Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002499.1 Kokia drynarioides strain JFW-HI SEQ_114655, 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: 92794
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:276 original size:23 final size:22
Alignment explanation
Indices: 200--318 Score: 92
Period size: 23 Copynumber: 5.5 Consensus size: 22
190 AAGTGCTGAG
200 TAAT-AGAGAGCACACAAAGTGC
1 TAATCAGAGAGCACACAAA-TGC
* *
222 TAAACAGAGAGTACACAAA-G-
1 TAATCAGAGAGCACACAAATGC
* *
242 T-A-C--TGAGCACACAAAGTGT
1 TAATCAGAGAGCACACAAA-TGC
261 TAATCAGAGAGCACACGAAATGC
1 TAATCAGAGAGCACAC-AAATGC
*
284 TAATTAGAGAGCACACACAATGC
1 TAATCAGAGAGCACACA-AATGC
307 TAAAT-AGAGAGC
1 T-AATCAGAGAGC
319 GCACTAGTGT
Statistics
Matches: 79, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
16 10 0.13
18 2 0.03
19 2 0.03
20 2 0.03
21 2 0.03
22 4 0.05
23 51 0.65
24 6 0.08
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (22 bp):
TAATCAGAGAGCACACAAATGC
Found at i:3648 original size:26 final size:26
Alignment explanation
Indices: 3619--3683 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
3609 TTCCTACAGT
3619 GACAATTTTGGGCAT-GCTCATGCAGC
1 GACAATTTTGGGCATCG-TCATGCAGC
* * *
3645 GACATTTTTGGACATCGTCATGCAGT
1 GACAATTTTGGGCATCGTCATGCAGC
3671 GACAATTTTGGGC
1 GACAATTTTGGGC
3684 GCAATTCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (26 bp):
GACAATTTTGGGCATCGTCATGCAGC
Found at i:13966 original size:9 final size:9
Alignment explanation
Indices: 13923--13971 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
13913 AAAATTTAAA
13923 TAAAATTAT
1 TAAAATTAT
* *
13932 TAAATTTTTT
1 TAAA-ATTAT
13942 TAAAATTAATT
1 TAAAATT-A-T
13953 TAAAATTAT
1 TAAAATTAT
13962 TAAAATTAT
1 TAAAATTAT
13971 T
1 T
13972 TTTTGAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 17 0.52
10 8 0.24
11 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAAAATTAT
Found at i:14321 original size:18 final size:18
Alignment explanation
Indices: 14298--14340 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
14288 TTACAAAATC
**
14298 ACAAGCACTGTACTGGGA
1 ACAAGCACAATACTGGGA
*
14316 ACAAGCTCAATACTGGGA
1 ACAAGCACAATACTGGGA
*
14334 AAAAGCA
1 ACAAGCA
14341 TGGGCTTTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (18 bp):
ACAAGCACAATACTGGGA
Found at i:14867 original size:9 final size:9
Alignment explanation
Indices: 14853--14901 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 9
14843 TTAAAAATAA
14853 TAATAATTT
1 TAATAATTT
14862 TAATAATTT
1 TAATAATTT
14871 TAAAATAATTT
1 T--AATAATTT
14882 TAAAATAATTT
1 T--AATAATTT
14893 TAATAATTT
1 TAATAATTT
14902 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 18 0.47
11 20 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATAATTT
Found at i:14867 original size:31 final size:31
Alignment explanation
Indices: 14829--14932 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 31
14819 ATTAAAATTA
14829 TTTAATAATTTTATTTAAAAATAATAATAAT
1 TTTAATAATTTTATTTAAAAATAATAATAAT
** ***
14860 TTTAATAATTTTAAAATAATTTTAA-AATAAT
1 TTTAATAATTTT-ATTTAAAAATAATAATAAT
14891 TTTAATAATTTATATTTTAAAAAATAACTTTAATAAT
1 TTTAATAATTT-TA-TTT-AAAAATAA---TAATAAT
14928 TTTAA
1 TTTAA
14933 AATCATTTGC
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
31 30 0.55
32 9 0.16
33 5 0.09
37 11 0.20
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTAATAATTTTATTTAAAAATAATAATAAT
Found at i:14879 original size:20 final size:20
Alignment explanation
Indices: 14854--14940 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
14844 TAAAAATAAT
14854 AATAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
14874 AATAATTTTAAAATAATTTT--
1 AATAATTTT--AATAATTTTAA
14894 AATAA-TTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTT--AA
*
14913 AATAACTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
*
14933 AATCATTT
1 AATAATTT
14941 GCTGACGTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
15 5 0.09
16 2 0.04
19 8 0.14
20 25 0.45
21 2 0.04
22 14 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:14929 original size:59 final size:60
Alignment explanation
Indices: 14820--14940 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 60
14810 AAATTGGAAA
* *
14820 TTAAAATTATTTAATAATTTTATTTAAAAATAATAATAATTTTAATAATTTTAAAATAATT
1 TTAAAATAATTTAATAATTTTATTT-AAAATAATAATAACTTTAATAATTTTAAAATAATT
* *
14881 TTAAAATAATTTTAATAATTTATATTT-TAA-AA-AATAACTTTAATAATTTTAAAATCATT
1 TTAAAATAA-TTTAATAATTT-TATTTAAAATAATAATAACTTTAATAATTTTAAAATAATT
14940 T
1 T
14941 GCTGACGTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
59 26 0.48
60 2 0.04
61 10 0.19
62 11 0.20
63 5 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (60 bp):
TTAAAATAATTTAATAATTTTATTTAAAATAATAATAACTTTAATAATTTTAAAATAATT
Found at i:25390 original size:12 final size:13
Alignment explanation
Indices: 25373--25402 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25363 ATATTTTTTG
25373 TTTTTA-ATTTAA
1 TTTTTACATTTAA
25385 TTTTTACATTTAA
1 TTTTTACATTTAA
25398 TTTTT
1 TTTTT
25403 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:25408 original size:13 final size:13
Alignment explanation
Indices: 25373--25414 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
25363 ATATTTTTTG
25373 TTTTTAATTTAA-
1 TTTTTAATTTAAT
25385 TTTTTACATTTAAT
1 TTTTTA-ATTTAAT
* *
25399 TTTTTTATTTTAT
1 TTTTTAATTTAAT
25412 TTT
1 TTT
25415 ATAGGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:29252 original size:52 final size:52
Alignment explanation
Indices: 29177--29518 Score: 506
Period size: 52 Copynumber: 6.6 Consensus size: 52
29167 ATAAAGAAAG
* * *
29177 GGTCTGATGACTATGAGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
29229 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
* * *
29281 GGTCCAATGACCATGTGTTATCATGAGTATATGAATCCTTTATGGATTAAAA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
29333 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
* * * *
29385 GGTCCAATGACCATGTGTCATCATGGGTATATGAATCCTTTAAGGATTAAAA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
* * * * * *
29437 GGTCCGATGACTATGTGTCATCCTGAGTATATGACTCCTTCACGGATTAAGA
1 GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
* *
29489 GGTCCGATGACTC-TATATCATCGTGAGTAT
1 GGTCCGATGAC-CATGTGTCATCGTGAGTAT
29519 CAAATGCGAA
Statistics
Matches: 264, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
52 264 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (52 bp):
GGTCCGATGACCATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAA
Found at i:32954 original size:11 final size:10
Alignment explanation
Indices: 32938--32971 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
32928 TTTGTTTTTC
32938 CTATTTGTCTT
1 CTATTT-TCTT
32949 CTATTTTGCTT
1 CTATTTT-CTT
32960 CTATTTTCTT
1 CTATTTTCTT
32970 CT
1 CT
32972 TTGATGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.09, C:0.21, G:0.06, T:0.65
Consensus pattern (10 bp):
CTATTTTCTT
Found at i:33950 original size:8 final size:8
Alignment explanation
Indices: 33937--33971 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
33927 ATTTGTTTTT
33937 AAAAAAGG
1 AAAAAAGG
33945 AAAAAAGG
1 AAAAAAGG
*
33953 AAAAAA-A
1 AAAAAAGG
33960 AAAAAAGG
1 AAAAAAGG
33968 AAAA
1 AAAA
33972 GAAAGAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:34585 original size:30 final size:30
Alignment explanation
Indices: 34549--34624 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
34539 ATTTTATTTA
* *
34549 AAAATTATATTTTGACTCCT-GAACTTCTTT
1 AAAATTAAATTTTAAC-CCTCGAACTTCTTT
*
34579 AAAATTAAATCTTAACCCTCGAACTTCTTT
1 AAAATTAAATTTTAACCCTCGAACTTCTTT
*
34609 -AAATTACA-TTTAACCC
1 AAAATTAAATTTTAACCC
34625 CTAAACTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.17
29 10 0.25
30 23 0.57
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTAAATTTTAACCCTCGAACTTCTTT
Found at i:34626 original size:29 final size:30
Alignment explanation
Indices: 34569--34624 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
34559 TTTGACTCCT
34569 GAACTTCTTTAAAATTAAATCTTAACCCTC
1 GAACTTCTTTAAAATTAAATCTTAACCCTC
*
34599 GAACTTCTTT-AAATTACAT-TTAACCC
1 GAACTTCTTTAAAATTAAATCTTAACCC
34625 CTAAACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.28
29 8 0.32
30 10 0.40
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (30 bp):
GAACTTCTTTAAAATTAAATCTTAACCCTC
Found at i:34653 original size:30 final size:30
Alignment explanation
Indices: 34609--34684 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
34599 GAACTTCTTT
34609 AAATTACA-TTTAACCCCTAAACTTTACCA
1 AAATTACATTTTAACCCCTAAACTTTACCA
* * *
34638 AAATTGCATTTTAACCCCTAAACTTTTCTA
1 AAATTACATTTTAACCCCTAAACTTTACCA
34668 AAATTACATTTT-ACCCC
1 AAATTACATTTTAACCCC
34685 AAAATTCTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 12 0.29
30 30 0.71
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTAACCCCTAAACTTTACCA
Found at i:34705 original size:28 final size:30
Alignment explanation
Indices: 34609--34707 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
34599 GAACTTCTTT
* *
34609 AAATTACA-TTTAACCCCTAAACTT-TACCA
1 AAATTACATTTTAACCCCTAAAATTCT-CTA
* * *
34638 AAATTGCATTTTAACCCCTAAACTTTTCTA
1 AAATTACATTTTAACCCCTAAAATTCTCTA
34668 AAATTACATTTT-ACCCC-AAAATTCTCTA
1 AAATTACATTTTAACCCCTAAAATTCTCTA
34696 AAACTT-CATTTT
1 AAA-TTACATTTT
34708 TTGACCCTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 18 0.29
29 14 0.23
30 29 0.47
31 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
AAATTACATTTTAACCCCTAAAATTCTCTA
Found at i:56631 original size:148 final size:147
Alignment explanation
Indices: 56023--56827 Score: 1107
Period size: 148 Copynumber: 5.4 Consensus size: 147
56013 TGATTAAACA
* * * *
56023 AAAATCATTATTTTACTTAAAAATTCAAATTTTTATTTCGAAATAGTT-AAAAAGATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* * *
56087 TGTTAAAAATTTAAACTTTTTGTTTAAAATAACCAAAAAACAGATTTCTATTTTTTTAAAAAAAA
66 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTT-T-TATTTTT---AAAAA
*
56152 TCTAAACTTTCTCTTTTTTAAAG
126 TATAAACTTTCTC-TTTTTAAAG
* * *
56175 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTT-GAAATTGTTAGAAAAAGTCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
56239 TGTTATAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAAATAGATTTTTATTTTTAAAAATAT
66 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACT--AAAAAACAGATTTTTATTTTTAAAAATAT
56304 AAACTTTCTCTTTTTTAAAG
129 AAACTTTCTC-TTTTTAAAG
* * *
56324 AAAATCACTATTTTACCTAAAAATCCAAATTTTTATTTTGAAATAGTTAAAAAAAAATCAAAACT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAAATCAAAACT
* *
56389 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-TTTTTTATTTTTAAAAATTTA
65 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
* * *
56453 AACTTTATTTTTTTAAAT
130 AACTTTCTCTTTTTAAAG
* *
56471 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
56536 TGTTAAAAATTTAAATTTTTTCTTTAAAATAATTAAAAAAACAGATTTTTATTTTTAAAAATATA
66 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACAGATTTTTATTTTTAAAAATATA
*
56601 AACTTCCTCTTTTTAAAG
130 AACTTTCTCTTTTTAAAG
*
56619 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
56684 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACAAATTTTTATTTTTAAAAATCTAA
66 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
*
56748 AATTTCTCTTTTTTTAAAG
131 ACTTTCTC--TTTTTAAAG
* * *
56767 AAAATCACTA-TTTGCTTAAAAAAATAATCAAAGCTTTTATTTCGAAATTGTTTAAAAAAAA
1 AAAATCACTATTTTACTT--AAAAAT--CCAAA-CTTTTATTTCGAAATAG-TTAAAAAAAA
56828 AACCAAAACA
Statistics
Matches: 587, Mismatches: 51, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
146 83 0.14
147 64 0.11
148 172 0.29
149 76 0.13
150 8 0.01
151 60 0.10
152 101 0.17
153 11 0.02
154 12 0.02
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (147 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
ACTTTCTCTTTTTAAAG
Found at i:57271 original size:3 final size:3
Alignment explanation
Indices: 57260--57314 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
57250 CCCTAAAAAA
* * *
57260 AAT AA- AAT AAT AAT AAA AAT AAT AAT AA- AAT AAT AAT AAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
57306 AAT AAT AAT
1 AAT AAT AAT
57315 TTGAACCCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:57276 original size:11 final size:11
Alignment explanation
Indices: 57260--57298 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
57250 CCCTAAAAAA
57260 AATAAAATAAT
1 AATAAAATAAT
57271 AATAAAAATAAT
1 AAT-AAAATAAT
57283 AATAAAATAAT
1 AATAAAATAAT
57294 AATAA
1 AATAA
57299 TGATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:57278 original size:20 final size:22
Alignment explanation
Indices: 57253--57298 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
57243 CATGAAACCC
57253 TAAAA-AA-AATAAAATAATAA
1 TAAAATAATAATAAAATAATAA
57273 TAAAAATAATAATAAAATAATAA
1 T-AAAATAATAATAAAATAATAA
57296 TAA
1 TAA
57299 TGATGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.04
21 4 0.17
22 4 0.17
23 14 0.61
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAATAATAATAAAATAATAA
Found at i:57739 original size:42 final size:42
Alignment explanation
Indices: 57691--58172 Score: 678
Period size: 42 Copynumber: 11.5 Consensus size: 42
57681 CCTCCTTGCT
** * *
57691 TAGGCCTCCGAATGCAATGAAAAGTAAATGGGCCTCCACACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * ** *
57733 TGGGCCTCTAAATGCAATGAAAAGTAAAAGGGTCTCTACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
57775 TGGGCCTCTAAATGCAATGAAAAGTAAATGGATCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
57817 TAGGCCTCTAAATGTAATGAAAAGTAAATTGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
57859 TAGGCCTCTAAATGCAACGAAAAGTAAATGAACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
57901 TGGGCCTCTAAATGCAATGAAAA-TTAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
*
57942 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
** *
57984 TAGGCCTCTAAATGTGATGAAAAGTAAATAGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
58026 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * * * *
58068 TAAGCCTCTGAATGCAATGAAAAATAAATGAACCTCCACACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * *
58110 TGGGCCTCTAAATTCAATGAAAAGTAAATGGACCTCGACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
58152 TAGGCCTCTAAATGCAATGAA
1 TAGGCCTCTAAATGCAATGAA
58173 TGCTTTCTTT
Statistics
Matches: 390, Mismatches: 49, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
41 38 0.10
42 352 0.90
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (42 bp):
TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
Found at i:58605 original size:34 final size:33
Alignment explanation
Indices: 58567--58635 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
58557 TTATCTTGCT
*
58567 TTCTC-TTTCTATTTTTTCTATTTTTTA-TTTTTTC
1 TTCTCTTTTCT-TTTTTT-T-TTTTGTACTTTTTTC
58601 TTCTCTTTTCTTTTTTTTTTTTGTACTTTTTTC
1 TTCTCTTTTCTTTTTTTTTTTTGTACTTTTTTC
58634 TT
1 TT
58636 GATTTAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 6 0.19
33 10 0.31
34 11 0.34
35 5 0.16
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.78
Consensus pattern (33 bp):
TTCTCTTTTCTTTTTTTTTTTTGTACTTTTTTC
Found at i:58609 original size:19 final size:18
Alignment explanation
Indices: 58578--58620 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
58568 TCTCTTTCTA
58578 TTTTTTCTATTTT-TTATT
1 TTTTTTCTATTTTCTT-TT
*
58596 TTTTCTTCTCTTTTCTTTT
1 TTTT-TTCTATTTTCTTTT
58615 TTTTTT
1 TTTTTT
58621 TTGTACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 14 0.64
20 2 0.09
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTATTTTCTTTT
Found at i:71957 original size:4 final size:4
Alignment explanation
Indices: 71950--71992 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
71940 ACAAATGAGC
* * * *
71950 GAAT GAAT GAAT GAAT GAGT GAGT GAGT GAGT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
71993 ATTGGGGCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:75620 original size:20 final size:20
Alignment explanation
Indices: 75583--75622 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
75573 GGGTTTATGA
* *
75583 TTTATCTTACTTTAAAATTC
1 TTTATCTAAATTTAAAATTC
*
75603 TTTATCTAAATTTTAAATTC
1 TTTATCTAAATTTAAAATTC
75623 GTTAAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATCTAAATTTAAAATTC
Found at i:76781 original size:147 final size:147
Alignment explanation
Indices: 76533--77290 Score: 1048
Period size: 147 Copynumber: 5.2 Consensus size: 147
76523 TGATTAAATA
* * * * *
76533 AAAATTACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAACTTT
1 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
76598 GTTAAAAATTTAAA-TTTTTCTTTAAAATAACT-AAAAACATATTTTATTTTTTTAAAAATCTAA
66 GTT-AAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTT-TATTTTTAAAAATCTAA
* *
76661 ATTTTCTCTTTTTTTAAAC
129 ACTTTCTCTTTTTTTAAAG
* * * *
76680 AAAATCATTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACAGTTAGAATAAATCAAAATTT
1 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
* * * *
76745 TGTTAAAATTTTAA-TTTTT-TTTAAAATAACTAAAAAAACATATTTTAATTATTAAAAATATAA
65 TGTTAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACATATTTTTATTTTTAAAAATCTAA
*
76808 ACTTTCTC-CTTTTTAAAG
129 ACTTTCTCTTTTTTTAAAG
* * *
76826 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * *
76891 GTTAAAATTTTAAACTTTTTCTGTAAAATATCTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
66 GTTAAAA-TTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
*
76956 CTTTTTCTTTTTTTAAA-
130 CTTTCTCTTTTTTTAAAG
* *
76973 AAAATCACTATTTTGCTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAGAACTTT
1 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
77038 GTTAAAAACTTAAACTTTTTCTTTAAAATAACTAAAAAAACATATTTTTATTTTTAAAAATATAA
66 GTT-AAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACATATTTTTATTTTTAAAAATCTAA
*
77103 ACTTTGT-TTTTTTTAAAG
129 ACTTTCTCTTTTTTTAAAG
* *
77121 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTT
1 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
77185 GTTAAAAGATTAAACTTTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTAA
66 GTTAAAA-TTTAAAC-TTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAA
77250 ACTTTCTC-TTTTTTAAAG
129 ACTTTCTCTTTTTTTAAAG
** *
77268 AAAATTGCTATTTTGCATAAAAA
1 AAAATCACTATTTTGCTTAAAAA
77291 ATAATAAAAG
Statistics
Matches: 542, Mismatches: 56, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
145 21 0.04
146 73 0.13
147 299 0.55
148 149 0.27
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (147 bp):
AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAAC
TTTCTCTTTTTTTAAAG
Found at i:77152 original size:295 final size:294
Alignment explanation
Indices: 76533--77290 Score: 1118
Period size: 295 Copynumber: 2.6 Consensus size: 294
76523 TGATTAAATA
* * * *
76533 AAAATTACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
76598 GTTAAAAATTTAAA-TTTTTCTTTAAAATAACT-AAAAACATATTTTATTTTTTTAAAAATCTAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTT-TATTTTTAAAAATCTAA
*
76661 A-TTTTCTCTTTTTTTAAACAAAATCATTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACA
130 ACTTTT-TCTTTTTTTAAACAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACA
* * * *
76725 GTTAGAATAAATCAAAATTTTGTTAAAATTTTAATTTTTTTTAAAATAACTAAAAAAACATATTT
194 GTTAGAAAAAATCAAAACTTTGTTAAAACTTAAATTTTTTTTAAAATAACTAAAAAAACATATTT
76790 TAATTATTAAAAATATAAACTTTCTCCTTTTTAAAG
259 TAATTATTAAAAATATAAACTTTCTCCTTTTTAAAG
* *
76826 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *
76891 GTTAAAATTTTAAACTTTTTCTGTAAAATATCTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
* *
76956 CTTTTTCTTTTTTTAAA-AAAATCACTATTTTGCTTAAAAATCTAAACTTTTATTTCGAAATAGT
131 CTTTTTCTTTTTTTAAACAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACAGT
*
77020 TA-AAAAAATCAGAACTTTGTTAAAAACTTAAACTTTTTCTTTAAAATAACTAAAAAAACATATT
196 TAGAAAAAATCAAAACTTTGTT-AAAACTTAAA-TTTTT-TTTAAAATAACTAAAAAAACATATT
* * * **
77084 TTTATTTTTAAAAATATAAACTTTGTTTTTTTTAAAG
258 TTAATTATTAAAAATATAAACTTTCTCCTTTTTAAAG
*
77121 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
77185 GTTAAAAGA-TTAAACTTTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTA
66 GTTAAAA-ATTTAAAC-TTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTA
* * ** *
77249 AACTTTCTC-TTTTTTAAAGAAAATTGCTATTTTGCATAAAAA
129 AACTTTTTCTTTTTTTAAACAAAATCACTATTTTGCTTAAAAA
77291 ATAATAAAAG
Statistics
Matches: 420, Mismatches: 36, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
292 16 0.04
293 126 0.30
294 88 0.21
295 190 0.45
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (294 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
CTTTTTCTTTTTTTAAACAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACAGT
TAGAAAAAATCAAAACTTTGTTAAAACTTAAATTTTTTTTAAAATAACTAAAAAAACATATTTTA
ATTATTAAAAATATAAACTTTCTCCTTTTTAAAG
Found at i:77372 original size:295 final size:284
Alignment explanation
Indices: 76533--77384 Score: 952
Period size: 295 Copynumber: 2.9 Consensus size: 284
76523 TGATTAAATA
* * * *
76533 AAAATTACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
76598 GTTAAAAATTTAAA-TTTTTCTTTAAAATAACTAAAAACATAT-TTTATT-TTTTTAAAAATCTA
66 GTTAAAAA-TTAAACTTTTTCTTTAAAATAACTAAAAA-ATATATTT-TTATTTTTAAAAATCTA
* * * *
76660 AATTTTCTCTTTTTTTAAACAAAATCATTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAACA
128 AACTTTCTCTTTTTTTAAA-AAAATCACTATTTTGCTTAAAAAT-TAAACTTTTATTTCGAAATA
* *
76725 GTTAGAATAAATCAAAATTTTGTTAAAATTTTAA-TTTTTT-TTAAAATAACTAAAAAAACATAT
191 GTTA-AAAAAATCAAAA-TTT-TTAAAAATTTAACTTTTTTCTT---A-AA--AAAAAAACATAT
* *
76788 TTTAATTATTAAAAATATAAACTTTCTCCTTTTTAAAG
247 TTTTATTTTTAAAAATATAAACTTTCTCCTTTTTAAAG
* *
76826 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * * *
76891 GTTAAAATTTTAAACTTTTTCTGTAAAATATCTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
66 GTTAAAA-ATTAAACTTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTAAA
*
76956 CTTTTTCTTTTTTTAAAAAAATCACTATTTTGCTTAAAAATCTAAACTTTTATTTCGAAATAGTT
130 CTTTCTCTTTTTTTAAAAAAATCACTATTTTGCTTAAAAAT-TAAACTTTTATTTCGAAATAGTT
* *
77021 AAAAAAATCAGAACTTTGTTAAAAACTTAAAC-TTTTTCTTTAAAATAACTAAAAAAACATATTT
194 AAAAAAATCA-AAATTT-TTAAAAA-TTTAACTTTTTTC-TT---A-AA--AAAAAAACATATTT
* **
77085 TTATTTTTAAAAATATAAACTTTGTTTTTTTTAAAG
249 TTATTTTTAAAAATATAAACTTTCTCCTTTTTAAAG
*
77121 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
77185 GTTAAAAGATTAAACTTTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTAA
66 GTTAAAA-ATTAAAC-TTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTAA
** * *
77250 ACTTTCTC-TTTTTTAAAGAAAATTGCTATTTTGCATAAAAAATAATAAAAGATTTTATTTCGAA
129 ACTTTCTCTTTTTTTAAA-AAAATCACTATTTTGC-TTAAAAAT--T-AAA-CTTTTATTTCGAA
* * * * *
77314 ATTGTTTAAAAAGAACCAAAATATTTTCCAAAA-TCAAGCTATTTTTCTTAAAAAAAAAA-A-AC
188 ATAG-TTAAAAA-AATCAAAAT-TTTT-AAAAATTTAA-CT-TTTTTCTTAAAAAAAAAACATAT
77376 TTTTATTTT
247 TTTTATTTT
77385 AGCAAATGGA
Statistics
Matches: 491, Mismatches: 46, Indels: 44
0.85 0.08 0.08
Matches are distributed among these distances:
292 18 0.04
293 142 0.29
294 94 0.19
295 174 0.35
296 7 0.01
297 3 0.01
298 4 0.01
299 18 0.04
300 13 0.03
301 12 0.02
302 6 0.01
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (284 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTAAACTTTTTCTTTAAAATAACTAAAAAATATATTTTTATTTTTAAAAATCTAAAC
TTTCTCTTTTTTTAAAAAAATCACTATTTTGCTTAAAAATTAAACTTTTATTTCGAAATAGTTAA
AAAAATCAAAATTTTTAAAAATTTAACTTTTTTCTTAAAAAAAAAACATATTTTTATTTTTAAAA
ATATAAACTTTCTCCTTTTTAAAG
Found at i:77666 original size:12 final size:14
Alignment explanation
Indices: 77645--77678 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
77635 ATTAATCTTG
77645 TTTATTTGTAAT-T
1 TTTATTTGTAATGT
77658 TTT-TTTGTAATGT
1 TTTATTTGTAATGT
77671 TTTATTTG
1 TTTATTTG
77679 ATCTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 7 0.37
14 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (14 bp):
TTTATTTGTAATGT
Found at i:81605 original size:16 final size:16
Alignment explanation
Indices: 81570--81603 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
81560 TATACTTAAC
81570 AAAGCATTTGGGAGCG
1 AAAGCATTTGGGAGCG
81586 AAAGCATTTGGGAG-G
1 AAAGCATTTGGGAGCG
81601 AAA
1 AAA
81604 AGGAGCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.38, C:0.09, G:0.35, T:0.18
Consensus pattern (16 bp):
AAAGCATTTGGGAGCG
Found at i:81917 original size:23 final size:25
Alignment explanation
Indices: 81891--81936 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
81881 CCAATTAGGG
81891 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
81914 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
81937 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:85136 original size:11 final size:11
Alignment explanation
Indices: 85103--85146 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
85093 AAATAGTATA
*
85103 TTTATTTTCAT
1 TTTATTTTTAT
85114 TTTCATTTTTAT
1 TTT-ATTTTTAT
85126 TTT-TATTTTAT
1 TTTAT-TTTTAT
85137 TTTATTTTTA
1 TTTATTTTTA
85147 ATTATGCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 1 0.03
11 17 0.59
12 11 0.38
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:85165 original size:6 final size:6
Alignment explanation
Indices: 85103--85146 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
85093 AAATAGTATA
* *
85103 TTTATT TTCATT TTCATT TTTATT TTTA-T TTTA-T TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
85147 ATTATGCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:86115 original size:19 final size:18
Alignment explanation
Indices: 86093--86134 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
86083 AAAAAAGTCG
86093 AAAAGAAAATTTGAAAAAA
1 AAAAGAAAA-TTGAAAAAA
*
86112 AAAAGAAAATTGAGAAAA
1 AAAAGAAAATTGAAAAAA
86130 AAAAG
1 AAAAG
86135 GAAGAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (18 bp):
AAAAGAAAATTGAAAAAA
Found at i:87211 original size:23 final size:25
Alignment explanation
Indices: 87185--87230 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
87175 CCAATTAAGG
87185 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
87208 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
87231 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:92534 original size:19 final size:19
Alignment explanation
Indices: 92510--92552 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
92500 AAACATAAAT
92510 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
92529 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
92548 TAAAT
1 TAAAT
92553 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:92771 original size:2 final size:2
Alignment explanation
Indices: 92764--92794 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92754 CATACTCTAA
92764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.