Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013953.1 Corchorus capsularis cultivar CVL-1 contig13974, 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: 51448
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--36 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA
3 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
37 ACTTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1869 original size:17 final size:17
Alignment explanation
Indices: 1847--1879 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1837 GGTTGCCCAA
1847 AAAAAAAAAAAAGAAAG
1 AAAAAAAAAAAAGAAAG
*
1864 AAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAGAAA
1880 TGGAATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAG
Found at i:7298 original size:21 final size:21
Alignment explanation
Indices: 7274--7313 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
7264 TTTCTCCGTT
7274 TTTCT-TTTGCTTTTATTTTTC
1 TTTCTATTT-CTTTTATTTTTC
7295 TTTCTATTTCTTTTATTTT
1 TTTCTATTTCTTTTATTTT
7314 CTCCAGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTCTATTTCTTTTATTTTTC
Found at i:8418 original size:314 final size:313
Alignment explanation
Indices: 7830--8462 Score: 1079
Period size: 314 Copynumber: 2.0 Consensus size: 313
7820 ATGGATGTTG
*
7830 GTCCAAATAGTGCTTTGAAACCAACTTTGTTCGCAATGTTTGGATGGAAACAGACATGTCATCTG
1 GTCCAAATAGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCTG
*
7895 AAATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGAAGGGTGATTTTGTTATTCTCAAAAT
66 AAATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAAAAT
*
7960 TGTGTAAGGGTCGCTATTCCTAGTGGCACCGAATAATCATTTCTGAGGTGGGGGTTCAAAATGAC
131 TGTGTAAGGGTCGCTATTCCTAGTGGCACCGAATAATCATTTCAGAGGTGGGGGTTCAAAATGAC
* * *
8025 CATCCAATCGTTTTAATGAATACACCTCGAACAGCTATTACAAGTTACAACGGTTCTTGAACCAC
196 CATCCAATCGCTTTAATGAATACACCTCGAACAGCTATTACAAGTAACAACAGTTCTTGAACCAC
* *
8090 ATGCATGGACAGAGCATAGGCATGAAATACAGGACAAAAGGATTAGCCATTTA
261 ATGCATGGACAGAGCATAGGCATGAAATAAAGGAAAAAAGGATTAGCCATTTA
* *
8143 GTCCAAATCAGTGTTTTGAGACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCT
1 GTCCAAAT-AGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCT
**
8208 GAAATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGTGGGGTGATTTTGTGATTCTCAAAA
65 GAAATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAAAA
8273 TTGTGTAAGGGTCGCTATTCCTAGTGGCACCGAATAATCATTTCAGAGGTGGGGGTTTCAAAATG
130 TTGTGTAAGGGTCGCTATTCCTAGTGGCACCGAATAATCATTTCAGAGGTGGGGG-TTCAAAATG
* * **
8338 ACCATCCAATC-CTTTAATGAATACACCTCGAACAGCTTTTACATGTAACGGCAGTTCTTGAACC
194 ACCATCCAATCGCTTTAATGAATACACCTCGAACAGCTATTACAAGTAACAACAGTTCTTGAACC
* *
8402 ACGTGCATGGACAGAGCATGGGCATGAAATAAAGGAAAAAAGGATTAGCCATTTA
259 ACATGCATGGACAGAGCATAGGCATGAAATAAAGGAAAAAAGGATTAGCCATTTA
8457 GTCCAA
1 GTCCAA
8463 CCAAACATAG
Statistics
Matches: 300, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
313 8 0.03
314 272 0.91
315 20 0.07
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (313 bp):
GTCCAAATAGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCTG
AAATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAAAAT
TGTGTAAGGGTCGCTATTCCTAGTGGCACCGAATAATCATTTCAGAGGTGGGGGTTCAAAATGAC
CATCCAATCGCTTTAATGAATACACCTCGAACAGCTATTACAAGTAACAACAGTTCTTGAACCAC
ATGCATGGACAGAGCATAGGCATGAAATAAAGGAAAAAAGGATTAGCCATTTA
Found at i:9666 original size:2 final size:2
Alignment explanation
Indices: 9661--9690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9651 TATATATATA
9661 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9691 CTGAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17422 original size:2 final size:2
Alignment explanation
Indices: 17417--17448 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17407 TCTGTGTGTG
17417 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
17449 ATTTGATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19997 original size:152 final size:152
Alignment explanation
Indices: 19721--20022 Score: 532
Period size: 152 Copynumber: 2.0 Consensus size: 152
19711 TCATAATCGG
* *
19721 GTTAAAATGTTGAGAGGTACCCCATTTCATAATTAATTAAATATTTAATATTTAAATCTATTCTC
1 GTTAAAATGTTGACAGGTACCCAATTTCATAATTAATTAAATATTTAATATTTAAATCTATTCTC
* * *
19786 TAATGAACCACATGTCAACCCTTAAACCCCGCACATGCAATTTGCTAAACTCCACTGACAGTGGA
66 TAATAAACCACATGCCAACCCTTAAACCACGCACATGCAATTTGCTAAACTCCACTGACAGTGGA
*
19851 TATGATAATTTTCCGAGTACGT
131 TACGATAATTTTCCGAGTACGT
19873 GTTAAAATGTTGACAGGTACCCAATTTCATAATTAATTAAATATTTAATATTTAAATCTATTCTC
1 GTTAAAATGTTGACAGGTACCCAATTTCATAATTAATTAAATATTTAATATTTAAATCTATTCTC
* *
19938 TAATAAACCACATGCCAACCCTTAAACCATGCACATGCAGTTTGCTAAACTCCACTGACAGTGGA
66 TAATAAACCACATGCCAACCCTTAAACCACGCACATGCAATTTGCTAAACTCCACTGACAGTGGA
20003 TACGATAATTTTCCGAGTAC
131 TACGATAATTTTCCGAGTAC
20023 TTAAGGATAA
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
152 142 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (152 bp):
GTTAAAATGTTGACAGGTACCCAATTTCATAATTAATTAAATATTTAATATTTAAATCTATTCTC
TAATAAACCACATGCCAACCCTTAAACCACGCACATGCAATTTGCTAAACTCCACTGACAGTGGA
TACGATAATTTTCCGAGTACGT
Found at i:21972 original size:2 final size:2
Alignment explanation
Indices: 21965--21995 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21955 ATCGGTTTAA
21965 AT AT 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 A
21996 ATAACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25997 original size:15 final size:16
Alignment explanation
Indices: 25974--26006 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25964 AAGTTGCCAA
25974 TTCTCGGTTT-TAGAT
1 TTCTCGGTTTATAGAT
*
25989 TTCTGGGTTTATAGAT
1 TTCTCGGTTTATAGAT
26005 TT
1 TT
26007 TCTTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (16 bp):
TTCTCGGTTTATAGAT
Found at i:32897 original size:26 final size:27
Alignment explanation
Indices: 32843--32896 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
32833 GCTCCTTAAC
32843 TTGTACTTAAGGGGCATTTTGGTCATT
1 TTGTACTTAAGGGGCATTTTGGTCATT
*
32870 TTGTAC-TAA-GGGCATTTTTGTCATT
1 TTGTACTTAAGGGGCATTTTGGTCATT
32895 TT
1 TT
32897 TAATTCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.65
26 3 0.12
27 6 0.23
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (27 bp):
TTGTACTTAAGGGGCATTTTGGTCATT
Found at i:33132 original size:31 final size:32
Alignment explanation
Indices: 33097--33166 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
33087 ATTGGGCGGA
33097 TTCGGGCT-GGTTCGGGTTCGGGTACTTT-GGG
1 TTCGGG-TAGGTTCGGGTTCGGGTACTTTCGGG
** *
33128 TTCGGGTATTTTCGGGTTCGGGTATTTTCGGG
1 TTCGGGTAGGTTCGGGTTCGGGTACTTTCGGG
33160 TTCGGGT
1 TTCGGGT
33167 TCGGGTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.68
32 10 0.29
ACGTcount: A:0.04, C:0.14, G:0.41, T:0.40
Consensus pattern (32 bp):
TTCGGGTAGGTTCGGGTTCGGGTACTTTCGGG
Found at i:33163 original size:6 final size:6
Alignment explanation
Indices: 33154--33224 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
33144 TTCGGGTATT
* * *
33154 TTCGGG TTCGGG TTCGGG TTC--T TTCGGG TTCGGG -TCCGG ATCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
33199 TTCGGG -TCCGG ATCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTC
33225 ACTTAGAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
4 3 0.06
5 8 0.15
6 42 0.79
ACGTcount: A:0.03, C:0.21, G:0.44, T:0.32
Consensus pattern (6 bp):
TTCGGG
Found at i:33163 original size:22 final size:22
Alignment explanation
Indices: 33138--33188 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
33128 TTCGGGTATT
33138 TTCGGGTTCGGGTAT-TTTCGGG
1 TTCGGGTTCGGGT-TCTTTCGGG
33160 TTCGGGTTCGGGTTCTTTCGGG
1 TTCGGGTTCGGGTTCTTTCGGG
33182 TTCGGGT
1 TTCGGGT
33189 CCGGATCGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.02, C:0.16, G:0.41, T:0.41
Consensus pattern (22 bp):
TTCGGGTTCGGGTTCTTTCGGG
Found at i:33188 original size:16 final size:16
Alignment explanation
Indices: 33107--33166 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
33097 TTCGGGCTGG
*
33107 TTCGGGTTCGGGTACT
1 TTCGGGTTCGGGTATT
33123 TT-GGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
33138 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
33154 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
33167 TCGGGTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
15 14 0.33
16 28 0.67
ACGTcount: A:0.05, C:0.13, G:0.40, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:33199 original size:17 final size:17
Alignment explanation
Indices: 33177--33222 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
33167 TCGGGTTCTT
33177 TCGGGTTCGGGTCCGGA
1 TCGGGTTCGGGTCCGGA
33194 TCGGGTTCGGGTCCGGA
1 TCGGGTTCGGGTCCGGA
33211 TCGGGTTCGGGT
1 TCGGGTTCGGGT
33223 TCACTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.04, C:0.22, G:0.48, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGTCCGGA
Found at i:34013 original size:16 final size:16
Alignment explanation
Indices: 33994--34032 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
33984 CGGGTTCAGG
*
33994 CGGGTTCGGGTTATCT
1 CGGGTTCGGGTAATCT
*
34010 CGGGTTCGGGTAATTT
1 CGGGTTCGGGTAATCT
34026 CGGGTTC
1 CGGGTTC
34033 AGGACGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.18, G:0.38, T:0.36
Consensus pattern (16 bp):
CGGGTTCGGGTAATCT
Found at i:37342 original size:20 final size:21
Alignment explanation
Indices: 37317--37356 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
37307 ATTTCTAAAT
*
37317 AAAGATT-AATTTTTTAAGTG
1 AAAGATTAAATCTTTTAAGTG
37337 AAAGATTAAATCTTTTAAGT
1 AAAGATTAAATCTTTTAAGT
37357 AGTTTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
AAAGATTAAATCTTTTAAGTG
Found at i:37556 original size:51 final size:50
Alignment explanation
Indices: 37500--37691 Score: 158
Period size: 50 Copynumber: 3.8 Consensus size: 50
37490 TGAGAAGATT
* *
37500 AAGTAAAAGATTGAACCTTTTGGTTAACTTGTAAATAAAAGTGAGATCTTT-
1 AAGTAAAAGATTG-ACCTTTTGGTCAATTTGT-AATAAAAGTGAGATCTTTG
* * ** *
37551 AAGTAAAAGACTAACCTTTCAAG-CAATTTGTAAATAAAAATGAGATCTTTG
1 AAGTAAAAGATTGACCTTT-TGGTCAATTTGT-AATAAAAGTGAGATCTTTG
* * * * ** * *
37602 GATTAAGAGATTGACATTTTGGTTGATTTGTGATAAAA-TGAGACCTTTG
1 AAGTAAAAGATTGACCTTTTGGTCAATTTGTAATAAAAGTGAGATCTTTG
* * *
37651 AACTAAAAGATAGA-CTTTTGATCAATTTGTAATAAAAGTGA
1 AAGTAAAAGATTGACCTTTTGGTCAATTTGTAATAAAAGTGA
37692 AGTTTTAAAG
Statistics
Matches: 109, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
48 18 0.17
49 23 0.21
50 37 0.34
51 31 0.28
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (50 bp):
AAGTAAAAGATTGACCTTTTGGTCAATTTGTAATAAAAGTGAGATCTTTG
Found at i:38361 original size:50 final size:50
Alignment explanation
Indices: 38296--38612 Score: 402
Period size: 50 Copynumber: 6.4 Consensus size: 50
38286 ACTTCACTTA
* ** *
38296 TTCCAAAAATG-CCCTTCCTGGTCGGAAGGTTTCTGTTTTCTCTATTTGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
38345 TTCCCAAAATGCCCCTTCCTGGTCAGAAAGTCCTTGTTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
** * * *
38395 TTCCCAAAATGCCCCTTCCCAGTCGGAAGGTCCCCGTTTTCTTTGTTTGC
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
38445 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTAAATTGC
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
38495 TTCCCAAAATGCCCCTTCCTAGTTGGAAGGTCCCTGTTTTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
** * *
38545 TTCCCAAAATGCCCCTTTTTGGTCGGAAGGTCCATGTTTTCTTAATTTGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
*
38595 TTCCCAAAATGTCCCTTC
1 TTCCCAAAATGCCCCTTC
38613 TCGGCCGGAA
Statistics
Matches: 231, Mismatches: 36, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
49 10 0.04
50 221 0.96
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (50 bp):
TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
Found at i:45178 original size:30 final size:30
Alignment explanation
Indices: 45144--45203 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
45134 CAATTCTTGC
*
45144 TTCTTGAAATAATTCTTCAATG-GTCTTCAA
1 TTCTTGAAATAA-TCTTCAATGAATCTTCAA
*
45174 TTCTTGAAATTATCTTCAATGAATCTTCAA
1 TTCTTGAAATAATCTTCAATGAATCTTCAA
45204 ACACGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (30 bp):
TTCTTGAAATAATCTTCAATGAATCTTCAA
Found at i:46392 original size:14 final size:14
Alignment explanation
Indices: 46369--46407 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
46359 GGGTCAGATT
46369 GGGTTCGGGCCATC
1 GGGTTCGGGCCATC
*
46383 GGGTTTGGGCCATC
1 GGGTTCGGGCCATC
*
46397 GGGTTCAGGCC
1 GGGTTCGGGCC
46408 GTTTTCAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.26, G:0.44, T:0.23
Consensus pattern (14 bp):
GGGTTCGGGCCATC
Found at i:46480 original size:32 final size:32
Alignment explanation
Indices: 46439--46533 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 32
46429 TCAGCTTCTG
* ** *
46439 GTTAAATTTGGGTTGGGTTGATTTGGGTTCAT
1 GTTAAATTTGGATCAGGTTGATTCGGGTTCAT
**
46471 GTTAAATTTGGATCAGGTTGATTCGGGTTCGG
1 GTTAAATTTGGATCAGGTTGATTCGGGTTCAT
* * *
46503 GTTAATTTTAGG-TCAGATTAATTCGGGTTCA
1 GTTAAATTT-GGATCAGGTTGATTCGGGTTCA
46534 GGCTCGGGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 50 0.96
33 2 0.04
ACGTcount: A:0.20, C:0.07, G:0.31, T:0.42
Consensus pattern (32 bp):
GTTAAATTTGGATCAGGTTGATTCGGGTTCAT
Found at i:46710 original size:20 final size:20
Alignment explanation
Indices: 46677--46715 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
46667 CATAGATGAA
*
46677 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
46697 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
46716 GAATTTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:46840 original size:16 final size:16
Alignment explanation
Indices: 46778--46842 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
46768 TCGAGTTTCA
*
46778 GATTTTTCGGGTTC-T
1 GATTTTTCGGGTTCGG
*
46793 GATTTTTTCGGGTTTGAG
1 GA-TTTTTCGGGTTCG-G
*
46811 CA-TTTTCGGGTTCGG
1 GATTTTTCGGGTTCGG
*
46826 GATTTTTTGGGTTCGG
1 GATTTTTCGGGTTCGG
46842 G
1 G
46843 TTCGGGCGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 4 0.10
16 35 0.88
18 1 0.03
ACGTcount: A:0.08, C:0.11, G:0.34, T:0.48
Consensus pattern (16 bp):
GATTTTTCGGGTTCGG
Found at i:47181 original size:18 final size:19
Alignment explanation
Indices: 47158--47198 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
47148 AAATTAAACA
47158 TTCTTAAAAATTC-TAGTT
1 TTCTTAAAAATTCATAGTT
* *
47176 TTCTTAAAATTTCATGGTT
1 TTCTTAAAAATTCATAGTT
47195 TTCT
1 TTCT
47199 ATGCATGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (19 bp):
TTCTTAAAAATTCATAGTT
Found at i:47512 original size:16 final size:16
Alignment explanation
Indices: 47487--47517 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47477 AGGAATAGGC
47487 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
47503 AATCATTCAAAGCAA
1 AATCAATCAAAGCAA
47518 AACAATGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Done.