Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015171.1 Kokia drynarioides strain JFW-HI SEQ_130215, 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: 239922
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 316 characters in sequence are not A, C, G, or T
Found at i:4621 original size:204 final size:203
Alignment explanation
Indices: 4247--4641 Score: 501
Period size: 204 Copynumber: 1.9 Consensus size: 203
4237 ACATGGCGTG
* * * **
4247 ACACATGCTTTCCTCGGTCCTTCTCAAAGGTTGGGTTTGAATTCCTCATCCCCTATTATACATAC
1 ACACATGCTTTCCCCAGCCCTAATCAAAGGTTGGGTTTGAATTCCTCATCCCCTATTATACATAC
* *
4312 ACATACATCTATAGTAGGAATCACCGTGTCACCGAACTATTACTCAATTCCCGAGAAACATGTCA
66 ACATACATCTATAGTAGGAATCACCATATCACCGAACTATTACTCAATTCCCGAGAAACATGTCA
* **
4377 GATAAGATGTGCAGTGCAACTGCTTATACAACCCAAGAGGCCTTCATTTTCCTAACCAATGCGGG
131 GATAAGATGTGCAGTGCAACTGCTTATAC-ACCAAAGAGGCCTTCACGTTCCTAACCAATGCGGG
4442 ATTCCTTAA
195 ATTCCTTAA
*
4451 ACACATGCTTTCCCCAGCCCTAATCAAAGGTTGGGTTTGAATTCCTCATCTCCTGA-TATACA-A
1 ACACATGCTTTCCCCAGCCCTAATCAAAGGTTGGGTTTGAATTCCTCATCCCCT-ATTATACATA
* * * * ** *
4514 TCACATATATTTATAGTAGGAATCACCATATCATTCGGACTATTACTCAATT-TTGTGAAACATG
65 -CACATACATCTATAGTAGGAATCACCATATCA-CCGAACTATTACTCAATTCCCGAGAAACATG
* * * * *
4578 TCTGATAAGATGTGTAGTGTAACTGTCTATATGC-CCAAAGAGGCCTTCACGTTCCTATCCAATG
128 TCAGATAAGATGTGCAGTGCAACTG-CT-TATACACCAAAGAGGCCTTCACGTTCCTAACCAATG
4642 TGGTATTAAC
Statistics
Matches: 163, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
203 1 0.01
204 139 0.85
205 19 0.12
206 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (203 bp):
ACACATGCTTTCCCCAGCCCTAATCAAAGGTTGGGTTTGAATTCCTCATCCCCTATTATACATAC
ACATACATCTATAGTAGGAATCACCATATCACCGAACTATTACTCAATTCCCGAGAAACATGTCA
GATAAGATGTGCAGTGCAACTGCTTATACACCAAAGAGGCCTTCACGTTCCTAACCAATGCGGGA
TTCCTTAA
Found at i:10645 original size:112 final size:112
Alignment explanation
Indices: 10507--10722 Score: 389
Period size: 112 Copynumber: 1.9 Consensus size: 112
10497 AAAAGTTAGA
* *
10507 GTTATTTAATTTTTTGTAATAGTATAAGAACTGAAATATAATAGAAGGATCAATTTGAAAAATTA
1 GTTATTTAATTTTTTGTAATAATATAAGAACTGAAATATAATAGAAGGATAAATTTGAAAAATTA
10572 ATAATTTTACATATTTTTAAAATTTGTA-ATACACATCACAAGATAGG
66 ATAATTTTACATATTTTTAAAATTTG-AGATACACATCACAAGATAGG
*
10619 GTTATTTGATTTTTTGTAATAATATAAGAACTGAAATATAATAGAAGGATAAATTTGAAAAATTA
1 GTTATTTAATTTTTTGTAATAATATAAGAACTGAAATATAATAGAAGGATAAATTTGAAAAATTA
10684 ATAATTTTACATATTTTTAAAATTTGAGATACACATCAC
66 ATAATTTTACATATTTTTAAAATTTGAGATACACATCAC
10723 GTAAATCATA
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
111 1 0.01
112 99 0.99
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (112 bp):
GTTATTTAATTTTTTGTAATAATATAAGAACTGAAATATAATAGAAGGATAAATTTGAAAAATTA
ATAATTTTACATATTTTTAAAATTTGAGATACACATCACAAGATAGG
Found at i:29966 original size:20 final size:20
Alignment explanation
Indices: 29941--29985 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
29931 AATCATTGGA
29941 TATTTATTGTTAGTATTTTT
1 TATTTATTGTTAGTATTTTT
29961 TATTTATTGTTAGTATTTTT
1 TATTTATTGTTAGTATTTTT
29981 TATTT
1 TATTT
29986 TGAACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (20 bp):
TATTTATTGTTAGTATTTTT
Found at i:30018 original size:21 final size:20
Alignment explanation
Indices: 29992--30033 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
29982 ATTTTGAACA
29992 TTAAATTCTGAATCACAAATT
1 TTAAATTCTGAA-CACAAATT
*
30013 TTAAATTCTGAACTCAAATT
1 TTAAATTCTGAACACAAATT
30033 T
1 T
30034 GAGTTTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (20 bp):
TTAAATTCTGAACACAAATT
Found at i:32664 original size:10 final size:10
Alignment explanation
Indices: 32649--32682 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
32639 TAAAAATTAA
32649 ATTTTTTTAT
1 ATTTTTTTAT
32659 ATTTTTTTAT
1 ATTTTTTTAT
*
32669 ATTTTTTAAT
1 ATTTTTTTAT
32679 ATTT
1 ATTT
32683 ATAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:32993 original size:18 final size:17
Alignment explanation
Indices: 32970--33022 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
32960 TTTTGAGTTA
32970 AATTAATCGAGTTTTTTG
1 AATTAATCGA-TTTTTTG
*
32988 AATTAATCGAATTATTTG
1 AATTAATCG-ATTTTTTG
*
33006 AATCAACTCGATTTTTT
1 AATTAA-TCGATTTTTT
33023 TTCGAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.47
Consensus pattern (17 bp):
AATTAATCGATTTTTTG
Found at i:35274 original size:12 final size:13
Alignment explanation
Indices: 35251--35297 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
35241 AATATCTCTC
35251 TATTATTTTAATT
1 TATTATTTTAATT
35264 TATTATTTAATAATTT
1 TATTATTT--TAA-TT
35280 TATATATTTT-ATT
1 TAT-TATTTTAATT
35293 TATTA
1 TATTA
35298 AAATTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 13 0.43
14 1 0.03
15 4 0.13
16 5 0.17
17 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTTTAATT
Found at i:35302 original size:24 final size:25
Alignment explanation
Indices: 35262--35310 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
35252 ATTATTTTAA
35262 TTTATTATTTAATAATTTTATATAT
1 TTTATTATTTAATAATTTTATATAT
35287 TTTATT-TATTAA-AATTTTATATAT
1 TTTATTAT-TTAATAATTTTATATAT
35311 AATCATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTATTATTTAATAATTTTATATAT
Found at i:43239 original size:31 final size:32
Alignment explanation
Indices: 43183--43248 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
43173 TATTCATTTC
* *
43183 TTTTAATGTGTACAATTTAATCAAAATCAAAA
1 TTTTAATGTATACAATTTAACCAAAATCAAAA
*
43215 TTTT-ATGTATACATTTTAACCAAAATCAAAA
1 TTTTAATGTATACAATTTAACCAAAATCAAAA
43246 TTT
1 TTT
43249 AATACGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (32 bp):
TTTTAATGTATACAATTTAACCAAAATCAAAA
Found at i:45184 original size:18 final size:17
Alignment explanation
Indices: 45161--45198 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
45151 TAAATACATT
45161 ATTAAAAAATTATAAAAA
1 ATTAAAAAATTA-AAAAA
*
45179 ATTAAAATATTAAAAAA
1 ATTAAAAAATTAAAAAA
45196 ATT
1 ATT
45199 GATTCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAAAAATTAAAAAA
Found at i:47656 original size:2 final size:2
Alignment explanation
Indices: 47649--47697 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
47639 ACAATTAATT
*
47649 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47691 TC TC TC T
1 TC TC TC T
47698 TTTTGTTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:55426 original size:17 final size:17
Alignment explanation
Indices: 55402--55481 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
55392 ACCCAACAGG
*
55402 ATTTAAATTCATTTTAA
1 ATTTAAATTTATTTTAA
*
55419 AATTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
*
55436 GTTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
55453 GTTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
55470 ATTTAAAGTTTA
1 ATTTAAA-TTTA
55482 AATCTATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
17 52 0.93
18 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:55478 original size:24 final size:23
Alignment explanation
Indices: 55446--55494 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
55436 GTTTAAATTT
* *
55446 ATTTTAAGTTTAAATTTATTATAA
1 ATTTAAAGTTTAAATCTATT-TAA
55470 ATTTAAAGTTTAAATCTATTTAA
1 ATTTAAAGTTTAAATCTATTTAA
55493 AT
1 AT
55495 CAAGTCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTAAAGTTTAAATCTATTTAA
Found at i:55483 original size:7 final size:6
Alignment explanation
Indices: 55414--55484 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
55404 TTAAATTCAT
* * * * *
55414 TTTAAA ATTAAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
55460 TTT--A TTATAAA TTTAAA GTTTAAA T
1 TTTAAA TT-TAAA TTTAAA -TTTAAA T
55485 CTATTTAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 30 0.59
7 9 0.18
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:56168 original size:3 final size:3
Alignment explanation
Indices: 56160--56227 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
56150 ATAACTGTTT
** * *
56160 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TGC T-T TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* *
56205 TAA TAA TTA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
56228 TTGTTATTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 1 0.02
3 51 0.93
4 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:56174 original size:21 final size:22
Alignment explanation
Indices: 56134--56174 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56124 TTTTCAAAAC
*
56134 GTTTTAATAACTATTAATAACT
1 GTTTTAATAACTAATAATAACT
56156 GTTTTAATAA-TAATAATAA
1 GTTTTAATAACTAATAATAA
56175 TAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (22 bp):
GTTTTAATAACTAATAATAACT
Found at i:56186 original size:33 final size:33
Alignment explanation
Indices: 56138--56211 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
56128 CAAAACGTTT
* * *
56138 TAATAACTATTAATAACTGTTTTAATAATAATAA
1 TAATAA-TAATAATAAATGCTTTAATAATAATAA
*
56172 TAATAATAATAATAAATGCTTTAATGATAATAA
1 TAATAATAATAATAAATGCTTTAATAATAATAA
56205 TAATAAT
1 TAATAAT
56212 TATTATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (33 bp):
TAATAATAATAATAAATGCTTTAATAATAATAA
Found at i:56196 original size:24 final size:24
Alignment explanation
Indices: 56168--56227 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
56158 TTTAATAATA
*
56168 ATAATAATAATAATAATAAATGCTT
1 ATAATAATAATAATAAT-AATGATT
* *
56193 -TAATGATAATAATAATAATTATT
1 ATAATAATAATAATAATAATGATT
56216 ATAATAATAATA
1 ATAATAATAATA
56228 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATAATAATAATAATAATGATT
Found at i:56237 original size:3 final size:3
Alignment explanation
Indices: 56226--56260 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
56216 ATAATAATAA
*
56226 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT T
56261 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56664 original size:64 final size:66
Alignment explanation
Indices: 56556--56751 Score: 274
Period size: 64 Copynumber: 3.0 Consensus size: 66
56546 TGTACCAGCA
*
56556 GGTGACGGATGTCGAAGCATGGTGGTCACACGCGCC-AATCGACGAGGCGCGTGCAACGGAGCCA
1 GGTGACGGACGTCGAAGCATGGTGGTCACACGCGCCGAATCGACGAGGCGCGTGCAACGGAGCCA
56620 C
66 C
*
56621 GGTGACGGACGT-GAAGCATGGTGGTCACACGCGCCGACT-GACGAGGCGCGTGCAACGGAGCCA
1 GGTGACGGACGTCGAAGCATGGTGGTCACACGCGCCGAATCGACGAGGCGCGTGCAACGGAGCCA
56684 C
66 C
* * * * * * *
56685 GGTGGTCGGACGTCGAAGCATGGTGGTCACGCACACCG-GTCGACGAGGCGCTTGCAGCGGAGCC
1 GGT-GACGGACGTCGAAGCATGGTGGTCACACGCGCCGAATCGACGAGGCGCGTGCAACGGAGCC
56749 AC
65 AC
56751 G
1 G
56752 ATGGCCGGAC
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
64 51 0.43
65 22 0.19
66 45 0.38
ACGTcount: A:0.21, C:0.28, G:0.39, T:0.12
Consensus pattern (66 bp):
GGTGACGGACGTCGAAGCATGGTGGTCACACGCGCCGAATCGACGAGGCGCGTGCAACGGAGCCA
C
Found at i:56746 original size:66 final size:65
Alignment explanation
Indices: 56559--56762 Score: 268
Period size: 66 Copynumber: 3.1 Consensus size: 65
56549 ACCAGCAGGT
* *
56559 GACGGATGTCGAAGCATGGTGGTCACACGCGCCAATCGACGAGGCGCGTGCAACGGAGCCACGGT
1 GACGGACGTCGAAGCATGGTGGTCACACGCGCC-GTCGACGAGGCGCGTGCAACGGAGCCACGGT
56624 -
65 G
*
56624 GACGGACGT-GAAGCATGGTGGTCACACGCGCCGACTGACGAGGCGCGTGCAACGGAGCCACGGT
1 GACGGACGTCGAAGCATGGTGGTCACACGCGCCGTC-GACGAGGCGCGTGCAACGGAGCCACGGT
56688 G
65 G
* * * * * * *
56689 GTCGGACGTCGAAGCATGGTGGTCACGCACACCGGTCGACGAGGCGCTTGCAGCGGAGCCACGAT
1 GACGGACGTCGAAGCATGGTGGTCACACGCGCC-GTCGACGAGGCGCGTGCAACGGAGCCACGGT
56754 G
65 G
*
56755 GCCGGACG
1 GACGGACG
56763 GCTTGGGAGT
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 51 0.41
65 16 0.13
66 53 0.43
67 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.39, T:0.12
Consensus pattern (65 bp):
GACGGACGTCGAAGCATGGTGGTCACACGCGCCGTCGACGAGGCGCGTGCAACGGAGCCACGGTG
Found at i:57506 original size:30 final size:29
Alignment explanation
Indices: 57399--57567 Score: 207
Period size: 29 Copynumber: 5.8 Consensus size: 29
57389 CCTTAATCTA
** * *
57399 TCCAAAAATTTGATTTTCACCCCTGAACT
1 TCCAAAAATTCCATTTTGACCCCTAAACT
* *
57428 TCCAAAAATTCCTTTTTGATCCCTAAACT
1 TCCAAAAATTCCATTTTGACCCCTAAACT
57457 TCCAAAAATTCCATTTTGACCCCTAAACT
1 TCCAAAAATTCCATTTTGACCCCTAAACT
* *
57486 TCCAAAAATTCCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCA-TTTTGACCCCTAAACT
*
57516 TCCAAAAATTCCAATTTT-ACCCTCGAAACT
1 TCCAAAAATTCC-ATTTTGACCC-CTAAACT
57546 TCCAAAAATTCCAATTTT-ACCC
1 TCCAAAAATTCC-ATTTTGACCC
57568 TCAGGTGTCC
Statistics
Matches: 126, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
29 66 0.52
30 59 0.47
31 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTGACCCCTAAACT
Found at i:57568 original size:30 final size:31
Alignment explanation
Indices: 57424--57569 Score: 200
Period size: 30 Copynumber: 4.9 Consensus size: 31
57414 TTCACCCCTG
*
57424 AACTTCCAAAAATTCC-TTTTTGATCCCT--A
1 AACTTCCAAAAATTCCAATTTTGA-CCCTCGA
*
57453 AACTTCCAAAAATTCC-ATTTTGACCC-CTA
1 AACTTCCAAAAATTCCAATTTTGACCCTCGA
*
57482 AACTTCCAAAAATTCCATTTTTGA-CCTCGA
1 AACTTCCAAAAATTCCAATTTTGACCCTCGA
57512 AACTTCCAAAAATTCCAATTTT-ACCCTCGA
1 AACTTCCAAAAATTCCAATTTTGACCCTCGA
57542 AACTTCCAAAAATTCCAATTTT-ACCCTC
1 AACTTCCAAAAATTCCAATTTTGACCCTC
57570 AGGTGTCCAA
Statistics
Matches: 108, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
28 3 0.03
29 42 0.39
30 63 0.58
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33
Consensus pattern (31 bp):
AACTTCCAAAAATTCCAATTTTGACCCTCGA
Found at i:57650 original size:29 final size:29
Alignment explanation
Indices: 57399--57651 Score: 184
Period size: 29 Copynumber: 8.7 Consensus size: 29
57389 CCTTAATCTA
** *
57399 TCCAAAAATTTGATTTTCACCC-CTGAACT
1 TCCAAAAATTCCATTTTTACCCTC-GAACT
*
57428 TCCAAAAATTCC-TTTTTGATCCCT-AAACT
1 TCCAAAAATTCCATTTTT-A-CCCTCGAACT
* *
57457 TCCAAAAATTCCATTTTGACCC-CTAAACT
1 TCCAAAAATTCCATTTTTACCCTC-GAACT
57486 TCCAAAAATTCCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCTCG-AACT
*
57516 TCCAAAAATTCCAATTTTACCCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCG-AACT
* **
57546 TCCAAAAATTCCAATTTTACCCTC-AGGT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
* *
57574 GTCCAAAAACTCCATTTTCGA-CCTCGAAAC-
1 -TCCAAAAATTCCATTTT-TACCCTCG-AACT
* * *
57604 TCTC-AAAATTACACTTTTACCCTTGAA-T
1 TC-CAAAAATTCCATTTTTACCCTCGAACT
*
57632 GTCTAAAAATTCCATTTTTA
1 -TCCAAAAATTCCATTTTTA
57652 AACCCCAAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
28 12 0.07
29 103 0.57
30 66 0.36
31 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTCGAACT
Found at i:58058 original size:96 final size:96
Alignment explanation
Indices: 57958--58132 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
57948 ATAATATTCT
* **
57958 TTTA-TTTCGAGTTTCAAAAATTTGTGCCTTAACTTTCTAGGTGCAATTTTTCTTCAAATCGAAA
1 TTTATTTTCGAGTTTCAAAAA-TTGTGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAA
58022 TAATCGAATACCCTTAATCGAGGCAATGTTTC
65 TAATCGAATACCCTTAATCGAGGCAATGTTTC
* * * *
58054 TTTATTTTCGATTTTGAAATATTGTGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGAT
1 TTTATTTTCGAGTTTCAAAAATTGTGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAAT
*
58119 AATCGAATATCCTT
66 AATCGAATACCCTT
58133 TTCCCAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
96 57 0.81
97 13 0.19
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (96 bp):
TTTATTTTCGAGTTTCAAAAATTGTGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAAT
AATCGAATACCCTTAATCGAGGCAATGTTTC
Found at i:69780 original size:2 final size:2
Alignment explanation
Indices: 69773--69797 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
69763 AACTTGTCTC
69773 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 A
69798 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73272 original size:2 final size:2
Alignment explanation
Indices: 73265--73295 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73255 TAAGAATTTA
73265 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
73296 AACTCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76412 original size:21 final size:21
Alignment explanation
Indices: 76370--76412 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
76360 TAATTTATAT
* * * *
76370 TTTATAATTTTTAAATATTAA
1 TTTAAAATTTTAAAAAAATAA
76391 TTTAAAATTTTAAAAAAATAA
1 TTTAAAATTTTAAAAAAATAA
76412 T
1 T
76413 AAAACTTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAAATTTTAAAAAAATAA
Found at i:77982 original size:18 final size:18
Alignment explanation
Indices: 77930--77986 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
77920 TTATACATTT
*
77930 TATATATACATACATACA
1 TATATATACATACATATA
* *
77948 CATATATACGTACATATA
1 TATATATACATACATATA
77966 TATATATACATACATATA
1 TATATATACATACATATA
77984 TAT
1 TAT
77987 GGTGTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (18 bp):
TATATATACATACATATA
Found at i:77986 original size:14 final size:14
Alignment explanation
Indices: 77933--77983 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
77923 TACATTTTAT
*
77933 ATATACATACATAC
1 ATATATATACATAC
* *
77947 ACATATATACGTAC
1 ATATATATACATAC
*
77961 ATATATATATATAC
1 ATATATATACATAC
*
77975 ATACATATA
1 ATATATATA
77984 TATGGTGTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:81524 original size:17 final size:16
Alignment explanation
Indices: 81502--81544 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
81492 TTTACTCAAA
81502 TGATAAGTATTTTTTGT
1 TGATAA-TATTTTTTGT
*
81519 TGATAATTTTTTTTG-
1 TGATAATATTTTTTGT
*
81534 TGTTAATATTT
1 TGATAATATTT
81545 GATACACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (16 bp):
TGATAATATTTTTTGT
Found at i:81964 original size:1 final size:1
Alignment explanation
Indices: 81921--81945 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
81911 ATTCAATCAA
81921 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
81946 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:84117 original size:3 final size:3
Alignment explanation
Indices: 84109--84136 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
84099 GCATACTTCT
84109 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
84137 ATTTTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:84340 original size:28 final size:29
Alignment explanation
Indices: 84282--84348 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
84272 TGAGTTATAA
*
84282 ATTTTTAAGAAATTAAATATAATTTTATT
1 ATTTTTAAAAAATTAAATATAATTTTATT
84311 ATTTTTTAAAATAATTAAATA-AA-TTT-TT
1 A-TTTTTAAAA-AATTAAATATAATTTTATT
84339 ATTTTTAAAA
1 ATTTTTAAAA
84349 GTTTTATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 9 0.26
28 3 0.09
29 4 0.11
30 10 0.29
31 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
ATTTTTAAAAAATTAAATATAATTTTATT
Found at i:86442 original size:21 final size:22
Alignment explanation
Indices: 86401--86442 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
86391 AATTAAAATT
*
86401 ATTATTAAATTTATCATAAGAA
1 ATTATTAAATTTATCAAAAGAA
86423 ATTA-TAAATTCTAT-AAAAGA
1 ATTATTAAATT-TATCAAAAGA
86443 GACCAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
ATTATTAAATTTATCAAAAGAA
Found at i:86717 original size:30 final size:30
Alignment explanation
Indices: 86666--86725 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
86656 ACAGGTGGAC
86666 TTAAATTTTAAAATGTGAAAAA-TATAGGGA
1 TTAAATTTTAAAATGTGAAAAAGTAT-GGGA
*
86696 TTAAATTTTAAATAT-TTAAAAAGTATGGGA
1 TTAAATTTTAAA-ATGTGAAAAAGTATGGGA
86726 ACTTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (30 bp):
TTAAATTTTAAAATGTGAAAAAGTATGGGA
Found at i:93458 original size:109 final size:109
Alignment explanation
Indices: 93267--93484 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
93257 TAAATAACCA
*
93267 CATGCATGACTGTACTAAGCAACAAATCAATAGAATTAATCACTAAACAAAATTCCCACAATTAT
1 CATGCATGACTGTACTAAGCAACAAATCAATAGAACTAATCACTAAACAAAATTCCCACAATTAT
93332 TTAATAATGAGAAAAAAGACATACCAGCCATGCAGCTTCATTTT
66 TTAATAATGAGAAAAAAGACATACCAGCCATGCAGCTTCATTTT
93376 CATGCATGACTGTACTAAGCAACAAATCAATAGAACTAATCACTAAACAAAATTCCCACAATTAT
1 CATGCATGACTGTACTAAGCAACAAATCAATAGAACTAATCACTAAACAAAATTCCCACAATTAT
93441 TTAATAATGAGAAAAAAGACATACCAGCCATGCAGCTTCATTTT
66 TTAATAATGAGAAAAAAGACATACCAGCCATGCAGCTTCATTTT
93485 GAAGTACAGA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (109 bp):
CATGCATGACTGTACTAAGCAACAAATCAATAGAACTAATCACTAAACAAAATTCCCACAATTAT
TTAATAATGAGAAAAAAGACATACCAGCCATGCAGCTTCATTTT
Found at i:95792 original size:13 final size:13
Alignment explanation
Indices: 95774--95838 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
95764 AATTTAGAAT
95774 TACTTTTGAAAAG
1 TACTTTTGAAAAG
**
95787 TACTTTAAAAAATG
1 TACTTTTGAAAA-G
*
95801 T--TTTGGAAAAG
1 TACTTTTGAAAAG
*
95812 TGAC-TTTGAAAAA
1 T-ACTTTTGAAAAG
95825 TACTTTTGAAAAG
1 TACTTTTGAAAAG
95838 T
1 T
95839 TTAGTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
11 2 0.05
12 9 0.22
13 27 0.68
14 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:95824 original size:26 final size:25
Alignment explanation
Indices: 95774--95838 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
95764 AATTTAGAAT
95774 TACTTTTGAAAAGTACTTTAAAAAA
1 TACTTTTGAAAAGTACTTTAAAAAA
* *
95799 T-GTTTTGGAAAAGTGACTTTGAAAAA
1 TACTTTT-GAAAAGT-ACTTTAAAAAA
95825 TACTTTTGAAAAGT
1 TACTTTTGAAAAGT
95839 TTAGTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 18 0.53
27 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (25 bp):
TACTTTTGAAAAGTACTTTAAAAAA
Found at i:96675 original size:43 final size:41
Alignment explanation
Indices: 96610--96699 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 41
96600 CAGTAGCACC
* *
96610 AACATTTTATTGATCTTTCTAA-CTCACGGTGACATTTTCACA
1 AACATTTTATTGATCTTACTAACCTCA--GTGACATTTCCACA
96652 AACACTTTTATTGAT-TATACTAACCTCAGTGACATTTCCACA
1 AACA-TTTTATTGATCT-TACTAACCTCAGTGACATTTCCACA
96694 AACATT
1 AACATT
96700 ATACTAACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
41 2 0.05
42 22 0.51
43 15 0.35
44 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (41 bp):
AACATTTTATTGATCTTACTAACCTCAGTGACATTTCCACA
Found at i:96706 original size:32 final size:32
Alignment explanation
Indices: 96665--96729 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
96655 ACTTTTATTG
96665 ATTATACTAACCTCAGTGACATTTCCACAAAC
1 ATTATACTAACCTCAGTGACATTTCCACAAAC
96697 ATTATACTAACCTCAGTGACATTTCCACAAAC
1 ATTATACTAACCTCAGTGACATTTCCACAAAC
96729 A
1 A
96730 CTTGGTAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (32 bp):
ATTATACTAACCTCAGTGACATTTCCACAAAC
Found at i:100391 original size:49 final size:49
Alignment explanation
Indices: 100330--100424 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
100320 AAATGTATAA
* *
100330 TTTGAAACTAATTAATAATAACATATGAAATATGTACGTTATTAAATAG
1 TTTGAAACTAATTAATAAAAACACATGAAATATGTACGTTATTAAATAG
*
100379 TTTGAAATTAATTAATAAAAACACATGAAATATGTACGTTATTAAA
1 TTTGAAACTAATTAATAAAAACACATGAAATATGTACGTTATTAAA
100425 ATGAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (49 bp):
TTTGAAACTAATTAATAAAAACACATGAAATATGTACGTTATTAAATAG
Found at i:101810 original size:18 final size:17
Alignment explanation
Indices: 101783--101816 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
101773 AAAATGTAGT
*
101783 AAAAAAATAACAAAACA
1 AAAAAAATAAAAAAACA
101800 AAAAGAAATAAAAAAAC
1 AAAA-AAATAAAAAAAC
101817 TAGAAAACAA
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:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAATAAAAAAACA
Found at i:102643 original size:11 final size:11
Alignment explanation
Indices: 102627--102688 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
102617 CCACGTTAGC
102627 AAATTATTTTA
1 AAATTATTTTA
102638 AAATTA--TTA
1 AAATTATTTTA
102647 AAATTATTTTTTA
1 AAATTA--TTTTA
*
102660 AAA--A-TATA
1 AAATTATTTTA
102668 AAATTATTTTA
1 AAATTATTTTA
102679 AAATTATTTT
1 AAATTATTTT
102689 TTAAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
8 6 0.14
9 9 0.21
10 1 0.02
11 20 0.48
13 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:102650 original size:20 final size:20
Alignment explanation
Indices: 102627--102686 Score: 86
Period size: 19 Copynumber: 3.0 Consensus size: 20
102617 CCACGTTAGC
102627 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
102647 AAATTATTTTTTAAAAATA-TA
1 AAATTA--TTTTAAAATTATTA
102668 AAATTATTTTAAAATTATT
1 AAATTATTTTAAAATTATT
102687 TTTTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 10 0.29
20 7 0.20
21 8 0.23
22 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:102662 original size:13 final size:13
Alignment explanation
Indices: 102644--102695 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
102634 TTTAAAATTA
102644 TTAAAATTATTTT
1 TTAAAATTATTTT
102657 TTAAAAATATAAAATTATT
1 TT-AAAAT-T---ATT-TT
102676 TTAAAATTATTTT
1 TTAAAATTATTTT
102689 TTAAAAT
1 TTAAAAT
102696 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.33
14 8 0.24
15 1 0.03
17 1 0.03
18 8 0.24
19 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:102669 original size:21 final size:22
Alignment explanation
Indices: 102633--102677 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
102623 TAGCAAATTA
*
102633 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
102655 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
102676 TT
1 TT
102678 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:102695 original size:31 final size:32
Alignment explanation
Indices: 102636--102706 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
102626 CAAATTATTT
102636 TAAAATTA--TTAAAATTATTTTTTAAAAATA
1 TAAAATTATTTTAAAATTATTTTTTAAAAATA
102666 TAAAATTATTTTAAAATTATTTTTT-AAAATA
1 TAAAATTATTTTAAAATTATTTTTTAAAAATA
102697 TAAAATTATT
1 TAAAATTATT
102707 AAAATCATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 8 0.21
31 16 0.41
32 15 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAAATTATTTTAAAATTATTTTTTAAAAATA
Found at i:102801 original size:13 final size:13
Alignment explanation
Indices: 102783--102807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
102773 TAAGTTTCTA
102783 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
102796 GGTTTTTTTTTT
1 GGTTTTTTTTTT
102808 CGCAATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:103600 original size:9 final size:9
Alignment explanation
Indices: 103586--103614 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
103576 GATGATGATG
103586 ATTTTAATA
1 ATTTTAATA
103595 ATTTTAATA
1 ATTTTAATA
103604 ATTTTAA-A
1 ATTTTAATA
103612 ATT
1 ATT
103615 ATTTACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTTAATA
Found at i:109455 original size:50 final size:50
Alignment explanation
Indices: 109398--109499 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
109388 AATTTTTTTG
109398 GTGTTTTACTTTATAAATTAAAATTAACTCAAAAATTTTAAATGATAATA
1 GTGTTTTACTTTATAAATTAAAATTAACTCAAAAATTTTAAATGATAATA
109448 GTGTTTTACTTTATAAATTAAAATTAACTCAAAAATTTTAAATGATAATA
1 GTGTTTTACTTTATAAATTAAAATTAACTCAAAAATTTTAAATGATAATA
109498 GT
1 GT
109500 CTATATCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (50 bp):
GTGTTTTACTTTATAAATTAAAATTAACTCAAAAATTTTAAATGATAATA
Found at i:110783 original size:18 final size:16
Alignment explanation
Indices: 110752--110795 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
110742 AGTTTAGGAT
*
110752 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
110769 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
110783 TTAAAAATTTATT
1 TTAAAAATTTATT
110796 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:112834 original size:23 final size:23
Alignment explanation
Indices: 112804--112850 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
112794 TCTCTTGTCC
112804 CTGTGTGGACCATGTTAGTTCTT
1 CTGTGTGGACCATGTTAGTTCTT
112827 CTGTGTGGACCATGTTAGTTCTT
1 CTGTGTGGACCATGTTAGTTCTT
112850 C
1 C
112851 CTAAGATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (23 bp):
CTGTGTGGACCATGTTAGTTCTT
Found at i:116071 original size:84 final size:82
Alignment explanation
Indices: 115938--116112 Score: 187
Period size: 84 Copynumber: 2.1 Consensus size: 82
115928 NNNNNNNNNN
* * *
115938 TACTTGAACTTTCAAAATGCATAAAAAAGCTCTCAATATTTAAAAAAAAAAACCAATTTAAGT-T
1 TACTTGAACTTCCAAAATGCATAAAAAAGCCCTCAATATTTAAAAAAAAAAA-CAA-TGAAGTCT
116002 TTTTTTT-GCACTCAATTGAG
64 TTTTTTTAG--CTCAATTGAG
* ***
116022 TACTTGAACTTCCAAAATGTATTAAAAAAGCCCTCAACT-TTT-TCTAAAAAAACAATGAAGTCT
1 TACTTGAACTTCCAAAATGCA-TAAAAAAGCCCTCAA-TATTTAAAAAAAAAAACAATGAAGTCT
* *
116085 TTTTTTTAGTTCAATTGGG
64 TTTTTTTAGCTCAATTGAG
116104 TACTTGAAC
1 TACTTGAAC
116113 CATCTAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
82 22 0.28
83 11 0.14
84 27 0.35
85 17 0.22
86 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (82 bp):
TACTTGAACTTCCAAAATGCATAAAAAAGCCCTCAATATTTAAAAAAAAAAACAATGAAGTCTTT
TTTTTAGCTCAATTGAG
Found at i:116486 original size:9 final size:9
Alignment explanation
Indices: 116461--116573 Score: 64
Period size: 9 Copynumber: 11.7 Consensus size: 9
116451 TTTTTATCTA
*
116461 TTTTATATT
1 TTTTATAAT
116470 TTTTATAAT
1 TTTTATAAT
*
116479 TTTTATAAAA
1 TTTTAT-AAT
* *
116489 GTTTACAATT
1 TTTTATAA-T
116499 TTTTATAACT
1 TTTTATAA-T
***
116509 TTTTACGTT
1 TTTTATAAT
116518 TTTTATAATTTT
1 TTTTATAA---T
*
116530 TTTTCTAAT
1 TTTTATAAT
116539 TTTTATAAT
1 TTTTATAAT
*
116548 TTTTATTAAAA
1 TTTTA-T-AAT
*
116559 TTTAATAAT
1 TTTTATAAT
116568 TTTTAT
1 TTTTAT
116574 TGATATTTAT
Statistics
Matches: 77, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
9 43 0.56
10 20 0.26
11 6 0.08
12 8 0.10
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:116550 original size:19 final size:19
Alignment explanation
Indices: 116461--116572 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 19
116451 TTTTTATCTA
*
116461 TTTTATATTTTTTA-TAAT
1 TTTTATAATTTTTACTAAT
**
116479 TTTTATAAAAGTTTAC-AATT
1 TTTTAT-AATTTTTACTAA-T
116499 TTTTATAACTTTTTACGT--T
1 TTTTATAA-TTTTTAC-TAAT
*
116518 TTTTATAATTTTTTTTCTAAT
1 TTTTATAA--TTTTTACTAAT
* *
116539 TTTTATAATTTTTATTAAAA
1 TTTTATAATTTTTACT-AAT
*
116559 TTTAATAATTTTTA
1 TTTTATAATTTTTA
116573 TTGATATTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
18 6 0.08
19 25 0.34
20 33 0.45
21 9 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTACTAAT
Found at i:116560 original size:21 final size:21
Alignment explanation
Indices: 116517--116574 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
116507 CTTTTTACGT
* **
116517 TTTTTATAATTTTTTTTCTAA
1 TTTTTATAATTTTTATTAAAA
116538 TTTTTATAATTTTTATTAAAA
1 TTTTTATAATTTTTATTAAAA
*
116559 -TTTAATAATTTTTATT
1 TTTTTATAATTTTTATT
116575 GATATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTATAATTTTTATTAAAA
Found at i:122252 original size:132 final size:129
Alignment explanation
Indices: 122005--122861 Score: 732
Period size: 132 Copynumber: 6.7 Consensus size: 129
121995 GTCACTTCCA
* * * * * * *
122005 ATGGGCTTCAGTCTCAGGCGTTGAGCAATGCAAGTGGAACGGTGGTTCCGGCAAAAAGCAGCCCA
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCT-CGACAAAAAGCAGCCCA
* ** * * * *
122070 GCATGGGATGAAGCCTGGGAATCTGCCCAGAG-AGGAGCTGCCAATGCCACTGCCA-TGACCACC
65 GCATGGGATGAAGACTGGGGCTCTACCAACAGCA-GAGCTG-CAATGCCA-TGCCACT-ACCACT
*
122133 GCAG
126 GGAG
* *
122137 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCGAGTGGAACTGTGGATCTGACAAAAAGCAGCCCA
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTC-GACAAAAAGCAGCCCA
* * * *
122202 GCATGGGATGAAGAGTGGGGCTCTGCC-A-A-CAGAG--G--A-G-C-TGTCACTACCACTGCAG
65 GCATGGGATGAAGACTGGGGCTCTACCAACAGCAGAGCTGCAATGCCATGCCACTACCACTGGAG
* * * *
122257 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCGAGTGGAACTGTAGCTCCTG-CAAAAAGCAACGC
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCT-C-GACAAAAAGCAGCCC
* * * **
122321 AGAATGGGATGAAGAGTAGGGCTCTACCCCCAGCAGAGCT----T-CCAATGCCACTACCACTGG
64 AGCATGGGATGAAGACTGGGGCTCTACCAACAGCAGAGCTGCAATGCC-ATGCCACTACCACTGG
122381 AG
128 AG
* * * *
122383 AT-GGACTTCGGTTTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCCAGCAAAAAGCAGACC
1 ATGGGA-TTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCGA-CAAAAAGCAGCCC
* * *
122447 AGCATGGGATGAAAACTGGGGCTCTAACACCAGCAGAGCTGCTAATGCCAATGCCACTACCACTG
64 AGCATGGGATGAAGACTGGGGCTCTACCAACAGCAGAGCTGC-AATGCC-ATGCCACTACCACTG
122512 GAG
127 GAG
* * * * *
122515 ATGGGCTTCGGTCTCAAGCCTTGAGCAACGCTAGTAGAACTGTGGCTCCAGCAAAAAGCAGCCCA
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCGA-CAAAAAGCAGCCCA
* *
122580 GCATGGGATGAAAACTGGGGCTCTACCACCAGCAGAGCTGCTAATGCCAATGCCACTACCACTGG
65 GCATGGGATGAAGACTGGGGCTCTACCAACAGCAGAGCTGC-AATGCC-ATGCCACTACCACTGG
122645 AG
128 AG
* * * * * * * *
122647 ATGGGCTTCGGTCTCAAGCCTTGAGCAGCGCAAGTGGAACTGTGGCACCAGCAAGATGCAGCTCA
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCGA-CAAAAAGCAGCCCA
* * * * *
122712 TCATGGGATGAAGACAGGTGCTCTATCAACAG-AGGAGCTGC----CCATGCCACT-GCA---G-
65 GCATGGGATGAAGACTGGGGCTCTACCAACAGCA-GAGCTGCAATGCCATGCCACTACCACTGGA
122767 G
129 G
* ** * * * *
122768 -TGGGGTTCAGTCTCAAGCCTTGAGCAGTGCAAGTGGAACTGCGGCTCCAGCAAAAAGCTGCTCA
1 ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCGA-CAAAAAGCAGCCCA
*
122832 GCATGGGGTGAAGAC-GGGGACTCTACCAAC
65 GCATGGGATGAAGACTGGGG-CTCTACCAAC
122862 CGAGGTGCTG
Statistics
Matches: 630, Mismatches: 70, Indels: 62
0.83 0.09 0.08
Matches are distributed among these distances:
119 3 0.00
120 172 0.27
121 5 0.01
122 3 0.00
123 6 0.01
124 2 0.00
125 6 0.01
126 106 0.17
127 3 0.00
129 3 0.00
130 2 0.00
131 4 0.01
132 313 0.50
133 2 0.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (129 bp):
ATGGGATTCAGTCTCAAGCCTTGAGCAACGCAAGTGGAACTGTGGCTCGACAAAAAGCAGCCCAG
CATGGGATGAAGACTGGGGCTCTACCAACAGCAGAGCTGCAATGCCATGCCACTACCACTGGAG
Found at i:123031 original size:72 final size:72
Alignment explanation
Indices: 122941--123085 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
122931 GATAAATCAA
122941 GTGAACCAACACCTTGGTAATCTCATTCTCCCATGATGTCCACCATATCTAGCCAGCAAATGCAT
1 GTGAACCAACACCTTGGTAATCTCATTCTCCCATGATGTCCACCATATCTAGCCAGCAAATGCAT
123006 GCTTCTT
66 GCTTCTT
*
123013 GTGAACCAACACCTTGGTAATCTCATTCTCCCATGATGTCCACTATATCTAGCCAGCAAATGCAT
1 GTGAACCAACACCTTGGTAATCTCATTCTCCCATGATGTCCACCATATCTAGCCAGCAAATGCAT
123078 GCTTCTT
66 GCTTCTT
123085 G
1 G
123086 CCCTGCGGTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (72 bp):
GTGAACCAACACCTTGGTAATCTCATTCTCCCATGATGTCCACCATATCTAGCCAGCAAATGCAT
GCTTCTT
Found at i:125466 original size:168 final size:169
Alignment explanation
Indices: 125095--125555 Score: 545
Period size: 172 Copynumber: 2.7 Consensus size: 169
125085 CAATGTTCAC
* ** ** * * *
125095 ATGCACAGACCTTATAAACCGAAAGCGTTCAACACGTTTGACAATATGCTATCACTCTGGCGCTT
1 ATGCACAGACCTTATAAGCC-AAAGCACTCAACGTGTTTGACAATATGCTATCATTCTGGAGTTT
* **
125160 AGAACAAAGTAAAACCCACCATATCAATGACAAAACCTTCTAAACATGATGGATGATACGGTAAT
65 AGAACAAAGTAAAACACACCATATCAA-GACAAAACCTTCTAAACATGATGGATGATACGACAAT
* *
125225 GCGACCATTGAATACTCCCAATACACCAAATTCTATAAACAT
129 GCGA-CATAGAAGACTCCCAATACACCAAATTCTATAAACAT
* * * *
125267 GTACACAGACCTTCTAAGCCAATAACACTCAACGTGTTTGACAATATGCTATCATTCTGCG-GTT
1 ATGCACAGACCTTATAAGCCAA-AGCACTCAACGTGTTTGACAATATGCTATCATTCTG-GAGTT
* * * *
125331 TAGAACAAAGTAATACACACTATATC-A-ACAAAACCTTCTAAACATGATGGATGATATGACCAT
64 TAGAACAAAGTAAAACACACCATATCAAGACAAAACCTTCTAAACATGATGGATGATACGACAAT
* * * *
125394 -TGA-ATAGAGTAGACTCTCAATACACCGAATTCTATGAACAT
129 GCGACATAGA--AGACTCCCAATACACCAAATTCTATAAACAT
*
125435 ATGCACAGACCTTATAAGCCAAGAGCACTCAACGTGTTTGACAATATGTTATCATTCTGGAGTTT
1 ATGCACAGACCTTATAAGCCAA-AGCACTCAACGTGTTTGACAATATGCTATCATTCTGGAGTTT
* *
125500 AGAACAAGGGTAAAACACACCGTATCAATGACAAAACCTTCTAAACATGATGGATG
65 AGAACAA-AGTAAAACACACCATATCAA-GACAAAACCTTCTAAACATGATGGATG
125556 GATGATATGA
Statistics
Matches: 246, Mismatches: 34, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
166 4 0.02
167 1 0.00
168 93 0.38
169 46 0.19
170 1 0.00
171 3 0.01
172 97 0.39
173 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (169 bp):
ATGCACAGACCTTATAAGCCAAAGCACTCAACGTGTTTGACAATATGCTATCATTCTGGAGTTTA
GAACAAAGTAAAACACACCATATCAAGACAAAACCTTCTAAACATGATGGATGATACGACAATGC
GACATAGAAGACTCCCAATACACCAAATTCTATAAACAT
Found at i:131852 original size:75 final size:75
Alignment explanation
Indices: 131729--131880 Score: 250
Period size: 75 Copynumber: 2.0 Consensus size: 75
131719 CAATGGTGCC
* * * * *
131729 ATCAACTATTGTTTAAATGATAAGGTTGGAGGTTCGAGAATTTTAAAATCATAGATTTTAATCCA
1 ATCAACTATTATTTAAATGATAACGTTGGAAGTTCGAGAATTTAAAAATCATAGATTTCAATCCA
131794 TCCATCGATT
66 TCCATCGATT
*
131804 ATCAACTATTATTTAAATGGTAACGTTGGAAGTTCGAGAATTTAAAAATCATAGATTTCAATCCA
1 ATCAACTATTATTTAAATGATAACGTTGGAAGTTCGAGAATTTAAAAATCATAGATTTCAATCCA
131869 TCCATCGATT
66 TCCATCGATT
131879 AT
1 AT
131881 AGTGGAACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (75 bp):
ATCAACTATTATTTAAATGATAACGTTGGAAGTTCGAGAATTTAAAAATCATAGATTTCAATCCA
TCCATCGATT
Found at i:142426 original size:10 final size:9
Alignment explanation
Indices: 142410--142436 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
142400 AGGGCTCCTC
142410 CTTTTTTTT
1 CTTTTTTTT
142419 CTTTTTTTT
1 CTTTTTTTT
142428 CTTTTTTTT
1 CTTTTTTTT
142437 GCAAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:148008 original size:18 final size:18
Alignment explanation
Indices: 147968--148002 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
147958 TATTTATTTA
*
147968 AAATAAAATATTAAAATT
1 AAATAAAATATAAAAATT
147986 AAATAAAA-ATAAAAATT
1 AAATAAAATATAAAAATT
148003 CTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAATATAAAAATT
Found at i:148370 original size:15 final size:14
Alignment explanation
Indices: 148349--148399 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
148339 AAGTTAATTT
148349 TTTTAATATTTAAA
1 TTTTAATATTTAAA
148363 TATTTAATATTATAAA
1 T-TTTAATATT-TAAA
*
148379 TTTT-ATTTTTAAA
1 TTTTAATATTTAAA
148392 -TTTAATAT
1 TTTTAATAT
148400 CTTTTATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 3 0.09
13 7 0.22
14 5 0.16
15 12 0.38
16 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAATATTTAAA
Found at i:148371 original size:7 final size:7
Alignment explanation
Indices: 148350--148399 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
148340 AGTTAATTTT
148350 TTTAATA
1 TTTAATA
148357 TTTAAATA
1 TTT-AATA
148365 TTTAATA
1 TTTAATA
148372 TTATAA-A
1 TT-TAATA
* *
148379 TTTTATT
1 TTTAATA
148386 TTTAA-A
1 TTTAATA
148392 TTTAATA
1 TTTAATA
148399 T
1 T
148400 CTTTTATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 7 0.20
7 18 0.51
8 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAATA
Found at i:150029 original size:16 final size:16
Alignment explanation
Indices: 150008--150038 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
149998 AGAATATTAC
150008 TTAATTAATAAATATT
1 TTAATTAATAAATATT
*
150024 TTAATTGATAAATAT
1 TTAATTAATAAATAT
150039 ATAAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTAATTAATAAATATT
Found at i:152811 original size:88 final size:88
Alignment explanation
Indices: 152650--152875 Score: 312
Period size: 88 Copynumber: 2.5 Consensus size: 88
152640 CTTAAGGGTG
* * * * *
152650 CAAAAAG-CCTTCAAACTTTTTCACAAAAAGCAATTAATCCCTTCCATTTTTTTTGCACTCATTT
1 CAAAAAGACCCTCAAACTTTTTCA-AAAAAGCAATTAAGCCCCTAC-TTTTTTTTGCACTCAATT
* * *
152714 AGGTACTTGAACTTTCAAAGTGCAT
64 AGATACTTGAACTATCAAAATGCAT
152739 CAAAAAGACCCTCAAACGTTTTT-AAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTA
1 CAAAAAGACCCTCAAAC-TTTTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTA
152803 GATACTTGAACTATCAAAATGCAT
65 GATACTTGAACTATCAAAATGCAT
*
152827 AAAAAAGACCCTCAAACTTTTTCAAAGAAAAGCAATTAAGCCCCTACTT
1 CAAAAAGACCCTCAAACTTTTTC-AA-AAAAGCAATTAAGCCCCTACTT
152876 ATATTAAAAT
Statistics
Matches: 123, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
87 5 0.04
88 55 0.45
89 27 0.22
90 31 0.25
91 5 0.04
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.31
Consensus pattern (88 bp):
CAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTAG
ATACTTGAACTATCAAAATGCAT
Found at i:152994 original size:28 final size:28
Alignment explanation
Indices: 152957--153089 Score: 107
Period size: 28 Copynumber: 4.7 Consensus size: 28
152947 TAAAAAATTC
*
152957 AAATATTAAAAATTTAATAAAAAT-TAGAA
1 AAATA-TAAAAATTTTATAAAAATATA-AA
* *
152986 AAATATAAAAATCGTGA-AAAAATATAAA
1 AAATATAAAAAT-TTTATAAAAATATAAA
*
153014 AAAT-TGTAAAATTTTATAAAAATCATAAA
1 AAATAT-AAAAATTTTATAAAAAT-ATAAA
* *
153043 AAATAT-AAAA-TATATAGAAATATTAAA
1 AAATATAAAAATTTTATAAAAATA-TAAA
153070 AAAT-TATAAAATTTTATAAA
1 AAATATA-AAAATTTTATAAA
153090 GTCGTAAGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
26 2 0.02
27 20 0.24
28 38 0.45
29 24 0.28
30 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (28 bp):
AAATATAAAAATTTTATAAAAATATAAA
Found at i:152996 original size:9 final size:9
Alignment explanation
Indices: 152957--153080 Score: 58
Period size: 10 Copynumber: 13.1 Consensus size: 9
152947 TAAAAAATTC
*
152957 AAATATTAA
1 AAATATAAA
*
152966 AAATTTAATA
1 AAATATAA-A
152976 AAA-ATTAGAA
1 AAATA-TA-AA
152986 AAATAT-AA
1 AAATATAAA
*
152994 AAATCGTGAAA
1 AAAT-AT-AAA
153005 AAATATAAA
1 AAATATAAA
*
153014 AAAT-TGTAA
1 AAATAT-AAA
* *
153023 AATTTTATAA
1 AAATATA-AA
153033 AAATCATAAA
1 AAAT-ATAAA
153043 AAATATAAA
1 AAATATAAA
* *
153052 ATATAT-AG
1 AAATATAAA
153060 AAATATTAAA
1 AAATA-TAAA
153070 AAATTATAAA
1 AAA-TATAAA
153080 A
1 A
153081 TTTTATAAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
8 12 0.14
9 30 0.34
10 33 0.38
11 12 0.14
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AAATATAAA
Found at i:153053 original size:56 final size:56
Alignment explanation
Indices: 152946--153089 Score: 156
Period size: 56 Copynumber: 2.6 Consensus size: 56
152936 TTAAATTTTA
* * * *
152946 ATAAAAA-ATTCAAATATTA-AAAATTTAATAAAAATTAGAAAAATATAAAAATCGT
1 ATAAAAATATTAAAAAATTATAAAATTTTATAAAAATTAGAAAAATATAAAAAT-AT
*
153001 GA-AAAAATA-TAAAAAATTGTAAAATTTTATAAAAATCATA-AAAAATAT-AAAATAT
1 -ATAAAAATATTAAAAAATTATAAAATTTTATAAAAAT--TAGAAAAATATAAAAATAT
*
153056 ATAGAAATATTAAAAAATTATAAAATTTTATAAA
1 ATAAAAATATTAAAAAATTATAAAATTTTATAAA
153090 GTCGTAAGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
54 1 0.01
55 19 0.25
56 45 0.60
57 8 0.11
58 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (56 bp):
ATAAAAATATTAAAAAATTATAAAATTTTATAAAAATTAGAAAAATATAAAAATAT
Found at i:153147 original size:20 final size:20
Alignment explanation
Indices: 152984--153150 Score: 79
Period size: 19 Copynumber: 8.8 Consensus size: 20
152974 TAAAAATTAG
*
152984 AAAAA-TATAAAAATCGTGA
1 AAAAATTATAAAAATCGTAA
*
153003 AAAAA-TATAAAAAATTGT-A
1 AAAAATTAT-AAAAATCGTAA
** *
153022 AAATTTTATAAAAATCAT-A
1 AAAAATTATAAAAATCGTAA
* *
153041 AAAAA-TATAAAATAT-ATAG
1 AAAAATTATAAAA-ATCGTAA
*
153060 AAATATTA-AAAAAT--T-A
1 AAAAATTATAAAAATCGTAA
* * *
153076 TAAAATTTTATAAAGTCGTAA
1 AAAAATTATA-AAAATCGTAA
*
153097 GAAAATTATACAAAAT-GTAA
1 AAAAATTATA-AAAATCGTAA
* **
153117 AGAAA-TATAAATTTCGTAA
1 AAAAATTATAAAAATCGTAA
153136 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
153151 TATTGTACCA
Statistics
Matches: 111, Mismatches: 25, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.05
17 2 0.02
18 18 0.16
19 45 0.41
20 28 0.25
21 13 0.12
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATCGTAA
Found at i:153610 original size:90 final size:90
Alignment explanation
Indices: 153453--153670 Score: 289
Period size: 90 Copynumber: 2.4 Consensus size: 90
153443 AAGAGCAAGA
* *
153453 GCTTAATTGCTTTTTTGAAAAATTTTGAGGG-TCTTTTTGATGCATTTTGAAAGTTTAAGTACCC
1 GCTTAATTGCTTTTTTGAAAAAATTTGAGGGCT-TTTTTGATGCATTTTGAAAGTTCAAGTACCC
* *
153517 AATTGAGTG-AAAAAGAAAAGCAGGG
65 AATTGAGTGAAAAAAAAAAAGCAGAG
* * * *
153542 GCTTAATTGCTTTTCTTGAAGAAGTTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGTGCTC
1 GCTTAATTGCTTTT-TTGAAAAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCC
*
153607 AATTGAGTGCAAAAAAAAAAAGGAGAG
65 AATTGAGTG-AAAAAAAAAAAGCAGAG
*
153634 ACTTAATTGCTTTTTTTGAAAAAATTTGA-GGCTTTTT
1 GCTTAATTGC-TTTTTTGAAAAAATTTGAGGGCTTTTT
153671 ACACCCTTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
89 14 0.12
90 52 0.46
91 9 0.08
92 34 0.30
93 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38
Consensus pattern (90 bp):
GCTTAATTGCTTTTTTGAAAAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
ATTGAGTGAAAAAAAAAAAGCAGAG
Found at i:159103 original size:22 final size:22
Alignment explanation
Indices: 159077--159141 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 22
159067 TAATTTAATT
159077 ATTTAAAAATTATAAAAATATA
1 ATTTAAAAATTATAAAAATATA
*
159099 ATTTATTAAAATAATAAAAATATA
1 ATTTA--AAAATTATAAAAATATA
* **
159123 ATTTTACTATTATAAAAAT
1 ATTTAAAAATTATAAAAAT
159142 TACAATGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.44
24 20 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAAAATTATAAAAATATA
Found at i:170047 original size:17 final size:17
Alignment explanation
Indices: 170025--170070 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
170015 ATTAACGGTT
170025 TAACAATAATAAATAAA
1 TAACAATAATAAATAAA
* *
170042 TAACAAAAATTAATAAA
1 TAACAATAATAAATAAA
*
170059 -AA-AATTATAAAT
1 TAACAATAATAAAT
170071 TAATTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 7 0.29
16 2 0.08
17 15 0.62
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (17 bp):
TAACAATAATAAATAAA
Found at i:171007 original size:62 final size:62
Alignment explanation
Indices: 170925--171048 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
170915 CTTGCTTTAT
170925 ACAGGCATTCCGTGCACAGAATATCGAAAGCGCTACATCTAGACTCATTATGTGTGCGGAAG
1 ACAGGCATTCCGTGCACAGAATATCGAAAGCGCTACATCTAGACTCATTATGTGTGCGGAAG
170987 ACAGGCATTCCGTGCACAGAATATCGAAAGCGCTACATCTAGACTCATTATGTGTGCGGAAG
1 ACAGGCATTCCGTGCACAGAATATCGAAAGCGCTACATCTAGACTCATTATGTGTGCGGAAG
171049 CAATTAGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (62 bp):
ACAGGCATTCCGTGCACAGAATATCGAAAGCGCTACATCTAGACTCATTATGTGTGCGGAAG
Found at i:171443 original size:28 final size:29
Alignment explanation
Indices: 171411--171498 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 29
171401 AGGCCAAGAC
171411 TAATGATATGATGCATCTTTATTGAAC-T
1 TAATGATATGATGCATCTTTATTGAACTT
* *
171439 TAATG-TATTGAAG-A---ATATTGAACTTT
1 TAATGATA-TGATGCATCTTTATTGAAC-TT
*
171465 CTAATGATATGATGCATCTTTATTG-ACAT
1 -TAATGATATGATGCATCTTTATTGAACTT
171494 TAATG
1 TAATG
171499 TTGCAGAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
24 8 0.17
26 1 0.02
27 12 0.26
28 17 0.37
29 1 0.02
30 2 0.04
31 5 0.11
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (29 bp):
TAATGATATGATGCATCTTTATTGAACTT
Found at i:176300 original size:32 final size:33
Alignment explanation
Indices: 176264--176325 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
176254 AGAAAAATTG
*
176264 AATTGGATTGAATTGAA-AGAAAGAAAAAACCT
1 AATTGAATTGAATTGAATAGAAAGAAAAAACCT
* *
176296 AATTGAATTGGATTGAATTGAAAGAAAAAA
1 AATTGAATTGAATTGAATAGAAAGAAAAAA
176326 AAAAAAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.24
Consensus pattern (33 bp):
AATTGAATTGAATTGAATAGAAAGAAAAAACCT
Found at i:176302 original size:37 final size:37
Alignment explanation
Indices: 176259--176329 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
176249 AATTAAGAAA
*
176259 AATTGAATTGGATTGAATTGAAAGAAAGAAAAAACCT
1 AATTGAATTGGATTGAATTGAAAGAAAAAAAAAACCT
176296 AATTGAATTGGATTGAATTGAAAGAAAAAAAAAA
1 AATTGAATTGGATTGAATTGAAAGAAAAAAAAAA
176330 AAAACCTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (37 bp):
AATTGAATTGGATTGAATTGAAAGAAAAAAAAAACCT
Found at i:180668 original size:29 final size:29
Alignment explanation
Indices: 180625--180702 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 29
180615 TTAATTTTTT
*
180625 TTATT-TTAATATAATATATATTTAATATA
1 TTATTATTAAT-TAATATATATTAAATATA
*
180654 TTATTATTAATTAAT-T-T-TAAAATATA
1 TTATTATTAATTAATATATATTAAATATA
* * *
180680 TTTTTATTATTTATTATATATTA
1 TTATTATTAATTAATATATATTA
180703 TATTCATGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
26 19 0.49
27 2 0.05
28 2 0.05
29 11 0.28
30 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTATTATTAATTAATATATATTAAATATA
Found at i:193747 original size:17 final size:18
Alignment explanation
Indices: 193715--193748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
193705 ATTCATTATT
*
193715 CAACTACTTAATTTGAAC
1 CAACTACATAATTTGAAC
193733 CAACTACAT-ATTTGAA
1 CAACTACATAATTTGAA
193749 ATTTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (18 bp):
CAACTACATAATTTGAAC
Found at i:200477 original size:14 final size:14
Alignment explanation
Indices: 200443--200481 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
200433 AACTTTTAAA
200443 TAATTATAATTTTT
1 TAATTATAATTTTT
200457 TGAAATTATAATTTTT
1 T--AATTATAATTTTT
200473 TAATTATAA
1 TAATTATAA
200482 AAATCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
16 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TAATTATAATTTTT
Found at i:202965 original size:46 final size:46
Alignment explanation
Indices: 202898--202990 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
202888 TTGGTGCAGG
202898 ACATAAAATTTGAGGTTTCTTAGAATGCAGCCTCTAGGATTCTACA
1 ACATAAAATTTGAGGTTTCTTAGAATGCAGCCTCTAGGATTCTACA
202944 ACATAAAATTTGAGGTTTCTTAGAATGCAGCCTCTAGGATTCTACA
1 ACATAAAATTTGAGGTTTCTTAGAATGCAGCCTCTAGGATTCTACA
202990 A
1 A
202991 GTTAATATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (46 bp):
ACATAAAATTTGAGGTTTCTTAGAATGCAGCCTCTAGGATTCTACA
Found at i:208692 original size:27 final size:25
Alignment explanation
Indices: 208662--208719 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
208652 TTATATAATA
*
208662 AAAAAAAAATAGAGAAATTAAATTCTT
1 AAAAAAAAA-AGAGAAACTAAATTC-T
* *
208689 AAAATAAAAAATATAAACTAAATTCT
1 AAAA-AAAAAAGAGAAACTAAATTCT
208715 AAAAA
1 AAAAA
208720 TACAAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.04
26 5 0.19
27 16 0.59
28 5 0.19
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.24
Consensus pattern (25 bp):
AAAAAAAAAAGAGAAACTAAATTCT
Found at i:209641 original size:18 final size:18
Alignment explanation
Indices: 209596--209647 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
209586 TATTGTATTG
209596 ATTATATATATATATATCAT
1 ATTATA-AT-TATATATCAT
209616 ATTATAATTATA-ATCAT
1 ATTATAATTATATATCAT
*
209633 ATGTTTAATTATATA
1 AT-TATAATTATATA
209648 AATATGCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 13 0.45
19 3 0.10
20 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTATAATTATATATCAT
Found at i:223984 original size:18 final size:20
Alignment explanation
Indices: 223947--223986 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
223937 GCTAATTATT
*
223947 TTGGTAAATTTATATAAATA
1 TTGGTAAAGTTATATAAATA
223967 TTGGTAAAGTT-T-TAAATA
1 TTGGTAAAGTTATATAAATA
223985 TT
1 TT
223987 TTAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (20 bp):
TTGGTAAAGTTATATAAATA
Found at i:226524 original size:13 final size:13
Alignment explanation
Indices: 226506--226531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
226496 TATTGATACG
226506 AAATTTAAATTCT
1 AAATTTAAATTCT
226519 AAATTTAAATTCT
1 AAATTTAAATTCT
226532 TCAGATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTAAATTCT
Found at i:226603 original size:29 final size:31
Alignment explanation
Indices: 226541--226606 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
226531 TTCAGATTAA
*
226541 AAAAATTATTAAAATTATTTATTAATGACAT
1 AAAAATTATTAAAATTATTTATTAATAACAT
226572 AAAAATTATTAAAA-TA-TTATTAAATAAC-T
1 AAAAATTATTAAAATTATTTATT-AATAACAT
226601 AAAAAT
1 AAAAAT
226607 AATGAGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 12 0.36
30 7 0.21
31 14 0.42
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAAATTATTAAAATTATTTATTAATAACAT
Found at i:228743 original size:4 final size:4
Alignment explanation
Indices: 228736--228821 Score: 50
Period size: 4 Copynumber: 21.0 Consensus size: 4
228726 AAATAAATGG
* * *
228736 GAAA GAAA GAAA GAAAA GAAA GAAA GGAAG GAAA -AAG GAGAA GAAA TAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA -GAAA GAAA GAAA GA-AA GAAA GAAA
* * * * *
228786 GGAA GAAG GAGAG GAAA GAAA -TAA GAAG GAAA GAAA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
228822 TGTAATGTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
3 4 0.06
4 44 0.71
5 14 0.23
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:228755 original size:13 final size:13
Alignment explanation
Indices: 228737--228761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
228727 AATAAATGGG
228737 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
228750 AAAGAAAGAAAG
1 AAAGAAAGAAAG
228762 GAAGGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:228761 original size:21 final size:22
Alignment explanation
Indices: 228736--228806 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 22
228726 AAATAAATGG
*
228736 GAAAGAAAGAAAGAAAAGA-AA
1 GAAAGAAAGGAAGAAAAGAGAA
* *
228757 GAAAGGAAGGAA-AAAGGAGAA
1 GAAAGAAAGGAAGAAAAGAGAA
* * *
228778 GAAATAAAGGAAG-AAGGAGAG
1 GAAAGAAAGGAAGAAAAGAGAA
228799 GAAAGAAA
1 GAAAGAAA
228807 TAAGAAGGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (22 bp):
GAAAGAAAGGAAGAAAAGAGAA
Found at i:228804 original size:25 final size:24
Alignment explanation
Indices: 228745--228817 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
228735 GGAAAGAAAG
* *
228745 AAAGAAAAGAAAGAAAGGAAGGAA
1 AAAGGAAAGAAATAAAGGAAGGAA
228769 AAAGGAGAAGAAATAAAGGAA-GAA
1 AAAGGA-AAGAAATAAAGGAAGGAA
*
228793 GGAGAGGAAAGAAAT-AA-GAAGGAA
1 --AAAGGAAAGAAATAAAGGAAGGAA
228817 A
1 A
228818 GAAATGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
22 1 0.02
23 3 0.07
24 13 0.31
25 20 0.48
26 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (24 bp):
AAAGGAAAGAAATAAAGGAAGGAA
Found at i:234671 original size:12 final size:12
Alignment explanation
Indices: 234656--234680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
234646 AAATTAAAAT
234656 ATTTTAAAATTA
1 ATTTTAAAATTA
234668 ATTTTAAAATTA
1 ATTTTAAAATTA
234680 A
1 A
234681 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:239401 original size:16 final size:16
Alignment explanation
Indices: 239380--239417 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
239370 AACCATATTT
239380 TTTTTATTTTTAAT-AA
1 TTTTTATTTTT-ATGAA
239396 TTTTTATTTTTATGAA
1 TTTTTATTTTTATGAA
239412 TTTTTA
1 TTTTTA
239418 ATGATCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTATTTTTATGAA
Done.