Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009797.1 Corchorus capsularis cultivar CVL-1 contig09818, 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: 36979
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:2449 original size:49 final size:49
Alignment explanation
Indices: 2367--2769 Score: 372
Period size: 49 Copynumber: 8.2 Consensus size: 49
2357 TCTTTCAATT
*
2367 TTCAGTTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
1 TTCA-TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
* * *
2417 TTCATTTTTACTTGCAATTTCCCAAAGTGCCCTTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
*
2466 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCG
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
* * *
2515 TTTATCTTTACTTGCTATTTCCCAAAAGCGCCCTTCCCGGACGGAAGGCA
1 TTCATTTTTACTTGCTATTTCCC-AAAGCGCCCTTCCCGGACGGAAGCCA
* * * * * ** *
2565 CTAATTTTT-CCTG-TTTTTCCGAAAATGCCCTTCCCGGACGGAAGACA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
* * * ** *
2612 --CGTATTTTACTTGCTATTTTTCAAAAATGCCCTTCCCGGATGGAAGACGC-
1 TTCAT-TTTTACTTGCTA-TTTCCCAAAGCGCCCTTCCCGGACGGAAG-C-CA
** * * *
2662 TT-ATTTTTACCCGCT-TTTCCCCAAAGTGCCCTTCCCCGACGGAAGGCA
1 TTCATTTTTACTTGCTATTT-CCCAAAGCGCCCTTCCCGGACGGAAGCCA
* * * * * * *
2710 CTAATTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGGCA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
*
2759 TT-AGTTTTACT
1 TTCATTTTTACT
2770 CGTTTTTTCT
Statistics
Matches: 294, Mismatches: 46, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.00
46 4 0.01
47 27 0.09
48 19 0.06
49 195 0.66
50 46 0.16
51 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (49 bp):
TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCA
Found at i:2791 original size:195 final size:195
Alignment explanation
Indices: 2396--2758 Score: 450
Period size: 195 Copynumber: 1.9 Consensus size: 195
2386 TTCCCAAAGC
* * * * *
2396 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCAATTTCCCAAAGTGCCCTTCCCAGACGGA
1 GCCCTTCCCGGACGGAAGACAGTCATTTTTACTTGCAATTTCCAAAAATGCCCTTCCCAGACGGA
** * ** *
2461 AGCCATTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGCCGTTTATCTTTAC
66 AGCCATTCATTTTTACCCGCTATTTCCCAAAGCGCCCTTCCCCGACGGAAGCCACTAATCTTTAC
2526 TTGCTATTTCCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAATTTTTCCTGTTTTTCCGAAAAT
131 TTGCTATTTCCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAATTTTTCCTGTTTTTCCGAAAAT
* * * *
2591 GCCCTTCCCGGACGGAAGACACGT-A-TTTTACTTGCTATTTTTCAAAAATGCCCTTCCCGGATG
1 GCCCTTCCCGGACGGAAGACA-GTCATTTTTACTTGC-AATTTCCAAAAATGCCCTTCCCAGACG
* * *
2654 GAAGACGC-TT-ATTTTTACCCGCT-TTTCCCCAAAGTGCCCTTCCCCGACGGAAGGCACTAATT
64 GAAG-C-CATTCATTTTTACCCGCTATTT-CCCAAAGCGCCCTTCCCCGACGGAAGCCACTAATC
* * *
2716 TTTACTTGCTTTTTCCTAAAA-CGCCCTTCCCGGATGGAAGGCA
126 TTTACTTGCTATTTCCCAAAAGCGCCCTTCCCGGACGGAAGGCA
2759 TTAGTTTTAC
Statistics
Matches: 142, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
194 34 0.24
195 103 0.73
196 4 0.03
197 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (195 bp):
GCCCTTCCCGGACGGAAGACAGTCATTTTTACTTGCAATTTCCAAAAATGCCCTTCCCAGACGGA
AGCCATTCATTTTTACCCGCTATTTCCCAAAGCGCCCTTCCCCGACGGAAGCCACTAATCTTTAC
TTGCTATTTCCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAATTTTTCCTGTTTTTCCGAAAAT
Found at i:6621 original size:14 final size:15
Alignment explanation
Indices: 6589--6640 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
6579 CAAGAGACGT
6589 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
*
6604 TTTTCAAGAAAA-GG
1 TTTTCAAAAAAATGG
*
6618 TTTTC--GAAAATGAG
1 TTTTCAAAAAAATG-G
6632 TTTTCAAAA
1 TTTTCAAAA
6641 GATTTTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 13 0.42
15 11 0.35
16 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:7406 original size:86 final size:85
Alignment explanation
Indices: 7249--7407 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 85
7239 AGAAAAGTGT
* * * **
7249 TTTTTTCTCAAAAAGGCTTTCAGACAAAATTAGTTTTAAAAGCTTTTCAGAGGCAAGCGCATAGT
1 TTTTTTCTCAAAAAGGCTTTCAGACAAAATTAGTTTCAAAAGCTTTTCAAAAGCAAGCGCATAAA
7314 GAAAAAATAACAAAAAATAG
66 GAAAAAATAACAAAAAATAG
* * * * *
7334 TTTTTTCTCAAAAAGGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTTCAAAAGCAAGCGCATGA
1 TTTTTTCTCAAAAA-GGCTTTCAGACAAAATTAGTTTCAAAAGCTTTTCAAAAGCAAGCGCAT-A
7399 AAGAAAAAA
64 AAGAAAAAA
7408 GAAAAGGGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 14 0.23
86 40 0.65
87 8 0.13
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (85 bp):
TTTTTTCTCAAAAAGGCTTTCAGACAAAATTAGTTTCAAAAGCTTTTCAAAAGCAAGCGCATAAA
GAAAAAATAACAAAAAATAG
Found at i:8497 original size:38 final size:38
Alignment explanation
Indices: 8455--8545 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
8445 TGGTCCCTTT
* *
8455 CAGGTCATCTTTCAGCAATAAACAAAGTTGGCTGGAAA
1 CAGGTCATCTTTCAACAATAAACAAAGTTGACTGGAAA
* *
8493 CAGGTCATCTTTCAACAGTAATCAAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACAATAAACAAAGTTGACTGGAAA
8531 CAGGTCATCTTTCAA
1 CAGGTCATCTTTCAA
8546 GTTATCAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (38 bp):
CAGGTCATCTTTCAACAATAAACAAAGTTGACTGGAAA
Found at i:8705 original size:39 final size:38
Alignment explanation
Indices: 8557--8828 Score: 222
Period size: 39 Copynumber: 7.3 Consensus size: 38
8547 TTATCAGAGA
* *
8557 TCATC-TTCCAAA-TTATCAAAGTTGACTGGAAACAGG
1 TCATCTTTCAAAACTTATCTAAGTTGACTGGAAACAGG
* * *
8593 TCATCTTTCAAAAATTATCTTA--CGACTGGAAACAGG
1 TCATCTTTCAAAACTTATCTAAGTTGACTGGAAACAGG
** ** *
8629 TTGTCTTTCAGCACTTAT-TAGGTTTGACTGGAAACAGG
1 TCATCTTTCAAAACTTATCTAAG-TTGACTGGAAACAGG
* *
8667 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGG
1 TCATCTTTCAA-AACTTATCTAAGTTGACTGGAAACAGG
* * *
8706 TCATCTTTCAGCAA-TTATCTTA--CGACTGGAAACAGG
1 TCATCTTTCA-AAACTTATCTAAGTTGACTGGAAACAGG
* * * **
8742 TCGTCTTTCAACACTT-GCTCGGTTTGACTGGAAACAGG
1 TCATCTTTCAAAACTTATCTAAG-TTGACTGGAAACAGG
* *
8780 TCATCTTTCAACAAGTTATC-AAGATCGACTGGAAACAGG
1 TCATCTTTCAA-AACTTATCTAAG-TTGACTGGAAACAGG
8819 TCATCTTTCA
1 TCATCTTTCA
8829 GCAGTTTTCG
Statistics
Matches: 184, Mismatches: 38, Indels: 25
0.74 0.15 0.10
Matches are distributed among these distances:
35 4 0.02
36 55 0.30
37 6 0.03
38 56 0.30
39 60 0.33
40 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (38 bp):
TCATCTTTCAAAACTTATCTAAGTTGACTGGAAACAGG
Found at i:8709 original size:113 final size:113
Alignment explanation
Indices: 8569--8828 Score: 423
Period size: 113 Copynumber: 2.3 Consensus size: 113
8559 ATCTTCCAAA
*
8569 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAAAAATTATCTTACGACTGGAAACAGGTTGTC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAAAAATTATCTTACGACTGGAAACAGGTCGTC
* * *
8634 TTTCAGCACTTATTAGGTTTGACTGGAAACAGGTCATCTTTCAATAAG
66 TTTCAACACTTACTAGGTTTGACTGGAAACAGGTCATCTTTCAACAAG
**
8682 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGGTCGTC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAAAAATTATCTTACGACTGGAAACAGGTCGTC
* *
8747 TTTCAACACTTGCTCGGTTTGACTGGAAACAGGTCATCTTTCAACAAG
66 TTTCAACACTTACTAGGTTTGACTGGAAACAGGTCATCTTTCAACAAG
*
8795 TTATC-AAGATCGACTGGAAACAGGTCATCTTTCA
1 TTATCAAAG-TTGACTGGAAACAGGTCATCTTTCA
8829 GCAGTTTTCG
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
112 3 0.02
113 134 0.98
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (113 bp):
TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAAAAATTATCTTACGACTGGAAACAGGTCGTC
TTTCAACACTTACTAGGTTTGACTGGAAACAGGTCATCTTTCAACAAG
Found at i:8884 original size:15 final size:16
Alignment explanation
Indices: 8863--8922 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 16
8853 GAGCATTTCA
8863 ACAACTTTTCAACTTT
1 ACAACTTTTCAACTTT
* *
8879 -CAACTTTACAGCATTT
1 ACAACTTTTCAAC-TTT
8895 CGACAACTTTTCAA-TTT
1 --ACAACTTTTCAACTTT
8912 ACAACTTTTCA
1 ACAACTTTTCA
8923 GCATTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 21 0.58
16 3 0.08
17 3 0.08
19 9 0.25
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (16 bp):
ACAACTTTTCAACTTT
Found at i:8892 original size:34 final size:34
Alignment explanation
Indices: 8854--8931 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
8844 CCCCAAGCGG
8854 AGCATTTCAACAACTTTTCAACTTT-CAACTTTAC
1 AGCATTTCAACAACTTTTCAA-TTTACAACTTTAC
* *
8888 AGCATTTCGACAACTTTTCAATTTACAACTTTTC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTAC
8922 AGCATTTCAA
1 AGCATTTCAA
8932 TTCACAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (34 bp):
AGCATTTCAACAACTTTTCAATTTACAACTTTAC
Found at i:8921 original size:26 final size:25
Alignment explanation
Indices: 8872--8945 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 25
8862 AACAACTTTT
* *
8872 CAACTTTCAACTTTACAGCATTTC-G
1 CAACTTTCAA-TTTACAACTTTTCAG
8897 ACAACTTTTCAATTTACAACTTTTCAG
1 -CAAC-TTTCAATTTACAACTTTTCAG
*
8924 C-A-TTTCAATTCACAACTTTTCA
1 CAACTTTCAATTTACAACTTTTCA
8946 ACTGACAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 19 0.44
25 1 0.02
26 16 0.37
27 7 0.16
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (25 bp):
CAACTTTCAATTTACAACTTTTCAG
Found at i:9042 original size:48 final size:47
Alignment explanation
Indices: 8953--9099 Score: 217
Period size: 47 Copynumber: 3.1 Consensus size: 47
8943 TCAACTGACA
*
8953 ACTTCCATGTGAGTCAGCAATCCTTCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
*
9000 ACTTCCATGTGAGTCAGAAATCATTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGTCTTTCCTC
* *
9048 ACTTCCA-GATGGGTCAGAAATCCTTCGACCAAAGTTGGTCTTGT-CTC
1 ACTTCCATG-TGAGTCAGAAATCCTTCGACCCAAGTTGGTCTT-TCCTC
9095 ACTTC
1 ACTTC
9100 TTTGCAAAGT
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
47 48 0.52
48 44 0.48
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (47 bp):
ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
Found at i:10831 original size:16 final size:17
Alignment explanation
Indices: 10805--10837 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10795 AAACAGTTTT
10805 CAAAGCATTTCAATTCG
1 CAAAGCATTTCAATTCG
*
10822 CAAA-CATTTCCATTCG
1 CAAAGCATTTCAATTCG
10838 TACATAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (17 bp):
CAAAGCATTTCAATTCG
Found at i:12213 original size:49 final size:48
Alignment explanation
Indices: 12141--12539 Score: 408
Period size: 49 Copynumber: 8.2 Consensus size: 48
12131 CAATTTTCAG
* *
12141 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCA
1 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGACATT-A
* * *
12190 TTTTTACTTGCAATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCA
1 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGACATT-A
* * *
12239 TTTTTACTTGCTATTTCCCAAAGTGCCCTTCCCGGACGGAAGCCGTTTA
1 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGAC-ATTA
* * * *
12288 TCTTTACTTGCTATTTCCCAAAAGCACCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACTTGCTATTTCCC-AAAGCGCCCTTCCCGGACGGAAGACA-TTA
* * **
12338 TTTTTACCTG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGACACTTA
1 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGACA-TTA
* ** *
12386 -TTTTACTTGCTATTTTCCAAAAATGCCCTTCCCGGATGGAAGACACTTA
1 TTTTTACTTGCTA-TTTCCCAAAGCGCCCTTCCCGGACGGAAGACA-TTA
** * * *
12435 TTTTTACCCGCT-TTTCCCCAAAGTGCCCTTCCCCGACGGAAGACACTAA
1 TTTTTACTTGCTATTT-CCCAAAGCGCCCTTCCCGGACGGAAGACA-TTA
* * * * *
12484 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGGCATTA
1 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGACATTA
*
12532 GTTTTACT
1 TTTTTACT
12540 CGTTTTTTCT
Statistics
Matches: 302, Mismatches: 40, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
47 8 0.03
48 38 0.13
49 210 0.70
50 46 0.15
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (48 bp):
TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCGGACGGAAGACATTA
Found at i:12354 original size:98 final size:99
Alignment explanation
Indices: 12141--12528 Score: 453
Period size: 98 Copynumber: 4.0 Consensus size: 99
12131 CAATTTTCAG
* * * * * *
12141 TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCAATT
1 TTTTTACCTGCTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGACACTT-ATTTTTACTTGCTATT
* * * *
12205 TCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTCA
65 TCCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAA
* * * ** *
12239 TTTTTACTTGCTATTTCCCAAAGTGCCCTTCCCGGACGGAAGCCGTTTATCTTTACTTGCTATTT
1 TTTTTACCTGCTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGACACTTATTTTTACTTGCTATTT
*
12304 CCCAAAAGCACCCTTCCCGGACGGAAGGCACTAA
66 CCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAA
*
12338 TTTTTACCTG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGACACTTA-TTTTACTTGCTATTT
1 TTTTTACCTGCTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGACACTTATTTTTACTTGCTATTT
* ** * * *
12401 TCCAAAAATGCCCTTCCCGGATGGAAGACACTTA
66 CCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAA
* * * * *
12435 TTTTTACCCGCTTTTCCCCAAAGTGCCCTTCCCCGACGGAAGACACTAATTTTTACTTGCTTTTT
1 TTTTTACCTGCTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGACACTTATTTTTACTTGCTATTT
* *
12500 CCTAAAA-CGCCCTTCCCGGATGGAAGGCA
66 CCCAAAAGCGCCCTTCCCGGACGGAAGGCA
12529 TTAGTTTTAC
Statistics
Matches: 252, Mismatches: 34, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
97 50 0.20
98 147 0.58
99 55 0.22
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.31
Consensus pattern (99 bp):
TTTTTACCTGCTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGACACTTATTTTTACTTGCTATTT
CCCAAAAGCGCCCTTCCCGGACGGAAGGCACTAA
Found at i:12413 original size:147 final size:146
Alignment explanation
Indices: 12143--12539 Score: 476
Period size: 147 Copynumber: 2.7 Consensus size: 146
12133 ATTTTCAGTT
* * * **
12143 TTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCAATTTCC
1 TTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGCTTTTTCC
* * * * * *
12208 CAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGTGCCCTTCCCG
66 CAAAACGCCCTTCCCGGACGGAAGACATT-AGTTTTACTTGCTATTTCCAAAAATGCCCTTCCCG
* **
12273 GACGGAAGCCGTTTATC
130 GACGGAAGACACTTATC
* * * *
12290 TTTACTTGCTATTTCCCAAAAGCACCCTTCCCGGACGGAAGGCACTAATTTTTACCTG-TTTTTC
1 TTTACTTGCTATTTCCC-AAAGCGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGCTTTTTC
*
12354 CCAAAATGCCCTTCCCGGACGGAAGACACTTA-TTTTACTTGCTATTTTCCAAAAATGCCCTTCC
65 CCAAAACGCCCTTCCCGGACGGAAGACA-TTAGTTTTACTTGCTA-TTTCCAAAAATGCCCTTCC
* *
12418 CGGATGGAAGACACTTATT
128 CGGACGGAAGACACTTATC
** * *
12437 TTTACCCGCT-TTTCCCCAAAGTGCCCTTCCCCGACGGAAGACACTAATTTTTACTTGCTTTTTC
1 TTTACTTGCTATTT-CCCAAAGCGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGCTTTTTC
* * *
12501 CTAAAACGCCCTTCCCGGATGGAAGGCATTAGTTTTACT
65 CCAAAACGCCCTTCCCGGACGGAAGACATTAGTTTTACT
12540 CGTTTTTTCT
Statistics
Matches: 214, Mismatches: 30, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
146 53 0.25
147 125 0.58
148 36 0.17
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (146 bp):
TTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGCTTTTTCC
CAAAACGCCCTTCCCGGACGGAAGACATTAGTTTTACTTGCTATTTCCAAAAATGCCCTTCCCGG
ACGGAAGACACTTATC
Found at i:14224 original size:22 final size:22
Alignment explanation
Indices: 14199--14258 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 22
14189 CTTGCATATA
*
14199 TTATAGCTTTGTATAAGCTATT
1 TTATAGCTTTGTACAAGCTATT
14221 TTATAGCTTTGCTCTGTACAAGCTATT
1 TTATAGC--T--T-TGTACAAGCTATT
14248 TTATAGCTTTG
1 TTATAGCTTTG
14259 CTCAAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
22 9 0.28
23 1 0.03
24 1 0.03
25 1 0.03
26 1 0.03
27 19 0.59
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.48
Consensus pattern (22 bp):
TTATAGCTTTGTACAAGCTATT
Found at i:14225 original size:27 final size:26
Alignment explanation
Indices: 14208--14261 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
14198 ATTATAGCTT
*
14208 TGTATAAGCTATTTTATAGCTTTGCTC
1 TGTACAAGCTATTTTATA-CTTTGCTC
14235 TGTACAAGCTATTTTATAGCTTTGCTC
1 TGTACAAGCTATTTTATA-CTTTGCTC
14262 AAAAAAGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (26 bp):
TGTACAAGCTATTTTATACTTTGCTC
Found at i:16311 original size:30 final size:31
Alignment explanation
Indices: 16247--16331 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 31
16237 TACACTTGAG
* *
16247 ACAAAATTAGTACTGTGTATCCATAAAAAAT
1 ACAAAATTAGTACTATGTATTCATAAAAAAT
*
16278 ACAAAATTAGTACTATGTATTCAT-AAGAAT
1 ACAAAATTAGTACTATGTATTCATAAAAAAT
*
16308 ACAAAATTAGTGCTATGTATTCAT
1 ACAAAATTAGTACTATGTATTCAT
16332 TAAAGAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 28 0.56
31 22 0.44
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
ACAAAATTAGTACTATGTATTCATAAAAAAT
Found at i:21994 original size:22 final size:23
Alignment explanation
Indices: 21968--22016 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
21958 GTCATTTTCT
*
21968 AATTCACT-TTTGGCATTTAGTA
1 AATTCACTCTTTGGCATTAAGTA
21990 AATTCACTCTTTGGCATTAAGTA
1 AATTCACTCTTTGGCATTAAGTA
22013 AATT
1 AATT
22017 GTGTTCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (23 bp):
AATTCACTCTTTGGCATTAAGTA
Found at i:25214 original size:15 final size:15
Alignment explanation
Indices: 25190--25222 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25180 AGGAGAATAA
25190 AAATAGTAATT-AGT
1 AAATAGTAATTAAGT
25204 AAATCAGTAATTAAGT
1 AAAT-AGTAATTAAGT
25220 AAA
1 AAA
25223 AAGAGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (15 bp):
AAATAGTAATTAAGT
Found at i:25235 original size:26 final size:26
Alignment explanation
Indices: 25205--25294 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
25195 GTAATTAGTA
25205 AATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAATTAAGTAAAAAGAGATT
* * * *
25231 AATCAG-AGTCAAGGTAATAGTAATCAG-TG
1 AATCAGTAATTAA-GTAA-A--AA-GAGATT
*
25260 AATCAGTAATTAAGTAAAAAGGGATT
1 AATCAGTAATTAAGTAAAAAGAGATT
25286 AATCAGTAA
1 AATCAGTAA
25295 ATTGATAGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 5 0.10
26 22 0.46
27 1 0.02
28 1 0.02
29 13 0.27
30 6 0.12
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (26 bp):
AATCAGTAATTAAGTAAAAAGAGATT
Found at i:25312 original size:71 final size:70
Alignment explanation
Indices: 25230--25404 Score: 195
Period size: 63 Copynumber: 2.6 Consensus size: 70
25220 AAAAAGAGAT
* *
25230 TAATC-AGAGTCAAGGTAATAGTAATCAGTGAATCAGTAATTAAGTAAAAAGGGATTAATCAGTA
1 TAATCAAGAGTCAAGGTAATAGTAATCAGTGAATCAGTAATT-AGTAAAAAGAGACTAATCAGTA
25294 AATTGA
65 AATTGA
* * *
25300 TAGTCAAGAGTCAAGGTAATAATAATCA--G--T-A--AATTAGTGAAAAGAGACTAATCAGTAA
1 TAATCAAGAGTCAAGGTAATAGTAATCAGTGAATCAGTAATTAGTAAAAAGAGACTAATCAGTAA
25358 ATTGA
66 ATTGA
* * * *
25363 TAATTAAGAGTCAAGATAATAGTGATCAGTAAAGTCAGTAAT
1 TAATCAAGAGTCAAGGTAATAGTAATCAGTGAA-TCAGTAAT
25405 CAAGAGCCAA
Statistics
Matches: 85, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
63 48 0.56
64 4 0.05
66 1 0.01
67 1 0.01
68 1 0.01
69 2 0.02
70 4 0.05
71 24 0.28
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.27
Consensus pattern (70 bp):
TAATCAAGAGTCAAGGTAATAGTAATCAGTGAATCAGTAATTAGTAAAAAGAGACTAATCAGTAA
ATTGA
Found at i:25587 original size:23 final size:23
Alignment explanation
Indices: 25561--25604 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25551 AAGGAAGCAA
25561 AAGGGACTAATAAGTAAATTGAG
1 AAGGGACTAATAAGTAAATTGAG
* *
25584 AAGGGATTAATAATTAAATTG
1 AAGGGACTAATAAGTAAATTG
25605 GTAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (23 bp):
AAGGGACTAATAAGTAAATTGAG
Found at i:25884 original size:26 final size:26
Alignment explanation
Indices: 25855--25918 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
25845 GTAAAATGAC
*
25855 AAATGGTAATTAAATTCAAAGAGTAA
1 AAATAGTAATTAAATTCAAAGAGTAA
*
25881 AAATAGTGATTAAATTCAAGAGAGT-A
1 AAATAGTAATTAAATTCAA-AGAGTAA
25907 AAATAGTAATTA
1 AAATAGTAATTA
25919 GTAAAGAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 29 0.85
27 5 0.15
ACGTcount: A:0.53, C:0.03, G:0.16, T:0.28
Consensus pattern (26 bp):
AAATAGTAATTAAATTCAAAGAGTAA
Found at i:25926 original size:22 final size:22
Alignment explanation
Indices: 25901--25951 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
25891 TAAATTCAAG
*
25901 AGAGTAAAATAGT-AATTAGTAA
1 AGAGTAAAATAGTGAA-GAGTAA
*
25923 AGAGTAAAATGGTGAAGAGTAA
1 AGAGTAAAATAGTGAAGAGTAA
25945 AGAGTAA
1 AGAGTAA
25952 TAAGTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (22 bp):
AGAGTAAAATAGTGAAGAGTAA
Found at i:25958 original size:36 final size:37
Alignment explanation
Indices: 25901--26016 Score: 123
Period size: 36 Copynumber: 3.2 Consensus size: 37
25891 TAAATTCAAG
* * *
25901 AGAGTAAAATAGTAATTAGTAAAGAGTAAAATGGT-GA
1 AGAGT-AAAGAGTAATAAGTAAAGAGTAAAATGGTAAA
25938 AGAGTAAAGAGTAATAAGTAAA-AG-AAGAATGGTAAA
1 AGAGTAAAGAGTAATAAGTAAAGAGTAA-AATGGTAAA
* * * *
25974 AAAGTAAAGGGTAATCAGTAAAGAGTAAAATAGTAAA
1 AGAGTAAAGAGTAATAAGTAAAGAGTAAAATGGTAAA
26011 AG-GTAA
1 AGAGTAA
26017 TCAGTAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
34 2 0.03
35 8 0.12
36 39 0.58
37 16 0.24
38 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.24, T:0.20
Consensus pattern (37 bp):
AGAGTAAAGAGTAATAAGTAAAGAGTAAAATGGTAAA
Found at i:26001 original size:29 final size:29
Alignment explanation
Indices: 25969--26024 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
25959 AAGAAGAATG
*
25969 GTAAAAAAGTAAAGGGTAATCAGTAAAGA
1 GTAAAAAAGTAAAAGGTAATCAGTAAAGA
*
25998 GTAAAATAGTAAAAGGTAATCAGTAAA
1 GTAAAAAAGTAAAAGGTAATCAGTAAA
26025 AAAGTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (29 bp):
GTAAAAAAGTAAAAGGTAATCAGTAAAGA
Found at i:26063 original size:22 final size:22
Alignment explanation
Indices: 26035--26213 Score: 102
Period size: 22 Copynumber: 8.5 Consensus size: 22
26025 AAAGTGATGA
*
26035 TAATCAGTAAAAGGTAAGATAG
1 TAATCAGTAAAAGGTAAAATAG
26057 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
*
26079 TAATCAGTAAAA-G-ATAATCAG
1 TAATCAGTAAAAGGTAAAAT-AG
*
26100 TAA--AG--CAA---AAAATAG
1 TAATCAGTAAAAGGTAAAATAG
*
26115 TAATCAGTAAAAGAGTAAAATGG
1 TAATCAGTAAAAG-GTAAAATAG
* * *
26138 TAATCAGTAAAAAGTAGGAA-GG
1 TAATCAGTAAAAGGTA-AAATAG
*
26160 TAATCA--ACAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
*
26181 TAATCAGTACAAA-TTAAAGA-A-
1 TAATCAGTA-AAAGGTAAA-ATAG
26202 TAATCAGTAAAA
1 TAATCAGTAAAA
26214 TAGTGATGGT
Statistics
Matches: 125, Mismatches: 14, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
15 5 0.04
16 4 0.03
17 4 0.03
19 4 0.03
20 12 0.10
21 29 0.23
22 40 0.32
23 25 0.20
24 2 0.02
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:26098 original size:14 final size:15
Alignment explanation
Indices: 25979--26103 Score: 57
Period size: 14 Copynumber: 8.1 Consensus size: 15
25969 GTAAAAAAGT
*
25979 AAAGGGTAATCAGT-
1 AAAGAGTAATCAGTA
25993 AAAGAGTAAAAT-AGTA
1 AAAGAGT--AATCAGTA
26009 AAAG-GTAATCAGTAAA
1 AAAGAGTAATCAGT--A
26025 AAAGTGATGATAATCAGTA
1 AAA--GA-G-TAATCAGTA
26044 AAAG-GTAAGAT-AGT-
1 AAAGAGT-A-ATCAGTA
** **
26058 AATCAGTAAAGAGTA
1 AAAGAGTAATCAGTA
*
26073 AAATAGTAATCAGTA
1 AAAGAGTAATCAGTA
26088 AAAGA-TAATCAGTA
1 AAAGAGTAATCAGTA
26102 AA
1 AA
26104 GCAAAAAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 32
0.68 0.07 0.25
Matches are distributed among these distances:
13 4 0.05
14 27 0.31
15 27 0.31
16 13 0.15
17 1 0.01
18 1 0.01
19 4 0.05
20 1 0.01
21 8 0.09
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (15 bp):
AAAGAGTAATCAGTA
Found at i:26098 original size:36 final size:36
Alignment explanation
Indices: 26057--26128 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
26047 GGTAAGATAG
*
26057 TAATCAGTAAAG-AGTAAAATAGTAATCAGTAAAAGA
1 TAATCAGTAAAGCA-AAAAATAGTAATCAGTAAAAGA
26093 TAATCAGTAAAGCAAAAAATAGTAATCAGTAAAAGA
1 TAATCAGTAAAGCAAAAAATAGTAATCAGTAAAAGA
26129 GTAAAATGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (36 bp):
TAATCAGTAAAGCAAAAAATAGTAATCAGTAAAAGA
Found at i:28255 original size:14 final size:14
Alignment explanation
Indices: 28238--28264 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28228 TCTTTTAGTC
28238 TTTAGTGTTTAGGG
1 TTTAGTGTTTAGGG
28252 TTTAGTGTTTAGG
1 TTTAGTGTTTAGG
28265 ACTTAAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
TTTAGTGTTTAGGG
Found at i:32854 original size:35 final size:35
Alignment explanation
Indices: 32782--32991 Score: 261
Period size: 35 Copynumber: 6.1 Consensus size: 35
32772 GCAGTTTTTG
* *
32782 GAGATCAACTCTAACCATC-G-AAA-TTTTTGAAAT
1 GAGATCAACTCTGACC-TCTGAAAACTTCTTGAAAT
* *
32815 GAGATCAACTCTGATCATC-AAAAACTTCTTGAAAT
1 GAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAAT
* *
32850 GAGATCAACTCTGATCGTC-GAAAATTTCTTGAAAT
1 GAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAAT
*
32885 GAGATCAACTCTGACCTCTGAAAACTTATTGAAAT
1 GAGATCAACTCTGACCTCTGAAAACTTCTTGAAAT
*
32920 GAGATCAACTCTGACCTC-GAAAAACTTCTTGCAAT
1 GAGATCAACTCTGACCTCTG-AAAACTTCTTGAAAT
*
32955 AAGATCAACTCTGACCTCTGAAAACTTCTTGAAAT
1 GAGATCAACTCTGACCTCTGAAAACTTCTTGAAAT
32990 GA
1 GA
32992 CACTACAAGA
Statistics
Matches: 156, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
33 15 0.10
34 8 0.05
35 132 0.85
36 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (35 bp):
GAGATCAACTCTGACCTCTGAAAACTTCTTGAAAT
Found at i:32990 original size:105 final size:103
Alignment explanation
Indices: 32782--32991 Score: 291
Period size: 105 Copynumber: 2.0 Consensus size: 103
32772 GCAGTTTTTG
*
32782 GAGATCAACTCTAACCATCGAAATTTTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTGA
1 GAGATCAACTCTAACCATCGAAATTATTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTGA
* * *
32847 AATGAGATCAACTCTGATCGTCGAAAATTTCTTGAAAT
66 AATAAGATCAACTCTGATCCTCGAAAACTTCTTGAAAT
* *
32885 GAGATCAACTCTGACC-TCTGAAAACTTATTGAAATGAGATCAACTCTGA-CCTCGAAAAACTTC
1 GAGATCAACTCTAACCATC-G-AAA-TTATTGAAATGAGATCAACTCTGATCATC-AAAAACTTC
*
32948 TTGCAATAAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAAT
62 TTGAAATAAGATCAACTCTGATCCTC-GAAAACTTCTTGAAAT
32990 GA
1 GA
32992 CACTACAAGA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
102 2 0.02
103 16 0.17
104 9 0.09
105 68 0.72
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (103 bp):
GAGATCAACTCTAACCATCGAAATTATTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTGA
AATAAGATCAACTCTGATCCTCGAAAACTTCTTGAAAT
Found at i:33705 original size:124 final size:124
Alignment explanation
Indices: 33433--34040 Score: 839
Period size: 124 Copynumber: 4.9 Consensus size: 124
33423 TCAACATGGT
* * ** * * * *
33433 TTCGTCACAAAAAACAAGTACATTATTTGTGTCGATATTGTTGTAACTATTGT-TTCATTTGTCG
1 TTCGTCACAATAAA-TA-TACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTT-ATTTATCG
* *
33497 TCACAAATAAATATGCAAAAATGAC-AAAGAAAAATGATTTAGTGACCATGTCCTAGCGTAA
63 TCACAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCAAGCATAA
*
33558 TTCGTCACAATAAATGTACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTATCGTCA
1 TTCGTCACAATAAATATACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTATCGTCA
* * * *
33623 CAAATAAATATGCAAAGATGACAACATAAAAATGATTTAGTGACCATGTCCAAGAATAA
66 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCAAGCATAA
* * * * *
33682 TTCGTCACAATAAATGTGCATTATGAGTGACCAAATTGTTGTCACTATTGTTTTATTAATCGTCA
1 TTCGTCACAATAAATATACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTATCGTCA
* *
33747 CAGATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAGCATAA
66 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCAAGCATAA
*
33806 TTCGTCACAATAAATATACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTTTCGTCA
1 TTCGTCACAATAAATATACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTATCGTCA
* * * *
33871 CTAATAAATATGCAAAGATGACAACAGAAAAATGATTTAGTGACCATGTCCTAA-CATAT
66 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCC-AAGCATAA
* * *
33930 TTCGTCACAATAAATATACATTATGAGTGT-CAAACATGTTGTCACTATTGTTTTATTTATCATC
1 TTCGTCACAATAAATATACATTATGAGTGTCCAAA-TTGTTGTCACTATTGTGTTATTTATCGTC
* *
33994 ACAAATAAATATGCAAAATTGAGAAAAGACAAAA-GATTTAGTGACCA
65 ACAAATAAATATGCAAAAATGACAAAAGA-AAAATGATTTAGTGACCA
34041 CTAACTAATA
Statistics
Matches: 432, Mismatches: 46, Indels: 11
0.88 0.09 0.02
Matches are distributed among these distances:
123 65 0.15
124 349 0.81
125 18 0.04
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (124 bp):
TTCGTCACAATAAATATACATTATGAGTGTCCAAATTGTTGTCACTATTGTGTTATTTATCGTCA
CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCAAGCATAA
Found at i:34754 original size:57 final size:57
Alignment explanation
Indices: 34682--34789 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
34672 TAGGAGCACT
** *
34682 TGGAGAATCAATAGAGGCTGATGCATTCACTATCACACTTGGA-ATTGTTCCTTGAGC
1 TGGAGAATCAATAGAGGCCAATGCATTCACTAACACACTT-GACATTGTTCCTTGAGC
*
34739 TGGAGAATCAGTAGAGGCCAATGCATTCACTAACACACTTGACATTGTTCC
1 TGGAGAATCAATAGAGGCCAATGCATTCACTAACACACTTGACATTGTTCC
34790 ACTAGCTGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
56 2 0.04
57 44 0.96
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (57 bp):
TGGAGAATCAATAGAGGCCAATGCATTCACTAACACACTTGACATTGTTCCTTGAGC
Found at i:35591 original size:19 final size:19
Alignment explanation
Indices: 35567--35603 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35557 TAGAATTATT
*
35567 TTGAAATGTAAATTAAAAA
1 TTGAAATATAAATTAAAAA
35586 TTGAAATATAAATTAAAA
1 TTGAAATATAAATTAAAA
35604 TATAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
TTGAAATATAAATTAAAAA
Found at i:35602 original size:24 final size:24
Alignment explanation
Indices: 35570--35627 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
35560 AATTATTTTG
*
35570 AAATGTAAATTAAAAATTGAAATAT
1 AAAT-TAAATTAAAAATTAAAATAT
* *
35595 AAATTAAAATATAAATTAAAATAT
1 AAATTAAATTAAAAATTAAAATAT
*
35619 ACA-TAAATT
1 AAATTAAATT
35628 TATAATTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 5 0.18
24 19 0.68
25 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (24 bp):
AAATTAAATTAAAAATTAAAATAT
Found at i:35604 original size:12 final size:12
Alignment explanation
Indices: 35583--35619 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
35573 TGTAAATTAA
*
35583 AAATTGAAATAT
1 AAATTAAAATAT
35595 AAATTAAAATAT
1 AAATTAAAATAT
35607 AAATTAAAATAT
1 AAATTAAAATAT
35619 A
1 A
35620 CATAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAATTAAAATAT
Done.