Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013241.1 Corchorus capsularis cultivar CVL-1 contig13262, 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: 54153
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:293 original size:28 final size:30
Alignment explanation
Indices: 234--312 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 30
224 GGCTAAATAC
* * *
234 CAAAAAAATCTCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTCTGGGA
265 CAAAATAATCCCTTATGTTTT-TTCT-GGA
1 CAAAATAATCCCTTATGTTTTCTTCTGGGA
* *
293 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
313 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 21 0.49
29 3 0.07
31 19 0.44
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTCTGGGA
Found at i:473 original size:33 final size:31
Alignment explanation
Indices: 424--518 Score: 138
Period size: 31 Copynumber: 3.0 Consensus size: 31
414 AATGGACTAA
*
424 TTTGTCACAAAAAAAAACATAAGGGATTTTT
1 TTTGTCCCAAAAAAAAACATAAGGGATTTTT
455 TTTGGTCCCAAAAGAAAAACATAAGGGA-TTTT
1 TTT-GTCCCAAAA-AAAAACATAAGGGATTTTT
* *
487 TTTGTTCCAAAATAAAACATAAGGGATTTTT
1 TTTGTCCCAAAAAAAAACATAAGGGATTTTT
518 T
1 T
519 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
30 13 0.22
31 16 0.28
32 15 0.26
33 14 0.24
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAAAAAACATAAGGGATTTTT
Found at i:504 original size:30 final size:31
Alignment explanation
Indices: 431--518 Score: 133
Period size: 30 Copynumber: 2.8 Consensus size: 31
421 TAATTTGTCA
431 CAAAAAAAAACATAAGGGATTTTTTTTGGTCC
1 CAAAAAAAAACATAAGGGA-TTTTTTTGGTCC
*
463 CAAAAGAAAAACATAAGGGATTTTTTT-GTTC
1 CAAAA-AAAAACATAAGGGATTTTTTTGGTCC
*
494 CAAAATAAAACATAAGGGATTTTTT
1 CAAAAAAAAACATAAGGGATTTTTT
519 AGTATTTAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 19 0.36
31 8 0.15
32 12 0.23
33 14 0.26
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (31 bp):
CAAAAAAAAACATAAGGGATTTTTTTGGTCC
Found at i:758 original size:13 final size:13
Alignment explanation
Indices: 714--763 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
704 AAACGATGAC
714 ATTTAAGAAATAT
1 ATTTAAGAAATAT
727 ATTTGAA-AAATA-
1 ATTT-AAGAAATAT
*
739 AGGTTAAGAAATAT
1 A-TTTAAGAAATAT
*
753 ATTTAAAAAAT
1 ATTTAAGAAAT
764 TCTAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (13 bp):
ATTTAAGAAATAT
Found at i:1245 original size:13 final size:13
Alignment explanation
Indices: 1224--1273 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1214 ATATAATAGA
*
1224 ATTTTTTAAATAT
1 ATTTCTTAAATAT
*
1237 ATTTCTTAACCT-T
1 ATTTCTTAA-ATAT
1250 ATTT-TTCAAATAT
1 ATTTCTT-AAATAT
1263 ATTTCTTAAAT
1 ATTTCTTAAAT
1274 GTCATTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTCTTAAATAT
Found at i:1378 original size:179 final size:178
Alignment explanation
Indices: 1071--1415 Score: 521
Period size: 179 Copynumber: 1.9 Consensus size: 178
1061 TAAAGGCATG
* * * * * ** *
1071 TTTTTTAAATATATTTCTTAAATGACATTATTTAAATTTTTATAGTTATATTTTACCAAAAATTT
1 TTTTTCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTATACTCAACCAAAAATAT
*
1136 CTATTTTTATTTAATTTAATTTAATATATTTATAAATATTTTATTTTTACCATTTTACTATTTTA
66 CTATTTTTATTTAATTAAATTTAATATATTTATAAATATTTTATTTTTACCATTTTACTATTTTA
1201 ATTAAAAATTTAGATATAATAGAATTTTTTAAATATATTTCTTAACCTTA
131 ATTAAAAA-TTAGATATAATAGAA-TTTTTAAATATATTTCTTAACCTTA
* * * **
1251 TTTTTCAAATATATTTCTTAAATGTCATTGTTTAAACTTTTACAATTTTACTCAATTAAAAA-AT
1 TTTTTCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTATACTCAACCAAAAATAT
*
1315 CTATTTTTATTTAATTAAATTTAATATATTTATAATTATTTTATTTTTACCATTTTACTATTTTA
66 CTATTTTTATTTAATTAAATTTAATATATTTATAAATATTTTATTTTTACCATTTTACTATTTTA
*
1380 ATTAAAAATTAGATATATTAGAATTTTTAAATATAT
131 ATTAAAAATTAGATATAATAGAATTTTTAAATATAT
1416 ATATTTTAAA
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
177 13 0.09
178 14 0.09
179 72 0.48
180 50 0.34
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (178 bp):
TTTTTCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTATACTCAACCAAAAATAT
CTATTTTTATTTAATTAAATTTAATATATTTATAAATATTTTATTTTTACCATTTTACTATTTTA
ATTAAAAATTAGATATAATAGAATTTTTAAATATATTTCTTAACCTTA
Found at i:1521 original size:31 final size:31
Alignment explanation
Indices: 1470--1564 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
1460 ACTAAATACT
1470 AAAAAAATCCCTTATG-TTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1500 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1531 AAAAAAATCCCTTATGTTTTT-TTTTGGGAAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGG-AC
1562 AAA
1 AAA
1565 CTAGTCTCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
30 23 0.37
31 40 0.63
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:1715 original size:27 final size:27
Alignment explanation
Indices: 1676--1730 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1666 CTCATTTTTG
* * *
1676 AAACGTAAGGGATTAATTTGTCCGAAA
1 AAACATAAAGGATTAATTTGTCCCAAA
*
1703 AAACATAAAGGATTATTTTGTCCCAAA
1 AAACATAAAGGATTAATTTGTCCCAAA
1730 A
1 A
1731 GCAAAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (27 bp):
AAACATAAAGGATTAATTTGTCCCAAA
Found at i:7225 original size:20 final size:20
Alignment explanation
Indices: 7202--7241 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7192 ATACTAATTA
7202 CCATTTTAATAATTTATACT
1 CCATTTTAATAATTTATACT
*
7222 CCATTTTAATCATTTATACT
1 CCATTTTAATAATTTATACT
7242 TTCAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
CCATTTTAATAATTTATACT
Found at i:7840 original size:18 final size:17
Alignment explanation
Indices: 7813--7871 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
7803 AATGGAACAC
*
7813 CACCATCAAATCCACCCT
1 CACCACCAAA-CCACCCT
*
7831 CACCACCAAAGCCACCGT
1 CACCACCAAA-CCACCCT
* *
7849 CGCCA--AAACCACCTT
1 CACCACCAAACCACCCT
7864 CACCACCA
1 CACCACCA
7872 CCAAAGGTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 10 0.30
16 3 0.09
17 1 0.03
18 19 0.58
ACGTcount: A:0.34, C:0.51, G:0.05, T:0.10
Consensus pattern (17 bp):
CACCACCAAACCACCCT
Found at i:7951 original size:81 final size:83
Alignment explanation
Indices: 7810--7982 Score: 251
Period size: 81 Copynumber: 2.1 Consensus size: 83
7800 GACAATGGAA
7810 CACCACCATCAAATCCACCCTCACCACCAAAGCCACCGTCGCCAAAACCACCTTCACCACCACCA
1 CACCACCATCAAATCCACCCTCACCACCAAAGCCACCG-CGCCAAAACCACCTTCACCACCACCA
*
7875 AAGGTACCGTCGCCTCCTT
65 AAGGTACCATCGCCTCCTT
* * * ** *
7894 CACCATCATCTAATCCACCCTCACCACCAAAGGCA-C-CGCCAAAAGTACCTTCCCCACCACCAA
1 CACCACCATCAAATCCACCCTCACCACCAAAGCCACCGCGCCAAAACCACCTTCACCACCACCAA
*
7957 AGGTACTATCGCCTCCTT
66 AGGTACCATCGCCTCCTT
7975 CACCACCA
1 CACCACCA
7983 AAGATACCTC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 47 0.59
83 1 0.01
84 32 0.40
ACGTcount: A:0.30, C:0.47, G:0.08, T:0.14
Consensus pattern (83 bp):
CACCACCATCAAATCCACCCTCACCACCAAAGCCACCGCGCCAAAACCACCTTCACCACCACCAA
AGGTACCATCGCCTCCTT
Found at i:8048 original size:33 final size:33
Alignment explanation
Indices: 8010--8093 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
8000 AGCACCTACA
* *
8010 CCACCGCCAAAGGTACCATCGCCGCCTCCTTCG
1 CCACCGTCAAAGGCACCATCGCCGCCTCCTTCG
8043 CCACCGTCAAAGGCACCATCGCCGCCTCCTTCG
1 CCACCGTCAAAGGCACCATCGCCGCCTCCTTCG
8076 CCACCGTCAAAGGCACCA
1 CCACCGTCAAAGGCACCA
8094 GCACCAAAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.21, C:0.48, G:0.18, T:0.13
Consensus pattern (33 bp):
CCACCGTCAAAGGCACCATCGCCGCCTCCTTCG
Found at i:8149 original size:69 final size:69
Alignment explanation
Indices: 8068--8270 Score: 318
Period size: 69 Copynumber: 2.9 Consensus size: 69
8058 CCATCGCCGC
8068 CTCCTTCGCCACCGTCAAAGGCACCAGCACCAAAAGCACCCACACCAATACCATCACCAAAACCA
1 CTCCTTCGCCACCGTCAAAGGCACCAGCACCAAAAGCACCCACACCAATACCATCACCAAAACCA
8133 CCTT
66 CCTT
*
8137 CTCCTTCACCACCGTCAAAGGCA-CAGTCACCAAAAGCACCCACACCAATACCATCACCAAAACC
1 CTCCTTCGCCACCGTCAAAGGCACCAG-CACCAAAAGCACCCACACCAATACCATCACCAAAACC
8201 ACCTT
65 ACCTT
* * * *
8206 CACCTTCGCCACCGTCAAAGGTGGCACCACCACCAAAAGCACCTACACCGATACCATCACCAAAA
1 CTCCTTCGCCACCGTCAAA---GGCACCAGCACCAAAAGCACCCACACCAATACCATCACCAAAA
8271 GCGCCCTCAC
Statistics
Matches: 123, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
68 3 0.02
69 81 0.66
72 37 0.30
73 2 0.02
ACGTcount: A:0.35, C:0.43, G:0.09, T:0.12
Consensus pattern (69 bp):
CTCCTTCGCCACCGTCAAAGGCACCAGCACCAAAAGCACCCACACCAATACCATCACCAAAACCA
CCTT
Found at i:8464 original size:24 final size:24
Alignment explanation
Indices: 8437--8490 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
8427 GCGCCAACAC
8437 CGAAAGAATTGGCACCTAATCCAT
1 CGAAAGAATTGGCACCTAATCCAT
8461 CGAAAGAATTGGCACCTAATCCAT
1 CGAAAGAATTGGCACCTAATCCAT
*
8485 CAAAAG
1 CGAAAG
8491 CGCCAACACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (24 bp):
CGAAAGAATTGGCACCTAATCCAT
Found at i:8917 original size:28 final size:28
Alignment explanation
Indices: 8885--8939 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
8875 CGAAAAAGGA
8885 AAGATCTACAATACAAGAAAGTAATTAG
1 AAGATCTACAATACAAGAAAGTAATTAG
8913 AAGATCTACAATACAAGAAAGTAATTA
1 AAGATCTACAATACAAGAAAGTAATTA
8940 CTACCAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.22
Consensus pattern (28 bp):
AAGATCTACAATACAAGAAAGTAATTAG
Found at i:11839 original size:12 final size:12
Alignment explanation
Indices: 11822--11854 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
11812 TGAAATTCTT
11822 GCCTCCACCGCC
1 GCCTCCACCGCC
11834 GCCTCCACCGCC
1 GCCTCCACCGCC
11846 GCCTCCACC
1 GCCTCCACC
11855 ACCACCACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.67, G:0.15, T:0.09
Consensus pattern (12 bp):
GCCTCCACCGCC
Found at i:12210 original size:3 final size:3
Alignment explanation
Indices: 12202--12226 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12192 TTCTTTTCAA
12202 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
12227 TCCTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:12485 original size:12 final size:12
Alignment explanation
Indices: 12468--12536 Score: 95
Period size: 12 Copynumber: 5.8 Consensus size: 12
12458 TTCCTCATCT
12468 TCATCATCAAAC
1 TCATCATCAAAC
*
12480 TCATCATCAAAT
1 TCATCATCAAAC
12492 TCATCATCAAAC
1 TCATCATCAAAC
**
12504 TCATCCCCAAAC
1 TCATCATCAAAC
12516 TCATCATCATAA-
1 TCATCATCA-AAC
12528 TCATCATCA
1 TCATCATCA
12537 CTATCATCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
12 48 0.96
13 2 0.04
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:17102 original size:55 final size:55
Alignment explanation
Indices: 17031--17211 Score: 206
Period size: 55 Copynumber: 3.3 Consensus size: 55
17021 GACAAATAAC
* *
17031 TTGAACCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAA
1 TTGATCCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACCAAAAAA
* * * * * ** *
17086 TTGGTCCTGATGGTGTTGTCAATTAAAAATTA-C--TCAAATCATCGGGACTGATAAA
1 TTGATCCTGATGGTGTTG-C-CTT-CAAATTATCATTCAGATCATCTGGACCAAAAAA
* *
17141 TTGATCATGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAA
1 TTGATCCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACCAAAAAA
17196 TTGATCCTGATGGTGT
1 TTGATCCTGATGGTGT
17212 AAGAAAATAT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
52 5 0.05
53 3 0.03
54 1 0.01
55 81 0.82
56 1 0.01
57 3 0.03
58 5 0.05
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (55 bp):
TTGATCCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACCAAAAAA
Found at i:18867 original size:2 final size:2
Alignment explanation
Indices: 18856--18892 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
18846 CTAGTATGAC
18856 AT AT -T AT AT AT AT -T AT AT AT AT AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
18893 TAAGAAGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18870 original size:9 final size:8
Alignment explanation
Indices: 18856--18892 Score: 51
Period size: 7 Copynumber: 4.8 Consensus size: 8
18846 CTAGTATGAC
18856 ATAT-TAT
1 ATATATAT
18863 ATATAT-T
1 ATATATAT
18870 ATATATAT
1 ATATATAT
18878 ATACTATAT
1 ATA-TATAT
18887 ATATAT
1 ATATAT
18893 TAAGAAGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 11 0.41
8 8 0.30
9 8 0.30
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (8 bp):
ATATATAT
Found at i:18876 original size:11 final size:11
Alignment explanation
Indices: 18856--18894 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18846 CTAGTATGAC
18856 ATATTATATAT
1 ATATTATATAT
18867 AT-TATATATAT
1 ATAT-TATATAT
*
18878 ATACTATATAT
1 ATATTATATAT
18889 ATATTA
1 ATATTA
18895 AGAAGCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTATATAT
Found at i:18878 original size:13 final size:13
Alignment explanation
Indices: 18860--18892 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18850 TATGACATAT
*
18860 TATATATATTATA
1 TATATATACTATA
18873 TATATATACTATA
1 TATATATACTATA
18886 TATATAT
1 TATATAT
18893 TAAGAAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATACTATA
Found at i:19600 original size:16 final size:14
Alignment explanation
Indices: 19567--19594 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19557 AATATTGGAA
19567 CTTATAATAAATAT
1 CTTATAATAAATAT
19581 CTTATAATAAATAT
1 CTTATAATAAATAT
19595 ATCTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
CTTATAATAAATAT
Found at i:19602 original size:14 final size:14
Alignment explanation
Indices: 19568--19605 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19558 ATATTGGAAC
*
19568 TTATAATAAATATC
1 TTATAATAAATATA
19582 TTATAATAAATATA
1 TTATAATAAATATA
19596 TCT-TAATAAA
1 T-TATAATAAA
19606 GGGTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
TTATAATAAATATA
Found at i:24929 original size:5 final size:5
Alignment explanation
Indices: 24919--24953 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
24909 GTGGCACATA
*
24919 TGTTC TGTTC TGTTC TGTTA TGTTC TGTTAC TGTT
1 TGTTC TGTTC TGTTC TGTTC TGTTC TGTT-C TGTT
24954 AGGCAGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.06, C:0.14, G:0.20, T:0.60
Consensus pattern (5 bp):
TGTTC
Found at i:27326 original size:41 final size:41
Alignment explanation
Indices: 27279--27360 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
27269 ATTTGTTTAC
*
27279 GCAATTTTTTTCTACAGTGTGCTTACGCTCCGTTTATATTA
1 GCAATTTTTTTCTACAGTGTGCTCACGCTCCGTTTATATTA
27320 GCAATTTTTTTCTACAGTGTGCTCACGCTCCGTTTATATTA
1 GCAATTTTTTTCTACAGTGTGCTCACGCTCCGTTTATATTA
27361 ACAGAATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (41 bp):
GCAATTTTTTTCTACAGTGTGCTCACGCTCCGTTTATATTA
Found at i:36584 original size:11 final size:11
Alignment explanation
Indices: 36568--36593 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36558 CAATATTTTC
36568 CACAAACTTTG
1 CACAAACTTTG
36579 CACAAACTTTG
1 CACAAACTTTG
36590 CACA
1 CACA
36594 TGGGCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (11 bp):
CACAAACTTTG
Found at i:40278 original size:242 final size:237
Alignment explanation
Indices: 39855--40312 Score: 754
Period size: 242 Copynumber: 1.9 Consensus size: 237
39845 GATTTATGGT
39855 ACTCACTTTGTGAGTGTAGAAAAAAAAAGTAGTTTATAGAAGTTTTTTTTTGACAAATTTAAATT
1 ACTCACTTTGTGAGTGTAGAAAAAAAAAGTAGTTTATAGAAGTTTTTTTTTGACAAATTTAAATT
39920 GGTAGTTTTTTTTAAATGATATAAATAAAAATTAATTATTATATATATCCTTGGTGGTTTATTTT
66 GGTAGTTTTTTTTAAATGATATAAATAAAAATTAATTATTATATATATCCTTGGTGGTTTATTTT
* * **
39985 CAAATGATTAGTTTTTAATCTTTTAAAAATTGAGTTTGTATTTGAGTCAACTCGTGACACAAACT
131 CAAATGAGTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACT
40050 CAGGACTTCACATTATAATTACTAGATTACTAGATCCATGAC
196 CAGGACTTCACATTATAATTACTAGATTACTAGATCCATGAC
* * * *
40092 ACTCACTTTGTGAGTGTAGAAATAAAATGATAGTTTATAGTAATTTTCTTTTTTGACACATTTAA
1 ACTCACTTTGTGAGTGTAGAAAAAAAAAG-TAGTTTATAG-AAGTTT-TTTTTTGACAAATTTAA
40157 ATTGGTAGTTTTTTTTAAATGATATAAATAAAAATTAATTATTATATATATATCCTTGGTGGTTT
63 ATTGGTAGTTTTTTTTAAATGATATAAATAAAAATTAATTA-T-TATATATATCCTTGGTGGTTT
* * *
40222 ATTTTGAAATGGGTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTTGTGACAC
126 ATTTTCAAATGAGTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACAC
* *
40287 AAACTCATGACTTCGCATTATAATTA
191 AAACTCAGGACTTCACATTATAATTA
40313 ATATAGATTA
Statistics
Matches: 203, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
237 27 0.13
238 10 0.05
239 5 0.02
240 57 0.28
241 1 0.00
242 103 0.51
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (237 bp):
ACTCACTTTGTGAGTGTAGAAAAAAAAAGTAGTTTATAGAAGTTTTTTTTTGACAAATTTAAATT
GGTAGTTTTTTTTAAATGATATAAATAAAAATTAATTATTATATATATCCTTGGTGGTTTATTTT
CAAATGAGTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACT
CAGGACTTCACATTATAATTACTAGATTACTAGATCCATGAC
Found at i:40397 original size:6 final size:6
Alignment explanation
Indices: 40388--40457 Score: 79
Period size: 6 Copynumber: 11.5 Consensus size: 6
40378 AATCCTTTCC
* *
40388 GGATTG GGATTG GGATTG GGATTG GGAATTTG GGATTG GG-TAG GGATAG
1 GGATTG GGATTG GGATTG GGATTG GG-A-TTG GGATTG GGATTG GGATTG
* *
40437 GGATTG GGAGTG GGAGTG GGA
1 GGATTG GGATTG GGATTG GGA
40458 AGGGTCTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
5 4 0.07
6 47 0.81
7 2 0.03
8 5 0.09
ACGTcount: A:0.20, C:0.00, G:0.53, T:0.27
Consensus pattern (6 bp):
GGATTG
Found at i:40780 original size:7 final size:7
Alignment explanation
Indices: 40768--40797 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
40758 CAGAAGTTTG
40768 GTGACTA
1 GTGACTA
40775 GTGACTA
1 GTGACTA
40782 GTGACTA
1 GTGACTA
40789 GTGACTA
1 GTGACTA
40796 GT
1 GT
40798 AAGTAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (7 bp):
GTGACTA
Found at i:41515 original size:29 final size:28
Alignment explanation
Indices: 41453--41515 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
41443 AACTTGTATG
* *
41453 ATTTTGACATTTTGCCCCCTAAACTTTA
1 ATTTGGACATTTTGCCCCCTAAACTTCA
* *
41481 ATTTTGGACATTTTGCCCCTTTAACTTGCA
1 A-TTTGGACATTTTGCCCCCTAAACTT-CA
41511 ATTTG
1 ATTTG
41516 AAGCCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.90
30 2 0.07
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (28 bp):
ATTTGGACATTTTGCCCCCTAAACTTCA
Found at i:41633 original size:31 final size:31
Alignment explanation
Indices: 41605--41664 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
41595 AATGTTTATC
41605 GAAGAAAAG-GTCAATTTTAGACAAGTTTAA
1 GAAGAAAAGTGTCAATTTTAGACAAGTTTAA
** *
41635 GGCGCAAAGTGTCAATTTTAGACAAGTTTA
1 GAAGAAAAGTGTCAATTTTAGACAAGTTTA
41665 GGGGGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (31 bp):
GAAGAAAAGTGTCAATTTTAGACAAGTTTAA
Found at i:41928 original size:42 final size:42
Alignment explanation
Indices: 41869--41975 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
41859 TTCCAAACCA
*
41869 ACTCCCCATTCTTCATAATCCCT-CCCAACTCTCGCTTATGGT
1 ACTCCCCATTCATCATAATCCCTCCCCAA-TCTCGCTTATGGT
*** * *
41911 ACTCCCCATTCATCATAATGGTTCCCCAATCTCGGTTTTGGT
1 ACTCCCCATTCATCATAATCCCTCCCCAATCTCGCTTATGGT
* *
41953 AATCCCCATTCATCACAATCCCT
1 ACTCCCCATTCATCATAATCCCT
41976 AATCTGAAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.21, C:0.37, G:0.08, T:0.33
Consensus pattern (42 bp):
ACTCCCCATTCATCATAATCCCTCCCCAATCTCGCTTATGGT
Found at i:53663 original size:19 final size:20
Alignment explanation
Indices: 53639--53684 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
53629 TTACTCATTC
53639 TAATTTAGCCACGTGG-ATT
1 TAATTTAGCCACGTGGAATT
53658 TAATTTAGCCACGTGGAATT
1 TAATTTAGCCACGTGGAATT
*
53678 TTATTTA
1 TAATTTA
53685 AACTAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TAATTTAGCCACGTGGAATT
Found at i:53724 original size:16 final size:15
Alignment explanation
Indices: 53705--53734 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
53695 AAATGTAAAT
53705 AGAAAATACAAAAAAC
1 AGAAAATA-AAAAAAC
53721 AGAAAATAAAAAAA
1 AGAAAATAAAAAAA
53735 TTAATTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (15 bp):
AGAAAATAAAAAAAC
Done.