Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011163.1 Kokia drynarioides strain JFW-HI SEQ_126137, 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: 614243
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2821 original size:6 final size:6
Alignment explanation
Indices: 2811--2842 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2801 ATGGATGTCC
*
2811 ATCAAC ATCAAG ATCAAG ATCAAG ATCAAG AT
1 ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG AT
2843 AATGTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (6 bp):
ATCAAG
Found at i:3001 original size:34 final size:34
Alignment explanation
Indices: 2958--3023 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
2948 CTTCTATTGA
2958 TCAATAAAATATACTCTCTCTCTTGCTCTCTCGT
1 TCAATAAAATATACTCTCTCTCTTGCTCTCTCGT
2992 TCAATAAAATATACTCTCTCTCTTGCTCTCTC
1 TCAATAAAATATACTCTCTCTCTTGCTCTCTC
3024 ATTCTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.30, G:0.05, T:0.41
Consensus pattern (34 bp):
TCAATAAAATATACTCTCTCTCTTGCTCTCTCGT
Found at i:3742 original size:19 final size:19
Alignment explanation
Indices: 3718--3769 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3708 TTCTATTTCT
3718 TATTAAATAATAAAATATA
1 TATTAAATAATAAAATATA
* *
3737 TATTAAAT-ATATATATTTA
1 TATTAAATAATA-AAATATA
*
3756 TGTTAAATAATAAA
1 TATTAAATAATAAA
3770 TTTATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TATTAAATAATAAAATATA
Found at i:3781 original size:19 final size:19
Alignment explanation
Indices: 3721--3783 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
3711 TATTTCTTAT
*
3721 TAAATAATAAA-ATATATA
1 TAAATAATAAATTTATATA
* *
3739 TTAAATATATATATTTATGT-
1 -TAAATA-ATAAATTTATATA
3759 TAAATAATAAATTTAT-TAA
1 TAAATAATAAATTTATAT-A
3778 TAAATA
1 TAAATA
3784 GTTAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 9 0.25
19 18 0.50
20 4 0.11
21 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAATAATAAATTTATATA
Found at i:6023 original size:14 final size:15
Alignment explanation
Indices: 5995--6023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5985 AGAAAAAGGT
5995 AAAAAAAATAGAAGA
1 AAAAAAAATAGAAGA
6010 AAAAAAAATA-AAGA
1 AAAAAAAATAGAAGA
6024 GAGAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAAAATAGAAGA
Found at i:6050 original size:40 final size:39
Alignment explanation
Indices: 5980--6057 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
5970 AAAGAAGAAG
5980 AAAGGAGAAAAAGGTAAAAAAAATAGAAGAAAAAAAAAT
1 AAAGGAGAAAAAGGTAAAAAAAATAGAAGAAAAAAAAAT
* *
6019 AAAGAGAGAAATAATGTAAAAGAAAA-A-AAGAAAATAAAA
1 AAAG-GAGAAA-AAGGTAAAA-AAAATAGAAGAAAAAAAAA
6058 GAATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 4 0.12
40 17 0.50
41 9 0.26
42 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (39 bp):
AAAGGAGAAAAAGGTAAAAAAAATAGAAGAAAAAAAAAT
Found at i:7824 original size:28 final size:26
Alignment explanation
Indices: 7778--7833 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
7768 ATTGTATTGA
7778 ATATTAAAATATAATAAAATCA-ATTT
1 ATATTAAAATATAATAAAAT-ATATTT
7804 ATATTAAAGA-ATAATTAAAAATATATTT
1 ATATTAAA-ATATAA-T-AAAATATATTT
7832 AT
1 AT
7834 GACAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
26 12 0.46
27 3 0.12
28 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
ATATTAAAATATAATAAAATATATTT
Found at i:9575 original size:22 final size:22
Alignment explanation
Indices: 9545--9588 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9535 AACTAAGTAT
*
9545 AAATAGGTTTGATTAAGG-TTAA
1 AAATAGG-TTAATTAAGGCTTAA
*
9567 AAATGGGTTAATTAAGGCTTAA
1 AAATAGGTTAATTAAGGCTTAA
9589 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (22 bp):
AAATAGGTTAATTAAGGCTTAA
Found at i:13886 original size:21 final size:22
Alignment explanation
Indices: 13861--13902 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13851 TCCTTCGTTT
*
13861 TTATTTA-TTTTTTATTTTTTC
1 TTATTTACTTTTTTATGTTTTC
13882 TTATTTACTTTTTTATGTTTT
1 TTATTTACTTTTTTATGTTTT
13903 GTTTTATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
TTATTTACTTTTTTATGTTTTC
Found at i:27394 original size:15 final size:16
Alignment explanation
Indices: 27371--27403 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27361 TCTAAAACCC
27371 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
*
27387 AAAG-AAAAGAAGAAA
1 AAAGAAAAAAAAGAAA
27402 AA
1 AA
27404 GTCGAGACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:28291 original size:5 final size:5
Alignment explanation
Indices: 28283--28345 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
28273 AGGAAGAAGG
* *
28283 GAAAA GAAAA GAAAA GAAAA GACAAA -AGAA -AAAA GAAAT GAAAA -AGAAA
1 GAAAA GAAAA GAAAA GAAAA GA-AAA GAAAA GAAAA GAAAA GAAAA GA-AAA
*
28332 -AAAA GCAAA GAAAA
1 GAAAA GAAAA GAAAA
28346 AAGAAATGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 9 0.19
5 36 0.75
6 3 0.06
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:28318 original size:19 final size:18
Alignment explanation
Indices: 28283--28351 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
28273 AGGAAGAAGG
28283 GAAAAG-AAAAG--AAAA
1 GAAAAGAAAAAGAAAAAA
28298 GAAAAGACAAAAGAAAAAA
1 GAAAAGA-AAAAGAAAAAA
*
28317 GAAATGAAAAAGAAAAAAA
1 GAAAAGAAAAAG-AAAAAA
*
28336 GCAAAGAAAAAAGAAA
1 GAAAAG-AAAAAGAAA
28352 TGGTATATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
15 6 0.13
17 5 0.11
18 5 0.11
19 23 0.51
20 6 0.13
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.01
Consensus pattern (18 bp):
GAAAAGAAAAAGAAAAAA
Found at i:28327 original size:18 final size:19
Alignment explanation
Indices: 28294--28351 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
28284 AAAAGAAAAG
28294 AAAAGAAAAGACAAAAGAA
1 AAAAGAAAAGACAAAAGAA
*
28313 AAAAGAAATGA-AAAAGAAA
1 AAAAGAAAAGACAAAAG-AA
* *
28332 AAAAGCAAAGAAAAAAGAA
1 AAAAGAAAAGACAAAAGAA
28351 A
1 A
28352 TGGTATATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.15
19 24 0.71
20 5 0.15
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAGACAAAAGAA
Found at i:28341 original size:24 final size:24
Alignment explanation
Indices: 28284--28345 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
28274 GGAAGAAGGG
28284 AAAAGAAAAGAAAAGAAAAGACAA
1 AAAAGAAAAGAAAAGAAAAGACAA
*
28308 AAGAA-AAAAGAAATGAAAAAGA-AA
1 AA-AAGAAAAGAAAAG-AAAAGACAA
*
28332 AAAAGCAAAGAAAA
1 AAAAGAAAAGAAAA
28346 AAGAAATGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.06
24 22 0.69
25 8 0.25
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAGAAAAGAAAAGACAA
Found at i:28345 original size:31 final size:35
Alignment explanation
Indices: 28289--28353 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 35
28279 AAGGGAAAAG
28289 AAAAGAAAAGAAAAGACAAAAGAAAAAAGAAATGA
1 AAAAGAAAAGAAAAGACAAAAGAAAAAAGAAATGA
28324 AAAAG-AAA-AAAAG-C-AAAGAAAAAAGAAATG
1 AAAAGAAAAGAAAAGACAAAAGAAAAAAGAAATG
28354 GTATATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 16 0.53
32 1 0.03
33 5 0.17
34 3 0.10
35 5 0.17
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (35 bp):
AAAAGAAAAGAAAAGACAAAAGAAAAAAGAAATGA
Found at i:29070 original size:14 final size:13
Alignment explanation
Indices: 29050--29082 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
29040 CGGCCTTGTT
29050 CTCGTTGCTCCAC
1 CTCGTTGCTCCAC
29063 CTTCGTTGCTCCAC
1 C-TCGTTGCTCCAC
29077 CTCGTT
1 CTCGTT
29083 TTTGCCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.06, C:0.42, G:0.15, T:0.36
Consensus pattern (13 bp):
CTCGTTGCTCCAC
Found at i:31199 original size:22 final size:20
Alignment explanation
Indices: 31156--31209 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
31146 TTGGTTTTTA
*
31156 TTTTATTTTATATTATTTCT
1 TTTTATTTTTTATTATTTCT
*
31176 TTTTATTTTTTCTTATTTACCT
1 TTTTATTTTTTATTATTT--CT
31198 TTTTATGTTTTT
1 TTTTAT-TTTTT
31210 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.55
22 8 0.28
23 5 0.17
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTTATTATTTCT
Found at i:32179 original size:50 final size:51
Alignment explanation
Indices: 32069--32165 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
32059 GGTTTTAACA
* * * * * *
32069 ACATGCACTATGTAACTCTCATGATTATTTAAGTTTGCATCATAAATAATG
1 ACATGCATTATTTGACTCTCATGATTAGTAAAGATTGCATCATAAATAATG
32120 ACATGCATTATTTGACTCTCATG-TTAGTAAAGATTGCATCATAAAT
1 ACATGCATTATTTGACTCTCATGATTAGTAAAGATTGCATCATAAAT
32166 TATGTTCTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 20 0.50
51 20 0.50
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (51 bp):
ACATGCATTATTTGACTCTCATGATTAGTAAAGATTGCATCATAAATAATG
Found at i:32226 original size:49 final size:49
Alignment explanation
Indices: 32081--32227 Score: 142
Period size: 50 Copynumber: 3.0 Consensus size: 49
32071 ATGCACTATG
* *
32081 TAACTCTCATGATTA-TTTAAGTTTGCATCATAAA-TAATGACATGCATTA
1 TAACTCTCATGA-TAGTTAAAGTTTGCATCATAAATTAA-GTCATGCATTA
* * * *
32130 TTTGACTCTCATGTTAG-TAAAGATTGCATCATAAATTATGTTC-TGCATTA
1 --TAACTCTCATGATAGTTAAAGTTTGCATCATAAATTAAG-TCATGCATTA
*
32180 -AACTCCCATGATAGTTAAAGTTTGCATCAATAAATTAAGTCATGCATT
1 TAACTCTCATGATAGTTAAAGTTTGCATC-ATAAATTAAGTCATGCATT
32228 TAGTAACTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
47 11 0.14
48 14 0.18
49 15 0.19
50 26 0.33
51 13 0.16
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (49 bp):
TAACTCTCATGATAGTTAAAGTTTGCATCATAAATTAAGTCATGCATTA
Found at i:38600 original size:21 final size:21
Alignment explanation
Indices: 38574--38629 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
38564 GACTTATGTT
38574 GTATCGATAGTA-ACATAATAA
1 GTATCGATAGTATACATAAT-A
*
38595 GTATCGGTAGTACTGTACATAATA
1 GTATCGATAGTA---TACATAATA
38619 GTATCGATAGT
1 GTATCGATAGT
38630 TTAAGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 11 0.38
24 11 0.38
25 7 0.24
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (21 bp):
GTATCGATAGTATACATAATA
Found at i:63119 original size:17 final size:17
Alignment explanation
Indices: 63088--63146 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
63078 TAATTGTCCA
* *
63088 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
63105 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
63122 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
63139 TGCATTTT
1 TGCATTTT
63147 CATATATATT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:63126 original size:34 final size:34
Alignment explanation
Indices: 63080--63146 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
63070 CTATAGTATA
*
63080 ATTGTCCATGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCATGCATCTA-CAATGTCATTGCATTTTT
*
63114 ATTGTCGC-TGCATCTACATTGTCATTGCATTTT
1 ATTGTC-CATGCATCTACAATGTCATTGCATTTT
63147 CATATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (34 bp):
ATTGTCCATGCATCTACAATGTCATTGCATTTTT
Found at i:63733 original size:15 final size:15
Alignment explanation
Indices: 63693--63738 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
63683 TCAGTCACTT
*
63693 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
63708 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAGAAAAA
63724 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
63739 AATTTATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 10 0.36
17 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:66416 original size:16 final size:16
Alignment explanation
Indices: 66395--66425 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66385 TGAGAACTCG
66395 ATATCATAAGGGAAAA
1 ATATCATAAGGGAAAA
66411 ATATCATAAGGGAAA
1 ATATCATAAGGGAAA
66426 GAGCATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
ATATCATAAGGGAAAA
Found at i:78482 original size:75 final size:74
Alignment explanation
Indices: 78350--78517 Score: 212
Period size: 75 Copynumber: 2.3 Consensus size: 74
78340 CGTAACTTCT
** * * * * *
78350 GTCAGTTTATCTGACTAGTGTTGGGCACATTTTCGTTGGTTTATCCAGCTAGAGCTGGGCTCATT
1 GTCAGTTTATCTGACTAGCATTGGGCAAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCA-C
78415 AA-TAATATC
65 AATTAATATC
* *
78424 GTCAGTTTATCCGACTAGCATTGGGCATAAATATCGTTGTTTTATCCAACTAGAGCTGGGCTCAC
1 GTCAGTTTATCTGACTAGCATTGGGCA-AAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCAC
*
78489 AATTAATATT
65 AATTAATATC
*
78499 GTCAGTTTATTTGACTAGC
1 GTCAGTTTATCTGACTAGC
78518 TTTAGGCACA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 26 0.32
75 54 0.68
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (74 bp):
GTCAGTTTATCTGACTAGCATTGGGCAAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACA
ATTAATATC
Found at i:78484 original size:35 final size:37
Alignment explanation
Indices: 78382--78484 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 37
78372 GGGCACATTT
*
78382 TCGTTGGTTTATCCAGCTAGAGCTGGGCTCATTAATAATA
1 TCGTT-GTTTATCCAACTAGAGCTGGG--CATTAATAATA
* * *
78422 TCGTCAGTTTATCCGACTAGCA-TTGGGCA-T-A-AATA
1 TCGT-TGTTTATCCAACTAG-AGCTGGGCATTAATAATA
78457 TCGTTGTTTTATCCAACTAGAGCTGGGC
1 TCGTTG-TTTATCCAACTAGAGCTGGGC
78485 TCACAATTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
34 2 0.04
35 25 0.48
36 1 0.02
37 1 0.02
38 2 0.04
40 20 0.38
41 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (37 bp):
TCGTTGTTTATCCAACTAGAGCTGGGCATTAATAATA
Found at i:79762 original size:22 final size:22
Alignment explanation
Indices: 79711--79762 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
79701 TAGGGGTACT
*
79711 GGCGTGTAAAAGTAGGCACACG
1 GGCGTGTGAAAGTAGGCACACG
* *
79733 GGCATGTGAAAGTAGGTACACG
1 GGCGTGTGAAAGTAGGCACACG
*
79755 GTCGTGTG
1 GGCGTGTG
79763 TTTGAGACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.19
Consensus pattern (22 bp):
GGCGTGTGAAAGTAGGCACACG
Found at i:86716 original size:116 final size:115
Alignment explanation
Indices: 86504--86722 Score: 266
Period size: 116 Copynumber: 1.9 Consensus size: 115
86494 TTTTCATTGC
* * * * *
86504 TTTCAAGTATCTGGTCTTTAAGAGTTTTGATCGTGTTTTTTGTTTTCCATTTCATGTACATTTGC
1 TTTCAAGCATCTGGTCTTT-AGAGTTCTGATCATGTTTTCTGTTTTCCATTTCATATACATTTGC
* * *
86569 ATTTTCTATCAGTTCAGTGGAGTGAGTTTTTCAGGTTTTTCATTTTGTCGA
65 ATTTTCCATCAGTTCAATGGACTGAGTTTTTCAGGTTTTTCATTTTGTCGA
*
86620 TTTCAAGCATCTGGTCCTTT-GAGTTCTGTTCATGTTTTCTG-TTTCCATTTCATTATACATTTT
1 TTTCAAGCATCTGGT-CTTTAGAGTTCTGATCATGTTTTCTGTTTTCCATTTCA-TATACA-TTT
*
86683 GCATTTTCCATCCA-TTGAATGGACTGACG-TTTTCAGGTTT
63 GCATTTTCCAT-CAGTTCAATGGACTGA-GTTTTTCAGGTTT
86723 CCTTTTCATT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
114 11 0.12
115 22 0.25
116 48 0.55
117 7 0.08
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.49
Consensus pattern (115 bp):
TTTCAAGCATCTGGTCTTTAGAGTTCTGATCATGTTTTCTGTTTTCCATTTCATATACATTTGCA
TTTTCCATCAGTTCAATGGACTGAGTTTTTCAGGTTTTTCATTTTGTCGA
Found at i:86776 original size:116 final size:115
Alignment explanation
Indices: 86473--87216 Score: 421
Period size: 124 Copynumber: 6.3 Consensus size: 115
86463 CTATTGATCA
* * *
86473 GAGTGA-GTTTTTCGGGTTTCCTTTTCATTGCTTTCAAGTATCTGGTCTTTA-AGAGTTTTGATC
1 GAGTGACG-TTTTCAGGTTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATA-AGTTCTGATC
* * * * *
86536 GTGTTTTTTGTTTTCCATTTCA-TGTACA-TTTGCATTTTCTATCAGTTCAGTG
64 GTGTTTTCTG-TTTCCATTTCATTTTACATTTTGCATTTTCCATCA-TTGAATG
* ** * * * * * *
86588 GAGTGA-GTTTTTCAGGTTTTTCATTTTGTCGATTTCAAGCATCTGGTCCTT-TGAGTTCTGTTC
1 GAGTGACG-TTTTCAGG-TTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTTCTGATC
* *
86651 ATGTTTTCTGTTTCCATTTCATTATACATTTTGCATTTTCCATCCATTGAATG
64 GTGTTTTCTGTTTCCATTTCATTTTACATTTTGCATTTTCCAT-CATTGAATG
* * * * *
86704 GACTGACGTTTTCAGGTTTCCTTTTCATTTCTTTCAAGTGTCTGGTCTTTATAAGGTCTGATCGT
1 GAGTGACGTTTTCAGGTTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTTCTGATCGT
* * * * **
86769 ATCTTCTG-TTCCATTTCATTTTACGTTTTGTATTTTCCATGGGTTGAATG
66 GTTTTCTGTTTCCATTTCATTTTACATTTTGCATTTTCCAT-CATTGAATG
* * * * * *
86819 GAGTAAC-TTTTCCGGGTTTCCATTTCACTGCTTTCAAGTGTCTGGTCTTTATAAGTTCCG-TTG
1 GAGTGACGTTTT-CAGGTTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTTCTGATCG
* * *
86882 CTGTTTTCTGTTTCCATTTCATTTTGCATTTTCCA---TCCA-C--TAAATG
65 -TGTTTTCTGTTTCCATTTCATTTTACATTTTGCATTTTCCATCATTGAATG
** * * * * * * *
86928 GAGTGA-GTTTTTTGGGTTTTCTAGTTCATTGCTTTCAAGTATTTGCTCTTTGTATGTTCCAT-T
1 GAGTGACG-TTTTCAGG-TTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTT-C-TGA
* * *
86991 TCGTGTTTTCTGATTCCATTCCATTTCATTGTATATTTTGCATTTTCTATTCATTGAATG
62 TCGTGTTTTCTG--T---TTCCATTTCATTTTACATTTTGCATTTTCCA-TCATTGAATG
* * ** * * * * * *
87051 GTGCGA-GTTTTTTTGGGTTTTCCAATTCATTGCTTTCAAGTATTTGCTCATTGTATGTTCCAT-
1 GAGTGACG--TTTTCAGG-TTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTT-C-TG
* * *
87114 TTCGTGTTTTCTGATTCCATTCCATTTCATTGTACATTTTGCATTTTCTATTCATTGAATG
61 ATCGTGTTTTCTG--T---TTCCATTTCATTTTACATTTTGCATTTTCCA-TCATTGAATG
* * ** *
87175 GTGAGA-GTTTTTTTGGGTTTTCCAATTCATTGCTTTCAAGTA
1 GAGTGACG--TTTTCAGG-TTTCCATTTCATTGCTTTCAAGTA
87217 CTCTTTATAA
Statistics
Matches: 517, Mismatches: 83, Indels: 49
0.80 0.13 0.08
Matches are distributed among these distances:
109 13 0.03
110 37 0.07
111 10 0.02
112 2 0.00
113 5 0.01
114 17 0.03
115 150 0.29
116 113 0.22
117 3 0.01
119 3 0.01
121 1 0.00
123 10 0.02
124 153 0.30
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (115 bp):
GAGTGACGTTTTCAGGTTTCCATTTCATTGCTTTCAAGTATCTGGTCTTTATAAGTTCTGATCGT
GTTTTCTGTTTCCATTTCATTTTACATTTTGCATTTTCCATCATTGAATG
Found at i:87105 original size:124 final size:124
Alignment explanation
Indices: 86901--87216 Score: 526
Period size: 124 Copynumber: 2.6 Consensus size: 124
86891 GTTTCCATTT
* * * * * * * *
86901 CATTTTGCATTTTCCATCCACTAAATGGAGTGAG-TTTTTTGGGTTTTCTAGTTCATTGCTTTCA
1 CATTTTGCATTTTCTATTCATTGAATGGTGAGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
*
86965 AGTATTTGCTCTTTGTATGTTCCATTTCGTGTTTTCTGATTCCATTCCATTTCATTGTA
66 AGTATTTGCTCATTGTATGTTCCATTTCGTGTTTTCTGATTCCATTCCATTTCATTGTA
* *
87024 TATTTTGCATTTTCTATTCATTGAATGGTGCGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
1 CATTTTGCATTTTCTATTCATTGAATGGTGAGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
87089 AGTATTTGCTCATTGTATGTTCCATTTCGTGTTTTCTGATTCCATTCCATTTCATTGTA
66 AGTATTTGCTCATTGTATGTTCCATTTCGTGTTTTCTGATTCCATTCCATTTCATTGTA
87148 CATTTTGCATTTTCTATTCATTGAATGGTGAGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
1 CATTTTGCATTTTCTATTCATTGAATGGTGAGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
87213 AGTA
66 AGTA
87217 CTCTTTATAA
Statistics
Matches: 180, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 27 0.15
124 153 0.85
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (124 bp):
CATTTTGCATTTTCTATTCATTGAATGGTGAGAGTTTTTTTGGGTTTTCCAATTCATTGCTTTCA
AGTATTTGCTCATTGTATGTTCCATTTCGTGTTTTCTGATTCCATTCCATTTCATTGTA
Found at i:91313 original size:15 final size:14
Alignment explanation
Indices: 91287--91317 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
91277 TAGATATAAC
91287 TAATAAAATAAATG
1 TAATAAAATAAATG
91301 TAATAATAATAAATG
1 TAATAA-AATAAATG
91316 TA
1 TA
91318 TTTGGCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
TAATAAAATAAATG
Found at i:99739 original size:19 final size:19
Alignment explanation
Indices: 99717--99756 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
99707 CATAAAATTA
99717 ATTTTCTAAAAATATT-TTT
1 ATTTT-TAAAAATATTATTT
*
99736 ATTTTTAGAAATATTATTT
1 ATTTTTAAAAATATTATTT
99755 AT
1 AT
99757 CGATTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTTAAAAATATTATTT
Found at i:102632 original size:41 final size:42
Alignment explanation
Indices: 102570--102661 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
102560 ACATTTAAAA
* * ** *
102570 ATCGAGTCGTAAATCTTCCTTTTTAAACAATCTTATGCTC-T
1 ATCGAGTCATAAATCTCCCTTTAAAAACAATCTCATGCTCAT
* *
102611 ATCGAGTCATAAGTCTCCCTTTAAAAATAATCTCATGCTCAT
1 ATCGAGTCATAAATCTCCCTTTAAAAACAATCTCATGCTCAT
*
102653 TTCGAGTCA
1 ATCGAGTCA
102662 CGAGTCTTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 33 0.79
42 9 0.21
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (42 bp):
ATCGAGTCATAAATCTCCCTTTAAAAACAATCTCATGCTCAT
Found at i:102751 original size:43 final size:43
Alignment explanation
Indices: 102704--102883 Score: 272
Period size: 43 Copynumber: 4.2 Consensus size: 43
102694 TTCAAGTCAC
* *
102704 GAGTCTTCCATTTATAAATAATTTCATGCTCGTCCTGAGACAT
1 GAGTCTTCCATTTATAAATAATCTCATGCTCATCCTGAGACAT
* *
102747 GAGTCTTCCATTTATAAATAATTTCATGCTCGTCCTGAGACAT
1 GAGTCTTCCATTTATAAATAATCTCATGCTCATCCTGAGACAT
*
102790 GAGTCTTCCATTTATACATAATCTCATGCTCAT-CTCGAGACAT
1 GAGTCTTCCATTTATAAATAATCTCATGCTCATCCT-GAGACAT
* * *
102833 GAGTCTTCCATTTATACATAATCTCATGCTCATCCGGAGACAC
1 GAGTCTTCCATTTATAAATAATCTCATGCTCATCCTGAGACAT
102876 GAGTCTTC
1 GAGTCTTC
102884 TAGTTAAGCC
Statistics
Matches: 130, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
42 2 0.02
43 127 0.98
44 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (43 bp):
GAGTCTTCCATTTATAAATAATCTCATGCTCATCCTGAGACAT
Found at i:102802 original size:86 final size:86
Alignment explanation
Indices: 102622--102883 Score: 293
Period size: 86 Copynumber: 3.1 Consensus size: 86
102612 TCGAGTCATA
* * * * *
102622 AGTC-TCCCTTTAAAAATAATCTCATGCTCATTTCGAGTCACGAGTCTTCC--TTA-AAGATAAT
1 AGTCTTCCATTTATAAATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAA-ATAAT
* * * * *
102683 CCCATGCTGATTTC-AAGTCACG
65 CTCATGCTCA-TCCGGAGACACG
* *
102705 AGTCTTCCATTTATAAATAATTTCATGCTCGTC-CTGAGACATGAGTCTTCCATTTATAAATAAT
1 AGTCTTCCATTTATAAATAATCTCATGCTCATCTC-GAGACATGAGTCTTCCATTTATAAATAAT
* * * *
102769 TTCATGCTCGTCCTGAGACATG
65 CTCATGCTCATCCGGAGACACG
* *
102791 AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATACATAATC
1 AGTCTTCCATTTATAAATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAAATAATC
102856 TCATGCTCATCCGGAGACACG
66 TCATGCTCATCCGGAGACACG
102877 AGTCTTC
1 AGTCTTC
102884 TAGTTAAGCC
Statistics
Matches: 149, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
83 5 0.03
84 37 0.25
85 2 0.01
86 102 0.68
87 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (86 bp):
AGTCTTCCATTTATAAATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAAATAATC
TCATGCTCATCCGGAGACACG
Found at i:106008 original size:8 final size:8
Alignment explanation
Indices: 105995--106038 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
105985 TCCTCAATTC
105995 TATTATTT
1 TATTATTT
106003 TATTATTT
1 TATTATTT
106011 TATTATTAT
1 TATTATT-T
106020 T-TTATTT
1 TATTATTT
*
106027 TATTTTTT
1 TATTATTT
106035 TATT
1 TATT
106039 GAGTAGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 2 0.06
8 29 0.88
9 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTATTT
Found at i:106016 original size:11 final size:11
Alignment explanation
Indices: 106002--106038 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
105992 TTCTATTATT
106002 TTATTATTTTA
1 TTATTATTTTA
106013 TTATTATTTTA
1 TTATTATTTTA
*
106024 TT-TTATTTTT
1 TTATTATTTTA
106034 TTATT
1 TTATT
106039 GAGTAGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:107171 original size:21 final size:21
Alignment explanation
Indices: 107127--107175 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
107117 CCTGTGCTAG
*
107127 TTCTACCGATACAATTATAAC
1 TTCTACCGATACAATCATAAC
*
107148 TTCTACCGATACAAGTCAT-GC
1 TTCTACCGATACAA-TCATAAC
107169 TTCTACC
1 TTCTACC
107176 AATGTTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAATCATAAC
Found at i:110234 original size:41 final size:41
Alignment explanation
Indices: 110183--110295 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 41
110173 CTTTTTAAAC
* *
110183 AATCTTATGCTC-TATTGAATCATAAGTCTTCCTTTAAAAAT
1 AATCTCATGCTCATATTGAATCACAAGTCTTCC-TTAAAAAT
* * * **
110224 AATCTCATGCTCATTTTGAGTCACGAGTCTTCCTTAAGCAT
1 AATCTCATGCTCATATTGAATCACAAGTCTTCCTTAAAAAT
* * *
110265 AATCCCATGCTCAT-TTCGAGTCACGAGTCTT
1 AATCTCATGCTCATATT-GAATCACAAGTCTT
110296 TTATTTATAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 44 0.71
42 16 0.26
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (41 bp):
AATCTCATGCTCATATTGAATCACAAGTCTTCCTTAAAAAT
Found at i:110336 original size:43 final size:43
Alignment explanation
Indices: 110262--110635 Score: 479
Period size: 43 Copynumber: 8.8 Consensus size: 43
110252 CTTCCTTAAG
* ** * *
110262 CATAATCCCATGCTCATTTCGAGTCACGAGTCTTTTATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
* * **
110305 CATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
*
110348 CATAA-CTCATGCTTATCCCGAGACATGAGTCTTTTATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
110390 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
* * * * **
110433 CATAATCTCATGCTCGTCACGAGTCACGAGTC--TTCCTTA-A
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
* ** * *
110473 GCATAATCCCATGCTCATTTCGAGTCACGAGTCTTTTATTTATA
1 -CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
* * **
110517 CATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
110560 CATAA-CTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
110602 CATAATCTCATGCTCATCCCGAGACATGAGTCTT
1 CATAATCTCATGCTCATCCCGAGACATGAGTCTT
110636 CCATTTACGC
Statistics
Matches: 287, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.00
41 33 0.11
42 75 0.26
43 177 0.62
44 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (43 bp):
CATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATA
Found at i:110507 original size:169 final size:169
Alignment explanation
Indices: 110305--110637 Score: 497
Period size: 169 Copynumber: 2.0 Consensus size: 169
110295 TTTATTTATA
* * * * *
110305 CATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATAA-CTCATGCTTATCCCGA
1 CATAATCCCATGCTCATCACGAGACACGAGTCTTCCATTTATACATAATCTCATGCTCATCACGA
**
110369 GACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACATGAGTCTTTTATTTATAC
66 GACATGAGTCTTCCATTTATACATAA-CTCATGCTCATCCCGAGACATGAGTCTTTTATTTATAC
* *
110434 ATAATCTCATGCTCGTCACGAGTCACGAGTCTTCCTTAAG
130 ATAATCTCATGCTCATCACGAGACACGAGTCTTCCTTAAG
** * ** *
110474 CATAATCCCATGCTCATTTCGAGTCACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGA
1 CATAATCCCATGCTCATCACGAGACACGAGTCTTCCATTTATACATAATCTCATGCTCATCACGA
110539 GACATGAGTCTTCCATTTATACATAACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACA
66 GACATGAGTCTTCCATTTATACATAACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACA
* *
110604 TAATCTCATGCTCATCCCGAGACATGAGTCTTCC
131 TAATCTCATGCTCATCACGAGACACGAGTCTTCC
110638 ATTTACGCCA
Statistics
Matches: 146, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
169 109 0.75
170 37 0.25
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (169 bp):
CATAATCCCATGCTCATCACGAGACACGAGTCTTCCATTTATACATAATCTCATGCTCATCACGA
GACATGAGTCTTCCATTTATACATAACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACA
TAATCTCATGCTCATCACGAGACACGAGTCTTCCTTAAG
Found at i:110589 original size:212 final size:212
Alignment explanation
Indices: 110222--110635 Score: 783
Period size: 212 Copynumber: 2.0 Consensus size: 212
110212 TCCTTTAAAA
***
110222 ATAATCTCATGCTCATTTTGAGTCACGAGTCTTCCTTAAGCATAATCCCATGCTCATTTCGAGTC
1 ATAATCTCATGCTCATCACGAGTCACGAGTCTTCCTTAAGCATAATCCCATGCTCATTTCGAGTC
110287 ACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATA
66 ACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATA
*
110352 ACTCATGCTTATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACAT
131 ACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACAT
110417 GAGTCTTTTATTTATAC
196 GAGTCTTTTATTTATAC
*
110434 ATAATCTCATGCTCGTCACGAGTCACGAGTCTTCCTTAAGCATAATCCCATGCTCATTTCGAGTC
1 ATAATCTCATGCTCATCACGAGTCACGAGTCTTCCTTAAGCATAATCCCATGCTCATTTCGAGTC
110499 ACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATA
66 ACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATA
110564 ACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACAT
131 ACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACAT
110629 GAGTCTT
196 GAGTCTT
110636 CCATTTACGC
Statistics
Matches: 197, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
212 197 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (212 bp):
ATAATCTCATGCTCATCACGAGTCACGAGTCTTCCTTAAGCATAATCCCATGCTCATTTCGAGTC
ACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATA
ACTCATGCTCATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACAT
GAGTCTTTTATTTATAC
Found at i:110636 original size:85 final size:86
Alignment explanation
Indices: 110262--110642 Score: 493
Period size: 85 Copynumber: 4.5 Consensus size: 86
110252 CTTCCTTAAG
* ** * * ** * *
110262 CATAATCCCATGCTCATTTCGAGTCACGAGTCTTTTATTTATACATAATCTCATGCTCGTCACGA
1 CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTATACATAATCTCATGCTCATCCCGA
**
110327 GACATGAGTCTTCCATTTATA
66 GACATGAGTCTTTTATTTATA
* * **
110348 CATAA-CTCATGCTTATCCCGAGACATGAGTCTTTTATTTATACATAATCTCATGCTCATCCCGA
1 CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTATACATAATCTCATGCTCATCCCGA
110412 GACATGAGTCTTTTATTTATA
66 GACATGAGTCTTTTATTTATA
* * * * **
110433 CATAATCTCATGCTCGTCACGAGTCACGAGTCTTCC--TTA-AGCATAATCCCATGCTCATTTCG
1 CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTATA-CATAATCTCATGCTCATCCCG
* *
110495 AGTCACGAGTCTTTTATTTATA
65 AGACATGAGTCTTTTATTTATA
*
110517 CATAATCTCATGCTCGTCACGAGACATGAGTCTTCCATTTATACATAA-CTCATGCTCATCCCGA
1 CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTATACATAATCTCATGCTCATCCCGA
110581 GACATGAGTCTTTTATTTATA
66 GACATGAGTCTTTTATTTATA
*
110602 CATAATCTCATGCTCATCCCGAGACATGAGTCTTCCATTTA
1 CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTA
110643 CGCCAAGTGA
Statistics
Matches: 259, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
83 1 0.00
84 75 0.29
85 146 0.56
86 36 0.14
87 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (86 bp):
CATAATCTCATGCTCATCACGAGACATGAGTCTTCCATTTATACATAATCTCATGCTCATCCCGA
GACATGAGTCTTTTATTTATA
Found at i:110642 original size:43 final size:43
Alignment explanation
Indices: 110207--110642 Score: 467
Period size: 43 Copynumber: 10.3 Consensus size: 43
110197 TTGAATCATA
* * *** * *
110207 AGTCTTCC-TTTAAAAATAATCTCATGCTCATTTTGAGTCACG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
* ** * *
110249 AGTCTTCC--TTA-AGCATAATCCCATGCTCATTTCGAGTCACG
1 AGTCTTCCATTTATA-CATAATCTCATGCTCATCCCGAGACATG
** * *
110290 AGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
*
110333 AGTCTTCCATTTATACATAA-CTCATGCTTATCCCGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
**
110375 AGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
** * * * *
110418 AGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGTCACG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
* ** * *
110461 AGTCTTCC--TTA-AGCATAATCCCATGCTCATTTCGAGTCACG
1 AGTCTTCCATTTATA-CATAATCTCATGCTCATCCCGAGACATG
** * *
110502 AGTCTTTTATTTATACATAATCTCATGCTCGTCACGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
110545 AGTCTTCCATTTATACATAA-CTCATGCTCATCCCGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
**
110587 AGTCTTTTATTTATACATAATCTCATGCTCATCCCGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
110630 AGTCTTCCATTTA
1 AGTCTTCCATTTA
110643 CGCCAAGTGA
Statistics
Matches: 339, Mismatches: 45, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.01
41 67 0.20
42 83 0.24
43 185 0.55
44 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.36
Consensus pattern (43 bp):
AGTCTTCCATTTATACATAATCTCATGCTCATCCCGAGACATG
Found at i:112062 original size:150 final size:150
Alignment explanation
Indices: 111892--112278 Score: 535
Period size: 150 Copynumber: 2.6 Consensus size: 150
111882 GTTTTTTTAG
*
111892 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCATAATAAAAGTTTGGATTT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCA-AATAAAAGTTTAGATTT
** * * * *
111957 TTAAGTGGAGTAGTGATTTTCATTAAAAAAAAAAGAAAGTTTATATTTT-TAAAAATAAAAATCT
65 TTAAGTAAAGTAGTGATTTTCATT-AAAAAAAAAGAAAGTTCAGATTTTAAAAAAATAAAAATAT
*
112021 ATTTTTTAGTTATTTTAAAG-A
129 ATTTTTTAGTGATTTTAAAGAA
*
112042 AAAAATTTAAATTTTTAAATAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTC-AAATAAAAGTTTAGATTT
* * * *
112107 TTAAGTAAAGTAGTTATTTTCATTAAAAAAAATGAAAGTTCGGATTTTAAAAAAATAAAAATATG
65 TTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAGAAAGTTCAGATTTTAAAAAAATAAAAATATA
112172 TTTTTTAGTGATTTTAAAGAA
130 TTTTTTAGTGATTTTAAAGAA
* * * * * *
112193 AAAAATTAAAAATTTTAAACAAAGTTTTGATTTTTTTTAACTATTTTGAAATAAAATTTTTGATT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTA-TTTCAAATAAAAGTTTAGATT
*
112258 TTGAAGTAAAGTAGTGATTTT
64 TTTAAGTAAAGTAGTGATTTT
112279 GTTTTAATTA
Statistics
Matches: 210, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
149 20 0.10
150 113 0.54
151 28 0.13
152 46 0.22
153 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (150 bp):
AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCAAATAAAAGTTTAGATTTT
TAAGTAAAGTAGTGATTTTCATTAAAAAAAAAGAAAGTTCAGATTTTAAAAAAATAAAAATATAT
TTTTTAGTGATTTTAAAGAA
Found at i:113756 original size:239 final size:238
Alignment explanation
Indices: 113331--113802 Score: 768
Period size: 239 Copynumber: 2.0 Consensus size: 238
113321 AAAATCATAA
* * *
113331 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTTTCTTAATTCAATAGTAACTT
1 TAATGAGAAAAGATCGAATAAGGTGTAGATGAATTTTAATATTTCTCTTAATTCAATAGTAACTT
113396 TTAGGATTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATT
66 TTAGGATTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATT
* *
113461 ATTTAAGTATCTTTTAGGATTCTCGTTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
*
113526 AGTTTGGTGAACACGTCTTAATCAAGTTACAAGTAAATCGGAG
196 AGTTTGGTAAACACGTCTTAATCAAGTTACAAGTAAATCGGAG
* *
113569 TAATGAGAAAAGATCGAATAAGGTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTT
1 TAATGAGAAAAGATCGAATAAGGTGTAGATGAATTTTAATATTTCTCTTAATTCAATAGTAA--C
* *
113634 TTTTAGG-TTTTTTTAGGATTCTAAACTAGAATTAATTTTAAGAATTGAA-AGTATTTTATTAGA
64 TTTTAGGATTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGA-TATTTTACTAGA
* * * *
113697 ATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAG
128 ATTATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAG
*
113762 ATAAGTTTGGTAAACACGTCTTAGTCAAGTTACAAGTAAAT
193 ATAAGTTTGGTAAACACGTCTTAATCAAGTTACAAGTAAAT
113803 TGAATGCATT
Statistics
Matches: 216, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
238 59 0.27
239 150 0.69
240 7 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (238 bp):
TAATGAGAAAAGATCGAATAAGGTGTAGATGAATTTTAATATTTCTCTTAATTCAATAGTAACTT
TTAGGATTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATT
ATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTGGTAAACACGTCTTAATCAAGTTACAAGTAAATCGGAG
Found at i:124492 original size:19 final size:19
Alignment explanation
Indices: 124470--124531 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
124460 GAGCACCGAG
124470 GTGCTAAAAGGGCACAAAA
1 GTGCTAAAAGGGCACAAAA
* *
124489 GTGC-ATACAGGAGCACCAAA
1 GTGCTA-AAAGG-GCACAAAA
124509 GTGCTAACAA-GGCACAAAA
1 GTGCTAA-AAGGGCACAAAA
124528 GTGC
1 GTGC
124532 ATACAGGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 13 0.37
21 2 0.06
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (19 bp):
GTGCTAAAAGGGCACAAAA
Found at i:124504 original size:39 final size:39
Alignment explanation
Indices: 124459--124558 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
124449 GCAATATCAG
* *
124459 GGAGCACCGAGGTGCTAA-AAGGGCACAAAAGTGCATACA
1 GGAGCACCAAAGTGCTAACAA-GGCACAAAAGTGCATACA
124498 GGAGCACCAAAGTGCTAACAAGGCACAAAAGTGCATACA
1 GGAGCACCAAAGTGCTAACAAGGCACAAAAGTGCATACA
** *
124537 GGAGCACTGAAGTGCAAACAAG
1 GGAGCACCAAAGTGCTAACAAG
124559 ACACCTTAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 53 0.96
40 2 0.04
ACGTcount: A:0.41, C:0.21, G:0.28, T:0.10
Consensus pattern (39 bp):
GGAGCACCAAAGTGCTAACAAGGCACAAAAGTGCATACA
Found at i:124552 original size:20 final size:20
Alignment explanation
Indices: 124481--124543 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
124471 TGCTAAAAGG
124481 GCACAAAAGTGCATACAGGA
1 GCACAAAAGTGCATACAGGA
* *
124501 GCACCAAAGTGC-TAACAAG-
1 GCACAAAAGTGCAT-ACAGGA
124520 GCACAAAAGTGCATACAGGA
1 GCACAAAAGTGCATACAGGA
124540 GCAC
1 GCAC
124544 TGAAGTGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.10
Consensus pattern (20 bp):
GCACAAAAGTGCATACAGGA
Found at i:124731 original size:40 final size:40
Alignment explanation
Indices: 124617--124885 Score: 193
Period size: 40 Copynumber: 6.7 Consensus size: 40
124607 TGCAAACAAA
* **
124617 AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTTTTACA
1 AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTATTAGG
* *
124657 AGTAAGAAAGTACTATCAAGAGCATTGTAGTGCTATTAGG
1 AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTATTAGG
* * * *
124697 AGTACGAAAATACTATCAGGAGCACTATAATGCTATCT-GG
1 AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTAT-TAGG
* * ** * * * * *
124737 AGTATTG-CAGTGTTGTCAGGAGCATCGCAGTGTTATCAGG
1 AGTA-CGAAAGTACTATCAGGAGCATTGTAGTGCTATTAGG
* * * * * *
124777 AGTATGAAAGTACTGTCAGGAGAACTGTAGTGCTATCAAG
1 AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTATTAGG
* * ** *
124817 AGTACGAAAGTATTGTC-GAGAGCACCGTAGTGCTATCAGG
1 AGTACGAAAGTACTATCAG-GAGCATTGTAGTGCTATTAGG
* * * *
124857 TGTACGAAAGTATTGTCAGGAGCACTGTA
1 AGTACGAAAGTACTATCAGGAGCATTGTA
124886 ATGCAATCAA
Statistics
Matches: 183, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
39 3 0.02
40 177 0.97
41 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (40 bp):
AGTACGAAAGTACTATCAGGAGCATTGTAGTGCTATTAGG
Found at i:124760 original size:80 final size:80
Alignment explanation
Indices: 124598--124895 Score: 260
Period size: 80 Copynumber: 3.7 Consensus size: 80
124588 AGAAATTAGG
* * ** * * * * * *
124598 GCATCGTAGTGCAAACAAAAGTACGAAAGTACTATCAGGAGCATTGTAGTGCTTTTACA-AGTAA
1 GCATCGTAGTGCTATCAGGAGTACGAAAGTACTGTCAGGAGCACTGTAATGCTATCA-AGAGTAC
* * *
124662 GAAAGTACTATCAAGA
65 GAAAGTATTGTCGAGA
* * * * * ** *
124678 GCATTGTAGTGCTATTAGGAGTACGAAAATACTATCAGGAGCACTATAATGCTATCTGGAGTATT
1 GCATCGTAGTGCTATCAGGAGTACGAAAGTACTGTCAGGAGCACTGTAATGCTATCAAGAGTA-C
* *
124743 G-CAGTGTTGTC-AGGA
65 GAAAGTATTGTCGA-GA
* * * * *
124758 GCATCGCAGTGTTATCAGGAGTATGAAAGTACTGTCAGGAGAACTGTAGTGCTATCAAGAGTACG
1 GCATCGTAGTGCTATCAGGAGTACGAAAGTACTGTCAGGAGCACTGTAATGCTATCAAGAGTACG
124823 AAAGTATTGTCGAGA
66 AAAGTATTGTCGAGA
* * * *
124838 GCACCGTAGTGCTATCAGGTGTACGAAAGTATTGTCAGGAGCACTGTAATGCAATCAA
1 GCATCGTAGTGCTATCAGGAGTACGAAAGTACTGTCAGGAGCACTGTAATGCTATCAA
124896 AAGCACTTAT
Statistics
Matches: 170, Mismatches: 43, Indels: 10
0.76 0.19 0.04
Matches are distributed among these distances:
79 2 0.01
80 166 0.98
81 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (80 bp):
GCATCGTAGTGCTATCAGGAGTACGAAAGTACTGTCAGGAGCACTGTAATGCTATCAAGAGTACG
AAAGTATTGTCGAGA
Found at i:129645 original size:26 final size:27
Alignment explanation
Indices: 129615--129673 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
129605 TTAACCCAAT
129615 TTATTAATGAAATAA-TTTAT-TTTTAA
1 TTATTAAT-AAATAATTTTATGTTTTAA
*
129641 TTATTAA-ATATAATTTTATGTTTTAA
1 TTATTAATAAATAATTTTATGTTTTAA
129667 -TATTAAT
1 TTATTAAT
129674 TAATTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 5 0.17
25 11 0.38
26 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (27 bp):
TTATTAATAAATAATTTTATGTTTTAA
Found at i:129670 original size:25 final size:24
Alignment explanation
Indices: 129626--129679 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
129616 TATTAATGAA
129626 ATAA-TTTATTTTTAATTATTAAAT
1 ATAATTTTATTTTTAATTATT-AAT
129650 ATAATTTTATGTTTTAA-TATTAAT
1 ATAATTTTAT-TTTTAATTATTAAT
129674 -TAATTT
1 ATAATTT
129680 ATGAATGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.21
24 7 0.25
25 9 0.32
26 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATAATTTTATTTTTAATTATTAAT
Found at i:133822 original size:18 final size:18
Alignment explanation
Indices: 133772--133813 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
133762 GCAGGCACAT
* *
133772 CATGATCAGATGCAGTCA
1 CATGCTCAGATGCAATCA
133790 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAATCA
133808 CATGCT
1 CATGCT
133814 TATATGCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (18 bp):
CATGCTCAGATGCAATCA
Found at i:139876 original size:15 final size:15
Alignment explanation
Indices: 139856--139901 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
139846 AGGGGTATCA
139856 AGAAGG-AGAAGGAAG
1 AGAAGGAAGAA-GAAG
139871 AGAAGGAAGAAGAAG
1 AGAAGGAAGAAGAAG
* *
139886 AAAAGAAAGAAGAAG
1 AGAAGGAAGAAGAAG
139901 A
1 A
139902 AAAAGAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AGAAGGAAGAAGAAG
Found at i:139906 original size:12 final size:13
Alignment explanation
Indices: 139855--139912 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
139845 TAGGGGTATC
* *
139855 AAGAAGGAGAAGG
1 AAGAAGAAGAAGA
139868 AAG-AGAAGGAAG-
1 AAGAAGAA-GAAGA
139880 AAGAAGAA-AAGA
1 AAGAAGAAGAAGA
139892 AAGAAGAAGAA-A
1 AAGAAGAAGAAGA
*
139904 AAGAGGAAG
1 AAGAAGAAG
139913 TTTTTGTCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 3 0.08
12 23 0.59
13 13 0.33
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:139912 original size:15 final size:15
Alignment explanation
Indices: 139862--139904 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
139852 ATCAAGAAGG
* *
139862 AGAAGGAAGAGAAGGA
1 AGAA-GAAGAAAAGAA
139878 AGAAGAAGAAAAGAA
1 AGAAGAAGAAAAGAA
139893 AGAAGAAGAAAA
1 AGAAGAAGAAAA
139905 AGAGGAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAGAA
Found at i:173011 original size:5 final size:5
Alignment explanation
Indices: 173001--173026 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
172991 CATGACAGCT
173001 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
173027 TTTAAGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:177105 original size:19 final size:19
Alignment explanation
Indices: 177083--177123 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
177073 CTTAAAATAA
177083 AAAAAG-TAAACTAAAACCT
1 AAAAAGATAAA-TAAAACCT
*
177102 AAAAAGATGAATAAAACCT
1 AAAAAGATAAATAAAACCT
177121 AAA
1 AAA
177124 CTAAAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAAAGATAAATAAAACCT
Found at i:178990 original size:73 final size:74
Alignment explanation
Indices: 178892--179037 Score: 204
Period size: 73 Copynumber: 2.0 Consensus size: 74
178882 AGACAGTCCG
* * *
178892 AATACACCGGCACGAAGCCTACTAGGCACATAGCCCAAATACACAAACACGAA-CCTGCTAGGCA
1 AATACACCGGCACAAAGCCTACTAGGAACATAGCCCAAATACACAAACACAAAGCCTGCTAGGCA
178956 CATAGCCCT
66 CATAGCCCT
* * * **
178965 AATACACCGGCACAAAGCTTGCTAGGAACATAGCCCGAATACACTGACACAAAGCCTGCTAGGCA
1 AATACACCGGCACAAAGCCTACTAGGAACATAGCCCAAATACACAAACACAAAGCCTGCTAGGCA
*
179030 TATAGCCC
66 CATAGCCC
179038 GAATTCTTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
73 45 0.71
74 18 0.29
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.14
Consensus pattern (74 bp):
AATACACCGGCACAAAGCCTACTAGGAACATAGCCCAAATACACAAACACAAAGCCTGCTAGGCA
CATAGCCCT
Found at i:179038 original size:37 final size:37
Alignment explanation
Indices: 178889--179041 Score: 182
Period size: 37 Copynumber: 4.2 Consensus size: 37
178879 TAGAGACAGT
* * *
178889 CCGAATACACCGGCACGAAGCCTACTAGGCACATAGC
1 CCGAATACACCGACACAAAGCCTGCTAGGCACATAGC
* ** *
178926 CCAAATACACAAACACGAA-CCTGCTAGGCACATAGC
1 CCGAATACACCGACACAAAGCCTGCTAGGCACATAGC
* * * *
178962 CCTAATACACCGGCACAAAGCTTGCTAGGAACATAGC
1 CCGAATACACCGACACAAAGCCTGCTAGGCACATAGC
* *
178999 CCGAATACACTGACACAAAGCCTGCTAGGCATATAGC
1 CCGAATACACCGACACAAAGCCTGCTAGGCACATAGC
179036 CCGAAT
1 CCGAAT
179042 TCTTAGATGT
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
36 30 0.31
37 67 0.69
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.14
Consensus pattern (37 bp):
CCGAATACACCGACACAAAGCCTGCTAGGCACATAGC
Found at i:194618 original size:18 final size:18
Alignment explanation
Indices: 194592--194645 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
194582 ATGCATTTTA
* *
194592 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
*
194610 TTTATTTGTCACTACA-T
1 TTTATTTGTCACTGCATT
* *
194627 TTTATTTGTTAGTGCATT
1 TTTATTTGTCACTGCATT
194645 T
1 T
194646 GCATTGTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:194644 original size:17 final size:17
Alignment explanation
Indices: 194592--194645 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
194582 ATGCATTTTA
* *
194592 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
*
194610 TTTATTTGTCACTACAT
1 TTTATTTGTCACTGCAT
* *
194627 TTTATTTGTTAGTGCAT
1 TTTATTTGTCACTGCAT
194644 TT
1 TT
194646 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:196290 original size:12 final size:12
Alignment explanation
Indices: 196273--196299 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
196263 GTTGTGCTTA
196273 AATTCCTCTGTT
1 AATTCCTCTGTT
196285 AATTCCTCTGTT
1 AATTCCTCTGTT
196297 AAT
1 AAT
196300 GCTGATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (12 bp):
AATTCCTCTGTT
Found at i:205147 original size:37 final size:37
Alignment explanation
Indices: 205091--205316 Score: 317
Period size: 37 Copynumber: 6.1 Consensus size: 37
205081 GATACAGTCT
* *
205091 GAATACACCAGCACGAAGCCTACTAGGCACATAGCCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
*
205128 GAATACACCGGCACAAAGCCTGCTAGGCACATAGCCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
*
205165 GAATACACCGGCACAAAGCCTGCTAGGCACATAGCCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
* *
205202 AAATACACCGACACAAAGCCTACTAGGCACATAGCCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
* * *
205239 GAATACACCGGCACAAAGCCTGCTAGGAACATAACCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
* *** * *
205276 AAATACACAAACACAAAGCCTACTAGGTACATAGTCC
1 GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
205313 GAAT
1 GAAT
205317 TCTTAGATGT
Statistics
Matches: 169, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 169 1.00
ACGTcount: A:0.38, C:0.33, G:0.18, T:0.12
Consensus pattern (37 bp):
GAATACACCGGCACAAAGCCTACTAGGCACATAGCCC
Found at i:207067 original size:17 final size:18
Alignment explanation
Indices: 207037--207076 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
207027 AAGCATATTA
*
207037 ATTTC-CAAATATTTCCC
1 ATTTCTCAAATATTTACC
207054 ATTTCTCAAA-ATTTACC
1 ATTTCTCAAATATTTACC
207071 ATTTCT
1 ATTTCT
207077 ATCCATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTCTCAAATATTTACC
Found at i:212961 original size:50 final size:50
Alignment explanation
Indices: 212883--213053 Score: 254
Period size: 50 Copynumber: 3.4 Consensus size: 50
212873 TTTAGTAAAA
*
212883 GTCATGCATTATGTAACTCTCATTTTAGTTAAGTATGCATCATAAATAAT
1 GTCATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAAT
*
212933 GACATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAAT
1 GTCATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAAT
* * *
212983 GTCGTGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATTAA-
1 GTCATGCATTATGTAACTCTCATGTTAGTT-AAGTATGCATCA-TAAA-TAAT
*
213035 GTCATGCATTAAGTAACTC
1 GTCATGCATTATGTAACTC
213054 ATTTGTTCAA
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
50 75 0.68
51 11 0.10
52 21 0.19
53 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (50 bp):
GTCATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAAT
Found at i:217786 original size:72 final size:70
Alignment explanation
Indices: 217668--217862 Score: 230
Period size: 72 Copynumber: 2.7 Consensus size: 70
217658 TGACAACTAT
* *
217668 TGTGAAAGTAAATATGTGGTAATGTTATTCATGCCATTAGATAGTAAATATGTGGGTATGTTATT
1 TGTGAAAGTAAATATGTGGT-ATGTTATTCATGTCATT-GATAGTAAATATGTGGGTATATTATT
217733 CATGCCA
64 CATGCCA
* * * *
217740 TGTGATAGTAAATATGTAGGTATGTTATTTATGTCATGTGACAGTAAATGTGTGGGTATATTATT
1 TGTGAAAGTAAATATGT-GGTATGTTATTCATGTCAT-TGATAGTAAATATGTGGGTATATTATT
*
217805 GATGCCA
64 CATGCCA
* * *
217812 TATGACAA-TAAATATATGGGTATGTTATTCATGTCATATGATAGTGAATAT
1 TGTGA-AAGTAAATATGT-GGTATGTTATTCATGTCAT-TGATAGTAAATAT
217863 ATTATGCTAA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
72 99 0.95
73 5 0.05
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (70 bp):
TGTGAAAGTAAATATGTGGTATGTTATTCATGTCATTGATAGTAAATATGTGGGTATATTATTCA
TGCCA
Found at i:217862 original size:108 final size:108
Alignment explanation
Indices: 217668--217862 Score: 268
Period size: 108 Copynumber: 1.8 Consensus size: 108
217658 TGACAACTAT
* * * *
217668 TGTGAAAGTAAATATGTGGTAATGTTATTCATGCCATTAGATAGTAAATATGTGGGTATGTTATT
1 TGTGAAAGTAAATATGTGGTAATATTATTCATGCCATTAGACAATAAATATATGGGTATGTTATT
*
217733 CATGCCATGTGATAGTAAATATGTAGGTATGTTATTTATGTCA
66 CATGCCATATGATAGTAAATATGTAGGTATGTTATTTATGTCA
* * *
217776 TGTGACAGTAAATGTGTGGGT-ATATTATTGATGCCA-TATGACAATAAATATATGGGTATGTTA
1 TGTGAAAGTAAATATGT-GGTAATATTATTCATGCCATTA-GACAATAAATATATGGGTATGTTA
* *
217839 TTCATGTCATATGATAGTGAATAT
64 TTCATGCCATATGATAGTAAATAT
217863 ATTATGCTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
107 2 0.03
108 70 0.93
109 3 0.04
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (108 bp):
TGTGAAAGTAAATATGTGGTAATATTATTCATGCCATTAGACAATAAATATATGGGTATGTTATT
CATGCCATATGATAGTAAATATGTAGGTATGTTATTTATGTCA
Found at i:217863 original size:36 final size:36
Alignment explanation
Indices: 217674--217864 Score: 197
Period size: 36 Copynumber: 5.3 Consensus size: 36
217664 CTATTGTGAA
*
217674 AGTAAATATGT-GGTAATGTTATTCATGCCAT-TAGAT
1 AGTAAATATATGGGT-ATGTTATTCATGCCATAT-GAT
* *
217710 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAT
1 AGTAAATATATGGGTATGTTATTCATGCCATATGAT
* * * * * *
217746 AGTAAATATGTAGGTATGTTATTTATGTCATGTGAC
1 AGTAAATATATGGGTATGTTATTCATGCCATATGAT
* * * * *
217782 AGTAAATGTGTGGGTATATTATTGATGCCATATGAC
1 AGTAAATATATGGGTATGTTATTCATGCCATATGAT
* *
217818 AATAAATATATGGGTATGTTATTCATGTCATATGAT
1 AGTAAATATATGGGTATGTTATTCATGCCATATGAT
*
217854 AGTGAATATAT
1 AGTAAATATAT
217865 TATGCTAATG
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
36 130 0.97
37 4 0.03
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (36 bp):
AGTAAATATATGGGTATGTTATTCATGCCATATGAT
Found at i:218294 original size:23 final size:23
Alignment explanation
Indices: 218264--218395 Score: 192
Period size: 23 Copynumber: 5.7 Consensus size: 23
218254 TGCGTTATAT
218264 GCTTAAATATTAATGTGATTTGC
1 GCTTAAATATTAATGTGATTTGC
*
218287 GCTTAAATATTAATGTGATTTAC
1 GCTTAAATATTAATGTGATTTGC
* *
218310 GCATAAATATTAATGTGGTTTGC
1 GCTTAAATATTAATGTGATTTGC
*
218333 GCTTAAATATTAATGTGATTTGT
1 GCTTAAATATTAATGTGATTTGC
**
218356 GCTTAAATATTAATGTGATTTAT
1 GCTTAAATATTAATGTGATTTGC
* *
218379 GCTGAAATATTCATGTG
1 GCTTAAATATTAATGTG
218396 GTTAAATGTA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 99 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (23 bp):
GCTTAAATATTAATGTGATTTGC
Found at i:218375 original size:69 final size:69
Alignment explanation
Indices: 218264--218398 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
218254 TGCGTTATAT
218264 GCTTAAATATTAATGTGATTTGCGCTTAAATATTAATGTGATTTACGCAT-AAATATTAATGTGG
1 GCTTAAATATTAATGTGATTTGCGCTTAAATATTAATGTGATTTACGC-TGAAATATTAATGTGG
218328 TTTGC
65 TTTGC
* * *
218333 GCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTGAAATATTCATGTGGT
1 GCTTAAATATTAATGTGATTTGCGCTTAAATATTAATGTGATTTACGCTGAAATATTAATGTGGT
218398 T
66 T
218399 AAATGTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (69 bp):
GCTTAAATATTAATGTGATTTGCGCTTAAATATTAATGTGATTTACGCTGAAATATTAATGTGGT
TTGC
Found at i:218436 original size:49 final size:49
Alignment explanation
Indices: 218381--218678 Score: 291
Period size: 49 Copynumber: 5.8 Consensus size: 49
218371 TGATTTATGC
* *
218381 TGAAATATTCATGTGGTTAAATGTAATTAATATGTGATATGATAAATGT
1 TGAAATATTCATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGT
218430 TGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAT-T
1 TGAAATATTCATGTG-------GT---TAAATGTGATTAATATGTGATGTGATAAATGT
* *
218488 CTGAAATATTCAAGTGATTAAATGTGATTAATATGTGATGTGATAAATGT
1 -TGAAATATTCATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGT
218538 TGAAATATTCATGTGACTAATGTGAGTAAATGTGATTAATATGTGATGTGATAAATGT
1 TGAAATATTCATGTG------GT---TAAATGTGATTAATATGTGATGTGATAAATGT
* ** *
218596 TGAGATATTCATGT-GACAAATGTGATT-ATATGTGATGTGATAAATGG
1 TGAAATATTCATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGT
**
218643 TGAAATATTCATGTGACT-AATGTGATT-ATATGTGAT
1 TGAAATATTCATGTGGTTAAATGTGATTAATATGTGAT
218679 TATATGTGAT
Statistics
Matches: 213, Mismatches: 14, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
47 50 0.23
48 10 0.05
49 59 0.28
50 1 0.00
51 1 0.00
52 1 0.00
55 1 0.00
56 2 0.01
58 46 0.22
59 42 0.20
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39
Consensus pattern (49 bp):
TGAAATATTCATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGT
Found at i:218455 original size:10 final size:10
Alignment explanation
Indices: 218440--218477 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
218430 TGAAATATTC
218440 ATGTGATTAA
1 ATGTGATTAA
*
218450 ATGTGACTAA
1 ATGTGATTAA
218460 ATGTGATTAA
1 ATGTGATTAA
218470 TATGTGAT
1 -ATGTGAT
218478 GTGATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:218461 original size:59 final size:59
Alignment explanation
Indices: 218398--218523 Score: 191
Period size: 59 Copynumber: 2.1 Consensus size: 59
218388 TTCATGTGGT
*
218398 TAAATGTAATTAATATGTGATATGATAAATGT-TGAAATATTCATGTGATTAAATGTGAC
1 TAAATGTAATTAATATGTGATATGATAAAT-TCTGAAATATTCAAGTGATTAAATGTGAC
* * *
218457 TAAATGTGATTAATATGTGATGTGATAAATTCTGAAATATTCAAGTGATTAAATGTGAT
1 TAAATGTAATTAATATGTGATATGATAAATTCTGAAATATTCAAGTGATTAAATGTGAC
218516 TAATATGT
1 TAA-ATGT
218524 GATGTGATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 1 0.02
59 56 0.92
60 4 0.07
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (59 bp):
TAAATGTAATTAATATGTGATATGATAAATTCTGAAATATTCAAGTGATTAAATGTGAC
Found at i:218560 original size:23 final size:23
Alignment explanation
Indices: 218450--218553 Score: 79
Period size: 26 Copynumber: 4.3 Consensus size: 23
218440 ATGTGATTAA
*
218450 ATGTGACTAAATG-TGATTAATATGTG
1 ATGTGA-TAAATGTTGA--AATAT-TC
218476 ATGTGATAAAT-TCTGAAATATTC
1 ATGTGATAAATGT-TGAAATATTC
* *
218499 AAGTGATTAAATG-TGATTAATATGTG
1 ATGTGA-TAAATGTTGA--AATAT-TC
218525 ATGTGATAAATGTTGAAATATTC
1 ATGTGATAAATGTTGAAATATTC
218548 ATGTGA
1 ATGTGA
218554 CTAATGTGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
23 16 0.25
24 15 0.23
25 16 0.25
26 18 0.28
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (23 bp):
ATGTGATAAATGTTGAAATATTC
Found at i:218574 original size:58 final size:57
Alignment explanation
Indices: 218501--218688 Score: 252
Period size: 58 Copynumber: 3.4 Consensus size: 57
218491 AAATATTCAA
218501 GTGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAAT
1 GTGATTAAATGTGATT-ATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAAT
* *
218559 GTGAGTAAATGTGATTAATATGTGATGTGATAAATGTTGAGATATTCATGTGAC----
1 GTGATTAAATGTGATT-ATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAAT
*
218613 ------AAATGTGATTATATGTGATGTGATAAATGGTGAAATATTCATGTGACTAAT
1 GTGATTAAATGTGATTATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAAT
*
218664 GTGATTATATGTGATTATATGTGAT
1 GTGATTAAATGTGATTATATGTGAT
218689 TAATATGTGT
Statistics
Matches: 115, Mismatches: 5, Indels: 21
0.82 0.04 0.15
Matches are distributed among these distances:
47 35 0.30
48 10 0.09
57 18 0.16
58 52 0.45
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (57 bp):
GTGATTAAATGTGATTATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAAT
Found at i:218633 original size:47 final size:47
Alignment explanation
Indices: 218565--218678 Score: 192
Period size: 47 Copynumber: 2.4 Consensus size: 47
218555 TAATGTGAGT
* *
218565 AAATGTGATTAATATGTGATGTGATAAATGTTGAGATATTCATGTGAC
1 AAATGTGATT-ATATGTGATGTGATAAATGGTGAAATATTCATGTGAC
218613 AAATGTGATTATATGTGATGTGATAAATGGTGAAATATTCATGTGAC
1 AAATGTGATTATATGTGATGTGATAAATGGTGAAATATTCATGTGAC
*
218660 TAATGTGATTATATGTGAT
1 AAATGTGATTATATGTGAT
218679 TATATGTGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
47 53 0.84
48 10 0.16
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.39
Consensus pattern (47 bp):
AAATGTGATTATATGTGATGTGATAAATGGTGAAATATTCATGTGAC
Found at i:218673 original size:23 final size:24
Alignment explanation
Indices: 218557--218675 Score: 113
Period size: 23 Copynumber: 5.0 Consensus size: 24
218547 CATGTGACTA
*
218557 ATGTGAGTAAATGTGATTAATATGTG
1 ATGTGA-TAAATGTGATT-ATATGTC
*
218583 ATGTGATAAATGTTGA-GATAT-TC
1 ATGTGATAAATG-TGATTATATGTC
* *
218606 ATGTGACAAATGTGATTATATGTG
1 ATGTGATAAATGTGATTATATGTC
*
218630 ATGTGATAAATGGTGA-AATAT-TC
1 ATGTGATAAAT-GTGATTATATGTC
218653 ATGTGACT-AATGTGATTATATGT
1 ATGTGA-TAAATGTGATTATATGT
218676 GATTATATGT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
22 7 0.09
23 30 0.39
24 21 0.27
25 10 0.13
26 9 0.12
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (24 bp):
ATGTGATAAATGTGATTATATGTC
Found at i:218677 original size:10 final size:10
Alignment explanation
Indices: 218653--218697 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
218643 TGAAATATTC
*
218653 ATGTGACTA-
1 ATGTGATTAT
218662 ATGTGATTAT
1 ATGTGATTAT
218672 ATGTGATTAT
1 ATGTGATTAT
218682 ATGTGATTAAT
1 ATGTGATT-AT
218693 ATGTG
1 ATGTG
218698 TCGTGTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 8 0.24
10 18 0.55
11 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.44
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:219421 original size:20 final size:17
Alignment explanation
Indices: 219377--219410 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
219367 GAGAGAATTG
219377 GCGATACCACTCTATTA
1 GCGATACCACTCTATTA
219394 GCGATACCACTCTATTA
1 GCGATACCACTCTATTA
219411 CTATCGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
GCGATACCACTCTATTA
Found at i:221204 original size:29 final size:30
Alignment explanation
Indices: 221165--221233 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
221155 TTTAATGTGC
* *
221165 AATTGTATACATG-AACTTTGATTTTATGT
1 AATTTTATACATGAAACTTTGATTTGATGT
* *
221194 AATTTTATACATGAAATTTTGATTTGATTT
1 AATTTTATACATGAAACTTTGATTTGATGT
221224 AATTCTTATA
1 AATT-TTATA
221234 AATTATTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.35
30 17 0.50
31 5 0.15
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (30 bp):
AATTTTATACATGAAACTTTGATTTGATGT
Found at i:221792 original size:31 final size:31
Alignment explanation
Indices: 221754--221815 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
221744 CATTAGGGAG
221754 ATTGCGGGGAAGCCGTTATTGGGATTACCCT
1 ATTGCGGGGAAGCCGTTATTGGGATTACCCT
221785 ATTGCGGGGAAGCCGTTATTGGGATTACCCT
1 ATTGCGGGGAAGCCGTTATTGGGATTACCCT
221816 TGGATGGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29
Consensus pattern (31 bp):
ATTGCGGGGAAGCCGTTATTGGGATTACCCT
Found at i:222919 original size:19 final size:19
Alignment explanation
Indices: 222895--222933 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
222885 TCTTATCACT
*
222895 ATATATTTTGAAAT-TAAAA
1 ATATATATT-AAATATAAAA
222914 ATATATATTAAATATAAAA
1 ATATATATTAAATATAAAA
222933 A
1 A
222934 AATGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATATATTAAATATAAAA
Found at i:225925 original size:19 final size:19
Alignment explanation
Indices: 225903--225947 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
225893 TTATATTAGG
225903 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
225922 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
225941 ATTTAAT
1 ATTTAAT
225948 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:226772 original size:15 final size:16
Alignment explanation
Indices: 226754--226783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
226744 CTTCCCTATT
226754 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
226769 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
226784 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:226776 original size:22 final size:22
Alignment explanation
Indices: 226749--226809 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
226739 TTCGACTTCC
226749 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
226771 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
226793 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
226810 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:226799 original size:21 final size:22
Alignment explanation
Indices: 226763--226809 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
226753 TTTCTATTTC
*
226763 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
226785 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
226806 TTTT
1 TTTT
226810 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:236962 original size:24 final size:23
Alignment explanation
Indices: 236907--236969 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
236897 ATGAACATTA
236907 AAAATCCTAA--TAATAAAACCCT
1 AAAATCCTAATTTAA-AAAACCCT
*
236929 -AAATCTTAATTTAAACAAACCCT
1 AAAATCCTAATTTAAA-AAACCCT
236952 AAAATCCTAATTTAAAAA
1 AAAATCCTAATTTAAAAA
236970 TCCTAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 8 0.23
22 1 0.03
23 12 0.34
24 14 0.40
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATCCTAATTTAAAAAACCCT
Found at i:241436 original size:15 final size:17
Alignment explanation
Indices: 241410--241444 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
241400 AATATATATA
241410 TAAACTATATAGCAA-T
1 TAAACTATATAGCAACT
241426 TAAACTA-ATAGCAACT
1 TAAACTATATAGCAACT
241442 TAA
1 TAA
241445 GCATTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAACTATATAGCAACT
Found at i:247575 original size:15 final size:16
Alignment explanation
Indices: 247555--247588 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
247545 AATCATTTAA
*
247555 AGAAATT-TGACATCC
1 AGAAATTATGAAATCC
247570 AGAAATTATGAAATCC
1 AGAAATTATGAAATCC
247586 AGA
1 AGA
247589 TCTAACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (16 bp):
AGAAATTATGAAATCC
Found at i:249403 original size:20 final size:20
Alignment explanation
Indices: 249362--249405 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
249352 GTTAAGAGTT
*
249362 TAAATAATAATCAATATAAA
1 TAAATAATAATCAAGATAAA
*
249382 TAAATAATTAATGAAGAT-AA
1 TAAATAA-TAATCAAGATAAA
249402 TAAA
1 TAAA
249406 ATGTGTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAATAATAATCAAGATAAA
Found at i:249551 original size:66 final size:70
Alignment explanation
Indices: 249480--249631 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 70
249470 AGTAACGTTG
* * * * * * *
249480 ATTCAAATTCCTTTATATACACA-TTTTA-T-TTTTAAAATAAAAAGATTATAGTACCTTTG-AT
1 ATTCAAATCCCTCTATATACACATTTTTATTATTTTAAAATAAAAAGACTAAAGTAACATGGTAT
249541 AATAT
66 AATAT
*
249546 ATTCAAATCCCTCTATATACATATTTTTTTATTACTTTTAAAATAAAAAGACTAAAGTAACATGG
1 ATTCAAATCCCTCTATATACACA--TTTTTATTA-TTTTAAAATAAAAAGACTAAAGTAACATGG
249611 TATAATAT
63 TATAATAT
249619 ATTCAAATCCCTC
1 ATTCAAATCCCTC
249632 AACTTTTATT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
66 20 0.28
69 5 0.07
70 1 0.01
72 25 0.35
73 20 0.28
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (70 bp):
ATTCAAATCCCTCTATATACACATTTTTATTATTTTAAAATAAAAAGACTAAAGTAACATGGTAT
AATAT
Found at i:255480 original size:17 final size:17
Alignment explanation
Indices: 255455--255490 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
255445 TAAAAAAATA
255455 ATTTATAATTATAAGAT
1 ATTTATAATTATAAGAT
* *
255472 ATTTTTAATTATAATAT
1 ATTTATAATTATAAGAT
255489 AT
1 AT
255491 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTATAATTATAAGAT
Found at i:258268 original size:58 final size:60
Alignment explanation
Indices: 258166--258277 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 60
258156 ATTGAATCTA
* * * *
258166 AAAAAAAGTTTAGGTATCAAATTAAAAAAAAAGTTTTAAATTCAAGTACCAAATTAGGTC
1 AAAAAAAGTTTAGATACCAAATTAAAAAAAAAGTTTCAAATTCAAATACCAAATTAGGTC
*
258226 AAAAAAA-TTTAGATACCAAATT-AAGAAAAA-TTGTCAAATTCAAATACCAAAT
1 AAAAAAAGTTTAGATACCAAATTAAAAAAAAAGTT-TCAAATTCAAATACCAAAT
258278 GTTATATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.04
58 24 0.52
59 13 0.28
60 7 0.15
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (60 bp):
AAAAAAAGTTTAGATACCAAATTAAAAAAAAAGTTTCAAATTCAAATACCAAATTAGGTC
Found at i:258599 original size:14 final size:15
Alignment explanation
Indices: 258582--258612 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
258572 TTTTAATTGA
258582 AATAAT-AAAATTAT
1 AATAATAAAAATTAT
258596 AATAATAAAAATTAT
1 AATAATAAAAATTAT
258611 AA
1 AA
258613 CACCTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATAAAAATTAT
Found at i:262615 original size:16 final size:18
Alignment explanation
Indices: 262576--262609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
262566 TAAGTTTATA
262576 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
262593 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
262610 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:263957 original size:18 final size:18
Alignment explanation
Indices: 263923--263956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
263913 TGGAGTGAGT
263923 AAAACTTGATTTGTTTTG
1 AAAACTTGATTTGTTTTG
*
263941 AAAAGTTGATTT-TTTT
1 AAAACTTGATTTGTTTT
263957 TTTAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (18 bp):
AAAACTTGATTTGTTTTG
Found at i:266798 original size:29 final size:29
Alignment explanation
Indices: 266756--266815 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
266746 ACAACATGCC
266756 ATTTGGGAAAACAATGTGTAAGCACAATA
1 ATTTGGGAAAACAATGTGTAAGCACAATA
266785 ATTTGGGAAAACAATGTGTAAGCACAATA
1 ATTTGGGAAAACAATGTGTAAGCACAATA
266814 AT
1 AT
266816 AATGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (29 bp):
ATTTGGGAAAACAATGTGTAAGCACAATA
Found at i:271101 original size:6 final size:6
Alignment explanation
Indices: 271085--271114 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
271075 CAAATGTATA
271085 ATTTCTC ATTTTC ATTTTC ATTTTC ATTTT
1 ATTT-TC ATTTTC ATTTTC ATTTTC ATTTT
271115 GAGAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTC
Found at i:272183 original size:13 final size:14
Alignment explanation
Indices: 272160--272191 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
272150 AAATATTTAA
272160 AATATTAAAATATT
1 AATATTAAAATATT
272174 AATA-TAAAATATT
1 AATATTAAAATATT
272187 -ATATT
1 AATATT
272192 TTTCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:272258 original size:16 final size:16
Alignment explanation
Indices: 272237--272286 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
272227 ATATTTAGTC
272237 ATATAATAAATTATTA
1 ATATAATAAATTATTA
272253 ATATAAT---TTATTA
1 ATATAATAAATTATTA
*
272266 ATTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
272283 ATAT
1 ATAT
272287 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 12 0.43
16 10 0.36
17 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:272262 original size:29 final size:30
Alignment explanation
Indices: 272229--272286 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
272219 AATTATTTAT
*
272229 ATTTAGTCATATAATAAATTA-TTAATATA
1 ATTTAGTAATATAATAAATTATTTAATATA
* *
272258 ATTTATTAATTTAATAAATTATTTAATAT
1 ATTTAGTAATATAATAAATTATTTAATAT
272287 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTAGTAATATAATAAATTATTTAATATA
Found at i:272312 original size:13 final size:14
Alignment explanation
Indices: 272296--272337 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
272286 TTTCAATTTT
272296 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
272309 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
272324 ATTTTAAATAATAT
1 ATTTT-AATAATAT
272338 TCTTTACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:272322 original size:16 final size:16
Alignment explanation
Indices: 272300--272336 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
272290 AATTTTATTT
272300 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
272317 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
272332 TAATA
1 TAATA
272337 TTCTTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:284902 original size:29 final size:30
Alignment explanation
Indices: 284828--284953 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 30
284818 TTTGTAGAAT
* * * * *
284828 TTTAGGGGTAAAAATGTAATATTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTAGAAAAA
* * ** *
284858 TTTAAGGGTCAAAATATAATTTTAGGGAAG
1 TTTAGGGGTTAAAATATAATTTTAGAAAAA
284888 TTT-GGGGTTAAAATATAATTTTAGAAAAA
1 TTTAGGGGTTAAAATATAATTTTAGAAAAA
* * * *
284917 TTTAGGCGTTAAAATAAAATTTTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTAGAAAAA
284947 TTTAGGG
1 TTTAGGG
284954 TTTCAAAAGT
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
29 24 0.31
30 54 0.69
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATAATTTTAGAAAAA
Found at i:284948 original size:59 final size:59
Alignment explanation
Indices: 284832--284955 Score: 135
Period size: 59 Copynumber: 2.1 Consensus size: 59
284822 TAGAATTTTA
* * * * * *
284832 GGGGTAAAAATGTAATATTGGAAAAGTTTAAGGGTCAAAATATAATTTTAGGGAAGTTT
1 GGGGTTAAAATATAATATTAGAAAAATTTAAGGGTCAAAATAAAATTTTAGGAAAGTTT
* *
284891 GGGGTTAAAATATAATTTTAGAAAAATTT-AGGCGTTAAAATAAAATTTT-GGAAAAGTTT
1 GGGGTTAAAATATAATATTAGAAAAATTTAAGG-GTCAAAATAAAATTTTAGG-AAAGTTT
*
284950 AGGGTT
1 GGGGTT
284956 TCAAAAGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 5 0.09
59 49 0.91
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
GGGGTTAAAATATAATATTAGAAAAATTTAAGGGTCAAAATAAAATTTTAGGAAAGTTT
Found at i:284963 original size:16 final size:16
Alignment explanation
Indices: 284942--284973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
284932 AAAATTTTGG
284942 AAAAGTTTAGGGTTTC
1 AAAAGTTTAGGGTTTC
*
284958 AAAAGTTTAGGTTTTC
1 AAAAGTTTAGGGTTTC
284974 GTTTTGGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (16 bp):
AAAAGTTTAGGGTTTC
Found at i:289822 original size:18 final size:18
Alignment explanation
Indices: 289788--289836 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
289778 TTGACAAAAA
*
289788 TTTGAAACCTCGAGTGAAG
1 TTTGAAATCT-GAGTGAAG
289807 TTTGAAATCTGAGTGAAG
1 TTTGAAATCTGAGTGAAG
289825 TTTGAAATCTGA
1 TTTGAAATCTGA
289837 TCCATGTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (18 bp):
TTTGAAATCTGAGTGAAG
Found at i:290423 original size:30 final size:29
Alignment explanation
Indices: 290383--290465 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 29
290373 GAGGAAAAAA
*
290383 AGGGTCAAAATG-AAGTTTTGGAAAAGTTCG
1 AGGGTTAAAATGTAA-TTTTGGAAAAGTT-G
* *
290413 AGGGTTAAAATGTAATTTTAGAAAAGTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTG
290442 AGGGGTTAAAATGTAATTTTGGAA
1 A-GGGTTAAAATGTAATTTTGGAA
290466 TAAAAAGGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.94
31 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.33
Consensus pattern (29 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTG
Found at i:301056 original size:23 final size:24
Alignment explanation
Indices: 301007--301058 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
300997 ATAACCATTC
301007 CATTGATATCCATTTCAATCTTTT
1 CATTGATATCCATTTCAATCTTTT
*
301031 CATTGATATCCTTTTCAA-CTTTT
1 CATTGATATCCATTTCAATCTTTT
301054 CATTG
1 CATTG
301059 TTCCAAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (24 bp):
CATTGATATCCATTTCAATCTTTT
Found at i:301234 original size:2 final size:2
Alignment explanation
Indices: 301227--301285 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
301217 CACTTTATAG
* *
301227 AC AC AC AC AT AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
301269 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
301286 TATGTATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.53, C:0.46, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:303686 original size:7 final size:7
Alignment explanation
Indices: 303674--303699 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
303664 ATCCCTTCAT
303674 TCATCAA
1 TCATCAA
303681 TCATCAA
1 TCATCAA
303688 TCATCAA
1 TCATCAA
303695 TCATC
1 TCATC
303700 TCTCATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCAA
Found at i:309635 original size:18 final size:17
Alignment explanation
Indices: 309604--309641 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
309594 CTAAAAATCG
309604 ATAAATAATATTTTAGAA
1 ATAAATAATATTTTA-AA
309622 ATAAA-AATATTTTTAAA
1 ATAAATAATA-TTTTAAA
309639 ATA
1 ATA
309642 TTAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAAATAATATTTTAAA
Found at i:327736 original size:23 final size:23
Alignment explanation
Indices: 327710--327766 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
327700 TGACGTGGCA
327710 TCCAGTCAGCAGCTTCTAAAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
*
327733 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
*
327756 TCTAGTCAGCA
1 TCCAGTCAGCA
327767 ATGATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAAAAGG
Found at i:331569 original size:50 final size:50
Alignment explanation
Indices: 331494--331593 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
331484 GGGACTTAGT
331494 CCCTCGACTTGTATGCATAAAATAAAGATCAAAGGAGGAGCAAAACCATC
1 CCCTCGACTTGTATGCATAAAATAAAGATCAAAGGAGGAGCAAAACCATC
331544 CCCTCGACTTGTATGCATAAAATAAAGATCAAAGGAGGAGCAAAACCATC
1 CCCTCGACTTGTATGCATAAAATAAAGATCAAAGGAGGAGCAAAACCATC
331594 ACGAGAAGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (50 bp):
CCCTCGACTTGTATGCATAAAATAAAGATCAAAGGAGGAGCAAAACCATC
Found at i:332251 original size:6 final size:6
Alignment explanation
Indices: 332240--332344 Score: 88
Period size: 6 Copynumber: 17.3 Consensus size: 6
332230 ACCCATTGTT
* * * *
332240 TTTTTA TTTTTA -TTTTA TTATTA -ATTTA TTTCTA TTATTTA TATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA
* ** * *
332287 TTTTTA TTTTTA TCTTTA TTTTTA TTTAAAA TTTTTA TTTATTA ATATTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTT-TTA TTTTTA
332337 TTTTTA TT
1 TTTTTA TT
332345 CTTTCTCAGG
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
5 8 0.11
6 56 0.74
7 12 0.16
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:332325 original size:47 final size:50
Alignment explanation
Indices: 332240--332344 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 50
332230 ACCCATTGTT
*
332240 TTTTTATTTTTATTTTATTATTAATTTATTTCTATTATTTA-T-AT-TTA
1 TTTTTATTTTTATTTTATTATTAATTTAATTCTATTATTTATTAATATTA
*
332287 TTTTTATTTTTATCTTTATT-TTTATTTAAAATT-T-TTATTTATTAATATTA
1 TTTTTATTTTTAT-TTTATTATTAATTT--AATTCTATTATTTATTAATATTA
332337 TTTTTATT
1 TTTTTATT
332345 CTTTCTCAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
47 26 0.52
48 8 0.16
49 5 0.10
50 11 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (50 bp):
TTTTTATTTTTATTTTATTATTAATTTAATTCTATTATTTATTAATATTA
Found at i:332339 original size:19 final size:18
Alignment explanation
Indices: 332252--332344 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
332242 TTTATTTTTA
332252 TTTTATTATTAAT-TTAT
1 TTTTATTATTAATATTAT
* *
332269 TTCTATTATTTATATTTAT
1 TTTTATTATTAATA-TTAT
* *
332288 TTTTATT-TTTATCTTTAT
1 TTTTATTATTAAT-ATTAT
332306 TTTTA-T-TTAA-A--AT
1 TTTTATTATTAATATTAT
332319 TTTTATTTATTAATATTAT
1 TTTTA-TTATTAATATTAT
332338 TTTTATT
1 TTTTATT
332345 CTTTCTCAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.11
15 1 0.02
16 4 0.07
17 16 0.26
18 16 0.26
19 17 0.28
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTATTAATATTAT
Found at i:334023 original size:23 final size:23
Alignment explanation
Indices: 333996--334053 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
333986 TAACGTGGCA
333996 TCCAGTCAGCAACTTCTAGAAGG
1 TCCAGTCAGCAACTTCTAGAAGG
*
334019 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAACTTCTAGAAGG
*
334042 TCTAGTCAGCAA
1 TCCAGTCAGCAA
334054 TGATGAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
TCCAGTCAGCAACTTCTAGAAGG
Done.