Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014024.1 Corchorus olitorius cultivar O-4 contig14057, 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: 100061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:914 original size:26 final size:27
Alignment explanation
Indices: 883--959 Score: 111
Period size: 26 Copynumber: 2.9 Consensus size: 27
873 GCATTAAGGT
883 CATTCAGGGGCATTTTGGTCATTTGCA
1 CATTCAGGGGCATTTTGGTCATTTGCA
* *
910 C-TTCAGGGGCATTTTTGTCATCTGCA
1 CATTCAGGGGCATTTTGGTCATTTGCA
* *
936 CATTCAGGGGCGTTTTGGTAATTT
1 CATTCAGGGGCATTTTGGTCATTT
960 TAAGTTCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 24 0.56
27 19 0.44
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTGCA
Found at i:3203 original size:21 final size:22
Alignment explanation
Indices: 3179--3219 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3169 TAATTAAATG
*
3179 CAATTTGATCCCTG-TTTTATT
1 CAATTTGACCCCTGATTTTATT
3200 CAATTTGACCCCTGATTTTA
1 CAATTTGACCCCTGATTTTA
3220 GAAATTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (22 bp):
CAATTTGACCCCTGATTTTATT
Found at i:4257 original size:9 final size:8
Alignment explanation
Indices: 4234--4267 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
4224 GTTGAAGAAT
4234 AAATG-AA
1 AAATGAAA
4241 AAATGAAA
1 AAATGAAA
4249 AAATGGAAA
1 AAAT-GAAA
4258 AAATGAAA
1 AAATGAAA
4266 AA
1 AA
4268 TGGAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 5 0.20
8 12 0.48
9 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:4259 original size:16 final size:15
Alignment explanation
Indices: 4234--4274 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
4224 GTTGAAGAAT
4234 AAAT-GAAAAATGAAA
1 AAATGGAAAAATG-AA
4249 AAATGGAAAAAATGAA
1 AAATGG-AAAAATGAA
4265 AAATGGAAAA
1 AAATGGAAAA
4275 GAATCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (15 bp):
AAATGGAAAAATGAA
Found at i:4273 original size:8 final size:8
Alignment explanation
Indices: 4234--4274 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4224 GTTGAAGAAT
4234 AAAT-GAA
1 AAATGGAA
*
4241 AAATGAAA
1 AAATGGAA
4249 AAATGGAAA
1 AAATGG-AA
4258 AAAT-GAA
1 AAATGGAA
4265 AAATGGAA
1 AAATGGAA
4273 AA
1 AA
4275 GAATCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 10 0.34
8 13 0.45
9 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (8 bp):
AAATGGAA
Found at i:23370 original size:20 final size:20
Alignment explanation
Indices: 23330--23371 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
23320 ATAAATATTC
23330 AAATGCATGAGAATGGGATGA
1 AAATGCATGAGAA-GGGATGA
23351 AAATGCATGAGGAA-GGATGA
1 AAATGCATGA-GAAGGGATGA
23371 A
1 A
23372 GTGCAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 10 0.50
22 3 0.15
ACGTcount: A:0.45, C:0.05, G:0.33, T:0.17
Consensus pattern (20 bp):
AAATGCATGAGAAGGGATGA
Found at i:34420 original size:44 final size:44
Alignment explanation
Indices: 34349--34498 Score: 143
Period size: 44 Copynumber: 3.4 Consensus size: 44
34339 ACTCATAGGG
*
34349 AGGTTA-CAAAATTTCATA-GGAAGGTTTATTAAAATTTAATAGTT
1 AGGTTATCAAAATTTCATATGG-A-GTTTATCAAAATTTAATAGTT
* * *
34393 AGGTTATCAAAGTTTCATATGGAGTTTATCACAATTTCATAGGTT
1 AGGTTATCAAAATTTCATATGGAGTTTATCAAAATTTAATA-GTT
*
34438 A--TTATCAAAATTTCATAATGTG-G-TTATCAAAATTTAATAGGGT
1 AGGTTATCAAAATTTCAT-ATG-GAGTTTATCAAAATTTAATA-GTT
*
34481 A-GTTATAAAAATTTCATA
1 AGGTTATCAAAATTTCATA
34499 AAAATATTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 13
0.81 0.08 0.12
Matches are distributed among these distances:
43 33 0.36
44 39 0.43
45 17 0.19
46 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATATGGAGTTTATCAAAATTTAATAGTT
Found at i:34490 original size:21 final size:22
Alignment explanation
Indices: 34300--34498 Score: 119
Period size: 22 Copynumber: 9.1 Consensus size: 22
34290 TCAAAAAATT
* *
34300 ATAGGG-AGATTAACAAAATCTC
1 ATAGGGTAG-TTATCAAAATTTC
* *
34322 ATAGTG-AGGTTATCAAAA-CTC
1 ATAGGGTA-GTTATCAAAATTTC
34343 ATAGGG-AGGTTA-CAAAATTTC
1 ATAGGGTA-GTTATCAAAATTTC
* * *
34364 ATA-GGAAGGTTTATTAAAATTTA
1 ATAGGGTA-G-TTATCAAAATTTC
* *
34387 ATA-GTTAGGTTATCAAAGTTTC
1 ATAGGGTA-GTTATCAAAATTTC
* *
34409 ATATGG-AGTTTATCACAATTTC
1 ATAGGGTAG-TTATCAAAATTTC
*
34431 ATAGGTTA-TTATCAAAATTTC
1 ATAGGGTAGTTATCAAAATTTC
** * *
34452 ATAATGTGGTTATCAAAATTTA
1 ATAGGGTAGTTATCAAAATTTC
*
34474 ATAGGGTAGTTATAAAAATTTC
1 ATAGGGTAGTTATCAAAATTTC
34496 ATA
1 ATA
34499 AAAATATTCA
Statistics
Matches: 141, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
20 7 0.05
21 39 0.28
22 78 0.55
23 17 0.12
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
ATAGGGTAGTTATCAAAATTTC
Found at i:44820 original size:1 final size:1
Alignment explanation
Indices: 44816--44842 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
44806 CCCCCTCCAA
44816 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
44843 ACACCCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:56237 original size:31 final size:30
Alignment explanation
Indices: 56168--56238 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
56158 TCCTTTCCTC
** *
56168 TTTTTTCCGATGATGGATCAAAGGTTTTGG
1 TTTTTTCCGATGAAAGATCAAAGGTTTGGG
* *
56198 TATATTTCCGATGAAAAGATTAAAGGTTTGGG
1 T-TTTTTCCGATG-AAAGATCAAAGGTTTGGG
56230 TTTTTTCCG
1 TTTTTTCCG
56239 TTAGCCGGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 1 0.03
31 17 0.52
32 15 0.45
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (30 bp):
TTTTTTCCGATGAAAGATCAAAGGTTTGGG
Found at i:65323 original size:40 final size:40
Alignment explanation
Indices: 65261--65341 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
65251 ACTTGACCCT
* *
65261 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
*
65301 CCTAATAATTAAGGTAAGAAATTAAATCCAGATTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
65341 C
1 C
65342 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
Found at i:66118 original size:15 final size:15
Alignment explanation
Indices: 66098--66136 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
66088 TTTAATTATA
66098 TTTTTTCTGTTTT-CT
1 TTTTTTCT-TTTTACT
*
66113 TTTTTTCTTTTTAGT
1 TTTTTTCTTTTTACT
66128 TTTTTTCTT
1 TTTTTTCTT
66137 GTCAGACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTACT
Found at i:67855 original size:42 final size:43
Alignment explanation
Indices: 67805--67898 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
67795 AGTGTATTAC
** * *
67805 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATTAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
*
67846 CTAATATTCTACTCCTCCATCTCTAAATAGTTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAAATAATTCATCAAAATAAAG
67891 CTAATATT
1 CTAATATT
67899 AGTTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
Found at i:69463 original size:12 final size:12
Alignment explanation
Indices: 69448--69473 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
69438 AATATGTACT
69448 TAAATGAAATTA
1 TAAATGAAATTA
69460 TAAATGAAATTA
1 TAAATGAAATTA
69472 TA
1 TA
69474 TCAGAGTAGA
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:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TAAATGAAATTA
Found at i:81967 original size:6 final size:6
Alignment explanation
Indices: 81956--81986 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
81946 TATATCATAT
*
81956 TTTATA TTTATA TTTATA ATTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA T
81987 AATTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:82006 original size:14 final size:13
Alignment explanation
Indices: 81970--82008 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
81960 TATTTATATT
*
81970 TATAATTATATTTA
1 TATAATTA-ATTAA
81984 TATAATTAATTAA
1 TATAATTAATTAA
81997 TATAATTTAATT
1 TATAA-TTAATT
82009 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:87272 original size:24 final size:24
Alignment explanation
Indices: 87205--87278 Score: 139
Period size: 24 Copynumber: 3.1 Consensus size: 24
87195 ATGGACAGAC
87205 GATTTGAAACATTAATTTAGACAT
1 GATTTGAAACATTAATTTAGACAT
*
87229 GATTTGAAACATTAAGTTAGACAT
1 GATTTGAAACATTAATTTAGACAT
87253 GATTTGAAACATTAATTTAGACAT
1 GATTTGAAACATTAATTTAGACAT
87277 GA
1 GA
87279 AGGATTAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (24 bp):
GATTTGAAACATTAATTTAGACAT
Found at i:87276 original size:12 final size:12
Alignment explanation
Indices: 87213--87276 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
87203 ACGATTTGAA
87213 ACATTAATTTAG
1 ACATTAATTTAG
* *
87225 ACA-TGATTTGAA
1 ACATTAATTT-AG
*
87237 ACATTAAGTTAG
1 ACATTAATTTAG
* *
87249 ACA-TGATTTGAA
1 ACATTAATTT-AG
87261 ACATTAATTTAG
1 ACATTAATTTAG
87273 ACAT
1 ACAT
87277 GAAGGATTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
11 9 0.24
12 20 0.53
13 9 0.24
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (12 bp):
ACATTAATTTAG
Found at i:89668 original size:30 final size:30
Alignment explanation
Indices: 89632--89689 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
89622 TTGTTGCCCA
*
89632 AACATGCCACCCCAACCATGAATTTCAATG
1 AACATGCCACCCCAACCATGAACTTCAATG
*
89662 AACATGCCACCCCAAGCATGAACTTCAA
1 AACATGCCACCCCAACCATGAACTTCAA
89690 GAATCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (30 bp):
AACATGCCACCCCAACCATGAACTTCAATG
Found at i:93390 original size:96 final size:94
Alignment explanation
Indices: 93209--93402 Score: 336
Period size: 96 Copynumber: 2.0 Consensus size: 94
93199 GGTGCGTGAA
*
93209 AATATCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTCTTGTTCCAGCACAAA
1 AATACCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTCTTGTTCCAGCACAAA
93274 AAAATCACCGAAGAAATCTTGAAAAGAAT
66 AAAATCACCGAAGAAATCTTGAAAAGAAT
*
93303 AATACCCATTGAATTTGTCCACGATAAACCCCCAAAAGCCCATCCTTTTTTTCTTGTTCCAGCTC
1 AATACCCATTGAATTTGTCCACGATAAA-CCCCAAAAGCCCATCC--TTTTTCTTGTTCCAGCAC
93368 AAAAAAA-CACCGAAGAAATCTTGAAAAGAAT
63 AAAAAAATCACCGAAGAAATCTTGAAAAGAAT
93399 AATA
1 AATA
93403 AAAGGAGATT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
94 27 0.28
95 16 0.17
96 28 0.29
97 24 0.25
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (94 bp):
AATACCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTCTTGTTCCAGCACAAA
AAAATCACCGAAGAAATCTTGAAAAGAAT
Found at i:95692 original size:198 final size:199
Alignment explanation
Indices: 95302--96166 Score: 1155
Period size: 198 Copynumber: 4.3 Consensus size: 199
95292 CTCTCAAAAA
* * * * * *
95302 ATTATACAATATATTGTCAATATAAATTTTGGACTCCATAAACGGGTTAAGAAAGTTGACACATA
1 ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAG-AAGTTGACACATA
*
95367 -TCATATTTCATAATTAATTAAATATTTAATATATAATATTAGTACATATTCCCTAAGGGGACAC
65 CTC-TATTTCATAATTAATT-AA-A--T-ATA-A-AATATTAATACATATTCCCTAAGGGGACAC
* * * * *
95431 ATGTCAACCTTTAAACCATGCACGTGCAGTCTGCTAAACTCCACTGGCGGCGTATTGTATAATTT
122 ATGTCAACCCTTAAGCCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTT
95496 TTTTTATAGGATT
187 TTTTTATAGGATT
* * *
95509 GTTATACAATACATTGTCAGTGTAAATTTTGAACTCTATAAGCGGGTTAAGAAGTTGACACATAC
1 ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATAC
*
95574 TCTATTTCATAATTAATTAAATATAAAATATTAATAAATATTCCCTAAGGGGACACATGTC-ACC
66 TCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
**
95638 CTTAAGCCCTGTGCGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTTATAG
131 CTTAAGCCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTTATAG
95703 GATT
196 GATT
* * *
95707 GTTATACAATACACTGTCAATGTAAATTTTAAACTCCATAAGCGGGTTAAGAAGTTGACACATAC
1 ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATAC
*
95772 CCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
66 TCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
* * *
95837 CTTAAG-TCTGCGCGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAA-TTTTTTTATAT
131 CTTAAGCCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTTATA-
*
95900 GATATT
195 G-GATT
* * *
95906 ATTATACAATACACTGTTAGTGTATATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATAC
1 ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATAC
** * *
95971 -CTCATTTCATAATTAATTAAATATTTAATATTAATACATATTTCCTAAGGGTACACATGTCAAC
66 TCT-ATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTCAAC
* * *
96035 CCTTAAAGTTAAACCCTGCATGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAAATTTT
130 CCTT-AAG-----CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
** *
96100 CCTATAGGATC
189 TTTATAGGATT
* * *
96111 ATTATACAATACCCTGTCAGTGTAAATTTTAAACTCCATAAACGGGTTAAGAAGTT
1 ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTT
96167 TTTGTGCCAA
Statistics
Matches: 596, Mismatches: 49, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
197 10 0.02
198 231 0.39
199 165 0.28
200 4 0.01
201 3 0.01
202 1 0.00
204 1 0.00
205 54 0.09
206 73 0.12
207 54 0.09
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (199 bp):
ATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATAC
TCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
CTTAAGCCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTTATAG
GATT
Found at i:97568 original size:2 final size:2
Alignment explanation
Indices: 97561--97588 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
97551 ATGTCTCCAA
97561 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
97589 TGTATCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98702 original size:1 final size:1
Alignment explanation
Indices: 98691--98722 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
98681 GCTAGTTTAG
*
98691 TTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
98723 GTCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:99978 original size:2 final size:2
Alignment explanation
Indices: 99971--100061 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
99961 GGGAGGGAGG
99971 GA GA GA GA GA 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 GA GA GA GA GA
100013 GA GA GA GA GA 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 GA GA GA GA GA
100055 GA GA GA G
1 GA GA GA G
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.