Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013590.1 Kokia drynarioides strain JFW-HI SEQ_128617, 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: 51269
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:212 original size:26 final size:25
Alignment explanation
Indices: 157--221 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
147 ACAGAAGTAG
* *
157 AAAACGGTGCGTTTTGTGTTTAAAT
1 AAAACGGTGCATTTTGGGTTTAAAT
*
182 AAAACGGTGCATTTTGGGTCTTAAGT
1 AAAACGGTGCATTTTGGGT-TTAAAT
* *
208 TAAACGGAGCATTT
1 AAAACGGTGCATTT
222 AGAGGAGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (25 bp):
AAAACGGTGCATTTTGGGTTTAAAT
Found at i:4453 original size:367 final size:373
Alignment explanation
Indices: 3915--4630 Score: 957
Period size: 367 Copynumber: 1.9 Consensus size: 373
3905 GTTTAAATTC
* * *
3915 ATTTACTAATCATGTACTATACGTACAGTTATAGATTTAGTATATATATTCTTCAATTGAATCAT
1 ATTTACTAATCATGTACTATACATACAGTTATAGATTTAGTATATATATTCTCCAATTGAATAAT
* * * *
3980 TCTAAGTCCTTATATTTTTTTTCAAAATTTGATATTTCAATCTCGGCACAAATGATAGTCCAATC
66 TCTAAGCCCTTATATTTTTTTTCAAAATTTGAAATTTCAATCTCGACACAAATAATAGTCCAATC
* *
4045 TATTAACTAAAATTTTAGTGAGTAATATGCGAAAATAAC-AA-G-TTA-A-A-AT-TGATATGTT
131 CATTAACTAAAATTTTAGTGAGTAATATGCGAAAATAACAAATGATTACACATATATGATATATT
* **
4103 TGTTGCATCAAATTTTGGAAATAACAGAA-TTTAATTTAATGAATTTAACAATTATTGTTTAGCA
196 TGTTGCATCAAATTTTGGAAATAACA-AAGTTTAACTTAATGAATTTAACAATTATCATTTAGCA
* *
4167 AGAACTGAAA-TTCTAAAAATTGAAAAGTGCGAGCATTAAAAGTGACCAAATTAAAATATGAGAA
260 AGAACTGAAATTTCTAAAAATTGAAAAGTACGAGCATTAAAAGTGACCAAATTAAAATATAAGAA
* *
4231 TTAAATTCATAACTTTGAAATTTGAAAATAACAGAATTTAATTTAATGA
325 CTAAATTCACAACTTTGAAATTTGAAAATAACAGAATTTAATTTAATGA
* * * *
4280 ATTTACTAGTCATGTACTATACATGCAGTTGTAGATTTAGTGTATATATTCTCCAATTGAATAAT
1 ATTTACTAATCATGTACTATACATACAGTTATAGATTTAGTATATATATTCTCCAATTGAATAAT
* *
4345 TCTAAGACCCTATATTTTTTTTTTCAAAATTTGAAATTTCAATCTCGACACAAATAATAGTCTAA
66 TCTAAG-CCCT-TATATTTTTTTTCAAAATTTGAAATTTCAATCTCGACACAAATAATAGTCCAA
** *
4410 TCCATTAACT-GGATTTTCAGTGAGTAATATGTGAAAATAACAAGTTAAAATGTCATTACACATA
129 TCCATTAACTAAAATTTT-AGTGAGTAATATGCGAAAATAAC------AAATG--ATTACACATA
* *
4474 TGATGATATATTTGTTGCATCAAATTTTGGAAATAATAAAGTTTAACTTAATGAGTTTAACAATT
185 T-ATGATATATTTGTTGCATCAAATTTTGGAAATAACAAAGTTTAACTTAATGAATTTAACAATT
** * *
4539 ATCATTTAGTGAGAACTGAAATTTTTAAAAATTGAAAAGTACGAGGATTAAAAGTGACCAAATTA
249 ATCATTTAGCAAGAACTGAAATTTCTAAAAATTGAAAAGTACGAGCATTAAAAGTGACCAAATTA
*
4604 AAATTTAAGAACTAAATTCACAACTTT
314 AAATATAAGAACTAAATTCACAACTTT
4631 TACAAAATAC
Statistics
Matches: 298, Mismatches: 32, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
365 64 0.21
366 8 0.03
367 79 0.27
374 2 0.01
375 1 0.00
378 3 0.01
379 1 0.00
380 1 0.00
381 2 0.01
382 2 0.01
383 72 0.24
384 63 0.21
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (373 bp):
ATTTACTAATCATGTACTATACATACAGTTATAGATTTAGTATATATATTCTCCAATTGAATAAT
TCTAAGCCCTTATATTTTTTTTCAAAATTTGAAATTTCAATCTCGACACAAATAATAGTCCAATC
CATTAACTAAAATTTTAGTGAGTAATATGCGAAAATAACAAATGATTACACATATATGATATATT
TGTTGCATCAAATTTTGGAAATAACAAAGTTTAACTTAATGAATTTAACAATTATCATTTAGCAA
GAACTGAAATTTCTAAAAATTGAAAAGTACGAGCATTAAAAGTGACCAAATTAAAATATAAGAAC
TAAATTCACAACTTTGAAATTTGAAAATAACAGAATTTAATTTAATGA
Found at i:7455 original size:27 final size:26
Alignment explanation
Indices: 7416--7470 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
7406 GTAGATTGAC
*
7416 TTCAAGTGGCGGCACTGAAAGAGG-GTT
1 TTCAAGTGACGGCACT-AAA-AGGTGTT
7443 TTCAAGTGACGGCACTAAAAGGTGTT
1 TTCAAGTGACGGCACTAAAAGGTGTT
7469 TT
1 TT
7471 GCCACTTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 3 0.12
26 8 0.31
27 15 0.58
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (26 bp):
TTCAAGTGACGGCACTAAAAGGTGTT
Found at i:7651 original size:16 final size:16
Alignment explanation
Indices: 7630--7674 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
7620 ATAATGAGAT
7630 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
7646 ATTATTTT--TATATT-
1 ATTATTTTGGTA-ATTA
7660 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
7675 TTTAGCTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 5 0.20
16 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:7870 original size:21 final size:23
Alignment explanation
Indices: 7846--7888 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
7836 AATTAAAATA
7846 TTTAAAATTTTA-TAT-TAATTT
1 TTTAAAATTTTATTATATAATTT
*
7867 TTTATAATTTTATTATATAATT
1 TTTAAAATTTTATTATATAATT
7889 AATTTTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAAAATTTTATTATATAATTT
Found at i:8756 original size:16 final size:16
Alignment explanation
Indices: 8737--8768 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8727 ATAATAAAAG
*
8737 AAAAGTTTGATAAGTA
1 AAAAGTGTGATAAGTA
8753 AAAAGTGTGATAAGTA
1 AAAAGTGTGATAAGTA
8769 CCAAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (16 bp):
AAAAGTGTGATAAGTA
Found at i:8906 original size:31 final size:31
Alignment explanation
Indices: 8862--8921 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
8852 ACTAACTTAA
* *
8862 GAAAAAATGTCAAGTT-TAGATATCAAATTAG
1 GAAAAAATATCAAGTTCAAG-TATCAAATTAG
*
8893 GAAAAAGTATCAAGTTCAAGTATCAAATT
1 GAAAAAATATCAAGTTCAAGTATCAAATT
8922 GAACCAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.28
Consensus pattern (31 bp):
GAAAAAATATCAAGTTCAAGTATCAAATTAG
Found at i:9166 original size:23 final size:23
Alignment explanation
Indices: 9136--9181 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9126 TCTATTGCAC
9136 TATCATATGATTGAAATGTGATA
1 TATCATATGATTGAAATGTGATA
9159 TATCATATGATTGAAATGTGATA
1 TATCATATGATTGAAATGTGATA
9182 ATCTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (23 bp):
TATCATATGATTGAAATGTGATA
Found at i:13410 original size:17 final size:17
Alignment explanation
Indices: 13388--13430 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
13378 TAAAGAGCGA
13388 TCATTGTCTCCACGTCT
1 TCATTGTCTCCACGTCT
13405 TCATTGTCTCCACGTCT
1 TCATTGTCTCCACGTCT
*
13422 TCATCGTCT
1 TCATTGTCT
13431 ACAAGTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.35, G:0.12, T:0.42
Consensus pattern (17 bp):
TCATTGTCTCCACGTCT
Found at i:15121 original size:20 final size:18
Alignment explanation
Indices: 15093--15178 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 18
15083 CCACGTCAAC
*
15093 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
*
15113 AAATTATTTTTTTAAATATA
1 AAATTA--TTTTAAAATATA
15133 AAATTA--TTAAAACTATTTTA
1 AAATTATTTTAAAA-TA---TA
*
15153 AAATTAATTTAAAATATA
1 AAATTATTTTAAAATATA
15171 AAATTATT
1 AAATTATT
15179 AAATCATCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
16 5 0.09
17 2 0.04
18 9 0.17
20 21 0.39
21 4 0.07
22 13 0.24
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:16254 original size:28 final size:28
Alignment explanation
Indices: 16217--16273 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
16207 AACGTTAGAG
16217 ACTAATTTTGCACTTATGCCTAAAAACT
1 ACTAATTTTGCACTTATGCCTAAAAACT
16245 ACTAATTTTGCACTTATGCCTAAAAACT
1 ACTAATTTTGCACTTATGCCTAAAAACT
16273 A
1 A
16274 TACTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (28 bp):
ACTAATTTTGCACTTATGCCTAAAAACT
Found at i:17862 original size:30 final size:29
Alignment explanation
Indices: 17826--18254 Score: 298
Period size: 30 Copynumber: 14.6 Consensus size: 29
17816 GCACGGGGGC
* * *
17826 AAAATGGTAGTTTTAGAAGGTTCGGAGTCA
1 AAAATGGTATTTTTGGAA-GTTCGGGGTCA
*
17856 AAAATGGGATTTTTGGAAGTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGTTCG-GGGTCA
* *
17884 AAAATGGTAATTTCTGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAA-GTTCGGGGTCA
* * * *
17915 AAAAGGGGATTTTTGGGATTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGTTCG-GGGTCA
* *
17943 AAAATGGTAAATTTTAGAAAGTTCGAGGGTCA
1 AAAATGGT--ATTTTTGGAAGTTCG-GGGTCA
17975 AAAATGAG-ATTTTTGGAAGTTCAGGGGT--
1 AAAATG-GTATTTTTGGAAGTTC-GGGGTCA
* * *
18003 AAAATGGTAATTTTGGAAGGTTCGGAGTCG
1 AAAATGGTATTTTTGGAA-GTTCGGGGTCA
*
18033 AAAATGGGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGTATTTTTGGAAGTTC-GGGGTCA
* * **
18061 AAAATGGTAATTTTAGAAGGTTCGGGGTTG
1 AAAATGGTATTTTTGGAA-GTTCGGGGTCA
*
18091 AAAATGGGATTTTTGGAAGTTCAGGGG--A
1 AAAATGGTATTTTTGGAAGTTC-GGGGTCA
* *
18119 AAAATGGTAATTTTTAGAAGGTTCGGAGTCA
1 AAAATGGT-ATTTTTGGAA-GTTCGGGGTCA
*
18150 AAAATAAG-ATTTTTGGAAGTTCGGGGT--
1 AAAAT-GGTATTTTTGGAAGTTCGGGGTCA
* **
18177 AAAATGGTAATTTTTAGAAGGTTCGGAATCA
1 AAAATGGT-ATTTTTGGAA-GTTCGGGGTCA
18208 AAAATGAG-ATTTTTGGAAGTTCGGGGGT--
1 AAAATG-GTATTTTTGGAAGTTC-GGGGTCA
18236 AAAATGGTAATTTTTGGAA
1 AAAATGGT-ATTTTTGGAA
18255 AGTTTAGGGA
Statistics
Matches: 318, Mismatches: 46, Indels: 71
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.00
27 7 0.02
28 74 0.23
29 78 0.25
30 130 0.41
31 19 0.06
32 8 0.03
33 1 0.00
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.31
Consensus pattern (29 bp):
AAAATGGTATTTTTGGAAGTTCGGGGTCA
Found at i:17890 original size:58 final size:58
Alignment explanation
Indices: 17826--18249 Score: 568
Period size: 58 Copynumber: 7.2 Consensus size: 58
17816 GCACGGGGGC
*
17826 AAAATGGTAGTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
17884 AAAATGGTAATTTCT-GAAAGGTTCGGGGTCAAAAAGGGGATTTTTGGGATTTCGAGGGT
1 AAAATGGTAATTT-TAG-AAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
17943 AAAATGGTAAATTTTAGAAAGTTCGAGGGTCAAAAATGAGATTTTTGGAAGTTC-AGGGGT
1 AAAATGGT-AATTTTAGAAGGTTCG-GAGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* * *
18003 AAAATGGTAATTTTGGAAGGTTCGGAGTCGAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* ** *
18061 AAAATGGTAATTTTAGAAGGTTCGGGGTTGAAAATGGGATTTTTGGAAGTTC-AGGGGA
1 AAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
**
18119 AAAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATAAGATTTTTGGAAGTTCG-GGGT
1 AAAATGGTAA-TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
18177 AAAATGGTAATTTTTAGAAGGTTCGGAATCAAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAA-TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
18236 AAAATGGTAATTTT
1 AAAATGGTAATTTT
18250 TGGAAAGTTT
Statistics
Matches: 326, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
58 163 0.50
59 121 0.37
60 42 0.13
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:18162 original size:117 final size:116
Alignment explanation
Indices: 17819--18251 Score: 600
Period size: 117 Copynumber: 3.7 Consensus size: 116
17809 TTAGGATGCA
* * *
17819 CGGGGGCAAAATGGTAGTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTC-GAGGG
1 CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCAG-GGG
* * * * *
17883 TAAAATGGTAATTTCTGAAAGGTTCGGGGTCAAAAAGGGGATTTTTGGGATTT
65 TAAAATGGTAATTTTTG-AAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
* * *
17936 CGAGGGTAAAATGGTAAATTTTAGAAAGTTCGAGGGTCAAAAATGAGATTTTTGGAAGTTCAGGG
1 CGGGGGTAAAATGGT-AATTTTAGAAGGTTCG-GAGTCAAAAATGAGATTTTTGGAAGTTCAGGG
* *
18001 GTAAAATGGTAATTTTGGAAGGTTCGGAGTCGAAAATGGGATTTTTGGAAGTT
64 GTAAAATGGTAATTTTTGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
* ** * *
18054 CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTTGAAAATGGGATTTTTGGAAGTTCAGGGGA
1 CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCAGGGGT
**
18119 AAAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATAAGATTTTTGGAAGTT
66 AAAATGGTAATTTTT-GAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
* *
18171 C-GGGGTAAAATGGTAATTTTTAGAAGGTTCGGAATCAAAAATGAGATTTTTGGAAGTTCGGGGG
1 CGGGGGTAAAATGGTAA-TTTTAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCAGGGG
18235 TAAAATGGTAATTTTTG
65 TAAAATGGTAATTTTTG
18252 GAAAGTTTAG
Statistics
Matches: 281, Mismatches: 30, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
116 60 0.21
117 118 0.42
118 58 0.21
119 44 0.16
120 1 0.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.31
Consensus pattern (116 bp):
CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCAGGGGT
AAAATGGTAATTTTTGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
Found at i:20191 original size:6 final size:6
Alignment explanation
Indices: 20163--20223 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
20153 TTATAATAAT
* * *
20163 TTTAAA TTTGAAA -ATAAA TTTAAA ATTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
20210 TTT-AA TTTAAA TTT
1 TTTAAA TTTAAA TTT
20224 TTAACAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 12 0.27
6 30 0.67
7 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:20203 original size:11 final size:11
Alignment explanation
Indices: 20165--20220 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
20155 ATAATAATTT
20165 TAAATTTGAAAA
1 TAAATTT-AAAA
20177 TAAATTTAAAA
1 TAAATTTAAAA
20188 TTAAATTTAAAA
1 -TAAATTTAAAA
*
20200 TAAATTTAAAT
1 TAAATTTAAAA
*
20211 TTAATTTAAA
1 TAAATTTAAA
20221 TTTTTAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
11 23 0.56
12 18 0.44
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:20208 original size:17 final size:17
Alignment explanation
Indices: 20147--20253 Score: 74
Period size: 17 Copynumber: 6.2 Consensus size: 17
20137 GAACTTTATC
* * *
20147 TTAATTTTATAATAATT
1 TTAAATTTAAAATAAAT
20164 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
20182 TTAAAATTAAATTTAAA-
1 TTAAATTTAAA-ATAAAT
* * *
20199 ATAAATTTAAATTTAAT
1 TTAAATTTAAAATAAAT
** *
20216 TTAAATTTTTAACAAAT
1 TTAAATTTAAAATAAAT
20233 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
20250 TTAA
1 TTAA
20254 GGGGGAGTTT
Statistics
Matches: 68, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
16 7 0.10
17 42 0.62
18 19 0.28
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:30653 original size:97 final size:96
Alignment explanation
Indices: 30479--30660 Score: 235
Period size: 97 Copynumber: 1.9 Consensus size: 96
30469 AGAATGTTCT
* ** *
30479 ATTATCTCGATTTGAGGAAATGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGAT
1 ATTATCTCGATTTGAGAAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAAT
**
30544 ACGGAAACATTGCCTCGATTAAGGGTATTCG
66 AAAGAAACATTGCCTCGATTAAGGGTATTCG
*
30575 ATTATTTCGATTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC-AA
1 ATTATCTCGATTTG-AGAAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGAA
*
30638 AATAAA-AGAATATTGCCTCGATT
63 AATAAAGA-AACATTGCCTCGATT
30661 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
96 15 0.20
97 57 0.77
98 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAGAAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAAT
AAAGAAACATTGCCTCGATTAAGGGTATTCG
Found at i:31132 original size:30 final size:29
Alignment explanation
Indices: 31034--31413 Score: 245
Period size: 29 Copynumber: 12.9 Consensus size: 29
31024 TGGACATCCA
* * *
31034 GGGGT-AAAAGGGTAATTTTTGAAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
* * * * *
31063 GAGGTTAATAATGAAAATTTTGG-AGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
*
31092 GAGGGTAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* *** * *
31122 GGGGTCAAAAATGTAATTTTCAAACAATTGT
1 GGGGT-AAAAATGGAATTTTTGGA-AGTTTT
*
31153 GGGGTCGAAAATGGAATTTTTGGAAG-TTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
31182 GAGGGTAAAAATGGAA-TTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * **
31211 GAGGTTAAAAATGGAAATTTTT-GAGGTTCG
1 G-GGGTAAAAATGG-AATTTTTGGAAGTTTT
*
31241 GGGGTAAAAATGGAATTTTTGAAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * * *
31270 AGTGTAAAAAATGTAATTTTT-CATCAATTTT
1 GGGGT-AAAAATGGAATTTTTGGA--AGTTTT
* *
31301 GGGGTCGAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * * *
31330 GAGGGTGAAAATAGAATTTTTAGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* *
31360 GGGGTTAAAAATGGAAATTTTGGAAG-TTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTT
* *
31389 GGGTTGAAAATGGAATTTTTGGAAG
1 GGGGTAAAAATGGAATTTTTGGAAG
31414 CTCGAGGGTA
Statistics
Matches: 279, Mismatches: 55, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
28 35 0.13
29 107 0.38
30 84 0.30
31 52 0.19
32 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:31280 original size:148 final size:149
Alignment explanation
Indices: 31047--31437 Score: 502
Period size: 148 Copynumber: 2.6 Consensus size: 149
31037 GTAAAAGGGT
* * * * * *
31047 AATTTTTGAAAGTTTCGAGGTTAATAATGAAAATTTTGGAGTTTCGAGGGTAAAAATGTAATTTT
1 AATTTTTGGAAGTTTCGAGGTTAAAAATGGAAATTTTGGAGGTTCGGGGGTAAAAATGGAATTTT
* * *
31112 TGGAAGTTTTGGGGTCAAAAATGTAA-TTTTCAAACAATTGTGGGGTCGAAAATGGAATTTTTGG
66 TGAAAGTTTTAGGGTAAAAAATGTAATTTTTC-AACAATTGTGGGGTCGAAAATGGAATTTTTGG
* *
31176 AAGTTTGAGGGTAAAAATGG
130 AAGTTCGAGGGTAAAAATAG
* *
31196 AA-TTTTGGAAGTTTTGAGGTTAAAAATGGAAATTTTTGAGGTTCGGGGGTAAAAATGGAATTTT
1 AATTTTTGGAAGTTTCGAGGTTAAAAATGGAAATTTTGGAGGTTCGGGGGTAAAAATGGAATTTT
* * *
31260 TGAAAGTTTTAGTGTAAAAAATGTAATTTTTCATCAATTTTGGGGTCGAAAATGGAATTTTTGGA
66 TGAAAGTTTTAGGGTAAAAAATGTAATTTTTCAACAATTGTGGGGTCGAAAATGGAATTTTTGGA
*
31325 AGTTCGAGGGTGAAAATAG
131 AGTTCGAGGGTAAAAATAG
* * * * *
31344 AATTTTTAGAAGTTTCGGGGTTAAAAATGGAAATTTTGGAAGTTC-GGGTTGAAAATGGAATTTT
1 AATTTTTGGAAGTTTCGAGGTTAAAAATGGAAATTTTGGAGGTTCGGGGGTAAAAATGGAATTTT
* * ** *
31408 TGGAAGCTCGAGGGT-AGAAATGTAATTTTT
66 TGAAAGTTTTAGGGTAAAAAATGTAATTTTT
31438 GAATAGTTTA
Statistics
Matches: 210, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
147 14 0.07
148 152 0.72
149 44 0.21
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (149 bp):
AATTTTTGGAAGTTTCGAGGTTAAAAATGGAAATTTTGGAGGTTCGGGGGTAAAAATGGAATTTT
TGAAAGTTTTAGGGTAAAAAATGTAATTTTTCAACAATTGTGGGGTCGAAAATGGAATTTTTGGA
AGTTCGAGGGTAAAAATAG
Found at i:33264 original size:6 final size:6
Alignment explanation
Indices: 33250--33292 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
33240 TTTTAAATCC
* *
33250 ATTTAA ATTTTA A-TTAA ATTTAAA ATATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA A
33293 ATAAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:44958 original size:18 final size:20
Alignment explanation
Indices: 44937--44975 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
44927 TGAGTTTGAA
44937 TTTTTAAT-AAATAT-TAAT
1 TTTTTAATCAAATATATAAT
*
44955 TTTTTATTCAAATATATAAT
1 TTTTTAATCAAATATATAAT
44975 T
1 T
44976 ATAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTAATCAAATATATAAT
Found at i:45210 original size:16 final size:18
Alignment explanation
Indices: 45189--45229 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
45179 AAATAGTTTT
*
45189 TTAATTATAAA-TTTAA-
1 TTAATTAAAAATTTTAAG
45205 TTAATTAAAAATTTTAAG
1 TTAATTAAAAATTTTAAG
45223 TTAATTA
1 TTAATTA
45230 CACCTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAG
Found at i:45450 original size:15 final size:15
Alignment explanation
Indices: 45430--45480 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
45420 ACAAAATAAT
45430 AATATAACTGATTAA
1 AATATAACTGATTAA
*
45445 AATATAAC--ATTTCA
1 AATATAACTGA-TTAA
*
45459 AATATAAGTGATTAA
1 AATATAACTGATTAA
45474 AATATAA
1 AATATAA
45481 TCTAAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 18 0.60
16 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
AATATAACTGATTAA
Found at i:45453 original size:31 final size:29
Alignment explanation
Indices: 45418--45480 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
45408 AACTATTTCG
45418 TAACAAAATAATAATATAACTGATTAAAATA
1 TAAC-AAATAA-AATATAACTGATTAAAATA
** * *
45449 TAACATTTCAAATATAAGTGATTAAAATA
1 TAACAAATAAAATATAACTGATTAAAATA
45478 TAA
1 TAA
45481 TCTAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 3 0.11
31 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (29 bp):
TAACAAATAAAATATAACTGATTAAAATA
Found at i:48336 original size:19 final size:19
Alignment explanation
Indices: 48309--48349 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48299 GTTGAATTGA
*
48309 TTAAATTTAATTAATTTAT
1 TTAAATTTAATTAATTAAT
* *
48328 TTAATTTTAATTTATTAAT
1 TTAAATTTAATTAATTAAT
48347 TTA
1 TTA
48350 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTTAATTAATTAAT
Found at i:48339 original size:15 final size:14
Alignment explanation
Indices: 48319--48348 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
48309 TTAAATTTAA
48319 TTAATTTATTTAATT
1 TTAATTTA-TTAATT
48334 TTAATTTATTAATT
1 TTAATTTATTAATT
48348 T
1 T
48349 ATTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAATTTATTAATT
Found at i:48359 original size:23 final size:24
Alignment explanation
Indices: 48312--48359 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
48302 GAATTGATTA
* *
48312 AATTTAATTAATTTATTTAATTTT
1 AATTTAATTAATTTATTAAAATTT
48336 AATTT-ATTAATTTATTAAAATTT
1 AATTTAATTAATTTATTAAAATTT
48359 A
1 A
48360 TAGATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTAATTAATTTATTAAAATTT
Found at i:48360 original size:10 final size:8
Alignment explanation
Indices: 48312--48353 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
48302 GAATTGATTA
48312 AATTTAATT
1 AATTT-ATT
48321 AATTTATTT
1 AATTTA-TT
48330 AA-TT-TT
1 AATTTATT
48336 AATTTATT
1 AATTTATT
48344 AATTTATT
1 AATTTATT
48352 AA
1 AA
48354 AATTTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.13
7 2 0.07
8 15 0.50
9 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTATT
Found at i:48699 original size:25 final size:27
Alignment explanation
Indices: 48660--48713 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
48650 TAACAAAGTG
*
48660 AAATAAATTTTAAAAAATATAT-ACTT
1 AAATAAATATTAAAAAATATATAACTT
*
48686 AAAT-AATATTAAAATATATATAACTT
1 AAATAAATATTAAAAAATATATAACTT
48712 AA
1 AA
48714 CAAATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATAAATATTAAAAAATATATAACTT
Found at i:48719 original size:26 final size:24
Alignment explanation
Indices: 48664--48719 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
48654 AAAGTGAAAT
*
48664 AAATTTTAAAAAATATATACTTAA
1 AAATATTAAAAAATATATACTTAA
*
48688 ATAATATTAAAATATATATAACTTAA
1 A-AATATTAAAAAATATAT-ACTTAA
48714 CAAATA
1 -AAATA
48720 AATGTCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 15 0.56
26 10 0.37
27 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATTAAAAAATATATACTTAA
Found at i:48808 original size:22 final size:22
Alignment explanation
Indices: 48760--48831 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
48750 TAAAATAAGT
48760 AATAACAACAAAATAGTAATAA
1 AATAACAACAAAATAGTAATAA
* * * * *
48782 CATAATAATAAAATTGTAGTAA
1 AATAACAACAAAATAGTAATAA
* * * *
48804 AATAAGAA-AAAACAATAAGAA
1 AATAACAACAAAATAGTAATAA
48825 AATAACA
1 AATAACA
48832 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (22 bp):
AATAACAACAAAATAGTAATAA
Found at i:48939 original size:17 final size:18
Alignment explanation
Indices: 48905--48949 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
48895 ATTTGACTTT
*
48905 TTTTTTAAATAGATTTAA
1 TTTTTTAAATAGAATTAA
*
48923 TTTTTTACATA-AATTAA
1 TTTTTTAAATAGAATTAA
*
48940 TTTTTCAAAT
1 TTTTTTAAAT
48950 TTATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTTTAAATAGAATTAA
Done.