Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007143.1 Corchorus capsularis cultivar CVL-1 contig07164, 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: 56075
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2950 original size:5 final size:5
Alignment explanation
Indices: 2911--3013 Score: 73
Period size: 5 Copynumber: 22.6 Consensus size: 5
2901 CAAATCTTAC
* * * * *
2911 TATCC TATCC TATCC TATCC TATCT TATCT TATCT TATCT AAT-T T-TCT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
* *
2959 TATCT TA-C- TATCT TA-C- TATCT TATTT TATCT TA-C- TATCT TAT-A
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
3002 T-TCT TATCT TAT
1 TATCT TATCT TAT
3014 ACTACCATAC
Statistics
Matches: 81, Mismatches: 7, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
3 8 0.10
4 11 0.14
5 62 0.77
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.55
Consensus pattern (5 bp):
TATCT
Found at i:2972 original size:8 final size:8
Alignment explanation
Indices: 2959--2999 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
2949 CTAATTTTCT
2959 TATCTTAC
1 TATCTTAC
2967 TATCTTAC
1 TATCTTAC
*
2975 TATCTTATTT
1 TATCTTA--C
2985 TATCTTAC
1 TATCTTAC
2993 TATCTTA
1 TATCTTA
3000 TATTCTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (8 bp):
TATCTTAC
Found at i:2987 original size:26 final size:26
Alignment explanation
Indices: 2956--3013 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
2946 TATCTAATTT
2956 TCTTATCTTACTATCTTACTA-TCTTA
1 TCTTATCTTACTATCTTA-TATTCTTA
*
2982 TTTTATCTTACTATCTTATATTCTTA
1 TCTTATCTTACTATCTTATATTCTTA
3008 TCTTAT
1 TCTTAT
3014 ACTACCATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (26 bp):
TCTTATCTTACTATCTTATATTCTTA
Found at i:4956 original size:22 final size:22
Alignment explanation
Indices: 4907--4961 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
4897 GTCACTGTGT
*
4907 GGTTATCAAAATTCCATAAAAA
1 GGTTATCAAAAGTCCATAAAAA
* ***
4929 GATTATCAAAAGTCCATATGGA
1 GGTTATCAAAAGTCCATAAAAA
4951 GGTTATCAAAA
1 GGTTATCAAAA
4962 TTTCGTTGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (22 bp):
GGTTATCAAAAGTCCATAAAAA
Found at i:5005 original size:22 final size:22
Alignment explanation
Indices: 4909--5015 Score: 58
Period size: 22 Copynumber: 4.9 Consensus size: 22
4899 CACTGTGTGG
* **
4909 TTATCAAAATTCCATAAAAAGA
1 TTATCAAAATTTCATAGGAAGA
* * *
4931 TTATCAAAAGTCCATATGG-AGG
1 TTATCAAAATTTCATA-GGAAGA
* * * *
4953 TTATCAAAATTTCGTTGTG-TGG
1 TTATCAAAATTTCATAG-GAAGA
4975 TTA-CTAAAATTTCATAGGAAGA
1 TTATC-AAAATTTCATAGGAAGA
* *
4997 TTATCAAAATATCTTAGGA
1 TTATCAAAATTTCATAGGA
5016 TTAGGTCATT
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
21 3 0.05
22 61 0.94
23 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAGA
Found at i:5095 original size:22 final size:21
Alignment explanation
Indices: 5068--5167 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 21
5058 ACGAGGTTAG
5068 AAAATTTTATAGTGTGGTTATC
1 AAAATTTTATAG-GTGGTTATC
* * **
5090 AAAATTTCATAAGGAGAATA-C
1 AAAATTTTAT-AGGTGGTTATC
* * *
5111 TAAAATTATATAAGGAGTTTATC
1 -AAAATTTTAT-AGGTGGTTATC
* *
5134 AAAATTTTATAGCATTGTTATC
1 AAAATTTTATAG-GTGGTTATC
5156 AAAATTTTATAG
1 AAAATTTTATAG
5168 TGTTGCTACC
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.05
22 55 0.90
23 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (21 bp):
AAAATTTTATAGGTGGTTATC
Found at i:5180 original size:22 final size:22
Alignment explanation
Indices: 5133--5180 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5123 AGGAGTTTAT
* *
5133 CAAAATTTTATAGCATTGTTAT
1 CAAAATTTTATAGCATTGCTAC
**
5155 CAAAATTTTATAGTGTTGCTAC
1 CAAAATTTTATAGCATTGCTAC
5177 CAAA
1 CAAA
5181 TTGGGGCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
CAAAATTTTATAGCATTGCTAC
Found at i:5225 original size:31 final size:31
Alignment explanation
Indices: 5178--5267 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
5168 TGTTGCTACC
* *
5178 AAATTGGGGCCCTTATTTGAGCAATTTTGGTA
1 AAATT-GGACCCTTATTTGAGCAATTTTCGTA
* * *
5210 ACATTTGACCCTTATTTGAGAAATTTTCGTA
1 AAATTGGACCCTTATTTGAGCAATTTTCGTA
5241 AAATTGGACCCTTATTTGAGCAATTTT
1 AAATTGGACCCTTATTTGAGCAATTTT
5268 TTCCTTTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 46 0.92
32 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (31 bp):
AAATTGGACCCTTATTTGAGCAATTTTCGTA
Found at i:5291 original size:29 final size:32
Alignment explanation
Indices: 5187--5325 Score: 116
Period size: 31 Copynumber: 4.5 Consensus size: 32
5177 CAAATTGGGG
* *
5187 CCCTTATTTGAGCAATTTTGGTAACAT-TT--GA
1 CCCTTATTTGAGCAATTTT-TTAA-ATATTAGGT
* * *
5218 CCCTTATTTGAGAAATTTTCGTAAA-ATT-GGA
1 CCCTTATTTGAGCAATTTT-TTAAATATTAGGT
**
5249 CCCTTATTTGAGCAATTTTTT-CCT-TTAGG-
1 CCCTTATTTGAGCAATTTTTTAAATATTAGGT
5278 CCCTTATTTGAGC-ATTTTTTAAATATTAGGT
1 CCCTTATTTGAGCAATTTTTTAAATATTAGGT
*
5309 CCTTTATTTGAGCAATT
1 CCCTTATTTGAGCAATT
5326 AGCCATTTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.08
29 16 0.18
30 11 0.12
31 54 0.59
32 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (32 bp):
CCCTTATTTGAGCAATTTTTTAAATATTAGGT
Found at i:5319 original size:31 final size:28
Alignment explanation
Indices: 5249--5322 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
5239 TAAAATTGGA
**
5249 CCCTTATTTGAGCAATTTTTTCCTTTAGG
1 CCCTTATTTGAGC-ATTTTTTAATTTAGG
5278 CCCTTATTTGAGCATTTTTTAAATATTAGG
1 CCCTTATTTGAGCATTTTTT-AAT-TTAGG
*
5308 TCCTTTATTTGAGCA
1 -CCCTTATTTGAGCA
5323 ATTAGCCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 7 0.18
29 14 0.36
30 5 0.13
31 13 0.33
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.47
Consensus pattern (28 bp):
CCCTTATTTGAGCATTTTTTAATTTAGG
Found at i:11155 original size:1 final size:1
Alignment explanation
Indices: 11151--11185 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
11141 GATAAAAATT
**
11151 AAAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11186 TCTTAGAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:12889 original size:61 final size:61
Alignment explanation
Indices: 12794--12916 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
12784 CCATAAGAGC
12794 ATTGTACATATAAATAAGAGTATGTTTAATTAAAAGTTCTATTTCCTTTTTGATAATTATA
1 ATTGTACATATAAATAAGAGTATGTTTAATTAAAAGTTCTATTTCCTTTTTGATAATTATA
12855 ATTGTACATATAAATAAGAGTATGTTTAATTAAAAGTTCTATTTCCTTTTTGATAATTATA
1 ATTGTACATATAAATAAGAGTATGTTTAATTAAAAGTTCTATTTCCTTTTTGATAATTATA
12916 A
1 A
12917 GTTAGCATGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (61 bp):
ATTGTACATATAAATAAGAGTATGTTTAATTAAAAGTTCTATTTCCTTTTTGATAATTATA
Found at i:13349 original size:22 final size:22
Alignment explanation
Indices: 13319--13360 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
13309 GGAATTCATG
13319 TATT-TTTTTTAAATATATTTGT
1 TATTATTTTTTAAA-ATATTTGT
13341 TATTATTTTTTAAAATATTT
1 TATTATTTTTTAAAATATTT
13361 TCAAGTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTTTAAAATATTTGT
Found at i:23744 original size:20 final size:20
Alignment explanation
Indices: 23714--23761 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
23704 TATCTAGCGA
*
23714 AAAATTAATTATAAGTCAAAC
1 AAAA-TAATTACAAGTCAAAC
*
23735 AAAATAATTACACGTCAAAC
1 AAAATAATTACAAGTCAAAC
23755 -AAATAAT
1 AAAATAAT
23762 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAATTACAAGTCAAAC
Found at i:25335 original size:33 final size:32
Alignment explanation
Indices: 25282--25388 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
25272 AAATGGCCTA
*
25282 GCCGCCCAAGTTGGGCGGCTAGCCATGGGCCAG
1 GCCGCCCAAGCTGGGCGGCTAGCCATGGG-CAG
* * *
25315 GCCGCCTAAGCTGGGTGGCTAGCCATGGGTCAA
1 GCCGCCCAAGCTGGGCGGCTAGCCATGGG-CAG
*
25348 GCTGCCCAAGCTGGGCGGCTTAGTCCAT-GGCAG
1 GCCGCCCAAGCTGGGCGGC-TAG-CCATGGGCAG
25381 GCCGCCCA
1 GCCGCCCA
25389 GCTTGGGAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 53 0.85
34 5 0.08
35 4 0.06
ACGTcount: A:0.16, C:0.33, G:0.36, T:0.15
Consensus pattern (32 bp):
GCCGCCCAAGCTGGGCGGCTAGCCATGGGCAG
Found at i:25401 original size:33 final size:33
Alignment explanation
Indices: 25351--25454 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
25341 GGGTCAAGCT
*
25351 GCCCAAGC-TGGGCGGCTTAGTCCATGGC-AGGCC
1 GCCC-AGCTTGGGAGGCTTAGTCCATGGCTA-GCC
*
25384 GCCCAGCTTGGGAGGCTTTGTCCATGGCTAGCC
1 GCCCAGCTTGGGAGGCTTAGTCCATGGCTAGCC
* * * * *
25417 GCCCAACTTGGGCGGCCTGGCCCATGGCTAGCC
1 GCCCAGCTTGGGAGGCTTAGTCCATGGCTAGCC
*
25450 ACCCA
1 GCCCA
25455 ACTTAGGCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.05
33 57 0.93
34 1 0.02
ACGTcount: A:0.14, C:0.36, G:0.33, T:0.17
Consensus pattern (33 bp):
GCCCAGCTTGGGAGGCTTAGTCCATGGCTAGCC
Found at i:25421 original size:66 final size:65
Alignment explanation
Indices: 25274--25432 Score: 157
Period size: 66 Copynumber: 2.4 Consensus size: 65
25264 TTTAAAAAAA
* *
25274 ATGGCCTAGCCGCCCAAGTTGGGCGGCTAGCCATGGGCCAGGCCGCCTAAGCTGGGTGGCTAGCC
1 ATGGCCTAGCCGCCCAAGCTGGGCGGCTAGCCATGGGCCAGGCCGCCTAAGCTGGGAGGCTAGCC
* * * *
25339 ATGGGTCAAGCTGCCCAAGCTGGGCGGCTTAGTCCAT-GG-CAGGCCGCC-CAGCTTGGGAGGCT
1 AT-GGCCTAGCCGCCCAAGCTGGGCGGC-TAG-CCATGGGCCAGGCCGCCTAAGC-TGGGAGGC-
*
25401 TTGTCC
61 TAG-CC
25407 ATGG-CTAGCCGCCCAA-CTTGGGCGGC
1 ATGGCCTAGCCGCCCAAGC-TGGGCGGC
25433 CTGGCCCATG
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
65 6 0.08
66 55 0.71
67 9 0.12
68 8 0.10
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (65 bp):
ATGGCCTAGCCGCCCAAGCTGGGCGGCTAGCCATGGGCCAGGCCGCCTAAGCTGGGAGGCTAGCC
Found at i:25576 original size:15 final size:15
Alignment explanation
Indices: 25552--25623 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 15
25542 AAATTACTTA
25552 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
25566 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
25578 -TCTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
25592 GATTAATTAG--TA-
1 GTTTAATTAGTTTAT
25604 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
25618 GATTAA
1 GTTTAA
25624 AATGAAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
11 16 0.36
13 8 0.18
14 4 0.09
15 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:25585 original size:26 final size:26
Alignment explanation
Indices: 25556--25623 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
25546 TACTTAGTTT
*
25556 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
25582 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
25608 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
25624 AATGAAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:25790 original size:20 final size:21
Alignment explanation
Indices: 25762--25806 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
25752 CAAAATTGTA
25762 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTATTTAGC
*
25783 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTATTTAGC
25804 AAA
1 AAA
25807 CCAGTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.42, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGCGGTATTTAGC
Found at i:28481 original size:154 final size:151
Alignment explanation
Indices: 28177--28463 Score: 334
Period size: 154 Copynumber: 1.9 Consensus size: 151
28167 TTCCAATTTT
* *
28177 TTAAAATTAAAATGGTAAAAAATAAAATATTTATAAAAATATTGAATTTAATTAAATAAAAATAG
1 TTAAAATTAAAACGGTAAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAG
* * * *
28242 AGTTTTTTTAGAATAAAACTATAAAAGTTTAAACAATATCATTTAAGAAATATATTTAAGAATTT
66 AGTTTTTTTAG-ATAAAACTATAAAAGTTTAAACAATAGCATTTAAGAAATATATTGAAGAAATA
* ***
28307 CTAACATATCTAAGTTTTTTAA
130 ATAACATATCTAAAAATTTTAA
28329 TTAAAATAGTAAAACGGT-AAAAATAAAATAGTTA-AAAAGATATT-AGATTTAATTAAGA-AAA
1 TTAAAAT--TAAAACGGTAAAAAATAAAATAGTTATAAAA-ATATTGA-ATTTAATTAA-ATAAA
* *
28390 AATAGAGTTTTCAGTTTAG-TAAAACTATAAAAGTTTAAATAATGGCATTTAAGAAATATATTCG
61 AATAGAGTTTT---TTTAGATAAAACTATAAAAGTTTAAACAATAGCATTTAAGAAATATATT-G
28454 AA-AAATAATA
122 AAGAAATAATA
28464 GGTGATTCAA
Statistics
Matches: 117, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
152 12 0.10
153 44 0.38
154 54 0.46
155 2 0.02
156 5 0.04
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (151 bp):
TTAAAATTAAAACGGTAAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAG
AGTTTTTTTAGATAAAACTATAAAAGTTTAAACAATAGCATTTAAGAAATATATTGAAGAAATAA
TAACATATCTAAAAATTTTAA
Found at i:29891 original size:8 final size:8
Alignment explanation
Indices: 29878--29912 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
29868 TATGAGGAAG
29878 TAGGATTA
1 TAGGATTA
29886 TAGGATTA
1 TAGGATTA
29894 TAGGATTA
1 TAGGATTA
29902 TAGGATTA
1 TAGGATTA
29910 TAG
1 TAG
29913 TGCATTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (8 bp):
TAGGATTA
Found at i:34901 original size:34 final size:35
Alignment explanation
Indices: 34845--34912 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
34835 TGCCACTTTT
*
34845 TTGAAATGAAGACTTGGAGTTTT-AGTCGATTAATG
1 TTGAAATGAAGACTTGAAGTTTTCA-TCGATTAATG
34880 TTGAAACTGAA-ACTT-AAGTTTTCATCGATTAAT
1 TTGAAA-TGAAGACTTGAAGTTTTCATCGATTAAT
34913 ACTGCCTCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 15 0.50
35 11 0.37
36 4 0.13
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (35 bp):
TTGAAATGAAGACTTGAAGTTTTCATCGATTAATG
Found at i:34946 original size:104 final size:105
Alignment explanation
Indices: 34761--35020 Score: 396
Period size: 104 Copynumber: 2.5 Consensus size: 105
34751 TGAAAGAAAG
* * *
34761 TTTAATCGATGAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGCCTCCGGGTTTGC
1 TTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGCCTCCGGGTTCGC
* * *
34826 TGTCAACACTGCCACTTTTTTGAAA-TGAAGACTTGGAGT
66 TGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAGAGC
* * **
34865 TTTAGTCGATTAATGTTGAAACTGAAACTTAAGTTTTCATCGATTAATACTGCCTCCGGGTTCGC
1 TTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGCCTCCGGGTTCGC
34930 TGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAGAGC
66 TGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAGAGC
** *
34970 TTTAGTCGATTAATACTGGAATTAAAACTGGAGTTTTCATCGATTAATACT
1 TTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACT
35021 TTTCTCACAG
Statistics
Matches: 138, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
104 82 0.59
105 56 0.41
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (105 bp):
TTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGCCTCCGGGTTCGC
TGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAGAGC
Found at i:40569 original size:34 final size:35
Alignment explanation
Indices: 40513--40580 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
40503 TGCCACTTTT
*
40513 TTGAAATGAAGACTTGGAGTTTT-AGTCGATTAATG
1 TTGAAATGAAGACTTGAAGTTTTCA-TCGATTAATG
40548 TTGAAACTGAA-ACTT-AAGTTTTCATCGATTAAT
1 TTGAAA-TGAAGACTTGAAGTTTTCATCGATTAAT
40581 ACTGACTCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 15 0.50
35 11 0.37
36 4 0.13
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (35 bp):
TTGAAATGAAGACTTGAAGTTTTCATCGATTAATG
Found at i:40606 original size:104 final size:105
Alignment explanation
Indices: 40426--40688 Score: 402
Period size: 104 Copynumber: 2.5 Consensus size: 105
40416 AATGAAACAA
* * *
40426 AGTTTTAATCGATGAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGCCTCCGGGTT
1 AGTTTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGACTCCGGGTT
* *
40491 CGCTGTCAACACTGCCACTTTTTTGAAA-TGAAGACTTGG
66 CGCTGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAG
* * **
40530 AGTTTTAGTCGATTAATGTTGAAACTGAAACTTAAGTTTTCATCGATTAATACTGACTCCGGGTT
1 AGTTTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGACTCCGGGTT
40595 CGCTGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAG
66 CGCTGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAG
** * *
40635 AGTTTTAGTCGATTAATACTGGAATTAAAACTGGAGCTTTCATCGATTAATACT
1 AGTTTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACT
40689 TTTCTAACAG
Statistics
Matches: 141, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
104 85 0.60
105 56 0.40
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (105 bp):
AGTTTTAGTCGATTAATGTTGAAATTAAAACTGGAGTTTTCATCGATTAATACTGACTCCGGGTT
CGCTGTCAACACTGCCACTTTTTTAAAAGTGAAGACTTAG
Found at i:41832 original size:48 final size:49
Alignment explanation
Indices: 41776--41875 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 49
41766 CTGGCCATAA
41776 TTGAAAATTAAGATTGAAACAATTGAAAAATC-TATCAACACATGCATG
1 TTGAAAATTAAGATTGAAACAATTGAAAAATCATATCAACACATGCATG
* * *
41824 TTGAAAATTAAGATTGAAATAATTGAAAAATCATATTAACATATGCATG
1 TTGAAAATTAAGATTGAAACAATTGAAAAATCATATCAACACATGCATG
41873 TTG
1 TTG
41876 TATTGAGTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 31 0.65
49 17 0.35
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (49 bp):
TTGAAAATTAAGATTGAAACAATTGAAAAATCATATCAACACATGCATG
Found at i:45678 original size:21 final size:21
Alignment explanation
Indices: 45654--45694 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45644 TGAAATGGTG
*
45654 AGATTAGTTACTGTACAGATA
1 AGATTAGATACTGTACAGATA
45675 AGATTAGATACTGTACAGAT
1 AGATTAGATACTGTACAGAT
45695 GAGAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (21 bp):
AGATTAGATACTGTACAGATA
Found at i:49924 original size:58 final size:58
Alignment explanation
Indices: 49832--50106 Score: 403
Period size: 58 Copynumber: 4.7 Consensus size: 58
49822 AGCAATAACG
*
49832 ATCGAGCATCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
* * *
49890 ATCGAGCATCCCTCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAATAGATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
* * * *
49948 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTTACGCAATAAGA-AA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAA
*
50006 A-CGGAGCATCCCTCGGTCACACGGCCAAGTGGGCCTCCCCCACTCATGTAATAAATAA
1 ATC-GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
* *
50064 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCAC
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCAC
50107 ACGTGCAAGA
Statistics
Matches: 193, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
57 2 0.01
58 185 0.96
59 6 0.03
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (58 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAA
Found at i:50133 original size:58 final size:57
Alignment explanation
Indices: 49836--50139 Score: 278
Period size: 58 Copynumber: 5.2 Consensus size: 57
49826 ATAACGATCG
* * * * *
49836 AGCATCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAAATCG
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACAC-TGCAATAAGA-AAAACA
* * * * * *
49894 AGCATCCCTCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAAT-AGATAAATCG
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACAC-TGCAATAAGA-AAAACA
* *
49952 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTTAC-GCAATAAG-AAAACGG
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCAC--ACTGCAATAAGAAAAAC-A
* * * *
50010 AGCATCCCTCGGTCACACGGCCAAGTGGGCCTCCCCCACTCATGTAATAA-ATAAATCA
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACAC-TGCAATAAGA-AAAACA
* *
50068 AGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACA
1 AGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCACAC-TGCAATAAGAAAAACA
* *
50126 AGAATCCCTTGGTC
1 AGCATCCCTCGGTC
50140 GCACAACCTA
Statistics
Matches: 211, Mismatches: 24, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 193 0.91
59 11 0.05
60 1 0.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (57 bp):
AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACACTGCAATAAGAAAAACA
Found at i:50133 original size:116 final size:115
Alignment explanation
Indices: 49836--50139 Score: 382
Period size: 116 Copynumber: 2.6 Consensus size: 115
49826 ATAACGATCG
* * * *
49836 AGCATCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAAATCGAGCATC
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACAC-TGCAATAAGA-AAAACGAGCATC
* *
49900 CCTCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAATAGATAAATCG
64 CCTCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAATAAATAAATCA
*
49952 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTTAC-GCAATAAG-AAAACGGAGCAT
1 AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCAC--ACTGCAATAAGAAAAAC-GAGCAT
* * *
50015 CCCTCGGTCACACGGCCAAGTGGGCCTCCCCCACTCATGTAATAAATAAATCA
63 CCCTCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAATAAATAAATCA
* * * *
50068 AGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACAAGAATC
1 AGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCACAC-TGCAATAAGAAAAACGAGCATC
*
50132 CCTTGGTC
64 CCTCGGTC
50140 GCACAACCTA
Statistics
Matches: 164, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
114 2 0.01
115 4 0.02
116 148 0.90
117 9 0.05
118 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (115 bp):
AGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACACTGCAATAAGAAAAACGAGCATCCC
TCGGTCACACGACCAAGCGGGCATCCCCCACTCATGTAATAAATAAATCA
Found at i:50203 original size:28 final size:28
Alignment explanation
Indices: 50163--50240 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
50153 TGTGCACCCC
*
50163 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTAAATAAAATTT
50191 CCAAAGGCATACAGCCTAAATAAAATTT
1 CCAAAGGCATACAGCCTAAATAAAATTT
*
50219 CCAAAGGCATACAGCCAAAATA
1 CCAAAGGCATACAGCCTAAATA
50241 GAGCCCAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (28 bp):
CCAAAGGCATACAGCCTAAATAAAATTT
Found at i:50624 original size:29 final size:29
Alignment explanation
Indices: 50602--50802 Score: 287
Period size: 29 Copynumber: 6.9 Consensus size: 29
50592 TGGTTGTATG
50602 CCCTCCAAAGTTCACGAAGTGGTAGTACT
1 CCCTCCAAAGTTCACGAAGTGGTAGTACT
*
50631 CCCTCCAAAGTTTACGAAGTGGTAGTACT
1 CCCTCCAAAGTTCACGAAGTGGTAGTACT
*
50660 CCCTCCAAAGTTCAAGAAGTGGTAGTACT
1 CCCTCCAAAGTTCACGAAGTGGTAGTACT
** *
50689 CCCTCCAAAACTCAAGAAGTGGTAGTACT
1 CCCTCCAAAGTTCACGAAGTGGTAGTACT
*
50718 CCCTCCAAAGTTCCCGAAGTGGTAGTACT
1 CCCTCCAAAGTTCACGAAGTGGTAGTACT
** *
50747 CCCTCCAAAACTCAAGAAGTGGTAGTACGT
1 CCCTCCAAAGTTCACGAAGTGGTAGTAC-T
**
50777 -CCTCCAAAACTCACGAAGTGGTAGTA
1 CCCTCCAAAGTTCACGAAGTGGTAGTA
50803 TGCCCCCTAG
Statistics
Matches: 157, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
29 156 0.99
30 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (29 bp):
CCCTCCAAAGTTCACGAAGTGGTAGTACT
Found at i:50737 original size:87 final size:88
Alignment explanation
Indices: 50602--50802 Score: 325
Period size: 87 Copynumber: 2.3 Consensus size: 88
50592 TGGTTGTATG
** *
50602 CCCTCCAAAGTTCACGAAGTGGTAGTACTCCCTCCAAAGTTTACGAAGTGGTAGTACTCCCTCCA
1 CCCTCCAAAACTCACGAAGTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTACTCCCTCCA
**
50667 AAGTTCAAGAAGTGGTAGTAC-T
66 AAACTCAAGAAGTGGTAGTACGT
* *
50689 CCCTCCAAAACTCAAGAAGTGGTAGTACTCCCTCCAAAGTTCCCGAAGTGGTAGTACTCCCTCCA
1 CCCTCCAAAACTCACGAAGTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTACTCCCTCCA
50754 AAACTCAAGAAGTGGTAGTACGT
66 AAACTCAAGAAGTGGTAGTACGT
50777 -CCTCCAAAACTCACGAAGTGGTAGTA
1 CCCTCCAAAACTCACGAAGTGGTAGTA
50803 TGCCCCCTAG
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 104 0.99
88 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (88 bp):
CCCTCCAAAACTCACGAAGTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTACTCCCTCCA
AAACTCAAGAAGTGGTAGTACGT
Found at i:50975 original size:29 final size:28
Alignment explanation
Indices: 50940--51433 Score: 441
Period size: 29 Copynumber: 18.2 Consensus size: 28
50930 AGAGAGCGTT
*
50940 GTACATCCACCATTATGGACATGAGCGCC
1 GTACATCCACCATTTTGGACA-GAGCGCC
*
50969 GTACATCCACCATTTTGGAC-GAGCGCT
1 GTACATCCACCATTTTGGACAGAGCGCC
* *
50996 GTACATCCACCATTATAGACATGAGCGCC
1 GTACATCCACCATTTTGGACA-GAGCGCC
51025 GTACATCCACCATTTTGGAC-GAGCGCC
1 GTACATCCACCATTTTGGACAGAGCGCC
* *
51052 GTACA---ACCATCTTGGAAGAGAGCGCC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
* *
51078 GTACATCCACCATTTTGGA-TGAGTGCC
1 GTACATCCACCATTTTGGACAGAGCGCC
* *
51105 GTACA---ACCATCTTGGAAGAGAGCGCC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
*
51131 TTACA---ACCATTTTGGAC-GAGCGCC
1 GTACATCCACCATTTTGGACAGAGCGCC
* *
51155 GTACA---ACCATCTTGGAAGAGAGCGCC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
51181 GTACATCCACCATTTTGGAC-GAGCGCC
1 GTACATCCACCATTTTGGACAGAGCGCC
* *
51208 GTACA---ACCATTTTGGAAGAGAGCGTC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
* *
51234 GTACA---ACCATCTTGGAAGAGAGCGCC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
*
51260 GTAGATCCACCATTTTGGAC-GAGCGCC
1 GTACATCCACCATTTTGGACAGAGCGCC
* * *
51287 GTACA---ACCATCTTGGAAGAGAGCGTC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
*
51313 GTACATCCACCATTTTGGAC-GAGCGCT
1 GTACATCCACCATTTTGGACAGAGCGCC
51340 GTACATCCACCATTTTGGACATGAGCGCC
1 GTACATCCACCATTTTGGACA-GAGCGCC
* *
51369 GTACATCCACCATTTTGGACGACAGCGCT
1 GTACATCCACCATTTTGGAC-AGAGCGCC
* * * *
51398 ATACATCCACCATCTTGGAAGAGAGCGTC
1 GTACATCCACCATTTTGG-ACAGAGCGCC
51427 GTACATC
1 GTACATC
51434 AATCTTGGAA
Statistics
Matches: 389, Mismatches: 48, Indels: 56
0.79 0.10 0.11
Matches are distributed among these distances:
24 57 0.15
25 6 0.02
26 88 0.23
27 95 0.24
28 4 0.01
29 137 0.35
30 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (28 bp):
GTACATCCACCATTTTGGACAGAGCGCC
Found at i:51084 original size:53 final size:53
Alignment explanation
Indices: 50962--51452 Score: 414
Period size: 53 Copynumber: 9.1 Consensus size: 53
50952 TTATGGACAT
* * * ** *
50962 GAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCACCATTATAGACA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATC-TTGGA-AGA
51017 TGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
1 -GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
* *
51071 GAGCGCCGTACATCCACCATTTTGGATGAGTGCCGTACAACCATCTTGGAAGA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
*
51124 GAGCGCCTTACA---ACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
*
51174 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
* * * * * *
51227 GAGCGTCGTACA---ACCATCTTGGAAGAGAGCGCCGTAGATCCACCATTTTGG-A-C
1 GAGCGCCGTACATCCACCATTTTGG-A-CGAGCGCCGT--A-CAACCATCTTGGAAGA
* * * * *
51280 GAGCGCCGTACA---ACCATCTTGGAAGAGAGCGTCGTACATCCACCATTTTGG-A-C
1 GAGCGCCGTACATCCACCATTTTGG-A-CGAGCGCCGTACA---ACCATCTTGGAAGA
* * *
51333 GAGCGCTGTACATCCACCATTTTGGACATGAGCGCCGTACATCCACCATTTTGGACGA
1 GAGCGCCGTACATCCACCATTTTGGAC--GAGCGCCGTACA---ACCATCTTGGAAGA
* ** * * * * *
51391 CAGCGCTATACATCCACCATCTTGGAAGAGAGCGTCGTACATCAATCTTGGAAGA
1 GAGCGCCGTACATCCACCATTTTGG-A-CGAGCGCCGTACAACCATCTTGGAAGA
*
51446 GGGCGCC
1 GAGCGCC
51453 ATAGGCCAAC
Statistics
Matches: 376, Mismatches: 39, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
50 57 0.15
51 2 0.01
52 9 0.02
53 166 0.44
54 4 0.01
55 29 0.08
56 75 0.20
58 33 0.09
59 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.21
Consensus pattern (53 bp):
GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
Found at i:51146 original size:79 final size:78
Alignment explanation
Indices: 50947--51420 Score: 414
Period size: 79 Copynumber: 5.9 Consensus size: 78
50937 GTTGTACATC
* * *
50947 CACCATTATGGACATGAGCGCCGTACATCCACCATTTTGG-A-CGAGCGCTGTACATCCACCAT-
1 CACCATTTTGGAC--GAGCGCCGTACA---ACCATTTTGGAAGAGAGCGCCGTACATCCACCATC
*
51009 TATAGACATGAGCGCCGTACA
61 T-TGGA-A-GAGCGCCGTACA
* *
51030 TCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTG
1 --CACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGCCGTACATCCACCATCTTG
* *
51095 GATGAGTGCCGTACA
64 GAAGAGCGCCGTACA
* * * *
51110 -ACCATCTTGGAAGAGAGCGCCTTACAACCATTTTGG-A-CGAGCGCCGTACA---ACCATCTTG
1 CACCATTTTGG-A-CGAGCGCCGTACAACCATTTTGGAAGAGAGCGCCGTACATCCACCATCTTG
51169 GAAGAGAGCGCCGTACA
64 G-A-AGAGCGCCGTACA
*
51186 TCCACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGTCGTACA---ACCATCTTG
1 --CACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGCCGTACATCCACCATCTTG
*
51248 GAAGAGAGCGCCGTAGA
64 G-A-AGAGCGCCGTACA
* * *
51265 TCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGAGAGCGTCGTACATCCACCATTTTG
1 --CACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGCCGTACATCCACCATCTTG
* *
51330 GACGAGCGCTGTACA
64 GAAGAGCGCCGTACA
* * **
51345 TCCACCATTTTGGACATGAGCGCCGTACATCCACCATTTTGGACGACAGCGCTATACATCCACCA
1 --CACCATTTTGGAC--GAGCGCCGTACA---ACCATTTTGGAAGAGAGCGCCGTACATCCACCA
51410 TCTTGGAAGAG
59 TCTTGGAAGAG
51421 AGCGTCGTAC
Statistics
Matches: 335, Mismatches: 34, Indels: 40
0.82 0.08 0.10
Matches are distributed among these distances:
74 9 0.03
75 1 0.00
76 11 0.03
77 42 0.13
78 4 0.01
79 117 0.35
80 45 0.13
81 2 0.01
82 43 0.13
83 13 0.04
85 48 0.14
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (78 bp):
CACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGCCGTACATCCACCATCTTGGA
AGAGCGCCGTACA
Found at i:51170 original size:103 final size:103
Alignment explanation
Indices: 50962--51249 Score: 414
Period size: 103 Copynumber: 2.7 Consensus size: 103
50952 TTATGGACAT
* * * ** *
50962 GAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCACCATTATAGACATGAGCGCCGT
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATC-TTGGA-AGA-GAGCGCCGT
51027 ACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
63 ACA---ACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
* * *
51071 GAGCGCCGTACATCCACCATTTTGGATGAGTGCCGTACAACCATCTTGGAAGAGAGCGCCTTACA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGAGAGCGCCGTACA
51136 ACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
66 ACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
* *
51174 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATTTTGGAAGAGAGCGTCGTACA
1 GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGAGAGCGCCGTACA
*
51239 ACCATCTTGGA
66 ACCATTTTGGA
51250 AGAGAGCGCC
Statistics
Matches: 164, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
103 108 0.66
106 11 0.07
107 2 0.01
108 3 0.02
109 40 0.24
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (103 bp):
GAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGAGAGCGCCGTACA
ACCATTTTGGACGAGCGCCGTACAACCATCTTGGAAGA
Found at i:51627 original size:19 final size:19
Alignment explanation
Indices: 51603--51639 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
51593 ATGACCGCGA
51603 AGCGGTAGTACGCTCCAAT
1 AGCGGTAGTACGCTCCAAT
51622 AGCGGTAGTACGCTCCAA
1 AGCGGTAGTACGCTCCAA
51640 ACGACCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (19 bp):
AGCGGTAGTACGCTCCAAT
Found at i:51662 original size:28 final size:28
Alignment explanation
Indices: 51622--51696 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
51612 ACGCTCCAAT
*
51622 AGCGGTAGTACGCTCCAAACGACCACGA
1 AGCGGTAGTACGCTCCAAACGACCACAA
* * *
51650 AGCGGTAGTACGCTCCCAATGACCGCAA
1 AGCGGTAGTACGCTCCAAACGACCACAA
*
51678 AGCGATAGTACGCTCCAAA
1 AGCGGTAGTACGCTCCAAA
51697 AGCGGTAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13
Consensus pattern (28 bp):
AGCGGTAGTACGCTCCAAACGACCACAA
Found at i:51700 original size:19 final size:19
Alignment explanation
Indices: 51676--51716 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
51666 CAATGACCGC
*
51676 AAAGCGATAGTACGCTCCA
1 AAAGCGATAGAACGCTCCA
*
51695 AAAGCGGTAGAACGCTCCA
1 AAAGCGATAGAACGCTCCA
51714 AAA
1 AAA
51717 AAAATCCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAGCGATAGAACGCTCCA
Done.