Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009257.1 Corchorus capsularis cultivar CVL-1 contig09278, 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: 85541
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4411 original size:24 final size:24
Alignment explanation
Indices: 4377--4428 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
4367 CTGCAAGGAG
4377 GAGAGAAAAACAGAGAAAATAGAA
1 GAGAGAAAAACAGAGAAAATAGAA
*
4401 GAGAGAGAAACAGAGAAAATAGAA
1 GAGAGAAAAACAGAGAAAATAGAA
4425 GAGA
1 GAGA
4429 AACATATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.63, C:0.04, G:0.29, T:0.04
Consensus pattern (24 bp):
GAGAGAAAAACAGAGAAAATAGAA
Found at i:5039 original size:24 final size:24
Alignment explanation
Indices: 5006--5059 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4996 GGTCGGTAGA
* *
5006 GAAGAGCAAGGGAAGGTTAACAGC
1 GAAGAACAAGGAAAGGTTAACAGC
5030 GAAGAACAAGGAAAGGTTAACAGC
1 GAAGAACAAGGAAAGGTTAACAGC
5054 GAAGAA
1 GAAGAA
5060 TACCAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.33, T:0.07
Consensus pattern (24 bp):
GAAGAACAAGGAAAGGTTAACAGC
Found at i:6526 original size:31 final size:32
Alignment explanation
Indices: 6451--6527 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
6441 ATATGGTATA
*
6451 AGACGCCACCATTTAGCGGCGTCTATGACATC
1 AGACGCCACTATTTAGCGGCGTCTATGACATC
* * *
6483 AGACGCCACTATTTAGCGGCGTTTATGGCCT-
1 AGACGCCACTATTTAGCGGCGTCTATGACATC
*
6514 AGACGCCGCTATTT
1 AGACGCCACTATTT
6528 GTTAGGCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 13 0.32
32 27 0.68
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (32 bp):
AGACGCCACTATTTAGCGGCGTCTATGACATC
Found at i:6626 original size:32 final size:32
Alignment explanation
Indices: 6576--6646 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
6566 ATTAAGTATG
*
6576 GCGGCGTCTAAGATATAAGACGCCACTATTTA
1 GCGGCGTCTAAGACATAAGACGCCACTATTTA
**
6608 GCGGCGTCTTCGACATAAGACGCCACTATTTA
1 GCGGCGTCTAAGACATAAGACGCCACTATTTA
6640 GCGGCGT
1 GCGGCGT
6647 TTAGCGCCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (32 bp):
GCGGCGTCTAAGACATAAGACGCCACTATTTA
Found at i:6644 original size:142 final size:143
Alignment explanation
Indices: 6323--6784 Score: 636
Period size: 142 Copynumber: 3.2 Consensus size: 143
6313 GGGATATAGT
6323 GGCGTCT-TACGACATAAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
1 GGCGTCTAT-CGACATAAGACGCCACTATTTAGCGGCGTTTA-GGCCTAGACGCCGCTATTTGTT
* *
6387 AGGCTTTATTTTTACTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGC--ATATGGTAT
64 AGGCTTTA---TTACTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGCGTCTATGATAT
*
6450 AAGACGCCACCATTTAGC
126 AAGACGCCACTATTTAGC
*
6468 GGCGTCTAT-GACATCAGACGCCACTATTTAGCGGCGTTTATGGCCTAGACGCCGCTATTTGTTA
1 GGCGTCTATCGACATAAGACGCCACTATTTAGCGGCGTTTA-GGCCTAGACGCCGCTATTTGTTA
*
6532 GGCTTTATT-CTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGCGTCTAAGATATAAGA
65 GGCTTTATTACTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGCGTCTATGATATAAGA
6596 CGCCACTATTTAGC
130 CGCCACTATTTAGC
*
6610 GGCGTCT-TCGACATAAGACGCCACTATTTAGCGGCGTTTAGCGCCTAGACACCGCTATTTGTTA
1 GGCGTCTATCGACATAAGACGCCACTATTTAGCGGCGTTTAG-GCCTAGACGCCGCTATTTGTTA
* * * * * *
6674 GGCTTCATTTTTACTCAATTTGCATTTCTTCG-AAAAAATTAAGTATGGCGGCGTCTGTGACATC
65 GGC-T--TTATTACTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGCGTCTATGATATA
6738 AGACGCCACTATTTAGC
127 AGACGCCACTATTTAGC
* * *
6755 GGCGTTTATGGTC--AAGACGCCACTATTTAG
1 GGCGTCTATCGACATAAGACGCCACTATTTAG
6785 GGTTGCTTTT
Statistics
Matches: 289, Mismatches: 18, Indels: 21
0.88 0.05 0.06
Matches are distributed among these distances:
140 40 0.14
141 4 0.01
142 84 0.29
143 1 0.00
144 77 0.27
145 62 0.21
146 21 0.07
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (143 bp):
GGCGTCTATCGACATAAGACGCCACTATTTAGCGGCGTTTAGGCCTAGACGCCGCTATTTGTTAG
GCTTTATTACTCAATTTACATTTCTCCGAAAAAAATTAAGTATGGCGGCGTCTATGATATAAGAC
GCCACTATTTAGC
Found at i:10675 original size:20 final size:20
Alignment explanation
Indices: 10650--10688 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10640 AAAAAGAGCA
*
10650 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
10670 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
10689 CCTTGTATTT
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:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:11211 original size:28 final size:27
Alignment explanation
Indices: 11176--11276 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
11166 AAGTGAACTT
*
11176 AAAACGACCCAAGATACCCCTGAATGCA
1 AAAACGA-CCAAAATACCCCTGAATGCA
**
11204 AAAACGACCAAAATACCCCTGAATGTG
1 AAAACGACCAAAATACCCCTGAATGCA
* * * *
11231 GAAATGACCAAAATGCCCCTGAATGTA
1 AAAACGACCAAAATACCCCTGAATGCA
*
11258 AAAATGACCAAAATGACCC
1 AAAACGACCAAAAT-ACCC
11277 TAGGTGACCC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 53 0.84
28 10 0.16
ACGTcount: A:0.45, C:0.27, G:0.15, T:0.14
Consensus pattern (27 bp):
AAAACGACCAAAATACCCCTGAATGCA
Found at i:13086 original size:35 final size:36
Alignment explanation
Indices: 13005--13087 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
12995 TTATTTTCGG
13005 AACAATGGTTTGTAATCCTTAATTTCTAGTTTCAAA
1 AACAATGGTTTGTAATCCTTAATTTCTAGTTTCAAA
**
13041 AACAATGGTTTGTAATCCTTAATTTCTAGTTT-GGA
1 AACAATGGTTTGTAATCCTTAATTTCTAGTTTCAAA
13076 AACAATGGTTTG
1 AACAATGGTTTG
13088 ATGTTTGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 13 0.29
36 32 0.71
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
AACAATGGTTTGTAATCCTTAATTTCTAGTTTCAAA
Found at i:26708 original size:41 final size:41
Alignment explanation
Indices: 26621--26729 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
26611 GCACATCTAA
26621 AACCTTAATTCAGTGTAATTAAG-AAAAATTAAGAAAAGTG
1 AACCTTAATTCAGTGTAATTAAGAAAAAATTAAGAAAAGTG
26661 AACCTTAATTCAGTGTAATTAAGAAAAAATTAAGAAAAGT-
1 AACCTTAATTCAGTGTAATTAAGAAAAAATTAAGAAAAGTG
*
26701 AAGCCTTAATTTAGTGTAATTAA-AAAAAA
1 AA-CCTTAATTCAGTGTAATTAAGAAAAAA
26730 GGAAAAAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
40 31 0.47
41 35 0.53
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.28
Consensus pattern (41 bp):
AACCTTAATTCAGTGTAATTAAGAAAAAATTAAGAAAAGTG
Found at i:26801 original size:41 final size:41
Alignment explanation
Indices: 26752--27220 Score: 480
Period size: 41 Copynumber: 11.9 Consensus size: 41
26742 TTAAGAAAAG
* * * *
26752 TAAA-TCTTAATTCAGGGAAATTAACAAGACCAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
*
26792 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACGGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* * *
26833 TAAAGTCTAAATT--TGGTAATTAAGAAAAACAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
*
26872 TAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
*
26913 TAAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACATAGT
1 T-AAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* * *
26955 CAAAGTCTTAATT--TGGTAATT-----AAG----CAGAG-
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* ** * *
26984 T-AAGTCTTAATT-TGGTAATTA-AGAAAAGCAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
27022 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* * * *
27063 CAGAGTCTTAATT--TGGTAATTAAGAAAAGTAAACACAGT
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* * * *
27102 CAGAA-TCTTAATTCAGGGTAATTAAGAAGAGCATACACATT
1 TA-AAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
* * *
27143 TAAAGTCTTAATTCATGGTAATTAAGGAAAGTAAACACAG-
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
27183 TAAGAGTCTTAATTCAGGGTAATTAAGAAGAA-CAAACA
1 TAA-AGTCTTAATTCAGGGTAATTAAGAA-AAGCAAACA
27221 TAGTCAAGGT
Statistics
Matches: 356, Mismatches: 50, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
28 11 0.03
29 3 0.01
30 4 0.01
33 3 0.01
34 3 0.01
37 4 0.01
38 1 0.00
39 86 0.24
40 14 0.04
41 187 0.53
42 40 0.11
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (41 bp):
TAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
Found at i:26870 original size:80 final size:80
Alignment explanation
Indices: 26782--27248 Score: 543
Period size: 80 Copynumber: 5.9 Consensus size: 80
26772 TTAACAAGAC
* *
26782 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACGGTTAAAGTCTAAATTT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTT
*
26847 GGTAATTAAGAAAAA
66 GGTAATTAAGAAAAG
*
26862 CAAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAAGTCTTAATT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTT-AAAGTCTTAATT
*
26927 CAGGGTAATTAAGAAAAG
65 --TGGTAATTAAGAAAAG
* * * *
26945 CAAACATAGTCAAAGTCTTAATT--TGGTAATT-----AAG----CAGAG-T-AAGTCTTAATTT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTT
26997 GGTAATTAAGAAAAG
66 GGTAATTAAGAAAAG
* *
27012 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAGAGTCTTAATTT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTT
27077 GGTAATTAAGAAAAG
66 GGTAATTAAGAAAAG
* * * * *
27092 TAAACACAGTCAGAA-TCTTAATTCAGGGTAATTAAGAAGAGCATACACATTTAAAGTCTTAATT
1 CAAACACAGTTA-AAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAGTCTTAATT
*
27156 CATGGTAATTAAGGAAAG
65 --TGGTAATTAAGAAAAG
* * * * *
27174 TAAACACAG-TAAGAGTCTTAATTCAGGGTAATTAAGAAGAA-CAAACATAGTCAAGGTCCTAAT
1 CAAACACAGTTAA-AGTCTTAATTCAGGGTAATTAAGAA-AAGCAAACACAGTTAAAGTCTTAAT
*
27237 TTGGTAAGTAAG
64 TTGGTAATTAAG
27249 TCTTAATTCA
Statistics
Matches: 331, Mismatches: 34, Indels: 44
0.81 0.08 0.11
Matches are distributed among these distances:
67 36 0.11
69 18 0.05
71 1 0.00
72 4 0.01
74 3 0.01
76 3 0.01
78 4 0.01
80 141 0.43
81 22 0.07
82 64 0.19
83 35 0.11
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (80 bp):
CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTT
GGTAATTAAGAAAAG
Found at i:27243 original size:121 final size:119
Alignment explanation
Indices: 26782--27248 Score: 487
Period size: 121 Copynumber: 4.0 Consensus size: 119
26772 TTAACAAGAC
* *
26782 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACGGTTAA-AGTCTAAATT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAG-TAAGAGTCTTAATT
* * * * * *
26846 TGGTAATTAAGAAAAACAAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAG
65 GGGTAATTAAGAAAAGCAAACACAGTCAGAATCCTAATT--TGGTAATTAAGAAAAG
*
26903 CAAACACAGTTAAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACATAGTCAA-AGTCTTAAT
1 CAAACACAGTT-AAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT-AAGAGTCTTAAT
* * * *
26967 TTGGTAATT-----AAG----CAGAGT-A-AGTCTTAATTTGGTAATTAAGAAAAG
64 TGGGTAATTAAGAAAAGCAAACACAGTCAGAATCCTAATTTGGTAATTAAGAAAAG
* *
27012 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAGAGTCTTAATTT
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTAAGAGTCTTAATTG
* * * *
27077 GGTAATTAAGAAAAGTAAACACAGTCAGAATCTTAATTCAGGGTAATTAAGAAGAG
66 GGTAATTAAGAAAAGCAAACACAGTCAGAATCCTAATT--TGGTAATTAAGAAAAG
* * * * *
27133 CATACACATTTAAAGTCTTAATTCATGGTAATTAAGGAAAGTAAACACAGTAAGAGTCTTAATTC
1 CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTAAGAGTCTTAATT-
* * *
27198 AGGGTAATTAAGAAGAA-CAAACATAGTCA-AGGTCCTAATTTGGTAAGTAAG
65 -GGGTAATTAAGAA-AAGCAAACACAGTCAGA-ATCCTAATTTGGTAATTAAG
27249 TCTTAATTCA
Statistics
Matches: 301, Mismatches: 25, Indels: 40
0.82 0.07 0.11
Matches are distributed among these distances:
107 1 0.00
108 57 0.19
109 26 0.09
111 10 0.03
112 1 0.00
113 8 0.03
117 7 0.02
118 1 0.00
119 9 0.03
121 93 0.31
122 57 0.19
123 29 0.10
124 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (119 bp):
CAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTAAGAGTCTTAATTG
GGTAATTAAGAAAAGCAAACACAGTCAGAATCCTAATTTGGTAATTAAGAAAAG
Found at i:27305 original size:41 final size:41
Alignment explanation
Indices: 27246--27601 Score: 414
Period size: 41 Copynumber: 8.7 Consensus size: 41
27236 TTTGGTAAGT
* *
27246 AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTA
1 AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
*
27287 AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACATAGTTA
1 AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
* * *
27328 AGGTCTTAATTCAGGGTAATTAAG-AAAGTCAAACACAGTCA
1 AAGTCTTAATTCATGGTAATTAAGAAAAG-CAAACACAGTTA
* *
27369 AAGTCTTAATT-AGGGGTAATTAAG-AAAGTCAAATACAGTTA
1 AAGTCTTAATTCA-TGGTAATTAAGAAAAG-CAAACACAGTTA
* * * * *
27410 AAGTCTTAATTCTTGGTAATTAAGGAGAGAAAACATAGTTA
1 AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
* * * * *
27451 AAGTCTTATTTCATGGTAATTAAGGAAAGTAAGCACAGTCA
1 AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
* * *
27492 GAA-TCTTAATTCAGGGTAATTAAGAAGAGCATACACAGTTA
1 -AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
* ** *
27533 AGGTCTTAATTCATAATAATTAAGGAAAAGTAAACACAGTTA
1 AAGTCTTAATTCATGGTAATTAA-GAAAAGCAAACACAGTTA
27575 AAGTCTTAATTCATGGTAATTAAGAAA
1 AAGTCTTAATTCATGGTAATTAAGAAA
27602 GGTAATCATA
Statistics
Matches: 267, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
40 6 0.02
41 221 0.83
42 40 0.15
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (41 bp):
AAGTCTTAATTCATGGTAATTAAGAAAAGCAAACACAGTTA
Found at i:27320 original size:101 final size:101
Alignment explanation
Indices: 27145--27338 Score: 302
Period size: 101 Copynumber: 1.9 Consensus size: 101
27135 TACACATTTA
* * *
27145 AAGTCTTAATTCATGGTAATTAAGGAAAGTAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAG
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAG
27210 AAGAACAAACATAGTCAAGGTCCTAATTTGGTAAGT
66 AAGAACAAACATAGTCAAGGTCCTAATTTGGTAAGT
*
27246 AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAA-AGTCTTAATTCATGGTAATTAA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAG-TAAGAGTCTTAATTCAGGGTAATTAA
* *
27310 GAA-AAGCAAACATAGTTAAGGTCTTAATT
65 GAAGAA-CAAACATAGTCAAGGTCCTAATT
27339 CAGGGTAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
100 2 0.02
101 80 0.94
102 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.28
Consensus pattern (101 bp):
AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAG
AAGAACAAACATAGTCAAGGTCCTAATTTGGTAAGT
Found at i:27368 original size:142 final size:142
Alignment explanation
Indices: 27107--27379 Score: 415
Period size: 142 Copynumber: 1.9 Consensus size: 142
27097 ACAGTCAGAA
* * * * *
27107 TCTTAATTCAGGGTAATTAAGAAGAGCATACACATTTAAAGTCTTAATTCATGGTAATTAAGGAA
1 TCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAA
* * *
27172 AGTAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAGAAGAACAAACATAGTCAAGGTCCTAAT
66 AGCAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAGAAGAACAAACACAGTCAAAGTCCTAAT
27237 TTGGTAAGTAAG
131 TTGGTAAGTAAG
27249 TCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAA
* * *
27314 AGCAAACATAGTTAAG-GTCTTAATTCAGGGTAATTAAGAA-AGTCAAACACAGTCAAAGTCTTA
66 AGCAAACACAG-TAAGAGTCTTAATTCAGGGTAATTAAGAAGA-ACAAACACAGTCAAAGTCCTA
27377 ATT
129 ATT
27380 AGGGGTAATT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 1 0.01
142 113 0.96
143 4 0.03
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (142 bp):
TCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAA
AGCAAACACAGTAAGAGTCTTAATTCAGGGTAATTAAGAAGAACAAACACAGTCAAAGTCCTAAT
TTGGTAAGTAAG
Found at i:27469 original size:123 final size:122
Alignment explanation
Indices: 27246--27602 Score: 486
Period size: 123 Copynumber: 2.9 Consensus size: 122
27236 TTTGGTAAGT
*
27246 AAGTCTTAATTCAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCATGGTAATTAAG
1 AAGTCTTAATTCAGGGTAATTAAG-AAAGCAAACACAGTTAAAGTCTTAATTCATGGTAATTAAG
* * * *
27311 AAAAGCAAACATAGTTAAGGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGTCA-
65 GAAAGAAAACATAGTTAAAGTCTTAATTCATGGTAATTAAGAAAGT-AAACACAGTCAG
* *
27369 AAGTCTTAATT-AGGGGTAATTAAGAAAGTCAAATACAGTTAAAGTCTTAATTCTTGGTAATTAA
1 AAGTCTTAATTCA-GGGTAATTAAGAAAG-CAAACACAGTTAAAGTCTTAATTCATGGTAATTAA
* * *
27433 GGAGAGAAAACATAGTTAAAGTCTTATTTCATGGTAATTAAGGAAAGTAAGCACAGTCAG
64 GGAAAGAAAACATAGTTAAAGTCTTAATTCATGGTAATTAA-GAAAGTAAACACAGTCAG
* * **
27493 AA-TCTTAATTCAGGGTAATTAAGAAGAGCATACACAGTTAAGGTCTTAATTCATAATAATTAAG
1 AAGTCTTAATTCAGGGTAATTAAGAA-AGCAAACACAGTTAAAGTCTTAATTCATGGTAATTAAG
* *
27557 GAAAAGTAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAAG
65 G-AAAGAAAACATAGTTAAAGTCTTAATTCATGGTAATTAAGAAAG
27603 GTAATCATAA
Statistics
Matches: 207, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
122 5 0.02
123 156 0.75
124 46 0.22
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (122 bp):
AAGTCTTAATTCAGGGTAATTAAGAAAGCAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGG
AAAGAAAACATAGTTAAAGTCTTAATTCATGGTAATTAAGAAAGTAAACACAGTCAG
Found at i:27691 original size:41 final size:41
Alignment explanation
Indices: 27635--27728 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
27625 AGTAATTAAG
* *
27635 AAGTAAGGCATAGACTTAATTTCAAGGAAAGAAATTAGGTA
1 AAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
*
27676 AAGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
1 AAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
27717 AAGTAAAGCACA
1 AAGTAAAGCACA
27729 AAATTTAGGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
Found at i:27848 original size:32 final size:32
Alignment explanation
Indices: 27730--27850 Score: 134
Period size: 32 Copynumber: 3.7 Consensus size: 32
27720 TAAAGCACAA
* **
27730 AATTTAGGGTAATTAAGTAGAGTCAATAAAGGGCTT
1 AATTCAGGGTAATTAAGT-G-G--AATAAAGAACTT
* **
27766 AATTCAGGGTAATTAAGTAGAATAAAGAACAA
1 AATTCAGGGTAATTAAGTGGAATAAAGAACTT
*
27798 AATTCTGGGTAATTAAGTGGAATAAAGAACTT
1 AATTCAGGGTAATTAAGTGGAATAAAGAACTT
*
27830 AATTCAAGGTAATTAAGTGGA
1 AATTCAGGGTAATTAAGTGGA
27851 GTCAATAGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
32 55 0.75
34 1 0.01
36 17 0.23
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (32 bp):
AATTCAGGGTAATTAAGTGGAATAAAGAACTT
Found at i:27865 original size:64 final size:67
Alignment explanation
Indices: 27703--27847 Score: 174
Period size: 68 Copynumber: 2.2 Consensus size: 67
27693 AATTTCAAGG
* * * **
27703 AAGGAAATTAGGTA-AAGTAAAGCACAAAATT-TAGGGTAATTAAGTAGAGTCAATAAAGGGCTT
1 AAGGTAATTAAGTAGAA-TAAAGAACAAAATTCT-GGGTAATTAAGTAGAG-CAATAAAGAACTT
27766 AATTC
63 AATTC
*
27771 AGGGTAATTAAGTAGAATAAAGAACAAAATTCTGGGTAATTAAGT-G-G-AATAAAGAACTTAAT
1 AAGGTAATTAAGTAGAATAAAGAACAAAATTCTGGGTAATTAAGTAGAGCAATAAAGAACTTAAT
27833 TC
66 TC
27835 AAGGTAATTAAGT
1 AAGGTAATTAAGT
27848 GGAGTCAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
64 27 0.40
66 1 0.01
67 1 0.01
68 36 0.53
69 3 0.04
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (67 bp):
AAGGTAATTAAGTAGAATAAAGAACAAAATTCTGGGTAATTAAGTAGAGCAATAAAGAACTTAAT
TC
Found at i:34681 original size:122 final size:122
Alignment explanation
Indices: 34464--34708 Score: 427
Period size: 122 Copynumber: 2.0 Consensus size: 122
34454 TGAGGCCCAC
* *
34464 CAACGTGGCCTATATATACCTGTCGGACACCAACTTGAACCGAAAAGTTTAAGCCTATGTGTTCT
1 CAACGTGGCCCATATATACCTGTAGGACACCAACTTGAACCGAAAAGTTTAAGCCTATGTGTTCT
*
34529 TGGATCTTTCAGGTATATATGCCACTTTTACAGCCCATCCCTTTATGATATGGGATG
66 TGGATCTTTCAGGTATATATGCCACTTTTACAACCCATCCCTTTATGATATGGGATG
* * *
34586 CAACGTGGCCCATATATACCTGTAGGACACCAACTTGAACCTAAAAGTTTAAGCTTGTGTGTTCT
1 CAACGTGGCCCATATATACCTGTAGGACACCAACTTGAACCGAAAAGTTTAAGCCTATGTGTTCT
*
34651 TGGGTCTTTCAGGTATATATGCCACTTTTACAACCCATCCCTTTATGATATGGGATG
66 TGGATCTTTCAGGTATATATGCCACTTTTACAACCCATCCCTTTATGATATGGGATG
34708 C
1 C
34709 TGTCGCAACG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (122 bp):
CAACGTGGCCCATATATACCTGTAGGACACCAACTTGAACCGAAAAGTTTAAGCCTATGTGTTCT
TGGATCTTTCAGGTATATATGCCACTTTTACAACCCATCCCTTTATGATATGGGATG
Found at i:35576 original size:35 final size:35
Alignment explanation
Indices: 35531--35753 Score: 268
Period size: 35 Copynumber: 6.3 Consensus size: 35
35521 TAAGCCATAT
*** **
35531 ATTTACTTAATTACACCGAATTAAGGCCATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
* * **
35566 ATTTATTTAATTACACCGAATTAAATTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
* *
35601 ATTTACTTAATTACACTGAATTAAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
*
35636 ATTTACTTAACTACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
* *
35671 AATTAATTAATTACACCGAATTAAGCTT-ATTACCA
1 ATTTACTTAATTACACCGAATTAAG-TTGATTACCA
*
35706 AATTACTTAATTACACCGAATTAAGTTGATTACCCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTA-CCA
* *
35742 AATCACTTAATT
1 ATTTACTTAATT
35754 CAATTACCAA
Statistics
Matches: 166, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
34 2 0.01
35 148 0.89
36 16 0.10
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:36418 original size:22 final size:23
Alignment explanation
Indices: 36371--36421 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
36361 TTATGAACGT
36371 AATTTACTAAATGCCAAAGAGTG
1 AATTTACTAAATGCCAAAGAGTG
36394 AATTTACTAAATGCCAAA-AGTG
1 AATTTACTAAATGCCAAAGAGTG
36416 AATTTA
1 AATTTA
36422 GAAAATGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (23 bp):
AATTTACTAAATGCCAAAGAGTG
Found at i:36427 original size:22 final size:23
Alignment explanation
Indices: 36371--36428 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
36361 TTATGAACGT
*
36371 AATTTACTAAATGCCAAAGAGTG
1 AATTTACAAAATGCCAAAGAGTG
*
36394 AATTTACTAAATGCCAAA-AGTG
1 AATTTACAAAATGCCAAAGAGTG
*
36416 AATTTAGAAAATG
1 AATTTACAAAATG
36429 ACCTTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (23 bp):
AATTTACAAAATGCCAAAGAGTG
Found at i:36849 original size:80 final size:80
Alignment explanation
Indices: 36702--36938 Score: 368
Period size: 80 Copynumber: 3.0 Consensus size: 80
36692 ATCTTGAAGA
* ** * * *
36702 AATAATGCACCGCA-TTAACTTGATTCACCGAATCACCCTGAACTGTTTGAGAATGTGCTGCACC
1 AATAATGCACCACATTTAACTTGATTCACCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
36766 GAGCTCACCGAATAC
66 GAGCTCACCGAATAC
* *
36781 AATAATGTACGACATTTAACTTGATTCACCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
1 AATAATGCACCACATTTAACTTGATTCACCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
*
36846 GAGCTCACCGAATCC
66 GAGCTCACCGAATAC
*
36861 AATAATGCACCACATTTAACTTGATTCATCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
1 AATAATGCACCACATTTAACTTGATTCACCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
*
36926 AAGCTCACCGAAT
66 GAGCTCACCGAAT
36939 TCCAATCTTT
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 11 0.08
80 133 0.92
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (80 bp):
AATAATGCACCACATTTAACTTGATTCACCGAATCGTCCTGAACTGTTTGAAAATATGCTACACC
GAGCTCACCGAATAC
Found at i:37000 original size:89 final size:88
Alignment explanation
Indices: 36864--37035 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 88
36854 CGAATCCAAT
* * *
36864 AATGCACCACATTTAACTTGATTCATCGAATCGTCCTGAACTGTTTGAAAATATGCTACACCAAG
1 AATGCACCACATTTAACTTGATTCACCGAATCGACCTGAACTATTTGAAAATATGCTACACCAAG
36929 CTCACCGAATTCCAATCTTTGAATA
66 CTCACCGAA-TCCAA-CTTTGAATA
* * * ** *
36954 AATGCACCGCA-TTAACTTGATTCACCGAATC-ACCATGATCTATTTGAAAATGTGCTGTACCGA
1 AATGCACCACATTTAACTTGATTCACCGAATCGACC-TGAACTATTTGAAAATATGCTACACCAA
*
37017 GCTCACTGAATCCAACTTT
65 GCTCACCGAATCCAACTTT
37036 AAAGAAATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
87 4 0.06
88 7 0.10
89 50 0.70
90 10 0.14
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (88 bp):
AATGCACCACATTTAACTTGATTCACCGAATCGACCTGAACTATTTGAAAATATGCTACACCAAG
CTCACCGAATCCAACTTTGAATA
Found at i:38880 original size:29 final size:29
Alignment explanation
Indices: 38814--38898 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
38804 TGGGCATCCA
* *
38814 ACGTGGCATGCCACATGTACCAAAAAAATGTC
1 ACGTGGCATGCCACATGTA-C--AAAAAGGAC
* *
38846 ATGTGGCATGCCACGTGTACAAAAAGGAC
1 ACGTGGCATGCCACATGTACAAAAAGGAC
*
38875 ACGTGGTATGCCACATGT-CAAAAA
1 ACGTGGCATGCCACATGTACAAAAA
38899 TACCATGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.13
29 22 0.48
31 1 0.02
32 17 0.37
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (29 bp):
ACGTGGCATGCCACATGTACAAAAAGGAC
Found at i:45642 original size:13 final size:14
Alignment explanation
Indices: 45610--45642 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
45600 CTCCCTTGTC
45610 AATAAAGATTAGTA
1 AATAAAGATTAGTA
45624 AATAAAGATTAGT-
1 AATAAAGATTAGTA
45637 AATAAA
1 AATAAA
45643 AATGTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (14 bp):
AATAAAGATTAGTA
Found at i:47200 original size:2 final size:2
Alignment explanation
Indices: 47193--47219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47183 AGAAGTACCC
47193 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47220 CGCCAAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52311 original size:37 final size:37
Alignment explanation
Indices: 52244--52489 Score: 187
Period size: 37 Copynumber: 6.6 Consensus size: 37
52234 CAGTGTTTTA
* *
52244 TAAGGAGAGCTCTGCGATAAAGAGGGTGCTACCGCAG
1 TAAGGAGAGCTCTACGATAAAGAGGATGCTACCGCAG
* * * * *
52281 TAAGGAGAGCTCTATGATGAAGATGATGCTATCGTAG
1 TAAGGAGAGCTCTACGATAAAGAGGATGCTACCGCAG
* * *
52318 TAAGAAGAGCTCT-CCAGTAAAGAGGGTGCTACCGCAG
1 TAAGGAGAGCTCTACGA-TAAAGAGGATGCTACCGCAG
* * * * * *
52355 TAA-TAGAGCTCTACGGTGAAAGAGGGTGCTAGCACTG
1 TAAGGAGAGCTCTACGAT-AAAGAGGATGCTACCGCAG
* * * * *
52392 TAAGGATAGCTCTGCGGTAAAGAGGTTGCTATCGCAG
1 TAAGGAGAGCTCTACGATAAAGAGGATGCTACCGCAG
* * *
52429 TAA-GAGGAGCTCTGCGGTAAAGAGGGTGCTATCACG-A-
1 TAAGGA-GAGCTCTACGATAAAGAGGATGCTA-C-CGCAG
*
52466 TAAGGAGAGCTCTGCGATAAAGAG
1 TAAGGAGAGCTCTACGATAAAGAG
52490 TGCTATCGCA
Statistics
Matches: 169, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
36 12 0.07
37 141 0.83
38 14 0.08
39 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (37 bp):
TAAGGAGAGCTCTACGATAAAGAGGATGCTACCGCAG
Found at i:52385 original size:74 final size:73
Alignment explanation
Indices: 52244--52489 Score: 275
Period size: 74 Copynumber: 3.3 Consensus size: 73
52234 CAGTGTTTTA
* * * *
52244 TAAGGAGAGCTCTGCGATAAAGAGGGTGCTACCGCAGTAAGGAGAGCTCTATGATG-AAGATGAT
1 TAAGGAGAGCTCTGCG-TAAAGAGGGTGCTACCGCAGTAA-GAGAGCTCTACGGTGAAAGAGGGT
*
52308 GCTATC-GTAG
64 GCTATCACT-G
* * *
52318 TAAGAAGAGCTCTCCAGTAAAGAGGGTGCTACCGCAGTAATAGAGCTCTACGGTGAAAGAGGGTG
1 TAAGGAGAGCTCTGC-GTAAAGAGGGTGCTACCGCAGTAAGAGAGCTCTACGGTGAAAGAGGGTG
*
52383 CTAGCACTG
65 CTATCACTG
* * * *
52392 TAAGGATAGCTCTGCGGTAAAGAGGTTGCTATCGCAGTAAGAGGAGCTCTGCGGT-AAAGAGGGT
1 TAAGGAGAGCTCTGC-GTAAAGAGGGTGCTACCGCAGTAAGA-GAGCTCTACGGTGAAAGAGGGT
52456 GCTATCAC-G
64 GCTATCACTG
52465 ATAAGGAGAGCTCTGCGATAAAGAG
1 -TAAGGAGAGCTCTGCG-TAAAGAG
52490 TGCTATCGCA
Statistics
Matches: 147, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
73 14 0.10
74 120 0.82
75 13 0.09
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (73 bp):
TAAGGAGAGCTCTGCGTAAAGAGGGTGCTACCGCAGTAAGAGAGCTCTACGGTGAAAGAGGGTGC
TATCACTG
Found at i:52453 original size:18 final size:19
Alignment explanation
Indices: 52398--52453 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
52388 ACTGTAAGGA
52398 TAGCTCTGCGGTAAAGAGG
1 TAGCTCTGCGGTAAAGAGG
* * *
52417 TTGCTATCGCAGT-AAGAGG
1 TAGCTCT-GCGGTAAAGAGG
52436 -AGCTCTGCGGTAAAGAGG
1 TAGCTCTGCGGTAAAGAGG
52454 GTGCTATCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 11 0.38
20 4 0.14
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.21
Consensus pattern (19 bp):
TAGCTCTGCGGTAAAGAGG
Found at i:52456 original size:111 final size:110
Alignment explanation
Indices: 52249--52489 Score: 270
Period size: 111 Copynumber: 2.2 Consensus size: 110
52239 TTTTATAAGG
* * * * *
52249 AGAGCTCTGCGATAAAGAGGGTGCTACCGCAGTAAGGAGAGCTCTATGATGAAGATGATGCTATC
1 AGAGCTCTACGATAAAGAGGGTGCTACCACAGTAAGGAGAGCTCTACGATAAAGAGGATGCTATC
*
52314 GTAGTAAGAAGAGCTCTCCAGTAAAGAGGGTGCTACCGCAGTAAT
66 GCAGTAAGAAGAGCTCTCCAGTAAAGAGGGTGCTACCGCAGTAAT
* * * * * * *
52359 AGAGCTCTACGGTGAAAGAGGGTGCTAGCACTGTAAGGATAGCTCTGCGGTAAAGAGGTTGCTAT
1 AGAGCTCTACGAT-AAAGAGGGTGCTACCACAGTAAGGAGAGCTCTACGATAAAGAGGATGCTAT
* * * *
52424 CGCAGTAAGAGGAGCTCTGCGGTAAAGAGGGTGCTATCACG-A-TAAGG
65 CGCAGTAAGAAGAGCTCTCCAGTAAAGAGGGTGCTA-C-CGCAGTAA-T
*
52471 AGAGCTCTGCGATAAAGAG
1 AGAGCTCTACGATAAAGAG
52490 TGCTATCGCA
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
110 11 0.10
111 82 0.76
112 13 0.12
113 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.32, T:0.20
Consensus pattern (110 bp):
AGAGCTCTACGATAAAGAGGGTGCTACCACAGTAAGGAGAGCTCTACGATAAAGAGGATGCTATC
GCAGTAAGAAGAGCTCTCCAGTAAAGAGGGTGCTACCGCAGTAAT
Found at i:57633 original size:13 final size:13
Alignment explanation
Indices: 57615--57639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57605 TATTGTTATT
57615 TTGTAGATCTAGG
1 TTGTAGATCTAGG
57628 TTGTAGATCTAG
1 TTGTAGATCTAG
57640 AATTATGTAA
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAGG
Found at i:57990 original size:22 final size:22
Alignment explanation
Indices: 57959--58004 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
57949 TCAAAAGTGT
* *
57959 AAAAAATGGGACGGTGTTTAGC
1 AAAAAATGGGACAGTATTTAGC
*
57981 AAAAACTGGGACAGTATTTAGC
1 AAAAAATGGGACAGTATTTAGC
58003 AA
1 AA
58005 CACCCATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (22 bp):
AAAAAATGGGACAGTATTTAGC
Found at i:59957 original size:16 final size:16
Alignment explanation
Indices: 59935--59980 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
59925 AATAAGTACT
*
59935 ATAACCCGAAACCGAT
1 ATAACCCGAAACCGAG
* *
59951 TTAACCCG-AATCGAG
1 ATAACCCGAAACCGAG
59966 ATAACCCGAAACCGA
1 ATAACCCGAAACCGA
59981 CAAAATTCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (16 bp):
ATAACCCGAAACCGAG
Found at i:61385 original size:6 final size:6
Alignment explanation
Indices: 61370--61408 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
61360 AAAGCAAAGC
*
61370 AAATCA AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
61409 GCAAATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:61397 original size:18 final size:18
Alignment explanation
Indices: 61370--61413 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
61360 AAAGCAAAGC
61370 AAATCAAAATCTAAATCT
1 AAATCAAAATCTAAATCT
*
61388 AAATCTAAATCTAAATCT
1 AAATCAAAATCTAAATCT
*
61406 AAAGCAAA
1 AAATCAAA
61414 TTAATAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATCAAAATCTAAATCT
Found at i:62358 original size:10 final size:10
Alignment explanation
Indices: 62343--62367 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
62333 GAGGACTCTA
62343 GAATTTTCTG
1 GAATTTTCTG
62353 GAATTTTCTG
1 GAATTTTCTG
62363 GAATT
1 GAATT
62368 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:66256 original size:35 final size:35
Alignment explanation
Indices: 66210--66306 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 35
66200 ACAATAGTAG
*
66210 CTCTTCCGGAGCCTTCAATCAAATTTGAATACTGA
1 CTCTTCTGGAGCCTTCAATCAAATTTGAATACTGA
* * * *
66245 CTCTTCTGGAGCCTTTAATCAATTTTAAATACTGG
1 CTCTTCTGGAGCCTTCAATCAAATTTGAATACTGA
66280 CTCTTCTGGAGCCTTCAATCAAATTTG
1 CTCTTCTGGAGCCTTCAATCAAATTTG
66307 CACCATCTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (35 bp):
CTCTTCTGGAGCCTTCAATCAAATTTGAATACTGA
Found at i:67014 original size:37 final size:38
Alignment explanation
Indices: 66948--67024 Score: 129
Period size: 37 Copynumber: 2.0 Consensus size: 38
66938 GATGTATTAT
66948 TAGAATAATCTCCATGATGATATTCATTACTACAATCACG
1 TAGAATAATCTCCA--ATGATATTCATTACTACAATCACG
66988 TAGAATAATCTCC-ATGATATTCATTACTACAATCACG
1 TAGAATAATCTCCAATGATATTCATTACTACAATCACG
67025 ATCATGACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
37 24 0.65
40 13 0.35
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (38 bp):
TAGAATAATCTCCAATGATATTCATTACTACAATCACG
Found at i:67717 original size:53 final size:54
Alignment explanation
Indices: 67607--67717 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
67597 AACATATATA
* *
67607 TAAAATTTAAAGTGGATAGTATGACAACTTCGAGTGTCAAACTTTGGCAACAAT
1 TAAAATTTAAAGTGGATAGTATGACAACTTCGAGTGTCAAACTCTGACAACAAT
* * *
67661 TAAAGTTTTAAGTGGATAGTATGACAACTT-GGGTGTCAAACTCTGACAACAAT
1 TAAAATTTAAAGTGGATAGTATGACAACTTCGAGTGTCAAACTCTGACAACAAT
67714 TAAA
1 TAAA
67718 CAAATATTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 24 0.46
54 28 0.54
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (54 bp):
TAAAATTTAAAGTGGATAGTATGACAACTTCGAGTGTCAAACTCTGACAACAAT
Found at i:67794 original size:29 final size:29
Alignment explanation
Indices: 67738--67794 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
67728 CATCCTTAAT
* *
67738 ATGACAATTTCGGGTGTCAAAATGATACG
1 ATGACAACTTCGGGTGTCAAAATAATACG
*
67767 ATGACAACTTCGGGTGTCAAAGTAATAC
1 ATGACAACTTCGGGTGTCAAAATAATAC
67795 TATATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (29 bp):
ATGACAACTTCGGGTGTCAAAATAATACG
Found at i:67846 original size:33 final size:33
Alignment explanation
Indices: 67804--67887 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
67794 CTATATTTTA
* *
67804 GATGTGACAACTTCATGTGCAACTAATATGCTT
1 GATGTGACAACTTCAGGTGCAACTAATATACTT
* * *
67837 GATGTGACAACTTCAGGTGCCACTGATATATTT
1 GATGTGACAACTTCAGGTGCAACTAATATACTT
67870 GATGTGACAACTTCAGGT
1 GATGTGACAACTTCAGGT
67888 CTCACTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (33 bp):
GATGTGACAACTTCAGGTGCAACTAATATACTT
Found at i:67997 original size:32 final size:33
Alignment explanation
Indices: 67932--68004 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
67922 ATAATTTTTA
* *
67932 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
67965 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
*
67997 ATGTTAAA
1 ATGATAAA
68005 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 18 0.49
33 19 0.51
ACGTcount: A:0.48, C:0.04, G:0.29, T:0.19
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
Found at i:69891 original size:26 final size:26
Alignment explanation
Indices: 69855--69910 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
69845 ATTAGTATGT
*
69855 AAGACCAACAAACTTTCTGTAAAACA
1 AAGACCAACAAACTTTCTCTAAAACA
*
69881 AAGACCAACAAACTTTCTCTAGAACA
1 AAGACCAACAAACTTTCTCTAAAACA
69907 AAGA
1 AAGA
69911 TAATACCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (26 bp):
AAGACCAACAAACTTTCTCTAAAACA
Found at i:71110 original size:324 final size:324
Alignment explanation
Indices: 70509--71301 Score: 1313
Period size: 324 Copynumber: 2.4 Consensus size: 324
70499 ATCCTTGATG
* * *
70509 GGGATCATTTATTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
1 GGGATCTTTTAGTAATTCCACTACTCTAATCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
* *
70574 TTTAATCCCCTCAAGAATCAAAATTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
66 TTTAATCCCTTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
*
70639 GAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
131 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
* * *
70704 TGAAAGTTTTGGACATTTACGTAATCTGCCAGGTAGGTAAAGACGAAAAATATTACTTATCCAGC
196 TGAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTATCCAGC
*
70769 TCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTCTCATTAATTCGGGGTA
261 TCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
*
70833 GGGATCTTTTAGTAATTCCACTACTCTAATCAAATCCATTGAAAAATGACCAAAAAGATTACTTA
1 GGGATCTTTTAGTAATTCCACTACTCTAATCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
*
70898 TTTAATCCCTTCAAGAAACAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
66 TTTAATCCCTTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
*
70963 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAGTTCCACTACTCTA
131 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
* *
71028 TTAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTCTCCAGC
196 TGAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTATCCAGC
*
71093 TCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTTATCATTAATTCGGGGTA
261 TCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
* * * *
71157 GGGATCTTTTAGTAATTCCACTACTC-AATTAAAGTCAAATGAGAAATGACCAAAAAG-TCTAGT
1 GGGATCTTTTAGTAATTCCACTACTCTAATCAAA-TCCATTGAGAAATGACCAAAAAGAT-TACT
* * *
71220 TATTTAATCACCTT-AAGAATCAAAAGTTAGGGCATTTAAGTAATCTGCCAAGTGGGAAAAAACG
64 TATTTAATC-CCTTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACG
*
71284 AAAAAAAATTAGTTCTCT
128 -AAAAAAATAAGTTCTCT
71302 CGCTCCTCAT
Statistics
Matches: 439, Mismatches: 26, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
323 7 0.02
324 412 0.94
325 20 0.05
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (324 bp):
GGGATCTTTTAGTAATTCCACTACTCTAATCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
TTTAATCCCTTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
TGAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTATCCAGC
TCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
Found at i:71138 original size:45 final size:45
Alignment explanation
Indices: 71088--71177 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
71078 GATTACTTCT
71088 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
* *
71133 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
71178 TACTCAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:72368 original size:2 final size:2
Alignment explanation
Indices: 72361--72403 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
72351 AGCCAAATCT
72361 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
72403 A
1 A
72404 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:72408 original size:2 final size:2
Alignment explanation
Indices: 72403--72428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72393 ACACACACAC
72403 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
72429 TCACACACTA
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:73784 original size:40 final size:40
Alignment explanation
Indices: 73736--73895 Score: 275
Period size: 40 Copynumber: 4.0 Consensus size: 40
73726 TACCCAATAA
*
73736 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCGC
1 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
* *
73776 TCACAGTCCTTAAACACATATAACACAAGGGCAATCTCTC
1 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
73816 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
1 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
* *
73856 TCAAAGTCCCTAAGCACATGTAACACAAGGGCAATCTCTC
1 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
73896 AAAGGTGATA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (40 bp):
TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
Found at i:78715 original size:52 final size:52
Alignment explanation
Indices: 78636--78738 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
78626 CAGTAATTTG
78636 AGGTTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTA
1 AGGTTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACAT-TTCATTA
78689 AGGTT-CCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACATTTCATT
1 AGGTTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACATTTCATT
78739 TTGGAAACCC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 6 0.12
52 39 0.78
53 5 0.10
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (52 bp):
AGGTTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACATTTCATTA
Found at i:78753 original size:52 final size:52
Alignment explanation
Indices: 78645--78755 Score: 161
Period size: 52 Copynumber: 2.1 Consensus size: 52
78635 GAGGTTCCCT
** *
78645 TTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTAAGGTTCCT
1 TTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTAAGGAACCC
**
78697 TTAATTATTGATATGTTAAGTGGGTTTTTAAGACAT-TTCATTTTGGAAACCC
1 TTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTAAGG-AACCC
78749 TTAATTA
1 TTAATTA
78756 CTTCAGTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 8 0.15
52 45 0.85
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (52 bp):
TTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTAAGGAACCC
Found at i:81189 original size:27 final size:27
Alignment explanation
Indices: 81151--81203 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
81141 TACTCAACCT
* **
81151 TTCCTACTCCTTTACATTACCAAACTG
1 TTCCTACTCCTTAACAACACCAAACTG
81178 TTCCTACTCCTTAACAACACCAAACT
1 TTCCTACTCCTTAACAACACCAAACT
81204 ACATAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACTG
Found at i:81354 original size:11 final size:11
Alignment explanation
Indices: 81338--81364 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
81328 AAACATAATC
81338 ATTTATCAAAT
1 ATTTATCAAAT
81349 ATTTATCAAAT
1 ATTTATCAAAT
81360 ATTTA
1 ATTTA
81365 GCCTCGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTATCAAAT
Found at i:81876 original size:25 final size:26
Alignment explanation
Indices: 81842--81891 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
81832 AGTATTGTAG
81842 AAATTGAATTTTGCT-AATAAAATAA
1 AAATTGAATTTTGCTAAATAAAATAA
*
81867 AAATTGAATTTTTCTAAATAAAATA
1 AAATTGAATTTTGCTAAATAAAATA
81892 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTGCTAAATAAAATAA
Found at i:82071 original size:27 final size:28
Alignment explanation
Indices: 82012--82077 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
82002 AAAAATACAC
*
82012 AAAAT-TATATTTTAATAGTGGCATAATT
1 AAAATATAT-TTTTAATAATGGCATAATT
*
82040 AAAATA-ATTTTTAATAATGGCA-ATTT
1 AAAATATATTTTTAATAATGGCATAATT
82066 AGAAATATATTT
1 A-AAATATATTT
82078 GAAAAAAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 18 0.55
28 11 0.33
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (28 bp):
AAAATATATTTTTAATAATGGCATAATT
Found at i:84118 original size:16 final size:16
Alignment explanation
Indices: 84097--84128 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
84087 ATATTTAAAT
84097 GACCCGAACCTGAAAA
1 GACCCGAACCTGAAAA
*
84113 GACCCGAATCTGAAAA
1 GACCCGAACCTGAAAA
84129 TCCAAGGCTT
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:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (16 bp):
GACCCGAACCTGAAAA
Done.