Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014633.1 Kokia drynarioides strain JFW-HI SEQ_129672, 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: 24462
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:1258 original size:61 final size:60
Alignment explanation
Indices: 1149--1392 Score: 241
Period size: 61 Copynumber: 4.1 Consensus size: 60
1139 ATATCCCTTT
* * * * * * *
1149 TTTTATTTGAT-AAAAAACT-AATTTTTTTTGTGTTGGTCAT-TATATGGTCGACATCACG
1 TTTTATCTGATAAAAAAATTCAATTTTTTTGGTGTTGGCCATGCAT-TGGTCGACACCACC
* *
1207 TTTTATCTTATAAAAAAATTTCAATTTTTTTGGTGTTGGCCAAGCATTGGTCGACACCACC
1 TTTTATCTGATAAAAAAA-TTCAATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACC
* * * *
1268 TATTATCTGATTAAAAAAATT-AA-ATTTTTGGTGTTGGTCATTGCA-TGG-CCAGCACCACC
1 TTTTATCTGA-TAAAAAAATTCAATTTTTTTGGTGTTGGCCA-TGCATTGGTCGA-CACCACC
* *
1327 TTTCTATCTGATAAAAAAATTCAAATTTTTTTTGTGTTGGCCATGCATTGATCGACACCACC
1 TTT-TATCTGATAAAAAAATTC-AATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACC
1389 TTTT
1 TTTT
1393 TATTTGAAAA
Statistics
Matches: 152, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
58 11 0.07
59 43 0.28
60 13 0.09
61 47 0.31
62 36 0.24
63 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (60 bp):
TTTTATCTGATAAAAAAATTCAATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACC
Found at i:1347 original size:121 final size:118
Alignment explanation
Indices: 1171--1428 Score: 317
Period size: 121 Copynumber: 2.2 Consensus size: 118
1161 AAAAACTAAT
* ** * * * *
1171 TTTTTTTGTGTTGGTCATTATATGGTC-GACATCACGTTT-TATCTTATAAAAAAATTTC-AATT
1 TTTTTTGGTGTTGGTCATTGCATGGCCAG-CACCACCTTTCTATCTGATAAAAAAA-TTCAAATT
* *
1233 TTTTTGGTGTTGGCCAAGCATTGGTCGACACCACCTATTATCTGATTAAAAAAATTAAA
64 TTTTTGGTGTTGGCCAAGCATTGATCGACACCACCT-TT-T-T-ATTAAAAAAATCAAA
1292 -TTTTTGGTGTTGGTCATTGCATGGCCAGCACCACCTTTCTATCTGATAAAAAAATTCAAATTTT
1 TTTTTTGGTGTTGGTCATTGCATGGCCAGCACCACCTTTCTATCTGATAAAAAAATTCAAATTTT
* * **
1356 TTTTGTGTTGGCCATGCATTGATCGACACCACCTTTTTATTTGAAAAATCAAA
66 TTTGGTGTTGGCCAAGCATTGATCGACACCACCTTTTTATTAAAAAAATCAAA
1409 TTTTTTGGTGTTGGTCATTG
1 TTTTTTGGTGTTGGTCATTG
1429 TTTGGTCGAT
Statistics
Matches: 120, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
117 12 0.10
118 20 0.17
119 1 0.01
120 35 0.29
121 52 0.43
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (118 bp):
TTTTTTGGTGTTGGTCATTGCATGGCCAGCACCACCTTTCTATCTGATAAAAAAATTCAAATTTT
TTTGGTGTTGGCCAAGCATTGATCGACACCACCTTTTTATTAAAAAAATCAAA
Found at i:1389 original size:62 final size:61
Alignment explanation
Indices: 1168--1422 Score: 239
Period size: 61 Copynumber: 4.3 Consensus size: 61
1158 ATAAAAAACT
* * * * * *
1168 AATTTTTTTTGTGTTGGTCAT-TATATGGTCGACATCACGTTTTATCTTATAAAAAAATTTC-
1 AATTTTTTTGGTGTTGGCCATGCAT-TGGTCGACACCACCTTTTATCTGATAAAAAAA-TTCA
* *
1229 AATTTTTTTGGTGTTGGCCAAGCATTGGTCGACACCACCTATTATCTGATTAAAAAAATT-A
1 AATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTATCTGA-TAAAAAAATTCA
* *
1290 AA--TTTTTGGTGTTGGTCATTGCA-TGG-CCAGCACCACCTTTCTATCTGATAAAAAAATTCA
1 AATTTTTTTGGTGTTGGCCA-TGCATTGGTCGA-CACCACCTTT-TATCTGATAAAAAAATTCA
* * *
1350 AATTTTTTTTGTGTTGGCCATGCATTGATCGACACCACCTTTTTAT-T--T-GAAAAA-TCA
1 AATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACC-TTTTATCTGATAAAAAAATTCA
1407 AA-TTTTTTGGTGTTGG
1 AATTTTTTTGGTGTTGG
1423 TCATTGTTTG
Statistics
Matches: 164, Mismatches: 18, Indels: 29
0.78 0.09 0.14
Matches are distributed among these distances:
56 13 0.08
57 5 0.03
58 7 0.04
59 38 0.23
60 13 0.08
61 47 0.29
62 36 0.22
63 5 0.03
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (61 bp):
AATTTTTTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTATCTGATAAAAAAATTCA
Found at i:2320 original size:30 final size:30
Alignment explanation
Indices: 2286--2407 Score: 154
Period size: 30 Copynumber: 4.1 Consensus size: 30
2276 AAAAACTAAT
* * *
2286 AATTAGAAATGAAATTTAAAATATAAATGA
1 AATTACAAATTAAATTTAAAATATAAACGA
* * * *
2316 AATTACAAGTTAAAATTAAAATATATAGGA
1 AATTACAAATTAAATTTAAAATATAAACGA
*
2346 AATTAGAAATTAAATTTAAAATATAAACGA
1 AATTACAAATTAAATTTAAAATATAAACGA
* *
2376 AATTACAAATTAAATTAAAAAAATAAACGA
1 AATTACAAATTAAATTTAAAATATAAACGA
2406 AA
1 AA
2408 AATATCAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.28
Consensus pattern (30 bp):
AATTACAAATTAAATTTAAAATATAAACGA
Found at i:5106 original size:94 final size:94
Alignment explanation
Indices: 4940--5460 Score: 889
Period size: 94 Copynumber: 5.5 Consensus size: 94
4930 TAAATATAAA
* *
4940 ATTTGATAAAAATTATAAAATAATAATTGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
5005 TAAATAATGTATTGTCAAATCAACACATT
66 TAAATAATGTATTGTCAAATCAACACATT
* *
5034 ATTTAATAAAAATTGTAAAATAATAATAGTTTTTAATTTAAATAATTTTAAATATTAAAAATTGG
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
5099 TAAATAATGTATTGTCAAATCAACACATT
66 TAAATAATGTATTGTCAAATCAACACATT
*
5128 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTAATTTAAATAATTTTAAATATTAAAAATTGG
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
*
5193 TAAATAATGTATTGTCAAATTAACACATT
66 TAAATAATGTATTGTCAAATCAACACATT
* * **
5222 ATTTAATAAAATTTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTAA
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
*
5287 TAAATAATGTATTGTCAAATAAACACATT
66 TAAATAATGTATTGTCAAATCAACACATT
* * *
5316 ATTTTATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAAATTGA
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
* *
5381 TAAATAATGCATTGTCAAAACAACACATT
66 TAAATAATGTATTGTCAAATCAACACATT
*
5410 ATTTGATAAAAATTATAAAATAATAATAGTTTTTTATTTAAATAATTTTAA
1 ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAA
5461 CATAATTTTA
Statistics
Matches: 405, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 405 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (94 bp):
ATTTGATAAAAATTGTAAAATAATAATAGTTTTTTATTTAAATAATTTTAAATATTAAAAATTGG
TAAATAATGTATTGTCAAATCAACACATT
Found at i:5590 original size:17 final size:17
Alignment explanation
Indices: 5568--5603 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5558 AATATGTACC
5568 TTAATTTTCAAATTAAT
1 TTAATTTTCAAATTAAT
5585 TTAATTTTCAAATTAAT
1 TTAATTTTCAAATTAAT
5602 TT
1 TT
5604 TTACACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTTCAAATTAAT
Found at i:7140 original size:26 final size:26
Alignment explanation
Indices: 7111--7161 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
7101 TTTTTTTCGT
7111 TTATTTCTTAAAAT-TATTTTTAATTA
1 TTATTT-TTAAAATATATTTTTAATTA
**
7137 TTATTTTTTCAATATATTTTTAATT
1 TTATTTTTAAAATATATTTTTAATT
7162 TGTCGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTTTAAAATATATTTTTAATTA
Found at i:8079 original size:61 final size:58
Alignment explanation
Indices: 7970--8188 Score: 240
Period size: 59 Copynumber: 3.6 Consensus size: 58
7960 GAAAGGAGGG
* * * *
7970 AAAGTTGGTATCGACCATGCAATGGTTAACACCAAAAAAATTTGATTTTTTACCAGATAAA
1 AAAG-TGGTGTCGGCCATGCAAT-GATAACACC-AAAAAATTTGATTTTTTATCAGATAAA
* * *
8031 AAATGTGGCGTCGGCCATGCAATGACTAACACCAAAAAATTTGAATTTTTTATCTGACAAA
1 AAA-GTGGTGTCGGCCATGCAATGA-TAACACCAAAAAATTTG-ATTTTTTATCAGATAAA
* * * *
8092 AAGGTAGTGTCGACCACGCAATGATCAACACCAAAAAATTTGATTTTTTATCAGATAAA
1 AAAGTGGTGTCGGCCATGCAATGAT-AACACCAAAAAATTTGATTTTTTATCAGATAAA
* * *
8151 TAAGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAA
1 AAAGTGGTGTCGGCCATGCAATGAT-AACACCAAAAAA
8189 ATTAATACAT
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
59 47 0.35
60 44 0.33
61 41 0.31
62 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (58 bp):
AAAGTGGTGTCGGCCATGCAATGATAACACCAAAAAATTTGATTTTTTATCAGATAAA
Found at i:8161 original size:59 final size:59
Alignment explanation
Indices: 7970--8188 Score: 244
Period size: 60 Copynumber: 3.7 Consensus size: 59
7960 GAAAGGAGGG
* * * * *
7970 AAAGTTGGTATCGACCATGCAATGGTTAACACCAAAAAAATTTGATTTTTTACCAGATAAA
1 AAAGGTGGTGTCGACCATGCAATGATCAACACC-AAAAAATTTGATTTTTTATCAGAT-AA
* * * * *
8031 AAATGTGGCGTCGGCCATGCAATGA-CTAACACCAAAAAATTTGAATTTTTTATCTGACAA
1 AAAGGTGGTGTCGACCATGCAATGATC-AACACCAAAAAATTTG-ATTTTTTATCAGATAA
* *
8091 AAAGGTAGTGTCGACCACGCAATGATCAACACCAAAAAATTTGATTTTTTATCAGATAA
1 AAAGGTGGTGTCGACCATGCAATGATCAACACCAAAAAATTTGATTTTTTATCAGATAA
* * *
8150 ATAA-GTGGTGTCGGCCATGCAATGGTCAACACAAAAAAA
1 A-AAGGTGGTGTCGACCATGCAATGATCAACACCAAAAAA
8189 ATTAATACAT
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
59 45 0.34
60 50 0.38
61 37 0.28
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAGGTGGTGTCGACCATGCAATGATCAACACCAAAAAATTTGATTTTTTATCAGATAA
Found at i:10994 original size:28 final size:29
Alignment explanation
Indices: 10962--11213 Score: 148
Period size: 29 Copynumber: 8.7 Consensus size: 29
10952 TGGACATCCA
* *
10962 GGGGT-AAAAGGGTAATTTTGAAAGTTTT
1 GGGGTCAAAATGGTAATTTTGGAAGTTTT
* *
10990 TGGGTCAAAAATGG-AATTTTGGAAGTTTG
1 GGGGTC-AAAATGGTAATTTTGGAAGTTTT
* *
11019 GGGGT-AAAATAGTAATTTTTGAGAG-TTT
1 GGGGTCAAAATGGTAATTTTGGA-AGTTTT
* * **
11047 AGGGTCAAAATTAGG-ATTTTTGGAAGTTCG
1 GGGGTCAAAA-T-GGTAATTTTGGAAGTTTT
11077 GGGGT-AAAATGGTAATTTTGGAAGTTTT
1 GGGGTCAAAATGGTAATTTTGGAAGTTTT
* * *
11105 TGGGTCAAAATCGAG-ATTTTTGGAAG-TTC
1 GGGGTCAAAAT-G-GTAATTTTGGAAGTTTT
* * * *
11134 GAAGGTAAAAAT-GTAATTTTTGGGAGTTTC
1 G-GGGTCAAAATGGTAA-TTTTGGAAGTTTT
* *
11164 GAGGTCAAAAGTGG-AATTTTAGAGAAGTTTG
1 GGGGTCAAAA-TGGTAATTTT-G-GAAGTTTT
*
11195 GGGGTCAAAAT-ATAATTTT
1 GGGGTCAAAATGGTAATTTT
11214 TAGACAGTTT
Statistics
Matches: 172, Mismatches: 31, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
27 9 0.05
28 36 0.21
29 56 0.33
30 53 0.31
31 18 0.10
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGGTAATTTTGGAAGTTTT
Found at i:10999 original size:29 final size:28
Alignment explanation
Indices: 10962--11132 Score: 125
Period size: 28 Copynumber: 5.9 Consensus size: 28
10952 TGGACATCCA
* *
10962 GGGGTAAAAGGGTAATTTTGAAAGTTTT
1 GGGGTAAAATGGTAATTTTGGAAGTTTT
* *
10990 TGGGTCAAAAATGG-AATTTTGGAAGTTTG
1 GGGGT--AAAATGGTAATTTTGGAAGTTTT
* *
11019 GGGGTAAAATAGTAATTTTTGAGAG-TTT
1 GGGGTAAAATGGTAATTTTGGA-AGTTTT
* * **
11047 AGGGTCAAAATTAGG-ATTTTTGGAAGTTCG
1 GGGGT-AAAA-T-GGTAATTTTGGAAGTTTT
11077 GGGGTAAAATGGTAATTTTGGAAGTTTT
1 GGGGTAAAATGGTAATTTTGGAAGTTTT
* *
11105 TGGGTCAAAATCGAG-ATTTTTGGAAGTT
1 GGGGT-AAAAT-G-GTAATTTTGGAAGTT
11133 CGAAGGTAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
27 8 0.07
28 35 0.32
29 34 0.31
30 32 0.29
31 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAGTTTT
Found at i:11039 original size:58 final size:59
Alignment explanation
Indices: 10962--11223 Score: 227
Period size: 58 Copynumber: 4.5 Consensus size: 59
10952 TGGACATCCA
** *
10962 GGGGTAAAAGGGTAA-TTTTGAAAGTTTTTGGGTCAAAAAT-GGAATTTTGGAAGTTTG
1 GGGGTAAAATAGTAATTTTTGAAAGTTTTTGGGTCAAAAATAGGAATTTTGGAAGTTCG
* * * *
11019 GGGGTAAAATAGTAATTTTTGAGAG-TTTAGGGTCAAAATTAGGATTTTTGGAAGTTCG
1 GGGGTAAAATAGTAATTTTTGAAAGTTTTTGGGTCAAAAATAGGAATTTTGGAAGTTCG
* * * *
11077 GGGGTAAAATGGTAA-TTTTGGAAGTTTTTGGGTC-AAAATCGAGATTTTTGGAAGTTCG
1 GGGGTAAAATAGTAATTTTTGAAAGTTTTTGGGTCAAAAATAG-GAATTTTGGAAGTTCG
** ** * * *
11135 AAGGTAAAA-ATGTAATTTTTGGGAG-TTTCGAGGTCAAAAGT-GGAATTTTAGAGAAGTTTG
1 GGGGTAAAATA-GTAATTTTTGAAAGTTTTTG-GGTCAAAAATAGGAATTTT-G-GAAGTTCG
*
11195 GGGGTCAAAATA-TAATTTTTAGACAGTTT
1 GGGGT-AAAATAGTAATTTTT-GAAAGTTT
11224 AGGGACCTTA
Statistics
Matches: 166, Mismatches: 25, Indels: 23
0.78 0.12 0.11
Matches are distributed among these distances:
57 38 0.23
58 82 0.49
59 14 0.08
60 22 0.13
61 7 0.04
62 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
GGGGTAAAATAGTAATTTTTGAAAGTTTTTGGGTCAAAAATAGGAATTTTGGAAGTTCG
Found at i:11165 original size:30 final size:29
Alignment explanation
Indices: 10992--11192 Score: 93
Period size: 30 Copynumber: 6.9 Consensus size: 29
10982 AAAGTTTTTG
* *
10992 GGTCAAAAATGGAA-TTTTGGAAGTTTGGG
1 GGTCAAAAATGGAATTTTTGGAAG-TTCGA
* *
11021 GGT--AAAATAGTAATTTTT-GAGAGTT-TA
1 GGTCAAAAAT-GGAATTTTTGGA-AGTTCGA
* *
11048 GGGTCAAAATTAGG-ATTTTTGGAAGTTCGGG
1 -GGTCAAAAAT-GGAATTTTTGGAAGTTC-GA
*
11079 GGT--AAAATGGTAA-TTTTGGAAGTTTTTG-
1 GGTCAAAAATGG-AATTTTTGGAAG--TTCGA
*
11107 GGTC-AAAATCGAGATTTTTGGAAGTTCGAA
1 GGTCAAAAATGGA-ATTTTTGGAAGTTCG-A
* *
11137 GGT-AAAAATGTAATTTTTGGGAGTTTCGA
1 GGTCAAAAATGGAATTTTTGGAAG-TTCGA
* *
11166 GGTCAAAAGTGGAATTTTAGAGAAGTT
1 GGTCAAAAATGGAATTTTTG-GAAGTT
11193 TGGGGGTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 43
0.68 0.09 0.22
Matches are distributed among these distances:
27 7 0.05
28 30 0.23
29 42 0.32
30 50 0.38
31 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
GGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:13970 original size:39 final size:39
Alignment explanation
Indices: 13854--13994 Score: 169
Period size: 39 Copynumber: 3.6 Consensus size: 39
13844 CCCCGTGATT
* * *
13854 GGGGTAGGAGATTGGTTGACGGTGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTC
* ** * * *
13893 GGGGTAAGAGATCGAATGGCTG-TAATCT-ACCCATGGCTC
1 GGGGTAAGAGATTGGTTGAC-GATGATCTGCCCCA-GGCTC
13932 GGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTC
13971 GGGGTAAGAGATTGGTTGACGATG
1 GGGGTAAGAGATTGGTTGACGATG
13995 TAACTTCACT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
38 5 0.06
39 74 0.88
40 5 0.06
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (39 bp):
GGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTC
Found at i:14250 original size:101 final size:101
Alignment explanation
Indices: 14049--14243 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 101
14039 GCTGCTGTAG
* * * * * * * * *
14049 TTTTATTCCAACTTTTCTGTGACTTTAAGAAGATAAGATTTGATGTTGAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTTACTGTAACTTAAAGAAGATAAGAATTAACGTTAAAGCTTCATCTCGCTCT
*
14114 TACTACAACTTTAGAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
* * * *
14150 TTTTAATCCAACTTTACTGTAACTTAAAGAGGATAGGAATTAACGTTAAAGTTTTATCTCGCTCT
1 TTTTAATCCAACTTTACTGTAACTTAAAGAAGATAAGAATTAACGTTAAAGCTTCATCTCGCTCT
*
14215 TACTGCAACTTCAGAGAGATAAAGACTTG
66 TACTACAACTTCAGAGAGATAAAGACTTG
14244 TCATTGTAGT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (101 bp):
TTTTAATCCAACTTTACTGTAACTTAAAGAAGATAAGAATTAACGTTAAAGCTTCATCTCGCTCT
TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
Found at i:14524 original size:100 final size:101
Alignment explanation
Indices: 14348--14626 Score: 335
Period size: 100 Copynumber: 2.8 Consensus size: 101
14338 TCGTCATTGC
* * * * * *
14348 GACTTAAACCTTTCCCCTTCAAATCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAATATTTCC
1 GACTTAAACCTTTCCCTTTTATATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
* * * * * *
14413 TTTCTTATCTTCTTAGGTATACGGT-CAACCGTTGT
66 CTTCATGTCTTCTGAGGTACACGGTCCAACCGTTGA
* * *
14448 GACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCC
1 GACTTAAACCTTTCCCTTTTATATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
* ***
14513 CTTCGTGTCTTCTGAGGTACACGGTCCTGTCGTTGA
66 CTTCATGTCTTCTGAGGTACACGGTCCAACCGTTGA
* * * *
14549 GACTTAGACCTTTCCCTTTTATATCTTTGTGGTACTAGATCCGCCGTTGCGGTCTTAGATCTTTC
1 GACTTAAACCTTTCCCTTTTATATCTTTGTGGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTC
14614 CCTTCATGTCTTC
65 CCTTCATGTCTTC
14627 ATGGTGCTGA
Statistics
Matches: 151, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
100 76 0.50
101 52 0.34
102 23 0.15
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (101 bp):
GACTTAAACCTTTCCCTTTTATATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
CTTCATGTCTTCTGAGGTACACGGTCCAACCGTTGA
Found at i:14583 original size:51 final size:50
Alignment explanation
Indices: 14440--14597 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 50
14430 TATACGGTCA
* * *
14440 ACCGTTGTGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTC
1 ACCGTTGAGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACCGGATCC
* * * *
14490 ACCGTTGCAG-CTTAAATCTTTCCC-TTCGTGTCTTCTGAGGTACACGG-TCC
1 ACCGTTG-AGACTTAAACCTTTCCCTTTTGTATCTT-TGTGGTAC-CGGATCC
** * * **
14540 TGTCGTTGAGACTTAGACCTTTCCCTTTTATATCTTTGTGGTACTAGATCC
1 -ACCGTTGAGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACCGGATCC
*
14591 GCCGTTG
1 ACCGTTG
14598 CGGTCTTAGA
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
49 8 0.10
50 38 0.46
51 30 0.36
52 7 0.08
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.40
Consensus pattern (50 bp):
ACCGTTGAGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACCGGATCC
Found at i:14606 original size:51 final size:50
Alignment explanation
Indices: 14450--14617 Score: 144
Period size: 51 Copynumber: 3.3 Consensus size: 50
14440 ACCGTTGTGA
* * *
14450 CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCAG
1 CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCCGCCGTTGCAG
* * * * * *
14500 CTTAAATCTTTCCC-TTCGTGTCTTCTGAGGTAC-ACGGTCCTGTCGTTG-AG
1 CTTAAACCTTTCCCTTTTGTATCTT-TGTGGTACTA-GATCC-GCCGTTGCAG
* * *
14550 ACTTAGACCTTTCCCTTTTATATCTTTGTGGTACTAGATCCGCCGTTGCGG
1 -CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCCGCCGTTGCAG
* *
14601 TCTTAGATCTTTCCCTT
1 -CTTAAACCTTTCCCTT
14618 CATGTCTTCA
Statistics
Matches: 91, Mismatches: 20, Indels: 13
0.73 0.16 0.10
Matches are distributed among these distances:
49 8 0.09
50 31 0.34
51 44 0.48
52 8 0.09
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (50 bp):
CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCCGCCGTTGCAG
Found at i:15883 original size:27 final size:25
Alignment explanation
Indices: 15815--15885 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
15805 TCTCCCTTTT
* * *
15815 TTCTATTTTTGTTTTTCTTCTTGTTT
1 TTCT-TTTTTTTTTTTCTTCTTCTTC
*
15841 TTGCTTTTCTTTTTTTCTCTCTTCTTC
1 TT-CTTTTTTTTTTTTCT-TCTTCTTC
15868 TTCTTTTTTTATTTTTCT
1 TTCTTTTTTT-TTTTTCT
15886 ATTTATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.76
Consensus pattern (25 bp):
TTCTTTTTTTTTTTTCTTCTTCTTC
Found at i:17349 original size:157 final size:156
Alignment explanation
Indices: 17064--17381 Score: 609
Period size: 157 Copynumber: 2.0 Consensus size: 156
17054 ATGTCTTACT
*
17064 CAAAAGGATTTAAGTCAATAGCAGTGTTGCTCATATCCTTGATATCAAGGGCCTAGCATAAAGAC
1 CAAAAGGATTTAAGTCAACAGCAGTGTTGCTCATATCCTTGATATCAAGGGCCTAGCATAAAGAC
17129 GAAAAGGGGATCCAAAGAATAATTGGACTAAAGAATGGTTAATTGTGGTATGAACGAATGAAAAG
66 GAAAAGGGGATCCAAAGAATAATTGGACTAAAGAATGGTTAATTGTGGTATGAACGAATGAAAAG
17194 AATGGGAAGGTATTTGCCAAATGGGA
131 AATGGGAAGGTATTTGCCAAATGGGA
*
17220 CAAAAGGATTTAAGTCAACAGCAGTGTTGCTCATATCCTTGATATCAAGGGACTTAGCATAAAGA
1 CAAAAGGATTTAAGTCAACAGCAGTGTTGCTCATATCCTTGATATCAAGGG-CCTAGCATAAAGA
17285 CGAAAAGGGGATCCAAAGAATAATTGGACTAAAGAATGGTTAATTGTGGTATGAACGAATGAAAA
65 CGAAAAGGGGATCCAAAGAATAATTGGACTAAAGAATGGTTAATTGTGGTATGAACGAATGAAAA
17350 GAATGGGAAGGTATTTGCCAAATGGGA
130 GAATGGGAAGGTATTTGCCAAATGGGA
17377 CAAAA
1 CAAAA
17382 AATAATGCAT
Statistics
Matches: 159, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
156 50 0.31
157 109 0.69
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (156 bp):
CAAAAGGATTTAAGTCAACAGCAGTGTTGCTCATATCCTTGATATCAAGGGCCTAGCATAAAGAC
GAAAAGGGGATCCAAAGAATAATTGGACTAAAGAATGGTTAATTGTGGTATGAACGAATGAAAAG
AATGGGAAGGTATTTGCCAAATGGGA
Found at i:21758 original size:29 final size:28
Alignment explanation
Indices: 21674--21993 Score: 175
Period size: 30 Copynumber: 10.9 Consensus size: 28
21664 TTCTAGGTCA
* * *
21674 AAAATGGAA-TTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGGGTT
* * *
21702 AAAAAGTAATTTTT-GAGAGTTTTGGGGTT
1 AAAATGGAATTTTTGGA-AG-TTTAGGGTT
*
21731 AAAAATGGAATTTTTGGAGGTTTAGGG-T
1 -AAAATGGAATTTTTGGAAGTTTAGGGTT
* * *
21759 ATAATGGTAATTTTTGAAAGTTTCGAGGTT
1 AAAATGG-AATTTTTGGAAGTTTAG-GGTT
**
21789 AAAATCTAGATTTTTGGAAGTTTAAGGG-T
1 AAAATGGA-ATTTTTGGAAGTTT-AGGGTT
*
21818 AAAATGGTAAATTTTGGAAGTTTTAGGGTT
1 AAAATGG-AATTTTTGGAAG-TTTAGGGTT
* ** *
21848 AAATTGGGTTTTTTTGGAAG-TTCGGGTGT
1 AAAAT-GGAATTTTTGGAAGTTTAGGGT-T
* * * *
21877 AAATTGGTAATTTTTGAAAGTTTTGGGGTC
1 AAAATGG-AATTTTTGGAAG-TTTAGGGTT
* *
21907 AAAATTGAGATTTTTGGAAGTTTGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTT-AGGGTT
* * *
21937 AAAATGTAATTTTT-AAGAGTTTCGAGGTT
1 AAAATGGAATTTTTGGA-AGTTTAG-GGTT
*
21966 AAAAGTGGAATTTTGGAGAAGTTTAGGG
1 AAAA-TGGAATTTTTG-GAAGTTTAGGG
21994 GTCATAATAT
Statistics
Matches: 224, Mismatches: 43, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
27 6 0.03
28 34 0.15
29 77 0.34
30 89 0.40
31 17 0.08
32 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.28, T:0.39
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTT
Found at i:21832 original size:30 final size:29
Alignment explanation
Indices: 21615--21993 Score: 209
Period size: 29 Copynumber: 13.0 Consensus size: 29
21605 ATCGAGATAA
**
21615 AAAATGG-AATTTTTGGACA-TCCGAGGGT
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGT
* * *
21643 AAAAGGGTAATTTTTGAAAGTTTCTA-GGT
1 AAAATGGTAATTTTTGGAAGTTT-GAGGGT
* *
21672 CAAAAATGG-AA-TTTTAGAAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTGAGGGT
**
21701 AAAAAAGTAATTTTT-GAGAGTTTTG-GGGTT
1 AAAATGGTAATTTTTGGA-AG-TTTGAGGG-T
*
21731 AAAAATGG-AATTTTTGGAGGTTT-AGGGT
1 -AAAATGGTAATTTTTGGAAGTTTGAGGGT
* * *
21759 ATAATGGTAATTTTTGAAAGTTTCGAGGTT
1 AAAATGGTAATTTTTGGAAGTTT-GAGGGT
* *
21789 AAAAT-CTAGATTTTTGGAAGTTTAAGGGT
1 AAAATGGTA-ATTTTTGGAAGTTTGAGGGT
* *
21818 AAAATGGTAAATTTTGGAAGTTTTAGGGTT
1 AAAATGGTAATTTTTGGAAGTTTGAGGG-T
* * *
21848 AAATTGGGT-TTTTTTGGAAGTTCG-GGTGT
1 AAAAT-GGTAATTTTTGGAAGTTTGAGG-GT
* *
21877 AAATTGGTAATTTTTGAAAGTTTTG-GGGT
1 AAAATGGTAATTTTTGGAAG-TTTGAGGGT
*
21906 CAAAATTG-AGATTTTTGGAAGTTTGAGGGT
1 -AAAATGGTA-ATTTTTGGAAGTTTGAGGGT
* *
21936 AAAAAT-GTAATTTTT-AAGAGTTTCGAGGTT
1 -AAAATGGTAATTTTTGGA-AGTTT-GAGGGT
*
21966 AAAAGTGG-AATTTTGGAGAAGTTT-AGGG
1 AAAA-TGGTAATTTTTG-GAAGTTTGAGGG
21994 GTCATAATAT
Statistics
Matches: 273, Mismatches: 44, Indels: 67
0.71 0.11 0.17
Matches are distributed among these distances:
27 11 0.04
28 29 0.11
29 112 0.41
30 98 0.36
31 22 0.08
32 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTGAGGGT
Found at i:21839 original size:59 final size:58
Alignment explanation
Indices: 21637--21982 Score: 281
Period size: 59 Copynumber: 5.9 Consensus size: 58
21627 TTGGACATCC
* * * * * * *
21637 GAGGGTAAAAGGGTAATTTTTGAAAGTTTCTAGGTCAAAAATGGAATTTTAGAAGTTT
1 GAGGGTAAAATGGTAAATTTTGAAAGTTTCGAGGTTAAAATTGGATTTTTGGAAGTTT
* ** * * * * * *
21695 GGGGGTAAAAAAGTAATTTTTGAGAGTTTTGGGGTTAAAAATGGAATTTTTGGAGGTTT
1 GAGGGTAAAATGGTAAATTTTGAAAGTTTCGAGGTTAAAATTGG-ATTTTTGGAAGTTT
* * *
21754 -AGGGTATAATGGTAATTTTTGAAAGTTTCGAGGTTAAAATCTAGATTTTTGGAAGTTT
1 GAGGGTAAAATGGTAAATTTTGAAAGTTTCGAGGTTAAAAT-TGGATTTTTGGAAGTTT
* * * * *
21812 AAGGGTAAAATGGTAAATTTTGGAAGTTT-TAGGGTT-AAATTGGGTTTTTTTGGAAGTTC
1 GAGGGTAAAATGGTAAATTTTGAAAGTTTCGA-GGTTAAAATT-GG-ATTTTTGGAAGTTT
* * * * *
21871 G-GGTGTAAATTGGTAATTTTTGAAAGTTTTGGGGTCAAAATTGAGATTTTTGGAAGTTT
1 GAGG-GTAAAATGGTAAATTTTGAAAGTTTCGAGGTTAAAATTG-GATTTTTGGAAGTTT
* * *
21930 GAGGGTAAAAAT-GT-AATTTTTAAGAGTTTCGAGGTTAAAAGTGGAATTTTGGA
1 GAGGGT-AAAATGGTAAATTTTGAA-AGTTTCGAGGTTAAAATTGGATTTTTGGA
21983 GAAGTTTAGG
Statistics
Matches: 230, Mismatches: 45, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
57 1 0.00
58 105 0.46
59 112 0.49
60 12 0.05
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (58 bp):
GAGGGTAAAATGGTAAATTTTGAAAGTTTCGAGGTTAAAATTGGATTTTTGGAAGTTT
Found at i:23722 original size:12 final size:13
Alignment explanation
Indices: 23705--23733 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23695 AATGATTACC
23705 AAACT-GGTTTTA
1 AAACTGGGTTTTA
23717 AAACTGGGTTTTA
1 AAACTGGGTTTTA
23730 AAAC
1 AAAC
23734 CCAGTTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (13 bp):
AAACTGGGTTTTA
Done.