Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005454.1 Hibiscus syriacus cultivar Beakdansim tig00012493_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: 374245
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:214370 original size:2 final size:2
Alignment explanation
Indices: 214363--214447 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
214353 GGTGACAAGG
214363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
214405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
214447 T
1 T
214448 GTACACCTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:215372 original size:55 final size:55
Alignment explanation
Indices: 215313--215555 Score: 271
Period size: 55 Copynumber: 4.4 Consensus size: 55
215303 AGATTTAGAC
* * *
215313 TGAAGCACAGAGGTGCTCAGTCATTTTTGGCTGCACAGAGGTGTCAGTCCTCGAT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTCGAT
* *
215368 TGAAGCACAGAGGTGCTCAATC-GTCTTAGCTACACAGAGGTGTCAGCTCC-CGGA-
1 TGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC-GAT
* * * * *
215422 TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGAT
1 TGAAGCACAGAGGTGCTCAATC--ATTTTTAGCTACACAGAGGTGTCAGTCCTCGAT
* * *
215479 TGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTCGGT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTCGAT
*
215534 TGAAGCAC-GAATGTGCTCAATC
1 TGAAGCACAG-AGGTGCTCAATC
215556 GTTAATTCTA
Statistics
Matches: 159, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
54 43 0.27
55 70 0.44
56 4 0.03
57 42 0.26
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (55 bp):
TGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTCGAT
Found at i:215375 original size:27 final size:27
Alignment explanation
Indices: 215345--215493 Score: 110
Period size: 27 Copynumber: 5.4 Consensus size: 27
215335 ATTTTTGGCT
215345 GCACAGAGGTGTCAGTCCTCGATTGAA
1 GCACAGAGGTGTCAGTCCTCGATTGAA
* * *
215372 GCACAGAGGTGCTCAATCGTC--TTAGCTA
1 GCACAGAGGTG-TCAGTCCTCGATT-G-AA
215400 -CACAGAGGTGTCAGCTCC-CGGA-TGAA
1 GCACAGAGGTGTCAG-TCCTC-GATTGAA
* *** *
215426 GCACAGAGGTGCTCAGTCGTTTTTTTAA
1 GCACAGAGGTG-TCAGTCCTCGATTGAA
*
215454 CTGCACAGAGGTGTCAGTTCTCGATTGAA
1 --GCACAGAGGTGTCAGTCCTCGATTGAA
215483 GCACAGAGGTG
1 GCACAGAGGTG
215494 CTCAATCACT
Statistics
Matches: 92, Mismatches: 17, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
26 7 0.08
27 48 0.52
28 16 0.17
29 10 0.11
30 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (27 bp):
GCACAGAGGTGTCAGTCCTCGATTGAA
Found at i:215486 original size:111 final size:112
Alignment explanation
Indices: 215313--215558 Score: 356
Period size: 111 Copynumber: 2.2 Consensus size: 112
215303 AGATTTAGAC
* **
215313 TGAAGCACAGAGGTGCTCAGTC--ATTTTTGGCTGCACAGAGGTGTCAGTCCTCGATTGAAGCAC
1 TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCAC
*
215376 AGAGGTGCTCAATC-GTCTTAGCTACACAGAGGTGTCAGCTCCCGGA
66 AGAGGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGGA
*
215422 TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGAAGCAC
1 TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCAC
* * * *
215487 AGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTCGGT
66 AGAGGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGGA
* *
215534 TGAAGCAC-GAATGTGCTCAATCGTT
1 TGAAGCACAG-AGGTGCTCAGTCGTT
215559 AATTCTAGCA
Statistics
Matches: 122, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
109 22 0.18
111 52 0.43
112 48 0.39
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (112 bp):
TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCAC
AGAGGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGGA
Found at i:215571 original size:55 final size:54
Alignment explanation
Indices: 215257--215575 Score: 237
Period size: 55 Copynumber: 5.8 Consensus size: 54
215247 CTTGATTTTA
* * * * * * *
215257 GATTGTAGCACTGATGTGCTCAATC---ATTCTAATGCACAGAGGTGCCAGATTTA
1 GATTGAAGCACAGAGGTGCTCAATCGTTATTCT-A-GCACAGAGGTGTCAGCTCTC
* * * *
215310 GACTGAAGCACAGAGGTGCTCAGTCATTTTTGGCT-GCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCGTTATT--CTAGCACAGAGGTGTCAGCT-CTC
* *
215365 GATTGAAGCACAGAGGTGCTCAATCGTCT-TAGCTA-CACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCGT-TAT-TCTAGCACAGAGGTGTCAGCTCTC
* * * *
215419 GGA-TGAAGCACAGAGGTGCTCAGTCGTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 -GATTGAAGCACAGAGGTGCTCAATCGTTATTCT-A--GCACAGAGGTGTCAGCTCTC
*
215476 GATTGAAGCACAGAGGTGCTCAATCACTT-TTGGCTA-CACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATC-GTTATT--CTAGCACAGAGGTGTCAGCTCTC
* *
215531 GGTTGAAGCAC-GAATGTGCTCAATCGTTAATTCTAGCACAGAGGT
1 GATTGAAGCACAG-AGGTGCTCAATCGTT-ATTCTAGCACAGAGGT
215576 ACTATGGATT
Statistics
Matches: 216, Mismatches: 26, Indels: 46
0.75 0.09 0.16
Matches are distributed among these distances:
53 22 0.10
54 50 0.23
55 91 0.42
56 7 0.03
57 40 0.19
58 5 0.02
59 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (54 bp):
GATTGAAGCACAGAGGTGCTCAATCGTTATTCTAGCACAGAGGTGTCAGCTCTC
Found at i:226967 original size:4 final size:4
Alignment explanation
Indices: 226960--226987 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
226950 TATATATATA
226960 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
226988 CTTTTAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:227762 original size:230 final size:227
Alignment explanation
Indices: 227351--227800 Score: 783
Period size: 230 Copynumber: 2.0 Consensus size: 227
227341 GTAAATTATC
* * *
227351 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
227416 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
227481 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTTAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTA-TTAAAAAAATT
227546 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
227580 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
227645 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
227710 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
227775 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
227801 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 68 0.32
230 138 0.66
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:227888 original size:20 final size:20
Alignment explanation
Indices: 227865--227914 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
227855 CGATATACCA
227865 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
227885 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
227905 GGTAAAATTA
1 GGTAAAATTA
227915 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:228054 original size:20 final size:19
Alignment explanation
Indices: 228031--228077 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
228021 CGATATAACA
*
228031 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
228051 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
228071 GGTAAAA
1 GGTAAAA
228078 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:230430 original size:33 final size:33
Alignment explanation
Indices: 230388--230453 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
230378 AAATAGATGG
*
230388 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
230421 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
230454 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:232310 original size:19 final size:19
Alignment explanation
Indices: 232247--232304 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
232237 AATGTCGAGT
*
232247 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
232266 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
232285 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
232304 T
1 T
232305 TTTTTTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:232823 original size:198 final size:199
Alignment explanation
Indices: 232391--234005 Score: 2861
Period size: 198 Copynumber: 8.1 Consensus size: 199
232381 TTAAGGGTCA
* * *** *
232391 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
232456 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
232521 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
232585 AATG
196 AATG
*
232589 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
232654 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
232719 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
232784 AATG
196 AATG
232788 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
232852 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
232917 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
232981 TAATG
195 TAATG
* *** *
232986 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
233051 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
233115 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
233180 AATG
196 AATG
233184 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
233249 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
233314 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
233379 TAATG
195 TAATG
* *** * *
233384 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
233449 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
233513 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
233577 AATG
196 AATG
233581 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
233645 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
233710 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
233775 TAATG
195 TAATG
* *** * *
233780 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
233845 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
233909 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
233974 AATG
196 AATG
233978 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
234006 CTAATTTAAA
Statistics
Matches: 1364, Mismatches: 43, Indels: 21
0.96 0.03 0.01
Matches are distributed among these distances:
196 18 0.01
197 204 0.15
198 571 0.42
199 393 0.29
200 178 0.13
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:233194 original size:396 final size:398
Alignment explanation
Indices: 232391--234005 Score: 3001
Period size: 397 Copynumber: 4.1 Consensus size: 398
232381 TTAAGGGTCA
* * *** *
232391 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
232455 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
232520 GTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* ***
232584 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
* * *
232649 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 AATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
232714 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
232779 TAAATAATG
390 TAAATAATG
232788 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
232852 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
232917 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
232981 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
*
233046 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
233111 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
233176 AAATAATG
391 AAATAATG
233184 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
233249 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
233314 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
233379 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
233444 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
233509 AATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
233573 AAATAATG
391 AAATAATG
233581 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
233645 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
233710 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
233775 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
233840 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
233905 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
233970 AAATAATG
391 AAATAATG
233978 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
234006 CTAATTTAAA
Statistics
Matches: 1197, Mismatches: 16, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
396 484 0.40
397 518 0.43
398 195 0.16
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:235490 original size:18 final size:18
Alignment explanation
Indices: 235467--235528 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
235457 ATCGGTCGCA
* * *
235467 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
235485 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
235503 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
235521 GAAGATGA
1 GAAGATGA
235529 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:235491 original size:6 final size:6
Alignment explanation
Indices: 235467--235528 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
235457 ATCGGTCGCA
* * * * * *
235467 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
235515 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
235529 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:235502 original size:3 final size:3
Alignment explanation
Indices: 235482--235532 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
235472 TGAAGCTGAC
* * * *
235482 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
235530 GAT
1 GAT
235533 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:235529 original size:12 final size:12
Alignment explanation
Indices: 235470--235532 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
235460 GGTCGCAGAA
* *
235470 GATGAAGCTGAC
1 GATGAAGATGAT
*
235482 GATGAAGATGAC
1 GATGAAGATGAT
*
235494 GATGATGATGAT
1 GATGAAGATGAT
*
235506 GATGACGATGAT
1 GATGAAGATGAT
235518 GATGAAGATGAT
1 GATGAAGATGAT
235530 GAT
1 GAT
235533 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:238701 original size:23 final size:23
Alignment explanation
Indices: 238670--238732 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
238660 ATAGGTAAAC
*
238670 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
238693 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
238716 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
238733 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:238740 original size:23 final size:23
Alignment explanation
Indices: 238670--238742 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
238660 ATAGGTAAAC
* * **
238670 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
238693 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
238716 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
238739 ATAT
1 ATAT
238743 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:239126 original size:23 final size:23
Alignment explanation
Indices: 239095--239157 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
239085 ATAGGTAAAC
*
239095 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
239118 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
239141 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
239158 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:239165 original size:23 final size:23
Alignment explanation
Indices: 239095--239167 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
239085 ATAGGTAAAC
* * **
239095 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
239118 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
239141 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
239164 ATAT
1 ATAT
239168 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:239556 original size:23 final size:23
Alignment explanation
Indices: 239525--239587 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
239515 ATAGGTAAAC
*
239525 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
239548 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
239571 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
239588 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:239595 original size:23 final size:23
Alignment explanation
Indices: 239525--239597 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
239515 ATAGGTAAAC
* * **
239525 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
239548 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
239571 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
239594 ATAT
1 ATAT
239598 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:239668 original size:430 final size:431
Alignment explanation
Indices: 238571--239867 Score: 2545
Period size: 430 Copynumber: 3.0 Consensus size: 431
238561 AATTCGCAGT
238571 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
238636 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
238701 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
238766 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
238830 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGG--TATA-TATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
238891 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
238955 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
238996 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
239061 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
239126 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
239191 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
239256 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
239321 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
239386 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
239427 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
239491 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
239556 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
239621 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
239686 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
239751 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
239816 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
239857 ACACTGTTAAA
1 ACACTGTTAAA
239868 GTATCGATCC
Statistics
Matches: 866, Mismatches: 0, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
425 245 0.28
426 53 0.06
427 14 0.02
429 4 0.00
430 427 0.49
431 123 0.14
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:249497 original size:18 final size:18
Alignment explanation
Indices: 249456--249498 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
249446 AAACAACATA
*
249456 ATATTCTTTTCATTCAGAC
1 ATATT-TTTTCATTCAAAC
* *
249475 TTATTTTTTCATTTAAAC
1 ATATTTTTTCATTCAAAC
249493 ATATTT
1 ATATTT
249499 CAGAACTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTTTTTCATTCAAAC
Found at i:249781 original size:2 final size:2
Alignment explanation
Indices: 249774--249814 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
249764 AAGCACATCA
249774 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 A
249815 CTAGTGCACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:251316 original size:25 final size:23
Alignment explanation
Indices: 251271--251317 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
251261 TTCTTTTTAG
* *
251271 AATTCATATTAACTTTCCCATTT
1 AATTCATAATAACCTTCCCATTT
251294 AATTCATAATAACCCTTCACCATT
1 AATTCATAATAA-CCTTC-CCATT
251318 ATGATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTCATAATAACCTTCCCATTT
Found at i:254278 original size:2 final size:2
Alignment explanation
Indices: 254271--254295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
254261 TCACTTCAAT
254271 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
254296 TTCTTTAAAA
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:264798 original size:36 final size:36
Alignment explanation
Indices: 264758--264829 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
264748 ATGAAAAAGA
264758 ACATCTATCGTCTCATCTTCAGCTGCCTGTCTTTCT
1 ACATCTATCGTCTCATCTTCAGCTGCCTGTCTTTCT
* * *
264794 ACATCTATTGTCTCATCTTCGGCTGCTTGTCTTTCT
1 ACATCTATCGTCTCATCTTCAGCTGCCTGTCTTTCT
264830 TTGTGAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.44
Consensus pattern (36 bp):
ACATCTATCGTCTCATCTTCAGCTGCCTGTCTTTCT
Found at i:274212 original size:2 final size:2
Alignment explanation
Indices: 274205--274246 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
274195 CTATCTATCG
274205 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
274247 GTTAGAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274417 original size:2 final size:2
Alignment explanation
Indices: 274410--274442 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
274400 TTGTTCTCAA
274410 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 A
274443 AAAGTAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:278522 original size:14 final size:13
Alignment explanation
Indices: 278500--278528 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
278490 TAAGTTTACT
278500 TACAAAAAAAGAA
1 TACAAAAAAAGAA
278513 TACAAAAAAAGAA
1 TACAAAAAAAGAA
278526 TAC
1 TAC
278529 TTTTAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.10, G:0.07, T:0.10
Consensus pattern (13 bp):
TACAAAAAAAGAA
Found at i:279897 original size:11 final size:12
Alignment explanation
Indices: 279850--279884 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
279840 AACTAATTAA
*
279850 TATAATAAAAAT
1 TATAATATAAAT
279862 TATAATATAAAT
1 TATAATATAAAT
279874 T-TAATATAAAT
1 TATAATATAAAT
279885 AAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAATATAAAT
Found at i:280306 original size:11 final size:11
Alignment explanation
Indices: 280290--280352 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
280280 GTATTATAGA
280290 ATTTTTAATAT
1 ATTTTTAATAT
280301 ATTTTTAA-A-
1 ATTTTTAATAT
280310 ATTTTATAAT-T
1 ATTTT-TAATAT
***
280321 ATCAATAATAT
1 ATTTTTAATAT
280332 ATTTTTAATAT
1 ATTTTTAATAT
280343 ATTTTTAATA
1 ATTTTTAATA
280353 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:283202 original size:73 final size:73
Alignment explanation
Indices: 283083--283224 Score: 284
Period size: 73 Copynumber: 1.9 Consensus size: 73
283073 AGCGAGTCCA
283083 TCTCATCTTTCATGGAAGACTCCCACTTGACTGAATCCTCCACCTGCATTGCTTCATCATAGCAC
1 TCTCATCTTTCATGGAAGACTCCCACTTGACTGAATCCTCCACCTGCATTGCTTCATCATAGCAC
283148 TCTGCGAG
66 TCTGCGAG
283156 TCTCATCTTTCATGGAAGACTCCCACTTGACTGAATCCTCCACCTGCATTGCTTCATCATAGCAC
1 TCTCATCTTTCATGGAAGACTCCCACTTGACTGAATCCTCCACCTGCATTGCTTCATCATAGCAC
283221 TCTG
66 TCTG
283225 GTTCACCATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (73 bp):
TCTCATCTTTCATGGAAGACTCCCACTTGACTGAATCCTCCACCTGCATTGCTTCATCATAGCAC
TCTGCGAG
Found at i:288139 original size:16 final size:17
Alignment explanation
Indices: 288114--288148 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
288104 CATACACATG
288114 ATATATCATATATACTT
1 ATATATCATATATACTT
*
288131 ATATA-CATATATATTT
1 ATATATCATATATACTT
288147 AT
1 AT
288149 TAAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATCATATATACTT
Found at i:288196 original size:34 final size:34
Alignment explanation
Indices: 288152--288246 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 34
288142 TATTTATTAA
*
288152 ATTTATTCATATATAAATATATTACTAATGTT-T
1 ATTTATTCATATATAAATATATTACTAATCTTGT
* ** **
288185 ATTTTATTCATATATAAATTTATTTTTACCCTTGT
1 A-TTTATTCATATATAAATATATTACTAATCTTGT
288220 A--TATTCATATATAAATATATTACTAAT
1 ATTTATTCATATATAAATATATTACTAAT
288247 ACAACAACAA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
32 21 0.43
33 1 0.02
34 25 0.51
35 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (34 bp):
ATTTATTCATATATAAATATATTACTAATCTTGT
Found at i:289127 original size:23 final size:23
Alignment explanation
Indices: 289101--289164 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
289091 ACACTCATAT
*
289101 AATTACACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
289124 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
*
289147 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
289165 TATAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:289351 original size:103 final size:103
Alignment explanation
Indices: 289180--289397 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
289170 TAATGTCCAT
* * *
289180 AAGGACCACATATCATTCCTTAAGAATCATATGCATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
289245 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
289283 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
289348 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
289386 AAGGACCACATA
1 AAGGACCACATA
289398 GACCATCTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:289958 original size:64 final size:67
Alignment explanation
Indices: 289846--289973 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 67
289836 ATTTTCATCT
289846 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
289911 TA
66 TA
**
289913 TTTAATGG-GG-ATGCATCGATGCACTAC-TTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTT
289974 TCTTTTTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 32 0.54
65 17 0.29
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:289991 original size:64 final size:63
Alignment explanation
Indices: 289858--290018 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
289848 TAATGGAGGT
* * *
289858 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
289923 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
289987 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
290019 CCTTAAATAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 58 0.68
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:296149 original size:23 final size:23
Alignment explanation
Indices: 296123--296176 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
296113 ATTACATCGA
296123 AGTGCCATGTAGAATTGCACCAG-
1 AGTGCCATGTAGAATTGCACC-GT
**
296146 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCATGTAGAATTGCACCGT
296169 AGTGCCAT
1 AGTGCCAT
296177 ATAATAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (23 bp):
AGTGCCATGTAGAATTGCACCGT
Found at i:296362 original size:103 final size:103
Alignment explanation
Indices: 296191--296408 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
296181 TAATGTCCAT
* *
296191 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
296256 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * * *
296294 AAGGACCACATATCATTCCTTAAGAGTCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
296359 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
296397 AAGGACCACATA
1 AAGGACCACATA
296409 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:305071 original size:336 final size:335
Alignment explanation
Indices: 304502--305409 Score: 892
Period size: 336 Copynumber: 2.6 Consensus size: 335
304492 TATTAAATTT
** * *
304502 TGTATTGATTAGTATATTTTTTTATATGTTCAGCTAATGATGCTATAGCCAGTCAAGTTGCATCT
1 TGTATTGATTAGTATATTTTTCGATA--TTCAGCTGATGATGCTAAAGCCAGTCAAGTTGCATCT
* * *
304567 AAAGGTTGCTTGGTACCAAATATTGAAGCTGATGATGATTTTGGCAATTGTTCTGCT-GAACA-T
64 GAAGGTTGCTTGGTACCAAAAACTGAAGC---TGATGATTTTGGC-A-TGTTCTGCTGGAA-ATT
* * * * * * *
304630 CGTAGTCCTGCTGCCGAACTCACTACAATAGGATATCAAGAAGATCGAGGGCAAGTCAATCCTAG
123 C-TAGTCCTGCTGCCCAACTCACCACAAGAGGAAATCAAGAAAATCAAGGGCAAATCAATCCTAG
*
304695 TAAGTATATCTGCAATATCCTCACTTTAAACCTGACAATACTAGATACAACACGAACAAGAAATG
187 TAAGTATATCTGCAATAGCCTCACTTTAAACCTGACAATACTAGATACAACA-G-ACAAGAAATG
* * * * *
304760 AAAAAAAAAACTAATAAT-AGGATACAAAACACAATGA-GACAATAAAAAATAAGC-A-C-G-GG
250 --AAAAAAAACTAACAATAAGCA-ACAAAACACAA-CATGACAAGAAAAAAGAAGCTAGCAGAGG
** * *
304819 CAAATACATTAATATGTCAAAA-TC
311 CAAATACACAAACATGTCAAAACCC
* * *
304843 TGTATTGATGAGTATATTTTTCGATATTCAGCTGACGCTGCTAAAGCCAGTCAAGTTGCATCTGA
1 TGTATTGATTAGTATATTTTTCGATATTCAGCTGATGATGCTAAAGCCAGTCAAGTTGCATCTGA
* *
304908 AGGTTGCTTGGTACCAAAAACTGAAGCTGATGATTTTGGC-GGTTCTGCTGGAAATTCTAGCCCT
66 AGGTTGCTTGGTACCAAAAACTGAAGCTGATGATTTTGGCATGTTCTGCTGGAAATTCTAGTCCT
*
304972 GCTGCCCAACTCACCACCATAGGAGGAAATCAAGAAAATCAAGAGG-AAATCAATCCTGGTAAGT
131 GCTGCCCAACTCACCA-CA-A-GAGGAAATCAAGAAAATCAAG-GGCAAATCAATCCTAGTAAGT
* * ** *
305036 -TCATCTGCAA-AGCACTCACTTTAAGCCTGACAATACTAGATACAACAGAGAAGATTTGGAAAA
192 AT-ATCTGCAATAGC-CTCACTTTAAACCTGACAATACTAGATACAACAGACAAGAAATGAAAAA
* ** *
305099 AAACTAACAATAAGCAACAAAATACAACATGACAAGAAAAAAGAAGCTTGAGCATGATTCTAATA
255 AAACTAACAATAAGCAACAAAACACAACATGACAAGAAAAAAGAAGC-T-AGCA-GAGGCAAATA
305164 CACAAACATGTCAAAACCC
317 CACAAACATGTCAAAACCC
* * *
305183 T-TTTTGATTTATATATTATTTTTTCTGATATATTCAGCTGATTATGCTAAAGCCAGTCAAGTTG
1 TGTATTGA-TTA-GTA-TA-TTTTTC-G--ATATTCAGCTGATGATGCTAAAGCCAGTCAAGTTG
*
305247 CATCTGAAGGTAGCTTGGTACCAAAAACTGAAGCTGATGGTGATTTTGGCAATTGTTCTGCTGGA
59 CATCTGAAGGTTGCTTGGTACCAAAAACTGAAGCTGA---TGATTTTGGC-A-TGTTCTGCTGGA
* ** * * * * *
305312 AATTCTTGTCCTGCTGCCCAACTCACTGCCACAGGATACCAAGAAAATC-AGGAGCAGATCAATC
119 AATTCTAGTCCTGCTGCCCAACTCACCACAAGAGGAAATCAAGAAAATCAAGG-GCAAATCAATC
** *
305376 CTAGTAAGTATATCTGCAATTTCCTCTCTTTAAA
183 CTAGTAAGTATATCTGCAATAGCCTCACTTTAAA
305410 TCTGGAAACA
Statistics
Matches: 471, Mismatches: 61, Indels: 62
0.79 0.10 0.10
Matches are distributed among these distances:
331 1 0.00
332 39 0.08
333 32 0.07
334 14 0.03
335 6 0.01
336 87 0.18
337 2 0.00
338 1 0.00
339 82 0.17
340 4 0.01
341 25 0.05
342 2 0.00
343 6 0.01
344 1 0.00
346 68 0.14
347 1 0.00
348 3 0.01
349 58 0.12
350 3 0.01
351 1 0.00
352 35 0.07
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (335 bp):
TGTATTGATTAGTATATTTTTCGATATTCAGCTGATGATGCTAAAGCCAGTCAAGTTGCATCTGA
AGGTTGCTTGGTACCAAAAACTGAAGCTGATGATTTTGGCATGTTCTGCTGGAAATTCTAGTCCT
GCTGCCCAACTCACCACAAGAGGAAATCAAGAAAATCAAGGGCAAATCAATCCTAGTAAGTATAT
CTGCAATAGCCTCACTTTAAACCTGACAATACTAGATACAACAGACAAGAAATGAAAAAAAACTA
ACAATAAGCAACAAAACACAACATGACAAGAAAAAAGAAGCTAGCAGAGGCAAATACACAAACAT
GTCAAAACCC
Found at i:307455 original size:17 final size:17
Alignment explanation
Indices: 307433--307472 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
307423 AGTAGCCATT
307433 GACAGTTTGCCAACTTA
1 GACAGTTTGCCAACTTA
*
307450 GACAGTTTGCCAACTTT
1 GACAGTTTGCCAACTTA
307467 GACAGT
1 GACAGT
307473 AGCAGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (17 bp):
GACAGTTTGCCAACTTA
Found at i:307733 original size:31 final size:31
Alignment explanation
Indices: 307659--307720 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
307649 TTACGTCAGA
*
307659 GACCATATTGCAAACGGACTAAATGTTGAGG
1 GACCATATTGCAAACGGACTAAATATTGAGG
*
307690 GACCATATTGCAAATGGACTAAATATT-AGG
1 GACCATATTGCAAACGGACTAAATATTGAGG
307720 G
1 G
307721 GATTGTATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATATTGAGG
Found at i:307843 original size:30 final size:31
Alignment explanation
Indices: 307808--307904 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
307798 ATCCTTAATT
*
307808 TTAATTTGATCTCTAAATTTTA-ATAAAATA
1 TTAATTTGATCTCTGAATTTTAGATAAAATA
* *
307838 TTAATTTGA-CTTTGATTTTTAGATAAAATA
1 TTAATTTGATCTCTGAATTTTAGATAAAATA
* *
307868 CTAATTTAAT-TCATGAATTTTAGATAAAAATA
1 TTAATTTGATCTC-TGAATTTTAGAT-AAAATA
307900 TTAAT
1 TTAAT
307905 ATCATCCTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
29 9 0.16
30 25 0.45
31 11 0.20
32 10 0.18
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAATTTGATCTCTGAATTTTAGATAAAATA
Found at i:307892 original size:31 final size:30
Alignment explanation
Indices: 307823--307896 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
307813 TTGATCTCTA
* *
307823 AATTTTA-ATAAAATATTAATTTGACTTTG
1 AATTTTAGATAAAATACTAATTTGAATTTG
*
307852 ATTTTTAGATAAAATACTAATTT-AATTCATG
1 AATTTTAGATAAAATACTAATTTGAATT--TG
307883 AATTTTAGATAAAA
1 AATTTTAGATAAAA
307897 ATATTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 9 0.24
30 14 0.37
31 15 0.39
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (30 bp):
AATTTTAGATAAAATACTAATTTGAATTTG
Found at i:308706 original size:3 final size:3
Alignment explanation
Indices: 308700--308749 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
308690 TTTTTATCCA
*
308700 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
308748 TA
1 TA
308750 AATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:309245 original size:20 final size:20
Alignment explanation
Indices: 309222--309260 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
309212 AGAACGGGAC
*
309222 AGAGAGACAGAAAAAAAAAG
1 AGAGAAACAGAAAAAAAAAG
309242 AGAGAAACAGAAAAAAAAA
1 AGAGAAACAGAAAAAAAAA
309261 ACAGAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (20 bp):
AGAGAAACAGAAAAAAAAAG
Found at i:309258 original size:21 final size:20
Alignment explanation
Indices: 309220--309268 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
309210 AGAGAACGGG
*
309220 ACAGAGAGACAGAAAAAAAA
1 ACAGAGAAACAGAAAAAAAA
*
309240 AGAGAGAAACAGAAAAAAAAA
1 ACAGAGAAACAG-AAAAAAAA
309261 ACAGAGAA
1 ACAGAGAA
309269 GATACAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.71, C:0.08, G:0.20, T:0.00
Consensus pattern (20 bp):
ACAGAGAAACAGAAAAAAAA
Found at i:321939 original size:19 final size:20
Alignment explanation
Indices: 321906--321947 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
321896 TTCAAGTTCA
*
321906 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
321926 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
321945 ATT
1 ATT
321948 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:322812 original size:84 final size:84
Alignment explanation
Indices: 322713--323781 Score: 1996
Period size: 84 Copynumber: 12.7 Consensus size: 84
322703 CATTAACTGA
*
322713 AAGATGAATTTGCTCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
322778 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
*
322797 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
*
322862 AACCAATCATTGAATTTGA
66 AACCAATCATTGAATTTGG
*
322881 AAGATGAATTTGCTCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
*
322946 AACCAATCATTGAATTTGA
66 AACCAATCATTGAATTTGG
* *
322965 AAGATGAATTTGCTCAATAGCATTTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323030 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
323049 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323114 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
323133 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323198 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
*
323217 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323282 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
323301 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
*
323366 AACCAATCATTGAATTTAG
66 AACCAATCATTGAATTTGG
*
323385 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGAAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323450 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
*
323469 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323534 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
*
323553 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323618 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
323637 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
323702 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
* * *
323721 AAGATGAATTTGC-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG
323782 TAAAAATTAC
Statistics
Matches: 965, Mismatches: 20, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 45 0.05
84 920 0.95
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (84 bp):
AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
AACCAATCATTGAATTTGG
Found at i:324713 original size:113 final size:113
Alignment explanation
Indices: 324510--325069 Score: 1030
Period size: 113 Copynumber: 5.0 Consensus size: 113
324500 CAAAGATTCA
* * * * * *
324510 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAATTCATCTGAAAA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
324575 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
324623 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
324688 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
324736 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
324801 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
324849 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
324914 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
324962 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
325027 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
325070 GCATAATTCT
Statistics
Matches: 436, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 436 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:325395 original size:3 final size:3
Alignment explanation
Indices: 325389--325438 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
325379 TTTTTATCCA
*
325389 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
325437 TA
1 TA
325439 AATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:332653 original size:35 final size:35
Alignment explanation
Indices: 332582--332654 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
332572 ACACATCATA
* **
332582 TAAGGCCCTGAGCACAAAGCCGAGGATCCGGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
* *
332617 TAAGGCCCTGAGCACACAGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
332652 TAA
1 TAA
332655 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
Found at i:332758 original size:24 final size:24
Alignment explanation
Indices: 332731--332814 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
332721 CATAATTCAA
332731 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * *
332755 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
332779 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
*
332802 GTCAGGTATCATA
1 GTCAAGTATCATA
332815 ATAGAATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:332821 original size:47 final size:48
Alignment explanation
Indices: 332731--332821 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 48
332721 CATAATTCAA
* *
332731 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAAATCAGAATCCAT
332779 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAAT-AGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCA-AATCAGAAT
332822 TCAAATTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 33 0.82
48 7 0.17
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAAATCAGAATCCAT
Found at i:335313 original size:18 final size:18
Alignment explanation
Indices: 335290--335331 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
335280 CAACAGTCAA
335290 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
335308 CGGGTCAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGT
335326 CGGGTC
1 CGGGTC
335332 GGGTTGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:337359 original size:35 final size:35
Alignment explanation
Indices: 337288--337360 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
337278 ACACATCATA
* **
337288 TAAGGCCCTGAGCATAAAGCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
* *
337323 TAAGGCCCTGAGCACACAGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
337358 TAA
1 TAA
337361 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.27, T:0.11
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
Found at i:337464 original size:24 final size:24
Alignment explanation
Indices: 337437--337527 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
337427 CATAATTCAA
337437 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
337461 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
337485 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
337508 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
337528 TCAAATTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 21 0.35
24 39 0.65
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:337507 original size:47 final size:48
Alignment explanation
Indices: 337437--337527 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 48
337427 CATAATTCAA
* *
337437 GTCAAGTATCATATCAGAATCCAGGTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAATCCAT
337485 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
337528 TCAAATTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 36 0.88
48 5 0.12
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAATCCAT
Found at i:341573 original size:36 final size:36
Alignment explanation
Indices: 341533--341776 Score: 303
Period size: 36 Copynumber: 6.8 Consensus size: 36
341523 TCAAACAATC
* * *
341533 CGATGCTTCTTTCCATTCGATTTGAATCGGAAGTGT
1 CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* * * *
341569 CGATGATTCCTTCCGTTTGA-TTCGAATCGAAAGTGC
1 CGATGCTTCCTTCCGTTCGACTT-GAATCGGAAGTGT
* * *
341605 CGATGATTCCCTCCGTTCGACTTGAATCGAAAGTGT
1 CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* *
341641 CGATGCTTCTTTTCGTTC-ACTTGAATCGGAAGTGT
1 CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* *
341676 CGATGCTTCCTTCCGTTTGATTTGAATCGGAAGTGT
1 CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* *
341712 CGATGCTTCCCTCCGTTCAACTTGAATCGGAAGTGT
1 CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* *
341748 CGATGTTTCCCTCCGTTCGACTTGAATCG
1 CGATGCTTCCTTCCGTTCGACTTGAATCG
341777 ATGCAAACTT
Statistics
Matches: 181, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
35 33 0.18
36 146 0.81
37 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (36 bp):
CGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
Found at i:341703 original size:107 final size:108
Alignment explanation
Indices: 341533--341776 Score: 364
Period size: 107 Copynumber: 2.3 Consensus size: 108
341523 TCAAACAATC
* *
341533 CGATGCTTCTTTCCATTCGATTTGAATCGGAAGTGTCGATGATTCCTTCCGTTTGATTCGAATCG
1 CGATGCTTCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGATTCCTTCCGTTTGATTCGAATCG
*
341598 AAAGTGCCGATGATTCCCTCCGTTCGACTTGAATCGAAAGTGT
66 AAAGTGCCGATGATTCCCTCCGTTCAACTTGAATCGAAAGTGT
* * *
341641 CGATGCTTCTTTTCGTTC-ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTTGATTTGAATCG
1 CGATGCTTCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGATTCCTTCCGTTTGATTCGAATCG
* * * *
341705 GAAGTGTCGATGCTTCCCTCCGTTCAACTTGAATCGGAAGTGT
66 AAAGTGCCGATGATTCCCTCCGTTCAACTTGAATCGAAAGTGT
* **
341748 CGATGTTTCCCTCCGTTCGACTTGAATCG
1 CGATGCTTCTTTCCGTTCGACTTGAATCG
341777 ATGCAAACTT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
107 95 0.79
108 26 0.21
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (108 bp):
CGATGCTTCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGATTCCTTCCGTTTGATTCGAATCG
AAAGTGCCGATGATTCCCTCCGTTCAACTTGAATCGAAAGTGT
Found at i:344335 original size:20 final size:21
Alignment explanation
Indices: 344300--344340 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
344290 GTTTATTTTT
*
344300 TTTTTTAATTTTTAAATAATA
1 TTTTTTAATTTTTAAAAAATA
344321 TTTTTT-ATTTTTAAAAAATA
1 TTTTTTAATTTTTAAAAAATA
344341 AAAAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAATTTTTAAAAAATA
Found at i:346510 original size:26 final size:26
Alignment explanation
Indices: 346477--346530 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
346467 TAGTAATTTG
*
346477 AAGTAATTATAATATAGTATATATTA
1 AAGTAATTATAAGATAGTATATATTA
*
346503 AAGTAATTATAAGGTAGTATATATTA
1 AAGTAATTATAAGATAGTATATATTA
346529 AA
1 AA
346531 AAATTGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (26 bp):
AAGTAATTATAAGATAGTATATATTA
Found at i:348651 original size:15 final size:15
Alignment explanation
Indices: 348631--348670 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
348621 TCAATCATAG
348631 CTGCATTTGCCAAAT
1 CTGCATTTGCCAAAT
348646 CTGCATTTGCCAAAT
1 CTGCATTTGCCAAAT
348661 CTGCATTTGC
1 CTGCATTTGC
348671 ATGGAGAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (15 bp):
CTGCATTTGCCAAAT
Found at i:351039 original size:24 final size:23
Alignment explanation
Indices: 351003--351048 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
350993 CTGCTGTGTC
*
351003 ATTTAATAATTATATTGTATTTT
1 ATTTAATAATTATATAGTATTTT
*
351026 ATTTATTATATTATATAGTATTT
1 ATTTAATA-ATTATATAGTATTT
351049 CCAAAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTAATAATTATATAGTATTTT
Found at i:353208 original size:20 final size:19
Alignment explanation
Indices: 353185--353229 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
353175 TATTTTTTAT
* *
353185 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
353205 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
353224 TATTTA
1 TATTTA
353230 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:353219 original size:26 final size:30
Alignment explanation
Indices: 353180--353235 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
353170 AATTATATTT
*
353180 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
353207 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
353236 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:353236 original size:3 final size:3
Alignment explanation
Indices: 353228--353334 Score: 178
Period size: 3 Copynumber: 35.7 Consensus size: 3
353218 TTAATATATT
*
353228 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
353276 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
353324 TAA TAA TAA TA
1 TAA TAA TAA TA
353335 TGGATAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:354195 original size:113 final size:113
Alignment explanation
Indices: 353653--354175 Score: 960
Period size: 113 Copynumber: 4.6 Consensus size: 113
353643 GAATTATGCC
* * *
353653 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
353717 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
353764 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
353829 TATGAACTTTTTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
353877 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
353942 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
353990 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
354055 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
354103 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
354168 TATGAACT
66 TATGAACT
354176 CGAACTGGAA
Statistics
Matches: 401, Mismatches: 9, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
111 4 0.01
112 64 0.16
113 333 0.83
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:355367 original size:250 final size:249
Alignment explanation
Indices: 354927--355465 Score: 990
Period size: 250 Copynumber: 2.2 Consensus size: 249
354917 CCTACTGAAT
*
354927 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
354992 TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
66 TGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
*
355057 TTCATCTTCCAAATTCAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
355122 GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
196 GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
*
355176 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAACACATTCATCTTCCAAATTCA
*
355241 ATGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCA
65 ATGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACA
355305 CATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTC
129 CATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTC
*
355370 CAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAT
194 CAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
*
355426 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
355466 TGGTAAATTC
Statistics
Matches: 281, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
249 39 0.14
250 240 0.85
251 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (249 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
TGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
TTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
Found at i:355466 original size:83 final size:83
Alignment explanation
Indices: 354927--355477 Score: 971
Period size: 83 Copynumber: 6.6 Consensus size: 83
354917 CCTACTGAAT
* *
354927 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
354991 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
*
355010 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
355074 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
355093 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
355158 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
355176 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
*
355241 ATGATTGGATTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
355260 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
355325 TGATTGGTTCTGTCAAAC
66 TGATTGGTTTTGTCAAAC
355343 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
355408 TGATTGGTTTTGTCAAAT
66 TGATTGGTTTTGTCAAAC
* * *
355426 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCAT
355478 TTGTTCTATT
Statistics
Matches: 454, Mismatches: 12, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
83 371 0.82
84 83 0.18
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:356166 original size:19 final size:16
Alignment explanation
Indices: 356144--356189 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
356134 AATAGAAAAG
356144 AATAAATTGAATTTCCAAA
1 AATAAATTGAATTT-C--A
*
356163 AATAAATTTAATTTCA
1 AATAAATTGAATTTCA
356179 AATAAATTGAA
1 AATAAATTGAA
356190 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
18 1 0.04
19 13 0.52
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (16 bp):
AATAAATTGAATTTCA
Found at i:369354 original size:27 final size:27
Alignment explanation
Indices: 369307--369360 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
369297 AATTATATTT
* *
369307 TTTATTATTTATTTATTTTTAATAATA
1 TTTATTATTTATATATATTTAATAATA
369334 TTTATGTATTTA-ATATATTTAATAATA
1 TTTAT-TATTTATATATATTTAATAATA
369361 ATAGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATTATTTATATATATTTAATAATA
Found at i:369361 original size:3 final size:3
Alignment explanation
Indices: 369353--369450 Score: 112
Period size: 3 Copynumber: 32.7 Consensus size: 3
369343 TTAATATATT
*
369353 TAA TAA TAA TAG TAA TATA TAA TAA TAA TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * *
369400 TAA T-A TGA TAA TAG TAA TAA TAA TAA T-A TAA T-A TATA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
369443 TAA TAA TA
1 TAA TAA TA
369451 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.07
3 68 0.83
4 8 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:369431 original size:41 final size:41
Alignment explanation
Indices: 369357--369450 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 41
369347 TATATTTAAT
369357 AATAATAGTAATATATAATAATAATAATAATAATATATAAT
1 AATAATAGTAATATATAATAATAATAATAATAATATATAAT
369398 AATAATATGATAATAGTAATAATAATAAT-ATAATATATATTATAAT
1 AATAATA-G-TAATA-T-ATAATAATAATAATAATA-ATA-TATAAT
369444 AATAATA
1 AATAATA
369451 TGGATAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
41 7 0.15
42 1 0.02
43 5 0.11
44 7 0.15
45 14 0.30
46 13 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (41 bp):
AATAATAGTAATATATAATAATAATAATAATAATATATAAT
Found at i:369437 original size:9 final size:10
Alignment explanation
Indices: 369344--369450 Score: 96
Period size: 10 Copynumber: 10.5 Consensus size: 10
369334 TTTATGTATT
*
369344 TAAT-ATATT
1 TAATAATATA
369353 TAATAATA-A
1 TAATAATATA
*
369362 TAGTAATATA
1 TAATAATATA
369372 TAATAATAATAA
1 TAATAAT-AT-A
369384 TAATAATATA
1 TAATAATATA
369394 TAATAATAATA
1 TAATAAT-ATA
*
369405 TGATAATAGTAA
1 TAATAATA-T-A
369417 TAATAATAATA
1 TAATAAT-ATA
369428 TAAT-ATATA
1 TAATAATATA
*
369437 TTATAATA-A
1 TAATAATATA
369446 TAATA
1 TAATA
369451 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
9 22 0.27
10 24 0.29
11 19 0.23
12 16 0.20
13 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TAATAATATA
Done.