Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013281.1 Corchorus olitorius cultivar O-4 contig13314, 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: 40279
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1826 original size:21 final size:21
Alignment explanation
Indices: 1793--1841 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1783 AAGAATTGTA
**
1793 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
1813 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
1834 GCATTCCT
1 GC-TTCCT
1842 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:7654 original size:43 final size:41
Alignment explanation
Indices: 7589--7669 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
7579 AAATCGTTCC
* * *
7589 TTTTAATCCTCTTTTTTTAGAAAAATAAATTTTCATTCTTGT
1 TTTTAATCCTCTTTTTTAAG-AAAACAAACTTTCATTCTTGT
*
7631 TTTTAGTCTCTCTTTTTTAAGAAAACAAACTTTCATTCT
1 TTTTAATC-CTCTTTTTTAAGAAAACAAACTTTCATTCT
7670 CTCCCTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 23 0.68
43 11 0.32
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.52
Consensus pattern (41 bp):
TTTTAATCCTCTTTTTTAAGAAAACAAACTTTCATTCTTGT
Found at i:9131 original size:11 final size:11
Alignment explanation
Indices: 9111--9140 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9101 CTAAGGGTAA
9111 AGGAAAGAGCT
1 AGGAAAGAGCT
*
9122 AGGAAGGAGCT
1 AGGAAAGAGCT
9133 AGGAAAGA
1 AGGAAAGA
9141 TCCTACTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (11 bp):
AGGAAAGAGCT
Found at i:9555 original size:21 final size:21
Alignment explanation
Indices: 9517--9557 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9507 CACCTTACGT
**
9517 AACTCCGATGAGTTTGAAACC
1 AACTCCGATGAGCGTGAAACC
9538 AACTCCGATGAGCGTGAAAC
1 AACTCCGATGAGCGTGAAAC
9558 TTCTTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
AACTCCGATGAGCGTGAAACC
Found at i:16261 original size:17 final size:17
Alignment explanation
Indices: 16239--16271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16229 CCAACCTAAT
*
16239 TAAAACGTGCACGTGAC
1 TAAAACGTACACGTGAC
16256 TAAAACGTACACGTGA
1 TAAAACGTACACGTGA
16272 ACGAACTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (17 bp):
TAAAACGTACACGTGAC
Found at i:18734 original size:51 final size:50
Alignment explanation
Indices: 18568--18757 Score: 308
Period size: 50 Copynumber: 3.8 Consensus size: 50
18558 TAAAGAGTCA
18568 TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCG
1 TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCG
* * *
18618 TCTTCCGCTTACCCTTTGAACTTTCTTCCAATCCAATCTTAAAAGGATCG
1 TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCG
* *
18668 TTTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCG
1 TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTT-AAAAGGACCG
* *
18719 TCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCT
1 TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCT
18758 CGAGAAAAAC
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 83 0.64
51 46 0.36
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (50 bp):
TCTTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCG
Found at i:18756 original size:101 final size:100
Alignment explanation
Indices: 18570--18757 Score: 322
Period size: 101 Copynumber: 1.9 Consensus size: 100
18560 AAGAGTCATC
18570 TTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCGTCTTCCGCTTACCCTTT
1 TTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCGTCTTCCGCTTACCCTTT
* *
18635 GAACTTTCTTCCAATCCAATCTTAAAAGGATCGTT
66 GAACTGTCTCCCAATCCAATCTTAAAAGGATCGTT
* *
18670 TTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTT
1 TTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTT-AAAAGGACCGTCTTCCGCTTACCCTT
*
18735 TGAACTGTCTCCCAATTCAATCT
65 TGAACTGTCTCCCAATCCAATCT
18758 CGAGAAAAAC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 37 0.45
101 45 0.55
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (100 bp):
TTCCGCTTATCCTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCGTCTTCCGCTTACCCTTT
GAACTGTCTCCCAATCCAATCTTAAAAGGATCGTT
Found at i:19131 original size:64 final size:64
Alignment explanation
Indices: 19005--19245 Score: 302
Period size: 64 Copynumber: 3.7 Consensus size: 64
18995 AAGAATTGTT
* * * * *
19005 TTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTGCTTTTTAACAAGATCGTC
1 TTCCGATCAACTTCTGAAA-ATTTTTGAGAAACCATCTTCTGGTGTACTTTTTGACAAGATCGTC
* * * * *
19070 TTCCGATCGACTTCTGAAAATTTTTGATAAACCATCTTCTGGCGTAATTCTTGACAAGATCGTC
1 TTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTTTTGACAAGATCGTC
* * * *
19134 TTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGCACTTTTTGACAAGATCTTC
1 TTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTTTTGACAAGATCGTC
* * *
19198 TTCCGATCAACTTCTTTAAAAACTCTTGAGAAACCATCTTCTGGTGTA
1 TTCCGATCAACTTC--TGAAAATTTTTGAGAAACCATCTTCTGGTGTA
19246 TTCCTTAATA
Statistics
Matches: 150, Mismatches: 24, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
64 104 0.69
65 18 0.12
66 28 0.19
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (64 bp):
TTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTTTTGACAAGATCGTC
Found at i:19266 original size:66 final size:63
Alignment explanation
Indices: 18969--19266 Score: 294
Period size: 64 Copynumber: 4.6 Consensus size: 63
18959 ACTTCTAAAT
* * * * *
18969 AACCGTCTTCTGGTGCATCTCTTAACAAGAATTGTTTTCCGATCAACTTCTGAAACCTTTTCGAG
1 AACCATCTTCTGGTGTAT-TCTTAACAAG-ATCGTCTTCCGATCAACTTCTGAAAACTTTT-GAG
19034 A
63 A
* * * * * *
19035 AACTATCTTCTGGTGTGCTTTTTAACAAGATCGTCTTCCGATCGACTTCTGAAAATTTTTGATA
1 AACCATCTTCTGGTGT-ATTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGA
* * *
19099 AACCATCTTCTGGCGTAATTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAA-TTGTTGAGA
1 AACCATCTTCTGGTGT-ATTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTT-TTGAGA
* * * * * *
19163 AACCATCTTCTGGTGCACTTTTTGACAAGATCTTCTTCCGATCAACTTCTTTAAAAACTCTTGAG
1 AACCATCTTCTGGTGTA-TTCTTAACAAGATCGTCTTCCGATCAACTTC--TGAAAACTTTTGAG
19228 A
63 A
*
19229 AACCATCTTCTGGTGTATTCCTTAATAAGAAT-GTCTTC
1 AACCATCTTCTGGTGTATT-CTTAACAAG-ATCGTCTTC
19267 TAATCAGCAT
Statistics
Matches: 192, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
63 3 0.02
64 97 0.51
65 28 0.15
66 60 0.31
67 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (63 bp):
AACCATCTTCTGGTGTATTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGA
Found at i:21224 original size:12 final size:12
Alignment explanation
Indices: 21207--21231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21197 TTTGATTCAC
21207 TTTTGATTTGAA
1 TTTTGATTTGAA
21219 TTTTGATTTGAA
1 TTTTGATTTGAA
21231 T
1 T
21232 CACTTGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TTTTGATTTGAA
Found at i:28881 original size:8 final size:8
Alignment explanation
Indices: 28868--28911 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
28858 GAAACCACAA
28868 TGAATTTT
1 TGAATTTT
28876 TGAATTTT
1 TGAATTTT
*
28884 CAGAATTTT
1 -TGAATTTT
28893 TGAATTTT
1 TGAATTTT
*
28901 CAGAATTTT
1 -TGAATTTT
28910 TG
1 TG
28912 GATCTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (8 bp):
TGAATTTT
Found at i:28891 original size:9 final size:9
Alignment explanation
Indices: 28877--28909 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28867 ATGAATTTTT
28877 GAATTTTCA
1 GAATTTTCA
*
28886 GAATTTT-T
1 GAATTTTCA
28894 GAATTTTCA
1 GAATTTTCA
28903 GAATTTT
1 GAATTTT
28910 TGGATCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (9 bp):
GAATTTTCA
Found at i:28891 original size:17 final size:17
Alignment explanation
Indices: 28869--28911 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
28859 AAACCACAAT
28869 GAATTTTTGAATTTTCA
1 GAATTTTTGAATTTTCA
28886 GAATTTTTGAATTTTCA
1 GAATTTTTGAATTTTCA
28903 GAATTTTTG
1 GAATTTTTG
28912 GATCTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (17 bp):
GAATTTTTGAATTTTCA
Found at i:34109 original size:69 final size:69
Alignment explanation
Indices: 34017--34481 Score: 646
Period size: 69 Copynumber: 6.9 Consensus size: 69
34007 TGCTGCTGTA
* * * * * ** * * *
34017 TGGATGGAACCAATGTTTAAACTGACTCGCATTGAAACGAGTTTGATTTATGGAAAAGTCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34082 GGCT
66 GGCT
* * * *
34086 TGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACTAGTTTGGCTTGTGGGAAAGCCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34151 GGCT
66 GGCT
34155 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34220 GGCT
66 GGCT
34224 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34289 GGCT
66 GGCT
*
34293 TGGATGGAACCAAGGCTTGAACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34358 GGCT
66 GGCT
* * *
34362 TGGATGGGACCAAGGCTTCAATTGA--C---T------GAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
34416 GGCT
66 GGCT
* * * * *
34420 TGGATGGGACCAAGGCTTAAATTGACTCGTATGGAAATGAGTTTGGCTTATGGAAAAGCCTA
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
34482 AGCATTTGGA
Statistics
Matches: 363, Mismatches: 22, Indels: 22
0.89 0.05 0.05
Matches are distributed among these distances:
58 55 0.15
60 1 0.00
63 1 0.00
64 1 0.00
67 1 0.00
69 304 0.84
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (69 bp):
TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
GGCT
Found at i:34421 original size:58 final size:58
Alignment explanation
Indices: 34331--34446 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
34321 ATATGGAAAC
*
34331 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGACCAAGGCTTCAATTGACT
1 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGACCAAGGCTTAAATTGACT
34389 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGACCAAGGCTTAAATTGACT
1 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGACCAAGGCTTAAATTGACT
34447 CGTATGGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (58 bp):
GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGACCAAGGCTTAAATTGACT
Found at i:35363 original size:49 final size:50
Alignment explanation
Indices: 35298--35490 Score: 282
Period size: 50 Copynumber: 3.9 Consensus size: 50
35288 CCCTTCGAAT
* * ** *
35298 AGCGAACTTTGGTCTTGGTCTCACAAATGGAATGCAATCTTATATT-AAA
1 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATTTTGAAA
* * *
35347 AGCGAATTTTGCTCTTGGACTCACAAATGCAATGCAAT-TTCATTTTGAAA
1 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTT-ATTTTGAAA
*
35397 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATTTTATTTTGAAA
1 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATTTTGAAA
35447 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATT
1 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATT
35491 ATAAAACTTC
Statistics
Matches: 132, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
48 2 0.02
49 38 0.29
50 90 0.68
51 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (50 bp):
AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATTTTGAAA
Found at i:35421 original size:99 final size:100
Alignment explanation
Indices: 35298--35484 Score: 286
Period size: 99 Copynumber: 1.9 Consensus size: 100
35288 CCCTTCGAAT
* ** *
35298 AGCGAACTTTGGTCTTGGTCTCACAAATGGAATGCAATCTTATATT-AAAAGCGAATTTTGCTCT
1 AGCGAACTTTGATCTTGAACTCACAAATGGAATGCAATCTTATATTGAAAAGCGAATTTTGATCT
*
35362 TGGACTCACAAATGCAATGCAATTTCATTTTGAAA
66 TGAACTCACAAATGCAATGCAATTTCATTTTGAAA
* * *
35397 AGCGAATTTTGATCTTGAACTCACAAATGGAATGCAATTTTATTTTGAAAAGCGAATTTTGATCT
1 AGCGAACTTTGATCTTGAACTCACAAATGGAATGCAATCTTATATTGAAAAGCGAATTTTGATCT
*
35462 TGAACTCACAAATGGAATGCAAT
66 TGAACTCACAAATGCAATGCAAT
35485 CTTATTATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 40 0.51
100 38 0.49
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (100 bp):
AGCGAACTTTGATCTTGAACTCACAAATGGAATGCAATCTTATATTGAAAAGCGAATTTTGATCT
TGAACTCACAAATGCAATGCAATTTCATTTTGAAA
Found at i:36101 original size:22 final size:22
Alignment explanation
Indices: 36065--36133 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
36055 TCCATTCTCT
**
36065 TTTGATTTTGATTTTGATTTGA
1 TTTGATTTTTTTTTTGATTTGA
36087 TTTGATTTTTTTTTTTTGATTT--
1 TTTGA--TTTTTTTTTTGATTTGA
*
36109 TTTGATTTTTTGTATTGA-TTGA
1 TTTGATTTTTT-TTTTGATTTGA
36131 TTT
1 TTT
36134 TTTTGAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 8 0.21
21 5 0.13
22 13 0.33
24 13 0.33
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (22 bp):
TTTGATTTTTTTTTTGATTTGA
Found at i:36109 original size:6 final size:6
Alignment explanation
Indices: 36064--36095 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
36054 ATCCATTCTC
36064 TTTTGA TTTTGA TTTTGA -TTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
36096 TTTTTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:36119 original size:17 final size:17
Alignment explanation
Indices: 36076--36139 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
36066 TTGATTTTGA
*
36076 TTTTGATTTGATTTGA-T
1 TTTTGATTT-TTTTGATT
36093 TTTT--TTTTTTTGATT
1 TTTTGATTTTTTTGATT
36108 TTTTGA-TTTTTTGTATT
1 TTTTGATTTTTTTG-ATT
**
36125 GATTGATTTTTTTGA
1 TTTTGATTTTTTTGA
36140 ATTTCTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.13
15 8 0.21
16 7 0.18
17 12 0.31
18 7 0.18
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (17 bp):
TTTTGATTTTTTTGATT
Found at i:36531 original size:11 final size:11
Alignment explanation
Indices: 36515--36540 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36505 CATTTTTTCA
36515 TTTTTTCATTT
1 TTTTTTCATTT
36526 TTTTTTCATTT
1 TTTTTTCATTT
36537 TTTT
1 TTTT
36541 CTTTTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:36539 original size:8 final size:8
Alignment explanation
Indices: 36492--36528 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
36482 TTGCAAGTGC
36492 TTTTTCAT
1 TTTTTCAT
36500 TTTTTCAT
1 TTTTTCAT
36508 TTTTTCAT
1 TTTTTCAT
36516 TTTTTCAT
1 TTTTTCAT
36524 TTTTT
1 TTTTT
36529 TTTCATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:36545 original size:8 final size:8
Alignment explanation
Indices: 36492--36557 Score: 51
Period size: 8 Copynumber: 7.5 Consensus size: 8
36482 TTGCAAGTGC
*
36492 TTTTTCAT
1 TTTTTCTT
*
36500 TTTTTCAT
1 TTTTTCTT
36508 TTTTTCATT
1 TTTTTC-TT
*
36517 TTTTCATTTT
1 TTTT--TCTT
36527 TTTTTCATT
1 TTTTTC-TT
36536 TTTTTCTT
1 TTTTTCTT
36544 TTCTTCTCTT
1 TT-TT-TCTT
36554 TTTT
1 TTTT
36558 ATTATTGGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
8 19 0.39
9 17 0.35
10 12 0.24
11 1 0.02
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:36545 original size:19 final size:19
Alignment explanation
Indices: 36492--36539 Score: 75
Period size: 16 Copynumber: 2.7 Consensus size: 19
36482 TTGCAAGTGC
36492 TTTTTCATTTTTTCA---T
1 TTTTTCATTTTTTCATTTT
36508 TTTTTCATTTTTTCATTTT
1 TTTTTCATTTTTTCATTTT
36527 TTTTTCATTTTTT
1 TTTTTCATTTTTT
36540 TCTTTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.52
19 14 0.48
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCATTTTTTCATTTT
Found at i:36555 original size:27 final size:27
Alignment explanation
Indices: 36499--36557 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
36489 TGCTTTTTCA
*
36499 TTTTTTCATTTTTTCATTTTTTCATTT
1 TTTTTTCATTTTTTCATTTTTTCATCT
36526 TTTTTTCATTTTTTTC-TTTTCTTC-TCT
1 TTTTTTCA-TTTTTTCATTTT-TTCATCT
36553 TTTTT
1 TTTTT
36558 ATTATTGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTCATTTTTTCATTTTTTCATCT
Done.