Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014172.1 Kokia drynarioides strain JFW-HI SEQ_129205, 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: 53254
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1298 original size:43 final size:43
Alignment explanation
Indices: 1240--1332 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
1230 TCTTATTTAG
* *
1240 GGTTTAAGGATTTAAAGTTATGAATTTGGGGTTTAATGTTCAT
1 GGTTTTAGGAATTAAAGTTATGAATTTGGGGTTTAATGTTCAT
*
1283 GGTTTTAGGAATTAAAGTTATGAGTTTGGGGTTTAATGTTCAT
1 GGTTTTAGGAATTAAAGTTATGAATTTGGGGTTTAATGTTCAT
1326 GGTTTTA
1 GGTTTTA
1333 TTTAAACATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.45
Consensus pattern (43 bp):
GGTTTTAGGAATTAAAGTTATGAATTTGGGGTTTAATGTTCAT
Found at i:1309 original size:22 final size:22
Alignment explanation
Indices: 1241--1309 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
1231 CTTATTTAGG
*
1241 GTTTAAGGATTTAAAGTTATGA
1 GTTTTAGGATTTAAAGTTATGA
* * * *
1263 -ATTTGGGGTTTAATGTTCATG-
1 GTTTTAGGATTTAAAGTT-ATGA
*
1284 GTTTTAGGAATTAAAGTTATGA
1 GTTTTAGGATTTAAAGTTATGA
1306 GTTT
1 GTTT
1310 GGGGTTTAAT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (22 bp):
GTTTTAGGATTTAAAGTTATGA
Found at i:1330 original size:21 final size:21
Alignment explanation
Indices: 1264--1330 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
1254 AAGTTATGAA
1264 TTTGGGGTTTAATGTTCATGG
1 TTTGGGGTTTAATGTTCATGG
* ** *
1285 TTTTAGGAATTAAAGTT-ATGAG
1 -TTTGGGGTTTAATGTTCATG-G
1307 TTTGGGGTTTAATGTTCATGG
1 TTTGGGGTTTAATGTTCATGG
1328 TTT
1 TTT
1331 TATTTAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTGGGGTTTAATGTTCATGG
Found at i:22243 original size:18 final size:18
Alignment explanation
Indices: 22220--22254 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22210 TTTGAGATTA
22220 AAAGGAATAATCAAAAGT
1 AAAGGAATAATCAAAAGT
*
22238 AAAGGAGTAATCAAAAG
1 AAAGGAATAATCAAAAG
22255 GTGAGCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.20, T:0.14
Consensus pattern (18 bp):
AAAGGAATAATCAAAAGT
Found at i:23221 original size:15 final size:15
Alignment explanation
Indices: 23201--23232 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23191 GCATTTGATT
23201 GAGTCAAATCAAATC
1 GAGTCAAATCAAATC
23216 GAGTCAAATCAAATC
1 GAGTCAAATCAAATC
23231 GA
1 GA
23233 ATCGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
GAGTCAAATCAAATC
Found at i:25100 original size:14 final size:15
Alignment explanation
Indices: 25067--25098 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25057 TAATTTCTTC
*
25067 AAATTTTAATTTAAT
1 AAATTTTAATTAAAT
25082 AAATTTTAATTAAAT
1 AAATTTTAATTAAAT
25097 AA
1 AA
25099 TTGATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTTAATTAAAT
Found at i:28958 original size:31 final size:31
Alignment explanation
Indices: 28898--28969 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
28888 GGTTATTGGG
28898 TTTGGGGA-TTTTGGTTTAGGTTTAAAAAA-
1 TTTGGGGATTTTTGGTTTAGGTTTAAAAAAT
*
28927 TTTGGGGATTTTTAGGTTTCAGGTTT-TAAAAT
1 TTTGGGGATTTTT-GGTTT-AGGTTTAAAAAAT
*
28959 TTTTGGGATTT
1 TTTGGGGATTT
28970 AGGTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.22
30 4 0.11
31 9 0.24
32 16 0.43
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.50
Consensus pattern (31 bp):
TTTGGGGATTTTTGGTTTAGGTTTAAAAAAT
Found at i:28967 original size:32 final size:30
Alignment explanation
Indices: 28898--29153 Score: 104
Period size: 29 Copynumber: 8.4 Consensus size: 30
28888 GGTTATTGGG
28898 TTTGGGGA-TTTTGGTTTAGGTTTAAAAAA
1 TTTGGGGATTTTTGGTTTAGGTTTAAAAAA
* *
28927 TTTGGGGATTTTTAGGTTTCAGGTTTTAAAAT
1 TTTGGGGATTTTT-GGTTT-AGGTTTAAAAAA
* *
28959 TTTTGGGA-------TTTAGGTTTTAAAAA
1 TTTGGGGATTTTTGGTTTAGGTTTAAAAAA
* ******
28982 TTTGGGGATTTTTGGGATTTTTAGGGTTGTTGGG
1 TTTGGGGATTTTT-GG---TTTAGGTTTAAAAAA
29016 TTTGGGGA-TTTTGGTTTAGGTTTAAAAAA
1 TTTGGGGATTTTTGGTTTAGGTTTAAAAAA
* ****
29045 TTTGAGGATTTTTGGGATTTTTATGGTTGT--TGGG
1 TTTGGGGATTTTT-GG---TTTA-GGTT-TAAAAAA
*
29079 TTTGGGGA-TTTTGGTTTAAGTTTAAAAAA
1 TTTGGGGATTTTTGGTTTAGGTTTAAAAAA
* *
29108 TTTGGGGATTTTCGAGATTTAGGTTTCAAAAAC
1 TTTGGGGATTTTTG-G-TTTAGGTTT-AAAAAA
**
29141 TTTGAAGATTTTT
1 TTTGGGGATTTTT
29154 AGTGTTCTAT
Statistics
Matches: 164, Mismatches: 36, Indels: 50
0.66 0.14 0.20
Matches are distributed among these distances:
23 18 0.11
24 3 0.02
27 1 0.01
28 3 0.02
29 35 0.21
30 12 0.07
31 8 0.05
32 29 0.18
33 23 0.14
34 27 0.16
35 4 0.02
36 1 0.01
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.48
Consensus pattern (30 bp):
TTTGGGGATTTTTGGTTTAGGTTTAAAAAA
Found at i:28981 original size:24 final size:24
Alignment explanation
Indices: 28934--28992 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
28924 AAATTTGGGG
*
28934 ATTTTTAGG-TTTCAGGTTTTAAA
1 ATTTTTGGGATTTCAGGTTTTAAA
28957 ATTTTTGGGATTT-AGGTTTTAAA
1 ATTTTTGGGATTTCAGGTTTTAAA
* *
28980 AATTTGGGGATTT
1 ATTTTTGGGATTT
28993 TTGGGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.51
Consensus pattern (24 bp):
ATTTTTGGGATTTCAGGTTTTAAA
Found at i:29127 original size:63 final size:63
Alignment explanation
Indices: 28967--29119 Score: 270
Period size: 63 Copynumber: 2.4 Consensus size: 63
28957 ATTTTTGGGA
*
28967 TTTAGGTTTTAAAAATTTGGGGATTTTTGGGATTTTTAGGGTTGTTGGGTTTGGGGATTTTGG
1 TTTAGGTTTAAAAAATTTGGGGATTTTTGGGATTTTTAGGGTTGTTGGGTTTGGGGATTTTGG
* *
29030 TTTAGGTTTAAAAAATTTGAGGATTTTTGGGATTTTTATGGTTGTTGGGTTTGGGGATTTTGG
1 TTTAGGTTTAAAAAATTTGGGGATTTTTGGGATTTTTAGGGTTGTTGGGTTTGGGGATTTTGG
*
29093 TTTAAGTTTAAAAAATTTGGGGATTTT
1 TTTAGGTTTAAAAAATTTGGGGATTTT
29120 CGAGATTTAG
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (63 bp):
TTTAGGTTTAAAAAATTTGGGGATTTTTGGGATTTTTAGGGTTGTTGGGTTTGGGGATTTTGG
Found at i:30093 original size:42 final size:41
Alignment explanation
Indices: 30045--30177 Score: 107
Period size: 42 Copynumber: 3.2 Consensus size: 41
30035 AATTGAATGG
30045 TAATTTATATATTTGACATGTTGATAATTCATTGAATCGTAT
1 TAATTTATATATTTGACATGTTGATAATT-ATTGAATCGTAT
* * * *
30087 TAATTTA-AAACTTGATAAT-TT-AT-A-TATTTGACATGTCTGCT-G
1 TAATTTATATATTTGA-CATGTTGATAATTA-TTGA-A--TC-G-TAT
30129 TAATTTATATATTTGACATGTTGATAATTTATTGAATCGTAT
1 TAATTTATATATTTGACATGTTGATAA-TTATTGAATCGTAT
30171 TAATTTA
1 TAATTTA
30178 AAACTTGGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 28
0.66 0.08 0.27
Matches are distributed among these distances:
37 1 0.01
38 5 0.07
39 2 0.03
40 2 0.03
41 11 0.16
42 27 0.39
43 11 0.16
44 2 0.03
45 2 0.03
46 4 0.06
47 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (41 bp):
TAATTTATATATTTGACATGTTGATAATTATTGAATCGTAT
Found at i:30190 original size:84 final size:84
Alignment explanation
Indices: 30044--30206 Score: 308
Period size: 84 Copynumber: 1.9 Consensus size: 84
30034 TAATTGAATG
30044 GTAATTTATATATTTGACATGTTGATAATTCATTGAATCGTATTAATTTAAAACTTGATAATTTA
1 GTAATTTATATATTTGACATGTTGATAATTCATTGAATCGTATTAATTTAAAACTTGATAATTTA
30109 TATATTTGACATGTCTGCT
66 TATATTTGACATGTCTGCT
* *
30128 GTAATTTATATATTTGACATGTTGATAATTTATTGAATCGTATTAATTTAAAACTTGGTAATTTA
1 GTAATTTATATATTTGACATGTTGATAATTCATTGAATCGTATTAATTTAAAACTTGATAATTTA
30193 TATATTTGACATGT
66 TATATTTGACATGT
30207 TGATAATTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (84 bp):
GTAATTTATATATTTGACATGTTGATAATTCATTGAATCGTATTAATTTAAAACTTGATAATTTA
TATATTTGACATGTCTGCT
Found at i:30216 original size:57 final size:57
Alignment explanation
Indices: 30128--30263 Score: 245
Period size: 57 Copynumber: 2.4 Consensus size: 57
30118 CATGTCTGCT
30128 GTAATTTATATATTTGACATGTTGATAATTTATTGAATCGTATTAATTTAAAACTTG
1 GTAATTTATATATTTGACATGTTGATAATTTATTGAATCGTATTAATTTAAAACTTG
*
30185 GTAATTTATATATTTGACATGTTGATAATTTATTGAATTGTATTAATTTAAAACTTG
1 GTAATTTATATATTTGACATGTTGATAATTTATTGAATCGTATTAATTTAAAACTTG
**
30242 AAAATTTATATATTTGACATGT
1 GTAATTTATATATTTGACATGT
30264 CTGCTCATTG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 76 1.00
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (57 bp):
GTAATTTATATATTTGACATGTTGATAATTTATTGAATCGTATTAATTTAAAACTTG
Found at i:30984 original size:18 final size:18
Alignment explanation
Indices: 30961--31030 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
30951 TGGCAGTAAT
*
30961 GGTGGTGAGGGTTTGAGA
1 GGTGGTGAGGGTTAGAGA
* *
30979 GGTGGTAAGGGTTCGAGTAA
1 GGTGGTGAGGGTTAGAG--A
* * *
30999 GGGTGTTGATGGTGAGAGA
1 -GGTGGTGAGGGTTAGAGA
31018 GGTGGTGAGGGTT
1 GGTGGTGAGGGTT
31031 CGGGTAAGGG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 25 0.64
19 1 0.03
20 1 0.03
21 12 0.31
ACGTcount: A:0.19, C:0.01, G:0.53, T:0.27
Consensus pattern (18 bp):
GGTGGTGAGGGTTAGAGA
Found at i:30998 original size:39 final size:39
Alignment explanation
Indices: 30955--31041 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
30945 AGATGATGGC
* **
30955 AGTAATGGTGGTGAGGGTTTGAGAGGTGGTAAGGGTTCG
1 AGTAAGGGTGGTGAGGGTGAGAGAGGTGGTAAGGGTTCG
* * *
30994 AGTAAGGGTGTTGATGGTGAGAGAGGTGGTGAGGGTTCG
1 AGTAAGGGTGGTGAGGGTGAGAGAGGTGGTAAGGGTTCG
*
31033 GGTAAGGGT
1 AGTAAGGGT
31042 AAGGGTGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.02, G:0.51, T:0.26
Consensus pattern (39 bp):
AGTAAGGGTGGTGAGGGTGAGAGAGGTGGTAAGGGTTCG
Found at i:31071 original size:69 final size:63
Alignment explanation
Indices: 30998--31296 Score: 193
Period size: 54 Copynumber: 5.1 Consensus size: 63
30988 GGTTCGAGTA
* * * *
30998 AGGGTGTTGATGGTGAGAGAGGTGGTGAGGGTTCGGGTAAGGGTAAGGGTGTTGTTAGTGAAGGT
1 AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTT----T-A-GGTAAGGGTGCTATTAGTGAAGGT
31063 GTTG
60 GTTG
* *
31067 AGGGTGTTGAGGGTGAGGGATATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
1 AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
* * *
31130 A-GG-G-TGA--G-GA-AG-G-TGGTGAGGGTTTGGGTAATGGTGCTATTAATGAAGGTGTTG
1 AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
* * ** * *
31184 A-GG-G-TGA-----A-AGAGGTGGTGAAGGTTCGGGTAAGGGTGCTGTTAATGAAGGTGTTG
1 AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
* * *
31238 A-GG-G-TGA-----A-AGAGGTGGTGAGGGTTCAGGTAAGGGTGCTGTTAGTGAAGGTGTTG
1 AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
31292 AGGGT
1 AGGGT
31297 CAGGGTGAGG
Statistics
Matches: 208, Mismatches: 18, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
52 3 0.01
53 1 0.00
54 134 0.64
55 2 0.01
56 1 0.00
57 2 0.01
58 1 0.00
60 3 0.01
61 1 0.00
62 2 0.01
63 27 0.13
64 1 0.00
65 1 0.00
69 29 0.14
ACGTcount: A:0.21, C:0.02, G:0.48, T:0.28
Consensus pattern (63 bp):
AGGGTGTTGAGGGTGAGAGAGATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAAGGTGTTG
Found at i:31135 original size:54 final size:54
Alignment explanation
Indices: 31069--31301 Score: 304
Period size: 54 Copynumber: 4.3 Consensus size: 54
31059 AGGTGTTGAG
** * *
31069 GGTGTTGAGGGTGAGGGATATGGTGAGGGTTTAGGTAAGGGTGCTATTAGTGAA
1 GGTGTTGAGGGTGAGGGAGGTGGTGAGGGTTCAGGTAAGGGTGCTATTAATGAA
* ** *
31123 GGTGTTGAGGGTGAGGAAGGTGGTGAGGGTTTGGGTAATGGTGCTATTAATGAA
1 GGTGTTGAGGGTGAGGGAGGTGGTGAGGGTTCAGGTAAGGGTGCTATTAATGAA
** * * *
31177 GGTGTTGAGGGTGAAAGAGGTGGTGAAGGTTCGGGTAAGGGTGCTGTTAATGAA
1 GGTGTTGAGGGTGAGGGAGGTGGTGAGGGTTCAGGTAAGGGTGCTATTAATGAA
** * *
31231 GGTGTTGAGGGTGAAAGAGGTGGTGAGGGTTCAGGTAAGGGTGCTGTTAGTGAA
1 GGTGTTGAGGGTGAGGGAGGTGGTGAGGGTTCAGGTAAGGGTGCTATTAATGAA
*
31285 GGTGTTGAGGGTCAGGG
1 GGTGTTGAGGGTGAGGG
31302 TGAGGTTGAT
Statistics
Matches: 160, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 160 1.00
ACGTcount: A:0.22, C:0.03, G:0.48, T:0.27
Consensus pattern (54 bp):
GGTGTTGAGGGTGAGGGAGGTGGTGAGGGTTCAGGTAAGGGTGCTATTAATGAA
Found at i:34816 original size:161 final size:161
Alignment explanation
Indices: 34536--34931 Score: 537
Period size: 161 Copynumber: 2.5 Consensus size: 161
34526 CAAACAAGAT
* * * * *
34536 CCTAACACAACGAGAACACAAGTATATTGTAAACACTTTCTCATTGTCAAATCCAAATTATAATA
1 CCTAACACAACTAGACCACAGGTATATTGTAAACATTTTCTCATTGTCAATTCCAAATTATAATA
* * * *
34601 ATCTAATTTCGGTTTTTATTTTTTGTGCTTTAGTCTAGTATGAGTACAAGAACTACAACCCCAAA
66 ATCTAATTTCGATTTTGATTTTTTGTGCTTTAGCCTAGTACGAGTACAAGAACTACAA-CCCAAA
* * *
34666 AAAAG-ATGGCAGAACACCACCATGCATTTAA
130 AAAAGAACGACAGAACACCACCATGCATTCAA
* *
34697 CCTAACACAATTGGACCACAGGTATATTGTAAACATTTTCTCATTGTCAATTCCAAATTATAATA
1 CCTAACACAACTAGACCACAGGTATATTGTAAACATTTTCTCATTGTCAATTCCAAATTATAATA
** * *
34762 ATCTAATTTTTATTTTGATTTTTTGTG-TCTTAGCCTGGTACGAGTACGAGAACTACAACCCAAA
66 ATCTAATTTCGATTTTGATTTTTTGTGCT-TTAGCCTAGTACGAGTACAAGAACTACAACCCAAA
* *
34826 AAAAGAACGATAGAACACCACCATGCATTCAG
130 AAAAGAACGACAGAACACCACCATGCATTCAA
** *
34858 CCTAACACAACTAGACCACAGGTATATCATAAACATTTTCTCATTGTCAATTCCAAATTAT-TTA
1 CCTAACACAACTAGACCACAGGTATATTGTAAACATTTTCTCATTGTCAATTCCAAATTATAAT-
34922 AATCTAATTT
65 AATCTAATTT
34932 GGGTTCTAAT
Statistics
Matches: 207, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
160 13 0.06
161 194 0.94
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (161 bp):
CCTAACACAACTAGACCACAGGTATATTGTAAACATTTTCTCATTGTCAATTCCAAATTATAATA
ATCTAATTTCGATTTTGATTTTTTGTGCTTTAGCCTAGTACGAGTACAAGAACTACAACCCAAAA
AAAGAACGACAGAACACCACCATGCATTCAA
Found at i:36688 original size:22 final size:21
Alignment explanation
Indices: 36662--36702 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36652 GCTTTTTTTC
*
36662 TTGTTTGGCTATTGAGAAAATT
1 TTGTTT-GCTATCGAGAAAATT
*
36684 TTGTTTTCTATCGAGAAAA
1 TTGTTTGCTATCGAGAAAA
36703 AATTTGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (21 bp):
TTGTTTGCTATCGAGAAAATT
Found at i:36703 original size:22 final size:21
Alignment explanation
Indices: 36670--36710 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
36660 TCTTGTTTGG
* *
36670 CTATTGAGAAAATTTTGTTTT
1 CTATCGAGAAAAATTTGTTTT
36691 CTATCGAGAAAAAATTTGTT
1 CTATCGAG-AAAAATTTGTT
36711 CTTTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (21 bp):
CTATCGAGAAAAATTTGTTTT
Found at i:36801 original size:22 final size:22
Alignment explanation
Indices: 36774--36822 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
36764 AGGGAATAAA
* * *
36774 AAACAAAATAGCAATATCGATT
1 AAACAAAAGAACAACATCGATT
36796 AAACAAAAGAACAACATCGATT
1 AAACAAAAGAACAACATCGATT
36818 AAACA
1 AAACA
36823 TGATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.16
Consensus pattern (22 bp):
AAACAAAAGAACAACATCGATT
Found at i:37347 original size:18 final size:19
Alignment explanation
Indices: 37310--37349 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
37300 AGTTTTTACT
*
37310 TTTATTTTTTAAAATTTAA
1 TTTATGTTTTAAAATTTAA
*
37329 TTTATGTTTT-AACTTTAA
1 TTTATGTTTTAAAATTTAA
37347 TTT
1 TTT
37350 TTTTTGCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTATGTTTTAAAATTTAA
Found at i:40041 original size:30 final size:29
Alignment explanation
Indices: 39971--40127 Score: 97
Period size: 30 Copynumber: 5.4 Consensus size: 29
39961 AAAAGAATAC
* * *
39971 GGGGTTAAAACATAATTTTGGAAATATTTA
1 GGGGTCAAAATATAATTTTGGAAA-GTTTA
* *
40001 AGGGTAAAAATATAATTTTGGAAAGGTTTA
1 GGGGTCAAAATATAATTTTGGAAA-GTTTA
* * * *
40031 GGGGTCAAAATGTGATATTAGGAAAG-TTC
1 GGGGTCAAAATATAAT-TTTGGAAAGTTTA
* * *
40060 GGGGATCAAAATGTAAATTTGGAAAATTT-
1 GGGG-TCAAAATATAATTTTGGAAAGTTTA
* * *
40089 TGGGT-TAAATGTAATTTTGGGAAAGTTTA
1 GGGGTCAAAATATAATTTT-GGAAAGTTTA
*
40118 -GGTTCAAAAT
1 GGGGTCAAAAT
40128 GTAGCTTTTA
Statistics
Matches: 100, Mismatches: 21, Indels: 13
0.75 0.16 0.10
Matches are distributed among these distances:
27 11 0.11
28 12 0.12
29 20 0.20
30 50 0.50
31 7 0.07
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
GGGGTCAAAATATAATTTTGGAAAGTTTA
Found at i:40121 original size:27 final size:28
Alignment explanation
Indices: 40067--40130 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
40057 TTCGGGGATC
* *
40067 AAAATGTAAATTTGGAAAATTTTGGGTT
1 AAAATGTAAATTTGGAAAAGTTTAGGTT
* *
40095 -AAATGTAATTTTGGGAAAGTTTAGGTT
1 AAAATGTAAATTTGGAAAAGTTTAGGTT
40122 CAAAATGTA
1 -AAAATGTA
40131 GCTTTTAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.77
29 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (28 bp):
AAAATGTAAATTTGGAAAAGTTTAGGTT
Found at i:41797 original size:6 final size:6
Alignment explanation
Indices: 41786--41831 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
41776 TTGGACATTT
*
41786 TTTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA TTTAAA GTTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTA
41832 TTCATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:41810 original size:17 final size:17
Alignment explanation
Indices: 41788--41820 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41778 GGACATTTTT
41788 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
41805 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
41821 TTTAAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:44277 original size:42 final size:43
Alignment explanation
Indices: 44213--44306 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
44203 TTTGGAAAAG
* * *
44213 CGCCGCTAAAGACCATGTTCTTTAGCGGCG-TTTTCCCACAAA
1 CGCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTCCCACAAA
44255 CGCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTCCCACAAA
1 CGCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTCCCACAAA
44298 CGCCACTAA
1 CGCCACTAA
44307 CATTAACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 27 0.56
43 21 0.44
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTCCCACAAA
Found at i:45979 original size:19 final size:19
Alignment explanation
Indices: 45924--45986 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
45914 TCATTTGTTA
*
45924 ATTTTTTATAATTTTTTATG
1 ATTTTTTATTA-TTTTTATG
*
45944 -TTTTATGTA-TATATTTATG
1 ATTTT-T-TATTATTTTTATG
*
45963 ATTTTTTATTATTTTTATA
1 ATTTTTTATTATTTTTATG
45982 ATTTT
1 ATTTT
45987 CTCTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.06
19 25 0.71
20 6 0.17
21 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTTTATTATTTTTATG
Found at i:48090 original size:22 final size:23
Alignment explanation
Indices: 48064--48107 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
48054 TAAAACGCTG
*
48064 CATTAGTAGAATAT-CAAAGCAA
1 CATTAGTAAAATATCCAAAGCAA
48086 CATTAGTAAAATATCCAAAGCA
1 CATTAGTAAAATATCCAAAGCA
48108 GGCACAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (23 bp):
CATTAGTAAAATATCCAAAGCAA
Found at i:48847 original size:41 final size:41
Alignment explanation
Indices: 48784--49001 Score: 321
Period size: 41 Copynumber: 5.3 Consensus size: 41
48774 TTTAAAATTT
*
48784 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
* * **
48825 CGTTATTGCTCTGACTTTTAGCGGCATTTTCCCATAAGCGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
* * *
48866 CACTATTGCTTTGACCTTTAGCGGTGCTTTCCCATAAGCGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
* *
48907 CGCTATTGCTCTGACCTTTAGCGACGTTTTCCCATAAGCGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
*
48948 CGCTATTGC-CTTAACCTTTAGCGGCGCTTTCCCATAAGCGC
1 CGCTATTGCTC-TGACCTTTAGCGGCGCTTTCCCATAAGCGC
48989 CGCTATTGCTCTG
1 CGCTATTGCTCTG
49002 TCTTTTGCGG
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 152 0.99
42 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (41 bp):
CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGC
Done.