Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016199.1 Corchorus capsularis cultivar CVL-1 contig16220, 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: 23500
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3953 original size:14 final size:14
Alignment explanation
Indices: 3934--3966 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3924 GAAGGAGGCC
*
3934 TTGAAAGATTGAAA
1 TTGAAACATTGAAA
3948 TTGAAACATTGAAA
1 TTGAAACATTGAAA
3962 TTGAA
1 TTGAA
3967 CTCGAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (14 bp):
TTGAAACATTGAAA
Found at i:3964 original size:20 final size:20
Alignment explanation
Indices: 3941--3986 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3931 GCCTTGAAAG
*
3941 ATTGAAATTGAA-ACATTGAA
1 ATTGAAATCGAAGA-ATTGAA
*
3961 ATTGAACTCGAAGAATTGAA
1 ATTGAAATCGAAGAATTGAA
3981 ATTGAA
1 ATTGAA
3987 GCATTGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (20 bp):
ATTGAAATCGAAGAATTGAA
Found at i:4008 original size:22 final size:21
Alignment explanation
Indices: 3980--4049 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
3970 GAAGAATTGA
3980 AATTGAAGCATTGACATGTTGG
1 AATTGAAGCATTGACAT-TTGG
* *
4002 AATTGAAACATTGGCATTTGG
1 AATTGAAGCATTGACATTTGG
* * *
4023 AGTTTGAAGAATTGA-AATT-G
1 A-ATTGAAGCATTGACATTTGG
4043 AATTGAA
1 AATTGAA
4050 ATTTAAGCAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 8 0.21
22 24 0.62
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (21 bp):
AATTGAAGCATTGACATTTGG
Found at i:4069 original size:22 final size:22
Alignment explanation
Indices: 4042--4139 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
4032 AATTGAAATT
*
4042 GAATTGAAATTTAAGCATTGAA
1 GAATTGAAATTGAAGCATTGAA
* **
4064 GAATTGAGATTGAAGCATCAAA
1 GAATTGAAATTGAAGCATTGAA
* * * *
4086 GATTTGAAATTGAGGTATTGAG
1 GAATTGAAATTGAAGCATTGAA
**
4108 GAATTGAAGTATTGAATAATTGAA
1 GAATTGAA--ATTGAAGCATTGAA
*
4132 GGATTGAA
1 GAATTGAA
4140 GAAAGATCAC
Statistics
Matches: 57, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 40 0.70
24 17 0.30
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (22 bp):
GAATTGAAATTGAAGCATTGAA
Found at i:4128 original size:16 final size:16
Alignment explanation
Indices: 4026--4142 Score: 68
Period size: 16 Copynumber: 7.5 Consensus size: 16
4016 CATTTGGAGT
4026 TTGAAGAATTGAA--A
1 TTGAAGAATTGAAGTA
* *
4040 TTGAATTGAAATTTAAGCA
1 TTGAA--G-AATTGAAGTA
4059 TTGAAGAATTG-AG-A
1 TTGAAGAATTGAAGTA
* **
4073 TTGAAGCATCAAAG-A
1 TTGAAGAATTGAAGTA
*
4088 TTTG-A-AATTGAGGTA
1 -TTGAAGAATTGAAGTA
*
4103 TTGAGGAATTGAAGTA
1 TTGAAGAATTGAAGTA
* *
4119 TTGAATAATTGAAGGA
1 TTGAAGAATTGAAGTA
4135 TTGAAGAA
1 TTGAAGAA
4143 AGATCACCCT
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
14 21 0.27
15 7 0.09
16 37 0.47
17 7 0.09
19 6 0.08
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.31
Consensus pattern (16 bp):
TTGAAGAATTGAAGTA
Found at i:4328 original size:8 final size:7
Alignment explanation
Indices: 4291--4453 Score: 52
Period size: 8 Copynumber: 22.3 Consensus size: 7
4281 GGAAGAAGTG
4291 AAATTGA
1 AAATTGA
4298 AACATTGA
1 AA-ATTGA
* *
4306 GATAGTG-
1 -AAATTGA
4313 AAATTGA
1 AAATTGA
4320 AACATTGA
1 AA-ATTGA
4328 AGAATTG-
1 A-AATTGA
4335 AAATTGA
1 AAATTGA
*
4342 AACGTTGA
1 AA-ATTGA
**
4350 TGGATTG-
1 -AAATTGA
*
4357 AATTTGA
1 AAATTGA
4364 AGAATTG-
1 A-AATTGA
4371 AAATTGA
1 AAATTGA
*
4378 AGCATTGA
1 A-AATTGA
4386 AAGATTG-
1 AA-ATTGA
*
4393 AATTTGA
1 AAATTGA
4400 AGAATTGA
1 A-AATTGA
4408 AAA-TGA
1 AAATTGA
** *
4414 GGCACTG-
1 -AAATTGA
4421 AAATTGA
1 AAATTGA
4428 AACATTGA
1 AA-ATTGA
4436 AGAATTGA
1 A-AATTGA
4444 AATATTGA
1 AA-ATTGA
4452 AA
1 AA
4454 TATACGAAGA
Statistics
Matches: 114, Mismatches: 21, Indels: 41
0.65 0.12 0.23
Matches are distributed among these distances:
6 26 0.23
7 19 0.17
8 66 0.58
9 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.28
Consensus pattern (7 bp):
AAATTGA
Found at i:4356 original size:22 final size:21
Alignment explanation
Indices: 4289--4514 Score: 105
Period size: 22 Copynumber: 10.5 Consensus size: 21
4279 CAGGAAGAAG
4289 TGAAATTGAAACATTGA-GAT
1 TGAAATTGAAACATTGAGGAT
*
4309 AGTGAAATTGAAACATTGAAGAAT
1 --TGAAATTGAAACATTG-AGGAT
*
4333 TGAAATTGAAACGTTGATGGAT
1 TGAAATTGAAACATTGA-GGAT
* *
4355 TGAATTTGAAGA-ATTGA-AAT
1 TGAAATTGAA-ACATTGAGGAT
*
4375 TGAAGCATTGAAAGATTGA--ATT
1 TGAA--ATTGAAACATTGAGGA-T
*
4397 TGAAGAATTGAAA-A-TGAGGCAC
1 TG-A-AATTGAAACATTGAGG-AT
*
4419 TGAAATTGAAACATTGAAGAAT
1 TGAAATTGAAACATTG-AGGAT
* *
4441 TGAAATATTGAAATA-T-ACGA-
1 TG-AA-ATTGAAACATTGAGGAT
* *
4461 AG-AATTGAAGCATTTGAAGGAT
1 TGAAATTGAAACA-TTG-AGGAT
*
4483 TGAAATTGAAACATTGAAGGTT
1 TGAAATTGAAACATTG-AGGAT
*
4505 TGAATTTGAA
1 TGAAATTGAA
4515 GAATTGAAAT
Statistics
Matches: 159, Mismatches: 21, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
17 7 0.04
18 1 0.01
19 1 0.01
20 18 0.11
21 11 0.07
22 92 0.58
23 18 0.11
24 11 0.07
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (21 bp):
TGAAATTGAAACATTGAGGAT
Found at i:4364 original size:36 final size:36
Alignment explanation
Indices: 4324--4546 Score: 200
Period size: 36 Copynumber: 6.0 Consensus size: 36
4314 AATTGAAACA
* *
4324 TTGAAGAATTGAAATTGAAACGTTGATGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* *
4360 TTGAAGAATTGAAATTGAAGCATTGAAAGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* ** * *
4396 TTGAAGAATTGAAAATGAGGCACTGAA--ATTGAAACA
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTG-AA-T
* * *
4432 TTGAAGAATTGAAATATTGAAATATACGAAGAATTGAAGCAT
1 TTGAAGAATTG-AA-ATTGAAACAT-TGAAGGATTG-A--AT
* *
4474 TTGAAGGATTGAAATTGAAACATTGAAGGTTTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* *
4510 TTGAAGAATTGAAATTG-AGCATTGAAGAATTGGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATT-GAAT
4546 T
1 T
4547 GAAACATTAA
Statistics
Matches: 153, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
34 4 0.03
35 13 0.08
36 90 0.59
37 2 0.01
38 6 0.04
39 10 0.07
40 9 0.06
41 8 0.05
42 10 0.07
43 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
Found at i:4470 original size:8 final size:8
Alignment explanation
Indices: 4360--4549 Score: 55
Period size: 8 Copynumber: 25.6 Consensus size: 8
4350 TGGATTGAAT
4360 TTGAAGAA
1 TTGAAGAA
4368 TTG-A-AA
1 TTGAAGAA
*
4374 TTGAAGCA
1 TTGAAGAA
4382 TTGAA-AGA
1 TTGAAGA-A
*
4390 TTG-A-AT
1 TTGAAGAA
4396 TTGAAGAA
1 TTGAAGAA
4404 TTGAA-AA
1 TTGAAGAA
* *
4411 -TGAGGCA
1 TTGAAGAA
*
4418 CTG-A-AA
1 TTGAAGAA
4424 TTGAA-ACA
1 TTGAAGA-A
4432 TTGAAGAA
1 TTGAAGAA
4440 TTGAA-ATA
1 TTGAAGA-A
4448 TTGAA-ATA
1 TTGAAGA-A
*
4456 TACGAAGAA
1 T-TGAAGAA
*
4465 TTGAAGCAT
1 TTGAAG-AA
*
4474 TTGAAGGA
1 TTGAAGAA
4482 TTG-A-AA
1 TTGAAGAA
4488 TTGAA-ACA
1 TTGAAGA-A
**
4496 TTGAAGGT
1 TTGAAGAA
*
4504 TTG-A-AT
1 TTGAAGAA
4510 TTGAAGAA
1 TTGAAGAA
4518 TTG-A-AA
1 TTGAAGAA
*
4524 TTG-AGCA
1 TTGAAGAA
4531 TTGAAGAA
1 TTGAAGAA
4539 TTG--GAA
1 TTGAAGAA
4545 TTGAA
1 TTGAA
4550 ACATTAAATA
Statistics
Matches: 138, Mismatches: 21, Indels: 46
0.67 0.10 0.22
Matches are distributed among these distances:
6 34 0.25
7 21 0.15
8 69 0.50
9 13 0.09
10 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (8 bp):
TTGAAGAA
Found at i:4643 original size:8 final size:8
Alignment explanation
Indices: 4630--4794 Score: 55
Period size: 8 Copynumber: 21.4 Consensus size: 8
4620 TCATTGAAGT
4630 GAATTGAA
1 GAATTGAA
4638 GAATTGAA
1 GAATTGAA
* *
4646 GCATT-TA
1 GAATTGAA
4653 GTAATTGAA
1 G-AATTGAA
*
4662 GAATTTAA
1 GAATTGAA
4670 GCAA-T-AA
1 G-AATTGAA
* *
4677 GTGATCGAA
1 G-AATTGAA
4686 GAATTGAA
1 GAATTGAA
4694 GGAA-T--A
1 -GAATTGAA
4700 -AATTGAA
1 GAATTGAA
*
4707 GTATTGAA
1 GAATTGAA
* *
4715 TAATTAAA
1 GAATTGAA
* *
4723 GAGTCGAA
1 GAATTGAA
4731 G-A--GATA
1 GAATTGA-A
4737 -AATTGAA
1 GAATTGAA
**
4744 TCATTGAA
1 GAATTGAA
4752 GAATTGAA
1 GAATTGAA
*
4760 AAATTGAA
1 GAATTGAA
* *
4768 TAATGGAA
1 GAATTGAA
*
4776 GCATTGAA
1 GAATTGAA
*
4784 TAATTGAA
1 GAATTGAA
4792 GAA
1 GAA
4795 AGAGATCATT
Statistics
Matches: 111, Mismatches: 31, Indels: 30
0.65 0.18 0.17
Matches are distributed among these distances:
4 2 0.02
5 3 0.03
6 3 0.03
7 8 0.07
8 85 0.77
9 10 0.09
ACGTcount: A:0.48, C:0.04, G:0.21, T:0.27
Consensus pattern (8 bp):
GAATTGAA
Found at i:4658 original size:24 final size:24
Alignment explanation
Indices: 4626--4700 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
4616 TGGGTCATTG
*
4626 AAGTGAATTGAAGAATTGAAGCATT
1 AAGT-AATTGAAGAATTGAAGCAAT
* *
4651 TAGTAATTGAAGAATTTAAGCAAT
1 AAGTAATTGAAGAATTGAAGCAAT
* * *
4675 AAGTGATCGAAGAATTGAAGGAAT
1 AAGTAATTGAAGAATTGAAGCAAT
4699 AA
1 AA
4701 ATTGAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 39 0.93
25 3 0.07
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.27
Consensus pattern (24 bp):
AAGTAATTGAAGAATTGAAGCAAT
Found at i:4792 original size:16 final size:16
Alignment explanation
Indices: 4737--4792 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
4727 CGAAGAGATA
* *
4737 AATTGAATCATTGAAG
1 AATTGAAGCATTGAAT
**
4753 AATTGAAAAATTGAAT
1 AATTGAAGCATTGAAT
*
4769 AATGGAAGCATTGAAT
1 AATTGAAGCATTGAAT
4785 AATTGAAG
1 AATTGAAG
4793 AAAGAGATCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.29
Consensus pattern (16 bp):
AATTGAAGCATTGAAT
Found at i:4840 original size:24 final size:24
Alignment explanation
Indices: 4737--4845 Score: 76
Period size: 24 Copynumber: 4.4 Consensus size: 24
4727 CGAAGAGATA
* * *
4737 AATTGAATCATTGAAGAATTGAAA
1 AATTGAAGCATTGAAGCATTGAAT
** *
4761 AATTGAATAATGGAAGCATTGAAT
1 AATTGAAGCATTGAAGCATTGAAT
** *
4785 AATTGAAG-AAAGAGATCATTTTGAGAT
1 AATTGAAGCATTGA-AGCA--TTGA-AT
*
4812 AAATTGAAGCATTGAAGGATTGAAT
1 -AATTGAAGCATTGAAGCATTGAAT
4837 AATTGAAGC
1 AATTGAAGC
4846 GAATTGAACA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
23 3 0.04
24 39 0.58
25 2 0.03
26 8 0.12
27 2 0.03
28 10 0.15
29 3 0.04
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (24 bp):
AATTGAAGCATTGAAGCATTGAAT
Found at i:6149 original size:16 final size:16
Alignment explanation
Indices: 6119--6148 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6109 TACTTTTCAA
6119 TTTCTTTTCTTTTTTC
1 TTTCTTTTCTTTTTTC
6135 TTTC-TTTCTTTTTT
1 TTTCTTTTCTTTTTT
6149 TTCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTCTTTTTTC
Found at i:6509 original size:13 final size:13
Alignment explanation
Indices: 6493--6527 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6483 TCAATTTTTT
*
6493 TTTTGAAAGACAC
1 TTTTGAAAAACAC
*
6506 TTTTGAAAAACAT
1 TTTTGAAAAACAC
6519 TTTTGAAAA
1 TTTTGAAAA
6528 TCATGACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTTGAAAAACAC
Found at i:6548 original size:32 final size:33
Alignment explanation
Indices: 6505--6569 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
6495 TTGAAAGACA
6505 CTTTTGAAAAACATTTTTGAAAATCATGACTCT
1 CTTTTGAAAAACATTTTTGAAAATCATGACTCT
6538 CTTTT-AAAAACATTTTTGAAAATCATGACTCT
1 CTTTTGAAAAACATTTTTGAAAATCATGACTCT
6570 ACTTATTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.84
33 5 0.16
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (33 bp):
CTTTTGAAAAACATTTTTGAAAATCATGACTCT
Found at i:12003 original size:2 final size:2
Alignment explanation
Indices: 11996--12035 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
11986 TCTATTCAAC
* *
11996 AT AT AT AT AT AT AT AT AT AT AT AT GT CT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12036 ACAATTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14710 original size:21 final size:21
Alignment explanation
Indices: 14686--14725 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14676 GAGGTGACCA
14686 CTCAA-ATAATGGAGTCAAATG
1 CTCAACATAA-GGAGTCAAATG
*
14707 CTCAACTTAAGGAGTCAAA
1 CTCAACATAAGGAGTCAAA
14726 CGACTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
CTCAACATAAGGAGTCAAATG
Found at i:14750 original size:20 final size:21
Alignment explanation
Indices: 14711--14750 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
14701 CAAATGCTCA
*
14711 ACTTAAGGAGTCAAACGACTT
1 ACTTAAAGAGTCAAACGACTT
*
14732 ACTTAAAGAG-CAAATGACT
1 ACTTAAAGAGTCAAACGACT
14751 CAAGATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
ACTTAAAGAGTCAAACGACTT
Found at i:18215 original size:156 final size:154
Alignment explanation
Indices: 17744--18280 Score: 497
Period size: 155 Copynumber: 3.5 Consensus size: 154
17734 AGGACAAATG
* * *
17744 GACTTA-AGATGAAAAACTTATGCTAGTTTTTCATTTAGGGACATTTTGGGGT-TAGAAACC-AC
1 GACTTAGA-ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGT-GAAACCTAG
* * * * * *
17806 TTCACCATGATAG-GGAG-TTGAGTTTAACTTAGAATTTTTTCCATAAGT-TTTTGGAGATAATC
64 TTCACCATCA-AGAGAAGCTCG-GTTTGACTTAGAATTTTTTCCAT-AGTCTTATGGAAATAATC
** * ** * **
17868 TAAGTTTCT-TGGCCAAGTTTCACCTCAAACA
126 TAAGCCTATGTGG--AAAATT-AACTCATTCA
* * ** ** *
17899 GACTTAGAATGAAAAACTTATGCTGGTTTTTCAGTTAAGGACAATTTGACGTGTGAAGTC-GGTT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTT
* * *
17963 CACTACCAAGGGAAGCTCGGTTTGACTTAGAATTTTTTCCATAGTCTTATGGAAATAATCTAAGC
66 CACCATCAAGAGAAGCTCGGTTTGACTTAGAATTTTTTCCATAGTCTTATGGAAATAATCTAAGC
*
18028 CTACTGGTGGAAAATTAGCTCATTCA
131 CTA-T-GTGGAAAATTAACTCATTCA
**
18054 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGTG-GAAACCTAGT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAA-TTTGGGGTGTGAAACCTAGT
* * * *
18118 TCACCATCAACGAG-AGCTCTGTTTTACTTAGAATTTTTTCCATAGTCTTATGTG-TATATTCTA
65 TCACCATCAA-GAGAAGCTCGGTTTGACTTAGAATTTTTTCCATAGTCTTATG-GAAATAATCTA
*
18181 AGTCCT-T-TGGAAAAATTTCAACTCGTTCA
128 AG-CCTATGTGG-AAAA-TT-AACTCATTCA
* *
18210 TACTTAGAATAAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTT
18275 CACCAT
66 CACCAT
18281 GAATTGAGGG
Statistics
Matches: 317, Mismatches: 48, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
153 3 0.01
154 9 0.03
155 160 0.50
156 136 0.43
157 6 0.02
158 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (154 bp):
GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAGTT
CACCATCAAGAGAAGCTCGGTTTGACTTAGAATTTTTTCCATAGTCTTATGGAAATAATCTAAGC
CTATGTGGAAAATTAACTCATTCA
Found at i:21277 original size:38 final size:38
Alignment explanation
Indices: 21226--21305 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
21216 CGTGGAAGTG
21226 AAGACTAATATATCAAAAAAGAAGATGAAACTTTTATT
1 AAGACTAATATATCAAAAAAGAAGATGAAACTTTTATT
*
21264 AAGACTAGTATATCAAAAAAGAAGATGAAACTTTTATT
1 AAGACTAATATATCAAAAAAGAAGATGAAACTTTTATT
21302 AAGA
1 AAGA
21306 AAAGAGAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (38 bp):
AAGACTAATATATCAAAAAAGAAGATGAAACTTTTATT
Found at i:22001 original size:15 final size:16
Alignment explanation
Indices: 21981--22018 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
21971 TGTGTAAGTG
21981 ACCCGAACCTG-ATTA
1 ACCCGAACCTGAATTA
*
21996 ACCCGAA-TTGAATTA
1 ACCCGAACCTGAATTA
22011 ACCCGAAC
1 ACCCGAAC
22019 TCAATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (16 bp):
ACCCGAACCTGAATTA
Done.