Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002725.1 Kokia drynarioides strain JFW-HI SEQ_115026, 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: 67320
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:818 original size:23 final size:23
Alignment explanation
Indices: 715--840 Score: 114
Period size: 23 Copynumber: 5.5 Consensus size: 23
705 ACACTAGCGC
* *
715 GCTCTCTGTTTATCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
738 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
763 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
786 ACTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
809 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
830 ACTCTCTGTTT
1 GCTCTCTGTTT
841 GTTCCGTATA
Statistics
Matches: 84, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
21 9 0.11
22 11 0.13
23 44 0.52
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:833 original size:44 final size:46
Alignment explanation
Indices: 739--840 Score: 163
Period size: 46 Copynumber: 2.2 Consensus size: 46
729 ACGTCTCGTG
739 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
*
787 CTCTTTGTTTAGCACTGTGTGTGCTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
831 CTCTCTGTTT
1 CTCTCTGTTT
841 GTTCCGTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
44 12 0.23
45 11 0.21
46 22 0.42
47 1 0.02
48 6 0.12
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.48
Consensus pattern (46 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
Found at i:3571 original size:20 final size:20
Alignment explanation
Indices: 3532--3584 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3522 TAAATTTTTT
* * *
3532 TTAAAAATTTGAGGGTAAAA
1 TTAAAAATTTCAAGGAAAAA
3552 TTAAAAATTTCAAGGAAAAA
1 TTAAAAATTTCAAGGAAAAA
* *
3572 TGAAAATTTTCAA
1 TTAAAAATTTCAA
3585 AAACTTTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.30
Consensus pattern (20 bp):
TTAAAAATTTCAAGGAAAAA
Found at i:5673 original size:16 final size:17
Alignment explanation
Indices: 5645--5681 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5635 ATTAATATAT
5645 TTTATATTTATTC-AAA
1 TTTATATTTATTCAAAA
5661 TTTA-ATTTGATTCAAAA
1 TTTATATTT-ATTCAAAA
5678 TTTA
1 TTTA
5682 GACTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 8 0.42
17 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTATATTTATTCAAAA
Found at i:5910 original size:14 final size:15
Alignment explanation
Indices: 5891--5920 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5881 ATTATAAAAT
5891 ATATAAAATA-CATA
1 ATATAAAATATCATA
5905 ATATAAAATATCATA
1 ATATAAAATATCATA
5920 A
1 A
5921 ATTTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAAAATATCATA
Found at i:14458 original size:89 final size:89
Alignment explanation
Indices: 14363--14547 Score: 352
Period size: 89 Copynumber: 2.1 Consensus size: 89
14353 ATGAGTAAAT
14363 TAATCACTATAATATATATTACATCAAAGAACAGGCCAATTATTCTGTTAAAAAATCCATCATTT
1 TAATCACTATAATATATATTACATCAAAGAACAGGCCAATTATTCTGTTAAAAAATCCATCATTT
14428 CTTATTGTTAAAAATTAATCACTA
66 CTTATTGTTAAAAATTAATCACTA
*
14452 TAATCACTATAATATATATTACATCAAAGAACAGGCCAATTCTTCTGTTAAAAAATCCATCATTT
1 TAATCACTATAATATATATTACATCAAAGAACAGGCCAATTATTCTGTTAAAAAATCCATCATTT
14517 CTTATTGTTAAAAATTAATCACTA
66 CTTATTGTTAAAAATTAATCACTA
14541 TACATCA
1 TA-ATCA
14548 ACATGAGATA
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 90 0.96
90 4 0.04
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (89 bp):
TAATCACTATAATATATATTACATCAAAGAACAGGCCAATTATTCTGTTAAAAAATCCATCATTT
CTTATTGTTAAAAATTAATCACTA
Found at i:16848 original size:54 final size:54
Alignment explanation
Indices: 16785--16987 Score: 157
Period size: 54 Copynumber: 3.8 Consensus size: 54
16775 GTAATTTGGT
16785 TTTTC-GTAATGATCCCATCAGAAGTAG-AGGTTGATTCCCTTCTAGAAATTCG
1 TTTTCGGTAATGATCCCATCAGAAGTAGAAGGTTGATTCCCTTCTAGAAATTCG
* * ** *
16837 TTTTATGGTAATGATCCTATCAG-AGGCGAAGGTTGATTCCTTTCTAG-AATTCTG
1 TTTT-CGGTAATGATCCCATCAGAAGTAGAAGGTTGATTCCCTTCTAGAAATTC-G
* * * * * ** *
16891 ATTTCGAGCAATCATCCTACCAGGGGT-GAAGGTTGATTCCCTTCTAGAAATTTG
1 TTTTCG-GTAATGATCCCATCAGAAGTAGAAGGTTGATTCCCTTCTAGAAATTCG
* * * * * *
16945 TTCTCCAGTAATGATCCCAACGGAAGTAG-TGGTCGATTCCCTT
1 TT-TTCGGTAATGATCCCATCAGAAGTAGAAGGTTGATTCCCTT
16988 GTAGGAATCG
Statistics
Matches: 116, Mismatches: 26, Indels: 16
0.73 0.16 0.10
Matches are distributed among these distances:
52 4 0.03
53 9 0.08
54 95 0.82
55 8 0.07
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (54 bp):
TTTTCGGTAATGATCCCATCAGAAGTAGAAGGTTGATTCCCTTCTAGAAATTCG
Found at i:21143 original size:41 final size:42
Alignment explanation
Indices: 21098--21202 Score: 185
Period size: 41 Copynumber: 2.5 Consensus size: 42
21088 AATTCGTAAT
21098 AAATGCAAAATAAGCTAAGAACTAACTTCA-AAATTAAATAA
1 AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
*
21139 AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTGAATAA
1 AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
21181 AAATGCAAAAATAAGCTAAGAA
1 AAATGC-AAAATAAGCTAAGAA
21203 AAAACAATAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
41 30 0.49
42 16 0.26
43 15 0.25
ACGTcount: A:0.58, C:0.11, G:0.10, T:0.20
Consensus pattern (42 bp):
AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
Found at i:21900 original size:17 final size:18
Alignment explanation
Indices: 21874--21907 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21864 TTTCTGAATT
*
21874 ATGTTTAAAAT-ATTATC
1 ATGTTAAAAATAATTATC
21891 ATGTTAAAAATAATTAT
1 ATGTTAAAAATAATTAT
21908 GGTAGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGTTAAAAATAATTATC
Found at i:26653 original size:181 final size:180
Alignment explanation
Indices: 26348--27214 Score: 1376
Period size: 181 Copynumber: 4.7 Consensus size: 180
26338 ACATATGGCC
26348 TATGGGCATAGCTAACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGA
1 TATGGGCATAGCTAACTTCTAA-TTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGA
*
26413 GTAAAAAGATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
65 GTAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
*
26478 AGATACCATCTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATGTCTTTACA
130 AGATACCATTTGTTCTTGGATTTCAGCTAATAAAAAAAAAAAT-TCTTTACA
*
26530 TATGGGCATAGCTAACTTCTAATTTATGTATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
*
26595 TAAAAAGATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAA
66 TAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAA
* *
26660 GATACCATTTGTTCTTGGATTTCAGCTAACAGAAAAAAAAATTCTTTACA
131 GATACCATTTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATTCTTTACA
26710 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
* * *
26775 TAAAATAAAATTGATCAATTTATCCACAATTATCAAATCAAAATTAATAAGCAAAGAAAGAAAGA
66 T-AAA-AAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAA--ACA-AAA-ACAGA
** *
26840 AAGAAAGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAACGAATTTCTTTACA
125 AAGAAAGATACCATTTGTTCTTGGATTTCAGCTAATA-AAAAAAAAAATTCTTTACA
* *
26897 TATGGACATAGCTAAGTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
* *
26962 TAAAAAAAATTGATCAATTTATCCACAATTATCAAATCAAAATTAATAAACAAAAGCAGAAAGAA
66 T-AAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
* *
27027 AGAAAGATTCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAAATTC-TTACA
130 AG--ATA-CCATTTGTTCTTGGATTTCAGCTAATA-AAAAAAAAAATTCTTTACA
* * *
27081 TAAGGGCATAGCTAACTTCTAATTTAGATATATGAACTAAAACAACTTAAAAATCTTAAAACAAG
1 TATGGGCATAGCTAACTTCTAATTT--ATATATGAACTAAAACAACTTCAAATTCTTAAAACAAG
* *
27146 AGTAAAAAAATTGATCAAATTAACCACAATTATCAAATTAAAATTAATAAACAAAAACAGAAAGA
64 AGTAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGA
27211 AAGA
129 AAGA
27215 AAGAAAGAAA
Statistics
Matches: 640, Mismatches: 33, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
180 73 0.11
181 149 0.23
182 74 0.12
183 4 0.01
184 33 0.05
185 101 0.16
186 123 0.19
187 83 0.13
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (180 bp):
TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
TAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAA
GATACCATTTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATTCTTTACA
Found at i:27210 original size:367 final size:361
Alignment explanation
Indices: 26351--27214 Score: 1388
Period size: 367 Copynumber: 2.4 Consensus size: 361
26341 TATGGCCTAT
26351 GGGCATAGCTAACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTA
1 GGGCATAGCTAACTTCTAA-TTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTA
*
26416 AAAAGATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGA
65 AAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGA
*
26481 TACCATCTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATGTCTTTACATATGGGCATAGCTAAC
130 TACCATCTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATGTCTTTACATATGGACATAGCTAAC
* *
26546 TTCTAATTTATGTATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAGATTGATCAA
195 TTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAAATTGATCAA
*
26611 ATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGATACCATTTGTTCTT
260 ATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAGACCATTTGTTCTT
*
26676 GGATTTCAGCTAACAGAAAAAAAAATTCTTTACATAT
325 GGATTTCAGCTAACAGAAAAAAAAATTCTTTACATAA
26713 GGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAA
1 GGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGT-A
* * *
26778 AATAAAATTGATCAATTTATCCACAATTATCAAATCAAAATTAATAAGCAAAGAAAGAAAGAAAG
65 AA-AAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAA--ACA-AAA-ACAGAAAG
* * ** *
26843 AAAGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAACGAATTTCTTTACATATGGACATAG
125 AAAGATACCATCTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATGTCTTTACATATGGACATAG
*
26908 CTAAGTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAAAATT
190 CTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGT-AAAAAAATT
* * *
26973 GATCAATTTATCCACAATTATCAAATCAAAATTAATAAACAAAAGCAGAAAGAAAGAAAGATTCA
254 GATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAG--AGA-CCA
*
27038 TTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAAATTC-TTACATAA
316 TTTGTTCTTGGATTTCAGCTAACAG-AAAAAAAAATTCTTTACATAA
* *
27084 GGGCATAGCTAACTTCTAATTTAGATATATGAACTAAAACAACTTAAAAATCTTAAAACAAGAGT
1 GGGCATAGCTAACTTCTAATTT--ATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGT
* *
27149 AAAAAAATTGATCAAATTAACCACAATTATCAAATTAAAATTAATAAACAAAAACAGAAAGAAAG
64 AAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAG
27214 A
129 A
27215 AAGAAAGAAA
Statistics
Matches: 463, Mismatches: 26, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
361 44 0.10
362 22 0.05
363 42 0.09
365 2 0.00
366 3 0.01
367 131 0.28
368 65 0.14
369 2 0.00
370 2 0.00
371 96 0.21
372 15 0.03
373 39 0.08
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (361 bp):
GGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAA
AAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAT
ACCATCTGTTCTTGGATTTCAGCTAATAAAAAAAAAAATGTCTTTACATATGGACATAGCTAACT
TCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAAATTGATCAAA
TTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAGACCATTTGTTCTTG
GATTTCAGCTAACAGAAAAAAAAATTCTTTACATAA
Found at i:30307 original size:29 final size:29
Alignment explanation
Indices: 30262--30330 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
30252 TGACAGGGAT
* * *
30262 TAGATCAAATTAGTCCCTCTATTATTAAA
1 TAGATCAAATTAATCCCTATACTATTAAA
*
30291 TAGATCAATTTAATCCCTATACTATTAAA
1 TAGATCAAATTAATCCCTATACTATTAAA
*
30320 AAGAATCAAAT
1 TAG-ATCAAAT
30331 AAGTCCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (29 bp):
TAGATCAAATTAATCCCTATACTATTAAA
Found at i:35872 original size:83 final size:84
Alignment explanation
Indices: 35732--35896 Score: 235
Period size: 83 Copynumber: 2.0 Consensus size: 84
35722 CAGTTTCACG
* ** * *
35732 CTAGAATCTAGATTGAAATTTAAAAAATCCACCGCAAAATTAACACCTCCCAGATGCCCGAATCA
1 CTAGAATCTACATCCAAATTTAAAAAATCCAACGCAAAATTAACACCTCCCAGATGCCCAAATCA
*
35797 ATAGTCCGTTTGAATCATA
66 ATAGTCCATTTGAATCATA
* *
35816 CTAGAATCTACATCCAAATTTCAAAAAT-CAATGCAAAATTAACA-CTGCCCAGATGCCCAAATC
1 CTAGAATCTACATCCAAATTTAAAAAATCCAACGCAAAATTAACACCT-CCCAGATGCCCAAATC
35879 AATAGTCCATTTGAATCA
65 AATAGTCCATTTGAATCA
35897 ATAAAAATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
82 2 0.03
83 46 0.64
84 24 0.33
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (84 bp):
CTAGAATCTACATCCAAATTTAAAAAATCCAACGCAAAATTAACACCTCCCAGATGCCCAAATCA
ATAGTCCATTTGAATCATA
Found at i:36028 original size:186 final size:184
Alignment explanation
Indices: 35722--36169 Score: 592
Period size: 186 Copynumber: 2.4 Consensus size: 184
35712 ATCAATAAAG
* * * * *
35722 CAGTTTCACGCTAGAATCTAGATTGAAATTTAAAAAATCCACCGCAAAATTAACACCTCCCAGAT
1 CAGTGTCATGCTAGAATCTA-ATTCAAA-TTAAAAAATCCAACGCAAAATTAACACTTCCCAGAT
* * * *
35787 GCCCGAATCAATAGTCCGTTTGAATCATACTAGAATCTACATCCAAATTTCAAAAATCAATGCAA
64 GCCCAAATCACTAGTCCATTTGAATCATACTAGAATCTACATCCAAATTTCAAAAATCAACGCAA
* *
35852 AATTAACACTGCCCAGATGCCCAAATCAATAGTCCATTTGAATCAATAAAAA-TAA
129 AATTAACACTACCCAGATGCACAAATCAATAGTCCATTTGAATCAATAAAAATTAA
* * * *
35907 CAGTGTCATGTTAGAATCTACATTCAAATATAAAAAATCCATCGAAAAATTAACACTTCCCAGAC
1 CAGTGTCATGCTAGAATCTA-ATTCAAAT-TAAAAAATCCAACGCAAAATTAACACTTCCCAGAT
**
35972 GCCCAAAATCACTAGTCCATTTGAATCATACTAGAATCTACATCCAAATTTCAAAAATCCCCGCA
64 GCCC-AAATCACTAGTCCATTTGAATCATACTAGAATCTACATCCAAATTTCAAAAATCAACGCA
* *
36037 AAATTAACACTACCCAGATGCACAAATCAATAGTTCATTTGCATCAATAAAAATTAA
128 AAATTAACACTACCCAGATGCACAAATCAATAGTCCATTTGAATCAATAAAAATTAA
* * * ** * * * *
36094 TAGTTTCATGCTAGAATCTAGTTCAAATTTCAAAATTCAAAGCAAAATTAATACTACCCAGATGC
1 CAGTGTCATGCTAGAATCTAATTCAAATTAAAAAATCCAACGCAAAATTAACACTTCCCAGATGC
36159 CCAAATCACTA
66 CCAAATCACTA
36170 AATCCCCCCC
Statistics
Matches: 228, Mismatches: 32, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
184 10 0.04
185 88 0.39
186 110 0.48
187 20 0.09
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (184 bp):
CAGTGTCATGCTAGAATCTAATTCAAATTAAAAAATCCAACGCAAAATTAACACTTCCCAGATGC
CCAAATCACTAGTCCATTTGAATCATACTAGAATCTACATCCAAATTTCAAAAATCAACGCAAAA
TTAACACTACCCAGATGCACAAATCAATAGTCCATTTGAATCAATAAAAATTAA
Found at i:40386 original size:33 final size:33
Alignment explanation
Indices: 40329--40391 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
40319 ACTTAAACTC
** *
40329 AAAAATTGATTTTCTTTTTATTTTTTAAAAGTA
1 AAAAATTGATTTTCAATTTATTTTTCAAAAGTA
40362 AAAAATTGATATTTCAATTT-TTTTTCAAAA
1 AAAAATTGAT-TTTCAATTTATTTTTCAAAA
40392 CATGACTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 19 0.73
34 7 0.27
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (33 bp):
AAAAATTGATTTTCAATTTATTTTTCAAAAGTA
Found at i:41149 original size:31 final size:31
Alignment explanation
Indices: 41089--41149 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
41079 ATATTTTAAA
* *
41089 TAAATTTAATTTTTTATCTAAATTCATTTTT
1 TAAATTTAATTTTTTATCAAAAATCATTTTT
41120 TAAATTTAATATTTTTATCAAAAAT-ATTTT
1 TAAATTTAAT-TTTTTATCAAAAATCATTTT
41150 AAATTCTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
TAAATTTAATTTTTTATCAAAAATCATTTTT
Found at i:41561 original size:11 final size:11
Alignment explanation
Indices: 41545--41569 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41535 TCTAGAGGGT
41545 TTTTTTTTTTC
1 TTTTTTTTTTC
41556 TTTTTTTTTTC
1 TTTTTTTTTTC
41567 TTT
1 TTT
41570 CTTTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:41564 original size:15 final size:15
Alignment explanation
Indices: 41544--41573 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41534 ATCTAGAGGG
41544 TTTTTTTT-TTTCTT
1 TTTTTTTTCTTTCTT
41558 TTTTTTTTCTTTCTT
1 TTTTTTTTCTTTCTT
41573 T
1 T
41574 CATGTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCTTTCTT
Found at i:41777 original size:96 final size:93
Alignment explanation
Indices: 41579--41991 Score: 434
Period size: 86 Copynumber: 4.5 Consensus size: 93
41569 TCTTTCATGT
* * *
41579 TTTTCTTTTAGTAATATTTTTGTCTAAGATGGGAAAATTAGGGGAAAAAATCGAAAATCAACAGA
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
*
41644 TTTCTGGATC----TA-TTTTTT--ATG
66 TTTCTGGATCTAGGTATTTTTTTCCCTG
**
41665 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGGGAAAATCGAAAATCAACAAA
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
41730 TTTCTGGATCTAGGGTATTTTTTTTCCCTG
66 TTTCTGGATCTA-GGTA-TTTTTTTCCCTG
* * * * * *
41760 TTTTCCTTTTGGTAATATTTTTTTCTACGAGACGGGAAAAATAGGGG-AAAAATTGAAAATTACC
1 TTTT-CTTTTAGTAATATTTTTCTCTA--AGACGGGAAAATTAGGGGAAAAAATCGAAAATCAAC
* ** *
41824 AAATTTCTGGCT-TTCG-ATTCTTTTCCCTGTTG
63 AAATTTCTGGATCTAGGTATTTTTTTCCC---TG
* * * *
41856 TTTTTCTTTTATTAATATTTTTCTCTGAGACGGGAAAATTAGGGAAAGAAAATCGAGAATCAACA
1 -TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAA-AAAATCGAAAATCAACA
* **
41921 AATTTCTGGATCTAGGTTTTTTTTTCGTTG
64 AATTTCTGGATCTAGGTATTTTTTTCCCTG
* *
41951 TTTTCTTTTAGTAATA-TTTTCTCTGAGACGAGAAAATTAGG
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGG
41992 AAAAAAAAAA
Statistics
Matches: 271, Mismatches: 36, Indels: 33
0.80 0.11 0.10
Matches are distributed among these distances:
86 70 0.26
91 2 0.01
93 39 0.14
94 32 0.12
95 10 0.04
96 64 0.24
97 30 0.11
98 24 0.09
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (93 bp):
TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
TTTCTGGATCTAGGTATTTTTTTCCCTG
Found at i:63909 original size:313 final size:314
Alignment explanation
Indices: 63301--63910 Score: 872
Period size: 314 Copynumber: 1.9 Consensus size: 314
63291 ATACGAAACG
* * *
63301 TTATTGTTGCATTCTTCATTATTTTTGTTGATCGTCATTTCCATGCTTACTCGAGTTAAAATTAG
1 TTATTGTTGCATTCTTCATAATTTTTGTTGATCGCCATTTCCATGCTTACTCGAGTGAAAATTAG
* * *
63366 TTGTTAATCTCTCTATATTGTTAAAAATTAAATATGCTCTGCAAGTTCAGTGAAATTATGAAATT
66 TTGTTAACCTCTATATATTGTTAAAAATTAAATATACTCTGCAAGTTCAGTGAAATTATGAAATT
* *
63431 TGAAGTCATAAAGTTTGTCTATGTTACCTGCGATGGATAATTTAGTAGATGTAAGTTTTTTATTA
131 TGAAGTCATAAAGTTTGTCTATGTTACCTGCGATGGATAATTTAGTAGATGTAAGTTGTTAATTA
* ** * *
63496 ATTGTTTTTCACTTAATTAGGAATAGGAATTTATTATTATTTTTTTTGGTATTTCTTTTTATTAA
196 ATTGTTTTTCACTTAATTAAGAATAGGAATTTATTAAAATTTTTTTTGCTATTTCTTTTGATTAA
*
63561 ATTGAGATGATTATGCAATGTTTGGAAAACTTATTTTTTAGTTTAGATGATACT
261 ATTAAGATGATTATGCAATGTTTGGAAAACTTATTTTTTAGTTTAGATGATACT
* * * * * *
63615 TTATTGTTGCATTCTTCATAATTTTT-TT-ATGGCCGTTTCCTTGCTTATTTGAGCTGGAAATTA
1 TTATTGTTGCATTCTTCATAATTTTTGTTGATCGCCATTTCCATGCTTACTCGAG-TGAAAATTA
*
63678 GTTGTTAACCTCTATATATTGTTAAAAATTAAATATACTCTGCAAGTTTTAGTGAAATTATGAAA
65 GTTGTTAACCTCTATATATTGTTAAAAATTAAATATACTCTGCAAG-TTCAGTGAAATTATGAAA
* * *
63743 TTTGAAGTCATAAAGTTTGTCTATGTTGCTTTCGATGGATAATTTAGTAGATGTAAGTTGTTAAT
129 TTTGAAGTCATAAAGTTTGTCTATGTTACCTGCGATGGATAATTTAGTAGATGTAAGTTGTTAAT
* * *
63808 T-ATTTTTTTTCACTTAATTAAGAATAGG-ATTTTTTAAAATTATTTTTTGCTTTTTCTTTTCGA
194 TAATTGTTTTTCACTTAATTAAGAATAGGAATTTATTAAAATT-TTTTTTGCTATTTCTTTT-GA
* *
63871 TTAGAA-TAAGATGATTAT-CCATGTTTGGAAATCTTATTTT
257 TTA-AATTAAGATGATTATGCAATGTTTGGAAAACTTATTTT
63911 CAGTTTTAAG
Statistics
Matches: 262, Mismatches: 29, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
312 29 0.11
313 113 0.43
314 118 0.45
315 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.48
Consensus pattern (314 bp):
TTATTGTTGCATTCTTCATAATTTTTGTTGATCGCCATTTCCATGCTTACTCGAGTGAAAATTAG
TTGTTAACCTCTATATATTGTTAAAAATTAAATATACTCTGCAAGTTCAGTGAAATTATGAAATT
TGAAGTCATAAAGTTTGTCTATGTTACCTGCGATGGATAATTTAGTAGATGTAAGTTGTTAATTA
ATTGTTTTTCACTTAATTAAGAATAGGAATTTATTAAAATTTTTTTTGCTATTTCTTTTGATTAA
ATTAAGATGATTATGCAATGTTTGGAAAACTTATTTTTTAGTTTAGATGATACT
Done.