Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014451.1 Corchorus olitorius cultivar O-4 contig14484, 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: 88929
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:718 original size:20 final size:18
Alignment explanation
Indices: 679--714 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
669 CTAGCCCTAA
*
679 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
697 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
715 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:3231 original size:15 final size:15
Alignment explanation
Indices: 3201--3242 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
3191 TTACTCTGCT
3201 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
3217 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
3232 TTGCTTTCTGT
1 TTGTTTTCTGT
3243 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:5091 original size:15 final size:15
Alignment explanation
Indices: 5071--5099 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5061 AATTCAGAGA
5071 GATTATTAATTTATC
1 GATTATTAATTTATC
5086 GATTATTAATTTAT
1 GATTATTAATTTAT
5100 GGAGGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
GATTATTAATTTATC
Found at i:7405 original size:178 final size:178
Alignment explanation
Indices: 7136--7474 Score: 506
Period size: 178 Copynumber: 1.9 Consensus size: 178
7126 CCGATTAAGG
*
7136 TGATTTAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
7201 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTA-TTGTTTCGATTAACGGGAATA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAA-TTAGTTGTTTCGATTAACGGAAATA
*
7264 GACGGTCCACTTAATATTATATAACTTT-TGCTTCAGTTGTCTAATTGAGA
129 GACGGTCCACTTAATATTACATAA-TTTGTGCTTCAGTTGTCTAATTGAGA
* * * * *
7314 TGATTCAAGTGTCTCTTGAAAGTTTGTTCCATGATCTACAACTTTCATGAAGGATTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
7379 AATTTATTG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGGAAATAG
*
7443 ACGGTCTACTTAATATTACATAATTTGTGCTT
130 ACGGTCCACTTAATATTACATAATTTGTGCTT
7475 ATGGTGGAAA
Statistics
Matches: 145, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
177 14 0.10
178 131 0.90
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGGAAATAGA
CGGTCCACTTAATATTACATAATTTGTGCTTCAGTTGTCTAATTGAGA
Found at i:8189 original size:7 final size:7
Alignment explanation
Indices: 8177--8203 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
8167 CCTACAGAGG
8177 GCCATGA
1 GCCATGA
8184 GCCATGA
1 GCCATGA
8191 GCCATGA
1 GCCATGA
8198 GCCATG
1 GCCATG
8204 CAAGAAGGAA
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:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (7 bp):
GCCATGA
Found at i:23871 original size:32 final size:32
Alignment explanation
Indices: 23835--23897 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
23825 AAATTTCGGG
* *
23835 TTCAACTCGATTGACTATTCAAACTACTTGAA
1 TTCAACTCCATTGACTATCCAAACTACTTGAA
*
23867 TTCAACTCCATTGACTATCCAAGCTACTTGA
1 TTCAACTCCATTGACTATCCAAACTACTTGA
23898 GCTTGAGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (32 bp):
TTCAACTCCATTGACTATCCAAACTACTTGAA
Found at i:31433 original size:3 final size:3
Alignment explanation
Indices: 31425--31450 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31415 GATGGGCTGC
31425 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
31451 CTTCATCTTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35213 original size:13 final size:12
Alignment explanation
Indices: 35195--35227 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
35185 TGTTTGTTAA
35195 AGAGAGAAGAGAG
1 AGAGAGAA-AGAG
35208 AGAGAGAAAGAG
1 AGAGAGAAAGAG
35220 A-AGAGAAA
1 AGAGAGAAA
35228 AAAAAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 5 0.25
13 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAGAG
Found at i:36784 original size:22 final size:22
Alignment explanation
Indices: 36759--36801 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36749 TTTTTTCCCC
36759 TTGTAAATTTAATTAATTTCTT
1 TTGTAAATTTAATTAATTTCTT
***
36781 TTGTCCCTTTAATTAATTTCT
1 TTGTAAATTTAATTAATTTCT
36802 ATTTTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TTGTAAATTTAATTAATTTCTT
Found at i:37229 original size:123 final size:123
Alignment explanation
Indices: 37091--37423 Score: 630
Period size: 123 Copynumber: 2.7 Consensus size: 123
37081 CATTGTTTAA
*
37091 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
37156 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
37214 ACTTTTACAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
*
37279 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTATAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
37337 ACTTTTACAGTTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
37402 TTTTACCATTTTACTATTTTAA
66 TTTTACCATTTTACTATTTTAA
37424 ATCTAATATC
Statistics
Matches: 205, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 205 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:39104 original size:2 final size:2
Alignment explanation
Indices: 39097--39130 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
39087 TTCGTACTTT
39097 TA TA TA TA GTA 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
39131 TGAGAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49984 original size:53 final size:53
Alignment explanation
Indices: 49919--50024 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
49909 ATCAAACTTC
49919 TCAAGCTTCGAAGTTCAAATATGTTCAGAACAAGTAGAATCAAATACCCACAT
1 TCAAGCTTCGAAGTTCAAATATGTTCAGAACAAGTAGAATCAAATACCCACAT
49972 TCAAGCTTCGAAGTTCAAATATGTTCAGAACAAGTAGAATCAAATACCCACAT
1 TCAAGCTTCGAAGTTCAAATATGTTCAGAACAAGTAGAATCAAATACCCACAT
50025 ATTTCTAGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (53 bp):
TCAAGCTTCGAAGTTCAAATATGTTCAGAACAAGTAGAATCAAATACCCACAT
Found at i:50017 original size:25 final size:25
Alignment explanation
Indices: 49933--50017 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
49923 GCTTCGAAGT
49933 TCAAATATGTTCAGAACAAGTAGAA
1 TCAAATATGTTCAGAACAAGTAGAA
** * * *
49958 TCAAATA--CCCACATTCAAGCTTCGAA
1 TCAAATATGTTCAGA-ACAAG--TAGAA
49984 GTTCAAATATGTTCAGAACAAGTAGAA
1 --TCAAATATGTTCAGAACAAGTAGAA
50011 TCAAATA
1 TCAAATA
50018 CCCACATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 14 0.33
26 4 0.09
27 4 0.09
28 7 0.16
29 4 0.09
30 3 0.07
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.25
Consensus pattern (25 bp):
TCAAATATGTTCAGAACAAGTAGAA
Found at i:56054 original size:16 final size:17
Alignment explanation
Indices: 56012--56055 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
56002 TTTCGACTAT
56012 AATTACCAAACATAACA
1 AATTACCAAACATAACA
*
56029 AA-TACACAAACA-AATA
1 AATTAC-CAAACATAACA
56045 AATTACCAAAC
1 AATTACCAAAC
56056 TAAACTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (17 bp):
AATTACCAAACATAACA
Found at i:60457 original size:15 final size:15
Alignment explanation
Indices: 60437--60465 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
60427 TAAAAGGACC
60437 TCCCATCCCGTCCCG
1 TCCCATCCCGTCCCG
60452 TCCCATCCCGTCCC
1 TCCCATCCCGTCCC
60466 TTACTGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.62, G:0.10, T:0.21
Consensus pattern (15 bp):
TCCCATCCCGTCCCG
Found at i:65025 original size:13 final size:13
Alignment explanation
Indices: 65007--65033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64997 TGTCTTTTAT
65007 TTATATATATATA
1 TTATATATATATA
65020 TTATATATATATA
1 TTATATATATATA
65033 T
1 T
65034 ATGCATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:65028 original size:17 final size:17
Alignment explanation
Indices: 65003--65035 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
64993 TGTTTGTCTT
*
65003 TTATTTATATATATATA
1 TTATATATATATATATA
65020 TTATATATATATATAT
1 TTATATATATATATAT
65036 GCATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATATATATATATA
Found at i:73072 original size:67 final size:67
Alignment explanation
Indices: 72992--73127 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
72982 AGTTTTTCTC
72992 TCTTCTCCGTTTTTTTTAATGAGAAAATTACACTTTTATATTTAAAATTGATTCTTATTTTAAAA
1 TCTTCTCCGTTTTTTTTAATGAGAAAATTACACTTTTATATTTAAAATTGATTCTTATTTTAAAA
73057 AG
66 AG
73059 TCTTCTCCGTTTTTTTTAATGAGAAAATTACACTTTTATATTTAAAATTGATTCTTATTTTAAAA
1 TCTTCTCCGTTTTTTTTAATGAGAAAATTACACTTTTATATTTAAAATTGATTCTTATTTTAAAA
73124 AG
66 AG
73126 TC
1 TC
73128 ATATACACCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49
Consensus pattern (67 bp):
TCTTCTCCGTTTTTTTTAATGAGAAAATTACACTTTTATATTTAAAATTGATTCTTATTTTAAAA
AG
Found at i:78444 original size:3 final size:3
Alignment explanation
Indices: 78436--78569 Score: 94
Period size: 3 Copynumber: 43.3 Consensus size: 3
78426 ATTTCCACTA
78436 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * *** * * *
78481 ATAA TAT ATAT GTAT ATAT TAT TAT TAT TGAC CAA CCC AAT T-T CCAC
1 -TAT TAT -TAT -TAT -TAT TAT TAT TAT T-AT TAT TAT TAT TAT -TAT
78528 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
78570 TATGATTTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
2 5 0.05
3 87 0.81
4 16 0.15
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:78538 original size:94 final size:95
Alignment explanation
Indices: 78372--78568 Score: 342
Period size: 94 Copynumber: 2.1 Consensus size: 95
78362 GACTTTTATG
* *
78372 TTATATATATATATATATGTATATAAATATATATTATTATTATTGGCCAACCCAATTTCCACTAT
1 TTAT-TATATATATATATATATATAAATATATATTATTATTATTGACCAACCCAATTTCCACTAT
78437 ATTATTATTATTATTATTATTATTATTATTA
65 ATTATTATTATTATTATTATTATTATTATTA
**
78468 TTATTATATATATATA-ATATATATGTATATATTATTATTATTGACCAACCCAATTTCCACTATA
1 TTATTATATATATATATATATATAAATATATATTATTATTATTGACCAACCCAATTTCCACTATA
78532 TTATTATTATTATTATTATTATTATTATTA
66 TTATTATTATTATTATTATTATTATTATTA
78562 TTATTAT
1 TTATTAT
78569 TTATGATTTA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 81 0.84
95 12 0.12
96 4 0.04
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (95 bp):
TTATTATATATATATATATATATAAATATATATTATTATTATTGACCAACCCAATTTCCACTATA
TTATTATTATTATTATTATTATTATTATTA
Found at i:80000 original size:63 final size:64
Alignment explanation
Indices: 79933--80078 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 64
79923 TTATAAGTAT
79933 GTTATCAAAATTTTATAA-GATGG-TTATCAAAATTTC-A-TGAGGTTATCAAAATTTCAAATG-
1 GTTATCAAAATTTTATAAGGA-GGTTTAT-AAAATTTCAAGTGAGG-TATCAAAATTTC--ATGA
79993 GA-G
61 GATG
* *
79996 GTTATCAAAATTTTATAAGGAGGTTTATAAAATTTCATAGTGAGGTATCACAATTTCATGATATG
1 GTTATCAAAATTTTATAAGGAGGTTTATAAAATTTCA-AGTGAGGTATCAAAATTTCATGAGATG
80061 GTTATCAAAATTTTATAA
1 GTTATCAAAATTTTATAA
80079 TGTGATTACC
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
63 31 0.42
64 7 0.09
65 31 0.42
66 5 0.07
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (64 bp):
GTTATCAAAATTTTATAAGGAGGTTTATAAAATTTCAAGTGAGGTATCAAAATTTCATGAGATG
Found at i:80017 original size:22 final size:22
Alignment explanation
Indices: 79884--80366 Score: 196
Period size: 22 Copynumber: 22.1 Consensus size: 22
79874 ATACTTCTCT
79884 AGGAGGTTCA-CAAAATTTTATA
1 AGGAGGTT-ATCAAAATTTTATA
* *
79906 AGGAAGTTAT-AGAAAATTTATA
1 AGGAGGTTATCA-AAATTTTATA
* *
79928 AGTATGTTATCAAAATTTTATA
1 AGGAGGTTATCAAAATTTTATA
*
79950 A-GATGGTTATCAAAATTTCAT-
1 AGGA-GGTTATCAAAATTTTATA
*
79971 --GAGGTTATCAAAATTTCA-A
1 AGGAGGTTATCAAAATTTTATA
79990 ATGGAGGTTATCAAAATTTTATA
1 A-GGAGGTTATCAAAATTTTATA
*
80013 AGGAGGTTTAT-AAAATTTCAT-
1 AGGAGG-TTATCAAAATTTTATA
* * *
80034 AGTGAGG-TATCACAATTTCATG
1 AG-GAGGTTATCAAAATTTTATA
*
80056 A-TATGGTTATCAAAATTTTATA
1 AGGA-GGTTATCAAAATTTTATA
* * * * * *
80078 ATGTGATTACCAATATTTTTTA
1 AGGAGGTTATCAAAATTTTATA
* *
80100 TTGGAAGGTTATCAAAATTTCATA
1 -AGG-AGGTTATCAAAATTTTATA
* * * * * *
80124 ATGTGCGCTTACCAACATTTCATT
1 A-G-GAGGTTATCAAAATTTTATA
* *
80148 GGGAGGTTATCAAAATTTCATA
1 AGGAGGTTATCAAAATTTTATA
* * * *
80170 GGGTGGTTATCAAAATTTCATT
1 AGGAGGTTATCAAAATTTTATA
**
80192 AGGTA-GTTATTTAAATTTTAT-
1 AGG-AGGTTATCAAAATTTTATA
* *
80213 AGGTA-ATGTAACAAAATTTTATA
1 AGG-AGGT-TATCAAAATTTTATA
* * * *
80236 GGGAAGTTAACACAATTTTATA
1 AGGAGGTTATCAAAATTTTATA
* * * *
80258 TGGAGGTTCTCGAGATTTTAT-
1 AGGAGGTTATCAAAATTTTATA
* * * * *
80279 AGTATTGTCATAAAAACTTTAT-
1 AGGA-GGTTATCAAAATTTTATA
*
80301 AGTGTA-ATTATCAAAATTTTATA
1 AG-G-AGGTTATCAAAATTTTATA
* *
80324 TGGAGATTATCAAAATTTTATA
1 AGGAGGTTATCAAAATTTTATA
* *
80346 ATGA--TTATC-AAATTTCATA
1 AGGAGGTTATCAAAATTTTATA
80365 AG
1 AG
80367 AATATTTAAT
Statistics
Matches: 351, Mismatches: 81, Indels: 61
0.71 0.16 0.12
Matches are distributed among these distances:
19 26 0.07
20 11 0.03
21 25 0.07
22 246 0.70
23 13 0.04
24 29 0.08
25 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
AGGAGGTTATCAAAATTTTATA
Found at i:80041 original size:44 final size:41
Alignment explanation
Indices: 79933--80195 Score: 135
Period size: 46 Copynumber: 6.0 Consensus size: 41
79923 TTATAAGTAT
*
79933 GTTATCAAAATTTTATAA--GATGGTTATCAAAATTTCATGAG
1 GTTATCAAAATTTCA-AATGGA-GGTTATCAAAATTTCATGAG
*
79974 GTTATCAAAATTTCAAATGGAGGTTATCAAAATTTTATAAGGAG
1 GTTATCAAAATTTCAAATGGAGGTTATCAAAATTTCAT---GAG
* *
80018 GTTTAT-AAAATTTCATA-GTGAGG-TATCACAATTTCATGATATG
1 G-TTATCAAAATTTCAAATG-GAGGTTATCAAAATTTCATG--A-G
* * * *
80061 GTTATCAAAATTTTATAATGTGA--TTACCAATATTTTTTATTGGAAG
1 GTTATCAAAATTTCA-AATG-GAGGTTATCAA-A-ATTTCA-T-G-AG
* * * *
80107 GTTATCAAAATTTCATAATGTGCGCTTACCAACATTTCATTGGGAG
1 GTTATCAAAATTTCA-AATG-GAGGTTATCAAAATTTCA-T--GAG
* * * *
80153 GTTATCAAAATTTCATAGGGTGGTTATCAAAATTTCATTAG
1 GTTATCAAAATTTCAAATGGAGGTTATCAAAATTTCATGAG
80194 GT
1 GT
80196 AGTTATTTAA
Statistics
Matches: 177, Mismatches: 24, Indels: 42
0.73 0.10 0.17
Matches are distributed among these distances:
40 3 0.02
41 34 0.19
42 7 0.04
43 24 0.14
44 37 0.21
45 11 0.06
46 49 0.28
47 4 0.02
48 8 0.05
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (41 bp):
GTTATCAAAATTTCAAATGGAGGTTATCAAAATTTCATGAG
Found at i:80112 original size:46 final size:45
Alignment explanation
Indices: 80060--80169 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 45
80050 TTCATGATAT
* * *
80060 GGTTATCAAAATTTTATAATGT-GATTACCAATATTTTTTATTGGAA
1 GGTTATCAAAATTTCATAATGTCGATTACCAACA--TTTCATTGGAA
* *
80106 GGTTATCAAAATTTCATAATGTGCGCTTACCAACATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGT-CGATTACCAACATTTCATTGGAA
80152 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
80170 GGGTGGTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 48 0.84
48 9 0.16
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAATGTCGATTACCAACATTTCATTGGAA
Found at i:80360 original size:19 final size:20
Alignment explanation
Indices: 80328--80365 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
80318 TTTATATGGA
*
80328 GATTATCAAAATTTTATAAT
1 GATTATCAAAATTTCATAAT
80348 GATTATC-AAATTTCATAA
1 GATTATCAAAATTTCATAA
80366 GAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
GATTATCAAAATTTCATAAT
Found at i:82216 original size:31 final size:31
Alignment explanation
Indices: 82178--82241 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
82168 ACTTCTTCGA
82178 AACTCTTGAAGCTTCTGCTGTTAGTGTAAAT
1 AACTCTTGAAGCTTCTGCTGTTAGTGTAAAT
82209 AACTCTTGAAGCTTCTGCTGTTAGTGTAAAT
1 AACTCTTGAAGCTTCTGCTGTTAGTGTAAAT
82240 AA
1 AA
82242 TTCAATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (31 bp):
AACTCTTGAAGCTTCTGCTGTTAGTGTAAAT
Found at i:83165 original size:28 final size:29
Alignment explanation
Indices: 83134--83191 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
83124 AAATAAGATA
* *
83134 TATATATAATAATC-AGAATCATTGTACT
1 TATATATAATAATCAAAAATCATCGTACT
*
83162 TATATATAATATTCAAAAATCATCGTACT
1 TATATATAATAATCAAAAATCATCGTACT
83191 T
1 T
83192 GTAAGCTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (29 bp):
TATATATAATAATCAAAAATCATCGTACT
Found at i:85417 original size:161 final size:161
Alignment explanation
Indices: 85143--85433 Score: 406
Period size: 161 Copynumber: 1.8 Consensus size: 161
85133 CCAAGGTGCG
* *
85143 GGAAGAACAAAATAGCGAAGAAAGAACAAAACCACAACCTAAAAGCGTAAAAAAATGAAAGTAAC
1 GGAAGAACAAAATAGCGAAGAAAGAACAAAACCACAACATAAAAGCGTAAAAAAATCAAAGTAAC
* * * *
85208 GATAACTTACGATGGGTGAATAAAAACAGAGGTTGAAAATGCCAGAGCAGGGGCCAAGAACAGTT
66 GATAACTCACGATGAGTGAATAAAAACAGAGGCTGAAAAAGCCAGAGCAGGGGCCAAGAACAGTT
85273 ATCATGAGAGGATGAGGAAAAATGAGGTGTC
131 ATCATGAGAGGATGAGGAAAAATGAGGTGTC
* * * * *
85304 GGAAGAACAAAATAGCGAGGAAGGAACAAAAGCGCAACATAAAAGTGTAAAAAAATCAAAGTAAC
1 GGAAGAACAAAATAGCGAAGAAAGAACAAAACCACAACATAAAAGCGTAAAAAAATCAAAGTAAC
* * * **
85369 GATAACTCACGGTGAGTGAATAGGAAA-GGAGGCTGAAAACAG-CAGAGCAGGGGCTGAGAACAG
66 GATAACTCACGATGAGTGAATA-AAAACAGAGGCTGAAAA-AGCCAGAGCAGGGGCCAAGAACAG
85432 TT
129 TT
85434 TCAGACAACA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
161 108 0.96
162 4 0.04
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (161 bp):
GGAAGAACAAAATAGCGAAGAAAGAACAAAACCACAACATAAAAGCGTAAAAAAATCAAAGTAAC
GATAACTCACGATGAGTGAATAAAAACAGAGGCTGAAAAAGCCAGAGCAGGGGCCAAGAACAGTT
ATCATGAGAGGATGAGGAAAAATGAGGTGTC
Done.