Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012127.1 Corchorus capsularis cultivar CVL-1 contig12148, 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: 42232
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3031 original size:20 final size:20
Alignment explanation
Indices: 2992--3031 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2982 CATCATTCGA
*
2992 ATTACATCATTCAAATTTTG
1 ATTACATCACTCAAATTTTG
3012 ATTACATCACT-AAATATTTG
1 ATTACATCACTCAAAT-TTTG
3032 TCTGTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTACATCACTCAAATTTTG
Found at i:6894 original size:97 final size:97
Alignment explanation
Indices: 6727--7008 Score: 465
Period size: 97 Copynumber: 2.9 Consensus size: 97
6717 GTGCCTTCCG
* * * * *
6727 TCCGGGAAGGGCGTTTTAAGAAAAAGCAAGTAAAAATCAGTTCATTCCATCCGGGAAGAGCACTT
1 TCCGGGAAGGGCGTTTTAGGAAAAA-CAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTT
* *
6792 TGGGAAAATGCAAATAGAGATTAGTACCGTCCA
65 TGGGAAAATGCAAGTAAAGATTAGTACCGTCCA
6825 TCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTT
1 TCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTT
*
6890 GGGAATATGCAAGTAAAGATTAGTACCGTCCA
66 GGGAAAATGCAAGTAAAGATTAGTACCGTCCA
* *
6922 TCCGGGAATGGCGTTTTAGGAAAACCAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTT
1 TCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTT
6987 GGGAAAATGCAAGTAAAGATTA
66 GGGAAAATGCAAGTAAAGATTA
7009 AAAATTGAGA
Statistics
Matches: 173, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
97 149 0.86
98 24 0.14
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (97 bp):
TCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTT
GGGAAAATGCAAGTAAAGATTAGTACCGTCCA
Found at i:6992 original size:48 final size:48
Alignment explanation
Indices: 6636--7003 Score: 281
Period size: 49 Copynumber: 7.6 Consensus size: 48
6626 TGCGTCCAGA
* * * * *
6636 AAGGGC-CTTTTAAGAATAAGCGAGT-AAAATTAGCGCCTTCCGTCCGGG
1 AAGGGCAC-TTTAGGAA-AAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
** * * * ** *
6684 AAGGGCGTTTTAGAAAAAAACGAGTAAAAATTGGTGCCTTCCGTCCGGG
1 AAGGGCACTTTAG-GAAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
** * * *
6733 AAGGGCGTTTTAAGAAAAAGCAAGTAAAAATCAGTTCATTCCATCCGGG
1 AAGGGCACTTT-AGGAAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
* * * * * * * *
6782 AAGAGCACTTTGGGAAAATGCAAATAGAGATTAGTACCGTCCATCCGGG
1 AAGGGCACTTTAGGAAAA-GCAAGTAAAAATCAGTGCCTTCCATCCGGG
** * *
6831 AAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGTGCCTTCCATCCGGG
1 AAGGGCACTTTAGGAAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
* * * * * *
6879 AAGGGCACTTTGGGAATATGCAAGTAAAGATTAGTACCGTCCATCCGGG
1 AAGGGCACTTTAGGAA-AAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
* ** * *
6928 AATGGCGTTTTAGGAAAACCAGGTAAAAATCAGTGCCTTCCATCCGGG
1 AAGGGCACTTTAGGAAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
*
6976 AAGGGCACTTTGGGAAAATGCAAGTAAA
1 AAGGGCACTTTAGGAAAA-GCAAGTAAA
7004 GATTAAAAAT
Statistics
Matches: 249, Mismatches: 64, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
48 96 0.39
49 151 0.61
50 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (48 bp):
AAGGGCACTTTAGGAAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGG
Found at i:9791 original size:20 final size:20
Alignment explanation
Indices: 9766--9814 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
9756 CAAAGCTACT
9766 ACCCAAAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
9786 ACCCAAAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
9806 AGCCCAAAA
1 A-CCCAAAA
9815 TGATGGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.47, C:0.31, G:0.10, T:0.12
Consensus pattern (20 bp):
ACCCAAAAGCCCAAGTTTAA
Found at i:10726 original size:59 final size:60
Alignment explanation
Indices: 10578--10749 Score: 274
Period size: 59 Copynumber: 2.9 Consensus size: 60
10568 TGATGGAATG
* *
10578 AATCAAGTAGGTCTACCGCAGGATCATGATGGAAGCATGATTACAGCGGGATCCAAAATC
1 AATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCAAAATC
* * *
10638 AATCAAGCAGGTCTACCGCAGGATTATGATTGAAGCATGATTACAACGGGATTC-AAATC
1 AATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCAAAATC
* *
10697 AATCAAGCAGGTCTACCGCAAGATCATGATTGAAGCATGATTATAGCGGGATC
1 AATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATC
10750 TAAGATTGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 53 0.52
60 49 0.48
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (60 bp):
AATCAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCAAAATC
Found at i:11244 original size:42 final size:41
Alignment explanation
Indices: 11185--11427 Score: 285
Period size: 42 Copynumber: 5.7 Consensus size: 41
11175 TCCCGCTGGT
11185 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAG-TCCTTGCGGAG
1 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAGTTCC-TGCGG-G
11227 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAG-TCCTTGCAGGG
1 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAGTTCC-TGC-GGG
* *
11269 TGGCGTAAAAACCTTCGAGAAGGGGAGGTTAGTTCCTGCGCAGGG
1 TGGC-TTAAAACCTTCGAAAAGGGGAGGTTAGTTCCT--GC-GGG
* * *
11314 TGGCGTAGAACCTTCGAAAAGGGGAGGTTAGTTCCTGTAGGG
1 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTG-CGGG
* * *
11356 TGACGTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTACAGGG
1 TGGCTTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGC-GGG
*
11398 TGG-TGTAGAACCTTCGAAAAGGGGAGGTTA
1 TGGCT-TAAAACCTTCGAAAAGGGGAGGTTA
11428 ATCAAAAGCT
Statistics
Matches: 179, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
42 110 0.61
43 28 0.16
44 31 0.17
45 10 0.06
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.23
Consensus pattern (41 bp):
TGGCTTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGG
Found at i:12108 original size:79 final size:79
Alignment explanation
Indices: 11977--12213 Score: 386
Period size: 79 Copynumber: 3.0 Consensus size: 79
11967 ACAAGGATTG
* *
11977 ATTTGAATCTTTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCACCAACTTGAGGAGGGAGTG
1 ATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCTCCAACTTGAGGAGGGAGTG
12042 ATGAAATCAGATCA
66 ATGAAATCAGATCA
* *
12056 ATTTGAATCATTAGTGTTCAAGTTGGACGTTGCAAATCTTCACGCTCCAACTTGAAGAGGGAGTG
1 ATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCTCCAACTTGAGGAGGGAGTG
12121 ATGAAATCAGATCA
66 ATGAAATCAGATCA
* * * *
12135 ATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCGAATCTTCATGCTCCAACTTGAGGAAGGTGTG
1 ATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCTCCAACTTGAGGAGGGAGTG
*
12200 ATGGAATCA-ATCA
66 ATGAAATCAGATCA
12213 A
1 A
12214 GCAGGTCTAC
Statistics
Matches: 147, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 5 0.03
79 142 0.97
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (79 bp):
ATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCTCCAACTTGAGGAGGGAGTG
ATGAAATCAGATCA
Found at i:12277 original size:67 final size:60
Alignment explanation
Indices: 12204--12389 Score: 214
Period size: 59 Copynumber: 3.0 Consensus size: 60
12194 GGTGTGATGG
12204 AATCAATCAAGCAGGTCTACCGTAGCCCGTAGGATCATGATGGAAGCATGATTACAGCGGGATCC
1 AATCAATCAAGCAGGTCTACCG-A---C--AGGATCATGATGGAAGCATGATTACAGCGGGATCC
12269 AA
60 -A
* * * *
12271 AATCAATCAAGCAGGTCTACC-ACAGGATCATGATTGAAGCATGATTATAGTGGGATTCA
1 AATCAATCAAGCAGGTCTACCGACAGGATCATGATGGAAGCATGATTACAGCGGGATCCA
* * * * *
12330 AATCAATCAAGCAAGTCTACCG-CAAGATCATGATTGAAGCATGATTATAGTGGGATCCA
1 AATCAATCAAGCAGGTCTACCGACAGGATCATGATGGAAGCATGATTACAGCGGGATCCA
12389 A
1 A
12390 GATTGAAGTC
Statistics
Matches: 111, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
59 57 0.51
60 31 0.28
62 1 0.01
65 1 0.01
67 21 0.19
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (60 bp):
AATCAATCAAGCAGGTCTACCGACAGGATCATGATGGAAGCATGATTACAGCGGGATCCA
Found at i:12361 original size:59 final size:60
Alignment explanation
Indices: 12236--12389 Score: 238
Period size: 59 Copynumber: 2.6 Consensus size: 60
12226 TAGCCCGTAG
* * * * *
12236 GATCATGATGGAAGCATGATTACAGCGGGATCCAAAATCAATCAAGCAGGTCTACCACAG
1 GATCATGATTGAAGCATGATTATAGTGGGATCCAAAATCAATCAAGCAAGTCTACCACAA
* *
12296 GATCATGATTGAAGCATGATTATAGTGGGATTC-AAATCAATCAAGCAAGTCTACCGCAA
1 GATCATGATTGAAGCATGATTATAGTGGGATCCAAAATCAATCAAGCAAGTCTACCACAA
12355 GATCATGATTGAAGCATGATTATAGTGGGATCCAA
1 GATCATGATTGAAGCATGATTATAGTGGGATCCAA
12390 GATTGAAGTC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 55 0.65
60 30 0.35
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (60 bp):
GATCATGATTGAAGCATGATTATAGTGGGATCCAAAATCAATCAAGCAAGTCTACCACAA
Found at i:13107 original size:26 final size:25
Alignment explanation
Indices: 13065--13112 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
13055 TAATACATCT
13065 TATTAGAAAAACTAAAAATTGATCC
1 TATTAGAAAAACTAAAAATTGATCC
13090 TATTAGAAAAACTAAAAATTGAT
1 TATTAGAAAAACTAAAAATTGAT
13113 GAGGTGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (25 bp):
TATTAGAAAAACTAAAAATTGATCC
Found at i:14155 original size:2 final size:2
Alignment explanation
Indices: 14148--14178 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14138 CAGTTCCTTT
14148 TA TA TA TA 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 T
14179 TCAAATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15074 original size:2 final size:2
Alignment explanation
Indices: 15063--15095 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15053 AATTTTATTG
15063 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15096 GTTGTCAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:16300 original size:28 final size:28
Alignment explanation
Indices: 16246--16303 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
16236 ATGATTCATG
**
16246 AAAGTCGTAGATCATGGAATAACCTTTT
1 AAAGTCGTAGATCATCAAATAACCTTTT
* * *
16274 AAAGTTGTAGATCATCAAATTATCTTTT
1 AAAGTCGTAGATCATCAAATAACCTTTT
16302 AA
1 AA
16304 TAAACACTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (28 bp):
AAAGTCGTAGATCATCAAATAACCTTTT
Found at i:17110 original size:434 final size:432
Alignment explanation
Indices: 16274--17218 Score: 1159
Period size: 434 Copynumber: 2.2 Consensus size: 432
16264 ATAACCTTTT
* * * *
16274 AAAGTTGTAGATCATCAAATTATCTTTTAATAAACACTTGAATTATCTTAATCAGACAAATAGAA
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACACTTGAATCATCTTAATCAGACAAACAGAA
* * * * * *
16339 AAGAATAATAAAGTTGAACCTTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAA
66 AAAAAAAATAAAGCTGAAACGTTAAA-C-ATTAAGATAGAATTAGTAAAAGACTAAGTAGTATAA
* * * * * * *
16404 AATAGAAAAATGTGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGGTGGAGATC
129 AATAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATATTTGTTGATGGAAATC
* *
16469 TTGAAACATAAAATTTCTTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGACC
194 TTGAAACATAAAATTTCGTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGAACC
* * * *
16534 CTTCATGAAAGTCATAGATCACGCAATAACCTTTTAACCGAAACTTGAATAATTTTAATCGGACA
259 CTTCATGAAAGTCATAGATCACGCAATAAACTTTTAAACGAAACGTGAATAACTTTAATCGGACA
*** ** * * * * ** * *
16599 TGTAGATTAAAAATTATTTGGTATTAAATAGACTGTTAATCGAAACCACCAAATTTTAAAAATAT
324 CACAGACCAAAAATAATATGATATTAAATAGACCGGCAATCAAAACCACCAAATTTCAAAAATAT
* * *
16664 TTTTTAGAATTGAAACATAAAAATTGACTTTTGACTTCTTCATG
389 TTTTTAGAATTGAAACATAAAAATTGACTTTTGAATCCTTCACG
* * * * *
16708 GAAGTTGTAGATCATGAAATTATCTTTTAATAGACATTTGAATCACCTTAATCCGACAAGCAGAA
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACACTTGAATCATCTTAATCAGACAAACAGAA
*
16773 AAAAAAAATAAAGCTGAAACGTT-AA-ATTAAGATAGAATTAGTAAAAGATTAAGTAGTATGAAG
66 AAAAAAAATAAAGCTGAAACGTTAAACATTAAGATAGAATTAGTAAAAGACTAAGTAGTAT-AA-
* *
16836 TAA-AAAAAATATATGATGATCATTCGATAAATAATCCAAATGAGAAAATATTTGTTGATGGAAA
129 -AATAAAAAA-ATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATATTTGTTGATGGAAA
* * *
16900 TTTTGAAACATGAAAATTAT-GTTTTGAGCCCTTTATGAAACTCGTATATCAAATTTAGCTTTCG
192 TCTTGAAACAT-AAAATT-TCGTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCG
* ** *
16964 AATCCTTCATGAAAGTGGTAGATCATGCAATAAACTTTTAAACGATAA-GTGAATAACTTTAATC
255 AACCCTTCATGAAAGTCATAGATCACGCAATAAACTTTTAAACGA-AACGTGAATAACTTTAATC
*
17028 GGACACACAGACCAAAAATAATATGATATTAAATAGACCGGCAATCAAAACCACTAAATTTCAGA
319 GGACACACAGACCAAAAATAATATGATATTAAATAGACCGGCAATCAAAACCACCAAATTTCA-A
* * *
17093 AGCA-ATTTTTT-GAATTGAAACATTAAAATTGCCTTTTGAATCCTTCACG
383 A-AATATTTTTTAGAATTGAAACATAAAAATTGACTTTTGAATCCTTCACG
* * * * *
17142 AAAGTTGTAGATTATGAGATTACCTTTTAATAGACACATGAATCATCTTAATCGGACAAACAG-A
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACACTTGAATCATCTTAATCAGACAAACAGAA
*
17206 ACAAAAAATAAAG
66 AAAAAAAATAAAG
17219 AAAATAAAGC
Statistics
Matches: 434, Mismatches: 68, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
430 32 0.07
431 2 0.00
432 5 0.01
433 73 0.17
434 309 0.71
435 12 0.03
436 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (432 bp):
AAAGTTGTAGATCATGAAATTATCTTTTAATAGACACTTGAATCATCTTAATCAGACAAACAGAA
AAAAAAAATAAAGCTGAAACGTTAAACATTAAGATAGAATTAGTAAAAGACTAAGTAGTATAAAA
TAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATATTTGTTGATGGAAATCTT
GAAACATAAAATTTCGTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGAACCCT
TCATGAAAGTCATAGATCACGCAATAAACTTTTAAACGAAACGTGAATAACTTTAATCGGACACA
CAGACCAAAAATAATATGATATTAAATAGACCGGCAATCAAAACCACCAAATTTCAAAAATATTT
TTTAGAATTGAAACATAAAAATTGACTTTTGAATCCTTCACG
Found at i:17666 original size:2 final size:2
Alignment explanation
Indices: 17659--17686 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17649 TTTTTGGTAC
17659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17687 GCCGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24750 original size:193 final size:193
Alignment explanation
Indices: 24421--25049 Score: 1258
Period size: 193 Copynumber: 3.3 Consensus size: 193
24411 GCCGAATGCA
24421 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
1 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
24486 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
66 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
24551 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
131 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
24614 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
1 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
24679 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
66 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
24744 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
131 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
24807 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
1 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
24872 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
66 AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
24937 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
131 ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
25000 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGT
1 CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGT
25050 GTCAGAAGGG
Statistics
Matches: 436, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 436 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (193 bp):
CCAACTAGCTAAATTTCTAAGTTAAATCATGCTGATGGCCACATCTGAGTTTATCAACTCCTTTC
AATGGTTTATTACCTAGTCTAACCCTTTCAGAGATGATGGTGTATAAACTCACTTCAAAAATTAT
ATCAGATTTTATTCTTCGTTTATTTTCTTGACCATCTCCACTCAACATAAATTTATTCATCTT
Found at i:30457 original size:10 final size:10
Alignment explanation
Indices: 30442--30467 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30432 TGATCTCAAT
30442 GCTCAAGCAA
1 GCTCAAGCAA
30452 GCTCAAGCAA
1 GCTCAAGCAA
30462 GCTCAA
1 GCTCAA
30468 TCTCTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (10 bp):
GCTCAAGCAA
Found at i:39133 original size:1 final size:1
Alignment explanation
Indices: 39127--39152 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
39117 TCATGATGTT
39127 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
39153 TGACCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41769 original size:14 final size:16
Alignment explanation
Indices: 41737--41777 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
41727 ATAAATAATT
*
41737 AAAAAATAATGTAGCA
1 AAAAAATAATGTAGAA
41753 AAAAAATAAT-TA-AA
1 AAAAAATAATGTAGAA
*
41767 AAATAATAATG
1 AAAAAATAATG
41778 GAATTATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 10 0.45
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (16 bp):
AAAAAATAATGTAGAA
Found at i:42202 original size:2 final size:2
Alignment explanation
Indices: 42195--42232 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42185 TTTATGTTAG
42195 TA TA TA TA 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 TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.