Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016301.1 Corchorus olitorius cultivar O-4 contig16334, 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: 43578
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:126 original size:15 final size:14
Alignment explanation
Indices: 82--128 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
72 ATTCGGTCTA
82 AATTGAAATTTT-AT
1 AATT-AAATTTTAAT
*
96 AATTAATTTTTAAAT
1 AATTAAATTTT-AAT
111 AATATAAATTTTAAT
1 AAT-TAAATTTTAAT
126 AAT
1 AAT
129 GTCAATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 11 0.39
16 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AATTAAATTTTAAT
Found at i:394 original size:14 final size:14
Alignment explanation
Indices: 375--409 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
365 CAAGTCCACT
375 CAGTAATTATGATG
1 CAGTAATTATGATG
389 CAGTAATTATGATG
1 CAGTAATTATGATG
403 CAGTAAT
1 CAGTAAT
410 GATTCAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (14 bp):
CAGTAATTATGATG
Found at i:11368 original size:15 final size:16
Alignment explanation
Indices: 11341--11372 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11331 AAAGTCTTGC
11341 TTATAACTTAATTATT
1 TTATAACTTAATTATT
11357 TTATAA-TTAATTATT
1 TTATAACTTAATTATT
11372 T
1 T
11373 AATTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAACTTAATTATT
Found at i:14364 original size:483 final size:483
Alignment explanation
Indices: 13607--14696 Score: 1730
Period size: 483 Copynumber: 2.3 Consensus size: 483
13597 CAAAACTGAG
*
13607 ATAGGATTTAACAATGTTGCATCAGGATTGAATCATTACTGCATCATAATTACTGATTGGACTTG
1 ATAGGATTTAACAATG-TGCATCAAGATTGAATCATTACTGCATCATAATTACTGATTGGACTTG
* *
13672 GACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTAT---AATATCAGATTTAGGCTTGAC
65 GACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTATAAGAATATCAGATTTAGACTTAAC
* *
13734 AAATTGCCGTTATTAAATAATATTTTAATTATTACCACTATTTAAATAATGAAAATTTAGATTAT
130 AAATTGCCATTATTAAATAATATTTTAA-TATTACCACTATTAAAATAATGAAAATTTAGATTAT
*
13799 CCTCATTAATTAGGATCCAACATGGCCAATAGAGATGCCCCACATTATCTTTAGCATCTGAATTC
194 CCTCATTAATTAGGATCCAACATGGCCAATAGAGATGCCCCACATCATCTTTAGCATCTGAATTC
* *
13864 TCATCCAAAACATTCTCCAAGTCGGTTTAGAAGAAGATCCATTCTGTCCAAAAATTGCAAGGGCA
259 TCATCCAAAACATTCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAAAAATTGCAAGGGCA
* *
13929 AAATTGTCCACAAAAACAGCATAATTAGGTCTAAAGATAAACATAAAAGTTGTAGATCTCGAAAT
324 AAATTGTCCACAAAAACAACAGAATTAGGTCT-AAGATAAACATAAAAGTTGTAGATCTCGAAAT
* * *
13994 TCTCTTTCCAACGGCACCTCATTTGTAATTTTCTA-AGCTCTGGATTAAAAGTTATGAATTTTCT
388 CCTCTTTCCAACGGCACCTCATTTGCAATTTTC-AGAGCTCTGGATCAAAAGTTATGAATTTTCT
14058 TCCAAAACTGCTCTTGTGAAGTCCTCCTTTAA
452 TCCAAAACTGCTCTTGTGAAGTCCTCCTTTAA
* * *
14090 ATAGAATTTAACAATGCTACATCAAGTTTTGAATCATTACTGCATCATAATTACTGATTGGACTT
1 ATAGGATTTAACAATG-TGCATCAAG-ATTGAATCATTACTGCATCATAATTACTGATTGGACTT
*
14155 GGACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTATAAGAATATCGGATTTAGACTTAA
64 GGACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTATAAGAATATCAGATTTAGACTTAA
*
14220 CAAATTGCCATTATTAAATAATATTTT-A-ATT-CCACTATTAAAATAATGGAAATTTAGATTAT
129 CAAATTGCCATTATTAAATAATATTTTAATATTACCACTATTAAAATAATGAAAATTTAGATTAT
* * *
14282 CCTCATTAATTAGGATCCAACATGGCCAATAGGGATGCCCCACATCATCTTTAGCATTTGAATTT
194 CCTCATTAATTAGGATCCAACATGGCCAATAGAGATGCCCCACATCATCTTTAGCATCTGAATTC
* * * * *
14347 TCGTCCAAAATATTCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAGGGCA
259 TCATCCAAAACATTCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAAAAATTGCAAGGGCA
* *
14412 AAATTGTCCACCAAAACAACAGAATTAGGTCTCAGATAAACATAAAAGTTGTAGATCTCGAAATC
324 AAATTGTCCACAAAAACAACAGAATTAGGTCTAAGATAAACATAAAAGTTGTAGATCTCGAAATC
* *
14477 CTCTTTCCAACGGTACCTCATTTGCATTTTTCAGAGCTCTGGATCAAAAGTTATGAATTTTCTTC
389 CTCTTTCCAACGGCACCTCATTTGCAATTTTCAGAGCTCTGGATCAAAAGTTATGAATTTTCTTC
*
14542 TAAAACTGCTCTTGTGAAGTCCTCCTTTAA
454 CAAAACTGCTCTTGTGAAGTCCTCCTTTAA
** *
14572 ATAGGATTTAACAATGTGGCATCAAGGCTGAATCATTACTGCATCATAATTACTGGTTGGACTTG
1 ATAGGATTTAACAATGT-GCATCAAGATTGAATCATTACTGCATCATAATTACTGATTGGACTTG
* *
14637 GACTCCTTCTTTGGGCTTCCATATTAACGAATTGGGCC--TAAGAATATCAGATTTAGACTT
65 GACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTATAAGAATATCAGATTTAGACTT
14697 CAAGACATCT
Statistics
Matches: 561, Mismatches: 40, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
479 21 0.04
481 74 0.13
482 141 0.25
483 199 0.35
484 82 0.15
486 1 0.00
487 43 0.08
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (483 bp):
ATAGGATTTAACAATGTGCATCAAGATTGAATCATTACTGCATCATAATTACTGATTGGACTTGG
ACTTCTTCTTTGGACTTCCATATTAACGAATTGGGCCTATAAGAATATCAGATTTAGACTTAACA
AATTGCCATTATTAAATAATATTTTAATATTACCACTATTAAAATAATGAAAATTTAGATTATCC
TCATTAATTAGGATCCAACATGGCCAATAGAGATGCCCCACATCATCTTTAGCATCTGAATTCTC
ATCCAAAACATTCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAAAAATTGCAAGGGCAAA
ATTGTCCACAAAAACAACAGAATTAGGTCTAAGATAAACATAAAAGTTGTAGATCTCGAAATCCT
CTTTCCAACGGCACCTCATTTGCAATTTTCAGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCA
AAACTGCTCTTGTGAAGTCCTCCTTTAA
Found at i:15185 original size:19 final size:19
Alignment explanation
Indices: 15171--15208 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15161 ACTATTATTT
15171 TTTGAATTTAATATTTTAC
1 TTTGAATTTAATATTTTAC
*
15190 TTTGAATTTCAATTTTTTA
1 TTTGAATTT-AATATTTTA
15209 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTGAATTTAATATTTTAC
Found at i:15437 original size:22 final size:21
Alignment explanation
Indices: 15365--15467 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
15355 CTTGTCTCTG
15365 TGTGGTTATCAAAATTTCATAA
1 TGTGGTTATCAAAA-TTCATAA
* * * *
15387 -GATGATTATTATAATTCATGA
1 TG-TGGTTATCAAAATTCATAA
* *
15408 GGAGGTTATCAAAATTGCATAA
1 TGTGGTTATCAAAATT-CATAA
*
15430 TGTGGTTACCAAAATTCCAT-A
1 TGTGGTTATCAAAATT-CATAA
15451 TG-GAAGTTATCAAAATT
1 TGTG--GTTATCAAAATT
15468 TCATGGGAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
21 20 0.32
22 41 0.66
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
TGTGGTTATCAAAATTCATAA
Found at i:15446 original size:43 final size:44
Alignment explanation
Indices: 15368--15467 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 44
15358 GTCTCTGTGT
* ** *
15368 GGTTATCAAAATTTCATAAGATGATTATTATAATT-CATGA-GGA
1 GGTTATCAAAATTGCATAAGATGATTACCAAAATTCCAT-ATGGA
*
15411 GGTTATCAAAATTGCATAATG-TGGTTACCAAAATTCCATATGGA
1 GGTTATCAAAATTGCATAA-GATGATTACCAAAATTCCATATGGA
*
15455 AGTTATCAAAATT
1 GGTTATCAAAATT
15468 TCATGGGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
43 29 0.60
44 19 0.40
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTGCATAAGATGATTACCAAAATTCCATATGGA
Found at i:15481 original size:22 final size:22
Alignment explanation
Indices: 15434--15486 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
15424 GCATAATGTG
* *
15434 GTTACCAAAATTCCATATGGAA
1 GTTATCAAAATTCCATAGGGAA
*
15456 GTTATCAAAATTTCAT-GGGAA
1 GTTATCAAAATTCCATAGGGAA
15477 TGTTATCAAA
1 -GTTATCAAA
15487 TTTTTATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (22 bp):
GTTATCAAAATTCCATAGGGAA
Found at i:15628 original size:22 final size:21
Alignment explanation
Indices: 15603--16936 Score: 360
Period size: 22 Copynumber: 61.0 Consensus size: 21
15593 ATCAAAGAGA
*
15603 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
15625 TTAT-AAGAATTTCATAGTATGG
1 TTATCAA-AATTTCATAGGA-GG
*
15647 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
15669 TTA-C-TAATATTCATGGGGAGG
1 TTATCAAAAT-TTCAT-AGGAGG
*
15690 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
** *
15712 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
*
15734 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
15756 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
15781 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
* *
15803 TTATC-AAATCTAATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* * *
15823 AGTATCGAAATTTCATAGAAATCGG
1 -TTATCAAAATTTCATAG-GA--GG
*
15848 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
* ***
15870 TTATCAAAATTTAATAGTGTTA
1 TTATCAAAATTTCATAG-GAGG
*
15892 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
15914 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
15936 TTATCAAAATTTCATAGAGTGG
1 TTATCAAAATTTCATAG-GAGG
* * *
15958 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
15980 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * * * *
16002 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTC-ATAGGAGG
* * *
16024 TTACCAAAATGTCATA-GTGG
1 TTATCAAAATTTCATAGGAGG
* * ** *
16044 TATTTCTGGGGAGGTTATCA-A--AAG
1 T-TATC----AAAATT-TCATAGGAGG
* *
16068 TAATCAAAATTTCA-GGGAGG
1 TTATCAAAATTTCATAGGAGG
* *
16088 ATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
16110 TTCTCAAAATTTCATAGTTTA-C
1 TTATCAAAATTTCATAG--GAGG
* *
16132 TTTTCAAAATTTCATAAGAGAG
1 TTATCAAAATTTCATAGGAG-G
* *
16154 TTATCAAAATTTCATAGTATG
1 TTATCAAAATTTCATAGGAGG
* *
16175 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATA-GGAGG
* * * **
16198 TTAACAAAATTTTATAATGAAA
1 TTATCAAAATTTCAT-AGGAGG
*
16220 TTATCAAAA-ATCATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
16241 TTATTAAAA-TT--T-GTA-G
1 TTATCAAAATTTCATAGGAGG
*
16257 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
16279 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
16301 TTTATCAAAATTTTATAGGAAGG
1 -TTATCAAAATTTCATAGG-AGG
*
16324 TTTATCAAAATTTCATAACGAGG
1 -TTATCAAAATTTCAT-AGGAGG
** * *
16347 TTATCACGATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* *
16369 TTATCAAAATTTCAGAGTAGG
1 TTATCAAAATTTCATAGGAGG
*
16390 ATTATTAACAA-TTCATATGGAGG
1 -TTATCAA-AATTTCATA-GGAGG
* * * *
16413 CTT-TTAAATTTTCATAACGTGG
1 -TTATCAAAATTTCAT-AGGAGG
* *
16435 TTATCAATATATCAT-GGAGG
1 TTATCAAAATTTCATAGGAGG
* * *
16455 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* *
16478 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCA-TAGGAGG
16500 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
16522 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATA-GGAGG
*
16544 TTAGCAAAATTTCATA--AGG
1 TTATCAAAATTTCATAGGAGG
** * ** *
16563 TTAAAAAAAAATT-ATAAAAAAG
1 TT-ATCAAAATTTCAT-AGGAGG
* * * * *
16585 TTCTCGAAATTGCATAGTATCG
1 TTATCAAAATTTCATAGGA-GG
**
16607 TTATCACGATTTCATAGCGA-G
1 TTATCAAAATTTCATAG-GAGG
* * ** *
16628 TAATCACAATTTCATAATATGA
1 TTATCAAAATTTCATAGGA-GG
* * *
16650 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
16672 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * * *
16694 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
16716 TTATCAATATATGATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* ** *
16738 TTATCAACATCACATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* * *
16761 TTATCAAAATTTTATTGGGAAG
1 TTATCAAAATTTCA-TAGGAGG
16783 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
16805 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATA-GGAGG
*
16827 TTAACAAAATTTCATA--AGG
1 TTATCAAAATTTCATAGGAGG
** ** *
16846 TTAAAAAAAAAATTT-ATAAAAAGA
1 TT---ATCAAAATTTCAT-AGGAGG
* * * * *
16870 TTCTCGAAATTGCATAGTATCG
1 TTATCAAAATTTCATAGGA-GG
*
16892 TTATTAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
16914 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
16936 T
1 T
16937 CACAAAAAAT
Statistics
Matches: 956, Mismatches: 247, Indels: 218
0.67 0.17 0.15
Matches are distributed among these distances:
16 8 0.01
17 4 0.00
18 3 0.00
19 19 0.02
20 65 0.07
21 108 0.11
22 587 0.61
23 109 0.11
24 18 0.02
25 20 0.02
26 6 0.01
28 9 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:16309 original size:23 final size:23
Alignment explanation
Indices: 16257--16336 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
16247 AAATTTGTAG
* * *
16257 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
16279 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
16302 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
16325 TTATCAAAATTT
1 TTATCAAAATTT
16337 CATAACGAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 19 0.36
23 34 0.64
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:16944 original size:22 final size:22
Alignment explanation
Indices: 16897--16943 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16887 TATCGTTATT
*
16897 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATC
16919 AAAATTTCATAAGG-AGGTCA-C
1 AAAATTTCAT-AGGAAGGTCATC
16940 AAAA
1 AAAA
16944 AATAGTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 15 0.65
23 3 0.13
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATC
Found at i:22067 original size:9 final size:9
Alignment explanation
Indices: 22053--22084 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
22043 TTCCTAAATT
22053 AATTATGGA
1 AATTATGGA
22062 AATTATGGA
1 AATTATGGA
*
22071 AATTAAGGA
1 AATTATGGA
22080 AATTA
1 AATTA
22085 AATATTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (9 bp):
AATTATGGA
Found at i:23383 original size:49 final size:49
Alignment explanation
Indices: 23278--23406 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
23268 TTACATTTCC
* *
23278 TGCA-CTTTTTCTCAATTTTTACA-ACAAAATTGAACCTTTATTTTTCCT
1 TGCACCTTTTTCTCAATTTTTA-AGACAAAATTGAACATTTATTTTTCAT
*
23326 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGAATATTTACTTTTT-AT
1 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGAACATTTA-TTTTTCAT
* * * *
23375 TGCTCC-TTTTATCAATTTCT-GGACAAAATTGA
1 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGA
23407 TTGGCACACT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 11 0.15
48 17 0.24
49 38 0.54
50 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (49 bp):
TGCACCTTTTTCTCAATTTTTAAGACAAAATTGAACATTTATTTTTCAT
Found at i:23710 original size:33 final size:33
Alignment explanation
Indices: 23668--23763 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
23658 AAAAAATCTC
23668 GGGGCGCCCCCAGAGGGCGCCTTTACCATGATT
1 GGGGCGCCCCCAGAGGGCGCCTTTACCATGATT
* * * * *
23701 GGGGCGCCCCAAGAAGGCGCCTCTGCCATGGTT
1 GGGGCGCCCCCAGAGGGCGCCTTTACCATGATT
* * * *
23734 GGGGCGCCCTCGGAGGGTGCCTTCACCATG
1 GGGGCGCCCCCAGAGGGCGCCTTTACCATG
23764 GTAGAGCCCA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.14, C:0.33, G:0.36, T:0.17
Consensus pattern (33 bp):
GGGGCGCCCCCAGAGGGCGCCTTTACCATGATT
Found at i:30645 original size:13 final size:13
Alignment explanation
Indices: 30627--30653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30617 AAATAACATC
30627 TGCATATATTAAG
1 TGCATATATTAAG
30640 TGCATATATTAAG
1 TGCATATATTAAG
30653 T
1 T
30654 AGAAACTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TGCATATATTAAG
Found at i:35671 original size:8 final size:8
Alignment explanation
Indices: 35658--35695 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
35648 CCTGCAAACC
35658 CAAATGGG
1 CAAATGGG
35666 CAAATGGG
1 CAAATGGG
35674 CAAATGGG
1 CAAATGGG
35682 CAAATGGG
1 CAAATGGG
35690 CAAATG
1 CAAATG
35696 TAGTTTTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.34, T:0.13
Consensus pattern (8 bp):
CAAATGGG
Done.