Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011473.1 Kokia drynarioides strain JFW-HI SEQ_126457, 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: 65489
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7270 original size:10 final size:9
Alignment explanation
Indices: 7248--7296 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 9
7238 TGAGCCAACT
7248 GCATCAGCAA
1 GCATCAGC-A
7258 GCATCTAGCA
1 GCATC-AGCA
7268 GCATCAGGCA
1 GCATCA-GCA
*
7278 ACATCGAGCA
1 GCATC-AGCA
7288 GCATCAGCA
1 GCATCAGCA
7297 AGAAGTTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 5 0.15
10 25 0.74
11 4 0.12
ACGTcount: A:0.35, C:0.31, G:0.22, T:0.12
Consensus pattern (9 bp):
GCATCAGCA
Found at i:7273 original size:20 final size:20
Alignment explanation
Indices: 7248--7298 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
7238 TGAGCCAACT
*
7248 GCATCAGCAAGCATCTAGCA
1 GCATCAGCAAGCATCGAGCA
7268 GCATCAGGCAA-CATCGAGCA
1 GCATCA-GCAAGCATCGAGCA
7288 GCATCAGCAAG
1 GCATCAGCAAG
7299 AAGTTGGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 20 0.71
21 4 0.14
ACGTcount: A:0.35, C:0.29, G:0.24, T:0.12
Consensus pattern (20 bp):
GCATCAGCAAGCATCGAGCA
Found at i:11799 original size:10 final size:10
Alignment explanation
Indices: 11767--11799 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
11757 TGAGCCAATT
11767 GCATCAGCAA
1 GCATCAGCAA
11777 GCATCGAGC-A
1 GCATC-AGCAA
11787 GCATCAGCAA
1 GCATCAGCAA
11797 GCA
1 GCA
11800 ATTGGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.14
10 15 0.71
11 3 0.14
ACGTcount: A:0.36, C:0.30, G:0.24, T:0.09
Consensus pattern (10 bp):
GCATCAGCAA
Found at i:20487 original size:23 final size:23
Alignment explanation
Indices: 20456--20509 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
20446 TGTCCATCCT
*
20456 TGCTTACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
20479 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
20502 TGCTGACT
1 TGCTGACT
20510 GGATGTCACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:28831 original size:23 final size:23
Alignment explanation
Indices: 28777--28833 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
28767 CGTCCATCCT
*
28777 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
28800 TGCTGACTGGACCTTTTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
28823 TGCTGACTGGA
1 TGCTGACTGGA
28834 TGCCACGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:34871 original size:22 final size:22
Alignment explanation
Indices: 34846--34889 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34836 CCCTTTCAAA
34846 AAAATATAAAATATAATGCAAT
1 AAAATATAAAATATAATGCAAT
* *
34868 AAAATATAAACTATAATTCAAT
1 AAAATATAAAATATAATGCAAT
34890 GAATTTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATATAAAATATAATGCAAT
Found at i:35807 original size:9 final size:10
Alignment explanation
Indices: 35786--35810 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35776 TATTAATGAA
35786 TTTAAATATT
1 TTTAAATATT
35796 TTTAAATATT
1 TTTAAATATT
35806 TTTAA
1 TTTAA
35811 CTGTACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTAAATATT
Found at i:36933 original size:3 final size:3
Alignment explanation
Indices: 36925--36975 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
36915 ATAGCCATTG
* * * * *
36925 AAT AAT AAT AAC AAT AAC AAC AAC AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36973 AAT
1 AAT
36976 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:40219 original size:148 final size:147
Alignment explanation
Indices: 39950--40243 Score: 561
Period size: 148 Copynumber: 2.0 Consensus size: 147
39940 CTCCACCATC
39950 GACAGCGTCCGACCGTCGAGATTACACACGTAATTTCACTCCAAATCGAAGCCACAACACAAATC
1 GACAGCGTCCGACCGTCGAGATTACACACGTAATTTCACTCCAAATCGAAGCCACAACACAAATC
*
40015 AAAGCTCACCTTCACAAAAATCAGCCAATCGAATGGCGGAAGGAACAACGTTGCAAGCCGAAAGC
66 AAAGCTCACCTTCACAAAAATCAGCCAATCGAATGGCGGAAGGAACAACGTCGCAAGCCGAAAGC
40080 TTAACTCACAATTTGCNT
131 TTAACTCACAATTTGC-T
*
40098 GACAGCGTCCGACCGTCGAGATTACACACGTAATTTCACTCCAAATCGAAGGCACAACACAAATC
1 GACAGCGTCCGACCGTCGAGATTACACACGTAATTTCACTCCAAATCGAAGCCACAACACAAATC
40163 AAAGCTCACCTTCACAAAAATCAGCCAATCGAATGGCGGAAGGAACAACGTCGCAAGCCGAAAGC
66 AAAGCTCACCTTCACAAAAATCAGCCAATCGAATGGCGGAAGGAACAACGTCGCAAGCCGAAAGC
40228 TTAACTCACAATTTGC
131 TTAACTCACAATTTGC
40244 ACAAATGAGG
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 144 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (147 bp):
GACAGCGTCCGACCGTCGAGATTACACACGTAATTTCACTCCAAATCGAAGCCACAACACAAATC
AAAGCTCACCTTCACAAAAATCAGCCAATCGAATGGCGGAAGGAACAACGTCGCAAGCCGAAAGC
TTAACTCACAATTTGCT
Found at i:44920 original size:28 final size:27
Alignment explanation
Indices: 44888--44963 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
44878 ATACGAAGTT
*
44888 AAAAATGCAATTTTTGGATACCCGAGGG
1 AAAAATGTAATTTTTGGATACCCGA-GG
* * *
44916 TAAAATGATAATTTTTGGACACTCGAGG
1 AAAAATG-TAATTTTTGGATACCCGAGG
44944 AAAAATGGTAATTTTTGGAT
1 AAAAAT-GTAATTTTTGGAT
44964 GTTCGGGGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (27 bp):
AAAAATGTAATTTTTGGATACCCGAGG
Found at i:44976 original size:28 final size:28
Alignment explanation
Indices: 44896--45072 Score: 153
Period size: 28 Copynumber: 6.2 Consensus size: 28
44886 TTAAAAATGC
** *
44896 AATTTTTGGATACCCGAGGGTAAAATGAT
1 AATTTTTGGATATTCG-GGGTAAAATGGT
* * * *
44925 AATTTTTGGACACTCGAGGAAAAATGGT
1 AATTTTTGGATATTCGGGGTAAAATGGT
*
44953 AATTTTTGGATGTTCGGGGTAAAATGGT
1 AATTTTTGGATATTCGGGGTAAAATGGT
*
44981 AA-TTTTGGATGTTCAGGGGT-AAATGGT
1 AATTTTTGGATATTC-GGGGTAAAATGGT
* * * *
45008 AATTTTTCGAAAATTTGAGGTCAAAAT-GT
1 AATTTTT-GGATATTCGGGGT-AAAATGGT
* *
45037 AATTTTTGGACATTTGGGGGTAAAATGGT
1 AATTTTTGGATA-TTCGGGGTAAAATGGT
45066 AATTTTT
1 AATTTTT
45073 TTGAAAATTA
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
27 21 0.17
28 55 0.45
29 42 0.34
30 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (28 bp):
AATTTTTGGATATTCGGGGTAAAATGGT
Found at i:45040 original size:29 final size:29
Alignment explanation
Indices: 45001--45258 Score: 184
Period size: 29 Copynumber: 8.8 Consensus size: 29
44991 GTTCAGGGGT
* *
45001 AAATGGTAATTTTTCGAAAATTTGAGGTCA
1 AAAT-GTAATTTTTGGAAAATTTAAGGTCA
* **
45031 AAATGTAATTTTTGG-ACATTTGGGGGT-A
1 AAATGTAATTTTTGGAAAATTT-AAGGTCA
*
45059 AAATGGTAATTTTTTTGAAAA-TTAAGTGTCA
1 AAAT-GTAA-TTTTTGGAAAATTTAAG-GTCA
* * **
45090 AAATGTAATTTTGGGAAAGTTTGGGGTCA
1 AAATGTAATTTTTGGAAAATTTAAGGTCA
*
45119 AAATGTAGTTTTTGGAAAATTTAAGGATCA
1 AAATGTAATTTTTGGAAAATTTAAGG-TCA
* * * **
45149 AAATATAATTTCTAGAAAGCTTAAGGGTCA
1 AAATGTAATTTTTGGAAAATTTAA-GGTCA
* * *
45179 AAATATAATTTTTGGAAAGTAT-AGGATCA
1 AAATGTAATTTTTGGAAAATTTAAGG-TCA
* * *
45208 AAATGTAATTTTT-GAAAGTTTAGGGTTA
1 AAATGTAATTTTTGGAAAATTTAAGGTCA
* * *
45236 AAACGTGATTTTTAGAAAATTTA
1 AAATGTAATTTTTGGAAAATTTA
45259 GGGACCTTCT
Statistics
Matches: 182, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
28 32 0.18
29 78 0.43
30 63 0.35
31 9 0.05
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (29 bp):
AAATGTAATTTTTGGAAAATTTAAGGTCA
Found at i:45092 original size:59 final size:58
Alignment explanation
Indices: 44996--45258 Score: 202
Period size: 59 Copynumber: 4.5 Consensus size: 58
44986 TGGATGTTCA
* * *
44996 GGGGT-AAATGGTAATTTTTCGAAAATTTGAGGTCAAAATGTAATTTTTGGACA-TTT
1 GGGGTAAAATGGTAATTTTTCGAAAATTTAAGGTCAAAATGTAATTTTGGGAAAGTTT
*
45052 GGGGGTAAAATGGTAATTTTTTTGAAAA-TTAAGTGTCAAAATGTAATTTTGGGAAAGTTT
1 -GGGGTAAAATGGTAA-TTTTTCGAAAATTTAAG-GTCAAAATGTAATTTTGGGAAAGTTT
* * * * *
45112 GGGGTCAAAAT-GTAGTTTTTGGAAAATTTAAGGATCAAAATATAATTTCT-AGAAAGCTTA
1 GGGGT-AAAATGGTAATTTTTCGAAAATTTAAGG-TCAAAATGTAATTT-TGGGAAAG-TTT
* * * * * *
45172 AGGGTCAAAAT-ATAATTTTTGGAAAGTAT-AGGATCAAAATGTAATTTT-TGAAAGTTT
1 GGGGT-AAAATGGTAATTTTTCGAAAATTTAAGG-TCAAAATGTAATTTTGGGAAAGTTT
* * * *
45229 AGGGTTAAAA-CGTGATTTTTAGAAAATTTA
1 -GGGGTAAAATGGTAATTTTTCGAAAATTTA
45259 GGGACCTTCT
Statistics
Matches: 170, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
57 24 0.14
58 33 0.19
59 78 0.46
60 35 0.21
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTCGAAAATTTAAGGTCAAAATGTAATTTTGGGAAAGTTT
Found at i:47025 original size:17 final size:17
Alignment explanation
Indices: 46972--47082 Score: 132
Period size: 17 Copynumber: 6.5 Consensus size: 17
46962 GACTTTTATT
*
46972 AATTTAAACTTAGAATA
1 AATTTAAACTTAAAATA
* * *
46989 ATTTTTAATTTAAAAATA
1 AATTTAAACTT-AAAATA
*
47007 AATTTAAACTTAAATTA
1 AATTTAAACTTAAAATA
* *
47024 AATTTAAATTTAAAACA
1 AATTTAAACTTAAAATA
*
47041 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
*
47058 AATTTAATCTTAAAATA
1 AATTTAAACTTAAAATA
47075 AATTTAAA
1 AATTTAAA
47083 AAAGTGGGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 65 0.83
18 13 0.17
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:47030 original size:11 final size:11
Alignment explanation
Indices: 46995--47082 Score: 63
Period size: 11 Copynumber: 7.7 Consensus size: 11
46985 AATAATTTTT
*
46995 AATTTAAAAATA
1 AATTT-AAATTA
47007 AATTTAAACTTA
1 AATTTAAA-TTA
47019 AA-TTAAATTTA
1 AATTTAAA-TTA
**
47030 AATTTAAAACA
1 AATTTAAATTA
47041 AATTTAAATTTA
1 AATTTAAA-TTA
* *
47053 AA-ATAAATTT
1 AATTTAAATTA
*
47063 AATCTTAAAATA
1 AAT-TTAAATTA
47075 AATTTAAA
1 AATTTAAA
47083 AAAGTGGGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
10 4 0.07
11 31 0.52
12 25 0.42
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:47674 original size:37 final size:37
Alignment explanation
Indices: 47614--47713 Score: 164
Period size: 37 Copynumber: 2.7 Consensus size: 37
47604 CATTACTTGT
* *
47614 TTTGATCCACTTCTCTGTATCTCATCAGGAAGTCGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
*
47651 TTTGGTCCATTTCTCTGTATCTCATCAGGAAGGCGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
*
47688 TTTGGTCCACTTCTTTGTATCTCATC
1 TTTGGTCCACTTCTCTGTATCTCATC
47714 CGAAAGACAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (37 bp):
TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
Found at i:47902 original size:249 final size:246
Alignment explanation
Indices: 47445--47931 Score: 706
Period size: 249 Copynumber: 2.0 Consensus size: 246
47435 TTCATCTCTC
* * * *
47445 GGTCTACTTCTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTTAACCTGCTTCTCTGTAT
1 GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTAT
* * *
47510 CTCATCAGGAAGCTGAGATTCGAAGTTTCGCTCATATTGAGCTTGGTTTCATTGATTTGGTCTAC
66 CTCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTCTAC
* * * *
47575 TTCTCAGTATCTCATCAGGAAGATGACTGCATTACTTGTTTTGATCCACTTCTCTGTATCTCATC
131 TTCTCAGTATCTCATCAGAAACATGACTGCATCACTTGTTTTGATCCACTTCTCTATATCTCATC
* * * *
47640 AGGAAGTCGGATTTGGTCCATTTCTCTGTATCTCATCAGGAAGGCGGATTT
196 AGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAGGCGGATTT
* * * * *
47691 GGTCCACTTCTTTGTATCTCATCCGAAAGACAACCGCTTTATTGCTTCGACCTGCTTCTCAGTAT
1 GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTA-
* * *
47756 CTCATCATCAAGAAGCTGGGATTCGAAGTTTCACTCATATTGAGCTTTGTTTTATTGATTAGGTC
65 -TC-TCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTC
*
47821 TACTTCTCAGTATCTCATTAGAAACATGA-TCGCATCACTTGTTTTGATCCACTTCTCTATATCT
128 TACTTCTCAGTATCTCATCAGAAACATGACT-GCATCACTTGTTTTGATCCACTTCTCTATATCT
*
47885 CATTAGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAG
192 CATCAGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAG
47932 ACGACCGCTT
Statistics
Matches: 212, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
246 55 0.26
248 3 0.01
249 154 0.73
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (246 bp):
GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTAT
CTCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTCTAC
TTCTCAGTATCTCATCAGAAACATGACTGCATCACTTGTTTTGATCCACTTCTCTATATCTCATC
AGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAGGCGGATTT
Found at i:47922 original size:37 final size:37
Alignment explanation
Indices: 47863--47934 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
47853 CATCACTTGT
* * *
47863 TTTGATCCACTTCTCTATATCTCATTAGGAAGACGGA
1 TTTGATCCACTTCTCTACATCTCATCAAGAAGACGGA
* *
47900 TTTGGTCCACTTCTCTGCATCTCATCAAGAAGACG
1 TTTGATCCACTTCTCTACATCTCATCAAGAAGACG
47935 ACCGCTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (37 bp):
TTTGATCCACTTCTCTACATCTCATCAAGAAGACGGA
Found at i:56250 original size:24 final size:24
Alignment explanation
Indices: 56223--56269 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
56213 AATATGCAAA
** *
56223 TATGCAATGTGAATAAAATGCATG
1 TATGCAATGCAAAAAAAATGCATG
*
56247 TATGTAATGCAAAAAAAATGCAT
1 TATGCAATGCAAAAAAAATGCAT
56270 TGATTTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (24 bp):
TATGCAATGCAAAAAAAATGCATG
Found at i:60263 original size:29 final size:29
Alignment explanation
Indices: 60231--60422 Score: 126
Period size: 29 Copynumber: 6.7 Consensus size: 29
60221 TGGATGCCCG
60231 AGGGTAAAATGGTAATTTTTAGATGTTCA
1 AGGGTAAAATGGTAATTTTTAGATGTTCA
*** * *
60260 AGGGTAAAACAATAATTTTGGACACT-TT-A
1 AGGGTAAAATGGTAATTTT-TAGA-TGTTCA
* * **
60289 GGGGCAAAATGGTAATTTTTAGACACTT--
1 AGGGTAAAATGGTAATTTTTAGA-TGTTCA
* * **
60317 GGGGAAAAATGGTAATTTTCGGATGTTCA
1 AGGGTAAAATGGTAATTTTTAGATGTTCA
* * * *
60346 GGGGTAAAACGGTAA-TTTTGGATGTTTA
1 AGGGTAAAATGGTAATTTTTAGATGTTCA
**
60374 AGGGTAAAAAAT-GTAATTTTTAGACATTCA
1 AGGGT--AAAATGGTAATTTTTAGATGTTCA
60404 AGGGTAAAATGGTAATTTT
1 AGGGTAAAATGGTAATTTT
60423 GGAAAATTTA
Statistics
Matches: 126, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
27 2 0.02
28 43 0.34
29 58 0.46
30 22 0.17
31 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTAGATGTTCA
Found at i:60326 original size:28 final size:30
Alignment explanation
Indices: 60275--60335 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
60265 AAAACAATAA
* *
60275 TTTTGGACACTTTAGGGGCAAAATGGTAAT
1 TTTTAGACACTTTAGGGGAAAAATGGTAAT
60305 TTTTAGACAC-TT-GGGGAAAAATGGTAAT
1 TTTTAGACACTTTAGGGGAAAAATGGTAAT
60333 TTT
1 TTT
60336 CGGATGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.62
29 2 0.07
30 9 0.31
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTTAGACACTTTAGGGGAAAAATGGTAAT
Found at i:60390 original size:86 final size:86
Alignment explanation
Indices: 60231--60422 Score: 219
Period size: 86 Copynumber: 2.2 Consensus size: 86
60221 TGGATGCCCG
* * **
60231 AGGGTAAAATGGTAATTTTTAGATGTTCAAGGGTAAAACAATAATTTTGGACACTTTAGGGGCAA
1 AGGGAAAAATGGTAATTTTCAGATGTTCAAGGGTAAAACAATAATTTTGGACACTTTAGGGAAAA
60296 AATGGTAATTTTTAGACACTT-
66 AATGGTAATTTTTAGACA-TTA
* * * ** **
60317 GGGGAAAAATGGTAATTTTCGGATGTTCAGGGGTAAAACGGTAATTTTGGA-TGTTTAAGGGTAA
1 AGGGAAAAATGGTAATTTTCAGATGTTCAAGGGTAAAACAATAATTTTGGACACTTT-AGGG-AA
60381 AAAAT-GTAATTTTTAGACATTCA
64 AAAATGGTAATTTTTAGACATT-A
*
60404 AGGGTAAAATGGTAATTTT
1 AGGGAAAAATGGTAATTTT
60423 GGAAAATTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 5 0.06
86 62 0.70
87 22 0.25
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (86 bp):
AGGGAAAAATGGTAATTTTCAGATGTTCAAGGGTAAAACAATAATTTTGGACACTTTAGGGAAAA
AATGGTAATTTTTAGACATTA
Found at i:60409 original size:58 final size:57
Alignment explanation
Indices: 60342--60511 Score: 155
Period size: 59 Copynumber: 2.9 Consensus size: 57
60332 TTTTCGGATG
* **
60342 TTCAGGGGTAAAACGGTAATTTTGG-ATGTTTAAGGGTAAAAAATGTAATTTTTAGACA
1 TTCAAGGGTAAAACGGTAATTTTGGAAAATTTAAGGGT-AAAAATGT-ATTTTTAGACA
* * * *
60400 TTCAAGGGTAAAATGGTAATTTTGGAAAATTTAAGGGTTAAAATGTATTTTTGGGAAA
1 TTCAAGGGTAAAACGGTAATTTTGGAAAATTTAAGGGTAAAAATGTATTTTT-AGACA
* * * * * *
60458 GTTTAAGGGTCAAAA-TGTAGTTTTTGAAAATTTAAGGGTCAAAATATAATTTTT
1 -TTCAAGGGT-AAAACGGTAATTTTGGAAAATTTAAGGGTAAAAATGT-ATTTTT
60512 GGAAAGCTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.06
58 33 0.35
59 45 0.48
60 10 0.11
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (57 bp):
TTCAAGGGTAAAACGGTAATTTTGGAAAATTTAAGGGTAAAAATGTATTTTTAGACA
Found at i:60487 original size:59 final size:58
Alignment explanation
Indices: 60370--60608 Score: 223
Period size: 59 Copynumber: 4.0 Consensus size: 58
60360 ATTTTGGATG
* * * * * *
60370 TTTAAGGGTAAAAAATGTAATTTTTAGACA-TTCAAGGGTAAAATGGTAATTTTGGAAAA
1 TTTAAGGGT-TAAAATATAATTTTTGGAAAGTTTAAGGGTAAAAT-GTAATTTTTGAAAA
* *
60429 TTTAAGGGTTAAAATGT-ATTTTTGGGAAAGTTTAAGGGTCAAAATGTAGTTTTTGAAAA
1 TTTAAGGGTTAAAATATAATTTTT-GGAAAGTTTAAGGGT-AAAATGTAATTTTTGAAAA
* * * * *
60488 TTTAAGGGTCAAAATATAATTTTTGGAAAGCTTAGGGGGTTAAAATATAATTTTTGGAAAG
1 TTTAAGGGTTAAAATATAATTTTTGGAAAGTTTA-AGGG-TAAAATGTAATTTTT-GAAAA
* * * * *
60549 TTTGAGGGTTAAAATATAATTTTT-AAAAGTTTAAGGTTAAAACGTGATTTTTGGAAAA
1 TTTAAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTAAAATGTAATTTTT-GAAAA
60607 TT
1 TT
60609 CATGGACCTT
Statistics
Matches: 150, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
57 6 0.04
58 29 0.19
59 55 0.37
60 33 0.22
61 27 0.18
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (58 bp):
TTTAAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTAAAATGTAATTTTTGAAAA
Found at i:60536 original size:31 final size:30
Alignment explanation
Indices: 60361--60605 Score: 209
Period size: 30 Copynumber: 8.3 Consensus size: 30
60351 AAAACGGTAA
* * *
60361 TTTTGG-ATGTTTAAGGGTAAAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGT-TAAAATATAAT
* * * *
60391 TTTTAGACA-TTCAAGGG-TAAAATGGTAA-
1 TTTTGGAAAGTTTAAGGGTTAAAAT-ATAAT
* *
60419 TTTTGGAAAATTTAAGGGTTAAAATGT-AT
1 TTTTGGAAAGTTTAAGGGTTAAAATATAAT
* * *
60448 TTTTGGGAAAGTTTAAGGGTCAAAATGTAGT
1 TTTT-GGAAAGTTTAAGGGTTAAAATATAAT
* *
60479 TTTT-GAAAATTTAAGGGTCAAAATATAAT
1 TTTTGGAAAGTTTAAGGGTTAAAATATAAT
* *
60508 TTTTGGAAAGCTTAGGGGGTTAAAATATAAT
1 TTTTGGAAAGTTTA-AGGGTTAAAATATAAT
*
60539 TTTTGGAAAGTTTGAGGGTTAAAATATAAT
1 TTTTGGAAAGTTTAAGGGTTAAAATATAAT
* ** *
60569 TTTT-AAAAGTTTAA-GGTTAAAACGTGAT
1 TTTTGGAAAGTTTAAGGGTTAAAATATAAT
60597 TTTTGGAAA
1 TTTTGGAAA
60606 ATTCATGGAC
Statistics
Matches: 178, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
28 28 0.16
29 54 0.30
30 65 0.37
31 31 0.17
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAGTTTAAGGGTTAAAATATAAT
Found at i:61685 original size:27 final size:23
Alignment explanation
Indices: 61630--61677 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
61620 GACCCTTTTT
*
61630 TTATTAATTATTATTATTATTAA
1 TTATTAATTATTATTAATATTAA
*
61653 TTATTATTTATTTATTAATATTAA
1 TTATTAATTA-TTATTAATATTAA
61677 T
1 T
61678 ATACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTAATTATTATTAATATTAA
Found at i:62361 original size:17 final size:17
Alignment explanation
Indices: 62308--62418 Score: 132
Period size: 17 Copynumber: 6.5 Consensus size: 17
62298 GACTTTTATT
*
62308 AATTTAAACTTAGAATA
1 AATTTAAACTTAAAATA
* * *
62325 ATTTTTAATTTAAAAATA
1 AATTTAAACTT-AAAATA
*
62343 AATTTAAACTTAAATTA
1 AATTTAAACTTAAAATA
* *
62360 AATTTAAATTTAAAACA
1 AATTTAAACTTAAAATA
*
62377 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
*
62394 AATTTAATCTTAAAATA
1 AATTTAAACTTAAAATA
62411 AATTTAAA
1 AATTTAAA
62419 AAAGTGGGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 65 0.83
18 13 0.17
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:62366 original size:11 final size:11
Alignment explanation
Indices: 62331--62418 Score: 63
Period size: 11 Copynumber: 7.7 Consensus size: 11
62321 AATAATTTTT
*
62331 AATTTAAAAATA
1 AATTT-AAATTA
62343 AATTTAAACTTA
1 AATTTAAA-TTA
62355 AA-TTAAATTTA
1 AATTTAAA-TTA
**
62366 AATTTAAAACA
1 AATTTAAATTA
62377 AATTTAAATTTA
1 AATTTAAA-TTA
* *
62389 AA-ATAAATTT
1 AATTTAAATTA
*
62399 AATCTTAAAATA
1 AAT-TTAAATTA
62411 AATTTAAA
1 AATTTAAA
62419 AAAGTGGGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
10 4 0.07
11 31 0.52
12 25 0.42
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:63010 original size:37 final size:37
Alignment explanation
Indices: 62950--63049 Score: 164
Period size: 37 Copynumber: 2.7 Consensus size: 37
62940 CATTACTTGT
* *
62950 TTTGATCCACTTCTCTGTATCTCATCAGGAAGTCGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
*
62987 TTTGGTCCATTTCTCTGTATCTCATCAGGAAGGCGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
*
63024 TTTGGTCCACTTCTTTGTATCTCATC
1 TTTGGTCCACTTCTCTGTATCTCATC
63050 CGAAAGACAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (37 bp):
TTTGGTCCACTTCTCTGTATCTCATCAGGAAGGCGGA
Found at i:63238 original size:249 final size:246
Alignment explanation
Indices: 62781--63267 Score: 706
Period size: 249 Copynumber: 2.0 Consensus size: 246
62771 TTCATCTCTC
* * * *
62781 GGTCTACTTCTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTTAACCTGCTTCTCTGTAT
1 GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTAT
* * *
62846 CTCATCAGGAAGCTGAGATTCGAAGTTTCGCTCATATTGAGCTTGGTTTCATTGATTTGGTCTAC
66 CTCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTCTAC
* * * *
62911 TTCTCAGTATCTCATCAGGAAGATGACTGCATTACTTGTTTTGATCCACTTCTCTGTATCTCATC
131 TTCTCAGTATCTCATCAGAAACATGACTGCATCACTTGTTTTGATCCACTTCTCTATATCTCATC
* * * *
62976 AGGAAGTCGGATTTGGTCCATTTCTCTGTATCTCATCAGGAAGGCGGATTT
196 AGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAGGCGGATTT
* * * * *
63027 GGTCCACTTCTTTGTATCTCATCCGAAAGACAACCGCTTTATTGCTTCGACCTGCTTCTCAGTAT
1 GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTA-
* * *
63092 CTCATCATCAAGAAGCTGGGATTCGAAGTTTCACTCATATTGAGCTTTGTTTTATTGATTAGGTC
65 -TC-TCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTC
*
63157 TACTTCTCAGTATCTCATTAGAAACATGA-TCGCATCACTTGTTTTGATCCACTTCTCTATATCT
128 TACTTCTCAGTATCTCATCAGAAACATGACT-GCATCACTTGTTTTGATCCACTTCTCTATATCT
*
63221 CATTAGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAG
192 CATCAGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAG
63268 ACGACCGCTT
Statistics
Matches: 212, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
246 55 0.26
248 3 0.01
249 154 0.73
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (246 bp):
GGTCCACTTCTCTATATCTCATCAGAAAGACAACCACTTTATTGCTTCAACCTGCTTCTCAGTAT
CTCATCAAGAAGCTGAGATTCGAAGTTTCACTCATATTGAGCTTGGTTTCATTGATTAGGTCTAC
TTCTCAGTATCTCATCAGAAACATGACTGCATCACTTGTTTTGATCCACTTCTCTATATCTCATC
AGGAAGACGGATTTGGTCCACTTCTCTGCATCTCATCAAGAAGGCGGATTT
Found at i:63258 original size:37 final size:37
Alignment explanation
Indices: 63199--63270 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
63189 CATCACTTGT
* * *
63199 TTTGATCCACTTCTCTATATCTCATTAGGAAGACGGA
1 TTTGATCCACTTCTCTACATCTCATCAAGAAGACGGA
* *
63236 TTTGGTCCACTTCTCTGCATCTCATCAAGAAGACG
1 TTTGATCCACTTCTCTACATCTCATCAAGAAGACG
63271 ACCGCTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (37 bp):
TTTGATCCACTTCTCTACATCTCATCAAGAAGACGGA
Done.