Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017351.1 Corchorus olitorius cultivar O-4 contig17384, 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: 36873
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:802 original size:32 final size:32
Alignment explanation
Indices: 761--824 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
751 CTTAAAATGT
761 TTATATTGATTGAATTAAATGATTGATTACAA
1 TTATATTGATTGAATTAAATGATTGATTACAA
793 TTATATTGATTGAATTAAATGATTGATTACAA
1 TTATATTGATTGAATTAAATGATTGATTACAA
825 AGTTACAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (32 bp):
TTATATTGATTGAATTAAATGATTGATTACAA
Found at i:3499 original size:7 final size:7
Alignment explanation
Indices: 3489--3513 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3479 AACACAAAAA
3489 AATTTGC
1 AATTTGC
3496 AATTTGC
1 AATTTGC
3503 AATTTGC
1 AATTTGC
3510 AATT
1 AATT
3514 CACTCCCCTT
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:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTGC
Found at i:6999 original size:29 final size:29
Alignment explanation
Indices: 6966--7087 Score: 208
Period size: 29 Copynumber: 4.2 Consensus size: 29
6956 TGGCAGATTA
6966 CACGTCAGCAAAGTTGACGACGTCACTGC
1 CACGTCAGCAAAGTTGACGACGTCACTGC
* *
6995 AACGTCAGCAAAGTTGACGGCGTCACTGC
1 CACGTCAGCAAAGTTGACGACGTCACTGC
* *
7024 CACATCAGCAAAGTTGACGGCGTCACTGC
1 CACGTCAGCAAAGTTGACGACGTCACTGC
7053 CACGTCAGCAAAGTTGACGACGTCACTGC
1 CACGTCAGCAAAGTTGACGACGTCACTGC
7082 CACGTC
1 CACGTC
7088 GGACGATTTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (29 bp):
CACGTCAGCAAAGTTGACGACGTCACTGC
Found at i:8740 original size:2 final size:2
Alignment explanation
Indices: 8733--8776 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
8723 TAAGACTTTG
*
8733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
8776 A
1 A
8777 AGTCTAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9048 original size:39 final size:40
Alignment explanation
Indices: 8992--9072 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
8982 TTTAATTCCT
8992 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
9032 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
9071 AT
1 AT
9073 TATTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:9103 original size:25 final size:24
Alignment explanation
Indices: 9063--9109 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
9053 AATACTTACA
9063 TTAATTAAATTATTAGGTATTTTC
1 TTAATTAAATTATTAGGTATTTTC
*
9087 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTATTAGGTATTT
9110 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTATTAGGTATTTTC
Found at i:9574 original size:204 final size:204
Alignment explanation
Indices: 9182--9594 Score: 663
Period size: 204 Copynumber: 2.0 Consensus size: 204
9172 TTCCTTAATA
*
9182 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTTTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * * *
9247 AATTTAATAAATCAACCAATAATGTTTAACTGATTGTTTTTGGTATGGTTCTATATATATAATAG
66 AATTTAATAAATCAACCAATAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
* *
9312 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTCATCTTAGACTTTAAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
9377 TCACCATTG
196 TCACCATTG
* *
9386 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGATATTTATCTAA-TT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
9450 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAA
66 AATTTAATAAATCAACCAATAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
9513 TAATGTGTTGTATCTTATT-ACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAAATTAATA
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT--AAA--AAATTAATA
9577 ACATTCACCATTG
192 ACATTCACCATTG
9590 ATAAA
1 ATAAA
9595 GTTATTAAGC
Statistics
Matches: 194, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
200 28 0.14
201 30 0.15
202 3 0.02
203 47 0.24
204 86 0.44
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCAATAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:10157 original size:36 final size:36
Alignment explanation
Indices: 10110--10179 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
10100 GAGATTTTGG
* *
10110 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
*
10146 AGAAATATGATAAGCAAAATCACAAAAGATGTAA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAA
10180 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
Found at i:11547 original size:58 final size:58
Alignment explanation
Indices: 11446--11558 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 58
11436 AGCATCATGC
*
11446 CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
* * *
11504 CTCGGTCCGAAAACGTCTTTTTTAATGCATCTAAT-AAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTCTTTTTT-AGGCATCTAATAAAAAAACATGTCACTCGATA
11559 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 40 0.80
59 10 0.20
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (58 bp):
CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
Found at i:14181 original size:30 final size:30
Alignment explanation
Indices: 14145--14202 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
14135 GGTTAATTAT
*
14145 TTCTTGACTTCACTCAAGTTCTCATTTGCA
1 TTCTTGACTTCACCCAAGTTCTCATTTGCA
*
14175 TTCTTGACTTGACCCAAGTTCTCATTTG
1 TTCTTGACTTCACCCAAGTTCTCATTTG
14203 TATAGATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (30 bp):
TTCTTGACTTCACCCAAGTTCTCATTTGCA
Found at i:14644 original size:14 final size:15
Alignment explanation
Indices: 14625--14657 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
14615 CTGTCGCGGA
14625 CGCGGTTACG-GTGT
1 CGCGGTTACGAGTGT
*
14639 CGCGGTTGCGAGTGT
1 CGCGGTTACGAGTGT
14654 CGCG
1 CGCG
14658 AACGTTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.06, C:0.24, G:0.45, T:0.24
Consensus pattern (15 bp):
CGCGGTTACGAGTGT
Found at i:16329 original size:72 final size:72
Alignment explanation
Indices: 16245--16397 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 72
16235 ATAACTTCTT
* * ** **
16245 TGGATCAATCCCTTCTTCCATAGGAAAC-ATGACCCAATTGTCTAGTCTTTCCCTTGA-TGAAAA
1 TGGATCAATCCCTGCTTCCATAGG-AACTATAACAAAATTGTCTACCCTTTCCCTT-ACTGAAAA
16308 TCAGATTTC
64 TCAGATTTC
* *
16317 TGGATCAGTCCCTGCTTCCATAGGAACTTTAACAAAATTGTCTACCCTTTCCCTTACTGAAAATC
1 TGGATCAATCCCTGCTTCCATAGGAACTATAACAAAATTGTCTACCCTTTCCCTTACTGAAAATC
16382 AGATTTC
66 AGATTTC
*
16389 TGGGTCAAT
1 TGGATCAAT
16398 ACCTCAAGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 4 0.06
72 65 0.94
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (72 bp):
TGGATCAATCCCTGCTTCCATAGGAACTATAACAAAATTGTCTACCCTTTCCCTTACTGAAAATC
AGATTTC
Found at i:22888 original size:19 final size:18
Alignment explanation
Indices: 22864--22908 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
22854 ATGCATACCG
* *
22864 CTATATACTAATCTTACTA
1 CTATATA-TAATATTAATA
22883 CTATATATAATATTAATA
1 CTATATATAATATTAATA
22901 -TATATATA
1 CTATATATA
22909 TACTAGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
CTATATATAATATTAATA
Found at i:22999 original size:21 final size:20
Alignment explanation
Indices: 22965--23029 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
22955 TGCAATCATT
22965 TATATATATTAATATATATA
1 TATATATATTAATATATATA
* *
22985 TATACTATCTTAATATCTATA
1 TATA-TATATTAATATATATA
23006 TACTATATATCT-ATATACTATA
1 TA-TATATAT-TAATATA-TATA
23028 TA
1 TA
23030 AGTCTAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 24 0.65
22 9 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATATATTAATATATATA
Found at i:23015 original size:15 final size:15
Alignment explanation
Indices: 22997--23029 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
22987 TACTATCTTA
22997 ATATCTATATACTAT
1 ATATCTATATACTAT
23012 ATATCTATATACTAT
1 ATATCTATATACTAT
23027 ATA
1 ATA
23030 AGTCTAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATCTATATACTAT
Found at i:23249 original size:21 final size:21
Alignment explanation
Indices: 23225--23288 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 21
23215 GTAATATATA
*
23225 TAATAACTAAAATACTTACAT
1 TAATAACTGAAATACTTACAT
* *
23246 TAATTAAATGTAATA-TT--A-
1 TAA-TAACTGAAATACTTACAT
23264 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTACAT
23285 TAAT
1 TAAT
23289 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 1 0.03
20 1 0.03
21 9 0.27
22 8 0.24
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAACTGAAATACTTACAT
Found at i:23270 original size:39 final size:40
Alignment explanation
Indices: 23213--23293 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
23203 TTTAATTCCT
23213 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
23253 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
23292 AT
1 AT
23294 TCTTAGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:24205 original size:36 final size:36
Alignment explanation
Indices: 24151--24220 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
24141 GAGATTTTGG
* *
24151 AGAAATATAATAATCAAAATTACAAAAGATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAGATGTAATA
* *
24187 AGAAATTTGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAGATGTAA
24221 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAGATGTAATA
Found at i:25599 original size:59 final size:58
Alignment explanation
Indices: 25487--25602 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 58
25477 ATAGCATCAT
*
25487 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
* * *
25545 GCCTTGGTCCGAAAACGTCTTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTC--TTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATA
25603 TTTGATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 17 0.33
59 19 0.37
60 16 0.31
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
Found at i:32039 original size:32 final size:33
Alignment explanation
Indices: 32003--32066 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
31993 TAAAATAATA
32003 GCTCAAGGAGACAAAAAAAAAC-TGACATGAAG
1 GCTCAAGGAGACAAAAAAAAACATGACATGAAG
* *
32035 GCTCAAGGATACAAAAAAAGACATGACATGAA
1 GCTCAAGGAGACAAAAAAAAACATGACATGAA
32067 ACTCAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.53, C:0.16, G:0.20, T:0.11
Consensus pattern (33 bp):
GCTCAAGGAGACAAAAAAAAACATGACATGAAG
Found at i:32143 original size:25 final size:23
Alignment explanation
Indices: 32056--32147 Score: 66
Period size: 25 Copynumber: 3.9 Consensus size: 23
32046 CAAAAAAAGA
32056 CATGACATGAAACTCAAACCCTAAC
1 CATGACATG-AAC-CAAACCCTAAC
* *
32081 CATGAAATG-A-CAAACCCGAA-
1 CATGACATGAACCAAACCCTAAC
* *
32101 -GTGAGATGAAGCCTAAACCCTAAC
1 CATGACATGAA-CC-AAACCCTAAC
32125 CATGACATGAAAGCCAAACCCTA
1 CATGACATG-AA-CCAAACCCTA
32148 CATGTCATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
19 6 0.11
20 1 0.02
21 9 0.17
22 1 0.02
23 9 0.17
25 22 0.42
26 5 0.09
ACGTcount: A:0.43, C:0.28, G:0.14, T:0.14
Consensus pattern (23 bp):
CATGACATGAACCAAACCCTAAC
Found at i:32224 original size:31 final size:32
Alignment explanation
Indices: 32178--32241 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
32168 GTAAAAAAGA
*
32178 ATTGGAATGCCCAAATTATCCTCAAGGCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
* *
32210 ATTGG-ATGTCCAAATTACCCTCAAGTCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
32241 A
1 A
32242 CAAAATAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (32 bp):
ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
Found at i:36141 original size:31 final size:31
Alignment explanation
Indices: 36084--36143 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
36074 GGTTAATTAA
*
36084 GTCCCTAACGTTATAAATTCGACTCAAATTT
1 GTCCCTAACGTTATAAAATCGACTCAAATTT
*
36115 GTCCCTAACGTTGTAAAATC-AGCTCAAAT
1 GTCCCTAACGTTATAAAATCGA-CTCAAAT
36144 CAGTGCCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (31 bp):
GTCCCTAACGTTATAAAATCGACTCAAATTT
Found at i:36616 original size:100 final size:99
Alignment explanation
Indices: 36427--36621 Score: 300
Period size: 100 Copynumber: 2.0 Consensus size: 99
36417 ATACAATACA
* * *
36427 CTATCAATGTAAATTTTGAAATCTACAAGCGGGTTAAGAAGTTGACACATACACATTTTTTTGAT
1 CTATCAAAGTAAATTTTGAAATCTACAAGCGGGTTAAAAAGTTGACACATACACATTTTCTTGAT
36492 TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
66 TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
* * *
36526 CTATCAAGAGTAAATTTTGGACTCTACAAGCGGGTTAAAAAGTTGATACATACACATTTTCTTGA
1 CTATCAA-AGTAAATTTTGAAATCTACAAGCGGGTTAAAAAGTTGACACATACACATTTTCTTGA
** *
36591 TTAATTTTGTTTTTGTAATTTAAAACTATTC
65 TTAATTTTGTTTTTAAAATTCAAAACTATTC
36622 GCTAAAGGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 7 0.08
100 79 0.92
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (99 bp):
CTATCAAAGTAAATTTTGAAATCTACAAGCGGGTTAAAAAGTTGACACATACACATTTTCTTGAT
TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
Found at i:36740 original size:23 final size:23
Alignment explanation
Indices: 36710--36780 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
36700 TACGATGAAT
*
36710 GGGGTGCGCAGGTACGAGAAATG
1 GGGGTGCGCAGCTACGAGAAATG
* *
36733 GGGGTGCGGACCTACGAGAAAT-
1 GGGGTGCGCAGCTACGAGAAATG
* * * *
36755 GGGGTGCTCAGTTGCGAGAGATG
1 GGGGTGCGCAGCTACGAGAAATG
36778 GGG
1 GGG
36781 TGGGTGGCCT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 16 0.42
23 22 0.58
ACGTcount: A:0.23, C:0.14, G:0.48, T:0.15
Consensus pattern (23 bp):
GGGGTGCGCAGCTACGAGAAATG
Found at i:36761 original size:22 final size:22
Alignment explanation
Indices: 36698--36761 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
36688 TTTATATGAT
36698 CCTACGATG-AATGGGGTGCGCA
1 CCTACGA-GAAATGGGGTGCGCA
** *
36720 GGTACGAGAAATGGGGGTGCGGA
1 CCTACGAGAAAT-GGGGTGCGCA
36743 CCTACGAGAAATGGGGTGC
1 CCTACGAGAAATGGGGTGC
36762 TCAGTTGCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 19 0.54
ACGTcount: A:0.25, C:0.17, G:0.42, T:0.16
Consensus pattern (22 bp):
CCTACGAGAAATGGGGTGCGCA
Done.