Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013615.1 Corchorus olitorius cultivar O-4 contig13648, 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: 36140
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:5264 original size:22 final size:22
Alignment explanation
Indices: 5208--5270 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
5198 GACCCTTGAA
* *
5208 TCAAATTATCAAACTT-GAGCTC
1 TCAAATTATC-AAGTTCAAGCTC
5230 TCAAATTATCAAGTTCAAGCTC
1 TCAAATTATCAAGTTCAAGCTC
*
5252 TCAAATTATCAAGATCAAG
1 TCAAATTATCAAGTTCAAG
5271 ATCGAGTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (22 bp):
TCAAATTATCAAGTTCAAGCTC
Found at i:17220 original size:31 final size:30
Alignment explanation
Indices: 17185--17254 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
17175 ATAGGTCCCT
17185 CTACTTACAAAAAGCGATCAATTTGGTCTCA
1 CTACTTACAAAAA-CGATCAATTTGGTCTCA
* ** *
17216 CTAC-TGCAAAAATTATCAATTTGGTCTCT
1 CTACTTACAAAAACGATCAATTTGGTCTCA
17245 CTACTTACAA
1 CTACTTACAA
17255 TTTGGTGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 18 0.55
30 11 0.33
31 4 0.12
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (30 bp):
CTACTTACAAAAACGATCAATTTGGTCTCA
Found at i:17759 original size:22 final size:22
Alignment explanation
Indices: 17732--17795 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
17722 AATTCCTTAT
17732 GTGATTTCTAAAATTTTATAGC
1 GTGATTTCTAAAATTTTATAGC
*
17754 GTGA-TTCTCAAAATTTTATAGT
1 GTGATTTCT-AAAATTTTATAGC
*
17776 GTGGTTATC-AAAATTTTATA
1 GTGATT-TCTAAAATTTTATA
17796 ATGAGGTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 4 0.11
22 30 0.81
23 1 0.03
24 2 0.05
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (22 bp):
GTGATTTCTAAAATTTTATAGC
Found at i:17803 original size:22 final size:22
Alignment explanation
Indices: 17761--18123 Score: 145
Period size: 22 Copynumber: 16.4 Consensus size: 22
17751 AGCGTGATTC
*
17761 TCAAAATTTTAT-AGTGTGGTTA
1 TCAAAATTTTATAAG-GAGGTTA
*
17783 TCAAAATTTTATAATGAGGTTA
1 TCAAAATTTTATAAGGAGGTTA
* * *
17805 CCAAAATTTCAT-AGGTAGGATA
1 TCAAAATTTTATAAGG-AGGTTA
*
17827 TTAAAATTTTAT-AGTGTA-GTTA
1 TCAAAATTTTATAAG-G-AGGTTA
* * *
17849 TCAAAATTTCAT-GGGATGTTA
1 TCAAAATTTTATAAGGAGGTTA
*
17870 TCAAAATTTCATAAGGAGGTTA
1 TCAAAATTTTATAAGGAGGTTA
* *
17892 TTAAAATAAAATTTCATAAGGATGTTA
1 TCAAAAT----TTT-ATAAGGAGGTTA
* *
17919 TCAAAATTTTGTATGGAGGTTA
1 TCAAAATTTTATAAGGAGGTTA
* * *
17941 TCAAAATTTCATAACGAGATTA
1 TCAAAATTTTATAAGGAGGTTA
* * * *
17963 TC-GAA-TTCAT-GGGAAGGTTG
1 TCAAAATTTTATAAGG-AGGTTA
* * * * *
17983 TCGAAATTTCACAGGGAGGATA
1 TCAAAATTTTATAAGGAGGTTA
* ****
18005 -CTAAAATTTCATATTTTGGTTA
1 TC-AAAATTTTATAAGGAGGTTA
* *
18027 TCAAAATTTCAT-AGGAAGGCTA
1 TCAAAATTTTATAAGG-AGGTTA
* * * * *
18049 ACAAAATTTCATAGGGCGATTA
1 TCAAAATTTTATAAGGAGGTTA
* *
18071 TCGAAATTTTATATGGAGGTTA
1 TCAAAATTTTATAAGGAGGTTA
* *
18093 TCAAATTTTTAT-AGGAAGATTA
1 TCAAAATTTTATAAGG-AGGTTA
*
18115 ACAAAATTT
1 TCAAAATTT
18124 CATATTTTGC
Statistics
Matches: 257, Mismatches: 65, Indels: 38
0.71 0.18 0.11
Matches are distributed among these distances:
19 1 0.00
20 12 0.05
21 26 0.10
22 186 0.72
23 13 0.05
26 2 0.01
27 17 0.07
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.36
Consensus pattern (22 bp):
TCAAAATTTTATAAGGAGGTTA
Found at i:17834 original size:66 final size:65
Alignment explanation
Indices: 17763--17898 Score: 184
Period size: 66 Copynumber: 2.1 Consensus size: 65
17753 CGTGATTCTC
* * *
17763 AAAATTTTATAGTGTGGTTATCAAAATTTTATAATGAGGTTACCAAAATTTCAT-AGGTAGGATA
1 AAAATTTTATAGTGTAGTTATCAAAATTTCAT-AGGAGGTTACCAAAATTTCATAAGG-AGGATA
17827 TT
64 TT
* * * *
17829 AAAATTTTATAGTGTAGTTATCAAAATTTCATGGGATGTTATCAAAATTTCATAAGGAGGTTATT
1 AAAATTTTATAGTGTAGTTATCAAAATTTCATAGGAGGTTACCAAAATTTCATAAGGAGGATATT
17894 AAAAT
1 AAAAT
17899 AAAATTTCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
65 29 0.47
66 33 0.53
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (65 bp):
AAAATTTTATAGTGTAGTTATCAAAATTTCATAGGAGGTTACCAAAATTTCATAAGGAGGATATT
Found at i:17910 original size:27 final size:27
Alignment explanation
Indices: 17872--17925 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
17862 GGATGTTATC
*
17872 AAAATTTCATAAGGAGGTTATTAAAAT
1 AAAATTTCATAAGGAGGTTATCAAAAT
*
17899 AAAATTTCATAAGGATGTTATCAAAAT
1 AAAATTTCATAAGGAGGTTATCAAAAT
17926 TTTGTATGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (27 bp):
AAAATTTCATAAGGAGGTTATCAAAAT
Found at i:17922 original size:49 final size:48
Alignment explanation
Indices: 17851--17947 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
17841 TGTAGTTATC
* *
17851 AAAATTTCATGGGATGTTATCAAAATTTCATAAGGAGGTTATTAAAAT
1 AAAATTTCATAGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAAT
** *
17899 AAAATTTCATAAGGATGTTATCAAAATTTTGTATGGAGGTTATCAAAAT
1 AAAATTTCAT-AGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAAT
17948 TTCATAACGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 10 0.23
49 33 0.77
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.36
Consensus pattern (48 bp):
AAAATTTCATAGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAAT
Found at i:17954 original size:44 final size:43
Alignment explanation
Indices: 17709--18127 Score: 169
Period size: 44 Copynumber: 9.5 Consensus size: 43
17699 CTTTTAATTT
* * *
17709 TGGAGGTTATCAAAATTCCTTATG-TGATT-TCTAAAATTTTATA
1 TGGAGGTTATCAAAATTTCATAGGATG-TTATC-AAAATTTTATA
* * * *
17752 -GCGTGATTCTCAAAATTTTATAGTG-TGGTTATCAAAATTTTATAA
1 TG-GAGGTTATCAAAATTTCATAG-GAT-GTTATCAAAATTTTAT-A
* * * *
17797 T-GAGGTTACCAAAATTTCATAGGTAGGATATTAAAATTTTATA
1 TGGAGGTTATCAAAATTTCATAGG-ATGTTATCAAAATTTTATA
* * *
17840 GTGTA-GTTATCAAAATTTCATGGGATGTTATCAAAATTTCATA
1 -TGGAGGTTATCAAAATTTCATAGGATGTTATCAAAATTTTATA
* * *
17883 AGGAGGTTATTAAAATAAAATTTCATAAGGATGTTATCAAAATTTTGTA
1 TGGAGGTTA-T----CAAAATTTCAT-AGGATGTTATCAAAATTTTATA
* * *
17932 TGGAGGTTATCAAAATTTCATAACGA-GATTATC-GAA-TTCAT-
1 TGGAGGTTATCAAAATTTCAT-AGGATG-TTATCAAAATTTTATA
* * * * * * *
17973 GGGAAGGTTGTCGAAATTTCACAGGGAGGATA-CTAAAATTTCATA
1 TGG-AGGTTATCAAAATTTCATA-GGATGTTATC-AAAATTTTATA
*** * * * *
18018 TTTTGGTTATCAAAATTTCATAGGAAGGCTAACAAAATTTCATA
1 TGGAGGTTATCAAAATTTCATAGG-ATGTTATCAAAATTTTATA
* * * * * * *
18062 GGGCGATTATCGAAATTTTATATGGAGGTTATCAAATTTTTATA
1 TGGAGGTTATCAAAATTTCATA-GGATGTTATCAAAATTTTATA
* *
18106 -GGAAGATTAACAAAATTTCATA
1 TGG-AGGTTATCAAAATTTCATA
18128 TTTTGCTTAT
Statistics
Matches: 283, Mismatches: 64, Indels: 57
0.70 0.16 0.14
Matches are distributed among these distances:
41 4 0.01
42 25 0.09
43 45 0.16
44 163 0.58
45 8 0.03
48 11 0.04
49 27 0.10
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (43 bp):
TGGAGGTTATCAAAATTTCATAGGATGTTATCAAAATTTTATA
Found at i:18219 original size:22 final size:22
Alignment explanation
Indices: 18168--18284 Score: 82
Period size: 22 Copynumber: 5.5 Consensus size: 22
18158 AAGTGAGCTT
* *
18168 ATCAAAATTTCA-AGTGTCGTT
1 ATCAAAATTTCATAGTGTAGTA
*
18189 ACCAAAATTTCATAGTGTAGTA
1 ATCAAAATTTCATAGTGTAGTA
* *
18211 ATCACAATTTCATAGAG--GTTA
1 ATCAAAATTTCATAGTGTAG-TA
* * * *
18232 A-CCAAATTTCAT-GGGGAGGTT
1 ATCAAAATTTCATAGTGTA-GTA
* *
18253 ATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAGTGTAGTA
18275 ATCAAAATTT
1 ATCAAAATTT
18285 TATAATATGG
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
19 2 0.03
20 10 0.13
21 16 0.21
22 45 0.60
23 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGTAGTA
Found at i:18295 original size:22 final size:22
Alignment explanation
Indices: 18249--18295 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
18239 TTCATGGGGA
* *
18249 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAATAT
*
18271 GGTTATCAAAATTTTATAATAT
1 GGTTATCAAAATTTCATAATAT
18293 GGT
1 GGT
18296 ATTTCAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAATAT
Found at i:18612 original size:22 final size:21
Alignment explanation
Indices: 18513--18740 Score: 144
Period size: 22 Copynumber: 10.6 Consensus size: 21
18503 TATAGTGTTC
* *
18513 TTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCATAAGAGG
* * *
18534 TCAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATAA-GAGG
* *
18556 TTATAAAAAATTT-ATAAGTATG
1 TTAT-CAAAATTTCATAAG-AGG
18578 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAAGA-GG
* *
18600 TTATCAAAATTTCATGAGGTGG
1 TTATCAAAATTTCAT-AAGAGG
*
18622 TTTTCAAAATTTCAT--GAGG
1 TTATCAAAATTTCATAAGAGG
*
18641 TTATCAAAATTT-TTAAAGGAGG
1 TTATCAAAATTTCAT-AA-GAGG
* * *
18663 TTATCAAAATTTTATAGGGAGCT
1 TTATCAAAATTTCATA-AGAG-G
* *
18686 TTATAAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATA-AGAGG
* *
18708 -TATCACAATTTCAT-GGTACGG
1 TTATCAAAATTTCATAAG-A-GG
18729 TTATCAAAATTT
1 TTATCAAAATTT
18741 TGTAATGTGA
Statistics
Matches: 163, Mismatches: 28, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
18 1 0.01
19 15 0.09
20 1 0.01
21 35 0.21
22 83 0.51
23 28 0.17
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAAGAGG
Found at i:19110 original size:3 final size:3
Alignment explanation
Indices: 19102--19136 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19092 AATATTTTTC
19102 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19137 AAGTCGATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20062 original size:6 final size:6
Alignment explanation
Indices: 20051--20080 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20041 CGAGCAACTT
20051 GAGCTC GAGCTC GAGCTC GAGCTC -AGCTC G
1 GAGCTC GAGCTC GAGCTC GAGCTC GAGCTC G
20081 TGAATAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
GAGCTC
Found at i:21096 original size:437 final size:435
Alignment explanation
Indices: 20277--21102 Score: 1031
Period size: 437 Copynumber: 1.9 Consensus size: 435
20267 TAAAACATAA
* ** *
20277 AAATTAGCTTTCGAGTCCTTCATGAAAGTCGTAGATCACGGAACAACCTTTAAACCGACATTTGA
1 AAATTAGCTTTCGAGTCCTTAATGAAAGTCGTAGATCACAAAACAACCTTTAAACCGACACTTGA
** * * * * *
20342 ATTACTTTAATCGAAAATCTGGATCGAAAATTATACGATATTAAATAGACGGTCGATCGAAACCA
66 ACAACTTCAATCGAAAATCTGGACCGAAAATTATACGATATTAAATAGACCGACAATCGAAACCA
* * ** * **
20407 CAAAATTTCAGAAGCATTTTTCGAGTTGAAACATAAAAATTGGCTTTTAAGTCCTTAATGAAAGT
131 CAAAATTTCAGAAGCATTTTTAGAATCAAAACATAAAAATCGGCTCCTAAGTCCTTAATGAAAGT
* * *
20472 TGTAAGTCATGAAATTACCTTTCAATAAACACTGGATCACCTTAATCGGACAAATAAAACCAAAA
196 TGTAAGTAATGAAATTACCTTTCAATAAACACTGAATCACCTCAATCGGACAAATAAAACCAAAA
** * * *
20537 AATACAAAAATAAAGTTGAAGAATTAAATCGATTAAGATGAAATCGTAAAGGATTCAATAGCATA
261 AATACAAAAATAAAGCCGAAGAATTAAATCGATCAACAT-AAATCGTAAAGGATTAAATAGCATA
* * * ** *
20602 CATCATAAATGTATGAGAATCATTAGATAAATAATCCAGCAAAAAAATGATTAGTTTATAGAGAT
325 AAACAGAAAACTATGAGAATCATTAGATAAATAATCCAACAAAAAAATGATTAGTTTATAGAGAT
20667 GAAACATAAAAATTCCCTCTTGAACCCTTAATGAAACTCGTCAATC
390 GAAACATAAAAATTCCCTCTTGAACCCTTAATGAAACTCGTCAATC
* * *
20713 AAATTCAGCTTTCGGGTCCTTAATGAAAGTCGTAGATCACAAAATAACCTTTTAACCGACACTTG
1 AAATT-AGCTTTCGAGTCCTTAATGAAAGTCGTAGATCACAAAACAACCTTTAAACCGACACTTG
* *
20778 AACAACTTCAATCAGACAA-GTGGACCGAAAATTATACGATATTAAATAGACCGACAATCGAAAC
65 AACAACTTCAATC-GAAAATCTGGACCGAAAATTATACGATATTAAATAGACCGACAATCGAAAC
* * * *
20842 CACAAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAATCGGCTCCTGAGTTC-TATATGA
129 CACAAAATTTCAGAAGCA-TTTTTAGAATCAAAACATAAAAATCGGCTCCTAAGTCCTTA-ATGA
* * * * *
20906 AAGTTGT-AGATAATGAAATTACCTTTTAATAGACACTTGAATCATCTCAATCGGACATATAGAA
192 AAGTTGTAAG-TAATGAAATTACCTTTCAATAAACAC-TGAATCACCTCAATCGGACAAATAAAA
*
20970 -CAAAAAATACAAAAATAAAAGCCG-AGACATTAAATCG-TCCAACCCAT-AATTGTAAAGGATT
255 CCAAAAAATACAAAAAT-AAAGCCGAAGA-ATTAAATCGAT-CAA--CATAAATCGTAAAGGATT
* *
21031 AAATAGCATAAAAGAGAAAACTATGAGGATCATTAGATAAATAATCCAAC-AAAAAAT-ATTAGT
315 AAATAGCATAAAACAGAAAACTATGAGAATCATTAGATAAATAATCCAACAAAAAAATGATTAGT
*
21094 TTATGGAGA
380 TTATAGAGA
21103 ATGGGATCCA
Statistics
Matches: 329, Mismatches: 50, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
436 5 0.02
437 137 0.42
438 93 0.28
439 92 0.28
441 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (435 bp):
AAATTAGCTTTCGAGTCCTTAATGAAAGTCGTAGATCACAAAACAACCTTTAAACCGACACTTGA
ACAACTTCAATCGAAAATCTGGACCGAAAATTATACGATATTAAATAGACCGACAATCGAAACCA
CAAAATTTCAGAAGCATTTTTAGAATCAAAACATAAAAATCGGCTCCTAAGTCCTTAATGAAAGT
TGTAAGTAATGAAATTACCTTTCAATAAACACTGAATCACCTCAATCGGACAAATAAAACCAAAA
AATACAAAAATAAAGCCGAAGAATTAAATCGATCAACATAAATCGTAAAGGATTAAATAGCATAA
AACAGAAAACTATGAGAATCATTAGATAAATAATCCAACAAAAAAATGATTAGTTTATAGAGATG
AAACATAAAAATTCCCTCTTGAACCCTTAATGAAACTCGTCAATC
Found at i:21834 original size:21 final size:21
Alignment explanation
Indices: 21810--21851 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21800 TCAAAGTTAA
*
21810 AAGTGAATTAAGACAAATAAT
1 AAGTAAATTAAGACAAATAAT
* *
21831 AAGTAAATTAAGTCAATTAAT
1 AAGTAAATTAAGACAAATAAT
21852 GCATATCATG
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:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGTAAATTAAGACAAATAAT
Found at i:27040 original size:30 final size:30
Alignment explanation
Indices: 26961--27136 Score: 183
Period size: 30 Copynumber: 5.7 Consensus size: 30
26951 AATATTGTAT
* *
26961 ATGACAACTGCTGGTGTCAATTGAATAAAATT
1 ATGACAACTTCTGGTGTCAATTG--TAAAATC
* * **
26993 ATGGCATCTTCAAGTGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATC
*
27023 ATGACAACTT-TCGGTGTCAATTGCAAAATC
1 ATGACAACTTCT-GGTGTCAATTGTAAAATC
* *
27053 ATGACAACTTCTGGTGTCAATTGTGAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATC
** *
27083 ATGACAACTTCTAATGTCAATTATTGTAAGATC
1 ATGACAACTTCTGGTGTC-A--ATTGTAAAATC
27116 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
27137 AATTTCCTCA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
30 73 0.61
31 2 0.02
32 19 0.16
33 26 0.22
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAAATC
Found at i:27084 original size:60 final size:62
Alignment explanation
Indices: 27006--27136 Score: 169
Period size: 63 Copynumber: 2.1 Consensus size: 62
26996 GCATCTTCAA
**
27006 GTGTCAATTGTAAAATCATGACAACTT-TCGGTGTC-A-ATTGCAAAATCATGACAACTTCTG
1 GTGTCAATTGTAAAATCATGACAACTTCT-AATGTCAATATTGCAAAATCATGACAACTTCTG
* * * *
27066 GTGTCAATTGTGAGATCATGACAACTTCTAATGTCAATTATTGTAAGATCATGACAACTTCTG
1 GTGTCAATTGTAAAATCATGACAACTTCTAATGTCAA-TATTGCAAAATCATGACAACTTCTG
27129 GTGTCAAT
1 GTGTCAAT
27137 AATTTCCTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
60 29 0.48
61 2 0.03
63 30 0.49
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (62 bp):
GTGTCAATTGTAAAATCATGACAACTTCTAATGTCAATATTGCAAAATCATGACAACTTCTG
Found at i:27115 original size:33 final size:32
Alignment explanation
Indices: 27012--27176 Score: 155
Period size: 30 Copynumber: 5.2 Consensus size: 32
27002 TCAAGTGTCA
*
27012 ATTGTAAAATCATGACAACTT-TCGGTGTC-A-
1 ATTGTAAGATCATGACAACTTCT-GGTGTCAAT
* *
27042 ATTGCAAAATCATGACAACTTCTGGTGTC-A-
1 ATTGTAAGATCATGACAACTTCTGGTGTCAAT
* **
27072 ATTGTGAGATCATGACAACTTCTAATGTCAATT
1 ATTGTAAGATCATGACAACTTCTGGTGTCAA-T
27105 ATTGTAAGATCATGACAACTTCTGGTGTCAAT
1 ATTGTAAGATCATGACAACTTCTGGTGTCAAT
* * *
27137 AATTTCCTCAG--CATGACAACTTCTGGTGTCAAG
1 -A-TT-GTAAGATCATGACAACTTCTGGTGTCAAT
27170 ATTGTAA
1 ATTGTAA
27177 TTTAATTGTA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
30 53 0.46
31 4 0.04
32 2 0.02
33 50 0.44
34 2 0.02
35 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (32 bp):
ATTGTAAGATCATGACAACTTCTGGTGTCAAT
Found at i:30422 original size:2 final size:2
Alignment explanation
Indices: 30415--30441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30405 CAATAATGTT
30415 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30442 TGAAGGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31954 original size:92 final size:92
Alignment explanation
Indices: 31847--32029 Score: 251
Period size: 92 Copynumber: 2.0 Consensus size: 92
31837 CTTAACGAAT
* * * * *
31847 GAATCATGAAGAAGGAAGAAGAAGGAAGCATAAACTAGCAACAAAACTTCAGAACCCATAACCT-
1 GAATCATGAAGAAGGAAGAAGAAAGAAGCATAAAATAACAACAAAACTTCAAAACCCAGAACCTG
31911 AAGCAATCTATCAGCACGAAAAACCAAG
66 AAGC-ATCTATCAGCACGAAAAACCAAG
** * *
31939 GAATCATGAAGAAGGAAGAAGAAAGAAGTGTAAAATAACATCAAAACTTCAAAACCCAGAATCTG
1 GAATCATGAAGAAGGAAGAAGAAAGAAGCATAAAATAACAACAAAACTTCAAAACCCAGAACCTG
* *
32004 AATCATCTATCAGCACGGAAAACCAA
66 AAGCATCTATCAGCACGAAAAACCAA
32030 TGAGTTGATG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 76 0.96
93 3 0.04
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (92 bp):
GAATCATGAAGAAGGAAGAAGAAAGAAGCATAAAATAACAACAAAACTTCAAAACCCAGAACCTG
AAGCATCTATCAGCACGAAAAACCAAG
Found at i:33470 original size:29 final size:30
Alignment explanation
Indices: 33432--33506 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
33422 TATTGGGTTA
*
33432 AGGACGTTTTGCCCCCTGAACTT-CAAATT
1 AGGACATTTTGCCCCCTGAACTTCCAAATT
**
33461 AGGACATTTTGCCTTCTGAACTTCCAAATT
1 AGGACATTTTGCCCCCTGAACTTCCAAATT
* *
33491 TGAGACATTTAGCCCC
1 AG-GACATTTTGCCCC
33507 TTATGCCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 20 0.54
30 7 0.19
31 10 0.27
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (30 bp):
AGGACATTTTGCCCCCTGAACTTCCAAATT
Found at i:35515 original size:19 final size:19
Alignment explanation
Indices: 35472--35518 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
35462 TTGGAATTTT
*
35472 TTTTAA-AAAAAAAAGGAA
1 TTTTAAGAAAAAAAAGAAA
**
35490 -TAAAAGAAAAAAAAGAAA
1 TTTTAAGAAAAAAAAGAAA
35508 TTTTAAGAAAA
1 TTTTAAGAAAA
35519 TATGAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (19 bp):
TTTTAAGAAAAAAAAGAAA
Done.