Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012863.1 Corchorus olitorius cultivar O-4 contig12896, 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: 27093
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:588 original size:7 final size:7
Alignment explanation
Indices: 555--607 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
545 CCCAAGCTAG
555 AAAGAAA
1 AAAGAAA
562 AAA-AATA
1 AAAGAA-A
569 ATAA-AAA
1 A-AAGAAA
576 AAAGAAA
1 AAAGAAA
*
583 AGAGAAAA
1 AAAG-AAA
591 AAAGAAA
1 AAAGAAA
598 AAAGAAA
1 AAAGAAA
605 AAA
1 AAA
608 AAAGGGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 4 0.10
7 26 0.65
8 10 0.25
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:590 original size:15 final size:15
Alignment explanation
Indices: 555--608 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
545 CCCAAGCTAG
*
555 AAAGAAAAAAA-ATA
1 AAAGAAAAAAAGAAA
*
569 ATA-AAAAAAAGAAA
1 AAAGAAAAAAAGAAA
*
583 AGAGAAAAAAAGAAA
1 AAAGAAAAAAAGAAA
598 AAAGAAAAAAA
1 AAAGAAAAAAA
609 AAGGGAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 21 0.62
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAGAAAAAAAGAAA
Found at i:593 original size:10 final size:9
Alignment explanation
Indices: 555--611 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
545 CCCAAGCTAG
555 AAAGAAAAA
1 AAAGAAAAA
* *
564 AAATAATAA
1 AAAGAAAAA
*
573 AAA-AAAGA
1 AAAGAAAAA
581 AAAGAGAAAA
1 AAAGA-AAAA
591 AAAGAAAAA
1 AAAGAAAAA
*
600 AGA-AAAAA
1 AAAGAAAAA
608 AAAG
1 AAAG
612 GGAATGGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 13 0.34
9 17 0.45
10 8 0.21
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:610 original size:17 final size:17
Alignment explanation
Indices: 555--611 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
545 CCCAAGCTAG
555 AAAGAAAAAA-AATAATAA
1 AAAGAAAAAAGAA-AA-AA
* *
573 AAAAAAGAAAAGAGAAAA
1 AAAGAA-AAAAGAAAAAA
591 AAAGAAAAAAGAAAAAA
1 AAAGAAAAAAGAAAAAA
608 AAAG
1 AAAG
612 GGAATGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 14 0.42
18 12 0.36
19 6 0.18
20 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAA
Found at i:4502 original size:949 final size:953
Alignment explanation
Indices: 2825--5044 Score: 3654
Period size: 949 Copynumber: 2.3 Consensus size: 953
2815 GGGCGTGACA
* *
2825 AAAATAGAATGGGTCTTTTTGAAAGTATGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
1 AAAATAGAATGGGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
2890 CCTAATTTTATTTGTCTCGTCAACTTTGCATTATGTCTCAGACATAATGCAAAAGTCATCGATGG
66 CCTAATTTTATTTGTCTCGTCAACTTTGCATTA---CT-AG-----ATGC---A-TCATCGATGG
*
2955 TTACTCCAAATTTTCAGACAAGAAGGTGAAATACATCACAGAAGCCTTACCGTTGATATTCATGT
118 TTACTTCAAATTTTCAGACAAGAAGGTGAAATACATCACAGAAGCCTTACCGTTGATATTCATGT
*
3020 GGAGCATACTGTTTCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAAT
183 GGAGCATACTGCTTCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAAT
* *
3085 ATCTCAACTTAACATTATACTGAACGTGCTTATAATCTCTTCCTGAGGTCATGGCATTCATTGTC
248 ATCTCAACTTAACTTTATACTGAACGTGCTTATAATCTCTTCCTGAGGTCATGGCATTCATGGTC
*
3150 TTTCCAAATCCAAAATTTGATGAATTATTCGCTTGAATAGGTGGTGTACTCAGAGTGGCTAGTTG
313 TTTCCAAATCCAAAATTTGATGAAATATTCGCTTGAATAGGTGGTGTACTC--A--GGC-AGTTG
* *
3215 TGTCTATATTCTATTTTGCTTTATTTTTTAACATGATATCAAAGCTGAGGTTTTATCCTACCTAA
373 TGTCTATATTCTATTTTGCTTTATTTTTTAACATGATATCAAAGCTCAGGTTTTATCATACCTAA
3280 AACCCTAATTATATAAAACTATTTAGTTTGGATATCAAGTGTCTTGGTTTTCGAAAATGATCCTA
438 AACCCTAATTATATAAAACTATTTAGTTTGGATATCAAGTGTCTTGGTTTTCGAAAATGATCCTA
* *
3345 AAATTTTCTAATGAATTTAAAAAATATAGAAATCAGCTCTGATACGTATCCTGATTTGGCACCTA
503 AAATTTTCTAATGAATTTAAAAAATATAAAAATCAGCTCTGATACGTATCCTGATTTGGCAACTA
3410 TGATTTATATATTTTTCCTTTTAGATTTTTTATTTTCATAATTTTTTTTTTCAAAAAGAGGAAAT
568 TGATTTATATATTTTTCCTTTTAGATTTTTTATTTTCATAATTTTTTTTTTCAAAAAGAGGAAAT
3475 TTAATCAACTAACGATTGATGTTTTAAGTCGTTAAAGTGTGTCTCACCTATATTGAGCAAGTCAC
633 TTAATCAACTAACGATTGATGTTTTAAGTCGTTAAAGTGTGTCTCACCTATATTGAGCAAGTCAC
*
3540 CTTAAGATTCAAGAGTGCAAAATCTTCACACCTATATATAAAGTTGACTCTGATACGTATCCTGA
698 CTTAAGATTCAAGAGTGCAAAATCTTCACACCTATATATAAAGTCGACTCTGATACGTATCCTGA
*
3605 TTTGACAACTATGATTTATATGTTTTTCCTTTCTTCTTGCATCAAACCCTGGCCCTCACTCTTGT
763 TTTGACAACTATGATTTATATGTTTTTCCTTTCTTCTTGCATCAAACCCTGACCCTCACTCTTGT
3670 TTCAATTTCAGCAAAATAAAAAAAAAAAAATCTCCCTCTCCCCCTCTTCTGTAGTACCTTTTTAA
828 TTCAATTTCAGC-AAA-AAAAAAAAAAAAATCTCCCTCTCCCCCTCTTCTGTAGTACCTTTTTAA
*
3735 AAATGGCTTTACTAGTTTCCCACGACCATGAGGAACATAATTTCCTCGAAAAAAGCGAAAACT
891 AAATGGCCTTACTAGTTTCCCACGACCATGAGGAACATAATTTCCTCGAAAAAAGCGAAAACT
* * * *
3798 AAAGTAGAATGAGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAATATTCTATTCAACGT
1 AAAATAGAATGGGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
3863 CCTAATTTTATTTGTCTCGTCAACTTTGCATTA-T-G-T-C-TCATCGATGGTTACTTCAAATTT
66 CCTAATTTTATTTGTCTCGTCAACTTTGCATTACTAGATGCATCATCGATGGTTACTTCAAATTT
* * *
3923 TCAGACAGGAAGGTGAAATACATCACAGAATCCTTACCGTTGATATTCATGTGGAGTATACTGCT
131 TCAGACAAGAAGGTGAAATACATCACAGAAGCCTTACCGTTGATATTCATGTGGAGCATACTGCT
3988 TCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAATATCTCAACTTAAC
196 TCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAATATCTCAACTTAAC
* *
4053 TTTATACTGAACGTGCTTGTAATCTCTTCCTGAGGTCATGGTATTCATGGTCTTTACC-AAT-CA
261 TTTATACTGAACGTGCTTATAATCTCTTCCTGAGGTCATGGCATTCATGGTCTTT-CCAAATCCA
*
4116 ACTATTTGATGAAATATTCGCTTGAATAGGTGGTGTACTC-GG-AGTTGCTGTCTATATTCTATT
325 A-AATTTGATGAAATATTCGCTTGAATAGGTGGTGTACTCAGGCAGTTG-TGTCTATATTCTATT
4179 TTGCTTTATTTTTTAACATGATATCAAAGCTCAGGTTTTATCATACCTAAAACCCTAATTATATA
388 TTGCTTTATTTTTTAACATGATATCAAAGCTCAGGTTTTATCATACCTAAAACCCTAATTATATA
* *
4244 AAACTGTTTAGTTTGGATGTCAAGTGTCTTGGTTTTCGAAAATGATCCTAAAATTTTCTAATGAA
453 AAACTATTTAGTTTGGATATCAAGTGTCTTGGTTTTCGAAAATGATCCTAAAATTTTCTAATGAA
* *
4309 TTTAAAAAATATATAAAATCGGCTCTGATACGTATCCTGATTTGGCAACTATGATTTATATTTTT
518 TTTAAAAAATATA-AAAATCAGCTCTGATACGTATCCTGATTTGGCAACTATGATTTATATATTT
4374 TTCCTTTTAGATTTTTTATTTTCATAA-TTTTTTTTTCAAAAAGAGGAAATTTAATCAACTAAAC
582 TTCCTTTTAGATTTTTTATTTTCATAATTTTTTTTTTCAAAAAGAGGAAATTTAATCAACT-AAC
4438 -ATTGATGTTTTAAGTCGTTAAAGTGTGTCTCACCTATATTGAGCAAGTCACCTTAAGATTCAAG
646 GATTGATGTTTTAAGTCGTTAAAGTGTGTCTCACCTATATTGAGCAAGTCACCTTAAGATTCAAG
4502 AGTGCAAAATCTTCACACCTATATATAAAGTCGACTCTGATACGTATCCTGATTTGACAACTATG
711 AGTGCAAAATCTTCACACCTATATATAAAGTCGACTCTGATACGTATCCTGATTTGACAACTATG
* *
4567 ATTTATATGTTTTTCCTTTCTTCTTGCATCAAACCCTGACCCTCCCTCTTGTTTCAGTTTCAGCA
776 ATTTATATGTTTTTCCTTTCTTCTTGCATCAAACCCTGACCCTCACTCTTGTTTCAATTTCAGCA
*
4632 AAAAAAAAAAAAAACTCTCCCTCTCCCCCTCTTCTGTAGTACCTTTTTAAAAATGGCCTTACTAG
841 AAAAAAAAAAAAAAATCTCCCTCTCCCCCTCTTCTGTAGTACCTTTTTAAAAATGGCCTTACTAG
*
4697 TTTCCCACGACCATGAGGAACATAATTTCCTCGGAAAAAGCGAAAACT
906 TTTCCCACGACCATGAGGAACATAATTTCCTCGAAAAAAGCGAAAACT
4745 AAAATAGAATGGGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
1 AAAATAGAATGGGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
* *
4810 CCTAATTTTATTTGTCTCGTCAATTTTGCATTACGCTGAGACATAATGCAAAAGCTATCGATGGT
66 CCTAATTTTATTTGTCTCGTCAACTTTGCATTA--CT-AG-----ATGC---ATC-ATCGATGGT
* * * *
4875 TACTTCAAATTTTCGGACAACAAGGTGAAATACACCACAAAAGCCTTACCGTTGATATTCATGTG
119 TACTTCAAATTTTCAGACAAGAAGGTGAAATACATCACAGAAGCCTTACCGTTGATATTCATGTG
*
4940 GAGCATACCT-CTTCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATTAT
184 GAGCATA-CTGCTTCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAAT
*
5004 ATCTCAACTTAACTTTATACTGAATGTGCTTATAATCTCTT
248 ATCTCAACTTAACTTTATACTGAACGTGCTTATAATCTCTT
5045 TAACTATTGT
Statistics
Matches: 1176, Mismatches: 48, Indels: 55
0.92 0.04 0.04
Matches are distributed among these distances:
947 201 0.17
948 8 0.01
949 376 0.32
950 80 0.07
952 1 0.00
954 3 0.00
955 238 0.20
956 2 0.00
958 1 0.00
959 1 0.00
960 1 0.00
961 1 0.00
963 1 0.00
964 166 0.14
965 2 0.00
967 1 0.00
969 1 0.00
973 92 0.08
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (953 bp):
AAAATAGAATGGGTCTTTTTGAAGGTGTGTGCTCACTGTGAGCATAGGAACATCCTATTCAACGT
CCTAATTTTATTTGTCTCGTCAACTTTGCATTACTAGATGCATCATCGATGGTTACTTCAAATTT
TCAGACAAGAAGGTGAAATACATCACAGAAGCCTTACCGTTGATATTCATGTGGAGCATACTGCT
TCTTATAAAAGAATCTCATAAGACCAATGGACAAACGTAAAGGTTCAATAATATCTCAACTTAAC
TTTATACTGAACGTGCTTATAATCTCTTCCTGAGGTCATGGCATTCATGGTCTTTCCAAATCCAA
AATTTGATGAAATATTCGCTTGAATAGGTGGTGTACTCAGGCAGTTGTGTCTATATTCTATTTTG
CTTTATTTTTTAACATGATATCAAAGCTCAGGTTTTATCATACCTAAAACCCTAATTATATAAAA
CTATTTAGTTTGGATATCAAGTGTCTTGGTTTTCGAAAATGATCCTAAAATTTTCTAATGAATTT
AAAAAATATAAAAATCAGCTCTGATACGTATCCTGATTTGGCAACTATGATTTATATATTTTTCC
TTTTAGATTTTTTATTTTCATAATTTTTTTTTTCAAAAAGAGGAAATTTAATCAACTAACGATTG
ATGTTTTAAGTCGTTAAAGTGTGTCTCACCTATATTGAGCAAGTCACCTTAAGATTCAAGAGTGC
AAAATCTTCACACCTATATATAAAGTCGACTCTGATACGTATCCTGATTTGACAACTATGATTTA
TATGTTTTTCCTTTCTTCTTGCATCAAACCCTGACCCTCACTCTTGTTTCAATTTCAGCAAAAAA
AAAAAAAAAATCTCCCTCTCCCCCTCTTCTGTAGTACCTTTTTAAAAATGGCCTTACTAGTTTCC
CACGACCATGAGGAACATAATTTCCTCGAAAAAAGCGAAAACT
Found at i:8681 original size:21 final size:21
Alignment explanation
Indices: 8656--8780 Score: 67
Period size: 27 Copynumber: 5.5 Consensus size: 21
8646 TAATAATTAT
*
8656 TATCAATGTCATTATTATCAA
1 TATCAATATCATTATTATCAA
* *
8677 TATCAATATCAGTATCAATGTCATTAT
1 TATCAATATCA-T-T--AT-T-ATCAA
*
8704 TATCAATATCA--A-TATCAG
1 TATCAATATCATTATTATCAA
* *
8722 TATCAATGTCATTAATATCAA
1 TATCAATATCATTATTATCAA
8743 TATCAATATCAATATCAATACTATCAA
1 TATCAATATC-AT-T--AT--TATCAA
8770 TATCAATATCA
1 TATCAATATCA
8781 ATGCCATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
18 13 0.16
19 1 0.01
20 1 0.01
21 25 0.31
22 3 0.04
23 2 0.03
25 3 0.04
26 2 0.03
27 30 0.38
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (21 bp):
TATCAATATCATTATTATCAA
Found at i:8682 original size:6 final size:6
Alignment explanation
Indices: 8671--8782 Score: 119
Period size: 6 Copynumber: 19.2 Consensus size: 6
8661 ATGTCATTAT
* * *
8671 TATCAA TATCAA TATCAG TATCAA TGTCATTA TTATCAA TATCAA TATCAG
1 TATCAA TATCAA TATCAA TATCAA TATCA--A -TATCAA TATCAA TATCAA
*
8722 TATCAA TGTC-A T-T-AA TATCAA TATCAA TATCAA TATCAA TA-C--
1 TATCAA TATCAA TATCAA TATCAA TATCAA TATCAA TATCAA TATCAA
8764 TATCAA TATCAA TATCAA T
1 TATCAA TATCAA TATCAA T
8783 GCCATTATTA
Statistics
Matches: 90, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
3 2 0.02
4 4 0.04
5 4 0.04
6 74 0.82
7 1 0.01
8 1 0.01
9 4 0.04
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.37
Consensus pattern (6 bp):
TATCAA
Found at i:8686 original size:27 final size:27
Alignment explanation
Indices: 8677--8794 Score: 128
Period size: 27 Copynumber: 4.1 Consensus size: 27
8667 TTATTATCAA
*
8677 TATCAATATCAGTATCAATGTCATTAT
1 TATCAATATCAATATCAATGTCATTAT
*
8704 TATCAATATCAATATCAGTATCAATGTCATTAA
1 TATCAATATC---A--A-TATCAATGTCATTAT
* * *
8737 TATCAATATCAATATCAATATCAATAC
1 TATCAATATCAATATCAATGTCATTAT
*
8764 TATCAATATCAATATCAATGCCATTAT
1 TATCAATATCAATATCAATGTCATTAT
8791 TATC
1 TATC
8795 TCTCTCTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
27 49 0.64
28 1 0.01
30 2 0.03
33 24 0.32
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (27 bp):
TATCAATATCAATATCAATGTCATTAT
Found at i:8698 original size:33 final size:33
Alignment explanation
Indices: 8656--8761 Score: 194
Period size: 33 Copynumber: 3.2 Consensus size: 33
8646 TAATAATTAT
8656 TATCAATGTCATTATTATCAATATCAATATCAG
1 TATCAATGTCATTATTATCAATATCAATATCAG
8689 TATCAATGTCATTATTATCAATATCAATATCAG
1 TATCAATGTCATTATTATCAATATCAATATCAG
* *
8722 TATCAATGTCATTAATATCAATATCAATATCAA
1 TATCAATGTCATTATTATCAATATCAATATCAG
8755 TATCAAT
1 TATCAAT
8762 ACTATCAATA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.39
Consensus pattern (33 bp):
TATCAATGTCATTATTATCAATATCAATATCAG
Found at i:8781 original size:21 final size:21
Alignment explanation
Indices: 8743--8782 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8733 TTAATATCAA
8743 TATCAATATCAATATCAATAC
1 TATCAATATCAATATCAATAC
8764 TATCAATATCAATATCAAT
1 TATCAATATCAATATCAAT
8783 GCCATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
TATCAATATCAATATCAATAC
Found at i:8794 original size:21 final size:21
Alignment explanation
Indices: 8744--8787 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8734 TAATATCAAT
*
8744 ATCAATATCAATATCAATACT
1 ATCAATATCAATATCAATACC
*
8765 ATCAATATCAATATCAATGCC
1 ATCAATATCAATATCAATACC
8786 AT
1 AT
8788 TATTATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (21 bp):
ATCAATATCAATATCAATACC
Found at i:23342 original size:26 final size:26
Alignment explanation
Indices: 23313--23365 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
23303 ATAGATGAAG
23313 AGCAAAGGAGCGTGTTGAGCTTTGTA
1 AGCAAAGGAGCGTGTTGAGCTTTGTA
* *
23339 AGCAAAGGAGTGTTTTGAGCTTTGTA
1 AGCAAAGGAGCGTGTTGAGCTTTGTA
23365 A
1 A
23366 ACTATCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.30
Consensus pattern (26 bp):
AGCAAAGGAGCGTGTTGAGCTTTGTA
Found at i:23858 original size:53 final size:53
Alignment explanation
Indices: 23801--23972 Score: 168
Period size: 53 Copynumber: 3.1 Consensus size: 53
23791 TAAGACAATT
*
23801 TGCATTTACAACTTTAAAGAATGCTCCTCCAATATTATCTGATTAGGACAAAC
1 TGCATTTTCAACTTTAAAGAATGCTCCTCCAATATTATCTGATTAGGACAAAC
*
23854 TGCATTTTCAACTTTAAAGGATGCTCCTCTATATTATCTGAATATTATCTGATTAAGG-CAAAC
1 TGCATTTTCAACTTTAAAGAATGCTCCTC--------C--AATATTATCTGATT-AGGACAAAC
* * * *
23917 TGCATTTTCAACTCTAAATAGA-GCTCCTCCAATATTATCCGATTAAGACAAAC
1 TGCATTTTCAACTTTAAAGA-ATGCTCCTCCAATATTATCTGATTAGGACAAAC
23970 TGC
1 TGC
23973 TCCAATATTA
Statistics
Matches: 99, Mismatches: 7, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
52 2 0.02
53 48 0.48
55 1 0.01
61 1 0.01
63 43 0.43
64 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (53 bp):
TGCATTTTCAACTTTAAAGAATGCTCCTCCAATATTATCTGATTAGGACAAAC
Found at i:23943 original size:63 final size:64
Alignment explanation
Indices: 23831--23955 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 64
23821 ATGCTCCTCC
* * *
23831 AATATTATCTGATTAGGACAAACTGCATTTTCAACTTTAAAGGATGCTCCT-CTATATTATCTG
1 AATATTATCTGATTAGGACAAACTGCATTTTCAACTCTAAAAGATGCTCCTCCAATATTATCTG
23894 AATATTATCTGATTAAGG-CAAACTGCATTTTCAACTCTAAATAGA-GCTCCTCCAATATTATC
1 AATATTATCTGATT-AGGACAAACTGCATTTTCAACTCTAAA-AGATGCTCCTCCAATATTATC
23956 CGATTAAGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 42 0.75
64 14 0.25
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (64 bp):
AATATTATCTGATTAGGACAAACTGCATTTTCAACTCTAAAAGATGCTCCTCCAATATTATCTG
Found at i:23943 original size:116 final size:116
Alignment explanation
Indices: 23733--23972 Score: 288
Period size: 116 Copynumber: 2.1 Consensus size: 116
23723 TCTCTTTCAT
23733 CAAACTGCATTTTCAACTTTAAAGAAAGCTACTCCAATATTATCCAAATATTTTAAAATAAGACA
1 CAAACTGCATTTTCAACTTTAAAGAAAGCTACTCCAATATTATCCAAATATTTTAAAATAAGACA
** * * *
23798 ATTTGCATTTACAACTTTAAAGAATGCTCCTCCAATATTATCTGATTAGGA
66 AACTGCATTTACAACTCTAAAGAATGCTCCTCCAATATTATCCGATTAAGA
* * * * ** * * *
23849 CAAACTGCATTTTCAACTTTAAAGGATGCTCCT-CTATATTATCTGAATATTATCT-GATTAAGG
1 CAAACTGCATTTTCAACTTTAAAGAAAGCTACTCCAATATTATCCAAATATT-T-TAAAATAAGA
* *
23912 CAAACTGCATTTTCAACTCTAAATAGA-GCTCCTCCAATATTATCCGATTAAGA
64 CAAACTGCATTTACAACTCTAAAGA-ATGCTCCTCCAATATTATCCGATTAAGA
23965 CAAACTGC
1 CAAACTGC
23973 TCCAATATTA
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
115 15 0.14
116 88 0.84
117 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (116 bp):
CAAACTGCATTTTCAACTTTAAAGAAAGCTACTCCAATATTATCCAAATATTTTAAAATAAGACA
AACTGCATTTACAACTCTAAAGAATGCTCCTCCAATATTATCCGATTAAGA
Found at i:23984 original size:29 final size:29
Alignment explanation
Indices: 23943--24001 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
23933 AATAGAGCTC
23943 CTCCAATATTATCCGATTAAGACAAACTG
1 CTCCAATATTATCCGATTAAGACAAACTG
23972 CTCCAATATTATCCGATTAAGACAAACTG
1 CTCCAATATTATCCGATTAAGACAAACTG
24001 C
1 C
24002 ATTTTTCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (29 bp):
CTCCAATATTATCCGATTAAGACAAACTG
Done.