Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012529.1 Corchorus olitorius cultivar O-4 contig12562, 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: 31017
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:27 original size:21 final size:21
Alignment explanation
Indices: 1--103 Score: 170
Period size: 21 Copynumber: 4.9 Consensus size: 21
1 AGGTTCCAAGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
*
22 AGGTTCCATGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
43 AGGTTCCAAGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
*
64 AGGTTCCAAGATCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
* *
85 AGGTTTCAAGCTCATTGGA
1 AGGTTCCAAGTTCATTGGA
104 ATTGCCTAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (21 bp):
AGGTTCCAAGTTCATTGGAGA
Found at i:4240 original size:35 final size:35
Alignment explanation
Indices: 4158--4241 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
4148 CCATATCATA
*
4158 AAACCATTGTTCCGAGAATAGAAATTAAGGATTAC
1 AAACCATTGTTCTGAGAATAGAAATTAAGGATTAC
4193 AAACCATTGTTCTGAGAATAGAAATTAAAGG-TTAC
1 AAACCATTGTTCTGAGAATAGAAATT-AAGGATTAC
4228 AAACCATTGTTCTG
1 AAACCATTGTTCTG
4242 CACATAAACT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 43 0.91
36 4 0.09
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (35 bp):
AAACCATTGTTCTGAGAATAGAAATTAAGGATTAC
Found at i:8993 original size:33 final size:33
Alignment explanation
Indices: 8927--9060 Score: 146
Period size: 33 Copynumber: 3.9 Consensus size: 33
8917 TAATGTCCTC
*
8927 ACTTAATTACCTTGAATTAAGTTCTTTATTGACTTT
1 ACTTAATTACCTCGAATTAAG---TTTATTGACTTT
*
8963 ACTTAATTACCTCGAATTAAGTTTATTGACTCT
1 ACTTAATTACCTCGAATTAAGTTTATTGACTTT
8996 ACTTAATTACC-CAGAATTAAGTTTATTGACTCTTT
1 ACTTAATTACCTC-GAATTAAGTTTATTGA--CTTT
* * * *
9031 ACATAATTTCCTTGAATTAAGTCT-TTGACT
1 ACTTAATTACCTCGAATTAAGTTTATTGACT
9061 AATTTTACCT
Statistics
Matches: 87, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
32 3 0.03
33 38 0.44
34 4 0.05
35 22 0.25
36 20 0.23
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (33 bp):
ACTTAATTACCTCGAATTAAGTTTATTGACTTT
Found at i:9016 original size:69 final size:66
Alignment explanation
Indices: 8927--9060 Score: 162
Period size: 68 Copynumber: 2.0 Consensus size: 66
8917 TAATGTCCTC
** * *
8927 ACTTAATTACCTTGAATTAAGTTCTTTATTGA-CTTTACTTAATTACCTCGAATTAAGTTTATTG
1 ACTTAATTACCCAGAATTAAG---TTTATTGACCTTTACATAATTACCTCGAATTAAGTCT-TTG
8991 ACTCT
62 ACTCT
* *
8996 ACTTAATTACCCAGAATTAAGTTTATTGACTCTTTACATAATTTCCTTGAATTAAGTCTTTGACT
1 ACTTAATTACCCAGAATTAAGTTTATTGAC-CTTTACATAATTACCTCGAATTAAGTCTTTGACT
9061 AATTTTACCT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
66 8 0.14
67 6 0.11
68 24 0.42
69 19 0.33
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (66 bp):
ACTTAATTACCCAGAATTAAGTTTATTGACCTTTACATAATTACCTCGAATTAAGTCTTTGACTC
T
Found at i:10000 original size:36 final size:36
Alignment explanation
Indices: 9028--9996 Score: 972
Period size: 36 Copynumber: 26.8 Consensus size: 36
9018 TTATTGACTC
* *
9028 TTTACATAATTTCCTTGAATTAAGTCTTTGAC-TAAT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTG-CTTGAT
* * * *
9064 TTTACCTAATTTCCCTAAATTAAGTCTTTGTTTGCT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
* * *
9100 TCTACCTAATTTCCTTGGATCAAGTCTTTGCTTG-T
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
*
9135 TCTTACCTAATTTCCTTGAAATTAAGTCTTTGATTGA-
1 T-TTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * * * *
9172 CTTACTTAATTACCCTGAATTAAGTCTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
* *
9208 TTTACCTAA-TTCCTTGAAATGAAGTCTTTACTTGAT
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
9244 TTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGA-
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * * *
9280 CTTACTTAATTACCCTGAATTAAGT-TTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTT-TGCTTGAT
* *
9316 TTTACCTAATTTCCTTGAAATTAAGTCTTTACTAGAT
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
*
9353 TTTACGTAATTTCCTTGAAATTAAGTCTTTGCTTG-T
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
*
9389 TCTTACCTAATTTCCTTGAAATTAAGCCTTTGCTTG-T
1 T-TTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
9426 TCTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGA-
1 T-TTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * * *
9463 TTTACTTAATTACCCTGAAATAAGT-TTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTT-TGCTTGAT
*
9499 TTTACCTAATTTCCTTGAAATTAAGTCTTTGCTT-AA
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * * *
9535 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
9571 TTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGA-
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * *
9607 TTTACTTAATTACCCTGAATTAAGT-TTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTT-TGCTTGAT
* *
9643 TTTACCTAATTTTCTTGAAATTAAGT-TTTTCTTGA-
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * * * *
9678 TTTACTTAATTACCCTGAATTAAGTCTGTGCTAGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
9714 TTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTG-T
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * *
9750 TCTTACCCAATTTTCTTGAAATTAAGTCGTTGCTTGA-
1 T-TTACCTAATTTCCTTG-AATTAAGTCTTTGCTTGAT
* * *
9787 TTTACTTAATTACCCTGAATTAAGT-TTGTGCTTGAT
1 TTTACCTAATTTCCTTGAATTAAGTCTT-TGCTTGAT
9823 TTTACCTAATTTCCTTGAAATTAAGTCTTTGAC-TGA-
1 TTTACCTAATTTCCTTG-AATTAAGTCTTTG-CTTGAT
* * * *
9859 TTTACTTAATTTCCCTGAATTAAGTCTATGCTTGTT
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
* * *
9895 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTG-T
1 TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
* * * * * * *
9930 ACTTACTTAATTACCCTAAATTAAGTCTTTGATTGTT
1 -TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
* * *
9967 TTTACTTAATTACCCTGAATTAAGTCTTTG
1 TTTACCTAATTTCCTTGAATTAAGTCTTTG
9997 ATTGCGTGAT
Statistics
Matches: 789, Mismatches: 108, Indels: 72
0.81 0.11 0.07
Matches are distributed among these distances:
34 16 0.02
35 131 0.17
36 382 0.48
37 253 0.32
38 7 0.01
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (36 bp):
TTTACCTAATTTCCTTGAATTAAGTCTTTGCTTGAT
Found at i:10140 original size:21 final size:21
Alignment explanation
Indices: 10121--10284 Score: 251
Period size: 21 Copynumber: 7.8 Consensus size: 21
10111 ATTACAGCAA
10121 GTTCCAAGCTCATTGGAGCAA-
1 GTTCCAAGCTCATTGGAG-AAG
10142 GTTCCAAGCTCATTGGAGCAA-
1 GTTCCAAGCTCATTGGAG-AAG
10163 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
10184 GTTCCAAGTTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
10205 GTTCCAAGTTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
10226 GTTCCAAGATCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
10247 GTTCCAAGATCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
10268 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
10285 ATTGCCTAAG
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
20 2 0.01
21 136 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:11168 original size:36 final size:36
Alignment explanation
Indices: 11093--11424 Score: 467
Period size: 36 Copynumber: 9.3 Consensus size: 36
11083 TATCATTGTG
*
11093 TTTACTTAATTA-CCTGAATTAAGTCTCTGCTTGCT
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
* *
11128 TTTACTTAATTACCCTGAATTACGTCTTTGATTG-T
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
*
11163 GTTTACTTAATTA-CCTGAATTAAGTCTCTGCTTGCT
1 -TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
*
11199 TTTACTTAATTACCCTGAATTACGTCTTTGCTTGCT
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
* *
11235 TTTACTTAATTACCCTGAATTAAGTTTTTGATTG-T
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
*
11270 GTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
1 -TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
* * *
11307 TTTACTTAGTTACACTGAATTAAGTCTTTGCTTGGT
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
* * *
11343 TTTACTTAATTACCTTGAATTAAGTCCTTGATTG-T
1 TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
*
11378 GTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
1 -TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
11415 TTTACTTAAT
1 TTTACTTAAT
11425 GCATGGATGC
Statistics
Matches: 262, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
35 45 0.17
36 215 0.82
37 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (36 bp):
TTTACTTAATTACCCTGAATTAAGTCTTTGCTTGCT
Found at i:11351 original size:108 final size:107
Alignment explanation
Indices: 11093--11424 Score: 549
Period size: 108 Copynumber: 3.1 Consensus size: 107
11083 TATCATTGTG
* *
11093 TTTACTTAATTACCTGAATTAAGTCTCTGCTTGCTTTTACTTAATTACCCTGAATTACGTCTTTG
1 TTTACTTAATTACCTGAATTAAGTCTTTGCTTGCTTTTACTTAATTACCCTGAATTAAGTCTTTG
* *
11158 ATTGTGTTTACTTAATTA-CCTGAATTAAGTCTCTGCTTGCT
66 ATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
* *
11199 TTTACTTAATTACCCTGAATTACGTCTTTGCTTGCTTTTACTTAATTACCCTGAATTAAGTTTTT
1 TTTACTTAATTA-CCTGAATTAAGTCTTTGCTTGCTTTTACTTAATTACCCTGAATTAAGTCTTT
11264 GATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
65 GATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
* * * *
11307 TTTACTTAGTTACACTGAATTAAGTCTTTGCTTGGTTTTACTTAATTACCTTGAATTAAGTCCTT
1 TTTACTTAATTAC-CTGAATTAAGTCTTTGCTTGCTTTTACTTAATTACCCTGAATTAAGTCTTT
11372 GATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
65 GATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
11415 TTTACTTAAT
1 TTTACTTAAT
11425 GCATGGATGC
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
106 12 0.06
107 68 0.32
108 130 0.62
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (107 bp):
TTTACTTAATTACCTGAATTAAGTCTTTGCTTGCTTTTACTTAATTACCCTGAATTAAGTCTTTG
ATTGTGTTTACTTAATTACCCTGGATTAAGTCTTTGCTTGCT
Found at i:13398 original size:15 final size:17
Alignment explanation
Indices: 13378--13410 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13368 CGCTCAAATG
13378 TCGGGTC-A-TTTGGGT
1 TCGGGTCAATTTTGGGT
13393 TCGGGTCAATTTTGGGT
1 TCGGGTCAATTTTGGGT
13410 T
1 T
13411 GGATCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.09, C:0.12, G:0.36, T:0.42
Consensus pattern (17 bp):
TCGGGTCAATTTTGGGT
Found at i:14244 original size:17 final size:18
Alignment explanation
Indices: 14219--14252 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14209 TTTAAAAAAA
*
14219 TATATATATATT-TATAG
1 TATACATATATTATATAG
14236 TATACATATATTATATA
1 TATACATATATTATATA
14253 AGAATCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATACATATATTATATAG
Found at i:14928 original size:65 final size:65
Alignment explanation
Indices: 14820--14949 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
14810 TTTAGCATAA
* *
14820 TTCGTAAGTATAATATTAGGAGTTAGTTTGCTAACTATCATTTAGCTTTAATTGCATTCAAAAAG
1 TTCGTAAGTATAATATTAAGAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAG
*
14885 TTCGTAAGTATAATATTAATAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAG
1 TTCGTAAGTATAATATTAAGAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAG
14950 AGGGTCCAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (65 bp):
TTCGTAAGTATAATATTAAGAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAG
Found at i:19011 original size:9 final size:9
Alignment explanation
Indices: 18997--19022 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18987 AAATGGTTGC
18997 TTTGTTTTG
1 TTTGTTTTG
19006 TTTGTTTTG
1 TTTGTTTTG
19015 TTTGTTTT
1 TTTGTTTT
19023 CATGCTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:20217 original size:42 final size:42
Alignment explanation
Indices: 20111--20203 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
20101 ATTTGATAAG
* * *
20111 TTATCCATATCTACATTGATATATG-TCATACATCCTTCATGCA
1 TTATCCATGTCTCCA-T-ATATATGTTCATACATCCGTCATGCA
*
20154 TTGTCCATGTCTCCATATATATGTTCATACATCCGTCATGCA
1 TTATCCATGTCTCCATATATATGTTCATACATCCGTCATGCA
20196 TTATCCAT
1 TTATCCAT
20204 TCCTTTGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
41 7 0.16
42 25 0.57
43 12 0.27
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.40
Consensus pattern (42 bp):
TTATCCATGTCTCCATATATATGTTCATACATCCGTCATGCA
Found at i:20223 original size:42 final size:42
Alignment explanation
Indices: 20111--20243 Score: 117
Period size: 42 Copynumber: 3.1 Consensus size: 42
20101 ATTTGATAAG
* * *
20111 TTATCCATATCTACAT-TGATATATGTCATACATCCTTCATGCA
1 TTATCCATGTCTCCATAT-ATATAT-TCATACATCCGTCATGCA
* *
20154 TTGTCCATGTCTCCATATATATGTTCATACATCCGTCATGCA
1 TTATCCATGTCTCCATATATATATTCATACATCCGTCATGCA
*** * ** *
20196 TTATCCAT-TCCTTTGTATATATATTCATGCATAGGTCGTGCA
1 TTATCCATGT-CTCCATATATATATTCATACATCCGTCATGCA
20238 TTATCC
1 TTATCC
20244 TTTCATTACT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.01
42 54 0.73
43 18 0.24
44 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.41
Consensus pattern (42 bp):
TTATCCATGTCTCCATATATATATTCATACATCCGTCATGCA
Found at i:21429 original size:14 final size:15
Alignment explanation
Indices: 21378--21426 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
21368 CAAGACATGT
*
21378 TTTTCAAGAAAT-TG
1 TTTTCAAGAAATAGG
*
21392 TTTTCAAGAAA-AGC
1 TTTTCAAGAAATAGG
21406 TTTTCAA-AAATAGG
1 TTTTCAAGAAATAGG
21420 TTTTCAA
1 TTTTCAA
21427 AAAGGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 3 0.10
14 27 0.90
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAATAGG
Found at i:21432 original size:12 final size:13
Alignment explanation
Indices: 21391--21435 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
21381 TCAAGAAATT
21391 GTTTTCAAGAAAAG
1 GTTTTCAA-AAAAG
*
21405 CTTTTCAAAAATAG
1 GTTTTCAAAAA-AG
21419 GTTTTC-AAAAAG
1 GTTTTCAAAAAAG
21431 GTTTT
1 GTTTT
21436 GGGTTTTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.25
13 7 0.25
14 14 0.50
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (13 bp):
GTTTTCAAAAAAG
Found at i:23933 original size:50 final size:50
Alignment explanation
Indices: 23858--24045 Score: 331
Period size: 50 Copynumber: 3.8 Consensus size: 50
23848 CGAATGTTTT
*
23858 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
23908 GGCTTTTCCACAAGCCAAACTCGTTTCCATACTAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
23958 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
24008 GGCTTTTCCACAAGCCGAACTTGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
24046 TTTCAAACCT
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 132 1.00
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:24175 original size:50 final size:50
Alignment explanation
Indices: 24101--24384 Score: 462
Period size: 50 Copynumber: 5.6 Consensus size: 50
24091 GCATTACCTT
*
24101 TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAGGACGGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
24152 TTTTAAGATTGAATTTGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
24202 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
24254 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
24304 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGAAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * *
24354 TTTTAATATT-AGATTGGAAGACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
24385 AAGTTGATCG
Statistics
Matches: 221, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
49 1 0.00
50 166 0.75
51 8 0.04
52 46 0.21
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:24285 original size:102 final size:100
Alignment explanation
Indices: 24101--24384 Score: 462
Period size: 102 Copynumber: 2.8 Consensus size: 100
24091 GCATTACCTT
*
24101 TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAGGACGGTCCTTTTAAGATTGAAT
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAAT
*
24166 TTGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
65 TGGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
24202 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAA
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAA
*
24267 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
64 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
* *
24304 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAATATT-AGAT
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA-AT
* *
24368 TGGAAGACAATTCAAAG
65 TGGTAGACAGTTCAAAG
24385 AAGTTGATCG
Statistics
Matches: 173, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
99 1 0.01
100 69 0.40
101 8 0.05
102 95 0.55
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (100 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
GGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
Found at i:24405 original size:152 final size:153
Alignment explanation
Indices: 24101--24384 Score: 468
Period size: 152 Copynumber: 1.9 Consensus size: 153
24091 GCATTACCTT
*
24101 TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAGGACGGTCCTTTTAAGATTGAAT
1 TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAAT
* * * *
24166 TTGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTATAGAATTGAATTGGTAGACAGTTC
66 TGGTAGACAGTTCAAAGGATAAGCGAAAGACAGTCCTTTTATAGAATTGAATTGGAAGACAATTC
24231 AAAGGATAAGCGGAAGACGGTCC
131 AAAGGATAAGCGGAAGACGGTCC
24254 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAAT
1 TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAAT
* *
24318 TGGTAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTA-A-TATT-AGATTGGAAGACAATT
66 TGGTAGACAGTTCAAAGGATAAGCGAAAGACAGTCCTTTTATAGAATTGA-ATTGGAAGACAATT
24380 CAAAG
130 CAAAG
24385 AAGTTGATCG
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
149 1 0.01
150 20 0.16
151 1 0.01
152 97 0.79
153 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (153 bp):
TTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAAT
TGGTAGACAGTTCAAAGGATAAGCGAAAGACAGTCCTTTTATAGAATTGAATTGGAAGACAATTC
AAAGGATAAGCGGAAGACGGTCC
Found at i:24914 original size:66 final size:66
Alignment explanation
Indices: 24805--24934 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
24795 TTTAGCATAA
** *
24805 TTCGTAAGTATAATATTAGGAGTTAGTTTGCTAACTATCATTTAGCTTTAATTGCATTCAAAAAA
1 TTCGTAAGTATAATATTAAAAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAA
24870 G
66 G
24871 TTCGTAAGTATAATATTAAAAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAA
1 TTCGTAAGTATAATATTAAAAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAA
24935 GAGGGTCCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (66 bp):
TTCGTAAGTATAATATTAAAAGTTAGTTTGCTAACTATAATTTAGCTTTAATTGCATTCAAAAAA
G
Found at i:27734 original size:21 final size:21
Alignment explanation
Indices: 27710--27864 Score: 224
Period size: 21 Copynumber: 7.4 Consensus size: 21
27700 CTTAGGCAAT
*
27710 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
27731 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
27752 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
27773 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
27794 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
*
27815 TCCAATGAGCTTGGAACTTTC
1 TCCAATGAGCTTGGAACCTTC
*
27836 TCCAATAAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
27857 TCCAATGA
1 TCCAATGA
27865 ACTTCTATCA
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
20 5 0.04
21 116 0.94
22 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:29743 original size:33 final size:34
Alignment explanation
Indices: 29706--29833 Score: 131
Period size: 33 Copynumber: 3.9 Consensus size: 34
29696 ATTAGCATCC
*
29706 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAGAATTTAGTATCATCACAAACAACACCT
*
29739 AAAACA-AATTTAGTATCATCACAAACAACACTT
1 AAAACAGAATTTAGTATCATCACAAACAACACCT
** * * *
29772 AAATTAG-GTTTAGTATCATCACTAACAACATCT
1 AAAACAGAATTTAGTATCATCACAAACAACACCT
* *
29805 AAAACAG-ATTTCA-TGTCATTACAAACAAC
1 AAAACAGAATTT-AGTATCATCACAAACAAC
29834 CCTCAAATCA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
32 5 0.06
33 72 0.92
34 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (34 bp):
AAAACAGAATTTAGTATCATCACAAACAACACCT
Found at i:29793 original size:66 final size:66
Alignment explanation
Indices: 29721--29847 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
29711 AGAATTTGTT
* *
29721 TCATCACAAACAACACCTAAAACAAATTT-AGTATCATCACAAACAACACTTAAATTAGGTTTAG
1 TCATCACAAACAACACCTAAAACAAATTTCA-TATCATCACAAACAACACTCAAATCAGGTTTAG
29785 TA
65 TA
* * * * * *
29787 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTACAAACAACCCTCAAATCAGGTT
1 TCATCACAAACAACACCTAAAACAAATTTCATATCATCACAAACAACACTCAAATCAGGTT
29848 CAGAATTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAAATTTCATATCATCACAAACAACACTCAAATCAGGTTTAGT
A
Done.