Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014819.1 Kokia drynarioides strain JFW-HI SEQ_129861, 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: 131914
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 194 characters in sequence are not A, C, G, or T
Found at i:55 original size:13 final size:14
Alignment explanation
Indices: 39--80 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
29 TTTTAATTTT
39 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
52 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
67 ATTTTAAATAATAT
1 ATTTT-AATAATAT
81 TCTTGACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:65 original size:16 final size:16
Alignment explanation
Indices: 43--79 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
33 AATTTTATTT
43 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
60 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
75 TAATA
1 TAATA
80 TTCTTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:641 original size:15 final size:15
Alignment explanation
Indices: 621--651 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
611 GGAATAAAAA
621 ATGAAGAAGAAGAAG
1 ATGAAGAAGAAGAAG
*
636 ATGAAGATGAAGAAG
1 ATGAAGAAGAAGAAG
651 A
1 A
652 GAGGTGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.10
Consensus pattern (15 bp):
ATGAAGAAGAAGAAG
Found at i:1045 original size:29 final size:30
Alignment explanation
Indices: 1013--1071 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1003 TATGGTTTAA
*
1013 TGTGCAATTGTATACATAAACTTTT-ATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
*
1042 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
1072 GATTCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATAAAATTTTGATTT
Found at i:13942 original size:14 final size:14
Alignment explanation
Indices: 13923--14012 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
13913 TTTTATTACT
13923 TTTAAAATGGTGTA
1 TTTAAAATGGTGTA
**
13937 TTTAAAAAAGTG-A
1 TTTAAAATGGTGTA
*
13950 TTATATAA--GTGTA
1 TT-TAAAATGGTGTA
13963 TTTAAAATGGTGTA
1 TTTAAAATGGTGTA
*
13977 TTT---AT--TACT-
1 TTTAAAATGGT-GTA
13986 TTTAAAATGGTGTA
1 TTTAAAATGGTGTA
14000 TTTAAAATGGTGT
1 TTTAAAATGGTGT
14013 GGAATAGTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
9 4 0.07
10 1 0.02
11 2 0.03
12 9 0.15
13 7 0.12
14 36 0.61
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.44
Consensus pattern (14 bp):
TTTAAAATGGTGTA
Found at i:17709 original size:52 final size:52
Alignment explanation
Indices: 17631--17735 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
17621 ATTGACAACG
* * *
17631 CACACACAGACGCTCGAACGCGGGATCTCTAAAACAAACAACATCTTCTTTT
1 CACACACAGACGCTCGAACACGGGATCCCTAAAACAAACAACATCCTCTTTT
* ** *
17683 CACACACAGACGTTCGAACACGGGATCCCTAAAATGAACAATATCCTCTTTT
1 CACACACAGACGCTCGAACACGGGATCCCTAAAACAAACAACATCCTCTTTT
17735 C
1 C
17736 CATTGATAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.22
Consensus pattern (52 bp):
CACACACAGACGCTCGAACACGGGATCCCTAAAACAAACAACATCCTCTTTT
Found at i:20532 original size:7 final size:7
Alignment explanation
Indices: 20522--20595 Score: 112
Period size: 7 Copynumber: 10.6 Consensus size: 7
20512 TGTGGAGTCT
*
20522 GGAGGTG
1 GGAGATG
*
20529 GGAGGTG
1 GGAGATG
*
20536 GGAGGTG
1 GGAGATG
20543 GGAGATG
1 GGAGATG
20550 GGAGATG
1 GGAGATG
20557 GGAGATG
1 GGAGATG
20564 GGAGATG
1 GGAGATG
20571 GGAGATG
1 GGAGATG
20578 GGAGATG
1 GGAGATG
*
20585 GGAGAGG
1 GGAGATG
20592 GGAG
1 GGAG
20596 TGGTGGTGGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 65 1.00
ACGTcount: A:0.24, C:0.00, G:0.64, T:0.12
Consensus pattern (7 bp):
GGAGATG
Found at i:22986 original size:30 final size:28
Alignment explanation
Indices: 22944--23327 Score: 134
Period size: 30 Copynumber: 12.9 Consensus size: 28
22934 CCCGGGGGGC
22944 AAAATGGTAATTTTGGAGAAGTTCGAGGTCA
1 AAAATGG-AATTTTGGA-AAGTTCGAGGT-A
* *
22975 AAAATGGAATTTT-TAGAAGTTCAGGGGT-
1 AAAATGGAATTTTGGA-AAGTTC-GAGGTA
** *
23003 AAAATGGTAATTTTTGGAAAAATCGGGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTCGAGGT-A
* ** *
23034 ATAAT-GAATTTTTTGGAAAAAT-AAGGGT-
1 AAAATGGAA--TTTTGGAAAGTTCGA-GGTA
*** *
23062 AAAATGGTAATTTTGGAAAAAAACAAGGTTA
1 AAAATGG-AATTTTGG-AAAGTTCGAGG-TA
* **
23093 AAAATGGAATTTTGGGAAGTTTAAGGGT-
1 AAAATGGAATTTTGGAAAGTTCGA-GGTA
** *
23121 AAAATGGTAATTTTTAAAAGATCGAGGTTA
1 AAAATGG-AATTTTGGAAAGTTCGAGG-TA
* * * *
23151 AAAATGAAATTTT-TAGAGGTTCAGGGGTA
1 AAAATGGAATTTTGGA-AAGTTC-GAGGTA
**
23180 AAAATGGTAATATTTGGAAAGTTTAAGGTTA
1 AAAATGG-AAT-TTTGGAAAGTTCGAGG-TA
* *
23211 AAAATGGAATTTTTGGAAAGTTTGAGGGTTT
1 AAAATGGAA-TTTTGGAAAGTTCGA-GG-TA
* **
23242 AAAATGGGATTTTGGAAAGTTTAAGGGTA
1 AAAATGGAATTTTGGAAAGTTCGA-GGTA
* * *
23271 AAAATGTAATTTTTGAAATGTTCGAGGGTT
1 AAAATGGAATTTTGGAAA-GTTCGA-GGTA
** *
23301 AAAATATAATTTTGGAGAAGTTTGAGG
1 AAAATGGAATTTTGGA-AAGTTCGAGG
23328 GTTAAAATAT
Statistics
Matches: 279, Mismatches: 46, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
28 27 0.10
29 78 0.28
30 123 0.44
31 50 0.18
32 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGAGGTA
Found at i:23007 original size:59 final size:59
Alignment explanation
Indices: 22939--23334 Score: 304
Period size: 59 Copynumber: 6.6 Consensus size: 59
22929 GGTCACCCGG
* * *
22939 GGGGCAAAATGGTAATTTTGGAGAAGTTCGAGGTCAAAAATGGAATTTTTAG-AAGTTCA
1 GGGGTAAAATGGTAATTTTGGA-AAGTTCGAGGTTAAAAATGGAATTTTTGGAAAGTTCA
** * * * **
22998 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAATAAT-GAATTTTTTGGAAAAAT-A
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTCGAGGTTAAAAATGGAA-TTTTTGGAAAGTTCA
* *** * * *
23057 AGGGTAAAATGGTAATTTTGGAAAAAAACAAGGTTAAAAATGGAA-TTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTGG-AAAGTTCGAGGTTAAAAATGGAATTTTTGGAAAGTTCA
* ** * * * *
23116 AGGGTAAAATGGTAATTTTTAAAAGATCGAGGTTAAAAATGAAATTTTTAG-AGGTTCA
1 GGGGTAAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGAAAGTTCA
** *
23174 GGGGTAAAAATGGTAATATTTGGAAAGTTTAAGGTTAAAAATGGAATTTTTGGAAAGTTTGA
1 GGGGT-AAAATGGTAAT-TTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGAAAG-TTCA
* * ** * *
23236 GGGTTTAAAATGG-GATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTT-GAAATGTTCGA
1 GGG-GTAAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGAAA-GTTC-A
* * *
23296 GGGTTAAAAT-ATAATTTTGGAGAAGTTTGAGGGTTAAAA
1 GGGGTAAAATGGTAATTTTGGA-AAGTTCGA-GGTTAAAA
23335 TATAATTTTT
Statistics
Matches: 275, Mismatches: 45, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
58 46 0.17
59 120 0.44
60 84 0.31
61 11 0.04
62 13 0.05
63 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGAAAGTTCA
Found at i:23285 original size:60 final size:59
Alignment explanation
Indices: 23149--23344 Score: 191
Period size: 60 Copynumber: 3.3 Consensus size: 59
23139 AGATCGAGGT
* * * * * *
23149 TAAAAATGAAATTTTT-AGAGGTTC-AGGGGTAAAAATGGTAATATTTGGAAAGTTTAAGGT
1 TAAAAATGTAATTTTTGAAATGTTCGA-GGGTTAAAATAG-AAT-TTTGGAAAGTTTAAGGG
* * * *
23209 TAAAAATGGAATTTTTGGAAA-GTTTGAGGGTTTAAAATGGGATTTTGGAAAGTTTAAGGG
1 TAAAAATGTAATTTTT-GAAATGTTCGAGGG-TTAAAATAGAATTTTGGAAAGTTTAAGGG
* *
23269 TAAAAATGTAATTTTTGAAATGTTCGAGGGTTAAAATATAATTTTGGAGAAGTTTGAGGG
1 TAAAAATGTAATTTTTGAAATGTTCGAGGGTTAAAATAGAATTTTGGA-AAGTTTAAGGG
* *
23329 TTAAAATATAATTTTT
1 TAAAAATGTAATTTTT
23345 TTATAATTTA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
59 19 0.16
60 78 0.67
61 8 0.07
62 11 0.09
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (59 bp):
TAAAAATGTAATTTTTGAAATGTTCGAGGGTTAAAATAGAATTTTGGAAAGTTTAAGGG
Found at i:23328 original size:30 final size:29
Alignment explanation
Indices: 23187--23343 Score: 156
Period size: 30 Copynumber: 5.2 Consensus size: 29
23177 GTAAAAATGG
*
23187 TAATATTTGGAAAGTTT-AAGGTTAAAA-A
1 TAAT-TTTGGAAAGTTTGAGGGTTAAAATA
*
23215 TGGAATTTTTGGAAAGTTTGAGGGTTTAAAATG
1 T--AA-TTTTGGAAAGTTTGAGGG-TTAAAATA
** * * *
23248 GGATTTTGGAAAGTTTAAGGGTAAAAATG
1 TAATTTTGGAAAGTTTGAGGGTTAAAATA
* *
23277 TAATTTTTGAAATGTTCGAGGGTTAAAATA
1 TAATTTTGGAAA-GTTTGAGGGTTAAAATA
23307 TAATTTTGGAGAAGTTTGAGGGTTAAAATA
1 TAATTTTGGA-AAGTTTGAGGGTTAAAATA
23337 TAATTTT
1 TAATTTT
23344 TTTATAATTT
Statistics
Matches: 106, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
28 1 0.01
29 16 0.15
30 76 0.72
31 7 0.07
32 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (29 bp):
TAATTTTGGAAAGTTTGAGGGTTAAAATA
Found at i:29289 original size:3 final size:3
Alignment explanation
Indices: 29275--29316 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
29265 TTCTTTTCGG
* *
29275 TTA TTA TCA TTA TTA CTA -TA TTCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
29317 ACATTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:33258 original size:44 final size:44
Alignment explanation
Indices: 33186--33306 Score: 179
Period size: 47 Copynumber: 2.7 Consensus size: 44
33176 GTTTTTTTTT
* *
33186 TTTTTTTTTTAATTTTGAAGCAAATAAGATTATATATTTCAATTA
1 TTTTATTTTT-ATTTTGAAGCAAGTAAGATTATATATTTCAATTA
*
33231 TTTTATTTTTATTTTGAAGCAAGTAAGATAATTATATATTTTAATTA
1 TTTTATTTTTATTTTGAAGCAAGTAAG---ATTATATATTTCAATTA
33278 TTTTATTTTTATTTTGAAGCAAGTAAGAT
1 TTTTATTTTTATTTTGAAGCAAGTAAGAT
33307 CAATTTTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
44 18 0.26
45 9 0.13
47 43 0.61
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (44 bp):
TTTTATTTTTATTTTGAAGCAAGTAAGATTATATATTTCAATTA
Found at i:37374 original size:6 final size:6
Alignment explanation
Indices: 37363--37387 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
37353 TCGGCTTCTC
37363 TTTCCA TTTCCA TTTCCA TTTCCA T
1 TTTCCA TTTCCA TTTCCA TTTCCA T
37388 CTTACCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCCA
Found at i:63009 original size:21 final size:21
Alignment explanation
Indices: 62985--63026 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62975 ATCGTGAAAG
*
62985 AAGGATTGGAGACGGCAGAGA
1 AAGGACTGGAGACGGCAGAGA
* *
63006 AAGGGCTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCAGAGA
63027 GAGGGATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.48, T:0.07
Consensus pattern (21 bp):
AAGGACTGGAGACGGCAGAGA
Found at i:63031 original size:21 final size:21
Alignment explanation
Indices: 62991--63031 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62981 AAAGAAGGAT
62991 TGGAGACGGCAGAGAAAGGGC
1 TGGAGACGGCAGAGAAAGGGC
* *
63012 TGGAGACGGCGGAGAGAGGG
1 TGGAGACGGCAGAGAAAGGG
63032 ATCTTTACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.54, T:0.05
Consensus pattern (21 bp):
TGGAGACGGCAGAGAAAGGGC
Found at i:64111 original size:14 final size:14
Alignment explanation
Indices: 64092--64122 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64082 TTGAAAGTGG
64092 TTTTTGAAAAATAA
1 TTTTTGAAAAATAA
*
64106 TTTTTGGAAAATAA
1 TTTTTGAAAAATAA
64120 TTT
1 TTT
64123 ATTTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAAATAA
Found at i:64530 original size:19 final size:20
Alignment explanation
Indices: 64494--64545 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
64484 TATTATTAAT
* **
64494 ATATTTATAATTGTAATA-A
1 ATATTTATTATTAAAATATA
64513 ATATTTATTATTAAAATATTA
1 ATATTTATTATTAAAATA-TA
*
64534 ATATTTAATATT
1 ATATTTATTATT
64546 TTCAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTTATTATTAAAATATA
Found at i:88827 original size:14 final size:14
Alignment explanation
Indices: 88810--88843 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88800 TACAATATTT
*
88810 AAATAATAATAATA
1 AAATAATAACAATA
88824 AAATAATAACAATA
1 AAATAATAACAATA
*
88838 TAATAA
1 AAATAA
88844 CAAAATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:88828 original size:11 final size:11
Alignment explanation
Indices: 88814--88849 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
88804 ATATTTAAAT
*
88814 AATAATAATAA
1 AATAATAACAA
88825 AATAATAACAA
1 AATAATAACAA
*
88836 TATAATAACAA
1 AATAATAACAA
88847 AAT
1 AAT
88850 GACATCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAATAACAA
Found at i:88862 original size:22 final size:22
Alignment explanation
Indices: 88814--88862 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
88804 ATATTTAAAT
* *
88814 AATAATAATAAAATAATAACAA
1 AATAATAACAAAATAACAACAA
* * *
88836 TATAATAACAAAATGACATCAA
1 AATAATAACAAAATAACAACAA
88858 AATAA
1 AATAA
88863 CAGTAAACAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.22
Consensus pattern (22 bp):
AATAATAACAAAATAACAACAA
Found at i:89881 original size:21 final size:18
Alignment explanation
Indices: 89836--89881 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
89826 AATCAAACGG
89836 ACAAAAATAAACCAGAAA
1 ACAAAAATAAACCAGAAA
*
89854 ATCAAAATATAACAGCAGAAA
1 A-CAAAA-ATAA-ACCAGAAA
89875 ACAAAAA
1 ACAAAAA
89882 ACAGGAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 6 0.25
20 9 0.38
21 8 0.33
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.09
Consensus pattern (18 bp):
ACAAAAATAAACCAGAAA
Found at i:91617 original size:16 final size:17
Alignment explanation
Indices: 91598--91633 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
91588 CAATAAACTT
91598 AAATG-TTATTATAAAA
1 AAATGATTATTATAAAA
*
91614 AAATGATTGTTATAAAA
1 AAATGATTATTATAAAA
91631 AAA
1 AAA
91634 AACTACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (17 bp):
AAATGATTATTATAAAA
Found at i:92860 original size:15 final size:14
Alignment explanation
Indices: 92839--92881 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
92829 ATTAACGTTT
92839 AAAAATATTTAAAC
1 AAAAATATTTAAAC
92853 ATAAAATATTTAGAAC
1 A-AAAATATTTA-AAC
92869 AAATAA-ATTTAAA
1 AAA-AATATTTAAA
92882 TCTAAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 17 0.65
16 6 0.23
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAAATATTTAAAC
Found at i:97930 original size:30 final size:31
Alignment explanation
Indices: 97894--97953 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
97884 AAAAATATAT
*
97894 TTTAAGAT-TCGTTTGATAAATGATT-GAAAA
1 TTTAAGATGT-GTTTGATAAATCATTAGAAAA
97924 TTTAAGATGTGTTTGATAAATCATTAGAAA
1 TTTAAGATGTGTTTGATAAATCATTAGAAA
97954 TTTTTGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (31 bp):
TTTAAGATGTGTTTGATAAATCATTAGAAAA
Found at i:104448 original size:2 final size:2
Alignment explanation
Indices: 104443--104467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104433 ATATATATAA
104443 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
104468 ATGTATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:105678 original size:2 final size:2
Alignment explanation
Indices: 105671--105701 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
105661 CTTTGTTAGA
105671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105702 AATTAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114872 original size:28 final size:29
Alignment explanation
Indices: 114840--114902 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
114830 ATTGTATTTT
* *
114840 ATTTTTATAT-TTAAAAATAA-ATTAATTG
1 ATTTTTATATGTTAAAAA-AATATAAATTA
114868 ATTTTTATATGTTAAAAAAATATAAATTA
1 ATTTTTATATGTTAAAAAAATATAAATTA
114897 ATTTTT
1 ATTTTT
114903 TTTTAGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTTTATATGTTAAAAAAATATAAATTA
Found at i:126576 original size:2 final size:2
Alignment explanation
Indices: 126569--126601 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
126559 AAGTTCTGAT
126569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
126602 TGACAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.