Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 17
Found at i:1254 original size:19 final size:19
Alignment explanation
Indices: 1230--1279 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1220 GAAACCCCTT
**
1230 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTAAA
1249 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
1268 TGAATATACATG
1 TGAAAATACATG
1280 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:2446 original size:13 final size:12
Alignment explanation
Indices: 2427--2512 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2417 ATATAGGCGT
2427 GATATGGTGATG
1 GATATGGTGATG
2439 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2451 GATATAGGCG-T-
1 GATAT-GGTGATG
2462 GATAATGGTGATG
1 GAT-ATGGTGATG
2475 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2487 GATATAGGCG-T-
1 GATAT-GGTGATG
2498 GATAATGGTGATG
1 GAT-ATGGTGATG
2511 GA
1 GA
2513 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2482 original size:36 final size:36
Alignment explanation
Indices: 2409--2513 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
2399 ATTTATAAGT
* *
2409 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2444 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2480 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2514 ATATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:2900 original size:19 final size:20
Alignment explanation
Indices: 2853--2903 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2843 GAAACCCATT
**
2853 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2873 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2892 TGAAGATACATG
1 TGAAAATACATG
2904 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:15288 original size:9 final size:9
Alignment explanation
Indices: 15258--15314 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
15248 TTTTTTGAAA
*
15258 TTTTGGCTT
1 TTTTGGTTT
*
15267 TTTTGGCTT
1 TTTTGGTTT
15276 TTTTGGTTT
1 TTTTGGTTT
15285 TTTT--TTT
1 TTTTGGTTT
*
15292 TTTTGCCTTT
1 TTTTG-GTTT
*
15302 TTTTTGTTT
1 TTTTGGTTT
15311 TTTT
1 TTTT
15315 TTTGTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.17
9 28 0.67
10 7 0.17
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.79
Consensus pattern (9 bp):
TTTTGGTTT
Found at i:15288 original size:11 final size:10
Alignment explanation
Indices: 15282--15325 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
15272 GCTTTTTTGG
15282 TTTTT-TTTT
1 TTTTTGTTTT
*
15291 TTTTTGCCTTT
1 TTTTTG-TTTT
15302 TTTTTGTTTTT
1 TTTTTG-TTTT
15313 TTTTTGTTTT
1 TTTTTGTTTT
15323 TTT
1 TTT
15326 GAAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 5 0.17
10 7 0.23
11 18 0.60
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.89
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:15311 original size:22 final size:19
Alignment explanation
Indices: 15282--15325 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
15272 GCTTTTTTGG
15282 TTTTTTTTTTTTTTGCCTTTT
1 TTTTTTTTTTTTTTG--TTTT
15303 TTTTGTTTTTTTTTTGTTTT
1 TTTT-TTTTTTTTTTGTTTT
15323 TTT
1 TTT
15326 GAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTTTGTTTT
Found at i:15311 original size:25 final size:25
Alignment explanation
Indices: 15265--15322 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
15255 AAATTTTGGC
*
15265 TTTTTTGGCTTTTTTGGTTTTTTTT
1 TTTTTTGCCTTTTTTGGTTTTTTTT
*
15290 TTTTTTGCCTTTTTTTTGTTTTTTTT
1 TTTTTTGCC-TTTTTTGGTTTTTTTT
15316 TTGTTTT
1 TT-TTTT
15323 TTTGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.28
26 17 0.59
27 4 0.14
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (25 bp):
TTTTTTGCCTTTTTTGGTTTTTTTT
Found at i:15697 original size:15 final size:16
Alignment explanation
Indices: 15677--15718 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
15667 GATTAGAATA
15677 AAATAAATAAAAGAT-
1 AAATAAATAAAAGATG
*
15692 AAATAAATGAAAGATG
1 AAATAAATAAAAGATG
15708 AAATAAGATAA
1 AAATAA-ATAA
15719 TAAAGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 6 0.26
17 3 0.13
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (16 bp):
AAATAAATAAAAGATG
Found at i:21391 original size:15 final size:15
Alignment explanation
Indices: 21356--21391 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21346 ATGAGTAATT
*
21356 AAGAAATGAAATGGA
1 AAGAATTGAAATGGA
21371 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
21386 TAGAAT
1 AAGAAT
21392 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:23979 original size:5 final size:5
Alignment explanation
Indices: 23969--23999 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
23959 CTTCAACTTC
*
23969 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
24000 CTTTTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:28009 original size:16 final size:16
Alignment explanation
Indices: 27976--28024 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
27966 TAAGGTAATG
27976 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
27994 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
28010 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
28025 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:29457 original size:200 final size:200
Alignment explanation
Indices: 29115--29516 Score: 779
Period size: 200 Copynumber: 2.0 Consensus size: 200
29105 TCAAGTAGGC
29115 TGCCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAACACCAAGGG
1 TGCCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAACACCAAGGG
29180 ATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCA
66 ATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCA
29245 TTCAAATCATCCTTAGGGCCGAACCAACACAT-ACCATTCGGCCAAGAGCATGTATCTTCATTAA
131 TTCAAATCATCCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAA
29309 AATCA
196 AATCA
29314 TGCCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGG
1 TGCCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCC-AAACACCAAGG
29379 GATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGC
65 GATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGC
*
29444 ATTCAAATCATCCTTAGGGCCGAACCAACACATAACTATTCGGCCAAGAGCATGTATCTTCATTA
130 ATTCAAATCATCCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTA
29509 AAATCA
195 AAATCA
29515 TG
1 TG
29517 TATTTTCATC
Statistics
Matches: 200, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
199 53 0.26
200 109 0.55
201 38 0.19
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (200 bp):
TGCCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAACACCAAGGG
ATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCA
TTCAAATCATCCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAA
AATCA
Found at i:29518 original size:19 final size:20
Alignment explanation
Indices: 29494--29544 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
29484 CGGCCAAGAG
* *
29494 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
29513 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
29533 AATGTATTTTCA
1 CATGTATTTTCA
29545 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:29995 original size:18 final size:19
Alignment explanation
Indices: 29954--29992 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29944 TATCCTTTCT
29954 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
29973 TTATTT-ATTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
29992 T
1 T
29993 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:30312 original size:7 final size:7
Alignment explanation
Indices: 30300--30346 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
30290 GATGTATGAG
30300 TCTTTTT
1 TCTTTTT
30307 TCTTTTT
1 TCTTTTT
30314 T-TTTTT
1 TCTTTTT
*
30320 T-GTTTT
1 TCTTTTT
*
30326 TCTTCTT
1 TCTTTTT
30333 TCTTTTT
1 TCTTTTT
30340 CTCTTTT
1 -TCTTTT
30347 GTTACTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 11 0.32
7 17 0.50
8 6 0.18
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (7 bp):
TCTTTTT
Found at i:30320 original size:13 final size:13
Alignment explanation
Indices: 30300--30346 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
30290 GATGTATGAG
30300 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
* *
30313 TTTTTTTTGTTTT
1 TCTTTTTTCTTTT
*
30326 TCTTCTTTCTTTT
1 TCTTTTTTCTTTT
30339 TCTCTTTT
1 TCT-TTTT
30347 GTTACTTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 24 0.89
14 3 0.11
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:30336 original size:26 final size:26
Alignment explanation
Indices: 30300--30349 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
30290 GATGTATGAG
* * *
30300 TCTTTTTTCTTTTTTTTTTTTGTTTT
1 TCTTCTTTCTTTTTCTCTTTTGTTTT
30326 TCTTCTTTCTTTTTCTCTTTTGTT
1 TCTTCTTTCTTTTTCTCTTTTGTT
30350 ACTTTGTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (26 bp):
TCTTCTTTCTTTTTCTCTTTTGTTTT
Found at i:32474 original size:19 final size:20
Alignment explanation
Indices: 32432--32475 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
32422 TGAAACCCTT
*
32432 TGAAAATACATGATTTTTATA
1 TGAAAATACATGA-TTTTAAA
32453 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
32472 TGAA
1 TGAA
32476 GATCAAGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:37932 original size:28 final size:29
Alignment explanation
Indices: 37881--37936 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
37871 AGGCTAACCA
37881 GCTTCTTTAATAATAGAGAAGTTGGCAAG
1 GCTTCTTTAATAATAGAGAAGTTGGCAAG
37910 GCTTCTTTAAT-ATAGAGAAGTTGGCAA
1 GCTTCTTTAATAATAGAGAAGTTGGCAA
37937 ACATGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (29 bp):
GCTTCTTTAATAATAGAGAAGTTGGCAAG
Found at i:38075 original size:15 final size:15
Alignment explanation
Indices: 38011--38067 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
38001 AAAATTAAAG
38011 AAAGAAATGATTAA-A
1 AAAGAAATGA-TAAGA
*
38026 ATAGAATATGAAATAAGA
1 AAAGAA-ATG--ATAAGA
*
38044 AAGGAAATGATAAGA
1 AAAGAAATGATAAGA
38059 AAAGAAATG
1 AAAGAAATG
38068 GATAGAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 19 0.56
16 3 0.09
17 6 0.18
18 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.18
Consensus pattern (15 bp):
AAAGAAATGATAAGA
Found at i:38654 original size:19 final size:19
Alignment explanation
Indices: 38611--38657 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38601 AACCCTTTGA
**
38611 AAATACATGATTTTTGATG
1 AAATACATGATTTTAAATG
38630 AAATACATGA-TTTAAATG
1 AAATACATGATTTTAAATG
38648 AAGATACATG
1 AA-ATACATG
38658 CTCTTGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (19 bp):
AAATACATGATTTTAAATG
Found at i:47090 original size:19 final size:19
Alignment explanation
Indices: 47066--47110 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
47056 TTCTTTTTCT
47066 TTCTTTTCT-TCTTTTCTTC
1 TTCTTTT-TGTCTTTTCTTC
47085 TTCTTTTTGTCTTTTC-T-
1 TTCTTTTTGTCTTTTCTTC
47102 TTCTTTTTG
1 TTCTTTTTG
47111 CACTCCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 14 0.56
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (19 bp):
TTCTTTTTGTCTTTTCTTC
Found at i:47104 original size:23 final size:23
Alignment explanation
Indices: 47056--47106 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
47046 TTCTTTTGAA
* *
47056 TTCTTTTTCTTTCTTTTCTTCTT
1 TTCTTCTTCTTTCTTGTCTTCTT
*
47079 TTCTTCTTCTTT-TTGTCTTTTCT
1 TTCTTCTTCTTTCTTGTCTTCT-T
47102 TTCTT
1 TTCTT
47107 TTTGCACTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (23 bp):
TTCTTCTTCTTTCTTGTCTTCTT
Found at i:49066 original size:6 final size:6
Alignment explanation
Indices: 49055--49098 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
49045 GTTGTAGGAG
*
49055 TCTTTT TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
49099 GTTGCTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:49087 original size:19 final size:18
Alignment explanation
Indices: 49055--49098 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
49045 GTTGTAGGAG
49055 TCTTTTTCTTTTTCTTTT
1 TCTTTTTCTTTTTCTTTT
*
49073 TGTTTTTCTTCTTTCTTTT
1 TCTTTTTCTT-TTTCTTTT
49092 TCTTTTT
1 TCTTTTT
49099 GTTGCTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TCTTTTTCTTTTTCTTTT
Found at i:49088 original size:25 final size:24
Alignment explanation
Indices: 49055--49101 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
49045 GTTGTAGGAG
49055 TCTTTTTCTTTTTCTTTTTGTTTT
1 TCTTTTTCTTTTTCTTTTTGTTTT
49079 TCTTCTTTCTTTTTCTTTTTGTT
1 TCTT-TTTCTTTTTCTTTTTGTT
49102 GCTTTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (24 bp):
TCTTTTTCTTTTTCTTTTTGTTTT
Found at i:49547 original size:13 final size:13
Alignment explanation
Indices: 49523--49557 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
49513 TGTTATAGGC
49523 ATGAAA-ATGGTG
1 ATGAAAGATGGTG
49535 ATGAAAGATGGTG
1 ATGAAAGATGGTG
49548 ATGAACAGAT
1 ATGAA-AGAT
49558 TGTATCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 11 0.52
14 4 0.19
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23
Consensus pattern (13 bp):
ATGAAAGATGGTG
Found at i:50953 original size:19 final size:20
Alignment explanation
Indices: 50929--50972 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
50919 AGTAAAGATG
50929 TGAAAA-CATAT-GTTATGCA
1 TGAAAATCATATAG-TATGCA
50948 TGAAAATCATATAGTATGCA
1 TGAAAATCATATAGTATGCA
*
50968 AGAAA
1 TGAAA
50973 GTGATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (20 bp):
TGAAAATCATATAGTATGCA
Found at i:51739 original size:17 final size:17
Alignment explanation
Indices: 51717--51749 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
51707 AAATTAGAGT
51717 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
*
51734 ACAAAAGGAAAGAAAA
1 ACAAAAAGAAAGAAAA
51750 TAAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:51766 original size:21 final size:20
Alignment explanation
Indices: 51720--51770 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
51710 TTAGAGTACA
*
51720 AAAAGAAAGAAAAGACAAAAG
1 AAAAGAAA-AAAAGAAAAAAG
* *
51741 GAAAGAAAATAAGAAAATAAG
1 AAAAGAAAAAAAGAAAA-AAG
51762 AAAAGAAAA
1 AAAAGAAAA
51771 GGAATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAAAAG
Found at i:52023 original size:12 final size:14
Alignment explanation
Indices: 51993--52024 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
51983 TAATCTTTTC
51993 TTCTACTTTTCCAT
1 TTCTACTTTTCCAT
52007 TTCTA-TTTTCC-T
1 TTCTACTTTTCCAT
52019 TTCTAC
1 TTCTAC
52025 CCTAACCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTACTTTTCCAT
Found at i:53407 original size:19 final size:21
Alignment explanation
Indices: 53383--53434 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
53373 CGGCCAAGAG
*
53383 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
53402 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
53423 CATGTATTTTCA
1 CATGTATTTTCA
53435 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:55414 original size:28 final size:29
Alignment explanation
Indices: 55383--55438 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
55373 TTTGTTTTGC
55383 AGGACA-ATTCAAGAGA-CATATCTTTTCA
1 AGGACAGATTCAAGA-ATCATATCTTTTCA
*
55411 AGGAGATGATTCAAGAATCATATCTTTT
1 AGGACA-GATTCAAGAATCATATCTTTT
55439 GGAGGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 1 0.04
30 18 0.75
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (29 bp):
AGGACAGATTCAAGAATCATATCTTTTCA
Found at i:57564 original size:19 final size:21
Alignment explanation
Indices: 57540--57591 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
57530 CGGCCAAGAG
*
57540 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
57559 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
57580 CATGTATTTTCA
1 CATGTATTTTCA
57592 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:61258 original size:22 final size:21
Alignment explanation
Indices: 61227--61268 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
61217 CATCTCCATT
61227 TCATCATCAAGACCATCAATA
1 TCATCATCAAGACCATCAATA
61248 TCATCCATCAAGACCATCAAT
1 TCAT-CATCAAGACCATCAAT
61269 TCTGCAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAATA
Found at i:66814 original size:19 final size:21
Alignment explanation
Indices: 66790--66841 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
66780 TGGCCAAGAG
*
66790 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
66809 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
66830 CATGTATTTTCA
1 CATGTATTTTCA
66842 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:71173 original size:11 final size:11
Alignment explanation
Indices: 71159--71214 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
71149 TCTTTTTGAA
71159 TTCTTTTTCTT
1 TTCTTTTTCTT
71170 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
71183 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
71196 TGTCTTTTTC-T
1 T-TCTTTTTCTT
71207 TTCTTTTT
1 TTCTTTTT
71215 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:71183 original size:19 final size:18
Alignment explanation
Indices: 71159--71214 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
71149 TCTTTTTGAA
71159 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
71177 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
71196 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
71214 T
1 T
71215 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:80693 original size:2 final size:2
Alignment explanation
Indices: 80681--80723 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
80671 TCATAATAAC
*
80681 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80723 T
1 T
80724 GAAAATAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:86136 original size:30 final size:31
Alignment explanation
Indices: 86095--86153 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
86085 ACATGCTGCC
*
86095 ATGATATCT-AAATGATATGCAAACATAATAA
1 ATGATATCTAAAACG-TATGCAAACATAATAA
*
86126 ATGA-ATCTAAAACGTATGTAAACATAAT
1 ATGATATCTAAAACGTATGCAAACATAAT
86154 TTAAAGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
ATGATATCTAAAACGTATGCAAACATAATAA
Found at i:89029 original size:19 final size:18
Alignment explanation
Indices: 89007--89047 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
88997 CTTTTTGAAA
89007 TTCTATTCTTTTTCTTTTC
1 TTCTATTCTTTTT-TTTTC
*
89026 TTCTTTTCTTTTTTTTTC
1 TTCTATTCTTTTTTTTTC
89044 TTCT
1 TTCT
89048 TTTTGTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTATTCTTTTTTTTTC
Found at i:89056 original size:26 final size:27
Alignment explanation
Indices: 89018--89069 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
89008 TCTATTCTTT
89018 TTCTTTTCTTCTTTTCTTT-TTTTTTC
1 TTCTTTTCTTCTTTTCTTTCTTTTTTC
89044 TTCTTTT-TGTCTTTTCTTTCTTTTTT
1 TTCTTTTCT-TCTTTTCTTTCTTTTTT
89070 TTACTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.71
27 6 0.25
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (27 bp):
TTCTTTTCTTCTTTTCTTTCTTTTTTC
Found at i:89071 original size:13 final size:12
Alignment explanation
Indices: 89015--89071 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 12
89005 AATTCTATTC
89015 TTTTTCTTTTCTT
1 TTTTTCTTTT-TT
*
89028 CTTTTCTTTTTT
1 TTTTTCTTTTTT
89040 TTTCTTCTTTTTGT
1 TTT-TTCTTTTT-T
*
89054 CTTTTCTTTCTTT
1 TTTTTCTTT-TTT
89067 TTTTT
1 TTTTT
89072 ACTCCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 28 0.76
14 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:90392 original size:26 final size:26
Alignment explanation
Indices: 90353--90423 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
90343 CCCTAGAACA
* *
90353 CCCATGTGCTTTGCATATGATCATCC
1 CCCATGTGCCTTGCATATGATCAGCC
90379 CCCATGTGCCTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
*
90405 CCCATGTGCCTTGGATATG
1 CCCATGTGCCTTGCATATG
90424 GTTCATTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGATCAGCC
Found at i:91282 original size:27 final size:28
Alignment explanation
Indices: 91221--91282 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
91211 AAAGAAAATC
*
91221 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
91249 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
91276 AGAAAAG
1 AGAAAAG
91283 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:95263 original size:20 final size:19
Alignment explanation
Indices: 95235--95273 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
95225 TGAAATGGAT
*
95235 TCCTTACGATCACTCACAAA
1 TCCTCACGATCACT-ACAAA
95255 TCCTCACGATCACTACAAA
1 TCCTCACGATCACTACAAA
95274 AAAAATGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.36, C:0.36, G:0.05, T:0.23
Consensus pattern (19 bp):
TCCTCACGATCACTACAAA
Found at i:98195 original size:9 final size:9
Alignment explanation
Indices: 98181--98224 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
98171 TTTTTTTTCC
98181 AAAAAACAA
1 AAAAAACAA
98190 AAAAAACAA
1 AAAAAACAA
98199 AAAAAAGGCAA
1 AAAAAA--CAA
**
98210 AAAAAGGAA
1 AAAAAACAA
98219 AAAAAA
1 AAAAAA
98225 ATCCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 22 0.73
11 8 0.27
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:98210 original size:20 final size:20
Alignment explanation
Indices: 98187--98224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
98177 TTCCAAAAAA
98187 CAAAAAAAACAAAAAAAAGG
1 CAAAAAAAACAAAAAAAAGG
**
98207 CAAAAAAAGGAAAAAAAA
1 CAAAAAAAACAAAAAAAA
98225 ATCCAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (20 bp):
CAAAAAAAACAAAAAAAAGG
Found at i:102265 original size:10 final size:10
Alignment explanation
Indices: 102250--102298 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
102240 TTTTTTTTTC
102250 AAAAAAACAA
1 AAAAAAACAA
102260 AAAAAAACAA
1 AAAAAAACAA
*
102270 AAAAAAGGCAA
1 AAAAAA-ACAA
102281 AAAAAGGAA-AA
1 AAAAA--AACAA
102292 AAAAAAA
1 AAAAAAA
102299 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 2 0.06
10 16 0.47
11 15 0.44
13 1 0.03
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:108503 original size:25 final size:26
Alignment explanation
Indices: 108442--108505 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
108432 CCCTAGAACA
* *
108442 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
108468 CCCATGTGCCTTGCATATGACCAG-C
1 CCCATGTGCCTTGCATATGACCAGCC
*
108493 CCCATGAGCCTTG
1 CCCATGTGCCTTG
108506 TATGTGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.19, C:0.34, G:0.20, T:0.27
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:110557 original size:2 final size:2
Alignment explanation
Indices: 110550--110576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110540 TCATAATAAC
110550 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 T
110577 GAAAATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113320 original size:15 final size:16
Alignment explanation
Indices: 113277--113322 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
113267 TGTGAAATAA
*
113277 GAAATGGAAGAAGAATG
1 GAAATGG-AGAAGAAAG
*
113294 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
113309 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
113323 AGATAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:113327 original size:25 final size:25
Alignment explanation
Indices: 113294--113352 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
113284 AAGAAGAATG
113294 GAAATGATAAGAAAGGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
* *
113319 GAAAAGATAAGAAATGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
113344 GAAATGATA
1 GAAATGATA
113353 TCAAAGTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (25 bp):
GAAATGATAAGAAAGGAAATGGAAA
Found at i:116905 original size:12 final size:13
Alignment explanation
Indices: 116888--116916 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
116878 TTATATATTG
116888 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
116900 GAAATAAAGAAAT
1 GAAATAAAGAAAT
116913 GAAA
1 GAAA
116917 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:119601 original size:12 final size:12
Alignment explanation
Indices: 119584--119621 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
119574 TATTTTTTCG
119584 AAAAAAAGGCAA
1 AAAAAAAGGCAA
119596 AAAAAAAGG-AA
1 AAAAAAAGGCAA
119607 ACAAAAAAGGCAA
1 A-AAAAAAGGCAA
119620 AA
1 AA
119622 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:122537 original size:35 final size:36
Alignment explanation
Indices: 122457--122539 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
122447 AGATACTATC
* *
122457 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
122494 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
122529 TATTATCACCA
1 TATTATCACCA
122540 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:123025 original size:14 final size:15
Alignment explanation
Indices: 122991--123037 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
122981 AATTTGGAGT
122991 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
123006 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
123020 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
123037 G
1 G
123038 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:123192 original size:17 final size:18
Alignment explanation
Indices: 123164--123197 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
123154 GAGTTGTAAG
*
123164 TTATCTTCATTTTCTTTA
1 TTATCTTCATTTCCTTTA
123182 TTATC-TCATTTCCTTT
1 TTATCTTCATTTCCTTT
123198 TCTTTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATCTTCATTTCCTTTA
Found at i:128029 original size:14 final size:14
Alignment explanation
Indices: 128010--128038 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
128000 AAGCTTGTGG
128010 CATCATTCCTTCAC
1 CATCATTCCTTCAC
128024 CATCATTCCTTCAC
1 CATCATTCCTTCAC
128038 C
1 C
128039 TTGATACTTT
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:0.45, G:0.00, T:0.34
Consensus pattern (14 bp):
CATCATTCCTTCAC
Found at i:128252 original size:35 final size:36
Alignment explanation
Indices: 128172--128254 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
128162 AGATACTATG
* *
128172 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
128209 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
128244 TATTATCACCA
1 TATTATCACCA
128255 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:133124 original size:12 final size:12
Alignment explanation
Indices: 133096--133130 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
133086 TATATTTTGT
133096 TTATCTTG-TTC
1 TTATCTTGTTTC
*
133107 TAATCTTGTTTC
1 TTATCTTGTTTC
133119 TTATCTTGTTTC
1 TTATCTTGTTTC
133131 CAGCACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:138019 original size:6 final size:6
Alignment explanation
Indices: 138008--138056 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
137998 TATGTAGGAG
*
138008 TCTTTT TC-TTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT
138056 T
1 T
138057 TGTTGCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
5 10 0.26
6 18 0.47
7 10 0.26
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:138038 original size:12 final size:12
Alignment explanation
Indices: 138008--138056 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
137998 TATGTAGGAG
138008 TCTTTTTC-TTT
1 TCTTTTTCTTTT
138019 TC-TTTTCTTTT
1 TCTTTTTCTTTT
*
138030 TGTTTTTCTTCTT
1 TCTTTTTCTT-TT
138043 TCTTTTTCTCTTT
1 TCTTTTTCT-TTT
138056 T
1 T
138057 TGTTGCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 7 0.22
13 13 0.41
14 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:138049 original size:25 final size:23
Alignment explanation
Indices: 138010--138056 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
138000 TGTAGGAGTC
138010 TTTTTCTTTTCTTTTCT-TTTTG
1 TTTTTCTTTTCTTTTCTCTTTTG
138032 TTTTTCTTCTTTCTTTTTCTCTTTT
1 TTTTTC-T-TTTC-TTTTCTCTTTT
138057 TGTTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 4 0.19
25 6 0.29
26 4 0.19
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTTCTTTTCTCTTTTG
Found at i:138499 original size:14 final size:14
Alignment explanation
Indices: 138467--138509 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
138457 ATAGGAGTGA
* *
138467 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
138480 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
138494 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
138508 AT
1 AT
138510 AATATCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:139579 original size:22 final size:22
Alignment explanation
Indices: 139539--139580 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
139529 AAATATGTGG
*
139539 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
139561 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
139581 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:141137 original size:90 final size:91
Alignment explanation
Indices: 141013--141194 Score: 294
Period size: 90 Copynumber: 2.0 Consensus size: 91
141003 CCTAGAACAC
141013 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
141078 AAGAGTTCTCTCCCCATTCGGCCAAG
66 AAGAGTTCTCTCCCCATTCGGCCAAG
** * * **
141104 CCATGTGTTTTGCATGTGA-CAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
*
141168 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCCATTCGGCCAAG
141194 C
1 C
141195 ATCAACTACC
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 68 0.81
91 16 0.19
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCCATTCGGCCAAG
Found at i:142007 original size:28 final size:28
Alignment explanation
Indices: 141973--142039 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
141963 AAAGAAAATC
* * *
141973 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
142001 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
142029 AGAAAAGAAAA
1 AGAAAAGAAAA
142040 GAAAGAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.63, C:0.13, G:0.16, T:0.07
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:144822 original size:13 final size:12
Alignment explanation
Indices: 144803--144888 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
144793 ATATAGGCGT
144803 GATATGGTGATG
1 GATATGGTGATG
144815 GAATATGGTGAT-
1 G-ATATGGTGATG
*
144827 GATATAGGCG-T-
1 GATAT-GGTGATG
144838 GATAATGGTGATG
1 GAT-ATGGTGATG
144851 GACTATGGTGAT-
1 GA-TATGGTGATG
*
144863 GATATAGGCG-T-
1 GATAT-GGTGATG
144874 GATAATGGTGATG
1 GAT-ATGGTGATG
144887 GA
1 GA
144889 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:144858 original size:36 final size:36
Alignment explanation
Indices: 144785--144889 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
144775 ATTTATAAGT
* *
144785 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
144820 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
144856 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
144890 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:145274 original size:19 final size:20
Alignment explanation
Indices: 145227--145277 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
145217 GAAACCCCTT
**
145227 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
145247 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
145266 TGAAGATACATG
1 TGAAAATACATG
145278 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:148960 original size:36 final size:36
Alignment explanation
Indices: 148887--148991 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
148877 ATTTATAAGT
* * *
148887 TGGTGATAATATAGGCGTGAT-ATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
148922 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
148958 TGGTAATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
148992 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:149379 original size:19 final size:20
Alignment explanation
Indices: 149329--149379 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
149319 GAAACCCCTT
**
149329 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
*
149349 TGAAAATGCATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
149368 TGAAGATACATG
1 TGAAAATACATG
149380 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:151600 original size:12 final size:12
Alignment explanation
Indices: 151583--151614 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
151573 TTAAGTGTTG
151583 GAAACAAGGTAA
1 GAAACAAGGTAA
151595 GAAACAAGGTAA
1 GAAACAAGGTAA
151607 GAAACAAG
1 GAAACAAG
151615 ATTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.25, T:0.06
Consensus pattern (12 bp):
GAAACAAGGTAA
Found at i:155987 original size:12 final size:11
Alignment explanation
Indices: 155958--155985 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
155948 AAATTTTGGA
155958 TTTTTTGGCTT
1 TTTTTTGGCTT
155969 TTTTTTGGCTT
1 TTTTTTGGCTT
155980 TTTTTT
1 TTTTTT
155986 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.79
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:156361 original size:20 final size:21
Alignment explanation
Indices: 156336--156385 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
156326 ATAAGATTAT
156336 AATAAAATAAACAAAAGAT-A
1 AATAAAATAAACAAAAGATGA
**
156356 AAT-AAATAAACGGAAGATGA
1 AATAAAATAAACAAAAGATGA
*
156376 AATAAGATAA
1 AATAAAATAA
156386 TAAAGAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.52
20 7 0.28
21 5 0.20
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (21 bp):
AATAAAATAAACAAAAGATGA
Found at i:158269 original size:28 final size:28
Alignment explanation
Indices: 158235--158301 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
158225 AAAGAAAATC
* * *
158235 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
158263 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
158291 AGAAAAGAAAA
1 AGAAAAGAAAA
158302 GAAAGAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.63, C:0.13, G:0.16, T:0.07
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:160346 original size:19 final size:20
Alignment explanation
Indices: 160322--160372 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
160312 CGGCCAAGAG
* *
160322 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
160341 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
160361 CATGTATTTTCA
1 CATGTATTTTCA
160373 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:169880 original size:11 final size:11
Alignment explanation
Indices: 169857--169905 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 11
169847 ATACAATCTC
169857 CATCACCATTAT
1 CATCACCA-TAT
169869 CA-CACCTATAT
1 CATCACC-ATAT
169880 CATCACCATATT
1 CATCACCATA-T
169892 CCATCACCATAT
1 -CATCACCATAT
169904 CA
1 CA
169906 CGCCAATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 14 0.42
12 9 0.27
13 10 0.30
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:169934 original size:33 final size:33
Alignment explanation
Indices: 169890--169958 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
169880 CATCACCATA
*
169890 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
169923 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
169956 TTC
1 TTC
169959 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:175536 original size:33 final size:33
Alignment explanation
Indices: 175457--175560 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
175447 ATACAATCTA
* *
175457 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
175493 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
175526 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
175559 TC
1 TC
175561 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:175984 original size:28 final size:28
Alignment explanation
Indices: 175944--176016 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
175934 AAAGAAAAAG
* * * *
175944 AAAATAAGAAAAGAAATTGAAGCACTCC
1 AAAAGAAGAAAAGAAAATCAAGCACTCA
*
175972 AAAAGAA-AGAAAGAAAATCCAGCACTCA
1 AAAAGAAGA-AAAGAAAATCAAGCACTCA
176000 AAAAGAAGAAAAGAAAA
1 AAAAGAAGAAAAGAAAA
176017 GAAAGAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 36 0.95
29 1 0.03
ACGTcount: A:0.64, C:0.12, G:0.15, T:0.08
Consensus pattern (28 bp):
AAAAGAAGAAAAGAAAATCAAGCACTCA
Found at i:179794 original size:9 final size:9
Alignment explanation
Indices: 179780--179847 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
179770 TTGGAATGCA
179780 AAAAGAAAG
1 AAAAGAAAG
*
179789 AAAAGACA-
1 AAAAGAAAG
179797 AAAAG-AAG
1 AAAAGAAAG
179805 AAAA-AGAAG
1 AAAAGA-AAG
179814 AAAAG-AAG
1 AAAAGAAAG
179822 AAAA-AGAAG
1 AAAAGA-AAG
179831 AAAAG-AAG
1 AAAAGAAAG
179839 AAAAAGAAA
1 -AAAAGAAA
179848 AAGATTTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
7 1 0.02
8 19 0.40
9 26 0.54
10 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:179800 original size:17 final size:16
Alignment explanation
Indices: 179779--179849 Score: 99
Period size: 17 Copynumber: 4.2 Consensus size: 16
179769 ATTGGAATGC
179779 AAAAAGAA-AGAAAAGA
1 AAAAAGAAGA-AAAAGA
179795 CAAAAAGAAGAAAAAGA
1 -AAAAAGAAGAAAAAGA
179812 AGAAAAGAAGAAAAAGA
1 A-AAAAGAAGAAAAAGA
179829 AGAAAAGAAGAAAAAGA
1 A-AAAAGAAGAAAAAGA
179846 AAAA
1 AAAA
179850 GATTTCAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.08
17 47 0.90
18 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAAAGA
Found at i:179859 original size:25 final size:23
Alignment explanation
Indices: 179780--179851 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 23
179770 TTGGAATGCA
* *
179780 AAAAGAAAGAAAAGACAAAAAGAAGA
1 AAAAG-AAGAAAA-AGAAAAAGAA-C
*
179806 AAAAGAAGAAAAGAAGAAAAAGAAG
1 AAAAGAAG-AAA-AAGAAAAAGAAC
179831 AAAAGAAGAAAAAGAAAAAGA
1 AAAAGAAGAAAAAGAAAAAGA
179852 TTTCAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 10 0.24
24 3 0.07
25 11 0.26
26 17 0.40
27 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAGAAGAAAAAGAAAAAGAAC
Found at i:180838 original size:15 final size:17
Alignment explanation
Indices: 180818--180850 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
180808 CTTTTACCAA
180818 ATCAAG-TG-TTTGAAG
1 ATCAAGATGCTTTGAAG
180833 ATCAAGATGCTTTGAAG
1 ATCAAGATGCTTTGAAG
180850 A
1 A
180851 AAAGCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (17 bp):
ATCAAGATGCTTTGAAG
Found at i:182098 original size:15 final size:15
Alignment explanation
Indices: 182078--182113 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
182068 ATTATTAGCT
*
182078 TTATAATATATGTTA
1 TTATAATATATATTA
182093 TTATAATATATATTA
1 TTATAATATATATTA
*
182108 TGATAA
1 TTATAA
182114 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:202520 original size:19 final size:22
Alignment explanation
Indices: 202496--202544 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
202486 AAAAATCAGC
202496 AAAGAAAA-T-AAAGCACTC-A
1 AAAGAAAATTGAAAGCACTCGA
202515 AAAGAAGAAATTGAAAGCACTCGA
1 AAAG-A-AAATTGAAAGCACTCGA
202539 AAAGAA
1 AAAGAA
202545 GAAAAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.16
20 1 0.04
21 3 0.12
22 2 0.08
23 10 0.40
24 5 0.20
ACGTcount: A:0.61, C:0.12, G:0.16, T:0.10
Consensus pattern (22 bp):
AAAGAAAATTGAAAGCACTCGA
Found at i:202533 original size:23 final size:23
Alignment explanation
Indices: 202497--202549 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
202487 AAAATCAGCA
202497 AAGAAAATAAAGCACTC-AAAAG
1 AAGAAAATAAAGCACTCGAAAAG
*
202519 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAT-AAAGCACTCGAAAAG
202543 AAGAAAA
1 AAGAAAA
202550 AGAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 9 0.33
24 11 0.41
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.09
Consensus pattern (23 bp):
AAGAAAATAAAGCACTCGAAAAG
Found at i:205809 original size:19 final size:20
Alignment explanation
Indices: 205785--205833 Score: 91
Period size: 19 Copynumber: 2.5 Consensus size: 20
205775 GAGCATGTAG
205785 TTTCATTAAAGTCTTA-TTT
1 TTTCATTAAAGTCTTATTTT
205804 TTTCATTAAAGTCTTATTTT
1 TTTCATTAAAGTCTTATTTT
205824 TTTCATTAAA
1 TTTCATTAAA
205834 AATCATGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTCATTAAAGTCTTATTTT
Found at i:207555 original size:22 final size:24
Alignment explanation
Indices: 207511--207555 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
207501 TTCTTCTTCT
207511 TCCTTTTTGAGTGCTTTTAATTTC
1 TCCTTTTTGAGTGCTTTTAATTTC
*
207535 TCCTTTTT-AGTG-TTTTGATTT
1 TCCTTTTTGAGTGCTTTTAATTT
207556 TATTTGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.62
Consensus pattern (24 bp):
TCCTTTTTGAGTGCTTTTAATTTC
Found at i:210572 original size:12 final size:13
Alignment explanation
Indices: 210549--210573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210539 AACGTCAACG
210549 AAAATACAAAAAA
1 AAAATACAAAAAA
210562 AAAATACAAAAA
1 AAAATACAAAAA
210574 GAAGTTCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:216153 original size:17 final size:17
Alignment explanation
Indices: 216114--216156 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
216104 GTACTACAAC
216114 AAAA-AAAACAACAAGA
1 AAAAGAAAACAACAAGA
216130 AAGAAGAAAACAA-AAGA
1 AA-AAGAAAACAACAAGA
216147 GAAAAGAAAA
1 -AAAAGAAAA
216157 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAACAAGA
Found at i:216216 original size:14 final size:15
Alignment explanation
Indices: 216181--216209 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
216171 AATTTGGAGT
216181 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
216196 GAAAAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
216210 TCAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAAA
Found at i:216382 original size:17 final size:18
Alignment explanation
Indices: 216354--216387 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
216344 GAGTTGCAAG
*
216354 TTATCTTCATTTTCTTTA
1 TTATCTTCATTTCCTTTA
216372 TTATC-TCATTTCCTTT
1 TTATCTTCATTTCCTTT
216388 TCTTTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATCTTCATTTCCTTTA
Found at i:216739 original size:2 final size:2
Alignment explanation
Indices: 216732--216797 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
216722 TATCACCATC
216732 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
216774 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
216798 GACGCTACCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:221108 original size:19 final size:19
Alignment explanation
Indices: 221084--221133 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
221074 GAAACCCCTT
**
221084 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTAAA
221103 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
221122 TGAATATACATG
1 TGAAAATACATG
221134 CCCTTGTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:222312 original size:22 final size:23
Alignment explanation
Indices: 222284--222335 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
222274 ATTTATAAGT
222284 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
222306 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
222329 TGGTGAT
1 TGGTGAT
222336 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:222327 original size:36 final size:38
Alignment explanation
Indices: 222286--222365 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 38
222276 TTATAAGTTG
222286 GTGATAATATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGCGATGGACTATGGTGATGATATAGGC
*
222322 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
*
222358 ATGATAAT
1 GTGATAAT
222366 GGTGATGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.08
34 3 0.08
35 3 0.08
36 27 0.73
37 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
Found at i:222366 original size:36 final size:36
Alignment explanation
Indices: 222304--222373 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
222294 ATAGGCGTGA
*
222304 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
222340 TATGGTGATGATATAGGCATGATAATGGTGATGG
1 TATGGTGATGATATAGGCATGATAATGGTGATGG
222374 GCAGATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCATGATAATGGTGATGGAC
Found at i:222758 original size:19 final size:20
Alignment explanation
Indices: 222717--222767 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
222707 GAAACCCCTT
* **
222717 TGAAAAAACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
222737 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
222756 TGAAGATACATG
1 TGAAAATACATG
222768 CTCTTGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:226044 original size:5 final size:5
Alignment explanation
Indices: 226034--226064 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
226024 CTTCAACTTC
*
226034 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
226065 CTTTTCGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:228079 original size:19 final size:20
Alignment explanation
Indices: 228031--228080 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
228021 GAAACCCCTT
*
228031 TGAAAATACATGATTTATTTA
1 TGAAAATACATGATTTA-TAA
228052 TGAAAATACATGATTTA-AA
1 TGAAAATACATGATTTATAA
*
228071 TGAAGATACA
1 TGAAAATACA
228081 AGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
21 17 0.63
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTATAA
Found at i:231909 original size:22 final size:21
Alignment explanation
Indices: 231878--231918 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
231868 CATCTCCATT
*
231878 TCATCATCAATACCATCAACA
1 TCATCATCAAGACCATCAACA
*
231899 TCATCCATCAAGACTATCAA
1 TCAT-CATCAAGACCATCAA
231919 TTCCGCAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAACA
Found at i:237586 original size:11 final size:11
Alignment explanation
Indices: 237570--237612 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
237560 TGCAAATTGC
237570 TTCTTTTCATT
1 TTCTTTTCATT
237581 TTCTTTTCATT
1 TTCTTTTCATT
*
237592 TTC--TTCTTT
1 TTCTTTTCATT
237601 TTCTTTTC-TT
1 TTCTTTTCATT
237611 TT
1 TT
237613 GCACTCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTCATT
Found at i:237607 original size:5 final size:5
Alignment explanation
Indices: 237570--237612 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
237560 TGCAAATTGC
*
237570 TTCTT TTCATT TTCTT TTCATT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TTC-TT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
237613 GCACTCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:237658 original size:15 final size:16
Alignment explanation
Indices: 237638--237671 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
237628 TGTAGGAGTC
237638 TTTTTCTT-TCTCTTT
1 TTTTTCTTCTCTCTTT
*
237653 TTTTTCTTCTTTCTTT
1 TTTTTCTTCTCTCTTT
237669 TTT
1 TTT
237672 GTTGCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTCTCTCTTT
Found at i:240312 original size:17 final size:17
Alignment explanation
Indices: 240290--240324 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
240280 AAATTAGAGT
240290 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
*
240307 ACAAAAGGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
240324 A
1 A
240325 AGAAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:240339 original size:21 final size:20
Alignment explanation
Indices: 240293--240344 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
240283 TTAGAGTACA
* *
240293 AAAAGAAAGAAAAGACAAAAG
1 AAAAGAAA-AGAAGAAAAAAG
*
240314 GAAAGAAAAGAAGAAAATAAG
1 AAAAGAAAAGAAGAAAA-AAG
240335 AAAAGAAAAG
1 AAAAGAAAAG
240345 GAATAGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAGAAGAAAAAAG
Found at i:241974 original size:19 final size:21
Alignment explanation
Indices: 241950--242001 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
241940 CGGTCAAGAG
*
241950 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
241969 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
241990 CATGTATTTTCA
1 CATGTATTTTCA
242002 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:242754 original size:8 final size:8
Alignment explanation
Indices: 242743--242767 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
242733 GAGAAAAATC
242743 AGAAAAGA
1 AGAAAAGA
242751 AGAAAAGA
1 AGAAAAGA
242759 AGAAAAGA
1 AGAAAAGA
242767 A
1 A
242768 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:246130 original size:19 final size:21
Alignment explanation
Indices: 246106--246157 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
246096 CGGCCAAGAG
*
246106 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
246125 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
246146 CATGTATTTTCA
1 CATGTATTTTCA
246158 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:249970 original size:22 final size:21
Alignment explanation
Indices: 249939--249980 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
249929 CATCTCCATT
249939 TCATCATCAAGACCATCAATA
1 TCATCATCAAGACCATCAATA
249960 TCATCCATCAAGACCATCAAT
1 TCAT-CATCAAGACCATCAAT
249981 TCCGCATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAATA
Found at i:253981 original size:22 final size:22
Alignment explanation
Indices: 253956--254001 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
253946 TCTATTTTAT
253956 ATAAGAGATGAGATGATTACAA
1 ATAAGAGATGAGATGATTACAA
253978 ATAAGAGATGAGATGATTACAA
1 ATAAGAGATGAGATGATTACAA
254000 AT
1 AT
254002 GAAGGCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (22 bp):
ATAAGAGATGAGATGATTACAA
Found at i:255400 original size:19 final size:21
Alignment explanation
Indices: 255376--255427 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
255366 CGGCCAAGAG
*
255376 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
255395 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
255416 CATGTATTTTCA
1 CATGTATTTTCA
255428 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:261440 original size:22 final size:20
Alignment explanation
Indices: 261415--261454 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
261405 ATGTTTGTTT
261415 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
261437 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
261455 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:261685 original size:15 final size:15
Alignment explanation
Indices: 261662--261697 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
261652 ACTAATATTC
* *
261662 TTATCATAATATATA
1 TTATAATAACATATA
261677 TTATAATAACATATA
1 TTATAATAACATATA
261692 TTATAA
1 TTATAA
261698 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:265694 original size:22 final size:20
Alignment explanation
Indices: 265669--265708 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
265659 ATGTTTGTTT
265669 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
265691 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
265709 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:265941 original size:15 final size:15
Alignment explanation
Indices: 265918--265953 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
265908 ACTAATATTC
* *
265918 TTATCATAATATATA
1 TTATAATAACATATA
265933 TTATAATAACATATA
1 TTATAATAACATATA
265948 TTATAA
1 TTATAA
265954 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Done.