Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009469.1 Kokia drynarioides strain JFW-HI SEQ_124177, 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: 332091
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 151 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:263036 original size:29 final size:29
Alignment explanation
Indices: 262992--263073 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
262982 CAAAAATGCG
** *
262992 ATTTTTGGATGCTCGAGGGTAAAACAATA
1 ATTTTTGGACACTCGAGGGCAAAACAATA
***
263021 A-TTTTGGACACTTCGAGGGCAAAATGGTA
1 ATTTTTGGACAC-TCGAGGGCAAAACAATA
263050 ATTTTTGGACACTCGAGGGCAAAA
1 ATTTTTGGACACTCGAGGGCAAAA
263074 TGGTAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.18
29 27 0.60
30 10 0.22
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (29 bp):
ATTTTTGGACACTCGAGGGCAAAACAATA
Found at i:263058 original size:30 final size:30
Alignment explanation
Indices: 263022--263260 Score: 185
Period size: 29 Copynumber: 8.2 Consensus size: 30
263012 AAAACAATAA
263022 TTTTGGACACTTCGAGGGCAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
263052 TTTTGGACAC-TCGAGGGCAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
* ** ** *
263081 TTTTAGA-TGTTC-AGGGGTGAAACGGTAA-
1 TTTTGGACACTTCGA-GGGCAAAATGGTAAT
*
263109 TTTTGAACACTT-G-GGGCAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
*
263137 TTTTGGACAC-TCGAGGGCAAAATTGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
* * * *
263166 TTTTGGAAATTTAG-GGGTAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
* * * *
263195 TTTTAGA-AGTTTGAGGGGTAAAAAT-GTAAT
1 TTTTGGACACTTCGA-GGG-CAAAATGGTAAT
* * * * *
263225 TTTTAGATATTTAG-GGGTAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAAT
263254 TTTTGGA
1 TTTTGGA
263261 AGTTTAGGGG
Statistics
Matches: 168, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
27 12 0.07
28 25 0.15
29 95 0.57
30 27 0.16
31 9 0.05
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (30 bp):
TTTTGGACACTTCGAGGGCAAAATGGTAAT
Found at i:263081 original size:58 final size:59
Alignment explanation
Indices: 263022--263198 Score: 177
Period size: 56 Copynumber: 3.1 Consensus size: 59
263012 AAAACAATAA
263022 TTTTGGACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAAATGGTAAT
* ** ** * * *
263081 TTTTAGA-TGTTC-AGGGGTGAAACGGTAA-TTTTGAACACTTG-GGGCAAAATGGTAAT
1 TTTTGGACACTTCGA-GGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAAATGGTAAT
* * ** *
263137 TTTTGGACAC-TCGAGGGCAAAATTGTAATTTTTGGA-AATTTAGGGGTAAAATGGTAAT
1 TTTTGGACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGA-GGGCAAAATGGTAAT
263195 TTTT
1 TTTT
263199 AGAAGTTTGA
Statistics
Matches: 93, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
56 36 0.39
57 19 0.20
58 32 0.34
59 6 0.06
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (59 bp):
TTTTGGACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAAATGGTAAT
Found at i:263146 original size:85 final size:87
Alignment explanation
Indices: 263008--263197 Score: 276
Period size: 85 Copynumber: 2.2 Consensus size: 87
262998 GGATGCTCGA
** *
263008 GGGTAAAACAATAATTTTGGACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAA
1 GGGTAAAACGGTAATTTTGAACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAA
**
263073 ATGGTAATTTTTAGATGTTCAG
66 ATGGTAATTTTTAGAAATTCAG
*
263095 GGGTGAAACGGTAATTTTGAACACTT-G-GGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAA
1 GGGTAAAACGGTAATTTTGAACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAA
* * *
263158 ATTGTAATTTTTGGAAATTTAG
66 ATGGTAATTTTTAGAAATTCAG
*
263180 GGGTAAAATGGTAATTTT
1 GGGTAAAACGGTAATTTT
263198 TAGAAGTTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 69 0.75
86 1 0.01
87 22 0.24
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (87 bp):
GGGTAAAACGGTAATTTTGAACACTTCGAGGGCAAAATGGTAATTTTTGGACACTCGAGGGCAAA
ATGGTAATTTTTAGAAATTCAG
Found at i:263211 original size:58 final size:58
Alignment explanation
Indices: 263035--263484 Score: 264
Period size: 58 Copynumber: 7.7 Consensus size: 58
263025 TGGACACTTC
* * * * * * *
263035 GAGGGCAAAATGGTAATTTTTGGACA-CTCGAGGGCAAAATGGTAATTTTTAGATG-TT
1 GAGGGGAAAATGGTAATTTTTGGAAATTTAG-GGGTAAAATGGTAATTTTTGGAAGTTT
* * * * * * *
263092 CAGGGGTGAAACGGTAA-TTTT-GAACACTT-GGGGCAAAATGGTAATTTTTGGACA-CTC
1 GAGGGG-AAAATGGTAATTTTTGGAA-ATTTAGGGGTAAAATGGTAATTTTTGGA-AGTTT
* * *
263149 GAGGGCAAAATTGTAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTAGAAGTTT
1 GAGGGGAAAATGGTAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAGTTT
* *
263207 GAGGGGTAAAAAT-GTAATTTTTAGATATTTAGGGGTAAAATGGTAATTTTTGGAAGTTT
1 GAGGGG--AAAATGGTAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAGTTT
* *** * *
263266 -AGGGGAAAATAGTAATTTTCAAAAATTTCA-AGGTCAAAAATGAT-ATTTTTGGAAGTTT
1 GAGGGGAAAATGGTAATTTTTGGAAATTT-AGGGGT--AAAATGGTAATTTTTGGAAGTTT
* * * * * * ** *
263324 G-GGGGTAAATAGTAATTTTTGGAAGTTCAAGGATAAAAATGTGATTTTTTTTTGGAGGTTT
1 GAGGGGAAAATGGTAATTTTTGGAAATTTAGGGGT-AAAATG-G--TAATTTTTGGAAGTTT
* * * ** *
263385 -AGGGGTAAATGGTAATCTTTGGAAGTTTAGAGGCAAAAAT-GCAATTTTTGGAAAGTTT
1 GAGGGGAAAATGGTAATTTTTGGAAATTTAG-GGGTAAAATGGTAATTTTTGG-AAGTTT
*
263443 GAGGGTAAAAAT-GTAA-TTTTGGAAAGTTTAGGGGTCAAAATG
1 GAGGG-GAAAATGGTAATTTTTGGAAA-TTTAGGGGT-AAAATG
263485 TGATTACTGA
Statistics
Matches: 309, Mismatches: 55, Indels: 55
0.74 0.13 0.13
Matches are distributed among these distances:
56 35 0.11
57 55 0.18
58 96 0.31
59 69 0.22
60 10 0.03
61 42 0.14
62 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (58 bp):
GAGGGGAAAATGGTAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAGTTT
Found at i:263241 original size:29 final size:29
Alignment explanation
Indices: 263070--263484 Score: 203
Period size: 29 Copynumber: 14.2 Consensus size: 29
263060 ACTCGAGGGC
* *
263070 AAAATGGTAATTTTTAGATGTTCAGGGGT
1 AAAATGGTAATTTTTAGAAGTTTAGGGGT
* * ** *
263099 GAAACGGTAA-TTTT-GAACACTT-GGGGC
1 AAAATGGTAATTTTTAGAA-GTTTAGGGGT
* * ** *
263126 AAAATGGTAATTTTTGGACACTCGA-GGGC
1 AAAATGGTAATTTTTAGA-AGTTTAGGGGT
* * *
263155 AAAATTGTAATTTTTGGAAATTTAGGGGT
1 AAAATGGTAATTTTTAGAAGTTTAGGGGT
263184 AAAATGGTAATTTTTAGAAGTTTGAGGGGT
1 AAAATGGTAATTTTTAGAAGTTT-AGGGGT
263214 AAAAAT-GTAATTTTTAGATA-TTTAGGGGT
1 -AAAATGGTAATTTTTAGA-AGTTTAGGGGT
*
263243 AAAATGGTAATTTTTGGAAGTTTAGGGG-
1 AAAATGGTAATTTTTAGAAGTTTAGGGGT
* * * * *
263271 AAAATAGTAATTTTCAAAAATTTCA-AGGT
1 AAAATGGTAATTTTTAGAAGTTT-AGGGGT
* * *
263300 CAAAAATGAT-ATTTTTGGAAGTTTGGGGGT
1 --AAAATGGTAATTTTTAGAAGTTTAGGGGT
* * * * *
263330 -AAATAGTAATTTTTGGAAGTTCAAGGAT
1 AAAATGGTAATTTTTAGAAGTTTAGGGGT
** * *
263358 AAAAATGTGATTTTTTTTTGGAGGTTTAGGGGT
1 -AAAATG-G--TAATTTTTAGAAGTTTAGGGGT
* * **
263391 -AAATGGTAATCTTTGGAAGTTTAGAGGCA
1 AAAATGGTAATTTTTAGAAGTTTAG-GGGT
* *
263420 AAAAT-GCAATTTTTGGAAAGTTT-GAGGGT
1 AAAATGGTAATTTTTAG-AAGTTTAG-GGGT
*
263449 AAAAAT-GTAA-TTTTGGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTTAG-AAGTTTAGGGGT
263478 CAAAATG
1 -AAAATG
263485 TGATTACTGA
Statistics
Matches: 297, Mismatches: 61, Indels: 55
0.72 0.15 0.13
Matches are distributed among these distances:
27 19 0.06
28 68 0.23
29 117 0.39
30 59 0.20
31 18 0.06
33 16 0.05
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGAAGTTTAGGGGT
Found at i:263423 original size:61 final size:61
Alignment explanation
Indices: 263253--263425 Score: 169
Period size: 61 Copynumber: 2.9 Consensus size: 61
263243 AAAATGGTAA
* ** * * *
263253 TTTTTGGAAGTTTAGGGGAAAATAGTAAT-TTTCAAAAATTTCAAGGTCAAAAA--TGA--TA
1 TTTTTGGAAGTTTAGGGGTAAATAGTAATCTTT--GGAAGTTCAAGGACAAAAATGTGATTTT
* * *
263311 TTTTTGGAAGTTTGGGGGTAAATAGTAATTTTTGGAAGTTCAAGGATAAAAATGTGATTTT
1 TTTTTGGAAGTTTAGGGGTAAATAGTAATCTTTGGAAGTTCAAGGACAAAAATGTGATTTT
* * *
263372 TTTTTGGAGGTTTAGGGGTAAATGGTAATCTTTGGAAGTTTAGAGG-CAAAAATG
1 TTTTTGGAAGTTTAGGGGTAAATAGTAATCTTTGGAAGTTCA-AGGACAAAAATG
263426 CAATTTTTGG
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
57 14 0.15
58 27 0.28
59 6 0.06
61 45 0.47
62 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.37
Consensus pattern (61 bp):
TTTTTGGAAGTTTAGGGGTAAATAGTAATCTTTGGAAGTTCAAGGACAAAAATGTGATTTT
Found at i:264420 original size:3 final size:3
Alignment explanation
Indices: 264414--264455 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
264404 TTTTTATTCT
* **
264414 TTA TTA TTA ATA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
264456 ATTCATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:265127 original size:11 final size:11
Alignment explanation
Indices: 265111--265186 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 11
265101 ATTTTGGACT
265111 TTTAAATTAAA
1 TTTAAATTAAA
*
265122 TTTAAAATTAAG
1 TTT-AAATTAAA
*
265134 TTTAAA--ACTA
1 TTTAAATTA-AA
265144 TTTCAAATTTAAA
1 TTT-AAA-TTAAA
265157 -TTAAATTTAAA
1 TTTAAA-TTAAA
**
265168 TTTAAAACAAA
1 TTTAAATTAAA
265179 TTTAAATT
1 TTTAAATT
265187 TAAAAATCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
9 1 0.02
10 3 0.06
11 27 0.54
12 17 0.34
13 1 0.02
14 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:265157 original size:6 final size:6
Alignment explanation
Indices: 265111--265190 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
265101 ATTTTGGACT
* * **
265111 TTTAAA -TTAAA TTTAAA ATTAAG TTTAAA ACT--A TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
**
265157 -TTAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
265191 AATCAATTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 37 0.66
7 4 0.07
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:265198 original size:18 final size:17
Alignment explanation
Indices: 265129--265237 Score: 79
Period size: 17 Copynumber: 6.7 Consensus size: 17
265119 AAATTTAAAA
* *
265129 TTAAGTTTAAAAC-TAT
1 TTAAATTTAAAACAAAT
**
265145 TTCAAATTTAAATTAAAT
1 TT-AAATTTAAAACAAAT
265163 TTAAATTTAAAACAAAT
1 TTAAATTTAAAACAAAT
265180 TTAAATTT--AA-AAA-
1 TTAAATTTAAAACAAAT
* *
265193 -TCAATTTAAAACTAAT
1 TTAAATTTAAAACAAAT
*
265209 TTAAACTTAATAA-AAAT
1 TTAAATTTAA-AACAAAT
*
265226 TTAAAATTAAAA
1 TTAAATTTAAAA
265238 GTTTGATTCG
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.08
14 5 0.07
15 4 0.05
16 4 0.05
17 48 0.66
18 6 0.08
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (17 bp):
TTAAATTTAAAACAAAT
Found at i:268856 original size:15 final size:15
Alignment explanation
Indices: 268832--268861 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
268822 TGACTGAAAA
268832 TTAATATTTTTAAAT
1 TTAATATTTTTAAAT
*
268847 TTAATTTTTTTAAAT
1 TTAATATTTTTAAAT
268862 ACATTTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATATTTTTAAAT
Found at i:269250 original size:21 final size:22
Alignment explanation
Indices: 269224--269274 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
269214 TGAAAATTTT
269224 ATATTAAATAAA-AAATTTAAA
1 ATATTAAATAAACAAATTTAAA
* *
269245 ATATT-ATTAAACACATTTAAA
1 ATATTAAATAAACAAATTTAAA
*
269266 AAATTAAAT
1 ATATTAAAT
269275 GTTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATTAAATAAACAAATTTAAA
Found at i:289546 original size:19 final size:19
Alignment explanation
Indices: 289522--289599 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 19
289512 CCAAATTCAA
289522 TTTAAATAATAAAAATATT
1 TTTAAATAATAAAAATATT
* * *
289541 TTTAAA-ATTAAAATTAAT
1 TTTAAATAATAAAAATATT
* *
289559 TATAAAAAATATAAAATA--
1 TTTAAATAATA-AAAATATT
289577 -TTAATATAA-AAAAATATT
1 TTTAA-ATAATAAAAATATT
289595 TTTAA
1 TTTAA
289600 TAGTTTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
16 6 0.13
17 4 0.09
18 17 0.38
19 13 0.29
20 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAAATAATAAAAATATT
Found at i:289837 original size:6 final size:7
Alignment explanation
Indices: 289812--289836 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
289802 ATTTAAACGT
289812 TTTTTAG
1 TTTTTAG
289819 TTTTTAG
1 TTTTTAG
289826 TTTTTAG
1 TTTTTAG
289833 TTTT
1 TTTT
289837 AAAGAGTTTA
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:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTTAG
Found at i:306549 original size:18 final size:17
Alignment explanation
Indices: 306518--306553 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
306508 TATTTCAAAT
306518 TTATTTTAAGTTTAAAA
1 TTATTTTAAGTTTAAAA
* *
306535 TTATTTTAAATTTTAAA
1 TTATTTTAAGTTTAAAA
306552 TT
1 TT
306554 TAAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATTTTAAGTTTAAAA
Found at i:307257 original size:13 final size:13
Alignment explanation
Indices: 307239--307272 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
307229 ATTAATTACG
307239 CATTATTTTTTAT
1 CATTATTTTTTAT
*
307252 CATTATTATTTAT
1 CATTATTTTTTAT
*
307265 TATTATTT
1 CATTATTT
307273 ACTTCAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
CATTATTTTTTAT
Found at i:308388 original size:30 final size:28
Alignment explanation
Indices: 308347--308839 Score: 295
Period size: 29 Copynumber: 16.9 Consensus size: 28
308337 AAAGTTCATG
308347 AACTGTCCAAAAATTACATTTTAACCCTA
1 AACT-TCCAAAAATTACATTTTAACCCTA
*
308376 GAACTTCACAAAAATTACATTTTTTACCCTTA
1 -AACTTC-CAAAAATTACA-TTTTAACCC-TA
* *
308408 AACTTCTCAAAAATTTCATTTTTACCCTAA
1 AACTTC-CAAAAATTACATTTTAACCCT-A
* * * *
308438 AACTTCCAAAAATTCCATTTTTGATCTTA
1 AACTTCCAAAAATTACA-TTTTAACCCTA
* * * *
308467 AATTTTTCCAAAAATCACCTTTTACCCCTA
1 AA--CTTCCAAAAATTACATTTTAACCCTA
* * * *
308497 AACTTTCTAAAATTACATTTTTACTCTA
1 AACTTCCAAAAATTACATTTTAACCCTA
*
308525 AACTTTCCAAAAATTACAATTTAACCCTA
1 AAC-TTCCAAAAATTACATTTTAACCCTA
* *
308554 AATTTCAAAAAATT-CTATTTTTAA-CCTCA
1 AACTTCCAAAAATTAC-A-TTTTAACCCT-A
*
308583 AACTTTCCAAAAATTACCATTTTACCCCTA
1 AAC-TTCCAAAAATTA-CATTTTAACCCTA
* * * * * *
308613 AATTTCCAAAAACTCCATTTTTGACCTTG
1 AACTTCCAAAAATTACA-TTTTAACCCTA
* * *
308642 AATTTCCAAAAAATTACCATTTTAGCCCCA
1 AACTTCC-AAAAATTA-CATTTTAACCCTA
* * * *
308672 AA-TTCCAAAAATTCCATTTTGACCATG
1 AACTTCCAAAAATTACATTTTAACCCTA
308699 AAC-TCCTAAAAATTACCATTTT-ACCCTTA
1 AACTTCC-AAAAATTA-CATTTTAACCC-TA
*
308728 AACTTCCAAAAA-TATCATTTTTGACCC-A
1 AACTTCCAAAAATTA-CA-TTTTAACCCTA
* * *
308756 AATTTTCCAAAAATTACA-ATTGACCCTA
1 AA-CTTCCAAAAATTACATTTTAACCCTA
* *
308784 AACTTTCC-AAAATTACCATTTTACCCCTCG
1 AAC-TTCCAAAAATTA-CATTTTAACCCT-A
* *
308814 AA-TGTTCAAAAATTACATTTTTACCC
1 AACT-TCCAAAAATTACATTTTAACCC
308840 CCGAGTGTCC
Statistics
Matches: 361, Mismatches: 68, Indels: 69
0.72 0.14 0.14
Matches are distributed among these distances:
27 28 0.08
28 71 0.20
29 121 0.34
30 97 0.27
31 41 0.11
32 3 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTAACCCTA
Found at i:308493 original size:59 final size:57
Alignment explanation
Indices: 308352--308805 Score: 354
Period size: 59 Copynumber: 7.8 Consensus size: 57
308342 TCATGAACTG
* * * *
308352 TCCAAAAATTACATTTTAACCCTAGAACTTCACAAAAATTACATTTTTTACCCTTAAA-CT
1 TCCAAAAATTACCTTTT-ACCCTA-AACTTC-CAAAAATTCCATTTTTGA-CCTTAAATTT
* * *
308412 TCTCAAAAATTTCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTGATCTTAAATTTT
1 TC-CAAAAATTAC-CTTTTACCCT-AAACTTCCAAAAATTCCATTTTTGACCTTAAA-TTT
* * * * *
308473 TCCAAAAATCACCTTTTACCCCTAAACTTTCTAAAATTACATTTTT-A-CTCTAAACTT
1 TCCAAAAATTACCTTTTA-CCCTAAACTTCCAAAAATTCCATTTTTGACCT-TAAATTT
* * * * * * * *
308530 TCCAAAAATTACAATTTAACCCTAAATTTCAAAAAATTCTATTTTTAACCTCAAACTT
1 TCCAAAAATTAC-CTTTTACCCTAAACTTCCAAAAATTCCATTTTTGACCTTAAATTT
* * *
308588 TCCAAAAATTACCATTTTACCCCTAAATTTCCAAAAACTCCATTTTTGACCTTGAA-TT
1 TCCAAAAATTACC-TTTTA-CCCTAAACTTCCAAAAATTCCATTTTTGACCTTAAATTT
* * * *
308646 TCCAAAAAATTACCATTTTAGCCCCAAA-TTCCAAAAATTCCA-TTTTGACCATGAA--C
1 TCC-AAAAATTACC-TTTTA-CCCTAAACTTCCAAAAATTCCATTTTTGACCTTAAATTT
*
308702 TCCTAAAAATTACCATTTTACCCTTAAACTTCCAAAAATAT-CATTTTTGACC-CAAATTT
1 TCC-AAAAATTACC-TTTTACCC-TAAACTTCCAAAAAT-TCCATTTTTGACCTTAAATTT
** *
308761 TCCAAAAATTACAATTGACCCTAAACTTTCC-AAAATTACCATTTT
1 TCCAAAAATTACCTTTTACCCTAAAC-TTCCAAAAATT-CCATTTT
308806 ACCCCTCGAA
Statistics
Matches: 328, Mismatches: 44, Indels: 47
0.78 0.11 0.11
Matches are distributed among these distances:
55 4 0.01
56 32 0.10
57 78 0.24
58 68 0.21
59 88 0.27
60 30 0.09
61 23 0.07
62 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (57 bp):
TCCAAAAATTACCTTTTACCCTAAACTTCCAAAAATTCCATTTTTGACCTTAAATTT
Found at i:308795 original size:27 final size:27
Alignment explanation
Indices: 308748--308799 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
308738 AATATCATTT
*
308748 TTGACCCAAATTTTCCAAAAATTACAA
1 TTGACCCAAACTTTCCAAAAATTACAA
308775 TTGACCCTAAACTTTCC-AAAATTAC
1 TTGACCC-AAACTTTCCAAAAATTAC
308800 CATTTTACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (27 bp):
TTGACCCAAACTTTCCAAAAATTACAA
Found at i:308823 original size:29 final size:28
Alignment explanation
Indices: 308789--308855 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
308779 CCCTAAACTT
308789 TCCAAAATTACCA-TTTTACCCCTCGAATG
1 TCCAAAATTA-CATTTTTACCCC-CGAATG
* *
308818 TTCAAAAATTACATTTTTACCCCCGAGTG
1 -TCCAAAATTACATTTTTACCCCCGAATG
308847 TCCAAAATT
1 TCCAAAATT
308856 TTCGTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
29 7 0.21
30 18 0.55
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (28 bp):
TCCAAAATTACATTTTTACCCCCGAATG
Found at i:312403 original size:11 final size:11
Alignment explanation
Indices: 312389--312414 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
312379 AGAGTAGTAT
312389 TATATATTTAG
1 TATATATTTAG
312400 TATATATTTAG
1 TATATATTTAG
312411 TATA
1 TATA
312415 ATCATCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATATTTAG
Found at i:315053 original size:31 final size:29
Alignment explanation
Indices: 314986--315054 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
314976 AAATAAATGG
*
314986 ATTTTTT--AATAAAAAATTAATTTATTC
1 ATTTTTTAAAATAAAAAATTAATTTACTC
*
315013 ATTGATTTAAAATAAAAATATTAATTTACTC
1 ATT-TTTTAAAATAAAAA-ATTAATTTACTC
315044 AATTTTTTAAA
1 -ATTTTTTAAA
315055 TAGACAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 3 0.09
28 3 0.09
30 8 0.24
31 17 0.50
32 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTTTTTAAAATAAAAAATTAATTTACTC
Found at i:315056 original size:30 final size:28
Alignment explanation
Indices: 314986--315056 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
314976 AAATAAATGG
*
314986 ATTTTTT-AATAAAAAATTAATTTATTC
1 ATTTTTTAAATAAAAAATTAATTTACTC
*
315013 ATTGATTTAAAATAAAAATATTAATTTACTC
1 ATT--TTTTAAATAAAAA-ATTAATTTACTC
315044 AATTTTTTAAATA
1 -ATTTTTTAAATA
315057 GACAAGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.08
29 3 0.08
30 16 0.44
31 11 0.31
32 3 0.08
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (28 bp):
ATTTTTTAAATAAAAAATTAATTTACTC
Found at i:315817 original size:2 final size:2
Alignment explanation
Indices: 315812--315857 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
315802 ATATATATAT
*
315812 AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
315854 AG AG
1 AG AG
315858 TCCAACATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:319860 original size:24 final size:26
Alignment explanation
Indices: 319832--319905 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
319822 CGAGCTCATT
319832 CAAAAACACATATTTTAATTTATTAA
1 CAAAAACACATATTTTAATTTATTAA
* * * *
319858 AAAAAACACGTCTTTTAAGTTATT-A
1 CAAAAACACATATTTTAATTTATTAA
* * *
319883 CAATAACA-ATAATTTAATATATT
1 CAAAAACACATATTTTAATTTATT
319906 TTAATATAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
24 10 0.27
25 7 0.19
26 20 0.54
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (26 bp):
CAAAAACACATATTTTAATTTATTAA
Found at i:319873 original size:26 final size:26
Alignment explanation
Indices: 319833--319882 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
319823 GAGCTCATTC
*
319833 AAAAACACATATTTTAATTTATTAAA
1 AAAAACACATATTTTAAGTTATTAAA
* *
319859 AAAAACACGTCTTTTAAGTTATTA
1 AAAAACACATATTTTAAGTTATTA
319883 CAATAACAAT
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:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (26 bp):
AAAAACACATATTTTAAGTTATTAAA
Found at i:319915 original size:15 final size:14
Alignment explanation
Indices: 319892--319936 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
319882 ACAATAACAA
*
319892 TAATTTAATATATTT
1 TAATATAATA-ATTT
*
319907 TAATATAATAAATT
1 TAATATAATAATTT
319921 TAATATAATAAATTT
1 TAATATAAT-AATTT
319936 T
1 T
319937 TAAGACATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATATAATAATTT
Found at i:319924 original size:14 final size:14
Alignment explanation
Indices: 319905--319935 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
319895 TTTAATATAT
319905 TTTAATATAATAAA
1 TTTAATATAATAAA
319919 TTTAATATAATAAA
1 TTTAATATAATAAA
319933 TTT
1 TTT
319936 TTAAGACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAATATAATAAA
Found at i:327616 original size:24 final size:23
Alignment explanation
Indices: 327589--327638 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
327579 TTTTATAAAA
327589 ATTAAATTGTA-ATTTTATCATTTT
1 ATTAAATT-TATATTTTAT-ATTTT
327613 ATT-AATTTATATTTTATATTTT
1 ATTAAATTTATATTTTATATTTT
327635 -TTAA
1 ATTAA
327639 TGATTAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.08
22 8 0.33
23 11 0.46
24 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTAAATTTATATTTTATATTTT
Done.