Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007799.1 Hibiscus syriacus cultivar Beakdansim tig00110109_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: 1433344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:196805 original size:15 final size:16
Alignment explanation
Indices: 196785--196828 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
196775 CTATCTGTAT
196785 ATGTTAATAAAAAC-C
1 ATGTTAATAAAAACTC
* *
196800 ATGTTAATGACAACTC
1 ATGTTAATAAAAACTC
196816 ATGTTAATAAAAA
1 ATGTTAATAAAAA
196829 TACTAGGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (16 bp):
ATGTTAATAAAAACTC
Found at i:197299 original size:59 final size:59
Alignment explanation
Indices: 197215--197369 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 59
197205 AAACTATAAA
* *
197215 TCTCATTCTAAATTCATCC-CTAAACTTTTGAACATTCTAATTTTGA-CCC-AAACAATGAC
1 TCTCATTCTAAATTAATCCAC-AAACTTTTGAACATTCTAATTTT-ATCCCAAAAC-ACGAC
* *
197274 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTTTAATTTTATTCCAAAATCACGAC
1 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTCTAATTTTATCCCAAAA-CACGAC
* * *
197334 TCTCATTCTAAATTAGTCTATAAACTTTTGAACATT
1 TCTCATTCTAAATTAATCCACAAACTTTTGAACATT
197370 TTAAACTCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 42 0.49
60 41 0.48
61 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
TCTCATTCTAAATTAATCCACAAACTTTTGAACATTCTAATTTTATCCCAAAACACGAC
Found at i:197363 original size:60 final size:58
Alignment explanation
Indices: 197215--197373 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 58
197205 AAACTATAAA
* * * *
197215 TCTCATTCTAAATTCATCCCTAAACTTTTGAACATTCTAATTTTGACCCAAACAATGAC
1 TCTCATTCTAAATT-ATCCATAAACTTTTGAACATTTTAATTTTGACCAAAACAACGAC
*
197274 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTTTAATTTT-ATTCCAAAATC-ACGAC
1 TCTCATTCTAAATT-ATCCATAAACTTTTGAACATTTTAATTTTGA--CCAAAA-CAACGAC
*
197334 TCTCATTCTAAATTAGTCTATAAACTTTTGAACATTTTAA
1 TCTCATTCTAAATTA-TCCATAAACTTTTGAACATTTTAA
197374 ACTCATCCTA
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 41 0.47
60 45 0.51
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.39
Consensus pattern (58 bp):
TCTCATTCTAAATTATCCATAAACTTTTGAACATTTTAATTTTGACCAAAACAACGAC
Found at i:197619 original size:60 final size:59
Alignment explanation
Indices: 197541--197703 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 59
197531 GAAAGCTTTG
* *
197541 AAAGTTTAGGGATCAATTTAGAATAAGGGTCATAATATGAGGATGA-AATTAGAATATTCA
1 AAAGTTTAGGGATCAATTTAGAAT-AGGGTCATAGT-TGAGGATAAGAATTAGAATATTCA
* * * * *
197601 AAAGTTATAGGAAT-AATTTAAAATAGGAGTCAT-GTTTAAGAAAAGAATTAGAATATTCA
1 AAAGTT-TAGGGATCAATTTAGAATAGG-GTCATAGTTGAGGATAAGAATTAGAATATTCA
*
197660 AAACTTTAGGGATCAATTTAGAATGAGGG-CATAGTTTGAGGATA
1 AAAGTTTAGGGATCAATTTAGAAT-AGGGTCATAG-TTGAGGATA
197704 TATGATGTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
58 14 0.17
59 34 0.41
60 29 0.35
61 6 0.07
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (59 bp):
AAAGTTTAGGGATCAATTTAGAATAGGGTCATAGTTGAGGATAAGAATTAGAATATTCA
Found at i:203414 original size:3 final size:3
Alignment explanation
Indices: 203406--203440 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
203396 ATCCTATGTT
203406 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
203441 ATCATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:214328 original size:13 final size:13
Alignment explanation
Indices: 214310--214353 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
214300 ACCGGTCACA
214310 ACCCGTTTACCCG
1 ACCCGTTTACCCG
214323 ACCCGTTTACCCG
1 ACCCGTTTACCCG
214336 ACCCGTTTACCCG
1 ACCCGTTTACCCG
214349 ACCCG
1 ACCCG
214354 ACCCGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGTTTACCCG
Found at i:214352 original size:18 final size:18
Alignment explanation
Indices: 214331--214371 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
214321 CGACCCGTTT
*
214331 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
214349 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
214367 GCCCG
1 ACCCG
214372 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.51, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:214364 original size:13 final size:13
Alignment explanation
Indices: 214310--214394 Score: 71
Period size: 13 Copynumber: 6.0 Consensus size: 13
214300 ACCGGTCACA
*
214310 ACCCGTTTACCCG
1 ACCCGTTGACCCG
*
214323 ACCCGTTTACCCG
1 ACCCGTTGACCCG
214336 ACCCGTTTACCCGACCCG
1 ACCCG-TT----GACCCG
214354 ACCCGTTGACCCG
1 ACCCGTTGACCCG
* *
214367 GCCCGTTGACCGTTG
1 ACCCGTTGACC--CG
214382 ACCCGTTGACCCG
1 ACCCGTTGACCCG
214395 TTGACCGGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
13 35 0.58
14 2 0.03
15 11 0.18
17 2 0.03
18 10 0.17
ACGTcount: A:0.14, C:0.45, G:0.21, T:0.20
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:214377 original size:26 final size:26
Alignment explanation
Indices: 214310--214394 Score: 71
Period size: 31 Copynumber: 3.0 Consensus size: 26
214300 ACCGGTCACA
* *
214310 ACCCGTTTACCCGACCCGTTTACCCG
1 ACCCGTTGACCCGACCCGTTGACCCG
214336 ACCCGTTTACCCGACCCGACCCGTTGACCCG
1 ACCCG-TT----GACCCGACCCGTTGACCCG
* *
214367 GCCCGTTGACCGTTGACCCGTTGACCCG
1 ACCCGTTGACC--CGACCCGTTGACCCG
214395 TTGACCGGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 9 0.19
27 2 0.04
28 14 0.29
30 2 0.04
31 21 0.44
ACGTcount: A:0.14, C:0.45, G:0.21, T:0.20
Consensus pattern (26 bp):
ACCCGTTGACCCGACCCGTTGACCCG
Found at i:214381 original size:7 final size:8
Alignment explanation
Indices: 214353--214400 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
214343 TACCCGACCC
214353 GACCCGTT
1 GACCCGTT
214361 GACCCG--
1 GACCCGTT
214367 G-CCCGTT
1 GACCCGTT
214374 GA-CCGTT
1 GACCCGTT
214381 GACCCGTT
1 GACCCGTT
214389 GACCCGTT
1 GACCCGTT
214397 GACC
1 GACC
214401 GGAGTTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 8 0.22
8 23 0.64
ACGTcount: A:0.12, C:0.40, G:0.27, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:217143 original size:52 final size:52
Alignment explanation
Indices: 217048--217154 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
217038 AAATGTTCCA
** *
217048 ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCTTAAACTTT-TGAAC
1 ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCCCAAACTTTGTAAAC
**
217099 ATTTCATCCCAAACTATGACCTTCATTCTAAATTGGTCCCAAACTTTGTAAAC
1 ATTT-ATCCCAAACTATGACCTTCATTCTAAATTAATCCCAAACTTTGTAAAC
217152 ATT
1 ATT
217155 CCAATTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
51 4 0.08
52 38 0.78
53 7 0.14
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (52 bp):
ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCCCAAACTTTGTAAAC
Found at i:217939 original size:2 final size:2
Alignment explanation
Indices: 217932--217960 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
217922 GTTACAGTAT
217932 TA TA 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 TA TA T
217961 TCTAACTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:219625 original size:2 final size:2
Alignment explanation
Indices: 219618--219651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
219608 TAATTCTATC
219618 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
219652 CCCTACCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220221 original size:7 final size:7
Alignment explanation
Indices: 220200--220241 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
220190 ATCTCAACAG
220200 TTAAA-T
1 TTAAATT
*
220206 TTGAATT
1 TTAAATT
220213 TTAAATT
1 TTAAATT
220220 TTAAAATT
1 TT-AAATT
220228 TTAAATT
1 TTAAATT
*
220235 TAAAATT
1 TTAAATT
220242 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 4 0.13
7 20 0.65
8 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
TTAAATT
Found at i:220238 original size:14 final size:14
Alignment explanation
Indices: 220200--220241 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
220190 ATCTCAACAG
*
220200 TTAAATTT-GAATT
1 TTAAATTTAAAATT
220213 TTAAATTTTAAAATT
1 TTAAA-TTTAAAATT
220228 TTAAATTTAAAATT
1 TTAAATTTAAAATT
220242 CAAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TTAAATTTAAAATT
Found at i:230155 original size:17 final size:17
Alignment explanation
Indices: 230131--230178 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
230121 GTGATGAATG
230131 AAAA-TAATATAAATTA
1 AAAATTAATATAAATTA
* * *
230147 AATATTAATTTAATTTA
1 AAAATTAATATAAATTA
230164 AAAATTAATA-AAATT
1 AAAATTAATATAAATT
230179 TCCATGTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTAATATAAATTA
Found at i:230209 original size:117 final size:118
Alignment explanation
Indices: 230003--230238 Score: 438
Period size: 117 Copynumber: 2.0 Consensus size: 118
229993 ATAAATGAGC
*
230003 AGTGAAGAATGAAAATAATATTAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATG
1 AGTGAAGAATGAAAATAATATAAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATG
230068 TCATCTTAAAGTTATGGAAAAATTGATGGAGTGAT-AAAAAATTCAATGTATA
66 TCATCTTAAAGTTATGGAAAAATTGATGGAGTGATAAAAAAATTCAATGTATA
* *
230120 AGTGATGAATGAAAATAATATAAATTAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATG
1 AGTGAAGAATGAAAATAATATAAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATG
230185 TCATCTTAAAGTTATGGAAAAATTGATGGAGTGATAAAAAAATTCAATGTATA
66 TCATCTTAAAGTTATGGAAAAATTGATGGAGTGATAAAAAAATTCAATGTATA
230238 A
1 A
230239 AGTTCAGTGA
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
117 97 0.84
118 18 0.16
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (118 bp):
AGTGAAGAATGAAAATAATATAAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATG
TCATCTTAAAGTTATGGAAAAATTGATGGAGTGATAAAAAAATTCAATGTATA
Found at i:230931 original size:204 final size:204
Alignment explanation
Indices: 230576--230989 Score: 765
Period size: 204 Copynumber: 2.0 Consensus size: 204
230566 AGTCTCTTTC
230576 TATCTTTCTCTTTTCTTTTCAATTGGTTTCTTTCCTTTATCTTCAATTTTGATTTCTTTATGGCT
1 TATC-TTCTCTTTTCTTTTCAATTGGTTTCTTTCCTTTATCTTCAATTTTGATTTCTTTATGGCT
*
230641 TCTTGATTACTCTTTGAATACCTTACGTCAATACAAGTTCCCAAAATGTTGTTCTTGTTTCTTGA
65 TCTTGATTACTCTTTGAATACCTTACGTCAATACAAGTTCCCAAAATATTGTTCTTGTTTCTTGA
230706 GGGCACGGGCTTCACTGGAAGAAGTGTTTGATTTTGTTGCAATTGTTGTGGTTTTACATCTCAAT
130 GGGCACGGGCTTCACTGGAAGAAGTGTTTGATTTTGTTGCAATTGTTGTGGTTTTACATCTCAAT
230771 ATGTTAGTTG
195 ATGTTAGTTG
*
230781 TATCTTCTCTTTTCTTTTCAATTGGTTTCTTTCCTTTATCTTCAATTTTGATTTCTTTATGGTTT
1 TATCTTCTCTTTTCTTTTCAATTGGTTTCTTTCCTTTATCTTCAATTTTGATTTCTTTATGGCTT
*
230846 CTTGATTACTCTTTGAATACCTTACGTCAATGCAAGTTCCCAAAATATTGTTCTTGTTTCTTGAG
66 CTTGATTACTCTTTGAATACCTTACGTCAATACAAGTTCCCAAAATATTGTTCTTGTTTCTTGAG
* * *
230911 GGCATGGGCTTCACTGGAAGAATTGTTTGATTTTGTTGCAATTGTTGTGGTTTTACGTCTCAATA
131 GGCACGGGCTTCACTGGAAGAAGTGTTTGATTTTGTTGCAATTGTTGTGGTTTTACATCTCAATA
230976 TGTTAGTTG
196 TGTTAGTTG
230985 TATCT
1 TATCT
230990 CAAACCGGGA
Statistics
Matches: 203, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
204 199 0.98
205 4 0.02
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (204 bp):
TATCTTCTCTTTTCTTTTCAATTGGTTTCTTTCCTTTATCTTCAATTTTGATTTCTTTATGGCTT
CTTGATTACTCTTTGAATACCTTACGTCAATACAAGTTCCCAAAATATTGTTCTTGTTTCTTGAG
GGCACGGGCTTCACTGGAAGAAGTGTTTGATTTTGTTGCAATTGTTGTGGTTTTACATCTCAATA
TGTTAGTTG
Found at i:232280 original size:22 final size:22
Alignment explanation
Indices: 232250--232293 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
232240 CCTTGAGGAG
232250 TTAAGCTTCACAATTATACAGA
1 TTAAGCTTCACAATTATACAGA
*
232272 TTAATCTTCACAATTATACAGA
1 TTAAGCTTCACAATTATACAGA
232294 CAGTGTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (22 bp):
TTAAGCTTCACAATTATACAGA
Found at i:236114 original size:135 final size:135
Alignment explanation
Indices: 235934--236203 Score: 459
Period size: 135 Copynumber: 2.0 Consensus size: 135
235924 AAGTGCAAGA
* * * *
235934 AAGCTAATAGATATTTTGTCCAAATTAAACAAAATGGCAGGGTATGGTTCTGATGAAGAGAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
* * * *
235999 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATGGAGCAATTCCAGTTCTCAGTCATTTT
66 TCTTAATGAGATTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATACCAGTTCTCAGTCATTTT
236064 TCTCT
131 TCTCT
*
236069 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGATAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
236134 TCTTAATGAGATTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATACCAGTTCTCAGTCATTTT
66 TCTTAATGAGATTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATACCAGTTCTCAGTCATTTT
236199 TCTCT
131 TCTCT
236204 TTTTTCCCTT
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 126 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (135 bp):
AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
TCTTAATGAGATTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATACCAGTTCTCAGTCATTTT
TCTCT
Found at i:241042 original size:135 final size:135
Alignment explanation
Indices: 240800--241204 Score: 738
Period size: 135 Copynumber: 3.0 Consensus size: 135
240790 AAGTGCAAGA
* * * * *
240800 AAGCCAATTGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTTCTGATGAAGAGAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
240865 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
66 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
240930 TCTCT
131 TCTCT
240935 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
241000 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
66 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
241065 TCTCT
131 TCTCT
241070 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
* * *
241135 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGTGCAATACCAGTTCTCAGTCATTTT
66 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
241200 TCTCT
131 TCTCT
241205 TTTTTCCTTT
Statistics
Matches: 262, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 262 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (135 bp):
AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGAAGGTTATGCTCCTGATGAAGATAACAA
TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCAGTTCTCTGTCATTTT
TCTCT
Found at i:255993 original size:2 final size:2
Alignment explanation
Indices: 255986--256010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
255976 CCTCCTTTCC
255986 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
256011 CACTCCCTCG
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:261053 original size:30 final size:30
Alignment explanation
Indices: 261018--261078 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
261008 CTCGATCCCA
*
261018 CCACTTCCCTCCTTTCCCCTTCCTC-TCCTC
1 CCACTTCCCTCCCTT-CCCTTCCTCTTCCTC
*
261048 CCACTTCCTTCCCTTCCCTTCCTCTTCCTC
1 CCACTTCCCTCCCTTCCCTTCCTCTTCCTC
261078 C
1 C
261079 TCTCCTCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (30 bp):
CCACTTCCCTCCCTTCCCTTCCTCTTCCTC
Found at i:261054 original size:15 final size:14
Alignment explanation
Indices: 261032--261087 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
261022 TTCCCTCCTT
261032 TCCCCTTCCTCTCC
1 TCCCCTTCCTCTCC
261046 TCCCACTTCCT-TCCC
1 TCCC-CTTCCTCT-CC
*
261061 TTCCCTTCCTCTTCC
1 TCCCCTTCCTC-TCC
*
261076 TCCTC-TCCTCTC
1 TCCCCTTCCTCTC
261088 ATCTTCTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 2 0.06
14 16 0.46
15 16 0.46
16 1 0.03
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (14 bp):
TCCCCTTCCTCTCC
Found at i:261082 original size:38 final size:40
Alignment explanation
Indices: 261038--261114 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 40
261028 CCTTTCCCCT
*
261038 TCCTCTCCTCCCA-CTTCCTT-CCCTTCCCT-TCCTCTTCC
1 TCCTCTCCTCCCATCTT-CTTCCCCTGCCCTCTCCTCTTCC
*
261076 TCCTCTCCTCTCATCTTCTTCCCCTGCCCTCTCCTCTTC
1 TCCTCTCCTCCCATCTTCTTCCCCTGCCCTCTCCTCTTC
261115 TTCACTCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 15 0.44
39 11 0.32
40 8 0.24
ACGTcount: A:0.03, C:0.56, G:0.01, T:0.40
Consensus pattern (40 bp):
TCCTCTCCTCCCATCTTCTTCCCCTGCCCTCTCCTCTTCC
Found at i:261879 original size:15 final size:16
Alignment explanation
Indices: 261851--261881 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
261841 TGTGGGATAA
261851 GGTCATCAATGTTAGG
1 GGTCATCAATGTTAGG
261867 GGTCATC-ATGTTAGG
1 GGTCATCAATGTTAGG
261882 CCTTATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (16 bp):
GGTCATCAATGTTAGG
Found at i:267509 original size:10 final size:10
Alignment explanation
Indices: 267494--267552 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
267484 CATTTAATAA
267494 ATAAACGAAC
1 ATAAACGAAC
267504 ATAAACGAAC
1 ATAAACGAAC
** *
267514 ACGAAC-ATAA
1 ATAAACGA-AC
267524 ATGAACACGAAC
1 AT-AA-ACGAAC
267536 ATAAACGAAC
1 ATAAACGAAC
267546 ATAAACG
1 ATAAACG
267553 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:267519 original size:16 final size:16
Alignment explanation
Indices: 267498--267546 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
267488 TAATAAATAA
267498 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
267514 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
267530 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
267546 A
1 A
267547 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:268312 original size:14 final size:14
Alignment explanation
Indices: 268295--268324 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
268285 AATGAACATA
*
268295 AACGAACATAATCG
1 AACGAACATAAACG
268309 AACGAACATAAACG
1 AACGAACATAAACG
268323 AA
1 AA
268325 TATAACCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:268315 original size:24 final size:24
Alignment explanation
Indices: 268288--268336 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
268278 ATAAATGAAT
*
268288 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
268312 GAACATAAACGAATATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
268336 G
1 G
268337 TTCACGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:269749 original size:21 final size:21
Alignment explanation
Indices: 269723--269832 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
269713 CTGTATTTCT
269723 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* * ** ** *
269744 CGTTGCAAT-TTTCCATTTCA
1 CGTTGCGATAGTTGAAAATCG
269764 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* * ** **
269785 CGTTGCGGT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
269805 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
269826 CGTTGCG
1 CGTTGCG
269833 GTTTTTCATT
Statistics
Matches: 61, Mismatches: 26, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 27 0.44
21 34 0.56
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:269762 original size:41 final size:41
Alignment explanation
Indices: 269744--270021 Score: 366
Period size: 41 Copynumber: 6.8 Consensus size: 41
269734 TTGAAAATCG
* * * *
269744 CGTTGCAATTTTCCATTTCACGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GT
* * *
269785 CGTTGCGGTTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GT
* *
269826 CGTTGCGGTTTTTCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
269867 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
* * *
269908 CGTTGCGGTTTTCCATTTCGTGTTACGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
*
269949 TGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
*
269990 CGTTGTGATTTTCCATTTCGCGTTGCGATAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
270022 TTTAAAAATG
Statistics
Matches: 218, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 1 0.00
41 216 0.99
42 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:269892 original size:20 final size:20
Alignment explanation
Indices: 269741--269895 Score: 89
Period size: 20 Copynumber: 7.6 Consensus size: 20
269731 TAGTTGAAAA
*
269741 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
269761 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
269782 TCGCGTTGCGGTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
269802 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
* *
269823 TCGCGTTGCGGTTTTTCATT
1 TCGCGTTGCGATTTTCCATT
* * *
269843 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
269864 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
269884 TCGCGTTGCGAT
1 TCGCGTTGCGAT
269896 AGTCTACAGT
Statistics
Matches: 95, Mismatches: 33, Indels: 14
0.67 0.23 0.10
Matches are distributed among these distances:
19 4 0.04
20 49 0.52
21 38 0.40
22 4 0.04
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:269975 original size:20 final size:20
Alignment explanation
Indices: 269950--270018 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
269940 CTACAGTGTT
269950 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* * *
269970 GTTGCGATAGTCTACA-GT-GTC
1 GTTGCGAT--TTTCCATTTCG-C
*
269991 GTTGTGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
270011 GTTGCGAT
1 GTTGCGAT
270019 AGTTTTAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
21 10 0.28
22 4 0.11
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:270986 original size:20 final size:20
Alignment explanation
Indices: 270961--271178 Score: 142
Period size: 20 Copynumber: 10.6 Consensus size: 20
270951 TTTTAAAACT
270961 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
270981 ATCGCAA--CGACATTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
271002 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
271022 ATCACAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
271043 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
271063 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
271084 ATCACAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * ** *
271104 ACCGCAACGCGATATTTTCAACT
1 ATCGCAACGCGA-A-ATGGAA-A
271127 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
271147 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
271167 ATCGCAACGCGA
1 ATCGCAACGCGA
271179 TTTTCAACTA
Statistics
Matches: 148, Mismatches: 32, Indels: 36
0.69 0.15 0.17
Matches are distributed among these distances:
18 9 0.06
19 9 0.06
20 68 0.46
21 29 0.20
22 13 0.09
23 20 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:271015 original size:41 final size:41
Alignment explanation
Indices: 270958--271155 Score: 299
Period size: 41 Copynumber: 4.8 Consensus size: 41
270948 CATTTTTAAA
*
270958 ACTATCGCAACGCGAAATGGAAAATCGCAACGACATTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
270999 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
271040 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* * * * *
271081 ACTATCACAACGCGAAATGGAAAACCGCAACGCGATATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCGCAA--CGACACTGT-AG
271124 ACTATCGCAACGCGAAATGGAAAATCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
271156 CGAAATGGAA
Statistics
Matches: 144, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
41 109 0.76
43 34 0.24
44 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:272681 original size:23 final size:22
Alignment explanation
Indices: 272655--272699 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
272645 AGGTTGGACG
* *
272655 ATTTATTAAATGGTTATATAAAT
1 ATTTATT-AATAGCTATATAAAT
*
272678 ATTTGTTAATAGCTATATAAAT
1 ATTTATTAATAGCTATATAAAT
272700 GTTAGTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTATTAATAGCTATATAAAT
Found at i:276497 original size:22 final size:23
Alignment explanation
Indices: 276451--276498 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
276441 TGGTGGTTAG
*
276451 TTTAATGGATGTTTAGACTTTAT
1 TTTAATGGATATTTAGACTTTAT
* *
276474 TTTAATGGTTATTTA-AGTTTAT
1 TTTAATGGATATTTAGACTTTAT
276496 TTT
1 TTT
276499 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (23 bp):
TTTAATGGATATTTAGACTTTAT
Found at i:279087 original size:50 final size:50
Alignment explanation
Indices: 279006--279120 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
278996 ATAAAAATAC
*
279006 TCATTAAATTTGTATACTTACTCTATCACAACGATTATTCTGTAACAGAT
1 TCATTAATTTTGTATACTTACTCTATCACAACGATTATTCTGTAACAGAT
* * *
279056 TCATTAATTTTTTATACTTACTGCGT-T-ACAACGATTATTTTGTAATAGAT
1 TCATTAATTTTGTATACTTACT-C-TATCACAACGATTATTCTGTAACAGAT
* * *
279106 TAATCAATTTAGTAT
1 TCATTAATTTTGTAT
279121 TATTTTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 52 0.95
51 2 0.04
52 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (50 bp):
TCATTAATTTTGTATACTTACTCTATCACAACGATTATTCTGTAACAGAT
Found at i:281208 original size:13 final size:13
Alignment explanation
Indices: 281190--281216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
281180 AACATGATAA
281190 GCATTAGAAAAAG
1 GCATTAGAAAAAG
281203 GCATTAGAAAAAG
1 GCATTAGAAAAAG
281216 G
1 G
281217 GAATCTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (13 bp):
GCATTAGAAAAAG
Found at i:286322 original size:28 final size:28
Alignment explanation
Indices: 286286--286341 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
286276 TATTATTCAT
*
286286 TAATTTTTATT-TTTTTAACAACAATTAA
1 TAATGTTTATTATTTTTAACAA-AATTAA
*
286314 TAATGTTTATTCATTTTTAATAAAATTA
1 TAATGTTTATT-ATTTTTAACAAAATTA
286342 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 5 0.21
30 9 0.38
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (28 bp):
TAATGTTTATTATTTTTAACAAAATTAA
Found at i:288950 original size:20 final size:20
Alignment explanation
Indices: 288916--288971 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
288906 AAACTATGGA
* *
288916 ATATATATATATATATATAT
1 ATATGTATATGTATATATAT
* *
288936 ATATGTATTTGTATATGTAT
1 ATATGTATATGTATATATAT
*
288956 GTATGTATATGTATAT
1 ATATGTATATGTATAT
288972 CACATGGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (20 bp):
ATATGTATATGTATATATAT
Found at i:289583 original size:21 final size:22
Alignment explanation
Indices: 289538--289583 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
289528 TAATTTTCGA
289538 TAGAAAAAATAATGTTTTACCGG
1 TAGAAAAAATAATGTTTTA-CGG
289561 TAGAAAAAATAATGTTTTA-GG
1 TAGAAAAAATAATGTTTTACGG
289582 TA
1 TA
289584 ACGCTTTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.17
23 19 0.83
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
TAGAAAAAATAATGTTTTACGG
Found at i:290304 original size:60 final size:59
Alignment explanation
Indices: 290194--290375 Score: 183
Period size: 60 Copynumber: 3.1 Consensus size: 59
290184 GATACGTATA
* * * *
290194 TTTGGGATGAGATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGA-AGGTCATAG
1 TTTGGGATGAAATTGAAATGTT-AAAAAGTTTGAGGACCAATTTAAAATGATA-GTCATAG
* * *
290254 TTTGTGGATGAAATTGAAATGTTAAAAAGTTTGAGGACTATTTTAAAATGATAGTTATAG
1 TTTG-GGATGAAATTGAAATGTTAAAAAGTTTGAGGACCAATTTAAAATGATAGTCATAG
* * * * *
290314 TTTAGGAATGAAATTAAAATATTTAAAAGTTT-AGTGACCAATTTAAAAT--TAGTCATAT
1 TTT-GGGATGAAATTGAAATGTTAAAAAGTTTGAG-GACCAATTTAAAATGATAGTCATAG
290372 TTTG
1 TTTG
290376 AGAACATGTG
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
57 1 0.01
58 10 0.10
59 2 0.02
60 72 0.70
61 18 0.17
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (59 bp):
TTTGGGATGAAATTGAAATGTTAAAAAGTTTGAGGACCAATTTAAAATGATAGTCATAG
Found at i:292790 original size:2 final size:2
Alignment explanation
Indices: 292783--292826 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
292773 ATAATTTGGA
292783 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
292825 AT
1 AT
292827 CTTGAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:293077 original size:12 final size:12
Alignment explanation
Indices: 293062--293090 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
293052 TTAAAAAAAT
293062 AAAAAAAGATTA
1 AAAAAAAGATTA
293074 AAAAAAAGATTA
1 AAAAAAAGATTA
293086 AAAAA
1 AAAAA
293091 TAAGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAGATTA
Found at i:299637 original size:57 final size:56
Alignment explanation
Indices: 299558--299681 Score: 205
Period size: 57 Copynumber: 2.2 Consensus size: 56
299548 CTTCGTTTTC
*
299558 CTCTTCTT-TTTGACCTTTCAGCATTTATGGAAACAGGATGATCATCATCTTCGTT
1 CTCTTCTTCTTTGACCTTTCAGCATTTATGGAAACAGGATGATCATCATCTTCCTT
*
299613 CTCTTCTTCATTTGACCTTTCAGCATTTATGGAAACAGGATGATCATCGTCTTCCTT
1 CTCTTCTTC-TTTGACCTTTCAGCATTTATGGAAACAGGATGATCATCATCTTCCTT
*
299670 CTCCTCTTCTTT
1 CTCTTCTTCTTT
299682 CCCCTCTTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
55 8 0.12
56 3 0.05
57 53 0.83
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (56 bp):
CTCTTCTTCTTTGACCTTTCAGCATTTATGGAAACAGGATGATCATCATCTTCCTT
Found at i:301986 original size:145 final size:143
Alignment explanation
Indices: 301723--302151 Score: 689
Period size: 145 Copynumber: 3.0 Consensus size: 143
301713 TTTTCTGGGT
*
301723 TTTCTTTTTCGTGTTTATGAATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGTGAAGAATTC
1 TTTCTTTTTCATGTTTATGAATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGTGAAGAATTC
*
301788 GGTGATCTTTGAGTTTACTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGT
66 GGT-ATC-TTGAGTTTATTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGT
301853 AGCTGCAAATTTCAA
129 AGCTGCAAATTTCAA
*
301868 TTTCTTTTTCATGTTTATGAATTTGGTGGTTGAGCTTGAACGGATTGTAATTTGGTGAAGAATTC
1 TTTCTTTTTCATGTTTATGAATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGTGAAGAATTC
301933 GGTAATCTTCGAGTTTATTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGT
66 GGT-ATCTT-GAGTTTATTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGT
301998 AGCTGCAAATTTCAA
129 AGCTGCAAATTTCAA
*
302013 TTTCTTTTTCATGTTTATGGATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGT---G-A-TC
1 TTTCTTTTTCATGTTTATGAATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGTGAAGAATTC
* * *
302073 ----T-TTGAGTTTATTGCTAGTTATGGTCTTTGAGTTTGTCTTCAATGAAGTTCAATTTTGTAG
66 GGTATCTTGAGTTTATTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGTAG
302133 CTGCAAATTTCAA
131 CTGCAAATTTCAA
302146 TTTCTT
1 TTTCTT
302152 GATTCATACT
Statistics
Matches: 274, Mismatches: 9, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
133 73 0.27
134 2 0.01
135 1 0.00
140 2 0.01
141 1 0.00
142 1 0.00
144 2 0.01
145 192 0.70
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.47
Consensus pattern (143 bp):
TTTCTTTTTCATGTTTATGAATTTGGTGGTTGAGCTTGAATGGATTGTAATTTGGTGAAGAATTC
GGTATCTTGAGTTTATTGCTAATTATGGTCTTTGAGTTTGTCTTTAGTGAAGTTCAATTTTGTAG
CTGCAAATTTCAA
Found at i:305525 original size:27 final size:25
Alignment explanation
Indices: 305495--305561 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
305485 AATTAAGTTA
305495 ATAATAAAATTTATTTAAGAAGTTAAT
1 ATAATAAAATTTATTT--GAAGTTAAT
*
305522 ATAA-ACATATTT-TTTGAAGTTAAT
1 ATAATA-AAATTTATTTGAAGTTAAT
305546 ATATATAAAATATTAT
1 ATA-ATAAAAT-TTAT
305562 AAATTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
24 12 0.36
25 4 0.12
26 7 0.21
27 10 0.30
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (25 bp):
ATAATAAAATTTATTTGAAGTTAAT
Found at i:305566 original size:61 final size:61
Alignment explanation
Indices: 305447--305622 Score: 145
Period size: 62 Copynumber: 2.9 Consensus size: 61
305437 TATATTTTTA
* * *
305447 TAAGTTTAG-A-TAATAATAAAATATATATTTTTAAA-TTAA-AT-TAAGTTAATAATA-AAATT
1 TAAGTTTAGAATTAAT-ATAAAAAATAT-TTTTTAAAGTTAATATAT-A-TAAATATTATAAATT
* *
305506 T-A-TTTAAGAAGTTAATAT-AAACATATTTTTTGAAGTTAATATATATAAAATATTATAAATT
1 TAAGTTT-AGAA-TTAATATAAAAAATATTTTTTAAAGTTAATATATAT-AAATATTATAAATT
* * * *
305567 TAAGTTTAGTATTTATATAAAAAATATTTTTTAAAGTTTATATATATATATATTAT
1 TAAGTTTAGAATTAATATAAAAAATATTTTTTAAAGTTAATATATATAAATATTAT
305623 GCCATGTGGC
Statistics
Matches: 95, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
57 3 0.03
58 10 0.11
59 14 0.15
60 11 0.12
61 25 0.26
62 29 0.31
63 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.46
Consensus pattern (61 bp):
TAAGTTTAGAATTAATATAAAAAATATTTTTTAAAGTTAATATATATAAATATTATAAATT
Found at i:305615 original size:31 final size:30
Alignment explanation
Indices: 305520--305616 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
305510 TAAGAAGTTA
*
305520 ATAT-AAACATATTTTTTGAAG-TTA-ATAT
1 ATATAAAAAATATTTTTT-AAGTTTATATAT
* ** *
305548 ATATAAAATATTATAAATTTAAGTTTAGTATTT
1 ATATAAAA-AATAT-TTTTTAAGTTTA-TATAT
305581 ATATAAAAAATATTTTTTAAAGTTTATATAT
1 ATATAAAAAATATTTTTT-AAGTTTATATAT
305612 ATATA
1 ATATA
305617 TATTATGCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 6 0.11
31 18 0.34
32 11 0.21
33 11 0.21
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (30 bp):
ATATAAAAAATATTTTTTAAGTTTATATAT
Found at i:307015 original size:18 final size:18
Alignment explanation
Indices: 306989--307024 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
306979 TGTTACACAT
* *
306989 ATAATATATTTTATAAAA
1 ATAAAATATTATATAAAA
307007 ATAAAATATTATATAAAA
1 ATAAAATATTATATAAAA
307025 GATATTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAATATTATATAAAA
Found at i:307610 original size:28 final size:28
Alignment explanation
Indices: 307557--307613 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
307547 TTGTCGTTGC
*
307557 TTTCAAGCACTAGCTCGCCAACATAATA
1 TTTCAAGCACTAGCTCGACAACATAATA
* *
307585 TTTCAAGCACT-GCCTCGACGATATAATA
1 TTTCAAGCACTAG-CTCGACAACATAATA
307613 T
1 T
307614 AAACAGACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACAACATAATA
Found at i:307886 original size:60 final size:60
Alignment explanation
Indices: 307763--307887 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
307753 GCCAAGTGAC
* ** ** * *
307763 CATTTTGTAACTTTTAATAGTCGGAGGACTCAATAAAATATTGTCCTATCGTTAAGGGTT
1 CATTTTGTAAATTTTAATAGTAAGAGGACTCAATAAAATATACTCCTATAGTTAAGGGAT
*
307823 CATTTTGTAAATTTTAATAGTTAAGA-GACTCAATAAAATAATACT-CTATAGTTAGGGGAT
1 CATTTTGTAAATTTTAATAG-TAAGAGGACTCAATAAAAT-ATACTCCTATAGTTAAGGGAT
307883 CATTT
1 CATTT
307888 ATACAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 49 0.89
61 6 0.11
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (60 bp):
CATTTTGTAAATTTTAATAGTAAGAGGACTCAATAAAATATACTCCTATAGTTAAGGGAT
Found at i:309246 original size:30 final size:30
Alignment explanation
Indices: 309212--309275 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
309202 ATATCAAATC
309212 AGCTTTCAATGTTTATCCTATGACCACTTT
1 AGCTTTCAATGTTTATCCTATGACCACTTT
* *
309242 AGCTTTCAATGTTTATCCTATGATCATTTT
1 AGCTTTCAATGTTTATCCTATGACCACTTT
309272 AGCT
1 AGCT
309276 CTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (30 bp):
AGCTTTCAATGTTTATCCTATGACCACTTT
Found at i:309303 original size:20 final size:18
Alignment explanation
Indices: 309270--309307 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
309260 TATGATCATT
309270 TTAGCTCTTATATATATA
1 TTAGCTCTTATATATATA
309288 TTAGCTCTTATATATATA
1 TTAGCTCTTATATATATA
309306 TT
1 TT
309308 TGAAGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTAGCTCTTATATATATA
Found at i:311496 original size:2 final size:2
Alignment explanation
Indices: 311489--311519 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
311479 CCAACCTGAC
311489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
311520 ATTCTCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:314148 original size:2 final size:2
Alignment explanation
Indices: 314141--314165 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
314131 ACAATTTTTA
314141 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
314166 AAAGACAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:315373 original size:4 final size:4
Alignment explanation
Indices: 315364--315408 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
315354 ACGCCATGTG
315364 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
315409 ATTTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:322826 original size:31 final size:31
Alignment explanation
Indices: 322769--322827 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
322759 TTATGTATTA
***
322769 AATGAACGAACATGAACAAGCTATATTTCTT
1 AATGAACGAACATGAACAAAAAATATTTCTT
322800 AATGAACGAACATGAACAAAAAATATTT
1 AATGAACGAACATGAACAAAAAATATTT
322828 GTTCGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (31 bp):
AATGAACGAACATGAACAAAAAATATTTCTT
Found at i:324031 original size:14 final size:14
Alignment explanation
Indices: 324014--324046 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
324004 ATTTCTATGT
*
324014 AGGGAATTATTTGC
1 AGGGAATTATTTAC
324028 AGGGAATTATTTAC
1 AGGGAATTATTTAC
324042 AGGGA
1 AGGGA
324047 TTACTCCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:334506 original size:20 final size:20
Alignment explanation
Indices: 334451--334497 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
334441 ACAGGTTCCA
*
334451 AAATCGCAACACGAATAAGT
1 AAATCGCAACGCGAATAAGT
*
334471 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATAAGT
334491 AAATCGC
1 AAATCGC
334498 GTTGCGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATAAGT
Found at i:334545 original size:20 final size:20
Alignment explanation
Indices: 334516--334557 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
334506 TTTGAAAATC
334516 ACATTACGATAGTACTGTTT
1 ACATTACGATAGTACTGTTT
*
334536 ACATTGCGATAGTACTGTTT
1 ACATTACGATAGTACTGTTT
334556 AC
1 AC
334558 CTATATTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
ACATTACGATAGTACTGTTT
Found at i:334626 original size:57 final size:57
Alignment explanation
Indices: 334536--334658 Score: 210
Period size: 57 Copynumber: 2.2 Consensus size: 57
334526 AGTACTGTTT
* * * *
334536 ACATTGCGATAGTACTGTTTACCTATATTGGTAATTAGCGTTGCGAATTTGAAAATC
1 ACATTGCGATAGTACTGTTTACCTAAATCGGTAAATACCGTTGCGAATTTGAAAATC
334593 ACATTGCGATAGTACTGTTTACCTAAATCGGTAAATACCGTTGCGAATTTGAAAATC
1 ACATTGCGATAGTACTGTTTACCTAAATCGGTAAATACCGTTGCGAATTTGAAAATC
334650 ACATTGCGA
1 ACATTGCGA
334659 ATTTGGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (57 bp):
ACATTGCGATAGTACTGTTTACCTAAATCGGTAAATACCGTTGCGAATTTGAAAATC
Found at i:334741 original size:20 final size:20
Alignment explanation
Indices: 334700--334789 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
334690 GAACTCTAAT
*
334700 TTCGCAACTC-ATTTTCGGAAA
1 TTCGCAACGCAATTTTC--AAA
*
334721 -TCGCAACGTAATTTTCCAAA
1 TTCGCAACGCAATTTT-CAAA
* *
334741 TTCGCAATGCGATTTTCAAA
1 TTCGCAACGCAATTTTCAAA
* *
334761 TTCCCAACGCGATTTTCAAA
1 TTCGCAACGCAATTTTCAAA
334781 TTCGCAACG
1 TTCGCAACG
334790 GTAATTACCG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
20 40 0.69
21 17 0.29
22 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
TTCGCAACGCAATTTTCAAA
Found at i:334745 original size:41 final size:41
Alignment explanation
Indices: 334700--334788 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 41
334690 GAACTCTAAT
* *
334700 TTCGCAACT-C-ATTTTCGGAAA-TCGCAACGTAATTTTCCAAA
1 TTCGCAACTGCGATTTTC--AAATTCCCAACGCAATTTT-CAAA
*
334741 TTCGCAA-TGCGATTTTCAAATTCCCAACGCGATTTTCAAA
1 TTCGCAACTGCGATTTTCAAATTCCCAACGCAATTTTCAAA
334781 TTCGCAAC
1 TTCGCAAC
334789 GGTAATTACC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
40 15 0.37
41 20 0.49
42 6 0.15
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (41 bp):
TTCGCAACTGCGATTTTCAAATTCCCAACGCAATTTTCAAA
Found at i:334837 original size:57 final size:57
Alignment explanation
Indices: 334769--335066 Score: 373
Period size: 57 Copynumber: 5.3 Consensus size: 57
334759 AATTCCCAAC
*
334769 GCGATTTTCAAATTCGCAACGGTAATTACCGATATAGGTAAACAGTACTATCGCAAT
1 GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
334826 GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
1 GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
* * *
334883 ACGATTTTCAAATTCGCAACGCTAATTACCGATATTGGTAAACAATACTATCGCAAT
1 GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
*** * * * *
334940 --G-TAAACAGTACTATCACTATCGC-AA-T-GCG----AGGTAAACAGTACTATCGCAAT
1 GCGATTTTCA--AAT-TCGC-AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
* *
334991 GCGATTTTCAAATTCGCAACGCTAATTATCGATATAGGTAAATAGTACTATCGCAAT
1 GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
335048 GCGATTTTCAAATTCGCAA
1 GCGATTTTCAAATTCGCAA
335067 TGCGATTTTC
Statistics
Matches: 206, Mismatches: 21, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
50 4 0.02
51 25 0.12
52 3 0.01
53 3 0.01
54 6 0.03
55 3 0.01
56 3 0.01
57 155 0.75
58 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (57 bp):
GCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
Found at i:335103 original size:20 final size:20
Alignment explanation
Indices: 335041--335094 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
335031 AATAGTACTA
335041 TCGCAATGCGATTTTCAAAT
1 TCGCAATGCGATTTTCAAAT
335061 TCGCAATGCGATTTTCAAAT
1 TCGCAATGCGATTTTCAAAT
*
335081 TCGCAACGCGATTT
1 TCGCAATGCGATTT
335095 ACATATTCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
TCGCAATGCGATTTTCAAAT
Found at i:336607 original size:6 final size:6
Alignment explanation
Indices: 336596--336628 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
336586 CGAACAAAAT
*
336596 TTCTTG TTCTTG TTCTTG TTCTTG TTCGTG TTC
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTC
336629 ATTCGTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.64
Consensus pattern (6 bp):
TTCTTG
Found at i:347611 original size:22 final size:22
Alignment explanation
Indices: 347586--347630 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
347576 AAACTAGCGT
*
347586 ACAATATAACTAATGTGTGTGC
1 ACAATAGAACTAATGTGTGTGC
*
347608 ACAATAGAACTACTGTGTGTGC
1 ACAATAGAACTAATGTGTGTGC
347630 A
1 A
347631 ACGGAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (22 bp):
ACAATAGAACTAATGTGTGTGC
Found at i:349975 original size:51 final size:51
Alignment explanation
Indices: 349915--350020 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
349905 CGATCGAATA
349915 CGACATAAAAAGATAACACGAACACGATACGAACATAACATATATTGCTAT
1 CGACATAAAAAGATAACACGAACACGATACGAACATAACATATATTGCTAT
349966 CGACATAAAAAGATAACACGAACACGATACGAACATAACATATATTGCTAT
1 CGACATAAAAAGATAACACGAACACGATACGAACATAACATATATTGCTAT
350017 CGAC
1 CGAC
350021 GGACGAAGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (51 bp):
CGACATAAAAAGATAACACGAACACGATACGAACATAACATATATTGCTAT
Found at i:359659 original size:60 final size:60
Alignment explanation
Indices: 359566--359724 Score: 248
Period size: 60 Copynumber: 2.6 Consensus size: 60
359556 ACGTAGTTAA
** * *
359566 AAAACCTAAAGACCGATGTAGGTAATCGTTGTTACTTAGGGAAATTTAGGTAATCGCATG
1 AAAACCTAATTACCGATGTAGGTAATCATTGTTACTTAGGAAAATTTAGGTAATCGCATG
359626 AAAACCTAATTACCGATGTAGGTAATCATTGTTACTTAGGAAAATTTAGGTAATCGCATG
1 AAAACCTAATTACCGATGTAGGTAATCATTGTTACTTAGGAAAATTTAGGTAATCGCATG
**
359686 AAAGTCTAATTACCGATGTAGGTAAT-ATTTGTTACTTAG
1 AAAACCTAATTACCGATGTAGGTAATCA-TTGTTACTTAG
359725 CCCAGCGTGT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 91 0.99
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (60 bp):
AAAACCTAATTACCGATGTAGGTAATCATTGTTACTTAGGAAAATTTAGGTAATCGCATG
Found at i:359810 original size:24 final size:24
Alignment explanation
Indices: 359753--359810 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
359743 CTACCCCTCA
*
359753 GATGGTCTCGGTCGAATGCGCTCG
1 GATGCTCTCGGTCGAATGCGCTCG
* * *
359777 GATGCCCTCGGTCGGATG-GCCTTG
1 GATGCTCTCGGTCGAATGCG-CTCG
359801 GATGCTCTCG
1 GATGCTCTCG
359811 CATAACTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.26
Consensus pattern (24 bp):
GATGCTCTCGGTCGAATGCGCTCG
Found at i:361695 original size:2 final size:2
Alignment explanation
Indices: 361688--361713 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
361678 ATACAAGTAG
361688 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
361714 GTGTGTGCGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:371442 original size:4 final size:4
Alignment explanation
Indices: 371433--371460 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
371423 GTATTTGTAG
371433 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
371461 TCAACTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:375925 original size:32 final size:32
Alignment explanation
Indices: 375858--375926 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
375848 ACATGTATCG
* ***
375858 CATCATCATTTTGGATGATATAACACATGTTA
1 CATCATCACTTTGGATGATATAACACATACCA
* *
375890 CATCATTACTTTGGATGATATGACACATACCA
1 CATCATCACTTTGGATGATATAACACATACCA
375922 CATCA
1 CATCA
375927 ACAATATGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (32 bp):
CATCATCACTTTGGATGATATAACACATACCA
Found at i:378548 original size:186 final size:182
Alignment explanation
Indices: 378234--378621 Score: 600
Period size: 186 Copynumber: 2.1 Consensus size: 182
378224 ATTAAATTTT
378234 AAATATTAAATATATTATATATAACATATGTGCTCAGCCCAAACCATTCAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGTGCTCAGCCCAAACCATTCAAAACCCAATTAATAA
* **
378299 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTAAAATTT
*
378364 TTATTTTATAATAATATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAAA
131 TTATTTTATAATAATATATTATTTAAATTAATTAT-AA-T-TTTTTTTGAATT-AA
* * * *
378420 AAATATTATATATATTATATATAACATATAG-GCTCAGCTCAAACCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATAT-GTGCTCAGCCCAAACCATTCAAAACCCAATTAATA
* *
378484 ATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAGTTAATTAAAAAAATTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTAAAATT
*
378549 TTTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAA
130 TTTATTTTATAATAATATATTATTTAAATTAATTATAATTTTTTTTGAATTAA
* *
378602 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
378622 AATTATAAAT
Statistics
Matches: 187, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
181 8 0.04
182 11 0.06
183 12 0.06
184 1 0.01
185 2 0.01
186 152 0.81
187 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGTGCTCAGCCCAAACCATTCAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTAAAATTT
TTATTTTATAATAATATATTATTTAAATTAATTATAATTTTTTTTGAATTAA
Found at i:381154 original size:37 final size:38
Alignment explanation
Indices: 381105--381180 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
381095 TTTAAAAAGA
381105 TATGAAACAATTTTAAAATT-AAATTTTCTTTGATTTC
1 TATGAAACAATTTTAAAATTCAAATTTTCTTTGATTTC
* *
381142 TATGAAATAATTTTATAATTCAAATTTTCTTTGATTTC
1 TATGAAACAATTTTAAAATTCAAATTTTCTTTGATTTC
381180 T
1 T
381181 TGATGAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 18 0.50
38 18 0.50
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (38 bp):
TATGAAACAATTTTAAAATTCAAATTTTCTTTGATTTC
Found at i:382894 original size:15 final size:16
Alignment explanation
Indices: 382856--382896 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
382846 CCAGAGCCTC
* *
382856 TGAATCATTCAGCATT
1 TGAATCATTCAGAACT
382872 TGAATCATTCAGAACT
1 TGAATCATTCAGAACT
382888 T-AATCATTC
1 TGAATCATTC
382897 TGAAGTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGAACT
Found at i:390902 original size:18 final size:18
Alignment explanation
Indices: 390879--390915 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
390869 TTCTAATCGA
390879 TTATTTTTTCATTT-TAAT
1 TTATTTTTT-ATTTGTAAT
390897 TTATTTTTTATTTGTAAT
1 TTATTTTTTATTTGTAAT
390915 T
1 T
390916 GCTATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (18 bp):
TTATTTTTTATTTGTAAT
Found at i:391362 original size:18 final size:19
Alignment explanation
Indices: 391339--391387 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
391329 CATTAAAACG
391339 TTTATTTTTTCA-TTTT-AA
1 TTTATTTTTT-ATTTTTAAA
391357 TTTATTTTTTATTTTTAAAA
1 TTTATTTTTTATTTTT-AAA
391377 TTTATTTTTTA
1 TTTATTTTTTA
391388 ATATTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.04
18 14 0.50
20 13 0.46
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTTTTATTTTTAAA
Found at i:391394 original size:20 final size:20
Alignment explanation
Indices: 391355--391396 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
391345 TTTTCATTTT
* *
391355 AATTTATTTTTTATTTTTAA
1 AATTTATTTTTTAATATTAA
391375 AATTTATTTTTTAATATTAA
1 AATTTATTTTTTAATATTAA
391395 AA
1 AA
391397 AATAAGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTATTTTTTAATATTAA
Found at i:398153 original size:3 final size:3
Alignment explanation
Indices: 398145--398184 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
398135 TAGCACAATA
398145 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
398185 TAAGATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:401475 original size:290 final size:289
Alignment explanation
Indices: 400951--401524 Score: 995
Period size: 290 Copynumber: 2.0 Consensus size: 289
400941 TCTTTTCAAG
** *
400951 GTTAATTGAAAGTGGAACATACCATGCAATCAGAGAGGTCAAAATAAGACGGTGACAAAGGAAAT
1 GTTAATTGAAAGCAGAACATACCATGCAATCAGAGAGGTCAAAATAAGACAGTGACAAAGGAAAT
* * * *
401016 TGATAAACTGTGAATAATATCAACAATATACTAATAGACTATTTCTGCTCATATTAGTTTAAACA
66 TGATAAACTGTGAATAATATCAAAAATATACTAATAGACCATGTCTGCTCAGATTAGTTTAAACA
* * *
401081 GTACGGTTATTTCTGACCATCAAACCGAAGCTCTATATCCCTAGAGGGCCCGGATTCGAGCAGTT
131 GTACAGTTATTTCCGACCATCAAACCGAAGCTCTATATCCCTAGAGGACCCGGATTCGAGCAGTT
*
401146 AATTGCAAAACACCGCAAGGCAAGTACATTTTGCTATATAAAAACGAAGAATGAAAGCTAACCTT
196 AATTGCAAAACACCGCAAGGCAAGTAAATTTTGCTATATAAAAACGAAGAATGAAAGCTAACCTT
401211 CTCTTATCATTTCTCGGAGCAACAGTACA
261 CTCTTATCATTTCTCGGAGCAACAGTACA
* *
401240 GTTATTTGAAAGCAGAACATACCATGCAATTAGAGAGGTCAAAATAAGACAGTGACAAAGGAAAA
1 GTTAATTGAAAGCAGAACATACCATGCAATCAGAGAGGTCAAAATAAGACAGTGACAAAGG-AAA
*
401305 TTGATAAACTGTGAATAATATCAAAAATATGCTAATAGACCATGTCTGCTCAGATTAGTTTAAAC
65 TTGATAAACTGTGAATAATATCAAAAATATACTAATAGACCATGTCTGCTCAGATTAGTTTAAAC
401370 AGTACAGTTATTTCCGACCATCAAACCGAAGCTCTATATCCCTAGAGGACCCGGATTCGAGCAGT
130 AGTACAGTTATTTCCGACCATCAAACCGAAGCTCTATATCCCTAGAGGACCCGGATTCGAGCAGT
* *
401435 TAATTGCAAAACACCGTAAGGCAAGTAAATTTTGCTATATAAAAACGAAGGATGAAAGCTAACCT
195 TAATTGCAAAACACCGCAAGGCAAGTAAATTTTGCTATATAAAAACGAAGAATGAAAGCTAACCT
401500 TCTCTTATCATTTCTCGGAGCAACA
260 TCTCTTATCATTTCTCGGAGCAACA
401525 TAAATGCATT
Statistics
Matches: 268, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
289 56 0.21
290 212 0.79
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (289 bp):
GTTAATTGAAAGCAGAACATACCATGCAATCAGAGAGGTCAAAATAAGACAGTGACAAAGGAAAT
TGATAAACTGTGAATAATATCAAAAATATACTAATAGACCATGTCTGCTCAGATTAGTTTAAACA
GTACAGTTATTTCCGACCATCAAACCGAAGCTCTATATCCCTAGAGGACCCGGATTCGAGCAGTT
AATTGCAAAACACCGCAAGGCAAGTAAATTTTGCTATATAAAAACGAAGAATGAAAGCTAACCTT
CTCTTATCATTTCTCGGAGCAACAGTACA
Found at i:404779 original size:30 final size:30
Alignment explanation
Indices: 404717--404796 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
404707 GTACCTATGT
* * *
404717 TTTTTGTCCAATTTGGTACTTAAATTTTTCA
1 TTTTT-TCCAATTTGGTACATAAACTTGTCA
*
404748 TTTTTTCCAATTTGGTACATGAACTTGTCA
1 TTTTTTCCAATTTGGTACATAAACTTGTCA
* *
404778 TTTTGTTCTAATGTGGTAC
1 TTTT-TTCCAATTTGGTAC
404797 CTGTCGTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 25 0.60
31 17 0.40
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (30 bp):
TTTTTTCCAATTTGGTACATAAACTTGTCA
Found at i:406095 original size:25 final size:25
Alignment explanation
Indices: 406067--406115 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
406057 TTTATTTTCT
*
406067 TTTTCTATAAAATTCTT-TAAATTTA
1 TTTTCTACAAAATT-TTATAAATTTA
*
406092 TTTTCTCCAAAATTTTATAAATTT
1 TTTTCTACAAAATTTTATAAATTT
406116 TAAATTAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTCTACAAAATTTTATAAATTTA
Found at i:413501 original size:27 final size:27
Alignment explanation
Indices: 413471--413537 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 27
413461 CTTTATTTTG
413471 TTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
* *
413498 TTCGGGTTGAGTTTTTTTAAGTGTGATA
1 TTCGGGTCG-GGTTTTTTAAGTGTGATA
413526 TTCGGGTCGGGT
1 TTCGGGTCGGGT
413538 CGGGTCGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.13, C:0.07, G:0.34, T:0.45
Consensus pattern (27 bp):
TTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:414152 original size:16 final size:18
Alignment explanation
Indices: 414127--414172 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
414117 TATGGAATTG
*
414127 GATTCCAATTCC-T-ACA
1 GATTCTAATTCCTTCACA
414143 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
*
414161 GATTTTAATTCC
1 GATTCTAATTCC
414173 CTCATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:418327 original size:12 final size:12
Alignment explanation
Indices: 418310--418334 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
418300 TGGTTTTGTT
418310 AAAAAAATAATA
1 AAAAAAATAATA
418322 AAAAAAATAATA
1 AAAAAAATAATA
418334 A
1 A
418335 CGTTTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:418782 original size:21 final size:21
Alignment explanation
Indices: 418758--418803 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
418748 GTATAATATT
*
418758 GCAATTTATCTTTAAGTTGAG
1 GCAACTTATCTTTAAGTTGAG
418779 GCAACTTATCTTTAAGTTGAG
1 GCAACTTATCTTTAAGTTGAG
418800 GCAA
1 GCAA
418804 ATATCGTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (21 bp):
GCAACTTATCTTTAAGTTGAG
Found at i:428482 original size:109 final size:112
Alignment explanation
Indices: 428288--428505 Score: 316
Period size: 109 Copynumber: 2.0 Consensus size: 112
428278 CCGCGCAGTA
* *
428288 CCCAAAAAATCCCAAAAAAAAAGTATATATATAGTGACGTTTTTCCAATAAACGCCACTATAGAT
1 CCCAAAAAATACC-AAAAAAAAGTATATATATAGTGACGTTTTTCCAATAAACACCACTATAGAT
*
428353 ATACCTATTGCGACGGTTTTTC-AAAAAACGCCACTATTATTGCGCAG
65 AGACCTATTGCGACGGTTTTTCAAAAAAACGCCACTATTATTGCGCAG
** *
428400 CCCAAAAAATACC-AAAAAAAGTAT-TATATAGTGGTGTTTTTCCAATAAACACCACTATAGATG
1 CCCAAAAAATACCAAAAAAAAGTATATATATAGTGACGTTTTTCCAATAAACACCACTATAGATA
* * * *
428463 GACTTATTGCGCCGTTTTTTCAAAAAAACGCCACTATTGTTGC
66 GACCTATTGCGACGGTTTTTCAAAAAAACGCCACTATTATTGC
428506 CCCAAGATCG
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 52 0.55
110 31 0.33
112 12 0.13
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (112 bp):
CCCAAAAAATACCAAAAAAAAGTATATATATAGTGACGTTTTTCCAATAAACACCACTATAGATA
GACCTATTGCGACGGTTTTTCAAAAAAACGCCACTATTATTGCGCAG
Found at i:439995 original size:12 final size:12
Alignment explanation
Indices: 439978--440003 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
439968 AATTAACGGG
439978 ATTTGAAATAAT
1 ATTTGAAATAAT
439990 ATTTGAAATAAT
1 ATTTGAAATAAT
440002 AT
1 AT
440004 AAACAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTGAAATAAT
Found at i:442374 original size:4 final size:4
Alignment explanation
Indices: 442367--442393 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
442357 ATATTCTTAA
442367 ATCT ATCT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATCT ATC
442394 ACTATATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
ATCT
Found at i:445276 original size:3 final size:3
Alignment explanation
Indices: 445268--445322 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
445258 TTATCTAAAT
445268 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
445316 ATA ATA A
1 ATA ATA A
445323 GTGTAAACCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:454249 original size:27 final size:27
Alignment explanation
Indices: 454211--454270 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
454201 ATTTTGTTCA
454211 GGTCGGGTTTTTTAAGTGTGATATGCG
1 GGTCGGGTTTTTTAAGTGTGATATGCG
*
454238 GGTCGGGTTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTAAGTGTGATATGCG
*
454265 AGTCGG
1 GGTCGG
454271 ATTGGATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.15, C:0.08, G:0.37, T:0.40
Consensus pattern (27 bp):
GGTCGGGTTTTTTAAGTGTGATATGCG
Found at i:456752 original size:31 final size:31
Alignment explanation
Indices: 456717--456814 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
456707 TTATTCTCGC
456717 ATAATATTAACGTGTGTCATTAGATCCTGAA
1 ATAATATTAACGTGTGTCATTAGATCCTGAA
* * * * *
456748 ATAATTTTATAGGT-TG-GATT--ATTCTCG-C
1 ATAATATTA-ACGTGTGTCATTAGATCCT-GAA
*
456776 ATAATATTAACGTGTATCATTAGATCCTGAA
1 ATAATATTAACGTGTGTCATTAGATCCTGAA
456807 ATAATATT
1 ATAATATT
456815 TCTATATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
27 3 0.06
28 13 0.27
29 4 0.08
30 4 0.08
31 22 0.45
32 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (31 bp):
ATAATATTAACGTGTGTCATTAGATCCTGAA
Found at i:467464 original size:78 final size:77
Alignment explanation
Indices: 467329--467482 Score: 218
Period size: 78 Copynumber: 2.0 Consensus size: 77
467319 CGCGGGGTAT
* * * * *
467329 ATATATCTGAGGAGCATAAACCCTAATATGCCATTTTAGCGGGTAAAAGCTTGTTTAAGCCCAAT
1 ATATATATGAGGAGCATAAACCCTAATATACCATTTTAGCGGGTAAAACCCTCTTTAAGCCC-AT
467394 TAACATGACTCGG
65 TAACATGACTCGG
* * *
467407 ATATATATGCGGAGCATAAACCCTAATTTACGATTTTAGCGGGTAAAACCCTCTTTAAGCCCATT
1 ATATATATGAGGAGCATAAACCCTAATATACCATTTTAGCGGGTAAAACCCTCTTTAAGCCCATT
*
467472 AATATGACTCG
66 AACATGACTCG
467483 TAGCCCAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 13 0.19
78 54 0.81
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (77 bp):
ATATATATGAGGAGCATAAACCCTAATATACCATTTTAGCGGGTAAAACCCTCTTTAAGCCCATT
AACATGACTCGG
Found at i:467792 original size:28 final size:28
Alignment explanation
Indices: 467707--467793 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
467697 ATAATATTTA
*
467707 AAATAATTAAAATAATATATTTT-TTA-
1 AAATAATTATAATAATATATTTTATTAT
* * *
467733 ACAATATATTTATAATTATTTATTATATTAT
1 A-AATA-A-TTATAATAATATATTTTATTAT
* *
467764 AAATAGTTATAATAATATATTTTACTAT
1 AAATAATTATAATAATATATTTTATTAT
467792 AA
1 AA
467794 CTTTTATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 21 0.45
29 13 0.28
30 7 0.15
31 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (28 bp):
AAATAATTATAATAATATATTTTATTAT
Found at i:475077 original size:23 final size:23
Alignment explanation
Indices: 475028--475078 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
475018 TGTGACACGT
* * *
475028 TTTTCTCTGTCTTTATAATATGT
1 TTTTCTATGTCTTTATAATACGA
* *
475051 TTTTCTATGTCTTTGTAGTACGA
1 TTTTCTATGTCTTTATAATACGA
475074 TTTTC
1 TTTTC
475079 ATTTTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.59
Consensus pattern (23 bp):
TTTTCTATGTCTTTATAATACGA
Found at i:475610 original size:3 final size:3
Alignment explanation
Indices: 475602--475671 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
475592 AATGATAAAC
475602 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
475650 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
475672 TAAATTGATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:482090 original size:104 final size:105
Alignment explanation
Indices: 481948--482157 Score: 356
Period size: 104 Copynumber: 2.0 Consensus size: 105
481938 CTAATAACAT
*
481948 ACATAAACGTAGAAAACCACTAATATATTGCATAAACCAGTCTCTACAAGTTATGAAATCCATAA
1 ACATAAACGTAGAAAACCAATAATATATTGCATAAACCAGTCTCTACAAGTTATGAAA-CCATAA
482013 ACAGAACCCTTAAGGTATGGTTTTC-TCAGTGTGTTCAACAAA
65 ACAGAACCCTTAAGGTATGGTTTTCTTCA--GTGTTCAACAAA
482055 ACATAAACGTAG-AAACCAAT-A-ATATTGCATAAACCAGTCTCTACAAGTTATGAAACCATAAA
1 ACATAAACGTAGAAAACCAATAATATATTGCATAAACCAGTCTCTACAAGTTATGAAACCATAAA
482117 CAGAACCCTTAAGGTATGGTTTTCTTCAGTGTTCAACAAA
66 CAGAACCCTTAAGGTATGGTTTTCTTCAGTGTTCAACAAA
482157 A
1 A
482158 GATAGGATCC
Statistics
Matches: 101, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
102 13 0.13
103 31 0.31
104 37 0.37
105 1 0.01
106 7 0.07
107 12 0.12
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (105 bp):
ACATAAACGTAGAAAACCAATAATATATTGCATAAACCAGTCTCTACAAGTTATGAAACCATAAA
CAGAACCCTTAAGGTATGGTTTTCTTCAGTGTTCAACAAA
Found at i:484337 original size:17 final size:18
Alignment explanation
Indices: 484300--484340 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
484290 ATATTATGTA
*
484300 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
484318 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
484335 TTTACT
1 TTTACT
484341 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:486076 original size:141 final size:141
Alignment explanation
Indices: 485822--486103 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
485812 ATCATCATCA
485822 TCGGAGTTGAATTGTGGTGATTCTGGGTGAATGAATAGTCCGGTCTCAGCACCATTCGCACCAGG
1 TCGGAGTTGAATTGTGGTGATTCTGGGTGAATGAATAGTCCGGTCTCAGCACCATTCGCACCAGG
485887 CTCACGAAGCGGTTCTTCTGGTGGAGATGATGCTTCCTCCATGCGCTCCACATTTAGGTCGAAGA
66 CTCACGAAGCGGTTCTTCTGGTGGAGATGATGCTTCCTCCATGCGCTCCACATTTAGGTCGAAGA
485952 ACCTACTACTT
131 ACCTACTACTT
485963 TCGGAGTTGAATTGTGGTGATTCTGGGTGAATGAATAGTCCGGTCTCAGCACCATTCGCACCAGG
1 TCGGAGTTGAATTGTGGTGATTCTGGGTGAATGAATAGTCCGGTCTCAGCACCATTCGCACCAGG
486028 CTCACGAAGCGGTTCTTCTGGTGGAGATGATGCTTCCTCCATGCGCTCCACATTTAGGTCGAAGA
66 CTCACGAAGCGGTTCTTCTGGTGGAGATGATGCTTCCTCCATGCGCTCCACATTTAGGTCGAAGA
486093 ACCTACTACTT
131 ACCTACTACTT
486104 GCATGTCTTC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (141 bp):
TCGGAGTTGAATTGTGGTGATTCTGGGTGAATGAATAGTCCGGTCTCAGCACCATTCGCACCAGG
CTCACGAAGCGGTTCTTCTGGTGGAGATGATGCTTCCTCCATGCGCTCCACATTTAGGTCGAAGA
ACCTACTACTT
Found at i:490482 original size:60 final size:60
Alignment explanation
Indices: 490388--490547 Score: 178
Period size: 60 Copynumber: 2.6 Consensus size: 60
490378 TCCCTTATAT
* * * * *
490388 TAAATTGATCCTTAAACTTTTAAATGTTCCAATTTCATCCCTAAACTATGA-CTATCATGC
1 TAAATTAATCCTTAAATTTTTGAATATTCCAATTTCATCCCCAAACTATGACCT-TCATGC
** *
490448 TAAATTAATCCTTAAATTTTTGAATATTTTAATTTCATCCCCAAACTATGACCTTCATTC
1 TAAATTAATCCTTAAATTTTTGAATATTCCAATTTCATCCCCAAACTATGACCTTCATGC
** * * *
490508 TAAATTAATCCCCAAACTTTTTGAACATTACAGTTTCATC
1 TAAATTAATCCTTAAA-TTTTTGAATATTCCAATTTCATC
490548 TGAAACTATA
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 63 0.75
61 21 0.25
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTAATCCTTAAATTTTTGAATATTCCAATTTCATCCCCAAACTATGACCTTCATGC
Found at i:491255 original size:24 final size:24
Alignment explanation
Indices: 491223--491270 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
491213 TGAATAGTTG
491223 AGTGATCATTTTGTAACTTTTAAT
1 AGTGATCATTTTGTAACTTTTAAT
491247 AGTGATCATTTTGTAACTTTTAAT
1 AGTGATCATTTTGTAACTTTTAAT
491271 GGTTAGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (24 bp):
AGTGATCATTTTGTAACTTTTAAT
Found at i:495463 original size:16 final size:16
Alignment explanation
Indices: 495444--495477 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
495434 CAATATACGA
495444 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
495460 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
495476 AT
1 AT
495478 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:495549 original size:14 final size:16
Alignment explanation
Indices: 495513--495549 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
495503 CATATATGTA
495513 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
495530 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
495545 T-AATA
1 TGAATA
495550 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:495784 original size:25 final size:24
Alignment explanation
Indices: 495736--495798 Score: 101
Period size: 24 Copynumber: 2.6 Consensus size: 24
495726 ACAATTTATC
495736 AAATATAATATTTT-TATTGTAAAA
1 AAATATAATATTTTCTATTGT-AAA
495760 AAATATAATATTTTCTATTGTAAA
1 AAATATAATATTTTCTATTGTAAA
*
495784 AAACATAATATTTTC
1 AAATATAATATTTTC
495799 CCATCATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
24 31 0.84
25 6 0.16
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (24 bp):
AAATATAATATTTTCTATTGTAAA
Found at i:496241 original size:130 final size:130
Alignment explanation
Indices: 496037--496284 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
496027 AATTTTATTC
* *
496037 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
496102 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
496167 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
496232 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
496285 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:496730 original size:35 final size:35
Alignment explanation
Indices: 496680--496755 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
496670 AATTGAATTT
* *
496680 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
496715 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
496750 AATTGA
1 AATTGA
496756 GGTCTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:507564 original size:12 final size:12
Alignment explanation
Indices: 507547--507576 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
507537 TTAGTAAAAT
507547 AAAGCACGGTGA
1 AAAGCACGGTGA
507559 AAAGCACGGTGA
1 AAAGCACGGTGA
507571 AAAGCA
1 AAAGCA
507577 AACTTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.30, T:0.07
Consensus pattern (12 bp):
AAAGCACGGTGA
Found at i:520412 original size:2 final size:2
Alignment explanation
Indices: 520405--520482 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
520395 ATAAAATGTC
520405 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
520447 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
520483 AGTCCAAGTT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:529230 original size:23 final size:23
Alignment explanation
Indices: 529204--529256 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
529194 TGATACGTCG
* *
529204 TCATTTTGAATAAATGACATGTA
1 TCATGTTGAATAAATAACATGTA
* *
529227 TCATGTTGGATACATAACATGTA
1 TCATGTTGAATAAATAACATGTA
529250 TCATGTT
1 TCATGTT
529257 ATTCTTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (23 bp):
TCATGTTGAATAAATAACATGTA
Found at i:532819 original size:16 final size:16
Alignment explanation
Indices: 532798--532832 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
532788 ATTATTTTAA
* *
532798 TTTTTTGTCTTTTATT
1 TTTTTTCTCTTTCATT
532814 TTTTTTCTCTTTCATT
1 TTTTTTCTCTTTCATT
532830 TTT
1 TTT
532833 CAGTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTTCTCTTTCATT
Found at i:532896 original size:2 final size:2
Alignment explanation
Indices: 532889--532945 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
532879 TATTTTAATC
532889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
532931 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
532946 GCATGTTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:535458 original size:22 final size:24
Alignment explanation
Indices: 535411--535464 Score: 85
Period size: 22 Copynumber: 2.3 Consensus size: 24
535401 CTAAACCGGT
*
535411 GAACCGCTATTAGTGAACTGGCCA
1 GAACCGCTATTAGTGAACCGGCCA
535435 GAACCGCTA-TAGTG-ACCGGCCA
1 GAACCGCTATTAGTGAACCGGCCA
535457 GAACCGCT
1 GAACCGCT
535465 TAACCGTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 15 0.52
23 5 0.17
24 9 0.31
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (24 bp):
GAACCGCTATTAGTGAACCGGCCA
Found at i:537567 original size:22 final size:19
Alignment explanation
Indices: 537531--537591 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
537521 AAAATCGAAA
537531 TCGGTTTTTTTGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
***
537550 TCGGTTTTTTT--AAAGGT
1 TCGGTTTTTTTGGTTCGGT
* *
537567 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
537586 TCGGTT
1 TCGGTT
537592 CGATTTATCG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 12 0.39
19 19 0.61
ACGTcount: A:0.05, C:0.11, G:0.31, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTTGGTTCGGT
Found at i:539384 original size:21 final size:22
Alignment explanation
Indices: 539357--539419 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
539347 GCAACGAATA
539357 AATCGCAACGCGAACTTCGACT
1 AATCGCAACGCGAACTTCGACT
* * *
539379 -ATCGCAA--CGAATTTGGAAT
1 AATCGCAACGCGAACTTCGACT
539398 AAATCGCAACGCGAACTTCGAC
1 -AATCGCAACGCGAACTTCGAC
539420 CACGACCACG
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 9 0.29
21 14 0.45
23 8 0.26
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (22 bp):
AATCGCAACGCGAACTTCGACT
Found at i:539936 original size:6 final size:6
Alignment explanation
Indices: 539925--539949 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
539915 TCTCGGGTCG
539925 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
539950 ATGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:547372 original size:8 final size:8
Alignment explanation
Indices: 547359--547397 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
547349 TGTTAGTATT
547359 TTATTTAA
1 TTATTTAA
547367 TTATTTAA
1 TTATTTAA
547375 TTA-TT--
1 TTATTTAA
547380 TTATTTAA
1 TTATTTAA
547388 TTATTTAA
1 TTATTTAA
547396 TT
1 TT
547398 TTTTTGCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 3 0.11
6 2 0.07
7 2 0.07
8 21 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATTTAA
Done.