Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015846.1 Corchorus olitorius cultivar O-4 contig15879, 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: 53525
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1109 original size:30 final size:30
Alignment explanation
Indices: 1033--1110 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
1023 AAACTTACAC
*
1033 AAAACGGCCAAATAAGCACATGAACTCTAAT
1 AAAA-GGCCAAATAAGCCCATGAACTCTAAT
*** * * *
1064 TGCA-GCCAAAGAAGCCCCTGAACTCTTAT
1 AAAAGGCCAAATAAGCCCATGAACTCTAAT
1093 AAAAGGCCAAATAAGCCC
1 AAAAGGCCAAATAAGCCC
1111 TTTTCTGATG
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
29 22 0.63
30 12 0.34
31 1 0.03
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (30 bp):
AAAAGGCCAAATAAGCCCATGAACTCTAAT
Found at i:12335 original size:35 final size:35
Alignment explanation
Indices: 12283--12353 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
12273 CTTTGTTCAA
* *
12283 GTTCGGCTCGTGTTCGTTTAAATATTTTG-GTGTTC
1 GTTCGGCTCGTGCTCGTTTAAA-ATTTAGAGTGTTC
12318 GTTCGAGCTCG-GCTCGTTTAAAATTTAGAGTGTTC
1 GTTCG-GCTCGTGCTCGTTTAAAATTTAGAGTGTTC
12353 G
1 G
12354 AAACTCGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.16
35 22 0.69
36 5 0.16
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (35 bp):
GTTCGGCTCGTGCTCGTTTAAAATTTAGAGTGTTC
Found at i:12470 original size:18 final size:18
Alignment explanation
Indices: 12447--12481 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12437 ACAAAAATTG
12447 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
12465 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
12482 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:12548 original size:15 final size:14
Alignment explanation
Indices: 12520--12561 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
12510 AACGAACAAA
12520 ATAT-TATATAATT
1 ATATATATATAATT
12533 ATATATATATATATT
1 ATATATATATA-ATT
12548 ATATATA-ATAATT
1 ATATATATATAATT
12561 A
1 A
12562 ATTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 9 0.33
15 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATATAATT
Found at i:12634 original size:16 final size:16
Alignment explanation
Indices: 12613--12644 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12603 TTTATAATTT
12613 TTATTAATAATATATA
1 TTATTAATAATATATA
*
12629 TTATTATTAATATATA
1 TTATTAATAATATATA
12645 AATGATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:12637 original size:19 final size:18
Alignment explanation
Indices: 12613--12658 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
12603 TTTATAATTT
* *
12613 TTATTAATAATATATATTA
1 TTATTAAT-ATATAAATGA
12632 TTATTAATATATAAATGA
1 TTATTAATATATAAATGA
12650 TTATATAAT
1 TTAT-TAAT
12659 TAATGAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATTAATATATAAATGA
Found at i:12662 original size:23 final size:19
Alignment explanation
Indices: 12578--12653 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 19
12568 AATTTAAATA
12578 TATTAGATAATAGAATATTAT
1 TATTA-ATAATA-AATATTAT
* *
12599 TATT-TTTAT-AAT-TT-T
1 TATTAATAATAAATATTAT
*
12614 TATTAATAATATATATTAT
1 TATTAATAATAAATATTAT
12633 TATTAATATATAAATGATTAT
1 TATTAATA-ATAAAT-ATTAT
12654 ATAATTAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.12
16 5 0.12
17 5 0.12
18 2 0.05
19 12 0.28
20 5 0.12
21 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTAATAATAAATATTAT
Found at i:12725 original size:35 final size:35
Alignment explanation
Indices: 12681--12757 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
12671 GATTATTATA
12681 TAAACGAACAATAAACGAGCCTGTTCGTGAACACT
1 TAAACGAACAATAAACGAGCCTGTTCGTGAACACT
*
12716 TAAATGAACAATAAACGAGCCTGTTCGTGAACA--
1 TAAACGAACAATAAACGAGCCTGTTCGTGAACACT
12749 TAAACGAAC
1 TAAACGAAC
12758 TGAACACATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 8 0.20
35 32 0.80
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (35 bp):
TAAACGAACAATAAACGAGCCTGTTCGTGAACACT
Found at i:13867 original size:12 final size:12
Alignment explanation
Indices: 13850--13875 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13840 ATTGCTAACG
13850 AAAAATCAAACT
1 AAAAATCAAACT
13862 AAAAATCAAACT
1 AAAAATCAAACT
13874 AA
1 AA
13876 TTAAGGAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATCAAACT
Found at i:16301 original size:21 final size:21
Alignment explanation
Indices: 16275--16316 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16265 TGTAATCACT
*
16275 AAAAAATCCAATACGAAGGCG
1 AAAAAATCCAATACAAAGGCG
*
16296 AAAAAATGCAATACAAAGGCG
1 AAAAAATCCAATACAAAGGCG
16317 CCCTTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.19, T:0.10
Consensus pattern (21 bp):
AAAAAATCCAATACAAAGGCG
Found at i:17460 original size:7 final size:7
Alignment explanation
Indices: 17450--17475 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17440 TAAAAATAAG
17450 ACATACT
1 ACATACT
17457 ACATACT
1 ACATACT
17464 ACATACT
1 ACATACT
17471 ACATA
1 ACATA
17476 AAATAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
ACATACT
Found at i:17549 original size:41 final size:41
Alignment explanation
Indices: 17492--17573 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17482 AAGTTGTAAT
17492 TGAGAATTTATATATTTTATATACTATACATACTTAGAAAA
1 TGAGAATTTATATATTTTATATACTATACATACTTAGAAAA
17533 TGAGAATTTATATATTTTATATACTATACATACTTAGAAAA
1 TGAGAATTTATATATTTTATATACTATACATACTTAGAAAA
17574 GGGTGAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (41 bp):
TGAGAATTTATATATTTTATATACTATACATACTTAGAAAA
Found at i:27743 original size:41 final size:41
Alignment explanation
Indices: 27686--27772 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
27676 GCATATAATC
27686 TATATCTATACTATATATAAAAGTATGAATATGAGAAACTT
1 TATATCTATACTATATATAAAAGTATGAATATGAGAAACTT
27727 TATATCTATACTATATATAAAAGTATGAATATGAGAAACTT
1 TATATCTATACTATATATAAAAGTATGAATATGAGAAACTT
27768 TATAT
1 TATAT
27773 TTTCCGAGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (41 bp):
TATATCTATACTATATATAAAAGTATGAATATGAGAAACTT
Found at i:33291 original size:73 final size:73
Alignment explanation
Indices: 33172--33315 Score: 288
Period size: 73 Copynumber: 2.0 Consensus size: 73
33162 ACTATGTTAC
33172 GAGACCAGAAGTTTGAGTTATTTTGTTGCTTCCATTGTCTAAAGCCTCTTTTTCTTCTTTATTTG
1 GAGACCAGAAGTTTGAGTTATTTTGTTGCTTCCATTGTCTAAAGCCTCTTTTTCTTCTTTATTTG
33237 TTTCCCAT
66 TTTCCCAT
33245 GAGACCAGAAGTTTGAGTTATTTTGTTGCTTCCATTGTCTAAAGCCTCTTTTTCTTCTTTATTTG
1 GAGACCAGAAGTTTGAGTTATTTTGTTGCTTCCATTGTCTAAAGCCTCTTTTTCTTCTTTATTTG
33310 TTTCCC
66 TTTCCC
33316 TACAGGGAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.48
Consensus pattern (73 bp):
GAGACCAGAAGTTTGAGTTATTTTGTTGCTTCCATTGTCTAAAGCCTCTTTTTCTTCTTTATTTG
TTTCCCAT
Found at i:35286 original size:20 final size:19
Alignment explanation
Indices: 35258--35309 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
35248 TGGGCTGCAC
*
35258 ATGCACATTAAACAAAACGA
1 ATGCCCATTAAA-AAAACGA
**
35278 ATGCCCATTTGAAAAACGA
1 ATGCCCATTAAAAAAACGA
*
35297 ATGCCCTTTAAAA
1 ATGCCCATTAAAA
35310 GGCTCTTTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (19 bp):
ATGCCCATTAAAAAAACGA
Found at i:44245 original size:14 final size:14
Alignment explanation
Indices: 44226--44261 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
44216 AAAAGCTTAA
44226 TTTTGAAAAAGTGC
1 TTTTGAAAAAGTGC
44240 TTTTG-AAAAGTGC
1 TTTTGAAAAAGTGC
*
44253 TTTTTAAAA
1 TTTTGAAAA
44262 TTGGGGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (14 bp):
TTTTGAAAAAGTGC
Found at i:45897 original size:15 final size:15
Alignment explanation
Indices: 45879--45911 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45869 TATCATTCAC
45879 ATGGTAAGCCAGTAT
1 ATGGTAAGCCAGTAT
45894 ATGGTAAGCCAGTAT
1 ATGGTAAGCCAGTAT
45909 ATG
1 ATG
45912 CTAGCTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (15 bp):
ATGGTAAGCCAGTAT
Found at i:46662 original size:13 final size:13
Alignment explanation
Indices: 46644--46670 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46634 TTTGTTTTGC
46644 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
46657 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
46670 T
1 T
46671 ATGTCCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTGTTTTTTGTT
Found at i:47782 original size:31 final size:31
Alignment explanation
Indices: 47729--48311 Score: 948
Period size: 31 Copynumber: 19.0 Consensus size: 31
47719 AGTGTGGCTG
* *
47729 TTGCATATAGTTCATTTTTAGGTTTATCGTCA
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTA
* *
47761 TAGTATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
47792 TTGCATATAGTTC----TAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
47819 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
47850 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
*
47881 TTGCATATAATTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
47912 TTGCATATAGTTCATTTTTAGGTCTATCGTTA
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTA
*
47944 TTGTCATATAGTTCATTCTAGGTCTATCGTTA
1 TTG-CATATAGTTCATTTTAGGTCTATCGTTA
*
47976 TTGCATATAGTTCATTCTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48007 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48038 TTGCATATAGTTC----TAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48065 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
* * * *
48096 TTGCATATAGTTCATCTTAGGTTTTTTGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
*
48127 TTGCATATAGTTCATCTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48158 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48189 TTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
*
48220 TTGCATATAGTTCATTTAAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
* *
48251 TTGCATATAGTTCATTTAAGGTCTATTGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTA
48282 TTGCATATAGTTCATTTTAGGTCTATCGTT
1 TTGCATATAGTTCATTTTAGGTCTATCGTT
48312 TCATTTTAGG
Statistics
Matches: 519, Mismatches: 22, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
27 54 0.10
31 403 0.78
32 51 0.10
33 11 0.02
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (31 bp):
TTGCATATAGTTCATTTTAGGTCTATCGTTA
Found at i:47902 original size:62 final size:62
Alignment explanation
Indices: 47729--48483 Score: 1108
Period size: 62 Copynumber: 12.5 Consensus size: 62
47719 AGTGTGGCTG
* * * *
47729 TTGCATATAGTTCATTTTTAGGTTTATCGTCATAGTATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
47792 TTGCATATAGTTC----TAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
*
47850 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAATTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
*
47912 TTGCATATAGTTCATTTTTAGGTCTATCGTTATTGTCATATAGTTCATTCTAGGTCTATCGTTA
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTATTG-CATATAGTTCATTTTAGGTCTATCGTTA
*
47976 TTGCATATAGTTCATTCTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
48038 TTGCATATAGTTC----TAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
* * * * *
48096 TTGCATATAGTTCATCTTAGGTTTTTTGTTATTGCATATAGTTCATCTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
48158 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
* * *
48220 TTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATTGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
*
48282 TTGCATATAGTTCATTTTAGGTCTATC------G----T--TTCATTTTAGGTCTATCGTTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
* * * *
48332 TTGCATATGGTTCATTTTAGGTCTATCGTTGTTGCATATGGTTCATTTTAGGTCTATCGTTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
* *
48394 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATTGTTCAGTTTAGGTCTATCGTTA
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
*
48456 ATGCATATAG----TTTTAGGTCTATCGTTAT
1 TTGCATATAGTTCATTTTAGGTCTATCGTTAT
48484 AGTTCATTTG
Statistics
Matches: 638, Mismatches: 32, Indels: 49
0.89 0.04 0.07
Matches are distributed among these distances:
50 44 0.07
52 1 0.00
56 2 0.00
58 130 0.20
60 1 0.00
62 368 0.58
63 52 0.08
64 40 0.06
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (62 bp):
TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTA
Found at i:48210 original size:93 final size:93
Alignment explanation
Indices: 47729--48483 Score: 1108
Period size: 93 Copynumber: 8.3 Consensus size: 93
47719 AGTGTGGCTG
* * * *
47729 TTGCATATAGTTCATTTTTAGGTTTATCGTCATAGTATATAGTTCATTTTAGGTCTATCGTTATT
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATT
47794 GCATATAGTTC----TAGGTCTATCGTTA
65 GCATATAGTTCATTTTAGGTCTATCGTTA
47819 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
*
47884 CATATAATTCATTTTAGGTCTATCGTTA
66 CATATAGTTCATTTTAGGTCTATCGTTA
*
47912 TTGCATATAGTTCATTTTTAGGTCTATCGTTATTGTCATATAGTTCATTCTAGGTCTATCGTTAT
1 TTGCATATAGTTCA-TTTTAGGTCTATCGTTATTG-CATATAGTTCATTTTAGGTCTATCGTTAT
*
47977 TGCATATAGTTCATTCTAGGTCTATCGTTA
64 TGCATATAGTTCATTTTAGGTCTATCGTTA
48007 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTC----TAGGTCTATCGTTATTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
48068 CATATAGTTCATTTTAGGTCTATCGTTA
66 CATATAGTTCATTTTAGGTCTATCGTTA
* * * * *
48096 TTGCATATAGTTCATCTTAGGTTTTTTGTTATTGCATATAGTTCATCTTAGGTCTATCGTTATTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
48161 CATATAGTTCATTTTAGGTCTATCGTTA
66 CATATAGTTCATTTTAGGTCTATCGTTA
*
48189 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
* *
48254 CATATAGTTCATTTAAGGTCTATTGTTA
66 CATATAGTTCATTTTAGGTCTATCGTTA
*
48282 TTGCATATAGTTCATTTTAGGTCTATC------G----T--TTCATTTTAGGTCTATCGTTGTTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
* *
48335 CATATGGTTCATTTTAGGTCTATCGTTG
66 CATATAGTTCATTTTAGGTCTATCGTTA
* *
48363 TTGCATATGGTTCATTTTAGGTCTATCGTTGTTGCATATAGTTCATTTTAGGTCTATCGTTATTG
1 TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
* *
48428 CATATTGTTCAGTTTAGGTCTATCGTTA
66 CATATAGTTCATTTTAGGTCTATCGTTA
*
48456 ATGCATATAG----TTTTAGGTCTATCGTTAT
1 TTGCATATAGTTCATTTTAGGTCTATCGTTAT
48484 AGTTCATTTG
Statistics
Matches: 608, Mismatches: 35, Indels: 45
0.88 0.05 0.07
Matches are distributed among these distances:
81 72 0.12
83 1 0.00
87 2 0.00
89 157 0.26
90 14 0.02
91 1 0.00
93 251 0.41
94 40 0.07
95 70 0.12
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (93 bp):
TTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTG
CATATAGTTCATTTTAGGTCTATCGTTA
Found at i:48316 original size:19 final size:19
Alignment explanation
Indices: 48292--48330 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
48282 TTGCATATAG
48292 TTCATTTTAGGTCTATCGT
1 TTCATTTTAGGTCTATCGT
48311 TTCATTTTAGGTCTATCGT
1 TTCATTTTAGGTCTATCGT
48330 T
1 T
48331 GTTGCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (19 bp):
TTCATTTTAGGTCTATCGT
Found at i:48349 original size:31 final size:31
Alignment explanation
Indices: 48311--48463 Score: 252
Period size: 31 Copynumber: 4.9 Consensus size: 31
48301 GGTCTATCGT
48311 TTCATTTTAGGTCTATCGTTGTTGCATATGG
1 TTCATTTTAGGTCTATCGTTGTTGCATATGG
48342 TTCATTTTAGGTCTATCGTTGTTGCATATGG
1 TTCATTTTAGGTCTATCGTTGTTGCATATGG
*
48373 TTCATTTTAGGTCTATCGTTGTTGCATATAG
1 TTCATTTTAGGTCTATCGTTGTTGCATATGG
* *
48404 TTCATTTTAGGTCTATCGTTATTGCATATTG
1 TTCATTTTAGGTCTATCGTTGTTGCATATGG
* **
48435 TTCAGTTTAGGTCTATCGTTAATGCATAT
1 TTCATTTTAGGTCTATCGTTGTTGCATAT
48464 AGTTTTAGGT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 117 1.00
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.48
Consensus pattern (31 bp):
TTCATTTTAGGTCTATCGTTGTTGCATATGG
Found at i:48367 original size:81 final size:81
Alignment explanation
Indices: 48230--48481 Score: 271
Period size: 81 Copynumber: 3.0 Consensus size: 81
48220 TTGCATATAG
*
48230 TTCATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATTGTTATTGCATATAGTTC
1 TTCATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
48295 ATTTTAGGTCTATCGT
66 ATTTTAGGTCTATCGT
* * * * * *
48311 TTCATTTTAGGTCTATCGTTGTTGCATATGGTTCATTTTAGGTCTATCGTTGTTGCATATGGTTC
1 TTCATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
48376 ATTTTAGGTCTATCGTT
66 ATTTTAGGTCTATCG-T
* *
48393 GTTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATTGTTCAGTTT-AGGTCTATCGTTAA
1 -TT-C--AT--TT-A----AGGTCTATCGTTATTGCATATAGTTCA-TTTAAGGTCTATCGTTAT
48457 TGCATATAG----TTTTAGGTCTATCGT
54 TGCATATAGTTCATTTTAGGTCTATCGT
48481 T
1 T
48482 ATAGTTCATT
Statistics
Matches: 145, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
81 73 0.50
82 1 0.01
83 2 0.01
84 1 0.01
86 2 0.01
87 1 0.01
88 3 0.02
89 14 0.10
93 45 0.31
94 3 0.02
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (81 bp):
TTCATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
ATTTTAGGTCTATCGT
Found at i:48398 original size:112 final size:112
Alignment explanation
Indices: 48199--48423 Score: 378
Period size: 112 Copynumber: 2.0 Consensus size: 112
48189 TTGCATATAG
48199 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
1 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
*
48264 ATTTAAGGTCTATTGTTATTGCATATAGTTCATTTTAGGTCTATCGT
66 ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGT
* * * * *
48311 TTCATTTTAGGTCTATCGTTGTTGCATATGGTTCATTTTAGGTCTATCGTTGTTGCATATGGTTC
1 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
* *
48376 ATTTTAGGTCTATCGTTGTTGCATATAGTTCATTTTAGGTCTATCGT
66 ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGT
48423 T
1 T
48424 ATTGCATATT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (112 bp):
TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTC
ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGT
Found at i:48426 original size:143 final size:143
Alignment explanation
Indices: 48168--48454 Score: 484
Period size: 143 Copynumber: 2.0 Consensus size: 143
48158 TTGCATATAG
48168 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTC
1 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTC
* *
48233 ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATTGTTATTGCATATAGTTCATT
66 ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTCAGT
48298 TTAGGTCTATCGT
131 TTAGGTCTATCGT
* * * *
48311 TTCATTTTAGGTCTATCGTTGTTGCATATGGTTCATTTTAGGTCTATCGTTGTTGCATATGGTTC
1 TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTC
* * * *
48376 ATTTTAGGTCTATCGTTGTTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATTGTTCAGT
66 ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTCAGT
48441 TTAGGTCTATCGT
131 TTAGGTCTATCGT
48454 T
1 T
48455 AATGCATATA
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
143 134 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (143 bp):
TTCATTTTAGGTCTATCGTTATTGCATATAGTTCATTTTAGGTCTATCGTTATTGCATATAGTTC
ATTTAAGGTCTATCGTTATTGCATATAGTTCATTTAAGGTCTATCGTTATTGCATATAGTTCAGT
TTAGGTCTATCGT
Found at i:48527 original size:22 final size:22
Alignment explanation
Indices: 48492--48541 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
48482 ATAGTTCATT
* *
48492 TGTCCATGGGGACAATCCTATC
1 TGTCCATGGCGACAATCCCATC
* *
48514 TGTCCGTGGCGACAATCCCATT
1 TGTCCATGGCGACAATCCCATC
48536 TGTCCA
1 TGTCCA
48542 CTTGCAAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (22 bp):
TGTCCATGGCGACAATCCCATC
Found at i:52880 original size:321 final size:317
Alignment explanation
Indices: 52298--53525 Score: 1382
Period size: 321 Copynumber: 3.8 Consensus size: 317
52288 ATTCCTGAGT
* * * * * *
52298 CCCGGCTCAATTTTGCATGATTTTTGG-TGTAAAGAATCCTTCAAATATCTATACTCATCAAACC
1 CCCGGCTCAATTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * *
52362 AAATCCCAGCCACATTGTATATAAGAATTT-ATTTTTACTAGCATCTGAATCTTATTTCGATTTA
66 AAATCTCAGCCACAATGTATATAAGGATTTGA-TTTTACGAGCATCTGAATCTTATTTCGATTTA
*
52426 ATTAGAAATTAATTC-GAAAAAAAAGGAAAAACGAAATTAGAAGCGTGAAAAGTTCGTCAATTTT
130 ATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAA-TTT
*
52490 TTTGACGTTGAATTATATATTTTTTCTGAATATTTTGCAAAACATTAGAAAAACTTTTCGGGTTA
194 TTTGACGTTGAATTATATATTTTTTCTGAATATTTTGCAAAACATTAGAAAAACTTTTCGGGCTA
* * * *
52555 CTTTTTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTACTAGAAATGCATTTCACGC
259 CTTTTTAGCCGAAATCGTGTACTAACAATTACGGTTTTTTACTA-AAATGCATTTCAAGC
*
52615 CCCGGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATTTAACC
1 CCCGGCTCAATTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATCTAACC
* *
52679 AAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTTATTTCGATTTA
66 AAATCTCAGCCACAATGTATATAAGGATTTGATTTTACGAGCATCTGAATC-TTATTTCGATTTA
52744 ATTAGAAATTAATTCGGAAAAAAAAAGGGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAACT
130 ATTAGAAATTAATTCGG-AAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAA-T
* *
52809 TTTTTGACGTTGAATTATATATTTTTTCTGAATATTTTGCAAATCATTTGAAAAACTTTTCGGGC
192 TTTTTGACGTTGAATTATATATTTTTTCTGAATATTTTGCAAAACATTAGAAAAACTTTTCGGGC
* * **
52874 TACTTTTTAGCAGAAATCGTGTACTAACAATTACGGTTTTTTACTAAATGTGCATTTCGGGGC
257 TACTTTTTAGCCGAAATCGTGTACTAACAATTACGGTTTTTTACTAAA-ATGCATTTC-AAGC
** * *
52937 CCCCACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTTATCTAACC
1 CCCGGCTCAATTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * * * *
53001 AAATCTCAGCCACAATGAATTTAAAGATTTG-TGTTTACGAGTATCTCAATCTTTGTTTCGATTT
66 AAATCTCAGCCACAATGTATATAAGGATTTGAT-TTTACGAGCATCTGAATC-TTATTTCGATTT
* * *** *
53065 AATTAGAAATGAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCTTGAAAAACACATCAATTT
129 AATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAATTT
* * ** * *
53130 TTTTAGCGTTGAATAATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG
194 TTTGA-CGTTGAATTATATATTTTTTCTGAATATT-TTGCAAAACATT-A-GAAAAACTTTTCGG
** * * ** *
53195 GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACGTTA-TATTACGGTTTTTGGCTAAAAACG
255 G-C------T---ACTTTTTAGCCGAAATCGTGTAC-TAACAATTACGGTTTTTTACT-AAAATG
* *
53259 C-GTTCAGGAGT
308 CATTTCA--AGC
* * * *
53270 GCCGGCTAAATTTTGCATGATTTTTGGC-GCAAAGA-TTCTTCGAAATATCTATATTCATCGAAC
1 CCCGGCTCAATTTTGCATGATTTTTGGCAGCAAAGACTCCTT-GAAATATCTATATTCATCTAAC
* * * *
53333 CAAATGTCAGCCACATTGTATATAAGGATTTGTTTTTTACGAGCATCTGAATC-TAGTTTTGATT
65 CAAATCTCAGCCACAATGTATATAAGGATTTG-ATTTTACGAGCATCTGAATCTTA-TTTCGATT
* * *
53397 TAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAG-CCTGTTAA
128 TAATTAGAAATTAATTCGGAAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAGTTC-GTCAA
* * * * * *
53461 TCTTTTTGTCATTAAATTATATATTTTTTTCTGAATATTTCGCAAAAAATTGAGAAAAACCTTTC
191 T-TTTTTGACGTTGAATTATATA-TTTTTTCTGAATATTTTGCAAAACATT-AGAAAAACTTTTC
Statistics
Matches: 781, Mismatches: 94, Indels: 56
0.84 0.10 0.06
Matches are distributed among these distances:
317 99 0.13
318 30 0.04
319 8 0.01
320 67 0.09
321 166 0.21
322 135 0.17
323 15 0.02
324 1 0.00
330 1 0.00
332 9 0.01
333 157 0.20
334 74 0.09
335 19 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (317 bp):
CCCGGCTCAATTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATCTAACC
AAATCTCAGCCACAATGTATATAAGGATTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAA
TTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAATTTTT
TGACGTTGAATTATATATTTTTTCTGAATATTTTGCAAAACATTAGAAAAACTTTTCGGGCTACT
TTTTAGCCGAAATCGTGTACTAACAATTACGGTTTTTTACTAAAATGCATTTCAAGC
Done.