Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007195.1 Corchorus capsularis cultivar CVL-1 contig07216, 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: 33389
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1481 original size:15 final size:16
Alignment explanation
Indices: 1458--1519 Score: 67
Period size: 15 Copynumber: 4.0 Consensus size: 16
1448 AGAATGCTTT
1458 CCAAGGAGAGTGATTC
1 CCAAGGAGAGTGATTC
*
1474 CCAA-GAGAGTG-CTC
1 CCAAGGAGAGTGATTC
* *
1488 TCCATGGAGAGTCATT-
1 -CCAAGGAGAGTGATTC
1504 CCAAGGAGAGTGATTC
1 CCAAGGAGAGTGATTC
1520 TAAGAGTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 2 0.06
15 23 0.64
16 10 0.28
17 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (16 bp):
CCAAGGAGAGTGATTC
Found at i:1505 original size:31 final size:31
Alignment explanation
Indices: 1446--1515 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1436 CTTTTCGATC
* * *
1446 GGAGAATGCTTTCCAAGGAGAGTGATTCCCAA
1 GGAGAGTGCTCTCCAAGGAGAGTCATT-CCAA
*
1478 -GAGAGTGCTCTCCATGGAGAGTCATTCCAA
1 GGAGAGTGCTCTCCAAGGAGAGTCATTCCAA
1508 GGAGAGTG
1 GGAGAGTG
1516 ATTCTAAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (31 bp):
GGAGAGTGCTCTCCAAGGAGAGTCATTCCAA
Found at i:14314 original size:31 final size:30
Alignment explanation
Indices: 14279--14337 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
14269 ATGTTTTTTG
*
14279 ATTGTACCCTTATTTT-TAAAACATATTTCCA
1 ATTGTA-CCTT-TTTTAAAAAACATATTTCCA
*
14310 ATTGTATCTTTTTTAAAAAACATATTTC
1 ATTGTACCTTTTTTAAAAAACATATTTC
14338 TAAATTGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.16
30 15 0.60
31 6 0.24
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTGTACCTTTTTTAAAAAACATATTTCCA
Found at i:14410 original size:15 final size:15
Alignment explanation
Indices: 14365--14413 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
14355 ATAATATTTG
14365 AATTATTCCATTATT
1 AATTATTCCATTATT
** *
14380 --TT-TTAAATTATA
1 AATTATTCCATTATT
14392 AATTATTCCATTATT
1 AATTATTCCATTATT
14407 AATTATT
1 AATTATT
14414 AGATTATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
12 7 0.28
13 2 0.08
14 2 0.08
15 14 0.56
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTATTCCATTATT
Found at i:14574 original size:19 final size:20
Alignment explanation
Indices: 14547--14584 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
14537 TACTAGTAGT
14547 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
14567 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
14585 ATGTCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:14774 original size:22 final size:22
Alignment explanation
Indices: 14749--14910 Score: 150
Period size: 22 Copynumber: 7.3 Consensus size: 22
14739 TGTCTCTATG
*
14749 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
14771 TGGTTATTATAATTTCATAAGGA
1 TGGTTATCAAAATTTCAT-AGGA
14794 -GGTTATCAAAATTTCATACGGA
1 TGGTTATCAAAATTTCATA-GGA
*
14816 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
14837 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
14859 TCAGATTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
14883 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
14905 TGGTTA
1 TGGTTA
14911 ATTATCACAA
Statistics
Matches: 116, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
21 3 0.03
22 93 0.80
23 3 0.03
24 17 0.15
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:15013 original size:22 final size:21
Alignment explanation
Indices: 14988--15081 Score: 73
Period size: 22 Copynumber: 4.3 Consensus size: 21
14978 TTCGTAGTGT
14988 GGTTAACAAAATTTCATTAGGA
1 GGTTAACAAAATTTCA-TAGGA
* *
15010 GGTT-ACTAATATTTCATGGGAA
1 GGTTAAC-AAAATTTCATAGG-A
* * *
15032 GGTTATCAAAATTTTATAGTGT
1 GGTTAACAAAATTTCATAG-GA
* *
15054 GGTTATCAAAATTTCATATGAA
1 GGTTAACAAAATTTCATA-GGA
15076 GGTTAA
1 GGTTAA
15082 TAGTCTTAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
21 5 0.09
22 48 0.86
23 3 0.05
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
GGTTAACAAAATTTCATAGGA
Found at i:15058 original size:44 final size:44
Alignment explanation
Indices: 14988--15081 Score: 102
Period size: 44 Copynumber: 2.1 Consensus size: 44
14978 TTCGTAGTGT
* *
14988 GGTTAACAAAATTTCATTAGGAGGTTA-CTAATATTTCATGGGAA
1 GGTTAACAAAATTTCATTAGGAGGTTATC-AAAATTTCATAGGAA
* * * *
15032 GGTTATCAAAATTTTA-TAGTGTGGTTATCAAAATTTCATATGAA
1 GGTTAACAAAATTTCATTAG-GAGGTTATCAAAATTTCATAGGAA
15076 GGTTAA
1 GGTTAA
15082 TAGTCTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.07
44 37 0.90
45 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (44 bp):
GGTTAACAAAATTTCATTAGGAGGTTATCAAAATTTCATAGGAA
Found at i:15158 original size:22 final size:23
Alignment explanation
Indices: 15106--15360 Score: 112
Period size: 22 Copynumber: 11.6 Consensus size: 23
15096 TAAAGACAAC
* *
15106 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
15127 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
15148 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
15173 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
15194 TAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
15216 CAAAATTTCA-AAACGA-GGTTAT
1 CAAAATTTCATAGA-GATGATTAT
*
15238 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * * *
15260 CAGAATTTCATATAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * * *
15282 CAAAATTTTATA-AAAAGGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
15304 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
15326 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
15347 CAAAAATTTCATAG
1 C-AAAATTTCATAG
15361 TGGTATTTCT
Statistics
Matches: 181, Mismatches: 34, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
20 10 0.06
21 27 0.15
22 117 0.65
23 10 0.06
24 4 0.02
25 13 0.07
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:15261 original size:44 final size:44
Alignment explanation
Indices: 15167--15359 Score: 164
Period size: 44 Copynumber: 4.4 Consensus size: 44
15157 ATAGAGATCA
* *
15167 GATTATCAAAATTT-ATAGGAAGA--TTATTAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATA--AAGAGGTTATCAAAATTTCATAATG-T
*
15211 G-TTATCAAAATTTCA-AAACGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAA-GAGGTTATCAAAATTTCATAATGT
* * * * * * ***
15254 GATTATCAGAATTTCATATAGGGGTCAACAAAATTTTATAAAAA
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
* * *
15298 GGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
15342 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
15360 GTGGTATTTC
Statistics
Matches: 116, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 16 0.14
44 94 0.81
45 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
Found at i:15469 original size:20 final size:20
Alignment explanation
Indices: 15444--15535 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
15434 TGGAGTAATC
15444 AAAATTTCAGAGAGGATATA
1 AAAATTTCAGAGAGGATATA
* *
15464 AAAATTTCAGAGATGATATT
1 AAAATTTCAGAGAGGATATA
* * *
15484 AAAATTTCAGGGATGATATC
1 AAAATTTCAGAGAGGATATA
* *
15504 AAAATTTCATATGAAGGTTATAA
1 AAAATTTCAGA-G-AGGATAT-A
15527 AAAATTTCA
1 AAAATTTCA
15536 TAGTTTAGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
20 45 0.75
21 1 0.02
22 5 0.08
23 9 0.15
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (20 bp):
AAAATTTCAGAGAGGATATA
Found at i:15730 original size:23 final size:23
Alignment explanation
Indices: 15700--15802 Score: 104
Period size: 23 Copynumber: 4.5 Consensus size: 23
15690 TATAAGCAAG
15700 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
15723 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
15746 TTATCAAAATTTCAT-GGCGAAGT
1 TTATCAAAATTTTATAGG-GAGGT
* * *
15769 TTATCACAAA-TTTATAGTG-TGA
1 TTATCA-AAATTTTATAGGGAGGT
15791 TTATCAAAATTT
1 TTATCAAAATTT
15803 CAGAGTGTGA
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
21 3 0.05
22 11 0.17
23 48 0.73
24 4 0.06
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:15771 original size:46 final size:45
Alignment explanation
Indices: 15700--15804 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 45
15690 TATAAGCAAG
* *
15700 TTATCAAAATTTTATAGGGAGGTTTATCA-AAATTTTATAG-GAAGA
1 TTATCAAAATTTCATAGGGAAGTTTATCACAAA-TTTATAGTG-AGA
*
15745 TTTATCAAAATTTCAT-GGCGAAGTTTATCACAAATTTATAGTGTGA
1 -TTATCAAAATTTCATAGG-GAAGTTTATCACAAATTTATAGTGAGA
15791 TTATCAAAATTTCA
1 TTATCAAAATTTCA
15805 GAGTGTGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 16 0.30
46 33 0.62
47 4 0.08
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGGAAGTTTATCACAAATTTATAGTGAGA
Found at i:15826 original size:22 final size:22
Alignment explanation
Indices: 15769--15815 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
15759 ATGGCGAAGT
*
15769 TTATCACAAATTT-ATAGTGTGA
1 TTATCA-AAATTTCAGAGTGTGA
15791 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
15813 TTA
1 TTA
15816 CTAACAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:19355 original size:33 final size:32
Alignment explanation
Indices: 19267--19356 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 32
19257 CTCTTTCTTT
19267 TCAACCAAAAC-AATCCTATTTTCAATGCTATGA
1 TCAACCAAAACAAAT--TATTTTCAATGCTATGA
* *
19300 TCAACCAAAACAAATTTGTTTTCCATGCTATGA
1 TCAACCAAAACAAA-TTATTTTCAATGCTATGA
19333 TCAACCAAAACAGAATTATTTTCA
1 TCAACCAAAACA-AATTATTTTCA
19357 TCACAAGTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
33 45 0.90
34 4 0.08
35 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (32 bp):
TCAACCAAAACAAATTATTTTCAATGCTATGA
Found at i:19408 original size:33 final size:33
Alignment explanation
Indices: 19371--19467 Score: 86
Period size: 33 Copynumber: 2.9 Consensus size: 33
19361 AAGTAGAATC
* * *
19371 CAAAACAGATTTTGTTTCATCACAAACAACACA
1 CAAAAAAGATTTAGTGTCATCACAAACAACACA
** *
19404 CAAAAAAGATTTAGTGTCATTGCAAACAACACT
1 CAAAAAAGATTTAGTGTCATCACAAACAACACA
** * ** *
19437 CAAATTAGGTTTAGCATCATCGCAAACAACA
1 CAAAAAAGATTTAGTGTCATCACAAACAACA
19468 TCTAAAACAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (33 bp):
CAAAAAAGATTTAGTGTCATCACAAACAACACA
Found at i:21902 original size:22 final size:22
Alignment explanation
Indices: 21877--21931 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
21867 CTTAGAGAGA
*
21877 TTAACAAAATTTTATAAGAAGG
1 TTAACAAAATTTTATAAAAAGG
*
21899 TTAA-AAAAATTTATAAAAAGG
1 TTAACAAAATTTTATAAAAAGG
**
21920 TTCTCAAAATTT
1 TTAACAAAATTT
21932 CATAGTATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (22 bp):
TTAACAAAATTTTATAAAAAGG
Found at i:21967 original size:22 final size:22
Alignment explanation
Indices: 21881--21980 Score: 87
Period size: 22 Copynumber: 4.6 Consensus size: 22
21871 GAGAGATTAA
* *
21881 CAAAATTTTATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAT
* * *
21903 AAAAATTT-ATAAAAAGGTTCT
1 CAAAATTTCATAAGAAGGTTAT
***
21924 CAAAATTTCAT-AGTATCATTAT
1 CAAAATTTCATAAG-AAGGTTAT
* *
21946 TAAAATTTCATAGGAAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
21968 CAAAATTTCATAA
1 CAAAATTTCATAA
21981 TGGGATCATA
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
21 18 0.31
22 39 0.67
23 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAT
Found at i:33177 original size:22 final size:22
Alignment explanation
Indices: 33152--33258 Score: 121
Period size: 22 Copynumber: 5.0 Consensus size: 22
33142 TAATTACCAC
33152 TTACTGATTACTATTTTACTCT
1 TTACTGATTACTATTTTACTCT
*
33174 TTACTGATTACT-CTTTACTCT
1 TTACTGATTACTATTTTACTCT
* * *
33195 TTACTGATTAATATTCTATTCT
1 TTACTGATTACTATTTTACTCT
* * *
33217 TTACTGATTGC--CTTTACTTT
1 TTACTGATTACTATTTTACTCT
*
33237 TTACTGATTAATATTTTACTCT
1 TTACTGATTACTATTTTACTCT
33259 CTACCATTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.21
21 19 0.28
22 34 0.51
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (22 bp):
TTACTGATTACTATTTTACTCT
Found at i:33185 original size:43 final size:43
Alignment explanation
Indices: 33138--33258 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
33128 TATTTCACGC
* *
33138 TTACTAATTAC-CACTTACTGATTACTATTTTACTCTTTACTGA
1 TTACTAATTACTC-CTTACTGATTAATATTCTACTCTTTACTGA
** * *
33181 TTACTCTTTACTCTTTACTGATTAATATTCTATTCTTTACTGA
1 TTACTAATTACTCCTTACTGATTAATATTCTACTCTTTACTGA
* ** *
33224 TTGCCT--TTACTTTTTACTGATTAATATTTTACTCT
1 TT-ACTAATTACTCCTTACTGATTAATATTCTACTCT
33259 CTACCATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
42 26 0.39
43 37 0.56
44 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (43 bp):
TTACTAATTACTCCTTACTGATTAATATTCTACTCTTTACTGA
Found at i:33198 original size:14 final size:14
Alignment explanation
Indices: 33166--33199 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33156 TGATTACTAT
*
33166 TTTACTCTTTACTG
1 TTTACTCTTTACTC
*
33180 ATTACTCTTTACTC
1 TTTACTCTTTACTC
33194 TTTACT
1 TTTACT
33200 GATTAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTACTCTTTACTC
Found at i:33275 original size:35 final size:34
Alignment explanation
Indices: 33236--33302 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
33226 GCCTTTACTT
33236 TTTACTGATTAATATTTTACTCTCTACCATTTTTC
1 TTTACTGATTAATATTTTAC-CTCTACCATTTTTC
* * *
33271 TTTACTGATTACTCTTTTACCTTTACCATTTT
1 TTTACTGATTAATATTTTACCTCTACCATTTT
33303 ACTGATTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTACTGATTAATATTTTACCTCTACCATTTTTC
Found at i:33283 original size:42 final size:43
Alignment explanation
Indices: 33152--33276 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 43
33142 TAATTACCAC
* *
33152 TTACTGATTACTATTTTACTCTTTACTGATTACTCTTTACTCT
1 TTACTGATTAATATTTTACTCTTTACTGATTTCTCTTTACTCT
* * * *
33195 TTACTGATTAATATTCTATTCTTTACTGATTGC-CTTTACTTT
1 TTACTGATTAATATTTTACTCTTTACTGATTTCTCTTTACTCT
* * *
33237 TTACTGATTAATATTTTACTCTCTAC-CATTTTTCTTTACT
1 TTACTGATTAATATTTTACTCTTTACTGATTTCTCTTTACT
33277 GATTACTCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.04
42 38 0.54
43 29 0.41
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (43 bp):
TTACTGATTAATATTTTACTCTTTACTGATTTCTCTTTACTCT
Found at i:33379 original size:14 final size:14
Alignment explanation
Indices: 33336--33385 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
33326 TATTTTTTTC
33336 CTTTACTGATTACT
1 CTTTACTGATTACT
**
33350 -TTTCATCTCTTTACT
1 CTTT-A-CTGATTACT
33365 CTTTACTGATTACT
1 CTTTACTGATTACT
33379 CTTTACT
1 CTTTACT
33386 TTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
15 8 0.28
16 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (14 bp):
CTTTACTGATTACT
Done.