Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012852.1 Corchorus capsularis cultivar CVL-1 contig12873, 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: 87955
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7597 original size:21 final size:21
Alignment explanation
Indices: 7568--7607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7558 TAACGGGTTT
* *
7568 TTTTTTTTTTTTTTTATTTGG
1 TTTTGTTTTTGTTTTATTTGG
7589 TTTTGTTTTTGTTTTATTT
1 TTTTGTTTTTGTTTTATTT
7608 TTTGGCGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.00, G:0.10, T:0.85
Consensus pattern (21 bp):
TTTTGTTTTTGTTTTATTTGG
Found at i:7597 original size:24 final size:24
Alignment explanation
Indices: 7563--7612 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
7553 ATAAGTAACG
* *
7563 GGTTTT-TTTTTTTTTTTTTTATTT
1 GGTTTTGTTTTTGTTTTATTT-TTT
7587 GGTTTTGTTTTTGTTTTATTTTTT
1 GGTTTTGTTTTTGTTTTATTTTTT
7611 GG
1 GG
7613 CGAAGAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.04, C:0.00, G:0.16, T:0.80
Consensus pattern (24 bp):
GGTTTTGTTTTTGTTTTATTTTTT
Found at i:27849 original size:39 final size:40
Alignment explanation
Indices: 27785--27864 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 40
27775 TAGTACAAAC
*
27785 ATATATCATTCATATTGAACTCCTCC-CTTTGGTAGTAGAT
1 ATATATCATTCATATTGAACTCCTCCAC-TCGGTAGTAGAT
*
27825 ATATAT-ATTCGA-ATTGAGCTCCTCCACTCGGTAGTAGAT
1 ATATATCATTC-ATATTGAACTCCTCCACTCGGTAGTAGAT
27864 A
1 A
27865 CAACACGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (40 bp):
ATATATCATTCATATTGAACTCCTCCACTCGGTAGTAGAT
Found at i:29760 original size:31 final size:31
Alignment explanation
Indices: 29695--29760 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
29685 TGACAATTTA
* *
29695 GAAATATATTTTTTAAAAAAAGGTATAATTG
1 GAAATATATTTTTTAAAAAAAGGTACAATCG
*
29726 GAAATATA-TTTTTAAAAAAGGGGTACAATCG
1 GAAATATATTTTTTAAAAAA-AGGTACAATCG
29757 GAAA
1 GAAA
29761 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTTTAAAAAAAGGTACAATCG
Found at i:30772 original size:15 final size:15
Alignment explanation
Indices: 30752--30785 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30742 AGCTTAATGT
*
30752 ATTTTGGCATGCCAA
1 ATTTTGGCATGACAA
30767 ATTTTGGCATGACAA
1 ATTTTGGCATGACAA
30782 ATTT
1 ATTT
30786 GACCAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (15 bp):
ATTTTGGCATGACAA
Found at i:33556 original size:27 final size:27
Alignment explanation
Indices: 33480--33558 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
33470 TACATTAATG
* *
33480 AATAATGTGATTATACATGAATTAATT
1 AATAATGTGATTATTCATGAATCAATT
*
33507 AATATTGTGATTATTCATGAATCAATT
1 AATAATGTGATTATTCATGAATCAATT
33534 AATAATGTGATTATTCATGAATCAA
1 AATAATGTGATTATTCATGAATCAA
33559 GAGTTGTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (27 bp):
AATAATGTGATTATTCATGAATCAATT
Found at i:43091 original size:24 final size:24
Alignment explanation
Indices: 43064--43116 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
43054 AATCATTCTT
* *
43064 CTATTGTAGATTGACTAATTAAAA
1 CTATTGTAGATTGACAAATGAAAA
*
43088 CTATTGTGGATTGACAAATGAAAA
1 CTATTGTAGATTGACAAATGAAAA
43112 CTATT
1 CTATT
43117 ATAACTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (24 bp):
CTATTGTAGATTGACAAATGAAAA
Found at i:53422 original size:6 final size:6
Alignment explanation
Indices: 53403--53435 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
53393 GGGACCCGTC
53403 TTTCATT TTT-TT TTTCTT TTTCTT TTTCTT TTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTT
53436 AGGGAGGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 17 0.68
7 3 0.12
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:56114 original size:15 final size:15
Alignment explanation
Indices: 56081--56118 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
56071 ATTCCTTTTA
56081 AATA-AATATACTAT
1 AATATAATATACTAT
56095 AATATAATATTACTAT
1 AATATAATA-TACTAT
56111 -ATATAATA
1 AATATAATA
56119 ATATAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAATATACTAT
Found at i:57344 original size:16 final size:15
Alignment explanation
Indices: 57317--57346 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
57307 ATTTTTTTTA
57317 TTAAAAAAATATATT
1 TTAAAAAAATATATT
57332 TTAAAAAATATATAT
1 TTAAAAAA-ATATAT
57347 ATATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAAATATATT
Found at i:62202 original size:28 final size:29
Alignment explanation
Indices: 62144--62202 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
62134 ATATTTATCT
* *
62144 TATAATGGGTGTTTTTTTCCTAAAATTGG
1 TATAATGGGTGTTTTTATCCTAAAATGGG
*
62173 TATAAT-GGTAGTTTTTAT-CTAAAGTGGG
1 TATAATGGGT-GTTTTTATCCTAAAATGGG
62201 TA
1 TA
62203 GTTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (29 bp):
TATAATGGGTGTTTTTATCCTAAAATGGG
Found at i:63277 original size:108 final size:109
Alignment explanation
Indices: 63149--63422 Score: 419
Period size: 109 Copynumber: 2.5 Consensus size: 109
63139 AAAAAAATTA
*
63149 TATAAA-ATATT-GAATTTAATTAAATG-AAATAGAGTTTTTAGTAGAATAAAGTTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
*
63211 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAAGAAAGTAAT
63256 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
63321 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAAGAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAAGAAAGTAAT
** *
63365 TATAAAGATATTAGATTTAATTTAATTTAAAAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
63423 CTATAATAGT
Statistics
Matches: 153, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
107 6 0.04
108 18 0.12
109 99 0.65
110 2 0.01
111 1 0.01
114 27 0.18
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAAGAAAGTAAT
Found at i:77389 original size:6 final size:6
Alignment explanation
Indices: 77380--77410 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
77370 CCAGCTCCAC
*
77380 CACCGG CACCGG CACCAG CACCGG CACCGG C
1 CACCGG CACCGG CACCGG CACCGG CACCGG C
77411 TCCAACTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.52, G:0.29, T:0.00
Consensus pattern (6 bp):
CACCGG
Found at i:77524 original size:24 final size:23
Alignment explanation
Indices: 77493--77570 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
77483 TCCACCACCC
77493 GCACCACCCCCAACACCTCCTCCT
1 GCACCACCCCCAACACC-CCTCCT
* *
77517 GCACCACCGCCAGCACCCACTCCT
1 GCACCACCCCCAACACCC-CTCCT
* * *
77541 CCACCAACACCC-ACACCACCTCCA
1 GCACC-ACCCCCAACACC-CCTCCT
77565 GCACCA
1 GCACCA
77571 GTTCGNACCC
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.05
24 36 0.84
25 5 0.12
ACGTcount: A:0.26, C:0.60, G:0.06, T:0.08
Consensus pattern (23 bp):
GCACCACCCCCAACACCCCTCCT
Found at i:77569 original size:18 final size:18
Alignment explanation
Indices: 77518--77569 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
77508 CCTCCTCCTG
*
77518 CACCACCGCCAGCACCCA
1 CACCACCACCAGCACCCA
* * *
77536 CTCCTCCACCAACACCCA
1 CACCACCACCAGCACCCA
*
77554 CACCACCTCCAGCACC
1 CACCACCACCAGCACC
77570 AGTTCGNACC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.62, G:0.06, T:0.06
Consensus pattern (18 bp):
CACCACCACCAGCACCCA
Found at i:77636 original size:79 final size:78
Alignment explanation
Indices: 77498--77648 Score: 171
Period size: 79 Copynumber: 1.9 Consensus size: 78
77488 CACCCGCACC
* * * * * * *
77498 ACCCCCAACACCTCCTCCTGCACCACCGCCAGCACCCACTCCTCCACCAACACCCACACCACCTC
1 ACCCCCAACACCTCCACCTCCACCACCACCACCACCAACACCTACACCAACACCCACACCACCTC
*
77563 CAGCACCAGTTCG
66 CAACACCAGTTCG
* *
77576 NACCCCCAACACCTCCACCTCCACCTCGCACCACCACCAACACCTACACC-AC-CCCGACACCTC
1 -ACCCCCAACACCTCCACCTCCACCAC-CACCACCACCAACACCTACACCAACACCC-ACACCAC
77639 CTCCAACACC
63 CTCCAACACC
77649 GCCACCAGCA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 3 0.05
79 40 0.67
80 17 0.28
ACGTcount: A:0.26, C:0.59, G:0.05, T:0.09
Consensus pattern (78 bp):
ACCCCCAACACCTCCACCTCCACCACCACCACCACCAACACCTACACCAACACCCACACCACCTC
CAACACCAGTTCG
Found at i:77720 original size:3 final size:3
Alignment explanation
Indices: 77714--78141 Score: 82
Period size: 3 Copynumber: 142.3 Consensus size: 3
77704 CCTCCACCTG
* * * * * * *
77714 CAC CAC CTC CAA CAC CCC CTC CAG CAC CAC CAC CAA CAC CTC CAC CTA-
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C-AC
* * * * * * * * * * *
77762 CGC CAC CAC CAA CAC CTC CTC CTC CTC CAC CTC TAC CAC CGC CGC TAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * * * * * * *
77810 CAC CAG CAC CAC CTC CAA CAC CAC CAC CAG CAC CTC CTC CTC C-C CTAA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C-AC
* * * * * *
77858 CAC CTC CTC CTA- CAC CAC CAC CAA CAC CAC CAC CGA- CTC CTC CTC
1 CAC CAC CAC C-AC CAC CAC CAC CAC CAC CAC CAC C-AC CAC CAC CAC
* * * * * * *
77903 CAA CAC CAC CAC CAG CAC CTA- CTC CTC CCC CAA CAC CTC CAC CTA-
1 CAC CAC CAC CAC CAC CAC C-AC CAC CAC CAC CAC CAC CAC CAC C-AC
* * * * * *
77948 CGC CAC CAC CAG CAC CGC CTC TAC CAC CAA CAC CAC CAC CTGA- CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C--AC CAC
* * * * * * *
77994 CAC CTC CAA CAC CAC CAC CAG CAC CTC CTC CGA- CGC CAC CAC CAG
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C-AC CAC CAC CAC CAC
* * * * * * *
78039 CAC CTA- CAC CAC CTC CTC CTC CAC CTC TAC CAC CAC CGC CTC CAC
1 CAC C-AC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * ** * * * * *
78084 CAC CAG CAC CTC CAC CTG CAC CAC CTC CAG CAC CTC CTC CAA CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
*
78132 CAC CAG CAC C
1 CAC CAC CAC C
78142 TACTCCTCCC
Statistics
Matches: 301, Mismatches: 105, Indels: 38
0.68 0.24 0.09
Matches are distributed among these distances:
2 5 0.02
3 288 0.96
4 7 0.02
5 1 0.00
ACGTcount: A:0.25, C:0.59, G:0.05, T:0.11
Consensus pattern (3 bp):
CAC
Found at i:77791 original size:24 final size:24
Alignment explanation
Indices: 77704--77885 Score: 102
Period size: 24 Copynumber: 8.1 Consensus size: 24
77694 TCCACCACTG
* * *
77704 CCTCCACCTGCACCACCTCCAACA
1 CCTCCTCCTACACCACCACCAACA
*
77728 CCCCCTCC-AGCACCACCACCAACA
1 CCTCCTCCTA-CACCACCACCAACA
* *
77752 CCTCCACCTACGCCACCACCAACA
1 CCTCCTCCTACACCACCACCAACA
* * * * *
77776 CCTCCTCCTCCTCCACCTCTACCA
1 CCTCCTCCTACACCACCACCAACA
* * *
77800 CCGCC-GCT-----ACCACCAGCA
1 CCTCCTCCTACACCACCACCAACA
* * *
77818 CCACCTCCAACACCACCACCAGCA
1 CCTCCTCCTACACCACCACCAACA
*
77842 CCTCCTCCT----C-CC-CTAACA
1 CCTCCTCCTACACCACCACCAACA
77860 CCTCCTCCTACACCACCACCAACA
1 CCTCCTCCTACACCACCACCAACA
77884 CC
1 CC
77886 ACCACCGACT
Statistics
Matches: 118, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
18 24 0.20
19 3 0.03
20 1 0.01
22 1 0.01
23 4 0.03
24 84 0.71
25 1 0.01
ACGTcount: A:0.25, C:0.60, G:0.04, T:0.12
Consensus pattern (24 bp):
CCTCCTCCTACACCACCACCAACA
Found at i:77864 original size:78 final size:78
Alignment explanation
Indices: 77808--78378 Score: 257
Period size: 78 Copynumber: 7.5 Consensus size: 78
77798 CACCGCCGCT
* *
77808 ACCACC-AGCACCACCTCCAACACCACCACCAGCACCTCCTCCTCCCCTAACACCTCCTCCTACA
1 ACCACCGA-CACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACA
77872 CCACCACCAACACC
65 CCACCACCAACACC
* * * *
77886 ACCACCGACTCCTCCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCACCTACGC
1 ACCACCGACACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACAC
*
77951 CACCACCAGCACC
66 CACCACCAACACC
* * * * * * * * * * * * * *
77964 GCC-TCTACCACCAACACCACCACCTGA-CACCACCTCCAACACCACCACCAGCACCTCCTCCGA
1 ACCACCGA-CACCACCTCCAACACC--ACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTA
* *
78027 CGCCACCACCAGCACC
63 CACCACCACCAACACC
* ** * * * * * * * *
78043 TA-CA-C--CACCTCCTCCTCCACCTCTACCACCA-C--CGCCTCCACCACCAGCACCT-C--CA
1 -ACCACCGACACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACA
**
78098 CCTGCA-C--CACC
65 CCACCACCAACACC
* * *
78109 TCCA--G-CACCTCCTCCAACACCACCACCAGCACCTACTCCTCCCCCAATACCTCCTCCTACAC
1 ACCACCGACACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACAC
* * *
78171 TACCACCGACTCC
66 CACCACCAACACC
* * ** ** * * * * * *
78184 TCCTCC-AGCACCTA--TGCCGCCACCAATACCACCTCCTCCTCCTCCACCTCTACCACCACCGC
1 ACCACCGA-CACC-ACCT-CCAACACCACCACCAGCACCTACTCCTCC-CC-C-AACACCTCCTC
78246 CT---CCACCACCAACACC
60 CTACACCACCACCAACACC
*
78262 TCCACCTGA-ACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCT---
1 ACCACC-GACACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACA
* *
78323 CCTCCACC-TCTACC
65 CCACCACCAAC-ACC
* * * * *
78337 ACCACCGCCTCCACCACCAACACCTCCACCAGCACCTCCTCC
1 ACCACCGACACCACCTCCAACACCACCACCAGCACCTACTCC
78379 AACACCACCA
Statistics
Matches: 369, Mismatches: 91, Indels: 69
0.70 0.17 0.13
Matches are distributed among these distances:
66 27 0.07
67 1 0.00
68 1 0.00
69 19 0.05
70 1 0.00
71 1 0.00
72 20 0.05
73 1 0.00
74 3 0.01
75 66 0.18
76 13 0.04
77 6 0.02
78 149 0.40
79 49 0.13
80 3 0.01
81 9 0.02
ACGTcount: A:0.25, C:0.58, G:0.05, T:0.12
Consensus pattern (78 bp):
ACCACCGACACCACCTCCAACACCACCACCAGCACCTACTCCTCCCCCAACACCTCCTCCTACAC
CACCACCAACACC
Found at i:77927 original size:24 final size:24
Alignment explanation
Indices: 77900--78147 Score: 128
Period size: 24 Copynumber: 10.2 Consensus size: 24
77890 CCGACTCCTC
77900 CTCCAACACCACCACCAGCACCTA
1 CTCCAACACCACCACCAGCACCTA
** * * **
77924 CTCCTCCCCCAACACCTCCACCTA
1 CTCCAACACCACCACCAGCACCTA
* * *
77948 CGCCACCACCAGCACC-GC-CTCTA
1 CTCCAACACCACCACCAGCAC-CTA
* *
77971 CCACCAACACCACCACCTGACACC-A
1 -CTCCAACACCACCACCAG-CACCTA
*
77996 CCTCCAACACCACCACCAGCACCTC
1 -CTCCAACACCACCACCAGCACCTA
* *
78021 CTCCGACGCCACCACCAGCACCTA
1 CTCCAACACCACCACCAGCACCTA
* * * * *
78045 CACCACCTCCTCCTCCA-C-CTCTA
1 CTCCAACACCACCACCAGCAC-CTA
* * * *
78068 CCACCACCGCCTCCACCACCAGCACCTC
1 -CTCCA---ACACCACCACCAGCACCTA
* ** * *
78096 CACCTGCACCACCTCCAGCACCTC
1 CTCCAACACCACCACCAGCACCTA
78120 CTCCAACACCACCACCAGCACCTA
1 CTCCAACACCACCACCAGCACCTA
78144 CTCC
1 CTCC
78148 TCCCCCAATA
Statistics
Matches: 173, Mismatches: 38, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
22 2 0.01
23 8 0.05
24 123 0.71
25 19 0.11
26 2 0.01
27 15 0.09
28 3 0.02
29 1 0.01
ACGTcount: A:0.25, C:0.58, G:0.06, T:0.10
Consensus pattern (24 bp):
CTCCAACACCACCACCAGCACCTA
Found at i:78095 original size:15 final size:15
Alignment explanation
Indices: 77683--78390 Score: 143
Period size: 15 Copynumber: 47.5 Consensus size: 15
77673 TCCTACGCCT
**
77683 CCACCACCTCTTCCA
1 CCACCACCTCCACCA
** *
77698 CCACTGCCTCCACCT
1 CCACCACCTCCACCA
*
77713 GCACCACCTCCA--A
1 CCACCACCTCCACCA
* *
77726 -CACCCCCTCCAGCA
1 CCACCACCTCCACCA
** *
77740 CCACCACCAACACCT
1 CCACCACCTCCACCA
*
77755 CCACCTA-CGCCACCA
1 CCACC-ACCTCCACCA
* * *
77770 CCAACACCTCCTCCT
1 CCACCACCTCCACCA
* *
77785 CCTCCACCTCTACCA
1 CCACCACCTCCACCA
* *
77800 CCGCC-GCTACCACCA
1 CCACCACCT-CCACCA
*
77815 GCACCACCTCCA--A
1 CCACCACCTCCACCA
* *
77828 -CACCACCACCAGCA
1 CCACCACCTCCACCA
* *
77842 CCTCCTCCTCC-CCTA
1 CCACCACCTCCACC-A
* *
77857 ACACCTCCTCCTA-CA
1 CCACCACCTCC-ACCA
**
77872 CCACCACCAACACCA
1 CCACCACCTCCACCA
* *
77887 CCACCGA-CTCCTCCT
1 CCACC-ACCTCCACCA
* *
77902 CCAACACCACCACCA
1 CCACCACCTCCACCA
* * *
77917 GCACCTA-CTCCTCCC
1 CCACC-ACCTCCACCA
*
77932 CCAACACCTCCACCTA
1 CCACCACCTCCACC-A
** *
77948 CGCCACCACCAGCACCG
1 --CCACCACCTCCACCA
* * * *
77965 CCTCTACCACCAACA
1 CCACCACCTCCACCA
*
77980 CCACCACCTGACACCA
1 CCACCACCT-CCACCA
* * *
77996 CCTCCAACACCACCA
1 CCACCACCTCCACCA
* *
78011 CCAGCACCTCCTCCGA
1 CCACCACCTCCACC-A
* * *
78027 -CGCCACCACCAGCA
1 CCACCACCTCCACCA
* * *
78041 CCTA-CACCACCTCCT
1 CC-ACCACCTCCACCA
* *
78056 CCTCCACCTCTACCA
1 CCACCACCTCCACCA
*
78071 CCACCGCCTCCACCA
1 CCACCACCTCCACCA
* *
78086 CCAGCACCTCCACCT
1 CCACCACCTCCACCA
*
78101 GCACCACCT---CCA
1 CCACCACCTCCACCA
* * *
78113 GCACCTCCTCCAACA
1 CCACCACCTCCACCA
**
78128 CCACCACCAGCACCTA
1 CCACCACCTCCACC-A
* * * **
78144 -CTCCTCCCCCAATA
1 CCACCACCTCCACCA
* * * *
78158 CCTCCTCCTACACTA
1 CCACCACCTCCACCA
*
78173 CCACCGACTCCTCCTCCA
1 CCACC-A--CCTCCACCA
* *
78191 GCACCTATGCCGCCACCA
1 CCACC-A--CCTCCACCA
** * *
78209 ATACCACCTCCTCCT
1 CCACCACCTCCACCA
* *
78224 CCTCCACCTCTACCA
1 CCACCACCTCCACCA
*
78239 CCACCGCCTCCACCA
1 CCACCACCTCCACCA
* *
78254 CCAACACCTCCACCT
1 CCACCACCTCCACCA
**
78269 GAACCACCTCCA--A
1 CCACCACCTCCACCA
78282 -CACCA---CCACCA
1 CCACCACCTCCACCA
* * *
78293 GCACCTA-CTCCTCCC
1 CCACC-ACCTCCACCA
* * *
78308 CCAACACCTCCTCCT
1 CCACCACCTCCACCA
* *
78323 CCTCCACCTCTACCA
1 CCACCACCTCCACCA
*
78338 CCACCGCCTCCACCA
1 CCACCACCTCCACCA
*
78353 CCAACACCTCCACCA
1 CCACCACCTCCACCA
* * *
78368 GCACCTCCTCCAACA
1 CCACCACCTCCACCA
78383 CCACCACC
1 CCACCACC
78391 AGCACCTACT
Statistics
Matches: 475, Mismatches: 177, Indels: 82
0.65 0.24 0.11
Matches are distributed among these distances:
9 3 0.01
11 1 0.00
12 38 0.08
13 2 0.00
14 12 0.03
15 368 0.77
16 18 0.04
17 1 0.00
18 32 0.07
ACGTcount: A:0.24, C:0.59, G:0.05, T:0.12
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:78095 original size:42 final size:41
Alignment explanation
Indices: 78045--78264 Score: 106
Period size: 42 Copynumber: 5.2 Consensus size: 41
78035 CCAGCACCTA
78045 CACCACCTCCTCCTCCACCTCTACCACCACCGCCTCCACCAC
1 CACCACCTCCTCCTCCACCTC-ACCACCACCGCCTCCACCAC
* * * * * * * *
78087 CAGCACCTCCACCTGCACCACCTCCAGCACCTCCTCCAACAC
1 CACCACCTCCTCCTCCACC-TCACCACCACCGCCTCCACCAC
** * * * * ** *
78129 CACCACCAGCACCTACTCCTCCCCCAATACCTCCTCCTACACTAC
1 CACCACCTCCTCCTCCACCT-CACCACCACCGCCTCC-AC-C-AC
* ** * **
78174 CACCGA-CTCCTCCTCCA--GCACCTA-TGCCGCCACCAATAC
1 CACC-ACCTCCTCCTCCACCTCACC-ACCACCGCCTCCACCAC
*
78213 CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCAC
1 CACCACCTCCTCCTCCACCTC-ACCACCACCGCCTCCACCAC
*
78255 CAACACCTCC
1 CACCACCTCC
78265 ACCTGAACCA
Statistics
Matches: 127, Mismatches: 39, Indels: 24
0.67 0.21 0.13
Matches are distributed among these distances:
39 17 0.13
41 3 0.02
42 90 0.71
43 3 0.02
44 1 0.01
45 12 0.09
46 1 0.01
ACGTcount: A:0.22, C:0.59, G:0.05, T:0.15
Consensus pattern (41 bp):
CACCACCTCCTCCTCCACCTCACCACCACCGCCTCCACCAC
Found at i:78266 original size:24 final size:24
Alignment explanation
Indices: 78239--78366 Score: 66
Period size: 24 Copynumber: 5.2 Consensus size: 24
78229 ACCTCTACCA
78239 CCACCGCCTCCACCACCAACACCT
1 CCACCGCCTCCACCACCAACACCT
** * *
78263 CCACCTG-AACCACCTCCAACACCA
1 CCACC-GCCTCCACCACCAACACCT
* *
78287 CCACCAGCACCTACTCCTCCCCCAACACCT
1 CCACC-G---C--CTCCACCACCAACACCT
* * * * *
78317 CCTCCTCCTCCACC-TC--TACCA
1 CCACCGCCTCCACCACCAACACCT
78338 CCACCGCCTCCACCACCAACACCT
1 CCACCGCCTCCACCACCAACACCT
78362 CCACC
1 CCACC
78367 AGCACCTCCT
Statistics
Matches: 73, Mismatches: 21, Indels: 20
0.64 0.18 0.18
Matches are distributed among these distances:
21 15 0.21
22 1 0.01
23 1 0.01
24 38 0.52
25 1 0.01
26 1 0.01
30 16 0.22
ACGTcount: A:0.24, C:0.61, G:0.03, T:0.12
Consensus pattern (24 bp):
CCACCGCCTCCACCACCAACACCT
Found at i:78326 original size:21 final size:21
Alignment explanation
Indices: 78300--78363 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
78290 CCAGCACCTA
*
78300 CTCCTCCCCCAACACCTCCTC
1 CTCCTCCCCCAACACCTCCGC
* *
78321 CTCCTCCACCTCTACCACCACCGC
1 CTCCTCC-CC-C-AACACCTCCGC
* *
78345 CTCCACCACCAACACCTCC
1 CTCCTCCCCCAACACCTCC
78364 ACCAGCACCT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 14 0.42
22 3 0.09
23 2 0.06
24 14 0.42
ACGTcount: A:0.19, C:0.64, G:0.02, T:0.16
Consensus pattern (21 bp):
CTCCTCCCCCAACACCTCCGC
Found at i:78365 original size:12 final size:12
Alignment explanation
Indices: 78350--78397 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
78340 ACCGCCTCCA
78350 CCACCAACACCT
1 CCACCAACACCT
*
78362 CCACCAGCACCT
1 CCACCAACACCT
* *
78374 CCTCCAACACCA
1 CCACCAACACCT
*
78386 CCACCAGCACCT
1 CCACCAACACCT
78398 ACTCCTCCCC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.29, C:0.58, G:0.04, T:0.08
Consensus pattern (12 bp):
CCACCAACACCT
Found at i:78380 original size:24 final size:24
Alignment explanation
Indices: 78353--78402 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
78343 GCCTCCACCA
* *
78353 CCAACACCTCCACCAGCACCTCCT
1 CCAACACCACCACCAGCACCTACT
78377 CCAACACCACCACCAGCACCTACT
1 CCAACACCACCACCAGCACCTACT
78401 CC
1 CC
78403 TCCCCCAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.58, G:0.04, T:0.10
Consensus pattern (24 bp):
CCAACACCACCACCAGCACCTACT
Found at i:78405 original size:42 final size:42
Alignment explanation
Indices: 78359--78441 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
78349 ACCACCAACA
* *
78359 CCTCCACCAGCACCTCCTCCAACACCACCACCAGCACCTACT
1 CCTCCACCAACACCTCCTCCAACACCACCACCAACACCTACT
* * *
78401 CCTCCCCCAACACCTCCTCCGACGCCACCACCAACACCTAC
1 CCTCCACCAACACCTCCTCCAACACCACCACCAACACCTAC
78442 ACCACCTCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.59, G:0.05, T:0.11
Consensus pattern (42 bp):
CCTCCACCAACACCTCCTCCAACACCACCACCAACACCTACT
Found at i:78429 original size:99 final size:99
Alignment explanation
Indices: 78213--78420 Score: 389
Period size: 99 Copynumber: 2.1 Consensus size: 99
78203 CCACCAATAC
*
78213 CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCACCAACACCTCCACCTGAACCACCT
1 CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCACCAACACCTCCACCAGAACCACCT
78278 CCAACACCACCACCAGCACCTACTCCTCCCCCAA
66 CCAACACCACCACCAGCACCTACTCCTCCCCCAA
* *
78312 CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCACCAACACCTCCACCAGCACCTCCT
1 CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCACCAACACCTCCACCAGAACCACCT
78377 CCAACACCACCACCAGCACCTACTCCTCCCCCAA
66 CCAACACCACCACCAGCACCTACTCCTCCCCCAA
78411 CACCTCCTCC
1 CACCTCCTCC
78421 GACGCCACCA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 106 1.00
ACGTcount: A:0.23, C:0.61, G:0.03, T:0.13
Consensus pattern (99 bp):
CACCTCCTCCTCCTCCACCTCTACCACCACCGCCTCCACCACCAACACCTCCACCAGAACCACCT
CCAACACCACCACCAGCACCTACTCCTCCCCCAA
Found at i:78459 original size:66 final size:66
Alignment explanation
Indices: 78389--78513 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
78379 AACACCACCA
* * * *
78389 CCAGCACCTACT-CCTCCCCCAACACCTCCTCCGACGCCACCACCAACACCTACACCACCTCCTC
1 CCAGCACCTA-TGCCACCACCAACACCACCCCCGACGCCACCACCAACACCTACACCACCTCCTC
78453 CT
65 CT
* * * * *
78455 CCAGCACCTATGCCACCACCAATACCACCCCCTACGCCTCCTCCAGCACCTACACCACC
1 CCAGCACCTATGCCACCACCAACACCACCCCCGACGCCACCACCAACACCTACACCACC
78514 ACCAACACCT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 48 0.98
ACGTcount: A:0.24, C:0.58, G:0.06, T:0.13
Consensus pattern (66 bp):
CCAGCACCTATGCCACCACCAACACCACCCCCGACGCCACCACCAACACCTACACCACCTCCTCC
T
Found at i:78470 original size:42 final size:41
Alignment explanation
Indices: 78422--78533 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
78412 ACCTCCTCCG
78422 ACGCCACCACCAACACCTACACCACCTCCTCCTCCAGCACCT
1 ACGCCACCACCAACACCTAC-CCACCTCCTCCTCCAGCACCT
* *
78464 ATGCCACCACCAATACC-ACCC-CCTACGCCTCCTCCAGCACCT
1 ACGCCACCACCAACACCTACCCACCT---CCTCCTCCAGCACCT
* *
78506 ACACCACCACCAACACCTCCTCCACCTC
1 ACGCCACCACCAACACCTAC-CCACCTC
78534 TACCACCACC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
39 3 0.05
40 2 0.03
41 2 0.03
42 45 0.78
43 1 0.02
44 2 0.03
45 3 0.05
ACGTcount: A:0.26, C:0.57, G:0.04, T:0.12
Consensus pattern (41 bp):
ACGCCACCACCAACACCTACCCACCTCCTCCTCCAGCACCT
Found at i:78599 original size:24 final size:24
Alignment explanation
Indices: 78572--78618 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
78562 ACCTGTACCA
78572 CCTCCAACACCACCACCACCACCT
1 CCTCCAACACCACCACCACCACCT
* * *
78596 CCTCCTACGCCACCACCAGCACC
1 CCTCCAACACCACCACCACCACC
78619 AACACCTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.62, G:0.04, T:0.09
Consensus pattern (24 bp):
CCTCCAACACCACCACCACCACCT
Found at i:78613 original size:30 final size:30
Alignment explanation
Indices: 78579--78642 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
78569 CCACCTCCAA
* *
78579 CACCACCACCACCACCTCCTCCTACGCCAC
1 CACCACCACCAACACCTCCTCCTACACCAC
* *
78609 CACCAGCACCAACACCTCCTCCTACACTAC
1 CACCACCACCAACACCTCCTCCTACACCAC
78639 CACC
1 CACC
78643 GGCTCCTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.59, G:0.03, T:0.11
Consensus pattern (30 bp):
CACCACCACCAACACCTCCTCCTACACCAC
Found at i:78630 original size:54 final size:53
Alignment explanation
Indices: 78572--78699 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 53
78562 ACCTGTACCA
*
78572 CCTCCAACACCACCACCACCACCTCCTCCTACGCCACC-A-CCAG-CACCAACACCT
1 CCTCCTACACCACCACCACCACCTCCTCC-A-G-CACCTAGCC-GCCACCAACACCT
* ** *
78626 CCTCCTACACTACCACCGGCTCCTCCTCCAGCACCTATGCCGCCACCAACACCT
1 CCTCCTACACCACCACCACCACCTCCTCCAGCACCTA-GCCGCCACCAACACCT
*
78680 CCTCCTCCACCACCACCACC
1 CCTCCTACACCACCACCACC
78700 TCCACTTCCA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
51 4 0.07
52 2 0.03
53 2 0.03
54 53 0.87
ACGTcount: A:0.23, C:0.59, G:0.05, T:0.12
Consensus pattern (53 bp):
CCTCCTACACCACCACCACCACCTCCTCCAGCACCTAGCCGCCACCAACACCT
Found at i:78689 original size:18 final size:18
Alignment explanation
Indices: 78615--78702 Score: 61
Period size: 18 Copynumber: 4.9 Consensus size: 18
78605 CCACCACCAG
*
78615 CACCAACACCTCCTCCTA
1 CACCAACACCTCCTCCTC
* * **
78633 CACTACCACCGGCTCCTC
1 CACCAACACCTCCTCCTC
* * * *
78651 CTCCAGCACCT-ATGCCGC
1 CACCAACACCTCCT-CCTC
78669 CACCAACACCTCCTCCTC
1 CACCAACACCTCCTCCTC
* *
78687 CACCACCACCACCTCC
1 CACCAACACCTCCTCC
78703 ACTTCCACCA
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
17 1 0.02
18 49 0.96
19 1 0.02
ACGTcount: A:0.22, C:0.58, G:0.06, T:0.15
Consensus pattern (18 bp):
CACCAACACCTCCTCCTC
Found at i:78701 original size:15 final size:15
Alignment explanation
Indices: 78683--78725 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
78673 AACACCTCCT
78683 CCTCCACCACCACCA
1 CCTCCACCACCACCA
**
78698 CCTCCACTTCCACCA
1 CCTCCACCACCACCA
* *
78713 CCTACACCCCCAC
1 CCTCCACCACCAC
78726 TTGCTCCACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.65, G:0.00, T:0.12
Consensus pattern (15 bp):
CCTCCACCACCACCA
Found at i:78725 original size:21 final size:22
Alignment explanation
Indices: 78685--78736 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
78675 CACCTCCTCC
*
78685 TCCACCACC-ACCACCTCCACT
1 TCCACCACCTACCACCCCCACT
78706 TCCACCACCTA-CACCCCCACT
1 TCCACCACCTACCACCCCCACT
* *
78727 TGCTCCACCT
1 TCCACCACCT
78737 CCGCCTCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.21, C:0.60, G:0.02, T:0.17
Consensus pattern (22 bp):
TCCACCACCTACCACCCCCACT
Found at i:78763 original size:30 final size:30
Alignment explanation
Indices: 78687--78765 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
78677 CCTCCTCCTC
* * *
78687 CACCACCACCACCTCCACTTCCACCACCTA
1 CACCACCACCAACTCCACCTCCACCACCGA
* *** * *
78717 CACCCCCACTTGCTCCACCTCCGCCTCCGA
1 CACCACCACCAACTCCACCTCCACCACCGA
78747 CACCACCACCAACTCCACC
1 CACCACCACCAACTCCACC
78766 GCCCTTTCCA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.23, C:0.61, G:0.04, T:0.13
Consensus pattern (30 bp):
CACCACCACCAACTCCACCTCCACCACCGA
Found at i:83589 original size:21 final size:21
Alignment explanation
Indices: 83559--83611 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
83549 CCTTGGGGGA
* *
83559 TGAGGTTGGTTGCGTTGGTTGT
1 TGAGG-TGGTTACGGTGGTTGT
* *
83581 TGTGGTGGTTACGGTGGTTTT
1 TGAGGTGGTTACGGTGGTTGT
83602 TGAGGTGGTT
1 TGAGGTGGTT
83612 TTGAGTGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.06, C:0.04, G:0.45, T:0.45
Consensus pattern (21 bp):
TGAGGTGGTTACGGTGGTTGT
Done.