Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015987.1 Corchorus capsularis cultivar CVL-1 contig16008, 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: 38473
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:2822 original size:17 final size:17
Alignment explanation
Indices: 2800--2860 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
2790 ATTGGGCCTA
2800 AAAAAGAAAGAGGTCGC
1 AAAAAGAAAGAGGTCGC
* *
2817 AAAAAGAAAAACTGGGC-C
1 AAAAAGAAAGA--GGTCGC
2835 TAAAAAAGAAAGAGGTCGC
1 --AAAAAGAAAGAGGTCGC
2854 AAAAAGA
1 AAAAAGA
2861 GAATAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 17 0.49
18 4 0.11
19 4 0.11
20 10 0.29
ACGTcount: A:0.57, C:0.11, G:0.25, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAGAGGTCGC
Found at i:2833 original size:37 final size:37
Alignment explanation
Indices: 2786--2860 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2776 TTAAAGAAGA
*
2786 AAAAATTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAG
1 AAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAG
2823 AAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAG
1 AAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAG
2860 A
1 A
2861 GAATAAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.55, C:0.12, G:0.24, T:0.09
Consensus pattern (37 bp):
AAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAG
Found at i:2858 original size:19 final size:19
Alignment explanation
Indices: 2799--2863 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
2789 AATTGGGCCT
2799 AAAAAAGAAAGAGGTCGCA
1 AAAAAAGAAAGAGGTCGCA
** * *
2818 AAAAGAA-AAACTGGGC-CT
1 AAAA-AAGAAAGAGGTCGCA
2836 AAAAAAGAAAGAGGTCGCA
1 AAAAAAGAAAGAGGTCGCA
*
2855 AAAAGAGAA
1 AAAAAAGAA
2864 TAAAAAGAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 11 0.32
19 19 0.56
20 2 0.06
ACGTcount: A:0.58, C:0.11, G:0.25, T:0.06
Consensus pattern (19 bp):
AAAAAAGAAAGAGGTCGCA
Found at i:2960 original size:14 final size:15
Alignment explanation
Indices: 2928--2966 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2918 CAAGAGACGT
2928 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
*
2943 TTTTCAAGAAAA-GG
1 TTTTCAAAAAAATGG
2957 TTTTCCAAAA
1 TTTT-CAAAA
2967 TGAGTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:3620 original size:21 final size:22
Alignment explanation
Indices: 3579--3622 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3569 GATTGTCCAA
3579 AAAAATTGATTTATCACAAAAG
1 AAAAATTGATTTATCACAAAAG
* * *
3601 AAAAATTGTTTTCTCAAAAAAG
1 AAAAATTGATTTATCACAAAAG
3623 GTTTTTAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAATTGATTTATCACAAAAG
Found at i:3707 original size:15 final size:14
Alignment explanation
Indices: 3683--3745 Score: 74
Period size: 15 Copynumber: 4.4 Consensus size: 14
3673 TTAGGCAATC
3683 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
3697 GAAAGAAGAAAAAAGA
1 GAAA-AAGAAAAAA-A
3713 GAAAAAG-AAAAAA
1 GAAAAAGAAAAAAA
* *
3726 GAAAGAGCAAAAGAA
1 GAAAAAG-AAAAAAA
3741 GAAAA
1 GAAAA
3746 GAGATGAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.17
14 9 0.21
15 21 0.50
16 5 0.12
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:3711 original size:22 final size:22
Alignment explanation
Indices: 3684--3729 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3674 TAGGCAATCG
*
3684 AAAAAGAAAAAAAGAAAGAAGA
1 AAAAAGAAAAAAAGAAAAAAGA
*
3706 AAAAAGAGAAAAAGAAAAAAGA
1 AAAAAGAAAAAAAGAAAAAAGA
3728 AA
1 AA
3730 GAGCAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAGAAAAAAGA
Found at i:3742 original size:22 final size:20
Alignment explanation
Indices: 3693--3745 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
3683 GAAAAAGAAA
*
3693 AAAAGAAAGAAGAAAAAAGAG
1 AAAAG-AAGAAAAAAAAAGAG
3714 -AAA-AAGAAAAAAGAAAGAG
1 AAAAGAAGAAAAAA-AAAGAG
3733 CAAAAGAAGAAAA
1 -AAAAGAAGAAAA
3746 GAGATGAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 3 0.11
21 3 0.11
22 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAGAAGAAAAAAAAAGAG
Found at i:5149 original size:35 final size:35
Alignment explanation
Indices: 5108--5653 Score: 333
Period size: 35 Copynumber: 15.6 Consensus size: 35
5098 CAGTTTAACA
* * *
5108 CAGGGTGGTCTTTCATCAGTTTATGTCAAATGATC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
* * * *
5143 GAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
* *
5178 CAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCA-GATGATC
* * * * * * *
5214 GAGGGTGGTCATTCTTCAGTATATTCCAGTTAACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
* * * *
5249 CAGAGTGGTCTTACATCAGTTTATGTCA-AGTGATC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGA-TGATC
* * * *
5284 GAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
* *
5319 CAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCA-GATGATC
* * * * *
5355 GAGGGTGGTCATTCTTCAGTATATTTCAGTTGACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
** * * * *
5390 CAGGGTGGTCTTTCAACAGTTTGTGTCGGAATGATT
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAG-ATGATC
* * * * *
5426 CAGGGTGATCTTCCTTTAGTTTATTTCAGTTGACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
* * * * * *
5461 CAGGGTGGTCTTCCGTCAATTTGTGTCAGAATAATC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAG-ATGATC
* * * * * * *
5497 GAGGGTGGT-TGTTTTTCGGTTCAGTCCGGAATGATC
1 CAGGGTGGTCT-TTCTTCAGTTTATTTCAG-ATGATC
* * *
5533 GAGGGTGGTCGTTCTTCAGTTTATTTCA-ATTGACC
1 CAGGGTGGTCTTTCTTCAGTTTATTTCAGA-TGATC
5568 CAGGGTGGTCTTT-TTGC-G------TCAGAATGATC
1 CAGGGTGGTCTTTCTT-CAGTTTATTTCAG-ATGATC
* * * * *
5597 AAGGGTGGTCGTTCTTCAATTCAGTTT-GGAATGATC
1 CAGGGTGGTCTTTCTTCAGTTTA-TTTCAG-ATGATC
5633 CAGGGTGGTCTTTCTTCAGTT
1 CAGGGTGGTCTTTCTTCAGTT
5654 ACTTATTTGA
Statistics
Matches: 374, Mismatches: 116, Indels: 41
0.70 0.22 0.08
Matches are distributed among these distances:
28 3 0.01
29 16 0.04
30 3 0.01
34 4 0.01
35 198 0.53
36 149 0.40
37 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (35 bp):
CAGGGTGGTCTTTCTTCAGTTTATTTCAGATGATC
Found at i:5229 original size:71 final size:71
Alignment explanation
Indices: 5108--5505 Score: 527
Period size: 71 Copynumber: 5.6 Consensus size: 71
5098 CAGTTTAACA
* * *
5108 CAGGGTGGTCTTTCATCAGTTTATGTCA-AATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAG
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG
5172 TTGACC
66 TTGACC
* * *
5178 CAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCATTCTTCAGTATATTCCAG
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG
*
5243 TTAACC
66 TTGACC
* * * *
5249 CAGAGTGGTCTTACATCAGTTTATGTCAAG-TGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAG
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG
5313 TTGACC
66 TTGACC
* *
5319 CAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCATTCTTCAGTATATTTCAG
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG
5384 TTGACC
66 TTGACC
* * * * *
5390 CAGGGTGGTCTTTCAACAGTTTGTGTC-GGAATGATTC-AGGGTGATC-TTCCTTTAGTTTATTT
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGG-ATGA-TCGAGGGTGGTCATT-CTTCAGTTTATTT
5452 CAGTTGACC
63 CAGTTGACC
* * * * *
5461 CAGGGTGGTCTTCCGTCAATTTGTGTCAGAATAATCGAGGGTGGT
1 CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGT
5506 TGTTTTTCGG
Statistics
Matches: 286, Mismatches: 35, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
70 94 0.33
71 189 0.66
72 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (71 bp):
CAGGGTGGTCTTCCATCAGTTTATGTCAGGATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG
TTGACC
Found at i:5283 original size:141 final size:140
Alignment explanation
Indices: 5095--5505 Score: 610
Period size: 141 Copynumber: 2.9 Consensus size: 140
5085 TTCTTTAGAC
*
5095 TTCCAGTTTAACACAGGGTGGTCTTTCATCAGTTTATGTCAAATGATCGAGGGTGGTCGTTCTTC
1 TTCCAG-TTAACCCAGGGTGGTCTTTCATCAGTTTATGTC-AATGATCGAGGGTGGTCGTTCTTC
5160 AGTTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCA
64 AGTTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCA
5225 TTCTTCAGTATA
129 TTCTTCAGTATA
* *
5237 TTCCAGTTAACCCAGAGTGGTCTTACATCAGTTTATGTCAAGTGATCGAGGGTGGTCGTTCTTCA
1 TTCCAGTTAACCCAGGGTGGTCTTTCATCAGTTTATGTCAA-TGATCGAGGGTGGTCGTTCTTCA
5302 GTTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCAT
65 GTTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCAT
5367 TCTTCAGTATA
130 TCTTCAGTATA
* * * * *
5378 TTTCAGTTGACCCAGGGTGGTCTTTCAACAGTTTGTGTCGGAATGATTC-AGGGTGATC-TTCCT
1 TTCCAGTTAACCCAGGGTGGTCTTTCATCAGTTTATGTC--AATGA-TCGAGGGTGGTCGTT-CT
* * * * * * *
5441 TTAGTTTATTTCAGTTGACCCAGGGTGGTCTTCCGTCAATTTGTGTCAGAATAATCGAGGGTGGT
62 TCAGTTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGT
5506 TGTTTTTCGG
Statistics
Matches: 247, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
140 2 0.01
141 164 0.66
142 77 0.31
143 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (140 bp):
TTCCAGTTAACCCAGGGTGGTCTTTCATCAGTTTATGTCAATGATCGAGGGTGGTCGTTCTTCAG
TTTATTTCAGTTGACCCAGGGTGGTCTTCCATCAGTTTATTTCAGGATGATCGAGGGTGGTCATT
CTTCAGTATA
Found at i:5638 original size:100 final size:102
Alignment explanation
Indices: 5416--5653 Score: 266
Period size: 100 Copynumber: 2.3 Consensus size: 102
5406 CAGTTTGTGT
* * * *
5416 CGGAATGATTCAGGGTGATCTTCCTTTAGTTTATTTCAGTTGACCCAGGGTGGTCTTCCGTCAAT
1 CGGAATGATCCAGGGTGGTCTT-CTTCAGTTTATTTCAATTGACCCAGGGTGGTCTT-C-T--AT
* * * * **
5481 TTGTGTCAGAATAATCGAGGGTGGTTGTTTTTCGGTTCAGTC
61 TTGCGTCAGAATAATCAAGGGTGGTCGTTCTTCAATTCAGTC
*
5523 CGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAATTGACCCAGGGTGGTC-T-T-TTTGC
1 CGGAATGATCCAGGGTGGTC-TTCTTCAGTTTATTTCAATTGACCCAGGGTGGTCTTCTATTTGC
* *
5585 GTCAGAATGATCAAGGGTGGTCGTTCTTCAATTCAGTT
65 GTCAGAATAATCAAGGGTGGTCGTTCTTCAATTCAGTC
*
5623 TGGAATGATCCAGGGTGGTCTTTCTTCAGTT
1 CGGAATGATCCAGGGTGGTC-TTCTTCAGTT
5654 ACTTATTTGA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
100 63 0.55
103 1 0.01
106 1 0.01
107 47 0.41
108 2 0.02
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.37
Consensus pattern (102 bp):
CGGAATGATCCAGGGTGGTCTTCTTCAGTTTATTTCAATTGACCCAGGGTGGTCTTCTATTTGCG
TCAGAATAATCAAGGGTGGTCGTTCTTCAATTCAGTC
Found at i:8912 original size:35 final size:34
Alignment explanation
Indices: 8768--9232 Score: 387
Period size: 35 Copynumber: 13.8 Consensus size: 34
8758 AGTAATTCAG
8768 AAACTTAATTCAGGGTAATTAAGT-A--AGTAAT
1 AAACTTAATTCAGGGTAATTAAGTAATCAGTAAT
*
8799 AGGTAACTTAATTCAGGGCAATTAAG---TCAGTAAGT
1 A---AACTTAATTCAGGGTAATTAAGTAATCAGTAA-T
* *
8834 -AGCTTAATTCAGGGTAATTAAGTAA--AGTCAGT
1 AAACTTAATTCAGGGTAATTAAGTAATCAGT-AAT
*
8866 -AACTTAATTCAGGGTAATTGAGTGAATCAGTAAT
1 AAACTTAATTCAGGGTAATTAAGT-AATCAGTAAT
*
8900 AAACTTAATTCAGGGTAATTAAGTAATTCAATAAT
1 AAACTTAATTCAGGGTAATTAAGTAA-TCAGTAAT
* *
8935 CAACTTAATTCAGGGTAATTGAGTAAGTCAG----
1 AAACTTAATTCAGGGTAATTAAGTAA-TCAGTAAT
8966 AAACTTAATTCAGGGTAATTAAGT-A--AGTAAT
1 AAACTTAATTCAGGGTAATTAAGTAATCAGTAAT
* *
8997 AGGTAACTTAATTCAGGGCAGTTAAG---TCAGTAAGT
1 A---AACTTAATTCAGGGTAATTAAGTAATCAGTAA-T
* *
9032 -AGCTTAATTCAGGGTAATTAAGTAAAGTCAGTTAT
1 AAACTTAATTCAGGGTAATTAAGT-AA-TCAGTAAT
* * * * *
9067 TAACTTAATTCAGGGTAGTTCAGTGAGTCAATAAT
1 AAACTTAATTCAGGGTAATTAAGT-AATCAGTAAT
* * * *
9102 CAACTTAATTCAGGGTAAATAAGTGAGTTAGTAAT
1 AAACTTAATTCAGGGTAATTAAGT-AATCAGTAAT
*
9137 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 AAACTTAATTCAGGGTAATTAAGTAA-TCAGTAAT
* * * *
9172 CAGCTTAATTCGGGGTAATTAAGTGAGTCAGTAAT
1 AAACTTAATTCAGGGTAATTAAGT-AATCAGTAAT
*
9207 CAACTTAATTCAGGGTAATTAAGTAA
1 AAACTTAATTCAGGGTAATTAAGTAA
9233 GGGTAATTAA
Statistics
Matches: 358, Mismatches: 43, Indels: 63
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.01
30 1 0.00
31 63 0.18
32 25 0.07
33 3 0.01
34 57 0.16
35 179 0.50
36 28 0.08
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (34 bp):
AAACTTAATTCAGGGTAATTAAGTAATCAGTAAT
Found at i:8993 original size:70 final size:68
Alignment explanation
Indices: 8737--9233 Score: 433
Period size: 70 Copynumber: 7.4 Consensus size: 68
8727 AGTAAATCAG
* * *
8737 CAACTTAATTCAGGGTAATTGAGTAATTCAGAAACTTAATTCAGGGTAATTAAGT--AAGT-AAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAGAAGTCAGT
*
8799 AGGT
66 A-AT
* * * * *
8803 -AACTTAATTCAGGGCAATTAAGTCAGTAAGTAGCTTAATTCAGGGTAATTAAGTA-AAGTCAG-
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAGAAGTCAGT
8865 --T
66 AAT
* *
8866 -AACTTAATTCAGGGTAATTGAGTGAA-TCAGTAATAAACTTAATTCAGGGTAATTAAGT--AAT
1 CAACTTAATTCAGGGTAATTAAGT-AAGTCAG----AAACTTAATTCAGGGTAATTAAGTAGAAG
*
8927 TCAATAAT
61 TCAGTAAT
* *
8935 CAACTTAATTCAGGGTAATTGAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGT--AAGT-AAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAGAAGTCAGT
*
8997 AGGT
66 A-AT
* * * * * *
9001 -AACTTAATTCAGGGCAGTTAAGTCAGTAAGTAGCTTAATTCAGGGTAATTAAGTA-AAGTCAGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAGAAGTCAGT
*
9064 TAT
66 AAT
* * * * * *
9067 TAACTTAATTCAGGGTAGTTCAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGT-G-AGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTC-A-GA--AACTTAATTCAGGGTAATTAAGTAGAAGT
*
9130 TAGTAAT
62 CAGTAAT
* *
9137 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAGCTTAATTCGGGGTAATTAAGT-G-AGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG-AA--A-CTTAATTCAGGGTAATTAAGTAGAAGT
9200 CAGTAAT
62 CAGTAAT
9207 CAACTTAATTCAGGGTAATTAAGTAAG
1 CAACTTAATTCAGGGTAATTAAGTAAG
9234 GGTAATTAAG
Statistics
Matches: 358, Mismatches: 48, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
63 25 0.07
64 1 0.00
65 98 0.27
66 42 0.12
67 50 0.14
68 1 0.00
69 6 0.02
70 114 0.32
71 21 0.06
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (68 bp):
CAACTTAATTCAGGGTAATTAAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAGAAGTCAGT
AAT
Found at i:9009 original size:167 final size:165
Alignment explanation
Indices: 8720--9230 Score: 539
Period size: 167 Copynumber: 3.0 Consensus size: 165
8710 GTAAGGAAAG
* *
8720 GTGAATCAGTAAATCAGCAACTTAATTCAGGGTAATTGAGTAATTC-A-GA--AACTTAATTCAG
1 GTGAATCAGT-AAT-A--AACTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAG
* * * *
8781 GGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGCAATTAAGTCAGT-A-AGTAGCTTAATTC
62 GGTAATTGAGTAAGT-A-A-GAAACTTAATTCAGGGTAATTAAGTAAGTAATAGTAGCTTAATTC
*
8844 AGGGTAATTAAGTAAAGTCAGTAACTTAATTCAGGGTAATTGA
124 AGGGTAATTAAGT-AAGTCAGTAACTTAATTCAGGGTAATTAA
8887 GTGAATCAGTAATAAACTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 GTGAATCAGTAATAAACTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
* * *
8952 ATTGAGTAAGTCAGAAACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGCA
66 ATTGAGTAAGTAAGAAACTTAATTCAGGGTAATTAAGTAAGTAATA-GTAGCTTAATTCAGGGTA
* * * *
9017 GTTAAGTCAGTAAGTAGCTTAATTCAGGGTAATTAA
130 ATTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAA
* * * * * * *
9053 GTAAAGTCAGTTATTAACTTAATTCAGGGTAGTTCAGTGAGTCAATAATCAACTTAATTCAGGGT
1 GTGAA-TCAGTAATAAACTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAGGGT
* ** * * *
9118 AAATAAGTGAGTTAGTAATCAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAGCTTAATTC
65 -AAT---TGAGTAAGTAAGAAACTTAATTCAGGGTAATTAAGTAAGT-AATAGT-AGCTTAATTC
* *
9183 GGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAA
124 AGGGTAATTAAGTAAGTCAG---T-AACTTAATTCAGGGTAATTAA
9229 GT
1 GT
9231 AAGGGTAATT
Statistics
Matches: 291, Mismatches: 35, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
163 27 0.09
164 27 0.09
165 4 0.01
166 33 0.11
167 111 0.38
168 3 0.01
171 36 0.12
172 27 0.09
175 1 0.00
176 22 0.08
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (165 bp):
GTGAATCAGTAATAAACTTAATTCAGGGTAATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
ATTGAGTAAGTAAGAAACTTAATTCAGGGTAATTAAGTAAGTAATAGTAGCTTAATTCAGGGTAA
TTAAGTAAGTCAGTAACTTAATTCAGGGTAATTAA
Found at i:9207 original size:105 final size:106
Alignment explanation
Indices: 8769--9230 Score: 448
Period size: 105 Copynumber: 4.5 Consensus size: 106
8759 GTAATTCAGA
* * * * *
8769 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-AACTTAATTCAGGGCAATTAAGTCAG-TA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAATA-ATCAACTTAATTCAGGGTAAATAAGTGAGTTA
* *
8831 --AGT-AGCTTAATTCAGGGTAATTAAGTAAAGTCAG---T-
65 GTAATCAACTTAATTCAGGGTAATTAAGTAAAGTCAGTAATC
* * * * * *
8866 AACTTAATTCAGGGTAATTGAGTGAATCAGTAATAAACTTAATTCAGGGTAATTAAGT-AATTCA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGTGAGTT-A
* *
8930 ATAATCAACTTAATTCAGGGTAATTGAGT-AAGTCAG--A--
65 GTAATCAACTTAATTCAGGGTAATTAAGTAAAGTCAGTAATC
* * * ** *
8967 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-AACTTAATTCAGGGCAGTTAAGTCAG-TA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAATA-ATCAACTTAATTCAGGGTAAATAAGTGAGTTA
* * * *
9029 --AGT-AGCTTAATTCAGGGTAATTAAGTAAAGTCAGTTATT
65 GTAATCAACTTAATTCAGGGTAATTAAGTAAAGTCAGTAATC
* *
9068 AACTTAATTCAGGGTAGTTCAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGTGAGTTAG
1 AACTTAATTCAGGGTAATTAAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGTGAGTTAG
*
9133 TAATCAACTTAATTCAGGGTAATTAAGT-AATTCAGTAATC
66 TAATCAACTTAATTCAGGGTAATTAAGTAAAGTCAGTAATC
* * * *
9173 AGCTTAATTCGGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGT
9231 AAGGGTAATT
Statistics
Matches: 304, Mismatches: 40, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
96 21 0.07
97 35 0.12
98 26 0.09
99 3 0.01
100 25 0.08
101 60 0.20
102 47 0.15
103 2 0.01
105 63 0.21
106 22 0.07
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (106 bp):
AACTTAATTCAGGGTAATTAAGTGAGTCAATAATCAACTTAATTCAGGGTAAATAAGTGAGTTAG
TAATCAACTTAATTCAGGGTAATTAAGTAAAGTCAGTAATC
Found at i:9235 original size:14 final size:14
Alignment explanation
Indices: 9218--9244 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9208 AACTTAATTC
9218 AGGGTAATTAAGTA
1 AGGGTAATTAAGTA
9232 AGGGTAATTAAGT
1 AGGGTAATTAAGT
9245 TTAGTAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGTAATTAAGTA
Found at i:12093 original size:72 final size:72
Alignment explanation
Indices: 11985--12396 Score: 598
Period size: 72 Copynumber: 5.7 Consensus size: 72
11975 GTAGTAGCAT
* *
11985 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCCGCTACAATCGCAATGA-GGAAGATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT-ATGGAAGATTA
*
12048 TCACATAA
65 TCATATAA
* * * *
12056 GGATGGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCACAATGAT-GAATATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT-ATGGAAGATTA
**
12120 TCGCATAA
65 TCATATAA
* * *
12128 GGGTTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAGTATGGAAGATTAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATATGGAAGATTAT
*
12193 CATTTAA
66 CATATAA
* * *
12200 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCACAATATGGAAGATTGT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATATGGAAGATTAT
*
12265 CATGTAA
66 CATATAA
*
12272 GGATTGTGCGAAGGACTGCCACATGTGGGAACTGCCTCGGCTACAA-CTGCAATATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATC-GCAATATGGAAGATTA
*
12336 TCATGTAA
65 TCATATAA
12344 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT
12397 GAAGAAGAAG
Statistics
Matches: 312, Mismatches: 24, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
71 22 0.07
72 289 0.93
73 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATATGGAAGATTAT
CATATAA
Found at i:12880 original size:35 final size:35
Alignment explanation
Indices: 12759--12882 Score: 151
Period size: 35 Copynumber: 3.5 Consensus size: 35
12749 GAAGTTTTCA
* * * * *
12759 TTGTTGAAG-CCCTCAAGTATTGAATGAAGAATGAG
1 TTGTTGGAGTCCC-CAAGTGTTGAATGAGGAAGGGG
* * *
12794 TTGCTGGAGTACCCAACTGTTGAATGAGGAAGGGG
1 TTGTTGGAGTCCCCAAGTGTTGAATGAGGAAGGGG
*
12829 TTGTTAGAGTCCCCAAGTGTTGAATGAGGAAGGGG
1 TTGTTGGAGTCCCCAAGTGTTGAATGAGGAAGGGG
12864 TTGTTGGAGTCCCCAAGTG
1 TTGTTGGAGTCCCCAAGTG
12883 CTAAATCTGA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
35 73 0.97
36 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.27
Consensus pattern (35 bp):
TTGTTGGAGTCCCCAAGTGTTGAATGAGGAAGGGG
Found at i:16846 original size:42 final size:41
Alignment explanation
Indices: 16744--16858 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 41
16734 ATGTAGAGAA
* ** * *
16744 AATTGCCCTTGTGTTGCATGTGTTT-AGGGACTTTAGTATAG
1 AATTGCCCCTGTGTTATATGTGTTTGA-GGACTTTAGAAGAG
*
16785 -A-TGCCTCTGTGTTATATGTGTTTGAGGACTTTAGAAGGAG
1 AATTGCCCCTGTGTTATATGTGTTTGAGGACTTTAGAA-GAG
*
16825 AATTGCCCCTGTGTTATATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATATGTGTTTGAGGACTTT
16859 GGGGAGAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
39 28 0.45
40 4 0.06
41 1 0.02
42 29 0.47
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (41 bp):
AATTGCCCCTGTGTTATATGTGTTTGAGGACTTTAGAAGAG
Found at i:17604 original size:16 final size:17
Alignment explanation
Indices: 17560--17604 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
17550 GCGGGTCAGG
17560 TCGGGTTCGGGTTGAAT
1 TCGGGTTCGGGTTGAAT
* *
17577 TTGGG-TCAGGTT-AAT
1 TCGGGTTCGGGTTGAAT
17592 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
17605 CAGTTTGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (17 bp):
TCGGGTTCGGGTTGAAT
Found at i:17796 original size:32 final size:32
Alignment explanation
Indices: 17752--17841 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
17742 TTTTAATAAA
*
17752 TTTTCGGATTCGGGTTTTTTC-GAGTTTGAACT
1 TTTTCGGGTTCGGGTTTTTTCAG-GTTTGAACT
17784 TTTTCGGGTTCGGGTTTTTTCAGGTTTGAACT
1 TTTTCGGGTTCGGGTTTTTTCAGGTTTGAACT
* *
17816 TTTTCGGGTTTGGATTTTTTCAGGTT
1 TTTTCGGGTTCGGGTTTTTTCAGGTT
17842 CAGGTTCAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 53 0.98
33 1 0.02
ACGTcount: A:0.10, C:0.11, G:0.27, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCAGGTTTGAACT
Found at i:17809 original size:16 final size:16
Alignment explanation
Indices: 17783--17842 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
17773 GAGTTTGAAC
* *
17783 TTTTTCGGGTTCGGGT
1 TTTTTCAGGTTCGGAT
* * *
17799 TTTTTCAGGTTTGAAC
1 TTTTTCAGGTTCGGAT
* *
17815 TTTTTCGGGTTTGGAT
1 TTTTTCAGGTTCGGAT
17831 TTTTTCAGGTTC
1 TTTTTCAGGTTC
17843 AGGTTCAGGC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.08, C:0.12, G:0.27, T:0.53
Consensus pattern (16 bp):
TTTTTCAGGTTCGGAT
Found at i:34545 original size:30 final size:30
Alignment explanation
Indices: 34509--34569 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
34499 CTAAACAAGA
*
34509 GGCATTAGTGGCACTACGTATAGAAATAGT
1 GGCATTAGTGGCACTACGCATAGAAATAGT
* * *
34539 GGCATTAGTTGCAGTAGGCATAGAAATAGT
1 GGCATTAGTGGCACTACGCATAGAAATAGT
34569 G
1 G
34570 TTTATGGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (30 bp):
GGCATTAGTGGCACTACGCATAGAAATAGT
Done.