Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007029.1 Corchorus capsularis cultivar CVL-1 contig07050, 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: 24482
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:2651 original size:21 final size:20
Alignment explanation
Indices: 2627--2673 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2617 AAAAGAGAGG
*
2627 AAGATAAAATAAAAGGAAAAA
1 AAGA-AAAATAAAAAGAAAAA
*
2648 AAGAAGAATAAAAAG-AAAA
1 AAGAAAAATAAAAAGAAAAA
2667 AAGAAAA
1 AAGAAAA
2674 GGAAAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.43
20 9 0.39
21 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (20 bp):
AAGAAAAATAAAAAGAAAAA
Found at i:2759 original size:15 final size:14
Alignment explanation
Indices: 2739--2790 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2729 CAAGATACAT
*
2739 TTTTCAAAAAAATTG
1 TTTTCAAAAAAA-GG
*
2754 TTTTCAATAAAAGG
1 TTTTCAAAAAAAGG
**
2768 TTTTCAAAAATGGG
1 TTTTCAAAAAAAGG
2782 TTTTCAAAA
1 TTTTCAAAA
2791 CGGTTTTGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (14 bp):
TTTTCAAAAAAAGG
Found at i:3162 original size:13 final size:13
Alignment explanation
Indices: 3133--3161 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3123 AAAAAGAAGC
3133 AAAAGCGAAAAAG
1 AAAAGCGAAAAAG
3146 AAAAG-GAAAAAG
1 AAAAGCGAAAAAG
3158 AAAA
1 AAAA
3162 AAATAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGCGAAAAAG
Found at i:3802 original size:10 final size:10
Alignment explanation
Indices: 3789--3826 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3779 AATTTTGGAT
3789 AAAAAAAAGA
1 AAAAAAAAGA
3799 AAAAAAAAGA
1 AAAAAAAAGA
3809 AAAAGAAAA-A
1 AAAA-AAAAGA
3819 AAACAAAA
1 AAA-AAAA
3827 TTGGGAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 21 0.81
11 5 0.19
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:4644 original size:35 final size:35
Alignment explanation
Indices: 4593--4760 Score: 192
Period size: 35 Copynumber: 4.8 Consensus size: 35
4583 GGAACGATTG
* * * *
4593 AGGGTGGTCATTCTTCAATTTATTTCGGTTTACCC
1 AGGGCGGTCATTCTTCAGTTTATTTCAGTTGACCC
*
4628 AGGGCGGTCATTCTTCAGTTTATTTTAGTTGACCC
1 AGGGCGGTCATTCTTCAGTTTATTTCAGTTGACCC
* * * *
4663 AGGGCAGTCTTTCTTCAGTTTATCTCAGTTAACCC
1 AGGGCGGTCATTCTTCAGTTTATTTCAGTTGACCC
* *
4698 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGCGGTCATTCTTCAGTTTATTTCAGTTGACCC
* * * * *
4733 ATGACGGTCTTTCTCCAGTTTATGTCAG
1 AGGGCGGTCATTCTTCAGTTTATTTCAG
4761 AATGATCGAT
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 114 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (35 bp):
AGGGCGGTCATTCTTCAGTTTATTTCAGTTGACCC
Found at i:4923 original size:70 final size:70
Alignment explanation
Indices: 4749--5023 Score: 415
Period size: 70 Copynumber: 3.9 Consensus size: 70
4739 GTCTTTCTCC
* *
4749 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTTTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
4814 ATTCCA
66 A-TCCA
* * *
4820 AGTTTATATCAGAATGATCGATTCAGTCAACCCAGGGCGGTCTTTCTTCAATTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
4885 ATCCA
66 ATCCA
* * * *
4890 AGTTTATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
4955 ATCCA
66 ATCCA
* * * * *
4960 AGTTTGTGACAGAATGATCGATTCAGTCGACCTAGGCCGGTTTTTCTTCAGTTGTTTCCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
5024 GATTCAAGGG
Statistics
Matches: 183, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
70 122 0.67
71 61 0.33
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:5073 original size:36 final size:36
Alignment explanation
Indices: 5022--5110 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 36
5012 TGTTTCCAAG
*
5022 TTGATTCAAGGGTGGTCAG-TTCGTCCATGCATTTTAA
1 TTGATTC-AGGGTGGTCAGCTT-GTCAATGCATTTTAA
*
5059 TTGATTCAGGGTGGTCAGCTTTTCAATGCATTTTAA
1 TTGATTCAGGGTGGTCAGCTTGTCAATGCATTTTAA
*
5095 TTGATACAGGGTGGTC
1 TTGATTCAGGGTGGTC
5111 GGTCTTCAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
36 39 0.81
37 9 0.19
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (36 bp):
TTGATTCAGGGTGGTCAGCTTGTCAATGCATTTTAA
Found at i:5631 original size:27 final size:27
Alignment explanation
Indices: 5598--5672 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
5588 TAGAGTTATA
*
5598 CAAGGGCATTTTGGTCATTTTTACATT
1 CAAGGGCATTTAGGTCATTTTTACATT
*
5625 CAGGGGCATTTAGGTCATTTTTACATT
1 CAAGGGCATTTAGGTCATTTTTACATT
5652 CAAGGGCATTTAGGTCATTTT
1 CAAGGGCATTTAGGTCATTTT
5673 AAGTTTACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (27 bp):
CAAGGGCATTTAGGTCATTTTTACATT
Found at i:10767 original size:16 final size:16
Alignment explanation
Indices: 10746--10864 Score: 125
Period size: 16 Copynumber: 7.5 Consensus size: 16
10736 CATGCAGTTT
* *
10746 TTTCGGGTCATTTGGA
1 TTTCGGGTCATTCGGG
*
10762 TTTCGGGTCA-TCTAGG
1 TTTCGGGTCATTC-GGG
*
10778 -TTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* *
10793 TCTCGGGTCGTTCGGG
1 TTTCGGGTCATTCGGG
* *
10809 TCTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
10825 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
10841 TCTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
10857 TCTCGGGT
1 TTTCGGGT
10865 TGGGCGGGTT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
15 11 0.13
16 76 0.87
ACGTcount: A:0.08, C:0.20, G:0.37, T:0.35
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:10825 original size:32 final size:32
Alignment explanation
Indices: 10748--10864 Score: 139
Period size: 32 Copynumber: 3.7 Consensus size: 32
10738 TGCAGTTTTT
* * * *
10748 TCGGGTCATTTGGATTTCGGGTCA-TCTAGGT-
1 TCGGGTCATTCGGGTCTCGGGTCATTC-GGGTC
* *
10779 TCGGGTTATTCGGGTCTCGGGTCGTTCGGGTC
1 TCGGGTCATTCGGGTCTCGGGTCATTCGGGTC
* *
10811 TCGGGTCATACGGGTTTCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTCTCGGGTCATTCGGGTC
10843 TCGGGTCATTCGGGTCTCGGGT
1 TCGGGTCATTCGGGTCTCGGGT
10865 TGGGCGGGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
31 22 0.31
32 50 0.69
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.34
Consensus pattern (32 bp):
TCGGGTCATTCGGGTCTCGGGTCATTCGGGTC
Found at i:10873 original size:48 final size:47
Alignment explanation
Indices: 10776--10879 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 47
10766 GGGTCATCTA
* * *
10776 GGTTCGGGTTATTCGGGTCTCGGGTCGTTCGGGTCTCGGGTCATACG
1 GGTTCGGGTCATTCGGGTCTCGGGTCATTCGGGTCTCGGGTCAGACG
** *
10823 GGTTTCGGGTCATTCGGGTCTCGGGTCATTCGGGTCTCGGGTTGGGCG
1 GG-TTCGGGTCATTCGGGTCTCGGGTCATTCGGGTCTCGGGTCAGACG
10871 GGTTCGGGT
1 GGTTCGGGT
10880 TTTAACTTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
47 9 0.18
48 41 0.82
ACGTcount: A:0.05, C:0.20, G:0.43, T:0.32
Consensus pattern (47 bp):
GGTTCGGGTCATTCGGGTCTCGGGTCATTCGGGTCTCGGGTCAGACG
Found at i:11292 original size:21 final size:21
Alignment explanation
Indices: 11265--11311 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
11255 TAACCAATTT
11265 ATAATTGGTAAAATCATAACA
1 ATAATTGGTAAAATCATAACA
* *
11286 TTAATTGGTAAAATTATAACA
1 ATAATTGGTAAAATCATAACA
11307 ATAAT
1 ATAAT
11312 ATAAATTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (21 bp):
ATAATTGGTAAAATCATAACA
Found at i:11448 original size:16 final size:15
Alignment explanation
Indices: 11428--11520 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 15
11418 CTTGGGTTAT
*
11428 TCGGGTTTCGGGTCA
1 TCGGGTCTCGGGTCA
11443 TACGGGTCTCGGGTCA
1 T-CGGGTCTCGGGTCA
11459 TCTGGGT-TACGGGTCA
1 TC-GGGTCT-CGGGTCA
*
11475 TTCGGGTCTCGGGTAA
1 -TCGGGTCTCGGGTCA
*
11491 TCTGGGT-TGTGGGTCA
1 TC-GGGTCT-CGGGTCA
*
11507 TTCGGGTCACGGGT
1 -TCGGGTCTCGGGT
11521 TCGTCGTGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
15 6 0.10
16 52 0.83
17 5 0.08
ACGTcount: A:0.10, C:0.19, G:0.40, T:0.31
Consensus pattern (15 bp):
TCGGGTCTCGGGTCA
Found at i:11472 original size:32 final size:32
Alignment explanation
Indices: 11430--11520 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
11420 TGGGTTATTC
* * *
11430 GGGTTTCGGGTCATACGGGTCTCGGGTCATCT
1 GGGTTACGGGTCATTCGGGTCTCGGGTAATCT
11462 GGGTTACGGGTCATTCGGGTCTCGGGTAATCT
1 GGGTTACGGGTCATTCGGGTCTCGGGTAATCT
** *
11494 GGGTTGTGGGTCATTCGGGTCACGGGT
1 GGGTTACGGGTCATTCGGGTCTCGGGT
11521 TCGTCGTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.10, C:0.19, G:0.41, T:0.31
Consensus pattern (32 bp):
GGGTTACGGGTCATTCGGGTCTCGGGTAATCT
Found at i:11612 original size:26 final size:27
Alignment explanation
Indices: 11575--11626 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
11565 CTGGTCAAAT
*
11575 CGGGTTGCGCGGGTTA-CGGGTTCGGA
1 CGGGTTGCGCGGATTATCGGGTTCGGA
*
11601 CGGGTTGGGCGGATTATCGGGTTCGG
1 CGGGTTGCGCGGATTATCGGGTTCGG
11627 GTCAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.08, C:0.17, G:0.50, T:0.25
Consensus pattern (27 bp):
CGGGTTGCGCGGATTATCGGGTTCGGA
Found at i:13845 original size:42 final size:41
Alignment explanation
Indices: 13726--13862 Score: 192
Period size: 39 Copynumber: 3.4 Consensus size: 41
13716 CAATTAAAGT
*
13726 CTTAATTTAGTGTAATTAAG-AA-AAATTAAGAAAAGTAAGC
1 CTTAATTCAGTGTAA-TAAGAAAGAAATTAAGAAAAGTAAGC
13766 CTTAATTCAGTGTAAT-A-AAAGAAATTAAGAAAAGTAAGC
1 CTTAATTCAGTGTAATAAGAAAGAAATTAAGAAAAGTAAGC
*
13805 CTTAATTCAGTGTAATCAAGAAAGAAATTAAGAAATGTAAGC
1 CTTAATTCAGTGTAAT-AAGAAAGAAATTAAGAAAAGTAAGC
* *
13847 CTCAATTCAGTATAAT
1 CTTAATTCAGTGTAAT
13863 TAAGCAAAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
38 3 0.03
39 35 0.40
40 14 0.16
41 1 0.01
42 35 0.40
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (41 bp):
CTTAATTCAGTGTAATAAGAAAGAAATTAAGAAAAGTAAGC
Found at i:13888 original size:32 final size:30
Alignment explanation
Indices: 13830--14107 Score: 139
Period size: 31 Copynumber: 8.4 Consensus size: 30
13820 TCAAGAAAGA
* * * * *
13830 AATTAAGAAATGTAAGCCTCAATTCAGTAT
1 AATTAAGAAAAGAAAGTCTTAATTCAGGAT
*
13860 AATTAAGCAAAAGCAAAGTCTTAATTCAGGGT
1 AATTAAG-AAAAG-AAAGTCTTAATTCAGGAT
*
13892 AATTAAGAAAAGAAAGTACATTCAAGGTCTTAATCTGG-T
1 AATTAAGAAAAGAAAGT-C-TT-AA-----T--TCAGGAT
*
13931 AATTAAGTAAAAGCAAAGTCTTAATTCAGGGT
1 AATTAAG-AAAAG-AAAGTCTTAATTCAGGAT
* * *
13963 AATTAAGAAAAGTAAGCACAGTCAAGGTCTTAATCCGG-T
1 AATTAAGAAAAG--A--A-AGTC----T-TAATTCAGGAT
*
14002 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAG-AAAGTCTTAATTCAGGAT
* *
14033 AATTAAGAAAAGAAAGTATAGTCAATTAAGGA-
1 AATTAAGAAAAGAAAGTCT--T-AATTCAGGAT
*
14065 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAG-AAAGTCTTAATTCAGGAT
14096 AATTAAGAAAAG
1 AATTAAGAAAAG
14108 TAAGCATAGT
Statistics
Matches: 196, Mismatches: 22, Indels: 59
0.71 0.08 0.21
Matches are distributed among these distances:
30 31 0.16
31 46 0.23
32 44 0.22
33 16 0.08
34 1 0.01
35 8 0.04
36 1 0.01
38 4 0.02
39 24 0.12
40 16 0.08
41 5 0.03
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.26
Consensus pattern (30 bp):
AATTAAGAAAAGAAAGTCTTAATTCAGGAT
Found at i:13935 original size:39 final size:38
Alignment explanation
Indices: 13889--14019 Score: 116
Period size: 39 Copynumber: 3.5 Consensus size: 38
13879 CTTAATTCAG
*
13889 GGTAATTAAGAAAAGAAAGTACATTCAAGGTCTTAATCT
1 GGTAATTAAGAAAAGAAAGTACA-TCAAGGTCTTAATCC
* *
13928 GGTAATTAAG--TA-AAAG--CA--AA-GTCTTAATTCAG
1 GGTAATTAAGAAAAGAAAGTACATCAAGGTCTTAA-TC-C
* *
13960 GGTAATTAAGAAAAGTAAGCACAGTCAAGGTCTTAATCC
1 GGTAATTAAGAAAAGAAAGTACA-TCAAGGTCTTAATCC
13999 GGTAATTAAGAAAAGTAAAGT
1 GGTAATTAAGAAAAG-AAAGT
14020 CTTAATTCAG
Statistics
Matches: 73, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
30 7 0.10
31 4 0.05
32 10 0.14
34 3 0.04
35 3 0.04
36 4 0.05
37 3 0.04
39 25 0.34
40 7 0.10
41 7 0.10
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (38 bp):
GGTAATTAAGAAAAGAAAGTACATCAAGGTCTTAATCC
Found at i:14037 original size:31 final size:31
Alignment explanation
Indices: 13999--14110 Score: 156
Period size: 31 Copynumber: 3.6 Consensus size: 31
13989 GTCTTAATCC
13999 GGTAATTAAGAAAAGTAAAGTCTTAATTCAG
1 GGTAATTAAGAAAAGTAAAGTCTTAATTCAG
* *
14030 GGTAATTAAGAAAAG-AAAGTATAGTCAATT-AA
1 GGTAATTAAGAAAAGTAAAGTCT--T-AATTCAG
*
14062 GGAAATTAAGAAAAGTAAAGTCTTAATTCAG
1 GGTAATTAAGAAAAGTAAAGTCTTAATTCAG
14093 GGTAATTAAGAAAAGTAA
1 GGTAATTAAGAAAAGTAA
14111 GCATAGTCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
30 10 0.14
31 34 0.49
32 16 0.23
33 10 0.14
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (31 bp):
GGTAATTAAGAAAAGTAAAGTCTTAATTCAG
Found at i:14056 original size:70 final size:70
Alignment explanation
Indices: 13859--14311 Score: 659
Period size: 70 Copynumber: 6.5 Consensus size: 70
13849 CAATTCAGTA
* * * *
13859 TAATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACATTCAAGGTCTTA
1 TAATTAAG-AAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
*
13924 ATCTGG
65 ATTTGG
*
13930 TAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAGGTCTTA
1 TAATTAAG-AAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
**
13995 ATCCGG
65 ATTTGG
* * *
14001 TAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAA----TTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
14062 ---GG
66 TTTGG
* *
14064 AAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
14129 TTTGG
66 TTTGG
*
14134 TAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
14199 TTTGG
66 TTTGG
* *
14204 TAATTAAGAAAAGCAATGTCTTAATCCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
14269 TTTGG
66 TTTGG
* * * *
14274 TGATTAAGAAAAGCAATGTCTTAATCCAGGATAATTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAA
14312 TTAGAGTAAA
Statistics
Matches: 357, Mismatches: 18, Indels: 15
0.92 0.05 0.04
Matches are distributed among these distances:
63 56 0.16
66 4 0.01
67 4 0.01
70 219 0.61
71 74 0.21
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (70 bp):
TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
TTTGG
Found at i:14103 original size:133 final size:135
Alignment explanation
Indices: 13859--14311 Score: 631
Period size: 133 Copynumber: 3.3 Consensus size: 135
13849 CAATTCAGTA
* *
13859 TAATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACATTCAAGGTCTTA
1 TAATTAAG-AAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAA-G--TTA
*
13924 ATCTGGTAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAG
62 A--TGGTAATTAAG-AAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAG
**
13989 GTCTTAATCCGG
124 GTCTTAATTTGG
*
14001 TAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAA-TTAA-GG
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGTTAATGG
* *
14064 AAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
66 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
14129 TTTGG
131 TTTGG
* * *
14134 TAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAA-G--TTAA
* *
14199 TTTGGTAATTAAGAAAAGCAATGTCTTAATCCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGT
63 --TGGTAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGT
14264 CTTAATTTGG
126 CTTAATTTGG
* * * *
14274 TGATTAAGAAAAGCAATGTCTTAATCCAGGATAATTAA
1 TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAA
14312 TTAGAGTAAA
Statistics
Matches: 285, Mismatches: 19, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
133 113 0.40
134 9 0.03
137 8 0.03
140 101 0.35
141 46 0.16
142 8 0.03
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (135 bp):
TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGTTAATGG
TAATTAAGAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
TTTGG
Found at i:14138 original size:39 final size:39
Alignment explanation
Indices: 14093--14286 Score: 176
Period size: 39 Copynumber: 5.4 Consensus size: 39
14083 CTTAATTCAG
14093 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
*
14132 GGTAATTAAG--AA--AAG--TA---AA-GTCTTAATTCAG
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATT--T
14163 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
**
14202 GGTAATTAAG--AA--AAGCA-A-T----GTCTTAATCCAG
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAAT--TT
14233 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
*
14272 GGTGATTAAGAAAAG
1 GGTAATTAAGAAAAG
14287 CAATGTCTTA
Statistics
Matches: 124, Mismatches: 7, Indels: 48
0.69 0.04 0.27
Matches are distributed among these distances:
29 17 0.14
30 2 0.02
31 20 0.16
33 7 0.06
34 1 0.01
35 16 0.13
36 1 0.01
37 7 0.06
39 34 0.27
40 2 0.02
41 17 0.14
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (39 bp):
GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
Found at i:14155 original size:29 final size:30
Alignment explanation
Indices: 14122--14180 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
14112 CATAGTCAAG
*
14122 GTCTTAATT-TGGTAATTAAGAAAAGTAAA
1 GTCTTAATTAGGGTAATTAAGAAAAGTAAA
14151 GTCTTAATTCAGGGTAATTAAGAAAAGTAA
1 GTCTTAATT-AGGGTAATTAAGAAAAGTAA
14181 GCATAGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
31 18 0.67
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (30 bp):
GTCTTAATTAGGGTAATTAAGAAAAGTAAA
Found at i:14192 original size:203 final size:205
Alignment explanation
Indices: 13860--14260 Score: 653
Period size: 203 Copynumber: 2.0 Consensus size: 205
13850 AATTCAGTAT
* *
13860 AATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACATTCAAGGTCTTAA
1 AATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCTTAA
13925 TCTGGTAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAGG
66 TCTGGTAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAGG
* * *
13990 TCTTAATCCGGTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGT
131 TCTTAATCCGGTAATTAAGAAAAGCAAAGTCTTAATCCAGGGTAATTAAGAAAAGAAAGCATAGT
14055 CAATTAAGGA
196 CAATTAAGGA
* * *
14065 AATTAAG-AAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAA
1 AATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCTTAA
* * *
14129 TTTGGTAATTAAG-AAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGG
66 TCTGGTAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAGG
** * *
14193 TCTTAATTTGGTAATTAAGAAAAGCAATGTCTTAATCCAGGGTAATTAAGAAAAGTAAGCATAGT
131 TCTTAATCCGGTAATTAAGAAAAGCAAAGTCTTAATCCAGGGTAATTAAGAAAAGAAAGCATAGT
14258 CAA
196 CAA
14261 GGTCTTAATT
Statistics
Matches: 181, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
203 110 0.61
204 64 0.35
205 7 0.04
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (205 bp):
AATTAAGCAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCTTAA
TCTGGTAATTAAGTAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCACAGTCAAGG
TCTTAATCCGGTAATTAAGAAAAGCAAAGTCTTAATCCAGGGTAATTAAGAAAAGAAAGCATAGT
CAATTAAGGA
Found at i:14500 original size:40 final size:40
Alignment explanation
Indices: 14334--14479 Score: 229
Period size: 40 Copynumber: 3.6 Consensus size: 40
14324 CAGTCTGGGG
*
14334 CTTAATTCATAGAAATTAAGTAAAAATAGCAGTTAAAGGA
1 CTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAAAGGA
*
14374 CTTAATTCATAGCAATTAAGTAAAAACAGCAGTTAAAGGA
1 CTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAAAGGA
* * * *
14414 CTTAATTCATGGAAATTAAGTGAAAACAACAGTTAAAAGA
1 CTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAAAGGA
*
14454 CTTAATTCATGGAAATTAAGTAAAAA
1 CTTAATTCATAGAAATTAAGTAAAAA
14480 TAGACAAGCA
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (40 bp):
CTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAAAGGA
Found at i:14539 original size:41 final size:41
Alignment explanation
Indices: 14485--14807 Score: 494
Period size: 41 Copynumber: 8.0 Consensus size: 41
14475 AAAAATAGAC
14485 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
* *
14526 AAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
14567 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
* *
14608 AAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
* * *
14649 AAGCACATACTTAATTTC---G-AGGAAATTAGGTCAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
*
14686 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
*
14727 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAA-GA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
* **
14767 AAGGCACAGGCTTAATTTCAAGGAATAAAATTAGGTAAAGG
1 AA-GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGG
14808 CAATAAAAGG
Statistics
Matches: 257, Mismatches: 19, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
37 33 0.13
38 1 0.00
40 4 0.02
41 218 0.85
42 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
Found at i:14691 original size:160 final size:162
Alignment explanation
Indices: 14485--14806 Score: 517
Period size: 160 Copynumber: 2.0 Consensus size: 162
14475 AAAAATAGAC
*
14485 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGAAAGCACGGACTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTC-A-GAAGGAAATTAGGTAAAGGAAAGCACAGACTTAATTTCAAGGAA
14550 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGAAA-GCAC
64 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-GAAAGGCAC
*
14614 -GGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
128 AGG-CTTAATTTCAAGGAAGAAAATTAGGTAAAGAA
* * *
14649 AAGCACATACTTAATTTC-G-AGGAAATTAGGTCAAGTAAAGCACAGACTTAATTTCAAGGAAGG
1 AAGCACAGACTTAATTTCAGAAGGAAATTAGGTAAAGGAAAGCACAGACTTAATTTCAAGGAAGG
*
14712 AAATTAGGTAAAGAAAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGGCACAGG
66 AAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGGCACAGG
*
14777 CTTAATTTCAAGGAATAAAATTAGGTAAAG
131 CTTAATTTCAAGGAAGAAAATTAGGTAAAG
14807 GCAATAAAAG
Statistics
Matches: 149, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
159 4 0.03
160 125 0.84
161 3 0.02
164 17 0.11
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (162 bp):
AAGCACAGACTTAATTTCAGAAGGAAATTAGGTAAAGGAAAGCACAGACTTAATTTCAAGGAAGG
AAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGGCACAGG
CTTAATTTCAAGGAAGAAAATTAGGTAAAGAA
Found at i:14718 original size:119 final size:119
Alignment explanation
Indices: 14485--14791 Score: 479
Period size: 119 Copynumber: 2.5 Consensus size: 119
14475 AAAAATAGAC
* *
14485 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGAAAGCACGGACTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC---G-A
*
14550 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGA
62 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
* *
14608 AAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACATACTTAATTTCGAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCGAGGAA
* *
14673 ATTAGGTCAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
66 ATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
* * * *
14727 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGGCACAGGCTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCGAGGAA
14792 TAAAATTAGG
Statistics
Matches: 171, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
119 115 0.67
120 1 0.01
123 55 0.32
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (119 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCGAGGAA
ATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
Found at i:17160 original size:30 final size:30
Alignment explanation
Indices: 17124--17186 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
17114 TGTCTTCAAG
17124 TCCATGATAAGTCCTT-GGCACATCATTCCC
1 TCCATGATAAG-CCTTGGGCACATCATTCCC
* *
17154 TCCATGATATGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCACATCATTCCC
17184 TCC
1 TCC
17187 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCACATCATTCCC
Found at i:20950 original size:10 final size:10
Alignment explanation
Indices: 20935--20960 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20925 GAGGACTCTA
20935 GAATTTTCTG
1 GAATTTTCTG
20945 GAATTTTCTG
1 GAATTTTCTG
20955 GAATTT
1 GAATTT
20961 GGCAGCAATT
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:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Done.