Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016164.1 Corchorus olitorius cultivar O-4 contig16197, 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: 123087
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1066 original size:34 final size:34
Alignment explanation
Indices: 1014--1110 Score: 169
Period size: 34 Copynumber: 2.9 Consensus size: 34
1004 AGTTTTTATT
* *
1014 AGAGCTTCGTTTC-AAATCTTGTTTTAGGTTGGA
1 AGAGTTTCGCTTCAAAATCTTGTTTTAGGTTGGA
1047 AGAGTTTCGCTTCAAAATCTTGTTTTAGGTTGGA
1 AGAGTTTCGCTTCAAAATCTTGTTTTAGGTTGGA
1081 AGAGTTTCGCTTCAAAATCTTGTTTTAGGT
1 AGAGTTTCGCTTCAAAATCTTGTTTTAGGT
1111 CTCTGGTCGA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 11 0.18
34 50 0.82
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (34 bp):
AGAGTTTCGCTTCAAAATCTTGTTTTAGGTTGGA
Found at i:1216 original size:60 final size:60
Alignment explanation
Indices: 1107--1554 Score: 518
Period size: 60 Copynumber: 7.5 Consensus size: 60
1097 ATCTTGTTTT
* ** * *
1107 AGGTCTCTGGTCGAGAGTGTT-C-AATCCAAAATCTTGTTTCATTTTAAAATCTTGCTCG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG
* * * *
1165 AGTTCTCTAGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTACTTG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG
* *
1225 TGGTCTCTAGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTT-AAAATCCTGCTCG
* *
1286 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAGAAATCTTGTTTCATTTTAAAATCATGCTCG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG
* * * *
1346 ATGTCTCCGGTCGAGAGTTTT-CGTTTCAGGAAATCTTGTTTCATTTTAAAAACTCTTGCTCG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCA-AAAATCTTGTTTCATTTT-AAAA-TCCTGCTCG
* ** *
1408 AGGTCTCTGGTCGAGAGTTAT-C-AATCCAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTT-AAAATCCTGCTCG
* * ** *
1467 AGGTCTCTGGT-GAAGAG-TGTCTGTTTCAAAAA-CTTGTTTTGTCTTAAAATCCTGCTCG
1 AGGTCTCTGGTCG-AGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG
** *
1525 AGGTCTCTAATCGAGAATTTT-CGTTTCAAA
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAA
1555 GTCTAAAAAT
Statistics
Matches: 338, Mismatches: 41, Indels: 22
0.84 0.10 0.05
Matches are distributed among these distances:
58 54 0.16
59 44 0.13
60 152 0.45
61 61 0.18
62 27 0.08
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (60 bp):
AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG
Found at i:1302 original size:121 final size:119
Alignment explanation
Indices: 1108--1554 Score: 505
Period size: 121 Copynumber: 3.7 Consensus size: 119
1098 TCTTGTTTTA
* ** * * *
1108 GGTCTCTGGTCGAGAGTGTT-C-AATCCAAAATCTTGTTTCATTTTAAAATCTTGCTCGAGTTCT
1 GGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCT
* *
1171 CTAGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTACTTGT
66 CTAGTCGAGAGTTTT-CGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCGT
*
1226 GGTCTCTAGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCGAGGTC
1 GGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTT-AAAATCCTGCTCGAGGTC
* * *
1291 TCTGGTCGAGAGTTTTCCGTTTCAGAAATCTTGTTTCATTTTAAAATCATGCTCGAT
65 TCTAGTCGAGAGTTTT-CGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCG-T
* * *
1348 -GTCTCCGGTCGAGAGTTTT-CGTTTCAGGAAATCTTGTTTCATTTTAAAAACTCTTGCTCGAGG
1 GGTCTCTGGTCGAGAGTTTTCCGTTTCA-AAAATCTTGTTTCATTTT-AAAA-TCCTGCTCGAGG
* * ** * *
1411 TCTCTGGTCGAGAGTTATC-AATCCAAAATCTTGTTTCATTTTAAAAATCCTGCTCGA
63 TCTCTAGTCGAGAGTTTTCGTTTCAAAAATCTTGTTTCATTTT-AAAATCCTGCTCGT
* * ** *
1468 GGTCTCTGGT-GAAGAG-TGTCTGTTTCAAAAA-CTTGTTTTGTCTTAAAATCCTGCTCGAGGTC
1 GGTCTCTGGTCG-AGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTC
* *
1530 TCTAATCGAGAATTTTCGTTTCAAA
65 TCTAGTCGAGAGTTTTCGTTTCAAA
1555 GTCTAAAAAT
Statistics
Matches: 280, Mismatches: 38, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
117 26 0.09
118 26 0.09
119 11 0.04
120 52 0.19
121 136 0.49
122 29 0.10
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (119 bp):
GGTCTCTGGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCT
CTAGTCGAGAGTTTTCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTGCTCGT
Found at i:1441 original size:181 final size:178
Alignment explanation
Indices: 1107--1554 Score: 546
Period size: 181 Copynumber: 2.5 Consensus size: 178
1097 ATCTTGTTTT
* ** * *
1107 AGGTCTCTGGTCGAGAGTGTT-CAATCCAAAATCTTGTTTCATTTTAAAATCTTGCTCGAGTTCT
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAATCTTGTTTCATTTTAAAATCATGCTCGAG-TCT
* *
1171 CTAGTCGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTACTTGTGGTCTCTAGT
65 CTAGTCGAGAGTTTT-CGTTTCAAAAATCTTGTTTCATTTTAAAATCCTACTCGAGGTCTCTAGT
* **
1236 CGAGAGTTTTCCGTTTCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
129 CGAGAGTTATCCGAATCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
1286 AGGTCTCTGGTCGAGAGTTTTCCGTTTCAGAAATCTTGTTTCATTTTAAAATCATGCTCGATGTC
1 AGGTCTCTGGTCGAGAGTTTTCCGTTTCA-AAATCTTGTTTCATTTTAAAATCATGCTCGA-GTC
** * * *
1351 TCCGGTCGAGAGTTTTCGTTTCAGGAAATCTTGTTTCATTTTAAAAACTCTTGCTCGAGGTCTCT
64 TCTAGTCGAGAGTTTTCGTTTCA-AAAATCTTGTTTCATTTT-AAAA-TCCTACTCGAGGTCTCT
* *
1416 GGTCGAGAGTTAT-C-AATCCAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
126 AGTCGAGAGTTATCCGAATCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
* * * ** * *
1467 AGGTCTCTGGT-GAAGAG-TGTCTGTTTCAAAAACTTGTTTTGTCTTAAAATCCTGCTCGAGGTC
1 AGGTCTCTGGTCG-AGAGTTTTCCGTTTCAAAATCTTGTTTCATTTTAAAATCATGCTCGA-GTC
* *
1530 TCTAATCGAGAATTTTCGTTTCAAA
64 TCTAGTCGAGAGTTTTCGTTTCAAA
1555 GTCTAAAAAT
Statistics
Matches: 232, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
178 1 0.00
179 68 0.29
180 21 0.09
181 112 0.48
182 6 0.03
183 24 0.10
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (178 bp):
AGGTCTCTGGTCGAGAGTTTTCCGTTTCAAAATCTTGTTTCATTTTAAAATCATGCTCGAGTCTC
TAGTCGAGAGTTTTCGTTTCAAAAATCTTGTTTCATTTTAAAATCCTACTCGAGGTCTCTAGTCG
AGAGTTATCCGAATCAAAAATCTTGTTTCATTTTAAAAATCCTGCTCG
Found at i:1666 original size:2 final size:2
Alignment explanation
Indices: 1659--1746 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
1649 AAGTGCTTGA
*
1659 AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1701 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1743 AC AC
1 AC AC
1747 TATTTGTGAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:11643 original size:23 final size:22
Alignment explanation
Indices: 11617--11684 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 22
11607 AAAACACCTT
11617 TTTTTTTTTTTCAAAAACGCAAA
1 TTTTTTTTTTT-AAAAACGCAAA
*
11640 TTTTTTTTTTTTGAAAACGC-AA
1 -TTTTTTTTTTTAAAAACGCAAA
*
11662 TTTTTTTTTAGTAAAAACGCAAA
1 TTTTTTTTT-TTAAAAACGCAAA
11685 AAAGAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.23
22 10 0.26
23 9 0.23
24 11 0.28
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTTTTTTTTTAAAAACGCAAA
Found at i:11969 original size:22 final size:22
Alignment explanation
Indices: 11937--11978 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11927 AAAATTAACT
*
11937 AAGAAAGCAATCAAGAAAATTA
1 AAGAAAACAATCAAGAAAATTA
* *
11959 AAGAAAACAATTAATAAAAT
1 AAGAAAACAATCAAGAAAAT
11979 AGCAGTGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
AAGAAAACAATCAAGAAAATTA
Found at i:23880 original size:74 final size:73
Alignment explanation
Indices: 23722--23863 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 73
23712 TCATCAGGTC
* * *
23722 AAAGTTTTTTAACTTAGGAAAG-TCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCA
1 AAAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCAGTCA
23786 GTTTTTTT
66 GTTTTTTT
*
23794 AAAGTTTTTTAAATTGGGAAAGTTCCCACCAAGTTTAAGTTTTCAATTTAGGGAAAGTTCCC-GT
1 AAAGTTTTTTAAATTGGGAAAGTTCCCACC-AGTTTAAGTTTTCAAATT-GGGAAAGTTCCCAGT
23858 CA-TTTT
64 CAGTTTT
23864 CGGTTTTAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
72 20 0.32
73 11 0.17
74 20 0.32
75 12 0.19
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (73 bp):
AAAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCAGTCA
GTTTTTTT
Found at i:23886 original size:74 final size:73
Alignment explanation
Indices: 23722--23892 Score: 199
Period size: 74 Copynumber: 2.3 Consensus size: 73
23712 TCATCAGGTC
** * *
23722 AAAGTTTTTTAACTTAGGAAAG-TCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCA
1 AAAGTTTTTTAAAATGGGAAAGTTCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCAGTCA
23786 GTTTTTTT
66 GTTTTTTT
* *
23794 AAAGTTTTTTAAATTGGGAAAGTTCCCACCAAGTTTAAGTTTTCAATTTAGGGAAAGTTCCC-GT
1 AAAGTTTTTTAAAATGGGAAAGTTCCCACC-AGTTTAAGTTTTCAAATT-GGGAAAGTTCCCAGT
23858 CA-TTTTCGGTTT
64 CAGTTTT---TTT
*
23870 -TAG-TTTTTAAAATGGGAAAGTTC
1 AAAGTTTTTTAAAATGGGAAAGTTC
23893 TCATCAAAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
72 20 0.23
73 11 0.13
74 39 0.45
75 14 0.16
76 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (73 bp):
AAAGTTTTTTAAAATGGGAAAGTTCCCACCAGTTTAAGTTTTCAAATTGGGAAAGTTCCCAGTCA
GTTTTTTT
Found at i:26008 original size:16 final size:16
Alignment explanation
Indices: 25987--26018 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25977 CAAGCCCATA
*
25987 TTAGCCCATTTACTCT
1 TTAGCCCAATTACTCT
26003 TTAGCCCAATTACTCT
1 TTAGCCCAATTACTCT
26019 ATGTTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (16 bp):
TTAGCCCAATTACTCT
Found at i:31484 original size:21 final size:21
Alignment explanation
Indices: 31460--31500 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31450 TCTTAGACAA
* *
31460 GGTTTTTCATCTTTTGGGTTT
1 GGTTGTTCATCTTTTAGGTTT
31481 GGTTGTTCATCTTTTAGGTT
1 GGTTGTTCATCTTTTAGGTT
31501 CAATTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.24, T:0.59
Consensus pattern (21 bp):
GGTTGTTCATCTTTTAGGTTT
Found at i:33741 original size:33 final size:33
Alignment explanation
Indices: 33688--33788 Score: 168
Period size: 33 Copynumber: 3.1 Consensus size: 33
33678 GCTCTTACAA
33688 ACAATGAAGTT-ACGGGCCTTCATCACGCCGTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
* *
33720 CCAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
*
33753 ACAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
33786 ACA
1 ACA
33789 TGTTGAGCAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 10 0.15
33 55 0.85
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
Found at i:35750 original size:22 final size:22
Alignment explanation
Indices: 35722--35766 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35712 AATGTGTTCA
*
35722 TAAAAGGGTCTGTTGAGGAAGC
1 TAAAAGGGTCTGTTAAGGAAGC
35744 TAAAAGGGTCTGTTAAGGAAGC
1 TAAAAGGGTCTGTTAAGGAAGC
35766 T
1 T
35767 GAAACACAAC
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:0.33, C:0.09, G:0.33, T:0.24
Consensus pattern (22 bp):
TAAAAGGGTCTGTTAAGGAAGC
Found at i:36585 original size:34 final size:34
Alignment explanation
Indices: 36539--36607 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
36529 GGTTTACCAC
* * * *
36539 ATGTGGATTTAGATTTTATAGGGAGAGCATTCAA
1 ATGTGGAGTTAGATTTGATAAGGAGAGCAATCAA
36573 ATGTGGAGTTAGATTTGATAAGGAGAGCAATCAA
1 ATGTGGAGTTAGATTTGATAAGGAGAGCAATCAA
36607 A
1 A
36608 CATTTGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (34 bp):
ATGTGGAGTTAGATTTGATAAGGAGAGCAATCAA
Found at i:38784 original size:22 final size:21
Alignment explanation
Indices: 38758--38811 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
38748 GAAGTTCGTG
38758 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
38780 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
38799 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
38812 TCAAGAGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:42951 original size:48 final size:48
Alignment explanation
Indices: 42880--43058 Score: 313
Period size: 48 Copynumber: 3.7 Consensus size: 48
42870 AGGGAAGCAA
42880 AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
1 AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
42928 AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
1 AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
* * *
42976 AAAATTAACTCTAATGGTACAACATACAAGCTCATATAAGAAATCCAA
1 AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
* *
43024 AAAATTAACTCTAATGGTACAACATGCAAAATCAT
1 AAAATTAACTCTAATGGTACAACATACAAACTCAT
43059 CTCATAGAAT
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 125 1.00
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (48 bp):
AAAATTAACTCTAATGGTACAACATACAAACTCATACAAGAAATCCAG
Found at i:44818 original size:42 final size:43
Alignment explanation
Indices: 44767--44860 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
44757 AGTGCATTAC
* *
44767 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
44808 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
44853 CTAATATT
1 CTAATATT
44861 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:46066 original size:20 final size:20
Alignment explanation
Indices: 46038--46080 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
46028 ATCAGAAAAG
*
46038 AAGAAAAAAGAGGTGAAGAGAA
1 AAGAAAAAAGA--TAAAGAGAA
46060 AAGAAAAAAGATAAAGAGAA
1 AAGAAAAAAGATAAAGAGAA
46080 A
1 A
46081 TTGAATTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAGATAAAGAGAA
Found at i:46924 original size:6 final size:6
Alignment explanation
Indices: 46862--46917 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
46852 ATGGTGAAGT
* * **
46862 AAAATA AAAA-A AATAGA AAAA-A AAAATC AAAAGAA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA
46909 AAAAGA AAA
1 AAAAGA AAA
46918 GATAAAGCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 9 0.21
6 28 0.67
7 5 0.12
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:48145 original size:36 final size:35
Alignment explanation
Indices: 48100--48240 Score: 178
Period size: 35 Copynumber: 4.0 Consensus size: 35
48090 TAGTTTCATA
48100 TTGACCCAGGGCGGTCTTTCTTCAGTTGT-TTTCAAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTT-TATTTC-AG
* * * *
48136 TTGATCCAGGGCGATCATTCTTCATTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
48171 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
48206 TTGA-CCAGGGTGGTCTTTTCTTCAATTTATGTCAG
1 TTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAG
48241 AATGATCGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
34 10 0.11
35 55 0.60
36 27 0.29
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (35 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:49028 original size:35 final size:35
Alignment explanation
Indices: 48989--49532 Score: 432
Period size: 35 Copynumber: 15.5 Consensus size: 35
48979 TTTACAGTCG
* * *
48989 TTCTTCAGTTTATTTTAGTTGACCCAGGGCGGTCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * * * * * *
49024 TTCTTCAATTTACTTTAATTGATCCATGGCGATC-
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * *
49058 ATCTTCAGTTTACTTCAGTTGACCCAGGGCGGTTT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* *
49093 TTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCTT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTC-T
* * * *
49129 TTCTTCAGTTTACGTCAGAATT-ATCGAGGGTGGTCG
1 TTCTTCAGTTTACTTCAG--TTGACCCAGGGTGGTCT
* **
49165 TTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * * *
49200 TTCATCGGTTTA-TT-TGTCGACCCAGGGTGGTCTT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTC-T
* * * * *
49234 TTCTTCAGTTTACGTCAGAATGATCGAGGGTGGTCG
1 TTCTTCAGTTTACTTCAG-TTGACCCAGGGTGGTCT
* * *
49270 TTCTTCACTTTATTTCAGTTGACCCAGGGCGGTCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* *
49305 TTCTTCAGTTTATTTCAGTTGACCCAGGGTAGTCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * ** * *
49340 CTCTTCAGTTTA-TGTCAGAATGTTCGAGGGTGGTCG
1 TTCTTCAGTTTACT-TCAG-TTGACCCAGGGTGGTCT
* *
49376 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * * * * *
49411 TTTTTCAATTTACTTCAATTGATCCAGGGTGATCA
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * *
49446 TTCTTCAGTTTACTTCAATTGATCCAGGGTGATCT
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
* * * ** * * * *
49481 TTCTTCAGTTAATTTCAATCAATCCAGGGCGATCA
1 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
49516 TTCTTCAGTTTACTTCA
1 TTCTTCAGTTTACTTCA
49533 ATAGATCTAA
Statistics
Matches: 405, Mismatches: 92, Indels: 24
0.78 0.18 0.05
Matches are distributed among these distances:
33 13 0.03
34 42 0.10
35 249 0.61
36 76 0.19
37 24 0.06
38 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (35 bp):
TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
Found at i:49237 original size:105 final size:106
Alignment explanation
Indices: 48989--49527 Score: 549
Period size: 105 Copynumber: 5.1 Consensus size: 106
48979 TTTACAGTCG
* * * ** * *
48989 TTCTTCAGTTTATTTTAGTTGACCCAGGGCGGTC-TTTCTTCAATTTAC-T-TTAATTGATCCAT
1 TTCTTCAGTTTA-TTTAGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATT-ATCGAG
* * * *
49051 GGCGATC-ATCTTCAGTTTACTTCAGTTGACCCAGGGCGGTTT
64 GGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
49093 TTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATTATCGAGG
1 TTCTTCAGTTTATTT-AGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATTATCGAGG
* *
49158 GTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCT
65 GTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
* * * *
49200 TTCATCGGTTTATTT-GTCGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATGATCGAGGG
1 TTCTTCAGTTTATTTAGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATTATCGAGGG
* *
49264 TGGTCGTTCTTCACTTTATTTCAGTTGACCCAGGGCGGTCT
66 TGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
* * * *
49305 TTCTTCAGTTTATTTCAGTTGACCCAGGGTAGTC-TCTCTTCAGTTTATGTCAGAATGT-TCGAG
1 TTCTTCAGTTTATTT-AGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAAT-TATCGAG
*
49368 GGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCT
64 GGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
* * * * * * * * * *
49411 TTTTTCAATTTACTTCAATTGATCCAGGGTGATC-ATTCTTCAGTTTACTTC--AATTGATCCAG
1 TTCTTCAGTTTA-TTTAGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATT-ATCGAG
* * * * * ** * * *
49473 GGTGATCTTTCTTCAGTTAATTTCAATCAATCCAGGGCGATCA
64 GGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
49516 TTCTTCAGTTTA
1 TTCTTCAGTTTA
49528 CTTCAATAGA
Statistics
Matches: 372, Mismatches: 52, Indels: 21
0.84 0.12 0.05
Matches are distributed among these distances:
103 4 0.01
104 31 0.08
105 158 0.42
106 114 0.31
107 65 0.17
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (106 bp):
TTCTTCAGTTTATTTAGTAGACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATTATCGAGGG
TGGTCGTTCTTCAGTTTACTTCAGTTGACCCAGGGCGGTCT
Found at i:49487 original size:211 final size:210
Alignment explanation
Indices: 49009--49537 Score: 616
Period size: 211 Copynumber: 2.5 Consensus size: 210
48999 TATTTTAGTT
* * * * * * * *
49009 GACCCAGGGCGGTCT-TTCTTCAATTTACTTTAATTGATCCATGGCGATCATCTTCAGTTTACTT
1 GACCCAGGGTGATCTATTCTTCAGTTTACTTCAATTGATCCAGGGTGATCTTCTTCAGTTTATTT
* * *
49073 CAGTTGACCCAGGGCGGTTTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCTTTTCTTCAGT
66 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTAGTCTTCTCTTCAGT
49138 TTACGTCAGAATTATCGAGGGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCTTTC
131 TTACGTCAGAATTATCGAGGGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCTTTC
** **
49203 ATCGGTTTATTTGTC
196 ATCAATTTATTAATC
* * * * * * *
49218 GACCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATGATCGAGGGTGGTCGTTCTTCACTTTAT
1 GACCCAGGGTGATCTATTCTTCAGTTTACTTCA-ATTGATCCAGGGTGATC-TTCTTCAGTTTAT
*
49283 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTAGTC-TCTCTTCA
64 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTAGTCTTCTCTTCA
* * * *
49347 GTTTATGTCAGAATGT-TCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCT
129 GTTTACGTCAGAAT-TATCGAGGGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCT
** *
49411 TTTTTCAATTTACTTCAATT
193 TTCATCAATTTA-TT-AATC
* *
49431 GATCCAGGGTGATC-ATTCTTCAGTTTACTTCAATTGATCCAGGGTGATCTTTCTTCAGTTAATT
1 GACCCAGGGTGATCTATTCTTCAGTTTACTTCAATTGATCCAGGGTGATC-TTCTTCAGTTTATT
* ** * * * * *
49495 TCAATCAATCCAGGGCGATCATTCTTCAGTTTACTTCAATAGA
65 TCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTAGA
49538 TCTAATGCGA
Statistics
Matches: 268, Mismatches: 46, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
209 14 0.05
210 14 0.05
211 145 0.54
212 82 0.31
213 13 0.05
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (210 bp):
GACCCAGGGTGATCTATTCTTCAGTTTACTTCAATTGATCCAGGGTGATCTTCTTCAGTTTATTT
CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTAGTCTTCTCTTCAGT
TTACGTCAGAATTATCGAGGGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCTTTC
ATCAATTTATTAATC
Found at i:49489 original size:141 final size:140
Alignment explanation
Indices: 49007--49490 Score: 399
Period size: 141 Copynumber: 3.4 Consensus size: 140
48997 TTTATTTTAG
* * * * * * * * *
49007 TTGACCCAGGGCGGTCTTTCTTCAATTTACTTTAATTGATCCATGGCGATC-ATCTTCAGTTTAC
1 TTGATCCAGGGTGGTCATTCTTCAGTTTACTTCAATTGACCCAGGGCGATCTTTCTTCAGTTTAT
* * * *
49071 T-TCAGTTGACCCAGGGCGGTTTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCTTTTCTTC
66 TGTCAGATG-CCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTT-TTC
* *
49135 AGTTTACGTCAGAA
129 AATTTACTTC--AA
* * * * * * * *
49149 TT-ATCGAGGGTGGTCGTTCTTCAGTTTACTTCAGTTGACCCAAGACGGTCTTTCATCGGTTTAT
1 TTGATCCAGGGTGGTCATTCTTCAGTTTACTTCAATTGACCCAGGGCGATCTTTCTTCAGTTTA-
** * * * * *
49213 TTGTC-GA--CCCAGGGTGGTCTTTTCTTCAGTTTACGTCAGAATGATCGAGGGTGGTCGTTCTT
65 TTGTCAGATGCCCAGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTTTT
* * *
49275 CACTTTATTTCAG
128 CAATTTACTTCAA
* * * * * * *
49288 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGG-TAGTCTCTCTTCAGTTTA
1 TTGATCCAGGGTGGTCATTCTTCAGTTTACTTCAATTGACCCAGGGCGA-TCTTTCTTCAGTTTA
* * * *
49352 -TGTCAGAATGTTCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTTT
65 TTGTCAG-ATG-CCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTTT
49416 CAATTTACTTCAA
128 CAATTTACTTCAA
* * *
49429 TTGATCCAGGGTGATCATTCTTCAGTTTACTTCAATTGATCCAGGGTGATCTTTCTTCAGTT
1 TTGATCCAGGGTGGTCATTCTTCAGTTTACTTCAATTGACCCAGGGCGATCTTTCTTCAGTT
49491 AATTTCAATC
Statistics
Matches: 264, Mismatches: 65, Indels: 27
0.74 0.18 0.08
Matches are distributed among these distances:
138 4 0.02
139 4 0.02
140 59 0.22
141 141 0.53
142 42 0.16
143 12 0.05
144 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (140 bp):
TTGATCCAGGGTGGTCATTCTTCAGTTTACTTCAATTGACCCAGGGCGATCTTTCTTCAGTTTAT
TGTCAGATGCCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTTTCAA
TTTACTTCAA
Found at i:49598 original size:50 final size:50
Alignment explanation
Indices: 49543--50009 Score: 735
Period size: 50 Copynumber: 9.4 Consensus size: 50
49533 ATAGATCTAA
*
49543 TGCGATCAATCAAGTTTATAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
*
49593 TGCGATCAATCAAGTTTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC-AAGTGATCCAG
* * *
49644 TGTGATCAATCAAGTTTACAGTGGTTTAAG-TTTCCTTCAAGTGATCTAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
* *
49693 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAATGATCCCG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
*
49743 TGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
* *
49793 TGCGATCAATCAAGTTTACAATGGTTTAAG-TTTT-TTCAAGTGATCTAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
* *
49841 TGCGATCAATCAAGTTTATAGTGGTTTAAGTTTTTCTTCAAAGTGCTCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC-AAGTGATCCAG
* *
49892 TGGGATCAATCAAGTTTACAGTGGTTTAAG-TTTCCTTCAAGTGATCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
* *
49941 TGCGATCAATCAAGTTTATAGTGATTTAAGTTTTTCTTCAAGTGATCCAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
*
49991 TGTGATCAATCAAGTTTAC
1 TGCGATCAATCAAGTTTAC
50010 TTCTTCAAAG
Statistics
Matches: 380, Mismatches: 31, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
48 41 0.11
49 84 0.22
50 178 0.47
51 77 0.20
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (50 bp):
TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAG
Found at i:49701 original size:100 final size:100
Alignment explanation
Indices: 49543--50091 Score: 742
Period size: 100 Copynumber: 5.6 Consensus size: 100
49533 ATAGATCTAA
*
49543 TGCGATCAATCAAGTTTATAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
49608 TTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAG
66 TTACAGTGGTTTAAGT-TTTCTTCAAAGTGATCCAG
* * *
49644 TGTGATCAATCAAGTTTACAGTGGTTTAAG-TTTCCTTCAAGTGATCTAGTGCGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
*
49708 TTACAGTGGTTTAAGTTTTTCTTCAAA-TGATCCCG
66 TTACAGTGGTTTAAG-TTTTCTTCAAAGTGATCCAG
*
49743 TGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
* *
49808 TTACAATGGTTTAAGTTTT-TTC-AAGTGATCTAG
66 TTACAGTGGTTTAAGTTTTCTTCAAAGTGATCCAG
* * *
49841 TGCGATCAATCAAGTTTATAGTGGTTTAAGTTTTTCTTCAAAGTGCTCCAGTGGGATCAATCAAG
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC-AAGTGATCCAGTGCGATCAATCAAG
*
49906 TTTACAGTGGTTTAAGTTTCCTTC-AAGTGATCCAG
65 TTTACAGTGGTTTAAGTTTTCTTCAAAGTGATCCAG
* * *
49941 TGCGATCAATCAAGTTTATAGTGATTTAAGTTTTTCTTCAAGTGATCCAGTGTGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
50006 TTAC-------------TTCTTCAAAGTGATCCAG
66 TTACAGTGGTTTAAGTTTTCTTCAAAGTGATCCAG
* ** *
50028 TGTGATCAATCAAGTTTACAGTGGTTTAAG--TTTCATAAAAGTGATCCAAGTGCGGTCAATCAA
1 TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC-TTCAAGTGATCC-AGTGCGATCAATCAA
50091 G
64 G
50092 AAAGTTTCCT
Statistics
Matches: 410, Mismatches: 30, Indels: 30
0.87 0.06 0.06
Matches are distributed among these distances:
85 4 0.01
86 15 0.04
87 52 0.13
97 2 0.00
98 46 0.11
99 108 0.26
100 154 0.38
101 29 0.07
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (100 bp):
TGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
TTACAGTGGTTTAAGTTTTCTTCAAAGTGATCCAG
Found at i:49867 original size:248 final size:250
Alignment explanation
Indices: 49543--50009 Score: 803
Period size: 248 Copynumber: 1.9 Consensus size: 250
49533 ATAGATCTAA
* *
49543 TGCGATCAATCAAGTTTATAGTGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAATGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
*
49608 TTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAGTGTGATCAATCAAGTTTACAGTGGTTTAA
66 TTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAGTGGGATCAATCAAGTTTACAGTGGTTTAA
* *
49673 GTTTCCTTCAAGTGATCTAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTCAAATGA
131 GTTTCCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAATGA
*
49738 TCCCGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAG
196 TCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAG
*
49793 TGCGATCAATCAAGTTTACAATGGTTTAAG-TTTT-TTCAAGTGATCTAGTGCGATCAATCAAGT
1 TGCGATCAATCAAGTTTACAATGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
* * *
49856 TTATAGTGGTTTAAGTTTTTCTTCAAAGTGCTCCAGTGGGATCAATCAAGTTTACAGTGGTTTAA
66 TTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAGTGGGATCAATCAAGTTTACAGTGGTTTAA
* *
49921 GTTTCCTTCAAGTGATCCAGTGCGATCAATCAAGTTTATAGTGATTTAAGTTTTTCTTCAAGTGA
131 GTTTCCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAATGA
*
49986 TCCAGTGTGATCAATCAAGTTTAC
196 TCCAGTGCGATCAATCAAGTTTAC
50010 TTCTTCAAAG
Statistics
Matches: 204, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
248 172 0.84
249 4 0.02
250 28 0.14
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (250 bp):
TGCGATCAATCAAGTTTACAATGGTTTAAGTTTTTCTTCAAGTGATCCAGTGCGATCAATCAAGT
TTACAGTGGTTTAAGTCTTTCTTCAAAGTGATCCAGTGGGATCAATCAAGTTTACAGTGGTTTAA
GTTTCCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAATGA
TCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAG
Found at i:50024 original size:37 final size:36
Alignment explanation
Indices: 49974--50046 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 36
49964 ATTTAAGTTT
49974 TTCTTCAAGTGATCCAGTGTGATCAATCAAGTTTAC
1 TTCTTCAAGTGATCCAGTGTGATCAATCAAGTTTAC
50010 TTCTTCAAAGTGATCCAGTGTGATCAATCAAGTTTAC
1 TTCTTC-AAGTGATCCAGTGTGATCAATCAAGTTTAC
50047 AGTGGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 6 0.17
37 30 0.83
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (36 bp):
TTCTTCAAGTGATCCAGTGTGATCAATCAAGTTTAC
Found at i:50110 original size:87 final size:85
Alignment explanation
Indices: 49919--50151 Score: 227
Period size: 87 Copynumber: 2.6 Consensus size: 85
49909 ACAGTGGTTT
* * * **
49919 AAGTTTCCTTCAAGTGATCCAGTGCGATCAATCAAGTTTATAGTGATTTAAGTTTTTCTTCAAGT
1 AAGTTTCC-TAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAG--TTTCTAAAAGT
* *
49984 GATCCAGTGTGATCAATCAAGTT
63 GATCCAGTGCGATCAATCAAGTA
* * * *
50007 TA-CTTCTTCAAAGTGATCCAGTGTGATCAATCAAGTTTACAGTGGTTTAAGTTTCATAAAAGTG
1 AAGTTTCCT-AAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTC-TAAAAGTG
*
50071 ATCCAAGTGCGGTCAATCAAG-A
64 ATCC-AGTGCGATCAATCAAGTA
* *
50093 AAGTTTCCTAAAGGTGATCCAGAGCGGTCAATCAAGAAAATTTACAGTGGTTTAAGTTT
1 AAGTTTCCTAAA-GTGATCCAGTGCGATCAATCAAG----TTTACAGTGGTTTAAGTTT
50152 ATCTTCAAGT
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
85 4 0.03
86 15 0.13
87 79 0.67
88 1 0.01
91 19 0.16
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (85 bp):
AAGTTTCCTAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTCTAAAAGTGAT
CCAGTGCGATCAATCAAGTA
Found at i:50129 original size:37 final size:38
Alignment explanation
Indices: 50055--50131 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 38
50045 ACAGTGGTTT
*
50055 AAGTTTCATAAAAGTGATCCAAGTGCGGTCAATCAAGA
1 AAGTTTCATAAAAGTGATCCAAGAGCGGTCAATCAAGA
* *
50093 AAGTTTCCTAAAGGTGATCC-AGAGCGGTCAATCAAGA
1 AAGTTTCATAAAAGTGATCCAAGAGCGGTCAATCAAGA
50130 AA
1 AA
50132 ATTTACAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 18 0.50
38 18 0.50
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (38 bp):
AAGTTTCATAAAAGTGATCCAAGAGCGGTCAATCAAGA
Found at i:50270 original size:42 final size:42
Alignment explanation
Indices: 50216--50464 Score: 354
Period size: 42 Copynumber: 5.9 Consensus size: 42
50206 ATCTTCAAGC
* * * *
50216 GATTCGGAGAATCAAATGACTCGGTGTAGCAACTTCAAGCGG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
* * *
50258 GATTCGGTGAATCAGATAACTTGGTGTCGCATCTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
* * * *
50300 GAATCAGTGAATCAGATAACTCGGTGTAGCATTTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
*
50342 GATTCGGTGAATCAGATGACTCGGCGTAGCATCTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
* *
50384 GATTCAGTGAATCAGATGACTCGGTGCAGCATCTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
* *
50426 GATTCGGTGAATTAGATGACTCGGTGTAACATCTTCAAG
1 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAG
50465 ATTGGAATTC
Statistics
Matches: 183, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 183 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
Found at i:50607 original size:89 final size:88
Alignment explanation
Indices: 50457--50631 Score: 208
Period size: 89 Copynumber: 2.0 Consensus size: 88
50447 CGGTGTAACA
* * * * ** *
50457 TCTTCAAGATTGGAATTCGGTAAGCTCGGGGCAGCACATTTTCAGATAGATCAGGGTGATTCTGT
1 TCTTCAAGAGTGGAATTCAGTAAGCTCGGGGCAGCACATTTTCAAACAGATCAGGACGATTCGGT
*
50522 GAATCAAGTTAATTCGGTGCATC
66 GAATCAAGTTAATACGGTGCATC
* * *
50545 TCTTCAAAGAGTGGAATTCAGTGAA-CTCGGTGCAGCACATTTTCAAACAGTTGAGGACGATTCG
1 TCTTC-AAGAGTGGAATTCAGT-AAGCTCGGGGCAGCACATTTTCAAACAGATCAGGACGATTCG
* *
50609 GTGAATTAAGTTACTACGGTGCA
64 GTGAATCAAGTTAATACGGTGCA
50632 GTATTTCTTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
88 5 0.07
89 65 0.90
90 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (88 bp):
TCTTCAAGAGTGGAATTCAGTAAGCTCGGGGCAGCACATTTTCAAACAGATCAGGACGATTCGGT
GAATCAAGTTAATACGGTGCATC
Found at i:52506 original size:46 final size:47
Alignment explanation
Indices: 52451--52559 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 47
52441 GATCACAGCT
* *
52451 TCTCT-GAAAAAAAAAAGT-TCACCTCTCTCTCTCGAAGGAACTCTC
1 TCTCTAGAAAAAAAAAAGTCTCACCTCTCTCTCTCGAAAGAACTCAC
* *
52496 TCTCTAGAAAAGAAGAA-TCTCACCTCTCTCTCTCGAAAGAACTCAC
1 TCTCTAGAAAAAAAAAAGTCTCACCTCTCTCTCTCGAAAGAACTCAC
52542 TCTCTAGAAAAAAAAAAG
1 TCTCTAGAAAAAAAAAAG
52560 ACTCTGGCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
45 6 0.11
46 49 0.89
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.24
Consensus pattern (47 bp):
TCTCTAGAAAAAAAAAAGTCTCACCTCTCTCTCTCGAAAGAACTCAC
Found at i:53697 original size:18 final size:18
Alignment explanation
Indices: 53645--53688 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
53635 TTAGTTTGAA
*
53645 ATTAATTT-CTAAGTTAG
1 ATTAATTTACTAAATTAG
* *
53662 CTTAATTTACAAAATTAG
1 ATTAATTTACTAAATTAG
53680 ATTAATTTA
1 ATTAATTTA
53689 GTAATTTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTAATTTACTAAATTAG
Found at i:58394 original size:25 final size:25
Alignment explanation
Indices: 58366--58416 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
58356 ATAAATATAA
*
58366 TTTAATTCAAGTGCATACAAAATTG
1 TTTAATTCAAGTGCATAAAAAATTG
58391 TTTAATTCAAGTGCATAAAAAATTG
1 TTTAATTCAAGTGCATAAAAAATTG
58416 T
1 T
58417 ATTGTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (25 bp):
TTTAATTCAAGTGCATAAAAAATTG
Found at i:58540 original size:2 final size:2
Alignment explanation
Indices: 58533--58557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58523 GTTACTACAA
58533 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
58558 TGGGAAGAAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59354 original size:13 final size:13
Alignment explanation
Indices: 59338--59362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59328 TTTTATATTA
59338 TATATATTAATAC
1 TATATATTAATAC
59351 TATATATTAATA
1 TATATATTAATA
59363 TTAATAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATTAATAC
Found at i:75775 original size:11 final size:11
Alignment explanation
Indices: 75759--75786 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
75749 GGAATGTGAG
75759 TTTGTTAGTAA
1 TTTGTTAGTAA
75770 TTTGTTAGTAA
1 TTTGTTAGTAA
75781 TTTGTT
1 TTTGTT
75787 TGTTTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (11 bp):
TTTGTTAGTAA
Found at i:78691 original size:15 final size:16
Alignment explanation
Indices: 78671--78700 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
78661 ACACTAGGTA
78671 CACCGGAATT-TATGG
1 CACCGGAATTATATGG
78686 CACCGGAATTATATG
1 CACCGGAATTATATG
78701 AAGAGGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (16 bp):
CACCGGAATTATATGG
Found at i:86965 original size:2 final size:2
Alignment explanation
Indices: 86958--86983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86948 TTAGATATGA
86958 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
86984 GTATTAGCCT
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):
AT
Found at i:90847 original size:85 final size:85
Alignment explanation
Indices: 90752--91079 Score: 448
Period size: 84 Copynumber: 3.9 Consensus size: 85
90742 ATAGAAGTGT
* **
90752 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAGGTGCCCCTGTGTTATAAATGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAAATGTGTTT
* *
90817 GGGGACTTT-AGTATGGATGT
66 GGGGACTTTGA-TATAGATGC
* *
90837 CTCTGTGTTATAAATGTGTTTGAGGACTTTT-AGAGAGAATTTCCCTTGTGTTATAAATGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAAATGTGTTT
90901 GGGGACTTTGATATAGATGC
66 GGGGACTTTGATATAGATGC
* * * *
90921 CTTTGTGTTATAAATGTGTTTGAGGACTTTGGA-ATAGAGA-TGCCACTGTGTTATAAATGTGTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGA-ATTGCCCCTGTGTTATAAATGTGTT
90984 TGGGGACTTTTGATATAGATGC
65 TGGGGAC-TTTGATATAGATGC
* * * * * *
91006 CTATATGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAATTGCCCCTGTGTTATAATTGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAAATGTGTTT
91071 GGGGACTTT
66 GGGGACTTT
91080 TGGTTATTGG
Statistics
Matches: 217, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
84 104 0.48
85 81 0.37
86 32 0.15
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (85 bp):
CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAAATGTGTTT
GGGGACTTTGATATAGATGC
Found at i:90899 original size:43 final size:42
Alignment explanation
Indices: 90755--91080 Score: 292
Period size: 43 Copynumber: 7.7 Consensus size: 42
90745 GAAGTGTCTC
* *
90755 TGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAGGTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTT-AGATAGA-ATGCCCT
* * *
90799 TGTGTTATAAATGTGTTTGGGGAC-TTTAG-TATGGATG-TCT
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGATA-GAATGCCCT
* *
90839 CTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAATTTCCCT
1 -TGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAA-TGCCCT
* * * *
90883 TGTGTTATAAATGTGTTTGGGGACTTTGATATAG-ATGCCTT
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAATGCCCT
*
90924 TGTGTTATAAATGTGTTTGAGGAC-TTTGGAATAGAGATGCCAC-
1 TGTGTTATAAATGTGTTTGAGGACTTTTAG-ATAGA-ATGCC-CT
* *
90967 TGTGTTATAAATGTGTTTGGGGACTTTT-GATATAGATG-CCT
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGATAGA-ATGCCCT
* * * *
91008 ATATGTTATAATTGTGTTTGAGGAC-TTTAGAAAGAGAATTGCCCC
1 -TGTGTTATAAATGTGTTTGAGGACTTTTAG--ATAGAA-TGCCCT
* *
91053 TGTGTTATAATTGTGTTTGGGGACTTTT
1 TGTGTTATAAATGTGTTTGAGGACTTTT
91081 GGTTATTGGG
Statistics
Matches: 232, Mismatches: 31, Indels: 37
0.77 0.10 0.12
Matches are distributed among these distances:
40 4 0.02
41 62 0.27
42 41 0.18
43 65 0.28
44 55 0.24
45 5 0.02
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.41
Consensus pattern (42 bp):
TGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAATGCCCT
Found at i:93469 original size:43 final size:43
Alignment explanation
Indices: 93416--93745 Score: 438
Period size: 43 Copynumber: 7.8 Consensus size: 43
93406 ATAAGGAGAA
*
93416 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
93459 ATGCTCCTGTGTTATATATGTGTTTGGGGACTTTGTAAT--AG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
93500 TTGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
93543 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAAT--AG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
93584 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
93627 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTG-AATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * * * *
93668 GTGTCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
*
93712 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
93746 TGGTTATTGG
Statistics
Matches: 251, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
41 107 0.43
42 3 0.01
43 109 0.43
44 32 0.13
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.42
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:93530 original size:84 final size:84
Alignment explanation
Indices: 93416--93745 Score: 536
Period size: 84 Copynumber: 3.9 Consensus size: 84
93406 ATAAGGAGAA
* *
93416 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCTCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
93481 TTTGGGGACTTTGTAATAG
66 TTTGGGGACTTTGTAATAG
* *
93500 TTGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAGGTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
93565 TTTGGGGACTTTGTAATAG
66 TTTGGGGACTTTGTAATAG
* * *
93584 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
*
93649 TTTGGGGAC-TTGAATATAG
66 TTTGGGGACTTTGTA-ATAG
* * *
93668 GTGTCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTAAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATATGT
93733 GTTTGGGGACTTT
65 GTTTGGGGACTTT
93746 TGGTTATTGG
Statistics
Matches: 229, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
83 4 0.02
84 183 0.80
85 40 0.17
86 2 0.01
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGTAATAG
Found at i:94702 original size:6 final size:6
Alignment explanation
Indices: 94693--94717 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
94683 CTTAAACATG
94693 CTTGAA CTTGAA CTTGAA CTTGAA C
1 CTTGAA CTTGAA CTTGAA CTTGAA C
94718 CGTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (6 bp):
CTTGAA
Found at i:96126 original size:16 final size:15
Alignment explanation
Indices: 96095--96139 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
96085 TTGAAGGATA
* *
96095 TTTAAGAATGTATTT
1 TTTAAGGATATATTT
*
96110 TTTAAAGGATTTATTT
1 TTT-AAGGATATATTT
96126 TTTAAGGATATATT
1 TTTAAGGATATATT
96140 ATGATGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTAAGGATATATTT
Found at i:98367 original size:290 final size:289
Alignment explanation
Indices: 97814--98394 Score: 1126
Period size: 290 Copynumber: 2.0 Consensus size: 289
97804 TCAATAATAC
97814 TAAATTAAACGATCGCATATGATAGGACTTAAATATAAAGGTTTAGGAAGTATATACACCAACCA
1 TAAATTAAACGATCGCATATGATAGGACTTAAATATAAAGGTTTAGGAAGTATATACACCAACCA
97879 ATTTAGTTAAATGCATCAATAATTTGTACAAAGACAAAAATTAAGCTAAACTACAAAACCTCAAA
66 ATTTAGTTAAATGCATCAATAATTTGTACAAAGACAAAAATTAAGCTAAACTACAAAACCTCAAA
97944 AATGATACTTATTACAACTTCTTCGTTGAAAAAAGGGAGACCGGAAAAATTATTAGGTGAGATTG
131 AATGATACTTATTACAACTTCTTCGTTGAAAAAAGGGAGACCGGAAAAATTATTAGGTGAGATTG
98009 ACCCACCACGTCAGTCATGAGATTAAAAATTAAAATTTTTTTTATTCAAGATTAAAAATTAAAAT
196 ACCCACCACGTCAGTCATGAGATTAAAAATTAAAATTTTTTTTATTCAAGATTAAAAATTAAAAT
*
98074 TGTGACATATCAAATCAACTCTTAATATT
261 TGTGACATATCAAATCAACTCTTAAAATT
* *
98103 TAAATTAAACGATCGCATATGATATGACTTAAATATAAAGGTTTAGGAAGTATATATACCAACCA
1 TAAATTAAACGATCGCATATGATAGGACTTAAATATAAAGGTTTAGGAAGTATATACACCAACCA
98168 ATTTAGTTAAATGCATCAATAATTTGTACAAAGACAAAAATTAAGCTAAACTACAAAACCTCAAA
66 ATTTAGTTAAATGCATCAATAATTTGTACAAAGACAAAAATTAAGCTAAACTACAAAACCTC-AA
98233 AAATGATACTTATTACAACTTCTTCGTTGAAAAAAGGGAGACCGGAAAAATTATTAGGTGAGATT
130 AAATGATACTTATTACAACTTCTTCGTTGAAAAAAGGGAGACCGGAAAAATTATTAGGTGAGATT
98298 GACCCACCACGTCAGTCATGAGATTAAAAATTAAAATTTTTTTTATTCAAGATTAAAAATTAAAA
195 GACCCACCACGTCAGTCATGAGATTAAAAATTAAAATTTTTTTTATTCAAGATTAAAAATTAAAA
98363 TTGTGACATATCAAATCAACTCTTAAAATT
260 TTGTGACATATCAAATCAACTCTTAAAATT
98393 TA
1 TA
98395 GTCATAATTT
Statistics
Matches: 288, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
289 125 0.43
290 163 0.57
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (289 bp):
TAAATTAAACGATCGCATATGATAGGACTTAAATATAAAGGTTTAGGAAGTATATACACCAACCA
ATTTAGTTAAATGCATCAATAATTTGTACAAAGACAAAAATTAAGCTAAACTACAAAACCTCAAA
AATGATACTTATTACAACTTCTTCGTTGAAAAAAGGGAGACCGGAAAAATTATTAGGTGAGATTG
ACCCACCACGTCAGTCATGAGATTAAAAATTAAAATTTTTTTTATTCAAGATTAAAAATTAAAAT
TGTGACATATCAAATCAACTCTTAAAATT
Found at i:101477 original size:18 final size:18
Alignment explanation
Indices: 101456--101495 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
101446 GCTGTCAATT
101456 TTTGAAAACAAAAAGATG
1 TTTGAAAACAAAAAGATG
101474 TTTGAAAACAAAAAGATG
1 TTTGAAAACAAAAAGATG
101492 TTTG
1 TTTG
101496 GATATACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (18 bp):
TTTGAAAACAAAAAGATG
Found at i:102518 original size:3 final size:3
Alignment explanation
Indices: 102510--102542 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
102500 ATGATTTTTC
102510 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
102543 GTAGAAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:118699 original size:60 final size:60
Alignment explanation
Indices: 118601--118761 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
118591 GCTAATTGCT
* * **
118601 CAAATAAGCGCCTAACGTTTGCTAAAAATACTCAAATAAGGGTTTGATCTTTTAATTTAGC
1 CAAATAAGGGCCTAACGTTTGC-CAAAATACTCAAATAAGGGCCTGATCTTTTAATTTAGC
* *
118662 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGCCTGATCTTTTAATTTAGC
118722 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGG
118762 ATATGGCGTC
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 72 0.77
61 21 0.23
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGCCTGATCTTTTAATTTAGC
Found at i:118700 original size:31 final size:31
Alignment explanation
Indices: 118662--118761 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
118652 TTAATTTAGC
118662 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
* * **
118693 CAAATAAGGGCCTGATC-TTT--TAATTTGGC-
1 CAAATAAGGGCCT-AACGTTTGCCAAAAT-GCT
*
118722 CAAATAAGGGCCTAACGTTTGCCAAAATACT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
118753 CAAATAAGG
1 CAAATAAGG
118762 ATATGGCGTC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 2 0.04
29 19 0.35
30 3 0.06
31 28 0.52
32 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCT
Found at i:118734 original size:29 final size:28
Alignment explanation
Indices: 118633--118734 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
118623 TAAAAATACT
**
118633 CAAATAAGGGTTTGATCTTTTAATTTAGC
1 CAAATAAGGGCCTGATCTTTTAATTT-GC
* * **
118662 CAAATAAGGGCCT-AACGTTTGCCAAAATGC
1 CAAATAAGGGCCTGATC-TTT--TAATTTGC
118692 TCAAATAAGGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTT-GC
118722 CAAATAAGGGCCT
1 CAAATAAGGGCCT
118735 AACGTTTGCC
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.04
29 30 0.53
30 4 0.07
31 19 0.33
32 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (28 bp):
CAAATAAGGGCCTGATCTTTTAATTTGC
Found at i:118842 original size:31 final size:31
Alignment explanation
Indices: 118804--118879 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
118794 AACTGACGCC
* * *
118804 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAACATTTTCAATAACGTA
* *
118835 AGGCCCTTATTTAAATATTTTCAATAACGTA
1 AGGCCCTTATTTGAACATTTTCAATAACGTA
*
118866 AGACCCTTATTTGA
1 AGGCCCTTATTTGA
118880 CGAAATTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAACATTTTCAATAACGTA
Found at i:120179 original size:4 final size:4
Alignment explanation
Indices: 120172--120206 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
120162 TTTTTTTTTT
120172 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
120207 GGTTTGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Done.