Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013783.1 Kokia drynarioides strain JFW-HI SEQ_128811, 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: 58429
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:2057 original size:49 final size:49
Alignment explanation
Indices: 1993--2204 Score: 225
Period size: 49 Copynumber: 4.6 Consensus size: 49
1983 GATTTGGTCT
*
1993 ACTTCTCTGTGTCTCATCAGGAAGACGATCGCCTCATTTGTTTTAATCC
1 ACTTCTCTGTATCTCATCAGGAAGACGATCGCCTCATTTGTTTTAATCC
* * * *
2042 ACTTCTCTATTTCTCATCTA-GAAGATGACCGCCTCATTTGTTTTAATCC
1 ACTTCTCTGTATCTCATC-AGGAAGACGATCGCCTCATTTGTTTTAATCC
* * *
2091 ATTTCTCTGTATCTCATCAAGAAGACG---G----ATTTG-----GTCC
1 ACTTCTCTGTATCTCATCAGGAAGACGATCGCCTCATTTGTTTTAATCC
* * *
2128 ACTTCTCTATATCTCATCTGGAAGATGATCGCCTCATTTGTTTTAATCC
1 ACTTCTCTGTATCTCATCAGGAAGACGATCGCCTCATTTGTTTTAATCC
2177 ACTTCTCTGTATCTCATCAGGAAGACGA
1 ACTTCTCTGTATCTCATCAGGAAGACGA
2205 CCGCTTTCTT
Statistics
Matches: 131, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
37 25 0.19
40 1 0.01
42 5 0.04
44 5 0.04
46 1 0.01
48 1 0.01
49 92 0.70
50 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (49 bp):
ACTTCTCTGTATCTCATCAGGAAGACGATCGCCTCATTTGTTTTAATCC
Found at i:2184 original size:86 final size:86
Alignment explanation
Indices: 2039--2203 Score: 285
Period size: 86 Copynumber: 1.9 Consensus size: 86
2029 TTTGTTTTAA
* *
2039 TCCACTTCTCTATTTCTCATCTAGAAGATGACCGCCTCATTTGTTTTAATCCATTTCTCTGTATC
1 TCCACTTCTCTATATCTCATCTAGAAGATGACCGCCTCATTTGTTTTAATCCACTTCTCTGTATC
2104 TCATCAAGAAGACGGATTTGG
66 TCATCAAGAAGACGGATTTGG
* *
2125 TCCACTTCTCTATATCTCATCTGGAAGATGATCGCCTCATTTGTTTTAATCCACTTCTCTGTATC
1 TCCACTTCTCTATATCTCATCTAGAAGATGACCGCCTCATTTGTTTTAATCCACTTCTCTGTATC
*
2190 TCATCAGGAAGACG
66 TCATCAAGAAGACG
2204 ACCGCTTTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (86 bp):
TCCACTTCTCTATATCTCATCTAGAAGATGACCGCCTCATTTGTTTTAATCCACTTCTCTGTATC
TCATCAAGAAGACGGATTTGG
Found at i:2421 original size:125 final size:124
Alignment explanation
Indices: 2242--2495 Score: 409
Period size: 125 Copynumber: 2.0 Consensus size: 124
2232 ATTTCATAAG
*
2242 GAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTTGTTGAATTGGTCTACTTCTCTGT
1 GAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTTATTGAATTGGTCTACTTCTCTGT
* *
2307 ATCTCATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAA
66 ATATAATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAA
** *
2366 GAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTTATTGATTTGGTCTACTTCTCTG
1 GAAGATGGGGTTT-GAAGTTTCACTCACATTGAGCTTCACTTTATTGAATTGGTCTACTTCTCTG
* * * *
2431 TATATAATTAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTCTGTATCTCATCAG
65 TATATAATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAA
2491 GAAGA
1 GAAGA
2496 CGGATTTGGT
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
124 13 0.11
125 106 0.89
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (124 bp):
GAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTTATTGAATTGGTCTACTTCTCTGT
ATATAATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAA
Found at i:2714 original size:210 final size:210
Alignment explanation
Indices: 2290--2805 Score: 721
Period size: 210 Copynumber: 2.5 Consensus size: 210
2280 CTTTGTTGAA
* * * * * ** * * *
2290 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTG
1 TTGGTCCACTTTTCTGTATCTCATCAGGAAGACGACCACTTTA-TTACTTTGACCCACTTCTCAG
* *
2355 TATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTTATTGATTTGGT
65 TATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGT
* *
2420 CTACTTCTCTGTATATAATTAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTCTGTATCT
130 CTACTTCTCTATATATAATCAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTCTGTATCT
* *
2485 CATCAGGAAGACGGAT
195 CATCAAGAAGACAGAT
* * * *
2501 TTGGTCCACTTCTT-TGTATCTCATTAGGAAGACGATCGCTTTATTACTTTGACCCACTTCTAAG
1 TTGGTCCACTT-TTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTTGACCCACTTCTCAG
*
2565 TATCTCATCAGGAAGATGAGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGT
65 TATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGT
* * *
2630 CTACTTCTCTATATCTCATCAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTTTGTATCT
130 CTACTTCTCTATATATAATCAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTCTGTATCT
*
2695 CATCAAGTAGACAGAT
195 CATCAAGAAGACAGAT
* ** **
2711 TTGGTCTACTTTTCTGTATCTCATCAGGAAGACGACCACTTTATTGTTTTGACAGACTTCTCAGT
1 TTGGTCCACTTTTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTTGACCCACTTCTCAGT
*
2776 ATCTCATTAGGAAGATGGGGTTT-GAAGTTT
66 ATCTCATCAGGAAGATGGGGTTTGGAAGTTT
2806 TAGTTTTCCC
Statistics
Matches: 267, Mismatches: 36, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
209 9 0.03
210 224 0.84
211 33 0.12
212 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (210 bp):
TTGGTCCACTTTTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTTGACCCACTTCTCAGT
ATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTC
TACTTCTCTATATATAATCAGGAAGATGACCACCTCATTTGTTTTAATCCACTTCTCTGTATCTC
ATCAAGAAGACAGAT
Found at i:15280 original size:29 final size:29
Alignment explanation
Indices: 15165--15519 Score: 265
Period size: 29 Copynumber: 12.0 Consensus size: 29
15155 GGTTAAAACA
** * *
15165 TAATTTTGGAAAACTTTAGGAGTAAAAATG
1 TAATTTTTAAAAAGTTTAGG-GTCAAAATG
* *
15195 TAA-TTTTAAGAAAGTTTGGGGGTTAAAATG
1 TAATTTTTAA-AAAGTTT-AGGGTCAAAATG
* * *
15225 TGA--TTTAGTAAAGTTTAGGGGTTAAAATG
1 TAATTTTTA-AAAAGTTTA-GGGTCAAAATG
* * * * *
15254 TAATGTTAAAAAAGTTAAGTGTCAAAATA
1 TAATTTTTAAAAAGTTTAGGGTCAAAATG
* *
15283 TAATTTTTGAGAAGTTTAGGGGTCAAAATG
1 TAATTTTTAAAAAGTTTA-GGGTCAAAATG
* * *
15313 -AATTTTTTGAGAAGTTTAGGGTCAAAATA
1 TAA-TTTTTAAAAAGTTTAGGGTCAAAATG
* *
15342 TAATTTTTAATAAGTTTAAGGGTCTAAATG
1 TAATTTTTAAAAAGTTT-AGGGTCAAAATG
*
15372 TAA-TTTTAAAAAGGTTTGGGGTCAAAATG
1 TAATTTTTAAAAA-GTTTAGGGTCAAAATG
* *
15401 TAATTTTTAAGAAGTTTAGGGATTAAAATG
1 TAATTTTTAAAAAGTTTAGGG-TCAAAATG
* *
15431 TAA-TTTTAAAAAGGTTTAGTGTTAAAATG
1 TAATTTTTAAAAA-GTTTAGGGTCAAAATG
* **
15460 TAATTTTTAAGAAGTTTAGGGGTTGAAATG
1 TAATTTTTAAAAAGTTTA-GGGTCAAAATG
* *
15490 TAA-TTTTAGAAAGGTTTGGGGTCAAAATG
1 TAATTTTTA-AAAAGTTTAGGGTCAAAATG
15519 T
1 T
15520 GATATTTGGA
Statistics
Matches: 265, Mismatches: 43, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
29 140 0.53
30 120 0.45
31 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
TAATTTTTAAAAAGTTTAGGGTCAAAATG
Found at i:15534 original size:59 final size:59
Alignment explanation
Indices: 15179--15519 Score: 361
Period size: 59 Copynumber: 5.8 Consensus size: 59
15169 TTTGGAAAAC
* * * * * *
15179 TTTAGGAGTAAAAATGTAATTTTAAGAAA-GTTTGGGGGTTAAAATGTGATTTAGT-A-AAG
1 TTTAGGGGTTAAAATGTAATTTTAA-AAAGGTTT-AGGGTCAAAATGTAATTT-TTAAGAAG
* * * * * *
15238 TTTAGGGGTTAAAATGTAATGTTAAAAAAGTTAAGTGTCAAAATATAATTTTTGAGAAG
1 TTTAGGGGTTAAAATGTAATTTTAAAAAGGTTTAGGGTCAAAATGTAATTTTTAAGAAG
* * * * *
15297 TTTAGGGGTCAAAATG-AATTTTTTGAGAA-GTTTAGGGTCAAAATATAATTTTTAATAAG
1 TTTAGGGGTTAAAATGTAA--TTTTAAAAAGGTTTAGGGTCAAAATGTAATTTTTAAGAAG
* *
15356 TTTAAGGGTCT-AAATGTAATTTTAAAAAGGTTTGGGGTCAAAATGTAATTTTTAAGAAG
1 TTTAGGGGT-TAAAATGTAATTTTAAAAAGGTTTAGGGTCAAAATGTAATTTTTAAGAAG
* * *
15415 TTTAGGGATTAAAATGTAATTTTAAAAAGGTTTAGTGTTAAAATGTAATTTTTAAGAAG
1 TTTAGGGGTTAAAATGTAATTTTAAAAAGGTTTAGGGTCAAAATGTAATTTTTAAGAAG
* * *
15474 TTTAGGGGTTGAAATGTAATTTTAGAAAGGTTTGGGGTCAAAATGT
1 TTTAGGGGTTAAAATGTAATTTTAAAAAGGTTTAGGGTCAAAATGT
15520 GATATTTGGA
Statistics
Matches: 237, Mismatches: 36, Indels: 18
0.81 0.12 0.06
Matches are distributed among these distances:
57 1 0.00
58 27 0.11
59 201 0.85
60 8 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (59 bp):
TTTAGGGGTTAAAATGTAATTTTAAAAAGGTTTAGGGTCAAAATGTAATTTTTAAGAAG
Found at i:16226 original size:3 final size:3
Alignment explanation
Indices: 16218--16254 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16208 GATTTGTTAC
16218 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16255 TTGCAGATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16381 original size:4 final size:4
Alignment explanation
Indices: 16372--16418 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
16362 TTTAATCTAC
*
16372 TTTA TTTA TTTA TTTA TTTAA TATA TTATA TTTA -TTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTT-A TTTA TT-TA TTTA TTTA TTTA TTTA TT
16419 AAAACGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:16999 original size:19 final size:19
Alignment explanation
Indices: 16955--17002 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
16945 TAAATAAATT
*
16955 TAAATTTAAAAATGTACAG
1 TAAATTTAAAAATGTAAAG
* *
16974 GACATTTAAAAATGTAAAG
1 TAAATTTAAAAATGTAAAG
16993 TAAATTTAAA
1 TAAATTTAAA
17003 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (19 bp):
TAAATTTAAAAATGTAAAG
Found at i:22847 original size:16 final size:17
Alignment explanation
Indices: 22813--22849 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
22803 GTTTTAAAAT
22813 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
22831 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
22847 TTT
1 TTT
22850 TTATCCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:22852 original size:18 final size:18
Alignment explanation
Indices: 22811--22850 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22801 GGGTTTTAAA
22811 ATTTTAATTAATTAAATTT
1 ATTTTAATTAA-TAAATTT
22830 A-TTTAATTAA-AAATTT
1 ATTTTAATTAATAAATTT
22846 ATTTT
1 ATTTT
22851 TATCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 9 0.45
19 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAATAAATTT
Found at i:23039 original size:31 final size:29
Alignment explanation
Indices: 22975--23040 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
22965 ATAACATAAG
* * *
22975 TGACTAAAATGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACATGTCAAACAAAAA
*
23004 TGACTAAAATGTAACCTGAGTCAAACAAAAA
1 TGACTAAAATGTAACAT--GTCAAACAAAAA
23035 TGACTA
1 TGACTA
23041 TTTTTGTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.24
Consensus pattern (29 bp):
TGACTAAAATGTAACATGTCAAACAAAAA
Found at i:25718 original size:76 final size:77
Alignment explanation
Indices: 25561--25718 Score: 189
Period size: 76 Copynumber: 2.1 Consensus size: 77
25551 AAAGTGGAAT
* * *
25561 ACTAATTGTACTAAATGCTTGCTCAAGCGAGCGAATCTACTGATTATACTGAATGCTTGTTCAAA
1 ACTAATTGTACGAAATGCTCGCTCAAGCGAGCGAAACTACTGATTATACTGAATGCTTGTTCAAA
* *
25626 ATGAGCAAATCT
66 AGGAGCAAATCC
* *
25638 ACTAATTTTACGAAATG-TCGCTCAA-CGAGCGATAACTACTGATTATATTGAATGCTT-TCTC-
1 ACTAATTGTACGAAATGCTCGCTCAAGCGAGCGA-AACTACTGATTATACTGAATGCTTGT-TCA
*
25699 AAAGGAGCATTATCC
64 AAAGGAGCA-AATCC
25714 ACTAA
1 ACTAA
25719 CTATACTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
75 16 0.23
76 39 0.56
77 15 0.21
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (77 bp):
ACTAATTGTACGAAATGCTCGCTCAAGCGAGCGAAACTACTGATTATACTGAATGCTTGTTCAAA
AGGAGCAAATCC
Found at i:29084 original size:6 final size:6
Alignment explanation
Indices: 29075--29101 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29065 AATACAAATG
29075 AATATA AATATA AATATA AATATA AAT
1 AATATA AATATA AATATA AATATA AAT
29102 GTAAGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:29111 original size:18 final size:18
Alignment explanation
Indices: 29075--29114 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29065 AATACAAATG
*
29075 AATATAAATATAAATATA
1 AATATAAATATAAAGATA
* *
29093 AATATAAATGTAAGGATA
1 AATATAAATATAAAGATA
29111 AATA
1 AATA
29115 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (18 bp):
AATATAAATATAAAGATA
Found at i:43300 original size:40 final size:40
Alignment explanation
Indices: 43198--43682 Score: 297
Period size: 40 Copynumber: 12.3 Consensus size: 40
43188 ACAACCTCGA
* *
43198 ATCTTTTACCTCAACCATG-GGGCACATTGAAGTA--ATTCG
1 ATCTTTTACC-CAACCATGAGGGCAGATTGAAG-ACCATCCG
** * *
43237 ATCTCTTGCCCCGACCATG-GGGCAGATTAAAGACCATCCG
1 ATCT-TTTACCCAACCATGAGGGCAGATTGAAGACCATCCG
* * *
43277 ATCTTTTACCTCGACTA-GAGGGCAGATTGAAGACCATCTG
1 ATCTTTTACC-CAACCATGAGGGCAGATTGAAGACCATCCG
* * * *
43317 ATCTCTTACCCTGACCATG-TGGCAGATTGAAG-CAATCC-
1 ATCTTTTACCC-AACCATGAGGGCAGATTGAAGACCATCCG
* * *
43355 ACTCTTTTACCCTAACTA-AAGGGCAGATTAAAGACCATCCG
1 A-TCTTTTACCC-AACCATGAGGGCAGATTGAAGACCATCCG
* * * **
43396 ATCTCTTACCCCAACTATG-GGGCAGATTGAAG-CAATCTA
1 ATCTTTTA-CCCAACCATGAGGGCAGATTGAAGACCATCCG
* *
43435 ATCTTTTACCCTAACTA-GCGGGCAGATTGAAGACCATCCG
1 ATCTTTTACCC-AACCATGAGGGCAGATTGAAGACCATCCG
* * * * *
43475 ATCTCTTATCCCGACCATG-GGTCAGATTGAAGGCCATCTG
1 ATCTTTTA-CCCAACCATGAGGGCAGATTGAAGACCATCCG
* * * * *
43515 ATCTTTTTCCTCGACCA-GAAGGTAGATTGAAGGCCATCCG
1 ATCTTTTACC-CAACCATGAGGGCAGATTGAAGACCATCCG
* * * * * **
43555 ATCTCTTGCCCAAACTATG-GGGAAGATTGAAG-CAATCTA
1 ATCTTTTACCC-AACCATGAGGGCAGATTGAAGACCATCCG
* * *
43594 ATCTTTTACCTAACCA-AAGGGCAGATTGAAGACCATTCG
1 ATCTTTTACCCAACCATGAGGGCAGATTGAAGACCATCCG
* * **
43633 ATCTTTTACCCCGACCATGA-GGCAGATTGAA-ACAATCAA
1 ATCTTTTA-CCCAACCATGAGGGCAGATTGAAGACCATCCG
43672 ATCTTTTACCC
1 ATCTTTTACCC
43683 CTAAAACTAA
Statistics
Matches: 349, Mismatches: 71, Indels: 53
0.74 0.15 0.11
Matches are distributed among these distances:
38 25 0.07
39 124 0.36
40 189 0.54
41 11 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (40 bp):
ATCTTTTACCCAACCATGAGGGCAGATTGAAGACCATCCG
Found at i:43361 original size:79 final size:79
Alignment explanation
Indices: 43197--43681 Score: 496
Period size: 79 Copynumber: 6.1 Consensus size: 79
43187 TACAACCTCG
* * * *
43197 AATCTTTTACCTCAACCATG-GGGCACATTGAAGTA--ATTCGATCTCTTGCCCCGACCATGGGG
1 AATCTTTTACCTCAACTA-GAGGGCAGATTGAAG-ACCATCCGATCTCTTACCCCGACCATGGGG
* *
43259 CAGATTAAAGACCATCC
64 CAGATTGAAG-CAATCC
* * * * *
43276 GATCTTTTACCTCGACTAGAGGGCAGATTGAAGACCATCTGATCTCTTACCCTGACCATGTGGCA
1 AATCTTTTACCTCAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCA
43341 GATTGAAGCAATCC
66 GATTGAAGCAATCC
* * * * *
43355 ACTCTTTTACC-CTAACTAAAGGGCAGATTAAAGACCATCCGATCTCTTACCCCAACTATGGGGC
1 AATCTTTTACCTC-AACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGC
*
43419 AGATTGAAGCAATCT
65 AGATTGAAGCAATCC
* * *
43434 AATCTTTTACC-CTAACTAGCGGGCAGATTGAAGACCATCCGATCTCTTATCCCGACCATGGGTC
1 AATCTTTTACCTC-AACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGC
* *
43498 AGATTGAAGGCCATCT
65 AGATTGAA-GCAATCC
* * * * * * * * ** * *
43514 GATCTTTTTCCTCGACCAGAAGGTAGATTGAAGGCCATCCGATCTCTTGCCCAAACTATGGGGAA
1 AATCTTTTACCTCAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCA
*
43579 GATTGAAGCAATCT
66 GATTGAAGCAATCC
* * * * *
43593 AATCTTTTACCT-AACCAAAGGGCAGATTGAAGACCATTCGATCTTTTACCCCGACCATGAGGCA
1 AATCTTTTACCTCAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCA
* *
43657 GATTGAAACAATCA
66 GATTGAAGCAATCC
43671 AATCTTTTACC
1 AATCTTTTACC
43682 CCTAAAACTA
Statistics
Matches: 336, Mismatches: 64, Indels: 13
0.81 0.15 0.03
Matches are distributed among these distances:
78 65 0.19
79 178 0.53
80 92 0.27
81 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (79 bp):
AATCTTTTACCTCAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCA
GATTGAAGCAATCC
Found at i:44755 original size:20 final size:19
Alignment explanation
Indices: 44705--44760 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
44695 TTGTAAAAAA
*
44705 TTGTTATTTTCTTATTTTTG
1 TTGTTATTTTCTT-TTTTAG
* *
44725 TTTTTATTTTTATTTTTTAAG
1 TTGTTA-TTTTCTTTTTT-AG
44746 TTGTTATTTTCTTTT
1 TTGTTATTTTCTTTT
44761 GACTAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.77
Consensus pattern (19 bp):
TTGTTATTTTCTTTTTTAG
Found at i:51481 original size:16 final size:15
Alignment explanation
Indices: 51445--51486 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
51435 AAACAAATAC
51445 CCAAATACCC-AATT
1 CCAAATACCCAAATT
*
51459 CAAAAATACCCAAATTT
1 C-CAAATACCCAAA-TT
51476 CCAAATACCCA
1 CCAAATACCCA
51487 TTTCCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 11 0.48
17 3 0.13
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
CCAAATACCCAAATT
Done.