Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021113.1 Corchorus olitorius cultivar O-4 contig21146, 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: 101544
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:3103 original size:34 final size:35
Alignment explanation
Indices: 3037--3104 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
3027 AAATTAACCA
*
3037 AGAATAAAAAAGAAAAGAAAAGAAGGAAAGACTCT
1 AGAATAAAAAAGAAAAGAAAAGAAGAAAAGACTCT
* *
3072 AGAAT-AAAAAGTAAAGAAGAGAA-AAAGAGACTC
1 AGAATAAAAAAGAAAAGAAAAGAAGAAA-AGACTC
3105 GGGATTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 2 0.07
34 22 0.76
35 5 0.17
ACGTcount: A:0.65, C:0.06, G:0.21, T:0.09
Consensus pattern (35 bp):
AGAATAAAAAAGAAAAGAAAAGAAGAAAAGACTCT
Found at i:3473 original size:11 final size:11
Alignment explanation
Indices: 3457--3485 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3447 GAATAAAAAG
3457 ATATTTTATAT
1 ATATTTTATAT
3468 ATATTTTATAT
1 ATATTTTATAT
3479 ATATTTT
1 ATATTTT
3486 TGAGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATATTTTATAT
Found at i:6821 original size:13 final size:14
Alignment explanation
Indices: 6798--6828 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
6788 GAATAAAAAA
6798 AAAAGTAATTTGAG
1 AAAAGTAATTTGAG
6812 AAAA-TAATTTGAG
1 AAAAGTAATTTGAG
6825 AAAA
1 AAAA
6829 CATCCTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (14 bp):
AAAAGTAATTTGAG
Found at i:16720 original size:348 final size:347
Alignment explanation
Indices: 16054--17802 Score: 2462
Period size: 348 Copynumber: 5.0 Consensus size: 347
16044 TCCAAGGTCC
16054 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
1 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* * *
16119 GCCAGCAATGGTACACACAT-TCCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAACGGAA
66 ACCAGCAATGGTACACATATAT-CCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAA
* ** * * * *
16183 ACAAACCTGACGTGCCCAATGAGGATTCAAACAGGTTTTTAGCTAACAATATGGTAGGAAATCAG
130 ACAAACCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTAGCAAACAATATGGCAGGAAATCAG
* * * * *
16248 CTAAAAATCAAGGAAAATGTACAAGACCAGCAGCAAATTGAGAAGAAACATGCTGGGGATATGAA
195 CTAAACA-CAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGATAAGAA
* * * * *
16313 TCCTCAATTTCGGTGCACCATCTGTCACATAAACTGCACTCGTTTGGAGGACATGAACTGTCACC
259 TCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACC
*
16378 TCTCGGGAAAGAAGCATTTGGCCA
324 TCTCGGGAAAGAAGCACTTGGCCA
* *
16402 AAGTCTCAGCTGCATCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGGGCA
1 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* * * *
16467 ACCAGCAATGGTACACATATATCCAGCAAAGTAGTGGATCTTCCAACTGGAATAAGCGATGGAAA
66 ACCAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
* * * *
16532 CAAAGCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTGGCAAACAATACGACAGGAAATCAGC
131 CAAACCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTAGCAAACAATATGGCAGGAAATCAGC
* *
16597 TACAACACAAGGAAATTGTACAAGACCAGCAGCAGATTGGGACTAAACATGCTGGGGATAAGAAT
196 TA-AACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGATAAGAAT
* **
16662 CCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCGCTCGTTCAGAGGACTTGAACTGTCACCT
260 CCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACCT
* *
16727 TTCTGGAAAGAAGCACTTGGCCA
325 CTCGGGAAAGAAGCACTTGGCCA
* * * *
16750 AAGTCTCAGCCGCTTCAGTGGCTAAGAAATCTGATGTTACCAAAAATGATGCCGAGAAATGTGCA
1 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
** *
16815 ACCAGCAACAGTACACATATATCCACCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
66 ACCAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
* * * * *
16880 CAAACCTGACCTGCCCAATGAGGAACAAAACAGGTTTTTAGCAAACAATATGGCAGGAGATCAAC
131 CAAACCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTAGCAAACAATATGGCAGGAAATCAGC
* *
16945 TAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTAGGGATGAGAATC
196 TAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGATAAGAATC
* *
17010 CCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTGGTTTGGAGAACTTGAACTGTCACCTC
261 CCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACCTC
*
17075 TCGGGAAAGAAGCATTTGGCCA
326 TCGGGAAAGAAGCACTTGGCCA
* * * *
17097 AAGTCTCAGCTGCTTCAGTGGCTAAGAACACTGATGTTTCCCAAAATAATGCTGAAAAATGTGCA
1 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* *
17162 TCAAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
66 ACCAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
** * * * * **
17227 CAAACCCAACCTACCCAATGAGGAAACAAACAAGTTTCTAGCAAACAATATGACAGGATATTGGC
131 CAAACCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTAGCAAACAATATGGCAGGAAATCAGC
* *
17292 TACAAGTACAAGACAAGGAAAATGTACCAGACCAGCAGCAGATTGGGACGAAACATGCTAGGGAT
196 T--AA--AC---ACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGAT
* * *
17357 GAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGGATTG
254 AAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTG
* *
17422 TCACCTTTCAGGAAAGAAGCACTTGGCCA
319 TCACCTCTCGGGAAAGAAGCACTTGGCCA
* * *
17451 AAGTCTCAGCCGCTTCAGTGGCTAAAAACTCTGATGTTTCCAGAAATGATGCTGAGAAATGTGCA
1 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* * * *
17516 ACCAGCAACGGTACACATATATCCAGAAAAGCAATGGATCTTACAACTGGGGTAAGCAATGGAAA
66 ACCAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
* * *
17581 CAAACCTGACCTGCCAAATGAGGAACCAAACAAGTTGT-TACCAAACAATATGGCAGGAAATCAA
131 CAAACCTGACCTGCCCAATGAGGAACCAAACAAGTT-TCTAGCAAACAATATGGCAGGAAATCAG
*
17645 CTAAAACGTGAGGACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGA
195 CT-AAAC------ACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGA
* * **
17710 TCAGAATCCTCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTCAGAGGACTT-ACAC
253 TAAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGA-AC
* *
17774 TGTCACGT-TGGGGAAAGAAGCACTTGGCC
317 TGTCACCTCTCGGGAAAGAAGCACTTGGCC
17803 CAGATTCGAG
Statistics
Matches: 1244, Mismatches: 143, Indels: 23
0.88 0.10 0.02
Matches are distributed among these distances:
347 309 0.25
348 479 0.39
349 6 0.00
351 4 0.00
353 21 0.02
354 424 0.34
355 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (347 bp):
AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
ACCAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
CAAACCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTAGCAAACAATATGGCAGGAAATCAGC
TAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTGGGGATAAGAATC
CCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACCTC
TCGGGAAAGAAGCACTTGGCCA
Found at i:17628 original size:701 final size:694
Alignment explanation
Indices: 16054--17802 Score: 2606
Period size: 701 Copynumber: 2.5 Consensus size: 694
16044 TCCAAGGTCC
* *
16054 AAGTCTCAGCTGCTTCAGTGGCTAAGAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
1 AAGTCTCAGCCGCTTCAGTGGCTAAAAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* * * *
16119 GCCAGCAATGGTACACACAT-TCCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAACGGAA
66 ACCAGCAACGGTACACATATAT-CCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAA
* ** * * *
16183 ACAAACCTGACGTGCCCAATGAGGATTCAAACAGGTTTTTAGCTAACAATATGGTAGGAAATCAG
130 ACAAACCTGACCTGCCCAATGAGGAACCAAACAGGTTTTTAGCAAACAATATGGCAGGAAATCAA
* * *
16248 CTAAAAATCAAGGAAAATGTACAAGACCAGCAGCAAATTGAGAAGAAACATGCTGGGGATATGAA
195 CTAAACA-CAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGATA-GAA
* * * *
16313 TCCTCAATTTCGGTGCACCATCTGTCACATAAACTGCACTCGTTTGGAGGACATGAACTGTCACC
258 TCCTCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACC
*
16378 TCTCGGGAAAGAAGCATTTGGCCAAAGTCTCAGCTGCATCAGTGGCTAAGAACTCTGATGTTTCC
323 TCTCGGGAAAGAAGCATTTGGCCAAAGTCTCAGCTGCATCAGTGGCTAAGAACACTGATGTTTCC
* * * *
16443 AAAAATGATGCTGAGAAATGGGCAACCAGCAATGGTACACATATATCCAGCAAAGTAGTGGATCT
388 AAAAATAATGCTGAAAAATGGGCAACAAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCT
* * * ** * * *
16508 TCCAACTGGAATAAGCGATGGAAACAAAGCTGACCTGCCCAATGAGGAACCAAACAAGTTTCTGG
453 TACAACTGGAATAAGCAATGGAAACAAACCCAACCTACCCAATGAGGAAACAAACAAGTTTCTAG
*
16573 CAAACAATACGACAGGAAATCAGCTACAACACAAGGAAATTGTACAAGACCAGCAGCAGATTGGG
518 CAAACAATACGACAGGAAATCAGCTACAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGG
* * *
16638 ACTAAACATGCTGGGGATAAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCGCTCG
583 ACGAAACATGCTAGGGATAAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCG
*
16703 TTCAGAGGACTTGAACTGTCACCTTTCTGGAAAGAAGCACTTGGCCA
648 TTCAGAGGACTTGAACTGTCACCTTTCAGGAAAGAAGCACTTGGCCA
* *
16750 AAGTCTCAGCCGCTTCAGTGGCTAAGAAA-TCTGATGTTACCAAAAATGATGCCGAGAAATGTGC
1 AAGTCTCAGCCGCTTCAGTGGCTAA-AAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGC
* *
16814 AACCAGCAACAGTACACATATATCCACCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAA
65 AACCAGCAACGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAA
* *
16879 ACAAACCTGACCTGCCCAATGAGGAACAAAACAGGTTTTTAGCAAACAATATGGCAGGAGATCAA
130 ACAAACCTGACCTGCCCAATGAGGAACCAAACAGGTTTTTAGCAAACAATATGGCAGGAAATCAA
* *
16944 CTAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACGAAACATGCTAGGGATGAGAAT
195 CTAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGAT-AGAAT
* * *
17009 CCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTGGTTTGGAGAACTTGAACTGTCACCT
259 CCTCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACCT
* *
17074 CTCGGGAAAGAAGCATTTGGCCAAAGTCTCAGCTGCTTCAGTGGCTAAGAACACTGATGTTTCCC
324 CTCGGGAAAGAAGCATTTGGCCAAAGTCTCAGCTGCATCAGTGGCTAAGAACACTGATGTTTCCA
* *
17139 AAAATAATGCTGAAAAATGTGCATCAAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTT
389 AAAATAATGCTGAAAAATGGGCAACAAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTT
*
17204 ACAACTGGGATAAGCAATGGAAACAAACCCAACCTACCCAATGAGGAAACAAACAAGTTTCTAGC
454 ACAACTGGAATAAGCAATGGAAACAAACCCAACCTACCCAATGAGGAAACAAACAAGTTTCTAGC
* * ** *
17269 AAACAATATGACAGGATATTGGCTACAAGTACAAGACAAGGAAAATGTACCAGACCAGCAGCAGA
519 AAACAATACGACAGGAAATCAGCTAC-A--AC---ACAAGGAAAATGTACAAGACCAGCAGCAGA
*
17334 TTGGGACGAAACATGCTAGGGATGAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGC
578 TTGGGACGAAACATGCTAGGGATAAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGC
** * *
17399 ACTCGTTTGGAGGACTTGGATTGTCACCTTTCAGGAAAGAAGCACTTGGCCA
643 ACTCGTTCAGAGGACTTGAACTGTCACCTTTCAGGAAAGAAGCACTTGGCCA
*
17451 AAGTCTCAGCCGCTTCAGTGGCTAAAAACTCTGATGTTTCCAGAAATGATGCTGAGAAATGTGCA
1 AAGTCTCAGCCGCTTCAGTGGCTAAAAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
* * *
17516 ACCAGCAACGGTACACATATATCCAGAAAAGCAATGGATCTTACAACTGGGGTAAGCAATGGAAA
66 ACCAGCAACGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
* * * *
17581 CAAACCTGACCTGCCAAATGAGGAACCAAACAAGTTGTTACCAAACAATATGGCAGGAAATCAAC
131 CAAACCTGACCTGCCCAATGAGGAACCAAACAGGTTTTTAGCAAACAATATGGCAGGAAATCAAC
17646 TAAAACGTGAGGACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGAT
196 T-AAAC------ACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGAT
**
17711 CAGAATCCTCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTCAGAGGACTT-ACACT
254 -AGAATCCTCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGA-ACT
* * *
17775 GTCACGT-TGGGGAAAGAAGCACTTGGCC
317 GTCACCTCTCGGGAAAGAAGCATTTGGCC
17803 CAGATTCGAG
Statistics
Matches: 947, Mismatches: 88, Indels: 25
0.89 0.08 0.02
Matches are distributed among these distances:
695 309 0.33
696 179 0.19
697 3 0.00
698 2 0.00
700 3 0.00
701 314 0.33
702 4 0.00
707 20 0.02
708 113 0.12
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (694 bp):
AAGTCTCAGCCGCTTCAGTGGCTAAAAACTCTGATGTTTCCAAAAATGATGCTGAGAAATGTGCA
ACCAGCAACGGTACACATATATCCAGCAAAGCAGTGGATCTTACAACTGGGATAAGCAATGGAAA
CAAACCTGACCTGCCCAATGAGGAACCAAACAGGTTTTTAGCAAACAATATGGCAGGAAATCAAC
TAAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGAAGAAACATGCTGGGGATAGAATCC
TCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTTGGAGGACTTGAACTGTCACCTCT
CGGGAAAGAAGCATTTGGCCAAAGTCTCAGCTGCATCAGTGGCTAAGAACACTGATGTTTCCAAA
AATAATGCTGAAAAATGGGCAACAAGCAATGGTACACATATATCCAGCAAAGCAGTGGATCTTAC
AACTGGAATAAGCAATGGAAACAAACCCAACCTACCCAATGAGGAAACAAACAAGTTTCTAGCAA
ACAATACGACAGGAAATCAGCTACAACACAAGGAAAATGTACAAGACCAGCAGCAGATTGGGACG
AAACATGCTAGGGATAAGAATCCCCAATTTCAGTGCACCATCTGTAACATAAGCTGCACTCGTTC
AGAGGACTTGAACTGTCACCTTTCAGGAAAGAAGCACTTGGCCA
Found at i:34440 original size:122 final size:122
Alignment explanation
Indices: 34216--34439 Score: 407
Period size: 121 Copynumber: 1.8 Consensus size: 122
34206 ATGTAGAGTT
34216 ATGGATTCAATTTTTAATATGAAAGTTATGATTATATATATAATTTTTTTTAGGGTATGATTATA
1 ATGGATTCAATTTTTAATATGAAAGTTATGATTATATATATAATTTTTTTTAGGGTATGATTATA
*
34281 TAATGTTAATAATAATTGTCAATGTTCCTTTTCTTTTTCCTTTTTGCTGAATTTTCA
66 TAATGTTAATAACAATTGTCAATGTTCCTTTTCTTTTTCCTTTTTGCTGAATTTTCA
34338 ATGGATTCAATTTTTAATATGAAAGTTATGA-T-TATATATAATGTTTTTTTAGGGTATGATTAT
1 ATGGATTCAATTTTTAATATGAAAGTTATGATTATATATATAAT-TTTTTTTAGGGTATGATTAT
*
34401 ATAATGTTAATAGCAATTGTCAATGTTCCTTTTCTTTTT
65 ATAATGTTAATAACAATTGTCAATGTTCCTTTTCTTTTT
34440 TTGCTGAATT
Statistics
Matches: 99, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
120 10 0.10
121 58 0.59
122 31 0.31
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (122 bp):
ATGGATTCAATTTTTAATATGAAAGTTATGATTATATATATAATTTTTTTTAGGGTATGATTATA
TAATGTTAATAACAATTGTCAATGTTCCTTTTCTTTTTCCTTTTTGCTGAATTTTCA
Found at i:39249 original size:29 final size:28
Alignment explanation
Indices: 39197--39255 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
39187 ACTTGTGGTG
* * * *
39197 TTTGGACTTTTTGTTCTCGAACTTTAAT
1 TTTGGACATTTTGTCCTCAAACTTCAAT
39225 TTTGGACATTTTGTCCTCTAAACTTCAAT
1 TTTGGACATTTTGTCCTC-AAACTTCAAT
39254 TT
1 TT
39256 CGGGACGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTGGACATTTTGTCCTCAAACTTCAAT
Found at i:39470 original size:29 final size:30
Alignment explanation
Indices: 39423--39481 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
39413 CAAAACGTTA
*
39423 TAAAATTGAAATTTAAGGA-ATAAAATATC
1 TAAAATTGAAAGTTAAGGAGATAAAATATC
*
39452 TAAAATTGAAAGTTCAGGAGATAAAATATC
1 TAAAATTGAAAGTTAAGGAGATAAAATATC
39482 CAAACACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.29
Consensus pattern (30 bp):
TAAAATTGAAAGTTAAGGAGATAAAATATC
Found at i:50785 original size:19 final size:19
Alignment explanation
Indices: 50753--50808 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
50743 ACTCATGAGG
*
50753 TTTATCTTTA-TATAATTTT
1 TTTAT-TTTATTATAATTTA
50772 TTTATTTTATTAT-ATTTA
1 TTTATTTTATTATAATTTA
*
50790 TTTATATT-TTATAATTTA
1 TTTATTTTATTATAATTTA
50808 T
1 T
50809 ATAGATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 4 0.12
18 21 0.64
19 8 0.24
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTTATTATAATTTA
Found at i:50788 original size:18 final size:20
Alignment explanation
Indices: 50753--50801 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
50743 ACTCATGAGG
50753 TTTATCTTTA-TATAATTT-T
1 TTTAT-TTTATTATAATTTAT
50772 TTTATTTTATTAT-ATTTAT
1 TTTATTTTATTATAATTTAT
50791 TTATATTTTAT
1 TT-TATTTTAT
50802 AATTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.30
19 11 0.41
20 8 0.30
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTTATTATAATTTAT
Found at i:50816 original size:18 final size:20
Alignment explanation
Indices: 50775--50816 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
50765 TAATTTTTTT
* *
50775 ATTTTATTATATTTATTTAT
1 ATTTTATTATATTTATATAG
50795 ATTTTA-TA-ATTTATATAG
1 ATTTTATTATATTTATATAG
50813 ATTT
1 ATTT
50817 ATAGATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 2 0.10
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTATTATATTTATATAG
Found at i:60875 original size:57 final size:57
Alignment explanation
Indices: 60787--60899 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
60777 ACGTTTCCTC
*
60787 TCACACAATAAATGTTATAATAAATCATATCCCCTCTATCTCTACTTAATTATTCTT
1 TCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTT
* *
60844 TCACACAATAAATGTTATAATAAATCCTATCCCCCCTATTTCTACTTAATTATTCT
1 TCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCT
60900 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (57 bp):
TCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTT
Found at i:61764 original size:268 final size:268
Alignment explanation
Indices: 61287--61820 Score: 1023
Period size: 268 Copynumber: 2.0 Consensus size: 268
61277 TCCAAAATCG
61287 AAGATGGTCAATCATCAAGTTATTGATTTGTTTTTCAATAATGTTAACTTAGCTAAAGATGCAAT
1 AAGATGGTCAATCATCAAGTTATTGATTTGTTTTTCAATAATGTTAACTTAGCTAAAGATGCAAT
* *
61352 TTGTGAATTCTTAAGAGACCACAAACTATTTGTTTCCAGTGATGCAATGTTTTATCAAACAACTA
66 TTGTGAATTCTTAAGAGACCACAAACCATTTGTTTCCAGTGATGCAATGTCTTATCAAACAACTA
61417 ATAATAATTTCTAAATGTCCATACGAAGAAGAGAGTGAACTTAGTTTTTGTTTTAAGTGCTATAC
131 ATAATAATTTCTAAATGTCCATACGAAGAAGAGAGTGAACTTAGTTTTTGTTTTAAGTGCTATAC
*
61482 ACTTTAGAGGAGGAAACAAAATTGGAGCTATTGCACCTGTCCATATACAAACTAATATTTACTAT
196 ACTTTAGAGGAGGAAACAAAATTGAAGCTATTGCACCTGTCCATATACAAACTAATATTTACTAT
61547 TTATTGCT
261 TTATTGCT
*
61555 AAGATGGTTAATCATCAAGTTATTGATTTGTTTTTCAATAATGTTAACTTAGCTAAAGATGCAAT
1 AAGATGGTCAATCATCAAGTTATTGATTTGTTTTTCAATAATGTTAACTTAGCTAAAGATGCAAT
61620 TTGTGAATTCTTAAGAGACCACAAACCATTTGTTTCCAGTGATGCAATGTCTTATCAAACAACTA
66 TTGTGAATTCTTAAGAGACCACAAACCATTTGTTTCCAGTGATGCAATGTCTTATCAAACAACTA
*
61685 ATAATAATTTCTAAATGTCCATACGAAGAAGAGAGTGAACTTAGTTTTTGTTTTAAGTGTTATAC
131 ATAATAATTTCTAAATGTCCATACGAAGAAGAGAGTGAACTTAGTTTTTGTTTTAAGTGCTATAC
61750 ACTTTAGAGGAGGAAACAAAATTGAAGCTATTGCACCTGTCCATATACAAACTAATATTTACTAT
196 ACTTTAGAGGAGGAAACAAAATTGAAGCTATTGCACCTGTCCATATACAAACTAATATTTACTAT
61815 TTATTG
261 TTATTG
61821 TTAACTTTAG
Statistics
Matches: 261, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
268 261 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (268 bp):
AAGATGGTCAATCATCAAGTTATTGATTTGTTTTTCAATAATGTTAACTTAGCTAAAGATGCAAT
TTGTGAATTCTTAAGAGACCACAAACCATTTGTTTCCAGTGATGCAATGTCTTATCAAACAACTA
ATAATAATTTCTAAATGTCCATACGAAGAAGAGAGTGAACTTAGTTTTTGTTTTAAGTGCTATAC
ACTTTAGAGGAGGAAACAAAATTGAAGCTATTGCACCTGTCCATATACAAACTAATATTTACTAT
TTATTGCT
Found at i:62535 original size:37 final size:40
Alignment explanation
Indices: 62465--62542 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 40
62455 TTATTTCTTG
*
62465 AAGCTTAAAAACTTAATGGTAATATAAGTAATTAAATTAA
1 AAGCTTAAAAACTTAATAGTAATATAAGTAATTAAATTAA
62505 AAGCTTAAAAA-TTAATAGT-A-ATAAGTAATTAAATTAA
1 AAGCTTAAAAACTTAATAGTAATATAAGTAATTAAATTAA
62542 A
1 A
62543 TAAGATGTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 18 0.49
38 1 0.03
39 7 0.19
40 11 0.30
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (40 bp):
AAGCTTAAAAACTTAATAGTAATATAAGTAATTAAATTAA
Found at i:63059 original size:22 final size:23
Alignment explanation
Indices: 63020--63065 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
63010 AATTTACTAT
63020 TTTTATATTCATGATTAAGTGTG
1 TTTTATATTCATGATTAAGTGTG
*
63043 TTTTA-ATTACAT-ATTAATTGTG
1 TTTTATATT-CATGATTAAGTGTG
63065 T
1 T
63066 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (23 bp):
TTTTATATTCATGATTAAGTGTG
Found at i:63876 original size:45 final size:45
Alignment explanation
Indices: 63812--63943 Score: 219
Period size: 45 Copynumber: 2.9 Consensus size: 45
63802 AGCAACAATT
* *
63812 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGTAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTAG
* * *
63857 AATATTAGCTTTATTTTGATGAATTACTTAGAGATGAAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTAG
63902 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
63944 AATTTAGGTA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTAG
Found at i:83405 original size:58 final size:58
Alignment explanation
Indices: 83309--83423 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
83299 ATTAATCAAA
*
83309 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * * *
83367 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGC
83424 ATGATGCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 36 0.71
59 15 0.29
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:85290 original size:206 final size:207
Alignment explanation
Indices: 84905--85326 Score: 672
Period size: 206 Copynumber: 2.0 Consensus size: 207
84895 GCTTAATAAC
* *
84905 TTTATGAATGGTGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAACGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
84970 GATACAACACATTATTATTATTATTATATATATAACTATAACGAAAAAAAGTAGTTGAACATTAG
66 GATACAACAC--TATTACTATTATTATATATAGAACTATAACAAAAAAAAGTAGTTGAACATTAG
*
85035 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-A-AAAGATAT
129 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAAATAT
85098 TAAAGATCCGATTTA
194 T-AAGATCCGATTTA
*
85113 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAACGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
85178 GATACAACAC-ATTACTATTA-TATATATAGAACTATGCAATAAAAAAAATTAGTTGAACATTAG
66 GATACAACACTATTACTATTATTATATATAGAACTAT--AACAAAAAAAAGTAGTTGAACATTAG
85241 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAATTAAAAAT
129 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-AA-TAAAAAT
85306 ATTAAGATCCGATTTA
192 ATTAAGATCCGATTTA
85322 TTTAT
1 TTTAT
85327 TATTGAGGAA
Statistics
Matches: 199, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
204 14 0.07
205 9 0.05
206 77 0.39
208 73 0.37
209 18 0.09
210 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (207 bp):
TTTATCAATGGTGAACGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACTATTACTATTATTATATATAGAACTATAACAAAAAAAAGTAGTTGAACATTAGTG
GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAAATATTA
AGATCCGATTTA
Found at i:85431 original size:25 final size:24
Alignment explanation
Indices: 85397--85443 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
85387 ACGTTTGCAC
85397 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
85422 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
85444 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:86930 original size:36 final size:36
Alignment explanation
Indices: 86883--86951 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
86873 GTATGCGGCA
* *
86883 TGTGAAAAATCTATCAAGTGCAGAGCTTCTTTAATT
1 TGTGAAAAATCTATCAACTGCAAAGCTTCTTTAATT
**
86919 TGTGAAAAATCTATTGACTGCAAAGCTTCTTTA
1 TGTGAAAAATCTATCAACTGCAAAGCTTCTTTA
86952 GACTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (36 bp):
TGTGAAAAATCTATCAACTGCAAAGCTTCTTTAATT
Found at i:87450 original size:32 final size:32
Alignment explanation
Indices: 87409--87497 Score: 139
Period size: 32 Copynumber: 2.9 Consensus size: 32
87399 AATGATGCGA
87409 TAAACCAATCCTTATTTCATTGTTTAAACTAT
1 TAAACCAATCCTTATTTCATTGTTTAAACTAT
*
87441 TAAACCAATCCTTATTTCACTGTTTAAACTAT
1 TAAACCAATCCTTATTTCATTGTTTAAACTAT
*
87473 T-AATCAA-CCTTA-TTCATTGTTTAAA
1 TAAACCAATCCTTATTTCATTGTTTAAA
87498 GATCCTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
29 12 0.22
30 5 0.09
31 5 0.09
32 32 0.59
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (32 bp):
TAAACCAATCCTTATTTCATTGTTTAAACTAT
Found at i:88259 original size:25 final size:25
Alignment explanation
Indices: 88231--88279 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
88221 ACTAAAGTTC
*
88231 AAACTCAATCTAATAAATTTAACCA
1 AAACCCAATCTAATAAATTTAACCA
88256 AAACCCAATCTAATAAATTTAACC
1 AAACCCAATCTAATAAATTTAACC
88280 CAACAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (25 bp):
AAACCCAATCTAATAAATTTAACCA
Found at i:97375 original size:14 final size:14
Alignment explanation
Indices: 97356--97396 Score: 75
Period size: 13 Copynumber: 3.0 Consensus size: 14
97346 ACAGTAGTTT
97356 CTGTTGGTAGATTC
1 CTGTTGGTAGATTC
97370 CTGTTGGTAG-TTC
1 CTGTTGGTAGATTC
97383 CTGTTGGTAGATTC
1 CTGTTGGTAGATTC
97397 ATATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.44
Consensus pattern (14 bp):
CTGTTGGTAGATTC
Found at i:97383 original size:13 final size:13
Alignment explanation
Indices: 97349--97392 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
97339 TGCCCATACA
*
97349 GTAGTTTCTGTTG
1 GTAGTTCCTGTTG
97362 GTAGATTCCTGTTG
1 GTAG-TTCCTGTTG
97376 GTAGTTCCTGTTG
1 GTAGTTCCTGTTG
97389 GTAG
1 GTAG
97393 ATTCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.45
Consensus pattern (13 bp):
GTAGTTCCTGTTG
Done.