Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014683.1 Corchorus olitorius cultivar O-4 contig14716, 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: 77866
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6306 original size:60 final size:60
Alignment explanation
Indices: 6233--6372 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
6223 ATGATTTGAT
* * ** * * *
6233 AAAATGTTTAAATAAGGGCCCGATCTTTTCATTTGGCCAAATAAAGGTCTAACGTTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAAAGTTATCG
* * *
6293 AAAATGCTCAAATAAGGGTCCGATCTTTGAATTTGACCAAATTAGGGCCTAAAGTTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAAAGTTATCG
6353 AAAATGCTCAAATAAGGGCC
1 AAAATGCTCAAATAAGGGCC
6373 TGACGTAAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAAAGTTATCG
Found at i:7840 original size:21 final size:21
Alignment explanation
Indices: 7815--7897 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
7805 TATCTTAGAT
7815 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
7836 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
7857 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
7879 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
7898 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:7848 original size:25 final size:25
Alignment explanation
Indices: 7817--7865 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
7807 TCTTAGATAT
*
7817 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
7842 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
7866 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:9569 original size:2 final size:2
Alignment explanation
Indices: 9562--9594 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
9552 TAATATTTAG
9562 TA TA TA TA TA TA TA T- TA GTA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T
9595 TTACAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9581 original size:18 final size:18
Alignment explanation
Indices: 9554--9595 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
9544 GTTTCAAATA
9554 ATAT-TTAGTATATATAT
1 ATATATTAGTATATATAT
9571 ATATATTAGTATATATAT
1 ATATATTAGTATATATAT
9589 ATATATT
1 ATATATT
9596 TACAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
ATATATTAGTATATATAT
Found at i:11857 original size:27 final size:27
Alignment explanation
Indices: 11818--11872 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
11808 TACTTATTGA
* *
11818 TGGAGTACTCCTTGGAGAATCAGGTTT
1 TGGAATACCCCTTGGAGAATCAGGTTT
*
11845 TGGAATACCCCTTGGAGAGTCAGGTTT
1 TGGAATACCCCTTGGAGAATCAGGTTT
11872 T
1 T
11873 CCTGCAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (27 bp):
TGGAATACCCCTTGGAGAATCAGGTTT
Found at i:15681 original size:75 final size:75
Alignment explanation
Indices: 15183--15674 Score: 702
Period size: 75 Copynumber: 6.6 Consensus size: 75
15173 TCAAGATTGT
* * * * * * * *
15183 TTTTATCATTTTCTTTCATTAACTTTCTGTTT-TCTTCTTCAAGTTTCT-TGACTTCTAATGCCT
1 TTTTACCATGTTCTTCCATTAACTTCCT-TTTCTCCTCTTCAAATTTCTGT-AATTCTAAT-TCT
* *
15246 TT-TCAAGAATTT
63 TTCTCAAGACTTC
* * * *
15258 TTTTATCATTTTCTTCCATTAACTTTCTTTTCTCCTCTTCAACTTTCTGTAATTCTAATTCTTTC
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
*
15323 TCAAGAATTC
66 TCAAGACTTC
* * * *
15333 TTTTATCACGTTCTTCCATTAGCTTCCTTTTCTCCTCTTCAAATTTCTGTATTTCTAATTCTTTC
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
15398 TCAAGACTTC
66 TCAAGACTTC
* *
15408 TTTTACCATGTTCTTCCATTAGCTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCCAATTCTTTC
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
15473 TCAAGACTTC
66 TCAAGACTTC
* * *
15483 TTTTACCATGTTCTTCCATCAGCTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCCAATTCTTTC
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
*
15548 TCAAGACTTA
66 TCAAGACTTC
15558 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
*
15623 TCAAGACTTA
66 TCAAGACTTC
15633 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAA
1 TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAA
15675 CCTTCTGCTT
Statistics
Matches: 392, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
74 7 0.02
75 384 0.98
76 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.51
Consensus pattern (75 bp):
TTTTACCATGTTCTTCCATTAACTTCCTTTTCTCCTCTTCAAATTTCTGTAATTCTAATTCTTTC
TCAAGACTTC
Found at i:19558 original size:17 final size:16
Alignment explanation
Indices: 19532--19586 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
19522 CAACGCCAAT
19532 AAAAACATTAAGAAGACG
1 AAAAA-ATTAAGAAGA-G
*
19550 AAAAAATTAA-AAGAA
1 AAAAAATTAAGAAGAG
19565 AAAAAATTAAAGAAGATG
1 AAAAAATT-AAGAAGA-G
19583 AAAA
1 AAAA
19587 GTAGAGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 8 0.25
16 6 0.19
17 9 0.28
18 9 0.28
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAAAATTAAGAAGAG
Found at i:28073 original size:100 final size:100
Alignment explanation
Indices: 27900--28092 Score: 359
Period size: 100 Copynumber: 1.9 Consensus size: 100
27890 TCATATAACA
27900 TGTTTCCAACTTTATAAGGAAATGAATTTGTATTCATCAGAAGTGAATACATTACAATCGACCCT
1 TGTTTCCAACTTTATAAGGAAATGAATTTGTATTCATCAGAAGTGAATACATTACAATCGACCCT
27965 AGTTCTCTAAGTGAACCCTTGGGCTACAGGTCGGG
66 AGTTCTCTAAGTGAACCCTTGGGCTACAGGTCGGG
* * *
28000 TGTTTCCAACTTTATGAGGAAATGAATTTGTATTCATTAGAAGTGAATACATTACAATCGACTCT
1 TGTTTCCAACTTTATAAGGAAATGAATTTGTATTCATCAGAAGTGAATACATTACAATCGACCCT
28065 AGTTCTCTAAGTGAACCCTTGGGCTACA
66 AGTTCTCTAAGTGAACCCTTGGGCTACA
28093 AATCGGGTTT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (100 bp):
TGTTTCCAACTTTATAAGGAAATGAATTTGTATTCATCAGAAGTGAATACATTACAATCGACCCT
AGTTCTCTAAGTGAACCCTTGGGCTACAGGTCGGG
Found at i:30625 original size:30 final size:30
Alignment explanation
Indices: 30478--30896 Score: 541
Period size: 30 Copynumber: 13.7 Consensus size: 30
30468 GAAAGGTAAA
* *
30478 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ** * * *
30510 ATTATGACATCTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATT-GCAA--G
* *
30543 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
** * **
30575 ATTGTGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
30605 ATCATGACAACTTATGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30635 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30665 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30695 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
30725 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30755 ACCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30785 ACCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
30815 ACCATGACAACTTCTAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
30845 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
30875 ATCATGACAACTTTTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
30897 TTTAGAGAGT
Statistics
Matches: 344, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
30 277 0.81
31 2 0.01
32 42 0.12
33 21 0.06
34 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:32811 original size:26 final size:26
Alignment explanation
Indices: 32782--32838 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
32772 TATATTAAAA
* *
32782 TAGCATTCGCATTAGTAATTAGGTAT
1 TAGCATTCGCATTAGCAATTAGGCAT
*
32808 TAGCATTTGCATTAGCAATTAGGCAT
1 TAGCATTCGCATTAGCAATTAGGCAT
32834 TAGCA
1 TAGCA
32839 GTTTGGCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (26 bp):
TAGCATTCGCATTAGCAATTAGGCAT
Found at i:32835 original size:14 final size:14
Alignment explanation
Indices: 32790--32838 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
32780 AATAGCATTC
*
32790 GCATTAGTAATTAG
1 GCATTAGCAATTAG
* *
32804 GTATTAGC-ATT-T
1 GCATTAGCAATTAG
32816 GCATTAGCAATTAG
1 GCATTAGCAATTAG
32830 GCATTAGCA
1 GCATTAGCA
32839 GTTTGGCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 7 0.25
13 6 0.21
14 15 0.54
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (14 bp):
GCATTAGCAATTAG
Found at i:36403 original size:22 final size:22
Alignment explanation
Indices: 36331--36495 Score: 142
Period size: 22 Copynumber: 7.6 Consensus size: 22
36321 AATGGTAATC
* **
36331 AGTAAAATGGTAATGA-TAATC
1 AGTAAAATGGTAATTAGTAAAA
* *
36352 AGTAAAATGGTGA-T-GTAAAT
1 AGTAAAATGGTAATTAGTAAAA
36372 AGT--AATGGTAATTAGTAAAA
1 AGTAAAATGGTAATTAGTAAAA
* * *
36392 AGTAAAATGGTAGTCAGTAAAG
1 AGTAAAATGGTAATTAGTAAAA
36414 AGTAAAATGGTAATTAGTAAGAA
1 AGTAAAATGGTAATTAGTAA-AA
* * * *
36437 AGGAAAAAAGGGAATAAGTAAAA
1 A-GTAAAATGGTAATTAGTAAAA
* * *
36460 AGTAAAATGGTAGTCAGTAAAG
1 AGTAAAATGGTAATTAGTAAAA
36482 AGTAAAATGGTAAT
1 AGTAAAATGGTAAT
36496 CAATATGAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
18 7 0.06
19 1 0.01
20 14 0.12
21 12 0.11
22 60 0.53
23 5 0.04
24 15 0.13
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24
Consensus pattern (22 bp):
AGTAAAATGGTAATTAGTAAAA
Found at i:36494 original size:68 final size:69
Alignment explanation
Indices: 36385--36569 Score: 270
Period size: 68 Copynumber: 2.7 Consensus size: 69
36375 AATGGTAATT
* *
36385 AGTAAAAAGTAAAATGGTAGTCAGTAAAGAGTAAAATGGTAATTAGTAAGAAAGG-AAAAAAGGG
1 AGTAAAAAGTAAAATGGTAGTCAGTAAAGAGTAAAATGGTAATCAGTAAGAAAGGAAAAAAAAGG
*
36449 AATA
66 AAGA
* *
36453 AGTAAAAAGTAAAATGGTAGTCAGTAAAGAGTAAAATGGTAATCAATATGAAAGGAAAAAAAAGG
1 AGTAAAAAGTAAAATGGTAGTCAGTAAAGAGTAAAATGGTAATCAGTAAGAAAGGAAAAAAAAGG
36518 AAGA
66 AAGA
*
36522 AG-AAGAAAGT-AAATGGTAATCAGT-AAGAGTAAAAATGGTAATCAGTAA
1 AGTAA-AAAGTAAAATGGTAGTCAGTAAAGAGT-AAAATGGTAATCAGTAA
36570 TTAAAGTCAA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
67 6 0.06
68 82 0.77
69 18 0.17
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.19
Consensus pattern (69 bp):
AGTAAAAAGTAAAATGGTAGTCAGTAAAGAGTAAAATGGTAATCAGTAAGAAAGGAAAAAAAAGG
AAGA
Found at i:36586 original size:32 final size:34
Alignment explanation
Indices: 36578--36769 Score: 118
Period size: 38 Copynumber: 5.6 Consensus size: 34
36568 AATTAAAGTC
* *
36578 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
1 AAGAGTAAAAATGGTAATCAGTAATTAAAGAT-AA
* *
36613 AAGAGTAGGAAAAAGGGTATTCAGTAATTAAAG----
1 AAGAGT---AAAAATGGTAATCAGTAATTAAAGATAA
* * *
36646 -AGAGTAAAAATGGTATTTAATAATT-AAGATAAA
1 AAGAGTAAAAATGGTAATCAGTAATTAAAGAT-AA
* *
36679 AATAGTATAAAAAATGGTAATCAGTAATTAAAGCTAA
1 AAGAG--T-AAAAATGGTAATCAGTAATTAAAGATAA
*
36716 AAGGAGTAAAAATGGT-ATCTAGTAATT-AAGGTCAA
1 AA-GAGTAAAAATGGTAATC-AGTAATTAAAGAT-AA
36751 AA-AGT-AAAA-GGTAATCAGT
1 AAGAGTAAAAATGGTAATCAGT
36770 GGTTAAGTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 38
0.72 0.06 0.21
Matches are distributed among these distances:
28 3 0.02
29 17 0.13
31 6 0.05
32 12 0.09
33 3 0.02
34 10 0.08
35 26 0.20
36 2 0.02
37 21 0.16
38 29 0.22
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (34 bp):
AAGAGTAAAAATGGTAATCAGTAATTAAAGATAA
Found at i:36612 original size:38 final size:36
Alignment explanation
Indices: 36546--36754 Score: 115
Period size: 32 Copynumber: 6.1 Consensus size: 36
36536 GGTAATCAGT
* * *
36546 AAGAGT-AAAAATGGTAATCAGTAATTAAAG-T--C
1 AAGAGTGAAAAAGGGTATTCAGTAATTAAAGTTAAA
*
36578 AAGAGT-AAAAATGGTATTCAGTAATTAAAGTTAAA
1 AAGAGTGAAAAAGGGTATTCAGTAATTAAAGTTAAA
36613 AAGAGTAGGAAAAAGGGTATTCAGTAATTAAAG-----
1 AAGAGT--GAAAAAGGGTATTCAGTAATTAAAGTTAAA
* * * *
36646 -AGAGT-AAAAATGGTATTTAATAATT-AAGATAAA
1 AAGAGTGAAAAAGGGTATTCAGTAATTAAAGTTAAA
* * * * *
36679 AATAGTATAAAAAATGGTAATCAGTAATTAAAGCTAAA
1 AAGAG--TGAAAAAGGGTATTCAGTAATTAAAGTTAAA
* * * *
36717 AGGAGT-AAAAATGGTA-TCTAGTAATTAAGGTCAAA
1 AAGAGTGAAAAAGGGTATTC-AGTAATTAAAGTTAAA
36752 AAG
1 AAG
36755 TAAAAGGTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.02
29 17 0.12
32 34 0.24
33 1 0.01
34 5 0.03
35 31 0.22
36 2 0.01
37 17 0.12
38 33 0.23
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (36 bp):
AAGAGTGAAAAAGGGTATTCAGTAATTAAAGTTAAA
Found at i:36662 original size:29 final size:30
Alignment explanation
Indices: 36612--36672 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
36602 TTAAAGTTAA
*
36612 AAAGAGTAGGAAAAAGGGTATTCAGTAATT
1 AAAGAGTAGGAAAAAGGGTATTCAATAATT
* * *
36642 AAAGAG-AGTAAAAATGGTATTTAATAATT
1 AAAGAGTAGGAAAAAGGGTATTCAATAATT
36671 AA
1 AA
36673 GATAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (30 bp):
AAAGAGTAGGAAAAAGGGTATTCAATAATT
Found at i:36711 original size:66 final size:68
Alignment explanation
Indices: 36552--36711 Score: 216
Period size: 66 Copynumber: 2.4 Consensus size: 68
36542 CAGTAAGAGT
* *
36552 AAAAATGGTAATCAGTAATTAAAGTCAAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAAAAGA
1 AAAAATGGTAATCAGTAATTAAAG--AAGAGTAAAAATGGTATTCAATAATTAAAGATAAAAAGA
*
36617 GTAGG
64 GTAGA
* * * *
36622 AAAAAGGGTATTCAGTAATTAAAG-AGAGTAAAAATGGTATTTAATAATT-AAGATAAAAATAGT
1 AAAAATGGTAATCAGTAATTAAAGAAGAGTAAAAATGGTATTCAATAATTAAAGATAAAAAGAGT
*
36685 ATA
66 AGA
36688 AAAAATGGTAATCAGTAATTAAAG
1 AAAAATGGTAATCAGTAATTAAAG
36712 CTAAAAGGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
66 35 0.44
67 23 0.29
70 22 0.28
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.27
Consensus pattern (68 bp):
AAAAATGGTAATCAGTAATTAAAGAAGAGTAAAAATGGTATTCAATAATTAAAGATAAAAAGAGT
AGA
Found at i:36740 original size:35 final size:35
Alignment explanation
Indices: 36642--36744 Score: 102
Period size: 35 Copynumber: 2.9 Consensus size: 35
36632 TTCAGTAATT
* *
36642 AAAGAGAGTAAAAATGGTATTTAATAATT-AAGATA
1 AAAG-GAGTAAAAATGGTATCTAGTAATTAAAGATA
** *
36677 AAAATAGTATAAAAAATGGTAATC-AGTAATTAAAGCTA
1 AAAGGAG--T-AAAAATGGT-ATCTAGTAATTAAAGATA
36715 AAAGGAGTAAAAATGGTATCTAGTAATTAA
1 AAAGGAGTAAAAATGGTATCTAGTAATTAA
36745 GGTCAAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
34 5 0.09
35 21 0.38
36 2 0.04
37 15 0.27
38 12 0.22
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (35 bp):
AAAGGAGTAAAAATGGTATCTAGTAATTAAAGATA
Found at i:39241 original size:77 final size:77
Alignment explanation
Indices: 39153--39300 Score: 219
Period size: 77 Copynumber: 1.9 Consensus size: 77
39143 TTTTTTAAAT
* *
39153 TAAAATAGTAAAATGGT-AAATAT-AATAGTTATAAGGATATTATACTTAGTTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAT-TGAATAGTTATAAAGATATTAGACTTA-TTAAATAAAAATAG
*
39216 ATTTTTTAGTTGAC
64 AGTTTTTAGTTGAC
* *
39230 TAAAATGGTAAAATGGTAAAATTGAATAGTTATAAAGATATTAGATTTATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGGTAAAATTGAATAGTTATAAAGATATTAGACTTATTAAATAAAAATAGAG
39295 TTTTTA
66 TTTTTA
39301 TTAGAATAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 38 0.59
78 26 0.41
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGGTAAAATTGAATAGTTATAAAGATATTAGACTTATTAAATAAAAATAGAG
TTTTTAGTTGAC
Found at i:39318 original size:77 final size:77
Alignment explanation
Indices: 39160--39319 Score: 209
Period size: 77 Copynumber: 2.1 Consensus size: 77
39150 AATTAAAATA
* * *
39160 GTAAAATGGTAAATATAATAGTTATAAGGATATTATACTTAGTTAAATAAAAATAGATTTTTTAG
1 GTAAAATGGTAAATATAATAGTTATAAAGATATTAGACTTAGTTAAATAAAAATAGAGTTTTTAG
* **
39225 TTGACTAAAATG
66 TTGAATAAAACC
*
39237 GTAAAATGGTAAA-ATTGAATAGTTATAAAGATATTAGATTTA-TTAAATAAAAATAGAGTTTTT
1 GTAAAATGGTAAATA-T-AATAGTTATAAAGATATTAGACTTAGTTAAATAAAAATAGAGTTTTT
39300 A-TTAGAATAAAACC
64 AGTT-GAATAAAACC
39314 GTAAAA
1 GTAAAA
39320 GTTTATTTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
76 3 0.04
77 48 0.66
78 22 0.30
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.36
Consensus pattern (77 bp):
GTAAAATGGTAAATATAATAGTTATAAAGATATTAGACTTAGTTAAATAAAAATAGAGTTTTTAG
TTGAATAAAACC
Found at i:39603 original size:22 final size:24
Alignment explanation
Indices: 39560--39603 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
39550 TCGTACTTTT
*
39560 ATATATAGTATAGATACTAAAATC
1 ATATATAGTATAGATACAAAAATC
*
39584 ATATTTAGTAT-G-TACAAAAA
1 ATATATAGTATAGATACAAAAA
39604 AAAATCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 1 0.06
24 10 0.56
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (24 bp):
ATATATAGTATAGATACAAAAATC
Found at i:39630 original size:26 final size:26
Alignment explanation
Indices: 39578--39630 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39568 TATAGATACT
*
39578 AAAATCATATTTAGTATGTACAAAAA
1 AAAATCATATTTAGTATATACAAAAA
*
39604 AAAATCATATTTAGTAATATACTAAAA
1 AAAATCATATTTAGT-ATATACAAAAA
39631 TTTAGGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAATCATATTTAGTATATACAAAAA
Found at i:41303 original size:438 final size:436
Alignment explanation
Indices: 40439--41413 Score: 1314
Period size: 438 Copynumber: 2.2 Consensus size: 436
40429 AGTCAAAGCG
* * * * *
40439 TTAAATCGTCCAACCTATAATTGTAAAGGCTTCAATAGCATGAAACATAAAAGTATGAGGGTCAT
1 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCAT-AAACATAAAAGTATAAGGATCAT
* * **** * *
40504 TAGATAAATAATCCGGCAAAAAA-AAAAACTTTATGAAGAAAAAACATAAAAATTCCCTCTTGAA
65 TTGATAAATAATCCAGCAAAAAATAATTTGTTTATGAACAAAAAACATAAAAATTCCCTCTTCAA
* * * *
40568 TCCTCCACGAAACTCATTAATCAAATTCAACTTTCATGCTCTTAATGAAAGTCGTAGATAACACA
130 TCCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCTCTTAACGAAAGTCATAGATAACACA
*
40633 ATAACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACGATAAT
195 ATAACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACAATAAT
* *
40698 AAATAGACCGGCAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCGAAACATTAAAATT
260 AAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCGAAACATGAAAATT
* ** * *
40763 GGCTTCTGAGTTTTTCATGAAAGTTGTAGATCATGAGATTACCTTTTAATAGACACTTGAATCAC
325 GGCTTCTGAATCCTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATCAC
* * * **
40828 TTTGATCGGACAAATAGAACAGAAAATAAAAAATAAAAGCCGACGCA
390 CTTGATCGGACAAATAAAACAAAAAATAAAAAATAAAAGCCGAAACA
40875 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAATCATAAAAGTATAAGGATCAT
1 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAA-CATAAAAGTATAAGGATCAT
* **
40940 TTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGACATCAAACATAAAAATTCCCTC-TCA
65 TTGATAAATAATCCAGCAAAAAATA-ATTTGTTTATGAACAAAAAACATAAAAATTCCCTCTTCA
* * * *
41004 ATCCCTCCACGAAACTCATTAATCAAATTCAGCCTTCAGG-TCCTTGACGAAAGTCATAGATCAT
129 AT-CCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCT-CTTAACGAAAGTCATAGATAAC
* * *
41068 ACAATAACCTTTTAACCGACACTTGAACAA-TCTCAATCGGATAAGTGGATCGAAAATTATACAA
192 ACAATAACCTTTTAACCGACACTTGAACAACT-TCAATCGAACAAGTGGACCGAAAATTATACAA
* * * * *
41132 TATTAGATAGACCGACAATCGAGACCATAAAATTTAAGAAGCATTTTTTAGAATCGAAACATGAA
256 TAATAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCGAAACATGAA
41197 AATTGG-TT-TGCAATCCTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGA
321 AATTGGCTTCTG-AATCCTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGA
* *
41260 ATCACCTTGATCGGACAAGTAAAACAAAAAATAAAAGAATAAAAGCCGAAACG
385 ATCACCTTGATCGGACAAATAAAACAAAAAATAAAA-AATAAAAGCCGAAACA
* * * * *
41313 TTCAATCGTCCAACCCAGAATTTGTGAGGGATTAAATAGCATAAAGCATAAAAGTATAGGGATCA
1 TTAAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAA-CATAAAAGTATAAGGATCA
* * * *
41378 TTTGATAAACAATTCAGTAAAAAATGATTTGTTTAT
64 TTTGATAAATAATCCAGCAAAAAATAATTTGTTTAT
41414 TGAGAGCGGG
Statistics
Matches: 473, Mismatches: 57, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
435 3 0.01
436 79 0.17
437 88 0.19
438 241 0.51
439 62 0.13
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (436 bp):
TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAACATAAAAGTATAAGGATCATT
TGATAAATAATCCAGCAAAAAATAATTTGTTTATGAACAAAAAACATAAAAATTCCCTCTTCAAT
CCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCTCTTAACGAAAGTCATAGATAACACAA
TAACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACAATAATA
AATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCGAAACATGAAAATTG
GCTTCTGAATCCTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATCACC
TTGATCGGACAAATAAAACAAAAAATAAAAAATAAAAGCCGAAACA
Found at i:43184 original size:2 final size:2
Alignment explanation
Indices: 43177--43210 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
43167 CCCGTACTTT
43177 TA TA TA TA GTA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
43211 ATAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46317 original size:15 final size:15
Alignment explanation
Indices: 46277--46319 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
46267 TTAATTTATT
46277 TATTGAAAATAAAAA
1 TATTGAAAATAAAAA
*
46292 TATT-ATTAATAAAAA
1 TATTGA-AAATAAAAA
46307 TATTGAAAATAAA
1 TATTGAAAATAAA
46320 TTTTGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
TATTGAAAATAAAAA
Found at i:46375 original size:13 final size:13
Alignment explanation
Indices: 46359--46391 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
46349 AAATTAAATC
46359 TTAAAAATAATTA
1 TTAAAAATAATTA
46372 TTAAAAATAATTA
1 TTAAAAATAATTA
*
46385 TGAAAAA
1 TTAAAAA
46392 AACATATTCA
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TTAAAAATAATTA
Found at i:55198 original size:18 final size:18
Alignment explanation
Indices: 55175--55209 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55165 AATATCAATC
55175 ATCAATAAGATCAATTAA
1 ATCAATAAGATCAATTAA
* *
55193 ATCAATTAGATCTATTA
1 ATCAATAAGATCAATTA
55210 GTTAAATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (18 bp):
ATCAATAAGATCAATTAA
Found at i:57067 original size:9 final size:9
Alignment explanation
Indices: 57053--57077 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57043 AGTGCTAGGG
57053 TTAATTGGC
1 TTAATTGGC
57062 TTAATTGGC
1 TTAATTGGC
57071 TTAATTG
1 TTAATTG
57078 TGGTGATAAG
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (9 bp):
TTAATTGGC
Found at i:66040 original size:11 final size:11
Alignment explanation
Indices: 66024--66071 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
66014 GAAGTTCGTG
66024 TTTGAAGACTA
1 TTTGAAGACTA
66035 TTTGAAGA-TAA
1 TTTGAAGACT-A
66046 TTTGAAGAC--
1 TTTGAAGACTA
66055 -TTGAAGACTA
1 TTTGAAGACTA
66065 -TTGAAGA
1 TTTGAAGA
66072 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:71589 original size:21 final size:21
Alignment explanation
Indices: 71551--71590 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
71541 GAAGAGCGCA
* *
71551 TGGACCGCATGGAGGAGGCGG
1 TGGAACGCATGCAGGAGGCGG
*
71572 TGGAACGCATGCATGAGGC
1 TGGAACGCATGCAGGAGGC
71591 TGTTGAGGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.45, T:0.12
Consensus pattern (21 bp):
TGGAACGCATGCAGGAGGCGG
Found at i:74075 original size:19 final size:18
Alignment explanation
Indices: 74051--74086 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
74041 TGAAGACCAT
74051 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
74070 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
74087 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Done.