Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013944.1 Corchorus olitorius cultivar O-4 contig13977, 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: 60512
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:5780 original size:2 final size:2
Alignment explanation
Indices: 5773--5798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5763 CAACATATCA
5773 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5799 TTAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6890 original size:2 final size:2
Alignment explanation
Indices: 6883--6907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6873 TTCCATCCTC
6883 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 T
6908 TCCTCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14562 original size:57 final size:57
Alignment explanation
Indices: 14484--14599 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
14474 TTTATTTCGT
*
14484 AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
* *
14541 AGAATAATTAAGTAGAGATAGGGTGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
14598 AG
1 AG
14600 GAAACGAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAAATAGGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:16900 original size:157 final size:157
Alignment explanation
Indices: 16614--16918 Score: 583
Period size: 157 Copynumber: 1.9 Consensus size: 157
16604 CCACTTTTCT
16614 TTGATGTTCCAAACACTTCTGTTTGCAACTCCCATTGAATCATACTTCTTCTCCCTTCCACTTCA
1 TTGATGTTCCAAACACTTCTGTTTGCAACTCCCATTGAATCATACTTCTTCTCCCTTCCACTTCA
* *
16679 TACTTTCTTTGCTATTTTGGCTGATTCATTAAAACTTTCCATAACCGGCAAACTATCTGAAAATA
66 TACTTTCTTTGCTATTTTGGCTGATTCATTAAAACTTCCCATAACCAGCAAACTATCTGAAAATA
16744 ATATAAAACAAGCAGGGCGGCCTGCGC
131 ATATAAAACAAGCAGGGCGGCCTGCGC
*
16771 TTGATGTTCCAAACACTTCTGTTTGCAACTCCCCTTGAATCATACTTCTTCTCCCTTCCACTTCA
1 TTGATGTTCCAAACACTTCTGTTTGCAACTCCCATTGAATCATACTTCTTCTCCCTTCCACTTCA
16836 TACTTTCTTTGCTATTTTGGCTGATTCATTAAAACTTCCCATAACCAGCAAACTATCTGAAAATA
66 TACTTTCTTTGCTATTTTGGCTGATTCATTAAAACTTCCCATAACCAGCAAACTATCTGAAAATA
16901 ATATAAAACAAGCAGGGC
131 ATATAAAACAAGCAGGGC
16919 AGCATGTGCT
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (157 bp):
TTGATGTTCCAAACACTTCTGTTTGCAACTCCCATTGAATCATACTTCTTCTCCCTTCCACTTCA
TACTTTCTTTGCTATTTTGGCTGATTCATTAAAACTTCCCATAACCAGCAAACTATCTGAAAATA
ATATAAAACAAGCAGGGCGGCCTGCGC
Found at i:17162 original size:42 final size:43
Alignment explanation
Indices: 17111--17204 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
17101 AGTGCATTAC
* *
17111 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
17152 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
17197 CTAATATT
1 CTAATATT
17205 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:18034 original size:2 final size:2
Alignment explanation
Indices: 18021--18056 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
18011 ACTAAAAATA
18021 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
18057 ATTTTCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19530 original size:10 final size:10
Alignment explanation
Indices: 19514--19544 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19504 AACTTCCCTC
19514 CCCTTTCCTT
1 CCCTTTCCTT
*
19524 TCCTTTCCTT
1 CCCTTTCCTT
19534 CCCTTTCCTT
1 CCCTTTCCTT
19544 C
1 C
19545 AATTACTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (10 bp):
CCCTTTCCTT
Found at i:19690 original size:2 final size:2
Alignment explanation
Indices: 19672--19732 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
19662 CAATGAGAAG
* * * *
19672 TA TA CA TA TA TA CA TA TA TA TA TA TG TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19714 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
19733 GCACACAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30790 original size:19 final size:19
Alignment explanation
Indices: 30768--30816 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
30758 TACCATATAT
30768 ATTACCATTTAGAGTTTAC
1 ATTACCATTTAGAGTTTAC
*
30787 ATTACCATTTAGAGTTTAT
1 ATTACCATTTAGAGTTTAC
30806 ATTACCATTTA
1 ATTACCATTTA
30817 ACAATGAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTACCATTTAGAGTTTAC
Found at i:32457 original size:83 final size:83
Alignment explanation
Indices: 32318--32484 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
32308 CTTTTTTTTG
32318 GGAAAATTTTTTTCTCTTACTTGCTAATAAAAACATGGAAAATTATTCAATACACCGTCAGTAGA
1 GGAAAATTTTTTTCTCTTACTTGCTAATAAAAACATGGAAAATTATTCAATACACCGTCAGTAGA
32383 GTTTAGCAGACTACACAT
66 GTTTAGCAGACTACACAT
*
32401 GGAAAATTTTTTTCTCTTACTTGCTAATAAAAACATGGAAAATTATTCAATACACCGTCAGTGGA
1 GGAAAATTTTTTTCTCTTACTTGCTAATAAAAACATGGAAAATTATTCAATACACCGTCAGTAGA
32466 GTTTAGCAGACTACACAT
66 GTTTAGCAGACTACACAT
32484 G
1 G
32485 AAGAGTTTAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (83 bp):
GGAAAATTTTTTTCTCTTACTTGCTAATAAAAACATGGAAAATTATTCAATACACCGTCAGTAGA
GTTTAGCAGACTACACAT
Found at i:37303 original size:15 final size:15
Alignment explanation
Indices: 37283--37324 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
37273 TATTGGCTAG
37283 TTTTCATTTTCAATA
1 TTTTCATTTTCAATA
37298 TTTTCATTTTCAATA
1 TTTTCATTTTCAATA
37313 TTTTCATTTTCA
1 TTTTCATTTTCA
37325 TTGCTATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTCATTTTCAATA
Found at i:40970 original size:19 final size:19
Alignment explanation
Indices: 40946--40982 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40936 GTATAGTATC
40946 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
40965 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
40983 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:41758 original size:2 final size:2
Alignment explanation
Indices: 41751--41800 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
41741 AACACCCTTT
*
41751 TA TA TA TA TA CTA TA GCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41795 TA TA TA
1 TA TA TA
41801 CCATTATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:45543 original size:19 final size:20
Alignment explanation
Indices: 45519--45574 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
45509 GTTTAGTAAG
45519 TGTACAGATGAGATTA-CAC
1 TGTACAGATGAGATTAGCAC
* *
45538 TGTACAGATTAGATTAGGTAC
1 TGTACAGATGAGATTA-GCAC
*
45559 TGTACATATGAGATTA
1 TGTACAGATGAGATTA
45575 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTACAGATGAGATTAGCAC
Found at i:50806 original size:21 final size:21
Alignment explanation
Indices: 50780--50823 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
50770 CTTGTACTCA
50780 ATTACAACAAGAGCCAATTTG
1 ATTACAACAAGAGCCAATTTG
50801 ATTACAACAAGAGCCAATTTG
1 ATTACAACAAGAGCCAATTTG
50822 AT
1 AT
50824 CACTATGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (21 bp):
ATTACAACAAGAGCCAATTTG
Found at i:51176 original size:43 final size:43
Alignment explanation
Indices: 51115--51200 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
51105 GGATTCAAAG
51115 AGTTTTACTGTCAATGATGTTGGCTCCAACATTAATTACAGCT
1 AGTTTTACTGTCAATGATGTTGGCTCCAACATTAATTACAGCT
51158 AGTTTTACTGTCAATGATGTTGGCTCCAACATTAATTACAGCT
1 AGTTTTACTGTCAATGATGTTGGCTCCAACATTAATTACAGCT
51201 TTGATGAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (43 bp):
AGTTTTACTGTCAATGATGTTGGCTCCAACATTAATTACAGCT
Found at i:51528 original size:14 final size:14
Alignment explanation
Indices: 51509--51539 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
51499 CCATATTATA
51509 TATTACGCTTCTTC
1 TATTACGCTTCTTC
51523 TATTACGCTTCTTC
1 TATTACGCTTCTTC
51537 TAT
1 TAT
51540 CATTCATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.06, T:0.52
Consensus pattern (14 bp):
TATTACGCTTCTTC
Found at i:53338 original size:9 final size:9
Alignment explanation
Indices: 53324--53352 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53314 GGCCTGGGTT
53324 CCCAAGTGC
1 CCCAAGTGC
53333 CCCAAGTGC
1 CCCAAGTGC
53342 CCCAAGTGC
1 CCCAAGTGC
53351 CC
1 CC
53353 TCATCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (9 bp):
CCCAAGTGC
Found at i:53695 original size:20 final size:20
Alignment explanation
Indices: 53666--53730 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
53656 TTTTATGAAA
*
53666 TTTGAAAATCACTATAAAAT
1 TTTGATAATCACTATAAAAT
*
53686 TTTGATAATCTCCATATAAAAT
1 TTTGATAATC-AC-TATAAAAT
* *
53708 TTTTATAATTAC-ACTAAAAT
1 TTTGATAATCACTA-TAAAAT
53728 TTT
1 TTT
53731 TATGACGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 18 0.49
21 2 0.05
22 16 0.43
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTGATAATCACTATAAAAT
Found at i:53781 original size:22 final size:22
Alignment explanation
Indices: 53742--53800 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
53732 ATGACGATAC
* **
53742 TATAAAATTTCGAGAACTTCCA
1 TATAAAATTTTGTTAACTTCCA
* *
53764 TATGAAATTTTGTTAACTTCCC
1 TATAAAATTTTGTTAACTTCCA
53786 TATAAAATTTTGTTA
1 TATAAAATTTTGTTA
53801 CACTCCGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (22 bp):
TATAAAATTTTGTTAACTTCCA
Found at i:53862 original size:22 final size:23
Alignment explanation
Indices: 53818--53865 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
53808 GATCCCTATA
53818 AAAATTTTAATAACCACCAAATG
1 AAAATTTTAATAACCACCAAATG
* * *
53841 AAAA-TTTGATAACCTCCCAATG
1 AAAATTTTAATAACCACCAAATG
53863 AAA
1 AAA
53866 TGTTGGTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (23 bp):
AAAATTTTAATAACCACCAAATG
Found at i:53998 original size:44 final size:45
Alignment explanation
Indices: 53927--54071 Score: 128
Period size: 41 Copynumber: 3.4 Consensus size: 45
53917 GTAATCACAT
53927 TATGAAATTTTGAT-AACCATACCATAAAATTGTGAT-ACCT-CA
1 TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
* * *
53969 CTATGAAATTTTTATAAACC-TTCCTATAAAATTTTGATAACCTCCA
1 -TATGAAATTTTGATAAACCATACC-ATAAAATTGTGATAACCTCCA
* * * * *
54015 TTTGAAATTTTGAT-AACC-T--CATGAAATTTTGAAAACCACC-
1 TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
54055 TCATGAAATTTTGATAA
1 T-ATGAAATTTTGATAA
54072 CATCCCTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
40 1 0.01
41 29 0.33
42 2 0.02
43 16 0.18
44 21 0.24
45 16 0.18
46 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (45 bp):
TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
Found at i:54010 original size:22 final size:21
Alignment explanation
Indices: 53927--54176 Score: 190
Period size: 22 Copynumber: 11.8 Consensus size: 21
53917 GTAATCACAT
53927 TATGAAATTTTGATAACCATACC
1 TATGAAATTTTGATAACC-T-CC
* *
53950 -ATAAAATTGTGAT-ACCTCAC
1 TATGAAATTTTGATAACCTC-C
*
53970 TATGAAATTTTTATAAACCTTCC
1 TATGAAATTTTGAT-AACC-TCC
*
53993 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
*
54014 ATTTGAAATTTTGATAACCT-C
1 -TATGAAATTTTGATAACCTCC
* *
54035 -ATGAAATTTTGAAAACCACC
1 TATGAAATTTTGATAACCTCC
*
54055 TCATGAAATTTTGATAACATCCC
1 T-ATGAAATTTTGATAACCT-CC
*
54078 TAT-AAATTTTTTATAACCT-C
1 TATGAAA-TTTTGATAACCTCC
** * *
54098 -AAAAAATTTTGTTAACCTCA
1 TATGAAATTTTGATAACCTCC
***
54118 TATGAAATTTTGATAAGAACAC
1 TATGAAATTTTGATAACCTC-C
* *
54140 TATTAAATTTTGATAACCCCC
1 TATGAAATTTTGATAACCTCC
*
54161 AATGAAATTTTGATAA
1 TATGAAATTTTGATAA
54177 TTAATTACAC
Statistics
Matches: 178, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
19 27 0.15
20 7 0.04
21 48 0.27
22 75 0.42
23 19 0.11
24 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:54094 original size:63 final size:62
Alignment explanation
Indices: 53927--54173 Score: 214
Period size: 63 Copynumber: 3.9 Consensus size: 62
53917 GTAATCACAT
* * *
53927 TATGAAATTTTGATAACCATACC-ATAAAATTGTGAT-ACCTCACTATGAAATTTTTATAAACCT
1 TATGAAATTTTGATAA-CATCCCTAT-AAATTTTGATAACCTCA--ATGAAATTTTGA-AAACC-
53990 TCC
60 TCC
* * * * *
53993 TATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTC-ATGAAATTTTGAAAACCACC
1 TATGAAATTTTGATAACATCCCTAT-AAATTTTGATAACCTCAATGAAATTTTGAAAACCTCC
* * ** *
54055 TCATGAAATTTTGATAACATCCCTATAAATTTTTTATAACCTCAA-AAAATTTTGTTAACCTCA
1 T-ATGAAATTTTGATAACATCCCTATAAA-TTTTGATAACCTCAATGAAATTTTGAAAACCTCC
* * * *
54118 TATGAAATTTTGATAAGAACACTATTAAATTTTGATAACCCCCAATGAAATTTTGA
1 TATGAAATTTTGATAACATCCCTA-TAAATTTTGATAA-CCTCAATGAAATTTTGA
54174 TAATTAATTA
Statistics
Matches: 147, Mismatches: 26, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
62 34 0.23
63 60 0.41
64 20 0.14
65 3 0.02
66 25 0.17
67 5 0.03
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (62 bp):
TATGAAATTTTGATAACATCCCTATAAATTTTGATAACCTCAATGAAATTTTGAAAACCTCC
Found at i:54156 original size:62 final size:62
Alignment explanation
Indices: 54019--54157 Score: 163
Period size: 62 Copynumber: 2.2 Consensus size: 62
54009 CCTCCATTTG
** * * *
54019 AAATTTTGATAACCTCATGAAATTTTGAAAACCACCTCATGAAATTTTGATAACATCCCTAT
1 AAATTTTGATAACCTCAAAAAATTTTGAAAACCACATCATGAAATTTTGATAACAACACTAT
* ** * *
54081 AAATTTTTTATAACCTCAAAAAATTTTGTTAACCTCAT-ATGAAATTTTGATAAGAACACTATT
1 AAA-TTTTGATAACCTCAAAAAATTTTGAAAACCACATCATGAAATTTTGATAACAACACTA-T
54144 AAATTTTGATAACC
1 AAATTTTGATAACC
54158 CCCAATGAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
62 33 0.52
63 31 0.48
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (62 bp):
AAATTTTGATAACCTCAAAAAATTTTGAAAACCACATCATGAAATTTTGATAACAACACTAT
Found at i:54531 original size:22 final size:22
Alignment explanation
Indices: 54491--54549 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
54481 CACTCTATCT
*
54491 CACTATGTAATTTCTATAAGC-A
1 CACTATGAAATTT-TATAAGCTA
* *
54513 CACTATGAAATTTTGATAATCTT
1 CACTATGAAATTTT-ATAAGCTA
54536 C-CTATGAAATTTTA
1 CACTATGAAATTTTA
54550 ATAACCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 2 0.06
22 29 0.91
23 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
CACTATGAAATTTTATAAGCTA
Found at i:54642 original size:22 final size:22
Alignment explanation
Indices: 54515--54885 Score: 188
Period size: 22 Copynumber: 16.8 Consensus size: 22
54505 TATAAGCACA
* *
54515 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAACCTCC
*
54537 CTATGAAATTTTAATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* * *
54559 ATA-CAAGATTTCGATAA--TCGC
1 CTATGAA-ATTTTGATAACCTC-C
* ***
54580 ATATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAACCTCC
* *
54602 GTATGAAATTCT-AGTAACCTCC
1 CTATGAAATTTTGA-TAACCTCC
* *
54624 CTGTGAAATTTTGACAACCTTCC
1 CTATGAAATTTTGATAACC-TCC
*
54647 C-ATG-AATTTCGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* *
54667 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAACCTCC
* *
54689 ATATGAAATTTTGATAACATCC
1 CTATGAAATTTTGATAACCTCC
* *
54711 TTATGAAATTTTATTTTAATAACCTCC
1 CTATG-AA----ATTTTGATAACCTCC
* *
54738 TTATGAAATTTTGATAACATCC
1 CTATGAAATTTTGATAACCTCC
* *
54760 C-ATGGAATTTTGATAA-CTACA
1 CTATGAAATTTTGATAACCT-CC
* * * ** *
54781 CTATAAAATTTTAACATGCTAC
1 CTATGAAATTTTGATAACCTCC
* * *
54803 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTCC
* * *
54825 CTAT-AAGATTTTGAGAACCACA
1 CTATGAA-ATTTTGATAACCTCC
* * *
54847 CTATAAAATTTT-AGTAACCACA
1 CTATGAAATTTTGA-TAACCTCC
*
54869 CAATG-AATTTTGATAAC
1 CTATGAAATTTTGATAAC
54886 TTTCAAAATT
Statistics
Matches: 267, Mismatches: 60, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
20 6 0.02
21 59 0.22
22 171 0.64
23 11 0.04
26 2 0.01
27 18 0.07
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:54677 original size:43 final size:44
Alignment explanation
Indices: 54616--54722 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 44
54606 GAAATTCTAG
* * *
54616 TAACCTCCCTGTGAAATTTTGACAACCT-TCCCATG-AATTTCGA
1 TAACCTCCTTATGAAATTTTGACAACCTCT-ACATGAAATTTCGA
* * *
54659 TAACCTCCTTATGAAATTTTGATAACCTCTATATGAAATTTTGA
1 TAACCTCCTTATGAAATTTTGACAACCTCTACATGAAATTTCGA
*
54703 TAACATCCTTATGAAATTTT
1 TAACCTCCTTATGAAATTTT
54723 ATTTTAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
43 28 0.51
44 27 0.49
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (44 bp):
TAACCTCCTTATGAAATTTTGACAACCTCTACATGAAATTTCGA
Found at i:54718 original size:87 final size:85
Alignment explanation
Indices: 54516--54723 Score: 201
Period size: 87 Copynumber: 2.4 Consensus size: 85
54506 ATAAGCACAC
* *
54516 TATGAAATTTTGATAATCTTCCTATGAAATTTTAATAACCTCCATACAAGATTTCGATAATCGCA
1 TATGAAATTTTGATAA-CATCCTATGAAATTTTAACAACCTCCATA-AAGATTTCGATAATCGCA
54581 TATGAAATTTTGATAACCAGAG
64 TATGAAATTTTGATAACCAGAG
* * * * *
54603 TATGAAATTCT-AGTAACCTCCCTGTGAAATTTTGACAACCTTCCCAT-GA-ATTTCGATAACCT
1 TATGAAATTTTGA-TAACAT-CCTATGAAATTTTAACAACC-T-CCATAAAGATTTCGATAA--T
* **
54665 C-CTTATGAAATTTTGATAACCTCTA-
60 CGCATATGAAATTTTGATAACC-AGAG
54690 TATGAAATTTTGATAACATCCTTATGAAATTTTA
1 TATGAAATTTTGATAACATCC-TATGAAATTTTA
54724 TTTTAATAAC
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
86 15 0.15
87 75 0.76
88 5 0.05
89 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (85 bp):
TATGAAATTTTGATAACATCCTATGAAATTTTAACAACCTCCATAAAGATTTCGATAATCGCATA
TGAAATTTTGATAACCAGAG
Found at i:54738 original size:27 final size:27
Alignment explanation
Indices: 54696--54749 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
54686 TCTATATGAA
*
54696 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
*
54723 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
54750 GATAACATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTTTAATAACATCCTTATGAAATTTT
Found at i:60025 original size:39 final size:40
Alignment explanation
Indices: 59969--60049 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
59959 TTTAATTCCT
59969 ATGTAATATATATAATAACAAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACAAAAATACTTACATTAATTAA
* **
60009 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACAAAAATACTTACATTAATTAA
60048 AT
1 AT
60050 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACAAAAATACTTACATTAATTAA
Found at i:60076 original size:25 final size:24
Alignment explanation
Indices: 60040--60086 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
60030 AATACTTACA
60040 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
60064 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
60087 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.