Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017714.1 Corchorus olitorius cultivar O-4 contig17747, 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: 34106
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:217 original size:21 final size:21
Alignment explanation
Indices: 1--216 Score: 285
Period size: 21 Copynumber: 10.2 Consensus size: 21
*
1 CAAACTTTGGGGTTTGACTAC
1 CAAACTTTGGGGTTTGACTAT
22 CAAACTTTGGGGTTTGACTAT
1 CAAACTTTGGGGTTTGACTAT
43 CAAACTTTTAGGGG-TTGACTAT
1 CAAAC-TTT-GGGGTTTGACTAT
65 CAAACTTTTGGGGTTTGACTAT
1 CAAAC-TTTGGGGTTTGACTAT
87 CAAACTTTGGGGTTTGACTAT
1 CAAACTTTGGGGTTTGACTAT
* * * *
108 TAAACTTTGGGATTTAACTAC
1 CAAACTTTGGGGTTTGACTAT
129 CAAACTTTGGGGTTTGACTAT
1 CAAACTTTGGGGTTTGACTAT
150 CAAACTTTGGGGTTTGA-TAGT
1 CAAACTTTGGGGTTTGACTA-T
* * *
171 TAAAATTTGGGGTTTAACTAT
1 CAAACTTTGGGGTTTGACTAT
*
192 CAAAATTTGGTGG-TTGACTAT
1 CAAACTTTGG-GGTTTGACTAT
213 CAAA
1 CAAA
217 ACATCATTGT
Statistics
Matches: 175, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
20 2 0.01
21 132 0.75
22 37 0.21
23 4 0.02
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (21 bp):
CAAACTTTGGGGTTTGACTAT
Found at i:374 original size:53 final size:53
Alignment explanation
Indices: 254--427 Score: 251
Period size: 53 Copynumber: 3.3 Consensus size: 53
244 CCAAAGGATG
* *
254 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AATCACCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
306 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* * * * * * *
359 ATGGTTAAACCCCAAAATTTAATATTCAAATCATATAACATCATTATACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
*
412 ATGGTCAAATCCCAAA
1 ATGGTCAAACCCCAAA
428 GGATGATGGT
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 34 0.31
53 76 0.69
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.24
Consensus pattern (53 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
Found at i:477 original size:126 final size:127
Alignment explanation
Indices: 306--591 Score: 394
Period size: 126 Copynumber: 2.3 Consensus size: 127
296 TTGTACATGC
* * *
306 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTTAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
* * * * * * * *
371 CAAAATTTAATATTCAAATCATATAACATCATTATACATGCATGGTCAAATCCCAAAGGATG
66 CAAAATTCAATAGTCAAACCACAAAACATCATTATACATGCATAGTCAAACCCCAAAAGATG
* *
433 ATGGTCAATCCCCAAAATTCAATAGTCAAACCAC-AATCACCATTGTACATGCATAGTCAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
* *
497 CAAAATTCAATAGTCAAACCACAAAATATCATTGTACATGCATAGTCAAACCCCAAAAGATG
66 CAAAATTCAATAGTCAAACCACAAAACATCATTATACATGCATAGTCAAACCCCAAAAGATG
* * * *
559 ATGTTCAAACCCCAACATTCGATAATCAAACCA
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCA
592 TGAAAAACAT
Statistics
Matches: 139, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
126 106 0.76
127 33 0.24
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (127 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
CAAAATTCAATAGTCAAACCACAAAACATCATTATACATGCATAGTCAAACCCCAAAAGATG
Found at i:494 original size:179 final size:179
Alignment explanation
Indices: 216--554 Score: 606
Period size: 179 Copynumber: 1.9 Consensus size: 179
206 TGACTATCAA
* *
216 AACATCATTGTACATGTATGGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTC
1 AACATCATTATACATGCATGGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTC
*
281 AAACCACAATCACCATTGTACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACA
66 AAACCACAATCACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACA
* *
346 TCATTGTACATGCATGGTTAAACCCCAAAATTTAATATTCAAATCATAT
131 TCATTGTACATGCATAGTCAAACCCCAAAATTTAATATTCAAATCATAT
* *
395 AACATCATTATACATGCATGGTCAAATCCCAAAGGATGATGGTCAATCCCCAAAATTCAATAGTC
1 AACATCATTATACATGCATGGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTC
*
460 AAACCACAATCACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCACAAAATA
66 AAACCACAATCACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACA
525 TCATTGTACATGCATAGTCAAACCCCAAAA
131 TCATTGTACATGCATAGTCAAACCCCAAAA
555 GATGATGTTC
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 152 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23
Consensus pattern (179 bp):
AACATCATTATACATGCATGGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTC
AAACCACAATCACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACA
TCATTGTACATGCATAGTCAAACCCCAAAATTTAATATTCAAATCATAT
Found at i:499 original size:73 final size:74
Alignment explanation
Indices: 359--500 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 74
349 TTGTACATGC
* * * * * * * *
359 ATGGTTAAACCCCAAAATTTAATATTCAAATCATATAACATCATTATACATGCATGGTCAAATCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCC
424 CAAAGGATG
66 CAAAGGATG
* * *
433 ATGGTCAATCCCCAAAATTCAATAGTCAAACCACA-ATCACCATTGTACATGCATAGTCAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCC
497 CAAA
66 CAAA
501 ATTCAATAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
73 28 0.49
74 29 0.51
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.25
Consensus pattern (74 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCC
CAAAGGATG
Found at i:552 original size:53 final size:52
Alignment explanation
Indices: 436--554 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
426 AAGGATGATG
*
436 GTCAATCCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
1 GTCAAACCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
*
488 GTCAAACCCCAAAATTCAATAGTCAAACCACAAAAT-ATCATTGTACATGCATA
1 GTCAAACCCCAAAATTCAATAGTCAAACCAC--AATCACCATTGTACATGCATA
541 GTCAAACCCCAAAA
1 GTCAAACCCCAAAA
555 GATGATGTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
52 30 0.48
53 30 0.48
54 3 0.05
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.21
Consensus pattern (52 bp):
GTCAAACCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
Found at i:7824 original size:50 final size:50
Alignment explanation
Indices: 7749--7845 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
7739 TTGTCCAAAA
7749 TTGATTGGTTGGGTAAATTTAATATTTTCACTCACCCAAAATAATATAAG
1 TTGATTGGTTGGGTAAATTTAATATTTTCACTCACCCAAAATAATATAAG
7799 TTGATTGGTTGGGTAAATTTAATATTTTCACTCACCCAAAATAATAT
1 TTGATTGGTTGGGTAAATTTAATATTTTCACTCACCCAAAATAATAT
7846 GTTGGGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (50 bp):
TTGATTGGTTGGGTAAATTTAATATTTTCACTCACCCAAAATAATATAAG
Found at i:12747 original size:2 final size:2
Alignment explanation
Indices: 12740--12767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12730 GACAACTTCA
12740 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
12768 TTAATATACT
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:22328 original size:46 final size:46
Alignment explanation
Indices: 22275--22459 Score: 370
Period size: 46 Copynumber: 4.0 Consensus size: 46
22265 TTTCCTTAAA
22275 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
1 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
22321 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
1 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
22367 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
1 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
22413 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
1 TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
22459 T
1 T
22460 TTGCAAAGTG
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 139 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (46 bp):
TAATACTGTAATTTGTGTATAGCTACTCTTATTAATTCTCATAATG
Found at i:26320 original size:2 final size:2
Alignment explanation
Indices: 26300--26345 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
26290 TTGAAAAGTG
* * *
26300 TA TA TA CA TA CA TA CA 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 TA TA
26342 TA TA
1 TA TA
26346 AGTACGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:27163 original size:3 final size:3
Alignment explanation
Indices: 27155--27276 Score: 244
Period size: 3 Copynumber: 40.7 Consensus size: 3
27145 CTACTATTTT
27155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27203 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27251 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
27277 GATGATTTAA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28513 original size:35 final size:35
Alignment explanation
Indices: 28458--28524 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
28448 TTTTTTATAT
*
28458 TGAAGTTAGTAGGATATTAAGGTGTTTGGAGATAC
1 TGAAGTTAGTAGGATATTAAGGTGTTTAGAGATAC
* * *
28493 TGAAGTTAGTGGGGTTTTAAGGTGTTTAGAGA
1 TGAAGTTAGTAGGATATTAAGGTGTTTAGAGA
28525 GCTTAAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.28, C:0.01, G:0.34, T:0.36
Consensus pattern (35 bp):
TGAAGTTAGTAGGATATTAAGGTGTTTAGAGATAC
Found at i:28625 original size:22 final size:21
Alignment explanation
Indices: 28589--28899 Score: 140
Period size: 22 Copynumber: 14.2 Consensus size: 21
28579 TCTCTAGCAT
*
28589 GTTAACAAAATTTTATAAGGAG
1 GTTATCAAAA-TTTATAAGGAG
* *
28611 GTTATAGAAAATTTAT-AGGTAT
1 GTTAT-CAAAATTTATAAGG-AG
28633 GTTATCAAAATTTATAA-GATG
1 GTTATCAAAATTTATAAGGA-G
28654 GTTATCAAAATTTCAT---GAG
1 GTTATCAAAATTT-ATAAGGAG
28673 GTTATCAAAATTTCA-AATGGAG
1 GTTATCAAAATTT-ATAA-GGAG
28695 GTTATCAAAATTTTATAAGGAG
1 GTTATCAAAA-TTTATAAGGAG
28717 GTTTAT-AAAATTT-TCATAGTGAG
1 G-TTATCAAAATTTAT-A-AG-GAG
* * *
28740 G-TATCACAATTTCATGA-TATG
1 GTTATCAAAATTT-ATAAGGA-G
* *
28761 GTTATCAAAATTTTATAATGTG
1 GTTATCAAAA-TTTATAAGGAG
* * * *
28783 ATTACCAATATTT-TATCGGAAG
1 GTTATCAAAATTTATA-AGG-AG
*
28805 GTTATCAAAATTTCATAATGTGCG
1 GTTATCAAAATTT-ATAA-G-GAG
* * * **
28829 CTTACCAACATTTCATTGGGAG
1 GTTATCAAAATTT-ATAAGGAG
* *
28851 GTTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTT-ATAAGGAG
* *
28873 GTTATCAAAATTTCATTAGGTG
1 GTTATCAAAATTT-ATAAGGAG
28895 GTTAT
1 GTTAT
28900 TTGAAGTTTA
Statistics
Matches: 225, Mismatches: 36, Indels: 56
0.71 0.11 0.18
Matches are distributed among these distances:
19 16 0.07
20 7 0.03
21 39 0.17
22 123 0.55
23 21 0.09
24 18 0.08
25 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTTATAAGGAG
Found at i:28808 original size:44 final size:45
Alignment explanation
Indices: 28760--28867 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 45
28750 TTCATGATAT
* * *
28760 GGTTATCAAAATTTTATAATGT-GATTACCAATATTTTATCGGAA
1 GGTTATCAAAATTTCATAATGTCGATTACCAACATTTCATCGGAA
* * *
28804 GGTTATCAAAATTTCATAATGTGCGCTTACCAACATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGT-CGATTACCAACATTTCATCGGAA
28850 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
28868 GGGTGGTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 21 0.38
46 35 0.62
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAATGTCGATTACCAACATTTCATCGGAA
Found at i:28934 original size:24 final size:22
Alignment explanation
Indices: 28906--28980 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
28896 TTATTTGAAG
*
28906 TTTATAGGTATAGTGTAACAAAAT
1 TTTATAGGGA-AGT-TAACAAAAT
*
28930 TTTATAGGGAAGTTAACACAAT
1 TTTATAGGGAAGTTAACAAAAT
* * ** *
28952 TTTATATGGAGGTTCTCGAAAT
1 TTTATAGGGAAGTTAACAAAAT
28974 TTTATAG
1 TTTATAG
28981 TATCGTCATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 30 0.71
23 3 0.07
24 9 0.21
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (22 bp):
TTTATAGGGAAGTTAACAAAAT
Found at i:28952 original size:22 final size:24
Alignment explanation
Indices: 28906--28957 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
28896 TTATTTGAAG
*
28906 TTTATAGGTATAGTGTAACAAAAT
1 TTTATAGGGATAGTGTAACAAAAT
*
28930 TTTATAGGGA-AGT-TAACACAAT
1 TTTATAGGGATAGTGTAACAAAAT
28952 TTTATA
1 TTTATA
28958 TGGAGGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 14 0.54
23 3 0.12
24 9 0.35
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (24 bp):
TTTATAGGGATAGTGTAACAAAAT
Found at i:29016 original size:22 final size:21
Alignment explanation
Indices: 28991--29057 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
28981 TATCGTCATA
*
28991 AAAACTTTATAGTGTAATTATC
1 AAAATTTTATAGTG-AATTATC
29013 AAAATTTTATA-TGGAGATTATC
1 AAAATTTTATAGT-GA-ATTATC
29035 AAAATTTTATAGTG-ATTATC
1 AAAATTTTATAGTGAATTATC
29055 AAA
1 AAA
29058 TTTCATAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 9 0.22
21 2 0.05
22 29 0.71
23 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAATTTTATAGTGAATTATC
Found at i:29087 original size:2 final size:2
Alignment explanation
Indices: 29080--29117 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29070 ATTTAATCTA
29080 AT AT AT AT AT 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 AT AT AT AT AT
29118 GAATCGAACA
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):
AT
Found at i:29582 original size:31 final size:31
Alignment explanation
Indices: 29533--29603 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
29523 ACCTTTTAAT
29533 GGGGTTGTAACCCTCGGATCACAAATTTACC
1 GGGGTTGTAACCCTCGGATCACAAATTTACC
29564 GGGGATTGTAA-CCTCGGATCACAAATTTACC
1 GGGG-TTGTAACCCTCGGATCACAAATTTACC
29595 GGGGGTTGT
1 -GGGGTTGT
29604 CGGACCCTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 28 0.74
32 10 0.26
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (31 bp):
GGGGTTGTAACCCTCGGATCACAAATTTACC
Found at i:32477 original size:22 final size:22
Alignment explanation
Indices: 32447--32651 Score: 118
Period size: 22 Copynumber: 9.5 Consensus size: 22
32437 TCCAATGTAG
*
32447 AAATATTGATAACCACATTGTGA
1 AAAT-TTGATAACCACATTATGA
* *
32470 AAATTTGATAATCTCATTATG-
1 AAATTTGATAACCACATTATGA
32491 AAATTTCGAT-A--ACA-TATGA
1 AAATTT-GATAACCACATTATGA
*
32510 AAATTTGATAACCACATTGTGA
1 AAATTTGATAACCACATTATGA
* * *
32532 AATTTTGATCACCACACTATGA
1 AAATTTGATAACCACATTATGA
* ** * *
32554 AATTTTGATAACCTTAGTGTGA
1 AAATTTGATAACCACATTATGA
* * * **
32576 AATTTTGATAATCTCCCTATGA
1 AAATTTGATAACCACATTATGA
* * *
32598 AATTTTGATAATCACACTAT-A
1 AAATTTGATAACCACATTATGA
* ** *
32619 AAA-TTGGTAACCGTACTATGA
1 AAATTTGATAACCACATTATGA
32640 AAATTTTGATAA
1 AAA-TTTGATAA
32652 TCTCTTCATA
Statistics
Matches: 146, Mismatches: 27, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
18 7 0.05
19 9 0.06
20 12 0.08
21 17 0.12
22 91 0.62
23 10 0.07
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (22 bp):
AAATTTGATAACCACATTATGA
Found at i:32510 original size:18 final size:18
Alignment explanation
Indices: 32467--32521 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 18
32457 AACCACATTG
32467 TGAAAATTTGATAATCTCATTA
1 TGAAAATTTGATAA---CA-TA
32489 TG-AAATTTCGATAACATA
1 TGAAAATTT-GATAACATA
32507 TGAAAATTTGATAAC
1 TGAAAATTTGATAAC
32522 CACATTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
21 6 0.19
22 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
TGAAAATTTGATAACATA
Found at i:32517 original size:40 final size:43
Alignment explanation
Indices: 32467--32566 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 43
32457 AACCACATTG
* *
32467 TGAAAATTTGATAATCTCATTATGAAATTTCGAT-A-ACA-TA
1 TGAAAATTTGATAACCACATTATGAAATTTCGATCACACACTA
* *
32507 TGAAAATTTGATAACCACATTGTGAAATTTTGATCACCACACTA
1 TGAAAATTTGATAACCACATTATGAAATTTCGATCA-CACACTA
*
32551 TGAAATTTTGATAACC
1 TGAAAATTTGATAACC
32567 TTAGTGTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 30 0.59
41 1 0.02
43 3 0.06
44 17 0.33
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (43 bp):
TGAAAATTTGATAACCACATTATGAAATTTCGATCACACACTA
Found at i:32553 original size:62 final size:63
Alignment explanation
Indices: 32447--32565 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 63
32437 TCCAATGTAG
* * *
32447 AAATATTGATAACCACATTGTGAAAATTTGATAATCTCATTATGAAATTTCGATAACATATGA
1 AAATATTGATAACCACATTGTGAAAATTTGATAACCACACTATGAAATTTCGATAACATATGA
* * *
32510 AAAT-TTGATAACCACATTGTGAAATTTTGATCACCACACTATGAAATTTTGATAAC
1 AAATATTGATAACCACATTGTGAAAATTTGATAACCACACTATGAAATTTCGATAAC
32566 CTTAGTGTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 46 0.92
63 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (63 bp):
AAATATTGATAACCACATTGTGAAAATTTGATAACCACACTATGAAATTTCGATAACATATGA
Found at i:32561 original size:44 final size:44
Alignment explanation
Indices: 32446--32613 Score: 155
Period size: 44 Copynumber: 3.9 Consensus size: 44
32436 CTCCAATGTA
* * * * * *
32446 GAAATATTGATAACCACATTGTGAAAATTTGATAATCTCATTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACATTGT
*
32490 GAAATTTCGAT-A--ACA-TATGAAAATTTGATAACCACATTGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACATTGT
* * ** *
32530 GAAATTTTGATCACCACACTATGAAATTTTGATAACCTTAGTGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACATTGT
* * * * *
32574 GAAATTTTGATAATCTCCCTATGAAATTTTGATAATCACA
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACA
32614 CTATAAAATT
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
40 31 0.30
41 4 0.04
43 4 0.04
44 63 0.62
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCACATTGT
Found at i:32602 original size:66 final size:65
Alignment explanation
Indices: 32529--32673 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 65
32519 AACCACATTG
* * * * *
32529 TGAAATTTTGATCACCACACTATGAAATTTTGATAACCTTAGTGTG-AAATTTTGATAATCTCCC
1 TGAAATTTTGATAACCACACTAT-AAA-ATTGATAACCGTACTATGAAAATTTTGATAATCTCCC
32593 TA
64 TA
* * *
32595 TGAAATTTTGATAATCACACTATAAAATTGGTAACCGTACTATGAAAATTTTGATAATCT-CTTC
1 TGAAATTTTGATAACCACACTATAAAATTGATAACCGTACTATGAAAATTTTGATAATCTCCCT-
32659 A
65 A
*
32660 TAAAATTTTGATAA
1 TGAAATTTTGATAA
32674 AACCTCATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 15 0.22
65 32 0.47
66 21 0.31
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (65 bp):
TGAAATTTTGATAACCACACTATAAAATTGATAACCGTACTATGAAAATTTTGATAATCTCCCTA
Found at i:32623 original size:44 final size:44
Alignment explanation
Indices: 32447--32673 Score: 137
Period size: 44 Copynumber: 5.3 Consensus size: 44
32437 TCCAATGTAG
* * * * * * * *
32447 AAATATTGATAACCACATTGTGAAAATTTGATAATCTCATTATG
1 AAATTTTGATAACCTCACTATGAAATTTTGATAACCACATTATA
* * * *
32491 AAATTTCGATAA---CA-TATGAAAATTTGATAACCACATTGTG
1 AAATTTTGATAACCTCACTATGAAATTTTGATAACCACATTATA
* * ** * * *
32531 AAATTTTGATCACCACACTATGAAATTTTGATAACCTTAGTGTG
1 AAATTTTGATAACCTCACTATGAAATTTTGATAACCACATTATA
* * * *
32575 AAATTTTGATAATCTCCCTATGAAATTTTGATAATCACACTATA
1 AAATTTTGATAACCTCACTATGAAATTTTGATAACCACATTATA
* * *
32619 AAA--TTGGTAACCGT-ACTATGAAAATTTTGATAATCTC-TTCATA
1 AAATTTTGATAACC-TCACTATG-AAATTTTGATAACCACATT-ATA
32662 AAATTTTGATAA
1 AAATTTTGATAA
32674 AACCTCATTA
Statistics
Matches: 146, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
40 32 0.22
41 2 0.01
42 13 0.09
43 24 0.16
44 69 0.47
45 6 0.04
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (44 bp):
AAATTTTGATAACCTCACTATGAAATTTTGATAACCACATTATA
Done.