Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014439.1 Corchorus capsularis cultivar CVL-1 contig14460, 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: 139135
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1662 original size:62 final size:62
Alignment explanation
Indices: 1595--1723 Score: 188
Period size: 62 Copynumber: 2.1 Consensus size: 62
1585 AAAAAATTAA
* *
1595 AAATTATTATTATTACACT-TTTTTTGATGACATCCTTATGAAATTTTGATAACCTTCATATG
1 AAATTATGATAATTACACTATTTTTT-ATGACATCCTTATGAAATTTTGATAACCTTCATATG
** * *
1657 AAATTATGATAATTACACTATTTTTTATGATGTCCTTATGAAATTTTGATAAGCTTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCATATG
1719 AAATT
1 AAATT
1724 TCAATAACGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 54 0.90
63 6 0.10
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (62 bp):
AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCATATG
Found at i:1966 original size:23 final size:22
Alignment explanation
Indices: 1918--1974 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1908 CCTCCATATG
*
1918 AATTGTCAGTAATCACACTCTGA
1 AATTGTGA-TAATCACACTCTGA
*
1941 AATTTTGATAATCACAC-CTTGAA
1 AATTGTGATAATCACACTC-TG-A
1964 AATTGTGATAA
1 AATTGTGATAA
1975 CCTCGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 11 0.38
23 17 0.59
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
AATTGTGATAATCACACTCTGA
Found at i:1986 original size:23 final size:23
Alignment explanation
Indices: 1940--2218 Score: 123
Period size: 22 Copynumber: 12.8 Consensus size: 23
1930 TCACACTCTG
* *
1940 AAATTTTGATAATCACACCT-TGA
1 AAATTTTGATAACCTC-CCTATGA
* **
1963 AAATTGTGATAACCTCGGTATG-
1 AAATTTTGATAACCTCCCTATGA
*
1985 AAATTTTGATAAATCTCCCTAT-A
1 AAATTTTGAT-AACCTCCCTATGA
* *
2008 AAATTTTGATAACCTCCTTAAGA
1 AAATTTTGATAACCTCCCTATGA
* *
2031 AAATCTTGATAA-----CTA--C
1 AAATTTTGATAACCTCCCTATGA
2047 AAATTTTGATAACCTCCCTATG-
1 AAATTTTGATAACCTCCCTATGA
* * **
2069 -ATTTTTAATAACCTCATTATG-
1 AAATTTTGATAACCTCCCTATGA
* *
2090 AAATTTTGTTAATCTCCCTATG-
1 AAATTTTGATAACCTCCCTATGA
* * *
2112 AAATTTTGATCTACAT-ACTATG-
1 AAATTTTGAT-AACCTCCCTATGA
* *
2134 AAATTTTGATAACC-CTCT-TGTG
1 AAATTTTGATAACCTCCCTATG-A
* **
2156 AAATTTTGA-AAACTAAACTATG-
1 AAATTTTGATAACCT-CCCTATGA
* *
2178 AAATTTTGATAACCTTCATATG-
1 AAATTTTGATAACCTCCCTATGA
*
2200 AAATTTTGATATCCTCCCT
1 AAATTTTGATAACCTCCCT
2219 GAAATTTGAT
Statistics
Matches: 192, Mismatches: 44, Indels: 41
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.06
18 2 0.01
20 2 0.01
21 27 0.14
22 95 0.49
23 53 0.28
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAACCTCCCTATGA
Found at i:1988 original size:45 final size:45
Alignment explanation
Indices: 1938--2023 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
1928 AATCACACTC
1938 TGAAATTTTGAT-AATCACACCT-TGAAAATTGTGATAACCTCGGTA
1 TGAAATTTTGATAAATCAC-CCTAT-AAAATTGTGATAACCTCGGTA
* *
1983 TGAAATTTTGATAAATCTCCCTATAAAATTTTGATAACCTC
1 TGAAATTTTGATAAATCACCCTATAAAATTGTGATAACCTC
2024 CTTAAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
45 31 0.84
46 6 0.16
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (45 bp):
TGAAATTTTGATAAATCACCCTATAAAATTGTGATAACCTCGGTA
Found at i:2089 original size:21 final size:21
Alignment explanation
Indices: 2050--2090 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2040 TAACTACAAA
* *
2050 TTTTGATAACCTCCCTATGAT
1 TTTTAATAACCTCACTATGAT
*
2071 TTTTAATAACCTCATTATGA
1 TTTTAATAACCTCACTATGA
2091 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (21 bp):
TTTTAATAACCTCACTATGAT
Found at i:2359 original size:22 final size:22
Alignment explanation
Indices: 2334--2454 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
2324 TATCACATTT
2334 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
2356 TGAAATTTTGATGACCTATCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
2378 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
2400 TAAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
2422 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
2444 TGAAATTTTGA
1 TGAAATTTTGA
2455 AATTAGACCA
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 77 0.97
23 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:2360 original size:44 final size:44
Alignment explanation
Indices: 2310--2454 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
2300 TAAATACTAC
* * *
2310 TATGAAATTTTGGTTATCACATTTTGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTT
* * * * * *
2354 TATGAAATTTTGATGA-C-CTATCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCAC-AT-TATGAAATTTTGATAACCTCTT
* * *
2398 TATAAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTC-TT
2443 T-TGAAATTTTGA
1 TATGAAATTTTGA
2455 AATTAGACCA
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.04
44 69 0.88
45 4 0.05
46 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTT
Found at i:2795 original size:31 final size:30
Alignment explanation
Indices: 2731--2795 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2721 TGGCAATTTA
* * * *
2731 GAAATATGTTTTTAAAAAATGGTACAATTG
1 GAAATATATTTTAAAAAAAGGGTACAATCG
*
2761 GAAATATATTTTAAAAATAAGGGTACACTCG
1 GAAATATATTTTAAAAA-AAGGGTACAATCG
2792 GAAA
1 GAAA
2796 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (30 bp):
GAAATATATTTTAAAAAAAGGGTACAATCG
Found at i:14846 original size:30 final size:30
Alignment explanation
Indices: 14810--14869 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
14800 TCAACTCTTT
*
14810 GCAGTACACAGACTACAACTTTAAACAAGC
1 GCAGTACACAGACCACAACTTTAAACAAGC
14840 GCAGTACACAGACCACAACTTTAAACAAGC
1 GCAGTACACAGACCACAACTTTAAACAAGC
14870 AAAGGTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (30 bp):
GCAGTACACAGACCACAACTTTAAACAAGC
Found at i:15160 original size:12 final size:12
Alignment explanation
Indices: 15143--15169 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15133 AGTTGGTAAC
15143 AATGATGTAGAG
1 AATGATGTAGAG
15155 AATGATGTAGAG
1 AATGATGTAGAG
15167 AAT
1 AAT
15170 TGCTTTTCTC
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:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (12 bp):
AATGATGTAGAG
Found at i:17557 original size:81 final size:81
Alignment explanation
Indices: 17460--17609 Score: 246
Period size: 81 Copynumber: 1.9 Consensus size: 81
17450 ACACGTTATT
* * * *
17460 TAATTTGTTTTAAATTATATAAAGATTAAAATCTTAAGCATATTACTAATTTTGTCTTAAAGAAA
1 TAATTTGTTTTAAATTATATAAAGATTAAAATCTTAAGCATACTACTAAATTTATCCTAAAGAAA
17525 CCTAGCGCACGTGACC
66 CCTAGCGCACGTGACC
* *
17541 TAATTTGTTTTAAATTATATGAAGATTAAAATCTTAAGCATACTACTAAATTTATCCTAAAGAAG
1 TAATTTGTTTTAAATTATATAAAGATTAAAATCTTAAGCATACTACTAAATTTATCCTAAAGAAA
17606 CCTA
66 CCTA
17610 TTATTAGAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (81 bp):
TAATTTGTTTTAAATTATATAAAGATTAAAATCTTAAGCATACTACTAAATTTATCCTAAAGAAA
CCTAGCGCACGTGACC
Found at i:23140 original size:10 final size:10
Alignment explanation
Indices: 23125--23154 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
23115 CTTTTTCTCA
23125 CCATTTTCTT
1 CCATTTTCTT
23135 CCATTTTCTT
1 CCATTTTCTT
*
23145 TCATTTTCTT
1 CCATTTTCTT
23155 GACTCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (10 bp):
CCATTTTCTT
Found at i:32186 original size:2 final size:2
Alignment explanation
Indices: 32179--32206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32169 TTCATCGACT
32179 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
32207 ATTAAATAAC
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:41855 original size:2 final size:2
Alignment explanation
Indices: 41848--41884 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41838 AATGAAGGAC
41848 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
41885 TCTCACCTTT
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:42184 original size:42 final size:42
Alignment explanation
Indices: 42137--42222 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
42127 CATATACTAA
42137 TATTTACCATGATGAATTTTTGCTAAATCCCCGGCAGACTCG
1 TATTTACCATGATGAATTTTTGCTAAATCCCCGGCAGACTCG
42179 TATTTACCATGATGAATTTTTGCTAAATCCCCGGCAGACTCG
1 TATTTACCATGATGAATTTTTGCTAAATCCCCGGCAGACTCG
42221 TA
1 TA
42223 CACATTGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (42 bp):
TATTTACCATGATGAATTTTTGCTAAATCCCCGGCAGACTCG
Found at i:42998 original size:24 final size:24
Alignment explanation
Indices: 42954--43001 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42944 ATCAGGGGAC
* **
42954 GCAAATTCATCATTTGTATCCTCA
1 GCAAATTCATCATCTAAATCCTCA
42978 GCAAATTCATCATCTAAATCCTCA
1 GCAAATTCATCATCTAAATCCTCA
43002 TTTCGAAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (24 bp):
GCAAATTCATCATCTAAATCCTCA
Found at i:63402 original size:19 final size:20
Alignment explanation
Indices: 63364--63407 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
63354 GGATCCTCTC
*
63364 TCTTCAGACGTTGATGAGTT
1 TCTTCAGAAGTTGATGAGTT
*
63384 TCTTCAGAAGTT-TTGAGTT
1 TCTTCAGAAGTTGATGAGTT
63403 TCTTC
1 TCTTC
63408 CCATTTCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (20 bp):
TCTTCAGAAGTTGATGAGTT
Found at i:63998 original size:39 final size:39
Alignment explanation
Indices: 63955--64429 Score: 624
Period size: 39 Copynumber: 12.3 Consensus size: 39
63945 TTCTCTTTCC
63955 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
*
63994 TCTCATGTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
64033 TCTCA------TCTCGTTCACGAGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
64066 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* *
64105 TCTCATGTTCTTCTCGTTCGCGAGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
*
64144 TCTCATTTTCTTCTCGTTCACGGGCTT-CTCTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCT-TCAATCTCT
* * * * *
64183 TCTCATTTTCTTCTTGCTCACGGGCTTCCCTCAGTCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* * * * *
64222 TCTCATTTTCTTCTTGTTCACGGGCTTCCCTCAGTCTCC
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* *
64261 TCTC-TTTCTCTTCTCGTTCACGAGCTTCCCTCAATCTCC
1 TCTCATTT-TCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* * * *
64300 TCTCCTTCTCTTCTCGTTCACGAGCTTCCCTCAATCTCC
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* * *
64339 TCTCTTTTTCTTCTCGTTCACGAGCTTCCTTCAAACTCC
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
* ** *
64378 TCTCTTTTTCTTCTCGTTCGTGGGCTTCCTTCAATCTCT
1 TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
*
64417 TCTCCTTTTCTTC
1 TCTCATTTTCTTC
64430 CTGCTCAAGG
Statistics
Matches: 400, Mismatches: 26, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
33 33 0.08
38 5 0.01
39 359 0.90
40 3 0.01
ACGTcount: A:0.10, C:0.36, G:0.10, T:0.44
Consensus pattern (39 bp):
TCTCATTTTCTTCTCGTTCACGAGCTTCCTTCAATCTCT
Found at i:75642 original size:1 final size:1
Alignment explanation
Indices: 75636--75668 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
75626 ATTGCGTTGG
75636 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
75669 CTCCCTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:79824 original size:17 final size:17
Alignment explanation
Indices: 79796--79840 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
79786 ACGGTGCACC
79796 TTTTATTTTATTTT-TTAA
1 TTTTA-TTTATTTTATT-A
79814 TTTTATTTATTTTATTA
1 TTTTATTTATTTTATTA
79831 TTTTATTTAT
1 TTTTATTTAT
79841 GAACAGCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTATTTTATTA
Found at i:92205 original size:26 final size:26
Alignment explanation
Indices: 92175--92227 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
92165 AATTTTAAAG
92175 TTTGGCACCAAACTTAATTGCTTGTT
1 TTTGGCACCAAACTTAATTGCTTGTT
*
92201 TTTGGCACCAAATTTAATTGCTTGTT
1 TTTGGCACCAAACTTAATTGCTTGTT
92227 T
1 T
92228 AAATAGTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (26 bp):
TTTGGCACCAAACTTAATTGCTTGTT
Found at i:99392 original size:4 final size:4
Alignment explanation
Indices: 99383--99407 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
99373 AAGCAAACGG
99383 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
99408 CAGAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:119154 original size:41 final size:41
Alignment explanation
Indices: 119092--119172 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
119082 CAACATGCTT
* * *
119092 AGTTCTTTTCAATTAAGGACAAGATTCTACATTTCACATTC
1 AGTTCTCTTCAATCAAGGACAAGATTCCACATTTCACATTC
* *
119133 AGTTCTCTTCAATC-AGAGACAATATTCCACATTTGACATT
1 AGTTCTCTTCAATCAAG-GACAAGATTCCACATTTCACATT
119173 GCACGTCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (41 bp):
AGTTCTCTTCAATCAAGGACAAGATTCCACATTTCACATTC
Found at i:134455 original size:3 final size:3
Alignment explanation
Indices: 134449--134496 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
134439 CAAAAAAAAA
134449 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
134497 CTTAATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:138577 original size:15 final size:16
Alignment explanation
Indices: 138546--138580 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
138536 GTGGAGTGAG
*
138546 AGAAAATGAAGGGAGA
1 AGAAAATGAAGGAAGA
138562 AGAAAATG-AGGAAGA
1 AGAAAATGAAGGAAGA
138577 AGAA
1 AGAA
138581 GAAGTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (16 bp):
AGAAAATGAAGGAAGA
Found at i:138610 original size:18 final size:17
Alignment explanation
Indices: 138589--138622 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
138579 AAGAAGTAGG
138589 AAAAGACAAAAAAAAAGT
1 AAAAGA-AAAAAAAAAGT
*
138607 AAAAGAAAGAAAAAAG
1 AAAAGAAAAAAAAAAG
138623 AAATCTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGT
Done.