Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018762.1 Corchorus olitorius cultivar O-4 contig18795, 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: 63491
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:559 original size:21 final size:21
Alignment explanation
Indices: 535--574 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
525 GCCGAATTAA
535 GGAATTAAGGAATTTTTCATT
1 GGAATTAAGGAATTTTTCATT
556 GGAATTAAGGAATTTTTCA
1 GGAATTAAGGAATTTTTCA
575 CATAGTGCTG
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:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (21 bp):
GGAATTAAGGAATTTTTCATT
Found at i:7166 original size:16 final size:15
Alignment explanation
Indices: 7128--7169 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7118 ACAGCGATTG
*
7128 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
7143 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7158 ACTAGAAAACAA
1 AC-AGAAAACAA
7170 AGCAAAATAA
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:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:14045 original size:1 final size:1
Alignment explanation
Indices: 14041--14075 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
14031 GATTTTTCTG
14041 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14076 GTGAAGGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14147 original size:22 final size:22
Alignment explanation
Indices: 14114--14168 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
14104 CTTAGCTATG
14114 TCCCC-TTTTCTAACTAATTCT
1 TCCCCTTTTTCTAACTAATTCT
14135 TCCCCTTTTTCTAACTAATTCT
1 TCCCCTTTTTCTAACTAATTCT
14157 TCCCCTTTTTCT
1 TCCCCTTTTTCT
14169 CCTGTGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.51
Consensus pattern (22 bp):
TCCCCTTTTTCTAACTAATTCT
Found at i:16043 original size:25 final size:25
Alignment explanation
Indices: 16015--16063 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
16005 CAATTCTCTA
16015 ATCTACCATG-TAGTATAACAATGCC
1 ATCTACCATGAT-GTATAACAATGCC
16040 ATCTACCATGATGTATAACAATGC
1 ATCTACCATGATGTATAACAATGC
16064 TATGCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (25 bp):
ATCTACCATGATGTATAACAATGCC
Found at i:16356 original size:10 final size:9
Alignment explanation
Indices: 16319--16402 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
16309 CCAAAATGCC
*
16319 GCCCTAAAT
1 GCCCAAAAT
*
16328 GCAC-AAAT
1 GCCCAAAAT
*
16336 GACCAAAAT
1 GCCCAAAAT
16345 GCCCATAAAT
1 GCCCA-AAAT
16355 GCACC--AAT
1 GC-CCAAAAT
*
16363 GACCAAAAT
1 GCCCAAAAT
*
16372 GCCGCTAAAT
1 GCC-CAAAAT
*
16382 GCAC-AAAT
1 GCCCAAAAT
*
16390 GACCAAAAT
1 GCCCAAAAT
16399 GCCC
1 GCCC
16403 CTGAATGTGC
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
7 2 0.04
8 16 0.28
9 24 0.42
10 13 0.23
11 2 0.04
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.14
Consensus pattern (9 bp):
GCCCAAAAT
Found at i:16363 original size:27 final size:26
Alignment explanation
Indices: 16303--16432 Score: 152
Period size: 27 Copynumber: 4.7 Consensus size: 26
16293 CTATGGACTA
16303 AAATGACCAAAATGCCGCCCTAAATGCAC
1 AAATGACCAAAAT---GCCCTAAATGCAC
16332 AAATGACCAAAATGCCCATAAATGCAC
1 AAATGACCAAAATGCCC-TAAATGCAC
*
16359 CAATGACCAAAATGCCGCTAAATGCAC
1 AAATGACCAAAATGCC-CTAAATGCAC
* **
16386 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACCAAAATG-CCCTAAATGCAC
*
16413 AAATCACCAAAATGCACCTA
1 AAATGACCAAAATGC-CCTA
16433 GGGGATCCTA
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.06
27 69 0.77
28 3 0.03
29 13 0.14
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (26 bp):
AAATGACCAAAATGCCCTAAATGCAC
Found at i:16422 original size:54 final size:55
Alignment explanation
Indices: 16303--16427 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 55
16293 CTATGGACTA
16303 AAATGACCAAAATGCCGCCCTAAATGCACAAATGACCAAAATGCCCATAAATGCAC
1 AAATGACCAAAATGCCG-CCTAAATGCACAAATGACCAAAATGCCCATAAATGCAC
* * * **
16359 CAATGACCAAAATGCCG-CTAAATGCACAAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCGCCTAAATGCACAAATGACCAAAATGCCCATAAATGCAC
*
16413 AAATCACCAAAATGC
1 AAATGACCAAAATGC
16428 ACCTAGGGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 46 0.74
56 16 0.26
ACGTcount: A:0.43, C:0.28, G:0.14, T:0.15
Consensus pattern (55 bp):
AAATGACCAAAATGCCGCCTAAATGCACAAATGACCAAAATGCCCATAAATGCAC
Found at i:20126 original size:39 final size:39
Alignment explanation
Indices: 20083--20179 Score: 176
Period size: 39 Copynumber: 2.5 Consensus size: 39
20073 TTGCAAGACC
20083 TAGCCATATGCATTTTTCAATCCACTACATCACAAAACT
1 TAGCCATATGCATTTTTCAATCCACTACATCACAAAACT
* *
20122 TAGCCATATGCATTTTTCAATCCACTGCATCTCAAAACT
1 TAGCCATATGCATTTTTCAATCCACTACATCACAAAACT
20161 TAGCCATATGCATTTTTCA
1 TAGCCATATGCATTTTTCA
20180 GTTCACTATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (39 bp):
TAGCCATATGCATTTTTCAATCCACTACATCACAAAACT
Found at i:21755 original size:12 final size:13
Alignment explanation
Indices: 21737--21766 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
21727 GTTTTCTTTA
21737 ATTTTCTTGATTG
1 ATTTTCTTGATTG
21750 -TTTTCTTGATTG
1 ATTTTCTTGATTG
21762 ATTTT
1 ATTTT
21767 AATTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:21771 original size:22 final size:21
Alignment explanation
Indices: 21718--21773 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
21708 CACTGCTTTC
21718 TTTTTAATTGTTTTCTTTAAT
1 TTTTTAATTGTTTTCTTTAAT
* *
21739 TTTCTTGATTGTTTTC-TTGAT
1 TTT-TTAATTGTTTTCTTTAAT
21760 TGATTTTAATTGTT
1 T--TTTTAATTGTT
21774 AGTTTGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.28
22 19 0.66
23 2 0.07
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (21 bp):
TTTTTAATTGTTTTCTTTAAT
Found at i:21998 original size:16 final size:17
Alignment explanation
Indices: 21977--22008 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21967 GAGATTGCGT
21977 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
21993 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
22009 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:31702 original size:12 final size:13
Alignment explanation
Indices: 31684--31713 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
31674 GTTTTCTTTA
31684 ATTTTCTTGATTG
1 ATTTTCTTGATTG
31697 -TTTTCTTGATTG
1 ATTTTCTTGATTG
31709 ATTTT
1 ATTTT
31714 AATTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:33527 original size:2 final size:2
Alignment explanation
Indices: 33520--33546 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33510 AGATAGCAAG
33520 AT 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 AT A
33547 CATAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41276 original size:23 final size:22
Alignment explanation
Indices: 41250--41294 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41240 TTCTTACCTT
41250 TTTGAAATT-TTATTTCTTTTTTA
1 TTTG-AATTCTTATTT-TTTTTTA
*
41273 TTTGAATTCTTCTTTTTTTTTA
1 TTTGAATTCTTATTTTTTTTTA
41295 GGATTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTGAATTCTTATTTTTTTTTA
Found at i:43544 original size:87 final size:87
Alignment explanation
Indices: 43424--43598 Score: 253
Period size: 87 Copynumber: 2.0 Consensus size: 87
43414 ACTCTAATCT
* * *
43424 TCTGATTACTCTTTCTCTTACTTCTGATGACTCTTTCTTCTGCTTCTGATTACTCTTTCTTTTGC
1 TCTGATTACTCTTTCTCTTACTTCTGATGACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTGC
*
43489 TTTTGATTACTCTTCCTTTTAC
66 TTCTGATTACTCTTCCTTTTAC
* * * *
43511 TCTGATTACTCTTTCT-TCTGCTTTTGATTACTCTTCCTTTTACTCCTGATTACTCTTTCTTTTG
1 TCTGATTACTCTTTCTCT-TACTTCTGATGACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTG
*
43575 CTTCTGATTACTCTTTCTTTTAC
65 CTTCTGATTACTCTTCCTTTTAC
43598 T
1 T
43599 GCTTAGCTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 77 0.99
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.56
Consensus pattern (87 bp):
TCTGATTACTCTTTCTCTTACTTCTGATGACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTGC
TTCTGATTACTCTTCCTTTTAC
Found at i:43613 original size:28 final size:22
Alignment explanation
Indices: 43422--43595 Score: 233
Period size: 22 Copynumber: 8.0 Consensus size: 22
43412 TTACTCTAAT
* *
43422 CTTCTGATTACTCTTTCTCTTA
1 CTTCTGATTACTCTTTCTTTTG
* *
43444 CTTCTGATGACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTG
43466 CTTCTGATTACTCTTTCTTTTG
1 CTTCTGATTACTCTTTCTTTTG
* * *
43488 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTG
*
43510 C-TCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTG
* * *
43531 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTG
*
43553 CTCCTGATTACTCTTTCTTTTG
1 CTTCTGATTACTCTTTCTTTTG
43575 CTTCTGATTACTCTTTCTTTT
1 CTTCTGATTACTCTTTCTTTT
43596 ACTGCTTAGC
Statistics
Matches: 129, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
21 17 0.13
22 112 0.87
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.56
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTG
Found at i:43662 original size:47 final size:47
Alignment explanation
Indices: 43609--44180 Score: 599
Period size: 47 Copynumber: 11.7 Consensus size: 47
43599 GCTTAGCTTG
* *
43609 ATTACCCAGAATCAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
43656 ATTACCCCA-AATTAAACTCTTTTCTTCTTCTTTTACTTTTTAGTTTA
1 ATTA-CCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
43703 ATTACCCAAAATTAAACTAGTCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTA
* * *
43757 ATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * *
43804 ATTACCCCGAATTAAACTCCTTTT-TTCTCCTCTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACT-CTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* *
43851 ATTACCCAGAATTAAACTAACCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATT--A--AA-CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTA
*
43905 ATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
43952 ATTACTCTGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * *
43999 ATTACTCTGAATTAAACTGTTTTCTTCTTCTCTTGCACTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
44046 ATTACTCTGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * * *
44093 ATTATCCATAATTAAACTAGCCTCTGTTTACTTTTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTA
* * *
44147 ATTACCAAGAATTAAAATGTTTTCTTCTTCTCTT
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTT
44181 AATTTTTTTA
Statistics
Matches: 449, Mismatches: 51, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
46 4 0.01
47 284 0.63
48 21 0.05
49 10 0.02
50 4 0.01
51 6 0.01
52 14 0.03
53 10 0.02
54 96 0.21
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
Found at i:43761 original size:148 final size:147
Alignment explanation
Indices: 43589--44110 Score: 695
Period size: 148 Copynumber: 3.6 Consensus size: 147
43579 TGATTACTCT
* * * * *
43589 TTCTTTTACTGC-TTAGCTTGATTACCCAGAATCAAACTATTTTCTTCTTCTCTTGCTCTTTAGT
1 TTCTTTTACT-CTTTAGTTTAATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGT
*
43653 TTAATTACCCCAAATTAAACTCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAA
65 TTAATTACCCCAAATTAAACTCTTTTCTTCTTCTCTTACTTTTTAGTTTAATTACCCAAAATTAA
43718 ACTAGTCTCTGTTTACTTC
130 ACTAG-CTCTGTTTACTTC
* *
43737 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTT
* * *
43802 TAATTACCCCGAATTAAACTCCTTTT-TTCTCCTCTTACTTTTTAGTTTAATTACCCAGAATTAA
66 TAATTACCCCAAATTAAACT-CTTTTCTTCTTCTCTTACTTTTTAGTTTAATTACCCAAAATTAA
*
43866 ACTAACCTCTGTTTACTTC
130 ACT-AGCTCTGTTTACTTC
43885 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTT
* ** * * **
43950 TAATTACTCTGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACTCTGAATTAAA
66 TAATTACCCCAAATTAAACTCTTTTCTTCTTCTCTTACTTTTTAGTTTAATTACCCAAAATTAAA
44015 CT-G---T-TTT-CTTC
131 CTAGCTCTGTTTACTTC
* * * * *
44026 TTCTCTTGCACTTTAGTTTAATTACTC-TGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGT
1 TTCTTTTACTCTTTAGTTTAATTAC-CAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGT
*
44090 TTAATTA-TCCATAATTAAACT
65 TTAATTACCCCA-AATTAAACT
44111 AGCCTCTGTT
Statistics
Matches: 341, Mismatches: 27, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
140 2 0.01
141 77 0.23
142 4 0.01
143 1 0.00
147 6 0.02
148 245 0.72
149 6 0.02
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (147 bp):
TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTT
TAATTACCCCAAATTAAACTCTTTTCTTCTTCTCTTACTTTTTAGTTTAATTACCCAAAATTAAA
CTAGCTCTGTTTACTTC
Found at i:43934 original size:195 final size:193
Alignment explanation
Indices: 43609--44180 Score: 721
Period size: 195 Copynumber: 2.9 Consensus size: 193
43599 GCTTAGCTTG
*
43609 ATTACCCAGAATCAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCCA-AATTAAAC
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTA-CCCAGAATTAAAC
43673 TCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAACTAGTCTCTGTTTACTTCT
65 TCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAAC-AG-CTCTGTTTACTTCT
43738 TCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTT
128 TCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTT
43803 A
193 A
* * * * *
43804 ATTACCCCGAATTAAACTCCTTTT-TTCTCCTCTTACTTTTTAGTTTAATTACCCAGAATTAAAC
1 ATTACCCAGAATTAAACT-ATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATT--A-
*
43868 TAACCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAATTA-CCAAGAATT-AA-A-CTCT-TTT
62 -AA-CTCT-TTT-CTTCTTCTTTTACTTTTTAGTTTAATTACCCAA-AATTAAACAGCTCTGTTT
* * * * *
43928 -CTTCTTCTCTTGCTCTTTAGTTTAATTACTC-TGAATTAAACTCTTTTCTTCTTCTCTTGCTTT
122 ACTTCTTCTTTTACTCTTTAGTTTAATTAC-CAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCT
*
43991 TTAGTTTA
186 TCAGTTTA
* * * * * *
43999 ATTACTCTGAATTAAACTGTTTTCTTCTTCTCTTGCACTTTAGTTTAATTACTCTGAATTAAACT
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
* * * * *
44064 CTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTATCCATAATTAAACTAGCCTCTGTTTACTTTTT
66 CTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAAC-AG-CTCTGTTTACTTCTT
*
44129 CTTTTACTCTTTAGTTTAATTACCAAGAATTAAAATGTTTTCTTCTTCTCTT
129 CTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTT
44181 AATTTTTTTA
Statistics
Matches: 324, Mismatches: 32, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
188 29 0.09
189 8 0.02
190 4 0.01
191 3 0.01
193 5 0.02
194 12 0.04
195 203 0.63
196 8 0.02
197 5 0.02
199 3 0.01
200 4 0.01
201 9 0.03
202 31 0.10
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (193 bp):
ATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
CTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAACAGCTCTGTTTACTTCTTCT
TTTACTCTTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTTA
Found at i:44106 original size:94 final size:93
Alignment explanation
Indices: 43609--44180 Score: 581
Period size: 101 Copynumber: 5.9 Consensus size: 93
43599 GCTTAGCTTG
* *
43609 ATTACCCAGAATCAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCCA-AATTAAAC
1 ATTA-CCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTA-CCCAGAATTAAAC
* *
43673 TCTTTTCTTCTTCTTTTACTTTTTAGTTTA
64 TCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
* * * *
43703 ATTACCCAAAATTAAACTAGTCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCAAGAA
1 ATTA-CCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAA
* * *
43768 TTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTTA
58 TTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
* * * *
43804 ATTACCCCGAATTAAACTCCTTTT-TTCTCCTCTTACTTTTTAGTTTAATTACCCAGAATTAAAC
1 ATTA-CCAGAATTAAACT-CTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATT--A-
* * *
43868 TAACCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
61 -AA-CTCT-TTT-CTTCTTCTCTTGCTTTTTAGTTTA
* *
43905 ATTACCAAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACT
1 ATTACC-AGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
43970 CTTTTCTTCTTCTCTTGCTTTTTAGTTTA
65 CTTTTCTTCTTCTCTTGCTTTTTAGTTTA
* * * * *
43999 ATTACTCTGAATTAAACTGTTTTCTTCTTCTCTTGCACTTTAGTTTAATTACTCTGAATTAAACT
1 ATTAC-CAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
44064 CTTTTCTTCTTCTCTTGCTTTTTAGTTTA
65 CTTTTCTTCTTCTCTTGCTTTTTAGTTTA
* * * * *
44093 ATTATCCATAATTAAACTAGCCTCTGTTTACTTTTTCTTTTACTCTTTAGTTTAATTACCAAGAA
1 ATTA-CCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAA
* *
44158 TTAAAATGTTTTCTTCTTCTCTT
58 TTAAACTCTTTTCTTCTTCTCTT
44181 AATTTTTTTA
Statistics
Matches: 406, Mismatches: 45, Indels: 47
0.82 0.09 0.09
Matches are distributed among these distances:
94 162 0.40
95 9 0.02
96 10 0.02
97 6 0.01
98 3 0.01
99 10 0.02
100 21 0.05
101 185 0.46
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (93 bp):
ATTACCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACTC
TTTTCTTCTTCTCTTGCTTTTTAGTTTA
Found at i:44192 original size:141 final size:138
Alignment explanation
Indices: 43617--44180 Score: 456
Period size: 148 Copynumber: 3.9 Consensus size: 138
43607 TGATTACCCA
* * * **
43617 GAATCAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCCAAATTAAACTCTTTTCTT
1 GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACTCTTTTCTT
* * * * * * *
43682 CTTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAACTAGTCTCTGTTTACTTCTTCTTTTACT
66 CTTCTCTTACTCTTTAGTTTAATTACTCAGAATTAAA--A-----TGTTTTCTTCTTCTCTT-CA
* *
43747 CTTTAGTTTAATTAC-CAA
123 CATTA-TTT-ATTACTC-T
* * * *
43765 GAATTAAACTGTTTTCTTCTTCTCTTGCTCTTCAGTTTAATTACCCCGAATTAAACTCCTTTT-T
1 GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACT-CTTTTCT
* * * * *
43829 TCTCCTCTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCTCTGTTTACTTCTTCTTTTAC
65 TCTTCTCTTACTCTTTAGTTTAATTACTCAGAATT-AA--AA----TGTTTTCTTCTTCTCTT-C
* * *
43894 TCTTTAGTTTAATTAC-CAA
122 ACATTA-TTT-ATTACTC-T
43913 GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACTCTTTTCTT
1 GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACTCTTTTCTT
* * * * *
43978 CTTCTCTTGCTTTTTAGTTTAATTACTCTGAATTAAACTGTTTTCTTCTTCTCTTGCACTTTAGT
66 CTTCTCTTACTCTTTAGTTTAATTACTCAGAATTAAAATGTTTTCTTCTTCTCTT-CACATTA-T
44043 TTAATTACTCT
129 TT-ATTACTCT
*
44054 GAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTA-TCCAT-AATTAAACTAGCCTC
1 GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACT-C-TGAATT-AA--A--CTC
* *
44117 TGTTTACTTTTTCTTTTACTCTTTAGTTTAATTAC-CAAGAATTAAAATGTTTTCTTCTTCTCTT
59 T-TTT-CTTCTTCTCTTACTCTTTAGTTTAATTACTC-AGAATTAAAATGTTTTCTTCTTCTCTT
44181 AATTTTTTTA
Statistics
Matches: 371, Mismatches: 29, Indels: 32
0.86 0.07 0.07
Matches are distributed among these distances:
140 1 0.00
141 78 0.21
142 4 0.01
144 1 0.00
145 1 0.00
146 4 0.01
147 11 0.03
148 262 0.71
149 8 0.02
151 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (138 bp):
GAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACTCTGAATTAAACTCTTTTCTT
CTTCTCTTACTCTTTAGTTTAATTACTCAGAATTAAAATGTTTTCTTCTTCTCTTCACATTATTT
ATTACTCT
Found at i:44243 original size:56 final size:56
Alignment explanation
Indices: 44130--44243 Score: 122
Period size: 56 Copynumber: 2.0 Consensus size: 56
44120 TTACTTTTTC
** ** *
44130 TTTTACTCTTTAGTTTAATTACCAAGAATTAAAATGTTTTCTTCTTCTCTTAATTT
1 TTTTACTCTTTAGTTTAATTACCAAGAATTAAAATAATCCCTTATTCTCTTAATTT
* * * * *
44186 TTTTACTAC-TTAGTTTAATTTCCTAGAATTAAACTAATCCCTTATTCTTTTACTTT
1 TTTTACT-CTTTAGTTTAATTACCAAGAATTAAAATAATCCCTTATTCTCTTAATTT
44242 TT
1 TT
44244 AGTTTAAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
56 46 0.98
57 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (56 bp):
TTTTACTCTTTAGTTTAATTACCAAGAATTAAAATAATCCCTTATTCTCTTAATTT
Found at i:49321 original size:64 final size:64
Alignment explanation
Indices: 49247--49375 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
49237 TTTAATGACC
49247 TATATTAATCCCAGTCTCTATATGCATGAATGCACGTGATGCATGGCTTCCGATTAATATAAGT
1 TATATTAATCCCAGTCTCTATATGCATGAATGCACGTGATGCATGGCTTCCGATTAATATAAGT
*
49311 TATATTAATCCTAGTCTCTATATGCATGAATGCACGTGATGCATGGCTTCCGATTAATATAAGT
1 TATATTAATCCCAGTCTCTATATGCATGAATGCACGTGATGCATGGCTTCCGATTAATATAAGT
49375 T
1 T
49376 TTACCGGGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (64 bp):
TATATTAATCCCAGTCTCTATATGCATGAATGCACGTGATGCATGGCTTCCGATTAATATAAGT
Found at i:52067 original size:17 final size:18
Alignment explanation
Indices: 52038--52078 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
52028 TATGTGTGCA
*
52038 TGCTCTGTTTTTTT-CTT
1 TGCTTTGTTTTTTTGCTT
52055 TG-TTTGTTTTTTTGCTT
1 TGCTTTGTTTTTTTGCTT
52072 TGCTTTG
1 TGCTTTG
52079 CTTGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.00, C:0.12, G:0.17, T:0.71
Consensus pattern (18 bp):
TGCTTTGTTTTTTTGCTT
Found at i:54502 original size:39 final size:39
Alignment explanation
Indices: 54250--54576 Score: 302
Period size: 39 Copynumber: 8.4 Consensus size: 39
54240 GAAATGAAGG
* *
54250 CCTAAGCAAGTTTGCTTAAACGAAAATTCTAAACAGGGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
* ** * * *
54289 CCTAAGTAGGTTTAATT-AACGAAAGTTCTAAAGAAAGGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGA-GA
* * * *
54328 CCTAAGCAGGTTTGATTAAACGAAAGTTCTAAAGAAAGGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGA-GA
* *
54368 CCTAAGCAGGTTTGATTAAACG-AAGTTCTAAACA-AGGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGA-GA
** *
54406 CCTAAGCAGGTTCACTTAAACGAAAATTCTAAACCGAGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
**
54445 CCTAAGCAGGTTCACTTAAACGAAAATTCTAAACAGAGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
* * * ** *
54484 CCAAAGCAGGTTTTCTTAAATG-GGATTCTAAACACAGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
* * ** * ** *
54522 CCTAAACAGGTTTGCTTAAATGGCAATTCTGAATGGGGA
1 CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
54561 CCTAAGCAGGTTTGCT
1 CCTAAGCAGGTTTGCT
54577 AGGATAATCA
Statistics
Matches: 248, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
38 70 0.28
39 133 0.54
40 45 0.18
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (39 bp):
CCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAGAGA
Found at i:54523 original size:38 final size:38
Alignment explanation
Indices: 54470--54544 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
54460 TTAAACGAAA
* *
54470 ATTCTAAACAGAGACC-AAAGCAGGTTTTCTTAAATGGG
1 ATTCTAAACACAGACCTAAA-CAGGTTTGCTTAAATGGG
54508 ATTCTAAACACAGACCTAAACAGGTTTGCTTAAATGG
1 ATTCTAAACACAGACCTAAACAGGTTTGCTTAAATGG
54545 CAATTCTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 31 0.91
39 3 0.09
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (38 bp):
ATTCTAAACACAGACCTAAACAGGTTTGCTTAAATGGG
Found at i:54563 original size:116 final size:116
Alignment explanation
Indices: 54253--54572 Score: 279
Period size: 116 Copynumber: 2.7 Consensus size: 116
54243 ATGAAGGCCT
* * * * ** * * *
54253 AAGCAAGTTTGCTTAAACGAAAATTCTAAACAGGGACCTAAGTAGGTTTAATT-AACGAAAGTTC
1 AAGCAGGTTTGATTAAACG-AAGTTCTAAACAAGGACCTAAACAGGTTCACTTAAACGAAAATTC
*** * * * *
54317 TAAAGAAAGGACCTAAGCAGGTTTGATTAAACGAAAGTTCTAAAGAAAGGACCT
65 TAAA-CCGGGACCTAAGCAGG-TTCATTAAACGAAAATTCTAAACAAAGGACCA
*
54371 AAGCAGGTTTGATTAAACGAAGTTCTAAACAAGGACCTAAGCAGGTTCACTTAAACGAAAATTCT
1 AAGCAGGTTTGATTAAACGAAGTTCTAAACAAGGACCTAAACAGGTTCACTTAAACGAAAATTCT
* *
54436 AAACCGAGACCTAAGCAGGTTCACTTAAACGAAAATTCTAAACAGA-GACCA
66 AAACCGGGACCTAAGCAGGTTCA-TTAAACGAAAATTCTAAACAAAGGACCA
** * * ** * **
54487 AAGCAGGTTTTCTTAAATG-GGATTCTAAACACA-GACCTAAACAGGTTTGCTTAAATGGCAATT
1 AAGCAGGTTTGATTAAACGAAG-TTCTAAACA-AGGACCTAAACAGGTTCACTTAAACGAAAATT
* **
54550 CTGAATGGGGACCTAAGCAGGTT
64 CTAAACCGGGACCTAAGCAGGTT
54573 TGCTAGGATA
Statistics
Matches: 167, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
115 1 0.01
116 75 0.45
117 60 0.36
118 31 0.19
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (116 bp):
AAGCAGGTTTGATTAAACGAAGTTCTAAACAAGGACCTAAACAGGTTCACTTAAACGAAAATTCT
AAACCGGGACCTAAGCAGGTTCATTAAACGAAAATTCTAAACAAAGGACCA
Found at i:60024 original size:21 final size:22
Alignment explanation
Indices: 60000--60043 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59990 TGTTTGCTAT
*
60000 CTTCCTCTTCC-TCGACTCAAA
1 CTTCCTCTTCCTTCCACTCAAA
*
60021 CTTCTTCTTCCTTCCACTCAAA
1 CTTCCTCTTCCTTCCACTCAAA
60043 C
1 C
60044 CCTAGATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.18, C:0.43, G:0.02, T:0.36
Consensus pattern (22 bp):
CTTCCTCTTCCTTCCACTCAAA
Found at i:62625 original size:29 final size:29
Alignment explanation
Indices: 62585--62797 Score: 248
Period size: 29 Copynumber: 7.4 Consensus size: 29
62575 ACCCAGAGTA
*
62585 TGCAAAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
*
62614 TGCAAAAGTGACCAAAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
** * * **
62643 AACAAAAATGATCAAACTGCCCCTGGACA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
62672 TTCAAAAATGACCATAATGCCCTTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* *
62701 GGCAAAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* *
62730 TGCAAAAATGACCAAAATGCCCATGGACG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
62759 TGC-AAATTGACCAAAATGCCCCTGGGTA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
*
62787 AGCAAAAATGA
1 TGCAAAAATGA
62798 TCAATTAGAA
Statistics
Matches: 150, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
28 22 0.15
29 128 0.85
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGGATG
Found at i:63162 original size:58 final size:58
Alignment explanation
Indices: 63012--63297 Score: 437
Period size: 58 Copynumber: 4.8 Consensus size: 58
63002 TTAAATATAG
* * * *
63012 ACTCTCAAACAGAGACCTCGACCAGGATTTTAAAACAAGATGAGATTTTGAATTGAAAAAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTG-----AAA
63075 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
*
63133 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
* *
63191 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
* * *
63249 ACTCTCTAACAGAGACCTCGACCAGGATTTTAAAACAAGATAAGATTTT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTT
63298 GTTTTAAACT
Statistics
Matches: 214, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
58 163 0.76
63 51 0.24
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (58 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATGAGATTTTAAATTGAAA
Done.