Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002321.1 Kokia drynarioides strain JFW-HI SEQ_114367, 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: 146625
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:19841 original size:24 final size:25
Alignment explanation
Indices: 19773--19870 Score: 101
Period size: 25 Copynumber: 3.9 Consensus size: 25
19763 CAAGTTACAA
**
19773 CTTGAATTTAATAATTTTTTTTACGT
1 CTTGAATTTTGTAA-TTTTTTTACGT
*
19799 CTTGAATTTTGTAATTTTTTTAGGT
1 CTTGAATTTTGTAATTTTTTTACGT
*
19824 TTTGAATTTTGTAATTTTTTT-CGT
1 CTTGAATTTTGTAATTTTTTTACGT
* *
19848 ATTGAGA-TTTGAAATTTTCTTTA
1 CTTGA-ATTTTGTAATTTT-TTTA
19871 TTTAGTTTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
24 16 0.26
25 34 0.55
26 12 0.19
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.59
Consensus pattern (25 bp):
CTTGAATTTTGTAATTTTTTTACGT
Found at i:21560 original size:12 final size:12
Alignment explanation
Indices: 21545--21618 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 12
21535 AATGGCAACC
*
21545 AAAACAAGAGCA
1 AAAACAACAGCA
*
21557 AAAATAACAGC-
1 AAAACAACAGCA
21568 AAAAC-A-A-CA
1 AAAACAACAGCA
* *
21577 AAAACAGCAACA
1 AAAACAACAGCA
* *
21589 AAAATAACAACA
1 AAAACAACAGCA
*
21601 AAAACAACA-CG
1 AAAACAACAGCA
21612 AAAACAA
1 AAAACAA
21619 TAACCAAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
8 1 0.02
9 6 0.12
10 1 0.02
11 13 0.26
12 29 0.58
ACGTcount: A:0.70, C:0.20, G:0.07, T:0.03
Consensus pattern (12 bp):
AAAACAACAGCA
Found at i:21587 original size:44 final size:44
Alignment explanation
Indices: 21525--21618 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
21515 AATAAAATTC
** * * * *
21525 AAACAACAAAAATGGCAACCAAAACAAGAGCAAAAATAACA-GCA
1 AAACAACAAAAACAGCAACAAAAACAACAACAAAAACAACACG-A
*
21569 AAACAACAAAAACAGCAACAAAAATAACAACAAAAACAACACGA
1 AAACAACAAAAACAGCAACAAAAACAACAACAAAAACAACACGA
21613 AAACAA
1 AAACAA
21619 TAACCAAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.68, C:0.21, G:0.07, T:0.03
Consensus pattern (44 bp):
AAACAACAAAAACAGCAACAAAAACAACAACAAAAACAACACGA
Found at i:21627 original size:56 final size:55
Alignment explanation
Indices: 21528--21636 Score: 130
Period size: 56 Copynumber: 1.9 Consensus size: 55
21518 AAAATTCAAA
** * * *
21528 CAACAAAAATGGCAACCAAAACAAGAGCAAAAATAACAGCAAAACAACAAAAACAG
1 CAACAAAAATAACAACAAAAACAACAGAAAAAATAACA-CAAAACAACAAAAACAG
*
21584 CAACAAAAATAACAACAAAAACAACACGAAAACAATAAC-CAAAACAATAAAAA
1 CAACAAAAATAACAACAAAAACAACA-GAAAA-AATAACACAAAACAACAAAAA
21637 AAAGTACTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 35 0.78
57 4 0.09
58 6 0.13
ACGTcount: A:0.68, C:0.21, G:0.06, T:0.05
Consensus pattern (55 bp):
CAACAAAAATAACAACAAAAACAACAGAAAAAATAACACAAAACAACAAAAACAG
Found at i:21670 original size:22 final size:21
Alignment explanation
Indices: 21620--21680 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
21610 CGAAAACAAT
21620 AACCAAAACAATAAAAAAAAG
1 AACCAAAACAATAAAAAAAAG
* * * *
21641 TACTAAAATAATAAAAAACAG
1 AACCAAAACAATAAAAAAAAG
*
21662 CAACCAAAACAGTAAAAAA
1 -AACCAAAACAATAAAAAA
21681 GCACAAAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.10
Consensus pattern (21 bp):
AACCAAAACAATAAAAAAAAG
Found at i:24075 original size:25 final size:24
Alignment explanation
Indices: 24043--24092 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
24033 TATCAAATTT
24043 TGTTTTTC-AACTTGAACACAAATA
1 TGTTTTTCTAACTTGAA-ACAAATA
* *
24067 TGTTATTTCTTACTTGAATCAAATA
1 TGTT-TTTCTAACTTGAAACAAATA
24092 T
1 T
24093 CAAATAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 7 0.32
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (24 bp):
TGTTTTTCTAACTTGAAACAAATA
Found at i:27626 original size:17 final size:17
Alignment explanation
Indices: 27604--27637 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27594 ATAAAATATT
27604 AAAAAGATAATAT-ATAA
1 AAAAAGA-AATATGATAA
27621 AAAAAGAAATATGATAA
1 AAAAAGAAATATGATAA
27638 TATATAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAAAGAAATATGATAA
Found at i:34336 original size:62 final size:62
Alignment explanation
Indices: 34239--34357 Score: 229
Period size: 62 Copynumber: 1.9 Consensus size: 62
34229 TTGAAGGACG
34239 ATAATAATTTGGTGGCCTTTAGATCAAGTGATGTAGCATTGCAATATATTCCAAGATGAACA
1 ATAATAATTTGGTGGCCTTTAGATCAAGTGATGTAGCATTGCAATATATTCCAAGATGAACA
*
34301 ATAATAATTTGGTGGCCTTTAGATCAAGTGATGTAGCGTTGCAATATATTCCAAGAT
1 ATAATAATTTGGTGGCCTTTAGATCAAGTGATGTAGCATTGCAATATATTCCAAGAT
34358 AAATCACGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (62 bp):
ATAATAATTTGGTGGCCTTTAGATCAAGTGATGTAGCATTGCAATATATTCCAAGATGAACA
Found at i:38336 original size:21 final size:21
Alignment explanation
Indices: 38312--38354 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38302 AGTTACGAAC
* *
38312 AAGAACAAGAATAAGAACAAA
1 AAGAACAAAAAAAAGAACAAA
*
38333 AAGAATAAAAAAAAGAACAAA
1 AAGAACAAAAAAAAGAACAAA
38354 A
1 A
38355 TGAAGAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.77, C:0.07, G:0.12, T:0.05
Consensus pattern (21 bp):
AAGAACAAAAAAAAGAACAAA
Found at i:42245 original size:26 final size:26
Alignment explanation
Indices: 42216--42265 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42206 AAAACCAAAA
*
42216 AATTTATAAAAAATT-TCAAAATTTAT
1 AATTT-TAAAAAATTATAAAAATTTAT
*
42242 AATTTTAGAAAATTATAAAAATTT
1 AATTTTAAAAAATTATAAAAATTT
42266 TAAATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
AATTTTAAAAAATTATAAAAATTTAT
Found at i:42349 original size:16 final size:17
Alignment explanation
Indices: 42319--42351 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42309 TTTGAAAAAA
42319 GTTTTCAAATCTATATG
1 GTTTTCAAATCTATATG
*
42336 GTTTT-AAATTTATATG
1 GTTTTCAAATCTATATG
42352 TTCGAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (17 bp):
GTTTTCAAATCTATATG
Found at i:58391 original size:27 final size:25
Alignment explanation
Indices: 58353--58415 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
58343 AAGATTTATA
*
58353 TTTATATTTTTTTAATTAAAAAATTG
1 TTTAT-TTTTTTTTATTAAAAAATTG
*
58379 TTTATTTTCTTTTTATTAAAAATTTG
1 TTTATTTT-TTTTTATTAAAAAATTG
*
58405 TTTAATTTTTT
1 TTTATTTTTTT
58416 AGGGATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (25 bp):
TTTATTTTTTTTTATTAAAAAATTG
Found at i:60172 original size:29 final size:28
Alignment explanation
Indices: 60118--60172 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
60108 TTTAGTGTTT
** **
60118 TTTATTTTATTTTTGTTAATTGTTTTAA
1 TTTATTTTATTTTTCATAATAATTTTAA
60146 TTTATTTTAATTTTTCATAATAATTTT
1 TTTATTTT-ATTTTTCATAATAATTTT
60173 TCTTTGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (28 bp):
TTTATTTTATTTTTCATAATAATTTTAA
Found at i:64752 original size:30 final size:29
Alignment explanation
Indices: 64718--64792 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
64708 AAAATTGGGC
64718 CTAAATCTTGAAATTTGAAAAGTAAAAGGA
1 CTAAATCTTGAAATTTG-AAAGTAAAAGGA
* *
64748 CTAAATTACTAGAAA--TGAAAGTACAAGGA
1 CTAAA-T-CTTGAAATTTGAAAGTAAAAGGA
*
64777 CTAAAT-TTCAAATTTG
1 CTAAATCTTGAAATTTG
64793 TGAAGTACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
26 4 0.11
28 3 0.08
29 16 0.43
30 7 0.19
31 1 0.03
32 6 0.16
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (29 bp):
CTAAATCTTGAAATTTGAAAGTAAAAGGA
Found at i:65303 original size:6 final size:6
Alignment explanation
Indices: 65292--65319 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
65282 ATTTGGCTGA
65292 CCATAG CCATAG CCATAG CCATAG CCAT
1 CCATAG CCATAG CCATAG CCATAG CCAT
65320 GAATAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (6 bp):
CCATAG
Found at i:67465 original size:20 final size:21
Alignment explanation
Indices: 67436--67479 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
67426 TAGAAATGCT
67436 TTTTAATAATAT-TTAAA-CA
1 TTTTAATAATATCTTAAACCA
*
67455 TTTTAATTAATGTCTTAAACCA
1 TTTTAA-TAATATCTTAAACCA
67477 TTT
1 TTT
67480 CATTAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 5 0.24
22 5 0.24
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTAATAATATCTTAAACCA
Found at i:67584 original size:18 final size:19
Alignment explanation
Indices: 67542--67577 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
67532 TTTCATGTAT
67542 ATATTTGAATCATAAATAA
1 ATATTTGAATCATAAATAA
67561 ATATTTGAATCA-AAATA
1 ATATTTGAATCATAAATA
67578 GGTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (19 bp):
ATATTTGAATCATAAATAA
Found at i:68231 original size:17 final size:18
Alignment explanation
Indices: 68211--68248 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
68201 TTTTGTTTCG
*
68211 ATTTAGTTTTTGTT-ATT
1 ATTTAATTTTTGTTAATT
*
68228 ATTTAATTTTTTTTAATT
1 ATTTAATTTTTGTTAATT
68246 ATT
1 ATT
68249 GGATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
ATTTAATTTTTGTTAATT
Found at i:68257 original size:20 final size:19
Alignment explanation
Indices: 68234--68279 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
68224 TATTATTTAA
*
68234 TTTTTTTTAATTATTGGAT
1 TTTTTTTTTATTATTGGAT
* *
68253 TTTTTTATTTCTTATTGTAT
1 TTTTTT-TTTATTATTGGAT
68273 TTTTTTT
1 TTTTTTT
68280 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTATTATTGGAT
Found at i:70701 original size:38 final size:39
Alignment explanation
Indices: 70659--70733 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
70649 GACTAAATCA
* * *
70659 TAAAAACT-ACAAAAATGGAATTTCAGGGACTGTTTTTT
1 TAAAAACTGACAAAAATGAAAGTGCAGGGACTGTTTTTT
* *
70697 TAAAAACTGTCAAAATTGAAAGTGCAGGGACTGTTTT
1 TAAAAACTGACAAAAATGAAAGTGCAGGGACTGTTTT
70734 GTAATTCCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 8 0.26
39 23 0.74
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (39 bp):
TAAAAACTGACAAAAATGAAAGTGCAGGGACTGTTTTTT
Found at i:77513 original size:20 final size:20
Alignment explanation
Indices: 77478--77515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
77468 CAGGGAAAGT
* *
77478 TTTTCAATTGAGCATTCATC
1 TTTTCAATTCAACATTCATC
77498 TTTTCAATTCAACATTCA
1 TTTTCAATTCAACATTCA
77516 CATGTGTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTCAATTCAACATTCATC
Found at i:87030 original size:13 final size:13
Alignment explanation
Indices: 87012--87036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87002 TTCTCCTATT
87012 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
87025 AAAAGAAAAAAA
1 AAAAGAAAAAAA
87037 CAACGAAAAG
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:93516 original size:17 final size:17
Alignment explanation
Indices: 93489--93523 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
93479 CATTAAAGAC
93489 TATCTGACTCTTTGGTTT
1 TATCTGACTCTTT-GTTT
93507 TATC-GACTCTTTGTTT
1 TATCTGACTCTTTGTTT
93523 T
1 T
93524 CCCAGGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.57
Consensus pattern (17 bp):
TATCTGACTCTTTGTTT
Found at i:98600 original size:3 final size:3
Alignment explanation
Indices: 98592--98629 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
98582 TCCTAAACAA
*
98592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
98630 AATCCTAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:99135 original size:12 final size:12
Alignment explanation
Indices: 99118--99169 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
99108 CTGATAAACG
99118 AAAATAGAAATA
1 AAAATAGAAATA
*
99130 AAAATAGAGATA
1 AAAATAGAAATA
99142 AATGAATAGAAATA
1 AA--AATAGAAATA
*
99156 AAAATAGAGATA
1 AAAATAGAAATA
99168 AA
1 AA
99170 TGAATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 24 0.69
14 11 0.31
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.17
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:99151 original size:26 final size:26
Alignment explanation
Indices: 99120--99175 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
99110 GATAAACGAA
99120 AATAGAAATAAAAATAGAGATAAATG
1 AATAGAAATAAAAATAGAGATAAATG
99146 AATAGAAATAAAAATAGAGATAAATG
1 AATAGAAATAAAAATAGAGATAAATG
99172 AATA
1 AATA
99176 AATAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (26 bp):
AATAGAAATAAAAATAGAGATAAATG
Found at i:112171 original size:13 final size:13
Alignment explanation
Indices: 112153--112177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112143 AAACAAATTC
112153 ATACATTTATATA
1 ATACATTTATATA
112166 ATACATTTATAT
1 ATACATTTATAT
112178 TTGAAGTGTT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
ATACATTTATATA
Found at i:112437 original size:31 final size:31
Alignment explanation
Indices: 112399--112467 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
112389 TTTTTTTACT
112399 TAATTTGGTACATGAACTT-GACATTTTCTCC
1 TAATTTGGTACATGAACTTAG-CATTTTCTCC
* *
112430 TAATTTGGTACTTGAACTTAGCATTTTTTCC
1 TAATTTGGTACATGAACTTAGCATTTTCTCC
112461 TAATTTG
1 TAATTTG
112468 CTACCTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (31 bp):
TAATTTGGTACATGAACTTAGCATTTTCTCC
Found at i:114441 original size:34 final size:31
Alignment explanation
Indices: 114396--114457 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 31
114386 ATTGATCCAT
114396 TTTTATAGAAAAAAGAGAACATACATCTATATATA
1 TTTTATAG--AAAA-AGAA-ATACATCTATATATA
114431 TTTTAT-GAAAAAGAAATACATCTATAT
1 TTTTATAGAAAAAGAAATACATCTATAT
114458 TTGACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 12 0.44
31 4 0.15
32 4 0.15
34 1 0.04
35 6 0.22
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (31 bp):
TTTTATAGAAAAAGAAATACATCTATATATA
Found at i:124700 original size:13 final size:13
Alignment explanation
Indices: 124682--124709 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
124672 ATAGTGTATG
124682 AGTTTAGGGTTTA
1 AGTTTAGGGTTTA
124695 AGTTTAGGGTTTA
1 AGTTTAGGGTTTA
124708 AG
1 AG
124710 GGTCTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (13 bp):
AGTTTAGGGTTTA
Found at i:126059 original size:6 final size:6
Alignment explanation
Indices: 126048--126076 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
126038 TATATCCCAA
126048 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
126077 ATGATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:130651 original size:22 final size:20
Alignment explanation
Indices: 130625--130664 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
130615 ATTTTTTAAA
130625 ATTTTAAAAAAGTTATAAAAAT
1 ATTTTAAAAAA-TTA-AAAAAT
130647 ATTTTAAAAAATTAAAAA
1 ATTTTAAAAAATTAAAAA
130665 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
ATTTTAAAAAATTAAAAAAT
Found at i:131400 original size:5 final size:5
Alignment explanation
Indices: 131390--131436 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
131380 CTATGGGGTT
*
131390 GATAG GATAG GTTAG GATAG GATAG GATAG GATAG GATAG GATAG GA
1 GATAG GATAG GATAG GATAG GATAG GATAG GATAG GATAG GATAG GA
131437 AAGTTTTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.21
Consensus pattern (5 bp):
GATAG
Found at i:141547 original size:29 final size:27
Alignment explanation
Indices: 141509--141777 Score: 227
Period size: 29 Copynumber: 9.4 Consensus size: 27
141499 TCGGTGATAC
*
141509 AATGGTAATTTTTAAAAGTTTCAGGGTCAA
1 AATGG-AATTTTTAGAAGTTT-AGGGT-AA
* **
141539 AATGGAATTTTTGGAAGTTTAGGGGGA
1 AATGGAATTTTTAGAAGTTTAGGGTAA
* *
141566 AATGTAATTTTTAGAAGTTTTGGGGTTAA
1 AATGGAATTTTTAGAAG-TTTAGGG-TAA
141595 AATGGAATTTTTAGAAGTTTAAGGGTAA
1 AATGGAATTTTTAGAAGTTT-AGGGTAA
* *
141623 AATGTAATTTTT-GAAAGTTTCGAGGTTAA
1 AATGGAATTTTTAG-AAGTTT--AGGGTAA
*
141652 AATGGAATTTTTAGAAGTTTGGGGGTAA
1 AATGGAATTTTTAGAAGTTT-AGGGTAA
* *
141680 AATGTATATTTTGA-AAGTTTTAGGGTTAA
1 AATGGA-ATTTTTAGAAG-TTTAGGG-TAA
*
141709 AATGGAATTTTTGGAAGTTTAGGGGTAA
1 AATGGAATTTTTAGAAGTTTA-GGGTAA
* * * *
141737 AATGTAATTTTTGGACAATTTAAGTGTAA
1 AATGGAATTTTTAGA-AGTTT-AGGGTAA
*
141766 AATGTAATTTTT
1 AATGGAATTTTT
141778 GGACAATTTA
Statistics
Matches: 200, Mismatches: 26, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
27 17 0.09
28 76 0.38
29 100 0.50
30 7 0.04
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.40
Consensus pattern (27 bp):
AATGGAATTTTTAGAAGTTTAGGGTAA
Found at i:141767 original size:57 final size:57
Alignment explanation
Indices: 141479--141790 Score: 334
Period size: 57 Copynumber: 5.5 Consensus size: 57
141469 ATCGAGATCA
* * * * * *
141479 AAAATGGAATTTTTGGACA--TTCGGTGATACAATGGTAATTTTTAAAAGTTTCAGGGTC
1 AAAATGGAATTTTTGGA-AGTTTAGG-GGTAAAAT-GTAATTTTTGAAAGTTTTAGGGTT
* *
141537 AAAATGGAATTTTTGGAAGTTTAGGGG-GAAATGTAATTTTT-AGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGA-AAGTTTTAGGGTT
* * *
141593 AAAATGGAATTTTTAGAAGTTTAAGGGTAAAATGTAATTTTTGAAAG-TTTCGAGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGAAAGTTTTAG-GGTT
* *
141650 AAAATGGAATTTTTAGAAGTTTGGGGGTAAAATGT-ATATTTTGAAAGTTTTAGGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAAT-TTTTGAAAGTTTTAGGGTT
* *
141707 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGGACAA-TTTAAGTG-T
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTT-GA-AAGTTTTAGGGTT
* *
141764 AAAATGTAATTTTTGGACAATTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
141791 ACCTCAATGG
Statistics
Matches: 222, Mismatches: 20, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
55 1 0.00
56 50 0.23
57 124 0.56
58 41 0.18
59 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGAAAGTTTTAGGGTT
Found at i:142882 original size:20 final size:20
Alignment explanation
Indices: 142849--142887 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
142839 TCTTTTTTTA
142849 TTTTAATTAATTATTATTAG
1 TTTTAATTAATTATTATTAG
* *
142869 TTTTATTTATTTATTATTA
1 TTTTAATTAATTATTATTA
142888 ATTAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATTAATTATTATTAG
Found at i:143626 original size:17 final size:17
Alignment explanation
Indices: 143606--143689 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
143596 AATATTAAGT
143606 TTTAAATCAATTTAAAA
1 TTTAAATCAATTTAAAA
* *
143623 TTTAATTAAATTT-AAA
1 TTTAAATCAATTTAAAA
*
143639 TTTAAAGCAAATTT-AAA
1 TTTAAATC-AATTTAAAA
* **
143656 TTTAAATTTAA-GAATAAA
1 TTTAAA-TCAATTTA-AAA
143674 TTTAAATCAATTTAAA
1 TTTAAATCAATTTAAA
143690 CCCAATCTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
16 8 0.16
17 32 0.64
18 10 0.20
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATCAATTTAAAA
Found at i:143639 original size:6 final size:6
Alignment explanation
Indices: 143614--143680 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
143604 GTTTTAAATC
**
143614 AATTTAA AATTT- AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
143660 AATTTA AGA-ATA AATTTA AAT
1 AATTTA A-ATTTA AATTTA AAT
143681 CAATTTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.04
5 8 0.16
6 33 0.67
7 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:143640 original size:23 final size:24
Alignment explanation
Indices: 143628--143680 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
143618 TAAAATTTAA
143628 TTAAATTTAAATTT-AAAGCAAAT
1 TTAAATTTAAATTTAAAAGCAAAT
*
143651 TTAAATTTAAATTTAAGAA-TAAAT
1 TTAAATTTAAATTTAA-AAGCAAAT
143675 TTAAAT
1 TTAAAT
143681 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 14 0.52
24 11 0.41
25 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAAATTTAAATTTAAAAGCAAAT
Found at i:144591 original size:38 final size:38
Alignment explanation
Indices: 144547--144624 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
144537 TTTGGAACTC
*
144547 TATATCAATTTGTTTATTTGAAATAAGTATATTCATAA
1 TATATCAATTTGTTCATTTGAAATAAGTATATTCATAA
144585 TATATCAATTTGTTCATTTGAAATAAGTATATTCATAA
1 TATATCAATTTGTTCATTTGAAATAAGTATATTCATAA
144623 TA
1 TA
144625 ATTATTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (38 bp):
TATATCAATTTGTTCATTTGAAATAAGTATATTCATAA
Found at i:144619 original size:19 final size:19
Alignment explanation
Indices: 144562--144620 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
144552 CAATTTGTTT
144562 ATTTGAAATAAGTATATTC
1 ATTTGAAATAAGTATATTC
* * * *
144581 ATAAT-ATATCAA-TTTGTTC
1 AT-TTGAAAT-AAGTATATTC
144600 ATTTGAAATAAGTATATTC
1 ATTTGAAATAAGTATATTC
144619 AT
1 AT
144621 AATAATTATT
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTTGAAATAAGTATATTC
Done.