Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014034.1 Kokia drynarioides strain JFW-HI SEQ_129065, 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: 43384
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:769 original size:19 final size:20
Alignment explanation
Indices: 728--770 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
718 CCAATTGGGC
*
728 ATTTGTAATTTGGACATTTA
1 ATTTGTAATATGGACATTTA
748 ATTTGTAA-ATGGAC-TTTGA
1 ATTTGTAATATGGACATTT-A
767 ATTT
1 ATTT
771 AATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (20 bp):
ATTTGTAATATGGACATTTA
Found at i:839 original size:6 final size:6
Alignment explanation
Indices: 766--883 Score: 75
Period size: 6 Copynumber: 20.0 Consensus size: 6
756 ATGGACTTTG
* * * *
766 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
* ** ** *
814 AATTGA AATTTA AA-ACA AATTTA AATTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
861 AATTTA AA-GTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
884 GAAATAAATC
Statistics
Matches: 82, Mismatches: 22, Indels: 16
0.68 0.18 0.13
Matches are distributed among these distances:
4 3 0.04
5 11 0.13
6 54 0.66
7 14 0.17
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:857 original size:41 final size:41
Alignment explanation
Indices: 807--897 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
797 ATTTCAAATT
807 TAAA-CTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
* * * ** *
847 TGAATTTAAATTTAAATTTAAAGTAAATTTAAATTTAGAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
888 TAAATCTAAA
1 TAAATCTAAA
898 ATAATTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.36
Consensus pattern (41 bp):
TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:897 original size:18 final size:17
Alignment explanation
Indices: 788--862 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
778 AAGTTTAAGT
*
788 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
* *
805 TTTAAACTAAATTGAAA
1 TTTAAAATAAATTTAAA
*
822 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
*
839 TTTAAAAATGAATTTAAA
1 TTT-AAAATAAATTTAAA
857 TTTAAA
1 TTTAAA
863 TTTAAAGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 30 0.62
18 18 0.38
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:2297 original size:19 final size:20
Alignment explanation
Indices: 2256--2298 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2246 CCAATTGGGC
*
2256 ATTTGTAATTTGGACATTTA
1 ATTTGTAATATGGACATTTA
2276 ATTTGTAA-ATGGAC-TTTGA
1 ATTTGTAATATGGACATTT-A
2295 ATTT
1 ATTT
2299 AATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (20 bp):
ATTTGTAATATGGACATTTA
Found at i:2367 original size:6 final size:6
Alignment explanation
Indices: 2294--2411 Score: 75
Period size: 6 Copynumber: 20.0 Consensus size: 6
2284 ATGGACTTTG
* * * *
2294 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
* ** ** *
2342 AATTGA AATTTA AA-ACA AATTTA AATTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
2389 AATTTA AA-GTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
2412 GAAATAAATC
Statistics
Matches: 82, Mismatches: 22, Indels: 16
0.68 0.18 0.13
Matches are distributed among these distances:
4 3 0.04
5 11 0.13
6 54 0.66
7 14 0.17
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:2385 original size:41 final size:41
Alignment explanation
Indices: 2335--2425 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
2325 ATTTCAAATT
2335 TAAA-CTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
* * * ** *
2375 TGAATTTAAATTTAAATTTAAAGTAAATTTAAATTTAGAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
2416 TAAATCTAAA
1 TAAATCTAAA
2426 ATAATTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.36
Consensus pattern (41 bp):
TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:2425 original size:18 final size:17
Alignment explanation
Indices: 2316--2390 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
2306 AAGTTTAAGT
*
2316 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
* *
2333 TTTAAACTAAATTGAAA
1 TTTAAAATAAATTTAAA
*
2350 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
*
2367 TTTAAAAATGAATTTAAA
1 TTT-AAAATAAATTTAAA
2385 TTTAAA
1 TTTAAA
2391 TTTAAAGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 30 0.62
18 18 0.38
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:3144 original size:206 final size:206
Alignment explanation
Indices: 2790--3521 Score: 1142
Period size: 206 Copynumber: 3.6 Consensus size: 206
2780 TTGACTAAGC
* * ** * * *
2790 CTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTTGATTCACTTCTCTGTGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCCACTTCTCTGTATCT
* * * * * *
2855 CATCAGGAAGACGGATTAGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
* *
2920 CGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCGAGCGTGGG
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTGGG
2985 TTTGATTTGGT
196 TTTGATTTGGT
*
2996 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT-TCGTATC
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCCACTTCTCT-GTATC
3060 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
65 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
* * *
3125 TTGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCATATCGAGCGTGA
130 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTGG
*
3190 GTTTAATTTGGT
195 GTTTGATTTGGT
* * * *
3202 CTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTATCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCCACTTCTCTGTATCT
**
3267 CATCAGGAAGACGAATTTGGTCCACTTCTTGGTATCTCATCAGGAAGCTAACCATTTTATTACTT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
* * * *
3332 CGACTTGATTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTGGG
3397 TTTGATTTGGT
196 TTTGATTTGGT
* * * *
3408 CTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTGTATCA
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCCACTTCTCTGTATCT
3473 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
3522 GGGATTCGAA
Statistics
Matches: 483, Mismatches: 41, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
205 1 0.00
206 481 1.00
207 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (206 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCCACTTCTCTGTATCT
CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTGGG
TTTGATTTGGT
Found at i:3532 original size:158 final size:158
Alignment explanation
Indices: 3340--3680 Score: 612
Period size: 158 Copynumber: 2.2 Consensus size: 158
3330 TTCGACTTGA
*
3340 TTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTT
1 TTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTGATTT
3405 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTGTA
66 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTGTA
3470 TCACATCAGGAAGACGAATTTGGTCCAC
131 TCACATCAGGAAGACGAATTTGGTCCAC
3498 TTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
1 TTCTCAGTATCTCATCAGGAAGCTAGGG-TTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
* *
3562 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGT
65 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTGT
* *
3627 ATCATATCAGGAAGACGAATTTGGTCCGC
130 ATCACATCAGGAAGACGAATTTGGTCCAC
*
3656 TTCTCAGTATCTCATTAGGAAGCTA
1 TTCTCAGTATCTCATCAGGAAGCTA
3681 ACCATTTTAT
Statistics
Matches: 175, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
157 3 0.02
158 172 0.98
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (158 bp):
TTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTGATTT
GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTGTA
TCACATCAGGAAGACGAATTTGGTCCAC
Found at i:3568 original size:364 final size:364
Alignment explanation
Indices: 3133--3885 Score: 1233
Period size: 364 Copynumber: 2.1 Consensus size: 364
3123 CTTTGACCTG
* * * *
3133 CTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCATATCGAGCGTGAGTTTAATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGAGTTTAATT
*
3198 TGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTATCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTATCTGT
**
3263 ATC-TCATCAGGAAGACGAATTTGGTCCACTTCTTGGTATCTCATCAGGAAGCTAACCATTTTAT
131 ATCAT-ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
** * *
3327 TACTTCGA-CTTGATTCTCAGTATCTCATCAGGAAGCTAG-GGTTCGAAGATTTGCTCACATCGA
195 TACTTC-ATCCCGATTCTCAGTATCTCATCAAGAAGCT-GTGATTCGAAGATTTGCTCACATCGA
*
3390 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCA
258 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCACGTCATTTGTTTCA
3455 ATCCGCTTCTCTGTATCACATCAGGAAGACGAATTTGGTCCA
323 ATCCGCTTCTCTGTATCACATCAGGAAGACGAATTTGGTCCA
* *
3497 CTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGAGTTTAATT
* *
3562 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTATCTGT
* *
3627 ATCATATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATT
131 ATCATATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
* * * *
3692 GCTTCATCCCGCTTCTCAGTATCTCATCAAGAAGCTGTGATTCGAAGTTTTGCTCATATCGAGCG
196 ACTTCATCCCGATTCTCAGTATCTCATCAAGAAGCTGTGATTCGAAGATTTGCTCACATCGAGCG
*
3757 TGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTCATTTGTTTCAATC
261 TGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCACGTCATTTGTTTCAATC
*
3822 CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCA
326 CGCTTCTCTGTATCACATCAGGAAGACGAATTTGGTCCA
*
3861 CTTCCCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
3886 AACCATTTTA
Statistics
Matches: 361, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
363 2 0.01
364 358 0.99
365 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (364 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGAGTTTAATT
TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTATCTGT
ATCATATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
ACTTCATCCCGATTCTCAGTATCTCATCAAGAAGCTGTGATTCGAAGATTTGCTCACATCGAGCG
TGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCACGTCATTTGTTTCAATC
CGCTTCTCTGTATCACATCAGGAAGACGAATTTGGTCCA
Found at i:3851 original size:206 final size:206
Alignment explanation
Indices: 3497--3954 Score: 785
Period size: 206 Copynumber: 2.2 Consensus size: 206
3487 ATTTGGTCCA
*
3497 CTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
1 CTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
* *
3562 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
* * *
3627 ATCATATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATT
131 ATCATATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTTATT
3692 GCTTC-ATCCCG
196 GCTTCGA-CCCG
* * * *
3703 CTTCTCAGTATCTCATCAAGAAGCTGTGATTCGAAGTTTTGCTCATATCGAGCGTGGGTTTGATT
1 CTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
3768 TGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
3833 ATC-TCATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTTAT
131 ATCAT-ATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTTAT
*
3897 TGCTTCGACTCG
195 TGCTTCGACCCG
3909 CTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCAC
1 CTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCAC
3955 CTTTGAGTTG
Statistics
Matches: 236, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
205 1 0.00
206 234 0.99
207 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTGATT
TGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGT
ATCATATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTTATT
GCTTCGACCCG
Found at i:4309 original size:102 final size:102
Alignment explanation
Indices: 4155--4348 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 102
4145 GCTGCTGTAG
* * * * * *
4155 TTTTATTCCAACTTCACTGCAACTTCAAGAAGATAGGATTTGATGTTGAAGCTTTATCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGAAATTGACGTTAAAGCTTCATCTTGCTCT
4220 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGCT
66 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGCT
* * * *
4257 TTTTAATCCAACTTTACTGCAACTTCAAGAGGATAGAAATTGACGTTAAAGCTTCATTTTTCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGAAATTGACGTTAAAGCTTCATCTTGCTCT
*
4322 TACTACAACTTTAGAGAGATAAAGACT
66 TACTACAACTTCAGAGAGATAAAGACT
4349 GACCATTGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (102 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGAAATTGACGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAGAGAGATAAAGACTTGCTATTGCT
Found at i:4604 original size:50 final size:50
Alignment explanation
Indices: 4497--4913 Score: 228
Period size: 50 Copynumber: 8.3 Consensus size: 50
4487 GCATTAGATT
* * * *
4497 CGCCGCTGCGGCTTAAATCTTTCCCTTAT-TATCTTCTGAGGTACACGG-TC
1 CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTT-TGTGGTAC-CGGATC
** * *
4547 CATCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATC
1 CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTTTGTGGTACCGGATC
* * ** * ** ** *
4597 CGCCGTTGTGGTCTTTGATCTTTCCCTTCATG--TCTTCATGGTACCAAATT
1 CGCCGTTG-CGACTTAAATCTTTCCCTT-TTGTATCTTTGTGGTACCGGATC
* * * * *
4647 GGCCGTTGC-AGGTTAAATCTTTCCC-TTCGTGTCTTCTGAGGTACACGG-TC
1 CGCCGTTGCGA-CTTAAATCTTTCCCTTTTGTATCTT-TGTGGTAC-CGGATC
* * * * * * *
4697 TTGTCGTTGTGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATT
1 -CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTTTGTGGTACCGGATC
* * * *
4748 CGCCGTTGCGGCTTAAATCTTTCCC-TTCGTGTCTTCTGAGGTACAC-GATC
1 CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTT-TGTGGTAC-CGGATC
* * * * *
4798 CTACCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTATGGTACTGGATC
1 C-GCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTTTGTGGTACCGGATC
* * * *
4849 CGCTGTTGCGGCTTAAATCTTTCCC-TTCGTGTCTTT-TAAGGTACACGG-TC
1 CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTTTGT--GGTAC-CGGATC
4899 CTGCCGTTGCGACTT
1 C-GCCGTTGCGACTT
4914 TGACCTTTCC
Statistics
Matches: 268, Mismatches: 77, Indels: 43
0.69 0.20 0.11
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 34 0.13
50 122 0.46
51 90 0.34
52 19 0.07
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (50 bp):
CGCCGTTGCGACTTAAATCTTTCCCTTTTGTATCTTTGTGGTACCGGATC
Found at i:4764 original size:101 final size:101
Alignment explanation
Indices: 4648--4926 Score: 443
Period size: 101 Copynumber: 2.8 Consensus size: 101
4638 TACCAAATTG
* * *
4648 GCCGTTGCAGG-TTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGTCGTTGTGACTT
1 GCCGTTGC-GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGCCGTTGCGACTT
* *
4712 AGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTC
65 AGACCTTTCCCTTTTGTATCTTTATGGTACTGGATCC
* *
4749 GCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTACCGTTGCGACTTA
1 GCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGCCGTTGCGACTTA
4814 GACCTTTCCCTTTTGTATCTTTATGGTACTGGATCC
66 GACCTTTCCCTTTTGTATCTTTATGGTACTGGATCC
* * * *
4850 GCTGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTT
1 GCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGCCGTTGCGACTTA
4915 GACCTTTCCCTT
66 GACCTTTCCCTT
4927 CATGTCTTCA
Statistics
Matches: 164, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
100 2 0.01
101 162 0.99
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (101 bp):
GCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGCCGTTGCGACTTA
GACCTTTCCCTTTTGTATCTTTATGGTACTGGATCC
Found at i:4791 original size:151 final size:150
Alignment explanation
Indices: 4509--4783 Score: 426
Period size: 150 Copynumber: 1.8 Consensus size: 150
4499 CCGCTGCGGC
*
4509 TTAAATCTTTCCCTTATTATCTTCTGAGGTACACGGTCCATCGTTGCGACTTAAACCTTTCCCTT
1 TTAAATCTTTCCCTTAGTATCTTCTGAGGTACACGGTCCATCGTTGCGACTTAAACCTTTCCCTT
* **
4574 TTGTATCTTTGTGGTACTGGATCCGCCGTTGTGGTCTTTGATCTTTCCCTTCATGTCTTCATGGT
66 TTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTCATGGT
4639 ACCAAATTGGCCGTTGCAGG
131 ACCAAATTGGCCGTTGCAGG
* * ** * *
4659 TTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGTCGTTGTGACTTAGACCTTTCCCT
1 TTAAATCTTTCCCTTAGTATCTTCTGAGGTACACGGTC-CATCGTTGCGACTTAAACCTTTCCCT
* *
4724 TTTGTATCTTTGTGGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTCGTGTCTTC
65 TTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTC
4784 TGAGGTACAC
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
150 57 0.51
151 55 0.49
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (150 bp):
TTAAATCTTTCCCTTAGTATCTTCTGAGGTACACGGTCCATCGTTGCGACTTAAACCTTTCCCTT
TTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATGTCTTCATGGT
ACCAAATTGGCCGTTGCAGG
Found at i:4925 original size:51 final size:51
Alignment explanation
Indices: 4665--4934 Score: 212
Period size: 51 Copynumber: 5.3 Consensus size: 51
4655 CAGGTTAAAT
* * * * *
4665 CTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGTCGTTGTGACTTAGAC
1 CTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTAGAC
* * * * * * *
4716 CTTTCCCTTTTGTATCTTTGT--GGTAC-TGGATTC-GCCGTTGCGGCTTAAAT
1 CTTTCCC-TTCGTGTCTTT-TAAGGTACACGG-TCCTGCCGTTGCGACTTAGAC
* * * *
4766 CTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTACCGTTGCGACTTAGAC
1 CTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTAGAC
* * * * * * * *
4817 CTTTCCCTT-TTGTATCTTTATGGTAC-TGGATCC-GCTGTTGCGGCTTAAAT
1 CTTTCCCTTCGTGTCT-TTTAAGGTACACGG-TCCTGCCGTTGCGACTTAGAC
*
4867 CTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTTGAC
1 CTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTAGAC
*
4918 CTTTCCCTTCATGTCTT
1 CTTTCCCTTCGTGTCTT
4935 CATGGTACTG
Statistics
Matches: 164, Mismatches: 43, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
48 1 0.01
49 8 0.05
50 66 0.40
51 80 0.49
52 8 0.05
53 1 0.01
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (51 bp):
CTTTCCCTTCGTGTCTTTTAAGGTACACGGTCCTGCCGTTGCGACTTAGAC
Found at i:11697 original size:28 final size:28
Alignment explanation
Indices: 11666--11723 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
11656 AAAATGAGAC
*
11666 TTTGGATACCCGAGGGCAAAATGGTAAT
1 TTTGGACACCCGAGGGCAAAATGGTAAT
* *
11694 TTTGGACACTCGGGGGCAAAATGGTAAT
1 TTTGGACACCCGAGGGCAAAATGGTAAT
11722 TT
1 TT
11724 CAGGAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (28 bp):
TTTGGACACCCGAGGGCAAAATGGTAAT
Found at i:11856 original size:29 final size:28
Alignment explanation
Indices: 11824--12113 Score: 111
Period size: 29 Copynumber: 9.9 Consensus size: 28
11814 GGACATCTGA
*
11824 GGGT-AAAATGGTTATTTTTAAAAGCTTCG
1 GGGTAAAAATGG-AATTTTTAAAAG-TTCG
**
11853 GGGTAAAAATGGAATTTTTGGAAGTTCG
1 GGGTAAAAATGGAATTTTTAAAAGTTCG
*
11881 AGGATAAAAATGGAATTTTTGAAAAGTTCG
1 -GGGTAAAAATGGAATTTTT-AAAAGTTCG
* *
11911 GGGT-TAAATGGTAATTTTTGGTGAAA-TT-G
1 GGGTAAAAATGG-AA-TTTT--TAAAAGTTCG
** *
11940 GGGTAAAAAATGGAATTTTGGAAAGTTTAAG
1 GGGT-AAAAATGGAATTTTTAAAAG-TT-CG
*
11971 GGGT-AAAATGGTAATTTTTGGTGAAA---CG
1 GGGTAAAAATGG-AA-TTTT--TAAAAGTTCG
* *
11999 AGGTTAAAAATGGAA-TTTTAGAAAGTTTAG
1 -GGGTAAAAATGGAATTTTTA-AAAG-TTCG
* * *
12029 GGGT-AAAATGGTACTTTTGGTTAAA--TCAA
1 GGGTAAAAATGG-AATTTT--TAAAAGTTC-G
*
12058 GGGTCAAAATGGAA-TTTTAGAAAGTTCG
1 GGGTAAAAATGGAATTTTTA-AAAGTTCG
*
12086 AGGGTAAAAATGTAATTTTTAGAAAGTT
1 -GGGTAAAAATGGAATTTTTA-AAAGTT
12114 TAAGGTTAAA
Statistics
Matches: 200, Mismatches: 26, Indels: 69
0.68 0.09 0.23
Matches are distributed among these distances:
25 1 0.00
26 4 0.02
27 10 0.05
28 22 0.11
29 82 0.41
30 54 0.27
31 21 0.10
32 2 0.01
33 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTAAAAGTTCG
Found at i:11889 original size:58 final size:58
Alignment explanation
Indices: 11828--12105 Score: 193
Period size: 58 Copynumber: 4.7 Consensus size: 58
11818 ATCTGAGGGT
*
11828 AAAATGGTTATTTTT-AAAAGCTTCGGGGTAAAAATGG-AATTTTTGGAAGTTCGAGGATA
1 AAAATGG-AATTTTTGAAAAG-TTCGGGGT-AAAATGGTAATTTTTGGAAGTTCGAGGATA
* * *
11887 AAAATGGAATTTTTGAAAAGTTCGGGGTTAAATGGTAATTTTTGGTGAAATT-G-GGGTAA
1 AAAATGGAATTTTTGAAAAGTTCGGGGTAAAATGGTAATTTTT-G-GAAGTTCGAGGAT-A
* * * *
11946 AAAATGGAA-TTTTGGAAAGTTTAAGGGGTAAAATGGTAATTTTTGGTGAA--ACGAGGTTA
1 AAAATGGAATTTTTGAAAAG-TT-CGGGGTAAAATGGTAATTTTT-G-GAAGTTCGAGGATA
* * * * * * *
12005 AAAATGGAATTTTAG-AAAGTTTAGGGGTAAAATGGT-ACTTTTGGTTAA-ATCAAGGGTC
1 AAAATGGAATTTTTGAAAAG-TTCGGGGTAAAATGGTAATTTTTGG--AAGTTCGAGGATA
*
12063 AAAATGGAATTTTAG-AAAGTTCGAGGGTAAAAAT-GTAATTTTT
1 AAAATGGAATTTTTGAAAAGTTCG-GGGT-AAAATGGTAATTTTT
12106 AGAAAGTTTA
Statistics
Matches: 186, Mismatches: 17, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
55 1 0.01
56 1 0.01
57 16 0.09
58 77 0.41
59 54 0.29
60 37 0.20
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGAAAAGTTCGGGGTAAAATGGTAATTTTTGGAAGTTCGAGGATA
Found at i:11951 original size:59 final size:59
Alignment explanation
Indices: 11828--12105 Score: 243
Period size: 59 Copynumber: 4.7 Consensus size: 59
11818 ATCTGAGGGT
* * * *
11828 AAAATGGTTATTTTTAAAAGCTTCGGGGTAAAAATGG-AATTTTT-G-GAAGTTCGAGG-ATA
1 AAAATGG-AATTTTTGAAAGTTTCGGGGT-AAAATGGTAATTTTTGGTGAAATT-GAGGTA-A
* *
11887 AAAATGGAATTTTTGAAAAG-TTCGGGGTTAAATGGTAATTTTTGGTGAAATTGGGGTAA
1 AAAATGGAATTTTTG-AAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTAA
* * * *
11946 AAAATGGAATTTTGGAAAGTTTAAGGGGTAAAATGGTAATTTTTGGTGAAA-CGAGGTTA
1 AAAATGGAATTTTTGAAAGTTT-CGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTAA
* * * * ** *
12005 AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGT-ACTTTTGGTTAAATCAAGGGT-C
1 AAAATGGAATTTTTGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATTGA-GGTAA
*
12063 AAAATGGAATTTTAGAAAG-TTCGAGGGTAAAAAT-GTAATTTTT
1 AAAATGGAATTTTTGAAAGTTTCG-GGGT-AAAATGGTAATTTTT
12106 AGAAAGTTTA
Statistics
Matches: 189, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
57 20 0.11
58 66 0.35
59 71 0.38
60 32 0.17
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTAA
Found at i:12124 original size:29 final size:29
Alignment explanation
Indices: 12063--12147 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
12053 ATCAAGGGTC
* * *
12063 AAAATGGAA-TTTTAGAAAGTTCGAGGGTA
1 AAAATGTAATTTTTAGAAAGTT-TAAGGTA
*
12092 AAAATGTAATTTTTAGAAAGTTTAAGGTT
1 AAAATGTAATTTTTAGAAAGTTTAAGGTA
*
12121 AAAATGTAATTTTTAGATAGTTTAAGG
1 AAAATGTAATTTTTAGAAAGTTTAAGG
12148 GCCTCAAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 38 0.76
30 12 0.24
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAAGTTTAAGGTA
Found at i:27894 original size:58 final size:58
Alignment explanation
Indices: 27826--27940 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
27816 ACCAACAAAC
*
27826 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCATAAAG
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAG
* *
27884 TAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAA
27941 CAACTCCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
57 3 0.06
58 50 0.94
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAG
Found at i:31018 original size:7 final size:7
Alignment explanation
Indices: 31008--31032 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30998 AATTAGTAAT
31008 GGCCCTA
1 GGCCCTA
31015 GGCCCTA
1 GGCCCTA
31022 GGCCCTA
1 GGCCCTA
31029 GGCC
1 GGCC
31033 TAGTTACACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.32, T:0.12
Consensus pattern (7 bp):
GGCCCTA
Done.