Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017223.1 Corchorus olitorius cultivar O-4 contig17256, 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: 45190
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:3071 original size:22 final size:22
Alignment explanation
Indices: 3044--3088 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3034 CATACTCGAC
3044 ACAAGCAAGAAAAAAAACTTTG
1 ACAAGCAAGAAAAAAAACTTTG
*
3066 ACAAGCAAGAGAAAAAACTTTG
1 ACAAGCAAGAAAAAAAACTTTG
3088 A
1 A
3089 AACTCACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (22 bp):
ACAAGCAAGAAAAAAAACTTTG
Found at i:16760 original size:21 final size:21
Alignment explanation
Indices: 16713--17160 Score: 367
Period size: 21 Copynumber: 21.4 Consensus size: 21
16703 AGATGGGGTC
16713 AATCAGTAAAAGAGTAA-AGAAT
1 AATCAGTAAAAGAGTAATAG--T
16735 AATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAATAGT
*
16756 AATCAGT-AAAGAGTAAAGAGT
1 AATCAGTAAAAGAGT-AATAGT
* * * *
16777 AATGAAG-AAATGGGTAAGAGT
1 AAT-CAGTAAAAGAGTAATAGT
*
16798 AATCACTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAATAGT
*
16819 AATCAGTAAAAGAGTAAAGAGT
1 AATCAGTAAAAGAGT-AATAGT
*
16841 AATCAGTAAAAGGGTAATAGT
1 AATCAGTAAAAGAGTAATAGT
16862 AATCAGTAAAAGAGTAA-AGAAT
1 AATCAGTAAAAGAGTAATAG--T
16884 AATCAGTAAAAAGAGTAATAGT
1 AATCAGT-AAAAGAGTAATAGT
*
16906 AATCAGT-AAAGAGTAAAGAGT
1 AATCAGTAAAAGAGT-AATAGT
* ** * *
16927 AATGAACAAATG-GTAAGAGT
1 AATCAGTAAAAGAGTAATAGT
16947 AATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAATAGT
*
16968 AATCAGTGAAAGAGTAA-AGAAT
1 AATCAGTAAAAGAGTAATAG--T
16990 AATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAATAGT
* * *
17011 AATTAGT-AAAGTGTAAAGAGT
1 AATCAGTAAAAGAGT-AATAGT
17032 AATCAGTAAAAGAGTAA-AG-
1 AATCAGTAAAAGAGTAATAGT
* * *
17051 ----AGTAAAGGAGTAGTAAT
1 AATCAGTAAAAGAGTAATAGT
** *
17068 GGTCAGTAAA-GAGTAAAGAGT
1 AATCAGTAAAAGAGT-AATAGT
* *
17089 AATCA--AGGAAGAGTCATAGT
1 AATCAGTA-AAAGAGTAATAGT
*
17109 AATCAGTAAAAGAGTAAACAGT
1 AATCAGTAAAAGAGT-AATAGT
17131 GAA-CAGTAAAATGA-TAATAGT
1 -AATCAGTAAAA-GAGTAATAGT
17152 AATCAGTAA
1 AATCAGTAA
17161 GGAGTATATG
Statistics
Matches: 347, Mismatches: 46, Indels: 67
0.75 0.10 0.15
Matches are distributed among these distances:
15 11 0.03
16 1 0.00
19 1 0.00
20 57 0.16
21 158 0.46
22 99 0.29
23 18 0.05
24 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (21 bp):
AATCAGTAAAAGAGTAATAGT
Found at i:16761 original size:43 final size:42
Alignment explanation
Indices: 16713--17055 Score: 353
Period size: 43 Copynumber: 8.0 Consensus size: 42
16703 AGATGGGGTC
*
16713 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAAAG-ATAATCAGTAAAAGAGTAAGAGT
* * *
16756 AATCAGT-AAAGAGTAAAGAGTAATGAAG-AAATGGGTAAGAGT
1 AATCAGTAAAAGAGTAAAGA-TAAT-CAGTAAAAGAGTAAGAGT
*
16798 AATCACTAAAAGAGTAATAG-TAATCAGTAAAAGAGTAAAGAGT
1 AATCAGTAAAAGAGTAA-AGATAATCAGTAAAAGAGT-AAGAGT
* *
16841 AATCAGTAAAAGGGTAATAG-TAATCAGTAAAAGAGTAAAGAAT
1 AATCAGTAAAAGAGTAA-AGATAATCAGTAAAAGAGT-AAGAGT
16884 AATCAGTAAAAAGAGTAATAG-TAATCAGT-AAAGAGTAAAGAGT
1 AATCAGT-AAAAGAGTAA-AGATAATCAGTAAAAGAGT-AAGAGT
* ** * *
16927 AATGAACAAATG-GT-AAGAGTAATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAAAGA-TAATCAGTAAAAGAGTAAGAGT
* *
16968 AATCAGTGAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGT
1 AATCAGTAAAAGAGTAAAG-ATAATCAGTAAAAGAGTAAGAGT
* *
17011 AATTAGT-AAAGTGTAAAGAGTAATCAGTAAAAGAGTAAAGAGT
1 AATCAGTAAAAGAGTAAAGA-TAATCAGTAAAAGAGT-AAGAGT
17054 AA
1 AA
17056 AGGAGTAGTA
Statistics
Matches: 259, Mismatches: 26, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.01
40 1 0.00
41 26 0.10
42 81 0.31
43 126 0.49
44 23 0.09
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (42 bp):
AATCAGTAAAAGAGTAAAGATAATCAGTAAAAGAGTAAGAGT
Found at i:16770 original size:7 final size:7
Alignment explanation
Indices: 16721--17090 Score: 94
Period size: 7 Copynumber: 51.3 Consensus size: 7
16711 TCAATCAGTA
16721 AAAGAGT
1 AAAGAGT
*
16728 AAAGAAT
1 AAAGAGT
**
16735 AATCAGT
1 AAAGAGT
16742 AAAAGAGT
1 -AAAGAGT
*
16750 -AATAGT
1 AAAGAGT
**
16756 AATCAGT
1 AAAGAGT
16763 AAAGAGT
1 AAAGAGT
16770 AAAGAGT
1 AAAGAGT
*
16777 AATGAAG-
1 AAAG-AGT
*
16784 AAATGGGT
1 AAA-GAGT
16792 -AAGAGT
1 AAAGAGT
** *
16798 AATCACT
1 AAAGAGT
16805 AAAAGAGT
1 -AAAGAGT
*
16813 -AATAGT
1 AAAGAGT
**
16819 AATCAGT
1 AAAGAGT
16826 AAAAGAGT
1 -AAAGAGT
16834 AAAGAGT
1 AAAGAGT
**
16841 AATCAGT
1 AAAGAGT
*
16848 AAAAGGGT
1 -AAAGAGT
*
16856 -AATAGT
1 AAAGAGT
**
16862 AATCAGT
1 AAAGAGT
16869 AAAAGAGT
1 -AAAGAGT
*
16877 AAAGAAT
1 AAAGAGT
**
16884 AATCAGT
1 AAAGAGT
16891 AAAAAGAGT
1 --AAAGAGT
*
16900 -AATAGT
1 AAAGAGT
**
16906 AATCAGT
1 AAAGAGT
16913 AAAGAGT
1 AAAGAGT
16920 AAAGAGT
1 AAAGAGT
* **
16927 AATGAAC
1 AAAGAGT
16934 AAATG-GT
1 AAA-GAGT
16941 -AAGAGT
1 AAAGAGT
**
16947 AATCAGT
1 AAAGAGT
16954 AAAAGAGT
1 -AAAGAGT
*
16962 -AATAGT
1 AAAGAGT
**
16968 AATCAGT
1 AAAGAGT
16975 GAAAGAGT
1 -AAAGAGT
*
16983 AAAGAAT
1 AAAGAGT
**
16990 AATCAGT
1 AAAGAGT
16997 AAAAGAGT
1 -AAAGAGT
*
17005 -AATAGT
1 AAAGAGT
**
17011 AATTAGT
1 AAAGAGT
*
17018 AAAGTGT
1 AAAGAGT
17025 AAAGAGT
1 AAAGAGT
**
17032 AATCAGT
1 AAAGAGT
17039 AAAAGAGT
1 -AAAGAGT
17047 AAAGAGT
1 AAAGAGT
17054 AAAGGAGT
1 AAA-GAGT
17062 AGTAATGGTCAGT
1 A--AA--G--AGT
17075 AAAGAGT
1 AAAGAGT
17082 AAAGAGT
1 AAAGAGT
17089 AA
1 AA
17091 TCAAGGAAGA
Statistics
Matches: 254, Mismatches: 79, Indels: 60
0.65 0.20 0.15
Matches are distributed among these distances:
5 1 0.00
6 36 0.14
7 149 0.59
8 52 0.20
9 6 0.02
10 2 0.01
11 4 0.02
13 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (7 bp):
AAAGAGT
Found at i:16850 original size:106 final size:106
Alignment explanation
Indices: 16713--17160 Score: 464
Period size: 106 Copynumber: 4.3 Consensus size: 106
16703 AGATGGGGTC
* *
16713 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGT
1 AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAAT
* * * *
16777 AATGAAGAAATGGGTAAGAGTAATCACTAAAAGAGT-AATAGT
66 AATGAAGAAA-GAGTAATAGTAATCAGT-AAAGAGTAAAGAGT
*
16819 AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGGGTAATAGTAATCAGTAAAAGAGTAAAGAAT
1 AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAAT
16884 AATCAGTAA-AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
66 AAT--G-AAGAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
* ** * *
16927 AATGAACAAATG-GT-AAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTGAAAGAGTAAAGAAT
1 AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAAT
* * *
16990 AAT-CAGTAAAAGAGTAATAGTAATTAGTAAAGTGTAAAGAGT
66 AATGAAG--AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
* * *
17032 AATCAGTAAAAGAGTAAAGAGTAA--AG---GAGTAGTAAT-G--GTCAGT-AAAGAGTAAAGAG
1 AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAG-AGTAATAGTAATCAGTAAAAGAGTAAAGAA
* * * *
17088 TAATCAAGGAAGAGTCATAGTAATCAGTAAAAGAGTAAACAGT
65 TAATGAAGAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGT
*
17131 GAA-CAGTAAAATGA-T-AATAGTAATCAGTAA
1 -AATCAGTAAAA-GAGTAAAGAGTAATCAGTAA
17161 GGAGTATATG
Statistics
Matches: 292, Mismatches: 30, Indels: 43
0.80 0.08 0.12
Matches are distributed among these distances:
98 24 0.08
99 37 0.13
100 13 0.04
102 4 0.01
103 6 0.02
105 42 0.14
106 100 0.34
107 33 0.11
108 27 0.09
109 4 0.01
110 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (106 bp):
AATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAAT
AATGAAGAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
Found at i:16951 original size:149 final size:149
Alignment explanation
Indices: 16713--17048 Score: 577
Period size: 149 Copynumber: 2.3 Consensus size: 149
16703 AGATGGGGTC
16713 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTA
1 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTA
* *
16778 ATGAAGAAATGGGTAAGAGTAATCACTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAGTAA
66 ATGAACAAATGGGTAAGAGTAATCACTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAATAA
*
16843 TCAGTAAAAGGGTAATAGT
131 TCAGTAAAAGAGTAATAGT
16862 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
1 AATCAGTAAAAGAGTAAAGAATAATCAGT-AAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGT
* *
16927 AATGAACAAAT-GGTAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGTGAAAGAGTAAAGAATA
65 AATGAACAAATGGGTAAGAGTAATCACTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAATA
16991 ATCAGTAAAAGAGTAATAGT
130 ATCAGTAAAAGAGTAATAGT
* * *
17011 AATTAGT-AAAGTGTAAAGAGTAATCAGTAAAAGAGTAA
1 AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAA
17049 AGAGTAAAGG
Statistics
Matches: 178, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
147 10 0.06
148 19 0.11
149 104 0.58
150 45 0.25
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (149 bp):
AATCAGTAAAAGAGTAAAGAATAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTA
ATGAACAAATGGGTAAGAGTAATCACTAAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAATAA
TCAGTAAAAGAGTAATAGT
Found at i:17336 original size:26 final size:26
Alignment explanation
Indices: 17295--17345 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17285 AATAGGTAAG
17295 AAAATGGTAATAAGT-AAAAAGAGTA
1 AAAATGGTAATAAGTAAAAAAGAGTA
*
17320 AAAATTGGTAATCAGTAAAAAAGAGT
1 AAAA-TGGTAATAAGTAAAAAAGAGT
17346 GAGGGTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 9 0.39
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.22
Consensus pattern (26 bp):
AAAATGGTAATAAGTAAAAAAGAGTA
Found at i:23536 original size:175 final size:175
Alignment explanation
Indices: 23245--23599 Score: 629
Period size: 175 Copynumber: 2.0 Consensus size: 175
23235 GAAACAAAAT
23245 TGAAGCTATTGCACATATCCATGCACAAATTAATATTTACTATTTATTGCCAACTTTAGGGCATA
1 TGAAGCTATTGCACATATCCATGCACAAATTAATATTTACTATTTATTGCCAACTTTAGGGCATA
23310 TGCTCAATGTTAATAGTATAGTCTTTTAAAGATGCAACAAATTTAAAATCATAGTACTTTCGAAA
66 TGCTCAATGTTAATAGTATAGTCTTTTAAAGATGCAACAAATTTAAAATCATAGTACTTTCGAAA
*
23375 TTTTCTACGTATCAAACAATTTAAGTCAAATAGAAATTTGTTCAA
131 TTTTCTACGTATCAAACAATTTAAGTCAAATAGAAAATTGTTCAA
* * * * *
23420 TGAAGCTATTGCACCTGTTCATGTACAAATTAATATTTACTATTTATTGTCAACTTTAGGGCATA
1 TGAAGCTATTGCACATATCCATGCACAAATTAATATTTACTATTTATTGCCAACTTTAGGGCATA
*
23485 TGCTCAATGTTGATAGTATAGTCTTTTAAAGATGCAACAAATTTAAAATCATAGTACTTTCGAAA
66 TGCTCAATGTTAATAGTATAGTCTTTTAAAGATGCAACAAATTTAAAATCATAGTACTTTCGAAA
* *
23550 TTTTCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAA
131 TTTTCTACGTATCAAACAATTTAAGTCAAATAGAAAATTGTTCAA
23595 TGAAG
1 TGAAG
23600 TAGATTTCTG
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
175 171 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (175 bp):
TGAAGCTATTGCACATATCCATGCACAAATTAATATTTACTATTTATTGCCAACTTTAGGGCATA
TGCTCAATGTTAATAGTATAGTCTTTTAAAGATGCAACAAATTTAAAATCATAGTACTTTCGAAA
TTTTCTACGTATCAAACAATTTAAGTCAAATAGAAAATTGTTCAA
Found at i:25722 original size:6 final size:6
Alignment explanation
Indices: 25711--25738 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25701 TGGTGCTCTC
25711 TTCATT TTCATT TTCATT TTCATT TTCA
1 TTCATT TTCATT TTCATT TTCATT TTCA
25739 ATATTTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:27448 original size:100 final size:100
Alignment explanation
Indices: 27334--27521 Score: 313
Period size: 100 Copynumber: 1.9 Consensus size: 100
27324 GTCCTTTAGC
* * *
27334 GAATAATTTTGAATTACAAAAACAAAATTAATCAAGAAAATGTGTATGTATCAACTTTTTAACCC
1 GAATAATTTTGAATTACAAAAACAAAATTAATCAAGAAAATGTGTACGCATCAACTTCTTAACCC
27399 GCTTGTAGAGTCCAAAATTTACACCTAATAGAGTG
66 GCTTGTAGAGTCCAAAATTTACACCTAATAGAGTG
* **
27434 GAATAGTTTTGAATTTTAAAAACAAAATTAATCAAGAAAATGTGTACGCATCAACTTCTTAACCC
1 GAATAATTTTGAATTACAAAAACAAAATTAATCAAGAAAATGTGTACGCATCAACTTCTTAACCC
*
27499 GCTTGTAGAGTTCAAAATTTACA
66 GCTTGTAGAGTCCAAAATTTACA
27522 TTGATAGTGT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (100 bp):
GAATAATTTTGAATTACAAAAACAAAATTAATCAAGAAAATGTGTACGCATCAACTTCTTAACCC
GCTTGTAGAGTCCAAAATTTACACCTAATAGAGTG
Found at i:27848 original size:31 final size:31
Alignment explanation
Indices: 27810--27869 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
27800 TCTAGGCACT
*
27810 GATTTGAGCCGATTTTACAACGTTAGGGACA
1 GATTTGAGCCGAATTTACAACGTTAGGGACA
* * *
27841 GATTTGAGTCGAATTTATAATGTTAGGGA
1 GATTTGAGCCGAATTTACAACGTTAGGGA
27870 TTTAATTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (31 bp):
GATTTGAGCCGAATTTACAACGTTAGGGACA
Found at i:29126 original size:196 final size:195
Alignment explanation
Indices: 28747--29133 Score: 587
Period size: 196 Copynumber: 2.0 Consensus size: 195
28737 CTTACCAAAC
*
28747 TACCAAACAAATAAACAAAAAAATTAAACTCAAATTTCTTGAGACTTGAAGCTAGGACCTCACAG
1 TACCAAACAAATAAACAAAAAAATTAAACTCAAATTTCTTGAGACTTGAAGCAAGGACCTCACAG
** *
28812 TCCAAGCATAATGCACTCATGAGTTGAGTTAACAATTCAGGTCCATCAATATGTATATATGTAAT
66 TCCAAGCATAATGCACTCACCAGTTGAGTTAACAACTCAGGTCCATCAATATGTATATA-GTAAT
*
28877 TAATTATACACGTTTACAAAAGGGACATTTTTCCCCCTGGATTTTTATTTTGGAACTTGTATTGC
130 TAATTATACACGTTTACAAAAGGGACATTTTTCCCCCTGAATTTTTATTTTGGAACTTGTATTGC
28942 T
195 T
* * * *
28943 TACCAAAGAAATAAACCAAAAAATTAAACTCAAATTTCTTGAGATTTGAATCAAGGACCTCACAG
1 TACCAAACAAATAAACAAAAAAATTAAACTCAAATTTCTTGAGACTTGAAGCAAGGACCTCACAG
* * * *
29008 TTCAAGCATAGTGCACTCACCAGTTGAGTTAACAACTCGGGTGCATCAATATGTATATA-TAATT
66 TCCAAGCATAATGCACTCACCAGTTGAGTTAACAACTCAGGTCCATCAATATGTATATAGTAATT
* * * *
29072 AATTGTACACTTTTACAAAAGGGACATTTTTCCTCCTGAATTTTTTTTTTTTGGAACTTGTA
131 AATTATACACGTTTACAAAAGGGACATTTTTCCCCCTGAA--TTTTTATTTTGGAACTTGTA
29134 GTCCTTAAAC
Statistics
Matches: 172, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
194 41 0.24
196 131 0.76
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (195 bp):
TACCAAACAAATAAACAAAAAAATTAAACTCAAATTTCTTGAGACTTGAAGCAAGGACCTCACAG
TCCAAGCATAATGCACTCACCAGTTGAGTTAACAACTCAGGTCCATCAATATGTATATAGTAATT
AATTATACACGTTTACAAAAGGGACATTTTTCCCCCTGAATTTTTATTTTGGAACTTGTATTGCT
Found at i:30367 original size:11 final size:11
Alignment explanation
Indices: 30351--30380 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
30341 TACCCGTGAC
30351 GGGTTCGGGTA
1 GGGTTCGGGTA
30362 GGGTTCGGGTA
1 GGGTTCGGGTA
30373 GGGTTCGG
1 GGGTTCGG
30381 ATAGTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.57, T:0.27
Consensus pattern (11 bp):
GGGTTCGGGTA
Found at i:30451 original size:19 final size:19
Alignment explanation
Indices: 30431--30467 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30421 AATTAATTAT
30431 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
30449 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
30468 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:30832 original size:5 final size:5
Alignment explanation
Indices: 30814--30849 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
30804 TATATAGTAG
30814 TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TAAGA TAA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAA
30850 TTTGTAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 4 0.14
5 24 0.83
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:34091 original size:31 final size:31
Alignment explanation
Indices: 34053--34115 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
34043 AAGGTCATAA
34053 ATATTTTCTTACAATTGTGGATGACTTTAGC
1 ATATTTTCTTACAATTGTGGATGACTTTAGC
34084 ATATTTTCTTACAATTGTGGATGACTTTAGC
1 ATATTTTCTTACAATTGTGGATGACTTTAGC
34115 A
1 A
34116 GATTCACCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (31 bp):
ATATTTTCTTACAATTGTGGATGACTTTAGC
Found at i:35732 original size:15 final size:15
Alignment explanation
Indices: 35704--35743 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35694 TTTTGGCGCG
*
35704 AAAATTTCAAAATTC
1 AAAATTTGAAAATTC
* *
35719 GAATTTTGAAAATTC
1 AAAATTTGAAAATTC
35734 AAAATTTGAA
1 AAAATTTGAA
35744 TTTTGGAAGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (15 bp):
AAAATTTGAAAATTC
Found at i:35737 original size:22 final size:23
Alignment explanation
Indices: 35703--35748 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
35693 TTTTTGGCGC
35703 GAAAATTTCAAAATTCGAATTTT
1 GAAAATTTCAAAATTCGAATTTT
*
35726 GAAAA-TTCAAAATTTGAATTTT
1 GAAAATTTCAAAATTCGAATTTT
35748 G
1 G
35749 GAAGTTGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
GAAAATTTCAAAATTCGAATTTT
Found at i:39265 original size:2 final size:2
Alignment explanation
Indices: 39258--39291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39248 TGGACAAACA
39258 AT AT AT AT 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 AT AT AT AT
39292 TTATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39695 original size:76 final size:75
Alignment explanation
Indices: 39516--39780 Score: 363
Period size: 76 Copynumber: 3.5 Consensus size: 75
39506 CCTCTAGGGA
* * *
39516 AGACGAACGGGGGCGCCAGTTTAGGCACTCCATCGTTGAGTGAGCGGCGTCAGCATGGACG--CT
1 AGACGAACGGGGGCGCCAGTCTAGGCACT-CACCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
39579 GTCTCACTGGT
65 GTCTCACTGGT
* *
39590 GGACGAACGGGAGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
1 AGACGAACGGGGGCGCCAGTCTAGGCACTCA-CCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
* *
39655 GTCCCATTGGT
65 GTCTCACTGGT
*
39666 AGACGAACGGGGGCGCCAGTCTAGACACTCAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
1 AGACGAACGGGGGCGCCAGTCTAGGCACTCA-CCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
39731 GTCTCACTGGT
65 GTCTCACTGGT
* * * *
39742 GGGCAGAACGGAGGTGCCAGTCTAGGCACTCTACCGTTG
1 AGAC-GAACGGGGGCGCCAGTCTAGGCACTC-ACCGTTG
39781 TTTGAAATAT
Statistics
Matches: 169, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
73 2 0.01
74 53 0.31
76 84 0.50
77 29 0.17
78 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.19
Consensus pattern (75 bp):
AGACGAACGGGGGCGCCAGTCTAGGCACTCACCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCTG
TCTCACTGGT
Done.