Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014860.1 Kokia drynarioides strain JFW-HI SEQ_129903, 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: 177976
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 260 characters in sequence are not A, C, G, or T
Found at i:11960 original size:31 final size:31
Alignment explanation
Indices: 11925--11988 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
11915 GTACCAAAAT
*
11925 AGTCACTGAATTATTCAAAAGTTTTCATTTA
1 AGTCACTGAACTATTCAAAAGTTTTCATTTA
* *
11956 AGTCATTGAACTATTCAAAAGTTTTTATTTA
1 AGTCACTGAACTATTCAAAAGTTTTCATTTA
11987 AG
1 AG
11989 ATATTAGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (31 bp):
AGTCACTGAACTATTCAAAAGTTTTCATTTA
Found at i:16792 original size:50 final size:50
Alignment explanation
Indices: 16697--16801 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
16687 CTGATATGAG
*
16697 AGGTGAATCTAGTCTTATCTAGGTTGTAGGCATTTCAGGGTATTGTTCTA
1 AGGTGAATCTAGTCTTATCTAGGTTGTAGGCATTTCAGGGCATTGTTCTA
* * * ** ** *
16747 AGGTGAATTTGGTCTTATCTCGGTTGTAGGTGTTTGGGGGCATTGTTCTT
1 AGGTGAATCTAGTCTTATCTAGGTTGTAGGCATTTCAGGGCATTGTTCTA
16797 AGGTG
1 AGGTG
16802 TTATGTTGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.41
Consensus pattern (50 bp):
AGGTGAATCTAGTCTTATCTAGGTTGTAGGCATTTCAGGGCATTGTTCTA
Found at i:19449 original size:22 final size:23
Alignment explanation
Indices: 19424--19473 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19414 ATCTTTAATT
19424 AAAT-AAATTTAATCCCATTTGA
1 AAATCAAATTTAATCCCATTTGA
* * *
19446 AAATCTATTTTAATCCCATTTTA
1 AAATCAAATTTAATCCCATTTGA
19469 AAATC
1 AAATC
19474 CAAGTTGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATCAAATTTAATCCCATTTGA
Found at i:21024 original size:17 final size:18
Alignment explanation
Indices: 21002--21035 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20992 AATACATTCA
21002 AAATTTATT-TTCTTTTC
1 AAATTTATTCTTCTTTTC
*
21019 AAATTTTTTCTTCTTTT
1 AAATTTATTCTTCTTTT
21036 ATCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (18 bp):
AAATTTATTCTTCTTTTC
Found at i:21156 original size:57 final size:57
Alignment explanation
Indices: 21090--21208 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 57
21080 AGATTTTGAC
21090 AATT-ATAAATGTTGAGTTTCATTCAAAGCATATAGTAGAACTATGTTTTTAAATTT
1 AATTAATAAATGTTGAGTTTCATTCAAAGCATATAGTAGAACTATGTTTTTAAATTT
* *
21146 AATTAATAAATGTTGAGTTTCATTCAAAGCATCTAGTAGAATTATGTTTTTAAATTT
1 AATTAATAAATGTTGAGTTTCATTCAAAGCATATAGTAGAACTATGTTTTTAAATTT
21203 AATTAA
1 AATTAA
21209 AGAGCAGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 4 0.07
57 56 0.93
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.43
Consensus pattern (57 bp):
AATTAATAAATGTTGAGTTTCATTCAAAGCATATAGTAGAACTATGTTTTTAAATTT
Found at i:23885 original size:32 final size:32
Alignment explanation
Indices: 23805--23937 Score: 164
Period size: 29 Copynumber: 4.1 Consensus size: 32
23795 TTTCTTTGCA
* *
23805 ATTTTTTAACGAATTTAATCTTTATGGATTGTT
1 ATTTTTTAATGAATTTAATC-TAATGGATTGTT
23838 ATTCTTTTTTAAATGAATTTAATCTAATGGATTGTT
1 A---TTTTTT-AATGAATTTAATCTAATGGATTGTT
*
23874 ATTTTTTAATGAATTTAATCAAATGGA---TT
1 ATTTTTTAATGAATTTAATCTAATGGATTGTT
*
23903 ATTATTTAATGAATTTAATCTAATGGATTGTT
1 ATTTTTTAATGAATTTAATCTAATGGATTGTT
23935 ATT
1 ATT
23938 CTTTCTTTCT
Statistics
Matches: 88, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
29 27 0.31
32 24 0.27
33 7 0.08
36 18 0.20
37 12 0.14
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (32 bp):
ATTTTTTAATGAATTTAATCTAATGGATTGTT
Found at i:43236 original size:6 final size:6
Alignment explanation
Indices: 43225--43251 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43215 ATGGAAAGGC
43225 CCCCCT CCCCCT CCCCCT CCCCCT CCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCC
43252 TTTTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:56317 original size:22 final size:21
Alignment explanation
Indices: 56292--56332 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
56282 ATTTTTTAAA
*
56292 TAATATTTATATTATTTTATTT
1 TAATATTTA-ATAATTTTATTT
56314 TAATATTTAATAATTTTAT
1 TAATATTTAATAATTTTAT
56333 ACCTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATATTTAATAATTTTATTT
Found at i:65662 original size:4 final size:4
Alignment explanation
Indices: 65653--65688 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
65643 AGAAATGGTA
65653 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
65689 ATGGCAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGAT
Found at i:66610 original size:17 final size:17
Alignment explanation
Indices: 66573--66612 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
66563 GGGAAATATT
*
66573 TATTTTAATATTTTTAG
1 TATTTTAATATTTATAG
66590 TATTTTAATATATTATA-
1 TATTTTAATAT-TTATAG
66607 TATTTT
1 TATTTT
66613 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTATAG
Found at i:68487 original size:27 final size:28
Alignment explanation
Indices: 68457--68510 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
68447 TTATTATCAA
* *
68457 AATTTTAAAATATA-TTAAAAAAATAAT
1 AATTATAAAATAAAGTTAAAAAAATAAT
* *
68484 AATTATAAATTAAAGTTAAAAATATAA
1 AATTATAAAATAAAGTTAAAAAAATAA
68511 CGAAAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
AATTATAAAATAAAGTTAAAAAAATAAT
Found at i:68696 original size:51 final size:51
Alignment explanation
Indices: 68615--68719 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
68605 TTCTTGAGGT
*
68615 TTTACATAGTTGCTCGGTTTGGCCTCCGGTGTCCCAATACCCAAAAAAATA
1 TTTACATAGTTGCTCGGTTCGGCCTCCGGTGTCCCAATACCCAAAAAAATA
* *
68666 TTTACATAGTTGCTCGGTTCGGCCTTCGGTGTCTCAATACCCAAAAAAATA
1 TTTACATAGTTGCTCGGTTCGGCCTCCGGTGTCCCAATACCCAAAAAAATA
68717 TTT
1 TTT
68720 TTAAATCTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (51 bp):
TTTACATAGTTGCTCGGTTCGGCCTCCGGTGTCCCAATACCCAAAAAAATA
Found at i:69016 original size:56 final size:56
Alignment explanation
Indices: 68887--69040 Score: 218
Period size: 56 Copynumber: 2.7 Consensus size: 56
68877 AAAAATTTGA
* * * * *
68887 GAAAGGTGGTGTAAGTCATTGGATGATAAACACTCAAAAAAAATATTTTTAAATCTGG
1 GAAATGTGGTGTAGGCCATTGGATGACAAACAC-C-CAAAAAATATTTTTAAATCTGG
* * *
68945 AAAATATGGTATAGGCCATTGGATGACAAACACCCAAAAAATATTTTTAAATCTGG
1 GAAATGTGGTGTAGGCCATTGGATGACAAACACCCAAAAAATATTTTTAAATCTGG
69001 GAAATGTGGTGTAGGCCATTGGATGACAAACACCCAAAAA
1 GAAATGTGGTGTAGGCCATTGGATGACAAACACCCAAAAA
69041 CTATGTTTGG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 58 0.68
57 1 0.01
58 26 0.31
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (56 bp):
GAAATGTGGTGTAGGCCATTGGATGACAAACACCCAAAAAATATTTTTAAATCTGG
Found at i:70974 original size:14 final size:14
Alignment explanation
Indices: 70955--70985 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
70945 ATGTCATCAA
70955 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
*
70969 TTTTCTTTNTTTTT
1 TTTTCTTTCTTTTT
70983 TTT
1 TTT
70986 CCAAAATTAA
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:0.00, C:0.10, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:87874 original size:17 final size:17
Alignment explanation
Indices: 87815--87874 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
87805 TCATGCTATT
87815 TTTTTAATATTTATGAAC
1 TTTTTAATATTTAT-AAC
*
87833 TTTTT-ATAATTT-TAAT
1 TTTTTAAT-ATTTATAAC
87849 TTTTCTAATAGTTTATAA-
1 TTTT-TAATA-TTTATAAC
87867 TTTTTAAT
1 TTTTTAAT
87875 TTTGTTAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
16 6 0.17
17 9 0.25
18 18 0.50
19 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTAATATTTATAAC
Found at i:94908 original size:59 final size:61
Alignment explanation
Indices: 94796--94921 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 61
94786 AAAATCCAAG
* *
94796 ATAGTTGGGTGAACAAAAAACAAAATTTACTAATAGTTAGGTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGAACAAAAAACAAAATTTACTAATAATTAAGTGATCATTTTGTAACTTTTC
*
94857 ATAGTTGGGTG-ACAAAAAA-TAAATTTACTAATAATTAAGTGA-C-TGTGTTGTAACTTTTC
1 ATAGTTGGGTGAACAAAAAACAAAATTTACTAATAATTAAGTGATCAT-T-TTGTAACTTTTC
94916 ATAGTT
1 ATAGTT
94922 TTATGACTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
57 1 0.02
58 2 0.03
59 38 0.63
60 8 0.13
61 11 0.18
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (61 bp):
ATAGTTGGGTGAACAAAAAACAAAATTTACTAATAATTAAGTGATCATTTTGTAACTTTTC
Found at i:95854 original size:56 final size:56
Alignment explanation
Indices: 95768--95880 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
95758 AGGTAGAAAA
95768 AACAAAGATGAATTTCAATTTCCTCCTGTTTGTGAAGTTAGGCCATATGTGTTGTT
1 AACAAAGATGAATTTCAATTTCCTCCTGTTTGTGAAGTTAGGCCATATGTGTTGTT
95824 AACAAAGATGAATTTCAATTTCCTCCTGTTTGTGAAGTTAGGCCATATGTGTTGTT
1 AACAAAGATGAATTTCAATTTCCTCCTGTTTGTGAAGTTAGGCCATATGTGTTGTT
95880 A
1 A
95881 TTGATGAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (56 bp):
AACAAAGATGAATTTCAATTTCCTCCTGTTTGTGAAGTTAGGCCATATGTGTTGTT
Found at i:96515 original size:46 final size:45
Alignment explanation
Indices: 96442--96528 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
96432 TCTATATATA
*
96442 TAAACATTAAAAAAGTTAAAATAATTATATATAAAATTTTATAGG
1 TAAACATTAAAAAAGCTAAAATAATTATATATAAAATTTTATAGG
*
96487 TAAACATTAAAACATGCTAAAATAATTATATATAAAATTTTA
1 TAAACATTAAAA-AAGCTAAAATAATTATATATAAAATTTTA
96529 ATAAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 12 0.31
46 27 0.69
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (45 bp):
TAAACATTAAAAAAGCTAAAATAATTATATATAAAATTTTATAGG
Found at i:96524 original size:15 final size:15
Alignment explanation
Indices: 96504--96577 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
96494 TAAAACATGC
96504 TAAAATAATTATATA
1 TAAAATAATTATATA
96519 TAAAAT--TT-TA-A
1 TAAAATAATTATATA
**
96530 T-AAATAAAAATATA
1 TAAAATAATTATATA
* *
96544 TAAAATTATTAAATA
1 TAAAATAATTATATA
*
96559 TTAAATTAATATATATA
1 -TAAAATAAT-TATATA
96576 TA
1 TA
96578 TATTCTATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 13
0.66 0.14 0.20
Matches are distributed among these distances:
10 4 0.09
11 2 0.05
12 2 0.05
13 4 0.09
14 2 0.05
15 15 0.35
16 9 0.21
17 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATAATTATATA
Found at i:96966 original size:31 final size:29
Alignment explanation
Indices: 96931--96996 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
96921 TAGTAAAATT
*
96931 AAAATTGCACTTTGACCCTTTAAAAATGATA
1 AAAATTG-A-TTTAACCCTTTAAAAATGATA
* *
96962 AAAATTTGATTTAATCCTTTAAAAATTATA
1 AAAA-TTGATTTAACCCTTTAAAAATGATA
96992 AAAAT
1 AAAAT
96997 ATAATCTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 22 0.71
31 5 0.16
32 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTGATTTAACCCTTTAAAAATGATA
Found at i:105260 original size:18 final size:17
Alignment explanation
Indices: 105224--105280 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
105214 TCACATTAAT
*
105224 AAATAATTTAAAATTATAA
1 AAAT-ATTTAAAA-AATAA
105243 AAATATTTTAAAAAATAA
1 AAATA-TTTAAAAAATAA
* *
105261 AAA-ATTCAAAAAAAAA
1 AAATATTTAAAAAATAA
105277 AAAT
1 AAAT
105281 GTAAAAGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.39
17 1 0.03
18 8 0.24
19 11 0.33
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATTTAAAAAATAA
Found at i:108785 original size:57 final size:57
Alignment explanation
Indices: 108697--108810 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
108687 AGTTGACCAG
108697 AGTAAATGCGACGAGTAAGGTACATTCGGAACACTTTGATAGTGTTTTGCATTCTAA
1 AGTAAATGCGACGAGTAAGGTACATTCGGAACACTTTGATAGTGTTTTGCATTCTAA
108754 AGTAAATGCGACGAGTAAGGTACATTCGGAACACTTTGATAGTGTTTTGCATTCTAA
1 AGTAAATGCGACGAGTAAGGTACATTCGGAACACTTTGATAGTGTTTTGCATTCTAA
108811 CTTGGTTGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (57 bp):
AGTAAATGCGACGAGTAAGGTACATTCGGAACACTTTGATAGTGTTTTGCATTCTAA
Found at i:118163 original size:21 final size:21
Alignment explanation
Indices: 118139--118179 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
118129 AACCCTATTA
* *
118139 TTTTGTTATTGTTTTCTCATG
1 TTTTGCTATTATTTTCTCATG
*
118160 TTTTGCTGTTATTTTCTCAT
1 TTTTGCTATTATTTTCTCAT
118180 TCGTTACAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.66
Consensus pattern (21 bp):
TTTTGCTATTATTTTCTCATG
Found at i:132746 original size:21 final size:20
Alignment explanation
Indices: 132722--132760 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
132712 AATTAATAAC
* *
132722 AATTTTATATATAGAAGATAT
1 AATTATATAGATA-AAGATAT
132743 AATTATATAGATAAAGAT
1 AATTATATAGATAAAGAT
132761 TTTTAGCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
AATTATATAGATAAAGATAT
Found at i:140162 original size:16 final size:16
Alignment explanation
Indices: 140141--140177 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
140131 CTTTTCAACT
* *
140141 TTCTCTTTTGCTTTTG
1 TTCTCTTTTGCCTTGG
140157 TTCTCTTTTGCCTTGG
1 TTCTCTTTTGCCTTGG
140173 TTCTC
1 TTCTC
140178 ATTGATGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.14, T:0.62
Consensus pattern (16 bp):
TTCTCTTTTGCCTTGG
Found at i:146715 original size:8 final size:8
Alignment explanation
Indices: 146702--146728 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
146692 GTCATTGTAC
146702 TTTTAAAA
1 TTTTAAAA
146710 TTTTAAAA
1 TTTTAAAA
146718 TTTTAAAA
1 TTTTAAAA
146726 TTT
1 TTT
146729 AAGCCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:147420 original size:2 final size:2
Alignment explanation
Indices: 147413--147439 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
147403 CCCCTCTTTG
147413 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 T
147440 GGAAGAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156369 original size:21 final size:24
Alignment explanation
Indices: 156343--156386 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
156333 ATAAATATTC
156343 TATT-AATTTAAT-AAA-AATTAA
1 TATTAAATTTAATCAAATAATTAA
156364 TATTAAATTTAATCAAATAATTA
1 TATTAAATTTAATCAAATAATTA
156387 TCTTGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 3 0.15
24 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAATTTAATCAAATAATTAA
Found at i:163027 original size:20 final size:20
Alignment explanation
Indices: 163004--163042 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
162994 ACTATATCAA
163004 AGGA-TTTTATAATATAAATT
1 AGGAGTTTTATAAT-TAAATT
*
163024 AGGAGTTTTTTAATTAAAT
1 AGGAGTTTTATAATTAAAT
163043 ATTATATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (20 bp):
AGGAGTTTTATAATTAAATT
Found at i:164229 original size:17 final size:18
Alignment explanation
Indices: 164207--164240 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
164197 AATATTTTAT
164207 TATAAAT-TTTGAAAAAA
1 TATAAATGTTTGAAAAAA
*
164224 TATAAATGTTTTAAAAA
1 TATAAATGTTTGAAAAA
164241 TTTTAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TATAAATGTTTGAAAAAA
Found at i:167787 original size:182 final size:188
Alignment explanation
Indices: 167467--168051 Score: 720
Period size: 196 Copynumber: 3.0 Consensus size: 188
167457 ATTTGCACAC
*
167467 ATATATA-A-ATAT-ATATATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGAC
1 ATATATACATATATGATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGAC
167529 AGCCATTGATAACCCTTTCTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTG
66 AGCCATTG--AA-----T-TACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTG
*
167594 TGATCTGTCTTAAGTTTTGCATTAATCACCTCTTTGGGTTTTTCTTAAATATCATTTGGCATATA
123 TGATCTGTCTTAAGTTTTGCATTAATCACCTCTTTGGGTTTTTCTTAAATATCATTTTGCATATA
167659 T
188 T
* * * * *
167660 AT-T-TGCATATATG-TGTATGTATTTGCAGGTATGGCCTTAATATGTGCCTCTCATTGTATGGC
1 ATATATACATATATGATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGAC
* * * * *
167722 AGCCATTG-A-TAC-TTGATATACCTTGCTTCCATCTTAATCATTAAGTGATATTCGTGATATGT
66 AGCCATTGAATTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTGTGATCTGT
* *
167784 CTTAAGTTTTACATTAATTAACCAGCTCTTTGGGTTTTTCTTAAATATCATTTTGCAAATATATA
131 CTTAAGTTTTGCATTAA-T---CACCTCTTTGGGTTTTTCTTAAATATCATTTTGC------ATA
167849 TAT
186 TAT
*
167852 ATATATATATATATGTATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGA
1 ATATATACATATATG-ATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGA
167917 CAGCCATTGATAACCTTTTTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTG
65 CAGCCATTG--AA-----TTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTG
* *
167982 TGATCTGTCTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTTAAATGTCATTTTGCATATA
123 TGATCTGTCTTAAGTTTTGCATTAATCACCTCTTTGGGTTTTTCTTAAATATCATTTTGCATATA
168047 T
188 T
168048 ATAT
1 ATAT
168052 GTATTTGAAG
Statistics
Matches: 336, Mismatches: 29, Indels: 51
0.81 0.07 0.12
Matches are distributed among these distances:
182 61 0.18
183 4 0.01
186 32 0.10
190 1 0.00
191 1 0.00
192 10 0.03
193 59 0.18
194 8 0.02
196 63 0.19
199 1 0.00
202 32 0.10
205 4 0.01
206 60 0.18
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (188 bp):
ATATATACATATATGATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGAC
AGCCATTGAATTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTGTGATCTGT
CTTAAGTTTTGCATTAATCACCTCTTTGGGTTTTTCTTAAATATCATTTTGCATATAT
Found at i:167897 original size:196 final size:193
Alignment explanation
Indices: 167666--168051 Score: 508
Period size: 206 Copynumber: 1.9 Consensus size: 193
167656 ATATATTTGC
* * * *
167666 ATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGTGCCTCTCATTGTATGGCAGCCATTG-
1 ATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGACAGCCATTGA
*
167730 A-TAC-TTGATATACCTTGCTTCCATCTTAATCATTAAGTGATATTCGTGATATGTCTTAAGTTT
66 ATTACTTTGATATACCTTGCTGCCATCTTAATCATTAAGTGATATTCGTGATATGTCTTAAGTTT
* *
167793 TACATTAATTAACCAGCTCTTTGGGTTTTTCTTAAATATCATTTTGCAAATATATATATATATAT
131 TACATCAA-T---CACCTCTTTGGGTTTTTCTTAAATATCATTTTGCAAATATATATATATATAT
167858 AT
192 AT
167860 ATATATGTATGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGACAGCCATT
1 ATATATG--TGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGACAGCCATT
* * * *
167925 GATAACCTTTTTACTTTGATATACCTTTCTGCCATCTTAATTATTAAGTGATATTTGTGATCTGT
64 G--AA-----TTACTTTGATATACCTTGCTGCCATCTTAATCATTAAGTGATATTCGTGATATGT
* * *
167990 CTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTTAAATGTCATTTTGCATATATATAT
122 CTTAAGTTTTACATCAATCACCTCTTTGGGTTTTTCTTAAATATCATTTTGCAAATATATAT
168052 GTATTTGAAG
Statistics
Matches: 166, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
194 7 0.04
196 53 0.32
199 1 0.01
202 41 0.25
205 4 0.02
206 60 0.36
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (193 bp):
ATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGTACCTCACATTGCATGACAGCCATTGA
ATTACTTTGATATACCTTGCTGCCATCTTAATCATTAAGTGATATTCGTGATATGTCTTAAGTTT
TACATCAATCACCTCTTTGGGTTTTTCTTAAATATCATTTTGCAAATATATATATATATATAT
Found at i:168046 original size:388 final size:386
Alignment explanation
Indices: 167318--168049 Score: 1234
Period size: 388 Copynumber: 1.9 Consensus size: 386
167308 GCGCGCGCGC
*
167318 GCCTCTCATTGCATGGCAGCCATTGATACTTGATATACCTTGCTTCCATCTTAATTATTAAGTGA
1 GCCTCTCATTGCATGGCAGCCATTGATACTTGATATACCTTGCTTCCATCTTAATCATTAAGTGA
* * *
167383 TATTTGTGATCTGTCTTCAGTTTTACATTAACCAGCTCCTTAGGTTTTTCTTAAATATCATTTTG
66 TATTCGTGATATGTCTTAAGTTTTACATTAACCAGCTCCTTAGGTTTTTCTTAAATATCATTTTG
* * *
167448 GATATATATATTTGCACACATATATAAATATATATATGTATTTGCAGGTATGGCCTTAATATGTA
131 CAAATATATATAT-CACACATATATAAATATATATATGTATTTGCAGGTATGGCCTTAATATGTA
167513 CCTCACATTGCATGACAGCCATTGATAACCCTTTCTACTTTGATATACCTTTCTGCCATCTTAAT
195 CCTCACATTGCATGACAGCCATTGATAACCCTTTCTACTTTGATATACCTTTCTGCCATCTTAAT
*
167578 TATTAAGTGATATTTGTGATCTGTCTTAAGTTTTGCATTAATCACCTCTTTGGGTTTTTCTTAAA
260 TATTAAGTGATATTTGTGATCTGTCTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTTAAA
167643 TATCATTTGGCATATATATTTGCATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGT
325 TATCATTTGGCATATATATTTGCATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGT
*
167705 GCCTCTCATTGTATGGCAGCCATTGATACTTGATATACCTTGCTTCCATCTTAATCATTAAGTGA
1 GCCTCTCATTGCATGGCAGCCATTGATACTTGATATACCTTGCTTCCATCTTAATCATTAAGTGA
* *
167770 TATTCGTGATATGTCTTAAGTTTTACATTAATTAACCAGCTCTTTGGGTTTTTCTTAAATATCAT
66 TATTCGTGATATGTCTTAAGTTTTAC----ATTAACCAGCTCCTTAGGTTTTTCTTAAATATCAT
* * * * *
167835 TTTGCAAATATATATAT-ATATATATATATATGTATGTATGTATTTGCAGGTATGGCCTTAATAT
127 TTTGCAAATATATATATCACACATATATAAATATATATATGTATTTGCAGGTATGGCCTTAATAT
*
167899 GTACCTCACATTGCATGACAGCCATTGATAA-CCTTTTTACTTTGATATACCTTTCTGCCATCTT
192 GTACCTCACATTGCATGACAGCCATTGATAACCCTTTCTACTTTGATATACCTTTCTGCCATCTT
167963 AATTATTAAGTGATATTTGTGATCTGTCTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTT
257 AATTATTAAGTGATATTTGTGATCTGTCTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTT
* *
168028 AAATGTCATTTTGCATATATAT
322 AAATATCATTTGGCATATATAT
168050 ATGTATTTGA
Statistics
Matches: 322, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
387 86 0.27
388 116 0.36
389 73 0.23
391 47 0.15
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (386 bp):
GCCTCTCATTGCATGGCAGCCATTGATACTTGATATACCTTGCTTCCATCTTAATCATTAAGTGA
TATTCGTGATATGTCTTAAGTTTTACATTAACCAGCTCCTTAGGTTTTTCTTAAATATCATTTTG
CAAATATATATATCACACATATATAAATATATATATGTATTTGCAGGTATGGCCTTAATATGTAC
CTCACATTGCATGACAGCCATTGATAACCCTTTCTACTTTGATATACCTTTCTGCCATCTTAATT
ATTAAGTGATATTTGTGATCTGTCTTAAGTTTTGCATCAATCACCTCTTTGGGTTTTTCTTAAAT
ATCATTTGGCATATATATTTGCATATATGTGTATGTATTTGCAGGTATGGCCTTAATATGT
Found at i:171002 original size:46 final size:46
Alignment explanation
Indices: 170935--171032 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
170925 ATTGATTATC
* *
170935 TTTGACGATCTCTCGAATTATGCAAGAGATTTTTTAAAAGAGGATA
1 TTTGACGATCTCTCGAATTATGCAAAAGACTTTTTAAAAGAGGATA
*
170981 TTTGACGATCTCTTGAATTATGCAAAAGACTTTTTAAAAGAGGATA
1 TTTGACGATCTCTCGAATTATGCAAAAGACTTTTTAAAAGAGGATA
171027 TTTGAC
1 TTTGAC
171033 AATTTTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (46 bp):
TTTGACGATCTCTCGAATTATGCAAAAGACTTTTTAAAAGAGGATA
Found at i:176635 original size:29 final size:30
Alignment explanation
Indices: 176604--176748 Score: 110
Period size: 29 Copynumber: 4.9 Consensus size: 30
176594 AGACAACCGG
176604 GGGTAAAATGGTAATTTTTGGTGAAATCG-
1 GGGTAAAATGGTAATTTTTGGTGAAATCGA
176633 GGGTTAAAAATGG-AA-TTTT-G-GAAAGTTCGA
1 GGG-T-AAAATGGTAATTTTTGGTGAAA--TCGA
* * *
176663 GGGTAAAATTGTATTTTTTGGTGAAATAGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGA
* * *
176693 GGCTAAAAATGG--AGTTTT-G-GAATTTCGA
1 GGGT-AAAATGGTAATTTTTGGTGAA-ATCGA
*
176721 GGGAAAAATGGTAATTTTTGGTGAAATC
1 GGGTAAAATGGTAATTTTTGGTGAAATC
176749 AGAGTTAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
27 14 0.16
28 13 0.15
29 21 0.24
30 19 0.22
31 17 0.19
32 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGA
Found at i:176641 original size:30 final size:31
Alignment explanation
Indices: 176607--176758 Score: 103
Period size: 30 Copynumber: 5.2 Consensus size: 31
176597 CAACCGGGGG
176607 TAAAATGGTAATTTTTGGTGAAATCG-GGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGGT
176637 TAAAAATGG-AA-TTTT-G-GAAAGTTCGAGGG-
1 T-AAAATGGTAATTTTTGGTGAAA--TCGAGGGT
* * * *
176666 TAAAATTGTATTTTTTGGTGAAATAGAGGCT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGGT
* * *
176697 AAAAATGG--AGTTTT-G-GAATTTCGAGGG-
1 TAAAATGGTAATTTTTGGTGAA-ATCGAGGGT
* *
176724 AAAAATGGTAATTTTTGGTGAAATC-AGAGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGGT
176754 TAAAA
1 TAAAA
176759 ATCAAATTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
27 15 0.16
28 13 0.14
29 21 0.23
30 22 0.24
31 17 0.18
32 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (31 bp):
TAAAATGGTAATTTTTGGTGAAATCGAGGGT
Found at i:176670 original size:59 final size:59
Alignment explanation
Indices: 176604--176795 Score: 246
Period size: 59 Copynumber: 3.3 Consensus size: 59
176594 AGACAACCGG
176604 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * * * * * *
176663 GGGTAAAATTGTATTTTTTGGTGAAATAGAGGCTAAAAATGGAGTTTTGG-AATTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * * **
176721 GGGAAAAATGGTAATTTTTGGTGAAATCAGAGTTAAAAATCAAATTTTGGAAAGTTC--
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
*
176778 GGGTAAAATTGTAATTTT
1 GGGTAAAATGGTAATTTT
176796 GAAAAGTTTA
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
57 16 0.14
58 46 0.41
59 49 0.44
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
Found at i:176820 original size:29 final size:29
Alignment explanation
Indices: 176778--176912 Score: 150
Period size: 29 Copynumber: 4.6 Consensus size: 29
176768 TGGAAAGTTC
* *
176778 GGGTAAAATTGTAATTTTGAAAAGTTTAG
1 GGGTAAAATGGTAATTTTAAAAAGTTTAG
*
176807 GGGTATAATGGTAATTTTAAAAAGTTTAG
1 GGGTAAAATGGTAATTTTAAAAAGTTTAG
* *
176836 GGGTAAAATGGTAATTTAAAAAAGTTTAA
1 GGGTAAAATGGTAATTTTAAAAAGTTTAG
* *
176865 GGGTAAAAAT-GTAATTTTCAAGAAG-TTCG
1 GGGT-AAAATGGTAATTTT-AAAAAGTTTAG
176894 AGGGTAAAAAT-GTAATTTT
1 -GGGT-AAAATGGTAATTTT
176913 TAGAACGTGG
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
29 65 0.70
30 28 0.30
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTAAAAAGTTTAG
Found at i:177945 original size:19 final size:19
Alignment explanation
Indices: 177921--177975 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
177911 CATTTTTTAT
177921 TTATTATAAATATTAATTA
1 TTATTATAAATATTAATTA
* *
177940 TTATTATAAATAAT-ATTT
1 TTATTATAAATATTAATTA
*
177958 TTATTCATAATTATTAAT
1 TTATT-ATAAATATTAAT
177976 G
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 8 0.27
19 20 0.67
20 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTATAAATATTAATTA
Done.