Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 20
Found at i:257261 original size:2 final size:2
Alignment explanation
Indices: 257254--257278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257244 ATTTTGCATG
257254 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
257279 CTTTCCCCAC
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:260623 original size:201 final size:199
Alignment explanation
Indices: 260241--260632 Score: 435
Period size: 201 Copynumber: 2.0 Consensus size: 199
260231 TACATTCCAG
* * *
260241 TCAAAATTCAAACTAAGGGCTTCAAGTAGAAGAAAACCCAAATCGGCTGTGATTTATCAACGAGG
1 TCAAAATTAAAACTAAGGGCTTCAAGTAGAAGAAAACCCAAATCGACTGCGATTTATCAACGAGG
* * * *
260306 AACTATCTCCCAACCCAGATTTCCACATAGCTTAAGGCGATAAGAGTTATCTGTCAACAAAAGCT
66 AACTATCTCCCAACCCAAATTTCCACATAGCTTAAGGCGAGAAGAATTATCTATCAACAAAAGCT
*** * * * * *
260371 TTCAAGTTTTGTTCCACTCAACTCGGGAGCACATTGACCACATGGTAGCAATAAGGAACTACCCT
131 TTCAAGTTTTGTTCCACTCAACTCAAAAACACATTAACCACAAGATAGCAATAAAGAACTACCCT
260436 CCGA
196 CCGA
* * * *
260440 TCAAAATTAAAACTAAGGGCTTCAAGTCTAGAAGAAGACTCAGATCGACTGCGATTTATCAAGGA
1 TCAAAATTAAAACTAAGGGCTTCAAG--TAGAAGAAAACCCAAATCGACTGCGATTTATCAACGA
* * * * ** * * ** ***
260505 GTAATTATCTTCCATCCCAAATTTTGATATAGCTTAAGTCGAGAAGAATTATCTATTGATTGAAG
64 GGAACTATCTCCCAACCCAAATTTCCACATAGCTTAAGGCGAGAAGAATTATCTATCAACAAAAG
* * *
260570 CTTTCAAG-TTTGATTCCACTGAACTCAAAAACATATTAACCATAAGATAGCAATAAAGAACTA
129 CTTTCAAGTTTTG-TTCCACTCAACTCAAAAACACATTAACCACAAGATAGCAATAAAGAACTA
260633 TCTTTTAATC
Statistics
Matches: 155, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
199 25 0.16
200 4 0.03
201 126 0.81
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (199 bp):
TCAAAATTAAAACTAAGGGCTTCAAGTAGAAGAAAACCCAAATCGACTGCGATTTATCAACGAGG
AACTATCTCCCAACCCAAATTTCCACATAGCTTAAGGCGAGAAGAATTATCTATCAACAAAAGCT
TTCAAGTTTTGTTCCACTCAACTCAAAAACACATTAACCACAAGATAGCAATAAAGAACTACCCT
CCGA
Found at i:261132 original size:3 final size:3
Alignment explanation
Indices: 261126--261181 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
261116 ATTTAAGTCT
*
261126 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA -TA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
261171 TTA TTA -TA TTA
1 TTA TTA TTA TTA
261182 AATAAATCAG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:276301 original size:22 final size:21
Alignment explanation
Indices: 276257--276302 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
276247 CACTGTTCAT
*
276257 TACACATGATGTAATCATGAA
1 TACACATGATGTAATCATAAA
* *
276278 TACATATGATGTTTATCATAAA
1 TACACATGATG-TAATCATAAA
276300 TAC
1 TAC
276303 TATTTCGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (21 bp):
TACACATGATGTAATCATAAA
Found at i:282874 original size:16 final size:16
Alignment explanation
Indices: 282853--282886 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
282843 TTTTATGCTT
282853 GAATCAAATCAAAATC
1 GAATCAAATCAAAATC
282869 GAATCAAATCAAAATC
1 GAATCAAATCAAAATC
282885 GA
1 GA
282887 TTAAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (16 bp):
GAATCAAATCAAAATC
Found at i:282893 original size:16 final size:16
Alignment explanation
Indices: 282853--282895 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
282843 TTTTATGCTT
*
282853 GAATCAAATCAAAATC
1 GAATAAAATCAAAATC
*
282869 GAATCAAATCAAAATC
1 GAATAAAATCAAAATC
*
282885 GATTAAAATCA
1 GAATAAAATCA
282896 TGAAAACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (16 bp):
GAATAAAATCAAAATC
Found at i:293620 original size:2 final size:2
Alignment explanation
Indices: 293613--293638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
293603 AAACACAAAT
293613 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
293639 CCAACTGCTG
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):
TA
Found at i:296898 original size:3 final size:3
Alignment explanation
Indices: 296890--296927 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
296880 TGTAATTATT
*
296890 TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
296928 TAAATATCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:296932 original size:12 final size:11
Alignment explanation
Indices: 296894--296933 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
296884 ATTATTTAAT
296894 AATAATAATAA
1 AATAATAATAA
296905 TAATAATAATAAA
1 -AATAATAAT-AA
296918 AATAATAATATA
1 AATAATAATA-A
296930 AATA
1 AATA
296934 TCGGGGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.88
13 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAATAATAA
Found at i:297368 original size:135 final size:134
Alignment explanation
Indices: 297121--297453 Score: 468
Period size: 135 Copynumber: 2.5 Consensus size: 134
297111 ATTCCACTGT
* * * * *
297121 TCTTCAGGGAAAATTGAATTGAACTTGATTTGCTTCGCGGCTCTTTAGGAAGGCCAAATATGAAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATATGAAA
* *
297186 GAAGAAGAATCTGCTCCGCTACTCTTTAGGGAAGACCAGACTCGAGAAAAATTGTGATCCACTTC
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGAAGACAAGACTCGAGAAAAATTGTGATCCAC-TC
297251 ACTAC
130 ACTAC
* * * * *
297256 TCTTTAGGGAAGATTGAATCGAACTTGATTTACTTAGCTGCTATTCAAGAAGACCAAATATGAAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATATGAAA
* * * * *
297321 GAAGAAGAATCTGCTTCACTACTCTTTAGGGGAGATAAGACTCGAGAAAAATTTTGATCCACTCG
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGAAGACAAGACTCGAGAAAAATTGTGATCCACTCA
*
297386 CTGC
131 CTAC
* * *
297390 TCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCGTTGCTCTTCAGGAAGACCAAATCTGAA
1 TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATATGAA
297454 GGATTAGAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
134 61 0.35
135 111 0.65
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (134 bp):
TCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATATGAAA
GAAGAAGAATCTGCTCCACTACTCTTTAGGGAAGACAAGACTCGAGAAAAATTGTGATCCACTCA
CTAC
Found at i:305056 original size:41 final size:41
Alignment explanation
Indices: 304995--305076 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
304985 GATATCTTTT
*
304995 CCATGCTATGCAACAAAAGTCCATTGGGCCTCACATCCTTC
1 CCATGCTATGCAACAAAAGTCAATTGGGCCTCACATCCTTC
* * * *
305036 CCATGCTCTGCAACACAAGTCAATTGGGCCTTACATTCTTC
1 CCATGCTATGCAACAAAAGTCAATTGGGCCTCACATCCTTC
305077 ACGTTCTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.27
Consensus pattern (41 bp):
CCATGCTATGCAACAAAAGTCAATTGGGCCTCACATCCTTC
Found at i:311220 original size:17 final size:18
Alignment explanation
Indices: 311198--311232 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
311188 TTCAAAAGAA
*
311198 GCTCTCTATTT-TTTTTT
1 GCTCTCCATTTCTTTTTT
311215 GCTCTCCATTTCTTTTTT
1 GCTCTCCATTTCTTTTTT
311233 ATATCGACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.66
Consensus pattern (18 bp):
GCTCTCCATTTCTTTTTT
Found at i:317114 original size:12 final size:12
Alignment explanation
Indices: 317097--317161 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 12
317087 TCAAATAAAG
317097 AGAAAAGAGAAA
1 AGAAAAGAGAAA
317109 AGAAAAGAGAAAAAA
1 AGAAAAGAG---AAA
*
317124 AGAAGAATAGAAA
1 AGAA-AAGAGAAA
317137 A-AAATAGA-AAA
1 AGAAA-AGAGAAA
317148 AGAAGAAGAGAAA
1 AGAA-AAGAGAAA
317161 A
1 A
317162 AATGTGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
11 5 0.12
12 18 0.42
13 9 0.21
15 7 0.16
16 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (12 bp):
AGAAAAGAGAAA
Found at i:317145 original size:15 final size:16
Alignment explanation
Indices: 317106--317140 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
317096 GAGAAAAGAG
*
317106 AAAAGAA-AAGAGAAA
1 AAAAGAAGAATAGAAA
317121 AAAAGAAGAATAGAAA
1 AAAAGAAGAATAGAAA
317137 AAAA
1 AAAA
317141 TAGAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAGAATAGAAA
Found at i:317148 original size:27 final size:28
Alignment explanation
Indices: 317104--317156 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
317094 AAGAGAAAAG
317104 AGAAAAGAAAAGAGAAAAAAAGAAGAAT
1 AGAAAAGAAAAGAGAAAAAAAGAAGAAT
*
317132 AGAAAA-AAATAGA-AAAAGAAGAAGA
1 AGAAAAGAAA-AGAGAAAAAAAGAAGA
317157 GAAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (28 bp):
AGAAAAGAAAAGAGAAAAAAAGAAGAAT
Found at i:319657 original size:19 final size:21
Alignment explanation
Indices: 319633--319741 Score: 124
Period size: 20 Copynumber: 5.5 Consensus size: 21
319623 AAAAAAAGTT
319633 TATGAATAGTATC-G-TATTG
1 TATGAATAGTATCTGATATTG
319652 TATGAATAGTA-CTGATATTG
1 TATGAATAGTATCTGATATTG
*
319672 TATGAATAATAT-T-ATATTG
1 TATGAATAGTATCTGATATTG
*
319691 TATGAATAGTA-CTGATACTG
1 TATGAATAGTATCTGATATTG
*
319711 TATGAATAGTAT-TGATACTG
1 TATGAATAGTATCTGATATTG
* *
319731 TGTGAACAGTA
1 TATGAATAGTA
319742 GTATCGATAC
Statistics
Matches: 79, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.01
19 29 0.37
20 49 0.62
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (21 bp):
TATGAATAGTATCTGATATTG
Found at i:319690 original size:39 final size:39
Alignment explanation
Indices: 319633--319741 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 39
319623 AAAAAAAGTT
** *
319633 TATGAATAGTATCGTATTGTATGAATAGTACTGATATTG
1 TATGAATAGTATTATATTGTATGAATAGTACTGATACTG
*
319672 TATGAATAATATTATATTGTATGAATAGTACTGATACTG
1 TATGAATAGTATTATATTGTATGAATAGTACTGATACTG
* * *
319711 TATGAATAGTATTGATACTGTGTGAACAGTA
1 TATGAATAGTATT-ATATTGTATGAATAGTA
319742 GTATCGATAC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 47 0.77
40 14 0.23
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (39 bp):
TATGAATAGTATTATATTGTATGAATAGTACTGATACTG
Found at i:319759 original size:21 final size:21
Alignment explanation
Indices: 319733--319783 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
319723 TGATACTGTG
319733 TGAACAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
*
319754 TGAACAATAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
*
319775 TAAACAGTA
1 TGAACAGTA
319784 CCGATGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (21 bp):
TGAACAGTAGTATCGATACCA
Found at i:319860 original size:21 final size:21
Alignment explanation
Indices: 319835--319886 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
319825 TGCTACAATT
319835 GTATCGATACCATAAACAGTA
1 GTATCGATACCATAAACAGTA
*
319856 GTATCGATACCTTAAACAGTA
1 GTATCGATACCATAAACAGTA
*
319877 GTATAGATAC
1 GTATCGATAC
319887 TATCAAGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (21 bp):
GTATCGATACCATAAACAGTA
Found at i:320308 original size:33 final size:34
Alignment explanation
Indices: 320241--320309 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
320231 TGTAAAAGGG
320241 GATTGGTTATATCTTAGCCAAGTGAAAAGATAGA
1 GATTGGTTATATCTTAGCCAAGTGAAAAGATAGA
* * *
320275 GATTGGTTCTAGT-TTAGCC-ATTGAAAAGCTAGA
1 GATTGGTTATA-TCTTAGCCAAGTGAAAAGATAGA
320308 GA
1 GA
320310 GTTATAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 14 0.45
34 16 0.52
35 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (34 bp):
GATTGGTTATATCTTAGCCAAGTGAAAAGATAGA
Found at i:321140 original size:79 final size:80
Alignment explanation
Indices: 320929--321145 Score: 240
Period size: 81 Copynumber: 2.7 Consensus size: 80
320919 AGTAAATTAT
* ** *
320929 TTCCAAAATTGATATGACTACCCAAAAAAGAGGAACAAATCAAGTTTGATCTCCCTTAAAGAAGA
1 TTCCAAAA-TGATCTGACTACCCAAAAAAGAGGAACAAATCAAGCCTGATCTCCCCTAAAGAAGA
* *
320994 ATGGAGCATACCCATC
65 ATGGAACAAACCCATC
* * *
321010 TTCCAAAATTGATCTTACAACCCGAAAAAGAGGAACAAATCAAGTCC-GATCTCCCCTAAAGAAG
1 TTCCAAAA-TGATCTGACTACCCAAAAAAGAGGAACAAATCAAG-CCTGATCTCCCCTAAAGAAG
* *
321074 AGTTGAACAAACCCATC
64 AATGGAACAAACCCATC
*** * * *
321091 TTCCTTCA-GATCTGACTACCCAAAAAAGATGAACAGATCAAGCCTGATCTACCCT
1 TTCCAAAATGATCTGACTACCCAAAAAAGAGGAACAAATCAAGCCTGATCTCCCCT
321146 GGAGAAATAG
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
78 2 0.02
79 38 0.33
81 74 0.65
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (80 bp):
TTCCAAAATGATCTGACTACCCAAAAAAGAGGAACAAATCAAGCCTGATCTCCCCTAAAGAAGAA
TGGAACAAACCCATC
Found at i:321307 original size:3 final size:3
Alignment explanation
Indices: 321292--321343 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
321282 TTTTGTCCCG
*
321292 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
321340 ATT A
1 ATT A
321344 CATTTTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:328782 original size:13 final size:13
Alignment explanation
Indices: 328743--328809 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
328733 CCCAATAAGG
328743 AGAA-AAGAGAAA
1 AGAAGAAGAGAAA
*
328755 AGGAA-ATAGAAAAA
1 A-GAAGA-AGAGAAA
328769 AGAAGAAGAGAAA
1 AGAAGAAGAGAAA
* *
328782 AAATAGATA-AAAAA
1 AGA-AGA-AGAGAAA
328796 AGAAGAAGAGAAA
1 AGAAGAAGAGAAA
328809 A
1 A
328810 AAATGAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
12 2 0.05
13 23 0.53
14 17 0.40
15 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (13 bp):
AGAAGAAGAGAAA
Found at i:328824 original size:27 final size:26
Alignment explanation
Indices: 328743--328824 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
328733 CCCAATAAGG
328743 AGAA-AAGAGAAAAGGAAAT-AGAAAAA
1 AGAAGAAGAGAAAA--AAATGAGAAAAA
*
328769 AGAAGAAGAG-AAAAAATAGATAAAAAA
1 AGAAGAAGAGAAAAAAAT-GA-GAAAAA
328796 AGAAGAAGAGAAAAAAATGAGAAATAA
1 AGAAGAAGAGAAAAAAATGAGAAA-AA
328823 AG
1 AG
328825 TAAATCAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.08
26 11 0.23
27 26 0.54
28 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (26 bp):
AGAAGAAGAGAAAAAAATGAGAAAAA
Found at i:331104 original size:42 final size:41
Alignment explanation
Indices: 331042--331129 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
331032 AAATTGTAAG
*
331042 TCCTTCGGGACATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGACATCAATAAGTCTTTCGAGCAAGATGA-TAAA
* ** *
331084 TCCTTCGGGTCATCTTTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGACATCAATAAGTCTTTCGAGCAAGATGATAAA
331125 TCCTT
1 TCCTT
331130 TGGGCTATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 8 0.20
42 33 0.80
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
TCCTTCGGGACATCAATAAGTCTTTCGAGCAAGATGATAAA
Found at i:331411 original size:80 final size:79
Alignment explanation
Indices: 331277--331488 Score: 214
Period size: 80 Copynumber: 2.6 Consensus size: 79
331267 CAATAAACTA
* * * * ** *
331277 TTTCCAAAATTGATCTAACTATCCGAAAAAGTGGAACAAATCAAGTTTGATCTCCCTTAAAGAAG
1 TTTCCAAAATTGATCT-GCTA-CCAAAAAAGAGGAACAGATCAAGTCCGATCTCCCCTAAAGAAG
*
331342 AATGGAGC-GTACTTGT
64 AATGGAACAG-ACTTGT
*
331358 TTTCCAAAATTGATCTGCTACCTAAAAAAGAGAAACAGATCAAGTCCGATCTCCCCTAAAGAAGA
1 TTTCCAAAATTGATCTGCTACC-AAAAAAGAGGAACAGATCAAGTCCGATCTCCCCTAAAGAAGA
*
331423 GTGGAACAGACTTGT
65 ATGGAACAGACTTGT
* *** *
331438 CTTCCTTCA--GATCTGACTACCCAAAAAAGAGGAACAGATCAAGACCGATCT
1 TTTCCAAAATTGATCTG-CTA-CCAAAAAAGAGGAACAGATCAAGTCCGATCT
331489 ACCATAGAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 6 0.05
79 32 0.29
80 56 0.50
81 17 0.15
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (79 bp):
TTTCCAAAATTGATCTGCTACCAAAAAAGAGGAACAGATCAAGTCCGATCTCCCCTAAAGAAGAA
TGGAACAGACTTGT
Found at i:334292 original size:22 final size:22
Alignment explanation
Indices: 334251--334294 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
334241 ATAATTATCA
*
334251 CATTTTTCTTTTTATATATTTT
1 CATTTTTCTTTTAATATATTTT
334273 CATTTTTCTTTTAA-ATTATTTT
1 CATTTTTCTTTTAATA-TATTTT
334295 TAGAGAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (22 bp):
CATTTTTCTTTTAATATATTTT
Found at i:334703 original size:2 final size:2
Alignment explanation
Indices: 334696--334720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
334686 TGTTTCGTAT
334696 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
334721 GGGAATGAAA
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:336004 original size:134 final size:134
Alignment explanation
Indices: 335597--336198 Score: 712
Period size: 133 Copynumber: 4.5 Consensus size: 134
335587 ATTAATTTCT
* * * * * **
335597 CTACTTTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTACCCTTCAAAAAGACCAAATCT
1 CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATC-
* * * * * *
335662 TG-AAGAAGAAAAATATGCTCCACTACT-TTTTAGGGAGAACAGACTCGAGGATATTTTGATCCA
65 TGAAAGAAGAAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCA
*
335725 CTTTA
130 CTTCA
* * *
335730 CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCAACTCTTCAGGAATACCAAATAT
1 CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATCT
** * * * *
335795 GAAAGAAGAA-AATATGCTCCACTACTAATGAGGGGAGATTAGACTAGAGAAAACTTTGATCCAC
66 GAAAGAAGAAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCAC
335859 TTCA
131 TTCA
* * * * * *
335863 CTACTCTTCAGGGAAGATTGAATCGAATGTCATTTGTTTTGCTGCTCTTCAGGAAGACTAAATCT
1 CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATCT
335928 GAAAGAA-ATAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCA
66 GAAAGAAGA-AGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCA
*
335992 CTTCG
130 CTTCA
* * * * * * *
335997 TTGCTCTTCAGCGAAGATTGAATCGAACATGAGTTGCTTCGCTGCTCTTCAAGAAGACCAAATCT
1 CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATCT
* * * *
336062 GAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAC-TTGATTCAC
66 GAAAGAAGAAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCAC
336126 TTCA
131 TTCA
* * * ** *
336130 CTACTCTTCAGGGAATATTGAATCAAAAAGT-ATTTGCTTTACTACTCTTCAGGAAGACCAAATT
1 CTACTCTTCAGGGAAGATTGAATC-GAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATC
336194 TGAAA
65 TGAAA
336199 ATCAGACATT
Statistics
Matches: 398, Mismatches: 65, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
132 19 0.05
133 219 0.55
134 159 0.40
135 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (134 bp):
CTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATCT
GAAAGAAGAAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCAC
TTCA
Found at i:336129 original size:267 final size:265
Alignment explanation
Indices: 335579--336198 Score: 769
Period size: 267 Copynumber: 2.3 Consensus size: 265
335569 TCATATCAAG
* * * * * *
335579 AAACGTTGATTAATTTCTCTACTTTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTACCC
1 AAACGTTGATTCACTTCACTACTCTTCAGGGAAGATTGAATCAAATGT-ATTTGCTTTACTACTC
** *
335644 TTCAAAAAGACCAAATCTTG-AAGAAGAAAAATATGCTCCACTACTTTTTAGGGAGAACAGACTC
65 TTCAGGAAGACCAAATC-TGAAAGAAGAAAAATATGCTCCACTACTTTTAAGGGAGAACAGACTC
* * * * * * *
335708 GAGGATATTTTGATCCACTTTACTACTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTCGCA
129 GAGAAAACTTTGATCCACTTCACTACTCTTCAGCGAAGATTGAATCGAACATGAGTTGCTTCGCA
* * * *
335773 ACTCTTCAGGAATACCAAATATGAAAGAAGAAAATATGCTCCACTACTAATGAGGGGAGATTAGA
194 ACTCTTCAAGAAGACCAAATATGAAAGAAAAAAATATGCTCCACTACTAATGAGGGGAGATCAGA
335838 CTAGAGA
259 CTAGAGA
* * * * * *
335845 AAACTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCGAATGTCATTTGTTTTGCTGCTC
1 AAACGTTGATTCACTTCACTACTCTTCAGGGAAGATTGAATCAAATGT-ATTTGCTTTACTACTC
* * *
335910 TTCAGGAAGACTAAATCTGAAAGAA-ATAGAATATGCTCCACTACTCTTTAAGGGAGATCAGACT
65 TTCAGGAAGACCAAATCTGAAAGAAGA-AAAATATGCTCCACTACT-TTTAAGGGAGAACAGACT
** *
335974 CGAGAAAACTTTGATCCACTTCGTTGCTCTTCAGCGAAGATTGAATCGAACATGAGTTGCTTCGC
128 CGAGAAAACTTTGATCCACTTCACTACTCTTCAGCGAAGATTGAATCGAACATGAGTTGCTTCGC
** * * ** *
336039 TGCTCTTCAAGAAGACCAAATCTGAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCA
193 AACTCTTCAAGAAGACCAAATATGAAAGAAAAA-AATATGCTCCACTACTAATGAGGGGAGATCA
*
336104 GACTCGAGA
257 GACTAGAGA
* *
336113 AAAC-TTGATTCACTTCACTACTCTTCAGGGAATATTGAATCAAAAAGTATTTGCTTTACTACTC
1 AAACGTTGATTCACTTCACTACTCTTCAGGGAAGATTGAATC-AAATGTATTTGCTTTACTACTC
*
336177 TTCAGGAAGACCAAATTTGAAA
65 TTCAGGAAGACCAAATCTGAAA
336199 ATCAGACATT
Statistics
Matches: 299, Mismatches: 50, Indels: 9
0.84 0.14 0.03
Matches are distributed among these distances:
265 3 0.01
266 88 0.29
267 166 0.56
268 42 0.14
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (265 bp):
AAACGTTGATTCACTTCACTACTCTTCAGGGAAGATTGAATCAAATGTATTTGCTTTACTACTCT
TCAGGAAGACCAAATCTGAAAGAAGAAAAATATGCTCCACTACTTTTAAGGGAGAACAGACTCGA
GAAAACTTTGATCCACTTCACTACTCTTCAGCGAAGATTGAATCGAACATGAGTTGCTTCGCAAC
TCTTCAAGAAGACCAAATATGAAAGAAAAAAATATGCTCCACTACTAATGAGGGGAGATCAGACT
AGAGA
Found at i:336968 original size:44 final size:45
Alignment explanation
Indices: 336920--337113 Score: 152
Period size: 38 Copynumber: 4.6 Consensus size: 45
336910 CAATATTAAG
* *
336920 AGATTGACTTATCTTCACGA-CAAGTCAAGGAATAAACCACTGAA
1 AGATTGACTTCTCTTCACGAGAAAGTCAAGGAATAAACCACTGAA
* * * * *
336964 AGATTGACTCCTCTTCGCGAGAAAGTC-AGG-ATGGACATCATTGAA
1 AGATTGACTTCTCTTCACGAGAAAGTCAAGGAAT--AAACCACTGAA
337009 AGATTGACTTCTCTTCACGAGAAAGTCAA-GAAT--A--A-T-AA
1 AGATTGACTTCTCTTCACGAGAAAGTCAAGGAATAAACCACTGAA
* *
337047 AGATTGAGTTCTCTTCACGAGGAAGTCAA-GAAT--A--AC--AA
1 AGATTGACTTCTCTTCACGAGAAAGTCAAGGAATAAACCACTGAA
* *
337085 AGATCGACTTCTCTTTACGAGAAAGTCAA
1 AGATTGACTTCTCTTCACGAGAAAGTCAA
337114 TAATAATAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
38 62 0.48
39 1 0.01
40 1 0.01
42 1 0.01
43 2 0.02
44 20 0.16
45 39 0.30
46 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (45 bp):
AGATTGACTTCTCTTCACGAGAAAGTCAAGGAATAAACCACTGAA
Found at i:337059 original size:38 final size:38
Alignment explanation
Indices: 337007--337733 Score: 821
Period size: 38 Copynumber: 18.8 Consensus size: 38
336997 GACATCATTG
* *
337007 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
337045 AAAGATTGAGTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
337083 AAAGATCGACTTCTCTTTACGAGAAAGTCAATAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337121 AAAGATCGATTTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337159 ATTGAAAGATTGAC-TCATCTTCGCGAGGGAGTAAAGAATAAC
1 ----AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* *
337201 AAAGATTAACTTCTCTTCACGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337239 AATGATTGACTTCTCTTTACGAGGAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* **
337277 AAAGATCGGTTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
337315 ATTGAATGATTGACTCCTCTTCGCTAGGGAGTCAGGAATAAC
1 A---AA-GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337357 AAAGATTGACTTCTCTTCGCGAGAAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337395 AAAGATTAAATTCTCTTCACGAGGAACTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
337433 AAAGATTGACTTCCCTTCAC-AGGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGA-GGAAGTCAAGAATAAC
* ** * *
337471 ATTGAAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337513 AACGATTGACTTTTCTTCACGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
337551 AAAGATTGACTTCTCTTCACGAGG-AGTCAATATTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** *
337588 ACAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
337626 AAAGATCGAATTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
337664 AAAGATTGACTTCTCTTCATGAGGAAGTTAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
337702 AAAGATTGACTTCTCTTCAAGAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
337734 TTGAAGCTTC
Statistics
Matches: 577, Mismatches: 95, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
37 33 0.06
38 448 0.78
39 4 0.01
41 4 0.01
42 87 0.15
43 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:337281 original size:156 final size:155
Alignment explanation
Indices: 337002--337732 Score: 961
Period size: 156 Copynumber: 4.7 Consensus size: 155
336992 GGATGGACAT
* ** * *
337002 CATTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAAAGATTGAGTTCTCTTCACGA
1 CATTGAAAGATTGAC-TCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA
* * * * * *
337067 GGAAGTCAAGAATAACAAAGATCGACTTCTCTTTACGAGAAAGTCAATAATAATAAAGATCGATT
65 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAAAGATCGACT
*
337132 TCTCTTCATGAGGAAGTCAAGAATAA
130 TCTCTTCACGAGGAAGTCAAGAATAA
* *
337158 CATTGAAAGATTGACTCATCTTCGCGAGGGAGTAAAGAATAACAAAGATTAACTTCTCTTCACGA
1 CATTGAAAGATTGACTC-TCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA
* * **
337223 GGAAGTCAAGAGTAACAATGATTGACTTCTCTTTACGAGGAAGTCAATAATAACAAAGATCGGTT
65 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAAAGATCGACT
337288 TCTCTTCACGAGGAAGTCAAGAATAA
130 TCTCTTCACGAGGAAGTCAAGAATAA
* * * *
337314 CATTGAATGATTGACTCCTCTTCGCTAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCGCGA
1 CATTGAAAGATTGACT-CTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA
* * * * * *
337379 GAAAGTCAAGAGTAACAAAGATTAAATTCTCTTCACGAGGAACTCAAGAATAACAAAGATTGACT
65 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAAAGATCGACT
*
337444 TCCCTTCAC-AGGGAAGTCAAGAATAA
130 TCTCTTCACGA-GGAAGTCAAGAATAA
* * * *
337470 CATTGAAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAACAACGATTGACTTTTCTTCACGA
1 CATTGAAAGATTGACT-CTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA
* * *
337535 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGG-AGTCAATATTAACACAGATCAACT
65 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAAAGATCGACT
337599 TCTCTTCACGAGGAAGTCAAGAATAA
130 TCTCTTCACGAGGAAGTCAAGAATAA
* * ** * *
337625 -A---AAAGATCGAATTCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATGA
1 CATTGAAAGATTG-ACTCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA
* * *
337686 GGAAGTTAAGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAA
65 GGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
337733 GTTGAAGCTT
Statistics
Matches: 511, Mismatches: 58, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
151 86 0.17
152 8 0.02
154 1 0.00
155 44 0.09
156 371 0.73
157 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (155 bp):
CATTGAAAGATTGACTCTCTTCGCGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAG
GAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAAAGATCGACTT
CTCTTCACGAGGAAGTCAAGAATAA
Found at i:339704 original size:12 final size:11
Alignment explanation
Indices: 339654--339731 Score: 54
Period size: 12 Copynumber: 7.1 Consensus size: 11
339644 AGGTTTCTTT
*
339654 TTTTCCTTTTC
1 TTTTCTTTTTC
*
339665 -TCTCTTTTTC
1 TTTTCTTTTTC
339675 TTCTTCTTTTTC
1 TT-TTCTTTTTC
*
339687 -TATCTTTTCTC
1 TTTTCTTTT-TC
339698 TTTTCTTTTT-
1 TTTTCTTTTTC
* * *
339708 ATATCTTTTCC
1 TTTTCTTTTTC
339719 TTTTTCTTTTTC
1 -TTTTCTTTTTC
339731 T
1 T
339732 ATATTTTCCC
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
10 21 0.42
11 6 0.12
12 23 0.46
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:339738 original size:15 final size:15
Alignment explanation
Indices: 339660--339739 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 15
339650 CTTTTTTTCC
*
339660 TTTTCTCTCTTTT-TC
1 TTTT-TCTCTTTTCTA
*
339675 TTCTTCT-TTTTCTA
1 TTTTTCTCTTTTCTA
339689 TCTTTTCTCTTTTCT-
1 T-TTTTCTCTTTTCTA
* *
339704 TTTTATATCTTTTC-C
1 TTTT-TCTCTTTTCTA
339719 TTTTTCT-TTTTCTA
1 TTTTTCTCTTTTCTA
339733 TATTTTC
1 T-TTTTC
339740 CCCTTTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
13 9 0.17
14 11 0.21
15 26 0.50
16 6 0.12
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCTCTTTTCTA
Found at i:339769 original size:15 final size:16
Alignment explanation
Indices: 339748--339788 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
339738 TCCCCTTTAT
339748 TTCTTTTTATTTTTTC
1 TTCTTTTTATTTTTTC
*
339764 -TCTTTTT-CTTTTTC
1 TTCTTTTTATTTTTTC
339778 TTCTTTTTATT
1 TTCTTTTTATT
339789 GGATGAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.29
15 14 0.67
16 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTATTTTTTC
Found at i:339776 original size:16 final size:16
Alignment explanation
Indices: 339647--339723 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 16
339637 TTTTCTCAGG
339647 TTTCTTTTTTTC-CTTT
1 TTTCTTTTTTTCTC-TT
339663 TCTCTCTTTTTCTTCTTCTT
1 T-T-TCTTTTT-TTC-TCTT
*
339683 TTTCTATCTTTTCTC-T
1 TTTCT-TTTTTTCTCTT
* *
339699 TTTCTTTTTATATCTT
1 TTTCTTTTTTTCTCTT
*
339715 TTCCTTTTT
1 TTTCTTTTT
339724 CTTTTTCTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
15 6 0.12
16 16 0.33
17 3 0.06
18 13 0.27
19 7 0.14
20 3 0.06
21 1 0.02
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTTTTCTCTT
Found at i:339784 original size:22 final size:23
Alignment explanation
Indices: 339647--339784 Score: 135
Period size: 22 Copynumber: 6.1 Consensus size: 23
339637 TTTTCTCAGG
* * *
339647 TTTCTTTTTTTCCTTTTCTCTCT
1 TTTCTCTTTTTCTTTTTCTATCT
*
339670 TTT-TCTTCTTCTTTTTCTATCT
1 TTTCTCTTTTTCTTTTTCTATCT
*
339692 TTTCTC-TTTTCTTTTTATATCT
1 TTTCTCTTTTTCTTTTTCTATCT
*
339714 TTTC-CTTTTTCTTTTTCTATAT
1 TTTCTCTTTTTCTTTTTCTATCT
* *
339736 TTTCCCCTTTATT-TCTTTT-TATTT
1 TTT-CTCTTT-TTCT-TTTTCTATCT
339760 TTTCTCTTTTTCTTTTTCT-TCT
1 TTTCTCTTTTTCTTTTTCTATCT
339782 TTT
1 TTT
339785 TATTGGATGA
Statistics
Matches: 96, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.01
22 64 0.67
23 13 0.14
24 12 0.12
25 6 0.06
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTCTCTTTTTCTTTTTCTATCT
Found at i:345578 original size:2 final size:2
Alignment explanation
Indices: 345571--345617 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
345561 ATGTTTCGTG
345571 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
345613 TA TA T
1 TA TA T
345618 GGGAATGATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:349133 original size:2 final size:2
Alignment explanation
Indices: 349106--349167 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
349096 ACTTTACATG
* *
349106 AT AT AT GT AT AT -T AC AT AT A- 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
349146 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
349168 TTACAATTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:349573 original size:60 final size:60
Alignment explanation
Indices: 349464--349576 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
349454 TCGGTTGACT
* *
349464 ATTTTGTAACTTTTAACAGTCAAGGGACTCAACAAAGTAACATTCTATAGTCAAAGGATC
1 ATTTTGTAACTTTTAACAGTCAAGGGACTCAACAAAATAACACTCTATAGTCAAAGGATC
* * * * * *
349524 ATTTTGTAATTTTTAATAGTCGAGGGACTTAATAAAATAGCAC-CTTATAGTCA
1 ATTTTGTAACTTTTAACAGTCAAGGGACTCAACAAAATAACACTC-TATAGTCA
349577 GGGACCATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 43 0.98
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (60 bp):
ATTTTGTAACTTTTAACAGTCAAGGGACTCAACAAAATAACACTCTATAGTCAAAGGATC
Found at i:350559 original size:68 final size:68
Alignment explanation
Indices: 350450--350585 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
350440 TCATACAAAA
*
350450 AATTAAATAAAACAAATGATTATTTAACTGATGAAAATTACCATGACATTCTAATACAAAAATTA
1 AATTAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAATTA
350515 TAT
66 TAT
*
350518 AATTAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTGATACAAAAATTA
1 AATTAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAATTA
350583 TAT
66 TAT
350586 GCATTTATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (68 bp):
AATTAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAATTA
TAT
Found at i:350934 original size:2 final size:2
Alignment explanation
Indices: 350929--350961 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
350919 CTCCAATAAT
350929 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
350962 CCAACTAAGC
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:352199 original size:14 final size:14
Alignment explanation
Indices: 352180--352221 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
352170 GATATTAGTA
*
352180 ATAATAATTATAAT
1 ATAATAATAATAAT
352194 ATAATAATAATAAT
1 ATAATAATAATAAT
352208 A-AAT-ATAAT-AT
1 ATAATAATAATAAT
352219 ATA
1 ATA
352222 TTTTAATCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 3 0.12
14 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:355621 original size:16 final size:18
Alignment explanation
Indices: 355590--355622 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
355580 ATTTGTATAC
355590 AATTACTTATGTTATTAA
1 AATTACTTATGTTATTAA
355608 AATTA-TTA-GTTATTA
1 AATTACTTATGTTATTA
355623 TAAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (18 bp):
AATTACTTATGTTATTAA
Found at i:356627 original size:24 final size:24
Alignment explanation
Indices: 356600--356651 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
356590 AGAATTCAAA
*
356600 TCAGGTATTATAA-CAAAATCCAGG
1 TCAGGTATCA-AATCAAAATCCAGG
*
356624 TCAGGTATCAAATCAGAATCCAGG
1 TCAGGTATCAAATCAAAATCCAGG
356648 TCAG
1 TCAG
356652 AAATCAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
TCAGGTATCAAATCAAAATCCAGG
Found at i:365796 original size:17 final size:17
Alignment explanation
Indices: 365753--365831 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
365743 CATGAATAAA
* *
365753 TAAGCATGCTACTTCATC
1 TAAGCATGC-AGTTCATT
365771 TAGAGCATGCAGTTCATT
1 TA-AGCATGCAGTTCATT
* *
365789 TAAGCATGTAGTACATT
1 TAAGCATGCAGTTCATT
* * *
365806 AAAAGCATGTAGTTCAAT
1 -TAAGCATGCAGTTCATT
365824 TAAGCATG
1 TAAGCATG
365832 TTAATTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 20 0.39
18 24 0.47
19 7 0.14
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (17 bp):
TAAGCATGCAGTTCATT
Found at i:365832 original size:17 final size:17
Alignment explanation
Indices: 365774--365832 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
365764 CTTCATCTAG
* *
365774 AGCATGCAGTTCATTTA
1 AGCATGTAGTTCAATTA
*
365791 AGCATGTAGTAC-ATTAAA
1 AGCATGTAGTTCAATT--A
365809 AGCATGTAGTTCAATTA
1 AGCATGTAGTTCAATTA
365826 AGCATGT
1 AGCATGT
365833 TAATTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.06
17 18 0.51
18 12 0.34
19 3 0.09
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (17 bp):
AGCATGTAGTTCAATTA
Found at i:365846 original size:18 final size:18
Alignment explanation
Indices: 365818--365862 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
365808 AAGCATGTAG
* *
365818 TTCAATTAAGCATGTTAA
1 TTCATTTAAGCACGTTAA
* *
365836 TTTATTTAAGCACGTTGA
1 TTCATTTAAGCACGTTAA
365854 TTCATTTAA
1 TTCATTTAA
365863 TAAACCTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
TTCATTTAAGCACGTTAA
Found at i:366364 original size:17 final size:17
Alignment explanation
Indices: 366342--366375 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
366332 TGGGCTGCCT
*
366342 AAGTGTCTACATACATC
1 AAGTGTCAACATACATC
*
366359 AAGTGTCAACATTCATC
1 AAGTGTCAACATACATC
366376 CTCCATTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
AAGTGTCAACATACATC
Found at i:368856 original size:29 final size:30
Alignment explanation
Indices: 368823--368884 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
368813 AAATTTTGAC
* *
368823 TAGTGACTAAAATAT-AAGTTTAGAAAGTT
1 TAGTGACTAAAATATAAACTTTAAAAAGTT
** *
368852 TAGTGGTTAAAGTATAAACTTTAAAAAGTT
1 TAGTGACTAAAATATAAACTTTAAAAAGTT
368882 TAG
1 TAG
368885 GGATCGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTAAAAAGTT
Found at i:371887 original size:116 final size:116
Alignment explanation
Indices: 371683--371915 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
371673 CGTGTGCAGA
371683 TCATATGTAATATCAGTATCAATAAGACATCACCGATGTTTCTTTTGACTAGTAGTGGCATGTAT
1 TCATATGTAATATCAGTATCAATAAGACATCACCGATGTTTCTTTTGACTAGTAGTGGCATGTAT
371748 ATTTATGTTATTAACTTGTTTTATCATTTATGACTAAATGATCTGTAATAG
66 ATTTATGTTATTAACTTGTTTTATCATTTATGACTAAATGATCTGTAATAG
371799 TCATATGTAATATCAGTATCAATAAGACATCACCGATGTTTCTTTTGACTAGTAGTGGCATGTAT
1 TCATATGTAATATCAGTATCAATAAGACATCACCGATGTTTCTTTTGACTAGTAGTGGCATGTAT
371864 ATTTATGTTATTAACTTGTTTTATCATTTATGACTAAATGATCTGTAATAG
66 ATTTATGTTATTAACTTGTTTTATCATTTATGACTAAATGATCTGTAATAG
371915 T
1 T
371916 AAATTAGGAC
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (116 bp):
TCATATGTAATATCAGTATCAATAAGACATCACCGATGTTTCTTTTGACTAGTAGTGGCATGTAT
ATTTATGTTATTAACTTGTTTTATCATTTATGACTAAATGATCTGTAATAG
Found at i:374219 original size:15 final size:15
Alignment explanation
Indices: 374199--374236 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
374189 ACCTATTTCA
374199 ATGGCTCCGTACAGG
1 ATGGCTCCGTACAGG
*
374214 ATGGCTCCGTATAGG
1 ATGGCTCCGTACAGG
374229 ATGGCTCC
1 ATGGCTCC
374237 AACGGAACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (15 bp):
ATGGCTCCGTACAGG
Found at i:381271 original size:17 final size:18
Alignment explanation
Indices: 381249--381285 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
381239 CTGCCGAAGC
381249 TCCCGCTGTC-AAAAGAG
1 TCCCGCTGTCAAAAAGAG
381266 TCCCGCTGTCAAAAAGAG
1 TCCCGCTGTCAAAAAGAG
381284 TC
1 TC
381286 AGCATTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
TCCCGCTGTCAAAAAGAG
Found at i:383141 original size:32 final size:32
Alignment explanation
Indices: 383045--383165 Score: 143
Period size: 32 Copynumber: 3.8 Consensus size: 32
383035 AATTCGGGTT
** *
383045 GGGTTAATATTAGATTGGTTGGTTTTCAGGTC
1 GGGTTAATATCGGATCGGTTGGTTTTCAGGTC
** * * *
383077 AAGTCAAAATCGGATCGGTTGGTTTTCGGGTC
1 GGGTTAATATCGGATCGGTTGGTTTTCAGGTC
*
383109 GGGTTAATATCGGATCAGTTGGTTTTCAGGTC
1 GGGTTAATATCGGATCGGTTGGTTTTCAGGTC
**
383141 GGGTTAATATCATATCGGTTGGTTT
1 GGGTTAATATCGGATCGGTTGGTTT
383166 CGAGTCTTGT
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.39
Consensus pattern (32 bp):
GGGTTAATATCGGATCGGTTGGTTTTCAGGTC
Found at i:383158 original size:64 final size:64
Alignment explanation
Indices: 383037--383165 Score: 159
Period size: 64 Copynumber: 2.0 Consensus size: 64
383027 GGAAATTCAA
* * ** *
383037 TTCGGGTTGGGTTAATATTAGATTGGTTGGTTTTCAGGTCAAGTCAAAATCGGATCGGTTGGTT
1 TTCGGGTCGGGTTAATATCAGATCAGTTGGTTTTCAGGTCAAGTCAAAATCAGATCGGTTGGTT
* ** * * *
383101 TTCGGGTCGGGTTAATATCGGATCAGTTGGTTTTCAGGTCGGGTTAATATCATATCGGTTGGTT
1 TTCGGGTCGGGTTAATATCAGATCAGTTGGTTTTCAGGTCAAGTCAAAATCAGATCGGTTGGTT
383165 T
1 T
383166 CGAGTCTTGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.19, C:0.11, G:0.31, T:0.40
Consensus pattern (64 bp):
TTCGGGTCGGGTTAATATCAGATCAGTTGGTTTTCAGGTCAAGTCAAAATCAGATCGGTTGGTT
Found at i:390819 original size:8 final size:8
Alignment explanation
Indices: 390806--390841 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
390796 AACTCACAAT
390806 AAAGAGTG
1 AAAGAGTG
390814 AAAGAGTG
1 AAAGAGTG
390822 AAAGAGTG
1 AAAGAGTG
390830 AAAGAGTG
1 AAAGAGTG
390838 AAAG
1 AAAG
390842 GGCTTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.36, T:0.11
Consensus pattern (8 bp):
AAAGAGTG
Found at i:392856 original size:3 final size:3
Alignment explanation
Indices: 392848--392903 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
392838 TTGTCTGGTC
*
392848 TTA TTA TTA TTA TTA TTA TTA CTA -TA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
392893 ATA TTA TTA TT
1 TTA TTA TTA TT
392904 TTAAAAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:392907 original size:14 final size:15
Alignment explanation
Indices: 392848--392907 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
392838 TTGTCTGGTC
*
392848 TTATTATTATTATTA
1 TTATTATTATTAATA
*
392863 TTATTACTATATTATTA
1 TTATTA-T-TATTAATA
392880 TTATTATATATTAATA
1 TTATTAT-TATTAATA
392896 TTATTATT-TTAA
1 TTATTATTATTAA
392908 AAATATTACA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 17 0.40
17 14 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:393704 original size:19 final size:19
Alignment explanation
Indices: 393670--393706 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
393660 CGACGATGGT
*
393670 TGAAATAGTGGGCGGTGGC
1 TGAAATAGTGCGCGGTGGC
*
393689 TGAAATAGTGCTCGGTGG
1 TGAAATAGTGCGCGGTGG
393707 TAGCCTGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.43, T:0.24
Consensus pattern (19 bp):
TGAAATAGTGCGCGGTGGC
Found at i:395113 original size:59 final size:59
Alignment explanation
Indices: 395057--395200 Score: 236
Period size: 59 Copynumber: 2.5 Consensus size: 59
395047 ATGGCACTTT
* *
395057 GTGTGCTAAAATGATAAGAAAATCATACTGATTGTATAGATTGTCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGAAAATCATACCGAGTGTATAGATTGTCATATGGAGCACTGA
*
395116 GTGTGCTAAAATGATAAGAAAATCATACCGAGTGTATAGATTTTCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGAAAATCATACCGAGTGTATAGATTGTCATATGGAGCACTGA
* *
395175 GTGTACT-AAATGATAAGGAAATCATA
1 GTGTGCTAAAATGATAAGAAAATCATA
395201 TTGAAAATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 18 0.22
59 62 0.77
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAAATCATACCGAGTGTATAGATTGTCATATGGAGCACTGA
Found at i:395491 original size:17 final size:18
Alignment explanation
Indices: 395466--395499 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
395456 ATTGTAGTAT
395466 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
395483 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
395500 TATCATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:402101 original size:59 final size:59
Alignment explanation
Indices: 402046--402188 Score: 234
Period size: 59 Copynumber: 2.4 Consensus size: 59
402036 TGGCACTTTC
* * *
402046 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTATAGATTTTCATATGTAGCACTGAG
1 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTATACATTTTCATATGGAGCACTTAG
*
402105 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTATACATTTTCATATGGAGGACTTAG
1 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTATACATTTTCATATGGAGCACTTAG
*
402164 TGTGCT-AAATGATAAGGAAATCATA
1 TGTGCTAAAATGATAAGAAAATCATA
402189 TTGAAAATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 18 0.23
59 61 0.77
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGAAAATCATACTGAGTGTATACATTTTCATATGGAGCACTTAG
Found at i:402480 original size:17 final size:18
Alignment explanation
Indices: 402455--402488 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
402445 ATTGTAGTAT
402455 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
402472 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
402489 TATCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:405519 original size:19 final size:19
Alignment explanation
Indices: 405495--405531 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
405485 TAATTAATCC
405495 TACTATGTTA-TATTTTAAT
1 TACTAT-TTATTATTTTAAT
405514 TACTATTTATTATTTTAA
1 TACTATTTATTATTTTAA
405532 GAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TACTATTTATTATTTTAAT
Found at i:411454 original size:42 final size:42
Alignment explanation
Indices: 411395--411476 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
411385 ATTGGAATGT
* * *
411395 TGGGGTATGCTGAAGGCCCATTTCAGTCAGAAATGATCTATA
1 TGGGGCATGCTGAAGGCCCATTTCAGACAAAAATGATCTATA
*
411437 TGGGGCATGCTGAAGGCCCATTTTAGACAAAAATGATCTA
1 TGGGGCATGCTGAAGGCCCATTTCAGACAAAAATGATCTA
411477 AGTAGGATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (42 bp):
TGGGGCATGCTGAAGGCCCATTTCAGACAAAAATGATCTATA
Found at i:412016 original size:22 final size:22
Alignment explanation
Indices: 411988--412037 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
411978 TTACATTCTG
*
411988 CAAAGATGATAGATTCTCTTTT
1 CAAAGATAATAGATTCTCTTTT
*
412010 CAAAGATAATATATTCTCTTTT
1 CAAAGATAATAGATTCTCTTTT
412032 CAAAGA
1 CAAAGA
412038 CGAAAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
CAAAGATAATAGATTCTCTTTT
Found at i:412917 original size:3 final size:3
Alignment explanation
Indices: 412909--412974 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
412899 TTTCGTTCGG
* *
412909 TAT TAT TAT TAT TAT TAT TA- TAT TAC TA- TAT TAT TAT TA- TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
412954 TAT TAT TA- TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
412975 CAAATATTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
2 10 0.18
3 45 0.82
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:412938 original size:8 final size:8
Alignment explanation
Indices: 412912--412974 Score: 83
Period size: 8 Copynumber: 7.6 Consensus size: 8
412902 CGTTCGGTAT
412912 TATTATTA
1 TATTATTA
412920 TTATTATTA
1 -TATTATTA
*
412929 TATTACTA
1 TATTATTA
412937 TATTATTA
1 TATTATTA
412945 T-TATATTA
1 TAT-TATTA
412953 GTATTATTA
1 -TATTATTA
412962 TATTATTA
1 TATTATTA
412970 TATTA
1 TATTA
412975 CAAATATTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
7 1 0.02
8 33 0.67
9 14 0.29
10 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (8 bp):
TATTATTA
Found at i:412946 original size:25 final size:26
Alignment explanation
Indices: 412912--412974 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
412902 CGTTCGGTAT
412912 TATTATTATTATTATTA-TATTACTA
1 TATTATTATTATTATTAGTATTACTA
*
412937 TATTATTATTA-TATTAGTATTATTA
1 TATTATTATTATTATTAGTATTACTA
412962 TATTATTA-TATTA
1 TATTATTATTATTA
412975 CAAATATTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTATTATTATTATTAGTATTACTA
Found at i:412982 original size:22 final size:21
Alignment explanation
Indices: 412915--412983 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
412905 TCGGTATTAT
*
412915 TATTATTATTATTATATTACTA
1 TATTA-TATTATTATATTACAA
* *
412937 TA-T-TATTATTATATTAGTAT
1 TATTATATTATTATATTA-CAA
412957 TATTATATTATTATATTACAAA
1 TATTATATTATTATATTAC-AA
412979 TATTA
1 TATTA
412984 CAAAATTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTATATTATTATATTACAA
Found at i:413743 original size:22 final size:22
Alignment explanation
Indices: 413718--413770 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
413708 TTATATTTTC
*
413718 CGGTGGCCGAAATAGTGACCGG
1 CGGTGGCCGAAATAGTGACCGA
* * **
413740 CGGTGGTCAAAATAGTGGTCGA
1 CGGTGGCCGAAATAGTGACCGA
413762 CGGTGGCCG
1 CGGTGGCCG
413771 GCCGGTGACA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.17
Consensus pattern (22 bp):
CGGTGGCCGAAATAGTGACCGA
Found at i:414246 original size:19 final size:19
Alignment explanation
Indices: 414222--414258 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
414212 TAATTAATCC
414222 TACTATGTTA-TATTTTAAT
1 TACTAT-TTATTATTTTAAT
414241 TACTATTTATTATTTTAA
1 TACTATTTATTATTTTAA
414259 GACTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TACTATTTATTATTTTAAT
Found at i:414263 original size:18 final size:19
Alignment explanation
Indices: 414223--414268 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
414213 AATTAATCCT
*
414223 ACTATGTTA-TATTTTAATT
1 ACTAT-TTATTATTTTAATG
414242 ACTATTTATTATTTTAA-G
1 ACTATTTATTATTTTAATG
*
414260 ACTAATTAT
1 ACTATTTAT
414269 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (19 bp):
ACTATTTATTATTTTAATG
Found at i:414305 original size:15 final size:15
Alignment explanation
Indices: 414285--414339 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
414275 AATATACTTT
414285 TATATATTATGATAA
1 TATATATTATGATAA
414300 TATATAATT-TGAT-A
1 TATAT-ATTATGATAA
* *
414314 TATATAGTTATAATAT
1 TATATA-TTATGATAA
*
414330 TAAATATTAT
1 TATATATTAT
414340 TATAGCATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 1 0.03
14 8 0.24
15 16 0.48
16 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TATATATTATGATAA
Found at i:414342 original size:18 final size:18
Alignment explanation
Indices: 414264--414343 Score: 51
Period size: 18 Copynumber: 4.3 Consensus size: 18
414254 TTTAAGACTA
414264 ATTATAATATTAATATACTT
1 ATTATAATATTAA-ATA-TT
* *
414284 -TTAT-ATATTATGATAAT
1 ATTATAATATTA-AATATT
*
414301 A-TATAAT-TTGATATATAT
1 ATTATAATATT-AAATAT-T
414319 AGTTATAATATTAAATATT
1 A-TTATAATATTAAATATT
414338 ATTATA
1 ATTATA
414344 GCATTAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
17 9 0.19
18 19 0.40
19 6 0.13
20 11 0.23
21 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (18 bp):
ATTATAATATTAAATATT
Found at i:418072 original size:24 final size:24
Alignment explanation
Indices: 418014--418072 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
418004 TTTGACCGAA
*
418014 CATATCCTTTGGACTTCTAATAGT
1 CATATCCTTTGGACTTCTAAGAGT
* ** *
418038 CACATTATTTGGTATTTCT-AGAGT
1 CATATCCTTTGG-ACTTCTAAGAGT
418062 CATATCCTTTG
1 CATATCCTTTG
418073 AATCATGAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.44
Consensus pattern (24 bp):
CATATCCTTTGGACTTCTAAGAGT
Found at i:425115 original size:14 final size:14
Alignment explanation
Indices: 425096--425124 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
425086 TGAAATTTGA
425096 AGAATCAATGGGCG
1 AGAATCAATGGGCG
425110 AGAATCAATGGGCG
1 AGAATCAATGGGCG
425124 A
1 A
425125 TTGGATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (14 bp):
AGAATCAATGGGCG
Found at i:430144 original size:18 final size:18
Alignment explanation
Indices: 430121--430160 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
430111 AGAACTTGAG
* * *
430121 GAAATTAATTTTGAATTA
1 GAAATTAAATGTGAATCA
430139 GAAATTAAATGTGAATCA
1 GAAATTAAATGTGAATCA
430157 GAAA
1 GAAA
430161 AAAATAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (18 bp):
GAAATTAAATGTGAATCA
Found at i:431399 original size:24 final size:24
Alignment explanation
Indices: 431362--431433 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
431352 GTGGCATCAA
431362 TTGATAGG-TCTGATTCGACCTCAG
1 TTGATAGGCT-TGATTCGACCTCAG
*
431386 TTGATAGGCTTGATTTGACCTCAG
1 TTGATAGGCTTGATTCGACCTCAG
*
431410 TTGATAGGCCTGATTCGACCTCAG
1 TTGATAGGCTTGATTCGACCTCAG
431434 ATTTTGCACA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TTGATAGGCTTGATTCGACCTCAG
Found at i:432895 original size:11 final size:11
Alignment explanation
Indices: 432879--432904 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
432869 AAATGAAAAA
432879 AATTAAATTTT
1 AATTAAATTTT
432890 AATTAAATTTT
1 AATTAAATTTT
432901 AATT
1 AATT
432905 GTAAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTAAATTTT
Found at i:433502 original size:15 final size:15
Alignment explanation
Indices: 433469--433502 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
433459 TTTTAAAAAG
433469 AAAATAAAAACTTGA
1 AAAATAAAAACTTGA
*
433484 AAAAGTAAAAACTTCA
1 AAAA-TAAAAACTTGA
433500 AAA
1 AAA
433503 CAAAAGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATAAAAACTTGA
Found at i:433674 original size:24 final size:24
Alignment explanation
Indices: 433611--433681 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
433601 CTCCTTAAAA
*
433611 CTCTAAATATC-CTAAGAGATAATT
1 CTCTAAAAATCACTAA-AGATAATT
433635 C-CTAATAAAT-AC-AAAGATAATT
1 CTCTAA-AAATCACTAAAGATAATT
433657 CTCTAAAAATCACTAAAGATAATT
1 CTCTAAAAATCACTAAAGATAATT
433681 C
1 C
433682 CCATAATTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 13 0.32
23 12 0.29
24 16 0.39
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.30
Consensus pattern (24 bp):
CTCTAAAAATCACTAAAGATAATT
Found at i:434324 original size:20 final size:21
Alignment explanation
Indices: 434285--434324 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
434275 TTAGGGGTTA
* *
434285 AATATTGATACTGGGATGAAC
1 AATATCGATACTGAGATGAAC
434306 AATATCGATACT-AGATGAA
1 AATATCGATACTGAGATGAA
434325 TTGGGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
AATATCGATACTGAGATGAAC
Found at i:437152 original size:12 final size:12
Alignment explanation
Indices: 437137--437171 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
437127 TGTTGGTATT
437137 GATGTTGATGTC
1 GATGTTGATGTC
*
437149 GATGTCGATGTC
1 GATGTTGATGTC
*
437161 GATATTGATGT
1 GATGTTGATGT
437172 ATATGTCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (12 bp):
GATGTTGATGTC
Found at i:438855 original size:18 final size:18
Alignment explanation
Indices: 438810--438859 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
438800 CTCATATGGG
438810 GAGTATCGATACTCTACCT
1 GAGTATCGATACTC-ACCT
*
438829 TAGGTATCGATACTC-CCAT
1 GA-GTATCGATACTCACC-T
438848 GAGTATCGATAC
1 GAGTATCGATAC
438860 AAAATTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 12 0.44
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (18 bp):
GAGTATCGATACTCACCT
Found at i:440673 original size:31 final size:31
Alignment explanation
Indices: 440638--440698 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
440628 TTGGCTTAAA
*
440638 GAAGATAATAAGGTTGAGGTGTTTTGGTTTG
1 GAAGATAATAAGGTTGAGGTGTCTTGGTTTG
**
440669 GAAGATGGTAAGGTTGAGGTGTCTTGGTTT
1 GAAGATAATAAGGTTGAGGTGTCTTGGTTT
440699 CATTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.38, T:0.38
Consensus pattern (31 bp):
GAAGATAATAAGGTTGAGGTGTCTTGGTTTG
Found at i:443028 original size:40 final size:40
Alignment explanation
Indices: 442954--443033 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
442944 ATAGTGTACA
* *
442954 AGGTGGGTAAAGCCCGACCTCAGCACTACGGTGCATTATT
1 AGGTGAGTAAAGCCCGACCTCAGCACTACGGTGCAATATT
* * **
442994 AGGTGAGTAAAGCTCGACCTCATCACTATTGTGCAATATT
1 AGGTGAGTAAAGCCCGACCTCAGCACTACGGTGCAATATT
443034 TGACTCTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (40 bp):
AGGTGAGTAAAGCCCGACCTCAGCACTACGGTGCAATATT
Found at i:455295 original size:17 final size:18
Alignment explanation
Indices: 455259--455295 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
455249 TCGTGAAGAA
455259 TTTCTCCATCAAGACTATT
1 TTTCTCCATCAAGAC-ATT
455278 TTTCTCCATCAAGA-ATT
1 TTTCTCCATCAAGACATT
455295 T
1 T
455296 CTTGGCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTCTCCATCAAGACATT
Found at i:456700 original size:111 final size:112
Alignment explanation
Indices: 456506--456731 Score: 445
Period size: 111 Copynumber: 2.0 Consensus size: 112
456496 TTGAGATTTT
456506 GGAAATCCTTGCACAAAGCTTTGGGAACTCGACTAAACTTCAACAAAACTTTCCATCCATAAACA
1 GGAAATCCTTGCACAAAGCTTTGGGAACTCGACTAAACTTCAACAAAACTTTCCATCCATAAACA
456571 TATTATCAATCTGAGTGAACCTTGTAGATACTTGAAGATATG-TAAG
66 TATTATCAATCTGAGTGAACCTTGTAGATACTTGAAGATATGTTAAG
456617 GGAAATCCTTGCACAAAGCTTTGGGAACTCGACTAAACTTCAACAAAACTTTCCATCCATAAACA
1 GGAAATCCTTGCACAAAGCTTTGGGAACTCGACTAAACTTCAACAAAACTTTCCATCCATAAACA
456682 TATTATCAATCTGAGTGAACCTTGTAGATACTTGAAGATATGTTAAG
66 TATTATCAATCTGAGTGAACCTTGTAGATACTTGAAGATATGTTAAG
456729 GGA
1 GGA
456732 GTGTGTTATT
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 107 0.94
112 7 0.06
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (112 bp):
GGAAATCCTTGCACAAAGCTTTGGGAACTCGACTAAACTTCAACAAAACTTTCCATCCATAAACA
TATTATCAATCTGAGTGAACCTTGTAGATACTTGAAGATATGTTAAG
Found at i:463898 original size:21 final size:21
Alignment explanation
Indices: 463874--463913 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
463864 TCATTTCCCC
*
463874 TTCCCGATCTTCAATCCCTAA
1 TTCCCCATCTTCAATCCCTAA
* *
463895 TTCCCCTTTTTCAATCCCT
1 TTCCCCATCTTCAATCCCT
463914 TCTCTTGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.40, G:0.03, T:0.40
Consensus pattern (21 bp):
TTCCCCATCTTCAATCCCTAA
Found at i:467265 original size:135 final size:135
Alignment explanation
Indices: 467023--467296 Score: 512
Period size: 135 Copynumber: 2.0 Consensus size: 135
467013 AATAATTTTT
*
467023 TGCCCTTGATATTGAAAACTTAGTGTCATTTGATTAAAATCCATCAAGATAGGAATAAATAGTTT
1 TGCCCTTGATATTGAAAACTCAGTGTCATTTGATTAAAATCCATCAAGATAGGAATAAATAGTTT
*
467088 TATCCAATCTACCCCCAACACCATATCACTGCCACCTAGTTTCAAGAGTCTGAAATCATGTACAA
66 CATCCAATCTACCCCCAACACCATATCACTGCCACCTAGTTTCAAGAGTCTGAAATCATGTACAA
467153 AGGAA
131 AGGAA
* *
467158 TGCCCTTGATGTTGAAAACTCAGTGTCATTTGATTAAAATCCATCAAGATAGGACTAAATAGTTT
1 TGCCCTTGATATTGAAAACTCAGTGTCATTTGATTAAAATCCATCAAGATAGGAATAAATAGTTT
467223 CATCCAATCTACCCCCAACACCATATCACTGCCACCTAGTTTCAAGAGTCTGAAATCATGTACAA
66 CATCCAATCTACCCCCAACACCATATCACTGCCACCTAGTTTCAAGAGTCTGAAATCATGTACAA
467288 AGGAA
131 AGGAA
467293 TGCC
1 TGCC
467297 ATTGCATTTG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (135 bp):
TGCCCTTGATATTGAAAACTCAGTGTCATTTGATTAAAATCCATCAAGATAGGAATAAATAGTTT
CATCCAATCTACCCCCAACACCATATCACTGCCACCTAGTTTCAAGAGTCTGAAATCATGTACAA
AGGAA
Found at i:469569 original size:81 final size:82
Alignment explanation
Indices: 469355--469951 Score: 813
Period size: 82 Copynumber: 7.3 Consensus size: 82
469345 ACACATTCAT
* * * * * * *
469355 GTTATATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTCAATGCCTAGCTATACATTCGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
469420 AGGTGCCAATCATGCCA
66 AGGTGCCAATCATGCCA
* * *
469437 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTCAAATGCCTAGTTGTGCATCTGGCAAAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
469502 AGGTGCCAATCATGCCA
66 AGGTGCCAATCATGCCA
*
469519 GTGAGATGAAAGGCT-AATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
* *
469583 AGGTGCCAATCTTG-TA
66 AGGTGCCAATCATGCCA
* *
469599 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAACATTTAAATGCCTAGCTGTGCATTTGGCAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
** * *
469664 AGGTGTGAATTATGTCA
66 AGGTGCCAATCATGCCA
* * * * *
469681 GTTAGATGAAAGGCTAGATACCTTTGAGTAAAATATTTAAATGCCTGGTTGTGCATTTGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
*
469746 AGTTGCCAATCATGCCA
66 AGGTGCCAATCATGCCA
* *
469763 GTTAGATGAAAGGCTAAATGCCTTTGGGTAAAAGA-TTAAATGCCTAGCTGTGCATTTGGCAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
* * * *
469827 ATGTGTCACTCATGCTA
66 AGGTGCCAATCATGCCA
* * * *
469844 ATTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAATTGTACATTTGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
* *
469909 AGGTGCCAATAATGCTA
66 AGGTGCCAATCATGCCA
* * *
469926 GTTAAATGAAAGGTTAAATTCCTTTG
1 GTTAGATGAAAGGCTAAATGCCTTTG
469952 GGATGAGACT
Statistics
Matches: 451, Mismatches: 61, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
80 15 0.03
81 187 0.41
82 249 0.55
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (82 bp):
GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
AGGTGCCAATCATGCCA
Found at i:469953 original size:163 final size:163
Alignment explanation
Indices: 469355--469951 Score: 840
Period size: 163 Copynumber: 3.7 Consensus size: 163
469345 ACACATTCAT
* * * * *
469355 GTTATATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTCAATGCCTAGCTATACATTCGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTACATTTGGTAGAA
469420 AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTCAAATGCCTAG
66 AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATT-AAATGCCTAG
* * * * *
469485 TTGTGCATCTGGCAAAAAGGTGCCAATCATGCCA
130 CTGTGCATTTGGCAGAAAGGTGTCAATCATGCTA
* * *
469519 GTGAGATGAAAGGCT-AATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTACATTTGGTAGAA
* * *
469583 AGGTGCCAATCTTG-TAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAACATTTAAATGCCTAG
66 AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGA-TTAAATGCCTAG
* *
469647 CTGTGCATTTGGCAGAAAGGTGTGAATTATG-TCA
130 CTGTGCATTTGGCAGAAAGGTGTCAATCATGCT-A
* * * * *
469681 GTTAGATGAAAGGCTAGATACCTTTGAGTAAAATATTTAAATGCCTGGTTGTGCATTTGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTACATTTGGTAGAA
* *
469746 AGTTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAAGATTAAATGCCTAGC
66 AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGC
* *
469811 TGTGCATTTGGCAGAAATGTGTCACTCATGCTA
131 TGTGCATTTGGCAGAAAGGTGTCAATCATGCTA
* *
469844 ATTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAATTGTACATTTGGTAGAA
1 GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTACATTTGGTAGAA
* * * * *
469909 AGGTGCCAATAATGCTAGTTAAATGAAAGGTTAAATTCCTTTG
66 AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTG
469952 GGATGAGACT
Statistics
Matches: 382, Mismatches: 46, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
162 85 0.22
163 249 0.65
164 48 0.13
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (163 bp):
GTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGTTGTACATTTGGTAGAA
AGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGC
TGTGCATTTGGCAGAAAGGTGTCAATCATGCTA
Found at i:470076 original size:49 final size:49
Alignment explanation
Indices: 469979--470077 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
469969 TATCGGTGTT
* * * **
469979 TTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGCCTAATTGTGCA
1 TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGCATAACAGTGCA
* * *
470028 TTTTTGGCATAAAGGTGCCACTAATGCAGGTTAGATGTATAACAGTGCA
1 TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGCATAACAGTGCA
470077 T
1 T
470078 AATTGGCTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (49 bp):
TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGCATAACAGTGCA
Found at i:474912 original size:30 final size:30
Alignment explanation
Indices: 474855--474918 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
474845 TCTTCATCAA
* * *
474855 TTTTCCAAAATTTATGAATTTATCCCAAAC
1 TTTTCCAAAACTTATGAAATGATCCCAAAC
* *
474885 TTTT-CAAAACTTATGAAATGATCCCCAAT
1 TTTTCCAAAACTTATGAAATGATCCCAAAC
474914 TTTTC
1 TTTTC
474919 TAAGGCTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTCCAAAACTTATGAAATGATCCCAAAC
Found at i:478082 original size:82 final size:82
Alignment explanation
Indices: 477937--478131 Score: 282
Period size: 82 Copynumber: 2.4 Consensus size: 82
477927 TGTTTAAAGT
* *
477937 AAAAGATTTAAATGCCTAGTTGTACATTTGGCAGAAAGATGCTAATCATACCAATTAGATGAAAG
1 AAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAAAGATGCCAATCATACCAATTAGATGAAAG
*
478002 GTTAAATGCCTTTGAGA
66 GCTAAATGCCTTTGAGA
* * * * * * *
478019 AAAAGATTTAAATACCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATACTAGTTAGTTGAAAG
1 AAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAAAGATGCCAATCATACCAATTAGATGAAAG
*
478084 GCTAAATGCCTTTGAGT
66 GCTAAATGCCTTTGAGA
*
478101 AAAATATTTAAATGCCTAGTTGTGCATTTGG
1 AAAAGATTTAAATGCCTAGTTGTGCATTTGG
478132 TAATTAGATG
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (82 bp):
AAAAGATTTAAATGCCTAGTTGTGCATTTGGCAGAAAGATGCCAATCATACCAATTAGATGAAAG
GCTAAATGCCTTTGAGA
Found at i:478175 original size:62 final size:62
Alignment explanation
Indices: 478073--478193 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 62
478063 ATTATACTAG
* * * * *
478073 TTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTAGTTGTGCATTTGGTAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGTAA
*
478135 TTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGG
1 TTAGATGAAAGGCTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGG
478194 CAGAAAGGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (62 bp):
TTAGATGAAAGGCTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGTAA
Found at i:478249 original size:144 final size:144
Alignment explanation
Indices: 477989--478277 Score: 578
Period size: 144 Copynumber: 2.0 Consensus size: 144
477979 TAATCATACC
477989 AATTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGA
1 AATTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGA
478054 AAGGTGCCAATTATACTAGTTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTA
66 AAGGTGCCAATTATACTAGTTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTA
478119 GTTGTGCATTTGGT
131 GTTGTGCATTTGGT
478133 AATTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGA
1 AATTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGA
478198 AAGGTGCCAATTATACTAGTTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTA
66 AAGGTGCCAATTATACTAGTTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTA
478263 GTTGTGCATTTGGT
131 GTTGTGCATTTGGT
478277 A
1 A
478278 GAATGGTGTC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (144 bp):
AATTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGA
AAGGTGCCAATTATACTAGTTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTA
GTTGTGCATTTGGT
Found at i:478299 original size:82 final size:82
Alignment explanation
Indices: 478135--478889 Score: 1010
Period size: 82 Copynumber: 9.2 Consensus size: 82
478125 CATTTGGTAA
* * *
478135 TTAGATGAAAGGTTAAATGCCTTTGAGAAAAAGATTTAAATACCTAGCTGTGCATTTGGCAGAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
* * *
478200 GGTGCCAATTATACTAG
66 GGTGCCAATCATGCCAG
* * * * *
478217 TTAGTTGAAAGGCTAAATGCCTTTGAGTAAAATATTTAAATGCCTAGTTGTGCATTTGGTAGAAT
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
* *
478282 GGTGTCAATCATGCTAG
66 GGTGCCAATCATGCCAG
* * * *
478299 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTCACTGCCTAGCTATGCATTCGGCAGAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
478364 GGTGCCAATCATGCCAG
66 GGTGCCAATCATGCCAG
* * *
478381 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTATGAATTTGACAGAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
* *
478446 GGTGTCAATCATG-CAT
66 GGTGCCAATCATGCCAG
** * *
478462 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTATTTGTGCATTTGGAAAAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGG-CAGAA
* *
478527 AGTTGTCAATCATGCCAG
65 AGGTGCCAATCATGCCAG
* * *
478545 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAACTGTACAATTGGCAGAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
478610 GGTGCCAATCATGCCAG
66 GGTGCCAATCATGCCAG
* * ** * * *
478627 TTAGATGAGAGGCTGAATGCCTTTGAGTAAAAGATTTAAATGGTTAGTTGTGCATTTGGAATAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
* *
478692 GGTTCCAATTATGCCAG
66 GGTGCCAATCATGCCAG
* * *
478709 TTAGATGAAAGGCTAAATGCCTTTGAGCAAAAGA-TTAAATGGCTAGTTGTGCATTTGGCAGAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
*
478773 AGTGCCAATCATGCCAG
66 GGTGCCAATCATGCCAG
* * * * * *
478790 TTAGATGAAAGGTTAAATGACTTTGAGTAAAAGATTTAATTGCCTAACTGTGTATTTGGCATAAA
1 TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
*
478855 GGTGCCAATAATGCCAG
66 GGTGCCAATCATGCCAG
* *
478872 TTAAATGAAAGGTTAAAT
1 TTAGATGAAAGGCTAAAT
478890 TCTTTTGGGA
Statistics
Matches: 591, Mismatches: 79, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
81 128 0.22
82 406 0.69
83 57 0.10
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (82 bp):
TTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTTAAATGCCTAGCTGTGCATTTGGCAGAAA
GGTGCCAATCATGCCAG
Found at i:480851 original size:2 final size:2
Alignment explanation
Indices: 480844--480919 Score: 110
Period size: 2 Copynumber: 41.0 Consensus size: 2
480834 ATGCGTAATA
480844 AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT -T 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
480883 AT A- AT AT AT A- AT AT AT AT AT AT AT AT A- 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
480920 GTTTTTAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
1 6 0.09
2 62 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:500572 original size:2 final size:2
Alignment explanation
Indices: 500565--500592 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
500555 TGCGTAAATA
500565 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
500593 TATGTTTTTA
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:502985 original size:21 final size:20
Alignment explanation
Indices: 502961--503010 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
502951 CTCAAAATCA
*
502961 TTTTTCAAAATTTAATTTTG
1 TTTTTCAAAATCTAATTTTG
502981 TTTTTCAAAATCTAATTTT-
1 TTTTTCAAAATCTAATTTTG
*
503000 TCTTTCAAAAT
1 TTTTTCAAAAT
503011 AAAATCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:504554 original size:20 final size:20
Alignment explanation
Indices: 504529--504600 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
504519 TCTTACCTTT
504529 AGTATTGATACTGCAAGAAC
1 AGTATTGATACTGCAAGAAC
* *
504549 AGTATTGATATTGTTCATG--C
1 AGTATTGATACTG--CAAGAAC
*
504569 AGTATTGATACTGTAAGAAC
1 AGTATTGATACTGCAAGAAC
* *
504589 AATATCGATACT
1 AGTATTGATACT
504601 TACCTAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
20 36 0.88
22 3 0.07
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
AGTATTGATACTGCAAGAAC
Found at i:508562 original size:14 final size:14
Alignment explanation
Indices: 508541--508580 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
508531 GACTCTATTT
508541 GAGTTGACTCAATC
1 GAGTTGACTCAATC
*
508555 GGGTTGACTC-ATC
1 GAGTTGACTCAATC
*
508568 GAGTTAACTCAAT
1 GAGTTGACTCAAT
508581 AAGTTAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (14 bp):
GAGTTGACTCAATC
Found at i:508622 original size:18 final size:19
Alignment explanation
Indices: 508599--508642 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
508589 TTAGCTTGAC
508599 CCGGTTCAGTCT-ATTGGA
1 CCGGTTCAGTCTAATTGGA
508617 CCGGTTCAGTCTAATTGGA
1 CCGGTTCAGTCTAATTGGA
*
508636 TCGGTTC
1 CCGGTTC
508643 CATAAGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (19 bp):
CCGGTTCAGTCTAATTGGA
Found at i:509351 original size:47 final size:47
Alignment explanation
Indices: 509300--509693 Score: 661
Period size: 47 Copynumber: 8.4 Consensus size: 47
509290 CTATTTATCT
* * *
509300 CATAAGATCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
509347 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTA
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
* *
509394 CATAAGCTCGTAAAGCTTATTTTATCAACATACTTATCATTTAAATTC
1 CATAAGCTCGT-AAGCTTATTTTATCAATATACTTACCATTTAAATTC
509442 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
509489 CATAAGCTCGTAAGCTTATTTTATCAACATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
509536 CATAAGCTCGTAATCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
509583 CATAAGCTCATAAGCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
509630 CATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT--ATT-
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
509673 CATAAGCTCGTAAGCTTATTT
1 CATAAGCTCGTAAGCTTATTT
509694 GCATACTTAC
Statistics
Matches: 330, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
43 21 0.06
44 3 0.01
46 2 0.01
47 260 0.79
48 44 0.13
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (47 bp):
CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
Found at i:510906 original size:29 final size:29
Alignment explanation
Indices: 510848--510913 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
510838 AGGTTCTTCA
* * *
510848 TCAATTTTCCAAAATTTACGAATTTATCC
1 TCAATTTTCCAAAACTTACGAAATGATCC
*
510877 TCAACTTTT-CAAAACTTACGAAATGGTCC
1 TCAA-TTTTCCAAAACTTACGAAATGATCC
510906 TCAATTTT
1 TCAATTTT
510914 ACTAAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.75
30 4 0.12
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (29 bp):
TCAATTTTCCAAAACTTACGAAATGATCC
Found at i:515210 original size:36 final size:35
Alignment explanation
Indices: 515144--515212 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
515134 CCTTAGGTCC
* * *
515144 ATAAGGAATTACCAGTTGATCGGTGTTAAACCTAT
1 ATAAGGAATTACCAGTTGATCAGAGCTAAACCTAT
515179 ATAAGGAATTACCAGTTTGATCAGAGCTAAACCT
1 ATAAGGAATTACCAG-TTGATCAGAGCTAAACCT
515213 GCAGAGACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGATCAGAGCTAAACCTAT
Found at i:518007 original size:32 final size:32
Alignment explanation
Indices: 517963--518049 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
517953 ATACTGATAC
* *
517963 ACATTATTTGAATGCAAACCTGAACGTACTTT
1 ACATTATCTGAATGCAAACCTGAACGTACTGT
** * *
517995 ACATTATCTGAATGCAAATTTAAATGTACTGT
1 ACATTATCTGAATGCAAACCTGAACGTACTGT
518027 ACATTATCTGAATGCAAACCTGA
1 ACATTATCTGAATGCAAACCTGA
518050 CTAGTATCTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
ACATTATCTGAATGCAAACCTGAACGTACTGT
Found at i:519779 original size:54 final size:54
Alignment explanation
Indices: 519700--519988 Score: 344
Period size: 54 Copynumber: 5.4 Consensus size: 54
519690 TTCTTTGAGA
* * * * *
519700 TGCACACATAGTGTCGATACTGTCGTTCATCAACATATGATGAATTTTTTGGGT
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
* * * * *
519754 TGCACACTTAGTGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
* * *
519808 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATACGATGAATTCTATGGGT
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
* * * * * * * *
519862 TACATACTTAGTGCCTATACGGTTGTTCATAAATATCTTATGAATTTTGTGGGT
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
* * * *
519916 TGCACACTTAGTGCCTATACATTCGCTCCTCAACATATGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
*
519970 TGCACACTTAGTTCCTATA
1 TGCACACTTAGTGCCTATA
519989 GTACACATAG
Statistics
Matches: 194, Mismatches: 41, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 194 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTTGTGGGT
Found at i:519871 original size:108 final size:107
Alignment explanation
Indices: 519700--519988 Score: 391
Period size: 108 Copynumber: 2.7 Consensus size: 107
519690 TTCTTTGAGA
* * * * *
519700 TGCACACATAGTGTCGATACTGTCGTTCATCAACATATGATGAATTTTTTGGGTTGCACACTTAG
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAA-TTTATGGGTTGCACACTTAG
519765 TGCCTATACGGTCGTTCATAAACA-CATTATGAATTTCGTGGGT
65 TGCCTATACGGTCGTTCATAAACATC-TTATGAATTTCGTGGGT
* * *
519808 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATACGATGAATTCTATGGGTTACATACTTAG
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATT-TATGGGTTGCACACTTAG
* * *
519873 TGCCTATACGGTTGTTCATAAATATCTTATGAATTTTGTGGGT
65 TGCCTATACGGTCGTTCATAAACATCTTATGAATTTCGTGGGT
* * * *
519916 TGCACACTTAGTGCCTATACATTCGCTCCTCAACATATGATGAATTTCGTGGGTTGCACACTTAG
1 TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTT-ATGGGTTGCACACTTAG
*
519981 TTCCTATA
65 TGCCTATA
519989 GTACACATAG
Statistics
Matches: 159, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
107 3 0.02
108 155 0.97
109 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (107 bp):
TGCACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTATGGGTTGCACACTTAGT
GCCTATACGGTCGTTCATAAACATCTTATGAATTTCGTGGGT
Found at i:526588 original size:54 final size:54
Alignment explanation
Indices: 526522--526856 Score: 395
Period size: 54 Copynumber: 6.2 Consensus size: 54
526512 GATGCATATG
* * * *
526522 TAGTGACTATACGGTCATTCATAAACATATTATGAATTCTGTGGGTTGCACATT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGCACACT
* * * * *
526576 TAGTGTCGATACGGTCGTTCATTAACATATGATGATTTCTGTGGGTTTCACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGCACACT
* * * * * *
526630 TACTGCCTATACGGTCATTCATAAACACATTATGAATTATGTGGGTTGTACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGCACACT
* * * *
526684 TAGTGCCTATATGGTTGTTCATCAACATATGATGAATTCTGTGGGTTACACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGCACACT
* * * * *
526738 TAGTGCCTATATGGTCGTTCATAAATATATTATGAATT-TCGTGGGTTACAAACT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCT-GTGGGTTGCACACT
** *
526792 TAGTGCCTATATAGTCGTTCATCAACATATGATGAATT-TCGTGGGTTGCACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCT-GTGGGTTGCACACT
526846 TAGTGCCTATA
1 TAGTGCCTATA
526857 GTACACATAG
Statistics
Matches: 240, Mismatches: 40, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 1 0.00
54 239 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (54 bp):
TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGCACACT
Found at i:526704 original size:108 final size:107
Alignment explanation
Indices: 526522--526856 Score: 456
Period size: 108 Copynumber: 3.1 Consensus size: 107
526512 GATGCATATG
* * * *
526522 TAGTGACTATACGGTCATTCATAAACATATTATGAATTCTGTGGGTTGCACATTTAGTGTCGATA
1 TAGTGCCTATACGGTCATTCATAAACATATTATGAATT-TGTGGGTTGCACACTTAGTGCCTATA
* * *
526587 CGGTCGTTCATTAACATATGATGATTTCTGTGGGTTTCACACT
65 TGGTCGTTCATCAACATATGATGATTTCTGTGGGTTACACACT
* * *
526630 TACTGCCTATACGGTCATTCATAAACACATTATGAATTATGTGGGTTGTACACTTAGTGCCTATA
1 TAGTGCCTATACGGTCATTCATAAACATATTATGAATT-TGTGGGTTGCACACTTAGTGCCTATA
* *
526695 TGGTTGTTCATCAACATATGATGAATTCTGTGGGTTACACACT
65 TGGTCGTTCATCAACATATGATGATTTCTGTGGGTTACACACT
* * * * *
526738 TAGTGCCTATATGGTCGTTCATAAATATATTATGAATTTCGTGGGTTACAAACTTAGTGCCTATA
1 TAGTGCCTATACGGTCATTCATAAACATATTATGAATTT-GTGGGTTGCACACTTAGTGCCTATA
* *
526803 TAGTCGTTCATCAACATATGATGAATTTC-GTGGGTTGCACACT
65 TGGTCGTTCATCAACATATGATG-ATTTCTGTGGGTTACACACT
526846 TAGTGCCTATA
1 TAGTGCCTATA
526857 GTACACATAG
Statistics
Matches: 200, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.00
108 195 0.98
109 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (107 bp):
TAGTGCCTATACGGTCATTCATAAACATATTATGAATTTGTGGGTTGCACACTTAGTGCCTATAT
GGTCGTTCATCAACATATGATGATTTCTGTGGGTTACACACT
Found at i:529225 original size:2 final size:2
Alignment explanation
Indices: 529218--529248 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
529208 CAAAAATTAA
529218 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
529249 AACAAATATT
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:540908 original size:24 final size:24
Alignment explanation
Indices: 540881--540926 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
540871 GTGACATGAT
540881 TTTCCTCTACTCTTGTAGCACGCG
1 TTTCCTCTACTCTTGTAGCACGCG
*
540905 TTTCCTCTGCTCTTGTAGCACG
1 TTTCCTCTACTCTTGTAGCACG
540927 ATCCTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.33, G:0.17, T:0.39
Consensus pattern (24 bp):
TTTCCTCTACTCTTGTAGCACGCG
Found at i:541239 original size:33 final size:33
Alignment explanation
Indices: 541197--541265 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
541187 GGTTATTGGA
* *
541197 TTTTGATATTGGTCTTCATTCTAAATGGAAGTT
1 TTTTGATATTGGTCGTCATTCTAAATGGAAGGT
*
541230 TTTTTATATTGGTCGTCATTCTAAATGGAAGGT
1 TTTTGATATTGGTCGTCATTCTAAATGGAAGGT
541263 TTT
1 TTT
541266 AATTTTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTTGATATTGGTCGTCATTCTAAATGGAAGGT
Found at i:541478 original size:13 final size:13
Alignment explanation
Indices: 541460--541484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541450 CAATGATTCA
541460 ATTTAAAATTTTG
1 ATTTAAAATTTTG
541473 ATTTAAAATTTT
1 ATTTAAAATTTT
541485 AGTGTTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTAAAATTTTG
Found at i:541864 original size:17 final size:17
Alignment explanation
Indices: 541842--541874 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
541832 TTAATTAATA
541842 TTTTATTAAT-TTAAAAT
1 TTTTA-TAATATTAAAAT
541859 TTTTATAATATTAAAA
1 TTTTATAATATTAAAA
541875 GAGTTAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAATATTAAAAT
Found at i:544359 original size:15 final size:15
Alignment explanation
Indices: 544336--544383 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
544326 GAGAGGTTCC
*
544336 ACTAACCAACCTTCA
1 ACTATCCAACCTTCA
*
544351 ACTATCCAATC-TCTA
1 ACTATCCAACCTTC-A
*
544366 ACTATCCAACCTCCA
1 ACTATCCAACCTTCA
544381 ACT
1 ACT
544384 TAGCAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.89
16 1 0.04
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (15 bp):
ACTATCCAACCTTCA
Done.