Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001807.1 Kokia drynarioides strain JFW-HI SEQ_113544, 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: 71931
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 174 characters in sequence are not A, C, G, or T
Found at i:226 original size:12 final size:13
Alignment explanation
Indices: 209--242 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
199 TTATTAACCA
209 TTAATAATATT-T
1 TTAATAATATTCT
221 TTAATAATATTCT
1 TTAATAATATTCT
234 TTAATAATA
1 TTAATAATA
243 ATAAAATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATAATATTCT
Found at i:898 original size:11 final size:11
Alignment explanation
Indices: 867--922 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
857 TTTGGACAAA
*
867 AATAAATTTTAA
1 AATAAA-TTTAT
879 AATTAAATTTAT
1 AA-TAAATTTAT
*
891 GATAAATTT-T
1 AATAAATTTAT
901 AATTAAATTTAT
1 AA-TAAATTTAT
913 AATAAATTTA
1 AATAAATTTA
923 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.05
11 22 0.58
12 10 0.26
13 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
AATAAATTTAT
Found at i:907 original size:22 final size:22
Alignment explanation
Indices: 867--925 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
857 TTTGGACAAA
867 AATAAATTTTAAAATTAAATTTAT
1 AATAAATTTT--AATTAAATTTAT
*
891 GATAAATTTTAATTAAATTTAT
1 AATAAATTTTAATTAAATTTAT
913 AATAAA-TTTAATT
1 AATAAATTTTAATT
926 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 7 0.21
22 17 0.52
24 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATAAATTTTAATTAAATTTAT
Found at i:923 original size:17 final size:18
Alignment explanation
Indices: 903--947 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
893 TAAATTTTAA
903 TTAAATTTATAAT-AAAT
1 TTAAATTTATAATAAAAT
* *
920 TTAATTTTAAAATAAAAT
1 TTAAATTTATAATAAAAT
*
938 TTAAGTTTAT
1 TTAAATTTAT
948 TGGGCTCAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAAATTTATAATAAAAT
Found at i:1168 original size:22 final size:22
Alignment explanation
Indices: 1120--1169 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1110 GAGGATAATA
**
1120 ATTATTATTGGATATTATTTAT
1 ATTATTATTGGATATTATCAAT
*
1142 ATTATTATTGTATAATTATCAAT
1 ATTATTATTGGAT-ATTATCAAT
1165 -TTATT
1 ATTATT
1170 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
ATTATTATTGGATATTATCAAT
Found at i:1912 original size:26 final size:27
Alignment explanation
Indices: 1865--1915 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1855 CGACTTTAAA
* **
1865 AAAATAGAAAATAGAACTTATTTTCTT
1 AAAATAGAAAATAAAAAATATTTTCTT
1892 AAAAT-GAAAATAAAAAATATTTTC
1 AAAATAGAAAATAAAAAATATTTTC
1916 GAAAATCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (27 bp):
AAAATAGAAAATAAAAAATATTTTCTT
Found at i:6322 original size:58 final size:57
Alignment explanation
Indices: 6250--6358 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 57
6240 TTAATATAAC
*
6250 ATTTGATACTTGAACTTAATACTTTTTT-ATAATTTGGTACCTAAACTTTTTTGACTCA
1 ATTTGATACTTGAACTTAACA-TTTTTTCATAATTTGGTACCT-AACTTTTTTGACTCA
** *
6308 ATTTGATA-TCTGAACTTGGCATTTTTTCCTAATTTGGTACCTAACTTTTTT
1 ATTTGATACT-TGAACTTAACATTTTTTCATAATTTGGTACCTAACTTTTTT
6359 TTAGATTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
57 16 0.36
58 29 0.64
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.50
Consensus pattern (57 bp):
ATTTGATACTTGAACTTAACATTTTTTCATAATTTGGTACCTAACTTTTTTGACTCA
Found at i:8300 original size:24 final size:24
Alignment explanation
Indices: 8248--8300 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
8238 TTTTTTAAAT
* *
8248 ATTTGTTTTTTTAAATTGTATTTA
1 ATTTTTTTTTTTAAATTGTATGTA
* *
8272 ATTTTTTTTTTTTAATTTTATGT-
1 ATTTTTTTTTTTAAATTGTATGTA
8295 ATTTTT
1 ATTTTT
8301 GAAATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (24 bp):
ATTTTTTTTTTTAAATTGTATGTA
Found at i:8866 original size:7 final size:7
Alignment explanation
Indices: 8854--8880 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
8844 TATTTTTATT
8854 TATTTTA
1 TATTTTA
8861 TATTTTA
1 TATTTTA
8868 TATTTTA
1 TATTTTA
8875 TATTTT
1 TATTTT
8881 TCATACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:9121 original size:21 final size:18
Alignment explanation
Indices: 9080--9136 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
9070 TTTAACTTTA
*
9080 TTTAATATTTTTATAAAT
1 TTTAATATTTTTACAAAT
9098 TTTAATAATGTTTTACAAATT
1 TTTAAT-AT-TTTTACAAA-T
9119 TTTAA-ATTTTTA-AAAT
1 TTTAATATTTTTACAAAT
9135 TT
1 TT
9137 AAAAAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 11 0.31
19 4 0.11
20 8 0.23
21 6 0.17
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAATATTTTTACAAAT
Found at i:15219 original size:17 final size:18
Alignment explanation
Indices: 15185--15221 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
15175 TTTCATCAGC
15185 TCCAAGTAACAAACATTA
1 TCCAAGTAACAAACATTA
15203 TCCAA-TAACATAA-ATTA
1 TCCAAGTAACA-AACATTA
15220 TC
1 TC
15222 ACAACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.27
Consensus pattern (18 bp):
TCCAAGTAACAAACATTA
Found at i:15387 original size:48 final size:51
Alignment explanation
Indices: 15290--15389 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 51
15280 AGTTGTGTAA
*
15290 TTACACAAACTATTACCCAATAACGAAAAATTATTACAATATCTGTAATGT
1 TTACACAAACTATTACCCAATAACGAAAAATTATTACAATATCTATAATGT
* * * *
15341 TTACA-AAAC-ATTACCCAATTA-TACAAATTATTACAA-CTCTCATAATGT
1 TTACACAAACTATTACCCAATAACGAAAAATTATTACAATATCT-ATAATGT
15389 T
1 T
15390 GTGTAACACG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
47 3 0.07
48 20 0.47
49 11 0.26
50 4 0.09
51 5 0.12
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (51 bp):
TTACACAAACTATTACCCAATAACGAAAAATTATTACAATATCTATAATGT
Found at i:19182 original size:22 final size:21
Alignment explanation
Indices: 19157--19198 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19147 ATGAAAGGAT
19157 AAAATT-AAAAGAAATAAAATTG
1 AAAATTGAAAA-AAA-AAAATTG
19179 AAAATTGAAAAAAAAAAATT
1 AAAATTGAAAAAAAAAAATT
19199 TACGACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAATTGAAAAAAAAAAATTG
Found at i:27704 original size:31 final size:31
Alignment explanation
Indices: 27669--27738 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
27659 TTTACAAATT
*
27669 AGTCATTGAAATATTCAAAACTTTTCATTTA
1 AGTCATTGAAATATTCAAAACTTTTCATGTA
* * *
27700 AGTCATTGAATTATTCAAAAGTTTTTATGTA
1 AGTCATTGAAATATTCAAAACTTTTCATGTA
27731 AGTCATTG
1 AGTCATTG
27739 GGTTGTTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (31 bp):
AGTCATTGAAATATTCAAAACTTTTCATGTA
Found at i:28909 original size:15 final size:16
Alignment explanation
Indices: 28877--28911 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28867 GCAAAAAATC
*
28877 ATTTATTTTTTTATAT
1 ATTTATTTTTATATAT
28893 ATTTATTTTTATA-AT
1 ATTTATTTTTATATAT
28908 ATTT
1 ATTT
28912 TAATGTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTATTTTTATATAT
Found at i:31024 original size:48 final size:48
Alignment explanation
Indices: 30971--31067 Score: 99
Period size: 48 Copynumber: 2.0 Consensus size: 48
30961 ATTTATTATA
* ** *
30971 TAATAT-TTAAATATTTAATTTAA-TTTAAATGTATATTTTTATTTTAAC
1 TAATATATTAAA-TTTTAATTTAATTTTAAAACT-TATTTTTATTTAAAC
** *
31019 TAATATATTCTATTTTTATTTAATTTTAAAACTTATTTTTATTTAAAC
1 TAATATATTAAATTTTAATTTAATTTTAAAACTTATTTTTATTTAAAC
31067 T
1 T
31068 TTTTTCTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
48 30 0.75
49 10 0.25
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (48 bp):
TAATATATTAAATTTTAATTTAATTTTAAAACTTATTTTTATTTAAAC
Found at i:31303 original size:19 final size:19
Alignment explanation
Indices: 31258--31303 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
31248 TTATTTTTAA
*
31258 AAATTAAAATAGAATATAT
1 AAATTAAAATAGAAAATAT
*
31277 TAATTAAAAT-GAAAATAT
1 AAATTAAAATAGAAAATAT
31295 AAATATAAA
1 AAAT-TAAA
31304 TATTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAATTAAAATAGAAAATAT
Found at i:32351 original size:60 final size:59
Alignment explanation
Indices: 32112--32541 Score: 323
Period size: 61 Copynumber: 7.1 Consensus size: 59
32102 AAAAAAAAAA
*
32112 TTTGGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTAAT-ATGATAAAAAAAATCAAATT
1 TTTGGGTGTTGGCCATGAAATGGCCGACA-CCCTTTTT-ATCA-GATAAAAAAAATCAAATT
* * * * *
32173 TTTAGATGTTGGCCATGTAATGGCCGACATCCCTTTTTTGTCAGATAAAAAATA-C-AATT
1 TTTGGGTGTTGGCCATGAAATGGCCGACA-CCC-TTTTTATCAGATAAAAAAAATCAAATT
** * *
32232 TTTTTGTGTTGGCCAT-ACAATGGTCGACACTCTTATTTATCTA-ATAAAAAAAAATCAAATT
1 TTTGGGTGTTGGCCATGA-AATGGCCGACACCCTT-TTTATC-AGAT-AAAAAAAATCAAATT
* * *
32293 TTTGGGTGTTGGCCATGAAATGGCTGACATCCCTATTTATCTGATAAAAAAAATCAAATT
1 TTTGGGTGTTGGCCATGAAATGGCCGACA-CCCTTTTTATCAGATAAAAAAAATCAAATT
* * ** *
32353 TTTGGGTGTTGGTCAT-ACAATGGCCGACACCCCCTTTTCCCAGATAAAAAAATTTCAAATT
1 TTTGGGTGTTGGCCATGA-AATGGCCGACA-CCCTTTTTATCAGATAAAAAAA-ATCAAATT
** ** * * * *
32414 CTTTTAGTGTTGATCATGCAATGGCTGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTTT
1 -TTTGGGTGTTGGCCATGAAATGGCCGACACCCT-TTTTATCAGATAAAAAAA-ATCAAA--TT
* * ** * * * * *
32478 TTTTGGTATTGATCATGCAATGGTCGACGCTCCCTTTTATCAGATAAAAAAATTTCAAATT
1 TTTGGGTGTTGGCCATGAAATGGCCGACAC-CCTTTTTATCAGATAAAAAAA-ATCAAATT
32539 TTT
1 TTT
32542 TTATTGTTAG
Statistics
Matches: 305, Mismatches: 45, Indels: 38
0.79 0.12 0.10
Matches are distributed among these distances:
57 2 0.01
58 9 0.03
59 36 0.12
60 59 0.19
61 90 0.30
62 56 0.18
63 49 0.16
64 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (59 bp):
TTTGGGTGTTGGCCATGAAATGGCCGACACCCTTTTTATCAGATAAAAAAAATCAAATT
Found at i:32402 original size:120 final size:121
Alignment explanation
Indices: 32112--32658 Score: 408
Period size: 120 Copynumber: 4.5 Consensus size: 121
32102 AAAAAAAAAA
* * **
32112 TTTGGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTAATATGATAAAAAAA-ATCAAATTTTT
1 TTTGGGTGTTGGCCATACAATGGCCGACACCCCCTTTTACCA-GATAAAAAAATATCAAATTTTT
* * * * *
32176 AGATGTTGGCCATGTAATGGCCGACATCCCTTTTTTGTCAGATAAAAAATA-C-AATT
65 AGGTGTTGGCCATGAAATGGCTGACATCCC-TTTTTATCAGATAAAAAAAATCAAATT
** * * * * *
32232 TTTTTGTGTTGGCCATACAATGGTCGACA-CTCTTATTTATCTA-ATAAAAAAAAATCAAATTTT
1 TTTGGGTGTTGGCCATACAATGGCCGACACCCCCT-TTTA-CCAGATAAAAAAATATCAAATTTT
* * *
32295 TGGGTGTTGGCCATGAAATGGCTGACATCCCTATTTATCTGATAAAAAAAATCAAATT
64 TAGGTGTTGGCCATGAAATGGCTGACATCCCTTTTTATCAGATAAAAAAAATCAAATT
* * *
32353 TTTGGGTGTTGGTCATACAATGGCCGACACCCCCTTTTCCCAGATAAAAAAATTTCAAATTCTTT
1 TTTGGGTGTTGGCCATACAATGGCCGACACCCCCTTTTACCAGATAAAAAAATATCAAA-T-TTT
** * * *
32418 TA-GTGTTGATCATGCAATGGCTGACA-CCCTCTTTTTTCAGATAAAAAAATTTCAAATTTT
64 TAGGTGTTGGCCATGAAATGGCTGACATCCCT-TTTTATCAGATAAAAAAA-ATCAAA--TT
* * ** * * * * * *
32478 TTTTGGTATTGATCATGCAATGGTCGACGCTCCCTTTTATCAGATAAAAAAATTTCAAATTTTTT
1 TTTGGGTGTTGGCCATACAATGGCCGACACCCCCTTTTACCAGATAAAAAAATATCAAA--TTTT
* * * * * *
32543 TA-TTGTTAGCCATGCAATGG-T--C-T--CTTTTT-TCAGCTAAAAAAATTCAATTTTT
64 TAGGTGTTGGCCATGAAATGGCTGACATCCCTTTTTATCAGATAAAAAAAATCAA--ATT
* * * *
32595 TTTTGGTGTTGGCCATGCAATGGTCC-ACATCCCCTTTT-CTCAGATAAAAAAATTTCAAATTTT
1 TTTGGGTGTTGGCCATACAATGG-CCGACACCCCCTTTTAC-CAGATAAAAAAATATCAAATTTT
32658 T
64 T
32659 TTTGTGTTGA
Statistics
Matches: 353, Mismatches: 55, Indels: 43
0.78 0.12 0.10
Matches are distributed among these distances:
115 5 0.01
117 55 0.16
118 13 0.04
119 33 0.09
120 71 0.20
121 52 0.15
122 41 0.12
123 9 0.03
124 1 0.00
125 71 0.20
126 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (121 bp):
TTTGGGTGTTGGCCATACAATGGCCGACACCCCCTTTTACCAGATAAAAAAATATCAAATTTTTA
GGTGTTGGCCATGAAATGGCTGACATCCCTTTTTATCAGATAAAAAAAATCAAATT
Found at i:32436 original size:62 final size:62
Alignment explanation
Indices: 32116--32668 Score: 333
Period size: 62 Copynumber: 9.1 Consensus size: 62
32106 AAAAAATTTG
** * * * *
32116 GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTAAT-ATGATAAAAAAA-ATCAAA-TTTTTA
1 GGTGTTGATCATGCAATGGCCGACACCCCCTTTT-CTCA-GATAAAAAAATTTCAAATTTTTTT
* ** * ** * *
32177 GATGTTGGCCATGTAATGGCCGACATCCCTTTTTTGTCAGAT-AAAAAA-TAC-AATTTTTTT
1 GGTGTTGATCATGCAATGGCCGACA-CCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
** * * * * * ** *
32237 -GTGTTGGCCATACAATGGTCGACA-CTCTTATTTATCTA-ATAAAAAAAAATCAAA-TTTTTG
1 GGTGTTGATCATGCAATGGCCGACACCCCCT-TTTCTC-AGATAAAAAAATTTCAAATTTTTTT
** * * * * * * *
32297 GGTGTTGGCCATGAAATGGCTGACA-TCCCTATTTATCTGATAAAAAAA-ATCAAA-TTTTTG
1 GGTGTTGATCATGCAATGGCCGACACCCCCT-TTTCTCAGATAAAAAAATTTCAAATTTTTTT
* * * *
32357 GGTGTTGGTCATACAATGGCCGACACCCCCTTTTCCCAGATAAAAAAATTTCAAATTCTTTT
1 GGTGTTGATCATGCAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
* * * *
32419 AGTGTTGATCATGCAATGGCTGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTT
1 GGTGTTGATCATGCAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAA-TTTTTTT
* * * * *
32482 GGTATTGATCATGCAATGGTCGACGCTCCCTTTTATCAGATAAAAAAATTTCAAATTTTTTT
1 GGTGTTGATCATGCAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
** * * * * * *
32544 ATTGTT-AGCCATGCAAT-G--G----TCTCTTTTTTCAGCTAAAAAAA-TTCAATTTTTTTTT
1 GGTGTTGA-TCATGCAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAA-ATTTTTTT
** *
32599 GGTGTTGGCCATGCAATGGTCC-ACATCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
1 GGTGTTGATCATGCAATGG-CCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
*
32661 TGTGTTGA
1 GGTGTTGA
32669 AATTTTTTTA
Statistics
Matches: 396, Mismatches: 70, Indels: 51
0.77 0.14 0.10
Matches are distributed among these distances:
54 5 0.01
55 39 0.10
56 1 0.00
57 3 0.01
58 7 0.02
59 30 0.08
60 65 0.16
61 78 0.20
62 110 0.28
63 58 0.15
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (62 bp):
GGTGTTGATCATGCAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTT
Found at i:32616 original size:117 final size:119
Alignment explanation
Indices: 32335--32668 Score: 376
Period size: 125 Copynumber: 2.8 Consensus size: 119
32325 CTATTTATCT
* * * * * *
32335 GATAAAAAAA-ATCAAA--TTTTTGGGTGTTGGTCATACAATGGCCGACACCCCCTTTTCCCAGA
1 GATAAAAAAATTTCAAATTTTTTTTGGTGTTGGTCATGCAATGGTCGAC-CTCCCTTTTCTCAGA
* *
32397 TAAAAAAATTTCAAATTCTTTTAGTGTTGATCATGCAATGGCTGACACCCTCTTTTTTCA
65 TAAAAAAATTTCAAATTTTTTTAGTGTTGACCATGCAATGGCT-----CCTCTTTTTTCA
* * *
32457 GATAAAAAAATTTCAAATTTTTTTTGGTATTGATCATGCAATGGTCGACGCTCCCTTTTATCAGA
1 GATAAAAAAATTTCAAATTTTTTTTGGTGTTGGTCATGCAATGGTCGAC-CTCCCTTTTCTCAGA
*
32522 TAAAAAAATTTCAAATTTTTTTATTGTT-AGCCATGCAATGG-T-CTCTTTTTTCA
65 TAAAAAAATTTCAAATTTTTTTAGTGTTGA-CCATGCAATGGCTCCTCTTTTTTCA
* * * * *
32575 GCTAAAAAAA-TTCAATTTTTTTTTGGTGTTGGCCATGCAATGGTCCACATCCCCTTTTCTCAGA
1 GATAAAAAAATTTCAAATTTTTTTTGGTGTTGGTCATGCAATGGTCGACCT-CCCTTTTCTCAGA
*
32639 TAAAAAAATTTCAAATTTTTTTTGTGTTGA
65 TAAAAAAATTTCAAATTTTTTTAGTGTTGA
32669 AATTTTTTTA
Statistics
Matches: 183, Mismatches: 23, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
116 1 0.01
117 71 0.39
118 21 0.11
122 10 0.05
123 5 0.03
124 2 0.01
125 73 0.40
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (119 bp):
GATAAAAAAATTTCAAATTTTTTTTGGTGTTGGTCATGCAATGGTCGACCTCCCTTTTCTCAGAT
AAAAAAATTTCAAATTTTTTTAGTGTTGACCATGCAATGGCTCCTCTTTTTTCA
Found at i:33359 original size:7 final size:7
Alignment explanation
Indices: 33347--33382 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
33337 TATTGTACAT
33347 AAGATAG
1 AAGATAG
33354 AAGATAG
1 AAGATAG
*
33361 AAGATGG
1 AAGATAG
33368 AAGATAG
1 AAGATAG
33375 AAGATAG
1 AAGATAG
33382 A
1 A
33383 TTCTTGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.14
Consensus pattern (7 bp):
AAGATAG
Found at i:35009 original size:16 final size:16
Alignment explanation
Indices: 34964--35001 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
34954 GTTACTTACA
* *
34964 AAATATTATTCATTTT
1 AAATATTATTTATATT
34980 AAATATTATTTATATT
1 AAATATTATTTATATT
34996 AAATAT
1 AAATAT
35002 ATTATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTATTTATATT
Found at i:40976 original size:6 final size:6
Alignment explanation
Indices: 40965--41005 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
40955 CCTCTCTCCT
*
40965 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC TTCTT
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTT
41006 GCTCCATAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
CTCTTC
Found at i:46037 original size:41 final size:41
Alignment explanation
Indices: 45992--46388 Score: 405
Period size: 41 Copynumber: 9.7 Consensus size: 41
45982 AAACGTTGCA
* **
45992 AAAGGT-AAAGCAATAGCGGCGTTTAT-AGGAAAAGCATCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGA-G-AAAGCGCCGCT
* ** * * *
46033 AAAGGTTAGGGCATTAGCGGCATTTATGAGAAAGTGTCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
* *
46074 AAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
** *
46115 AAAGGTCAGGGCATTAGCGGCGTTTATGAGAAAGCGCCACT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
46156 AAAGGTCAAAGCATTAGCGGCGTTTATTGA-AAAGCGCCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTA-TGAGAAAGCGCCGCT
* * * *
46197 AAAAGTCAAAGCATTAACGGCGTTTATGGGAAAACGCCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
* * * *
46238 AAAGGTCAGAGCATTAACGACGTTTATTGA-AAAGCGCCGTT
1 AAAGGTCAAAGCATTAGCGGCGTTTA-TGAGAAAGCGCCGCT
* * ** **
46279 AAAGGTTAGAGCATTAGCGGTATTTATGAGAAAGCGCCTAT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
* *
46320 AAA-ATCAGAGCATTAGCGGCGTTTATGATG-AAGCGCCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGA-GAAAGCGCCGCT
46360 AAA-G-CATAGAGCATTAGCGGCGTTTATGA
1 AAAGGTCA-A-AGCATTAGCGGCGTTTATGA
46389 TAACAATGCC
Statistics
Matches: 304, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 37 0.12
41 242 0.80
42 22 0.07
43 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (41 bp):
AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
Found at i:46115 original size:82 final size:82
Alignment explanation
Indices: 45992--46388 Score: 446
Period size: 82 Copynumber: 4.9 Consensus size: 82
45982 AAACGTTGCA
* * ** * *
45992 AAAGGT-AAAGCAATAGCGGCGTTTAT-AGGAAAAGCATCGCTAAAGGTTAGGGCATTAGCGGCA
1 AAAGGTCAGAGCATTAGCGGCGTTTATGA-G-AAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCG
* *
46055 TTTATGAGAAAGTGTCGCT
64 TTTATGAGAAAGCGCCGCT
* * *
46074 AAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACCGCTAAAGGTCAGGGCATTAGCGGCGTT
1 AAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCGTT
*
46139 TATGAGAAAGCGCCACT
66 TATGAGAAAGCGCCGCT
* * * * *
46156 AAAGGTCAAAGCATTAGCGGCGTTTATTGA-AAAGCGCCGCTAAAAGTCAAAGCATTAACGGCGT
1 AAAGGTCAGAGCATTAGCGGCGTTTA-TGAGAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCGT
* *
46220 TTATGGGAAAACGCCGCT
65 TTATGAGAAAGCGCCGCT
* * * **
46238 AAAGGTCAGAGCATTAACGACGTTTATTGA-AAAGCGCCGTTAAAGGTTAGAGCATTAGCGGTAT
1 AAAGGTCAGAGCATTAGCGGCGTTTA-TGAGAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCGT
**
46302 TTATGAGAAAGCGCCTAT
65 TTATGAGAAAGCGCCGCT
* **
46320 AAA-ATCAGAGCATTAGCGGCGTTTATGATG-AAGCGCCGCTAAAGCATAGAGCATTAGCGGCGT
1 AAAGGTCAGAGCATTAGCGGCGTTTATGA-GAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCGT
46383 TTATGA
65 TTATGA
46389 TAACAATGCC
Statistics
Matches: 271, Mismatches: 39, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
80 3 0.01
81 53 0.20
82 192 0.71
83 22 0.08
84 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (82 bp):
AAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCGTT
TATGAGAAAGCGCCGCT
Found at i:46890 original size:24 final size:24
Alignment explanation
Indices: 46822--46892 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
46812 AGAAATAATC
* * *
46822 TTTCAGTTAAATTCTGTTTAATTA
1 TTTCAATTAAACTCTGTTTATTTA
*
46846 TTTCAATTAAACTCTATTTATTTA
1 TTTCAATTAAACTCTGTTTATTTA
46870 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
46893 GTTTGAGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTA
Found at i:46905 original size:24 final size:24
Alignment explanation
Indices: 46838--46908 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
46828 TTAAATTCTG
* *
46838 TTTAATTATTTCAATTAAACTCTA
1 TTTATTTATTTCAATCAAACTCTA
* *
46862 TTTATTTATTTCAATTAAACTCTG
1 TTTATTTATTTCAATCAAACTCTA
* * *
46886 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTATTTCAATCAAACTCT
46909 TATTAGTCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.52
Consensus pattern (24 bp):
TTTATTTATTTCAATCAAACTCTA
Found at i:48885 original size:24 final size:24
Alignment explanation
Indices: 48802--48888 Score: 113
Period size: 24 Copynumber: 3.6 Consensus size: 24
48792 TGAAATAATT
* *
48802 TTTGAGTTAAACTCTGTTTAATTG
1 TTTGAGTTAAACTCTATTTATTTG
48826 TTTCGA-TTAAACTCTATTTATTTG
1 TTT-GAGTTAAACTCTATTTATTTG
* *
48850 TTTCAATTAAACTCTATTTATTTG
1 TTTGAGTTAAACTCTATTTATTTG
*
48874 TTTGAGTCAAACTCT
1 TTTGAGTTAAACTCT
48889 TATTAGTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.95
25 2 0.04
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTGAGTTAAACTCTATTTATTTG
Found at i:49674 original size:22 final size:23
Alignment explanation
Indices: 49634--49679 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
49624 AGATTTGTGC
* *
49634 CTGCTTTGGATATTTTACTAATG
1 CTGCTTTGAATATTATACTAATG
49657 CTGCTTT-AATATTATACTAATG
1 CTGCTTTGAATATTATACTAATG
49679 C
1 C
49680 AGCATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (23 bp):
CTGCTTTGAATATTATACTAATG
Found at i:52334 original size:43 final size:42
Alignment explanation
Indices: 52273--52386 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 42
52263 AAGAAAAGCG
*
52273 GGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCTG-TGTTGGTT
1 GGAAAAGTGCCGCTAAAGATCATGTTCTTTAGC-GACGTTGG-T
*
52316 GGAAAAGTGCCGCTAAAGA-CTATGTTCTTTAGCGACGTTTGT
1 GGAAAAGTGCCGCTAAAGATC-ATGTTCTTTAGCGACGTTGGT
* *
52358 GG--GAGCGCCGCTAAAGATCATGTTCTTTA
1 GGAAAAGTGCCGCTAAAGATCATGTTCTTTA
52387 ACGGCGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
40 23 0.36
41 1 0.02
42 5 0.08
43 35 0.55
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
GGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGACGTTGGT
Found at i:59226 original size:61 final size:61
Alignment explanation
Indices: 59145--59275 Score: 208
Period size: 61 Copynumber: 2.1 Consensus size: 61
59135 TTCAATGAAG
* * * *
59145 TTATATTTTTATTTCTTCATTACATCTTTTATTTTCCAACCTCATGATTAAAATTGACATT
1 TTATCTTTTTATTCCTTCATTACATCTTTTATTTTCCAACATAATGATTAAAATTGACATT
**
59206 TTATCTTTTTATTCCTTCATTACATCTTTTATTTTCCAACATAATGATTAAAATTGATGTT
1 TTATCTTTTTATTCCTTCATTACATCTTTTATTTTCCAACATAATGATTAAAATTGACATT
59267 TTATCTTTT
1 TTATCTTTT
59276 CAAAAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (61 bp):
TTATCTTTTTATTCCTTCATTACATCTTTTATTTTCCAACATAATGATTAAAATTGACATT
Found at i:60867 original size:7 final size:7
Alignment explanation
Indices: 60855--60879 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
60845 TTATTTTAAA
60855 ATTTTAG
1 ATTTTAG
60862 ATTTTAG
1 ATTTTAG
60869 ATTTTAG
1 ATTTTAG
60876 ATTT
1 ATTT
60880 ATTCGATTTA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
ATTTTAG
Found at i:71787 original size:22 final size:21
Alignment explanation
Indices: 71760--71809 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
71750 GCAATATAAT
71760 AACAAAATGACAGCAAAACAAC
1 AACAAAATGACAGC-AAACAAC
* **
71782 ATCAAAATGGTAGCAAACAAC
1 AACAAAATGACAGCAAACAAC
71803 AACAAAA
1 AACAAAA
71810 CATTAGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.62, C:0.20, G:0.10, T:0.08
Consensus pattern (21 bp):
AACAAAATGACAGCAAACAAC
Done.