Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_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: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:390496 original size:31 final size:30
Alignment explanation
Indices: 390461--390541 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
390451 CTAAAATAGT
*
390461 GACTAAAT-TGATAGAATATGTAAATATTAAG
1 GACTAAATAT-ATA-AATATGCAAATATTAAG
* *
390492 GACTAAATATATAATTATGCCAATATTAAG
1 GACTAAATATATAAATATGCAAATATTAAG
*
390522 GACAAAATATATAAATATGC
1 GACTAAATATATAAATATGC
390542 TAATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 32 0.73
31 11 0.25
32 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (30 bp):
GACTAAATATATAAATATGCAAATATTAAG
Found at i:391011 original size:5 final size:5
Alignment explanation
Indices: 391001--391161 Score: 322
Period size: 5 Copynumber: 32.2 Consensus size: 5
390991 TAGATGAATA
391001 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
391051 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
391101 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
391151 ATTAT ATTAT A
1 ATTAT ATTAT A
391162 CCTACCAATC
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 156 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:392877 original size:228 final size:228
Alignment explanation
Indices: 392477--392889 Score: 582
Period size: 228 Copynumber: 1.8 Consensus size: 228
392467 AAATAGAGGT
** * *
392477 TTTATGGGTTTGGGGTTTTCAAAGTAAAGAAGCGTTTGAGACTGATTACAGGTAGAAAGTAATAT
1 TTTATGGGTTTCAGGTTTTCAAAGCAAAGAAGCGTTTGAGACCGATTACAGGTAGAAAGTAATAT
* ** * * * *
392542 TCTATGTAGAAAATAAATATTGATATTTTTATATAATATTATTTTAAGAAAATTATATTGTAGGT
66 TCTAGGTAGAAAATAAATATCAATACTTGTATATAATATTATTATAAGAAAATGATATTGTAGGT
* * *
392607 TGTATAATTGTACCGATACTTGTAATAGAGTATTCACATTCCTATGAAGGAAACCTTAGTTTGTT
131 TGTATAAATGTACCAATACTTGTAAGAGAGTATTCACATTCCTATGAAGGAAACCTTAGTTTGTT
392672 TAGTATTATAGTATTCAGAAATAGGGATTAGGG
196 TAGTATTATAGTATTCAGAAATAGGGATTAGGG
* * * *
392705 TTTATGGGTTTCAGGTTTTCAAAGCAAATAAG-GATTTGAGACCGATTAGAGTTAGAAAGTGATA
1 TTTATGGGTTTCAGGTTTTCAAAGCAAAGAAGCG-TTTGAGACCGATTACAGGTAGAAAGTAATA
392769 TTCTAGGTAGAAAA-AAATATCAATACTTGTATATAATATTA-TATATAGAAAATGATATTGTAG
65 TTCTAGGTAGAAAATAAATATCAATACTTGTATATAATATTATTATA-AGAAAATGATATTGTAG
* *
392832 GTTGTATAAATGTATCAATACTTGTAGTAGAGAGTATTC-CATTCCTTTGAAGGAAACC
129 GTTGTATAAATGTACCAATACTTGTA--AGAGAGTATTCACATTCCTATGAAGGAAACC
392890 GTCTTACTAT
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
226 3 0.02
227 63 0.39
228 85 0.53
229 10 0.06
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (228 bp):
TTTATGGGTTTCAGGTTTTCAAAGCAAAGAAGCGTTTGAGACCGATTACAGGTAGAAAGTAATAT
TCTAGGTAGAAAATAAATATCAATACTTGTATATAATATTATTATAAGAAAATGATATTGTAGGT
TGTATAAATGTACCAATACTTGTAAGAGAGTATTCACATTCCTATGAAGGAAACCTTAGTTTGTT
TAGTATTATAGTATTCAGAAATAGGGATTAGGG
Found at i:396441 original size:18 final size:18
Alignment explanation
Indices: 396395--396442 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
396385 GATGTAAACC
* *
396395 AAATTTTGTACGTGAATT
1 AAATTTTGTATGTGAATG
396413 ATAATTTTGTATGTGAATG
1 A-AATTTTGTATGTGAATG
*
396432 AAATTATGTAT
1 AAATTTTGTAT
396443 AAGATGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:399662 original size:198 final size:197
Alignment explanation
Indices: 399060--399976 Score: 1032
Period size: 198 Copynumber: 4.5 Consensus size: 197
399050 TTCAACATTT
* * * * *
399060 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACCAGTTAAATGAAAAA
1 ATTAATTTAAAGTAATAGGTAAATTTACAATGT-AGCGGTAAAAAGATACCA-TTTAATGACAAA
* * * *
399125 ATGCGTAAACATAAAGTTTCGATCCTTTTTGTAT-ATGTATCGATACTTTTTGTCCAGTATGCTT
64 ATACGTTAACATAAAG-TTCGATACTTTTTGTATGA-GTATCGATACTTTTTGTCAAGTATGCTT
* * * * * * *
399189 CCCAAACGAGATGCACATATAAAGTATCGATACACGTATGAAAAATATCAATTCTTAAAACTTCA
127 CCCAAACGAGATGCACACAGAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCG
399254 AAACCG
192 AAACCG
* **
399260 ATTAATTTAAAGTAATAGGTAAATTTTCAATGTTAGCGGTAAAAAGATATCGGTTTAATGACAAA
1 ATTAATTTAAAGTAATAGGTAAATTTACAATG-TAGCGGTAAAAAGATA-CCATTTAATGACAAA
* * *
399325 ATACGTTAACATAAAGTATCGATACTTTTT-TATGAGTATCAATACTTTTTGTCCAGTATTCTTC
64 ATACGTTAACATAAAGT-TCGATACTTTTTGTATGAGTATCGATACTTTTTGTCAAGTATGCTTC
* * *
399389 CCAAACTAGATACACACAGAAAATATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGA
128 CCAAACGAGATGCACACAGAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGA
*
399454 AACTG
193 AACCG
*
399459 ATTAATTTAAAGTAATAGGTAAATTTACAATGCTAGCGGTAAAAAGATACCGATTTAATGAAAAA
1 ATTAATTTAAAGTAATAGGTAAATTTACAATG-TAGCGGTAAAAAGATACC-ATTTAATGACAAA
* *
399524 ATACGTTAACATAAAG-TCGATACGTTTTGTATGAGTATCGATATTTTTTGTCAAGTATGCTTCC
64 ATACGTTAACATAAAGTTCGATACTTTTTGTATGAGTATCGATACTTTTTGTCAAGTATGCTTCC
* * * *
399588 CAAACTAAATGCACACATAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTTGAA
129 CAAACGAGATGCACACAGAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGAA
399653 ACCG
194 ACCG
* *
399657 ATTAATTTAAAGTAATAGGTAAATTTACTATGTTAGTGGTAAAAAGA-ATCCAATTTAATGACAA
1 ATTAATTTAAAGTAATAGGTAAATTTACAATG-TAGCGGTAAAAAGATA-CC-ATTTAATGACAA
* *
399721 AATATGTTAACATAAAGTATCGATACTTTTTATATGAGTATCGATACTTTTTATATGAGTATCGA
63 AATACGTTAACATAAAGT-TCGATACTTTTTGTATGAGTATCGATAC--TTT-T-T--G--TC-A
* * *
399786 TACTTTTTGTTCAGTAGGCTTCCCAAACGAGATGCACGCAGAAAGTATTGATACACATATGAAAA
118 -A------G-T-A-T--GCTTCCCAAACGAGATGCACACAGAAAGTATCGATACACATATCAAAA
* *
399851 GTATCGATTCTTAGAACTTCGAAACTG
171 GTATCGATTCTTAAAACTTCGAAACCG
* * *
399878 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCAGTTTAATGACAAA
1 ATTAATTTAAAGTAATAGGTAAATTTACAATGT-AGCGGTAAAAAGATACCA-TTTAATGACAAA
* * * *
399943 ATACGTAAATATAAATTATCGATACTTTTAGTAT
64 ATACGTTAACATAAAGT-TCGATACTTTTTGTAT
399977 ATGTGTAAAT
Statistics
Matches: 617, Mismatches: 67, Indels: 45
0.85 0.09 0.06
Matches are distributed among these distances:
197 12 0.02
198 168 0.27
199 164 0.27
200 104 0.17
201 2 0.00
202 3 0.00
203 1 0.00
204 1 0.00
206 1 0.00
208 2 0.00
209 1 0.00
210 1 0.00
216 1 0.00
217 1 0.00
218 1 0.00
219 1 0.00
220 2 0.00
221 150 0.24
222 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (197 bp):
ATTAATTTAAAGTAATAGGTAAATTTACAATGTAGCGGTAAAAAGATACCATTTAATGACAAAAT
ACGTTAACATAAAGTTCGATACTTTTTGTATGAGTATCGATACTTTTTGTCAAGTATGCTTCCCA
AACGAGATGCACACAGAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGAAAC
CG
Found at i:399801 original size:20 final size:21
Alignment explanation
Indices: 399736--399793 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
399726 GTTAACATAA
399736 AGTATCGATACTTTTTATATG
1 AGTATCGATACTTTTTATATG
399757 AGTATCGATACTTTTTATATG
1 AGTATCGATACTTTTTATATG
399778 AGTATCGATACTTTTT
1 AGTATCGATACTTTTT
399794 GTTCAGTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
AGTATCGATACTTTTTATATG
Found at i:399937 original size:221 final size:221
Alignment explanation
Indices: 399540--399971 Score: 634
Period size: 221 Copynumber: 2.0 Consensus size: 221
399530 TAACATAAAG
* * * *
399540 TCGATACGTTTTGTATGAGTATCGATATTTTTTGTCAAGTATGCTTCCCAAACTAAATGCACACA
1 TCGATACGTTTTATATGAGTATCGATACTTTTTGTCAAGTAGGCTTCCCAAACGAAATGCACACA
* *
399605 TAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTTGAAACCGATTAATTTAAAGT
66 GAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGAAACCGATTAATTTAAAGT
* * * *
399670 AATAGGTAAATTTACTATGTTAGTGGTAAAAAGAATCCAATTTAATGACAAAATATGTTAACATA
131 AATAGGTAAATTTACAATGTAAGTGGTAAAAAGAATCCAATTTAATGACAAAATACGTAAACATA
399735 AAGTATCGATACTTTTTATATGAGTA
196 AAGTATCGATACTTTTTATATGAGTA
* * *
399761 TCGATACTTTTTATATGAGTATCGATACTTTTTGTTC-AGTAGGCTTCCCAAACGAGATGCACGC
1 TCGATACGTTTTATATGAGTATCGATACTTTTTG-TCAAGTAGGCTTCCCAAACGAAATGCACAC
* * * * *
399825 AGAAAGTATTGATACACATATGAAAAGTATCGATTCTTAGAACTTCGAAACTGATTACTTTAAAG
65 AGAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGAAACCGATTAATTTAAAG
* * *
399890 TAATAGGTAAATTTACAATGTAAGTGGTAAAAA-TATACCAGTTTAATGACAAAATACGTAAATA
130 TAATAGGTAAATTTACAATGTAAGTGGTAAAAAGAAT-CCAATTTAATGACAAAATACGTAAACA
*
399954 TAAATTATCGATACTTTT
194 TAAAGTATCGATACTTTT
399972 AGTATATGTG
Statistics
Matches: 187, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
220 2 0.01
221 183 0.98
222 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (221 bp):
TCGATACGTTTTATATGAGTATCGATACTTTTTGTCAAGTAGGCTTCCCAAACGAAATGCACACA
GAAAGTATCGATACACATATCAAAAGTATCGATTCTTAAAACTTCGAAACCGATTAATTTAAAGT
AATAGGTAAATTTACAATGTAAGTGGTAAAAAGAATCCAATTTAATGACAAAATACGTAAACATA
AAGTATCGATACTTTTTATATGAGTA
Found at i:407537 original size:21 final size:23
Alignment explanation
Indices: 407513--407571 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
407503 AAATCAAGAC
* *
407513 GAGCATAGAAGAAAA-GA-AAAA
1 GAGCAAAGAAAAAAAGGAGAAAA
407534 GAGCAAAGAAAAAAAGGAGAAAA
1 GAGCAAAGAAAAAAAGGAGAAAA
**
407557 GAAAAAAGAAAAAAA
1 GAGCAAAGAAAAAAA
407572 AAGAGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.41
22 2 0.06
23 17 0.53
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.02
Consensus pattern (23 bp):
GAGCAAAGAAAAAAAGGAGAAAA
Found at i:407557 original size:16 final size:15
Alignment explanation
Indices: 407529--407597 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 15
407519 AGAAGAAAAG
*
407529 AAAAAGAGCAAAGAA
1 AAAAAGAGAAAAGAA
407544 AAAAAGGAGAAAAG--
1 AAAAA-GAGAAAAGAA
407558 AAAAA-AGAAAA-AA
1 AAAAAGAGAAAAGAA
*
407571 AAAGAGAGAAAAGAA
1 AAAAAGAGAAAAGAA
407586 AAATAA-AGAAAA
1 AAA-AAGAGAAAA
407598 AACAAAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.13
13 4 0.09
14 11 0.24
15 16 0.36
16 8 0.18
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (15 bp):
AAAAAGAGAAAAGAA
Found at i:407573 original size:40 final size:39
Alignment explanation
Indices: 407521--407610 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 39
407511 ACGAGCATAG
*
407521 AAGAAAAGAAAA-AGAGCAAAGAAAAA-AAGGAGAAAAGAAAA
1 AAGAAAA-AAAAGAGAGAAAAGAAAAATAA--AGAAAA-AAAA
*
407562 AAGAAAAAAAAAGAGAGAAAAGAAAAATAAAGAAAAAACA
1 AAG-AAAAAAAAGAGAGAAAAGAAAAATAAAGAAAAAAAA
407602 AAGAAAAAA
1 AAGAAAAAA
407611 GAGGACAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
39 6 0.14
40 6 0.14
41 13 0.30
42 17 0.39
43 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.01
Consensus pattern (39 bp):
AAGAAAAAAAAGAGAGAAAAGAAAAATAAAGAAAAAAAA
Found at i:407579 original size:26 final size:29
Alignment explanation
Indices: 407522--407588 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 29
407512 CGAGCATAGA
407522 AGAAAAGAAAAAGAGCAAAGAAAAAAAGG
1 AGAAAAGAAAAAGAGCAAAGAAAAAAAGG
407551 AGAAAAGAAAAA-AG--AA-AAAAAAAGAG
1 AGAAAAGAAAAAGAGCAAAGAAAAAAAG-G
407577 AGAAAAGAAAAA
1 AGAAAAGAAAAA
407589 TAAAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.22
26 15 0.41
28 2 0.05
29 12 0.32
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (29 bp):
AGAAAAGAAAAAGAGCAAAGAAAAAAAGG
Found at i:407588 original size:41 final size:40
Alignment explanation
Indices: 407521--407610 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
407511 ACGAGCATAG
* * *
407521 AAGAAAAGAAAAAGAGCAAAGAAAAAA-AGGAGAAAAGAAAA
1 AAGAAAAAAAAAAGAGAAAAGAAAAAATA-AAGAAAA-AAAA
*
407562 AAGAAAAAAAAAGAGAGAAAAG-AAAAATAAAGAAAAAACA
1 AAGAAAAAAAAA-AGAGAAAAGAAAAAATAAAGAAAAAAAA
407602 AAGAAAAAA
1 AAGAAAAAA
407611 GAGGACAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
40 12 0.28
41 22 0.51
42 9 0.21
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.01
Consensus pattern (40 bp):
AAGAAAAAAAAAAGAGAAAAGAAAAAATAAAGAAAAAAAA
Found at i:407597 original size:26 final size:24
Alignment explanation
Indices: 407538--407608 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 24
407528 GAAAAAGAGC
407538 AAAGAAAAAAAGGAGAAAAGAAAAA
1 AAAGAAAAAAA-GAGAAAAGAAAAA
*
407563 AGAAAAAAAAAGAGAGAAAAGAAAAA
1 A-AAGAAAAAA-AGAGAAAAGAAAAA
*
407589 TAAAGAAAAAACAAAGAAAA
1 -AAAGAAAAAA-AGAGAAAA
407609 AAGAGGACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 36 0.92
27 2 0.05
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (24 bp):
AAAGAAAAAAAGAGAAAAGAAAAA
Found at i:408775 original size:38 final size:37
Alignment explanation
Indices: 408733--408828 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 37
408723 TTGCGTGTTG
* *
408733 TTTCTCTTGAAACAAAATTTTGCCTCACTTGAGCCATT
1 TTTCTCTTGAAACAAAATTTCGCCTCACTTGAGACA-T
* * *
408771 TTTCTCTTAAAAC-AAATTTCGTCTCACTTGATACAT
1 TTTCTCTTGAAACAAAATTTCGCCTCACTTGAGACAT
408807 TTTC-CTTCGAAACAAAAATTTC
1 TTTCTCTT-GAAAC-AAAATTTC
408829 AAAGTCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 3 0.06
36 9 0.18
37 18 0.37
38 19 0.39
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTCGCCTCACTTGAGACAT
Found at i:408808 original size:37 final size:38
Alignment explanation
Indices: 408733--408809 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 38
408723 TTGCGTGTTG
* * *
408733 TTTCTCTTGAAACAAAATTTTGCCTCACTTGAGCCATT
1 TTTCTCTTAAAACAAAATTTCGCCTCACTTGAGACATT
* *
408771 TTTCTCTTAAAAC-AAATTTCGTCTCACTTGATACATT
1 TTTCTCTTAAAACAAAATTTCGCCTCACTTGAGACATT
408808 TT
1 TT
408810 CCTTCGAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (38 bp):
TTTCTCTTAAAACAAAATTTCGCCTCACTTGAGACATT
Found at i:408893 original size:66 final size:67
Alignment explanation
Indices: 408775--408940 Score: 248
Period size: 67 Copynumber: 2.5 Consensus size: 67
408765 GCCATTTTTC
* *
408775 TCTT-AAAACAAATTTCGTCTCACTTGATACA-TTTTCCTTCGAAACAAAAATTTCAAAG-TCAT
1 TCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCCTTCGAAACAAAAATTTCAAAGTTCAT
408837 TT
66 TT
* * **
408839 TCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCCTTCGGAACACAAATTTCAAAGTTGTT
1 TCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCCTTCGAAACAAAAATTTCAAAGTTCAT
408904 TT
66 TT
*
408906 TCTTAAAAACAAATTTTGTCTCGCTTGAGACATTT
1 TCTTAAAAACAAATTTTGTCTCACTTGAGACATTT
408941 CTCTCTCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
64 4 0.04
65 25 0.27
66 25 0.27
67 38 0.41
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (67 bp):
TCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCCTTCGAAACAAAAATTTCAAAGTTCAT
TT
Found at i:409103 original size:36 final size:36
Alignment explanation
Indices: 408999--409108 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 36
408989 TGAAATATTT
* **
408999 AGAACAAAATTGATCTCAAATGAGATAGTTTTCCTA
1 AGAACAAAATTAATCTCACTTGAGATAGTTTTCCTA
* ** * * * *
409035 AGAACAAATTTTGTCTCGCTAGAGACAATTTTCCTTA
1 AGAACAAAATTAATCTCACTTGAGATAGTTTTCC-TA
*
409072 A-AACAAAATTAATCTCACTTGAGATTGTTTTCTCTA
1 AGAACAAAATTAATCTCACTTGAGATAGTTTTC-CTA
409108 A
1 A
409109 AAAAAACAAA
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
36 51 0.93
37 4 0.07
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (36 bp):
AGAACAAAATTAATCTCACTTGAGATAGTTTTCCTA
Found at i:409180 original size:76 final size:76
Alignment explanation
Indices: 409037--409182 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
409027 TTTTCCTAAG
* * *
409037 AACAAATTTTGTCTCGCTAGAGACAATTTTCCTTAAAACAAAATTAATCTCACTTGAGATTGTTT
1 AACAAATTTTGTCTCACTAGAGACAATTTTCCTTAAAACAAAATTAATATCACTTGAGATAGTTT
409102 TCTCTAAAAAA
66 TCTCTAAAAAA
* * * **
409113 AACAAATTTTGTCTCACTTGATAC-ATTTTCCTCTCAAAACAAAGTTTGTATC-CTTTGAGATAG
1 AACAAATTTTGTCTCACTAGAGACAATTTTCCT-T-AAAACAAAATTAATATCAC-TTGAGATAG
409176 -TTTCTCT
63 TTTTCTCT
409183 TGAAACAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 8 0.14
76 30 0.51
77 21 0.36
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (76 bp):
AACAAATTTTGTCTCACTAGAGACAATTTTCCTTAAAACAAAATTAATATCACTTGAGATAGTTT
TCTCTAAAAAA
Found at i:409246 original size:65 final size:63
Alignment explanation
Indices: 409149--409386 Score: 264
Period size: 65 Copynumber: 3.7 Consensus size: 63
409139 TTTCCTCTCA
* *
409149 AAACAAAGTTTGTATC-CTTTGAGATAGTTTCTCTTGAAACAAAAAATCATTAAATATGTTTCCC
1 AAACAAA-TTTGTATCTC-TTGAGACAGTTTCTCTTGAAAC--AAAATC-TTGAATATGTTTCCC
409213 TTG
61 TTG
* * * * *
409216 AAACAAATTT-TATCTTTTGAGACATTTTCTCCTGAAACAAAATCTTTGAATCTATTTCCCTTG
1 AAACAAATTTGTATCTCTTGAGACAGTTTCTCTTGAAACAAAATC-TTGAATATGTTTCCCTTG
* * *
409279 AAACAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACATCTATGAATTTGTTTCCCTTG
1 AAAC-AAATTTGTATCTCTTGAGACAGTTTCTCTTGAAACAAAATCT-TGAATATGTTTCCCTTG
* * *
409344 AAACAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACAAA
1 AAACAAA-TTTGTATCTCTTGAGACAGTTTCTCTTGAAACAAA
409387 TTTTGTCTAT
Statistics
Matches: 148, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 25 0.17
64 10 0.07
65 103 0.70
66 3 0.02
67 7 0.05
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (63 bp):
AAACAAATTTGTATCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTGAATATGTTTCCCTTG
Found at i:409382 original size:130 final size:130
Alignment explanation
Indices: 409149--409459 Score: 339
Period size: 130 Copynumber: 2.3 Consensus size: 130
409139 TTTCCTCTCA
* * *
409149 AAACAAAGTTTGTATC-CTTTGAGATAGTTTCTCTTGAAACAAAAAATCATTAAATATGTTTCCC
1 AAACAAAATTTGTCTCTC-TTGAGACAGTTTCTCTTGAAAC--AAAATCATTAAATATGTTTCCC
*
409213 TTGAAACAAATTTTATCTTTTGAGACATTTTCTCCTGAAACAAAATCTTTG-AATC-T-A-TTTC
63 TTGAAACAAATTTTATCTCTTGAGACATTTTCTCCTGAAAC-AAAT-TTTGCAATCTTGAGTTTC
409274 CCTTG
126 CCTTG
* * *
409279 AAACAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACATC-TATGAATTTGTTTCCCTT
1 AAACAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCAT-TAAATATGTTTCCCTT
* * *
409343 GAAACAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTATCTTGAGGCAGT
65 GAAACAAATTTTATCT--CTTGAGACATTTTCTCCTGAAACAAATTTTG-CAATCTT---G-AGT
409408 TTCCCTTG
123 TTCCCTTG
*
409416 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTC-CTTTGAAACAAA
1 AAACAAA-ATTTGTCTCTCTTGAGACAGTTTCTC-TTGAAACAAA
409460 TTTTTCTCCC
Statistics
Matches: 154, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
127 1 0.01
128 38 0.25
129 4 0.03
130 59 0.38
131 2 0.01
136 1 0.01
137 17 0.11
138 32 0.21
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (130 bp):
AAACAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCATTAAATATGTTTCCCTTG
AAACAAATTTTATCTCTTGAGACATTTTCTCCTGAAACAAATTTTGCAATCTTGAGTTTCCCTTG
Found at i:409401 original size:21 final size:20
Alignment explanation
Indices: 409340--409401 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
409330 ATTTGTTTCC
*
409340 CTTGAAACAAATTTTGTCTCC
1 CTTGAAACAAATTTTGTCT-T
*
409361 CTTGAGAC--A-TTT-TC-T
1 CTTGAAACAAATTTTGTCTT
409376 CTTGAAACAAATTTTGTCTAT
1 CTTGAAACAAATTTTGTCT-T
409397 CTTGA
1 CTTGA
409402 GGCAGTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
15 7 0.22
17 3 0.09
18 6 0.19
19 3 0.09
21 13 0.41
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (20 bp):
CTTGAAACAAATTTTGTCTT
Found at i:409437 original size:37 final size:36
Alignment explanation
Indices: 409334--409531 Score: 209
Period size: 36 Copynumber: 5.3 Consensus size: 36
409324 CTATGAATTT
409334 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* * ** *
409370 TTTTCTCTTGAAACAAATTTTGTCTATCTTGAGGCA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
409406 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGACA
* *
409443 GTTTCCTTTGAAACAAATTTT-TCTCCCTCGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* *
409478 GTTTACAATTTCCCTTAAAACAAATTTTGTCTCCATTGAGACA
1 G-------TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
**
409521 GTGCCCCTTGA
1 GTTTCCCTTGA
409532 GATAGTTTAC
Statistics
Matches: 134, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
35 13 0.10
36 57 0.43
37 33 0.25
42 18 0.13
43 13 0.10
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:409596 original size:172 final size:167
Alignment explanation
Indices: 409371--409697 Score: 444
Period size: 172 Copynumber: 1.9 Consensus size: 167
409361 CTTGAGACAT
* * * **
409371 TTTCTCTTGAAACAAATTTTGTCTATCTTGAGGCAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCAATTGAAACAAAGTTTTGTCTCTCT
*
409436 TGAGACAGTTTCCTTTGAAACAAATTT-T-TCTCCCTCGAGACAGTTTACAATTTCCCTTAAAAC
66 TGAGACAGTTTCCCTTGAAAC-AATTTGTGTCTCCCTCGAGACAG-------TTTCCCTTAAAAC
409499 AAATTTTGTCTCCATTGAGACAGTGCCCCTTGAGATAGTTTACAG
123 AAATTTTGTCTCCATTGAGACAGTGCCCCTTGAGATAGTTTACAG
* *
409544 TTTCCCTTGAAACAGATTTT-TCTCCCTTGAGACAGTTTCAATTGAAACAAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCAATTGAAACAAAGTTTTGTCTCTCT
* * *
409608 TGAGACAGTTTCCCTTGAAACAATTTGTGTCTCCCTTGAGACAGTTTCCCTTGAAGCAAATTTTG
66 TGAGACAGTTTCCCTTGAAACAATTTGTGTCTCCCTCGAGACAGTTTCCCTTAAAACAAATTTTG
**
409673 TCTCCATTGAGACAGTTTCCCTTGA
131 TCTCCATTGAGACAGTGCCCCTTGA
409698 AACAAATTTT
Statistics
Matches: 139, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
166 42 0.30
171 5 0.04
172 60 0.43
173 32 0.23
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (167 bp):
TTTCCCTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCAATTGAAACAAAGTTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAATTTGTGTCTCCCTCGAGACAGTTTCCCTTAAAACAAATTTTG
TCTCCATTGAGACAGTGCCCCTTGAGATAGTTTACAG
Found at i:409639 original size:130 final size:131
Alignment explanation
Indices: 409404--409661 Score: 317
Period size: 130 Copynumber: 1.9 Consensus size: 131
409394 TATCTTGAGG
* **
409404 CAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCTTTGAAACAAATTTTTCTCC
1 CAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCAATTGAAACAAATTTTTCTCC
409469 CTCGAGACAGTTTACAATTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGTGCCCCTTGAGA
66 CTCGAGACAG------ATTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGTGCCCCTTGAGA
409534 TAGTTTA
125 TAGTTTA
*
409541 CAGTTTCCCTTGAAACAGA-TTTT-TCTCCCTTGAGACAGTTTCAATTGAAACAAAGTTTTGTCT
1 CAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCAATTGAAACAAA-TTTT-TCT
* * * * **
409604 CTCTTGAGACAG-TTTCCCTTGAAAC-AATTTGTGTCTCCCTTGAGACAGTTTCCCTTGA
64 CCCTCGAGACAGATTTCCCTTAAAACAAATTT-TGTCTCCATTGAGACAGTGCCCCTTGA
409662 AGCAAATTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
129 5 0.05
130 36 0.33
135 28 0.26
136 8 0.07
137 31 0.29
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (131 bp):
CAGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCAATTGAAACAAATTTTTCTCC
CTCGAGACAGATTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGTGCCCCTTGAGATAGTTT
A
Found at i:409646 original size:36 final size:36
Alignment explanation
Indices: 409540--409733 Score: 284
Period size: 36 Copynumber: 5.4 Consensus size: 36
409530 GAGATAGTTT
*
409540 ACAGTTTCCCTTGAAACAGATTTT-TCTCCCTTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
** *
409575 ACAGTTTCAATTGAAACAAAGTTTTGTCTCTCTTGAG
1 ACAGTTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAG
409612 ACAGTTTCCCTTGAAAC-AATTTGTGTCTCCCTTGAG
1 ACAGTTTCCCTTGAAACAAATTT-TGTCTCCCTTGAG
* *
409648 ACAGTTTCCCTTGAAGCAAATTTTGTCTCCATTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
*
409684 ACAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
*
409720 ACAGTCTCCCTTGA
1 ACAGTTTCCCTTGA
409734 GACAGTTTCC
Statistics
Matches: 142, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
35 20 0.14
36 92 0.65
37 30 0.21
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (36 bp):
ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
Found at i:409659 original size:15 final size:15
Alignment explanation
Indices: 409606--409748 Score: 70
Period size: 15 Copynumber: 8.3 Consensus size: 15
409596 TTTTGTCTCT
409606 CTTGAGACAGTTTCC
1 CTTGAGACAGTTTCC
*
409621 CTTGAAACAATTTGTGTCTCC
1 CTTGAGAC-A---GT-T-TCC
409642 CTTGAGACAGTTTCC
1 CTTGAGACAGTTTCC
* *
409657 CTTGAAGCAAATTTTGTCTC
1 CTTG-AG-ACA-GTT-TC-C
409677 CATTGAGACAGTTTCC
1 C-TTGAGACAGTTTCC
* *
409693 CTTGAAACAAATTTTGTCTC
1 CTTGAGAC--A-GTT-TC-C
*
409713 ACTTGAGACAGTCTCC
1 -CTTGAGACAGTTTCC
409729 CTTGAGACAGTTTCC
1 CTTGAGACAGTTTCC
409744 CTTGA
1 CTTGA
409749 AACAACCTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 36
0.67 0.08 0.25
Matches are distributed among these distances:
15 39 0.40
16 7 0.07
17 9 0.09
18 7 0.07
19 9 0.09
20 7 0.07
21 20 0.20
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (15 bp):
CTTGAGACAGTTTCC
Found at i:413465 original size:6 final size:6
Alignment explanation
Indices: 413456--413539 Score: 96
Period size: 6 Copynumber: 14.0 Consensus size: 6
413446 TTTGAGACTG
* * * *
413456 AATTTC AATTTC AATTTT AATTTG AGTTTG AATTTC AATTTC AATTTC
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* * * *
413504 AATTTT AATTTG AGTTTG AATTTC AATTTC AATTTC
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
413540 GACTCCACTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (6 bp):
AATTTC
Found at i:413516 original size:30 final size:30
Alignment explanation
Indices: 413434--413538 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
413424 ATTTATCCAG
* *
413434 TTTCAATTTTAATTTGAGA-CTGAATTTCAA
1 TTTCAATTTCAATTTGA-ATTTGAATTTCAA
* *
413464 TTTCAATTTTAATTTGAGTTTGAATTTCAA
1 TTTCAATTTCAATTTGAATTTGAATTTCAA
* * *
413494 TTTCAATTTCAATTTTAATTTGAGTTTGAA
1 TTTCAATTTCAATTTGAATTTGAATTTCAA
413524 TTTCAATTTCAATTT
1 TTTCAATTTCAATTT
413539 CGACTCCACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (30 bp):
TTTCAATTTCAATTTGAATTTGAATTTCAA
Found at i:413539 original size:36 final size:36
Alignment explanation
Indices: 413456--413539 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
413446 TTTGAGACTG
413456 AATTTCAATTTCAATTTTAATTTGAGTTTGAATTTC
1 AATTTCAATTTCAATTTTAATTTGAGTTTGAATTTC
413492 AATTTCAATTTCAATTTTAATTTGAGTTTGAATTTC
1 AATTTCAATTTCAATTTTAATTTGAGTTTGAATTTC
413528 AATTTCAATTTC
1 AATTTCAATTTC
413540 GACTCCACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (36 bp):
AATTTCAATTTCAATTTTAATTTGAGTTTGAATTTC
Found at i:415417 original size:19 final size:19
Alignment explanation
Indices: 415377--415416 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
415367 CCAAGTAACG
*
415377 AATTTGACAAAATGGTTAA
1 AATTTGACAAAATGATTAA
415396 AATTTGACAAAATCGATTAA
1 AATTTGACAAAAT-GATTAA
415416 A
1 A
415417 TATAACAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (19 bp):
AATTTGACAAAATGATTAA
Found at i:415861 original size:247 final size:247
Alignment explanation
Indices: 415418--416627 Score: 1677
Period size: 247 Copynumber: 4.9 Consensus size: 247
415408 TCGATTAAAT
* * * * * * * *
415418 ATAACAGGTTGAAAATTGACAAAACCGGTTTCAATAATAGCACTTATAAAGTATCAATAACTTAT
1 ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCAG
* * * *
415483 ACACATATATCGATACATGACAATATAACAGGTTGAAAATTGATAAAATCAGTTTCAATATGACA
66 ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGACA
* * * * * * * *
415548 AAATCAGTAAAGTGCTACCAGTTTACAAAAAAATGAAACGTCTCAAAAGTATCGATGCCCTACAC
131 AAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCGATACCTTACAC
*
415613 AAAAGTATCAACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
196 AAAAGTATCGACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
* *
415665 ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCAATATCTCAG
1 ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCAG
* *
415730 ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTAACAAAATCGGTTTCAGTATGACA
66 ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGACA
* * * *
415795 TAACCGATAAAGCACTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCAATACCTTACAC
131 AAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCGATACCTTACAC
* *
415860 AAAAGTATCGACACTTCGGTAAGGGTAATGGTATCGATTAAATATAAATAAT
196 AAAAGTATCGACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
* * * ** * *
415912 ATAACATGTTAAAAATTCACAAAACCATTTTCAATAATTACGCCTATAAAGTATGGATACCTCAG
1 ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCAG
* * *
415977 ACACATGTATCGATACATAACAGTATAACAGGTTGAAAATTGACAAAACCAGTTTCAATATGACA
66 ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGACA
* * * * * * *
416042 AAACCGGTAAAACGCTATCGGTTTACACAAAAACAAAACATCTCGAAAGTAACGATACCTTGCAC
131 AAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCGATACCTTACAC
* * *
416107 AAAAGTATCGACACTTCGGTAAGGGTAATTGTATCGATAAAATATAAATAAC
196 AAAAGTATCGACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
* * * * *
416159 ATAACAGGTTGAAAATTAACATAACCGGTTTCAATAATTGCGTCTATAAAATATCGATACCTCAG
1 ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCAG
*** * * * * * *
416224 AGTTATCTATCGATACATAGCAATACAACATGTTGAAAATTGATAAAATCGATTTCAATATGACA
66 ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGACA
* *
416289 AAACCGGTAAAGCGCTACCGGTTTACACAAAAACAAAACGTCTCAAAAGTATCGATACCTTACAT
131 AAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCGATACCTTACAC
* *
416354 AAAAGTATCAACACTTCAGTAAGGGTAATGGTATAGATTAAATATAAATAAC
196 AAAAGTATCGACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
*
416406 ATAA-AAGTTTGAAAATTGACAAAACCGGCTTCAATAATTGCGCCTATAAAGTATCGATACCTCA
1 ATAACAAG-TTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCA
* * *
416470 GACACATGTATCGATACATAACAATATAACATGTTGAAAATTGACAAAACCGATTTCAATATGAC
65 GACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGAC
* * * * *
416535 AAAACCGGTAAAGCGTTATCGGTATACACAAAAATGAAATGTCT-AGAAAGTATCGATACCTTAC
130 AAAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCA-AAAGTATCGATACCTTAC
*
416599 ATAAAAGTATCGACACTTCAGTAAGGGTA
194 ACAAAAGTATCGACACTTCAGTAAGGGTA
416628 TTCAATATAA
Statistics
Matches: 850, Mismatches: 111, Indels: 4
0.88 0.12 0.00
Matches are distributed among these distances:
246 3 0.00
247 847 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (247 bp):
ATAACAAGTTGAAAATTGACAAAACCGGTTTCAATAATTGCGCCTATAAAGTATCGATACCTCAG
ACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAATCGGTTTCAATATGACA
AAACCGGTAAAGCGCTACCGGTTTACACAAAAACGAAACGTCTCAAAAGTATCGATACCTTACAC
AAAAGTATCGACACTTCAGTAAGGGTAATGGTATCGATTAAATATAAATAAC
Found at i:418495 original size:2 final size:2
Alignment explanation
Indices: 418488--418514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
418478 GTATCGATAA
418488 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
418515 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:419052 original size:108 final size:108
Alignment explanation
Indices: 418893--419531 Score: 434
Period size: 108 Copynumber: 5.7 Consensus size: 108
418883 ATGAAGATGG
* * *
418893 TAATATGTTGATAA-AGCTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCGTTGAATTTC
1 TAATATGTTGATAATA--TTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGAATTTC
*
418957 TAAGTCTCCATCAGCTTAAACTTTGTTAACATTTTAGGCGTTACC
64 TAAGGCTCCATCAGCTTAAACTTTGTTAACATTTTAGGCGTTACC
* * * * *
419002 TAATATGTTGATAATAATGATAACAAATTAAGTAATTAATCTATTTTGTTA-CGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGAATTTCTA
* * * ** *
419066 AGGCCCCATCAGCTTTAATA-TTGCGCTACCTATTACATTAAATAAACGCTACC
66 AGGCTCCATCAGC-TTAA-ACTT-TG-T---TA--ACATT--TTAGGCGTTACC
** *** * * *
419119 TAATATGTT-ATAACGCTTGATAA-TGTTTCTAGTAATTAACCGGTTATGTTATCGTCGGATTTC
1 TAATATGTTGATAA-TATTGATAACAAATT-AAGTAATTAACCGATTATGTTATCGTCGAATTTC
* * *
419182 TAAGGTTCCATCAGCTTAAACTTT-TGTAATATTTTAGGTGTTACC
64 TAAGGCTCCATCAGCTTAAACTTTGT-TAACATTTTAGGCGTTACC
* * * * *
419227 TAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTC-AGATTTTT
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGA-ATTTCT
* * *** * * * *
419291 AAAGCCCCATCAGCTTTAAAAAGGTGCTACCATTACGTTACATAAGCGCTACC
65 AAGGCTCCATCAGC-TT-AAACTTTGTTAACA-T---TT---TAGGCGTTACC
* * *** *
419344 TAATATGTT-ATTATGCTTGATAA-TGTTTCCAGTAATTAACCGATTATGTTATCGTC-AGATTT
1 TAATATGTTGATAAT-ATTGATAACAAATT-AAGTAATTAACCGATTATGTTATCGTCGA-ATTT
* *
419406 CTAAGGCTCCATCAGCTTAAACTTTGGTAATATTTTAGGCGTTACC
63 CTAAGGCTCCATCAGCTTAAACTTTGTTAACATTTTAGGCGTTACC
* * * * * **
419452 TAATATATTGATAATACTGATAACAAATTAAATAATTAACCTATTTTGTTATTATCGAATTTCTA
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGAATTTCTA
**
419517 AGGCAACATCAGCTT
66 AGGCTCCATCAGCTT
419532 TAATATTGCG
Statistics
Matches: 399, Mismatches: 97, Indels: 69
0.71 0.17 0.12
Matches are distributed among these distances:
107 22 0.06
108 159 0.40
109 31 0.08
110 13 0.03
111 3 0.01
112 2 0.01
113 2 0.01
114 4 0.01
115 13 0.03
116 15 0.04
117 111 0.28
118 24 0.06
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (108 bp):
TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGAATTTCTA
AGGCTCCATCAGCTTAAACTTTGTTAACATTTTAGGCGTTACC
Found at i:419343 original size:225 final size:226
Alignment explanation
Indices: 418924--419827 Score: 1119
Period size: 225 Copynumber: 4.1 Consensus size: 226
418914 TAACAAATCA
* * *
418924 AGTAATTAACCGGTTATGTTATCGTTGAATTTCTAAGTCTCCATCAGCTTAAAC-TTTGTTAACA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTTG-TAACA
* *
418988 TTTTAGGCGTTACCTAATATGTTGATAATAATGATAACAAATTAAGTAATTAATCTATTTTGTTA
65 TTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
* * * ** * * *
419053 -CGTCGGATTTCTAAGGCCCCATCAGCTTTAATATTGCGCTACCTATTACATTAAATAAACGCTA
130 TCATCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
* * *
419117 CCTAATATGTTATAACGCTTGATAATGTTTCT
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* *
419149 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGTTCCATCAGCTTAAACTTTTGTAATAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTTGTAACAT
* *
419214 TTTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
419279 CGTCAGATTTTTAAAGCCCCATCAGCTTTAAAAAGGTGCTACC-ATTACGTTACATAAGCGCTAC
131 CATCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
419343 CTAATATGTTATTATGCTTGATAATGTTTCC
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * * *
419374 AGTAATTAACCGATTATGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAATAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTTGTAACAT
* *
419439 TTTAGGCGTTACCTAATATATTGATAATACTGATAACAAATTAAATAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * ** * **
419504 TATCGAATTTCTAAGGCAACATCAGCTTTAATATTGCGCTACCTATTACGTTACATAAGCAG-TA
131 CATCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGC-GCTA
419568 CCTAATATGTTATTATGCTTGATAATGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* ** * *
419600 AATAATTAATTGGTTATGTTATCGTTGGATTCCTAAGGCTCCATCAGCTT----TGTTTGTAACA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACT-TTTGTAACA
419661 TTTTAGGCGTTACCTAATATG-T--T-AT-C-G-T--C---------AATTAACCTATTTTGTTA
65 TTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
* * *
419708 TCATCGGATTTCT-AAGGCCC-T-AGCTTTAAAAAGGTGCTACCTATTACGTTACATAAGTGCTA
130 TCATCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
* * *
419770 CCTAATCTGTTATCATGCTTGATAATGTTTCT
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* *
419802 AGTAATTAACTGATTATGTTATCGTC
1 AGTAATTAACCGGTTATGTTATCGTC
419828 AATATTTTTT
Statistics
Matches: 603, Mismatches: 70, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
201 1 0.00
202 85 0.14
203 1 0.00
204 3 0.00
205 29 0.05
214 1 0.00
216 1 0.00
217 1 0.00
218 1 0.00
219 2 0.00
220 1 0.00
222 2 0.00
223 27 0.04
225 314 0.52
226 133 0.22
227 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (226 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTTGTAACAT
TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CATCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
CTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:422448 original size:24 final size:26
Alignment explanation
Indices: 422421--422612 Score: 87
Period size: 28 Copynumber: 7.1 Consensus size: 26
422411 ATTAGATTAA
422421 AATATTA-A-TATTAAATATATAAAT
1 AATATTATATTATTAAATATATAAAT
422445 AATATTATTCATTATTAAATATATAAAT
1 AATATTA-T-ATTATTAAATATATAAAT
*
422473 AATTTATTATATATTATTAAA-ATAAAAATAT
1 AA--TA-T-TATATTATTAAATAT-ATAA-AT
* *
422504 AATATCTTATATTATTATA-ATATAATT
1 AATA--TTATATTATTAAATATATAAAT
* * *
422531 GATTATT-TTTTATTATAATATTAAAAATAT
1 -AATATTATATTATTA-AATA-T-ATAA-AT
*
422561 AATATTATATTATTAGAA-ATATTAAT
1 AATATTATATTATTA-AATATATAAAT
* * *
422587 -A-AGTATATT-TTAAATATTTTAAT
1 AATATTATATTATTAAATATATAAAT
422610 AAT
1 AAT
422613 TAATATTTTG
Statistics
Matches: 130, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
22 2 0.02
23 10 0.08
24 15 0.12
25 8 0.06
26 5 0.04
27 5 0.04
28 26 0.20
29 26 0.20
30 25 0.19
31 6 0.05
32 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATTATATTATTAAATATATAAAT
Found at i:422463 original size:28 final size:29
Alignment explanation
Indices: 422429--422588 Score: 108
Period size: 29 Copynumber: 5.6 Consensus size: 29
422419 AAAATATTAA
422429 TATTAAATATATAAATAA-TATTAT-TCAT
1 TATTAAATATATAAATAATTATTATAT-AT
422457 TATTAAATATATAAATAATTTATTATATAT
1 TATTAAATATATAAATAA-TTATTATATAT
* *
422487 TATTAAA-ATAAAAATATAATATCT-TATAT
1 TATTAAATATATAAATA-ATTAT-TATATAT
* * *
422516 TATTATA-ATATAATTGATTATT-T-T-T
1 TATTAAATATATAAATAATTATTATATAT
*
422541 TATTATAATAT-TAAA-AATATAATATTATAT
1 TATTA-AATATATAAATAAT-TATTA-TATAT
*
422571 TATTAGAA-ATATTAATAA
1 TATTA-AATATATAAATAA
422589 GTATATTTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 25
0.73 0.09 0.17
Matches are distributed among these distances:
25 8 0.08
26 8 0.08
27 4 0.04
28 23 0.22
29 31 0.30
30 28 0.27
31 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TATTAAATATATAAATAATTATTATATAT
Found at i:422481 original size:30 final size:28
Alignment explanation
Indices: 422429--422527 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 28
422419 AAAATATTAA
422429 TATTAAATATATAAATAATATTAT-TCAT
1 TATTAAATATATAAATAATATTATAT-AT
422457 TATTAAATATATAAATAATTTATTATATAT
1 TATTAAATATATAAATAA--TATTATATAT
*
422487 TATTAAA-ATAAAAATATAATATCT-TATAT
1 TATTAAATAT-ATAA-ATAATAT-TATATAT
422516 TATTATAATATA
1 TATTA-AATATA
422528 ATTGATTATT
Statistics
Matches: 62, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
28 18 0.29
29 15 0.24
30 22 0.35
31 7 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTAAATATATAAATAATATTATATAT
Found at i:422569 original size:22 final size:23
Alignment explanation
Indices: 422541--422587 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
422531 GATTATTTTT
422541 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
422563 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
422586 TA
1 TA
422588 AGTATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:422876 original size:41 final size:42
Alignment explanation
Indices: 422817--422905 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 42
422807 TTCCTCCAAC
* *
422817 CAAACATTGGAAAACATTTTCCGGAAAACGTATTACGTGAAA
1 CAAACATTGGAAAACATTTTCCGGAAAACGAAGTACGTGAAA
* *
422859 TAAACA-TGGAGAACATTTTCCGGAAAACGAAGTACGTGAAA
1 CAAACATTGGAAAACATTTTCCGGAAAACGAAGTACGTGAAA
422900 CAAACA
1 CAAACA
422906 CGGGATTTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (42 bp):
CAAACATTGGAAAACATTTTCCGGAAAACGAAGTACGTGAAA
Found at i:423092 original size:18 final size:18
Alignment explanation
Indices: 423069--423106 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
423059 GATTTAATTA
423069 TTGATTTTGTATAATCTG
1 TTGATTTTGTATAATCTG
*
423087 TTGATTTTGTATAATTTG
1 TTGATTTTGTATAATCTG
423105 TT
1 TT
423107 CTAAATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.61
Consensus pattern (18 bp):
TTGATTTTGTATAATCTG
Found at i:425258 original size:17 final size:18
Alignment explanation
Indices: 425236--425269 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
425226 ACTTAGCATT
425236 TTTGAAAAA-AAAAGAAC
1 TTTGAAAAAGAAAAGAAC
425253 TTTGAAAAAGAAAAGAA
1 TTTGAAAAAGAAAAGAA
425270 AAACTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (18 bp):
TTTGAAAAAGAAAAGAAC
Found at i:428910 original size:37 final size:38
Alignment explanation
Indices: 428866--428948 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
428856 TTAAAAAGGT
*
428866 ATATAAAATAA-ATAATTATAAATTAAAAAAAG-AA-AA
1 ATATAAAATAATA-AATAATAAATTAAAAAAAGTAATAA
* *
428902 ATAATAAAATAATAAATAATGAATTAAAAATAGTAATAA
1 AT-ATAAAATAATAAATAATAAATTAAAAAAAGTAATAA
428941 ATATAAAA
1 ATATAAAA
428949 GGGGATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 2 0.05
37 25 0.62
38 9 0.22
39 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (38 bp):
ATATAAAATAATAAATAATAAATTAAAAAAAGTAATAA
Found at i:429781 original size:75 final size:75
Alignment explanation
Indices: 429628--429832 Score: 301
Period size: 75 Copynumber: 2.8 Consensus size: 75
429618 TCTTAAATCA
* * *
429628 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAA-AAA-ATAATAT-TTAAAATAAT
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAAAATAAT
* *
429689 ATTCTAAATCC
65 ATCCTAAAACC
*
429700 TAATTAAAATACTAAAACCTATTTAAACTAAAATATCTAAACAAAGATAAAATATAAAAATAATA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAAAATAATA
*
429765 TCCTAAAACT
66 TCCTAAAACC
429775 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAA
429833 TGTTTAAAAT
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
71 5 0.04
72 33 0.28
73 3 0.03
74 6 0.05
75 54 0.45
76 19 0.16
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAAAATAATA
TCCTAAAACC
Found at i:437264 original size:15 final size:15
Alignment explanation
Indices: 437246--437297 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
437236 ATAAATAATT
437246 ATAAATTAAAAAATA
1 ATAAATTAAAAAATA
* **
437261 ATAAAATAATGAATA
1 ATAAATTAAAAAATA
*
437276 ATGAATTAAAAATAGTA
1 ATAAATTAAAAA-A-TA
437293 ATAAA
1 ATAAA
437298 GGTAAAAGGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 20 0.74
16 1 0.04
17 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (15 bp):
ATAAATTAAAAAATA
Found at i:437265 original size:33 final size:33
Alignment explanation
Indices: 437215--437277 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
437205 ATTCCAGGTA
*
437215 AAATTAAAAAGGTATAAAAAAATAAATAATTAT
1 AAATTAAAAAGATATAAAAAAATAAATAATTAT
* *
437248 AAATTAAAAA-ATAATAAAATAATGAATAAT
1 AAATTAAAAAGAT-ATAAAAAAATAAATAAT
437278 GAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (33 bp):
AAATTAAAAAGATATAAAAAAATAAATAATTAT
Found at i:437269 original size:30 final size:31
Alignment explanation
Indices: 437215--437297 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 31
437205 ATTCCAGGTA
* *
437215 AAATTAAAAAGGTATAAAAAAATAAAT-AATTAT
1 AAATTAAAAA--TATAATAAAAT-AATGAATAAT
437248 AAATTAAAAA-ATAATAAAATAATGAATAAT
1 AAATTAAAAATATAATAAAATAATGAATAAT
*
437278 GAATTAAAAATAGTAATAAA
1 AAATTAAAAATA-TAATAAA
437298 GGTAAAAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.07
30 23 0.52
31 1 0.02
32 7 0.16
33 10 0.23
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (31 bp):
AAATTAAAAATATAATAAAATAATGAATAAT
Found at i:437587 original size:76 final size:76
Alignment explanation
Indices: 437495--437646 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
437485 AATTCTTCAC
437495 TTCCAACACGGATTGTGTTGTTTCAACAATAACTGATTTTGATCTCAGTTTCCTTTTAGCAAACA
1 TTCCAACACGGATTGTGTTGTTTCAACAATAACTGATTTTGATCTCAGTTTCCTTTTAGCAAACA
437560 ATTTTGCTAAA
66 ATTTTGCTAAA
437571 TTCCAACACGGATTGTGTTGTTTCAACAATAACTGATTTTGATCTCAGTTTCCTTTTAGCAAACA
1 TTCCAACACGGATTGTGTTGTTTCAACAATAACTGATTTTGATCTCAGTTTCCTTTTAGCAAACA
437636 ATTTTGCTAAA
66 ATTTTGCTAAA
437647 CGTGTTCTCG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (76 bp):
TTCCAACACGGATTGTGTTGTTTCAACAATAACTGATTTTGATCTCAGTTTCCTTTTAGCAAACA
ATTTTGCTAAA
Found at i:438112 original size:12 final size:12
Alignment explanation
Indices: 438095--438122 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
438085 AAATACTAAA
438095 AAATAATATTCT
1 AAATAATATTCT
438107 AAATAATATTCT
1 AAATAATATTCT
438119 AAAT
1 AAAT
438123 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:438205 original size:76 final size:76
Alignment explanation
Indices: 438048--438258 Score: 233
Period size: 76 Copynumber: 2.9 Consensus size: 76
438038 TAAAACATCT
* *
438048 TAAATCCTAATTAAAA-AGCTTAAAAC-TATTTAAACTAAAATA-CT---A-AAAAATAATAT-T
1 TAAATCCTAATTAAAATA-C-TAAAACATATTGAAACTAAAATACCTAAAACAAAAATAAAATAT
** *
438105 CTAAATAATATTC
64 AAAAATAATATCC
* *
438118 TAAATCCTAATTAAATTACTAAAACCTATTGAAACTAAAATACCTAAAACAAAAATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACATATTGAAACTAAAATACCTAAAACAAAAATAAAATATAA
438183 AAATAATATCC
66 AAATAATATCC
* * * *
438194 TACAA-CTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAATAAAGATAAAATATA
1 TA-AATCCTAATTAAAATACTAAAACATATTGAAACTAAAATACCTAAAACAAAAATAAAATATA
438258 A
65 A
438259 TGTTTAAAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
69 6 0.05
70 31 0.26
71 3 0.03
74 1 0.01
75 10 0.08
76 67 0.56
77 2 0.02
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACATATTGAAACTAAAATACCTAAAACAAAAATAAAATATAA
AAATAATATCC
Found at i:443430 original size:21 final size:21
Alignment explanation
Indices: 443406--443452 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
443396 GCTTTGGAAT
*
443406 TTTTCCTGGGATACAACTAGC
1 TTTTCCTGGGATACAACCAGC
**
443427 TTTTCCTGGGATGTAACCAGC
1 TTTTCCTGGGATACAACCAGC
443448 TTTTC
1 TTTTC
443453 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TTTTCCTGGGATACAACCAGC
Found at i:444928 original size:11 final size:11
Alignment explanation
Indices: 444912--444942 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
444902 TAAGATAAAG
444912 AAAAATAATAA
1 AAAAATAATAA
444923 AAAAATAATAA
1 AAAAATAATAA
444934 ATAAAATAA
1 A-AAAATAA
444943 AATAGTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:444936 original size:15 final size:14
Alignment explanation
Indices: 444898--444946 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
444888 AGACTGTTTG
*
444898 AAAATAAGATAAAGA
1 AAAATAA-ATAAAAA
444913 AAAAT-AATAAAAA
1 AAAATAAATAAAAA
*
444926 AATAATAAATAAAAT
1 AA-AATAAATAAAAA
444941 AAAATA
1 AAAATA
444947 GTCATTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 8 0.27
14 8 0.27
15 14 0.47
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (14 bp):
AAAATAAATAAAAA
Found at i:445791 original size:5 final size:5
Alignment explanation
Indices: 445783--445812 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
445773 GATAAGATAA
445783 AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
445813 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:447632 original size:2 final size:2
Alignment explanation
Indices: 447625--447660 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
447615 TTTTCACAAT
447625 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
447661 CTTTGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:447710 original size:22 final size:23
Alignment explanation
Indices: 447680--447722 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
447670 TTTGATATAC
447680 TAAAATTAAT-TAATATTTTAAA
1 TAAAATTAATATAATATTTTAAA
* *
447702 TAAATTTAATATTATATTTTA
1 TAAAATTAATATAATATTTTA
447723 TTCGGTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAAATTAATATAATATTTTAAA
Found at i:448245 original size:21 final size:21
Alignment explanation
Indices: 448221--448268 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
448211 GGTAGTACAA
**
448221 ATACTCCAAGATTGAGTACCG
1 ATACTCCAAGAACGAGTACCG
*
448242 ATACTCCAAGAACGAGTATCG
1 ATACTCCAAGAACGAGTACCG
448263 ATACTC
1 ATACTC
448269 AAGGCATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (21 bp):
ATACTCCAAGAACGAGTACCG
Found at i:451559 original size:27 final size:27
Alignment explanation
Indices: 451529--451580 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
451519 TTCGAAAAAG
451529 AAAATAACCTTGAAGTGTAAAATGATC
1 AAAATAACCTTGAAGTGTAAAATGATC
*
451556 AAAATACCCTTGAAGTGTAAAATGA
1 AAAATAACCTTGAAGTGTAAAATGA
451581 CTATATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (27 bp):
AAAATAACCTTGAAGTGTAAAATGATC
Found at i:453524 original size:26 final size:27
Alignment explanation
Indices: 453491--453547 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
453481 CCTGATTATG
*
453491 AAATGACCAAAATA-CCTTGAATTGTA
1 AAATGACCAAAATACCCTTGAAGTGTA
453517 AAATGACCAAAATACCCTTGAAGTGTA
1 AAATGACCAAAATACCCTTGAAGTGTA
453544 AAAT
1 AAAT
453548 AACTATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (27 bp):
AAATGACCAAAATACCCTTGAAGTGTA
Found at i:454900 original size:32 final size:32
Alignment explanation
Indices: 454833--454904 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
454823 TAAGGTGACC
* *
454833 CTTGGGTAGGCTTCGAGGCCCCGAGAAACTTT
1 CTTGGGTAGGCTTCGAGGCCCCAAGAAACTCT
* **
454865 CTTGGGTAGGCTCTC-AGGCCTCAAGGCACTCT
1 CTTGGGTAGGCT-TCGAGGCCCCAAGAAACTCT
454897 CTTGGGTA
1 CTTGGGTA
454905 AATCATATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (32 bp):
CTTGGGTAGGCTTCGAGGCCCCAAGAAACTCT
Found at i:458158 original size:27 final size:27
Alignment explanation
Indices: 458128--458213 Score: 145
Period size: 27 Copynumber: 3.2 Consensus size: 27
458118 CCTGATTATG
458128 AAATGACCAAAATACCCTTGAAGTGTA
1 AAATGACCAAAATACCCTTGAAGTGTA
458155 AAATGACCAAAATACCCTTGAAGTGTA
1 AAATGACCAAAATACCCTTGAAGTGTA
* * *
458182 AAATGACCAAAATATCATTGAAGTATA
1 AAATGACCAAAATACCCTTGAAGTGTA
458209 AAATG
1 AAATG
458214 TCTATATTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (27 bp):
AAATGACCAAAATACCCTTGAAGTGTA
Found at i:460498 original size:45 final size:45
Alignment explanation
Indices: 460434--460603 Score: 279
Period size: 45 Copynumber: 3.8 Consensus size: 45
460424 GTAAGTATGC
460434 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
460479 AAATAAGCTAACAAGCTTATCGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
460524 AAATAAGCTTACAAGCTTATGGAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
460569 AAATAAGCTTACGAGCTTATAGG-ATAAATGATAAG
1 AAATAAGCTTACAAGCTTAT-GGAATAAATGGTAAG
460604 AAATTGTATA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 114 0.98
46 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:461035 original size:21 final size:21
Alignment explanation
Indices: 460993--461036 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
460983 TGCTGAAATT
* * *
460993 ACTGTAGCAATGCATTGGTAC
1 ACTGTAGCAATACATCGATAC
*
461014 ACTGTAGCAGTACATCGATAC
1 ACTGTAGCAATACATCGATAC
461035 AC
1 AC
461037 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAATACATCGATAC
Found at i:464707 original size:147 final size:147
Alignment explanation
Indices: 464501--464794 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
464491 TTTCATGGGA
464501 AATTTCGTAAATTAAAGTCAAATTAATTCATCTTTGACTTTGAAATATGTTAAGGATGAGGTGTT
1 AATTTCGTAAATTAAAGTCAAATTAATTCATCTTTGACTTTGAAATATGTTAAGGATGAGGTGTT
464566 TTGGTTTTATGGTGAATAAGAAGATTCATTAAGGGTGTTTTGGTCTTATCTCAATTAAATGAATA
66 TTGGTTTTATGGTGAATAAGAAGATTCATTAAGGGTGTTTTGGTCTTATCTCAATTAAATGAATA
464631 TTTTATTCATTTATAGT
131 TTTTATTCATTTATAGT
464648 AATTTCGTAAATTAAAGTCAAATTAATTCATCTTTGACTTTGAAATATGTTAAGGATGAGGTGTT
1 AATTTCGTAAATTAAAGTCAAATTAATTCATCTTTGACTTTGAAATATGTTAAGGATGAGGTGTT
464713 TTGGTTTTATGGTGAATAAGAAGATTCATTAAGGGTGTTTTGGTCTTATCTCAATTAAATGAATA
66 TTGGTTTTATGGTGAATAAGAAGATTCATTAAGGGTGTTTTGGTCTTATCTCAATTAAATGAATA
464778 TTTTATTCATTTATAGT
131 TTTTATTCATTTATAGT
464795 GGAATTAAAT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (147 bp):
AATTTCGTAAATTAAAGTCAAATTAATTCATCTTTGACTTTGAAATATGTTAAGGATGAGGTGTT
TTGGTTTTATGGTGAATAAGAAGATTCATTAAGGGTGTTTTGGTCTTATCTCAATTAAATGAATA
TTTTATTCATTTATAGT
Found at i:466506 original size:45 final size:45
Alignment explanation
Indices: 466442--466606 Score: 287
Period size: 45 Copynumber: 3.7 Consensus size: 45
466432 GTAAGCATGC
466442 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
*
466487 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
* *
466532 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
466577 AAATAAGCTTACGAGCTTATA-AGATAAATG
1 AAATAAGCTTACGAGCTTATAGA-ATAAATG
466607 ATAATAAATG
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
44 1 0.01
45 114 0.99
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
Found at i:466536 original size:24 final size:24
Alignment explanation
Indices: 466509--466582 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
466499 GAGCTTATGG
466509 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* ***
466533 AATAAGCTTACAAGCT-TA-TGG---
1 AATAA-ATGGTAAG-TATATTGGTAA
466554 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
466578 AATAA
1 AATAA
466583 GCTTACGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 8 0.23
24 13 0.37
25 6 0.17
26 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:475270 original size:30 final size:30
Alignment explanation
Indices: 475236--475292 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
475226 AAAACCAGTA
*
475236 GAATCTACTGAAAA-CTGATAAAATCGGGGT
1 GAATCGACTGAAAATC-GATAAAATCGGGGT
*
475266 GAATCGACTGAAAATCGGTAAAATCGG
1 GAATCGACTGAAAATCGATAAAATCGG
475293 TTTGAACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
GAATCGACTGAAAATCGATAAAATCGGGGT
Found at i:481055 original size:70 final size:70
Alignment explanation
Indices: 480942--481082 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
480932 ATGTTATTCT
480942 CCGGAACTGAAATGGCATTTCAGTTGCGATAAAATCTAGAATAACCATATTTATCTTCTTAGCAC
1 CCGGAACTGAAATGGCATTTCAGTTGCGATAAAATCTAGAATAACCATATTTATCTTCTTAGCAC
481007 ATCTG
66 ATCTG
481012 CCGGAACTGAAATGGCATTTCAGTTGCGATAAAATCTAGAATAACCATATTTATCTTCTTAGCAC
1 CCGGAACTGAAATGGCATTTCAGTTGCGATAAAATCTAGAATAACCATATTTATCTTCTTAGCAC
481077 ATCTG
66 ATCTG
481082 C
1 C
481083 ACCTACACTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (70 bp):
CCGGAACTGAAATGGCATTTCAGTTGCGATAAAATCTAGAATAACCATATTTATCTTCTTAGCAC
ATCTG
Found at i:485306 original size:46 final size:45
Alignment explanation
Indices: 485250--485356 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
485240 TGCACATATC
* * *
485250 ATGCACCGATGCACTGAAGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAAGATATTT-TG-AAACATCGAATGCACTTG
** *
485296 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
485341 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
485357 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.61
46 18 0.33
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
Found at i:485354 original size:17 final size:19
Alignment explanation
Indices: 485326--485374 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
485316 TATTTTGAAA
485326 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
485344 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
485363 CACCGATGCACT
1 CATCGATGCACT
485375 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:493818 original size:17 final size:17
Alignment explanation
Indices: 493796--493838 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
493786 GAAACATCAA
*
493796 ATGCACTTAATGCATCG
1 ATGCACTTAATGCACCG
*
493813 ATGCACTCTTAGTGCACCG
1 ATGCA--CTTAATGCACCG
493832 ATGCACT
1 ATGCACT
493839 AAGGATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (17 bp):
ATGCACTTAATGCACCG
Found at i:493828 original size:19 final size:19
Alignment explanation
Indices: 493801--493838 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
493791 ATCAAATGCA
*
493801 CTTAATGCATCGATGCACT
1 CTTAATGCACCGATGCACT
*
493820 CTTAGTGCACCGATGCACT
1 CTTAATGCACCGATGCACT
493839 AAGGATCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CTTAATGCACCGATGCACT
Found at i:496237 original size:19 final size:19
Alignment explanation
Indices: 496178--496237 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
496168 GCATTGGTAC
496178 ACTGTTCACGGTACTG--T
1 ACTGTTCACGGTACTGTTT
* *
496195 AGTAGTGCATCGGTACATTGTTT
1 ACT-GTTCA-CGGTAC--TGTTT
496218 ACTGTTCACGGTACTGTTT
1 ACTGTTCACGGTACTGTTT
496237 A
1 A
496238 TTATTATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 2 0.06
18 4 0.12
19 12 0.36
21 8 0.24
22 4 0.12
23 3 0.09
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
ACTGTTCACGGTACTGTTT
Found at i:498552 original size:131 final size:131
Alignment explanation
Indices: 498318--498581 Score: 501
Period size: 131 Copynumber: 2.0 Consensus size: 131
498308 CAACAAATTT
*
498318 TGGAACCTTGTTTAGGCTGAGTTAGCCCCTCAAAAGGTTCAGGCATTTGCCTAGAAGGCTGTCTT
1 TGGAACCATGTTTAGGCTGAGTTAGCCCCTCAAAAGGTTCAGGCATTTGCCTAGAAGGCTGTCTT
*
498383 GCAAAGGGTACCCTCGTTTGTGGAATTAGCTAAACGGGGAGTGATCAGATCGGATGTTGTTCTTT
66 GCAAAGGGTACCATCGTTTGTGGAATTAGCTAAACGGGGAGTGATCAGATCGGATGTTGTTCTTT
498448 G
131 G
498449 TGGAACCATGTTTAGGCTGAGTTAGCCCCTCAAAAGGTTCAGGCATTTGCCTAGAAGGCTGTCTT
1 TGGAACCATGTTTAGGCTGAGTTAGCCCCTCAAAAGGTTCAGGCATTTGCCTAGAAGGCTGTCTT
*
498514 GCAAAGGGTACCATCGTTTGTGGAATTAGCTAAACGGGGAGTGATCAGATCGGATTTTGTTCTTT
66 GCAAAGGGTACCATCGTTTGTGGAATTAGCTAAACGGGGAGTGATCAGATCGGATGTTGTTCTTT
498579 G
131 G
498580 TG
1 TG
498582 TTTTGTGTCG
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (131 bp):
TGGAACCATGTTTAGGCTGAGTTAGCCCCTCAAAAGGTTCAGGCATTTGCCTAGAAGGCTGTCTT
GCAAAGGGTACCATCGTTTGTGGAATTAGCTAAACGGGGAGTGATCAGATCGGATGTTGTTCTTT
G
Found at i:505090 original size:7 final size:7
Alignment explanation
Indices: 505080--505179 Score: 69
Period size: 7 Copynumber: 14.0 Consensus size: 7
505070 TGTTATTCTT
*
505080 TATAGTA
1 TATATTA
*
505087 TATAGTA
1 TATATTA
505094 TATATGTA
1 TATAT-TA
505102 TTATATTA
1 -TATATTA
* *
505110 TGTAATA
1 TATATTA
*
505117 TATACATA
1 TATA-TTA
505125 CTATATTA
1 -TATATTA
505133 TATATTA
1 TATATTA
505140 TATATTA
1 TATATTA
505147 TA-ATTA
1 TATATTA
**
505153 TATAACA
1 TATATTA
505160 TATATTA
1 TATATTA
* *
505167 CATA-CA
1 TATATTA
505173 TATATTA
1 TATATTA
505180 ATTTGGTTCC
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
6 10 0.14
7 46 0.62
8 9 0.12
9 9 0.12
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (7 bp):
TATATTA
Found at i:505111 original size:12 final size:12
Alignment explanation
Indices: 505079--505155 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
505069 GTGTTATTCT
*
505079 TTATAGTATATA
1 TTATATTATATA
* *
505091 GTATA-TATGTA
1 TTATATTATATA
*
505102 TTATATTATGTA
1 TTATATTATATA
* *
505114 ATATA-TACATA
1 TTATATTATATA
*
505125 CTATATTATATA
1 TTATATTATATA
505137 TTATA-TATTATAA
1 TTATATTA-TAT-A
505150 TTATAT
1 TTATAT
505156 AACATATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 19 0.37
12 26 0.51
13 6 0.12
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (12 bp):
TTATATTATATA
Found at i:505118 original size:23 final size:21
Alignment explanation
Indices: 505080--505166 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 21
505070 TGTTATTCTT
* *
505080 TATAGTATATAGTATATATGTA
1 TATATTATATAATATATAT-TA
* *
505102 TTATATTATGTAATATATACATA
1 -TATATTATATAATATATA-TTA
*
505125 CTATATTATATATTATATATTA
1 -TATATTATATAATATATATTA
*
505147 TA-ATTATATAACATATATTA
1 TATATTATATAATATATATTA
505167 CATACATATA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 16 0.30
21 2 0.04
22 2 0.04
23 33 0.62
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATTATATAATATATATTA
Found at i:505152 original size:20 final size:20
Alignment explanation
Indices: 505129--505166 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
505119 TACATACTAT
**
505129 ATTATATATTATATATTATA
1 ATTATATAACATATATTATA
505149 ATTATATAACATATATTA
1 ATTATATAACATATATTA
505167 CATACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATATAACATATATTATA
Found at i:506290 original size:15 final size:15
Alignment explanation
Indices: 506270--506344 Score: 64
Period size: 15 Copynumber: 4.9 Consensus size: 15
506260 TAATATATAT
506270 TTTTTATTATTTTTA
1 TTTTTATTATTTTTA
*
506285 TTTTTATCATTTTTA
1 TTTTTATTATTTTTA
*
506300 TTCTTTACTATTTTTCCA
1 TT-TTTATTATTTTT--A
**
506318 TTTTT-TGGTTTTCT-
1 TTTTTATTATTTT-TA
506332 TTTTTATTATTTT
1 TTTTTATTATTTT
506345 CTTTTTCTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
14 5 0.11
15 21 0.45
16 14 0.30
17 4 0.09
18 3 0.06
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:506343 original size:31 final size:29
Alignment explanation
Indices: 506269--506344 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
506259 TTAATATATA
506269 TTTTTTATTATTTTTATTTTTATCATTTT
1 TTTTTTATTATTTTTATTTTTATCATTTT
* **
506298 TATTCTTTACTATTTTTCCATTTTT-TGGTTTT
1 T-TT-TTTATTATTTTT--ATTTTTATCATTTT
506330 CTTTTTTATTATTTT
1 -TTTTTTATTATTTT
506345 CTTTTTCTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 1 0.03
30 2 0.05
31 21 0.55
32 7 0.18
33 7 0.18
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (29 bp):
TTTTTTATTATTTTTATTTTTATCATTTT
Found at i:506373 original size:2 final size:2
Alignment explanation
Indices: 506366--506408 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
506356 CCCCTGACGT
506366 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
506408 T
1 T
506409 TACTTTATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:506451 original size:9 final size:9
Alignment explanation
Indices: 506437--506461 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
506427 ATTTGTTTGT
506437 TTTTTTTCC
1 TTTTTTTCC
506446 TTTTTTTCC
1 TTTTTTTCC
506455 TTTTTTT
1 TTTTTTT
506462 TATTTTGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:506762 original size:10 final size:10
Alignment explanation
Indices: 506747--506776 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
506737 GAATTTGTTC
506747 AAAGTTTTCA
1 AAAGTTTTCA
506757 AAAGTTTTCA
1 AAAGTTTTCA
506767 AAAGTTTTCA
1 AAAGTTTTCA
506777 GAAATAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (10 bp):
AAAGTTTTCA
Found at i:506790 original size:20 final size:19
Alignment explanation
Indices: 506744--506791 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
506734 ATTGAATTTG
*
506744 TTCAAAGTTTTCAAAAGTT
1 TTCAAAGTTTTCAAAAGTA
506763 TTCAAAAGTTTTCAGAAA-TAA
1 TTC-AAAGTTTTCA-AAAGT-A
506784 TTCAAAGT
1 TTCAAAGT
506792 CTATTAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 16 0.64
21 6 0.24
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (19 bp):
TTCAAAGTTTTCAAAAGTA
Found at i:506937 original size:19 final size:19
Alignment explanation
Indices: 506913--506950 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
506903 ATACCGAAGG
506913 TAAGAGAAGTATCGATATT
1 TAAGAGAAGTATCGATATT
506932 TAAGAGAAGTATCGATATT
1 TAAGAGAAGTATCGATATT
506951 CTCTAGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TAAGAGAAGTATCGATATT
Found at i:507212 original size:20 final size:20
Alignment explanation
Indices: 507184--507226 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
507174 TTATGTAGAA
* * *
507184 AAATTATCCCCAATGGCTCC
1 AAATCATCCCCAACGGCTAC
507204 AAATCATCCCCAACGGCTAC
1 AAATCATCCCCAACGGCTAC
507224 AAA
1 AAA
507227 CGGCTACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.35, G:0.09, T:0.19
Consensus pattern (20 bp):
AAATCATCCCCAACGGCTAC
Found at i:524976 original size:22 final size:21
Alignment explanation
Indices: 524934--524973 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
524924 GAGTTTGTTT
*
524934 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
524955 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
524974 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:530473 original size:19 final size:18
Alignment explanation
Indices: 530449--530486 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
530439 TATATGTATA
530449 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
530468 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
530486 T
1 T
530487 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:530486 original size:10 final size:9
Alignment explanation
Indices: 530449--530486 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
530439 TATATGTATA
530449 TATTTAATT
1 TATTTAATT
530458 ATATTTAATT
1 -TATTTAATT
530468 TATTT-ATT
1 TATTTAATT
530476 TATTATAATT
1 TATT-TAATT
530486 T
1 T
530487 TTTTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:530534 original size:2 final size:2
Alignment explanation
Indices: 530527--530559 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
530517 ATTTTCCTAT
530527 TA TA 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 TA TA T
530560 TATTTTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:530622 original size:2 final size:2
Alignment explanation
Indices: 530615--530665 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
530605 TTCCTAACGT
530615 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
530657 TA TA TA TA T
1 TA TA TA TA T
530666 TCTTACTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:530825 original size:32 final size:32
Alignment explanation
Indices: 530737--530832 Score: 83
Period size: 32 Copynumber: 3.0 Consensus size: 32
530727 ATTTTTTTCA
*
530737 TTTATTTATTATTATTT-TACTATTTA-GTA-TT
1 TTTA-TTATT-TTATTTATACTATTTATATATTT
* * **
530768 TTTATTATATCATACATAC-ATTTTATATATTT
1 TTTATTATTTTATTTATACTA-TTTATATATTT
*
530800 TTTATTATTTTATTTATACTATTTATTTATTT
1 TTTATTATTTTATTTATACTATTTATATATTT
530832 T
1 T
530833 CATTATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
29 4 0.08
30 11 0.22
31 6 0.12
32 28 0.56
33 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (32 bp):
TTTATTATTTTATTTATACTATTTATATATTT
Found at i:535460 original size:15 final size:14
Alignment explanation
Indices: 535442--535500 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
535432 GGCAAAACAA
535442 AAAAAGAAAAGAAAC
1 AAAAA-AAAAGAAAC
*
535457 AAAAAAGAAGAAAAC
1 AAAAAAAAAG-AAAC
*
535472 AAAAAAAAAGAACAA
1 AAAAAAAAAGAA-AC
535487 AAATAAAAAAGAAA
1 AAA-AAAAAAGAAA
535501 AAGGGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.16
15 23 0.61
16 9 0.24
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAGAAAC
Found at i:535478 original size:18 final size:18
Alignment explanation
Indices: 535434--535488 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
535424 ACAAAAAGGG
535434 CAAAACAAAAA-AAGAAAA
1 CAAAA-AAAAAGAAGAAAA
*
535452 GAAACAAAAAAGAAGAAAA
1 CAAA-AAAAAAGAAGAAAA
*
535471 CAAAAAAAAAGAACAAAA
1 CAAAAAAAAAGAAGAAAA
535489 ATAAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 21 0.66
19 11 0.34
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAGAAGAAAA
Found at i:535494 original size:18 final size:16
Alignment explanation
Indices: 535435--535502 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
535425 CAAAAAGGGC
*
535435 AAAACAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
* *
535451 AGAAACAAAAAAGAAGA
1 AAAAAAAAAAAAGAA-A
*
535468 AAACAAAAAAAAAGAAC
1 AAA-AAAAAAAAAGAAA
*
535485 AAAAATAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
535501 AA
1 AA
535503 GGGAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
16 25 0.60
17 6 0.14
18 11 0.26
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:536132 original size:22 final size:22
Alignment explanation
Indices: 536104--536158 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
536094 GCTACCCCAT
536104 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
536126 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
536148 CAAACCTTTGA
1 CAAACCTTTGA
536159 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:537247 original size:106 final size:106
Alignment explanation
Indices: 537120--538395 Score: 1843
Period size: 106 Copynumber: 12.0 Consensus size: 106
537110 ATATCGTGCC
* * * * **
537120 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGAGATGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
537185 AAATTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
537226 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
537291 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
537332 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
537397 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
537438 ACTCAAGACAACGCAAGTTCAAATTCATGACGAAGGGACCACTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
537503 AATTTAAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
537544 ACTCTAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
537609 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
537650 ACTCCAAACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
537715 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * **
537756 ACTCGAGACAATGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCAT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
537821 AATTTCGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** *
537862 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
537927 AATTTCGGAGCCAATTTCAATTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
537968 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
538033 AATTTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
538074 ACTCCAGACTACGCAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
538139 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
538180 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
538245 AATTTCGGAGCCAATTTCAACTTCAGAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * * * *
538286 ACTTGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAGCAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
538351 AATTCCAGAGACAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
538392 ACTC
1 ACTC
538396 AGAACAATGC
Statistics
Matches: 1057, Mismatches: 112, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
106 1057 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:539238 original size:37 final size:37
Alignment explanation
Indices: 539144--539248 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 37
539134 TCTTTTCGTC
*
539144 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATGCAAACTCCTAAAAATAGGATAGAATT
* * *
539181 TTTCTAGGATGCAAAATCCTAAAAATAGGATA-AAGTT
1 CTACTAGGATGCAAACTCCTAAAAATAGGATAGAA-TT
** ** *
539218 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATGCAAACTCCTAAAAATAGGAT
539249 CCACAAGCAT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 2 0.04
37 53 0.96
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATGCAAACTCCTAAAAATAGGATAGAATT
Found at i:539695 original size:23 final size:24
Alignment explanation
Indices: 539644--539691 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
539634 TAACCCTTAT
539644 TATTTATATGTATATATTTAATTA
1 TATTTATATGTATATATTTAATTA
* *
539668 TATTT-TATTTATTTATTT-ATTA
1 TATTTATATGTATATATTTAATTA
539690 TA
1 TA
539692 ATTTGTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTTATATGTATATATTTAATTA
Found at i:539798 original size:14 final size:14
Alignment explanation
Indices: 539781--539808 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
539771 TGTTTACTTA
539781 TTTACTATATTTTC
1 TTTACTATATTTTC
539795 TTTACTATATTTTC
1 TTTACTATATTTTC
539809 CTAACATTAT
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:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTACTATATTTTC
Found at i:539930 original size:19 final size:18
Alignment explanation
Indices: 539908--539943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
539898 ATTTTTCATT
*
539908 TATTTATTATTATTATTAC
1 TATTTAATATT-TTATTAC
539927 TATTTAATATTTTATTA
1 TATTTAATATTTTATTA
539944 TATCATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTAATATTTTATTAC
Found at i:539987 original size:21 final size:20
Alignment explanation
Indices: 539956--540026 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 20
539946 TCATACATAC
539956 ATTTTTATATTTTTATATATAT
1 ATTTTT-TATTTTTAT-TATAT
539978 ATTTTTTATTATTTTATTTATACT
1 ATTTTTTA-T-TTTTA-TTATA-T
*
540002 ATTTATTTATTTTCATTATAT
1 ATTT-TTTATTTTTATTATAT
540023 -TTTT
1 ATTTT
540027 AGTTTCTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 3 0.07
22 12 0.28
23 13 0.30
24 7 0.16
25 4 0.09
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTTATTTTTATTATAT
Found at i:540023 original size:28 final size:27
Alignment explanation
Indices: 539967--540024 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
539957 TTTTTATATT
* *
539967 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
539994 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
540022 TTT
1 TTT
540025 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:541382 original size:15 final size:15
Alignment explanation
Indices: 541364--541393 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
541354 TATAATCTTA
541364 TTTTAGTTTTAAATAT
1 TTTTA-TTTTAAATAT
541380 TTTTATTTTAAATA
1 TTTTATTTTAAATA
541394 AAACTAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTTATTTTAAATAT
Found at i:541532 original size:21 final size:20
Alignment explanation
Indices: 541503--541552 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
541493 TTAACTATTT
* * *
541503 AAATTTAAAACATTTACAATA
1 AAATATAAAACAATTA-AACA
541524 AAATATAAAAACAATTAAACA
1 AAATAT-AAAACAATTAAACA
541545 AAATATAA
1 AAATATAA
541553 TTTAGGGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATATAAAACAATTAAACA
Found at i:546381 original size:23 final size:24
Alignment explanation
Indices: 546355--546399 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
546345 TTGCCTGACC
*
546355 TCTCCTATTA-GTTTCAAACTCCT
1 TCTCCTATCACGTTTCAAACTCCT
* *
546378 TCTCTTATCACTTTTCAAACTC
1 TCTCCTATCACGTTTCAAACTC
546400 TACCTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.44
Consensus pattern (24 bp):
TCTCCTATCACGTTTCAAACTCCT
Found at i:547396 original size:267 final size:267
Alignment explanation
Indices: 546921--547457 Score: 993
Period size: 267 Copynumber: 2.0 Consensus size: 267
546911 TATCAAAGAC
**
546921 TGAAGGATTGAAGGGCAAAGTGGTCTTTTGACATGAAATGAATTTTAAATTCATTTTATGTTAAT
1 TGAAGGATTGAAGGAAAAAGTGGTCTTTTGACATGAAATGAATTTTAAATTCATTTTATGTTAAT
*
546986 ATAACATGCGACGAATTAGAGAAAAAGGAAAAGAAAAATCTAGAATATATCTTCATCTCCTATCC
66 ATAACATGCGACGAATTAAAGAAAAAGGAAAAGAAAAATCTAGAATATATCTTCATCTCCTATCC
* *
547051 TTCATTTTATACCGTGAACGTCCCCTTTTGCTAAGGTAAGTGATTGAAGTTGGTTATTTCTTTCA
131 TTCATTTTATACCGTGAACCTCCCATTTTGCTAAGGTAAGTGATTGAAGTTGGTTATTTCTTTCA
547116 TTTTTGAGTTGGTTTTTAGTCCTTGGATGGTATAGAAACTTAAATAAAGCTTAAGGATGATTAAA
196 TTTTTGAGTTGGTTTTTAGTCCTTGGATGGTATAGAAACTTAAATAAAGCTTAAGGATGATTAAA
547181 AACTATG
261 AACTATG
*
547188 TGAAGGATTGAAGGAAAAAGTGGTCTTTTGACATGAAATGAATTTTAAATTTATTTTATGTTAAT
1 TGAAGGATTGAAGGAAAAAGTGGTCTTTTGACATGAAATGAATTTTAAATTCATTTTATGTTAAT
* *
547253 ATAACATGTGATGAATTAAAGAAAAAGGAAAAGAAAAATCTAGAATATATCTTCATCTCCTATCC
66 ATAACATGCGACGAATTAAAGAAAAAGGAAAAGAAAAATCTAGAATATATCTTCATCTCCTATCC
*
547318 TTCATTTTATACCGTGAACCTCCCATTTTGCTCAGGTAAGTGATTGAAGTTGGTTATTTCTTTCA
131 TTCATTTTATACCGTGAACCTCCCATTTTGCTAAGGTAAGTGATTGAAGTTGGTTATTTCTTTCA
547383 TTTTTGAGTTGGTTTTTAGTCCTTGGATGGTATAGAAACTTAAATAAAGCTTAAGGATGATTAAA
196 TTTTTGAGTTGGTTTTTAGTCCTTGGATGGTATAGAAACTTAAATAAAGCTTAAGGATGATTAAA
547448 AACTATG
261 AACTATG
547455 TGA
1 TGA
547458 TTGATGAATT
Statistics
Matches: 261, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 261 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (267 bp):
TGAAGGATTGAAGGAAAAAGTGGTCTTTTGACATGAAATGAATTTTAAATTCATTTTATGTTAAT
ATAACATGCGACGAATTAAAGAAAAAGGAAAAGAAAAATCTAGAATATATCTTCATCTCCTATCC
TTCATTTTATACCGTGAACCTCCCATTTTGCTAAGGTAAGTGATTGAAGTTGGTTATTTCTTTCA
TTTTTGAGTTGGTTTTTAGTCCTTGGATGGTATAGAAACTTAAATAAAGCTTAAGGATGATTAAA
AACTATG
Found at i:548417 original size:15 final size:15
Alignment explanation
Indices: 548397--548462 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
548387 TATTAGTATT
*
548397 TGAATATGTTATATG
1 TGAATATGTTCTATG
*
548412 TGAATATGTTCTACG
1 TGAATATGTTCTATG
* *
548427 TAAAAATGTTCTATG
1 TGAATATGTTCTATG
* *
548442 TGAATGTGCTCTATG
1 TGAATATGTTCTATG
548457 TGAATA
1 TGAATA
548463 AATGATACTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (15 bp):
TGAATATGTTCTATG
Found at i:548599 original size:23 final size:23
Alignment explanation
Indices: 548573--548651 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
548563 GGTTCTACGC
*
548573 GGTCCTTCAGGAAAATTCTATGT
1 GGTCCTTCGGGAAAATTCTATGT
* *
548596 GGTCCTTCGGGATAATTCTACGT
1 GGTCCTTCGGGAAAATTCTATGT
*
548619 GGTCCTTTGGGATAAA-TCTATGT
1 GGTCCTTCGGGA-AAATTCTATGT
548642 -GTCACTTCGG
1 GGTC-CTTCGG
548652 TGCATATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 3 0.06
23 42 0.89
24 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (23 bp):
GGTCCTTCGGGAAAATTCTATGT
Found at i:549172 original size:12 final size:12
Alignment explanation
Indices: 549155--549179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
549145 TGAGGGGTTC
549155 ACCACTAAAATA
1 ACCACTAAAATA
549167 ACCACTAAAATA
1 ACCACTAAAATA
549179 A
1 A
549180 AAGAAAAATA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ACCACTAAAATA
Found at i:554823 original size:20 final size:20
Alignment explanation
Indices: 554798--554841 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
554788 GTAAGAATCA
*
554798 AATGAA-TAATATCTATACT
1 AATGAAGTAATATCAATACT
*
554817 GAATGAAGTAGTATCAATACT
1 -AATGAAGTAATATCAATACT
554838 AATG
1 AATG
554842 TGGGGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGAAGTAATATCAATACT
Found at i:555517 original size:23 final size:23
Alignment explanation
Indices: 555491--555556 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
555481 GTTCTACGCA
555491 GTCCTTCGGGTCAATTCTATGTG
1 GTCCTTCGGGTCAATTCTATGTG
*
555514 GTCCTTCAGGAT-AATTCTATGTG
1 GTCCTTC-GGGTCAATTCTATGTG
* *
555537 GTCCTTCGGGACAAATCTAT
1 GTCCTTCGGGTCAATTCTAT
555557 ATGGCACTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.05
23 32 0.86
24 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
GTCCTTCGGGTCAATTCTATGTG
Found at i:555580 original size:24 final size:24
Alignment explanation
Indices: 555548--555603 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
555538 TCCTTCGGGA
555548 CAAA-TCTATATGGCACTTCGATG
1 CAAATTCTATATGGCACTTCGATG
* * * *
555571 CATATTCTATGTGTCACTTCGGTG
1 CAAATTCTATATGGCACTTCGATG
555595 CAAATTCTA
1 CAAATTCTA
555604 CGTGGTAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (24 bp):
CAAATTCTATATGGCACTTCGATG
Found at i:566645 original size:2 final size:2
Alignment explanation
Indices: 566638--566671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
566628 TGTGAAAAGA
566638 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
566672 CTTATATGGT
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:569192 original size:22 final size:22
Alignment explanation
Indices: 569166--569236 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
569156 CAAATAACGG
*
569166 AAGTGTCTTTTCACTGATACTA
1 AAGTGTCTTTACACTGATACTA
* * * *
569188 AAGTGCCTCTACA-TTAGTACAA
1 AAGTGTCTTTACACTGA-TACTA
* *
569210 AAGTGTATTTGCACTGATACTA
1 AAGTGTCTTTACACTGATACTA
569232 AAGTG
1 AAGTG
569237 CCTCAACACT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (22 bp):
AAGTGTCTTTACACTGATACTA
Found at i:569246 original size:22 final size:22
Alignment explanation
Indices: 569177--569246 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
569167 AGTGTCTTTT
569177 CACTGATACTAAAGTGCCTCTA
1 CACTGATACTAAAGTGCCTCTA
* * ** * *
569199 CA-TTAGTACAAAAGTGTATTTG
1 CACTGA-TACTAAAGTGCCTCTA
*
569221 CACTGATACTAAAGTGCCTCAA
1 CACTGATACTAAAGTGCCTCTA
569243 CACT
1 CACT
569247 AATAAGAAAA
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (22 bp):
CACTGATACTAAAGTGCCTCTA
Found at i:575126 original size:18 final size:18
Alignment explanation
Indices: 575103--575144 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
575093 GGTTTTACTT
575103 TTTCATGATTTTAGATTA
1 TTTCATGATTTTAGATTA
575121 TTTCATGATTTTAGATTA
1 TTTCATGATTTTAGATTA
575139 TTTCAT
1 TTTCAT
575145 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTCATGATTTTAGATTA
Found at i:575150 original size:2 final size:2
Alignment explanation
Indices: 575143--575174 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
575133 AGATTATTTC
575143 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
575175 TAAATTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:576717 original size:31 final size:31
Alignment explanation
Indices: 576674--576739 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
576664 TAGTATATGA
*
576674 TCACTTCTGTTTTTATTTATTTAAGATATAG
1 TCACTTCTGTTTTTATTTAATTAAGATATAG
* *
576705 TCACTT-TGGTTTTTATTTAATTAAGGTGTAG
1 TCACTTCT-GTTTTTATTTAATTAAGATATAG
576736 TCAC
1 TCAC
576740 CACGAGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.52
Consensus pattern (31 bp):
TCACTTCTGTTTTTATTTAATTAAGATATAG
Found at i:577014 original size:15 final size:15
Alignment explanation
Indices: 576985--577026 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
576975 TTAATCTTAC
*
576985 ATTAAAATAAAAATAT
1 ATTAAAAT-AAAATAA
*
577001 ATTCAAATAAAATAA
1 ATTAAAATAAAATAA
577016 ATTAAAATAAA
1 ATTAAAATAAA
577027 GTTAATCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAATAA
Found at i:580311 original size:23 final size:24
Alignment explanation
Indices: 580281--580327 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
580271 AGTCTTCCAT
580281 ACGATGTATAAAA-ATCTATGTAC
1 ACGATGTATAAAACATCTATGTAC
580304 ACGATGTATAAAACATCTATGTAC
1 ACGATGTATAAAACATCTATGTAC
580328 CATACCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
ACGATGTATAAAACATCTATGTAC
Done.