Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013518.1 Corchorus capsularis cultivar CVL-1 contig13539, 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: 26844
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:81 original size:21 final size:21
Alignment explanation
Indices: 55--94 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
45 GATATTGGTG
55 TTGAGACAAACTATAGCTCAC
1 TTGAGACAAACTATAGCTCAC
76 TTGAGACAAACTATAGCTC
1 TTGAGACAAACTATAGCTC
95 TCACCTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
TTGAGACAAACTATAGCTCAC
Found at i:154 original size:90 final size:90
Alignment explanation
Indices: 1--274 Score: 449
Period size: 90 Copynumber: 3.0 Consensus size: 90
*
1 GCTCTCACCTTCTCTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
1 GCTCTCACCTTATCTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
66 TATAGCTCACTTGAGACAAACTATA
66 TATAGCTCACTTGAGACAAACTATA
* *
91 GCTCTCACCTTGTGTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
1 GCTCTCACCTTATCTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
*
156 TATAGCTCACTTGAGGCAAACTATA
66 TATAGCTCACTTGAGACAAACTATA
* ** *
181 GCTCTCACCTTATCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAAC
1 GCTCTCACCTTATCTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
* * *
246 TATAGCTCACGTAAGACAAACTTTA
66 TATAGCTCACTTGAGACAAACTATA
271 GCTC
1 GCTC
275 GTTATAGCTC
Statistics
Matches: 171, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 171 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (90 bp):
GCTCTCACCTTATCTTTATTTACAAAAGGTCCACCTTGTGGCAAGATATTGGTGTTGAGACAAAC
TATAGCTCACTTGAGACAAACTATA
Found at i:175 original size:21 final size:21
Alignment explanation
Indices: 145--184 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
135 GATATTGGTG
145 TTGAGACAAACTATAGCTCAC
1 TTGAGACAAACTATAGCTCAC
*
166 TTGAGGCAAACTATAGCTC
1 TTGAGACAAACTATAGCTC
185 TCACCTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (21 bp):
TTGAGACAAACTATAGCTCAC
Found at i:284 original size:31 final size:31
Alignment explanation
Indices: 246--305 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
236 TGAGGCAAAC
*
246 TATAGCTCACGTAAGACAAACTTTAGCTCGT
1 TATAGCTCACGTAAGACAAACTATAGCTCGT
* *
277 TATAGCTCACGTGAGACAACCTATAGCTC
1 TATAGCTCACGTAAGACAAACTATAGCTC
306 TCACCTTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (31 bp):
TATAGCTCACGTAAGACAAACTATAGCTCGT
Found at i:7502 original size:16 final size:16
Alignment explanation
Indices: 7483--7594 Score: 80
Period size: 16 Copynumber: 7.0 Consensus size: 16
7473 AACCCGACTG
*
7483 AACTTGAATCCGAAAA
1 AACTCGAATCCGAAAA
*
7499 AACTCGAATCCGAAAG
1 AACTCGAATCCGAAAA
** * *
7515 AGTTCAAACCCGAAAA
1 AACTCGAATCCGAAAA
* *
7531 AACACGAACCCGAAAA
1 AACTCGAATCCGAAAA
* * * *
7547 AACCCAAACCCGAAAT
1 AACTCGAATCCGAAAA
* * *
7563 AGCTCAAACCCGAAAA
1 AACTCGAATCCGAAAA
*
7579 AACCCGAATCCGAAAA
1 AACTCGAATCCGAAAA
7595 TTTATGAAAA
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 75 1.00
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.09
Consensus pattern (16 bp):
AACTCGAATCCGAAAA
Found at i:7546 original size:48 final size:48
Alignment explanation
Indices: 7492--7594 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
7482 GAACTTGAAT
* * * *
7492 CCGAAAAAACTCGAATCCGAAAGAGTTCAAACCCGAAAAAACACGAAC
1 CCGAAAAAACCCAAACCCGAAAGAGCTCAAACCCGAAAAAACACGAAC
* * *
7540 CCGAAAAAACCCAAACCCGAAATAGCTCAAACCCGAAAAAACCCGAAT
1 CCGAAAAAACCCAAACCCGAAAGAGCTCAAACCCGAAAAAACACGAAC
7588 CCGAAAA
1 CCGAAAA
7595 TTTATGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.30, G:0.13, T:0.07
Consensus pattern (48 bp):
CCGAAAAAACCCAAACCCGAAAGAGCTCAAACCCGAAAAAACACGAAC
Found at i:7555 original size:32 final size:32
Alignment explanation
Indices: 7492--7594 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
7482 GAACTTGAAT
* * ***
7492 CCGAAAAAACTCGAATCCGAAAGAGTTCAAAC
1 CCGAAAAAACTCGAACCCGAAAAAACCCAAAC
*
7524 CCGAAAAAACACGAACCCGAAAAAACCCAAAC
1 CCGAAAAAACTCGAACCCGAAAAAACCCAAAC
* * * * *
7556 CCGAAATAGCTCAAACCCGAAAAAACCCGAAT
1 CCGAAAAAACTCGAACCCGAAAAAACCCAAAC
7588 CCGAAAA
1 CCGAAAA
7595 TTTATGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.50, C:0.30, G:0.13, T:0.07
Consensus pattern (32 bp):
CCGAAAAAACTCGAACCCGAAAAAACCCAAAC
Found at i:7778 original size:16 final size:15
Alignment explanation
Indices: 7750--7804 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
7740 CAGAACCCGA
*
7750 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
*
7765 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
*
7781 AACCCGAATTAACCTG
1 -ACCCAAATTAACCTG
7797 ACCCAAAT
1 ACCCAAAT
7805 CCAACCTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 15 0.45
16 10 0.30
17 8 0.24
ACGTcount: A:0.38, C:0.36, G:0.09, T:0.16
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:7779 original size:32 final size:32
Alignment explanation
Indices: 7743--7819 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
7733 ACCCAAACAG
*
7743 AACCCGAACCCGAATTAACCTGACCCAAATTC
1 AACCCGAACCCGAATTAACCTGACCCAAATCC
7775 AACCCGAACCCGAATTAACCTGACCCAAATCC
1 AACCCGAACCCGAATTAACCTGACCCAAATCC
*
7807 AACCTGAACCCGA
1 AACCCGAACCCGA
7820 CTCAAGTCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.38, C:0.39, G:0.10, T:0.13
Consensus pattern (32 bp):
AACCCGAACCCGAATTAACCTGACCCAAATCC
Found at i:7810 original size:16 final size:15
Alignment explanation
Indices: 7759--7813 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
7749 AACCCGAATT
7759 AACCTGACCCAAATTC
1 AACCTGACCCAAA-TC
* * *
7775 AACCCGAACCCGAATT
1 AACCTG-ACCCAAATC
7791 AACCTGACCCAAATCC
1 AACCTGACCCAAAT-C
7807 AACCTGA
1 AACCTGA
7814 ACCCGACTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 7 0.23
16 18 0.58
17 6 0.19
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (15 bp):
AACCTGACCCAAATC
Found at i:10378 original size:59 final size:59
Alignment explanation
Indices: 10304--10517 Score: 356
Period size: 59 Copynumber: 3.6 Consensus size: 59
10294 GGTTGACCAT
* * * *
10304 AGGATTATGATTGAAGCTTCATTACAGCGGGATCCAAATCAATCAAGCAGGTCTACCGC
1 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAAATCAATCAAGCAAGTCTACCGC
* * *
10363 AGGATCATGAATGAAGCATGATTACAACGGGATCCAAATCAATCAAGCAAGTCTATCGC
1 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAAATCAATCAAGCAAGTCTACCGC
*
10422 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAAATCAATCAAGCAAGTCTATCGC
1 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAAATCAATCAAGCAAGTCTACCGC
10481 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAA
1 AGGATCATGATTGAAGCATGATTACAGCGGGATCCAA
10518 GATTGAAGTC
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 146 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (59 bp):
AGGATCATGATTGAAGCATGATTACAGCGGGATCCAAATCAATCAAGCAAGTCTACCGC
Found at i:10411 original size:31 final size:31
Alignment explanation
Indices: 10324--10470 Score: 105
Period size: 28 Copynumber: 4.9 Consensus size: 31
10314 TTGAAGCTTC
10324 ATTACAGCGGGATCCAAATCAATCAAGCA-G
1 ATTACAGCGGGATCCAAATCAATCAAGCATG
* * * * *
10354 GTCTACCGCAGGAT-C--ATGAATGAAGCATG
1 AT-TACAGCGGGATCCAAATCAATCAAGCATG
* *
10383 ATTACAACGGGATCCAAATCAATCAAGCAAG
1 ATTACAGCGGGATCCAAATCAATCAAGCATG
* * * *
10414 -TCTATC-GCAGGAT-C--ATGATTGAAGCATG
1 AT-TA-CAGCGGGATCCAAATCAATCAAGCATG
10442 ATTACAGCGGGATCCAAATCAATCAAGCA
1 ATTACAGCGGGATCCAAATCAATCAAGCA
10471 AGTCTATCGC
Statistics
Matches: 83, Mismatches: 22, Indels: 23
0.65 0.17 0.18
Matches are distributed among these distances:
27 1 0.01
28 36 0.43
29 5 0.06
30 4 0.05
31 36 0.43
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
ATTACAGCGGGATCCAAATCAATCAAGCATG
Found at i:10454 original size:28 final size:29
Alignment explanation
Indices: 10310--10525 Score: 88
Period size: 28 Copynumber: 7.3 Consensus size: 29
10300 CCATAGGATT
* *
10310 ATGATTGAAGCTTCATTACAGCGGGATCC
1 ATGATTGAAGCATGATTACAGCGGGATCC
* * * * * *
10339 AAATCAATCAAGCA-GGTCTACCGCAGGAT-C
1 --ATGATTGAAGCATGAT-TACAGCGGGATCC
* *
10369 ATGAATGAAGCATGATTACAACGGGATCC
1 ATGATTGAAGCATGATTACAGCGGGATCC
* * * * *
10398 AAATCAATCAAGCAAG-TCTATC-GCAGGAT-C
1 --ATGATTGAAGCATGAT-TA-CAGCGGGATCC
10428 ATGATTGAAGCATGATTACAGCGGGATCC
1 ATGATTGAAGCATGATTACAGCGGGATCC
* * * * *
10457 AAATCAATCAAGCAAG-TCTATC-GCAGGAT-C
1 --ATGATTGAAGCATGAT-TA-CAGCGGGATCC
10487 ATGATTGAAGCATGATTACAGCGGGATCC
1 ATGATTGAAGCATGATTACAGCGGGATCC
*
10516 AAGATTGAAG
1 ATGATTGAAG
10526 TCGCAAATCA
Statistics
Matches: 133, Mismatches: 35, Indels: 36
0.65 0.17 0.18
Matches are distributed among these distances:
27 2 0.02
28 54 0.41
29 16 0.12
30 6 0.05
31 53 0.40
32 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (29 bp):
ATGATTGAAGCATGATTACAGCGGGATCC
Found at i:10486 original size:31 final size:30
Alignment explanation
Indices: 10333--10486 Score: 90
Period size: 31 Copynumber: 5.2 Consensus size: 30
10323 CATTACAGCG
*
10333 GGATCCAAATCAATCAAGCAGGTCTACCGCA
1 GGATCCAAATCAATCAAGCAAGTCTA-CGCA
* * * * *
10364 GGAT-C--ATGAATGAAGCATGAT-TACAACG
1 GGATCCAAATCAATCAAGCAAG-TCTAC-GCA
10392 GGATCCAAATCAATCAAGCAAGTCTATCGCA
1 GGATCCAAATCAATCAAGCAAGTCTA-CGCA
* * * * *
10423 GGAT-C--ATGATTGAAGCATGAT-TACAGCG
1 GGATCCAAATCAATCAAGCAAG-TCTAC-GCA
10451 GGATCCAAATCAATCAAGCAAGTCTATCGCA
1 GGATCCAAATCAATCAAGCAAGTCTA-CGCA
10482 GGATC
1 GGATC
10487 ATGATTGAAG
Statistics
Matches: 89, Mismatches: 20, Indels: 28
0.65 0.15 0.20
Matches are distributed among these distances:
27 2 0.02
28 36 0.40
29 4 0.04
30 4 0.04
31 41 0.46
32 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (30 bp):
GGATCCAAATCAATCAAGCAAGTCTACGCA
Found at i:10561 original size:21 final size:21
Alignment explanation
Indices: 10535--10576 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10525 GTCGCAAATC
* *
10535 ATGGTCAATGATTTGTACCGT
1 ATGGTCAAAGATTTATACCGT
10556 ATGGTCAAAGATTTATACCGT
1 ATGGTCAAAGATTTATACCGT
10577 GTACATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGGTCAAAGATTTATACCGT
Found at i:10937 original size:60 final size:60
Alignment explanation
Indices: 10812--10928 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
10802 CCATAGTCAG
** * * * **
10812 ATCTAACAGAGAGAGCAGTGAATATGCATCCTCTAGTAGATCAGATAGAGCCATGGCCAC
1 ATCTAACAGAGAGAGCAGCAAATATGCATACTCTAGTAGATCAGACAGAGACATGAACAC
* *
10872 ATCTAACAGAGAGAGCAGCAAATCTGCATACTCTAGTAGATCAGACAGAGAGATGAA
1 ATCTAACAGAGAGAGCAGCAAATATGCATACTCTAGTAGATCAGACAGAGACATGAA
10929 ACCTTCTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (60 bp):
ATCTAACAGAGAGAGCAGCAAATATGCATACTCTAGTAGATCAGACAGAGACATGAACAC
Found at i:11266 original size:42 final size:42
Alignment explanation
Indices: 11197--11538 Score: 402
Period size: 42 Copynumber: 8.0 Consensus size: 42
11187 TCCTTGGATA
* *
11197 TCCTGTAGGTTGGCGTAAAACCTTCGAAAAGGGGAGGTTAG-
1 TCCTGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
* * *
11238 TCCGTGCAAGGTGGCGTAAAATCTTCGAAAAGGAGAGGTTAGT
1 TCC-TGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
* * *
11281 TCTTGCAGGGATGGCGTAAAACCTTCAAAAAGGGAAGGTTAGT
1 TCCTGCAGGG-TGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
*
11324 TCCTGCGGGGTGGCGTGGTGTAAAACCTTCGAAAAGGGGAGGTTAGT
1 TCCTGCAGGGTGGC-----GTAAAACCTTCGAAAAGGGGAGGTTAGT
* *
11371 TCCTGC-TGGTGGCGT-AAACCTTCGAAAAGAGGAGGTTAGT
1 TCCTGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
* * *
11411 TCCTACGGAGGTGGTGTAAAAACCTTCGAAAAGGGGAGGTTAGT
1 TCCTGCAG-GGTGGCGT-AAAACCTTCGAAAAGGGGAGGTTAGT
* * *
11455 TCCTGCGGGGTGGCGTAAAACCTTCCAAAATGGGAGGTTAGT
1 TCCTGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
* * *
11497 TCCTGGAGGGTGGCGTAGAACCTTCCAAAAGGGGAGGTTAGT
1 TCCTGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
11539 CAAAAGCTGC
Statistics
Matches: 260, Mismatches: 29, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
40 29 0.11
41 5 0.02
42 112 0.43
43 45 0.17
44 31 0.12
46 6 0.02
47 32 0.12
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (42 bp):
TCCTGCAGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGT
Found at i:11901 original size:55 final size:55
Alignment explanation
Indices: 11827--11936 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
11817 GTTGTGTTGC
* *
11827 CGCGGATAATGAGTGAGAAGAGGTCATTCCATTACCGCAGGTAAATTGTGATGAA
1 CGCGGATAATGAGTAAGAAGAGGTCATTACATTACCGCAGGTAAATTGTGATGAA
11882 CGCGGATAATGAGTAAGAAGAGGTCATTACATTACCGCAGGTAAATTGTGATGAA
1 CGCGGATAATGAGTAAGAAGAGGTCATTACATTACCGCAGGTAAATTGTGATGAA
11937 ATCAAATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.24
Consensus pattern (55 bp):
CGCGGATAATGAGTAAGAAGAGGTCATTACATTACCGCAGGTAAATTGTGATGAA
Found at i:12065 original size:79 final size:79
Alignment explanation
Indices: 11929--12170 Score: 376
Period size: 79 Copynumber: 3.1 Consensus size: 79
11919 CAGGTAAATT
* *
11929 GTGATGAAATCAAATTGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTTCGAGTCTTCACGCGCC
1 GTGATGAAATCAGATTGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTTCGAATCTTCACGCGCC
11994 AACTTGAGGAGGGA
66 AACTTGAGGAGGGA
* *
12008 GTGATGAAATCAGATCGGTTTGAACCATTAGTGTTCAAGTTGGGCGTTTCGAATCTTCACGCGCC
1 GTGATGAAATCAGATTGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTTCGAATCTTCACGCGCC
12073 AACTTGAGGAGGGA
66 AACTTGAGGAGGGA
** * * * *
12087 GTGATGAAATCAGATTAATTTGAATGATTAGTGTTCAAGTTGGGCGTTGCGAATCTTCACCCTCC
1 GTGATGAAATCAGATTGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTTCGAATCTTCACGCGCC
* *
12152 AACTTGAGGAAGGT
66 AACTTGAGGAGGGA
12166 GTGAT
1 GTGAT
12171 CAATCAAGCA
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 149 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (79 bp):
GTGATGAAATCAGATTGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTTCGAATCTTCACGCGCC
AACTTGAGGAGGGA
Found at i:12260 original size:59 final size:57
Alignment explanation
Indices: 12169--12341 Score: 253
Period size: 59 Copynumber: 3.0 Consensus size: 57
12159 GGAAGGTGTG
12169 ATCAATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCTTCATTACAGCGGGATCCAA
1 ATCAATCAAGCAGGTCTACCGCAGGATCATGATTGAAGC-T-ATTACAGCGGGATCCAA
*
12228 ATCAATCAAGCAGGTCTACCACAGGATCATGATTGAAG--ATTGA-AGCGGGATCCAA
1 ATCAATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCTATT-ACAGCGGGATCCAA
* *
12283 ATCAATCAAGCAGGTCTATCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAA
1 ATCAATCAAGCAGGTCTACCGCAGGATCATGATTGAAGC-T-ATTACAGCGGGATCCAA
12342 GATTGAAGTC
Statistics
Matches: 104, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
55 50 0.48
56 1 0.01
58 1 0.01
59 52 0.50
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (57 bp):
ATCAATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCTATTACAGCGGGATCCAA
Found at i:16920 original size:11 final size:11
Alignment explanation
Indices: 16904--16945 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
16894 TCGTCTACTT
16904 GTGCGTAGCAA
1 GTGCGTAGCAA
16915 GTGCGTAGCAA
1 GTGCGTAGCAA
16926 GTGCGTAGCAA
1 GTGCGTAGCAA
*
16937 GTTCGTAGC
1 GTGCGTAGC
16946 TAAATGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (11 bp):
GTGCGTAGCAA
Found at i:17115 original size:27 final size:28
Alignment explanation
Indices: 17058--17115 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
17048 ATTTAATTAC
* *
17058 AAAAGAAATTACAATATTCATATTAATTAT
1 AAAAGAAATTAC-A-ATTCATATGAAATAT
17088 AAAAGAAATTAC-ATTCATATGAAATAT
1 AAAAGAAATTACAATTCATATGAAATAT
17115 A
1 A
17116 CGATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 14 0.54
30 12 0.46
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAAGAAATTACAATTCATATGAAATAT
Found at i:22837 original size:15 final size:15
Alignment explanation
Indices: 22813--22846 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
22803 CATAGATGAT
22813 ATATTCTAAATAGAA
1 ATATTCTAAATAGAA
*
22828 ATATTTTAAATAGAA
1 ATATTCTAAATAGAA
22843 ATAT
1 ATAT
22847 ATATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (15 bp):
ATATTCTAAATAGAA
Found at i:22848 original size:17 final size:16
Alignment explanation
Indices: 22811--22848 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
22801 CGCATAGATG
22811 ATATATTCTAAATAGA
1 ATATATTCTAAATAGA
*
22827 A-ATATTTTAAATAGAA
1 ATATATTCTAAATAG-A
22843 ATATAT
1 ATATAT
22849 ATATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 3 0.16
17 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (16 bp):
ATATATTCTAAATAGA
Done.