Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015462.1 Corchorus olitorius cultivar O-4 contig15495, 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: 47270
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:18929 original size:15 final size:15
Alignment explanation
Indices: 18906--18944 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
18896 TTTTATCAAA
*
18906 CTTTGTTTTTC-TTT
1 CTTTTTTTTTCTTTT
*
18920 CTTTTCTTTTCTTTT
1 CTTTTTTTTTCTTTT
18935 CTTTTTTTTT
1 CTTTTTTTTT
18945 TGGTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTTCTTTT
Found at i:18945 original size:5 final size:5
Alignment explanation
Indices: 18912--18943 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
18902 CAAACTTTGT
18912 TTTTC -TTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
18944 TTGGTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:30728 original size:6 final size:6
Alignment explanation
Indices: 30717--30748 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
30707 AGAAAAGCGT
30717 CGCCAA CGCCAA CGCCAA CGCCAA CG-CAA CGC
1 CGCCAA CGCCAA CGCCAA CGCCAA CGCCAA CGC
30749 AGGACTCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
CGCCAA
Found at i:31702 original size:62 final size:62
Alignment explanation
Indices: 31632--31804 Score: 337
Period size: 62 Copynumber: 2.8 Consensus size: 62
31622 ATGTGATCAT
*
31632 TCACAATCTATACTTTCATGTATTAAAGAATTTCATTATAACTAAAATCTGATCATTTCAAA
1 TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATCTGATCATTTCAAA
31694 TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATCTGATCATTTCAAA
1 TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATCTGATCATTTCAAA
31756 TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATC
1 TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATC
31805 CTTGAAGCTT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 110 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (62 bp):
TCACAATCTATACTTTCATGCATTAAAGAATTTCATTATAACTAAAATCTGATCATTTCAAA
Found at i:33969 original size:3 final size:3
Alignment explanation
Indices: 33961--33994 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
33951 TCAGGTTCAA
* *
33961 ACG ACG ACG ACG ACG ACG ACG TCG ACG GCG ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG A
33995 GTAGCCAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.32, G:0.35, T:0.03
Consensus pattern (3 bp):
ACG
Found at i:44542 original size:50 final size:51
Alignment explanation
Indices: 44351--44560 Score: 264
Period size: 51 Copynumber: 4.1 Consensus size: 51
44341 TCCATATGTT
* * ** * * *
44351 TAAAAAAATTTAGTAATTAGGAGACTGATTAGAGCTATCTCTCTAAACAT-
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
* *
44401 TAAAAAAGTTTTAGTAATTAGGAGACTGATGGGAGTTGTCTCCCCAAACATC
1 TAAAAAA-TTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
* * *
44453 TAAAAAATTTTAGTAATTAGAAGACCTATGGGAGCTGTCTCCCCAAATATC
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
*
44504 TAAAAAATTTTAGTAATTAGGAGACCGAT-GGAGCTGTCTCCCCTAACAAT-
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAAC-ATC
44554 TAAAAAA
1 TAAAAAA
44561 GTGACCGATG
Statistics
Matches: 141, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
50 30 0.21
51 104 0.74
52 7 0.05
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (51 bp):
TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
Found at i:44610 original size:49 final size:49
Alignment explanation
Indices: 44555--44653 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
44545 CCTAACAATT
44555 AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATTGAAAAGA
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATTGAAAAGA
44604 AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATTGAAAAGA
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATTGAAAAGA
44653 A
1 A
44654 GTGACCGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (49 bp):
AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATTGAAAAGA
Found at i:44736 original size:41 final size:42
Alignment explanation
Indices: 44604--44801 Score: 216
Period size: 41 Copynumber: 4.9 Consensus size: 42
44594 ATTGAAAAGA
* * * *
44604 AAAAAAGTGACCGATGAGAGCTGTCTCTCGAAACATTTAATT
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATT
44646 GAAAAGAAGTGACCGATGAGAG----CTCTCCAAAC----AATT
1 -AAAA-AAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATT
* *
44682 AAAAAAGTGACTGATGAGAGTTATCTCTCCAAACAATAAATT
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATT
* * * *
44724 -AAAAAGTGACTGATAAGAGCTATCTCTTCAAACATTAAATT
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATT
*
44765 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAAT
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAAT
44802 TAAAAAAGTG
Statistics
Matches: 134, Mismatches: 11, Indels: 21
0.81 0.07 0.13
Matches are distributed among these distances:
34 15 0.11
35 4 0.03
36 4 0.03
38 10 0.07
40 9 0.07
41 37 0.28
42 35 0.26
43 4 0.03
44 16 0.12
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (42 bp):
AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATT
Found at i:44852 original size:59 final size:60
Alignment explanation
Indices: 44765--44878 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 60
44755 ACATTAAATT
*
44765 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAA-AAAA-GTGACCAACATAAA
1 AAAAAAGTGACCGAAGAGAGCTGTCTCTCCAAACAATTAATAAAATGTGACCAACATAAA
*
44823 AAAAAATGTGACCGAAGAGAGCTGTCTCTCCAAACATTTAATTAAAATGTGACCAA
1 AAAAAA-GTGACCGAAGAGAGCTGTCTCTCCAAACAATTAA-TAAAATGTGACCAA
44879 TGAGAGCTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
58 6 0.12
59 32 0.64
61 4 0.08
62 8 0.16
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (60 bp):
AAAAAAGTGACCGAAGAGAGCTGTCTCTCCAAACAATTAATAAAATGTGACCAACATAAA
Found at i:44871 original size:41 final size:41
Alignment explanation
Indices: 44825--44910 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
44815 AACATAAAAA
* *
44825 AAAATGTGACCGAA-GAGAGCTGTCTCTCCAAACATTTAATT
1 AAAATGTGACC-AATGAGAGCTATCTCTCCAAACAATTAATT
44866 AAAATGTGACCAATGAGAGCTATCTCTCCAAACAATTAATT
1 AAAATGTGACCAATGAGAGCTATCTCTCCAAACAATTAATT
44907 AAAA
1 AAAA
44911 AACTGACCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 2 0.05
41 40 0.95
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (41 bp):
AAAATGTGACCAATGAGAGCTATCTCTCCAAACAATTAATT
Found at i:44941 original size:42 final size:41
Alignment explanation
Indices: 44831--44941 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 41
44821 AAAAAAAATG
* **
44831 TGACCGAA-GAGAGCTGTCTCTCCAAACATTTAATTAAAATG
1 TGACC-AATGAGAGCTGTCTCTCCAAACAATTAATTAAAAAC
*
44872 TGACCAATGAGAGCTATCTCTCCAAACAATTAATTAAAAAAC
1 TGACCAATGAGAGCTGTCTCTCCAAACAATTAATT-AAAAAC
** *
44914 TGACCTGTGGGAGCTGTCTC-CCTAAACA
1 TGACCAATGAGAGCTGTCTCTCC-AAACA
44942 TCTAAAAAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 2 0.03
41 32 0.54
42 25 0.42
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (41 bp):
TGACCAATGAGAGCTGTCTCTCCAAACAATTAATTAAAAAC
Found at i:44941 original size:142 final size:140
Alignment explanation
Indices: 44682--44955 Score: 349
Period size: 142 Copynumber: 1.9 Consensus size: 140
44672 CCAAACAATT
* * * **
44682 AAAAAAGTGACTGATGAGAGTTATCTCTCCAAACAATAAATTAAAAAGTGACTGATAAGAGCTAT
1 AAAAAAGTGACCGAAGAGAGCTATCTCTCCAAACAATAAATTAAAAAGTGACCAATAAGAGCTAT
* *
44747 CTCTTCAAACATTAAATTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAAT-TAAAAAAGT
66 CTCTCCAAACATTAAATTAAAAAACTGACCGATGAGAGCTGTCTCTCCAAAC-ATCT-AAAAAGT
44811 GACCAACATAAA
129 GACCAACATAAA
* * * * *
44823 AAAAAATGTGACCGAAGAGAGCTGTCTCTCCAAACATTTAATTAAAATGTGACCAATGAGAGCTA
1 AAAAAA-GTGACCGAAGAGAGCTATCTCTCCAAACAATAAATTAAAAAGTGACCAATAAGAGCTA
*
44888 TCTCTCCAAACAATT-AATTAAAAAACTGACCTG-TGGGAGCTGTCTC-CCTAAACATCTAAAAA
65 TCTCTCCAAAC-ATTAAATTAAAAAACTGACC-GATGAGAGCTGTCTCTCC-AAACATCTAAAAA
44950 GTGACC
127 GTGACC
44956 GATAAGAGTT
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
141 21 0.18
142 90 0.78
143 4 0.03
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (140 bp):
AAAAAAGTGACCGAAGAGAGCTATCTCTCCAAACAATAAATTAAAAAGTGACCAATAAGAGCTAT
CTCTCCAAACATTAAATTAAAAAACTGACCGATGAGAGCTGTCTCTCCAAACATCTAAAAAGTGA
CCAACATAAA
Found at i:45000 original size:179 final size:179
Alignment explanation
Indices: 44766--45091 Score: 496
Period size: 179 Copynumber: 1.8 Consensus size: 179
44756 CATTAAATTA
* *
44766 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCAACATAAAAAAAAATG
1 AAAAAGTGACCGATAAGAGCTGTCTCTCCAAAAAATTAAAAAAGTGACCAACATAAAAAAAAA-G
* * * *
44831 TGACCGAAGAGAGCTGTCTCTCCAAACATTTAA-TTAAAATGTGACCAATGAGAGCTATCTCTCC
65 TGACCGAAGAGAGCTGTCTCTCCAAACATTAAATTTAAAAAGTGACCAATGAAAGCCATCTCTCC
44895 AAACAATT-AATTAAAAAACTGACCTGTGGGAGCTGTCTCCCTAAACATCT
130 AAAC-ATTAAATTAAAAAACTGACCTGTGGGAGCTGTCTCCCTAAACATCT
* * *
44945 AAAAAGTGACCGATAAGAGTTGTCTTTCCAAAAAAATT-AAAAAGTGACCAACATAAAAAAGAAG
1 AAAAAGTGACCGATAAGAGCTGTCTCTCC-AAAAAATTAAAAAAGTGACCAACATAAAAAAAAAG
* * *
45009 TGACCGATGAGAGCTGTCTCTCCAAACATTAAATTTAAAAAGTGACCGATGAAAGCCGTCTCTCC
65 TGACCGAAGAGAGCTGTCTCTCCAAACATTAAATTTAAAAAGTGACCAATGAAAGCCATCTCTCC
45074 AAACATTAAATTAAAAAA
130 AAACATTAAATTAAAAAA
45092 GTAACCGATG
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
178 35 0.27
179 90 0.68
180 7 0.05
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (179 bp):
AAAAAGTGACCGATAAGAGCTGTCTCTCCAAAAAATTAAAAAAGTGACCAACATAAAAAAAAAGT
GACCGAAGAGAGCTGTCTCTCCAAACATTAAATTTAAAAAGTGACCAATGAAAGCCATCTCTCCA
AACATTAAATTAAAAAACTGACCTGTGGGAGCTGTCTCCCTAAACATCT
Found at i:45053 original size:42 final size:42
Alignment explanation
Indices: 45001--45996 Score: 745
Period size: 42 Copynumber: 23.8 Consensus size: 42
44991 ACCAACATAA
*
45001 AAAAGAAGTGACCGATGAGAGCTGTCTCTCCAAACATTAAATT
1 AAAA-AAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * *
45044 TAAAAAGTGACCGATGAAAGCCGTCTCTCCAAACATTAAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
45086 AAAAAAGTAACCGATGAGAGCCGTCTCTCCAAACATTTAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *** *
45128 AAAAAAAATGATTAATGAGAGCTGTCTCTCCAAGCATTTAATT
1 -AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
45171 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAAC----AATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45209 -AAAAAGTGACCGATGGGAGCTGTCTCCCCAAACATCTAAAAGTTTTAGTACT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCC-AA-A-C----A--TTTA--ATT
45261 AAAAGAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAA--AAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45305 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATAAATTT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAA-TT
** * * * *
45348 TTAAAAGTGACTGATGGGAGCTGTCTCCCCAAACA--T--CT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
45386 AAAAAAGTGGCCGATGAGAGC--TCTCTCCAAACATTTAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * *
45426 -AAAATGTGACCAATGAGAGCTATCTCTCCAAACAATTAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * * * *
45467 -AAAAACTGACCCATGGGAGCTGTCTCCCCAAAC--GT--CT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
45504 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAATCATTAAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
45546 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAGCATTTAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
45588 AAGAAAATTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AA-AAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
45631 AAAAAAAAGTGACCGATTAGAGCTGTCTCTCCAAGCATTTAATT
1 --AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45675 AAAAAAGTGACCAATGTGAGCCGTCTCTCCAAAC----AATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * * *
45713 -AAAAAGTAACCGATGGGA-CTATCTCCCCAAACATCTAAAAAATTT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAT-T---TAA-TT
*** ** * * * ** * * *
45758 ATTAATTAAAAAAAGTGACCGATGAG-AGTTGTCTCTCCGA-ACATTTAAT
1 A--AA--AAAGTGACCGA-TGA-GAGCTG-TCTCTC-CAAACA-TTTAATT
* * *
45807 TAAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTTAATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
45849 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAAC---T-ATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * *
45887 -AAAAAGTGACCGATGGGAGTTGTCTCCCCAAACA--T--CT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45924 AAAAAATTGACTGATAAGAGCTGTCTCTCCAAAC----AATT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45962 AAAAAAGTGACCGATGAAAGCTATTTCTCCAAACA
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACA
45997 ATATTAGAAG
Statistics
Matches: 758, Mismatches: 134, Indels: 126
0.74 0.13 0.12
Matches are distributed among these distances:
36 22 0.03
37 73 0.10
38 116 0.15
39 20 0.03
40 2 0.00
41 45 0.06
42 244 0.32
43 115 0.15
44 48 0.06
45 10 0.01
46 4 0.01
47 2 0.00
48 3 0.00
49 1 0.00
50 9 0.01
51 1 0.00
52 5 0.01
53 10 0.01
54 4 0.01
55 24 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (42 bp):
AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
Found at i:45188 original size:85 final size:84
Alignment explanation
Indices: 45001--45996 Score: 745
Period size: 85 Copynumber: 11.9 Consensus size: 84
44991 ACCAACATAA
* * * *
45001 AAAAGAAGTGACCGATGAGAGCTGTCTCTCCAAACATTAAATTTAAAAAGTGACCGATGAAAGCC
1 AAAA-AAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCT
*
45066 GTCTCTCCAAACATTAAATT
65 GTCTCTCCAAACATTTAATT
* * * ***
45086 AAAAAAGTAACCGATGAGAGCCGTCTCTCCAAACATTTAATTAAAAAAAATGATTAATGAGAGCT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT-AAAAAAGTGACCGATGAGAGCT
*
45151 GTCTCTCCAAGCATTTAATT
65 GTCTCTCCAAACATTTAATT
*
45171 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAAC----AATT-AAAAAGTGACCGATGGGAGCTG
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
* *
45231 TCTCCCCAAACATCTAAAAGTTTTAGTACT
66 TCTCTCC-AA-A-C----A--TTTA--ATT
45261 AAAAGAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGC
1 AAAA--AAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGC
* * *
45326 TATCTCTCCAAACAATAAATTT
64 TGTCTCTCCAAACATTTAA-TT
** * * * * *
45348 TTAAAAGTGACTGATGGGAGCTGTCTCCCCAAACA--T--CTAAAAAAGTGGCCGATGAGAGC--
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
45407 TCTCTCCAAACATTTAATT
66 TCTCTCCAAACATTTAATT
* * * * * * *
45426 -AAAATGTGACCAATGAGAGCTATCTCTCCAAACAATTAATT-AAAAACTGACCCATGGGAGCTG
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
* * *
45489 TCTCCCCAAAC--GT--CT
66 TCTCTCCAAACATTTAATT
* *
45504 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAATCATTAAATTAAAAAAGTGACCGATGAGAGCTG
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
*
45569 TCTCTCCAAGCATTTAATT
66 TCTCTCCAAACATTTAATT
* *
45588 AAGAAAATTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAAAGTGACCGATTAGAG
1 AA-AAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT--AAAAAAGTGACCGATGAGAG
*
45653 CTGTCTCTCCAAGCATTTAATT
63 CTGTCTCTCCAAACATTTAATT
* * * * * *
45675 AAAAAAGTGACCAATGTGAGCCGTCTCTCCAAAC----AATT-AAAAAGTAACCGATGGGA-CTA
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
* *
45734 TCTCCCCAAACATCTAAAAAATTT
66 TCTCTCCAAACAT-T---TAA-TT
*** ** * * * ** * * * *
45758 ATTAATTAAAAAAAGTGACCGATGAG-AGTTGTCTCTCCGA-ACATTTAATTAAAAAGTGACCGA
1 A--AA--AAAGTGACCGA-TGA-GAGCTG-TCTCTC-CAAACA-TTTAATTAAAAAAGTGACCGA
* *
45821 TGAAAGTTGTCTCTCCAAACATTTAATT
57 TGAGAGCTGTCTCTCCAAACATTTAATT
* * *
45849 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAAC---T-ATT-AAAAAGTGACCGATGGGAGTTG
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
* *
45909 TCTCCCCAAACA--T--CT
66 TCTCTCCAAACATTTAATT
* * * * *
45924 AAAAAATTGACTGATAAGAGCTGTCTCTCCAAAC----AATTAAAAAAGTGACCGATGAAAGCTA
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
*
45985 TTTCTCCAAACA
66 TCTCTCCAAACA
45997 ATATTAGAAG
Statistics
Matches: 726, Mismatches: 126, Indels: 127
0.74 0.13 0.13
Matches are distributed among these distances:
75 34 0.05
76 28 0.04
77 28 0.04
78 16 0.02
79 121 0.17
80 49 0.07
81 27 0.04
82 18 0.02
83 4 0.01
84 40 0.06
85 144 0.20
86 33 0.05
87 57 0.08
88 8 0.01
89 10 0.01
90 9 0.01
91 3 0.00
92 32 0.04
94 3 0.00
95 17 0.02
96 19 0.03
97 26 0.04
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (84 bp):
AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATGAGAGCTG
TCTCTCCAAACATTTAATT
Found at i:45829 original size:41 final size:40
Alignment explanation
Indices: 45767--45996 Score: 224
Period size: 38 Copynumber: 5.8 Consensus size: 40
45757 TATTAATTAA
* *
45767 AAAAAGTGACCGATGAGAGTTGTCTCTCCGAACATTTAATT
1 AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTT-ATT
45808 AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTT-ATT
* * *
45849 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAAC---TATT
1 -AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTTATT
** * *
45887 AAAAAGTGACCGATGGGAGTTGTCTCCCCAAACATCTA--
1 AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTTATT
* * * *
45925 AAAAATTGACTGAT-AAGAGCTGTCTCTCCAAACAATTA--
1 AAAAAGTGACCGATGAA-AGTTGTCTCTCCAAACATTTATT
* * *
45963 AAAAAGTGACCGATGAAAGCTATTTCTCCAAACA
1 AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACA
45997 ATATTAGAAG
Statistics
Matches: 162, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
37 29 0.18
38 59 0.36
39 3 0.02
40 2 0.01
41 39 0.24
42 30 0.19
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (40 bp):
AAAAAGTGACCGATGAAAGTTGTCTCTCCAAACATTTATT
Found at i:45877 original size:174 final size:176
Alignment explanation
Indices: 45582--45931 Score: 524
Period size: 174 Copynumber: 2.0 Consensus size: 176
45572 CTCCAAGCAT
* *
45582 TTAATTAAGAAAATTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAAAGTGACCGA
1 TTAATTAAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT--AAAAAAGTGACCGA
* * * *
45647 TTAGAGCTGTCTCTCCAAGCATTTAATTAAAAAAGTGACCAATGTGAGCCGTCTCTCCAAACAAT
64 TGAAAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCAATGAGAGCCGTCTCTCCAAACAAT
45712 TAAAAAGTAACCGATGGGA-CTATCTCCCCAAACATCTAAAAAATTTA
129 TAAAAAGTAACCGATGGGAGCTATCTCCCCAAACATCTAAAAAATTTA
* *
45759 TTAATTAAAAAAAGTGACCGATGAGAGTTGTCTCTCCGAACATTTAATT-AAAAAGTGACCGATG
1 TTAATTAAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATG
* * * * *
45823 AAAGTTGTCTCTCCAAACATTTAATTAAAAAAGTGATCGATGAGAGCTGTCTCTCCAAACTATTA
66 AAAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCAATGAGAGCCGTCTCTCCAAACAATTA
* * *
45888 AAAAGTGACCGATGGGAGTTGTCTCCCCAAACATCTAAAAAATT
131 AAAAGTAACCGATGGGAGCTATCTCCCCAAACATCTAAAAAATT
45932 GACTGATAAG
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
174 87 0.56
175 24 0.15
177 45 0.29
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (176 bp):
TTAATTAAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCGATG
AAAGCTGTCTCTCCAAACATTTAATTAAAAAAGTGACCAATGAGAGCCGTCTCTCCAAACAATTA
AAAAGTAACCGATGGGAGCTATCTCCCCAAACATCTAAAAAATTTA
Found at i:45918 original size:79 final size:77
Alignment explanation
Indices: 45758--45981 Score: 256
Period size: 75 Copynumber: 2.8 Consensus size: 77
45748 TAAAAAATTT
* *
45758 ATTAATTAAAAAAAGTGACCGATGAGAGTTGTCTCTCCGAACATTTAATTAAAAAGTGACCGATG
1 ATTAATT-AAAAAAGTGA-CGATGAGAGCTGTCTCTCC-AA-A-CT-ATTAAAAAGTGACCGATG
*
45823 AAAGTTGTCTCTCCAAAC
60 AAAGTTGTCTCCCCAAAC
**
45841 ATTTAATTAAAAAAGTGATCGATGAGAGCTGTCTCTCCAAACTATTAAAAAGTGACCGATGGGAG
1 A-TTAATTAAAAAAGTGA-CGATGAGAGCTGTCTCTCCAAACTATTAAAAAGTGACCGATGAAAG
45906 TTGTCTCCCCAAAC
64 TTGTCTCCCCAAAC
* * * *
45920 A-T--CTAAAAAATTGACTGATAAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCGATGAAAG
1 ATTAATTAAAAAAGTGAC-GATGAGAGCTGTCTCTCCAAACTATT-AAAAAGTGACCGATGAAAG
45982 CTATTTCTCC
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
74 1 0.01
75 34 0.27
76 17 0.13
77 1 0.01
79 34 0.27
80 1 0.01
81 1 0.01
82 2 0.02
83 29 0.23
84 6 0.05
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (77 bp):
ATTAATTAAAAAAGTGACGATGAGAGCTGTCTCTCCAAACTATTAAAAAGTGACCGATGAAAGTT
GTCTCCCCAAAC
Found at i:46979 original size:332 final size:331
Alignment explanation
Indices: 45992--47268 Score: 1659
Period size: 332 Copynumber: 3.8 Consensus size: 331
45982 CTATTTCTCC
* * *
45992 AAACAATATTAGAAGCGTGAAAATCACTTCAATATTTTTGGCGTTGAATTATATATTCTTTATGA
1 AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
* * * *
46057 GTATAGTGGCTAAAAATTTAGGAAAAATCTTTCGGTTCAATTTTTTTGCAAAATTTTAGCCAAAA
66 GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAA-TTTTTTGCAAAATTTTAGCCAAAA
* * * * * *
46122 TCGTGTTCTAACCATTACAGTTTTTGGCTAAAAAACATGTTTCGGGTCCCCGGCTCAGTTTTGCA
130 TCGTATACTAACCATCACAGTTTTTGGCTAAAAAACATGTTCCGGG-ACCCGGCTCAGTTATGCA
* * * * * *
46187 TGATTTTTGGCATC-AAGACTCCTTGAAATATATATATATATATTCATCTAACCAATTCTCTGCC
194 TGATTTTTGGC-GCGAAGATTCATTG--A-A-ATATCTATA-A-TCATCTAACCAATTCTCAGCT
* * * * * * *
46251 ACATTGGATTTGAGGATTTGTTTTTACAAG-ATTCTGAATCATATTTCAATTTAATATGAAATCA
252 ACATTAGATTTAAGGATTTGTTTTTACGAGCA-TCTGAATCTTGTTTCGATTTAATA-GAAATTA
*
46315 ATTCAAATAAAATTGGAA
315 ATTCGAA-AAAATTGGAA
* * * * * **
46333 AAACGATATTGGAAGCGTGAAAAGCTATTCATTCTTTTTGTTGTTGAATTATATATTTTTTATGA
1 AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
* * * * * * * ** *
46398 GTGTTGTGGCTAAGAATTT-TGAAAAAA-TATTTCGCGTCAATTTTTGGCAAAATTTTAGCTGAT
66 GTATAGTGCCTAAAAATTTAGGAAAAAACT-TTT-GGGTCAATTTTTTGCAAAATTTTAGCCAAA
* * * ** * * ** *
46461 ATCATATACTAACCATCACAGTTTTTGCCAAAAAAACGCGTTTCGGGGCCTTAGCTCAGTTTTGC
129 ATCGTATACTAACCATCACAGTTTTTGGCTAAAAAACATGTTCCGGGACC-CGGCTCAGTTATGC
* * * * * *
46526 ATGATTTTTGGCGCCAAGACTTC-TTGAAATATCTTTATTCTTCTAACCAAATCTCAGCGACATT
193 ATGATTTTTGGCGCGAAGA-TTCATTGAAATATCTATAATCATCTAACCAATTCTCAGCTACATT
* *
46590 AGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGAATTAATAAGAAATTAATTCTG
257 AGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT-AGAAATTAATTC-G
46655 AAAAAATTGGAA
320 AAAAAATTGGAA
*
46667 AAACAATATTAGAAGCGTGAAAATCTCTTCAGTCTTTTTGGCGTTGAATTATATATTTTTTATGA
1 AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
46732 GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAATTTTTTGCAAAATTTTAGCCAAAAT
66 GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAATTTTTTGCAAAATTTTAGCCAAAAT
46797 CGTATACT-ACCATCACAGTTTTTGGCTAAAAAACATGTTCCGGGACCCGGCTCAGTTATGCATG
131 CGTATACTAACCATCACAGTTTTTGGCTAAAAAACATGTTCCGGGACCCGGCTCAGTTATGCATG
*
46861 ATTTTTGGCGCGAAGATTCATTGAAATATCTATAATCATCTAACTAATTCTCAGCTACATTAGAT
196 ATTTTTGGCGCGAAGATTCATTGAAATATCTATAATCATCTAACCAATTCTCAGCTACATTAGAT
* *
46926 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATCAGAAATTAATTCAGATAA
261 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT-AGAAATTAATTC-GAAAA
*
46991 AATTCGAA
324 AATTGGAA
46999 AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
1 AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
*
47064 GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAATTTTTTGCAAAATTTTAGCCAAAAC
66 GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAATTTTTTGCAAAATTTTAGCCAAAAT
47129 CGTATACT-ACCATCACAGTTTTTGGCTAAAAAACATGTTACCGGGACCCGGCTCGACGTTATGC
131 CGTATACTAACCATCACAGTTTTTGGCTAAAAAACATGTT-CCGGGACCCGGCTC-A-GTTATGC
*
47193 TATGATTTTTGGCGTCGAAGATTCATTGAAATATCTATAATCATCTAACTAATTCTCAGCTACAT
193 -ATGATTTTTGGCG-CGAAGATTCATTGAAATATCTATAATCATCTAACCAATTCTCAGCTACAT
47258 TAGATTTAAGG
256 TAGATTTAAGG
47269 TA
Statistics
Matches: 825, Mismatches: 95, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
331 3 0.00
332 301 0.36
333 47 0.06
334 190 0.23
335 21 0.03
336 21 0.03
337 62 0.08
338 1 0.00
339 4 0.00
340 97 0.12
341 78 0.09
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (331 bp):
AAACAATATTAGAAGCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
GTATAGTGCCTAAAAATTTAGGAAAAAACTTTTGGGTCAATTTTTTGCAAAATTTTAGCCAAAAT
CGTATACTAACCATCACAGTTTTTGGCTAAAAAACATGTTCCGGGACCCGGCTCAGTTATGCATG
ATTTTTGGCGCGAAGATTCATTGAAATATCTATAATCATCTAACCAATTCTCAGCTACATTAGAT
TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATAGAAATTAATTCGAAAAAA
TTGGAA
Done.