Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012278.1 Kokia drynarioides strain JFW-HI SEQ_127279, 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: 30492
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1775 original size:59 final size:59
Alignment explanation
Indices: 1678--1987 Score: 437
Period size: 59 Copynumber: 5.3 Consensus size: 59
1668 TAAATTGTCC
* * *
1678 AAAAATCTCATTTTTAA-CCTCGAAACTTTCAAATATTCTATTTCTACCCCCAAACTTCT
1 AAAAATCCCATTTTTAACCCT-GAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
* * *
1737 AAAAATCCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCTCGAACTTCC
1 AAAAATCCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
* * * *
1796 AAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCTCGAACTTCT
1 AAAAATCCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
* * * *
1855 AAAAATCTCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
1 AAAAATCCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
*
1914 AAAAATCCCATTTTTAAACCC-AAAACTTTCAAAAATTCTATTTTTACCCCCAAACTT-T
1 AAAAATCCCATTTTT-AACCCTGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
1972 CAAAAATCCCATTTTT
1 -AAAAATCCCATTTTT
1988 GACCTCGAAT
Statistics
Matches: 228, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
59 220 0.96
60 8 0.04
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAAATCCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCT
Found at i:2001 original size:29 final size:28
Alignment explanation
Indices: 1677--2001 Score: 190
Period size: 29 Copynumber: 11.0 Consensus size: 28
1667 CTAAATTGTC
*
1677 CAAAAATCTCATTTTTAACCTCGAAACTTT
1 CAAAAATCCCATTTTT-ACCTCG-AACTTT
* * * * * *
1707 CAAATATTCTATTTCTACCCCCAAAC-TT
1 CAAAAATCCCATTTTTA-CCTCGAACTTT
1735 CTAAAAATCCCATTTTTAACC-CTGAAACTTT
1 C-AAAAATCCCATTTTT-ACCTC-G-AACTTT
* * *
1766 CAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATCCCATTTTTA-CCTCGAACTTT
*
1795 CAAAAATCCCATTTTTAACCCCGAAACTTT
1 CAAAAATCCCATTTTT-ACCTCG-AACTTT
* * *
1825 CAAAAATTCTACTTTTACCCTCGAAC-TT
1 CAAAAATCCCATTTTTA-CCTCGAACTTT
* **
1853 CTAAAAATCTCATTTTTAACCCTAAAACTTT
1 C-AAAAATCCCATTTTT-A-CCTCGAACTTT
* * * * *
1884 CAAAAATTCTATTTTTACCCCTAAACTTC
1 CAAAAATCCCATTTTTACCTC-GAACTTT
*
1913 CAAAAATCCCATTTTTAAACC-CAAAACTTT
1 CAAAAATCCCATTTTT--ACCTC-GAACTTT
* * * *
1943 CAAAAATTCTATTTTTACCCCCAAACTTT
1 CAAAAATCCCATTTTTA-CCTCGAACTTT
*
1972 CAAAAATCCCATTTTTGACCTCGAATTTT
1 CAAAAATCCCATTTTT-ACCTCGAACTTT
2001 C
1 C
2002 CCAAAATTAT
Statistics
Matches: 229, Mismatches: 46, Indels: 41
0.72 0.15 0.13
Matches are distributed among these distances:
28 10 0.04
29 109 0.48
30 100 0.44
31 10 0.04
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (28 bp):
CAAAAATCCCATTTTTACCTCGAACTTT
Found at i:2035 original size:177 final size:177
Alignment explanation
Indices: 1678--2046 Score: 478
Period size: 177 Copynumber: 2.1 Consensus size: 177
1668 TAAATTGTCC
* * *
1678 AAAAATCTCATTTTTAACCTCGAAACTTTCAAATATTCTATTTCTACCCCCAAACTTCTAAAAAT
1 AAAAATCTCATTTTTAACCTCAAAACTTTCAAAAATTCTATTTCTACCCCCAAACTTCCAAAAAT
* * *
1743 CCCATTTTTAACCCTGAAACTTTCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATT
66 CCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCATT
* * * *
1808 TTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCTCGAACTTCT
131 TTTAACCCCGAAACTTTCAAAAATTATACTTTCACCCCCGAACATCT
* *
1855 AAAAATCTCATTTTTAACC-CTAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCCAAAAA
1 AAAAATCTCATTTTTAACCTC-AAAACTTTCAAAAATTCTATTTCTACCCCCAAACTTCCAAAAA
*
1919 TCCCATTTTTAAACCC-AAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTTCAAAAATCCCA
65 TCCCATTTTT-AACCCTAAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCA
* * * * *
1983 TTTTTGACCTCG-AATTTTCCCAAAATTAT-CGTTTCGCCCCCGAGA-ATCT
129 TTTTTAACCCCGAAACTTT-CAAAAATTATAC-TTTCACCCCCGA-ACATCT
* *
2032 AAAATTATCATTTTT
1 AAAAATCTCATTTTT
2047 GCCCCCAGGA
Statistics
Matches: 167, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
176 7 0.04
177 154 0.92
178 6 0.04
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (177 bp):
AAAAATCTCATTTTTAACCTCAAAACTTTCAAAAATTCTATTTCTACCCCCAAACTTCCAAAAAT
CCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCATT
TTTAACCCCGAAACTTTCAAAAATTATACTTTCACCCCCGAACATCT
Found at i:13140 original size:32 final size:30
Alignment explanation
Indices: 13104--13171 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 30
13094 TACTTGACAA
13104 TTTTTAACTAATGATTGTTTCCTTTGATCCTC
1 TTTTTAA-TAAT-ATTGTTTCCTTTGATCCTC
13136 -TTTT--TAATATTGTTTCCTTTGATCCTC
1 TTTTTAATAATATTGTTTCCTTTGATCCTC
*
13163 TTCTTAATA
1 TTTTTAATA
13172 GAATTTTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
27 19 0.59
28 7 0.22
30 2 0.06
31 4 0.12
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTTTAATAATATTGTTTCCTTTGATCCTC
Found at i:13148 original size:27 final size:27
Alignment explanation
Indices: 13112--13171 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
13102 AATTTTTAAC
*
13112 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTCT
13140 TAATATTGTTTCCTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
13167 TAATA
1 TAATA
13172 GAATTTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:14207 original size:206 final size:206
Alignment explanation
Indices: 13743--14287 Score: 770
Period size: 205 Copynumber: 2.6 Consensus size: 206
13733 TGATTAAGAG
* *
13743 GCAGGTCGAAGCAATAAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAAATTCGTCT
1 GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACC-AAATTCGTCT
* * * *
13808 TCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATAACT
65 TCCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAAT-ACT
* * * *
13873 AAGAAGAAGACCAAATCAAGCCCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGAT
129 GAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGAT
13938 GAGACACCGAGAA
194 GAGACACCGAGAA
* *
13951 GTAGGTCGAAACAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
1 GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
* *
14016 CCTGATGAAATACAGAGAAGCGGATTGGAACAAACGACGCAGTCATCTTCCTGATGAAATACTGA
66 CCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTGA
* * * * * * *
14081 GAAGAAGACCAAATCAAACCCATGCTCGATGTG-GGCAAATCTTTGAACCACAGCTTCCTGATTA
131 GAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGATGA
* * *
14145 GATACTGAGGA
196 GACACCGAGAA
* * *
14156 GCAGGTCGAAGTAATAAGATGGTTAGCTTCTTGATGAGATACTGAGAAGTCAACCAAATTCGTCT
1 GCAGGTCGAAGCAATAA-ACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCT
* * * *
14221 TCCTGATG-AATACAAAGAAGCGGATTGAAACAAATGATGCAGCCGTCTTCCTGATGAAATACTG
65 TCCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTG
14285 AGA
130 AGA
14288 GAAAGGTCAA
Statistics
Matches: 301, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
205 101 0.34
206 85 0.28
207 65 0.22
208 50 0.17
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (206 bp):
GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
CCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTGA
GAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGATGA
GACACCGAGAA
Found at i:14578 original size:16 final size:16
Alignment explanation
Indices: 14559--14620 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
14549 TTGGATTTTG
*
14559 AATTTATTTTATTTAA
1 AATTTAATTTATTTAA
*
14575 AATTTAAATTTATTTGA
1 AATTT-AATTTATTTAA
14592 AATTTAAATTTA-TTATA
1 AATTT-AATTTATTTA-A
14609 AATTTAAATTTA
1 AATTT-AATTTA
14621 AAATGTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTAATTTATTTAA
Found at i:14585 original size:6 final size:6
Alignment explanation
Indices: 14569--14622 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
14559 AATTTATTTT
14569 ATTTAAA ATTTAA ATTT-- ATTTGAA ATTTAA ATTT-- ATTATAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATT-TAA ATTTAA
14616 ATTTAA A
1 ATTTAA A
14623 ATGTCCAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.17
5 1 0.02
6 22 0.54
7 11 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:14588 original size:17 final size:17
Alignment explanation
Indices: 14566--14620 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
14556 TTGAATTTAT
14566 TTTATTTAAAATTTAAA
1 TTTATTTAAAATTTAAA
*
14583 TTTATTTGAAATTTAAA
1 TTTATTTAAAATTTAAA
14600 TTTA-TTATAAATTTAAA
1 TTTATTTA-AAATTTAAA
14617 TTTA
1 TTTA
14621 AAATGTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 2 0.06
17 33 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATTTAAAATTTAAA
Found at i:26500 original size:32 final size:30
Alignment explanation
Indices: 26464--26531 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 30
26454 TACTTGACAA
26464 TTTTTAACTAATGATTGTTTCCTTTGATCCTC
1 TTTTTAA-TAAT-ATTGTTTCCTTTGATCCTC
26496 -TTTT--TAATATTGTTTCCTTTGATCCTC
1 TTTTTAATAATATTGTTTCCTTTGATCCTC
*
26523 TTCTTAATA
1 TTTTTAATA
26532 GAATTTTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
27 19 0.59
28 7 0.22
30 2 0.06
31 4 0.12
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTTTAATAATATTGTTTCCTTTGATCCTC
Found at i:26508 original size:27 final size:27
Alignment explanation
Indices: 26472--26531 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
26462 AATTTTTAAC
*
26472 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTCT
26500 TAATATTGTTTCCTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
26527 TAATA
1 TAATA
26532 GAATTTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:27567 original size:206 final size:206
Alignment explanation
Indices: 27103--27647 Score: 770
Period size: 205 Copynumber: 2.6 Consensus size: 206
27093 TGATTAAGAG
* *
27103 GCAGGTCGAAGCAATAAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAAATTCGTCT
1 GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACC-AAATTCGTCT
* * * *
27168 TCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATAACT
65 TCCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAAT-ACT
* * * *
27233 AAGAAGAAGACCAAATCAAGCCCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGAT
129 GAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGAT
27298 GAGACACCGAGAA
194 GAGACACCGAGAA
* *
27311 GTAGGTCGAAACAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
1 GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
* *
27376 CCTGATGAAATACAGAGAAGCGGATTGGAACAAACGACGCAGTCATCTTCCTGATGAAATACTGA
66 CCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTGA
* * * * * * *
27441 GAAGAAGACCAAATCAAACCCATGCTCGATGTG-GGCAAATCTTTGAACCACAGCTTCCTGATTA
131 GAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGATGA
* * *
27505 GATACTGAGGA
196 GACACCGAGAA
* * *
27516 GCAGGTCGAAGTAATAAGATGGTTAGCTTCTTGATGAGATACTGAGAAGTCAACCAAATTCGTCT
1 GCAGGTCGAAGCAATAA-ACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCT
* * * *
27581 TCCTGATG-AATACAAAGAAGCGGATTGAAACAAATGATGCAGCCGTCTTCCTGATGAAATACTG
65 TCCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTG
27645 AGA
130 AGA
27648 GAAAGGTCAA
Statistics
Matches: 301, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
205 101 0.34
206 85 0.28
207 65 0.22
208 50 0.17
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (206 bp):
GCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTT
CCTGATGAAATACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAAATACTGA
GAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGGAAAATCTTCGAACCACAGCTTCCTGATGA
GACACCGAGAA
Found at i:27938 original size:16 final size:16
Alignment explanation
Indices: 27919--27980 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
27909 TTGGATTTTG
*
27919 AATTTATTTTATTTAA
1 AATTTAATTTATTTAA
*
27935 AATTTAAATTTATTTGA
1 AATTT-AATTTATTTAA
27952 AATTTAAATTTA-TTATA
1 AATTT-AATTTATTTA-A
27969 AATTTAAATTTA
1 AATTT-AATTTA
27981 AAATGTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTAATTTATTTAA
Found at i:27945 original size:6 final size:6
Alignment explanation
Indices: 27929--27982 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
27919 AATTTATTTT
27929 ATTTAAA ATTTAA ATTT-- ATTTGAA ATTTAA ATTT-- ATTATAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATT-TAA ATTTAA
27976 ATTTAA A
1 ATTTAA A
27983 ATGTCCAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.17
5 1 0.02
6 22 0.54
7 11 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:27948 original size:17 final size:17
Alignment explanation
Indices: 27926--27980 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
27916 TTGAATTTAT
27926 TTTATTTAAAATTTAAA
1 TTTATTTAAAATTTAAA
*
27943 TTTATTTGAAATTTAAA
1 TTTATTTAAAATTTAAA
27960 TTTA-TTATAAATTTAAA
1 TTTATTTA-AAATTTAAA
27977 TTTA
1 TTTA
27981 AAATGTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 2 0.06
17 33 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATTTAAAATTTAAA
Found at i:29827 original size:29 final size:30
Alignment explanation
Indices: 29781--30091 Score: 262
Period size: 29 Copynumber: 10.9 Consensus size: 30
29771 CCCTAAATTG
29781 TTCAAAAA-TCTCATTTTTAACCCCGAAACT
1 TTCAAAAATTC-CATTTTTAACCCCGAAACT
* *
29811 TTTAAAAATTCTATTTTT-ACCCTCG-AACT
1 TTCAAAAATTCCATTTTTAACCC-CGAAACT
* *
29840 TCCAAAAATCCCATTTTTAACCCCGAAACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
** * *
29870 TTCAAAAATTATACTTTTACCCCCG-AACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* *
29899 TCCAAAAA-TCCATTTTTAACCCCAAAACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* * ** *
29928 TTAAAAAATTCTACATTTACCCCCG-AACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* *
29957 TCCAAAAATCCCATTTTTAACCCCGAAACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
*
29987 TTCAAAAATTCC---CTT------G-AACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* *
30007 TCCAAAAATCCCATTTTTAA-CCCGAAACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* *
30036 TTCAAAAATTCTATTTTT-ACCCCCAAACT
1 TTCAAAAATTCCATTTTTAACCCCGAAACT
* *
30065 TTCAAAAATCCCATTTTTGACCCCGAA
1 TTCAAAAATTCCATTTTTAACCCCGAA
30092 TTTTCCTAAA
Statistics
Matches: 218, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
20 14 0.06
21 1 0.00
23 2 0.01
27 2 0.01
28 13 0.06
29 110 0.50
30 74 0.34
31 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (30 bp):
TTCAAAAATTCCATTTTTAACCCCGAAACT
Found at i:29947 original size:58 final size:59
Alignment explanation
Indices: 29783--30091 Score: 424
Period size: 59 Copynumber: 5.4 Consensus size: 59
29773 CTAAATTGTT
* * * *
29783 CAAAAATCTCATTTTTAACCCCGAAACTTTTAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
*
29842 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTATACTTTTACCCCCGAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
* * *
29901 CAAAAAT-CCATTTTTAACCCCAAAACTTTAAAAAATTCTACATTTACCCCCGAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
*
29959 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTC--C-CTT------GAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
* * *
30009 CAAAAATCCCATTTTTAA-CCCGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTTT
1 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
*
30067 CAAAAATCCCATTTTTGACCCCGAA
1 CAAAAATCCCATTTTTAACCCCGAA
30092 TTTTCCTAAA
Statistics
Matches: 222, Mismatches: 17, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
49 20 0.09
50 25 0.11
52 2 0.01
56 2 0.01
57 1 0.00
58 76 0.34
59 96 0.43
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (59 bp):
CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCTACTTTTACCCCCGAACTTC
Found at i:30011 original size:50 final size:49
Alignment explanation
Indices: 29952--30046 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 49
29942 ATTTACCCCC
29952 GAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCCCTT
1 GAACTTCCAAAAATCCCATTTTTAA-CCCGAAACTTTCAAAAATTCCCTT
30002 GAACTTCCAAAAATCCCATTTTTAACCCGAAACTTTCAAAAATTC
1 GAACTTCCAAAAATCCCATTTTTAACCCGAAACTTTCAAAAATTC
30047 TATTTTTACC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 20 0.44
50 25 0.56
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.29
Consensus pattern (49 bp):
GAACTTCCAAAAATCCCATTTTTAACCCGAAACTTTCAAAAATTCCCTT
Found at i:30104 original size:108 final size:108
Alignment explanation
Indices: 29894--30091 Score: 317
Period size: 108 Copynumber: 1.8 Consensus size: 108
29884 TTTTACCCCC
*
29894 GAACTTCCAAAAATCCATTTTTAACCCCAAAACTTTAAAAAATTCTACATTTACCCCCGAACTTC
1 GAACTTCCAAAAATCCATTTTTAACCCCAAAACTTTAAAAAATTCTACATTTACCCCCAAACTTC
29959 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCCCTT
66 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCCCTT
* * **
30002 GAACTTCCAAAAATCCCATTTTTAA-CCCGAAACTTTCAAAAATTCTATTTTTACCCCCAAACTT
1 GAACTTCCAAAAAT-CCATTTTTAACCCCAAAACTTTAAAAAATTCTACATTTACCCCCAAACTT
* *
30066 TCAAAAATCCCATTTTTGACCCCGAA
65 CCAAAAATCCCATTTTTAACCCCGAA
30092 TTTTCCTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 72 0.88
109 10 0.12
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (108 bp):
GAACTTCCAAAAATCCATTTTTAACCCCAAAACTTTAAAAAATTCTACATTTACCCCCAAACTTC
CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCCCTT
Done.