Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015175.1 Corchorus olitorius cultivar O-4 contig15208, 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: 66996
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:15907 original size:13 final size:13
Alignment explanation
Indices: 15889--15914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15879 CCTTTGATTG
15889 TAATATCAAATCA
1 TAATATCAAATCA
15902 TAATATCAAATCA
1 TAATATCAAATCA
15915 GACATGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATATCAAATCA
Found at i:22581 original size:174 final size:175
Alignment explanation
Indices: 22003--22871 Score: 1115
Period size: 174 Copynumber: 5.0 Consensus size: 175
21993 TTGCATTTTT
* * * ** *
22003 TTTTATGAAAAACAGTGGGCAACTAAGGTTTGTAAGTTTAGTGGGCGAGAAAATCCAAAATTGGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGGA
22068 AAGAG-T--AAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
* * * *
22130 GTAGGCGATCGAGATAACCCACCTCGCAATCAGTGCAAAGGTATC
131 GTAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * * * **
22175 TTGTT-TGAAAAATAGTGGGCAACCGAGGTTTGTAAGTTTAGTGGGCAAGATAATTGAAAATTGG
1 TT-TTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGG
** * * * * * **
22239 AAAGAGCGCAAAGTTGAATGACAACGAGGG-GAAAACACATGAAA-CATGTGAAGTTTATAACCT
65 AAAGAGTTCAAAGGTGAATGACAACAAGGGAG-GAACACGTGAAATC-TATGAAGTTTATAAAGT
*
22302 TTAGTAGGCGGTCGAGATAACCCATCTCGCAATCAGTGCAAAGGTGTC
128 TTAGTAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * * * *
22350 TTTTGTGAAAAACAGTGGGCGACTGAGGTTTGTAAGTTTAGTCGGCCAGATAATCCAAAATTAGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGGA
* *
22415 AAGAGTTTAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAGGTTTATAAAGTTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
* *
22480 GCAGGCGGTCGAGATAACCCACCTC-CAATCGGTGCAAAGGTGTC
131 GTAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* ** * *
22524 TTTTGTGAAAAACAATGGGTGACCGAGGTTTACAAGTTCAGTGGGCGAGATAATCCAAAATTAGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGGA
* * * * *
22589 AAGAGTTCAAAGGTGAATGAAAACATGGGAAGAACACGCGGAATCTATGAAGTTTATAAAG-TTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
* * *
22653 GTAGGCGGTCAAGATAACCCATCTCGGAGTCGGTGCAAAGGTGTC
131 GTAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * * *
22698 TTTTGTGAAAAACAATGGGCGACCAAGGTTTGTAAGTTCAATGGGTGAGATAATCCAAAATTGGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGGA
* * *
22763 AAGAGTTCAAAGGTGAATGACAACAAGGAAGGAACACGCGAAATCTGTGAAGTTTATAAAGTTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
* * * *
22828 GCAGGCGATCAAGATAACCCAATCTCTCAATCGGTGCAAAGGTG
131 GTAGGCGGTCGAGATAACCC-ATCTCGCAATCGGTGCAAAGGTG
22872 AATAACAACA
Statistics
Matches: 607, Mismatches: 78, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
172 60 0.10
173 27 0.04
174 263 0.43
175 235 0.39
176 22 0.04
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (175 bp):
TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTTAGTGGGCGAGATAATCCAAAATTGGA
AAGAGTTCAAAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTATGAAGTTTATAAAGTTTA
GTAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
Found at i:22955 original size:91 final size:89
Alignment explanation
Indices: 22838--23220 Score: 238
Period size: 91 Copynumber: 4.2 Consensus size: 89
22828 GCAGGCGATC
* * ** *
22838 AAGATAACCCAATCTCTCAATCGGTGCAAAGGTGAATAACAACAGGGGAGGTATACATGTGAAGT
1 AAGATAACCCAAAC-CGCAATCGGTGCAAAGGTGAATAACAACAGGGGAGG-A-ACACATGAAAT
** * *
22903 CGGTGAAGTTTGTAAATTTATCA-GGA-
63 CAATGAAATTTGTAAATTTAT-ATAGAT
* * * **
22929 GAGATAACCCAAACGCGCAATTGGTGCAACGACGAATAACAACAGGGGAGGAACACATGAAATCA
1 AAGATAACCCAAAC-CGCAATCGGTGCAAAGGTGAATAACAACAGGGGAGGAACACATGAAATCA
*
22994 ATGAAATTTGTACATTTATATTAGAT
65 ATGAAATTTGTAAATTTATA-TAGAT
* * ** *
23020 AAGTTAACCCAAACCTGCAAGCGGTGCAAAGGTGAATAACAACAGGAAAGG--TACATGTAAAGT
1 AAGATAACCCAAACC-GCAATCGGTGCAAAGGTGAATAACAACAGGGGAGGAACACATG-AAA-T
* * * * **
23083 CAATTGTAACTTGTAAGTTTA-AGAGGG
63 CAA-TGAAATTTGTAAATTTATATAGAT
** * ** * *
23110 AAGATAACCCAAACTCGCAATCAATGCAAAGGCAAAT-AATAACATCAATGGAGAAACACGTGAA
1 AAGATAACCCAAAC-CGCAATCGGTGCAAAGG----TGAATAACAACAGGGGAGGAACACATGAA
* * * *
23174 ATCAGTGAAAATTTGTACATTTATATTGGAC
61 ATCAATG-AAATTTGTAAATTTATA-TAGAT
23205 AAGATAACCCAAACCG
1 AAGATAACCCAAACCG
23221 ACCGCAATCT
Statistics
Matches: 221, Mismatches: 54, Indels: 31
0.72 0.18 0.10
Matches are distributed among these distances:
88 1 0.00
89 30 0.14
90 35 0.16
91 89 0.40
92 15 0.07
93 25 0.11
94 7 0.03
95 19 0.09
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (89 bp):
AAGATAACCCAAACCGCAATCGGTGCAAAGGTGAATAACAACAGGGGAGGAACACATGAAATCAA
TGAAATTTGTAAATTTATATAGAT
Found at i:27840 original size:25 final size:27
Alignment explanation
Indices: 27783--27841 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
27773 GGGAATTCAT
* * *
27783 AAAATTTAAAGATTTTTTTTGAGATAA
1 AAAATTTAAAGATTTTTTATGAAAGAA
27810 AAAATTTAAAGA-TTTTTAT-AAAGAA
1 AAAATTTAAAGATTTTTTATGAAAGAA
*
27835 AGAATTT
1 AAAATTT
27842 TGAAATGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 6 0.21
27 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (27 bp):
AAAATTTAAAGATTTTTTATGAAAGAA
Found at i:28305 original size:12 final size:12
Alignment explanation
Indices: 28288--28312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28278 ATTTTAGATT
28288 TTAAAAAATCTC
1 TTAAAAAATCTC
28300 TTAAAAAATCTC
1 TTAAAAAATCTC
28312 T
1 T
28313 ATCCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAAAATCTC
Found at i:28405 original size:67 final size:67
Alignment explanation
Indices: 28297--28432 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
28287 TTTAAAAAAT
28297 CTCTTAAAAAATCTCTATCCAAATGAATCTCCCTCTTGAATATCCTCATCCAAACACACTCTTTA
1 CTCTTAAAAAATCTCTATCCAAATGAATCTCCCTCTTGAATATCCTCATCCAAACACACTCTTTA
28362 AA
66 AA
28364 CTCTTAAAAAATCTCTATCCAAATGAATCTCCCTCTTGAATATCCTCATCCAAACACACTCTTTA
1 CTCTTAAAAAATCTCTATCCAAATGAATCTCCCTCTTGAATATCCTCATCCAAACACACTCTTTA
28429 AA
66 AA
28431 CT
1 CT
28433 TGGTTTGGCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (67 bp):
CTCTTAAAAAATCTCTATCCAAATGAATCTCCCTCTTGAATATCCTCATCCAAACACACTCTTTA
AA
Found at i:28480 original size:12 final size:12
Alignment explanation
Indices: 28463--28488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28453 TGGGTTTTAG
28463 ATATCTTAGGAA
1 ATATCTTAGGAA
28475 ATATCTTAGGAA
1 ATATCTTAGGAA
28487 AT
1 AT
28489 TGGGAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATATCTTAGGAA
Found at i:31110 original size:3 final size:3
Alignment explanation
Indices: 31102--31155 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
31092 ACTGCTTTTC
31102 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31150 AAT AAT
1 AAT AAT
31156 TATTGACGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41668 original size:17 final size:16
Alignment explanation
Indices: 41646--41692 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
41636 TATTTATTAC
41646 ATATATTATTATATAAT
1 ATATATTATTATAT-AT
*
41663 ATATATAATTATCATAT
1 ATATATTATTAT-ATAT
*
41680 ATTTATT-TTATAT
1 ATATATTATTATAT
41693 TTCAGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 4 0.15
17 18 0.69
18 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTATTATATAT
Found at i:43759 original size:13 final size:13
Alignment explanation
Indices: 43738--43774 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
43728 GATAATTCTT
43738 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
43751 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
43764 CTTGACCCTCC
1 TTTGACCCTCC
43775 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:43818 original size:41 final size:41
Alignment explanation
Indices: 43768--43854 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
43758 CTCCAACTTG
* *
43768 ACCCTCCTAATAATTAAGGAAATAAATTAAATCCAAGTTTA
1 ACCCCCCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
* *
43809 ACCCCCCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTA
1 ACCCCCCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
*
43850 GCCCC
1 ACCCC
43855 TAGTTATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26
Consensus pattern (41 bp):
ACCCCCCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
Found at i:46235 original size:331 final size:327
Alignment explanation
Indices: 45572--46755 Score: 1214
Period size: 331 Copynumber: 3.6 Consensus size: 327
45562 ATATAATTAT
* * * *
45572 TTTAATTAG--ATTCAATTCGGAAAAAGGTAGGAAAAGCGATATTAGAAGTATGAAAAGCCCTTC
1 TTTAATTAGAAATT-AATTCGGAAAAA--TAAGAAAAACGATATTAGAAGCATGAAAA-CCTTTC
* ** * * * * *
45635 AGTCTTTTCAGAATTGACTTATATATTTTTTATTAGTATTGTGGCCCAAAATTGAGGAGAAATT-
62 AATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAATTC
* ** * * * *
45699 TCTCAAGTCAATTTTTGCAACATTTTCGCTGAAATCGTGTATTAACCATCACGGTTTTTTGACTA
126 TTTCGGGTCAATTTTTACAAAATTTTAGC-GAAATCGTGTATTAACCATCACAG-TTTTTGACTA
* * * * * *
45764 AAAACGCGTTCCGGAGCCCCGGCTCAATTTGGCACGATTTTTGGCGCCAAGTCTCATTGAAATAT
189 AAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAT
* * * * *
45829 CTATATCCATCTAACTAAATCTTACCCGCATTGTATTTAAGGATTTGTTTTTACGAGCATATGAA
254 CTATATCCATCTAA-TAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCAT-TTAA
45894 TCATGTTTCGA
317 TCATGTTTCGA
* *
45905 TTCAATTAGAAATTAATTCGGAAAAATAAGAAAAATGATATTAGAAGCATGAATAACCTTTCAAT
1 TTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCATGAA-AACCTTTCAAT
** * *
45970 CTTTTTGGTGTTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGA-GAATCATTCTTT
65 CTTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAA-AATTCTTT
* * * *
46034 CGGGTCAATTTTTACAAAATTTTAGTCGAAATCGTCTATTAACTATCACGGTTTTTGGCTAAAAA
129 CGGGTCAATTTTTACAAAATTTTAG-CGAAATCGTGTATTAACCATCACAGTTTTTGACTAAAAA
* * *
46099 CGTGTTCTGGGGCCCCAGCTCAGTTTTGCATGGTTTTTGGCGCCAAGACTCATTGAAATATCTAT
193 CGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTAT
** ** * * **
46164 ATTTATCTAATGAAATCTCAGTCACATTGGATTTAAGAATTTGTTTCTACGAGCATCTTAATCCG
258 ATCCATCTAAT-AAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCAT-TTAATCAT
46229 GTTTCGA
321 GTTTCGA
* * * * *
46236 TTTAATTAGAAATTAATTCGGAAAAATAGAAAAAAACAATATTAGATGCGTGAGAAGCCTTTCAA
1 TTTAATTAGAAATTAATTCGGAAAAATA-AGAAAAACGATATTAGAAGCATGA-AAACCTTTCAA
* * * * *** * *
46301 TCTTTTTGGCAATGAGTTATATATTTTTTATGAATATGGTGG-TGGAGATTGAGGAGAAA-TGTT
64 TCTTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAATTCTT
* * * * *
46364 TCGTGTTAATTTTTACAAAATTTTAGCCGAAATCGTATACTAACTATCACAGTTTTTGACTAAAA
128 TCGGGTCAATTTTTACAAAATTTTAG-CGAAATCGTGTATTAACCATCACAGTTTTTGACTAAAA
* * * *
46429 ACGCGTT-TCGGGGTCCCGGCTCTGTTTTGCATGATTTTTAGCGCCAAGCCTCATTGAAATATCT
192 ACGCGTTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCT
* * * *
46493 ATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTATTTTTATGAGCATTTGAATT
256 ATATCCATCTAA-TAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATTT-AATC
46558 ATGTTTCGA
319 ATGTTTCGA
* * * * * * *
46567 TTTAACTAAAAATTATTTTGGAAAAAAAAAGGAAAACTGATATTAGAAGCGTGAAAAACCTTTCA
1 TTTAATTAGAAATTAATTCGG-AAAAATAAGAAAAAC-GATATTAGAAGCATG-AAAACCTTTCA
** * * * *
46632 ATCTTTTTTACGTTGAATTATATATTTTTTTATGAGT-TCCGGGGCAAAAAATTTAGGAAAATTC
63 ATCTTTTTGGCATTGAATTATATA-TTTTTTATGAGTAT-CGTGGCCAAAAATTGAGGAAAATTC
* * * *
46696 TTTTGGGTAAATTTTTGCAAAATTTTAAGCGAAATCGTGTATTAACCATCACAATTTTTG
126 TTTCGGGTCAATTTTTACAAAATTTT-AGCGAAATCGTGTATTAACCATCACAGTTTTTG
46756 GTAACAAAGG
Statistics
Matches: 703, Mismatches: 126, Indels: 43
0.81 0.14 0.05
Matches are distributed among these distances:
330 5 0.01
331 361 0.51
332 231 0.33
333 31 0.04
334 70 0.10
335 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (327 bp):
TTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCATGAAAACCTTTCAATC
TTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCG
GGTCAATTTTTACAAAATTTTAGCGAAATCGTGTATTAACCATCACAGTTTTTGACTAAAAACGC
GTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATC
CATCTAATAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTAATCATGTTTC
GA
Found at i:49971 original size:95 final size:96
Alignment explanation
Indices: 49803--49994 Score: 314
Period size: 95 Copynumber: 2.0 Consensus size: 96
49793 TGTACAAAAA
*
49803 TAGTGTGGCTAGTGATAGTATGCCTAGCCTTATATCCTAAAAATAAAACCAAGCTGGATTCGGA-
1 TAGTGTGGCTAGTGATAGTATACCTAGCCTTATATCCTAAAAATAAAACCAAGCTGGATTCGGAT
49867 TTTTGTTTTTTTTTTACTTTTGATCGTAGAG
66 TTTTGTTTTTTTTTTACTTTTGATCGTAGAG
* *
49898 TAGTGTGGCTAGTGGTAGTATACCTAGCCTTATATCCTAAAAATAAAACCAAGCTGGATTTGGAT
1 TAGTGTGGCTAGTGATAGTATACCTAGCCTTATATCCTAAAAATAAAACCAAGCTGGATTCGGA-
*
49963 TTTTTTTTTTTTTTTTTTACTTTTGATCGTAG
65 --TTTTTGTTTTTTTTTTACTTTTGATCGTAG
49995 TTGGACTTGT
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
95 61 0.69
99 28 0.31
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (96 bp):
TAGTGTGGCTAGTGATAGTATACCTAGCCTTATATCCTAAAAATAAAACCAAGCTGGATTCGGAT
TTTTGTTTTTTTTTTACTTTTGATCGTAGAG
Found at i:58230 original size:36 final size:34
Alignment explanation
Indices: 58148--58246 Score: 105
Period size: 33 Copynumber: 2.9 Consensus size: 34
58138 CCAGAAATAG
*
58148 CAGGTCGCGCGCGGATCGTGACCC-GCCATGGTC
1 CAGGTCGCGCGCGGATCGCGACCCGGCCATGGTC
*
58181 CGGGTCGCGCGCGGATCGCGACCCGGGTCCATGG-C
1 CAGGTCGCGCGCGGATCGCGACCC-GG-CCATGGTC
* * *
58216 CATGTCGCGACGCGGGTCACGACCC-GCCATG
1 CAGGTCGCG-CGCGGATCGCGACCCGGCCATG
58247 ACTCGGTGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 27 0.48
34 1 0.02
35 9 0.16
36 19 0.34
ACGTcount: A:0.12, C:0.37, G:0.37, T:0.13
Consensus pattern (34 bp):
CAGGTCGCGCGCGGATCGCGACCCGGCCATGGTC
Found at i:63741 original size:3 final size:3
Alignment explanation
Indices: 63681--63719 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
63671 TATAGTATAA
63681 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
63720 ATTAATAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:65265 original size:14 final size:16
Alignment explanation
Indices: 65232--65278 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
65222 GGATCATTAT
65232 TATATATATAATA-ATAA
1 TATATATA-AATATA-AA
65249 TAATAATATAAATATAAA
1 T-AT-ATATAAATATAAA
65267 TATATATAAATA
1 TATATATAAATA
65279 AATGTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 9 0.33
19 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATATAAATATAAA
Found at i:66150 original size:31 final size:31
Alignment explanation
Indices: 66105--66218 Score: 126
Period size: 31 Copynumber: 3.7 Consensus size: 31
66095 GTCGAATGGA
* *
66105 GTTTTGCACGTTTTGTCCCCTAAACTTGTAC
1 GTTTTGGACATTTTGTCCCCTAAACTTGTAC
* *
66136 ATTTTGGACATTTTG-CCCCATGAACTTGTAC
1 GTTTTGGACATTTTGTCCCC-TAAACTTGTAC
* *
66167 GTTTTGGACCTTTTGTCCCCTAAACAT-TA-
1 GTTTTGGACATTTTGTCCCCTAAACTTGTAC
**
66196 GTTTTGGACATTTTACCCCCTAA
1 GTTTTGGACATTTTGTCCCCTAA
66219 GCAACAAGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 20 0.29
30 6 0.09
31 40 0.57
32 4 0.06
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (31 bp):
GTTTTGGACATTTTGTCCCCTAAACTTGTAC
Done.