Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019400.1 Corchorus olitorius cultivar O-4 contig19433, 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: 53701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:53 original size:13 final size:13
Alignment explanation
Indices: 35--65 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25 TCAAAAATAA
*
35 CTGAAAAGCACTT
1 CTGAAAAACACTT
48 CTGAAAAACACTT
1 CTGAAAAACACTT
61 CTGAA
1 CTGAA
66 TTTTCCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (13 bp):
CTGAAAAACACTT
Found at i:6907 original size:18 final size:17
Alignment explanation
Indices: 6873--6907 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6863 TTTTTACTGC
*
6873 ACTTTTCTTTGCCTTTA
1 ACTTTTCTTTCCCTTTA
6890 ACTTTTCTTTTCCCTTTA
1 ACTTTTC-TTTCCCTTTA
6908 TAAAAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.11, C:0.26, G:0.03, T:0.60
Consensus pattern (17 bp):
ACTTTTCTTTCCCTTTA
Found at i:9383 original size:12 final size:12
Alignment explanation
Indices: 9366--9392 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9356 AGGACATAGG
9366 AAAACAGAGAAA
1 AAAACAGAGAAA
9378 AAAACAGAGAAA
1 AAAACAGAGAAA
9390 AAA
1 AAA
9393 GTGGGGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAACAGAGAAA
Found at i:10705 original size:13 final size:13
Alignment explanation
Indices: 10687--10711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10677 TAAGCCATTT
10687 TTTTTTCTTTCTC
1 TTTTTTCTTTCTC
10700 TTTTTTCTTTCT
1 TTTTTTCTTTCT
10712 GTTGCAGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTTCTC
Found at i:19595 original size:97 final size:97
Alignment explanation
Indices: 19424--19806 Score: 662
Period size: 97 Copynumber: 4.0 Consensus size: 97
19414 CCTAATTTTT
* * *
19424 TTCATTAAAAATACAAAGTAATATGTTGAACTTTTAATTTCAGAATTCAGACCATTATATCATCA
1 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
19489 AGACGTCACCCATTAAGTATCTCTAATACGTA
66 AGACGTCACCCATTAAGTATCTCTAATACGTA
19521 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
1 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
* *
19586 AGACTTCACCTATTAAGTATCTCTAATACGTA
66 AGACGTCACCCATTAAGTATCTCTAATACGTA
* * *
19618 TTCATTAAAAATACAAAGTAAAATGTTGAACTTTTAATTTC--AATTCAAATCATTATATCGTCA
1 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
*
19681 AGACGTCACCCATTAAGTATCTCTATTACGTA
66 AGACGTCACCCATTAAGTATCTCTAATACGTA
19713 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
1 TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
*
19778 AGACATCACCCATTAAGTATCTCTAATAC
66 AGACGTCACCCATTAAGTATCTCTAATAC
19807 ATCATACCTA
Statistics
Matches: 268, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
95 89 0.33
97 179 0.67
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (97 bp):
TTCATTAAAAATACAAAGTAAAATATTGAACTTTTAATTTCAGAATTCAGACCATTATATCGTCA
AGACGTCACCCATTAAGTATCTCTAATACGTA
Found at i:19753 original size:192 final size:193
Alignment explanation
Indices: 19424--19806 Score: 687
Period size: 192 Copynumber: 2.0 Consensus size: 193
19414 CCTAATTTTT
* *
19424 TTCATTAAAAATACAAAGTAATATGTTGAACTTTTAATTTCAGAATTCAGACCATTATATCATCA
1 TTCATTAAAAATACAAAGTAAAATGTTGAACTTTTAATTTCA-AATTCAAACCATTATATCATCA
19489 AGACGTCACCCATTAAGTATCTCTAATACGTATTCATTAAAAATACAAAGTAAAATATTGAACTT
65 AGACGTCACCCATTAAGTATCTCTAATACGTATTCATTAAAAATACAAAGTAAAATATTGAACTT
* *
19554 TTAATTTCAGAATTCAGACCATTATATCGTCAAGACTTCACCTATTAAGTATCTCTAATACGTA
130 TTAATTTCAGAATTCAGACCATTATATCGTCAAGACATCACCCATTAAGTATCTCTAATACGTA
* *
19618 TTCATTAAAAATACAAAGTAAAATGTTGAACTTTTAATTTC-AATTCAAATCATTATATCGTCAA
1 TTCATTAAAAATACAAAGTAAAATGTTGAACTTTTAATTTCAAATTCAAACCATTATATCATCAA
*
19682 GACGTCACCCATTAAGTATCTCTATTACGTATTCATTAAAAATACAAAGTAAAATATTGAACTTT
66 GACGTCACCCATTAAGTATCTCTAATACGTATTCATTAAAAATACAAAGTAAAATATTGAACTTT
19747 TAATTTCAGAATTCAGACCATTATATCGTCAAGACATCACCCATTAAGTATCTCTAATAC
131 TAATTTCAGAATTCAGACCATTATATCGTCAAGACATCACCCATTAAGTATCTCTAATAC
19807 ATCATACCTA
Statistics
Matches: 182, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
192 142 0.78
194 40 0.22
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (193 bp):
TTCATTAAAAATACAAAGTAAAATGTTGAACTTTTAATTTCAAATTCAAACCATTATATCATCAA
GACGTCACCCATTAAGTATCTCTAATACGTATTCATTAAAAATACAAAGTAAAATATTGAACTTT
TAATTTCAGAATTCAGACCATTATATCGTCAAGACATCACCCATTAAGTATCTCTAATACGTA
Found at i:21496 original size:2 final size:2
Alignment explanation
Indices: 21439--21479 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
21429 AATTGATTAT
*
21439 TA TA TA TA TA TA TA TA TA TA TA -A TCA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T
21480 TTAAGGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24007 original size:9 final size:9
Alignment explanation
Indices: 23993--24017 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23983 GGTGGGTGGT
23993 GCCTGGTTG
1 GCCTGGTTG
24002 GCCTGGTTG
1 GCCTGGTTG
24011 GCCTGGT
1 GCCTGGT
24018 AGGCATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.44, T:0.32
Consensus pattern (9 bp):
GCCTGGTTG
Found at i:29360 original size:13 final size:13
Alignment explanation
Indices: 29342--29370 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29332 TTTTGGGAAA
29342 ACGACATGCCACC
1 ACGACATGCCACC
29355 ACGACATGCCACC
1 ACGACATGCCACC
29368 ACG
1 ACG
29371 CCATACTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.45, G:0.17, T:0.07
Consensus pattern (13 bp):
ACGACATGCCACC
Found at i:30448 original size:45 final size:45
Alignment explanation
Indices: 30396--30486 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
30386 GGAAAAGGAA
*
30396 TATTAGACATTGTGATAGACATAAACATGACACAACAAATTAGAT
1 TATTAGACATTGTGATAGACATAAACATGAAACAACAAATTAGAT
30441 TATTAGACATTGTGATAGACATAAACATGAAACAACAAATTAGAT
1 TATTAGACATTGTGATAGACATAAACATGAAACAACAAATTAGAT
30486 T
1 T
30487 CAAAATACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.27
Consensus pattern (45 bp):
TATTAGACATTGTGATAGACATAAACATGAAACAACAAATTAGAT
Found at i:36332 original size:29 final size:30
Alignment explanation
Indices: 36272--36351 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
36262 GCTAAATACC
* *
36272 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
*
36303 CAAAATAATCGCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
36332 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
36352 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:36562 original size:32 final size:31
Alignment explanation
Indices: 36477--36574 Score: 133
Period size: 31 Copynumber: 3.1 Consensus size: 31
36467 AAGGGACTGA
* *
36477 TTTGTCCCAAAAGATAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
36508 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
** *
36539 TTTGTTTCAAAAGAAAAATTATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAA-TATAAG-GGATTTT
36572 TTT
1 TTT
36575 AGTATTTAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 45 0.75
32 6 0.10
33 9 0.15
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAATATAAGGGATTTT
Found at i:37721 original size:31 final size:31
Alignment explanation
Indices: 37615--37711 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
37605 ACTAAATACT
* *
37615 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
37647 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
37678 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
37709 AAA
1 AAA
37712 TCAGTCCCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 56 0.89
32 7 0.11
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:37901 original size:31 final size:29
Alignment explanation
Indices: 37835--37914 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
37825 TTCATTTTTG
* *
37835 AAACGTAAGGGATTAATTTGTCCCAAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
37864 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
37895 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
37915 GGTATTTAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.57
31 20 0.43
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:42741 original size:19 final size:18
Alignment explanation
Indices: 42703--42748 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42693 TTTCTTTTGG
* *
42703 AGTTTGTTTTTTTGATTC
1 AGTTTGTTTTTTCGAGTC
42721 AGTTTGTTTTTATCGAGTC
1 AGTTTGTTTTT-TCGAGTC
42740 AGTTT-TTTT
1 AGTTTGTTTT
42749 AGTCTCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.13, C:0.07, G:0.17, T:0.63
Consensus pattern (18 bp):
AGTTTGTTTTTTCGAGTC
Found at i:44667 original size:3 final size:3
Alignment explanation
Indices: 44659--44683 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44649 ATATATATAT
44659 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
44684 ATCCGAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:45408 original size:18 final size:18
Alignment explanation
Indices: 45387--45421 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45377 ATGAATTAGT
45387 AATAAAA-AATTAATAATG
1 AATAAAAGAATT-ATAATG
45405 AATAAAAGAATTATAAT
1 AATAAAAGAATTATAAT
45422 AACTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATAAAAGAATTATAATG
Found at i:45842 original size:60 final size:60
Alignment explanation
Indices: 45765--45924 Score: 198
Period size: 60 Copynumber: 2.6 Consensus size: 60
45755 CTAATTGCTT
* * * *
45765 AAATAAGGGTCTAATGTTTGCCAAAATACTTAAATAAGGGT-CTGATATTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTT-CGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGCC
* * * *
45825 AAATAAGAGCCTAATGTTATCGAAAATGCTCAAATAA-GGTCCTGGTCTTTTAATTTAGCC
1 AAATAAGGGCCTAATGTT-TCGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGCC
*
45885 AAATAAGGGCCTAATGTCATCGAAAATACTCAAATAAGGG
1 AAATAAGGGCCTAATGT-TTCGAAAATACTCAAATAAGGG
45925 CATGGCGTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
59 3 0.04
60 79 0.93
61 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTTCGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGCC
Found at i:45922 original size:31 final size:31
Alignment explanation
Indices: 45824--45925 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 31
45814 TTAATTTGGC
* * *
45824 CAAATAAGAGCCTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATGTCATCGAAAATACT
* * * ** **
45855 CAAATAAGGTCCT--GGTCTTTTAATTTAGC-
1 CAAATAAGGGCCTAATGTCATCGAAAATA-CT
45884 CAAATAAGGGCCTAATGTCATCGAAAATACT
1 CAAATAAGGGCCTAATGTCATCGAAAATACT
45915 CAAATAAGGGC
1 CAAATAAGGGC
45926 ATGGCGTCGA
Statistics
Matches: 50, Mismatches: 17, Indels: 8
0.67 0.23 0.11
Matches are distributed among these distances:
29 18 0.36
30 2 0.04
31 30 0.60
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTCATCGAAAATACT
Found at i:46384 original size:60 final size:61
Alignment explanation
Indices: 46288--46448 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 61
46278 GCTAATTGCT
* * * *
46288 CAAATAAGGGTCTAATATT-TGCTAAAATACTTAAATAAGGGTCC-GATATTTTAATTTGGC
1 CAAATAAGGGTCTAATGTTAT-CGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGC
* * *
46348 CAAATAAGAGTCTAATGTTATCGAAAATGCTCAAATAA-GGTCCTGGTATTTTAATTTAGC
1 CAAATAAGGGTCTAATGTTATCGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGC
*
46408 CAAATAAGGGTCTAATGTCATCGAAAATACTCAAATAAGGG
1 CAAATAAGGGTCTAATGTTATCGAAAATACTCAAATAAGGG
46449 CATGGCATCG
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 5 0.06
60 80 0.91
61 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (61 bp):
CAAATAAGGGTCTAATGTTATCGAAAATACTCAAATAAGGGTCCTGATATTTTAATTTAGC
Found at i:46463 original size:28 final size:30
Alignment explanation
Indices: 46408--46468 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
46398 TTAATTTAGC
*
46408 CAAATAAGGGTCTAATGTCATCGAAAATACT
1 CAAATAAGGGTC-AATGGCATCGAAAATACT
*
46439 CAAATAAGGG-C-ATGGCATCGAAAATTCT
1 CAAATAAGGGTCAATGGCATCGAAAATACT
46467 CA
1 CA
46469 CGCGTCATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.61
30 1 0.04
31 10 0.36
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (30 bp):
CAAATAAGGGTCAATGGCATCGAAAATACT
Found at i:46511 original size:524 final size:523
Alignment explanation
Indices: 45516--46563 Score: 1979
Period size: 524 Copynumber: 2.0 Consensus size: 523
45506 AAGTTTAGTT
* *
45516 GAGGGAAGGCTGTCACAGTTCAGGGTGAGGGTATGCCACAAGCCTCAGAGAGGGCTTATAGTGAT
1 GAGGGAAGGCTGTCACAGTCCAGGGTGAGGGTATGCCACAAGCCTCAGAGAGGGCTTACAGTGAT
45581 ACTTACAGATCACCCACTAATGAGAACCATTGACACGACTCGAACCCCAAACCTTACAAGTAGAG
66 ACTTACAGATCACCCACTAATGAGAACCATTGACACGACTCGAACCCCAAACCTTACAAGTAGAG
45646 GTCCAAAGGCTTACTAACTCAACCAACCTCAATTGGCAATTGCAAGCTTTACATAACTTTTCATA
131 GTCCAAAGGCTTACTAACTCAACCAACCTCAATTGGCAATTGCAAGCTTTACATAACTTTTCATA
*
45711 ACTGAATCGGTTATTGAATCCGTATAGCAAAATGAATATTAAGGCTAATTGCTTAAATAAGGGTC
196 ACTGAATCGGTTATTGAATCCGTATAGCAAAATGAATATTAAGGCTAATTGCTCAAATAAGGGTC
* *
45776 TAATGTTTGCCAAAATACTTAAATAAGGGTCTGATATTTTAATTTGGCCAAATAAGAGCCTAATG
261 TAATATTTGCCAAAATACTTAAATAAGGGTCCGATATTTTAATTTGGCCAAATAAGAGCCTAATG
*
45841 TTATCGAAAATGCTCAAATAAGGTCCTGGTCTTTTAATTTAGCCAAATAAGGGCCTAATGTCATC
326 TTATCGAAAATGCTCAAATAAGGTCCTGGTATTTTAATTTAGCCAAATAAGGGCCTAATGTCATC
*
45906 GAAAATACTCAAATAAGGGCATGGCGTCGAAAATTCTCACGCGTCATCCAAACTGACGCAGGCCC
391 GAAAATACTCAAATAAGGGCATGGCATCGAAAATTCTCACGCGTCATCCAAACTGACGCAGGCCC
45971 TTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTTTTCCAAATTACAAGATCAGGCCCTTAT
456 TTATTTGAGCATTTTCGATAACGCTAGGCCCTTA-TTTTTCCAAATTACAAGATCAGGCCCTTAT
46036 TTGA
520 TTGA
46040 GAGGGAAGGCTGTCACAGTCCAGGGTGAGGGTATGCCACAAGCCTCAGAGAGGGCTTACAGTGAT
1 GAGGGAAGGCTGTCACAGTCCAGGGTGAGGGTATGCCACAAGCCTCAGAGAGGGCTTACAGTGAT
46105 ACTTACAGATCACCCACTAATGAGAACCATTGACACGACTCGAACCCCAAACCTTACAAGTAGAG
66 ACTTACAGATCACCCACTAATGAGAACCATTGACACGACTCGAACCCCAAACCTTACAAGTAGAG
*
46170 GTCCAAAGGCTTACTAACTCAACCAACCTCAATTGGCAATTGCAAGCTTTTCATAACTTTTCATA
131 GTCCAAAGGCTTACTAACTCAACCAACCTCAATTGGCAATTGCAAGCTTTACATAACTTTTCATA
46235 ACTGAATCGGTTATTGAATCCGTATAGCAAAATGAATATTAAGGCTAATTGCTCAAATAAGGGTC
196 ACTGAATCGGTTATTGAATCCGTATAGCAAAATGAATATTAAGGCTAATTGCTCAAATAAGGGTC
* *
46300 TAATATTTGCTAAAATACTTAAATAAGGGTCCGATATTTTAATTTGGCCAAATAAGAGTCTAATG
261 TAATATTTGCCAAAATACTTAAATAAGGGTCCGATATTTTAATTTGGCCAAATAAGAGCCTAATG
*
46365 TTATCGAAAATGCTCAAATAAGGTCCTGGTATTTTAATTTAGCCAAATAAGGGTCTAATGTCATC
326 TTATCGAAAATGCTCAAATAAGGTCCTGGTATTTTAATTTAGCCAAATAAGGGCCTAATGTCATC
46430 GAAAATACTCAAATAAGGGCATGGCATCGAAAATTCTCACGCGTCATCCAAACTGACGCAGGCCC
391 GAAAATACTCAAATAAGGGCATGGCATCGAAAATTCTCACGCGTCATCCAAACTGACGCAGGCCC
*
46495 TTATTTGAGTATTTTCGATAACGCTAGGCCCTTATTTTTCCAAATTACAAGATCAGGCCCTTATT
456 TTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTTTCCAAATTACAAGATCAGGCCCTTATT
46560 TGA
521 TGA
46563 G
1 G
46564 GATTTTCGAT
Statistics
Matches: 512, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
523 35 0.07
524 477 0.93
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (523 bp):
GAGGGAAGGCTGTCACAGTCCAGGGTGAGGGTATGCCACAAGCCTCAGAGAGGGCTTACAGTGAT
ACTTACAGATCACCCACTAATGAGAACCATTGACACGACTCGAACCCCAAACCTTACAAGTAGAG
GTCCAAAGGCTTACTAACTCAACCAACCTCAATTGGCAATTGCAAGCTTTACATAACTTTTCATA
ACTGAATCGGTTATTGAATCCGTATAGCAAAATGAATATTAAGGCTAATTGCTCAAATAAGGGTC
TAATATTTGCCAAAATACTTAAATAAGGGTCCGATATTTTAATTTGGCCAAATAAGAGCCTAATG
TTATCGAAAATGCTCAAATAAGGTCCTGGTATTTTAATTTAGCCAAATAAGGGCCTAATGTCATC
GAAAATACTCAAATAAGGGCATGGCATCGAAAATTCTCACGCGTCATCCAAACTGACGCAGGCCC
TTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTTTCCAAATTACAAGATCAGGCCCTTATT
TGA
Found at i:46569 original size:60 final size:60
Alignment explanation
Indices: 46488--46629 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 60
46478 CAAACTGACG
* ** *
46488 CAGGCCCTTATTTGAGTATTTTCGATAACGCTAGGCCCTTATTTTTCCAAATTACAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTGACCAAATTAAAAGAT
* * **
46548 CAGGCCCTTATTTGAGGATTTTCGATAACGTTAGGTTCTTATTTGACCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTGACCAAATTAAAAGAT
* *
46608 CAGACGCTTATTTGAGCATTTT
1 CAGGCCCTTATTTGAGCATTTT
46630 TACAAACGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTGACCAAATTAAAAGAT
Found at i:46649 original size:60 final size:60
Alignment explanation
Indices: 46492--46661 Score: 193
Period size: 60 Copynumber: 2.9 Consensus size: 60
46482 CTGACGCAGG
* * ** * *
46492 CCCTTATTTGAGTATTTTCGATAACGCTAGGCCCTTATTTTTCCAAATTACAAGATCAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* **
46552 CCCTTATTTGAGGATTTTCGATAACGTTAGGTTCTTATTTGACCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* * *
46612 CGCTTATTTGAGCATTTTTAC-A-AACGTTAGACCCTTATTTGAGC-AATTAA
1 CCCTTATTTGAGCA-TTTT-CGATAACGTTAGGCCCTTATTTGACCAAATTAA
46662 CTATGTTAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
59 6 0.06
60 82 0.87
61 5 0.05
62 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
Found at i:47912 original size:19 final size:19
Alignment explanation
Indices: 47892--47928 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47882 AATTAATTAT
47892 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
47910 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
47929 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:47939 original size:19 final size:19
Alignment explanation
Indices: 47898--47939 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47888 TTATTTTAAT
* * *
47898 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
47917 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
47936 ATTA
1 ATTA
47940 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:50945 original size:1 final size:1
Alignment explanation
Indices: 50939--50965 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50929 CGATGGTGGG
50939 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
50966 CATGTCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.