Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011454.1 Corchorus capsularis cultivar CVL-1 contig11475, 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: 34102
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:38 original size:19 final size:19
Alignment explanation
Indices: 3--50 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1 TA
3 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
23 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
*
42 ATCTAAATT
1 ATCAAAATT
51 TCATATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:71 original size:22 final size:22
Alignment explanation
Indices: 41--602 Score: 182
Period size: 22 Copynumber: 25.7 Consensus size: 22
31 TCAGGGAGGA
*
41 TATCTAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
63 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
85 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
107 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
128 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
151 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
173 TATCAAAAAATTCATAGGGAGGT
1 TATC-AAAATTTCATATGAAGGT
*
196 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
212 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
234 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
257 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
280 TATCAAAATTTCATA-GCTAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
302 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
324 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
346 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
368 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
390 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
412 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
435 CATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
457 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
479 CT-TCAAAATTCCTTAGGGAA-GT
1 -TATCAAAATTTCATA-TGAAGGT
* * *
501 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * * *
523 TAAAAAAAATT-ATA-AAATGAT
1 TATCAAAATTTCATATGAA-GGT
* * **
544 TCTCAAAATTCCATA-GTATTGT
1 TATCAAAATTTCATATG-AAGGT
*
566 TATTC-AAATTTCATAGGAAGGT
1 TA-TCAAAATTTCATATGAAGGT
588 TATCAAAATTTCATA
1 TATCAAAATTTCATA
603 ATGGGATCAT
Statistics
Matches: 402, Mismatches: 97, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 4 0.01
21 30 0.07
22 266 0.66
23 87 0.22
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:186 original size:23 final size:23
Alignment explanation
Indices: 133--203 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
123 TATGTAGATC
* * *
133 AAAATTTCATAGGGAGATTAAC-
1 AAAAATTCATAAGGAGATTATCA
* *
155 AAAATTTCATAATGAGATTATCA
1 AAAAATTCATAAGGAGATTATCA
* *
178 AAAAATTCATAGGGAGGTTATCA
1 AAAAATTCATAAGGAGATTATCA
201 AAA
1 AAA
204 TTTGTAGTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.28
Consensus pattern (23 bp):
AAAAATTCATAAGGAGATTATCA
Found at i:2574 original size:2 final size:2
Alignment explanation
Indices: 2560--2601 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2550 AATTAAATAC
*
2560 TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2601 T
1 T
2602 TAGAAGGTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3774 original size:2 final size:2
Alignment explanation
Indices: 3767--3798 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3757 GCTGTGTATC
*
3767 TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3799 CTCCCTCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4224 original size:51 final size:49
Alignment explanation
Indices: 4151--4263 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 49
4141 TAATTCATAA
4151 AAAAAATAAATAAATATAATAAATCACATATTAATTTGTAATCATAAATCAT
1 AAAAAATAAATAAATATAATAAATCACATATTAATTTGTAA-CAT-AAT-AT
* *
4203 AAAAAA-AAATTAATATGATAAATCACATATTAATTTGTAACATAATAT
1 AAAAAATAAATAAATATAATAAATCACATATTAATTTGTAACATAATAT
4251 -AAAAATAATATAA
1 AAAAAATAA-ATAA
4264 TTTTTCGTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
47 5 0.09
48 4 0.07
49 6 0.11
50 3 0.05
51 32 0.57
52 6 0.11
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (49 bp):
AAAAAATAAATAAATATAATAAATCACATATTAATTTGTAACATAATAT
Found at i:7021 original size:27 final size:27
Alignment explanation
Indices: 6991--7072 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
6981 TACCAAAATA
*
6991 TTATGAGATTAGAGGAAATCATAACAC
1 TTATGAGATTAGAGCAAATCATAACAC
* * *
7018 TTATGA-ATTTGA-TACAA--A-AATA-
1 TTATGAGATTAGAGCA-AATCATAACAC
*
7040 TTATGAGATTAAAGCAAATCATAACAC
1 TTATGAGATTAGAGCAAATCATAACAC
7067 TTATGA
1 TTATGA
7073 ATTTAATACA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 6 0.15
23 9 0.22
24 2 0.05
25 2 0.05
26 10 0.24
27 12 0.29
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (27 bp):
TTATGAGATTAGAGCAAATCATAACAC
Found at i:7046 original size:49 final size:49
Alignment explanation
Indices: 6974--7116 Score: 241
Period size: 49 Copynumber: 2.9 Consensus size: 49
6964 TATCAACGTT
* *
6974 AATTTAATACCAAAATATTATGAGATTAGAGGAAATCATAACACTTATG
1 AATTTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTTATG
* *
7023 AATTTGATACAAAAATATTATGAGATTAAAGCAAATCATAACACTTATG
1 AATTTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTTATG
*
7072 AATTTAATACAAAAATATTATGAAATTAGAGCAAATCATAACACT
1 AATTTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACT
7117 CATAAATCAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 87 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (49 bp):
AATTTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTTATG
Found at i:7084 original size:27 final size:27
Alignment explanation
Indices: 7006--7084 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
6996 AGATTAGAGG
*
7006 AAATCATAACACTTATGAATTTGATAC
1 AAATCATAACACTTATGAATTTAATAC
*
7033 -AA--A-AATA-TTATGAGA-TTAA-AGC
1 AAATCATAACACTTATGA-ATTTAATA-C
7055 AAATCATAACACTTATGAATTTAATAC
1 AAATCATAACACTTATGAATTTAATAC
7082 AAA
1 AAA
7085 AATATTATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 18
0.66 0.05 0.30
Matches are distributed among these distances:
21 1 0.03
22 10 0.25
23 6 0.15
24 1 0.03
25 1 0.03
26 6 0.15
27 14 0.35
28 1 0.03
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATCATAACACTTATGAATTTAATAC
Found at i:7095 original size:22 final size:22
Alignment explanation
Indices: 7018--7095 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 22
7008 ATCATAACAC
*
7018 TTATGAATTTGATACAAAAATA
1 TTATGAATTTAATACAAAAATA
*
7040 TTATGAGA-TTAA-AGCAAATCATAACA
1 TTATGA-ATTTAATA-C-AA--A-AATA
7066 CTTATGAATTTAATACAAAAATA
1 -TTATGAATTTAATACAAAAATA
7089 TTATGAA
1 TTATGAA
7096 ATTAGAGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 18
0.68 0.05 0.28
Matches are distributed among these distances:
21 1 0.02
22 17 0.39
23 6 0.14
24 1 0.02
25 1 0.02
26 6 0.14
27 11 0.25
28 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (22 bp):
TTATGAATTTAATACAAAAATA
Found at i:10604 original size:22 final size:21
Alignment explanation
Indices: 10566--10607 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10556 AAATCTATCC
10566 TTCTATTCATCATTCATCAAG
1 TTCTATTCATCATTCATCAAG
10587 TTCTAGTTCCATC-TTCATCAA
1 TTCTA-TT-CATCATTCATCAA
10608 TATCACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.43
Consensus pattern (21 bp):
TTCTATTCATCATTCATCAAG
Found at i:12720 original size:11 final size:10
Alignment explanation
Indices: 12699--12739 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
12689 ATGAAATTCC
12699 TTTTTTGATT
1 TTTTTTGATT
12709 TTTTTTGA--
1 TTTTTTGATT
*
12717 ATTTTTGATT
1 TTTTTTGATT
*
12727 TTTTTGGATT
1 TTTTTTGATT
12737 TTT
1 TTT
12740 GGAAAACCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.27
10 19 0.73
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (10 bp):
TTTTTTGATT
Found at i:12728 original size:17 final size:18
Alignment explanation
Indices: 12700--12740 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
12690 TGAAATTCCT
12700 TTTTTGATTTTTTTTGAA
1 TTTTTGATTTTTTTTGAA
*
12718 TTTTTGA-TTTTTTTGGA
1 TTTTTGATTTTTTTTGAA
12735 TTTTTG
1 TTTTTG
12741 GAAAACCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (18 bp):
TTTTTGATTTTTTTTGAA
Found at i:13261 original size:16 final size:15
Alignment explanation
Indices: 13235--13265 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
13225 CTTATCATAA
13235 CACTAAAGCCCAAAT
1 CACTAAAGCCCAAAT
13250 CACTAGAAGCCCAAAT
1 CACTA-AAGCCCAAAT
13266 AAGTAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.32, G:0.10, T:0.13
Consensus pattern (15 bp):
CACTAAAGCCCAAAT
Found at i:13772 original size:16 final size:16
Alignment explanation
Indices: 13632--13780 Score: 169
Period size: 16 Copynumber: 9.4 Consensus size: 16
13622 TGTAGTTTTT
* *
13632 TCGGGTCATTTGGGTT
1 TCGGGTCATTCGGGTC
*
13648 TCAGGTCA-TCTGGGT-
1 TCGGGTCATTC-GGGTC
*
13663 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
*
13679 TCGGGTCGTTCGGGTC
1 TCGGGTCATTCGGGTC
* *
13695 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
13711 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
*
13727 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
*
13743 TCGGGTCATTCGGGTG
1 TCGGGTCATTCGGGTC
*
13759 TCGGGTC-TACCGGGTC
1 TCGGGTCAT-TCGGGTC
13775 TCGGGT
1 TCGGGT
13781 TGGGCGGGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.11
16 102 0.89
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:14252 original size:21 final size:21
Alignment explanation
Indices: 14227--14274 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
14217 TAGCTAATTT
14227 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
14248 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
14269 ATAATA
1 ATAATA
14275 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:14403 original size:16 final size:16
Alignment explanation
Indices: 14382--14491 Score: 89
Period size: 16 Copynumber: 6.9 Consensus size: 16
14372 GGTTAATGTC
*
14382 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
14398 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
* *
14414 ACGGGTCATTCAGGTT
1 TCGGGTCATTCGGGTT
* *
14430 TCGGATCA-TCTGGTT
1 TCGGGTCATTCGGGTT
* * *
14445 ACCGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
14461 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
14477 GCGGGTCATTGGGGT
1 TCGGGTCATTCGGGT
14492 CACAGGTTCA
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
15 13 0.18
16 57 0.80
17 1 0.01
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:14455 original size:31 final size:31
Alignment explanation
Indices: 14389--14473 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
14379 GTCTCGGGTT
* *
14389 ATTCGGGTTTCGGGTCATACGGGTCACGGGTC
1 ATTCGGGTTTCGGGTCAT-CTGGTCACCGGTC
* * *
14421 ATTCAGGTTTCGGATCATCTGGTTACCGGTC
1 ATTCGGGTTTCGGGTCATCTGGTCACCGGTC
*
14452 ATTCGGGTCTCGGGTCATCTGG
1 ATTCGGGTTTCGGGTCATCTGG
14474 GTTGCGGGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 29 0.64
32 16 0.36
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.32
Consensus pattern (31 bp):
ATTCGGGTTTCGGGTCATCTGGTCACCGGTC
Found at i:14492 original size:32 final size:32
Alignment explanation
Indices: 14383--14492 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 32
14373 GTTAATGTCT
* * *
14383 CGGGTTATTCGGGTTTCGGGTCATAC-GGGTCA
1 CGGGTCATTCGGGTCTCGGGTCAT-CTGGGTTA
* * *
14415 CGGGTCATTCAGGTTTCGGATCATCT-GGTTA
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
* *
14446 CCGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
*
14478 CGGGTCATTGGGGTC
1 CGGGTCATTCGGGTC
14493 ACAGGTTCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 27 0.42
32 38 0.58
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (32 bp):
CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
Found at i:14514 original size:32 final size:32
Alignment explanation
Indices: 14383--14515 Score: 85
Period size: 32 Copynumber: 4.2 Consensus size: 32
14373 GTTAATGTCT
* ** **
14383 CGGGTTATTCGGGTTTCGGGTCATAC-GGGTCA
1 CGGGTCATTCGGGTCACGGGTCAT-CTGGGTTG
* ** * *
14415 CGGGTCATTCAGGTTTCGGATCATCT-GGTTA
1 CGGGTCATTCGGGTCACGGGTCATCTGGGTTG
* *
14446 CCGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCACGGGTCATCTGGGTTG
* *
14478 CGGGTCATTGGGGTCACAGGTTCATC-GGGTCT-
1 CGGGTCATTCGGGTCAC-GGGTCATCTGGGT-TG
14510 CGGGTC
1 CGGGTC
14516 GGGCGGGTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
31 27 0.32
32 49 0.58
33 8 0.10
ACGTcount: A:0.11, C:0.22, G:0.36, T:0.31
Consensus pattern (32 bp):
CGGGTCATTCGGGTCACGGGTCATCTGGGTTG
Found at i:14591 original size:18 final size:18
Alignment explanation
Indices: 14550--14593 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
14540 TTCTGGTCAA
*
14550 ATCGGGTT-GGACGGGTT
1 ATCGGGTTCGAACGGGTT
14567 A-CGGGTTCGAACGGGTT
1 ATCGGGTTCGAACGGGTT
14584 ATCGGGTTCG
1 ATCGGGTTCG
14594 GGTCAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 10 0.42
18 8 0.33
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
ATCGGGTTCGAACGGGTT
Found at i:16325 original size:28 final size:29
Alignment explanation
Indices: 16292--16359 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
16282 TTGCAAGGAA
*
16292 TGGAGAAAAGAATGT-AAAATGAAGGTAG
1 TGGAGAAAAGAATGTGAAAAGGAAGGTAG
*
16320 TGGAGAAAAGAATGTGAAAGGGAAGGTAG
1 TGGAGAAAAGAATGTGAAAAGGAAGGTAG
*
16349 TGGAGAGAAGA
1 TGGAGAAAAGA
16360 CGCGAAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.47, C:0.00, G:0.38, T:0.15
Consensus pattern (29 bp):
TGGAGAAAAGAATGTGAAAAGGAAGGTAG
Found at i:16512 original size:29 final size:30
Alignment explanation
Indices: 16480--16536 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
16470 ACACCATGAA
16480 TTGGGAAATAA-TTTTAAAAGTATAATAAT
1 TTGGGAAATAAGTTTTAAAAGTATAATAAT
*
16509 TTGGGAAATAAGTTTTCAAAGTATAATA
1 TTGGGAAATAAGTTTTAAAAGTATAATA
16537 CTTAGGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.37
Consensus pattern (30 bp):
TTGGGAAATAAGTTTTAAAAGTATAATAAT
Found at i:18050 original size:16 final size:16
Alignment explanation
Indices: 18031--18086 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
18021 GAACCTGAAT
18031 CCGAAAAAACCCGAAC
1 CCGAAAAAACCCGAAC
*** *
18047 CCGAAAAAGTTCAAAC
1 CCGAAAAAACCCGAAC
* *
18063 TCGAAAAAACCCGAAT
1 CCGAAAAAACCCGAAC
18079 CCGAAAAA
1 CCGAAAAA
18087 TTATGAAAAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (16 bp):
CCGAAAAAACCCGAAC
Found at i:18284 original size:17 final size:16
Alignment explanation
Indices: 18226--18291 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
18216 CAAAACCCAA
*
18226 ATTCAACCCGAATCCG
1 ATTCAACCCGAACCCG
* *
18242 AATT-AA-CCTAACCCAA
1 -ATTCAACCCGAACCC-G
18258 ATTCAACCCGAACCCG
1 ATTCAACCCGAACCCG
18274 ATTCAAGCCCGAACCCG
1 ATTCAA-CCCGAACCCG
18291 A
1 A
18292 AAATGGCCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
15 9 0.22
16 10 0.25
17 21 0.52
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (16 bp):
ATTCAACCCGAACCCG
Found at i:18986 original size:24 final size:25
Alignment explanation
Indices: 18959--19006 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
18949 TTGGATGCTG
*
18959 AATTTAGGGCTAAAGAAA-ATAGTA
1 AATTTAGGGCAAAAGAAAGATAGTA
* *
18983 AATTTGGGGGAAAAGAAAGATAGT
1 AATTTAGGGCAAAAGAAAGATAGT
19007 TCAAAGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.23
Consensus pattern (25 bp):
AATTTAGGGCAAAAGAAAGATAGTA
Found at i:29260 original size:33 final size:33
Alignment explanation
Indices: 29193--29308 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
29183 TTCTCGTCAC
29193 CCAAAACA-GATTTATTTTCAATGC--T-ATCAA
1 CCAAAACAGGA-TTATTTTCAATGCTATGATCAA
*
29223 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGGATTATTTTCAATGCTATGATCAA
* ** * *
29256 CCAAAATAAAATTATTTTTAATGCTATGTTCAA
1 CCAAAACAGGATTATTTTCAATGCTATGATCAA
* *
29289 CCAAAACAGAATTGTTTTCA
1 CCAAAACAGGATTATTTTCA
29309 TCACAATTAG
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
30 20 0.28
31 2 0.03
32 1 0.01
33 48 0.68
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (33 bp):
CCAAAACAGGATTATTTTCAATGCTATGATCAA
Found at i:29369 original size:33 final size:33
Alignment explanation
Indices: 29344--29452 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
29334 TAGTTTTATT
29344 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
** * * *
29377 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC
*
29410 GCAAACAACACTAAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
29443 GCAAACAACA
1 GCAAACAACA
29453 TCTAAAACAC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.95
34 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (33 bp):
GCAAACAACACTCAAATTAGGTTTAGTATCATC
Found at i:29401 original size:66 final size:66
Alignment explanation
Indices: 29319--29461 Score: 250
Period size: 66 Copynumber: 2.2 Consensus size: 66
29309 TCACAATTAG
* * * *
29319 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
29384 A
66 A
29385 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
1 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
29450 A
66 A
29451 CATCTAAAACA
1 CATCTAAAACA
29462 CTCTTTTCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (66 bp):
CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
A
Done.