Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015751.1 Corchorus capsularis cultivar CVL-1 contig15772, 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: 42074
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:385 original size:19 final size:18
Alignment explanation
Indices: 352--387 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
342 TTGAAATAAT
352 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
370 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
388 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:1306 original size:19 final size:18
Alignment explanation
Indices: 1282--1318 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1272 TTGAAGATTT
1282 CTTGAAGACAATCTGAAGA
1 CTTGAAGACAAT-TGAAGA
*
1301 CTTGAAGACCATTGAAGA
1 CTTGAAGACAATTGAAGA
1319 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
CTTGAAGACAATTGAAGA
Found at i:7376 original size:40 final size:41
Alignment explanation
Indices: 7326--7409 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 41
7316 AGATGAAGCC
*
7326 AAACCCTAAAAAACA-ATATAAACCCTATGTGACAT-AAAAG
1 AAACCCTAAAAAACATAT-TAAACCCTAGGTGACATAAAAAG
* *
7366 AAACCTTAAAAAACATATTAAACCCTAGGTGAGATAAAAAG
1 AAACCCTAAAAAACATATTAAACCCTAGGTGACATAAAAAG
7407 AAA
1 AAA
7410 AAAACATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 29 0.74
41 10 0.26
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.18
Consensus pattern (41 bp):
AAACCCTAAAAAACATATTAAACCCTAGGTGACATAAAAAG
Found at i:10568 original size:919 final size:910
Alignment explanation
Indices: 7824--10748 Score: 3797
Period size: 905 Copynumber: 3.2 Consensus size: 910
7814 TAAAAATATC
* * * * *
7824 TTATGTGCAACACCACCACTGTAAGGGGGATCAGCTTTTCTCTTCTTACTTATTGTGCGAAGTCC
1 TTATGTGCAACACCACCACTGGACGGAGGATCAGCCTTTATCTTCTTACTTATTGTGCGAAGTCC
* * * * *
7889 AACGACTTCAATGCTTTTATGTTTCTTCTATTCAAAGAATTGAGGATTATCGATCTATCCTACAA
66 AACTACGTCAATGCTTCTATGTTTCTTCCATTCAAAGAATTGAGGATTCTCGATCTATCCTACAA
* * ** *
7954 TGCCAATCTATTCAATGGATCTATAAATATGAAAGGTAGATTATATGTACACTTTCATACTGTTT
131 TGCCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATACACTTTCATATTGTTT
* * * * *
8019 AAACCCTAATTTACAATTTGGTTAATTAAATAATTTTGCCAAATTGACTTGGTCCCAAAGCCCTA
196 ATACCCTAATTTACAAATTGG-TAATTAAGTAATTGTGGCAAATTGACTTGGTCCCAAAG-CCT-
* * * * * * *
8084 ATCCACCCTTAAAAATTTCACGAATGTCACAAGAAACACGCACAAAATTGCAATTCAGCCCAAAT
258 ATCCACCCTTCAAAATTTCACGAATGTCGCACGAAACCCGCATAGAATTGCAATTCAGCCAAAAT
* * * * * *
8149 ATG-AAAGTTGGGC-TTTAGTGTTCTTTGCAAGCCTCTACGCCTTCATCGCTAGCCTCGTTCATA
323 ATGCAAAGTTGGGCTTTTGGTGTTCTTTTCAAGCCTTTACGCCTTCCTCGCTTGCCTCGTTCATT
** * * * * *
8212 TCGTTTCAATAACGGACGCTTTTCTAAGAATTTTGATATTTTT-TTCCTACGTCAAAAAGATACA
388 TCGTTTCGGTAACGGACGCTTCTCTAAGGATTTTGATGTTTTTCGTCCTACGTCAAAAAGAGACA
* *
8276 ACTGACAAGCTACTGCTTAGCTTACAATTGAACTTCTAATTTTAAAATTTTCATAGAAGACGTAA
453 ACTGACAAGC-ACTACTTAGCTTACAATTGAACTTCTAATTTTACAATTTTCATAGAAGACGTAA
*
8341 TACTATGATATTAAAGAAAATAATTTATAGTTGTACCCAATTGACTTACTATGCTCGAGGCCCTT
517 TACTATG--ATTAAAGGAAAT-ATTT-TA-TTGTACCCAATTGACTTACTATGCTCGAGGCCCTT
* * * *
8406 ATATAAGCTCAAACGAAGTAATAATTGTTC--CGAACCTCCTCTTATACATCCAAATTTTATTTT
577 -TATAAGCTCAAACGAAGTGAT-ATT-TTCTGCCAACCTCCTCTTATACATCCAACTTTTATTTC
* *
8469 TATTTTCAACGAAAAAAAAAAAG-AAACGCTTTCTACAAGTCATTAGGGTGTTGTTACCTCTCAA
639 TATTTTCAACGAAAAAAAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTGTTACCTTTCAA
*
8533 AAGAAAATTCATTAGAGTGTTCTAGAATATGGGTTCAAAAAGGTTATTGA-TCGTACTCATGATC
704 AA-AAAATTCATTAGAGTGTT-TAGAAGATGGGTTCAAAAAGGTTATTGATTC-TACTCATGATC
* * ***
8597 ATAGTAATCATTCTAGGATACAAATGGTCGAATGGGTGTGTTCATAGGGGCCGAATTGCTTTGTT
766 ATAGTAATCATTCTAGGATCCAAATGGTCGAATGGGTGTGTTCATAAGGAAAGAATTGCTTTGTT
* *
8662 TCAACTCAAATCTCCCATCGATCTTCAACTTCCAATTCATCAATCATGGGTGGATAATGATTGTT
831 TCAACTCAAATCTTCCATCGATCTTCAACTTCCAGTTCATCAATCATGGGTGGATAATGATTGTT
* *
8727 GTCAATAGAGTGGTC
896 GTCAATGGAGTGGTG
* * *
8742 TTATGTTCAACACCACCACTGGACGGATGATCAACCTTTATCTTCTTACTTATTGTG-GAAAGTC
1 TTATGTGCAACACCACCACTGGACGGAGGATCAGCCTTTATCTTCTTACTTATTGTGCG-AAGTC
* * *
8806 CAACTACGTCAATGCTTCTATGTTTCTTTCATTCGAAGAATTGAGGATTCTCGATCTGTCCTACA
65 CAACTACGTCAATGCTTCTATGTTTCTTCCATTCAAAGAATTGAGGATTCTCGATCTATCCTACA
*
8871 ATGCCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATATATACACTTTCATGCAGTT
130 ATGCCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATACACTTTCAT--A-TT
* * *
8936 -TAATATACCCTAATTTAC-AATTGTGTTATTAAGTGATTGTGGCAAATTGACTTGGTCCCAAAG
192 GT-TTATACCCTAATTTACAAATTG-GTAATTAAGTAATTGTGGCAAATTGACTTGGTCCCAAAG
* * * * * * *
8999 CCATAATCCACCATTCAATATTCCACCAATATCGCACGAAA-CCGCATAGAATTGCAAGTCTGCC
255 CC-T-ATCCACCCTTCAAAATTTCACGAATGTCGCACGAAACCCGCATAGAATTGCAATTCAGCC
* * * *
9063 AAAATATGCAAAGTTGTGCTTTTGGTGTTCTTTTCAAGCTTTTAGGCCTTCCTCGCATGCCTCGT
318 AAAATATGCAAAGTTGGGCTTTTGGTGTTCTTTTCAAGCCTTTACGCCTTCCTCGCTTGCCTCGT
* * ** *
9128 CCATTTTGTTTCGGTAATAGATGCTTCTCTAAGGATTTTGATGTTTTTCGTCCTACGTCAAAAAG
383 TCATTTCGTTTCGGTAACGGACGCTTCTCTAAGGATTTTGATGTTTTTCGTCCTACGTCAAAAAG
* * * * *
9193 AGACAACTGACAAGCAACTATTTAGCTTACAATTGAGCTTCTACTTTTACAATTTTAATAGACGA
448 AGACAACTGACAAGC-ACTACTTAGCTTACAATTGAACTTCTAATTTTACAATTTTCATAGAAGA
* * ** *
9258 TGTAATACTATGATTAAAGGAAATAATTTATAATACCCAATTGGCTTACTATGCTCGAGG-CC--
512 CGTAATACTATGATTAAAGGAAATATTTTATTGTACCCAATTGACTTACTATGCTCGAGGCCCTT
* * ** *
9320 --T----TCAAAGGAAGTGATA-ATAGTGCCCAACCTCCTCTTATACATCCAACTTTTATTTCTC
577 TATAAGCTCAAACGAAGTGATATTTTCTG-CCAACCTCCTCTTATACATCCAACTTTTATTTCTA
* *
9378 TTTTCAATGAAAAACAAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTCTTACCTTTCAAA
641 TTTTCAACGAAAAA-AAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTGTTACCTTTCAAA
* * *
9443 AAAAATTCA-TAGTGT-TTTGGAAGATGGGTTCAAAAAGGTTATTGATTGTACTCATGATCATAG
705 AAAAATTCATTAGAGTGTTTAGAAGATGGGTTCAAAAAGGTTATTGATTCTACTCATGATCATAG
* *
9506 TAATCATTCTA-GATTCCAAATGGTTGAATGGGTGTGTTCATATGGAAAGAATTGCTTTGTTTCA
770 TAATCATTCTAGGA-TCCAAATGGTCGAATGGGTGTGTTCATAAGGAAAGAATTGCTTTGTTTCA
* *
9570 ACTCAAATCTTCCATCTATCTTCAACTTCCAGTTCATCAATCATGGTTGGATAATGATTGTTGTC
834 ACTCAAATCTTCCATCGATCTTCAACTTCCAGTTCATCAATCATGGGTGGATAATGATTGTTGTC
9635 AATGGAGTGGTG
899 AATGGAGTGGTG
* * * *
9647 TTATGTGCAACACCACCACTGGATGGAGGATCAGCCTTTAT-TGTCTTCCTTAGTGTGTGAAGTC
1 TTATGTGCAACACCACCACTGGACGGAGGATCAGCCTTTATCT-TCTTACTTATTGTGCGAAGTC
* * * **
9711 CAACTACGTCAATGCTTTTATGTTTCTTCCGTTCAAAAAATTGATTATTCTCGATCTATCCTACA
65 CAACTACGTCAATGCTTCTATGTTTCTTCCATTCAAAGAATTGAGGATTCTCGATCTATCCTACA
*
9776 ATGCCAATTTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATACACTTTCATATTGTT
130 ATGCCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATACACTTTCATATTGTT
*
9841 TATACCCTAATTTACAAATTGAGTAATTAAGTAATTGTGGAAAATTGACTTGGTCCCAAAGCCT-
195 TATACCCTAATTTACAAATTG-GTAATTAAGTAATTGTGGCAAATTGACTTGGTCCCAAAGCCTA
* * * *
9905 TCCACCCTTCAAAATTTCAGGAATGTCGCACGAAACCCGCATAGAACTGCAATTCGGCAAAAATA
259 TCCACCCTTCAAAATTTCACGAATGTCGCACGAAACCCGCATAGAATTGCAATTCAGCCAAAATA
*
9970 TGCACAA-TTGGGCTTTTGGTGTTCTTTTCAAGCCTTTACGCGTTCCTCGCTTGCCTCGTTCATT
324 TGCA-AAGTTGGGCTTTTGGTGTTCTTTTCAAGCCTTTACGCCTTCCTCGCTTGCCTCGTTCATT
* * * * * *
10034 TCATTTTGGTAACGGACCCTTCTCTAAGGATTTTGATGTTTTTCGTCCTAGGTCAGAAAGAGCCA
388 TCGTTTCGGTAACGGACGCTTCTCTAAGGATTTTGATGTTTTTCGTCCTACGTCAAAAAGAGACA
* *
10099 ACTAACAAGCAGCTACTTAGCTTACAATTGAAC-TCTTAATTTTACAATTTTCATAAAAGACGTA
453 ACTGACAAGCA-CTACTTAGCTTACAATTGAACTTC-TAATTTTACAATTTTCATAGAAGACGTA
*
10163 ATACTATGATTAAAGGAAATAGTTTGTACTTGTACCCAATTGCCTTACTATGCTTC-AGGCCCTA
516 ATACTATGATTAAAGGAAATA-TTT-TA-TTGTACCCAATTGACTTACTATGC-TCGAGGCCC--
* *
10227 TTTATAAGCTCAAATGAAGTGATATTTTCTGACCAACCTCCTCTTATACTTCCAACTTTTATTTC
575 TTTATAAGCTCAAACGAAGTGATATTTTCTG-CCAACCTCCTCTTATACATCCAACTTTTATTT-
***
10292 CT-TTTTCAACGGGGGGAAAAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTGTTACCTTT
638 CTATTTTCAAC--GAAAAAAAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTGTTACCTTT
*
10356 CAAAAAAAATTCATTAGAGTCGTTTAGAAGATGGGTTCAAAAAGGTTATTGATTCCACTC-TGAT
701 CAAAAAAAATTCATTAGAGT-GTTTAGAAGATGGGTTCAAAAAGGTTATTGATTCTACTCATGAT
* *
10420 CATAGTAATTATTCTAGGATCCAAATGGTCGAACGGGTGTGTTCATAAGGAAAGAATTGCTTTGT
765 CATAGTAATCATTCTAGGATCCAAATGGTCGAATGGGTGTGTTCATAAGGAAAGAATTGCTTTGT
10485 TTCAACTCAAATCTTCCATCGATCTTCAACTTCCAGTTCATCAATCATGGGTGGATAATGATTGT
830 TTCAACTCAAATCTTCCATCGATCTTCAACTTCCAGTTCATCAATCATGGGTGGATAATGATTGT
*
10550 TGTCGATGGAGTGGTG
895 TGTCAATGGAGTGGTG
* * * * *
10566 TTATGTGCAACACAACCACTAGACGGATGACCAGCCTTTATCTTCTTCCTTATTGTGCGAAGTCC
1 TTATGTGCAACACCACCACTGGACGGAGGATCAGCCTTTATCTTCTTACTTATTGTGCGAAGTCC
* * * * * * *
10631 AACTACGCCAATGCTTCTATGTTTTTTCCATTCGAAGAGTTGAGGATTCTCGGTTTATCCAACAA
66 AACTACGTCAATGCTTCTATGTTTCTTCCATTCAAAGAATTGAGGATTCTCGATCTATCCTACAA
** *
10696 TGCTTCCAATCTATTCAGCGGATCTATAAATATGAAAGGTAGACTATACATAC
131 TG---CCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATAC
10749 TAGAAGTCCA
Statistics
Matches: 1744, Mismatches: 211, Indels: 100
0.85 0.10 0.05
Matches are distributed among these distances:
900 32 0.02
901 207 0.12
902 22 0.01
903 47 0.03
904 28 0.02
905 339 0.19
906 5 0.00
907 61 0.03
908 15 0.01
909 40 0.02
911 2 0.00
915 14 0.01
916 43 0.02
917 88 0.05
918 177 0.10
919 281 0.16
920 127 0.07
921 90 0.05
922 126 0.07
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (910 bp):
TTATGTGCAACACCACCACTGGACGGAGGATCAGCCTTTATCTTCTTACTTATTGTGCGAAGTCC
AACTACGTCAATGCTTCTATGTTTCTTCCATTCAAAGAATTGAGGATTCTCGATCTATCCTACAA
TGCCAATCTATTCAATGGATCAATAAATATGAAAGGTAGACTATACATACACTTTCATATTGTTT
ATACCCTAATTTACAAATTGGTAATTAAGTAATTGTGGCAAATTGACTTGGTCCCAAAGCCTATC
CACCCTTCAAAATTTCACGAATGTCGCACGAAACCCGCATAGAATTGCAATTCAGCCAAAATATG
CAAAGTTGGGCTTTTGGTGTTCTTTTCAAGCCTTTACGCCTTCCTCGCTTGCCTCGTTCATTTCG
TTTCGGTAACGGACGCTTCTCTAAGGATTTTGATGTTTTTCGTCCTACGTCAAAAAGAGACAACT
GACAAGCACTACTTAGCTTACAATTGAACTTCTAATTTTACAATTTTCATAGAAGACGTAATACT
ATGATTAAAGGAAATATTTTATTGTACCCAATTGACTTACTATGCTCGAGGCCCTTTATAAGCTC
AAACGAAGTGATATTTTCTGCCAACCTCCTCTTATACATCCAACTTTTATTTCTATTTTCAACGA
AAAAAAAAAAGAAAACGCTTTCTACAAGTCATTAGAGTGTTGTTACCTTTCAAAAAAAATTCATT
AGAGTGTTTAGAAGATGGGTTCAAAAAGGTTATTGATTCTACTCATGATCATAGTAATCATTCTA
GGATCCAAATGGTCGAATGGGTGTGTTCATAAGGAAAGAATTGCTTTGTTTCAACTCAAATCTTC
CATCGATCTTCAACTTCCAGTTCATCAATCATGGGTGGATAATGATTGTTGTCAATGGAGTGGTG
Found at i:28901 original size:21 final size:21
Alignment explanation
Indices: 28877--28925 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28867 TAAATTTAGA
* *
28877 TTTAATTTACTTTGCTTTATT
1 TTTAATTTAATTTACTTTATT
* *
28898 TTTAGTTTAATTTACTTTCTT
1 TTTAATTTAATTTACTTTATT
*
28919 TCTAATT
1 TTTAATT
28926 GATAATTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAATTTAATTTACTTTATT
Found at i:30376 original size:26 final size:26
Alignment explanation
Indices: 30340--30431 Score: 132
Period size: 26 Copynumber: 3.5 Consensus size: 26
30330 CACGCGCGAT
* *
30340 GTCACGTGTGGAGGT-GTCCGTTGAAG
1 GTCACGTGTGGA-GTCGTACGTTGGAG
*
30366 GTCACGTGTGGAGTCGTACATTGGAG
1 GTCACGTGTGGAGTCGTACGTTGGAG
*
30392 GTCACGTGTGGAGTCATACGTTGGAG
1 GTCACGTGTGGAGTCGTACGTTGGAG
30418 GTCACGTGTGGAGT
1 GTCACGTGTGGAGT
30432 GCCAGCTGGC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 2 0.03
26 58 0.97
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.27
Consensus pattern (26 bp):
GTCACGTGTGGAGTCGTACGTTGGAG
Found at i:30403 original size:13 final size:13
Alignment explanation
Indices: 30340--30430 Score: 68
Period size: 13 Copynumber: 7.0 Consensus size: 13
30330 CACGCGCGAT
30340 GTCACGTGTGGAGG
1 GTCACGTGTGGA-G
*
30354 TGTC-CGT-TGAAG
1 -GTCACGTGTGGAG
30366 GTCACGTGTGGA-
1 GTCACGTGTGGAG
*
30378 GTCGTACAT-TGGAG
1 GTC--ACGTGTGGAG
30392 GTCACGTGTGGA-
1 GTCACGTGTGGAG
30404 GTCATACGT-TGGAG
1 GTC--ACGTGTGGAG
30418 GTCACGTGTGGAG
1 GTCACGTGTGGAG
30431 TGCCAGCTGG
Statistics
Matches: 62, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
11 3 0.05
12 17 0.27
13 23 0.37
14 16 0.26
15 3 0.05
ACGTcount: A:0.18, C:0.15, G:0.41, T:0.26
Consensus pattern (13 bp):
GTCACGTGTGGAG
Found at i:30497 original size:23 final size:23
Alignment explanation
Indices: 30471--30525 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
30461 TTGTGGTCCT
30471 AAGTGGTCGATCGCCAAACATGG
1 AAGTGGTCGATCGCCAAACATGG
* * * *
30494 AAGTGGTCGGTCGCTAAGCTTGG
1 AAGTGGTCGATCGCCAAACATGG
*
30517 AAGTAGTCG
1 AAGTGGTCG
30526 GACACCAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (23 bp):
AAGTGGTCGATCGCCAAACATGG
Found at i:30535 original size:23 final size:23
Alignment explanation
Indices: 30491--30535 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
30481 TCGCCAAACA
* * * *
30491 TGGAAGTGGTCGGTCGCTAAGCT
1 TGGAAGTAGTCGGACACCAAGCT
30514 TGGAAGTAGTCGGACACCAAGC
1 TGGAAGTAGTCGGACACCAAGC
30536 AATTGTGCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (23 bp):
TGGAAGTAGTCGGACACCAAGCT
Found at i:34320 original size:11 final size:11
Alignment explanation
Indices: 34304--34328 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34294 CCACTTGATT
34304 TTTGAATTGTG
1 TTTGAATTGTG
34315 TTTGAATTGTG
1 TTTGAATTGTG
34326 TTT
1 TTT
34329 TGTGCAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTGAATTGTG
Found at i:38867 original size:21 final size:21
Alignment explanation
Indices: 38841--38882 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38831 GTACAACTGA
*
38841 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
38862 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
38883 GCCTGCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:38913 original size:33 final size:33
Alignment explanation
Indices: 38862--38954 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
38852 ACTTGGAGAT
* *
38862 CCGGCCACGCGACTTGGAGATGCCTGCG-CAACA
1 CCGGCCACGCGACATGGAGATGCCCG-GTCAACA
* * *
38895 CCGGCCATGCAACATGGAGATGCCCGGTCATCA
1 CCGGCCACGCGACATGGAGATGCCCGGTCAACA
**
38928 CCGGCCACGCGACATGGCCATGCCCGG
1 CCGGCCACGCGACATGGAGATGCCCGG
38955 CTTCACCCGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 1 0.02
33 49 0.98
ACGTcount: A:0.20, C:0.38, G:0.30, T:0.12
Consensus pattern (33 bp):
CCGGCCACGCGACATGGAGATGCCCGGTCAACA
Found at i:40026 original size:5 final size:5
Alignment explanation
Indices: 40016--40046 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
40006 ATCGAAAAAT
40016 ATAAA ATAAA ATAAA ATAAA ATAAA A-AAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
40047 TTTCGACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:40036 original size:15 final size:14
Alignment explanation
Indices: 40010--40046 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
40000 AGTTATATCG
*
40010 AAAAATATAAAATA
1 AAAAAAATAAAATA
40024 AAATAAAATAAAATA
1 AAA-AAAATAAAATA
40039 AAAAAAAT
1 AAAAAAAT
40047 TTTCGACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAAAATAAAATA
Done.