Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005078.1 Corchorus capsularis cultivar CVL-1 contig05096, 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: 9412
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Found at i:5626 original size:40 final size:41
Alignment explanation
Indices: 5582--5660 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
5572 TGAAAATGTG
* *
5582 ATCTTTA-GCTAAGAGATGAAACTTTTAATTGATTTATATA
1 ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATATA
* *
5622 ATCTTTATGTTAAAAGATGAAATTTTTAATTGACTTATA
1 ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATA
5661 ATAAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 7 0.21
41 27 0.79
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (41 bp):
ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATATA
Found at i:5717 original size:29 final size:29
Alignment explanation
Indices: 5684--5748 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
5674 CATTGTGTTG
5684 AAAGATGAAGTCTTTAAGTAATTTGTAAA-
1 AAAGATGAA-TCTTTAAGTAATTTGTAAAT
* *
5713 AAAGATTGGATTTTTAAGTAATTTGTAAAT
1 AAAGA-TGAATCTTTAAGTAATTTGTAAAT
5743 AAAGAT
1 AAAGAT
5749 TAAATGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.37
Consensus pattern (29 bp):
AAAGATGAATCTTTAAGTAATTTGTAAAT
Found at i:5759 original size:30 final size:29
Alignment explanation
Indices: 5696--5761 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
5686 AGATGAAGTC
** *
5696 TTTAAGTAATTTGTAAAAAAGATTGGATT
1 TTTAAGTAATTTGTAAAAAAGATTAAATG
5725 TTTAAGTAATTTGTAAATAAAGATTAAATG
1 TTTAAGTAATTTGTAAA-AAAGATTAAATG
5755 TTTAAGT
1 TTTAAGT
5762 GAAAGATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (29 bp):
TTTAAGTAATTTGTAAAAAAGATTAAATG
Found at i:5838 original size:51 final size:51
Alignment explanation
Indices: 5783--6197 Score: 259
Period size: 51 Copynumber: 8.4 Consensus size: 51
5773 TCTTTTAAGA
**
5783 AATTTGTAAATAAAAATGTGATCTTTGAACTAAAAGATGAAACTTTGGATT
1 AATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTTTGGATT
* ** * * * *
5834 AATTTGGT-GATAAAGGTGAAATCTTT-AAGGTAATA-ATTAAACTTTTGATT
1 AATTT-GTAAATAAAAATGAAATCTTTGAA-CTAAAAGATGAAACTTTGGATT
* * * *
5884 AACTTGTAAAT-AAAATGAGATCTTAGAACT-----A--AAA--TTAGA--
1 AATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTTTGGATT
5923 AATTTGTAAATAAAAATGAAA-CTTTTGAACTAAAAGATGAAACTTTGGATT
1 AATTTGTAAATAAAAATGAAATC-TTTGAACTAAAAGATGAAACTTTGGATT
* ** ** * *
5974 AATTTGGT-GATAAAGGTGAAATCTTT-AAGCTAGTA-ATTAAACTTTTGATT
1 AATTT-GTAAATAAAAATGAAATCTTTGAA-CTAAAAGATGAAACTTTGGATT
* * * * * * *
6024 AACTTATGAATAAAAATGAGATCTTTGAACCAAATGATGGAACTTAT-GATT
1 AATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTT-TGGATT
* * *
6075 AATTTGTAAATAAAACT-AAGATCTTTGAACTAAAAGATGGAACTTTTGATT
1 AATTTGTAAATAAAAATGAA-ATCTTTGAACTAAAAGATGAAACTTTGGATT
** *
6126 AATTTGT-AATAAAGGTGAAATCTTT-AAGCTAAAAGTTTGAAA--TTGTGATT
1 AATTTGTAAATAAAAATGAAATCTTTGAA-CTAAAAG-ATGAAACTTTG-GATT
*
6176 AATTTGTAAATAAAAGTGAAAT
1 AATTTGTAAATAAAAATGAAAT
6198 TTGTAATCTA
Statistics
Matches: 280, Mismatches: 53, Indels: 62
0.71 0.13 0.16
Matches are distributed among these distances:
39 11 0.04
40 15 0.05
41 4 0.01
43 3 0.01
45 2 0.01
47 3 0.01
49 22 0.08
50 91 0.32
51 123 0.44
52 6 0.02
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (51 bp):
AATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTTTGGATT
Found at i:5949 original size:21 final size:21
Alignment explanation
Indices: 5925--5968 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5915 AAATTAGAAA
5925 TTTGTAAATAAAA-ATGAAACT
1 TTTG-AAATAAAAGATGAAACT
*
5946 TTTGAACTAAAAGATGAAACT
1 TTTGAAATAAAAGATGAAACT
5967 TT
1 TT
5969 GGATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TTTGAAATAAAAGATGAAACT
Found at i:6036 original size:140 final size:145
Alignment explanation
Indices: 5780--6157 Score: 511
Period size: 140 Copynumber: 2.6 Consensus size: 145
5770 GAATCTTTTA
**
5780 AGAAATTTGTAAATAAAAATGTGATCTTTGAACTAAAAGATGAAACTTTGGATTAATTTGGTGAT
1 AGAAATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTTTGGATTAATTTGGTGAT
* *
5845 AAAGGTGAAATCTTTAAGGTAATAATTAAACTTTTGATTAACTTGTAAAT-AAAATGAGATCTTA
66 AAAGGTGAAATCTTTAAGCTAATAATTAAACTTTTGATTAACTTATAAATAAAAATGAGATCTTA
5909 GAA-C-T-A-AAATT
131 GAACCATGAGAAATT
5920 AGAAATTTGTAAATAAAAATGAAA-CTTTTGAACTAAAAGATGAAACTTTGGATTAATTTGGTGA
1 AGAAATTTGTAAATAAAAATGAAATC-TTTGAACTAAAAGATGAAACTTTGGATTAATTTGGTGA
* *
5984 TAAAGGTGAAATCTTTAAGCTAGTAATTAAACTTTTGATTAACTTATGAATAAAAATGAGATCTT
65 TAAAGGTGAAATCTTTAAGCTAATAATTAAACTTTTGATTAACTTATAAATAAAAATGAGATCTT
* *
6049 TGAACCAAATGATGGAACTT
130 AGAACC--ATGA--GAAATT
* * *
6069 ATGATTAATTTGTAAATAAAACT-AAGATCTTTGAACTAAAAGATGGAACTTTTGATTAATTT-G
1 A-GA--AATTTGTAAATAAAAATGAA-ATCTTTGAACTAAAAGATGAAACTTTGGATTAATTTGG
*
6132 TAATAAAGGTGAAATCTTTAAGCTAA
62 TGATAAAGGTGAAATCTTTAAGCTAA
6158 AAGTTTGAAA
Statistics
Matches: 210, Mismatches: 13, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
139 1 0.00
140 107 0.51
141 16 0.08
142 1 0.00
145 1 0.00
146 1 0.00
149 5 0.02
150 2 0.01
151 27 0.13
152 48 0.23
153 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.35
Consensus pattern (145 bp):
AGAAATTTGTAAATAAAAATGAAATCTTTGAACTAAAAGATGAAACTTTGGATTAATTTGGTGAT
AAAGGTGAAATCTTTAAGCTAATAATTAAACTTTTGATTAACTTATAAATAAAAATGAGATCTTA
GAACCATGAGAAATT
Found at i:6137 original size:101 final size:101
Alignment explanation
Indices: 6013--6245 Score: 242
Period size: 101 Copynumber: 2.3 Consensus size: 101
6003 CTAGTAATTA
* * *
6013 AACTTTTGATTAACTTATG-AATAAAAATGAGATCTTTGAA-CCAAATGATGGAACTTATGATTA
1 AACTTTTGATTAA-TT-TGTAATAAAAATGAAATCTTT-AAGCCAAAAGATGGAAATTATGATTA
6076 ATTTGTAAATAAAACT-AAGATCTT-TGAA-CTAAAAGATGG
63 ATTTGTAAATAAAACTGAA-AT-TTGT-AATCTAAAAGATGG
** * * * *
6115 AACTTTTGATTAATTTGTAATAAAGGTGAAATCTTTAAGCTAAAAGTTTGAAATTGTGATTAATT
1 AACTTTTGATTAATTTGTAATAAAAATGAAATCTTTAAGCCAAAAGATGGAAATTATGATTAATT
* * * *
6180 TGTAAATAAAAGTGAAATTTGTAATCTAAACGGTTG
66 TGTAAATAAAACTGAAATTTGTAATCTAAAAGATGG
* *
6216 AACTTTTGATCAATTTGTAATAAAAGTGAA
1 AACTTTTGATTAATTTGTAATAAAAATGAA
6246 GTTTTAAAGC
Statistics
Matches: 111, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
100 8 0.07
101 88 0.79
102 15 0.14
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (101 bp):
AACTTTTGATTAATTTGTAATAAAAATGAAATCTTTAAGCCAAAAGATGGAAATTATGATTAATT
TGTAAATAAAACTGAAATTTGTAATCTAAAAGATGG
Found at i:6209 original size:51 final size:52
Alignment explanation
Indices: 5923--6289 Score: 266
Period size: 51 Copynumber: 7.3 Consensus size: 52
5913 TAAAATTAGA
* * * *
5923 AATTTGTAAATAAAAATGAAA-CTTTTGAA-CTAAAA-GATGAAACTTTGGATT
1 AATTTGTAAATAAAAGTGAAATC-TTTAAAGCTAAAAGGTTG-AACTTTTGATT
* * * *
5974 AATTTGGT-GATAAAGGTGAAATCTTT-AAGCTAGTAA--TTAAACTTTTGATT
1 AATTT-GTAAATAAAAGTGAAATCTTTAAAGCTA-AAAGGTTGAACTTTTGATT
* * * * * * * * * * *
6024 AACTTATGAATAAAAATGAGATCTTTGAA-CCAAATGATGGAACTTATGATT
1 AATTTGTAAATAAAAGTGAAATCTTTAAAGCTAAAAGGTTGAACTTTTGATT
* * * *
6075 AATTTGTAAATAAAACT-AAGATCTTTGAA-CTAAAAGATGGAACTTTTGATT
1 AATTTGTAAATAAAAGTGAA-ATCTTTAAAGCTAAAAGGTTGAACTTTTGATT
* * * *
6126 AATTTGT-AATAAAGGTGAAATCTTT-AAGCTAAAAGTTTGAAATTGTGATT
1 AATTTGTAAATAAAAGTGAAATCTTTAAAGCTAAAAGGTTGAACTTTTGATT
* * *
6176 AATTTGTAAATAAAAGTGAAAT-TTGT-AATCTAAACGGTTGAACTTTTGATC
1 AATTTGTAAATAAAAGTGAAATCTT-TAAAGCTAAAAGGTTGAACTTTTGATT
* *
6227 AATTTGT-AATAAAAGTGAAGT-TTTAAAGCTAAAAGGTTG-ACTTTTGATA
1 AATTTGTAAATAAAAGTGAAATCTTTAAAGCTAAAAGGTTGAACTTTTGATT
6276 AATTTG-AAATAAAA
1 AATTTGTAAATAAAA
6290 CTTTTAAGTG
Statistics
Matches: 257, Mismatches: 44, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
49 27 0.11
50 100 0.39
51 125 0.49
52 5 0.02
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (52 bp):
AATTTGTAAATAAAAGTGAAATCTTTAAAGCTAAAAGGTTGAACTTTTGATT
Found at i:6256 original size:101 final size:100
Alignment explanation
Indices: 6070--6291 Score: 265
Period size: 101 Copynumber: 2.2 Consensus size: 100
6060 ATGGAACTTA
*
6070 TGATTAATTTGTAAATAAAACTAAGATCTTTGAACTAAAAGATGGAACTTTTGATTAATTTGTAA
1 TGATTAATTTGTAAATAAAACTAAGATCTTTGAACTAAAAGATGGAACTTTTGATCAATTTGTAA
* *
6135 TAAAGGTGAAATCTTTAAGCTAAAAGTTTGAAATTG
66 TAAAAGTGAAATCTTTAAGCTAAAAGGTTG-AATTG
* * * *
6171 TGATTAATTTGTAAATAAAAGTGAA-A--TTTGTAATCTAAACGGTTGAACTTTTGATCAATTTG
1 TGATTAATTTGTAAATAAAACT-AAGATCTTTG-AA-CTAAAAGATGGAACTTTTGATCAATTTG
* * *
6233 TAATAAAAGTGAAGT-TTTAAAGCTAAAAGGTTGACTTT
63 TAATAAAAGTGAAATCTTT-AAGCTAAAAGGTTGAATTG
*
6271 TGATAAATTTG-AAATAAAACT
1 TGATTAATTTGTAAATAAAACT
6292 TTTAAGTGAG
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
99 13 0.12
100 18 0.17
101 72 0.69
102 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (100 bp):
TGATTAATTTGTAAATAAAACTAAGATCTTTGAACTAAAAGATGGAACTTTTGATCAATTTGTAA
TAAAAGTGAAATCTTTAAGCTAAAAGGTTGAATTG
Found at i:6912 original size:50 final size:49
Alignment explanation
Indices: 6841--7991 Score: 1087
Period size: 49 Copynumber: 23.2 Consensus size: 49
6831 GGAAGATGTT
* * * *
6841 TTTTCTTTCTTGTTTCCCAAAAATGCCCCTTCCTGGTTGGAAGGTTCCTG
1 TTTTCTTTTTTGTTT-CCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * * * * *
6891 TTTTCTTTATTTGTTTCCAAAAAATGGCCATTCCTGATTGGAAGGTCCTTG
1 TTTTCTTT-TTTGTTTCC-AAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* ** * *
6942 -TTCCTTTATTTGTTTCCCGAAATTCCCCTTCCTGGTCGGAAGGT-CCTG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* *
6990 TTTTCTTTGTTTGTTTCCAAAAATGCCCCTTCACAGTCGGAAGGTCCCTG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* ** ** * *
7040 TTTTCTTTGTTTGTTTCCAAAGATGCCCCTTCCCAATTAGAAGGTCACAG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * * ** * *
7090 TTTTCTTCATTT-ATTCC-AAAA-GCCTCTTCCAAGTCGTAAGGTCACAT-
1 TTTTCTT-TTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC-CCTG
* * * *
7137 TTTTATTCATTT-ATTCC-AAAA-GCCCCTTCCCGGTCGGAAGGT-CATAG
1 TTTTCTT-TTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCT-G
* ** * *
7184 TTTTCTTCTCTT-ACTCCAAAAACGTCCCTTCCCGGTCGGAAGGTCCCTG
1 TTTTCTT-TTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
7233 TTTTCTTTGTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * * **
7283 TTTTGTTTGTTTGTTTCCAAAAACGCCCCTTCCCGGTCGGAAGGTCACAA
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * ** *
7333 TTTTCTTCTCTT-ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTAACAG
1 TTTTCTT-TTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * * *
7382 TTTTCTCCTCTT-ATTCCAAAAATGCCCCTTCCTGGTCGGAAGG-CCACTG
1 TTTTCT-TTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-CTG
* * ** *
7431 TTTTCTTTATTTATTTCCAAAAATTCCCCTTCTTGGTCGGAAGGTCCCTC
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * *
7481 TTTTCTTTGTTGTTTCCAAAAATGCCCATTCCCGGTCGGAAGGTCCCTC
1 TTTTCTTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* *
7530 TTTTCTTTGTTGTTTCCAAAAATGCCCCTTCCCGATCGGAAGGTCCCTG
1 TTTTCTTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* ** *
7579 TTTTCTTTGTTTGTTTCCAAAAATGACCCTTCCTAGTTGGAAGGTCCCTG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* *
7629 TTTTCTTTGTCTCATCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACTG
1 TTTTCTTT-T-T--T-GT-TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * * **
7684 TTTTCTTTATTTATTTCCAAAAATTCCCCTTCTTC-GTCGGAAGGTCCCCC
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTC-CCGGTCGGAAGGTCCCTG
* *
7734 TTTTCTTTGTTGTTTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCTG
1 TTTTCTTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* *
7783 TTTTCTTTGTTGTTTCCAAAAATGCCCCTTCCCGATCGGAAGGTCCCTG
1 TTTTCTTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* * ** *
7832 TTTTCTTTGTTTTTTTTTTCCAAAAATACCCCTTCCTAGTCGAAAGGTCCCTG
1 TTTTC----TTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
* *
7885 TTTTCTTTGTTTGTTTCCACAAATGCCCCTTCCTGGTCGGAAGGTCCCTG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
**
7935 TTTTCTTTGTTTGTTTCC-AAAATGCCCCTTCTTGGTCGGAAGGT--CTAG
1 TTTTCTTT-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCT-G
7983 TTTTCTTTT
1 TTTTCTTTT
7992 CACATTTGAG
Statistics
Matches: 938, Mismatches: 130, Indels: 69
0.82 0.11 0.06
Matches are distributed among these distances:
45 3 0.00
47 69 0.07
48 22 0.02
49 374 0.40
50 345 0.37
51 39 0.04
52 1 0.00
53 43 0.05
54 2 0.00
55 40 0.04
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.39
Consensus pattern (49 bp):
TTTTCTTTTTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG
Found at i:6934 original size:99 final size:99
Alignment explanation
Indices: 6812--7990 Score: 355
Period size: 99 Copynumber: 11.9 Consensus size: 99
6802 CTGCTTTTCG
* * * * *
6812 AAAATTGCCCTTCCTCATCGGAAGAT-GTTTTTTCTTT-CTTGTTTCCCAAAAATGCCCCTTCCT
1 AAAATGGCCATTCCTCATCGGAAGATCCTTGTTCCTTTACTTGTTTCCC-AAAATGCCCCTTCCT
*
6875 GGTTGGAAGGTTCCTGTTTTCTTTATTTGTTTCCAA
65 GGTCGGAAGG-TCCTGTTTTCTTTATTTGTTTCCAA
* * * * * *
6911 AAAATGGCCATTCCTGATTGGAAGGTCCTTGTTCCTTTATTTGTTTCCCGAAATTCCCCTTCCTG
1 AAAATGGCCATTCCTCATCGGAAGATCCTTGTTCCTTTACTTGTTTCCCAAAATGCCCCTTCCTG
*
6976 GTCGGAAGGTCCTGTTTTCTTTGTTTGTTTCC-A
66 GTCGGAAGGTCCTGTTTTCTTTATTTGTTTCCAA
* * * * * * **
7009 AAAATGCCCCTT-CACAGTCGGAAGGTCCCTGTTTTCTTTGTTTGTTT-CCAAAGATGCCCCTTC
1 AAAATGGCCATTCCTCA-TCGGAAGATCCTTG-TTCCTTTACTTGTTTCCCAAA-ATGCCCCTTC
*** ** * * *
7072 CCAATTAGAAGGTCACAGTTTTCTTCATTT-ATTCC--
63 CTGGTCGGAAGGTC-CTGTTTTCTTTATTTGTTTCCAA
* * * * ** *
7107 AAAA--GCCTCTTCC-AAGTCGTAAGGTCACATT-TTTATTCA-TT-TATT-CCAAAA-GCCCCT
1 AAAATGGCC-ATTCCTCA-TCGGAAGATC-C-TTGTTCCTTTACTTGT-TTCCCAAAATGCCCCT
* * * **
7164 TCCCGGTCGGAAGGTCATAGTTTTCTTCT-CTT-ACTCC-A
61 TCCTGGTCGGAAGGTCCT-GTTTTCTT-TATTTGTTTCCAA
* * * * * * * ** *
7202 AAAACGTCCCTTCC-CGGTCGGAAGGTCCCTGTTTTCTTTGTTTGTTTCCAAAAATGCCCCTTCC
1 AAAATGGCCATTCCTC-ATCGGAAGATCCTTG-TTCCTTTACTTGTTTCCCAAAATGCCCCTTCC
* * *
7266 CGGTCGGAAGGTCCCTGTTTTGTTTGTTTGTTTCC-A
64 TGGTCGGAAGGT-CCTGTTTTCTTTATTTGTTTCCAA
* * * * * * *
7302 AAAACGCCCCTTCC-CGGTCGGAAGGTCACAATT-TT-CTTCT-CTT-ATTCCAAAAATGCCCCT
1 AAAATGGCCATTCCTC-ATCGGAAGATC-C--TTGTTCCTT-TACTTGTTTCCCAAAATGCCCCT
* * * * * *
7362 TCCCGGTCGGAAGGTAACAGTTTTCTCCT-CTT-ATTCC-A
61 TCCTGGTCGGAAGGT-CCTGTTTTCT-TTATTTGTTTCCAA
* * ** * * * * * * * *
7400 AAAATGCCCCTTCCTGGTCGGAAG-GCCACTGTTTTCTTTATTTATTTCCAAAAATTCCCCTTCT
1 AAAATGGCCATTCCTCATCGGAAGATCC-TTG-TTCCTTTACTTGTTTCCCAAAATGCCCCTTCC
* *
7464 TGGTCGGAAGGTCCCTCTTTTCTTT-GTTGTTTCC-A
64 TGGTCGGAAGGT-CCTGTTTTCTTTATTTGTTTCCAA
* * * * * *
7499 AAAATGCCCATTCC-CGGTCGGAAGGTCCCTCT-TTTCTTT-GTTGTTTCCAAAAATGCCCCTTC
1 AAAATGGCCATTCCTC-ATCGGAAGAT-CCT-TGTTCCTTTACTTGTTTCCCAAAATGCCCCTTC
* * *
7561 CCGATCGGAAGGTCCCTGTTTTCTTTGTTTGTTTCC-A
63 CTGGTCGGAAGGT-CCTGTTTTCTTTATTTGTTTCCAA
* * * * * * * * *
7598 AAAATGACCCTTCCT-AGTTGGAAGGTCCCTGTTTTCTTTGTCTCATCTTATTCCAAAAATGCCC
1 AAAATGGCCATTCCTCA-TCGGAAGATCCTTG-TTCCTTT-ACT--T-GT-TTCCCAAAATGCCC
* *
7662 CTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTATTTCC-A
59 CTTCCTGGTCGGAAGGTC-CTGTTTTCTTTATTTGTTTCCAA
** * * * * * *
7703 AAAATTCCCCTTCTTCGTCGGAAGGTCCCCCTT-TT-CTTT-GTTGTTTCCAAAAATGCCCCTTC
1 AAAATGGCCATTCCTCATCGGAAGAT---CCTTGTTCCTTTACTTGTTTCCCAAAATGCCCCTTC
** *
7765 CCAGTCGGAAGGTCCCTGTTTTCTTT-GTTGTTTCC-A
63 CTGGTCGGAAGGT-CCTGTTTTCTTTATTTGTTTCCAA
* * * * * ** * * *
7801 AAAATGCCCCTTCC-CGATCGGAAGGTCCCTGTTTTCTTTGTTTTTTTTTTCCAAAAATACCCCT
1 AAAATGGCCATTCCTC-ATCGGAAGAT-CCT-TGTTC-CT-TTACTTGTTTCCCAAAATGCCCCT
* * *
7865 TCCTAGTCGAAAGGTCCCTGTTTTCTTTGTTTGTTTCC-A
61 TCCTGGTCGGAAGGT-CCTGTTTTCTTTATTTGTTTCCAA
* * * ** * * * ** *
7904 CAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTTGTTTGTTT-CCAAAATGCCCCTTCTT
1 AAAATGGCCATTCCTCATCGGAAGATCCTTG-TTCCTTTACTTGTTTCCCAAAATGCCCCTTCCT
7968 GGTCGGAAGGT-CTAGTTTTCTTT
65 GGTCGGAAGGTCCT-GTTTTCTTT
7991 TCACATTTGA
Statistics
Matches: 864, Mismatches: 146, Indels: 141
0.75 0.13 0.12
Matches are distributed among these distances:
94 33 0.04
95 9 0.01
96 35 0.04
97 36 0.04
98 158 0.18
99 317 0.37
100 91 0.11
101 22 0.03
102 48 0.06
103 34 0.04
104 2 0.00
105 74 0.09
106 2 0.00
108 3 0.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.39
Consensus pattern (99 bp):
AAAATGGCCATTCCTCATCGGAAGATCCTTGTTCCTTTACTTGTTTCCCAAAATGCCCCTTCCTG
GTCGGAAGGTCCTGTTTTCTTTATTTGTTTCCAA
Found at i:8801 original size:27 final size:27
Alignment explanation
Indices: 8722--8802 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
8712 GCATTAGGGT
* * **
8722 CACCCAAGGGTATTTTGGTCATTTTCG
1 CACCCAGGGGCATTTTGGTCATTTTTA
*
8749 CACCCAGGGGCATTTTGGTAATTTTTA
1 CACCCAGGGGCATTTTGGTCATTTTTA
* *
8776 CACTCAGGGGCATTTTAGTCATTTTTA
1 CACCCAGGGGCATTTTGGTCATTTTTA
8803 AGTTCACCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
CACCCAGGGGCATTTTGGTCATTTTTA
Done.