Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008874.1 Kokia drynarioides strain JFW-HI SEQ_123560, 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: 78066
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:9966 original size:29 final size:30
Alignment explanation
Indices: 9913--10167 Score: 181
Period size: 29 Copynumber: 8.7 Consensus size: 30
9903 GTAATTTTGG
* *
9913 GAAAGTTTG-GGGTCAAAAATAGAATTTTTA
1 GAAAGTTCGAGGGT-AAAAATGGAATTTTTA
* * *
9943 GACA-TTCGAGGATAAAAATGGAATTTTTT
1 GAAAGTTCGAGGGTAAAAATGGAATTTTTA
*
9972 G-AAGTTCGGGGGT-AAAATGGTAATTTTTAA
1 GAAAGTTCGAGGGTAAAAATGG-AATTTTT-A
* **
10002 AAAAAATCGA-GGTAAAAAATGGAATTTTT-
1 GAAAGTTCGAGGGT-AAAAATGGAATTTTTA
* ** * *
10031 GGAAGTTCG-GGGGCAAAACGGTAA-TTTTG
1 GAAAGTTCGAGGGTAAAAATGG-AATTTTTA
** *
10060 GAAAAATCGA-GGTCAAAATGGAA-TTTTA
1 GAAAGTTCGAGGGTAAAAATGGAATTTTTA
* *
10088 GAAAGTTCGAGGGTAAAAATGTAATTTTTG
1 GAAAGTTCGAGGGTAAAAATGGAATTTTTA
** *
10118 GAAAAATCGAGGTTAAAAATGGAA-TTTTA
1 GAAAGTTCGAGGGTAAAAATGGAATTTTTA
*
10147 AAAAGTTCGAGGGTAAAAATG
1 GAAAGTTCGAGGGTAAAAATG
10168 TAATAATCAA
Statistics
Matches: 172, Mismatches: 40, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
28 32 0.19
29 88 0.51
30 33 0.19
31 12 0.07
32 7 0.04
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (30 bp):
GAAAGTTCGAGGGTAAAAATGGAATTTTTA
Found at i:10026 original size:60 final size:59
Alignment explanation
Indices: 9948--10164 Score: 255
Period size: 60 Copynumber: 3.7 Consensus size: 59
9938 TTTTAGACAT
* * **
9948 TCGAGG-ATAAAAATGGAATTTTTTGAAGTTCGGGGGTAAAATGGTAATTTTTAAAAAAAA
1 TCGAGGTA-AAAAATGGAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTT-GGAAAAA
* * * *
10008 TCGAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGCAAAACGGTAA-TTTTGGAAAAA
1 TCGAGGTAAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAA
*
10066 TCGAGGT-CAAAATGGAA-TTTTAGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAAA
1 TCGAGGTAAAAAATGGAATTTTTAG-AAGTTCGAGGGT-AAAATGGTAATTTTTGGAAAAA
* * *
10124 TCGAGGTTAAAAATGGAATTTTAAAAAGTTCGAGGGTAAAA
1 TCGAGGTAAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAA
10165 ATGTAATAAT
Statistics
Matches: 138, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
56 5 0.04
57 23 0.17
58 38 0.28
59 25 0.18
60 46 0.33
61 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (59 bp):
TCGAGGTAAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAA
Found at i:10152 original size:59 final size:59
Alignment explanation
Indices: 9905--10342 Score: 367
Period size: 58 Copynumber: 7.6 Consensus size: 59
9895 GTAAAATAGT
* * * * *
9905 AATTTTGGGAAAGTT-TGGGGTCAAAAATAG-AATTTTTAG-ACATTCGAGGATAAAAATGG
1 AATTTT-GGAAAGTTCGGGGGT-AAAAAT-GTAATTTTTGGAAAAATCGAGGTTAAAAATGG
* ** *
9964 AATTTTTTG-AAGTTCGGGGGT-AAAATGGTAATTTTTAAAAAAAATCGAGGTAAAAAATGG
1 AA-TTTTGGAAAGTTCGGGGGTAAAAAT-GTAATTTTT-GGAAAAATCGAGGTTAAAAATGG
* ** *
10024 AATTTTTGG-AAGTTCGGGGGCAAAACGGTAA-TTTTGGAAAAATCGAGG-TCAAAATGG
1 AA-TTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
* *
10081 AATTTTAGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
1 AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
** * * * *
10140 AATTTTAAAAAGTTCGAGGGTAAAAATGTAA----T-----AATCAAGATTAAAAATGA
1 AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
* * * **
10190 AATTTTGGAAAGTTCGGGGGTAAAAATGGTAACTTTTGGAAAATTAG-GGTT-AAAATAA
1 AATTTTGGAAAGTTCGGGGGTAAAAAT-GTAATTTTTGGAAAAATCGAGGTTAAAAATGG
** * * *
10248 AATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGG-AAAATTGATGTTAAAAATAG
1 AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
* *
10306 AATTTTGGAAAGTTTGGGGGTAAAAATGTATTTTTTG
1 AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTG
10343 ACAATTTAGG
Statistics
Matches: 315, Mismatches: 43, Indels: 43
0.79 0.11 0.11
Matches are distributed among these distances:
50 39 0.12
51 4 0.01
55 2 0.01
56 10 0.03
57 46 0.15
58 112 0.36
59 54 0.17
60 45 0.14
61 3 0.01
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
Found at i:10241 original size:109 final size:108
Alignment explanation
Indices: 10074--10279 Score: 272
Period size: 109 Copynumber: 1.9 Consensus size: 108
10064 AATCGAGGTC
* * * *
10074 AAAATGGAATTTTAGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATG
1 AAAATGAAATTTTAGAAAGTTCGAGGGTAAAAATGTAACTTTTGGAAAAATAGAGGTT-AAAATA
*
10139 GAATTTTAAAAAGTTCGA-GGGTAAAAATGTAATAATCAAGATTA
65 AAATTTTAAAAAGTT-GAGGGGTAAAAATGTAATAATCAAGATTA
* * *
10183 AAAATGAAATTTTGGAAAGTTCGGGGGTAAAAATGGTAACTTTTGGAAAATTAG-GGTTAAAATA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTAAAAAT-GTAACTTTTGGAAAAATAGAGGTTAAAATA
** *
10247 AAATTTTGGAAAGTTTAGGGGTAAAAATGTAAT
65 AAATTTTAAAAAGTTGAGGGGTAAAAATGTAAT
10280 TTTTGGAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 32 0.38
109 35 0.42
110 16 0.19
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (108 bp):
AAAATGAAATTTTAGAAAGTTCGAGGGTAAAAATGTAACTTTTGGAAAAATAGAGGTTAAAATAA
AATTTTAAAAAGTTGAGGGGTAAAAATGTAATAATCAAGATTA
Found at i:10311 original size:166 final size:166
Alignment explanation
Indices: 10016--10335 Score: 423
Period size: 166 Copynumber: 1.9 Consensus size: 166
10006 AATCGAGGTA
* * * **
10016 AAAAATGGAATTTTTGGAAGTTCGGGGGCAAAACGGTAATTTTGGAAAAATCGAGGTCAAAATGG
1 AAAAATGGAAATTTTGGAAGTTCGGGGGAAAAACGGTAATTTTGGAAAAATAGAGGTCAAAATAA
* *
10081 AATTTTAGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTT
66 AATTTTAGAAAGTTAGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTT
10146 AAAAAGTTCGAGGGTAAAAATGTAATAATCAAGATT
131 AAAAAGTTCGAGGGTAAAAATGTAATAATCAAGATT
* * *
10182 AAAAAT-GAAATTTTGGAAAGTTCGGGGGTAAAAATGGTAACTTTTGGAAAATTAG-GGTTAAAA
1 AAAAATGGAAATTTTGG-AAGTTCGGGGG-AAAAACGGTAA-TTTTGGAAAAATAGAGGTCAAAA
* * *
10245 TAAAATTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTTGG-AAAATTGATGTTAAAAATAGAA
63 TAAAATTTTAGAAAG-TTAGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATAGAA
** * *
10308 TTTTGGAAAGTTTGGGGGTAAAAATGTA
127 TTTTAAAAAGTTCGAGGGTAAAAATGTA
10336 TTTTTTGACA
Statistics
Matches: 133, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
165 9 0.07
166 60 0.45
167 49 0.37
168 15 0.11
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.30
Consensus pattern (166 bp):
AAAAATGGAAATTTTGGAAGTTCGGGGGAAAAACGGTAATTTTGGAAAAATAGAGGTCAAAATAA
AATTTTAGAAAGTTAGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTT
AAAAAGTTCGAGGGTAAAAATGTAATAATCAAGATT
Found at i:10340 original size:29 final size:29
Alignment explanation
Indices: 10181--10340 Score: 139
Period size: 29 Copynumber: 5.5 Consensus size: 29
10171 TAATCAAGAT
* *
10181 TAAAAATGAAATTTTGGAAAGTTCGGGGG
1 TAAAAATGTAATTTTGGAAAGTTTGGGGG
* *
10210 TAAAAATGGTAACTTTTGGAAA-ATT-AGGG
1 TAAAAAT-GTAA-TTTTGGAAAGTTTGGGGG
* ** *
10239 TTAAAATAAAATTTTGGAAAGTTTAGGGG
1 TAAAAATGTAATTTTGGAAAGTTTGGGGG
* ** *
10268 TAAAAATGTAATTTTTGGAAA-ATTGATGT
1 TAAAAATGTAA-TTTTGGAAAGTTTGGGGG
10297 TAAAAATAG-AATTTTGGAAAGTTTGGGGG
1 TAAAAAT-GTAATTTTGGAAAGTTTGGGGG
*
10326 TAAAAATGTATTTTT
1 TAAAAATGTAATTTT
10341 TGACAATTTA
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
27 9 0.09
28 14 0.14
29 55 0.54
30 14 0.14
31 9 0.09
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAAATGTAATTTTGGAAAGTTTGGGGG
Found at i:11432 original size:3 final size:3
Alignment explanation
Indices: 11419--11487 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
11409 CCCTTTTTAT
** * **
11419 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA AAA TTA TTT TTA AAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
11466 TTA TTA CTA TTA ATA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA
11488 CGAATAATGT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12240 original size:6 final size:6
Alignment explanation
Indices: 12220--12279 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
12210 CTTTGAAATT
* ** ** *
12220 AATTTA AA-CTA AATTTA AATTTA AA-ACA AATTTA AATTTA AAAATG
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
12266 AATTTA AATTTA AA
1 AATTTA AATTTA AA
12280 AATAAATCTA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
5 7 0.17
6 33 0.82
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:12242 original size:17 final size:18
Alignment explanation
Indices: 12220--12291 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
12210 CTTTGAAATT
12220 AATTT-AAACTAAATTTA
1 AATTTAAAACTAAATTTA
12237 AATTTAAAAC-AAATTTA
1 AATTTAAAACTAAATTTA
* *
12254 AATTTAAAAATGAATTTA
1 AATTTAAAACTAAATTTA
* *
12272 AATTTAAAAATAAATCTA
1 AATTTAAAACTAAATTTA
12290 AA
1 AA
12292 ACCAATCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
17 21 0.43
18 28 0.57
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (18 bp):
AATTTAAAACTAAATTTA
Found at i:12891 original size:96 final size:95
Alignment explanation
Indices: 12766--13153 Score: 268
Period size: 96 Copynumber: 4.0 Consensus size: 95
12756 CTTTCATGCT
* * * *
12766 TTTGAGGTACAAGGTTCGCCATTGCGACTTACACCTTTCTC-TTCGTATTTTCGTGGTACTGGAT
1 TTTGTGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCATT-G--TTTTCGTGGTACTGGAT
** * *
12830 TTACTGTTGCGGCTTAAATCTTTCCCTT-TGTC
63 CCACCGTTACGGCTTAAATCTTTCCCTTATGTC
* * *
12862 TTTGTGGTACTAGGTTCGCCATTGTGACTTAAACTTTTCCCATTGTTTTCGTGGTACTGGATCCG
1 TTTGTGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCATTGTTTTCGTGGTACTGGATCCA
*
12927 CCGTTACGGCTTAGATCTTTCCCTTCATGTC
66 CCGTTACGGCTTAAATCTTTCCCTT-ATGTC
* * * * * * *
12958 TTCGTGGTACT-GGATTCG-CAGTTGCGTCTTTAAATCTTTTCCCTTTATGTCTCCGAGGTACT-
1 TTTGTGGTACTAGG-TTCGCCA-TTGCGAC-TTAAA-CCTTTCCC-AT-TGTTTTCGTGGTACTG
* * * * * * * *
13020 AAGTTCGCCATTGCGACTTAAA-CTTTTCCCTTCGTGCC
60 GA-TCCACCGTTACGGCTTAAATC-TTTCCCTT-ATGTC
** * * * *
13058 TTTAAGGTACTAGGTTTGCCATTGCGACTTAAGCATTTCCC-TTGTGTCTTCGTGGTACTGGATT
1 TTTGTGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCATTGT-T-TTCGTGGTACTGGATC
* *
13122 CGCCGTTGCGGCTTAAATCTTTCCCTTCATGT
64 CACCGTTACGGCTTAAATCTTTCCCTT-ATGT
13154 TTATGACTTG
Statistics
Matches: 233, Mismatches: 42, Indels: 33
0.76 0.14 0.11
Matches are distributed among these distances:
94 39 0.17
95 7 0.03
96 60 0.26
97 44 0.19
98 17 0.07
99 7 0.03
100 55 0.24
101 4 0.02
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.40
Consensus pattern (95 bp):
TTTGTGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCATTGTTTTCGTGGTACTGGATCCA
CCGTTACGGCTTAAATCTTTCCCTTATGTC
Found at i:12967 original size:49 final size:49
Alignment explanation
Indices: 12837--13153 Score: 224
Period size: 49 Copynumber: 6.5 Consensus size: 49
12827 GATTTACTGT
* * *
12837 TGCGGCTTAAATC-TTTCCCTT--TGTCTTTGTGGTACTAGG-TTCGCCAT
1 TGCGACTT-AATCTTTTCCCTTCATGTCTTCGTGGTACT-GGATTCGCCGT
* * * * *
12884 TGTGACTTAAACTTTTCCCAT--TGTTTTCGTGGTACTGGATCCGCCGT
1 TGCGACTTAATCTTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGT
* * *
12931 TACGGCTTAGATC-TTTCCCTTCATGTCTTCGTGGTACTGGATTCGCAGT
1 TGCGACTTA-ATCTTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGT
* * * * * *
12980 TGCGTCTTTAAATCTTTTCCCTTTATGTCTCCGAGGTACT-AAGTTCGCCAT
1 TGCGAC-TT-AATCTTTTCCCTTCATGTCTTCGTGGTACTGGA-TTCGCCGT
* * * *** * *
13031 TGCGACTTAAACTTTTCCCTTCGTGCCTTTAAGGTACTAGG-TTTGCCAT
1 TGCGACTTAATCTTTTCCCTTCATGTCTTCGTGGTACT-GGATTCGCCGT
* * *
13080 TGCGACTTAAGCATTTCCCTT-GTGTCTTCGTGGTACTGGATTCGCCGT
1 TGCGACTTAATCTTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGT
*
13128 TGCGGCTTAAATC-TTTCCCTTCATGT
1 TGCGACTT-AATCTTTTCCCTTCATGT
13154 TTATGACTTG
Statistics
Matches: 211, Mismatches: 45, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
46 5 0.02
47 47 0.22
48 35 0.17
49 82 0.39
50 8 0.04
51 34 0.16
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (49 bp):
TGCGACTTAATCTTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGT
Found at i:13426 original size:18 final size:18
Alignment explanation
Indices: 13400--13434 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13390 AAAATTGCCG
* *
13400 AATATTTACATGGAACAA
1 AATAATTACAAGGAACAA
13418 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
13435 GTATTAGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:24493 original size:28 final size:28
Alignment explanation
Indices: 24462--24524 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
24452 AAAATGAGAT
* *
24462 TTTTGGATACTCGAGGGTAAAATAGTAA
1 TTTTGGACACTCGAGGGCAAAATAGTAA
*
24490 TTTTGGACATTCGAGGGCAAAATAGTAA
1 TTTTGGACACTCGAGGGCAAAATAGTAA
24518 TTTTGGA
1 TTTTGGA
24525 AAAGTTTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGAGGGCAAAATAGTAA
Found at i:24556 original size:57 final size:58
Alignment explanation
Indices: 24488--24608 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
24478 GTAAAATAGT
** * *
24488 AATTTTGGACATTCGAGGGCAAAATAGTAATTTTGGAAAAGTTTAGGGTCAAAAATTG
1 AATTTTGGACATTCGAGGGCAAAATAGTAATTTTCAAAAAGTTCAGGGTCAAAAATGG
* * * *
24546 AATTTT-GACATTCGGGGGTAAAATGGTAATTTTCAAAAAGTTCGGGGTCAAAAATGG
1 AATTTTGGACATTCGAGGGCAAAATAGTAATTTTCAAAAAGTTCAGGGTCAAAAATGG
24603 AATTTT
1 AATTTT
24609 TTGAAGTTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 49 0.89
58 6 0.11
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.32
Consensus pattern (58 bp):
AATTTTGGACATTCGAGGGCAAAATAGTAATTTTCAAAAAGTTCAGGGTCAAAAATGG
Found at i:24674 original size:59 final size:58
Alignment explanation
Indices: 24606--24759 Score: 175
Period size: 59 Copynumber: 2.6 Consensus size: 58
24596 AAAATGGAAT
* ** *
24606 TTTTTGAAGTTCAAGGGT-AAAATAGTTGTTTTTGGAAAAAATCGAGGTCAAAAGCGAAA
1 TTTTGGAAGTTCAAGGGTAAAAAT-GTAATTTTTGG-AAAAATCAAGGTCAAAAGCGAAA
* * ** *
24665 TTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAAAATTAAGGTCAAAATTGGAA
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAGCGAAA
* *
24723 TTTTGGAAAGTTCGAGGGTAAAAATATAATTTTTGGA
1 TTTTGG-AAGTTCAAGGGTAAAAATGTAATTTTTGGA
24760 CAATTTAGGG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 24 0.30
59 52 0.64
60 5 0.06
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (58 bp):
TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAGCGAAA
Found at i:24698 original size:29 final size:30
Alignment explanation
Indices: 24665--24759 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 30
24655 AAAAGCGAAA
24665 TTTTGG-AAGTTTAAGGGTAAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTAAT
** * *
24694 TTTTGGAAAAATTAA-GGTCAAAATTGGAA-
1 TTTTGGAAAGTTTAAGGGT-AAAAATGTAAT
** *
24723 TTTTGGAAAGTTCGAGGGTAAAAATATAAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTAAT
24753 TTTTGGA
1 TTTTGGA
24760 CAATTTAGGG
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
29 27 0.53
30 24 0.47
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTTAAGGGTAAAAATGTAAT
Found at i:24747 original size:30 final size:30
Alignment explanation
Indices: 24472--24747 Score: 86
Period size: 29 Copynumber: 9.5 Consensus size: 30
24462 TTTTGGATAC
* * *
24472 TCGAGGGT-AAAATAGTAATTTTGGACA-T
1 TCGAGGGTAAAAATTGGAATTTTGGAAAGT
* * *
24500 TCGAGGG-CAAAATAGTAATTTTGGAAAAGT
1 TCGAGGGTAAAAATTGGAATTTTGG-AAAGT
* *
24530 T-TAGGGTCAAAAATT-GAATTTT-GACA-T
1 TCGAGGGT-AAAAATTGGAATTTTGGAAAGT
* **
24557 TCGGGGGT-AAAA-TGGTAATTTTCAAAAAGT
1 TCGAGGGTAAAAATTGG-AATTTT-GGAAAGT
*
24587 TCG-GGGTCAAAAA-TGGAATTTTTTG-AAGT
1 TCGAGGGT-AAAAATTGGAA-TTTTGGAAAGT
* * **
24616 TCAAGGGTAAAATAGTT-G-TTTTTGGAAAAAA
1 TCGAGGGTAAAA-A-TTGGAATTTTGG-AAAGT
* ** *
24647 TCGA-GGTCAAAAGCGAAATTTTGG-AAGT
1 TCGAGGGTAAAAATTGGAATTTTGGAAAGT
** * *
24675 TTAAGGGTAAAAA-TGTAATTTTTGGAAAAAT
1 TCGAGGGTAAAAATTGGAA-TTTTGG-AAAGT
* *
24706 T--AAGGTCAAAATTGGAATTTTGGAAAGT
1 TCGAGGGTAAAAATTGGAATTTTGGAAAGT
24734 TCGAGGGTAAAAAT
1 TCGAGGGTAAAAAT
24748 ATAATTTTTG
Statistics
Matches: 182, Mismatches: 37, Indels: 56
0.66 0.13 0.20
Matches are distributed among these distances:
25 1 0.01
26 5 0.03
27 8 0.04
28 41 0.23
29 56 0.31
30 44 0.24
31 26 0.14
32 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (30 bp):
TCGAGGGTAAAAATTGGAATTTTGGAAAGT
Found at i:25967 original size:5 final size:6
Alignment explanation
Indices: 25948--25978 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
25938 TTAAAAATGG
25948 AAATAA AAATAA AAATAA AAATAA AATATAA
1 AAATAA AAATAA AAATAA AAATAA AA-ATAA
25979 CTGATGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:26660 original size:17 final size:16
Alignment explanation
Indices: 26632--26712 Score: 81
Period size: 17 Copynumber: 4.8 Consensus size: 16
26622 AAATTTAAAG
* **
26632 TTTAAGTTTAAAATTA
1 TTTAAATTTAAAAAAA
26648 TTTCAAATTTAAACAAAA
1 TTT-AAATTTAAA-AAAA
26666 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAA-AAA
*
26683 TTTAAAATTAAAAATAAA
1 TTT-AAATTTAAAA-AAA
26701 TTTAAATTTAAA
1 TTTAAATTTAAA
26713 TTTAAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 4 0.07
17 31 0.56
18 20 0.36
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAAAAAA
Found at i:26679 original size:18 final size:18
Alignment explanation
Indices: 26647--26712 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
26637 GTTTAAAATT
26647 ATTTCAAATTT-AAACAAA
1 ATTT-AAATTTAAAACAAA
26665 ATTTAAATTTAAAAC-AA
1 ATTTAAATTTAAAACAAA
*
26682 ATTTAAAATTAAAA-ATAA
1 ATTTAAATTTAAAACA-AA
26700 ATTTAAATTTAAA
1 ATTTAAATTTAAA
26713 TTTAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 21 0.49
18 22 0.51
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTAAATTTAAAACAAA
Found at i:26705 original size:12 final size:12
Alignment explanation
Indices: 26685--26731 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
26675 AAAACAAATT
*
26685 TAAAATTAAAAA
1 TAAATTTAAAAA
**
26697 TAAATTTAAATT
1 TAAATTTAAAAA
26709 TAAATTTAAAAA
1 TAAATTTAAAAA
*
26721 TAAATCTAAAA
1 TAAATTTAAAA
26732 CCAATCTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:26707 original size:24 final size:24
Alignment explanation
Indices: 26680--26730 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
26670 AATTTAAAAC
*
26680 AAATTTAAAATTAAAAATAAATTT
1 AAATTTAAAATTAAAAATAAATCT
*
26704 AAATTTAAATTTAAAAATAAATCT
1 AAATTTAAAATTAAAAATAAATCT
26728 AAA
1 AAA
26731 ACCAATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTTAAAATTAAAAATAAATCT
Found at i:26718 original size:18 final size:17
Alignment explanation
Indices: 26620--26714 Score: 68
Period size: 17 Copynumber: 5.4 Consensus size: 17
26610 AACTTTGAAA
*
26620 TTAAATTTAAAGTTTAAGT
1 TTAAA-TTAAA-TTTAAAT
26639 TTAAAATT--ATTTCAAAT
1 TT-AAATTAAATTT-AAAT
**
26656 TTAAACAAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
26673 TTAAAACAAATTTAAAAT
1 TTAAATTAAATTT-AAAT
* *
26691 TAAAAATAAATTTAAAT
1 TTAAATTAAATTTAAAT
26708 TTAAATT
1 TTAAATT
26715 TAAAAATAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
16 6 0.10
17 30 0.48
18 19 0.31
19 4 0.06
20 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:26730 original size:6 final size:6
Alignment explanation
Indices: 26620--26718 Score: 71
Period size: 6 Copynumber: 16.8 Consensus size: 6
26610 AACTTTGAAA
* * **
26620 TTAAAT TTAAAGT TTAAGT TTAAAA TT--AT TTCAAAT TTAAA- CAAAAT
1 TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT
** * * *
26667 TTAAAT TTAAA- ACAAAT TTAAAA TTAAAA ATAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
26714 TTAAA
1 TTAAA
26719 AATAAATCTA
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
4 3 0.04
5 6 0.08
6 53 0.75
7 9 0.13
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:26730 original size:18 final size:17
Alignment explanation
Indices: 26647--26712 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
26637 GTTTAAAATT
*
26647 ATTTCAAATTTAAACAAA
1 ATTT-AAATTTAAAAAAA
*
26665 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAAAAA
*
26682 ATTTAAAATTAAAAATAA
1 ATTTAAATTTAAAAA-AA
26700 ATTTAAATTTAAA
1 ATTTAAATTTAAA
26713 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 24 0.57
18 18 0.43
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAAATTTAAAAAAA
Found at i:33200 original size:25 final size:25
Alignment explanation
Indices: 33172--33219 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
33162 AAAAAGCAAT
33172 AAAAATTAATTATATCAATATATTC
1 AAAAATTAATTATATCAATATATTC
33197 AAAAATTAATTATATCAATATAT
1 AAAAATTAATTATATCAATATAT
33220 GTAACATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATTAATTATATCAATATATTC
Found at i:41532 original size:24 final size:23
Alignment explanation
Indices: 41497--41546 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
41487 TGTGAAGTTG
*
41497 TATATATTTAAA-ATTTAATAAA
1 TATATATTTAAATATTAAATAAA
*
41519 TATATATTACTAAATATTAAATTAA
1 TATATATT--TAAATATTAAATAAA
41544 TAT
1 TAT
41547 TAACAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
24 4 0.17
25 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TATATATTTAAATATTAAATAAA
Found at i:52288 original size:31 final size:31
Alignment explanation
Indices: 52250--52312 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
52240 AAAAAAAAAA
52250 AACTTAAATAAAAACTTACAAATAATTCAAT
1 AACTTAAATAAAAACTTACAAATAATTCAAT
* ** *
52281 AACTTAAATAAAAATTTTTAAATAATTTAAT
1 AACTTAAATAAAAACTTACAAATAATTCAAT
52312 A
1 A
52313 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (31 bp):
AACTTAAATAAAAACTTACAAATAATTCAAT
Found at i:56563 original size:17 final size:18
Alignment explanation
Indices: 56525--56563 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56515 TTATTGATTC
*
56525 TCAATATAATTGATTTGA
1 TCAATATAATTGATTAGA
*
56543 TCAATTTAATTG-TTAGA
1 TCAATATAATTGATTAGA
56560 TCAA
1 TCAA
56564 ACCATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (18 bp):
TCAATATAATTGATTAGA
Found at i:61008 original size:21 final size:20
Alignment explanation
Indices: 60974--61016 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
60964 ATATTTTATA
*
60974 TTTTAAAACCAAATATAAAAT
1 TTTTAAAACCAAAT-CAAAAT
* *
60995 TTTTAATACTAAATCAAAAT
1 TTTTAAAACCAAATCAAAAT
61015 TT
1 TT
61017 ACCGATTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAACCAAATCAAAAT
Found at i:61781 original size:3 final size:3
Alignment explanation
Indices: 61773--61798 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61763 ATTCCATCCA
61773 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
61799 TTTTCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:64099 original size:22 final size:21
Alignment explanation
Indices: 64064--64106 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
64054 GCTCATATTA
64064 ATTTTAATTTTTTTAAAAATT
1 ATTTTAATTTTTTTAAAAATT
* *
64085 ATTTTATTTTATTTTAATAATT
1 ATTTTAATTT-TTTTAAAAATT
64107 TTATACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTAATTTTTTTAAAAATT
Found at i:64226 original size:18 final size:17
Alignment explanation
Indices: 64205--64257 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
64195 TATGTATTTT
64205 AAATTATATAATATATAA
1 AAATTATATAATATA-AA
* *
64223 AAATAACATAATATAAA
1 AAATTATATAATATAAA
* *
64240 ATATTATA-AATTTAAA
1 AAATTATATAATATAAA
64256 AA
1 AA
64258 CAGATCAAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:64460 original size:20 final size:20
Alignment explanation
Indices: 64435--64473 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
64425 TTCCAATAAA
64435 ATAAATTTTAGTT-TAAAATG
1 ATAAATTTTA-TTATAAAATG
64455 ATAAATTTTATTATAAAAT
1 ATAAATTTTATTATAAAAT
64474 TTTCAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATAAATTTTATTATAAAATG
Found at i:66825 original size:31 final size:32
Alignment explanation
Indices: 66763--66825 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
66753 TAGATACATG
*
66763 AAATATGATATGAATACACAAAATTATCGATC
1 AAATATGATATGAATACACAAAATTACCGATC
*
66795 AAATATGATATGAATACAC-GAATTACCGATC
1 AAATATGATATGAATACACAAAATTACCGATC
66826 GACAACCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (32 bp):
AAATATGATATGAATACACAAAATTACCGATC
Found at i:71050 original size:19 final size:18
Alignment explanation
Indices: 70999--71050 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
70989 ATAATGTATC
*
70999 TTTTTCAATGATTTAATA
1 TTTTTCAATGAATTAATA
* * *
71017 CTTTCCAATGCATTAATA
1 TTTTTCAATGAATTAATA
71035 TTTTTTCAATGAATTA
1 -TTTTTCAATGAATTA
71051 TAAAATAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTTCAATGAATTAATA
Found at i:76094 original size:17 final size:17
Alignment explanation
Indices: 76072--76104 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
76062 GTAGTTACAA
76072 GAAGATGAAAGGTTAAG
1 GAAGATGAAAGGTTAAG
*
76089 GAAGATGGAAGGTTAA
1 GAAGATGAAAGGTTAA
76105 AAGTTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (17 bp):
GAAGATGAAAGGTTAAG
Done.