Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005680.1 Hibiscus syriacus cultivar Beakdansim tig00013285_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: 1821426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 6
Found at i:244221 original size:60 final size:60
Alignment explanation
Indices: 244075--244188 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
244065 AACATAATGA
* * * * *
244075 ATAGTCAAGTGACCATTTTATAAATTTTAATAGTCGAGGGACCCAACAAAGTAACTCCCT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAAGGACCCAACAAAGCAACTCCCT
* *
244135 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCTAAGGACTCAACAAAGCAA
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAAGGACCCAACAAAGCAA
244189 TATCTTATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAAGGACCCAACAAAGCAACTCCCT
Found at i:244571 original size:2 final size:2
Alignment explanation
Indices: 244531--244558 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
244521 ATTTCATACC
244531 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
244559 TATTAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245640 original size:3 final size:3
Alignment explanation
Indices: 245632--245661 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
245622 CTTGCTCTAT
*
245632 TTC TTC TTC TTC TTC TTC TTC ATC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
245662 GTTGTGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:246113 original size:25 final size:25
Alignment explanation
Indices: 246084--246135 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
246074 AGCATACCAC
246084 TTGAATCCTAATTAAACATTATTAT
1 TTGAATCCTAATTAAACATTATTAT
*
246109 TTGAATCGTAATTAAACATTATTAT
1 TTGAATCCTAATTAAACATTATTAT
246134 TT
1 TT
246136 ATATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (25 bp):
TTGAATCCTAATTAAACATTATTAT
Found at i:248353 original size:16 final size:16
Alignment explanation
Indices: 248328--248385 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
248318 TGAAGAATTA
*
248328 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
248344 GCAAAATTGAAAGTTA
1 GCAAAATTGAAAGTTG
*
248360 ACAAAATTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
248376 GCAAAGTTGA
1 GCAAAATTGA
248386 CATATTGGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:260292 original size:59 final size:60
Alignment explanation
Indices: 260200--260336 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
260190 TAAAGCACAC
* *
260200 AAATGGTCCCTCGACTATAGGATATTACTTTGTTGAGTC-CCCAACTACTAAAAGTTACA
1 AAATGGTCCCCCGACTATAGGATATTACTTTGTTGAATCTCCCAACTACTAAAAGTTACA
* ** * * *
260259 AAATGGTCCCCCGACTATAGAGA-GTTGTTTTGTTGAATCTCTCGACTATTAAAAGTTACA
1 AAATGGTCCCCCGACTATAG-GATATTACTTTGTTGAATCTCCCAACTACTAAAAGTTACA
* *
260319 AAATAGTCACCCGACTAT
1 AAATGGTCCCCCGACTAT
260337 TCATTATGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
59 31 0.47
60 35 0.53
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (60 bp):
AAATGGTCCCCCGACTATAGGATATTACTTTGTTGAATCTCCCAACTACTAAAAGTTACA
Found at i:262292 original size:2 final size:2
Alignment explanation
Indices: 262285--262315 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
262275 TTGAAGAAAC
262285 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 T
262316 TCAAGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262872 original size:34 final size:35
Alignment explanation
Indices: 262810--262875 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
262800 GCCACCAAAA
262810 GCCATCTAGAAGCACATGCAATTGTCAACAATGCT
1 GCCATCTAGAAGCACATGCAATTGTCAACAATGCT
* *
262845 GCCATCTAGAAGC-CATGCATTTTTCAACAAT
1 GCCATCTAGAAGCACATGCAATTGTCAACAAT
262876 CTCCCACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (35 bp):
GCCATCTAGAAGCACATGCAATTGTCAACAATGCT
Found at i:264730 original size:16 final size:17
Alignment explanation
Indices: 264702--264735 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
264692 CGTATCGCTG
264702 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
264719 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
264735 A
1 A
264736 TGTGAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:269899 original size:2 final size:2
Alignment explanation
Indices: 269892--269928 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
269882 TTAAATGGAT
269892 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
269929 TAATTAATCA
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:281679 original size:20 final size:20
Alignment explanation
Indices: 281656--281875 Score: 269
Period size: 20 Copynumber: 10.8 Consensus size: 20
281646 CTCAGTTTCC
281656 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
* * *
281676 AAAATTCTCAAAGTGAATAAT
1 AAAA-TCGCAACGTGAATAGT
281697 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
* * *
281717 AAAATTCTCAAAGTGAATAAT
1 AAAA-TCGCAACGTGAATAGT
281738 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
* * *
281758 AAAATTCTCAAAGTGAATAAT
1 AAAA-TCGCAACGTGAATAGT
281779 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
281799 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
* * *
281819 AAAATCGCAACGCGAATTGG
1 AAAATCGCAACGTGAATAGT
* * *
281839 AAAATCGCAACGAGAATTGA
1 AAAATCGCAACGTGAATAGT
*
281859 AAAATCGCAACGCGAAT
1 AAAATCGCAACGTGAAT
281876 TTAGAAAATC
Statistics
Matches: 173, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
20 122 0.71
21 51 0.29
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:281713 original size:41 final size:41
Alignment explanation
Indices: 281656--281835 Score: 317
Period size: 41 Copynumber: 4.4 Consensus size: 41
281646 CTCAGTTTCC
281656 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
1 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
281697 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
1 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
281738 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
1 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
* * *
281779 AAAATCGCAACGTGAATAGTAAAA-TCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
*
281819 AAAATCGCAACGCGAAT
1 AAAATCGCAACGTGAAT
281836 TGGAAAATCG
Statistics
Matches: 135, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 29 0.21
41 106 0.79
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATAAT
Found at i:281876 original size:40 final size:40
Alignment explanation
Indices: 281656--281885 Score: 151
Period size: 41 Copynumber: 5.7 Consensus size: 40
281646 CTCAGTTTCC
* * * * * *
281656 AAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATA-A
1 AAAATCGCAACGCGAATTGGAAAA-TCGCAACGAGAATAGA
* * * * * *
281696 TAAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATA-A
1 -AAAATCGCAACGCGAATTGGAAAA-TCGCAACGAGAATAGA
* * * * * *
281737 TAAAATCGCAACGTGAATAGTAAAATTCTCAAAGTGAATA-A
1 -AAAATCGCAACGCGAATTGGAAAA-TCGCAACGAGAATAGA
* * * * *
281778 TAAAATCGCAACGTGAATAGTAAAATCGCAACGTGAATAGT
1 -AAAATCGCAACGCGAATTGGAAAATCGCAACGAGAATAGA
*
281819 AAAATCGCAACGCGAATTGGAAAATCGCAACGAGAATTGA
1 AAAATCGCAACGCGAATTGGAAAATCGCAACGAGAATAGA
*
281859 AAAATCGCAACGCGAATTTAGAAAATC
1 AAAATCGCAACGCGAA-TTGGAAAATC
281886 ACAAAATCGC
Statistics
Matches: 177, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 62 0.35
41 115 0.65
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.21
Consensus pattern (40 bp):
AAAATCGCAACGCGAATTGGAAAATCGCAACGAGAATAGA
Found at i:282349 original size:21 final size:21
Alignment explanation
Indices: 282246--282392 Score: 185
Period size: 20 Copynumber: 7.2 Consensus size: 21
282236 ATTCGTTGTC
282246 ATTTTACTATTCACGTTGCG-
1 ATTTTACTATTCACGTTGCGA
*
282266 ATTTTACTATTCACGTTGTG-
1 ATTTTACTATTCACGTTGCGA
*
282286 ATTTTACTATTCACATTGCGA
1 ATTTTACTATTCACGTTGCGA
*
282307 TTTTTACTATTCACGTTGCGA
1 ATTTTACTATTCACGTTGCGA
282328 ATTTTACTATTCACGTTGCGA
1 ATTTTACTATTCACGTTGCGA
* ***
282349 ATTTGACT-TTTGTGTTGCGA
1 ATTTTACTATTCACGTTGCGA
* *
282369 ATTTGACTA-TCGCGTTGCGA
1 ATTTTACTATTCACGTTGCGA
282389 ATTT
1 ATTT
282393 GACTTCTGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
20 67 0.59
21 46 0.41
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (21 bp):
ATTTTACTATTCACGTTGCGA
Found at i:282367 original size:20 final size:20
Alignment explanation
Indices: 282342--282408 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
282332 TACTATTCAC
282342 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
282362 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
282382 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
282402 GTTGCGA
1 GTTGCGA
282409 TTTACAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:282396 original size:40 final size:41
Alignment explanation
Indices: 282321--282408 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 41
282311 TACTATTCAC
* *
282321 GTTGCGAATTTTACTATTCACGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATTCACGTTGCGAATTTGACTTCTGT
*
282362 GTTGCGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATTCACGTTGCGAATTTGACTTCTGT
282402 GTTGCGA
1 GTTGCGA
282409 TTTACAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 29 0.66
41 15 0.34
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (41 bp):
GTTGCGAATTTGACTATTCACGTTGCGAATTTGACTTCTGT
Found at i:282446 original size:20 final size:20
Alignment explanation
Indices: 282402--282448 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
282392 TGACTTCTGT
*
282402 GTTGCGATTTACAAATTCGT
1 GTTGCGATTTACAAATTCGC
* *
282422 ATTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
282442 GTTGCGA
1 GTTGCGA
282449 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:282462 original size:21 final size:21
Alignment explanation
Indices: 282438--282555 Score: 53
Period size: 20 Copynumber: 5.8 Consensus size: 21
282428 ATTTACAGAT
282438 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
*****
282459 TCGCAACATGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** ** * *
282480 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* * *
282500 TCACGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * **
282521 T-GGGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
282540 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
282556 TTGGTCATTT
Statistics
Matches: 69, Mismatches: 26, Indels: 5
0.69 0.26 0.05
Matches are distributed among these distances:
19 2 0.03
20 38 0.55
21 29 0.42
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:282788 original size:19 final size:20
Alignment explanation
Indices: 282764--282802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
282754 TGTTTGCCTC
282764 TTAATG-GAACCATTCAGCG
1 TTAATGTGAACCATTCAGCG
*
282783 TTAATGTTGAACCGTTCAGC
1 TTAATG-TGAACCATTCAGC
282803 ATTCAGCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
TTAATGTGAACCATTCAGCG
Found at i:286898 original size:2 final size:2
Alignment explanation
Indices: 286893--286918 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
286883 GCACTTTTTC
286893 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
286919 CATCAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286995 original size:2 final size:2
Alignment explanation
Indices: 286988--287018 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
286978 TTCCTCTTTC
286988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
287019 CATACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:288801 original size:4 final size:4
Alignment explanation
Indices: 288792--288822 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
288782 AATTCTCCAT
288792 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
288823 TGTCTCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:296030 original size:55 final size:54
Alignment explanation
Indices: 295973--296628 Score: 346
Period size: 51 Copynumber: 12.6 Consensus size: 54
295963 TGACGAGCCT
*
295973 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACG-GTCC
* * * *
296028 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC-TTCATAAAAC-GGTCC
* *
296084 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCA-ATAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAAC-GGTCC
* * * * *
296139 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCA-ACGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * *
296190 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * * *
296241 GCTCTCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
296292 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * * *
296343 GCTCTCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
296394 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
296445 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * *
296496 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * *
296547 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* *
296598 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
296629 AATCTTCAAC
Statistics
Matches: 565, Mismatches: 29, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
51 444 0.79
54 1 0.00
55 72 0.13
56 47 0.08
57 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGGTCC
Found at i:296195 original size:51 final size:51
Alignment explanation
Indices: 296080--296638 Score: 947
Period size: 51 Copynumber: 10.9 Consensus size: 51
296070 AATAAAACGG
* * * ** **
296080 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
296135 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
296186 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
296237 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
296288 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
296339 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
296390 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
296441 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
296492 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
296543 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
296594 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
296639 AAACGAATTG
Statistics
Matches: 486, Mismatches: 18, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
51 455 0.94
55 31 0.06
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:296263 original size:102 final size:102
Alignment explanation
Indices: 295973--296638 Score: 949
Period size: 102 Copynumber: 6.4 Consensus size: 102
295963 TGACGAGCCT
* * * * *
295973 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACGAACTTGTCCGCTCCCTA
* * ** **
296036 TTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
60 TTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCC
* * ** **
296084 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCCTATT
* * *
296149 CTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTAGTCC
62 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
296190 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCTCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
296255 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
296292 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCTCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
296357 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
296394 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
296459 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
296496 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
296561 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
296598 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
296639 AAACGAATTG
Statistics
Matches: 519, Mismatches: 30, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
102 405 0.78
106 36 0.07
107 10 0.02
110 2 0.00
111 65 0.13
112 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (102 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:298007 original size:29 final size:29
Alignment explanation
Indices: 297963--298036 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
297953 CTTTTATTTC
297963 TCTTTTTTCA-TTTTTCTCTTATTATTAT
1 TCTTTTTTCATTTTTTCTCTTATTATTAT
* * *
297991 T-TTTTTTCCATTTTTTCTCTTCTTTTTTT
1 TCTTTTTT-CATTTTTTCTCTTATTATTAT
298020 TCTTTTTTTCATTTTTT
1 TC-TTTTTTCATTTTTT
298037 TTCGTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 6 0.15
28 3 0.08
29 16 0.41
30 8 0.21
31 6 0.15
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (29 bp):
TCTTTTTTCATTTTTTCTCTTATTATTAT
Found at i:307814 original size:44 final size:47
Alignment explanation
Indices: 307750--307846 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 47
307740 TGTTATCCAT
307750 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATTC-
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
307795 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
307842 AAAAA
1 AAAAA
307847 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 8 0.17
46 6 0.13
47 5 0.11
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:311973 original size:34 final size:31
Alignment explanation
Indices: 311935--312012 Score: 77
Period size: 34 Copynumber: 2.4 Consensus size: 31
311925 CACATAATAT
* *
311935 TTTTCAATCTACCACCTGCCCAC-CAGGGTACAAA
1 TTTTCAATCCA-CACCCGCCCACGC-GGGTAC--A
311969 TTTTCAAATCCACACCCGCCCACGCGGGTACA
1 TTTTC-AATCCACACCCGCCCACGCGGGTACA
312001 TTTTCAAATCCA
1 TTTTC-AATCCA
312013 TCCCCATACC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 13 0.32
34 21 0.52
35 6 0.15
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (31 bp):
TTTTCAATCCACACCCGCCCACGCGGGTACA
Found at i:313854 original size:10 final size:11
Alignment explanation
Indices: 313834--313867 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
313824 ATTTTTTTAA
313834 TAAAAATATAT
1 TAAAAATATAT
313845 TAAAAAATATAT
1 T-AAAAATATAT
*
313857 TTAAAATATAT
1 TAAAAATATAT
313868 GATAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:324225 original size:217 final size:218
Alignment explanation
Indices: 323836--324262 Score: 766
Period size: 217 Copynumber: 2.0 Consensus size: 218
323826 GCGGACAGGT
*
323836 GTGTCTATTTCCACCTGCGATCAATTTAGGTAAACTTTATAGCATGAAAAACAGAAGTAACTGTT
1 GTGTCTATTTCCACCTGCGATCAATTTAGGTAAAATTTATAGCATGAAAAACAGAAGTAACTGTT
*
323901 AAGTTTTATTTTAGGCAGAAAGTTCTTAAATTGGGTTATTTAACATGGTTAAATCATAATGTTAC
66 AAGTTTTATTTTAGGCAGAAAGTTCTTAAATTGAGTTATTTAACATGGTTAAATCATAATGTTAC
323966 AGATTCCTAACTGTTTTAGTGCTGGTATCTCTGTCAAATATACAATTTGAAATCACCTAGTCATA
131 AGATTCCTAACTGTTTTAGTGCTGGTATCTCTGTCAAATATACAATTTGAAATCACCTAGTCATA
324031 ATTCTATAACAGAATGCCGGCAG
196 ATTCTATAACAGAATGCCGGCAG
* *
324054 GTGTCT-TTTCCACCTGCGATCACTTTGGGTAAAATTTATAGCATGAAAAACAGAAGTAACTGTT
1 GTGTCTATTTCCACCTGCGATCAATTTAGGTAAAATTTATAGCATGAAAAACAGAAGTAACTGTT
* *
324118 AAGTTTTATTTTAGGCAGAAAGTTCTTAAATTTATTTATTTAACATGGTTAAATCATAATGTTAC
66 AAGTTTTATTTTAGGCAGAAAGTTCTTAAATTGAGTTATTTAACATGGTTAAATCATAATGTTAC
* **
324183 AGATTCCTAACTGTTTTAGTGCTGGTATTTCTGTTGAATATACAATTTGAAATCACCTAGTCATA
131 AGATTCCTAACTGTTTTAGTGCTGGTATCTCTGTCAAATATACAATTTGAAATCACCTAGTCATA
324248 ATTCTATAACAGAAT
196 ATTCTATAACAGAAT
324263 CAGTATGCTT
Statistics
Matches: 200, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
217 194 0.97
218 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (218 bp):
GTGTCTATTTCCACCTGCGATCAATTTAGGTAAAATTTATAGCATGAAAAACAGAAGTAACTGTT
AAGTTTTATTTTAGGCAGAAAGTTCTTAAATTGAGTTATTTAACATGGTTAAATCATAATGTTAC
AGATTCCTAACTGTTTTAGTGCTGGTATCTCTGTCAAATATACAATTTGAAATCACCTAGTCATA
ATTCTATAACAGAATGCCGGCAG
Found at i:339354 original size:20 final size:20
Alignment explanation
Indices: 339307--339700 Score: 351
Period size: 20 Copynumber: 19.2 Consensus size: 20
339297 AATGACCAAC
339307 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
339326 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
339346 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
339366 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
339388 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
339408 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
339430 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
339450 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
339470 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
339492 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
339512 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
339534 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
339554 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
339574 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
339594 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
339614 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
339634 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
339654 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
339676 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
339696 AAAAT
1 AAAAT
339701 GAGTAAATTC
Statistics
Matches: 314, Mismatches: 33, Indels: 55
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.00
19 29 0.09
20 195 0.62
21 6 0.02
22 75 0.24
23 8 0.03
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:339415 original size:42 final size:39
Alignment explanation
Indices: 339369--339692 Score: 366
Period size: 42 Copynumber: 7.9 Consensus size: 39
339359 TGAAAAGAAG
* *
339369 ATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAA
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCA-AAA
339411 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAA
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCA-AAA
* *
339453 ATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-CAAAA
* *
339495 ATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-CAAAA
* *
339537 ATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGATT-CAAAA
339577 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAA
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCA-AAA
*
339617 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCA-AAA
339657 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT
339693 AAGAAAATGA
Statistics
Matches: 266, Mismatches: 8, Indels: 16
0.92 0.03 0.06
Matches are distributed among these distances:
39 4 0.02
40 107 0.40
41 2 0.01
42 151 0.57
43 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (39 bp):
ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAAAA
Found at i:339456 original size:62 final size:61
Alignment explanation
Indices: 339390--339700 Score: 386
Period size: 62 Copynumber: 5.0 Consensus size: 61
339380 ATCTTCCAAG
*
339390 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
339452 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
* *
339514 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCCA-A
1 AATCGCAACGCGA--TT-CAAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-CAGA
*
339575 G
61 A
* * *
339576 AATCGCAACGCGATTCCAAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-CAGAA
* *
339636 AATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
339698 AAT
1 AAT
339701 GAGTAAATTC
Statistics
Matches: 229, Mismatches: 10, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
59 1 0.00
60 76 0.33
61 3 0.01
62 127 0.55
63 4 0.02
64 16 0.07
65 2 0.01
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (61 bp):
AATCGCAACGCGATTCAAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
Found at i:339807 original size:6 final size:6
Alignment explanation
Indices: 339796--339922 Score: 240
Period size: 6 Copynumber: 21.5 Consensus size: 6
339786 GACACGTATT
339796 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
339844 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
339892 ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
339923 CGAGACGGCG
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.08
6 111 0.92
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:340430 original size:6 final size:6
Alignment explanation
Indices: 340414--340793 Score: 753
Period size: 6 Copynumber: 63.5 Consensus size: 6
340404 TCTCGTCTCG
340414 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340461 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340509 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340557 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340605 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340653 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340701 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
340749 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
340794 AATACGTGTC
Statistics
Matches: 374, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
5 5 0.01
6 369 0.99
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:340945 original size:20 final size:20
Alignment explanation
Indices: 340889--341263 Score: 324
Period size: 20 Copynumber: 18.2 Consensus size: 20
340879 GAATTTACTC
*
340889 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
340909 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
340931 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
340951 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
340973 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
340993 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
341015 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
341035 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
341055 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
341075 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
341095 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
341117 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* *
341137 ATTTTATGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* *
341157 ATTTTATGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
341177 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
341197 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
341219 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
341239 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
341259 ATTTT
1 ATTTT
341264 GTTGGTCATT
Statistics
Matches: 296, Mismatches: 44, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
19 6 0.02
20 187 0.63
21 32 0.11
22 71 0.24
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:340948 original size:42 final size:41
Alignment explanation
Indices: 340889--341263 Score: 344
Period size: 42 Copynumber: 9.1 Consensus size: 41
340879 GAATTTACTC
*
340889 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCG
340931 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCG
340973 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCG
*
341015 A--TTCTTGGAATCGCGTTGCGATTTTCTG-A-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTTT-GGAAGATCGCGTTGCG
***
341055 A--TTCTTGGAATCGCGTTGCGATTTTCTTA-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTTTGGAAGATCGCGTTGCG
*** *
341095 ATTCTTGGAAGATCGCGTTGCGATTTTCTG-A-ATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTTT-GGAAGATCGCGTTGCG
* * *
341137 ATTTTATGAATCGCGTTGCGATTTT--ATGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTTTGGAAG-ATCGCGTTGCG
* * *
341177 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCG
* * * * **
341219 ATCTTCTT-TTCAACGTTGCGCTTTTCTAA-ATCGCGTTGCG
1 ATTTTCTTAATC-GCGTTGCGATTTTGGAAGATCGCGTTGCG
341259 ATTTT
1 ATTTT
341264 GTTGGTCATT
Statistics
Matches: 292, Mismatches: 25, Indels: 34
0.83 0.07 0.10
Matches are distributed among these distances:
40 118 0.40
41 15 0.05
42 155 0.53
43 4 0.01
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
ATTTTCTTAATCGCGTTGCGATTTTGGAAGATCGCGTTGCG
Found at i:341103 original size:102 final size:102
Alignment explanation
Indices: 340898--341261 Score: 518
Period size: 102 Copynumber: 3.5 Consensus size: 102
340888 CATTTTCTGA
*
340898 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGA
1 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG-A-A
340963 TCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
62 TCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
341004 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGC
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGC
341069 GTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
66 GTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
* * *
341106 ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTATGAATCGCGTTGCGATT-TTATGAATC
1 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GGAATC
* * *
341169 GCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
64 GCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
**** * * *
341208 ATCGCGTTGCGA-TCTTCTTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGATT
1 ATCGCGTTGCGATTCTTGGAATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATT
341262 TTGTTGGTCA
Statistics
Matches: 239, Mismatches: 15, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
101 7 0.03
102 173 0.72
103 1 0.00
104 38 0.16
105 1 0.00
106 19 0.08
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (102 bp):
ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGC
GTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
Found at i:341236 original size:82 final size:78
Alignment explanation
Indices: 340892--341264 Score: 331
Period size: 82 Copynumber: 4.5 Consensus size: 78
340882 TTTACTCATT
* **
340892 TTCTGAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
1 TTCT-AATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTT-GGAATCGCGTTGCGATT-T
*
340956 T-GGAAGATCGCGTTGCGATT
60 TCGG-A-ATCGCGTTGCGATC
*
340976 TTCTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTT
1 TTC-TAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATT-TTGGAATCGCGTTGCGATTTT
*
341040 CTGAATCGCGTTGCGATTC
61 CGGAATCGCGTTGCGA-TC
** * *
341059 TTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 TTCTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGATTTTCG
*
341124 GAATCGCGTTGCGATT
63 GAATCGCGTTGCGATC
* * * *
341140 TTATGAATCGCGTTGCGATTTTATGAATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTT-G
1 TTCT-AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTT-GGAATCGCGTTGCGATT-TTCG
341204 GAAGATCGCGTTGCGATC
63 G-A-ATCGCGTTGCGATC
** * * *
341222 TTCTTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGATTTTG
1 TTCTAATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATTTTG
341265 TTGGTCATTT
Statistics
Matches: 251, Mismatches: 25, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
80 33 0.13
81 15 0.06
82 138 0.55
83 6 0.02
84 56 0.22
85 3 0.01
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (78 bp):
TTCTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTGGAATCGCGTTGCGATTTTCGGAA
TCGCGTTGCGATC
Found at i:350096 original size:21 final size:22
Alignment explanation
Indices: 350072--350116 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
350062 CGGAAATTTA
**
350072 AAAAATATTAATA-TTTTAGAT
1 AAAAATAAAAATATTTTTAGAT
350093 AAAAATAAAAATATTTTTAGAT
1 AAAAATAAAAATATTTTTAGAT
350115 AA
1 AA
350117 TATTTTACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAATAAAAATATTTTTAGAT
Found at i:350714 original size:3 final size:3
Alignment explanation
Indices: 350708--350733 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
350698 TTGATTAAGA
350708 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
350734 ACTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:354451 original size:13 final size:12
Alignment explanation
Indices: 354428--354464 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
354418 ACCCCCCCCC
354428 CCCAAAAAAAAA
1 CCCAAAAAAAAA
354440 CCCAACAAAAAAA
1 CCCAA-AAAAAAA
354453 CCCAAAAAAAAA
1 CCCAAAAAAAAA
354465 ATTAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (12 bp):
CCCAAAAAAAAA
Found at i:354465 original size:13 final size:13
Alignment explanation
Indices: 354431--354465 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
354421 CCCCCCCCCC
354431 AAAAAAAAACCCA
1 AAAAAAAAACCCA
*
354444 ACAAAAAAACCCA
1 AAAAAAAAACCCA
354457 AAAAAAAAA
1 AAAAAAAAA
354466 TTAAAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACCCA
Found at i:359526 original size:22 final size:22
Alignment explanation
Indices: 359500--359579 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
359490 ACAAGACTCT
359500 TAAACACAATTAACAGAGCAGA
1 TAAACACAATTAACAGAGCAGA
** * *
359522 TAAACAC-A-GGACAGTTGGAGA
1 TAAACACAATTAACAG-AGCAGA
*
359543 TAAACACAATTAGCAGAGCAGA
1 TAAACACAATTAACAGAGCAGA
359565 TAAACACAATTAACA
1 TAAACACAATTAACA
359580 TGTGAATACA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 26 0.58
23 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.15
Consensus pattern (22 bp):
TAAACACAATTAACAGAGCAGA
Found at i:361820 original size:33 final size:33
Alignment explanation
Indices: 361783--361849 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
361773 GTAATAAGAG
*
361783 AAGGACAGAAAGCTCGAAACGAGTAAGAACGCA
1 AAGGACAGAAAGCTCAAAACGAGTAAGAACGCA
361816 AAGGACAGAAAGCTCAAAACGAGTAAGAACGCA
1 AAGGACAGAAAGCTCAAAACGAGTAAGAACGCA
361849 A
1 A
361850 CGCACCGCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.18, G:0.25, T:0.06
Consensus pattern (33 bp):
AAGGACAGAAAGCTCAAAACGAGTAAGAACGCA
Found at i:362390 original size:3 final size:3
Alignment explanation
Indices: 362384--362413 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
362374 GATGATGATG
362384 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
362414 GGTAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:365229 original size:16 final size:18
Alignment explanation
Indices: 365204--365244 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
365194 TTTGATTGTA
365204 ATTTTTTTTA-AA-TA-T
1 ATTTTTTTTATAACTATT
365219 ATTTTTGTTTATAACTATT
1 ATTTTT-TTTATAACTATT
365238 ATTTTTT
1 ATTTTTT
365245 CCTTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 2 0.09
18 3 0.14
19 7 0.32
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTTTTTATAACTATT
Found at i:370091 original size:20 final size:20
Alignment explanation
Indices: 370066--370107 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
370056 CCACATCCTT
*
370066 AATCATGGATTCCATAACAC
1 AATCATGGAGTCCATAACAC
370086 AATCATGGAGTCCATAACAC
1 AATCATGGAGTCCATAACAC
370106 AA
1 AA
370108 ACAATAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (20 bp):
AATCATGGAGTCCATAACAC
Found at i:377926 original size:68 final size:68
Alignment explanation
Indices: 377813--378018 Score: 342
Period size: 68 Copynumber: 3.0 Consensus size: 68
377803 TAGGAATTTT
* * *
377813 TTTAGGGTAAACTACATATTTGGTCGCTTATATATTATCTAATTTATGTTTTAGTCATTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCATTCGATTA
377878 TTA
66 TTA
* *
377881 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTTATTTATGCTTTGGTCACTT-GATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCA-TTCGATT
377945 ATTA
65 ATTA
*
377949 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCATTCGATTA
378014 TTA
66 TTA
378017 TT
1 TT
378019 ATTTTTCAAA
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.01
68 125 0.98
69 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCATTCGATTA
TTA
Found at i:377937 original size:31 final size:31
Alignment explanation
Indices: 377899--378007 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
377889 AAACTACCTA
377899 TTTGGTCACTTATATATTATCTTATTTATGC
1 TTTGGTCACTTATATATTATCTTATTTATGC
** *
377930 TTTGGTCACTTGAT-TATTAT-TTAGGGTAAACTACC
1 TTTGGTCACTT-ATATATTATCTTA---TTTA-T-GC
* *
377965 TATTTGGTCACTTATATATTATCTAATTTATGT
1 --TTTGGTCACTTATATATTATCTTATTTATGC
377998 TTTGGTCACT
1 TTTGGTCACT
378008 CGATTATTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
30 3 0.05
31 27 0.45
32 2 0.03
33 2 0.03
34 2 0.03
35 3 0.05
36 2 0.03
37 17 0.28
38 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTTATTTATGC
Found at i:377985 original size:37 final size:37
Alignment explanation
Indices: 377876--377986 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 37
377866 GTCATTCGAT
377876 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
** *
377913 TATTATCTTA---TTTA-T-GC--TTTGGTCACTTGAT-
1 TATTAT-TTAGGGTAAACTACCTATTTGGTCACTT-ATA
377944 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
377981 TATTAT
1 TATTAT
377987 CTAATTTATG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
30 3 0.05
31 17 0.29
32 2 0.03
33 3 0.05
34 2 0.03
35 3 0.05
36 2 0.03
37 23 0.40
38 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (37 bp):
TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
Found at i:378138 original size:32 final size:32
Alignment explanation
Indices: 378102--378164 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
378092 GCTAACATGG
*
378102 CATTTTTTAATTATGTTTGGATGTTGGACTAA
1 CATTTTTTAATTATGTTTGGATGTTAGACTAA
378134 CATTTTTTAATTATGTTTGGATGTTAGACTA
1 CATTTTTTAATTATGTTTGGATGTTAGACTA
378165 TGTAATTCGA
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:0.25, C:0.06, G:0.17, T:0.51
Consensus pattern (32 bp):
CATTTTTTAATTATGTTTGGATGTTAGACTAA
Found at i:390606 original size:22 final size:22
Alignment explanation
Indices: 390556--390607 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
390546 ATATTATATG
390556 ATTATAAAAAATTATTTAAATT
1 ATTATAAAAAATTATTTAAATT
**
390578 AAAATAAAATAA-TATTATAAA-T
1 ATTATAAAA-AATTATT-TAAATT
390600 ATTATAAA
1 ATTATAAA
390608 TATTTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTATAAAAAATTATTTAAATT
Found at i:399228 original size:141 final size:141
Alignment explanation
Indices: 398418--399391 Score: 1189
Period size: 141 Copynumber: 7.0 Consensus size: 141
398408 TCACCACCAA
* * * *
398418 CAGGAGTCAAGTCATTCATTTGATCAATATTGTAAACGAACTCACTCTTTGCAGCTCCATCACCA
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
** * * *
398483 TCATTGTCTTCACAGAAATTCTGAGATGACTCATGAGTAGAA---TGGCTCACATAATCTCGATC
66 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGATC
*
398545 TAGAGACAATC
131 TTGAGACAATC
* * *
398556 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAAC-AAGTTCGCTCTTTGCAACT-C--CACT
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAA-CTCACTCTTTGCAACTCCATCACC
** * *
398617 ATCATTGTCTTTGC--A-TTTTTGAGATGACTCGTGAGTAGAATGGTGGCTCACATCATCTCGAT
65 ATCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGAT
398679 CTTGAGACAATC
130 CTTGAGACAATC
***
398691 CAGGAGTCAAG---TTCATCTGTTCAATACCAAAAACGAACTCACTCTTTGCAACT-C--CACCA
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
* * ** * *
398750 TCATTGTCTTCACAGATTTTTTTAGATGATTTGTGAGTAGAATGGTGGTTCACATCATATTGATC
66 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGATC
398815 TTGAGACAATC
131 TTGAGACAATC
* * * * * *
398826 CAGGAGTCGAGTCTTTCATCTGTTGAATACTGCAAACAACAAACTCACTCTTTGCAGCTCCATCA
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTG--TA-AACGAACTCACTCTTTGCAACTCCATCA
* * * *
398891 CCATCATTGTCTTCACAGATTTTTTTAGATGACTCACGAGTAGAGTGGTGGCTCACATCATTTTG
63 CCATCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTG
398956 ATCTTGAGACAATC
128 ATCTTGAGACAATC
* ** * *
398970 CAGGAGTCGAGTCATTCATCTGTTCAATACCATAAACGAACTCGCTCTTTGCAACT--A-CACAA
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
399032 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGATC
66 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGATC
399097 TTGAGACAATC
131 TTGAGACAATC
* * * * * * *
399108 CAGGAGTCAAGTCATTCGTATGTTGAATACTGTAAACAAACTCACTCATTGCAGCTCCATCACCG
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
* * * * *
399173 CCATTGTCTTCACAGATTTTTTGAGATGACTCACGAGTAGAATGGTGACTCACATCGT-TCCGAT
66 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCT-TGAT
399237 CTTGAGACAATC
130 CTTGAGACAATC
* * * * *
399249 CAGGAGTCAAATCATTCATCTGTTCAATACTGTGAATGAACTCGCTCTTTGCAACTCCATCACCG
1 CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
* **
399314 TCATTGTCTTCACAGATTTTTGGAGATGGGTCATGAGTAGAATGGTGGCTCACATCAT-TTCGAT
66 TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTT-GAT
*
399378 CTTGATACAATC
130 CTTGAGACAATC
399390 CA
1 CA
399392 TCCATCCCTG
Statistics
Matches: 724, Mismatches: 90, Indels: 41
0.85 0.11 0.05
Matches are distributed among these distances:
132 72 0.10
133 3 0.00
134 1 0.00
135 118 0.16
137 3 0.00
138 184 0.25
139 1 0.00
140 4 0.01
141 234 0.32
142 2 0.00
144 102 0.14
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (141 bp):
CAGGAGTCAAGTCATTCATCTGTTCAATACTGTAAACGAACTCACTCTTTGCAACTCCATCACCA
TCATTGTCTTCACAGATTTTTTGAGATGACTCATGAGTAGAATGGTGGCTCACATCATCTTGATC
TTGAGACAATC
Found at i:400529 original size:30 final size:29
Alignment explanation
Indices: 400493--400584 Score: 79
Period size: 30 Copynumber: 3.3 Consensus size: 29
400483 AAAATCATGT
400493 CTCTCTTGTAATAATGTAGGATACCTGTCA
1 CTCTCTTGTAATAATGTA-GATACCTGTCA
* * *
400523 CTCTCTTGCT-GT--TGTAAAT-CATGT--
1 CTCTCTTG-TAATAATGTAGATACCTGTCA
*
400547 CTGTCTTGTAATAATGTAAGATACCTGTCA
1 CTCTCTTGTAATAATGT-AGATACCTGTCA
400577 CTCTCTTG
1 CTCTCTTG
400585 CTGTTCAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
26 7 0.15
27 5 0.11
28 8 0.17
30 16 0.35
31 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (29 bp):
CTCTCTTGTAATAATGTAGATACCTGTCA
Found at i:400554 original size:54 final size:54
Alignment explanation
Indices: 400468--400626 Score: 246
Period size: 54 Copynumber: 2.9 Consensus size: 54
400458 CATCATTTTT
*
400468 ACTCTCTTGCAGTTGAAAATCATGTCTCTCTTGTAATAATGTAGGATACCTGTC
1 ACTCTCTTGCTGTTGAAAATCATGTCTCTCTTGTAATAATGTAGGATACCTGTC
* * *
400522 ACTCTCTTGCTGTTGTAAATCATGTCTGTCTTGTAATAATGTAAGATACCTGTC
1 ACTCTCTTGCTGTTGAAAATCATGTCTCTCTTGTAATAATGTAGGATACCTGTC
* * **
400576 ACTCTCTTGCTGTTCAAAATCATGTCTTTCTTGTAATAACATAGGATACCT
1 ACTCTCTTGCTGTTGAAAATCATGTCTCTCTTGTAATAATGTAGGATACCT
400627 ATCAGAAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (54 bp):
ACTCTCTTGCTGTTGAAAATCATGTCTCTCTTGTAATAATGTAGGATACCTGTC
Found at i:401686 original size:36 final size:36
Alignment explanation
Indices: 401639--401728 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
401629 ACGTGGTACT
401639 TGATTTCTCATTGGAGACCTAGCAGCTAGTTTTCCA
1 TGATTTCTCATTGGAGACCTAGCAGCTAGTTTTCCA
401675 TGATTTCTCATTGGAGACCTAGCAGCTAGTTTTCCA
1 TGATTTCTCATTGGAGACCTAGCAGCTAGTTTTCCA
401711 TGATTTCTCATTGGAGAC
1 TGATTTCTCATTGGAGAC
401729 TTATCAACTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (36 bp):
TGATTTCTCATTGGAGACCTAGCAGCTAGTTTTCCA
Found at i:405977 original size:2 final size:2
Alignment explanation
Indices: 405970--406003 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
405960 CTTCATTTTG
405970 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
406004 TTCTTAAAAT
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:407379 original size:17 final size:17
Alignment explanation
Indices: 407357--407391 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
407347 CTTGATGCCG
407357 GAACTGAAATCAGACGA
1 GAACTGAAATCAGACGA
*
407374 GAACTGAAATCGGACGA
1 GAACTGAAATCAGACGA
407391 G
1 G
407392 TTGTAAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.29, T:0.11
Consensus pattern (17 bp):
GAACTGAAATCAGACGA
Found at i:416672 original size:60 final size:59
Alignment explanation
Indices: 416594--416710 Score: 135
Period size: 59 Copynumber: 2.0 Consensus size: 59
416584 AATGGTCTCC
* * *
416594 CGACTATAGGGCGCTACTTTATTAAATCTTTCGACTATTAAAAGGTACAAAATAGTCATT
1 CGACTATAAGGCGCTACTTTATTAAATC-CTCAACTATTAAAAGGTACAAAATAGTCATT
* * * * * * *
416654 CGACTATAAGGTGTTACTTTGTTGAGTCCTCAACTATTAGAAGTTACAAAATAGTCA
1 CGACTATAAGGCGCTACTTTATTAAATCCTCAACTATTAAAAGGTACAAAATAGTCA
416711 CCTAACCATT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 25 0.53
60 22 0.47
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (59 bp):
CGACTATAAGGCGCTACTTTATTAAATCCTCAACTATTAAAAGGTACAAAATAGTCATT
Found at i:421136 original size:15 final size:15
Alignment explanation
Indices: 421116--421152 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
421106 ATATTTAGCT
*
421116 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
421131 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
421146 GGGCGGG
1 GGGCGGG
421153 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:421825 original size:4 final size:4
Alignment explanation
Indices: 421816--421868 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
421806 TTACATGCAC
** * *
421816 AATA AATA AATA AATA AATA GTTT AATG AAT- AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
421863 AATA AA
1 AATA AA
421869 GCACTCAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:425830 original size:22 final size:22
Alignment explanation
Indices: 425776--425831 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
425766 ATAATCTGTT
425776 TTCGTCCCCTAAAATTTTATAAA
1 TTCGT-CCCTAAAATTTTATAAA
*
425799 TTC-CCTCCTAAAATTTTATAAA
1 TTCGTC-CCTAAAATTTTATAAA
425821 TTCGTCCCTAA
1 TTCGTCCCTAA
425832 GAATCACGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 24 0.83
23 4 0.14
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (22 bp):
TTCGTCCCTAAAATTTTATAAA
Found at i:432407 original size:3 final size:3
Alignment explanation
Indices: 432399--432424 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
432389 TAGTAACCAA
432399 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
432425 TCCATTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:432463 original size:39 final size:39
Alignment explanation
Indices: 432420--432510 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
432410 GCAGCAGCAG
* * *
432420 CAGCATCCATTGTTTAATAGCCAACAGCAACAGCAGGCC-
1 CAGCATCCACTGTTTAATAACCAACAGCAACAACA-GCCA
* * *
432459 CAGCATCCGCTGTTTACTAATCAACAGCAACAACAGCCA
1 CAGCATCCACTGTTTAATAACCAACAGCAACAACAGCCA
*
432498 CAGCATGCACTGT
1 CAGCATCCACTGT
432511 CACAGCAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 3 0.07
39 40 0.93
ACGTcount: A:0.33, C:0.32, G:0.16, T:0.19
Consensus pattern (39 bp):
CAGCATCCACTGTTTAATAACCAACAGCAACAACAGCCA
Found at i:444426 original size:14 final size:14
Alignment explanation
Indices: 444407--444434 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
444397 GAATACAAAG
444407 GAATATTATGGAAA
1 GAATATTATGGAAA
444421 GAATATTATGGAAA
1 GAATATTATGGAAA
444435 TGATGAATAC
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
GAATATTATGGAAA
Found at i:445124 original size:20 final size:20
Alignment explanation
Indices: 445080--445467 Score: 390
Period size: 20 Copynumber: 19.2 Consensus size: 20
445070 AATGACCAAC
*
445080 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
445099 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
445119 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
445139 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
445159 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
445181 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
445201 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
445223 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445243 AAAATCGCAACGCGATTCA-
1 AAAATCGCAACGCGATTCAG
445262 AAGAATCGCAACGCGATTCA-
1 AA-AATCGCAACGCGATTCAG
445282 AAGAATCGCAACGCGATTCA-
1 AA-AATCGCAACGCGATTCAG
445302 AAGAATCGCAACGCGATTCCA-
1 AA-AATCGCAACGCGATT-CAG
*
445323 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
445343 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
445363 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
445383 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
445403 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
445423 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
445443 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445463 AAAAT
1 AAAAT
445468 GAGTAAATTC
Statistics
Matches: 323, Mismatches: 22, Indels: 47
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.01
19 26 0.08
20 253 0.78
21 8 0.02
22 29 0.09
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:445314 original size:60 final size:60
Alignment explanation
Indices: 445157--445467 Score: 434
Period size: 60 Copynumber: 5.1 Consensus size: 60
445147 AACGGTCAAA
* * * *
445157 AGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT-AAGAGAATCGCAACGCGATCTTC
1 AGAAAATCGCAACGCG--ATTCAAAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-
445221 C
60 C
* * *
445222 A-AGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCAAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
*
445281 A-AAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAA-AATCGCAACGCGATTCAAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
445341 AGAAAATCGCAACGCGATT-AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCAA-AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
445401 AGAAAATCGCAACGCGATT-AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCAA-AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
445461 AGAAAAT
1 AGAAAAT
445468 GAGTAAATTC
Statistics
Matches: 232, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
59 5 0.02
60 175 0.75
61 2 0.01
62 34 0.15
63 2 0.01
64 13 0.06
65 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (60 bp):
AGAAAATCGCAACGCGATTCAAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
Found at i:445572 original size:6 final size:6
Alignment explanation
Indices: 445561--445670 Score: 204
Period size: 6 Copynumber: 18.5 Consensus size: 6
445551 GACACGTATT
445561 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
445608 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
445656 ACCACC ACCACG ACC
1 ACCACG ACCACG ACC
445671 CGAGACGAGA
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
5 5 0.05
6 96 0.95
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:446157 original size:6 final size:6
Alignment explanation
Indices: 446148--446270 Score: 218
Period size: 6 Copynumber: 21.2 Consensus size: 6
446138 CCGTCTCGTC
446148 TCGTGG TCGTGG TCGTGG TCGTGG TC---G TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
446193 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT-G TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
446240 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
446271 AATACGTGTC
Statistics
Matches: 113, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.03
5 5 0.04
6 105 0.93
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:446394 original size:20 final size:20
Alignment explanation
Indices: 446369--446783 Score: 497
Period size: 20 Copynumber: 20.8 Consensus size: 20
446359 CTCATTTTCT
446369 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446389 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446409 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
446430 -AAT--CGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446447 GAATCGCGTTGCGATT-TT-
1 GAATCGCGTTGCGATTCTTG
**
446465 -CTTCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446484 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
446505 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446524 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
446545 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446564 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
446585 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446604 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
*
446625 -AATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
446644 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446664 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
446684 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
446704 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446724 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
446746 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
446766 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
446784 TTTTTGACCG
Statistics
Matches: 349, Mismatches: 11, Indels: 68
0.82 0.03 0.16
Matches are distributed among these distances:
16 5 0.01
17 15 0.04
18 30 0.09
19 5 0.01
20 232 0.66
21 7 0.02
22 54 0.15
23 1 0.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:446816 original size:19 final size:19
Alignment explanation
Indices: 446774--446824 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
446764 TGGAATATCG
* *
446774 CGTTGCGATTTT-TTTGAC
1 CGTTGCGATTTTCTTTCAA
446792 CGTTGCGATTTTCTTTCAA
1 CGTTGCGATTTTCTTTCAA
446811 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
446825 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCTTTCAA
Found at i:446836 original size:20 final size:20
Alignment explanation
Indices: 446362--446862 Score: 461
Period size: 20 Copynumber: 25.2 Consensus size: 20
446352 GAATTTACTC
446362 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446382 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446402 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446422 ATTTTCTTAAT--CGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446440 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
446460 ATTTTCT---TCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446477 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446497 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446517 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446537 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446557 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446577 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446597 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446617 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
446637 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446657 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446677 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
446697 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446717 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
446739 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446759 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
446781 ATTTTTTTG-A-C-CGTTGCG
1 A-TTTTCTGAATCGCGTTGCG
* *
446799 ATTTTCT--TTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
446818 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
* *
446838 ATTTT-TTATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
446858 ATTTT
1 ATTTT
446863 GTTGGTCATT
Statistics
Matches: 407, Mismatches: 40, Indels: 68
0.79 0.08 0.13
Matches are distributed among these distances:
17 19 0.05
18 23 0.06
19 33 0.08
20 283 0.70
21 19 0.05
22 27 0.07
23 3 0.01
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:446862 original size:40 final size:40
Alignment explanation
Indices: 446369--446862 Score: 660
Period size: 40 Copynumber: 12.4 Consensus size: 40
446359 CTCATTTTCT
446369 GAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTG
446409 GAATCGCGTTGCGATTTTCTTAAT--CGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
446447 GAATCGCGTTGCGATTTTC-T--TCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
446484 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
446524 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
446564 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
*
446604 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTT-G
446644 GAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTG
*
446684 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
446724 GAAGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* * *
446766 GAATATCGCGTTGCGATTTTTTTGA-C-CGTTGCGATTTTCTTT
1 G-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGA--TTCTTG
* * *
446808 CAA---CGTTGCGATTTTCTAAATCGCGTTGCGATT-TTT
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
446844 TATTTCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
446863 GTTGGTCATT
Statistics
Matches: 413, Mismatches: 18, Indels: 46
0.87 0.04 0.10
Matches are distributed among these distances:
35 1 0.00
36 4 0.01
37 50 0.12
38 40 0.10
39 10 0.02
40 233 0.56
41 5 0.01
42 70 0.17
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:448255 original size:15 final size:15
Alignment explanation
Indices: 448231--448260 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
448221 ATCTATCAAT
448231 TGAAACGCCAATCCC
1 TGAAACGCCAATCCC
*
448246 TGAAATGCCAATCCC
1 TGAAACGCCAATCCC
448261 GTACTATGTT
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:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (15 bp):
TGAAACGCCAATCCC
Found at i:461339 original size:2 final size:2
Alignment explanation
Indices: 461332--461379 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
461322 GAAGAAGATG
461332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
461374 AT AT AT
1 AT AT AT
461380 TACTTTCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464262 original size:2 final size:2
Alignment explanation
Indices: 464255--464286 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
464245 CAGATCTTAC
464255 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
464287 TTTGGAACAG
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:465837 original size:2 final size:2
Alignment explanation
Indices: 465832--465864 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
465822 TTTTTTAAAT
465832 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
465865 TATTTCGACA
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:473312 original size:15 final size:15
Alignment explanation
Indices: 473294--473323 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
473284 AAAAGAAAGG
473294 GAAAAAAAAATAAGT
1 GAAAAAAAAATAAGT
*
473309 GAAAAATAAATAAGT
1 GAAAAAAAAATAAGT
473324 CCAAGAGGAT
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:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
GAAAAAAAAATAAGT
Found at i:473903 original size:21 final size:21
Alignment explanation
Indices: 473878--473926 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
473868 AGAGGAAAAG
473878 GTGGCGGAGCCGCGACTGCAA
1 GTGGCGGAGCCGCGACTGCAA
473899 GTGGCGGAGCCGCGACTGCAA
1 GTGGCGGAGCCGCGACTGCAA
*
473920 GCGGCGG
1 GTGGCGG
473927 CGCACGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.47, T:0.08
Consensus pattern (21 bp):
GTGGCGGAGCCGCGACTGCAA
Found at i:474759 original size:22 final size:23
Alignment explanation
Indices: 474715--474772 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
474705 TGACACGGGA
474715 AAAAATAA-AATAAAATAAGTGAT
1 AAAAATAATAAT-AAATAAGTGAT
474738 AAAAATAATAATAAATAA-TGAT
1 AAAAATAATAATAAATAAGTGAT
* *
474760 GATAATAATAATA
1 AAAAATAATAATA
474773 TATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATAATAATAAATAAGTGAT
Found at i:474858 original size:38 final size:36
Alignment explanation
Indices: 474784--474969 Score: 169
Period size: 38 Copynumber: 5.0 Consensus size: 36
474774 ATATATAAAC
* * * *
474784 GTTTTCAAAAAC-ATATAATATACAAATTTTTTAAAAT
1 GTTTT-AAAAACTATATATTATATATA-TTTTCAAAAT
474821 GTTTTTAAAAAACTATATATTATATATATTTTCAAAAT
1 G-TTTT-AAAAACTATATATTATATATATTTTCAAAAT
* * *
474859 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAT
1 -G-TTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
* * * * *
474899 GTTTTCAAAAGTATCTATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATATATTATATATATTTTCAAAAT
474935 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 GTTTT-AAAAACTATATATTATATATATTTTCAAAA
474970 AATATATTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
36 23 0.19
37 17 0.14
38 55 0.44
39 18 0.15
40 11 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:474864 original size:76 final size:74
Alignment explanation
Indices: 474780--474957 Score: 205
Period size: 76 Copynumber: 2.4 Consensus size: 74
474770 ATATATATAT
* *
474780 AAACGTTTTCAAAAACATATAATATACAAAT-TTTTTAAAATGTTTTTAAAAAACTATATATTAT
1 AAACGTTTTCAAAAACATATATTATACAAATGTTTTCAAAATG-TTTT-AAAAACTATATATTAT
474844 ATATATTTTCAA
64 ATATATTTT-AA
** * * * * * * *
474856 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAAGTATCTATTATA
1 AAACGTTTTCAAAAA-CATATATTATACAAATGTTTTCAAAATGTTTTAAAAACTATATATTATA
474921 TATATTTTAA
65 TATATTTTAA
474931 AAACGTTTTCAAAAACTATATATTATA
1 AAACGTTTTCAAAAAC-ATATATTATA
474958 TAATTTTCAA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
75 24 0.29
76 34 0.40
77 17 0.20
78 9 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAACGTTTTCAAAAACATATATTATACAAATGTTTTCAAAATGTTTTAAAAACTATATATTATAT
ATATTTTAA
Found at i:474968 original size:25 final size:25
Alignment explanation
Indices: 474936--475012 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
474926 TTTAAAAACG
*
474936 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
474961 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
474988 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
475013 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:474980 original size:15 final size:16
Alignment explanation
Indices: 474955--474984 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
474945 ACTATATATT
474955 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
474971 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
474985 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:474984 original size:76 final size:74
Alignment explanation
Indices: 474780--474984 Score: 191
Period size: 76 Copynumber: 2.7 Consensus size: 74
474770 ATATATATAT
* * * * *
474780 AAACGTTTTCAAAAAC-ATATAATATACAAATTTTTTAAAATGTTTTTAAAAAACTATATATTAT
1 AAACGTTTTCAAAAACTATATATTATA-TAA-TTTTCAAAATATTTTT-CAAAACTATATATTAT
474844 ATATATTTTCAA
63 ATATATTTTCAA
** * * * * * *
474856 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAT-GTTTTCAAAAGTATCTATTAT
1 AAACGTTTTCAAAAACTATATATTATAT-AA--TTTTCAAAATATTTTTCAAAACTATATATTAT
474920 ATATATTTT-AA
63 ATATATTTTCAA
474931 AAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAATATATTTTCAAAA
1 AAACGTTTTCAAAAACTATATATTATATAATTTTC--AAAATAT-TTTTCAAAA
474985 TGGTTTTTAA
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
72 5 0.05
74 6 0.06
75 26 0.25
76 43 0.42
77 15 0.15
78 8 0.08
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAACGTTTTCAAAAACTATATATTATATAATTTTCAAAATATTTTTCAAAACTATATATTATATA
TATTTTCAA
Found at i:475066 original size:36 final size:37
Alignment explanation
Indices: 474971--475097 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 37
474961 TTTTCAAAAA
** * * *
474971 ATAT-ATTTTCAAAATGGTTTTTAAAAATTATATATT
1 ATATAATTTTCAAAAACGTTTTCAAAAACTATACATT
* *
475007 ATATAAATGTTTTC-ATAACGTTTTC-AAAAGTATACATT
1 ATAT-AA--TTTTCAAAAACGTTTTCAAAAACTATACATT
*
475045 ATATATATTTT-AAAAACGTTTTCAAAAACTATATATT
1 ATATA-ATTTTCAAAAACGTTTTCAAAAACTATACATT
475082 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
475098 ATATACTTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
36 23 0.31
37 22 0.30
38 17 0.23
39 7 0.09
40 5 0.07
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAATTTTCAAAAACGTTTTCAAAAACTATACATT
Found at i:475219 original size:36 final size:34
Alignment explanation
Indices: 475174--475287 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 34
475164 GTATACATTA
475174 TATATATTTT-AAAAACGTTTTCAAAAACTATATAT
1 TATATATTTTCAAAAACGTTTT--AAAACTATATAT
**
475209 TATATGATTTTCAAAAATATTTTAAAAACTATATAAT
1 TATAT-ATTTTCAAAAACGTTTT-AAAACTATAT-AT
* *
475246 ATACATATTTTCAAAAAATGTTTT-AAACTATATAT
1 -TATATATTTTC-AAAAACGTTTTAAAACTATATAT
475281 TATATAT
1 TATATAT
475288 GTATTTTCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.09
35 7 0.10
36 25 0.36
37 17 0.25
38 14 0.20
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (34 bp):
TATATATTTTCAAAAACGTTTTAAAACTATATAT
Found at i:475228 original size:127 final size:127
Alignment explanation
Indices: 474844--475225 Score: 685
Period size: 127 Copynumber: 3.0 Consensus size: 127
474834 TATATATTAT
*
474844 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
474909 GTAT-CTATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATAC-ATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
474971 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
475036 GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
* * * *
475098 ATATACTTTCAAATTGTTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCTAA
1 ATATATTTTCAAAATG-GTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
*
475163 AGTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATGATTTTCAAAAA
65 AGTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
475226 TATTTTAAAA
Statistics
Matches: 247, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
127 138 0.56
128 109 0.44
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:475263 original size:75 final size:73
Alignment explanation
Indices: 475172--475323 Score: 184
Period size: 75 Copynumber: 2.1 Consensus size: 73
475162 AAGTATACAT
* * *
475172 TATATATATTTTAAAAACGTTTTCAAAAACTATATA-T-TATATG-ATTTTCAAAAATATTTTAA
1 TATACATATTTTAAAAACGTTTT---AAACTATATATTATATATGTATTTTCAAAAACAATTTAA
475234 AAACTATATAA
63 AAACTATATAA
* **
475245 TATACATATTTTCAAAAAATGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTGCA
1 TATACATATTTT--AAAAACGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTAAA
475310 AACTATATAA
64 AACTATATAA
475320 TATA
1 TATA
475324 TATGTGTATA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
72 10 0.15
73 12 0.18
74 6 0.09
75 40 0.59
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (73 bp):
TATACATATTTTAAAAACGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTAAAAA
CTATATAA
Found at i:475271 original size:38 final size:37
Alignment explanation
Indices: 475172--475326 Score: 149
Period size: 37 Copynumber: 4.2 Consensus size: 37
475162 AAGTATACAT
*
475172 TATATATATTTT-AAAAACGTTTTCAAAAACTATAT-A
1 TATATATATTTTCAAAAATGTTTT-AAAAACTATATAA
*
475208 T-TATATGATTTTCAAAAATATTTTAAAAACTATATAA
1 TATATAT-ATTTTCAAAAATGTTTTAAAAACTATATAA
*
475245 TATACATATTTTCAAAAAATGTTTT--AAACTATATATTA
1 TATATATATTTTC-AAAAATGTTTTAAAAACTATATA--A
* *** **
475283 TATATGTATTTTCAAAAACAATTTGCAAACTATATAA
1 TATATATATTTTCAAAAATGTTTTAAAAACTATATAA
475320 TATATAT
1 TATATAT
475327 GTGTATATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
35 5 0.05
36 27 0.27
37 32 0.32
38 26 0.26
39 10 0.10
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (37 bp):
TATATATATTTTCAAAAATGTTTTAAAAACTATATAA
Found at i:476219 original size:105 final size:105
Alignment explanation
Indices: 475916--477121 Score: 2132
Period size: 105 Copynumber: 11.4 Consensus size: 105
475906 TCCTTTGCTA
*
475916 TGAAGTTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTG
1 TGAAG-TTGAAATTGGCTCTG-AATTGACGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTTG
475980 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
63 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* **
476023 TGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCAT
1 TGAAGTTGAAATTGGCTCTG-AATTGACGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTTGT
476087 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
64 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476129 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
*
476194 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTCG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476234 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
476299 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
476339 TGAAGTTGAGATTGGCTCTGAATTGACGAAATATTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
476404 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476444 TGAAGTTGAAATTGGCTCTGAATTGACGAAATATTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
476509 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476549 TGAAGTTGAAATTGGCTCTGAATTTGA-GAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTG
1 TGAAGTTGAAATTGGCTCTGAA-TTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTG
476613 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* **
476654 TGAAGTTGAAATTGGCTCTGAATTGACGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCATGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
476719 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476759 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
*
476824 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTCG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
476864 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
476929 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
476969 TGAAGTTGAGATTGGCTCTGAATTGACGAAATATTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
477034 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
477074 TGAAGTTGAAATTGGCTCTGAATTTGA-GAAATTGTTTATTGACAACCA
1 TGAAGTTGAAATTGGCTCTGAA-TTGACGAAA-TGTTTGTTGACAACCA
477122 ACTTTTCTTG
Statistics
Matches: 1068, Mismatches: 26, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
104 4 0.00
105 916 0.86
106 143 0.13
107 5 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
TGAAGTTGAAATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
Found at i:481603 original size:21 final size:21
Alignment explanation
Indices: 481578--481626 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
481568 AGAGGAAAAG
481578 GTGGCGGAGCCGCGACTGCAA
1 GTGGCGGAGCCGCGACTGCAA
481599 GTGGCGGAGCCGCGACTGCAA
1 GTGGCGGAGCCGCGACTGCAA
*
481620 GCGGCGG
1 GTGGCGG
481627 CGCACGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.47, T:0.08
Consensus pattern (21 bp):
GTGGCGGAGCCGCGACTGCAA
Found at i:482462 original size:22 final size:23
Alignment explanation
Indices: 482418--482475 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
482408 TGACACGGGA
482418 AAAAATAA-AATAAAATAAGTGAT
1 AAAAATAATAAT-AAATAAGTGAT
482441 AAAAATAATAATAAATAA-TGAT
1 AAAAATAATAATAAATAAGTGAT
* *
482463 GATAATAATAATA
1 AAAAATAATAATA
482476 TATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATAATAATAAATAAGTGAT
Found at i:482561 original size:38 final size:36
Alignment explanation
Indices: 482487--482672 Score: 169
Period size: 38 Copynumber: 5.0 Consensus size: 36
482477 ATATATAAAC
* * * *
482487 GTTTTCAAAAAC-ATATAATATACAAATTTTTTAAAAT
1 GTTTT-AAAAACTATATATTATATATA-TTTTCAAAAT
482524 GTTTTTAAAAAACTATATATTATATATATTTTCAAAAT
1 G-TTTT-AAAAACTATATATTATATATATTTTCAAAAT
* * *
482562 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAT
1 -G-TTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
* * * * *
482602 GTTTTCAAAAGTATCTATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATATATTATATATATTTTCAAAAT
482638 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 GTTTT-AAAAACTATATATTATATATATTTTCAAAA
482673 AATATATTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
36 23 0.19
37 17 0.14
38 55 0.44
39 18 0.15
40 11 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:482567 original size:76 final size:74
Alignment explanation
Indices: 482483--482660 Score: 205
Period size: 76 Copynumber: 2.4 Consensus size: 74
482473 ATATATATAT
* *
482483 AAACGTTTTCAAAAACATATAATATACAAAT-TTTTTAAAATGTTTTTAAAAAACTATATATTAT
1 AAACGTTTTCAAAAACATATATTATACAAATGTTTTCAAAATG-TTTT-AAAAACTATATATTAT
482547 ATATATTTTCAA
64 ATATATTTT-AA
** * * * * * * *
482559 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAAGTATCTATTATA
1 AAACGTTTTCAAAAA-CATATATTATACAAATGTTTTCAAAATGTTTTAAAAACTATATATTATA
482624 TATATTTTAA
65 TATATTTTAA
482634 AAACGTTTTCAAAAACTATATATTATA
1 AAACGTTTTCAAAAAC-ATATATTATA
482661 TAATTTTCAA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
75 24 0.29
76 34 0.40
77 17 0.20
78 9 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAACGTTTTCAAAAACATATATTATACAAATGTTTTCAAAATGTTTTAAAAACTATATATTATAT
ATATTTTAA
Found at i:482671 original size:25 final size:25
Alignment explanation
Indices: 482639--482715 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
482629 TTTAAAAACG
*
482639 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
482664 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
482691 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
482716 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:482683 original size:15 final size:16
Alignment explanation
Indices: 482658--482687 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
482648 ACTATATATT
482658 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
482674 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
482688 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:482687 original size:76 final size:74
Alignment explanation
Indices: 482483--482687 Score: 191
Period size: 76 Copynumber: 2.7 Consensus size: 74
482473 ATATATATAT
* * * * *
482483 AAACGTTTTCAAAAAC-ATATAATATACAAATTTTTTAAAATGTTTTTAAAAAACTATATATTAT
1 AAACGTTTTCAAAAACTATATATTATA-TAA-TTTTCAAAATATTTTT-CAAAACTATATATTAT
482547 ATATATTTTCAA
63 ATATATTTTCAA
** * * * * * *
482559 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAT-GTTTTCAAAAGTATCTATTAT
1 AAACGTTTTCAAAAACTATATATTATAT-AA--TTTTCAAAATATTTTTCAAAACTATATATTAT
482623 ATATATTTT-AA
63 ATATATTTTCAA
482634 AAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAATATATTTTCAAAA
1 AAACGTTTTCAAAAACTATATATTATATAATTTTC--AAAATAT-TTTTCAAAA
482688 TGGTTTTTAA
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
72 5 0.05
74 6 0.06
75 26 0.25
76 43 0.42
77 15 0.15
78 8 0.08
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAACGTTTTCAAAAACTATATATTATATAATTTTCAAAATATTTTTCAAAACTATATATTATATA
TATTTTCAA
Found at i:482769 original size:36 final size:37
Alignment explanation
Indices: 482674--482800 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 37
482664 TTTTCAAAAA
** * * *
482674 ATAT-ATTTTCAAAATGGTTTTTAAAAATTATATATT
1 ATATAATTTTCAAAAACGTTTTCAAAAACTATACATT
* *
482710 ATATAAATGTTTTC-ATAACGTTTTC-AAAAGTATACATT
1 ATAT-AA--TTTTCAAAAACGTTTTCAAAAACTATACATT
*
482748 ATATATATTTT-AAAAACGTTTTCAAAAACTATATATT
1 ATATA-ATTTTCAAAAACGTTTTCAAAAACTATACATT
482785 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
482801 ATATACTTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
36 23 0.31
37 22 0.30
38 17 0.23
39 7 0.09
40 5 0.07
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAATTTTCAAAAACGTTTTCAAAAACTATACATT
Found at i:482922 original size:36 final size:34
Alignment explanation
Indices: 482877--482990 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 34
482867 GTATACATTA
482877 TATATATTTT-AAAAACGTTTTCAAAAACTATATAT
1 TATATATTTTCAAAAACGTTTT--AAAACTATATAT
**
482912 TATATGATTTTCAAAAATATTTTAAAAACTATATAAT
1 TATAT-ATTTTCAAAAACGTTTT-AAAACTATAT-AT
* *
482949 ATACATATTTTCAAAAAATGTTTT-AAACTATATAT
1 -TATATATTTTC-AAAAACGTTTTAAAACTATATAT
482984 TATATAT
1 TATATAT
482991 GTATTTTCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.09
35 7 0.10
36 25 0.36
37 17 0.25
38 14 0.20
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (34 bp):
TATATATTTTCAAAAACGTTTTAAAACTATATAT
Found at i:482931 original size:127 final size:127
Alignment explanation
Indices: 482547--482928 Score: 685
Period size: 127 Copynumber: 3.0 Consensus size: 127
482537 TATATATTAT
*
482547 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
482612 GTAT-CTATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATAC-ATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
482674 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
482739 GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
* * * *
482801 ATATACTTTCAAATTGTTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCTAA
1 ATATATTTTCAAAATG-GTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
*
482866 AGTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATGATTTTCAAAAA
65 AGTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
482929 TATTTTAAAA
Statistics
Matches: 247, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
127 138 0.56
128 109 0.44
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATACATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:482966 original size:75 final size:73
Alignment explanation
Indices: 482875--483026 Score: 184
Period size: 75 Copynumber: 2.1 Consensus size: 73
482865 AAGTATACAT
* * *
482875 TATATATATTTTAAAAACGTTTTCAAAAACTATATA-T-TATATG-ATTTTCAAAAATATTTTAA
1 TATACATATTTTAAAAACGTTTT---AAACTATATATTATATATGTATTTTCAAAAACAATTTAA
482937 AAACTATATAA
63 AAACTATATAA
* **
482948 TATACATATTTTCAAAAAATGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTGCA
1 TATACATATTTT--AAAAACGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTAAA
483013 AACTATATAA
64 AACTATATAA
483023 TATA
1 TATA
483027 TATGTGTATA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
72 10 0.15
73 12 0.18
74 6 0.09
75 40 0.59
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (73 bp):
TATACATATTTTAAAAACGTTTTAAACTATATATTATATATGTATTTTCAAAAACAATTTAAAAA
CTATATAA
Found at i:482974 original size:38 final size:37
Alignment explanation
Indices: 482875--483029 Score: 149
Period size: 37 Copynumber: 4.2 Consensus size: 37
482865 AAGTATACAT
*
482875 TATATATATTTT-AAAAACGTTTTCAAAAACTATAT-A
1 TATATATATTTTCAAAAATGTTTT-AAAAACTATATAA
*
482911 T-TATATGATTTTCAAAAATATTTTAAAAACTATATAA
1 TATATAT-ATTTTCAAAAATGTTTTAAAAACTATATAA
*
482948 TATACATATTTTCAAAAAATGTTTT--AAACTATATATTA
1 TATATATATTTTC-AAAAATGTTTTAAAAACTATATA--A
* *** **
482986 TATATGTATTTTCAAAAACAATTTGCAAACTATATAA
1 TATATATATTTTCAAAAATGTTTTAAAAACTATATAA
483023 TATATAT
1 TATATAT
483030 GTGTATATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
35 5 0.05
36 27 0.27
37 32 0.32
38 26 0.26
39 10 0.10
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (37 bp):
TATATATATTTTCAAAAATGTTTTAAAAACTATATAA
Found at i:493489 original size:70 final size:70
Alignment explanation
Indices: 493376--493554 Score: 331
Period size: 70 Copynumber: 2.6 Consensus size: 70
493366 AGTTAGTTGG
*
493376 GATGCTCTTTTATGTTTCTTAGCAATGTGAGATTGTTTTGTTCTCATATTTTTACTCTTTAGACT
1 GATGCTCTTCTATGTTTCTTAGCAATGTGAGATTGTTTTGTTCTCATATTTTTACTCTTTAGACT
493441 TTTGT
66 TTTGT
493446 GATGCTCTTCTATGTTTCTTAGCAATGTGAGATTGTTTTGTTCTCATATTTTTACTCTTTAGACT
1 GATGCTCTTCTATGTTTCTTAGCAATGTGAGATTGTTTTGTTCTCATATTTTTACTCTTTAGACT
493511 TTTGT
66 TTTGT
* *
493516 GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTT
1 GATGCTCTTCTATGTTTCTTAGCAATGTGAGATTGTTTT
493555 TAAAAAAAAA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 106 1.00
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (70 bp):
GATGCTCTTCTATGTTTCTTAGCAATGTGAGATTGTTTTGTTCTCATATTTTTACTCTTTAGACT
TTTGT
Found at i:493799 original size:23 final size:21
Alignment explanation
Indices: 493772--493814 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
493762 ATATAAAAAA
493772 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
493793 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
493814 T
1 T
493815 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:494127 original size:2 final size:2
Alignment explanation
Indices: 494122--494170 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
494112 ACACACGCGC
494122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494163 AT A- AT AT A
1 AT AT AT AT A
494171 AAATCTTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:499922 original size:37 final size:37
Alignment explanation
Indices: 499846--499922 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
499836 TTTTTATATT
*
499846 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
499883 TTTAATTTTTTAAAGAAAA-TGTATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
499920 TTT
1 TTT
499923 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:501563 original size:15 final size:16
Alignment explanation
Indices: 501543--501583 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
501533 GTTTACTTCA
*
501543 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
501558 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
501574 GAATGATTCA
1 GAATGATTCA
501584 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:501776 original size:20 final size:21
Alignment explanation
Indices: 501737--501776 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
501727 CGCGCTGAAT
501737 GCTGAACGATTCAACATTCAGC
1 GCTGAACGATTC-ACATTCAGC
*
501759 GCTGAATGATTC-CATTCA
1 GCTGAACGATTCACATTCA
501777 AAACCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
GCTGAACGATTCACATTCAGC
Found at i:509287 original size:2 final size:2
Alignment explanation
Indices: 509280--509335 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
509270 TAGAAGAAAC
509280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509322 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
509336 TTGTATCTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509529 original size:2 final size:2
Alignment explanation
Indices: 509522--509549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
509512 GTGGTGATTG
509522 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
509550 CCCTTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:518020 original size:2 final size:2
Alignment explanation
Indices: 518008--518038 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
517998 AATAATTCAT
518008 TA TA T- 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
518039 ATAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:518689 original size:23 final size:24
Alignment explanation
Indices: 518640--518714 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 24
518630 GTGTTCGTTT
* * *
518640 ATTTAT-TAATCGCGAACATATTC
1 ATTTATATATTCGCGAACGTGTTC
* *
518663 ATTTA-ATGTTCGCGAACGTGTTT
1 ATTTATATATTCGCGAACGTGTTC
* *
518686 ATTTATATATTCACAAACGTGTTC
1 ATTTATATATTCGCGAACGTGTTC
518710 ATTTA
1 ATTTA
518715 GCATTATGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (24 bp):
ATTTATATATTCGCGAACGTGTTC
Found at i:519179 original size:2 final size:2
Alignment explanation
Indices: 519172--519196 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
519162 ACTAACTATC
519172 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
519197 GATAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:527350 original size:23 final size:23
Alignment explanation
Indices: 527310--527355 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
527300 TGTGCTTTTG
527310 ATTTTTTTATATAATTT-ATAAT
1 ATTTTTTTATATAATTTAATAAT
* *
527332 ATTTTATTTATTTATTTTAATAAT
1 ATTTT-TTTATATAATTTAATAAT
527356 GTGCATTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTTATATAATTTAATAAT
Found at i:528552 original size:20 final size:20
Alignment explanation
Indices: 528527--528619 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
528517 TTTTCCCAAT
528527 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
528547 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
528567 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
528588 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
528609 TCGCAATGCGA
1 TCGCAATGCGA
528620 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:528569 original size:41 final size:41
Alignment explanation
Indices: 528524--528619 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
528514 CGATTTTCCC
528524 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
528565 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
528606 AAATCGCAATGCGA
1 AATTCGCAATGCGA
528620 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:528573 original size:21 final size:20
Alignment explanation
Indices: 528527--528619 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
528517 TTTTCCCAAT
*
528527 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
528547 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
528567 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
528588 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
528609 TCGCAATGCGA
1 TCGCAATGCGA
528620 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:528633 original size:20 final size:20
Alignment explanation
Indices: 528608--528702 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
528598 AATTGGGAAA
*
528608 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
528628 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
528649 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
528669 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
528689 TTCGCAACGCGATA
1 ATCGCAACGCGATA
528703 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Done.