Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014406.1 Corchorus capsularis cultivar CVL-1 contig14427, 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: 68704
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4838 original size:2 final size:2
Alignment explanation
Indices: 4833--4865 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4823 TTCAATTGTG
4833 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
4866 CAAATTACTT
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:5208 original size:21 final size:21
Alignment explanation
Indices: 5165--5211 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5155 GTAACATGTT
*
5165 TTGTTGTTGTTGATCTGATTG
1 TTGTTGTTGTTGATCTGACTG
*
5186 TTGTTGTTGTTGCTGCTG-CTG
1 TTGTTGTTGTTGAT-CTGACTG
5207 TTGTT
1 TTGTT
5212 TTTCAGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.04, C:0.09, G:0.30, T:0.57
Consensus pattern (21 bp):
TTGTTGTTGTTGATCTGACTG
Found at i:10087 original size:27 final size:27
Alignment explanation
Indices: 9951--10077 Score: 236
Period size: 27 Copynumber: 4.7 Consensus size: 27
9941 CTTTTCCCCA
*
9951 TCATCAGAGTCAGATTTCTTCTCATTC
1 TCATCAGACTCAGATTTCTTCTCATTC
*
9978 TCATCAGAGTCAGATTTCTTCTCATTC
1 TCATCAGACTCAGATTTCTTCTCATTC
10005 TCATCAGACTCAGATTTCTTCTCATTC
1 TCATCAGACTCAGATTTCTTCTCATTC
10032 TCATCAGACTCAGATTTCTTCTCATTC
1 TCATCAGACTCAGATTTCTTCTCATTC
10059 TCATCAGACTCAGATTTCT
1 TCATCAGACTCAGATTTCT
10078 CATTGCTCTC
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (27 bp):
TCATCAGACTCAGATTTCTTCTCATTC
Found at i:10873 original size:8 final size:8
Alignment explanation
Indices: 10860--10885 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
10850 GGACGGATCT
10860 GAAGAGAA
1 GAAGAGAA
10868 GAAGAGAA
1 GAAGAGAA
10876 GAAGAGAA
1 GAAGAGAA
10884 GA
1 GA
10886 GAGCTTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
GAAGAGAA
Found at i:13621 original size:14 final size:14
Alignment explanation
Indices: 13602--13630 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13592 TTACAATCAG
13602 GGGGAGAGGGAGGA
1 GGGGAGAGGGAGGA
13616 GGGGAGAGGGAGGA
1 GGGGAGAGGGAGGA
13630 G
1 G
13631 TGGGGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (14 bp):
GGGGAGAGGGAGGA
Found at i:14124 original size:22 final size:22
Alignment explanation
Indices: 14098--14170 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
14088 AGTTATAATA
14098 AACTAATAATCTACCTCATTAT
1 AACTAATAATCTACCTCATTAT
* *
14120 AACTAATATATATGA--TGATTA-
1 AACTAATA-ATCT-ACCTCATTAT
*
14141 AACTAATAATCTACCTTATTAT
1 AACTAATAATCTACCTCATTAT
14163 AACTAATA
1 AACTAATA
14171 TATATGATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 13 0.31
22 21 0.50
23 3 0.07
24 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (22 bp):
AACTAATAATCTACCTCATTAT
Found at i:14144 original size:43 final size:43
Alignment explanation
Indices: 14096--14196 Score: 193
Period size: 43 Copynumber: 2.3 Consensus size: 43
14086 TTAGTTATAA
14096 TAAACTAATAATCTACCTCATTATAACTAATATATATGATGAT
1 TAAACTAATAATCTACCTCATTATAACTAATATATATGATGAT
*
14139 TAAACTAATAATCTACCTTATTATAACTAATATATATGATGAT
1 TAAACTAATAATCTACCTCATTATAACTAATATATATGATGAT
14182 TAAACTAATAATCTA
1 TAAACTAATAATCTA
14197 ACTTTAATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.38
Consensus pattern (43 bp):
TAAACTAATAATCTACCTCATTATAACTAATATATATGATGAT
Found at i:14146 original size:21 final size:22
Alignment explanation
Indices: 14115--14191 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 22
14105 AATCTACCTC
14115 ATTATAACTAATATATATGATG
1 ATTATAACTAATATATATGATG
* *
14137 ATTA-AACTAATA-ATCT-ACCTT
1 ATTATAACTAATATATATGA--TG
14158 ATTATAACTAATATATATGATG
1 ATTATAACTAATATATATGATG
14180 ATTA-AACTAATA
1 ATTATAACTAATA
14192 ATCTAACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 21 0.46
22 17 0.37
23 3 0.07
24 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (22 bp):
ATTATAACTAATATATATGATG
Found at i:17331 original size:7 final size:7
Alignment explanation
Indices: 17319--17359 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
17309 ATTATATGTG
17319 TTTTAGA
1 TTTTAGA
17326 TTTTAGA
1 TTTTAGA
17333 TTTTAGA
1 TTTTAGA
17340 TTTTAGA
1 TTTTAGA
*
17347 --CTAGA
1 TTTTAGA
17352 TTTTAGA
1 TTTTAGA
17359 T
1 T
17360 GAATATGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
7 26 0.87
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (7 bp):
TTTTAGA
Found at i:19333 original size:21 final size:20
Alignment explanation
Indices: 19304--19344 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19294 TGATCAGGTC
*
19304 TTTTTTTTTGTTGTTTTTTG
1 TTTTTTTTTGTTGCTTTTTG
*
19324 TTTTTGTTTTTTTGCTTTTTG
1 TTTTT-TTTTGTTGCTTTTTG
19345 GCTTTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTGTTGCTTTTTG
Found at i:19342 original size:15 final size:14
Alignment explanation
Indices: 19304--19344 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19294 TGATCAGGTC
*
19304 TTTTTTT-TTGTTG
1 TTTTTTTGTTTTTG
19317 -TTTTTTGTTTTTG
1 TTTTTTTGTTTTTG
19330 TTTTTTTGCTTTTTG
1 TTTTTTTG-TTTTTG
19345 GCTTTTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.25
13 5 0.21
14 7 0.29
15 6 0.25
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (14 bp):
TTTTTTTGTTTTTG
Found at i:19343 original size:16 final size:15
Alignment explanation
Indices: 19304--19336 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19294 TGATCAGGTC
19304 TTTTTTTTTGTTGTT
1 TTTTTTTTTGTTGTT
19319 TTTTGTTTTTGTT-TT
1 TTTT-TTTTTGTTGTT
19334 TTT
1 TTT
19337 GCTTTTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTGTTGTT
Found at i:20294 original size:18 final size:18
Alignment explanation
Indices: 20246--20288 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20236 AAGCTTCAGC
** *
20246 TCTTGATGTTTCTTTTGG
1 TCTTGATGACTCTGTTGG
20264 TCTTGATGACTCTGTTGG
1 TCTTGATGACTCTGTTGG
20282 TCTTGAT
1 TCTTGAT
20289 CGCTCTCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53
Consensus pattern (18 bp):
TCTTGATGACTCTGTTGG
Found at i:24483 original size:18 final size:18
Alignment explanation
Indices: 24460--24494 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24450 ACAAAAACTG
*
24460 AAATTGTTCATAAACAAA
1 AAATTGCTCATAAACAAA
*
24478 AAATTGCTCATGAACAA
1 AAATTGCTCATAAACAA
24495 TGTAATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATTGCTCATAAACAAA
Found at i:25962 original size:16 final size:16
Alignment explanation
Indices: 25913--25971 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
25903 TAGCTTTTAT
*
25913 TATATATATAA-AATGA
1 TATATATA-AATAATAA
* *
25929 TATAT-TTAATTATAAA
1 TATATATAAATAAT-AA
25945 TATATATAAATAATAA
1 TATATATAAATAATAA
25961 TATATAATAAA
1 TATAT-ATAAA
25972 CGAACATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 18 0.53
17 11 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TATATATAAATAATAA
Found at i:26012 original size:35 final size:34
Alignment explanation
Indices: 25973--26055 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
25963 TATAATAAAC
* *
25973 GAACATTTAAACGAACAATAAGCGAGCTTGTTCGT
1 GAACA-TTAAACGAACAATAAACGAGCATGTTCGT
*
26008 GAACACTTAAATGAACAATAAACGAGCATGTTCGT
1 GAACA-TTAAACGAACAATAAACGAGCATGTTCGT
26043 GAACA-TAAACGAA
1 GAACATTAAACGAA
26056 TTGAACACGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 7 0.16
35 36 0.84
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (34 bp):
GAACATTAAACGAACAATAAACGAGCATGTTCGT
Found at i:26786 original size:31 final size:30
Alignment explanation
Indices: 26730--26788 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
26720 ATGTTTTTCG
*
26730 ATTGTACCTTATTTTTAAAGCATATTTCCA
1 ATTGTACCTTATTTTTAAAACATATTTCCA
*
26760 ATTGTACCATT-TTTGTTAAAATATATTTC
1 ATTGTACC-TTATTT-TTAAAACATATTTC
26789 TAAATTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.49
Consensus pattern (30 bp):
ATTGTACCTTATTTTTAAAACATATTTCCA
Found at i:26935 original size:97 final size:97
Alignment explanation
Indices: 26777--26957 Score: 344
Period size: 97 Copynumber: 1.9 Consensus size: 97
26767 CATTTTTGTT
* *
26777 AAAATATATTTCTAAATTGTCATTACTAAATAATATTTTAATTATTCCATTATTTTTTAATCATA
1 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTTTTTAATCATA
26842 AATTATTCCATTATTAATTCTTCCTTTTTTAA
66 AATTATTCCATTATTAATTCTTCCTTTTTTAA
26874 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTTTTTAATCATA
1 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTTTTTAATCATA
26939 AATTATTCCATTATTAATT
66 AATTATTCCATTATTAATT
26958 ATTAGATTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.50
Consensus pattern (97 bp):
AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTTTTTAATCATA
AATTATTCCATTATTAATTCTTCCTTTTTTAA
Found at i:27934 original size:19 final size:20
Alignment explanation
Indices: 27907--27944 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27897 TACTATTATT
27907 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
27927 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
27945 AATGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:28180 original size:22 final size:22
Alignment explanation
Indices: 28155--28217 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
28145 TTAATGAGGA
* *
28155 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
28177 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
28199 GATCACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
28218 GATCAGGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:28284 original size:22 final size:22
Alignment explanation
Indices: 28259--28492 Score: 136
Period size: 22 Copynumber: 10.6 Consensus size: 22
28249 ATAGGAAGAT
*
28259 TTATCAAAATTTTATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
28281 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
28303 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
28325 TTA-CTAACAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * * *
28347 TTTTTAAATTTTCATAATGTGG
1 TTATCAAAATTTCATAGTGAGG
** *
28369 TTATCAGTATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
28391 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* * * *
28414 TTATCAAAATTTTATTGGGAAG
1 TTATCAAAATTTCATAGTGAGG
*
28436 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
28458 TCT-TCAAAATTCCTTAGAGAGG
1 T-TATCAAAATTTCATAGTGAGG
*
28480 TTAACAAAATTTC
1 TTATCAAAATTTC
28493 GTAAGGTTAA
Statistics
Matches: 159, Mismatches: 42, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
21 5 0.03
22 133 0.84
23 21 0.13
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:28776 original size:10 final size:11
Alignment explanation
Indices: 28762--28794 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
28752 CTATTATTGT
28762 TTTTTATAATG
1 TTTTTATAATG
28773 TTTTTATAATG
1 TTTTTATAATG
28784 TTTTTTATAAT
1 -TTTTTATAAT
28795 TTAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (11 bp):
TTTTTATAATG
Found at i:28778 original size:11 final size:12
Alignment explanation
Indices: 28759--28794 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
28749 CTCCTATTAT
28759 TGTTTTTTATAA
1 TGTTTTTTATAA
28771 TG-TTTTTATAA
1 TGTTTTTTATAA
28782 TGTTTTTTATAA
1 TGTTTTTTATAA
28794 T
1 T
28795 TTAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (12 bp):
TGTTTTTTATAA
Found at i:30775 original size:11 final size:10
Alignment explanation
Indices: 30757--30790 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
30747 GAAGTTCGTG
30757 TTTTGAAGAT
1 TTTTGAAGAT
30767 TTCTTGAAGAT
1 TT-TTGAAGAT
30778 ATTTTGAAGAT
1 -TTTTGAAGAT
30789 TT
1 TT
30791 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:36596 original size:12 final size:12
Alignment explanation
Indices: 36579--36603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36569 GGTGACCAAA
36579 TCCCCAATCTTT
1 TCCCCAATCTTT
36591 TCCCCAATCTTT
1 TCCCCAATCTTT
36603 T
1 T
36604 TTGCCCAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCCCAATCTTT
Found at i:37983 original size:52 final size:52
Alignment explanation
Indices: 37921--38023 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
37911 ATTTTTTAAG
* * * *
37921 GAATTACTTCCACATATATGGTAGTCATATTAGAATTTAGTTAATCTGTAAC
1 GAATTACTTCCACATATATGATAGTCATATTAAAATTTAATTAATATGTAAC
37973 GAATTACTTCCACATATATGATAGTCATATTAAAATTTAATTAATATGTAA
1 GAATTACTTCCACATATATGATAGTCATATTAAAATTTAATTAATATGTAA
38024 TAGACGCGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (52 bp):
GAATTACTTCCACATATATGATAGTCATATTAAAATTTAATTAATATGTAAC
Found at i:38120 original size:219 final size:221
Alignment explanation
Indices: 37730--38140 Score: 711
Period size: 219 Copynumber: 1.9 Consensus size: 221
37720 AGAATTTATC
37730 AATTTAGCTAATCTGTAACGAATTACTTTCATTCCAAATATATGATAGTCATATTAAAATTTAAT
1 AATTTAGCTAATCTGTAACGAATTA---TCATTCCAAATATATGATAGTCATATTAAAATTTAAT
37795 TAATATGCAATAGACGCGAGTTAGATCTCAAATGCAATGAATATCTTATAGTTTCTATTTTCTCC
63 TAATATGCAATAGACGCGAGTTAGATCTCAAATGCAATGAATATCTTATAGTTTCTATTTTCTCC
*
37860 ATTTATAAAACTTATTCCAAAAATTTTTTATCTCAAAAAAAAAATTCCAAAATTTTTTAAGGAAT
128 ATTTATAAAAATTATTCCAAAAATTTTTTATCTCAAAAAAAAAATTCCAAAATTTTTTAAGGAAT
37925 TACTTCCACATATATGGTAGTCATATTAG
193 TACTTCCACATATATGGTAGTCATATTAG
* *
37954 AATTTAGTTAATCTGTAACGAATTA-C-TTCCACATATATGATAGTCATATTAAAATTTAATTAA
1 AATTTAGCTAATCTGTAACGAATTATCATTCCAAATATATGATAGTCATATTAAAATTTAATTAA
*
38017 TATGTAATAGACGCGAGTTAGATCTCAAATGCAATGAATATCTTATAGTTTCTATTTTCTCCATT
66 TATGCAATAGACGCGAGTTAGATCTCAAATGCAATGAATATCTTATAGTTTCTATTTTCTCCATT
* *
38082 TATAAAAATTAATTTCAAAATTTTTTTATCTC-AAAAAAAAATTCCAAAATTTTTTAAGG
131 TATAAAAATT-ATTCCAAAAATTTTTTATCTCAAAAAAAAAATTCCAAAATTTTTTAAGG
38141 GATTTTTTTT
Statistics
Matches: 180, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
219 136 0.76
220 20 0.11
224 24 0.13
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (221 bp):
AATTTAGCTAATCTGTAACGAATTATCATTCCAAATATATGATAGTCATATTAAAATTTAATTAA
TATGCAATAGACGCGAGTTAGATCTCAAATGCAATGAATATCTTATAGTTTCTATTTTCTCCATT
TATAAAAATTATTCCAAAAATTTTTTATCTCAAAAAAAAAATTCCAAAATTTTTTAAGGAATTAC
TTCCACATATATGGTAGTCATATTAG
Found at i:41070 original size:32 final size:32
Alignment explanation
Indices: 41029--41100 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
41019 GTTTTTGTGC
41029 ATACTTGTCTTTTATTGTCTTTGTACCATAAT
1 ATACTTGTCTTTTATTGTCTTTGTACCATAAT
41061 ATACTTGTCTTTTATTGTCTTTGTACCATAAT
1 ATACTTGTCTTTTATTGTCTTTGTACCATAAT
*
41093 AAACTTGT
1 ATACTTGT
41101 TTAATTACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (32 bp):
ATACTTGTCTTTTATTGTCTTTGTACCATAAT
Found at i:45439 original size:29 final size:29
Alignment explanation
Indices: 45384--45458 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
45374 GCTTATAGTG
* *
45384 TTTGGACGTTTTGTCACATCAACTTCAAT
1 TTTGGACGTTTTGCCCCATCAACTTCAAT
* * *
45413 TTTGGACATTTTGCCCCATGAATTTCAAT
1 TTTGGACGTTTTGCCCCATCAACTTCAAT
*
45442 TATGGGACGTTTTGCCC
1 T-TTGGACGTTTTGCCC
45459 TCTGAACCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCATCAACTTCAAT
Found at i:47988 original size:22 final size:22
Alignment explanation
Indices: 47958--48060 Score: 98
Period size: 22 Copynumber: 4.6 Consensus size: 22
47948 TCCAACGTAG
*
47958 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* * *
47981 AAATTTGATAACCTCATTACGA
1 AAATTTGATAACCACACTATGA
* * *
48003 AACTTTGATAACCTCTCTATGA
1 AAATTTGATAACCACACTATGA
* * *
48025 AAATTTGATAACCATACTGTGT
1 AAATTTGATAACCACACTATGA
*
48047 AATTTTGATAACCA
1 AAATTTGATAACCA
48061 TAATCTAGAG
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
22 61 0.94
23 4 0.06
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:48439 original size:29 final size:30
Alignment explanation
Indices: 48389--48451 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
48379 TTAATTGATG
* *
48389 TATACATATAAATTATTCAATTTTATTATA
1 TATAAATATAAATTATTCAATTATATTATA
*
48419 TATAAATAT-AATTATAT-AATTATATTATT
1 TATAAATATAAATTAT-TCAATTATATTATA
48448 TATA
1 TATA
48452 TACAATACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TATAAATATAAATTATTCAATTATATTATA
Found at i:48818 original size:22 final size:22
Alignment explanation
Indices: 48746--48869 Score: 106
Period size: 22 Copynumber: 5.6 Consensus size: 22
48736 GAAACCATAG
* * *
48746 TATAAATTTTTTATAACCTCCC
1 TATAAAATTTTGATAACCTCCT
* ***
48768 TATAAAA-TTTGGTAACCGAAT
1 TATAAAATTTTGATAACCTCCT
* *
48789 TCTGAAATTTTGATAACCTCCT
1 TATAAAATTTTGATAACCTCCT
*
48811 TATAAAATTTTTGATTACCTCCT
1 TATAAAA-TTTTGATAACCTCCT
* * *
48834 TATGAAATTTTGATAATCTCAT
1 TATAAAATTTTGATAACCTCCT
*
48856 TATGAAATTTTGAT
1 TATAAAATTTTGAT
48870 TACCAAACAA
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 13 0.16
22 47 0.59
23 20 0.25
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCT
Found at i:48830 original size:23 final size:22
Alignment explanation
Indices: 48791--48869 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
48781 AACCGAATTC
48791 TGAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCCTTA
* *
48813 TAAAATTTTTGATTACCTCCTTA
1 TGAAA-TTTTGATAACCTCCTTA
* *
48836 TGAAATTTTGATAATCTCATTA
1 TGAAATTTTGATAACCTCCTTA
48858 TGAAATTTTGAT
1 TGAAATTTTGAT
48870 TACCAAACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
22 30 0.60
23 20 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCTTA
Found at i:50942 original size:29 final size:28
Alignment explanation
Indices: 50894--50968 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
50884 TTAGGCTGAG
50894 GGGGCAAAACGTCCCAAAATTGATA-TTCA
1 GGGGCAAAACGT-CCAAAATTGA-AGTTCA
*
50923 GGAGGCAAAATGTCCAAAATTGAAGTTCA
1 GG-GGCAAAACGTCCAAAATTGAAGTTCA
*
50952 GGGACAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
50969 CGCTACAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 14 0.34
29 18 0.44
30 9 0.22
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (28 bp):
GGGGCAAAACGTCCAAAATTGAAGTTCA
Found at i:55926 original size:31 final size:31
Alignment explanation
Indices: 55848--55932 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
55838 TGATATGGCC
* *
55848 TTGCAACGTGGCATTTTGGTCCAACATGGCA
1 TTGCCACGTGGCATTTTGGTCCAACATGACA
* * **
55879 TTGCTACGCGTTATTTTGGTCCAACGA-GACA
1 TTGCCACGTGGCATTTTGGTCCAAC-ATGACA
*
55910 TTGCCATGTGGCATTTTCGGTCC
1 TTGCCACGTGGCATTTT-GGTCC
55933 GACGTGGCAT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
31 36 0.86
32 6 0.14
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.33
Consensus pattern (31 bp):
TTGCCACGTGGCATTTTGGTCCAACATGACA
Found at i:62551 original size:36 final size:36
Alignment explanation
Indices: 62511--62616 Score: 90
Period size: 39 Copynumber: 2.9 Consensus size: 36
62501 CACCATCAAG
62511 TGAAGAACAGTTCATCGAATCTTCTTCATCATCAGC
1 TGAAGAACAGTTCATCGAATCTTCTTCATCATCAGC
* * * * *
62547 TGAAGATCAAGTT-A-CAGAATCTTCTGCAGCACCATCTGG
1 TGAAGAAC-AGTTCATC-GAATCTTCT---TCATCATCAGC
* *
62586 TGAAGAACAGTTCATAGAGTCTTCTTCATCA
1 TGAAGAACAGTTCATCGAATCTTCTTCATCA
62617 GCTGAAGATA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
35 1 0.02
36 21 0.40
37 4 0.08
38 4 0.08
39 23 0.43
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (36 bp):
TGAAGAACAGTTCATCGAATCTTCTTCATCATCAGC
Found at i:62645 original size:75 final size:74
Alignment explanation
Indices: 62492--62636 Score: 197
Period size: 75 Copynumber: 2.0 Consensus size: 74
62482 CCTGGAGTGC
* *
62492 CTTCTCCATCACCATCAAGTGAAGAACAGTTCATCGAATCTTCTTCATCATCAGCTGAAGATCAA
1 CTTCTCCAGCACCATCAAGTGAAGAACAGTTCATAGAATCTTCTT-ATCATCAGCTGAAGATCAA
62557 GTTACAGAAT
65 GTTACAGAAT
* ** *
62567 CTTCTGCAGCACCATCTGGTGAAGAACAGTTCATAGAGTCTTC-T-TCATCAGCTGAAGAT-AAG
1 CTTCTCCAGCACCATCAAGTGAAGAACAGTTCATAGAATCTTCTTATCATCAGCTGAAGATCAAG
62629 CTTACAGA
66 -TTACAGA
62637 CCCTTCTTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 3 0.05
72 22 0.35
74 1 0.02
75 37 0.59
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (74 bp):
CTTCTCCAGCACCATCAAGTGAAGAACAGTTCATAGAATCTTCTTATCATCAGCTGAAGATCAAG
TTACAGAAT
Done.