Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008882.1 Kokia drynarioides strain JFW-HI SEQ_123569, 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: 44012
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--82 Score: 111
Period size: 2 Copynumber: 43.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42 GT A- AT -T A- AA AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80 AT A
1 AT A
83 AAGAATAAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
1 5 0.07
2 67 0.93
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2676 original size:20 final size:19
Alignment explanation
Indices: 2648--2686 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2638 GCATAAATCA
*
2648 AAATAAGAGATGAGATGATG
1 AAATAAGAGAGGAGA-GATG
*
2668 AAATGAGAGAGGAGAGATG
1 AAATAAGAGAGGAGAGATG
2687 CTTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.36, T:0.15
Consensus pattern (19 bp):
AAATAAGAGAGGAGAGATG
Found at i:4495 original size:2 final size:2
Alignment explanation
Indices: 4488--4512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4478 TCTAACCTTA
4488 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4513 ACCTAAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7241 original size:3 final size:3
Alignment explanation
Indices: 7233--7265 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
7223 GTTTATTTTC
7233 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7266 TAGGCTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9343 original size:20 final size:20
Alignment explanation
Indices: 9314--9355 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
9304 TTTTTAAAGT
9314 TCCTAATCTCGTATATTCTA
1 TCCTAATCTCGTATATTCTA
*
9334 TCCTACTCTCGTATATTCTA
1 TCCTAATCTCGTATATTCTA
9354 TC
1 TC
9356 ATTTATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (20 bp):
TCCTAATCTCGTATATTCTA
Found at i:10545 original size:15 final size:16
Alignment explanation
Indices: 10509--10544 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10499 AAGAATAGTG
*
10509 TTTTTGAGACTTTTAA
1 TTTTTGAGACTTGTAA
10525 TTTTTGAGACTTGTAA
1 TTTTTGAGACTTGTAA
10541 TTTT
1 TTTT
10545 GGGATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (16 bp):
TTTTTGAGACTTGTAA
Found at i:11475 original size:26 final size:27
Alignment explanation
Indices: 11445--11538 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 27
11435 TGAAATATTA
11445 AAAAGA-AAAATGAAATGAGTAGAAAC
1 AAAAGAGAAAATGAAATGAGTAGAAAC
* *
11471 AAAAGAGGAAAAT--CATGAGTAAGAAAGT
1 AAAAGA-GAAAATGAAATGAGT-AGAAA-C
*
11499 ATATAA-AGAAAAATGAAATTAGTAGAAAC
1 A-A-AAGAG-AAAATGAAATGAGTAGAAAC
11528 AAAAGAGAAAA
1 AAAAGAGAAAA
11539 ATCATGAGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 19
0.69 0.06 0.25
Matches are distributed among these distances:
26 12 0.23
27 11 0.21
28 10 0.19
29 8 0.15
30 7 0.13
31 5 0.09
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (27 bp):
AAAAGAGAAAATGAAATGAGTAGAAAC
Found at i:11482 original size:28 final size:28
Alignment explanation
Indices: 11444--11540 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
11434 GTGAAATATT
11444 AAAA-AGAAAAATGAAATGAGTAGAAAC
1 AAAAGAGAAAAATGAAATGAGTAGAAAC
* * *
11471 AAAAGAGGAAAAT--CATGAGTAAGAAAGT
1 AAAAGAGAAAAATGAAATGAGT-AGAAA-C
*
11499 ATATAA-AGAAAAATGAAATTAGTAGAAAC
1 A-A-AAGAGAAAAATGAAATGAGTAGAAAC
11528 AAAAGAGAAAAAT
1 AAAAGAGAAAAAT
11541 CATGAGTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
26 6 0.11
27 11 0.20
28 17 0.31
29 9 0.16
30 7 0.13
31 5 0.09
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (28 bp):
AAAAGAGAAAAATGAAATGAGTAGAAAC
Found at i:11507 original size:31 final size:30
Alignment explanation
Indices: 11472--11559 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 30
11462 AGTAGAAACA
11472 AAAGAGGAAAATCATGAGTAAGAAAGTATAT
1 AAAGA-GAAAATCATGAGTAAGAAAGTATAT
* * *
11503 AAAGA-AAAATGAAATTAGT-AG-AA--ACA-
1 AAAGAGAAAAT--CATGAGTAAGAAAGTATAT
11529 AAAGAGAAAAATCATGAGTAAGAAAGTATAT
1 AAAGAG-AAAATCATGAGTAAGAAAGTATAT
11560 GAAAAGTGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
26 10 0.24
27 4 0.10
28 7 0.17
29 7 0.17
30 4 0.10
31 10 0.24
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.18
Consensus pattern (30 bp):
AAAGAGAAAATCATGAGTAAGAAAGTATAT
Found at i:11510 original size:57 final size:57
Alignment explanation
Indices: 11446--11559 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
11436 GAAATATTAA
*
11446 AAAGAAAAATGAAATGAGTAGAAACAAAAGAGGAAAATCATGAGTAAGAAAGTATAT
1 AAAGAAAAATGAAATGAGTAGAAACAAAAGAGAAAAATCATGAGTAAGAAAGTATAT
*
11503 AAAGAAAAATGAAATTAGTAGAAACAAAAGAGAAAAATCATGAGTAAGAAAGTATAT
1 AAAGAAAAATGAAATGAGTAGAAACAAAAGAGAAAAATCATGAGTAAGAAAGTATAT
11560 GAAAAGTGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.61, C:0.04, G:0.19, T:0.17
Consensus pattern (57 bp):
AAAGAAAAATGAAATGAGTAGAAACAAAAGAGAAAAATCATGAGTAAGAAAGTATAT
Found at i:11548 original size:26 final size:27
Alignment explanation
Indices: 11459--11553 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 27
11449 GAAAAATGAA
*
11459 ATGAGT-AGAAACAAAAGAGGAAAATC
1 ATGAGTAAGAAACAAAAGAGAAAAATC
* *
11485 ATGAGTAAGAAAGTATATAA-AGAAAAATGAA
1 ATGAGTAAGAAA-CA-A-AAGAGAAAAAT--C
*
11516 ATTAGT-AGAAACAAAAGAGAAAAATC
1 ATGAGTAAGAAACAAAAGAGAAAAATC
11542 ATGAGTAAGAAA
1 ATGAGTAAGAAA
11554 GTATATGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
26 11 0.20
27 12 0.22
28 10 0.19
29 9 0.17
30 7 0.13
31 5 0.09
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (27 bp):
ATGAGTAAGAAACAAAAGAGAAAAATC
Found at i:16899 original size:78 final size:78
Alignment explanation
Indices: 16805--16961 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
16795 GATGCTTTTA
16805 TCCTAGCAAAGAGGAGTAAGAAAGACAGAAGGTTTGGGTTTTTGGGTGATAGCATTACAAAAGAC
1 TCCTAGCAAAGAGGAGTAAGAAAGACAGAAGGTTTGGGTTTTTGGGTGATAGCATTACAAAAGAC
16870 CATTGATTTCTCC
66 CATTGATTTCTCC
*
16883 TCCTAGCAAAGAGGAGTAAGAAAGACAGAAGGTTTGGGTTTTTGGGTGATAGTATTACAAAAGAC
1 TCCTAGCAAAGAGGAGTAAGAAAGACAGAAGGTTTGGGTTTTTGGGTGATAGCATTACAAAAGAC
16948 CATTGATTTCTCC
66 CATTGATTTCTCC
16961 T
1 T
16962 TACTTATGGT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (78 bp):
TCCTAGCAAAGAGGAGTAAGAAAGACAGAAGGTTTGGGTTTTTGGGTGATAGCATTACAAAAGAC
CATTGATTTCTCC
Found at i:17256 original size:37 final size:37
Alignment explanation
Indices: 17215--17298 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
17205 CCAAATTTAT
* * * *
17215 GCCCAAAACTGTCGCTGCATGAGCACTTCTAGATTGC
1 GCCCAAAACTGTCACCGAATGAGCACTTCCAGATTGC
17252 GCCCAAAACTGTCACCGAATGAGCACTTCCAGATTGC
1 GCCCAAAACTGTCACCGAATGAGCACTTCCAGATTGC
* *
17289 ACCTAAAACT
1 GCCCAAAACT
17299 ATCGTCGCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (37 bp):
GCCCAAAACTGTCACCGAATGAGCACTTCCAGATTGC
Found at i:18271 original size:16 final size:16
Alignment explanation
Indices: 18250--18280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18240 TTGTGGATCC
18250 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
18266 CATTTTATCTTTATT
1 CATTTTACCTTTATT
18281 CTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:21948 original size:37 final size:37
Alignment explanation
Indices: 21838--21948 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 37
21828 TCCCCGTAGG
* *
21838 AATATT-TTCGAAA-TGCACCCAAGACTGTTGCTGCAAA
1 AATATTCTTC-AAATTGCACCC-AGAATGTTGCTGCATA
* **
21875 AATATTCTTCAAATTGCATCCAGAACCATTGCTGCATA
1 AATATTCTTCAAATTGCACCCAGAA-TGTTGCTGCATA
* *
21913 AGTATTCTTC-AATTGCACCCAGGAATGTTGTTGCAT
1 AATATTCTTCAAATTGCACCCA-GAATGTTGCTGCAT
21949 TAACATGTCC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 30 0.50
38 30 0.50
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (37 bp):
AATATTCTTCAAATTGCACCCAGAATGTTGCTGCATA
Found at i:21973 original size:26 final size:26
Alignment explanation
Indices: 21944--21993 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
21934 GGAATGTTGT
* *
21944 TGCATTAACATGTCCAGAATTGTCAC
1 TGCATGAACATGTCCAAAATTGTCAC
*
21970 TGCATGAACGTGTCCAAAATTGTC
1 TGCATGAACATGTCCAAAATTGTC
21994 GCCACATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (26 bp):
TGCATGAACATGTCCAAAATTGTCAC
Found at i:27284 original size:21 final size:21
Alignment explanation
Indices: 27255--27305 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
27245 TGGAGTTTTA
*
27255 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCA-CACTT
*
27276 GTTTCGGTAGAAGTCACACTT
1 GTATCGGTAGAAGTCACACTT
27297 GTATCGGTA
1 GTATCGGTA
27306 AAACCATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCACACTT
Found at i:34212 original size:15 final size:17
Alignment explanation
Indices: 34192--34226 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34182 AACAAAATGC
34192 AAAA-ATGGTATTGATA
1 AAAATATGGTATTGATA
34208 AAAATATGGTATTGATA
1 AAAATATGGTATTGATA
34225 AA
1 AA
34227 TTTCAATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (17 bp):
AAAATATGGTATTGATA
Found at i:34361 original size:21 final size:19
Alignment explanation
Indices: 34306--34344 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
34296 CTCAATGAGC
*
34306 AATTTTGGTATCGATAAAA
1 AATTATGGTATCGATAAAA
34325 AATTATGGTATCGATAAAA
1 AATTATGGTATCGATAAAA
34344 A
1 A
34345 TCATATGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (19 bp):
AATTATGGTATCGATAAAA
Found at i:37211 original size:21 final size:21
Alignment explanation
Indices: 37186--37229 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
37176 ATTCTTATAC
37186 GATATATGTTTATGAAAATAT
1 GATATATGTTTATGAAAATAT
*
37207 GATATATGTTTCTGAAAATAT
1 GATATATGTTTATGAAAATAT
37228 GA
1 GA
37230 CATTCTGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (21 bp):
GATATATGTTTATGAAAATAT
Found at i:37265 original size:33 final size:35
Alignment explanation
Indices: 37202--37292 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 35
37192 TGTTTATGAA
* *
37202 AATATGATATATGT-T-TCTGAAAATATGACATTCT
1 AATATGATATATGTATATGTG-TAATATGACATTCT
*
37236 GAGT-TGATATATGT-TATG-GTAATATGACATTCT
1 -AATATGATATATGTATATGTGTAATATGACATTCT
37269 AATATGATATATGTATATGTGTAA
1 AATATGATATATGTATATGTGTAA
37293 ATTATAAGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.04
33 23 0.48
34 16 0.33
35 7 0.15
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (35 bp):
AATATGATATATGTATATGTGTAATATGACATTCT
Found at i:38448 original size:241 final size:241
Alignment explanation
Indices: 38157--38617 Score: 676
Period size: 241 Copynumber: 1.9 Consensus size: 241
38147 TATTATATTA
*
38157 TAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCATTTAT-TCATATATA
1 TAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCATTGATGTC-TATATA
* * * *
38221 TAAACTATTTATTTATTATATACTATATGATATAATATAACATTTTATAATATAAT-AGTAGGGC
65 TAAACTATTAATATATTATATACTATATGATATAATATAACATTATATAATATAATAAG-AAGGC
* * * * *
38285 TAACTTTCAAATATACAAAAAGTAT-AGGATTTTAAAACATATTTCAACCAGTATAACAATAAAT
129 TAACTTTCAAATACACAAAAAGTATAAGGA-CTCAAAACATATTTCAACCAATATAACAATAAAC
*
38349 AATAATATTTGATAATAATTAATATATAATATATAATTTTTTTTTTTTG
193 AATAATATATGATAATAATTAATATATAATATATAATTTTTTTTTTTTG
* * *
38398 TAGATTATAATAAAAGATATAGTATTGCATGATATTATAGTGTTTAATCATTGATGTCTATATAT
1 TAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCATTGATGTCTATATAT
* * *
38463 AAACTATTAATATATTATATACTATATGATATGATATATCATTATATAATATAATAAGAAGGTTA
66 AAACTATTAATATATTATATACTATATGATATAATATAACATTATATAATATAATAAGAAGGCTA
* * * * *
38528 ACTTTCAAATGCACAAAAATTATAAGGACTCAAAGCATATTTCAACCAATATAATAATAACCAAT
131 ACTTTCAAATACACAAAAAGTATAAGGACTCAAAACATATTTCAACCAATATAACAATAAACAAT
38593 AATATATGATAATAATTAATATATA
196 AATATATGATAATAATTAATATATA
38618 TGTACAACTC
Statistics
Matches: 195, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
241 187 0.96
242 8 0.04
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (241 bp):
TAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCATTGATGTCTATATAT
AAACTATTAATATATTATATACTATATGATATAATATAACATTATATAATATAATAAGAAGGCTA
ACTTTCAAATACACAAAAAGTATAAGGACTCAAAACATATTTCAACCAATATAACAATAAACAAT
AATATATGATAATAATTAATATATAATATATAATTTTTTTTTTTTG
Found at i:38613 original size:20 final size:19
Alignment explanation
Indices: 38576--38619 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
38566 ATTTCAACCA
*
38576 ATATAATAATAACCAATAAT
1 ATATGATAATAACCAAT-AT
**
38596 ATATGATAATAATTAATAT
1 ATATGATAATAACCAATAT
38615 ATATG
1 ATATG
38620 TACAACTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
ATATGATAATAACCAATAT
Found at i:39343 original size:27 final size:28
Alignment explanation
Indices: 39299--39368 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
39289 TATTTTGGAC
*
39299 TTGAGATTTGGGCTATAAT-TATTTTATT
1 TTGAG-TTTGGGCTATAATGTATATTATT
39327 TTGAGTTTGGG-TAATAATGAGTATATTATT
1 TTGAGTTTGGGCT-ATAAT--GTATATTATT
39357 TTG-GTTTGGGCT
1 TTGAGTTTGGGCT
39369 TAGTATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 1 0.03
27 11 0.31
28 5 0.14
29 7 0.19
30 12 0.33
ACGTcount: A:0.23, C:0.03, G:0.24, T:0.50
Consensus pattern (28 bp):
TTGAGTTTGGGCTATAATGTATATTATT
Found at i:41214 original size:15 final size:16
Alignment explanation
Indices: 41194--41231 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
41184 TGGCTCCCTC
41194 AAATTTAATTTTTTA-
1 AAATTTAATTTTTTAT
41209 AAATTTAATTTTTTAT
1 AAATTTAATTTTTTAT
41225 AAATTTA
1 AAATTTA
41232 TATTATGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTAATTTTTTAT
Found at i:42787 original size:96 final size:96
Alignment explanation
Indices: 42598--42789 Score: 212
Period size: 96 Copynumber: 2.0 Consensus size: 96
42588 ATCTTGGGAA
* * ** *
42598 AAGGATGTTTGATTATCCCGATTTGACGAAAGGTTGCACCTAGTAAGTTAAGGTGCAAATTTTCA
1 AAGGATGTTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGTGCAAATTTTCA
* * *
42663 GAATCGGAGATAAGGAAACATTGTCTCGATT
66 GAATCGGAAATAAAGAAACATTGCCTCGATT
* **
42694 AAGGGTGTTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGG-GACAAATTTTC
1 AAGGATGTTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGTG-CAAATTTTC
*
42758 -GAAACTC-GAAATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGGAAATAAAGA-AACATTGCCTCGATT
42790 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.94
97 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATGTTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGTGCAAATTTTCA
GAATCGGAAATAAAGAAACATTGCCTCGATT
Found at i:43135 original size:30 final size:30
Alignment explanation
Indices: 43099--43408 Score: 328
Period size: 29 Copynumber: 10.7 Consensus size: 30
43089 ATTCGGGGGT
43099 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
43129 AAAATGGAATTTTTGGAAG-TTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* * *
43158 AAAATGGGATTTTTTGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
43188 AAAATGGAA----T-----TTTTAGGGTTAA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTT-A
* **
43210 AAAATGGAATTTTTGGTAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
43239 AAAATGGTATTTTTGGAAGTTTTGGGGTT-
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
*
43268 AAAATGGAATTTTTGGAAGTTTTGGGGTT-
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
43297 AAAATGGAATTTTTGGAAG-TTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
43326 AAAATGGGATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
* *
43356 AAAACT-AAATTTTTGGAAG-TTTCGAGGTTA
1 AAAA-TGGAATTTTTGGAAGTTTTAG-GGTTA
*
43386 AAAATGGGATTTTTGGAAAGTTT
1 AAAATGGAATTTTTGG-AAGTTT
43409 AATGACCTTC
Statistics
Matches: 236, Mismatches: 25, Indels: 36
0.79 0.08 0.12
Matches are distributed among these distances:
21 9 0.04
22 10 0.04
26 2 0.01
28 6 0.03
29 120 0.51
30 77 0.33
31 10 0.04
32 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.39
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGTTA
Found at i:43201 original size:21 final size:22
Alignment explanation
Indices: 43177--43223 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
43167 TTTTTTGAAG
43177 TTTTAAGGTT-AAAAATGGAAT
1 TTTTAAGGTTAAAAAATGGAAT
*
43198 TTTTAGGGTTAAAAAATGGAAT
1 TTTTAAGGTTAAAAAATGGAAT
43220 TTTT
1 TTTT
43224 GGTAGTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (22 bp):
TTTTAAGGTTAAAAAATGGAAT
Found at i:43241 original size:51 final size:51
Alignment explanation
Indices: 43148--43252 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 51
43138 TTTTTGGAAG
* * * *
43148 TTTAGGGTTAAAAATGGGATTTTTTGAAGTTTTAAGGTTAAAAATGGAATT
1 TTTAGGGTTAAAAATGGAATTTTTGGAAGTTTCAAGGGTAAAAATGGAATT
* * *
43199 TTTAGGGTTAAAAAATGGAATTTTTGGTAG-TTCGAGGGTAAAAATGGTATT
1 TTTAGGGTT-AAAAATGGAATTTTTGGAAGTTTCAAGGGTAAAAATGGAATT
43250 TTT
1 TTT
43253 GGAAGTTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
51 29 0.63
52 17 0.37
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (51 bp):
TTTAGGGTTAAAAATGGAATTTTTGGAAGTTTCAAGGGTAAAAATGGAATT
Found at i:43253 original size:110 final size:110
Alignment explanation
Indices: 43099--43408 Score: 317
Period size: 110 Copynumber: 2.7 Consensus size: 110
43089 ATTCGGGGGT
**
43099 AAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAG-TTTAGGGTTAAAAAT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTTAGGGTT-AAAAT
* *
43163 GGGATTTTTTGAAGTTTTAAGGTTAAAAATGGAATTTTTAGGGTTAA
65 GGAATTTTTGGAAGTTTTAAGGTT-AAAATGGAATTTTTAGGGTTAA
* * *
43210 AAAATGGAATTTTTGGTAGTTCGAGGG-TAAAAATGGTATTTTTGGAAGTTTTGGGGTTAAAATG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAATG
**
43274 GAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTT-GGAAGTTCAGGGGTA
66 GAATTTTTGGAAGTTTTAAGGTTAAAATGGAATTTTTAGG--GTT-A-----A
* * * *
43326 AAAATGGGATTTTTGGAAGTTTTG-GGGTTAAAAACT-AAATTTTTGGAAG-TTTCGAGGTTAAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTTAAAAA-TGGAATTTTTGGAAGTTTTAG-GGTT-AA
*
43388 AATGGGATTTTTGGAAAGTTT
62 AATGGAATTTTTGG-AAGTTT
43409 AATGACCTTC
Statistics
Matches: 168, Mismatches: 16, Indels: 22
0.82 0.08 0.11
Matches are distributed among these distances:
108 2 0.01
109 14 0.08
110 48 0.29
111 33 0.20
116 25 0.15
117 24 0.14
118 16 0.10
119 6 0.04
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.39
Consensus pattern (110 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAATG
GAATTTTTGGAAGTTTTAAGGTTAAAATGGAATTTTTAGGGTTAA
Done.