Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013001.1 Corchorus olitorius cultivar O-4 contig13034, 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: 27966
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:6786 original size:22 final size:22
Alignment explanation
Indices: 6750--6793 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6740 AATTGCAGGA
*
6750 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
6772 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
6794 ACGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:8640 original size:2 final size:2
Alignment explanation
Indices: 8628--8674 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
8618 AGAAAATCCT
* *
8628 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
8670 CA CA C
1 CA CA C
8675 TTGTTTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9034 original size:20 final size:20
Alignment explanation
Indices: 9009--9061 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
8999 TTCAAGCCTT
9009 AAGAACCCTAATTGAAACTC
1 AAGAACCCTAATTGAAACTC
9029 AAGAACCCTAATTGAAACTC
1 AAGAACCCTAATTGAAACTC
*
9049 AAGAACCCCAATT
1 AAGAACCCTAATT
9062 TTGAATTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.26, G:0.09, T:0.19
Consensus pattern (20 bp):
AAGAACCCTAATTGAAACTC
Found at i:9218 original size:26 final size:26
Alignment explanation
Indices: 9188--9237 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
9178 CTAATCAAGA
*
9188 AATCCCCAAATAACCTCCAAAACCCT
1 AATCCCCAAAAAACCTCCAAAACCCT
9214 AATCCCCAAAAAACCTCCAAAACC
1 AATCCCCAAAAAACCTCCAAAACC
9238 ACAAACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.42, G:0.00, T:0.12
Consensus pattern (26 bp):
AATCCCCAAAAAACCTCCAAAACCCT
Found at i:14018 original size:30 final size:30
Alignment explanation
Indices: 13979--14067 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 30
13969 TGAACGACTT
*
13979 CGTCTTGGACATTGGCACATGAAAGACGAA
1 CGTCCTGGACATTGGCACATGAAAGACGAA
* * *
14009 CGTCCTGGACATT-GC-CATCGGAACACGAT
1 CGTCCTGGACATTGGCACAT-GAAAGACGAA
* * * *
14038 CGTCCTGGACTTTGCCACAGGAACGACGAA
1 CGTCCTGGACATTGGCACATGAAAGACGAA
14068 TGCTAGGAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
28 3 0.07
29 21 0.47
30 19 0.42
31 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (30 bp):
CGTCCTGGACATTGGCACATGAAAGACGAA
Found at i:14060 original size:29 final size:30
Alignment explanation
Indices: 14003--14067 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
13993 GCACATGAAA
14003 GACGAACGTCCTGGACATTGCCATCGGAAC
1 GACGAACGTCCTGGACATTGCCATCGGAAC
* *
14033 -ACGATCGTCCTGGACTTTGCCA-CAGGAAC
1 GACGAACGTCCTGGACATTGCCATC-GGAAC
14062 GACGAA
1 GACGAA
14068 TGCTAGGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.83
30 4 0.13
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (30 bp):
GACGAACGTCCTGGACATTGCCATCGGAAC
Found at i:17702 original size:31 final size:32
Alignment explanation
Indices: 17666--17730 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
17656 TGTTTTCGTT
17666 AACTGGGATTTCT-TTGTCTTGTTGATCGG-TC
1 AACTGGG-TTTCTATTGTCTTGTTGATCGGATC
*
17697 AACTGGGTTTCTATTGTTTTGTTGATCGGATC
1 AACTGGGTTTCTATTGTCTTGTTGATCGGATC
17729 AA
1 AA
17731 GTTATTGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 5 0.16
31 22 0.71
32 4 0.13
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.45
Consensus pattern (32 bp):
AACTGGGTTTCTATTGTCTTGTTGATCGGATC
Found at i:20115 original size:20 final size:20
Alignment explanation
Indices: 20090--20130 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20080 TTTGGTACCC
20090 CATTGGTATCTAGAACTTAG
1 CATTGGTATCTAGAACTTAG
20110 CATTGGTATCTAGAACTTAG
1 CATTGGTATCTAGAACTTAG
20130 C
1 C
20131 TTTCACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (20 bp):
CATTGGTATCTAGAACTTAG
Found at i:21198 original size:19 final size:20
Alignment explanation
Indices: 21174--21211 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21164 AAAGCCGTTT
*
21174 TCTTTA-TTTTTCTTTTTTC
1 TCTTTACTTTTCCTTTTTTC
21193 TCTTTACTTTTCCTTTTTT
1 TCTTTACTTTTCCTTTTTT
21212 TTCCTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTACTTTTCCTTTTTTC
Found at i:23056 original size:72 final size:71
Alignment explanation
Indices: 22979--23336 Score: 198
Period size: 72 Copynumber: 5.1 Consensus size: 71
22969 ATGATTACCT
* *
22979 TTTTTTCCTTTTAAACTTAATTACTGGTTACCTTTTTACTTTTTGACCTTAATTACTAAATATCA
1 TTTTTT-CTTTTAAACTTAATTACTGATTACCTTTTTACTTTTTGACCTTAATTACTAAATACCA
23044 TTTTTAC
65 TTTTTAC
** * * * * *
23051 TTTTTTAGC-TTTAATTAC-TAATTACCAATT---TTTCTACTCTTTTTAACTTTGATTACTGAA
1 TTTTTT--CTTTTAA--ACTTAATTACTGATTACCTTTTTA--CTTTTTGACCTTAATTACTAAA
*
23111 TACCATTTCTAC
60 TACCATTTTTAC
* * *
23123 -----TCTTTTTAACTTAAATATTGATTACCTTTTTACTTTTTGACCTTAATTACTAAATACCAT
1 TTTTTTCTTTTAAACTTAATTACTGATTACCTTTTTACTTTTTGACCTTAATTACTAAATACCAT
23183 TTTTAC
66 TTTTAC
* * * * *
23189 ---TTT-TTTTAAGCTTTAATTACTAATTACCAATTTTTCTACTCTTTTTAACTCTAATTACTGA
1 TTTTTTCTTTTAAAC-TTAATTACTGATTACC---TTTT-TACT-TTTTGACCT-TAATTACTAA
*
23250 ATACCATTTCTAC
59 ATACCATTTTTAC
* * * * * *
23263 -----TCTTTTTAACTTAATTAC-CATTTACCATTTTACTCTTTTTAACTTAATTACTGAATACC
1 TTTTTTCTTTTAAACTTAATTACTGA-TTACCTTTTTACT-TTTTGACCTTAATTACTAAATACC
23322 ATTTTTAC
64 ATTTTTAC
23330 TCTTTTT
1 T-TTTTT
23337 AACTTTAATT
Statistics
Matches: 223, Mismatches: 36, Indels: 53
0.71 0.12 0.17
Matches are distributed among these distances:
64 2 0.01
65 9 0.04
66 33 0.15
67 29 0.13
68 33 0.15
69 3 0.01
70 5 0.02
71 5 0.02
72 57 0.26
73 24 0.11
74 23 0.10
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (71 bp):
TTTTTTCTTTTAAACTTAATTACTGATTACCTTTTTACTTTTTGACCTTAATTACTAAATACCAT
TTTTAC
Found at i:23065 original size:34 final size:34
Alignment explanation
Indices: 22972--23685 Score: 685
Period size: 34 Copynumber: 21.0 Consensus size: 34
22962 TCAATTAATG
* * * *
22972 ATTACCTTTTTTTC-CTTTTAAACTTAATTACTG
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* * *
23005 GTTACC-TTTTTACT-TTTTGACCTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* * *
23037 AATATCATTTTTACT-TTTTTAGCTTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAAC-TTAATTACTA
*
23071 ATTACCAATTTTTCTACTCTTTTTAACTTTGATTACTGA
1 ATTACC-A-TTTT-TACTCTTTTTAAC-TTAATTACT-A
* * * *
23110 A-TACCATTTCTACTCTTTTTAACTTAAATATTG
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* *
23143 ATTACC-TTTTTACT-TTTTGACCTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* *
23175 AATACCATTTTTACTTTTTTTAAGCTTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAA-C-TTAATTACTA
23211 ATTACCAATTTTTCTACTCTTTTTAACTCTAATTACTGA
1 ATTACC-A-TTTT-TACTCTTTTTAACT-TAATTACT-A
* *
23250 A-TACCATTTCTACTCTTTTTAACTTAATTACCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
*
23283 TTTACCA-TTTTACTCTTTTTAACTTAATTACTGA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACT-A
23317 A-TACCATTTTTACTCTTTTTAACTTTAATTACTGA
1 ATTACCATTTTTACTCTTTTTAAC-TTAATTACT-A
* *
23352 A-TACCATTTCTACTCTTTTTAACTTAATT-GTCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACT-A
* * * *
23385 TTTACCA-TTTTAGTC-TTTTAA-TTATTTACCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* *
23416 TTTACCATTTTTACTCTTTTTAACTTAATTACCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* * *
23450 TTTATCA-TTTTACTTTTGTTTAACTTAATTACTGA
1 ATTACCATTTTTACTCTT-TTTAACTTAATTACT-A
* * *
23485 A-TACTATTTTTACTCTTTTTATCTTAATTACCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* *
23518 TTTACCA-TTTTACTCTTTTTAACTTAATTAATGA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACT-A
*
23552 A-TACCGTTTTTACTCTTTTTAACTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* * *
23585 CTTACCA-TTTTACTCTTTTTAACTTAATTCCCA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* *
23618 TTTACCATTTTTGCTCTTTTTAACTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
* * *
23652 AATACCATTTCTACTCTCTTTAACTTAATTACTA
1 ATTACCATTTTTACTCTTTTTAACTTAATTACTA
23686 CAAGCAGGGC
Statistics
Matches: 569, Mismatches: 77, Indels: 69
0.80 0.11 0.10
Matches are distributed among these distances:
31 13 0.02
32 55 0.10
33 145 0.25
34 199 0.35
35 72 0.13
36 25 0.04
37 8 0.01
38 37 0.07
39 15 0.03
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (34 bp):
ATTACCATTTTTACTCTTTTTAACTTAATTACTA
Found at i:23256 original size:140 final size:136
Alignment explanation
Indices: 22986--23682 Score: 737
Period size: 140 Copynumber: 5.1 Consensus size: 136
22976 CCTTTTTTTC
* * * * *
22986 CTTTTAAACTTAATTACTGGTTACCTTTTTACT-TTTTGACCTTAATTACTAAATATCATTTTTA
1 CTTTTTAACTTAATTA-TGATTACCTTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTTA
* * *
23050 C-TTTTTTAGCTTTAATTACTAATTACCAATTTTTCTACTCTTTTTAACTTTGATTACTGAATAC
65 CTTTTTTTAACTTTAATTACTAATTACC-A-TTTTCTACTCTTTTTAAC-TTAATTACTCAATAC
23114 CATTTCTACT
127 CATTTCTACT
* * *
23124 CTTTTTAACTTAAATATTGATTACCTTTTTACT-TTTTGACCTTAATTACTAAATACCATTTTTA
1 CTTTTTAACTTAATTA-TGATTACCTTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTTA
*
23188 CTTTTTTTAAGCTTTAATTACTAATTACCAATTTTTCTACTCTTTTTAACTCTAATTACTGAATA
65 CTTTTTTTAA-CTTTAATTACTAATTACC-A-TTTTCTACTCTTTTTAACT-TAATTACTCAATA
23253 CCATTTCTACT
126 CCATTTCTACT
** * *
23264 CTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTGAATACCATTTTTA
1 CTTTTTAACTTAATTATGA-TTACCTTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTTA
* * *
23329 CTCTTTTTAACTTTAATTACTGAA-TACCA-TTTCTACTCTTTTTAACTTAATT-GTCATTTACC
65 CTTTTTTTAACTTTAATTACT-AATTACCATTTTCTACTCTTTTTAACTTAATTACTCA-ATACC
*
23391 ATTT-TAGT
128 ATTTCTACT
* ** * ** *
23399 C-TTTTAA-TTATTTACCATTTACCATTTTTACTCTTTTTAACTTAATTACCATTTATCA-TTTT
1 CTTTTTAACTTAATTATGA-TTACC-TTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTT
* * *
23461 ACTTTTGTTTAAC-TTAATTACTGAA-TACTATTTT-TACTCTTTTTATCTTAATTAC-CATTTA
64 ACTTTT-TTTAACTTTAATTACT-AATTACCATTTTCTACTCTTTTTAACTTAATTACTCA-ATA
23522 CCATTT-TACT
126 CCATTTCTACT
* **
23532 CTTTTTAACTTAATTAATGAATACCGTTTTTACTCTTTTTAACTTAATTACTACTTACCA-TTTT
1 CTTTTTAACTTAATT-ATGATTACC-TTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTT
* * * * * *
23596 ACTCTTTTTAAC-TTAATTCCCATTTACCATTTT-TGCTCTTTTTAACTTAATTACTAAATACCA
64 ACTTTTTTTAACTTTAATTACTAATTACCATTTTCTACTCTTTTTAACTTAATTACTCAATACCA
23659 TTTCTACT
129 TTTCTACT
*
23667 CTCTTTAACTTAATTA
1 CTTTTTAACTTAATTA
23683 CTACAAGCAG
Statistics
Matches: 493, Mismatches: 49, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
133 75 0.15
134 98 0.20
135 74 0.15
136 15 0.03
137 18 0.04
138 60 0.12
139 10 0.02
140 104 0.21
141 39 0.08
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (136 bp):
CTTTTTAACTTAATTATGATTACCTTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTTAC
TTTTTTTAACTTTAATTACTAATTACCATTTTCTACTCTTTTTAACTTAATTACTCAATACCATT
TCTACT
Found at i:23315 original size:67 final size:67
Alignment explanation
Indices: 22986--23683 Score: 632
Period size: 67 Copynumber: 10.3 Consensus size: 67
22976 CCTTTTTTTC
* *** * * *
22986 CTTTTAAACTTAATTACTGGTTACC-TTTTTACT-TTTTGACCTTAATTACTAAATATCATTTTT
1 CTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCA-TTTT
23049 ACT
65 ACT
* * * * *
23052 -TTTTTAGCTTTAATTACTAATTACCAATTTTTCTACTCTTTTTAACTTTGATTACTGAATACCA
1 CTTTTTAAC-TTAATTACCATTTACC-A-TTTT-TACTCTTTTTAAC-TTAATTACTAAATACCA
23116 TTTCTACT
61 TTT-TACT
* ** * *
23124 CTTTTTAACTTAAATATTGA-TTACC-TTTTTACT-TTTTGACCTTAATTACTAAATACCATTTT
1 CTTTTTAACTTAATTA-CCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCA-TTT
23186 TACT
64 TACT
* * * *
23190 TTTTTTAAGCTTTAATTACTAATTACCAATTTTTCTACTCTTTTTAACTCTAATTACTGAATACC
1 CTTTTTAA-C-TTAATTACCATTTACC-A-TTTT-TACTCTTTTTAACT-TAATTACTAAATACC
23255 ATTTCTACT
60 ATTT-TACT
*
23264 CTTTTTAACTTAATTACCATTTACCA-TTTTACTCTTTTTAACTTAATTACTGAATACCATTTTT
1 CTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCA-TTTT
23328 ACT
65 ACT
* * * * **
23331 CTTTTTAACTTTAATTACTGA-ATACCATTTCTACTCTTTTTAACTTAATT-GTCATTTACCATT
1 CTTTTTAAC-TTAATTAC-CATTTACCATTTTTACTCTTTTTAACTTAATTACT-AAATACCATT
*
23394 TTAGT
63 TTACT
* * ** *
23399 C-TTTTAA-TTATTTACCATTTACCATTTTTACTCTTTTTAACTTAATTACCATTTATCATTTTA
1 CTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTA
23462 CT
66 CT
* * * * * * **
23464 TTTGTTTAACTTAATTACTGA-ATACTATTTTTACTCTTTTTATCTTAATTACCATTTACCATTT
1 CTT-TTTAACTTAATTAC-CATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCATTT
23528 TACT
64 TACT
* * **
23532 CTTTTTAACTTAATTA--ATGAATACCGTTTTTACTCTTTTTAACTTAATTACTACTTACCATTT
1 CTTTTTAACTTAATTACCAT--TTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCATTT
23595 TACT
64 TACT
* *
23599 CTTTTTAACTTAATTCCCATTTACCATTTTTGCTCTTTTTAACTTAATTACTAAATACCATTTCT
1 CTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCATTT-T
23664 ACT
65 ACT
*
23667 CTCTTTAACTTAATTAC
1 CTTTTTAACTTAATTAC
23684 TACAAGCAGG
Statistics
Matches: 530, Mismatches: 64, Indels: 74
0.79 0.10 0.11
Matches are distributed among these distances:
64 2 0.00
65 53 0.10
66 41 0.08
67 159 0.30
68 124 0.23
69 41 0.08
70 4 0.01
71 14 0.03
72 47 0.09
73 19 0.04
74 26 0.05
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (67 bp):
CTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTAAATACCATTTTA
CT
Found at i:23936 original size:42 final size:43
Alignment explanation
Indices: 23885--23978 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
23875 AGTGTATTAC
23885 CTAA-ATTCTA-CTCCATCTCTA-AGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGA-TAATTCATCAAAATAAAG
*
23926 CTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
23971 CTAATATT
1 CTAATATT
23979 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.77
46 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:25113 original size:67 final size:68
Alignment explanation
Indices: 24955--25552 Score: 743
Period size: 67 Copynumber: 8.9 Consensus size: 68
24945 ATAGTATATA
* *
24955 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTTTTTTTTAAGCTTAATTACTGA-AT
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTAC-TCTTTTTAA-CTTAATTACTCATAT
25019 ACCAT
64 ACCAT
* *
25024 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTAATCTTTTTAACTTAATTACTGA-ATAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCATATAC
25088 CAT
66 CAT
* * *
25091 TTTTACTCTTTTTAACTTAATTACCATTTACAATTTTACTTTTTTTAACTTAATTAC-CATTTAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCATATAC
25155 CAT
66 CAT
* * * *
25158 TTTTACTCTTTTTAACTTAATTACTGA-ATAGCATTTTTACTCTTTTTAACTTAATTAC-CATTT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACTCATAT
25221 ACCA-
64 ACCAT
* * *
25225 TTTTACTCTTTTTAACTTAATTACTGA-ATACCATTTTTACTCTTTTTAACTTAATTAC-CATTT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACTCATAT
*
25288 ATCA-
64 ACCAT
* * * * *
25292 TATTATTCTTTTAAACTTAATTACCATTTACCATTTTTACTCTTTTTAAGTTAATTACTGA-ATA
1 TTTTACTCTTTTTAACTTAATTACCATTTACCA-TTTTACTCTTTTTAACTTAATTACTCATATA
*
25356 TCAT
65 CCAT
* * *
25360 TTTTACTCTTTTTAAGTCAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACT-AAATAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCATATAC
*
25424 CGT
66 CAT
* * *
25427 TTTTACTCTTTTTAACTTAATTACTACTTACCATTTTACTCTTTTTAACTTAATT-CTCATTTAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCATATAC
25491 CAT
66 CAT
** ** *
25494 TTTTACTCTTTTTAACTTAATTATTAAATACCATTTCTACTCTCTTTAACTTAATTACT
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTT-TACTCTTTTTAACTTAATTACT
25553 ACAAGCAGTG
Statistics
Matches: 478, Mismatches: 41, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
66 5 0.01
67 345 0.72
68 88 0.18
69 40 0.08
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (68 bp):
TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCATATAC
CAT
Found at i:25237 original size:168 final size:167
Alignment explanation
Indices: 24954--25551 Score: 957
Period size: 168 Copynumber: 3.6 Consensus size: 167
24944 TATAGTATAT
*
24954 ATTTTACTCTTTTTAACTTAATTACCATTTACCA-TTTTACTTTTTTTTAAGCTTAATTACTGAA
1 ATTTTACTCTTTTTAACTTAATTACCATTTACCATTTTTAC-TCTTTTTAA-CTTAATTACTGAA
*
25018 TACCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTAATCTTTTTAACTTAATTACTG
64 TACCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTG
25083 AATACCATTTTTACTCTTTTTAACTTAATTACCATTTAC
129 AATACCATTTTTACTCTTTTTAACTTAATTACCATTTAC
*
25122 AATTTTACTTTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTGAAT
1 -ATTTTACTCTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTGAAT
*
25187 AGCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTGA
65 ACCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTGA
25252 ATACCATTTTTACTCTTTTTAACTTAATTACCATTTATC
130 ATACCATTTTTACTCTTTTTAACTTAATTACCATTTA-C
* * * *
25291 ATATTATTCTTTTAAACTTAATTACCATTTACCATTTTTACTCTTTTTAAGTTAATTACTGAATA
1 ATTTTACTCTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTGAATA
* * * *
25356 TCATTTTTACTCTTTTTAAGTCAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTAAA
66 CCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTGAA
* * *
25421 TACCGTTTTTACTCTTTTTAACTTAATTACTACTTACC
131 TACCATTTTTACTCTTTTTAACTTAATTACCATTTA-C
* *
25459 ATTTTACTCTTTTTAACTTAATT-CTCATTTACCATTTTTACTCTTTTTAACTTAATTATTAAAT
1 ATTTTACTCTTTTTAACTTAATTAC-CATTTACCATTTTTACTCTTTTTAACTTAATTACTGAAT
* *
25523 ACCATTTCTACTCTCTTTAACTTAATTAC
65 ACCATTTTTACTCTTTTTAACTTAATTAC
25552 TACAAGCAGT
Statistics
Matches: 398, Mismatches: 28, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
167 1 0.00
168 349 0.88
169 42 0.11
170 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.52
Consensus pattern (167 bp):
ATTTTACTCTTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTGAATA
CCATTTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTGAA
TACCATTTTTACTCTTTTTAACTTAATTACCATTTAC
Found at i:25554 original size:101 final size:100
Alignment explanation
Indices: 24955--25553 Score: 717
Period size: 101 Copynumber: 5.9 Consensus size: 100
24945 ATAGTATATA
* **
24955 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTTTTTTTTAAGCTTAATTACTGAATA
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTAC-TCTTTTTAA-CTTAATTACCAAATA
*
25020 CCATTTTTACTCTTTTTAACTTAATTACCATTTACCA-
64 CCATTTTTACTCTTTTTAACTTAATTACTA-TTACCAT
* * * **
25057 TTTTAATCTTTTTAACTTAATTACTGA-ATACCATTTTTACTCTTTTTAACTTAATTACCATTTA
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACCAAATA
* * *
25121 -CAATTTTACTTTTTTTAACTTAATTACCATTTACCAT
64 CCATTTTTACTCTTTTTAACTTAATTACTA-TTACCAT
* * * **
25158 TTTTACTCTTTTTAACTTAATTACTGA-ATAGCATTTTTACTCTTTTTAACTTAATTACCATTTA
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACCAAATA
*
25222 CCA-TTTTACTCTTTTTAACTTAATTACTGAATACCAT
64 CCATTTTTACTCTTTTTAACTTAATTACT-ATTACCAT
* * * * **
25259 TTTTACTCTTTTTAACTTAATTACCATTTATCATATTATTCTTTTAAACTTAATTACCATTTACC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACCAAATACC
* * *
25324 ATTTTTACTCTTTTTAAGTTAATTACTGAATATCAT
66 ATTTTTACTCTTTTTAACTTAATTACT-ATTACCAT
* * *
25360 TTTTACTCTTTTTAAGTCAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTAAATACC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACCAAATACC
*
25425 GTTTTTACTCTTTTTAACTTAATTACTACTTACCA-
66 ATTTTTACTCTTTTTAACTTAATTACTA-TTACCAT
**
25460 TTTTACTCTTTTTAACTTAATT-CTCATTTACCATTTTTACTCTTTTTAACTTAATTATTAAATA
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACCAAATA
* *
25524 CCATTTCTACTCTCTTTAACTTAATTACTA
64 CCATTTTTACTCTTTTTAACTTAATTACTA
25554 CAAGCAGTGT
Statistics
Matches: 445, Mismatches: 42, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
99 1 0.00
100 95 0.21
101 303 0.68
102 39 0.09
103 7 0.02
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.52
Consensus pattern (100 bp):
TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACCAAATACC
ATTTTTACTCTTTTTAACTTAATTACTATTACCAT
Found at i:25804 original size:42 final size:44
Alignment explanation
Indices: 25757--25847 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 44
25747 TATTACTTAA
25757 ATTCTA-CTCCATCTCTA-AGTAATTCATCAAAAT-AAAGCTAAT
1 ATTCTACCTCCATCTCTAGA-TAATTCATCAAAATAAAAGCTAAT
*
25799 ATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAAGCTAAT
25845 ATT
1 ATT
25848 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 6 0.14
45 24 0.56
46 13 0.30
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (44 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAAGCTAAT
Done.