Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015569.1 Corchorus olitorius cultivar O-4 contig15602, 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: 68875
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:60 original size:40 final size:39
Alignment explanation
Indices: 1--187 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 39
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTCCATTCCTGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTT-CATTCCTGTTT
*
41 TGCCCTTCCCCACCAGAAGGTGTTGTTT-ATTTTCCTGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTCA--TTCCTGTTT
** *
81 TGCCCTTCCCCACTAGAAGGTGTTGTTTTCATTCCCGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTG-TTTCATTCCTGTTT
* * ** *
121 TGGCCTTCCCGACCGGAAGGTGTTGTCTTTTTTCCAG-TT
1 TGCCCTTCCCCACCGGAAGGTGTTGT-TTCATTCCTGTTT
* *
160 TGCCCTTTCCTACCGGAAGGTGTTGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTT
188 ACCCCACCGG
Statistics
Matches: 129, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.02
39 26 0.20
40 96 0.74
41 3 0.02
42 1 0.01
ACGTcount: A:0.11, C:0.28, G:0.21, T:0.40
Consensus pattern (39 bp):
TGCCCTTCCCCACCGGAAGGTGTTGTTTCATTCCTGTTT
Found at i:140 original size:80 final size:79
Alignment explanation
Indices: 1--187 Score: 259
Period size: 80 Copynumber: 2.4 Consensus size: 79
*
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTCCATTCCTGTTTTGCCCTTCCCCACCAGAAGGTGTTG
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTCCATTCCCGTTTTGCCCTTCCCCACCAGAAGGTGTTG
*
66 T-TTATTTTCCTGTTT
66 TCTT-TTTTCCAG-TT
** * * * *
81 TGCCCTTCCCCACTAGAAGGTGTTGTTTTCATTCCCGTTTTGGCCTTCCCGACCGGAAGGTGTTG
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTCCATTCCCGTTTTGCCCTTCCCCACCAGAAGGTGTTG
146 TCTTTTTTCCAGTT
66 TCTTTTTTCCAGTT
* *
160 TGCCCTTTCCTACCGGAAGGTGTTGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTT
188 ACCCCACCGG
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 26 0.28
80 66 0.70
81 2 0.02
ACGTcount: A:0.11, C:0.28, G:0.21, T:0.40
Consensus pattern (79 bp):
TGCCCTTCCCCACCGGAAGGTGTTGTTTCCATTCCCGTTTTGCCCTTCCCCACCAGAAGGTGTTG
TCTTTTTTCCAGTT
Found at i:302 original size:141 final size:140
Alignment explanation
Indices: 48--328 Score: 354
Period size: 141 Copynumber: 2.0 Consensus size: 140
38 TTTTGCCCTT
* * *
48 CCCCACCAGAAGGTGTTGTTTATTTTCCTGTTTTGCCCTTCCCCACTAGAAGGTGTTGTTTTCAT
1 CCCCACCAGAAGGTGTTGTTCATTTTCCTGTTTTACCCTTCCCAACTAGAAGGTGTTGTTTT-AT
* * * *
113 TCCCGTTTTGGCCTTCCCGACCGGAAGGTGTTGTCTTTTTTCCAGTTTGCCCTT-TCCTACCGGA
65 TCCCGTTTTGCCCTTCCCGACCGGAAGGTGTTGTCTTTTTCCCAGTTTGCCATTCT-CGACCGGA
177 AGGTGTTGTTTA
129 AGGTGTTGTTTA
* * * *
189 CCCCACCGGAAGGTGTTGTTCCTTTTCTTGTTTTACCCTTCCCAA-TCGGAAGGTGTTGTTCCTT
1 CCCCACCAGAAGGTGTTGTTCATTTTCCTGTTTTACCCTTCCCAACT-AGAAGGTGTTGTT--TT
* * *
253 -TTCCTGTTTTGCCCTTCCCTACCGGAAGGTGTTGT-TTTATTCCCAGTTTGCCATTCTCGGCCG
63 ATTCCCGTTTTGCCCTTCCCGACCGGAAGGTGTTGTCTTT-TTCCCAGTTTGCCATTCTCGACCG
316 GAAGGTGTTGTTT
127 GAAGGTGTTGTTT
329 TATTCCTGTT
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
140 4 0.03
141 114 0.94
142 1 0.01
143 2 0.02
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (140 bp):
CCCCACCAGAAGGTGTTGTTCATTTTCCTGTTTTACCCTTCCCAACTAGAAGGTGTTGTTTTATT
CCCGTTTTGCCCTTCCCGACCGGAAGGTGTTGTCTTTTTCCCAGTTTGCCATTCTCGACCGGAAG
GTGTTGTTTA
Found at i:347 original size:79 final size:78
Alignment explanation
Indices: 235--506 Score: 243
Period size: 79 Copynumber: 3.4 Consensus size: 78
225 CCTTCCCAAT
235 CGGAAGGTGTTGTTCCTTTTCCTGTTTTGCCCTTCCCTACCGGAAGGTGTTGTTTTATTCCCA-G
1 CGGAAGGTGTTGTT--TTTTCCTGTTTTGCCCTTCCC-ACCGGAAGGTGTTGTTTTATTCCCATG
* **
299 -TTTGCCATTCT-CGGC
63 TTTTACCATT-TGCCAC
* * *
314 CGGAAGGTGTTGTTTTATTCCTGTTTTACCCCTTCCCACCGGAAAGTGTTGTTTCT-TT-TCATG
1 CGGAAGGTGTTGTTTT-TTCCTGTTTT-GCCCTTCCCACCGGAAGGTGTTGTTT-TATTCCCATG
*
377 TTTTACCCTTTGCCAC
63 TTTTACCATTTGCCAC
* * *
393 CGGAAGGTGTTTTTTTTTTCTTGTTTTGCCTTTCACCACCGGAAGGTGTTGTTTTATT-CC-TGT
1 CGGAAGGTG-TTGTTTTTTCCTGTTTTGCCCTTC-CCACCGGAAGGTGTTGTTTTATTCCCATGT
* * **
456 TTTGCCCTTCCCCAC
64 TTTACCATTTGCCAC
* * *
471 CGGAAGGTGTTTTTTCTGTTTCTGTTATGCCCTTCC
1 CGGAAGGTGTTGTTT-T-TTCCTGTTTTGCCCTTCC
507 AGGTCGGAAG
Statistics
Matches: 162, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
77 10 0.06
78 62 0.38
79 84 0.52
80 6 0.04
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (78 bp):
CGGAAGGTGTTGTTTTTTCCTGTTTTGCCCTTCCCACCGGAAGGTGTTGTTTTATTCCCATGTTT
TACCATTTGCCAC
Found at i:356 original size:39 final size:38
Alignment explanation
Indices: 190--506 Score: 298
Period size: 39 Copynumber: 8.1 Consensus size: 38
180 TGTTGTTTAC
* *
190 CCCACCGGAAGGTGTTGTTCCTT-TTCTTGTTTTACCCTT
1 CCCACCGGAAGGTGTTGTT--TTATTCCTGTTTTGCCCTT
*
229 CCCAATCGGAAGGTGTTGTTCCTT-TTCCTGTTTTGCCCTT
1 CCC-ACCGGAAGGTGTTGTT--TTATTCCTGTTTTGCCCTT
* *
269 CCCTACCGGAAGGTGTTGTTTTATTCCCAG-TTTGCCATT
1 CCC-ACCGGAAGGTGTTGTTTTATT-CCTGTTTTGCCCTT
** *
308 CTCGGCCGGAAGGTGTTGTTTTATTCCTGTTTTACCCCTT
1 C-CCACCGGAAGGTGTTGTTTTATTCCTGTTTT-GCCCTT
* * * *
348 CCCACCGGAAAGTGTTGTTTCTTTTCATGTTTTACCCTTT
1 CCCACCGGAAGGTGTTGTTT-TATTCCTGTTTTGCCC-TT
* * * * *
388 GCCACCGGAAGGTGTTTTTTTTTTCTTGTTTTGCCTTT
1 CCCACCGGAAGGTGTTGTTTTATTCCTGTTTTGCCCTT
426 CACCACCGGAAGGTGTTGTTTTATTCCTGTTTTGCCCTT
1 C-CCACCGGAAGGTGTTGTTTTATTCCTGTTTTGCCCTT
* * * *
465 CCCCACCGGAAGGTGTTTTTTCTGTTTCTGTTATGCCCTT
1 -CCCACCGGAAGGTGTTGTTT-TATTCCTGTTTTGCCCTT
505 CC
1 CC
507 AGGTCGGAAG
Statistics
Matches: 234, Mismatches: 33, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
38 7 0.03
39 122 0.52
40 105 0.45
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (38 bp):
CCCACCGGAAGGTGTTGTTTTATTCCTGTTTTGCCCTT
Found at i:515 original size:118 final size:115
Alignment explanation
Indices: 191--521 Score: 362
Period size: 118 Copynumber: 2.8 Consensus size: 115
181 GTTGTTTACC
* * * *
191 CCACCGGAAGGTGTTGTTCCTT-TTCTTGTTTTACCCTTCCCAATCGGAAGGTGTTGTTCCTTTT
1 CCACCGGAAGGTGTTGTT--TTATTCCTGTTTTACCCTTCCCCACCGGAAGGTGTTGTTTCTTTT
*
255 CCTGTTTTGCCCTTCCCTACCGGAAGGTGTTGTTTTATTCCCAGTTTGCCATTCT
64 -CTGTTTTGCCCTT-CC-ACCGGAAGGTGTTGTTTTATTCCCAGTTTGCCATTCA
** *
310 CGGCCGGAAGGTGTTGTTTTATTCCTGTTTTACCCCTT-CCCACCGGAAAGTGTTGTTTCTTTTC
1 CCACCGGAAGGTGTTGTTTTATTCCTGTTTTA-CCCTTCCCCACCGGAAGGTGTTGTTTCTTTTC
* * * ** *
374 ATGTTTTACCCTTTGCCACCGGAAGGTGTT-TTTTTTTTCTTGTTTTGCCTTTCA
65 -TGTTTTGCCC-TT-CCACCGGAAGGTGTTGTTTTATTCCCAG-TTTGCCATTCA
* *
428 CCACCGGAAGGTGTTGTTTTATTCCTGTTTTGCCCTTCCCCACCGGAAGGTGTTTTTTCTGTTTC
1 CCACCGGAAGGTGTTGTTTTATTCCTGTTTTACCCTTCCCCACCGGAAGGTGTTGTTTCT-TTTC
* *
493 TGTTATGCCCTTCCAGGTCGGAAGGTGTT
65 TGTTTTGCCCTTCCA--CCGGAAGGTGTT
522 ATTTAATTTT
Statistics
Matches: 180, Mismatches: 23, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
116 3 0.02
117 18 0.10
118 130 0.72
119 29 0.16
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.43
Consensus pattern (115 bp):
CCACCGGAAGGTGTTGTTTTATTCCTGTTTTACCCTTCCCCACCGGAAGGTGTTGTTTCTTTTCT
GTTTTGCCCTTCCACCGGAAGGTGTTGTTTTATTCCCAGTTTGCCATTCA
Found at i:5706 original size:26 final size:27
Alignment explanation
Indices: 5670--5733 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
5660 TCTTTCGACT
5670 TTGCATTTGGGCA-TTTTAGTTTGAGA
1 TTGCATTTGGGCATTTTTAGTTTGAGA
*
5696 TTGCATTTGGGCATTTTTAGTTTGGGA
1 TTGCATTTGGGCATTTTTAGTTTGAGA
5723 TTGCATTTGGG
1 TTGCATTTGGG
5734 GCACATTGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.36
27 23 0.64
ACGTcount: A:0.16, C:0.08, G:0.30, T:0.47
Consensus pattern (27 bp):
TTGCATTTGGGCATTTTTAGTTTGAGA
Found at i:7397 original size:19 final size:19
Alignment explanation
Indices: 7373--7411 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7363 ATATCAGCAT
7373 TTTCCAGTAGTGATATCAA
1 TTTCCAGTAGTGATATCAA
7392 TTTCCAGTAGTGATATCAA
1 TTTCCAGTAGTGATATCAA
7411 T
1 T
7412 AAAAGCACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTCCAGTAGTGATATCAA
Found at i:11352 original size:2 final size:2
Alignment explanation
Indices: 11340--11377 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
11330 CCTTTGTCAC
*
11340 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11378 GGAATTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11531 original size:43 final size:43
Alignment explanation
Indices: 11484--11813 Score: 410
Period size: 43 Copynumber: 7.8 Consensus size: 43
11474 ATAAGGAGAA
*
11484 ATGCCTCTATGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
11527 ATGCCCCTGTGTTATATATGTGTTTGTGGACTTTG-ATATA-A-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
11568 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
11610 ATTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTG-AATATAG
1 A-TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
11652 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * * *
11695 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGGATATAG-G
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
11737 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
* *
11779 ATTGCCACTGTGTTATATATGTGTTTGGGGACTTT
1 A-TGCCTCTGTGTTATATATGTGTTTGAGGACTTT
11814 TTGGTTATTG
Statistics
Matches: 254, Mismatches: 20, Indels: 26
0.85 0.07 0.09
Matches are distributed among these distances:
41 97 0.38
42 20 0.08
43 109 0.43
44 28 0.11
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (43 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:11596 original size:84 final size:84
Alignment explanation
Indices: 11482--11813 Score: 517
Period size: 84 Copynumber: 3.9 Consensus size: 84
11472 CCATAAGGAG
*
11482 AAATGCCTCTATGTTATATATGTGTTTGAGGACTTTGTAATAGAGA-TGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-ATTGCCCCTGTGTTATATAT
*
11546 GTGTTTGTGGACTTTGATAT
65 GTGTTTGGGGACTTTGATAT
11566 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
11631 TGTTTGGGGAC-TTGAATAT
66 TGTTTGGGGACTTTG-ATAT
** *
11650 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATA-AAGGTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-TTGCCCCTGTGTTATATAT
*
11714 GTGTTTGGGGACTTGGATAT
65 GTGTTTGGGGACTTTGATAT
** * *
11734 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAATTGCCACTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAATTGCCCCTGTGTTATATAT
11799 GTGTTTGGGGACTTT
65 GTGTTTGGGGACTTT
11814 TTGGTTATTG
Statistics
Matches: 232, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
83 6 0.03
84 183 0.79
85 41 0.18
86 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:24276 original size:2 final size:2
Alignment explanation
Indices: 24269--24304 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
24259 GGCCTTTGTC
*
24269 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24305 GGAATTTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24465 original size:43 final size:43
Alignment explanation
Indices: 24412--24657 Score: 299
Period size: 43 Copynumber: 5.8 Consensus size: 43
24402 ATAAGGAGAA
* *
24412 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAG
*
24455 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT-GATATAG-G
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAG
* * *
24497 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAG
* *
24539 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGGATATAG-G
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAG
**
24581 -TGCCTATGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAG
* *
24623 ATTGCCCATGTGTTATATATGTGTTTGGGGACTTT
1 A-TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
24658 TTGGTTATTG
Statistics
Matches: 177, Mismatches: 16, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
41 61 0.34
42 13 0.07
43 75 0.42
44 28 0.16
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAG
Found at i:24511 original size:84 final size:84
Alignment explanation
Indices: 24413--24657 Score: 411
Period size: 84 Copynumber: 2.9 Consensus size: 84
24403 TAAGGAGAAA
24413 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
24478 TTGGGGACTTTGATATAGG
66 TTGGGGACTTTGATATAGG
* *
24497 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
*
24562 TTGGGGACTTGGATATAGG
66 TTGGGGACTTTGATATAGG
* * *
24581 TGCCTATGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-ATTGCCCATGTGTTATATATGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGA-TGCCCCTGTGTTATATATGT
24645 GTTTGGGGACTTT
64 GTTTGGGGACTTT
24658 TTGGTTATTG
Statistics
Matches: 150, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
84 110 0.73
85 40 0.27
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.42
Consensus pattern (84 bp):
TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
TTGGGGACTTTGATATAGG
Found at i:26367 original size:13 final size:13
Alignment explanation
Indices: 26349--26374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26339 TTGGTTTAGG
26349 AAAAAGAAAATTA
1 AAAAAGAAAATTA
26362 AAAAAGAAAATTA
1 AAAAAGAAAATTA
26375 TGTTAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAGAAAATTA
Found at i:29137 original size:2 final size:2
Alignment explanation
Indices: 29130--29156 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29120 AAGAAACGCA
29130 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
29157 AAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30034 original size:17 final size:19
Alignment explanation
Indices: 29992--30031 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29982 GGACCGGGGG
29992 AGAAGGAGAGGAAGAGAGA
1 AGAAGGAGAGGAAGAGAGA
* *
30011 GGAAGGAGGGGAAGAGA-A
1 AGAAGGAGAGGAAGAGAGA
30029 AGA
1 AGA
30032 GGAAGAAGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (19 bp):
AGAAGGAGAGGAAGAGAGA
Found at i:33786 original size:6 final size:6
Alignment explanation
Indices: 33779--33809 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
33769 ATAGTTCAAT
*
33779 TCCAAT TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
33810 ATTAGTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (6 bp):
TCCAAA
Found at i:39199 original size:12 final size:12
Alignment explanation
Indices: 39181--39210 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39171 TAAAGGTTAG
39181 ATTTTCATATTC
1 ATTTTCATATTC
*
39193 TTTTTCATATTC
1 ATTTTCATATTC
39205 ATTTTC
1 ATTTTC
39211 CAAACGGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTTTCATATTC
Found at i:41664 original size:27 final size:26
Alignment explanation
Indices: 41604--41669 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
41594 TAAGTTGGCC
*
41604 ACCAA-ATCAATCAGAAATCATAAAA
1 ACCAAGATAAATCAGAAATCATAAAA
* *
41629 ACATAAAGATAAATCTGAAATCATAAAA
1 AC--CAAGATAAATCAGAAATCATAAAA
41657 TACCAAGATAAAT
1 -ACCAAGATAAAT
41670 AATCAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.06
27 11 0.33
28 18 0.55
29 2 0.06
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.20
Consensus pattern (26 bp):
ACCAAGATAAATCAGAAATCATAAAA
Found at i:44183 original size:3 final size:3
Alignment explanation
Indices: 44171--44205 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
44161 ACATCAACAA
* *
44171 CAG CAA CAG CAG CAG CAG CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
44206 ACAACAAGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.34, G:0.26, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:44189 original size:15 final size:15
Alignment explanation
Indices: 44171--44208 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
44161 ACATCAACAA
44171 CAGCAACAGCAGCAG
1 CAGCAACAGCAGCAG
44186 CAGCAACAGCAGCAG
1 CAGCAACAGCAGCAG
44201 CAGCAACA
1 CAGCAACA
44209 ACAAGCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.34, G:0.24, T:0.00
Consensus pattern (15 bp):
CAGCAACAGCAGCAG
Found at i:44426 original size:21 final size:21
Alignment explanation
Indices: 44402--44459 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
44392 ACCGTCTCCG
44402 CAGCAGCAACAGCAGCCACAA
1 CAGCAGCAACAGCAGCCACAA
* * *
44423 CAGCAACAACAACAGCCTCAA
1 CAGCAGCAACAGCAGCCACAA
* *
44444 AATCAGCAACAGCAGC
1 CAGCAGCAACAGCAGC
44460 AGCAGCAGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.36, G:0.16, T:0.03
Consensus pattern (21 bp):
CAGCAGCAACAGCAGCCACAA
Found at i:47499 original size:31 final size:30
Alignment explanation
Indices: 47464--47525 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 30
47454 GCGAAGTTGG
47464 GGAGTTTGATTTGAATAGTAGATGAGTTCAT
1 GGAGTTTGATTTGAATAGTAGATGAG-TCAT
47495 GGAGTTTGATTTGAATAGTAGATGAGTCAT
1 GGAGTTTGATTTGAATAGTAGATGAGTCAT
47525 G
1 G
47526 AACGGTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.37
Consensus pattern (30 bp):
GGAGTTTGATTTGAATAGTAGATGAGTCAT
Found at i:62479 original size:21 final size:22
Alignment explanation
Indices: 62350--62518 Score: 82
Period size: 21 Copynumber: 7.9 Consensus size: 22
62340 TGAATATTTT
**
62350 TATGAAATTTT-ATAA-CCACC
1 TATGAAATTTTGATAATCTTCC
*
62370 TATGAAATTTTCATAAT-TAT-C
1 TATGAAATTTTGATAATCT-TCC
* *
62391 TATGAAATTCTGATAAAC-TCC
1 TATGAAATTTTGATAATCTTCC
* * ***
62412 ATATGAAACTTTGATAACCTAAT
1 -TATGAAATTTTGATAATCTTCC
* * * *
62435 TATAAAAATTTAATAAACCTTCC
1 TATGAAATTTTGAT-AATCTTCC
62458 TATGAAATTTTG-TAATCTTCC
1 TATGAAATTTTGATAATCTTCC
* * *
62479 TATG-ATTTTTGATAATATTCT
1 TATGAAATTTTGATAATCTTCC
* * *
62500 TGTGAGATTTTGTTAATCT
1 TATGAAATTTTGATAATCT
62519 CTATATAACT
Statistics
Matches: 110, Mismatches: 29, Indels: 18
0.70 0.18 0.11
Matches are distributed among these distances:
20 18 0.16
21 41 0.37
22 37 0.34
23 14 0.13
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:64969 original size:51 final size:52
Alignment explanation
Indices: 64868--64969 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
64858 GTTCATCAAA
* **
64868 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
64920 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
64970 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:66907 original size:27 final size:27
Alignment explanation
Indices: 66870--66957 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
66860 GGGATTTTGG
66870 GGTCATTTGCATGTTCAGGGGCATTTT
1 GGTCATTTGCATGTTCAGGGGCATTTT
* * * * *
66897 AGTCATTTGCACGTCCAAGGGCATTTC
1 GGTCATTTGCATGTTCAGGGGCATTTT
*
66924 GGTCATTTGTATGTTC-GGAGGCATTTT
1 GGTCATTTGCATGTTCAGG-GGCATTTT
66951 GGTCATT
1 GGTCATT
66958 CTAGATTCAC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
26 1 0.02
27 48 0.98
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (27 bp):
GGTCATTTGCATGTTCAGGGGCATTTT
Found at i:67263 original size:36 final size:36
Alignment explanation
Indices: 67216--67305 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
67206 TATGCATTTT
67216 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
*
67252 TTATTAGTAATTAGGCATCATCGTTCACATTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
67288 TTATTAGTAATTAGGCAT
1 TTATTAGTAATTAGGCAT
67306 TGCATTCACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (36 bp):
TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
Done.