Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018666.1 Corchorus olitorius cultivar O-4 contig18699, 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: 17361
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:184 original size:28 final size:25
Alignment explanation
Indices: 132--187 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 25
122 ACTAAAAGCA
132 AATGAATAACTAAAAGTTGATTAAG
1 AATGAATAACTAAAAGTTGATTAAG
157 AATGAATCAACTAATTAAGTTGCA-TAAG
1 AATGAAT-AACTAA--AAGTTG-ATTAAG
185 AAT
1 AAT
188 TGCCTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 7 0.26
26 6 0.22
28 13 0.48
29 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (25 bp):
AATGAATAACTAAAAGTTGATTAAG
Found at i:2214 original size:23 final size:22
Alignment explanation
Indices: 2184--2227 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2174 TTCCATTGTT
*
2184 TACTTTAATATTAATACTATAC
1 TACTTTAAAATTAATACTATAC
2206 TACTCTTAAAATTAATACTATA
1 TACT-TTAAAATTAATACTATA
2228 TATATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (22 bp):
TACTTTAAAATTAATACTATAC
Found at i:2871 original size:42 final size:42
Alignment explanation
Indices: 2811--2900 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
2801 ACACAATTCC
* * ** *
2811 CTTCATCACCACGGCGTCGTTTTTGGCTGCTTACTTCTTCTT
1 CTTCATCAACACGGCGTCGTTTTCGGCCACTTACTTCTCCTT
* *
2853 CTTCATCAAGACGTCGTCGTTTTCGGCCACTTACTTCTCCTT
1 CTTCATCAACACGGCGTCGTTTTCGGCCACTTACTTCTCCTT
*
2895 CATCAT
1 CTTCAT
2901 GATGATCCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.13, C:0.32, G:0.14, T:0.40
Consensus pattern (42 bp):
CTTCATCAACACGGCGTCGTTTTCGGCCACTTACTTCTCCTT
Found at i:4222 original size:16 final size:16
Alignment explanation
Indices: 4201--4305 Score: 133
Period size: 16 Copynumber: 6.6 Consensus size: 16
4191 GGCAATTGGG
* **
4201 CGGGTTCGGGCAGGTT
1 CGGGTTCGGGTATTTT
*
4217 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
4232 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
4248 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
4264 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
4280 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
4296 CGGGTTCGGG
1 CGGGTTCGGG
4306 CTCGGGTAGG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
15 15 0.19
16 63 0.80
17 1 0.01
ACGTcount: A:0.06, C:0.16, G:0.43, T:0.35
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:4303 original size:6 final size:6
Alignment explanation
Indices: 4294--4344 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
4284 TTCGGGTATT
* * *
4294 TTCGGG TTCGGG CTCGGG -TAGGG TTCGGG TTCGGG CTCGGG -TCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
4340 TTCGG
1 TTCGG
4345 ACTCGGGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (6 bp):
TTCGGG
Found at i:4323 original size:11 final size:11
Alignment explanation
Indices: 4294--4344 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
4284 TTCGGGTATT
4294 TTCGGGTTCGGG
1 TTCGGG-TCGGG
* *
4306 CTCGGGTAGGG
1 TTCGGGTCGGG
4317 TTCGGGTTCGGG
1 TTCGGG-TCGGG
*
4329 CTCGGGTCGGG
1 TTCGGGTCGGG
4340 TTCGG
1 TTCGG
4345 ACTCGGGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (11 bp):
TTCGGGTCGGG
Found at i:4324 original size:23 final size:23
Alignment explanation
Indices: 4294--4344 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
4284 TTCGGGTATT
4294 TTCGGGTTCGGGCTCGGGTAGGG
1 TTCGGGTTCGGGCTCGGGTAGGG
*
4317 TTCGGGTTCGGGCTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGGTAGGG
4340 TTCGG
1 TTCGG
4345 ACTCGGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCGGGTAGGG
Found at i:4338 original size:17 final size:18
Alignment explanation
Indices: 4295--4353 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 18
4285 TCGGGTATTT
*
4295 TCGGGTTCGGGCTCGGG-
1 TCGGGTTCGGGTTCGGGC
*
4312 TAGGGTTCGGGTTCGGGC
1 TCGGGTTCGGGTTCGGGC
*
4330 TCGGG-TCGGGTTCGGAC
1 TCGGGTTCGGGTTCGGGC
4347 TCGGGTT
1 TCGGGTT
4354 TGATTTTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 31 0.86
18 5 0.14
ACGTcount: A:0.03, C:0.20, G:0.49, T:0.27
Consensus pattern (18 bp):
TCGGGTTCGGGTTCGGGC
Found at i:4350 original size:23 final size:23
Alignment explanation
Indices: 4301--4351 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
4291 ATTTTCGGGT
**
4301 TCGGGCTCGGGTAGGGTTCGGGT
1 TCGGGCTCGGGTAGGGTTCGGAC
*
4324 TCGGGCTCGGGTCGGGTTCGGAC
1 TCGGGCTCGGGTAGGGTTCGGAC
4347 TCGGG
1 TCGGG
4352 TTTGATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.22, G:0.51, T:0.24
Consensus pattern (23 bp):
TCGGGCTCGGGTAGGGTTCGGAC
Found at i:4800 original size:31 final size:31
Alignment explanation
Indices: 4765--4836 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
4755 TAAATTATTG
*
4765 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
4796 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
4827 CAAATTAAAA
1 CAAATTAAAA
4837 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:5203 original size:26 final size:22
Alignment explanation
Indices: 5146--5203 Score: 53
Period size: 26 Copynumber: 2.4 Consensus size: 22
5136 AATTGTGATC
*
5146 ATTATTATATAAATTTTATTAT
1 ATTAATATATAAATTTTATTAT
5168 ATTCATATATATAATAGTTTTATTTAAT
1 ATT-A-ATATATAA-A-TTTTA-TT-AT
5196 ATTAATAT
1 ATTAATAT
5204 GTTTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
22 3 0.10
23 1 0.03
24 7 0.24
25 1 0.03
26 9 0.31
27 3 0.10
28 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTAATATATAAATTTTATTAT
Found at i:5286 original size:11 final size:12
Alignment explanation
Indices: 5264--5330 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 12
5254 TCAAATTATT
5264 TCGGGTTCGGGC
1 TCGGGTTCGGGC
5276 TCGGG-TCGGGC
1 TCGGGTTCGGGC
5287 TC-GGTCTCGGG-
1 TCGGGT-TCGGGC
5298 TCGGGTTCGGGC
1 TCGGGTTCGGGC
* *
5310 TCGAGTT--GCC
1 TCGGGTTCGGGC
5320 TCGGGTTCGGG
1 TCGGGTTCGGG
5331 TATTTTCGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
10 10 0.22
11 15 0.33
12 20 0.44
ACGTcount: A:0.01, C:0.25, G:0.48, T:0.25
Consensus pattern (12 bp):
TCGGGTTCGGGC
Found at i:5290 original size:17 final size:17
Alignment explanation
Indices: 5264--5312 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
5254 TCAAATTATT
5264 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
* *
5281 TCGGGCTCGGTCTCGGG
1 TCGGGTTCGGGCTCGGG
5298 TCGGGTTCGGGCTCG
1 TCGGGTTCGGGCTCG
5313 AGTTGCCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.00, C:0.27, G:0.49, T:0.24
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:5339 original size:16 final size:16
Alignment explanation
Indices: 5320--5363 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
5310 TCGAGTTGCC
*
5320 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
*
5336 TCGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
5352 TCGGGTTCGGGT
1 TCGGGTTCGGGT
5364 TCGGGCGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.16, G:0.41, T:0.36
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:7660 original size:28 final size:27
Alignment explanation
Indices: 7566--7665 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
7556 GTGATCCTAG
* *
7566 AATGACCAAAATGCCCCTGAACATGCA
1 AATGACCAAAATGCCCCTGGATATGCA
* *
7593 AATGACCAAAATGCCCCTGGATGTGCG
1 AATGACCAAAATGCCCCTGGATATGCA
* *
7620 AATGACCAAAATGCCCCTGGATTTTGAA
1 AATGACCAAAATGCCCCTGGA-TATGCA
7648 AATGACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
7666 AGATGACCCT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 44 0.68
28 21 0.32
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGGATATGCA
Found at i:8099 original size:50 final size:50
Alignment explanation
Indices: 8037--8473 Score: 705
Period size: 50 Copynumber: 8.7 Consensus size: 50
8027 GAAGTAAGGC
* *
8037 TTGACTCATATGGAAACGAGTCTGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
*
8087 TCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
8137 TTGACTCGTATGG-AACGAGTTTGGCTTGTGGAAAAGCCATATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC-TATGTTGATAA
* *
8187 TTGACTCGTATGGAAAGGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
8237 TTGACTCGTATGGAGACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* **
8287 TCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGCGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
**
8337 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGGTGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
**
8387 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGGTGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* * *
8437 TTGACTCGTATGGAAACGAGCTTGACTTATGGAAAAG
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
8474 TCAAAGTATT
Statistics
Matches: 364, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 25 0.07
50 315 0.87
51 24 0.07
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (50 bp):
TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
Found at i:8699 original size:79 final size:80
Alignment explanation
Indices: 8561--8782 Score: 335
Period size: 79 Copynumber: 2.8 Consensus size: 80
8551 ATACCTTTGG
* * *
8561 AAAATAACTATGAATCTGATGTTGTAACTGAAAACTCCTTGA-CTGATGATGAAAA-AGGACCAA
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATC-GATGAT-AAAAGAGGACCAA
*
8624 TG-TGCGGTCAACTTGA
64 TGATGCGATCAACTTGA
*
8640 AAAATAACTCTGAGTCTGATGTTGTAAGTGAAAACTTCTTGATCGATGATAAAAGAGGACCAA-G
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATCGATGATAAAAGAGGACCAATG
8704 ATGCGATCAACTTGA
66 ATGCGATCAACTTGA
* *
8719 AAAATAACTCTAAGTCTGATGTTGTAACTGAAAACTTCTTGATCGATGATGAAAGAGGACCAAT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATCGATGATAAAAGAGGACCAAT
8783 AACTTTGGTC
Statistics
Matches: 131, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
78 5 0.04
79 125 0.95
80 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (80 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATCGATGATAAAAGAGGACCAATG
ATGCGATCAACTTGA
Found at i:9251 original size:50 final size:50
Alignment explanation
Indices: 9197--9340 Score: 238
Period size: 50 Copynumber: 2.9 Consensus size: 50
9187 CTTCAATGTC
* *
9197 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
*
9247 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
*
9297 --TTGTAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
9341 TTTATTGTAA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 43 0.48
50 47 0.52
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
Found at i:9324 original size:48 final size:48
Alignment explanation
Indices: 9203--9351 Score: 244
Period size: 48 Copynumber: 3.1 Consensus size: 48
9193 TGTCCTTTGA
* * * *
9203 AAAGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTACTTTGA
1 AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA--TTGT
9253 AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTATTGT
1 AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTATTGT
9301 AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTATTGT
1 AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTATTGT
9349 AAA
1 AAA
9352 ACTTCTTGTT
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 54 0.57
50 41 0.43
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (48 bp):
AAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTATTGT
Found at i:9642 original size:11 final size:11
Alignment explanation
Indices: 9626--9659 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
9616 GCTCCTTTTC
**
9626 TTTTTTTCTTT
1 TTTTTTTCACT
9637 TTTTTTTCACT
1 TTTTTTTCACT
9648 TTTTTTTCACT
1 TTTTTTTCACT
9659 T
1 T
9660 GGAAAACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTCACT
Found at i:9976 original size:14 final size:15
Alignment explanation
Indices: 9951--10002 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
9941 TCTCTTTTGA
9951 TTTTGATTTTGATTTT
1 TTTTGA-TTTGATTTT
* **
9967 TTTTTA-TTGATTGA
1 TTTTGATTTGATTTT
9981 TTTTGATTTGA-TTT
1 TTTTGATTTGATTTT
9995 TTTTGATT
1 TTTTGATT
10003 GACTTTGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 20 0.69
15 4 0.14
16 5 0.17
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.71
Consensus pattern (15 bp):
TTTTGATTTGATTTT
Found at i:9981 original size:30 final size:31
Alignment explanation
Indices: 9947--10034 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
9937 CCATTCTCTT
*
9947 TTGATTTTGATTTTGATTTTTTTTTATTGA-
1 TTGATTTTGATTTTGATTTTTTTTGATTGAC
9977 TTGATTTTGA-TTTGA-TTTTTTTGATTGAC
1 TTGATTTTGATTTTGATTTTTTTTGATTGAC
10006 TTTGA-TTTGATTTTTTGA-TTTTTTTGATT
1 -TTGATTTTGA--TTTTGATTTTTTTTGATT
10035 TTGAATTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
28 12 0.23
29 10 0.19
30 14 0.27
32 16 0.31
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.68
Consensus pattern (31 bp):
TTGATTTTGATTTTGATTTTTTTTGATTGAC
Found at i:10042 original size:24 final size:24
Alignment explanation
Indices: 9953--10043 Score: 98
Period size: 24 Copynumber: 3.8 Consensus size: 24
9943 TCTTTTGATT
**
9953 TTGATTTTGATTT-TTTTTTATTGA
1 TTGATTTTGATTTGAATTTT-TTGA
*
9977 TTGATTTTGATTTGATTTTTTTGA
1 TTGATTTTGATTTGAATTTTTTGA
*
10001 TTGACTTTGATTTG-ATTTTTTGA
1 TTGATTTTGATTTGAATTTTTTGA
*
10024 TT-TTTTTGATTTTGAATTTT
1 TTGATTTTGA-TTTGAATTTT
10044 CTGAATTTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 5 0.08
23 14 0.24
24 35 0.59
25 5 0.08
ACGTcount: A:0.16, C:0.01, G:0.14, T:0.68
Consensus pattern (24 bp):
TTGATTTTGATTTGAATTTTTTGA
Found at i:10043 original size:7 final size:6
Alignment explanation
Indices: 9945--9995 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
9935 ATCCATTCTC
*
9945 TTTTGA TTTTGA TTTTGA TTTT-- TTTTTA TTGATTGA TTTTGA -TTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT--TTGA TTTTGA TTTTGA
9992 TTTT
1 TTTT
9996 TTTGATTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 25 0.64
8 5 0.13
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:10082 original size:14 final size:14
Alignment explanation
Indices: 10040--10083 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
10030 TGATTTTGAA
*
10040 TTTTCTGAATTTCCT
1 TTTTTTGAATTT-CT
*
10055 TTTTTTGAACTTCT
1 TTTTTTGAATTTCT
10069 TTTTTTGAATTTCT
1 TTTTTTGAATTTCT
10083 T
1 T
10084 GATGGAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTTTGAATTTCT
Done.