Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020251.1 Corchorus olitorius cultivar O-4 contig20284, 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: 61306
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--80 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
1 TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
81 ATATATATAT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:85 original size:2 final size:2
Alignment explanation
Indices: 80--108 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70 TCTCTCTCTC
80 TA TA 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 TA TA T
109 TGTGGCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:875 original size:23 final size:21
Alignment explanation
Indices: 828--875 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
818 GGTTATCAAT
*
828 ATAGGAAGGTTGTAAAATTTT
1 ATAGGAAGGTTGTAAAATTTC
*
849 ATAGGAAGGTTTATTAAAATTTC
1 ATAGGAAGG-TT-GTAAAATTTC
872 ATAG
1 ATAG
876 TTACGTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 12 0.52
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (21 bp):
ATAGGAAGGTTGTAAAATTTC
Found at i:8326 original size:2 final size:2
Alignment explanation
Indices: 8319--8355 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8309 AAAAATTACA
8319 AT AT AT 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 AT AT AT A
8356 CAAATGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8656 original size:66 final size:66
Alignment explanation
Indices: 8580--8710 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
8570 TATGTACGTT
* *
8580 TCAATTTGTAAATAGGGAAGCTAATGTATTAGCACATCCTCTAGCTAAGATTGAGTTGGATAATC
1 TCAATATGTAAATAGGGAAGCTAATGTATTAGCACATCCTCTAGCTAAGATTGAGATGGATAATC
8645 G
66 G
*
8646 TCAATATGTAAATAGGGAAGCTAATGTATTAGCACATTCTCTAGCTAAGATTGAGATGGATAATC
1 TCAATATGTAAATAGGGAAGCTAATGTATTAGCACATCCTCTAGCTAAGATTGAGATGGATAATC
8711 ATGTGGTGCG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (66 bp):
TCAATATGTAAATAGGGAAGCTAATGTATTAGCACATCCTCTAGCTAAGATTGAGATGGATAATC
G
Found at i:9130 original size:22 final size:22
Alignment explanation
Indices: 9097--9174 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 22
9087 ATAAACATTT
9097 TTATG-ATATTTTGATAACCTCC
1 TTATGAAT-TTTTGATAACCTCC
* * *
9119 TTATGAATTTTTTAAAACC-AC
1 TTATGAATTTTTGATAACCTCC
* * *
9140 TCTATGAAATTTTGTTAATCTCC
1 T-TATGAATTTTTGATAACCTCC
* *
9163 CTATAAATTTTT
1 TTATGAATTTTT
9175 TATACCATAG
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
21 2 0.05
22 36 0.88
23 3 0.07
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.47
Consensus pattern (22 bp):
TTATGAATTTTTGATAACCTCC
Found at i:9190 original size:43 final size:44
Alignment explanation
Indices: 9098--9215 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
9088 TAAACATTTT
* * * *
9098 TATGATATTTTGATAACCTCCTTATGAATTTTTTAAAACCACTC
1 TATGAAATTTTGATAATCTCCCTATAAATTTTTTAAAACCACTC
* * *
9142 TATGAAATTTTGTTAATCTCCCTATAAATTTTTT-ATACCA-TAG
1 TATGAAATTTTGATAATCTCCCTATAAATTTTTTAAAACCACT-C
* *
9185 TATGAAATCTTGATAATCTCTCTATGAAATT
1 TATGAAATTTTGATAATCTCCCTAT-AAATT
9216 ATATATCATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 27 0.44
44 34 0.55
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTCCCTATAAATTTTTTAAAACCACTC
Found at i:10897 original size:14 final size:13
Alignment explanation
Indices: 10878--10916 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10868 AAATTGTAAA
10878 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
10891 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
10905 ATTTAAAAAATT
1 ATTTAAAAAATT
10917 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:11153 original size:122 final size:128
Alignment explanation
Indices: 10902--11155 Score: 385
Period size: 122 Copynumber: 2.0 Consensus size: 128
10892 ATTTAAGAAA
10902 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT---AATAAAA
* * * *
10967 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAA
11032 G
128 G
*
11033 TATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-C
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
*
11094 ATA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAATTAAGTAAAACTATAAAAG
66 ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAAG
11155 T
1 T
11156 TTAAACAATG
Statistics
Matches: 117, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
122 53 0.45
123 2 0.02
124 3 0.03
125 5 0.04
126 1 0.01
130 46 0.39
131 7 0.06
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAAG
Found at i:11861 original size:77 final size:74
Alignment explanation
Indices: 11768--11908 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
11758 AGCAAGACCG
* *
11768 ACCATACAAGCTCATTTATAATGGATCATTAAAGACCAAAATTTTCTTCTTAAACCCATTTGAAA
1 ACCATACAAGCCCATTTATAATGG---ATTAAACACCAAAATTTTCTTCTTAAACCCATTTGAAA
11833 TGTTATTACACA
63 TGTTATTACACA
* *
11845 ACCATACAAGCCCATTTATAATGGATTGAACACCAGAATTTTCTTCTTAAACCCATTTGAAATG
1 ACCATACAAGCCCATTTATAATGGATTAAACACCAAAATTTTCTTCTTAAACCCATTTGAAATG
11909 AATCGCCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 37 0.62
77 23 0.38
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (74 bp):
ACCATACAAGCCCATTTATAATGGATTAAACACCAAAATTTTCTTCTTAAACCCATTTGAAATGT
TATTACACA
Found at i:13884 original size:12 final size:11
Alignment explanation
Indices: 13867--13891 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13857 TCTGAATTTG
13867 AAAAAAAAATT
1 AAAAAAAAATT
13878 AAAAAAAAATT
1 AAAAAAAAATT
13889 AAA
1 AAA
13892 TGACTGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:14197 original size:3 final size:3
Alignment explanation
Indices: 14189--14235 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
14179 TATCTATACC
*
14189 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14236 AAGTTATCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:14538 original size:69 final size:69
Alignment explanation
Indices: 14459--14593 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 69
14449 CATTTAACTT
* *
14459 CATTGCTATTAAATAAGATAAAATTTGATTTAGAATTGAAATTCCTCA-GTTCCAATCATAAACG
1 CATTGCTATTAAATAAGATAAAATTTGATTTAAAATTGAAATT-ATCACGTTCCAATCATAAACG
14523 GAGCG
65 GAGCG
14528 CATTGCTATTAAATAAGATAAAATTTGATTTAAAATTGAAATTATCACGTTCCAATCATAAACGG
1 CATTGCTATTAAATAAGATAAAATTTGATTTAAAATTGAAATTATCACGTTCCAATCATAAACGG
14593 A
66 A
14594 AAAATCTGAC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 3 0.05
69 60 0.95
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (69 bp):
CATTGCTATTAAATAAGATAAAATTTGATTTAAAATTGAAATTATCACGTTCCAATCATAAACGG
AGCG
Found at i:15956 original size:29 final size:28
Alignment explanation
Indices: 15860--15959 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 28
15850 ACGTTTACAA
*
15860 TCAAAGAAAATA--TCTTTT-TTTTGGAG
1 TCAAAGAAAATATCTCTTTTGTTTTGG-T
**
15886 TCAAAGAAAATATCTCTTTTGTTTTTTTTT
1 TCAAAGAAAATATCTCTTTTG--TTTTGGT
* *
15916 TGAAGAAAAAATATCTCTTTTGTTTTGGT
1 TCAA-AGAAAATATCTCTTTTGTTTTGGT
15945 TACAAAGAAAATATC
1 T-CAAAGAAAATATC
15960 AAAATTAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
26 12 0.21
28 6 0.10
29 15 0.26
30 5 0.09
31 20 0.34
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (28 bp):
TCAAAGAAAATATCTCTTTTGTTTTGGT
Found at i:16583 original size:3 final size:3
Alignment explanation
Indices: 16577--16666 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
16567 AATAATAATG
16577 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16625 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16667 CTAATTTCTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17405 original size:42 final size:41
Alignment explanation
Indices: 17346--17427 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 41
17336 TCCAAAATGT
*
17346 CCCTCCTAATAATTAAGGTAATAAATTAAAATCCATGTTTAG
1 CCCTCCTAATAATTAAGGTAATAAA-TAAAATCCAGGTTTAG
*
17388 CCCTCCTAATAATTAAGGTAATAAATCAAATCCAGGTTTA
1 CCCTCCTAATAATTAAGGTAATAAATAAAATCCAGGTTTA
17428 ACCCCTAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 13 0.34
42 25 0.66
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (41 bp):
CCCTCCTAATAATTAAGGTAATAAATAAAATCCAGGTTTAG
Found at i:17800 original size:21 final size:24
Alignment explanation
Indices: 17771--17821 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
17761 TTTTGAACTC
17771 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
17794 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
17817 ATTAT
1 ATTAT
17822 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:17816 original size:25 final size:25
Alignment explanation
Indices: 17771--17819 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17761 TTTTGAACTC
*
17771 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
17796 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
17820 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:27350 original size:14 final size:16
Alignment explanation
Indices: 27326--27357 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27316 ATTAAAGAAG
27326 TAACATAATTC-AGCT
1 TAACATAATTCTAGCT
27341 TAAC-TAATTCTAGCT
1 TAACATAATTCTAGCT
27356 TA
1 TA
27358 GATAAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
TAACATAATTCTAGCT
Found at i:28578 original size:24 final size:24
Alignment explanation
Indices: 28542--28591 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28532 ACACCCTCCA
*
28542 CCACCACCGCCAAAGCCGCGCCCT
1 CCACCACCCCCAAAGCCGCGCCCT
28566 CCACCACCCCCAAAGCCGCGCCCT
1 CCACCACCCCCAAAGCCGCGCCCT
28590 CC
1 CC
28592 GAATCCTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.62, G:0.14, T:0.04
Consensus pattern (24 bp):
CCACCACCCCCAAAGCCGCGCCCT
Found at i:28946 original size:1 final size:1
Alignment explanation
Indices: 28942--28969 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28932 GAAATCAAGA
28942 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
28970 GAAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28999 original size:32 final size:32
Alignment explanation
Indices: 28957--29023 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
28947 TTTTTTTTTT
28957 TTTTTTTTTTTTTGAAGAAAAAAATGAAACAAG
1 TTTTTTTTTTTTTG-AGAAAAAAATGAAACAAG
28990 TTTTTTTTTTTTTGAGAAAAAAATGAAACAAG
1 TTTTTTTTTTTTTGAGAAAAAAATGAAACAAG
29022 TT
1 TT
29024 ATTAGTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (32 bp):
TTTTTTTTTTTTTGAGAAAAAAATGAAACAAG
Found at i:30061 original size:28 final size:28
Alignment explanation
Indices: 30005--30061 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
29995 TCTAAAGTAT
***
30005 AAAAAATATAGAAGGTATTGATGCCAAA
1 AAAAAATATAGAAGGTATTGATAAAAAA
30033 AAAAAATATAGAAGGTATT-ACTAAAAAA
1 AAAAAATATAGAAGGTATTGA-TAAAAAA
30061 A
1 A
30062 TAAAGAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAAAATATAGAAGGTATTGATAAAAAA
Found at i:30268 original size:20 final size:20
Alignment explanation
Indices: 30245--30287 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30235 ATCAGCTATA
30245 TTTGGAACACGTCAGCAATT
1 TTTGGAACACGTCAGCAATT
* * *
30265 TTTGGACCACTTCATCAATT
1 TTTGGAACACGTCAGCAATT
30285 TTT
1 TTT
30288 ATGGTGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (20 bp):
TTTGGAACACGTCAGCAATT
Found at i:30340 original size:37 final size:37
Alignment explanation
Indices: 30290--30364 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
30280 CAATTTTTAT
30290 GGTGGGGAAAATTGTCATGATATTAATAGTTTTGAGG
1 GGTGGGGAAAATTGTCATGATATTAATAGTTTTGAGG
30327 GGTGGGGAAAATTGTCATGATATTAATAGTTTTGAGG
1 GGTGGGGAAAATTGTCATGATATTAATAGTTTTGAGG
30364 G
1 G
30365 TAATAGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (37 bp):
GGTGGGGAAAATTGTCATGATATTAATAGTTTTGAGG
Found at i:30468 original size:32 final size:33
Alignment explanation
Indices: 30395--30470 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
30385 TTTGAAGGGG
*
30395 AAATGTTCCTATTGTGAAAAGTTCCAAGGGAGA
1 AAATGTCCCTATTGTGAAAAGTTCCAAGGGAGA
* *
30428 AAATGTCCCTATTGT-ATAAGTT-CAAGGGGGA
1 AAATGTCCCTATTGTGAAAAGTTCCAAGGGAGA
*
30459 AATTGGTCCCTA
1 AAAT-GTCCCTA
30471 AACTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 11 0.29
32 13 0.34
33 14 0.37
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (33 bp):
AAATGTCCCTATTGTGAAAAGTTCCAAGGGAGA
Found at i:33441 original size:255 final size:255
Alignment explanation
Indices: 32990--33498 Score: 982
Period size: 255 Copynumber: 2.0 Consensus size: 255
32980 GGCTTAACAA
32990 AACAAGTGGCCTAACATGCATTTTAACAACACAAAAGTAAAATTACAAGCCTAATTAAAACATTA
1 AACAAGTGGCCTAACATGCATTTTAACAACACAAAAGTAAAATTACAAGCCTAATTAAAACATTA
33055 CAGCAAATACTCAACACTGCATGCAACTAAACACTAACACTCCTCCTTAGTTGCTAGCTGCATTA
66 CAGCAAATACTCAACACTGCATGCAACTAAACACTAACACTCCTCCTTAGTTGCTAGCTGCATTA
33120 CTCCAATTTTCATTCCCAAATCTTCAAACTTAGCCTTTGACAAAGGCTTTGTCAAAATATCAGCA
131 CTCCAATTTTCATTCCCAAATCTTCAAACTTAGCCTTTGACAAAGGCTTTGTCAAAATATCAGCA
33185 AAATGATCATCAGTGCTGCAATGCTCAAGTTCAATCTCACCTTCACACAAGACTTATCTG
196 AAATGATCATCAGTGCTGCAATGCTCAAGTTCAATCTCACCTTCACACAAGACTTATCTG
33245 AACAAGTGGCCTAACATGCATTTTAACAACACAAAAGTAAAATTACAAGCCTAATTAAAACATTA
1 AACAAGTGGCCTAACATGCATTTTAACAACACAAAAGTAAAATTACAAGCCTAATTAAAACATTA
*
33310 CAGCAAATACTCAACGCTGCATGCAACTAAACACTAACACTCCTCCTTAGTTGCTAGCTGCATTA
66 CAGCAAATACTCAACACTGCATGCAACTAAACACTAACACTCCTCCTTAGTTGCTAGCTGCATTA
**
33375 CTTTAATTTTCATTCCCAAATCTTCAAACTTAGCCTTTGACAAAGGCTTTGTCAAAATATCAGCA
131 CTCCAATTTTCATTCCCAAATCTTCAAACTTAGCCTTTGACAAAGGCTTTGTCAAAATATCAGCA
*
33440 AACTGATCATCAGTGCTGCAATGCTCAAGTTCAATCTCACCTTCACACAAGACTTATCT
196 AAATGATCATCAGTGCTGCAATGCTCAAGTTCAATCTCACCTTCACACAAGACTTATCT
33499 AATAAAATGG
Statistics
Matches: 250, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
255 250 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (255 bp):
AACAAGTGGCCTAACATGCATTTTAACAACACAAAAGTAAAATTACAAGCCTAATTAAAACATTA
CAGCAAATACTCAACACTGCATGCAACTAAACACTAACACTCCTCCTTAGTTGCTAGCTGCATTA
CTCCAATTTTCATTCCCAAATCTTCAAACTTAGCCTTTGACAAAGGCTTTGTCAAAATATCAGCA
AAATGATCATCAGTGCTGCAATGCTCAAGTTCAATCTCACCTTCACACAAGACTTATCTG
Found at i:37094 original size:234 final size:234
Alignment explanation
Indices: 36685--37154 Score: 922
Period size: 234 Copynumber: 2.0 Consensus size: 234
36675 AACTGCTGCT
*
36685 TTAAACTTCCAGAAGACCTCTGCTACCTCAGACTTCTGCTTCAGAAAATACATCCAAGCATATCT
1 TTAAACTTCCAGAAGACCTCTGCTACCTCAGACTTCTGCTTCAGAAAATAAATCCAAGCATATCT
36750 AGTATAATCATCAATGATAAGGATGAAATACCTGCTTCCATTCAAGCTTGGTGTTCTTTGTGGGC
66 AGTATAATCATCAATGATAAGGATGAAATACCTGCTTCCATTCAAGCTTGGTGTTCTTTGTGGGC
*
36815 CACATACATCAAATGCACAAGCTGCAACTTTTCTAAAGCTCTCCAACTTGCTTTAGCAGGAAAAG
131 CACATACATCAAATGCACAAGCTACAACTTTTCTAAAGCTCTCCAACTTGCTTTAGCAGGAAAAG
36880 GATTCCTATTTTGCTTCCCAAACTTGCACACATTACAAA
196 GATTCCTATTTTGCTTCCCAAACTTGCACACATTACAAA
36919 TTAAACTTCCAGAAGACCTCTGCTACCTCAGACTTCTGCTTCAGAAAATAAATCCAAGCATATCT
1 TTAAACTTCCAGAAGACCTCTGCTACCTCAGACTTCTGCTTCAGAAAATAAATCCAAGCATATCT
36984 AGTATAATCATCAATGATAAGGATGAAATACCTGCTTCCATTCAAGCTTGGTGTTCTTTGTGGGC
66 AGTATAATCATCAATGATAAGGATGAAATACCTGCTTCCATTCAAGCTTGGTGTTCTTTGTGGGC
37049 CACATACATCAAATGCACAAGCTACAACTTTTCTAAAGCTCTCCAACTTGCTTTAGCAGGAAAAG
131 CACATACATCAAATGCACAAGCTACAACTTTTCTAAAGCTCTCCAACTTGCTTTAGCAGGAAAAG
37114 GATTCCTATTTTGCTTCCCAAACTTGCACACATTACAAA
196 GATTCCTATTTTGCTTCCCAAACTTGCACACATTACAAA
37153 TT
1 TT
37155 CCAGTTTGCA
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
234 234 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (234 bp):
TTAAACTTCCAGAAGACCTCTGCTACCTCAGACTTCTGCTTCAGAAAATAAATCCAAGCATATCT
AGTATAATCATCAATGATAAGGATGAAATACCTGCTTCCATTCAAGCTTGGTGTTCTTTGTGGGC
CACATACATCAAATGCACAAGCTACAACTTTTCTAAAGCTCTCCAACTTGCTTTAGCAGGAAAAG
GATTCCTATTTTGCTTCCCAAACTTGCACACATTACAAA
Found at i:53099 original size:29 final size:29
Alignment explanation
Indices: 53057--53115 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
53047 GCAGCCTTGG
53057 AGTTGGATCCGACTTTAGATAATATATAT
1 AGTTGGATCCGACTTTAGATAATATATAT
53086 AGTTGGATCCGACTTTAGATAATATATAT
1 AGTTGGATCCGACTTTAGATAATATATAT
53115 A
1 A
53116 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (29 bp):
AGTTGGATCCGACTTTAGATAATATATAT
Found at i:53114 original size:2 final size:2
Alignment explanation
Indices: 53107--53131 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53097 ACTTTAGATA
53107 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 A
53132 GTATTTTGCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53221 original size:14 final size:14
Alignment explanation
Indices: 53202--53228 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53192 ACATGCGAAT
53202 GTATTAATTCAATC
1 GTATTAATTCAATC
53216 GTATTAATTCAAT
1 GTATTAATTCAAT
53229 GTTTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (14 bp):
GTATTAATTCAATC
Found at i:53484 original size:32 final size:32
Alignment explanation
Indices: 53419--53488 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
53409 TCAAAGAACA
* * *
53419 TTTGTCCTACTTTGTCAAAATTTGAAGGTTAT
1 TTTGTCCTACTATGTCAAAATTCGAAGGCTAT
*
53451 TTTGTCCTTCTATGTCAAAATTCG-AGAGCTAT
1 TTTGTCCTACTATGTCAAAATTCGAAG-GCTAT
53483 TTTGTC
1 TTTGTC
53489 TATCAATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.46
Consensus pattern (32 bp):
TTTGTCCTACTATGTCAAAATTCGAAGGCTAT
Done.