Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003963.1 Kokia drynarioides strain JFW-HI SEQ_117056, 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: 116845
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:2908 original size:18 final size:17
Alignment explanation
Indices: 2885--2932 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
2875 TTCGCGTGCT
2885 TATTTTATTTATTTATAA
1 TATTTTATTTATTTAT-A
* *
2903 TATTTTATTAATATATA
1 TATTTTATTTATTTATA
*
2920 TTTTTTA-TTATTT
1 TATTTTATTTATTT
2933 TATGTCTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTATTTATTTATA
Found at i:6919 original size:28 final size:28
Alignment explanation
Indices: 6861--6921 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
6851 ATAGATTTAT
* * * *
6861 AATTTAGTTTTTTATTTTTATTTTTAGA
1 AATTTAGTCTTCTATTTTTATATTTACA
6889 AATTTAGTCTTCTACTTTTTATATTT-CA
1 AATTTAGTCTTCTA-TTTTTATATTTACA
6917 AATTT
1 AATTT
6922 CACTTTCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (28 bp):
AATTTAGTCTTCTATTTTTATATTTACA
Found at i:10067 original size:22 final size:22
Alignment explanation
Indices: 10041--10094 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
10031 ATATCAAAAC
*
10041 AATAACAATATAATAAAGAAAT
1 AATAACAAAATAATAAAGAAAT
* * **
10063 GATAATAAAATAATAGTGAAAT
1 AATAACAAAATAATAAAGAAAT
10085 AATAACAAAA
1 AATAACAAAA
10095 CAACAACAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (22 bp):
AATAACAAAATAATAAAGAAAT
Found at i:16513 original size:24 final size:24
Alignment explanation
Indices: 16485--16532 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16475 AAAAATCAAA
* **
16485 ATATTTATAAAAATTCTAAAATTT
1 ATATTTAAAAAAATTAAAAAATTT
16509 ATATTTAAAAAAATTAAAAAATTT
1 ATATTTAAAAAAATTAAAAAATTT
16533 CTAGAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTTAAAAAAATTAAAAAATTT
Found at i:19537 original size:20 final size:20
Alignment explanation
Indices: 19494--19537 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
19484 TACATATCAT
***
19494 TATTGTTCATGATATGATTT
1 TATTGTTCATGATATGACCC
*
19514 TATTGTTCATGATTTGACCC
1 TATTGTTCATGATATGACCC
19534 TATT
1 TATT
19538 ATTTTTAGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (20 bp):
TATTGTTCATGATATGACCC
Found at i:21335 original size:16 final size:17
Alignment explanation
Indices: 21300--21332 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21290 TACAATGATA
21300 AATATTAATTTTATTTT
1 AATATTAATTTTATTTT
21317 AATA-TAATTTTGATTT
1 AATATTAATTTT-ATTT
21333 AATTTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATATTAATTTTATTTT
Found at i:23967 original size:22 final size:21
Alignment explanation
Indices: 23935--24001 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
23925 AGGTGCTTTT
23935 TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTTG-TA
* *
23957 TTTTTTGCTGTTTTTG-TGT-
1 TTTTTTACTGTTTTGGTTGTA
*
23976 TTTTTTACTATTTTGGTTGTTA
1 TTTTTTACTGTTTTGGTTG-TA
23998 TTTT
1 TTTT
24002 CGTGTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 13 0.35
20 3 0.08
21 3 0.08
22 18 0.49
ACGTcount: A:0.07, C:0.06, G:0.16, T:0.70
Consensus pattern (21 bp):
TTTTTTACTGTTTTGGTTGTA
Found at i:24012 original size:41 final size:41
Alignment explanation
Indices: 23934--24023 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
23924 TAGGTGCTTT
* *
23934 TTTTTTTACTGTTTTGGTTGCTATTTTTTGCTGTTTTTGTG
1 TTTTTTTACTATTTTGGTTGCTATTTTGTGCTGTTTTTGTG
* * *
23975 TTTTTTTACTATTTTGGTTGTTATTTTCGTG-TTTTTTTTTG
1 TTTTTTTACTATTTTGGTTGCTATTTT-GTGCTGTTTTTGTG
24016 TTATTTTT
1 TT-TTTTT
24024 GTTGCTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 35 0.83
42 7 0.17
ACGTcount: A:0.07, C:0.06, G:0.16, T:0.72
Consensus pattern (41 bp):
TTTTTTTACTATTTTGGTTGCTATTTTGTGCTGTTTTTGTG
Found at i:24064 original size:43 final size:43
Alignment explanation
Indices: 24016--24098 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
24006 TTTTTTTTTG
**
24016 TTATTTTTGTTGCTATTATTGTTGTT-TTTAATGTTGTTTGCTA
1 TTATTTTTACTGCTATTATTGTTGTTATTT-ATGTTGTTTGCTA
* * *
24059 TTATTTTTACTGCTGTTTTTGTTGTTATTTTTGTTGTTTG
1 TTATTTTTACTGCTATTATTGTTGTTATTTATGTTGTTTG
24099 GATGTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 31 0.91
44 3 0.09
ACGTcount: A:0.11, C:0.05, G:0.17, T:0.67
Consensus pattern (43 bp):
TTATTTTTACTGCTATTATTGTTGTTATTTATGTTGTTTGCTA
Found at i:28796 original size:3 final size:3
Alignment explanation
Indices: 28775--28809 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
28765 GTGGTTGAAA
* *
28775 AAT AAT GAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28810 AATTAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30110 original size:22 final size:21
Alignment explanation
Indices: 30068--30110 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
30058 AATAGTATTC
*
30068 TTAAAAAATTCAATATTTTAA
1 TTAAAAAATTCAATATATTAA
30089 TTAAAATAATT-AATAATATTAA
1 TTAAAA-AATTCAAT-ATATTAA
30111 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAATTCAATATATTAA
Found at i:30861 original size:12 final size:12
Alignment explanation
Indices: 30834--30868 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
30824 CTTATTAAAT
30834 AATAAAA-AACA
1 AATAAAACAACA
30845 AATAAAACAACA
1 AATAAAACAACA
*
30857 TATAAAACAACA
1 AATAAAACAACA
30869 CTGGTCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (12 bp):
AATAAAACAACA
Found at i:35900 original size:6 final size:7
Alignment explanation
Indices: 35883--35908 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35873 AGATTTAAGC
35883 TTTTTAA
1 TTTTTAA
35890 TTTTTAA
1 TTTTTAA
35897 TTTTTAA
1 TTTTTAA
35904 TTTTT
1 TTTTT
35909 CGACTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:43499 original size:17 final size:18
Alignment explanation
Indices: 43477--43517 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
43467 GTTAAATGAA
43477 AATAGTTCTA-TTTTGAT
1 AATAGTTCTATTTTTGAT
43494 AATAGTTCTATTTTTTGAT
1 AATAGTTCTA-TTTTTGAT
43513 AATAG
1 AATAG
43518 ATTTTTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (18 bp):
AATAGTTCTATTTTTGAT
Found at i:44523 original size:20 final size:21
Alignment explanation
Indices: 44493--44539 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
44483 TTGCCATTAA
44493 AAATGCTTGATTTTAAT-TTCG
1 AAAT-CTTGATTTTAATATTCG
*
44514 AAATCTTGATTTTATTATTCG
1 AAATCTTGATTTTAATATTCG
44535 AAATC
1 AAATC
44540 GATAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (21 bp):
AAATCTTGATTTTAATATTCG
Found at i:51063 original size:23 final size:24
Alignment explanation
Indices: 51030--51080 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
51020 ACAAAAATGA
51030 TAAATTTAAAATTTATATTAATAT
1 TAAATTTAAAATTTATATTAATAT
51054 TAAA-TTAAAATTTATATTAATAT
1 TAAATTTAAAATTTATATTAATAT
51077 TAAA
1 TAAA
51081 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATTTAAAATTTATATTAATAT
Found at i:51086 original size:23 final size:23
Alignment explanation
Indices: 51037--51086 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
51027 TGATAAATTT
**
51037 AAAATTTATATTAATATTAAATT
1 AAAATTTATATTAATATTAAAAA
51060 AAAATTTATATTAATATTAAAAA
1 AAAATTTATATTAATATTAAAAA
51083 AAAA
1 AAAA
51087 AAAAAAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTTATATTAATATTAAAAA
Found at i:51811 original size:18 final size:17
Alignment explanation
Indices: 51779--51812 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
51769 TTTTTTTCAT
51779 TTAATAAAATATTAATA
1 TTAATAAAATATTAATA
*
51796 TTAATATAAATTTTAAT
1 TTAATA-AAATATTAAT
51813 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATAAAATATTAATA
Found at i:53935 original size:292 final size:292
Alignment explanation
Indices: 53405--53952 Score: 918
Period size: 292 Copynumber: 1.9 Consensus size: 292
53395 AGAAAATTCG
* * * **
53405 TTCTTGATTCTTACAATACAAGGTATTCATCAAAATGCGGTAATTCTTTTGGCCCATAGACAAAC
1 TTCTCGATTCTTACAATACAAGGCATTCACCAAAATGCAATAATTCTTTTGGCCCATAGACAAAC
* *
53470 CCCTCGTCTTCCAATCTTTGAGCAATTCAAAAGCATCATTACTCTTCCCTCCACTACACAACTCT
66 CCCTCGTCTTCCAATCCTCGAGCAATTCAAAAGCATCATTACTCTTCCCTCCACTACACAACTCT
*
53535 TCTAATACGGTCTTATAAGTCAATAAATACGGCGCCATCGAATTTTCCAACATATCATAAACAAC
131 TCCAATACGGTCTTATAAGTCAATAAATACGGCGCCATCGAATTTTCCAACATATCATAAACAAC
* *
53600 ATCAATAGCATCATCAAGCCTTTGCTCCCTTGCAAGGCTACAAATCAGAATCATATAAGCAAGAA
196 ATCAATAGCATCATCAAGCCTTTGCTCCATTGCAAGACTACAAATCAGAATCATATAAGCAAGAA
53665 CCACTTCGTTTTTGGACCATAGAGACCGGTCA
261 CCACTTCGTTTTTGGACCATAGAGACCGGTCA
* *
53697 TTCTCGATTCTTACAATGCAAGGCATTCACCAAAATGCAATAATTCTTTTGGCCCATAGACAAAT
1 TTCTCGATTCTTACAATACAAGGCATTCACCAAAATGCAATAATTCTTTTGGCCCATAGACAAAC
* * *
53762 CCCTCTTCTTCCACTCCTCGAGCAATTCAAAAGCATCATTACTCTTCCCTCCCCTACACAACTCT
66 CCCTCGTCTTCCAATCCTCGAGCAATTCAAAAGCATCATTACTCTTCCCTCCACTACACAACTCT
*
53827 TCCAATACGGTCTTATAAGTCAATAAAT-CTGGCGCCATCGAATTTTCCAACATATCGTAAACAA
131 TCCAATACGGTCTTATAAGTCAATAAATAC-GGCGCCATCGAATTTTCCAACATATCATAAACAA
* *
53891 CATCAATGGCGTCATCAAGCCTTTGCTCCATTGCAAGACTACAAATCAGAATCATATAAGCA
195 CATCAATAGCATCATCAAGCCTTTGCTCCATTGCAAGACTACAAATCAGAATCATATAAGCA
53953 CTCCCTTTCG
Statistics
Matches: 237, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
291 1 0.00
292 236 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (292 bp):
TTCTCGATTCTTACAATACAAGGCATTCACCAAAATGCAATAATTCTTTTGGCCCATAGACAAAC
CCCTCGTCTTCCAATCCTCGAGCAATTCAAAAGCATCATTACTCTTCCCTCCACTACACAACTCT
TCCAATACGGTCTTATAAGTCAATAAATACGGCGCCATCGAATTTTCCAACATATCATAAACAAC
ATCAATAGCATCATCAAGCCTTTGCTCCATTGCAAGACTACAAATCAGAATCATATAAGCAAGAA
CCACTTCGTTTTTGGACCATAGAGACCGGTCA
Found at i:60354 original size:25 final size:25
Alignment explanation
Indices: 60326--60373 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
60316 ATAAATTGTT
* *
60326 ATTACATACATGTAAATATATCTCA
1 ATTACATACATATAAAAATATCTCA
*
60351 ATTACATTCATATAAAAATATCT
1 ATTACATACATATAAAAATATCT
60374 ATATATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTACATACATATAAAAATATCTCA
Found at i:61248 original size:4 final size:4
Alignment explanation
Indices: 61241--61322 Score: 62
Period size: 4 Copynumber: 20.8 Consensus size: 4
61231 CTGGCAGAAG
* *
61241 AAGA AAGA AAGA AAGAA AAGA AAGA AAGA AAG- AAGG AAGA ATG- AAGA
1 AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * * * *
61288 AGGA ATGA GAGAA AAGA AAG- AAGA ATGA GAGA AAG
1 AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAG
61323 GTAGTGTGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
3 8 0.13
4 46 0.75
5 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (4 bp):
AAGA
Found at i:61263 original size:17 final size:18
Alignment explanation
Indices: 61236--61322 Score: 83
Period size: 17 Copynumber: 4.9 Consensus size: 18
61226 ACAAACTGGC
61236 AGAAGAAGAAAGAAAGAA
1 AGAAGAAGAAAGAAAGAA
61254 AGAA-AAGAAAGAAAGAA
1 AGAAGAAGAAAGAAAGAA
*
61271 AGAAGGAAGAATG-AAGAA
1 AGAA-GAAGAAAGAAAGAA
* *
61289 GGAATG-AGAGA-AAAGAA
1 AGAA-GAAGAAAGAAAGAA
*
61306 AGAAGAATGAGAGAAAG
1 AGAAGAA-GAAAGAAAG
61323 GTAGTGTGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 29 0.51
18 17 0.30
19 10 0.18
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAAAGAAAGAA
Found at i:61800 original size:24 final size:24
Alignment explanation
Indices: 61765--61810 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61755 ATGTTGAACT
*
61765 TAGAAAATGAAGACCCAACTCCAG
1 TAGAAAAAGAAGACCCAACTCCAG
*
61789 TAGAAAAAGAAGATCCAACTCC
1 TAGAAAAAGAAGACCCAACTCC
61811 GTGTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (24 bp):
TAGAAAAAGAAGACCCAACTCCAG
Found at i:65241 original size:30 final size:30
Alignment explanation
Indices: 65147--65241 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
65137 CCAAAATAGG
*
65147 TTATTTATTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
* * * * * * **
65177 TTATATACCAAAATGATATCCACA-CACCA-
1 TTATTTACTAAAATGGTA-CAAAATAAATAT
65206 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
65236 TTATTT
1 TTATTT
65242 TGTACCATTT
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.38
30 22 0.49
31 3 0.07
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (30 bp):
TTATTTACTAAAATGGTACAAAATAAATAT
Found at i:65294 original size:16 final size:16
Alignment explanation
Indices: 65273--65321 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
65263 GGATGAAGAT
65273 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
65289 ATTATTTT--TATATT-
1 ATTATTTTGGTA-ATTA
65303 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
65318 ATTA
1 ATTA
65322 GCTAAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:65726 original size:21 final size:21
Alignment explanation
Indices: 65701--65741 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
65691 TTACTTACTA
* *
65701 TTACTGACAACATAAAATTAC
1 TTACTAACAAAATAAAATTAC
*
65722 TTACTAACAAAATTAAATTA
1 TTACTAACAAAATAAAATTA
65742 AAATAAATTA
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:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (21 bp):
TTACTAACAAAATAAAATTAC
Found at i:66042 original size:13 final size:13
Alignment explanation
Indices: 66024--66052 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
66014 ACAAATTAAA
66024 AAATTTTAAAAAT
1 AAATTTTAAAAAT
66037 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
66049 AAAT
1 AAAT
66053 ACACTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:69132 original size:75 final size:75
Alignment explanation
Indices: 69046--69194 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
69036 TCATGCCACT
*
69046 GGTAAGATCATTGTGGAGCCTTAATCTATGAAATATTACTTTACACTTTCTACAGTGATGCTTGG
1 GGTAAGATCATTGTGGAGCCTTAATCTATGAAATATTACTTTACACTTACTACAGTGATGCTTGG
69111 AGGTCATGCC
66 AGGTCATGCC
*
69121 GGTAAGATCATTGTGGAGCCTTAATCTATGAAATATTACTTTATACTTACTACAGTGATGCTTGG
1 GGTAAGATCATTGTGGAGCCTTAATCTATGAAATATTACTTTACACTTACTACAGTGATGCTTGG
69186 AGGTCATGC
66 AGGTCATGC
69195 TGCTTGTGTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (75 bp):
GGTAAGATCATTGTGGAGCCTTAATCTATGAAATATTACTTTACACTTACTACAGTGATGCTTGG
AGGTCATGCC
Found at i:70060 original size:19 final size:19
Alignment explanation
Indices: 70036--70075 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
70026 TCTATAGTTG
*
70036 AAGCATACATTGAATAAAA
1 AAGCATACAGTGAATAAAA
70055 AAGCATACAGTGAATAAAA
1 AAGCATACAGTGAATAAAA
70074 AA
1 AA
70076 TTACTATCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.17
Consensus pattern (19 bp):
AAGCATACAGTGAATAAAA
Found at i:71585 original size:18 final size:17
Alignment explanation
Indices: 71543--71585 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
71533 ATTTTAAGTT
*
71543 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
71560 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
71578 TATAATTT
1 TATAATTT
71586 AAATCACGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:72070 original size:159 final size:167
Alignment explanation
Indices: 71856--72167 Score: 415
Period size: 176 Copynumber: 1.9 Consensus size: 167
71846 TCTTATGAAC
* *
71856 ACTTTTAATCTCAATTGATTTCGTTCTTAAGTTTTAATATAATAGATACT----TA--AAT-ATA
1 ACTTTTAATCTCAATCGATTCCGTTCTTAAGTTTTAATATAATAGATACTGAAATAGTAATAATA
* *
71914 AATAATTATTTTCCAAATATG-AATTAATACAAAATCTAAAACCTACCAATTAACATTTCGAAAG
66 GATAATTATTTTCCAAAAATGAAATTAATACAAAATCTAAAACCTACCAATTAACATTTCGAAAG
*
71978 ATTTCTTGTAAAATTTAATCTAACTCATCCCATGGAT
131 ATTTCTTGCAAAATTTAATCTAACTCATCCCATGGAT
*
72015 ACTTTTAATCTCAATCGATTCCGTTCTTAAGTTTTAATATAATAGATGCTGAAATATGGTAACAA
1 ACTTTTAATCTCAATCGATTCCGTTCTTAAGTTTTAATATAATAGATACTGAAATA--GT----A
*
72080 ATAATAGATAATTATTTTCCAAAAATGAAATAATTAATACAAAATCTAGAACCTACCAATTAACA
60 ATAATAGATAATTATTTTCCAAAAATG--A-AATTAATACAAAATCTAAAACCTACCAATTAACA
*
72145 TTTCGAGAGATTTCTTGCAAAAT
122 TTTCGAAAGATTTCTTGCAAAAT
72168 CATCGACGGT
Statistics
Matches: 128, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
159 47 0.37
163 2 0.02
171 3 0.02
172 22 0.17
176 54 0.42
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (167 bp):
ACTTTTAATCTCAATCGATTCCGTTCTTAAGTTTTAATATAATAGATACTGAAATAGTAATAATA
GATAATTATTTTCCAAAAATGAAATTAATACAAAATCTAAAACCTACCAATTAACATTTCGAAAG
ATTTCTTGCAAAATTTAATCTAACTCATCCCATGGAT
Found at i:81678 original size:13 final size:13
Alignment explanation
Indices: 81660--81684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81650 CATACATTTT
81660 TTATTATAATTGA
1 TTATTATAATTGA
81673 TTATTATAATTG
1 TTATTATAATTG
81685 TTTGTATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATTATAATTGA
Found at i:82115 original size:21 final size:21
Alignment explanation
Indices: 82089--82133 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
82079 TATAATATAA
82089 ATAATTTACAGATAAATTCTC
1 ATAATTTACAGATAAATTCTC
82110 ATAATTTACAGATAAATTCTC
1 ATAATTTACAGATAAATTCTC
82131 ATA
1 ATA
82134 TAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (21 bp):
ATAATTTACAGATAAATTCTC
Found at i:83037 original size:35 final size:35
Alignment explanation
Indices: 82991--83063 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
82981 CTGTTAAATA
82991 TAACAGTTATGGCGGAGGTGCCGATGCTTTGAAAG
1 TAACAGTTATGGCGGAGGTGCCGATGCTTTGAAAG
83026 TAACAGTTATGGCGGAGGTGCCGATGCTTTGAAAG
1 TAACAGTTATGGCGGAGGTGCCGATGCTTTGAAAG
83061 TAA
1 TAA
83064 TCTTCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (35 bp):
TAACAGTTATGGCGGAGGTGCCGATGCTTTGAAAG
Found at i:87542 original size:17 final size:17
Alignment explanation
Indices: 87510--87543 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
87500 CATTAACAAT
87510 TGAATCTAAATTTTAAA
1 TGAATCTAAATTTTAAA
87527 TGAAT-TAAATTCTTAAA
1 TGAATCTAAATT-TTAAA
87544 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TGAATCTAAATTTTAAA
Found at i:90192 original size:7 final size:7
Alignment explanation
Indices: 90180--90204 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
90170 TTTTATAGAC
90180 ATTTCAA
1 ATTTCAA
90187 ATTTCAA
1 ATTTCAA
90194 ATTTCAA
1 ATTTCAA
90201 ATTT
1 ATTT
90205 AATTGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTCAA
Found at i:92558 original size:42 final size:42
Alignment explanation
Indices: 92512--92611 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
92502 TCTGCCCAGC
* *
92512 CCACCACAATCACCA-TCATACAATAAGCTGCCGTCTCCACCA
1 CCACCACAACCACCACT-ATACAATAAGCTGCCCTCTCCACCA
*
92554 CCACCACCACCACCACTATACAATAAGCTGCCCTCTCCACCA
1 CCACCACAACCACCACTATACAATAAGCTGCCCTCTCCACCA
* *
92596 CCACCACCAGCACCAC
1 CCACCACAACCACCAC
92612 CTCATTATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.49, G:0.06, T:0.13
Consensus pattern (42 bp):
CCACCACAACCACCACTATACAATAAGCTGCCCTCTCCACCA
Found at i:99354 original size:21 final size:21
Alignment explanation
Indices: 99329--99378 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
99319 ATAATAGCAT
* *
99329 AATCCTAATATAAAGTTTAGA
1 AATCCAAACATAAAGTTTAGA
*
99350 AATCCAAACATAAAGTTTATA
1 AATCCAAACATAAAGTTTAGA
99371 AATCCAAA
1 AATCCAAA
99379 TCACATAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (21 bp):
AATCCAAACATAAAGTTTAGA
Found at i:106605 original size:6 final size:6
Alignment explanation
Indices: 106596--106663 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
106586 TTTAATTTAT
* * * *
106596 TTTAAA TTTAGA TTT-AT TTTTAA TTTAAA -TT-AA TCTTAAA TTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
106642 TTT-AA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
106664 TTTCAAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 35 0.70
7 3 0.06
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:106663 original size:17 final size:17
Alignment explanation
Indices: 106589--106666 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
106579 TTTTTTTTTT
*
106589 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
* * *
106606 GATTTATTTTTAATTTA
1 AATTTAATTTAAATTTA
*
106623 AA-TTAATCTTAAATTCA
1 AATTTAAT-TTAAATTTA
106640 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
106657 AATTTAATTT
1 AATTTAATTT
106667 CAAAATACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 4 0.08
17 43 0.83
18 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:106665 original size:11 final size:11
Alignment explanation
Indices: 106589--106666 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
106579 TTTTTTTTTT
*
106589 AATTTATTTTA
1 AATTTAATTTA
106600 AATTTAGATTTA
1 AATTTA-ATTTA
**
106612 TTTTTAATTTA
1 AATTTAATTTA
106623 AA-TTAATCTTA
1 AATTTAAT-TTA
*
106634 AATTCAAATTT-
1 AATT-TAATTTA
106645 AATTTAAATTTA
1 AATTT-AATTTA
106657 AATTTAATTT
1 AATTTAATTT
106667 CAAAATACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
10 5 0.09
11 30 0.56
12 16 0.30
13 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:108521 original size:30 final size:29
Alignment explanation
Indices: 108485--108689 Score: 195
Period size: 30 Copynumber: 6.9 Consensus size: 29
108475 AGAAGGTCCC
*
108485 GAAACTTCCAAAAATTCCATATTTGACCTT
1 GAAACTTCCAAAAATTCCAT-TTTGACCCT
* * * *
108515 GAAACTTCTAAAAAATCTATTTTTACACCT
1 GAAACTTCCAAAAATTCCATTTTGAC-CCT
108545 -AAACTTCCAAAAATTCCATTTTTGACCCT
1 GAAACTTCCAAAAATTCCA-TTTTGACCCT
* *
108574 AAAACTTCCAAAAAATTCCATTTTTACCCCT
1 GAAACTTCC-AAAAATTCCATTTTGA-CCCT
*
108605 G-AACTTCC-AAAATTCCATTTTTGACCCC
1 GAAACTTCCAAAAATTCCA-TTTTGACCCT
108633 GAAACTTCCAAAAATTACCATTTTG-CCCT
1 GAAACTTCCAAAAATT-CCATTTTGACCCT
* * *
108662 CAAA-TGTCTAAAAACTCCATTTTCGACC
1 GAAACT-TCCAAAAATTCCATTTT-GACC
108690 TCAAAACTCT
Statistics
Matches: 146, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
28 21 0.14
29 50 0.34
30 58 0.40
31 17 0.12
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
GAAACTTCCAAAAATTCCATTTTGACCCT
Found at i:108579 original size:59 final size:60
Alignment explanation
Indices: 108486--108656 Score: 240
Period size: 59 Copynumber: 2.9 Consensus size: 60
108476 GAAGGTCCCG
* * * *
108486 AAACTTCCAAAAATTCCATATTTGACCTTGAAACTTCTAAAAAA-TCTATTTTTACACCT
1 AAACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAAATTCCATTTTTACACCT
* *
108545 AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAAATTCCATTTTTACACCT
* *
108605 GAACTTCC-AAAATTCCATTTTTGACCCCGAAACTTCC-AAAAATTACCATTTT
1 AAACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAAATT-CCATTTT
108657 GCCCTCAAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
58 7 0.07
59 74 0.73
60 20 0.20
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAAATTCCATTTTTACACCT
Found at i:108681 original size:59 final size:59
Alignment explanation
Indices: 108493--108697 Score: 186
Period size: 59 Copynumber: 3.5 Consensus size: 59
108483 CCGAAACTTC
* *** * * *
108493 CAAAAATTCCATATTTGACCTTGAAACTTCTAAAAAA-TCTATTTTTACACCT-AAACTT
1 CAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATTCCATTTTTACCCCTCAAA-TT
* * *
108551 CCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAAATTCCATTTTTACCCCTGAACTT
1 -CAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATTCCATTTTTACCCCTCAAATT
* * *
108611 CCAAAATTCCATTTTTGACCCCGAAACTTCC-AAAAATTACCA-TTTT-GCCCTCAAATGT
1 CAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATT-CCATTTTTACCCCTCAAAT-T
* * *
108669 CTAAAAACTCCATTTTCGACCTCAAAACT
1 C-AAAAATTCCATTTTTGACCCCAAAACT
108698 CTCAAAATTA
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 7 0.06
58 13 0.11
59 86 0.70
60 15 0.12
61 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATTCCATTTTTACCCCTCAAATT
Found at i:108704 original size:29 final size:28
Alignment explanation
Indices: 108613--108704 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
108603 CTGAACTTCC
* * * *
108613 AAAATTCCATTTTTGACCCCGAAACTTCCA
1 AAAACTCCA-TTTTGACCTCAAAAC-TCTA
* * **
108643 AAAATTACCATTTTGCCCTCAAATGTCTA
1 AAAACT-CCATTTTGACCTCAAAACTCTA
*
108672 AAAACTCCATTTTCGACCTCAAAACTCTC
1 AAAACTCCATTTT-GACCTCAAAACTCTA
108701 AAAA
1 AAAA
108705 TTACTCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.14
29 23 0.47
30 16 0.33
31 3 0.06
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAACTCCATTTTGACCTCAAAACTCTA
Found at i:111490 original size:24 final size:25
Alignment explanation
Indices: 111443--111495 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
111433 TGTGTGTATT
*
111443 ATATATTTATAATAAAATTTATAAG
1 ATATATTTATAATAAAATTTATAAA
*
111468 ATATA-TTAT-ATAAATTTTGATAAA
1 ATATATTTATAATAAAATTT-ATAAA
111492 ATAT
1 ATAT
111496 TAAGCACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 12 0.48
25 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATATTTATAATAAAATTTATAAA
Found at i:111599 original size:18 final size:18
Alignment explanation
Indices: 111564--111606 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
111554 AATAAATATA
111564 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
111583 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
111601 AA-AAAT
1 AATAAAT
111607 AAAATAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:113986 original size:25 final size:27
Alignment explanation
Indices: 113911--114002 Score: 92
Period size: 25 Copynumber: 3.7 Consensus size: 27
113901 ATGCTTTTGA
113911 ATAATAAAA-TA-AT-TTTAACATAAT
1 ATAATAAAATTATATATTTAACATAAT
* *
113935 AT-ATAAAATTATATATTT-TCATTAT
1 ATAATAAAATTATATATTTAACATAAT
* *
113960 ATAATTACA-TAT-TATTTAACATAAT
1 ATAATAAAATTATATATTTAACATAAT
113985 AT-ATAAAATTATATATTT
1 ATAATAAAATTATATATTT
114003 TCTAATTGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
23 6 0.11
24 13 0.25
25 22 0.42
26 12 0.23
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAATAAAATTATATATTTAACATAAT
Found at i:114874 original size:30 final size:30
Alignment explanation
Indices: 114794--114886 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
114784 TTAAATGTGC
*
114794 ATAATTAAATCAAAATTAAAATTTCAAATAT
1 ATAATTAAA-CCAAATTAAAATTTCAAATAT
* * * *
114825 ATATTTAAACTATAATTAAAATTTCACATGT
1 ATAATTAAACCA-AATTAAAATTTCAAATAT
* *
114856 ATAATTACACCAAATTAAAATTTCAAGTAT
1 ATAATTAAACCAAATTAAAATTTCAAATAT
114886 A
1 A
114887 CTTCTAAGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
30 18 0.35
31 33 0.65
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (30 bp):
ATAATTAAACCAAATTAAAATTTCAAATAT
Done.