Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012223.1 Corchorus capsularis cultivar CVL-1 contig12244, 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: 227682
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3277 original size:18 final size:18
Alignment explanation
Indices: 3254--3289 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3244 GCAATTATTA
3254 TATCAT-TATATATATAAT
1 TATCATATATATA-ATAAT
3272 TATCATATATATAATAAT
1 TATCATATATATAATAAT
3290 ATATACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TATCATATATATAATAAT
Found at i:18406 original size:10 final size:10
Alignment explanation
Indices: 18391--18420 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18381 ATCAACCAAG
*
18391 AGAAAAACAA
1 AGAAAAAAAA
18401 AGAAAAAAAA
1 AGAAAAAAAA
18411 AGAAAAAAAA
1 AGAAAAAAAA
18421 CAATGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:18431 original size:14 final size:13
Alignment explanation
Indices: 18393--18437 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 13
18383 CAACCAAGAG
18393 AAAAACAA-AGAA
1 AAAAACAAGAGAA
18405 AAAAA-AAGA-AA
1 AAAAACAAGAGAA
18416 AAAAACAATGAGAA
1 AAAAACAA-GAGAA
*
18430 AAGAACAA
1 AAAAACAA
18438 CGGAGGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 2 0.07
14 9 0.32
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAACAAGAGAA
Found at i:19502 original size:27 final size:26
Alignment explanation
Indices: 19462--19512 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
19452 ACTTTGGTCA
19462 TTTCAGGGACATTTCGGTCATCTTTCG
1 TTTCAGGGACATTTCGGTCA-CTTTCG
* *
19489 TTTCAGGGATATTTTGGTCACTTT
1 TTTCAGGGACATTTCGGTCACTTT
19513 TGGGGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (26 bp):
TTTCAGGGACATTTCGGTCACTTTCG
Found at i:23380 original size:40 final size:40
Alignment explanation
Indices: 23331--23444 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
23321 GAAAGCGGTT
*
23331 AAAGAACTTAATTCATAGAAATTAAGTAAAAGCAACAATCA
1 AAAG-ACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
* * * * *
23372 GAGGACTTAATTCATAGAAATTAAGTAAAAACAGCAGTTA
1 AAAGACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
* *
23412 AAAGACTTAATCCATAGTAATTAAGTAAAAACA
1 AAAGACTTAATTCATAGAAATTAAGTAAAAACA
23445 TCAGAACACA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (40 bp):
AAAGACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
Found at i:23461 original size:40 final size:39
Alignment explanation
Indices: 23337--23463 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 39
23327 GGTTAAAGAA
* *
23337 CTTAATTCATAGAAATTAAGTAAAAGCAACA-ATCAGAGG
1 CTTAATTCATAGAAATTAAGTAAAAACAACAGAACA-AGG
* *
23376 ACTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAA-AAGA
1 -CTTAATTCATAGAAATTAAGTAAAAACAACAG--AACAAGG
* * *
23417 CTTAATCCATAGTAATTAAGTAAAAACATCAGAACACAGG
1 CTTAATTCATAGAAATTAAGTAAAAACAACAGAACA-AGG
23457 CTTAATT
1 CTTAATT
23464 TTAAGAAAGG
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 66 0.90
41 2 0.03
42 1 0.01
43 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (39 bp):
CTTAATTCATAGAAATTAAGTAAAAACAACAGAACAAGG
Found at i:23471 original size:80 final size:80
Alignment explanation
Indices: 23314--23463 Score: 189
Period size: 80 Copynumber: 1.9 Consensus size: 80
23304 AGTTAAGAAG
* * * * *
23314 AAGTAAAGAAAGCGGTTAAAGAACTTAATTCATAGAAATTAAGTAAAAGCAACAATCAGAGGACT
1 AAGTAAAGAAAGCAGTTAAAGAACTTAATCCATAGAAATTAAGTAAAAACAACAAACACAGGACT
23379 TAATTCATAGAAATT
66 TAATTCATAGAAATT
* *
23394 AAGTAAA-AACAGCAGTTAAA-AGACTTAATCCATAGTAATTAAGTAAAAACATCAGAACACAGG
1 AAGTAAAGAA-AGCAGTTAAAGA-ACTTAATCCATAGAAATTAAGTAAAAACAACA-AACACAGG
23457 -CTTAATT
63 ACTTAATT
23464 TTAAGAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 3 0.05
80 51 0.85
81 6 0.10
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (80 bp):
AAGTAAAGAAAGCAGTTAAAGAACTTAATCCATAGAAATTAAGTAAAAACAACAAACACAGGACT
TAATTCATAGAAATT
Found at i:23576 original size:22 final size:22
Alignment explanation
Indices: 23548--23971 Score: 289
Period size: 22 Copynumber: 19.3 Consensus size: 22
23538 TTGGAAAGTT
* *
23548 AGACTGAAATTAGACTGATAGA
1 AGACTGAAATTAGACTGAAATA
* *
23570 AGACTGATATTAGACTGAAATT
1 AGACTGAAATTAGACTGAAATA
* * *
23592 AGACTGATATTAAACTGAAATT
1 AGACTGAAATTAGACTGAAATA
* ** * *
23614 AGACTGATAGAAGACTGATATT
1 AGACTGAAATTAGACTGAAATA
*
23636 AGACTGAAATTAGACTGATATA
1 AGACTGAAATTAGACTGAAATA
* * * *
23658 AGATTGATATTAAACTGAAATC
1 AGACTGAAATTAGACTGAAATA
** *
23680 AGACTGAAAGAATACTGAAACT-
1 AGACTGAAATTAGACTGAAA-TA
* * *
23702 AGACTGATATAAGACTGATATTA
1 AGACTGAAATTAGACTGA-AATA
* *
23725 A-ACTGAAATCAGACTGAAAGA
1 AGACTGAAATTAGACTGAAATA
* * *
23746 ATACTGAAATTAGATTGATATA
1 AGACTGAAATTAGACTGAAATA
* * * **
23768 AGACTGATATTAAAATGAAACC
1 AGACTGAAATTAGACTGAAATA
** * *
23790 AGACTGAAAGAATACTGAAATT
1 AGACTGAAATTAGACTGAAATA
* *
23812 AGACTGAAAATAGACTGAAAGA
1 AGACTGAAATTAGACTGAAATA
* * * *
23834 AGATTGATATTAAACTGAAATC
1 AGACTGAAATTAGACTGAAATA
* *
23856 AGACTGAAA-GAGTACTGAAATT
1 AGACTGAAATTAG-ACTGAAATA
** *
23878 AGACTGAAAAAAGACTGAAATT
1 AGACTGAAATTAGACTGAAATA
** * *
23900 AGACTGAAAAAAGACTGATATT
1 AGACTGAAATTAGACTGAAATA
* *
23922 AGACTGAAATCAGACTGAAAGA
1 AGACTGAAATTAGACTGAAATA
*
23944 AGACTGAAATTAGGCTGATAA-A
1 AGACTGAAATTAGACTGA-AATA
23966 AGACTG
1 AGACTG
23972 GCTTAGTTTC
Statistics
Matches: 321, Mismatches: 74, Indels: 14
0.78 0.18 0.03
Matches are distributed among these distances:
21 4 0.01
22 310 0.97
23 7 0.02
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (22 bp):
AGACTGAAATTAGACTGAAATA
Found at i:23585 original size:33 final size:33
Alignment explanation
Indices: 23541--23971 Score: 305
Period size: 33 Copynumber: 13.0 Consensus size: 33
23531 AAGAAGATTG
*
23541 GAAAGTTAGACTGAAATTAGACTGATAGAAGACT
1 GAAA-TTAGACTGAAATTAGACTGATATAAGACT
*
23575 GATATTAGACTGAAATTAGACTGATATTAA-ACT
1 GAAATTAGACTGAAATTAGACTGATA-TAAGACT
* ** *
23608 GAAATTAGACTGATAGAAGACTGATATTAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
* * *
23641 GAAATTAGACTGATATAAGATTGATATTAA-ACT
1 GAAATTAGACTGAAATTAGACTGATA-TAAGACT
* ** * *
23674 GAAATCAGACTGAAAGAATACTGAAACT-AGACT
1 GAAATTAGACTGAAATTAGACTGATA-TAAGACT
* * * * * *
23707 GATATAAGACTGATATTAAACTGAAATCAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
** * *
23740 GAAAGAATACTGAAATTAGATTGATATAAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
* * * ** * * *
23773 GATATTAAAATGAAACCAGACTGAAAGAATACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
* * * *
23806 GAAATTAGACTGAAAATAGACTGAAAGAAGATT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
* * *
23839 GATATTAAACTGAAATCAGACTGA-A-AGAGTACT
1 GAAATTAGACTGAAATTAGACTGATATA-AG-ACT
** * *
23872 GAAATTAGACTGAAAAAAGACTGAAATTAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
** * * *
23905 GAAAAAAGACTGATATTAGACTGAAATCAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
** * *
23938 GAAAGAAGACTGAAATTAGGCTGATAAAAGACT
1 GAAATTAGACTGAAATTAGACTGATATAAGACT
23971 G
1 G
23972 GCTTAGTTTC
Statistics
Matches: 317, Mismatches: 71, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
31 1 0.00
32 7 0.02
33 299 0.94
34 10 0.03
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (33 bp):
GAAATTAGACTGAAATTAGACTGATATAAGACT
Found at i:23613 original size:55 final size:55
Alignment explanation
Indices: 23550--23971 Score: 350
Period size: 55 Copynumber: 7.5 Consensus size: 55
23540 GGAAAGTTAG
* *
23550 ACTGAAATTAGACTGATAGAAGACTGATATTAGACTGAAATTAGACTGATATTAA
1 ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
* *
23605 ACTGAAATTAGACTGATAGAAGACTGATATTAGACTGAAATTAGACTGATATAAGATTGATATTA
1 ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGAC-----------TGATATTA
23670 A
55 A
* * * * *
23671 ACTGAAATCAGACTGAAAGAATACTGAAACTAGACTGATATAAGACTGATATTAA
1 ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
* * * * *
23726 ACTGAAATCAGACTGAAAGAATACTGAAATTAGATTGATATAAGACTGATATTAA
1 ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
* ** * * **
23781 AATGAAACCAGACTGAAAGAATACTGAAATTAGACTGAAAATAGACTGA-AAGAA
1 ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
* * * ** * **
23835 GATTGATATTAAACTGAAATCAGACTGAAA-GAGTACTGAAATTAGACTGA-AAAAA
1 -ACTGAAATTAGACTGAAAGAAGACTGAAATTAG-ACTGAAATTAGACTGATATTAA
* * * **
23890 GACTGAAATTAGACTGAAAAAAGACTGATATTAGACTGAAATCAGACTGA-AAGAA
1 -ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
*
23945 GACTGAAATTAGGCTGATAA-AAGACTG
1 -ACTGAAATTAGACTGA-AAGAAGACTG
23972 GCTTAGTTTC
Statistics
Matches: 314, Mismatches: 38, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
54 5 0.02
55 257 0.82
56 4 0.01
66 48 0.15
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.24
Consensus pattern (55 bp):
ACTGAAATTAGACTGAAAGAAGACTGAAATTAGACTGAAATTAGACTGATATTAA
Found at i:24057 original size:35 final size:35
Alignment explanation
Indices: 23964--24214 Score: 270
Period size: 36 Copynumber: 7.0 Consensus size: 35
23954 TAGGCTGATA
* *
23964 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
23999 AATAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
1 AA-AGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * * *
24035 ATAGTCTGGCGTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * * *
24069 AAAGAATTGGCTTAGTTTCAAGGAAACTAGGTAAAAAAA
1 AAAG-ACTGGCTTAATTTCAAGGAAATTAGGT---AAAG
* *
24108 AAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAA-GACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
24144 AAAAGACTGACTTAATTTCAAGGAAATTAGGTGAAGG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGT-AAAG
* *
24181 AAAGACTGCCTTAATTTCAAGGAAATTAAGTAAA
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAA
24215 AAGACACATG
Statistics
Matches: 183, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.02
35 53 0.29
36 88 0.48
37 6 0.03
38 3 0.02
39 29 0.16
40 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (35 bp):
AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
Found at i:24230 original size:35 final size:34
Alignment explanation
Indices: 23949--24234 Score: 209
Period size: 36 Copynumber: 7.9 Consensus size: 34
23939 AAAGAAGACT
* *
23949 GAAATTAGGCTGATAAA-AGACTGGCTTAGTTTCAAG
1 GAAATTAGG-T-AAAAAGAGACT-GCTTAATTTCAAG
* *
23985 GAAACTAGGTAAAGAATAGACTGACTTAATTTCAAG
1 GAAATTAGGTAAA-AAGAGACTG-CTTAATTTCAAG
* * * *
24021 GAAATTAGGTAAAGATAGTCTGGCGTAATTTCAAG
1 GAAATTAGGTAAAAAGAGACT-GCTTAATTTCAAG
* * *
24056 GAAATTAAGTAAAAA-AGAATTGGCTTAGTTTCAAG
1 GAAATTAGGTAAAAAGAG-ACT-GCTTAATTTCAAG
* * *
24091 GAAACTAGGTAAAAAAAAAAGGACTGGCTTAGTTTCAAG
1 GAAATTAGGT---AAAAAGA-GACT-GCTTAATTTCAAG
* *
24130 GAAACTAGGTAAAGAAAAGACTGACTTAATTTCAAG
1 GAAATTAGGTAAA-AAGAGACTG-CTTAATTTCAAG
*
24166 GAAATTAGGTGAAGGAA-AGACTGCCTTAATTTCAAG
1 GAAATTAGGT-AA-AAAGAGACTG-CTTAATTTCAAG
* *
24202 GAAATTAAGTAAAAAGACACATGCTTAATTTCA
1 GAAATTAGGTAAAAAGAGAC-TGCTTAATTTCA
24235 GAAAAGGAAA
Statistics
Matches: 211, Mismatches: 23, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
34 6 0.03
35 71 0.34
36 93 0.44
37 8 0.04
38 5 0.02
39 27 0.13
40 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (34 bp):
GAAATTAGGTAAAAAGAGACTGCTTAATTTCAAG
Found at i:25247 original size:2 final size:2
Alignment explanation
Indices: 25240--25268 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25230 TTACAATTCT
25240 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 T
25269 TGTTTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27959 original size:14 final size:14
Alignment explanation
Indices: 27942--27970 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27932 ATGGTGATTA
27942 GAAGGGCAGCTCTT
1 GAAGGGCAGCTCTT
27956 GAAGGGCAGCTCTT
1 GAAGGGCAGCTCTT
27970 G
1 G
27971 GTCTCTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (14 bp):
GAAGGGCAGCTCTT
Found at i:30784 original size:19 final size:18
Alignment explanation
Indices: 30755--30790 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30745 TATTTTTACT
*
30755 CTTTTTTACTGAGTACCC
1 CTTTTTTACTGAATACCC
30773 CTTTTCTTACTGAATACC
1 CTTTT-TTACTGAATACC
30791 ACATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.44
Consensus pattern (18 bp):
CTTTTTTACTGAATACCC
Found at i:30826 original size:27 final size:27
Alignment explanation
Indices: 30796--30875 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
30786 ATACCACATT
*
30796 TTACTCTTTTTTATTGATCACCATTTC
1 TTACTCTTTTTTACTGATCACCATTTC
*
30823 TTACTCTTTTTTACTAATCACCATTTC
1 TTACTCTTTTTTACTGATCACCATTTC
30850 TTACTCTTTTTTACTGATCACCATTT
1 TTACTCTTTTTTACTGATCACCATTT
30876 TTTGCTCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.03, T:0.54
Consensus pattern (27 bp):
TTACTCTTTTTTACTGATCACCATTTC
Found at i:31058 original size:29 final size:29
Alignment explanation
Indices: 31013--31076 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
31003 CTGACTATCA
* *
31013 TTTTAC-TCTTTACTGATTATTATTTTTT
1 TTTTACTTCTTTACTGATTACTATTTTAT
* *
31041 TTTTACTTTTTTATTGATTACTATTTTAT
1 TTTTACTTCTTTACTGATTACTATTTTAT
31070 TTTTACT
1 TTTTACT
31077 GATTATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.19, C:0.09, G:0.03, T:0.69
Consensus pattern (29 bp):
TTTTACTTCTTTACTGATTACTATTTTAT
Found at i:31093 original size:21 final size:21
Alignment explanation
Indices: 31043--31473 Score: 96
Period size: 20 Copynumber: 20.1 Consensus size: 21
31033 TATTTTTTTT
*
31043 TTACTTTTTTATTGATTACTA
1 TTACTTTTTTACTGATTACTA
*
31064 TT-TTATTTTTACTGATTA-TCA
1 TTACT-TTTTTACTGATTACT-A
*
31085 TTACTTTTTGAACTTGATTACTGA
1 TTACTTTTT-TAC-TGATTACT-A
*
31109 TTACCCTTTTTACTTTTACTGTTTACTA
1 TTA--C---TT--TTTTACTGATTACTA
* *
31137 TTA-ATTCTTACTGATTACTA
1 TTACTTTTTTACTGATTACTA
* *
31157 TTAC-TCTTTACTGATTATTA
1 TTACTTTTTTACTGATTACTA
* * *
31177 CTTTACTCTTTT-CTAATTACCATT
1 --TTACTTTTTTACTGATTA-C-TA
** * *
31201 TTAC-CCTTTACAGA-TACCTTT
1 TTACTTTTTTACTGATTA-C-TA
*
31222 TTAC-TTTTTACTGATTACCTTT
1 TTACTTTTTTACTGATTA-C-TA
*
31244 TTACTTTTTTACTGTTTACTA
1 TTACTTTTTTACTGATTACTA
* * *
31265 TTAC-CTCTTACTGATTTCTA
1 TTACTTTTTTACTGATTACTA
* *
31285 TTAC-TCTTTACTGATTATTA
1 TTACTTTTTTACTGATTACTA
* * *
31305 TTTTAC-TCTTTACTAATTACCA
1 --TTACTTTTTTACTGATTACTA
* *
31327 TT--TTATCCTTT-CAGA-TACCTTT
1 TTACTT-T--TTTACTGATTA-C-TA
*
31349 TTA-TTTTTTACTGATTGC-A
1 TTACTTTTTTACTGATTACTA
*
31368 TTAC-TTCTTACTGATTACTA
1 TTACTTTTTTACTGATTACTA
*
31388 TTAC-TCTTTACTGATTACCATA
1 TTACTTTTTTACTGATTA-C-TA
* * * *
31410 TT-GTTCTTTACTAATTACCATT
1 TTACTTTTTTACTGATTA-C-TA
* * *
31432 TTAC-CTATTACTGATTACCA
1 TTACTTTTTTACTGATTACTA
31452 TTA-TTTTTTACTGATTACTA
1 TTACTTTTTTACTGATTACTA
31472 TT
1 TT
31474 TTACTATTTG
Statistics
Matches: 306, Mismatches: 64, Indels: 81
0.68 0.14 0.18
Matches are distributed among these distances:
19 16 0.05
20 99 0.32
21 56 0.18
22 87 0.28
23 23 0.08
24 6 0.02
26 1 0.00
28 4 0.01
29 9 0.03
30 2 0.01
31 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (21 bp):
TTACTTTTTTACTGATTACTA
Found at i:31274 original size:128 final size:125
Alignment explanation
Indices: 31102--31405 Score: 436
Period size: 128 Copynumber: 2.4 Consensus size: 125
31092 TTGAACTTGA
*
31102 TTACTGATTACCCTTTTTAC-TTTTACTGTTTACTATTAATTCTTACTGATTACTATTACTCTTT
1 TTACTGATTA-CCTTTTTACTTTTTACTGTTTACTATT-ACTCTTACTGATTACTATTACTCTTT
*
31166 ACTGATTATTACTTTACTCTTTTCTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
64 ACTGATTATTACTTTACTCTTTACTAATTACCATTTTACCCTTT-CAGATACCTTTTTACTTT
*
31229 TTACTGATTACCTTTTTACTTTTTTACTGTTTACTATTACCTCTTACTGATTTCTATTACTCTTT
1 TTACTGATTACCTTTTTAC-TTTTTACTGTTTACTATTA-CTCTTACTGATTACTATTACTCTTT
* * *
31294 ACTGATTATTATTTTACTCTTTACTAATTACCATTTTATCCTTTCAGATACCTTTTTATTTT
64 ACTGATTATTACTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTT
* * * *
31356 TTACTGATT-GC--ATTACTTCTTACTGATTACTATTACTCTTTACTGATTAC
1 TTACTGATTACCTTTTTACTTTTTACTGTTTACTATTACTC-TTACTGATTAC
31406 CATATTGTTC
Statistics
Matches: 162, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
122 3 0.02
123 27 0.17
124 4 0.02
126 10 0.06
127 37 0.23
128 81 0.50
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (125 bp):
TTACTGATTACCTTTTTACTTTTTACTGTTTACTATTACTCTTACTGATTACTATTACTCTTTAC
TGATTATTACTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTT
Found at i:31329 original size:22 final size:22
Alignment explanation
Indices: 31102--31478 Score: 208
Period size: 22 Copynumber: 17.9 Consensus size: 22
31092 TTGAACTTGA
*
31102 TTACTGATTACCCTTTTTACT-T
1 TTACTGATTA-CCATTTTACTCT
* * * *
31124 TTACTGTTTACTA-TTAATTC-
1 TTACTGATTACCATTTTACTCT
*
31144 TTACTGATTA-C-TATTACTCT
1 TTACTGATTACCATTTTACTCT
** *
31164 TTACTGATTATTACTTTACTCT
1 TTACTGATTACCATTTTACTCT
* * *
31186 TTTCTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
31208 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* *
31229 TTACTGATTACCTTTTTACTTTT
1 TTACTGATTACCATTTTAC-TCT
* *
31252 TTACTGTTTA-C-TATTAC-CT
1 TTACTGATTACCATTTTACTCT
* *
31271 CTTACTGATT-TC-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
**
31292 TTACTGATTATTATTTTACTCT
1 TTACTGATTACCATTTTACTCT
*
31314 TTACTAATTACCATTTTA-TCCT
1 TTACTGATTACCATTTTACT-CT
* * * *
31336 TT-CAGA-TACCTTTTTATTTT
1 TTACTGATTACCATTTTACTCT
*
31356 TTACTGATT-GCA--TTACT-T
1 TTACTGATTACCATTTTACTCT
*
31374 CTTACTGATTA-C-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
* **
31395 TTACTGATTACCATATTGTTCT
1 TTACTGATTACCATTTTACTCT
*
31417 TTACTAATTACCATTTTAC-CT
1 TTACTGATTACCATTTTACTCT
31438 ATTACTGATTACCATTATT--T-T
1 -TTACTGATTACCATT-TTACTCT
*
31459 TTACTGATTACTATTTTACT
1 TTACTGATTACCATTTTACT
31479 ATTTGAATTT
Statistics
Matches: 276, Mismatches: 51, Indels: 57
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.00
19 21 0.08
20 88 0.32
21 40 0.14
22 112 0.41
23 14 0.05
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:31389 original size:103 final size:106
Alignment explanation
Indices: 31144--31473 Score: 363
Period size: 103 Copynumber: 3.1 Consensus size: 106
31134 CTATTAATTC
* * * * *
31144 TTACTGATTACTATTA-CTCTTTACTGATTATTACTTTACTCTTTTCTAATTACCATTTTACCCT
1 TTACTGATTACTATTACCTC-TTACTGATTACTA--TTACTCTTTACTGATTACCATATTACTCT
* * * *
31208 TTAC-AGA-TACCTTTTTACTTTTTACTGATTACCTTTTTACTTTT
63 TTACTA-ATTACCATTTTACCTATTACAGATTACCTTTTTA-TTTT
* * ** *
31252 TTACTGTTTACTATTACCTCTTACTGATTTCTATTACTCTTTACTGATTATTATTTTACTCTTTA
1 TTACTGATTACTATTACCTCTTACTGATTACTATTACTCTTTACTGATTACCATATTACTCTTTA
31317 CTAATTACCATTTTATCCT-TT-CAGA-TACCTTTTTATTTT
66 CTAATTACCATTTTA-CCTATTACAGATTACCTTTTTATTTT
* * **
31356 TTACTGATTGC-ATTACTTCTTACTGATTACTATTACTCTTTACTGATTACCATATTGTTCTTTA
1 TTACTGATTACTATTACCTCTTACTGATTACTATTACTCTTTACTGATTACCATATTACTCTTTA
* *
31420 CTAATTACCATTTTACCTATTACTGATTACC--ATTATTTT
66 CTAATTACCATTTTACCTATTACAGATTACCTTTTTATTTT
31459 TTACTGATTACTATT
1 TTACTGATTACTATT
31474 TTACTATTTG
Statistics
Matches: 191, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
102 3 0.02
103 80 0.42
104 19 0.10
105 14 0.07
106 32 0.17
107 12 0.06
108 28 0.15
109 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (106 bp):
TTACTGATTACTATTACCTCTTACTGATTACTATTACTCTTTACTGATTACCATATTACTCTTTA
CTAATTACCATTTTACCTATTACAGATTACCTTTTTATTTT
Found at i:31565 original size:34 final size:33
Alignment explanation
Indices: 31525--31638 Score: 129
Period size: 34 Copynumber: 3.3 Consensus size: 33
31515 TACTAATTGC
*
31525 TTTTTTCTTATTGAACTTAATCACTGATTACTCT
1 TTTTTTCTTTTTGAACTTAATCACTGATTAC-CT
* *
31559 TTTTTTCTTTTTGAACTTAATTACTGATTGCCT
1 TTTTTTCTTTTTGAACTTAATCACTGATTACCT
* * *
31592 TTTTTACTTTTTGGAACTTAATTACTCTGATTACCC
1 TTTTTTCTTTTT-GAACTTAA-T-CACTGATTACCT
*
31628 TTTTTACTTTT
1 TTTTTTCTTTT
31639 CTGACTGATC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
33 13 0.19
34 36 0.52
35 1 0.01
36 19 0.28
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (33 bp):
TTTTTTCTTTTTGAACTTAATCACTGATTACCT
Found at i:34999 original size:21 final size:21
Alignment explanation
Indices: 34975--35021 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
34965 GTTTTTTGGT
34975 GTTTATGTGCATGCTATATGA
1 GTTTATGTGCATGCTATATGA
34996 GTTTATGTGCATGCTATATGA
1 GTTTATGTGCATGCTATATGA
35017 -TTTAT
1 GTTTAT
35022 TTTTGCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (21 bp):
GTTTATGTGCATGCTATATGA
Found at i:37717 original size:4 final size:4
Alignment explanation
Indices: 37710--37748 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
37700 TATATATATA
*
37710 TATG TATG TATG TATG TATG TATG TATG TATG TAGG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
37749 CTTGTTCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:44251 original size:31 final size:31
Alignment explanation
Indices: 44216--44280 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
44206 CCCGACCGAG
44216 TTAATC-AACTTAATCGAACCC-TTTAATCAAA
1 TTAATCGAA-TTAATCG-ACCCATTTAATCAAA
*
44247 TTAATCGAATTAATCGACCCGATTTACTCAAA
1 TTAATCGAATTAATCGACCC-ATTTAATCAAA
44279 TT
1 TT
44281 TGAACAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.13
31 13 0.43
32 13 0.43
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (31 bp):
TTAATCGAATTAATCGACCCATTTAATCAAA
Found at i:45506 original size:46 final size:46
Alignment explanation
Indices: 45453--45545 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
45443 TAGTTGTTGC
45453 GATTAAACTAGTCTAAAATAATAAATAAGAACAAGCAGATTTACGT
1 GATTAAACTAGTCTAAAATAATAAATAAGAACAAGCAGATTTACGT
45499 GATTAAACTAGTCTAAAATAATAAATAAGAACAAGCAGATTTACGT
1 GATTAAACTAGTCTAAAATAATAAATAAGAACAAGCAGATTTACGT
45545 G
1 G
45546 GTTCGATCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (46 bp):
GATTAAACTAGTCTAAAATAATAAATAAGAACAAGCAGATTTACGT
Found at i:54017 original size:6 final size:6
Alignment explanation
Indices: 54006--54034 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53996 GGGGGTATAC
54006 TCCCCG TCCCCG TCCCCG TCCCCG TCCCC
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCC
54035 CGGCGAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.14, T:0.17
Consensus pattern (6 bp):
TCCCCG
Found at i:54446 original size:8 final size:8
Alignment explanation
Indices: 54381--54446 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 8
54371 ATACTTATGT
54381 GTGA-TTA
1 GTGATTTA
*
54388 GTGATATA
1 GTGATTTA
54396 GTGATTGTA
1 GTGATT-TA
54405 GTGATTTA
1 GTGATTTA
54413 GTGACTTATA
1 GTGA-TT-TA
54423 GTCTGA-TTA
1 G--TGATTTA
54432 GTGATTTA
1 GTGATTTA
54440 GTGATTT
1 GTGATTT
54447 TATTTAACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
7 7 0.14
8 23 0.46
9 13 0.26
10 4 0.08
12 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (8 bp):
GTGATTTA
Found at i:55454 original size:2 final size:2
Alignment explanation
Indices: 55447--55505 Score: 50
Period size: 2 Copynumber: 29.5 Consensus size: 2
55437 ACCAATTATC
* * * *
55447 AT AT AT AT AT A- AT AT AT AT TT AT AT TT TT AT AT AT CT GA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
55488 AT AT CAT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT A
55506 AATAATAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:60814 original size:14 final size:16
Alignment explanation
Indices: 60795--60830 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
60785 GTCTAAACCA
60795 TTTTTTC-TTTTTC-T
1 TTTTTTCTTTTTTCAT
60809 TTTTTTCTTTTTTCAT
1 TTTTTTCTTTTTTCAT
60825 TTTTTT
1 TTTTTT
60831 GGAATATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCTTTTTTCAT
Found at i:63267 original size:106 final size:104
Alignment explanation
Indices: 63066--63291 Score: 344
Period size: 106 Copynumber: 2.2 Consensus size: 104
63056 AACTTAAGTA
* * * * *
63066 TTCATCAATTAATACTGGCTCCGGGTTCGCTGTCAACACTGCCACTTTTTCAAAGTGAAGACTTG
1 TTCATCGATTAATACTGCCTCCAGATTCGCTGTCAACACTGCCACTTTTTAAAAGTGAAGACTTG
63131 GAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
66 GAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
*
63170 TTCATCGATTAATACTGCCTCCAGATTCGCTGTCAACACTGCCACTTTTTTTAAAAGTGGAGACT
1 TTCATCGATTAATACTGCCTCCAGATTCGCTGTCAACACTGCCAC--TTTTTAAAAGTGAAGACT
** * *
63235 TGGAGTTTTAGTCGATTAATACTGGAATTAAAACTTGAGTT
64 TGGAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
63276 TTCATCGATTAATACT
1 TTCATCGATTAATACT
63292 TTTCTGACAG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 41 0.37
106 69 0.63
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (104 bp):
TTCATCGATTAATACTGCCTCCAGATTCGCTGTCAACACTGCCACTTTTTAAAAGTGAAGACTTG
GAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
Found at i:71376 original size:34 final size:31
Alignment explanation
Indices: 71336--71428 Score: 96
Period size: 34 Copynumber: 2.8 Consensus size: 31
71326 TTGTTTCTTT
71336 AAAACGCCAGCAAATAGGGGCGTTTGATGCAGAG
1 AAAACGCC-GCAAATAGGGGCGTTTG--GCAGAG
* * * *
71370 AAAACGCCGGGATATAGGGGCGTTTGGGATAG
1 AAAACGCC-GCAAATAGGGGCGTTTGGCAGAG
71402 AAAACGCCGCAATATAGGGGCGCTTTG
1 AAAACGCCGCAA-ATAGGGGCG-TTTG
71429 CCAACTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.04
32 21 0.42
33 4 0.08
34 23 0.46
ACGTcount: A:0.31, C:0.17, G:0.34, T:0.17
Consensus pattern (31 bp):
AAAACGCCGCAAATAGGGGCGTTTGGCAGAG
Found at i:71409 original size:32 final size:33
Alignment explanation
Indices: 71336--71428 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 33
71326 TTGTTTCTTT
71336 AAAACGCCAGCAA-ATAGGGGCGTTTGATGCAGAG
1 AAAACGCC-GCAATATAGGGGCGTTTGA-GCAGAG
** * *
71370 AAAACGCCGGGATATAGGGGCGTTTG-GGATAG
1 AAAACGCCGCAATATAGGGGCGTTTGAGCAGAG
71402 AAAACGCCGCAATATAGGGGCGCTTTG
1 AAAACGCCGCAATATAGGGGCG-TTTG
71429 CCAACTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 24 0.47
33 6 0.12
34 21 0.41
ACGTcount: A:0.31, C:0.17, G:0.34, T:0.17
Consensus pattern (33 bp):
AAAACGCCGCAATATAGGGGCGTTTGAGCAGAG
Found at i:76196 original size:104 final size:106
Alignment explanation
Indices: 76079--76305 Score: 314
Period size: 107 Copynumber: 2.2 Consensus size: 106
76069 AACTTAAGTA
* * * * *
76079 TTCATCAATTAATACTGGCTCCGGGTTCG-ATGTCAACACTGCCAC-TTTTTCAAAGTGAAGACT
1 TTCATCGATTAATACTGCCTCCAGATTCGCATGTCAACACTGCCACTTTTTTAAAAGTGAAGACT
76142 AAGAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
66 AAGAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
* *
76183 TTCATCGATTAATACTGCCTCCAGATTCGCTTGTCAACACTGCCACTTTTTTTAAAAGTGGAGAC
1 TTCATCGATTAATACTGCCTCCAGATTCGCATGTCAACACTGCCAC-TTTTTTAAAAGTGAAGAC
** ** * *
76248 TTGGAGTTTTAGTCGATTAATACTGGAATTAAAACTTGAGTT
65 TAAGAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
76290 TTCATCGATTAATACT
1 TTCATCGATTAATACT
76306 TTTCTGACAG
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
104 25 0.23
105 15 0.14
107 67 0.63
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (106 bp):
TTCATCGATTAATACTGCCTCCAGATTCGCATGTCAACACTGCCACTTTTTTAAAAGTGAAGACT
AAGAGTTTTAGTCGATTAATACTAAAACTAAAACTGGAGTT
Found at i:77757 original size:48 final size:47
Alignment explanation
Indices: 77647--77984 Score: 245
Period size: 48 Copynumber: 7.2 Consensus size: 47
77637 TACATGTCCT
* * * * *
77647 AAAACTCCCTTCCAGGACGGAAGACACTAATTTTTACTTGCTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGC-TTTATTTTTACTTGC-TTTTCCC
* **
77696 AAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTACTAACTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGC-TTTATTTTTACTTGCTTTTCCC
* * *
77744 AAAACGCCCTTCCCAGATGGAAGGC---A--CTTA--T--TTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCTTTATTTTTACTTGCTTTTCCC
*
77782 AAAACGCCCTTCCC-GATCGGAAGGCTCCTATTTTTACTTGCTTTTTCCC
1 AAAACGCCCTTCCCGGA-CGGAAGGCT-TTATTTTTACTTGC-TTTTCCC
**
77831 AAATA--CCCTTCCCGGACGGAAGGCACT-TTTTTACTTGCTTTTTCCC
1 AAA-ACGCCCTTCCCGGACGGAAGGCTTTATTTTTACTTGC-TTTTCCC
* * * * * *
77877 AAAACACCCTTCCCTGACGGAATGCACTTCTTTTTACTTGCTCTTT-CT
1 AAAACGCCCTTCCCGGACGGAAGGC-TTTATTTTTACTTGCT-TTTCCC
* * * *
77925 AAAACGCCCTTCCCGAACGGAAGGCGTTGATTTTTACTCGCTTTTTCTC
1 AAAACGCCCTTCCCGGACGGAAGGC-TTTATTTTTACTTGC-TTTTCCC
*
77974 AAAATGCCCTT
1 AAAACGCCCTT
77985 TTAGACAAAG
Statistics
Matches: 236, Mismatches: 32, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
37 2 0.01
38 28 0.12
42 4 0.02
44 4 0.02
45 1 0.00
46 23 0.10
47 19 0.08
48 85 0.36
49 69 0.29
50 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.33
Consensus pattern (47 bp):
AAAACGCCCTTCCCGGACGGAAGGCTTTATTTTTACTTGCTTTTCCC
Found at i:77788 original size:38 final size:38
Alignment explanation
Indices: 77737--77816 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
77727 TTTTACTAAC
*
77737 TTTTCCCAAAACGCCCTTCCCAGAT-GGAAGGCACTTAT
1 TTTTCCCAAAACGCCCTTCCC-GATCGGAAGGCACCTAT
*
77775 TTTTCCCAAAACGCCCTTCCCGATCGGAAGGCTCCTAT
1 TTTTCCCAAAACGCCCTTCCCGATCGGAAGGCACCTAT
77813 TTTT
1 TTTT
77817 ACTTGCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (38 bp):
TTTTCCCAAAACGCCCTTCCCGATCGGAAGGCACCTAT
Found at i:77840 original size:86 final size:84
Alignment explanation
Indices: 77688--77862 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 84
77678 TTTTACTTGC
*
77688 TTTTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTACTAACTTTTCCCAAAACGCCC
1 TTTTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTCTATTTTTACTAACTTTTCCCAAAAC-CCC
*
77753 TTCCCAGATGGAAGGCACTT
65 TTCCCAGACGGAAGGCACTT
**
77773 ATTTTTCCCAAAACGCCCTTCCC-GATCGGAAGGC-TCCTATTTTTACTTGCTTTTTCCCAAATA
1 -TTTTTCCCAAAACGCCCTTCCCGGAT-GGAAGGCGT-CTATTTTTACTAAC-TTTTCCCAAA-A
*
77836 -CCCTTCCCGGACGGAAGGCACTT
61 CCCCTTCCCAGACGGAAGGCACTT
77859 TTTT
1 TTTT
77863 ACTTGCTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
85 8 0.10
86 61 0.76
87 10 0.12
88 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (84 bp):
TTTTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTCTATTTTTACTAACTTTTCCCAAAACCCCT
TCCCAGACGGAAGGCACTT
Found at i:77890 original size:95 final size:96
Alignment explanation
Indices: 77774--77977 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 96
77764 AAGGCACTTA
* * * * *
77774 TTTTTCCCAAAACGCCCTTCCC-GATCGGAAGGCTCCTATTTTTACTTGCTTTTTCCCAAATACC
1 TTTTTCCCAAAACACCCTTCCCTGA-CGGAAGGCACCTATTTTTACTTGCTCTTTCCAAAACACC
* *
77838 CTTCCCGGACGGAAGGCACT-TTTTTACTTGC
65 CTTCCCGAACGGAAGGCACTATTTTTACTCGC
* * * * *
77869 TTTTTCCCAAAACACCCTTCCCTGACGGAATGCACTTCTTTTTACTTGCTCTTTCTAAAACGCCC
1 TTTTTCCCAAAACACCCTTCCCTGACGGAAGGCACCTATTTTTACTTGCTCTTTCCAAAACACCC
**
77934 TTCCCGAACGGAAGGCGTTGATTTTTACTCGC
66 TTCCCGAACGGAAGGCACT-ATTTTTACTCGC
*
77966 TTTTTCTCAAAA
1 TTTTTCCCAAAA
77978 TGCCCTTTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
95 68 0.75
96 2 0.02
97 21 0.23
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (96 bp):
TTTTTCCCAAAACACCCTTCCCTGACGGAAGGCACCTATTTTTACTTGCTCTTTCCAAAACACCC
TTCCCGAACGGAAGGCACTATTTTTACTCGC
Found at i:78055 original size:71 final size:64
Alignment explanation
Indices: 77973--78262 Score: 238
Period size: 63 Copynumber: 4.5 Consensus size: 64
77963 CGCTTTTTCT
* * * * *
77973 CAAAATGCCCTTTTAGACAAAGGGCTAATTTTGTCACATTCCCGCATTTAAGTTAAGTACTTTCG
1 CAAAATACCCTTTCAGACAAAGGG-TAGTTTTGTCACATTCCTGCATTTAAGTT-AGTA---GC-
78038 ATTCC
60 ATTCC
* * * *
78043 CAAAAATACCCTTTCGGACAAAGGGTTGGTTTTGTCACCTTCTTGCATTTAAGTT--TAGCATTC
1 C-AAAATACCCTTTCAGACAAAGGG-TAGTTTTGTCACATTCCTGCATTTAAGTTAGTAGCATTC
78106 C
64 C
* * *
78107 CAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTT--TAGTATTCC
1 CAAAATACCCTTTCAGACAAAGGGT-AGTTTTGTCACATTCCTGCATTTAAGTTAGTAGCATTCC
* * * *
78170 CAAAATACCCTTTCAGACTAAGGGTCAGTTTCT-TCACATTCCTGCACTT-AGATCA-TA--TTT
1 CAAAATACCCTTTCAGACAAAGGGT-AGTTT-TGTCACATTCCTGCATTTAAG-TTAGTAGCATT
78230 CC
63 CC
* *
78232 CAAAATACCCTTTCGGGCAAAGGGTCAGTTT
1 CAAAATACCCTTTCAGACAAAGGGT-AGTTT
78263 AGCCATGTTT
Statistics
Matches: 189, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
62 35 0.19
63 98 0.52
64 8 0.04
65 1 0.01
68 2 0.01
70 1 0.01
71 44 0.23
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (64 bp):
CAAAATACCCTTTCAGACAAAGGGTAGTTTTGTCACATTCCTGCATTTAAGTTAGTAGCATTCC
Found at i:78127 original size:63 final size:63
Alignment explanation
Indices: 78038--78262 Score: 265
Period size: 63 Copynumber: 3.6 Consensus size: 63
78028 AGTACTTTCG
* ** * * * *
78038 ATTCCCAAAAATACCCTTTCGGACAAAGGGTTGGTTTTGTCACCTTCTTGCATTTAAGTTTAGC
1 ATTCCC-AAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTTAGC
*
78102 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTTAGT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTTAGC
* * * * * * *
78165 ATTCCCAAAATACCCTTTCAGACTAAGGGTCAGTTTCTTCACATTCCTGCACTT-AGATCA-T
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTTAGC
* *
78226 ATTTCCCAAAATACCCTTTCGGGCAAAGGGTCAGTTT
1 A-TTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTT
78263 AGCCATGTTT
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
61 2 0.01
62 36 0.25
63 99 0.69
64 6 0.04
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (63 bp):
ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTTAGC
Found at i:85210 original size:21 final size:21
Alignment explanation
Indices: 85180--85232 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
85170 ACTAGCGCTG
85180 GGCGCCCATGTGGTATG-CTT
1 GGCGCCCATGTGGTATGCCTT
*
85200 GGCGCCCCATGTGGTTTGCCTT
1 GGCG-CCCATGTGGTATGCCTT
85222 -GCGACCCATGT
1 GGCG-CCCATGT
85233 ACACCAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 22 0.76
22 3 0.10
ACGTcount: A:0.09, C:0.30, G:0.32, T:0.28
Consensus pattern (21 bp):
GGCGCCCATGTGGTATGCCTT
Found at i:87199 original size:21 final size:22
Alignment explanation
Indices: 87163--87207 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 22
87153 ATATTGTCAT
87163 TCAATTCATTTTTTTTAACTAAA
1 TCAATTCA-TTTTTTTAACTAAA
87186 TCAATTCA-TTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
87207 T
1 T
87208 TATTGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (22 bp):
TCAATTCATTTTTTTAACTAAA
Found at i:89906 original size:16 final size:14
Alignment explanation
Indices: 89858--89909 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
89848 ATATAAAACA
*
89858 AAAATTAATTAAGG
1 AAAATTAATTAAGT
*
89872 AAAATTCAATTCAATT
1 AAAATT-AATT-AAGT
89888 AAAATTAATTAAAGCT
1 AAAATTAATT-AAG-T
89904 AAAATT
1 AAAATT
89910 TAAAAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 6 0.19
15 10 0.32
16 15 0.48
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAATTAATTAAGT
Found at i:98206 original size:26 final size:26
Alignment explanation
Indices: 98176--98474 Score: 161
Period size: 26 Copynumber: 11.2 Consensus size: 26
98166 TATTTCTTGA
98176 TTACTAATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* * * * *
98202 GTACTGATTACCATATTTAATCTTTTT
1 TTACTAATTACCATTTTTTA-CTCTTT
* * *
98229 TTACTGATTACCCCTTTTCTTACTGTTT
1 TTACTAATTA-CCATTTT-TTACTCTTT
**
98257 TTACTGAA-TACCGCTTTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
98283 TTACTTAATTACCATTTTTTTACTCTCCTTTT
1 TTAC-TAATTACCA-TTTTTTA--CT-C-TTT
*
98315 TTACTTAA-TACCA-TATTTACTC-TT
1 TTAC-TAATTACCATTTTTTACTCTTT
*
98339 TT--T--TTACCA-TTTTTACCCCTTT
1 TTACTAATTACCATTTTTTA-CTCTTT
* *
98361 TTATTGAA-TACCACTTTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
* * *
98387 TTACTGATCACCATTTCTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* *
98413 ATTATTAATTACTC-TCTTTTACTCTTTTT
1 -TTACTAATTAC-CATTTTTTACTC--TTT
* *
98442 TTACTGATCACCATTTTTTACTCATTT
1 TTACTAATTACCATTTTTTACTC-TTT
98469 CTTACT
1 -TTACT
98475 CTTTTTACTG
Statistics
Matches: 211, Mismatches: 35, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
20 10 0.05
21 3 0.01
22 4 0.02
24 5 0.02
25 1 0.00
26 60 0.28
27 52 0.25
28 46 0.22
29 11 0.05
30 2 0.01
31 6 0.03
32 11 0.05
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.55
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:98361 original size:20 final size:20
Alignment explanation
Indices: 98323--98362 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
98313 TTTTACTTAA
* *
98323 TACCATATTTACTCTTTTTT
1 TACCATATTTACCCCTTTTT
*
98343 TACCATTTTTACCCCTTTTT
1 TACCATATTTACCCCTTTTT
98363 ATTGAATACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (20 bp):
TACCATATTTACCCCTTTTT
Found at i:98486 original size:37 final size:37
Alignment explanation
Indices: 98421--98511 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
98411 TTATTATTAA
98421 TTACTCTCTT-TTACTCTTTTTTTACTGATCAC-CATTTT-
1 TTACTCT-TTCTTACTC--TTTTTACTGATCACTC-TTTTC
*
98459 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTC
1 TTACTC-TTTCTTACTCTTTTTACTGATCACTCTTTTC
*
98497 TTACTCTTTTTTACT
1 TTACTCTTTCTTACT
98512 GATTACCACA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
37 25 0.53
38 15 0.32
39 7 0.15
ACGTcount: A:0.15, C:0.23, G:0.02, T:0.59
Consensus pattern (37 bp):
TTACTCTTTCTTACTCTTTTTACTGATCACTCTTTTC
Found at i:98497 original size:27 final size:28
Alignment explanation
Indices: 98459--98517 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
98449 TCACCATTTT
98459 TTACTCATTTCTTACTC-TTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTTACTGA
*
98486 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTTACTGA
98514 TTAC
1 TTAC
98518 CACATTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (28 bp):
TTACTCATTTCTTACTCTTTTTTACTGA
Found at i:98526 original size:65 final size:66
Alignment explanation
Indices: 98398--98529 Score: 187
Period size: 65 Copynumber: 2.0 Consensus size: 66
98388 TACTGATCAC
* **
98398 CATTTCTTACTCTTTATTATTAATTACTCTCTTTTACTCTTTTTTTACTGATCACCATTTTTTAC
1 CATTTCTTACTCTTTATTACTAATTACTCTCTTTTACTCTTTTTTTACTGATCACCACATTTTAC
98463 T
66 T
* * *
98464 CATTTCTTACTCTTT-TTACTGATTACTCTTTTCTTACTC-TTTTTTACTGATTACCACATTTTA
1 CATTTCTTACTCTTTATTACTAATTACTCTCTT-TTACTCTTTTTTTACTGATCACCACATTTTA
98527 CT
65 CT
98529 C
1 C
98530 TTCTTCTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 38 0.64
66 21 0.36
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (66 bp):
CATTTCTTACTCTTTATTACTAATTACTCTCTTTTACTCTTTTTTTACTGATCACCACATTTTAC
T
Found at i:98527 original size:27 final size:28
Alignment explanation
Indices: 98459--98531 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
98449 TCACCATTTT
98459 TTACT-CATTTCTTACTC-TTTTTACTGA
1 TTACTCCA-TTCTTACTCTTTTTTACTGA
**
98486 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCCATTCTTACTCTTTTTTACTGA
98514 TTAC-CACATT-TTACTCTT
1 TTACTC-CATTCTTACTCTT
98532 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (28 bp):
TTACTCCATTCTTACTCTTTTTTACTGA
Found at i:98548 original size:39 final size:36
Alignment explanation
Indices: 98486--98569 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 36
98476 TTTTTACTGA
* * *
98486 TTACTCTTTTCTTACTCTTTTTTACTGATTACCACATT
1 TTACTCTTTTCTTACTCTCTTTTACTAACTA-C-CATT
**
98524 TTACTCTTCTTCTTTTTCTCTTTTACTAACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTAACTACCATT
98561 TTACTCTTT
1 TTACTCTTT
98570 GAATTTCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 1 0.03
37 12 0.30
38 9 0.22
39 18 0.45
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.57
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTAACTACCATT
Found at i:98630 original size:23 final size:23
Alignment explanation
Indices: 98590--98991 Score: 155
Period size: 22 Copynumber: 18.3 Consensus size: 23
98580 ACTGACTATC
*
98590 ATTTTAC-TCTTTACTGATTATT
1 ATTTTACTTCTTTACTGATTACT
* * *
98612 TTTTTACTTTTTTATTGATTACT
1 ATTTTACTTCTTTACTGATTACT
98635 ATTTTAC-TC-TTACTGATTACCATT
1 ATTTTACTTCTTTACTGATTA-C--T
* *
98659 ATTTTTTAATT-TGATTACTGATTACC
1 A--TTTTACTTCT--TTACTGATTACT
* * *
98685 CTTTTAC-T-TTAACTGATTACC
1 ATTTTACTTCTTTACTGATTACT
* *
98706 ATTTTAC-TCTTTACTAATTACC
1 ATTTTACTTCTTTACTGATTACT
* * * *
98728 ATCTTAC-CCTTTCCAGA-TACGT
1 ATTTTACTTCTTTACTGATTAC-T
*
98750 -TTTTACTT-TTTATTGATTACCT
1 ATTTTACTTCTTTACTGATTA-CT
* *
98772 -TTTTACTTTTTTACTGTTTACT
1 ATTTTACTTCTTTACTGATTACT
98794 A--TTACTTC-TTACTGATTACT
1 ATTTTACTTCTTTACTGATTACT
98814 A--TTAC-TCTTTACTGATTA-T
1 ATTTTACTTCTTTACTGATTACT
** * *
98833 CGCTTTAC-TCTTTACTAATTACC
1 -ATTTTACTTCTTTACTGATTACT
* *
98856 ATTGTAC--CTATTACTGACTACCT
1 ATTTTACTTCT-TTACTGATTA-CT
*
98879 -TTTTACTT-TTTACTGATTACC
1 ATTTTACTTCTTTACTGATTACT
* *
98900 A--TTACTTTTTTACTGTTTACT
1 ATTTTACTTCTTTACTGATTACT
*
98921 A--TTACTTC-TTATTGATTACT
1 ATTTTACTTCTTTACTGATTACT
* * ** *
98941 CTTTTAATT-TTTGTTGATTACC
1 ATTTTACTTCTTTACTGATTACT
* * *
98963 ATTTTACTT-TTTGCTAATTACC
1 ATTTTACTTCTTTACTGATTACT
98985 ATTTTAC
1 ATTTTAC
98992 ACTTAGTGAT
Statistics
Matches: 294, Mismatches: 55, Indels: 62
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.01
20 42 0.14
21 67 0.23
22 126 0.43
23 32 0.11
24 7 0.02
26 5 0.02
27 1 0.00
28 1 0.00
29 10 0.03
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.54
Consensus pattern (23 bp):
ATTTTACTTCTTTACTGATTACT
Found at i:98681 original size:50 final size:48
Alignment explanation
Indices: 98571--98710 Score: 130
Period size: 50 Copynumber: 2.9 Consensus size: 48
98561 TTACTCTTTG
*
98571 AATTTCATTACTGACTA-TCATTTTACTCTTTACTGATT---A-TTTTTTT
1 AATTT-ATTACTGATTACT-ATTTTACTC-TTACTGATTACCATTTTTTTT
* * *
98617 ACTTTTTTATTGATTACTATTTTACTCTTACTGATTACCATTATTTTTT
1 AATTTATTACTGATTACTATTTTACTCTTACTGATTACCATT-TTTTTT
**
98666 AATTTGATTACTGATTACCCTTTTACT-TTAACTGATTACCATTTT
1 AATTT-ATTACTGATTACTATTTTACTCTT-ACTGATTACCATTTT
98711 ACTCTTTACT
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
44 9 0.12
45 17 0.22
46 5 0.06
47 1 0.01
48 1 0.01
49 14 0.18
50 30 0.39
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (48 bp):
AATTTATTACTGATTACTATTTTACTCTTACTGATTACCATTTTTTTT
Found at i:98695 original size:29 final size:28
Alignment explanation
Indices: 98644--98704 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
98634 TATTTTACTC
* *
98644 TTACTGATTACCATTATTTTTTAATTTGA
1 TTACTGATTACCATTATTCTTTAA-CTGA
*
98673 TTACTGATTACCCTT-TTACTTTAACTGA
1 TTACTGATTACCATTATT-CTTTAACTGA
98701 TTAC
1 TTAC
98705 CATTTTACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (28 bp):
TTACTGATTACCATTATTCTTTAACTGA
Found at i:98807 original size:20 final size:20
Alignment explanation
Indices: 98782--98940 Score: 99
Period size: 20 Copynumber: 7.6 Consensus size: 20
98772 TTTTACTTTT
*
98782 TTACTGTTTACTATTACTTC
1 TTACTGATTACTATTACTTC
98802 TTACTGATTACTATTAC-TC
1 TTACTGATTACTATTACTTC
98821 TTTACTGATTATCGCT-TTAC-TC
1 -TTACTGATTA---CTATTACTTC
* * * *
98843 TTTACTAATTACCATTGTACCTA
1 -TTACTGATTACTA-T-TACTTC
* * *
98866 TTACTGACTACCTTTTTACTTT
1 TTACTGATTA-C-TATTACTTC
* *
98888 TTACTGATTACCATTACTTTT
1 TTACTGATTACTATTAC-TTC
*
98909 TTACTGTTTACTATTACTTC
1 TTACTGATTACTATTACTTC
*
98929 TTATTGATTACT
1 TTACTGATTACT
98941 CTTTTAATTT
Statistics
Matches: 110, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.03
20 42 0.38
21 20 0.18
22 40 0.36
23 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.52
Consensus pattern (20 bp):
TTACTGATTACTATTACTTC
Found at i:98990 original size:107 final size:107
Alignment explanation
Indices: 98750--98991 Score: 265
Period size: 107 Copynumber: 2.3 Consensus size: 107
98740 CCAGATACGT
* * *
98750 TTTTACTTTTTATTGATTACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTACTA
1 TTTTACTTTTTACTGATTACCTTTTTACTTTTTTACTGATTACCATTACTTCTTACTGATTACTA
*
98815 TTACTCTTTACTGATTATCGCTTTACTCTTTACTAATTACCA
66 TTACTCTTTACTGATTATCGCTTTAATCTTTACTAATTACCA
* * * * * *
98857 TTGTACCTATTACTGACTACCTTTTTAC-TTTTTACTGATTACCATTACTTTTTTACTGTTTACT
1 TTTTACTTTTTACTGATTACCTTTTTACTTTTTTACTGATTACCATTAC-TTCTTACTGATTACT
* * * ** *
98921 ATTACT-TCTTATTGATTACTC-TTTTAATTTTTGTTGATTACCA
65 ATTACTCT-TTACTGATTA-TCGCTTTAATCTTTACTAATTACCA
* * *
98964 TTTTACTTTTTGCTAATTACCATTTTAC
1 TTTTACTTTTTACTGATTACCTTTTTAC
98992 ACTTAGTGAT
Statistics
Matches: 109, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
106 19 0.17
107 88 0.81
108 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (107 bp):
TTTTACTTTTTACTGATTACCTTTTTACTTTTTTACTGATTACCATTACTTCTTACTGATTACTA
TTACTCTTTACTGATTATCGCTTTAATCTTTACTAATTACCA
Found at i:98991 original size:22 final size:21
Alignment explanation
Indices: 98933--99016 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
98923 TACTTCTTAT
*
98933 TGATTACTC-TTTTAATTTTTG
1 TGATTAC-CATTTTACTTTTTG
98954 TTGATTACCATTTTACTTTTTG
1 -TGATTACCATTTTACTTTTTG
* ** *
98976 CTAATTACCATTTTACACTTAG
1 -TGATTACCATTTTACTTTTTG
98998 TGATTACC-TTTTACTTTTT
1 TGATTACCATTTTACTTTTT
99017 ACCATTTTAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
20 8 0.16
21 8 0.16
22 35 0.69
ACGTcount: A:0.21, C:0.15, G:0.07, T:0.56
Consensus pattern (21 bp):
TGATTACCATTTTACTTTTTG
Found at i:99027 original size:43 final size:43
Alignment explanation
Indices: 98955--99039 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
98945 TAATTTTTGT
* *
98955 TGATTACCATTTTACTTTTTGCTAATTACCATTTTACACTTAG
1 TGATTACCATTTTACTTTTTACCAATTACCATTTTACACTTAG
* * *
98998 TGATTACC-TTTTACTTTTTACCATTTTACCTTTTTACTCTTA
1 TGATTACCATTTTACTTTTTACCA-ATTACCATTTTACACTTA
99040 CTATTACTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 13 0.36
43 23 0.64
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (43 bp):
TGATTACCATTTTACTTTTTACCAATTACCATTTTACACTTAG
Found at i:99088 original size:15 final size:15
Alignment explanation
Indices: 99068--99102 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
99058 CATTTTTGTC
99068 TCTACTGATTACTCT
1 TCTACTGATTACTCT
99083 TCTACTGATTACTCT
1 TCTACTGATTACTCT
99098 T-TACT
1 TCTACT
99103 CTTTACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.20, C:0.26, G:0.06, T:0.49
Consensus pattern (15 bp):
TCTACTGATTACTCT
Found at i:99101 original size:7 final size:7
Alignment explanation
Indices: 99076--99210 Score: 75
Period size: 7 Copynumber: 19.3 Consensus size: 7
99066 TCTCTACTGA
99076 TTACTCT
1 TTACTCT
**
99083 TCTACTGA
1 T-TACTCT
99091 TTACTCT
1 TTACTCT
99098 TTACTCT
1 TTACTCT
99105 TTAC-CAT
1 TTACTC-T
*
99112 TT-TTCT
1 TTACTCT
**
99118 TTACTGA
1 TTACTCT
99125 TTACTCTT
1 TTACTC-T
99133 TTACTCT
1 TTACTCT
99140 TTAC-CAT
1 TTACTC-T
99147 TT-CTCT
1 TTACTCT
**
99153 TTACTGA
1 TTACTCT
*
99160 TTACTTT
1 TTACTCT
99167 TTACTCT
1 TTACTCT
*
99174 TTACGATTT
1 TTAC--TCT
99183 TTA--CT
1 TTACTCT
**
99188 TTACTGA
1 TTACTCT
99195 TTACTCT
1 TTACTCT
99202 TTACTCT
1 TTACTCT
99209 TT
1 TT
99211 CCTGATTGCC
Statistics
Matches: 95, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
5 4 0.04
6 9 0.09
7 66 0.69
8 11 0.12
9 5 0.05
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:99128 original size:20 final size:20
Alignment explanation
Indices: 99095--99163 Score: 51
Period size: 20 Copynumber: 3.7 Consensus size: 20
99085 TACTGATTAC
**
99095 TCTTTACTCTTTACCATTTT
1 TCTTTACTGATTACCATTTT
99115 TCTTTACTGATTACTC-TTTT
1 TCTTTACTGATTAC-CATTTT
* *
99135 AC--T-CT--TTACCATTTC
1 TCTTTACTGATTACCATTTT
99150 TCTTTACTGATTAC
1 TCTTTACTGATTAC
99164 TTTTTACTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
14 1 0.03
15 8 0.22
17 3 0.08
18 3 0.08
20 21 0.57
21 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.55
Consensus pattern (20 bp):
TCTTTACTGATTACCATTTT
Found at i:99143 original size:35 final size:34
Alignment explanation
Indices: 99080--99210 Score: 208
Period size: 35 Copynumber: 3.8 Consensus size: 34
99070 TACTGATTAC
99080 TCTTCTACTGATTACTCTTTACTCTTTACCATTTT
1 TCTT-TACTGATTACTCTTTACTCTTTACCATTTT
*
99115 TCTTTACTGATTACTCTTTTACTCTTTACCATTTC
1 TCTTTACTGATTACTC-TTTACTCTTTACCATTTT
* *
99150 TCTTTACTGATTACTTTTTACTCTTTACGATTTT
1 TCTTTACTGATTACTCTTTACTCTTTACCATTTT
99184 TACTTTACTGATTACTCTTTACTCTTT
1 T-CTTTACTGATTACTCTTTACTCTTT
99211 CCTGATTGCC
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
34 29 0.33
35 60 0.67
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.56
Consensus pattern (34 bp):
TCTTTACTGATTACTCTTTACTCTTTACCATTTT
Found at i:99374 original size:26 final size:26
Alignment explanation
Indices: 99271--99375 Score: 122
Period size: 26 Copynumber: 4.0 Consensus size: 26
99261 TTATTGCTCT
*
99271 TTTCTTACTCTTTTTACTGGA-TATTG
1 TTTCTTACTCTTTTTACT-GATTACTG
* * * *
99297 TTTCCTACTCTTTTCACTGATGACTCT
1 TTTCTTACTCTTTTTACTGATTACT-G
*
99324 TTTCTTACTCTTTTTACTGAATACTG
1 TTTCTTACTCTTTTTACTGATTACTG
*
99350 TTTCTTACTCTTTTTATTGATTACTG
1 TTTCTTACTCTTTTTACTGATTACTG
99376 ATTACCAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.03
26 42 0.65
27 21 0.32
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.55
Consensus pattern (26 bp):
TTTCTTACTCTTTTTACTGATTACTG
Found at i:101354 original size:27 final size:27
Alignment explanation
Indices: 101324--101377 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
101314 TTACTTTACT
101324 TTGCTTGTAATTGCCTTATTCTCTGCC
1 TTGCTTGTAATTGCCTTATTCTCTGCC
101351 TTGCTTGTAATTGCCTTATTCTCTGCC
1 TTGCTTGTAATTGCCTTATTCTCTGCC
101378 ATGGGGTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (27 bp):
TTGCTTGTAATTGCCTTATTCTCTGCC
Found at i:108295 original size:13 final size:13
Alignment explanation
Indices: 108277--108311 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
108267 CATCTAAATC
108277 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
108290 TAAAGCAATTTAA
1 TAAAGCAAATTAA
108303 TAAAGCAAA
1 TAAAGCAAA
108312 CAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:109236 original size:10 final size:10
Alignment explanation
Indices: 109221--109245 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
109211 GAGGACTCTA
109221 GAATTTTCTG
1 GAATTTTCTG
109231 GAATTTTCTG
1 GAATTTTCTG
109241 GAATT
1 GAATT
109246 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:122741 original size:20 final size:20
Alignment explanation
Indices: 122704--122742 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
122694 CGACTCGAGA
** *
122704 AAAATTCGAGTTCGGCTCGG
1 AAAATTCGAGCCCAGCTCGG
122724 AAAATTCGAGCCCAGCTCG
1 AAAATTCGAGCCCAGCTCG
122743 AGCTCGAGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (20 bp):
AAAATTCGAGCCCAGCTCGG
Found at i:123456 original size:20 final size:20
Alignment explanation
Indices: 123431--123499 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
123421 CGTGTAGGCT
*
123431 CGAGCTCGACAGACTCGAGC
1 CGAGCTCGACAGGCTCGAGC
123451 CGAGCTCGACAGGCTCGAGC
1 CGAGCTCGACAGGCTCGAGC
123471 CGAGCTCGACAGGCTCGAGC
1 CGAGCTCGACAGGCTCGAGC
123491 CGAGCTCGA
1 CGAGCTCGA
123500 GCCTCATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.22, C:0.35, G:0.33, T:0.10
Consensus pattern (20 bp):
CGAGCTCGACAGGCTCGAGC
Found at i:123477 original size:11 final size:11
Alignment explanation
Indices: 123431--123502 Score: 75
Period size: 11 Copynumber: 7.1 Consensus size: 11
123421 CGTGTAGGCT
123431 CGAGCTCGA-C
1 CGAGCTCGAGC
*
123441 AGA-CTCGAGC
1 CGAGCTCGAGC
123451 CGAGCTCGA-C
1 CGAGCTCGAGC
*
123461 AG-GCTCGAGC
1 CGAGCTCGAGC
123471 CGAGCTCGA-C
1 CGAGCTCGAGC
*
123481 AG-GCTCGAGC
1 CGAGCTCGAGC
123491 CGAGCTCGAGC
1 CGAGCTCGAGC
123502 C
1 C
123503 TCATTTTGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 17 0.34
10 13 0.26
11 20 0.40
ACGTcount: A:0.21, C:0.36, G:0.33, T:0.10
Consensus pattern (11 bp):
CGAGCTCGAGC
Found at i:129539 original size:36 final size:36
Alignment explanation
Indices: 129496--129569 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
129486 GGTCAATAAC
129496 CGGTTCAATTAAAAAACCGTTAAAAACCCACCGGAT
1 CGGTTCAATTAAAAAACCGTTAAAAACCCACCGGAT
129532 CGGTTCAATTAAAAAACCGTTAAAAACCCACCGGAT
1 CGGTTCAATTAAAAAACCGTTAAAAACCCACCGGAT
129568 CG
1 CG
129570 ACTGGTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (36 bp):
CGGTTCAATTAAAAAACCGTTAAAAACCCACCGGAT
Found at i:131247 original size:30 final size:30
Alignment explanation
Indices: 131213--131269 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
131203 CAAATAAACT
131213 CAATTACAATTCAAATAAATCTCATGAACC
1 CAATTACAATTCAAATAAATCTCATGAACC
131243 CAATTACAATTCAAATAAATCTCATGA
1 CAATTACAATTCAAATAAATCTCATGA
131270 TTAGCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (30 bp):
CAATTACAATTCAAATAAATCTCATGAACC
Found at i:147208 original size:19 final size:20
Alignment explanation
Indices: 147172--147213 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
147162 GGTTACACTT
147172 AAAAAAGATACAATTACACC
1 AAAAAAGATACAATTACACC
147192 AAAAAAGA-ATCAA-TACACC
1 AAAAAAGATA-CAATTACACC
147211 AAA
1 AAA
147214 TGTTGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.64, C:0.19, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAAAGATACAATTACACC
Found at i:151528 original size:16 final size:15
Alignment explanation
Indices: 151499--151553 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
151489 CTCAAATGTC
*
151499 GGGTCATTTCGGTTT
1 GGGTCATTTTGGTTT
151514 GGGTCAATTTTGGTTT
1 GGGTC-ATTTTGGTTT
*
151530 GGGTCTTTTTCGGTTT
1 GGGTCATTTT-GGTTT
151546 CGGGTCAT
1 -GGGTCAT
151554 ATGGTTCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.26
16 19 0.56
17 6 0.18
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (15 bp):
GGGTCATTTTGGTTT
Found at i:159739 original size:30 final size:31
Alignment explanation
Indices: 159705--159778 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
159695 CGGTTGTGCT
** *
159705 CGGTCTTGTGCGATTGGC-CCATGCCATGGC
1 CGGTCTTGTGCGATTCCCTCCATGCAATGGC
*
159735 CGGTCATGTGCGA-TCCCTCCATGCAATGGC
1 CGGTCTTGTGCGATTCCCTCCATGCAATGGC
*
159765 CGGTCTTGTACGAT
1 CGGTCTTGTGCGAT
159779 GGCATCCTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (31 bp):
CGGTCTTGTGCGATTCCCTCCATGCAATGGC
Found at i:166208 original size:30 final size:30
Alignment explanation
Indices: 166174--166269 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
166164 CCGGTTGAGC
*
166174 CCGGTCTTGTGCGATTGGCCCATGCCATAG
1 CCGGTCTTGTGCGATTGGCCCATGCCATGG
* * ** *
166204 CCGGTCATGTACGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
166234 CCGGTCTTGTGCGATTGGCCCATGCCATGG
1 CCGGTCTTGTGCGATTGGCCCATGCCATGG
166264 CCGGTC
1 CCGGTC
166270 ATGCGATGGC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 2 0.04
30 49 0.92
31 2 0.04
ACGTcount: A:0.14, C:0.32, G:0.29, T:0.25
Consensus pattern (30 bp):
CCGGTCTTGTGCGATTGGCCCATGCCATGG
Found at i:168020 original size:2 final size:2
Alignment explanation
Indices: 168013--168048 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
168003 TTGGTATTAC
168013 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
168049 TTGGAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170917 original size:14 final size:14
Alignment explanation
Indices: 170900--170930 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
170890 TTTTCGGCAT
170900 TAATAATAAAAATA
1 TAATAATAAAAATA
*
170914 TAATTATAAAAATA
1 TAATAATAAAAATA
170928 TAA
1 TAA
170931 GAATTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAATAATAAAAATA
Found at i:176975 original size:72 final size:72
Alignment explanation
Indices: 176855--176991 Score: 229
Period size: 72 Copynumber: 1.9 Consensus size: 72
176845 AAACATTTAA
* *
176855 GGGATTTTAGTCATTTAATGACCAAAAACACTTTTGAAACACAGAAGCACCTAGAGATTAGCTTT
1 GGGATTTTAGTCATTTAATAACCAAAAACACTTTTGAAACACAAAAGCACCTAGAGATTAGCTTT
176920 TCGGATG
66 TCGGATG
** *
176927 GGGATTTTAGTCATTTAATAACCAAAAACACTTTTGAAATGCAAAAGCACCTAGGGATTAGCTTT
1 GGGATTTTAGTCATTTAATAACCAAAAACACTTTTGAAACACAAAAGCACCTAGAGATTAGCTTT
176992 GTTTTATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (72 bp):
GGGATTTTAGTCATTTAATAACCAAAAACACTTTTGAAACACAAAAGCACCTAGAGATTAGCTTT
TCGGATG
Found at i:177186 original size:18 final size:20
Alignment explanation
Indices: 177150--177200 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
177140 AAAGCACCTA
177150 AAGATTAGCTTTT-CGGGTG
1 AAGATTAGCTTTTGCGGGTG
*
177169 -GGATTAGCTTTTGC-GGTG
1 AAGATTAGCTTTTGCGGGTG
*
177187 AAAATTAGCTTTTG
1 AAGATTAGCTTTTG
177201 ACACAAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (20 bp):
AAGATTAGCTTTTGCGGGTG
Found at i:177600 original size:2 final size:2
Alignment explanation
Indices: 177593--177623 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
177583 CTAAATCCTA
177593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
177624 CCCTTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178200 original size:17 final size:17
Alignment explanation
Indices: 178146--178202 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
178136 CTAAACCCAG
* * *
178146 GTGATCTAAGATCACCA
1 GTGATCTTACATCACTA
*
178163 GTGATCTTACATCACTT
1 GTGATCTTACATCACTA
*
178180 GTGATCTTTA-ATCGCTA
1 GTGATC-TTACATCACTA
178197 GTGATC
1 GTGATC
178203 CGGGGGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 30 0.91
18 3 0.09
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (17 bp):
GTGATCTTACATCACTA
Found at i:181291 original size:16 final size:16
Alignment explanation
Indices: 181270--181330 Score: 88
Period size: 16 Copynumber: 3.8 Consensus size: 16
181260 CTGTAAGTGA
181270 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
181286 ACCCGAACTCGAAAGA-
1 ACCCGAACCCGAAA-AT
181302 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
181318 ACCCGATCCCGAA
1 ACCCGAACCCGAA
181331 CCCACCCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 1 0.03
16 38 0.95
17 1 0.03
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:186328 original size:23 final size:23
Alignment explanation
Indices: 186302--186351 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
186292 TAAAAATATG
*
186302 TTTTGAAAAATTTAAGTTTT-AAA
1 TTTTCAAAAATTT-AGTTTTAAAA
* *
186325 TTTTCCAAAATTTATTTTTAAAA
1 TTTTCAAAAATTTAGTTTTAAAA
186348 TTTT
1 TTTT
186352 TTGAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTCAAAAATTTAGTTTTAAAA
Found at i:186358 original size:24 final size:25
Alignment explanation
Indices: 186286--186360 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
186276 ATACAATTAA
186286 AATTTTTAAAAATATGTTTTGAAAAATTT
1 AATTTTT-AAAAT-T-TTTTG-AAAATTT
* **
186315 AAGTTTT-AAA-TTTTCCAAAATTT
1 AATTTTTAAAATTTTTTGAAAATTT
186338 -ATTTTTAAAATTTTTTGAAAATT
1 AATTTTTAAAATTTTTTGAAAATT
186361 AGTATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
22 5 0.13
23 10 0.26
24 13 0.34
25 1 0.03
27 3 0.08
29 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (25 bp):
AATTTTTAAAATTTTTTGAAAATTT
Found at i:189612 original size:156 final size:156
Alignment explanation
Indices: 189318--189727 Score: 597
Period size: 156 Copynumber: 2.6 Consensus size: 156
189308 TGTAGATCAT
* * * * *
189318 CTTGGCTAAGTTTCATCTCAAACGGGCTTAAGATGAAAAACTTATACATGTTTTTCAGTTAAGGA
1 CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAAGGA
* * * * *
189383 CAGTTTGGGGTAAGAAACCAAGTTCACCCTGAAGGAGAGCTCGGCCTTACTTAGAATTTTTTCCA
66 CAGTTTGGGGTGAGAAACCATGTTCACCATGAAAGAGAGCTCGACCTTACTTAGAATTTTTTCCA
189448 TAAACTTATGGAGATAATCTAAGTCC
131 TAAACTTATGGAGATAATCTAAGTCC
189474 CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAAGGA
1 CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAAGGA
* ** * *
189539 CAGTTTGGGGTGAGAGACCATGTTCACCATGAAAGAGAGCTCGATTTTACTTATAATTTTTTTCA
66 CAGTTTGGGGTGAGAAACCATGTTCACCATGAAAGAGAGCTCGACCTTACTTAGAATTTTTTCCA
**
189604 TAGTCTTATGGAGATAATCTAAGTCC
131 TAAACTTATGGAGATAATCTAAGTCC
* * * *
189630 CTTGGAAAAGTTTCATATCAATCATACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGGA
1 CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAAGGA
* *
189695 TAGTTTGGGGTGTGAAACC-TAGTTCACCATGAA
66 CAGTTTGGGGTGAGAAACCAT-GTTCACCATGAA
189728 GGAGGGTTCA
Statistics
Matches: 229, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
155 1 0.00
156 228 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (156 bp):
CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAAGGA
CAGTTTGGGGTGAGAAACCATGTTCACCATGAAAGAGAGCTCGACCTTACTTAGAATTTTTTCCA
TAAACTTATGGAGATAATCTAAGTCC
Found at i:190094 original size:28 final size:28
Alignment explanation
Indices: 190054--190115 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
190044 GTAACCAGTT
190054 AGAGGGAGAATTTTCCATCACCCATATC
1 AGAGGGAGAATTTTCCATCACCCATATC
*
190082 AGAGGGA-AGATTTTCCGTCACCCATATC
1 AGAGGGAGA-ATTTTCCATCACCCATATC
190110 AGAGGG
1 AGAGGG
190116 TAACGTCCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (28 bp):
AGAGGGAGAATTTTCCATCACCCATATC
Found at i:190831 original size:26 final size:28
Alignment explanation
Indices: 190802--190855 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
190792 CGCAACAATT
* *
190802 ACCTA-CAAAATAAA-AAGAAAAATATC
1 ACCTATCAAAAAAAAGAAAAAAAATATC
190828 ACCTATCAAAAAAAAGAAAAAAAATATC
1 ACCTATCAAAAAAAAGAAAAAAAATATC
190856 TTTTAATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 8 0.33
28 11 0.46
ACGTcount: A:0.67, C:0.15, G:0.04, T:0.15
Consensus pattern (28 bp):
ACCTATCAAAAAAAAGAAAAAAAATATC
Found at i:193311 original size:23 final size:23
Alignment explanation
Indices: 193284--193354 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 23
193274 TAAAGTAATT
193284 ATAAAGATATTAGATTTAATTGA
1 ATAAAGATATTAGATTTAATTGA
* ** * *
193307 ATAAA-AAAGGAGTTTTTATT--
1 ATAAAGATATTAGATTTAATTGA
193327 ATAAAGATATTAGATTTAATTGA
1 ATAAAGATATTAGATTTAATTGA
193350 ATAAA
1 ATAAA
193355 AATAGAGTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
22 10 0.29
23 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (23 bp):
ATAAAGATATTAGATTTAATTGA
Found at i:193329 original size:43 final size:43
Alignment explanation
Indices: 193281--193367 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
193271 AAATAAAGTA
193281 ATTATAAAGATATTAGATTTAATTGAATAAAAA-AGGAGTTTTT
1 ATTATAAAGATATTAGATTTAATTGAATAAAAATA-GAGTTTTT
193324 ATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTT
1 ATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTT
193367 A
1 A
193368 GTAGAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (43 bp):
ATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTT
Found at i:193360 original size:20 final size:20
Alignment explanation
Indices: 193294--193360 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
193284 ATAAAGATAT
193294 TAGATTTAATTGAATAAAAA
1 TAGATTTAATTGAATAAAAA
*
193314 -AGGAGTTTTTATT--ATAAAGATA
1 TA-GA--TTTAATTGAATAAA-A-A
193336 TTAGATTTAATTGAATAAAAA
1 -TAGATTTAATTGAATAAAAA
193357 TAGA
1 TAGA
193361 GTTTTTAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 8 0.22
22 8 0.22
23 7 0.19
24 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TAGATTTAATTGAATAAAAA
Found at i:193367 original size:23 final size:24
Alignment explanation
Indices: 193298--193378 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 24
193288 AGATATTAGA
193298 TTTAATTGAATAAAAA-AGGAGTT
1 TTTAATTGAATAAAAATAGGAGTT
* ** *
193321 TTT-ATT--ATAAAGATATTAG-A
1 TTTAATTGAATAAAAATAGGAGTT
193341 TTTAATTGAATAAAAATA-GAGTT
1 TTTAATTGAATAAAAATAGGAGTT
* *
193364 TTTAGTAGAATAAAA
1 TTTAATTGAATAAAA
193379 CTATAATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
20 9 0.20
21 6 0.14
22 5 0.11
23 24 0.55
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (24 bp):
TTTAATTGAATAAAAATAGGAGTT
Found at i:194331 original size:108 final size:108
Alignment explanation
Indices: 194183--194475 Score: 437
Period size: 108 Copynumber: 2.6 Consensus size: 108
194173 TAAATTAAAA
*
194183 TGGTAAAAATAAAAATATATATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTA
1 TGGTAAAAAT-AAAGTAT-TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTA
194246 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
63 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
*
194292 TGGTAAAAATAAAGTATTATAAAGATATTAGATTTAATTAAATGAAAACAGAGTTTTTAGTAGAA
1 TGGTAAAAATAAAGTATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
* *
194357 TAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
* *
194400 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGT-ATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
194465 GTAGAATAAAA
60 GTAGAATAAAA
194476 CTATAATAGT
Statistics
Matches: 169, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
107 6 0.04
108 100 0.59
109 33 0.20
110 2 0.01
111 1 0.01
114 27 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (108 bp):
TGGTAAAAATAAAGTATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
Found at i:202132 original size:3 final size:3
Alignment explanation
Indices: 202119--202170 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
202109 AGTCTTTCAC
202119 ATA AT- 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
202166 ATA AT
1 ATA AT
202171 CTACTCGAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:214372 original size:102 final size:102
Alignment explanation
Indices: 214169--214364 Score: 340
Period size: 102 Copynumber: 1.9 Consensus size: 102
214159 CATAAGTTCC
214169 TGTACGCTTGAACAGGTTCTTTAAAACAAAAAAAGTTAATCATGCACTCAAAACATTTTATAAAA
1 TGTACGCTTGAACAGGTTCTTTAAAACAAAAAAAGTTAATCATGCACTCAAAACATTTTATAAAA
214234 CATTTAAATAAAAGAAGTAATAAAACATTACCCTCAA
66 CATTTAAATAAAAGAAGTAATAAAACATTACCCTCAA
* * *
214271 TGTATGCTTGAATAGGTTCTTTAAAACAAAACAAGTTAATCATGCA-TCCAAAACATTTTATAAA
1 TGTACGCTTGAACAGGTTCTTTAAAACAAAAAAAGTTAATCATGCACT-CAAAACATTTTATAAA
*
214335 GCATTTAAATAAAAGAAGTAATAAAACATT
65 ACATTTAAATAAAAGAAGTAATAAAACATT
214365 TTTCTCAACG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 1 0.01
102 88 0.99
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (102 bp):
TGTACGCTTGAACAGGTTCTTTAAAACAAAAAAAGTTAATCATGCACTCAAAACATTTTATAAAA
CATTTAAATAAAAGAAGTAATAAAACATTACCCTCAA
Found at i:218065 original size:2 final size:2
Alignment explanation
Indices: 218052--218093 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
218042 CTACATTGAA
* **
218052 AT AT AT AA AT AT AT AT AT AT AT GG 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
218094 TAATAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Done.