Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002236.1 Hibiscus syriacus cultivar Beakdansim tig00004546_pilon, 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: 80378
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11660 original size:10 final size:10
Alignment explanation
Indices: 11645--11675 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
11635 CAAATATAAC
11645 CTAAATGCAA
1 CTAAATGCAA
11655 CTAAATGCAA
1 CTAAATGCAA
*
11665 CTACATGCAA
1 CTAAATGCAA
11675 C
1 C
11676 CAATATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:24508 original size:2 final size:2
Alignment explanation
Indices: 24503--24527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24493 TATGTGTGTG
24503 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 T
24528 TTGTTAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25335 original size:2 final size:2
Alignment explanation
Indices: 25328--25375 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
25318 GCTAAGTTTA
25328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25370 AT AT AT
1 AT AT AT
25376 GATGGTATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31251 original size:12 final size:12
Alignment explanation
Indices: 31236--31281 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
31226 ACTATTCACG
*
31236 GTACTTTTCATA
1 GTACTGTTCATA
31248 GTACTGTTCAT-
1 GTACTGTTCATA
* *
31259 -TATTGTTCATG
1 GTACTGTTCATA
31270 GTACTGTTCATA
1 GTACTGTTCATA
31282 CCATATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (12 bp):
GTACTGTTCATA
Found at i:34051 original size:20 final size:20
Alignment explanation
Indices: 34026--34100 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
34016 ACGAAATAAA
34026 AATCGCAATGCGATCTCCAG
1 AATCGCAATGCGATCTCCAG
*
34046 AATCGCAAAT-CAGTTC-CCAG
1 AATCGC-AATGC-GATCTCCAG
* * **
34066 AATCGCAACGCGATTATTAAG
1 AATCGCAATGCGA-TCTCCAG
34087 AATCGCAATGCGAT
1 AATCGCAATGCGAT
34101 AGTACAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 20 0.47
21 20 0.47
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGATCTCCAG
Found at i:34090 original size:21 final size:20
Alignment explanation
Indices: 34066--34183 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
34056 CAGTTCCCAG
34066 AATCGCAACGCGATTATTAA
1 AATCGCAACGCGATTATTAA
* *
34086 GAATCGCAATGCGA-TAGTACA
1 -AATCGCAACGCGATTATTA-A
* ** *
34107 AATTAGCATTGCGATT-TTCCAG
1 AA-TCGCAACGCGATTATT--AA
* *
34129 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATTAA
**
34149 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGATTATTA-A
34169 AATCGCAACGCGATT
1 AATCGCAACGCGATT
34184 CTGACTATCG
Statistics
Matches: 74, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
19 1 0.01
20 36 0.49
21 32 0.43
22 4 0.05
23 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATTAA
Found at i:34154 original size:20 final size:20
Alignment explanation
Indices: 34129--34326 Score: 98
Period size: 20 Copynumber: 9.8 Consensus size: 20
34119 GATTTTCCAG
34129 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
34149 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
34169 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * * **
34189 TATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
*
34210 AATCGCAACGCG--TATCCATA
1 AATCGCAACGCGAATAT-GA-A
*
34230 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* ** *
34251 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
* * *
34271 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
34291 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
* *
34311 AATTGCAACGAGAATA
1 AATCGCAACGCGAATA
34327 CGTAAATCAC
Statistics
Matches: 134, Mismatches: 34, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.02
20 101 0.75
21 27 0.20
22 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:34212 original size:61 final size:61
Alignment explanation
Indices: 34147--34332 Score: 166
Period size: 61 Copynumber: 3.0 Consensus size: 61
34137 CGCGAATATG
* * ** *
34147 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAATGAGTATCCGT
1 AAAATCGCAACGCGAACACATAAATCGCAACGCGATACGT-AAAATCGCAACGAGTATCCGT
* * *
34208 AAAATCGCAACGCGTATC-CATAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGCG-AACACATAAATCGCAACG-CGATACGTAAAATCGCAACGAGTATCCGT
* * * * * *
34270 -AAATCGCAACGAGAATACGTAAATCGCAACGCG-TATCTGT-AAATTGCAACGAGAATACGT
1 AAAATCGCAACGCGAACACATAAATCGCAACGCGATA-C-GTAAAATCGCAACGAGTATCCGT
34330 AAA
1 AAA
34333 TCACAATGTG
Statistics
Matches: 101, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
59 2 0.02
60 19 0.19
61 56 0.55
62 23 0.23
63 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (61 bp):
AAAATCGCAACGCGAACACATAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
Found at i:34235 original size:41 final size:41
Alignment explanation
Indices: 34190--34332 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 41
34180 GATTCTGACT
* * *
34190 ATCGCAATGAGTATCCGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCATAA
* *
34231 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCATAA
**
34272 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCATAA
*
34312 ATTGCAACGAGAATACGTAAA
1 ATCGCAACGAGAATACGTAAA
34333 TCACAATGTG
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 38 0.41
41 55 0.59
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCATAA
Found at i:34305 original size:40 final size:40
Alignment explanation
Indices: 34129--34350 Score: 214
Period size: 40 Copynumber: 5.5 Consensus size: 40
34119 GATTTTCCAG
* ** * * * **
34129 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * *
34169 AATCGCAACGCG-ATTC-TGACTATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
34210 AATCGCAACGCGTATCCATAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
34251 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
34291 AATCGCAACGCGTATCTGTAAATTGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
34331 AATCACAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34351 TTCGCATTGC
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 78 0.51
41 66 0.43
42 4 0.03
43 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:34331 original size:20 final size:20
Alignment explanation
Indices: 34190--34334 Score: 130
Period size: 20 Copynumber: 7.2 Consensus size: 20
34180 GATTCTGACT
* * *
34190 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGAGAATACGT-AA
* * * *
34211 ATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAA
*
34231 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATACGT-AA
* * *
34252 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAA
34272 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGAATACGTAA
* *
34292 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGAGAATAC-GTAA
*
34312 ATTGCAACGAGAATACGTAA
1 ATCGCAACGAGAATACGTAA
34332 ATC
1 ATC
34335 ACAATGTGTA
Statistics
Matches: 100, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
19 1 0.01
20 67 0.67
21 32 0.32
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGAATACGTAA
Found at i:34406 original size:20 final size:20
Alignment explanation
Indices: 34355--34393 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34345 TCCGTATTCG
34355 CATTGCGATTTACGTAATCA
1 CATTGCGATTTACGTAATCA
34375 CATTGCGATTTACGTAATC
1 CATTGCGATTTACGTAATC
34394 GTGTTGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
CATTGCGATTTACGTAATCA
Found at i:34414 original size:20 final size:20
Alignment explanation
Indices: 34357--34410 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
34347 CGTATTCGCA
***
34357 TTGCGATTTACGTAATCACA
1 TTGCGATTTACGTAATCGTG
34377 TTGCGATTTACGTAATCGTG
1 TTGCGATTTACGTAATCGTG
34397 TTGCGATTTA-GTAA
1 TTGCGATTTACGTAA
34411 ATCGCAACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGTG
Found at i:37888 original size:19 final size:19
Alignment explanation
Indices: 37821--37930 Score: 95
Period size: 19 Copynumber: 5.9 Consensus size: 19
37811 TCGCAACACG
37821 TGAAAATCGCAACGCGAATA
1 TGAAAATCGCAACGCGAA-A
* *
37841 TGAATATCGTAACGCGGAAA
1 TGAAAATCGCAACGC-GAAA
** *
37861 TGACTATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
37880 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
* * *
37895 -GAGAATCACAAAGCGAAA
1 TGAAAATCGCAACGCGAAA
37913 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
37931 TTTAGTTTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 28 0.39
20 26 0.36
21 3 0.04
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
TGAAAATCGCAACGCGAAA
Found at i:37961 original size:19 final size:19
Alignment explanation
Indices: 37926--38002 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
37916 AAATCGCAAC
*
37926 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
37945 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
37964 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
37978 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
37997 GCGATT
1 GCGATT
38003 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:37983 original size:33 final size:33
Alignment explanation
Indices: 37941--38034 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
37931 TTTAGTTTCG
* * *
37941 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
37974 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
38007 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
38035 AGTCATTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 56 0.98
34 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:38033 original size:19 final size:18
Alignment explanation
Indices: 37936--38034 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 18
37926 GCGAATTTAG
37936 TTTCGCGTTGCGATTTT-A
1 TTTCGC-TTGCGATTTTCA
37954 GTTTCGCGTTGCGA-TTT--
1 -TTTCGC-TTGCGATTTTCA
*
37971 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
37988 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
38004 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
38021 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
38035 AGTCATTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 12 0.18
15 3 0.05
16 11 0.17
17 11 0.17
18 3 0.05
19 26 0.39
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:38042 original size:19 final size:17
Alignment explanation
Indices: 37984--38034 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
37974 CGTTGCGATT
37984 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
38001 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
38015 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
38034 T
1 T
38035 AGTCATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:39578 original size:21 final size:21
Alignment explanation
Indices: 39512--39578 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
39502 GTGAATCGAG
39512 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
39532 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
39554 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
39575 CTCT
1 CTCT
39579 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:40070 original size:19 final size:19
Alignment explanation
Indices: 40031--40115 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
40021 TCTGGAACTT
*
40031 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GCAAAATG
**
40052 ACTATCGCAACGCAAAATG
1 AAAATCGCAACGCAAAATG
40071 AAAATCGCAACG----A-G
1 AAAATCGCAACGCAAAATG
* *
40085 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCAAAATG
40104 AAAATCGCAACG
1 AAAATCGCAACG
40116 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
18 1 0.02
19 29 0.56
21 9 0.17
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCAAAATG
Found at i:40090 original size:14 final size:14
Alignment explanation
Indices: 40073--40127 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40063 GCAAAATGAA
40073 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40087 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40106 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40120 AATCGCAA
1 AATCGCAA
40128 TACGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40092 original size:33 final size:33
Alignment explanation
Indices: 40055--40148 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
40045 AAAAATGACT
*
40055 ATCGCAACGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
40088 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
**
40121 ATCGCAATACGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
40149 CGATTATAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:40144 original size:19 final size:18
Alignment explanation
Indices: 40066--40146 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 18
40056 TCGCAACGCA
40066 AAATGAAAATCGC-AACG
1 AAATGAAAATCGCAAACG
* *
40083 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAA-ACG
40099 AAATGAAAATCGC-AACG
1 AAATGAAAATCGCAAACG
*
40116 --A-GAGAATCGCAATACG
1 AAATGAAAATCGCAA-ACG
40132 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
40147 CGCGATTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
14 16 0.33
15 4 0.08
16 5 0.10
17 2 0.04
18 3 0.06
19 18 0.38
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (18 bp):
AAATGAAAATCGCAAACG
Found at i:40183 original size:19 final size:19
Alignment explanation
Indices: 40148--40229 Score: 121
Period size: 19 Copynumber: 4.3 Consensus size: 19
40138 AAATCGCAAC
*
40148 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
40167 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
40186 GCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
40205 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
40224 GCGATT
1 GCGATT
40230 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 58 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:40476 original size:94 final size:94
Alignment explanation
Indices: 40330--40709 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
40320 ATGGATTGCA
* * *
40330 TTAC-TTCAACCAAAAGACAAAACAAAGGCAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
40394 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
40423 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
40488 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
40517 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
40582 TTAGCATAATTGACAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
40611 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
40675 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
40705 TTACT
1 TTACT
40710 AAGCAATCTA
Statistics
Matches: 272, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
93 22 0.08
94 250 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:42426 original size:40 final size:39
Alignment explanation
Indices: 42382--42489 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 39
42372 TCTTTTGGTT
**
42382 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGCG
** *
42422 GAAATGACTATCGCAACGCGAAATGAAAATCGCAA--C-
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGCG
* *
42458 --AA-GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAA
42490 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
33 28 0.46
34 2 0.03
37 1 0.02
39 12 0.20
40 18 0.30
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGCG
Found at i:42487 original size:19 final size:19
Alignment explanation
Indices: 42382--42494 Score: 110
Period size: 20 Copynumber: 6.1 Consensus size: 19
42372 TCTTTTGGTT
*
42382 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
42401 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
42421 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
42441 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
42458 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
42474 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
42493 GA
1 GA
42495 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
15 2 0.03
16 1 0.01
17 1 0.01
18 2 0.03
19 30 0.38
20 31 0.39
21 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:42512 original size:19 final size:19
Alignment explanation
Indices: 42490--42534 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42480 AAAATCGCAA
** *
42490 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTCATTTCGCGT
42509 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
42528 TGCGATT
1 TGCGATT
42535 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:42542 original size:33 final size:34
Alignment explanation
Indices: 42503--42568 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
42493 GATTTTGGTT
* **
42503 TCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTC
1 TCTCGTTGCAATAGTCATTTTCGCGTTGCGATTC
*
42536 TCTCGTTGCAATAGTCATTTTCGTGTTGCGATT
1 TCTCGTTGCAATAGTCATTTTCGCGTTGCGATT
42569 TTCATTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (34 bp):
TCTCGTTGCAATAGTCATTTTCGCGTTGCGATTC
Found at i:42573 original size:20 final size:20
Alignment explanation
Indices: 42540--42590 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42530 CGATTCTCTC
** *
42540 GTTGCAATAGTCATTTTCGT
1 GTTGCAATTTTCATTTTCAT
*
42560 GTTGCGATTTTCATTTTCAT
1 GTTGCAATTTTCATTTTCAT
42580 GTTGCAATTTT
1 GTTGCAATTTT
42591 AAGTTTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCAATTTTCATTTTCAT
Found at i:43198 original size:20 final size:20
Alignment explanation
Indices: 43149--43382 Score: 165
Period size: 20 Copynumber: 11.7 Consensus size: 20
43139 GCTTTAAAAA
*
43149 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACAGAT
* *
43169 ACGC-TTGCGATTTACATAT
1 TCGCGTTGCGATTTACAGAT
*
43188 TCTCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
* *
43208 ACGCGTTGCGATTTA-TGTAT
1 TCGCGTTGCGATTTACAG-AT
* * * *
43228 TCTCATTGCGATTTACGGGT
1 TCGCGTTGCGATTTACAGAT
*
43248 ACGCGTTGCGATTTTAC-GTAT
1 TCGCGTTGCGA-TTTACAG-AT
*
43269 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACAGAT
* *
43289 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACAGAT
* * * *
43310 ACTCGTTGCGATAGT-CAGAA
1 TCGCGTTGCGAT-TTACAGAT
* *
43330 TCGAGTTGCGATTTATATG-T
1 TCGCGTTGCGATTTACA-GAT
* *
43350 TCGCGTTGCGATTTATATAT
1 TCGCGTTGCGATTTACAGAT
43370 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43383 CTGGAAAATC
Statistics
Matches: 169, Mismatches: 32, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
19 17 0.10
20 114 0.67
21 38 0.22
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAGAT
Found at i:43229 original size:40 final size:40
Alignment explanation
Indices: 43152--43382 Score: 234
Period size: 40 Copynumber: 5.8 Consensus size: 40
43142 TTAAAAATCG
* *
43152 CGTTGCGATTTACGGATACGC-TTGCGATTTACATATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
*
43191 CGTTGCGATTTACAGATACGCGTTGCGATTTATGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* * * *
43231 CATTGCGATTTACGGGTACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
* * *
43272 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
* * ** * *
43313 CGTTGCGATAGT-CAGA-ATCGAGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCT
* * *
43353 CGTTGCGATTTATATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
43383 CTGGAAAATC
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
39 21 0.13
40 70 0.44
41 67 0.42
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:43281 original size:41 final size:40
Alignment explanation
Indices: 43152--43321 Score: 243
Period size: 41 Copynumber: 4.2 Consensus size: 40
43142 TTAAAAATCG
*
43152 CGTTGCGATTTACGGATACGC-TTGCGATTTACATATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
43191 CGTTGCGATTTACAGATACGCGTTGCGATTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
43231 CATTGCGATTTACGGGTACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* *
43272 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
43313 CGTTGCGAT
1 CGTTGCGAT
43322 AGTCAGAATC
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 20 0.17
40 41 0.35
41 55 0.47
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:43290 original size:81 final size:79
Alignment explanation
Indices: 43154--43302 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 79
43144 AAAAATCGCG
43154 TTGCGATTTACGGATACGCTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCGTTGCGA
1 TTGCGATTTACGGATACGCTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCGTTGCGA
43219 TTTATGTATTCTCA
66 TTTATGTATTCTCA
* * * *
43233 TTGCGATTTACGGGTACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
1 TTGCGATTTACGGATACGC-TTGCGA-TTTACATATTCTCGTTGCGATTTACAGATACGCGTTGC
43298 GATTT
64 GATTT
43303 TACGGATACT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 18 0.28
80 6 0.09
81 40 0.62
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (79 bp):
TTGCGATTTACGGATACGCTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCGTTGCGA
TTTATGTATTCTCA
Found at i:43357 original size:81 final size:81
Alignment explanation
Indices: 43154--43382 Score: 207
Period size: 81 Copynumber: 2.8 Consensus size: 81
43144 AAAAATCGCG
* * * * * *
43154 TTGCGATTTACGGATACG-CTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCGTTGCG
1 TTGCGATTCACGAATACGAGTTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTGCG
* * *
43218 A-TTTATGTATTCTCA
66 ATTTTACGGATACTCA
* ** * * * *
43233 TTGCGATTTACGGGTACGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATACGCGTTG
1 TTGCGATTCACGAATACGAGTTGCGATTTATATGT-TCG-CGTTGCGATTTACAGATACGCGTTG
*
43297 CGATTTTACGGATACTCG
64 CGATTTTACGGATACTCA
* * *
43315 TTGCGATAGTCA-GAAT-CGAGTTGCGATTTATATGTTCGCGTTGCGATTTATATATTCGCGTTG
1 TTGCGAT--TCACGAATACGAGTTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTG
43378 CGATT
64 CGATT
43383 CTGGAAAATC
Statistics
Matches: 121, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
79 19 0.16
80 10 0.08
81 53 0.44
82 31 0.26
83 6 0.05
84 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (81 bp):
TTGCGATTCACGAATACGAGTTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTGCG
ATTTTACGGATACTCA
Found at i:43485 original size:20 final size:19
Alignment explanation
Indices: 43431--43485 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
43421 GATTCTTCAT
43431 AATCGCGTTGTGATTCTGG
1 AATCGCGTTGTGATTCTGG
* ** *
43450 AAACTGATTTGCGATTCTGG
1 AATC-GCGTTGTGATTCTGG
43470 AGATCGCGTTGTGATT
1 A-ATCGCGTTGTGATT
43486 TTTATTTCGC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 3 0.12
20 21 0.81
21 2 0.08
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (19 bp):
AATCGCGTTGTGATTCTGG
Found at i:44962 original size:27 final size:26
Alignment explanation
Indices: 44915--44965 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
44905 TTTTTTATAC
*
44915 TTAAAAAAGGAAATACGGAAAAATCA
1 TTAAAAAAGGAAATACAGAAAAATCA
44941 TTAAAAATAGGAAATGA-AGAAAAAT
1 TTAAAAA-AGGAAAT-ACAGAAAAAT
44966 GAAAATACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 14 0.64
28 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.18
Consensus pattern (26 bp):
TTAAAAAAGGAAATACAGAAAAATCA
Found at i:47905 original size:84 final size:84
Alignment explanation
Indices: 47627--48269 Score: 720
Period size: 84 Copynumber: 7.7 Consensus size: 84
47617 TTGATATGCA
**
47627 GAGTGTAATCGAACTCGAAGGTC-TTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
** *
47691 AATTTGACATG-CTTCTGAGTT
66 AA--TGATGTGCCTT-TGAGCT
* * * * * * * * *
47712 GAATGTAATCGAACTCAAATGT-ATTTGTTGACAGGTAACCCTTCTCGCCTTAAGTTACGCTGTA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
* * * *
47776 ACTTTAATATGCCTTTGAGAT
66 A--ATGATGTGCCTTTGAGCT
* * * *
47797 GAGTGTAATCGAACTCGAATGTCTTTTTTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
*
47862 AATGATGTGCCTTTGAGTT
66 AATGATGTGCCTTTGAGCT
* * * * * * * *
47881 GAGCGTAATCGAGCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
*
47946 AATAATGTGCCTTTGAGCT
66 AATGATGTGCCTTTGAGCT
* * *
47965 GAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
48030 AATGATGTGCCTTTGAGCT
66 AATGATGTGCCTTTGAGCT
* * * * * * * * * *
48049 GAGTGTAATAGAACTCGAAGGTCTTTGGTTGGAAGAT-AGCCTTCTCGACTTAAGCTATACTGCA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
*
48113 AATGATATGCCTTTGAGCT
66 AATGATGTGCCTTTGAGCT
* *
48132 GAGTATAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
48196 AATGATGTGCCTTTGAGCT
66 AATGATGTGCCTTTGAGCT
* * * * * *
48215 GAATATAATCGAACTCGAAGGTCTTTTGTTAGCAGATAGCCCTTCTTGCATTGAG
1 GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG
48270 CTAAGTTGCA
Statistics
Matches: 469, Mismatches: 82, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
82 10 0.02
83 120 0.26
84 216 0.46
85 86 0.18
86 37 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (84 bp):
GAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
AATGATGTGCCTTTGAGCT
Found at i:47991 original size:168 final size:167
Alignment explanation
Indices: 47533--48260 Score: 837
Period size: 168 Copynumber: 4.4 Consensus size: 167
47523 ACCATGCGGT
* * * * * * *
47533 TGATATGCCTATGAGCTGAATGAAATCGAACTCGAAGGTCTTT-GATGACAGATAGCCCTTCTTG
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
* * ** * * *
47597 CCTTGAGCTATGCTTTAAAT--T-TG-ATAT--GCAGAGTGTAATCGAACTCGAAGGTCTTTGTT
66 ACTTAAGCTATGCTGCAAATAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT
*
47656 AACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
131 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
** * * * * * *
47693 TTTGACATG-CTTCTGAGTTGAATGTAATCGAACTCAAATGTATTT-GTTGACAGGTAACCCTTC
1 --TGATGTGCCTT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * * *
47756 TCGCCTTAAGTTACGCTGTAACTTTAATATGCCTTTGAGATGAGTGTAATCGAACTCGAATGTCT
63 TCGACTTAAGCTATGCTGCAA--ATAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-
* ** *
47821 TTTTTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAA
125 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
* ** *
47864 TGATGTGCCTTTGAGTTGAGCGTAATCGAGCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
* *
47929 ACTTAAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTAT
66 ACTTAAGCTATGCTGCAAATAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGT
* * *
47994 TGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
130 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
* * * *
48032 TGATGTGCCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTTGGTTGGAAGAT-AGCCTTCTCG
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
* * *
48096 ACTTAAGCTATACTGCAAATGATATGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTGTT
66 ACTTAAGCTATGCTGCAAATAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT
48161 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
131 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
* * * *
48198 TGATGTGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTTGTTAGCAGATAGCCCTTCT
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
48261 TGCATTGAGC
Statistics
Matches: 482, Mismatches: 71, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
161 2 0.00
162 64 0.13
164 1 0.00
166 88 0.18
167 72 0.15
168 127 0.26
169 31 0.06
170 59 0.12
171 38 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (167 bp):
TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
ACTTAAGCTATGCTGCAAATAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT
GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
Found at i:48502 original size:121 final size:121
Alignment explanation
Indices: 48286--48506 Score: 316
Period size: 121 Copynumber: 1.8 Consensus size: 121
48276 TGCAAATGAG
** *
48286 CACGATATCCTACGTCGTGAAGTTGAAATCATGAATGACCCCTTCGTTGTGAAGTTGAGCCTCAA
1 CACGATATCCTACGTCGTGAAGTTGAAATCATGAATGACCCCTTCGTCATGAAGTTGAACCTCAA
* *
48351 ATTAGATATCATTCGCCGTAAAGTTGAAATCCAAGGGTTGCATTGTTACTGGTGGA
66 ATTAGATATCATTCACCGTAAAGTTAAAATCCAAGGGTTGCATTGTTACTGGTGGA
* * * **
48407 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCATGAAGTTGAACCTTGA
1 CACGATATCCTACGTCGTGAAGTTGAAATCATGAATGACCCCTTCGTCATGAAGTTGAACCTCAA
* * * *
48472 ATTGGATATCCTTCATCGTGAAGTTAAAATCCAAG
66 ATTAGATATCATTCACCGTAAAGTTAAAATCCAAG
48507 TTAAGTTGCA
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
121 86 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (121 bp):
CACGATATCCTACGTCGTGAAGTTGAAATCATGAATGACCCCTTCGTCATGAAGTTGAACCTCAA
ATTAGATATCATTCACCGTAAAGTTAAAATCCAAGGGTTGCATTGTTACTGGTGGA
Found at i:48715 original size:43 final size:43
Alignment explanation
Indices: 48675--48818 Score: 207
Period size: 43 Copynumber: 3.3 Consensus size: 43
48665 TTCCCTTCGC
* * * * * *
48675 CGTGAAGTTAAAACCGTGGATGTGTGGGAACGATATCCTTCGT
1 CGTGAAGTTGAAATCGTGGATGCGTTGGTACGATATCCTCCGT
* *
48718 CGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGT
1 CGTGAAGTTGAAATCGTGGATGCGTTGGTACGATATCCTCCGT
*
48761 CGTGGAGTTGAAATCGTGGATGCGTTGGTACGATATCCTCCGT
1 CGTGAAGTTGAAATCGTGGATGCGTTGGTACGATATCCTCCGT
48804 CGTGAAGTTGAAATC
1 CGTGAAGTTGAAATC
48819 CAAGCTTGTG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
CGTGAAGTTGAAATCGTGGATGCGTTGGTACGATATCCTCCGT
Found at i:48990 original size:43 final size:41
Alignment explanation
Indices: 48926--49036 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 41
48916 GGATTCCCTT
* * *
48926 CGTTGTGAAGTTGAAACCGTGGATGTATGGGCACGATATCCTC
1 CGTTGTGGAGTTGAAATCGTGGATGT-T-GGCAAGATATCCTC
*
48969 CGTTGTGGAGTTGAAATCGTGGATCAGTTGGTAAGATATCCTC
1 CGTTGTGGAGTTGAAATCGTGGAT--GTTGGCAAGATATCCTC
* *
49012 TGTCGTGGAGTTGAAATCGTGGATG
1 CGTTGTGGAGTTGAAATCGTGGATG
49037 ACCCCTTCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
41 1 0.02
43 56 0.93
44 1 0.02
45 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.31
Consensus pattern (41 bp):
CGTTGTGGAGTTGAAATCGTGGATGTTGGCAAGATATCCTC
Found at i:49308 original size:64 final size:64
Alignment explanation
Indices: 49233--49363 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 64
49223 GAGCAAATTG
* * * *
49233 TGAGTTCAATATACTTCGCTGTGAAGTTGAAATTTACTTTGAATGAAACTGGAAAA-TTGTTTGT
1 TGAGTACAATATACTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAA-TGGAAAAGTTGTTTAT
* *
49297 TGAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTAT
1 TGAGTACAATATACTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATGGAAAAGTTGTTTAT
49361 TGA
1 TGA
49364 CAGACGCTCC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 6 0.10
64 54 0.90
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (64 bp):
TGAGTACAATATACTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATGGAAAAGTTGTTTAT
Found at i:49386 original size:63 final size:64
Alignment explanation
Indices: 49246--49389 Score: 184
Period size: 64 Copynumber: 2.3 Consensus size: 64
49236 GTTCAATATA
* * * * *
49246 CTTCGCTGTGAAGTTGAAATTTACTTTGAATGAAACTGGAAAATTGTTTGTTGAGTACAATATC
1 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGTTTATTGAGCACAAGATC
* * * *
49310 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAA-TTGAAAAGTTGTTTATTGA-CAGACGCTC
1 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAA-TTGTTTATTGAGCACAAGATC
49373 CTTCGCTGTGAAGTTGA
1 CTTCGCTGTGAAGTTGA
49390 GCACCCACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
63 27 0.39
64 43 0.61
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (64 bp):
CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGTTTATTGAGCACAAGATC
Found at i:49663 original size:32 final size:32
Alignment explanation
Indices: 49622--49696 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
49612 TTGCATCAGG
49622 ATGTTGAATC-CCAAAATATGCCACAATATTCA
1 ATGTTGAATCTCC-AAATATGCCACAATATTCA
* *
49654 ATGTTGAATCTCCAAATATGCCTCAATATTTA
1 ATGTTGAATCTCCAAATATGCCACAATATTCA
*
49686 CTGTTGAATCT
1 ATGTTGAATCT
49697 TTAAAGATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 37 0.95
33 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCACAATATTCA
Found at i:49707 original size:32 final size:32
Alignment explanation
Indices: 49622--49707 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
49612 TTGCATCAGG
*
49622 ATGTTGAATC-CCAAAATATGCCACAATATTCA
1 ATGTTGAATCTCC-AAAGATGCCACAATATTCA
* * *
49654 ATGTTGAATCTCCAAATATGCCTCAATATTTA
1 ATGTTGAATCTCCAAAGATGCCACAATATTCA
* **
49686 CTGTTGAATCTTTAAAGATGCC
1 ATGTTGAATCTCCAAAGATGCC
49708 CCGTTGTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 45 0.96
33 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (32 bp):
ATGTTGAATCTCCAAAGATGCCACAATATTCA
Found at i:57620 original size:76 final size:76
Alignment explanation
Indices: 57528--57688 Score: 295
Period size: 76 Copynumber: 2.1 Consensus size: 76
57518 AATAGTGACT
57528 AAAATAAAGGAAATGAAAGTTACAGACATAAATCATCACAAAATATAACATATTGGTGATCAAAT
1 AAAATAAAGGAAATGAAAGTTACAGACATAAATCATCACAAAATATAACATATTGGTGATCAAAT
*
57593 CGAAAATAACG
66 CAAAAATAACG
*
57604 AAAATAAAGGAAATGAAAGTTACATACATAAATCATCACAAAATATAACATATTGGTGATCAAAT
1 AAAATAAAGGAAATGAAAGTTACAGACATAAATCATCACAAAATATAACATATTGGTGATCAAAT
*
57669 TAAAAATAACG
66 CAAAAATAACG
57680 AAAATAAAG
1 AAAATAAAG
57689 CGCCAAAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.22
Consensus pattern (76 bp):
AAAATAAAGGAAATGAAAGTTACAGACATAAATCATCACAAAATATAACATATTGGTGATCAAAT
CAAAAATAACG
Found at i:60922 original size:3 final size:3
Alignment explanation
Indices: 60914--60979 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
60904 TTAGAAAAAT
60914 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60962 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
60980 TGATTAAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61878 original size:11 final size:11
Alignment explanation
Indices: 61862--61911 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
61852 AAAGTAAAAT
61862 AATTAAATCTG
1 AATTAAATCTG
61873 AATTAAAT-TG
1 AATTAAATCTG
* *
61883 AAGTAAA-AT-
1 AATTAAATCTG
*
61892 AATTAAAACTG
1 AATTAAATCTG
61903 AATTAAATC
1 AATTAAATC
61912 GAAAGATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 6 0.19
10 10 0.31
11 16 0.50
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (11 bp):
AATTAAATCTG
Found at i:61889 original size:30 final size:30
Alignment explanation
Indices: 61853--61910 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
61843 AGTTGTACTA
*
61853 AAGTAAAATAATTAAATCTGAATTAAATTG
1 AAGTAAAATAATTAAAACTGAATTAAATTG
61883 AAGTAAAATAATTAAAACTGAATTAAAT
1 AAGTAAAATAATTAAAACTGAATTAAAT
61911 CGAAAGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (30 bp):
AAGTAAAATAATTAAAACTGAATTAAATTG
Found at i:62660 original size:2 final size:2
Alignment explanation
Indices: 62653--62700 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
62643 GCGTCTATTA
62653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62695 AT AT AT
1 AT AT AT
62701 GAATTTCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63269 original size:17 final size:16
Alignment explanation
Indices: 63226--63273 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
63216 TGAAATAAGG
*
63226 AAAGTAATAAAAAAAT
1 AAAGTAATATAAAAAT
*
63242 AAAG-AAGATAAAAAT
1 AAAGTAATATAAAAAT
63257 AAAGTAAATATAAAAAT
1 AAAGT-AATATAAAAAT
63274 GAATAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 13 0.48
16 4 0.15
17 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AAAGTAATATAAAAAT
Found at i:63662 original size:16 final size:16
Alignment explanation
Indices: 63638--63674 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
63628 ATATATATAT
63638 AAAAA-AAATAA-TAA
1 AAAAATAAATAATTAA
63652 GAAAAATAAATAATTAA
1 -AAAAATAAATAATTAA
63669 AAAAAT
1 AAAAAT
63675 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 12 0.60
17 3 0.15
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAAATAATTAA
Found at i:65511 original size:37 final size:37
Alignment explanation
Indices: 65460--65844 Score: 192
Period size: 37 Copynumber: 11.1 Consensus size: 37
65450 GGTTTTTTTG
*
65460 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * *
65497 TGTTTCAAGGGAAACATAT-TC-A-A-AG-----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-T
* *
65527 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
65564 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAA-TT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
65600 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG-----ATTT
1 TGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTT
* *
65629 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAACTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
65666 AT-TTT-AAGAGAAAATGTCTCAAGAGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
65702 AG-TTCTAAAAGAAATTGTCTCAAGAGAGACGAAA-TT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * **
65738 TGTTTAAAG-GAAA-----AC-A-A-ATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ATTT
* * *
65767 TGTTTCAAGGGAAACTATCTCAAAAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
65803 TGTTTTAAGAGAAACTATATCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
65840 TGTTT
1 TGTTT
65845 TGAGTAAATT
Statistics
Matches: 263, Mismatches: 42, Indels: 86
0.67 0.11 0.22
Matches are distributed among these distances:
27 4 0.02
28 4 0.02
29 34 0.13
30 22 0.08
31 2 0.01
32 3 0.01
33 4 0.02
34 2 0.01
35 9 0.03
36 82 0.31
37 87 0.33
38 10 0.04
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:65654 original size:102 final size:102
Alignment explanation
Indices: 65469--65701 Score: 335
Period size: 101 Copynumber: 2.3 Consensus size: 102
65459 GTGTTTCAAG
* *
65469 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATATTCAAAGATTGGTATTTCA
1 AGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGAAAACAGATTCAAAGATTGGTATTTCA
65534 AGAGAAACTGTCTCAAGAGAGACAAAAC-TTAGTTCTAAA
65 AGAGAAACTGTCTCAAGAGAGAC-AAACTTTA-TTCTAAA
* * *
65573 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATT-TTGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTGGTATTTCAA
* * *
65637 GGGAAACTGTCTCAAGAGAGACAAACTTTATTTTAAG
66 GAGAAACTGTCTCAAGAGAGACAAACTTTATTCTAAA
* *
65674 AGAAAATGTCTCAAGAGAGACAAAATTT
1 AGAAACTGTCTCAAGGGAGACAAAATTT
65702 AGTTCTAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
101 34 0.29
102 31 0.26
103 28 0.24
104 24 0.21
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (102 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTGGTATTTCAA
GAGAAACTGTCTCAAGAGAGACAAACTTTATTCTAAA
Found at i:65691 original size:138 final size:138
Alignment explanation
Indices: 65527--65839 Score: 509
Period size: 138 Copynumber: 2.3 Consensus size: 138
65517 CAAAGATTGG
* *
65527 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGGAG
1 TATTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAGAG
* * * *
65592 ACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
66 ACGAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAAAGAG
*
65657 ACAAACTT
131 ACAAAATT
* * *
65665 TATTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAATTGTCTCAAGAGAG
1 TATTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAGAG
65730 ACGAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAAAGAG
66 ACGAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAAAGAG
65795 ACAAAATT
131 ACAAAATT
* * *
65803 TGTTTTAAGAGAAACTATATCAAGAGAGACAAAACTT
1 TATTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
65840 TGTTTTGAGT
Statistics
Matches: 160, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 160 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (138 bp):
TATTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAAAGAG
ACAAAATT
Found at i:65817 original size:36 final size:37
Alignment explanation
Indices: 65765--65845 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
65755 ATTCAAAGAT
* * *
65765 TTTGTTTCAAGGGAAACTATCTCAAAAGAGACAAAA-
1 TTTGTTTTAAGAGAAACTATATCAAAAGAGACAAAAC
*
65801 TTTGTTTTAAGAGAAACTATATCAAGAGAGACAAAAC
1 TTTGTTTTAAGAGAAACTATATCAAAAGAGACAAAAC
65838 TTTGTTTT
1 TTTGTTTT
65846 GAGTAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (37 bp):
TTTGTTTTAAGAGAAACTATATCAAAAGAGACAAAAC
Found at i:67367 original size:95 final size:95
Alignment explanation
Indices: 67165--67425 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 95
67155 AGCTAGCTGA
* * * *
67165 ATCCATAAAGCCGGGGCATTTAACCAATTTCTCTAGAGGGAGAACTTAA--TATTATTGTATATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTTTTCTAGAGGGAAAACTCAAGCT-TTATTG----TA
* * *
67228 TATTATAATCGCCTTTATCAGGCTAGCTGAATTTT
61 TATTATAATCACATTTATCAGGCTAGCTGAATCTT
67263 ATCCATAAAGCCGGGGCGTTTAACCAATTTTTCTAGAGGGAAAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTTTTCTAGAGGGAAAACTCAAGCTTTATTGTATATTA
*
67328 TACTCACATTTATCAGGCTAGCTGAATCTT
66 TAATCACATTTATCAGGCTAGCTGAATCTT
* * *
67358 ATCCGTAAAGTCGGGGCGTTTAACCAATTTCTT-TAGAGGGACAACTCAAGCTTTATTGTATATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTT-TTCTAGAGGGAAAACTCAAGCTTTATTGTATAT-
67422 TATA
64 TATA
67426 TAATTATAAT
Statistics
Matches: 148, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
95 90 0.61
96 6 0.04
98 45 0.30
99 6 0.04
100 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTTTTCTAGAGGGAAAACTCAAGCTTTATTGTATATTA
TAATCACATTTATCAGGCTAGCTGAATCTT
Found at i:71565 original size:17 final size:16
Alignment explanation
Indices: 71508--71555 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
71498 TGAAATAAGG
*
71508 AAAGTAATAAAAAAAT
1 AAAGTAATATAAAAAT
*
71524 AAAG-AAGATAAAAAT
1 AAAGTAATATAAAAAT
71539 AAAGTAAATATAAAAAT
1 AAAGT-AATATAAAAAT
71556 GGAAAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 13 0.48
16 4 0.15
17 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AAAGTAATATAAAAAT
Found at i:71582 original size:14 final size:14
Alignment explanation
Indices: 71518--71778 Score: 60
Period size: 14 Copynumber: 17.6 Consensus size: 14
71508 AAAGTAATAA
*
71518 AAAAATAAAGAAGAT
1 AAAAATAAATAA-AT
71533 AAAAATAAAGTAAATAT
1 AAAAATAAA-T-AA-AT
*
71550 AAAAATGGAAA-GAAT
1 AAAAAT--AAATAAAT
71565 -AAAATAAATAAAT
1 AAAAATAAATAAAT
71578 AAAAA-ATAAT-AAT
1 AAAAATA-AATAAAT
* *
71591 AATACTAATATATACAT
1 AA-A--AATAAATAAAT
* * *
71608 AGCAAACAACTAAAT
1 A-AAAATAAATAAAT
*
71623 TAAAATAAGAT-AAT
1 AAAAATAA-ATAAAT
**
71637 GCAAATAAATAAAT
1 AAAAATAAATAAAT
*
71651 AAAACT-AATAAA-
1 AAAAATAAATAAAT
*
71663 AGGAAGATAAA-AAGAT
1 A--AAAATAAATAA-AT
71679 AAAAATAGAAAATAGAAAT
1 AAAAAT---AAAT--AAAT
71698 AAAAAGTAAATAAAT
1 AAAAA-TAAATAAAT
71713 AAAATATAAA-AAAGT
1 AAAA-ATAAATAAA-T
* * *
71728 AAATATATATATAT
1 AAAAATAAATAAAT
71742 AAGTAAAT-AATAAAT
1 AA--AAATAAATAAAT
*
71757 TAAAA-AAAT-AAT
1 AAAAATAAATAAAT
71769 ATAAAATAAA
1 A-AAAATAAA
71779 AAACCAAAAG
Statistics
Matches: 180, Mismatches: 31, Indels: 71
0.64 0.11 0.25
Matches are distributed among these distances:
12 7 0.04
13 27 0.15
14 55 0.31
15 46 0.26
16 10 0.06
17 22 0.12
19 10 0.06
20 3 0.02
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:71591 original size:26 final size:29
Alignment explanation
Indices: 71508--71592 Score: 70
Period size: 31 Copynumber: 2.9 Consensus size: 29
71498 TGAAATAAGG
* *
71508 AAAGT-AATAAAAAAATAAAGAAGATAAAAAT
1 AAAGTAAATATAAAAATGAAG-A-AT-AAAAT
71539 AAAGTAAATATAAAAATGGAAAGAATAAAAT
1 AAAGTAAATATAAAAAT-G-AAGAATAAAAT
*
71570 AAA-TAAATA-AAAAAT-AATAATAA
1 AAAGTAAATATAAAAATGAAGAATAA
71593 TACTAATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 7 0.15
29 6 0.12
30 6 0.12
31 13 0.27
32 12 0.25
33 1 0.02
34 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (29 bp):
AAAGTAAATATAAAAATGAAGAATAAAAT
Found at i:71722 original size:41 final size:41
Alignment explanation
Indices: 71672--71766 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 41
71662 AAGGAAGATA
*
71672 AAAAGATAAAAATAGAAAATAGAAATA-AAAAGTAAATAAAT
1 AAAATATAAAAATAGAAAATAGAAATATAAAAGTAAAT-AAT
* * * *
71713 AAAATATAAAAA-AGTAAATATATATATATAAGTAAATAAT
1 AAAATATAAAAATAGAAAATAGAAATATAAAAGTAAATAAT
* *
71753 AAATTAAAAAAATA
1 AAAATATAAAAATA
71767 ATATAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
40 24 0.53
41 21 0.47
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (41 bp):
AAAATATAAAAATAGAAAATAGAAATATAAAAGTAAATAAT
Found at i:74218 original size:63 final size:62
Alignment explanation
Indices: 74116--74237 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 62
74106 TAGTCACATA
* * *
74116 ATTTTATTTATTTTGATTTTCGCATATTAATTTCATTATTTTACATTCTGGTCACATGTTTAC
1 ATTTTATTTATTTTAATTTTCGCATATTAATTTCATTA-TTTACAATATGGTCACATGTTTAC
* *
74179 ATTTTATTTATTTTAATTTT-G-ATACATTATTTTTC-TTATTTACAATATGGTCACTTGTT
1 ATTTTATTTATTTTAATTTTCGCAT--ATTA-ATTTCATTATTTACAATATGGTCACATGTT
74238 ATGCTTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
61 2 0.04
62 19 0.37
63 26 0.51
64 4 0.08
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (62 bp):
ATTTTATTTATTTTAATTTTCGCATATTAATTTCATTATTTACAATATGGTCACATGTTTAC
Found at i:74762 original size:14 final size:14
Alignment explanation
Indices: 74743--74778 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
74733 TTTTTATTTA
*
74743 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
74757 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
74771 TTTAATTT
1 TTTAATTT
74779 ATTTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:74796 original size:17 final size:18
Alignment explanation
Indices: 74771--74830 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 18
74761 ATTTCATTAC
*
74771 TTTAATTTATTTATAT-T
1 TTTATTTTATTTATATCT
*
74788 TTTATTTTATTTTTATCT
1 TTTATTTTATTTATATCT
* *
74806 TTCATTTT-TTTGTA-CT
1 TTTATTTTATTTATATCT
*
74822 TTAATTTTA
1 TTTATTTTA
74831 ATAGTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.25
17 19 0.53
18 8 0.22
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTTATTTATATCT
Found at i:74812 original size:13 final size:11
Alignment explanation
Indices: 74776--74814 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
74766 ATTACTTTAA
74776 TTTATTTATATT
1 TTTATTT-TATT
74788 TTTATTTTATT
1 TTTATTTTATT
74799 TTTATCTTTCATT
1 TTTAT-TTT-ATT
74812 TTT
1 TTT
74815 TTGTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
12 10 0.40
13 6 0.24
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:74850 original size:19 final size:19
Alignment explanation
Indices: 74826--74865 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
74816 TGTACTTTAA
74826 TTTTAATAGT-TTTATATAT
1 TTTTAATAGTCTTTA-ATAT
*
74845 TTTTAATTGTCTTTAATAT
1 TTTTAATAGTCTTTAATAT
74864 TT
1 TT
74866 GTATCCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTAATAGTCTTTAATAT
Done.