Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014886.1 Corchorus capsularis cultivar CVL-1 contig14907, 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: 144012
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:248 original size:37 final size:37
Alignment explanation
Indices: 201--296 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
191 ATATGACTTT
*
201 TTTGTTTCCAATGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTCTCCAATGTCCTATTTAATTTTGCCTTTTGTC
** **
238 TTTGTCTCCAATCGTTGTATTTAATTTTGTTTTTTGTC
1 TTTGTCTCCAAT-GTCCTATTTAATTTTGCCTTTTGTC
* *
276 TTCGTCTCCAACGTCCTATTT
1 TTTGTCTCCAATGTCCTATTT
297 GGGTTTAGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.14, C:0.20, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTGTCTCCAATGTCCTATTTAATTTTGCCTTTTGTC
Found at i:2484 original size:16 final size:16
Alignment explanation
Indices: 2463--2493 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2453 ATAAATCAAC
2463 TTTCTTCTCCTTCTTT
1 TTTCTTCTCCTTCTTT
*
2479 TTTCTTCTTCTTCTT
1 TTTCTTCTCCTTCTT
2494 CTTCTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTCTCCTTCTTT
Found at i:2486 original size:3 final size:3
Alignment explanation
Indices: 2464--2500 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2454 TAAATCAACT
*
2464 TTC TTC TCC TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2501 AAATCAGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:11990 original size:61 final size:59
Alignment explanation
Indices: 11895--12027 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 59
11885 ACCGACAAGG
*
11895 CCTTATTTGAGCAATTTTGGCAACATTGGGCCTTGATTTGAGCAATTTT-TTTTTGC-CTGAC
1 CCTTATTTGAGCAATTTTGGCAACATTGGACCTTGATTTGAGC--TTTTGTTTTT-CTCTG-C
* * *
11956 CCTTATTTGAGCAATTTTTGCAACGTTGGACCTTGATTTGAGCTTTTGTTTTTCTTTGC
1 CCTTATTTGAGCAATTTTGGCAACATTGGACCTTGATTTGAGCTTTTGTTTTTCTCTGC
12015 CCTTATTTGAGCA
1 CCTTATTTGAGCA
12028 TTTCCACAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
59 19 0.29
60 7 0.11
61 40 0.61
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (59 bp):
CCTTATTTGAGCAATTTTGGCAACATTGGACCTTGATTTGAGCTTTTGTTTTTCTCTGC
Found at i:11998 original size:31 final size:30
Alignment explanation
Indices: 11895--11998 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
11885 ACCGACAAGG
* * *
11895 CCTTATTTGAGCAATTTTGGCAACATTGGG
1 CCTTATTTGAGCAATTTTTGCAACGTTGGA
**** *
11925 CCTTGATTTGAGCAATTTTT-TTTTGCCT-GA
1 CCTT-ATTTGAGCAATTTTTGCAACG-TTGGA
11955 CCCTTATTTGAGCAATTTTTGCAACGTTGGA
1 -CCTTATTTGAGCAATTTTTGCAACGTTGGA
11986 CCTTGATTTGAGC
1 CCTT-ATTTGAGC
11999 TTTTGTTTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
30 25 0.45
31 30 0.55
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (30 bp):
CCTTATTTGAGCAATTTTTGCAACGTTGGA
Found at i:12626 original size:2 final size:2
Alignment explanation
Indices: 12619--12646 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12609 ATCAATATTG
12619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12647 GTTACATATT
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):
TA
Found at i:15710 original size:12 final size:12
Alignment explanation
Indices: 15695--15720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15685 GCAAAACTAT
15695 AAGGAAAAGATG
1 AAGGAAAAGATG
15707 AAGGAAAAGATG
1 AAGGAAAAGATG
15719 AA
1 AA
15721 TATATACAAG
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:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (12 bp):
AAGGAAAAGATG
Found at i:18916 original size:20 final size:20
Alignment explanation
Indices: 18891--18935 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
18881 AAAGATTAAG
*
18891 AAATAATTAATCCATGTAAA-
1 AAATAATTAAT-CATATAAAT
18911 AAATAATTAATCATATAAAT
1 AAATAATTAATCATATAAAT
18931 AAATA
1 AAATA
18936 GTATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAATTAATCATATAAAT
Found at i:21673 original size:17 final size:17
Alignment explanation
Indices: 21651--21684 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21641 GCACCTAAAT
21651 AAATTACAGAGAGCATA
1 AAATTACAGAGAGCATA
21668 AAATTACAGAGAGCATA
1 AAATTACAGAGAGCATA
21685 GAGCTCAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATTACAGAGAGCATA
Found at i:24008 original size:1 final size:1
Alignment explanation
Indices: 24002--24037 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
23992 GGCCTTTCAG
24002 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24038 ATGGGCTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38843 original size:7 final size:7
Alignment explanation
Indices: 38831--38857 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38821 ATTATTGTAT
38831 GTATAGA
1 GTATAGA
38838 GTATAGA
1 GTATAGA
38845 GTATAGA
1 GTATAGA
38852 GTATAG
1 GTATAG
38858 TTGGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
GTATAGA
Found at i:40783 original size:5 final size:5
Alignment explanation
Indices: 40773--40798 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40763 GAAACACACA
40773 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
40799 TTAAGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:48821 original size:109 final size:108
Alignment explanation
Indices: 48630--48841 Score: 372
Period size: 109 Copynumber: 2.0 Consensus size: 108
48620 ATTTTTGTGC
* *
48630 TTGTATTTTTCTTTAAATCTAATAGTTCATTGCACTTTTTATTATTTGGTATGTGTGCTTATTTA
1 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTTTATTACTTGGTATGTGTGCTTATTTA
48695 ATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTGA
66 ATAGGTTCAATTGAATAAA-AACACAATTAATAATAATAGGTGA
*
48739 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCA-TTTTGTATTGCTTGGTATGTGTGCTTATTT
1 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTT-TATTACTTGGTATGTGTGCTTATTT
48803 AATAGGTTCAATTGAATAAAAACACAATTAATAATAATA
65 AATAGGTTCAATTGAATAAAAACACAATTAATAATAATA
48842 TATAATAGAA
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
108 23 0.23
109 76 0.77
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (108 bp):
TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTTTATTACTTGGTATGTGTGCTTATTTA
ATAGGTTCAATTGAATAAAAACACAATTAATAATAATAGGTGA
Found at i:50332 original size:4 final size:4
Alignment explanation
Indices: 50323--50349 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50313 AATTTGAGAT
50323 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
50350 ACACATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:53035 original size:63 final size:63
Alignment explanation
Indices: 52932--53055 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
52922 CTCTCCCCCG
* * * *
52932 TGCGGTCCAACCCGTCAAGTCTTAAGTCAATTTCCTGCCATCTAAGACTTAACCCGCGGAGAA
1 TGCGGCCCAACCCGTCAAGTCTTAAGCCAATTTCCGGCCATCCAAGACTTAACCCGCGGAGAA
*
52995 TGCGGCCCAACCCGTCAAGTCTTAAGCCAATTTCCGGCCATCCAAGACTTAACCCGTGGAG
1 TGCGGCCCAACCCGTCAAGTCTTAAGCCAATTTCCGGCCATCCAAGACTTAACCCGCGGAG
53056 TGCGAGGGCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (63 bp):
TGCGGCCCAACCCGTCAAGTCTTAAGCCAATTTCCGGCCATCCAAGACTTAACCCGCGGAGAA
Found at i:54074 original size:18 final size:18
Alignment explanation
Indices: 54053--54088 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54043 AATTTGGTTG
54053 GGATTTACAATTTCATTA
1 GGATTTACAATTTCATTA
*
54071 GGATTTACGATTTCATTA
1 GGATTTACAATTTCATTA
54089 AACTTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (18 bp):
GGATTTACAATTTCATTA
Found at i:73627 original size:19 final size:21
Alignment explanation
Indices: 73575--73631 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
73565 ATATGACGTG
73575 GCTTTTTTCTTTTT-TAATTTC
1 GCTTTTTTCTTTTTCT-ATTTC
*
73596 TCTTTTCTTCTTTTTCT-TTT-
1 GCTTTT-TTCTTTTTCTATTTC
73616 GCTTTTTTCTTTTTCT
1 GCTTTTTTCTTTTTCT
73632 CTTCTTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 10 0.31
20 5 0.16
21 8 0.25
22 8 0.25
23 1 0.03
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (21 bp):
GCTTTTTTCTTTTTCTATTTC
Found at i:74866 original size:12 final size:12
Alignment explanation
Indices: 74851--74875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74841 AAAAAAAAAA
74851 AAAGTTTGGAAG
1 AAAGTTTGGAAG
74863 AAAGTTTGGAAG
1 AAAGTTTGGAAG
74875 A
1 A
74876 TTTTGCTGGA
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:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
AAAGTTTGGAAG
Found at i:76410 original size:31 final size:31
Alignment explanation
Indices: 76375--76437 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
76365 TTCTCCAATG
76375 GCAGACATACGTAATACTTTGAAAACCCTCA
1 GCAGACATACGTAATACTTTGAAAACCCTCA
76406 GCAGACATACGTAATACTTTGAAAACCCTCA
1 GCAGACATACGTAATACTTTGAAAACCCTCA
76437 G
1 G
76438 ACCACATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.22
Consensus pattern (31 bp):
GCAGACATACGTAATACTTTGAAAACCCTCA
Found at i:79997 original size:24 final size:24
Alignment explanation
Indices: 79959--80031 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
79949 TATTTTTTCC
79959 TTCAAA-CCCTTTTAAATCAGGGT
1 TTCAAACCCCTTTTAAATCAGGGT
79982 TTCAAACCCCTTTTAAATCAGGGT
1 TTCAAACCCCTTTTAAATCAGGGT
*
80006 TTCAAACCCCTTTTGAATCAGGGT
1 TTCAAACCCCTTTTAAATCAGGGT
80030 TT
1 TT
80032 TAGGGTTTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 6 0.12
24 42 0.88
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (24 bp):
TTCAAACCCCTTTTAAATCAGGGT
Found at i:80051 original size:32 final size:32
Alignment explanation
Indices: 80001--80063 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
79991 CTTTTAAATC
* *
80001 AGGGTTTCAAACCCCTTTTGAATCAGGGTTTT
1 AGGGTTTCAAAACCCTTTTAAATCAGGGTTTT
** *
80033 AGGGTTTCAAAATTCTTTTAAATCCGGGTTT
1 AGGGTTTCAAAACCCTTTTAAATCAGGGTTT
80064 AAAAAATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (32 bp):
AGGGTTTCAAAACCCTTTTAAATCAGGGTTTT
Found at i:80224 original size:96 final size:95
Alignment explanation
Indices: 80083--80260 Score: 311
Period size: 96 Copynumber: 1.9 Consensus size: 95
80073 CATTCAACTA
* *
80083 CAAATTCAAATTAATATTTCAACGATCTCTTCCTTCTCCCTCAGAAAACCTCATTTCTTACTTCC
1 CAAATTCAAATTAATATTTCAACGATATCTTCCTTCTCCATCAGAAAACCTCATTTCTTACTTCC
80148 TTTTTTATGTTTATCTCTTCTCTCTTTAACC
66 -TTTTTATGTTTATCTCTTCTCTCTTTAACC
*
80179 CAAATTCAAATTAATATTTCAACGTTATCTTCCTTCTCCATCAGAAAACCTCATTTCTTACTTCC
1 CAAATTCAAATTAATATTTCAACGATATCTTCCTTCTCCATCAGAAAACCTCATTTCTTACTTCC
*
80244 TTTTTGTGTTTATCTCT
66 TTTTTATGTTTATCTCT
80261 CCATGAGATA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 16 0.21
96 62 0.79
ACGTcount: A:0.25, C:0.26, G:0.04, T:0.45
Consensus pattern (95 bp):
CAAATTCAAATTAATATTTCAACGATATCTTCCTTCTCCATCAGAAAACCTCATTTCTTACTTCC
TTTTTATGTTTATCTCTTCTCTCTTTAACC
Found at i:80378 original size:30 final size:30
Alignment explanation
Indices: 80342--80398 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
80332 GCCGTAAGTT
80342 TTTTTTTCAATTTGAACTTTCAACTCTCAA
1 TTTTTTTCAATTTGAACTTTCAACTCTCAA
80372 TTTTTTTCAATTTGAACTTTCAACTCT
1 TTTTTTTCAATTTGAACTTTCAACTCT
80399 TTTACATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTTTTCAATTTGAACTTTCAACTCTCAA
Found at i:83111 original size:23 final size:23
Alignment explanation
Indices: 83081--83124 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
83071 AACAATCTTA
*
83081 AGCACTCTCGTTCGGTCTCTATG
1 AGCACTCTCGCTCGGTCTCTATG
83104 AGCACTCTCGCTCGGTCTCTA
1 AGCACTCTCGCTCGGTCTCTA
83125 CAAACTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (23 bp):
AGCACTCTCGCTCGGTCTCTATG
Found at i:83820 original size:32 final size:32
Alignment explanation
Indices: 83784--83864 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 32
83774 CCCTTTTAAA
83784 TCAGGGTTTCAAAATTCTTTTGAATCAGGGCT
1 TCAGGGTTTCAAAATTCTTTTGAATCAGGGCT
83816 TCAGGGTTTCAAAA-------GAATCAGGGCT
1 TCAGGGTTTCAAAATTCTTTTGAATCAGGGCT
*
83841 TTAGGGTTTCAAAATTCTTTTGAA
1 TCAGGGTTTCAAAATTCTTTTGAA
83865 ACCCCTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
25 24 0.59
32 17 0.41
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (32 bp):
TCAGGGTTTCAAAATTCTTTTGAATCAGGGCT
Found at i:83902 original size:24 final size:24
Alignment explanation
Indices: 83869--83914 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
83859 TTTGAAACCC
* * *
83869 CTTTTGAATCAGGGTTTCAAAATT
1 CTTTTAAATCAGGCTTTAAAAATT
83893 CTTTTAAATCAGGCTTTAAAAA
1 CTTTTAAATCAGGCTTTAAAAA
83915 AATCACATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (24 bp):
CTTTTAAATCAGGCTTTAAAAATT
Found at i:84062 original size:95 final size:95
Alignment explanation
Indices: 83930--84110 Score: 301
Period size: 95 Copynumber: 1.9 Consensus size: 95
83920 CATTCAACTT
* * * *
83930 CAAATTCAAATTAATATTTTAACGGTATCTTCCTTCTCCCTCAGAAAACCTCATTTCTTACTTCC
1 CAAATTCAAATTAATATTTCAACGGTATCTTCCTTCTCCATAAAAAAACCTCATTTCTTACTTCC
83995 TTTTTATGAT-TATCTCTTCTCTGTTTAACC
66 TTTTTATG-TGTATCTCTTCTCTGTTTAACC
*
84025 CAAATTCAAATTAATATTTCAACGGTATCTTCCTTCTCCATAAAAAAACCTCATTTCTTATTTCC
1 CAAATTCAAATTAATATTTCAACGGTATCTTCCTTCTCCATAAAAAAACCTCATTTCTTACTTCC
84090 TTTTTATGTGTATCTCTTCTC
66 TTTTTATGTGTATCTCTTCTC
84111 CATAAGATAC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 1 0.01
95 79 0.99
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (95 bp):
CAAATTCAAATTAATATTTCAACGGTATCTTCCTTCTCCATAAAAAAACCTCATTTCTTACTTCC
TTTTTATGTGTATCTCTTCTCTGTTTAACC
Found at i:84233 original size:30 final size:30
Alignment explanation
Indices: 84197--84254 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
84187 AGTTTTGTTT
84197 ATTTTTTTCAATTTGAACTTTCAACTCTCA
1 ATTTTTTTCAATTTGAACTTTCAACTCTCA
84227 ATTTTTTTCAATTTGAACTTTCAACTCT
1 ATTTTTTTCAATTTGAACTTTCAACTCT
84255 TTTACATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTTTTCAATTTGAACTTTCAACTCTCA
Found at i:86807 original size:16 final size:15
Alignment explanation
Indices: 86775--86804 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
86765 TGCTTACACC
86775 AAATTTTTTGTTTTT
1 AAATTTTTTGTTTTT
86790 AAATTTTTTGTTTTT
1 AAATTTTTTGTTTTT
86805 TAAGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
AAATTTTTTGTTTTT
Found at i:104255 original size:73 final size:73
Alignment explanation
Indices: 104136--104282 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
104126 TTAGGAAGCA
104136 TTGTAAGGATCTTACGGACGTGGTTATAGTTCGAATCTGAATAAATACAGAGTTTTCTCATATAG
1 TTGTAAGGATCTTACGGACGTGGTTATAGTTCGAATCTGAATAAATACAGAGTTTTCTCATATAG
104201 ACTTTGCT
66 ACTTTGCT
*
104209 TTGTAAGGATCTTATGGACGTGGTTATAGTTCGAATCTGAATAAATACAGAGTTTTCTCATATAG
1 TTGTAAGGATCTTACGGACGTGGTTATAGTTCGAATCTGAATAAATACAGAGTTTTCTCATATAG
104274 ACTTTGCT
66 ACTTTGCT
104282 T
1 T
104283 GACTCCATCC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (73 bp):
TTGTAAGGATCTTACGGACGTGGTTATAGTTCGAATCTGAATAAATACAGAGTTTTCTCATATAG
ACTTTGCT
Found at i:107954 original size:11 final size:12
Alignment explanation
Indices: 107929--107955 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
107919 GTTCTCATGG
107929 TTTTGCTCTGTT
1 TTTTGCTCTGTT
107941 TTTTGCTCTGTT
1 TTTTGCTCTGTT
107953 TTT
1 TTT
107956 CAGTTTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (12 bp):
TTTTGCTCTGTT
Found at i:135856 original size:3 final size:3
Alignment explanation
Indices: 135848--135876 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
135838 TTCCTTCCTC
135848 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
135877 CCCAGCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:137226 original size:6 final size:6
Alignment explanation
Indices: 137215--137240 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
137205 CATAATTACC
137215 CTAGTA CTAGTA CTAGTA CTAGTA CT
1 CTAGTA CTAGTA CTAGTA CTAGTA CT
137241 TAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (6 bp):
CTAGTA
Found at i:139827 original size:60 final size:60
Alignment explanation
Indices: 139724--139837 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
139714 AATACACACC
* *
139724 CTTATATGACTTTTCCAACCTTTCAATCCATCAAAGAGAGGAA-GCAAATAAGATGGTGAT
1 CTTATATAACTTCTCCAACCTTTCAATCCATCAAAGAGAGGAAGGCAAA-AAGATGGTGAT
* *
139784 CTTATATAACTTCTCCAACCTTTCAAT-CAGGTC-CAGAGGGGAAGGCAAAAAGAT
1 CTTATATAACTTCTCCAACCTTTCAATCCA--TCAAAGAGAGGAAGGCAAAAAGAT
139838 ATAAGTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
59 2 0.04
60 38 0.81
61 7 0.15
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (60 bp):
CTTATATAACTTCTCCAACCTTTCAATCCATCAAAGAGAGGAAGGCAAAAAGATGGTGAT
Done.