Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011824.1 Kokia drynarioides strain JFW-HI SEQ_126819, 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: 32891
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:12437 original size:11 final size:11
Alignment explanation
Indices: 12397--12441 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
12387 AAAACTAGGT
12397 TTTTTTTAT-A
1 TTTTTTTATAA
*
12407 TATTTTTA-AA
1 TTTTTTTATAA
12417 TATTTTTTATAA
1 T-TTTTTTATAA
12429 TTTTTTTATAA
1 TTTTTTTATAA
12440 TT
1 TT
12442 ATCTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.30
11 18 0.60
12 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:13505 original size:31 final size:31
Alignment explanation
Indices: 13470--13528 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
13460 CGAATTTCGA
13470 AGTTGAATTATATATTGTCATGTATTGCCGG
1 AGTTGAATTATATATTGTCATGTATTGCCGG
13501 AGTTGAATTATATATTGTCATGTATTGC
1 AGTTGAATTATATATTGTCATGTATTGC
13529 AGCAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.44
Consensus pattern (31 bp):
AGTTGAATTATATATTGTCATGTATTGCCGG
Found at i:14071 original size:34 final size:34
Alignment explanation
Indices: 14033--14108 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
14023 CCAAGTAAGC
* *
14033 AATATTTGGGTAAGGTAAAAGGTAAAAAATTAAA
1 AATATTTGGGTAAGATAAAAGGTAAAAAATAAAA
*
14067 AATATTTGGGTAAGATATAAGGTAAAAAATAAAA
1 AATATTTGGGTAAGATAAAAGGTAAAAAATAAAA
14101 AATATTTG
1 AATATTTG
14109 AGTTTAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (34 bp):
AATATTTGGGTAAGATAAAAGGTAAAAAATAAAA
Found at i:14269 original size:9 final size:9
Alignment explanation
Indices: 14257--14286 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
14247 TTTATTCAGT
14257 TTATTCGAA
1 TTATTCGAA
*
14266 TTATTCGAG
1 TTATTCGAA
14275 TTATTCGAA
1 TTATTCGAA
14284 TTA
1 TTA
14287 GAAAATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:14271 original size:18 final size:18
Alignment explanation
Indices: 14248--14286 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
14238 TAATATAGTT
14248 TTATTC-AGTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
14266 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
14284 TTA
1 TTA
14287 GAAAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:14677 original size:22 final size:21
Alignment explanation
Indices: 14635--14677 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
14625 TCTTATATCT
*
14635 GTAAATTTAATTTGTTGTGTA
1 GTAAATTTAATATGTTGTGTA
14656 GTAATATTTAATAATGTT-TGTA
1 GTAA-ATTTAAT-ATGTTGTGTA
14678 TTTTCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
GTAAATTTAATATGTTGTGTA
Found at i:14882 original size:6 final size:6
Alignment explanation
Indices: 14871--14900 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
14861 GGCCCTTTTT
14871 AATTTA AATTTA AATTT- AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
14901 TTCCAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:14890 original size:17 final size:17
Alignment explanation
Indices: 14868--14900 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
14858 CTGGGCCCTT
14868 TTTAATTTAAATTTAAA
1 TTTAATTTAAATTTAAA
14885 TTTAATTTAAATTTAA
1 TTTAATTTAAATTTAA
14901 TTCCAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATTTAAA
Found at i:14891 original size:11 final size:11
Alignment explanation
Indices: 14871--14902 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
14861 GGCCCTTTTT
14871 AATTTAAATTTA
1 AATTT-AATTTA
14883 AATTTAATTTA
1 AATTTAATTTA
14894 AATTTAATT
1 AATTTAATT
14903 CCAAAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:16636 original size:29 final size:29
Alignment explanation
Indices: 16598--16890 Score: 269
Period size: 29 Copynumber: 10.1 Consensus size: 29
16588 AGGCTCCCTA
* *
16598 AACTTTCAAAAATTCAATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
16627 AACTTCCAAAAATACAAATTTTGACCC-CG
1 AACTTCCAAAAATTC-CATTTTTACCCTCG
* *
16656 AAGCTTCCAAAAATTCCAATTTTACCCCCG
1 AA-CTTCCAAAAATTCCATTTTTACCCTCG
*
16686 AAGCTTCCAAAAATTCCA-TTTTACCCCCG
1 AA-CTTCCAAAAATTCCATTTTTACCCTCG
* *
16715 AACTTCCAAAAATCCCATTTTTGACCC-AG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
16744 AAACTTCCAAAAATTCCA-TTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
16773 AACTTCCAAAAATCCCATTTTTAGCCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* **
16802 AACTTCC-AAAATTCCATTTTTGACACTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
16831 AACTTTCAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATT-CCATTTTTACCCTCG
* *
16860 AA-TGTCCAAAAACTCAATTTTCTA-CCTCG
1 AACT-TCCAAAAATTCCATTTT-TACCCTCG
16889 AA
1 AA
16891 ACTCTCAAAA
Statistics
Matches: 222, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
28 50 0.23
29 95 0.43
30 74 0.33
31 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:16938 original size:58 final size:59
Alignment explanation
Indices: 16830--16948 Score: 134
Period size: 58 Copynumber: 2.0 Consensus size: 59
16820 TTTGACACTA
*
16830 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCAATTTTCT-ACCTCG
1 AAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCAATTTT-TAACCTCG
* ** ** ** *
16889 AAACTCTCAAAAA-TACCCTTTTACCCCTTAATGTTTAAAATTTCCATTTTTAACCTCG
1 AAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCAATTTTTAACCTCG
16947 AA
1 AA
16949 TTTTCCCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
57 1 0.02
58 37 0.74
59 12 0.24
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
AAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCAATTTTTAACCTCG
Found at i:20792 original size:17 final size:17
Alignment explanation
Indices: 20765--20797 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20755 TTTTAAGTCA
20765 TTTAATTGAAT-ATTTT
1 TTTAATTGAATCATTTT
20781 TTTAACTTGAATCATTT
1 TTTAA-TTGAATCATTT
20798 AAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTAATTGAATCATTTT
Found at i:21688 original size:142 final size:142
Alignment explanation
Indices: 21432--21716 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
21422 ATACATAACC
*
21432 CACTTCGGCTCTTCTTATCTCGTAGGGCAAAACCAAAACACCCTACTTTCTCCTTCGCTATCCTC
1 CACTTCGGCTCTTCTTATCTCGTAGGGCAAAACCAAAACACCCTACTTTCTCCTTCACTATCCTC
21497 CATTCCCCAGTGGCATCCCACTCTGCTTTGCCCTCTTTCACTATCGAATCCCTTATAGCTAGCTA
66 CATTCCCCAGTGGCATCCCACTCTGCTTTGCCCTCTTTCACTATCGAATCCCTTATAGCTAGCTA
21562 ATCTCTACTCCA
131 ATCTCTACTCCA
21574 CACTTCGGCTCTTCTTATCTCGTAGGGCAAAACCAAAACACCCTACTTTCTCCTTCACTATCCTC
1 CACTTCGGCTCTTCTTATCTCGTAGGGCAAAACCAAAACACCCTACTTTCTCCTTCACTATCCTC
21639 CATTCCCCAGTGGCATCCCACTCTGCTTTGCCCTCTTTCACTATCGAATCCCTTATAGCTAGCTA
66 CATTCCCCAGTGGCATCCCACTCTGCTTTGCCCTCTTTCACTATCGAATCCCTTATAGCTAGCTA
*
21704 ATCTCTCCTCCA
131 ATCTCTACTCCA
21716 C
1 C
21717 CCTCACTTTC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.20, C:0.38, G:0.10, T:0.32
Consensus pattern (142 bp):
CACTTCGGCTCTTCTTATCTCGTAGGGCAAAACCAAAACACCCTACTTTCTCCTTCACTATCCTC
CATTCCCCAGTGGCATCCCACTCTGCTTTGCCCTCTTTCACTATCGAATCCCTTATAGCTAGCTA
ATCTCTACTCCA
Found at i:27784 original size:9 final size:9
Alignment explanation
Indices: 27772--27796 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27762 TGAAAATTTT
27772 TCGAGTTAA
1 TCGAGTTAA
27781 TCGAGTTAA
1 TCGAGTTAA
27790 TCGAGTT
1 TCGAGTT
27797 GACGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (9 bp):
TCGAGTTAA
Found at i:30100 original size:11 final size:11
Alignment explanation
Indices: 30086--30156 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
30076 GACCTTTTTT
*
30086 AATTTATTTTA
1 AATTTAATTTA
*
30097 AATTTGATTTA
1 AATTTAATTTA
30108 AATTTAAATTTA
1 AATTT-AATTTA
*
30120 AA-TTGATATTA
1 AATTTAAT-TTA
* *
30131 AATTTAAATTG
1 AATTTAATTTA
30142 AATTTAATTTA
1 AATTTAATTTA
30153 AATT
1 AATT
30157 AAAAATTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 2 0.04
11 36 0.75
12 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:30114 original size:6 final size:6
Alignment explanation
Indices: 30093--30156 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
30083 TTTAATTTAT
* * *
30093 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA TTGATA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
30139 -TTGAA TTT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
30157 AAAAATTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 16 0.34
6 31 0.66
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:30115 original size:17 final size:17
Alignment explanation
Indices: 30093--30156 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
30083 TTTAATTTAT
* * *
30093 TTTAAATTTGATTTAAA
1 TTTAAATTTAAATTGAA
30110 TTTAAATTTAAATTG-A
1 TTTAAATTTAAATTGAA
30126 TATTAAATTTAAATTGAA
1 T-TTAAATTTAAATTGAA
30144 TTT-AATTTAAATT
1 TTTAAATTTAAATT
30157 AAAAATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 12 0.29
17 28 0.67
18 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTGAA
Found at i:31299 original size:206 final size:206
Alignment explanation
Indices: 30663--31619 Score: 1178
Period size: 206 Copynumber: 4.7 Consensus size: 206
30653 AGCAGATTGG
* *
30663 AGCAATAAACGGTTAACTTCCT-GATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGA
1 AGCAATAAACGGTTAGCTT-CTAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGA
* * * * ** *
30727 GATACAGAGAA-GCGAGTTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAG
65 GATACAGAGAAGGGGA-TTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAG
** * * * *
30791 ACCCAAA-C--G---AGGCTCAAAACGAG-CAAATCTTCGAACCCCAGCTTCATGATGAGACACC
129 A-CCAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATAAGACACC
30849 GAGAAGCAGGTCGA
193 GAGAAGCAGGTCGA
* * * *
30863 AGCAGTAAACGGTTAGCTT-TCAGATGATATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGA
1 AGCAATAAACGGTTAGCTTCT-AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGA
* *
30927 GATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCCGATGAGATACT--G-AGAAGA
65 GATACAGAGAAGGGGATTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGA
* * * *
30989 CCAAATCAAGCTCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGTTTCCTGATGAGACACCGA
130 CCAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATAAGACACCGA
31054 GAAGCAGGTCGA
195 GAAGCAGGTCGA
* ** *
31066 AGCAGTAAACAATTAGCTTCCAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAG
1 AGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAG
31131 ATACAGAGAAGGGGATTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGAC
66 ATACAGAGAAGGGGATTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGAC
*
31196 CAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAACTTCCTGATAAGACACCGAG
131 CAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATAAGACACCGAG
31261 AAGCAGGTCGA
196 AAGCAGGTCGA
*
31272 AGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAG
1 AGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAG
* * * * *
31337 ATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGGTACTGAGGAGAAGAC
66 ATACAGAGAAGGGGATTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGAC
* * * * * * * * *
31402 CAAACCAAACCCACACAC-GA-TGAAT-AAACCTTCGAACCCCAGCTTCCTGATAAGATACTGAG
131 CAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATAAGACACCGAG
*
31464 AAGTAGGTCGA
196 AAGCAGGTCGA
* * * *
31475 AGTAATAAAACGGATAGCTCCCT-GATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATG
1 AGCAAT-AAACGGTTAGCT-TCTAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATG
* * * * * *
31539 AGATGCAGAGAAACGGG-TTGAAACAAACGACGTGGTCATC-TCCCTGATGAGACACTGAGAAGA
64 AGATACAGAG-AAGGGGATTGAAACAAGCGATGCGGTCATCTTCCC-GATGAGATACTGAGAAGA
* * *
31602 AGTCCAAATTAAACCCAC
127 AGACCAAATCAAGCCCAC
31620 GCGCGATGAA
Statistics
Matches: 668, Mismatches: 71, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
196 5 0.01
197 7 0.01
198 2 0.00
199 1 0.00
200 98 0.15
201 2 0.00
202 12 0.02
203 206 0.31
204 114 0.17
205 8 0.01
206 213 0.32
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (206 bp):
AGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAG
ATACAGAGAAGGGGATTGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGAC
CAAATCAAGCCCACACTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATAAGACACCGAG
AAGCAGGTCGA
Found at i:31438 original size:409 final size:408
Alignment explanation
Indices: 30679--31619 Score: 1253
Period size: 409 Copynumber: 2.3 Consensus size: 408
30669 AAACGGTTAA
* *
30679 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAGT
1 CTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGGGA-T
* ** **
30744 TGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAA-C--G---AGG
65 TGAAACAAACGACGCGGTCATCTTCCCGATGAGACACTGAGAAGAAGA-CCAAATCAAGCCCACA
* * * *
30803 CTCAAAACGAGCAAATCTTCGAACCCCAGCTTCATGATGAGACACCGAGAAGCAGGTCGAAGCAG
129 CTCAAAACGAGAAAATCTTCGAACCCCAACTTCATGATAAGACACCGAGAAGCAGGTCGAAGCAA
*
30868 TAAACGGTTAGCTTTCAGATGATATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGAGATACA
194 TAAACGGTTAGCTTTCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGAGATACA
*
30933 GAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCCGATGAGATACTGAGAAGACCAAATCAA
259 GAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCCGATGAGATACTGAGAAGACCAAACCAA
* * * * * * * *
30998 GCTCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGTTTCCTGATGAGACACCGAGAAGCAGGT
324 ACCCACACACAAAGCGAATAAAACCTTCGAACCCCAGCTTCCTGATAAGACACCGAGAAGCAGGT
*
31063 CGAAGCAGT-AAAC-AATTAG
389 CGAAGCAATAAAACGAA-TAG
*
31082 CTTCCAGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGGGGAT
1 CTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAA-GGGAT
* * *
31147 TGAAACAAGCGATGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACAC
65 TGAAACAAACGACGCGGTCATCTTCCCGATGAGACACTGAGAAGAAGACCAAATCAAGCCCACAC
* *
31212 TCAAAGCGAGTAAAATCTTCGAACCCCAACTTCCTGATAAGACACCGAGAAGCAGGTCGAAGCAA
130 TCAAAACGAG-AAAATCTTCGAACCCCAACTTCATGATAAGACACCGAGAAGCAGGTCGAAGCAA
* * *
31277 TAAACGGTTAGC-TTCTAGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATAC
194 TAAACGGTTAGCTTTC-AGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGAGATAC
* *
31341 AGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGGTACTGAGGAGAAGACCAAA
258 AGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCCGATGAGATACT---GAGAAGACCAAA
* * * * *
31406 CCAAACCCACACAC-GA-TGAAT-AAACCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGT
320 CCAAACCCACACACAAAGCGAATAAAACCTTCGAACCCCAGCTTCCTGATAAGACACCGAGAAGC
* *
31468 AGGTCGAAGTAATAAAACGGATAG
385 AGGTCGAAGCAATAAAACGAATAG
* * *
31492 CTCCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATGCAGAGAAACGGG-
1 CTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAG-AA-GGGA
* * * *
31556 TTGAAACAAACGACGTGGTCATC-TCCCTGATGAGACACTGAGAAGAAGTCCAAATTAAACCCAC
64 TTGAAACAAACGACGCGGTCATCTTCCC-GATGAGACACTGAGAAGAAGACCAAATCAAGCCCAC
31620 GCGCGATGAA
Statistics
Matches: 470, Mismatches: 52, Indels: 25
0.86 0.10 0.05
Matches are distributed among these distances:
402 5 0.01
403 101 0.21
404 3 0.01
405 1 0.00
408 14 0.03
409 203 0.43
410 115 0.24
411 7 0.01
412 21 0.04
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (408 bp):
CTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGGGATT
GAAACAAACGACGCGGTCATCTTCCCGATGAGACACTGAGAAGAAGACCAAATCAAGCCCACACT
CAAAACGAGAAAATCTTCGAACCCCAACTTCATGATAAGACACCGAGAAGCAGGTCGAAGCAATA
AACGGTTAGCTTTCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGAGATACAGA
GAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCCGATGAGATACTGAGAAGACCAAACCAAAC
CCACACACAAAGCGAATAAAACCTTCGAACCCCAGCTTCCTGATAAGACACCGAGAAGCAGGTCG
AAGCAATAAAACGAATAG
Found at i:31709 original size:204 final size:201
Alignment explanation
Indices: 30686--31712 Score: 949
Period size: 203 Copynumber: 5.0 Consensus size: 201
30676 TAACTTCCTG
* * * *
30686 ATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAGTTGAAACA
1 ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGGTTGAAACA
* * * * * * ** * **
30751 AACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAA-CGAGGCTCA-AAACGA-
66 AGCGATGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGA-CCAAATC-AAACCCACACGCGAT
* * * * * * * *
30813 GCAAATCTTCGAACCCCAGCTTCATGATGAGACACCGAGAAGCAGGTCGAAGCAGT-AAACGGTT
129 GAAAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAAC-GAT
*
30877 AGCTTTC-A
193 AGCTTCCGA
* * * * * *
30885 GATGATATACTAAGGAGTGAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGCGGATTGAAAC
1 -ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGGTTGAAAC
*
30950 AAGCGATGCGGTCATCTTTCC-GATGAGATACT--G-AGAAGACCAAATCAAGCTCACGCTCA-A
65 AAGCGATGCGGTCATC-TCCCTGATGAGATACTGAGAAGAAGACCAAATCAA----AC-C-CACA
* * * * * * *
31010 AGCGA-GTAAAATCTTCGAACCCCAGTTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAGT-A
123 CGCGATG-AAAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAA
*
31073 AACAATTAGCTTCC-A
187 AACGA-TAGCTTCCGA
* *
31088 GATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAG-AAGGGGATTGAAA
1 -ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGG-TTGAAA
*
31152 CAAGCGATGCGGTCATCTTCCC-GATGAGATACTGAGAAGAAGACCAAATCAAGCCCACACTCAA
64 CAAGCGATGCGGTCATC-TCCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACA--C--
* * * *
31216 AGCGA-GTAAAATCTTCGAACCCCAACTTCCTGATAAGACACCGAGAAGCAGGTCGAAGCAAT-A
124 -GCGATG-AAAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAA
* *
31279 AACGGTTAGCTT-CTA
187 AAC-GATAGCTTCCGA
* *
31294 GATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
1 -ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGGTTGAAAC
** * * * *
31359 AAGCGATGCGGTCATCTTTCTGATGAGGTACTGAGGAGAAGACCAAACCAAACCCACACACGATG
65 AAGCGATGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACGCGATG
* *
31424 AATAAACCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGTAGGTCGAAGTAATAAAACGGA
130 -A-AAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAAC-GA
*
31489 TAGCTCCCTG-
192 TAGCTTCC-GA
*
31499 ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATGCAGAGAAACGGGTTGAAACA
1 ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGGTTGAAACA
* * * * * * *
31564 AACGACGTGGTCATCTCCCTGATGAGACACTGAGAAGAAGTCCAAATTAAACCCACGCGCGATGA
66 AGCGATGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACGCGATGA
* * * * * * * * *
31629 ACGAATCTTCAAACCCCAGCTTTCGGATCAGGTACTGAAAAGCAGGTTGAAGTAATAAAATGACC
131 A--AATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAACGA-T
*
31694 ATCTTCCGA
193 AGCTTCCGA
31703 ATGAGATACT
1 ATGAGATACT
31713 AAGAAGAAAG
Statistics
Matches: 708, Mismatches: 86, Indels: 62
0.83 0.10 0.07
Matches are distributed among these distances:
196 6 0.01
197 7 0.01
198 1 0.00
200 84 0.12
201 8 0.01
202 15 0.02
203 202 0.29
204 188 0.27
205 5 0.01
206 189 0.27
207 3 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (201 bp):
ATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGGTTGAAACA
AGCGATGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACGCGATGA
AAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAACGATAGC
TTCCGA
Found at i:31968 original size:11 final size:11
Alignment explanation
Indices: 31954--32024 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
31944 GGCCTTTTTT
*
31954 AATTTATTTTA
1 AATTTAATTTA
*
31965 AATTTGATTTA
1 AATTTAATTTA
31976 AATTTAAATTTA
1 AATTT-AATTTA
*
31988 AA-TTGATATTA
1 AATTTAAT-TTA
* *
31999 AATTTAAATTG
1 AATTTAATTTA
32010 AATTTAATTTA
1 AATTTAATTTA
32021 AATT
1 AATT
32025 AAAAAGTCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 2 0.04
11 36 0.75
12 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:31982 original size:6 final size:6
Alignment explanation
Indices: 31961--32024 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
31951 TTTAATTTAT
* * *
31961 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA TTGATA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
32007 -TTGAA TTT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
32025 AAAAAGTCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 16 0.34
6 31 0.66
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:31983 original size:17 final size:17
Alignment explanation
Indices: 31961--32024 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
31951 TTTAATTTAT
* * *
31961 TTTAAATTTGATTTAAA
1 TTTAAATTTAAATTGAA
31978 TTTAAATTTAAATTG-A
1 TTTAAATTTAAATTGAA
31994 TATTAAATTTAAATTGAA
1 T-TTAAATTTAAATTGAA
32012 TTT-AATTTAAATT
1 TTTAAATTTAAATT
32025 AAAAAGTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 12 0.29
17 28 0.67
18 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTGAA
Done.