Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010864.1 Kokia drynarioides strain JFW-HI SEQ_125832, 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: 152727
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:5211 original size:5 final size:5
Alignment explanation
Indices: 5193--5244 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
5183 TCATAGTATG
* ** *
5193 TTTAG TTTATT TTTAT TTTAT TTTAT TTTAT AGTAT TTAAT TTTAT TATTAT
1 TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT
5245 CGTATTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
5 30 0.79
6 8 0.21
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:5235 original size:20 final size:21
Alignment explanation
Indices: 5206--5250 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
5196 AGTTTATTTT
*
5206 TATTTTATTTTATT-TTATAG
1 TATTTAATTTTATTATTATAG
*
5226 TATTTAATTTTATTATTATCG
1 TATTTAATTTTATTATTATAG
5247 TATT
1 TATT
5251 AAATCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTTAATTTTATTATTATAG
Found at i:5834 original size:60 final size:60
Alignment explanation
Indices: 5764--5888 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
5754 ATATACTAAG
*
5764 ATTATTATTAAATATAATTTAATAAAA-AGATAATAAAGAATTTAAT-CATATTTTAATATA
1 ATTAGTATTAAATATAATTTAATAAAATA-ATAATAAAGAATTTAATACAT-TTTTAATATA
* * * *
5824 ATTAGTATTAAATATAGTTTAATAAAATAATAATATATAATTTAATAACATTTTTAGTATA
1 ATTAGTATTAAATATAATTTAATAAAATAATAATAAAGAATTTAAT-ACATTTTTAATATA
5885 ATTA
1 ATTA
5889 TTTTTATATT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
60 40 0.70
61 14 0.25
62 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (60 bp):
ATTAGTATTAAATATAATTTAATAAAATAATAATAAAGAATTTAATACATTTTTAATATA
Found at i:5923 original size:33 final size:33
Alignment explanation
Indices: 5886--5950 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5876 TTTAGTATAA
5886 TTATTTTTATATTAAATTATATCAAAATATTTT
1 TTATTTTTATATTAAATTATATCAAAATATTTT
*
5919 TTATTTTTATATTAAATTATATTAAAATATTT
1 TTATTTTTATATTAAATTATATCAAAATATTT
5951 CAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
TTATTTTTATATTAAATTATATCAAAATATTTT
Found at i:5940 original size:43 final size:43
Alignment explanation
Indices: 5892--5974 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
5882 ATAATTATTT
*
5892 TTATATTAAATTATATCAAAATATTTT-TTATTTTTATATTAAA
1 TTATATTAAAATATATC-AAATATTTTATTATTTTTATATTAAA
* *
5935 TTATATTAAAATATTTCAAATATTTTATTTTTTTTATATT
1 TTATATTAAAATATATCAAATATTTTATTATTTTTATATT
5975 TTTTGGGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 9 0.25
43 27 0.75
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (43 bp):
TTATATTAAAATATATCAAATATTTTATTATTTTTATATTAAA
Found at i:7518 original size:27 final size:27
Alignment explanation
Indices: 7468--7519 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
7458 AGTTTAAATA
*** *
7468 TAATAATTTTATTGGTAAATAAATATC
1 TAATAATTTTATTACAAAAAAAATATC
7495 TAATAATTTTATTACAAAAAAAATA
1 TAATAATTTTATTACAAAAAAAATA
7520 CTTCCATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (27 bp):
TAATAATTTTATTACAAAAAAAATATC
Found at i:11186 original size:18 final size:18
Alignment explanation
Indices: 11134--11186 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
11124 TCTATATTTT
*
11134 ATATTATTAA-TAATAAA
1 ATATTATTAATTAATATA
* * *
11151 ATATGATTATTTATTATA
1 ATATTATTAATTAATATA
11169 ATATTATTAATTAATATA
1 ATATTATTAATTAATATA
11187 TCTTTTGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATTATTAATTAATATA
Found at i:12327 original size:30 final size:30
Alignment explanation
Indices: 12291--12347 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12281 TTTTGGTTGC
12291 TTCGGGGAT-AAAATAGTAATTTTTAGAAGG
1 TTCGGGGATGAAAATAG-AATTTTTAGAAGG
*
12321 TTCGGGGTTGAAAATAGAATTTTTAGA
1 TTCGGGGATGAAAATAGAATTTTTAGA
12348 CATTCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
TTCGGGGATGAAAATAGAATTTTTAGAAGG
Found at i:12462 original size:30 final size:29
Alignment explanation
Indices: 12369--12487 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 29
12359 AAAATGGTAA
* * *
12369 TTTGGAAATTTTGAGGTCAAAAATGAAATT
1 TTTGGAAATTTGGGGGT-AAAAATGTAATT
* * * * *
12399 TTAGAAAATTTAGGGCTAAAAATGGAA-T
1 TTTGGAAATTTGGGGGTAAAAATGTAATT
12427 TTTGGAAGATTTGGGGGTAAAAATGTAATT
1 TTTGGAA-ATTTGGGGGTAAAAATGTAATT
*
12457 TTTGGAAATTTTGGGGTTAAAAA-GTAATT
1 TTTGGAAA-TTTGGGGGTAAAAATGTAATT
12486 TT
1 TT
12488 GAAAAGTTCA
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
28 6 0.08
29 35 0.47
30 33 0.45
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTGGAAATTTGGGGGTAAAAATGTAATT
Found at i:12486 original size:58 final size:58
Alignment explanation
Indices: 12359--12488 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 58
12349 ATTCAAGAGT
*
12359 AAAATGGTAA-TTTGGAAATTTTGAGGTCAAAAATGAAATTTTAGAAAATTTAGGGCTA
1 AAAAT-GTAATTTTGGAAATTTGGAGGTCAAAAATGAAATTTTAGAAAATTTAGGGCTA
* * * * * * *
12417 AAAATGGAATTTTGGAAGATTTGGGGGT-AAAAATGTAATTTTTGGAAATTTTGGGGTTA
1 AAAATGTAATTTTGGAA-ATTTGGAGGTCAAAAATG-AAATTTTAGAAAATTTAGGGCTA
12476 AAAA-GTAATTTTG
1 AAAATGTAATTTTG
12489 AAAAGTTCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
57 3 0.05
58 27 0.45
59 30 0.50
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAATTTGGAGGTCAAAAATGAAATTTTAGAAAATTTAGGGCTA
Found at i:13390 original size:18 final size:18
Alignment explanation
Indices: 13364--13398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13354 TTATTAAAAC
*
13364 ATTATTTAATACTTATTT
1 ATTAATTAATACTTATTT
*
13382 ATTAATTAATATTTATT
1 ATTAATTAATACTTATT
13399 AATACTTATT
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:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTAATTAATACTTATTT
Found at i:13408 original size:14 final size:14
Alignment explanation
Indices: 13369--13413 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
13359 AAAACATTAT
13369 TTAATACTTATTTA
1 TTAATACTTATTTA
*
13383 TTAATTA-ATATTTA
1 TTAA-TACTTATTTA
*
13397 TTAATACTTATTGA
1 TTAATACTTATTTA
13411 TTA
1 TTA
13414 TATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (14 bp):
TTAATACTTATTTA
Found at i:14084 original size:6 final size:6
Alignment explanation
Indices: 14073--14130 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
14063 ATTATTTAAA
* * * *
14073 TAAATT TAAATT TAAATT TAAATT TAAA-A TAAACT TAATTT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
14119 TAAATT TAAATT
1 TAAATT TAAATT
14131 CTGTTGGGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 8 0.19
6 35 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:14110 original size:17 final size:17
Alignment explanation
Indices: 14073--14130 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
14063 ATTATTTAAA
*
14073 TAAATTTAAATTTAAATT
1 TAAATTTAAA-ATAAATT
*
14091 TAAATTTAAAATAAACT
1 TAAATTTAAAATAAATT
*
14108 TAATTTTAAAATAAATT
1 TAAATTTAAAATAAATT
14125 TAAATT
1 TAAATT
14131 CTGTTGGGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 25 0.71
18 10 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:16144 original size:5 final size:5
Alignment explanation
Indices: 16136--16164 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16126 ATCTGGAAGG
16136 ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
1 ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
16165 AATCAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCCC
Found at i:21247 original size:19 final size:20
Alignment explanation
Indices: 21210--21247 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
21200 CAAAACCCTC
* *
21210 AAAACTTTTTATTTTCTCCT
1 AAAACTTTTTACTTCCTCCT
21230 AAAAC-TTTTACTTCCTCC
1 AAAACTTTTTACTTCCTCC
21248 CATCTCACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAACTTTTTACTTCCTCCT
Found at i:21504 original size:36 final size:36
Alignment explanation
Indices: 21464--21556 Score: 115
Period size: 34 Copynumber: 2.7 Consensus size: 36
21454 ATTTATATCT
* *
21464 AATATTTATATTATTAAATTAAATTTCA-CATTTTG
1 AATATTTATATTATTAAATTAAATTTAATCATATTG
*
21499 CAATATTTATATTATTGAATT--ATTTAATCATATTG
1 -AATATTTATATTATTAAATTAAATTTAATCATATTG
21534 AATATTTATATTA--AAATTAAATT
1 AATATTTATATTATTAAATTAAATT
21557 ATTAATGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
32 4 0.08
34 21 0.42
35 6 0.12
36 19 0.38
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (36 bp):
AATATTTATATTATTAAATTAAATTTAATCATATTG
Found at i:21543 original size:34 final size:35
Alignment explanation
Indices: 21464--21553 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 35
21454 ATTTATATCT
* *
21464 AATATTTATATTATTAAATTAAATTTCACATTTTGC
1 AATATTTATATTATTAAATT-AATTTAACATATTGC
*
21500 AATATTTATATTATTGAATT-ATTTAATCATATTG-
1 AATATTTATATTATTAAATTAATTTAA-CATATTGC
21534 AATATTTATATTA--AAATTAA
1 AATATTTATATTATTAAATTAA
21554 ATTATTAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.08
33 1 0.02
34 18 0.38
35 6 0.12
36 19 0.40
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (35 bp):
AATATTTATATTATTAAATTAATTTAACATATTGC
Found at i:22226 original size:24 final size:26
Alignment explanation
Indices: 22194--22252 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
22184 TCAACGTTTA
*
22194 CATTTTTTTTATTA-TTA-ATTTGAC
1 CATTATTTTTATTAGTTATATTTGAC
22218 CATTA-TTTT-TTAGTTATATTTGAC
1 CATTATTTTTATTAGTTATATTTGAC
* *
22242 CTTTATCTTTA
1 CATTATTTTTA
22253 AAAAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.11
23 7 0.25
24 15 0.54
25 3 0.11
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (26 bp):
CATTATTTTTATTAGTTATATTTGAC
Found at i:29346 original size:6 final size:6
Alignment explanation
Indices: 29335--29368 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
29325 AAAAAATAAA
29335 GAATAT GAATAT GAATAT GAATA- GAATAT GAATA
1 GAATAT GAATAT GAATAT GAATAT GAATAT GAATA
29369 GATGGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (6 bp):
GAATAT
Found at i:29363 original size:11 final size:11
Alignment explanation
Indices: 29334--29370 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
29324 CAAAAAATAA
29334 AGAATATGAAT
1 AGAATATGAAT
29345 ATGAATATGAAT
1 A-GAATATGAAT
29357 AGAATATGAAT
1 AGAATATGAAT
29368 AGA
1 AGA
29371 TGGTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (11 bp):
AGAATATGAAT
Found at i:29363 original size:17 final size:18
Alignment explanation
Indices: 29335--29368 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29325 AAAAAATAAA
29335 GAATATGAATATGAATAT
1 GAATATGAATATGAATAT
29353 GAATA-GAATATGAATA
1 GAATATGAATATGAATA
29369 GATGGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
GAATATGAATATGAATAT
Found at i:39976 original size:6 final size:6
Alignment explanation
Indices: 39957--40013 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
39947 ACAATTCATA
*
39957 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
40005 TCACTT TCA
1 TCACTT TCA
40014 ATTTTGATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:50556 original size:59 final size:59
Alignment explanation
Indices: 50459--50628 Score: 159
Period size: 59 Copynumber: 2.9 Consensus size: 59
50449 GGACACTCGG
** * * *
50459 GGGTAAAAT-AGTAATTTTTGGAAAGTTTGAAGTTAAAAACGTAATTCTTA-GATA-TCCGA
1 GGGTAAAATGA-TAATTTTTGGAAAAATCGAGGTTAAAAACGGAATT-TTAGGA-AGTCCGA
* * * **
50518 GGGTAAAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCTC
1 GGGTAAAATGATAATTTTTGGAAAAATCGAGGTTAAAAACGGAATTTTAGGAAGTCCGA
** * *
50577 GGGTAAAATGGGAAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTT-GGAA
1 GGGTAAAATGATAATTTTTGGAAAAATCGAGGTTAAAAACGGAATTTTAGGAA
50629 ATTTTAGGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 8 0.09
59 85 0.90
60 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (59 bp):
GGGTAAAATGATAATTTTTGGAAAAATCGAGGTTAAAAACGGAATTTTAGGAAGTCCGA
Found at i:50564 original size:30 final size:29
Alignment explanation
Indices: 50530--50747 Score: 115
Period size: 29 Copynumber: 7.4 Consensus size: 29
50520 GTAAAATGAT
50530 AATTTTTGGAAAAATCGAGGTCAAAAATGG
1 AATTTTTGGAAAAATCGAGGT-AAAAATGG
* ***
50560 AATTTTAGGAAGTTCTCG-GGT-AAAATGGG
1 AATTTTTGGAA-AAATCGAGGTAAAAAT-GG
*
50589 AAATTTTGGAAAAATCGAGGTTAAAAATGG
1 AATTTTTGGAAAAATCGAGG-TAAAAATGG
** * * *
50619 AA-TTTTGGAAATTTTAGGGGTAAAAATGTA
1 AATTTTTGGAAA-AATCGAGGTAAAAATG-G
* * * * *
50649 AATTTCTAGAAAATTTGAGGTTAAAATGG
1 AATTTTTGGAAAAATCGAGGTAAAAATGG
** * * *
50678 AA-TTTTGGAAATTTTAGGGGTAAAAATGT
1 AATTTTTGGAAA-AATCGAGGTAAAAATGG
**
50707 AATTTTTGG-AAAATTTAGGGTTAAAAAT-G
1 AATTTTTGGAAAAATCGA-GG-TAAAAATGG
50736 AATTTTTGGAAA
1 AATTTTTGGAAA
50748 GTTTAGGGGT
Statistics
Matches: 141, Mismatches: 34, Indels: 26
0.70 0.17 0.13
Matches are distributed among these distances:
28 16 0.11
29 59 0.42
30 51 0.36
31 15 0.11
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAAAATCGAGGTAAAAATGG
Found at i:50584 original size:29 final size:28
Alignment explanation
Indices: 50552--50747 Score: 130
Period size: 29 Copynumber: 6.7 Consensus size: 28
50542 AATCGAGGTC
* *
50552 AAAAATGGAATTTTAGGAAGTTCTCGGGT
1 AAAAATGGAATTTT-GGAAATTTTCGGGT
**
50581 -AAAATGGGAAATTTTGGAAA-AATCGAGGTT
1 AAAAAT-GG-AATTTTGGAAATTTTCG-GG-T
*
50611 AAAAATGGAATTTTGGAAATTTTAGGGGT
1 AAAAATGGAATTTTGGAAATTTT-CGGGT
* * *
50640 AAAAATGTAAATTTCTAGAAAATTT-GAGGT
1 AAAAATG-GAATTT-TGGAAATTTTCG-GGT
* *
50670 TAAAATGGAATTTTGGAAATTTTAGGGGT
1 AAAAATGGAATTTTGGAAATTTT-CGGGT
* * *
50699 AAAAATGTAATTTTTGGAAAATTTAGGGTT
1 AAAAATGGAA-TTTTGGAAATTTTCGGG-T
50729 AAAAAT-GAATTTTTGGAAA
1 AAAAATGGAA-TTTTGGAAA
50748 GTTTAGGGGT
Statistics
Matches: 135, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 16 0.12
29 59 0.44
30 46 0.34
31 14 0.10
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTGGAAATTTTCGGGT
Found at i:50640 original size:59 final size:59
Alignment explanation
Indices: 50518--50764 Score: 263
Period size: 59 Copynumber: 4.2 Consensus size: 59
50508 AGATATCCGA
* * * * * *
50518 GGGTAAAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCT-C
1 GGGTAAAATGGTAAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTT-GGAAATTTTAG
*
50577 GGGTAAAATGGGAAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAATTTTAG
1 GGGTAAAATGGTAAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAATTTTAG
* * *
50636 GGGTAAAAAT-GTAAATTTCTAGAAAATTTGAGGTT-AAAATGGAATTTTGGAAATTTTAG
1 GGGT-AAAATGGTAAATTT-TGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAATTTTAG
* ** *
50695 GGGTAAAAAT-GTAATTTTTGG-AAAATTTAGGGTTAAAAAT-GAATTTTTGGAAAGTTTAG
1 GGGT-AAAATGGTAAATTTTGGAAAAATCGA-GGTTAAAAATGGAA-TTTTGGAAATTTTAG
50754 GGGTAGAAATG
1 GGGTA-AAATG
50765 AGATTTCTAA
Statistics
Matches: 164, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
57 6 0.04
58 17 0.10
59 123 0.75
60 18 0.11
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAAATTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAATTTTAG
Found at i:50752 original size:29 final size:29
Alignment explanation
Indices: 50610--50770 Score: 166
Period size: 29 Copynumber: 5.4 Consensus size: 29
50600 AAATCGAGGT
*
50610 TAAAAATGGAA-TTTTGGAAATTTTAGGGG
1 TAAAAAT-GAATTTTTGGAAAATTTAGGGG
* * *
50639 TAAAAATGTAAATTTCTAGAAAATTT-GAGG
1 TAAAAATG--AATTTTTGGAAAATTTAGGGG
* *
50669 TTAAAATGGAA-TTTTGGAAATTTTAGGGG
1 TAAAAAT-GAATTTTTGGAAAATTTAGGGG
*
50698 TAAAAATGTAATTTTTGGAAAATTTAGGGT
1 TAAAAATG-AATTTTTGGAAAATTTAGGGG
*
50728 TAAAAATGAATTTTTGGAAAGTTTAGGGG
1 TAAAAATGAATTTTTGGAAAATTTAGGGG
*
50757 TAGAAATGAGATTT
1 TAAAAATGA-ATTT
50771 CTAAACTGTT
Statistics
Matches: 109, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
28 12 0.11
29 47 0.43
30 39 0.36
31 11 0.10
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.36
Consensus pattern (29 bp):
TAAAAATGAATTTTTGGAAAATTTAGGGG
Found at i:52538 original size:6 final size:6
Alignment explanation
Indices: 52515--52619 Score: 67
Period size: 6 Copynumber: 18.2 Consensus size: 6
52505 GTATTTGGAT
* *** *
52515 ATTTCAA ATTTAA TTTTAA ATTTAA A-ACCA TTTTAA ATTT-A A-TTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* ** * *
52561 ATTTAA ATTTAA ATTCAA AAATAA ATTTAA A-ATAA ATTTAA ACTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
52607 ATATAA ATTTAA A
1 ATTTAA ATTTAA A
52620 AGTTTAATCC
Statistics
Matches: 71, Mismatches: 22, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
4 2 0.03
5 12 0.17
6 53 0.75
7 4 0.06
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:52564 original size:17 final size:16
Alignment explanation
Indices: 52546--52619 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
52536 TTAAAACCAT
52546 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
52562 TTTAAATTTAAATTCAAA
1 TTTAAATTT-AATT-AAA
** *
52580 AATAAATTTAAAATAAA
1 TTTAAATTT-AATTAAA
*
52597 TTTAAACTTAATATAAA
1 TTTAAATTTAAT-TAAA
52614 TTTAAA
1 TTTAAA
52620 AGTTTAATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 11 0.23
17 23 0.48
18 14 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:52569 original size:11 final size:11
Alignment explanation
Indices: 52547--52607 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
52537 TAAAACCATT
52547 TTAAATTT-AA
1 TTAAATTTAAA
52557 TTAAATTTAAA
1 TTAAATTTAAA
*
52568 TTTAAATTCAAAA
1 -TTAAATT-TAAA
*
52581 ATAAATTTAAA
1 TTAAATTTAAA
*
52592 ATAAATTTAAA
1 TTAAATTTAAA
52603 CTTAA
1 -TTAA
52608 TATAAATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.19
11 16 0.37
12 16 0.37
13 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:53297 original size:147 final size:146
Alignment explanation
Indices: 53030--53511 Score: 525
Period size: 147 Copynumber: 3.3 Consensus size: 146
53020 TTAATTCGCA
* *** *
53030 TGGTACTAGATTCGCCGTTATGGCTTAAAT-TTT-CCTTTCATG-CTTCTGAGGTA-TAAGG-TT
1 TGGTACTAGATTCGCCATTGCAGCTTAAATCTTTCCCTTT-ATGTCTTC-GTGGTACT--GGATT
* * * * *
53090 CACCATTGCGACTTAAACCTTTCCCCTCGTGTC-TTCACAGTACT-GGATTCGCCGTTGCGACTT
62 CACCATTGCGACTTAAATCTTTCCCTTCATGTCTTTGAC-GTACTAGG-TTCGCCATTGCGACTT
**
53153 AAATCTTTCCCTTCATGTC-TCTG
125 AAA-CTTTCCCTTTGTGTCTTC-G
* * * *
53176 AGGTACTAGATTAGCCATTGC-GACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
1 TGGTACTAGATTCGCCATTGCAG-CTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCAC
* *
53240 CGTTGCTACTTAAATCTTTCCCTTCATGTCTTTGACGTACTAGGTTCGCCATTGCGACTTAAACC
65 CATTGCGACTTAAATCTTTCCCTTCATGTCTTTGACGTACTAGGTTCGCCATTGCGACTTAAA-C
53305 TTTCCCTTTGTGTCTTCG
129 TTTCCCTTTGTGTCTTCG
* * *
53323 TGGTACTGGATTCGTCATTGCAGCTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCC
1 TGGTACTAGATTCGCCATTGCAGCTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCACC
* ** * * **
53388 ATTGCGGCTTAAATCTTTCAATTCATGTCTCTGAGGTA-TAAGGTTCATCATTGCGACTTAAACT
66 ATTGCGACTTAAATCTTTCCCTTCATGTCTTTGACGTACT-AGGTTCGCCATTGCGACTTAAAC-
53452 TTTCCCTTTGTGTCTTCG
129 TTTCCCTTTGTGTCTTCG
*
53470 TGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTTAT
1 TGGTACTAGATTCGCCATTGCAGCTTAAATCTTTCCCTTTAT
53512 ACTTATGAGG
Statistics
Matches: 287, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
145 1 0.00
146 26 0.09
147 241 0.84
148 19 0.07
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (146 bp):
TGGTACTAGATTCGCCATTGCAGCTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCACC
ATTGCGACTTAAATCTTTCCCTTCATGTCTTTGACGTACTAGGTTCGCCATTGCGACTTAAACTT
TCCCTTTGTGTCTTCG
Found at i:53417 original size:98 final size:98
Alignment explanation
Indices: 53053--53509 Score: 457
Period size: 98 Copynumber: 4.7 Consensus size: 98
53043 GCCGTTATGG
* * *
53053 CTTAAAT-TTTCCTTTCATG-CTTCTGAGGTA-TAAGGTTCACCATTGCGACTTAAACCTTTCCC
1 CTTAAATCTTTCCCTTCATGTCTTC-GAGGTACT-AGATTCGCCATTGCGACTTAAACCTTTCCC
* * *** * *
53115 CTCGTGTCTTCACAGTACTGGATTCGCCGTTGCGA
64 TTTGTGTCTTCGTGGTACTGGATTCACCATTGCGA
*
53150 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGATTAGCCATTGCGACTTAAACCTTTCCCT
1 CTTAAATCTTTCCCTTCATGTCTTC-GAGGTACTAGATTCGCCATTGCGACTTAAACCTTTCCCT
* *
53214 TTGTGTCTTCGTGGTACTGGATTCACCGTTGCTA
65 TTGTGTCTTCGTGGTACTGGATTCACCATTGCGA
* * *
53248 CTTAAATCTTTCCCTTCATGTCTTTGACGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTTCGAGGTACTAGATTCGCCATTGCGACTTAAACCTTTCCCTT
**
53313 TGTGTCTTCGTGGTACTGGATTCGTCATTGC-A
66 TGTGTCTTCGTGGTACTGGATTCACCATTGCGA
* * * * * **
53345 GCTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCAAT
1 -CTTAAATCTTTCCCTTCATGTCTTCGAGGTACTAGATTCGCCATTGCGACTTAAACCTTTCCCT
** * *
53410 TCATGTC-TCTGAGGTA-TAAGG-TTCATCATTGCGA
65 TTGTGTCTTC-GTGGTACT--GGATTCACCATTGCGA
** * * *
53444 CTTAAA-CTTTTCCCTTTGTGTCTTCGTGGTACTAGATTCGCCGTTGC-AGCTTAAATCTTTCCC
1 CTTAAATC-TTTCCCTTCATGTCTTCGAGGTACTAGATTCGCCATTGCGA-CTTAAACCTTTCCC
53507 TTT
64 TTT
53510 ATACTTATGA
Statistics
Matches: 310, Mismatches: 39, Indels: 21
0.84 0.11 0.06
Matches are distributed among these distances:
97 12 0.04
98 292 0.94
99 6 0.02
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
CTTAAATCTTTCCCTTCATGTCTTCGAGGTACTAGATTCGCCATTGCGACTTAAACCTTTCCCTT
TGTGTCTTCGTGGTACTGGATTCACCATTGCGA
Found at i:53509 original size:49 final size:49
Alignment explanation
Indices: 53030--53573 Score: 410
Period size: 49 Copynumber: 11.1 Consensus size: 49
53020 TTAATTCGCA
* ** *
53030 TGGTACTAGATTCGCCGTTATGGCTTAAAT-TTT-CCTTTCATG-CTTCTG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTT-ATGTCTTC-G
* * * * * ** *
53078 AGGTA-TAAGGTTCACCATTGCGACTTAAACCTTTCCCCTCGTGTCTTCA
1 TGGTACT-AGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
** * * *
53127 CAGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTC-TCTG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTC-G
* * * *
53176 AGGTACTAGATTAGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
* * * * * *
53225 TGGTACTGGATTCACCGTTGCTACTTAAATCTTTCCCTTCATGTCTTTG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
** * * *
53274 ACGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
* *
53323 TGGTACTGGATTCGTCATTGC-AGCTTAAATCTTTCCCTTTATGTCTTCG
1 TGGTACTAGATTCGCCATTGCGA-CTTAAATCTTTCCCTTTATGTCTTCG
* * ** *
53372 TGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCAATTCATGTC-TCTG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTC-G
* * ** *
53421 AGGTA-TAAGGTTCATCATTGCGACTTAAA-CTTTTCCCTTTGTGTCTTCG
1 TGGTACT-AGATTCGCCATTGCGACTTAAATC-TTTCCCTTTATGTCTTCG
* * *
53470 TGGTACTAGATTCGCCGTTGC-AGCTTAAATCTTTCCCTTTAT-ACTTATG
1 TGGTACTAGATTCGCCATTGCGA-CTTAAATCTTTCCCTTTATGTCTT-CG
* * * * * * * * *
53519 AGGTACAAGGTTTGCCGTTGCGACTTAAACCTTTTCCTCTGTGT-TTCG
1 TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
53567 TGGTACT
1 TGGTACT
53574 GAGACCTGTG
Statistics
Matches: 384, Mismatches: 93, Indels: 38
0.75 0.18 0.07
Matches are distributed among these distances:
47 1 0.00
48 37 0.10
49 331 0.86
50 15 0.04
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (49 bp):
TGGTACTAGATTCGCCATTGCGACTTAAATCTTTCCCTTTATGTCTTCG
Found at i:54209 original size:22 final size:23
Alignment explanation
Indices: 54177--54231 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
54167 AGCTGCCCTT
*
54177 TTTTGGTTTTTAACTCCAAACCC
1 TTTTGGTTTTTAACTCAAAACCC
54200 TTTTGGTTTTTAACTCAAAACCC
1 TTTTGGTTTTTAACTCAAAACCC
54223 TTTTGGTTT
1 TTTTGGTTT
54232 CAAGATGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (23 bp):
TTTTGGTTTTTAACTCAAAACCC
Found at i:65436 original size:30 final size:30
Alignment explanation
Indices: 65394--65760 Score: 224
Period size: 29 Copynumber: 12.5 Consensus size: 30
65384 ACTCGAGAGC
* *
65394 AAAATGGTAATTTTTGGAAAGTTC-GGAGTCA
1 AAAATGG-AATTTTTGGAAAATTCAGGGGT-A
* * *
65425 AAAATAGAATTTTTCG-AGATTCAGGGGT-
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* *
65453 AAAATGGTAA-TTTTGGAAAAATC-GAGGTCA
1 AAAATGG-AATTTTTGGAAAATTCAGGGGT-A
* *
65483 AAAATGGAATTTTTGG-AAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* *
65511 AAAATGAGAAATTTTGGAAAAATC--GGGTAA
1 AAAATG-GAATTTTTGGAAAATTCAGGGGT-A
*
65541 AAAATGGAA-TTTTGGAAATTTCAGGGGTA
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* ** * *
65570 AAAATGTAATTTTTGG-AAATTTTGAGGTT
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* * * * * *
65599 AAAAT-AAAATTTTAGAAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* * * *
65628 AACATGTAATTTTTGGAAAATTC-GAGGTT
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* *
65657 AAAATGGAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* * * * *
65686 AAAATGTAATTTTTAGAAAATTTAAGGTTA
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
* * *
65716 AAAATGGAA-TTTTGGAGAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAATTCAGGGGTA
*
65745 AAAATGAGATTTTTTG
1 AAAATG-GAATTTTTG
65761 ACAGTTTAGG
Statistics
Matches: 257, Mismatches: 59, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
28 54 0.21
29 105 0.41
30 87 0.34
31 11 0.04
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAATTCAGGGGTA
Found at i:65483 original size:58 final size:58
Alignment explanation
Indices: 65394--65747 Score: 271
Period size: 58 Copynumber: 6.1 Consensus size: 58
65384 ACTCGAGAGC
** * *
65394 AAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAATAGAATTTTTCG-AGATTCAGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGG-GTCAAAAATGGAATTTTTGGAAG-TTCAGGGGT
*
65453 AAAATGGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCG-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGGT
* * *
65511 AAAATGAG-AAATTTTGGAAAAATCGGGTAAAAAATGGAA-TTTTGGAAATTTCAGGGGT
1 AAAATG-GTAATTTTTGGAAAAATCGGGTCAAAAATGGAATTTTTGG-AAGTTCAGGGGT
** * * ** * * * *
65569 AAAAAT-GTAATTTTTGGAAATTTTGAGGT-TAAAATAAAATTTTAGAAAGTTTAAGGGT
1 -AAAATGGTAATTTTTGGAAAAATCG-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGGT
* * *
65627 AAACAT-GTAATTTTTGGAAAATTCGAGGT-TAAAATGGAA-TTTTGGAAAGTTTAGGGGT
1 AAA-ATGGTAATTTTTGGAAAAATCG-GGTCAAAAATGGAATTTTTGG-AAGTTCAGGGGT
* * ** * *
65685 AAAAAT-GTAATTTTTAGAAAATTTAAGGTTAAAAATGGAA-TTTTGGAGAGTTTAGGGGT
1 -AAAATGGTAATTTTTGGAAAA-ATCGGGTCAAAAATGGAATTTTTGGA-AGTTCAGGGGT
65744 AAAA
1 AAAA
65748 ATGAGATTTT
Statistics
Matches: 249, Mismatches: 31, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
57 14 0.06
58 164 0.66
59 71 0.29
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATCGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGT
Found at i:65551 original size:116 final size:115
Alignment explanation
Indices: 65405--65753 Score: 357
Period size: 116 Copynumber: 3.0 Consensus size: 115
65395 AAATGGTAAT
* * * *
65405 TTTTGGAAAGTTCGGAGTCAAAAATAGAATTTTTCGAGA-TTCAGGGGT-AAAATGGTAA-TTTT
1 TTTTGGAAAATTCGG-GT-AAAAATGGAA-TTTTGGAAAGTTCAGGGGTAAAAAT-GTAATTTTT
* * **
65467 GGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGAGAAA
62 GGAAAATTTGAGGT-AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGAGAAA
* *
65522 TTTTGGAAAAATCGGGTAAAAAATGGAATTTTGGAAATTTCAGGGGTAAAAATGTAATTTTTGGA
1 TTTTGGAAAATTCGGGT-AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGA
* * ** * * * * *
65587 AATTTTGAGGTTAAAATAAAATTTTAGAAAGTTTAAGGGTAAACATG-TAAT
65 AAATTTGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAA-ATGAGAAA
* * *
65638 TTTTGGAAAATTCGAGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAGA
1 TTTTGGAAAATTCG-GGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGA
*
65703 AAATTTAAGGTTAAAAATGGAA-TTTTGGAGAGTTTAGGGGTAAAAATGAGA
65 AAATTTGAGG-TAAAAATGGAATTTTTGGA-AGTTTAGGGGT-AAAATGAGA
65754 TTTTTTGACA
Statistics
Matches: 190, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
115 7 0.04
116 119 0.63
117 60 0.32
118 4 0.02
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (115 bp):
TTTTGGAAAATTCGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGAA
AATTTGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGAGAAA
Found at i:65756 original size:29 final size:30
Alignment explanation
Indices: 65394--65771 Score: 223
Period size: 30 Copynumber: 12.9 Consensus size: 30
65384 ACTCGAGAGC
* *
65394 AAAATGGTAATTTTTGGAAAG-TTCGGAGTCA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGGT-A
* * * *
65425 AAAATAGAATTTTTCGAGA-TTCAGGGGT-
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
** * *
65453 AAAATGGTAA-TTTTGGAAA-AATCGAGGTCA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGGT-A
**
65483 AAAATGGAATTTTTGG-AAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
* ** *
65511 AAAATGAGAAATTTTGGAAA-AAT-CGGGTAA
1 AAAATG-GAATTTTTGGAAAGTTTAGGGGT-A
65541 AAAATGGAA-TTTTGGAAA-TTTCAGGGGTA
1 AAAATGGAATTTTTGGAAAGTTT-AGGGGTA
* * * *
65570 AAAATGTAATTTTTGGAAA-TTTTGAGGTT
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
* * * *
65599 AAAAT-AAAATTTTAGAAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
* * * * * *
65628 AACATGTAATTTTTGGAAA-ATTCGAGGTT
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
65657 AAAATGGAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
* * * * *
65686 AAAATGTAATTTTTAGAAAATTTAAGGTTA
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
*
65716 AAAATGGAA-TTTTGGAGAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAGTTTAGGGGTA
* *
65745 AAAAT-GAGATTTTTTGACAGTTTAGGG
1 AAAATGGA-ATTTTTGGAAAGTTTAGGG
65772 ACCTTCAAGG
Statistics
Matches: 262, Mismatches: 66, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
28 58 0.22
29 93 0.35
30 105 0.40
31 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTTAGGGGTA
Found at i:66784 original size:3 final size:3
Alignment explanation
Indices: 66776--66816 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
66766 TAAAATCAAC
66776 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
66817 CTAATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:67570 original size:16 final size:18
Alignment explanation
Indices: 67532--67594 Score: 80
Period size: 17 Copynumber: 3.7 Consensus size: 18
67522 CAAATTTAAT
* *
67532 TTTAAATTTAAA-ACCAT
1 TTTAAATTTAAATACAAG
67549 TTTAAATTTAAATA-AA-
1 TTTAAATTTAAATACAAG
67565 TTTAAATTTAAA-ACAAG
1 TTTAAATTTAAATACAAG
67582 TTTAAATTTAAAT
1 TTTAAATTTAAAT
67595 TCAGAAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.02
16 14 0.34
17 25 0.61
18 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TTTAAATTTAAATACAAG
Found at i:67574 original size:33 final size:33
Alignment explanation
Indices: 67532--67594 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
67522 CAAATTTAAT
* *
67532 TTTAAATTTAAAACCATTTTAAATTTAAATAAA
1 TTTAAATTTAAAACAAGTTTAAATTTAAATAAA
67565 TTTAAATTTAAAACAAGTTTAAATTTAAAT
1 TTTAAATTTAAAACAAGTTTAAATTTAAAT
67595 TCAGAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (33 bp):
TTTAAATTTAAAACAAGTTTAAATTTAAATAAA
Found at i:80889 original size:26 final size:26
Alignment explanation
Indices: 80825--80890 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
80815 ACATATTTTC
* * *
80825 TCAAAATTTTACCAAATGTAAGATCA
1 TCAAAATTTTACTAAAGGTAAAATCA
* *
80851 TCAAAATTTTACTGAAGGTAAAATCG
1 TCAAAATTTTACTAAAGGTAAAATCA
80877 TCAAAATTTTACTA
1 TCAAAATTTTACTA
80891 GGTTAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTAAAGGTAAAATCA
Found at i:86336 original size:82 final size:82
Alignment explanation
Indices: 86199--86417 Score: 298
Period size: 82 Copynumber: 2.7 Consensus size: 82
86189 AAATTATAAC
* * * *
86199 CATTTATGTATTTTGTGAT-ACGTATGGATAATATTTAAATAAATACTGAGACACATTGGTGTCA
1 CATTTATGTATTTTGTAATAAC-TATGGATAATATTTAAATAAACATTGAGACACATTGGTGTAA
*
86263 AGGGCTTATTTAAACAAA
65 AAGGCTTATTTAAACAAA
*
86281 CATTTATGTATTTTGTAATAATTATGGATAATATTTAAATAAACATTGAGACACATTGGTGTAAA
1 CATTTATGTATTTTGTAATAACTATGGATAATATTTAAATAAACATTGAGACACATTGGTGTAAA
*
86346 AGTCTTATTTAAACAAA
66 AGGCTTATTTAAACAAA
* * * * * *
86363 CATTTATATAATTTGTAAT-ACTGTGGATGATGTTTAAATAAACATTGACACACAT
1 CATTTATGTATTTTGTAATAACTATGGATAATATTTAAATAAACATTGAGACACAT
86418 GGTATAAGAG
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
81 31 0.25
82 90 0.74
83 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (82 bp):
CATTTATGTATTTTGTAATAACTATGGATAATATTTAAATAAACATTGAGACACATTGGTGTAAA
AGGCTTATTTAAACAAA
Found at i:87978 original size:21 final size:21
Alignment explanation
Indices: 87954--88007 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
87944 CTTGGGAAAG
*
87954 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* *
87975 TTCTACTGAAACAAGTCATAC
1 TTCTACCGATACAAGTCATAC
87996 TTCTACCGATAC
1 TTCTACCGATAC
88008 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:88176 original size:21 final size:21
Alignment explanation
Indices: 88150--88200 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
88140 CAACCTGTAC
88150 TTCTACCGATACATGCAAGAG
1 TTCTACCGATACATGCAAGAG
*
88171 TTCTACCGATACATGCGAGAG
1 TTCTACCGATACATGCAAGAG
88192 TTCTACCGA
1 TTCTACCGA
88201 AACAAGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TTCTACCGATACATGCAAGAG
Found at i:93896 original size:33 final size:33
Alignment explanation
Indices: 93858--93938 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
93848 AAGAATTTGA
93858 ATAAATTCTAAAAAAAACTTGACGTCAGTTTTC
1 ATAAATTCTAAAAAAAACTTGACGTCAGTTTTC
93891 ATAAATTCTAAAAAAAACTTGACGTCAGTTTTC
1 ATAAATTCTAAAAAAAACTTGACGTCAGTTTTC
*
93924 ATAAATTCTTAAAAA
1 ATAAATTCTAAAAAA
93939 CTCGCTATCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
ATAAATTCTAAAAAAAACTTGACGTCAGTTTTC
Found at i:95745 original size:18 final size:19
Alignment explanation
Indices: 95704--95746 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
95694 TGTATCAATC
*
95704 AAAAATAATTTAAAAATTA
1 AAAAATAATTTAAAAATAA
*
95723 TAAAAT-ATTTAAAAATAA
1 AAAAATAATTTAAAAATAA
95741 AAAAAT
1 AAAAAT
95747 CAAAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATAATTTAAAAATAA
Found at i:95769 original size:18 final size:16
Alignment explanation
Indices: 95705--95769 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 16
95695 GTATCAATCA
95705 AAAATAATTTAAAAATT
1 AAAA-AATTTAAAAATT
95722 ATAAAATATTTAAAAA-T
1 A-AAAA-ATTTAAAAATT
* *
95739 AAAAAA-ATCAAAATT
1 AAAAAATTTAAAAATT
95754 GAAAAAATTATAAAAA
1 -AAAAAATT-TAAAAA
95770 AAAATTGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 10 0.26
17 4 0.11
18 17 0.45
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAAATTTAAAAATT
Found at i:95773 original size:22 final size:23
Alignment explanation
Indices: 95739--95796 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
95729 ATTTAAAAAT
95739 AAAAAAATCAAAATTGAAAAAATT-
1 AAAAAAA--AAAATTGAAAAAATTC
* *
95763 ATAAAAAAAAATTGAGAAAATTC
1 AAAAAAAAAAATTGAAAAAATTC
95786 AAAAAAAAAAA
1 AAAAAAAAAAA
95797 AAAAGCACAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.47
23 10 0.33
24 6 0.20
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (23 bp):
AAAAAAAAAAATTGAAAAAATTC
Found at i:101376 original size:344 final size:338
Alignment explanation
Indices: 100743--101407 Score: 1107
Period size: 344 Copynumber: 1.9 Consensus size: 338
100733 CTCATGCTCA
**
100743 TGTCCAGATATGCATCAAACACGGATACTTCTAGAAAAATGAATAGTTGGAGCAACAAAGTGTGC
1 TGTCCAGATATGCATCAAACACGGATACTTCTAGAAAAATGAATAGTCAGAGCAACAAAGTGTGC
*
100808 TAGTGCGAGATTTCCGATGTTAGCTAAAGTTTTCTGTAATTGAAAGGTCTTTTTTCCCCCTTGCT
66 TAGTGCGAGATTTCCGATGTTAGCTAAAGTTTTCTGCAATTGAAAGGTCTTTTTTCCCCCTTGCT
*
100873 GGTTAGAAGTTGAGAAGATTTAGGCATGAGCTATGATCAGTCATATTTGCTTTGTGAACTAGTTT
131 GGTTAGAAGTTGAGAAGATTTAGGCATGAGCTATGACCAGTCATATTTGCTTTGTGAACTAGTTT
*
100938 CCGATGCCAAGGTGCATTAGGGTCCCAATAAAGAAAGATTAAAGAGCAATAAGTCGAGGCTTTTT
196 CCAATGCCAAGGTGCATTAGGGTCCCAATAAAGAAAGATTAAAGAGCAATAAGTCGAGGCTTTTT
* *
101003 TAATTTGCTGCATAACAGTTCGTTATTATTTTCTGTTAAAGATTTGGAAGTTTTCACACTGCTGT
261 TAATTTGCTGCATAACAGTTCGTTATTA-----T-TTAAAGATTGGGAAGTTTTCACACCGCTGT
101068 ACAGATTTCGTTATTATTT
320 ACAGATTTCGTTATTATTT
* *
101087 TGTCCGGATATGCATCAAACACTGATACTTCTAGAAAAATGAATAGTCAGAGCAACAAAGTGTGC
1 TGTCCAGATATGCATCAAACACGGATACTTCTAGAAAAATGAATAGTCAGAGCAACAAAGTGTGC
* * * *
101152 TAGTGCTAGATTTCCGATGTTAGCTAAAGTTTTCTGCACTTGAAAAGTTCTTTTTTTCCCCTTGC
66 TAGTGCGAGATTTCCGATGTTAGCTAAAGTTTTCTGCAATTG-AAAGGTCTTTTTTCCCCCTTGC
* *
101217 TGGTTAGAAGTTTAGAAGA-TTAGGCATGAGTTATGACCAGTCATATTTGCTTTGTGAACTAGTT
130 TGGTTAGAAGTTGAGAAGATTTAGGCATGAGCTATGACCAGTCATATTTGCTTTGTGAACTAGTT
101281 TCCAATGCCAAGGTGCATTAGGGTCCCAATAAAGAAAGATTAAAGAGCAATAAGTCGAGGCTTTT
195 TCCAATGCCAAGGTGCATTAGGGTCCCAATAAAGAAAGATTAAAGAGCAATAAGTCGAGGCTTTT
* *
101346 TTAATTTGTTGCATAACATTTCGTTATTATTTAAAGATTGGGAAGTTTTCACACCGCTGTAC
260 TTAATTTGCTGCATAACAGTTCGTTATTATTTAAAGATTGGGAAGTTTTCACACCGCTGTAC
101408 GGATGTGAAG
Statistics
Matches: 303, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
338 30 0.10
339 1 0.00
344 234 0.77
345 38 0.13
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (338 bp):
TGTCCAGATATGCATCAAACACGGATACTTCTAGAAAAATGAATAGTCAGAGCAACAAAGTGTGC
TAGTGCGAGATTTCCGATGTTAGCTAAAGTTTTCTGCAATTGAAAGGTCTTTTTTCCCCCTTGCT
GGTTAGAAGTTGAGAAGATTTAGGCATGAGCTATGACCAGTCATATTTGCTTTGTGAACTAGTTT
CCAATGCCAAGGTGCATTAGGGTCCCAATAAAGAAAGATTAAAGAGCAATAAGTCGAGGCTTTTT
TAATTTGCTGCATAACAGTTCGTTATTATTTAAAGATTGGGAAGTTTTCACACCGCTGTACAGAT
TTCGTTATTATTT
Found at i:105434 original size:58 final size:58
Alignment explanation
Indices: 105351--105465 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
105341 ATTTTGGGTT
* *
105351 TATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTC
1 TATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGTC
* *
105409 TATGAGTGTT-TTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGAGTTTAGT
1 TATGAGTGTTATTT-AAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGT
105466 TTGTTGATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (58 bp):
TATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGTC
Found at i:105722 original size:25 final size:25
Alignment explanation
Indices: 105677--105724 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
105667 AAAAAAATTC
*
105677 AACTCGATTCATTTAACTCGAAAAT
1 AACTCGATTCATATAACTCGAAAAT
*
105702 AACTCGATTCGA-ATAATTCGAAA
1 AACTCGATTC-ATATAACTCGAAA
105725 TTCAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (25 bp):
AACTCGATTCATATAACTCGAAAAT
Found at i:107977 original size:5 final size:5
Alignment explanation
Indices: 107940--107976 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
107930 CATATTTTAA
107940 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
107977 TAATTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:113823 original size:9 final size:9
Alignment explanation
Indices: 113809--113901 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 9
113799 AAATATAAAT
*
113809 TTTTATTTA
1 TTTTATATA
113818 TTTTATATA
1 TTTTATATA
113827 -TTTATATA
1 TTTTATATA
*
113835 TTTTTTATAA
1 TTTTATAT-A
* *
113845 ATTTATAAA
1 TTTTATATA
*
113854 TTTTA-AGCTC
1 TTTTATA--TA
113864 TTTTATATA
1 TTTTATATA
*
113873 -TTCATATA
1 TTTTATATA
* *
113881 TTGTA-ATT
1 TTTTATATA
113889 TTTTATATA
1 TTTTATATA
113898 TTTT
1 TTTT
113902 TCAAAATATT
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
8 22 0.35
9 28 0.45
10 11 0.18
11 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATATA
Found at i:113824 original size:19 final size:19
Alignment explanation
Indices: 113802--113857 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
113792 TTTATAAAAA
*
113802 TATAAATTTTTAT-TTATTT
1 TATAAATTTATATATT-TTT
*
113821 TATATATTTATATATTTTT
1 TATAAATTTATATATTTTT
*
113840 TATAAATTTATAAATTTT
1 TATAAATTTATATATTTT
113858 AAGCTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATAAATTTATATATTTTT
Found at i:113840 original size:46 final size:46
Alignment explanation
Indices: 113783--113882 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
113773 TTTAGTTCCC
* **
113783 TTATATA-TTTTTATAAAAATATAAATTTTTATTTATTTTATATAT
1 TTATATATTTTTTATAAAAATATAAATTTTAAGCTATTTTATATAT
** *
113828 TTATATATTTTTTATAAATTTATAAATTTTAAGCTCTTTTATATAT
1 TTATATATTTTTTATAAAAATATAAATTTTAAGCTATTTTATATAT
*
113874 TCATATATT
1 TTATATATT
113883 GTAATTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 7 0.15
46 40 0.85
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (46 bp):
TTATATATTTTTTATAAAAATATAAATTTTAAGCTATTTTATATAT
Found at i:115290 original size:31 final size:31
Alignment explanation
Indices: 115232--115292 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
115222 TTAACAACCC
* **
115232 AATAATTTAAAGAAAAAATTTTGAATAGTTT
1 AATAACTTAAAGAAAAAATTTCAAATAGTTT
* *
115263 AATAACTTAAATAAAAACTTTCAAATAGTT
1 AATAACTTAAAGAAAAAATTTCAAATAGTT
115293 CACTAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (31 bp):
AATAACTTAAAGAAAAAATTTCAAATAGTTT
Found at i:123044 original size:18 final size:19
Alignment explanation
Indices: 123012--123051 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
123002 AACATATAAA
123012 AAAATTAATCAAATTAACC
1 AAAATTAATCAAATTAACC
*
123031 AAAA-TAATCGAATTAACC
1 AAAATTAATCAAATTAACC
123049 AAA
1 AAA
123052 TCTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATTAATCAAATTAACC
Found at i:124044 original size:17 final size:18
Alignment explanation
Indices: 124024--124062 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
124014 AAAAAGCTTA
124024 AAGAAGAAAA-AGAAAAG
1 AAGAAGAAAAGAGAAAAG
*
124041 AAG-AGAAAAGATAAAAG
1 AAGAAGAAAAGAGAAAAG
124058 AAGAA
1 AAGAA
124063 TATTTAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 12 0.63
18 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAGAAGAAAAGAGAAAAG
Found at i:124131 original size:7 final size:7
Alignment explanation
Indices: 124119--124144 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
124109 GTCGTTGCCT
124119 AAATGGG
1 AAATGGG
124126 AAATGGG
1 AAATGGG
124133 AAATGGG
1 AAATGGG
124140 AAATG
1 AAATG
124145 TAGTACTAGT
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:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (7 bp):
AAATGGG
Found at i:130062 original size:21 final size:22
Alignment explanation
Indices: 130038--130090 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
130028 CTTGGGAAAG
*
130038 TTCTACCGATA-CAAGTGTAAC
1 TTCTACCGATACCAAGTCTAAC
* *
130059 TTCTATCGA-ACCAAGTCTTAC
1 TTCTACCGATACCAAGTCTAAC
130080 TTCTACCGATA
1 TTCTACCGATA
130091 TTAAAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (22 bp):
TTCTACCGATACCAAGTCTAAC
Found at i:132757 original size:21 final size:20
Alignment explanation
Indices: 132733--132807 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
132723 GAAATTTAAA
132733 ACAAACATAATGATGAGAGTT
1 ACAAACATAATGA-GAGAGTT
*
132754 ACAAA-ACTTATGAGCAGAGTT
1 ACAAACA-TAATGAG-AGAGTT
*
132775 ACAAACATTATGAGGAGAGTT
1 ACAAACATAATGA-GAGAGTT
*
132796 ACAAATATAATG
1 ACAAACATAATG
132808 TTTTGTAGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.24
Consensus pattern (20 bp):
ACAAACATAATGAGAGAGTT
Found at i:135429 original size:23 final size:23
Alignment explanation
Indices: 135351--135522 Score: 129
Period size: 23 Copynumber: 7.4 Consensus size: 23
135341 TATACGGAAC
* *
135351 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
135373 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
135394 GGGTAACAAAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
135420 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
**
135443 AATTAGAGAGC-CACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
135465 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
135488 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
135513 AAACAGAGAG
1 AAACAGAGAG
135523 TGCGCTAGTG
Statistics
Matches: 119, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
21 17 0.14
22 20 0.17
23 45 0.38
24 2 0.02
25 28 0.24
26 7 0.06
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:135472 original size:45 final size:46
Alignment explanation
Indices: 135403--135522 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 46
135393 TGGGTAACAA
* *
135403 AGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAATTAG
1 AGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATTAG
* * * *
135449 AGAGC-CACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAG
1 AGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT--TAG
* *
135496 AGAGCACGA-GACGTGCTAAACAGAGAG
1 AGAGCAC-ACAAAGTGCTAAACAGAGAG
135523 TGCGCTAGTG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
45 32 0.52
46 5 0.08
47 7 0.11
48 16 0.26
49 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (46 bp):
AGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATTAG
Found at i:135481 original size:70 final size:67
Alignment explanation
Indices: 135351--135499 Score: 187
Period size: 70 Copynumber: 2.1 Consensus size: 67
135341 TATACGGAAC
135351 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACAAAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGC---GTAACAAAGAGCACACACAG
135416 TGCT-
63 TGCTA
* *
135420 AAACAGAGAGTACACAAAGTACTAATTAGAGAGCCACA-AAGTGC-TAATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAG-CACATAAGTGCGTAA-CAAAGAGCACACACA
135483 GTGCTA
62 GTGCTA
135489 ATAACAGAGAG
1 A-AACAGAGAG
135500 CACGAGACGT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
67 3 0.04
68 19 0.26
69 14 0.19
70 20 0.28
71 12 0.17
72 4 0.06
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCGTAACAAAGAGCACACACAGTGC
TA
Found at i:146635 original size:19 final size:17
Alignment explanation
Indices: 146610--146667 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
146600 CACATTATGC
146610 TATTTTTTTGAATTTTTA
1 TATTTTTTT-AATTTTTA
146628 TGATTTTTTATAATTTTTA
1 T-ATTTTTT-TAATTTTTA
146647 T-TTTTTTTAATATTTTTA
1 TATTTTTTT-A-ATTTTTA
146665 TAT
1 TAT
146668 ATTTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 7 0.20
18 9 0.26
19 17 0.49
20 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTTTTAATTTTTA
Found at i:146649 original size:16 final size:17
Alignment explanation
Indices: 146630--146662 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
146620 AATTTTTATG
146630 ATTTTTTATAAT-TTTT
1 ATTTTTTATAATATTTT
*
146646 ATTTTTTTTAATATTTT
1 ATTTTTTATAATATTTT
146663 TATATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTATAATATTTT
Found at i:146669 original size:10 final size:10
Alignment explanation
Indices: 146621--146671 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
146611 ATTTTTTTGA
146621 ATTTTTATGAT
1 ATTTTTAT-AT
146632 -TTTTTATA-
1 ATTTTTATAT
146640 ATTTTTAT-T
1 ATTTTTATAT
*
146649 TTTTTTA-AT
1 ATTTTTATAT
146658 ATTTTTATAT
1 ATTTTTATAT
146668 ATTT
1 ATTT
146672 AAAATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 21 0.62
10 13 0.38
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:147278 original size:10 final size:10
Alignment explanation
Indices: 147258--147299 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
147248 TGAAATAAAC
147258 TTATAAAAATA
1 TTAT-AAAATA
147269 TTATAAAATA
1 TTATAAAATA
147279 TTATAAAATA
1 TTATAAAATA
*
147289 TAAT-AAATA
1 TTATAAAATA
147298 TT
1 TT
147300 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 6 0.21
10 19 0.66
11 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATAAAATA
Found at i:147298 original size:19 final size:21
Alignment explanation
Indices: 147258--147320 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
147248 TGAAATAAAC
*
147258 TTATAAAAATATTATAAAATA
1 TTATAAAAATATAATAAAATA
*
147279 TTAT-AAAATATAATAAATATT
1 TTATAAAAATATAATAAA-ATA
*
147300 TTTTATAAAAT-TAATAAAATA
1 TTATA-AAAATATAATAAAATA
147321 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.34
21 11 0.31
22 7 0.20
23 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATAAAAATATAATAAAATA
Found at i:147326 original size:22 final size:22
Alignment explanation
Indices: 147250--147326 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
147240 ATAAAAATTG
* *
147250 AAATAAACTTATAAAA-ATATT
1 AAATAAATTTATAAAATATAAT
*
147271 ATA-AAATATTATAAAATATAAT
1 AAATAAAT-TTATAAAATATAAT
**
147293 AAATATTTTTTATAAAAT-TAAT
1 AAATA-AATTTATAAAATATAAT
147315 AAAATAAATTTA
1 -AAATAAATTTA
147327 AAATTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 14 0.33
23 15 0.35
24 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAAATTTATAAAATATAAT
Found at i:147373 original size:12 final size:12
Alignment explanation
Indices: 147356--147380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
147346 AAAGCTCTAT
147356 AAAAATTATAAA
1 AAAAATTATAAA
147368 AAAAATTATAAA
1 AAAAATTATAAA
147380 A
1 A
147381 TGTATTAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:147979 original size:28 final size:30
Alignment explanation
Indices: 147948--148004 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
147938 CAAGAATTCT
147948 AATAA-TTTT-TTAACTTTTA-AATATTTTA
1 AATAAGTTTTATTAA-TTTTATAATATTTTA
*
147976 AATAAGTTTTATTAATTTTATAATTTTTT
1 AATAAGTTTTATTAATTTTATAATATTTT
148005 TGTAACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 9 0.36
30 11 0.44
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
AATAAGTTTTATTAATTTTATAATATTTTA
Found at i:148003 original size:9 final size:9
Alignment explanation
Indices: 147949--148127 Score: 57
Period size: 9 Copynumber: 19.2 Consensus size: 9
147939 AAGAATTCTA
147949 ATAATTTTT
1 ATAATTTTT
*
147958 -TAACTTTT
1 ATAATTTTT
147966 A-AATATTTT
1 ATAAT-TTTT
*
147975 AAATAAGTTTT
1 --ATAATTTTT
147986 ATTAA-TTTT
1 A-TAATTTTT
147995 ATAATTTTTTT
1 ATAA--TTTTT
* *
148006 GTAACTTATT
1 ATAA-TTTTT
* *
148016 AGATTTTTT
1 ATAATTTTT
148025 AT-A-TTTT
1 ATAATTTTT
*
148032 ATAATATTT
1 ATAATTTTT
148041 ATAAGTTTTT
1 ATAA-TTTTT
*
148051 ATAATTTTA
1 ATAATTTTT
*
148060 ATAAGTTTAT
1 ATAA-TTTTT
**
148070 ATCAATTTCA
1 AT-AATTTTT
148080 AT-ATTTTT
1 ATAATTTTT
*
148088 -TTATTTTT
1 ATAATTTTT
*
148096 ATAGTTTTTTT
1 ATA--ATTTTT
*
148107 ATGATTTTT
1 ATAATTTTT
*
148116 AATCATTTTT
1 -ATAATTTTT
148126 AT
1 AT
148128 GGGAAAATAT
Statistics
Matches: 125, Mismatches: 26, Indels: 38
0.66 0.14 0.20
Matches are distributed among these distances:
7 7 0.06
8 23 0.18
9 38 0.30
10 34 0.27
11 21 0.17
12 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:148040 original size:19 final size:19
Alignment explanation
Indices: 147968--148040 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
147958 TAACTTTTAA
147968 ATATTTTA-AATAAGTTTTATT
1 ATATTTTATAAT-A-TTTT-TT
147989 A-ATTTTATAAT-TTTTTT
1 ATATTTTATAATATTTTTT
* ** * *
148006 GTAACTTATTAGATTTTTT
1 ATATTTTATAATATTTTTT
148025 ATATTTTATAATATTT
1 ATATTTTATAATATTT
148041 ATAAGTTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
17 2 0.05
18 10 0.26
19 17 0.44
20 6 0.15
21 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (19 bp):
ATATTTTATAATATTTTTT
Found at i:148050 original size:19 final size:19
Alignment explanation
Indices: 148028--148082 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
148018 ATTTTTTATA
148028 TTTTATAATATTT-ATAAGT
1 TTTTATAAT-TTTAATAAGT
148047 TTTTATAATTTTAATAAGT
1 TTTTATAATTTTAATAAGT
* *
148066 TTATATCAATTTCAATA
1 TTTTAT-AATTTTAATA
148083 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 3 0.09
19 20 0.62
20 9 0.28
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTTATAATTTTAATAAGT
Found at i:149570 original size:21 final size:20
Alignment explanation
Indices: 149546--149598 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
149536 TATCATATTT
149546 ATTTATATATATTTAAAAAAC
1 ATTTATATATATTT-AAAAAC
*
149567 ATTTATCATAT-CTTAAAAAC
1 ATTTAT-ATATATTTAAAAAC
*
149587 ATTTATTTATAT
1 ATTTATATATAT
149599 ATATTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.11
20 12 0.44
21 8 0.30
22 4 0.15
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATATATATTTAAAAAC
Found at i:150899 original size:28 final size:29
Alignment explanation
Indices: 150868--150949 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 29
150858 TTATTATCTT
* * *
150868 TAAAAAATAGGTT-TTTACCCAAATAATA
1 TAAAAAATAGATTAATTACCAAAATAATA
*
150896 TAAAAAATA-ATTAATTACGAAAATAATA
1 TAAAAAATAGATTAATTACCAAAATAATA
*
150924 TAAAAAATAGATTAATTACGAAAATA
1 TAAAAAATAGATTAATTACCAAAATA
150950 GACATTTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
27 2 0.04
28 30 0.62
29 16 0.33
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (29 bp):
TAAAAAATAGATTAATTACCAAAATAATA
Found at i:150929 original size:29 final size:29
Alignment explanation
Indices: 150888--150949 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
150878 GTTTTTACCC
150888 AAATAATATAAAAAATA-ATTAATTACGA
1 AAATAATATAAAAAATAGATTAATTACGA
150916 AAATAATATAAAAAATAGATTAATTACGA
1 AAATAATATAAAAAATAGATTAATTACGA
150945 AAATA
1 AAATA
150950 GACATTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAATATAAAAAATAGATTAATTACGA
Found at i:150951 original size:17 final size:16
Alignment explanation
Indices: 150899--150949 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
150889 AATAATATAA
150899 AAAATAATTAATTACG
1 AAAATAATTAATTACG
*
150915 AAAATAA-T-A-TA-A
1 AAAATAATTAATTACG
150927 AAAATAGATTAATTACG
1 AAAATA-ATTAATTACG
150944 AAAATA
1 AAAATA
150950 GACATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 2 0.07
15 2 0.07
16 9 0.32
17 6 0.21
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAATAATTAATTACG
Found at i:151727 original size:26 final size:27
Alignment explanation
Indices: 151672--151735 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
151662 GTAACAAATA
* *
151672 TATATTTTCT-TAATTAATTGTTTTAC
1 TATATTTTTTATAATTAATTATTTTAC
*
151698 TATATTTTTTATAATTAATTATTTT-T
1 TATATTTTTTATAATTAATTATTTTAC
*
151724 TATATTATTTAT
1 TATATTTTTTAT
151736 GTAAAAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
TATATTTTTTATAATTAATTATTTTAC
Done.