Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024857.1 Corchorus olitorius cultivar O-4 contig24890, 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: 39866
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA TA TA TA TA TA 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 TA TA TA TA TA TA
39 CTTTTGATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1866 original size:13 final size:13
Alignment explanation
Indices: 1848--1872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1838 TTACAATTCC
1848 AAATAATATTTAT
1 AAATAATATTTAT
1861 AAATAATATTTA
1 AAATAATATTTA
1873 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:2861 original size:33 final size:33
Alignment explanation
Indices: 2819--2887 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2809 GTTACACAGC
2819 ATGTGTCAATGAAAACTAGCATATTTTTAGAGA
1 ATGTGTCAATGAAAACTAGCATATTTTTAGAGA
2852 ATGTGTCAATGAAAACTAGCATATTTTTAGAGA
1 ATGTGTCAATGAAAACTAGCATATTTTTAGAGA
2885 ATG
1 ATG
2888 GAGATGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (33 bp):
ATGTGTCAATGAAAACTAGCATATTTTTAGAGA
Found at i:7145 original size:23 final size:23
Alignment explanation
Indices: 7076--7145 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
7066 TAATTTTATG
*
7076 AAATTTTGATAACTACCCTAT--T
1 AAATTTTGATAACTA-CCTATGAA
* *
7098 AAATTTAGATAACCACGCTATGAA
1 AAATTTTGATAACTAC-CTATGAA
*
7122 AAATTTTGATAATTACCTATGAA
1 AAATTTTGATAACTACCTATGAA
7145 A
1 A
7146 TTGAGATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 17 0.44
23 8 0.21
24 13 0.33
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATTTTGATAACTACCTATGAA
Found at i:7165 original size:45 final size:43
Alignment explanation
Indices: 7072--7191 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 43
7062 TGAATAATTT
* * * *
7072 TATGAAATTTTGATAACTACCCTATTAAATTTAGATAACCACGC
1 TATGAAATTTTGATAATTA-CCTATGAAATTGAGATAAACACGC
**
7116 TATGAAAAATTTTGATAATTACCTATGAAATTGAGATAAATTC-C
1 TATG--AAATTTTGATAATTACCTATGAAATTGAGATAAACACGC
* *
7160 ATATGAAACTTTGATAATCTAACTATGAAATT
1 -TATGAAATTTTGATAAT-TACCTATGAAATT
7192 TTAATAAACC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 12 0.19
44 17 0.27
45 21 0.33
46 14 0.22
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (43 bp):
TATGAAATTTTGATAATTACCTATGAAATTGAGATAAACACGC
Found at i:7175 original size:22 final size:21
Alignment explanation
Indices: 7126--7192 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
7116 TATGAAAAAT
7126 TTTGAT-AATTACCTATGAAA
1 TTTGATAAATTACCTATGAAA
*
7146 TTGAGATAAATT-CCATATGAAA
1 TT-TGATAAATTACC-TATGAAA
*
7168 CTTTGAT-AATCTAACTATGAAA
1 -TTTGATAAAT-TACCTATGAAA
7190 TTT
1 TTT
7193 TAATAAACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
20 2 0.05
21 11 0.29
22 22 0.58
23 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTGATAAATTACCTATGAAA
Found at i:8008 original size:3 final size:3
Alignment explanation
Indices: 8000--8027 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7990 GTCATAAATA
8000 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8028 TATACTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8761 original size:8 final size:9
Alignment explanation
Indices: 8748--8781 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
8738 AGGTTGGCCA
8748 ATAATA-AT
1 ATAATATAT
8756 ATAATATAT
1 ATAATATAT
8765 ATATATATAT
1 ATA-ATATAT
8775 ATAATAT
1 ATAATAT
8782 TAGAGTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.25
9 9 0.38
10 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATATAT
Found at i:8833 original size:24 final size:24
Alignment explanation
Indices: 8799--8858 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
8789 TAATTTTAAG
*
8799 TAATGGTAATTTTCAAGGAAAAAA
1 TAATGGCAATTTTCAAGGAAAAAA
* *
8823 TCATGGCAATTTTTAAGGAAAAAA
1 TAATGGCAATTTTCAAGGAAAAAA
8847 TAATGGCAATTT
1 TAATGGCAATTT
8859 ACAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.32
Consensus pattern (24 bp):
TAATGGCAATTTTCAAGGAAAAAA
Found at i:9151 original size:697 final size:680
Alignment explanation
Indices: 7804--9881 Score: 2783
Period size: 697 Copynumber: 3.0 Consensus size: 680
7794 AAATTCAAAC
7804 TCTTTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAATGCAACAATCATAT
1 TCTTTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAATGCAACAATCATAT
7869 ATTTATCATCATC-TTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGATATAGTAG
66 ATTTATCATCATCATTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGATATAGTAG
*
7933 TTAGAAATATATATAATATAGTTTGGGTAAGATTTAAAATTTTAAACTTAAAATTAAGTCATAAA
131 TTAGAAATATATATAATATAGTTTGAGTAAGATTTAAAATTTTAAACTTAAAATTAAGTC-----
* *
7998 TAAATAATAATAATAATAATAATAATAATATATACTAGAAATAAGGTTGGCCAATAATAATATGA
191 ------AT-A-AATAA-AATAATAAT-ATATATAGTAGAAATTAGGTTGGCCAATAAT-A-AT-A
* * * * * * * * * *
8063 TAATATATAAAACATTAAAGTCTTTTTTG-GCCACAATATTACATTAAAGTCTAATTTTATGTAA
243 TAATATAT-ATATA-TATA-TATATATTGAGTC-TAATATTA-A-TAATG-CTAATTTTAAGTAA
* *
8127 TGGCAATTTTTAAGGAAAAAATAATGACAATTTAGAAATATTTTTTTAAAAAAAGGGTACAACTG
301 TGGCAATTTTTAAGGAAAAAATAATGGCAATTTAGAAATATTTTTTT-AAAAAAGGGTACAATTG
* *
8192 GAAAACACAAAGTTTT-CCATTATTCGTACATTTATATATAGTATATAAATTTGGAGAAACTATT
365 GAAAACACAAA-TTTTCCCATTATTCGTACTTTTATATATAGTATATAGATTTGGAGAAACTA-T
* * * * *
8256 A-ATTTTGTTTCATTTCGGCCCAGTAGGCCCATTAGATCCGTTTGAGTCCATGAAACCCGAATTG
428 AGATTTTGTCTCATTTCGGCCCAGTAGG-CCATTAGGTCCATTTGAGTCCATGAAGCCCGAATTC
* *
8320 CCAAGCCATATATCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATATGGAAGACC
492 CCAAGCCATATATCTTGAAGCCTAAATATGATATTCTTAGACCCAATTCATTAATATGGAAGCCC
* * *
8385 AAACAAGGAGTCCAAGTCCAATCAGTAATTATGATGCAATAATGATTCAGACTTGAGCATTGTTA
557 AAAGAAGGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAG-CCTGAGCATTGTTA
* *
8450 AATCCTATTTAAAGGAGGATTTCACAAGAGTAGTTTTGGAAGAAAATTTATAACTTTTGA
621 AATCCTATTTAAAGGAGGATTTCACAAGAGCAGTTTTGAAAGAAAATTTATAACTTTTGA
*
8510 T-TATTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAGTGCAACAATCATA
1 TCT-TTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAATGCAACAATCATA
8574 TATTTATCATCATCATTGTTTTTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGAT
65 TATTTATCATCATCA------TTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGAT
8639 ATAGTAGTTAGAAATATATATAATATAGTTTGAGTAAGATTTAAAATTTTAAACTTAAAATTAAG
124 ATAGTAGTTAGAAATATATATAATATAGTTTGAGTAAGATTTAAAATTTTAAACTTAAAATTAAG
8704 TCATAAAT-AAATAATAATATATATAGTAGAAATTAGGTTGGCCAATAATAATATAATATATATA
189 TCATAAATAAAATAATAATATATATAGTAGAAATTAGGTTGGCCAATAATAATATAATATATATA
* * *
8768 TATATATATAATATTAGAGTCTAATTTTAAGTAATGGTAATTTTCAAGGAAAAAATCATGGCAAT
254 TATATATAT-ATATT-GAGTCTAATATTAA-TAATGCTAATTTT-AA-G------TAATGGCAAT
* * *
8833 TTTTAAGGAAAAAATAATGGCAATTTACAAATATTTTTTTAATAAAGGGTACAGTTGGAAAACA-
308 TTTTAAGGAAAAAATAATGGCAATTTAGAAATATTTTTTTAAAAAAGGGTACAATTGGAAAACAC
* * * *
8897 AGAATTTTCCCATTATTCGCACTTTTATGTATAGAATATAGATTTGGAGAAACTATCGATTTTGT
373 A-AATTTTCCCATTATTCGTACTTTTATATATAGTATATAGATTTGGAGAAACTATAGATTTTGT
* * **
8962 CTCATTTCGGCCCAGTAGGCCATTAGGTCCATGTT-AGTCCATGAAGTCCGAATTTCCAAGTTAT
437 CTCATTTCGGCCCAGTAGGCCATTAGGTCCAT-TTGAGTCCATGAAGCCCGAATTCCCAAGCCAT
* * * *
9026 ATCTCTTGAAGCCTAAATATGATATTCTTAGACCCAATTCATTAATCTAGAAGCCCAAAGAAAGA
501 ATATCTTGAAGCCTAAATATGATATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGA
* *
9091 GTCCAAGTCCAATCAAG-AATTATGATGCAGTAATGATTCAGCCATGAGTACTGTTAAATCCTAT
566 GTCCAAGTCCAATC-AGTAATTATGATGCAGTAATGATTCAGCC-TGAGCATTGTTAAATCCTAT
* * * *
9155 TTAAAGGAGGATTTCCCAAGAGCAGTTTTGAAAGAAAAATTATAACTTATGG
629 TTAAAGGAGGATTTCACAAGAGCAGTTTTGAAAGAAAATTTATAACTTTTGA
* * * *
9207 TCTTTTCATGGCCATTGTAGCGTTTAAGAAAAATTATACCGAAATTACAAATGTAACAATCATAT
1 TCTTTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAATGCAACAATCATAT
9272 ATTTATCATCATCA--TTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGATATAGTAG
66 ATTTATCATCATCATTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGATATAGTAG
* * *
9335 TTAGAAATATGTATAATATAGTTTGAGTAAGATTTGATATTTTAAACTTAAAATTAAGTCATAAA
131 TTAGAAATATATATAATATAGTTTGAGTAAGATTTAAAATTTTAAACTTAAAATTAAGTCATAAA
* *
9400 TAAATTATAATATATATATATAGTAGAAATTGGGTTGGCCAATAAT-A-ACAATATA-ATATATA
196 TAAA--ATAATA-ATATATATAGTAGAAATTAGGTTGGCCAATAATAATATAATATATATATATA
* * *
9462 TATATATA-T-A-TATAACATTAA-AGT-CTAATTTTAAGTAATGGCAATTTTTAAGGAAAAAAT
258 TATATATATTGAGTCTAATATTAATAATGCTAATTTTAAGTAATGGCAATTTTTAAGGAAAAAAT
* *
9522 AATGGCAATTTAGAAATATTTTTTTAAAAAAGGGTACAATTGGAAAACACAAAGTTTCTCATTAT
323 AATGGCAATTTAGAAATATTTTTTTAAAAAAGGGTACAATTGGAAAACACAAATTTTCCCATTAT
* * *
9587 TCGTACTTTTATATATAGTATATAGATTTAGAAAAACTATAGGTTTTGTCTCATTTCGGCCCAGT
388 TCGTACTTTTATATATAGTATATAGATTTGGAGAAACTATAGATTTTGTCTCATTTCGGCCCAGT
* * **
9652 AGG-CATTAGGTCCATTTGAATCCATGAAGCCCGAATTCCCAAGCCATATGTCTTGAAGGTTAAA
453 AGGCCATTAGGTCCATTTGAGTCCATGAAGCCCGAATTCCCAAGCCATATATCTTGAAGCCTAAA
* * *
9716 TATGATATTTTTAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGATTTCAAGTCCAATCAGT
518 TATGATATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGAGTCCAAGTCCAATCAGT
*
9781 AATTATGATGCAGTAATGATGCAGACCTGAGCATTGTTAAATCCTATTTAAAGGAGGATTTCACA
583 AATTATGATGCAGTAATGATTCAG-CCTGAGCATTGTTAAATCCTATTTAAAGGAGGATTTCACA
* *
9846 AGAGCAGTTTTGCAAGAAAATTTATGACTTTTGA
647 AGAGCAGTTTTGAAAGAAAATTTATAACTTTTGA
9880 TC
1 TC
9882 AAGAGCTCAG
Statistics
Matches: 1233, Mismatches: 105, Indels: 101
0.86 0.07 0.07
Matches are distributed among these distances:
672 4 0.00
673 195 0.16
674 145 0.12
675 1 0.00
680 1 0.00
681 2 0.00
682 7 0.01
683 2 0.00
685 8 0.01
686 1 0.00
688 1 0.00
689 115 0.09
690 14 0.01
691 16 0.01
692 19 0.02
693 43 0.03
694 11 0.01
695 2 0.00
696 2 0.00
697 301 0.24
698 103 0.08
699 48 0.04
700 3 0.00
701 1 0.00
702 2 0.00
705 1 0.00
706 75 0.06
713 110 0.09
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (680 bp):
TCTTTTCATGGCCATTGTAACGTTTAAGAAAAATGATACCAAAATTACAAATGCAACAATCATAT
ATTTATCATCATCATTTTTTTTTGCTACATATTTATTATCATCGTTAATAATTTGGATATAGTAG
TTAGAAATATATATAATATAGTTTGAGTAAGATTTAAAATTTTAAACTTAAAATTAAGTCATAAA
TAAAATAATAATATATATAGTAGAAATTAGGTTGGCCAATAATAATATAATATATATATATATAT
ATATATTGAGTCTAATATTAATAATGCTAATTTTAAGTAATGGCAATTTTTAAGGAAAAAATAAT
GGCAATTTAGAAATATTTTTTTAAAAAAGGGTACAATTGGAAAACACAAATTTTCCCATTATTCG
TACTTTTATATATAGTATATAGATTTGGAGAAACTATAGATTTTGTCTCATTTCGGCCCAGTAGG
CCATTAGGTCCATTTGAGTCCATGAAGCCCGAATTCCCAAGCCATATATCTTGAAGCCTAAATAT
GATATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGAGTCCAAGTCCAATCAGTAAT
TATGATGCAGTAATGATTCAGCCTGAGCATTGTTAAATCCTATTTAAAGGAGGATTTCACAAGAG
CAGTTTTGAAAGAAAATTTATAACTTTTGA
Found at i:10199 original size:27 final size:26
Alignment explanation
Indices: 10139--10200 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
10129 AATTTTCCAT
10139 TATTTTAATAATGAAATAATTAAAATA
1 TATTTTAATAATGAAAT-ATTAAAATA
*
10166 T-TATTTAATAATGGCAAT-TTAGAAATA
1 TAT-TTTAATAAT-GAAATATTA-AAATA
10193 TATTTTAA
1 TATTTTAA
10201 AAAAAGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 4 0.13
27 21 0.70
28 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (26 bp):
TATTTTAATAATGAAATATTAAAATA
Found at i:17163 original size:6 final size:6
Alignment explanation
Indices: 17152--17253 Score: 204
Period size: 6 Copynumber: 17.0 Consensus size: 6
17142 TATTTATTTG
17152 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
17200 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
17248 TTTATA
1 TTTATA
17254 GTTCTTGCTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 96 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:25751 original size:21 final size:21
Alignment explanation
Indices: 25725--25766 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25715 TTTAAACCCT
25725 ATTGGAGAC-AAGTGGTACTAG
1 ATTGGA-ACTAAGTGGTACTAG
*
25746 ATTGGATCTAAGTGGTACTAG
1 ATTGGAACTAAGTGGTACTAG
25767 GGTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAG
Found at i:29814 original size:21 final size:21
Alignment explanation
Indices: 29789--29850 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
29779 TCACACAATG
29789 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
29810 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
*
29831 AGGTTTCAAGCTCATTGGAG
1 AAGTTTCAAGCTCATTGGAG
29851 TTGCCTAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:34239 original size:21 final size:21
Alignment explanation
Indices: 34213--34304 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
34203 TGCTAGGAGT
34213 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
34234 TCATTGTAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
34255 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
34276 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
34297 TCATTGGA
1 TCATTGGA
34305 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:34446 original size:21 final size:21
Alignment explanation
Indices: 34420--34461 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34410 TCTTGAAGAG
* *
34420 TTGAAGGCCATTGGAGATCAT
1 TTGAAGCCCATTAGAGATCAT
34441 TTGAAGCCCATTAGAGATCAT
1 TTGAAGCCCATTAGAGATCAT
34462 CACCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (21 bp):
TTGAAGCCCATTAGAGATCAT
Found at i:36625 original size:25 final size:25
Alignment explanation
Indices: 36591--36639 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
36581 CCAAGCAATC
36591 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
36616 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
36640 CAAACCAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:39836 original size:2 final size:2
Alignment explanation
Indices: 39829--39862 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39819 AGGTGTACAA
39829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39863 CATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.