Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018545.1 Corchorus olitorius cultivar O-4 contig18578, 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: 104766
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6666 original size:12 final size:11
Alignment explanation
Indices: 6640--6664 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6630 CTCCATCAAG
6640 AAATTCAAAAA
1 AAATTCAAAAA
6651 AAATTCAAAAA
1 AAATTCAAAAA
6662 AAA
1 AAA
6665 ATAATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:6735 original size:19 final size:20
Alignment explanation
Indices: 6693--6729 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
6683 AAAGTCAATA
6693 AAAAAAATTCAAATCAAAAT
1 AAAAAAATTCAAATCAAAAT
6713 AAAAAAA-TCAAATCAAA
1 AAAAAAATTCAAATCAAA
6730 TCAAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAATTCAAATCAAAAT
Found at i:7415 original size:50 final size:50
Alignment explanation
Indices: 7334--7491 Score: 246
Period size: 50 Copynumber: 3.2 Consensus size: 50
7324 GAACAAGAAG
*
7334 TTTCACAA-TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCT
1 TTTCA-AAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCT
* *
7384 TTTCAAAGTAAAATTGCTTTCAATTTGTGAGTTCAAGATCAAAATTTGCT
1 TTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCT
* * *
7434 TTTCAAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCT
1 TTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCT
7484 TTTCAAAG
1 TTTCAAAG
7492 GACATTGAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 2 0.02
50 97 0.98
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (50 bp):
TTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCT
Found at i:8029 original size:87 final size:85
Alignment explanation
Indices: 7883--8353 Score: 536
Period size: 87 Copynumber: 5.5 Consensus size: 85
7873 TTCGAGGCAA
* * * * * *
7883 CAATCCAGAAGTTTTAATCATAACATCAGACTCAGAGTTATTCTTCAAGGCAACAAAATTGACCG
1 CAATCAAGAAGTTTTAGTTACAACATCAGACTCAGAGTTATT-TTCAA-GTATCAAAATTGACCG
*
7948 CAAATTGGTCCTTTTTCATCAT
64 CACATTGGTCCTTTTTCATCAT
* * * *
7970 CAATCAAGAAGTTTTAATCATAACATCAGACTCAGAGCTATTCTTCAAGTCATCAAAATTGACCG
1 CAATCAAGAAGTTTTAGTTACAACATCAGACTCAGAGTTATT-TTCAAGT-ATCAAAATTGACCG
*
8035 CAAATTGGTCCTTTTTCATCATT
64 CACATTGGTCCTTTTTCATCA-T
* *
8058 CAATCAAGAAGTTTTCAGTTACAGCATCAGACTCAGAGTTA-TTT----T-TCAAGATTGACCGC
1 CAATCAAGAAGTTTT-AGTTACAACATCAGACTCAGAGTTATTTTCAAGTATCAAAATTGACCGC
8117 ACATTGGTCCTTTTTCATCAT
65 ACATTGGTCCTTTTTCATCAT
* * *
8138 CAATCAAGAAGTTTCCAGTTACAACATCAGACTTAGAGTTATTTTTCAAGTTATTTTTCAAGATT
1 CAATCAAGAAGTTT-TAGTTACAACATCAGACTCAGAGTTA-TTTTCAAG-TA----TCAAAATT
8203 GACCGCACATTGGTCCTTTTTCATCAT
59 GACCGCACATTGGTCCTTTTTCATCAT
*
8230 CAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTA-TTT----T-TC-AAGTTGACCGC
1 CAATCAAGAAGTTTT-AGTTACAACATCAGACTCAGAGTTATTTTCAAGTATCAAAATTGACCGC
8288 ACATTGGTCCTTTTTCATCAT
65 ACATTGGTCCTTTTTCATCAT
* *
8309 CAATCAAGAAGTTTTCTGTTACAACATCAGATTCAGAGTTATTTT
1 CAATCAAGAAGTTTT-AGTTACAACATCAGACTCAGAGTTATTTT
8354 TCAAAGGTAT
Statistics
Matches: 346, Mismatches: 20, Indels: 43
0.85 0.05 0.11
Matches are distributed among these distances:
79 69 0.20
80 43 0.12
81 32 0.09
82 3 0.01
83 1 0.00
85 1 0.00
86 1 0.00
87 83 0.24
88 17 0.05
89 20 0.06
90 3 0.01
92 73 0.21
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (85 bp):
CAATCAAGAAGTTTTAGTTACAACATCAGACTCAGAGTTATTTTCAAGTATCAAAATTGACCGCA
CATTGGTCCTTTTTCATCAT
Found at i:8191 original size:12 final size:12
Alignment explanation
Indices: 8174--8199 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8164 TCAGACTTAG
8174 AGTTATTTTTCA
1 AGTTATTTTTCA
8186 AGTTATTTTTCA
1 AGTTATTTTTCA
8198 AG
1 AG
8200 ATTGACCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (12 bp):
AGTTATTTTTCA
Found at i:8251 original size:92 final size:92
Alignment explanation
Indices: 8094--8281 Score: 358
Period size: 92 Copynumber: 2.0 Consensus size: 92
8084 TCAGACTCAG
8094 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTCCAGTTA
1 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTCCAGTTA
*
8159 CAACATCAGACTTAGAGTTATTTTTCA
66 CAACATCAGACTCAGAGTTATTTTTCA
*
8186 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTA
1 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTCCAGTTA
8251 CAACATCAGACTCAGAGTTATTTTTCA
66 CAACATCAGACTCAGAGTTATTTTTCA
8278 AGTT
1 AGTT
8282 GACCGCACAT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (92 bp):
AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTCCAGTTA
CAACATCAGACTCAGAGTTATTTTTCA
Found at i:8318 original size:79 final size:80
Alignment explanation
Indices: 8186--8357 Score: 319
Period size: 79 Copynumber: 2.2 Consensus size: 80
8176 TTATTTTTCA
8186 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTA
1 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTA
8251 CAACATCAGACTCAG
66 CAACATCAGACTCAG
*
8266 AGTTATTTTTCAAG-TTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCTGTTA
1 AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTA
*
8330 CAACATCAGATTCAG
66 CAACATCAGACTCAG
8345 AGTTATTTTTCAA
1 AGTTATTTTTCAA
8358 AGGTATTTTC
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
79 76 0.84
80 14 0.16
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (80 bp):
AGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTA
CAACATCAGACTCAG
Found at i:8332 original size:171 final size:173
Alignment explanation
Indices: 7940--8366 Score: 654
Period size: 171 Copynumber: 2.5 Consensus size: 173
7930 AGGCAACAAA
* * * * *
7940 ATTGACCGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTT-AATCATAACATCAGACTCA
1 ATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTTA
* * *
8004 GAGCTATTCTTCAAGTCA----TCAAAATTGACCGCAAATTGGTCCTTTTTCATCATTCAATCAA
66 GAGTTATTTTTCAAGTTATTTTTCAAAATTGACCGCAAATTGGTCCTTTTTCATCATTCAATCAA
*
8065 GAAGTTTTCAGTTACAGCATCAGACTCAGAGTTATTTTTCAAG
131 GAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAG
*
8108 ATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTCCAGTTACAACATCAGACTTA
1 ATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTTA
* *
8173 GAGTTATTTTTCAAGTTATTTTTCAAGATTGACCGCACATTGGTCCTTTTTCATCA-TCAATCAA
66 GAGTTATTTTTCAAGTTATTTTTCAAAATTGACCGCAAATTGGTCCTTTTTCATCATTCAATCAA
8237 GAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAG
131 GAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAG
*
8280 -TTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCTGTTACAACATCAGA-TTC
1 ATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTT-
*
8343 AGAGTTATTTTTCAAAGGTATTTT
65 AGAGTTATTTTTC-AAGTTATTTT
8367 CTTCCAAAAT
Statistics
Matches: 237, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
168 43 0.18
169 30 0.13
170 2 0.01
171 71 0.30
172 59 0.25
173 32 0.14
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (173 bp):
ATTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTTA
GAGTTATTTTTCAAGTTATTTTTCAAAATTGACCGCAAATTGGTCCTTTTTCATCATTCAATCAA
GAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAG
Found at i:8688 original size:50 final size:50
Alignment explanation
Indices: 8608--8801 Score: 309
Period size: 50 Copynumber: 3.9 Consensus size: 50
8598 TCCAAGCCAG
* *
8608 ATAGACTTTTCCACAAGCCAAGCTCGTTTCCACACGAGTCAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAAC
* *
8658 ATAGGCTTTTCCACAAGCCAAGCTCGTTTCCACACGAGTCAGTTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAAC
* * *
8708 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCCAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAAC
8758 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACAC-ATGTCAATT
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGA-GTCAATT
8802 TAAGCCTTGG
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 1 0.01
50 135 0.99
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.27
Consensus pattern (50 bp):
ATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATTATCAAC
Found at i:8833 original size:69 final size:69
Alignment explanation
Indices: 8754--9099 Score: 487
Period size: 69 Copynumber: 5.0 Consensus size: 69
8744 AGTCAGTTAT
* * *
8754 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACAC-ATGTCAATTTAAGCCTTGGTTCCAT
1 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGA-GTCAGTTCAAGCCTTGGTTCCAT
8818 CCAAG
65 CCAAG
8823 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
1 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
8888 CAAG
66 CAAG
* *
8892 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTAAGTTCAAGCCTTGGTTCCATC
1 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
8957 CAAG
66 CAAG
* * *
8961 CCATATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTTCA
1 CC--ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
*
9026 TCTAAG
64 TCCAAG
* * * ** * * * *
9032 CCATATAGACTTTCCCATGAGTCGAAACTCGTTTCCATACGAGTCAGTTTAAACATTGGTTCCAT
1 CCACATAGGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCAT
9097 CCA
65 CCA
9100 TACAGTAGTG
Statistics
Matches: 251, Mismatches: 22, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
69 148 0.59
70 40 0.16
71 63 0.25
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28
Consensus pattern (69 bp):
CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
CAAG
Found at i:8963 original size:138 final size:139
Alignment explanation
Indices: 8754--9099 Score: 500
Period size: 140 Copynumber: 2.5 Consensus size: 139
8744 AGTCAGTTAT
8754 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACAC-ATGTCAA-TTTAAGCCTTGGTTCCA
1 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGA-GT-AAGTTTAAGCCTTGGTTCCA
8817 TCCAAGCC-ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGG
64 TCCAAGCCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGG
8881 TTCCATCCAAG
129 TTCCATCCAAG
*
8892 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTAAGTTCAAGCCTTGGTTCCATC
1 CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTAAGTTTAAGCCTTGGTTCCATC
* *
8957 CAAGCCATATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGT
66 CAAGCCA-ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGT
* *
9022 TTCATCTAAG
130 TCCATCCAAG
* * * ** * * * * *
9032 CCATATAGACTTTCCCATGAGTCGAAACTCGTTTCCATACGAGTCAGTTTAAACATTGGTTCCAT
1 CCACATAGGCTTTTCCACAAG-CCAAACTCGTTTCCACACGAGTAAGTTTAAGCCTTGGTTCCAT
9097 CCA
65 CCA
9100 TACAGTAGTG
Statistics
Matches: 187, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
137 2 0.01
138 65 0.35
139 1 0.01
140 79 0.42
141 40 0.21
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28
Consensus pattern (139 bp):
CCACATAGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTAAGTTTAAGCCTTGGTTCCATC
CAAGCCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTT
CCATCCAAG
Found at i:9609 original size:29 final size:29
Alignment explanation
Indices: 9577--9735 Score: 133
Period size: 29 Copynumber: 5.5 Consensus size: 29
9567 AGGATCGCCT
***
9577 AGGGGCATTTTGGTCATTTTCAAAAATCC
1 AGGGGCATTTTGGTCATTTTTGCAAATCC
* * *
9606 AGGGGCATTTTGTTCATTTTT-CACATTC
1 AGGGGCATTTTGGTCATTTTTGCAAATCC
* * *
9634 AGTGGCATTATGGTCATTTTTGCACA-CTC
1 AGGGGCATTTTGGTCATTTTTGCAAATC-C
* *
9663 AGGGGGCATTTTGGTCATTTCTGCATATCC
1 A-GGGGCATTTTGGTCATTTTTGCAAATCC
** * * *
9693 AGGGGCATTTTGGTTGTTTGTGTACATCC
1 AGGGGCATTTTGGTCATTTTTGCAAATCC
*
9722 GGGGGCATTTTGGT
1 AGGGGCATTTTGGT
9736 TTTTTTTTTT
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
28 22 0.21
29 61 0.57
30 23 0.21
31 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCAAATCC
Found at i:15739 original size:27 final size:27
Alignment explanation
Indices: 15709--15798 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
15699 TACCTGAAGC
15709 GACCAAAATGCCCCTGGACGTGCAAAT
1 GACCAAAATGCCCCTGGACGTGCAAAT
* *
15736 GACCAAAATGCCCTTGGATGTGCAAAT
1 GACCAAAATGCCCCTGGACGTGCAAAT
* *
15763 GACCAAAATGCCCCTGGACATGTAAAT
1 GACCAAAATGCCCCTGGACGTGCAAAT
15790 GACCAAAAT
1 GACCAAAAT
15799 AAGAAGTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.18
Consensus pattern (27 bp):
GACCAAAATGCCCCTGGACGTGCAAAT
Found at i:19904 original size:14 final size:14
Alignment explanation
Indices: 19885--19912 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19875 AATTATAACC
19885 AAACTTATCTATGT
1 AAACTTATCTATGT
19899 AAACTTATCTATGT
1 AAACTTATCTATGT
19913 CTATCTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AAACTTATCTATGT
Found at i:27112 original size:22 final size:22
Alignment explanation
Indices: 27087--27156 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
27077 CAGGCCGCGC
27087 GGGCCTGCGCAGCAGGCCACTT
1 GGGCCTGCGCAGCAGGCCACTT
* * * *
27109 GGGCCAGCG-TGCGGGCCA-TGC
1 GGGCCTGCGCAGCAGGCCACT-T
27130 GTGGCCTG-GCAGCAGGCCACTT
1 G-GGCCTGCGCAGCAGGCCACTT
27152 GGGCC
1 GGGCC
27157 AGCGTGCGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
20 1 0.03
21 13 0.36
22 21 0.58
23 1 0.03
ACGTcount: A:0.11, C:0.34, G:0.41, T:0.13
Consensus pattern (22 bp):
GGGCCTGCGCAGCAGGCCACTT
Found at i:27126 original size:21 final size:21
Alignment explanation
Indices: 27101--27169 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
27091 CTGCGCAGCA
27101 GGCCACTTGGGCCAGCGTGCG
1 GGCCACTTGGGCCAGCGTGCG
* * * *
27122 GGCCA-TGCGTGGCCTG-GCAGCA
1 GGCCACT-TG-GGCCAGCG-TGCG
27144 GGCCACTTGGGCCAGCGTGCG
1 GGCCACTTGGGCCAGCGTGCG
27165 GGCCA
1 GGCCA
27170 TGCGTGGCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 19 0.54
22 14 0.40
23 1 0.03
ACGTcount: A:0.12, C:0.33, G:0.42, T:0.13
Consensus pattern (21 bp):
GGCCACTTGGGCCAGCGTGCG
Found at i:27143 original size:43 final size:43
Alignment explanation
Indices: 27088--27187 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
27078 AGGCCGCGCG
27088 GGCCTGCGCAGCAGGCCACTTGGGCCAGCGTGCGGGCCATGCGT
1 GGCCTG-GCAGCAGGCCACTTGGGCCAGCGTGCGGGCCATGCGT
27132 GGCCTGGCAGCAGGCCACTTGGGCCAGCGTGCGGGCCATGCGT
1 GGCCTGGCAGCAGGCCACTTGGGCCAGCGTGCGGGCCATGCGT
27175 GGCCTGGCAGCAG
1 GGCCTGGCAGCAG
27188 TTGGGGCCCC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 50 0.89
44 6 0.11
ACGTcount: A:0.12, C:0.33, G:0.42, T:0.13
Consensus pattern (43 bp):
GGCCTGGCAGCAGGCCACTTGGGCCAGCGTGCGGGCCATGCGT
Found at i:27262 original size:11 final size:11
Alignment explanation
Indices: 27242--27287 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
27232 AGCCCAAAAG
27242 AAAG-AAAGAA
1 AAAGAAAAGAA
27252 AAAGAAAAGAA
1 AAAGAAAAGAA
*
27263 AAAGAGAAAAAA
1 AAAGA-AAAGAA
27275 AAAGAAAAGAA
1 AAAGAAAAGAA
27286 AA
1 AA
27288 GGGAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 4 0.12
11 18 0.56
12 10 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:27270 original size:23 final size:23
Alignment explanation
Indices: 27244--27287 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27234 CCCAAAAGAA
*
27244 AGAAAGAAAAAGAAAAGAAAAAG
1 AGAAAAAAAAAGAAAAGAAAAAG
27267 AGAAAAAAAAAGAAAAGAAAA
1 AGAAAAAAAAAGAAAAGAAAA
27288 GGGAAAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAAGAAAAGAAAAAG
Found at i:27300 original size:23 final size:24
Alignment explanation
Indices: 27237--27300 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
27227 ATCCAAGCCC
*
27237 AAAAGAAAGAAAGAAAAAGAAAAGA
1 AAAAGAGA-AAAGAAAAAGAAAAGA
27262 AAAAGAGAAAA-AAAAAGAAAAG-
1 AAAAGAGAAAAGAAAAAGAAAAGA
* *
27284 AAAAGGGAAAAGGAAAA
1 AAAAGAGAAAAGAAAAA
27301 TAAGAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.29
23 15 0.43
24 3 0.09
25 7 0.20
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAAGAGAAAAGAAAAAGAAAAGA
Found at i:28108 original size:28 final size:27
Alignment explanation
Indices: 28068--28141 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
28058 TAAGATGTCA
*
28068 AAATTACTGTTTTGCCCTTGGTCAG-CT
1 AAATTACAGTTTTGCCCTTGGT-AGACT
* * *
28095 AAAATTAACA-TTTTACCCCTGGTTGACT
1 -AAATT-ACAGTTTTGCCCTTGGTAGACT
28123 AAATTACAGTTTTGCCCTT
1 AAATTACAGTTTTGCCCTT
28142 AAATGCCGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
26 3 0.08
27 14 0.38
28 18 0.49
29 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (27 bp):
AAATTACAGTTTTGCCCTTGGTAGACT
Found at i:34678 original size:15 final size:15
Alignment explanation
Indices: 34658--34686 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34648 TTTTTTAGGT
34658 TATATTTGAATCTAC
1 TATATTTGAATCTAC
34673 TATATTTGAATCTA
1 TATATTTGAATCTA
34687 TTATTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (15 bp):
TATATTTGAATCTAC
Found at i:43565 original size:32 final size:33
Alignment explanation
Indices: 43529--43591 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
43519 GATTTAGGAA
**
43529 TAGTGGCATTTCAGTATTA-AAACGCCGCTATT
1 TAGTGGCATTTCAGTACAACAAACGCCGCTATT
* *
43561 TAGTGGCGTTTCCGTACAACAAACGCCGCTA
1 TAGTGGCATTTCAGTACAACAAACGCCGCTA
43592 AATAGCGGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (33 bp):
TAGTGGCATTTCAGTACAACAAACGCCGCTATT
Found at i:54877 original size:14 final size:15
Alignment explanation
Indices: 54858--54886 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54848 TTATTTTGAA
54858 ATATAAATT-AAAAT
1 ATATAAATTCAAAAT
54872 ATATAAATTCAAAAT
1 ATATAAATTCAAAAT
54887 TATCTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAAATTCAAAAT
Found at i:56811 original size:2 final size:2
Alignment explanation
Indices: 56806--56837 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56796 TTTTGGTTGA
56806 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
56838 GCACTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74685 original size:42 final size:42
Alignment explanation
Indices: 74630--74713 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
74620 AGATTGATCC
74630 TTCGTATCAGTCTTGATCCTTCCTAATACTAAAACCATTTGA
1 TTCGTATCAGTCTTGATCCTTCCTAATACTAAAACCATTTGA
74672 TTCGTATCAGTCTTGATCCTTCCTAATACTAAAACCATTTGA
1 TTCGTATCAGTCTTGATCCTTCCTAATACTAAAACCATTTGA
74714 GAAGTGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (42 bp):
TTCGTATCAGTCTTGATCCTTCCTAATACTAAAACCATTTGA
Found at i:76744 original size:28 final size:28
Alignment explanation
Indices: 76713--76770 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
76703 TGGGAATTTG
* *
76713 AAATTACCGT-TTTACCCTTGTAACGGGT
1 AAATTACCATATTTACCCTCGTAA-GGGT
*
76741 AAATTACCATATTTATCCTCGTAAGGGT
1 AAATTACCATATTTACCCTCGTAAGGGT
76769 AA
1 AA
76771 GTTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (28 bp):
AAATTACCATATTTACCCTCGTAAGGGT
Found at i:79260 original size:8 final size:9
Alignment explanation
Indices: 79247--79271 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
79237 CCATTTTAAA
79247 ATTTTTGTT
1 ATTTTTGTT
79256 ATTTTTGTT
1 ATTTTTGTT
79265 ATTTTTG
1 ATTTTTG
79272 CAGTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (9 bp):
ATTTTTGTT
Found at i:81159 original size:22 final size:21
Alignment explanation
Indices: 81108--81184 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 21
81098 CTTATGAAGT
* *
81108 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAG
* *
81129 TTATAAAAATTTTATATGGTGG
1 TTATCAAAATTTTATA-GGTAG
*
81151 TTATCAAAATTTGATAGGATAG
1 TTATCAAAATTTTATAGG-TAG
*
81173 TTACCAAAATTT
1 TTATCAAAATTT
81185 CATAAAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.35
22 30 0.65
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAG
Found at i:89556 original size:19 final size:21
Alignment explanation
Indices: 89532--89572 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
89522 CAACAGTAAC
89532 CAACAA-TT-CAGTCAATTGA
1 CAACAATTTACAGTCAATTGA
*
89551 CAACAATTTACTGTCAATTGA
1 CAACAATTTACAGTCAATTGA
89572 C
1 C
89573 TCACAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
CAACAATTTACAGTCAATTGA
Found at i:92866 original size:13 final size:13
Alignment explanation
Indices: 92848--92874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
92838 GCCAAATACT
92848 AAAGACCAGGTGA
1 AAAGACCAGGTGA
92861 AAAGACCAGGTGA
1 AAAGACCAGGTGA
92874 A
1 A
92875 CTACATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.30, T:0.07
Consensus pattern (13 bp):
AAAGACCAGGTGA
Found at i:96434 original size:13 final size:13
Alignment explanation
Indices: 96416--96440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96406 AGAAGAAGAG
96416 AATATTCATATTA
1 AATATTCATATTA
96429 AATATTCATATT
1 AATATTCATATT
96441 GAGCAAGTAT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATTCATATTA
Done.