Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007473.1 Corchorus capsularis cultivar CVL-1 contig07494, 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: 51223
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3179 original size:67 final size:66
Alignment explanation
Indices: 3071--3205 Score: 207
Period size: 67 Copynumber: 2.0 Consensus size: 66
3061 ACTTAACTTT
* * *
3071 TTGGTTATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAAGGCTT
1 TTGGTCATTTCTCAATTGACTTTAATAGAGCAGTGGAATTACTAAAAGATCCCTACC-AAGCCTT
3136 GC
65 GC
* * *
3138 TTGGTCATTTCTTAATTGGCTTTAATTGAGCAGTGGAATTACTAAAAGATCCCTACCAAGCCTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAGCAGTGGAATTACTAAAAGATCCCTACCAAGCCTTG
3203 C
66 C
3204 TT
1 TT
3206 TTGCAGCTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 10 0.16
67 52 0.84
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (66 bp):
TTGGTCATTTCTCAATTGACTTTAATAGAGCAGTGGAATTACTAAAAGATCCCTACCAAGCCTTG
C
Found at i:3434 original size:166 final size:167
Alignment explanation
Indices: 3139--3489 Score: 449
Period size: 166 Copynumber: 2.1 Consensus size: 167
3129 AAGGCTTGCT
* * * * * *
3139 TGGTCATTTCTTAATTGGCTTTAATTGAGCAGTGGAATTACTAAAAGATCCCTACCAAGCCTTGC
1 TGGTCATTTCTCAA-TGGCTTGAATAGAGCAGTGGAATTACTAAAAGATCCCCACCAAGCATTGA
** * * *
3204 TTTTGCAGCTAGAGATAGAACTTATTTTTTTCGTCTTTTCCTACTTGACAGATTACAGAAATGTC
65 TGATGCAGCTA-AGA-AGAACTAATATTTTTCGTCTTTACCTACTTGACAGATTACAGAAATGTC
* *
3269 CTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTG
128 CTAACTTTTGATTCTTGA-GGGATTAAATAACTAAACTTTG
* * *
3310 TGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCCATCAAGGATTGA
1 TGGTCATTTCTCAATGG-CTTGAATAGAGCAGTGGAATTACTAAAAGATCCCCACCAAGCATTGA
**
3375 TGATG-AGCT-AG-AGAACTAATATTTTTCGTCTTTACCTACTTGGA-AGATTACTTAAATGTCC
65 TGATGCAGCTAAGAAGAACTAATATTTTTCGTCTTTACCTACTT-GACAGATTACAGAAATGTCC
*
3436 TAACTTTTGATTCTTGAGGGATTAAATAACTAAACTTTT
129 TAACTTTTGATTCTTGAGGGATTAAATAACTAAACTTTG
3475 TGGTCATTTCTCAAT
1 TGGTCATTTCTCAAT
3490 TGACAAATGA
Statistics
Matches: 159, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
165 34 0.21
166 59 0.37
167 2 0.01
168 2 0.01
170 7 0.04
171 55 0.35
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (167 bp):
TGGTCATTTCTCAATGGCTTGAATAGAGCAGTGGAATTACTAAAAGATCCCCACCAAGCATTGAT
GATGCAGCTAAGAAGAACTAATATTTTTCGTCTTTACCTACTTGACAGATTACAGAAATGTCCTA
ACTTTTGATTCTTGAGGGATTAAATAACTAAACTTTG
Found at i:4234 original size:16 final size:16
Alignment explanation
Indices: 4215--4304 Score: 110
Period size: 16 Copynumber: 5.6 Consensus size: 16
4205 CCTGAACCTG
4215 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
* * *
4231 AACCCGAAAAAACACG
1 AACCCGAAAAAGCTCA
*
4247 AACCCGAAAAAGCTTA
1 AACCCGAAAAAGCTCA
4263 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
*
4279 AACCCGGAAAAA-CTCG
1 AACCC-GAAAAAGCTCA
*
4295 AATCCGAAAA
1 AACCCGAAAA
4305 TTTATGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.08
16 52 0.83
17 6 0.10
ACGTcount: A:0.51, C:0.29, G:0.13, T:0.07
Consensus pattern (16 bp):
AACCCGAAAAAGCTCA
Found at i:4474 original size:16 final size:16
Alignment explanation
Indices: 4453--4506 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
4443 ACCCAAACAG
*
4453 AACCTGAACACGAATT
1 AACCTGAACCCGAATT
*
4469 AACCTG-ACCCAAATT
1 AACCTGAACCCGAATT
*
4484 AACCCGAACCCGAATT
1 AACCTGAACCCGAATT
4500 AACCTGA
1 AACCTGA
4507 CCCAAACCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.41, C:0.31, G:0.11, T:0.17
Consensus pattern (16 bp):
AACCTGAACCCGAATT
Found at i:4485 original size:15 final size:15
Alignment explanation
Indices: 4465--4512 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
4455 CCTGAACACG
4465 AATTAACCTGACCCA
1 AATTAACCTGACCCA
* *
4480 AATTAACCCGAACCCG
1 AATTAACCTG-ACCCA
4496 AATTAACCTGACCCA
1 AATTAACCTGACCCA
4511 AA
1 AA
4513 CCCAACCCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (15 bp):
AATTAACCTGACCCA
Found at i:4500 original size:31 final size:32
Alignment explanation
Indices: 4443--4528 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 32
4433 TCTGGCCAAA
** * *
4443 ACCCAAACAGAACCTGAACACGAATTAACCTG
1 ACCCAAACCCAACCCGAACCCGAATTAACCTG
**
4475 ACCCAAA-TTAACCCGAACCCGAATTAACCTG
1 ACCCAAACCCAACCCGAACCCGAATTAACCTG
4506 ACCCAAACCCAACCCGAACCCGA
1 ACCCAAACCCAACCCGAACCCGA
4529 CTCAAGCCCG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 27 0.57
32 20 0.43
ACGTcount: A:0.41, C:0.38, G:0.10, T:0.10
Consensus pattern (32 bp):
ACCCAAACCCAACCCGAACCCGAATTAACCTG
Found at i:15573 original size:59 final size:60
Alignment explanation
Indices: 15442--15629 Score: 200
Period size: 60 Copynumber: 3.1 Consensus size: 60
15432 TTATAACTAA
* ** *
15442 AATTTTACATAAATCCCCAAACAGAATTAAAATCCCC-ATATTTTAAAACCCTAAATCACC
1 AATTTTACATAAAACCCTTAACAGAATTAAAATCCCCAAT-TTTTAAAACCCTAAATCCCC
* * * *
15502 AATTTGACATAAAACCCTTAACCGAATTAATATCCCCAATTTTTAAAACCAT-AATCCCC
1 AATTTTACATAAAACCCTTAACAGAATTAAAATCCCCAATTTTTAAAACCCTAAATCCCC
*** * * * *
15561 AATTTTACATAAAATAGTTAAACTGAATTAAAAAACCCCAATTTTTGAAACCCTAAATCCCT
1 AATTTTACATAAAACCCTT-AACAGAATT-AAAATCCCCAATTTTTAAAACCCTAAATCCCC
15623 AATTTTA
1 AATTTTA
15630 AAAAGAAATT
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
59 21 0.20
60 50 0.47
61 22 0.21
62 13 0.12
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.30
Consensus pattern (60 bp):
AATTTTACATAAAACCCTTAACAGAATTAAAATCCCCAATTTTTAAAACCCTAAATCCCC
Found at i:16594 original size:30 final size:29
Alignment explanation
Indices: 16517--16594 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
16507 ACTTGTAGTG
*
16517 TTTGGACGTTTTGTCCCATGAACTTCAAT
1 TTTGGACGTTTTGTCCCCTGAACTTCAAT
* *
16546 TTTGGCCATTTTGTCCCCTGAACTTCAAT
1 TTTGGACGTTTTGTCCCCTGAACTTCAAT
*
16575 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGTCCCCT
16595 CAACCTAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGTCCCCTGAACTTCAAT
Found at i:16819 original size:28 final size:29
Alignment explanation
Indices: 16746--16819 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
16736 TAGGCTGACG
16746 AGGCAAAACGTCTCAAAATTGAAGTTCAAC
1 AGGCAAAACGTC-CAAAATTGAAGTTCAAC
* ** *
16776 AGACAAAATATCCAAAATTGAAGTTTAA-
1 AGGCAAAACGTCCAAAATTGAAGTTCAAC
*
16804 GGGCAAAACGTCCAAA
1 AGGCAAAACGTCCAAA
16820 CGCTAGAAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
28 12 0.33
29 15 0.42
30 9 0.25
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (29 bp):
AGGCAAAACGTCCAAAATTGAAGTTCAAC
Found at i:18370 original size:30 final size:30
Alignment explanation
Indices: 18334--18390 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
18324 CTGCTGCAGC
* *
18334 AACTGATTCTCTCACCACCCAACTTTCAGA
1 AACTGATCCACTCACCACCCAACTTTCAGA
*
18364 AACTGATCCACTCACCACCCAGCTTTC
1 AACTGATCCACTCACCACCCAACTTTC
18391 TTCTCAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.40, G:0.07, T:0.25
Consensus pattern (30 bp):
AACTGATCCACTCACCACCCAACTTTCAGA
Found at i:24016 original size:17 final size:15
Alignment explanation
Indices: 23978--24010 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23968 TGATTGGAAG
23978 AAAG-GAAAGAGAGA
1 AAAGTGAAAGAGAGA
*
23992 AGAGTGAAAGAGAGA
1 AAAGTGAAAGAGAGA
24007 AAAG
1 AAAG
24011 GCTGAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
AAAGTGAAAGAGAGA
Found at i:24538 original size:13 final size:14
Alignment explanation
Indices: 24520--24552 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24510 ATGTGTGTCG
24520 TTTTGGG-TAGCCA
1 TTTTGGGATAGCCA
*
24533 TTTTGGGATTGCCA
1 TTTTGGGATAGCCA
24547 TTTTGG
1 TTTTGG
24553 TTTTACCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.12, C:0.12, G:0.30, T:0.45
Consensus pattern (14 bp):
TTTTGGGATAGCCA
Found at i:25260 original size:81 final size:81
Alignment explanation
Indices: 25120--25297 Score: 250
Period size: 81 Copynumber: 2.2 Consensus size: 81
25110 GGTCATGTTG
* * * * * *
25120 GGGCTGGTGGGGGGTTAAATGAAGAAGTTAATGTGCAAGAAGTGGTTGGTGATGTTTTTTCAGA-
1 GGGCTGGTGAGGGTTTAAATGAAGAAGTAAATGTGCAAGAAGGGGTGGGTGATGATTTTTCA-AT
*
25184 GCATATTGAAGATGTAC
65 CCATATTGAAGATGTAC
*
25201 GGGCTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTGGGTGATGATTTTTCAATC
1 GGGCTGGTGAGGGTTTAAATGAAGAAGTAAATGTGCAAGAAGGGGTGGGTGATGATTTTTCAATC
*
25266 CATATTGAAGATTTAC
66 CATATTGAAGATGTAC
25282 GGGCTGGTGAAGGGTT
1 GGGCTGGTG-AGGGTT
25298 GGATGATGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 79 0.92
82 6 0.07
ACGTcount: A:0.27, C:0.07, G:0.37, T:0.30
Consensus pattern (81 bp):
GGGCTGGTGAGGGTTTAAATGAAGAAGTAAATGTGCAAGAAGGGGTGGGTGATGATTTTTCAATC
CATATTGAAGATGTAC
Found at i:30008 original size:17 final size:16
Alignment explanation
Indices: 29975--30005 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29965 TTCCACGTTA
29975 GCACTTAACACCCCCT
1 GCACTTAACACCCCCT
29991 GCACTTAACACCCCC
1 GCACTTAACACCCCC
30006 CTGACGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.52, G:0.06, T:0.16
Consensus pattern (16 bp):
GCACTTAACACCCCCT
Found at i:34064 original size:74 final size:73
Alignment explanation
Indices: 33986--34143 Score: 253
Period size: 74 Copynumber: 2.2 Consensus size: 73
33976 TTTGGTCTTT
*
33986 TTACACTTTTCGGGTGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCT
1 TTACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCC-ATTCCTTTTCCTTCTACCCT
34051 TTTTCGTAA
65 TTTTCGTAA
* * * *
34060 TTACACTTTTCGGATGACTGAAAAGTCCCTTTATGAGTTTCCCCCTTCCTTTTCCTTCTACCCTT
1 TTACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCATTCCTTTTCCTTCTACCCTT
34125 TTTCGTAA
66 TTTCGTAA
*
34133 TTACACATTTC
1 TTACACTTTTC
34144 TCTTGATTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 38 0.49
74 40 0.51
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (73 bp):
TTACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCATTCCTTTTCCTTCTACCCTT
TTTCGTAA
Found at i:35469 original size:24 final size:24
Alignment explanation
Indices: 35442--35489 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35432 CTCCTTCTGA
35442 ATTATATCACTCTGTCTTCAATGC
1 ATTATATCACTCTGTCTTCAATGC
35466 ATTATATCACTCTGTCTTCAATGC
1 ATTATATCACTCTGTCTTCAATGC
35490 GTCTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (24 bp):
ATTATATCACTCTGTCTTCAATGC
Found at i:36266 original size:1 final size:1
Alignment explanation
Indices: 36260--36288 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
36250 TCACCAAAAG
36260 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36289 GTACTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41208 original size:3 final size:3
Alignment explanation
Indices: 41200--41224 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41190 GGGATTTTGG
41200 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
41225 CAGAGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:42501 original size:15 final size:15
Alignment explanation
Indices: 42483--42526 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
42473 AGTTAGTATC
42483 TAATTAGTTTATGAT
1 TAATTAGTTTATGAT
42498 TAATTAG--TAT--T
1 TAATTAGTTTATGAT
42509 TAATTAGTTTATGAT
1 TAATTAGTTTATGAT
42524 TAA
1 TAA
42527 AATGAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.32
13 6 0.24
15 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (15 bp):
TAATTAGTTTATGAT
Found at i:42506 original size:26 final size:26
Alignment explanation
Indices: 42475--42526 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42465 AATTACTTAG
42475 TTAGTATCTAATTAGTTTATGATTAA
1 TTAGTATCTAATTAGTTTATGATTAA
*
42501 TTAGTATTTAATTAGTTTATGATTAA
1 TTAGTATCTAATTAGTTTATGATTAA
42527 AATGAAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (26 bp):
TTAGTATCTAATTAGTTTATGATTAA
Found at i:42572 original size:24 final size:24
Alignment explanation
Indices: 42536--42586 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
42526 AAATGAAGGA
*
42536 AAATGAATCTGAAG-ATTTGTTAG
1 AAATGAATCTGAAGAAGTTGTTAG
*
42559 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAA-TCTGAAGAAGTTGTTAG
42584 AAA
1 AAA
42587 GTTCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 6 0.25
25 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (24 bp):
AAATGAATCTGAAGAAGTTGTTAG
Found at i:43160 original size:20 final size:18
Alignment explanation
Indices: 43135--43171 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
43125 CAAGCCTACC
43135 AAAAGAAGAAGATAAAAAAG
1 AAAAGAA-AAGA-AAAAAAG
43155 AAAAGAAAAGAAAAAAA
1 AAAAGAAAAGAAAAAAA
43172 AATCTAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAG
Found at i:43173 original size:20 final size:20
Alignment explanation
Indices: 43135--43172 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
43125 CAAGCCTACC
*
43135 AAAAGAAGAAGATAAAAAAG
1 AAAAGAAGAAGAAAAAAAAG
43155 AAAAGAA-AAGAAAAAAAA
1 AAAAGAAGAAGAAAAAAAA
43173 ATCTAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAAGAAGAAGAAAAAAAAG
Found at i:44530 original size:33 final size:33
Alignment explanation
Indices: 44454--44530 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
44444 TAGACAAAGG
* * *
44454 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA
1 GTCGCGTGGCCAGTTGTAGCCGGACATGGCCGA
** *
44487 GTCGTTTGGCCAGTTGTAGCCGGACATGTCC-A
1 GTCGCGTGGCCAGTTGTAGCCGGACATGGCCGA
44519 TGTCGCGTGGCC
1 -GTCGCGTGGCC
44531 GGTCTTCTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.09, C:0.27, G:0.40, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCAGTTGTAGCCGGACATGGCCGA
Found at i:49940 original size:5 final size:5
Alignment explanation
Indices: 49930--49958 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
49920 CTGGTCGAAA
49930 TTTAT TTTAT TTTAT TTTAT TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
49959 ATTTTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:50065 original size:8 final size:8
Alignment explanation
Indices: 50037--50070 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
50027 GAATCGGCTA
50037 TGAATTTT
1 TGAATTTT
*
50045 TGAAGTTTC
1 TGAA-TTTT
50054 TGAATTTT
1 TGAATTTT
50062 TGAATTTT
1 TGAATTTT
50070 T
1 T
50071 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:51049 original size:33 final size:33
Alignment explanation
Indices: 51022--51085 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
51012 TGGCCGATTG
*
51022 TAGCCGTACATGTCCATGTCGCGTGGCCGGTGA
1 TAGCCGGACATGTCCATGTCGCGTGGCCGGTGA
*
51055 TGGCCGGACATGTCCATGTCGCGTGGCCGGT
1 TAGCCGGACATGTCCATGTCGCGTGGCCGGT
51086 CTTGTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.12, C:0.28, G:0.36, T:0.23
Consensus pattern (33 bp):
TAGCCGGACATGTCCATGTCGCGTGGCCGGTGA
Done.