Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019006.1 Corchorus olitorius cultivar O-4 contig19039, 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: 68890
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:794 original size:2 final size:2
Alignment explanation
Indices: 783--818 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
773 AAAAGTCTAT
783 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
819 AATCAGAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1444 original size:16 final size:15
Alignment explanation
Indices: 1420--1461 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
1410 CCGAAACCGA
1420 AAATGACCC-AACCC
1 AAATGACCCGAACCC
1434 ATAATTGACCCGAACCC
1 A-AA-TGACCCGAACCC
1451 AAATGACCCGA
1 AAATGACCCGA
1462 TATTTGAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 8 0.32
17 6 0.24
ACGTcount: A:0.40, C:0.36, G:0.12, T:0.12
Consensus pattern (15 bp):
AAATGACCCGAACCC
Found at i:7935 original size:18 final size:17
Alignment explanation
Indices: 7912--7949 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
7902 GCACGTATGT
7912 TAATAAATTATAAAATTA
1 TAATAAATTAT-AAATTA
7930 TAATAAATTATAAATTA
1 TAATAAATTATAAATTA
7947 TAA
1 TAA
7950 AACATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATTATAAATTA
Found at i:17851 original size:20 final size:21
Alignment explanation
Indices: 17828--17867 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17818 AATGTCTGAT
*
17828 GCAAAATGGTA-ATGTCCGTG
1 GCAAAAAGGTATATGTCCGTG
*
17848 GCAAAAAGTTATATGTCCGT
1 GCAAAAAGGTATATGTCCGT
17868 AGCCATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (21 bp):
GCAAAAAGGTATATGTCCGTG
Found at i:17964 original size:80 final size:80
Alignment explanation
Indices: 17872--18032 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
17862 GTCCGTAGCC
17872 ATTTTTTTAAACCCTAAAATAACATTTGTCGCAAATGTTTAATTGTGCGTAGCTAATTGGTATAC
1 ATTTTTTTAAACCCTAAAATAACATTTGTCGCAAATGTTTAATTGTGCGTAGCTAATTGGTATAC
17937 ATTCGTAGCCATTTT
66 ATTCGTAGCCATTTT
17952 ATTTTTTTAAACCCTAAAATAACATTTGTCGCAAATGTTTAATTGTGCGTAGCTAATTGGTATAC
1 ATTTTTTTAAACCCTAAAATAACATTTGTCGCAAATGTTTAATTGTGCGTAGCTAATTGGTATAC
18017 ATTCGTAGCCATTTT
66 ATTCGTAGCCATTTT
18032 A
1 A
18033 ATGAATGAGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (80 bp):
ATTTTTTTAAACCCTAAAATAACATTTGTCGCAAATGTTTAATTGTGCGTAGCTAATTGGTATAC
ATTCGTAGCCATTTT
Found at i:21684 original size:30 final size:30
Alignment explanation
Indices: 21650--21706 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21640 AGTTCGTGAT
21650 TGAAGATTAATTGAAG-ATAATTTCAAGATA
1 TGAAGA-TAATTGAAGAATAATTTCAAGATA
* *
21680 TGAAGATCATTGAAGAATTATTTCAAG
1 TGAAGATAATTGAAGAATAATTTCAAG
21707 GAGCATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (30 bp):
TGAAGATAATTGAAGAATAATTTCAAGATA
Found at i:32658 original size:2 final size:2
Alignment explanation
Indices: 32651--32688 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32641 AACTAACTAG
32651 TA TA 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 TA TA
32689 AGCTTAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38053 original size:11 final size:11
Alignment explanation
Indices: 38037--38061 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38027 AACAAGCAAC
38037 ACTCTTTCCTT
1 ACTCTTTCCTT
38048 ACTCTTTCCTT
1 ACTCTTTCCTT
38059 ACT
1 ACT
38062 AGTGCAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (11 bp):
ACTCTTTCCTT
Found at i:40499 original size:148 final size:148
Alignment explanation
Indices: 40230--40527 Score: 463
Period size: 148 Copynumber: 2.0 Consensus size: 148
40220 TAGACTACTT
* * * *
40230 AGTTGGCAGTGAGAATCAGTGCACTGTAAGTTGCTCTGATTCCAGTTCAATTGAGAAGAGATTAA
1 AGTTGGCAGAGAGAATCAGTACACTGTAAGTTGCCCTGACTCCAGTTCAATTGAGAAGAGATTAA
* * *
40295 AGAAAGGCAAACGTAATTCCATGAGGGGACCAAATCCTCATTAAAAAGCTCGCCAAGCTGTTTAG
66 AGAAAGGCAAACGCAATTCCATGAGGGGACCAAATCCTCATTAAAAAGCTCACCAAGCTGTTTAA
* *
40360 CAATTCAGTGAATCCTGC
131 CAATTAAGTGAATCATGC
40378 AGTTGGCAGAGAGAA-CTAGTACACTGTAAGTTGCCCTGACTCCAGTTCAATTGAGAAGAGATTA
1 AGTTGGCAGAGAGAATC-AGTACACTGTAAGTTGCCCTGACTCCAGTTCAATTGAGAAGAGATTA
* * * *
40442 AAGAAAGGGAAATGCAATTCCATGAGGGTATCAAATCCTCATTAAAAAGCTCACCAAGCTGTTTA
65 AAGAAAGGCAAACGCAATTCCATGAGGGGACCAAATCCTCATTAAAAAGCTCACCAAGCTGTTTA
40507 ACAATTAAGTGAATCATGC
130 ACAATTAAGTGAATCATGC
40526 AG
1 AG
40528 ATCAACAAAA
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 1 0.01
148 135 0.99
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (148 bp):
AGTTGGCAGAGAGAATCAGTACACTGTAAGTTGCCCTGACTCCAGTTCAATTGAGAAGAGATTAA
AGAAAGGCAAACGCAATTCCATGAGGGGACCAAATCCTCATTAAAAAGCTCACCAAGCTGTTTAA
CAATTAAGTGAATCATGC
Found at i:44562 original size:2 final size:2
Alignment explanation
Indices: 44555--44579 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44545 GCACAAGCGC
44555 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44580 AGTACGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45211 original size:30 final size:30
Alignment explanation
Indices: 45175--45236 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
45165 ATTCTTATCT
45175 TGACTTTGCTCTTATACCCTCAAATTTTAA
1 TGACTTTGCTCTTATACCCTCAAATTTTAA
*
45205 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTGCTCTTATACCCTCAAATTTTAA
45235 TG
1 TG
45237 GCTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
TGACTTTGCTCTTATACCCTCAAATTTTAA
Found at i:45762 original size:2 final size:2
Alignment explanation
Indices: 45757--45799 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
45747 TGTGTGTGTC
45757 TA TA TA TA 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 TA TA TA TA
45799 T
1 T
45800 TCATTCAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49723 original size:2 final size:2
Alignment explanation
Indices: 49716--49740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49706 GCAAAATGAT
49716 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49741 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49746 original size:3 final size:3
Alignment explanation
Indices: 49738--49772 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
49728 AGAGAGAGAG
49738 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
49773 CTTGAGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52286 original size:46 final size:46
Alignment explanation
Indices: 52219--52312 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
52209 CAAGTCGTAT
52219 TTGGGATGCAACAAAGTCACTTGAGAACATTCAGAGAGAAGTAGAA
1 TTGGGATGCAACAAAGTCACTTGAGAACATTCAGAGAGAAGTAGAA
52265 TTGGGATGCAACAAAGTCACTTGAGAACATTCAGAGAGAAGTAGAA
1 TTGGGATGCAACAAAGTCACTTGAGAACATTCAGAGAGAAGTAGAA
52311 TT
1 TT
52313 ATTGGTTGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (46 bp):
TTGGGATGCAACAAAGTCACTTGAGAACATTCAGAGAGAAGTAGAA
Found at i:52423 original size:40 final size:40
Alignment explanation
Indices: 52378--52548 Score: 198
Period size: 40 Copynumber: 4.0 Consensus size: 40
52368 CACACATGTC
52378 TTTTCAAAATACTAACTTTATTCCATACTAAATTGAGTTG
1 TTTTCAAAATACTAACTTTATTCCATACTAAATTGAGTTG
* *
52418 TTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTTG
1 TTTTCAAAATACTAACTTTATTCCATACTAAATTGAGTTG
* **
52458 TTAGTACTAAAATGTTAAGAGAGACTTTATTCCATACTAAATTGAGTTG
1 TT--TTC-AAAA---T-A-CTA-ACTTTATTCCATACTAAATTGAGTTG
* *
52507 TTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTTG
1 TTTTCAAAATACTAACTTTATTCCATACTAAATTGAGTTG
52547 TT
1 TT
52549 AGTACTAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
40 66 0.60
41 1 0.01
42 3 0.03
43 5 0.05
46 5 0.05
47 3 0.03
48 1 0.01
49 26 0.24
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (40 bp):
TTTTCAAAATACTAACTTTATTCCATACTAAATTGAGTTG
Found at i:52504 original size:49 final size:49
Alignment explanation
Indices: 52432--52569 Score: 168
Period size: 40 Copynumber: 3.0 Consensus size: 49
52422 CAAAATACTA
52432 ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
1 ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
* * * **
52481 ACTTTATTCCATACTAAATTGAGTTGTT--TTC-AAAA---T-A-CTA-
1 ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
52521 ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
1 ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
52570 GACGAGTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
40 26 0.37
41 1 0.01
42 3 0.04
43 5 0.07
46 5 0.07
47 3 0.04
48 1 0.01
49 26 0.37
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (49 bp):
ACTTTGTTCCGTACTAAATTGAGTTGTTAGTACTAAAATGTTAAGAGAG
Found at i:52543 original size:89 final size:89
Alignment explanation
Indices: 52392--52569 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
52382 CAAAATACTA
52392 ACTTTATTCCATACTAAATTGAGTTGTTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTT
1 ACTTTATTCCATACTAAATTGAGTTGTTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTT
52457 GTTAGTACTAAAATGTTAAGAGAG
66 GTTAGTACTAAAATGTTAAGAGAG
52481 ACTTTATTCCATACTAAATTGAGTTGTTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTT
1 ACTTTATTCCATACTAAATTGAGTTGTTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTT
52546 GTTAGTACTAAAATGTTAAGAGAG
66 GTTAGTACTAAAATGTTAAGAGAG
52570 GACGAGTTCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (89 bp):
ACTTTATTCCATACTAAATTGAGTTGTTTTCAAAATACTAACTTTGTTCCGTACTAAATTGAGTT
GTTAGTACTAAAATGTTAAGAGAG
Found at i:53106 original size:2 final size:2
Alignment explanation
Indices: 53099--53131 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53089 TAACTTTGAG
53099 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
53132 TATTTGAATC
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:60553 original size:12 final size:12
Alignment explanation
Indices: 60536--60568 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
60526 TCCTCAAATA
60536 ACATACACACAC
1 ACATACACACAC
60548 ACATACACACAC
1 ACATACACACAC
*
60560 ACACACACA
1 ACATACACA
60569 GAGAGAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (12 bp):
ACATACACACAC
Found at i:62792 original size:2 final size:2
Alignment explanation
Indices: 62785--62869 Score: 58
Period size: 2 Copynumber: 46.0 Consensus size: 2
62775 TAACCATTAT
* * * *
62785 TA TA TA TA CA TA TA TA AA T- TA TA TA -A TA TA TA AA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
62825 T- TA TA T- TA AA T- TA TA TA -A TA TA TA AA TC TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62862 TA TA TA TA
1 TA TA TA TA
62870 AAGTTTAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
1 7 0.11
2 55 0.89
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:62799 original size:8 final size:8
Alignment explanation
Indices: 62786--62867 Score: 71
Period size: 8 Copynumber: 9.9 Consensus size: 8
62776 AACCATTATT
*
62786 ATATATAC
1 ATATATAA
62794 ATATATAA
1 ATATATAA
62802 AT-TATATA
1 ATATATA-A
62810 ATATATAA
1 ATATATAA
62818 ATATA-AA
1 ATATATAA
*
62825 TTATATTAA
1 ATATA-TAA
62834 AT-TATATA
1 ATATATA-A
62842 ATATATAA
1 ATATATAA
62850 ATCTATATATA
1 A--TATATA-A
62861 ATATATA
1 ATATATA
62868 TAAAGTTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
7 12 0.19
8 25 0.40
9 17 0.27
10 6 0.10
11 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAA
Found at i:62807 original size:19 final size:17
Alignment explanation
Indices: 62785--62867 Score: 100
Period size: 16 Copynumber: 4.9 Consensus size: 17
62775 TAACCATTAT
62785 TATATATACATATATAAA
1 TATATATA-ATATATAAA
62803 T-TATATAATATATAAA
1 TATATATAATATATAAA
* *
62819 TATAAATTATAT-TAAA
1 TATATATAATATATAAA
62835 T-TATATAATATATAAA
1 TATATATAATATATAAA
62851 TCTATATATAATATATA
1 --TATATATAATATATA
62868 TAAAGTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.14
16 19 0.34
17 14 0.25
18 2 0.04
19 13 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATATAATATATAAA
Found at i:62865 original size:17 final size:16
Alignment explanation
Indices: 62787--62858 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
62777 ACCATTATTA
62787 TATATACATATATAAAT
1 TATATA-ATATATAAAT
62804 TATATAATATATAAA-
1 TATATAATATATAAAT
62819 TATA-AATTATATTAAAT
1 TATATAA-TATA-TAAAT
62836 TATATAATATATAAAT
1 TATATAATATATAAAT
62852 CTATATA
1 -TATATA
62859 TAATATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.04
15 8 0.16
16 18 0.36
17 20 0.40
18 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATAATATATAAAT
Found at i:64292 original size:180 final size:178
Alignment explanation
Indices: 63961--64488 Score: 519
Period size: 180 Copynumber: 2.9 Consensus size: 178
63951 AACGGATTCT
* * * * * *
63961 ACAACATTTGAAGGGTCACATAATCCAAAAAGTATATAAATAAA-GGCGACACCTCCGAACATAT
1 ACAACACTTGAAGGGTCACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATAT
* * * ** * *
64025 CATAGATAAGATTATTATTTCGTCAAATGACGTGAGGTTTTCTACAAATTAAGTAACAACTTCCA
66 CATAGAT-ATATTATTATTTCATCAAATGACATGAGGTTAGCCACAAACTAAGTAACAACTTCCA
* ** * *
64090 ATGCAGAAATGCATTGATTAACCCGAACATTGTATCCGTTTCAGTAATC
130 ATGCAGAAACGCATTGATTAACCCGAACATCCTATCCGTTCCAGAAATC
* * *
64139 ACAACACTTGAAGTGCCACATAATCCAAAAAGTAAATGTATAAAGGGCAACACCGCCAAACATAT
1 ACAACACTTGAAGGGTCACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATAT
* * * ** *
64204 CATGGATATATTATTTATTTCCATCAAATGACACGAGGTTAGCCAAAAACTGGGTGACAA-TTCC
66 CATAGATATATTA-TTATTT-CATCAAATGACATGAGGTTAGCCACAAACTAAGTAACAACTT-C
* * *
64268 CAATGCAGCAACGCCATT-ATTAACCCGAACATCCTATTCGTTCCGGAAATC
128 CAATGCAGAAACG-CATTGATTAACCCGAACATCCTATCCGTTCCAGAAATC
* ** * *
64319 ACAACACTTGAAGGGTCACATAATCTAAAAAG--AATATAT-AAGGTTTAACACTGCTAAACATA
1 ACAACACTTGAAGGGTCACATAATCCAAAAAGTAAATATATAAAGG-GCAACACCGCCAAACATA
* * * *
64381 TCATAGATATGATCATTATTTCATCACAAATGACATGAGGCTAGCCACAAACTAGGTAACAGCTT
65 TCATAGATAT-ATTATTATTTCAT--CAAATGACATGAGGTTAGCCACAAACTAAGTAACAACTT
** * ** * *
64446 CCAATGCAGAAGTGAATTTTTTAGCCCGAACATCCTAACCGTT
127 CCAATGCAGAAACGCATTGATTAACCCGAACATCCTATCCGTT
64489 TCAGCTATCA
Statistics
Matches: 285, Mismatches: 54, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
177 7 0.02
178 81 0.28
179 95 0.33
180 98 0.34
181 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (178 bp):
ACAACACTTGAAGGGTCACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATAT
CATAGATATATTATTATTTCATCAAATGACATGAGGTTAGCCACAAACTAAGTAACAACTTCCAA
TGCAGAAACGCATTGATTAACCCGAACATCCTATCCGTTCCAGAAATC
Found at i:64479 original size:179 final size:178
Alignment explanation
Indices: 63961--64488 Score: 498
Period size: 179 Copynumber: 2.9 Consensus size: 178
63951 AACGGATTCT
* * * * * * *
63961 ACAACATTTGAAGGGTCACATAATCCAAAAAGTATATAAATAAA-GGCGACACCTCCGAACATAT
1 ACAACACTTGAAGGGCCACATAATCCAAAAAG-AAATATATAAAGGGCAACACCGCCAAACATAT
* * ** * * *
64025 CATAGATAAGATTATTATTTCGT--CAAATGACGTGAGGTTTTCTACAAATTAAGTAACAACTTC
65 CATAGATATGATTATTATTTC-TCACAAATGACATGAGGTTAGCCACAAACTAGGTAAC-ACTTC
* * ** * *
64088 CAATGCAGAAATGCATTGATTAACCCGAACATTGTATCCGTTTCAGTAATC
128 CAATGCAGAAGTGCATTTATTAACCCGAACATCCTATCCGTTCCAGAAATC
* *
64139 ACAACACTTGAAGTGCCACATAATCCAAAAAGTAAATGTATAAAGGGCAACACCGCCAAACATAT
1 ACAACACTTGAAGGGCCACATAATCCAAAAAG-AAATATATAAAGGGCAACACCGCCAAACATAT
* * * * * *
64204 CATGGATAT-ATTATTTATTTC-CATCAAATGACACGAGGTTAGCCAAAAACTGGGTGACAATTC
65 CATAGATATGATTA-TTATTTCTCA-CAAATGACATGAGGTTAGCCACAAACTAGGTAACACTT-
* * *
64267 CCAATGCAGCAACG-CCA-TTATTAACCCGAACATCCTATTCGTTCCGGAAATC
127 CCAATGCAG-AA-GTGCATTTATTAACCCGAACATCCTATCCGTTCCAGAAATC
* * ** * *
64319 ACAACACTTGAAGGGTCACATAATCTAAAAAG-AATATAT-AAGGTTTAACACTGCTAAACATAT
1 ACAACACTTGAAGGGCCACATAATCCAAAAAGAAATATATAAAGG-GCAACACCGCCAAACATAT
* *
64382 CATAGATATGATCATTATTTCATCACAAATGACATGAGGCTAGCCACAAACTAGGTAACAGCTTC
65 CATAGATATGATTATTATTTC-TCACAAATGACATGAGGTTAGCCACAAACTAGGTAACA-CTTC
* * * *
64447 CAATGCAGAAGTGAATTTTTTAGCCCGAACATCCTAACCGTT
128 CAATGCAGAAGTGCATTTATTAACCCGAACATCCTATCCGTT
64489 TCAGCTATCA
Statistics
Matches: 282, Mismatches: 53, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
177 5 0.02
178 81 0.29
179 98 0.35
180 94 0.33
181 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (178 bp):
ACAACACTTGAAGGGCCACATAATCCAAAAAGAAATATATAAAGGGCAACACCGCCAAACATATC
ATAGATATGATTATTATTTCTCACAAATGACATGAGGTTAGCCACAAACTAGGTAACACTTCCAA
TGCAGAAGTGCATTTATTAACCCGAACATCCTATCCGTTCCAGAAATC
Found at i:65233 original size:7 final size:7
Alignment explanation
Indices: 65221--65247 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
65211 GGAGAATCAA
65221 GGGAGAG
1 GGGAGAG
65228 GGGAGAG
1 GGGAGAG
65235 GGGAGAG
1 GGGAGAG
65242 GGGAGA
1 GGGAGA
65248 AGGAATGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (7 bp):
GGGAGAG
Found at i:67751 original size:3 final size:3
Alignment explanation
Indices: 67743--67768 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
67733 AGGTTTTCCT
67743 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
67769 TATAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:68711 original size:17 final size:17
Alignment explanation
Indices: 68689--68726 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
68679 CTGCCACGTC
68689 ATATTTTTTATAAAAAA
1 ATATTTTTTATAAAAAA
*
68706 ATATTTTTTTTAAAAAA
1 ATATTTTTTATAAAAAA
68723 ATAT
1 ATAT
68727 ATATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTTTTATAAAAAA
Done.