Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022597.1 Corchorus olitorius cultivar O-4 contig22630, 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: 43980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:56 original size:22 final size:22
Alignment explanation
Indices: 28--91 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
18 TCTTATGAGG
28 TTATCAAAATTATATAGGGTCA
1 TTATCAAAATTATATAGGGTCA
* * * **
50 TTATCAAAATTACATATGATGG
1 TTATCAAAATTATATAGGGTCA
72 TTATCAAAATTTATATAGGG
1 TTATCAAAA-TTATATAGGG
92 CCCTCAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTATATAGGGTCA
Found at i:121 original size:21 final size:22
Alignment explanation
Indices: 50--321 Score: 95
Period size: 22 Copynumber: 12.6 Consensus size: 22
40 TATAGGGTCA
* *
50 TTATCAAAATTACATAT-GATGG
1 TTATCAAAATTTCAAATAGA-GG
*
72 TTATCAAAATTT-ATATAG-GG
1 TTATCAAAATTTCAAATAGAGG
***
92 CCCTCAAAATTTC-AATCA-AGG
1 TTATCAAAATTTCAAAT-AGAGG
* *
113 TTATCAAAATTACAAATAGTGG
1 TTATCAAAATTTCAAATAGAGG
* * *
135 TTATCAAAATTTCGAATGGTGG
1 TTATCAAAATTTCAAATAGAGG
* * *
157 ATT-TCAAATTTTCAAA-AAATAG
1 -TTATCAAAATTTCAAATAGA-GG
179 TTATCAAAATTTC--ATAGGACGG
1 TTATCAAAATTTCAAATA-GA-GG
* * * *
201 CTGTCAAAATTTC-AATCGAAG
1 TTATCAAAATTTCAAATAGAGG
* * *
222 TTATTAAAATTACAAAGA-ATGG
1 TTATCAAAATTTCAAATAGA-GG
* * * *
244 TTCTCATAA-TT-ATATAGGGCGG
1 TTATCAAAATTTCAAATA--GAGG
* *
266 TTGTCAAAA-TTCCAATAGAGG
1 TTATCAAAATTTCAAATAGAGG
* * *
287 TTATCAAGATTACAAATAGTGG
1 TTATCAAAATTTCAAATAGAGG
309 TTATCAAAATTTC
1 TTATCAAAATTTC
322 GAATGGTGAT
Statistics
Matches: 178, Mismatches: 53, Indels: 38
0.66 0.20 0.14
Matches are distributed among these distances:
20 17 0.10
21 42 0.24
22 112 0.63
23 7 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCAAATAGAGG
Found at i:123 original size:41 final size:44
Alignment explanation
Indices: 25--123 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 44
15 GTTTCTTATG
* *
25 AGGTTATCAAAA-TTATATAGGGTCATTATCAAAATTACATATGA
1 AGGTTATCAAAATTTATATAGGGTCA-CATCAAAATTACATATCA
* * *
69 TGGTTATCAAAATTTATATAGGG-C-CCTCAAAATTTCA-ATCA
1 AGGTTATCAAAATTTATATAGGGTCACATCAAAATTACATATCA
110 AGGTTATCAAAATT
1 AGGTTATCAAAATT
124 ACAAATAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 16 0.33
42 10 0.21
44 12 0.25
45 10 0.21
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (44 bp):
AGGTTATCAAAATTTATATAGGGTCACATCAAAATTACATATCA
Found at i:310 original size:65 final size:65
Alignment explanation
Indices: 160--319 Score: 169
Period size: 65 Copynumber: 2.5 Consensus size: 65
150 ATGGTGGATT
* * * * * *
160 TCAAATTTTCAAAAAATAGTTATCAAAATT-TCATAGGACGGCTGTCAAAATTTCAATCGAAGTT
1 TCAAAATTACAAAGAATGGTTATCAAAATTAT-ATAGGACGGCTGTCAAAATTCCAATAGAAGTT
224 A
65 A
* * * * * *
225 TTAAAATTACAAAGAATGGTTCTCATAATTATATAGGGCGGTTGTCAAAATTCCAATAGAGGTTA
1 TCAAAATTACAAAGAATGGTTATCAAAATTATATAGGACGGCTGTCAAAATTCCAATAGAAGTTA
* * *
290 TCAAGATTACAAATAGTGGTTATCAAAATT
1 TCAAAATTACAAAGAATGGTTATCAAAATT
320 TCGAATGGTG
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
65 75 0.99
66 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (65 bp):
TCAAAATTACAAAGAATGGTTATCAAAATTATATAGGACGGCTGTCAAAATTCCAATAGAAGTTA
Found at i:700 original size:2 final size:2
Alignment explanation
Indices: 693--722 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
683 AAAATATTAG
693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
723 GTTTAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13348 original size:6 final size:6
Alignment explanation
Indices: 13337--13361 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13327 TAAAAAGCAG
13337 AGGCTA AGGCTA AGGCTA AGGCTA A
1 AGGCTA AGGCTA AGGCTA AGGCTA A
13362 CAAATATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AGGCTA
Found at i:14133 original size:1 final size:1
Alignment explanation
Indices: 14127--14156 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
14117 AATCTAACTT
*
14127 AAAAAAAAACAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14157 CCCTTAGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15369 original size:13 final size:13
Alignment explanation
Indices: 15347--15386 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
15337 CAGAGAATAT
15347 TATCAACAGAAGA
1 TATCAACAGAAGA
*
15360 TATCACCAGAAGA
1 TATCAACAGAAGA
* *
15373 TTTCAACTGAAGA
1 TATCAACAGAAGA
15386 T
1 T
15387 TATATGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:15399 original size:11 final size:11
Alignment explanation
Indices: 15380--15409 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15370 AGATTTCAAC
15380 TGAAGATTATA
1 TGAAGATTATA
*
15391 TGGAGATTATA
1 TGAAGATTATA
15402 TGAAGATT
1 TGAAGATT
15410 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (11 bp):
TGAAGATTATA
Found at i:20968 original size:15 final size:16
Alignment explanation
Indices: 20950--20979 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20940 CTTTTTTGTT
20950 AAAAAATAT-TTTTTA
1 AAAAAATATGTTTTTA
20965 AAAAAATATGTTTTT
1 AAAAAATATGTTTTT
20980 TGAAGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAAAATATGTTTTTA
Found at i:22759 original size:51 final size:51
Alignment explanation
Indices: 22699--22805 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
22689 TTCCAGATTG
22699 TTGTAAGTAGATGAATTTTGTTCTTTGAGATTTGCATGGGTTAAATAGGGC
1 TTGTAAGTAGATGAATTTTGTTCTTTGAGATTTGCATGGGTTAAATAGGGC
22750 TTGTAAGTAGATGAATTTTGTTCTTTGAGATTTGCATGGGTTAAATAGGGC
1 TTGTAAGTAGATGAATTTTGTTCTTTGAGATTTGCATGGGTTAAATAGGGC
22801 TTGTA
1 TTGTA
22806 GCGTTTCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (51 bp):
TTGTAAGTAGATGAATTTTGTTCTTTGAGATTTGCATGGGTTAAATAGGGC
Found at i:23826 original size:15 final size:16
Alignment explanation
Indices: 23808--23837 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23798 GATTTTCCAA
23808 TCTTAAGTT-TTTATT
1 TCTTAAGTTGTTTATT
23823 TCTTAAGTTGTTTAT
1 TCTTAAGTTGTTTAT
23838 ATTGTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TCTTAAGTTGTTTATT
Found at i:24002 original size:40 final size:41
Alignment explanation
Indices: 23874--24002 Score: 188
Period size: 41 Copynumber: 3.2 Consensus size: 41
23864 AATAATATTG
* * *
23874 AAAATTACCTTTGACACCATAAGTTGTCATTTTTGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
23915 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
23956 AAAATTACCTTTGACACTAGAAG-TGCCACTCTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
*
23996 ATAATTA
1 AAAATTA
24003 ATGTTGCCCT
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 21 0.26
41 60 0.74
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:24098 original size:56 final size:56
Alignment explanation
Indices: 24031--24225 Score: 313
Period size: 56 Copynumber: 3.5 Consensus size: 56
24021 CACAGTTAAT
* *
24031 TTAT-TTTTGACACCAGAAGCTGTCATAATAAACATTACTTATTTACTACGGTAAA
1 TTATCTTTTGACACCGGAAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
*
24086 TTAT-TCTTTGACACCGGGAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
1 TTATCT-TTTGACACCGGAAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
*
24142 TTATCTTTTGACACTGGAAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
1 TTATCTTTTGACACCGGAAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
* *
24198 TCATCTTTTGACACCCGAAGTTGTCATA
1 TTATCTTTTGACACCGGAAGTTGTCATA
24226 GTATATTCTC
Statistics
Matches: 130, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
55 5 0.04
56 124 0.95
57 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (56 bp):
TTATCTTTTGACACCGGAAGTTGTCATAATAAACATTACTTATTTACTACGGTAAA
Found at i:24660 original size:101 final size:101
Alignment explanation
Indices: 24538--24740 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
24528 TATTCTCAAG
24538 TATAACATTGCGTAAAGCAAATGTTCACACTATATCTGGTCATATTAAGATTATAGATGGCTACG
1 TATAACATTGCGTAAAGCAAATGTTCACACTATATCTGGTCATATTAAGATTATAGATGGCTACG
24603 TGAATGCCACAATTATTTTGTCAAAATGATACTGAT
66 TGAATGCCACAATTATTTTGTCAAAATGATACTGAT
24639 TATAACATTGCGTAAAGCAAATGTTCACACTATATCTGGTCATATTAAGATTATAGATGGCTACG
1 TATAACATTGCGTAAAGCAAATGTTCACACTATATCTGGTCATATTAAGATTATAGATGGCTACG
24704 TGAATGCCACAATTATTTTGTCAAAATGATACTGAT
66 TGAATGCCACAATTATTTTGTCAAAATGATACTGAT
24740 T
1 T
24741 TGCGTCTTGA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (101 bp):
TATAACATTGCGTAAAGCAAATGTTCACACTATATCTGGTCATATTAAGATTATAGATGGCTACG
TGAATGCCACAATTATTTTGTCAAAATGATACTGAT
Found at i:25477 original size:137 final size:137
Alignment explanation
Indices: 25231--25505 Score: 523
Period size: 137 Copynumber: 2.0 Consensus size: 137
25221 TATAGATTAT
*
25231 GATAAGTGGCAATAACTTTTTGTATGAATAATGAGATGCATCTCCGCAAGGCCTTGCTAATAACA
1 GATAAGTGGCAATAACTTTTTGTATGAATAATGAGATGCATCCCCGCAAGGCCTTGCTAATAACA
*
25296 TTTGATGAAAAGTGAGATGCTAATTTATGCTAATGCGTAACAGTTATTGAAATAATCCTTAATTA
66 TTTGATGAAAAGTGAGATGCTAATTTACGCTAATGCGTAACAGTTATTGAAATAATCCTTAATTA
25361 ATGGGCC
131 ATGGGCC
*
25368 GATAAGTGGCAATAACTTTTTGTATGAATGATGAGATGCATCCCCGCAAGGCCTTGCTAATAACA
1 GATAAGTGGCAATAACTTTTTGTATGAATAATGAGATGCATCCCCGCAAGGCCTTGCTAATAACA
25433 TTTGATGAAAAGTGAGATGCTAATTTACGCTAATGCGTAACAGTTATTGAAATAATCCTTAATTA
66 TTTGATGAAAAGTGAGATGCTAATTTACGCTAATGCGTAACAGTTATTGAAATAATCCTTAATTA
25498 ATGGGCC
131 ATGGGCC
25505 G
1 G
25506 TTATAGAGGC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (137 bp):
GATAAGTGGCAATAACTTTTTGTATGAATAATGAGATGCATCCCCGCAAGGCCTTGCTAATAACA
TTTGATGAAAAGTGAGATGCTAATTTACGCTAATGCGTAACAGTTATTGAAATAATCCTTAATTA
ATGGGCC
Found at i:28992 original size:444 final size:441
Alignment explanation
Indices: 28122--29082 Score: 1343
Period size: 443 Copynumber: 2.2 Consensus size: 441
28112 CCCCTTCTAA
* * * *
28122 ATAAACAAATCATTTTTTTGTTGGTTTATCTATTAAATGATCCCTATACTTTTATGCTTTATGTT
1 ATAAACAAATCATTTTTTTGTTGG-TTATTTATTAAATGATCCTTAGACTTTTATGCTTTATGCT
* * * *
28187 ATTCAGTCCCTCACAATTTCTGGGTTGGACGACTAAACGTTTCGGCTTTAATTCTTTAATTTTTT
65 ATTTAATCCCTCACAATTTCTGGGTTGGACGACTAAACATTTCGACTTTAATTCTTTAATTTTTT
28252 TTGTTTTGCTTGTCCGATCAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAAC
130 TTGTTTTGCTTGTCCGATCAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAAC
* * *
28317 TTCCATGAAGGACTCAGAAGTCAATTTTAATATTTTGATTCTAAAAAATGCTTCTGAAATTTTGT
195 TTCCATGAAGGACTCAAAAGTCAATTTGAATATTTTGATTCTAAAAAATGCTTCTAAAATTTTGT
* *
28382 GGTCTCGATTGCCAGTCTGTCTAATATCATATAATTTTCGGTCCACTTGTCCGATTGAGGTTGTT
260 GGTCTCGATTGCCAGTCTATCTAATATCATATAATTTTCGGTCCACTTGTCCGATTGAGGTTATT
*
28447 CAAGTGTCGATTAAAAGGTTATTGTGTGATCTACGACTTTTATTAAGAGACTGAAAGCTGAAATT
325 CAAGTGTCGATTAAAAGGTTATTGTGTGATCTACGACTTTTATTAAGAGACTCAAAGCTGAAATT
* * *
28512 GATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTTGTCTCC
390 GATTAATAAGTTTCGTGGAGGGTTCAAGACGGAATTTTTATGTTTAGTCTCC
* *
28564 ATAAATAAATCATTTTTTTGTTGGATTATTTATTAAATGATCCTTAGACTTTTATGCTTTATACT
1 ATAAACAAATCATTTTTTTGTTGG-TTATTTATTAAATGATCCTTAGACTTTTATGCTTTATGCT
* *
28629 ATTTAATCCCTCACAATTTCTGGGTTGGACGACTGAACATTTCGACTTTAATTCTTTTATTTTTT
65 ATTTAATCCCTCACAATTTCTGGGTTGGACGACTAAACATTTCGACTTTAATTC-TTTAATTTTT
* * * *
28694 TTTGTTTTGCTTGTTCGATCAAGGTGACTT-AAGTGTCTATTAAATGGTAATTTCATGATCTGCA
129 TTTGTTTTGCTTGTCCGATCAAGCTGA-TTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACA
* * * * *
28758 ACTTCCATTAAGGA-TGCAAAAGTTAATTTGAATGTTTTGATT-TAAAAAAATGTTTTTAAAATT
193 ACTTCCATGAAGGACT-CAAAAGTCAATTTGAATATTTTGATTCT-AAAAAATGCTTCTAAAATT
* * * * * ** *
28821 TTGTGGTCTTGATTGCCGGTCTATTTGATATCGTATAAATTTTTTGTCCACTTGTCTGATTGAGG
256 TTGTGGTCTCGATTGCCAGTCTATCTAATATCATAT-AATTTTCGGTCCACTTGTCCGATTGAGG
* * * * *
28886 TTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGGCTTTTGTTAAGGGCCTCAAAGCTG
320 TTATTCAAGTGTCGATTAAAAGGTTATTGTGTGATCTACGACTTTTATTAAGAGACTCAAAGCTG
* * *
28951 AATTTGATTAATAAGTTTCGTTGAGGGTTCAAGACGGAATTTTTATGTTTAGTCTTC
385 AAATTGATTAATAAGTTTCGTGGAGGGTTCAAGACGGAATTTTTATGTTTAGTCTCC
* **** * * **
29008 ATAAACAAATAATTTTTTCCCAGGTTATTTATCAAATGATCCTTAGATTTTTATATTTTATGCTA
1 ATAAACAAATCATTTTTTTGTTGGTTATTTATTAAATGATCCTTAGACTTTTATGCTTTATGCTA
29073 TTTAATCCCT
66 TTTAATCCCT
29083 TATAATTATG
Statistics
Matches: 456, Mismatches: 58, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
442 109 0.24
443 193 0.42
444 154 0.34
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (441 bp):
ATAAACAAATCATTTTTTTGTTGGTTATTTATTAAATGATCCTTAGACTTTTATGCTTTATGCTA
TTTAATCCCTCACAATTTCTGGGTTGGACGACTAAACATTTCGACTTTAATTCTTTAATTTTTTT
TGTTTTGCTTGTCCGATCAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACT
TCCATGAAGGACTCAAAAGTCAATTTGAATATTTTGATTCTAAAAAATGCTTCTAAAATTTTGTG
GTCTCGATTGCCAGTCTATCTAATATCATATAATTTTCGGTCCACTTGTCCGATTGAGGTTATTC
AAGTGTCGATTAAAAGGTTATTGTGTGATCTACGACTTTTATTAAGAGACTCAAAGCTGAAATTG
ATTAATAAGTTTCGTGGAGGGTTCAAGACGGAATTTTTATGTTTAGTCTCC
Found at i:29770 original size:81 final size:81
Alignment explanation
Indices: 29635--29786 Score: 250
Period size: 81 Copynumber: 1.9 Consensus size: 81
29625 ATTGATGATG
**
29635 AAACACTTATTTTAATTGTATGAAGTTTGGGTACCCATTAGGCCTAACTAACAAACCCATTTCTT
1 AAACACTTATTTTAATTCCATGAAGTTTGGGTACCCATTAGGCCTAACTAACAAACCCATTTCTT
29700 TAATTTAGGAGGCCTT
66 TAATTTAGGAGGCCTT
* * * *
29716 AAACACTTATTTTAATTCCATGAAGTTTGGGTGCCCATTGGGCCTCACTAACAAATCCATTTCTT
1 AAACACTTATTTTAATTCCATGAAGTTTGGGTACCCATTAGGCCTAACTAACAAACCCATTTCTT
29781 TAATTT
66 TAATTT
29787 TTTGGGACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (81 bp):
AAACACTTATTTTAATTCCATGAAGTTTGGGTACCCATTAGGCCTAACTAACAAACCCATTTCTT
TAATTTAGGAGGCCTT
Found at i:32923 original size:18 final size:18
Alignment explanation
Indices: 32900--32934 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32890 ACTAAAAAAT
*
32900 GAGGTTGAGTGTTTGAAA
1 GAGGTTGAGTATTTGAAA
32918 GAGGTTGAGTATTTGAA
1 GAGGTTGAGTATTTGAA
32935 GTTGTTTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (18 bp):
GAGGTTGAGTATTTGAAA
Found at i:41607 original size:21 final size:21
Alignment explanation
Indices: 41583--41629 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
41573 GATCAAAATT
41583 CAAACTTAAATAAGTTCCGAC
1 CAAACTTAAATAAGTTCCGAC
*
41604 CAAAATTTAAATAAGTTCCGAC
1 C-AAACTTAAATAAGTTCCGAC
41626 CAAA
1 CAAA
41630 AGACAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (21 bp):
CAAACTTAAATAAGTTCCGAC
Found at i:41613 original size:22 final size:22
Alignment explanation
Indices: 41588--41630 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41578 AAATTCAAAC
41588 TTAAATAAGTTCCGACCAAAAT
1 TTAAATAAGTTCCGACCAAAAT
41610 TTAAATAAGTTCCGACCAAAA
1 TTAAATAAGTTCCGACCAAAA
41631 GACAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.26
Consensus pattern (22 bp):
TTAAATAAGTTCCGACCAAAAT
Found at i:41646 original size:29 final size:29
Alignment explanation
Indices: 41604--41661 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41594 AAGTTCCGAC
41604 CAAAATTTAAATAAGTTCCGACCAAAAGA
1 CAAAATTTAAATAAGTTCCGACCAAAAGA
*
41633 CAAAATTTAAATAATTTCCGACCAAAAGA
1 CAAAATTTAAATAAGTTCCGACCAAAAGA
41662 GATCTTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (29 bp):
CAAAATTTAAATAAGTTCCGACCAAAAGA
Found at i:43730 original size:19 final size:18
Alignment explanation
Indices: 43697--43732 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43687 TTGAAATTAT
43697 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
43715 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
43733 TAAGTCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.