Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007044.1 Corchorus capsularis cultivar CVL-1 contig07065, 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: 52591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1887 original size:33 final size:33
Alignment explanation
Indices: 1821--1928 Score: 123
Period size: 33 Copynumber: 3.4 Consensus size: 33
1811 TCTCGTCACA
* * *
1821 CAAAACAGATTTATTTTCAATGC---CATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
*
1851 CAAAACAGGATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
* ** *
1884 CAAAACAAAATTATTTTTAATGCTATGTTCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1917 CAAAACAGAATT
1 CAAAACAGAATT
1929 GTTTTCATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 20 0.31
33 45 0.69
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (33 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAAC
Found at i:2029 original size:33 final size:33
Alignment explanation
Indices: 1992--2079 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
1982 CTAGAACAGA
* *
1992 TTTAGTGTCATTACAAACAACATTCAAATTAGG
1 TTTAGTATCATTACAAACAACACTCAAATTAGG
*
2025 TTTAGTATCATTGCAAACAACACTCAAATTAGG
1 TTTAGTATCATTACAAACAACACTCAAATTAGG
* **
2058 TTTAGTATTATCGCAAACAACA
1 TTTAGTATCATTACAAACAACA
2080 TCTAAAACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
TTTAGTATCATTACAAACAACACTCAAATTAGG
Found at i:3703 original size:9 final size:8
Alignment explanation
Indices: 3669--3702 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3659 GAATCGGCTA
3669 TGAATTTT
1 TGAATTTT
*
3677 TGAAGTTTC
1 TGAA-TTTT
3686 TGAATTTT
1 TGAATTTT
3694 TGAATTTT
1 TGAATTTT
3702 T
1 T
3703 TCAAGAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:4667 original size:33 final size:34
Alignment explanation
Indices: 4592--4736 Score: 192
Period size: 33 Copynumber: 4.4 Consensus size: 34
4582 AGACAAAGGA
* *
4592 TCGCGTGGCCGGTTG-TGGCCGGGCATGGCCGA-G
1 TCGCGTGGCCGGTTGATGGCCGGACATGTCC-ATG
** *
4625 TCGTTTGGCCGGTTG-TAGCCGGACATGTCCATG
1 TCGCGTGGCCGGTTGATGGCCGGACATGTCCATG
4658 TCGCGTGGCCGG-TGATGGCCGGACATGTCCATG
1 TCGCGTGGCCGGTTGATGGCCGGACATGTCCATG
*
4691 TCGCGTGGTCGG-TGATGGCCGGACATGTCCATG
1 TCGCGTGGCCGGTTGATGGCCGGACATGTCCATG
4724 TCGCGTGGCCGGT
1 TCGCGTGGCCGGT
4737 CTTGTGGCCG
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
32 3 0.03
33 96 0.97
ACGTcount: A:0.10, C:0.26, G:0.41, T:0.23
Consensus pattern (34 bp):
TCGCGTGGCCGGTTGATGGCCGGACATGTCCATG
Found at i:5684 original size:53 final size:54
Alignment explanation
Indices: 5622--5726 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 54
5612 GATCATTTAA
*
5622 AGTTTTCAGAGATTTAAGCTGATCTGAAGATGA-CCAGTGTGGTCTTTCATAAG
1 AGTTTTCAGAGATCTAAGCTGATCTGAAGATGACCCAGTGTGGTCTTTCATAAG
*
5675 AGTTTTCAGAGATCTAAGCTGATCTTAAGATGACCCAGTGTGGTCTTTCATA
1 AGTTTTCAGAGATCTAAGCTGATCTGAAGATGACCCAGTGTGGTCTTTCATA
5727 GAAGTCTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 31 0.63
54 18 0.37
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (54 bp):
AGTTTTCAGAGATCTAAGCTGATCTGAAGATGACCCAGTGTGGTCTTTCATAAG
Found at i:5817 original size:107 final size:107
Alignment explanation
Indices: 5706--6235 Score: 547
Period size: 107 Copynumber: 4.9 Consensus size: 107
5696 ATCTTAAGAT
* * *
5706 GACCCAGTGTGGTCTTTC-ATAGAAGTCTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTGC
1 GACCCAGTGCGGTCATTCTA-AGAAGTTTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTGC
* * * * *
5770 GGTCACTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCTAGAT
65 GATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCAGAA
* * * *
5813 GACCCAGTGTC-GTCTTTC-ATAGAAGATTTCAATGGTCAGAGTTGATTCCTAGAAGATCCAGTA
1 GACCCAGTG-CGGTCATTCTA-AGAAGTTTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTG
* *
5876 CGGTCATTCCAAGAAGTTTTCAATGCTCAGAGTTGA-CCCAGAA
64 CGATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCAGAA
* *
5919 GATCTC-GTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCC-AGAAGATCCTGTGC
1 GA-CCCAGTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTGC
** ** *
5982 GATTGTTTTAAGAAATTTTCAATGGTCAGAGTTGATCACCAGAA
65 GATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC-CCAGAA
* * *
6026 GATCCAGTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGATTCAGTGCG
1 GACCCAGTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTGCG
* * *
6091 ATCATTCCAAGATGTTTTCAATGGTCAGAGTTGATCCCCATAT
66 ATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGAT-CCCAGAA
* * ** * * * * *
6134 GATCTAGTGCGACCATTCCAAAGAAGTTTTTAGA-GATCAGAGTTGGTCCCTAGATGATCCAGTG
1 GACCCAGTGCGGTCATT-CTAAGAAGTTTTCA-ATGGTCAGAGTTGATCCCTAGAAGATCCAGTG
* * * *
6198 CGGTCACTT-CAAAAAGCTTTCAGAT-ATCAGAGTTGATC
64 CGATCA-TTCCAAGAAGTTTTCA-ATGGTCAGAGTTGATC
6236 TCATTCCAAG
Statistics
Matches: 360, Mismatches: 50, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
105 41 0.11
106 45 0.12
107 144 0.40
108 61 0.17
109 64 0.18
110 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (107 bp):
GACCCAGTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCTAGAAGATCCAGTGCG
ATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCAGAA
Found at i:5951 original size:159 final size:160
Alignment explanation
Indices: 5726--6128 Score: 559
Period size: 159 Copynumber: 2.5 Consensus size: 160
5716 GGTCTTTCAT
* *
5726 AGAAGTCTTCAATGGTCAGAGTTGATCCCTAGAAGATC-CAGTGCGGTCACTCTAAGAAGTTTTC
1 AGAAGTTTTCAATGGTCAGAGTTGATCCC-AGAAGATCTCAGTGCGGTCATTCTAAGAAGTTTTC
* *
5790 AATGGTCAGAGTTGATCCTAGATGACCCAGTGTCG-TCTTTCATAGAAGA-TTTCAATGGTCAGA
65 AATGGTCAGAGTTGATCCCAGAAGACCCAGTG-CGATCTTTCA-AGAA-ATTTTCAATGGTCAGA
*
5853 GTTGATTC-CTAGAAGATCCAGTACGGTCATTCCA
127 GTTGA-TCACCAGAAGATCCAGTACGGTCATTCCA
*
5887 AGAAGTTTTCAATGCTCAGAGTTGA-CCCAGAAGATCTC-GTGCGGTCATTCTAAGAAGTTTTCA
1 AGAAGTTTTCAATGGTCAGAGTTGATCCCAGAAGATCTCAGTGCGGTCATTCTAAGAAGTTTTCA
* * * *
5950 ATGGTCAGAGTTGATCCCAGAAGATCCTGTGCGATTGTTTTAAGAAATTTTCAATGGTCAGAGTT
66 ATGGTCAGAGTTGATCCCAGAAGACCCAGTGCGA-TCTTTCAAGAAATTTTCAATGGTCAGAGTT
* *
6015 GATCACCAGAAGATCCAGTGCGGTCATTCTA
130 GATCACCAGAAGATCCAGTACGGTCATTCCA
* * *
6046 AGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT-TCAGTGCGATCATTCCAAGATGTTTTC
1 AGAAGTTTTCAATGGTCAGAGTTGAT-CCCAGAAGATCTCAGTGCGGTCATTCTAAGAAGTTTTC
6110 AATGGTCAGAGTTGATCCC
65 AATGGTCAGAGTTGATCCC
6129 CATATGATCT
Statistics
Matches: 218, Mismatches: 16, Indels: 16
0.87 0.06 0.06
Matches are distributed among these distances:
158 5 0.02
159 129 0.59
160 11 0.05
161 73 0.33
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (160 bp):
AGAAGTTTTCAATGGTCAGAGTTGATCCCAGAAGATCTCAGTGCGGTCATTCTAAGAAGTTTTCA
ATGGTCAGAGTTGATCCCAGAAGACCCAGTGCGATCTTTCAAGAAATTTTCAATGGTCAGAGTTG
ATCACCAGAAGATCCAGTACGGTCATTCCA
Found at i:6128 original size:54 final size:54
Alignment explanation
Indices: 5709--6235 Score: 536
Period size: 54 Copynumber: 9.8 Consensus size: 54
5699 TTAAGATGAC
* * * *
5709 CCAGTGTGGTC-TTTCATAGAAGTCTTCAATGGTCAGAGTTGATCCCTAGAAGAT
1 CCAGTGCGGTCATTCCA-AGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* * * * *
5763 CCAGTGCGGTCACTCTAAGAAGTTTTCAATGGTCAGAGTTGAT-CCTAGATGAC
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* * * *
5816 CCAGTGTC-GTC-TTTCATAGAAGATTTCAATGGTCAGAGTTGATTCCTAGAAGAT
1 CCAGTG-CGGTCATTCCA-AGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* *
5870 CCAGTACGGTCATTCCAAGAAGTTTTCAATGCTCAGAGTTGA--CCCAGAAGAT
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
*
5922 CTC-GTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGAT-CCCAGAAGAT
1 C-CAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* * ** ** * *
5975 CCTGTGCGATTGTTTTAAGAAATTTTCAATGGTCAGAGTTGATCACCAGAAGAT
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
*
6029 CCAGTGCGGTCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* * * * *
6083 TCAGTGCGATCATTCCAAGATGTTTTCAATGGTCAGAGTTGATCCCCATATGAT
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
* ** * * * * *
6137 CTAGTGCGACCATTCCAAAGAAGTTTTTAGA-GATCAGAGTTGGTCCCTAGATGAT
1 CCAGTGCGGTCATTCC-AAGAAGTTTTCA-ATGGTCAGAGTTGATCCCCAGAAGAT
* * *
6192 CCAGTGCGGTCACTT-CAAAAAGCTTTCAGAT-ATCAGAGTTGATC
1 CCAGTGCGGTCA-TTCCAAGAAGTTTTCA-ATGGTCAGAGTTGATC
6236 TCATTCCAAG
Statistics
Matches: 403, Mismatches: 56, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
52 49 0.12
53 90 0.22
54 215 0.53
55 46 0.11
56 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (54 bp):
CCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAGAAGAT
Found at i:7634 original size:13 final size:14
Alignment explanation
Indices: 7608--7638 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
7598 AAAAGTTTTT
7608 TTTTATTAAAGTTA
1 TTTTATTAAAGTTA
7622 TTTTATT-AAGTTA
1 TTTTATTAAAGTTA
7635 TTTT
1 TTTT
7639 CTTTATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTATTAAAGTTA
Found at i:7750 original size:15 final size:14
Alignment explanation
Indices: 7685--7762 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
7675 TTAGTTTTTT
7685 TTTATTTACTTACTTA
1 TTTATTTA-TTAC-TA
* *
7701 TCTATTTGTTA-TCA
1 TTTATTTATTACT-A
*
7715 -TTATTTATTATTA
1 TTTATTTATTACTA
*
7728 TCTATTTATCTACTA
1 TTTATTTAT-TACTA
7743 TTTATTTATTTACTA
1 TTTATTTA-TTACTA
7758 TTTAT
1 TTTAT
7763 CCTTTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
13 10 0.20
14 9 0.18
15 24 0.48
16 7 0.14
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (14 bp):
TTTATTTATTACTA
Found at i:7769 original size:15 final size:15
Alignment explanation
Indices: 7738--7796 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
7728 TCTATTTATC
*
7738 TACTATTTATTTATT
1 TACTATTTATCTATT
*
7753 TACTATTTATC-CTT
1 TACTATTTATCTATT
7767 T--TATTTATCTATT
1 TACTATTTATCTATT
*
7780 CAGCTA-TTATCTATT
1 TA-CTATTTATCTATT
7795 TA
1 TA
7797 TTTATCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 8 0.23
13 2 0.06
14 3 0.09
15 20 0.57
16 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (15 bp):
TACTATTTATCTATT
Found at i:7779 original size:27 final size:27
Alignment explanation
Indices: 7715--7851 Score: 83
Period size: 27 Copynumber: 5.2 Consensus size: 27
7705 TTTGTTATCA
*
7715 TTATTTAT-TA-TTATCTATTTATCTA-
1 TTATTTATCTATTTAGCTA-TTATCTAT
* *
7740 CTATTTATTTATTTA-CTATTTATCCT-T
1 TTATTTATCTATTTAGCTA-TTAT-CTAT
*
7767 TTATTTATCTATTCAGCTATTATCTAT
1 TTATTTATCTATTTAGCTATTATCTAT
* * *
7794 TTATTTATCTTTTTA--T-TTACCTAC
1 TTATTTATCTATTTAGCTATTATCTAT
* * * *
7818 CTAATTATTCTATTAAGCTATTATTTAT
1 TTATTTA-TCTATTTAGCTATTATCTAT
7846 TTATTT
1 TTATTT
7852 TTTTTACCTA
Statistics
Matches: 85, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
24 11 0.13
25 14 0.16
26 12 0.14
27 36 0.42
28 12 0.14
ACGTcount: A:0.26, C:0.12, G:0.01, T:0.61
Consensus pattern (27 bp):
TTATTTATCTATTTAGCTATTATCTAT
Found at i:8734 original size:33 final size:33
Alignment explanation
Indices: 8691--8765 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
8681 ACAAAGTTTA
* *
8691 TTTATCATGCATGATCTCCTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
* *
8724 TTTATTATGCATAATCTCCTCCTTTTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
8757 TTTTATCAT
1 -TTTATCAT
8766 TAAAAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 29 0.81
34 7 0.19
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:9829 original size:13 final size:13
Alignment explanation
Indices: 9811--9835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9801 GAAGGGAAAT
9811 GAAGGAAAAAGGA
1 GAAGGAAAAAGGA
9824 GAAGGAAAAAGG
1 GAAGGAAAAAGG
9836 TGAACAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
GAAGGAAAAAGGA
Found at i:10137 original size:25 final size:25
Alignment explanation
Indices: 10109--10161 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
10099 AAAAAATGAA
*
10109 TTCCTTATGTCCTGTATGTTTTATC
1 TTCCTTATGTCCTATATGTTTTATC
*
10134 TTCCTTATGTTCTATATGTTTTATC
1 TTCCTTATGTCCTATATGTTTTATC
10159 TTC
1 TTC
10162 TTTTGAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.13, C:0.19, G:0.09, T:0.58
Consensus pattern (25 bp):
TTCCTTATGTCCTATATGTTTTATC
Found at i:18353 original size:6 final size:6
Alignment explanation
Indices: 18295--18338 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
18285 CACTAAAACG
18295 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
18339 CGAAAAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:27541 original size:13 final size:15
Alignment explanation
Indices: 27512--27544 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
27502 CTAACCCTTA
27512 ATTTTTCTTTGTTTC
1 ATTTTTCTTTGTTTC
27527 ATTTTTC-TT-TTTC
1 ATTTTTCTTTGTTTC
27540 ATTTT
1 ATTTT
27545 AGGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (15 bp):
ATTTTTCTTTGTTTC
Found at i:38496 original size:3 final size:3
Alignment explanation
Indices: 38488--38513 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38478 AGGGTTGAGG
38488 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
38514 TAAAGGCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39375 original size:35 final size:35
Alignment explanation
Indices: 39287--40293 Score: 922
Period size: 35 Copynumber: 28.7 Consensus size: 35
39277 AGTAATAAGT
*
39287 AACTTAATTCAGGGTAATTAAGCAAGTT-AGTAAGTC
1 AACTTAATTCAGGGTAATTAAGTAA-TTCAGTAA-TC
* * *
39323 AGTAACTTAATTCAGGGTAATTAAGAAATTCAGTTATT
1 ---AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
39361 AATTTAATTCAGGGTAATTAAGTAATTTAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * *
39396 AACTTAATTCAGGGTAATTAAGTAAGTTATTAAGTTAGTA
1 AACTTAATTCAGGGTAATTAAGT-A---ATTCAG-TAATC
* *
39436 AGTAGCTTAATTCAGGGTAATTAAGTAAATT-AGTTAGC
1 A--A-CTTAATTCAGGGTAATTAAGT-AATTCAGTAATC
* *
39474 AACTTAATTCAGGGCAATTAAGTAAGTCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGT-AATC
* *
39509 AGCTTAATTCAGGGTAATTAAGTAAGTC---AA-C
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * * *
39540 AACTTAATTCAAGGTAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTA-ATC
* * * *
39574 AACTTAATTCAGGGTAATTAAGAAATTCAATTATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
** *
39609 ATTTTAATTCAGGGTAATTAAGTAATTTAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
39644 AACTTAATTCAGGGTAATTAAGTAAGTTATTAAGTCAGTAAGT-
1 AACTTAATTCAGGGTAATTAAGT-A---A-T---TCAGTAA-TC
* * * *
39687 AGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
39722 AACTTAATTCAGGGCAATTAAGTAAGTCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGT-AATC
* *
39757 AGCTTAATTCAGGGTAATTAAGTAAGTCAG----C
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * *
39788 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTA-ATC
39822 AACTTAATTCAGGGTAATTAAG----TCAGTAAGT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAA-TC
* * * *
39853 AGCTTAATTTAGGGTAATTAAGTAAAGTCAGTTAGT-
1 AACTTAATTCAGGGTAATTAAGT-AATTCAG-TAATC
* * * **
39889 AGCTTAGTTCAGGGAAATTAAGTAAGGCAG---T-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
39920 AACTTAATTCAGGGTAATTAAGTAATTCAATAGTC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
39955 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
39990 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
*
40025 AACTTAATTCAGGGTAAATAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
40060 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * *
40095 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAGTC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
40130 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
40165 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * * *
40200 AACTTTAATTCGGGGTAATTAAGTGAGTT-AATGAGT-
1 AAC-TTAATTCAGGGTAATTAAGT-AATTCAGT-AATC
* *
40236 AACTTAATTCAGGGTAATTAAGTAGTTCAATAAGT-
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAA-TC
40271 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
40294 TTAGTAAGAA
Statistics
Matches: 823, Mismatches: 92, Indels: 110
0.80 0.09 0.11
Matches are distributed among these distances:
30 2 0.00
31 102 0.12
33 1 0.00
34 56 0.07
35 499 0.61
36 54 0.07
37 5 0.01
38 5 0.01
39 37 0.04
40 8 0.01
42 2 0.00
43 51 0.06
44 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
Found at i:39762 original size:248 final size:242
Alignment explanation
Indices: 39287--40293 Score: 1114
Period size: 248 Copynumber: 4.1 Consensus size: 242
39277 AGTAATAAGT
* *
39287 AACTTAATTCAGGGTAATTAAGCAAGTTAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGAAAT
1 AACTTAATTCAGGGTAATTAAGTAAG-TAAT-AG---GTAACTTAATTCAGGGTAATTAAGAAAT
* * * *
39352 TCAGTTATTAATTTAATTCAGGGTAATTAAGTAATTTAGTAATCAACTTAATTCAGGGTAATTAA
61 TCAGTAATTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAA
* *
39417 GTAAGTTATTAAGTTAGTAAGTAGCTTAATTCAGGGTAATTAAGTAAATTAGTTAGCAACTTAAT
126 GTAAG--A-T--GTCAGTAA-TAGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGCAACTTAAT
*
39482 TCAGGGCAATTAAGTAAGTCAGTGAATAGCTTAATTCAGGGTAATTAAGTAAGTCAAC
185 TCAGGGCAATTAAGTAAGTCAGTGAATAACTTAATTCAGGGTAATTAAGTAAGTCAAC
* *
39540 AACTTAATTCAAGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGAAATTCAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGAAATTCAGT
* ** * *
39605 TATTATTTTAATTCAGGGTAATTAAGTAATTTAGTAATCAACTTAATTCAGGGTAATTAAGTAAG
66 AATTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAG
39670 TTATTAAGTCAGTAAGTAGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGCAACTTAATTCAGG
131 --A-T--GTCAGTAA-TAGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGCAACTTAATTCAGG
* *
39735 GCAATTAAGTAAGTCAGTGAATAGCTTAATTCAGGGTAATTAAGTAAGTCAGC
190 GCAATTAAGTAAGTCAGTGAATAACTTAATTCAGGGTAATTAAGTAAGTCAAC
39788 AACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAG----TCAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGAAATTCAGT
* * * * * * *
39849 AAGTAGCTTAATTTAGGGTAATTAAGTAAAGTCAGTTAGT-AGCTTAGTTCAGGGAAATTAAGTA
66 AATTAACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAATCAACTTAATTCAGGGTAATTAAGTA
* * *
39913 AG--G-CAGT-A-A-CTTAATTCAGGGTAATTAAGTAATTCA-ATAGTCAACTTAATTCAGGGTA
129 AGATGTCAGTAATAGCTTAATTCAGGGTAATTAAGTAAATCAGTTAG-CAACTTAATTCAGGGCA
* *
39971 ATTAAGTAATTCAGT-AATCAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
193 ATTAAGTAAGTCAGTGAAT-AACTTAATTCAGGGTAATTAAGTAAGTC---AA-C
* * * * ** *
40025 AACTTAATTCAGGGTAAATAAGTAATTCAGTA-ATCAACTTAATTCAGGGTAATTAAGTGAGTCA
1 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-AACTTAATTCAGGGTAATTAAGAAATTCA
* * *
40089 GTAATCAACTTAATTCAGGGTAATTAAGTGAGTCAGTAGTCAACTTAATTCAGGGTAATTAAGT-
64 GTAATTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTA
* * * * * * *
40153 A-AT-TCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTTAATTCGGGGT
129 AGATGTCAGTAAT-AGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGCAAC-TTAATTCAGGGC
* * * * *
40216 AATTAAGTGAGTTAATGAGTAACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT
192 AATTAAGTAAGTCAGTGAATAACTTAATTCAGGGTAATTAAGTAAG-TC---AA-C
40271 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
40294 TTAGTAAGAA
Statistics
Matches: 673, Mismatches: 55, Indels: 59
0.86 0.07 0.07
Matches are distributed among these distances:
232 6 0.01
233 82 0.12
234 1 0.00
236 2 0.00
237 31 0.05
238 26 0.04
240 5 0.01
241 30 0.04
242 29 0.04
244 27 0.04
245 59 0.09
246 78 0.12
247 2 0.00
248 266 0.40
251 2 0.00
252 3 0.00
253 24 0.04
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (242 bp):
AACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGAAATTCAGT
AATTAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAG
ATGTCAGTAATAGCTTAATTCAGGGTAATTAAGTAAATCAGTTAGCAACTTAATTCAGGGCAATT
AAGTAAGTCAGTGAATAACTTAATTCAGGGTAATTAAGTAAGTCAAC
Found at i:40136 original size:21 final size:21
Alignment explanation
Indices: 40077--40136 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
40067 TTCAGGGTAA
*
40077 TTAAGTGAGTCAGTAATCAAC
1 TTAAGTGAGTCAGTAGTCAAC
*
40098 TTAA-T---TCAG-GGT-AA-
1 TTAAGTGAGTCAGTAGTCAAC
40112 TTAAGTGAGTCAGTAGTCAAC
1 TTAAGTGAGTCAGTAGTCAAC
40133 TTAA
1 TTAA
40137 TTCAGGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 14
0.63 0.07 0.30
Matches are distributed among these distances:
14 4 0.14
15 3 0.10
16 1 0.03
17 4 0.14
18 4 0.14
19 2 0.07
20 3 0.10
21 8 0.28
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (21 bp):
TTAAGTGAGTCAGTAGTCAAC
Found at i:41550 original size:10 final size:10
Alignment explanation
Indices: 41535--41560 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41525 AGTTTCTGCC
41535 AAATTCCAGA
1 AAATTCCAGA
41545 AAATTCCAGA
1 AAATTCCAGA
41555 AAATTC
1 AAATTC
41561 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:42509 original size:6 final size:6
Alignment explanation
Indices: 42498--42526 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42488 ATTTTGCTTC
42498 AGATTT AGATTT AGATTT AGATTT AGATT
1 AGATTT AGATTT AGATTT AGATTT AGATT
42527 GCTTTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
AGATTT
Found at i:43266 original size:10 final size:10
Alignment explanation
Indices: 43251--43302 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
43241 TAAAGGATCA
43251 TGTGGCCGGT
1 TGTGGCCGGT
*
43261 TGTGGCCGGG
1 TGTGGCCGGT
**
43271 CATGGCCGAGT
1 TGTGGCCG-GT
43282 CATGTGGCCGGT
1 --TGTGGCCGGT
43294 TGTGGCCGG
1 TGTGGCCGG
43303 ACATGTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.06, C:0.23, G:0.48, T:0.23
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:43322 original size:33 final size:33
Alignment explanation
Indices: 43252--43359 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 33
43242 AAAGGATCAT
* *
43252 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGGTTGTGGCCGGACATGGCCGAGTCAC
* * *
43285 GTGGCCGGTTGTGGCCGGACAT-GTCTATGTCGC
1 GTGGCCGGTTGTGGCCGGACATGGCCGA-GTCAC
* * ** *
43318 GTGGCCGG-TGATGGTCGGGCATCTCCGAGTCGC
1 GTGGCCGGTTG-TGGCCGGACATGGCCGAGTCAC
43351 GTGGCCGGT
1 GTGGCCGGT
43360 CACAAGTGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
32 5 0.08
33 54 0.89
34 2 0.03
ACGTcount: A:0.08, C:0.25, G:0.44, T:0.23
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGACATGGCCGAGTCAC
Found at i:45186 original size:33 final size:33
Alignment explanation
Indices: 45147--45325 Score: 331
Period size: 33 Copynumber: 5.4 Consensus size: 33
45137 CTTTTCACCA
**
45147 AAAACAGAATTATTTTTAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
45180 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
45213 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
45246 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
*
45279 AAAACAGAATTATTTGCAATGTTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
45312 AAAACAGAATTATT
1 AAAACAGAATTATT
45326 ATCATCACAA
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 143 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (33 bp):
AAAACAGAATTATTTGCAATGCTATGATCAACC
Found at i:45349 original size:33 final size:33
Alignment explanation
Indices: 45311--45407 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
45301 TATGATCAAC
* *
45311 CAAAACAGAATTATTATCATCACAAACAACACT
1 CAAAACAGATTTATTATCATCGCAAACAACACT
* * * *
45344 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTATTATCATCGCAAACAACACT
** *
45377 CAAATTAGGTTTATTATCATCGCAAACAACA
1 CAAAACAGATTTATTATCATCGCAAACAACA
45408 TCTAAAAGAC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTATTATCATCGCAAACAACACT
Found at i:46827 original size:8 final size:9
Alignment explanation
Indices: 46812--46846 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
46802 TCTAGTCGAA
46812 ATTTTTTTT
1 ATTTTTTTT
46821 ATTTTTTTT
1 ATTTTTTTT
46830 ATTTTTTTT
1 ATTTTTTTT
46839 ATATTTTT
1 AT-TTTTT
46847 CGATATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:47901 original size:33 final size:33
Alignment explanation
Indices: 47859--48003 Score: 134
Period size: 33 Copynumber: 4.4 Consensus size: 33
47849 AGCTAAAGGA
*
47859 TCATGTGGCCGGTTG-TGGCCGGGCATGGCCGAG
1 TCATGTGGCCGG-TGATGGCCGGGCATGTCCGAG
* *
47892 TCATGTGGCCGGTTG-TGCCCGGACATGTCC-ATG
1 TCATGTGGCCGG-TGATGGCCGGGCATGTCCGA-G
** *
47925 TCGCGTGGCCGGTGATGGCCGGGCATCTCCGAG
1 TCATGTGGCCGGTGATGGCCGGGCATGTCCGAG
* * * *
47958 TCGTGTGGCCGGTGATGGTCGGGCATCTCCAAG
1 TCATGTGGCCGGTGATGGCCGGGCATGTCCGAG
**
47991 TCGCGTGGCCGGT
1 TCATGTGGCCGGT
48004 CACAAGTGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
32 3 0.03
33 93 0.96
34 1 0.01
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.23
Consensus pattern (33 bp):
TCATGTGGCCGGTGATGGCCGGGCATGTCCGAG
Found at i:47969 original size:66 final size:65
Alignment explanation
Indices: 47863--48003 Score: 176
Period size: 66 Copynumber: 2.1 Consensus size: 65
47853 AAAGGATCAT
* * *
47863 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCATGTGGCCGGTTG-TGCCCGGACATGTCCATGTC
1 GTGGCCGG-TGTGGCCGGGCATCGCCGAGTCATGTGGCCGG-TGATGCCCGGACATCTCCAAGTC
47927 GC
64 GC
* * ** *
47929 GTGGCCGGTGATGGCCGGGCATCTCCGAGTCGTGTGGCCGGTGATGGTCGGGCATCTCCAAGTCG
1 GTGGCCGGTG-TGGCCGGGCATCGCCGAGTCATGTGGCCGGTGATGCCCGGACATCTCCAAGTCG
47994 C
65 C
47995 GTGGCCGGT
1 GTGGCCGGT
48004 CACAAGTGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
65 4 0.06
66 61 0.94
ACGTcount: A:0.09, C:0.27, G:0.42, T:0.22
Consensus pattern (65 bp):
GTGGCCGGTGTGGCCGGGCATCGCCGAGTCATGTGGCCGGTGATGCCCGGACATCTCCAAGTCGC
Found at i:49940 original size:21 final size:20
Alignment explanation
Indices: 49895--49932 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49885 TAAATTTTAG
*
49895 AAGA-TTTTTCTGAAAGAGA
1 AAGAGTTTTTCGGAAAGAGA
49914 AAGAGTTTTTCGGAAAGAG
1 AAGAGTTTTTCGGAAAGAG
49933 GAAGGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (20 bp):
AAGAGTTTTTCGGAAAGAGA
Found at i:50841 original size:21 final size:21
Alignment explanation
Indices: 50815--50874 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
50805 GCATAACTTG
*
50815 GAATCGATTGGAATATTCCTA
1 GAATCGATTGGAATATTCATA
* * **
50836 GAATCGATTGTAGTAGACATA
1 GAATCGATTGGAATATTCATA
*
50857 GAATCGACTGGAATATTC
1 GAATCGATTGGAATATTC
50875 TTGCTCCAAA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (21 bp):
GAATCGATTGGAATATTCATA
Found at i:51372 original size:13 final size:14
Alignment explanation
Indices: 51348--51379 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
51338 GAATTAAAAT
51348 TAAATCTAACTAAG
1 TAAATCTAACTAAG
51362 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
51375 -AAATC
1 TAAATC
51380 AATCAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAATCTAACTAAG
Done.