Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009578.1 Hibiscus syriacus cultivar Beakdansim tig00116946_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: 651624
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:260704 original size:7 final size:7
Alignment explanation
Indices: 260692--260736 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
260682 TCTCTCGCGA
260692 AGAAGAG
1 AGAAGAG
260699 AGAAGAG
1 AGAAGAG
*
260706 AGAAAAG
1 AGAAGAG
260713 AGAAGAG
1 AGAAGAG
260720 AGAAGAG
1 AGAAGAG
260727 AGAAGAG
1 AGAAGAG
260734 AGA
1 AGA
260737 GTTTGGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:261002 original size:79 final size:79
Alignment explanation
Indices: 260852--261009 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 79
260842 AACGTTCGAT
*
260852 TTTTTTTCATGAAATGAAAGTTTTGTTTTTTCTGATTTCCCCTTTATTTTATTTTCATCCCAATC
1 TTTTTGTCATGAAATGAAAGTTTTGTTTTTTCTGATTTCCCCTTTATTTTATTTTCATCCCAATC
260917 TATTTTTTAATATA
66 TATTTTTTAATATA
*
260931 TTTTTGTCATGAAATGAAAGTTTT-TTTTTTCTGATTTCCCCTTTATTTTATTTTCATCCCAATT
1 TTTTTGTCATGAAATGAAAGTTTTGTTTTTTCTGATTTCCCCTTTATTTTATTTTCATCCCAATC
260995 TATTTTTTAATATA
66 TATTTTTTAATATA
261009 T
1 T
261010 GTGCCTCGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 54 0.70
79 23 0.30
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (79 bp):
TTTTTGTCATGAAATGAAAGTTTTGTTTTTTCTGATTTCCCCTTTATTTTATTTTCATCCCAATC
TATTTTTTAATATA
Found at i:262266 original size:16 final size:16
Alignment explanation
Indices: 262245--262277 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
262235 AAATATTGTC
262245 ATTTTAATAAATT-TTA
1 ATTTTAA-AAATTATTA
262261 ATTTTAAAAATTATTA
1 ATTTTAAAAATTATTA
262277 A
1 A
262278 AAAAATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAAAAATTATTA
Found at i:263739 original size:13 final size:13
Alignment explanation
Indices: 263723--263750 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
263713 AAGAAAAAGG
263723 AAAAAGAGAGAGA
1 AAAAAGAGAGAGA
263736 AAAAAGAGAGAGA
1 AAAAAGAGAGAGA
263749 AA
1 AA
263751 TAAGTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAGAGA
Found at i:263890 original size:15 final size:16
Alignment explanation
Indices: 263861--263893 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
263851 AGAAACCCGA
263861 AAAAGAAATAAAAAAC
1 AAAAGAAATAAAAAAC
263877 AAAAGAAA-AAAAAAC
1 AAAAGAAATAAAAAAC
263892 AA
1 AA
263894 CCATTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAGAAATAAAAAAC
Found at i:264651 original size:22 final size:21
Alignment explanation
Indices: 264626--264668 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
264616 GAAATGACCC
264626 TTAATAAATAGTTCAAAATAAA
1 TTAATAAATA-TTCAAAATAAA
**
264648 TTAATTTATATTCAAAATAAA
1 TTAATAAATATTCAAAATAAA
264669 AGGATCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAATAAATATTCAAAATAAA
Found at i:265822 original size:30 final size:30
Alignment explanation
Indices: 265778--265834 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
265768 ATTTTTTTGA
* *
265778 GGATTAAATTGAAATTT-TAATTAAATTCAG
1 GGATCAAAATGAAATTTCT-ATTAAATTCAG
265808 GGATCAAAATGAAATTTCTATTAAATT
1 GGATCAAAATGAAATTTCTATTAAATT
265835 TATACCCAAA
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:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (30 bp):
GGATCAAAATGAAATTTCTATTAAATTCAG
Found at i:275994 original size:20 final size:20
Alignment explanation
Indices: 275969--276029 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
275959 TTTTGGTGCA
*
275969 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
275989 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
276010 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
276030 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:276038 original size:21 final size:21
Alignment explanation
Indices: 276012--276051 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
276002 CCCCCTTTGA
*
276012 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
276033 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
276052 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:278046 original size:17 final size:17
Alignment explanation
Indices: 278013--278046 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
278003 TTGAATATTT
* *
278013 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
278030 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
278047 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:279734 original size:18 final size:18
Alignment explanation
Indices: 279713--279759 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
279703 CCGTTGACCA
279713 TTGATCGTTGATCGAACG
1 TTGATCGTTGATCGAACG
*
279731 TTGATCGTTGATCGACCG
1 TTGATCGTTGATCGAACG
*
279749 TTGATTGTTGA
1 TTGATCGTTGA
279760 CCTACCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (18 bp):
TTGATCGTTGATCGAACG
Found at i:279766 original size:18 final size:18
Alignment explanation
Indices: 279708--279770 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
279698 ACTGGCCGTT
* *
279708 GACCATTGATCGTTGATC
1 GACCGTTGATCGTTGACC
* *
279726 GAACGTTGATCGTTGATC
1 GACCGTTGATCGTTGACC
*
279744 GACCGTTGATTGTTGACC
1 GACCGTTGATCGTTGACC
*
279762 TACCGTTGA
1 GACCGTTGA
279771 CCATTAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (18 bp):
GACCGTTGATCGTTGACC
Found at i:280269 original size:13 final size:13
Alignment explanation
Indices: 280251--280275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
280241 ACATTACTGT
280251 TTTGAACTATTTA
1 TTTGAACTATTTA
280264 TTTGAACTATTT
1 TTTGAACTATTT
280276 TAGATTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTGAACTATTTA
Found at i:287513 original size:20 final size:20
Alignment explanation
Indices: 287470--287515 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
287460 GGTCAGTGGG
** *
287470 TCAGACCGATTCGGGTTGAC
1 TCAGACCGATTCGGACTGAA
*
287490 TCAGATCGATTCGGACTGAA
1 TCAGACCGATTCGGACTGAA
287510 TCAGAC
1 TCAGAC
287516 TGGTTTGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
TCAGACCGATTCGGACTGAA
Found at i:293429 original size:40 final size:40
Alignment explanation
Indices: 293384--293465 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
293374 TATAAAACAT
293384 TCTTGAATTATTAATATATAAAACAATGATTAAAAATCCA
1 TCTTGAATTATTAATATATAAAACAATGATTAAAAATCCA
*
293424 TCTTGAATTATTACTATATAAAACAATGATTAAAAATCCA
1 TCTTGAATTATTAATATATAAAACAATGATTAAAAATCCA
293464 TC
1 TC
293466 AAATAGTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (40 bp):
TCTTGAATTATTAATATATAAAACAATGATTAAAAATCCA
Found at i:295224 original size:17 final size:17
Alignment explanation
Indices: 295202--295238 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
295192 CTAATCAAAT
295202 TTCATCATAACATAAAC
1 TTCATCATAACATAAAC
295219 TTCATCATAACATAAAC
1 TTCATCATAACATAAAC
295236 TTC
1 TTC
295239 CTCTAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.32
Consensus pattern (17 bp):
TTCATCATAACATAAAC
Found at i:301097 original size:25 final size:23
Alignment explanation
Indices: 301059--301108 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
301049 ATGGAACTAT
301059 GGTGCAATTCTACGCGG-CACTTC
1 GGTGCAATTCTACGCGGTC-CTTC
301082 GGTGCAAATTTCTACGCGGTCCTTC
1 GGTGC-AA-TTCTACGCGGTCCTTC
301107 GG
1 GG
301109 AAAACAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 2 0.08
25 16 0.67
26 1 0.04
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGTCCTTC
Found at i:315258 original size:60 final size:59
Alignment explanation
Indices: 315193--315319 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 59
315183 GAACATATGA
* **
315193 ATAGTCGAGTGACCATTTTGTAACCTTAAATAG-CCGAAGAACTCAACAAAGCAACATTTT
1 ATAGTCGAG-GACCATGTTGTAACCTTAAATAGTCCGAAG-ACTCAACAAAGCAACACCTT
* * * * * *
315253 ATAGTCATAGGACCATGTTGTGACTTTTAATAGTCGGAAGACTCAACAAAGCATCACCTT
1 ATAGTC-GAGGACCATGTTGTAACCTTAAATAGTCCGAAGACTCAACAAAGCAACACCTT
315313 ATAGTCG
1 ATAGTCG
315320 TAGTCGAGGG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
60 48 0.87
61 7 0.13
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (59 bp):
ATAGTCGAGGACCATGTTGTAACCTTAAATAGTCCGAAGACTCAACAAAGCAACACCTT
Found at i:325343 original size:27 final size:27
Alignment explanation
Indices: 325294--325347 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
325284 AAGCATAAAG
*
325294 ATAAAAGAGATTTATTACCTCTTTTAT
1 ATAAAAGAGATTTAATACCTCTTTTAT
**
325321 ATAAAAGAGATTTAATAGTTCTTTTAT
1 ATAAAAGAGATTTAATACCTCTTTTAT
325348 TGGAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (27 bp):
ATAAAAGAGATTTAATACCTCTTTTAT
Found at i:327700 original size:3 final size:3
Alignment explanation
Indices: 327678--327725 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
327668 TTGCACATTA
*
327678 ATT ATT AGT ATT ACTT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
327723 ATT
1 ATT
327726 TCTTTTCGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:330599 original size:26 final size:25
Alignment explanation
Indices: 330553--330618 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
330543 TCTTCTTTAG
*
330553 TATTTTTATTGTTGAATTTTTTCCTT
1 TATTTTTATT-TTGAATTTTTTACTT
* * *
330579 TATTTTTATTTTTATTATTTTTATTT
1 TATTTTTATTTTGAAT-TTTTTACTT
330605 TATTGCTTTATTTT
1 TATT--TTTATTTT
330619 AGCCTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 21 0.64
28 8 0.24
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (25 bp):
TATTTTTATTTTGAATTTTTTACTT
Found at i:333346 original size:15 final size:15
Alignment explanation
Indices: 333326--333355 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
333316 AAGCAAGCAA
333326 CCTATAAGAAATAAG
1 CCTATAAGAAATAAG
*
333341 CCTATAAGAGATAAG
1 CCTATAAGAAATAAG
333356 GTAAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (15 bp):
CCTATAAGAAATAAG
Found at i:357547 original size:5 final size:5
Alignment explanation
Indices: 357514--357617 Score: 50
Period size: 6 Copynumber: 19.4 Consensus size: 5
357504 AAATATAATA
* * *
357514 TATAT ATATAT TCTAT TCTA- TATA- TATAT CATAT TATATT ATATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATA-T -TATAT
* * * *
357560 TATTAT TACTAT TATAA TAAAA TATAA TATATT TATAT TATTAT TAGTAT
1 TA-TAT TA-TAT TATAT TATAT TATAT TATA-T TATAT TA-TAT TA-TAT
357610 TATTAT TA
1 TA-TAT TA
357618 ATAATATTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
4 7 0.09
5 34 0.42
6 36 0.44
7 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:357551 original size:12 final size:11
Alignment explanation
Indices: 357506--357603 Score: 59
Period size: 10 Copynumber: 9.2 Consensus size: 11
357496 AGTTCTTGAA
357506 ATATA-ATA-T
1 ATATATATATT
357515 ATATATATATT
1 ATATATATATT
* *
357526 CTAT-TCTATAT
1 ATATATATAT-T
357537 ATATATCATATT
1 ATATAT-ATATT
357549 ATATTATATATT
1 ATA-TATATATT
357561 AT-TATTACTATT
1 ATATA-TA-TATT
* *
357573 ATA-ATAAAAT
1 ATATATATATT
357583 ATA-ATATATT
1 ATATATATATT
357593 -TATAT-TATT
1 ATATATATATT
357602 AT
1 AT
357604 TAGTATTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
9 11 0.16
10 22 0.31
11 12 0.17
12 19 0.27
13 6 0.09
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATATT
Found at i:357566 original size:18 final size:18
Alignment explanation
Indices: 357512--357617 Score: 76
Period size: 18 Copynumber: 5.8 Consensus size: 18
357502 TGAAATATAA
*
357512 TATATATATATATT-CTAT
1 TATAT-TATATATTATTAT
* *
357530 TCTATATATATATCA-TAT
1 TATAT-TATATATTATTAT
357548 TATATTATATATTATTAT
1 TATATTATATATTATTAT
** *
357566 TACTATTATAATAAAATATAA
1 TA-TATTAT-ATATTAT-TAT
357587 TATATT-TATATTATTAT
1 TATATTATATATTATTAT
357604 TAGTATTAT-TATTA
1 TA-TATTATATATTA
357618 ATAATATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
17 12 0.17
18 38 0.54
19 8 0.11
20 9 0.13
21 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.54
Consensus pattern (18 bp):
TATATTATATATTATTAT
Found at i:357620 original size:32 final size:35
Alignment explanation
Indices: 357505--357636 Score: 101
Period size: 35 Copynumber: 3.6 Consensus size: 35
357495 TAGTTCTTGA
*
357505 AATATAATATATATATATATT-CTATT-CTA-TATAT
1 AATATAATATAT-T-TATATTATTATTACTATTATAT
*
357539 ATATCATATTATATTATATATTATTATTACTATTATAAT
1 A-AT-ATAATATATT-TATATTATTATTACTATTAT-AT
*
357578 AAAATATAATATATTTATATTATTATTAGTATTAT-T
1 --AATATAATATATTTATATTATTATTACTATTATAT
* * *
357614 ATTAATAATATTTTTATTTTATT
1 AAT-ATAATATATTTATATTATT
357637 TTCTAGGGTC
Statistics
Matches: 82, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
34 3 0.04
35 27 0.33
36 13 0.16
37 3 0.04
38 22 0.27
39 11 0.13
40 2 0.02
41 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (35 bp):
AATATAATATATTTATATTATTATTACTATTATAT
Found at i:361797 original size:45 final size:45
Alignment explanation
Indices: 361730--361835 Score: 194
Period size: 45 Copynumber: 2.4 Consensus size: 45
361720 CGGTGCACTA
**
361730 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCC
361775 AGAGTGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCC
361820 AGAGTGCATCGATGCA
1 AGAGTGCATCGATGCA
361836 TGGCTGGTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (45 bp):
AGAGTGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCC
Found at i:361846 original size:64 final size:65
Alignment explanation
Indices: 361778--361902 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 65
361768 AATAGCCAGA
361778 GTGCATCGATGCACCAAATGCATTCGATG-TTTCA-AAATAGC-C-AGAGTGCATCGATGCATGG
1 GTGCATCGATGCACCAAATGCATTCGATGTTTTCATAAA-A-CTCTA-AGTGCATCGATGCATGG
361839 CTG
63 CTG
*
361842 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTAAGTGCATCGATGCATG
1 GTGCATCGATGCACCAAATGCATTCGATGTTTTCATAAAACTCTAAGTGCATCGATGCATG
361903 AAATGCATTC
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
64 29 0.52
65 23 0.41
66 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGATGCACCAAATGCATTCGATGTTTTCATAAAACTCTAAGTGCATCGATGCATGGCTG
Found at i:361915 original size:64 final size:64
Alignment explanation
Indices: 361779--361916 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
361769 ATAGCCAGAG
***
361779 TGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCAAA
*
361843 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTA-AGTGCATCGATGCAT-G-
1 TGCATCGATGCACCAAATGCATTCGATG-TTTCA-AAATAGC-C-AGAGTGCATCGATGCATGGC
361903 AAA
62 AAA
361906 TGCATTCGATG
1 TGCA-TCGATG
361917 TTCAATTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
63 4 0.06
64 35 0.54
65 22 0.34
66 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCACCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCAAA
Found at i:361938 original size:110 final size:110
Alignment explanation
Indices: 361733--361968 Score: 306
Period size: 110 Copynumber: 2.1 Consensus size: 110
361723 TGCACTAAGA
*
361733 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCACCAAATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCACCAAATG
361798 CATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG-CTG
66 CATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGACTG
**
361842 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTA-AGTGCATCGATGCATGA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGC-C-AGAGTGCATCGATGCACCA
* *
361904 AATGCATTCGATG-TTCAATTTATA-CCATG-GTGCATCGATGCATGGATTG
62 AATGCATTCGATGTTTCAA--AATAGCCA-GAGTGCATCGATGCATGGACTG
*
361953 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
361969 CTCTGAAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
109 34 0.30
110 54 0.48
111 25 0.22
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (110 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCACCAAATG
CATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGACTG
Found at i:364613 original size:23 final size:22
Alignment explanation
Indices: 364583--364662 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
364573 GCATGACCTT
364583 GTGCATCGATGCCCATTCAAGG
1 GTGCATCGATGCCCATTCAAGG
* *
364605 CGTGCATCGGTGCACC-TTC-ATG
1 -GTGCATCGATGC-CCATTCAAGG
* *
364627 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCCCATTC-AAGG
*
364650 GATACATCGATGC
1 G-TGCATCGATGC
364663 ACTGTTAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.02
21 13 0.30
22 2 0.05
23 17 0.39
24 11 0.25
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCCCATTCAAGG
Found at i:371230 original size:20 final size:19
Alignment explanation
Indices: 371207--371268 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
371197 AATTTTCAAT
371207 ACTTTCACAATAGTTTCGAA
1 ACTTTCACAA-AGTTTCGAA
* *
371227 ACTTTCATCAAAGTTACTAA
1 ACTTTCA-CAAAGTTTCGAA
*
371247 ACTTTCCTCAAAGTTTCGAA
1 ACTTT-CACAAAGTTTCGAA
371267 AC
1 AC
371269 ATCATGTGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (19 bp):
ACTTTCACAAAGTTTCGAA
Found at i:379194 original size:68 final size:67
Alignment explanation
Indices: 379090--379221 Score: 176
Period size: 68 Copynumber: 2.0 Consensus size: 67
379080 AACTGACAAA
* * * *
379090 ACATGTAGAGATTCATACTAGGAAATTGGTTTATGGTAATGAGGTCTTCATCCCTAAAATCAAAA
1 ACATATAGAGATTCATACTAAGAAATTGATTAATGGTAATGAGGTCTTCATCCCTAAAAT-AAAA
379155 AAT
65 AAT
* * *
379158 ACATATAGAGATTC-TCACTAAGCAATTGATTAATGGTGATGAGGTCTTCGTCCCTAAAATAAAA
1 ACATATAGAGATTCAT-ACTAAGAAATTGATTAATGGTAATGAGGTCTTCATCCCTAAAATAAAA
379222 TAAAAAAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 5 0.09
68 51 0.91
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (67 bp):
ACATATAGAGATTCATACTAAGAAATTGATTAATGGTAATGAGGTCTTCATCCCTAAAATAAAAA
AT
Found at i:383916 original size:2 final size:2
Alignment explanation
Indices: 383909--383945 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
383899 TACACTCATG
383909 TA TA 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 TA TA T
383946 CTACACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:385963 original size:8 final size:7
Alignment explanation
Indices: 385921--385961 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
385911 CATTTAATGA
385921 AAAAAAT
1 AAAAAAT
*
385928 AAAAAAG
1 AAAAAAT
*
385935 AAAAATT
1 AAAAAAT
*
385942 GAAAAAT
1 AAAAAAT
385949 AAAAAAT
1 AAAAAAT
385956 AAAAAA
1 AAAAAA
385962 ATGATGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:386730 original size:18 final size:19
Alignment explanation
Indices: 386684--386730 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
386674 AGCCTGGATT
*
386684 AATTACAAAGCCATAACCC
1 AATTACAAAGCCAAAACCC
* *
386703 AATCATAAAG-CAAAACCC
1 AATTACAAAGCCAAAACCC
*
386721 GATTACAAAG
1 AATTACAAAG
386731 TTGATGACCC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.15
Consensus pattern (19 bp):
AATTACAAAGCCAAAACCC
Found at i:386750 original size:21 final size:21
Alignment explanation
Indices: 386726--386785 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
386716 AACCCGATTA
386726 CAAAGTTGATGACCCATTATG
1 CAAAGTTGATGACCCATTATG
386747 CAAA----A--ACCCGATTA--
1 CAAAGTTGATGACCC-ATTATG
386761 CAAAGTTGATGACCCATTATG
1 CAAAGTTGATGACCCATTATG
386782 CAAA
1 CAAA
386786 AACCCGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 18
0.62 0.00 0.38
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 4 0.13
17 1 0.03
18 1 0.03
19 4 0.13
20 4 0.13
21 8 0.27
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (21 bp):
CAAAGTTGATGACCCATTATG
Found at i:386757 original size:35 final size:35
Alignment explanation
Indices: 386714--386799 Score: 172
Period size: 35 Copynumber: 2.5 Consensus size: 35
386704 ATCATAAAGC
386714 AAAACCCGATTACAAAGTTGATGACCCATTATGCA
1 AAAACCCGATTACAAAGTTGATGACCCATTATGCA
386749 AAAACCCGATTACAAAGTTGATGACCCATTATGCA
1 AAAACCCGATTACAAAGTTGATGACCCATTATGCA
386784 AAAACCCGATTACAAA
1 AAAACCCGATTACAAA
386800 CCCAAAGAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (35 bp):
AAAACCCGATTACAAAGTTGATGACCCATTATGCA
Found at i:388674 original size:7 final size:7
Alignment explanation
Indices: 388649--388681 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
388639 GAGTGTGTCA
*
388649 TATTTTT
1 TATTATT
388656 TATTATT
1 TATTATT
388663 T-TTATT
1 TATTATT
388669 TATTATT
1 TATTATT
388676 TATTAT
1 TATTAT
388682 ATTTTGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTATT
Found at i:432736 original size:35 final size:35
Alignment explanation
Indices: 432697--432780 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
432687 ATGTTGCATT
* * *
432697 TTGTATTTGGTTGATTTAGTAAGAATGTAAAATTA
1 TTGTATTTGGTTAATTTAATAAGAAAGTAAAATTA
* **
432732 TTGTATTTGATTAATTTAATAAGAAAGTAAGTTTA
1 TTGTATTTGGTTAATTTAATAAGAAAGTAAAATTA
*
432767 TCGTATTTGGTTAA
1 TTGTATTTGGTTAA
432781 AGGAATAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (35 bp):
TTGTATTTGGTTAATTTAATAAGAAAGTAAAATTA
Found at i:435711 original size:20 final size:20
Alignment explanation
Indices: 435674--435711 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
435664 GGCCGTTTCT
*
435674 AGCCGTTGGGGATGATTTGG
1 AGCCGTTGGGGATAATTTGG
*
435694 AGCCGTTGGGGGTAATTT
1 AGCCGTTGGGGATAATTT
435712 TTCTACAAAA
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:0.16, C:0.11, G:0.42, T:0.32
Consensus pattern (20 bp):
AGCCGTTGGGGATAATTTGG
Found at i:435766 original size:20 final size:21
Alignment explanation
Indices: 435741--435780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
435731 TCAGGATAGG
435741 GAGTATCGATACT-CCTTTAA
1 GAGTATCGATACTACCTTTAA
*
435761 GAGTATCGGTACTACCTTTA
1 GAGTATCGATACTACCTTTA
435781 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (21 bp):
GAGTATCGATACTACCTTTAA
Found at i:448856 original size:3 final size:3
Alignment explanation
Indices: 448835--448875 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
448825 CTACCAAAAA
*
448835 TAT TAT T-T TAT TAA T-T TAT TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
448876 ATCAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.15
3 28 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:448862 original size:8 final size:8
Alignment explanation
Indices: 448834--448875 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
448824 TCTACCAAAA
448834 ATATTATT
1 ATATTATT
*
448842 TTATTAATT
1 ATATT-ATT
448851 -TATTATT
1 ATATTATT
448858 ATATTATT
1 ATATTATT
448866 ATTATTATT
1 A-TATTATT
448875 A
1 A
448876 ATCAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 3 0.10
8 16 0.53
9 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATATTATT
Found at i:450723 original size:24 final size:20
Alignment explanation
Indices: 450670--450726 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
450660 TCCCTTTTGA
*
450670 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
450690 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
450713 ATGTGCATCGATGC
1 A-GTGCATCGATGC
450727 GCTACTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:454433 original size:26 final size:26
Alignment explanation
Indices: 454363--454419 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
454353 ATCATATATC
*
454363 ACATATGCATATTATTCATTATATAA
1 ACATAAGCATATTATTCATTATATAA
454389 ACATAAGCATATTATTCATTATATAA
1 ACATAAGCATATTATTCATTATATAA
454415 ACATA
1 ACATA
454420 TATTCATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
ACATAAGCATATTATTCATTATATAA
Found at i:454782 original size:18 final size:20
Alignment explanation
Indices: 454759--454809 Score: 79
Period size: 18 Copynumber: 2.6 Consensus size: 20
454749 TCCCCTTTGA
454759 AGTGCATCGATGTATTC-T-
1 AGTGCATCGATGTATTCTTC
454777 AGTGCATCGATGTATTCTTC
1 AGTGCATCGATGTATTCTTC
454797 ATGTGCATCGATG
1 A-GTGCATCGATG
454810 CGCTACTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.57
19 1 0.03
20 1 0.03
21 11 0.37
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGTATTCTTC
Found at i:455462 original size:10 final size:10
Alignment explanation
Indices: 455447--455473 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
455437 CACGAGAAGA
455447 AGAAGAAAGG
1 AGAAGAAAGG
455457 AGAAGAAAGG
1 AGAAGAAAGG
455467 AGAAGAA
1 AGAAGAA
455474 GAGAACTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGG
Found at i:459006 original size:19 final size:20
Alignment explanation
Indices: 458962--459006 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
458952 TTGGGATCAA
458962 CATTTTTGCATCTGCATTTG
1 CATTTTTGCATCTGCATTTG
*
458982 CA-TTTTGCATCTGTATTT-
1 CATTTTTGCATCTGCATTTG
459000 CATTTTT
1 CATTTTT
459007 TAAGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (20 bp):
CATTTTTGCATCTGCATTTG
Found at i:459874 original size:164 final size:159
Alignment explanation
Indices: 459577--459897 Score: 581
Period size: 164 Copynumber: 2.0 Consensus size: 159
459567 CCGATTTACC
459577 AGAATAATCATGGTCACTACCAAAGAACTGATTTTGACATTCCCTCTCTTTAGACCTTGAAACAT
1 AGAATAATCATGGTCACTACCAAAGAACTGATTTTGACATTCCCTCTCTTTAGACCTTGAAACAT
459642 GCATCTATCCTTCGATACATAAAAGTCATACACATACCTTTGTTGAGCCAATAAAGTCACAATTG
66 GCATCTATCCTTCGATACATAAAAGTCATACACATACCTTTGTTGAGCCAATAAAGTCACAATTG
459707 TCTTCTTAGA-GTCAAACCAACATTTTCT
131 TCTTCTTAGATGTCAAACCAACATTTTCT
459735 AGAATAATTCATGGTCACTACCAAAGAACTGATTTTTGACATTCCCTCTCTTTTAGACCTTGAAA
1 AGAATAA-TCATGGTCACTACCAAAGAACTGA-TTTTGACATTCCCTCTC-TTTAGACCTTGAAA
459800 CATTGCATCTATCCTTTCGATACATAAAAGTCATACACATACCTTTTGTTGAGCCAATAAAGTCA
63 CA-TGCATCTATCC-TTCGATACATAAAAGTCATACACATACC-TTTGTTGAGCCAATAAAGTCA
459865 CAATTGTCTTCTTAGATGTCAAACCAACATTTT
125 CAATTGTCTTCTTAGATGTCAAACCAACATTTT
459898 TCTACAAATA
Statistics
Matches: 156, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
158 7 0.04
159 24 0.15
160 17 0.11
161 16 0.10
162 11 0.07
163 28 0.18
164 37 0.24
165 16 0.10
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (159 bp):
AGAATAATCATGGTCACTACCAAAGAACTGATTTTGACATTCCCTCTCTTTAGACCTTGAAACAT
GCATCTATCCTTCGATACATAAAAGTCATACACATACCTTTGTTGAGCCAATAAAGTCACAATTG
TCTTCTTAGATGTCAAACCAACATTTTCT
Found at i:460443 original size:13 final size:13
Alignment explanation
Indices: 460425--460476 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
460415 GATAAATAAA
460425 CAAAGAGAAAAAG
1 CAAAGAGAAAAAG
460438 CAAAGA-AAAAGAG
1 CAAAGAGAAAA-AG
460451 CAAA-AGAAAAAG
1 CAAAGAGAAAAAG
460463 CAAAGAGCAAAAAG
1 CAAAGAG-AAAAAG
460477 AAAACAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.31
13 18 0.51
14 6 0.17
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (13 bp):
CAAAGAGAAAAAG
Found at i:461875 original size:31 final size:31
Alignment explanation
Indices: 461831--461907 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
461821 CATTAAGGCA
461831 GTTTCTTTAGAAACACAAA-ATCTTTGAGTAT-
1 GTTTCTTTAGAAACA-AAACATCTTTGAG-ATC
461862 GTTTCTGTT-GAAACAAAACCATCTTTGAGATC
1 GTTTCT-TTAGAAACAAAA-CATCTTTGAGATC
461894 GTTTCATTTA-AAAC
1 GTTTC-TTTAGAAAC
461908 GAATTTTGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
30 3 0.08
31 14 0.35
32 22 0.55
33 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
GTTTCTTTAGAAACAAAACATCTTTGAGATC
Found at i:463071 original size:91 final size:91
Alignment explanation
Indices: 462905--463076 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
462895 CCCATGTGCC
* *
462905 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGTCCT
* *
462970 CTCCCTATTCGGCCAAGCCATATGTT
66 CTACCAATTCGGCCAAGCCATATGTT
* * *
462996 TTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATGAATG-G-CC
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAA-GAGTCC
*
463059 ATCTATCAATTCGGCCAA
65 -TCTACCAATTCGGCCAA
463077 TCACCATTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 69 0.97
92 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGTCCT
CTACCAATTCGGCCAAGCCATATGTT
Found at i:463965 original size:81 final size:82
Alignment explanation
Indices: 463825--463980 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 82
463815 TGGTATGTCC
* * * * ***
463825 TCCTCATCGCGTAGGAACTGTGTCATCCCCTAACCAGACTTTCTCATCACTTTGGAGCCATGTCA
1 TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
463890 CCCCTGATAATCAGTCG
66 CCCCTGATAATCAGTCG
* * * *
463907 TCCTCATCGCGTAGGAACCGTTTCCTTCCC-GACCAGACCTCCTCATCACGTAAAAGCCATGTCA
1 TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
463971 CCCCTGATAA
66 CCCCTGATAA
463981 CTAGCCATCC
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
81 37 0.59
82 26 0.41
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (82 bp):
TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
CCCCTGATAATCAGTCG
Found at i:463992 original size:81 final size:82
Alignment explanation
Indices: 463825--464005 Score: 204
Period size: 81 Copynumber: 2.2 Consensus size: 82
463815 TGGTATGTCC
* * * * ***
463825 TCCTCATCGCGTAGGAACTGTGTCATCCCCTAACCAGACTTTCTCATCACTTTGGAGCCATGTCA
1 TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
* *
463890 CCCCTGATAATCAGTCG
66 CCCCTGATAATCAGCCA
* * * *
463907 TCCTCATCGCGTAGGAACCGTTTCCTTCCC-GACCAGACCTCCTCATCACGTAAAAGCCATGTCA
1 TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
463971 CCCCTGATAA-CTAGCCA
66 CCCCTGATAATC-AGCCA
* *
463988 TCCTCGTCACGTAGGAAC
1 TCCTCATCGCGTAGGAAC
464006 TATGTTATCA
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 56 0.67
82 26 0.31
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (82 bp):
TCCTCATCGCGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCACGTAAAAGCCATGTCA
CCCCTGATAATCAGCCA
Found at i:469641 original size:29 final size:30
Alignment explanation
Indices: 469580--469643 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
469570 AAGTTTTAGA
* * *
469580 AAATTTAAAATGTAAAAATATATTTTTAAT
1 AAATTTAAAATATAAAAATATATATTAAAT
469610 AAATTTAAAA-ATAAAAATAT-TATTAAACT
1 AAATTTAAAATATAAAAATATATATTAAA-T
469639 AAATT
1 AAATT
469644 GAAATTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 5 0.17
29 15 0.50
30 10 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
AAATTTAAAATATAAAAATATATATTAAAT
Found at i:469656 original size:16 final size:15
Alignment explanation
Indices: 469631--469664 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
469621 TAAAAATATT
469631 ATTAAACTAAATTGAA
1 ATTAAACTAAATT-AA
*
469647 ATTAATCTAAATTAA
1 ATTAAACTAAATTAA
469662 ATT
1 ATT
469665 CGAAGATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTAAACTAAATTAA
Found at i:471641 original size:24 final size:24
Alignment explanation
Indices: 471594--471642 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
471584 TAAAGTATGT
*
471594 TTTATATTTTATATATTTATTTTG
1 TTTATATTTTATATATTTACTTTG
471618 TTTATATTATTATATA-TTACTTTG
1 TTTATATT-TTATATATTTACTTTG
471642 T
1 T
471643 ACATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATATTTTATATATTTACTTTG
Found at i:471652 original size:24 final size:25
Alignment explanation
Indices: 471602--471655 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
471592 GTTTTATATT
* ** *
471602 TTATATATTTATTTTGTTTATATTA
1 TTATATATTTACTTTGTACATAATA
471627 TTATATA-TTACTTTGTACATAATA
1 TTATATATTTACTTTGTACATAATA
471651 TTATA
1 TTATA
471656 GAATGATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
TTATATATTTACTTTGTACATAATA
Found at i:476264 original size:32 final size:32
Alignment explanation
Indices: 476218--476280 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
476208 GACAATAACT
476218 TTTTAGGATCAATACCTCTTGCATACATTCAA
1 TTTTAGGATCAATACCTCTTGCATACATTCAA
*
476250 TTTTGGGATCAATACCTCTTGCATACATTCA
1 TTTTAGGATCAATACCTCTTGCATACATTCA
476281 TTCTTCATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (32 bp):
TTTTAGGATCAATACCTCTTGCATACATTCAA
Found at i:480103 original size:7 final size:7
Alignment explanation
Indices: 480091--480120 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
480081 TATTTATATT
480091 TTCATTC
1 TTCATTC
480098 TTCATTC
1 TTCATTC
*
480105 TTTATTC
1 TTCATTC
480112 TTCATTC
1 TTCATTC
480119 TT
1 TT
480121 TACATTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (7 bp):
TTCATTC
Found at i:480108 original size:22 final size:21
Alignment explanation
Indices: 480077--480120 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
480067 CAAATGGCCA
*
480077 TCATTATTTATATTTTCATTCT
1 TCATTATTTAT-TCTTCATTCT
*
480099 TCATTCTTTATTCTTCATTCT
1 TCATTATTTATTCTTCATTCT
480120 T
1 T
480121 TACATTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (21 bp):
TCATTATTTATTCTTCATTCT
Found at i:480113 original size:14 final size:14
Alignment explanation
Indices: 480094--480122 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
480084 TTATATTTTC
480094 ATTCTTCATTCTTT
1 ATTCTTCATTCTTT
480108 ATTCTTCATTCTTT
1 ATTCTTCATTCTTT
480122 A
1 A
480123 CATTCATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTCTTCATTCTTT
Found at i:482043 original size:15 final size:15
Alignment explanation
Indices: 482023--482072 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 15
482013 TTTCATTTAA
*
482023 ATATTATTTATATTT
1 ATATTATTTATAATT
482038 ATATTA-TTATAA-T
1 ATATTATTTATAATT
482051 -TATTA-TTATAATT
1 ATATTATTTATAATT
482064 ATTATTATT
1 A-TATTATT
482073 ATTATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 11 0.37
13 2 0.07
14 5 0.17
15 11 0.37
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTATTTATAATT
Found at i:482045 original size:3 final size:3
Alignment explanation
Indices: 482039--482079 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
482029 TTTATATTTA
* *
482039 TAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
482080 AAAAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:482054 original size:12 final size:12
Alignment explanation
Indices: 482039--482079 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
482029 TTTATATTTA
482039 TATTATTATAAT
1 TATTATTATAAT
482051 TATTATTATAAT
1 TATTATTATAAT
*
482063 TATTATTATTAT
1 TATTATTATAAT
482075 TATTA
1 TATTA
482080 AAAAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:494933 original size:7 final size:7
Alignment explanation
Indices: 494921--494974 Score: 76
Period size: 7 Copynumber: 7.9 Consensus size: 7
494911 ATGCTTGAAG
494921 AAAAAGA
1 AAAAAGA
494928 AAAAAGA
1 AAAAAGA
494935 AAAAA-A
1 AAAAAGA
*
494941 AGAAAGA
1 AAAAAGA
494948 AAAAA-A
1 AAAAAGA
494954 AGAAAAGA
1 A-AAAAGA
494962 AAAAAGA
1 AAAAAGA
494969 AAAAAG
1 AAAAAG
494975 GGTGTCAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 7 0.17
7 33 0.79
8 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:494936 original size:13 final size:13
Alignment explanation
Indices: 494918--494974 Score: 71
Period size: 13 Copynumber: 4.2 Consensus size: 13
494908 ATTATGCTTG
494918 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
494931 AAGAAAAA-AAAGA
1 AAGAAAAAGAAA-A
*
494944 AAGAAAAAAAAGAA
1 AAGAAAAAGAA-AA
494958 AAGAAAAAAGAAAA
1 AAG-AAAAAGAAAA
494972 AAG
1 AAG
494975 GGTGTCAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 3 0.08
13 17 0.44
14 11 0.28
15 8 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:494945 original size:22 final size:23
Alignment explanation
Indices: 494918--494973 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
494908 ATTATGCTTG
494918 AAGAAA-AAGAAAAAAGAAAA-AA
1 AAGAAAGAA-AAAAAAGAAAAGAA
494940 AAGAAAGAAAAAAAAGAAAAG-A
1 AAGAAAGAAAAAAAAGAAAAGAA
494962 AA-AAAGAAAAAA
1 AAGAAAGAAAAAA
494974 GGGTGTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.31
22 20 0.62
23 2 0.06
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAAAAAAAGAAAAGAA
Found at i:496135 original size:94 final size:93
Alignment explanation
Indices: 495973--496544 Score: 945
Period size: 94 Copynumber: 6.1 Consensus size: 93
495963 AAAAGTGCCG
495973 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC-A
496038 AAAACCAATCATTGAATTTGAAAGATGAA
65 AAAACCAATCATTGAATTTGAAAGATGAA
*
496067 TGTGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC-A
496132 AAAACCAATCATTGAATTTGAAAGATGAA
65 AAAACCAATCATTGAATTTGAAAGATGAA
*
496161 TATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC-A
*
496226 AAAACTAATCATTGAATTTGAAAGATGAA
65 AAAACCAATCATTGAATTTGAAAGATGAA
*
496255 TGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC-A
496320 AAAACCAATCATTGAATTTGAAAGATGAA
65 AAAACCAATCATTGAATTTGAAAGATGAA
*
496349 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
*
496414 AAACCAATCATTGGATTTG-AA-AT-AA
66 AAACCAATCATTGAATTTGAAAGATGAA
* * *
496439 AGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-ACC
1 TGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC
* * *
496503 ACAGAACCAATCATTGGATTTAAAAGATGAA
64 A-AAAACCAATCATTGAATTTGAAAGATGAA
496534 TGTGCTCATAG
1 TGTGCTCATAG
496545 TACAAATAAA
Statistics
Matches: 451, Mismatches: 21, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
90 4 0.01
91 8 0.02
92 71 0.16
93 26 0.06
94 338 0.75
95 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (93 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
AAACCAATCATTGAATTTGAAAGATGAA
Found at i:497542 original size:113 final size:113
Alignment explanation
Indices: 497375--498225 Score: 1251
Period size: 113 Copynumber: 7.5 Consensus size: 113
497365 CCAGAAAAAA
* *
497375 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * ** * *
497440 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCG
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
* * *
497488 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
497553 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
* * *
497601 AGTTTATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * ** * * *
497666 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGTTCG
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
* *
497714 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
497779 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
* *
497827 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * ** * * * * **
497892 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTGCCAGATAA
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCA-TTACCAGTTCG
*
497941 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG---AAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATAAGAAGAA--C-TCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTG
498002 TTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
63 TTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
* *
498053 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
*
498118 AAGTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
66 AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
*
498166 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACT
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
498226 CATCTGAAGA
Statistics
Matches: 661, Mismatches: 69, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
109 12 0.02
110 4 0.01
112 24 0.04
113 581 0.88
114 24 0.04
116 4 0.01
117 12 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCG
Found at i:497780 original size:226 final size:226
Alignment explanation
Indices: 497375--498225 Score: 1445
Period size: 226 Copynumber: 3.8 Consensus size: 226
497365 CCAGAAAAAA
* * * *
497375 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
497440 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCGAGTTCATAATGAGAAGA
*
497505 ACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
497570 CATCATTCAATGGATCAGCATTACCAGTTCG
196 CATCATTCAATGGATCAGCATTACCAGTTCG
*
497601 AGTTTATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
*
497666 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCGAGTTCATAATGAGAAGA
497731 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
497796 CATCATTCAATGGATCAGCATTACCAGTTCG
196 CATCATTCAATGGATCAGCATTACCAGTTCG
497827 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
* * **
497892 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTGCCAGATAAAGTTCATAATGAGAAG
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACA-TTACCAGTTCGAGTTCATAATGAGAAG
* **
497957 AACTCGTCAT-CTGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAA
130 AACTCATC-TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAA
498020 TTCATCATTCAATGGATCAGCATTACCAGTTCG
194 TTCATCATTCAATGGATCAGCATTACCAGTTCG
498053 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
** * * ** * * *
498118 AAGTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGA
66 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCGAGTTCATAATGAGAAGA
* *
498183 ACTCATCTGAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACT
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
498226 CATCTGAAGA
Statistics
Matches: 589, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
224 1 0.00
225 32 0.05
226 521 0.88
227 34 0.06
228 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (226 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGAACTTGTTC
AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTACCAGTTCGAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
CATCATTCAATGGATCAGCATTACCAGTTCG
Found at i:497994 original size:20 final size:20
Alignment explanation
Indices: 497940--497998 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
497930 TTGCCAGATA
497940 AAGTTCATAATGAGAAGAAC
1 AAGTTCATAATGAGAAGAAC
** * *
497960 TCG-TCAT-CTGAAGAAGAAG
1 AAGTTCATAATG-AGAAGAAC
497979 AAGTTCATAATGAGAAGAAC
1 AAGTTCATAATGAGAAGAAC
497999 TTGTTCAACT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 12 0.43
21 2 0.07
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (20 bp):
AAGTTCATAATGAGAAGAAC
Found at i:498004 original size:20 final size:20
Alignment explanation
Indices: 497941--498005 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
497931 TGCCAGATAA
497941 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * **
497961 CG-TCAT-CTGAAGAAGAAGA
1 AGTTCATAATG-AGAAGAACT
497980 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
498000 TGTTCA
1 AGTTCA
498006 ACTTTTTGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 17 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:498634 original size:3 final size:3
Alignment explanation
Indices: 498628--498680 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
498618 TTCATTTAAA
* *
498628 TAT TAT T-T ATAT TAT TAT TAT TAT AAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
498673 TAT TAT TA
1 TAT TAT TA
498681 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:502409 original size:8 final size:8
Alignment explanation
Indices: 502385--502456 Score: 68
Period size: 8 Copynumber: 9.9 Consensus size: 8
502375 TATGCTTGAA
502385 GAAAAAAT
1 GAAAAAAT
**
502393 GAATGAAT
1 GAAAAAAT
502401 GAAAAAAT
1 GAAAAAAT
502409 G--AAAAT
1 GAAAAAAT
502415 G-AAAAA-
1 GAAAAAAT
*
502421 GAGAAAAT
1 GAAAAAAT
502429 G--AAAA-
1 GAAAAAAT
502434 GAAAAAAT
1 GAAAAAAT
502442 GAAAAAAT
1 GAAAAAAT
502450 GAAAAAA
1 GAAAAAA
502457 GAAGAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
5 1 0.02
6 11 0.21
7 12 0.23
8 29 0.55
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:502415 original size:14 final size:14
Alignment explanation
Indices: 502385--502454 Score: 83
Period size: 14 Copynumber: 4.9 Consensus size: 14
502375 TATGCTTGAA
502385 GAAAAAATGAATGAAT
1 GAAAAAATGAA--AAT
502401 GAAAAAATGAAAAT
1 GAAAAAATGAAAAT
502415 GAAAAAGA-GAAAAT
1 GAAAAA-ATGAAAAT
502429 GAAAAGAA--AAAAT
1 GAAAA-AATGAAAAT
502442 GAAAAAATGAAAA
1 GAAAAAATGAAAA
502455 AAGAAGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.04
13 10 0.20
14 25 0.50
15 2 0.04
16 11 0.22
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (14 bp):
GAAAAAATGAAAAT
Found at i:502429 original size:20 final size:19
Alignment explanation
Indices: 502401--502490 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 19
502391 ATGAATGAAT
502401 GAAAAAATGAAAATGAAAAA
1 GAAAAAATGAAAA-GAAAAA
*
502421 GAGAAAATGAAAAGAAAAAA
1 GAAAAAATGAAAAG-AAAAA
*
502441 TGAAAAAATGAAAA-AAGAA
1 -GAAAAAATGAAAAGAAAAA
502460 GAAAAAAATGAAAAGAAAGAA
1 G-AAAAAATGAAAAGAAA-AA
502481 -AAGAAAATGA
1 GAA-AAAATGA
502491 GGGATCGAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
19 19 0.32
20 26 0.43
21 14 0.23
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
GAAAAAATGAAAAGAAAAA
Found at i:502433 original size:13 final size:13
Alignment explanation
Indices: 502398--502446 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
502388 AAAATGAATG
*
502398 AATGAAAAAATGAA
1 AATGAAAAGA-GAA
502412 AATGAAAAAGAGAA
1 AATG-AAAAGAGAA
*
502426 AATGAAAAGAAAA
1 AATGAAAAGAGAA
502439 AATGAAAA
1 AATGAAAA
502447 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 16 0.50
14 11 0.34
15 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (13 bp):
AATGAAAAGAGAA
Found at i:502477 original size:14 final size:14
Alignment explanation
Indices: 502410--502487 Score: 60
Period size: 14 Copynumber: 5.7 Consensus size: 14
502400 TGAAAAAATG
*
502410 AAAATGAAAA-AGAG
1 AAAATGAAAAGA-AA
502424 AAAATGAAAAG-AA
1 AAAATGAAAAGAAA
502437 AAAATGAAAA-AATGA
1 AAAATGAAAAGAA--A
*
502452 AAAA--AGAAGAAA
1 AAAATGAAAAGAAA
502464 AAAATGAAAAGAAA
1 AAAATGAAAAGAAA
502478 GAAAA-GAAAA
1 -AAAATGAAAA
502488 TGAGGGATCG
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
12 5 0.09
13 15 0.28
14 24 0.45
15 9 0.17
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAATGAAAAGAAA
Found at i:503522 original size:105 final size:105
Alignment explanation
Indices: 503332--503629 Score: 425
Period size: 105 Copynumber: 2.8 Consensus size: 105
503322 TATAATTCAC
* *
503332 CCCCAGAAGGAGGTGAATCAAAATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGA
1 CCCCAGAAAGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGA
503397 GAAGGTTCATAATGAGAAGAGTCTGTTCCTTTCAAATCCA
66 GAAGGTTCATAATGAGAAGAGTCTGTTCCTTTCAAATCCA
* * * *
503437 CCGCAGAATGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGA
1 CCCCAGAAAGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGA
* * * * *
503502 GAATGTTCGTAATGATAAGAGTCTGTTCCTTTCCAATTCA
66 GAAGGTTCATAATGAGAAGAGTCTGTTCCTTTCAAATCCA
* * *
503542 CCCCAGAAAGAGGTGAATCAACATTTCCAGAAGAGTACATAATGAGAAGAACTCATTCGACAAAA
1 CCCCAGAAAGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC-GTC--CTAAA
503607 GGAGAAGAAGTTCATAATGAGAA
63 GGAGAAG--GTTCATAATGAGAA
503630 AAACTTGTTC
Statistics
Matches: 168, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
105 145 0.86
106 2 0.01
108 9 0.05
110 12 0.07
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (105 bp):
CCCCAGAAAGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGA
GAAGGTTCATAATGAGAAGAGTCTGTTCCTTTCAAATCCA
Found at i:503764 original size:21 final size:21
Alignment explanation
Indices: 503739--503803 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
503729 AACTCATCTG
503739 ATGAGGGAAAAGAAGTTCATA
1 ATGAGGGAAAAGAAGTTCATA
*
503760 ATGA--G--AAGAACTAATC-TA
1 ATGAGGGAAAAGAAGT--TCATA
503778 ATGAGGGAAAAGAAGTTCATA
1 ATGAGGGAAAAGAAGTTCATA
503799 ATGAG
1 ATGAG
503804 AAGAACTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 6 0.17
18 6 0.17
19 3 0.09
20 3 0.09
21 11 0.31
22 6 0.17
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.20
Consensus pattern (21 bp):
ATGAGGGAAAAGAAGTTCATA
Found at i:503770 original size:39 final size:39
Alignment explanation
Indices: 503716--503810 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
503706 CAGTGGAGAG
* *
503716 TCATAATGAGAAGAACTCATCTGATGAGGGAAAAGAAGT
1 TCATAATGAGAAGAACTAATCTAATGAGGGAAAAGAAGT
503755 TCATAATGAGAAGAACTAATCTAATGAGGGAAAAGAAGT
1 TCATAATGAGAAGAACTAATCTAATGAGGGAAAAGAAGT
503794 TCATAATGAGAAGAACT
1 TCATAATGAGAAGAACT
503811 TGTTCAACCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.21
Consensus pattern (39 bp):
TCATAATGAGAAGAACTAATCTAATGAGGGAAAAGAAGT
Found at i:505395 original size:27 final size:25
Alignment explanation
Indices: 505342--505396 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
505332 CATTAAAGTA
*
505342 TGTTTTATATTTTATATATTTATTT
1 TGTTTTATATTTTATATATTTACTT
505367 TGTTTGTATTATTATTATATA-TTACTT
1 TGTTT-TA-TATT-TTATATATTTACTT
505394 TGT
1 TGT
505397 ACGCAGGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 2 0.08
27 12 0.46
28 7 0.27
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (25 bp):
TGTTTTATATTTTATATATTTACTT
Found at i:506977 original size:15 final size:15
Alignment explanation
Indices: 506949--506991 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
506939 TCTTTGTTAT
* *
506949 TTATATAAAGAAAAA
1 TTATAAAAAAAAAAA
*
506964 TTATAAAAAAAAAAT
1 TTATAAAAAAAAAAA
506979 TTATATAAAAAAA
1 TTATA-AAAAAAA
506992 TGCCGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
TTATAAAAAAAAAAA
Found at i:509947 original size:105 final size:106
Alignment explanation
Indices: 509764--509977 Score: 360
Period size: 105 Copynumber: 2.0 Consensus size: 106
509754 TAAGGATAAA
* *
509764 TTATATATTTAGTCACTCAATTATTCTCATAATTTTTGTTTTGGTCACTTAATTATTATTCTTCT
1 TTATATATTTAGTCACTCAATTATTCTCATAAGTTTTGTTTTGGTCACTCAATTATTATTCTTCT
509829 CATAATCATCACTAAACTTAAATTAATTTCTTAAATGAGTT
66 CATAATCATCACTAAACTTAAATTAATTTCTTAAATGAGTT
509870 TTATATATTTAGTCACTCAATTATTCTCAT-AGTTTTGTTTTGGTCACTCAATTATTATTCTTCT
1 TTATATATTTAGTCACTCAATTATTCTCATAAGTTTTGTTTTGGTCACTCAATTATTATTCTTCT
** *
509934 CGA-AATTGTCACTAAACTTAAATTAATTTCTTAAATGCGTT
66 C-ATAATCATCACTAAACTTAAATTAATTTCTTAAATGAGTT
509975 TTA
1 TTA
509978 ATTTGTTTGG
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
105 71 0.70
106 31 0.30
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (106 bp):
TTATATATTTAGTCACTCAATTATTCTCATAAGTTTTGTTTTGGTCACTCAATTATTATTCTTCT
CATAATCATCACTAAACTTAAATTAATTTCTTAAATGAGTT
Found at i:510582 original size:7 final size:7
Alignment explanation
Indices: 510570--511014 Score: 683
Period size: 7 Copynumber: 60.3 Consensus size: 7
510560 ACAGACCTAA
510570 GCTCATT
1 GCTCATT
510577 GCTCATT
1 GCTCATT
510584 GCTCATT
1 GCTCATT
510591 GCTCATT
1 GCTCATT
510598 GCTCATT
1 GCTCATT
510605 GCTCATT
1 GCTCATT
510612 GCTCATT
1 GCTCATT
510619 GCTCATT
1 GCTCATT
510626 GCTCATT
1 GCTCATT
510633 GCTCATT
1 GCTCATT
510640 GCTCATT
1 GCTCATT
510647 GCTCATTT
1 GCTCA-TT
510655 GCTCATT
1 GCTCATT
510662 GCTCATT
1 GCTCATT
510669 GCTCATT
1 GCTCATT
510676 GCTCATTT
1 GCTCA-TT
510684 GCTCATT
1 GCTCATT
510691 GCTCATT
1 GCTCATT
510698 GCTCATTT
1 GCTCA-TT
510706 GCTCATT
1 GCTCATT
510713 GCTCATT
1 GCTCATT
510720 GCTCATTT
1 GCTCA-TT
510728 GCTCATTT
1 GCTCA-TT
510736 GCTCATT
1 GCTCATT
510743 GCTCATTT
1 GCTCA-TT
510751 GCTCATTT
1 GCTCA-TT
510759 GCTCATTT
1 GCTCA-TT
510767 GCTCATT
1 GCTCATT
510774 GCTCATTT
1 GCTCA-TT
510782 GCTCATTT
1 GCTCA-TT
510790 GCTCATTT
1 GCTCA-TT
510798 GCTCATT
1 GCTCATT
510805 GCTCATT
1 GCTCATT
510812 GCTCATTT
1 GCTCA-TT
510820 GCTCATTT
1 GCTCA-TT
510828 GCTCATT
1 GCTCATT
510835 GCTCATT
1 GCTCATT
510842 GCTCATTT
1 GCTCA-TT
510850 GCTCATTT
1 GCTCA-TT
510858 GCTCATTT
1 GCTCA-TT
510866 GCTCATT
1 GCTCATT
510873 GCTCATTT
1 GCTCA-TT
510881 GCTCATT
1 GCTCATT
510888 GCTCATT
1 GCTCATT
510895 GCTCATTT
1 GCTCA-TT
510903 GCTCATTT
1 GCTCA-TT
510911 GCTCATTT
1 GCTCA-TT
510919 GCTCATT
1 GCTCATT
510926 GCTCATTT
1 GCTCA-TT
510934 GCTCATT
1 GCTCATT
510941 GCTCATT
1 GCTCATT
510948 GCTCATTT
1 GCTCA-TT
510956 GCTCATT
1 GCTCATT
510963 GCTCATT
1 GCTCATT
510970 GCTCATT
1 GCTCATT
510977 GCTCATT
1 GCTCATT
510984 GCTCATT
1 GCTCATT
510991 GCTCATTT
1 GCTCA-TT
510999 GCTCATT
1 GCTCATT
511006 GCTCATT
1 GCTCATT
511013 GC
1 GC
511015 AATGAGGGTT
Statistics
Matches: 425, Mismatches: 0, Indels: 26
0.94 0.00 0.06
Matches are distributed among these distances:
7 254 0.60
8 171 0.40
ACGTcount: A:0.13, C:0.27, G:0.14, T:0.46
Consensus pattern (7 bp):
GCTCATT
Found at i:510658 original size:15 final size:14
Alignment explanation
Indices: 510570--511014 Score: 683
Period size: 15 Copynumber: 30.1 Consensus size: 14
510560 ACAGACCTAA
510570 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510584 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510598 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510612 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510626 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510640 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510655 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510669 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510684 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510698 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510713 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510728 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510743 GCTCATTTGCTCATTT
1 GCTCA-TTGCTCA-TT
510759 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510774 GCTCATTTGCTCATTT
1 GCTCA-TTGCTCA-TT
510790 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510805 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510820 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510835 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510850 GCTCATTTGCTCATTT
1 GCTCA-TTGCTCA-TT
510866 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510881 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510895 GCTCATTTGCTCATTT
1 GCTCA-TTGCTCA-TT
510911 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510926 GCTCATTTGCTCATT
1 GCTCA-TTGCTCATT
510941 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510956 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510970 GCTCATTGCTCATT
1 GCTCATTGCTCATT
510984 GCTCATTGCTCATTT
1 GCTCATTGCTCA-TT
510999 GCTCATTGCTCATT
1 GCTCATTGCTCATT
511013 GC
1 GC
511015 AATGAGGGTT
Statistics
Matches: 416, Mismatches: 0, Indels: 30
0.93 0.00 0.07
Matches are distributed among these distances:
14 156 0.38
15 186 0.45
16 74 0.18
ACGTcount: A:0.13, C:0.27, G:0.14, T:0.46
Consensus pattern (14 bp):
GCTCATTGCTCATT
Found at i:510659 original size:22 final size:22
Alignment explanation
Indices: 510571--511014 Score: 637
Period size: 22 Copynumber: 20.0 Consensus size: 22
510561 CAGACCTAAG
510571 CTCATTGCTCA-TTGCTCATTG
1 CTCATTGCTCATTTGCTCATTG
510592 CTCATTGCTCA-TTGCTCATTG
1 CTCATTGCTCATTTGCTCATTG
510613 CTCATTGCTCA-TTGCTCATTG
1 CTCATTGCTCATTTGCTCATTG
510634 CTCATTGCTCA-TTGCTCATTTG
1 CTCATTGCTCATTTGCTCA-TTG
510656 CTCATTGCTCA-TTGCTCATTG
1 CTCATTGCTCATTTGCTCATTG
510677 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510699 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510721 CTCATTTGCTCATTTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510744 CTCATTTGCTCATTTGCTCATTTG
1 CTCA-TTGCTCATTTGCTCA-TTG
510768 CTCATTGCTCATTTGCTCATTTG
1 CTCATTGCTCATTTGCTCA-TTG
510791 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510813 CTCATTTGCTCATTTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510836 CTCATTGCTCATTTGCTCATTTG
1 CTCATTGCTCATTTGCTCA-TTG
510859 CTCATTTGCTCA-TTGCTCATTTG
1 CTCA-TTGCTCATTTGCTCA-TTG
510882 CTCATTGCTCA-TTGCTCATTTG
1 CTCATTGCTCATTTGCTCA-TTG
510904 CTCATTTGCTCATTTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510927 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510949 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
510971 CTCATTGCTCA-TTGCTCATTG
1 CTCATTGCTCATTTGCTCATTG
510992 CTCATTTGCTCA-TTGCTCATTG
1 CTCA-TTGCTCATTTGCTCATTG
511014 C
1 C
511015 AATGAGGGTT
Statistics
Matches: 412, Mismatches: 0, Indels: 21
0.95 0.00 0.05
Matches are distributed among these distances:
21 88 0.21
22 178 0.43
23 118 0.29
24 28 0.07
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.46
Consensus pattern (22 bp):
CTCATTGCTCATTTGCTCATTG
Found at i:518066 original size:29 final size:28
Alignment explanation
Indices: 518010--518081 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
518000 AATTGAAATA
* * * *
518010 AAAATCAAAATTCAGTGTTATAATTGGT
1 AAAATCAAAGTTCAGTGGTACAAATGGT
518038 AAAATCGAAAGTTCAGTGGTACAAATGGT
1 AAAATC-AAAGTTCAGTGGTACAAATGGT
518067 ATAACATCTAAAGTT
1 A-AA-ATC-AAAGTT
518082 TGATGGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.17
29 19 0.53
30 2 0.06
31 9 0.25
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (28 bp):
AAAATCAAAGTTCAGTGGTACAAATGGT
Found at i:518433 original size:13 final size:13
Alignment explanation
Indices: 518415--518439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518405 AGAGAATATT
518415 TTATTAATTTTAA
1 TTATTAATTTTAA
518428 TTATTAATTTTA
1 TTATTAATTTTA
518440 TTTTATTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTAATTTTAA
Found at i:519347 original size:251 final size:251
Alignment explanation
Indices: 518904--519405 Score: 995
Period size: 251 Copynumber: 2.0 Consensus size: 251
518894 CCCCTACATG
518904 AATGAAATTGATTATTTCAATCATTGAATCGATATGGTGATAGATTCTACGTTCGATATTTGCAT
1 AATGAAATTGATTATTTCAATCATTGAATCGATATGGTGATAGATTCTACGTTCGATATTTGCAT
518969 GGGATAGGTAGGCGTCCCCCTTTGAACCTTCCCTTGTGAAAATATATTTACCTTACTGGCTGTCC
66 GGGATAGGTAGGCGTCCCCCTTTGAACCTTCCCTTGTGAAAATATATTTACCTTACTGGCTGTCC
519034 AGTATATGTGATGTCCTTGAACTATCCTACCGTTGGTGTAAGCGATGACATACCTCACACAAATA
131 AGTATATGTGATGTCCTTGAACTATCCTACCGTTGGTGTAAGCGATGACATACCTCACACAAATA
519099 TCTCACTAACAAGAATTTGATTCTCATGGTTATGTCCATATAACTATGGACATCTC
196 TCTCACTAACAAGAATTTGATTCTCATGGTTATGTCCATATAACTATGGACATCTC
519155 AATGAAATTGATTATTTCAATCATTGAATCGATATGGTGATAGATTCTACGTTCGATATTTGCAT
1 AATGAAATTGATTATTTCAATCATTGAATCGATATGGTGATAGATTCTACGTTCGATATTTGCAT
519220 GGGATAGGTAGGCGTCCCCCTTTGAACCTTCCCTTGTGAAAATATATTTACCTTACTGGCTGTCC
66 GGGATAGGTAGGCGTCCCCCTTTGAACCTTCCCTTGTGAAAATATATTTACCTTACTGGCTGTCC
519285 AGTATATGTGATGTCCTTGAACTATCCTACCGTTGGTGTAAGCGATGACATACCTCACACAAATA
131 AGTATATGTGATGTCCTTGAACTATCCTACCGTTGGTGTAAGCGATGACATACCTCACACAAATA
*
519350 TCTCACTAACAAGAATTTGATTCTCATGGTTATGTCCATATAACTGTGGACATCTC
196 TCTCACTAACAAGAATTTGATTCTCATGGTTATGTCCATATAACTATGGACATCTC
519406 CTAATTCTAC
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 250 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (251 bp):
AATGAAATTGATTATTTCAATCATTGAATCGATATGGTGATAGATTCTACGTTCGATATTTGCAT
GGGATAGGTAGGCGTCCCCCTTTGAACCTTCCCTTGTGAAAATATATTTACCTTACTGGCTGTCC
AGTATATGTGATGTCCTTGAACTATCCTACCGTTGGTGTAAGCGATGACATACCTCACACAAATA
TCTCACTAACAAGAATTTGATTCTCATGGTTATGTCCATATAACTATGGACATCTC
Found at i:531480 original size:21 final size:21
Alignment explanation
Indices: 531454--531534 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 21
531444 TTTTGGTGCA
* *
531454 GAGGGAATCGATACCCCCCAT
1 GAGGGAACCGATACCCCCTAT
* *
531475 GAGGGAACCGAT-CTCCCTTT
1 GAGGGAACCGATACCCCCTAT
*
531495 GAAGGGGAACCGATTCCCCCTA-
1 G-A-GGGAACCGATACCCCCTAT
*
531517 G-GGGAATCGATACCCCCT
1 GAGGGAACCGATACCCCCT
531535 GGGGTTCTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 15 0.31
20 6 0.12
21 12 0.24
22 11 0.22
23 5 0.10
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATACCCCCTAT
Found at i:533532 original size:24 final size:24
Alignment explanation
Indices: 533505--533551 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
533495 TTGAATGTTT
533505 GATTT-TGTGGATTGTTAGACTTTG
1 GATTTGTGTGGA-TGTTAGACTTTG
* *
533529 GATTTGTTTGGATGTTTGACTTT
1 GATTTGTGTGGATGTTAGACTTT
533552 ATATATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.15, C:0.04, G:0.28, T:0.53
Consensus pattern (24 bp):
GATTTGTGTGGATGTTAGACTTTG
Found at i:538980 original size:6 final size:6
Alignment explanation
Indices: 538969--539002 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
538959 ATCGAATACA
538969 ATCTTT ATCTTT ATCTTT ATCTTT ATCTTT ATCT
1 ATCTTT ATCTTT ATCTTT ATCTTT ATCTTT ATCT
539003 ATCACCGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (6 bp):
ATCTTT
Found at i:540120 original size:77 final size:78
Alignment explanation
Indices: 539973--540127 Score: 267
Period size: 77 Copynumber: 2.0 Consensus size: 78
539963 TGTTCAAGCC
*
539973 CCTTGAAGGGCTGATATATTTCTTTGCAATATTTTGTAATGTCACCACTCTATTAGATATAAAAT
1 CCTTCAAGGGCTGATATATTTCTTTGCAATATTTTGTAATGTCACCACTCTATTAGATATAAAAT
*
540038 AGAATAAATTAAA
66 AGAATAAACTAAA
* *
540051 CCTTCAAGGGCTGATTTATTTCTTTGCAATATTTTGT-ATGTCACCACTTTATTAGATATAAAAT
1 CCTTCAAGGGCTGATATATTTCTTTGCAATATTTTGTAATGTCACCACTCTATTAGATATAAAAT
540115 AGAATAAACTAAA
66 AGAATAAACTAAA
540128 TAATTAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 38 0.52
78 35 0.48
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (78 bp):
CCTTCAAGGGCTGATATATTTCTTTGCAATATTTTGTAATGTCACCACTCTATTAGATATAAAAT
AGAATAAACTAAA
Found at i:541168 original size:24 final size:24
Alignment explanation
Indices: 541116--541165 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
541106 TATAATAATT
*
541116 ATTATTATTAGAAATATTAATATA
1 ATTATTATTAGAAATATTAAAATA
*
541140 ATTATTGTTA-AAATATTAAAATA
1 ATTATTATTAGAAATATTAAAATA
541163 ATT
1 ATT
541166 TATTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTATTATTAGAAATATTAAAATA
Found at i:541289 original size:18 final size:18
Alignment explanation
Indices: 541263--541315 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
541253 TAATTTTATT
541263 TATTAATAATTTTTTTAAA
1 TATT-ATAATTTTTTTAAA
**
541282 TATTATAATTTAATTAAA
1 TATTATAATTTTTTTAAA
541300 TATTATAATTTATTTT
1 TATTATAATTT-TTTT
541316 TTAAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATAATTTTTTTAAA
Found at i:541445 original size:17 final size:18
Alignment explanation
Indices: 541400--541446 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
541390 CTAAAAATAT
541400 TTTAATAATTAATAATTTAA
1 TTTAAT-ATT-ATAATTTAA
*
541420 TTAAATATTATAATTT-A
1 TTTAATATTATAATTTAA
541437 TTTAATATTA
1 TTTAATATTA
541447 CTTGTCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 3 0.12
20 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATATTATAATTTAA
Found at i:541521 original size:21 final size:21
Alignment explanation
Indices: 541495--541564 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 21
541485 TTAGGATTAA
541495 AATAATACTAAAATATTTTAT
1 AATAATACTAAAATATTTTAT
541516 AATAATA-T--AATATTTTAT
1 AATAATACTAAAATATTTTAT
*
541534 TATAAT-CTTAAAAATATTTTAAT
1 AATAATAC-T-AAAATATTTT-AT
541557 AATTAATA
1 AA-TAATA
541565 ATTTAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 1 0.03
21 7 0.18
22 8 0.21
23 3 0.08
24 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATACTAAAATATTTTAT
Found at i:543614 original size:7 final size:7
Alignment explanation
Indices: 543592--543624 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
543582 CATGGAGTCT
543592 CATATCA
1 CATATCA
543599 CATATTCA
1 CATA-TCA
543607 CATATCA
1 CATATCA
543614 CATAT-A
1 CATATCA
543620 CATAT
1 CATAT
543625 AATCATGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (7 bp):
CATATCA
Found at i:544343 original size:24 final size:24
Alignment explanation
Indices: 544315--544375 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
544305 TACCCACTAT
544315 AGGGTATCGATACTACCCTAGCTG
1 AGGGTATCGATACTACCCTAGCTG
544339 AGGGTATCGATACTACCCTAGCTG
1 AGGGTATCGATACTACCCTAGCTG
544363 AGGGTATCGATAC
1 AGGGTATCGATAC
544376 CAAGATGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (24 bp):
AGGGTATCGATACTACCCTAGCTG
Found at i:544387 original size:18 final size:18
Alignment explanation
Indices: 544364--544411 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
544354 CCCTAGCTGA
544364 GGGTATCGATACCAAGAT
1 GGGTATCGATACCAAGAT
544382 GGGTATCGATACCAAGAT
1 GGGTATCGATACCAAGAT
544400 GGGTATCGATAC
1 GGGTATCGATAC
544412 AGAAATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (18 bp):
GGGTATCGATACCAAGAT
Found at i:545946 original size:18 final size:18
Alignment explanation
Indices: 545925--545960 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
545915 TTCTTTCATA
545925 TTTGCATAAA-CCTTATTC
1 TTTGCA-AAATCCTTATTC
545943 TTTGCAAAATCCTTATTC
1 TTTGCAAAATCCTTATTC
545961 AAATCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTGCAAAATCCTTATTC
Found at i:547927 original size:15 final size:14
Alignment explanation
Indices: 547907--547944 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
547897 CATGGAGTCT
*
547907 CATATCAGATATGCA
1 CATATCACATAT-CA
547922 CATATCACATATCA
1 CATATCACATATCA
547936 CATAT-ACAT
1 CATATCACAT
547945 GTAATCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 7 0.32
15 11 0.50
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (14 bp):
CATATCACATATCA
Found at i:547930 original size:7 final size:7
Alignment explanation
Indices: 547907--547944 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
547897 CATGGAGTCT
547907 CATATCA
1 CATATCA
*
547914 GATATGCA
1 CATAT-CA
547922 CATATCA
1 CATATCA
547929 CATATCA
1 CATATCA
547936 CATAT-A
1 CATATCA
547942 CAT
1 CAT
547945 GTAATCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 4 0.14
7 18 0.64
8 6 0.21
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (7 bp):
CATATCA
Found at i:556646 original size:23 final size:20
Alignment explanation
Indices: 556614--556667 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
556604 CCTAGGCATG
*
556614 GTACCAATACCACATATAGGGAA
1 GTACCGATACCAC-TAT-GGG-A
*
556637 GTATCGATACC-CTATGGGA
1 GTACCGATACCACTATGGGA
556656 GTACCGATACCA
1 GTACCGATACCA
556668 TTGCTAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 3 0.11
22 1 0.04
23 9 0.33
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
GTACCGATACCACTATGGGA
Found at i:558383 original size:27 final size:26
Alignment explanation
Indices: 558353--558405 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
558343 TATACAATAC
558353 TATATGATATGATGATAT-ATGTGTATG
1 TATAT-AT-TGATGATATAATGTGTATG
*
558380 TATATATTTATGATATGAATGTGTAT
1 TATATATTGATGATAT-AATGTGTAT
558406 ATGAGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
26 2 0.09
27 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (26 bp):
TATATATTGATGATATAATGTGTATG
Found at i:562738 original size:16 final size:17
Alignment explanation
Indices: 562713--562744 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
562703 ACAAATGACT
562713 AAATTGAATATTTTATA
1 AAATTGAATATTTTATA
562730 AAATT-AATATTTTAT
1 AAATTGAATATTTTAT
562745 TCATTCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATTGAATATTTTATA
Found at i:567894 original size:20 final size:22
Alignment explanation
Indices: 567855--567894 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
567845 AGGAATCTCA
567855 TTTACATATCATTAAGAGAATC
1 TTTACATATCATTAAGAGAATC
*
567877 TTTAGATATC-TT-AGAGAA
1 TTTACATATCATTAAGAGAA
567895 ACTCCTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTACATATCATTAAGAGAATC
Found at i:568739 original size:19 final size:19
Alignment explanation
Indices: 568715--568753 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
568705 TTGTTCCGGA
568715 TGATTTTCTTGCTCAAAAT
1 TGATTTTCTTGCTCAAAAT
568734 TGATTTTCTTGCTCAAAAT
1 TGATTTTCTTGCTCAAAAT
568753 T
1 T
568754 AGTTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (19 bp):
TGATTTTCTTGCTCAAAAT
Found at i:580856 original size:21 final size:21
Alignment explanation
Indices: 580805--580857 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
580795 ATTATGACTA
580805 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* *
580826 TTGCATTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
580847 TCGCAATGCGA
1 TCGCAATGCGA
580858 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:580877 original size:41 final size:41
Alignment explanation
Indices: 580832--580923 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
580822 AATTTTGCAT
* * *
580832 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTACCAAAATCGCAATGCGAATAAGTAAATCGCAA
* ** *
580873 TGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACCAAAATCGCAATGCGAATAAGTAAATCGCAA
580914 TGCGATTTAC
1 TGCGATTTAC
580924 ATAGCGCCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
TGCGATTTACCAAAATCGCAATGCGAATAAGTAAATCGCAA
Found at i:580890 original size:21 final size:20
Alignment explanation
Indices: 580847--580918 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
580837 TTTTCCCAAT
580847 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
580867 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
580888 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
580908 TCGCAATGCGA
1 TCGCAATGCGA
580919 TTTACATAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:581483 original size:34 final size:33
Alignment explanation
Indices: 581440--581532 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
581430 CCAGAATGAA
*
581440 AATCGCAACGCGGAAAT-AACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAA-AATCGCAACGAGAG
*
581474 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* **
581507 AATCGCAATGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
581533 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:581498 original size:19 final size:19
Alignment explanation
Indices: 581434--581502 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
581424 TAGTTTCCAG
581434 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
581454 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
581470 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
581487 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
581503 AGATAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 15
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.18
15 2 0.05
16 2 0.05
17 1 0.03
18 2 0.05
19 14 0.37
20 10 0.26
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:581598 original size:20 final size:19
Alignment explanation
Indices: 581528--581621 Score: 90
Period size: 20 Copynumber: 5.1 Consensus size: 19
581518 GAAACCAAAA
*
581528 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
581547 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
581561 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
581580 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
581600 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
581620 TC
1 TC
581622 AACCAAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.16
16 2 0.03
17 3 0.05
19 13 0.21
20 32 0.52
21 1 0.02
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:583473 original size:95 final size:89
Alignment explanation
Indices: 583308--583492 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 89
583298 TAGATTGCTT
583308 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAATTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAATTGTTTATTAACACTGTGAAGTTAGTATTT
*
583373 TTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTGTCTTTTGGTTGA
* * * *
583399 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAA-T-TGT-TT-ATTAACACTGTGAAGTTAGT
583464 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
583492 A
1 A
583493 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 32 0.38
92 1 0.01
93 25 0.29
94 2 0.02
95 25 0.29
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTACTGCCAATACTGCTAAATTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGA
Found at i:585205 original size:14 final size:14
Alignment explanation
Indices: 585185--585221 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
585175 GATTGTTTAA
585185 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
585198 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
585213 TTGATTTGT
1 TTGATTTGT
585222 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:585350 original size:19 final size:19
Alignment explanation
Indices: 585328--585445 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
585318 AAAAATTACT
585328 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
585347 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
585361 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
585380 ATCGCAA--C--TA-GAGA
1 ATCGCAATGCGAAATGAAA
*
585394 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
585413 ATCGCAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
*
585432 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
585446 CTAAATTCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.25
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 49 0.61
20 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Done.