Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001972.1 Kokia drynarioides strain JFW-HI SEQ_113816, 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: 88283
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:5663 original size:52 final size:52
Alignment explanation
Indices: 5579--5812 Score: 258
Period size: 52 Copynumber: 4.5 Consensus size: 52
5569 CACTTCATTT
* * ** * *
5579 ATATACTCACGATGATACATAACCACCGGACC-TTATAATCCATAAGGGATTC
1 ATATACTCACGATGACACTTAGTCATCGGACCATT-TAATCCATAAAGGATTC
* * ** * * *
5631 GTATACTCACAATGACACAGAGTCATCGGACC-TCTTAATTCGTATAA-GATCC
1 ATATACTCACGATGACACTTAGTCATCGGACCAT-TTAATCCATA-AAGGATTC
*
5683 ATATACTCACGATAACACTTAGTCATCGGACCATTTAATCCATAAAGGATTC
1 ATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCATAAAGGATTC
* * *
5735 ATATACTCAGGATGACACTTAGTCATTGGACCATTTAATCCATAAAGGATTT
1 ATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCATAAAGGATTC
*
5787 GTATACTCACGATGACACTTAGTCAT
1 ATATACTCACGATGACACTTAGTCAT
5813 TGAACCTCTT
Statistics
Matches: 153, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
51 2 0.01
52 148 0.97
53 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATATACTCACGATGACACTTAGTCATCGGACCATTTAATCCATAAAGGATTC
Found at i:12767 original size:52 final size:52
Alignment explanation
Indices: 12696--12939 Score: 294
Period size: 52 Copynumber: 4.7 Consensus size: 52
12686 ATTTCACTTC
* * *
12696 ATTCATATACTCACGATGACACATAGCCATCGAACC-TTATAATCCGTAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCATT-TAATCCGTAAAGG
* * ** * * * *
12748 ATTCATATACTAACAATGACACAAAGTCATCGGACCACTTAATCCATAAATG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCATTTAATCCGTAAAGG
* * * *
12800 ATCCATATACTCACGATGACACTTAATCATC-AGACCGTTTAATCCGTATAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGA-ACCATTTAATCCGTAAAGG
* * *
12852 ATTCATATACTCATGATGACACTTAGTCATCAAACCATTTAATCCGTAAATG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCATTTAATCCGTAAAGG
12904 ATTCATATACTCACGATGACACTTAGTCATCGAACC
1 ATTCATATACTCACGATGACACTTAGTCATCGAACC
12940 TCTTCGTTTA
Statistics
Matches: 160, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
52 158 0.99
53 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGAACCATTTAATCCGTAAAGG
Found at i:21113 original size:24 final size:24
Alignment explanation
Indices: 21081--21131 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
21071 TAATTCAATC
* *
21081 AATATAAAATATATTATGCTAATA
1 AATACAAAATATATTATACTAATA
*
21105 AATACAAAATATATTATACTATTA
1 AATACAAAATATATTATACTAATA
21129 AAT
1 AAT
21132 TTTCTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AATACAAAATATATTATACTAATA
Found at i:23612 original size:20 final size:20
Alignment explanation
Indices: 23587--23626 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
23577 ACACATAAGA
23587 AAATAAATTGCTATATATAT
1 AAATAAATTGCTATATATAT
23607 AAATAAATTGCTATATATAT
1 AAATAAATTGCTATATATAT
23627 TATACTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
AAATAAATTGCTATATATAT
Found at i:33322 original size:15 final size:15
Alignment explanation
Indices: 33304--33358 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 15
33294 TATAACTTGA
33304 GGAGCTGGTTTGGGT
1 GGAGCTGGTTTGGGT
33319 GGAGCTGGTGGTTTGGGT
1 GGAGC---TGGTTTGGGT
33337 -G-G-TGGTTTGGGT
1 GGAGCTGGTTTGGGT
*
33349 GGTGCTGGTT
1 GGAGCTGGTT
33359 CTTTCGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 10 0.29
13 1 0.03
14 1 0.03
15 10 0.29
16 1 0.03
17 1 0.03
18 10 0.29
ACGTcount: A:0.04, C:0.05, G:0.55, T:0.36
Consensus pattern (15 bp):
GGAGCTGGTTTGGGT
Found at i:33341 original size:12 final size:12
Alignment explanation
Indices: 33324--33352 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33314 TGGGTGGAGC
33324 TGGTGGTTTGGG
1 TGGTGGTTTGGG
33336 TGGTGGTTTGGG
1 TGGTGGTTTGGG
33348 TGGTG
1 TGGTG
33353 CTGGTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (12 bp):
TGGTGGTTTGGG
Found at i:34053 original size:13 final size:13
Alignment explanation
Indices: 34035--34059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34025 CATTATGCTT
34035 TAAAAGAAGTCAC
1 TAAAAGAAGTCAC
34048 TAAAAGAAGTCA
1 TAAAAGAAGTCA
34060 AATCTCTCTC
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:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
TAAAAGAAGTCAC
Found at i:34444 original size:27 final size:28
Alignment explanation
Indices: 34396--34449 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
34386 GTCACCTCAA
*
34396 CAAACAATTCAAAAATTATAAATATATT
1 CAAACAAATCAAAAATTATAAATATATT
* *
34424 CAAACAAAT-AAAATTTTTAAATATAT
1 CAAACAAATCAAAAATTATAAATATAT
34450 ATAAATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (28 bp):
CAAACAAATCAAAAATTATAAATATATT
Found at i:35571 original size:9 final size:10
Alignment explanation
Indices: 35541--35582 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
35531 TTAATTAAAT
35541 AAATTATTAA
1 AAATTATTAA
*
35551 AAATCCATT-A
1 AAAT-TATTAA
35561 AAATTATTAA
1 AAATTATTAA
35571 AAATTA-TAA
1 AAATTATTAA
35580 AAA
1 AAA
35583 CGATTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 9 0.32
10 16 0.57
11 3 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATTATTAA
Found at i:35945 original size:21 final size:20
Alignment explanation
Indices: 35921--35959 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35911 ATCTAGAACA
*
35921 TTTTATTAGTTAAATTTGAAT
1 TTTTATTA-TAAAATTTGAAT
*
35942 TTTTTTTATAAAATTTGA
1 TTTTATTATAAAATTTGA
35960 GGATGAGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTATTATAAAATTTGAAT
Found at i:36301 original size:2 final size:2
Alignment explanation
Indices: 36294--36326 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36284 TTGGTACAAT
36294 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 T
36327 GAAATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37922 original size:20 final size:21
Alignment explanation
Indices: 37899--37938 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37889 AAAAATATTG
*
37899 TTTAT-TTTGAATCGATTGTT
1 TTTATGTTTAAATCGATTGTT
*
37919 TTTATGTTTAAATCTATTGT
1 TTTATGTTTAAATCGATTGT
37939 CATATTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTATGTTTAAATCGATTGTT
Found at i:37968 original size:55 final size:56
Alignment explanation
Indices: 37903--38015 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 56
37893 ATATTGTTTA
* * * *
37903 TTTTGAATCGATTGTTTTTATG-TTTAAATCTATTGTCATATTGGAATACTGCTTC
1 TTTTGAATCGATTGTTTCTATGTTTTAAAACGATTGTCATAGTGGAATACTGCTTC
* * *
37958 TTTTGAATCGATTGTTTCTATGTTTTAAAACGATTTTTATGGTGGAATACTGCTTC
1 TTTTGAATCGATTGTTTCTATGTTTTAAAACGATTGTCATAGTGGAATACTGCTTC
38014 TT
1 TT
38016 CTTCTTTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 21 0.42
56 29 0.58
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.50
Consensus pattern (56 bp):
TTTTGAATCGATTGTTTCTATGTTTTAAAACGATTGTCATAGTGGAATACTGCTTC
Found at i:48890 original size:15 final size:16
Alignment explanation
Indices: 48872--48901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48862 TTTCCCTATT
48872 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
48887 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
48902 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:48894 original size:22 final size:22
Alignment explanation
Indices: 48867--48927 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
48857 TTCGATTTCC
48867 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
48889 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
48911 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
48928 CTTCATATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:48917 original size:21 final size:22
Alignment explanation
Indices: 48881--48927 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
48871 TTTCTATTTC
*
48881 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
48903 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
48924 TTTT
1 TTTT
48928 CTTCATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:65844 original size:18 final size:18
Alignment explanation
Indices: 65821--65863 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
65811 TTTTTAGTTG
65821 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
65839 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
65857 TAATTAA
1 TAATTAA
65864 AAAATCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:67342 original size:40 final size:39
Alignment explanation
Indices: 67240--67355 Score: 124
Period size: 40 Copynumber: 2.8 Consensus size: 39
67230 TTTGGACAGA
* **
67240 AAACGCCGCAAAAAGTAAATCAATAGCGGCGTTTTTTTTCAT
1 AAACGCCGC-AAAAGTAAAGCAATAGCGGCG--TTTTCCCAT
**
67282 AAACATCGCAAAAGGTAAAGCAATAGCGGCGTTTTCCCAT
1 AAACGCCGCAAAA-GTAAAGCAATAGCGGCGTTTTCCCAT
* *
67322 AAACGCCGCAACAAGCAAAGCAATAGCAGCGTTT
1 AAACGCCGCAA-AAGTAAAGCAATAGCGGCGTTT
67356 ATGGGTAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 34 0.54
41 6 0.10
42 23 0.37
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAAAAGTAAAGCAATAGCGGCGTTTTCCCAT
Found at i:67407 original size:41 final size:41
Alignment explanation
Indices: 67239--67548 Score: 236
Period size: 41 Copynumber: 7.5 Consensus size: 41
67229 GTTTGGACAG
* * * * **
67239 AAAACGCCGCAAAAAGTAA-ATCAATAGCGGCGTTTTTTTTC
1 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCG-TTTATGAC
** * **
67280 ATAAACATCGCAAAAGGTAA-AGCAATAGCGGCGTTT-TCCC
1 A-AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAC
* * * **
67320 ATAAACGCCGCAACAA-GCAA-AGCAATAGCAGCGTTTATGGGT
1 A-AAACGCCGCAA-AAGGTAAGAGCATTAGCGGCGTTTAT-GAC
* * * *
67362 AAAACGCCGTAAAATGTAAGAGCATCAGTGGCGTTTATGAC
1 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAC
* * *
67403 AAAACACCGCAAAAGGTAAGAGCATTAGCGGGGTGTATGAC
1 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAC
*
67444 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTT-TCGAG
1 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTAT-GAC
** * * *
67485 AAAACGATGCAAAAGGTCAGAGCATTAGCGGCGTTCATGAG
1 AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAC
*
67526 AAATACGCCGCTAAAGGTTAAGA
1 AAA-ACGCCGCAAAAGG-TAAGA
67549 AATAATGGCA
Statistics
Matches: 219, Mismatches: 40, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
40 34 0.16
41 128 0.58
42 53 0.24
43 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAC
Found at i:68553 original size:21 final size:22
Alignment explanation
Indices: 68507--68559 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
68497 ATCCTAAAGC
* *
68507 TATACATGAATATGTGTAATTT
1 TATACATGAATATGTGCAATTG
68529 TATACATGTAAT-T-TGCAATTG
1 TATACATG-AATATGTGCAATTG
68550 TATACATGAA
1 TATACATGAA
68560 CTTTGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 14 0.50
22 9 0.32
23 3 0.11
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (22 bp):
TATACATGAATATGTGCAATTG
Found at i:74812 original size:50 final size:47
Alignment explanation
Indices: 74745--75060 Score: 203
Period size: 50 Copynumber: 6.4 Consensus size: 47
74735 AACATGAAAG
*
74745 GAAAGATTTAAGCCGCAACGGCGAATCCAATACCACAAAGATAATGGA
1 GAAAGATTTAAGCCGCAACGGCGAA-CCAGTACCACAAAGATAATGGA
* * * * *
74793 GAAAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCATGAA-GG-
1 G--AAAGATTTAAGCCGCAACGGCGAACC-AGTACCACA-AAG-AT-AATGGA
* * *
74844 GAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATAGAGG
1 GAAAGATTTAAGCCGCAACGGCGAA-CCAGTACCACAAAGATAAT-G-GA
* * * * * *
74894 GAAAGGTTTAAGTCGTAACGACGAACCTCGTACCTCAGAAGCATGAA-GG-
1 GAAAGATTTAAGCCGCAACGGCGAACC-AGTACCACA-AAG-AT-AATGGA
*
74943 GAAAGATTTAAGCCGCAACGGCGAACCCAGTACCACGAAGATAATGGA
1 GAAAGATTTAAGCCGCAACGGCGAA-CCAGTACCACAAAGATAATGGA
* * * * *
74991 GGGAAAGGTTTAAGTCGCAACGACGAACCTCGTACCTCAGAAGCATGAA--GA
1 --GAAAGATTTAAGCCGCAACGGCGAACC-AGTACCACA-AAG-AT-AATGGA
*
75042 GAAATATTTAAGCCGCAAC
1 GAAAGATTTAAGCCGCAAC
75061 AACGAATCTA
Statistics
Matches: 207, Mismatches: 37, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
46 4 0.02
47 6 0.03
48 8 0.04
49 76 0.37
50 86 0.42
51 13 0.06
52 8 0.04
53 6 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (47 bp):
GAAAGATTTAAGCCGCAACGGCGAACCAGTACCACAAAGATAATGGA
Found at i:74908 original size:99 final size:99
Alignment explanation
Indices: 74737--75060 Score: 531
Period size: 99 Copynumber: 3.3 Consensus size: 99
74727 ACCATGAAAA
* * **
74737 CATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACAAAGATAATGGAGAAAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATGGAGGGAAAGGT
** *
74802 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAAG
66 TTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
*
74836 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATAGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATGGAGGGAAAGGT
*
74901 TTAAGTCGTAACGACGAACCTCGTACCTCAGAAG
66 TTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
* *
74935 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCCAGTACCACGAAGATAATGGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATGGAGGGAAAGGT
75000 TTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
66 TTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
* *
75034 CATGAAGAGAAATATTTAAGCCGCAAC
1 CATGAAGGGAAAGATTTAAGCCGCAAC
75061 AACGAATCTA
Statistics
Matches: 210, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 210 1.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (99 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATAATGGAGGGAAAGGT
TTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
Found at i:75066 original size:49 final size:49
Alignment explanation
Indices: 74737--75110 Score: 257
Period size: 49 Copynumber: 7.6 Consensus size: 49
74727 ACCATGAAAA
* * ** *
74737 CATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCACA-AAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTCGTACCTCAGAAG
* * ** *
74785 -AT-AATGGAGAAAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAG
1 CATGAA-GG-G--AAAGATTTAAGCCGCAACGACGAACCTCGTACCTCAGAAG
* ** *
74836 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTCGTACCTCAGAAG
* * * *
74884 -ATAATAGAGGGAAAGGTTTAAGTCGTAACGACGAACCTCGTACCTCAGAAG
1 CAT--GA-AGGGAAAGATTTAAGCCGCAACGACGAACCTCGTACCTCAGAAG
* *
74935 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACC-CAGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTC-GTACCTCAGAAG
* * * *
74983 ATAATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
1 --CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTCGTACCTCAGAAG
* * * * * *
75034 CATGAAGAGAAATATTTAAGCCGCAACAACGAATCTAGTA-AT-ACGAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTCGTACCTCA-GAAG
* *
75082 ACATAAAGGGAAAGATTGAAGCCGCAACG
1 -CATGAAGGGAAAGATTTAAGCCGCAACG
75111 GCAAATCTTA
Statistics
Matches: 256, Mismatches: 48, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
46 2 0.01
47 6 0.02
48 15 0.06
49 117 0.46
50 95 0.37
51 13 0.05
52 6 0.02
53 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTCGTACCTCAGAAG
Found at i:75772 original size:22 final size:22
Alignment explanation
Indices: 75746--75787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
75736 CGTCAGCATC
75746 GCCACATCAGCACCACATCATT
1 GCCACATCAGCACCACATCATT
* *
75768 GCCACGTCATCACCACATCA
1 GCCACATCAGCACCACATCA
75788 ACCATGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.43, G:0.10, T:0.17
Consensus pattern (22 bp):
GCCACATCAGCACCACATCATT
Found at i:79767 original size:64 final size:59
Alignment explanation
Indices: 79652--79771 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
79642 ATCACTTTAA
* * *
79652 TATTAAATTAATATAATAGTTATCAAGATAAATATTAGATTAAATTTAATATTAAACAT
1 TATTAAATTAATAGAATAGTTATCAAAATAAATATTAGAATAAATTTAATATTAAACAT
*
79711 TATTAAATTAATAGAATATTTATCTACAAAATAAATATTA-AATAACCACTTTAATATTAAA
1 TATTAAATTAATAGAATAGTTA--T-CAAAATAAATATTAGAATAA--A-TTTAATATTAAA
79772 TTAATAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
59 20 0.39
61 5 0.10
62 13 0.25
63 1 0.02
64 12 0.24
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (59 bp):
TATTAAATTAATAGAATAGTTATCAAAATAAATATTAGAATAAATTTAATATTAAACAT
Done.