Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019231.1 Corchorus olitorius cultivar O-4 contig19264, 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: 108234
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:628 original size:230 final size:229
Alignment explanation
Indices: 200--661 Score: 762
Period size: 230 Copynumber: 2.0 Consensus size: 229
190 AAGTGTTACA
200 CACTTTAGAGGAGGAAACAAAATTGAAGGTATTGCACCTGTCTATGTACAAACTAATATTTACTA
1 CACTTTAGAGGAGGAAACAAAATTGAAGGTATTGCACCTGTCTATGTACAAACTAATATTTACTA
* *
265 TTTATTGCCAACTTTAGGGCATATGCTAATGTTAATAGTATAACCTTTTAAAGCTGCAACATATT
66 TTTATTGCCAACTTTAAGGCATATGCTAATGTTAATAGTATAACCTTTTAAAGCTGCAACACATT
* * * * *
330 TAAAATTATAGTACTTTCGAAATTTCTTACGTTTCACATAATTTAATTCGAATAAAAAATTGTTC
131 TAAAATCATAGTACTTTCGAAATTTCCTACATTTCAAACAATTTAATTCGAATAAAAAATTGTTC
* *
395 AAAAAAGTAGATTGTTGAATGCCCGACACGCCAG
196 AAAAAAGTAGATTATTGAACGCCCGACACGCCAG
* *
429 CACTTTAGAGGAGGAAACAAAATTGAAGGTATTGCATCTGTCTATGTACAAATTAATATTTACTA
1 CACTTTAGAGGAGGAAACAAAATTGAAGGTATTGCACCTGTCTATGTACAAACTAATATTTACTA
* *
494 TTTATTGCCAACTTTAAGGCATATGCTCAATGTTAATAGTATAGCCTTTTAAAGCTGCAACGCAT
66 TTTATTGCCAACTTTAAGGCATATGCT-AATGTTAATAGTATAACCTTTTAAAGCTGCAACACAT
* *
559 TTAAAATCATAGTACTTTCGAAATTTCCTACATTTTAAACAATTTAATTCGAATAGAAAATTGTT
130 TTAAAATCATAGTACTTTCGAAATTTCCTACATTTCAAACAATTTAATTCGAATAAAAAATTGTT
* *
624 CAAAAAAGTAGATTATTGAACGTCCGACACGTCAG
195 CAAAAAAGTAGATTATTGAACGCCCGACACGCCAG
659 CAC
1 CAC
662 AGACCGATCC
Statistics
Matches: 215, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
229 89 0.41
230 126 0.59
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (229 bp):
CACTTTAGAGGAGGAAACAAAATTGAAGGTATTGCACCTGTCTATGTACAAACTAATATTTACTA
TTTATTGCCAACTTTAAGGCATATGCTAATGTTAATAGTATAACCTTTTAAAGCTGCAACACATT
TAAAATCATAGTACTTTCGAAATTTCCTACATTTCAAACAATTTAATTCGAATAAAAAATTGTTC
AAAAAAGTAGATTATTGAACGCCCGACACGCCAG
Found at i:4488 original size:7 final size:7
Alignment explanation
Indices: 4476--4501 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4466 CATTTGCCTC
4476 TCCTAAG
1 TCCTAAG
4483 TCCTAAG
1 TCCTAAG
4490 TCCTAAG
1 TCCTAAG
4497 TCCTA
1 TCCTA
4502 TCTCTTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (7 bp):
TCCTAAG
Found at i:6069 original size:36 final size:37
Alignment explanation
Indices: 6014--6087 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 37
6004 TTTTTTTTGG
* *
6014 CAATAAAAAAATGCGGAGATAATTAGAAATTGGAATT
1 CAATAAAAAAATGCGGAGATAACTAGAAATTGCAATT
6051 CAATGAAAAAAAT-C-GAGATAACTAGAAATTGCAATT
1 CAAT-AAAAAAATGCGGAGATAACTAGAAATTGCAATT
6087 C
1 C
6088 GAGAGAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 21 0.62
37 5 0.15
38 8 0.24
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (37 bp):
CAATAAAAAAATGCGGAGATAACTAGAAATTGCAATT
Found at i:6325 original size:27 final size:27
Alignment explanation
Indices: 6295--6349 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6285 ATGAATGCCA
6295 AATTTATTTGTGAAAAAGCTAAAAGAC
1 AATTTATTTGTGAAAAAGCTAAAAGAC
6322 AATTTATTTGTGAAAAAGCTAAAAGAC
1 AATTTATTTGTGAAAAAGCTAAAAGAC
6349 A
1 A
6350 TGTTAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (27 bp):
AATTTATTTGTGAAAAAGCTAAAAGAC
Found at i:6359 original size:27 final size:27
Alignment explanation
Indices: 6295--6359 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
6285 ATGAATGCCA
*
6295 AATTTATTTGTGAAAAAGCTAAAAGAC
1 AATTTAATTGTGAAAAAGCTAAAAGAC
*
6322 AATTTATTTGTGAAAAAGCTAAAAGAC
1 AATTTAATTGTGAAAAAGCTAAAAGAC
6349 -ATGTTAATTGT
1 AAT-TTAATTGT
6360 TTAACACATC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (27 bp):
AATTTAATTGTGAAAAAGCTAAAAGAC
Found at i:19274 original size:16 final size:18
Alignment explanation
Indices: 19253--19299 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
19243 AAGGAAGAAA
19253 AGACAGAG-AG-AAACAG
1 AGACAGAGAAGAAAACAG
19269 AGACAGAGAAGAAAACAG
1 AGACAGAGAAGAAAACAG
19287 AGAAACAGAGAAG
1 AG--ACAGAGAAG
19300 GAAGCGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.30
17 2 0.07
18 8 0.30
20 9 0.33
ACGTcount: A:0.60, C:0.11, G:0.30, T:0.00
Consensus pattern (18 bp):
AGACAGAGAAGAAAACAG
Found at i:21976 original size:20 final size:21
Alignment explanation
Indices: 21951--21989 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
21941 GGATTTGCTA
*
21951 ATTGATTTAGTAAA-ATTGGG
1 ATTGATATAGTAAATATTGGG
21971 ATTGATATAGTAAATATTG
1 ATTGATATAGTAAATATTG
21990 AAAAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (21 bp):
ATTGATATAGTAAATATTGGG
Found at i:44532 original size:30 final size:30
Alignment explanation
Indices: 44497--44559 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
44487 TTCACACATC
*
44497 TATATCCCGCATGAAAACTATATGTAAAGA
1 TATATCCCACATGAAAACTATATGTAAAGA
44527 TATATCCCACATGAAAACTATATGTAAAGA
1 TATATCCCACATGAAAACTATATGTAAAGA
44557 TAT
1 TAT
44560 GAAAGAGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (30 bp):
TATATCCCACATGAAAACTATATGTAAAGA
Found at i:44928 original size:39 final size:39
Alignment explanation
Indices: 44874--44952 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
44864 CTCTATAGGT
44874 TTTTTAGTAATGGTATACATGGCTTAACACACTCTTCAC
1 TTTTTAGTAATGGTATACATGGCTTAACACACTCTTCAC
44913 TTTTTAGTAATGGTATACATGGCTTAACACACTCTTCAC
1 TTTTTAGTAATGGTATACATGGCTTAACACACTCTTCAC
44952 T
1 T
44953 CTAAATATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (39 bp):
TTTTTAGTAATGGTATACATGGCTTAACACACTCTTCAC
Found at i:45569 original size:43 final size:43
Alignment explanation
Indices: 45500--45588 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
45490 TTTTCACTTA
* *
45500 TCAGGTCCGACAATTGAACCGATCAAACAGACAACTGAAACCT
1 TCAGCTCCGACAATTAAACCGATCAAACAGACAACTGAAACCT
* * *
45543 TCAGCTCCGACGATTAAACCGGTCAAACCGACAACTGAAACCT
1 TCAGCTCCGACAATTAAACCGATCAAACAGACAACTGAAACCT
45586 TCA
1 TCA
45589 CCATTTACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (43 bp):
TCAGCTCCGACAATTAAACCGATCAAACAGACAACTGAAACCT
Found at i:45847 original size:18 final size:18
Alignment explanation
Indices: 45824--45860 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
45814 ACACACATGA
45824 AGTCCACATTTTCATAAC
1 AGTCCACATTTTCATAAC
*
45842 AGTCCATATTTTCATAAC
1 AGTCCACATTTTCATAAC
45860 A
1 A
45861 ACAGCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (18 bp):
AGTCCACATTTTCATAAC
Found at i:54371 original size:22 final size:22
Alignment explanation
Indices: 54319--54366 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
54309 ATTAAAAGAT
*
54319 AAAAAGAAATTAAAAGAAAATCC
1 AAAAAG-ATTTAAAAGAAAATCC
54342 AAAAAGATTTAAAA-AAAA-CC
1 AAAAAGATTTAAAAGAAAATCC
54362 AAAAA
1 AAAAA
54367 TAGATGGCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
22 7 0.29
23 6 0.25
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAAAGATTTAAAAGAAAATCC
Found at i:58039 original size:33 final size:31
Alignment explanation
Indices: 57976--58039 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
57966 ATTTTTATCC
* *
57976 GTGTTTAATGGGGTTTTTTTTTTTGGTGAAA
1 GTGTTTAATGGCGTTTTTTTTTTTGATGAAA
58007 GTGTTTAAT-GCGTTTTTATTAGTTTTGATGAAA
1 GTGTTTAATGGCGTTTTT-TT--TTTTGATGAAA
58040 CAAAATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.25
31 11 0.39
33 10 0.36
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (31 bp):
GTGTTTAATGGCGTTTTTTTTTTTGATGAAA
Found at i:62219 original size:102 final size:99
Alignment explanation
Indices: 62028--62229 Score: 296
Period size: 102 Copynumber: 2.0 Consensus size: 99
62018 TGGGCTCAGA
*
62028 ATTTTCCATATATTCATAAGACACTTCATTAAGTGAACAATGAGGTTCTTTTGTAGGATGAGGCA
1 ATTTTCCATATATTCATAAGACACTTCATTAAGAGAACAATGAGGTTCTTTTGTAGGATGAGGCA
*
62093 ACTCACTCTCCAGAATATGTACATTGGGAGTATC
66 ACTCACTCTCCAGAATATGCACATTGGGAGTATC
*
62127 ATTTTCCATATATTCATAGGACACTTCATTAAGAGAACAATATTGAGGTTCTTTTGTAGGATGAG
1 ATTTTCCATATATTCATAAGACACTTCATTAAGAGAAC-A-A-TGAGGTTCTTTTGTAGGATGAG
* *** * *
62192 GCGACTTTGTCTCCAGAATGTGCACATTGGTAGTATC
63 GCAACTCACTCTCCAGAATATGCACATTGGGAGTATC
62229 A
1 A
62230 GGACCCTCGT
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 36 0.40
100 1 0.01
101 1 0.01
102 53 0.58
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (99 bp):
ATTTTCCATATATTCATAAGACACTTCATTAAGAGAACAATGAGGTTCTTTTGTAGGATGAGGCA
ACTCACTCTCCAGAATATGCACATTGGGAGTATC
Found at i:65885 original size:91 final size:91
Alignment explanation
Indices: 65771--66120 Score: 455
Period size: 91 Copynumber: 4.0 Consensus size: 91
65761 GGTATTGGGT
65771 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
1 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
65836 TTATTTATGATATAGCTTCTTCTGAG
66 TTATTTATGATATAGCTTCTTCTGAG
65862 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
1 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
*
65927 TTATTTATGATATAGCTTC--CTCACG
66 TTATTTATGATATAGCTTCTTCTGA-G
* * * ** * *
65952 -GAA-TGTGA--GTTTGTTTGTAATTTG-TT-T-ATTTGTGTA-TT-TG------GTAGGTAGAT
1 TCAAGTCTCACGGAATG--TG-AGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGAT
* *
66002 AGTTTATTTATGATATAGCTTCTTCTAAA
63 AGTTTATTTATGATATAGCTTCTTCTGAG
66031 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
1 TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
66096 TTATTTATGATATAGCTTCTTCTGA
66 TTATTTATGATATAGCTTCTTCTGA
66121 CTTTGTTTGT
Statistics
Matches: 220, Mismatches: 18, Indels: 42
0.79 0.06 0.15
Matches are distributed among these distances:
78 32 0.15
80 10 0.05
81 7 0.03
82 1 0.00
83 11 0.05
84 4 0.02
85 4 0.02
86 11 0.05
87 1 0.00
88 7 0.03
89 10 0.05
90 1 0.00
91 121 0.55
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (91 bp):
TCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGT
TTATTTATGATATAGCTTCTTCTGAG
Found at i:65957 original size:78 final size:78
Alignment explanation
Indices: 65868--66023 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
65858 TGAGTCAAGT
65868 CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTT
1 CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTT
65933 ATGATATAGCTTC
66 ATGATATAGCTTC
65946 CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTT
1 CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTT
66011 ATGATATAGCTTC
66 ATGATATAGCTTC
66024 TTCTAAATCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.49
Consensus pattern (78 bp):
CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTT
ATGATATAGCTTC
Found at i:66056 original size:169 final size:168
Alignment explanation
Indices: 65776--66185 Score: 717
Period size: 169 Copynumber: 2.5 Consensus size: 168
65766 TGGGTTCAAG
65776 TCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATT
1 TCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATT
* *
65841 TATGATATAGCTTCTTCTGAGTCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTG
66 TATGATATAGCTTCTTCTAAATCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTG
65906 TGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCT
131 TGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCT
65944 TCCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTAT
1 T-CTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTAT
66009 TTATGATATAGCTTCTTCTAAATCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTT
65 TTATGATATAGCTTCTTCTAAATCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTT
66074 GTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCT
130 GTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCT
* *
66113 TCT-------TCTGACTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATT
1 TCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATT
*
66171 TATGATATAGTTTCT
66 TATGATATAGCTTCT
66186 AGTTTGCGCA
Statistics
Matches: 236, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
161 67 0.28
168 3 0.01
169 166 0.70
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.50
Consensus pattern (168 bp):
TCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATT
TATGATATAGCTTCTTCTAAATCAAGTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTATTTG
TGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCT
Found at i:66126 original size:70 final size:70
Alignment explanation
Indices: 66052--66185 Score: 259
Period size: 70 Copynumber: 1.9 Consensus size: 70
66042 GGAATGTGAG
66052 TTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCTTCTT
1 TTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCTTCTT
66117 CTGAC
66 CTGAC
*
66122 TTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGTTTCT
1 TTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCTTCT
66186 AGTTTGCGCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.56
Consensus pattern (70 bp):
TTTGTTTGTAATTTGTTTATTTGTGTATTTGGTAGGTAGATAGTTTATTTATGATATAGCTTCTT
CTGAC
Found at i:66896 original size:15 final size:15
Alignment explanation
Indices: 66876--66907 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66866 TGGGGCTCTC
*
66876 TATTAATTTTATTAA
1 TATTAATTTTAATAA
66891 TATTAATTTTAATAA
1 TATTAATTTTAATAA
66906 TA
1 TA
66908 GATTGTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATTTTAATAA
Found at i:72487 original size:15 final size:15
Alignment explanation
Indices: 72467--72506 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
72457 ACAAACGGTT
*
72467 TGAAGATGATGAAAA
1 TGAAGAAGATGAAAA
*
72482 TGAAGAAGATGAAGA
1 TGAAGAAGATGAAAA
*
72497 TGATGAAGAT
1 TGAAGAAGAT
72507 TTGGAGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (15 bp):
TGAAGAAGATGAAAA
Found at i:72506 original size:9 final size:9
Alignment explanation
Indices: 72467--72506 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
72457 ACAAACGGTT
72467 TGAAGATGA
1 TGAAGATGA
72476 TGAA-A--A
1 TGAAGATGA
*
72482 TGAAGAAGA
1 TGAAGATGA
72491 TGAAGATGA
1 TGAAGATGA
72500 TGAAGAT
1 TGAAGAT
72507 TTGGAGGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
6 5 0.19
7 1 0.04
8 1 0.04
9 20 0.74
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (9 bp):
TGAAGATGA
Found at i:77434 original size:14 final size:14
Alignment explanation
Indices: 77401--77428 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
77391 TTTGAAGCAG
77401 AGGTTCAAAAATCT
1 AGGTTCAAAAATCT
77415 AGGTTCAAAAATCT
1 AGGTTCAAAAATCT
77429 GTGTTCTTAT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AGGTTCAAAAATCT
Found at i:79011 original size:25 final size:24
Alignment explanation
Indices: 78960--79016 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
78950 GTCAGTCTTG
*
78960 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
78983 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
79008 AATTTATTT
1 AATTTATTT
79017 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:91217 original size:42 final size:42
Alignment explanation
Indices: 91158--91243 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
91148 CTTGAAATTA
91158 GCCTGGAATGCTTATTGTTATGTTATTTGGTGTGAACGTAAT
1 GCCTGGAATGCTTATTGTTATGTTATTTGGTGTGAACGTAAT
*
91200 GCCTGGAATGCTTATTGTTATGTTGTTTGGTGTGAACGTAAT
1 GCCTGGAATGCTTATTGTTATGTTATTTGGTGTGAACGTAAT
91242 GC
1 GC
91244 GATCTTCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (42 bp):
GCCTGGAATGCTTATTGTTATGTTATTTGGTGTGAACGTAAT
Found at i:103779 original size:17 final size:16
Alignment explanation
Indices: 103750--103781 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
103740 GTAGTGGTGA
103750 TCAGAGTCTCAGAGAC
1 TCAGAGTCTCAGAGAC
103766 TCAGAGTACTCAGAGA
1 TCAGAGT-CTCAGAGA
103782 GCCGTGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (16 bp):
TCAGAGTCTCAGAGAC
Found at i:108198 original size:2 final size:2
Alignment explanation
Indices: 108191--108227 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
108181 GCTTAAACCT
108191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
108228 TCAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.