Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013149.1 Corchorus capsularis cultivar CVL-1 contig13170, 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: 51562
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6978 original size:30 final size:30
Alignment explanation
Indices: 6938--7000 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
6928 TGTCTTCAAG
6938 TCCATAATAAGTCCTT-GGCACATCATTCCC
1 TCCATAATAAG-CCTTGGGCACATCATTCCC
* **
6968 TCCATGATAAGCCTTGGGTGCATCATTCCC
1 TCCATAATAAGCCTTGGGCACATCATTCCC
6998 TCC
1 TCC
7001 CCCTTGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.30
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCC
Found at i:22844 original size:31 final size:31
Alignment explanation
Indices: 22798--22868 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
22788 GGGGAAACTT
*
22798 TATATTTTCCGATTGTACCCTTATT-TTTAAAA
1 TATA-TTTCCAATTGTACCCTT-TTCTTTAAAA
22830 TATATTTCCAATTGTACCCTTTTCTTTAAAA
1 TATATTTCCAATTGTACCCTTTTCTTTAAAA
*
22861 CATATTTC
1 TATATTTC
22869 TAAATTGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.06
31 30 0.83
32 4 0.11
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.49
Consensus pattern (31 bp):
TATATTTCCAATTGTACCCTTTTCTTTAAAA
Found at i:23200 original size:19 final size:20
Alignment explanation
Indices: 23173--23210 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
23163 TACTATTATT
23173 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
23193 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
23211 AATGTCAATA
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:27031 original size:21 final size:20
Alignment explanation
Indices: 27007--27062 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 20
26997 CAGTAAATTA
*
27007 GTAATTAAGTTAAATCAGTT
1 GTAATTAAGTTAAATCAGGT
* * *
27027 GGTAATCAACTTAATTC-GGT
1 -GTAATTAAGTTAAATCAGGT
27047 GTAATTAAG-TAAATCA
1 GTAATTAAGTTAAATCA
27063 AGTAATTTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
18 5 0.19
19 7 0.26
20 2 0.07
21 13 0.48
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (20 bp):
GTAATTAAGTTAAATCAGGT
Found at i:27126 original size:43 final size:43
Alignment explanation
Indices: 27025--27155 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 43
27015 GTTAAATCAG
* * *
27025 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATCAAGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAAT-TAGTAAT
* * *
27069 TTGGTAAACTACTTAATTCAGTGTAATTAAGCAAATTAGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAATTAGTAAT
*
27112 TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAATTGGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAATTAGTAAT
27155 T
1 T
27156 AAGCTAAGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 46 0.59
44 32 0.41
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (43 bp):
TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAATTAGTAAT
Found at i:27151 original size:35 final size:35
Alignment explanation
Indices: 27112--27287 Score: 121
Period size: 35 Copynumber: 5.0 Consensus size: 35
27102 AATTAGTAAT
**
27112 TTGGTAAACAACTTAATTCGGTGTAATTAAGAAAA
1 TTGGTAATTAACTTAATTCGGTGTAATTAAGAAAA
*
27147 TTGGTAATTAAGCTAAGTAATT--TTGTAATT----AAA
1 TTGGTAATTAA-CT---TAATTCGGTGTAATTAAGAAAA
*
27180 TTAGGTAATTAACTTAATTCGGTGTAATTAAGTAAA
1 TT-GGTAATTAACTTAATTCGGTGTAATTAAGAAAA
** * ** *
27216 TCAGTAGTCGACTTAATTCGGTGTAATTAAGTAAA
1 TTGGTAATTAACTTAATTCGGTGTAATTAAGAAAA
** ** *
27251 TCAGTAATTGGCTTAATTTGGTGTAATTAAGTAAAA
1 TTGGTAATTAACTTAATTCGGTGTAATTAAG-AAAA
27287 T
1 T
27288 AAATGGCTTA
Statistics
Matches: 115, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
30 5 0.04
32 7 0.06
33 7 0.06
34 9 0.08
35 65 0.57
36 10 0.09
37 7 0.06
39 5 0.04
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (35 bp):
TTGGTAATTAACTTAATTCGGTGTAATTAAGAAAA
Found at i:27163 original size:21 final size:21
Alignment explanation
Indices: 27139--27178 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27129 TCGGTGTAAT
27139 TAAGAAAATTGGTAATTAAGC
1 TAAGAAAATTGGTAATTAAGC
* * *
27160 TAAGTAATTTTGTAATTAA
1 TAAGAAAATTGGTAATTAA
27179 ATTAGGTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (21 bp):
TAAGAAAATTGGTAATTAAGC
Found at i:27748 original size:24 final size:22
Alignment explanation
Indices: 27721--27779 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
27711 TGTGGTTACC
27721 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG-T-AGGTTATT
* * *
27745 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTAGGTTATT
*
27767 GAAATTTCATAGG
1 AAAATTTCATAGG
27780 GTGGTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 17 0.59
23 1 0.03
24 11 0.38
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGTAGGTTATT
Found at i:27766 original size:22 final size:22
Alignment explanation
Indices: 27738--27786 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
27728 CATAGGATCA
* *
27738 GGTTATTAAAATCTCTTAGGTT
1 GGTTATTAAAATCTCATAGGGT
* *
27760 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATCTCATAGGGT
27782 GGTTA
1 GGTTA
27787 ATTATCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (22 bp):
GGTTATTAAAATCTCATAGGGT
Found at i:27957 original size:22 final size:21
Alignment explanation
Indices: 27822--27961 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
27812 ATCAAAGAGA
* * *
27822 TTATCAAAATGTCATAACGAGA
1 TTATCAAAATTTCAT-ATGAGG
*
27844 TTAT-AAGAATTTCATAATGTGG
1 TTATCAA-AATTTCAT-ATGAGG
* *
27866 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TATGAGG
* **
27888 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-ATGAGG
* *
27910 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
27932 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
27954 TTAT-AAAA
1 TTATCAAAA
27962 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.11
22 80 0.85
23 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:28009 original size:20 final size:23
Alignment explanation
Indices: 27986--28058 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 23
27976 AGGAGTACCA
*
27986 AAATTTGATAGAAG-G-TTATC-
1 AAATTTCATAGAAGTGATTATCG
*
28006 AAATCTCATAG-AGTGATTATCG
1 AAATTTCATAGAAGTGATTATCG
* *
28028 AAATTTCATAGAAATTGGATTATCA
1 AAATTTCATAG-AAGT-GATTATCG
28053 AAATTT
1 AAATTT
28059 ATTTCATAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.05
20 10 0.24
21 5 0.12
22 10 0.24
24 2 0.05
25 13 0.31
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (23 bp):
AAATTTCATAGAAGTGATTATCG
Found at i:28127 original size:21 final size:22
Alignment explanation
Indices: 28059--28130 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
28049 ATCAAAATTT
* * * *
28059 ATTTCATAGAGGGGTCAACAAA
1 ATTTCATAAAGAGGTTATCAAA
*
28081 ATTTTATAAAGAGGTTATCAAA
1 ATTTCATAAAGAGGTTATCAAA
28103 ATTTCATAAAGAGGTTATCAAA
1 ATTTCATAAAGAGGTTATCAAA
*
28125 TTTTCA
1 ATTTCA
28131 AATGTGATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
ATTTCATAAAGAGGTTATCAAA
Found at i:28282 original size:22 final size:22
Alignment explanation
Indices: 28254--28812 Score: 193
Period size: 22 Copynumber: 25.7 Consensus size: 22
28244 TCAGGGAGGA
28254 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
28276 TATCAAAATTTCATA-GTTTGGT
1 TATCAAAATTTCATATG-AAGGT
* * * *
28298 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
28320 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
28341 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
28364 TAACAAAATTTCATAATGAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
28386 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
28408 TATC-AAA-TT--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * **
28424 TATCAAGATTTCATAAGAAATT
1 TATCAAAATTTCATATGAAGGT
*
28446 TATCAAAATTTTATA-G-AGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
28467 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
28490 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
28512 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
28534 TATCAAAATTTCAGAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
*
28556 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
28578 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
28600 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
28622 TATCAATATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
28645 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
28667 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
28689 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
28711 TA--AACGTATTTCATAAGAAGGT
1 TATCAA--AATTTCATATGAAGGT
** **
28733 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
28754 TCTCGAAATTCCATAGTGTCA--T
1 TATCAAAATTTCATA-TG-AAGGT
*
28776 TATTAAAATTTCATA-GAAAGGT
1 TATCAAAATTTCATATG-AAGGT
28798 TATCAAAATTTCATA
1 TATCAAAATTTCATA
28813 ATGGGGTCAT
Statistics
Matches: 399, Mismatches: 91, Indels: 94
0.68 0.16 0.16
Matches are distributed among these distances:
16 6 0.02
17 4 0.01
18 3 0.01
20 8 0.02
21 54 0.14
22 270 0.68
23 49 0.12
24 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:28669 original size:45 final size:45
Alignment explanation
Indices: 28596--28681 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
28586 TTTCATAACG
* * *
28596 TGGTTATCAATATATCATATGGAGGTTATCAATATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
28641 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
28682 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:35824 original size:2 final size:2
Alignment explanation
Indices: 35817--35842 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35807 TTCTGTTTTC
35817 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
35843 GTACAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41195 original size:22 final size:22
Alignment explanation
Indices: 41170--41290 Score: 111
Period size: 22 Copynumber: 5.5 Consensus size: 22
41160 TGATAATCAA
* * *
41170 ACCAAAATTACATAGTGTGGTT
1 ACCAAAATTTCATACTGAGGTT
41192 ACCAAAATTTCATA-TAGAGGTT
1 ACCAAAATTTCATACT-GAGGTT
* *
41214 ATCAAAACTTCATACTGTA-GTT
1 ACCAAAATTTCATACTG-AGGTT
* *
41236 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATACTGAGGTT
*** *
41258 ACCAAAATTTCATAAAAAGGGT
1 ACCAAAATTTCATACTGAGGTT
41280 ACCAAAATTTC
1 ACCAAAATTTC
41291 TTAGGCATGT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
21 2 0.02
22 81 0.95
23 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATACTGAGGTT
Found at i:41244 original size:44 final size:43
Alignment explanation
Indices: 41170--41271 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
41160 TGATAATCAA
* * *
41170 ACCAAAATTACATAGTGTGGTTACCAAAATTTCATATAGAGGTT
1 ACCAAAATT-CATACTGTAGTTACCAAAATTTCATACAGAGGTT
* *
41214 ATCAAAACTTCATACTGTAGTTATCAAAATTTCATACAGAGGTT
1 ACCAAAA-TTCATACTGTAGTTACCAAAATTTCATACAGAGGTT
41258 ACCAAAATTTCATA
1 ACCAAAA-TTCATA
41272 AAAAGGGTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 48 0.96
45 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (43 bp):
ACCAAAATTCATACTGTAGTTACCAAAATTTCATACAGAGGTT
Found at i:41303 original size:66 final size:66
Alignment explanation
Indices: 41188--41337 Score: 160
Period size: 66 Copynumber: 2.3 Consensus size: 66
41178 TACATAGTGT
* * * * * *
41188 GGTTACCAAAATTTCATATAGAGGTTATCAAAACTTCATACTGTAGTTATCAAAATTTCATACAG
1 GGTTACCAAAATTTCATAAAAAGGGTACCAAAACTTCATACGGCAGTTATCAAAATTTCATA-AG
41253 -A
65 AA
* * * *
41254 GGTTACCAAAATTTCATAAAAAGGGTACCAAAATTTCTTA-GGCATGTTATTAAAATTTCATATG
1 GGTTACCAAAATTTCATAAAAAGGGTACCAAAACTTCATACGGCA-GTTATCAAAATTTCATAAG
41318 AA
65 AA
* *
41320 AGTTAACAAAATTTCATA
1 GGTTACCAAAATTTCATA
41338 GGGAGGGAGG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 3 0.04
66 67 0.96
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (66 bp):
GGTTACCAAAATTTCATAAAAAGGGTACCAAAACTTCATACGGCAGTTATCAAAATTTCATAAGA
A
Found at i:41420 original size:22 final size:22
Alignment explanation
Indices: 41364--41440 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
41354 AATTTTGTGC
* **
41364 TTATCAAAATTTCCTAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
* *
41386 TTAAGAAAATTTTATAGGGAGA
1 TTATGAAAATTTTATAGGGAGG
41408 TTATGAAAATTTTAT-GGAGAGG
1 TTATGAAAATTTTATAGG-GAGG
41430 TTATCGAAAAT
1 TTAT-GAAAAT
41441 ACATAGAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 2 0.04
22 38 0.83
23 6 0.13
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (22 bp):
TTATGAAAATTTTATAGGGAGG
Found at i:43174 original size:34 final size:34
Alignment explanation
Indices: 43098--43175 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
43088 TAAAGATTTA
* *
43098 AATATTTGACATGAATATTTGTGTTGATATATTG
1 AATATTTGGCATGAATATTTGTGGTGATATATTG
43132 AATATTTGGCATGAATATTTGTGGTGATATATTG
1 AATATTTGGCATGAATATTTGTGGTGATATATTG
43166 AATATTTGGC
1 AATATTTGGC
43176 TTGGAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45
Consensus pattern (34 bp):
AATATTTGGCATGAATATTTGTGGTGATATATTG
Found at i:45781 original size:29 final size:31
Alignment explanation
Indices: 45736--45800 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
45726 AATTGTTGAC
45736 ATTAAGAC-TTCTGTTTTTGACC-AGGAGAT
1 ATTAAGACTTTCTGTTTTTGACCAAGGAGAT
* * * *
45765 ATTAAGACTTTTTTTTTTTGGCCAATGAGAT
1 ATTAAGACTTTCTGTTTTTGACCAAGGAGAT
45796 ATTAA
1 ATTAA
45801 ACAATATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 11 0.37
31 11 0.37
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (31 bp):
ATTAAGACTTTCTGTTTTTGACCAAGGAGAT
Found at i:48982 original size:15 final size:15
Alignment explanation
Indices: 48962--48990 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48952 CTTATCATCT
48962 TGTTGGATTTGAATC
1 TGTTGGATTTGAATC
48977 TGTTGGATTTGAAT
1 TGTTGGATTTGAAT
48991 TGGAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (15 bp):
TGTTGGATTTGAATC
Found at i:50709 original size:16 final size:16
Alignment explanation
Indices: 50688--50737 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
50678 GAGAACAATC
50688 TGGGAAGCAATATCAG
1 TGGGAAGCAATATCAG
50704 TGGGAA-C-A-ATC--
1 TGGGAAGCAATATCAG
*
50715 TGGGAAGCAATATTAG
1 TGGGAAGCAATATCAG
50731 TGGGAAG
1 TGGGAAG
50738 AATGGAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
11 6 0.21
12 1 0.04
13 4 0.14
14 3 0.11
15 1 0.04
16 13 0.46
ACGTcount: A:0.36, C:0.10, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGGAAGCAATATCAG
Found at i:50733 original size:27 final size:27
Alignment explanation
Indices: 50666--50736 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
50656 TTCTCTGAGG
*
50666 AGCAATATTAGTGAGAACAATCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
*
50693 AGCAATATCAGTGGGAACAATCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
50720 AGCAATATTAGTGGGAA
1 AGCAATATTAGTGGGAA
50737 GAATGGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.21
Consensus pattern (27 bp):
AGCAATATTAGTGGGAACAATCTGGGA
Done.