Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021183.1 Corchorus olitorius cultivar O-4 contig21216, 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: 175514
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2494 original size:5 final size:6
Alignment explanation
Indices: 2478--2511 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
2468 TATATATATG
2478 ATTTTT ATTTTT ATTTTT ATTTTTT CATTTTT AT
1 ATTTTT ATTTTT ATTTTT A-TTTTT -ATTTTT AT
2512 CATTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.58
7 10 0.38
8 1 0.04
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:4009 original size:21 final size:21
Alignment explanation
Indices: 3976--4017 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3966 TTTTGATCCT
*
3976 ATAAATTATTTTTAGTGTGAA
1 ATAAATTAGTTTTAGTGTGAA
* *
3997 ATAATTTAGTTTTGGTGTGAA
1 ATAAATTAGTTTTAGTGTGAA
4018 CATCATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (21 bp):
ATAAATTAGTTTTAGTGTGAA
Found at i:6460 original size:209 final size:209
Alignment explanation
Indices: 6087--6507 Score: 745
Period size: 209 Copynumber: 2.0 Consensus size: 209
6077 TGAATCACCC
6087 ATTATACCCTTATTTTTCAAACATATTTCTTAAATACCATTACTTAAATTATTATAGTTTTATTC
1 ATTATACCCTTATTTTTCAAACATATTTCTTAAATACCATTACTTAAATTATTATAGTTTTATTC
*
6152 TACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACTATT
66 TACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACTATT
*
6217 TTTCATTAAAAACTTGGATATATTCAAAAATTTTAATATACAGTTTTATTTTATTAAAAACTCTA
131 TTTCATTAAAAACTTGGATATATTCAAAAATTTTAATATACAGTTTTATTTTACTAAAAACTCTA
6282 TTTTCATTTAATTAA
196 TTTTCATTT-ATTAA
* * *
6297 ATTATAGCCTTA-TTTTCAAACATATTTCTTAAATGCCATTATTTAAATTATTATAGTTTTATTC
1 ATTATACCCTTATTTTTCAAACATATTTCTTAAATACCATTACTTAAATTATTATAGTTTTATTC
* *
6361 TGCTAAACACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACTATT
66 TACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACTATT
* *
6426 TTTTATTAAAAACTTGGATATATTCAAAAATTTTAATATATAGTTTTATTTTACTAAAAACTCTA
131 TTTCATTAAAAACTTGGATATATTCAAAAATTTTAATATACAGTTTTATTTTACTAAAAACTCTA
6491 TTTTCATTTATTAA
196 TTTTCATTTATTAA
6505 ATT
1 ATT
6508 CAATATTTTT
Statistics
Matches: 202, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
208 8 0.04
209 183 0.91
210 11 0.05
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.51
Consensus pattern (209 bp):
ATTATACCCTTATTTTTCAAACATATTTCTTAAATACCATTACTTAAATTATTATAGTTTTATTC
TACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACTATT
TTTCATTAAAAACTTGGATATATTCAAAAATTTTAATATACAGTTTTATTTTACTAAAAACTCTA
TTTTCATTTATTAA
Found at i:18142 original size:31 final size:31
Alignment explanation
Indices: 18090--18168 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
18080 ATTTTTAGCC
* * * *
18090 ACCACTTTGA-CCTTAACCTTTCAAAAGTTG
1 ACCAATTTGAGCCTAAAACTTTCAAAAGGTG
18120 -CTCAATTTGAGCCTAAAACTTTCAAAAGGTG
1 AC-CAATTTGAGCCTAAAACTTTCAAAAGGTG
*
18151 ACCAATTTGAGTCTAAAA
1 ACCAATTTGAGCCTAAAA
18169 ACAGAAACGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.02
30 7 0.17
31 32 0.78
32 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (31 bp):
ACCAATTTGAGCCTAAAACTTTCAAAAGGTG
Found at i:21184 original size:2 final size:2
Alignment explanation
Indices: 21175--21230 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
21165 TTTTATTTAG
* *
21175 TA TA -A TA TA TA T- TA TGA TG T- TA TA TA TA T- TT TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
21214 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
21231 TTCGAAGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.09
2 41 0.87
3 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21201 original size:19 final size:19
Alignment explanation
Indices: 21155--21230 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
21145 CATACTTTTT
* * *
21155 TATAAATATATTTTATTTA
1 TATATATATATATTATATA
*
21174 GTATA-ATATATATTATGATG
1 -TATATATATATATTAT-ATA
*
21194 T-TATATATATTTTATATA
1 TATATATATATATTATATA
21212 TATATATATATA-TATATA
1 TATATATATATATTATATA
21230 T
1 T
21231 TTCGAAGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 12 0.26
19 30 0.64
20 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATATATATATTATATA
Found at i:21502 original size:2 final size:2
Alignment explanation
Indices: 21495--21520 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21485 TATTAAAATA
21495 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
21521 CTAAAGACGC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31940 original size:21 final size:20
Alignment explanation
Indices: 31912--31958 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
31902 TTTCCACAAC
*
31912 AATCTCATTCGAATGATCTA
1 AATCTCATTCGAATCATCTA
*
31932 AATCATCATTTGAATCATCTA
1 AATC-TCATTCGAATCATCTA
*
31953 ACTCTC
1 AATCTC
31959 CTTCAACTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (20 bp):
AATCTCATTCGAATCATCTA
Found at i:35133 original size:627 final size:627
Alignment explanation
Indices: 33940--35199 Score: 2346
Period size: 627 Copynumber: 2.0 Consensus size: 627
33930 TCCAAACATT
33940 CTAAGTTTGACATAATCACTCACATCTTCACACCTAATACTAAACCTTCCAATATGCTCTAGTGT
1 CTAAGTTTGACATAATCACTCACATCTTCACACCTAATACTAAACCTTCCAATATGCTCTAGTGT
*
34005 AGACTGACCATCTTCACCAGAAAACACAGAAAAATCAGGAACCTTATATCCCCTTGGGAATGGAT
66 AGACTGACCATATTCACCAGAAAACACAGAAAAATCAGGAACCTTATATCCCCTTGGGAATGGAT
34070 TACATTGATCAATCCAATCTGGATATGGTTTCCTATACACAGGTCTTTGTCCACCTCTCCCACAG
131 TACATTGATCAATCCAATCTGGATATGGTTTCCTATACACAGGTCTTTGTCCACCTCTCCCACAG
34135 GCACTAACTGCTCTTGTAAGATTCCTAAAACCTGATCTCTTAACATATTTTAAAGATCATTATCT
196 GCACTAACTGCTCTTGTAAGATTCCTAAAACCTGATCTCTTAACATATTTTAAAGATCATTATCT
*
34200 CTTCTAATAGGATTTTGAACTTGTTCATAATTACCATGAACATTGGTTTCATTTCTAGGCTGAGT
261 CTTCTAACAGGATTTTGAACTTGTTCATAATTACCATGAACATTGGTTTCATTTCTAGGCTGAGT
*
34265 TTAGCCCCCAAGCCTCTGCAACATTCCTATTTTGACTACTTTGGACATTTCCAGCAACTCTATGA
326 TTAGCCCCCAAGCCTCTGCAACATTCCTATTTTGACTACCTTGGACATTTCCAGCAACTCTATGA
*
34330 TTTTCAAAAACTTCTTCAACAGATTTGCCTCGATTTGAAGTAAATCTGTCTGTTTGAGGAAAAAC
391 TTTTCAAAAACTTCTTCAACAGATTTGCCTCGATTTGAAGTAAATATGTCTGTTTGAGGAAAAAC
34395 ATTTTGACCTGGACTAATTCTTCCAGATTTTCCACTTGTATTATCCATAACATTACCTGTTATTG
456 ATTTTGACCTGGACTAATTCTTCCAGATTTTCCACTTGTATTATCCATAACATTACCTGTTATTG
34460 GATTCGAGCAAGTACCAAATTCCCTTAAGATTATATCTGGAGGAGGCCTGACATTACCTACCCTA
521 GATTCGAGCAAGTACCAAATTCCCTTAAGATTATATCTGGAGGAGGCCTGACATTACCTACCCTA
34525 ACCACATTGTTCT-GTGGACTTCCATTGACAAAATTTGACACC
586 ACCACATTGTT-TAGTGGACTTCCATTGACAAAATTTGACACC
34567 CTAAGTTTGACATAATCACTCACATCTTCACACCTAATACTAAACCTTCCAATATGCTCTAGTGT
1 CTAAGTTTGACATAATCACTCACATCTTCACACCTAATACTAAACCTTCCAATATGCTCTAGTGT
** *
34632 AGACTGACCATATTCACCAGAAAACACA-ATTTAATTAGGAACCTTATATCCCCTTGGGAATGGA
66 AGACTGACCATATTCACCAGAAAACACAGA-AAAATCAGGAACCTTATATCCCCTTGGGAATGGA
34696 TTACATTGATCAATCCAATCTGGATATGGTTTCCTATACACAGGTCTTTGTCCACCTCTTCCCAC
130 TTACATTGATCAATCCAATCTGGATATGGTTTCCTATACACAGGTCTTTGTCCACCTC-TCCCAC
* *
34761 AGGCACTAACTGCTCTTGTGAGATTCCTAAAACCTGATCTCTTAACATATTTTGAAGATCATTAT
194 AGGCACTAACTGCTCTTGTAAGATTCCTAAAACCTGATCTCTTAACATATTTTAAAGATCATTAT
34826 CTCTTCTAACAGGATTTTGAACTTGTTCATAATTACCATGAACATTGGTTTCATTTCTAGGCTGA
259 CTCTTCTAACAGGATTTTGAACTTGTTCATAATTACCATGAACATTGGTTTCATTTCTAGGCTGA
*
34891 GTTT-GCCCCCAAGCCTCTGCAACATTCCTATTTTGACTACCTTGGACATTTCCTGCAACTCTAT
324 GTTTAGCCCCCAAGCCTCTGCAACATTCCTATTTTGACTACCTTGGACATTTCCAGCAACTCTAT
34955 GATTTTCAAAAACTTCTTCAACAGATTTGCCTCGATTTGAAGTAAATATGTCTGTTTGAGGAAAA
389 GATTTTCAAAAACTTCTTCAACAGATTTGCCTCGATTTGAAGTAAATATGTCTGTTTGAGGAAAA
* *
35020 ACATTTTGATCTGGACTAATTCTTCCAGATTTTCCACTTGTATTATCCATAACATTACTTGTTAT
454 ACATTTTGACCTGGACTAATTCTTCCAGATTTTCCACTTGTATTATCCATAACATTACCTGTTAT
35085 TGGATTCGAGCAAGTACCAAATTCCCTTAAGATTATATCTGGAGGAGGCCTGACATTACCTACCC
519 TGGATTCGAGCAAGTACCAAATTCCCTTAAGATTATATCTGGAGGAGGCCTGACATTACCTACCC
* *
35150 TAACCACTTTGTTTAGTGGACTTCCATTGACAGAATTTGACACC
584 TAACCACATTGTTTAGTGGACTTCCATTGACAAAATTTGACACC
35194 CTAAGT
1 CTAAGT
35200 CCTTCTGGTA
Statistics
Matches: 616, Mismatches: 14, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
626 2 0.00
627 477 0.77
628 137 0.22
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (627 bp):
CTAAGTTTGACATAATCACTCACATCTTCACACCTAATACTAAACCTTCCAATATGCTCTAGTGT
AGACTGACCATATTCACCAGAAAACACAGAAAAATCAGGAACCTTATATCCCCTTGGGAATGGAT
TACATTGATCAATCCAATCTGGATATGGTTTCCTATACACAGGTCTTTGTCCACCTCTCCCACAG
GCACTAACTGCTCTTGTAAGATTCCTAAAACCTGATCTCTTAACATATTTTAAAGATCATTATCT
CTTCTAACAGGATTTTGAACTTGTTCATAATTACCATGAACATTGGTTTCATTTCTAGGCTGAGT
TTAGCCCCCAAGCCTCTGCAACATTCCTATTTTGACTACCTTGGACATTTCCAGCAACTCTATGA
TTTTCAAAAACTTCTTCAACAGATTTGCCTCGATTTGAAGTAAATATGTCTGTTTGAGGAAAAAC
ATTTTGACCTGGACTAATTCTTCCAGATTTTCCACTTGTATTATCCATAACATTACCTGTTATTG
GATTCGAGCAAGTACCAAATTCCCTTAAGATTATATCTGGAGGAGGCCTGACATTACCTACCCTA
ACCACATTGTTTAGTGGACTTCCATTGACAAAATTTGACACC
Found at i:36223 original size:2 final size:2
Alignment explanation
Indices: 36216--36251 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36206 AAGGGTGAGA
36216 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
36252 CAATTGGATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38559 original size:42 final size:43
Alignment explanation
Indices: 38508--38601 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
38498 AGTGCATTAT
*
38508 CTAA-ATTCTA-CTCTATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCTATCTCTAGATAATTCATCAAAATAAAG
*
38549 CTGATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCTATCTCTAGATAATTCATCAAAATAAAG
38594 CTAATATT
1 CTAATATT
38602 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
45 37 0.80
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCTATCTCTAGATAATTCATCAAAATAAAG
Found at i:41260 original size:18 final size:19
Alignment explanation
Indices: 41237--41280 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
41227 AAATTAAATA
*
41237 TTTTTAATT-TAATATATT
1 TTTTTAATTGAAATATATT
*
41255 TTTTT-ATTGAAATTTATT
1 TTTTTAATTGAAATATATT
41273 TTTTTAAT
1 TTTTTAAT
41281 AATAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 17 0.77
19 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTAATTGAAATATATT
Found at i:42074 original size:17 final size:18
Alignment explanation
Indices: 42034--42075 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42024 TTTTTATTAT
*
42034 TTAAAAAATAAATTTCAA
1 TTAAAAAATAAATTTAAA
* *
42052 TAAAAAAATATA-TTAAA
1 TTAAAAAATAAATTTAAA
42069 TTAAAAA
1 TTAAAAA
42076 TATTTAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAATAAATTTAAA
Found at i:43725 original size:3 final size:3
Alignment explanation
Indices: 43719--43761 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
43709 TGCTTAGTTC
* *
43719 ATT ATT ATT ACT CTT ATT ATT ATT ATT -TT ATT ATAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT A
43762 GAGGTTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:45032 original size:19 final size:19
Alignment explanation
Indices: 45005--45064 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
44995 ACTGTTTAGC
*
45005 TACTATACAGATGAGATTA
1 TACTGTACAGATGAGATTA
* *
45024 TACTGTACAGATCAAATTAGA
1 TACTGTACAGATGAGATT--A
*
45045 TACTGTACATATGAGATTA
1 TACTGTACAGATGAGATTA
45064 T
1 T
45065 TAGAGCAGCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (19 bp):
TACTGTACAGATGAGATTA
Found at i:45063 original size:21 final size:21
Alignment explanation
Indices: 45000--45063 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
44990 TCGACACTGT
* *
45000 TTAGCTACTATACAGATGAGA
1 TTAGATACTGTACAGATGAGA
* *
45021 TT--ATACTGTACAGATCAAA
1 TTAGATACTGTACAGATGAGA
*
45040 TTAGATACTGTACATATGAGA
1 TTAGATACTGTACAGATGAGA
45061 TTA
1 TTA
45064 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (21 bp):
TTAGATACTGTACAGATGAGA
Found at i:45132 original size:22 final size:22
Alignment explanation
Indices: 45104--45197 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 22
45094 TTAAAACTCC
**
45104 ATGTGGTTATTGAAATTTCATA
1 ATGTGGTTATCAAAATTTCATA
45126 ATGTGGTTATCAAAATTTCATA
1 ATGTGGTTATCAAAATTTCATA
* * * *
45148 TTGAGATTA-CAAAATTGCATA
1 ATGTGGTTATCAAAATTTCATA
* * * *
45169 GTATGGTTACCAAAACTT-ATA
1 ATGTGGTTATCAAAATTTCATA
45190 AGTGTGGT
1 A-TGTGGT
45198 ATTTCAGAGG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 19 0.34
22 37 0.66
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
ATGTGGTTATCAAAATTTCATA
Found at i:45305 original size:22 final size:22
Alignment explanation
Indices: 45280--45362 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
45270 TTGTGGGGTA
* *
45280 ATCAAAATCTCATAGCGAGATT
1 ATCAAAATTTCATAGAGAGATT
*
45302 ATCAAAATTTCATAGGGA-AGTT
1 ATCAAAATTTCATAGAGAGA-TT
* *
45324 AACAAAATTTCATAGAGAGTTT
1 ATCAAAATTTCATAGAGAGATT
45346 ATCGAGAAATTTCATAG
1 ATC-A-AAATTTCATAG
45363 TTTAGTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 38 0.75
23 1 0.02
24 11 0.22
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (22 bp):
ATCAAAATTTCATAGAGAGATT
Found at i:45309 original size:44 final size:44
Alignment explanation
Indices: 45205--45316 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 44
45195 GGTATTTCAG
* * * * * *
45205 AGGAAAGTTATCAAAATTGTATAGTGTGGTTACCAAAATTTTAT
1 AGGAAATTTATCAAAATTTTATAGTGGGGTAACCAAAATCTCAT
* * *
45249 AGGAAATTTATTAAAATTTTATTGTGGGGTAATCAAAATCTCAT
1 AGGAAATTTATCAAAATTTTATAGTGGGGTAACCAAAATCTCAT
* *
45293 AGCGAGA-TTATCAAAATTTCATAG
1 AG-GAAATTTATCAAAATTTTATAG
45317 GGAAGTTAAC
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
44 51 0.94
45 3 0.06
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (44 bp):
AGGAAATTTATCAAAATTTTATAGTGGGGTAACCAAAATCTCAT
Found at i:45479 original size:22 final size:21
Alignment explanation
Indices: 45462--45712 Score: 162
Period size: 22 Copynumber: 11.5 Consensus size: 21
45452 ACATTTGATA
45462 AGGAGGTTATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTCAT
*
45483 AGTGTGGTTATCAAAATTTCATT
1 AG-GAGGTTATCAAAATTTCA-T
*
45506 GGGAGGTTATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTCAT
* *
45527 TGTCAGGTT-TCCAAAATTTCAT
1 AG-GAGGTTAT-CAAAATTTCAT
* * * *
45549 AGAGAGGTTAACAAAAATCCAG
1 AG-GAGGTTATCAAAATTTCAT
* * * *
45571 ATGTAGGTTAACAAAATTTTAG
1 A-GGAGGTTATCAAAATTTCAT
* * * *
45593 AGGGATGTTCTCAAAGTTCCAT
1 A-GGAGGTTATCAAAATTTCAT
* * *
45615 AGGGAGGTTCTCGAAATTACAT
1 A-GGAGGTTATCAAAATTTCAT
**
45637 AGTGTCGTTATCAAAATTTCAT
1 AG-GAGGTTATCAAAATTTCAT
*
45659 AGGAAGGTTATCAATATTTCAT
1 AGG-AGGTTATCAAAATTTCAT
* * * *
45681 ATGTGATCATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTCAT
45702 AAGGAGGTTAT
1 -AGGAGGTTAT
45713 TACAATTTTA
Statistics
Matches: 175, Mismatches: 46, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
21 21 0.12
22 151 0.86
23 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (21 bp):
AGGAGGTTATCAAAATTTCAT
Found at i:45511 original size:44 final size:44
Alignment explanation
Indices: 45454--45712 Score: 179
Period size: 44 Copynumber: 5.9 Consensus size: 44
45444 GCTTAGCAAC
* * *
45454 ATTTGATAAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAA
* * *
45498 ATTTCATTGGGAGGTTATCAAAATTTCATTGTCAGGTT-TCCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTTAT-CAAA
* * * * * *
45542 ATTTCATAGAGAGGTTAACAAAAATCCAGA-TGTAGGTTAACAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTG-AGGTTATCAAA
* * * * * * * * *
45586 ATTTTAGAGGGATGTTCTCAAAGTTCCATAGGGAGGTTCTCGAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAA
* * ** *
45630 ATTACATAGTGTCGTTATCAAAATTTCATAG-GAAGGTTATCAAT
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTG-AGGTTATCAAA
* *
45674 ATTTCATATGTGA--TCATCAAAATTTCATAAG-GAGGTTAT
1 ATTTCATA-GGGAGGTTATCAAAATTTCAT-AGTGAGGTTAT
45713 TACAATTTTA
Statistics
Matches: 165, Mismatches: 43, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
43 24 0.15
44 137 0.83
45 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (44 bp):
ATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAA
Found at i:49243 original size:166 final size:166
Alignment explanation
Indices: 48929--49455 Score: 503
Period size: 166 Copynumber: 3.2 Consensus size: 166
48919 TCCAACACAT
* * * * * * * *
48929 AAATGATTGGAGACCTGAGATATAAAAGTAC-AATTTAGTAAATAGAAAAAATTTTGCAAATCCA
1 AAATGGTTGGAGACTTGAGACACAAAAGT-CTAATTTAGTAAATGGAAAAAA-ATTGGAAATCTA
** * * * * * *
48993 AATTCGCTCCGTATCCATATATCACGATCCAAATCCGCCCTAAA-TAGATTCGGACAGATCGGAT
64 AATTCGCTCAATATCCATATATCACGATTCAAATCCGACCTAAACGA-ATTCGAACGGATCAGAT
* * *
49057 ATCCGCCTCGGAGATCCAAACAACAATTGTCCGATACAC
128 ATCTGTCTCAGAGATCCAAACAACAATTGTCCGATACAC
* * ** *
49096 AAATGGTTGGAGACTTCG-GACACAAAAGTCTAATTTAGTAAGTGTAAAAATTTTGGAAATTTAA
1 AAATGGTTGGAGACTT-GAGACACAAAAGTCTAATTTAGTAAATGGAAAAAAATTGGAAATCTAA
* * * *
49160 ATTCGCTCAATATCTATATATTACTA-TCAAAATCC-ACCGTAAACGAATTCGAACGGATCATAT
65 ATTCGCTCAATATCCATATATCACGATTC-AAATCCGACC-TAAACGAATTCGAACGGATCAGAT
* * * * *
49223 ATCTG-CTTCAGAGGTCCAAACAACAATCGTTCGATATAT
128 ATCTGTC-TCAGAGATCCAAACAACAATTGTCCGATACAC
49262 AAATGGTTGGAGAAC-TGAGACACAAAAGTCTAATTTAGTAAATGGAAAAAAATTGGAAATCTAA
1 AAATGGTTGGAG-ACTTGAGACACAAAAGTCTAATTTAGTAAATGGAAAAAAATTGGAAATCTAA
* *** * * *
49326 ATTCGTTTTGTATCCATATATCACGATTCAAATCCGACCTAAACGGATTCGAATGGATCGGATAT
65 ATTCGCTCAATATCCATATATCACGATTCAAATCCGACCTAAACGAATTCGAACGGATCAGATAT
* * * * ** *
49391 CTGTCTCCGTGATCTAACCGGCAATTGTCTGATACAC
130 CTGTCTCAGAGATCCAAACAACAATTGTCCGATACAC
49428 AAATGGTTGGA-ACTTGAGACACAAAAGT
1 AAATGGTTGGAGACTTGAGACACAAAAGT
49456 ACATTTTTTT
Statistics
Matches: 290, Mismatches: 58, Indels: 26
0.78 0.16 0.07
Matches are distributed among these distances:
164 2 0.01
165 19 0.07
166 220 0.76
167 48 0.17
168 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (166 bp):
AAATGGTTGGAGACTTGAGACACAAAAGTCTAATTTAGTAAATGGAAAAAAATTGGAAATCTAAA
TTCGCTCAATATCCATATATCACGATTCAAATCCGACCTAAACGAATTCGAACGGATCAGATATC
TGTCTCAGAGATCCAAACAACAATTGTCCGATACAC
Found at i:50607 original size:15 final size:14
Alignment explanation
Indices: 50584--50613 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
50574 ATAAAAATTA
50584 AATATTTTTATTTT
1 AATATTTTTATTTT
50598 AATATATTTTATTTT
1 AATAT-TTTTATTTT
50613 A
1 A
50614 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:51800 original size:15 final size:14
Alignment explanation
Indices: 51782--51811 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
51772 TAAATTTCAA
51782 TAAAATAAAATATAT
1 TAAAATAAAA-ATAT
51797 TAAAATAAAAATAT
1 TAAAATAAAAATAT
51811 T
1 T
51812 TGATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATAAAAATAT
Found at i:56302 original size:19 final size:18
Alignment explanation
Indices: 56278--56313 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56268 TGAAGACTTA
56278 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
56297 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
56314 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:56320 original size:30 final size:30
Alignment explanation
Indices: 56266--56325 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
56256 GAAGTTCGTG
* *
56266 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
56296 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
56326 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:61382 original size:15 final size:15
Alignment explanation
Indices: 61362--61391 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61352 GGAACATGGT
61362 TGAGTAATTTCTTGA
1 TGAGTAATTTCTTGA
*
61377 TGAGTACTTTCTTGA
1 TGAGTAATTTCTTGA
61392 CTTAAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (15 bp):
TGAGTAATTTCTTGA
Found at i:61499 original size:20 final size:20
Alignment explanation
Indices: 61470--61525 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
61460 TATAAACACT
61470 AAAT-TTCAATTCATCTCAC
1 AAATATTCAATTCATCTCAC
61489 AAATATTCAATTCATCTCAC
1 AAATATTCAATTCATCTCAC
61509 AAATATTCAATTCATCT
1 AAATATTCAATTCATCT
61526 AAAACAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTCAATTCATCTCAC
Found at i:65466 original size:517 final size:517
Alignment explanation
Indices: 64480--65518 Score: 1934
Period size: 517 Copynumber: 2.0 Consensus size: 517
64470 GTCAGCAATC
* *
64480 ATAAATATAATCCCCACAAAATCCTAACTAAGTAGATAGGGCAAGCAGGGGTCGATCCCACAGAG
1 ATAAAAATAATCACCACAAAATCCTAACTAAGTAGATAGGGCAAGCAGGGGTCGATCCCACAGAG
64545 AAGGTGGATAGACTTTATCCGAAGATACAATCCTTAAAAATCTCTCAAAAGCAATGCGTAAGAAC
66 AAGGTGGATAGACTTTATCCGAAGATACAATCCTTAAAAATCTCTCAAAAGCAATGCGTAAGAAC
*
64610 AGGGGATTAAAAATAACAATTAAGAAGAAGGGAATTAAACTAAAAACAAAGCAAAGTAAATTAAA
131 AGGGGATTAAAAATAACAATTAAGAAGAAGGCAATTAAACTAAAAACAAAGCAAAGTAAATTAAA
* *
64675 TCTAGATCTATGGCAATTAAGAATGAAAACATTAACTAAAAGCATACTTCTTCTCCAATGGTAGA
196 TCTAGATCTATGGCAATTAAGAAAGAAAACAATAACTAAAAGCATACTTCTTCTCCAATGGTAGA
64740 AAACAATCAAATTGACTTTGGATCCTTGATTTAAAAGATGAATTCAATATTAAATCATTGATGAT
261 AAACAATCAAATTGACTTTGGATCCTTGATTTAAAAGATGAATTCAATATTAAATCATTGATGAT
* *
64805 AACTGGTTTAGGAAAACCTAACATACTATTTAGATAAGATTACCGGTTAAGGCTTAAATTACCCC
326 AACTGGTCTAGGAAAACCTAACATACTATTTAGATAAGATTACCGGTTAAGGCTTAAATTACCAC
*
64870 TATTGTTAACTTAACAAATCAATTACCGATTAAGACTTAAAGATTCATCAAGCAACAAAGCATTA
391 TATTGTTAACTTAACAAATCAATTACCGATTAAGACTTAAAGATTCACCAAGCAACAAAGCATTA
64935 AGATCAACTATTTAATTAGTTCTTTCACACATGCTTAACAAGTAAAACAATACAACAACCAG
456 AGATCAACTATTTAATTAGTTCTTTCACACATGCTTAACAAGTAAAACAATACAACAACCAG
64997 ATAAAAATAATCACCACAAAATCCTAACTAAGTAGATAGGGCAAGCAGGGGTCGATCCCACAGAG
1 ATAAAAATAATCACCACAAAATCCTAACTAAGTAGATAGGGCAAGCAGGGGTCGATCCCACAGAG
*
65062 AAGGTGGATAGACTTTATCCGAAGATACAATCCTTAAAAATCTCTTAAAAGCAATGCGTAAGAAC
66 AAGGTGGATAGACTTTATCCGAAGATACAATCCTTAAAAATCTCTCAAAAGCAATGCGTAAGAAC
*
65127 AGGGGATTAAAAATAATAATTAAGAAGAAGGCAATTAAACTAAAAACAAAGCAAAGTAAATTAAA
131 AGGGGATTAAAAATAACAATTAAGAAGAAGGCAATTAAACTAAAAACAAAGCAAAGTAAATTAAA
65192 TCTAGATCTATGGCAATTAAGAAAGAAAACAATAACTAAAAGCATACTTCTTCTCCAATGGTAGA
196 TCTAGATCTATGGCAATTAAGAAAGAAAACAATAACTAAAAGCATACTTCTTCTCCAATGGTAGA
*
65257 AAACAATCAAATTGACTTTGGATCCTTGATTTAAAAGATGAATTCAATATTAAATCCTTGATGAT
261 AAACAATCAAATTGACTTTGGATCCTTGATTTAAAAGATGAATTCAATATTAAATCATTGATGAT
* *
65322 AACTGGTCTAGGAAAACCTAACATGCTATTTAGATAAGATTACTGGTTAAGGCTTAAATTACCAC
326 AACTGGTCTAGGAAAACCTAACATACTATTTAGATAAGATTACCGGTTAAGGCTTAAATTACCAC
* *
65387 TATTGTTAACTTAACAAATCAATTACCGGTTAAGGCTTAAAGATTCACCAAGCAACAAAGCATTA
391 TATTGTTAACTTAACAAATCAATTACCGATTAAGACTTAAAGATTCACCAAGCAACAAAGCATTA
*
65452 AGATCAACTATTTAATTAGTTCTTTCACACATGCTTAACAAGTAAAACCATACAACAACCAG
456 AGATCAACTATTTAATTAGTTCTTTCACACATGCTTAACAAGTAAAACAATACAACAACCAG
65514 ATAAA
1 ATAAA
65519 TCTGATCACT
Statistics
Matches: 506, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
517 506 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (517 bp):
ATAAAAATAATCACCACAAAATCCTAACTAAGTAGATAGGGCAAGCAGGGGTCGATCCCACAGAG
AAGGTGGATAGACTTTATCCGAAGATACAATCCTTAAAAATCTCTCAAAAGCAATGCGTAAGAAC
AGGGGATTAAAAATAACAATTAAGAAGAAGGCAATTAAACTAAAAACAAAGCAAAGTAAATTAAA
TCTAGATCTATGGCAATTAAGAAAGAAAACAATAACTAAAAGCATACTTCTTCTCCAATGGTAGA
AAACAATCAAATTGACTTTGGATCCTTGATTTAAAAGATGAATTCAATATTAAATCATTGATGAT
AACTGGTCTAGGAAAACCTAACATACTATTTAGATAAGATTACCGGTTAAGGCTTAAATTACCAC
TATTGTTAACTTAACAAATCAATTACCGATTAAGACTTAAAGATTCACCAAGCAACAAAGCATTA
AGATCAACTATTTAATTAGTTCTTTCACACATGCTTAACAAGTAAAACAATACAACAACCAG
Found at i:65957 original size:18 final size:19
Alignment explanation
Indices: 65931--65968 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
65921 GCACCCTAGC
65931 ACTAAAACTAGAAGA-AAA
1 ACTAAAACTAGAAGAGAAA
*
65949 ACTAGAACTAGAAGAGAAA
1 ACTAAAACTAGAAGAGAAA
65968 A
1 A
65969 AGAAGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (19 bp):
ACTAAAACTAGAAGAGAAA
Found at i:67717 original size:59 final size:59
Alignment explanation
Indices: 67650--67765 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
67640 CGAATTTGGT
* *
67650 ATGCAAACTGCTGTGTTTGGCTTCTTTTCTTTTGTTTTCTAATAGTACCTACAATGGGC
1 ATGCAAACTGCTGTGTTTAGCTTCTTTTCTTTTGTTTTATAATAGTACCTACAATGGGC
* *
67709 ATGCAAACTGTTGTGTTTAGCTTCTTTTCTTTTGTTTTATAATAGTATCTACAATGG
1 ATGCAAACTGCTGTGTTTAGCTTCTTTTCTTTTGTTTTATAATAGTACCTACAATGG
67766 TCAAGGTAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (59 bp):
ATGCAAACTGCTGTGTTTAGCTTCTTTTCTTTTGTTTTATAATAGTACCTACAATGGGC
Found at i:73050 original size:21 final size:21
Alignment explanation
Indices: 73024--73064 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
73014 TTGAAGCCCT
73024 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
73045 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
73065 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:79732 original size:16 final size:16
Alignment explanation
Indices: 79711--79745 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
79701 CAAACATGAA
*
79711 TTTAACTTTGAATGCT
1 TTTAACTCTGAATGCT
79727 TTTAACTCTGAATGCT
1 TTTAACTCTGAATGCT
79743 TTT
1 TTT
79746 GATGACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAACTCTGAATGCT
Found at i:80861 original size:39 final size:38
Alignment explanation
Indices: 80817--81111 Score: 218
Period size: 38 Copynumber: 7.7 Consensus size: 38
80807 CTAATGCGAG
* **
80817 ATTCTAAAGAGGGACCTAAGCAGGTTTGATTAAATAAA
1 ATTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
* *
80855 ACTTCTAAACAAGGACCTAAGCAGGTTCGATTAAACGAA
1 A-TTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
* * * * ** *
80894 ATTTTAAGC-GGAAACCTAAGCAGATTTTCTTAAATGAA
1 ATTCTAAACAGG-GACCTAAGCAGGTTTGATTAAACGAA
** * *
80932 ATTCTAAACATTGACCTAAGCATGTTTGATTAAACAAA
1 ATTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
* *
80970 ACTTCTAAACAAGGACCTAAGCACGTTTGATTAAACGAA
1 A-TTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
* * * ** *
81009 ATTCT-AA-GGGGAAACCTAAACAGATTTTCTTAAATGAA
1 ATTCTAAACAGGG--ACCTAAGCAGGTTTGATTAAACGAA
** ** * *
81047 ATTCTAAACATTGACCTAAGCAGGTTTCCTTAAATGAG
1 ATTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
* * **
81085 ATTCCAAGCATAGACCTAAGCAGGTTT
1 ATTCTAAACAGGGACCTAAGCAGGTTT
81112 ACTTAGATGG
Statistics
Matches: 202, Mismatches: 47, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
36 2 0.01
37 3 0.01
38 127 0.63
39 69 0.34
40 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (38 bp):
ATTCTAAACAGGGACCTAAGCAGGTTTGATTAAACGAA
Found at i:81080 original size:115 final size:115
Alignment explanation
Indices: 80829--81073 Score: 427
Period size: 115 Copynumber: 2.1 Consensus size: 115
80819 TCTAAAGAGG
* *
80829 GACCTAAGCAGGTTTGATTAAATAAAACTTCTAAACAAGGACCTAAGCAGGTTCGATTAAACGAA
1 GACCTAAGCAGGTTTGATTAAACAAAACTTCTAAACAAGGACCTAAGCACGTTCGATTAAACGAA
* *
80894 ATTTTAAGCGGAAACCTAAGCAGATTTTCTTAAATGAAATTCTAAACATT
66 ATTCTAAGCGGAAACCTAAACAGATTTTCTTAAATGAAATTCTAAACATT
* *
80944 GACCTAAGCATGTTTGATTAAACAAAACTTCTAAACAAGGACCTAAGCACGTTTGATTAAACGAA
1 GACCTAAGCAGGTTTGATTAAACAAAACTTCTAAACAAGGACCTAAGCACGTTCGATTAAACGAA
*
81009 ATTCTAAGGGGAAACCTAAACAGATTTTCTTAAATGAAATTCTAAACATT
66 ATTCTAAGCGGAAACCTAAACAGATTTTCTTAAATGAAATTCTAAACATT
81059 GACCTAAGCAGGTTT
1 GACCTAAGCAGGTTT
81074 CCTTAAATGA
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 122 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (115 bp):
GACCTAAGCAGGTTTGATTAAACAAAACTTCTAAACAAGGACCTAAGCACGTTCGATTAAACGAA
ATTCTAAGCGGAAACCTAAACAGATTTTCTTAAATGAAATTCTAAACATT
Found at i:81260 original size:34 final size:36
Alignment explanation
Indices: 81175--81263 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 36
81165 TCTACACAAA
* *
81175 GTCCTAAGCAGGTTCACTTAACGAAACTCTAAGCAGAG
1 GTCCTAAGCAGGTTTAC-T-ACGAAACTCAAAGCAGAG
*
81213 GT-CTAAGCCGGTTTACT-CG-AACTCAAAGCAG-G
1 GTCCTAAGCAGGTTTACTACGAAACTCAAAGCAGAG
81245 GATCCTAAGCAGGTTTACT
1 G-TCCTAAGCAGGTTTACT
81264 TACCCAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 2 0.04
33 12 0.27
34 16 0.36
36 1 0.02
37 12 0.27
38 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (36 bp):
GTCCTAAGCAGGTTTACTACGAAACTCAAAGCAGAG
Found at i:82378 original size:11 final size:11
Alignment explanation
Indices: 82348--82388 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
82338 CTTTTTTAGG
82348 TTATGTTTTATT
1 TTAT-TTTTATT
82360 TTATTTTTTATT
1 TTA-TTTTTATT
82372 TTATTTTTATT
1 TTATTTTTATT
82383 TT-TTTT
1 TTATTTT
82389 AAGCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.14
11 10 0.36
12 13 0.46
13 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:82379 original size:18 final size:17
Alignment explanation
Indices: 82353--82386 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
82343 TTAGGTTATG
82353 TTTTATTTTATTTTTTA
1 TTTTATTTTATTTTTTA
82370 TTTTATTTTTATTTTTT
1 TTTTA-TTTTATTTTTT
82387 TTAAGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTATTTTATTTTTTA
Found at i:87250 original size:18 final size:19
Alignment explanation
Indices: 87222--87258 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
87212 ACACAGATAA
*
87222 TTTTCTCTTCTGGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
87241 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
87259 GACTAGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.08, C:0.14, G:0.14, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:92660 original size:21 final size:21
Alignment explanation
Indices: 92636--92680 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
92626 CGTCGCCTCC
92636 TCTCGGCGCTGTG-CTTCTTCA
1 TCTCGGCGCT-TGACTTCTTCA
* *
92657 TCTCTGCGCTTGAGTTCTTCA
1 TCTCGGCGCTTGACTTCTTCA
92678 TCT
1 TCT
92681 TTGCGCCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.07, C:0.31, G:0.20, T:0.42
Consensus pattern (21 bp):
TCTCGGCGCTTGACTTCTTCA
Found at i:96126 original size:19 final size:18
Alignment explanation
Indices: 96102--96137 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
96092 TGAAGATTTA
96102 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
96121 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
96138 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:96772 original size:18 final size:18
Alignment explanation
Indices: 96744--96794 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
96734 CTTTTTTTCT
96744 TTTTCTCTTCTAGTTCTAG
1 TTTT-TCTTCTAGTTCTAG
96763 TTTTTCTTCTAGTTCTAG
1 TTTTTCTTCTAGTTCTAG
96781 TTTTTCTTCTAGTT
1 TTTTTCTTCTAGTT
96795 TTAGGGCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.63
Consensus pattern (18 bp):
TTTTTCTTCTAGTTCTAG
Found at i:97762 original size:13 final size:13
Alignment explanation
Indices: 97744--97777 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
97734 GGAGATTGTG
97744 TTTTATTTTTCTT
1 TTTTATTTTTCTT
97757 TTTTATTTTTCTT
1 TTTTATTTTTCTT
97770 TTTCTATT
1 TTT-TATT
97778 CGATTTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTCTT
Found at i:101136 original size:21 final size:22
Alignment explanation
Indices: 101110--101158 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
101100 CTATTTCCCC
101110 AATTTTTGAA-A-AAAATTTCG
1 AATTTTTGAAGATAAAATTTCG
*
101130 GATTTTTGAAGATAAAATTTCG
1 AATTTTTGAAGATAAAATTTCG
101152 AATTTTT
1 AATTTTT
101159 CATGCATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 1 0.04
22 15 0.60
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (22 bp):
AATTTTTGAAGATAAAATTTCG
Found at i:102335 original size:19 final size:21
Alignment explanation
Indices: 102311--102349 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
102301 TGAAGACTTA
102311 TTGAAGA-CAAT-TTGAAGAT
1 TTGAAGACCAATATTGAAGAT
102330 TTGAAGACCAATATTGAAGA
1 TTGAAGACCAATATTGAAGA
102350 AGAATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (21 bp):
TTGAAGACCAATATTGAAGAT
Found at i:105838 original size:18 final size:19
Alignment explanation
Indices: 105804--105842 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
105794 TGAAGATTTC
105804 TTGAAGATAATTTGAAGAA
1 TTGAAGATAATTTGAAGAA
*
105823 TTGAAGATCA-TTGAAGAA
1 TTGAAGATAATTTGAAGAA
105841 TT
1 TT
105843 ATCTCAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAA
Found at i:110242 original size:15 final size:15
Alignment explanation
Indices: 110219--110248 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
110209 CCAGCTGTTC
*
110219 TATCTCCACCTTCAG
1 TATCACCACCTTCAG
110234 TATCACCACCTTCAG
1 TATCACCACCTTCAG
110249 CACATGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.40, G:0.07, T:0.30
Consensus pattern (15 bp):
TATCACCACCTTCAG
Found at i:111686 original size:20 final size:21
Alignment explanation
Indices: 111644--111699 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
111634 TTTTCTTCCT
111644 TTGCTTTGATTTGAATGATTA
1 TTGCTTTGATTTGAATGATTA
*
111665 TTGCTTTGA-TTGATTG-TCTA
1 TTGCTTTGATTTGAATGAT-TA
*
111685 TTCCTTT-ATTTGAAT
1 TTGCTTTGATTTGAAT
111700 TAGTTGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.07
20 19 0.63
21 9 0.30
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (21 bp):
TTGCTTTGATTTGAATGATTA
Found at i:117932 original size:19 final size:19
Alignment explanation
Indices: 117910--117949 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
117900 CTTGCTCCAC
117910 GCAAAAAACCAAGCTCCGT
1 GCAAAAAACCAAGCTCCGT
*
117929 GCAAAAAACCAAGCTTCGT
1 GCAAAAAACCAAGCTCCGT
117948 GC
1 GC
117950 TTATTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.12
Consensus pattern (19 bp):
GCAAAAAACCAAGCTCCGT
Found at i:118574 original size:15 final size:16
Alignment explanation
Indices: 118550--118589 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
118540 AGAGGTTGAA
*
118550 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
118565 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
118581 AGAAAACAA
1 AGAAAACAA
118590 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:124903 original size:24 final size:24
Alignment explanation
Indices: 124876--124923 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
124866 TTTTTTCAAA
**
124876 AAAAAAACACAAACGCAAAAAATT
1 AAAAAAACACAAACAAAAAAAATT
**
124900 AAAAACGCACAAACAAAAAAAATT
1 AAAAAAACACAAACAAAAAAAATT
124924 TTTTTTAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (24 bp):
AAAAAAACACAAACAAAAAAAATT
Found at i:125229 original size:15 final size:16
Alignment explanation
Indices: 125205--125244 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
125195 AGAGGTTGAA
*
125205 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
125220 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
125236 AGAAAACAA
1 AGAAAACAA
125245 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:129329 original size:15 final size:15
Alignment explanation
Indices: 129306--129340 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
129296 GGGGAATAAT
*
129306 CAATCCAAAAACAAA
1 CAATTCAAAAACAAA
129321 CAATTCAAAAACAAA
1 CAATTCAAAAACAAA
129336 CAATT
1 CAATT
129341 TTCTATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (15 bp):
CAATTCAAAAACAAA
Found at i:129653 original size:30 final size:29
Alignment explanation
Indices: 129614--129670 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
129604 GTTTATTAAT
129614 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
129645 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
129671 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Found at i:130866 original size:14 final size:15
Alignment explanation
Indices: 130844--130879 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
130834 AATTAGTGTA
130844 AAAATTAAAAATAAT
1 AAAATTAAAAATAAT
130859 AAAA-TAAAAAT-A-
1 AAAATTAAAAATAAT
130871 AAAATTAAA
1 AAAATTAAA
130880 TATGCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 7 0.35
15 4 0.20
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATTAAAAATAAT
Found at i:137777 original size:22 final size:22
Alignment explanation
Indices: 137749--137817 Score: 104
Period size: 22 Copynumber: 3.1 Consensus size: 22
137739 GCAAATCAAA
*
137749 TCAAGCTCCGTGCTTGCAAATC
1 TCAAGCTCCGTGCTTTCAAATC
137771 TCAAGCTCCGTGCTTTCAAATC
1 TCAAGCTCCGTGCTTTCAAATC
*
137793 TCAAGC-CCTTGGCTTTCAAATC
1 TCAAGCTCCGT-GCTTTCAAATC
137815 TCA
1 TCA
137818 TTTGTAAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 3 0.07
22 41 0.93
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.30
Consensus pattern (22 bp):
TCAAGCTCCGTGCTTTCAAATC
Found at i:140481 original size:14 final size:14
Alignment explanation
Indices: 140464--140614 Score: 78
Period size: 14 Copynumber: 10.3 Consensus size: 14
140454 TTCAAATTTT
140464 ATTTTCTAAATATA
1 ATTTTCTAAATATA
140478 A-TTTCTAAATATTTTAA
1 ATTTTCTAAATA---T-A
* *
140495 AATTTCTAAATATT
1 ATTTTCTAAATATA
*
140509 ATTTTCTAATTATA
1 ATTTTCTAAATATA
140523 A-TTTCATTACATATATA
1 ATTTTC--TA-A-ATATA
* * *
140540 A-TTGCTAATTATT
1 ATTTTCTAAATATA
140553 ATTTTCTAAATATA
1 ATTTTCTAAATATA
*
140567 ATTTT-TAAAAATTTTTA
1 ATTTTCT--AAA--TATA
*
140584 A-TTTCTAAATATT
1 ATTTTCTAAATATA
*
140597 ATTTTCTAATTATA
1 ATTTTCTAAATATA
140611 ATTT
1 ATTT
140615 CAATACATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
13 22 0.21
14 42 0.40
15 11 0.10
16 5 0.05
17 15 0.14
18 10 0.10
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.54
Consensus pattern (14 bp):
ATTTTCTAAATATA
Found at i:140567 original size:44 final size:43
Alignment explanation
Indices: 140457--140630 Score: 172
Period size: 44 Copynumber: 3.9 Consensus size: 43
140447 CGCTATATTC
* *
140457 AAATTTTATTTTCTAAATATAATTTC-TAAATATTTTAAAATTTCT
1 AAATATTATTTTCTAAATATAATTTCTTAAATA---TATAATTTCT
* * *
140502 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTGCT
1 AAATATTATTTTCTAAATATAATTTC-TTAAATATATAATTTCT
* * *
140546 AATTATTATTTTCTAAATATAATTT-TTAAAAATTTTTAATTTCT
1 AAATATTATTTTCTAAATATAATTTCTT--AAATATATAATTTCT
* * *
140590 AAATATTATTTTCTAATTATAATTTCAATACATATATAATT
1 AAATATTATTTTCTAAATATAATTTC-TTAAATATATAATT
140631 AAATAATATT
Statistics
Matches: 106, Mismatches: 17, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.02
44 74 0.70
45 24 0.23
46 1 0.01
47 5 0.05
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (43 bp):
AAATATTATTTTCTAAATATAATTTCTTAAATATATAATTTCT
Found at i:140612 original size:88 final size:88
Alignment explanation
Indices: 140458--140630 Score: 294
Period size: 88 Copynumber: 2.0 Consensus size: 88
140448 GCTATATTCA
*
140458 AATTTTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCTAAATATTATTTTCTAATTATA
1 AATTTTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTATA
*
140523 ATTTCATTACATATATAATTGCT
66 ATTTCAATACATATATAATTGCT
* *
140546 AATTATTATTTTCTAAATATAATTTTTAAAAATTTT-TAATTTCTAAATATTATTTTCTAATTAT
1 AATT-TTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
140610 AATTTCAATACATATATAATT
65 AATTTCAATACATATATAATT
140631 AAATAATATT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 51 0.64
89 29 0.36
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.53
Consensus pattern (88 bp):
AATTTTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTATA
ATTTCAATACATATATAATTGCT
Found at i:140629 original size:23 final size:23
Alignment explanation
Indices: 140603--140663 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 23
140593 TATTATTTTC
140603 TAATTATAATTTCAATACATATA
1 TAATTATAATTTCAATACATATA
*
140626 TAATTAAATAATATTTCATTACATATA
1 TAATT--AT-A-ATTTCAATACATATA
140653 TAATTTATAAT
1 TAA-TTATAAT
140664 ATAATTCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
23 5 0.16
24 2 0.06
25 3 0.09
26 3 0.09
27 17 0.53
28 2 0.06
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTATAATTTCAATACATATA
Found at i:140641 original size:27 final size:26
Alignment explanation
Indices: 140611--140665 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
140601 TCTAATTATA
140611 ATTTCAATACATATATAATTAAATAAT
1 ATTTCAATACATATATAATT-AATAAT
* *
140638 ATTTCATTACATATATAATTTATAAT
1 ATTTCAATACATATATAATTAATAAT
140664 AT
1 AT
140666 AATTCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTCAATACATATATAATTAATAAT
Found at i:140655 original size:44 final size:43
Alignment explanation
Indices: 140607--140795 Score: 171
Period size: 43 Copynumber: 4.4 Consensus size: 43
140597 ATTTTCTAAT
140607 TATAATTTCAATACATATATAATT-AAATAAT-ATTTCATTACATA
1 TATAATTTC-ATA-A-ATATAATTCAAATAATAATTTCATTACATA
* *
140651 TATAATTT-AT-AATATAATTCCTAATTATAATTTC-TTCACATA
1 TATAATTTCATAAATATAATT-CAAATAATAATTTCATT-ACATA
* *
140693 TATAGTTTC-TAAATATCATTTTCTAAATAAT-ATTTCATTACATA
1 TATAATTTCATAAATAT-A-ATTC-AAATAATAATTTCATTACATA
* *
140737 TATAATTT-ATAAATATAATTCCTAATTATAATTTCATTACATA
1 TATAATTTCATAAATATAATT-CAAATAATAATTTCATTACATA
*
140780 TATCATTTC-TAAATAT
1 TATAATTTCATAAATAT
140796 TATTTTCTCA
Statistics
Matches: 120, Mismatches: 11, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
39 8 0.07
40 1 0.01
41 7 0.06
42 27 0.22
43 34 0.28
44 34 0.28
45 9 0.08
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.47
Consensus pattern (43 bp):
TATAATTTCATAAATATAATTCAAATAATAATTTCATTACATA
Found at i:140708 original size:15 final size:14
Alignment explanation
Indices: 140466--140800 Score: 103
Period size: 13 Copynumber: 23.2 Consensus size: 14
140456 CAAATTTTAT
140466 TTTCTAAATATA-A
1 TTTCTAAATATATA
*
140479 TTTCTAAATATTTTAAAA
1 TTTCTAAATA---T-ATA
140497 TTTCTAAATAT-TA
1 TTTCTAAATATATA
*
140510 TTTTCTAATTATA-A
1 -TTTCTAAATATATA
*
140524 TTTCATTACATATATAA
1 TTTC--TAAATATAT-A
* *
140541 TTGCTAATTAT-TA
1 TTTCTAAATATATA
140554 TTTTCTAAATATA-A
1 -TTTCTAAATATATA
* * *
140568 TTTTTAAAAATTTTTAA
1 TTTCT--AAATATAT-A
140585 TTTCTAAATAT-TA
1 TTTCTAAATATATA
*
140598 TTTTCTAATTATA-A
1 -TTTCTAAATATATA
*
140612 TTTC-AATACATATA
1 TTTCTAA-ATATATA
*
140626 TAAT-TAAATA-ATA
1 T-TTCTAAATATATA
*
140639 TTTCATTACATATATA
1 TTTC--TAAATATATA
*
140655 ATT-TATAATATA-A
1 TTTCTA-AATATATA
* *
140668 TTCCTAATTATA-A
1 TTTCTAAATATATA
*
140681 TTTCTTCACATATATA
1 TTTC-T-AAATATATA
140697 GTTTCTAAATATCAT-
1 -TTTCTAAATAT-ATA
140712 TTTCTAAATA-ATA
1 TTTCTAAATATATA
*
140725 TTTCATTACATATATAA
1 TTTC--TAAATATAT-A
*
140742 TTTATAAATATA-A
1 TTTCTAAATATATA
* *
140755 TTCCTAATTATA-A
1 TTTCTAAATATATA
*
140768 TTTCATTACATATATCA
1 TTTC--TAAATATAT-A
140785 TTTCTAAATAT-TA
1 TTTCTAAATATATA
140798 TTT
1 TTT
140801 TCTCATTATA
Statistics
Matches: 239, Mismatches: 40, Indels: 86
0.65 0.11 0.24
Matches are distributed among these distances:
12 5 0.02
13 67 0.28
14 57 0.24
15 64 0.27
16 12 0.05
17 23 0.10
18 11 0.05
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.50
Consensus pattern (14 bp):
TTTCTAAATATATA
Found at i:140720 original size:86 final size:87
Alignment explanation
Indices: 140630--140803 Score: 300
Period size: 87 Copynumber: 2.0 Consensus size: 87
140620 CATATATAAT
140630 TAAATAATATTTCATTACATATATAATTTAT-AATATAATTCCTAATTATAATTTC-TTCACATA
1 TAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATT-ACATA
140693 TAT-AGTTTCTAAATATCATTTTC
65 TATCA-TTTCTAAATATCATTTTC
140716 TAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATAT
1 TAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATAT
*
140781 ATCATTTCTAAATATTATTTTC
66 ATCATTTCTAAATATCATTTTC
140803 T
1 T
140804 CATTATAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
86 31 0.37
87 50 0.60
88 3 0.04
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (87 bp):
TAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATAT
ATCATTTCTAAATATCATTTTC
Found at i:140752 original size:113 final size:115
Alignment explanation
Indices: 140523--140743 Score: 279
Period size: 113 Copynumber: 1.9 Consensus size: 115
140513 TCTAATTATA
* * * * *
140523 ATTTCATTACATATATAATTGCTAATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTT
1 ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTTTTAAAAATATATAATTT
* *
140588 CTAAATATTATTTTCTAATTATAATTTCAATACATATATAATTAAATAAT
66 CTAAATATCATTTTCTAATAATAATTTCAATACATATATAATTAAATAAT
* * * * *
140638 ATTTCATTACATATATAATTTATAA-TA-TAATTCCTAATTATAATTTCTT-CACATATATAGTT
1 ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTT-TTAAAAATATATAATT
*
140700 TCTAAATATCATTTTCTAAATAAT-ATTTCATTACATATATAATT
65 TCTAAATATCATTTTCT-AATAATAATTTCAATACATATATAATT
140744 TATAAATATA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
113 59 0.65
114 9 0.10
115 23 0.25
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (115 bp):
ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTTTTAAAAATATATAATTT
CTAAATATCATTTTCTAATAATAATTTCAATACATATATAATTAAATAAT
Found at i:141287 original size:20 final size:21
Alignment explanation
Indices: 141250--141289 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
141240 CTTTAAAGTC
* *
141250 TCGATTTGTTGTTGTAGGTCT
1 TCGATTTATGGTTGTAGGTCT
141271 TCGATTTATGGTT-TAGGTC
1 TCGATTTATGGTTGTAGGTC
141290 GAAAATCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.10, G:0.28, T:0.50
Consensus pattern (21 bp):
TCGATTTATGGTTGTAGGTCT
Found at i:151059 original size:14 final size:16
Alignment explanation
Indices: 151028--151059 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
151018 TGGATTTCTT
151028 CTTCAAGTGCTGAGAC
1 CTTCAAGTGCTGAGAC
151044 CTTCAAG-GCT-AGAC
1 CTTCAAGTGCTGAGAC
151058 CT
1 CT
151060 CTTTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (16 bp):
CTTCAAGTGCTGAGAC
Found at i:153338 original size:15 final size:16
Alignment explanation
Indices: 153314--153353 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
153304 AGAGGTTGAA
*
153314 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
153329 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
153345 AGAAAACAA
1 AGAAAACAA
153354 AGAAGAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:157378 original size:15 final size:16
Alignment explanation
Indices: 157354--157393 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
157344 AGAGGTTGAA
*
157354 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
157369 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
157385 AGAAAACAA
1 AGAAAACAA
157394 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:167966 original size:116 final size:117
Alignment explanation
Indices: 167744--167978 Score: 382
Period size: 116 Copynumber: 2.0 Consensus size: 117
167734 CTAGGCCGTG
* *
167744 ACAAATGTTGTCTTCTATCATGTCTTCAAGTGCCATTTTAATCTAATTATAACCCGAAAATCCAT
1 ACAAAGGTTGTCTTCTACCATGTCTTCAAGTGCCATTTTAATCTAATTATAACCCGAAAATCCAT
* *
167809 CCATGAAAGAGAATATCATTGTTTTCAAAACCGAACCGGACCGAGCGGTTGA
66 CCACGAAAGAGAATATCAATGTTTTCAAAACCGAACCGGACCGAGCGGTTGA
* * * *
167861 ACAAAGGTTGTCTTCT-CCATGTTTTCAGGTGCGATTTTAATCTAATTATAACCCTAAAATCCAT
1 ACAAAGGTTGTCTTCTACCATGTCTTCAAGTGCCATTTTAATCTAATTATAACCCGAAAATCCAT
*
167925 CCACGAAAGAGAATATCAATGTTTTCAAAACCGAACCGGACCGGGCGGTTGA
66 CCACGAAAGAGAATATCAATGTTTTCAAAACCGAACCGGACCGAGCGGTTGA
167977 AC
1 AC
167979 CGGGCACCAG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
116 94 0.86
117 15 0.14
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (117 bp):
ACAAAGGTTGTCTTCTACCATGTCTTCAAGTGCCATTTTAATCTAATTATAACCCGAAAATCCAT
CCACGAAAGAGAATATCAATGTTTTCAAAACCGAACCGGACCGAGCGGTTGA
Found at i:171866 original size:30 final size:30
Alignment explanation
Indices: 171809--171869 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
171799 TAATTCTTGT
* *
171809 TTCTTGAAATTATTCTTCAATGGTCTTCAA
1 TTCTTGAAATTAGTCTTCAATGATCTTCAA
*
171839 TTCTTGAAATT-GTCTTCAATATATCTTCAA
1 TTCTTGAAATTAGTCTTCAAT-GATCTTCAA
171869 T
1 T
171870 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (30 bp):
TTCTTGAAATTAGTCTTCAATGATCTTCAA
Done.