Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007848.1 Corchorus capsularis cultivar CVL-1 contig07869, 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: 57219
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:874 original size:2 final size:2
Alignment explanation
Indices: 867--904 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
857 TTATGACTAG
867 TA TA TA TA TA 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 TA TA TA TA TA
905 GTAGATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4682 original size:21 final size:20
Alignment explanation
Indices: 4654--4693 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4644 AGGTGAAATT
4654 AAGTCATGTGGCGAACCATC
1 AAGTCATGTGGCGAACCATC
*
4674 AAGTACATGTGGGGAACCAT
1 AAGT-CATGTGGCGAACCAT
4694 GCATGATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (20 bp):
AAGTCATGTGGCGAACCATC
Found at i:5555 original size:21 final size:22
Alignment explanation
Indices: 5512--5556 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5502 CTTTCGACAG
5512 TCCGACTACCACCTCCTCCTCC
1 TCCGACTACCACCTCCTCCTCC
*
5534 TCCGAC-ACC-CCATCCTCGTCC
1 TCCGACTACCACC-TCCTCCTCC
5555 TC
1 TC
5557 TGAAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.13, C:0.58, G:0.07, T:0.22
Consensus pattern (22 bp):
TCCGACTACCACCTCCTCCTCC
Found at i:8187 original size:12 final size:12
Alignment explanation
Indices: 8153--8187 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
8143 AAATGTAACA
8153 AAATAAAAAGAG
1 AAATAAAAAGAG
*
8165 AAAAAAAAAGAG
1 AAATAAAAAGAG
*
8177 AAATAAGAAGA
1 AAATAAAAAGA
8188 AAAGAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (12 bp):
AAATAAAAAGAG
Found at i:23945 original size:20 final size:20
Alignment explanation
Indices: 23920--23962 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
23910 TTAGTGTCCG
23920 TCCATTGCTCCGTTAATTCA
1 TCCATTGCTCCGTTAATTCA
23940 TCCATTGCTCCGTTAATTCA
1 TCCATTGCTCCGTTAATTCA
23960 TCC
1 TCC
23963 GACGTGGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (20 bp):
TCCATTGCTCCGTTAATTCA
Found at i:41395 original size:29 final size:29
Alignment explanation
Indices: 41353--41425 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
41343 TGATTAATGA
41353 GAATGGTTTATCTTCCTATAGATGTTATG
1 GAATGGTTTATCTTCCTATAGATGTTATG
*
41382 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATGGTTTATCTTCCTATAGATGTTATG
*
41411 GAATTGTTTATCTTC
1 GAATGGTTTATCTTC
41426 TTACATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.45
Consensus pattern (29 bp):
GAATGGTTTATCTTCCTATAGATGTTATG
Found at i:41749 original size:33 final size:33
Alignment explanation
Indices: 41707--41775 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
41697 ACAAAGTTTA
* * *
41707 TTTACCATGCATGATCCCCTTCTTCTACCTTTC
1 TTTACCATGCATAATCCCCTCCTCCTACCTTTC
* * *
41740 TTTATCATGCATAATCTCCTCCTCCTGCCTTTC
1 TTTACCATGCATAATCCCCTCCTCCTACCTTTC
41773 TTT
1 TTT
41776 TATTATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.14, C:0.35, G:0.06, T:0.45
Consensus pattern (33 bp):
TTTACCATGCATAATCCCCTCCTCCTACCTTTC
Found at i:44868 original size:30 final size:30
Alignment explanation
Indices: 44841--44902 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
44831 TAGAAGAGCT
44841 CACTCCTGAAGAGATTACTCCAAAAGAGTC
1 CACTCCTGAAGAGATTACTCCAAAAGAGTC
* * *
44871 CACTCTTGAAGAGATTACTCTAGAAGAGTC
1 CACTCCTGAAGAGATTACTCCAAAAGAGTC
44901 CA
1 CA
44903 TAGGCATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (30 bp):
CACTCCTGAAGAGATTACTCCAAAAGAGTC
Found at i:44891 original size:15 final size:15
Alignment explanation
Indices: 44825--44898 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
44815 GAGGATAAGG
*
44825 TTACTCTAGAAGAGC
1 TTACTCTAGAAGAGA
*
44840 TCACTCCT-GAAGAGA
1 TTACT-CTAGAAGAGA
* *
44855 TTACTCCAAAAGAG-
1 TTACTCTAGAAGAGA
* *
44869 TCCACTCTTGAAGAGA
1 T-TACTCTAGAAGAGA
44885 TTACTCTAGAAGAG
1 TTACTCTAGAAGAG
44899 TCCATAGGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
14 2 0.05
15 39 0.89
16 3 0.07
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (15 bp):
TTACTCTAGAAGAGA
Found at i:46847 original size:50 final size:49
Alignment explanation
Indices: 46790--47649 Score: 904
Period size: 50 Copynumber: 17.4 Consensus size: 49
46780 AGAAAAAACT
* *
46790 GGACCTTCCGACCGGGAAGGGGCCTTTTGGGAAACAAAATAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAA-AAGAAAACAG
* * * *
46840 GGACCTTCCGACCAGGAAGGAGCATTTTTGGAAACAAATAAAGAGAACGG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
* *
46890 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
*
46940 GGACCTTCCGA--GGGAAGGGGC-TTTTTGGAAACAAACAAAGAAAACAT
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
**
46987 GGACCTTCCGACTAGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
* * *
47037 GGACCTTCCGACCGGGAATGGGCATTTTT-TAAACAAAACAAGAAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAA-AAGAAAACAG
* *
47086 TGACCTTCCGACAC-GGAAGGGACATTTTTGGAAACAAACAAAGAAAACAG
1 GGACCTTCCGAC-CGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
* *
47136 GGACCTTCCGACCAGGAAGGAGCATTTTTGGAAACAAAGAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
* *
47186 GGACCTTCCGACCGGGAATGGGCATTTTTGG-AACAAGAGAAGAAAACTA-
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAA-AAAAGAAAAC-AG
* * *
47235 TGACCTTCCGACCGGGAAGGGGTATTTTTGG-AACAATCAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAA-AAAAGAAAACAG
* * *
47284 GGACCTTCCGACCAGGAATGGGCATTTTTGGAAACAAACAAAGAAAACAA
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AAAGAAAACAG
* ** **
47334 GGACCTTCCAACTAGGAAGGGGCATTTTTGGAAACTAGCAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAAC-AAAAAAGAAAACAG
* * **
47384 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAATA-AGAGGAGAAAAC-G
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAAAAGAAAACAG
* * * *
47432 GTGACCTTCCGACCGGGAAGCGGCATTTTTGGAATA-ACAGAAGAAAACTG
1 G-GACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAAAAGAAAACAG
* * * * * *
47482 TGACCTTCTGACAGGGAAGGGGCATTCTTT-GAATA-AGAGAAGAAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATT-TTTGGAA-ACAAAAAAGAAAACAG
* * *** * *
47531 TGACCTTCCGACCGGGAAAGGGCATTTTTGGAATA-AGGGAAGAAGACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAAAAGAAAACAG
* * * * *
47580 TGACCTTCCGACCGGGAAGAGGCATGTTTGGAATA-AGAAAAGAAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAAAAGAAAACAG
*
47629 TGACCTTCCGACCGGGAAGGG
1 GGACCTTCCGACCGGGAAGGG
47650 AAATTTAGGA
Statistics
Matches: 711, Mismatches: 79, Indels: 41
0.86 0.10 0.05
Matches are distributed among these distances:
47 33 0.05
48 17 0.02
49 325 0.46
50 332 0.47
51 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (49 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAAAAGAAAACAG
Found at i:47091 original size:49 final size:49
Alignment explanation
Indices: 46784--47649 Score: 760
Period size: 49 Copynumber: 17.6 Consensus size: 49
46774 ATGTTAAGAA
* * *
46784 AAAACT-GGACCTTCCGACCGGGAAGGGGCCTTTTGGGAAACAAAATAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTT-TGAAACAAAACAAG
* * *
46833 AAAACAGGGACCTTCCGACCAGGAAGGAGCATTTTTGGAAACAAATA-AAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAA-ACAAG
* * *
46883 AGAACGGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATA-AAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTT-TGAAACAAA-ACAAG
46933 AAAACTGGGACCTTCCGA--GGGAAGGGGC-TTTTTGGAAAC-AAACAAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAAAC-AAG
**
46980 AAAACAT-GGACCTTCCGACTAGGAAGGGGCATTTTTGGAAAC-AAACAAAG
1 AAAAC-TGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAAAC-AAG
* * *
47030 AAAACAGGGACCTTCCGACCGGGAATGGGCATTTTTTAAACAAAACAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
* *
47079 AAAACTGTGACCTTCCGACAC-GGAAGGGACATTTTTGGAAAC-AAACAAAG
1 AAAACTGGGACCTTCCGAC-CGGGAAGGGGCATTTTT-GAAACAAAAC-AAG
* * *
47129 AAAACAGGGACCTTCCGACCAGGAAGGAGCATTTTTGGAAACAAAGA-AAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAA-ACAAG
* * * * *
47179 AAAACAGGGACCTTCCGACCGGGAATGGGCATTTTTGGAACAAGAGAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
** * * *
47228 AAAACTATGACCTTCCGACCGGGAAGGGGTATTTTTGGAAC-AATCAAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAAC-AAG
* * *
47277 AAAACAGGGACCTTCCGACCAGGAATGGGCATTTTTGGAAAC-AAACAAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAAAC-AAG
** * ** * *
47327 AAAACAAGGACCTTCCAACTAGGAAGGGGCATTTTTGGAAAC-TAGCAAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT-GAAACAAAAC-AAG
* * * * * **
47377 AAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGGAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
* * * * *
47426 AAAAC-GGTGACCTTCCGACCGGGAAGCGGCATTTTTGGAATAACAGAAG
1 AAAACTGG-GACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
* * * * * *
47475 AAAACTGTGACCTTCTGACAGGGAAGGGGCATTCTTTG-AATAAGAGAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATT-TTTGAAACAAAACAAG
* * * * ***
47524 AAAACTGTGACCTTCCGACCGGGAAAGGGCATTTTTGGAATAAGGGAAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
* * * * * *
47573 AAGACTGTGACCTTCCGACCGGGAAGAGGCATGTTTGGAATAAGAA-AAG
1 AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAA-AACAAG
*
47622 AAAACTGTGACCTTCCGACCGGGAAGGG
1 AAAACTGGGACCTTCCGACCGGGAAGGG
47650 AAATTTAGGA
Statistics
Matches: 703, Mismatches: 86, Indels: 56
0.83 0.10 0.07
Matches are distributed among these distances:
45 1 0.00
46 2 0.00
47 28 0.04
48 19 0.03
49 326 0.46
50 323 0.46
51 3 0.00
52 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (49 bp):
AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGAAACAAAACAAG
Found at i:47312 original size:198 final size:197
Alignment explanation
Indices: 46790--47649 Score: 929
Period size: 198 Copynumber: 4.4 Consensus size: 197
46780 AGAAAAAACT
* * * *
46790 GGACCTTCCGACCGGGAAGGGGCCTTTTGGGAAACAA-AATAAGAAAACAGGGACCTTCCGACCA
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGG-AACAAGAA-AAGAAAACA-TGACCTTCCGACCG
* * * *
46854 GGAAGGAGCATTTTTGGAAACAA-ATAAAGAGAACGGGGACCTTCCGAC-CGGGAAGGGGCATTT
63 GGAAGGGGCATTTTTGG-AACAACA-CAAGAAAACTGGGACCTTCCGACAC-GGAAGGGGCATTT
* * * * *
46917 TGGGAAACAAATAAAGAAAACTGGGACCTTCCGA--GGGAAGGGGC-TTTTTGGAAACAAACAAA
125 TTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAACAAAGAAA
*
46979 GAAAACAT
190 GAAAACAG
** *
46987 GGACCTTCCGACTAGGAAGGGGCATTTTTGGAAACAA-ACAAAGAAAACAGGGACCTTCCGACCG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGG-AACAAGA-AAAGAAAACA-TGACCTTCCGACCG
* ** * * *
47051 GGAATGGGCATTTTTTAAACAAAACAAGAAAACTGTGACCTTCCGACACGGAAGGGACATTTTTG
63 GGAAGGGGCATTTTTGGAACAACACAAGAAAACTGGGACCTTCCGACACGGAAGGGGCATTTTTG
*
47116 GAAACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGAGCATTTTTGGAAACAAAGAAAGAA
128 GAAACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAACAAAGAAAGAA
47181 AACAG
193 AACAG
* *
47186 GGACCTTCCGACCGGGAATGGGCATTTTTGGAACAAGAGAAGAAAACTATGACCTTCCGACCGGG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAACAAGAAAAGAAAAC-ATGACCTTCCGACCGGG
* * *
47251 AAGGGGTATTTTTGGAACAATCA-AAGAAAACAGGGACCTTCCGAC-CAGGAATGGGCATTTTTG
65 AAGGGGCATTTTTGGAACAA-CACAAGAAAACTGGGACCTTCCGACAC-GGAAGGGGCATTTTTG
* * * *
47314 GAAACAAACAAAGAAAACAAGGACCTTCCAACTAGGAAGGGGCATTTTTGGAAAC-TAGCAAAGA
128 GAAACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAACAAAG-AAAGA
47378 AAACAG
192 AAACAG
* * ** *
47384 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGGAGAAAACGGTGACCTTCCGACCGGG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAACAAGAAAAGAAAAC-ATGACCTTCCGACCGGG
* * * * * *
47449 AAGCGGCATTTTTGGAATAACAGAAGAAAACTGTGACCTTCTGACAGGGAAGGGGCATTCTTT-G
65 AAGGGGCATTTTTGGAACAACACAAGAAAACTGGGACCTTCCGACACGGAAGGGGCATT-TTTGG
* * * * * * * * *
47513 AATA-AGA-GAAGAAAACTGTGACCTTCCGACCGGGAAAGGGCATTTTTGG-AATAAGGGAAGAA
129 AA-ACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAACAAAGAAAGAA
* *
47575 GACTG
193 AACAG
* * * * *
47580 TGACCTTCCGACCGGGAAGAGGCATGTTTGGAATAAGAAAAGAAAACTGTGACCTTCCGACCGGG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAACAAGAAAAGAAAAC-ATGACCTTCCGACCGGG
47645 AAGGG
65 AAGGG
47650 AAATTTAGGA
Statistics
Matches: 570, Mismatches: 77, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
196 139 0.24
197 112 0.20
198 260 0.46
199 59 0.10
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (197 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTTGGAACAAGAAAAGAAAACATGACCTTCCGACCGGGA
AGGGGCATTTTTGGAACAACACAAGAAAACTGGGACCTTCCGACACGGAAGGGGCATTTTTGGAA
ACAAACAAAGAAAACAGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAACAAAGAAAGAAAAC
AG
Found at i:48358 original size:50 final size:51
Alignment explanation
Indices: 48299--48425 Score: 202
Period size: 50 Copynumber: 2.5 Consensus size: 51
48289 CACCTTTATC
* * * *
48299 ACAAATTAATCAACAGTTTCATCTTTCACTTAAAAATTCCATTC-TTAATT
1 ACAACTTAATCAAAAATTCCATCTTTCACTTAAAAATTCCATTCTTTAATT
*
48349 ACAACTTAATCAAAAATTCCATCTTTCACTTAAAAATTCCATTCTTTATTT
1 ACAACTTAATCAAAAATTCCATCTTTCACTTAAAAATTCCATTCTTTAATT
48400 ACAACTTAATCAAAAATTCCATCTTT
1 ACAACTTAATCAAAAATTCCATCTTT
48426 TAGCTAAAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
50 40 0.56
51 31 0.44
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.39
Consensus pattern (51 bp):
ACAACTTAATCAAAAATTCCATCTTTCACTTAAAAATTCCATTCTTTAATT
Found at i:53008 original size:40 final size:40
Alignment explanation
Indices: 52954--53035 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
52944 CATTTAATAA
52954 AAAAGCAAGTAAAAGCAGCTCAATTTGGCAACTAATTGGT
1 AAAAGCAAGTAAAAGCAGCTCAATTTGGCAACTAATTGGT
52994 AAAAGCAAGTAAAAGCAGCTCAATTTGGCAACTAATTGGT
1 AAAAGCAAGTAAAAGCAGCTCAATTTGGCAACTAATTGGT
53034 AA
1 AA
53036 CTCGTAGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (40 bp):
AAAAGCAAGTAAAAGCAGCTCAATTTGGCAACTAATTGGT
Found at i:53108 original size:25 final size:25
Alignment explanation
Indices: 53080--53129 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53070 CAAAAGCTCG
53080 AGGCAT-TATGTTGATCATCCTGTCT
1 AGGCATAT-TGTTGATCATCCTGTCT
* *
53105 AGGCATATTGTTGTTCATCTTGTCT
1 AGGCATATTGTTGATCATCCTGTCT
53130 TCATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (25 bp):
AGGCATATTGTTGATCATCCTGTCT
Found at i:57045 original size:102 final size:98
Alignment explanation
Indices: 56906--57137 Score: 290
Period size: 102 Copynumber: 2.3 Consensus size: 98
56896 TAATTTTAAT
* * * * * *
56906 TTGGCCTAAACATAGTG-AATTAATTATATATTTTATTTCTAAAACCCTATAACAATAAGTTATT
1 TTGG-CTAAACTTAGTGAAATTAGTTTTATATTATATTTCTAAAACCCTAAAACAATAAATTATT
*
56970 AATTAT-GGAATTTACCCTTAAAATAAAAAAATT-AAC
65 AATT-TCGGAATTTACCCTTAAAAT---AAAATTAAAA
*
57006 TTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTATATTTCTAAAACCCTAAAACAATAAATTAT
1 TT--GGCTAAACTTAGTGAAATTAGTTTTATATTATATTTCTAAAACCCTAAAACAATAAATTAT
*
57071 TGATTTCGGAATTTACCCTTAAAATAAAATTAAAA
64 TAATTTCGGAATTTACCCTTAAAATAAAATTAAAA
*
57106 TTTGCTAAACTTAGTGAAATTAGTTTTATATT
1 TTGGCTAAACTTAGTGAAATTAGTTTTATATT
57138 TTATAAAACT
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
98 28 0.24
99 6 0.05
100 6 0.05
101 12 0.10
102 64 0.55
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (98 bp):
TTGGCTAAACTTAGTGAAATTAGTTTTATATTATATTTCTAAAACCCTAAAACAATAAATTATTA
ATTTCGGAATTTACCCTTAAAATAAAATTAAAA
Done.