Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018113.1 Corchorus olitorius cultivar O-4 contig18146, 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: 55373
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:6584 original size:51 final size:52
Alignment explanation
Indices: 6519--6737 Score: 274
Period size: 50 Copynumber: 4.3 Consensus size: 52
6509 TTCCAATTAG
* *
6519 CAAAAATTCAATCTTTTTAGTTCAAAGATCT-CATCTCTATTACAAATTAAT
1 CAAAAATTCAATCTTTTTAGTTTAAAGATCTCCATCTTTATTACAAATTAAT
* * *
6570 CAAAAAGTT-AATCTTTTTAGTTTAAGGAT-TCCATTTTTATCT-CAAGTTAAT
1 CAAAAA-TTCAATCTTTTTAGTTTAAAGATCTCCATCTTTAT-TACAAATTAAT
* *
6621 C-AAAATTCAATCTTATTAGTTAAAAGATCT-CATCTTTATTACAAATTAAT
1 CAAAAATTCAATCTTTTTAGTTTAAAGATCTCCATCTTTATTACAAATTAAT
* * *
6671 CAAAAATTCGATCTTTTTAGTTTAAAGA-CTCCAT-TTTATCACAAATTATT
1 CAAAAATTCAATCTTTTTAGTTTAAAGATCTCCATCTTTATTACAAATTAAT
6721 CAAAAATTCAATCTTTT
1 CAAAAATTCAATCTTTT
6738 AACTTGAAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
49 3 0.02
50 71 0.49
51 67 0.47
52 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (52 bp):
CAAAAATTCAATCTTTTTAGTTTAAAGATCTCCATCTTTATTACAAATTAAT
Found at i:6661 original size:101 final size:101
Alignment explanation
Indices: 6519--6735 Score: 321
Period size: 101 Copynumber: 2.1 Consensus size: 101
6509 TTCCAATTAG
* *
6519 CAAAAATTCAATCTTTTTAGTTCAAAGATCTCATCTCTATTACAAATTAATCAAAAAGTT-AATC
1 CAAAAATTCAATCTTATTAGTTAAAAGATCTCATCTCTATTACAAATTAATCAAAAA-TTCAATC
* * * *
6583 TTTTTAGTTTAAGGATTCCATTTTTATCTCAAGTTAAT
65 TTTTTAGTTTAAAGACTCCA-TTTTATCACAAATTAAT
* *
6621 C-AAAATTCAATCTTATTAGTTAAAAGATCTCATCTTTATTACAAATTAATCAAAAATTCGATCT
1 CAAAAATTCAATCTTATTAGTTAAAAGATCTCATCTCTATTACAAATTAATCAAAAATTCAATCT
*
6685 TTTTAGTTTAAAGACTCCATTTTATCACAAATTATT
66 TTTTAGTTTAAAGACTCCATTTTATCACAAATTAAT
6721 CAAAAATTCAATCTT
1 CAAAAATTCAATCTT
6736 TTAACTTGAA
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
100 17 0.16
101 86 0.83
102 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (101 bp):
CAAAAATTCAATCTTATTAGTTAAAAGATCTCATCTCTATTACAAATTAATCAAAAATTCAATCT
TTTTAGTTTAAAGACTCCATTTTATCACAAATTAAT
Found at i:6756 original size:50 final size:49
Alignment explanation
Indices: 6519--6783 Score: 237
Period size: 51 Copynumber: 5.2 Consensus size: 49
6509 TTCCAATTAG
* * *
6519 CAAAAATTCAATCTTTTTAGTTCAAAGATCTCATCTCTATTACAAATTAAT
1 CAAAAATTCAATCTTTTTAGTT-AAAGATTTCAT-TTTATCACAAATTAAT
* * * *
6570 CAAAAAGTT-AATCTTTTTAGTTTAAGGATTCCATTTTTATCTCAAGTTAAT
1 CAAAAA-TTCAATCTTTTTAG-TTAAAGATTTCA-TTTTATCACAAATTAAT
* * *
6621 C-AAAATTCAATCTTATTAGTTAAAAGATCTCATCTTTATTACAAATTAAT
1 CAAAAATTCAATCTTTTTAGTT-AAAGATTTCAT-TTTATCACAAATTAAT
* * * *
6671 CAAAAATTCGATCTTTTTAGTTTAAAGACTCCATTTTATCACAAATTATT
1 CAAAAATTCAATCTTTTTAG-TTAAAGATTTCATTTTATCACAAATTAAT
* * * * *
6721 CAAAAATTCAATCTTTTAACTTGAAAGGTTTCATTTTTGTCATAAATTAAT
1 CAAAAATTCAATCTTTTTAGTT-AAAGATTTCA-TTTTATCACAAATTAAT
* *
6772 CGAAAATCCAAT
1 CAAAAATTCAAT
6784 TTAGTTCCTA
Statistics
Matches: 172, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
49 7 0.04
50 73 0.42
51 85 0.49
52 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (49 bp):
CAAAAATTCAATCTTTTTAGTTAAAGATTTCATTTTATCACAAATTAAT
Found at i:6768 original size:101 final size:100
Alignment explanation
Indices: 6521--6778 Score: 286
Period size: 101 Copynumber: 2.6 Consensus size: 100
6511 CCAATTAGCA
* * * * *
6521 AAAATTCAATCTTTTTAGTTCAAAGATCTCATCTCTATTACAAATTAATCAAAAAGTTAATCTTT
1 AAAATTCAATCTTATTACTTAAAAGATCTCATCTTTATCACAAATTAATCAAAAA-TTAATCTTT
* * * *
6586 TTAGTTTAAGGATTCCATTTTTATCTCAAGTTAATC
65 TTAGTTTAAAGACTCCATTTTTATCACAAATTAATC
* * *
6622 AAAATTCAATCTTATTAGTTAAAAGATCTCATCTTTATTACAAATTAATCAAAAATTCGATCTTT
1 AAAATTCAATCTTATTACTTAAAAGATCTCATCTTTATCACAAATTAATCAAAAATT-AATCTTT
*
6687 TTAGTTTAAAGACTCCA-TTTTATCACAAATTATTC
65 TTAGTTTAAAGACTCCATTTTTATCACAAATTAATC
* * * * * * *
6722 AAAAATTCAATCTT-TTAACTTGAAAGGTTTCATTTTTGTCATAAATTAATCGAAAAT
1 -AAAATTCAATCTTATT-ACTTAAAAGATCTCATCTTTATCACAAATTAATCAAAAAT
6779 CCAATTTAGT
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
100 19 0.14
101 117 0.86
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (100 bp):
AAAATTCAATCTTATTACTTAAAAGATCTCATCTTTATCACAAATTAATCAAAAATTAATCTTTT
TAGTTTAAAGACTCCATTTTTATCACAAATTAATC
Found at i:15536 original size:21 final size:21
Alignment explanation
Indices: 15510--15549 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
15500 AAAACTACAA
15510 TTTCTATTAAAGAAAATGAAT
1 TTTCTATTAAAGAAAATGAAT
15531 TTTCTATTAAAGAAAATGA
1 TTTCTATTAAAGAAAATGA
15550 GTATGCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTCTATTAAAGAAAATGAAT
Found at i:17186 original size:21 final size:21
Alignment explanation
Indices: 17160--17203 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17150 TTTAGCCACC
*
17160 AATTTGAGTCTAAACCTTTCA
1 AATTTGAGGCTAAACCTTTCA
17181 AATTTGAGGCTAAACCTTTCA
1 AATTTGAGGCTAAACCTTTCA
17202 AA
1 AA
17204 AGTTGACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
AATTTGAGGCTAAACCTTTCA
Found at i:17854 original size:6 final size:6
Alignment explanation
Indices: 17843--18115 Score: 447
Period size: 6 Copynumber: 45.5 Consensus size: 6
17833 GAAAAAAAAT
* * *
17843 ATAATA ATAATA ATAATA GTAATA ATAATA ATAGTA ATAATA GTAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
17891 GTAATA ATAATA GTAATA GTAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
17939 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
17987 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* *
18035 ATAATA ATAATA ATAATA ATTATA ATAGTA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
18083 ATAGTA ATAATA GTAATA ATAGTA ATAATA ATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATA
18116 CAACAGTCCC
Statistics
Matches: 249, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 249 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.34
Consensus pattern (6 bp):
ATAATA
Found at i:17857 original size:9 final size:9
Alignment explanation
Indices: 17843--18115 Score: 447
Period size: 9 Copynumber: 30.3 Consensus size: 9
17833 GAAAAAAAAT
17843 ATAATAATA
1 ATAATAATA
17852 ATAATAATA
1 ATAATAATA
*
17861 GTAATAATA
1 ATAATAATA
*
17870 ATAATAGTA
1 ATAATAATA
*
17879 ATAATAGTA
1 ATAATAATA
*
17888 ATAGTAATA
1 ATAATAATA
*
17897 ATAATAGTA
1 ATAATAATA
*
17906 ATAGTAATA
1 ATAATAATA
17915 ATAATAATA
1 ATAATAATA
17924 ATAATAATA
1 ATAATAATA
17933 ATAATAATA
1 ATAATAATA
17942 ATAATAATA
1 ATAATAATA
17951 ATAATAATA
1 ATAATAATA
17960 ATAATAATA
1 ATAATAATA
17969 ATAATAATA
1 ATAATAATA
17978 ATAATAATA
1 ATAATAATA
17987 ATAATAATA
1 ATAATAATA
17996 ATAATAATA
1 ATAATAATA
18005 ATAATAATA
1 ATAATAATA
18014 ATAATAATA
1 ATAATAATA
18023 ATAATAATA
1 ATAATAATA
18032 ATAATAATA
1 ATAATAATA
18041 ATAATAATA
1 ATAATAATA
*
18050 ATAATTATA
1 ATAATAATA
*
18059 ATAGTAATA
1 ATAATAATA
18068 ATAATAATA
1 ATAATAATA
18077 ATAATAATA
1 ATAATAATA
*
18086 GTAATAATA
1 ATAATAATA
*
18095 GTAATAATA
1 ATAATAATA
*
18104 GTAATAATA
1 ATAATAATA
18113 ATA
1 ATA
18116 CAACAGTCCC
Statistics
Matches: 248, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 248 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAATAATA
Found at i:18618 original size:18 final size:19
Alignment explanation
Indices: 18595--18630 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18585 AGGTCTCTAG
*
18595 AAAA-TTTGGAAGTTTGAC
1 AAAATTTTGGAACTTTGAC
18613 AAAATTTTGGAACTTTGA
1 AAAATTTTGGAACTTTGA
18631 GAAAGACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (19 bp):
AAAATTTTGGAACTTTGAC
Found at i:21679 original size:3 final size:3
Alignment explanation
Indices: 21671--21712 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
21661 GGCCACCTTC
21671 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21713 ATCTTAACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:22159 original size:22 final size:22
Alignment explanation
Indices: 22132--22176 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
22122 TTTTCATTCT
*
22132 TATATAATATATAGTATAAATA
1 TATATAATATATACTATAAATA
*
22154 TATATAATATATACTATATATA
1 TATATAATATATACTATAAATA
22176 T
1 T
22177 TTGTGCCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATAATATATACTATAAATA
Found at i:26017 original size:18 final size:18
Alignment explanation
Indices: 25994--26085 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
25984 AAACTAAATT
25994 ACAATTAATAGAAAATCA
1 ACAATTAATAGAAAATCA
26012 ACAATTAATA-AGAAAT--
1 ACAATTAATAGA-AAATCA
*
26028 -CAATCAATAGAAAATCA
1 ACAATTAATAGAAAATCA
*
26045 ACAATAAATA-AGAAATCA
1 ACAATTAATAGA-AAATCA
26063 ATC-A-T--TAGAAAATCA
1 A-CAATTAATAGAAAATCA
26078 ACAATTAA
1 ACAATTAA
26086 GAAGAAATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 24
0.69 0.03 0.28
Matches are distributed among these distances:
14 1 0.02
15 22 0.37
16 3 0.05
17 2 0.03
18 30 0.51
19 1 0.02
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (18 bp):
ACAATTAATAGAAAATCA
Found at i:26036 original size:15 final size:15
Alignment explanation
Indices: 26013--26088 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
26003 AGAAAATCAA
*
26013 CAATTAATAAGAAAT
1 CAATCAATAAGAAAT
26028 CAATCAAT-AGAAAAT
1 CAATCAATAAG-AAAT
*
26043 CAACAATAAATAAGAAAT
1 ---CAATCAATAAGAAAT
*
26061 CAATC-ATTAGAAAAT
1 CAATCAATAAG-AAAT
26076 CAA-CAATTAAGAA
1 CAATCAA-TAAGAA
26089 GAAATCATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
14 7 0.15
15 25 0.52
16 3 0.06
18 11 0.23
19 2 0.04
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.21
Consensus pattern (15 bp):
CAATCAATAAGAAAT
Found at i:26042 original size:33 final size:33
Alignment explanation
Indices: 25995--26095 Score: 166
Period size: 33 Copynumber: 3.1 Consensus size: 33
25985 AACTAAATTA
*
25995 CAATTAATAGAAAATCAACAATTAATAAGAAAT
1 CAATCAATAGAAAATCAACAATTAATAAGAAAT
*
26028 CAATCAATAGAAAATCAACAATAAATAAGAAAT
1 CAATCAATAGAAAATCAACAATTAATAAGAAAT
* *
26061 CAATCATTAGAAAATCAACAATTAAGAAGAAAT
1 CAATCAATAGAAAATCAACAATTAATAAGAAAT
26094 CA
1 CA
26096 TTCCTCTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (33 bp):
CAATCAATAGAAAATCAACAATTAATAAGAAAT
Found at i:26093 original size:18 final size:18
Alignment explanation
Indices: 26006--26095 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
25996 AATTAATAGA
*
26006 AAATCAACAATTAATAAG
1 AAATCAACAATTAAGAAG
26024 AAATCAATCAA-T-AG-A-
1 AAATCAA-CAATTAAGAAG
* *
26039 AAATCAACAATAAATAAG
1 AAATCAACAATTAAGAAG
26057 AAATCAATC-ATT-AG-A-
1 AAATCAA-CAATTAAGAAG
26072 AAATCAACAATTAAGAAG
1 AAATCAACAATTAAGAAG
26090 AAATCA
1 AAATCA
26096 TTCCTCTAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 4 0.07
15 17 0.30
16 5 0.09
17 4 0.07
18 23 0.40
19 4 0.07
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (18 bp):
AAATCAACAATTAAGAAG
Found at i:30444 original size:20 final size:20
Alignment explanation
Indices: 30419--30458 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30409 GACTTGAGTT
* *
30419 TCATTATCATGATTGTTTTA
1 TCATTATCATAAGTGTTTTA
30439 TCATTATCATAAGTGTTTTA
1 TCATTATCATAAGTGTTTTA
30459 CCATAGATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TCATTATCATAAGTGTTTTA
Found at i:33525 original size:91 final size:91
Alignment explanation
Indices: 33422--33606 Score: 352
Period size: 91 Copynumber: 2.0 Consensus size: 91
33412 AAGCCACTTA
* *
33422 AAAACATCCAGAAAGAAGTAAAATTATTGGTTTATAGGACGTGATCAGAGTCATCTCTTCAAGGT
1 AAAACATACAGAAAGAAGTAAAATTATTGGTTTATAGGACGTGATCAGAGACATCTCTTCAAGGT
33487 AAACTGTTCGTCAACAGATATCTTTT
66 AAACTGTTCGTCAACAGATATCTTTT
33513 AAAACATACAGAAAGAAGTAAAATTATTGGTTTATAGGACGTGATCAGAGACATCTCTTCAAGGT
1 AAAACATACAGAAAGAAGTAAAATTATTGGTTTATAGGACGTGATCAGAGACATCTCTTCAAGGT
33578 AAACTGTTCGTCAACAGATATCTTTT
66 AAACTGTTCGTCAACAGATATCTTTT
33604 AAA
1 AAA
33607 CTTGAAAAAC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (91 bp):
AAAACATACAGAAAGAAGTAAAATTATTGGTTTATAGGACGTGATCAGAGACATCTCTTCAAGGT
AAACTGTTCGTCAACAGATATCTTTT
Found at i:36899 original size:4 final size:4
Alignment explanation
Indices: 36890--37107 Score: 80
Period size: 4 Copynumber: 55.0 Consensus size: 4
36880 TAATAATAAT
* ** *
36890 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
36936 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AA-A AGATG AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
36982 AGTA AATA AGTA GATA ATAGTT AA-A AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA A-ATA AATA AATA
** * * * *
37030 AATA AATA GTTA ATAGTT AA-G AATA AATA AATA GATA AAT- AGTA AATA
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA AATA
* *
37078 AATA TATA ATAGTA AATA AATA GATA AATA
1 AATA AATA A-A-TA AATA AATA AATA AATA
37108 GTTAAAAAAA
Statistics
Matches: 152, Mismatches: 42, Indels: 40
0.65 0.18 0.17
Matches are distributed among these distances:
3 22 0.14
4 113 0.74
5 10 0.07
6 7 0.05
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:36941 original size:19 final size:19
Alignment explanation
Indices: 36905--37145 Score: 158
Period size: 19 Copynumber: 12.5 Consensus size: 19
36895 ATAAATAGAT
* *
36905 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
*
36925 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
36944 AATAGAT-AATAATTAAATT
1 AATAGATAAAT-AGTAAATA
* * *
36963 AATAAATAAA-A--AGATG
1 AATAGATAAATAGTAAATA
*
36979 AATAG-TAAATAAGTAGAT-
1 AATAGATAAAT-AGTAAATA
* *
36997 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
*
37015 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
*
37034 AATAGTTAATAGTTAAGAATAAATA
1 AATAGATAA-A--T-AG--TAAATA
37059 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
*
37078 AATATAT-AATAGTAAATA
1 AATAGATAAATAGTAAATA
*
37096 AATAGATAAATAGTTAAAAAA
1 AATAGATAAATAG-T-AAATA
* *
37117 AATAAAATAAATAGTGAATA
1 AAT-AGATAAATAGTAAATA
37137 AATA-ATAAA
1 AATAGATAAA
37146 AAAAATCATT
Statistics
Matches: 178, Mismatches: 24, Indels: 40
0.74 0.10 0.17
Matches are distributed among these distances:
15 4 0.02
16 7 0.04
17 6 0.03
18 39 0.22
19 66 0.37
20 18 0.10
21 10 0.06
22 11 0.06
23 2 0.01
24 1 0.01
25 14 0.08
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Found at i:37015 original size:25 final size:26
Alignment explanation
Indices: 36984--37095 Score: 84
Period size: 25 Copynumber: 4.7 Consensus size: 26
36974 AGATGAATAG
*
36984 TAAATAAGTAGAT-AATAGTTAAAAA
1 TAAATAAATAGATAAATAGTTAAAAA
*
37009 TAAATAAAAAGATAAATAG-------
1 TAAATAAATAGATAAATAGTTAAAAA
* *
37028 TAAATAAATAG-TTAATAGTTAAGAA
1 TAAATAAATAGATAAATAGTTAAAAA
*
37053 TAAATAAATAGATAAATAGTAAATAAA
1 TAAATAAATAGATAAATAGTTAA-AAA
*
37080 TATAT-AATAG-TAAATA
1 TAAATAAATAGATAAATA
37096 AATAGATAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 6 0.09
19 10 0.14
25 28 0.41
26 19 0.28
27 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (26 bp):
TAAATAAATAGATAAATAGTTAAAAA
Found at i:37025 original size:12 final size:11
Alignment explanation
Indices: 36917--37037 Score: 55
Period size: 11 Copynumber: 10.7 Consensus size: 11
36907 TAGCTAAATT
36917 AATAAATAAAA
1 AATAAATAAAA
**
36928 AGATAAATAGTA
1 A-ATAAATAAAA
* *
36940 AATAAATAGAT
1 AATAAATAAAA
* *
36951 AATAATTAAATT
1 AATAAATAAA-A
36963 AATAAATAAAA
1 AATAAATAAAA
* **
36974 AGATGAATAGTA
1 A-ATAAATAAAA
* * *
36986 AATAAGTAGAT
1 AATAAATAAAA
* *
36997 AAT-AGTTAAA
1 AATAAATAAAA
37007 AATAAATAAAA
1 AATAAATAAAA
**
37018 AGATAAATAGTA
1 A-ATAAATAAAA
37030 AATAAATA
1 AATAAATA
37038 GTTAATAGTT
Statistics
Matches: 83, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
10 7 0.08
11 40 0.48
12 36 0.43
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:37027 original size:44 final size:44
Alignment explanation
Indices: 36887--37105 Score: 294
Period size: 44 Copynumber: 4.9 Consensus size: 44
36877 AAATAATAAT
* *
36887 AATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATA
* *
36933 AATAGTAAATAAATAGATAATAATTAAATTAATAAATAAAAAGATG
1 AATAGTAAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATA
*
36979 AATAGTAAATAAGTAGATAATAGTTAAAAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
* * *
37023 AATAGTAAATAAATAGTTAATAGTTAAGAATAAATAAATAGATA
1 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
* * *
37067 AATAGTAAATAAATATATAATAGTAAATAAATAGATAAA
1 AATAGTAAATAAATAGATAATAGTTAA-AAATAAATAAA
37106 TAGTTAAAAA
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
44 79 0.51
45 9 0.06
46 68 0.44
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.27
Consensus pattern (44 bp):
AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
Found at i:37095 original size:7 final size:8
Alignment explanation
Indices: 36812--37113 Score: 73
Period size: 8 Copynumber: 37.9 Consensus size: 8
36802 ATAATAAAAA
36812 AGATAAAT
1 AGATAAAT
* * *
36820 AGGTATAG
1 AGATAAAT
36828 AGATAAAT
1 AGATAAAT
36836 AGATAAAT
1 AGATAAAT
* *
36844 AGATACAG
1 AGATAAAT
36852 AGA-ATAAT
1 AGATA-AAT
*
36860 AAATAAAT
1 AGATAAAT
36868 AGGTAGCTAAAAT
1 A-G-A--T-AAAT
36881 A-AT-AAT
1 AGATAAAT
36887 A-AT-AAT
1 AGATAAAT
*
36893 AAATAAAT
1 AGATAAAT
36901 AGAT-AAT
1 AGATAAAT
*
36908 AGCTAAATT
1 AGATAAA-T
36917 A-ATAAAT
1 AGATAAAT
36924 --A-AAA-
1 AGATAAAT
36928 AGATAAAT
1 AGATAAAT
36936 AG-TAAAT
1 AGATAAAT
* *
36943 AAATAGAT
1 AGATAAAT
*
36951 A-ATAATT
1 AGATAAAT
* *
36958 AAATTAAT
1 AGATAAAT
* *
36966 AAATAAAA
1 AGATAAAT
*
36974 AGATGAAT
1 AGATAAAT
36982 AG-TAAAT
1 AGATAAAT
*
36989 AAGTAGATAAT
1 -AG-ATA-AAT
*
37000 AGTTAAAAAT
1 AG--ATAAAT
* *
37010 AAATAAAA
1 AGATAAAT
37018 AGATAAAT
1 AGATAAAT
37026 AGTAAATAAAT
1 AG---ATAAAT
*
37037 AG-TTAAT
1 AGATAAAT
*
37044 AGTTAAGAAT
1 AGAT-A-AAT
*
37054 AAATAAAT
1 AGATAAAT
37062 AGATAAAT
1 AGATAAAT
37070 AG-TAAAT
1 AGATAAAT
* *
37077 AAATATAT
1 AGATAAAT
*
37085 A-AT-AGT
1 AGATAAAT
*
37091 AAATAAAT
1 AGATAAAT
37099 AGATAAAT
1 AGATAAAT
*
37107 AGTTAAA
1 AGATAAA
37114 AAAAATAAAA
Statistics
Matches: 217, Mismatches: 46, Indels: 62
0.67 0.14 0.19
Matches are distributed among these distances:
5 3 0.01
6 14 0.06
7 44 0.20
8 118 0.54
9 4 0.02
10 14 0.06
11 14 0.06
12 1 0.00
13 5 0.02
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.27
Consensus pattern (8 bp):
AGATAAAT
Found at i:37143 original size:18 final size:18
Alignment explanation
Indices: 36877--37145 Score: 104
Period size: 19 Copynumber: 14.8 Consensus size: 18
36867 TAGGTAGCTA
*
36877 AAAT-AATAAT-AATAAT
1 AAATAAATAATAAATAGT
36893 AAATAAATAGAT-AATAGCT
1 AAATAAATA-ATAAATAG-T
* *
36912 AAATTAATAAATAAAAAGAT
1 AAATAAAT-AATAAATAG-T
*
36932 AAAT-AGTAAATAAATAG-
1 AAATAAAT-AATAAATAGT
*
36949 --AT-AATAATTAAATTAAT
1 AAATAAATAA-TAAA-TAGT
* *
36966 AAATAAAAAGATGAATAGT
1 AAATAAATA-ATAAATAGT
*
36985 AAATAAGTAGAT-AATAGT
1 AAATAAATA-ATAAATAGT
* *
37003 TAA-AAATAAATAAAAAGAT
1 AAATAAAT-AATAAATAG-T
*
37022 AAAT-AGTAAATAAATAGT
1 AAATAAAT-AATAAATAGT
* *
37040 TAAT-AGT--TAAGA-A-T
1 AAATAAATAATAA-ATAGT
37054 AAATAAATAGATAAATAGT
1 AAATAAATA-ATAAATAGT
37073 AAATAAAT-ATATAATAGT
1 AAATAAATAATA-AATAGT
37091 AAATAAATAGATAAATAGTT
1 AAATAAATA-ATAAATAG-T
*
37111 AAAAAAAATAAAATAAATAGT
1 -AAATAAAT--AATAAATAGT
*
37132 GAATAAATAATAAA
1 AAATAAATAATAAA
37146 AAAAATCATT
Statistics
Matches: 198, Mismatches: 25, Indels: 58
0.70 0.09 0.21
Matches are distributed among these distances:
14 6 0.03
15 14 0.07
16 7 0.04
17 13 0.07
18 50 0.25
19 64 0.32
20 26 0.13
21 9 0.05
22 8 0.04
23 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (18 bp):
AAATAAATAATAAATAGT
Found at i:38741 original size:54 final size:55
Alignment explanation
Indices: 38612--38974 Score: 433
Period size: 54 Copynumber: 6.7 Consensus size: 55
38602 ACGGAAACTT
* ** **
38612 TTCTTGGAGTGACCATACTGGATCAAAT-TGGA-GATCAACTCTGATCATCAAAAAC
1 TTCTTGGAATGACCGCACTGGATC--ATCTGGAGGATCAACTCTGATCATTGAAAAC
* * *
38667 TTCTT-GAACGAGCACACTGGATCATCTGGA-GATCAACTCTGATC-TTCGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATT-GAAAAC
* *
38720 TTCTTCGAATGACCGCACTGGATCAT-TTGAGGATCAACTCTGATCATTGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATTGAAAAC
* *
38774 TTCTTGGAATGACCGCACTGGATCATCT-GAGTATCAACTCTAATCATT-ATAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATTGA-AAAC
* * *
38828 TTCTTGGAATGACCACACTGGATCAT-TTGAGGATCAACTCTGACCATTGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATTGAAAAC
* * * *
38882 TTCTTGGAATGATCGCACTGGATCATCT-GAGGATCAACTCTGATAAATCAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATTGAAAAC
*
38936 TTCTTGGAATGACCGCACTGGATCATCT-GAGGATGAACT
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACT
38975 TTCTACAAAA
Statistics
Matches: 273, Mismatches: 25, Indels: 21
0.86 0.08 0.07
Matches are distributed among these distances:
52 3 0.01
53 33 0.12
54 227 0.83
55 10 0.04
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (55 bp):
TTCTTGGAATGACCGCACTGGATCATCTGGAGGATCAACTCTGATCATTGAAAAC
Found at i:38847 original size:162 final size:158
Alignment explanation
Indices: 38555--38966 Score: 483
Period size: 162 Copynumber: 2.5 Consensus size: 158
38545 TTCAAACTTG
* * * * *
38555 AACTTCTTAAATAACCGCACTGGATCATTT-AAGATGCAAC-CTCGATCACGGAAACTTTTCTTG
1 AACTTCTTGAATGACCGCACTGGATCATTTGAGGAT-CAACTCT-GATCATGAAAAC--TTCTTG
* ** * *
38618 GAGTGACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCAAAAACTTCTTGAACGAGCAC
62 GAATGACCGCACTGGATC--ATCT-GAGATCAACTCTAATCATCAAAAACTTCTTGAACGACCAC
*
38682 ACTGGATCATCTGGA-GATCAACTCTGATC-TTCGAA
124 ACTGGATCAT-TGGAGGATCAACTCTGACCATT-GAA
38717 AACTTCTTCGAATGACCGCACTGGATCATTTGAGGATCAACTCTGATCATTGAAAACTTCTTGGA
1 AACTTCTT-GAATGACCGCACTGGATCATTTGAGGATCAACTCTGATCA-TGAAAACTTCTTGGA
* * *
38782 ATGACCGCACTGGATCATCTGAGTATCAACTCTAATCATTATAAACTTCTTGGAATGACCACACT
64 ATGACCGCACTGGATCATCTGAG-ATCAACTCTAATCATCAAAAACTTCTT-GAACGACCACACT
*
38847 GGATCATTTGAGGATCAACTCTGACCATTGAA
127 GGATCATTGGAGGATCAACTCTGACCATTGAA
* * * *
38879 AACTTCTTGGAATGATCGCACTGGATCATCTGAGGATCAACTCTGATAAATCAAAACTTCTTGGA
1 AACTTCTT-GAATGACCGCACTGGATCATTTGAGGATCAACTCTGAT-CATGAAAACTTCTTGGA
38944 ATGACCGCACTGGATCATCTGAG
64 ATGACCGCACTGGATCATCTGAG
38967 GATGAACTTT
Statistics
Matches: 220, Mismatches: 20, Indels: 20
0.85 0.08 0.08
Matches are distributed among these distances:
160 5 0.02
161 28 0.13
162 144 0.65
163 32 0.15
164 11 0.05
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (158 bp):
AACTTCTTGAATGACCGCACTGGATCATTTGAGGATCAACTCTGATCATGAAAACTTCTTGGAAT
GACCGCACTGGATCATCTGAGATCAACTCTAATCATCAAAAACTTCTTGAACGACCACACTGGAT
CATTGGAGGATCAACTCTGACCATTGAA
Found at i:43400 original size:4 final size:4
Alignment explanation
Indices: 43393--43426 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
43383 TACCAAAGGA
43393 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
43427 GTGAATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:48146 original size:11 final size:11
Alignment explanation
Indices: 48130--48177 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
48120 GAAGTTCGTG
48130 TTTGAAGACCA
1 TTTGAAGACCA
**
48141 TTTGAAGATAA
1 TTTGAAGACCA
48152 TTTGAAGA-C-
1 TTTGAAGACCA
48161 -TTGAAGACCA
1 TTTGAAGACCA
48171 -TTGAAGA
1 TTTGAAGA
48178 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:50808 original size:15 final size:15
Alignment explanation
Indices: 50778--50819 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
50768 TTACTTTGTT
50778 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
50794 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
50809 TTGTTTTCTGT
1 TTGTTTTCTGT
50820 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:53806 original size:44 final size:44
Alignment explanation
Indices: 53743--53832 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
53733 AAAGAAAAGA
53743 AAAAAAATGCAACCAATTATTAAGATCCTAAATCTGGTTAAACT
1 AAAAAAATGCAACCAATTATTAAGATCCTAAATCTGGTTAAACT
53787 AAAAAAATGCAACCAATTATTAAGATCCTAAATCTGGTTAAACT
1 AAAAAAATGCAACCAATTATTAAGATCCTAAATCTGGTTAAACT
53831 AA
1 AA
53833 GTCTGGCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.27
Consensus pattern (44 bp):
AAAAAAATGCAACCAATTATTAAGATCCTAAATCTGGTTAAACT
Found at i:54295 original size:4 final size:4
Alignment explanation
Indices: 54262--54350 Score: 55
Period size: 4 Copynumber: 23.5 Consensus size: 4
54252 TATTAATAAC
* ** * *
54262 AAAT AAAT AGAT -AAT AGCT AAAT TAAT AAAT AAA- AAGAT AAAT -AGT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT
* * *
54308 AAAT AAAT AGAT -AAT -AAT TAA- AAAT AAAT AAAT AGAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
54351 TGTCACGCCC
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
3 13 0.20
4 49 0.77
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:54300 original size:27 final size:27
Alignment explanation
Indices: 54262--54347 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
54252 TATTAATAAC
* *
54262 AAATAAATAGAT-AATAGCTAAATTAAT
1 AAATAAAAAGATAAATAG-TAAATAAAT
54289 AAATAAAAAGATAAATAGTAAATAAAT
1 AAATAAAAAGATAAATAGTAAATAAAT
* * * *
54316 AGATAATAA-TTAAA-AATAAATAAAT
1 AAATAAAAAGATAAATAGTAAATAAAT
*
54341 AGATAAA
1 AAATAAA
54348 TAATGTCACG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
25 16 0.31
26 4 0.08
27 26 0.51
28 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATAAAAAGATAAATAGTAAATAAAT
Done.