Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007126.1 Corchorus capsularis cultivar CVL-1 contig07147, 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: 34047
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--30 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 T
2 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35 original size:2 final size:2
Alignment explanation
Indices: 30--57 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20 TCTCTCTCTC
30 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
58 AGTGAAAGCA
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):
TA
Found at i:2547 original size:16 final size:18
Alignment explanation
Indices: 2526--2560 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2516 AAAATCATAA
2526 TCAATTAAT-AT-ATTAT
1 TCAATTAATCATAATTAT
2542 TCAATTAATCATAATTAT
1 TCAATTAATCATAATTAT
2560 T
1 T
2561 ATATTCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TCAATTAATCATAATTAT
Found at i:3694 original size:437 final size:440
Alignment explanation
Indices: 2904--3747 Score: 1139
Period size: 437 Copynumber: 1.9 Consensus size: 440
2894 TTTTGAATAA
* * **
2904 TCCATGAAACTCATTAATCAAATTCAACTTTCAAGTCCTTAGTGAAAGTCATAGATCACACAATA
1 TCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTTAACGAAAGTCATAGATCACACAATA
* * * *
2969 ACCTTTCAACCGACACTTGAAGAACCTCAATCGGACATGTGGACCGAAAATTACACGATATTAAA
66 ACCTTTCAACCGACACTTAAACAACCTCAATCGGACAAGTGGACCGAAAATTACACAATATTAAA
* **
3034 TAGACCAAAATAGAAAGCACAAAATTTCGAAAACATTTTTTTAGAATCAAAACATCAAAATTAGT
131 TAGACCAAAATAGAAACCACAAAATTTCGAAAACATTTTTTTAGAATCAAAACATCAAAATTAAC
* * * *
3099 TTTTGAGTCTTTAATGAAAGTTGTAAATCATTAAATTACCTTTCAATAGACTCTTGAATCACCTT
196 TTTTGAGTCCTTAACGAAAGATGTAAATCATGAAATTACCTTTCAATAGACTCTTGAATCACCTT
* * * * * * *
3164 GATCCGACAAATAGAGCAAAAAATAAAAGAATTAAAGCCAAAACATTAAATCGTCTAACCCAGAA
261 CATCCGACAAACAAAACAAAAAATAAAAGAATTAAAGCCAAAACATTAAATCATCCAACCCAAAA
* * * * *
3229 TTTGTGAGGGATTAAATAGCATAAAGCATAAAAGTAT-GAGGACCATTTAATAAATAATCC-A-A
326 ATTGTGAGGGACTAAATAGCAAAAAGCATAAAAGTATAG-GGACCACTTAATAAATAAACCAACA
3291 AAAAAAT-ATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCAAACCC
390 AAAAAATGATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCAAACCC
* *
3341 TCCACGAAACTCATTAATCAAATTCAGCTTTC-AGCCCCTTAACGAAAGTCGTAGATCACACAAT
1 TCCACGAAACTCATTAATCAAATTCAACTTTCAAG-CCCTTAACGAAAGTCATAGATCACACAAT
* * * * *
3405 AATCTTTTAACCGACACTTAAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAG
65 AACCTTTCAACCGACACTTAAACAACCTCAATCGGACAAGTGGACCGAAAATTACACAATATTAA
* * * * *
3470 ATAGACCGACAATCGAGACCACAAAATTTC-ATAAGCA-TTTTTTAGAA-CTAAAACATTAAAAT
130 ATAGACC-AAAATAGAAACCACAAAATTTCGA-AAACATTTTTTTAGAATC-AAAACATCAAAAT
* * *
3532 TAACTTTTGAGTCCTTCACGAAAGATGTAGATCATGAAATTACCTTTTAATAGACAT-TTGAATC
192 TAACTTTTGAGTCCTTAACGAAAGATGTAAATCATGAAATTACCTTTCAATAGAC-TCTTGAATC
* ** * *
3596 ACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCTGAAACGTTCAATCATCCAACC
256 ACCTTCATCCGACAAACAAAACAAAAAATAAAAGAATTAAAGCCAAAACATTAAATCATCCAACC
*
3661 CAAAAATTGTGAGGGACTAAATAGCAAAAAGCATAAAAGTATAGGGACCACTTGATAAATAAACC
321 CAAAAATTGTGAGGGACTAAATAGCAAAAAGCATAAAAGTATAGGGACCACTTAATAAATAAACC
3726 AACAAAAAAATGATTTGTTTAT
386 AACAAAAAAATGATTTGTTTAT
3748 TATAAGTGGG
Statistics
Matches: 350, Mismatches: 48, Indels: 15
0.85 0.12 0.04
Matches are distributed among these distances:
436 3 0.01
437 304 0.87
438 25 0.07
439 8 0.02
440 10 0.03
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (440 bp):
TCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTTAACGAAAGTCATAGATCACACAATA
ACCTTTCAACCGACACTTAAACAACCTCAATCGGACAAGTGGACCGAAAATTACACAATATTAAA
TAGACCAAAATAGAAACCACAAAATTTCGAAAACATTTTTTTAGAATCAAAACATCAAAATTAAC
TTTTGAGTCCTTAACGAAAGATGTAAATCATGAAATTACCTTTCAATAGACTCTTGAATCACCTT
CATCCGACAAACAAAACAAAAAATAAAAGAATTAAAGCCAAAACATTAAATCATCCAACCCAAAA
ATTGTGAGGGACTAAATAGCAAAAAGCATAAAAGTATAGGGACCACTTAATAAATAAACCAACAA
AAAAATGATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCAAACCC
Found at i:6873 original size:2 final size:2
Alignment explanation
Indices: 6868--6893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6858 TATATAAGGC
6868 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
6894 TTTCAGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9356 original size:13 final size:14
Alignment explanation
Indices: 9338--9366 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9328 ATAACCGAAT
9338 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
9351 TTTGCATTCATGCA
1 TTTGCATTCATGCA
9365 TT
1 TT
9367 AAGTAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:10730 original size:175 final size:175
Alignment explanation
Indices: 10425--10769 Score: 600
Period size: 175 Copynumber: 2.0 Consensus size: 175
10415 TTAAAAGAGT
* *
10425 ATGATACGTCAAGGGCTTATCATGGTCTTGAAGAGCACAATGGAGCTAATGGAGATCATGCTAGG
1 ATGATACGCCAAGGGCTTATCATGGTCTTGAAGAGCACAATGGAGCTAATGGAGATCATGCTACG
* * *
10490 GATAAACATGGAGATGCCTTGGATATTCAAGAAGCTGCTATGGTTAATCCCGGCTTGAAAGGAAG
66 GATAAACATGGAGATGCCTTAGATATTCAAGAAGCTGCTAAGGTTAATCCCAGCTTGAAAGGAAG
* *
10555 CTTGGAGGAGCATGGAGATGATGGGATTGCGCATGGCCGGTCATG
131 CTTGGAGGAGCATGAAGATGATGGGATCGCGCATGGCCGGTCATG
*
10600 ATGATGCGCCAAGGGCTTATCATGGTCTTGAAGAGCACAATGGAGCTAATGGAGATCATGCTACG
1 ATGATACGCCAAGGGCTTATCATGGTCTTGAAGAGCACAATGGAGCTAATGGAGATCATGCTACG
* *
10665 GATAAACATGGAGATGCCTTAGATATTCAAGAAGCTGCTAAGGTTGATCCCAGCTTGAGAGGAAG
66 GATAAACATGGAGATGCCTTAGATATTCAAGAAGCTGCTAAGGTTAATCCCAGCTTGAAAGGAAG
10730 CTTGGAGGAGCATGAAGATGATGGGATCGCGCATGGCCGG
131 CTTGGAGGAGCATGAAGATGATGGGATCGCGCATGGCCGG
10770 CCATTGCATG
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 160 1.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (175 bp):
ATGATACGCCAAGGGCTTATCATGGTCTTGAAGAGCACAATGGAGCTAATGGAGATCATGCTACG
GATAAACATGGAGATGCCTTAGATATTCAAGAAGCTGCTAAGGTTAATCCCAGCTTGAAAGGAAG
CTTGGAGGAGCATGAAGATGATGGGATCGCGCATGGCCGGTCATG
Found at i:10833 original size:42 final size:42
Alignment explanation
Indices: 10761--10855 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
10751 TGGGATCGCG
* *
10761 CATGGCCGGCCATTGCATGAGGCAACCGCACAAGACCGGACA
1 CATGACCGGCCATGGCATGAGGCAACCGCACAAGACCGGACA
* * *
10803 CATGACCGGCCATGGCATG-GAGCAATCGCACATGACCGGGCA
1 CATGACCGGCCATGGCATGAG-GCAACCGCACAAGACCGGACA
10845 CA--ACCGGCCAT
1 CATGACCGGCCAT
10856 TTGATCCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 9 0.19
41 1 0.02
42 37 0.79
ACGTcount: A:0.27, C:0.34, G:0.28, T:0.11
Consensus pattern (42 bp):
CATGACCGGCCATGGCATGAGGCAACCGCACAAGACCGGACA
Found at i:11223 original size:14 final size:14
Alignment explanation
Indices: 11215--11255 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
11205 TAATAAATTT
11215 TACTAAATAAATAA
1 TACTAAATAAATAA
11229 TACTAAATAAATAA
1 TACTAAATAAATAA
11243 TA-T--ATAAATAA
1 TACTAAATAAATAA
11254 TA
1 TA
11256 GAATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.37
13 1 0.04
14 16 0.59
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (14 bp):
TACTAAATAAATAA
Found at i:11269 original size:14 final size:15
Alignment explanation
Indices: 11218--11273 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
11208 TAAATTTTAC
*
11218 TAAATAAATAATA-C
1 TAAATAAATAATATA
11232 TAAATAAATAATATA
1 TAAATAAATAATATA
11247 TAAAT-AATAGA-ATA
1 TAAATAAATA-ATATA
11261 -AAATAAAT-ATATA
1 TAAATAAATAATATA
11274 ATTTATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 1 0.03
13 7 0.19
14 23 0.62
15 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
TAAATAAATAATATA
Found at i:11286 original size:11 final size:11
Alignment explanation
Indices: 11267--11291 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11257 AATAAAATAA
11267 ATATATAATTT
1 ATATATAATTT
11278 ATATATAATTT
1 ATATATAATTT
11289 ATA
1 ATA
11292 ATTGTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATAATTT
Found at i:11321 original size:12 final size:13
Alignment explanation
Indices: 11304--11336 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11294 TGTATAATTG
11304 TAATTGTACT-TA
1 TAATTGTACTGTA
*
11316 TAATTGTATTGTA
1 TAATTGTACTGTA
11329 TAATTGTA
1 TAATTGTA
11337 ATTTGTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (13 bp):
TAATTGTACTGTA
Found at i:15350 original size:19 final size:18
Alignment explanation
Indices: 15326--15361 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15316 TGAAGATTTC
15326 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15345 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15362 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:18560 original size:37 final size:37
Alignment explanation
Indices: 18510--18662 Score: 247
Period size: 37 Copynumber: 4.2 Consensus size: 37
18500 CTCTTCTTAG
* *
18510 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGCCTCTTTATTGACGCTACTTAATTACCCTGA
*
18546 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCCTCTTTATTGACGCTACTTAATTACCCTGA
*
18583 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCCTCTTTATTGACGCTACTTAATTACCCTGA
18620 ATTAAGTCC-CTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAG-CCTCTTTATTGACGCTACTTAATTACCCTGA
18657 ATTAAG
1 ATTAAG
18663 TCCCTAACTT
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
36 6 0.05
37 103 0.93
38 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.39
Consensus pattern (37 bp):
ATTAAGCCTCTTTATTGACGCTACTTAATTACCCTGA
Found at i:18697 original size:37 final size:37
Alignment explanation
Indices: 18655--18902 Score: 319
Period size: 37 Copynumber: 6.8 Consensus size: 37
18645 TAATTACCCT
* * *
18655 GAATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTG
1 GAATCAAGTCCTTAACTCT-ACTTAATTCCCTTCCTTG
* * *
18692 AAATTAAGTCCTTAACTCTACTTAATTCCCCTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
18729 GAATCAAGT-C----CTCTACTTAATTTCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* * *
18761 AAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* *
18798 GAACCAAGTCCTTAGCTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
18835 GAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
18872 GAATCAAGTCCTTTACTCTACTTAATTCCCT
1 GAATCAAGTCCTTAACTCTACTTAATTCCCT
18903 GAGGTTAAGT
Statistics
Matches: 185, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
32 26 0.14
33 1 0.01
36 1 0.01
37 156 0.84
38 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.39
Consensus pattern (37 bp):
GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
Found at i:18747 original size:69 final size:69
Alignment explanation
Indices: 18674--18888 Score: 313
Period size: 69 Copynumber: 3.0 Consensus size: 69
18664 CCCTAACTTG
*
18674 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCCTCCTTGGAATCAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
18739 CTCT
66 CTCT
* *
18743 ACTTAATTTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAACCAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGT-
18808 CTTAGCTCT
65 C----CTCT
* * * *
18817 ACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
*
18882 CTTT
66 CTCT
18886 ACT
1 ACT
18889 CTACTTAATT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
69 67 0.51
70 1 0.01
73 1 0.01
74 62 0.47
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (69 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
CTCT
Found at i:18777 original size:106 final size:106
Alignment explanation
Indices: 18656--18902 Score: 307
Period size: 106 Copynumber: 2.3 Consensus size: 106
18646 AATTACCCTG
* * **
18656 AATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTC
1 AATTAAATCCCTAACTCT-ACTTAATTCCCTTCCTTGAAACCAAGTCCTTAACTCTACTTAATTC
18720 CCCTCCTTGGAATCAAGTCCTCTACTTAATTTCCTTCCTTGA
65 CCCTCCTTGGAATCAAGTCCTCTACTTAATTTCCTTCCTTGA
* * *
18762 AATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAACCAAGTCCTTAGCTCTACTTAATTCC
1 AATTAAATCCCTAACTCTACTTAATTCCCTTCCTTGAAACCAAGTCCTTAACTCTACTTAATTCC
* * *
18827 CTTCCTTGGAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTGG
66 CCTCCTTGGAATCAAGT-C----CTCTACTTAATTTCCTTCCTTGA
* * * *
18873 AATCAAGTCCTTTACTCTACTTAATTCCCT
1 AATTAAATCCCTAACTCTACTTAATTCCCT
18903 GAGGTTAAGT
Statistics
Matches: 122, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
106 72 0.59
107 2 0.02
111 48 0.39
ACGTcount: A:0.25, C:0.29, G:0.07, T:0.39
Consensus pattern (106 bp):
AATTAAATCCCTAACTCTACTTAATTCCCTTCCTTGAAACCAAGTCCTTAACTCTACTTAATTCC
CCTCCTTGGAATCAAGTCCTCTACTTAATTTCCTTCCTTGA
Found at i:19145 original size:76 final size:75
Alignment explanation
Indices: 19053--19562 Score: 840
Period size: 76 Copynumber: 6.7 Consensus size: 75
19043 CCTTCCTTGA
19053 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTC-CTGAAATTAAGTCTGTGCTTACTTTACT
*
19118 TAATTACTCTG
65 TAATTACCCTG
* *
19129 AATTAACTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCC-TGAAATTAAGTCTGTGCTTACTTTACT
19194 TAATTACCCTG
65 TAATTACCCTG
* *
19205 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAAATTAAGTTTGTGCTTATTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTC-CTGAAATTAAGTCTGTGCTTACTTTACT
19270 TAATTACCCTG
65 TAATTACCCTG
* * *
19281 AATTAAGTCTATGCTTGTCTTTACCTAACTTCTTTCTTGAAATTAAGTCTGTGCTTACTTTACTT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTGAAATTAAGTCTGTGCTTACTTTACTT
19346 AATTACCCTG
66 AATTACCCTG
19356 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCC-TGAAATTAAGTCTGTGCTTACTTTACT
19421 TAATTACCCTG
65 TAATTACCCTG
* * * *
19432 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCATTGAAATTATGTTTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTC-CTGAAATTAAGTCTGTGCTTACTTTACT
*
19497 TAATTACCCTA
65 TAATTACCCTG
*
19508 AATTAAGTCTATGCTTGTCTTTATCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCC-TGAAATTAAGTCTGTGC
19563 CTATCCTCAC
Statistics
Matches: 404, Mismatches: 25, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
75 71 0.18
76 332 0.82
77 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (75 bp):
AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTGAAATTAAGTCTGTGCTTACTTTACTT
AATTACCCTG
Found at i:19359 original size:227 final size:227
Alignment explanation
Indices: 19052--19562 Score: 887
Period size: 227 Copynumber: 2.2 Consensus size: 227
19042 TCCTTCCTTG
* *
19052 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAAATTAAGTCTGTGCTTACTTTAC
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCTTTC-TTGAAATTAAGTCTGTGCTTACTTTAC
*
19117 TTAATTACTCTGAATTAACTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGTCTGT
65 TTAATTACCCTGAATTAACTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGTCTGT
19182 GCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAA
130 GCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAA
*
19247 ATTAAGTTTGTGCTTATTTTACTTAATTACCCT
195 ATTAAGTTTGTGCTTACTTTACTTAATTACCCT
* *
19280 GAATTAAGTCTATGCTTGTCTTTACCTAACTTCTTTCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCTTTCTTGAAATTAAGTCTGTGCTTACTTTACT
* *
19345 TAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTG
66 TAATTACCCTGAATTAACTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGTCTGTG
* *
19410 CTTACTTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCATTGAAA
131 CTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAAA
*
19475 TTATGTTTGTGCTTACTTTACTTAATTACCCT
196 TTAAGTTTGTGCTTACTTTACTTAATTACCCT
* *
19507 AAATTAAGTCTATGCTTGTCTTTATCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTT-CTTTCTTGAAATTAAGTCTGTGC
19563 CTATCCTCAC
Statistics
Matches: 267, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
227 211 0.79
228 56 0.21
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (227 bp):
AAATTAAGTCTATGCTTGTCTTTACCTAATTTCTTTCTTGAAATTAAGTCTGTGCTTACTTTACT
TAATTACCCTGAATTAACTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGTCTGTG
CTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCACTGAAA
TTAAGTTTGTGCTTACTTTACTTAATTACCCT
Found at i:19619 original size:37 final size:37
Alignment explanation
Indices: 19578--19865 Score: 425
Period size: 37 Copynumber: 7.8 Consensus size: 37
19568 CTCACTGTTT
* * **
19578 TTTTACTTAATTACCCTGAATTAAGTCCTTCAACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
* *
19615 TTTTACTTAATTACCCTGAATTAAGTTC-TTAACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
** *
19651 TTTTACTTAATTGTCCTGAATTAAGCTCTTTGACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
* *
19688 TTTTACTTAATTCCCCTAAATTAAGTTTTTTGACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
*
19725 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGATTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
19762 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
* *
19799 TTTTACTTAATCCCCCTGAATTAGGTTCTTTGACTGC
1 TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
* *
19836 TTTTACTTAATTACCCTGAATTAGGTTCTT
1 TTTTACTTAATTCCCCTGAATTAAGTTCTT
19866 AACTATGTTT
Statistics
Matches: 231, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
36 32 0.14
37 199 0.86
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.46
Consensus pattern (37 bp):
TTTTACTTAATTCCCCTGAATTAAGTTCTTTGACTGC
Found at i:19910 original size:41 final size:40
Alignment explanation
Indices: 19864--19980 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 40
19854 AATTAGGTTC
19864 TTAACTATGTTTTCCTTTCTTAATCACCCTGGATTAAAAA
1 TTAACTATGTTTTCCTTTCTTAATCACCCTGGATTAAAAA
* * *
19904 TCTAACTATGTTTTCCTGTCTTAATCA-CCTGAATTAAAAC
1 T-TAACTATGTTTTCCTTTCTTAATCACCCTGGATTAAAAA
** *
19944 TTAACTATGTTTGACTTTCTTAATCGCCCTGGATTAA
1 TTAACTATGTTTTCCTTTCTTAATCACCCTGGATTAA
19981 CTATGTTTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 21 0.31
40 22 0.33
41 24 0.36
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (40 bp):
TTAACTATGTTTTCCTTTCTTAATCACCCTGGATTAAAAA
Found at i:19986 original size:33 final size:33
Alignment explanation
Indices: 19944--20013 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
19934 GAATTAAAAC
19944 TTAACTATGTTTGACTTTCTTAATCGCCCTGGA
1 TTAACTATGTTTGACTTTCTTAATCGCCCTGGA
19977 TTAACTATGTTTGACTTTCTTAATCGCCCTGGA
1 TTAACTATGTTTGACTTTCTTAATCGCCCTGGA
20010 TTAA
1 TTAA
20014 AACTTTACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (33 bp):
TTAACTATGTTTGACTTTCTTAATCGCCCTGGA
Found at i:20217 original size:40 final size:38
Alignment explanation
Indices: 20135--20218 Score: 89
Period size: 40 Copynumber: 2.2 Consensus size: 38
20125 TCTTAACTTT
***
20135 ATTAAGATTCACTTCTTTATGTTTCTTAATTTTACTGA
1 ATTAAGATTCACTTCTTTATGTTTCTTAATCACACTGA
* *
20173 ATTAAGATTTACTTCTCTTAAT-TTTCTTTAATCACACTGG
1 ATTAAGATTCACTTCT-TT-ATGTTTC-TTAATCACACTGA
20213 ATTAAG
1 ATTAAG
20219 GCTTTCATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
38 15 0.39
39 6 0.16
40 17 0.45
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (38 bp):
ATTAAGATTCACTTCTTTATGTTTCTTAATCACACTGA
Found at i:23696 original size:26 final size:26
Alignment explanation
Indices: 23652--23701 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
23642 ATGATTTAGG
* *
23652 GGTTACTAACGCCCTTTTTCTTTTGA
1 GGTTACTAACACCCATTTTCTTTTGA
* *
23678 GGTTACTAACACTCATTTTTTTTT
1 GGTTACTAACACCCATTTTCTTTT
23702 CAAGAGGGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (26 bp):
GGTTACTAACACCCATTTTCTTTTGA
Found at i:30638 original size:42 final size:40
Alignment explanation
Indices: 30570--30657 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 40
30560 TCGCGCATAG
* *
30570 CCGGCCATTGCATGGGGCAACTGCACAAGACCGGACACATGA
1 CCGGCCATGGCATGGAGCAACTGCACAAGACCGGACACA--A
* *
30612 CCGGCCATGGCATGGAGCAA-TCGCACATGACCGGGCACAA
1 CCGGCCATGGCATGGAGCAACT-GCACAAGACCGGACACAA
30652 CCGGCC
1 CCGGCC
30658 CTTTGATCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 7 0.17
41 1 0.02
42 33 0.80
ACGTcount: A:0.26, C:0.34, G:0.30, T:0.10
Consensus pattern (40 bp):
CCGGCCATGGCATGGAGCAACTGCACAAGACCGGACACAA
Found at i:32671 original size:21 final size:21
Alignment explanation
Indices: 32647--32698 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
32637 GCGCTGGGTG
* * *
32647 CCCATGTGCTATGCTTGGCGC
1 CCCATGTGCTATGCCTCGCGA
* *
32668 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGCTATGCCTCGCGA
32689 CCCATGTGCT
1 CCCATGTGCT
32699 CCAGTGCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.29
Consensus pattern (21 bp):
CCCATGTGCTATGCCTCGCGA
Done.