Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010165.1 Corchorus capsularis cultivar CVL-1 contig10186, 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: 52281
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:40 original size:14 final size:13
Alignment explanation
Indices: 17--52 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
7 GGCCCAGCCG
17 CTCCTCTCCCCTT
1 CTCCTCTCCCCTT
30 CTCCATCTCCCCTT
1 CTCC-TCTCCCCTT
44 CTCCCTCTC
1 CT-CCTCTC
53 TAGTTCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.03, C:0.61, G:0.00, T:0.36
Consensus pattern (13 bp):
CTCCTCTCCCCTT
Found at i:762 original size:2 final size:2
Alignment explanation
Indices: 755--791 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
745 TTTGTCTCAT
755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
792 AGAACTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14079 original size:25 final size:23
Alignment explanation
Indices: 14042--14087 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
14032 CAATATGCAT
*
14042 ATATATGGAGTAATACTATATATAC
1 ATATATAGAGTAAT--TATATATAC
*
14067 ATATATAGTGTAATTATATAT
1 ATATATAGAGTAATTATATAT
14088 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
25 12 0.63
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (23 bp):
ATATATAGAGTAATTATATATAC
Found at i:16467 original size:4 final size:4
Alignment explanation
Indices: 16458--16489 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16448 CACATCAATC
*
16458 TTCT TTCT TTCT TTCT TTCT TTCT TTGT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
16490 GTTTTTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:18941 original size:37 final size:37
Alignment explanation
Indices: 18891--18966 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
18881 TGAAATCGAA
* *
18891 CTGCATCAGACCCATATGAGAAAAACTTTTCAAACAC
1 CTGCATCAAACCCATATGAGAAAAACTCTTCAAACAC
18928 CTGCATCAAACCCATATGAGAAAAACTCTTCAAACAC
1 CTGCATCAAACCCATATGAGAAAAACTCTTCAAACAC
18965 CT
1 CT
18967 ATTTGTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (37 bp):
CTGCATCAAACCCATATGAGAAAAACTCTTCAAACAC
Found at i:19875 original size:195 final size:195
Alignment explanation
Indices: 19541--19931 Score: 710
Period size: 195 Copynumber: 2.0 Consensus size: 195
19531 TTGATCGGTT
*
19541 TATTTGGTTTGAACCGACTTATACTCACCCTATATAAACTTCTATTGGTCGCCAATCTATAGGAT
1 TATTTGGTTTGAACAGACTTATACTCACCCTATATAAACTTCTATTGGTCGCCAATCTATAGGAT
**
19606 TGAAAGATTCACAAATGAAAAAGTGATCCAATGTTTATTTGGTAGCTTACTTTGACCTTAGAGAT
66 TGAAAGATTCACAAATGAAAAAGTGATCCAATGTTTATTTGACAGCTTACTTTGACCTTAGAGAT
*
19671 AAGAGAGCCTATTATACTCCTAAACTTTTGTTCCGAAAAGAATACTCAAAAGAAGAAAAATAAAG
131 AAAAGAGCCTATTATACTCCTAAACTTTTGTTCCGAAAAGAATACTCAAAAGAAGAAAAATAAAG
*
19736 TATTTGGTTTGAACAGACTTATACTCACCCTATATAAACTTTTATTGGTCGCCAATCTATAGGAT
1 TATTTGGTTTGAACAGACTTATACTCACCCTATATAAACTTCTATTGGTCGCCAATCTATAGGAT
*
19801 TGAAAGATTCACAAATGAAAAAGTGATCCAATGTTTATTTGACAGTTTACTTTGACCTTAGAGAT
66 TGAAAGATTCACAAATGAAAAAGTGATCCAATGTTTATTTGACAGCTTACTTTGACCTTAGAGAT
* *
19866 AAAAGAGCCTATTATATTCTTAAACTTTTGTTCCGAAAAGAATACTCAAAAGAAGAAAAATAAAG
131 AAAAGAGCCTATTATACTCCTAAACTTTTGTTCCGAAAAGAATACTCAAAAGAAGAAAAATAAAG
19931 T
1 T
19932 TCAATGGAAA
Statistics
Matches: 188, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 188 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (195 bp):
TATTTGGTTTGAACAGACTTATACTCACCCTATATAAACTTCTATTGGTCGCCAATCTATAGGAT
TGAAAGATTCACAAATGAAAAAGTGATCCAATGTTTATTTGACAGCTTACTTTGACCTTAGAGAT
AAAAGAGCCTATTATACTCCTAAACTTTTGTTCCGAAAAGAATACTCAAAAGAAGAAAAATAAAG
Found at i:21176 original size:14 final size:14
Alignment explanation
Indices: 21157--21200 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
21147 TCACTCTGTT
21157 CCTTTTTAATTGTC
1 CCTTTTTAATTGTC
** *
21171 CC-TTTTCCTTGTT
1 CCTTTTTAATTGTC
21184 CCTTTTTAATTGTC
1 CCTTTTTAATTGTC
21198 CCT
1 CCT
21201 CATATTCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.09, C:0.27, G:0.07, T:0.57
Consensus pattern (14 bp):
CCTTTTTAATTGTC
Found at i:21401 original size:22 final size:22
Alignment explanation
Indices: 21373--21420 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
21363 CTTAAAGAAA
21373 TAAATCGGTTAAAAGAGACAAT
1 TAAATCGGTTAAAAGAGACAAT
*
21395 TAAATCGGTTAAAAGGGACAAT
1 TAAATCGGTTAAAAGAGACAAT
21417 TAAA
1 TAAA
21421 AAGGAACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (22 bp):
TAAATCGGTTAAAAGAGACAAT
Found at i:28064 original size:24 final size:25
Alignment explanation
Indices: 28004--28062 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
27994 TTCAAACCCT
*
28004 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
28029 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
28053 AAA-TTCATTT
1 AAACTTCATTT
28063 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:28096 original size:11 final size:11
Alignment explanation
Indices: 28082--28130 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
28072 TTAATCATAA
28082 ACTAATTAAAT
1 ACTAATTAAAT
28093 ACTAATTAATCAT
1 ACTAATTAA--AT
*
28106 AAACTAATTAGAT
1 --ACTAATTAAAT
28119 ACTAATTAAAT
1 ACTAATTAAAT
28130 A
1 A
28131 TAAACTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 20 0.62
13 4 0.12
15 8 0.25
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:28101 original size:26 final size:26
Alignment explanation
Indices: 28072--28139 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
28062 TTCCTTCATT
28072 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
28098 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
28124 TTAAAT-ATAAACTAAT
1 TT-AATCATAAACTAAT
28140 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:28102 original size:15 final size:15
Alignment explanation
Indices: 28072--28115 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
28062 TTCCTTCATT
28072 TTAATCATAAACTAA
1 TTAATCATAAACTAA
28087 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
28098 TTAATCATAAACTAA
1 TTAATCATAAACTAA
28113 TTA
1 TTA
28116 GATACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:28139 original size:15 final size:14
Alignment explanation
Indices: 28072--28139 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
28062 TTCCTTCATT
28072 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
28087 TTAA-AT--ACTAA
1 TTAATATAAACTAA
28098 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
*
28113 TT-AGAT--ACTAA
1 TTAATATAAACTAA
28124 TTAAATATAAACTAA
1 TT-AATATAAACTAA
28139 T
1 T
28140 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
13 9 0.21
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (14 bp):
TTAATATAAACTAA
Found at i:28292 original size:33 final size:33
Alignment explanation
Indices: 28244--28342 Score: 105
Period size: 33 Copynumber: 3.0 Consensus size: 33
28234 TCTAGCCTAG
*
28244 CCATGGGCTATGCCGCCCACGCTGGGCGGCATGT
1 CCATTGGCTA-GCCGCCCACGCTGGGCGGCATGT
* *
28278 CCATTGGCTAGCCGCCCA-GCGTGGGCAGTATAGT
1 CCATTGGCTAGCCGCCCACGC-TGGGCGGCAT-GT
*
28312 CCA-TGGCCAGCCGCCCAACG-TGGGCGGCATG
1 CCATTGGCTAGCCGCCC-ACGCTGGGCGGCATG
28343 ACCCATGGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
32 3 0.05
33 36 0.65
34 15 0.27
35 1 0.02
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.16
Consensus pattern (33 bp):
CCATTGGCTAGCCGCCCACGCTGGGCGGCATGT
Found at i:28383 original size:11 final size:11
Alignment explanation
Indices: 28367--28408 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
28357 GGCTAGGCCA
28367 TTTTTTTAAAG
1 TTTTTTTAAAG
* *
28378 TTTTTTTAGAT
1 TTTTTTTAAAG
28389 TTTTTTTAAAG
1 TTTTTTTAAAG
28400 ATTTTTTTA
1 -TTTTTTTA
28409 CCTCAACCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTTTTTAAAG
Found at i:28559 original size:20 final size:21
Alignment explanation
Indices: 28535--28579 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
28525 CAAAAATTAT
*
28535 AAAAAAGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTGTTTAGC
*
28556 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTGTTTAGC
28577 AAA
1 AAA
28580 CCCCATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.40, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTGTTTAGC
Found at i:28910 original size:45 final size:45
Alignment explanation
Indices: 28859--28944 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
28849 TAATAGAGTT
28859 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG
* *
28904 GTGGAATTACTAAAAGATCTCTACCCCGGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAG
28945 CTGGAGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG
Found at i:29939 original size:32 final size:32
Alignment explanation
Indices: 29898--29960 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
29888 AATTCAGAAC
29898 TCACATTTGTAGATATTTCTAAAGGGAATGGT
1 TCACATTTGTAGATATTTCTAAAGGGAATGGT
29930 TCACATTTGTAGATATTTCTAAAGGGAATGG
1 TCACATTTGTAGATATTTCTAAAGGGAATGG
29961 GTTAACCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (32 bp):
TCACATTTGTAGATATTTCTAAAGGGAATGGT
Found at i:35058 original size:19 final size:19
Alignment explanation
Indices: 35005--35058 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
34995 ACAAAGTTCA
*
35005 AAATGCATGAA-AAATGAG
1 AAATGCATGAAGAAAAGAG
**
35023 -AATGCATGAAGTGAAGAG
1 AAATGCATGAAGAAAAGAG
*
35041 AAATTCATGAAGAAAAGA
1 AAATGCATGAAGAAAAGA
35059 AGAAGTGCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.36
18 4 0.14
19 14 0.50
ACGTcount: A:0.54, C:0.06, G:0.24, T:0.17
Consensus pattern (19 bp):
AAATGCATGAAGAAAAGAG
Found at i:40849 original size:21 final size:21
Alignment explanation
Indices: 40824--40865 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40814 CCCTGTTATC
* *
40824 ATCATTCCTGTATCTTTCTCT
1 ATCATTCCTGAATCTGTCTCT
*
40845 ATCATTTCTGAATCTGTCTCT
1 ATCATTCCTGAATCTGTCTCT
40866 TCGATAGCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (21 bp):
ATCATTCCTGAATCTGTCTCT
Found at i:43161 original size:7 final size:7
Alignment explanation
Indices: 43151--43175 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43141 CCAAAAAAAA
43151 AAAAGAT
1 AAAAGAT
43158 AAAAGAT
1 AAAAGAT
43165 AAAAGAT
1 AAAAGAT
43172 AAAA
1 AAAA
43176 AAGAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAGAT
Found at i:43276 original size:21 final size:21
Alignment explanation
Indices: 43250--43301 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
43240 AAATAAGTGC
*
43250 ACAAAACAAAGATAAAAAAGAT
1 ACAAAACAAAGAT-AAAAAGAA
43272 A-AAAACAAAGATAAAAAGAA
1 ACAAAACAAAGATAAAAAGAA
43292 ACAAAACAAA
1 ACAAAACAAA
43302 TATCAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.29
21 19 0.68
22 1 0.04
ACGTcount: A:0.77, C:0.10, G:0.08, T:0.06
Consensus pattern (21 bp):
ACAAAACAAAGATAAAAAGAA
Found at i:43281 original size:12 final size:12
Alignment explanation
Indices: 43252--43288 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
43242 ATAAGTGCAC
43252 AAAACAAAGAT-
1 AAAACAAAGATA
43263 -AAA-AAAGATA
1 AAAACAAAGATA
43273 AAAACAAAGATA
1 AAAACAAAGATA
43285 AAAA
1 AAAA
43289 GAAACAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.26
10 3 0.13
11 3 0.13
12 11 0.48
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAACAAAGATA
Found at i:43614 original size:12 final size:13
Alignment explanation
Indices: 43596--43628 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
43586 GTGGGTTTAG
43596 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
43609 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
43621 TAGTTTGT
1 TAGTTTGT
43629 AATTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:43995 original size:16 final size:16
Alignment explanation
Indices: 43976--44037 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
43966 AACCCGTCTG
43976 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
*
43992 AACCCGAATCCGAAAA
1 AACCCGAACCCGAAAA
* * *
44008 AACTCAAACCTGAAAA
1 AACCCGAACCCGAAAA
*
44024 AATCCGAACCCGAA
1 AACCCGAACCCGAA
44038 TCCGAAAAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.50, C:0.32, G:0.11, T:0.06
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:44223 original size:26 final size:26
Alignment explanation
Indices: 44184--44256 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 26
44174 TCTGGCCAAA
44184 ACCCAAA-TCGAACCCGAATTAACCTG
1 ACCCAAATTC-AACCCGAATTAACCTG
44210 ACCCAAATTCAACCCGAATCCGAATTAACCTG
1 ACCCAAATTCAA--C----CCGAATTAACCTG
44242 ACCCAAATTCAACCC
1 ACCCAAATTCAACCC
44257 ATCCTGACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
26 11 0.28
27 2 0.05
28 1 0.03
30 1 0.03
32 25 0.62
ACGTcount: A:0.38, C:0.37, G:0.08, T:0.16
Consensus pattern (26 bp):
ACCCAAATTCAACCCGAATTAACCTG
Found at i:44233 original size:32 final size:32
Alignment explanation
Indices: 44192--44256 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
44182 AAACCCAAAT
44192 CGAACCCGAATTAACCTGACCCAAATTCAACC
1 CGAACCCGAATTAACCTGACCCAAATTCAACC
*
44224 CGAATCCGAATTAACCTGACCCAAATTCAACC
1 CGAACCCGAATTAACCTGACCCAAATTCAACC
44256 C
1 C
44257 ATCCTGACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.37, G:0.09, T:0.17
Consensus pattern (32 bp):
CGAACCCGAATTAACCTGACCCAAATTCAACC
Found at i:44255 original size:16 final size:15
Alignment explanation
Indices: 44195--44255 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
44185 CCCAAATCGA
*
44195 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
*
44210 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
* *
44226 AATCCGAATTAACCTG
1 -ACCCAAATTAACCTG
44242 ACCCAAATTCAACC
1 ACCCAAATT-AACC
44256 CATCCTGACT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 15 0.42
16 14 0.39
17 7 0.19
ACGTcount: A:0.38, C:0.36, G:0.08, T:0.18
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:46381 original size:199 final size:199
Alignment explanation
Indices: 45862--47407 Score: 1753
Period size: 199 Copynumber: 7.8 Consensus size: 199
45852 TCAAATTATT
* * * * *
45862 TTATATAATTTTTCTTATAGGATTATTATACAATACACTTTTCAGTGTAAATTTTAGACTCTATA
1 TTATATAAATTTTCTTATAGAATTATTATACAATACAC-TGTCAATGTAAATTTTGGACTCTATA
* * *
45927 AACGGGTTAAGAAGTTGACACATACCCCA-TTCATAATCAATTAAATAATTAATATTAATACATA
65 AGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA
* * * * * * *
45991 TTCCTTAAGGGGACACATGTCAACCCTTAAACCCTGCACATGCAGACTGCTAAATTCGATTGACG
130 TTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG
46056 GTGTA
195 GTGTA
* * * * *
46061 -TAGTTTAATTTTTCTAATATAAAATTATTATA-AATCCACTGTCAATGTAAATTTTGGACTCCA
1 TTA-TATAAATTTTCT--TATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCTA
* * *
46124 TAAGCGGGTTAAGAAGTTGACATATACCCTATTTCACAATTAATTAAATATTTAATATTAATACA
63 TAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACA
* * *
46189 TATTCCCTAAGGGGACAGATGTCAACCCTTAAACCCCGCACGTGTAGTCTGCTAAAATCCACTGA
128 TATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA
*
46254 CAGTGTA
193 CGGTGTA
* * ** *
46261 TTATATAAATTTTCTTATAGAATTATTATACAACACACTGTCAGTGTAAATTTTAAACTCTAAAA
1 TTATATAAATTTTCTTATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCTATAA
* * * *
46326 GCGGGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATATATAATATTAATACATAT
66 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* * * *
46391 TCCCCAAGGGGGCACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTTCACTGACGG
131 TCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGG
46456 TGTA
196 TGTA
* ** * *
46460 TAATATAGTTTTTCTTATAGAATTATTATACAATAAACTGTCAATGTAAATTTTGGACTTTATAA
1 TTATATAAATTTTCTTATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCTATAA
* * *
46525 GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATAAATTAAATATTTCATATTAATACATAT
66 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* * * * * * *
46590 TCCTTATGGGGACACATGTCAACCCTTAAACCCCACATGTGCAGTGTGCTAAACTCGACAGACGG
131 TCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGG
46655 TGTA
196 TGTA
* * * * *
46659 -TA-AT--A--TT-TTATAGGATTATCATACAGTACACAT-TCAGTGTAAATTTTGGA-TTTCAT
1 TTATATAAATTTTCTTATAGAATTATTATACAATACAC-TGTCAATGTAAATTTTGGACTCT-AT
* * * *
46715 AAGCGGGTTAAGAAGTTGACACATACCCTATTTCATAATTAATAAAATGTTTAATTTTAATACAT
64 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACAT
* ** * * * * * *
46780 ATTCCCTAAGAGGACATGTGACAACCCTTAAATCCTGCACGTGCAGTCTACTAAACTGCACCGAC
129 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAC
46845 GGTGTA
194 GGTGTA
* * * * * * *
46851 TTGTAT-AATTGTTCTTATAGGACTATTATACAATAAATTGTTAATGTAAATTTTGGACTCCATA
1 TTATATAAATT-TTCTTATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCTATA
* * * * * *
46915 AGCGGATTAAGAAATTGACACATACCCCATTTCATAATTAATTATAGATTTAAAATTGATACATA
65 AGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA
* * * *
46980 TTCCTTAAGGGGACAGATGTCAACCCTTAAACCTCGCACGTGCAGTCTGCTAAACTCGACT-AGC
130 TTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA-C
47044 GGTGTA
194 GGTGTA
** * * * *
47050 -TAGTATACTTTTTCTTATA-AGATTATTAAAGAATACACTGACAATGTAAATTTAGGACT-TCA
1 TTA-TATAAATTTTCTTATAGA-ATTATTATACAATACACTGTCAATGTAAATTTTGGACTCT-A
* * * ** *
47112 TAAGCGGGTTAAGAAGATGACCCTTACCCCATTTCATAATTAAAAAAATATTTAATATTAATGCA
63 TAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACA
* * * ** * **
47177 TATACCCTAAGGGGACACATGTCAATCCATAAACTTCGGACGTGCAGTCTGCTAAACTTTACTGA
128 TATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA
47242 CGGTGTA
193 CGGTGTA
* * * * *
47249 TTGTAT-AATTGTTCTTATAGGATTATTATACAATGCACTGTCAATGTAAATTTT-GAATTTCAT
1 TTATATAAATT-TTCTTATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCT-AT
* * * * *
47312 AAGCAGGTTAAGAAGTTGACATATTCCCCATTTCATAATTAATGAAATATTTAACATTAATACAT
64 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACAT
*
47377 ATTTCCTAAGGGGACACATGTCAACCCTTAA
129 ATTCCCTAAGGGGACACATGTCAACCCTTAA
47408 GGCCCTGTTT
Statistics
Matches: 1127, Mismatches: 193, Indels: 54
0.82 0.14 0.04
Matches are distributed among these distances:
191 3 0.00
192 152 0.13
193 4 0.00
194 2 0.00
195 1 0.00
197 2 0.00
198 27 0.02
199 808 0.72
200 113 0.10
201 15 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (199 bp):
TTATATAAATTTTCTTATAGAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCTATAA
GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
TCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGG
TGTA
Done.