Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006508.1 Corchorus capsularis cultivar CVL-1 contig06529, 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: 58537
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8982 original size:17 final size:17
Alignment explanation
Indices: 8957--8999 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
8947 TAGATGTTAT
* *
8957 CTAGCACCTTATGCTAC
1 CTAGTACCTCATGCTAC
*
8974 CTAGTACCTCATGTTAC
1 CTAGTACCTCATGCTAC
8991 CTAGGTACC
1 CTA-GTACC
9000 ATGAAGAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (17 bp):
CTAGTACCTCATGCTAC
Found at i:9289 original size:23 final size:23
Alignment explanation
Indices: 9245--9289 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9235 ACTTAACAAC
* *
9245 TTGCTCCGTGCTTATTTTCTCTA
1 TTGCTCCGAGCTTATTTACTCTA
9268 TTGCTCCGAGCCTT-TTTACTCT
1 TTGCTCCGAG-CTTATTTACTCT
9290 TGTTCATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.09, C:0.29, G:0.13, T:0.49
Consensus pattern (23 bp):
TTGCTCCGAGCTTATTTACTCTA
Found at i:12950 original size:49 final size:49
Alignment explanation
Indices: 12856--12952 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
12846 TGAGCTCATG
*
12856 CTAAAAATGTGCAAATTCGATTTTTTAAAAAAAATATGATCAAGCTTAA
1 CTAAAAATGTGCAAATTCGATTTTTTAAAAAAAATATAATCAAGCTTAA
* **
12905 CTAAAAATGTGCAAATTCGATTTTTT-TAAATGATATAATCAAAGCTTA
1 CTAAAAATGTGCAAATTCGATTTTTTAAAAAAAATATAATC-AAGCTTA
12953 TCGGTCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 10 0.23
49 33 0.77
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (49 bp):
CTAAAAATGTGCAAATTCGATTTTTTAAAAAAAATATAATCAAGCTTAA
Found at i:13853 original size:2 final size:2
Alignment explanation
Indices: 13846--13876 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13836 AAACATCAAA
13846 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
13877 CTAGTTTTAA
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:14272 original size:22 final size:22
Alignment explanation
Indices: 14247--14531 Score: 115
Period size: 22 Copynumber: 13.1 Consensus size: 22
14237 GAATTGTCAG
*
14247 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
14269 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * * *
14291 TAACCTCGCTATAAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
14313 TAAATCTTC-CTATGAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
14336 TAAAGCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
14359 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
14380 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
14397 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
14419 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
14441 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
14463 T-CTACATACTGTGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
14485 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
14507 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
14529 TAA
1 TAA
14532 CCTTCACATT
Statistics
Matches: 198, Mismatches: 48, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.01
19 2 0.01
21 8 0.04
22 136 0.69
23 40 0.20
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:14327 original size:45 final size:44
Alignment explanation
Indices: 14260--14384 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 44
14250 TCACACTCTG
* *
14260 AAATTTTGAT-AATC-ACACTATGAAATTGTGATAACCTCGCTATA
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAACCTCCCTATA
*
14304 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAAGCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGAT-AACCTCCCTATA
* *
14350 AAATTTTGATAACT-TTCTTATGAAATCTTGATAAC
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAAC
14385 TACAAATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
44 13 0.19
45 31 0.44
46 26 0.37
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAACCTCCCTATA
Found at i:14596 original size:19 final size:20
Alignment explanation
Indices: 14518--14590 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
14508 AACTAAACTA
* *
14518 TGAAATTTTGATAACCTTCACA
1 TGAAATTTTGATATCC-TC-CC
*
14540 TTAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
14560 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
14579 TGAAATTTTGAT
1 TGAAATTTTGAT
14591 TACTCCATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 18 0.40
20 11 0.24
21 2 0.04
22 14 0.31
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:14722 original size:44 final size:45
Alignment explanation
Indices: 14672--14799 Score: 122
Period size: 44 Copynumber: 2.9 Consensus size: 45
14662 GAAATACCAC
*
14672 TATGAAATTTTTGTAATCACATTT-TGAAAA-TTTGGTAACCTCTT
1 TATGAAATTTTTGTAATCACATTTAT-AAAATTTTGGTAACCCCTT
* * * *
14716 TATGAAA-TTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTTATAAAATTTTGGTAACCCCTT
* * * *
14760 TATGAAATTCTTATAATCACA-TTATATAATTTTGATAACC
1 TATGAAATTTTTGTAATCACATTTATAAAATTTTGGTAACC
14800 TCGCTTTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
43 12 0.18
44 52 0.78
45 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (45 bp):
TATGAAATTTTTGTAATCACATTTATAAAATTTTGGTAACCCCTT
Found at i:14767 original size:22 final size:22
Alignment explanation
Indices: 14696--14799 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
14686 AATCACATTT
* * *
14696 TGAAAATTTGGTAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
*
14718 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
14740 TAAAATTTTGTTGACCCCTTTA
1 TGAAATTTTGATAACCCCTTTA
* * *
14762 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAACCCCTTTA
14784 T-ATAATTTTGATAACC
1 TGA-AATTTTGATAACC
14800 TCGCTTTGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.05
22 61 0.92
23 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTTTA
Found at i:14876 original size:25 final size:23
Alignment explanation
Indices: 14822--14886 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 23
14812 TTTAACAATG
* *
14822 CTATGAAATTTTGACAAT-CTTC
1 CTATGAAATTTTGATAATCCATC
14844 CTAT-AAATTTTGATAATCCGATC
1 CTATGAAATTTTGATAATCC-ATC
*
14867 TCTATGAAATTTCGATAATC
1 -CTATGAAATTTTGATAATC
14887 ACTCTATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.33
22 5 0.14
23 2 0.06
24 4 0.11
25 13 0.36
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCCATC
Found at i:14894 original size:22 final size:22
Alignment explanation
Indices: 14671--14894 Score: 74
Period size: 22 Copynumber: 10.2 Consensus size: 22
14661 AGAAATACCA
14671 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * * *
14694 -TTTGAAAATTTGGTAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
14715 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
14737 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
14759 TTATGAAATTCTT-ATAATCACAT
1 CTATGAAATT-TTGATAATCAC-T
* * *
14782 -TAT-ATAATTTTGATAACCTCG
1 CTATGA-AATTTTGATAATCACT
* *
14803 CTTTGAAA-TTT--TAA-CAAT
1 CTATGAAATTTTGATAATCACT
* *
14821 GCTATGAAATTTTGACAATC-TT
1 -CTATGAAATTTTGATAATCACT
14843 CCTAT-AAATTTTGATAATCCGATCT
1 -CTATGAAATTTTGATAAT-C-A-CT
*
14868 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
14890 CTATG
1 CTATG
14895 GATTGGATAA
Statistics
Matches: 153, Mismatches: 30, Indels: 37
0.70 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 10 0.07
20 3 0.02
21 23 0.15
22 92 0.60
23 6 0.04
24 5 0.03
25 13 0.08
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:14973 original size:22 final size:23
Alignment explanation
Indices: 14944--14998 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
14934 AAATTGAGAC
*
14944 TTTT-ATAACCTTCA-TATAAAA
1 TTTTGATAACCTACACTATAAAA
14965 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
14987 TTTTGATAACCT
1 TTTTGATAACCT
14999 CCCCATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:15214 original size:22 final size:22
Alignment explanation
Indices: 15107--15246 Score: 95
Period size: 22 Copynumber: 6.3 Consensus size: 22
15097 TTGTGATAAT
* **
15107 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * * *
15129 TATCCGA-CCTAAGAGATTTTAA
1 TAACC-ATCCTATGAAATTTTGA
*
15151 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
* *
15175 TAACCATACTATGGAATTTTGA
1 TAACCATCCTATGAAATTTTGA
* *
15197 TAA-CATCCTCATGAAATTGTAA
1 TAACCATCCT-ATGAAATTTTGA
* * *
15219 TAACCATCTTATAAAATTTTGT
1 TAACCATCCTATGAAATTTTGA
15241 TAACCA
1 TAACCA
15247 CATAGAGAAA
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
21 5 0.05
22 63 0.68
23 8 0.09
24 16 0.17
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:15442 original size:18 final size:19
Alignment explanation
Indices: 15412--15448 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
15402 TATTGACATT
15412 TAAAAATTGAAATT-AAAA
1 TAAAAATTGAAATTCAAAA
15430 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
15449 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAAATTGAAATTCAAAA
Found at i:15827 original size:31 final size:31
Alignment explanation
Indices: 15762--15820 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
15752 TGACAATTTA
*
15762 GAAATATGTTTTAAAGAAAATGGTACAACTG
1 GAAATATGTTTTAAAGAAAAGGGTACAACTG
15793 GAAATATGTTTTAAA-AATAAGGGTACAA
1 GAAATATGTTTTAAAGAA-AAGGGTACAA
15821 TCGGAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGGTACAACTG
Found at i:16934 original size:27 final size:28
Alignment explanation
Indices: 16892--16950 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
16882 TTTATAAATT
16892 ATTTAAGAAAAGTCAGTTAAGAAACGAA
1 ATTTAAGAAAAGTCAGTTAAGAAACGAA
* *
16920 ATTT-AGAAAATTCAGTTAAGAAATGAA
1 ATTTAAGAAAAGTCAGTTAAGAAACGAA
16947 ATTT
1 ATTT
16951 TATTGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (28 bp):
ATTTAAGAAAAGTCAGTTAAGAAACGAA
Found at i:17020 original size:16 final size:16
Alignment explanation
Indices: 16999--17032 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16989 ATTGAAGTAT
16999 TAAAAAGACAAGAGAA
1 TAAAAAGACAAGAGAA
*
17015 TAAAAAGACAATAGAA
1 TAAAAAGACAAGAGAA
17031 TA
1 TA
17033 TGGAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (16 bp):
TAAAAAGACAAGAGAA
Found at i:17853 original size:15 final size:15
Alignment explanation
Indices: 17833--17886 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
17823 TTCGGGTTGG
*
17833 ATTTGGGTCAGCTTA
1 ATTTGGGTCAGGTTA
* *
17848 ATTTGGATTCGGGTTA
1 ATTTGG-GTCAGGTTA
17864 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
*
17879 ATTCGGGT
1 ATTTGGGT
17887 TCGGGTTCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:17866 original size:16 final size:15
Alignment explanation
Indices: 17821--17893 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 15
17811 GCTTGAGTCG
*
17821 GGTTCGGGTTGGATTT
1 GGTTCGGGTT-AATTT
* * *
17837 GGGTCAGCTTAATTT
1 GGTTCGGGTTAATTT
17852 GGATTCGGGTTAATTT
1 GG-TTCGGGTTAATTT
* * *
17868 GGGTCAGGTTAATTCG
1 GGTTCGGGTTAATT-T
17884 GGTTCGGGTT
1 GGTTCGGGTT
17894 CTGTTTGGGT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
15 16 0.37
16 27 0.63
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.40
Consensus pattern (15 bp):
GGTTCGGGTTAATTT
Found at i:17871 original size:31 final size:32
Alignment explanation
Indices: 17818--17893 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
17808 CGGGCTTGAG
* *
17818 TCGGGTTCGGGTTGGATTTGGGTCAGCTTAAT
1 TCGGATTCGGGTTGAATTTGGGTCAGCTTAAT
* *
17850 TTGGATTCGGGTT-AATTTGGGTCAGGTTAAT
1 TCGGATTCGGGTTGAATTTGGGTCAGCTTAAT
*
17881 TCGGGTTCGGGTT
1 TCGGATTCGGGTT
17894 CTGTTTGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.13, C:0.11, G:0.37, T:0.39
Consensus pattern (32 bp):
TCGGATTCGGGTTGAATTTGGGTCAGCTTAAT
Found at i:18062 original size:16 final size:16
Alignment explanation
Indices: 18041--18137 Score: 86
Period size: 16 Copynumber: 6.0 Consensus size: 16
18031 TTTTCATAAA
*
18041 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* *
18057 TTTTCGGGTTTGAGCTT
1 TTTTCGGGTTCG-GGTT
*
18074 TTTTCGGGTTCGTGTT
1 TTTTCGGGTTCGGGTT
* ***
18090 TTTTCGGGTTTGAACT
1 TTTTCGGGTTCGGGTT
*
18106 TTTTCGGGTTCGAGTT
1 TTTTCGGGTTCGGGTT
* *
18122 TTTTCGAGTTCAGGTT
1 TTTTCGGGTTCGGGTT
18138 CAGACGGGTT
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
16 50 0.78
17 14 0.22
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.52
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:18109 original size:32 final size:33
Alignment explanation
Indices: 18041--18127 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
18031 TTTTCATAAA
* * *
18041 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCTT
1 TTTTCGGGTTCGAGTTTTTTCGGGTTTGAACTT
*
18074 TTTTCGGGTTCGTGTTTTTTCGGGTTTGAAC-T
1 TTTTCGGGTTCGAGTTTTTTCGGGTTTGAACTT
18106 TTTTCGGGTTCGAGTTTTTTCG
1 TTTTCGGGTTCGAGTTTTTTCG
18128 AGTTCAGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 22 0.44
33 28 0.56
ACGTcount: A:0.06, C:0.13, G:0.29, T:0.53
Consensus pattern (33 bp):
TTTTCGGGTTCGAGTTTTTTCGGGTTTGAACTT
Found at i:18893 original size:22 final size:22
Alignment explanation
Indices: 18867--18915 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
18857 ATAAAACGCC
18867 AATAATTATATC-ATAAAAAAAT
1 AATAATTAT-TCAATAAAAAAAT
* *
18889 TATAATTATTCAATTAAAAAAT
1 AATAATTATTCAATAAAAAAAT
18911 AATAA
1 AATAA
18916 AAAATATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATTATTCAATAAAAAAAT
Found at i:18918 original size:10 final size:10
Alignment explanation
Indices: 18903--18940 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
18893 ATTATTCAAT
18903 TAAAAAATAA
1 TAAAAAATAA
18913 TAAAAAAT-A
1 TAAAAAATAA
18922 TAAAAATATAA
1 TAAAAA-ATAA
18933 -AAAAAATA
1 TAAAAAATA
18941 TTCTGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 10 0.38
10 15 0.58
11 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:18924 original size:9 final size:9
Alignment explanation
Indices: 18903--18936 Score: 52
Period size: 8 Copynumber: 3.8 Consensus size: 9
18893 ATTATTCAAT
18903 TAAAAAATAA
1 TAAAAAAT-A
18913 TAAAAAATA
1 TAAAAAATA
18922 T-AAAAATA
1 TAAAAAATA
18930 TAAAAAA
1 TAAAAAA
18937 AATATTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 7 0.30
10 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAAAAATA
Found at i:18925 original size:19 final size:19
Alignment explanation
Indices: 18903--18941 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18893 ATTATTCAAT
18903 TAAAAA-ATAATAAAAAATA
1 TAAAAATATAA-AAAAAATA
18922 TAAAAATATAAAAAAAATA
1 TAAAAATATAAAAAAAATA
18941 T
1 T
18942 TCTGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAAATATAAAAAAAATA
Found at i:22966 original size:21 final size:20
Alignment explanation
Indices: 22937--22986 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
22927 GTTATTAGAA
*
22937 ATAATTCATTAGAAATTAATTT
1 ATAA-TCATTACAAATT-ATTT
*
22959 ATAATCATTACATATTATTT
1 ATAATCATTACAAATTATTT
*
22979 CTAATCAT
1 ATAATCAT
22987 ATTTGTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.44
21 10 0.40
22 4 0.16
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATCATTACAAATTATTT
Found at i:27230 original size:24 final size:24
Alignment explanation
Indices: 27203--27248 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
27193 CTTGGTTTTG
* *
27203 GATTGATTATCTTGATTTTACTAT
1 GATTGATGATCCTGATTTTACTAT
* *
27227 GATTTATGATCCTGGTTTTACT
1 GATTGATGATCCTGATTTTACT
27249 GATTTTCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (24 bp):
GATTGATGATCCTGATTTTACTAT
Found at i:28637 original size:16 final size:16
Alignment explanation
Indices: 28612--28642 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28602 TTTTAATACT
*
28612 AACTTCATTTTGTTTC
1 AACTTAATTTTGTTTC
28628 AACTTAATTTTGTTT
1 AACTTAATTTTGTTT
28643 TGATCCTTGA
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:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (16 bp):
AACTTAATTTTGTTTC
Found at i:36325 original size:13 final size:13
Alignment explanation
Indices: 36307--36340 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
36297 ATAATTATTG
36307 TTTGCTTTATTAA
1 TTTGCTTTATTAA
36320 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
36333 TCTGCTTT
1 TTTGCTTT
36341 GGATTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.62
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:36400 original size:26 final size:27
Alignment explanation
Indices: 36350--36399 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
36340 TGGATTTAGA
36350 TTTATATTTAGATTTAATTTGTTTTGT
1 TTTATATTTAGATTTAATTTGTTTTGT
*
36377 TTTATTTTTAG-TTTAA-TTGTTTT
1 TTTATATTTAGATTTAATTTGTTTT
36400 TTAGGGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 5 0.23
27 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (27 bp):
TTTATATTTAGATTTAATTTGTTTTGT
Found at i:36735 original size:26 final size:26
Alignment explanation
Indices: 36706--36760 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
36696 AAAAAAAAAG
* *
36706 TTTGCGTCGA-TAAAAAAAAATTTGTT
1 TTTGCATCGATTAAAAAAAAAGTT-TT
36732 TTTGCATCGATTAAAAAAAAAGTTTT
1 TTTGCATCGATTAAAAAAAAAGTTTT
36758 TTT
1 TTT
36761 CCGTTTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (26 bp):
TTTGCATCGATTAAAAAAAAAGTTTT
Found at i:43324 original size:13 final size:13
Alignment explanation
Indices: 43306--43338 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43296 AGAAGAAGTA
*
43306 TGCTTTATTAATT
1 TGCTTTATTAATC
43319 TGCTTTATTAATC
1 TGCTTTATTAATC
43332 TGCTTTA
1 TGCTTTA
43339 GATTTAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:43346 original size:6 final size:6
Alignment explanation
Indices: 43335--43366 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43325 ATTAATCTGC
43335 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
43367 GTTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:45844 original size:21 final size:21
Alignment explanation
Indices: 45820--45860 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45810 ACTGGCGGGC
*
45820 TTTACTTGCTGAGGAAGGCGT
1 TTTACTAGCTGAGGAAGGCGT
45841 TTTACTAGCTGAGGAAGGCG
1 TTTACTAGCTGAGGAAGGCG
45861 AACTCTTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (21 bp):
TTTACTAGCTGAGGAAGGCGT
Found at i:46580 original size:156 final size:158
Alignment explanation
Indices: 46391--46770 Score: 427
Period size: 156 Copynumber: 2.4 Consensus size: 158
46381 AAGCTTCTCA
*
46391 CCTCAAACTGTCCTTAAATGAAAAAGTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
* * *
46456 TTTT-GAAAAG-GGTCTTAGAATATC-CACATAAGACTAT-GGAAAAAATTCTAAGTAAAACCGA
66 TTTTCCAAAAGTAGACTTAGAATATCAC-CATAAGACTATGGGAAAAAA-TCTAAGTAAAACCGA
* * * *
46517 GCTCCCCT-TGATGGTGAACTAGGTTTCTCT
129 ACT-CCCTATGATAGAGAACTAGGTTTCACT
** * *
46547 CC-CTAAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATG-AGCTGA
** * *
46609 -ATTTTCCACCAGTAGACTTAGATTATCACCATAAGGCTATGGGAAAAAATCTAAGTAAAACCGA
64 AATTTTCCAAAAGTAGACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCGA
* * * *
46673 ACTCTCTATGATAGAGAAGTTGGTTTGACT
129 ACTCCCTATGATAGAGAACTAGGTTTCACT
* * ** *
46703 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGTTTGAGATGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
46768 TTT
66 TTT
46771 CACCTAGATG
Statistics
Matches: 184, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
154 5 0.03
155 10 0.05
156 154 0.84
157 11 0.06
158 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (158 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
TTTTCCAAAAGTAGACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCGAAC
TCCCTATGATAGAGAACTAGGTTTCACT
Found at i:48130 original size:8 final size:8
Alignment explanation
Indices: 48117--48146 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
48107 AGCGGTAGAA
48117 GAAGAGAG
1 GAAGAGAG
48125 GAAGAGAG
1 GAAGAGAG
48133 GAAGAGAG
1 GAAGAGAG
48141 G-AGAGA
1 GAAGAGA
48147 AAGATGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (8 bp):
GAAGAGAG
Found at i:54111 original size:36 final size:35
Alignment explanation
Indices: 54063--54160 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 35
54053 TCCTATGTTT
* *
54063 ATTAAGCATTCCATTGTGCTTGTTGGCCATTATTCA
1 ATTAAGCTTTCCATGGTGCTTGTTGGCCATTATT-A
* *
54099 CTTAAGCTTTCCATGGTGCTTGTTGGCCTTTATTA
1 ATTAAGCTTTCCATGGTGCTTGTTGGCCATTATTA
54134 ATTAAGCTTTTCCATGGTGCTTGTTGG
1 ATTAAGC-TTTCCATGGTGCTTGTTGG
54161 GTGGTGTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 7 0.12
36 49 0.88
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.44
Consensus pattern (35 bp):
ATTAAGCTTTCCATGGTGCTTGTTGGCCATTATTA
Found at i:54724 original size:26 final size:26
Alignment explanation
Indices: 54668--54725 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
54658 TTTTCATTAA
* * * *
54668 AAAAATATTTTCTCTATTTTTTCTTT
1 AAAAATATTTACTCTACTATTTCTTC
54694 AAAAATATTTACTC-ACTATTTCTTC
1 AAAAATATTTACTCTACTATTTCTTC
54719 ATAAAAT
1 A-AAAAT
54726 TGGTGAGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (26 bp):
AAAAATATTTACTCTACTATTTCTTC
Done.