Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015661.1 Corchorus olitorius cultivar O-4 contig15694, 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: 112315
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:170 original size:2 final size:2
Alignment explanation
Indices: 163--197 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
153 GCTTTTAGTT
*
163 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
198 TTATCTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4228 original size:250 final size:250
Alignment explanation
Indices: 3787--4282 Score: 920
Period size: 250 Copynumber: 2.0 Consensus size: 250
3777 CTCAATCAAA
3787 GAATGATTCATACCGGTTTCGATGGTTTCACCATATCGTTTCGGGCTTTCAGGATTAGTATATAT
1 GAATGATTCATACCGGTTTCGATGGTTTCACCATATCGTTTCGGGCTTTCAGGATTAGTATATAT
3852 ATATAACAAATATTAAGATTTATATAATATAAAAACTAATTTTATGATATATAGAATTTTATATT
66 ATATAACAAATATTAAGATTTATATAATATAAAAACTAATTTTATGATATATAGAATTTTATATT
*
3917 TAGTATTTAACATTTAATAATACTTTCAAAGATCAATTAAACCGTTAAAAGGCAACGTTTCATGG
131 TAGTATTTAACATTTAATAATACTTTCAAAGATCAATTAAACCGCTAAAAGGCAACGTTTCATGG
*
3982 AAGGAGACTGCTAAAGCTTTGATTTTTTAGAAAGATAATTAAAATAATAGAGAAG
196 AAGGAGACTGCTAAAGCTTTGATTTTTTAGAAAGATAAGTAAAATAATAGAGAAG
* **
4037 GAATGATTCGTACCGGTTTCGATGGTTTCGTCATATCGTTTCGGGCTTTCAGGATTAGTATATAT
1 GAATGATTCATACCGGTTTCGATGGTTTCACCATATCGTTTCGGGCTTTCAGGATTAGTATATAT
*
4102 ATATAACAAATATTAAGATTTATATAATATAAAAATTAATTTTATGATATATAGAATTTTATATT
66 ATATAACAAATATTAAGATTTATATAATATAAAAACTAATTTTATGATATATAGAATTTTATATT
* *
4167 TAGTATTTAACATTTAATAATACTTTCAAAGGTCAATTAAACTGCTAAAAGGCAACGTTTCATGG
131 TAGTATTTAACATTTAATAATACTTTCAAAGATCAATTAAACCGCTAAAAGGCAACGTTTCATGG
4232 AAGGAGACTGCTAAAGCTTTGATTTTTTAGAAAGATAAGTAAAATAATAGA
196 AAGGAGACTGCTAAAGCTTTGATTTTTTAGAAAGATAAGTAAAATAATAGA
4283 AAAGTGGGGT
Statistics
Matches: 238, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
250 238 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (250 bp):
GAATGATTCATACCGGTTTCGATGGTTTCACCATATCGTTTCGGGCTTTCAGGATTAGTATATAT
ATATAACAAATATTAAGATTTATATAATATAAAAACTAATTTTATGATATATAGAATTTTATATT
TAGTATTTAACATTTAATAATACTTTCAAAGATCAATTAAACCGCTAAAAGGCAACGTTTCATGG
AAGGAGACTGCTAAAGCTTTGATTTTTTAGAAAGATAAGTAAAATAATAGAGAAG
Found at i:11366 original size:33 final size:33
Alignment explanation
Indices: 11327--11396 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 33
11317 TTTAAATACT
*
11327 ATTTTTTTTATAGAATGCGTTACTTTCATATCAC
1 ATTTTTTTCATAGAATGCGTTAC-TTCATATCAC
*
11361 ATTTTTTTCATAGAATTCGTTACTTCATATCAC
1 ATTTTTTTCATAGAATGCGTTACTTCATATCAC
11394 ATT
1 ATT
11397 AAAAGGTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (33 bp):
ATTTTTTTCATAGAATGCGTTACTTCATATCAC
Found at i:11650 original size:12 final size:13
Alignment explanation
Indices: 11630--11662 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11620 GTGAGTTAAG
11630 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
11643 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
11655 TAGTTTGT
1 TAGTTTGT
11663 AATTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:11973 original size:26 final size:27
Alignment explanation
Indices: 11944--11998 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
11934 ATTTACACAA
* *
11944 AATGGT-CAAATAAGCCCTTGAACTCT
1 AATGGTACAAATAAACCCTTAAACTCT
11970 AATGGTAGCCAAATAAACCCTTAAACTCT
1 AATGGTA--CAAATAAACCCTTAAACTCT
11999 TTAAGAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
29 18 0.75
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (27 bp):
AATGGTACAAATAAACCCTTAAACTCT
Found at i:12299 original size:2 final size:2
Alignment explanation
Indices: 12292--12316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12282 GTTTTTATTT
12292 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12317 TTCTCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13476 original size:2 final size:2
Alignment explanation
Indices: 13469--13495 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13459 TGAACAAGAA
13469 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 A
13496 AAGAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17207 original size:103 final size:102
Alignment explanation
Indices: 17098--17404 Score: 445
Period size: 103 Copynumber: 3.0 Consensus size: 102
17088 TTTGCTACAG
* * * *
17098 ATTTTGCCACAAAATTAATTTTCGTGGCAAATTAAAATTTGAATTCCCGCTCTCTCAAAAATTTT
1 ATTTTGCAACAAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCT-TCAAATATTTT
*
17163 GCGCCAAAATAAATTTTTGCAACGGAAATTATTACAAA
65 GCGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
* * * *
17201 ATTTTGCAACGAATTTAGTTTTCGTAACAAATCAAAATTTGAATTCCCGCTCGATT-AAATATTT
1 ATTTTGCAACAAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTC--TTCAAATATTT
17265 TGCGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
64 TGCGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
* * *
17304 TTTTTGCAACAAATTTAATTTTCGTGTCAAATTAAAATTTGAATTCCCGCTAGTTCAAATATTTT
1 ATTTTGCAACAAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCT-CTTCAAATATTTT
* *
17369 GCGCCAAAATAAATTGTTCCAACGGAAATTACTACA
65 GCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
17405 GAAAAATCCG
Statistics
Matches: 182, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
102 2 0.01
103 178 0.98
104 1 0.01
105 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (102 bp):
ATTTTGCAACAAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCTTCAAATATTTTG
CGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
Found at i:21170 original size:64 final size:64
Alignment explanation
Indices: 21069--21196 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
21059 GCCGGAGTTA
*
21069 GGATTTCACTGATCCTCAAAAGGATTCCTACAAGATAATAAACACCTGAGTGGCAGGGGATGCC
1 GGATTTCACTAATCCTCAAAAGGATTCCTACAAGATAATAAACACCTGAGTGGCAGGGGATGCC
21133 GGATTTCACTAATCCTCAAAAGGATTCCTACAAGATAATAAACACCTGAGTGGCAGGGGATGCC
1 GGATTTCACTAATCCTCAAAAGGATTCCTACAAGATAATAAACACCTGAGTGGCAGGGGATGCC
21197 CTGTGTTAAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (64 bp):
GGATTTCACTAATCCTCAAAAGGATTCCTACAAGATAATAAACACCTGAGTGGCAGGGGATGCC
Found at i:21730 original size:50 final size:50
Alignment explanation
Indices: 21676--21774 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
21666 CTATTGCAAT
21676 TTAATCCTACCTCTATCTTCAGTGTAAATATTATATATAGAACTTTATAA
1 TTAATCCTACCTCTATCTTCAGTGTAAATATTATATATAGAACTTTATAA
21726 TTAATCCTACCTCTATCTTCAGTGTAAATATTATATATAGAACTTTATA
1 TTAATCCTACCTCTATCTTCAGTGTAAATATTATATATAGAACTTTATA
21775 TATCATGCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (50 bp):
TTAATCCTACCTCTATCTTCAGTGTAAATATTATATATAGAACTTTATAA
Found at i:23411 original size:45 final size:45
Alignment explanation
Indices: 23338--23427 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
23328 ATATGTCTTC
*
23338 GATCACATCATTGGGTACTCCATAATCTATTTCTCTTGGCCTTTT
1 GATCACATCATTGGGTACTCCATAATCTATTTCTCTCGGCCTTTT
* *
23383 GATCACATCATTGGGTACTTCATTATCTATTTCTCTCGGCCTTTT
1 GATCACATCATTGGGTACTCCATAATCTATTTCTCTCGGCCTTTT
23428 TTTTGCCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.43
Consensus pattern (45 bp):
GATCACATCATTGGGTACTCCATAATCTATTTCTCTCGGCCTTTT
Found at i:24529 original size:17 final size:17
Alignment explanation
Indices: 24507--24544 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
24497 GATGTTAGTT
24507 TAGGGGCAAAATGTTGG
1 TAGGGGCAAAATGTTGG
24524 TAGGGGCAAAATGTTGG
1 TAGGGGCAAAATGTTGG
24541 TAGG
1 TAGG
24545 TCCATTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.42, T:0.24
Consensus pattern (17 bp):
TAGGGGCAAAATGTTGG
Found at i:28845 original size:12 final size:12
Alignment explanation
Indices: 28828--28852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28818 TCCTACTTGA
28828 CGAAGAAAAGCG
1 CGAAGAAAAGCG
28840 CGAAGAAAAGCG
1 CGAAGAAAAGCG
28852 C
1 C
28853 TAGTTTAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.20, G:0.32, T:0.00
Consensus pattern (12 bp):
CGAAGAAAAGCG
Found at i:29234 original size:8 final size:8
Alignment explanation
Indices: 29221--29247 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29211 CTCTTATTGG
29221 TCCCTCAA
1 TCCCTCAA
29229 TCCCTCAA
1 TCCCTCAA
29237 TCCCTCAA
1 TCCCTCAA
29245 TCC
1 TCC
29248 AAACACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.52, G:0.00, T:0.26
Consensus pattern (8 bp):
TCCCTCAA
Found at i:33843 original size:2 final size:2
Alignment explanation
Indices: 33836--33865 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33826 CACAGGGGGC
33836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33866 GTAATTTACC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34113 original size:2 final size:2
Alignment explanation
Indices: 34106--34131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34096 AAGGTTAACT
34106 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
34132 ACTACCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36403 original size:56 final size:57
Alignment explanation
Indices: 36311--36424 Score: 187
Period size: 56 Copynumber: 2.0 Consensus size: 57
36301 TTATAATTAG
*
36311 CAAAACTTAACAAATACTATAGTAGTCTAAATTAATGCCATTGTCATCCATTGAACAA
1 CAAAACTTAACAAATAC-ATAGTAGTCTAAATTAATGCCATTGCCATCCATTGAACAA
36369 CAAAACTTAAACAAATAC-TA-TAGTCTAAATTAATGCCATTGCCATCCATTGAACAA
1 CAAAACTT-AACAAATACATAGTAGTCTAAATTAATGCCATTGCCATCCATTGAACAA
36425 AAGAACTACT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
56 35 0.65
57 2 0.04
58 8 0.15
59 9 0.17
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (57 bp):
CAAAACTTAACAAATACATAGTAGTCTAAATTAATGCCATTGCCATCCATTGAACAA
Found at i:46186 original size:14 final size:15
Alignment explanation
Indices: 46166--46200 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46156 GTTTGATAAA
46166 ACTGAAA-ATTAAGT
1 ACTGAAAGATTAAGT
*
46180 GCTGAAAGATTAAGT
1 ACTGAAAGATTAAGT
46195 ACTGAA
1 ACTGAA
46201 TTTTTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (15 bp):
ACTGAAAGATTAAGT
Found at i:46229 original size:16 final size:15
Alignment explanation
Indices: 46190--46234 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
46180 GCTGAAAGAT
**
46190 TAAGTACTGAATTTT
1 TAAGTACTGAATTCA
46205 TAA-TACTGAATCTCA
1 TAAGTACTGAAT-TCA
46220 TAAGTACTGAATTCA
1 TAAGTACTGAATTCA
46235 GACTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (15 bp):
TAAGTACTGAATTCA
Found at i:47226 original size:164 final size:164
Alignment explanation
Indices: 46948--47258 Score: 545
Period size: 164 Copynumber: 1.9 Consensus size: 164
46938 ATTCAACCTA
46948 ACATATTGTTGACATTCATCAAATAATAAAAGGAAATAAGTTTAAGCAATTTAGCATCATAATAT
1 ACATATTGTTGACATTCATCAAATAATAAAAGGAAATAAGTTTAAGCAATTTAGCATCATAATAT
*
47013 ATCTATATTATTCATATCTTTAATTGAGTAAAACTTTTAGCTATTTTTTAGAAATTTAAGAAAAG
66 ATCAATATTATTCATATCTTTAATTGAGTAAAACTTTTAGCTATTTTTTAGAAATTTAAGAAAAG
*
47078 AAAATCATGAAAAGTGTCGGTCACTATTTTCTCT
131 AAAATAATGAAAAGTGTCGGTCACTATTTTCTCT
* *
47112 ACATATTGTTGACATTCATCAAGTAATAAAAGTAAATAAGTTTAAGCAATTTAGCATCAT-ATAT
1 ACATATTGTTGACATTCATCAAATAATAAAAGGAAATAAGTTTAAGCAATTTAGCATCATAATAT
*
47176 AT-AATATTATTCATATCTTTAATTGAGTAAAACTTTTAGCTATTTTTTTTATAAATTTAAGAAA
66 ATCAATATTATTCATATCTTTAATTGAGTAAAACTTTTAGCTA--TTTTTTAGAAATTTAAGAAA
47240 AGAAAATAATGAAAAGTGT
129 AGAAAATAATGAAAAGTGT
47259 GTCAATATTT
Statistics
Matches: 140, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
162 39 0.28
163 6 0.04
164 95 0.68
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (164 bp):
ACATATTGTTGACATTCATCAAATAATAAAAGGAAATAAGTTTAAGCAATTTAGCATCATAATAT
ATCAATATTATTCATATCTTTAATTGAGTAAAACTTTTAGCTATTTTTTAGAAATTTAAGAAAAG
AAAATAATGAAAAGTGTCGGTCACTATTTTCTCT
Found at i:49769 original size:13 final size:13
Alignment explanation
Indices: 49751--49776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49741 TACCAAATCT
49751 AGCGAGTGCATCA
1 AGCGAGTGCATCA
49764 AGCGAGTGCATCA
1 AGCGAGTGCATCA
49777 GTACAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
AGCGAGTGCATCA
Found at i:50177 original size:22 final size:23
Alignment explanation
Indices: 50149--50198 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
50139 AAATGACTCA
**
50149 ATTTTTGGCGGGGCCATTGATT-
1 ATTTTTGAAGGGGCCATTGATTG
50171 ATTTTTGAAGGGGCCATTGATTG
1 ATTTTTGAAGGGGCCATTGATTG
50194 ATTTT
1 ATTTT
50199 GGTATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (23 bp):
ATTTTTGAAGGGGCCATTGATTG
Found at i:55628 original size:21 final size:21
Alignment explanation
Indices: 55602--55645 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55592 CCCTAGTCAA
55602 TGGTAATTGAGG-AAGAAAGTT
1 TGGTAATTG-GGAAAGAAAGTT
*
55623 TGGTAATTGGGAAAGGAAGTT
1 TGGTAATTGGGAAAGAAAGTT
55644 TG
1 TG
55646 ACAGTAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (21 bp):
TGGTAATTGGGAAAGAAAGTT
Found at i:60264 original size:56 final size:56
Alignment explanation
Indices: 60173--60282 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
60163 CGTTTCCTTC
*
60173 CACATAATAAATGTTATAATAAATCATATCCCCCTATCTCTATTTAATTATTCTTT
1 CACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTATTTAATTATTCTTT
*
60229 CACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTATTTAATTATTCT
1 CACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTATTTAATTATTCT
60283 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (56 bp):
CACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTATTTAATTATTCTTT
Found at i:62392 original size:12 final size:13
Alignment explanation
Indices: 62373--62403 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
62363 CAAGGGTAAG
62373 TCTTTTCTTTTTT
1 TCTTTTCTTTTTT
62386 T-TTTTCTTTTTT
1 TCTTTTCTTTTTT
62398 TCTTTT
1 TCTTTT
62404 TTTGTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:62395 original size:8 final size:8
Alignment explanation
Indices: 62373--62406 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
62363 CAAGGGTAAG
62373 TCTTTTCTT
1 TCTTTT-TT
*
62382 TTTTTTTT
1 TCTTTTTT
62390 TCTTTTTT
1 TCTTTTTT
62398 TCTTTTTT
1 TCTTTTTT
62406 T
1 T
62407 GTGTGTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TCTTTTTT
Found at i:62395 original size:17 final size:17
Alignment explanation
Indices: 62373--62406 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
62363 CAAGGGTAAG
62373 TCTTTTCTTT-TTTTTTT
1 TCTTTT-TTTCTTTTTTT
62390 TCTTTTTTTCTTTTTTT
1 TCTTTTTTTCTTTTTTT
62407 GTGTGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TCTTTTTTTCTTTTTTT
Found at i:70973 original size:111 final size:112
Alignment explanation
Indices: 70779--71071 Score: 410
Period size: 111 Copynumber: 2.6 Consensus size: 112
70769 CTCAGCGTTT
* * * * *
70779 GTGACTTTAAGTTAGCCTTTCATGTAGACTTCATGAATAACTCCTCATAGCCCTTTGTAGGTTGC
1 GTGAC-TTAAGTTAGCCTTTCATGTAGAGTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGC
* * *
70844 ATG-TTCATATGTTGTGTTTCAGCATGGATGATCATTTCTCGTTCTTC
65 ATGTTTCATATGTTATGTTTCACCATCGATGATCATTTCTCGTTCTTC
* * *
70891 GTGACTTAAGTTTGCCTTTTATGTAGAGTTCATGAGTGACTCTTCATAGCCCCTTGTAGATTGCA
1 GTGACTTAAGTTAGCCTTTCATGTAGAGTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCA
* * * *
70956 TGTTTC-TTTGTTATGTTTCACCATCGATGATCATTTCTTGTTGTTT
66 TGTTTCATATGTTATGTTTCACCATCGATGATCATTTCTCGTTCTTC
* *
71002 GTGACTTAAATTAGCCTTTCATGTAGAGTTCATGAGTAACTCTTCATAGCCCCTTGTATATTGCA
1 GTGACTTAAGTTAGCCTTTCATGTAGAGTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCA
71067 TGTTT
66 TGTTT
71072 TTTTTGCTGT
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
111 152 0.95
112 8 0.05
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (112 bp):
GTGACTTAAGTTAGCCTTTCATGTAGAGTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCA
TGTTTCATATGTTATGTTTCACCATCGATGATCATTTCTCGTTCTTC
Found at i:99198 original size:20 final size:18
Alignment explanation
Indices: 99152--99199 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
99142 AAAAATGCAT
99152 TATATA-ATTTATATATG
1 TATATACATTTATATATG
99169 TATAATTACATTTATGTATATG
1 TAT-A-TACATTTA--TATATG
99191 TATATACAT
1 TATATACAT
99200 AATGATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 2 0.08
20 10 0.38
21 1 0.04
22 9 0.35
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATACATTTATATATG
Found at i:99960 original size:18 final size:18
Alignment explanation
Indices: 99937--99974 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
99927 TGTAACGAGA
99937 TTTCACTTATCTAACCAT
1 TTTCACTTATCTAACCAT
99955 TTTCACTTATCTAACCAT
1 TTTCACTTATCTAACCAT
99973 TT
1 TT
99975 ATTAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCACTTATCTAACCAT
Found at i:109128 original size:331 final size:327
Alignment explanation
Indices: 106971--109329 Score: 1775
Period size: 331 Copynumber: 7.2 Consensus size: 327
106961 TTGCATGATT
*
106971 TTCATCTAATCAAATCTCCGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * *
107036 TTTCGATTTAATTGGAAATTAATTTGAAAAAAATAGGAAAACGATATTAGAAA-TGTCAAAAGCC
66 TTTCGATTTAATTAGAAATTAA-TTCAAAAAAATAGGAAAACGATATTA-AAAGCGTGAAAAGTC
* * * * *
107100 CTTCAATCCTTTTGGCGTTGTATTATATA-TTTTTATGAGTATTT-TATCCAAAAATTGAGGAAA
129 CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTGGAT--AAAAATTGAGGAAA
* * * * * *
107163 TATCTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCATGTAATAACC-ATCACAG-ATTTT
192 AATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATC--GT-GT-ACCAATCACGGTTTTTT
* * * ** * * *
107226 AGCTAAAAAAGCGTTTCGGGGCCCCGTCTCAGTTTTGCATGATTTTTGG-CACCAAGATTGCTTG
253 GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGGCAAAG-CTCCTTG
* *
107290 AGATATCCATA
317 AAATATCTATA
* * * ** * *
107301 TT-ATTCTAATCAAATCTCAGCCACATCAGG-TTTAAGAATTT-ATTTTAAAAGCATCTAAATGT
1 TTCA-TCTAATCAAATCTCAGCCACAT-TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* * * * *
107363 TCTTTCGATTTAATT-GAAAATTAATTC-AGAAAATATGAAAAACGATATTAAAAGTGTAAAAAG
64 TGTTTCGATTTAATTAG-AAATTAATTCAAAAAAATA-GGAAAACGATATTAAAAGCGTGAAAAG
* * * * * *
107426 TCCTACAATCTTTTTAGCATTAAATTATATATATATT-T---TA-TT---CAAAAATTGAGGAAA
127 TCCTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTGGATAAAAATTGAGGAAA
* * * ** *
107483 ATTTTTTTGGGTCGTTTTTTTTGCAAAATTTTAGCCGAAATCGTACACGTTAAGTCAATATCACG
192 AATTTTTCGAGTC--AATTTTTGCAAAATTTTAGCCGAAATCGT----G-T-A--CCA-ATCACG
* ** * * * * * *
107548 ATTTTTTTCCTCTAAAAATGCGTTTCGGGGCCTCGACTCAATTTTGCATGAATTTTAGCGTCG-A
246 -GTTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATG-ATTTTTG-GTGGCA
*
107612 GAG-TCCTTGAAATATCTATA
307 AAGCTCCTTGAAATATCTATA
* *
107632 TTCATCTAGTCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* *
107697 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAATAACGATATTAAAAGCGTGAAAAGTCC
66 TTTCGATTTAATTAGAAATTAATTCAAAAAAATAGGAA-AACGATATTAAAAGCGTGAAAAGTCC
* * * * * *
107762 TCCAATCTTTTTGG-AGTTGAATTATGTATATATTTTATAAGTATTTAGACAAAACTTGAGAAAA
130 TCCAATCTTTTTGGCA-TTGAATTA--TATATTTTTTATGAGTATTTGGATAAAAATTGAGGAAA
* * * * ** *
107826 AATATTTCTG-GTCAATTTTTGCCAGATATTAGTAGAAATCGTGTACGTTAGTCAAAGTCATGG-
192 AATTTTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC------C-AA-TCACGGT
* * * * ** * * * * *
107889 TATTTGGCTAAAAATGTGTTCCGAAGCCCCGGTTTAGTGTTGCATGATTTTTGACGCGG-AGA-C
248 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTG--GTGGCAAAGC
107952 TCCTTGAAATATCTATA
311 TCCTTGAAATATCTATA
* **** * * *
107969 TTCATCTAA-CTAAATCTCAGCCACATTTGATTTAAGGATTTG-TAAGGCAAACATCTAAATCAT
1 TTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC-T
* *
108032 T-TTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAA-CATGAAA
64 TGTTTCGATTTAATTAGAAATTAATTC--AAAAAAATAGG-AAAACGATATTA-AAAGCGTGAAA
* * * * *
108095 A-ACTCTTCAATGTTTTTGGCATTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTGAG
125 AGTC-CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATT-TGGATAAAAATTGAG
* * * ** *
108159 GAAATAA-CTTGCGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATCATAGTT
188 GAAA-AATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAATCA-C---G-G
* * * * * * *
108223 TTTTTTGACTAAAAACGCGTTCCGGAAG-CCCGGCTAAGTTTTTCATGATTTTTGG-CGCCAAGA
247 TTTTTTGGCTAAAAACGCGTTTCGG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGTGGCAAAG-
* * * *
108286 CTCTTTGAGATATCCACA
310 CTCCTTGAAATATCTATA
* * * * *
108304 TTCATCTAATCAAATCTTAGCTACATTGGATTTAAGAATTTATTTTTACGAGCATTTGAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
108369 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGACAAATGATATTAAAAGCGTGAAAAGTCC
66 TTTCGATTTAATTAGAAATTAATTCAAAAAAATAGGA-AAACGATATTAAAAGCGTGAAAAGTCC
* * **
108434 TCCAATCTTTTTGGCGTT-ATATTATATATATATATATATTATGAGTATTTTAGCCAAAAATTGA
130 TCCAATCTTTTTGGCATTGA-A-T-TATATAT-T-T-T-TTATGAGTA-TTTGGATAAAAATTG-
* * *** *
108498 AGGAAAATTTTTTCGGGTTTTTTTTTTGCAAAATTTCAGCCGAAATCGTG---------CGG-TT
186 AGGAAAAATTTTTCGAG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAATCACGGTTT
* ** * * * *
108553 TATGGCTAAAAACGCGTTTCGGGGCCCCAACTTAGTTTTGCATGATTTTTGGCGTC-GAGACTCC
250 TTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGGCAAAG-CTCC
* *
108617 TTCAAATATTTATA
314 TTGAAATATCTATA
* * * * *
108631 TTCATCTAATCAAATCTCAACCACATTGAATTTAAGTA-TT-TTTTTACGAGCATTTGAGTCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
108694 TGTCGAATTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
66 TTTCGATTTAATTAGAAATTAATTCAAAAAAATA-GGAAAACGATATTAAAAGCGTGAAAAGTCC
* * *
108759 TCCAATCTTTTTGGCGTTGAATTACATATATTTTATGAGTATTGTGGATAAAAATTGAGGAAAAA
130 TCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATT-TGGATAAAAATTGAGGAAAAA
* *
108824 TTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACCAATCACGGTTTTTTGACTAA
194 TTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAATCACGGTTTTTTGGCTAA
* * * * *
108889 AAATGCG-TTCTGGGGCCCCCGGGTTAGTTTTGCATGAGTTTTGGTGGCAAAGCTCCATGAAATA
259 AAACGCGTTTC-GGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGTGGCAAAGCTCCTTGAAATA
108953 TCTATA
322 TCTATA
* ** * * *
108959 TTCATCTAACCAAATCTTGGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAAGCATG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* *
109024 TTTCGATTTAATTA-AAACTTAATTTGAAAAAAATAGGGAAAACGATATTAGAAGCGT-AAGAAG
66 TTTCGATTTAATTAGAAA-TTAA-TTCAAAAAAATA-GGAAAACGATATTAAAAGCGTGAA-AAG
* * *
109087 CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA-GAA
127 TCCTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATT-TGGATAAAAATTGAGGAA
* * * * * ** * * *
109151 TAATATTTCGGGTCAACTTTTGCAAAATTTTAGCCGAAATCTTGTA-TTATCATGGGTTTTCGGC
191 AAATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAATCACGGTTTTTTGGC
* ** **
109215 TAAAAACGCGTTTCAGGGCCCTATG-TCAGTTTTGCATGATTTTTGGCAGCAAA------T---A
256 TAAAAACGCGTTTCGGGGCCC-CGGCTCAGTTTTGCATGATTTTTGGTGGCAAAGCTCCTTGAAA
109270 TATCTATA
320 TATCTATA
* * * *
109278 TTCATCTAACCAAATCTCAGCCATATTGTATTTAAGGATTTGTTTTTTCGAG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
109330 TTTCTAAATC
Statistics
Matches: 1627, Mismatches: 289, Indels: 237
0.76 0.13 0.11
Matches are distributed among these distances:
317 27 0.02
318 17 0.01
319 75 0.05
320 25 0.02
321 1 0.00
322 25 0.02
323 6 0.00
324 6 0.00
325 101 0.06
326 12 0.01
327 121 0.07
328 155 0.10
329 77 0.05
330 124 0.08
331 171 0.11
332 52 0.03
333 62 0.04
334 43 0.03
335 104 0.06
336 108 0.07
337 140 0.09
338 53 0.03
339 10 0.01
340 28 0.02
341 35 0.02
342 27 0.02
343 21 0.01
344 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (327 bp):
TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
TTTCGATTTAATTAGAAATTAATTCAAAAAAATAGGAAAACGATATTAAAAGCGTGAAAAGTCCT
CCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTGGATAAAAATTGAGGAAAAATT
TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAATCACGGTTTTTTGGCTAAAA
ACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGGCAAAGCTCCTTGAAATATCTA
TA
Found at i:111076 original size:37 final size:37
Alignment explanation
Indices: 111035--111106 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
111025 GACATATTAT
* *
111035 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
111072 TCATAAAGTTATGTCTATATGAAAAGACATGTATT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATT
111107 TTGATCAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Done.