Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010180.1 Kokia drynarioides strain JFW-HI SEQ_124986, 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: 83748
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:10390 original size:30 final size:29
Alignment explanation
Indices: 10356--10535 Score: 154
Period size: 30 Copynumber: 6.1 Consensus size: 29
10346 TTTCAAGGTC
*
10356 AAAAATGGAATTTTTTGAAGTTCGAGGGTT
1 AAAAATGGAATTTTTAGAAGTTCG-GGGTT
** * *
10386 AAAAATGGGGTTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGTT
* *
10415 -AAAATGGTAATTTTTAGAAGTTTCGAGGTC
1 AAAAATGG-AATTTTTAGAAG-TTCGGGGTT
* * *
10445 AAAAATGCG-ATTTTTGGGAGTTCGGGGGT
1 AAAAATG-GAATTTTTAGAAGTTCGGGGTT
*
10474 -AAAATGGTAATTTTTAGAAGGTTCGGGGTC
1 AAAAATGG-AATTTTTAGAA-GTTCGGGGTT
*
10504 AAAAATGGGATTTTT-GAGAGTTCGGGG-T
1 AAAAATGGAATTTTTAGA-AGTTCGGGGTT
10532 AAAA
1 AAAA
10536 TGGTAACTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.01
28 17 0.14
29 37 0.31
30 51 0.43
31 13 0.11
32 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGTT
Found at i:10390 original size:89 final size:89
Alignment explanation
Indices: 10278--10477 Score: 192
Period size: 89 Copynumber: 2.2 Consensus size: 89
10268 AAAATGGTAA
* *
10278 TTTTGAGAGTTTCGA-GGTAAAAAACGGAGTCTTT-GAACATCCGAGAGTAAAATAGTATTTTTT
1 TTTTGA-AG-TTCGAGGGTTAAAAACGGAGTCTTTGGAA-ATCCGAGAGTAAAATAGTAATTTTT
* *
10341 GGATGTTTCAAGGTCAAAAATG-GAATT
63 AGAAGTTTCAAGGTCAAAAATGCG-ATT
* * * * * * * *
10368 TTTTGAAGTTCGAGGGTTAAAAATGGGGTTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGA
1 TTTTGAAGTTCGAGGGTTAAAAACGGAGTCTTTGGAAATCCGAGAGTAAAATAGTAATTTTTAGA
*
10433 AGTTTCGAGGTCAAAAATGCGATT
66 AGTTTCAAGGTCAAAAATGCGATT
* * *
10457 TTTGGGAGTTCG-GGGGTAAAA
1 TTTTGAAGTTCGAGGGTTAAAA
10478 TGGTAATTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
88 13 0.14
89 68 0.75
90 10 0.11
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (89 bp):
TTTTGAAGTTCGAGGGTTAAAAACGGAGTCTTTGGAAATCCGAGAGTAAAATAGTAATTTTTAGA
AGTTTCAAGGTCAAAAATGCGATT
Found at i:10436 original size:59 final size:59
Alignment explanation
Indices: 10357--10541 Score: 263
Period size: 59 Copynumber: 3.2 Consensus size: 59
10347 TTCAAGGTCA
* * *
10357 AAAATGG-AATTTTTTGAAGTTCGAGGGTTAAAAATGGGGTTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGTTCGAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
10415 AAAATGGTAATTTTTAGAAGTTTCGA-GGTCAAAAATGCGATTTTTGGGAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAG-TTCGAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
10474 AAAATGGTAATTTTTAGAAGGTTCG-GGGTCAAAAATGGGATTTTT-GAGAGTTC-GGGGT
1 AAAATGGTAATTTTTAGAA-GTTCGAGGGTCAAAAATGGGATTTTTGGA-AGTTCGGGGGT
10532 AAAATGGTAA
1 AAAATGGTAA
10542 CTTTGTCGTT
Statistics
Matches: 115, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
58 23 0.20
59 86 0.75
60 6 0.05
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGTTCGAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:10518 original size:89 final size:89
Alignment explanation
Indices: 10324--10501 Score: 209
Period size: 89 Copynumber: 2.0 Consensus size: 89
10314 ACATCCGAGA
* * * * * *
10324 GTAAAATAGTATTTTTTGGATGTTTCAAGGTCAAAAATGGAATTTTTTGAAGTTCGAGGGTTAAA
1 GTAAAATGGTAATTTTTAGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGGTAAA
** *
10389 AATGGGGTTTTTGGAAGTTCGGGG
66 AATGGAATTTTTAGAAGTTCGGGG
* *
10413 GTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGCG-ATTTTTGGGAGTTCG-GGGGT-A
1 GTAAAATGGTAATTTTTAGAAGTTTCAAGGTCAAAAATG-GAATTTTTGGAAGTTCGAGGGGTAA
10475 AAATGGTAATTTTTAGAAGGTTCGGGG
65 AAATGG-AATTTTTAGAA-GTTCGGGG
10502 TCAAAAATGG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
87 7 0.09
88 12 0.16
89 55 0.73
90 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.35
Consensus pattern (89 bp):
GTAAAATGGTAATTTTTAGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGGTAAA
AATGGAATTTTTAGAAGTTCGGGG
Found at i:22196 original size:58 final size:58
Alignment explanation
Indices: 22116--22304 Score: 181
Period size: 58 Copynumber: 3.3 Consensus size: 58
22106 GGTCAAATAT
* *
22116 ATTTTT-GAAAGTTC-GAGGGTAAAACGGTAAATTTTGGATAATTCGGGGGTAAAAATGGA
1 ATTTTTGGAAAGTTCAG-GGGTAAAATGGTAAATTTTGGA-AATT-GGGGGTAAAAATGAA
* * * * * *
22175 A-TTTTGGAAA-TTTAGGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGTTAAAATGAA
1 ATTTTTGGAAAGTTCAGGGGTAAAATGGTAAATTTTGGAAA-TTGGGGGTAAAAATGAA
* * * * *
22232 ATTTTTGGAAAGTTCAGGGTTAAAATGG-AATTTTTGGAAATTTGGGAGTAAAATTGTA
1 ATTTTTGGAAAGTTCAGGGGTAAAATGGTAAATTTTGGAAA-TTGGGGGTAAAAATGAA
22290 ATTTTTGGAAAGTTC
1 ATTTTTGGAAAGTTC
22305 GAGGTCAAAT
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
57 14 0.13
58 73 0.68
59 20 0.19
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
ATTTTTGGAAAGTTCAGGGGTAAAATGGTAAATTTTGGAAATTGGGGGTAAAAATGAA
Found at i:22229 original size:30 final size:29
Alignment explanation
Indices: 22167--22464 Score: 202
Period size: 29 Copynumber: 10.2 Consensus size: 29
22157 TTCGGGGGTA
* *
22167 AAAATGGAA-TTTTGGAAA-TTT-AGGGGT
1 AAAATGTAATTTTTGGAAAGTTTGA-GGTT
*
22194 AAAATGGTAATTTTTGAAAAGTTTGAGGTT
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGTT
* *
22224 AAAATGAAATTTTTGGAAAG-TTCAGGGTT
1 AAAATGTAATTTTTGGAAAGTTTGA-GGTT
* *
22253 AAAATGGAATTTTTGGAAA-TTTG-GGAGT
1 AAAATGTAATTTTTGGAAAGTTTGAGG-TT
* *
22281 AAAATTGTAATTTTTGGAAAGTTCGAGGTC
1 AAAA-TGTAATTTTTGGAAAGTTTGAGGTT
* * * * *
22311 AAATTTTGATTTTTGGAAAGTTTAGTGGTG
1 AAAATGTAATTTTTGGAAAGTTT-GAGGTT
**
22341 AAAATGCGATTTTT-GAGAAGTTT-AGGGTCT
1 AAAATGTAATTTTTGGA-AAGTTTGA-GGT-T
* *
22371 AAAATGTAAATTTTGGAAAATTTTG-GGTCT
1 AAAATGTAATTTTTGG-AAAGTTTGAGGT-T
* * * *
22401 -AAATGTAATTTTTAGATAGTTTCGTGATT
1 AAAATGTAATTTTTGGAAAGTTT-GAGGTT
*
22430 AAAATGTAATTTTTGGAAAGTTTGGAGGTC
1 AAAATGTAATTTTTGGAAAGTTT-GAGGTT
22460 AAAAT
1 AAAAT
22465 AAGATTTTTG
Statistics
Matches: 212, Mismatches: 39, Indels: 37
0.74 0.14 0.13
Matches are distributed among these distances:
27 7 0.03
28 16 0.08
29 95 0.45
30 84 0.40
31 9 0.04
32 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGTT
Found at i:22314 original size:29 final size:29
Alignment explanation
Indices: 22116--22451 Score: 159
Period size: 29 Copynumber: 11.5 Consensus size: 29
22106 GGTCAAATAT
**
22116 ATTTTT-GAAAGTTCGAGGGTAAAACGGTA
1 ATTTTTGGAAAGTTCGA-GGTAAAAATGTA
* * *
22145 AATTTTGGATAA-TTCGGGGGTAAAAATGGA
1 ATTTTTGGA-AAGTTC-GAGGTAAAAATGTA
* * *
22175 A-TTTTGGAAATTTAGGGGT-AAAATGGTA
1 ATTTTTGGAAAGTTCGAGGTAAAAAT-GTA
* * * *
22203 ATTTTTGAAAAGTTTGAGGTTAAAATGAA
1 ATTTTTGGAAAGTTCGAGGTAAAAATGTA
* *
22232 ATTTTTGGAAAGTTC-AGGGTTAAAATGGA
1 ATTTTTGGAAAGTTCGA-GGTAAAAATGTA
* * *
22261 ATTTTTGGAAA-TTTGGGAGTAAAATTGTA
1 ATTTTTGGAAAGTTCGAG-GTAAAAATGTA
* * * *
22290 ATTTTTGGAAAGTTCGAGGTCAAATTTTG
1 ATTTTTGGAAAGTTCGAGGTAAAAATGTA
* * * **
22319 ATTTTTGGAAAGTTTAGTGGTGAAAATGCG
1 ATTTTTGGAAAG-TTCGAGGTAAAAATGTA
* *
22349 ATTTTT-GAGAAGTT-TAGGGTCTAAAATGTA
1 ATTTTTGGA-AAGTTCGA-GGT-AAAAATGTA
* * * **
22379 AATTTTGGAAAATTTTG-GGTCTAAATGTA
1 ATTTTTGG-AAAGTTCGAGGTAAAAATGTA
* * * * *
22408 ATTTTTAGATAGTTTCGTGATTAAAATGTA
1 ATTTTTGGAAAG-TTCGAGGTAAAAATGTA
22438 ATTTTTGGAAAGTT
1 ATTTTTGGAAAGTT
22452 TGGAGGTCAA
Statistics
Matches: 236, Mismatches: 51, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
27 5 0.02
28 16 0.07
29 129 0.55
30 77 0.33
31 8 0.03
32 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
ATTTTTGGAAAGTTCGAGGTAAAAATGTA
Found at i:22472 original size:30 final size:29
Alignment explanation
Indices: 22203--22476 Score: 95
Period size: 30 Copynumber: 9.3 Consensus size: 29
22193 TAAAATGGTA
* *
22203 ATTTTTGAAAAGTTT-GAGGTTAAAATGAA-
1 ATTTTTGGAAAGTTTAG-GGTCAAAAT-AAG
* * *
22232 ATTTTTGGAAAGTTCAGGGTTAAAAT-GG
1 ATTTTTGGAAAGTTTAGGGTCAAAATAAG
* *
22260 AATTTTTGGAAA-TTTGGGAGT-AAAAT-TG
1 -ATTTTTGGAAAGTTTAGG-GTCAAAATAAG
* * **
22288 TAATTTTTGGAAAG-TTCGAGGTCAAATTTTG
1 --ATTTTTGGAAAGTTTAG-GGTCAAAATAAG
* **
22319 ATTTTTGGAAAGTTTAGTGGTGAAAATGCG
1 ATTTTTGGAAAGTTTAG-GGTCAAAATAAG
22349 ATTTTT-GAGAAGTTTAGGGTCTAAAATGTAA-
1 ATTTTTGGA-AAGTTTAGGGTC-AAAA--TAAG
* * * *
22380 A-TTTTGGAAAATTTTGGGTCTAAATGTA-
1 ATTTTTGGAAAGTTTAGGGTCAAAAT-AAG
* * * * * *
22408 ATTTTTAGATAGTTTCGTGATTAAAATGTA-
1 ATTTTTGGAAAGTTTAG-GGTCAAAAT-AAG
*
22438 ATTTTTGGAAAGTTTGGAGGTCAAAATAAG
1 ATTTTTGGAAAGTTTAG-GGTCAAAATAAG
22468 ATTTTTGGA
1 ATTTTTGGA
22477 CAATGCAAAG
Statistics
Matches: 191, Mismatches: 35, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 12 0.06
29 84 0.44
30 88 0.46
31 5 0.03
32 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (29 bp):
ATTTTTGGAAAGTTTAGGGTCAAAATAAG
Found at i:23545 original size:3 final size:3
Alignment explanation
Indices: 23537--23649 Score: 145
Period size: 3 Copynumber: 37.7 Consensus size: 3
23527 ACTTTCCCTT
* * * * *
23537 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
23585 TTG TTG TTA TTA TTG TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23633 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
23650 TAATATTTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23661 original size:13 final size:13
Alignment explanation
Indices: 23616--23664 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
23606 TTGTTATTAT
*
23616 TATTATTA-TTAT
1 TATTATTATTTAA
*
23628 TATTATTA-TTAT
1 TATTATTATTTAA
23640 TATTATTATTTAA
1 TATTATTATTTAA
*
23653 TATTTTTATTTA
1 TATTATTATTTA
23665 TTAAAATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 20 0.59
13 14 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTATTTAA
Found at i:24900 original size:12 final size:11
Alignment explanation
Indices: 24872--24913 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
24862 TTCAAGCTCA
*
24872 ATTAATTTTTT
1 ATTATTTTTTT
24883 A-TATTTTTTT
1 ATTATTTTTTT
*
24893 CTTCATTTTTTT
1 ATT-ATTTTTTT
24905 ATTATTTTT
1 ATTATTTTT
24914 CCATTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 10 0.38
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTATTTTTTT
Found at i:24905 original size:22 final size:22
Alignment explanation
Indices: 24877--24932 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 22
24867 GCTCAATTAA
24877 TTTTTTATATTTTT-TTCTTCAT
1 TTTTTTATATTTTTCTT-TTCAT
24899 TTTTTTATTATTTTTCCATTTTCAT
1 TTTTTTA-TATTTTT-C-TTTTCAT
24924 TTTTTTATA
1 TTTTTTATA
24933 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 2 0.07
25 12 0.40
26 2 0.07
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTATATTTTTCTTTTCAT
Found at i:25081 original size:14 final size:14
Alignment explanation
Indices: 25062--25090 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25052 TGTGGGTTAC
25062 GGGTTAGTATAAAT
1 GGGTTAGTATAAAT
25076 GGGTTAGTATAAAT
1 GGGTTAGTATAAAT
25090 G
1 G
25091 TCTCAGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
GGGTTAGTATAAAT
Found at i:26117 original size:17 final size:17
Alignment explanation
Indices: 26071--26120 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
26061 AGCAATTTGT
*
26071 TCAATAATATTTTTATC
1 TCAAAAATATTTTTATC
* *
26088 TCGAAAGTCATTTTTATC
1 TCAAAAAT-ATTTTTATC
26106 TCAAAAATATTTTTA
1 TCAAAAATATTTTTA
26121 AAAAGTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (17 bp):
TCAAAAATATTTTTATC
Found at i:30908 original size:6 final size:7
Alignment explanation
Indices: 30881--30906 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30871 TCAGATTTTA
30881 AAAAAAG
1 AAAAAAG
30888 AAAAAAG
1 AAAAAAG
30895 AAAAAAG
1 AAAAAAG
30902 AAAAA
1 AAAAA
30907 GAGCGTAGAT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:33691 original size:16 final size:16
Alignment explanation
Indices: 33670--33721 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33660 ACTTTTTAAA
*
33670 TAATTTTAATGATTTT
1 TAATTTTAATAATTTT
*
33686 TAATTTTTATAATTTTT
1 TAATTTTAATAA-TTTT
*
33703 TGAATTTTTA-AATTTT
1 T-AATTTTAATAATTTT
33719 TAA
1 TAA
33722 AAATTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 7 0.22
18 8 0.25
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TAATTTTAATAATTTT
Found at i:33708 original size:18 final size:16
Alignment explanation
Indices: 33682--33719 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
33672 ATTTTAATGA
33682 TTTTTAATTTTTATAAT
1 TTTTTAATTTTTA-AAT
33699 TTTTTGAATTTTTAAAT
1 TTTTT-AATTTTTAAAT
33716 TTTT
1 TTTT
33720 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTAATTTTTAAAT
Found at i:35228 original size:22 final size:26
Alignment explanation
Indices: 35190--35241 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
35180 ATTGTCTCTA
35190 AATAATTAGTACAAATATAAT-T-TT
1 AATAATTAGTACAAATATAATATATT
35214 AATAATT-G-ACAAATATAATATATT
1 AATAATTAGTACAAATATAATATATT
35238 AATA
1 AATA
35242 TTATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.42
23 2 0.08
24 13 0.50
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AATAATTAGTACAAATATAATATATT
Found at i:41056 original size:6 final size:6
Alignment explanation
Indices: 41045--41073 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41035 ATTGAATTGA
41045 TCCAAC TCCAAC TCCAAC TCCAAC TCCAA
1 TCCAAC TCCAAC TCCAAC TCCAAC TCCAA
41074 TTCACTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCAAC
Found at i:46453 original size:44 final size:44
Alignment explanation
Indices: 46364--46451 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
46354 TAATGTCGAG
* *
46364 TTAAGAGTTAGAATATGTGGCTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTGGCTAAAATAAGAAGATTAAGAAAAA
* * *
46408 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGT-GGCTAAAATAAG-AAGATTAAGAAAA
46452 TTTTAAGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 23 0.62
45 14 0.38
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.26
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTGGCTAAAATAAGAAGATTAAGAAAAA
Found at i:64481 original size:29 final size:29
Alignment explanation
Indices: 64449--64509 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
64439 AAAATGAGAC
* * *
64449 TTTTTGGATACCCGGGGGTAAAATGGTAA
1 TTTTTGGATACCCAGAGGCAAAATGGTAA
**
64478 -TTTTGGATTTCCAGAGGCAAAATGGTAA
1 TTTTTGGATACCCAGAGGCAAAATGGTAA
64506 TTTT
1 TTTT
64510 GGGACAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTTGGATACCCAGAGGCAAAATGGTAA
Found at i:64558 original size:29 final size:27
Alignment explanation
Indices: 64515--64772 Score: 119
Period size: 29 Copynumber: 8.9 Consensus size: 27
64505 ATTTTGGGAC
64515 AATTCGGGGTTAAAAATTGAATTTTTAG
1 AATTCGGGG-TAAAAATTGAATTTTTAG
**
64543 ATATTCAGGGGT-AAAAGGGTAATTTTTAG
1 A-ATTC-GGGGTAAAAATTG-AATTTTTAG
* * * * * *
64572 AGTTTCGAGGTCGAAAATAGAGTTTTTGG
1 A-ATTCGGGGT-AAAAATTGAATTTTTAG
* *
64601 ACATTCGGGGTAAAAATAGAATTTTTGG
1 A-ATTCGGGGTAAAAATTGAATTTTTAG
* *
64629 AAGTTTCGGGGTAAAAAATGAAATTTTTTG
1 AA--TTCGGGGTAAAAATTG-AATTTTTAG
*
64659 AAGTTCGAGGGTAAAATTTGAATTTTTCTAG
1 AA-TTCG-GGGTAAAAATTGAA-TTTT-TAG
* * * *
64690 -TTTTGGGGTTAAAAATGGAATTTTTGG
1 AATTCGGGG-TAAAAATTGAATTTTTAG
* *
64717 AAGTTTAGGGGTAAAAA-TGCAATTTTTGG
1 AA--TTCGGGGTAAAAATTG-AATTTTTAG
*
64746 AAGTTTGGGGGTAAAAA-TGAAATTTTT
1 AA--TTCGGGGTAAAAATTG-AATTTTT
64773 GAAAGTTTAG
Statistics
Matches: 183, Mismatches: 31, Indels: 31
0.75 0.13 0.13
Matches are distributed among these distances:
27 3 0.02
28 34 0.19
29 105 0.57
30 39 0.21
31 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (27 bp):
AATTCGGGGTAAAAATTGAATTTTTAG
Found at i:64647 original size:58 final size:57
Alignment explanation
Indices: 64517--64832 Score: 209
Period size: 58 Copynumber: 5.4 Consensus size: 57
64507 TTTGGGACAA
* * ** * *
64517 TTCGGGGTTAAAAATTGAATTTTTAGATA-TTCAGGGGTAAAAGGGTAATTTTTAG-AGT
1 TTCGGGG-TAAAAAATGAATTTTTGGA-AGTTC-GGGGTAAAAATGCAATTTTTGGAAGT
* ** *
64575 TTCGAGGTCGAAAATAGAGTTTTTGGACA-TTCGGGGTAAAAATAG-AATTTTTGGAAGT
1 TTCGGGGTAAAAAAT-GAATTTTTGGA-AGTTCGGGGTAAAAAT-GCAATTTTTGGAAGT
* * **
64633 TTCGGGGTAAAAAATGAAATTTTTTGAAGTTCGAGGGTAAAATTTG-AATTTTT-CTAGT
1 TTCGGGGTAAAAAATG-AATTTTTGGAAGTTCG-GGGTAAAA-ATGCAATTTTTGGAAGT
* * *
64691 TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGCAATTTTTGGAAGT
1 TTCGGGGTAAAAAAT-GAATTTTTGGAAG-TTCGGGGTAAAAATGCAATTTTTGGAAGT
* * * * * * *
64750 TTGGGGGT-AAAAATGAAATTTTTGAAAGTTTAGAGGTCGAAAATGGAATTTTTGAAAG-
1 TTCGGGGTAAAAAATG-AATTTTTGGAAG-TTCGGGGT-AAAAATGCAATTTTTGGAAGT
64808 TTCGGGTGT-AAAAATGTAATTTTTG
1 TTCGGG-GTAAAAAATG-AATTTTTG
64833 AACAGTTTAG
Statistics
Matches: 211, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
57 27 0.13
58 119 0.56
59 64 0.30
60 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (57 bp):
TTCGGGGTAAAAAATGAATTTTTGGAAGTTCGGGGTAAAAATGCAATTTTTGGAAGT
Found at i:64718 original size:88 final size:88
Alignment explanation
Indices: 64607--64832 Score: 262
Period size: 88 Copynumber: 2.6 Consensus size: 88
64597 TTGGACATTC
* *
64607 GGGG-TAAAAATAGAATTTTTGGAAGTTTCGGGGTAAAAAATGAAATTTTTTGAAGTTCGAGGGT
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGAAATTTTTGGAAGTTCGAGGGT
* ** *
64671 AAAATTTG-AATTTTT-CTAGTTTT
65 AAAA-ATGAAATTTTTGAAAGTTTA
* * * *
64694 GGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGCAATTTTTGGAAGTTTGGGGGTA
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGAAATTTTTGGAAGTTCGAGGGTA
64759 AAAATGAAATTTTTGAAAGTTTA
66 AAAATGAAATTTTTGAAAGTTTA
* ** * *
64782 GAGGTCGAAAATGGAATTTTTGAAAG-TTCGGGTGTAAAAATGTAATTTTTG
1 GGGGTTAAAAATGGAATTTTTGGAAGTTTCGGG-GTAAAAATGAAATTTTTG
64833 AACAGTTTAG
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
86 2 0.02
87 45 0.38
88 72 0.61
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (88 bp):
GGGGTTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGAAATTTTTGGAAGTTCGAGGGTA
AAAATGAAATTTTTGAAAGTTTA
Found at i:64833 original size:29 final size:29
Alignment explanation
Indices: 64604--64840 Score: 207
Period size: 29 Copynumber: 8.1 Consensus size: 29
64594 TTTTTGGACA
*
64604 TTCGGGGTAAAAAT-AGAATTTTTGGAAGT
1 TTCGGGGTAAAAATGA-AATTTTTGAAAGT
64633 TTCGGGGTAAAAAATGAAATTTTTTG-AAG-
1 TTCGGGGT-AAAAATGAAA-TTTTTGAAAGT
* **
64662 TTCGAGGGTAAAATTTG-AATTTTT-CTAGT
1 TTCG-GGGTAAAA-ATGAAATTTTTGAAAGT
* * *
64691 TTTGGGGTTAAAAATGGAATTTTTGGAAGT
1 TTCGGGG-TAAAAATGAAATTTTTGAAAGT
* * *
64721 TTAGGGGTAAAAATGCAATTTTTGGAAGT
1 TTCGGGGTAAAAATGAAATTTTTGAAAGT
*
64750 TTGGGGGTAAAAATGAAATTTTTGAAAGT
1 TTCGGGGTAAAAATGAAATTTTTGAAAGT
* * * *
64779 TTAGAGGTCGAAAATGGAATTTTTGAAAG-
1 TTCGGGGT-AAAAATGAAATTTTTGAAAGT
*
64808 TTCGGGTGTAAAAATGTAATTTTTGAACAGT
1 TTCGGG-GTAAAAATGAAATTTTTGAA-AGT
64839 TT
1 TT
64841 AGGGACCTTC
Statistics
Matches: 175, Mismatches: 19, Indels: 26
0.80 0.09 0.12
Matches are distributed among these distances:
28 12 0.07
29 106 0.61
30 48 0.27
31 9 0.05
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
TTCGGGGTAAAAATGAAATTTTTGAAAGT
Found at i:66014 original size:21 final size:21
Alignment explanation
Indices: 65982--66038 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
65972 TAATATTAAT
65982 TATTATTTATTATTGTTGTTAC
1 TATTA-TTATTATTGTTGTTAC
* *
66004 TATTATTATTACTGTTGTTAT
1 TATTATTATTATTGTTGTTAC
*
66025 TATTAATAGTTATT
1 TATTATTA-TTATT
66039 AAATAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (21 bp):
TATTATTATTATTGTTGTTAC
Found at i:66841 original size:17 final size:17
Alignment explanation
Indices: 66786--66849 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
66776 CAAATTTGAT
*
66786 TAAATTTAAATCTAA-A
1 TAAATTTAAATTTAAGA
*
66802 GCAAATTTAAATTTAAAAAGA
1 -TAAATTTAAATTT---AAGA
66823 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAGA
66840 TAAATTTAAA
1 TAAATTTAAA
66850 CCAATTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 25 0.62
20 14 0.35
21 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:77744 original size:23 final size:23
Alignment explanation
Indices: 77692--77745 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
77682 TAGAATAGAG
*
77692 TTAACATTTATTGTTTTAAAAAA
1 TTAATATTTATTGTTTTAAAAAA
*
77715 -TATTATTTATTG-TTTAACAAAA
1 TTAATATTTATTGTTTTAA-AAAA
77737 TTAATATTT
1 TTAATATTT
77746 TTAATGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAATATTTATTGTTTTAAAAAA
Done.