Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014259.1 Corchorus capsularis cultivar CVL-1 contig14280, 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: 60497
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5767 original size:14 final size:14
Alignment explanation
Indices: 5744--5777 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5734 TTAGGAGCTA
5744 GGTTTAGAGATTAG
1 GGTTTAGAGATTAG
* *
5758 GGTTTTGAGATTGG
1 GGTTTAGAGATTAG
5772 GGTTTA
1 GGTTTA
5778 AATGAGAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
GGTTTAGAGATTAG
Found at i:8636 original size:85 final size:85
Alignment explanation
Indices: 8516--8688 Score: 321
Period size: 85 Copynumber: 2.0 Consensus size: 85
8506 TTCAGCAAGC
8516 ACCGTCTTCAAAAACAATTAACAGGGTCTATAAAAAACGCACTTAGTATGTTAATAATTTCAGAA
1 ACCGTCTTCAAAAACAATTAACAGGGTCTATAAAAAACGCACTTAGTATGTTAATAATTTCAGAA
*
8581 AATGCAATTTACTC-TAATA
66 AATGCAATTTACTCAAAATA
8600 ACCGTCTTCAAAAAACAATTAACAGGGTCTATAAAAAACGCACTTAGTATGTTAATAATTTCAGA
1 ACCGTCTTC-AAAAACAATTAACAGGGTCTATAAAAAACGCACTTAGTATGTTAATAATTTCAGA
8665 AAATGCAATTTACTCAAAATA
65 AAATGCAATTTACTCAAAATA
8686 ACC
1 ACC
8689 CAACACACCC
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
84 9 0.10
85 70 0.81
86 7 0.08
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.28
Consensus pattern (85 bp):
ACCGTCTTCAAAAACAATTAACAGGGTCTATAAAAAACGCACTTAGTATGTTAATAATTTCAGAA
AATGCAATTTACTCAAAATA
Found at i:11744 original size:31 final size:32
Alignment explanation
Indices: 11700--11768 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
11690 CATGGCCTTA
*
11700 CCACATGGCA-TTTTGGTCCGACGTGGCAATG
1 CCACGTGGCATTTTTGGTCCGACGTGGCAATG
* * *
11731 CCACGTGGTATTTTTGGTCTGACGTGGCATTG
1 CCACGTGGCATTTTTGGTCCGACGTGGCAATG
11763 CCACGT
1 CCACGT
11769 CAGCAATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (32 bp):
CCACGTGGCATTTTTGGTCCGACGTGGCAATG
Found at i:11877 original size:31 final size:29
Alignment explanation
Indices: 11804--11877 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 29
11794 AAATGGTTCC
*
11804 AAATTGCAAGTTTAGAGGCAAAACATCCA
1 AAATTACAAGTTTAGAGGCAAAACATCCA
*
11833 AAATTA-AAGTTTAGAGGACAAAAC-TTCA
1 AAATTACAAGTTTAGAGG-CAAAACATCCA
11861 AAATCATACAAGTTTAG
1 AAAT--TACAAGTTTAG
11878 GAGACAGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 18 0.46
29 11 0.28
30 2 0.05
31 8 0.21
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AAATTACAAGTTTAGAGGCAAAACATCCA
Found at i:14979 original size:22 final size:22
Alignment explanation
Indices: 14949--15024 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
14939 TAACTTGATC
* *
14949 CTATGAAATTTTGGTAATCATA
1 CTATGAAATTTTGGTAACCACA
*
14971 CTATAAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
14993 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACA
15014 CTCATGAAATT
1 CT-ATGAAATT
15025 ACAATAACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:15053 original size:22 final size:23
Alignment explanation
Indices: 14954--15056 Score: 70
Period size: 22 Copynumber: 4.7 Consensus size: 23
14944 TGATCCTATG
* *
14954 AAATTTTGGTAATCATAC-TATA
1 AAATTTTGATAACCATACTTATA
* * *
14976 AAATTTTGGTAACCACAC-TATG
1 AAATTTTGATAACCATACTTATA
* * * *
14998 GAATTTTGATAACC-TCCTCATG
1 AAATTTTGATAACCATACTTATA
***
15020 AAATTACAATAACCAT-CTTATA
1 AAATTTTGATAACCATACTTATA
15042 AAATTTTGATAACCA
1 AAATTTTGATAACCA
15057 CATAGAGACA
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 1 0.02
22 60 0.97
23 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
AAATTTTGATAACCATACTTATA
Found at i:15246 original size:19 final size:20
Alignment explanation
Indices: 15222--15259 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15212 TATTGACATT
15222 TAAAAT-TTGAAATT-AAAAG
1 TAAAATATT-AAATTCAAAAG
15241 TAAAATATTAAATTCAAAA
1 TAAAATATTAAATTCAAAA
15260 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAATATTAAATTCAAAAG
Found at i:15464 original size:37 final size:36
Alignment explanation
Indices: 15389--15465 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
15379 AATTTAAGAC
*
15389 CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
1 CAAAGACAAAGAAAAATTAAATACAACGATTGGAAA
**
15425 CAAAGACAAAAGAATAAATTAAATAGGACG-TTGGAAA
1 CAAAGAC-AAAGAA-AAATTAAATACAACGATTGGAAA
15462 CAAA
1 CAAA
15466 AAGTCAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.19
37 16 0.44
38 13 0.36
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (36 bp):
CAAAGACAAAGAAAAATTAAATACAACGATTGGAAA
Found at i:17229 original size:1 final size:1
Alignment explanation
Indices: 17223--17256 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
17213 AAGAATACTC
17223 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17257 CCTATTTCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19635 original size:19 final size:20
Alignment explanation
Indices: 19589--19636 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
19579 TGTGGCACGC
*
19589 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
19611 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
19630 CACATGT
1 CACATGT
19637 CACGCCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:19641 original size:53 final size:53
Alignment explanation
Indices: 19556--19658 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
19546 GACGTGGCAC
* **
19556 GCCACATGTACCAAAAAGTGATATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
*
19609 GCCACATGTACCAAAAAGTGACACATGTCACGCCACATGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
19659 GACACGTGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:19697 original size:30 final size:31
Alignment explanation
Indices: 19608--19705 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 31
19598 CAAAAAGTCG
* *
19608 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
*
19639 CGCCACATGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
19670 TGCCACATGTTTCAAAAA-TGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
19700 TGCCAC
1 TGCCAC
19706 GTGCATAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 17 0.28
31 43 0.72
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:24281 original size:24 final size:24
Alignment explanation
Indices: 24254--24303 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
24244 AAATGATAAA
24254 ATATACTACAAATTAAGAACTTCT
1 ATATACTACAAATTAAGAACTTCT
24278 ATATACTACAAATTAAGAACTTCT
1 ATATACTACAAATTAAGAACTTCT
24302 AT
1 AT
24304 GTGCAGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATACTACAAATTAAGAACTTCT
Found at i:27327 original size:2 final size:2
Alignment explanation
Indices: 27311--27348 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
27301 TGGCTTTGCC
*
27311 AT AT AT GAT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27349 GACTGCAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30846 original size:31 final size:31
Alignment explanation
Indices: 30811--30918 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
30801 AATGGCTAAT
30811 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
** * **
30842 TGCTCAAATAAGGGCCCGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
* *
30871 TGGTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
30902 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
30919 GTCTCACGCG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
29 23 0.37
31 39 0.63
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
Found at i:31023 original size:60 final size:60
Alignment explanation
Indices: 30946--31077 Score: 203
Period size: 60 Copynumber: 2.2 Consensus size: 60
30936 AACTGACACC
* **
30946 AGGCCCTTATTTGGCCAAATTAAAAGATCGAACCCTTATTTGAGCATTTTCG-ATAATGTT
1 AGGCCCTTATTTAGCCAAATTAAAAGATCGAACCCTTATTTGAGCATTTTCGCA-AACATT
* *
31006 AGGCCCTTATTTAGCCAAATTAAAAGATCGAGCCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTAGCCAAATTAAAAGATCGAACCCTTATTTGAGCATTTTCGCAAACATT
31066 AGGCCCTTATTT
1 AGGCCCTTATTT
31078 GAGCAATTAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 65 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
AGGCCCTTATTTAGCCAAATTAAAAGATCGAACCCTTATTTGAGCATTTTCGCAAACATT
Found at i:31045 original size:29 final size:29
Alignment explanation
Indices: 30948--31046 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
30938 CTGACACCAG
*
30948 GCCCTTATTTGGCCAAATTAAAAGATCGA
1 GCCCTTATTTAGCCAAATTAAAAGATCGA
* ** * * *
30977 ACCCTTATTTGAG-CATTTTCGATAATGTTAG-
1 GCCCTTATTT-AGCCAAATT--A-AAAGATCGA
31008 GCCCTTATTTAGCCAAATTAAAAGATCGA
1 GCCCTTATTTAGCCAAATTAAAAGATCGA
31037 GCCCTTATTT
1 GCCCTTATTT
31047 GAGCATTTTG
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
28 5 0.10
29 24 0.47
30 3 0.06
31 14 0.27
32 5 0.10
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (29 bp):
GCCCTTATTTAGCCAAATTAAAAGATCGA
Found at i:34124 original size:31 final size:29
Alignment explanation
Indices: 34056--34191 Score: 151
Period size: 31 Copynumber: 4.8 Consensus size: 29
34046 TGCCACGTGC
34056 CACTTTTTGGTACACGTGGCGTGACATGT
1 CACTTTTTGGTACACGTGGCGTGACATGT
*
34085 CACATTTTGGTACACGTGGCGTGACATGTGT
1 CACTTTTTGGTACACGTGGCGTGACA--TGT
*
34116 CACTTTTTGGTACATGTGGC---AC--G-
1 CACTTTTTGGTACACGTGGCGTGACATGT
*
34139 -ACTTTTTGGTACATGTGGCGTGCCACATGT
1 CACTTTTTGGTACACGTGGCGTG--ACATGT
*
34169 CACTTTTTTGTACACGTGGCGTG
1 CACTTTTTGGTACACGTGGCGTG
34192 CCACGTCGGA
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
22 19 0.21
24 1 0.01
27 2 0.02
28 2 0.02
29 26 0.29
31 41 0.45
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (29 bp):
CACTTTTTGGTACACGTGGCGTGACATGT
Found at i:38165 original size:32 final size:33
Alignment explanation
Indices: 38129--38199 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
38119 ATTTTTAGGT
38129 TCAGGTTTAAGTCAGG-TCAAGTTGAATTTGGG
1 TCAGGTTTAAGTCAGGTTCAAGTTGAATTTGGG
* * * **
38161 TCAGG-CTAATTCGGGTTCGGGTTGAATTTGGG
1 TCAGGTTTAAGTCAGGTTCAAGTTGAATTTGGG
38193 TCAGGTT
1 TCAGGTT
38200 AATTAGGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.35
Consensus pattern (33 bp):
TCAGGTTTAAGTCAGGTTCAAGTTGAATTTGGG
Found at i:38176 original size:15 final size:15
Alignment explanation
Indices: 38143--38208 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
38133 GTTTAAGTCA
*
38143 GGTCAAGTTGAATTTG
1 GGTCAGGTT-AATTTG
* *
38159 GGTCAGGCTAATTCG
1 GGTCAGGTTAATTTG
*
38174 GGTTCGGGTTGAATTTG
1 GG-TCAGGTT-AATTTG
*
38191 GGTCAGGTTAATTAG
1 GGTCAGGTTAATTTG
38206 GGT
1 GGT
38209 TCGGGTTTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
15 15 0.38
16 18 0.45
17 7 0.17
ACGTcount: A:0.20, C:0.09, G:0.36, T:0.35
Consensus pattern (15 bp):
GGTCAGGTTAATTTG
Found at i:38203 original size:32 final size:32
Alignment explanation
Indices: 38149--38225 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
38139 GTCAGGTCAA
*
38149 GTTGAATTTGGGTCAGGCTAATTCGGGTTCGG
1 GTTGAATTTGGGTCAGGCTAATTAGGGTTCGG
*
38181 GTTGAATTTGGGTCAGGTTAATTAGGGTTCGG
1 GTTGAATTTGGGTCAGGCTAATTAGGGTTCGG
* *
38213 GTTTAGTTTGGGT
1 GTTGAATTTGGGT
38226 TTTGACCAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.16, C:0.08, G:0.38, T:0.39
Consensus pattern (32 bp):
GTTGAATTTGGGTCAGGCTAATTAGGGTTCGG
Found at i:38215 original size:16 final size:16
Alignment explanation
Indices: 38167--38215 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
38157 TGGGTCAGGC
*
38167 TAATTCGGGTTCGGGT
1 TAATTAGGGTTCGGGT
* *
38183 TGAATTTGGG-TCAGGT
1 T-AATTAGGGTTCGGGT
38199 TAATTAGGGTTCGGGT
1 TAATTAGGGTTCGGGT
38215 T
1 T
38216 TAGTTTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.26
16 13 0.48
17 7 0.26
ACGTcount: A:0.16, C:0.08, G:0.37, T:0.39
Consensus pattern (16 bp):
TAATTAGGGTTCGGGT
Found at i:38403 original size:16 final size:17
Alignment explanation
Indices: 38384--38427 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
38374 GGGTTAAGGT
38384 TTTTTCGGGTTCTGA-A
1 TTTTTCGGGTTCTGAGA
*
38400 TTTTTTGGGTT-TGAGA
1 TTTTTCGGGTTCTGAGA
38416 TTTTTCGGGTTC
1 TTTTTCGGGTTC
38428 GGGTTCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.09, C:0.09, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTTCGGGTTCTGAGA
Found at i:39730 original size:28 final size:28
Alignment explanation
Indices: 39691--39756 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
39681 TCGCAAAAAT
*
39691 AAGTATGAAAGAATTTATGTAGTGCAAA
1 AAGTATGAAAGAATCTATGTAGTGCAAA
* *
39719 AAGTATGGAAGAATCTATTTAGTGCAAA
1 AAGTATGAAAGAATCTATGTAGTGCAAA
39747 AAGTATGAAA
1 AAGTATGAAA
39757 TAATTACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (28 bp):
AAGTATGAAAGAATCTATGTAGTGCAAA
Found at i:40521 original size:28 final size:28
Alignment explanation
Indices: 40482--40547 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
40472 TCGCAAAAAT
*
40482 AAGTATGAAAGAATTTATGTAGTGCAAA
1 AAGTATGAAAGAATCTATGTAGTGCAAA
* *
40510 AAGTATGGAAGAATCTATTTAGTGCAAA
1 AAGTATGAAAGAATCTATGTAGTGCAAA
40538 AAGTATGAAA
1 AAGTATGAAA
40548 TAATTACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (28 bp):
AAGTATGAAAGAATCTATGTAGTGCAAA
Found at i:42587 original size:15 final size:16
Alignment explanation
Indices: 42557--42589 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42547 ACCTACCTAC
42557 CAAATTACATAAATAAA
1 CAAATTACA-AAATAAA
42574 CAAATTAC-AAATAAA
1 CAAATTACAAAATAAA
42589 C
1 C
42590 TCACATTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
CAAATTACAAAATAAA
Found at i:44782 original size:2 final size:2
Alignment explanation
Indices: 44777--44819 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
44767 ATAATGTGTG
44777 TA TA TA TA T- 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
44818 TA
1 TA
44820 CAAGTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44889 original size:30 final size:30
Alignment explanation
Indices: 44853--44915 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
44843 TCATATGAAA
44853 TGACTTTTAGCAAAGCAGTGTAACCATGAG
1 TGACTTTTAGCAAAGCAGTGTAACCATGAG
*
44883 TGACTTTTAGCAAAGCAGTGTAACCGTGAG
1 TGACTTTTAGCAAAGCAGTGTAACCATGAG
44913 TGA
1 TGA
44916 GAATTAGGAC
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:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (30 bp):
TGACTTTTAGCAAAGCAGTGTAACCATGAG
Found at i:47274 original size:6 final size:6
Alignment explanation
Indices: 47256--47288 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
47246 CACACCATTA
*
47256 AAAC-G AAAGGG AAACGG AAACGG AAACGG AAAC
1 AAACGG AAACGG AAACGG AAACGG AAACGG AAAC
47289 AAAGGACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 3 0.12
6 22 0.88
ACGTcount: A:0.55, C:0.15, G:0.30, T:0.00
Consensus pattern (6 bp):
AAACGG
Found at i:50184 original size:30 final size:28
Alignment explanation
Indices: 50115--50187 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
50105 GTAGCATTTA
50115 GACGTTTTGCCCACCGAACTTCAATTTTG
1 GACGTTTTGCCC-CCGAACTTCAATTTTG
* * *
50144 GACATTTTGCCCCTTGAATTTCAATTTTGG
1 GACGTTTTGCCCC-CGAACTTCAATTTT-G
50174 GACGTTTTGCCCCC
1 GACGTTTTGCCCCC
50188 TCAACTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 23 0.62
30 13 0.35
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (28 bp):
GACGTTTTGCCCCCGAACTTCAATTTTG
Found at i:50449 original size:29 final size:30
Alignment explanation
Indices: 50390--50456 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
50380 AGGTTGAGGA
*
50390 GGCAAAACGTCCCAAAATTGAAGTTTAGGG
1 GGCAAAACGTCCCAAAATTGAAGTTCAGGG
* *
50420 GGCAAAATGT-CCAAGATTGAAGTTC-GGG
1 GGCAAAACGTCCCAAAATTGAAGTTCAGGG
50448 GGACAAAAC
1 GG-CAAAAC
50457 ATCTAAACGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.16
29 18 0.56
30 9 0.28
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.18
Consensus pattern (30 bp):
GGCAAAACGTCCCAAAATTGAAGTTCAGGG
Found at i:52940 original size:24 final size:24
Alignment explanation
Indices: 52913--52960 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52903 GTATCTATTA
52913 TTTTTCTTCTTTCCTATCAAGTAT
1 TTTTTCTTCTTTCCTATCAAGTAT
52937 TTTTTCTTCTTTCCTATCAAGTAT
1 TTTTTCTTCTTTCCTATCAAGTAT
52961 CAAATGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTTCTTCTTTCCTATCAAGTAT
Found at i:53256 original size:20 final size:20
Alignment explanation
Indices: 53231--53283 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
53221 GTGCACCCAT
53231 TGTAATGCACCCACTTTCAA
1 TGTAATGCACCCACTTTCAA
53251 TGTAATGCACCCACTTTCAA
1 TGTAATGCACCCACTTTCAA
53271 TGTAATGCACCCA
1 TGTAATGCACCCA
53284 TTCAATTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (20 bp):
TGTAATGCACCCACTTTCAA
Found at i:56401 original size:76 final size:75
Alignment explanation
Indices: 56290--56499 Score: 316
Period size: 76 Copynumber: 2.8 Consensus size: 75
56280 TCCATCATTG
* * *
56290 ATTAATTAATTACAAATGG-CTTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATACTAATA
1 ATTAATTAATTACAAAGGGAATTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATAATAATA
*
56354 GTCATTGA-TA
66 CTC-TTGATTA
56364 ATTAATTAATTACAAAGGGAAATTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATAATAAT
1 ATTAATTAATTACAAAGGG-AATTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATAATAAT
*
56429 ACTCTTGATTG
65 ACTCTTGATTA
* *
56440 ATTAATTAATTACAAAGGGCAACTTTCTCAAGGGTTCTTCGCCCTCTAGGACAACATATA
1 ATTAATTAATTACAAAGGG-AATTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATA
56500 TATACTTACT
Statistics
Matches: 125, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 18 0.14
75 4 0.03
76 103 0.82
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (75 bp):
ATTAATTAATTACAAAGGGAATTTTCTCAAGGGTTCTTCGCCCCCTAGGACAACATATAATAATA
CTCTTGATTA
Done.