Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011326.1 Corchorus olitorius cultivar O-4 contig11359, 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: 118328
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:28058 original size:16 final size:16
Alignment explanation
Indices: 28028--28061 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28018 AAACTACTCG
28028 ATACAAATATATATAT
1 ATACAAATATATATAT
28044 ATACATAATAT-TATAT
1 ATACA-AATATATATAT
28060 AT
1 AT
28062 TTAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
ATACAAATATATATAT
Found at i:28526 original size:14 final size:15
Alignment explanation
Indices: 28503--28535 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28493 GGCCTAGCTT
*
28503 AAAGCTCTTCT-GAA
1 AAAGCGCTTCTGGAA
28517 AAAGCGCTTCTGGAA
1 AAAGCGCTTCTGGAA
28532 AAAG
1 AAAG
28536 TTTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (15 bp):
AAAGCGCTTCTGGAA
Found at i:29628 original size:2 final size:2
Alignment explanation
Indices: 29621--29655 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
29611 AGTTCGGATA
29621 AT AT AT AT AT AT AT AT AT AT -T AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
29656 ATTTTCGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34007 original size:23 final size:23
Alignment explanation
Indices: 33977--34047 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
33967 GGTATAGATA
33977 ATATAGGTATATATATGCTTTTC
1 ATATAGGTATATATATGCTTTTC
34000 ATATAGGTATATATATGCTTTTC
1 ATATAGGTATATATATGCTTTTC
34023 ATATAGGTATATATATGCTTTTC
1 ATATAGGTATATATATGCTTTTC
34046 AT
1 AT
34048 CATGATTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (23 bp):
ATATAGGTATATATATGCTTTTC
Found at i:36559 original size:3 final size:3
Alignment explanation
Indices: 36553--36615 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
36543 TTTTTTTTAC
*
36553 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
36599 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
36616 TAATTAGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:37793 original size:22 final size:22
Alignment explanation
Indices: 37768--37814 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
37758 ATTTTAGTTG
*
37768 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
37790 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
37812 AGT
1 AGT
37815 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:37793 original size:93 final size:93
Alignment explanation
Indices: 37691--37875 Score: 280
Period size: 93 Copynumber: 2.0 Consensus size: 93
37681 GCTTTTTAAT
* * *
37691 TAAATTAGTAATATCGTAAAAATGAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAG
*
37756 AAATTTTAGTTGAGTAAAACTATAAAAG
66 AAATTTTAGTTGACTAAAACTATAAAAG
* * * *
37784 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATATAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAG
**
37849 AGTTTTTAGTTGACTAAAACTATAAAA
66 AAATTTTAGTTGACTAAAACTATAAAA
37876 ATTTAAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAG
AAATTTTAGTTGACTAAAACTATAAAAG
Found at i:38573 original size:1 final size:1
Alignment explanation
Indices: 38567--38594 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
38557 AAGCTGGTAT
38567 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
38595 GGAACTTCTA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40439 original size:34 final size:34
Alignment explanation
Indices: 40396--40463 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
40386 TCATATATCA
40396 TAATAAAATCCATAAATAACATACATTTCAAATG
1 TAATAAAATCCATAAATAACATACATTTCAAATG
40430 TAATAAAATCCATAAATAACATACATTTCAAATG
1 TAATAAAATCCATAAATAACATACATTTCAAATG
40464 CACCATATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (34 bp):
TAATAAAATCCATAAATAACATACATTTCAAATG
Found at i:44958 original size:32 final size:32
Alignment explanation
Indices: 44922--44983 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
44912 ATAAATCTAT
*
44922 GGACTACTATGCAATTTTTCCATTTTTTGGAG
1 GGACTACTATGCAATCTTTCCATTTTTTGGAG
*
44954 GGACTACTATGTAATCTTTCCATTTTTTGG
1 GGACTACTATGCAATCTTTCCATTTTTTGG
44984 GGGGCCATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (32 bp):
GGACTACTATGCAATCTTTCCATTTTTTGGAG
Found at i:45837 original size:20 final size:20
Alignment explanation
Indices: 45812--45866 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
45802 AATTCACAAG
45812 GAACTAGACCAAGAAATAAT
1 GAACTAGACCAAGAAATAAT
45832 GAACTAGACCAAGAAATAAT
1 GAACTAGACCAAGAAATAAT
45852 GAACTAGACCAAGAA
1 GAACTAGACCAAGAA
45867 CTAAATTACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (20 bp):
GAACTAGACCAAGAAATAAT
Found at i:46660 original size:3 final size:3
Alignment explanation
Indices: 46654--46679 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46644 CTACAAGCTC
46654 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
46680 AAAGCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47312 original size:2 final size:2
Alignment explanation
Indices: 47305--47335 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47295 TTAAAATGTT
47305 TA 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 TA T
47336 GCATAATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48982 original size:43 final size:43
Alignment explanation
Indices: 48921--49002 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
48911 TATTACGTCA
*
48921 TTTTATTGTTGATAAAAGAATTATATTTTACGCAACAACACTG
1 TTTTATTGTTGATAAAAGAATTATATTTTACACAACAACACTG
*
48964 TTTTATTGTTGCTAAAAGAATTATATTTTACACAACAAC
1 TTTTATTGTTGATAAAAGAATTATATTTTACACAACAAC
49003 TCAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (43 bp):
TTTTATTGTTGATAAAAGAATTATATTTTACACAACAACACTG
Found at i:49013 original size:43 final size:43
Alignment explanation
Indices: 48923--49015 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
48913 TTACGTCATT
* ** *
48923 TTATTGTTGATAAAAGAATTATATTTTACGCAACAACACTGTT
1 TTATTGTTGATAAAAGAATTATATTTTACACAACAACACAATA
* *
48966 TTATTGTTGCTAAAAGAATTATATTTTACACAACAACTCAATA
1 TTATTGTTGATAAAAGAATTATATTTTACACAACAACACAATA
49009 TTATTGT
1 TTATTGT
49016 GTAAAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.41
Consensus pattern (43 bp):
TTATTGTTGATAAAAGAATTATATTTTACACAACAACACAATA
Found at i:49130 original size:42 final size:42
Alignment explanation
Indices: 49071--49156 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
49061 CTAATATAAC
49071 GATATTGTTTTCGCAATATAAGTATGAGTTCATTTGATGTAA
1 GATATTGTTTTCGCAATATAAGTATGAGTTCATTTGATGTAA
49113 GATATTGTTTTCGCAATATAAGTATGAGTTCATTTGATGTAA
1 GATATTGTTTTCGCAATATAAGTATGAGTTCATTTGATGTAA
49155 GA
1 GA
49157 AATGTCGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (42 bp):
GATATTGTTTTCGCAATATAAGTATGAGTTCATTTGATGTAA
Found at i:54463 original size:8 final size:8
Alignment explanation
Indices: 54450--54474 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54440 ATGGAGGTCT
54450 GGGATTTC
1 GGGATTTC
54458 GGGATTTC
1 GGGATTTC
54466 GGGATTTC
1 GGGATTTC
54474 G
1 G
54475 AATCTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.36
Consensus pattern (8 bp):
GGGATTTC
Found at i:59611 original size:178 final size:178
Alignment explanation
Indices: 59272--59618 Score: 421
Period size: 178 Copynumber: 1.9 Consensus size: 178
59262 AGTAGATTGT
*
59272 CTATTCCCGCTAACCGAAACAACTAATTATTTGGAAACATATTTTATACCTTGAACATTAAATTT
1 CTATTCCCGCTAACCGAAACAACAAATTATTTGGAAACATATTTTATACCTTGAACATTAAATTT
** * *
59337 AGTTTTTAAGTCCTTCAAGAAAATTGTAGATCATGGGACAACCTTTCAAGAGACAATTGAATCAC
66 AGTTTGCAAGTCCTTCAAGAAAATTGTAGATCATGGAACAACCTTTCAAGAGACAATTAAATCAC
* * *
59402 CTCAATCAGACATCTGGAACAAAAGTTATATAATATTAAGTGGACCGC
131 CTCAATCAGACAACTCGAACAAAAATTATATAATATTAAGTGGACCGC
* * *
59450 CTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATTTTTTATA-CTTGAAACATTAAAT
1 CTATTCCCGCTAACCGAAACAACAAATTATTT-GGAAACATATTTTATACCTTG-AACATTAAAT
* * * * * * * *
59513 TTAGTTTGCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAATCTTTTAATAGATACTTAAATC
64 TTAGTTTGCAAGTCCTTCAAGAAAATTGTAGATCATGGAACAACCTTTCAAGAGACAATTAAATC
** * * * *
59578 ACCTTGATCGGATAAC-CGAAGAGAAAATTATATAATGTTAA
129 ACCTCAATCAGACAACTCGAACA-AAAATTATATAATATTAA
59619 ATAGACCGTT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
177 11 0.08
178 130 0.92
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (178 bp):
CTATTCCCGCTAACCGAAACAACAAATTATTTGGAAACATATTTTATACCTTGAACATTAAATTT
AGTTTGCAAGTCCTTCAAGAAAATTGTAGATCATGGAACAACCTTTCAAGAGACAATTAAATCAC
CTCAATCAGACAACTCGAACAAAAATTATATAATATTAAGTGGACCGC
Found at i:64086 original size:23 final size:21
Alignment explanation
Indices: 64043--64087 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
64033 TTAAAATTTT
*
64043 TTTAAAATAAATTTTGGAAAA
1 TTTAAAATAAATTTTGCAAAA
*
64064 TTTAAAACTTAAATTTTTCAAAA
1 TTTAAAA--TAAATTTTGCAAAA
64087 T
1 T
64088 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
TTTAAAATAAATTTTGCAAAA
Found at i:66301 original size:31 final size:30
Alignment explanation
Indices: 66265--66324 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
66255 AGCAACTCTT
66265 TTTACTGGAAAACCAGAAAAAATGAAAAAAG
1 TTTACTGGAAAACCAG-AAAAATGAAAAAAG
**
66296 TTTACTGTCAAACCAGAAAAATGAAAAAA
1 TTTACTGGAAAACCAGAAAAATGAAAAAA
66325 CAAAAAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (30 bp):
TTTACTGGAAAACCAGAAAAATGAAAAAAG
Found at i:73589 original size:11 final size:11
Alignment explanation
Indices: 73555--73581 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
73545 TAATTTCTCC
73555 AAATTGATCCA
1 AAATTGATCCA
73566 AAATTGATCCA
1 AAATTGATCCA
73577 AAATT
1 AAATT
73582 ACTCCAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (11 bp):
AAATTGATCCA
Found at i:77383 original size:17 final size:17
Alignment explanation
Indices: 77350--77383 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
77340 GGTGTCTTAG
* *
77350 GGCTAGTTTAGAGTCAT
1 GGCTAGTTCAGACTCAT
77367 GGCTAGTTCAGACTCAT
1 GGCTAGTTCAGACTCAT
77384 CTCCTTGCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (17 bp):
GGCTAGTTCAGACTCAT
Found at i:78716 original size:8 final size:8
Alignment explanation
Indices: 78703--78730 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
78693 ACGCCTGTCA
78703 AAAAAAAT
1 AAAAAAAT
78711 AAAAAAAT
1 AAAAAAAT
78719 AAAAAAAT
1 AAAAAAAT
78727 AAAA
1 AAAA
78731 CTTTTGTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:79598 original size:4 final size:4
Alignment explanation
Indices: 79591--79683 Score: 186
Period size: 4 Copynumber: 23.2 Consensus size: 4
79581 ATTAATTGTA
79591 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
79639 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
79684 CTGTCTGGTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 89 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:80490 original size:7 final size:7
Alignment explanation
Indices: 80478--80568 Score: 182
Period size: 7 Copynumber: 13.0 Consensus size: 7
80468 TTTGCATTGC
80478 ATCTGCA
1 ATCTGCA
80485 ATCTGCA
1 ATCTGCA
80492 ATCTGCA
1 ATCTGCA
80499 ATCTGCA
1 ATCTGCA
80506 ATCTGCA
1 ATCTGCA
80513 ATCTGCA
1 ATCTGCA
80520 ATCTGCA
1 ATCTGCA
80527 ATCTGCA
1 ATCTGCA
80534 ATCTGCA
1 ATCTGCA
80541 ATCTGCA
1 ATCTGCA
80548 ATCTGCA
1 ATCTGCA
80555 ATCTGCA
1 ATCTGCA
80562 ATCTGCA
1 ATCTGCA
80569 TGATAAAAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 84 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
ATCTGCA
Found at i:82947 original size:9 final size:9
Alignment explanation
Indices: 82933--82963 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
82923 GTAAATGTAA
*
82933 ATTATTATT
1 ATTATTATG
82942 ATTATTATG
1 ATTATTATG
82951 ATTATTATG
1 ATTATTATG
82960 ATTA
1 ATTA
82964 GTGAATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (9 bp):
ATTATTATG
Found at i:82973 original size:6 final size:6
Alignment explanation
Indices: 82964--82993 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
82954 ATTATGATTA
82964 GTGAAT GTGAAT GTGAAT GTGAAT GTGAAT
1 GTGAAT GTGAAT GTGAAT GTGAAT GTGAAT
82994 TGATATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GTGAAT
Found at i:83084 original size:7 final size:7
Alignment explanation
Indices: 83074--83114 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
83064 GTTTTGTTGT
83074 TGATGAA
1 TGATGAA
**
83081 TGATGGT
1 TGATGAA
83088 TGATGAA
1 TGATGAA
83095 TGATGAA
1 TGATGAA
83102 TGATGAA
1 TGATGAA
83109 TGATGA
1 TGATGA
83115 TGGGGCCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (7 bp):
TGATGAA
Found at i:83127 original size:8 final size:8
Alignment explanation
Indices: 83114--83151 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
83104 ATGAATGATG
83114 ATGGGGCC
1 ATGGGGCC
83122 ATGGGGCC
1 ATGGGGCC
83130 ATGGGGCC
1 ATGGGGCC
83138 ATGGGGCC
1 ATGGGGCC
83146 ATGGGG
1 ATGGGG
83152 GAGGTGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.53, T:0.13
Consensus pattern (8 bp):
ATGGGGCC
Found at i:84586 original size:14 final size:13
Alignment explanation
Indices: 84555--84599 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
84545 TTCGGGTTTT
84555 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
84568 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
84582 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
84597 AGT
1 AGT
84600 GTGAGTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 9 0.33
15 4 0.15
16 3 0.11
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:100723 original size:22 final size:22
Alignment explanation
Indices: 100698--100751 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
100688 TCGAAACCGA
*
100698 AATGACCTGACCCTAAAAACTT
1 AATGACCCGACCCTAAAAACTT
**
100720 AATGACCCGACCCTAAATCCTT
1 AATGACCCGACCCTAAAAACTT
100742 AATGACCCGA
1 AATGACCCGA
100752 ACCCGATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (22 bp):
AATGACCCGACCCTAAAAACTT
Found at i:102725 original size:6 final size:6
Alignment explanation
Indices: 102714--102739 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
102704 CTCATCTCTA
102714 TGCCAT TGCCAT TGCCAT TGCCAT TG
1 TGCCAT TGCCAT TGCCAT TGCCAT TG
102740 GCTTTGGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.19, T:0.35
Consensus pattern (6 bp):
TGCCAT
Found at i:105379 original size:16 final size:16
Alignment explanation
Indices: 105358--105424 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
105348 AATCCGAACT
105358 CGAAAAAACTCAAATC
1 CGAAAAAACTCAAATC
105374 CG-AAAAAC-CAGAA-C
1 CGAAAAAACTCA-AATC
* * *
105388 CTGAAAAATCTAAAACC
1 C-GAAAAAACTCAAATC
* *
105405 CGAAAAAACCCGAATC
1 CGAAAAAACTCAAATC
105421 CGAA
1 CGAA
105425 CGTGAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
14 4 0.10
15 9 0.23
16 23 0.59
17 3 0.08
ACGTcount: A:0.54, C:0.27, G:0.10, T:0.09
Consensus pattern (16 bp):
CGAAAAAACTCAAATC
Found at i:105469 original size:20 final size:20
Alignment explanation
Indices: 105444--105482 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
105434 ACCCGAATTC
105444 AATAATAATTTCTGAAAATA
1 AATAATAATTTCTGAAAATA
105464 AATAATAATTTCTGAAAAT
1 AATAATAATTTCTGAAAAT
105483 TTTATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
AATAATAATTTCTGAAAATA
Found at i:105675 original size:32 final size:32
Alignment explanation
Indices: 105631--105714 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 32
105621 AAACCGAATT
* * *
105631 AACC-GACCCAAATTTGATCCAAACCCAGATC
1 AACCTGACACAAATTTAACCCAAACCCAGATC
* * *
105662 GACCTGACACAAATTTAACCCGAACCCATATC
1 AACCTGACACAAATTTAACCCAAACCCAGATC
* *
105694 AACCTGACCCGAATTTAACCC
1 AACCTGACACAAATTTAACCC
105715 GATCTAACTC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 3 0.07
32 40 0.93
ACGTcount: A:0.37, C:0.36, G:0.10, T:0.18
Consensus pattern (32 bp):
AACCTGACACAAATTTAACCCAAACCCAGATC
Found at i:105715 original size:32 final size:32
Alignment explanation
Indices: 105652--105716 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
105642 ATTTGATCCA
*
105652 AACCCAGATCGACCTGACACAAATTTAACCCG
1 AACCCAGATCAACCTGACACAAATTTAACCCG
* * *
105684 AACCCATATCAACCTGACCCGAATTTAACCCG
1 AACCCAGATCAACCTGACACAAATTTAACCCG
105716 A
1 A
105717 TCTAACTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.35, G:0.11, T:0.17
Consensus pattern (32 bp):
AACCCAGATCAACCTGACACAAATTTAACCCG
Found at i:115353 original size:12 final size:12
Alignment explanation
Indices: 115338--115362 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115328 GCAAAGCCAC
115338 CGGCAACGGCAG
1 CGGCAACGGCAG
115350 CGGCAACGGCAG
1 CGGCAACGGCAG
115362 C
1 C
115363 CCCTCTCAAC
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:0.24, C:0.36, G:0.40, T:0.00
Consensus pattern (12 bp):
CGGCAACGGCAG
Done.