Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007508.1 Corchorus capsularis cultivar CVL-1 contig07529, 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: 29027
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:4517 original size:60 final size:60
Alignment explanation
Indices: 4451--4596 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
4441 GGGCATAAGG
* *** * *
4451 TTTGTCAAAATGTTCAAATAAGGGTTTGATCTTTTAATTTGACCAAATAAAGGCTTAACA
1 TTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAACA
* * * * *
4511 TTTGTCAAAATACTCAAATAAGGGCCCGGTCTTTGAATTTGGCCAAATAAGGGCCTAACG
1 TTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAACA
*
4571 TTTGCCAAAATGCTCAAATAAGGGCC
1 TTTGTCAAAATGCTCAAATAAGGGCC
4597 TATCTCATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (60 bp):
TTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGACCAAATAAAGGCCTAACA
Found at i:4663 original size:31 final size:31
Alignment explanation
Indices: 4625--4823 Score: 157
Period size: 31 Copynumber: 6.5 Consensus size: 31
4615 AACTGAAACC
*
4625 AGGCCCTTATTTGAGTATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* *
4656 AGGCCCTTATTTGAGCATTTTCAATAATGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
** * *
4687 AGGCCCTTATTTG-GCCAAATT--AGAA-GATC
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
4716 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* * * *
4747 AGACCCTTATTTG-GCCGA-ATT--A-AAAGATC
1 AGGCCCTTATTTGAG-C-ATTTTCGATAACG-TT
* *
4776 AGACCCTTATTTGAGCATTTTGGCA-AACGTT
1 AGGCCCTTATTTGAGCATTTTCG-ATAACGTT
4807 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
4824 ATTAGCTCAC
Statistics
Matches: 135, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
28 5 0.04
29 39 0.29
30 4 0.03
31 81 0.60
32 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:4728 original size:60 final size:59
Alignment explanation
Indices: 4656--4819 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 59
4646 CGATAACGTT
* *
4656 AGGCCCTTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTGGCCAAATTAGAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* *
4716 AGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCGAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
*
4776 AGACCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
4820 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
60 93 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:7040 original size:2 final size:2
Alignment explanation
Indices: 7035--7066 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7025 TATAAGTACC
7035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7067 GAGGATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7764 original size:6 final size:6
Alignment explanation
Indices: 7753--7790 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
7743 ATTGAAAATT
7753 TAAAAA T-AAAA -AAAAA T-AAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
7791 GACCCATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 13 0.45
6 16 0.55
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:14382 original size:37 final size:37
Alignment explanation
Indices: 14332--15008 Score: 871
Period size: 37 Copynumber: 18.4 Consensus size: 37
14322 CAATCAATGT
*
14332 CTTAATTCAGGGTAATTAAATAAAAGCAGTTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
*
14369 CTTAATTCAGGGTAATTAAGTAAAAGCGGTTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* *
14406 CTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * * *
14443 CTTGATTCAGGGAAATTAAGTAAAAGTAGTTAACGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * *
14480 CTTAATTGAGGGAAATTAAGTAAAAGTAGTTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* *
14517 CTTAATTCAGGGAAATTAAGTAAAAGCAG-TAAAGGG
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * *
14553 CTTAGTTCAGGGAAATTAAGTAAAAGCAG-TAAAAGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* *
14589 CTTAATTCAGTGTAATTAAGTAAAAGCAGTTAAAGGG
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * *
14626 CTAAATTCAGGGGAATTAAGTAAAAGCAGTTAAAGGT
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
** *
14663 CTTAATTCAAGGAAAATTAAGTAAAAGCAGTGAAAGGA
1 CTTAATTC-AGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * * * *
14701 CCTAATTCAGGGTATTTAAATAAAAAACAGTTAAATGA
1 CTTAATTCAGGGTAATTAAGT-AAAAGCAGTTAAAGGA
*
14739 CTTAATTCAGAGTAATTAAGTAAAAGCAG-TAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * *
14775 CTTAATTCAGGGAAATTAAGTAAAAGCAATAAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * *
14812 CCTAATTCAGGGTAATTAAGTAAAAACAATTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
14849 CTTAATTCAGGGTAATTAAGTAAAAGCAG-TAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* *
14885 CTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAAGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * * *
14922 CTTAATTCAGGGTAATTAAATAAAAACAATCAAA-GA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
* * * *
14958 CTTAATTCAGGGTAATTAAGTGAAAGTA-CTCAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
*
14994 CTTAATTCAAGGTAA
1 CTTAATTCAGGGTAA
15009 GACAAGCACA
Statistics
Matches: 564, Mismatches: 70, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
35 2 0.00
36 174 0.31
37 326 0.58
38 62 0.11
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (37 bp):
CTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGA
Found at i:14967 original size:332 final size:331
Alignment explanation
Indices: 14330--15005 Score: 944
Period size: 332 Copynumber: 2.0 Consensus size: 331
14320 CACAATCAAT
** * * *
14330 GTCTTAATTC-AGGGTAATTAAATAAAAGCAGTTAAAGGACTTAATTCAGGGTAATTAAGTAAAA
1 GTCTTAATTCAAGGAAAATTAAATAAAAGCAGTGAAAGGACCTAATTCAGGGTAATTAAATAAAA
* * * * *
14394 GCGGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTGATTCAGGGAAAT
66 ACAGTTAAAGGACTTAATTCAGAGAAATTAAGTAAAAGCAGTTAAAGGACTTAATTCAGGGAAAT
* * * * * * ** *
14459 TAAGTAAAAGTAGTTAACGGACTTAATTGAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATT
131 TAAGTAAAAGCAATAAAAGGACCTAATTCAGGGAAATTAAGTAAAAACAATTAAAGGACTTAATT
* *
14524 CAGGGAAATTAAGTAAAAGCAGTAAAGGGCTTAGTTCAGGGAAATTAAGTAAAAGCAGTAAAAGA
196 CAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAAGA
* * * * * *
14589 CTTAATTCAGTGTAATTAAGTAAAAGCAGTTAAAGGGCTAAATTCAGGGGAATTAAGTAAAAGCA
261 CTTAATTCAGGGTAATTAAATAAAAACAATCAAAGGACTAAATTCAGGGGAATTAAGTAAAAGCA
*
14654 GTTAAAG
326 -CTAAAG
* *
14661 GTCTTAATTCAAGGAAAATTAAGTAAAAGCAGTGAAAGGACCTAATTCAGGGTATTTAAATAAAA
1 GTCTTAATTCAAGGAAAATTAAATAAAAGCAGTGAAAGGACCTAATTCAGGGTAATTAAAT-AAA
* *
14726 AACAGTTAAATGACTTAATTCAGAGTAATTAAGTAAAAGCAG-TAAAGGACTTAATTCAGGGAAA
65 AACAGTTAAAGGACTTAATTCAGAGAAATTAAGTAAAAGCAGTTAAAGGACTTAATTCAGGGAAA
*
14790 TTAAGTAAAAGCAATAAAAGGACCTAATTCAGGGTAATTAAGTAAAAACAATTAAAGGACTTAAT
130 TTAAGTAAAAGCAATAAAAGGACCTAATTCAGGGAAATTAAGTAAAAACAATTAAAGGACTTAAT
*
14855 TCAGGGTAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAA
195 TCAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAG-TAAAA
* * *
14920 GACTTAATTCAGGGTAATTAAATAAAAACAATCAAA-GACTTAATTCAGGGTAATTAAGTGAAAG
259 GACTTAATTCAGGGTAATTAAATAAAAACAATCAAAGGACTAAATTCAGGGGAATTAAGTAAAAG
* *
14984 TACTCAAG
324 CACTAAAG
*
14992 GACTTAATTCAAGG
1 GTCTTAATTCAAGG
15006 TAAGACAAGC
Statistics
Matches: 302, Mismatches: 40, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
331 27 0.09
332 200 0.66
333 75 0.25
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (331 bp):
GTCTTAATTCAAGGAAAATTAAATAAAAGCAGTGAAAGGACCTAATTCAGGGTAATTAAATAAAA
ACAGTTAAAGGACTTAATTCAGAGAAATTAAGTAAAAGCAGTTAAAGGACTTAATTCAGGGAAAT
TAAGTAAAAGCAATAAAAGGACCTAATTCAGGGAAATTAAGTAAAAACAATTAAAGGACTTAATT
CAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAAGA
CTTAATTCAGGGTAATTAAATAAAAACAATCAAAGGACTAAATTCAGGGGAATTAAGTAAAAGCA
CTAAAG
Found at i:15057 original size:41 final size:41
Alignment explanation
Indices: 15003--15210 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
14993 ACTTAATTCA
15003 AGGT-AAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
1 AGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
* *
15043 AAGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATT
1 AGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
*
15084 AAGTAAAGACCAA-CACAGACTTAATTTCAAGGAAGGAAATT
1 AGGTAAAGA-CAAGCACAGACTTAATTTCAAGGAAGGAAATT
*
15125 AGGTAAAGACAAGCACAGACTTAATTTC----ACGGAAATT
1 AGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
* *
15162 AGGTAAAGACAAGCACAGACTTAATTTCAATGAAAGAAATT
1 AGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
15203 AGGTAAAG
1 AGGTAAAG
15211 TGATGCGCTA
Statistics
Matches: 154, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
37 36 0.23
40 6 0.04
41 110 0.71
42 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (41 bp):
AGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATT
Found at i:15435 original size:12 final size:12
Alignment explanation
Indices: 15415--15448 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
15405 CATGACCGGC
15415 CATCGCATGGAA
1 CATCGCATGGAA
*
15427 CATCACATGGAA
1 CATCGCATGGAA
15439 CATCGCATGG
1 CATCGCATGG
15449 GGCAACCGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (12 bp):
CATCGCATGGAA
Found at i:15473 original size:30 final size:30
Alignment explanation
Indices: 15439--15501 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
15429 TCACATGGAA
*
15439 CATCGCATGGGGCAACCGGCCACAACCGGC
1 CATCGCATGGGCCAACCGGCCACAACCGGC
*
15469 CATCGCATGGGCCATCCGGCCACAACCGGC
1 CATCGCATGGGCCAACCGGCCACAACCGGC
15499 CAT
1 CAT
15502 TTGACCCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (30 bp):
CATCGCATGGGCCAACCGGCCACAACCGGC
Found at i:16380 original size:36 final size:36
Alignment explanation
Indices: 16325--16424 Score: 96
Period size: 36 Copynumber: 2.8 Consensus size: 36
16315 TAATTCAGGG
* * * *
16325 TAATTAACT-AAATTAGCAAACACTTAATTTCAAAGA
1 TAATTAAGTAAAATCAGCAAAAACTTAATCT-AAAGA
* *
16361 -AATTAAGTAAAATCAGCAAAGACTTGATCTAAAGA
1 TAATTAAGTAAAATCAGCAAAAACTTAATCTAAAGA
* *
16396 TGATTAAGTAAGATCAGACAAAAACTTAA
1 TAATTAAGTAAAATCAG-CAAAAACTTAA
16425 CCCAAGGGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
35 12 0.23
36 31 0.60
37 9 0.17
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (36 bp):
TAATTAAGTAAAATCAGCAAAAACTTAATCTAAAGA
Found at i:16493 original size:37 final size:37
Alignment explanation
Indices: 16447--16938 Score: 754
Period size: 37 Copynumber: 13.3 Consensus size: 37
16437 AAGTAAGAAA
*
16447 AAGGGCTTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
16484 AAGGACTTAATTTGAAGGAAGGAAATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
16521 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
16558 AAGGACTTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
16595 AAGGGCTTAATTTCAAGGAAGGAGATTAAGTAGTGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
16632 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
16669 AAGGGTTTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
16706 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
16743 AATGG-TTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*** * * *
16779 AAAAACTTAATTTCAAGGGAGGACATTAAGTAGGGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
16816 AAGGGCTTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
16853 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* * *
16890 AAGGACTTAATTTCAGGGAAGAAAATTAAGTCA-AGTC
1 AAGGGCTTAATTTCAAGGAAGGAAATTAAGT-AGAGTC
*
16927 AAGGACTTAATT
1 AAGGGCTTAATT
16939 CATGGTAATT
Statistics
Matches: 420, Mismatches: 33, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
36 32 0.08
37 387 0.92
38 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (37 bp):
AAGGGCTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
Found at i:16949 original size:32 final size:32
Alignment explanation
Indices: 16840--16983 Score: 130
Period size: 37 Copynumber: 4.2 Consensus size: 32
16830 AAGGAAGGAG
*
16840 ATTAAGT-AGAGTCAAGGACTTAATTTCAAGGAAGGAA
1 ATTAAGTCA-AGTCAAGGACTTAA-TTC-A-G--GGTA
*
16877 ATTAAGT-AGAGTCAAGGACTTAATTTCAGGGAAGAAA
1 ATTAAGTCA-AGTCAAGGACTTAA-TTCA-GG--G-TA
*
16914 ATTAAGTCAAGTCAAGGACTTAATTCATGGTA
1 ATTAAGTCAAGTCAAGGACTTAATTCAGGGTA
*
16946 ATTAAGTCAAGTCATGGACTTAATTCAGGGTA
1 ATTAAGTCAAGTCAAGGACTTAATTCAGGGTA
16978 ATTAAG
1 ATTAAG
16984 AAGCGTCAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 13
0.85 0.03 0.11
Matches are distributed among these distances:
32 37 0.37
33 1 0.01
34 1 0.01
35 1 0.01
36 8 0.08
37 50 0.51
38 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (32 bp):
ATTAAGTCAAGTCAAGGACTTAATTCAGGGTA
Found at i:16958 original size:37 final size:35
Alignment explanation
Indices: 16890--17114 Score: 194
Period size: 36 Copynumber: 6.3 Consensus size: 35
16880 AAGTAGAGTC
** * *
16890 AAGGACTTAATTTCAGGG-AAGAAAATTAAGTCAAGTC
1 AAGGACTTAA-TTCAGGGTAA-TTAAGTAAGTCAA-TA
*
16927 AAGGACTTAATTCATGGTAATTAAGTCAAGTC-AT-
1 AAGGACTTAATTCAGGGTAATTAAGT-AAGTCAATA
16961 --GGACTTAATTCAGGGTAATTAAG-AAGCGTCAATA
1 AAGGACTTAATTCAGGGTAATTAAGTAA--GTCAATA
* *
16995 AAGGGACTTAATTCAGTGTAATTAAGTAGCGTCAATA
1 AA-GGACTTAATTCAGGGTAATTAAGTA-AGTCAATA
* *
17032 AAGGGCTTAATTCAGGGTAATTAAGTGGAGTCAATAA
1 AAGGACTTAATTCAGGGTAATTAAGT-AAGTCAAT-A
* *
17069 AAGG-CTTAATTTAGGGTAATTAAGTGGAGTCAATA
1 AAGGACTTAATTCAGGGTAATTAAGT-AAGTCAATA
*
17104 AAGAACTTAAT
1 AAGGACTTAAT
17115 CTAAGTAAAA
Statistics
Matches: 161, Mismatches: 13, Indels: 29
0.79 0.06 0.14
Matches are distributed among these distances:
30 2 0.01
32 25 0.16
33 2 0.01
35 5 0.03
36 73 0.45
37 53 0.33
38 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (35 bp):
AAGGACTTAATTCAGGGTAATTAAGTAAGTCAATA
Found at i:17052 original size:36 final size:36
Alignment explanation
Indices: 16918--17106 Score: 208
Period size: 36 Copynumber: 5.3 Consensus size: 36
16908 AAGAAAATTA
* * *
16918 AGTCAAGTCAAGGACTTAATTCATGGTAATTAAGTCA-
1 AGTCAA-TAAAGGGCTTAATTCAGGGTAATTAAGT-AG
* *
16955 AGTC-AT---GGACTTAATTCAGGGTAATTAAGAAG
1 AGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAG
* *
16987 CGTCAATAAAGGGACTTAATTCAGTGTAATTAAGTAG
1 AGTCAATAAAGGG-CTTAATTCAGGGTAATTAAGTAG
* *
17024 CGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTGG
1 AGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAG
* * *
17060 AGTCAATAAAAGGCTTAATTTAGGGTAATTAAGTGG
1 AGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAG
17096 AGTCAATAAAG
1 AGTCAATAAAG
17107 AACTTAATCT
Statistics
Matches: 134, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
31 1 0.01
32 25 0.19
33 2 0.01
35 1 0.01
36 67 0.50
37 38 0.28
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (36 bp):
AGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAG
Found at i:17056 original size:73 final size:72
Alignment explanation
Indices: 16927--17106 Score: 208
Period size: 73 Copynumber: 2.5 Consensus size: 72
16917 AAGTCAAGTC
* *
16927 AAGGACTTAATTCATGGTAATTAAGTCA-AGTC-AT---GGACTTAATTCAGGGTAATTAAGAAG
1 AAGG-CTTAATTCAGGGTAATTAAGT-AGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGAAG
*
16987 CGTCAATAA
64 AGTCAATAA
* * * **
16996 AGGGACTTAATTCAGTGTAATTAAGTAGCGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTGGA
1 AAGG-CTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGAAGA
17061 GTCAATAA
65 GTCAATAA
* *
17069 AAGGCTTAATTTAGGGTAATTAAGTGGAGTCAATAAAG
1 AAGGCTTAATTCAGGGTAATTAAGTAGAGTCAATAAAG
17107 AACTTAATCT
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
68 1 0.01
69 26 0.28
70 2 0.02
72 30 0.32
73 34 0.37
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (72 bp):
AAGGCTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGAAGAG
TCAATAA
Found at i:26180 original size:22 final size:22
Alignment explanation
Indices: 26150--26206 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
26140 ATAAAGTTGC
* *
26150 AAAAAAAAATGATGATGAAATG
1 AAAAAAAAAAGATGAAGAAATG
* *
26172 AAAATAAAAAGATGAAGAAAAGG
1 AAAAAAAAAAGATGAAG-AAATG
*
26195 AAAGAAAAAAGA
1 AAAAAAAAAAGA
26207 AGTGAAAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (22 bp):
AAAAAAAAAAGATGAAGAAATG
Found at i:26197 original size:23 final size:21
Alignment explanation
Indices: 26150--26206 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
26140 ATAAAGTTGC
* *
26150 AAAAAAAAATGATGATGAAATG
1 AAAAAAAAA-GATGAAGAAAGG
26172 AAAATAAAAAGATGAAGAAAAGG
1 AAAA-AAAAAGATGAAG-AAAGG
26195 AAAGAAAAAAGA
1 AAA-AAAAAAGA
26207 AGTGAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAGATGAAGAAAGG
Found at i:27525 original size:24 final size:24
Alignment explanation
Indices: 27488--27611 Score: 106
Period size: 24 Copynumber: 4.9 Consensus size: 24
27478 GCTAATCTTG
**
27488 TTCAATTAGCTTCAATTATTCAATCC
1 TTCAATT--CTTCAATTATTCAATGA
*
27514 TTCAATGCTTCAATTTATCTCAAAATGA
1 TTCAATTCTTCAA-TTAT-TC--AATGA
* *
27542 TCTC-TTTCTTCAATTATTCAATGC
1 T-TCAATTCTTCAATTATTCAATGA
* *
27566 TTCAATTCTTCTATTATTCAATTA
1 TTCAATTCTTCAATTATTCAATGA
*
27590 TTCAATTCTTCAATGATTCAAT
1 TTCAATTCTTCAATTATTCAAT
27612 TTATCTCTTC
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
23 2 0.03
24 47 0.59
25 4 0.05
26 10 0.12
27 4 0.05
28 11 0.14
29 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (24 bp):
TTCAATTCTTCAATTATTCAATGA
Found at i:27563 original size:8 final size:8
Alignment explanation
Indices: 27550--27612 Score: 72
Period size: 8 Copynumber: 7.9 Consensus size: 8
27540 GATCTCTTTC
27550 TTCAATTA
1 TTCAATTA
**
27558 TTCAATGC
1 TTCAATTA
*
27566 TTCAATTC
1 TTCAATTA
*
27574 TTCTATTA
1 TTCAATTA
27582 TTCAATTA
1 TTCAATTA
*
27590 TTCAATTC
1 TTCAATTA
*
27598 TTCAATGA
1 TTCAATTA
27606 TTCAATT
1 TTCAATT
27613 TATCTCTTCG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.49
Consensus pattern (8 bp):
TTCAATTA
Found at i:27570 original size:16 final size:16
Alignment explanation
Indices: 27547--27612 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
27537 AATGATCTCT
27547 TTCTTCAATTATTCAA
1 TTCTTCAATTATTCAA
* * *
27563 TGCTTCAATTCTTCTA
1 TTCTTCAATTATTCAA
*
27579 TTATTCAATTATTCAA
1 TTCTTCAATTATTCAA
*
27595 TTCTTCAATGATTCAA
1 TTCTTCAATTATTCAA
27611 TT
1 TT
27613 TATCTCTTCG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (16 bp):
TTCTTCAATTATTCAA
Found at i:27830 original size:14 final size:14
Alignment explanation
Indices: 27813--28070 Score: 90
Period size: 14 Copynumber: 19.0 Consensus size: 14
27803 AATTCCAAAT
*
27813 TTTCAATGCTCCAA
1 TTTCAATGCTTCAA
*
27827 TTTCAATTCTTCAA
1 TTTCAATGCTTCAA
*
27841 ATTCAATGCTTCAA
1 TTTCAATGCTTCAA
27855 TGTTTCAAT--TTCAA
1 --TTTCAATGCTTCAA
27869 TCCTTCAAATGCTTCAA
1 T--TTC-AATGCTTCAA
* *
27886 -TTC--TTCGT-ATA
1 TTTCAATGCTTCA-A
*
27897 TTTCAAT-ATTCCAA
1 TTTCAATGCTT-CAA
* *
27911 TGTTTCAATGTTTTAA
1 --TTTCAATGCTTCAA
* *
27927 TTTCAGTGCCTCAA
1 TTTCAATGCTTCAA
*
27941 TTTCAATTCTTCAA
1 TTTCAATGCTTCAA
*
27955 ATTCAA----TC--
1 TTTCAATGCTTCAA
27963 TTTCAATGCTTCAA
1 TTTCAATGCTTCAA
*
27977 TTTCAATTCTTCAA
1 TTTCAATGCTTCAA
*
27991 ATTCAAT-C--C-A
1 TTTCAATGCTTCAA
*
28001 --TCAATGTTTCAA
1 TTTCAATGCTTCAA
* *
28013 ATTCAATCCTTCAA
1 TTTCAATGCTTCAA
28027 TGTTTCAAT--TTCAA
1 --TTTCAATGCTTCAA
28041 TATCTCAATGCTTCAA
1 T-T-TCAATGCTTCAA
*
28057 TTTCAATTCTTCAA
1 TTTCAATGCTTCAA
28071 ATCCCAAATG
Statistics
Matches: 183, Mismatches: 27, Indels: 68
0.66 0.10 0.24
Matches are distributed among these distances:
8 10 0.05
10 4 0.02
11 6 0.03
12 8 0.04
13 3 0.02
14 113 0.62
15 5 0.03
16 27 0.15
17 7 0.04
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTCAATGCTTCAA
Found at i:27853 original size:22 final size:22
Alignment explanation
Indices: 27828--27885 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
27818 ATGCTCCAAT
*
27828 TTCAATTCTTCAAATTCAATGC
1 TTCAATTCTTCAAATTCAATCC
*
27850 TTCAATGT-TTCAATTTCAATCC
1 TTCAAT-TCTTCAAATTCAATCC
*
27872 TTCAAATGCTTCAA
1 TTC-AATTCTTCAA
27886 TTCTTCGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (22 bp):
TTCAATTCTTCAAATTCAATCC
Found at i:27854 original size:36 final size:35
Alignment explanation
Indices: 27814--28072 Score: 173
Period size: 36 Copynumber: 6.8 Consensus size: 35
27804 ATTCCAAATT
*
27814 TTCAATGCTCCAATTTCAATTCTTCAAATTCAATGC
1 TTCAATGCTTCAATTTCAATTCTTCAAATTCAAT-C
* *
27850 TTCAATGTTTCAATTTCAATCCTTCAAATGCTTCAATTC
1 TTCAATGCTTCAATTTCAATTCTTCAAA---TTCAA-TC
* ** * *
27889 TTCGTATATTTCAATATTCCAATGT-TTCAATGTTTTAAT-
1 TTC-AATGCTTCAAT-TT-CAAT-TCTTCAA--ATTCAATC
* *
27928 TTCAGTGCCTCAATTTCAATTCTTCAAATTCAATC
1 TTCAATGCTTCAATTTCAATTCTTCAAATTCAATC
27963 TTTCAATGCTTCAATTTCAATTCTTCAAATTCAATCC
1 -TTCAATGCTTCAATTTCAATTCTTCAAATTCAAT-C
* * *
28000 ATCAATGTTTCAAATTCAATCCTTCAATGT-TTCAATTTCAATA
1 TTCAATG---C---TTCAAT--TTCAAT-TCTTCAAATTCAATC
28043 TCTCAATGCTTCAATTTCAATTCTTCAAAT
1 T-TCAATGCTTCAATTTCAATTCTTCAAAT
28073 CCCAAATGTC
Statistics
Matches: 176, Mismatches: 22, Indels: 50
0.71 0.09 0.20
Matches are distributed among these distances:
34 5 0.03
35 2 0.01
36 84 0.48
37 3 0.02
38 12 0.07
39 13 0.07
40 11 0.06
41 7 0.04
42 15 0.09
44 23 0.13
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (35 bp):
TTCAATGCTTCAATTTCAATTCTTCAAATTCAATC
Found at i:27990 original size:22 final size:22
Alignment explanation
Indices: 27941--27983 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27931 AGTGCCTCAA
*
27941 TTTCAATTCTTCAAATTCAATC
1 TTTCAATGCTTCAAATTCAATC
*
27963 TTTCAATGCTTCAATTTCAAT
1 TTTCAATGCTTCAAATTCAAT
27984 TCTTCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTCAATGCTTCAAATTCAATC
Found at i:28070 original size:22 final size:22
Alignment explanation
Indices: 27978--28070 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 22
27968 ATGCTTCAAT
*
27978 TTCAATTCTTCAAATTCAATCC
1 TTCAATGCTTCAAATTCAATCC
* *
28000 ATCAATGTTTCAAATTCAATCC
1 TTCAATGCTTCAAATTCAATCC
* * *
28022 TTCAATGTTTCAATTTCAAT-A
1 TTCAATGCTTCAAATTCAATCC
* *
28043 TCTCAATGCTTCAATTTCAATTC
1 T-TCAATGCTTCAAATTCAATCC
28066 TTCAA
1 TTCAA
28071 ATCCCAAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.02
22 59 0.97
23 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (22 bp):
TTCAATGCTTCAAATTCAATCC
Done.