Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021264.1 Corchorus olitorius cultivar O-4 contig21297, 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: 101607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2942 original size:2 final size:2
Alignment explanation
Indices: 2935--2965 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2925 AATATTTTAA
2935 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2966 CATAGAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5292 original size:2 final size:2
Alignment explanation
Indices: 5285--5321 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5275 ATCTAAAAAT
5285 TA TA TA TA 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 TA T
5322 TCTTGAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8983 original size:14 final size:14
Alignment explanation
Indices: 8945--8976 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8935 CTATATGGTG
8945 TATAAGCTAAGAGA
1 TATAAGCTAAGAGA
8959 TATAAGCTAAGAGA
1 TATAAGCTAAGAGA
8973 TATA
1 TATA
8977 CATTAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (14 bp):
TATAAGCTAAGAGA
Found at i:14267 original size:16 final size:16
Alignment explanation
Indices: 14246--14279 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14236 TTGCTTTACA
14246 TAAATAAAGTGAAATT
1 TAAATAAAGTGAAATT
* *
14262 TAAATAAATTGTAATT
1 TAAATAAAGTGAAATT
14278 TA
1 TA
14280 TTTAGATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAATAAAGTGAAATT
Found at i:16319 original size:20 final size:20
Alignment explanation
Indices: 16294--16332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16284 TTGGTGAAAA
**
16294 TTAAATCATTTACAATTAAT
1 TTAAATCATAAACAATTAAT
16314 TTAAATCATAAACAATTAA
1 TTAAATCATAAACAATTAA
16333 ATCATTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATCATAAACAATTAAT
Found at i:17150 original size:24 final size:24
Alignment explanation
Indices: 17117--17164 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17107 CCAATTGTTC
*
17117 GTTTAGTATCTTTGGAAAGTTGAA
1 GTTTAATATCTTTGGAAAGTTGAA
17141 GTTTAATATCTTTGGAAAGTTGAA
1 GTTTAATATCTTTGGAAAGTTGAA
17165 AGTTGAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (24 bp):
GTTTAATATCTTTGGAAAGTTGAA
Found at i:29846 original size:2 final size:2
Alignment explanation
Indices: 29839--29867 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29829 AATGCTAATG
29839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29868 GCTCTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32068 original size:13 final size:13
Alignment explanation
Indices: 32035--32068 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
32025 CTTTATCGTT
32035 TTTTTTTTCGATC
1 TTTTTTTTCGATC
*
32048 CTTTTTTTCGATC
1 TTTTTTTTCGATC
32061 TTTTTTTT
1 TTTTTTTT
32069 TGCTTGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGATC
Found at i:32179 original size:56 final size:59
Alignment explanation
Indices: 32117--32245 Score: 165
Period size: 56 Copynumber: 2.2 Consensus size: 59
32107 GCTAGGGGAG
** *
32117 TCTCCCCTGGCGTGCGGCGCTGGGGG-GTCTCTCCCCCGGTG-CGCA-CTGGGGGAGGC
1 TCTCCCCTGGCGCACGGCGCTGGGGGAGTCTCTCCCCCGGCGACGCAGCTGGGGGAGGC
* * * *
32173 TCTCCCCTGACGCACGGCGCTGGGGGAGTCTCTCCCCTGGCGCACGGAGCTGGGGGAGTC
1 TCTCCCCTGGCGCACGGCGCTGGGGGAGTCTCTCCCCCGGCG-ACGCAGCTGGGGGAGGC
32233 TCTCCCCTGGCGC
1 TCTCCCCTGGCGC
32246 TGGTTTTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 23 0.38
57 13 0.21
59 3 0.05
60 22 0.36
ACGTcount: A:0.06, C:0.37, G:0.39, T:0.18
Consensus pattern (59 bp):
TCTCCCCTGGCGCACGGCGCTGGGGGAGTCTCTCCCCCGGCGACGCAGCTGGGGGAGGC
Found at i:32242 original size:30 final size:30
Alignment explanation
Indices: 32117--32245 Score: 149
Period size: 30 Copynumber: 4.4 Consensus size: 30
32107 GCTAGGGGAG
** *
32117 TCTCCCCTGGCGTGCGGCGCTGGGGG-GTC
1 TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
* * * *
32146 TCTCCCCCGGTG--CGCA-CTGGGGGAGGC
1 TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
* *
32173 TCTCCCCTGACGCACGGCGCTGGGGGAGTC
1 TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
32203 TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
1 TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
32233 TCTCCCCTGGCGC
1 TCTCCCCTGGCGC
32246 TGGTTTTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
26 7 0.08
27 13 0.16
29 12 0.14
30 51 0.61
ACGTcount: A:0.06, C:0.37, G:0.39, T:0.18
Consensus pattern (30 bp):
TCTCCCCTGGCGCACGGAGCTGGGGGAGTC
Found at i:32319 original size:26 final size:26
Alignment explanation
Indices: 32290--32370 Score: 110
Period size: 26 Copynumber: 3.0 Consensus size: 26
32280 GCCTCCCCTA
*
32290 GTGCGCTGCTAGGGGTCTCCCTTGGG
1 GTGCGCTGCTAGGGGTCTCCCATGGG
32316 GTGCGCTGCTAGGGGTCTCCCATGGG
1 GTGCGCTGCTAGGGGTCTCCCATGGG
*
32342 G-GCGTGCTGCTAGGGGGTCTCCCCTGGG
1 GTGC--GCTGCTA-GGGGTCTCCCATGGG
32370 G
1 G
32371 GAGCCTCCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.04
26 26 0.52
27 7 0.14
28 15 0.30
ACGTcount: A:0.05, C:0.27, G:0.44, T:0.23
Consensus pattern (26 bp):
GTGCGCTGCTAGGGGTCTCCCATGGG
Found at i:42964 original size:12 final size:11
Alignment explanation
Indices: 42930--42982 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
42920 GTCTAACCGT
42930 TATATTATTATA
1 TATATTA-TATA
*
42942 TACATTA-ATA
1 TATATTATATA
42952 TATA-TATATA
1 TATATTATATA
42962 TATATTATATGA
1 TATATTATAT-A
42974 TA-ATTATAT
1 TATATTATAT
42983 GATTGAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 2 0.06
10 13 0.36
11 12 0.33
12 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
TATATTATATA
Found at i:42979 original size:11 final size:12
Alignment explanation
Indices: 42930--42985 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 12
42920 GTCTAACCGT
42930 TATATTATTAT-A
1 TATATTA-TATGA
*
42942 TACATTA-AT-A
1 TATATTATATGA
42952 TATA-TATAT-A
1 TATATTATATGA
42962 TATATTATATGA
1 TATATTATATGA
42974 TA-ATTATATGA
1 TATATTATATGA
42985 T
1 T
42986 TGAAATCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 13 0.33
11 15 0.38
12 9 0.23
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
TATATTATATGA
Found at i:45498 original size:15 final size:15
Alignment explanation
Indices: 45478--45510 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
45468 ATTAATCCAT
*
45478 TACCAAGTGAATTGA
1 TACCAAGTGAACTGA
45493 TACCAAGTGAACTGA
1 TACCAAGTGAACTGA
45508 TAC
1 TAC
45511 TAAATCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (15 bp):
TACCAAGTGAACTGA
Found at i:50532 original size:22 final size:24
Alignment explanation
Indices: 50507--50552 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
50497 CGTGCCAGCT
50507 TGGCACGCTGGGCC-GCG-CTGGC
1 TGGCACGCTGGGCCTGCGCCTGGC
50529 TGGCACGCTGGGCCTGCGCCTGGC
1 TGGCACGCTGGGCCTGCGCCTGGC
50553 CAGCCCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.64
23 3 0.14
24 5 0.23
ACGTcount: A:0.04, C:0.37, G:0.43, T:0.15
Consensus pattern (24 bp):
TGGCACGCTGGGCCTGCGCCTGGC
Found at i:54628 original size:18 final size:18
Alignment explanation
Indices: 54605--54655 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
54595 GTTAGGGTAC
54605 GGGTACCTCAAATTTGAT
1 GGGTACCTCAAATTTGAT
54623 GGGTACCTCAAATTTGAT
1 GGGTACCTCAAATTTGAT
54641 GGGTACCTCAAATTT
1 GGGTACCTCAAATTT
54656 CTCTAATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (18 bp):
GGGTACCTCAAATTTGAT
Found at i:55483 original size:2 final size:2
Alignment explanation
Indices: 55476--55503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55466 TACGTATCAA
55476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55504 TGAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56786 original size:2 final size:2
Alignment explanation
Indices: 56781--56829 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
56771 TAGTTTTTTT
*
56781 TG TG TG TG TG TG TG TG TG TG TG TT TG TG T- TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
56822 TG TG -G TG T
1 TG TG TG TG T
56830 TTATGAATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:58133 original size:3 final size:3
Alignment explanation
Indices: 58125--58165 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
58115 AAAATGATTA
58125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
58166 ATACTACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:59218 original size:3 final size:3
Alignment explanation
Indices: 59212--59241 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
59202 CCACTTGTTG
59212 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59242 GGAGAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66172 original size:51 final size:51
Alignment explanation
Indices: 66096--66198 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
66086 GGAGCTTGAT
* *
66096 ATCATGACAGTAATGTCTTTTATTTAGGTGAGCCTGCTTAGGTACGGGGAG
1 ATCATGACAGTAATGTCTTTTATTTAGGTGAGCCTGCTTAGGGACAGGGAG
66147 ATCATGACAGTAATGTCTTTTATTTAGGTGAGCCTGCTTAGGGACAGGGAG
1 ATCATGACAGTAATGTCTTTTATTTAGGTGAGCCTGCTTAGGGACAGGGAG
66198 A
1 A
66199 GACTGTTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (51 bp):
ATCATGACAGTAATGTCTTTTATTTAGGTGAGCCTGCTTAGGGACAGGGAG
Found at i:69329 original size:42 final size:43
Alignment explanation
Indices: 69273--69356 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
69263 CGTGTTTGAC
* *
69273 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCATGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
69315 TTATCATGTTTCGTGTCCCTAATCGTGTCAAGACACGATTAA
1 TTATCATGTCTCGTGT-CCTAATCGTGTCAAGACACGATTAA
69357 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 14 0.39
43 9 0.25
44 13 0.36
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (43 bp):
TTATCATGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:69369 original size:20 final size:21
Alignment explanation
Indices: 69344--69386 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
69334 TAATCGTGTC
*
69344 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
69364 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
69385 AA
1 AA
69387 TTATCGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:79184 original size:31 final size:31
Alignment explanation
Indices: 79135--79194 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
79125 AAATAAGACT
**
79135 TTTTTTTAAGGACATAAGCCCAAAAAAAACC
1 TTTTTTTAAGGACATAAGCAAAAAAAAAACC
*
79166 TTTTTTT-AGGATACTAAGCAAAAAAAAAA
1 TTTTTTTAAGGACA-TAAGCAAAAAAAAAA
79195 ACTTGAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (31 bp):
TTTTTTTAAGGACATAAGCAAAAAAAAAACC
Found at i:80083 original size:16 final size:16
Alignment explanation
Indices: 80058--80091 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
80048 GACCCTGAAA
80058 ACCCAAAAGCCGAATG
1 ACCCAAAAGCCGAATG
* *
80074 ACCCAGAAGCCGAGTG
1 ACCCAAAAGCCGAATG
80090 AC
1 AC
80092 TTTAGGCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.32, G:0.24, T:0.06
Consensus pattern (16 bp):
ACCCAAAAGCCGAATG
Found at i:81323 original size:28 final size:28
Alignment explanation
Indices: 81289--81344 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
81279 ACAAAAAAGG
*
81289 ACATGTGGCGGG-TCACGTGTCATTTTTT
1 ACATGTGGCGGGCT-ACATGTCATTTTTT
*
81317 ACATGTGGCGTGCTACATGTCATTTTTT
1 ACATGTGGCGGGCTACATGTCATTTTTT
81345 GGTACACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (28 bp):
ACATGTGGCGGGCTACATGTCATTTTTT
Found at i:81369 original size:31 final size:31
Alignment explanation
Indices: 81302--81385 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
81292 TGTGGCGGGT
* *
81302 CACGTGTCA-TTTTT--TACATGTGGCGTGC
1 CACGTGTCATTTTTTGGTACACGTGACGTGC
* *
81330 TACATGTCATTTTTTGGTACACGTGACGTGC
1 CACGTGTCATTTTTTGGTACACGTGACGTGC
81361 CACGTGTCATTTTTTGGTACACGTG
1 CACGTGTCATTTTTTGGTACACGTG
81386 GTGTTGCCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.15
29 5 0.11
31 35 0.74
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (31 bp):
CACGTGTCATTTTTTGGTACACGTGACGTGC
Found at i:81693 original size:71 final size:71
Alignment explanation
Indices: 81550--81731 Score: 215
Period size: 71 Copynumber: 2.6 Consensus size: 71
81540 GTATTTATAC
* * * * * *
81550 CCCTCCATTGTTGTGTAGCTCACC-TACATAATTAAAATA-GGGTTCGAACTCATATCTTATCGT
1 CCCTCTATTATTGTGTAACTCACCGAAC-TAATTAAAGTAGGGGTTCGAACTCATATCTTATCAT
*
81613 TTCTTAA
65 TTCTCAA
* * * * *
81620 CCCTCTATTATTGTGTGAGTCACTGAACTAATTAAAGTAGGGGTTCGAACTCCTATCTTGTCATT
1 CCCTCTATTATTGTGTAACTCACCGAACTAATTAAAGTAGGGGTTCGAACTCATATCTTATCATT
81685 TCTCAA
66 TCTCAA
* *
81691 CCCTCTTTTATTGTGTAACTCACCGAACTAATTAAGGTAGG
1 CCCTCTATTATTGTGTAACTCACCGAACTAATTAAAGTAGG
81732 TTCCCCCCTC
Statistics
Matches: 93, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
70 28 0.30
71 65 0.70
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (71 bp):
CCCTCTATTATTGTGTAACTCACCGAACTAATTAAAGTAGGGGTTCGAACTCATATCTTATCATT
TCTCAA
Found at i:83405 original size:7 final size:7
Alignment explanation
Indices: 83393--83420 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
83383 CTATGGCCCT
83393 GCTTGGG
1 GCTTGGG
83400 GCTTGGG
1 GCTTGGG
83407 GCTTGGG
1 GCTTGGG
83414 GCTTGGG
1 GCTTGGG
83421 ACTTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.57, T:0.29
Consensus pattern (7 bp):
GCTTGGG
Found at i:91703 original size:1 final size:1
Alignment explanation
Indices: 91697--91727 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
91687 TTTAGTTTAG
91697 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
91728 AATTTACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:92042 original size:26 final size:26
Alignment explanation
Indices: 92006--92055 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
91996 TCGGGTATAA
*
92006 TCATGTTTAGGGATGGCAATGGGGCG
1 TCATGTTTAGGGATAGCAATGGGGCG
92032 TCATGTTTAGGGATAGCAATGGGG
1 TCATGTTTAGGGATAGCAATGGGG
92056 TGGGGCGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.10, G:0.40, T:0.28
Consensus pattern (26 bp):
TCATGTTTAGGGATAGCAATGGGGCG
Found at i:92580 original size:29 final size:30
Alignment explanation
Indices: 92519--92582 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
92509 AAAGTTCAAA
* *
92519 TAAGGACCTGATTTTTAGGGAAAAGGTTATT
1 TAAGGACCTGATCTTTA-GGAAAAGGTCATT
*
92550 TAAGGGCCTGATCTTTA-GAAAAGGTCATT
1 TAAGGACCTGATCTTTAGGAAAAGGTCATT
92579 TAAG
1 TAAG
92583 TACCCAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 15 0.50
31 15 0.50
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (30 bp):
TAAGGACCTGATCTTTAGGAAAAGGTCATT
Found at i:94087 original size:15 final size:16
Alignment explanation
Indices: 94062--94100 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
94052 CTACAAAATT
94062 AAAGAATGAGTTTACA
1 AAAGAATGAGTTTACA
94078 AAAG-ATGAGTTTACAA
1 AAAGAATGAGTTTAC-A
94094 AAAGAAT
1 AAAGAAT
94101 ATAACCCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 9 0.43
17 2 0.10
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (16 bp):
AAAGAATGAGTTTACA
Found at i:94336 original size:23 final size:23
Alignment explanation
Indices: 94306--94353 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
94296 TTGACACATG
94306 TTCATTTTCTGAATTAATTAAAT
1 TTCATTTTCTGAATTAATTAAAT
94329 TTCATTTTCTGAATTAATTAAAT
1 TTCATTTTCTGAATTAATTAAAT
94352 TT
1 TT
94354 TTTAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (23 bp):
TTCATTTTCTGAATTAATTAAAT
Found at i:94419 original size:19 final size:19
Alignment explanation
Indices: 94395--94433 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
94385 ACAAACGGGT
94395 TAAAAGGCCGACAAGTACC
1 TAAAAGGCCGACAAGTACC
*
94414 TAAAAGGCTGACAAGTACC
1 TAAAAGGCCGACAAGTACC
94433 T
1 T
94434 TCTAAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (19 bp):
TAAAAGGCCGACAAGTACC
Found at i:100228 original size:9 final size:9
Alignment explanation
Indices: 100214--100248 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
100204 AATTACTTAT
100214 GGAAATTAA
1 GGAAATTAA
*
100223 GGAAATTAT
1 GGAAATTAA
100232 GGAAATT-A
1 GGAAATTAA
100240 GGAAATTAA
1 GGAAATTAA
100249 ATAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (9 bp):
GGAAATTAA
Found at i:100244 original size:17 final size:18
Alignment explanation
Indices: 100210--100247 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
100200 CCCAAATTAC
100210 TTATGGAAATTAAGGAAA
1 TTATGGAAATTAAGGAAA
100228 TTATGGAAATT-AGGAAA
1 TTATGGAAATTAAGGAAA
100245 TTA
1 TTA
100248 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (18 bp):
TTATGGAAATTAAGGAAA
Done.