Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013067.1 Kokia drynarioides strain JFW-HI SEQ_128085, 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: 118927
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:550 original size:13 final size:13
Alignment explanation
Indices: 532--556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522 TAAATATTTA
532 AACTTTAATAATT
1 AACTTTAATAATT
545 AACTTTAATAAT
1 AACTTTAATAAT
557 CACTTAATTA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AACTTTAATAATT
Found at i:4088 original size:9 final size:9
Alignment explanation
Indices: 4069--4098 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4059 TTAATTTTTT
4069 AAAAATT-A
1 AAAAATTCA
4077 AAAAATTCA
1 AAAAATTCA
4086 AAAAATTCA
1 AAAAATTCA
4095 AAAA
1 AAAA
4099 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATTCA
Found at i:10301 original size:29 final size:30
Alignment explanation
Indices: 10242--10301 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
10232 CTATATATAT
* * **
10242 TTAGTTTAAGATTTAATTAAGTTAATTTAA
1 TTAGTTTAAGACTTAATTAACTTAAACTAA
10272 TTAGTTTAAG-CTTAATTAACTTAAACTAA
1 TTAGTTTAAGACTTAATTAACTTAAACTAA
10301 T
1 T
10302 CATACCTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAGTTTAAGACTTAATTAACTTAAACTAA
Found at i:12418 original size:16 final size:16
Alignment explanation
Indices: 12395--12436 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
12385 GATTAGATGT
12395 TTAG-TTGATTAAGTC
1 TTAGTTTGATTAAGTC
**
12410 TTAGTTTGATTGGGTC
1 TTAGTTTGATTAAGTC
12426 TTAGTTTGATT
1 TTAGTTTGATT
12437 GGCATCGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.19, C:0.05, G:0.24, T:0.52
Consensus pattern (16 bp):
TTAGTTTGATTAAGTC
Found at i:12437 original size:16 final size:16
Alignment explanation
Indices: 12407--12438 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12397 AGTTGATTAA
12407 GTCTTAGTTTGATTGG
1 GTCTTAGTTTGATTGG
12423 GTCTTAGTTTGATTGG
1 GTCTTAGTTTGATTGG
12439 CATCGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
GTCTTAGTTTGATTGG
Found at i:13688 original size:30 final size:29
Alignment explanation
Indices: 13645--13703 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
13635 TAAAAACTTC
* *
13645 AATTTTTTTGTTCATATTCGTTTATTTAA
1 AATTTTTGTGTTCATATTCATTTATTTAA
*
13674 AATTATTTGTGTTCATATTCATTTGTTTAA
1 AATT-TTTGTGTTCATATTCATTTATTTAA
13704 TGTTCACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.25, C:0.07, G:0.08, T:0.59
Consensus pattern (29 bp):
AATTTTTGTGTTCATATTCATTTATTTAA
Found at i:13739 original size:23 final size:24
Alignment explanation
Indices: 13709--13769 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
13699 TTTAATGTTC
13709 ACGAACATGTTCACAAACAT-TAA
1 ACGAACATGTTCACAAACATATAA
* *
13732 ACGAACATGTTTATAAACATATAA
1 ACGAACATGTTCACAAACATATAA
***
13756 TTTAACATGTTCAC
1 ACGAACATGTTCAC
13770 GAATAATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (24 bp):
ACGAACATGTTCACAAACATATAA
Found at i:17348 original size:87 final size:88
Alignment explanation
Indices: 17202--17443 Score: 335
Period size: 88 Copynumber: 2.8 Consensus size: 88
17192 TCTTTCGGTT
* * * * *
17202 TGCCTAACAAAAATATT-TCCCTAAATTTGTCTTGCATTGTGCATGCCAATGTTATCTGAAATG-
1 TGCCTAGCAAAAATATTGT-CTTGAATTTGTCTTGTATTGTGCATGCCAATGTTACCTGAAATGA
17265 ATGCAGAACGATTCTATTTCAGTA
65 ATGCAGAACGATTCTATTTCAGTA
17289 TGCCTAGCAAAAATATTGTCTTGAATTTGTCTTGTATTGTGCATGCCAATGTTACCTGAAATGAA
1 TGCCTAGCAAAAATATTGTCTTGAATTTGTCTTGTATTGTGCATGCCAATGTTACCTGAAATGAA
*
17354 TGTAGAACGATTCTATTTCAGTA
66 TGCAGAACGATTCTATTTCAGTA
* * * * * * * *
17377 TGCCTAGTAAAAATATCGTCTTGAATTTGTCTTGTATCGTACATACCAATGTTTCTTAAAATGAA
1 TGCCTAGCAAAAATATTGTCTTGAATTTGTCTTGTATTGTGCATGCCAATGTTACCTGAAATGAA
17442 TG
66 TG
17444 TTGAAATGAA
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
87 56 0.40
88 83 0.60
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (88 bp):
TGCCTAGCAAAAATATTGTCTTGAATTTGTCTTGTATTGTGCATGCCAATGTTACCTGAAATGAA
TGCAGAACGATTCTATTTCAGTA
Found at i:17518 original size:100 final size:100
Alignment explanation
Indices: 17345--17541 Score: 261
Period size: 100 Copynumber: 2.0 Consensus size: 100
17335 CAATGTTACC
* * ** ** * *
17345 TGAAATGAATGTAGAACGATTCTATTTCAGTATGCCTAGTAAAAATATCGTCTTGAATTTGTCTT
1 TGAAATGAATGCAGAACGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCTT
*
17410 GTATCGTACATACCAATGTTTCTTAAAATGAATGT
66 GTATCGTACATACCAATGTTACTTAAAATGAATGT
* *
17445 TGAAATGAATGCA-AATCGATTCTATTTTAATATGCCTAACAAAAATATTACCCTGAACTTGTCT
1 TGAAATGAATGCAGAA-CGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCT
* *
17509 TGTGTCGTACATACCAATGTTACTTGAAATGAA
65 TGTATCGTACATACCAATGTTACTTAAAATGAA
17542 AACCAATTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 2 0.02
100 81 0.98
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (100 bp):
TGAAATGAATGCAGAACGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCTT
GTATCGTACATACCAATGTTACTTAAAATGAATGT
Found at i:17560 original size:100 final size:100
Alignment explanation
Indices: 17347--17566 Score: 230
Period size: 100 Copynumber: 2.2 Consensus size: 100
17337 ATGTTACCTG
* * ** ** * *
17347 AAATGAATGTAGAA-CGATTCTATTTCAGTATGCCTAGTAAAAATATCGTCTTGAATTTGTCTTG
1 AAATGAATGCA-AATCGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCTTG
* ****
17411 TATCGTACATACCAATGTTTCTTAAAATGAATGTTG
65 TATCGTACATACCAATGTTACTTAAAATGAATAACC
* *
17447 AAATGAATGCAAATCGATTCTATTTTAATATGCCTAACAAAAATATTACCCTGAACTTGTCTTGT
1 AAATGAATGCAAATCGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCTTGT
* *
17512 GTCGTACATACCAATGTTACTTGAAATGAA-AACC
66 ATCGTACATACCAATGTTACTTAAAATGAATAACC
*
17546 AATTGAA-GCACAAATCGATTC
1 AAATGAATG--CAAATCGATTC
17567 AAAATTTGGA
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
98 1 0.01
99 8 0.08
100 90 0.91
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (100 bp):
AAATGAATGCAAATCGATTCTATTTCAATATGCCTAACAAAAATATCACCCTGAACTTGTCTTGT
ATCGTACATACCAATGTTACTTAAAATGAATAACC
Found at i:26606 original size:3 final size:3
Alignment explanation
Indices: 26598--26640 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
26588 CTATTCTCAA
26598 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
26641 AGATTCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:27370 original size:21 final size:21
Alignment explanation
Indices: 27340--27379 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27330 CTCAAACAAA
*
27340 ATTTAAGGTTCATGATTCAAG
1 ATTTAAGGTTCACGATTCAAG
* *
27361 ATTTAGGGTTTACGATTCA
1 ATTTAAGGTTCACGATTCA
27380 TTATTATGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
ATTTAAGGTTCACGATTCAAG
Found at i:32523 original size:45 final size:45
Alignment explanation
Indices: 32458--32544 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
32448 CGATCACTGG
* *
32458 TTAATGTATGAGAGACCCTTGTCATCTCACTTAACTCCCGTGAGA
1 TTAATGTAGGAGAGACCCTTGCCATCTCACTTAACTCCCGTGAGA
* *
32503 TTAATGTAGGAGAGATCCTTGCCATCTCACTTAACTCTCGTG
1 TTAATGTAGGAGAGACCCTTGCCATCTCACTTAACTCCCGTG
32545 GTTTCAACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (45 bp):
TTAATGTAGGAGAGACCCTTGCCATCTCACTTAACTCCCGTGAGA
Found at i:38136 original size:23 final size:23
Alignment explanation
Indices: 38092--38137 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38082 AAAAAAAATT
**
38092 CAACTCGATTCGTTTAACTCGAA
1 CAACTCGATTCGAATAACTCGAA
*
38115 CAACTCGATTCGAATAATTCGAA
1 CAACTCGATTCGAATAACTCGAA
38138 ATACGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (23 bp):
CAACTCGATTCGAATAACTCGAA
Found at i:40098 original size:15 final size:15
Alignment explanation
Indices: 40056--40101 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
40046 TTTAGGCTTC
40056 TTTTTATT-ATATTT
1 TTTTTATTAATATTT
40070 TAATTTT-TTAAATATTT
1 T--TTTTATT-AATATTT
40087 TTTTTATTAATATTT
1 TTTTTATTAATATTT
40102 AATAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.04
15 13 0.48
16 6 0.22
17 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTAATATTT
Found at i:43760 original size:2 final size:2
Alignment explanation
Indices: 43753--43785 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43743 ATTATTCATT
43753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43786 TCAAACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48574 original size:3 final size:3
Alignment explanation
Indices: 48566--48597 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48556 CCCTAGCCAA
48566 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
48598 TGGATGTCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:52443 original size:24 final size:24
Alignment explanation
Indices: 52411--52457 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52401 ACCTTGAAAG
52411 CCTTGAGTTGTTCTTCCATTGTTA
1 CCTTGAGTTGTTCTTCCATTGTTA
*
52435 CCTTGAGTTGTTCTTCTATTGTT
1 CCTTGAGTTGTTCTTCCATTGTT
52458 GCATTGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (24 bp):
CCTTGAGTTGTTCTTCCATTGTTA
Found at i:52464 original size:24 final size:24
Alignment explanation
Indices: 52413--52465 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
52403 CTTGAAAGCC
*
52413 TTGAGTTGTTCTTCCATTGTTACC
1 TTGAGTTGTTCTTCCATTGTTACA
* *
52437 TTGAGTTGTTCTTCTATTGTTGCA
1 TTGAGTTGTTCTTCCATTGTTACA
52461 TTGAG
1 TTGAG
52466 AACTTTGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (24 bp):
TTGAGTTGTTCTTCCATTGTTACA
Found at i:66027 original size:30 final size:28
Alignment explanation
Indices: 65965--66119 Score: 132
Period size: 30 Copynumber: 5.4 Consensus size: 28
65955 CCCTACTTTA
** * *
65965 TTTTAAAATT-ATTTTTGACCCTAAACT
1 TTTTAAAATTCAAATTTAACCCTAAATT
*
65992 TTTTAAAATTCAAATTTAACCCCTAATTTT
1 TTTTAAAATTCAAATTTAA-CCCTAA-ATT
*
66022 TTTTAAAACTCAAATTTAACCCTAAATT
1 TTTTAAAATTCAAATTTAACCCTAAATT
** *
66050 TTCCAAAGATTCAAATTTGATCCCTAAATT
1 TTTTAAA-ATTCAAATTT-AACCCTAAATT
** * *
66080 TTCCAAAAATTTAAATTTAAGCCCTAAACT
1 TT-TTAAAATTCAAATTTAA-CCCTAAATT
66110 TTTTAAAATT
1 TTTTAAAATT
66120 TTTGATTTGA
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
27 10 0.10
28 12 0.12
29 28 0.27
30 50 0.48
31 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTTAAAATTCAAATTTAACCCTAAATT
Found at i:66158 original size:30 final size:29
Alignment explanation
Indices: 65978--66162 Score: 122
Period size: 30 Copynumber: 6.3 Consensus size: 29
65968 TAAAATTATT
**
65978 TTTGA-CCCTAAACTTTTTAAAATTCAAA
1 TTTGACCCCTAAACTTTCAAAAATTCAAA
* ** ** *
66006 TTTAACCCCTAATTTTTTTTAAAACTCAAA
1 TTTGACCCCTAA-ACTTTCAAAAATTCAAA
* * *
66036 TTT-AACCCTAAATTTTCCAAAGATTCAAA
1 TTTGACCCCTAAACTTT-CAAAAATTCAAA
* * *
66065 TTTGATCCCTAAATTTTCCAAAAATTTAAA
1 TTTGACCCCTAAACTTT-CAAAAATTCAAA
* * * * ***
66095 TTTAAGCCCTAAACTTTTTAAAATTTTTGA
1 TTTGACCCCTAAAC-TTTCAAAAATTCAAA
66125 TTTGACCCCTAAAGCTTTCAAAAATTCAAA
1 TTTGACCCCTAAA-CTTTCAAAAATTCAAA
66155 TTTGACCC
1 TTTGACCC
66163 GGTTTTAATG
Statistics
Matches: 124, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
28 8 0.06
29 24 0.19
30 88 0.71
31 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTGACCCCTAAACTTTCAAAAATTCAAA
Found at i:67587 original size:28 final size:28
Alignment explanation
Indices: 67543--67644 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 28
67533 TCAGCAAATG
*
67543 ATTTTAAAATTAATTTTTAAAATATAAAA
1 ATTTT-AAATTATTTTTTAAAATATAAAA
67572 ATTTTAAATTA-TTTTTAAAATATAAAA
1 ATTTTAAATTATTTTTTAAAATATAAAA
* *
67599 ATATTAAAATTACTTTTTTGAAATA-ATAAA
1 AT-TTTAAATTA-TTTTTTAAAATATA-AAA
*
67629 ATTATTAAATAATTTT
1 ATT-TTAAATTATTTT
67645 AATTTTCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
27 18 0.28
28 14 0.22
29 11 0.17
30 21 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTTTAAATTATTTTTTAAAATATAAAA
Found at i:68857 original size:30 final size:30
Alignment explanation
Indices: 68809--68895 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
68799 ATAATTTTGG
*
68809 GAAA-TTTTGGGATCAAAATGTGATTTTAA
1 GAAAGTTTAGGGATCAAAATGTGATTTTAA
* * *
68838 GAAAGTTTAGGGATTAAAATATGATTTTAG
1 GAAAGTTTAGGGATCAAAATGTGATTTTAA
* *
68868 GAAAGTTTAGGGGTCAAAATGTAATTTT
1 GAAAGTTTAGGGATCAAAATGTGATTTT
68896 GGAAAAGCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 4 0.08
30 45 0.92
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
GAAAGTTTAGGGATCAAAATGTGATTTTAA
Found at i:68908 original size:30 final size:30
Alignment explanation
Indices: 68800--69071 Score: 229
Period size: 29 Copynumber: 9.2 Consensus size: 30
68790 GGTTAAAACA
* * *
68800 TAATTTTGGGAAA-TTTTGGGATCAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
* * * * *
68829 TGATTTT-AAGAAAGTTTAGGGATTAAAATA
1 TAATTTTGGA-AAAGTTTAGGGGTCAAAATG
*
68859 TGATTTTAGG-AAAGTTTAGGGGTCAAAATG
1 TAATTTT-GGAAAAGTTTAGGGGTCAAAATG
* *
68889 TAATTTTGGAAAAGCTTAGGGG-CCAAATG
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
* *
68918 TAATTTTGGAAAAGCTTAGGGCT-AAAATG
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
* * *
68947 TAATTTTGGAAAAGTTTA-AGGTTAAAATA
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
* *
68976 TGATTTTGGAAAAGTTTAGGGG-CTAAAT-
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
* * *
69004 TCAATTTTTGAAAAGTTTAGAGG-CTAAAATA
1 T-AATTTTGGAAAAGTTTAGGGGTC-AAAATG
* *
69035 TAATTTTGGAAAAGTTTAGAGATCAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
*
69065 TGATTTT
1 TAATTTT
69072 TAAATAAAAT
Statistics
Matches: 200, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.01
29 105 0.52
30 90 0.45
31 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTAGGGGTCAAAATG
Found at i:72365 original size:28 final size:28
Alignment explanation
Indices: 72313--72367 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
72303 AAATGAGCAT
* * **
72313 CATGACCTTTGGGTCAATAGGGAGTAAG
1 CATGACCTTTGGGTAAACAAAGAGTAAG
72341 CATGACCTTTGGGTAAACAAAGAGTAA
1 CATGACCTTTGGGTAAACAAAGAGTAA
72368 ATCAGATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.24
Consensus pattern (28 bp):
CATGACCTTTGGGTAAACAAAGAGTAAG
Found at i:73124 original size:21 final size:21
Alignment explanation
Indices: 73076--73127 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
73066 GAAGTTTTTA
73076 GTATCGGTAGAAGAATGACAT
1 GTATCGGTAGAAGAATGACAT
* * *
73097 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-AATGACAT
73118 GTATCGGTAG
1 GTATCGGTAG
73128 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGAATGACAT
Found at i:74200 original size:37 final size:37
Alignment explanation
Indices: 74149--74220 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
74139 ATTTCATTGT
* *
74149 TTTAATCCATTTCTCT-CTATCTCATCAAGAAGATGGA
1 TTTAATCCACTTCTCTGC-ATATCATCAAGAAGATGGA
* *
74186 TTTAATTCACTTCTCTGCATATCGTCAAGAAGATG
1 TTTAATCCACTTCTCTGCATATCATCAAGAAGATG
74221 AACACTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTAATCCACTTCTCTGCATATCATCAAGAAGATGGA
Found at i:74281 original size:63 final size:63
Alignment explanation
Indices: 74179--74305 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
74169 CTCATCAAGA
*
74179 AGATGGATTTAATTCACTTCTCTGCATATCGTCAAGAAGATGAACACTTTATTGCTTCAACCC
1 AGATGAATTTAATTCACTTCTCTGCATATCGTCAAGAAGATGAACACTTTATTGCTTCAACCC
* *
74242 AGATGAATTTAATTCACTTCTCTGCATATCGTCAGGAAGATGAACACTTTATTGCTTTAACCC
1 AGATGAATTTAATTCACTTCTCTGCATATCGTCAAGAAGATGAACACTTTATTGCTTCAACCC
74305 A
1 A
74306 CTTCTCTGTA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (63 bp):
AGATGAATTTAATTCACTTCTCTGCATATCGTCAAGAAGATGAACACTTTATTGCTTCAACCC
Found at i:80682 original size:9 final size:9
Alignment explanation
Indices: 80668--80692 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
80658 GGCAGGGTTT
80668 TTCTCTTCA
1 TTCTCTTCA
80677 TTCTCTTCA
1 TTCTCTTCA
80686 TTCTCTT
1 TTCTCTT
80693 TTTCTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (9 bp):
TTCTCTTCA
Found at i:80708 original size:13 final size:15
Alignment explanation
Indices: 80680--80713 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
80670 CTCTTCATTC
80680 TCTTCATTCTCTTTT
1 TCTTCATTCTCTTTT
80695 TCTTC-TTC-CTTTT
1 TCTTCATTCTCTTTT
80708 TCTTCA
1 TCTTCA
80714 ACAGGTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTCATTCTCTTTT
Found at i:81773 original size:24 final size:23
Alignment explanation
Indices: 81720--81774 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
81710 AGCTCCATCA
* *
81720 ATGCATAAGTCCTTTATAATCTG
1 ATGCATAAGTCATTTACAATCTG
*
81743 ATCCATACAGTCATTATACAATC-G
1 ATGCATA-AGTCATT-TACAATCTG
81767 ATGCATAA
1 ATGCATAA
81775 ATGGTGTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
ATGCATAAGTCATTTACAATCTG
Found at i:92370 original size:23 final size:24
Alignment explanation
Indices: 92334--92383 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
92324 AATTGAAAGT
*
92334 AAAGTGAAAGTGAAATTG-GAATTG
1 AAAGTGAAAGTG-AATTGTAAATTG
*
92358 AAAGTGATA-TGAATTGTAAATTG
1 AAAGTGAAAGTGAATTGTAAATTG
92381 AAA
1 AAA
92384 ATCCCTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGTGAAAGTGAATTGTAAATTG
Found at i:96608 original size:18 final size:20
Alignment explanation
Indices: 96572--96608 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
96562 CTTGATTTGT
96572 TAAATATTTGAAAACACGAG
1 TAAATATTTGAAAACACGAG
*
96592 TAAA-ATTT-AAAATACGA
1 TAAATATTTGAAAACACGA
96609 TCCTTAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (20 bp):
TAAATATTTGAAAACACGAG
Found at i:97239 original size:59 final size:59
Alignment explanation
Indices: 97152--97281 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 59
97142 ACGGGGTTGA
* *
97152 AAAATG-AAGTTTAAGAGAATTTAAGGTT-AAATCATAATTTTAGGAAAATTTAAGGATC
1 AAAATGTAATTTTAAGAGAATTTAAGGTTAAAAT-ATAAATTTAGGAAAATTTAAGGATC
* * * * *
97210 AAAATGTAATTTTAAGA-AAGTTTAGGGTTAAAATGTAAATTTAGGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAAGAGAA-TTTAAGGTTAAAATATAAATTTAGGAAAATTTAAGGATC
97269 AAAATGTAATTTT
1 AAAATGTAATTTT
97282 TGAAAAGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.13
59 50 0.81
60 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTAAGAGAATTTAAGGTTAAAATATAAATTTAGGAAAATTTAAGGATC
Found at i:97289 original size:59 final size:58
Alignment explanation
Indices: 97190--97460 Score: 278
Period size: 59 Copynumber: 4.6 Consensus size: 58
97180 AAATCATAAT
* * * * * *
97190 TTTAGGAAAATTTAAGGATCAAAATGTAA-TTTTAAGAAAGTTTAGGGTTAAAATGTAAA
1 TTTAGGAAAGTTTAAGGGTTAAAATATAATTTTTGA-AAAGTTTAGGGCTAAAATGT-AA
* *
97249 TTTAGGAAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTTTAGAGGCTAAAATGCAA
1 TTTAGGAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTTTAG-GGCTAAAATGTAA
* *
97308 TTTTGGAAAAGTTTAAGGGCTAAAATATAA-TTTTGAAAAGTTTATGGGCTAAAATGTAA
1 TTTAGG-AAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTTTA-GGGCTAAAATGTAA
** * * * *
97367 TTGTAAAAAAGTTT-AGGGTTAAAATATAATTTTAGAAAAGTTTAAAGGTTAAAATGTGAT
1 TT-TAGGAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTTT-AGGGCTAAAATGT-AA
* * *
97427 TTTTGGAAAGTTTAAGGGTTAAAATCTGATTTTT
1 TTTAGGAAAGTTTAAGGGTTAAAATATAATTTTT
97461 AAATAAAATA
Statistics
Matches: 179, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
58 14 0.08
59 107 0.60
60 58 0.32
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (58 bp):
TTTAGGAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTTTAGGGCTAAAATGTAA
Found at i:97460 original size:30 final size:30
Alignment explanation
Indices: 97186--97451 Score: 281
Period size: 30 Copynumber: 9.0 Consensus size: 30
97176 GGTTAAATCA
* * *
97186 TAATTTTAGGAAAATTTAAGGATCAAAATG
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
*
97216 TAATTTTAAGAAAGTTT-AGGGTTAAAATG
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
*
97245 TAAATTTAGGAAAGTTTAAGGGTTAAAATG
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
* * *
97275 TAATTTTTGAAAAGTTT-AGAGGCTAAAATG
1 TAATTTTAGGAAAGTTTAAG-GGTTAAAATG
* * *
97305 CAATTTT-GGAAAAGTTTAAGGGCTAAAATA
1 TAATTTTAGG-AAAGTTTAAGGGTTAAAATG
* * *
97335 TAATTTT-GAAAAGTTTATGGGCTAAAATG
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
* ** *
97364 TAATTGTAAAAAAGTTT-AGGGTTAAAATA
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
* *
97393 TAATTTTAGAAAAGTTTAAAGGTTAAAATG
1 TAATTTTAGGAAAGTTTAAGGGTTAAAATG
* *
97423 TGATTTTTGGAAAGTTTAAGGGTTAAAAT
1 TAATTTTAGGAAAGTTTAAGGGTTAAAAT
97452 CTGATTTTTA
Statistics
Matches: 200, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
29 76 0.38
30 122 0.61
31 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (30 bp):
TAATTTTAGGAAAGTTTAAGGGTTAAAATG
Found at i:99713 original size:26 final size:24
Alignment explanation
Indices: 99683--99753 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
99673 AATTTGGAAA
* *
99683 TTAAAATTATTTAATAATTTTATATT
1 TTAAAATAATTTAA-AA-ATTATATT
99709 TTAAAAAATAATTTAAAAATTATATT
1 TT--AAAATAATTTAAAAATTATATT
*
99735 TTAAAAATAATTTTAAAAT
1 TT-AAAATAATTTAAAAAT
99754 CATTTGCTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 16 0.40
26 11 0.28
27 2 0.05
28 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAATAATTTAAAAATTATATT
Found at i:99725 original size:12 final size:12
Alignment explanation
Indices: 99708--99752 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
99698 AATTTTATAT
99708 TTTAAAAAATAA
1 TTTAAAAAATAA
*
99720 TTTAAAAATTATA
1 TTTAAAAAATA-A
*
99733 TTTTAAAAATAA
1 TTTAAAAAATAA
99745 TTTTAAAA
1 -TTTAAAA
99753 TCATTTGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAA
Found at i:99746 original size:25 final size:26
Alignment explanation
Indices: 99702--99753 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
99692 TTTAATAATT
99702 TTATATTTTAAAAAATAATTTAAAAA
1 TTATATTTTAAAAAATAATTTAAAAA
*
99728 TTATATTTT-AAAAATAATTTTAAAA
1 TTATATTTTAAAAAATAATTTAAAAA
99753 T
1 T
99754 CATTTGCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATATTTTAAAAAATAATTTAAAAA
Found at i:100431 original size:29 final size:29
Alignment explanation
Indices: 100306--100471 Score: 109
Period size: 30 Copynumber: 5.6 Consensus size: 29
100296 ATTAAAATCG
* * *
100306 GGTCAAATTAGAATTTTTGAAAAATTTAGG
1 GGTCAAATTTGAATTTTTGGAAAATTT-GA
* *** * * * *
100336 GGTTAAATCAAAAATTTTAGAAAGTTTAGG
1 GGTCAAATTTGAATTTTTGGAAAATTT-GA
* *
100366 GGTTAAATTTGAATTTTTGGAAAATTCG-
1 GGTCAAATTTGAATTTTTGGAAAATTTGA
*
100394 GGATAAAATTTGAATTTTTGGAAAATTTGA
1 GG-TCAAATTTGAATTTTTGGAAAATTTGA
** * * *
100424 GGTCAAATTCAAATTTTTAGAAAAAATCGA
1 GGTCAAATTTGAATTTTT-GGAAAATTTGA
100454 GGGTCAAATTTGAATTTT
1 -GGTCAAATTTGAATTTT
100472 AGAAAGTTCG
Statistics
Matches: 108, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
28 2 0.02
29 38 0.35
30 53 0.49
31 15 0.14
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.37
Consensus pattern (29 bp):
GGTCAAATTTGAATTTTTGGAAAATTTGA
Found at i:100474 original size:30 final size:30
Alignment explanation
Indices: 100348--100476 Score: 102
Period size: 29 Copynumber: 4.4 Consensus size: 30
100338 TTAAATCAAA
** * *
100348 AATTTTAGAAAGTTTAG-GGGTTAAATTTG
1 AATTTTAGAAAAATTCGAGGGTCAAATTTG
* * * *
100377 AATTTTTGGAAAATTCG-GGATAAAATTTG
1 AATTTTAGAAAAATTCGAGGGTCAAATTTG
* * * **
100406 AATTTTTGGAAAATTTGA-GGTCAAATTCA
1 AATTTTAGAAAAATTCGAGGGTCAAATTTG
*
100435 AATTTTTAGAAAAAATCGAGGGTCAAATTTG
1 AA-TTTTAGAAAAATTCGAGGGTCAAATTTG
100466 AATTTTAGAAA
1 AATTTTAGAAA
100477 GTTCGGGAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 47 0.59
30 21 0.27
31 11 0.14
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (30 bp):
AATTTTAGAAAAATTCGAGGGTCAAATTTG
Found at i:102475 original size:11 final size:12
Alignment explanation
Indices: 102454--102545 Score: 66
Period size: 11 Copynumber: 7.8 Consensus size: 12
102444 GATTTATTTC
*
102454 TAAAATTAAATT
1 TAAATTTAAATT
*
102466 T-ACTTTAAATT
1 TAAATTTAAATT
102477 TAAATTTAAATT
1 TAAATTTAAATT
***
102489 CTTTTTTTAAATT
1 -TAAATTTAAATT
*
102502 TAAATTT-AGTT
1 TAAATTTAAATT
102513 TAAATTTGAAA--
1 TAAATTT-AAATT
* *
102524 TAATTTTAAACT
1 TAAATTTAAATT
102536 TAAATTTAAA
1 TAAATTTAAA
102546 ATCAATTAGA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
10 3 0.05
11 25 0.41
12 23 0.38
13 10 0.16
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:102478 original size:6 final size:6
Alignment explanation
Indices: 102454--102545 Score: 66
Period size: 6 Copynumber: 15.7 Consensus size: 6
102444 GATTTATTTC
* * ***
102454 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CTTTTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
* * *
102502 TAAATT T-AGTT TAAATT TGAAA-- TAATTT TAAACT TAAATT TAAA
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAA
102546 ATCAATTAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
4 2 0.03
5 9 0.14
6 48 0.74
7 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:102479 original size:17 final size:18
Alignment explanation
Indices: 102440--102484 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
102430 TTAGATGAGT
* *
102440 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
102458 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
102475 TTTAAATTTA
1 TTTAAATTTA
102485 AATTCTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:102516 original size:17 final size:17
Alignment explanation
Indices: 102475--102543 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
102465 TTACTTTAAA
*
102475 TTTAAATTTAAATTCTTTT
1 TTTAAATTTAAA-T-TTAT
*
102494 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
102511 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
102528 TTTAAACTTAAATTTA
1 TTTAAATTTAAATTTA
102544 AAATCAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.07
17 23 0.55
18 4 0.10
19 12 0.29
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:102561 original size:23 final size:23
Alignment explanation
Indices: 102512--102562 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
102502 TAAATTTAGT
* **
102512 TTAAATTTGAAATAATTTTAAAC
1 TTAAATTTAAAATAATTAGAAAC
102535 TTAAATTTAAAATCAATTAGAAA-
1 TTAAATTTAAAAT-AATTAGAAAC
102558 TTAAA
1 TTAAA
102563 GTCCAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
TTAAATTTAAAATAATTAGAAAC
Found at i:102740 original size:32 final size:31
Alignment explanation
Indices: 102698--102761 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 31
102688 ACTTGTATTG
102698 CTGCTGCCACCCTCAACCAATCGGAATGCGC
1 CTGCTGCCACCCTCAACCAATCGGAATGCGC
*
102729 CNTGCTGCCACCCTCAACCAATCGGGATGCGC
1 C-TGCTGCCACCCTCAACCAATCGGAATGCGC
102761 C
1 C
102762 ACGTCATCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.16
Consensus pattern (31 bp):
CTGCTGCCACCCTCAACCAATCGGAATGCGC
Found at i:104403 original size:29 final size:29
Alignment explanation
Indices: 104358--104684 Score: 231
Period size: 29 Copynumber: 11.1 Consensus size: 29
104348 CCCTAGAAGT
*
104358 CCCT-AAACTATCTAAAAATTACATTTTTA
1 CCCTCAAACT-TCCAAAAATTACATTTTTA
* *
104387 CCCTCAAACTTCCAAAAAATCCATTTTTAA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
*
104417 CCC-CAAAACTTCCAAAAA-AACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* * *
104445 CCCTCGAACTTCAAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* ** *
104474 CCCCCAAAACTTTAAAAAATAACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* *
104504 CCCTTCCCAAACTTCCAAAAAATCCATTTTTA
1 CCC-T--CAAACTTCCAAAAATTACATTTTTA
***
104536 CCCTCAAAACTTTTGAAAATTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* *
104566 CCCCCAAACTTCCAAAAATTCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTACA-TTTTTA
* **
104596 -CCTCAAAAAATT-TGAAAATTACCA-TTTTA
1 CCCTC--AAACTTCCAAAAATTA-CATTTTTA
* * * *
104625 CCC-CGAACCTCCAAAAATTCCATTTTTGG
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
*
104654 CCC-CAAACTTTCAAAAATTACCA-TTTTA
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
104682 CCC
1 CCC
104685 GTGGATGTCC
Statistics
Matches: 232, Mismatches: 47, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
27 5 0.02
28 28 0.12
29 84 0.36
30 84 0.36
31 8 0.03
32 22 0.09
33 1 0.00
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:104600 original size:59 final size:60
Alignment explanation
Indices: 104372--104684 Score: 295
Period size: 58 Copynumber: 5.3 Consensus size: 60
104362 AAACTATCTA
* * * **
104372 AAAATTACATTTTTACCCTCAAACTTCCAAAAAATCCA-TTTTTAACCCCAAAAC-TTCC
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
** * * * **
104430 AAAAAAACATTTTTACCCTCGAACTTCAAAAAATTCCA-TTTTTACCCCCAAAACTTTAA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
* * *
104489 AAAATAACATTTTTACCCTTCCCAAACTTCCAAAAAATCCA-TTTTTACCCTCAAAACTTTTG
1 AAAATTACATTTTTA-CC--CCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
* **
104551 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTA-CCTCAAAAAATTTG
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
* * ** **
104610 AAAATTACCA-TTTTA-CCCCGAACCTCCAAAAATTCCA-TTTTTGGCCCC-AAACTTTCA
1 AAAATTA-CATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
104667 AAAATTACCA-TTTTACCC
1 AAAATTA-CATTTTTACCC
104685 GTGGATGTCC
Statistics
Matches: 219, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
57 25 0.11
58 73 0.33
59 60 0.27
60 10 0.05
61 2 0.01
62 49 0.22
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.32
Consensus pattern (60 bp):
AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCCAAAACTTTTG
Found at i:104696 original size:58 final size:56
Alignment explanation
Indices: 104576--104796 Score: 187
Period size: 58 Copynumber: 3.8 Consensus size: 56
104566 CCCCCAAACT
* * * * * **
104576 TCCAAAAATTCCATTTTTTACCTCAAAAAATTT-GAAAATTACCATTTTACCCCGAACC
1 TCCAAAAATTCCATTTTTGACC-C--CAAATTTCAAAAATTACCATTTTACCCTGGATG
*
104634 TCCAAAAATTCCATTTTTGGCCCCAAACTTTCAAAAATTACCATTTTACCCGTGGATG
1 TCCAAAAATTCCATTTTTGACCCCAAA-TTTCAAAAATTACCATTTTACCC-TGGATG
** * *
104692 TCCAAAAATTCTGTTTTTGATCCCTAATTTCTAAAAATTACCATTTTACCCCTGGATG
1 TCCAAAAATTCCATTTTTGACCCCAAATTTC-AAAAATTACCATTTTA-CCCTGGATG
* * * *
104750 T-CTAAAATAT-CATTTTTAACCCTAAATTTTCCCAAAATTACCATTTT
1 TCCAAAAAT-TCCATTTTTGACCCCAAA-TTT-CAAAAATTACCATTTT
104797 GCCGCCAAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
55 3 0.02
56 3 0.02
57 39 0.29
58 85 0.63
59 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (56 bp):
TCCAAAAATTCCATTTTTGACCCCAAATTTCAAAAATTACCATTTTACCCTGGATG
Found at i:104753 original size:29 final size:29
Alignment explanation
Indices: 104666--104756 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
104656 CCAAACTTTC
* *
104666 AAAAATTACCATTTTACCCGTGGATGTCC
1 AAAAATTACCATTTTACCCCTGGATGTCT
** * * *
104695 AAAAATT-CTGTTTTTGATCCCT-AATTTCT
1 AAAAATTAC-CATTTT-ACCCCTGGATGTCT
104724 AAAAATTACCATTTTACCCCTGGATGTCT
1 AAAAATTACCATTTTACCCCTGGATGTCT
104753 AAAA
1 AAAA
104757 TATCATTTTT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
28 6 0.13
29 35 0.76
30 5 0.11
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCTGGATGTCT
Found at i:117200 original size:206 final size:196
Alignment explanation
Indices: 116846--117434 Score: 754
Period size: 206 Copynumber: 3.0 Consensus size: 196
116836 CCAACTCGAG
* * * * * *
116846 GCTCAATGCGATCAAACCTTCAAACCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCA
116911 AT-AAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
66 ATAAAAAT-GTTAGCTT-CTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
* *
116975 ACAGAGAAGCGGATTGAAACAAGCGATGCGGTCACCTTCCTAATGAGATACTGAGAAGAAGACTA
129 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAG--T-
117040 AATCAAACACA
191 -AT---AC-CA
* *
117051 CGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGTAGGGCGAAGC
1 -GCTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGC
* * * *
117116 AATAAAAATTTTAGCTTCTTGATGAGATAATGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
65 AATAAAAATGTTAGCTTC-TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
* * *
117181 ACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCATGATGAGATAC--AG-AGAAGTATA
129 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGTATA
117243 CCA
194 CCA
* * * * *
117246 ACTCAATGCGAACAAATCTTCGACCCCCAACTTACTAATGAGATACTAAGAAGCAGGGCGAAGCA
1 GCTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCA
* * * * *
117311 ATAAAAAGGTTAGCTTCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACAC
66 ATAAAAATGTTAGCTTCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
* ** * *
117376 AGAGAAGTGGATCAAAACAAGTGATGCGGTCGTCTTCCTAATGAGATGCTGAGAAGAAG
131 AGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAG
117435 GCCAAGTCAA
Statistics
Matches: 338, Mismatches: 40, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
193 82 0.24
194 73 0.22
195 4 0.01
196 7 0.02
199 2 0.01
201 1 0.00
203 5 0.01
204 2 0.01
205 1 0.00
206 156 0.46
207 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (196 bp):
GCTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCA
ATAAAAATGTTAGCTTCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGTATACC
A
Found at i:117839 original size:6 final size:6
Alignment explanation
Indices: 117815--117891 Score: 77
Period size: 6 Copynumber: 12.8 Consensus size: 6
117805 GATTTATTTC
* * * *
117815 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAATTT TAATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT
*
117863 TAAATT TAAATT T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT TAAATT TAAATT T-AAAT
117892 ATTTTTAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
5 8 0.13
6 42 0.70
7 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:117840 original size:17 final size:17
Alignment explanation
Indices: 117801--117909 Score: 84
Period size: 17 Copynumber: 6.5 Consensus size: 17
117791 TTAGATGGGT
* *
117801 TTTAGATTTATTTCTAAA
1 TTTAAATTTAATT-TAAA
* *
117819 ATTAAATTTACTTTAAA
1 TTTAAATTTAATTTAAA
*
117836 TTTAAATTTAATTTTAA
1 TTTAAATTTAATTTAAA
*
117853 TTT---TTAAATTTAAA
1 TTTAAATTTAATTTAAA
*
117867 TTTAAATTTAGTTTAAA
1 TTTAAATTTAATTTAAA
117884 TTTGAAATATT--TTTAAA
1 TTT-AAAT-TTAATTTAAA
*
117901 CTTAAATTT
1 TTTAAATTT
117910 GAAATAATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.16
15 2 0.03
16 4 0.05
17 41 0.55
18 14 0.19
19 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Done.