Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016345.1 Corchorus olitorius cultivar O-4 contig16378, 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: 62930
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:876 original size:324 final size:321
Alignment explanation
Indices: 4--1031 Score: 1282
Period size: 312 Copynumber: 3.2 Consensus size: 321
1 CGT
* * * * *
4 GTTTTTAGCCCAAAAATTGTGATGAAATGTACACGATTTCGGCTAAAAACTGACCCCGAAAGTTT
1 GTTTTTAGCCCAAAAACTGTGATGATA-GTACACGATTTCGGCTAAAAATTGA-CTCGAAAATTT
* * *
69 TGTTCTGAAA-TTT-TTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA
64 TTTTCT-AAATTTTCTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAA
* ** *
132 GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTGAATTTAATTCTAATTAAATCGAAA
128 GGGTTTTTCACGCTTCTAATATCGTTTTTTCA-TTTTCCTGAATTTATTTCTAATTAAATCGAAA
* *
197 CAAGATTCAGATGCGCTTAAAAATAAATCCTTATATCCAATATGCCTGAGATTTGGTTAGATGAA
192 CAAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATATGCCTGAGATTTGGTTAGATGAA
* * * * * * * **
262 TATAAGATATTTCAAGGAGTCTTTCTGCTAAAAATCATGTAAAACTGAATCGGGGTCCCCACATG
257 TATAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG-AGCAGGATCCCAAAACA
327 C
321 C
* *
328 GTTTTAAGCCCAAAAAC-----TG-T-G---ACGTTTTCGGCTAAAAACTT-ACTCGAAAATTTT
1 GTTTTTAGCCCAAAAACTGTGATGATAGTACACGATTTCGGCTAAAAA-TTGACTCGAAAATTTT
* * * *
382 TTTCTTAATTTTC-TGCTAAAATACTCAGAAAAAATATATAATTCAACACCACGAATATTGAAGG
65 TTTCTAAATTTTCTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGG
* * *
446 GTTTTTACACGCTTCTAATATC-ATTTTTCGATTTTCCTGAATTTATCTCCAATTAAATCGAAAC
130 GTTTTT-CACGCTTCTAATATCGTTTTTTC-ATTTTCCTGAATTTATTTCTAATTAAATCGAAAC
*
510 AAGATTCAGATGCTCGTAAAAATAAATCCTTATATTCAATATGCCTGAGATTTGGTTAGATGAAT
193 AAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATATGCCTGAGATTTGGTTAGATGAAT
575 ATAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGATCCCAAAACAC
258 ATAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAG-CAGGATCCCAAAACAC
* * *
640 GTTTTTAGCCCAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTGTCTCAAAAATTTT
1 GTTTTTAGCCCAAAAACTGTGATGA-TAGTACACGATTTCGGCTAAAAATTGACTCGAAAATTTT
* * * * * *
705 TTTCTAAATTTTCTTGCCGAAATACTTAGACAAAAATATATAGTTCAACGCGAAGAATATTAAAA
65 TTTCTAAATTTTCTTGCCAAAATACTCAGA-AAAAATATATAATTCAACGCCAAGAATATTGAAG
*
770 GGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTCCCGAATTTATTTCTAATTAAATCGAAACA
129 GGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTCCTGAATTTATTTCTAATTAAATCGAAACA
* *
835 AGATTTAGATGCTCGTAAAAATAAATCCTTATATCCAATATGCCCGAGATTTGGTTAGATGAATA
194 AGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATATGCCTGAGATTTGGTTAGATGAATA
* * * * * * *
900 TAAAATATTTGATGGAGTCTTTTTGCCAAAAATCATGCAAAACTGAGCTGGTATCCCGAATCAC
259 TAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCAGG-ATCCCAAAACAC
* * * *
964 ATTTTTTA-CCCAAAAACTGTGATGGTTAGTACACGATTTCTCAGCTAAAAACTGAC-C-AAAAT
1 -GTTTTTAGCCCAAAAACTGTGAT-GATAGTACACGA-TT-TCGGCTAAAAATTGACTCGAAAAT
1026 TTTTTT
62 TTTTTT
1032 GCTTTTTAAC
Statistics
Matches: 610, Mismatches: 68, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
311 3 0.00
312 234 0.38
313 33 0.05
314 1 0.00
316 1 0.00
317 2 0.00
319 3 0.00
320 1 0.00
322 2 0.00
323 41 0.07
324 226 0.37
325 51 0.08
326 12 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (321 bp):
GTTTTTAGCCCAAAAACTGTGATGATAGTACACGATTTCGGCTAAAAATTGACTCGAAAATTTTT
TTCTAAATTTTCTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGG
TTTTTCACGCTTCTAATATCGTTTTTTCATTTTCCTGAATTTATTTCTAATTAAATCGAAACAAG
ATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATATGCCTGAGATTTGGTTAGATGAATATA
AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCAGGATCCCAAAACAC
Found at i:1947 original size:15 final size:15
Alignment explanation
Indices: 1927--1978 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1917 TATGCTACTG
1927 AATATGCAACTATAT
1 AATATGCAACTATAT
** ***
1942 AATATGACCCCTACCG
1 AATATG-CAACTATAT
1958 AATATGCAACTATAT
1 AATATGCAACTATAT
1973 AATATG
1 AATATG
1979 ACCCCTACCG
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (15 bp):
AATATGCAACTATAT
Found at i:1962 original size:31 final size:31
Alignment explanation
Indices: 1921--2000 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
1911 ACTGAATATG
*
1921 CTACTGAATATGCAACTATATAATATGACCC
1 CTACCGAATATGCAACTATATAATATGACCC
1952 CTACCGAATATGCAACTATATAATATGACCC
1 CTACCGAATATGCAACTATATAATATGACCC
*
1983 CTACCGAATATTCAACTA
1 CTACCGAATATGCAACTA
2001 CATGACCCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (31 bp):
CTACCGAATATGCAACTATATAATATGACCC
Found at i:1963 original size:16 final size:16
Alignment explanation
Indices: 1942--1993 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1932 GCAACTATAT
1942 AATATGACCCCTACCG
1 AATATGACCCCTACCG
** ***
1958 AATATG-CAACTATAT
1 AATATGACCCCTACCG
1973 AATATGACCCCTACCG
1 AATATGACCCCTACCG
1989 AATAT
1 AATAT
1994 TCAACTACAT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (16 bp):
AATATGACCCCTACCG
Found at i:2012 original size:26 final size:26
Alignment explanation
Indices: 1945--2039 Score: 118
Period size: 26 Copynumber: 3.5 Consensus size: 26
1935 ACTATATAAT
*
1945 ATGACCCCTACCGAATATGCAACTATATAAT
1 ATGACCCCTACCGAATATGCAAC----T-AC
*
1976 ATGACCCCTACCGAATATTCAACTAC
1 ATGACCCCTACCGAATATGCAACTAC
*
2002 ATGACCCCTACTGAATATGCAACTAC
1 ATGACCCCTACCGAATATGCAACTAC
2028 ATGACCCCTACC
1 ATGACCCCTACC
2040 CTACTAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 36 0.61
27 1 0.02
31 22 0.37
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.23
Consensus pattern (26 bp):
ATGACCCCTACCGAATATGCAACTAC
Found at i:2050 original size:31 final size:31
Alignment explanation
Indices: 2007--2069 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1997 ACTACATGAC
* *
2007 CCCTACTGAATATGCAACTACATGACCCCTA
1 CCCTACTAAATATACAACTACATGACCCCTA
*
2038 CCCTACTAAATATACAACTACATGATCCCTA
1 CCCTACTAAATATACAACTACATGACCCCTA
2069 C
1 C
2070 TGAATATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.24
Consensus pattern (31 bp):
CCCTACTAAATATACAACTACATGACCCCTA
Found at i:2067 original size:26 final size:26
Alignment explanation
Indices: 1976--2076 Score: 103
Period size: 26 Copynumber: 3.7 Consensus size: 26
1966 ACTATATAAT
* * *
1976 ATGACCCCTACCGAATATTCAACTAC
1 ATGATCCCTACTGAATATACAACTAC
* *
2002 ATGACCCCTACTGAATATGCAACTAC
1 ATGATCCCTACTGAATATACAACTAC
*
2028 ATGACCCCTACCCTACTAAATATACAACTAC
1 ATGA----T-CCCTACTGAATATACAACTAC
2059 ATGATCCCTACTGAATAT
1 ATGATCCCTACTGAATAT
2077 GTATGTACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
26 40 0.62
27 1 0.02
31 23 0.36
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.25
Consensus pattern (26 bp):
ATGATCCCTACTGAATATACAACTAC
Found at i:2125 original size:34 final size:34
Alignment explanation
Indices: 2082--2163 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
2072 AATATGTATG
*
2082 TACATGATGCAAATGACTCAACTAAATATGCAAC
1 TACATGATGCAAATGACCCAACTAAATATGCAAC
* * **
2116 TACACGATGCATATGACCCTGCTAAATATGCAAC
1 TACATGATGCAAATGACCCAACTAAATATGCAAC
2150 TACATGATGCAAAT
1 TACATGATGCAAAT
2164 CATACTGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (34 bp):
TACATGATGCAAATGACCCAACTAAATATGCAAC
Found at i:2202 original size:26 final size:26
Alignment explanation
Indices: 2166--2368 Score: 282
Period size: 26 Copynumber: 7.7 Consensus size: 26
2156 ATGCAAATCA
*
2166 TACTGAATATGTAACTACATGACCCC
1 TACTGAATATGCAACTACATGACCCC
** * * *
2192 TACTGTTTATGCAAATAAATGAACCC
1 TACTGAATATGCAACTACATGACCCC
2218 TACTGAATATGCAACTACATGACCCCACC
1 TACTGAATATGCAACTACATGA--CC-CC
*
2247 TACTGGATATGCAACTACATGACCCC
1 TACTGAATATGCAACTACATGACCCC
* *
2273 TACTGGATATGCAACTACATGACCGC
1 TACTGAATATGCAACTACATGACCCC
*
2299 TACTGGATATGCAACTACATGA-CCC
1 TACTGAATATGCAACTACATGACCCC
2324 TACTGAATATGCAACTACATGACCCC
1 TACTGAATATGCAACTACATGACCCC
2350 TACTGAATATGCAACTACA
1 TACTGAATATGCAACTACA
2369 CATGAATATA
Statistics
Matches: 158, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
25 23 0.15
26 109 0.69
27 2 0.01
28 1 0.01
29 23 0.15
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (26 bp):
TACTGAATATGCAACTACATGACCCC
Found at i:2226 original size:52 final size:52
Alignment explanation
Indices: 2166--2368 Score: 291
Period size: 51 Copynumber: 3.9 Consensus size: 52
2156 ATGCAAATCA
* ** * *
2166 TACTGAATATGTAACTACATGACCCCTACTGTTTATGCAAATAAATGAACCC
1 TACTGAATATGCAACTACATGACCCCTACTGGATATGCAACTACATGAACCC
*
2218 TACTGAATATGCAACTACATGACCCCACCTACTGGATATGCAACTACATGACCCC
1 TACTGAATATGCAACTACATGA--CC-CCTACTGGATATGCAACTACATGAACCC
* *
2273 TACTGGATATGCAACTACATGACCGCTACTGGATATGCAACTACATG-ACCC
1 TACTGAATATGCAACTACATGACCCCTACTGGATATGCAACTACATGAACCC
*
2324 TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACA
1 TACTGAATATGCAACTACATGACCCCTACTGGATATGCAACTACA
2369 CATGAATATA
Statistics
Matches: 136, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
51 45 0.33
52 43 0.32
53 2 0.01
54 2 0.01
55 44 0.32
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (52 bp):
TACTGAATATGCAACTACATGACCCCTACTGGATATGCAACTACATGAACCC
Found at i:2302 original size:81 final size:77
Alignment explanation
Indices: 2166--2368 Score: 282
Period size: 81 Copynumber: 2.6 Consensus size: 77
2156 ATGCAAATCA
* ** * *
2166 TACTGAATATGTAACTACATGACCCCTACTGTTTATGCAAATAAATGAACCCTACTGAATATGCA
1 TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACATGAACCCTACTGAATATGCA
2231 ACTACATGACCCCACC
66 ACTACATGA---C-CC
* * *
2247 TACTGGATATGCAACTACATGACCCCTACTGGATATGCAACTACATG-ACCGCTACTGGATATGC
1 TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACATGAACC-CTACTGAATATGC
2311 AACTACATGACCC
65 AACTACATGACCC
2324 TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACA
1 TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACA
2369 CATGAATATA
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
77 45 0.40
78 1 0.01
80 3 0.03
81 63 0.56
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (77 bp):
TACTGAATATGCAACTACATGACCCCTACTGAATATGCAACTACATGAACCCTACTGAATATGCA
ACTACATGACCC
Found at i:2436 original size:31 final size:31
Alignment explanation
Indices: 2386--2449 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
2376 ATACAACTAT
* *
2386 ATGAATATGATACAAATGACCCTACTGTAAA
1 ATGAATATGATACAAATGACCCTAATGAAAA
** *
2417 ATGAATATGATGGAGATGACCCTAATGAAAA
1 ATGAATATGATACAAATGACCCTAATGAAAA
2448 AT
1 AT
2450 AAACTATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (31 bp):
ATGAATATGATACAAATGACCCTAATGAAAA
Found at i:6682 original size:2 final size:2
Alignment explanation
Indices: 6675--6706 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6665 ATTTTTGAAT
6675 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6707 ATTTATCATG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6904 original size:1 final size:1
Alignment explanation
Indices: 6898--6928 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
6888 CACATATAAC
6898 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6929 CCCTAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11176 original size:25 final size:25
Alignment explanation
Indices: 11045--11169 Score: 196
Period size: 25 Copynumber: 5.0 Consensus size: 25
11035 TGTGTTTTCC
11045 AAACGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
* *
11070 AAACACAAGCACAGGCTCGTTTACT
1 AAACGCAAGCACAGGCTCGTTTGCT
* * *
11095 AAATGCAAACACAGGTTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
*
11120 AAACGCAAACACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
11145 AAACGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
11170 CAGCGCACAC
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 90 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (25 bp):
AAACGCAAGCACAGGCTCGTTTGCT
Found at i:16072 original size:22 final size:21
Alignment explanation
Indices: 16044--16095 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
16034 AATTTATTCC
*
16044 TTTTTTTTTAGGTATTACTGAA
1 TTTTTTTTTAAGTA-TACTGAA
*
16066 TTTTTTTTGAAGTATACTGAA
1 TTTTTTTTTAAGTATACTGAA
16087 TTTTTTTTT
1 TTTTTTTTT
16096 TTGAAGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.63
Consensus pattern (21 bp):
TTTTTTTTTAAGTATACTGAA
Found at i:18128 original size:82 final size:83
Alignment explanation
Indices: 17991--18152 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 83
17981 ATTAATAATT
* *
17991 AGGGTAATTATTTGATACACCGGTGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAATTGAC
1 AGGGTAATTATTTGATACACCGGCGGTGTAAACTTTGGACTCCACAAGCGGGTTGTGGAATTGAC
18056 ACATGT-CATTTTTTTTA
66 ACATGTCCATTTTTTTTA
*
18073 AGGGTAATTATTTGATACACCGGCGGTGTAAACTTTGGACTCCACAAGCGGGTTGTGGAGTTGAC
1 AGGGTAATTATTTGATACACCGGCGGTGTAAACTTTGGACTCCACAAGCGGGTTGTGGAATTGAC
18138 ACATGTCCATTTTTT
66 ACATGTCCATTTTTT
18153 GAATTAGTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 68 0.89
83 8 0.11
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (83 bp):
AGGGTAATTATTTGATACACCGGCGGTGTAAACTTTGGACTCCACAAGCGGGTTGTGGAATTGAC
ACATGTCCATTTTTTTTA
Found at i:40802 original size:25 final size:25
Alignment explanation
Indices: 40774--40825 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40764 ATCCGTACTG
40774 GTCCATTAAACAGCCTCAACAATCT
1 GTCCATTAAACAGCCTCAACAATCT
40799 GTCCATTAAACAGCCTCAACAATCT
1 GTCCATTAAACAGCCTCAACAATCT
40824 GT
1 GT
40826 TCTATAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.25
Consensus pattern (25 bp):
GTCCATTAAACAGCCTCAACAATCT
Found at i:41799 original size:38 final size:35
Alignment explanation
Indices: 41728--41799 Score: 90
Period size: 38 Copynumber: 2.0 Consensus size: 35
41718 AATGAGTGAA
*
41728 AAATGAAAAAAACAGAGAGGATTTATCGGAGAGAG
1 AAATGAAAAAAACAGAGAGGATTTATAGGAGAGAG
* *
41763 AAATGAAAAGAGAAGAGAGGGGTATTTATAGGAGAGA
1 AAATGAAAA-A-AACAGAGAGG-ATTTATAGGAGAGA
41800 ATCAGAGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.29
36 1 0.03
37 8 0.26
38 13 0.42
ACGTcount: A:0.50, C:0.03, G:0.32, T:0.15
Consensus pattern (35 bp):
AAATGAAAAAAACAGAGAGGATTTATAGGAGAGAG
Found at i:42549 original size:30 final size:30
Alignment explanation
Indices: 42513--42576 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
42503 TTTTTCCAAT
42513 ATATTCTCCAAATAAGTAAGTATAATTAAC
1 ATATTCTCCAAATAAGTAAGTATAATTAAC
42543 ATATTCTCCAAATAAGTAAGTATAATTAAC
1 ATATTCTCCAAATAAGTAAGTATAATTAAC
42573 ATAT
1 ATAT
42577 ACCAAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (30 bp):
ATATTCTCCAAATAAGTAAGTATAATTAAC
Found at i:42750 original size:21 final size:22
Alignment explanation
Indices: 42720--42760 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
42710 ATTCTTTTTT
* *
42720 ATTAAGTTTAG-CCCTAATTTC
1 ATTAAATTTAGTCCCAAATTTC
42741 ATTAAATTTAGTCCCAAATT
1 ATTAAATTTAGTCCCAAATT
42761 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (22 bp):
ATTAAATTTAGTCCCAAATTTC
Found at i:49445 original size:2 final size:2
Alignment explanation
Indices: 49438--49467 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49428 TCTGCAATCG
49438 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
49468 TAGATTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50024 original size:59 final size:59
Alignment explanation
Indices: 49940--50055 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
49930 AGCAACTCAA
* * *
49940 TTCGTTTCCATAAAAAGTCTATCATTACTCATTAGTGATCTGCAATCAGCAATGATAAT
1 TTCGCTTCAATAAAAAGTCTATCATTACTCATTAGTGACCTGCAATCAGCAATGATAAT
*
49999 TTCGCTTCAATAAGAAGTCTATCATTACTCATTAGTGACCTGCAATCAGCAATGATA
1 TTCGCTTCAATAAAAAGTCTATCATTACTCATTAGTGACCTGCAATCAGCAATGATA
50056 GTTCCCAAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (59 bp):
TTCGCTTCAATAAAAAGTCTATCATTACTCATTAGTGACCTGCAATCAGCAATGATAAT
Found at i:51198 original size:19 final size:19
Alignment explanation
Indices: 51158--51194 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
51148 AATTTTTAAG
51158 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
51177 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
51195 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:60525 original size:30 final size:28
Alignment explanation
Indices: 60468--60525 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
60458 TAAATTTGTA
* * *
60468 TAATTTTGACGTTTTGCCTCCTAAACTT
1 TAATTTTGACATTTTACCCCCTAAACTT
60496 TAATTTTGGACATTTTACCCCCATAAACTT
1 TAATTTT-GACATTTTACCCCC-TAAACTT
60526 GCAATTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 11 0.44
30 7 0.28
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (28 bp):
TAATTTTGACATTTTACCCCCTAAACTT
Found at i:61876 original size:99 final size:103
Alignment explanation
Indices: 61705--61905 Score: 329
Period size: 99 Copynumber: 2.0 Consensus size: 103
61695 GGTTTTAGGA
61705 TCAAATCCTGAGTCTGGATGGGTTTAGGGATGGGAGAAGGCTACTTCCCTTTGTGTAGCCCTATC
1 TCAAATCCTGAGTCTGGATGGGTTTAGGGATGGGAGAAGGCTACTTCCCTTTGTGTAGCCCTATC
61770 AT-CA-C-A-TTCATGTTCACATGTAACATAGAGCGGG
66 ATACATCAATTTCATGTTCACATGTAACATAGAGCGGG
* * *
61804 TCAAATCTTGAGTTTGGATGGGTTTAGGGATGGGAGAAGGCTATTTCCCTTTGTGTAGCCCTATC
1 TCAAATCCTGAGTCTGGATGGGTTTAGGGATGGGAGAAGGCTACTTCCCTTTGTGTAGCCCTATC
61869 ATCACATTCAATTTCATGTTCACATGTAACATAGAGC
66 AT-ACA-TCAATTTCATGTTCACATGTAACATAGAGC
61906 TAATTTGAGT
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
99 64 0.69
101 2 0.02
103 1 0.01
104 1 0.01
105 25 0.27
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (103 bp):
TCAAATCCTGAGTCTGGATGGGTTTAGGGATGGGAGAAGGCTACTTCCCTTTGTGTAGCCCTATC
ATACATCAATTTCATGTTCACATGTAACATAGAGCGGG
Done.