Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015119.1 Kokia drynarioides strain JFW-HI SEQ_130163, 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: 310394
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 528 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:259757 original size:21 final size:21
Alignment explanation
Indices: 259711--259750 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
259701 TAATTTTAAA
259711 AAATTA-T-AAAAAAATTATT
1 AAATTATTCAAAAAAATTATT
*
259730 AAATTATTCAAAAAATTTATT
1 AAATTATTCAAAAAAATTATT
259751 TTATTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTATTCAAAAAAATTATT
Found at i:261990 original size:30 final size:28
Alignment explanation
Indices: 261955--262097 Score: 108
Period size: 30 Copynumber: 4.8 Consensus size: 28
261945 ACTCGGGATG
* *
261955 AAAATGAAATTTTAGAGAAGTTCGAGGGTT
1 AAAATGAAATTTT-GAAAAGTT-AAGGGTT
* *
261985 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
1 AAAATGAAATTTT-GAAAAG-TTAAGGGTT
*
262015 AAAAT-ATAATTTTGAAAAAGTTTAGGGGTT
1 AAAATGA-AATTTTG-AAAAG-TTAAGGGTT
* *
262045 AAAATGTAATTTTGAAAAAAATTTAAGGGTT
1 AAAATGAAATTTTG---AAAAGTTAAGGGTT
*
262076 AAAATGTAATTTTGGAAAAGTT
1 AAAATGAAATTTT-GAAAAGTT
262098 TGGAAACCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
29 7 0.07
30 58 0.62
31 23 0.24
32 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.34
Consensus pattern (28 bp):
AAAATGAAATTTTGAAAAGTTAAGGGTT
Found at i:262075 original size:31 final size:30
Alignment explanation
Indices: 261979--262098 Score: 177
Period size: 30 Copynumber: 4.0 Consensus size: 30
261969 GAGAAGTTCG
*
261979 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGAAAAAGTTTA
* *
262009 AGGGTCAAAATATAATTTTGAAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGAAAAAGTTTA
* *
262039 GGGGTTAAAATGTAATTTTGAAAAAAATTTA
1 AGGGTTAAAATGTAATTTTG-AAAAAGTTTA
*
262070 AGGGTTAAAATGTAATTTTGGAAAAGTTT
1 AGGGTTAAAATGTAATTTTGAAAAAGTTT
262099 GGAAACCTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 51 0.65
31 28 0.35
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGAAAAAGTTTA
Found at i:262095 original size:61 final size:60
Alignment explanation
Indices: 261980--262098 Score: 184
Period size: 61 Copynumber: 2.0 Consensus size: 60
261970 AGAAGTTCGA
* *
261980 GGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGAAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGAAAAAATTTAAGGGTCAAAATATAATTTTGAAAAAGTTTAG
* * *
262040 GGGTTAAAATGTAATTTTGAAAAAAATTTAAGGGTTAAAATGTAATTTTGGAAAAGTTT
1 GGGTTAAAATGTAATTTTG-AAAAAATTTAAGGGTCAAAATATAATTTTGAAAAAGTTT
262099 GGAAACCTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 19 0.36
61 34 0.64
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (60 bp):
GGGTTAAAATGTAATTTTGAAAAAATTTAAGGGTCAAAATATAATTTTGAAAAAGTTTAG
Found at i:263182 original size:13 final size:13
Alignment explanation
Indices: 263166--263190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
263156 TTTGTATTGA
263166 TTTTGTATTTTTT
1 TTTTGTATTTTTT
263179 TTTTGTATTTTT
1 TTTTGTATTTTT
263191 CGTGGATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTGTATTTTTT
Found at i:264277 original size:49 final size:49
Alignment explanation
Indices: 264224--264642 Score: 316
Period size: 49 Copynumber: 8.6 Consensus size: 49
264214 CGGTCGTAAC
* *
264224 CTTTCCCTCCATATCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTCCATATCTTCGTGGTAATGGATTCGCCGTTGCGACTTAAAT
* * * * *
264273 CTTTCCCTTCAT-GCTTCTGAGGTACAAT-G-TTCGTCGTTGCGACTTAAAC
1 CTTTCCCTCCATATCTTC-GTGGT--AATGGATTCGCCGTTGCGACTTAAAT
* * * *
264322 CTTTCTCTCCATATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTCCATATCTTCGTGGTAATGGATTCGCCGTTGCGACTTAAAT
* * * * * * * *
264371 CTTTTCTTTCAT-GCTTCTTAGGTACAAGG-TTCGCTGTTGCGACTTAAAC
1 CTTTCCCTCCATATCTTCGT-GGTA-ATGGATTCGCCGTTGCGACTTAAAT
* * * * *
264420 CTTTCCCTCCATATCTTCGTGGTACTAGATTTGCTGTTGCGGCTTAAAT
1 CTTTCCCTCCATATCTTCGTGGTAATGGATTCGCCGTTGCGACTTAAAT
* * * * *
264469 CTTTCCCTTCAT-GCTTCTGAGGTACAAGG-TTCGCCGTTACGACTTAAAT
1 CTTTCCCTCCATATCTTC-GTGGTA-ATGGATTCGCCGTTGCGACTTAAAT
* * * * *
264518 CTTTCCCTCCACACCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTCCATATCTTCGTGGTAATGGATTCGCCGTTGCGACTTAAAT
* * * ** * *
264567 CTTTCCCTTCATGT-TTCTGAGGT-ATAAAGTTCGCCGTTACGACTTAAAC
1 CTTTCCCTCCATATCTTC-GTGGTAATGGA-TTCGCCGTTGCGACTTAAAT
*
264616 CTTTCCCTCCATGTCTTCGTGGTAATG
1 CTTTCCCTCCATATCTTCGTGGTAATG
264643 AAACCTGTAG
Statistics
Matches: 281, Mismatches: 71, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
47 2 0.01
48 21 0.07
49 235 0.84
50 21 0.07
51 2 0.01
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (49 bp):
CTTTCCCTCCATATCTTCGTGGTAATGGATTCGCCGTTGCGACTTAAAT
Found at i:264344 original size:98 final size:98
Alignment explanation
Indices: 264172--264639 Score: 659
Period size: 98 Copynumber: 4.8 Consensus size: 98
264162 TCATGGGTTC
* * * * * * *
264172 AATCTTTCTCGTCATGTTTCTAAGGTACTAGGTTCGCCGTTACGGTCGT-AACCTTTCCCTCCAT
1 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTAC-GACTTAAACCTTTCCCTCCAT
* *
264236 ATCTTCGTGGTATTGGATTCGCCGTTGCGGCTTA
65 ATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * * *
264270 AATCTTTCCCTTCATGCTTCTGAGGTACAATGTTCGTCGTTGCGACTTAAACCTTTCTCTCCATA
1 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATA
* *
264335 TCTTTGTGGTACTGGATTCGCCGTTGCGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * * * *
264368 AATCTTTTCTTTCATGCTTCTTAGGTACAAGGTTCGCTGTTGCGACTTAAACCTTTCCCTCCATA
1 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATA
* *
264433 TCTTCGTGGTACTAGATTTGCTGTTGCGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* *
264466 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAATCTTTCCCTCCACA
1 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATA
*
264531 CCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * * *
264564 AATCTTTCCCTTCATGTTTCTGAGGTATAAAGTTCGCCGTTACGACTTAAACCTTTCCCTCCATG
1 AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATA
264629 TCTTCGTGGTA
66 TCTTCGTGGTA
264640 ATGAAACCTG
Statistics
Matches: 328, Mismatches: 41, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
97 3 0.01
98 325 0.99
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (98 bp):
AATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATA
TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
Found at i:265122 original size:17 final size:17
Alignment explanation
Indices: 265096--265129 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
265086 TGAAATTAAA
*
265096 CTCGATTGAAGGCAAAG
1 CTCGAATGAAGGCAAAG
*
265113 CTCGAATGAATGCAAAG
1 CTCGAATGAAGGCAAAG
265130 ATCATTGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (17 bp):
CTCGAATGAAGGCAAAG
Found at i:266366 original size:37 final size:37
Alignment explanation
Indices: 266316--266392 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
266306 AGCTTTTGAT
*
266316 GAATTTGGCTCGGTAACGTCCATGTCCTACATAAAAA
1 GAATTTGGCTCGGTAACGTCCATGTCCCACATAAAAA
* *
266353 GAATTTGTCTCGGTGACGTCCATGTCCCACATAAAAA
1 GAATTTGGCTCGGTAACGTCCATGTCCCACATAAAAA
266390 GAA
1 GAA
266393 GCCATGACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (37 bp):
GAATTTGGCTCGGTAACGTCCATGTCCCACATAAAAA
Found at i:266487 original size:16 final size:17
Alignment explanation
Indices: 266466--266507 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
266456 TGATCTTAAC
266466 TTTCTTTTTCTTC-CTT
1 TTTCTTTTTCTTCTCTT
266482 TTTC-TTTTCTTCTTCTT
1 TTTCTTTTTCTTC-TCTT
*
266499 TTCCTTTTT
1 TTTCTTTTT
266508 TTTTAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 6 0.27
18 4 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTCTTCTCTT
Found at i:266496 original size:18 final size:17
Alignment explanation
Indices: 266473--266506 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
266463 AACTTTCTTT
*
266473 TTCTTCCTTTTTCTTTTC
1 TTCTT-CTTTTCCTTTTC
266491 TTCTTCTTTTCCTTTT
1 TTCTTCTTTTCCTTTT
266507 TTTTTAAAAG
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTCTTCTTTTCCTTTTC
Found at i:266640 original size:19 final size:18
Alignment explanation
Indices: 266616--266651 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
266606 CTTTTTTCGT
*
266616 TTTTCTTTATTTTATTTTA
1 TTTTCTTT-TTTGATTTTA
266635 TTTTCTTTTTTGATTTT
1 TTTTCTTTTTTGATTTT
266652 CTTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTCTTTTTTGATTTTA
Found at i:267063 original size:17 final size:18
Alignment explanation
Indices: 267033--267067 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
267023 ACATAGAAGC
267033 AAAATCGAATTCAAAGAA
1 AAAATCGAATTCAAAGAA
*
267051 AAAATTGAA-TCAAAGAA
1 AAAATCGAATTCAAAGAA
267068 TGGTTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAATCGAATTCAAAGAA
Found at i:270952 original size:29 final size:30
Alignment explanation
Indices: 270792--270986 Score: 214
Period size: 30 Copynumber: 6.5 Consensus size: 30
270782 ATGGAAATAA
* * **
270792 AATTTTAGAGAAGTTTGGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
*
270822 AATTTTGGAAAAGTTTAAGGGTCAAAAAT-T
1 AATTTTGGAAAAGTTTAAGGGT-TAAAATGT
* * *
270852 AATTTTGGAAAAGTTTAAGTGTCAAAATAT
1 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
* * *
270882 GATTTTGGAAAAATTTAAGGGTTAAAATAT
1 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
** *
270912 AATTTTAAAAAATTTTAAGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
*
270942 AA-TTTGGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
* *
270971 AATTTTAGAAACGTTT
1 AATTTTGGAAAAGTTT
270987 GGAGACCTCT
Statistics
Matches: 140, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
29 30 0.21
30 105 0.75
31 5 0.04
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.37
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTAAGGGTTAAAATGT
Found at i:271498 original size:2 final size:2
Alignment explanation
Indices: 271493--271537 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
271483 AAATTTGCTC
*
271493 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
271534 CT CT
1 CT CT
271538 TCCTTCTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:272205 original size:17 final size:17
Alignment explanation
Indices: 272183--272221 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
272173 TAAACTACTA
272183 TTCTTTTGCTGATGTTT
1 TTCTTTTGCTGATGTTT
272200 TTCTTTTGCTGATGTTT
1 TTCTTTTGCTGATGTTT
272217 TTCTT
1 TTCTT
272222 CTTCTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.13, G:0.15, T:0.67
Consensus pattern (17 bp):
TTCTTTTGCTGATGTTT
Found at i:274200 original size:18 final size:17
Alignment explanation
Indices: 274166--274206 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
274156 TTTAATCTTT
274166 TAAATATTATAAATATA
1 TAAATATTATAAATATA
274183 TAAACTATTA-AAAT-TA
1 TAAA-TATTATAAATATA
274199 TAAA-ATTA
1 TAAATATTA
274207 CATTCTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
16 6 0.26
17 8 0.35
18 5 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATATTATAAATATA
Found at i:275731 original size:43 final size:43
Alignment explanation
Indices: 275649--275729 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 43
275639 ATATATCCAT
*
275649 TTTTTAAATTTAATAGAAAATAATATTTTAAAATTATAATACG
1 TTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAATACG
275692 TTTTTAAA-TTAATAGAAAAT-A-ATCTTAAAATTATAATA
1 TTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAATA
275730 ATTAGATGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 16 0.43
41 1 0.03
42 12 0.32
43 8 0.22
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (43 bp):
TTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAATACG
Found at i:277786 original size:20 final size:20
Alignment explanation
Indices: 277734--277786 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
277724 TTTTAATATA
*
277734 TTTAATATAAAATAATATTT
1 TTTAATATAAAATAATATTC
* * *
277754 TTTGATAGAAAATATTATTC
1 TTTAATATAAAATAATATTC
*
277774 TTTAATATTAAAT
1 TTTAATATAAAAT
277787 TGATGCAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTAATATAAAATAATATTC
Found at i:281723 original size:72 final size:72
Alignment explanation
Indices: 281643--281789 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 72
281633 ACTTTAACCC
*
281643 AAATATATTAATTGTGTAAATTATCTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
1 AAATATATTAATTGTGTAAACTATCTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
281708 ATATTAT
66 ATATTAT
* * * *
281715 AAATATATTAATTGTGTAAACTATTTGAACTAATTAATAATATTAATTTATTTAAAAAGCAAATG
1 AAATATATTAATTGTGTAAACTATCTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
281780 ATATTAT
66 ATATTAT
281787 AAA
1 AAA
281790 AATAAAGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (72 bp):
AAATATATTAATTGTGTAAACTATCTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
ATATTAT
Found at i:282660 original size:9 final size:9
Alignment explanation
Indices: 282646--282675 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
282636 AAATTGTAAT
282646 TTTCTTTCA
1 TTTCTTTCA
282655 TTTCTTTCA
1 TTTCTTTCA
*
282664 TTTCTTTTA
1 TTTCTTTCA
282673 TTT
1 TTT
282676 TGGGTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTCTTTCA
Found at i:286240 original size:28 final size:29
Alignment explanation
Indices: 286164--286254 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 29
286154 CTTGTCATAT
*
286164 TATTTTTTAATTTTTTTAATAAATATTTATA
1 TATTTTTTAATTTATTTAAT-AAT-TTTATA
286195 TTATATTATTTCAA--TATTTAATAATTTTATA
1 -TAT-TT-TTT-AATTTATTTAATAATTTTATA
*
286226 TATTTTTT-ATTTATTGAA-AATTTT-TA
1 TATTTTTTAATTTATTTAATAATTTTATA
286252 TAT
1 TAT
286255 GTTCATCTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
26 6 0.12
27 6 0.12
28 9 0.17
29 2 0.04
30 3 0.06
31 6 0.12
32 6 0.12
33 9 0.17
34 3 0.06
35 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
TATTTTTTAATTTATTTAATAATTTTATA
Found at i:292146 original size:15 final size:15
Alignment explanation
Indices: 292126--292160 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
292116 CCAGATTTTT
292126 TTTTATTTTTTAATA
1 TTTTATTTTTTAATA
292141 TTTTATTTTTTAATA
1 TTTTATTTTTTAATA
292156 TTTTA
1 TTTTA
292161 ATGATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTTAATA
Found at i:292733 original size:19 final size:19
Alignment explanation
Indices: 292711--292748 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
292701 GTTAAATATG
*
292711 TTTTATTAATTTTAATAAT
1 TTTTATGAATTTTAATAAT
*
292730 TTTTATGAATTTTTATAAT
1 TTTTATGAATTTTAATAAT
292749 ACATAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATGAATTTTAATAAT
Found at i:292740 original size:10 final size:9
Alignment explanation
Indices: 292711--292827 Score: 53
Period size: 10 Copynumber: 12.7 Consensus size: 9
292701 GTTAAATATG
292711 TTTTATTAAT
1 TTTTA-TAAT
*
292721 TTTAATAAT
1 TTTTATAAT
292730 TTTTATGAAT
1 TTTTAT-AAT
292740 TTTTATAA-
1 TTTTATAAT
**
292748 -TACATAAGT
1 TTTTATAA-T
*
292757 TTTTATGAT
1 TTTTATAAT
*
292766 TTTT-TATAC
1 TTTTATA-AT
*
292775 TTTTATATT
1 TTTTATAAT
*
292784 TTTTATAAGA
1 TTTTATAA-T
* *
292794 TTATATCTAT
1 TTTTAT-AAT
292804 TTTT-TAAT
1 TTTTATAAT
*
292812 TTTCGATAAT
1 TTT-TATAAT
292822 TTTTAT
1 TTTTAT
292828 GGCTTTTATG
Statistics
Matches: 77, Mismatches: 20, Indels: 21
0.65 0.17 0.18
Matches are distributed among these distances:
7 5 0.06
8 6 0.08
9 31 0.40
10 34 0.44
11 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:292786 original size:17 final size:18
Alignment explanation
Indices: 292757--292790 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
292747 ATACATAAGT
292757 TTTTATGATTTTTTATAC
1 TTTTATGATTTTTTATAC
292775 TTTTAT-ATTTTTTATA
1 TTTTATGATTTTTTATA
292791 AGATTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTATGATTTTTTATAC
Found at i:293560 original size:2 final size:2
Alignment explanation
Indices: 293553--293583 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
293543 GTGTTCAAAG
293553 AT AT AT 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 AT AT AT A
293584 ATGAATTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:294215 original size:3 final size:3
Alignment explanation
Indices: 294207--294231 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
294197 TAAATGTAAT
294207 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
294232 ATTGGTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:300124 original size:42 final size:42
Alignment explanation
Indices: 300064--300143 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
300054 AAAGCATATG
*
300064 AATTTAATCCAAGTTTTAGCATAGTAAAGGGGATAAAATTGA
1 AATTTAATCCAAGGTTTAGCATAGTAAAGGGGATAAAATTGA
* *
300106 AATTTAATCCAAGGTTTAGCATAGTATAGGGGCTAAAA
1 AATTTAATCCAAGGTTTAGCATAGTAAAGGGGATAAAA
300144 GAAAGTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (42 bp):
AATTTAATCCAAGGTTTAGCATAGTAAAGGGGATAAAATTGA
Found at i:302151 original size:58 final size:58
Alignment explanation
Indices: 302078--302226 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 58
302068 TTGAATATTA
* * * * * * * *
302078 AAAAAAGATTGGATACCAAATTAGGAAAACA-TGTCAAGTTTAGGTACCAATTTGAGTC
1 AAAAAAGTTTAGATACCAAATTAAGAAAA-AGTATCAAGTTCAGATACCAAATTGAATC
302136 AAAAAAGTTTAGATACCAAATTAAGAAAAAGTATCAAGTTCAGATACCAAATTGAATC
1 AAAAAAGTTTAGATACCAAATTAAGAAAAAGTATCAAGTTCAGATACCAAATTGAATC
* * *
302194 AGAAAAAGTTTAAATACTAAATTATGAAAAAGT
1 A-AAAAAGTTTAGATACCAAATTAAGAAAAAGT
302227 GTCTTCAAGT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 1 0.01
58 49 0.63
59 28 0.36
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.26
Consensus pattern (58 bp):
AAAAAAGTTTAGATACCAAATTAAGAAAAAGTATCAAGTTCAGATACCAAATTGAATC
Found at i:303613 original size:2 final size:2
Alignment explanation
Indices: 303606--303639 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
303596 GAGTACGCGC
303606 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
303640 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:303644 original size:2 final size:2
Alignment explanation
Indices: 303639--303671 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
303629 TCTCTCTCTC
303639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
303672 GTACAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:307356 original size:20 final size:21
Alignment explanation
Indices: 307326--307364 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
307316 TAGACTTAAA
307326 ATTTAATATATTTATTTATAC
1 ATTTAATATATTTATTTATAC
307347 ATTT-ATATATTTATTTAT
1 ATTTAATATATTTATTTAT
307365 TAAAAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATATATTTATTTATAC
Found at i:307997 original size:6 final size:6
Alignment explanation
Indices: 307989--308020 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
307979 TTATTTTATA
*
307989 AAAATA AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AA
308021 CATATTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:308250 original size:40 final size:40
Alignment explanation
Indices: 308179--308263 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
308169 AATAATATTT
*
308179 TTAAAAAATAAAGAAAATATATATTATAAAAAATTAT-AAA
1 TTAAAAAATAAAGAAAATATATACT-TAAAAAATTATAAAA
* *
308219 TTAAAAAACTATAAGTAAA-ATATAC-TAAAAAATTGTAAAA
1 TTAAAAAA-TA-AAGAAAATATATACTTAAAAAATTATAAAA
308259 TTAAA
1 TTAAA
308264 TATATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
39 10 0.26
40 16 0.41
41 7 0.18
42 6 0.15
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (40 bp):
TTAAAAAATAAAGAAAATATATACTTAAAAAATTATAAAA
Found at i:308277 original size:27 final size:27
Alignment explanation
Indices: 308234--308286 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
308224 AAACTATAAG
308234 TAAAATATACTAAAAAA-TTGTAAAAT
1 TAAAATATACTAAAAAATTTGTAAAAT
* *
308260 TAAATATATATTATAAAATTTGTAAAA
1 TAAA-ATATACTAAAAAATTTGTAAAA
308287 ACTATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 11 0.48
28 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (27 bp):
TAAAATATACTAAAAAATTTGTAAAAT
Found at i:308285 original size:28 final size:26
Alignment explanation
Indices: 308234--308286 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
308224 AAACTATAAG
308234 TAAAATATACTAAAAAATTGTAAAAT
1 TAAAATATACTAAAAAATTGTAAAAT
* *
308260 TAAATATATATTATAAAATTTGTAAAA
1 TAAA-ATATACTA-AAAAATTGTAAAA
308287 ACTATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 7 0.30
28 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAAATATACTAAAAAATTGTAAAAT
Found at i:309731 original size:16 final size:16
Alignment explanation
Indices: 309710--309776 Score: 80
Period size: 16 Copynumber: 4.2 Consensus size: 16
309700 TGAATTACTA
309710 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
309726 ATTACAGCTTTATTCC
1 ATTACAACTCTATTCC
* * *
309742 ATTATAACTATATTCT
1 ATTACAACTCTATTCC
*
309758 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
309774 ATT
1 ATT
309777 CTAATGAACC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:309762 original size:32 final size:32
Alignment explanation
Indices: 309710--309776 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
309700 TGAATTACTA
* *
309710 ATTACAACTCTATTCCATTACAGCTTTATTCC
1 ATTACAACTATATTCCATTACAGCTCTATTCC
* *
309742 ATTATAACTATATTCTATTACAGCTCTATTCC
1 ATTACAACTATATTCCATTACAGCTCTATTCC
309774 ATT
1 ATT
309777 CTAATGAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (32 bp):
ATTACAACTATATTCCATTACAGCTCTATTCC
Done.