Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009093.1 Hibiscus syriacus cultivar Beakdansim tig00112540_pilon, 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: 447474
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:251580 original size:46 final size:46
Alignment explanation
Indices: 251521--251645 Score: 250
Period size: 46 Copynumber: 2.7 Consensus size: 46
251511 GAATGAATTG
251521 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
251567 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
251613 AACATCGAATGCATTTTATGCATCGATGCACTC
1 AACATCGAATGCATTTTATGCATCGATGCACTC
251646 TTAGTGCACC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (46 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
Found at i:257444 original size:21 final size:21
Alignment explanation
Indices: 257418--257474 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
257408 TTGTGCATAA
257418 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
257439 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
257463 TGCATCGATACA
1 TGCATCGATACA
257475 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:257488 original size:45 final size:42
Alignment explanation
Indices: 257418--257541 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 42
257408 TTGTGCATAA
257418 TGCATCGATACACTATGAAAGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACAC-ATGAAA-TGCATCGATGCATCCC-TTGAATG
*
257463 TGCATCGATACATCATGAAGATGCATTGATGCA-CGCCTTGAATG
1 TGCATCGATACA-CATGAA-ATGCATCGATGCATC-CCTTGAATG
* * **
257507 TGCATCGATGCACAAGGCCATGCATCGATGCATCC
1 TGCATCGATACAC-ATGAAATGCATCGATGCATCC
257542 GTCGGGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
43 14 0.21
44 22 0.32
45 30 0.44
46 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (42 bp):
TGCATCGATACACATGAAATGCATCGATGCATCCCTTGAATG
Found at i:260275 original size:65 final size:64
Alignment explanation
Indices: 260203--260362 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
260193 GAATAAATTG
*
260203 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTTGTT-T-
260266 AA
63 AA
* * *
260268 AACATCGAATACATTTTATGCATCGATGCACAAGCCATGCATCGATGCATTCTGGCTTGTTTAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTAA
*
260332 AACATCGAATGCATTTTATGCACCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
260363 TAAGGGTCCA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 32 0.37
65 51 0.59
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTAA
Found at i:262721 original size:15 final size:16
Alignment explanation
Indices: 262686--262719 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
262676 AATAAAAAAT
262686 AAATATTTTATAGAAA
1 AAATATTTTATAGAAA
*
262702 AAATATTTTATACAAA
1 AAATATTTTATAGAAA
262718 AA
1 AA
262720 TAAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATATTTTATAGAAA
Found at i:266727 original size:20 final size:20
Alignment explanation
Indices: 266694--266747 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
266684 TTTAGTTCAT
* *
266694 GGAATTTAAAATTATCAGTG
1 GGAATGTAAGATTATCAGTG
*
266714 GGAATGTAAGATTATTAGTG
1 GGAATGTAAGATTATCAGTG
*
266734 GAAATGTAAGATTA
1 GGAATGTAAGATTA
266748 CCAGAGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:266911 original size:19 final size:21
Alignment explanation
Indices: 266874--266912 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
266864 AATTATCCTT
*
266874 ATTATATATTTATTTTTTAAC
1 ATTATATATTTATTCTTTAAC
266895 ATTATATA-TT-TTCTTTAA
1 ATTATATATTTATTCTTTAA
266913 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 2 0.12
21 8 0.47
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATATATTTATTCTTTAAC
Found at i:268991 original size:21 final size:20
Alignment explanation
Indices: 268965--269003 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
268955 TATTGAGTTC
268965 ATATATAAATAATTTTTTTCT
1 ATATAT-AATAATTTTTTTCT
*
268986 ATATATAATGATTTTTTT
1 ATATATAATAATTTTTTT
269004 ACACTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATATAATAATTTTTTTCT
Found at i:277016 original size:2 final size:2
Alignment explanation
Indices: 277009--277046 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
276999 GTCCTTCGGG
277009 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
277047 CTGGAACATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277209 original size:23 final size:23
Alignment explanation
Indices: 277146--277214 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
277136 CATTATTATA
277146 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * **
277169 CGGCACTCCAGTATAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
277192 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
277215 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:277325 original size:14 final size:14
Alignment explanation
Indices: 277306--277333 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
277296 TTAATAATTT
277306 CTTATGAATGTGAA
1 CTTATGAATGTGAA
277320 CTTATGAATGTGAA
1 CTTATGAATGTGAA
277334 ATTTGATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
CTTATGAATGTGAA
Found at i:308696 original size:18 final size:18
Alignment explanation
Indices: 308673--308711 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
308663 CCAAGCTCAT
308673 CCGCCTTGGATAACAACC
1 CCGCCTTGGATAACAACC
*
308691 CCGCCTTGGATAACAGCC
1 CCGCCTTGGATAACAACC
308709 CCG
1 CCG
308712 AGAAACTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.41, G:0.21, T:0.15
Consensus pattern (18 bp):
CCGCCTTGGATAACAACC
Found at i:311037 original size:2 final size:2
Alignment explanation
Indices: 311032--311063 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
311022 TTTTTTTAAT
*
311032 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
311064 AAATACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:311345 original size:14 final size:15
Alignment explanation
Indices: 311326--311355 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
311316 AAACATGTTT
311326 TATTATCA-TATTTA
1 TATTATCAGTATTTA
311340 TATTATCAGTATTTA
1 TATTATCAGTATTTA
311355 T
1 T
311356 TCTAAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTATCAGTATTTA
Found at i:311767 original size:18 final size:18
Alignment explanation
Indices: 311726--311764 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
311716 TTTGGTTCAC
311726 GGAATGTAAATTACCAGTG
1 GGAATGTAAATTACCAG-G
*
311745 GGAATGTAAGATTACTAGG
1 GGAATGTAA-ATTACCAGG
311764 G
1 G
311765 AATAGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.26
Consensus pattern (18 bp):
GGAATGTAAATTACCAGG
Found at i:320572 original size:60 final size:60
Alignment explanation
Indices: 320471--320589 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
320461 CTGCCCCCCA
* * * *
320471 AGTATACACAGATATCAAAAATCGACTTTCTATCGTCCATATTGTCTCCCTAGTCTGCAG
1 AGTATACACAGATACCAAAAATCGACCTTCCATCGTCCATATTGCCTCCCTAGTCTGCAG
* * * *
320531 AGTATACACAGCTACCAGAAATTGACCTTCCATTGTCCATATTGCCTCCCTAGTCTGCA
1 AGTATACACAGATACCAAAAATCGACCTTCCATCGTCCATATTGCCTCCCTAGTCTGCA
320590 ACTGCAACTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (60 bp):
AGTATACACAGATACCAAAAATCGACCTTCCATCGTCCATATTGCCTCCCTAGTCTGCAG
Found at i:320596 original size:6 final size:6
Alignment explanation
Indices: 320585--320615 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
320575 CCTCCCTAGT
320585 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA C
1 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA C
320616 AGGTTGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CTGCAA
Found at i:325655 original size:218 final size:218
Alignment explanation
Indices: 325277--325712 Score: 872
Period size: 218 Copynumber: 2.0 Consensus size: 218
325267 GTTAAACCGA
325277 TGCCAACATCTATCTACTGAATGCACAGTTTTTTCACATAACTGACACTGTAGACGAGCACGACG
1 TGCCAACATCTATCTACTGAATGCACAGTTTTTTCACATAACTGACACTGTAGACGAGCACGACG
325342 ATGACCCCGAGATCCACTTTTTCCTGCTGAGTCTTGCCGTGGCCTTCCATATATGCTGAGTACCT
66 ATGACCCCGAGATCCACTTTTTCCTGCTGAGTCTTGCCGTGGCCTTCCATATATGCTGAGTACCT
325407 CTACTGTTGCCTTGATCATTACTATGAACACGCACCATGTTAGCACTCGTAGGTAGTTGGGTCTG
131 CTACTGTTGCCTTGATCATTACTATGAACACGCACCATGTTAGCACTCGTAGGTAGTTGGGTCTG
325472 GGCATGAAAACCCTTCAGTTGTG
196 GGCATGAAAACCCTTCAGTTGTG
325495 TGCCAACATCTATCTACTGAATGCACAGTTTTTTCACATAACTGACACTGTAGACGAGCACGACG
1 TGCCAACATCTATCTACTGAATGCACAGTTTTTTCACATAACTGACACTGTAGACGAGCACGACG
325560 ATGACCCCGAGATCCACTTTTTCCTGCTGAGTCTTGCCGTGGCCTTCCATATATGCTGAGTACCT
66 ATGACCCCGAGATCCACTTTTTCCTGCTGAGTCTTGCCGTGGCCTTCCATATATGCTGAGTACCT
325625 CTACTGTTGCCTTGATCATTACTATGAACACGCACCATGTTAGCACTCGTAGGTAGTTGGGTCTG
131 CTACTGTTGCCTTGATCATTACTATGAACACGCACCATGTTAGCACTCGTAGGTAGTTGGGTCTG
325690 GGCATGAAAACCCTTCAGTTGTG
196 GGCATGAAAACCCTTCAGTTGTG
325713 CTTCTGCATC
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 218 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (218 bp):
TGCCAACATCTATCTACTGAATGCACAGTTTTTTCACATAACTGACACTGTAGACGAGCACGACG
ATGACCCCGAGATCCACTTTTTCCTGCTGAGTCTTGCCGTGGCCTTCCATATATGCTGAGTACCT
CTACTGTTGCCTTGATCATTACTATGAACACGCACCATGTTAGCACTCGTAGGTAGTTGGGTCTG
GGCATGAAAACCCTTCAGTTGTG
Found at i:334835 original size:43 final size:45
Alignment explanation
Indices: 334721--334852 Score: 193
Period size: 43 Copynumber: 3.0 Consensus size: 45
334711 TAATTTAAGG
*
334721 ACCAAAGATGAAAT-TCCCATGTGCACAAGTTGGCCACTTG-TCA
1 ACCAAAGATGAATTATCCCATGTGCACAAGTTGGCCACTTGCTCA
*
334764 GCCAAAGATGAATTATCCCATGTGCACAAGTTGGCCACTTGCT-A
1 ACCAAAGATGAATTATCCCATGTGCACAAGTTGGCCACTTGCTCA
* *
334808 ACCAAAGAT-AATTATCCCATGTACACAAGTTGGCTACTTGC-CA
1 ACCAAAGATGAATTATCCCATGTGCACAAGTTGGCCACTTGCTCA
334851 AC
1 AC
334853 TTGGCCACTT
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
43 45 0.56
44 35 0.43
45 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (45 bp):
ACCAAAGATGAATTATCCCATGTGCACAAGTTGGCCACTTGCTCA
Found at i:334878 original size:25 final size:25
Alignment explanation
Indices: 334844--334905 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
334834 AAGTTGGCTA
334844 CTTGCCAACTTGGCCACTTGTCAAT
1 CTTGCCAACTTGGCCACTTGTCAAT
334869 CTTGCCAACTTGGCCACTTGTCAAT
1 CTTGCCAACTTGGCCACTTGTCAAT
334894 CTTGCCAACTTG
1 CTTGCCAACTTG
334906 CCAATTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (25 bp):
CTTGCCAACTTGGCCACTTGTCAAT
Found at i:334905 original size:8 final size:8
Alignment explanation
Indices: 334843--334914 Score: 67
Period size: 8 Copynumber: 8.8 Consensus size: 8
334833 CAAGTTGGCT
334843 ACTTGCCA
1 ACTTGCCA
334851 ACTTGGCC-
1 ACTT-GCCA
*
334859 ACTTGTCA
1 ACTTGCCA
334867 ATCTTGCCA
1 A-CTTGCCA
334876 ACTTGGCC-
1 ACTT-GCCA
*
334884 ACTTGTCA
1 ACTTGCCA
334892 ATCTTGCCA
1 A-CTTGCCA
334901 ACTTGCCA
1 ACTTGCCA
*
334909 ATTTGC
1 ACTTGC
334915 AAGCCACACA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 4 0.08
8 29 0.55
9 20 0.38
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (8 bp):
ACTTGCCA
Found at i:337283 original size:22 final size:22
Alignment explanation
Indices: 337255--337296 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
337245 CATTCTGTTA
337255 TGGTGTATTTCTAACAGTGAAG
1 TGGTGTATTTCTAACAGTGAAG
337277 TGGTGTATTTCTAACAGTGA
1 TGGTGTATTTCTAACAGTGA
337297 CGTGTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (22 bp):
TGGTGTATTTCTAACAGTGAAG
Found at i:338665 original size:36 final size:36
Alignment explanation
Indices: 338605--338675 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
338595 AGTTATGCAG
* *
338605 ACAAAGATCCTATTATATTAATACCAAAAGTATTCC
1 ACAAAGATCCTATTAGATTAATACCAAAAGCATTCC
* *
338641 ACAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 ACAAAGATCCTATTAGATTAATACCAAAAGCATTC
338676 TACGGTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (36 bp):
ACAAAGATCCTATTAGATTAATACCAAAAGCATTCC
Found at i:339279 original size:15 final size:13
Alignment explanation
Indices: 339259--339294 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
339249 CATACATGCA
339259 TTTGCATTTTGCATC
1 TTTGCATTTT-CA-C
339274 TTTGCATTTTCAC
1 TTTGCATTTTCAC
339287 TTTGCATT
1 TTTGCATT
339295 CGTACTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.43
14 2 0.10
15 10 0.48
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (13 bp):
TTTGCATTTTCAC
Found at i:339279 original size:21 final size:21
Alignment explanation
Indices: 339255--339342 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
339245 TTTTCATACA
339255 TGCATTTGCATTTTGCATCTT
1 TGCATTTGCATTTTGCATCTT
* * *
339276 TGCATTTTCACTTTGCAT-TCG
1 TGCATTTGCATTTTGCATCT-T
* * * *
339297 TACTTTTACATTTT-CATTTTT
1 TGCATTTGCATTTTGCA-TCTT
339318 TGCATTTGCA-TTTGCATCTT
1 TGCATTTGCATTTTGCATCTT
339338 TGCAT
1 TGCAT
339343 AGTTACATTT
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
20 14 0.27
21 36 0.71
22 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.53
Consensus pattern (21 bp):
TGCATTTGCATTTTGCATCTT
Found at i:343090 original size:64 final size:64
Alignment explanation
Indices: 342903--343081 Score: 288
Period size: 64 Copynumber: 2.8 Consensus size: 64
342893 TCTTTAACAT
342903 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
342967 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
* * * * * *
343031 GTGCATCGATGCACT-CCTTATGTATCGATGCACTAATTACATTCGATGTTT
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACCTTCGATGTTT
343082 CTTCTTTAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 2 0.02
64 106 0.98
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
Found at i:343958 original size:20 final size:19
Alignment explanation
Indices: 343935--343974 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
343925 TACTTAATTT
*
343935 TTCCTTTCTTTATTCCATTA
1 TTCCTTTATTTATTCC-TTA
343955 TTCCTTTATTTATTCCTTA
1 TTCCTTTATTTATTCCTTA
343974 T
1 T
343975 ATACAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCCTTTATTTATTCCTTA
Found at i:345844 original size:2 final size:2
Alignment explanation
Indices: 345837--345864 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
345827 ATATCACAAA
345837 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
345865 CACATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:346976 original size:64 final size:63
Alignment explanation
Indices: 346853--346989 Score: 141
Period size: 64 Copynumber: 2.2 Consensus size: 63
346843 TCTTTAACAT
* * * * *
346853 GTGCATCGATGCACTACGCATGCATCGATACACCGATCACCTTTGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACGCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* ** * * * *
346917 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACGCATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
346980 GTGCATCGAT
1 GTGCATCGAT
346990 ACACATTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 16 0.27
64 44 0.73
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACGCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:351636 original size:54 final size:54
Alignment explanation
Indices: 351553--351697 Score: 191
Period size: 54 Copynumber: 2.7 Consensus size: 54
351543 CACTGGCAAG
* * * * *
351553 CATCTATGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGTTTTACGAA
1 CATCTGTGCAGAAACCACAGGAAAGGATGAATATGTTGTCAAATGCTTTACAAA
* * *
351607 CATCTGTGTAGAAACCACAGGAAAGGATGAATGTATTGTCAAATGCTTTACAAA
1 CATCTGTGCAGAAACCACAGGAAAGGATGAATATGTTGTCAAATGCTTTACAAA
* * *
351661 CATCTGTACAGAAACCACAAGAAAGGACGAATATGTT
1 CATCTGTGCAGAAACCACAGGAAAGGATGAATATGTT
351698 ACGAACCAGT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (54 bp):
CATCTGTGCAGAAACCACAGGAAAGGATGAATATGTTGTCAAATGCTTTACAAA
Found at i:352097 original size:22 final size:22
Alignment explanation
Indices: 352069--352167 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
352059 ACATCTACAT
352069 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
352091 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
352113 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
352135 TCTTCAAAGATGATATATTATC
1 TCTTCAAAGATGATAGATTCTC
*
352157 TTTTCAAAGAT
1 TCTTCAAAGAT
352168 AAAAACTTTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:352991 original size:37 final size:36
Alignment explanation
Indices: 352884--353089 Score: 189
Period size: 36 Copynumber: 5.7 Consensus size: 36
352874 TTCAAATAAC
352884 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
*** ** ** **
352920 ACA-GCGTCTCACTTGAGACAGTTTCACTCGAAACAA
1 A-ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
*
352956 CAATTTATCTCACTTGAAATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * ** *
352993 AATTTGTCTCGCTTGAGATAGTTTCACTTGAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
353029 TAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* ** * *
353066 GATTCGTCTCGCTTGAGATAGTTT
1 AATTTATCTCACTTGAGATTGTTT
353090 CACTAGAAAC
Statistics
Matches: 129, Mismatches: 37, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
36 74 0.57
37 55 0.43
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:353002 original size:73 final size:73
Alignment explanation
Indices: 352881--353107 Score: 348
Period size: 73 Copynumber: 3.1 Consensus size: 73
352871 GTTTTCAAAT
* * *
352881 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACA-GCGTCTCACTTGAGACAGTTTC
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTCGTCTCGCTTGAGATAGTTTC
*
352945 ACTCGAAAC
65 ACTAGAAAC
* *
352954 AACAATTTATCTCACTTGAAATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGATAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGATAGTTTCA
*
353019 CTTGAAAC
66 CTAGAAAC
* *
353027 AATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGATAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGATAGTTTCA
353092 CTAGAAAC
66 CTAGAAAC
*
353100 AAAAATTT
1 AACAATTT
353108 CTATCACTCG
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
72 1 0.01
73 140 0.99
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (73 bp):
AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGATAGTTTCA
CTAGAAAC
Found at i:353346 original size:123 final size:122
Alignment explanation
Indices: 353122--353811 Score: 827
Period size: 122 Copynumber: 5.7 Consensus size: 122
353112 CACTCGATGG
*
353122 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* ** * * *
353187 ATGAGAAGAATTTGTTCAATTTTTTACTCGACTCTATCACAGAAGGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAGAAAGAGATAGATCAGC
* * * * *
353245 ACCAACATCTCCAGAGGAATTTTATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
353310 ATGAGAAGAATTTGTTCAACCTTTTGCTCGAGTCTATCAC---------TCGAT--GG
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAGAAAGAGATAGATCAGC
* * *
353357 ATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGGAGAAGTTCATA
1 ATCAACATTTCCAGA-GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
353422 ATGAGAAGAACTTGTTCAACCTTTTGCTCGATTTTATCCCA-AAAGGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAGAAA-GAGATAGATCAGC
* * * *
353480 ACCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAATTCATA
1 ATCAACATTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
** * * *
353544 ATGAGAAGAACTTGTTCAATGTTTTGCTTGACG-CTATCACAGAAAGAGATAAATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGA-GTCTATCACAGAAAGAGATAGATCAGC
*
353602 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
353666 ATGAGAAGAACTTGTTCAACCTTTTGAAT-GATTCTATCACAGAAAGAGATAAATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTG-CTCGAGTCTATCACAGAAAGAGATAGATCAGC
* *
353724 ATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAGGAAGTTCATA
1 ATCAACATTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
353789 ATGAGAATAATTTATTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
353812 GTCTTAATTC
Statistics
Matches: 498, Mismatches: 52, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
112 94 0.19
114 4 0.01
121 5 0.01
122 215 0.43
123 180 0.36
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAGAAAGAGATAGATCAGC
Found at i:354277 original size:25 final size:25
Alignment explanation
Indices: 354248--354302 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
354238 TAAAAACCCA
354248 ACAAAACAGGAGAATAAATATACAT
1 ACAAAACAGGAGAATAAATATACAT
***
354273 ACAAAACAGGAGAATGGTTATACAT
1 ACAAAACAGGAGAATAAATATACAT
354298 ACAAA
1 ACAAA
354303 GGATTGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.16
Consensus pattern (25 bp):
ACAAAACAGGAGAATAAATATACAT
Found at i:355006 original size:2 final size:2
Alignment explanation
Indices: 354999--355023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
354989 ATAAATATCT
354999 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
355024 TTACTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:355310 original size:23 final size:22
Alignment explanation
Indices: 355284--355337 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
355274 TTCTAAGTAA
*
355284 ATAAATATCTTATTTATAAAAAT
1 ATAAATAT-ATATTTATAAAAAT
355307 ATAAAATATATATTTATAAAAAT
1 AT-AAATATATATTTATAAAAAT
355330 -T-AATATAT
1 ATAAATATAT
355338 TTTCTTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.24
22 1 0.03
23 15 0.52
24 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAATATATATTTATAAAAAT
Found at i:355653 original size:16 final size:18
Alignment explanation
Indices: 355632--355664 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
355622 ATGGCGACTC
355632 TCAAAA-CATTT-TTTAA
1 TCAAAATCATTTATTTAA
355648 TCAAAATCATTTATTTA
1 TCAAAATCATTTATTTA
355665 CTCATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TCAAAATCATTTATTTAA
Found at i:360735 original size:55 final size:55
Alignment explanation
Indices: 360150--360734 Score: 836
Period size: 55 Copynumber: 10.7 Consensus size: 55
360140 CTCCATAGTC
* * *
360150 CTTCAGAGAGTATAAGACTAGAACAATCTTTAACAATCGCGTCTCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * ** * *
360205 TTTCAGAGAGTATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
360260 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
360313 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
360368 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
360421 CTTCGGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
360476 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
360531 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
360586 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
360641 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACGATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
360696 CTTCAGAGAGTATGATAATTGAACAATCTTCAACAATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
360735 TAGGGAACCT
Statistics
Matches: 470, Mismatches: 56, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
53 94 0.20
54 2 0.00
55 374 0.80
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:361754 original size:16 final size:15
Alignment explanation
Indices: 361733--361783 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
361723 TGTTTCTCTT
361733 TTTTTTATTCTTTTCA
1 TTTTTT-TTCTTTTCA
**
361749 -TTTTTTTCCATTCA
1 TTTTTTTTCTTTTCA
361763 TTTTTTTTCTTCTTCA
1 TTTTTTTTCTT-TTCA
361779 CTTTT
1 -TTTT
361784 CTTTAAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 7 0.25
15 13 0.46
16 4 0.14
17 4 0.14
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTTCTTTTCA
Found at i:387816 original size:18 final size:18
Alignment explanation
Indices: 387770--387816 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
387760 ATCTCGAAGG
*
387770 CTAACCTTAGTAGGCAAT
1 CTAACCTTAGTAGGAAAT
*
387788 CT-ATC-TAGTAGGAAAT
1 CTAACCTTAGTAGGAAAT
387804 CTAACCTTAGTAG
1 CTAACCTTAGTAG
387817 TCAAATGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.50
17 4 0.17
18 8 0.33
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (18 bp):
CTAACCTTAGTAGGAAAT
Found at i:389980 original size:27 final size:27
Alignment explanation
Indices: 389941--390003 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
389931 AATATTATTT
*
389941 ATATTATTATTATTATAATTA-TAATTA
1 ATATTATTATTATT-TAATTATTAATAA
* *
389968 TTATTATTATTATTTTATTATTAATAA
1 ATATTATTATTATTTAATTATTAATAA
389995 ATATTATTA
1 ATATTATTA
390004 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATATTATTATTATTTAATTATTAATAA
Found at i:390003 original size:3 final size:3
Alignment explanation
Indices: 389933--389990 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
389923 TTCATTTGAA
* *
389933 TAT TAT T-T ATAT TAT TAT TAT TAT AAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
389978 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
389991 ATAAATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:392080 original size:24 final size:24
Alignment explanation
Indices: 392023--392104 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 24
392013 ATTTTTTATA
* *
392023 TATACTTATTATTTTCATAGTATT
1 TATATTTATTATTTTCATAATATT
*
392047 TATATATATTATTTT-ATTAATATT
1 TATATTTATTATTTTCA-TAATATT
* *
392071 T-CA-TT-TTATTTTCA-AGTATT
1 TATATTTATTATTTTCATAATATT
392091 T-TATTTCATTATTT
1 TATATTT-ATTATTT
392105 ATTTTTCTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.15
21 9 0.20
22 2 0.04
23 8 0.17
24 20 0.43
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATTTATTATTTTCATAATATT
Found at i:399083 original size:9 final size:9
Alignment explanation
Indices: 399069--399100 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
399059 AAATGGCAAT
399069 CATTCTTTA
1 CATTCTTTA
399078 CATTCTTTA
1 CATTCTTTA
*
399087 CATTTTTTA
1 CATTCTTTA
399096 CATTC
1 CATTC
399101 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:402677 original size:26 final size:25
Alignment explanation
Indices: 402623--402689 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
402613 ATGCTTGAAG
*
402623 AAAAA-AATGAAATAAAGAGAAAAA
1 AAAAAGAATAAAATAAAGAGAAAAA
*
402647 TAAAAAGAATAAAATTAAGA-AAAAGA
1 -AAAAAGAATAAAATAAAGAGAAAA-A
*
402673 AAAAAGAAGAAAATAAA
1 AAAAAGAATAAAATAAA
402690 AAAGAGGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAAAGAATAAAATAAAGAGAAAAA
Found at i:402682 original size:16 final size:16
Alignment explanation
Indices: 402648--402694 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
402638 AGAGAAAAAT
*
402648 AAAAAGAATAAAATTAAG
1 AAAAAGAA-AAAA-GAAG
402666 AAAAAGAAAAAAGAAG
1 AAAAAGAAAAAAGAAG
*
402682 -AAAATAAAAAAGA
1 AAAAAGAAAAAAGA
402695 GGGTCAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 12 0.44
16 3 0.11
17 4 0.15
18 8 0.30
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:403058 original size:20 final size:19
Alignment explanation
Indices: 403022--403096 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
403012 TATTTATTAA
403022 TAAATTCTAAGTTTATTTTCTC
1 TAAATTC-AA-TTTATTTT-TC
*
403044 TAAATTCAATTTATTTTTTT
1 TAAATTCAATTTA-TTTTTC
*
403064 TAGATTCAATTTA-TTTTC
1 TAAATTCAATTTATTTTTC
*
403082 GAAATTCAATTTATT
1 TAAATTCAATTTATT
403097 CTTTTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.33
19 1 0.02
20 17 0.37
21 6 0.13
22 7 0.15
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (19 bp):
TAAATTCAATTTATTTTTC
Found at i:404444 original size:113 final size:113
Alignment explanation
Indices: 404247--404677 Score: 561
Period size: 113 Copynumber: 3.8 Consensus size: 113
404237 GATTCAAATC
* * *
404247 CATCATTCAATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGTAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
404311 AGAAGAAGTTCAAAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * *
404359 CATCATTCGATGGATCATCATTTCCAGGTCGAGTTCATAATGAGAAGAACCCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
404424 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT-TTTTGCTTGAATT
* * * * * * *
404472 CATCACTCGGTGGATCAACAGTGCCAGTTAGAGTTCATAATGAGAATAACTCATCTGAAGAAGAA
1 CATCATTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
404537 AGAAGAAATTCATAATGAGAATAATTTGTTCAACCTTTTGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * *
404585 CATCACTT-GATGGATCAACTTTTCTAGAG-AAAGTTCATAATGAGAAGAACTCATCTAAAGAA-
1 CATCA-TTCGATGGATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
404647 G--GAAGAAGTTCATAATGAGAAGAGCTTGTTC
64 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
404678 GTCCTTTTGC
Statistics
Matches: 275, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
110 26 0.09
112 25 0.09
113 223 0.81
114 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:405085 original size:3 final size:3
Alignment explanation
Indices: 405027--405072 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
405017 TTCATTTGAA
405027 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
405071 TA
1 TA
405073 ATAAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:405940 original size:17 final size:17
Alignment explanation
Indices: 405918--405951 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
405908 CCCAAGTTAA
*
405918 ATTAAAAAATATTTTTT
1 ATTAAAAAACATTTTTT
*
405935 ATTAAATAACATTTTTT
1 ATTAAAAAACATTTTTT
405952 TACAAAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAAAAACATTTTTT
Found at i:408488 original size:3 final size:3
Alignment explanation
Indices: 408480--408590 Score: 222
Period size: 3 Copynumber: 37.0 Consensus size: 3
408470 TTAATATCTC
408480 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
408528 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
408576 GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT
408591 TATTATTATT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:408595 original size:3 final size:3
Alignment explanation
Indices: 408589--408621 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
408579 GATGATGATG
*
408589 ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
408622 TAGGGTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:409375 original size:2 final size:2
Alignment explanation
Indices: 409368--409410 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
409358 ACATACATAC
409368 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
409410 A
1 A
409411 ACCAAGCGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:414649 original size:22 final size:22
Alignment explanation
Indices: 414621--414673 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
414611 GAGACTTAGT
414621 CAATACAGACCTCGAAGGAGGA
1 CAATACAGACCTCGAAGGAGGA
414643 CAATACAGACCTCGAAGGAGGA
1 CAATACAGACCTCGAAGGAGGA
*
414665 CGATACAGA
1 CAATACAGA
414674 TCAACCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (22 bp):
CAATACAGACCTCGAAGGAGGA
Found at i:429486 original size:29 final size:29
Alignment explanation
Indices: 429414--429497 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
429404 GACCTATTTA
* * *
429414 GGTCGCCATGCAGGCTGTGCACCATTGTT
1 GGTCGCCATGAAGGCTATGCGCCATTGTT
*
429443 GGTCGCCATGTAGGCTATGCGCCATTGTT
1 GGTCGCCATGAAGGCTATGCGCCATTGTT
* * *
429472 GGTCGCCACGAAGGCCATGCGACATT
1 GGTCGCCATGAAGGCTATGCGCCATT
429498 CTATCAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (29 bp):
GGTCGCCATGAAGGCTATGCGCCATTGTT
Found at i:429665 original size:29 final size:29
Alignment explanation
Indices: 429598--429686 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
429588 CCCCAACACC
* *
429598 CCTACAAGGTTGCCAAGCACTCCCAGCAA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
* *
429627 CCTACAAGGTCTCCATGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
*** * *
429656 CCTTGTAGGTCGCCAAGCAATCCCGGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
429685 CC
1 CC
429687 AAGCTTCACG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.25, C:0.39, G:0.20, T:0.16
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCACTCCCAGCGA
Found at i:430017 original size:13 final size:13
Alignment explanation
Indices: 429994--430040 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
429984 CAGTCGAGAA
429994 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
430006 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
430019 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
430033 AGATAAGG
1 AGA-AAGG
430041 CTCTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:430163 original size:22 final size:21
Alignment explanation
Indices: 430138--430178 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
430128 GTTAATTAGT
*
430138 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
430160 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
430179 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:430493 original size:8 final size:8
Alignment explanation
Indices: 430480--430514 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
430470 TTTAAAAAGT
*
430480 TTAGTTTG
1 TTAGTTTA
430488 TTAGTTTA
1 TTAGTTTA
430496 TTAGTTTA
1 TTAGTTTA
430504 TTAGTTTA
1 TTAGTTTA
430512 TTA
1 TTA
430515 TATTAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (8 bp):
TTAGTTTA
Found at i:432782 original size:14 final size:14
Alignment explanation
Indices: 432734--432782 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
432724 TTCAAGTCAT
*
432734 AAATCATTACTATC
1 AAATCATTAATATC
432748 AAATCATT-AT-T-
1 AAATCATTAATATC
432759 AAATCATTAATATC
1 AAATCATTAATATC
432773 AAATCATTAA
1 AAATCATTAA
432783 ATATTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 8 0.26
12 3 0.10
13 2 0.06
14 18 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:432797 original size:21 final size:22
Alignment explanation
Indices: 432725--432791 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 22
432715 TGTTCATTGT
* *
432725 TCAAGTCA-TAAATCATTACTA
1 TCAAATCATTAAATCATTAATA
432746 TCAAATCATTATTAAATCATTAATA
1 TCAAATC---ATTAAATCATTAATA
432771 TCAAATCATTAAAT-ATTAATA
1 TCAAATCATTAAATCATTAATA
432792 ATAAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 13 0.32
22 7 0.17
24 1 0.03
25 19 0.47
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.37
Consensus pattern (22 bp):
TCAAATCATTAAATCATTAATA
Found at i:432802 original size:21 final size:22
Alignment explanation
Indices: 432733--432802 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 22
432723 GTTCAAGTCA
*
432733 TAAATCATTACTATCAAATCATTAT
1 TAAATCATTAATATC-AA--ATTAT
*
432758 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
432780 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
432801 TA
1 TA
432803 TTACTAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.34
22 11 0.27
24 2 0.05
25 14 0.34
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:432817 original size:10 final size:10
Alignment explanation
Indices: 432802--432828 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
432792 ATAAATTATT
432802 ATTACTAATC
1 ATTACTAATC
432812 ATTACTAATC
1 ATTACTAATC
432822 ATTACTA
1 ATTACTA
432829 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:432868 original size:49 final size:49
Alignment explanation
Indices: 432812--433141 Score: 499
Period size: 49 Copynumber: 6.6 Consensus size: 49
432802 ATTACTAATC
432812 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
432861 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTCATT
432921 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
432970 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
433019 ATTACTAAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
433067 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
433116 ATTACTAATCATTA-T-T-AAATCATTAA
1 ATTACTAATCATTACTATCAAATCATTAA
433142 TATCAAATCA
Statistics
Matches: 263, Mismatches: 4, Indels: 31
0.88 0.01 0.10
Matches are distributed among these distances:
46 10 0.04
47 1 0.00
48 49 0.19
49 137 0.52
51 4 0.02
52 8 0.03
53 7 0.03
54 1 0.00
55 1 0.00
56 7 0.03
57 8 0.03
58 4 0.02
60 26 0.10
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:432938 original size:109 final size:109
Alignment explanation
Indices: 432812--433534 Score: 857
Period size: 109 Copynumber: 6.6 Consensus size: 109
432802 ATTACTAATC
432812 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
*
432877 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
66 AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
432921 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--T
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
432983 --A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATT
66 AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
433019 ATTACTAAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC-
* * * * * * *
433083 ATCAAATCATT-A-A--AAATTAATAATAATTTCATTATTACTAATCATT
65 -T-AAATCATTAATATCAAATCATTAA-AAATT-AATAATAAT-TTCATT
* *
433129 ATTA--AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
*
433192 AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
66 AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
* * * * *
433236 ATTACTAATCATTAC--T-AAATCATTACTATCAAATCATTAA-ATATTAATAATAATT--TTAT
1 ATTACTAATCATTACTATCAAATCATTA--A--AAATTAATAATA-ATT--TCATTATTACTAAT
* *
433295 TATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
59 CATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
*
433345 ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
*
433410 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
66 AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
* *
433454 ATTACTAATCATTATTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTAC
1 A-T--T-A-C-----T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
433519 TAATCATTACTAAATC
55 TAATCATTACTAAATC
433535 TTATAAATAC
Statistics
Matches: 528, Mismatches: 38, Indels: 85
0.81 0.06 0.13
Matches are distributed among these distances:
97 50 0.09
98 43 0.08
102 1 0.00
103 1 0.00
104 1 0.00
105 1 0.00
106 25 0.05
107 19 0.04
108 36 0.07
109 232 0.44
110 38 0.07
111 1 0.00
112 16 0.03
113 1 0.00
114 1 0.00
119 1 0.00
120 61 0.12
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (109 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:433047 original size:146 final size:145
Alignment explanation
Indices: 432871--433478 Score: 655
Period size: 146 Copynumber: 3.9 Consensus size: 145
432861 ATTACTAATC
*
432871 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
432936 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA-T-T-AAATCATTAAAA
433001 ATTAATAATAATTTCATT
128 ATTAATAATAATTTCATT
*
433019 ATTACT-AAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
433082 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTATTAAATCATTAATATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTATTAAATC------AT--
433147 AATCATTAAATATTAATAATAATTTCATT
123 --T-A--AAA-ATTAATAATAATTTCATT
*
433176 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1 ATTACT----------AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTC------A-
* *
433241 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
49 T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
433306 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
110 ATTA-T-T-AAATCATTAAAAATTAATAATAATTTCATT
* *
433345 ATTACT-AATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--
*
433409 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATTAAAT
63 T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTATTAAAT
433474 CATTA
120 CATTA
433479 CTATCAAATC
Statistics
Matches: 403, Mismatches: 6, Indels: 95
0.80 0.01 0.19
Matches are distributed among these distances:
143 5 0.01
144 1 0.00
145 1 0.00
146 100 0.25
147 8 0.02
148 13 0.03
149 3 0.01
150 1 0.00
151 1 0.00
152 2 0.00
153 2 0.00
154 1 0.00
155 9 0.02
156 4 0.01
157 25 0.06
158 86 0.21
168 3 0.01
169 60 0.15
170 3 0.01
172 1 0.00
173 1 0.00
175 1 0.00
176 1 0.00
177 2 0.00
178 1 0.00
179 6 0.01
180 55 0.14
181 1 0.00
182 1 0.00
183 5 0.01
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (145 bp):
ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTATTAAATCATTAAAAATT
AATAATAATTTCATT
Found at i:433171 original size:60 final size:60
Alignment explanation
Indices: 432749--433312 Score: 515
Period size: 60 Copynumber: 9.2 Consensus size: 60
432739 ATTACTATCA
* *
432749 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
432808 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
432867 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * * * * * *
432927 AATCATTACTATCAAATCATTAAAAAT-TAAT-AATAATTTCATTATTACTAA--TCATTACTAT
1 AATCATTAC--T-AAATCATT-AATATCAAATCATTAA-AT-ATTAATAATAATTTCATTATTA-
*
432988 CA
59 CT
* * * * * * * **
432990 AATCATTA--AAA--ATTAATAAT-AATTTCATT-ATTACTAATATTACTATCAAATCATTAAA
1 AATCATTACTAAATCATTAAT-ATCAA-ATCATTAAATATTAATAATAATTTC--ATTATTACT
* * * * * *
433048 AATTAATAATAATTTCATTATTACTAATC-ATTACTATCAAATCATTAAAAATTAATAATAATTT
1 AATCATTACTAA-ATCATTA--A-T-ATCAAAT-C-ATTAAAT-ATT---AA-TAAT---AATTT
433112 CATTATTACT
51 CATTATTACT
*
433122 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
433182 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
433242 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
433302 AATCATTACTA
1 AATCATTACTA
433313 TCAAATCATT
Statistics
Matches: 420, Mismatches: 48, Indels: 73
0.78 0.09 0.13
Matches are distributed among these distances:
55 9 0.02
56 8 0.02
57 4 0.01
58 48 0.11
59 33 0.08
60 199 0.47
62 13 0.03
63 29 0.07
64 15 0.04
65 3 0.01
66 6 0.01
67 5 0.01
68 8 0.02
69 6 0.01
70 3 0.01
71 1 0.00
72 2 0.00
73 9 0.02
74 15 0.04
76 4 0.01
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:433249 original size:49 final size:49
Alignment explanation
Indices: 433186--433410 Score: 315
Period size: 49 Copynumber: 4.3 Consensus size: 49
433176 ATTACTAATC
433186 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
* *
433245 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
433296 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
433345 ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
433394 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
433411 AATCATTAAT
Statistics
Matches: 159, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
49 105 0.66
50 6 0.04
51 1 0.01
53 1 0.01
54 1 0.01
60 45 0.28
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:433374 original size:278 final size:277
Alignment explanation
Indices: 432921--433534 Score: 1072
Period size: 278 Copynumber: 2.3 Consensus size: 277
432911 TAATTTCATT
432921 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAA-TT--TC---A-T--T-ATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTAC
432975 T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATATTACTATCAA
66 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATATTACTATCAA
433039 ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAAT
131 ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAAT
*
433104 AATAATTTCATTATTACTAATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAA
196 AATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
433169 TTTCATTATTACTAATC
261 TTTCATTATTACTAATC
*
433186 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTAC
* *
433251 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATCATTACTATCA
66 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT-ATTACTATCA
*
433316 AATCATTAAAAATTAATAATAATTTCATTATTACTAATTATTACTATCAAATCATTAAAAATTAA
130 AATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAA
433381 TAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
195 TAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
433446 ATTTCATTATTACTAATC
260 ATTTCATTATTACTAATC
* *
433464 ATTATTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTAC
433529 TAAATC
66 TAAATC
433535 TTATAAATAC
Statistics
Matches: 328, Mismatches: 8, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
265 6 0.02
266 36 0.11
267 2 0.01
269 1 0.00
272 1 0.00
273 1 0.00
275 1 0.00
276 6 0.02
277 50 0.15
278 224 0.68
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (277 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTAC
TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATATTACTATCAA
ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAAT
AATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
TTTCATTATTACTAATC
Found at i:433418 original size:21 final size:21
Alignment explanation
Indices: 433394--433534 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 21
433384 TAATTTCATT
*
433394 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTATTAAATC
* *
433415 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTATTAAATC
* ** *
433436 ATTAATAAT-A--ATTTCATT
1 ATTACTAATCATTATTAAATC
433454 ATTACTAATCATTATTAAATC
1 ATTACTAATCATTATTAAATC
*
433475 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTATTAAATC
* **
433496 ATTAATAAT-A--ATTTCATC
1 ATTACTAATCATTATTAAATC
*
433514 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTATTAAATC
433535 TTATAAATAC
Statistics
Matches: 89, Mismatches: 17, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
17 10 0.11
18 16 0.18
19 4 0.04
20 6 0.07
21 32 0.36
22 21 0.24
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTATTAAATC
Found at i:433427 original size:60 final size:60
Alignment explanation
Indices: 433345--433534 Score: 328
Period size: 60 Copynumber: 3.2 Consensus size: 60
433335 TAATTTCATT
* *
433345 ATTACT-AATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
433404 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
433464 ATTATTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
433524 ATTACTAAATC
1 ATTACTAAATC
433535 TTATAAATAC
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 6 0.05
60 117 0.95
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:437016 original size:43 final size:43
Alignment explanation
Indices: 436968--437061 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
436958 GATACTAACA
* * *
436968 AATTAATTAATTTTTTATAT-TTAATAACTTAAACTAAGAAACT
1 AATTAATGAATTTTTTATATAAT-ATAACTTAAACTAACAAACT
*
437011 AATTAACGAATTTTTTATATAATATAACTTAAACTAACAAACT
1 AATTAATGAATTTTTTATATAATATAACTTAAACTAACAAACT
437054 AATATAAT
1 AAT-TAAT
437062 ATAACTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (43 bp):
AATTAATGAATTTTTTATATAATATAACTTAAACTAACAAACT
Found at i:437058 original size:28 final size:28
Alignment explanation
Indices: 437027--437084 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
437017 CGAATTTTTT
437027 ATATAATATAACTTAAACTAACAAACTA
1 ATATAATATAACTTAAACTAACAAACTA
437055 ATATAATATAACTTAAACTAACAAACTA
1 ATATAATATAACTTAAACTAACAAACTA
437083 AT
1 AT
437085 TAACTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (28 bp):
ATATAATATAACTTAAACTAACAAACTA
Found at i:437717 original size:29 final size:29
Alignment explanation
Indices: 437600--437711 Score: 143
Period size: 29 Copynumber: 3.9 Consensus size: 29
437590 GTCGAGGCTT
*
437600 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
*
437629 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
* * ***
437658 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
* *
437687 GGTCGCTGGGAGTACTTGGCGACCT
1 GGTCGCCGGGAGTGCTTGGCGACCT
437712 TGTAGGGGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCTTGGCGACCTACAA
Found at i:437867 original size:29 final size:29
Alignment explanation
Indices: 437833--437929 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
437823 GCATGGCTTT
*
437833 CATGGCGACCAACAATGGCGCATAGCCTT
1 CATGGCGACCAACAATGGCGCATAGCCTA
*
437862 CGTGGCGACCAACAATGGCGCATAGCCTA
1 CATGGCGACCAACAATGGCGCATAGCCTA
*
437891 CATGGCGACCAACAATGGCGCACAGCCTA
1 CATGGCGACCAACAATGGCGCATAGCCTA
437920 CATGGCGACC
1 CATGGCGACC
437930 TAAATAGGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (29 bp):
CATGGCGACCAACAATGGCGCATAGCCTA
Found at i:438110 original size:5 final size:5
Alignment explanation
Indices: 438108--438135 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
438098 TTAATCAAAT
438108 CAATC CAATC CAATC CAATC CAATC CAA
1 CAATC CAATC CAATC CAATC CAATC CAA
438136 AAGACCTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (5 bp):
CAATC
Done.