Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015274.1 Kokia drynarioides strain JFW-HI SEQ_130319, 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: 742443
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:278 original size:11 final size:11
Alignment explanation
Indices: 258--287 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
248 TTTATTTTTT
*
258 AAAATTTTAAA
1 AAAATATTAAA
269 AAAATATTAAA
1 AAAATATTAAA
280 AAAATATT
1 AAAATATT
288 TCTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:2291 original size:4 final size:4
Alignment explanation
Indices: 2282--2309 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2272 CCAGACTAAA
2282 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2310 CCTCTCTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:3198 original size:32 final size:32
Alignment explanation
Indices: 3157--3228 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
3147 GATTACACAT
* * *
3157 ATTTTAAGGGTTAAACAACTTTGTTACGATCA
1 ATTTTAAGGGTCAAACAACCTTGTTACAATCA
*
3189 ATTTTAAGGGTCAAACAACCTTGTTATAATCA
1 ATTTTAAGGGTCAAACAACCTTGTTACAATCA
3221 ATGTTTAA
1 AT-TTTAA
3229 TAGAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
ATTTTAAGGGTCAAACAACCTTGTTACAATCA
Found at i:4458 original size:21 final size:21
Alignment explanation
Indices: 4432--4483 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
4422 CCCTTCTTTG
4432 AGATGAAAATGCTGAAATTCA
1 AGATGAAAATGCTGAAATTCA
4453 AGATGAAAATGCTGAAATTCA
1 AGATGAAAATGCTGAAATTCA
4474 AGATGAAAAT
1 AGATGAAAAT
4484 ACTAATGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (21 bp):
AGATGAAAATGCTGAAATTCA
Found at i:5191 original size:2 final size:2
Alignment explanation
Indices: 5184--5219 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5174 TTTGATATAC
5184 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5220 ATAATACACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:9713 original size:22 final size:23
Alignment explanation
Indices: 9673--9722 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
9663 CAAATGTATT
*
9673 AAAATCATTAATTTCAAATAATA
1 AAAATCATTAATTTAAAATAATA
*
9696 AAAATCATT-TTTTAAAATAATA
1 AAAATCATTAATTTAAAATAATA
*
9718 CAAAT
1 AAAAT
9723 GTGTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATCATTAATTTAAAATAATA
Found at i:16240 original size:4 final size:4
Alignment explanation
Indices: 16233--16300 Score: 75
Period size: 4 Copynumber: 16.5 Consensus size: 4
16223 GAAGGAAAAA
* *
16233 AAAG AAAG AAGAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG GAAG GAAG
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
16281 AATG AGAAG AAAG AGAAG AA
1 AAAG A-AAG AAAG A-AAG AA
16301 GGAGAAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
3 3 0.05
4 43 0.75
5 11 0.19
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:16261 original size:12 final size:12
Alignment explanation
Indices: 16233--16300 Score: 75
Period size: 13 Copynumber: 5.5 Consensus size: 12
16223 GAAGGAAAAA
16233 AAAGAAAGAAGAG
1 AAAGAAAGAA-AG
16246 AAAGAAAGAAAG
1 AAAGAAAGAAAG
16258 AAAGAAAGAAAG
1 AAAGAAAGAAAG
* *
16270 -AAGGAAGGAAG
1 AAAGAAAGAAAG
*
16281 AATGAGAAGAAAG
1 AAAGA-AAGAAAG
16294 AGAAGAA
1 A-AAGAA
16301 GGAGAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.20
12 16 0.35
13 18 0.39
14 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (12 bp):
AAAGAAAGAAAG
Found at i:18387 original size:43 final size:43
Alignment explanation
Indices: 18305--18389 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
18295 ATTAACATGT
* *
18305 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
18348 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
18390 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:19029 original size:45 final size:45
Alignment explanation
Indices: 18956--19092 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
18946 GCATAGCTCA
*
18956 TCAAGCCAAGGATATCAGTCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
19001 TCAAGCCAAGGATATCAGCCTTAATTTGACAAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * *
19046 TCAAGGGAAGGATATCAGGCTCAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
19091 TC
1 TC
19093 TATTCCTCCG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:19416 original size:28 final size:28
Alignment explanation
Indices: 19336--19416 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
19326 CATTAAACCC
** * * *
19336 TAAAA-CCTAAATTATAAACTCTAAACT
1 TAAAACCCTAAACCATAAACACTAGACA
19363 TAAAACCCTAAACCATAAACACTAGACA
1 TAAAACCCTAAACCATAAACACTAGACA
* * *
19391 TAAAACTCTAAACCGTAAACATTAGA
1 TAAAACCCTAAACCATAAACACTAGA
19417 TTGATTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (28 bp):
TAAAACCCTAAACCATAAACACTAGACA
Found at i:22475 original size:4 final size:4
Alignment explanation
Indices: 22466--22531 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
22456 AACACATTAC
* * * *
22466 CTTT CTTT CTTT C-TT CTTT ATTT CCTCT CTTT CTTC CTTT CTTT CCTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT
* *
22515 CCTT CTTC CTTT CTTT C
1 CTTT CTTT CTTT CTTT C
22532 CCGTTTATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
3 3 0.06
4 39 0.83
5 5 0.11
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:22510 original size:21 final size:21
Alignment explanation
Indices: 22473--22532 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
22463 TACCTTTCTT
*
22473 TCTTTCTT-CTTTATTTCCTC
1 TCTTTCTTCCTTTCTTTCCTC
22493 TCTTTCTTCCTTTCTTTCCTC
1 TCTTTCTTCCTTTCTTTCCTC
*
22514 TCCTTCTTCCTTTCTTTCC
1 TCTTTCTTCCTTTCTTTCC
22533 CGTTTATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
20 8 0.22
21 29 0.78
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTTCTTCCTTTCTTTCCTC
Found at i:32531 original size:3 final size:3
Alignment explanation
Indices: 32517--32554 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
32507 GTATCTTCAT
*
32517 TTC TTC TT- TTC TTC TTC TTT TTC -TC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
32555 ACTGTCCCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:32531 original size:11 final size:11
Alignment explanation
Indices: 32517--32554 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
32507 GTATCTTCAT
32517 TTCTTCTTTTC
1 TTCTTCTTTTC
32528 TTCTTCTTTT-
1 TTCTTCTTTTC
32538 TCTCTTCTTCTTC
1 T-TCTTCTT-TTC
32551 TTCT
1 TTCT
32555 ACTGTCCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 5 0.21
13 1 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCTTCTTTTC
Found at i:32543 original size:14 final size:14
Alignment explanation
Indices: 32517--32554 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
32507 GTATCTTCAT
32517 TTCTTCTTT-TCTTC
1 TTCTT-TTTCTCTTC
32531 TTCTTTTTCTCTTC
1 TTCTTTTTCTCTTC
*
32545 TTCTTCTTCT
1 TTCTTTTTCT
32555 ACTGTCCCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTTTTCTCTTC
Found at i:34282 original size:20 final size:20
Alignment explanation
Indices: 34254--34299 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
34244 AATATTTAAC
34254 AATAAT-AAATAAATAAATAT
1 AATAATAAAATAAATAAA-AT
* *
34274 AATATTAAAATTAATAAAAT
1 AATAATAAAATAAATAAAAT
34294 AATAAT
1 AATAAT
34300 TTCATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAAAATAAATAAAAT
Found at i:43211 original size:33 final size:31
Alignment explanation
Indices: 43167--43245 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
43157 TTACCCATAA
* *
43167 AAGTGACTAAAATGTTAACGACA-ATTAACGGCT
1 AAGTGATTAAAATGTTAA-AACACATTAA-GG-T
*
43200 CAA-TGATTAAAATATTAAAACACATTAAGGT
1 -AAGTGATTAAAATGTTAAAACACATTAAGGT
43231 AAGTGATTAAAATGT
1 AAGTGATTAAAATGT
43246 ATCATGAGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 2 0.05
31 12 0.31
32 5 0.13
33 18 0.46
34 2 0.05
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (31 bp):
AAGTGATTAAAATGTTAAAACACATTAAGGT
Found at i:44796 original size:17 final size:17
Alignment explanation
Indices: 44774--44837 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
44764 AAACTCCCCT
44774 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
* * *
44791 TTAAATTT-GTTAAAAA
1 TTAAATTTATTTTAAGA
* * *
44807 TTTAAATTAAATTTAAGT
1 -TTAAATTTATTTTAAGA
44825 TTAAATTTATTTT
1 TTAAATTTATTTT
44838 CAACTTTAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
16 5 0.14
17 26 0.74
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:46738 original size:29 final size:29
Alignment explanation
Indices: 46693--47042 Score: 251
Period size: 29 Copynumber: 12.0 Consensus size: 29
46683 ACCCGAAGGT
* *
46693 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
1 CCCCGAACCTTTCAAAAATTACCA-TTTT-A
46722 CCCCGAACCTTTCAAAAATTACCATTTTA
1 CCCCGAACCTTTCAAAAATTACCATTTTA
* * * *
46751 CCCCAAAACTTCCAAAAA-TCCCATCTTTGA
1 CCCCGAACCTTTCAAAAATTACCAT-TTT-A
46781 CCCCGAACC-TTCTAAAAATTACCATTTTA
1 CCCCGAACCTTTC-AAAAATTACCATTTTA
* * * *
46810 CCCCCAAACTTCCAAAAA-TCCCATTTTTAA
1 CCCCGAACCTTTCAAAAATTACCA-TTTT-A
* *
46840 CCCCAAACCTTTTAAAAATTACCATTTTA
1 CCCCGAACCTTTCAAAAATTACCATTTTA
* * *
46869 CCCTC-AAAC-TTCAAAAAATCCCATTTTTAA
1 CCC-CGAACCTTTCAAAAATTACCA-TTTT-A
*
46899 CCCCAAACC-TTCTAAAAATTACCATTTTA
1 CCCCGAACCTTTC-AAAAATTACCATTTTA
* *
46928 CCCTC-AA-ATTTCCAAAAA-TCCCATTTTGA
1 CCC-CGAACCTTT-CAAAAATTACCATTTT-A
46957 CCCCGAACCTTTCAAAAATTACCATTTTA
1 CCCCGAACCTTTCAAAAATTACCATTTTA
*
46986 CCCTCGAA-CTTTCAAAAA-TCCCATTTTTGA
1 CCC-CGAACCTTTCAAAAATTACCA-TTTT-A
* * *
47016 CTCCGAACC-TTCCAAAACTACCATTTT
1 CCCCGAACCTTTCAAAAATTACCATTTT
47043 TCCCTCGTGC
Statistics
Matches: 260, Mismatches: 34, Indels: 54
0.75 0.10 0.16
Matches are distributed among these distances:
28 33 0.13
29 115 0.44
30 90 0.35
31 22 0.08
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (29 bp):
CCCCGAACCTTTCAAAAATTACCATTTTA
Found at i:46772 original size:59 final size:58
Alignment explanation
Indices: 46698--47048 Score: 499
Period size: 59 Copynumber: 6.0 Consensus size: 58
46688 AAGGTCCCCG
46698 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTACCC-CAA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCAAAAATTACCATTTTACCCTC-A
* *
46757 AACTTCCAAAAATCCCATCTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC-AAAAATTACCATTTTACCCTCA
* * *
46816 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTTTAAAAATTACCATTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCAAAAATTACCATTTTACCCTCA
* * *
46875 AACTTCAAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAATTACCATTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC-AAAAATTACCATTTTACCCTCA
* *
46934 AATTTCCAAAAATCCCA-TTTTGACCCCGAACCTTTCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCAAAAATTACCATTTTACCCTCA
* * * * *
46992 AACTTTCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAACTACCATTTTTCCCTC
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCTC
47049 GTGCATCCGA
Statistics
Matches: 267, Mismatches: 19, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
58 75 0.28
59 189 0.71
60 3 0.01
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCTCA
Found at i:47396 original size:96 final size:96
Alignment explanation
Indices: 47250--47434 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 96
47240 TTTAAAAAAA
* * ***
47250 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCGCTAGGTGCATTT
1 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTATGCCTTAACTCACTAGGTGCAACC
47315 TTTCTTCAAATCGAAATAATCGAACACCCTT
66 TTTCTTCAAATCGAAATAATCGAACACCCTT
* *
47346 AATCGAGGCAATGTTTCC-TTATCTTCGA--TTCTG-AAATATTATGCCTTAACTTACTAGGTGC
1 AATCGAGGCAAT-ATTCCTTTAT-TTCGAGTTTC-GAAAAT-TTATGCCTTAACTCACTAGGTGC
* *
47407 AACCTTTCTTCGAATCGAGATAATCGAA
62 AACCTTTCTTCAAATCGAAATAATCGAA
47435 TATCCTTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
95 7 0.09
96 60 0.79
97 9 0.12
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTATGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAACACCCTT
Found at i:54314 original size:15 final size:15
Alignment explanation
Indices: 54294--54332 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
54284 TTCCATTTTA
54294 TACTCTTTCCATAAC
1 TACTCTTTCCATAAC
54309 TACTCTTTCCATAAC
1 TACTCTTTCCATAAC
54324 TACTCTTTC
1 TACTCTTTC
54333 ATTTCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (15 bp):
TACTCTTTCCATAAC
Found at i:58889 original size:120 final size:120
Alignment explanation
Indices: 58676--58931 Score: 458
Period size: 120 Copynumber: 2.1 Consensus size: 120
58666 ACAAAACGAC
58676 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAA
1 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAA
* *
58741 ATCTTCGAATCTCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGTAATAAA
66 ATCTTCAAATCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGTAATAAA
58796 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAA
1 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAA
** *
58861 ATCTTCAAATCCCAGCTTCCTGATGAGATACTGTGAAGCAAGTCGAAGTAGTAAA
66 ATCTTCAAATCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGTAATAAA
*
58916 ACGGTCAGCTTCCTGA
1 ACGGTCATCTTCCTGA
58932 CCATCTCCCT
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 130 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (120 bp):
ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAA
ATCTTCAAATCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGTAATAAA
Found at i:59595 original size:6 final size:6
Alignment explanation
Indices: 59586--59663 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
59576 AAATTTGTTA
* *
59586 AAATTT AAA-TT AAATTT AAATTT -ATTTT AAATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
59632 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
59664 ATAAAGTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 34 0.60
7 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:59602 original size:11 final size:11
Alignment explanation
Indices: 59556--59630 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
59546 TAAACTCCCC
* *
59556 TTTAAATTTAT
1 TTTAAATTAAA
59567 TTTAAGATTAAA
1 TTTAA-ATTAAA
*
59579 TTT--GTTAAAA
1 TTTAAATT-AAA
59589 TTTAAATTAAA
1 TTTAAATTAAA
* *
59600 TTTAAATTTAT
1 TTTAAATTAAA
*
59611 TTTAAATTTAAG
1 TTTAAA-TTAAA
59623 TTTAAATT
1 TTTAAATT
59631 TATTTTCAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 2 0.04
10 6 0.12
11 25 0.49
12 18 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:59608 original size:17 final size:17
Alignment explanation
Indices: 59586--59668 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
59576 AAATTTGTTA
59586 AAATTTAAATTAAATTT
1 AAATTTAAATTAAATTT
**
59603 AAATTTATTTTAAATTT
1 AAATTTAAATTAAATTT
* * *
59620 AAGTTTAAATTTATTTT
1 AAATTTAAATTAAATTT
59637 CAAATTTAAAATT--ATTAT
1 -AAATTT-AAATTAAATT-T
*
59655 AAATTTAAAATAAA
1 AAATTTAAATTAAA
59669 GTTCAAATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
16 4 0.08
17 35 0.69
18 7 0.14
19 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (17 bp):
AAATTTAAATTAAATTT
Found at i:59628 original size:12 final size:12
Alignment explanation
Indices: 59589--59645 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 12
59579 TTTGTTAAAA
*
59589 TTTAAA-TTAAA
1 TTTAAATTTAAT
59600 TTTAAATTT-AT
1 TTTAAATTTAAT
*
59611 TTTAAATTTAAG
1 TTTAAATTTAAT
59623 TTTAAATTT-AT
1 TTTAAATTTAAT
59634 TTTCAAATTTAA
1 TTT-AAATTTAA
59646 AATTATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 20 0.51
12 18 0.46
13 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAT
Found at i:60715 original size:21 final size:23
Alignment explanation
Indices: 60686--60729 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
60676 GGGGAAAACC
*
60686 GTTTAGATCTAG-GCTAGATCTG
1 GTTTAGATCTAGACCTAGATCTG
60708 GTTT-GATCTAGACCTAGATCTG
1 GTTTAGATCTAGACCTAGATCTG
60730 TTCTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (23 bp):
GTTTAGATCTAGACCTAGATCTG
Found at i:61609 original size:58 final size:59
Alignment explanation
Indices: 61534--61924 Score: 585
Period size: 58 Copynumber: 6.7 Consensus size: 59
61524 CCCCGAAGGT
61534 CCCT-GAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
**
61592 CCCTCGAACTT-CAAAAATCTCATTTTTGACCCCGAACCTTTCGAAAATTACCATTTTA
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
** *
61650 CCCTCGAACTT-CAAAAATCTCATTTTTGACCCCGAACCTTTCGAAATTTACCATTTTA
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
* * *
61708 CCCTTGAACTT-CAAAAATCTCATTTTTGACCCCGAACATTCTAAAAATTACCATTTTA
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
* * * * *
61766 CCC-CTGAACTTCCAAAAATCCCATTTTTAACCTCAAACCTTCTAAAAATTACCATTTTA
1 CCCTC-GAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
* *
61825 CCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
* *
61884 CCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTT
1 CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
61925 CCAAAACTAT
Statistics
Matches: 308, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
58 167 0.54
59 140 0.45
60 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (59 bp):
CCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTA
Found at i:61939 original size:30 final size:29
Alignment explanation
Indices: 61538--61940 Score: 277
Period size: 30 Copynumber: 13.8 Consensus size: 29
61528 GAAGGTCCCT
61538 GAACTTCCAAAAAT-CTCATTTTTGACCCC
1 GAACTTCCAAAAATAC-CATTTTTGACCCC
**
61567 GAACCTTTTAAAAATTACCA-TTTT-ACCCTC
1 GAA-CTTCCAAAAA-TACCATTTTTGACCC-C
61597 GAACTT-CAAAAAT-CTCATTTTTGACCCC
1 GAACTTCCAAAAATAC-CATTTTTGACCCC
* *
61625 GAACCTTTCGAAAATTACCA-TTTT-ACCCTC
1 GAA-C-TTCCAAAAATACCATTTTTGACCC-C
61655 GAACTT-CAAAAAT-CTCATTTTTGACCCC
1 GAACTTCCAAAAATAC-CATTTTTGACCCC
* ** *
61683 GAACCTTTCGAAATTTACCA-TTTT-ACCCTT
1 GAA-C-TTCCAAAAATACCATTTTTGACCC-C
61713 GAACTT-CAAAAAT-CTCATTTTTGACCCC
1 GAACTTCCAAAAATAC-CATTTTTGACCCC
*
61741 GAACATTCTAAAAATTACCA-TTTT-ACCCC
1 GAAC-TTCCAAAAA-TACCATTTTTGACCCC
* * *
61770 TGAACTTCCAAAAATCCCATTTTTAACCTC
1 -GAACTTCCAAAAATACCATTTTTGACCCC
* *
61800 AAACCTTCTAAAAATTACCA-TTTT-ACCCCC
1 GAA-CTTCCAAAAA-TACCATTTTTGA-CCCC
*
61830 GAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACTTCCAAAAATACCATTTTTGACCCC
**
61859 GAACCTTTTAAAAATTACCA-TTTT-ACCCTC
1 GAA-CTTCCAAAAA-TACCATTTTTGACCC-C
* *
61889 GAACTTCCAAAAATCCCATTTTTGACTCC
1 GAACTTCCAAAAATACCATTTTTGACCCC
* *
61918 GAACCTTCCAAAACTATCATTTT
1 GAA-CTTCCAAAAATACCATTTT
61941 GCCCCCGTGC
Statistics
Matches: 297, Mismatches: 36, Indels: 81
0.72 0.09 0.20
Matches are distributed among these distances:
26 3 0.01
27 16 0.05
28 45 0.15
29 96 0.32
30 106 0.36
31 27 0.09
32 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
GAACTTCCAAAAATACCATTTTTGACCCC
Found at i:78041 original size:2 final size:2
Alignment explanation
Indices: 78034--78078 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
78024 ATTTTGAGTG
78034 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
78074 GA GA G
1 GA GA G
78079 TGTTGGAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:78340 original size:14 final size:15
Alignment explanation
Indices: 78301--78346 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
78291 TTTTTCAAAA
78301 TTTT-AGAATTTAAT
1 TTTTAAGAATTTAAT
* *
78315 TTTT-A-ATTTTTAT
1 TTTTAAGAATTTAAT
78328 TTTTAAGAATTTAAT
1 TTTTAAGAATTTAAT
78343 TTTT
1 TTTT
78347 TTACTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 10 0.38
14 6 0.23
15 10 0.38
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTTAAGAATTTAAT
Found at i:79505 original size:2 final size:2
Alignment explanation
Indices: 79498--79549 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
79488 GATTGCATTG
79498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79540 AT AT AT AT AT
1 AT AT AT AT AT
79550 GTTTCATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80084 original size:26 final size:27
Alignment explanation
Indices: 80033--80084 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
80023 CATAAATTAA
* *
80033 AAATCTAAAATTTTAAAACAGGAAAAG
1 AAATCTAAAACTTTAAAACAGCAAAAG
80060 AAAT-TAAAACTTTAAAA-AGACAAAA
1 AAATCTAAAACTTTAAAACAG-CAAAA
80085 ACCAGTCGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 16 0.73
27 4 0.18
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (27 bp):
AAATCTAAAACTTTAAAACAGCAAAAG
Found at i:84395 original size:2 final size:2
Alignment explanation
Indices: 84388--84416 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84378 AATCGTGTAA
84388 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 A
84417 CTGGTGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85577 original size:39 final size:39
Alignment explanation
Indices: 85534--85609 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
85524 TTTTTATATA
**
85534 TTTTTTATAATTTTAATG-ATTTTTAATTTTTAAAAATAG
1 TTTTTTA-AATTTTAATGAATTTTTAAAATTTAAAAATAG
**
85573 TTTTTTAAATTTTTTTGAATTTTTAAAATTTAAAAAT
1 TTTTTTAAATTTTAATGAATTTTTAAAATTTAAAAAT
85610 TAAATATGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 8 0.25
39 24 0.75
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
TTTTTTAAATTTTAATGAATTTTTAAAATTTAAAAATAG
Found at i:93327 original size:7 final size:7
Alignment explanation
Indices: 93315--93343 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
93305 GCTCTTGCTC
93315 TTCTTTT
1 TTCTTTT
93322 TTCTTTT
1 TTCTTTT
93329 TTCTTTT
1 TTCTTTT
93336 TT-TTTT
1 TTCTTTT
93342 TT
1 TT
93344 GACCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTCTTTT
Found at i:96495 original size:15 final size:16
Alignment explanation
Indices: 96462--96492 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
96452 AAAAATATAT
96462 TAAAAATCCTAAACCC
1 TAAAAATCCTAAACCC
96478 TAAAAATCCTAAACC
1 TAAAAATCCTAAACC
96493 TAACAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAATCCTAAACCC
Found at i:102114 original size:9 final size:9
Alignment explanation
Indices: 102100--102148 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
102090 GCAAATGATT
102100 TTAAAATTA
1 TTAAAATTA
102109 TTAAAATTA
1 TTAAAATTA
*
102118 TTTTTAAAAATA
1 ---TTAAAATTA
102130 -TAAAATTA
1 TTAAAATTA
102138 TTAAAATTA
1 TTAAAATTA
102147 TT
1 TT
102149 GTATTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.21
9 19 0.56
12 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:102120 original size:20 final size:19
Alignment explanation
Indices: 102092--102177 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 19
102082 TCGCATCAGC
*
102092 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTA-TA
*
102112 AAATTATTTTTAAAAATATA
1 AAATTA-TTTTAAAATTATA
*
102132 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATA
**
102149 GTATTATTTTTAAAA-TATA
1 AAATTA-TTTTAAAATTATA
102168 AAATTATTTT
1 AAATTATTTT
102178 GTCTTTTTCC
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 13 0.25
18 4 0.08
19 7 0.13
20 19 0.36
21 10 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AAATTATTTTAAAATTATA
Found at i:102162 original size:29 final size:28
Alignment explanation
Indices: 102097--102177 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
102087 TCAGCAAATG
102097 ATTTTAAAATTATTAAAATTATTTTTAAA
1 ATTTTAAAATTATTAAAATTATTTTT-AA
* *
102126 AATATAAAATTATTAAAATTATTGTATT-A
1 ATTTTAAAATTATTAAAATTATT-T-TTAA
*
102155 TTTTTAAAA-TA-TAAAATTATTTT
1 ATTTTAAAATTATTAAAATTATTTT
102178 GTCTTTTTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 10 0.22
28 2 0.04
29 28 0.62
30 1 0.02
31 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTTAAAATTATTAAAATTATTTTTAA
Found at i:102171 original size:36 final size:38
Alignment explanation
Indices: 102100--102175 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 38
102090 GCAAATGATT
102100 TTAAAATTATTAAAATTATTTTTAAAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTAAAAATATAAAATTA
**
102138 TTAAAATTATT-GTATTATTTTT-AAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTAAAAATATAAAATTA
102174 TT
1 TT
102176 TTGTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 16 0.44
37 9 0.25
38 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
TTAAAATTATTAAAATTATTTTTAAAAATATAAAATTA
Found at i:103330 original size:2 final size:2
Alignment explanation
Indices: 103313--103353 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
103303 TCAGTGTGAG
*
103313 AT AT CT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103354 CAGCAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110981 original size:31 final size:31
Alignment explanation
Indices: 110943--111004 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
110933 AATCAAAGAA
110943 CAATTTCATCCATTTGTACTGTTGAAAACTG
1 CAATTTCATCCATTTGTACTGTTGAAAACTG
110974 CAATTTCATCCATTTGTACTGTTGAAAACTG
1 CAATTTCATCCATTTGTACTGTTGAAAACTG
111005 ACATGGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (31 bp):
CAATTTCATCCATTTGTACTGTTGAAAACTG
Found at i:111933 original size:31 final size:31
Alignment explanation
Indices: 111898--111971 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
111888 TAACGGTGGT
** * *
111898 CGTAAGATTAAATTTTGTAACGATATTGTAG
1 CGTAAGACAAAATATTGTAACGATACTGTAG
111929 CGTAAGACAAAATATTGTAACGATACTGTAG
1 CGTAAGACAAAATATTGTAACGATACTGTAG
*
111960 CGTGAGACAAAA
1 CGTAAGACAAAA
111972 AATAAGTTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (31 bp):
CGTAAGACAAAATATTGTAACGATACTGTAG
Found at i:114068 original size:14 final size:13
Alignment explanation
Indices: 114047--114090 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
114037 TAGTCAAATG
114047 AAAAAGAAAACTA
1 AAAAAGAAAACTA
114060 AAGAAAGAAAGAC--
1 AA-AAAGAAA-ACTA
114073 AAAAAGAAAACTA
1 AAAAAGAAAACTA
114086 AAAAA
1 AAAAA
114091 AGAGAGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.07
12 7 0.26
13 9 0.33
14 7 0.26
15 2 0.07
ACGTcount: A:0.77, C:0.07, G:0.11, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAACTA
Found at i:114092 original size:14 final size:14
Alignment explanation
Indices: 114047--114093 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
114037 TAGTCAAATG
114047 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
*
114061 AGAAAGAAAGAC---
1 AAAAAGAAA-ACTAA
114073 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
114087 AAAAAGA
1 AAAAAGA
114094 GAGGAGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 2 0.07
12 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAACTAA
Found at i:114134 original size:18 final size:16
Alignment explanation
Indices: 114111--114146 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
114101 TGAACAGTTT
114111 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
114129 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
114145 TT
1 TT
114147 CTCATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:115998 original size:26 final size:26
Alignment explanation
Indices: 115954--116026 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
115944 TATTTTCTTG
* * * *
115954 AAATTTTACCAAGGATAAAATTATCA
1 AAATTTTATCGAGGGTAAAATCATCA
* *
115980 AAATTTTATCGAGGGTAAAATCGTGA
1 AAATTTTATCGAGGGTAAAATCATCA
*
116006 AAATTTTAAT-GGGGGTAAAAT
1 AAATTTT-ATCGAGGGTAAAAT
116027 AGGGATGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (26 bp):
AAATTTTATCGAGGGTAAAATCATCA
Found at i:118216 original size:7 final size:7
Alignment explanation
Indices: 118160--118216 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 7
118150 TTTAAAATAA
118160 AAATATT
1 AAATATT
118167 AAAT-TT
1 AAATATT
118173 AAAT-TT
1 AAATATT
*
118179 AAA-ATA
1 AAATATT
*
118185 AAAAATT
1 AAATATT
118192 ATAATATT
1 A-AATATT
118200 AAATATTT
1 AAATA-TT
118208 AAATATT
1 AAATATT
118215 AA
1 AA
118217 GAAATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
6 15 0.35
7 15 0.35
8 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:118226 original size:33 final size:28
Alignment explanation
Indices: 118148--118226 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 28
118138 AAGTTAGATT
118148 TATTTAAAATAAAAATATTA-AATTTAA
1 TATTTAAAATAAAAATATTATAATTTAA
118175 -ATTTAAAATAAAAA-ATTATAATATTAAA
1 TATTTAAAATAAAAATATTATAAT-TT-AA
118203 TATTTAAATATTAAGAAATATTAT
1 TATTTAAA-A-TAA-AAATATTAT
118227 TGACTTTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.09
26 17 0.39
27 2 0.05
28 2 0.05
29 7 0.16
30 1 0.02
31 3 0.07
32 3 0.07
33 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
TATTTAAAATAAAAATATTATAATTTAA
Found at i:118410 original size:24 final size:23
Alignment explanation
Indices: 118369--118431 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
118359 TATTATATTC
* *
118369 ATTA-AAAATATAAAAAATTTATA
1 ATTATAAAAT-TATAAAATATATA
118392 TATTATAAAATTATAAAATATATA
1 -ATTATAAAATTATAAAATATATA
* *
118416 ATT-TTAAATTTTAAAA
1 ATTATAAAATTATAAAA
118432 ATTGAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 11 0.32
23 3 0.09
24 15 0.44
25 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTATAAAATTATAAAATATATA
Found at i:118556 original size:12 final size:11
Alignment explanation
Indices: 118527--118577 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
118517 AACCTTGAAA
118527 TTTAAATAATTT
1 TTTAAA-AATTT
118539 TATTAAAAATTAT
1 T-TTAAAAATT-T
*
118552 TTT-AAAACTT
1 TTTAAAAATTT
118562 TTTAAAATATTT
1 TTTAAAA-ATTT
118574 TTTA
1 TTTA
118578 CGTTTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 4 0.12
11 8 0.24
12 14 0.42
13 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAAAATTT
Found at i:118667 original size:16 final size:16
Alignment explanation
Indices: 118646--118694 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
118636 ATTATCATAT
* *
118646 TTTTTTGTAAATTTTA
1 TTTTTTATAAATTATA
118662 TTTTTTATAAATTATA
1 TTTTTTATAAATTATA
* *
118678 TTTTTTCTAGATTATA
1 TTTTTTATAAATTATA
118694 T
1 T
118695 ATAATGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTTTTATAAATTATA
Found at i:119215 original size:30 final size:29
Alignment explanation
Indices: 119146--119215 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
119136 TCAGAACCCC
* * * **
119146 TAAAATGATAAAATTTTAATTTAGATTTT
1 TAAAATTATAAAATTTTAAATTAGAATGG
*
119175 TATAATTTATAAAATTTTAAATTAGTAATGG
1 TA-AAATTATAAAATTTTAAATTAG-AATGG
119206 TAAAATTATA
1 TAAAATTATA
119216 TTTTGACTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 2 0.06
30 26 0.81
31 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (29 bp):
TAAAATTATAAAATTTTAAATTAGAATGG
Found at i:119566 original size:23 final size:21
Alignment explanation
Indices: 119533--119578 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
119523 GAAAAAGTTG
*
119533 AAGATAGATATAATACAAAAT
1 AAGATAGATATAAAACAAAAT
*
119554 AAGACTAGAATATAAAATAAAAT
1 AAGA-TAG-ATATAAAACAAAAT
119577 AA
1 AA
119579 AATGCTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 3 0.14
23 14 0.67
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
AAGATAGATATAAAACAAAAT
Found at i:121247 original size:2 final size:2
Alignment explanation
Indices: 121240--121283 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
121230 ATGTTAAATA
121240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121282 AT
1 AT
121284 TAAATCACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121484 original size:38 final size:36
Alignment explanation
Indices: 121403--121484 Score: 85
Period size: 38 Copynumber: 2.2 Consensus size: 36
121393 TATTTAATAC
* * *
121403 AATAAATTATTTATTATATTTATTTGTTTTTTTAAT
1 AATAAAATATTTATTATATTTATTAGTTTTCTTAAT
121439 AGAATAAAATATTTATTATATTTATAGTAGTGTTTCTTAAT
1 --AATAAAATATTTATTATATTTAT--TAGT-TTTCTTAAT
121480 -ATAAA
1 AATAAA
121485 TACTTTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
38 27 0.71
40 3 0.08
41 8 0.21
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (36 bp):
AATAAAATATTTATTATATTTATTAGTTTTCTTAAT
Found at i:123182 original size:59 final size:58
Alignment explanation
Indices: 122655--123229 Score: 344
Period size: 59 Copynumber: 9.5 Consensus size: 58
122645 AGAGAAAGTT
* *
122655 GGTGTCGACCATTGCATGGCCAACACCAAAAAATTTGATTTATTTATCAGATAAATAGG
1 GGTGTCGACCATTGCATGGCCAACACC-AAAAATTTGATTTTTTTATCAGATAAAAAGG
* * ** * * * *
122714 GGTGTCGGCCATGGCATGATCAACACCAAAAAAATTGA-ATTTTTATCTGACAAAAAGGG
1 GGTGTCGACCATTGCATGGCCAACACC-AAAAATTTGATTTTTTTATCAGATAAAAA-GG
* *
122773 GGTGTCGACCATGGTAT-GCCTAACACCCAAAAATTTGA-TTTTTTATTCAGATAAAAAGG
1 GGTGTCGACCATTGCATGGCC-AACA-CCAAAAATTTGATTTTTTTA-TCAGATAAAAAGG
* ** * * * *
122832 AGTGTCGGTCA-TGCAATGACCAACACAAAAAAAAAATTGAAATTTTTTTACCAGATAAAAAAAG
1 GGTGTCGACCATTGC-ATGGCCAACAC---CAAAAATTTG--ATTTTTTTATCAGAT--AAAAAG
122896 G
58 G
* ** *
122897 GGTGTCGACCATTGCATGGCCAACA-CAAAATTTTTTTTTATTTTTTACCAGATAAAAAAGG
1 GGTGTCGACCATTGCATGGCCAACACCAAAA--ATTTGAT-TTTTTTATCAGAT-AAAAAGG
*
122958 TGTGTCGACCA-TGACATGGCCAACACCCAAAAATTTGA-TTTTTTATTCAGATAAAAAGG
1 GGTGTCGACCATTG-CATGGCCAACA-CCAAAAATTTGATTTTTTTA-TCAGATAAAAAGG
* * * * ***** *
123017 AGTGTCGGCCA-TGCAATGGCCAATACCAAAAAAAATTTTAAAAAAAATTATCTG--AAAAAGAG
1 GGTGTCGACCATTGC-ATGGCCAACACC---AAAAA-TTT-GATTTTTTTATCAGATAAAAAG-G
* * * * *
123079 GGTGTCGATCATTGCATGACTAACACCAAAAAAATTGATTTTTTTATCAGATAAATAGG
1 GGTGTCGACCATTGCATGGCCAACACC-AAAAATTTGATTTTTTTATCAGATAAAAAGG
* ** *
123138 GGTGTTGGTCATTGCATGGCCAACACGCAAAAATTTGATTTTTTTTTTATCAGATTAAAAGGG
1 GGTGTCGACCATTGCATGGCCAACAC-CAAAAATTTGA---TTTTTTTATCAGA-TAAAAAGG
* **
123201 GGTCTCGGGCA-TGCAATGGCCAACACCAA
1 GGTGTCGACCATTGC-ATGGCCAACACCAA
123230 TTTTTTTTTA
Statistics
Matches: 402, Mismatches: 75, Indels: 75
0.73 0.14 0.14
Matches are distributed among these distances:
58 26 0.06
59 153 0.38
60 32 0.08
61 56 0.14
62 53 0.13
63 45 0.11
64 10 0.02
65 24 0.06
66 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (58 bp):
GGTGTCGACCATTGCATGGCCAACACCAAAAATTTGATTTTTTTATCAGATAAAAAGG
Found at i:125029 original size:16 final size:16
Alignment explanation
Indices: 124987--125035 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
124977 TTAAAATGAT
*
124987 AAATTTTTAATTTATA
1 AAATTTATAATTTATA
**
125003 ATCTTTATAATTTATA
1 AAATTTATAATTTATA
* *
125019 AAATTTCTAATTAATA
1 AAATTTATAATTTATA
125035 A
1 A
125036 TTTAATTTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTATAATTTATA
Found at i:126924 original size:20 final size:19
Alignment explanation
Indices: 126895--126985 Score: 110
Period size: 20 Copynumber: 4.6 Consensus size: 19
126885 CAGGGGGACA
*
126895 TCTACCCATACAAGTCGATT
1 TCTACCCATACAAGTC-ACT
*
126915 TCTACTCATACAAGTCACT
1 TCTACCCATACAAGTCACT
*
126934 TCTACCCATGCAAGTACACT
1 TCTACCCATACAAGT-CACT
*
126954 TCTACCTATACAAGTCCACT
1 TCTACCCATACAAGT-CACT
*
126974 TCTACCCTTACA
1 TCTACCCATACA
126986 TTTTGTGAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.25
20 46 0.75
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.30
Consensus pattern (19 bp):
TCTACCCATACAAGTCACT
Found at i:126939 original size:39 final size:40
Alignment explanation
Indices: 126895--126985 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 40
126885 CAGGGGGACA
*
126895 TCTACCCATACAAGT-CGATTTCTA-CTCATACAAGT-CACT
1 TCTACCCATACAAGTAC-ACTTCTACCT-ATACAAGTCCACT
*
126934 TCTACCCATGCAAGTACACTTCTACCTATACAAGTCCACT
1 TCTACCCATACAAGTACACTTCTACCTATACAAGTCCACT
*
126974 TCTACCCTTACA
1 TCTACCCATACA
126986 TTTTGTGAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 28 0.62
40 17 0.38
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.30
Consensus pattern (40 bp):
TCTACCCATACAAGTACACTTCTACCTATACAAGTCCACT
Found at i:128946 original size:6 final size:6
Alignment explanation
Indices: 128937--129014 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
128927 ATTTGTTTAA
* *
128937 AAATTT AAATTT -ACTTT AAATTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
128983 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
129015 ATTATCATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 16 0.28
6 37 0.65
7 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:128971 original size:11 final size:11
Alignment explanation
Indices: 128957--129012 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
128947 TTACTTTAAA
128957 TTTAAATTTAT
1 TTTAAATTTAT
*
128968 TTTAAATTTAAA
1 TTTAAATTT-AT
*
128980 TTT-AATTTAAG
1 TTTAAATTT-AT
*
128991 TTTAAAATTAT
1 TTTAAATTTAT
129002 TTTCAAATTTA
1 TTT-AAATTTA
129013 AAATTATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:128999 original size:35 final size:34
Alignment explanation
Indices: 128905--129031 Score: 139
Period size: 35 Copynumber: 3.7 Consensus size: 34
128895 CCAAACTCCC
* * * *
128905 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTT-TAAA
*
128940 TTTAAATTTACTTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTTAAA
* *
128974 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTT-AAA
* *
129009 TTTAAAATT-ATCATAAATTTAAA
1 TTTAAATTTAAT-TTAAATTTAAA
129032 ATAAATAAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
34 33 0.41
35 47 0.59
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (34 bp):
TTTAAATTTAATTTAAATTTAAATTTATTTTAAA
Found at i:128999 original size:52 final size:51
Alignment explanation
Indices: 128905--129031 Score: 141
Period size: 52 Copynumber: 2.5 Consensus size: 51
128895 CCAAACTCCC
* *
128905 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAATTTAAATTTACTTT-AAA
1 TTTAAATTTATTTTAAATTTAAATTTATTT-AAAATTTAAA-TTACTTTCAAA
* *
128957 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTT-ATTTAAAATTT-AAATTACTTTCAAA
* **
129009 TTTAAAATTATCATAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
129032 ATAAATAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
51 11 0.17
52 51 0.78
53 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (51 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAATTTAAATTACTTTCAAA
Found at i:129028 original size:17 final size:17
Alignment explanation
Indices: 128905--129033 Score: 123
Period size: 17 Copynumber: 7.5 Consensus size: 17
128895 CCAAACTCCC
*
128905 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * * *
128922 ATTAAATTTGTTTAAAAA
1 TTTAAAATTATTT-TAAA
* *
128940 TTTAAATTTACTTTAAA
1 TTTAAAATTATTTTAAA
*
128957 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * *
128974 TTTAAATTTAATTTAAG
1 TTTAAAATTATTTTAAA
128991 TTTAAAATTATTTTCAAA
1 TTTAAAATTATTTT-AAA
**
129009 TTTAAAATTATCATAAA
1 TTTAAAATTATTTTAAA
129026 TTTAAAAT
1 TTTAAAAT
129034 AAATAAAGCC
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
17 68 0.72
18 27 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:131232 original size:6 final size:6
Alignment explanation
Indices: 131221--131265 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
131211 AGATCAAAAT
* * *
131221 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
131266 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:134473 original size:20 final size:20
Alignment explanation
Indices: 134448--134489 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
134438 TGCTTCAATG
134448 TATCCAAGAACTGCTGATAC
1 TATCCAAGAACTGCTGATAC
134468 TATCCAAGAACTGCTGATAC
1 TATCCAAGAACTGCTGATAC
134488 TA
1 TA
134490 CTTATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (20 bp):
TATCCAAGAACTGCTGATAC
Found at i:135090 original size:21 final size:21
Alignment explanation
Indices: 135048--135091 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
135038 CTGATTCTAG
*
135048 TGTGGATGCATCTGGCTTTGC
1 TGTGGATGCATCTGGCTGTGC
135069 TGTGGATGCATCTGAG-TGTGC
1 TGTGGATGCATCTG-GCTGTGC
135090 TG
1 TG
135092 ATTGTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.11, C:0.16, G:0.36, T:0.36
Consensus pattern (21 bp):
TGTGGATGCATCTGGCTGTGC
Found at i:138245 original size:19 final size:19
Alignment explanation
Indices: 138218--138388 Score: 126
Period size: 19 Copynumber: 9.0 Consensus size: 19
138208 CCAGTACAGT
138218 ATATTGCTCTTACGAGCCA
1 ATATTGCTCTTACGAGCCA
* **
138237 ATATCGCTCTTACGAGGTA
1 ATATTGCTCTTACGAGCCA
* * *
138256 GTATTGCTCTCAAGAGCCA
1 ATATTGCTCTTACGAGCCA
* * *
138275 TTATTGCTCTGACGAGCTA
1 ATATTGCTCTTACGAGCCA
* *
138294 GTATTGCTCTTATGAGCCA
1 ATATTGCTCTTACGAGCCA
* ** * * *
138313 GTATTGGGCTCACAAGCTA
1 ATATTGCTCTTACGAGCCA
* * *
138332 GTATTACTCTTACGAGTCA
1 ATATTGCTCTTACGAGCCA
* **
138351 ATATTGCTCTGACGAGTTA
1 ATATTGCTCTTACGAGCCA
*
138370 GTATTGCTCTTACGAGCCA
1 ATATTGCTCTTACGAGCCA
138389 GTGTATCTTT
Statistics
Matches: 114, Mismatches: 38, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 114 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (19 bp):
ATATTGCTCTTACGAGCCA
Found at i:138273 original size:38 final size:38
Alignment explanation
Indices: 138219--138388 Score: 205
Period size: 38 Copynumber: 4.5 Consensus size: 38
138209 CAGTACAGTA
* * *
138219 TATTGCTCTTACGAGCCAATATCGCTCTTACGAGGTAG
1 TATTGCTCTTACGAGCCAATATTGCTCTGACGAGCTAG
* * *
138257 TATTGCTCTCAAGAGCCATTATTGCTCTGACGAGCTAG
1 TATTGCTCTTACGAGCCAATATTGCTCTGACGAGCTAG
* * ** * *
138295 TATTGCTCTTATGAGCCAGTATTGGGCTCACAAGCTAG
1 TATTGCTCTTACGAGCCAATATTGCTCTGACGAGCTAG
* * *
138333 TATTACTCTTACGAGTCAATATTGCTCTGACGAGTTAG
1 TATTGCTCTTACGAGCCAATATTGCTCTGACGAGCTAG
138371 TATTGCTCTTACGAGCCA
1 TATTGCTCTTACGAGCCA
138389 GTGTATCTTT
Statistics
Matches: 108, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 108 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (38 bp):
TATTGCTCTTACGAGCCAATATTGCTCTGACGAGCTAG
Found at i:138373 original size:57 final size:56
Alignment explanation
Indices: 138219--138390 Score: 157
Period size: 57 Copynumber: 3.0 Consensus size: 56
138209 CAGTACAGTA
* * * *
138219 TATTGCTCTTACGAGCCAATATCGCTCTTACGAGGTAGTATTGCTCTCAAGAGCCAT
1 TATTGCTCTTACGAG-CAATATTGCTCTTACGAGCTAGTATTGCGCTCAAGAGCCAG
* * * * * *
138276 TATTGCTCTGACGAGCTAGTATTGCTCTTATGAGCCAGTATTGGGCTCACA-AGCTAG
1 TATTGCTCTTACGAGC-AATATTGCTCTTACGAGCTAGTATTGCGCTCA-AGAGCCAG
* * * * * *
138333 TATTACTCTTACGAGTCAATATTGCTCTGACGAGTTAGTATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAG-CAATATTGCTCTTACGAGCTAGTATTGCGCTCAAGAGCCAG
138390 T
1 T
138391 GTATCTTTAG
Statistics
Matches: 89, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
56 1 0.01
57 86 0.97
58 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (56 bp):
TATTGCTCTTACGAGCAATATTGCTCTTACGAGCTAGTATTGCGCTCAAGAGCCAG
Found at i:144044 original size:40 final size:40
Alignment explanation
Indices: 143999--144281 Score: 249
Period size: 40 Copynumber: 7.2 Consensus size: 40
143989 AATATTGATG
*
143999 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
** * ** * * * *
144039 CTTCAATCTGCCCTTTAATTAGGGTAAAAGATTAG-AT-A
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
144077 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
* * ** * * *
144117 CTTCAATCTACCCTC-TAATTAGGGTAAAAAATTGG-ATG-
1 CTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGTGTGT
* *
144155 CTTCAATCTGCTCCATGATCGGGGTAAGGGATTGGTGTGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
* * *** * *
144195 TTTCAATTTGCCCTC-TGATTAAGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGTGTGT
*
144233 CTTCAAGCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
144273 CTTCAATCT
1 CTTCAATCT
144282 ACCCTTTGAT
Statistics
Matches: 180, Mismatches: 53, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
37 2 0.01
38 79 0.44
39 10 0.06
40 87 0.48
41 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (40 bp):
CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
Found at i:144087 original size:38 final size:38
Alignment explanation
Indices: 143963--144317 Score: 138
Period size: 40 Copynumber: 9.2 Consensus size: 38
143953 GTAACCTATT
* * * * *
143963 TTCACTCTGCCCTCTAGTTAGGGTAAAATATT-GATGC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
* * * ** * * *
144000 TTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGG-AT-AC
* *
144040 TTCAATCTGCCCTTTAATTAGGGTAAAAGATTAGATAC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
* * ** * * *
144078 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGG-AT-AC
* * * *
144118 TTCAATCTACCCTCTAATTAGGGTAAAAAATTGGATGC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
* ** ** * **
144156 TTCAATCTGCTCC-ATGATCGGGGTAAGGGATTGGTGTGTT
1 TTCAATCTGC-CCTATAATTAGGGTAAAAGATTGG-AT-AC
* * * * *
144196 TTCAATTTGCCCTCTGATTAAGGTAAAAGATTGGATGC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
* * * ** * * *
144234 TTCAAGCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGG-AT-AC
* * * * * *
144274 TTCAATCTACCCTTTGATTAGAGTAAAAGATTTGATGC
1 TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
144312 TTCAAT
1 TTCAAT
144318 AAGAGATTGG
Statistics
Matches: 224, Mismatches: 83, Indels: 21
0.68 0.25 0.06
Matches are distributed among these distances:
37 22 0.10
38 86 0.38
39 12 0.05
40 104 0.46
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (38 bp):
TTCAATCTGCCCTATAATTAGGGTAAAAGATTGGATAC
Found at i:144096 original size:78 final size:78
Alignment explanation
Indices: 143963--144317 Score: 514
Period size: 78 Copynumber: 4.6 Consensus size: 78
143953 GTAACCTATT
* * * *
143963 TTCACTCTGCCCTCTAGTTAGGGTAAAATATT-GATGCTTCAATCTACCCCATGATCGGGGTAAG
1 TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAG
144027 AGATTGGTGTGTC
66 AGATTGGTGTGTC
* * *
144040 TTCAATCTGCCCTTTAATTAGGGTAAAAGATTAGATACTTCAATCTGCCCCATGATCGGGGTAAG
1 TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAG
144105 AGATTGGTGTGTC
66 AGATTGGTGTGTC
* * *
144118 TTCAATCTACCCTCTAATTAGGGTAAAAAATTGGATGCTTCAATCTGCTCCATGATCGGGGTAAG
1 TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAG
* *
144183 GGATTGGTGTGTT
66 AGATTGGTGTGTC
* * * *
144196 TTCAATTTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAAGCTGCCCCATGATCGGGGTAAG
1 TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAG
144261 AGATTGGTGTGTC
66 AGATTGGTGTGTC
* * * * *
144274 TTCAATCTACCCTTTGATTAGAGTAAAAGATTTGATGCTTCAAT
1 TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAAT
144318 AAGAGATTGG
Statistics
Matches: 247, Mismatches: 30, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
77 28 0.11
78 219 0.89
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (78 bp):
TTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAG
AGATTGGTGTGTC
Found at i:144279 original size:156 final size:154
Alignment explanation
Indices: 143963--144411 Score: 561
Period size: 156 Copynumber: 3.0 Consensus size: 154
143953 GTAACCTATT
* * * * * *
143963 TTCACTCTGCCCTCTAGTTAGGGTAAAATATTGATGCTTCAATCTACCCCATGATCGGGGTAAGA
1 TTCAATCTACCCTCTAATTAGGGTAAAAAATTGATGCTTCAATCT-GCCCATGATCGGGGTAAGG
* * * * *
144028 GATTGGTGTGTCTTCAATCTGCCCTTTAATTAGGGTAAAAGATTAGATACTTCAATCTGCCCCAT
65 GATTGGTGTGTCTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCAT
144093 GATCGGGGTAAGAGATTGGTGTGTC
130 GATCGGGGTAAGAGATTGGTGTGTC
144118 TTCAATCTACCCTCTAATTAGGGTAAAAAATTGGATGCTTCAATCTGCTCCATGATCGGGGTAAG
1 TTCAATCTACCCTCTAATTAGGGTAAAAAATT-GATGCTTCAATCTGC-CCATGATCGGGGTAAG
* * *
144183 GGATTGGTGTGTTTTCAATTTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAAGCTGCCCCA
64 GGATTGGTGTGTCTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCA
144248 TGATCGGGGTAAGAGATTGGTGTGTC
129 TGATCGGGGTAAGAGATTGGTGTGTC
* * * * **
144274 TTCAATCTACCCTTTGATTAGAGTAAAAGATTTGATGCTTCAATAAG---A-GAT-----T---G
1 TTCAATCTACCCTCTAATTAGGGTAAAA-AATTGATGCTTCAATCTGCCCATGATCGGGGTAAGG
*
144327 G--T-GTGTGTCTTCAATTTGCCCTCTGCTTAGGGTAAAAG-TTGGATGCTTCAATCTGCCCCAT
65 GATTGGTGTGTCTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCAT
144388 GATCGGGGTAAGAGATTGGTGTGT
130 GATCGGGGTAAGAGATTGGTGTGT
144412 ACCTTCGCTT
Statistics
Matches: 267, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
139 46 0.17
140 33 0.12
141 1 0.00
143 2 0.01
146 1 0.00
151 3 0.01
152 1 0.00
155 29 0.11
156 148 0.55
157 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (154 bp):
TTCAATCTACCCTCTAATTAGGGTAAAAAATTGATGCTTCAATCTGCCCATGATCGGGGTAAGGG
ATTGGTGTGTCTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATG
ATCGGGGTAAGAGATTGGTGTGTC
Found at i:144362 original size:62 final size:59
Alignment explanation
Indices: 144257--144378 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 59
144247 ATGATCGGGG
* *
144257 TAAGAGATTGGTGTGTCTTCAATCTACCCTTTGATTAGAGTAAAAGATTTGATGCTTCAA
1 TAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGAGTAAAAG-TTGGATGCTTCAA
* * * *
144317 TAAGAGATTGGTGTGTGTCTTCAATTTGCCCTCTGCTTAGGGTAAAAGTTGGATGCTTCAA
1 TAAGAGATT-G-GTGTGTCTTCAATCTACCCTCTGATTAGAGTAAAAGTTGGATGCTTCAA
144378 T
1 T
144379 CTGCCCCATG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
60 9 0.17
61 14 0.26
62 31 0.57
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (59 bp):
TAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGAGTAAAAGTTGGATGCTTCAA
Found at i:149056 original size:18 final size:18
Alignment explanation
Indices: 149016--149058 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
149006 GTAGGCACAT
* * *
149016 CATGATCAGATGTAGTCA
1 CATGCTCAGATGCAATCA
*
149034 AATGCTCAGATGCAATCA
1 CATGCTCAGATGCAATCA
149052 CATGCTC
1 CATGCTC
149059 GTATGTAGCC
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:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (18 bp):
CATGCTCAGATGCAATCA
Found at i:172264 original size:16 final size:17
Alignment explanation
Indices: 172220--172269 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
172210 AAATGCGTTA
*
172220 ACAAATAAAATGCAAA-G
1 ACAAGTAAAATG-AAATG
*
172237 ACAAGTAAAATGTAATG
1 ACAAGTAAAATGAAATG
172254 ACAAG-AAAATGAAATG
1 ACAAGTAAAATGAAATG
172270 TATGCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (17 bp):
ACAAGTAAAATGAAATG
Found at i:172721 original size:15 final size:16
Alignment explanation
Indices: 172690--172730 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
172680 CATTTTCCTT
172690 TTCTTCTC-TTCCATC
1 TTCTTCTCTTTCCATC
*
172705 TTCTTCTCTTTTC-TC
1 TTCTTCTCTTTCCATC
172720 TTCTTCCTCTT
1 TTCTT-CTCTT
172731 CAAACCCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCTTCTCTTTCCATC
Found at i:173898 original size:48 final size:48
Alignment explanation
Indices: 173838--173956 Score: 177
Period size: 48 Copynumber: 2.5 Consensus size: 48
173828 TTTAACAAAA
*
173838 CATTTAACAAACAAAACAGTTAATAATGCATATTACTAAACAAAGATG
1 CATTTAACAAACAAAACAGTTAATAATGCATATTACTAAACAAAGAAG
* * * *
173886 CATTTAACAAACAAATCACTTAATGATGCATATTATTAAACAAAGAAG
1 CATTTAACAAACAAAACAGTTAATAATGCATATTACTAAACAAAGAAG
*
173934 CATTTAACAAA-AAAAAAGTTAAT
1 CATTTAACAAACAAAACAGTTAAT
173957 GAAACATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 9 0.14
48 54 0.86
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (48 bp):
CATTTAACAAACAAAACAGTTAATAATGCATATTACTAAACAAAGAAG
Found at i:177080 original size:6 final size:6
Alignment explanation
Indices: 177051--177132 Score: 58
Period size: 6 Copynumber: 13.2 Consensus size: 6
177041 TACCACAACC
* ** *
177051 TCTTTT TCTTGT TCTTTT AT-TTTT TCTTTT TCGCTC TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
* **
177099 CCCTCATGC TCTTTT TCTTTT TCTTTT TCTTTT T
1 ---TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
177133 TACATTCTCT
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
5 1 0.02
6 52 0.91
7 1 0.02
9 3 0.05
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:179999 original size:48 final size:47
Alignment explanation
Indices: 179944--180062 Score: 157
Period size: 48 Copynumber: 2.5 Consensus size: 47
179934 TTTAACAAAA
* *
179944 CATTTAACAAATAAAACAGTTACTAATGCAAATTACTAAACAGAGATG
1 CATTTAACAAA-AAAACAGTTAATAATGCAAATTACTAAACAAAGATG
* * * *
179992 CATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAAAGATG
1 CATTTAACAAA-AAAACAGTTAATAATGCAAATTACTAAACAAAGATG
*
180040 CATTTAACAAAAAAAAAGTTAAT
1 CATTTAACAAAAAAACAGTTAAT
180063 GAAACATAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
47 10 0.16
48 52 0.84
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.25
Consensus pattern (47 bp):
CATTTAACAAAAAAACAGTTAATAATGCAAATTACTAAACAAAGATG
Found at i:195415 original size:21 final size:21
Alignment explanation
Indices: 195389--195435 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
195379 CTCTCCTTCC
* *
195389 TCCTTGTGCTTCTTCTTTTTG
1 TCCTTGTGCTTCCTCTTATTG
*
195410 TCCTTGTGTTTCCTCTTATTG
1 TCCTTGTGCTTCCTCTTATTG
195431 TCCTT
1 TCCTT
195436 CGAACCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.26, G:0.13, T:0.60
Consensus pattern (21 bp):
TCCTTGTGCTTCCTCTTATTG
Found at i:210968 original size:8 final size:8
Alignment explanation
Indices: 210955--210979 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
210945 ATAAATAATT
210955 ATAAAATA
1 ATAAAATA
210963 ATAAAATA
1 ATAAAATA
210971 ATAAAATA
1 ATAAAATA
210979 A
1 A
210980 ATTGATTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAATA
Found at i:214278 original size:26 final size:25
Alignment explanation
Indices: 214209--214278 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
214199 GGGGGTAAGA
*
214209 ATTTAAATT-CTAAT-TTTTAATTT
1 ATTTAAATTATTAATATTTTAATTT
* * *
214232 ATTTAATTTATTAACAATTTAATTT
1 ATTTAAATTATTAATATTTTAATTT
214257 ATTTTAAATTATTAATATTTTA
1 A-TTTAAATTATTAATATTTTA
214279 TACAAGTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 8 0.22
24 3 0.08
25 9 0.24
26 17 0.46
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTAAATTATTAATATTTTAATTT
Found at i:218161 original size:36 final size:36
Alignment explanation
Indices: 218091--218161 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
218081 CACAACATAA
*
218091 TCTGTCACATGGCATGAAAAACAAACCCATATATTT
1 TCTGTCACATGGCATGAAAAACAAACCCACATATTT
* * *
218127 TCTGTCACATGGCATGAAGAACATACCTACATATT
1 TCTGTCACATGGCATGAAAAACAAACCCACATATT
218162 CACTTCTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (36 bp):
TCTGTCACATGGCATGAAAAACAAACCCACATATTT
Found at i:227197 original size:18 final size:18
Alignment explanation
Indices: 227174--227208 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
227164 TGTCTGGTTG
*
227174 CTATTATAACTCCCTTGT
1 CTATTATAACCCCCTTGT
227192 CTATTATAACCCCCTTG
1 CTATTATAACCCCCTTG
227209 ATTTGAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (18 bp):
CTATTATAACCCCCTTGT
Found at i:248602 original size:12 final size:14
Alignment explanation
Indices: 248570--248611 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
248560 AAGATAAAAT
248570 AGAAGAAGAAGGAAG
1 AGAAGAA-AAGGAAG
248585 AGAAGAAAAGGAA-
1 AGAAGAAAAGGAAG
*
248598 A-AAGAAAATGAAG
1 AGAAGAAAAGGAAG
248611 A
1 A
248612 AGATTTTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 6 0.24
15 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AGAAGAAAAGGAAG
Found at i:257908 original size:18 final size:19
Alignment explanation
Indices: 257865--257914 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
257855 GGAACCTGAG
*
257865 GAGAAGAAGGAA-ATTGAA
1 GAGAAGAAGGAAGATAGAA
257883 GA-AGAGAAGGAAGA-AGAA
1 GAGA-AGAAGGAAGATAGAA
*
257901 GAGAAGAATGAAGA
1 GAGAAGAAGGAAGA
257915 GATTGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.04
18 24 0.89
19 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.06
Consensus pattern (19 bp):
GAGAAGAAGGAAGATAGAA
Found at i:257913 original size:15 final size:15
Alignment explanation
Indices: 257867--257914 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
257857 AACCTGAGGA
*
257867 GAAGAAG-GAA-ATT
1 GAAGAAGAGAAGAAT
257880 GAAGAAGAGAAGGAA-
1 GAAGAAGAGAA-GAAT
257895 GAAGAAGAGAAGAAT
1 GAAGAAGAGAAGAAT
257910 GAAGA
1 GAAGA
257915 GATTGAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 16 0.53
16 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.06
Consensus pattern (15 bp):
GAAGAAGAGAAGAAT
Found at i:258924 original size:24 final size:24
Alignment explanation
Indices: 258892--258938 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
258882 TTTATAAAAA
*
258892 AAAAAAG-AAAGAAAGAAAGAAGAG
1 AAAAAAGAAAAG-AAGAAAAAAGAG
*
258916 AAAAGAGAAAAGAAGAAAAAAGA
1 AAAAAAGAAAAGAAGAAAAAAGA
258939 ACTATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAGAAGAAAAAAGAG
Found at i:279410 original size:239 final size:239
Alignment explanation
Indices: 278991--279468 Score: 947
Period size: 239 Copynumber: 2.0 Consensus size: 239
278981 AACAAAAATG
278991 TGACCATGGTTTTTATTTTTATGCATAAATCTTGAATTGTTTGGAATGTTGATATGTGAATTGGG
1 TGACCATGGTTTTTATTTTTATGCATAAATCTTGAATTGTTTGGAATGTTGATATGTGAATTGGG
279056 TGAATATGAATGAATACTGAATCTTCTATTTTTGGATGAATGATTGGAATTGCTTTAGTAATGAA
66 TGAATATGAATGAATACTGAATCTTCTATTTTTGGATGAATGATTGGAATTGCTTTAGTAATGAA
279121 TGGATAGTATCAACCCTTGAATTTTGAACTAACTTACCAATTGCAGGGACATTGTACTAATGAAA
131 TGGATAGTATCAACCCTTGAATTTTGAACTAACTTACCAATTGCAGGGACATTGTACTAATGAAA
*
279186 GGCACTCCAACGTGAGTGCATTGTGACTTGTCAAGGGAGAACAC
196 GACACTCCAACGTGAGTGCATTGTGACTTGTCAAGGGAGAACAC
279230 TGACCATGGTTTTTATTTTTATGCATAAATCTTGAATTGTTTGGAATGTTGATATGTGAATTGGG
1 TGACCATGGTTTTTATTTTTATGCATAAATCTTGAATTGTTTGGAATGTTGATATGTGAATTGGG
279295 TGAATATGAATGAATACTGAATCTTCTATTTTTGGATGAATGATTGGAATTGCTTTAGTAATGAA
66 TGAATATGAATGAATACTGAATCTTCTATTTTTGGATGAATGATTGGAATTGCTTTAGTAATGAA
279360 TGGATAGTATCAACCCTTGAATTTTGAACTAACTTACCAATTGCAGGGACATTGTACTAATGAAA
131 TGGATAGTATCAACCCTTGAATTTTGAACTAACTTACCAATTGCAGGGACATTGTACTAATGAAA
279425 GACACTCCAACGTGAGTGCATTGTGACTTGTCAAGGGAGAACAC
196 GACACTCCAACGTGAGTGCATTGTGACTTGTCAAGGGAGAACAC
279469 ACCGCTTCAT
Statistics
Matches: 238, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 238 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (239 bp):
TGACCATGGTTTTTATTTTTATGCATAAATCTTGAATTGTTTGGAATGTTGATATGTGAATTGGG
TGAATATGAATGAATACTGAATCTTCTATTTTTGGATGAATGATTGGAATTGCTTTAGTAATGAA
TGGATAGTATCAACCCTTGAATTTTGAACTAACTTACCAATTGCAGGGACATTGTACTAATGAAA
GACACTCCAACGTGAGTGCATTGTGACTTGTCAAGGGAGAACAC
Found at i:285876 original size:17 final size:17
Alignment explanation
Indices: 285856--285909 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
285846 ACTACAATGC
*
285856 AAATGTACTAACAACTA
1 AAATGTAATAACAACTA
* *
285873 AAATGCT-GTAACAATTAA
1 AAATG-TAATAACAACT-A
285891 AAATGTAATAACAACTA
1 AAATGTAATAACAACTA
285908 AA
1 AA
285910 TGCTATGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATGTAATAACAACTA
Found at i:286062 original size:21 final size:21
Alignment explanation
Indices: 286020--286063 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
286010 GCCTTCCTCT
*
286020 TTGCGTTTCTTTTTCTTATCC
1 TTGCGTTTCTCTTTCTTATCC
*
286041 TTGCGCTTTCTCTTT-TTGTCC
1 TTGCG-TTTCTCTTTCTTATCC
286062 TT
1 TT
286064 TGATTCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.25, G:0.11, T:0.61
Consensus pattern (21 bp):
TTGCGTTTCTCTTTCTTATCC
Found at i:300522 original size:43 final size:43
Alignment explanation
Indices: 300474--300773 Score: 370
Period size: 43 Copynumber: 7.0 Consensus size: 43
300464 TCTATTAATG
* * **
300474 TTAGTGGCGTTTGTGGGAAAAATGCCGCTAAAGACCATGTTCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
300517 TTAGTGGCATTTGTGGGAAAAAG-GCCGCTAAAGATCATGGTCT
1 TTAGCGGCATTTGTGGG-AAAAGCGCCGCTAAAGACCATGTTCT
* **
300560 TTAGCGGCATTTGTGGG-AAAGCACCGCTAAAGACCATGCCCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * * *
300602 TTAGTGGCGTTTATGAGAAAAGCGCCGCTAAAGACTATGATCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
300645 TTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGACGATGTTCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
300688 TTAGCGGTATTTGTGGGAAAAGCGCCGCTAAAGACGATGTTCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
300731 TTAGCGGTATTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCT
1 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
300774 ATAATGACAT
Statistics
Matches: 226, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.02
42 29 0.13
43 189 0.84
44 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (43 bp):
TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:309276 original size:24 final size:24
Alignment explanation
Indices: 309237--309665 Score: 482
Period size: 24 Copynumber: 17.9 Consensus size: 24
309227 GTTCAGTACA
** * *
309237 TTTACGCTCGTTAGCTAAGATACG
1 TTTACGCTCGCCAGCTAATATGCG
* *
309261 TTTACGTTCACCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATGCG
* *
309285 TTTACGCTCACCAGCTAATATACG
1 TTTACGCTCGCCAGCTAATATGCG
* *
309309 TTTATGCTCGTCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATGCG
*
309333 TTTACGCTCGCCAGCTAATATGCA
1 TTTACGCTCGCCAGCTAATATGCG
* *
309357 TTTACGCTCGCCAACTAATATACG
1 TTTACGCTCGCCAGCTAATATGCG
* *** *
309381 TTTATGCTCGTTTGCTAATATGCA
1 TTTACGCTCGCCAGCTAATATGCG
*
309405 TTTACGCTCGCCAGCTAATATGCA
1 TTTACGCTCGCCAGCTAATATGCG
*
309429 TTTACGCTCGCCAGCTAATATGCA
1 TTTACGCTCGCCAGCTAATATGCG
* *
309453 TTTACGCTTGCCAGCTAATATACG
1 TTTACGCTCGCCAGCTAATATGCG
*
309477 TTTACGCTCGCCAGCTAATACGCG
1 TTTACGCTCGCCAGCTAATATGCG
*
309501 TTTACGCTCGCCAGCTAATACGCG
1 TTTACGCTCGCCAGCTAATATGCG
* * *
309525 TTTATGCTCGCCAACTAATATACG
1 TTTACGCTCGCCAGCTAATATGCG
* * * **
309549 TTTACACTCGTCAGCTTATATATG
1 TTTACGCTCGCCAGCTAATATGCG
***
309573 TTTACGCTCATTAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATGCG
* * *
309597 TTTATGCTCGCCAACTAATATACG
1 TTTACGCTCGCCAGCTAATATGCG
* *
309621 TTTATGCTCACCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATGCG
309645 TTTACGCT-GACCAGCTAATAT
1 TTTACGCTCG-CCAGCTAATAT
309666 AAGAAAAATT
Statistics
Matches: 342, Mismatches: 62, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
24 342 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTAATATGCG
Found at i:312234 original size:26 final size:26
Alignment explanation
Indices: 312205--312256 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
312195 CACTTCTGAG
312205 AATGATTTCCTCACAATGCTCTTGCC
1 AATGATTTCCTCACAATGCTCTTGCC
312231 AATGATTTCCTCACAATGCTCTTGCC
1 AATGATTTCCTCACAATGCTCTTGCC
312257 CTTGTGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.35
Consensus pattern (26 bp):
AATGATTTCCTCACAATGCTCTTGCC
Found at i:322913 original size:25 final size:25
Alignment explanation
Indices: 322887--323055 Score: 230
Period size: 25 Copynumber: 6.8 Consensus size: 25
322877 TGAGTAATAC
* *
322887 TCTGTTTGGCTCGTAAGAGCGACAC
1 TCTGTTTGGCTCGTAAGAGCGATAT
*
322912 TCTGTTTGGCTCATAAGAGCGATAT
1 TCTGTTTGGCTCGTAAGAGCGATAT
* *
322937 TTTGTCTGGCTCGTAAGAGCGATAT
1 TCTGTTTGGCTCGTAAGAGCGATAT
**
322962 TCTGTTTGGCTCGTAAGAGTAATAT
1 TCTGTTTGGCTCGTAAGAGCGATAT
* *
322987 TCTATTTGGCTCGTAAGAGTGATAT
1 TCTGTTTGGCTCGTAAGAGCGATAT
* *
323012 TCTATTTGGCTCGTAAGAGTGATAT
1 TCTGTTTGGCTCGTAAGAGCGATAT
*
323037 TCTATTTGGCTCGTAAGAG
1 TCTGTTTGGCTCGTAAGAG
323056 TGTTAATCTA
Statistics
Matches: 132, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 132 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.37
Consensus pattern (25 bp):
TCTGTTTGGCTCGTAAGAGCGATAT
Found at i:323056 original size:25 final size:25
Alignment explanation
Indices: 322891--323075 Score: 226
Period size: 25 Copynumber: 7.4 Consensus size: 25
322881 TAATACTCTG
* * * *
322891 TTTGGCTCGTAAGAGCGACACTCTG
1 TTTGGCTCGTAAGAGTGATATTCTA
* * * *
322916 TTTGGCTCATAAGAGCGATATTTTG
1 TTTGGCTCGTAAGAGTGATATTCTA
* * *
322941 TCTGGCTCGTAAGAGCGATATTCTG
1 TTTGGCTCGTAAGAGTGATATTCTA
*
322966 TTTGGCTCGTAAGAGTAATATTCTA
1 TTTGGCTCGTAAGAGTGATATTCTA
322991 TTTGGCTCGTAAGAGTGATATTCTA
1 TTTGGCTCGTAAGAGTGATATTCTA
323016 TTTGGCTCGTAAGAGTGATATTCTA
1 TTTGGCTCGTAAGAGTGATATTCTA
* *
323041 TTTGGCTCGTAAGAGTGTTAATCTA
1 TTTGGCTCGTAAGAGTGATATTCTA
*
323066 TCTGAGCTCG
1 TTTG-GCTCG
323076 GTAAAGCTAA
Statistics
Matches: 144, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 139 0.97
26 5 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (25 bp):
TTTGGCTCGTAAGAGTGATATTCTA
Found at i:349027 original size:26 final size:26
Alignment explanation
Indices: 348998--349077 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
348988 TTAGCTTTAG
348998 TTTTCATGCATAGCATGTAGCGGTAA
1 TTTTCATGCATAGCATGTAGCGGTAA
* * * ** *
349024 TTTTTATTTCAGT-TC-T-TAGCTTTAG
1 TTTTCA-TGCA-TAGCATGTAGCGGTAA
349049 TTTTCATGCATAGCATGTAGCGGTAA
1 TTTTCATGCATAGCATGTAGCGGTAA
349075 TTT
1 TTT
349078 GTAATCTGTT
Statistics
Matches: 37, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 12 0.32
26 15 0.41
27 4 0.11
28 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (26 bp):
TTTTCATGCATAGCATGTAGCGGTAA
Found at i:349050 original size:51 final size:51
Alignment explanation
Indices: 348974--349077 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
348964 ATTGAGTTAG
348974 TTTTATTTCAGTTCTTAGCTTTAGTTTTCATGCATAGCATGTAGCGGTAAT
1 TTTTATTTCAGTTCTTAGCTTTAGTTTTCATGCATAGCATGTAGCGGTAAT
349025 TTTTATTTCAGTTCTTAGCTTTAGTTTTCATGCATAGCATGTAGCGGTAAT
1 TTTTATTTCAGTTCTTAGCTTTAGTTTTCATGCATAGCATGTAGCGGTAAT
349076 TT
1 TT
349078 GTAATCTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48
Consensus pattern (51 bp):
TTTTATTTCAGTTCTTAGCTTTAGTTTTCATGCATAGCATGTAGCGGTAAT
Found at i:349165 original size:17 final size:17
Alignment explanation
Indices: 349094--349170 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
349084 TGTTAGTAGG
* *
349094 CATTGTCATCACATTCC
1 CATTGTCATTACATTTC
* *
349111 CGTTGTCATTACATTTT
1 CATTGTCATTACATTTC
* * *
349128 AATTGTCATTGCATTTG
1 CATTGTCATTACATTTC
*
349145 CATTGTCATTGCATTTC
1 CATTGTCATTACATTTC
349162 CATTTGTCA
1 CA-TTGTCA
349171 ATAGAGTTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
17 43 0.88
18 6 0.12
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (17 bp):
CATTGTCATTACATTTC
Found at i:356561 original size:29 final size:31
Alignment explanation
Indices: 356508--356572 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
356498 AATTGTTTAT
*
356508 ATTTTTATAATATTTAAAAGAATAAATTA-A
1 ATTTTTATAATATTTAAAAGAATAAAGTATA
* * *
356538 ATTTTTATTAT-TTTTAAAGGATAAAGTATA
1 ATTTTTATAATATTTAAAAGAATAAAGTATA
356568 ATTTT
1 ATTTT
356573 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (31 bp):
ATTTTTATAATATTTAAAAGAATAAAGTATA
Found at i:356573 original size:29 final size:30
Alignment explanation
Indices: 356505--356575 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
356495 TTAAATTGTT
* * *
356505 TATATTTTTATAATATTTAAAAGAATAAAT
1 TATAATTTTATTATATTTAAAAGAATAAAG
* *
356535 TA-AATTTTTATTAT-TTTTAAAGGATAAAG
1 TATAA-TTTTATTATATTTAAAAGAATAAAG
356564 TATAATTTTATT
1 TATAATTTTATT
356576 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.51
Consensus pattern (30 bp):
TATAATTTTATTATATTTAAAAGAATAAAG
Found at i:369649 original size:18 final size:18
Alignment explanation
Indices: 369591--369651 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
369581 AAAGGGTGAG
* *
369591 AAGTAAAAGTTTAGGGGA
1 AAGTAAAATTTTATGGGA
* *
369609 AAATAAAAAATTTTGTGGG-
1 AAGT--AAAATTTTATGGGA
369628 -AGTAAAATTTTATGGGA
1 AAGTAAAATTTTATGGGA
369645 AAGTAAA
1 AAGTAAA
369652 TGAGAGAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 12 0.36
18 11 0.33
20 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.28
Consensus pattern (18 bp):
AAGTAAAATTTTATGGGA
Found at i:370763 original size:50 final size:50
Alignment explanation
Indices: 370707--370831 Score: 178
Period size: 50 Copynumber: 2.5 Consensus size: 50
370697 TTTGTGATTT
* ** *
370707 AATTATGTCAAGCATTATGTAATTTTCATATTAGTTAAGTTTGCATCTTA
1 AATTATGTCATGCATTATGTAATTCCCATATTAGTTAAGTTAGCATCTTA
* * * *
370757 AATTATGACATGTATTATGTAACTCCCATGTTAGTTAAGTTAGCATCTTA
1 AATTATGTCATGCATTATGTAATTCCCATATTAGTTAAGTTAGCATCTTA
370807 AATTATGTCATGCATTATGTAATTC
1 AATTATGTCATGCATTATGTAATTC
370832 ATTTGTTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (50 bp):
AATTATGTCATGCATTATGTAATTCCCATATTAGTTAAGTTAGCATCTTA
Found at i:370856 original size:50 final size:48
Alignment explanation
Indices: 370707--370857 Score: 135
Period size: 50 Copynumber: 3.0 Consensus size: 48
370697 TTTGTGATTT
*
370707 AATTATGTCAAGCATTATGTAATTTTCATATTAGTTA--AGTTTGCATCTTA
1 AATTATGTCATGCATTATGTAA--TTCAT-TT-GTTATTAGTTTGCATCTTA
* * * *** *
370757 AATTATGACATGTATTATGTAACTCCCATGTTAGTTAAGTTAGCATCTTA
1 AATTATGTCATGCATTATGTAATTCATTTGTTA-TT-AGTTTGCATCTTA
*
370807 AATTATGTCATGCATTATGTAATTCATTTGTTCATTTAGTTTGCTTCTTA
1 AATTATGTCATGCATTATGTAATTCATTTGTT-A-TTAGTTTGCATCTTA
370857 A
1 A
370858 TTAAACCATG
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
46 4 0.05
47 1 0.01
48 2 0.03
50 69 0.87
51 3 0.04
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (48 bp):
AATTATGTCATGCATTATGTAATTCATTTGTTATTAGTTTGCATCTTA
Found at i:378154 original size:16 final size:16
Alignment explanation
Indices: 378133--378163 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
378123 CCACTCAAAA
*
378133 TCACATATTGGAAGTC
1 TCACATAGTGGAAGTC
378149 TCACATAGTGGAAGT
1 TCACATAGTGGAAGT
378164 GGGAAAGAGT
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:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (16 bp):
TCACATAGTGGAAGTC
Found at i:383679 original size:6 final size:6
Alignment explanation
Indices: 383668--383701 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
383658 GTTATGGGTG
* *
383668 GAATAT GAATAT GAAAAT AAATAT GAATAT GAAT
1 GAATAT GAATAT GAATAT GAATAT GAATAT GAAT
383702 GATATGTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (6 bp):
GAATAT
Found at i:403452 original size:25 final size:25
Alignment explanation
Indices: 403424--403479 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
403414 CACCGGCTCA
*
403424 AAGCTTGCTAAAAATCACTATCTCG
1 AAGCCTGCTAAAAATCACTATCTCG
*
403449 AAGCCTGCTAACAATCACTATCTCG
1 AAGCCTGCTAAAAATCACTATCTCG
403474 AAGCCT
1 AAGCCT
403480 ATTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (25 bp):
AAGCCTGCTAAAAATCACTATCTCG
Found at i:403489 original size:25 final size:24
Alignment explanation
Indices: 403434--403491 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
403424 AAGCTTGCTA
*
403434 AAAATCACTATCTCGAAGCCTGCT
1 AAAATCACTATCTCGAAGCCTACT
*
403458 AACAATCACTATCTCGAAGCCTATT
1 AA-AATCACTATCTCGAAGCCTACT
403483 GAAAATCAC
1 -AAAATCAC
403492 CTCACATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 26 0.87
26 2 0.07
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (24 bp):
AAAATCACTATCTCGAAGCCTACT
Found at i:416406 original size:15 final size:15
Alignment explanation
Indices: 416386--416416 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
416376 ATCATAAATT
*
416386 TTTTTCTTCTTTTTC
1 TTTTTCTTCCTTTTC
416401 TTTTTCTTCCTTTTC
1 TTTTTCTTCCTTTTC
416416 T
1 T
416417 CATTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTCCTTTTC
Found at i:442995 original size:2 final size:2
Alignment explanation
Indices: 442988--443015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
442978 GCGTATTAGA
442988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
443016 GTATGATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:451311 original size:10 final size:10
Alignment explanation
Indices: 451298--451335 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
451288 TTCAAAAAAA
451298 ATATATAAAT
1 ATATATAAAT
451308 ATATATAAAT
1 ATATATAAAT
*
451318 AT-TTTCAAAT
1 ATATAT-AAAT
451328 ATATATAA
1 ATATATAA
451336 TAATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATAAAT
Found at i:452128 original size:27 final size:27
Alignment explanation
Indices: 452088--452155 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
452078 CATTTAAAAG
*
452088 TAATTATA-ATTTAATAAAAATTGTAA
1 TAATTACATATTTAATAAAAATTGTAA
*
452114 TAATTACATATTTAATAAAAGTTGTAA
1 TAATTACATATTTAATAAAAATTGTAA
452141 TAATTACATATTTAA
1 TAATTACATATTTAA
452156 AAATAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATTACATATTTAATAAAAATTGTAA
Found at i:452168 original size:27 final size:27
Alignment explanation
Indices: 452115--452168 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
452105 AAATTGTAAT
** *
452115 AATTACATATTTAATAAAAGTTGTAAT
1 AATTACATATTTAATAAAAAATATAAT
452142 AATTACATATTTAA-AAATAAATATAAT
1 AATTACATATTTAATAAA-AAATATAAT
452169 TTAAGCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (27 bp):
AATTACATATTTAATAAAAAATATAAT
Found at i:453678 original size:137 final size:137
Alignment explanation
Indices: 453427--453710 Score: 433
Period size: 137 Copynumber: 2.1 Consensus size: 137
453417 ATGTTCATGG
* * * **
453427 TTATCAACTATCATCAATCGGGCTCTACGTTTCGACCTAAACGGTTTCATTTGCTGTAGCTTATT
1 TTATTAACTATCATCAATCGGGCTCTACATTTCCACCTAAACGGTTTCATTTGCTGTAGCCCATT
* * *
453492 TATTGTGGGCCCCTTGAATGGGACCCTAATAAGTTAACTTACATTGCTAACTGCTTTGGGATCTT
66 TATTGTGGGCCCCCTAAATGGGACCCTAATAAGTTAACCTACATTGCTAACTGCTTTGGGATCTT
453557 TTGAATA
131 TTGAATA
* * *
453564 TTATTAACTATCATCGATCGGGCTCTATATTTCCACCTAAACGGTTTCGTTTGCTGTAGCCCATT
1 TTATTAACTATCATCAATCGGGCTCTACATTTCCACCTAAACGGTTTCATTTGCTGTAGCCCATT
* * * *
453629 TATTGTGGGCCCCCTAAATGGGACCCTAATATGTTAACCTGCATTGCTAATTGTTTTGGGATCTT
66 TATTGTGGGCCCCCTAAATGGGACCCTAATAAGTTAACCTACATTGCTAACTGCTTTGGGATCTT
453694 TTGAATA
131 TTGAATA
453701 TTATTAACTA
1 TTATTAACTA
453711 GTTCAATTTG
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (137 bp):
TTATTAACTATCATCAATCGGGCTCTACATTTCCACCTAAACGGTTTCATTTGCTGTAGCCCATT
TATTGTGGGCCCCCTAAATGGGACCCTAATAAGTTAACCTACATTGCTAACTGCTTTGGGATCTT
TTGAATA
Done.