Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020203.1 Corchorus olitorius cultivar O-4 contig20236, 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: 63549
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1031 original size:31 final size:31
Alignment explanation
Indices: 980--1154 Score: 190
Period size: 31 Copynumber: 5.7 Consensus size: 31
970 GGCACGTATC
* * *
980 CTTTTT-GTGCACGTGGCATGCCACGTGTCA
1 CTTTTTGGTACACATGGCATGCCATGTGTCA
**
1010 CTTTTTGAAACACATGGCATGCCATGTGTCA
1 CTTTTTGGTACACATGGCATGCCATGTGTCA
* **
1041 CTTTTTGGTACACATGGCGTGATATGTGTCA
1 CTTTTTGGTACACATGGCATGCCATGTGTCA
* ** *
1072 CTTTTTGGTACACATGGCGTGATATGTGCCA
1 CTTTTTGGTACACATGGCATGCCATGTGTCA
* ** *
1103 CTTTTTGGTACACATGGCGTGCCACATGTCG
1 CTTTTTGGTACACATGGCATGCCATGTGTCA
*
1134 CTTTTTGGTACACGTGGCATG
1 CTTTTTGGTACACATGGCATG
1155 TCACCGTCGG
Statistics
Matches: 125, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
30 6 0.05
31 119 0.95
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (31 bp):
CTTTTTGGTACACATGGCATGCCATGTGTCA
Found at i:3923 original size:64 final size:64
Alignment explanation
Indices: 3787--3916 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
3777 GACCCCTTGA
3787 GCAGAAAGACTACTGTGGGTGTAAATACTAAATATAAAGGGTGTAAAGTAATAGAAGGATCTCT
1 GCAGAAAGACTACTGTGGGTGTAAATACTAAATATAAAGGGTGTAAAGTAATAGAAGGATCTCT
3851 GCAGAAAGACTACTGTGGGTGTAAATACTAAATATAAAGGGTGTAAAGTAATAGAAGGATCTCT
1 GCAGAAAGACTACTGTGGGTGTAAATACTAAATATAAAGGGTGTAAAGTAATAGAAGGATCTCT
3915 GC
1 GC
3917 GTAAAGAGGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (64 bp):
GCAGAAAGACTACTGTGGGTGTAAATACTAAATATAAAGGGTGTAAAGTAATAGAAGGATCTCT
Found at i:15014 original size:22 final size:20
Alignment explanation
Indices: 14967--15038 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 20
14957 TAAATATTTT
14967 TATAAAA-TTTGATAATCAC
1 TATAAAATTTTGATAATCAC
14986 TATAAAATTTTGATAACCTC-C
1 TATAAAATTTTGATAA--TCAC
*
15007 ATATAAAATTTTGATATTACAC
1 -TATAAAATTTTGATAAT-CAC
15029 TAT-AAATTTT
1 TATAAAATTTT
15039 TTTTGGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
19 7 0.15
20 16 0.35
21 5 0.11
22 18 0.39
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (20 bp):
TATAAAATTTTGATAATCAC
Found at i:15112 original size:22 final size:22
Alignment explanation
Indices: 15087--15136 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
15077 CTCTGTATGG
15087 AATTTTGTTA-ACTTCCCTAT-AA
1 AATTTT-TTATAC-TCCCTATAAA
15109 AATTTTTTATACTCCCTATAAA
1 AATTTTTTATACTCCCTATAAA
15131 AATTTT
1 AATTTT
15137 AATAACCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTTTTTATACTCCCTATAAA
Found at i:15126 original size:21 final size:21
Alignment explanation
Indices: 15087--15136 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
15077 CTCTGTATGG
15087 AATTTTGTTAACTTCCCTATAA
1 AATTTT-TTAACTTCCCTATAA
15109 AATTTTTTATAC-TCCCTATAA
1 AATTTTTTA-ACTTCCCTATAA
*
15130 AAATTTT
1 AATTTTT
15137 AATAACCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTTTTTAACTTCCCTATAA
Found at i:15196 original size:22 final size:22
Alignment explanation
Indices: 15130--15431 Score: 97
Period size: 22 Copynumber: 13.8 Consensus size: 22
15120 CTCCCTATAA
* * **
15130 AAATTTTAATAACCACTTAATG
1 AAATTTTGATAACCTCCCAATG
* * *
15152 AAATTTTGATAA-ATATCCGATG
1 AAATTTTGATAACCT-CCCAATG
15174 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCTCCCAATG
* * * * *
15196 AAATGTTGGTAAGCGCACATTATG
1 AAATTTTGATAACCTCCCA--ATG
* * * *
15220 ATATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCTCCCAATG
* * *
15242 AAATATTGGTAA--TCACATTATG
1 AAATTTTGATAACCTCCCA--ATG
*
15264 AAATTTTGATAACCATACC-ATG
1 AAATTTTGATAACC-TCCCAATG
* * *
15286 AAATTGTGAT-ACCTCACTATG
1 AAATTTTGATAACCTCCCAATG
* * *
15307 AAAGTTTTTATAAACCTCCCTATA
1 AAA-TTTTGAT-AACCTCCCAATG
*
15331 AAATTTTGATAACCT-TCAATTG
1 AAATTTTGATAACCTCCCAA-TG
* *
15353 AAATTTT--TAA-ATCTC-ATG
1 AAATTTTGATAACCTCCCAATG
* **
15371 AAATTTTGAAAACCAT-CTTATG
1 AAATTTTGATAACC-TCCCAATG
* * *
15393 AAATTTTAATAACATCCCTAT-
1 AAATTTTGATAACCTCCCAATG
*
15414 AAATATTTTATAACCTCC
1 AAAT-TTTGATAACCTCC
15432 TACGAAATTA
Statistics
Matches: 201, Mismatches: 57, Indels: 44
0.67 0.19 0.15
Matches are distributed among these distances:
18 9 0.04
19 2 0.01
20 11 0.05
21 16 0.08
22 128 0.64
23 7 0.03
24 26 0.13
25 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCAATG
Found at i:15274 original size:44 final size:45
Alignment explanation
Indices: 15171--15277 Score: 144
Period size: 46 Copynumber: 2.4 Consensus size: 45
15161 TAAATATCCG
* *
15171 ATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACATT
1 ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAA-CGCACATT
* * * *
15217 ATGATATTTTGATAACCTTCCGATAAAATATTGGTAA-TCACATT
1 ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAACGCACATT
15261 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
15278 ATACCATGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 22 0.41
46 32 0.59
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAACGCACATT
Found at i:15720 original size:20 final size:22
Alignment explanation
Indices: 15695--15768 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
15685 TAACCTCCTC
*
15695 ATGAAATTTTG-TTAAT-CTCT
1 ATGAAATTTTGATTAATACACT
* *
15715 ATGAAATTGTGATTATTACACT
1 ATGAAATTTTGATTAATACACT
* *
15737 ATGAAATTTTG-GTAACGACACT
1 ATGAAATTTTGATTAA-TACACT
15759 -TGAAATTTTG
1 ATGAAATTTTG
15769 GTAAGCTCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.23
21 16 0.36
22 18 0.41
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
ATGAAATTTTGATTAATACACT
Found at i:15779 original size:21 final size:22
Alignment explanation
Indices: 15732--15772 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
15722 TGTGATTATT
15732 ACACTATGAAATTTTGGTAACG
1 ACACTATGAAATTTTGGTAACG
15754 ACACT-TGAAATTTTGGTAA
1 ACACTATGAAATTTTGGTAA
15773 GCTCACTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (22 bp):
ACACTATGAAATTTTGGTAACG
Found at i:15978 original size:22 final size:22
Alignment explanation
Indices: 15810--16089 Score: 112
Period size: 22 Copynumber: 12.6 Consensus size: 22
15800 TATAAGCACA
* *
15810 ATATGGAATTTTGATAATCTTCC
1 ATATGAAATTTTGATAA-CCTCC
* *
15833 -TATGGAATTTTAATAACCTCC
1 ATATGAAATTTTGATAACCTCC
* * * *
15854 ATATAAAATTTCGATATCGC-GC
1 ATATGAAATTTTGATAAC-CTCC
* **
15876 -TATGAAATTTTAATAACC-AG
1 ATATGAAATTTTGATAACCTCC
*
15896 AGTATGAAATTTT-AGTATCCTCC
1 A-TATGAAATTTTGA-TAACCTCC
* * * *
15919 CTGTGAAATTTTGACAACCTTC
1 ATATGAAATTTTGATAACCTCC
* * *
15941 -TCATG-GACTTCGATAACCTCC
1 AT-ATGAAATTTTGATAACCTCC
*
15962 ATATGAAATTTTGATAACCTGC
1 ATATGAAATTTTGATAACCTCC
*
15984 ATATGAAATTTTGATAACAAT-C
1 ATATGAAATTTTGATAAC-CTCC
* *
16006 TTATGAAATTTTATTTCAATAACCTCC
1 ATATGAAA---T-TTT-GATAACCTCC
* * *
16033 TTATGAAATTGTGATAA-CTAC
1 ATATGAAATTTTGATAACCTCC
* * *
16054 ACTATAAAATTTTAATATCCTACC
1 A-TATGAAATTTTGATAACCT-CC
16078 -TATGAAATTTTG
1 ATATGAAATTTTG
16090 CTAATCACAC
Statistics
Matches: 190, Mismatches: 47, Indels: 41
0.68 0.17 0.15
Matches are distributed among these distances:
20 1 0.01
21 36 0.19
22 125 0.66
23 7 0.04
24 2 0.01
25 1 0.01
26 4 0.02
27 14 0.07
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
ATATGAAATTTTGATAACCTCC
Found at i:16082 original size:71 final size:71
Alignment explanation
Indices: 15953--16088 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
15943 ATGGACTTCG
* * * * *
15953 ATAACCTCCATATGAAATTTTGATAACCTGCATATGAAATTTTGATAACAATCTTATGAAATTTT
1 ATAACCTCCATATGAAATTGTGATAACCTACATATAAAATTTTAATAACAATCCTATGAAATTTT
16018 ATTTCA
66 ATTTCA
* * *
16024 ATAACCTCCTTATGAAATTGTGATAA-CTACACTATAAAATTTTAATATC-CTACCTATGAAATT
1 ATAACCTCCATATGAAATTGTGATAACCTACA-TATAAAATTTTAATAACAAT-CCTATGAAATT
16087 TT
64 TT
16089 GCTAATCACA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 5 0.09
71 50 0.91
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.39
Consensus pattern (71 bp):
ATAACCTCCATATGAAATTGTGATAACCTACATATAAAATTTTAATAACAATCCTATGAAATTTT
ATTTCA
Found at i:16102 original size:22 final size:21
Alignment explanation
Indices: 16034--16159 Score: 78
Period size: 22 Copynumber: 5.8 Consensus size: 21
16024 ATAACCTCCT
* *
16034 TATGAAATTGTGATAACTACAC
1 TATGAAATTTTG-TAACCACAC
* * *
16056 TATAAAATTTTAATATCCTAC-C
1 TATGAAATTTT-GTAACC-ACAC
*
16078 TATGAAATTTTGCTAATCACAC
1 TATGAAATTTTG-TAACCACAC
* *
16100 TATAAAATTTTGAGAACCACAC
1 TATGAAATTTTG-TAACCACAC
16122 TAT-AAACTTTTAGTAACCACAC
1 TATGAAA-TTTT-GTAACCACAC
*
16144 AATG-AATTTTGATAAC
1 TATGAAATTTTG-TAAC
16160 TTCCAAAATT
Statistics
Matches: 81, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.01
21 13 0.16
22 64 0.79
23 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (21 bp):
TATGAAATTTTGTAACCACAC
Found at i:16143 original size:44 final size:44
Alignment explanation
Indices: 16026--16143 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 44
16016 TTATTTCAAT
* * * *
16026 AACCT-CCTTATGAAATTGTGATAACTACACTATAAAATTTTAAT
1 AACCTACC-TATGAAATTTTGCTAACCACACTATAAAATTTTAAG
* * *
16070 ATCCTACCTATGAAATTTTGCTAATCACACTATAAAATTTTGAG
1 AACCTACCTATGAAATTTTGCTAACCACACTATAAAATTTTAAG
16114 AACC-ACACTAT-AAACTTTTAG-TAACCACAC
1 AACCTAC-CTATGAAA-TTTT-GCTAACCACAC
16144 AATGAATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
43 5 0.08
44 53 0.87
45 3 0.05
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (44 bp):
AACCTACCTATGAAATTTTGCTAACCACACTATAAAATTTTAAG
Found at i:16766 original size:16 final size:16
Alignment explanation
Indices: 16745--16786 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
16735 TTAAAATTTC
16745 AAAGATTTTTAAAAAG
1 AAAGATTTTTAAAAAG
16761 AAAGATTTTTAAAAAG
1 AAAGATTTTTAAAAAG
16777 AAAGATTTTT
1 AAAGATTTTT
16787 GAAATGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (16 bp):
AAAGATTTTTAAAAAG
Found at i:17468 original size:22 final size:22
Alignment explanation
Indices: 17409--17490 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
17399 AAAACCTCCA
*
17409 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
** * *
17431 CCTGAAATTTTCATAATCACAC
1 TATGAAATTGTGATAATCACAC
* * *
17453 TATGAAATTGTGATAACCTCGC
1 TATGAAATTGTGATAATCACAC
*
17475 TATGAAATTTTGATAA
1 TATGAAATTGTGATAA
17491 ACCATCCTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 41 0.87
23 6 0.13
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:17555 original size:22 final size:21
Alignment explanation
Indices: 17433--17809 Score: 224
Period size: 22 Copynumber: 17.7 Consensus size: 21
17423 AATCACACCC
* * *
17433 TGAAATTTTCATAATCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
17455 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
17477 TGAAATTTTGATAAACCATCCTA
1 TGAAATTTTGAT-AACC-TCCTA
* *
17500 TAAAATTTTGATAAACATCCCTA
1 TGAAATTTTGAT-AACCT-CCTA
*
17523 TAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCC-TA
*
17545 TGAAATCTTGATAA----CTA
1 TGAAATTTTGATAACCTCCTA
17562 T-AAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
* * *
17583 T-AATTTTTTTATAACCTCATTA
1 TGAA-ATTTTGATAACCTC-CTA
* *
17605 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
* * *
17627 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACCTCCTA
*
17649 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCCTA
* *
17671 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT--CCTA
* *
17693 GGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACC-TCCTA
* *
17715 TGAAATTTTGATATCCT-CTC
1 TGAAATTTTGATAACCTCCTA
*
17735 TGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAACCTCC-T-A
* *
17757 TAAAATTTTAATAACCTTCC--
1 TGAAATTTTGATAACC-TCCTA
* *
17777 T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAACC-TCCTA
17796 TGAAATTTTGATAA
1 TGAAATTTTGATAA
17810 TCTCTCCATA
Statistics
Matches: 275, Mismatches: 51, Indels: 58
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.04
17 13 0.05
18 3 0.01
19 3 0.01
20 17 0.06
21 16 0.06
22 159 0.58
23 47 0.17
24 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:17941 original size:66 final size:66
Alignment explanation
Indices: 17852--17999 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
17842 AATCACATTT
* * * * * * * ** *
17852 TGAAAATTTGATAAACTCTTTATGGAATTTTTATAACCTC-TTTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCACATTATGGAATTTTGATAACCTCATTT-TAAAATTTTGATAACAACAC
17916 TA
65 TA
* * *
17918 TGAAATTTTGATAATCACATTATGTAATTTTGATAATCTCATTTTAAAATTTTGATAATAACACT
1 TGAAATTTTGATAATCACATTATGGAATTTTGATAACCTCATTTTAAAATTTTGATAACAACACT
17983 A
66 A
17984 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
18000 TTCCTATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 65 0.96
67 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGGAATTTTGATAACCTCATTTTAAAATTTTGATAACAACACT
A
Found at i:17976 original size:22 final size:22
Alignment explanation
Indices: 17828--18064 Score: 142
Period size: 22 Copynumber: 10.7 Consensus size: 22
17818 TAAATACCAC
*
17828 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAATCACAT
* * * * *
17850 TTTGAAAATTTGATAAACTCTT
1 TATGAAATTTTGATAATCACAT
* * * * *
17872 TATGGAATTTTTATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * * * *
17894 TATAAAATTTTGTTGA-CCCCT
1 TATGAAATTTTGATAATCACAT
17915 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
17938 TATGTAATTTTGATAATCTCAT
1 TATGAAATTTTGATAATCACAT
* * * *
17960 TTTAAAATTTTGATAATAACAC
1 TATGAAATTTTGATAATCACAT
* *
17982 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATC-ACAT
*
18004 TAT-AAATTTTGATAATCCAATCTT
1 TATGAAATTTTGATAAT-C-A-CAT
*
18028 TATGAAATTTCGATAATCAC-T
1 TATGAAATTTTGATAATCACAT
*
18049 CTATGAGA-TTTGATAA
1 -TATGAAATTTTGATAA
18065 CCTTCTATCA
Statistics
Matches: 166, Mismatches: 41, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
21 24 0.14
22 120 0.72
23 6 0.04
24 4 0.02
25 12 0.07
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:18081 original size:21 final size:22
Alignment explanation
Indices: 17827--18098 Score: 124
Period size: 22 Copynumber: 12.5 Consensus size: 22
17817 ATAAATACCA
*
17827 CTATGAAATTTTGGTAATCACATT
1 CTATGAAATTTTGATAATC-C-TT
* *
17851 -T-TGAAAATTTGATAAACTCTT
1 CTATGAAATTTTGATAATC-CTT
* *
17872 -TATGGAATTTTTATAA-CCTCT
1 CTATGAAATTTTGATAATCCT-T
* * * * * *
17893 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCCTT
*
17915 CTATGAAATTTTGATAATCACAT
1 CTATGAAATTTTGATAATC-CTT
*
17938 -TATGTAATTTTGATAATCTCATT
1 CTATGAAATTTTGATAATC-C-TT
* * *
17961 -T-TAAAATTTTGATAATAAC-A
1 CTATGAAATTTTGATAAT-CCTT
17981 CTATGAAATTTTGATAAT-CTT
1 CTATGAAATTTTGATAATCCTT
18002 CCTAT-AAATTTTGATAATCCAATCT
1 -CTATGAAATTTTGATAATCC--T-T
* *
18027 TTATGAAATTTCGATAATCAC-T
1 CTATGAAATTTTGATAATC-CTT
*
18049 CTATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCCTT
* * *
18069 CTATCAAATTTTGGTACTCC-T
1 CTATGAAATTTTGATAATCCTT
18090 C-ATGAAATT
1 CTATGAAATT
18099 GAGACTTTTA
Statistics
Matches: 190, Mismatches: 38, Indels: 44
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.01
20 18 0.09
21 34 0.18
22 111 0.58
23 7 0.04
24 4 0.02
25 14 0.07
26 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCCTT
Found at i:18150 original size:22 final size:22
Alignment explanation
Indices: 18122--18244 Score: 99
Period size: 22 Copynumber: 5.6 Consensus size: 22
18112 CTTTTATATG
18122 AAATTTTGATAACCACACTA-A
1 AAATTTTGATAACCACACTATA
*
18143 AAATTTTTGATAACCACACTATG
1 AAA-TTTTGATAACCACACTATA
* * *
18166 AAATTTTGATAACCTCCCCATA
1 AAATTTTGATAACCACACTATA
* * * *
18188 AAATATTAATAACCTC-CTTATC
1 AAATTTTGATAACCACAC-TATA
* * *
18210 AAATTTTGTTAATCACACTATG
1 AAATTTTGATAACCACACTATA
18232 AAATTCTT-ATAAC
1 AAATT-TTGATAAC
18245 TTTGCTATGA
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
21 4 0.05
22 70 0.88
23 6 0.08
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:18265 original size:22 final size:23
Alignment explanation
Indices: 18227--18270 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
18217 GTTAATCACA
18227 CTATGAAATTCTTATAA-CTTTG
1 CTATGAAATTCTTATAATCTTTG
*
18249 CTATGACATT-TTGATAATCTTT
1 CTATGAAATTCTT-ATAATCTTT
18271 TTGATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (23 bp):
CTATGAAATTCTTATAATCTTTG
Found at i:18379 original size:22 final size:22
Alignment explanation
Indices: 18351--18417 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
18341 TAACTTGATC
*
18351 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
** *
18373 CTATGAAATTTTGATAACTTCG
1 CTATGAAATTTTGATAACCACA
*
18395 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
18417 C
1 C
18418 AGAGACAAGA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:18381 original size:46 final size:44
Alignment explanation
Indices: 18331--18417 Score: 122
Period size: 44 Copynumber: 1.9 Consensus size: 44
18321 ACATTCCTAA
*
18331 GAAATTTTAATAACTT-GATCCTATGAAATTTTGGTAACCACACTAT
1 GAAATTTTAATAACTTCG-T--TATGAAATTTTGATAACCACACTAT
*
18377 GAAATTTTGATAACTTCGTTATGAAATTTTGATAACCACAC
1 GAAATTTTAATAACTTCGTTATGAAATTTTGATAACCACAC
18418 AGAGACAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 21 0.55
46 16 0.42
47 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (44 bp):
GAAATTTTAATAACTTCGTTATGAAATTTTGATAACCACACTAT
Found at i:21648 original size:2 final size:2
Alignment explanation
Indices: 21641--21679 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
21631 TTCGTACTTT
*
21641 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21680 GATTGTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:26765 original size:72 final size:71
Alignment explanation
Indices: 26677--26871 Score: 257
Period size: 72 Copynumber: 2.7 Consensus size: 71
26667 GCTCAATTAT
* *
26677 ATTATTACTTTCCAATTTTATCCTTATCTCTCTCTTCAATTATTTAATGAGAGTGAAAACCAGCT
1 ATTATTATTTTCCAATTTTATCCTTATCTCTCTCTTCAATTATTTAATGAGAGTGAAAACCAGAT
26742 CAGCAAA
66 -AGCAAA
* * * *
26749 ATTATTATTTTTCAATTCTATCCTTATTTCTCTCTTCAATTATTTAAAT-AGGAGTGAAAACTAG
1 ATTATTATTTTCCAATTTTATCCTTATCTCTCTCTTCAATTATTT-AATGA-GAGTGAAAACCAG
*
26813 ATAGTAAA
64 ATAGCAAA
* * * *
26821 ATTATTATTTTCCAATTTTACCCTTATCTTTCCCTTCAATTATGTAATGAG
1 ATTATTATTTTCCAATTTTATCCTTATCTCTCTCTTCAATTATTTAATGAG
26872 GCCTATGAAG
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
71 4 0.04
72 86 0.81
73 16 0.15
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (71 bp):
ATTATTATTTTCCAATTTTATCCTTATCTCTCTCTTCAATTATTTAATGAGAGTGAAAACCAGAT
AGCAAA
Found at i:27121 original size:14 final size:15
Alignment explanation
Indices: 27095--27124 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27085 ATAACGTATC
27095 TTTTTATCATCATTA
1 TTTTTATCATCATTA
27110 TTTTTATC-TCATTA
1 TTTTTATCATCATTA
27124 T
1 T
27125 ATATTGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTATCATCATTA
Found at i:46074 original size:11 final size:12
Alignment explanation
Indices: 46060--46106 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
46050 TTTTCTTGAG
46060 CTCTTC-TCTTT
1 CTCTTCTTCTTT
46071 CTCTTCTTCTTT
1 CTCTTCTTCTTT
* *
46083 ATTTTGCTCTCTTT
1 CTCTT-CT-TCTTT
46097 CTCTTCTTCT
1 CTCTTCTTCT
46107 GCATGGAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.21
12 11 0.38
13 4 0.14
14 8 0.28
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (12 bp):
CTCTTCTTCTTT
Found at i:46633 original size:6 final size:6
Alignment explanation
Indices: 46578--46629 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
46568 AAGGTTTCAA
* * *
46578 CTCAGC CTCAGC CTCAGC CTCGGC CTCAGC CTCAGC CTCAAC CTCAAC
1 CTCAGC CTCAGC CTCAGC CTCAGC CTCAGC CTCAGC CTCAGC CTCAGC
46626 CTCA
1 CTCA
46630 ACCTGATCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.19, C:0.50, G:0.13, T:0.17
Consensus pattern (6 bp):
CTCAGC
Found at i:47304 original size:20 final size:22
Alignment explanation
Indices: 47279--47321 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
47269 GAATTATACC
47279 ATATACAT-AT-ATCTACATAT
1 ATATACATGATCATCTACATAT
*
47299 ATATACATGATCATCTATATAT
1 ATATACATGATCATCTACATAT
47321 A
1 A
47322 CATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATACATGATCATCTACATAT
Found at i:47404 original size:2 final size:2
Alignment explanation
Indices: 47386--47495 Score: 94
Period size: 2 Copynumber: 54.5 Consensus size: 2
47376 ACAAAAAGAC
* *
47386 TA TA TCA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * ** * *
47429 CA CA CA CA TA CA TA CA TA CA TA CC TA CA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47471 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47496 GAATCAAAAC
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
2 87 0.98
3 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:48995 original size:6 final size:6
Alignment explanation
Indices: 48986--49047 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
48976 CGAACCCAAC
* * * * * *
48986 CATGAT CATGAT GATGAT GATGAT GATGAC CATCAT GATGAT CATGAT
1 CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT
49034 CATGAT CATGAT CA
1 CATGAT CATGAT CA
49048 GCTCGAAAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (6 bp):
CATGAT
Found at i:49005 original size:9 final size:9
Alignment explanation
Indices: 48987--49047 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
48977 GAACCCAACC
48987 ATGATCATG
1 ATGATCATG
*
48996 ATGATGATG
1 ATGATCATG
*
49005 ATGATGATG
1 ATGATCATG
**
49014 ACCATCATG
1 ATGATCATG
49023 ATGATCATG
1 ATGATCATG
* * *
49032 ATCATGATC
1 ATGATCATG
49041 ATGATCA
1 ATGATCA
49048 GCTCGAAAGC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (9 bp):
ATGATCATG
Found at i:49008 original size:12 final size:12
Alignment explanation
Indices: 48987--49045 Score: 82
Period size: 12 Copynumber: 4.9 Consensus size: 12
48977 GAACCCAACC
48987 ATGATCATGATG
1 ATGATCATGATG
*
48999 ATGATGATGATG
1 ATGATCATGATG
* *
49011 ATGACCATCATG
1 ATGATCATGATG
*
49023 ATGATCATGATC
1 ATGATCATGATG
49035 ATGATCATGAT
1 ATGATCATGAT
49046 CAGCTCGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (12 bp):
ATGATCATGATG
Found at i:51077 original size:2 final size:2
Alignment explanation
Indices: 51070--51102 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51060 ATGGAGGGAG
51070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51103 TTGTTGGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59938 original size:124 final size:123
Alignment explanation
Indices: 59693--59939 Score: 273
Period size: 124 Copynumber: 2.0 Consensus size: 123
59683 CCTTTTAAAT
**
59693 TAAAATAGTAAAAATAAAATAATTATAAAAATATTTTATTTAATTAAATGAAAATAGAGTTTTTA
1 TAAAATAGTAAAAATAAAATAATTATAAAAATATTACATTTAATTAAATGAAAATAGAGTTTTTA
* *** * ** * *
59758 GTAGAATAAAACTGTATATTAAATTTTTTTAATATATCCAAGTTTTTAATGGAAAATAG
66 GTAGAATAAAAC-GTATAATAAATTTAAGTAATACATCCAAGAATATAATGAAAAATAG
* * * * *
59817 TAAAATGGTAAAAATGAAGTAATTATAAAGATATTACATTTAATTAAATTAAAATAGAGTTTTTA
1 TAAAATAGTAAAAATAAAATAATTATAAAAATATTACATTTAATTAAATGAAAATAGAGTTTTTA
** *
59882 GTAGAATAAAAC-TATAAT-AATTTAAGTAATGACATTTAAGAAATATATTAGAAAAATA
66 GTAGAATAAAACGTATAATAAATTTAAGTAAT-ACATCCAAG-AATATAAT-GAAAAATA
59940 AGGGTATAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
121 9 0.09
122 11 0.11
123 4 0.04
124 77 0.76
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (123 bp):
TAAAATAGTAAAAATAAAATAATTATAAAAATATTACATTTAATTAAATGAAAATAGAGTTTTTA
GTAGAATAAAACGTATAATAAATTTAAGTAATACATCCAAGAATATAATGAAAAATAG
Found at i:63363 original size:2 final size:2
Alignment explanation
Indices: 63356--63389 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
63346 CTTGCTAATT
63356 TA 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 TA
63390 GCATGCCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.