Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019364.1 Corchorus olitorius cultivar O-4 contig19397, 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: 51960
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:750 original size:26 final size:26
Alignment explanation
Indices: 721--773 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
711 TCACAAATGA
721 ATTTAATTAGTGCAAGATTTTGTAGT
1 ATTTAATTAGTGCAAGATTTTGTAGT
747 ATTTAATTAGTGCAAGATTTTGTAGT
1 ATTTAATTAGTGCAAGATTTTGTAGT
773 A
1 A
774 ATGACAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (26 bp):
ATTTAATTAGTGCAAGATTTTGTAGT
Found at i:3529 original size:29 final size:30
Alignment explanation
Indices: 3491--3548 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3481 GATGCACTTG
*
3491 ACATATAAAACAT-TTTCTTGACATTGGTTT
1 ACATATAAAAAATATTT-TTGACATTGGTTT
*
3521 ACATA-AAAAAATATTTTTTACATTGGTT
1 ACATATAAAAAATATTTTTGACATTGGTT
3549 ATGGGTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (30 bp):
ACATATAAAAAATATTTTTGACATTGGTTT
Found at i:4862 original size:18 final size:18
Alignment explanation
Indices: 4815--4862 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
4805 TATATTATAC
*
4815 ACTCCATAATTGGTAGTA
1 ACTCCATAATTTGTAGTA
4833 ACTCCATAATTTGTAGTA
1 ACTCCATAATTTGTAGTA
*
4851 ACTCCTTAATTT
1 ACTCCATAATTT
4863 TCTTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (18 bp):
ACTCCATAATTTGTAGTA
Found at i:4995 original size:26 final size:26
Alignment explanation
Indices: 4966--5017 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4956 GCACAAATAC
4966 ATTTAATTAGTGCAA-GATTTTGTAGT
1 ATTTAATTAGTG-AAGGATTTTGTAGT
4992 ATTTAATTAGTGAAGGATTTTGTAGT
1 ATTTAATTAGTGAAGGATTTTGTAGT
5018 TTTGACAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (26 bp):
ATTTAATTAGTGAAGGATTTTGTAGT
Found at i:27982 original size:2 final size:2
Alignment explanation
Indices: 27975--28009 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27965 ATTGACTACT
27975 TA TA TA TA 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 TA TA TA TA T
28010 TTTGTATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32503 original size:31 final size:31
Alignment explanation
Indices: 32461--32522 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
32451 TTGTTATCCT
*
32461 AGTTTATCTTTTGAATAATTCATTTAACTGC
1 AGTTTACCTTTTGAATAATTCATTTAACTGC
32492 AGTTTACCTTTTGAATAATTCATTTAACTGC
1 AGTTTACCTTTTGAATAATTCATTTAACTGC
32523 TCGTCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.47
Consensus pattern (31 bp):
AGTTTACCTTTTGAATAATTCATTTAACTGC
Found at i:40193 original size:11 final size:11
Alignment explanation
Indices: 40152--40192 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
40142 TTGACTGCGC
40152 AACAAAAACAA
1 AACAAAAACAA
*
40163 AACGAAAACAA
1 AACAAAAACAA
40174 AACAAAAA-AA
1 AACAAAAACAA
40184 AACAGAAAA
1 AACA-AAAA
40193 ACGAAAGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:44286 original size:77 final size:70
Alignment explanation
Indices: 44148--44315 Score: 237
Period size: 77 Copynumber: 2.3 Consensus size: 70
44138 CGAAAAGTCT
* *
44148 AAAAATACTAAACTCTTGTAGAGATACTTTGATTACTTTGTTGTTTCACATTAAAAGAAAAATTC
1 AAAAATACTAAAATCTTGTAGAGATACTTTGATTACTTTGTAGTTTCACATTAAAAGAAAAATTC
44213 CGCAAAAA
66 CGC---AA
*
44221 AAAAATACTAAAATCTTGTAGAGATACTTTAATTATTTACTTTGTAGTTTCACATTAAAAGAAAA
1 AAAAATACTAAAATCTTGTAGAGATAC-TT--TGA-TTACTTTGTAGTTTCACATTAAAAGAAAA
44286 ATTCCGCAA
62 ATTCCGCAA
*
44295 ATAAATACTAAAATCTTGTAG
1 AAAAATACTAAAATCTTGTAG
44316 CATATGTATC
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
73 26 0.30
74 24 0.28
76 2 0.02
77 35 0.40
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (70 bp):
AAAAATACTAAAATCTTGTAGAGATACTTTGATTACTTTGTAGTTTCACATTAAAAGAAAAATTC
CGCAA
Found at i:45245 original size:15 final size:15
Alignment explanation
Indices: 45225--45255 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45215 AACCAGCTCT
*
45225 TCTTAATGTTTTCCA
1 TCTTAATGATTTCCA
45240 TCTTAATGATTTCCA
1 TCTTAATGATTTCCA
45255 T
1 T
45256 GAAACTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (15 bp):
TCTTAATGATTTCCA
Found at i:49886 original size:13 final size:13
Alignment explanation
Indices: 49868--49906 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
49858 CTAAATTGAC
49868 ATTATTAAAATTT
1 ATTATTAAAATTT
*
49881 ATTATTAAAAATTA
1 ATTATT-AAAATTT
49895 ATTA-TAAAATTT
1 ATTATTAAAATTT
49907 CAATTTAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 7 0.30
14 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTATTAAAATTT
Found at i:49911 original size:14 final size:14
Alignment explanation
Indices: 49868--49911 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
49858 CTAAATTGAC
49868 ATTATTAAAATTT-
1 ATTATTAAAATTTA
*
49881 ATTATTAAAAATTA
1 ATTATTAAAATTTA
49895 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
49909 ATT
1 ATT
49912 TAGACCGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 19 0.70
14 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:50193 original size:20 final size:20
Alignment explanation
Indices: 50156--50194 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50146 TACTATTATT
50156 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
50176 TTTT-AATTTGAATTTTTTA
1 TTTTGAATTT-AATATTTTA
50195 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:50440 original size:44 final size:43
Alignment explanation
Indices: 50361--51537 Score: 214
Period size: 44 Copynumber: 27.3 Consensus size: 43
50351 GTCTCTGTGT
* * ** *
50361 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCAT-AGGA
* *
50405 GGTTATCAAAATTCCATAGTGTA-GTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCATA-GGA
* * * *
50449 AGTTATCAAAATTTCATTGGAAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAG-GA
* ** *
50493 GGTTACCAAAATTTCATA-GAATCGGTTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGGAA--GG-TTACCAAAATTTCATAGG-A
* ** * * * * *
50539 GCTTATTGAAATTTCATAGTG-TGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCATAG-GA
* * **
50583 GGTTATC---A----A-A-G-AGATTATCAAAATGCCATAGCGA
1 GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAG-GA
* *
50617 GGTTAT-AAGAATTTCATAGTG-TGGTTAACAAAATTTCATAAGGA
1 GGTTATCAA-AATTTCATAG-GAAGGTTACCAAAATTTCAT-AGGA
* * * *
50661 GGTTA-CAAATAATATTTCATGGGGAGGTTATCAAAATTTCAATA--T
1 GGTTATC--A-AA-ATTTCATAGGAAGGTTACCAAAATTTC-ATAGGA
* ** * * *
50706 TGTTATCAAAATTTTTTAGTG-TGGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCATA-GGA
* * *
50750 GGTTATAAAAGTCTCAATTTCATAAGG-A-G-TACCAAAATTTGATAGAA
1 GGTTAT-CAA-----AATTTCAT-AGGAAGGTTACCAAAATTTCATAGGA
* *** *
50797 GGTTATC-AAATCTCATA-G-AGTGATTATTGAAACTTCATAGAGA
1 GGTTATCAAAATTTCATAGGAAG-G-TTACCAAAATTTCATAG-GA
* ** * * *
50840 TCGGATTATCAAAATTT-ATAGGAAGATTATTAGATTTTCATAGTGT
1 --GG-TTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAG-GA
* * * *
50886 TGTTATCAAAATTTCAAAGCG-AGGTTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCATAG-GA
* * * * *
50930 GGTCAACAAAATTTTATA-GAGAGGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGGA-AGGTTACCAAAATTTCAT-AGGA
*
50974 GGTTAT-AAAATTTTCA-A--AATGTGATTACCAAAATTTCATA-GT
1 GGTTATCAAAA-TTTCATAGGAA-G-G-TTACCAAAATTTCATAGGA
* * *
51016 GG---T----ATTTC-TAGGGAGGTTATCAAAATTTCATAGTA
1 GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGGA
* * ** * *
51051 TAGTTA-CCAAA--T--TAGGAAGGTTATTAAACTTTTATTATGGA
1 -GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCA-TA-GGA
* * * *
51092 -G-TACTCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAA
1 GGTTA-TCAAAATTTCATAGGAAGGTTACCAAAATTTCATA-GGA
* * * ** **
51133 AGTTTTCAAAATTTAATAGTTTA-GTTTTCAAAATTTCATA-G-
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCATAGGA
* * * *
51174 GGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGGAAGGT-TACCAAAATTTCATA-GGA
* * * * *
51218 GATTAACAAAATTTCATAATG-AGGTTATCAAAA-TT--T-GTA
1 GGTTATCAAAATTTCAT-AGGAAGGTTACCAAAATTTCATAGGA
* * *
51257 -GTTATCAAGATTTCATAAGG-AGGTTATCAAAATTTTATATGGA
1 GGTTATCAAAATTTCAT-AGGAAGGTTACCAAAATTTCATA-GGA
* * *
51300 GGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTTATAGGAA
1 GG-TTATCAAAATTTCATAGGAAGG-TTACCAAAATTTCATAGG-A
* * * *
51346 GGTTTATCAAAATTTCATAGCAAGGTTATCACAATTTCATAGTGT
1 GG-TTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAG-GA
* * * * *
51391 GATTATCAAAATTTCAGAGTG-TGATTACTAACAA-TTCATATGGA
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAA-AATTTCATA-GGA
* * * * * * * *
51435 GGTTTTTAAATTTTCATAACG-TGGTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCAT-AGGAAGGTTACCAAAATTTCATA-GGA
* * ** **
51479 GGTTATCAACATCTCATAGTGTTGGTTATGAAAATTTCATTAGGA
1 GGTTATCAAAATTTCATAG-GAAGGTTACCAAAATTTCA-TAGGA
*
51524 AGTTATCAAAATTT
1 GGTTATCAAAATTT
51538 ACTTCAAAAT
Statistics
Matches: 845, Mismatches: 176, Indels: 223
0.68 0.14 0.18
Matches are distributed among these distances:
34 37 0.04
35 6 0.01
36 4 0.00
37 3 0.00
38 32 0.04
39 27 0.03
40 17 0.02
41 43 0.05
42 67 0.08
43 38 0.04
44 315 0.37
45 90 0.11
46 99 0.12
47 39 0.05
48 18 0.02
49 1 0.00
50 7 0.01
51 2 0.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGAAGGTTACCAAAATTTCATAGGA
Found at i:50511 original size:22 final size:22
Alignment explanation
Indices: 50357--50579 Score: 152
Period size: 22 Copynumber: 10.0 Consensus size: 22
50347 TCTTGTCTCT
50357 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * *
50380 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
* *
50402 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
* *
50423 GTGTAGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
50445 -TG-GAAGTTATCAAAATTTCATT
1 GTGTG--GTTATCAAAATTTCATA
*
50467 G-GAAGGTTATCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
50489 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
** * *
50511 GAATCGGTTTATTAAAATTTCTTA
1 GTGT-GG-TTATCAAAATTTCATA
* * **
50535 G-GAAGCTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
* *
50557 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
50579 G
1 G
50580 AAAGGTTATC
Statistics
Matches: 154, Mismatches: 35, Indels: 23
0.73 0.17 0.11
Matches are distributed among these distances:
21 4 0.03
22 129 0.84
23 6 0.04
24 15 0.10
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:50988 original size:22 final size:22
Alignment explanation
Indices: 50592--51537 Score: 189
Period size: 22 Copynumber: 42.8 Consensus size: 22
50582 AGGTTATCAA
* **
50592 AGAGATTATCAAAATGCCATAG
1 AGAGGTTATCAAAATTTCATAG
*
50614 CGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTCATAG
* * *
50636 TGTGGTTAACAAAATTTCATA-
1 AGAGGTTATCAAAATTTCATAG
*
50657 AGGAGGTTA-CAAATAATATTTCATGG
1 A-GAGGTTATC--A-AA-ATTTCATAG
* *
50683 GGAGGTTATCAAAATTTCA-AT
1 AGAGGTTATCAAAATTTCATAG
** **
50704 A-TTGTTATCAAAATTTTTTAG
1 AGAGGTTATCAAAATTTCATAG
* *
50725 TGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
*
50748 A-AGGTTATAAAAGTCTCAATTTCATA-
1 AGAGGTTAT-CAA-----AATTTCATAG
* *
50774 AG-GAG-TACCAAAATTTGATAG
1 AGAG-GTTATCAAAATTTCATAG
*
50795 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * ** *
50815 AGTGATTATTGAAACTTCATAG
1 AGAGGTTATCAAAATTTCATAG
50837 AGATCGGATTATCAAAATTT-ATAG
1 AGA--GG-TTATCAAAATTTCATAG
* * * *
50861 -GAAGATTATTAGATTTTCATAG
1 AG-AGGTTATCAAAATTTCATAG
* ** *
50883 TGTTGTTATCAAAATTTCAAAG
1 AGAGGTTATCAAAATTTCATAG
*
50905 CGAGGTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * * *
50927 AGGGGTCAACAAAATTTTATAG
1 AGAGGTTATCAAAATTTCATAG
*
50949 AGAGGTTATCAAAATTTCATAA
1 AGAGGTTATCAAAATTTCATAG
*
50971 AGAGGTTAT-AAAATTTTCA-AA
1 AGAGGTTATCAAAA-TTTCATAG
* * *
50992 ATGTGATTACCAAAATTTCAT--
1 A-GAGGTTATCAAAATTTCATAG
* * **
51013 AGTGGTATTTCTAGGGAGGTTATCA-A-
1 AGAGGT-TATC-A---AAATT-TCATAG
*
51039 A-A--TT-TCATAGTATAGTTACCAAATTAG
1 AGAGGTTATCA-A--A-A-TT-TC--A-TAG
* * *
51066 -GAAGGTTATTAAACTTTTATTATG
1 AG-AGGTTATCAAAATTTCA-TA-G
51090 -GA-G-TACTCAAAATTTC--AG
1 AGAGGTTA-TCAAAATTTCATAG
* *
51108 GGAGGATATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
* * *
51131 A-AAGTTTTCAAAATTTAATAG
1 AGAGGTTATCAAAATTTCATAG
** *
51152 TTTA-GTTTTCAAAATTTCAT--
1 -AGAGGTTATCAAAATTTCATAG
51172 AG-GGTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
51193 -TATGTAGATCAAAATTTCATAG
1 AGAGGT-TATCAAAATTTCATAG
* * *
51215 GGAGATTAACAAAATTTCATA-
1 AGAGGTTATCAAAATTTCATAG
51236 ATGAGGTTATCAAAA-TT--T-G
1 A-GAGGTTATCAAAATTTCATAG
* *
51255 -TA-GTTATCAAGATTTCATA-
1 AGAGGTTATCAAAATTTCATAG
*
51274 AGGAGGTTATCAAAATTTTATATG
1 A-GAGGTTATCAAAATTTCATA-G
*
51298 -GAGGTTTATCAAAATTTTATAG
1 AGAGG-TTATCAAAATTTCATAG
*
51320 -GAAGGTTTATCAAAATTTTATAG
1 AG-AGG-TTATCAAAATTTCATAG
51343 -GAAGGTTTATCAAAATTTCATAG
1 AG-AGG-TTATCAAAATTTCATAG
*
51366 CA-AGGTTATCACAATTTCATAG
1 -AGAGGTTATCAAAATTTCATAG
* * * *
51388 TGTGATTATCAAAATTTCAGAG
1 AGAGGTTATCAAAATTTCATAG
* * *
51410 TGTGATTA-CTAACAA-TTCATATG
1 AGAGGTTATC-AA-AATTTCATA-G
* * *
51433 -GAGGTTTTTAAATTTTCATA-
1 AGAGGTTATCAAAATTTCATAG
* * *
51453 ACGTGGTTATCAATATATCATATG
1 A-GAGGTTATCAAAATTTCATA-G
* *
51477 -GAGGTTATCAACATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
51498 TGTTGGTTATGAAAATTTCATTAG
1 AG-AGGTTATCAAAATTTCA-TAG
*
51522 -GAAGTTATCAAAATTT
1 AGAGGTTATCAAAATTT
51538 ACTTCAAAAT
Statistics
Matches: 682, Mismatches: 142, Indels: 200
0.67 0.14 0.20
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 2 0.00
19 20 0.03
20 48 0.07
21 48 0.07
22 377 0.55
23 103 0.15
24 15 0.02
25 28 0.04
26 12 0.02
27 1 0.00
28 11 0.02
30 3 0.00
31 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:51187 original size:41 final size:41
Alignment explanation
Indices: 51115--51216 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 41
51105 CAGGGAGGAT
* *
51115 ATCAAAATTTCATATGAAAGTTTTCAAAATTTAATAGT-T-TAG
1 ATCAAAATTTCATA-G--GGTTATCAAAATTTAATAGTATGTAG
* *
51157 TTTTCAAAATTTCATAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAGGGTTATCAAAATTTAATAGTATGTAG
51200 ATCAAAATTTCATAGGG
1 ATCAAAATTTCATAGGG
51217 AGATTAACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
41 33 0.65
42 1 0.02
43 4 0.08
44 13 0.25
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (41 bp):
ATCAAAATTTCATAGGGTTATCAAAATTTAATAGTATGTAG
Found at i:51272 original size:60 final size:61
Alignment explanation
Indices: 51200--51314 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
51190 TAGTATGTAG
*
51200 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT-GAGG-TTATCAAAATTTGTAGTT
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCAT-ATGGAGGTTTATCAAAATTTGTAGTT
* * * *
51260 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATATGGAGGTTTATCAAAATTT
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATATGGAGGTTTATCAAAATTT
51315 TATAGGAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.04
60 34 0.71
61 12 0.25
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.37
Consensus pattern (61 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATATGGAGGTTTATCAAAATTTGTAGTT
Found at i:51310 original size:23 final size:23
Alignment explanation
Indices: 51258--51387 Score: 160
Period size: 23 Copynumber: 5.7 Consensus size: 23
51248 AAATTTGTAG
* *
51258 TTATCAAGATTTCATAAGG-AGG-
1 TTATCAAAATTTTAT-AGGAAGGT
51280 TTATCAAAATTTTATATGG-AGGT
1 TTATCAAAATTTTATA-GGAAGGT
51303 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
51326 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
* *
51349 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTTATAGGAAGGT
* *
51371 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
51388 TGTGATTATC
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.01
22 36 0.36
23 63 0.63
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:51672 original size:22 final size:22
Alignment explanation
Indices: 51627--51680 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
51617 CCATAGTTTC
*
51627 GTTATTAAAATTTCATAGGAAG
1 GTTATCAAAATTTCATAGGAAG
51649 GTTATCAAAATTTCATAAGG-AG
1 GTTATCAAAATTTCAT-AGGAAG
*
51671 GTCATCAAAA
1 GTTATCAAAA
51681 ATACTGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGAAG
Found at i:51793 original size:2 final size:2
Alignment explanation
Indices: 51786--51827 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
51776 TTAAAACTAG
51786 TA TA 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 TA TA
51828 GTTAGTTTAN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.