Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014862.1 Kokia drynarioides strain JFW-HI SEQ_129905, 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: 67717
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:67 original size:16 final size:16
Alignment explanation
Indices: 46--96 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
36 TGATGGAGAT
46 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
62 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
77 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
92 ATTAT
1 ATTAT
97 CTAGGTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:798 original size:12 final size:11
Alignment explanation
Indices: 781--819 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
771 TTCTTCCTTC
781 TTCTTTCTTTAT
1 TTCTTTCTTT-T
793 TTCTTTCTCTTTT
1 TTC-TT-TCTTTT
806 TTCTTTCTTTT
1 TTCTTTCTTTT
817 TTC
1 TTC
820 AGTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.36
12 5 0.20
13 6 0.24
14 5 0.20
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:808 original size:21 final size:20
Alignment explanation
Indices: 779--819 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
769 CCTTCTTCCT
779 TCTTCTTTCTTTATTTCTTTC
1 TCTTCTTTCTTTATTT-TTTC
* *
800 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTATTTTTTC
820 AGTCAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTCTTTCTTTATTTTTTC
Found at i:2961 original size:6 final size:6
Alignment explanation
Indices: 2950--2980 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2940 CGCACGTGAC
*
2950 GGCCGG GGCCGG GGCCGG GGCCAG GGCCGG G
1 GGCCGG GGCCGG GGCCGG GGCCGG GGCCGG G
2981 CAAGTATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.32, G:0.65, T:0.00
Consensus pattern (6 bp):
GGCCGG
Found at i:10059 original size:5 final size:5
Alignment explanation
Indices: 10049--10073 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10039 TGATGAAGTG
10049 GGTTT GGTTT GGTTT GGTTT GGTTT
1 GGTTT GGTTT GGTTT GGTTT GGTTT
10074 ATAACCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
GGTTT
Found at i:12105 original size:5 final size:5
Alignment explanation
Indices: 12095--12124 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
12085 TAATATTAAA
12095 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
12125 TTGACAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:14640 original size:23 final size:23
Alignment explanation
Indices: 14591--14641 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
14581 CTAGCGTGCT
* *
14591 TACTGTTTCGCACTTCGTATGCT
1 TACTGTTTCGCACTTCGTATACC
14614 TACTGTTTCGCACCTT-GTATACC
1 TACTGTTTCGCA-CTTCGTATACC
14637 TACTG
1 TACTG
14642 ATTTGCGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (23 bp):
TACTGTTTCGCACTTCGTATACC
Found at i:14704 original size:23 final size:22
Alignment explanation
Indices: 14637--14706 Score: 95
Period size: 23 Copynumber: 3.1 Consensus size: 22
14627 CTTGTATACC
* * *
14637 TACTGATTTGCGCTATGTGTGCC
1 TACTGA-TTGCACTGTGTGTGCT
14660 TACTGATTGCACTGTGTGTGCT
1 TACTGATTGCACTGTGTGTGCT
14682 TACTGGATTGCACTGTGTGTGCT
1 TACT-GATTGCACTGTGTGTGCT
14705 TA
1 TA
14707 TTGTTTCTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 17 0.40
23 26 0.60
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (22 bp):
TACTGATTGCACTGTGTGTGCT
Found at i:15224 original size:20 final size:21
Alignment explanation
Indices: 15186--15224 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15176 TTTGTACTAA
**
15186 AAATCATATTTTATTTCTTTT
1 AAATCATATTTTAAGTCTTTT
15207 AAATCA-ATTTTAAGTCTT
1 AAATCATATTTTAAGTCTT
15225 GATTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (21 bp):
AAATCATATTTTAAGTCTTTT
Found at i:17738 original size:6 final size:6
Alignment explanation
Indices: 17727--17767 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
17717 ATATTTGCAT
*
17727 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
17768 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:20972 original size:17 final size:17
Alignment explanation
Indices: 20950--20983 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20940 CTTACAATAA
*
20950 TTAAATAATATTTAAAT
1 TTAAATAATAGTTAAAT
20967 TTAAATAATAGTTAAAT
1 TTAAATAATAGTTAAAT
20984 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAATAATAGTTAAAT
Found at i:21308 original size:27 final size:27
Alignment explanation
Indices: 21276--21354 Score: 142
Period size: 27 Copynumber: 2.9 Consensus size: 27
21266 ATTGAGACCA
21276 GGTGCCGCCTGATAGGTAGGCACCATT
1 GGTGCCGCCTGATAGGTAGGCACCATT
21303 GGTGCCGCCTGATAGGTAGGCACCATT
1 GGTGCCGCCTGATAGGTAGGCACCATT
21330 GGTGCCGCCT-ATCAGGTAGGCACCA
1 GGTGCCGCCTGAT-AGGTAGGCACCA
21355 CCCAAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 2 0.04
27 49 0.96
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTGATAGGTAGGCACCATT
Found at i:21452 original size:16 final size:16
Alignment explanation
Indices: 21409--21452 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
21399 ACCATCAATA
*
21409 TATTTTTTTAATTTAT
1 TATTTATTTAATTTAT
** *
21425 TATTTAAATAATTTTT
1 TATTTATTTAATTTAT
21441 TATTTATTTAAT
1 TATTTATTTAAT
21453 ATTAATGAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTAATTTAT
Found at i:28962 original size:186 final size:184
Alignment explanation
Indices: 28648--29018 Score: 715
Period size: 186 Copynumber: 2.0 Consensus size: 184
28638 TTGAATATTA
28648 TGAAACATCTTAGAAACACAACTCGGTGAGCATATCGTCATAACATGCTGATTTCCTCATTAGTC
1 TGAAACATCTTAGAAACACAACTCGGTGAGCATATCGTCATAACATGCTGATTTCCTCATTAGTC
28713 TAAAGTCATATTAGGAAGATTTTATCGAAAAAAAGAAGGCATATTAGGAAGGTATCGACTTTTCT
66 TAAAGTCATATTAGGAAGATTTTATCGAAAAAAAGAAGGCATATTAGGAAGGTATCGACTTTTCT
28778 TTATTTAAATATTTGGGAAACCAAAGAGATAGATATCGGTTCTCTGAAGTCCGAAG
131 TTATTTAAATATTTGGGAAACCAAAGAG--AGATATCGGTTCTCTGAAGTCCGAAG
*
28834 TGAAACATCTTAGAAACACAATTCGGTGAGCATATCGTCATAACATGCTGATTTCCTCATTAGTC
1 TGAAACATCTTAGAAACACAACTCGGTGAGCATATCGTCATAACATGCTGATTTCCTCATTAGTC
28899 TAAAGTCATATTAGGAAGATTTTATCGAAAAAAAGAAGGCATATTAGGAAGGTATCGACTTTTCT
66 TAAAGTCATATTAGGAAGATTTTATCGAAAAAAAGAAGGCATATTAGGAAGGTATCGACTTTTCT
28964 TTATTTAAATATTTGGGAAACCAAAGAGAGATATCGGTTCTCTGAAGTCCGAAG
131 TTATTTAAATATTTGGGAAACCAAAGAGAGATATCGGTTCTCTGAAGTCCGAAG
29018 T
1 T
29019 TCCTAAACAG
Statistics
Matches: 184, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 27 0.15
186 157 0.85
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (184 bp):
TGAAACATCTTAGAAACACAACTCGGTGAGCATATCGTCATAACATGCTGATTTCCTCATTAGTC
TAAAGTCATATTAGGAAGATTTTATCGAAAAAAAGAAGGCATATTAGGAAGGTATCGACTTTTCT
TTATTTAAATATTTGGGAAACCAAAGAGAGATATCGGTTCTCTGAAGTCCGAAG
Found at i:47541 original size:99 final size:101
Alignment explanation
Indices: 47401--47589 Score: 319
Period size: 102 Copynumber: 1.9 Consensus size: 101
47391 TGGCTGAACC
*
47401 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGATGC-T-ATTGTCAATGATTCTCTGGCAGA
1 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCATCATTGTCAATGATTCTCTGGCAGA
*
47464 ATTATCCGAGCAACCGGCAGCGAACATAATGCGACA
66 ATTATCCGAGCAACCAGCAGCGAACATAATGCGACA
*
47500 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCTATCATTGTCAATGATTCTTTGGCAG
1 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGC-ATCATTGTCAATGATTCTCTGGCAG
*
47565 AGTTATCCGAGCAACCAGCAGCGAA
65 AATTATCCGAGCAACCAGCAGCGAA
47590 GAGGATGCGG
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
99 38 0.46
101 1 0.01
102 44 0.53
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (101 bp):
ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCATCATTGTCAATGATTCTCTGGCAGA
ATTATCCGAGCAACCAGCAGCGAACATAATGCGACA
Found at i:51098 original size:33 final size:33
Alignment explanation
Indices: 51056--51121 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
51046 AAGAGCCTCG
51056 CTTCAGCGAATGAGCTCGCTGAGGTTGAAGGTA
1 CTTCAGCGAATGAGCTCGCTGAGGTTGAAGGTA
51089 CTTCAGCGAATGAGCTCGCTGAGGTTGAAGGTA
1 CTTCAGCGAATGAGCTCGCTGAGGTTGAAGGTA
51122 AGGCTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (33 bp):
CTTCAGCGAATGAGCTCGCTGAGGTTGAAGGTA
Found at i:64691 original size:69 final size:68
Alignment explanation
Indices: 64526--64897 Score: 280
Period size: 69 Copynumber: 5.4 Consensus size: 68
64516 TGTTCCTCTA
* * * * * * *
64526 AAGGCTCGTTTATTTCATATCGTAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCCAACTGTCA
1 AAGGCTCGTTAATTTCATATCGCAACCTTCAACACAGTTAACGAGAGCAAAGCT-CCAGCTGTCA
* *
64591 TATA
65 CATT
* * * ** * * * *
64595 AAGGTTCG-CAAGTGAAGAGTCGTAACCTTCAACACAGTTAGCGAGAGTAAAGCTCTCAGCTGTC
1 AAGGCTCGTTAATTTCATA-TCGCAACCTTCAACACAGTTAACGAGAGCAAAGCTC-CAGCTGTC
*
64659 ATATT
64 ACATT
* * ** * * * *
64664 AAGGCTCTTTGATTTCATATCGCAACCTTCAACATGGTTAGCGAAAGCAAAGCTCCCAGTTATCA
1 AAGGCTCGTTAATTTCATATCGCAACCTTCAACACAGTTAACGAGAGCAAAGCT-CCAGCTGTCA
64729 CATT
65 CATT
* * * * **
64733 GAGGCTCATTAATTTCATATCGCAGCC-TCTAACACAGTTAACAAGAGCAAAGCTCCAAATTGTC
1 AAGGCTCGTTAATTTCATATCGCAACCTTC-AACACAGTTAACGAGAGCAAAGCTCC-AGCTGTC
64797 ACATT
64 ACATT
* * * * * * * * *
64802 AAGGTTCGCTGATTTCATATCGTAGCCTCCAATATAGTTAATGAGAGCAAAGCTCACAGCTGTCA
1 AAGGCTCGTTAATTTCATATCGCAACCTTCAACACAGTTAACGAGAGCAAAGCTC-CAGCTGTCA
64867 CATT
65 CATT
*
64871 AAGGCTCGTTAATTTCATATTGCAACC
1 AAGGCTCGTTAATTTCATATCGCAACC
64898 AGGTGTCATA
Statistics
Matches: 236, Mismatches: 59, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
68 9 0.04
69 220 0.93
70 7 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (68 bp):
AAGGCTCGTTAATTTCATATCGCAACCTTCAACACAGTTAACGAGAGCAAAGCTCCAGCTGTCAC
ATT
Found at i:64785 original size:138 final size:138
Alignment explanation
Indices: 64625--64890 Score: 318
Period size: 138 Copynumber: 1.9 Consensus size: 138
64615 CGTAACCTTC
* * * * * **
64625 AACACAGTTAGCGAGAGTAAAGCTCTC-AGCTGTCATATTAAGGCTCTTTGATTTCATATCGCAA
1 AACACAGTTAACAAGAGCAAAGCTC-CAAACTGTCACATTAAGGCTCGCTGATTTCATATCGCAA
* * * * * *
64689 CCTTCAACATGGTTAGCGAAAGCAAAGCTCCCAGTTATCACATTGAGGCTCATTAATTTCATATC
65 CCTCCAACATAGTTAACGAAAGCAAAGCTCACAGCTATCACATTAAGGCTCATTAATTTCATATC
64754 GCAGCCTCT
130 GCAGCCTCT
* * * *
64763 AACACAGTTAACAAGAGCAAAGCTCCAAATTGTCACATTAAGGTTCGCTGATTTCATATCGTAGC
1 AACACAGTTAACAAGAGCAAAGCTCCAAACTGTCACATTAAGGCTCGCTGATTTCATATCGCAAC
* * * * *
64828 CTCCAATATAGTTAATGAGAGCAAAGCTCACAGCTGTCACATTAAGGCTCGTTAATTTCATAT
66 CTCCAACATAGTTAACGAAAGCAAAGCTCACAGCTATCACATTAAGGCTCATTAATTTCATAT
64891 TGCAACCAGG
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
137 1 0.01
138 104 0.99
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (138 bp):
AACACAGTTAACAAGAGCAAAGCTCCAAACTGTCACATTAAGGCTCGCTGATTTCATATCGCAAC
CTCCAACATAGTTAACGAAAGCAAAGCTCACAGCTATCACATTAAGGCTCATTAATTTCATATCG
CAGCCTCT
Found at i:64982 original size:108 final size:108
Alignment explanation
Indices: 64793--64998 Score: 277
Period size: 108 Copynumber: 1.9 Consensus size: 108
64783 AGCTCCAAAT
* * * * * **
64793 TGTCACATTAAGGTTCGCTGATTTCATATCGTAGCCTCCAATATAGTTAATGAGAGCAAAGCTCA
1 TGTCACATTAAAGCTCGCTGATTTCATATCGAAGCCTCCAACACAGTTAACAAGAGCAAAGCTCA
* *
64858 CAGCTGTCACATTAAGGCTCGTTAATTTCATATTGCAACCAGG
66 CAACTGTCACATTAAGGCTCATTAATTTCATATTGCAACCAGG
* * * * *
64901 TGTCATATTAAAGCTCGTTGATTTCATATTGAAGCCTCTAACACAGTTAACAAGAGCAAAGCTCC
1 TGTCACATTAAAGCTCGCTGATTTCATATCGAAGCCTCCAACACAGTTAACAAGAGCAAAGCTCA
*
64966 CAACTGTCACATTAAGGCTCATTGATTTCATAT
66 CAACTGTCACATTAAGGCTCATTAATTTCATAT
64999 CGTAGCCTCC
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 83 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (108 bp):
TGTCACATTAAAGCTCGCTGATTTCATATCGAAGCCTCCAACACAGTTAACAAGAGCAAAGCTCA
CAACTGTCACATTAAGGCTCATTAATTTCATATTGCAACCAGG
Found at i:65026 original size:69 final size:69
Alignment explanation
Indices: 64901--65043 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 69
64891 TGCAACCAGG
* * * * *
64901 TGTCATATTAAAGCTCGTTGATTTCATATTGAAGCCTCTAACACAGTTAACAAGAGCAAAGCTCC
1 TGTCACATTAAAGCTCATTGATTTCATATCGAAGCCTCCAACACAATTAACAAGAGCAAAGCTCC
*
64966 CAAC
66 AAAC
* * * * *
64970 TGTCACATTAAGGCTCATTGATTTCATATCGTAGCCTCCAACATAATTAGCGAGAGCAAAGCTCC
1 TGTCACATTAAAGCTCATTGATTTCATATCGAAGCCTCCAACACAATTAACAAGAGCAAAGCTCC
65035 AAAC
66 AAAC
65039 TGTCA
1 TGTCA
65044 TATTGAGGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (69 bp):
TGTCACATTAAAGCTCATTGATTTCATATCGAAGCCTCCAACACAATTAACAAGAGCAAAGCTCC
AAAC
Found at i:65077 original size:69 final size:68
Alignment explanation
Indices: 65004--65469 Score: 398
Period size: 69 Copynumber: 6.8 Consensus size: 68
64994 CATATCGTAG
* * * * * *
65004 CCTCCAACATAATTAGCGAGAGCAAAGCTCCAAACTGTCATATTGAGGTTCGCAGGCAAAGAGTC
1 CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGTAGGCGAAGAG-C
65069 GCAA
65 GCAA
* * ** *
65073 CCTCCAACACTA-TTAGCAAGAGCAAAGCTCCTAGTTGTCATATTAAAGTTCGTAGGCGAAGAGC
1 CCTCCAACAC-AGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGTAGGCGAAGAGC
65137 TGCAA
65 -GCAA
* * * * * *
65142 CCTGCAACATAGTTAGTGAGAGCAAAGCT-CCAGGCTGTCATATTAAGGTTCGTAGGCAAAAAGC
1 CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCA-ACTGTCATATTAAGGTTCGTAGGCGAAGAG-
65206 CGCAA
64 CGCAA
* * * *
65211 CCTCCAACACAGTTAGCGAGAGTAAAGATCCCAACTATCATATTAAGGCTT-GCAGGCGAAGAGC
1 CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGG-TTCGTAGGCGAAGAGC
* *
65275 TGTAG
65 -GCAA
* * **
65280 CCTCTAACACAGTTAGAGAGAGCAAAGCTCCCAACTGTCATATTAAGACTCGTAGGCGAAGAGCC
1 CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGTAGGCGAAGAG-C
*
65345 ACAA
65 GCAA
* ** * * * * * * *
65349 CCTCCAACACATTTAAATGAGTGTAAAGCTCCCAACTGTCATATTAAGGCTCATAGGTGAAAATC
1 CCTCCAACACAGTT-AGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGTAGGCGAAGAGC
*
65414 GCAG
65 GCAA
* * * * * * * **
65418 CGTTCAACACAGTTAGCAATAGCCAAGCCCCCATCAATCATATTAAGGTTCG
1 CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCG
65470 CACGTCCAAA
Statistics
Matches: 316, Mismatches: 70, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
68 31 0.10
69 237 0.75
70 48 0.15
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (68 bp):
CCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGTAGGCGAAGAGCG
CAA
Found at i:65097 original size:246 final size:246
Alignment explanation
Indices: 64655--65102 Score: 528
Period size: 246 Copynumber: 1.8 Consensus size: 246
64645 AGCTCTCAGC
* * ** *
64655 TGTCATATTAAGGCTCTTTGATTTCATATCGCAACCTTCAACATGGTTAGCGAAAGCAAAGCTCC
1 TGTCATATTAAAGCTCGTTGATTTCATATCGCAACCTTCAACACAGTTAACGAAAGCAAAGCTCC
** * * *
64720 CAGTTATCACATTGAGGCTCATTAATTTCATATCGCAGCCTCTAACACAGTTAACAAGAGCAAAG
66 CAACTATCACATTAAGGCTCATTAATTTCATATCGCAGCCTCCAACACAATTAACAAGAGCAAAG
* * **** * * * * **
64785 CTCCAAATTGTCACATTAAGGTTCGCTGATTTCATATCGTAGCCTCCAATATAGTTAATGAGAGC
131 CTCCAAACTGTCACATTAAGGTTCGCAGAGCAAAGATCGCAACCTCCAACATAGTTAACAAGAGC
64850 AAAGCTCACAGCTGTCACATTAAGGCTCGTTAATTTCATATTGCAACCAGG
196 AAAGCTCACAGCTGTCACATTAAGGCTCGTTAATTTCATATTGCAACCAGG
*
64901 TGTCATATTAAAGCTCGTTGATTTCATATTG-AAGCC-TCTAACACAGTTAAC-AAGAGCAAAGC
1 TGTCATATTAAAGCTCGTTGATTTCATATCGCAA-CCTTC-AACACAGTTAACGAA-AGCAAAGC
* * * * * *
64963 TCCCAACTGTCACATTAAGGCTCATTGATTTCATATCGTAGCCTCCAACATAATTAGCGAGAGCA
63 TCCCAACTATCACATTAAGGCTCATTAATTTCATATCGCAGCCTCCAACACAATTAACAAGAGCA
* * *
65028 AAGCTCCAAACTGTCATATTGAGGTTCGCAG-GCAAAGAGTCGCAACCTCCAACACTA-TTAGCA
128 AAGCTCCAAACTGTCACATTAAGGTTCGCAGAGCAAAGA-TCGCAACCTCCAACA-TAGTTAACA
65091 AGAGCAAAGCTC
191 AGAGCAAAGCTC
65103 CTAGTTGTCA
Statistics
Matches: 165, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
245 8 0.05
246 155 0.94
247 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (246 bp):
TGTCATATTAAAGCTCGTTGATTTCATATCGCAACCTTCAACACAGTTAACGAAAGCAAAGCTCC
CAACTATCACATTAAGGCTCATTAATTTCATATCGCAGCCTCCAACACAATTAACAAGAGCAAAG
CTCCAAACTGTCACATTAAGGTTCGCAGAGCAAAGATCGCAACCTCCAACATAGTTAACAAGAGC
AAAGCTCACAGCTGTCACATTAAGGCTCGTTAATTTCATATTGCAACCAGG
Found at i:65428 original size:207 final size:206
Alignment explanation
Indices: 64935--65471 Score: 501
Period size: 207 Copynumber: 2.6 Consensus size: 206
64925 CATATTGAAG
* ** * * * ** *
64935 CCTCTAACACAGTTAACAAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCATTGATTTCATATC
1 CCTCCAACACAGTTAATGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCATAG-GTAAAAATC
* * * * * *
65000 GTAGCCTCCAACATAATTAGCGAGAGCAAAGCTCCAAACTGTCATATTGAGGTTCGCAGGCAAAG
65 GCAGCCTCCAACACAGTTAGCGAGAGCAAAGATCCAAACTATCATATTAAGGTTCGCAGGCAAAG
* ** *
65065 AGTCGCAACCTCCAACACTATTAGCAAGAGCAAAGCTCCTAGTTGTCATATTAAAGTTCGTAGGC
130 AGTCGCAACCTCCAACACTATTAGCAAGAGCAAAGCTCCCAACTGTCATATTAAAGCTCGTAGGC
**
65130 GAAGAGCTGCAA
195 GAAGAGCCACAA
* * * * * * * *
65142 CCTGCAACATAGTTAGTGAGAGCAAAGCT-CCAGGCTGTCATATTAAGGTTCGTAGGCAAAAAGC
1 CCTCCAACACAGTTAATGAGAGCAAAGCTCCCA-ACTGTCATATTAAGGCTCATAGGTAAAAA-T
* * * *
65206 CGCAACCTCCAACACAGTTAGCGAGAGTAAAGATCCCAACTATCATATTAAGGCTT-GCAGGCGA
64 CGCAGCCTCCAACACAGTTAGCGAGAGCAAAGATCCAAACTATCATATTAAGG-TTCGCAGGCAA
* * *
65270 AGAG-CTGTAGCCTCTAACAC-AGTTAG-AGAGAGCAAAGCTCCCAACTGTCATATT-AAGACTC
128 AGAGTC-GCAACCTCCAACACTA-TTAGCA-AGAGCAAAGCTCCCAACTGTCATATTAAAG-CTC
65331 GTAGGCGAAGAGCCACAA
189 GTAGGCGAAGAGCCACAA
* * * *
65349 CCTCCAACACATTTAAATGAGTGTAAAGCTCCCAACTGTCATATTAAGGCTCATAGGTGAAAATC
1 CCTCCAACACAGTT-AATGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCATAGGTAAAAATC
* * * * * ** * * *
65414 GCAGCGTTCAACACAGTTAGCAATAGCCAAGCCCCCATCAATCATATTAAGGTTCGCA
65 GCAGCCTCCAACACAGTTAGCGAGAGCAAAGATCCAAACTATCATATTAAGGTTCGCA
65472 CGTCCAAACA
Statistics
Matches: 261, Mismatches: 59, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
206 13 0.05
207 207 0.79
208 38 0.15
209 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (206 bp):
CCTCCAACACAGTTAATGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCATAGGTAAAAATCG
CAGCCTCCAACACAGTTAGCGAGAGCAAAGATCCAAACTATCATATTAAGGTTCGCAGGCAAAGA
GTCGCAACCTCCAACACTATTAGCAAGAGCAAAGCTCCCAACTGTCATATTAAAGCTCGTAGGCG
AAGAGCCACAA
Found at i:65795 original size:19 final size:21
Alignment explanation
Indices: 65771--65810 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
65761 GACCTCATTC
65771 TCCCTCC-CTTCA-CTCTCTT
1 TCCCTCCACTTCAGCTCTCTT
65790 TCCCTCCTACTTCAGCTCTCT
1 TCCCTCC-ACTTCAGCTCTCT
65811 CTTCTCCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.07, C:0.50, G:0.03, T:0.40
Consensus pattern (21 bp):
TCCCTCCACTTCAGCTCTCTT
Found at i:66009 original size:3 final size:3
Alignment explanation
Indices: 66003--66040 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
65993 TATTATCAAC
66003 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
66041 GTAAAACACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.