Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006351.1 Corchorus capsularis cultivar CVL-1 contig06372, 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: 52080
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:94 original size:55 final size:55
Alignment explanation
Indices: 1--389 Score: 674
Period size: 55 Copynumber: 7.1 Consensus size: 55
* * *
1 TTAAGT-AAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
*
55 TTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
* *
110 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGTAAATCGGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
*
165 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGTAAATCAGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
*
220 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTAAATCAGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
*
275 TTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
330 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATC-GATAA
1 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAG-TAA
385 TTAAG
1 TTAAG
390 AGTTAAAATG
Statistics
Matches: 320, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
54 7 0.02
55 313 0.98
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA
Found at i:631 original size:22 final size:22
Alignment explanation
Indices: 574--954 Score: 250
Period size: 22 Copynumber: 17.4 Consensus size: 22
564 AATAACGTGC
* *
574 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
596 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
616 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
*
638 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
**
660 AATCA--ACAAGAGTAAAATAAT
1 AATCAGTA-AAGAGTAAAATGGT
* * *
681 AGTCAGTAAAAAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
**
703 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAGAGTAAAATGGT
* *
724 AATAAGT-AAGAAGTAAAA-GGA
1 AATCAGTAAAG-AGTAAAATGGT
* *
745 AATTAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
* * *
766 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAATGGT
* *
788 AATCAG-CAAGAAGTAAAAAGGT
1 AATCAGTAAAG-AGTAAAATGGT
* * *
810 AATCAGTAAAAAGCAAAA-GGC
1 AATCAGTAAAGAGTAAAATGGT
*
831 AATCAGTAAAAAGTAAAA-GAGT
1 AATCAGTAAAGAGTAAAATG-GT
* *
853 AATCAGTAAAAAAGGAGCAGAAAATAGT
1 AATCAGT---AAA-GAG--TAAAATGGT
881 AATCAGTAAATGAGTAAAATGGT
1 AATCAGTAAA-GAGTAAAATGGT
*
904 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
* * *
926 AATCAAT-AAGAGTAGAATAGT
1 AATCAGTAAAGAGTAAAATGGT
947 AATCAGTA
1 AATCAGTA
955 CAAAATAAAG
Statistics
Matches: 287, Mismatches: 49, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
20 24 0.08
21 94 0.33
22 121 0.42
23 24 0.08
25 9 0.03
26 2 0.01
28 13 0.05
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:673 original size:43 final size:42
Alignment explanation
Indices: 606--963 Score: 263
Period size: 43 Copynumber: 8.1 Consensus size: 42
596 ATCTGAAAGG
* *
606 GTAAAATGGTAATTAGTAAAGAGTAAAATAGTAATCAGTAAAAA
1 GTAAAA-GGTAATCAAT-AAGAGTAAAATAGTAATCAGTAAAAA
* * *
650 GTAAGAAGGTAATCAACAAGAGTAAAATAATAGTCAGTAAAAA
1 GTAA-AAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
* * * * *
693 GTAAAATAGTAATCAGTAAGAGTAAAAAAGTAATAAGTAAGAA
1 GTAAAA-GGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
* * * * *
736 GTAAAAGGAAATTAGTAAGAGTAAAA-AGGTGATCAGTAAAGA
1 GTAAAAGGTAATCAATAAGAGTAAAATA-GTAATCAGTAAAAA
* **
778 GTAAAAAGCTAATCAGCAAGAAGTAAAA-AGGTAATCAGTAAAAA
1 GT-AAAAGGTAATCAATAAG-AGTAAAATA-GTAATCAGTAAAAA
* * * * *
822 GCAAAAGGCAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAGGA
1 GTAAAAGGTAATCAAT-AAGAGTAAAATAGTAATCAGT--AAAA--A
* * * *
869 GCAGAAAATAGTAATCAGTAAATGAGTAAAATGGTAATCAGTAAAAA
1 G--TAAAA-GGTAATCAAT-AA-GAGTAAAATAGTAATCAGTAAAAA
*
916 GTAAGAAGGTAATCAATAAGAGTAGAATAGTAATCAGTACAAAA
1 GTAA-AAGGTAATCAATAAGAGTAAAATAGTAATCAGTA-AAAA
960 -TAAA
1 GTAAA
964 GAATAATCAG
Statistics
Matches: 255, Mismatches: 42, Indels: 36
0.77 0.13 0.11
Matches are distributed among these distances:
41 1 0.00
42 32 0.13
43 123 0.48
44 42 0.16
45 16 0.06
46 2 0.01
47 4 0.02
49 8 0.03
50 11 0.04
51 16 0.06
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (42 bp):
GTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
Found at i:860 original size:15 final size:15
Alignment explanation
Indices: 842--897 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
832 ATCAGTAAAA
842 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
857 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
871 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
*
885 AGTAAATGAGTAA
1 AGTAAAAGAGTAA
898 AATGGTAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.26
15 17 0.55
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.18
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:991 original size:21 final size:21
Alignment explanation
Indices: 876--997 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 21
866 GGAGCAGAAA
876 ATAGTAATCAGTAAATGAGTAAA-
1 ATAGTAATCAGTAAA--A-TAAAG
*
899 ATGGTAATCAGTAAAA-AGTAAG
1 ATAGTAATCAGTAAAATA--AAG
* * *
921 A-AGGTAATCAATAAGAGTAGA-
1 ATA-GTAATCAGTAA-AATAAAG
942 ATAGTAATCAGTACAAAATAAAG
1 ATAGTAATCAGT--AAAATAAAG
**
965 A-A-TAATCAGTAAAATAGTG
1 ATAGTAATCAGTAAAATAAAG
984 ATAGTAATCAGTAA
1 ATAGTAATCAGTAA
998 TTCAGTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
19 9 0.12
20 1 0.01
21 30 0.39
22 18 0.23
23 18 0.23
24 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (21 bp):
ATAGTAATCAGTAAAATAAAG
Found at i:1814 original size:199 final size:198
Alignment explanation
Indices: 1465--2407 Score: 1152
Period size: 199 Copynumber: 4.7 Consensus size: 198
1455 GAGGTTTAAC
* * * *
1465 TTTAATGGTTGACATGTGTACCTTTAGAGAATATGTATTAATATTAAATA--T--TTAATTATGA
1 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* *
1526 AATTG-GGTATGTGTCAACTTCTTAACCCG-TTCACGGAGTCCAAAATTTACACTAACAGTGTAT
66 AA-TGAGGTATGTGTCAACTTCTTAACCCGCTT-ATGGAGTCCAAAATTTACACTGACAGTGTAT
* ** * * *
1589 TGTGTAATAATCCAATAAGGAAAATTATACAATAC-CCGTCAGTGGATTTTAGGACGACTGCACG
129 TGTATAATAATCTTATAA-AAAAATTATACAATACACCGTCAGTGGAGTTTAGCA-GACTGCACG
* *
1653 TGCAAGA
192 TGCAGGG
*
1660 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTGTTAATATTAAATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* * * *
1725 AATGAGGTATGTATCAACTTCTTAACTCGCTTATGGAGTCCAAAATTTATACTGATAGTGTATTG
66 AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
* * *
1790 TATAATAATCTTATAAGAAAAATTATGCAATACGCAGTCAGTGGAGTTTAGCAGACTGCACGTGC
131 TATAATAATCTTATAA-AAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC
*
1855 GGGG
195 AGGG
*
1859 TTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* * * * **
1924 AATGGGGTATGTGCCAACTTCTTAACTCACTTATATAGTCCAAAATTTACA-TAGACAGTGTATT
66 AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACT-GACAGTGTATT
* * * ** * *
1988 GTATAATAATCATATAAAAAAAATATACAATACACTGTCAGTGGAGTTTAGCAGACTATACGCGT
130 GTATAATAATCTTATAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC
*
2053 GGGG
195 AGGG
* * * *
2057 TTTAAGGGTTGACATGTGTCCTCTTAGAGAATATGTATTAATATT-TATATTTAATTAATTATGG
1 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* ** *
2121 AAT-AGTGTATGTGTCAACTTCTTAACCCGGTTATGGAGTTGAAAATTTACATTGACAGTGTATT
66 AATGAG-GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATT
* *
2185 GTATAATAATCTTATAAAAAAATTATACAATACATCGTCAGTGGTGTTTAGCAGACTGCACGTGC
130 GTATAATAATCTTATAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC
*
2250 ATGG
195 AGGG
* * * *
2254 TTTGAGGGTTGACATGTGTCCTCTTAGCGAATATGAATAATATATGATTAATATCAATTATTTAA
1 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG--T-AT-TA--A-T-AT-T-AAATATTTAA
* *
2319 TTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGA
56 TTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGA
2384 CAGTGT-TTGTATAATAATCCTTAT
121 CAGTGTATTGTATAATAAT-CTTAT
2408 TATAAAGCTT
Statistics
Matches: 650, Mismatches: 75, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
195 45 0.07
196 1 0.00
197 160 0.25
198 90 0.14
199 238 0.37
200 20 0.03
201 2 0.00
203 1 0.00
204 1 0.00
205 2 0.00
206 1 0.00
207 12 0.02
208 76 0.12
209 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (198 bp):
TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
TATAATAATCTTATAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCA
GGG
Found at i:7391 original size:48 final size:48
Alignment explanation
Indices: 7331--7428 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 48
7321 AAAAAGCTTG
7331 ATAAAATCTATTGATCTCAAAGAG-TCAAAGATAAATTTCTTAAAAATA
1 ATAAAATCTATTGATCTCAAAGAGCT-AAAGATAAATTTCTTAAAAATA
* * *
7379 ATAAAATCTATTGGTCTCAAAGAGCTACAGATAAATTTCTTAAAGATA
1 ATAAAATCTATTGATCTCAAAGAGCTAAAGATAAATTTCTTAAAAATA
7427 AT
1 AT
7429 GATGCCAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (48 bp):
ATAAAATCTATTGATCTCAAAGAGCTAAAGATAAATTTCTTAAAAATA
Found at i:12982 original size:19 final size:19
Alignment explanation
Indices: 12958--13011 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
12948 TGTATGATGA
12958 ATATATAAGCTCCTTTATG
1 ATATATAAGCTCCTTTATG
* *
12977 ATATATAAGCTCCTTAATT
1 ATATATAAGCTCCTTTATG
12996 A-ATATAAGCTCCTTTA
1 ATATATAAGCTCCTTTA
13012 GGTTTCAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (19 bp):
ATATATAAGCTCCTTTATG
Found at i:23596 original size:12 final size:12
Alignment explanation
Indices: 23568--23609 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
23558 GAACCAAGAT
23568 GCACCACCACCG
1 GCACCACCACCG
*
23580 CCACCAGCC-CCG
1 GCACCA-CCACCG
*
23592 GCACCACCACCA
1 GCACCACCACCG
23604 GCACCA
1 GCACCA
23610 AGGTGGTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.26, C:0.60, G:0.14, T:0.00
Consensus pattern (12 bp):
GCACCACCACCG
Found at i:27969 original size:21 final size:19
Alignment explanation
Indices: 27939--27977 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
27929 TACTCTGTTG
27939 TTTCCATGTGTTGCGCCAAAT
1 TTTCCATGTG-TGC-CCAAAT
*
27960 TTTCCTTGTGTGCCCAAA
1 TTTCCATGTGTGCCCAAA
27978 ATGGTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (19 bp):
TTTCCATGTGTGCCCAAAT
Found at i:32848 original size:36 final size:35
Alignment explanation
Indices: 32776--32875 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 35
32766 GCAACAGTTA
* *
32776 AAAGACTTAATTCACAATAATTAAGTAATATTAGC
1 AAAGACTTAATTCACAAGAATTAAGTAATATCAGC
32811 AAAGACTTAATTTCACAAGAATTAAGTAA-AGTCAGC
1 AAAGACTTAA-TTCACAAGAATTAAGTAATA-TCAGC
* * *
32847 AAATATTTAATCCA-AAGATGATTAAGTAA
1 AAAGACTTAATTCACAAGA--ATTAAGTAA
32876 GACCAGACGA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
34 4 0.07
35 14 0.25
36 38 0.68
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (35 bp):
AAAGACTTAATTCACAAGAATTAAGTAATATCAGC
Found at i:32996 original size:24 final size:23
Alignment explanation
Indices: 32913--33177 Score: 223
Period size: 24 Copynumber: 11.0 Consensus size: 23
32903 GAAATTAGGC
32913 AAAAGAAGACTGAAAACAAAAGACTG
1 AAAAGAAGACTG-AAAC--AAGACTG
* * *
32939 -AAAGAAGATTGAAAAAAATACTG
1 AAAAGAAGACTG-AAACAAGACTG
32962 -AAAGAAGACTGAAACAAGACTG
1 AAAAGAAGACTGAAACAAGACTG
*
32984 AAAGAGAAGACTGAAACAGAAGAGTG
1 AAA-AGAAGACTGAAAC--AAGACTG
* *
33010 -AAACAAGACTGAAAGAGAAGACTG
1 AAAAGAAGACTG-AA-ACAAGACTG
33034 AAAGAGAAGACTGAAACAAGACTG
1 AAA-AGAAGACTGAAACAAGACTG
*
33058 AAAGAGAAGACTGAAACAAGACTA
1 AAA-AGAAGACTGAAACAAGACTG
* *
33082 AAAGAGAAGCCTGGAAAAAAGACTG
1 AAA-AGAAGACT-GAAACAAGACTG
* * *
33107 AAAAAAAAACTGAAAGAAAGACTG
1 AAAAGAAGACTGAAA-CAAGACTG
* *
33131 AAAAAATAGACTGAAAGAAAGACTG
1 AAAAGA-AGACTGAAA-CAAGACTG
*
33156 -AAAGAAGACTGAAAGAAGACTG
1 AAAAGAAGACTGAAACAAGACTG
33178 GCTTAGTTTC
Statistics
Matches: 206, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
22 16 0.08
23 31 0.15
24 92 0.45
25 52 0.25
26 15 0.07
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.09
Consensus pattern (23 bp):
AAAAGAAGACTGAAACAAGACTG
Found at i:33012 original size:37 final size:37
Alignment explanation
Indices: 32916--33171 Score: 244
Period size: 37 Copynumber: 7.0 Consensus size: 37
32906 ATTAGGCAAA
* * *
32916 AGAAGACTGAAAACAAAAGACTGAAAGAAGATTGAAA-
1 AGAAGACTG-AAACAGAAGACTGAAACAAGACTGAAAG
* *
32953 AAAATACTG-AA-AGAAGACTGAAACAAGACTGAAAG
1 AGAAGACTGAAACAGAAGACTGAAACAAGACTGAAAG
*
32988 AGAAGACTGAAACAGAAGAGTGAAACAAGACTGAAAG
1 AGAAGACTGAAACAGAAGACTGAAACAAGACTGAAAG
*
33025 AGAAGACTGAAAGAGAAGACTGAAACAAGACTGAAAG
1 AGAAGACTGAAACAGAAGACTGAAACAAGACTGAAAG
* * *
33062 AGAAGACTGAAAC--AAGACTAAAAGAGAAGCCTGGAAA-
1 AGAAGACTGAAACAGAAGACT-GAA-ACAAGACT-GAAAG
* * *
33099 A-AAGACTGAAA-AAAAAACTGAAAGAAAGACTGAAA-
1 AGAAGACTGAAACAGAAGACTGAAA-CAAGACTGAAAG
* * *
33134 AAATAGACTGAAAGA-AAGACTGAAAGAAGACTGAAAG
1 AGA-AGACTGAAACAGAAGACTGAAACAAGACTGAAAG
33171 A
1 A
33172 AGACTGGCTT
Statistics
Matches: 186, Mismatches: 20, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
34 20 0.11
35 21 0.11
36 32 0.17
37 108 0.58
38 5 0.03
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.09
Consensus pattern (37 bp):
AGAAGACTGAAACAGAAGACTGAAACAAGACTGAAAG
Found at i:33078 original size:11 final size:11
Alignment explanation
Indices: 32932--33177 Score: 195
Period size: 11 Copynumber: 20.6 Consensus size: 11
32922 CTGAAAACAA
32932 AAGACTGAAAG
1 AAGACTGAAAG
* *
32943 AAGATTGAAAAA
1 AAGACTG-AAAG
*
32955 AATACTGAAAG
1 AAGACTGAAAG
*
32966 AAGACTGAAAC
1 AAGACTGAAAG
32977 AAGACTGAAAGAG
1 AAGACTG-AA-AG
32990 AAGACTGAAACAG
1 AAGACTG-AA-AG
* *
33003 AAGAGTGAAAC
1 AAGACTGAAAG
33014 AAGACTGAAAGAG
1 AAGACTG-AA-AG
33027 AAGACTGAAAGAG
1 AAGACTG-AA-AG
*
33040 AAGACTGAAAC
1 AAGACTGAAAG
33051 AAGACTGAAAGAG
1 AAGACTG-AA-AG
*
33064 AAGACTGAAAC
1 AAGACTGAAAG
*
33075 AAGACTAAAAGAG
1 AAGACT-GAA-AG
* *
33088 AAGCCTGGAAAA
1 AAGACT-GAAAG
*
33100 AAGACTGAAAAA
1 AAGACTG-AAAG
*
33112 AAAACTGAAAG
1 AAGACTGAAAG
*
33123 AAAGACTGAAAAA
1 -AAGACTG-AAAG
33136 ATAGACTGAAAG
1 A-AGACTGAAAG
33148 AAAGACTGAAAG
1 -AAGACTGAAAG
33160 AAGACTGAAAG
1 AAGACTGAAAG
33171 AAGACTG
1 AAGACTG
33178 GCTTAGTTTC
Statistics
Matches: 193, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
11 69 0.36
12 58 0.30
13 66 0.34
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (11 bp):
AAGACTGAAAG
Found at i:33265 original size:36 final size:36
Alignment explanation
Indices: 33171--33582 Score: 526
Period size: 36 Copynumber: 11.5 Consensus size: 36
33161 AGACTGAAAG
* *
33171 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG-AA
* * *
33208 AAGATTGGCTTAATTTCAAGGAAATTAAGTAAA-AC
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
33243 AAGAACTGGCTTAGTTTTAAGGAAACTAGGTAAAG-A
1 AAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
33279 TAGACTGACTTAATTTCAAGGAAATTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
33314 TAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
33350 AAGACTGGTTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * *
33386 AAGACTGGTTTAGTTTCAAGGAAACTGGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
33422 AAGACTGGCTTAGTTTCAAGGAAACTGGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
33458 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
33494 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
33530 AAGACTGGCTTAATTTCAAGGATATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
33565 GACACAGGCTTAATTTCA
1 AAGACTGGCTTAATTTCA
33583 GGAGAGGAAA
Statistics
Matches: 337, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
35 80 0.24
36 228 0.68
37 29 0.09
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
Found at i:33628 original size:32 final size:32
Alignment explanation
Indices: 33591--33698 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
33581 CAGGAGAGGA
33591 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
*
33623 AATTAAGTGAAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-AA---AATAAAGA-ACTTAATTCAGGGT
* *
33659 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
33691 AATTAAGT
1 AATTAAGT
33699 GAAGTCAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
32 34 0.52
33 3 0.05
35 2 0.03
36 27 0.41
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (32 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGGGT
Found at i:33641 original size:36 final size:36
Alignment explanation
Indices: 33601--33719 Score: 167
Period size: 36 Copynumber: 3.4 Consensus size: 36
33591 AATTAAGTAA
33601 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
*
33637 AATAAA-AGGCTTAATTCAGGGTAATTAAGT--AG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAAGTC
*
33669 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
*
33705 AATAAAGAGCTTAAT
1 AATAAAGAACTTAAT
33720 CTAGAAAAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
32 26 0.36
33 1 0.01
34 4 0.05
35 1 0.01
36 41 0.56
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (36 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
Found at i:33673 original size:68 final size:68
Alignment explanation
Indices: 33591--33719 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 68
33581 CAGGAGAGGA
*
33591 AATTAAGTAAAATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTCAATAAA-AGGCTTAATTCA
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGA-GCTTAATTCA
33655 GGGT
65 GGGT
*
33659 AATTAAGTAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
33720 CTAGAAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 57 0.98
69 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Found at i:41711 original size:8 final size:8
Alignment explanation
Indices: 41698--41738 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
41688 GAAGCATTTC
41698 AAAAAAAG
1 AAAAAAAG
41706 AAAAAAAG
1 AAAAAAAG
41714 AAAAAAAG
1 AAAAAAAG
41722 AAAAAAAG
1 AAAAAAAG
*
41730 AAAGAAAG
1 AAAAAAAG
41738 A
1 A
41739 CAAGTCTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:43011 original size:438 final size:435
Alignment explanation
Indices: 42189--43262 Score: 1322
Period size: 438 Copynumber: 2.5 Consensus size: 435
42179 AATCTTTGTT
* * * * * **** * *
42189 AATCGAACATTTGGAAAAAAAATAATATGAAATTAAATAGATTGTCAATCGAAATCACAAAATTT
1 AATCGGACATGTGGACAAAAAATTATACGAAATTAAATAGACCAACAATCAAAATCACAAACTTT
* * * * * * *
42254 TAAAAGTACTTTTTAGAATTGAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGAT
66 CAGAAGCA-TTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAAATTGTAGAT
* * * *
42319 CATAAAATTACCTTTTAATAAACACCTGAATTACCTTAATTGGACAAATAGAACAAAGAA-A-AA
130 CATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGAACAAAGAATACAA
* * * * *
42382 AAATGAAGCGTTAAATCAAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGT
195 AAATAAAGCGTTAAAGCAAATAAGATAGAATTTGTAAAGGACTAAGCAGCATAAAATAGAAAAAT
* * *
42447 ATGAGGGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGGATATCTTGAAACATAA
260 ATGAGGATCATTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAA
* * *
42512 AAATTCTCTTTTAAACCCTTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAA
325 AAATTCCCTTTTAAACCCTTTCATGAAACTCGCAGATCAAATTAACTTTCGGGTCCTTCATGAAA
* * * *
42577 GTCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTT
390 GTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * * * *
42623 AATCGGATATGTTGATC-GAAAATTATATGATATTAAATAGACCAACAATCGAAA-CGACCAAA-
1 AATCGGACATGTGGA-CAAAAAATTATACGAAATTAAATAGACCAACAATCAAAATC-A-CAAAC
*
42685 TTT-AGGAAGCAATTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCTTTCATGAAAATTGT
63 TTTCA-GAAGC-ATTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAAATTGT
* * * *
42749 AGATCATGAAATTACTTTTTAATAGACACATGAATCAACTTAATCGGACAAATATAACAAAGAAT
126 AGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGAACAAAGAAT
* * * *
42814 ACAAAAATAAATC-TTAAACGCTAGATTAAGATAGAATTTGTAAAGGACTAAGCAGTATAAAGTA
191 ACAAAAATAAAGCGTTAAA-GC-A-AATAAGATAGAATTTGTAAAGGACTAAGCAGCATAAAATA
* *
42878 GAAAAATATGAGGATCATTTGATAAATAA-TCTAAATAAGAAAATGTTTTTTAATGGAGATCTTG
253 GAAAAATATGAGGATCATTTGATAAATAATTC-AAATAAGAAAATATTTCTTAATGGAGATCTTG
* * * *
42942 AAGCATAAAAATTCCCTTTTGAACCC-TTCATGAAACTCGCAGATCAAATTTAGCTTTCTGGTCC
317 AAACATAAAAATTCCCTTTTAAACCCTTTCATGAAACTCGCAGATCAAA-TTAACTTTCGGGTCC
* *
43006 TTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACTGACACTTCAATAACTTC
381 TTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* **
43061 AATCGGACATGTGGACAAAAAATTATACGAAATTAAATTGACCGGCAATCAAAATCACAAACTTT
1 AATCGGACATGTGGACAAAAAATTATACGAAATTAAATAGACCAACAATCAAAATCACAAACTTT
* * *
43126 CAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGT-TCTTCATGAAAATTGTAGA
66 CAGAAGCATTTTTT-GAATTAAAACATAAAAATTAGCTTTTGAGTCT-TTCATGAAAATTGTAGA
* * * * *
43190 TCATGAAATTACCTTTTAATAGACACTTGAATCGCCTTAATTAGACAAATAGAAAAAAAAATACA
129 TCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGAACAAAGAATACA
43255 AAAATAAA
194 AAAATAAA
43263 AGCCAACGTG
Statistics
Matches: 547, Mismatches: 75, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
433 2 0.00
434 151 0.28
435 11 0.02
436 10 0.02
437 37 0.07
438 334 0.61
439 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (435 bp):
AATCGGACATGTGGACAAAAAATTATACGAAATTAAATAGACCAACAATCAAAATCACAAACTTT
CAGAAGCATTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAAATTGTAGATC
ATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGAACAAAGAATACAAA
AATAAAGCGTTAAAGCAAATAAGATAGAATTTGTAAAGGACTAAGCAGCATAAAATAGAAAAATA
TGAGGATCATTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
AATTCCCTTTTAAACCCTTTCATGAAACTCGCAGATCAAATTAACTTTCGGGTCCTTCATGAAAG
TCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
Found at i:43812 original size:37 final size:37
Alignment explanation
Indices: 43762--43832 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
43752 ATATAATTAT
*
43762 TCATAAAGTTATGTCTATTTTG-AAAGACATGTATTGA
1 TCATAAAGTTATGTCTA-TATGAAAAGACATGTATTGA
43799 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
43833 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 3 0.09
37 29 0.91
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:46000 original size:2 final size:2
Alignment explanation
Indices: 45993--46028 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
45983 TTATACGTTT
*
45993 TA TA TA TA TT TA T- 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
46029 CAGAATTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:47701 original size:37 final size:37
Alignment explanation
Indices: 47651--47721 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
47641 ATATAATTAT
* *
47651 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
47688 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
47722 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:48447 original size:114 final size:114
Alignment explanation
Indices: 48247--48474 Score: 411
Period size: 114 Copynumber: 2.0 Consensus size: 114
48237 TAGGGTTGAT
48247 CAAACAAGAGTTTGTATCAAGTAAAAGTTTTGCATCTCTGCAGGAGAGAAGTGTTTGCGCAGGGC
1 CAAACAAGAGTTTGTATCAAGTAAAAGTTTTGCATCTCTGCAGGAGAGAAGTGTTTGCGCAGGGC
* * *
48312 GAGGGTGTGTTCGGAGAGAGCTTTCACGTTGATGGGGACTCCACTTATA
66 AAGGGTGTGTCCGGAGAGAGCTTTCACGTTGATGGAGACTCCACTTATA
* *
48361 CAAACAAGAGTTTGTATCAAGTAAAAGTTTTGTATCTTTGCAGGAGAGAAGTGTTTGCGCAGGGC
1 CAAACAAGAGTTTGTATCAAGTAAAAGTTTTGCATCTCTGCAGGAGAGAAGTGTTTGCGCAGGGC
48426 AAGGGTGTGTCCGGAGAGAGCTTTCACGTTGATGGAGACTCCACTTATA
66 AAGGGTGTGTCCGGAGAGAGCTTTCACGTTGATGGAGACTCCACTTATA
48475 TAGGCATGGG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (114 bp):
CAAACAAGAGTTTGTATCAAGTAAAAGTTTTGCATCTCTGCAGGAGAGAAGTGTTTGCGCAGGGC
AAGGGTGTGTCCGGAGAGAGCTTTCACGTTGATGGAGACTCCACTTATA
Found at i:49317 original size:17 final size:18
Alignment explanation
Indices: 49279--49332 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 18
49269 CTCGGTCTCT
49279 ACAAAACAATCATCACATCA
1 ACAAAACAATCA-CACA-CA
49299 ACAAAACAATCAC-CACA
1 ACAAAACAATCACACACA
49316 AC-AAACAATCACACACA
1 ACAAAACAATCACACACA
49333 CACACACCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.30
17 8 0.24
18 2 0.06
19 1 0.03
20 12 0.36
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.09
Consensus pattern (18 bp):
ACAAAACAATCACACACA
Done.