Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011661.1 Corchorus capsularis cultivar CVL-1 contig11682, 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: 21413
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:648 original size:22 final size:22
Alignment explanation
Indices: 623--666 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
613 AAAATTTGGC
*
623 TTTTAGTTTATGATTTATGAGT
1 TTTTAGTTTATGATTAATGAGT
645 TTTTAGTTTATGATTAATGAGT
1 TTTTAGTTTATGATTAATGAGT
667 AGATCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTTAGTTTATGATTAATGAGT
Found at i:1147 original size:35 final size:35
Alignment explanation
Indices: 1096--1385 Score: 401
Period size: 35 Copynumber: 8.3 Consensus size: 35
1086 GAAGCAAAGA
*
1096 TAATTAAGTAATTCAGTAATCAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1131 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1166 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1201 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
* *
1236 TAATTAAGTGAGTCAGTAATCACATTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATCA-ACTTAATTCAGGG
* *
1272 TAATTAAGTAATTCAGTAAGT-AACTTAATTCATGG
1 TAATTAAGTAAGTCAGTAA-TCAACTTAATTCAGGG
* * * *
1307 TAATTAAGTGAGTTAATAATCAACTTAATTTAGGG
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
1342 -AAGTTAAGT-AGTTC-GATAAGT-AACTTAATTCAGGG
1 TAA-TTAAGTAAG-TCAG-TAA-TCAACTTAATTCAGGG
*
1377 AAATTAAGT
1 TAATTAAGT
1386 CTAGTAAGAA
Statistics
Matches: 231, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
34 5 0.02
35 192 0.83
36 33 0.14
37 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (35 bp):
TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGG
Found at i:1297 original size:141 final size:140
Alignment explanation
Indices: 1096--1385 Score: 401
Period size: 141 Copynumber: 2.1 Consensus size: 140
1086 GAAGCAAAGA
*
1096 TAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATT
1 TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATT
*
1161 CAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAA-TTAAGTAAG-TC-AGTAA-TC
66 CAGGGTAATTAAGTAAGTCAATAATCAACTTAATTCAGGG-AAGTTAAGT-AGTTCGA-TAAGT-
1222 AACTTAATTCAGGG
127 AACTTAATTCAGGG
* * *
1236 TAATTAAGTGAGTCAGTAATCACATTTAATTCAGGGTAATTAAGTAATTCAGTAAGT-AACTTAA
1 TAATTAAGTAAGTCAGTAATCA-ACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TCAACTTAA
* * * *
1300 TTCATGGTAATTAAGTGAGTTAATAATCAACTTAATTTAGGGAAGTTAAGTAGTTCGATAAGTAA
64 TTCAGGGTAATTAAGTAAGTCAATAATCAACTTAATTCAGGGAAGTTAAGTAGTTCGATAAGTAA
1365 CTTAATTCAGGG
129 CTTAATTCAGGG
*
1377 AAATTAAGT
1 TAATTAAGT
1386 CTAGTAAGAA
Statistics
Matches: 134, Mismatches: 10, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
140 24 0.18
141 107 0.80
142 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (140 bp):
TAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATT
CAGGGTAATTAAGTAAGTCAATAATCAACTTAATTCAGGGAAGTTAAGTAGTTCGATAAGTAACT
TAATTCAGGG
Found at i:4370 original size:40 final size:43
Alignment explanation
Indices: 4316--4403 Score: 137
Period size: 41 Copynumber: 2.1 Consensus size: 43
4306 TTAAAGAAGG
* *
4316 AAAAATTGGGCCT-AAAAAAGAAAGAGGTCGCAAAAAGA-AA-
1 AAAAACTGGACCTAAAAAAAGAAAGAGGTCGCAAAAAGATAAT
4356 AAAAACTGGACCTAAAAAAAGAAAGAGGTCGCAAAAAGATAAT
1 AAAAACTGGACCTAAAAAAAGAAAGAGGTCGCAAAAAGATAAT
4399 AAAAA
1 AAAAA
4404 GAATTGCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 11 0.26
41 25 0.58
42 2 0.05
43 5 0.12
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.10
Consensus pattern (43 bp):
AAAAACTGGACCTAAAAAAAGAAAGAGGTCGCAAAAAGATAAT
Found at i:6907 original size:36 final size:36
Alignment explanation
Indices: 6867--7242 Score: 238
Period size: 36 Copynumber: 10.5 Consensus size: 36
6857 AATGACCCAA
* * *
6867 GGTGGTTGCTCTTAAGTTCAGTTCGGAATGATCGAG
1 GGTGGTTGTTCTTCAGTTCAGTTCAGAATGATCGAG
* * * * ** *
6903 GGTGGTCGTT-TCTCAGTTTATTTCAG-TTGGCCCAG
1 GGTGGTTGTTCT-TCAGTTCAGTTCAGAATGATCGAG
* * *
6938 GGTGGTCT-TTCTTTAGGTTGAG-TAAGAATGATCGAG
1 GGTGGT-TGTTCTTCA-GTTCAGTTCAGAATGATCGAG
* * *
6974 GGTGGTTGTTCTTCAATTTA-TGTCGGAATGATCGAG
1 GGTGGTTGTTCTTCAGTTCAGT-TCAGAATGATCGAG
* * *
7010 GGTGGTCGTTCTTCAGTTCAGCTT-GGAATAATCGAG
1 GGTGGTTGTTCTTCAGTTCAG-TTCAGAATGATCGAG
* * *
7046 GGTGGTTTTTCATCAGTTTGAG-TCAGAATGATCGAG
1 GGTGGTTGTTCTTCAG-TTCAGTTCAGAATGATCGAG
* * * *
7082 GGTGGTTATTCTTCAGTTTAGTCCAGAATAATCGAG
1 GGTGGTTGTTCTTCAGTTCAGTTCAGAATGATCGAG
* * * * *
7118 GGTGGTTGTTCTTCAGTTTATTTCAG-TTGACCCAG
1 GGTGGTTGTTCTTCAGTTCAGTTCAGAATGATCGAG
* * *
7153 GGTGGTCT-TTCTTCAATTTGCA--TCGGAGTGATCGAG
1 GGTGGT-TGTTCTTC-AGTT-CAGTTCAGAATGATCGAG
* *
7189 GGTGGTCGTTCTTCAGTTCAGTTC-GAAATGATCCAG
1 GGTGGTTGTTCTTCAGTTCAGTTCAG-AATGATCGAG
7225 GGTGGTCT-TTCTTCAGTT
1 GGTGGT-TGTTCTTCAGTT
7243 ACTTATTTTA
Statistics
Matches: 261, Mismatches: 57, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
34 2 0.01
35 52 0.20
36 200 0.77
37 6 0.02
38 1 0.00
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (36 bp):
GGTGGTTGTTCTTCAGTTCAGTTCAGAATGATCGAG
Found at i:7047 original size:72 final size:70
Alignment explanation
Indices: 6889--7243 Score: 283
Period size: 72 Copynumber: 5.0 Consensus size: 70
6879 TAAGTTCAGT
* * * * ** *
6889 TCGGAATGATCGAGGGTGGTCGTT-TCTCAGTTTATTTCAG-TTGGCCCAGGGTGGTCTTTCTTT
1 TCGGAATAATCGAGGGTGGTTGTTCT-TCAGTTTA-GTCAGAATGATCCAGGGTGGTCTTTCTTC
6952 AGGTTGAG-
64 A-GTT-AGC
** * * * * *
6960 TAAGAATGATCGAGGGTGGTTGTTCTTCAATTTATGTCGGAATGATCGAGGGTGGTCGTTCTTCA
1 TCGGAATAATCGAGGGTGGTTGTTCTTCAGTTTA-GTCAGAATGATCCAGGGTGGTCTTTCTTCA
7025 GTTCAGC
65 GTT-AGC
* * * *
7032 TTGGAATAATCGAGGGTGGTTTTTCATCAGTTTGAGTCAGAATGATCGAGGGTGGT-TATTCTTC
1 TCGGAATAATCGAGGGTGGTTGTTCTTCAGTTT-AGTCAGAATGATCCAGGGTGGTCT-TTCTTC
7096 AGTTTAG-
64 AG-TTAGC
* * * *
7103 TCCAGAATAATCGAGGGTGGTTGTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCTTC
1 T-CGGAATAATCGAGGGTGGTTGTTCTTCAGTTTA-GTCAGAATGATCCAGGGTGGTCTTTCTTC
* *
7167 AATTTGC
64 AGTTAGC
* * * *
7174 ATCGGAGTGATCGAGGGTGGTCGTTCTTCAGTTCAGTTC-GAAATGATCCAGGGTGGTCTTTCTT
1 -TCGGAATAATCGAGGGTGGTTGTTCTTCAGTTTAG-TCAG-AATGATCCAGGGTGGTCTTTCTT
7238 CAGTTA
63 CAGTTA
7244 CTTATTTTAG
Statistics
Matches: 229, Mismatches: 41, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
70 4 0.02
71 88 0.38
72 134 0.59
73 3 0.01
ACGTcount: A:0.19, C:0.15, G:0.29, T:0.37
Consensus pattern (70 bp):
TCGGAATAATCGAGGGTGGTTGTTCTTCAGTTTAGTCAGAATGATCCAGGGTGGTCTTTCTTCAG
TTAGC
Found at i:7088 original size:108 final size:108
Alignment explanation
Indices: 6936--7135 Score: 294
Period size: 108 Copynumber: 1.9 Consensus size: 108
6926 CAGTTGGCCC
* * * *
6936 AGGGTGGTCTTTCTTTAGGTTGAGTAAGAATGATCGAGGGTGGTTGTTCTTCAATTTATGT-CGG
1 AGGGTGGTCTTTCATCAGGTTGAGTAAGAATGATCGAGGGTGGTTATTCTTCAATTTA-GTCCAG
*
7000 AATGATCGAGGGTGGTCGTTCTTCAGTTCAGCTTGGAATAATCG
65 AATAATCGAGGGTGGTCGTTCTTCAGTTCAGCTTGGAATAATCG
* * * *
7044 AGGGTGGTTTTTCATCAGTTTGAGTCAGAATGATCGAGGGTGGTTATTCTTCAGTTTAGTCCAGA
1 AGGGTGGTCTTTCATCAGGTTGAGTAAGAATGATCGAGGGTGGTTATTCTTCAATTTAGTCCAGA
*
7109 ATAATCGAGGGTGGTTGTTCTTCAGTT
66 ATAATCGAGGGTGGTCGTTCTTCAGTT
7136 TATTTCAGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 2 0.02
108 79 0.98
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.37
Consensus pattern (108 bp):
AGGGTGGTCTTTCATCAGGTTGAGTAAGAATGATCGAGGGTGGTTATTCTTCAATTTAGTCCAGA
ATAATCGAGGGTGGTCGTTCTTCAGTTCAGCTTGGAATAATCG
Found at i:10450 original size:35 final size:35
Alignment explanation
Indices: 10406--10814 Score: 475
Period size: 35 Copynumber: 11.8 Consensus size: 35
10396 GAATCAGTAA
10406 TAATCAACTTAATTC-GAGGTAATTAAGTGATTCAG
1 TAATCAACTTAATTCAG-GGTAATTAAGTGATTCAG
*
10441 TAATCAACTTAATTCAGGGTAATTAAGT-AGGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGA-TTCAG
* *
10476 TAATCAATTTAATTCAGGGTAATTAAGTAATTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGATTCAG
10511 TGAAT-AACTTAATTCAGGGTAATTAA--G--TCAG
1 T-AATCAACTTAATTCAGGGTAATTAAGTGATTCAG
* * * *
10542 TAAAT-AGCTTAATTCAGGTTAATTAAGTAAGTCAG
1 T-AATCAACTTAATTCAGGGTAATTAAGTGATTCAG
* *
10577 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGATTCAG
*
10612 TAATCAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGATTCAG
* *
10647 GAATCAACTTAATTCAGGGTAATTAAGTAATTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGATTCAG
*
10682 TAATTAACTTAATTCAGGGTAATTAAGTG-TGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTGAT-TCAG
* * *
10717 GAATCAACTTAATTCAGGGTAATTCAGTGAGTT-AA
1 TAATCAACTTAATTCAGGGTAATTAAGTGA-TTCAG
* *
10752 TAATCAACTTAATTTAGGG-AAGTTAAGT-AGTTCAA
1 TAATCAACTTAATTCAGGGTAA-TTAAGTGA-TTCAG
*
10787 TAAGT-AACTTAATTCAGGGAAATTAAGT
1 TAA-TCAACTTAATTCAGGGTAATTAAGT
10815 TTAGTAAGTA
Statistics
Matches: 332, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
31 27 0.08
34 11 0.03
35 284 0.86
36 9 0.03
37 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (35 bp):
TAATCAACTTAATTCAGGGTAATTAAGTGATTCAG
Found at i:10571 original size:27 final size:27
Alignment explanation
Indices: 10502--10571 Score: 68
Period size: 31 Copynumber: 2.4 Consensus size: 27
10492 GGGTAATTAA
* *
10502 GTAATTCAGTGAATAACTTAATTCAGG
1 GTAATTAAGTAAATAACTTAATTCAGG
*
10529 GTAATTAAGTCAGTAAATAGCTTAATTCAGG
1 GTAATT-A---AGTAAATAACTTAATTCAGG
*
10560 TTAATTAAGTAA
1 GTAATTAAGTAA
10572 GTCAGTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 11 0.31
30 1 0.03
31 23 0.66
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (27 bp):
GTAATTAAGTAAATAACTTAATTCAGG
Found at i:11677 original size:26 final size:26
Alignment explanation
Indices: 11637--11701 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
11627 TTGCGACAAT
*
11637 TGAATACCATTTTTACTCTTTTTCAC
1 TGAATACCATTTTTACTCTTTTTAAC
*
11663 TGATTACCATTTTTACTCTTTTTAAC
1 TGAATACCATTTTTACTCTTTTTAAC
11689 TGAATACCATTTT
1 TGAATACCATTTT
11702 CACTTTACTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.51
Consensus pattern (26 bp):
TGAATACCATTTTTACTCTTTTTAAC
Found at i:11711 original size:21 final size:21
Alignment explanation
Indices: 11687--11730 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
11677 ACTCTTTTTA
* *
11687 ACTGAATACCATTTTCACTTT
1 ACTGAATACAATTTACACTTT
* *
11708 ACTGATTACAATTTACTCTTT
1 ACTGAATACAATTTACACTTT
11729 AC
1 AC
11731 CATTTTACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (21 bp):
ACTGAATACAATTTACACTTT
Found at i:11729 original size:7 final size:7
Alignment explanation
Indices: 11719--11917 Score: 57
Period size: 7 Copynumber: 27.7 Consensus size: 7
11709 CTGATTACAA
11719 TTTACTC
1 TTTACTC
11726 TTTAC-C
1 TTTACTC
*
11732 ATTTTACTT
1 --TTTACTC
*
11741 TTTACTG
1 TTTACTC
*
11748 ATTACTC
1 TTTACTC
*
11755 TTTACTTT
1 TTTAC-TC
11763 TTTAC-C
1 TTTACTC
11769 ATTTTACTC
1 --TTTACTC
*
11778 TTTACTG
1 TTTACTC
*
11785 ATTACTC
1 TTTACTC
* *
11792 CTTGCTC
1 TTTACTC
11799 TTTAC-C
1 TTTACTC
*
11805 ATATAACTC
1 -T-TTACTC
* *
11814 TTTCCTG
1 TTTACTC
* *
11821 ATTATTC
1 TTTACTC
11828 TTTACTC
1 TTTACTC
11835 TTTAC-C
1 TTTACTC
*
11841 ATCTTACTA
1 -T-TTACTC
*
11850 TTTACTG
1 TTTACTC
*
11857 ATTACTC
1 TTTACTC
*
11864 TTTACTT
1 TTTACTC
* *
11871 TTTATTG
1 TTTACTC
*
11878 ATTACTC
1 TTTACTC
11885 TTTACT-
1 TTTACTC
*
11891 TTCTACTG
1 TT-TACTC
*
11899 ATTACTC
1 TTTACTC
* *
11906 GTTATTC
1 TTTACTC
11913 TTTAC
1 TTTAC
11918 CATTTTTCTT
Statistics
Matches: 135, Mismatches: 42, Indels: 30
0.65 0.20 0.14
Matches are distributed among these distances:
6 5 0.04
7 102 0.76
8 26 0.19
9 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.54
Consensus pattern (7 bp):
TTTACTC
Found at i:11749 original size:36 final size:36
Alignment explanation
Indices: 11693--11945 Score: 235
Period size: 36 Copynumber: 6.9 Consensus size: 36
11683 TTTAACTGAA
* **
11693 TACCATTTT-CACTTTACTGATTACAATTTACTCTT
1 TACCATTTTACTCTTTACTGATTACTCTTTACTCTT
* *
11728 TACCATTTTACTTTTTACTGATTACTCTTTACTTTTT
1 TACCATTTTACTCTTTACTGATTACTCTTTAC-TCTT
* *
11765 TACCATTTTACTCTTTACTGATTACTCCTTGCTCTT
1 TACCATTTTACTCTTTACTGATTACTCTTTACTCTT
* * * *
11801 TACCATATAACTCTTTCCTGATTATTCTTTACTCTT
1 TACCATTTTACTCTTTACTGATTACTCTTTACTCTT
* * *
11837 TACCATCTTACTATTTACTGATTACTCTTTACTTTTTAT
1 TACCATTTTACTCTTTACTGATTACTCTTTAC--TCT-T
** * *
11876 TGATTACTCTTTACT-TTCTACTGATTACTCGTTATTCTT
1 T-ACCA-T-TTTACTCTT-TACTGATTACTCTTTACTCTT
*
11915 TACCATTTT--TCTTTGCTGATTACTCTTTACT
1 TACCATTTTACTCTTTACTGATTACTCTTTACT
11946 GATTTACTGA
Statistics
Matches: 176, Mismatches: 32, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
34 16 0.09
35 11 0.06
36 81 0.46
37 33 0.19
38 4 0.02
39 4 0.02
40 4 0.02
41 3 0.02
42 20 0.11
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (36 bp):
TACCATTTTACTCTTTACTGATTACTCTTTACTCTT
Found at i:11765 original size:29 final size:30
Alignment explanation
Indices: 11720--11776 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
11710 TGATTACAAT
*
11720 TTACTCTTTACCATTTTA-CTTTTTACTGA
1 TTACTCTTTACCATTTTACCATTTTACTGA
**
11749 TTACTCTTTACTTTTTTACCATTTTACT
1 TTACTCTTTACCATTTTACCATTTTACT
11777 CTTTACTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (30 bp):
TTACTCTTTACCATTTTACCATTTTACTGA
Found at i:11786 original size:73 final size:72
Alignment explanation
Indices: 11693--11861 Score: 205
Period size: 73 Copynumber: 2.3 Consensus size: 72
11683 TTTAACTGAA
* * * * *
11693 TACCATTTT-CACTTTACTGATTACAATTTACTCTTTACCATTTTACTTTTTACTGATTACTCTT
1 TACCATTTTACTCTTTACTGATTACAACTTACTCTTTACCATATAACTCTTTACTGATTACTCTT
*
11757 TACTTTTT
66 TAC-TCTT
** * * *
11765 TACCATTTTACTCTTTACTGATTACTCCTTGCTCTTTACCATATAACTCTTTCCTGATTATTCTT
1 TACCATTTTACTCTTTACTGATTACAACTTACTCTTTACCATATAACTCTTTACTGATTACTCTT
11830 TACTCTT
66 TACTCTT
* *
11837 TACCATCTTACTATTTACTGATTAC
1 TACCATTTTACTCTTTACTGATTAC
11862 TCTTTACTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
72 35 0.42
73 48 0.58
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.51
Consensus pattern (72 bp):
TACCATTTTACTCTTTACTGATTACAACTTACTCTTTACCATATAACTCTTTACTGATTACTCTT
TACTCTT
Found at i:11874 original size:21 final size:21
Alignment explanation
Indices: 11844--11905 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
11834 CTTTACCATC
*
11844 TTACTATTTACTGATTACTCT
1 TTACTTTTTACTGATTACTCT
*
11865 TTACTTTTTATTGATTACTCT
1 TTACTTTTTACTGATTACTCT
*
11886 TTACTTTCTACTGATTACTC
1 TTACTTTTTACTGATTACTC
11906 GTTATTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (21 bp):
TTACTTTTTACTGATTACTCT
Found at i:12001 original size:40 final size:40
Alignment explanation
Indices: 11947--12096 Score: 246
Period size: 40 Copynumber: 3.8 Consensus size: 40
11937 CTCTTTACTG
* *
11947 ATTTACTGATTACTTCTTTTAATTTTACTCTTAATTACCA
1 ATTTACTGATTACTTCTTTTACTTTTACTCTTAATTATCA
*
11987 TTTTACTGATTACTTCTTTTACTTTTACTCTTAATTATCA
1 ATTTACTGATTACTTCTTTTACTTTTACTCTTAATTATCA
*
12027 ATTTACTGATTACTTCCTTTACTTTTACTCTTAATTATCA
1 ATTTACTGATTACTTCTTTTACTTTTACTCTTAATTATCA
* *
12067 ACTTACTGATTACTTCTTTTACTTTCACTC
1 ATTTACTGATTACTTCTTTTACTTTTACTC
12097 CATTCTACTG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.53
Consensus pattern (40 bp):
ATTTACTGATTACTTCTTTTACTTTTACTCTTAATTATCA
Found at i:12296 original size:32 final size:31
Alignment explanation
Indices: 12229--12300 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
12219 TGATTAATCT
* *
12229 TTTTACCTTGACTCTTAATTACTGACTTACCC
1 TTTTACTTTGACCCTTAATTACTGACTTA-CC
12261 TTTTACTTTGACCCTTAATTACTGACTGCTA-C
1 TTTTACTTTGACCCTTAATTACTGACT--TACC
12293 TTTTACTT
1 TTTTACTT
12301 CCTCTCTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 34 0.94
34 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.47
Consensus pattern (31 bp):
TTTTACTTTGACCCTTAATTACTGACTTACC
Found at i:12337 original size:40 final size:40
Alignment explanation
Indices: 12293--12479 Score: 141
Period size: 40 Copynumber: 4.5 Consensus size: 40
12283 TGACTGCTAC
*
12293 TTTTACTTCCTCTCTTAGTTATCAATTTACTAATTAATCT
1 TTTTACTTCCTCTCTTAATTATCAATTTACTAATTAATCT
*** *
12333 TTTTACTTTGACTCTTAATTATCAATTTACTGAA-TGATC-
1 TTTTACTTCCTCTCTTAATTATCAATTTACT-AATTAATCT
* * *
12372 -TTTACTTCCCCTCTTAATTATCAATCCTT-TTATTTAATTACT
1 TTTTACTTCCTCTCTTAATTATCAAT--TTACTAATTAA-T-CT
* *
12414 GATTACTACTT-TTACTTCCTTAATTATCAATTTACTAATTAATCT
1 --TT-TTACTTCCT-C-T-CTTAATTATCAATTTACTAATTAATCT
*
12459 TTTTACTTCCTCGCTTAATTA
1 TTTTACTTCCTCTCTTAATTA
12480 CTGGTTACCA
Statistics
Matches: 112, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
38 23 0.21
39 3 0.03
40 42 0.38
41 3 0.03
42 6 0.05
43 3 0.03
45 3 0.03
46 9 0.08
47 7 0.06
48 13 0.12
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (40 bp):
TTTTACTTCCTCTCTTAATTATCAATTTACTAATTAATCT
Found at i:15599 original size:18 final size:19
Alignment explanation
Indices: 15562--15603 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
15552 GGGTAAAAGC
*
15562 CCAAAAGATAAACTGAAGT
1 CCAAAAGATAAACAGAAGT
*
15581 CCAAAAGA-AAAGAGAAGT
1 CCAAAAGATAAACAGAAGT
15599 CCAAA
1 CCAAA
15604 TAGGATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.10
Consensus pattern (19 bp):
CCAAAAGATAAACAGAAGT
Found at i:19790 original size:25 final size:26
Alignment explanation
Indices: 19761--19832 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
19751 ATGAGATATG
*
19761 CATGGCAAAATTAT-AATTTTATGTA
1 CATGGCAAAATTATAAATTTTAGGTA
* * *
19786 CATGGCATAATTGTAAAATTT-GGTA
1 CATGGCAAAATTATAAATTTTAGGTA
* *
19811 TATGGCAAAATCATAAATTTTA
1 CATGGCAAAATTATAAATTTTA
19833 AATTTTCTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (26 bp):
CATGGCAAAATTATAAATTTTAGGTA
Found at i:20797 original size:2 final size:2
Alignment explanation
Indices: 20785--20819 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20775 TAAGTTGAAC
*
20785 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20820 TGAATATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.