Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 120 of 144
Found at i:28221840 original size:27 final size:25
Alignment explanation
Indices: 28221810--28221859 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
28221800 AAAGATTATT
28221810 AAAACTATTTTAAAAGAAAACTCAAGA
1 AAAACTATTTT-AAA-AAAACTCAAGA
* *
28221837 AAAATTCTTTTAAAAAAACTCAA
1 AAAACTATTTTAAAAAAACTCAA
28221860 AGTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 3 0.14
27 9 0.43
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAACTATTTTAAAAAAACTCAAGA
Found at i:28231024 original size:15 final size:15
Alignment explanation
Indices: 28230983--28231028 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
28230973 TTTTAACTTT
28230983 TTTG-AAAAGTGTT-
1 TTTGAAAAAGTGTTA
**
28230996 TTCCAAAAAG-GTTA
1 TTTGAAAAAGTGTTA
28231010 TTTGAAAAAGTGTTA
1 TTTGAAAAAGTGTTA
28231025 TTTG
1 TTTG
28231029 TAATTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
15 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (15 bp):
TTTGAAAAAGTGTTA
Found at i:28236955 original size:4 final size:4
Alignment explanation
Indices: 28236946--28236979 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
28236936 CTCTCAGTAC
28236946 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
28236980 TTTTCCTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:28239187 original size:311 final size:310
Alignment explanation
Indices: 28238625--28239246 Score: 1118
Period size: 311 Copynumber: 2.0 Consensus size: 310
28238615 TATATAAACT
*
28238625 AGTGCTTTTGTTAGGGTTCCTTGATTAATTTGCTGCATATATAAGGTGGTTGATCATGTTTCCAT
1 AGTGCTTTTGTTAGGGTTCCTTGATTAATTTGCTGCATATATAAGGGGGTTGATCATGTTTCCAT
28238690 TATGATCTTTGAAGTAGGATTTGACTATTACTAGGAATTTGATATATTTGACAGTGTGGTGTTTT
66 TATGATCTTTGAAGTAGGATTTGACTATTACTAGGAATTTGATATATTTGACAGTGTGGTGTTTT
* * *
28238755 GGTCACTGTCTCATTCTTAGTTCTCATATACATTGGTGTTTTGTACCAATTGACATGAATTTTCA
131 GGTCACAGCCTCATTCTTAGTTCTCATATACATTGGTGTTCTGTACCAATTGACATGAATTTTCA
* * *
28238820 ATGGGAAGTGTTGTTTGAAAAAATGGAGTTTTGCTAGTCTCCGAGGAAACATTTCCTTTGAATTT
196 ATGGAAAGGGTTGTTTGAAAAAATGGAGTTTTGCTAGTATCCGAGGAAACATTTCCTTTGAATTT
28238885 TCCAGGAAAACGCATTTGTCAGAAAAAACTGCAGCAAAAAAGAATAACAA
261 TCCAGGAAAACGCATTTGTCAGAAAAAACTGCAGCAAAAAAGAATAACAA
28238935 AGTGCTTTTGTTAGGGTTCCTTGATTAATTTGCTGCATATATAAGGCGGGTTGATCATGTTTCCA
1 AGTGCTTTTGTTAGGGTTCCTTGATTAATTTGCTGCATATATAAGG-GGGTTGATCATGTTTCCA
*
28239000 TTATGATCTTTGAAGTAGGATTTGACTATTACTAGGGATTTGATATATTTGACAGTGTGGTGTTT
65 TTATGATCTTTGAAGTAGGATTTGACTATTACTAGGAATTTGATATATTTGACAGTGTGGTGTTT
* *
28239065 TGGTCACAGCCTCATTCTTAGTTCTCATGTACATTGGTGTTCTGTATCAATTGACATGAATTTTC
130 TGGTCACAGCCTCATTCTTAGTTCTCATATACATTGGTGTTCTGTACCAATTGACATGAATTTTC
*
28239130 AATGGAAAGGGTTGTTTGAAAAATTGGAGTTTTGCTAGTATCCGAGGAAACATTTCCTTTGAATT
195 AATGGAAAGGGTTGTTTGAAAAAATGGAGTTTTGCTAGTATCCGAGGAAACATTTCCTTTGAATT
* *
28239195 TTCCAGGAAAACGGATTTGTCAGAAAAAATTGCAGCAAAAAAGAATAACAA
260 TTCCAGGAAAACGCATTTGTCAGAAAAAACTGCAGCAAAAAAGAATAACAA
28239246 A
1 A
28239247 AATTATTGGC
Statistics
Matches: 298, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
310 46 0.15
311 252 0.85
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (310 bp):
AGTGCTTTTGTTAGGGTTCCTTGATTAATTTGCTGCATATATAAGGGGGTTGATCATGTTTCCAT
TATGATCTTTGAAGTAGGATTTGACTATTACTAGGAATTTGATATATTTGACAGTGTGGTGTTTT
GGTCACAGCCTCATTCTTAGTTCTCATATACATTGGTGTTCTGTACCAATTGACATGAATTTTCA
ATGGAAAGGGTTGTTTGAAAAAATGGAGTTTTGCTAGTATCCGAGGAAACATTTCCTTTGAATTT
TCCAGGAAAACGCATTTGTCAGAAAAAACTGCAGCAAAAAAGAATAACAA
Found at i:28262656 original size:18 final size:18
Alignment explanation
Indices: 28262630--28262666 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28262620 CATCACTGTC
*
28262630 ACCGGAAAATAAAACAAA
1 ACCGAAAAATAAAACAAA
*
28262648 ACCGAAAAATAAATCAAA
1 ACCGAAAAATAAAACAAA
28262666 A
1 A
28262667 TCAAAACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (18 bp):
ACCGAAAAATAAAACAAA
Found at i:28266682 original size:33 final size:33
Alignment explanation
Indices: 28266641--28266707 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
28266631 TTAATGTTTT
*
28266641 TAACATTTACCCTCTCAATTTTTGTAAAATATG
1 TAACATTTACCCTCTCAATTTATGTAAAATATG
28266674 TAACATTTACCCTCTCAATTTATGTAAAATATG
1 TAACATTTACCCTCTCAATTTATGTAAAATATG
28266707 T
1 T
28266708 TTACCTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (33 bp):
TAACATTTACCCTCTCAATTTATGTAAAATATG
Found at i:28277342 original size:16 final size:16
Alignment explanation
Indices: 28277321--28277368 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
28277311 GGGATGAGAA
*
28277321 TAAAATTTTAATGAAT
1 TAAAATTTAAATGAAT
*
28277337 TAAAATTTAAATTAAT
1 TAAAATTTAAATGAAT
* *
28277353 TACACTTTAAACTGAA
1 TAAAATTTAAA-TGAA
28277369 AAAAAAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (16 bp):
TAAAATTTAAATGAAT
Found at i:28290609 original size:15 final size:15
Alignment explanation
Indices: 28290577--28290623 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
28290567 ATCGGTTTGT
*
28290577 ATAAATAATGAAATA
1 ATAAATAATGAAAAA
28290592 ATAAA-AATGAAAAAA
1 ATAAATAATG-AAAAA
28290607 ATAAATTACATGAAAAA
1 ATAAA-TA-ATGAAAAA
28290624 TTTTTACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
17 6 0.22
18 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (15 bp):
ATAAATAATGAAAAA
Found at i:28297870 original size:21 final size:20
Alignment explanation
Indices: 28297823--28297870 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
28297813 TTTTCTCACC
*
28297823 TAAATTTTAACAATTTTTTT
1 TAAATTTTAACAATTTTATT
28297843 TATAATTTATAA-AATTTTAATT
1 TA-AATTT-TAACAATTTT-ATT
28297865 TAAATT
1 TAAATT
28297871 AACATTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATTTTAACAATTTTATT
Found at i:28306135 original size:19 final size:19
Alignment explanation
Indices: 28306093--28306137 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28306083 TCAAAATCCT
**
28306093 TTAAAATATAAAAAGTTCA
1 TTAAAATATAAAAAAATCA
28306112 TTAAAATATAAAAAAAATCA
1 TTAAAATAT-AAAAAAATCA
28306132 -TAAAAT
1 TTAAAAT
28306138 TAGTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
TTAAAATATAAAAAAATCA
Found at i:28309372 original size:16 final size:16
Alignment explanation
Indices: 28309337--28309381 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
28309327 TTATTTATTT
*
28309337 TGAAAAG-ATATATGG
1 TGAAAAGAATATAAGG
*
28309352 AGAAAAGAATATAAGG
1 TGAAAAGAATATAAGG
28309368 TGAAAGAGAATATA
1 TGAAA-AGAATATA
28309382 TTAATTAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (16 bp):
TGAAAAGAATATAAGG
Found at i:28315151 original size:22 final size:20
Alignment explanation
Indices: 28315111--28315151 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
28315101 AACAAACTAC
*
28315111 TGTTGTTTCCATTGTTTTGG
1 TGTTGTTTCCACTGTTTTGG
28315131 TGTTGTTTTACCACTGTTTTG
1 TGTTG-TTT-CCACTGTTTTG
28315152 CTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (20 bp):
TGTTGTTTCCACTGTTTTGG
Found at i:28316369 original size:18 final size:19
Alignment explanation
Indices: 28316348--28316431 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 19
28316338 CATTAACAGG
*
28316348 TTAAAAT-TTGTTAAAATT
1 TTAAAATATTGTAAAAATT
28316366 TTAAAATATTGTAAAAATTAT
1 TTAAAATATTGTAAAAA-T-T
*
28316387 TTTAAA-A-TGT-AAAATT
1 TTAAAATATTGTAAAAATT
*
28316403 ATTAAAA-ATTGT-AAATTAT
1 -TTAAAATATTGTAAAAAT-T
28316422 TTAAAATATT
1 TTAAAATATT
28316432 AAAAAGTTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.02
17 7 0.13
18 24 0.44
19 15 0.27
20 2 0.04
21 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTAAAATATTGTAAAAATT
Found at i:28316418 original size:17 final size:18
Alignment explanation
Indices: 28316348--28316428 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 18
28316338 CATTAACAGG
*
28316348 TTAAAATTTGTTAAAATT-
1 TTAAAAATTG-TAAAATTA
28316366 TTAAAATATTGTAAAAATTA
1 TTAAAA-ATTGT-AAAATTA
*
28316386 TTTTAAAA-TGTAAAATTA
1 -TTAAAAATTGTAAAATTA
28316404 TTAAAAATTGT-AAATTA
1 TTAAAAATTGTAAAATTA
*
28316421 TTTAAAAT
1 TTAAAAAT
28316429 ATTAAAAAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
17 19 0.35
18 17 0.31
19 12 0.22
20 1 0.02
21 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTAAAAATTGTAAAATTA
Found at i:28316426 original size:9 final size:9
Alignment explanation
Indices: 28316348--28316435 Score: 51
Period size: 8 Copynumber: 9.7 Consensus size: 9
28316338 CATTAACAGG
*
28316348 TTAAAATTT
1 TTAAAATAT
28316357 GTTAAAAT-T
1 -TTAAAATAT
28316366 TTAAAATAT
1 TTAAAATAT
28316375 TGTAAAAATTAT
1 T-T-AAAA-TAT
*
28316387 TTTAAA-AT
1 TTAAAATAT
*
28316395 GTAAAAT-T
1 TTAAAATAT
28316403 ATTAAAA-AT
1 -TTAAAATAT
*
28316412 TGTAAATTAT
1 T-TAAAATAT
28316422 TTAAAATA-
1 TTAAAATAT
28316430 TTAAAA
1 TTAAAA
28316436 AGTTGAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
8 21 0.33
9 19 0.30
10 14 0.22
11 5 0.08
12 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (9 bp):
TTAAAATAT
Found at i:28316434 original size:17 final size:16
Alignment explanation
Indices: 28316380--28316434 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
28316370 AATATTGTAA
*
28316380 AAATTATTTTAAAATGTA
1 AAATTA-TTTAAAAT-TT
*
28316398 AAATTATTAAAAATTGT
1 AAATTATTTAAAATT-T
28316415 AAATTATTTAAAATATT
1 AAATTATTTAAAAT-TT
28316432 AAA
1 AAA
28316435 AAGTTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.03
17 24 0.75
18 7 0.22
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AAATTATTTAAAATTT
Found at i:28323628 original size:52 final size:53
Alignment explanation
Indices: 28323526--28323634 Score: 166
Period size: 53 Copynumber: 2.1 Consensus size: 53
28323516 ATGTATGATC
* *
28323526 ATAATTATAAATATAAAAAATAAATCCAAACAATTGCAACCATAATTAACATT
1 ATAATTATAAATACAAAAAATAAATCCAAACAACTGCAACCATAATTAACATT
* * *
28323579 ATAATTATGAATGCAAAAAATAAATCCAAACAACTGC-ATCATAATTAACATT
1 ATAATTATAAATACAAAAAATAAATCCAAACAACTGCAACCATAATTAACATT
28323631 ATAA
1 ATAA
28323635 AACATGGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 18 0.35
53 33 0.65
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.28
Consensus pattern (53 bp):
ATAATTATAAATACAAAAAATAAATCCAAACAACTGCAACCATAATTAACATT
Found at i:28332984 original size:16 final size:18
Alignment explanation
Indices: 28332957--28332989 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28332947 AAGTCTTCAA
28332957 AAAATAATATTA-AAAAC
1 AAAATAATATTATAAAAC
28332974 AAAAT-ATATTATAAAA
1 AAAATAATATTATAAAA
28332990 TATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAATATTATAAAAC
Found at i:28337282 original size:38 final size:37
Alignment explanation
Indices: 28337240--28337313 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
28337230 TTACATCACG
*
28337240 TTTGGTTCG-CTGTAATGGAATA-AAGCTGTAATCAGTAA
1 TTTGGTT-GACTGGAATGGAATAGAA-CTGTAAT-AGTAA
*
28337278 TTTGGTTGATTGGAATGGAATAGAACTGTAATAGTA
1 TTTGGTTGACTGGAATGGAATAGAACTGTAATAGTA
28337314 TTTTTGTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 5 0.16
38 25 0.78
39 2 0.06
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (37 bp):
TTTGGTTGACTGGAATGGAATAGAACTGTAATAGTAA
Found at i:28337502 original size:58 final size:59
Alignment explanation
Indices: 28337433--28337587 Score: 201
Period size: 58 Copynumber: 2.6 Consensus size: 59
28337423 AATTTTAATG
* *
28337433 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAATATTTTTAACATA
* *
28337491 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
*
28337549 ATTATTATTAAAATATGAA-TTAATAAAAATTATAATATA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
28337588 TAATATTAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
57 20 0.24
58 41 0.48
59 10 0.12
60 9 0.11
61 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:28338876 original size:12 final size:12
Alignment explanation
Indices: 28338835--28338878 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
28338825 TTTAGTTTAC
28338835 TGCAAGTAAACA
1 TGCAAGTAAACA
28338847 TGC-AGTATTAAGCA
1 TGCAAGTA--AA-CA
28338861 TGCAAGTAAACA
1 TGCAAGTAAACA
28338873 TGCAAG
1 TGCAAG
28338879 AAAATGTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.14
12 11 0.39
13 4 0.14
14 5 0.18
15 4 0.14
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (12 bp):
TGCAAGTAAACA
Found at i:28340515 original size:56 final size:56
Alignment explanation
Indices: 28340410--28340519 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
28340400 GAAAAAAACA
*
28340410 ATTTTTTGGTGTTGGCAATCAAATGGCCGACACCCCCTTTTCTCAAAAAAAATTGT
1 ATTTTTTGGTGTTGGCAATCAAATGGCCGACACCCCCTGTTCTCAAAAAAAATTGT
* *** * *
28340466 ATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCTCTGTT-TGAGAAAAAAATT
1 ATTTTTTGGTGTTGGCAATCAAATGGCCGACACCCCCTGTTCTCA-AAAAAAATT
28340520 CAAAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
55 2 0.04
56 44 0.96
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (56 bp):
ATTTTTTGGTGTTGGCAATCAAATGGCCGACACCCCCTGTTCTCAAAAAAAATTGT
Found at i:28340613 original size:97 final size:98
Alignment explanation
Indices: 28340433--28340632 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 98
28340423 GGCAATCAAA
** * ***
28340433 TGGCCGACACCCCCTTTTCTCAAAAAAAATTGTATTTTTTGGTGTTGGCCATTGCATGGCCGACA
1 TGGCCGACACCCCCTTTTCTCAAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCCGACA
*
28340498 CCCTCTGTTTGAGAAAAAAA-TTCAAAATTTTT
66 CCCCCTGTTTGAGAAAAAAATTTCAAAATTTTT
* * *
28340530 TGGCCGACACCCCTTTTTCTCGAAAAAAATTACATTTTTGGGTGTT-GCTTATCAAATGGCCGAC
1 TGGCCGACACCCCCTTTTCTCAAAAAAAATTACATTTTTGGGTGTTGGC-CATCAAATGGCCGAC
*
28340594 ACCCCCCT-TTTCGAGAAAAAAAATTTCAAATTTTTT
65 A-CCCCCTGTTT-GAG-AAAAAAATTTCAAAATTTTT
28340630 TGG
1 TGG
28340633 TGTGGCCATC
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
96 2 0.02
97 56 0.64
98 8 0.09
99 7 0.08
100 14 0.16
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (98 bp):
TGGCCGACACCCCCTTTTCTCAAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCCGACA
CCCCCTGTTTGAGAAAAAAATTTCAAAATTTTT
Found at i:28340734 original size:116 final size:115
Alignment explanation
Indices: 28340530--28340779 Score: 330
Period size: 116 Copynumber: 2.2 Consensus size: 115
28340520 CAAAATTTTT
* *
28340530 TGGCCGACACCCCTTTTTCTCGAAAAAAATTACATTTTTGGGTGTTGCTTATCAAATGGCCGACA
1 TGGCCGACACCCCTTTTTCTCCAAAAAAATTA-ATTTTTGGGTGTTGCTCATCAAATGGCCGACA
28340595 CCCCCCTTTTCGAGAAAAAAAATTTCAAATTTTTTTGGTG-TGGCCATCAAA
65 CCCCCCTTTTCGAGAAAAAAAATTT-AAATTTTTTTGGTGTTGGCCATCAAA
*** *
28340646 TGGCCGACACCCCTTTTTCTCCAAAAAAATGT-A-TTTTGGTGTGTTGGC-CATTTGATGGTCGA
1 TGGCCGACACCCCTTTTTCTCCAAAAAAAT-TAATTTTTGG-GTGTT-GCTCATCAAATGGCCGA
* *
28340708 CA-CCCTCTATTCTTGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAA
63 CACCCCCCT-TT-TCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAA
28340762 TGGCCGACACCCCTTTTT
1 TGGCCGACACCCCTTTTT
28340780 TTCGAATAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
114 11 0.09
115 33 0.28
116 75 0.62
117 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (115 bp):
TGGCCGACACCCCTTTTTCTCCAAAAAAATTAATTTTTGGGTGTTGCTCATCAAATGGCCGACAC
CCCCCTTTTCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAA
Found at i:28344776 original size:12 final size:12
Alignment explanation
Indices: 28344734--28344781 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
28344724 ATTTGTGTAA
*
28344734 AAATTAATTTGA
1 AAATTAATTTGG
28344746 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
28344762 AAATTAATTTGG
1 AAATTAATTTGG
28344774 AAATTAAT
1 AAATTAAT
28344782 GAACATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:28345104 original size:86 final size:87
Alignment explanation
Indices: 28344911--28345168 Score: 241
Period size: 84 Copynumber: 3.0 Consensus size: 87
28344901 AAAAAAATAG
* * * *
28344911 TTATTATATTACAATTTATATCAAATATT--GTGTTAATTTGACAATACATTATTTATCAAATTT
1 TTATTATATTACAATTTTTATC--ATATTAAATATTGATTTGACAATACATTATTTAT--AATTT
* *
28344974 TTGTATTTAAAGTACAAAA-TATTATTA
62 ATATATTTAAA-TA-AAAATTATTATTA
* * * *
28345001 -TA-T-TA-T--AATTTTTATCATA-TAATGTGTTGATTTGATAATACATTATTTA-ATTTTATA
1 TTATTATATTACAATTTTTATCATATTAA-ATATTGATTTGACAATACATTATTTATAATTTATA
*
28345058 TCTTTAAATAAAAATTATTATTA
65 TATTTAAATAAAAATTATTATTA
*
28345081 TTATTATATTACAATTTTTATCATATTTTAAATATTGATTTGACAATATATTATTTATTAATTTA
1 TTATTATATTACAATTTTTATCATA--TTAAATATTGATTTGACAATACATTATTTA-TAATTTA
28345146 TATATTTAAATAAAAATTATTAT
63 TATATTTAAATAAAAATTATTAT
28345169 CATATTACAA
Statistics
Matches: 140, Mismatches: 13, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
79 4 0.03
80 10 0.07
81 15 0.11
82 4 0.03
83 2 0.01
84 34 0.24
86 14 0.10
87 2 0.01
88 23 0.16
89 5 0.04
90 27 0.19
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (87 bp):
TTATTATATTACAATTTTTATCATATTAAATATTGATTTGACAATACATTATTTATAATTTATAT
ATTTAAATAAAAATTATTATTA
Found at i:28345194 original size:83 final size:83
Alignment explanation
Indices: 28344946--28345196 Score: 262
Period size: 84 Copynumber: 3.0 Consensus size: 83
28344936 TATTGTGTTA
* * *
28344946 ATTTGACAATACATTATTTATCAAATTTTTGTATTTAAAGTACAAAA-TATTATTATATTATAAT
1 ATTTGACAATACATTATTTAT--AATTTATATATTTAAA-TA-AAAATTATTATTATATTACAAT
* *
28345010 TTTTATCATA---TAATGTGTTG
62 TTTTATCATATTTTAA-ATATTG
* * *
28345030 ATTTGATAATACATTATTTA-ATTTTATATCTTTAAATAAAAATTATTATTATTATTATATTACA
1 ATTTGACAATACATTATTTATAATTTATATATTTAAAT--AAA--A--ATTATTATTATATTACA
28345094 ATTTTTATCATATTTTAAATATTG
60 ATTTTTATCATATTTTAAATATTG
* *
28345118 ATTTGACAATATATTATTTATTAATTTATATATTTAAATAAAAATTATTATCATATTACAA-TTT
1 ATTTGACAATACATTATTTA-TAATTTATATATTTAAATAAAAATTATTATTATATTACAATTTT
28345182 TATCATATTTTAAAT
65 TATCATATTTTAAAT
28345197 TTATTAACCA
Statistics
Matches: 142, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
80 1 0.01
81 14 0.10
82 1 0.01
83 19 0.13
84 36 0.25
85 1 0.01
86 27 0.19
88 25 0.18
89 3 0.02
90 15 0.11
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (83 bp):
ATTTGACAATACATTATTTATAATTTATATATTTAAATAAAAATTATTATTATATTACAATTTTT
ATCATATTTTAAATATTG
Found at i:28345310 original size:22 final size:22
Alignment explanation
Indices: 28345285--28345339 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28345275 ACCACCCACT
* * *
28345285 TTCCACCTCACTTAAACCAATA
1 TTCCAGCTCACTAAAACCAAAA
*
28345307 TTCCAGCTCAGTAAAACCAAAA
1 TTCCAGCTCACTAAAACCAAAA
28345329 TTCCAGCTCAC
1 TTCCAGCTCAC
28345340 CAAGTCCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.35, G:0.05, T:0.24
Consensus pattern (22 bp):
TTCCAGCTCACTAAAACCAAAA
Found at i:28345371 original size:10 final size:10
Alignment explanation
Indices: 28345358--28345413 Score: 87
Period size: 10 Copynumber: 5.6 Consensus size: 10
28345348 AAGACCGTCA
28345358 TTGACCATCG
1 TTGACCATCG
28345368 TTGACCGA-CG
1 TTGACC-ATCG
*
28345378 TTGACCACCG
1 TTGACCATCG
28345388 TTGACCATCG
1 TTGACCATCG
28345398 TTGACCATCG
1 TTGACCATCG
28345408 TTGACC
1 TTGACC
28345414 GACTTTGTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
9 1 0.02
10 41 0.95
11 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (10 bp):
TTGACCATCG
Found at i:28345381 original size:20 final size:20
Alignment explanation
Indices: 28345358--28345435 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
28345348 AAGACCGTCA
28345358 TTGACCATCGTTGACCGACG
1 TTGACCATCGTTGACCGACG
*
28345378 TTGACCACCGTTGACC-ATCG
1 TTGACCATCGTTGACCGA-CG
*
28345398 TTGACCATCGTTGACCGACT
1 TTGACCATCGTTGACCGACG
* **
28345418 TTGTCTGTCGTTGACCGA
1 TTGACCATCGTTGACCGA
28345436 GTTTCATCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (20 bp):
TTGACCATCGTTGACCGACG
Found at i:28348456 original size:30 final size:29
Alignment explanation
Indices: 28348422--28348515 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 29
28348412 GTAATAAAAT
28348422 ATTTTTGGTGAAACTGGGGTCAAAAATGAA
1 ATTTTT-GTGAAACTGGGGTCAAAAATGAA
* *
28348452 A-TTTTG-GAAAGTTCGAGGGT--AAAATGGTA
1 ATTTTTGTGAAA-CT-G-GGGTCAAAAAT-GAA
* *
28348481 ATTTTTCGTGAAACCGGGGTCAAAAATGGA
1 ATTTTT-GTGAAACTGGGGTCAAAAATGAA
28348511 ATTTT
1 ATTTT
28348516 AGAAAGTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
27 4 0.08
28 7 0.14
29 12 0.24
30 17 0.34
31 6 0.12
32 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (29 bp):
ATTTTTGTGAAACTGGGGTCAAAAATGAA
Found at i:28348492 original size:59 final size:59
Alignment explanation
Indices: 28348422--28348584 Score: 247
Period size: 59 Copynumber: 2.8 Consensus size: 59
28348412 GTAATAAAAT
* *
28348422 ATTTTTGGTGAAACTGGGGTCAAAAATGAAATTTTGGAAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGTGAAACCGGGGTCAAAAATGAAATTTTGGAAAGTTCGAGGGTAAAACGGTA
* * *
28348481 ATTTTTCGTGAAACCGGGGTCAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAACGGTA
1 ATTTTTGGTGAAACCGGGGTCAAAAATGAAATTTTGGAAAGTTCGAGGGTAAAACGGTA
* *
28348540 ATTTTTGGTGAAACCAGGGTCAAAAAT-AGAATTTTGAAAAGTTCG
1 ATTTTTGGTGAAACCGGGGTCAAAAATGA-AATTTTGGAAAGTTCG
28348585 GGGACTAGAG
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
59 93 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.29
Consensus pattern (59 bp):
ATTTTTGGTGAAACCGGGGTCAAAAATGAAATTTTGGAAAGTTCGAGGGTAAAACGGTA
Found at i:28348542 original size:29 final size:29
Alignment explanation
Indices: 28348451--28348544 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
28348441 TCAAAAATGA
*
28348451 AATTTTGGAAAGTTCGAGGGTAAAATGGT
1 AATTTTAGAAAGTTCGAGGGTAAAATGGT
* *
28348480 AATTTTTCGTGAAA--CCG-GGGTCAAAAATGG-
1 AA-TTTT--AGAAAGTTCGAGGGT--AAAATGGT
*
28348510 AATTTTAGAAAGTTCGAGGGTAAAACGGT
1 AATTTTAGAAAGTTCGAGGGTAAAATGGT
28348539 AATTTT
1 AATTTT
28348545 TGGTGAAACC
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
27 4 0.08
28 6 0.12
29 18 0.35
30 12 0.24
31 7 0.14
32 4 0.08
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (29 bp):
AATTTTAGAAAGTTCGAGGGTAAAATGGT
Found at i:28349379 original size:15 final size:16
Alignment explanation
Indices: 28349350--28349381 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28349340 TAAACCAAAC
28349350 CCAGATCTGGGAAAAT
1 CCAGATCTGGGAAAAT
*
28349366 CCAGATCTGGAAAAAT
1 CCAGATCTGGGAAAAT
28349382 TTCAAATCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (16 bp):
CCAGATCTGGGAAAAT
Found at i:28349685 original size:3 final size:3
Alignment explanation
Indices: 28349675--28349705 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28349665 TAATAATATC
28349675 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28349706 AAATAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28350408 original size:17 final size:17
Alignment explanation
Indices: 28350386--28350443 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
28350376 ATTTAATTTA
*
28350386 AAATTTAAATTTATAAT
1 AAATTTAAATTTAAAAT
*
28350403 AAATTTAAATTCAAAAT
1 AAATTTAAATTTAAAAT
*
28350420 AAATCTAAATTTTAAAACT
1 AAATTTAAA-TTTAAAA-T
28350439 AAATT
1 AAATT
28350444 CATTGGGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 23 0.68
18 6 0.18
19 5 0.15
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:28359187 original size:24 final size:24
Alignment explanation
Indices: 28359160--28359208 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28359150 TATTCCTGAC
28359160 ATGGGAAGGAGTGAAAAAGAATTG
1 ATGGGAAGGAGTGAAAAAGAATTG
28359184 ATGGGAAGGAGTGAAAAAGAATTG
1 ATGGGAAGGAGTGAAAAAGAATTG
28359208 A
1 A
28359209 ACACTTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.16
Consensus pattern (24 bp):
ATGGGAAGGAGTGAAAAAGAATTG
Found at i:28360923 original size:23 final size:26
Alignment explanation
Indices: 28360869--28360929 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 26
28360859 TACAAGGACT
28360869 TATGACATATTTTAACCTAGTATAAAA
1 TATGA-ATATTTTAACCTAGTATAAAA
*
28360896 TATGAATATTTTAA-TTA-TAT-AAA
1 TATGAATATTTTAACCTAGTATAAAA
*
28360919 TATGAGTATTT
1 TATGAATATTT
28360930 GTTTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 13 0.41
24 3 0.09
25 2 0.06
26 9 0.28
27 5 0.16
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (26 bp):
TATGAATATTTTAACCTAGTATAAAA
Found at i:28370721 original size:21 final size:21
Alignment explanation
Indices: 28370681--28370721 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28370671 GCATTCAATA
*
28370681 AAATAAATAAGAATTCAAATC
1 AAATAAATAAGAATTAAAATC
28370702 AAATAAATTAA-AATTAAAAT
1 AAATAAA-TAAGAATTAAAAT
28370722 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATAAGAATTAAAATC
Found at i:28382497 original size:99 final size:98
Alignment explanation
Indices: 28382293--28382631 Score: 333
Period size: 99 Copynumber: 3.4 Consensus size: 98
28382283 GTTTCATTAC
* * * * **
28382293 CATGAAGAGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGA-A-AGTACAAAGGGAAAGG
1 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGAGATAGT--GGAGGGAAAGG
* * *
28382356 TTTAAGTCGCAATGGCGAACCTTATACCTCAG-AG
64 TTTAAGTCGCAACGACGAACCTTACACCTCAGAAG
* * *
28382390 GATGTGAAGGGAAAGATTTAAGCCACGACGGCGAATCCAGTACCACGAGGATAGTGGAGGAAAAG
1 CA--TGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGA-GATAGTGGAGGGAAAG
* * *
28382455 GTTTAAGTTGCAACGACAAACCTCACACCTCAGAAG
63 GTTTAAGTCGCAACGACGAACCTTACACCTCAGAAG
* ** * * *
28382491 CATGAAGGGAAAGATTCAAGCCACAACGTTGAATCCGGTACCATGAAGATAATGGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACG-AGATAGTGGAGGGAAAGGT
* * * *
28382556 TTAAGTCGTAACGACGAGCCTTACACCTCAAAAA
65 TTAAGTCGCAACGACGAACCTTACACCTCAGAAG
* * ** *
28382590 CATGAAAGGAAAGATTTAAGTCGTAACGGCGAATCCATTACC
1 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACC
28382632 TTGGAAAATG
Statistics
Matches: 195, Mismatches: 40, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
97 1 0.01
99 152 0.78
100 35 0.18
101 4 0.02
102 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17
Consensus pattern (98 bp):
CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGAGATAGTGGAGGGAAAGGTT
TAAGTCGCAACGACGAACCTTACACCTCAGAAG
Found at i:28383317 original size:21 final size:21
Alignment explanation
Indices: 28383274--28383313 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
28383264 CAAGACCTAT
28383274 TTACAAATATACAAGCCCAAA
1 TTACAAATATACAAGCCCAAA
28383295 TTACAAA-A-ACAAGCCCAAA
1 TTACAAATATACAAGCCCAAA
28383314 AATTTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.55, C:0.25, G:0.05, T:0.15
Consensus pattern (21 bp):
TTACAAATATACAAGCCCAAA
Found at i:28398157 original size:22 final size:22
Alignment explanation
Indices: 28398132--28398173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28398122 ACAAAATAGT
* * *
28398132 AGCAATATAATAACGCAATGAA
1 AGCAAAATAACAACGAAATGAA
28398154 AGCAAAATAACAACGAAATG
1 AGCAAAATAACAACGAAATG
28398174 GCAAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
AGCAAAATAACAACGAAATGAA
Found at i:28403998 original size:5 final size:5
Alignment explanation
Indices: 28403988--28404021 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
28403978 AATTAGGGAC
28403988 AGCTG AGCTG AGCTG AGCTG AGCTG AGCTG AGCT
1 AGCTG AGCTG AGCTG AGCTG AGCTG AGCTG AGCT
28404022 TTCACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (5 bp):
AGCTG
Found at i:28414591 original size:83 final size:83
Alignment explanation
Indices: 28414431--28414590 Score: 245
Period size: 83 Copynumber: 1.9 Consensus size: 83
28414421 GAAAAATTCC
* * *
28414431 TATTTCAGTCCCCTCATAAATAATAAAATTATAAATTAATATATGGTACCATTGCACTTTGACCT
1 TATTTCAATCCCCTCATAAATAATAAAATTATAAATTAATATATGGTACAATTGCACTTTGACAT
28414496 CAAAAAATAAAAACTGGT
66 CAAAAAATAAAAACTGGT
*
28414514 TATTTCAATCCCCTCATAAA-AATTGAAATTATAAATTAATATATGGTGA-AATTGCACTTTGAC
1 TATTTCAATCCCCTCATAAATAA-TAAAATTATAAATTAATATATGGT-ACAATTGCACTTTGAC
28414577 ATC-AAAAATAAAAA
64 ATCAAAAAATAAAAA
28414591 AAATCTTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
82 13 0.18
83 57 0.80
84 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (83 bp):
TATTTCAATCCCCTCATAAATAATAAAATTATAAATTAATATATGGTACAATTGCACTTTGACAT
CAAAAAATAAAAACTGGT
Found at i:28415222 original size:18 final size:20
Alignment explanation
Indices: 28415195--28415232 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
28415185 TAAAACAAGT
28415195 AATAAAAAA-T-ATATTAAA
1 AATAAAAAATTCATATTAAA
*
28415213 AATAAGAAATTCATATTAAA
1 AATAAAAAATTCATATTAAA
28415233 GATTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AATAAAAAATTCATATTAAA
Found at i:28416237 original size:26 final size:26
Alignment explanation
Indices: 28416180--28416237 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
28416170 AGTTATCTAT
28416180 ATTA-ATTGAATGATAAATATTATAC
1 ATTATATTGAATGATAAATATTATAC
*
28416205 AAT-TATTGATATGAT-AAT-TTATATC
1 ATTATATTGA-ATGATAAATATTATA-C
28416230 ATTATATT
1 ATTATATT
28416238 ATGCAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
24 5 0.19
25 13 0.48
26 9 0.33
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (26 bp):
ATTATATTGAATGATAAATATTATAC
Found at i:28419005 original size:2 final size:2
Alignment explanation
Indices: 28418998--28419041 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28418988 TATAGTGTAC
28418998 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
28419040 AT
1 AT
28419042 CTCTTTGTAA
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:28419764 original size:23 final size:23
Alignment explanation
Indices: 28419726--28419773 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28419716 GCCCGACTAG
*
28419726 TTAATAGGGACTTTCAATTTACAA
1 TTAATAGGCACTTTCAATTT-CAA
28419750 TTAATA-GCACTTTCAATTTCAA
1 TTAATAGGCACTTTCAATTTCAA
28419772 TT
1 TT
28419774 TCACTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAATAGGCACTTTCAATTTCAA
Found at i:28420418 original size:17 final size:18
Alignment explanation
Indices: 28420389--28420423 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28420379 AATCCTAGTT
*
28420389 TTCCCTGTTTCTTTTTCC
1 TTCCCTGTTTCTTCTTCC
28420407 TTCCCT-TTTCTTCTTCC
1 TTCCCTGTTTCTTCTTCC
28420424 CCTGTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.60
Consensus pattern (18 bp):
TTCCCTGTTTCTTCTTCC
Found at i:28420537 original size:14 final size:14
Alignment explanation
Indices: 28420514--28420548 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28420504 AGATATTAGT
28420514 TAATAATAATAAAA
1 TAATAATAATAAAA
*
28420528 TAATACTAATAAAA
1 TAATAATAATAAAA
*
28420542 CAATAAT
1 TAATAAT
28420549 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:28421814 original size:23 final size:24
Alignment explanation
Indices: 28421775--28421824 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
28421765 TAATAGGGAT
28421775 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
28421798 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
28421822 TTT
1 TTT
28421825 TACTTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:28421819 original size:6 final size:6
Alignment explanation
Indices: 28421794--28421844 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
28421784 ACAATTCATA
* * * * *
28421794 TCACTT TCAATT CCAATT TCACTT TCACTT TTACTT TTACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
28421842 TCA
1 TCA
28421845 ATTTTGATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:28421849 original size:18 final size:18
Alignment explanation
Indices: 28421796--28421849 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
28421786 AATTCATATC
* * *
28421796 ACTTTCAATTCCAATTTC
1 ACTTTCACTTTCAATTTT
* *
28421814 ACTTTCACTTTTACTTTT
1 ACTTTCACTTTCAATTTT
28421832 ACTTTCACTTTCAATTTT
1 ACTTTCACTTTCAATTTT
28421850 GATCATAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (18 bp):
ACTTTCACTTTCAATTTT
Found at i:28424401 original size:24 final size:24
Alignment explanation
Indices: 28424373--28424429 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
28424363 TAGACTAATA
* *
28424373 AGAGTTTGACTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
28424397 AGAGTTTAATTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAT
*
28424421 AAAGTTTAA
1 AGAGTTTAA
28424430 TTGGAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:28424430 original size:24 final size:24
Alignment explanation
Indices: 28424385--28424431 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28424375 AGTTTGACTG
* *
28424385 AAACAAATAAATAGAGTTTAATTC
1 AAACAAATAAACAAAGTTTAATTC
28424409 AAACAAATAAACAAAGTTTAATT
1 AAACAAATAAACAAAGTTTAATT
28424432 GGAAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTC
Found at i:28436975 original size:6 final size:6
Alignment explanation
Indices: 28436964--28436997 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
28436954 TTCGTCTCCT
* *
28436964 TCACCA TCACCA TCACCA TCACCC TCATCA TCAC
1 TCACCA TCACCA TCACCA TCACCA TCACCA TCAC
28436998 TATATGAGAA
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:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (6 bp):
TCACCA
Found at i:28440098 original size:15 final size:15
Alignment explanation
Indices: 28440078--28440121 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
28440068 TGATAAAATG
* *
28440078 AAAAATAAAATGTTA
1 AAAAATTAAATATTA
*
28440093 AAAAATTAAGTATTA
1 AAAAATTAAATATTA
28440108 AAAAATTAAATATT
1 AAAAATTAAATATT
28440122 GAATTTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAAAATTAAATATTA
Found at i:28442594 original size:75 final size:75
Alignment explanation
Indices: 28442464--28442618 Score: 294
Period size: 75 Copynumber: 2.1 Consensus size: 75
28442454 AAGAAATACA
*
28442464 AAGA-AAAAATGAAAACATAAGGTGCAGAGTAAAAGAGAGAGAGACTGGGTTTGGTGGAAGCCAA
1 AAGATAAAAATGAAAACATAAGGTGCAGAGTAAAAGAGAGAGAGACTGGGTGTGGTGGAAGCCAA
28442528 CATTGTGGGG
66 CATTGTGGGG
28442538 AAGATAAAAATGAAAACATAAGGTGCAGAGTAAAAGAGAGAGAGACTGGGTGTGGTGGAAGCCAA
1 AAGATAAAAATGAAAACATAAGGTGCAGAGTAAAAGAGAGAGAGACTGGGTGTGGTGGAAGCCAA
28442603 CATTGTGGGG
66 CATTGTGGGG
28442613 AAGATA
1 AAGATA
28442619 CTGCTTCCTC
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
74 4 0.05
75 75 0.95
ACGTcount: A:0.43, C:0.08, G:0.34, T:0.16
Consensus pattern (75 bp):
AAGATAAAAATGAAAACATAAGGTGCAGAGTAAAAGAGAGAGAGACTGGGTGTGGTGGAAGCCAA
CATTGTGGGG
Found at i:28451316 original size:2 final size:2
Alignment explanation
Indices: 28451309--28451334 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28451299 ATGAAAATGT
28451309 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
28451335 AAGTGATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28455420 original size:18 final size:18
Alignment explanation
Indices: 28455388--28455439 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
28455378 CTAGGATGAG
28455388 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
28455404 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
28455422 AA-AATTTTTAATTAATTA
1 AATAA-ATTTAATTAATTA
28455440 CAATTGAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 2 0.06
18 21 0.66
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:28455432 original size:14 final size:15
Alignment explanation
Indices: 28455388--28455437 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 15
28455378 CTAGGATGAG
28455388 AATAAATTTTTAATT
1 AATAAATTTTTAATT
28455403 AAATAAATTTAATTAATT
1 -AATAAATTT--TTAATT
28455421 AA-AAATTTTTAATT
1 AATAAATTTTTAATT
28455435 AAT
1 AAT
28455438 TACAATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.26
16 15 0.48
17 2 0.06
18 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTTTTAATT
Found at i:28456372 original size:18 final size:18
Alignment explanation
Indices: 28456349--28456384 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28456339 GTTCACTCTC
*
28456349 TTTTTAATTTTTACTTTA
1 TTTTTAATTTTTAATTTA
*
28456367 TTTTTAGTTTTTAATTTA
1 TTTTTAATTTTTAATTTA
28456385 AAAGTTATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTAATTTTTAATTTA
Found at i:28457970 original size:24 final size:24
Alignment explanation
Indices: 28457924--28457970 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28457914 TTTACTAGAT
** **
28457924 CTAACATTTTTTTCTTTTCTTTTC
1 CTAACATTTTCCTCTTTAATTTTC
28457948 CTAACATTTTCCTCTTTAATTTT
1 CTAACATTTTCCTCTTTAATTTT
28457971 ATGTTTCTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (24 bp):
CTAACATTTTCCTCTTTAATTTTC
Found at i:28460065 original size:13 final size:14
Alignment explanation
Indices: 28460036--28460065 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28460026 CTAAAAAAGT
28460036 AAATCATTTTTCAG
1 AAATCATTTTTCAG
28460050 AAATCATTTTTC-G
1 AAATCATTTTTCAG
28460063 AAA
1 AAA
28460066 AACATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
AAATCATTTTTCAG
Found at i:28460302 original size:23 final size:24
Alignment explanation
Indices: 28460259--28460306 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
28460249 CGAAGAAAAC
*
28460259 ATTTTTGATTAAAAAATTAAAAATG
1 ATTTTTGA-TAAAAAAATAAAAATG
28460284 ATTTTTGA-AAAAAAATAAAAATG
1 ATTTTTGATAAAAAAATAAAAATG
28460307 TGAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
ATTTTTGATAAAAAAATAAAAATG
Found at i:28462992 original size:21 final size:21
Alignment explanation
Indices: 28462945--28463021 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
28462935 AATACTGCAG
*
28462945 ACTTCTACTGATACAAGTCAC
1 ACTTCTACCGATACAAGTCAC
* *
28462966 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTCAC
* * **
28462987 TCTTCTACCGAAACAAGTCTT
1 ACTTCTACCGATACAAGTCAC
*
28463008 ACTTTTACCGATAC
1 ACTTCTACCGATAC
28463022 TAAAAACTCC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCAC
Found at i:28467748 original size:15 final size:15
Alignment explanation
Indices: 28467728--28467760 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28467718 TTGGTGTTTA
28467728 AAAAAAAGGAAAGAG
1 AAAAAAAGGAAAGAG
28467743 AAAAAAAGGAAAGAG
1 AAAAAAAGGAAAGAG
28467758 AAA
1 AAA
28467761 TTGGGTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAAAGGAAAGAG
Found at i:28470931 original size:7 final size:7
Alignment explanation
Indices: 28470919--28470947 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28470909 CAAAGGCTGG
28470919 TAGTAAC
1 TAGTAAC
28470926 TAGTAAC
1 TAGTAAC
28470933 TAGTAAC
1 TAGTAAC
28470940 TAGTAAC
1 TAGTAAC
28470947 T
1 T
28470948 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (7 bp):
TAGTAAC
Found at i:28474398 original size:15 final size:15
Alignment explanation
Indices: 28474378--28474431 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
28474368 TCACCAATCG
28474378 TAATTAAAATTATAA
1 TAATTAAAATTATAA
* *
28474393 TAATTAATATTCTAA
1 TAATTAAAATTATAA
*
28474408 TAAGT-AAA-TATAA
1 TAATTAAAATTATAA
*
28474421 TAATTATAATT
1 TAATTAAAATT
28474432 TTAAAATATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
15 18 0.60
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATTAAAATTATAA
Found at i:28479761 original size:15 final size:17
Alignment explanation
Indices: 28479732--28479770 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28479722 AAAAAATTCG
*
28479732 ATTTTTTATATTTATA-
1 ATTTTTTATAGTTATAT
28479748 ATTTTTTAT-GTTATAT
1 ATTTTTTATAGTTATAT
28479764 ATTTTTT
1 ATTTTTT
28479771 GAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTTTTATAGTTATAT
Found at i:28484368 original size:39 final size:37
Alignment explanation
Indices: 28484316--28484406 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
28484306 CATTCATTTA
28484316 CAGCCTT--TTGTTGAAACCTTAG-TCTAAGAAAACTTAT
1 CAGCCTTCATTGTTGAAACCTTAGTTC-AA-AAAAC-TAT
28484353 CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
1 CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
** *
28484390 CTTCCTTCATTGCTGAA
1 CAGCCTTCATTGTTGAA
28484407 TATCACCTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 24 0.50
38 5 0.10
39 17 0.35
40 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (37 bp):
CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
Found at i:28491773 original size:30 final size:30
Alignment explanation
Indices: 28491751--28491898 Score: 125
Period size: 30 Copynumber: 5.0 Consensus size: 30
28491741 TTAACCTCAT
*
28491751 TTTCGCCAAAAATTACCATTTTACCCCCGAAC
1 TTTC-CCAAAAATTACCATTTTACCCTCG-AC
28491783 TTT-CC-AAAATT-CCATTTTTAACCC-CGA-
1 TTTCCCAAAAATTACCA-TTTT-ACCCTCGAC
*
28491810 TTTCACCAAAAATTACCATTTTATCCTCGAAC
1 TTTC-CCAAAAATTACCATTTTACCCTCG-AC
*
28491842 TTT-CC-AAAATT-CCATTTTGACCCT-GAT
1 TTTCCCAAAAATTACCATTTT-ACCCTCGAC
*
28491869 TTTACCAAAAAATTACCATTTTACCCTCGA
1 TTT-CCCAAAAATTACCATTTTACCCTCGA
28491899 ACCTTTCAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 31
0.73 0.03 0.23
Matches are distributed among these distances:
27 7 0.07
28 12 0.12
29 28 0.29
30 31 0.32
31 13 0.13
32 6 0.06
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTCCCAAAAATTACCATTTTACCCTCGAC
Found at i:28491790 original size:59 final size:58
Alignment explanation
Indices: 28491721--28491948 Score: 266
Period size: 59 Copynumber: 3.9 Consensus size: 58
28491711 TTAACCTCAA
*
28491721 AACTTTCCAAAATCCCATTTTTAACCTCATTTTCGCCAAAAATTACCATTTTACCCCCG
1 AACTTTCCAAAATCCCATTTTTAACCTCATTTTC-CCAAAAATTACCATTTTACCCTCG
* * *
28491780 AACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCAAAAATTACCATTTTATCCTCG
1 AACTTTCCAAAATCCCATTTTTAACCTC-ATTTTC-CCAAAAATTACCATTTTACCCTCG
* * * * *
28491839 AACTTTCCAAAATTCCATTTTGACCCTGATTTTACCAAAAAATTACCATTTTACCCTCG
1 AACTTTCCAAAATCCCATTTTTAACCTCATTTT-CCCAAAAATTACCATTTTACCCTCG
* *
28491898 AACCTTT-CAAAATCCCATTTTTAACCCTAAATTTT-CCTAAAATTA-CATTTT
1 AA-CTTTCCAAAATCCCATTTTTAA-CCT-CATTTTCCCAAAAATTACCATTTT
28491949 TGCCCCCGAA
Statistics
Matches: 146, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
58 7 0.05
59 125 0.86
60 9 0.06
61 5 0.03
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (58 bp):
AACTTTCCAAAATCCCATTTTTAACCTCATTTTCCCAAAAATTACCATTTTACCCTCG
Found at i:28491940 original size:118 final size:117
Alignment explanation
Indices: 28491698--28491948 Score: 301
Period size: 118 Copynumber: 2.1 Consensus size: 117
28491688 CTAAACTTCT
** * * * *
28491698 CAAAAATTGTATTTTAACCTCAAAACTTTCCAAAATCCCATTTTTAACCTCATTTTCGCCAAAAA
1 CAAAAATTACATTTTATCCTC-GAACTTTCCAAAATCCCATTTTGAACCTCATTTTCGCAAAAAA
* **
28491763 TTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
65 TTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCAAATTTCAC
* * *
28491816 CAAAAATTACCATTTTATCCTCGAACTTTCCAAAATTCCATTTTGACCCTGATTTTAC-CAAAAA
1 CAAAAATTA-CATTTTATCCTCGAACTTTCCAAAATCCCATTTTGAACCTCATTTT-CGCAAAAA
* *
28491880 ATTACCATTTTACCCTCGAACCTTT-CAAAATCCCATTTTTAACCCTAAATTT-TC
64 ATTACCATTTTACCCCCGAA-CTTTCCAAAATCCCATTTTTAACCC-AAATTTCAC
*
28491934 CTAAAATTACATTTT
1 CAAAAATTACATTTT
28491949 TGCCCCCGAA
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
117 6 0.05
118 89 0.78
119 19 0.17
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (117 bp):
CAAAAATTACATTTTATCCTCGAACTTTCCAAAATCCCATTTTGAACCTCATTTTCGCAAAAAAT
TACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCAAATTTCAC
Found at i:28491975 original size:118 final size:117
Alignment explanation
Indices: 28491758--28491982 Score: 264
Period size: 118 Copynumber: 1.9 Consensus size: 117
28491748 CATTTTCGCC
* **
28491758 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCAAATTTCACCAAAAAT
* **
28491823 TACCATTTTATCCTCGAACTTTCCAAAATTCCATTTTGACCCTGATTTTACCA
66 TACCATTTTATCCCCGAACAGTCCAAAATTCCATTTTG-CCCTGATTTTACCA
* * *
28491876 AAAAATTACCATTTTACCCTCGAACCTTT-CAAAATCCCATTTTTAACCCTAAATTT-TCCTAAA
1 AAAAATTACCATTTTACCCCCGAA-CTTTCCAAAATCCCATTTTTAACCC-AAATTTCACCAAAA
28491939 ATTA-CATTTT-TGCCCCCGAA-AGT-CAAAAGTTACCATTTTGCCCT
64 ATTACCATTTTAT--CCCCGAACAGTCCAAAA-TT-CCATTTTGCCCT
28491983 CGGATGTCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
116 6 0.07
117 13 0.14
118 65 0.71
119 8 0.09
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCAAATTTCACCAAAAAT
TACCATTTTATCCCCGAACAGTCCAAAATTCCATTTTGCCCTGATTTTACCA
Found at i:28501184 original size:58 final size:58
Alignment explanation
Indices: 28501097--28501226 Score: 206
Period size: 58 Copynumber: 2.2 Consensus size: 58
28501087 ACCCGGGGGA
**
28501097 AAAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTAAGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
* * *
28501156 GAAATGGTAATTTAAGTGAAATCGGGGTTTAAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTAATTTAAGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
28501214 AAAATGGTAATTT
1 AAAATGGTAATTT
28501227 TTGAAAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 57 0.88
59 8 0.12
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTAAGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
Found at i:28501226 original size:29 final size:29
Alignment explanation
Indices: 28501136--28501226 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 29
28501126 TAAAAATGAG
*
28501136 ATTTAGGGAAGTTTGAGGGTGAAATGGTA
1 ATTTAGGGAAGTTTGAGGGTAAAATGGTA
* * * *
28501165 ATTTAAGTGAA-ATCG-GGGTTTAAAATGG-G
1 ATTT-AGGGAAGTTTGAGGG--TAAAATGGTA
28501194 ATTTAGGGAAGTTTGAGGGTAAAATGGTA
1 ATTTAGGGAAGTTTGAGGGTAAAATGGTA
28501223 ATTT
1 ATTT
28501227 TTGAAAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
28 16 0.34
29 16 0.34
30 15 0.32
ACGTcount: A:0.33, C:0.01, G:0.33, T:0.33
Consensus pattern (29 bp):
ATTTAGGGAAGTTTGAGGGTAAAATGGTA
Found at i:28501278 original size:30 final size:30
Alignment explanation
Indices: 28501205--28501590 Score: 426
Period size: 30 Copynumber: 12.8 Consensus size: 30
28501195 TTTAGGGAAG
*
28501205 TTTGAGGGT-AAAATGGTAATTTTTGAAAA-T
1 TTTG-GGGTCAAAAT-GTAATTTTGGAAAAGT
* * *
28501235 TTCGAGGTAAAAATGTAATTTTTTGG-AAA-T
1 TTTGGGGTCAAAATGTAA--TTTTGGAAAAGT
* * *
28501265 TTTGGGGTTAAAATATGATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
*
28501295 TTTAGGGTCAAAATGTAATTTTGGAAAAGAT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAG-T
* **
28501326 TTTAGGGTCAGCATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* * *
28501356 TTTGGGGCCAAAATATAATTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
*
28501386 TTTGGGGTCAAAATGTAATTTCTAG-AAAGT
1 TTTGGGGTCAAAATGTAATTT-TGGAAAAGT
*
28501416 TTTGGGGTCAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
28501446 TTAGGGGTCAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
28501476 TTTGGGGTTAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* * *
28501506 TTAGGGGTCAAAATATAATTTTGAAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
28501536 TTAGGGGTCAAAATGTAATTTT-TAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGA-AAAGT
28501566 TTTGGGGTC-AAATGTAATTTCTGGA
1 TTTGGGGTCAAAATGTAATTT-TGGA
28501591 CAATTTAGGG
Statistics
Matches: 311, Mismatches: 34, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
28 6 0.02
29 24 0.08
30 244 0.78
31 37 0.12
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAGT
Found at i:28503222 original size:25 final size:24
Alignment explanation
Indices: 28503189--28503238 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
28503179 TCTAGGCAGT
28503189 GGTGATGGCAGG-GCATGGTGGAGCA
1 GGTGATGGCAGGAGC-TGGTGG-GCA
* *
28503214 GGTGGTGGCTGGAGCTGGTGGGCA
1 GGTGATGGCAGGAGCTGGTGGGCA
28503238 G
1 G
28503239 CAGCACGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.14, C:0.12, G:0.56, T:0.18
Consensus pattern (24 bp):
GGTGATGGCAGGAGCTGGTGGGCA
Found at i:28503449 original size:6 final size:6
Alignment explanation
Indices: 28503440--28503542 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
28503430 TAATATTATT
* *
28503440 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
28503487 TTTAAA TTTAAGA --T-AA TTTAAA TCTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
28503531 TTTAAA CTTAAA
1 TTTAAA TTTAAA
28503543 AATCAAAGTC
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
3 1 0.01
4 3 0.04
5 17 0.23
6 48 0.64
7 1 0.01
8 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:28503743 original size:19 final size:19
Alignment explanation
Indices: 28503696--28503743 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28503686 GCTAGGTTTT
* *
28503696 AAATTTTATTTTAATTTTA
1 AAATTTTAATTTAATTGTA
* *
28503715 AAACTATAATTTAATTGTA
1 AAATTTTAATTTAATTGTA
*
28503734 ATATTTTAAT
1 AAATTTTAAT
28503744 AATCTTTTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AAATTTTAATTTAATTGTA
Found at i:28506918 original size:2 final size:2
Alignment explanation
Indices: 28506911--28506940 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28506901 GCCAAAGACT
28506911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28506941 AGGTTTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28506960 original size:13 final size:13
Alignment explanation
Indices: 28506942--28506973 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28506932 ATATATATAA
28506942 GGTTTAGGTTTAG
1 GGTTTAGGTTTAG
28506955 GGTTTAGGTTTAG
1 GGTTTAGGTTTAG
*
28506968 AGTTTA
1 GGTTTA
28506974 AGGTGGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (13 bp):
GGTTTAGGTTTAG
Found at i:28510584 original size:30 final size:30
Alignment explanation
Indices: 28510548--28510608 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28510538 AATACGAAGC
*
28510548 AATATAATAAGCAGAT-AAATAATATGCGAA
1 AATATAAGAAGCAGATCAAATAA-ATGCGAA
*
28510578 AATATAAGATGCAGATGCAAATAAATGCGAA
1 AATATAAGAAGCAGAT-CAAATAAATGCGAA
28510609 TGTTGGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 14 0.52
31 7 0.26
32 6 0.22
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.21
Consensus pattern (30 bp):
AATATAAGAAGCAGATCAAATAAATGCGAA
Found at i:28510679 original size:28 final size:28
Alignment explanation
Indices: 28510646--28510715 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
28510636 ATCGGGGTTG
*
28510646 AAAATGGGACTTTTGGA-TACCCGGGGGC
1 AAAATGGGAATTTTGGACT-CCCGGGGGC
* **
28510674 AAAATGGTAATTTTGGACTTTCGGGGGC
1 AAAATGGGAATTTTGGACTCCCGGGGGC
*
28510702 AAAATGGTAATTTT
1 AAAATGGGAATTTT
28510716 CGTGAAATCG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAATGGGAATTTTGGACTCCCGGGGGC
Found at i:28510953 original size:30 final size:30
Alignment explanation
Indices: 28510786--28510955 Score: 225
Period size: 30 Copynumber: 5.6 Consensus size: 30
28510776 TGGCAAAATC
* *
28510786 GGGGTCAAAAATGTAATATTGGAAAAGTTTT
1 GGGGTC-AAAATGTAATTTTAGAAAAGTTTT
*
28510817 GGGGTCAAAATGTAATATTAGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAAGTTTT
* *
28510847 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAAGTTTT
* **
28510877 AGGGTCAAAACATAATTTTTAG-AAAGTTTT
1 GGGGTCAAAATGTAA-TTTTAGAAAAGTTTT
*
28510907 GGGGTCAAAATGTAATTTTAGAAAACTTTT
1 GGGGTCAAAATGTAATTTTAGAAAAGTTTT
*
28510937 GGGGGCAAAATGTAATTTT
1 GGGGTCAAAATGTAATTTT
28510956 TGGGTAGTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
29 6 0.05
30 108 0.86
31 11 0.09
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTAGAAAAGTTTT
Found at i:28511788 original size:23 final size:21
Alignment explanation
Indices: 28511740--28511790 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
28511730 TCTTTCGTTC
28511740 TTCCTTTTTTTTTCTTTTTAA
1 TTCCTTTTTTTTTCTTTTTAA
* * *
28511761 ATCCTTTTTATTTTGTTCTTTAT
1 TTCCTTTTT-TTTTCTT-TTTAA
28511784 TTCCTTT
1 TTCCTTT
28511791 ATTTAACCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.10, C:0.16, G:0.02, T:0.73
Consensus pattern (21 bp):
TTCCTTTTTTTTTCTTTTTAA
Found at i:28512076 original size:15 final size:15
Alignment explanation
Indices: 28512056--28512096 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28512046 CTCCCTTTTT
*
28512056 TATTTTATTAATTAA
1 TATTTTATTAAATAA
*
28512071 TATTTTAATAAATAA
1 TATTTTATTAAATAA
28512086 TATATTTATTA
1 TAT-TTTATTA
28512097 TTATTAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTATTAAATAA
Found at i:28512894 original size:6 final size:6
Alignment explanation
Indices: 28512885--28512988 Score: 78
Period size: 6 Copynumber: 17.8 Consensus size: 6
28512875 TTAATATTAT
* *
28512885 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
28512932 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -ATAAT TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
28512977 TTTAAA CTTTAA
1 TTTAAA -TTTAA
28512989 TTAAAAAATC
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
4 3 0.04
5 18 0.23
6 45 0.58
7 6 0.08
8 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:28512894 original size:17 final size:17
Alignment explanation
Indices: 28512869--28512988 Score: 122
Period size: 17 Copynumber: 7.2 Consensus size: 17
28512859 CTTTTATTTA
* * *
28512869 TTAAGTTTAATATTATT
1 TTAAATTTAATATAAAT
28512886 TTAAATTTAAT-TAAAT
1 TTAAATTTAATATAAAT
*
28512902 TTAAATTTAAAATAAAT
1 TTAAATTTAATATAAAT
28512919 TTAAA--TAA-ATAAAT
1 TTAAATTTAATATAAAT
*
28512933 TTAAATTTAAGATAAAT
1 TTAAATTTAATATAAAT
* *
28512950 TTAAATTTAAAATAATT
1 TTAAATTTAATATAAAT
* *
28512967 TTAAAATTAATTTAAACT
1 TTAAATTTAATATAAA-T
28512985 TTAA
1 TTAA
28512989 TTAAAAAATC
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
14 11 0.12
15 3 0.03
16 16 0.18
17 53 0.60
18 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAAATTTAATATAAAT
Found at i:28512908 original size:11 final size:11
Alignment explanation
Indices: 28512885--28512982 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
28512875 TTAATATTAT
*
28512885 TTTAAATTTAA
1 TTTAAATTAAA
28512896 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
28512907 TTTAAAATAAA
1 TTTAAATTAAA
28512918 TTTAAATAAATAAA
1 TTTAAAT---TAAA
*
28512932 TTTAAATTTAA
1 TTTAAATTAAA
**
28512943 GATAAATTTAAA
1 TTTAAA-TTAAA
* *
28512955 TTTAAAATAAT
1 TTTAAATTAAA
28512966 TTTAAAATT-AA
1 TTT-AAATTAAA
28512977 TTTAAA
1 TTTAAA
28512983 CTTTAATTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
10 8 0.12
11 31 0.46
12 17 0.25
14 11 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:28512935 original size:31 final size:31
Alignment explanation
Indices: 28512897--28512955 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
28512887 TAAATTTAAT
28512897 TAAATTTAAATTTAAAATAAATTTAAATAAA
1 TAAATTTAAATTTAAAATAAATTTAAATAAA
*
28512928 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATTTAAAATAAATTTAAAT
28512956 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAATTTAAATTTAAAATAAATTTAAATAAA
Found at i:28521479 original size:13 final size:12
Alignment explanation
Indices: 28521440--28521487 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
28521430 GAATTGTGGG
*
28521440 TAAAAAATTATA
1 TAAAAAATTTTA
28521452 TAATAAATATATTTA
1 TAA-AAA-AT-TTTA
28521467 TTAAAAAATTTTA
1 -TAAAAAATTTTA
28521480 TAAAAAAT
1 TAAAAAAT
28521488 AAATGAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 11 0.35
13 7 0.23
14 4 0.13
15 6 0.19
16 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAAAAATTTTA
Found at i:28522249 original size:21 final size:21
Alignment explanation
Indices: 28522225--28522264 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28522215 AATTTACAAG
28522225 TATAAATAATAA-AAAATAATA
1 TATAAATAA-AATAAAATAATA
28522246 TATAAATAAAATAAAATAA
1 TATAAATAAAATAAAATAA
28522265 AATAATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TATAAATAAAATAAAATAATA
Found at i:28522259 original size:5 final size:5
Alignment explanation
Indices: 28522228--28522269 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
28522218 TTACAAGTAT
*
28522228 AAATA ATAA-A AAATA ATATA TAAATA AAATA AAATA AAATA A
1 AAATA A-AATA AAATA AAATA -AAATA AAATA AAATA AAATA A
28522270 TATACATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.06
5 24 0.75
6 6 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:28523418 original size:22 final size:22
Alignment explanation
Indices: 28523390--28523451 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
28523380 ATTTATTTAT
28523390 ATAAAATAATAAAT-AAATAAAA
1 ATAAAATAA-AAATGAAATAAAA
*
28523412 ATAAAATAAGAATGAAATAAAA
1 ATAAAATAAAAATGAAATAAAA
* *
28523434 CA-AAAAGAAAAATTAAAT
1 -ATAAAATAAAAATGAAAT
28523452 TGAGTTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 30 0.88
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (22 bp):
ATAAAATAAAAATGAAATAAAA
Found at i:28526567 original size:23 final size:23
Alignment explanation
Indices: 28526529--28526602 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
28526519 TCCAAAAAAT
*
28526529 AAAAACAACAACCAAAATAGCAAC
1 AAAAACAATAA-CAAAATAGCAAC
* *
28526553 AAAAATAATAGC-AAA-AGCAAC
1 AAAAACAATAACAAAATAGCAAC
* *
28526574 ACCAAAACAATAAAAAAATAGCACC
1 A--AAAACAATAACAAAATAGCAAC
28526599 AAAA
1 AAAA
28526603 CAGCAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
21 7 0.18
22 3 0.08
23 12 0.31
24 11 0.28
25 6 0.15
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (23 bp):
AAAAACAATAACAAAATAGCAAC
Found at i:28526598 original size:22 final size:21
Alignment explanation
Indices: 28526573--28526623 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28526563 GCAAAAGCAA
* *
28526573 CACCAAAACAATAAAAAAATAG
1 CACCAAAAC-AGAAAAAAACAG
*
28526595 CACCAAAACAGCAAAAAACAG
1 CACCAAAACAGAAAAAAACAG
28526616 CACCAAAA
1 CACCAAAA
28526624 TAACAACACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.65, C:0.25, G:0.06, T:0.04
Consensus pattern (21 bp):
CACCAAAACAGAAAAAAACAG
Found at i:28531964 original size:31 final size:31
Alignment explanation
Indices: 28531928--28531986 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28531918 AATTACAATC
28531928 CAGTGACTTAAATAAAAACTTTCGAATAATT
1 CAGTGACTTAAATAAAAACTTTCGAATAATT
* * *
28531959 CAGTGACTTAAATCAAAATTTTTGAATA
1 CAGTGACTTAAATAAAAACTTTCGAATA
28531987 GTTTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCGAATAATT
Found at i:28549570 original size:63 final size:63
Alignment explanation
Indices: 28549502--28549627 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
28549492 CATTAAAGTC
28549502 ACAACAATAAAGGAGGTCAAAGATATTATCACTCTCAAGCTAGATGAGTTAGTAGGCTCACTT
1 ACAACAATAAAGGAGGTCAAAGATATTATCACTCTCAAGCTAGATGAGTTAGTAGGCTCACTT
28549565 ACAACAATAAAGGAGGTCAAAGATATTATCACTCTCAAGCTAGATGAGTTAGTAGGCTCACTT
1 ACAACAATAAAGGAGGTCAAAGATATTATCACTCTCAAGCTAGATGAGTTAGTAGGCTCACTT
28549628 CAAACCTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (63 bp):
ACAACAATAAAGGAGGTCAAAGATATTATCACTCTCAAGCTAGATGAGTTAGTAGGCTCACTT
Found at i:28551664 original size:24 final size:24
Alignment explanation
Indices: 28551637--28551688 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28551627 ATTATCAAGA
*
28551637 TAAGTAT-TAGATTAAATTTAATAT
1 TAAGTATAAAGATTAAATTTAAT-T
*
28551661 TAAG-ATAAATATTAAATTTAATT
1 TAAGTATAAAGATTAAATTTAATT
28551684 TAAGT
1 TAAGT
28551689 TAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (24 bp):
TAAGTATAAAGATTAAATTTAATT
Found at i:28555741 original size:22 final size:22
Alignment explanation
Indices: 28555715--28555760 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28555705 TAAACATATA
28555715 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
28555737 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
28555759 AT
1 AT
28555761 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:28555765 original size:18 final size:20
Alignment explanation
Indices: 28555719--28555768 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
28555709 CATATAATAT
28555719 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
28555740 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
28555760 -TCACATATA
1 TTCACATATA
28555769 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:28559783 original size:44 final size:44
Alignment explanation
Indices: 28559712--28559802 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
28559702 ATGAATTAAG
* * *
28559712 TTCACATCAACCTTAAAAGTCAGCAGTCTTTTTATATATCACCT
1 TTCACATCAACCATAAAAGTCAACAGTCCTTTTATATATCACCT
*
28559756 TTCACATCTAA-CATAAATGTCAACAGTCCTTTTATATATCACCT
1 TTCACATC-AACCATAAAAGTCAACAGTCCTTTTATATATCACCT
28559800 TTC
1 TTC
28559803 TCTCCCATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (44 bp):
TTCACATCAACCATAAAAGTCAACAGTCCTTTTATATATCACCT
Found at i:28570012 original size:36 final size:36
Alignment explanation
Indices: 28569947--28570016 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
28569937 TAAAGTTTCA
* *
28569947 GATAACTGAGTATTGAACTTATTATTTCTTAGGATG
1 GATAACTGAGTATTGAACTTATAAATTCTTAGGATG
28569983 GATAACTG-GTATTGTAA-TTAGTAAATTCTTAGGA
1 GATAACTGAGTATTG-AACTTA-TAAATTCTTAGGA
28570017 GGGCCTGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 9 0.30
36 21 0.70
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (36 bp):
GATAACTGAGTATTGAACTTATAAATTCTTAGGATG
Found at i:28575851 original size:29 final size:30
Alignment explanation
Indices: 28575818--28575895 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 30
28575808 ACTTAGAAAT
28575818 ATTATAAATATATTATATTATTAA-TAAAA
1 ATTATAAATATATTATATTATTAATTAAAA
* * * * *
28575847 ATTATGAATCATTTTA-AATCTTAATTAATA
1 ATTATAAAT-ATATTATATTATTAATTAAAA
28575877 ATT-TAAATTATATTATATT
1 ATTATAAA-TATATTATATT
28575896 TACATTTAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
ATTATAAATATATTATATTATTAATTAAAA
Found at i:28576614 original size:31 final size:31
Alignment explanation
Indices: 28576543--28576677 Score: 135
Period size: 31 Copynumber: 4.2 Consensus size: 31
28576533 ATATTTCGTA
* *
28576543 TATCATTATATTAAATTGTTTAAATATTTTATG
1 TATCATTATATTAAATTATTTAAATA--TTATT
* *
28576576 TATCATTATACTAAATTATTCAAATATTATT
1 TATCATTATATTAAATTATTTAAATATTATT
*
28576607 TATCATTATATTAAATTATTTAAATCTTATT
1 TATCATTATATTAAATTATTTAAATATTATT
* * * * *
28576638 TGTTATTATATTTAATTTTTTTAAAATATTTATA
1 TATCATTATA-TTAAATTATTT-AAATA-TTATT
28576672 TATCAT
1 TATCAT
28576678 CAAATTTACA
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
31 40 0.48
32 9 0.11
33 27 0.32
34 8 0.10
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (31 bp):
TATCATTATATTAAATTATTTAAATATTATT
Found at i:28576665 original size:64 final size:65
Alignment explanation
Indices: 28576541--28576677 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 65
28576531 TTATATTTCG
* *
28576541 TATATCATTATATTAAATTGTTTAAATATTTTATGTATCATTATACTAAATTATTCAAATA-TTA
1 TATATCATTATATTAAATTATTTAAATATTTTATGTATCATTATACTAAATTATTAAAATATTTA
* * * * *
28576605 TTTATCATTATATTAAATTATTTAAATCTTATT-TGT-T-ATTATATTTAATTTTTTTAAAATAT
1 TATATCATTATATTAAATTATTTAAATATT-TTATGTATCATTATA-CTAA-ATTATTAAAATAT
28576667 TTA
63 TTA
28576670 TATATCAT
1 TATATCAT
28576678 CAAATTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
62 6 0.10
63 4 0.07
64 39 0.64
65 12 0.20
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (65 bp):
TATATCATTATATTAAATTATTTAAATATTTTATGTATCATTATACTAAATTATTAAAATATTTA
Found at i:28583735 original size:21 final size:21
Alignment explanation
Indices: 28583692--28583735 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28583682 ATTATGAGGG
* *
28583692 AATACAAAAAATATATAAAAA
1 AATACAAAAAATACAAAAAAA
28583713 AATACAAAAAA-ACAAAAACAA
1 AATACAAAAAATACAAAAA-AA
28583734 AA
1 AA
28583736 AGCACCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (21 bp):
AATACAAAAAATACAAAAAAA
Found at i:28583815 original size:20 final size:19
Alignment explanation
Indices: 28583778--28583820 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
28583768 GAGAAAGTAC
*
28583778 AAAAAAATAGGAAGTATATA
1 AAAAAAAAAGGAAGTATA-A
28583798 AAAAAAAAAGAGAA-TATAA
1 AAAAAAAAAG-GAAGTATAA
28583817 AAAA
1 AAAA
28583821 TATGAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (19 bp):
AAAAAAAAAGGAAGTATAA
Found at i:28583828 original size:20 final size:18
Alignment explanation
Indices: 28583752--28583820 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
28583742 AAACATGAGG
* *
28583752 GAATATAAAAAAATATGA
1 GAATATAAAAAAAAAAGA
*
28583770 GAA-AGTACAAAAAAATAGGAA
1 GAATA-TA-AAAAAAA-AAG-A
*
28583791 GTATATAAAAAAAAAAGA
1 GAATATAAAAAAAAAAGA
28583809 GAATATAAAAAA
1 GAATATAAAAAA
28583821 TATGAAGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.02
18 17 0.41
19 8 0.20
20 9 0.22
21 5 0.12
22 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.13, T:0.16
Consensus pattern (18 bp):
GAATATAAAAAAAAAAGA
Found at i:28584270 original size:20 final size:20
Alignment explanation
Indices: 28584247--28584313 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
28584237 CATAAATACC
28584247 AAAAAAATATGAGGAAATAT
1 AAAAAAATATGAGGAAATAT
** * *
28584267 AAAAATTTATGAGGGAACA-
1 AAAAAAATATGAGGAAATAT
* * *
28584286 AAAAAAAAATGAAGAATTAT
1 AAAAAAATATGAGGAAATAT
28584306 AAAAAAAT
1 AAAAAAAT
28584314 TATAAGAGAA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
19 12 0.35
20 22 0.65
ACGTcount: A:0.66, C:0.01, G:0.13, T:0.19
Consensus pattern (20 bp):
AAAAAAATATGAGGAAATAT
Found at i:28584609 original size:20 final size:20
Alignment explanation
Indices: 28584560--28584615 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
28584550 AATTATGAAA
* *
28584560 AAGTACCAAAATTTATGAGG
1 AAGTACCAAAAATTATAAGG
* *
28584580 ATGTA-TAAAAATTATAAGG
1 AAGTACCAAAAATTATAAGG
*
28584599 AAGTACCAAAACTTATA
1 AAGTACCAAAAATTATA
28584616 TGTATAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (20 bp):
AAGTACCAAAAATTATAAGG
Found at i:28584672 original size:20 final size:20
Alignment explanation
Indices: 28584647--28584719 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
28584637 ATAAAAAAAC
28584647 AAAAATTACGAGGGAT-AACA
1 AAAAATTACGA-GGATGAACA
* *
28584667 AAAAA-TATGAGGATGCACA
1 AAAAATTACGAGGATGAACA
* * * *
28584686 AAAAATTATGAAGATGTATA
1 AAAAATTACGAGGATGAACA
28584706 AAAAAGTTACGAGG
1 AAAAA-TTACGAGG
28584720 GAATACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.09
19 12 0.28
20 21 0.49
21 6 0.14
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAAATTACGAGGATGAACA
Found at i:28584678 original size:19 final size:19
Alignment explanation
Indices: 28584644--28584749 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 19
28584634 GAAATAAAAA
* *
28584644 AACAAAAATTACGAGGGAT
1 AACAAAAAATATGAGGGAT
28584663 AACAAAAAATATGA-GGAT
1 AACAAAAAATATGAGGGAT
* *
28584681 GCACAAAAAATTATGAAGATGTAT
1 -AACAAAAAA-TATG-AG--GGAT
** *
28584705 AA-AAAAGTTACGAGGGA-
1 AACAAAAAATATGAGGGAT
*
28584722 ATACAAAAAATATGAAGGAT
1 A-ACAAAAAATATGAGGGAT
*
28584742 ACCAAAAA
1 AACAAAAA
28584750 TACATGGATG
Statistics
Matches: 64, Mismatches: 14, Indels: 18
0.67 0.15 0.19
Matches are distributed among these distances:
17 1 0.02
18 7 0.11
19 37 0.58
20 7 0.11
21 4 0.06
22 4 0.06
23 1 0.02
24 3 0.05
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (19 bp):
AACAAAAAATATGAGGGAT
Found at i:28584768 original size:20 final size:19
Alignment explanation
Indices: 28584742--28584787 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28584732 TATGAAGGAT
*
28584742 ACCAAAAATACATGGATGC
1 ACCAAAAATACAAGGATGC
*
28584761 ACGAAAAATACAAGGATGC
1 ACCAAAAATACAAGGATGC
28584780 ACCAAAAA
1 ACCAAAAA
28584788 ATATAAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.20, G:0.15, T:0.11
Consensus pattern (19 bp):
ACCAAAAATACAAGGATGC
Found at i:28584789 original size:20 final size:20
Alignment explanation
Indices: 28584725--28584790 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
28584715 CGAGGGAATA
*
28584725 CAAAAAATATGAAGGAT--AC
1 CAAAAAATA-CAAGGATGCAC
*
28584744 C-AAAAATACATGGATGCA-
1 CAAAAAATACAAGGATGCAC
*
28584762 CGAAAAATACAAGGATGCAC
1 CAAAAAATACAAGGATGCAC
28584782 CAAAAAATA
1 CAAAAAATA
28584791 TAAAGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 5 0.13
18 8 0.21
19 18 0.46
20 8 0.21
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.14
Consensus pattern (20 bp):
CAAAAAATACAAGGATGCAC
Found at i:28584798 original size:20 final size:19
Alignment explanation
Indices: 28584745--28584807 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
28584735 GAAGGATACC
** *
28584745 AAAAATACATGGATGCACG
1 AAAAATACAAAGATGCACA
*
28584764 AAAAATACAAGGATGCACCA
1 AAAAATACAAAGATGCA-CA
* *
28584784 AAAAATATAAAGATGTACA
1 AAAAATACAAAGATGCACA
28584803 AAAAA
1 AAAAA
28584808 AATGAGAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.59, C:0.13, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAAATACAAAGATGCACA
Found at i:28584808 original size:20 final size:20
Alignment explanation
Indices: 28584745--28584808 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
28584735 GAAGGATACC
** *
28584745 AAAAATACATGGATGCAC-G
1 AAAAATACAAAGATGCACAA
* *
28584764 AAAAATACAAGGATGCACCA
1 AAAAATACAAAGATGCACAA
* *
28584784 AAAAATATAAAGATGTACAA
1 AAAAATACAAAGATGCACAA
28584804 AAAAA
1 AAAAA
28584809 ATGAGAGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAATACAAAGATGCACAA
Found at i:28584878 original size:20 final size:19
Alignment explanation
Indices: 28584799--28584878 Score: 56
Period size: 20 Copynumber: 4.1 Consensus size: 19
28584789 TATAAAGATG
28584799 TACAAAAAAAATGAGAGAA
1 TACAAAAAAAATGAGAGAA
* * * *
28584818 TTCAAAAATATAATGAAATAT
1 TACAAAAA-A-AATGAGAGAA
*
28584839 TA-AAAAAATATGAG-GAAA
1 TACAAAAAAAATGAGAG-AA
*
28584857 TACAAAAAATTATGAGAGAA
1 TACAAAAAA-AATGAGAGAA
28584877 TA
1 TA
28584879 TCATAAAACC
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
18 7 0.15
19 14 0.30
20 16 0.35
21 9 0.20
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (19 bp):
TACAAAAAAAATGAGAGAA
Done.