Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007980.1 Hibiscus syriacus cultivar Beakdansim tig00110419_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: 1499237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:414920 original size:16 final size:17
Alignment explanation
Indices: 414896--414944 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
414886 AAATAGTAAT
414896 AAATATAATATAATATA
1 AAATATAATATAATATA
*
414913 ACAT-TAATA-AATAATA
1 AAATATAATATAAT-ATA
414929 AAATATAATAATAATA
1 AAATATAAT-ATAATA
414945 ATAGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 7 0.27
18 2 0.08
19 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAATATAATATA
Found at i:414939 original size:3 final size:3
Alignment explanation
Indices: 414870--414947 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
414860 AAAATATGAG
*
414870 TAA TATA TATA TAA TAA -AA TAG TAA TAA -ATA TAA T-A TAA T-A TAA
1 TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
414914 CAT TAA TAAA TAA TAA -AA T-A TAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA
414948 GTTTAAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
2 11 0.18
3 38 0.63
4 11 0.18
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:416725 original size:62 final size:65
Alignment explanation
Indices: 416647--416803 Score: 205
Period size: 62 Copynumber: 2.4 Consensus size: 65
416637 GACAAAATTT
* *
416647 TTTCAAGAGAAACTGTCTCGAGAGAGACGA-AATTTGTTT-AAAAAAAACAGATT-AAAGA-TTT
1 TTTCAAG-GGAACTGTCTCAAGAGAGAC-ACAATTTGTTTCAAAAAAAACAGATTCAAAGATTTT
416708 TG
64 TG
*** *
416710 TTTCAAGGGAACTGTCTCAAGAGAGACACAATTTGTTTCAAGGGAAATAGATTCAAAGATTTTTG
1 TTTCAAGGGAACTGTCTCAAGAGAGACACAATTTGTTTCAAAAAAAACAGATTCAAAGATTTTTG
416775 TTTCAAGGGAATCTGTCTCAAGAGAGACA
1 TTTCAAGGGAA-CTGTCTCAAGAGAGACA
416804 AAAAAATTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
61 1 0.01
62 27 0.33
63 17 0.20
64 5 0.06
65 16 0.19
66 17 0.20
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (65 bp):
TTTCAAGGGAACTGTCTCAAGAGAGACACAATTTGTTTCAAAAAAAACAGATTCAAAGATTTTTG
Found at i:416752 original size:35 final size:34
Alignment explanation
Indices: 416706--417146 Score: 205
Period size: 36 Copynumber: 13.0 Consensus size: 34
416696 GATTAAAGAT
*
416706 TTTGTTTCAAGGGAACTGTCTCAAGAGAGACACAA
1 TTTGTTTCAAGGAAACTGTCTCAAGAGAGACA-AA
**
416741 TTTGTTTCAAGGGAAA-TAGAT-TC-A-A-AG--ATT
1 TTTGTTTCAA-GGAAACT-G-TCTCAAGAGAGACAAA
*
416771 TTTGTTTCAAGGGAATCTGTCTCAAGAGAGACAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAA
**** *
416806 AAAATTT-AAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGAC-AAA
* * * *
416841 TTTGTTTTAAAAGAAACTGTCTCAAGGGAGATGAAA
1 TTTG-TTTCAAGGAAACTGTCTCAAGAGAGA-CAAA
* * * *
416877 TTTGTTTTAAGGAAACATAT-TC-----A-ACGAT
1 TTTGTTTCAAGGAAAC-TGTCTCAAGAGAGACAAA
416905 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAA
* *
416939 TTT-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGAC-AAA
* *
416974 TTTGTTTCTAAAAGAAACTATCTC-AGAGAGACAAA
1 TTTGTTTC--AAGGAAACTGTCTCAAGAGAGACAAA
** **
417009 CTTTGTTTCAAGGAAAACAAAT-TC-A-A-AG---TT
1 -TTTGTTTCAAGG-AAAC-TGTCTCAAGAGAGACAAA
*
417039 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGAC-AAA
* *
417075 TTTG-TTCAAGAGAGAAAATATCTCAAGAGAGACAAAA
1 TTTGTTTC-A-AG-GAAACTGTCTCAAGAGAGAC-AAA
* *
417112 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAA
417147 AACTTTGTTT
Statistics
Matches: 309, Mismatches: 51, Indels: 92
0.68 0.11 0.20
Matches are distributed among these distances:
28 13 0.04
29 26 0.08
30 22 0.07
31 4 0.01
32 4 0.01
33 30 0.10
34 30 0.10
35 54 0.17
36 83 0.27
37 39 0.13
38 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (34 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAA
Found at i:416850 original size:36 final size:36
Alignment explanation
Indices: 416788--417157 Score: 230
Period size: 36 Copynumber: 10.8 Consensus size: 36
416778 CAAGGGAATC
***
416788 TGTCTCAAGAGAGACAAAA--AAATTTAAGAGAAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
* *
416822 TGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
* **
416858 TGTCTCAAGGGAGATGAAATTTGTTTTAAG-GAAACA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAA-A
* * * * * *
416894 TAT-TC-----A-AC-GATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
416922 TGTCTCAAGAGAG--AAAATTT-TTTTAAGAGAAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
* *
416955 TGTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTT-TAAGAGAAAA
* * *
416992 TATCTC-AGAGAGACAAACTTTGTTTCAAG-GAAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
** * * * *
417026 -----C-A-A-ATTCAAAGTTTTTGTTTCAAGGGAAAC
1 TGTCTCAAGAGAGACAAA--ATTTGTTTTAAGAGAAAA
* **
417056 CGTCTCAAGAGAGACAAAATTTGTTCAAGAGAGAAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTTA-AGAGAAAA
* *
417093 TATCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
*
417129 CGTCTCAAGAGAGACAAAAACTTTGTTTT
1 TGTCTCAAGAGAGAC-AAAA-TTTGTTTT
417158 GAGTAAATTA
Statistics
Matches: 259, Mismatches: 47, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
27 5 0.02
28 14 0.05
29 20 0.08
30 5 0.02
33 23 0.09
34 28 0.11
35 16 0.06
36 87 0.34
37 48 0.19
38 13 0.05
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (36 bp):
TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAA
Found at i:416928 original size:134 final size:133
Alignment explanation
Indices: 416719--417146 Score: 574
Period size: 134 Copynumber: 3.2 Consensus size: 133
416709 GTTTCAAGGG
* *
416719 AACTGTCTCAAGAGAGACACAATTTGTTTCAAGGGAAATAGATTCAAAGATTTTTGTTTCAAGGG
1 AACTGTCTCAAGAGAGACA-AATTTGTTTCAA-GGAAACAAATTCAAAGA-TTTTGTTTCAAGGG
* **
416784 AATCTGTCTCAAGAGAGACAAAAAAATTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
63 AAACTGTCTCAAGAGAGACAAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
416849 AAAAGA
128 AAAAGA
* * * * *
416855 AACTGTCTCAAGGGAGATGAAATTTGTTTTAAGGAAACATATTCAACGATTTTGTTTCAAGGGAA
1 AACTGTCTCAAGAGAGA-CAAATTTGTTTCAAGGAAACAAATTCAAAGATTTTGTTTCAAGGGAA
**
416920 ACTGTCTCAAGAGAGA-AAATTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCTA
65 ACTGTCTCAAGAGAGACAAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTT-TA
416984 AAAGA
129 AAAGA
* *
416989 AACTATCTC-AGAGAGACAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAA-TTTGTTTCAAGG-AAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
417053 AACCGTCTCAAGAGAGAC-AAAATTTGTTCAAGAGAGAAAATATCTCAAGAGAGACAAAATTTGT
64 AACTGTCTCAAGAGAGACAAAAATTT-TT--A-AGAGAAAATGTCTCAAGAGAGACAAAATTTGT
*
417117 TTTAAGAGA
125 TTTAAAAGA
*
417126 AACCGTCTCAAGAGAGACAAA
1 AACTGTCTCAAGAGAGACAAA
417147 AACTTTGTTT
Statistics
Matches: 257, Mismatches: 25, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
132 3 0.01
133 58 0.23
134 94 0.37
135 16 0.06
136 27 0.11
137 15 0.06
138 44 0.17
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (133 bp):
AACTGTCTCAAGAGAGACAAATTTGTTTCAAGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAA
CTGTCTCAAGAGAGACAAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAA
AGA
Found at i:416964 original size:33 final size:33
Alignment explanation
Indices: 416903--417004 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 33
416893 ATATTCAACG
*
416903 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAA
1 ATTTT-TTT-AAGAGAAACTGTCTCAAGAGAGAAA
*
416938 ATTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
1 ATTTTTTTAAGAGAAACTGTCTCAAGAGAG--AAA
* *
416973 ATTTGTTTCTAAAAGAAACTATCTC-AGAGAGA
1 ATTT-TTT-TAAGAGAAACTGTCTCAAGAGAGA
417005 CAAACTTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 20 0.34
34 4 0.07
35 12 0.21
36 9 0.16
37 13 0.22
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (33 bp):
ATTTTTTTAAGAGAAACTGTCTCAAGAGAGAAA
Found at i:417085 original size:20 final size:20
Alignment explanation
Indices: 417060--417117 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
417050 GGAAACCGTC
417060 TCAAGAGAGACAAAATTTGT
1 TCAAGAGAGACAAAATTTGT
* *
417080 TCAAGAGAG--AAAATAT-C
1 TCAAGAGAGACAAAATTTGT
417097 TCAAGAGAGACAAAATTTGT
1 TCAAGAGAGACAAAATTTGT
417117 T
1 T
417118 TTAAGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 6 0.19
20 10 0.32
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (20 bp):
TCAAGAGAGACAAAATTTGT
Found at i:418360 original size:83 final size:86
Alignment explanation
Indices: 418251--418472 Score: 274
Period size: 91 Copynumber: 2.6 Consensus size: 86
418241 GACTAGCTAG
*
418251 ATCCATAAAGCCGGGGCGTTTTACCAATTGCTCTAGAGGGACAACTCA-TTATG-TA-AAT-ACC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCACTTATGATAGAATCACC
* *
418312 TTTATCAAGTTAGATGAATCTT
66 TTTATC-AGCTAGATGAATATT
** *
418334 ATCCATAAAGCTAGGGCGTTTAACCAATTAC-CTTAGAGGGACAACTCAAGCTTTATGTATAGTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-C-TTATG-ATAG-A
*
418398 ATCACCTTTATCAGCTAGTTGAATATT
60 ATCACCTTTATCAGCTAGATGAATATT
*
418425 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCA
418473 AGCTTATTGT
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
82 1 0.01
83 41 0.35
84 1 0.01
87 5 0.04
89 2 0.02
90 1 0.01
91 57 0.49
92 9 0.08
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (86 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCACTTATGATAGAATCACC
TTTATCAGCTAGATGAATATT
Found at i:419343 original size:79 final size:80
Alignment explanation
Indices: 419189--419347 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 80
419179 CTGCTTCCTC
419189 CAAATCATTTTCCTGGAAAATCCCACTTCTTCGTGATTTATCAGTATTTCCCTTCCTAGTTGCTG
1 CAAATCATTTTCCTGGAAAATCCCACTTCTTCGTGATTTATCAGTATTTCCCTTCCTAGTTGCTG
419254 GAAATTGGGCCCAAA
66 GAAATTGGGCCCAAA
419269 CAAATCATTTTCCTGGGAAAATCCCACTTCTTCGTGATTTATCA-TA-TTCCCTTCCTAGTTGCT
1 CAAATCATTTTCCT-GGAAAATCCCACTTCTTCGTGATTTATCAGTATTTCCCTTCCTAGTTGCT
419332 GGAAATTGGGCCCAAA
65 GGAAATTGGGCCCAAA
419348 TTTAGATCCA
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
79 33 0.42
80 16 0.21
81 29 0.37
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (80 bp):
CAAATCATTTTCCTGGAAAATCCCACTTCTTCGTGATTTATCAGTATTTCCCTTCCTAGTTGCTG
GAAATTGGGCCCAAA
Found at i:422396 original size:17 final size:16
Alignment explanation
Indices: 422374--422431 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
422364 TAAAAAAATA
422374 AATAAAAATATACGTAT
1 AATAAAAATATA-GTAT
*
422391 AATAAAAA-AT-GCAT
1 AATAAAAATATAGTAT
* *
422405 AAGAAAAATATATATAT
1 AATAAAAATATA-GTAT
422422 AATAAAAATA
1 AATAAAAATA
422432 AAAATATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.30
15 2 0.06
16 2 0.06
17 19 0.58
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (16 bp):
AATAAAAATATAGTAT
Found at i:422406 original size:28 final size:29
Alignment explanation
Indices: 422366--422433 Score: 68
Period size: 31 Copynumber: 2.3 Consensus size: 29
422356 AGTAAAATTA
*
422366 AAAAAATAAAT-AAAAATATACGTATAAT
1 AAAAAATAAATAAAAAATATACATATAAT
** *
422394 AAAAAATGCATAAGAAAAATATATATATAAT
1 AAAAAATAAAT-A-AAAAATATACATATAAT
422425 -AAAAATAAA
1 AAAAAATAAA
422434 AATATGATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 9 0.29
30 7 0.23
31 15 0.48
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (29 bp):
AAAAAATAAATAAAAAATATACATATAAT
Found at i:422485 original size:5 final size:5
Alignment explanation
Indices: 422464--422534 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
422454 ATATAATAAA
* * * * *
422464 AATAGT AATAA AATTT AATTT AATAT AATAT AATAT AATAG AATA- AATAA
1 AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
422514 AATAAT AATAAT AATAT AATA
1 AAT-AT AAT-AT AATAT AATA
422535 ATAGTTCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
4 4 0.07
5 39 0.68
6 14 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:422487 original size:15 final size:15
Alignment explanation
Indices: 422409--422535 Score: 73
Period size: 15 Copynumber: 8.1 Consensus size: 15
422399 ATGCATAAGA
422409 AAAATATATATATAAT
1 AAAATATA-ATATAAT
* *
422425 AAAAATAAAAATATGATT
1 -AAAAT-ATAATAT-AAT
422443 AATATATATATATATAAT
1 AA-A-ATATA-ATATAAT
*
422461 AAAA-AT-A-GTAAT
1 AAAATATAATATAAT
* *
422473 AAAATTTAATTTAAT
1 AAAATATAATATAAT
*
422488 ATAATATAATATAAT
1 AAAATATAATATAAT
* *
422503 AGAATA-AATAAAAT
1 AAAATATAATATAAT
422517 AATAATAATAATATAAT
1 AA-AAT-ATAATATAAT
422534 AA
1 AA
422536 TAGTTCAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
12 8 0.09
13 2 0.02
14 9 0.11
15 26 0.31
16 2 0.02
17 21 0.25
18 11 0.13
19 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATATAATATAAT
Found at i:422490 original size:36 final size:35
Alignment explanation
Indices: 422412--422510 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 35
422402 CATAAGAAAA
* **
422412 ATATATATATAATAAAAATAAAAATATGATTAATAT
1 ATATATATATAATAAAAAT-AGAATAAAATTAATAT
*
422448 ATATATATATAATAAAAATAGTAATAAAATTTAATTT
1 ATATATATATAATAAAAATAG-AATAAAA-TTAATAT
*
422485 A-ATATAATATAAT-ATAATAGAATAAA
1 ATATAT-ATATAATAAAAATAGAATAAA
422511 TAAAATAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
35 7 0.13
36 34 0.62
37 14 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (35 bp):
ATATATATATAATAAAAATAGAATAAAATTAATAT
Found at i:422492 original size:10 final size:10
Alignment explanation
Indices: 422411--422534 Score: 80
Period size: 10 Copynumber: 12.4 Consensus size: 10
422401 GCATAAGAAA
422411 AATATATATAT
1 AATATA-ATAT
*
422422 AATA-AAAAT
1 AATATAATAT
422431 AA-A-AATAT
1 AATATAATAT
*
422439 GAT-TAATAT
1 AATATAATAT
422448 -ATATATATAT
1 AATATA-ATAT
*
422458 AATAAAAATAGT
1 AAT-ATAATA-T
* *
422470 AATAAAATTT
1 AATATAATAT
*
422480 AATTTAATAT
1 AATATAATAT
422490 AATATAATAT
1 AATATAATAT
*
422500 AATAGAATA-
1 AATATAATAT
*
422509 AATAAAATAAT
1 AATATAAT-AT
422520 AATAATAATAT
1 AAT-ATAATAT
422531 AATA
1 AATA
422535 ATAGTTCAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
8 8 0.09
9 19 0.21
10 32 0.35
11 22 0.24
12 10 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AATATAATAT
Found at i:429212 original size:226 final size:227
Alignment explanation
Indices: 428813--429253 Score: 737
Period size: 226 Copynumber: 1.9 Consensus size: 227
428803 GTAAATTATC
* * *
428813 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
***
428878 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACATCAAATAATTTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACATCAAATAATAAATT
*
428943 TATGTAAATGAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTGA
131 TATGTAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGA
429007 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTTCAAAAAAGTATA
*
429039 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
429104 TTAATATTGTTAAATTTAAATTCTAAAT-A-ATTTTATAAAATATCAAAACAATCAAATAA-AAA
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAAC-ATCAAATAATAAA
*
429166 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTATGTAAA-TAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
429231 TGAAACATAAATTACATAACTTT
193 TGAAACATAAATTACATAACTTT
429254 TAAAGCAGTT
Statistics
Matches: 201, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
225 29 0.14
226 94 0.47
227 78 0.39
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACATCAAATAATAAATT
TATGTAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGA
AACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:429351 original size:19 final size:19
Alignment explanation
Indices: 429305--429359 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
429295 AATATCGATC
* *
429305 CAAAACGATATACCAGGTAA
1 CAAAATGATAAACC-GGTAA
429325 -AAATATGATAAACCGGTAA
1 CAAA-ATGATAAACCGGTAA
429344 CAAAATGATTAAACCG
1 CAAAATGA-TAAACCG
429360 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (19 bp):
CAAAATGATAAACCGGTAA
Found at i:429358 original size:20 final size:19
Alignment explanation
Indices: 429320--429363 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
429310 CGATATACCA
429320 GGTAAAAATATGATAAACC
1 GGTAAAAATATGATAAACC
429339 GGTAACAAA-ATGATTAAACC
1 GGTAA-AAATATGA-TAAACC
429359 -GTAAA
1 GGTAAA
429364 TTTAAAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 9 0.39
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.20
Consensus pattern (19 bp):
GGTAAAAATATGATAAACC
Found at i:429505 original size:20 final size:19
Alignment explanation
Indices: 429482--429528 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
429472 CGATATAACA
429482 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
429502 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
429522 GGTAAAA
1 GGTAAAA
429529 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:429530 original size:17 final size:18
Alignment explanation
Indices: 429486--429533 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
429476 ATAACAGGTA
429486 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
429505 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
429525 -AAAATGATA
1 AAAAATGATA
429534 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:431214 original size:50 final size:50
Alignment explanation
Indices: 431139--431240 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
431129 CAAGGAATAT
431139 ATGAAGCTCATTTGCGATGAAGGCTTGAAGGGTGAATTCAATTGGGCTGA
1 ATGAAGCTCATTTGCGATGAAGGCTTGAAGGGTGAATTCAATTGGGCTGA
431189 ATGAAGCTCATTTGCGATGAAGGCTTGAAGGGTGAATTCAATTGGGCTGA
1 ATGAAGCTCATTTGCGATGAAGGCTTGAAGGGTGAATTCAATTGGGCTGA
431239 AT
1 AT
431241 ATATCCATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (50 bp):
ATGAAGCTCATTTGCGATGAAGGCTTGAAGGGTGAATTCAATTGGGCTGA
Found at i:431824 original size:21 final size:21
Alignment explanation
Indices: 431777--431841 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
431767 AAGACAATCA
* *
431777 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
431799 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
431819 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
431840 AG
1 AG
431842 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:433735 original size:19 final size:19
Alignment explanation
Indices: 433711--433759 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
433701 AATGTAGGGT
433711 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
433730 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
433749 TATTTTTGTAT
1 TAATTTTGTAT
433760 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:434255 original size:197 final size:198
Alignment explanation
Indices: 433876--435230 Score: 2454
Period size: 198 Copynumber: 6.9 Consensus size: 198
433866 CAATATGGCC
* *
433876 ACAGGGTGCAACCC-CAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAA-CATCGAAA
1 ACAGGGTGC-ACCCATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCG-AA
*
433939 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG-ACAATTATACCGGTTTTATGAG
62 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
434003 AGAATATGTCTAAATAATGTGTTGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
127 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
434068 ATGGAAA
192 ATGGAAA
434075 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCA
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCA
*
434140 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAAAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
434205 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
434270 AAA
196 AAA
434273 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC
434338 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
65 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
434403 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTTTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
434467 GAAA
195 GAAA
434471 ACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCC-AAATCATCGAACCCA
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCA
434534 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA-AA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
*
434598 TATGTCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
434663 -AA
196 AAA
*
434665 ACAGGGTGCACCCATAAAGTGTCGATCCATTTATAAAAAGTGTCGATCCCAAAATCATCGAA-CC
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC
434729 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
65 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
434794 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
434859 GAAA
195 GAAA
434863 ACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCC-AAATCATCGAACCCA
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCA
434926 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA-AA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
434990 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTCCAGAATGAAT
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTTTCCAGAATGAAT
435055 GGAAA
194 GGAAA
435060 ACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCGAAACCC
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCG-AACCC
435124 -AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
65 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
435187 ATATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATA
130 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
435231 CTAATTTAAA
Statistics
Matches: 1129, Mismatches: 10, Indels: 36
0.96 0.01 0.03
Matches are distributed among these distances:
194 78 0.07
195 155 0.14
196 175 0.16
197 267 0.24
198 283 0.25
199 171 0.15
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (198 bp):
ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
AAA
Found at i:435115 original size:590 final size:594
Alignment explanation
Indices: 433876--435230 Score: 2470
Period size: 590 Copynumber: 2.3 Consensus size: 594
433866 CAATATGGCC
* *
433876 ACAGGGTGCAACCC-CAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAA-CATCGAAA
1 ACAGGGTGC-ACCCATAAAGTGTCGATCC--ATAT-AAAAAGTGTCGATCCCAAAATCATCGAAA
*
433939 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG-ACAATTATACCGGTTTTATGAG
62 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
434003 AGAATATGTCTAAATAATGTGTTGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
127 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
434068 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATC
192 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATC
434133 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
257 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
434198 GAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAA
322 GAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAA
434263 TGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
387 TGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
434328 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
452 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
434393 TTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTTCCA
517 TTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTTCCA
434458 GAATGAATGGAAA
582 GAATGAATGGAAA
434471 ACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCC-AAATCATCG-AACCCA
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAACCCA
434534 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA-AA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
*
434598 TATGTCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
*
434663 -AAACAGGGTGCACCCATAAAGTGTCGATCCATTTATAAAAAGTGTCGATCCCAAAATCATCGAA
196 AAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAA
434727 -CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
260 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
434791 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
325 AAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
434856 ATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCAT
390 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
434918 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
455 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
434983 TGAGA-AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTCCA
520 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCG--A-TTTTTTTTTCCA
435047 GAATGAATGGAAA
582 GAATGAATGGAAA
435060 ACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAACCC-
1 ACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAACCCA
435124 AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
435188 TATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATA
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
435231 CTAATTTAAA
Statistics
Matches: 742, Mismatches: 8, Indels: 26
0.96 0.01 0.03
Matches are distributed among these distances:
586 43 0.06
587 77 0.10
588 16 0.02
589 161 0.22
590 229 0.31
591 143 0.19
592 43 0.06
593 4 0.01
594 4 0.01
595 22 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (594 bp):
ACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
AAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
AAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTTCCAGAAT
GAATGGAAA
Found at i:436694 original size:18 final size:18
Alignment explanation
Indices: 436673--436734 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
436663 AGCGGTCGCA
436673 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
436691 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
436709 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
436727 GAAGATGA
1 GAAGATGA
436735 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:436697 original size:6 final size:6
Alignment explanation
Indices: 436673--436764 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
436663 AGCGGTCGCA
* * * * * *
436673 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
436721 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
436765 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:436708 original size:3 final size:3
Alignment explanation
Indices: 436688--436768 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
436678 TGAAGCTGAC
* * * * * ** *
436688 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
436736 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
436769 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:436727 original size:36 final size:36
Alignment explanation
Indices: 436676--436752 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
436666 GGTCGCAGAA
*
436676 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
436712 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
436748 GATGA
1 GATGA
436753 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:436768 original size:12 final size:12
Alignment explanation
Indices: 436676--436764 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
436666 GGTCGCAGAA
*
436676 GATGAAGCTGAC
1 GATGAAGATGAC
436688 GATGAAGATGAC
1 GATGAAGATGAC
*
436700 GATGATGATGAC
1 GATGAAGATGAC
* *
436712 GATGAAGCTGGC
1 GATGAAGATGAC
*
436724 GATGAAGATGAT
1 GATGAAGATGAC
* * *
436736 GACGATGATGAT
1 GATGAAGATGAC
* *
436748 GATGATGATGAA
1 GATGAAGATGAC
436760 GATGA
1 GATGA
436765 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:436768 original size:18 final size:18
Alignment explanation
Indices: 436673--436764 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
436663 AGCGGTCGCA
*
436673 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
436691 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
436709 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
436727 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
436745 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
436763 GA
1 GA
436765 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:438524 original size:184 final size:183
Alignment explanation
Indices: 438215--438627 Score: 720
Period size: 184 Copynumber: 2.3 Consensus size: 183
438205 CTTTCAACAT
** * * * *
438215 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGCGCGAATA
438280 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
438345 AATGTGCCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGCCGATACGATTTAAAAAAGTATCGACA-TTTACACATCGGAACCCAGA
438399 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGCGCGAATA
438464 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
438529 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGCCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
*
438582 TTTATAATGTAATAGAT-ATTTTGTAATATAACCGGTATAAATATAC
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATAC
438628 GGTATAAAAA
Statistics
Matches: 219, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 29 0.13
183 35 0.16
184 155 0.71
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGCCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
Found at i:441162 original size:25 final size:25
Alignment explanation
Indices: 441128--441192 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
441118 TTATCATTAA
441128 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
441153 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
441178 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
441193 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:441506 original size:23 final size:23
Alignment explanation
Indices: 441475--441538 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
441465 ATAGGTAAAC
*
441475 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
441498 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
441521 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
441539 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:441545 original size:23 final size:23
Alignment explanation
Indices: 441475--441547 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
441465 ATAGGTAAAC
* **
441475 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
441498 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
441521 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
441544 ATAT
1 ATAT
441548 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:441937 original size:23 final size:23
Alignment explanation
Indices: 441906--441969 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
441896 ATAGGTAAAC
*
441906 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
441929 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
441952 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
441970 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:441976 original size:23 final size:23
Alignment explanation
Indices: 441906--441978 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
441896 ATAGGTAAAC
* **
441906 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
441929 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
441952 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
441975 ATAT
1 ATAT
441979 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:442361 original size:23 final size:23
Alignment explanation
Indices: 442330--442393 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
442320 ATAGGTAAAC
*
442330 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
442353 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
442376 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
442394 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:442400 original size:23 final size:23
Alignment explanation
Indices: 442330--442402 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
442320 ATAGGTAAAC
* **
442330 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
442353 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
442376 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
442399 ATAT
1 ATAT
442403 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:442430 original size:20 final size:20
Alignment explanation
Indices: 442405--442443 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
442395 GGTTATATTG
* *
442405 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
442425 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
442444 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:442811 original size:22 final size:23
Alignment explanation
Indices: 442755--442817 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
442745 ATAGGTAAAC
*
442755 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
442778 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
442801 ATAT-ATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
442818 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:442824 original size:22 final size:23
Alignment explanation
Indices: 442755--442826 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
442745 ATAGGTAAAC
* **
442755 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
442778 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
442801 ATAT-ATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
442823 ATAT
1 ATAT
442827 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:442863 original size:425 final size:429
Alignment explanation
Indices: 441195--443057 Score: 3528
Period size: 424 Copynumber: 4.4 Consensus size: 429
441185 TATATACATC
441195 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
1 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
441260 ACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATC-AAAC-ATCAA
66 ACGA-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
* *
441323 ATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTA-GTGGAAAACATGAAACACTGTTA
130 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
441387 AAAAATTGAAACATAAATTACATAACTTTT-AAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
195 AAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
441451 ACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
260 ACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
441516 CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCC
325 CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCC
441581 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
390 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
441621 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
1 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
441686 ACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
66 ACGA-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
441751 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
130 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTT-
441816 AAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATG
194 AAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATG
441881 GACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTA
259 GACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTA
441946 TCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCC-TTTTATAAAAGTGTC
324 TCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTC
442010 CATACTTTTTTCACTGTGG-AAACATTAATTTAAGGTTATG
389 CATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
442050 -TTTGAGTGAGTTTTAAGATATTAA-TTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
1 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
442113 ACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
66 ACGA-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
442178 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
130 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
442243 AAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCC-TTTTAT-AAAAGTATGG
195 AAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
442306 ACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
260 ACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
442371 CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT-AAAGTGTCC
325 CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCC
442435 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
390 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
442475 TTTTGAGTGAGTTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTC-TACGT
1 TTTTGAGTGAG-TTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGT
442539 TACG-ATATATTATTATTAAATTAAAAATTCTAAATATTA-TTTATAAAATATCAAAACAATCAA
65 TACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
442602 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
130 ATAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTA
442667 AAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
195 AAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
442732 ACACTTTCAATAT-ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
260 ACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAT
442796 CGTTTATAT-ATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCC
325 CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCC
442860 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
390 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
442900 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTT-TTACGTT
1 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
442964 ACG-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAA
66 ACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAA
*
443028 TAATTTTTTGTGCAAATGAAATTATTAAAT
131 TAATTTTTTGTGCAAATGAAATCATTAAAT
443058 CAAATAATTC
Statistics
Matches: 1419, Mismatches: 3, Indels: 31
0.98 0.00 0.02
Matches are distributed among these distances:
424 421 0.30
425 248 0.17
426 200 0.14
427 195 0.14
428 100 0.07
429 43 0.03
430 65 0.05
431 147 0.10
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (429 bp):
TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTT
ACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAA
TAATTTTTTGTGCAAATGAAATCATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAA
AAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
CACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATC
GTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCA
TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATG
Found at i:443126 original size:25 final size:25
Alignment explanation
Indices: 443092--443140 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
443082 ACAACAAATC
*
443092 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
443117 AATTGAACATTGTTATGGGTACAT
1 AATTAAACATTGTTATGGGTACAT
443141 CATTTGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:443845 original size:39 final size:39
Alignment explanation
Indices: 443802--443888 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
443792 TCCGATGCTC
*
443802 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
443841 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
443880 ATCAAAATC
1 ATCAAAATC
443889 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:444323 original size:23 final size:23
Alignment explanation
Indices: 444292--444355 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
444282 ATAGGTAAAC
*
444292 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
444315 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
444338 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
444356 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:444362 original size:23 final size:23
Alignment explanation
Indices: 444292--444364 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
444282 ATAGGTAAAC
* **
444292 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
444315 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
444338 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
444361 ATAT
1 ATAT
444365 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:448289 original size:31 final size:31
Alignment explanation
Indices: 448254--448327 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
448244 TTCAAAAACA
* *
448254 TAAGTTTTGGTCACTTACGCCATTGTTTTAT
1 TAAGTTTTGGTCAATTACGCCATCGTTTTAT
**
448285 TAAGTTTTGGTCAATTACGTTATCGTTTTAT
1 TAAGTTTTGGTCAATTACGCCATCGTTTTAT
448316 TAAGTTTTGGTC
1 TAAGTTTTGGTC
448328 GCTTGGACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (31 bp):
TAAGTTTTGGTCAATTACGCCATCGTTTTAT
Found at i:448835 original size:32 final size:32
Alignment explanation
Indices: 448811--448943 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 32
448801 AACGCTCCTG
448811 TGCATTATCTGAATGCAACACTAACTCTGA-TA
1 TGCATTATCTGAATGCAACACTAACTCT-ACTA
* *
448843 TGCATTATCTGAATGCAATATTAACTCTACTA
1 TGCATTATCTGAATGCAACACTAACTCTACTA
* * * * * * * *
448875 TGCATTATCTAAATACAATATTGATTGTGCTA
1 TGCATTATCTGAATGCAACACTAACTCTACTA
* * *
448907 TGTATTATCTAAATGCAATACTAA-TACTACTA
1 TGCATTATCTGAATGCAACACTAACT-CTACTA
448939 TGCAT
1 TGCAT
448944 CACACAAGCT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
31 2 0.02
32 82 0.98
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTAACTCTACTA
Found at i:457308 original size:30 final size:30
Alignment explanation
Indices: 457260--457338 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
457250 ATTGTTTTTT
* * *
457260 AATTTGGTGCCCAACCTTTGTCTCGGTTCT
1 AATTTGGTGCCTAACCTTTGTCTCAGTTCC
* *
457290 AGTTTGATGCCTAACCTTTGTCTCAGTTCC
1 AATTTGGTGCCTAACCTTTGTCTCAGTTCC
*
457320 AATTTGGTTCCTAACCTTT
1 AATTTGGTGCCTAACCTTT
457339 AATTATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTGGTGCCTAACCTTTGTCTCAGTTCC
Found at i:460808 original size:31 final size:31
Alignment explanation
Indices: 460741--460800 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
460731 CAATTTAAGG
*
460741 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
460772 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
460801 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:460892 original size:19 final size:19
Alignment explanation
Indices: 460865--460930 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
460855 AATGTTTTTA
* *
460865 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
460884 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* * *
460903 TGAACAGTAAATCATTGTT
1 TGAACAGTAAATTACTATT
460922 TGAACAGTA
1 TGAACAGTA
460931 CCCCGAGGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:461063 original size:21 final size:21
Alignment explanation
Indices: 461037--461078 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
461027 ATTTAAATAT
*
461037 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
461058 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
461079 CCCCCATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:461402 original size:34 final size:32
Alignment explanation
Indices: 461363--461432 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
461353 TTTTGTAAAG
*
461363 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
461397 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
461429 GGGA
1 GGGA
461433 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:463153 original size:15 final size:15
Alignment explanation
Indices: 463133--463166 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
463123 AAAAAGGGTG
*
463133 GAGAATGAATGAGAA
1 GAGAATGAAGGAGAA
*
463148 GAGAATGAAGGGGAA
1 GAGAATGAAGGAGAA
463163 GAGA
1 GAGA
463167 GAGAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (15 bp):
GAGAATGAAGGAGAA
Found at i:471101 original size:3 final size:3
Alignment explanation
Indices: 471093--471148 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
471083 AATATATATT
* * *
471093 TAA TAA TAA TAA TAA AAA TGA TGA 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
471141 TAA TAA TA
1 TAA TAA TA
471149 TGGGTAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:471736 original size:113 final size:112
Alignment explanation
Indices: 471464--472239 Score: 1309
Period size: 113 Copynumber: 6.9 Consensus size: 112
471454 GATAGAATTA
* *
471464 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
471529 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAA-ATAATCCATCAA-GTGATGAATTCAGGTAAAAGG
*
471578 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
471643 CTTTCTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAA-ATAATCCATCAAGTGATGAATTCAGGTAAAAGG
*
471691 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
471756 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAA-AATAATCCATCAAGTGATGAATTCAGGTAAAAGG
471804 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
471869 CCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
471917 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
471982 CTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
472030 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
472095 CTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
472143 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* ** *
472208 CCTTCTCTGGAAATGTAAATCCATCAAATGAT
66 CTTTCTCTGGAAAAAT-AATCCATCAAGTGAT
472240 AGATTTGAAT
Statistics
Matches: 633, Mismatches: 26, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
112 4 0.01
113 539 0.85
114 90 0.14
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGG
Found at i:472448 original size:23 final size:23
Alignment explanation
Indices: 472404--472448 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
472394 AATTGTAAAA
* *
472404 AAAACAATAGATCTTTCTTCTTC
1 AAAACAATAGATCTATCATCTTC
472427 AAAACAA-AGAATCTATCATCTT
1 AAAACAATAG-ATCTATCATCTT
472449 TGACAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAACAATAGATCTATCATCTTC
Found at i:473112 original size:83 final size:83
Alignment explanation
Indices: 472973--473264 Score: 530
Period size: 83 Copynumber: 3.5 Consensus size: 83
472963 GTTCCTACCA
*
472973 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
473038 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCT
*
473056 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
473121 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCT
* *
473139 AACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
* *
473204 CAATGATTGGTTCTGCCA
66 CAATGATTGGTTCTGTCT
473222 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
473265 TGAGTCTCTT
Statistics
Matches: 201, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 201 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
CAATGATTGGTTCTGTCT
Found at i:474410 original size:6 final size:6
Alignment explanation
Indices: 474399--474471 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
474389 TTGACCCCCC
*
474399 CTTTTT CTTTTTT CTTTTT -TTCTTT -TTCTTT C-TTTT GTTTTT CTTTTT
1 CTTTTT C-TTTTT CTTTTT CTT-TTT CTT-TTT CTTTTT CTTTTT CTTTTT
* *
474447 C-TTTT CTCTTT -TTTTT CCTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT
474472 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
5 14 0.25
6 35 0.64
7 6 0.11
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:474425 original size:21 final size:21
Alignment explanation
Indices: 474399--474471 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
474389 TTGACCCCCC
474399 CTTTTTCTTTTTTCTTTTTTT
1 CTTTTTCTTTTTTCTTTTTTT
*
474420 CTTTTTCTTTCTTT-TGTTTTT
1 CTTTTTCTTT-TTTCTTTTTTT
*
474441 CTTTTTCTTTTCTCTTTTTTTT
1 CTTTTTCTTTTTTC-TTTTTTT
*
474463 CCTTTTCTT
1 CTTTTTCTT
474472 CAAGCATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 2 0.04
21 26 0.58
22 17 0.38
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (21 bp):
CTTTTTCTTTTTTCTTTTTTT
Found at i:474443 original size:11 final size:10
Alignment explanation
Indices: 474399--474468 Score: 70
Period size: 11 Copynumber: 6.5 Consensus size: 10
474389 TTGACCCCCC
474399 CTTTTTCTTTT
1 CTTTTT-TTTT
474410 -TTCTTTTTTT
1 CTT-TTTTTTT
*
474420 CTTTTTCTTT
1 CTTTTTTTTT
474430 CTTTTGTTTTT
1 CTTTT-TTTTT
474441 CTTTTTCTTTT
1 CTTTTT-TTTT
474452 CTCTTTTTTTT
1 CT-TTTTTTTT
474463 CCTTTT
1 -CTTTT
474469 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
10 18 0.35
11 27 0.53
12 6 0.12
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:485161 original size:28 final size:28
Alignment explanation
Indices: 485127--485197 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
485117 AAAATGAAAC
485127 ATATAAATATTATGAAA-ATAATAAATAA
1 ATATAAATATTATGAAAGATAA-AAATAA
* * *
485155 ATATAAAAATTTTGAAAAGATAAAATTAA
1 ATATAAATATTATG-AAAGATAAAAATAA
485184 AT-TAAATA-TATGAA
1 ATATAAATATTATGAA
485198 TTTTTAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 3 0.08
28 17 0.47
29 10 0.28
30 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (28 bp):
ATATAAATATTATGAAAGATAAAAATAA
Found at i:485162 original size:18 final size:19
Alignment explanation
Indices: 485084--485164 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 19
485074 TCTAACAGAC
*
485084 AAATAATGAAATAAAATAATTGC
1 AAATAAT-AAAT-AAAT-A-TGA
485107 AAATAA-AAATAAA-ATGA
1 AAATAATAAATAAATATGA
*
485124 AACAT-ATAAAT-ATTATGA
1 AA-ATAATAAATAAATATGA
*
485142 AAATAATAAATAAATATAA
1 AAATAATAAATAAATATGA
485161 AAAT
1 AAAT
485165 TTTGAAAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
17 8 0.16
18 19 0.39
19 9 0.18
20 3 0.06
21 4 0.08
23 6 0.12
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATAATAAATAAATATGA
Found at i:487321 original size:3 final size:3
Alignment explanation
Indices: 487313--487389 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
487303 AATATATATT
*
487313 TAA TAA TAA TAA TAA TGA 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
487361 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
487390 TGGGTAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:492232 original size:4 final size:4
Alignment explanation
Indices: 492223--492348 Score: 108
Period size: 4 Copynumber: 31.5 Consensus size: 4
492213 AAATTAAAGA
* * * *
492223 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT TTGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
492271 ATAT GTAT GTAT ATAT ATGT ATGT ATGT ATAT ATGT ATGT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
492319 ATGT ATGT ATAT ATAT GTAT GTAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
492349 GTATGTATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 108 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (4 bp):
ATAT
Found at i:492284 original size:32 final size:32
Alignment explanation
Indices: 492234--492360 Score: 199
Period size: 32 Copynumber: 4.1 Consensus size: 32
492224 TATATATATA
* * *
492234 TATATATATATATATATATATATGTTTGTATG
1 TATATATATGTATGTATATATATGTATGTATG
492266 TATATATATGTATGTATATATATGTATGTATG
1 TATATATATGTATGTATATATATGTATGTATG
492298 --TATATATGTATG--TATATATGTATGTATG
1 TATATATATGTATGTATATATATGTATGTATG
492326 TATATATATGTATGTATATATATGTATGTATG
1 TATATATATGTATGTATATATATGTATGTATG
492358 TAT
1 TAT
492361 GGAGGAAAAT
Statistics
Matches: 88, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
28 16 0.18
30 24 0.27
32 48 0.55
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (32 bp):
TATATATATGTATGTATATATATGTATGTATG
Found at i:492353 original size:4 final size:4
Alignment explanation
Indices: 492254--492361 Score: 97
Period size: 4 Copynumber: 29.0 Consensus size: 4
492244 TATATATATA
* * *
492254 TATG TTTG TATG TA-- TATA TATG TATG TA-- TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
492298 TATA TATG TATG TATA TATG TATG TATG TA-- TATA TATG TATG TA--
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
492342 TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG
492362 GAGGAAAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
2 8 0.09
4 78 0.91
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:492353 original size:14 final size:14
Alignment explanation
Indices: 492224--492356 Score: 176
Period size: 14 Copynumber: 9.2 Consensus size: 14
492214 AATTAAAGAA
* *
492224 TATATATATATATA
1 TATATATATGTATG
* *
492238 TATATATATATATA
1 TATATATATGTATG
* *
492252 TATATGTTTGTATG
1 TATATATATGTATG
492266 TATATATATGTATG
1 TATATATATGTATG
492280 TATATATATGTATG
1 TATATATATGTATG
492294 TATGTATATATGTATG
1 TA--TATATATGTATG
492310 TATATATGTATGTATG
1 TATATA--TATGTATG
492326 TATATATATGTATG
1 TATATATATGTATG
492340 TATATATATGTATG
1 TATATATATGTATG
492354 TAT
1 TAT
492357 GTATGGAGGA
Statistics
Matches: 109, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
14 81 0.74
16 28 0.26
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:492353 original size:18 final size:18
Alignment explanation
Indices: 492230--492360 Score: 145
Period size: 18 Copynumber: 7.2 Consensus size: 18
492220 AGAATATATA
* * *
492230 TATATATATATATATATA
1 TATATATATGTATGTATG
*
492248 TATATATATGTTTGTATG
1 TATATATATGTATGTATG
*
492266 TATATATATGTATGTATA
1 TATATATATGTATGTATG
* *
492284 TATATGTATGTATGTATA
1 TATATATATGTATGTATG
* *
492302 TATGTATGTATATATGTATG
1 TA--TATATATGTATGTATG
* *
492322 TATGTATATATATGTATG
1 TATATATATGTATGTATG
492340 TATATATATGTATGTATG
1 TATATATATGTATGTATG
492358 TAT
1 TAT
492361 GGAGGAAAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
18 82 0.84
20 16 0.16
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
TATATATATGTATGTATG
Found at i:495647 original size:42 final size:42
Alignment explanation
Indices: 495601--495733 Score: 205
Period size: 42 Copynumber: 3.2 Consensus size: 42
495591 CCGAAATCTC
*
495601 GTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTTTCC-
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATA-TTTTCCA
* * *
495643 GTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTCCT
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCA
*
495685 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCA
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCA
495727 GTGTTTG
1 GTGTTTG
495734 GTTGAAGGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 6 0.07
42 77 0.93
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCA
Found at i:495992 original size:26 final size:24
Alignment explanation
Indices: 495930--495992 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
495920 CAATTTAATC
495930 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
495954 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
495977 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
495993 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:495994 original size:22 final size:23
Alignment explanation
Indices: 495964--496010 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
495954 AAAATATATT
495964 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
495987 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
496009 TA
1 TA
496011 AAATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:496034 original size:23 final size:23
Alignment explanation
Indices: 496004--496048 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
495994 TTTTTAATAT
* *
496004 TATAATAAAATTATAAATTATAG
1 TATAATAAAATAAGAAATTATAG
*
496027 TATAATAATATAAGAAATTATA
1 TATAATAAAATAAGAAATTATA
496049 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TATAATAAAATAAGAAATTATAG
Found at i:496584 original size:14 final size:14
Alignment explanation
Indices: 496565--496620 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
496555 TCAGAAATGT
496565 AATTCATTTTCCAG
1 AATTCATTTTCCAG
*
496579 AATTCAATTTT-TAG
1 AATTC-ATTTTCCAG
*
496593 TAATTCATTTTCCAA
1 -AATTCATTTTCCAG
*
496608 AATTCAATTTCCA
1 AATTCATTTTCCA
496621 TAAAACCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.45
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:499424 original size:2 final size:2
Alignment explanation
Indices: 499417--499445 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
499407 ACAGTTAGGA
499417 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 A
499446 GAAAGAGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:502367 original size:35 final size:35
Alignment explanation
Indices: 502318--502406 Score: 162
Period size: 35 Copynumber: 2.5 Consensus size: 35
502308 AAATAATTAC
502318 TAAATATATC-ATTTTAAAATGTGTTAGTAAAATAA
1 TAAATA-ATCAATTTTAAAATGTGTTAGTAAAATAA
502353 TAAATAATCAATTTTAAAATGTGTTAGTAAAATAA
1 TAAATAATCAATTTTAAAATGTGTTAGTAAAATAA
502388 TAAATAATCAATTTTAAAA
1 TAAATAATCAATTTTAAAA
502407 AGTAACATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 3 0.06
35 50 0.94
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (35 bp):
TAAATAATCAATTTTAAAATGTGTTAGTAAAATAA
Found at i:504303 original size:22 final size:22
Alignment explanation
Indices: 504269--504336 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
504259 CATATATAGT
* *
504269 ATACAGAGATCCTTCGGGACAA
1 ATACATAGGTCCTTCGGGACAA
* *
504291 ATACATAGGTCCTTCGAGACAG
1 ATACATAGGTCCTTCGGGACAA
* *
504313 ATACATAGGTCTTTCGGGATAA
1 ATACATAGGTCCTTCGGGACAA
504335 AT
1 AT
504337 TTCACATGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
ATACATAGGTCCTTCGGGACAA
Found at i:519315 original size:16 final size:16
Alignment explanation
Indices: 519291--519365 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
519281 AACTGGTATT
519291 ACCTGACCTGTTTTCA
1 ACCTGACCTGTTTTCA
* * *
519307 ACCTAACCTGTTATGA
1 ACCTGACCTGTTTTCA
519323 ACCTGACCTGTTTTCA
1 ACCTGACCTGTTTTCA
* * * *
519339 ACTTGACATGTTATGA
1 ACCTGACCTGTTTTCA
519355 ACCTGACCTGT
1 ACCTGACCTGT
519366 AATTGGCTCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (16 bp):
ACCTGACCTGTTTTCA
Found at i:519332 original size:32 final size:32
Alignment explanation
Indices: 519291--519365 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
519281 AACTGGTATT
*
519291 ACCTGACCTGTTTTCAACCTAACCTGTTATGA
1 ACCTGACCTGTTTTCAACCTAACATGTTATGA
* *
519323 ACCTGACCTGTTTTCAACTTGACATGTTATGA
1 ACCTGACCTGTTTTCAACCTAACATGTTATGA
519355 ACCTGACCTGT
1 ACCTGACCTGT
519366 AATTGGCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (32 bp):
ACCTGACCTGTTTTCAACCTAACATGTTATGA
Found at i:519499 original size:17 final size:17
Alignment explanation
Indices: 519477--519517 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
519467 TATAATAAAC
519477 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
519494 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
519511 ATATGAT
1 TTATGAT
519518 TATTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:519545 original size:51 final size:52
Alignment explanation
Indices: 519487--519584 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 52
519477 TTATGATAAT
519487 TAAATTATTATGATAATTAAATTAATATGATTA-TTTTTTGAAATTTTATCA
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTTTATCA
519538 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTT
519585 AGTTTTATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 33 0.72
52 13 0.28
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (52 bp):
TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTTTATCA
Found at i:519558 original size:68 final size:67
Alignment explanation
Indices: 519439--519568 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 67
519429 GTGAAGTTAC
* * *
519439 AATTAATATAATTATGTTATTTTAAATTTATAATAAACTTATGATAATTAAATTATTATGATAAT
1 AATTAATATAATTATGTTATTTGAAATTTATAATAAAATTATGATAATTAAATTAATATGATAAT
519504 TA
66 TA
* *
519506 AATTAATATGATTAT-TT-TTTGAAATTTTATCATAAATTATTATGATAATTAAATTAATATGAT
1 AATTAATATAATTATGTTATTTGAAA-TTTATAATAAA--ATTATGATAATTAAATTAATATGAT
519569 TACTTTTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
65 6 0.11
66 12 0.22
67 14 0.25
68 23 0.42
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (67 bp):
AATTAATATAATTATGTTATTTGAAATTTATAATAAAATTATGATAATTAAATTAATATGATAAT
TA
Found at i:522807 original size:64 final size:64
Alignment explanation
Indices: 522754--522916 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
522744 CGGTGCACCA
***
522754 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCAAAGTGCATCGATGCATGG
** * *
522818 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAAAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATGCAAAGTGCATCGATGCATGG
* * *
522883 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
522917 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 31 0.37
65 51 0.61
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCAAAGTGCATCGATGCATGG
Found at i:522890 original size:19 final size:18
Alignment explanation
Indices: 522865--522914 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
522855 AAAATATTCA
522865 AAGTGCATCGATGCATGG
1 AAGTGCATCGATGCATGG
*
522883 AGAGTGCATCGGTGCATGG
1 A-AGTGCATCGATGCATGG
522902 AA-TGCATTCGATG
1 AAGTGCA-TCGATG
522915 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 17 0.61
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
AAGTGCATCGATGCATGG
Found at i:523148 original size:20 final size:21
Alignment explanation
Indices: 523125--523164 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
523115 GAATCGAATA
523125 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
523145 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
523165 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:529264 original size:19 final size:19
Alignment explanation
Indices: 529240--529290 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
529230 GAAAATATTC
529240 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
529259 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
529278 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
529291 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:529532 original size:20 final size:21
Alignment explanation
Indices: 529509--529548 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
529499 GAATCGAATA
529509 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
529529 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
529549 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:529627 original size:21 final size:21
Alignment explanation
Indices: 529601--529660 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
529591 AATTATATAT
529601 TATAATT-ATAATTAATATTAA
1 TATAATTAAT-ATTAATATTAA
*
529622 TATAATTAATTTTAATATTAA
1 TATAATTAATATTAATATTAA
529643 -ATTATATTAATA-TAATAT
1 TA-TA-ATTAATATTAATAT
529661 AGTTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAATTAATATTAATATTAA
Found at i:529717 original size:31 final size:30
Alignment explanation
Indices: 529675--529859 Score: 108
Period size: 31 Copynumber: 5.8 Consensus size: 30
529665 TATAATTTGT
*
529675 AATTAAAATTAATATAAAATATAGTATATAA
1 AATTAATATTAATATAAAATATAGT-TATAA
*
529706 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAAATATA-GTTATAA
* * *
529736 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTT-ATAA
* *
529772 AATTACTATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAAATATAG-TTATAA
*
529801 ACATTATACTATATTAATATAAATTATAGTTA-AGA
1 A-A-T-TA--ATATTAATATAAAATATAGTTATA-A
* *
529836 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAAATATA
529860 TAGTACATTA
Statistics
Matches: 124, Mismatches: 12, Indels: 36
0.72 0.07 0.21
Matches are distributed among these distances:
29 10 0.08
30 9 0.07
31 47 0.38
32 5 0.04
33 6 0.05
34 15 0.12
35 20 0.16
36 12 0.10
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATAGTTATAA
Found at i:529755 original size:14 final size:14
Alignment explanation
Indices: 529738--529799 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
529728 ATGTTATAAA
529738 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
529752 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
529766 TAATATAATTACTA-T
1 TTATAT-AGTA-TAGT
*
529781 TAATATAGTATAGT
1 TTATATAGTATAGT
529795 TTATA
1 TTATA
529800 AACATTATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:529807 original size:66 final size:63
Alignment explanation
Indices: 529682--529852 Score: 154
Period size: 66 Copynumber: 2.6 Consensus size: 63
529672 TGTAATTAAA
* *
529682 ATTAATATAAAATATAG-TATATAAAATTAATATTAATATAAACTATATGTTATAAATTATA-TA
1 ATTAATATAAAATATAGTTA-ATATAATTACTATTAATAT--ACTATATGTTATAAATTATACTA
529745 GT
63 -T
* * *
529747 A-TAGTTTATAAACTATAGTTAATATAATTACTATTAATATAGTATA-GTTTATAAACATTATAC
1 ATTA--ATATAAAATATAGTTAATATAATTACTATTAATATACTATATG-TTAT-AA-ATTATAC
529810 TAT
61 TAT
* *
529813 ATTAATATAAATTATAGTTAAGATAATTAAC-ATTAATATA
1 ATTAATATAAAATATAGTTAATATAATT-ACTATTAATATA
529853 AACTATATAG
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
63 1 0.01
64 11 0.12
65 33 0.37
66 38 0.43
67 6 0.07
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (63 bp):
ATTAATATAAAATATAGTTAATATAATTACTATTAATATACTATATGTTATAAATTATACTAT
Found at i:529899 original size:21 final size:21
Alignment explanation
Indices: 529874--529924 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
529864 ACATTAAGAT
*
529874 AACTATAGT-TTATAAATTATA
1 AACTATA-TATTATAAAGTATA
*
529895 TACTATATATTATAAAGTATA
1 AACTATATATTATAAAGTATA
529916 AACTATATA
1 AACTATATA
529925 GTACACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (21 bp):
AACTATATATTATAAAGTATA
Found at i:529927 original size:14 final size:14
Alignment explanation
Indices: 529884--529927 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
529874 AACTATAGTT
*
529884 TATAAATTATATAC
1 TATAAATTATATAG
* *
529898 TATATATTATAAAG
1 TATAAATTATATAG
*
529912 TATAAACTATATAG
1 TATAAATTATATAG
529926 TA
1 TA
529928 CACTAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
TATAAATTATATAG
Found at i:529998 original size:60 final size:60
Alignment explanation
Indices: 529934--530049 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
529924 AGTACACTAA
* *
529934 TATACATACATGTACTATAAGTTACATATATAGTTTACATTTATACATATACTATAAGTT
1 TATACATACAAGTACTATAAGTTACATATATAGTTTACATATATACATATACTATAAGTT
529994 TATACATACAAGTACTATAAGTTACATATATAGTTTACATATATACATATACTATA
1 TATACATACAAGTACTATAAGTTACATATATAGTTTACATATATACATATACTATA
530050 GGTTACTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (60 bp):
TATACATACAAGTACTATAAGTTACATATATAGTTTACATATATACATATACTATAAGTT
Found at i:530230 original size:21 final size:21
Alignment explanation
Indices: 530192--530231 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
530182 TAAACTATAG
* *
530192 TTTAGGGTTTATGATTTATGA
1 TTTAAGGTTTAGGATTTATGA
*
530213 TTTAAGGTTTAGGGTTTAT
1 TTTAAGGTTTAGGATTTAT
530232 ATAAAACTAT
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:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (21 bp):
TTTAAGGTTTAGGATTTATGA
Found at i:530488 original size:2 final size:2
Alignment explanation
Indices: 530477--530521 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
530467 TTAGTGTTTC
530477 TA TA -A 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
530518 TA TA
1 TA TA
530522 ATTTATAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:530620 original size:4 final size:4
Alignment explanation
Indices: 530611--530698 Score: 68
Period size: 4 Copynumber: 22.0 Consensus size: 4
530601 TTATATAGTT
* * * * * * * * * *
530611 CACA CACA CACG CACG CACG CACG CACG CACG CACG CACG CACA GACC
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* *
530659 CACA CCCA CACA CACC CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
530699 TAGAAAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 74 1.00
ACGTcount: A:0.38, C:0.52, G:0.10, T:0.00
Consensus pattern (4 bp):
CACA
Found at i:530667 original size:6 final size:6
Alignment explanation
Indices: 530659--530698 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
530649 CGCACAGACC
* *
530659 CACACC CACACA CACCCA CACACA CACACA CACACA CACA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACA
530699 TAGAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.45, C:0.55, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACA
Found at i:530670 original size:16 final size:16
Alignment explanation
Indices: 530611--530698 Score: 77
Period size: 16 Copynumber: 5.5 Consensus size: 16
530601 TTATATAGTT
* *
530611 CACACACACACGCACG
1 CACACACACACACACC
* * * *
530627 CACGCACGCACGCACG
1 CACACACACACACACC
* * *
530643 CACGCACGCACAGACC
1 CACACACACACACACC
*
530659 CACACCCACACACACC
1 CACACACACACACACC
*
530675 CACACACACACACACA
1 CACACACACACACACC
530691 CACACACA
1 CACACACA
530699 TAGAAAATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.38, C:0.52, G:0.10, T:0.00
Consensus pattern (16 bp):
CACACACACACACACC
Found at i:530674 original size:10 final size:10
Alignment explanation
Indices: 530611--530698 Score: 68
Period size: 10 Copynumber: 8.8 Consensus size: 10
530601 TTATATAGTT
530611 CACACACACA
1 CACACACACA
* * *
530621 CGCACGCACG
1 CACACACACA
* *
530631 CACGCACGCA
1 CACACACACA
* * *
530641 CGCACGCACG
1 CACACACACA
* *
530651 CACAGACCCA
1 CACACACACA
*
530661 CACCCACACA
1 CACACACACA
*
530671 CACCCACACA
1 CACACACACA
530681 CACACACACA
1 CACACACACA
530691 CACACACA
1 CACACACA
530699 TAGAAAATTA
Statistics
Matches: 56, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
10 56 1.00
ACGTcount: A:0.38, C:0.52, G:0.10, T:0.00
Consensus pattern (10 bp):
CACACACACA
Found at i:530938 original size:19 final size:19
Alignment explanation
Indices: 530887--530948 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
530877 ATAAAATCTC
*
530887 AATTCTCAATTTCCCTCCA
1 AATTCTCAATTTCCCTCTA
* * *
530906 TATTTTTCTA-TTCCCTCTA
1 -AATTCTCAATTTCCCTCTA
530925 AATTCTCAATTTCCCTCTA
1 AATTCTCAATTTCCCTCTA
530944 AATTC
1 AATTC
530949 CCAAATAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:531031 original size:2 final size:2
Alignment explanation
Indices: 531024--531050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
531014 CTCACTTTGA
531024 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 A
531051 AATTATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:531131 original size:13 final size:13
Alignment explanation
Indices: 531079--531180 Score: 69
Period size: 13 Copynumber: 7.2 Consensus size: 13
531069 ATATACTTTT
531079 TATAGTTTATACATA
1 TATAGTTTAT--ATA
* *
531094 TATAGTTTACAAA
1 TATAGTTTATATA
531107 TATAGTTTATATA
1 TATAGTTTATATA
*
531120 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
531135 CATAATTTATATA
1 TATAGTTTATATA
*
531148 TATAACTTATAATAATTA
1 TAT-AGTT-T-AT-A-TA
531166 TATAGTTTATATA
1 TATAGTTTATATA
531179 TA
1 TA
531181 AACTTATATT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
13 31 0.45
14 4 0.06
15 22 0.32
16 3 0.04
17 4 0.06
18 5 0.07
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:531143 original size:28 final size:26
Alignment explanation
Indices: 531091--531151 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 26
531081 TAGTTTATAC
* *
531091 ATATATAGTTTACAAATATAGTTTAT
1 ATATATAGTTTACAAACATAATTTAT
*
531117 ATATATAGTTCATATAAACATAATTTAT
1 ATATATAGTT--TACAAACATAATTTAT
531145 ATATATA
1 ATATATA
531152 ACTTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
28 20 0.67
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATATAGTTTACAAACATAATTTAT
Found at i:544154 original size:30 final size:30
Alignment explanation
Indices: 544118--544174 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
544108 AAGTTAGGGG
* *
544118 GATAAACTTTAACTTATAATATTTTAAGTC
1 GATAAACTTGAACTTATAAAATTTTAAGTC
544148 GATAAACTTGAACTTATAAAATTTTAA
1 GATAAACTTGAACTTATAAAATTTTAA
544175 AGAACGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (30 bp):
GATAAACTTGAACTTATAAAATTTTAAGTC
Found at i:544219 original size:17 final size:17
Alignment explanation
Indices: 544199--544232 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
544189 TTTTCAATAA
544199 AAAATACATAAAAATTT
1 AAAATACATAAAAATTT
* *
544216 AAAATATATAATAATTT
1 AAAATACATAAAAATTT
544233 TATATTTTTA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATACATAAAAATTT
Found at i:545478 original size:20 final size:21
Alignment explanation
Indices: 545445--545483 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
545435 AAATAAAGGG
545445 TAAATTATATG-TTTAGTATT
1 TAAATTATATGTTTTAGTATT
545465 TAAATTAT-TAGTTTTAGTA
1 TAAATTATAT-GTTTTAGTA
545484 ACTAAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 9 0.53
21 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (21 bp):
TAAATTATATGTTTTAGTATT
Found at i:545890 original size:14 final size:14
Alignment explanation
Indices: 545871--545900 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
545861 TAGTTGAGTG
*
545871 ATTTATTCATAAAA
1 ATTTATCCATAAAA
545885 ATTTATCCATAAAA
1 ATTTATCCATAAAA
545899 AT
1 AT
545901 GTACCACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTATCCATAAAA
Found at i:549272 original size:26 final size:26
Alignment explanation
Indices: 549236--549289 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
549226 TGGGTGCATG
549236 GGATGGGGATGCATGTGAAGAATTCC
1 GGATGGGGATGCATGTGAAGAATTCC
549262 GGATGGGGATGCATGTGAAGAATTCC
1 GGATGGGGATGCATGTGAAGAATTCC
549288 GG
1 GG
549290 CAAATACAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.41, T:0.22
Consensus pattern (26 bp):
GGATGGGGATGCATGTGAAGAATTCC
Found at i:549875 original size:22 final size:21
Alignment explanation
Indices: 549833--549888 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
549823 TTTGATTTTT
*
549833 TTTAAAATATAATTAATTTAAA
1 TTTAAAATATAA-AAATTTAAA
549855 TTTAAAATATAAAAATATTAAA
1 TTTAAAATATAAAAAT-TTAAA
549877 --T-AAATATAAAAA
1 TTTAAAATATAAAAA
549889 CACCAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 11 0.34
20 1 0.03
21 3 0.09
22 17 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAATATAAAAATTTAAA
Found at i:560009 original size:17 final size:17
Alignment explanation
Indices: 559983--560015 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
559973 TTACCGGATT
559983 AAAAACCGGTTTTTTTA
1 AAAAACCGGTTTTTTTA
*
560000 AAAAATCGGTTTTTTT
1 AAAAACCGGTTTTTTT
560016 TCAAACCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAAACCGGTTTTTTTA
Found at i:560159 original size:22 final size:22
Alignment explanation
Indices: 560119--560160 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
560109 AGTGAAAAAA
* **
560119 CCGGATCGGTTTTTTATCCGAT
1 CCGGATCGGATTTAAATCCGAT
560141 CCGGATCGGATTTAAATCCG
1 CCGGATCGGATTTAAATCCG
560161 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (22 bp):
CCGGATCGGATTTAAATCCGAT
Found at i:569741 original size:17 final size:18
Alignment explanation
Indices: 569702--569748 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
569692 TGTTTATGAG
569702 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
569720 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
569737 GGAATTGGAATC
1 GGAATTGAAATC
569749 CAATTCTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:570585 original size:256 final size:252
Alignment explanation
Indices: 570119--570658 Score: 745
Period size: 256 Copynumber: 2.1 Consensus size: 252
570109 ACATGACACA
* *
570119 AAATAATGAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTGGAAAAAAATTATATATA
1 AAATAAT-AAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTGGAAAAAAATTATATATA
570184 GAAGGGTATTATTGTAATTATTCCTAAACATATAAAGTAAAATTATATACTTTTTTCGGGTCGGT
65 GAAGGGTATTATTGTAATTATTCCTAAACATATAAAGTAAAATTATATACTTTTTTCGGGTCGG-
* * * *
570249 CCGGTTTTTTTTCACCCTAAACCCGAATTCGACCCGACCCGAATATCACACTTAAAAAACCCGAC
129 -CAGTTATTTTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAACCCGAC
*
570314 CCGAACAAAATAAAGTTTCACCCGACCCGATCCGAATATATGAATTAGAAATCCGACCCGACCCG
193 CCGAACAAAATAAAGTTTCACCCGA--C---CCGAATATATGAATTAGAAACCCGACCCGACCCG
* *
570379 AAATAATAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATT-G-AAAATA-TATATATAT
1 AAATAATAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTGGAAAAAAATTATATATAG
* * *
570441 ATGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TATTTTT-GGGTC-G-
66 AAGGGTATTATTGTAATTATTCCTAAACATATAAAGTAAAATTATATACT-TTTTTCGGGTCGGC
* *
570502 AG-TATTTTTCACCCTAAACTCGAACTCAACCCGACCCTAATATCACACTTAAAAAAAACCGACC
130 AGTTATTTTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTT---AAAAA---ACC
*
570566 CGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCG
189 CGACCCGAACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCG
*
570630 AAATAATAAAAAAATATTTTTATTCAATA
1 AAATAATAAAAAATTATTTTTATTCAATA
570659 TATAAATAAA
Statistics
Matches: 257, Mismatches: 16, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
250 43 0.17
251 62 0.24
253 5 0.02
254 2 0.01
255 6 0.02
256 89 0.35
257 5 0.02
258 1 0.00
259 37 0.14
260 7 0.03
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (252 bp):
AAATAATAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTGGAAAAAAATTATATATAG
AAGGGTATTATTGTAATTATTCCTAAACATATAAAGTAAAATTATATACTTTTTTCGGGTCGGCA
GTTATTTTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAACCCGACCCG
AACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCG
Found at i:577892 original size:53 final size:51
Alignment explanation
Indices: 577834--577944 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 51
577824 AAAAATTGTA
*
577834 TAAAATTTAAATTTTTTATCATTGACACAGAGACAGAGTGCAACATGATTAGT
1 TAAAATTTAAAATTTTTATCATTGACACAGAGAC--AGTGCAACATGATTAGT
577887 TAAAATTTAAAATTTTTATCATTGACACAGAGACAGTGCAACATGATTAGT
1 TAAAATTTAAAATTTTTATCATTGACACAGAGACAGTGCAACATGATTAGT
577938 TAAAATT
1 TAAAATT
577945 GCTTACGGGC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 24 0.42
53 33 0.58
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (51 bp):
TAAAATTTAAAATTTTTATCATTGACACAGAGACAGTGCAACATGATTAGT
Found at i:582973 original size:24 final size:24
Alignment explanation
Indices: 582942--582992 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 24
582932 ACTTTATTTG
582942 AAAAATTAT-ATTAAACTTAGTAA
1 AAAAATTATAATTAAACTTAGTAA
582965 AAAATATTATACAATTAAACTTAGTAA
1 AAAA-ATTAT--AATTAAACTTAGTAA
582992 A
1 A
582993 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
24 5 0.21
27 15 0.62
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAAATTATAATTAAACTTAGTAA
Found at i:583622 original size:30 final size:29
Alignment explanation
Indices: 583582--583665 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 29
583572 TCAATAAAGT
583582 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAATTATAAAATA-TTATTAAATTTA
* *
583612 TTAAAGATTATAAAATATTAATAAATTTA
1 TTAAAAATTATAAAATATTATTAAATTTA
* *
583641 TCTAAATACTATAAAATAATTATTA
1 T-TAAAAATTATAAAAT-ATTATTA
583666 TATTATCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 12 0.26
30 29 0.62
31 6 0.13
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:583631 original size:10 final size:10
Alignment explanation
Indices: 583583--583663 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 10
583573 CAATAAAGTT
583583 TAAAA-ATTA
1 TAAAATATTA
583592 TAAAATACTTA
1 TAAAATA-TTA
*
583603 TTAAAT-TTA
1 TAAAATATTA
* *
583612 TTAAAGATTA
1 TAAAATATTA
583622 TAAAATATTA
1 TAAAATATTA
583632 -ATAAAT-TTA
1 TA-AAATATTA
* *
583641 TCTAAATACTA
1 T-AAAATATTA
583652 TAAAATAATTA
1 TAAAAT-ATTA
583663 T
1 T
583664 TATATTATCG
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
9 17 0.30
10 24 0.43
11 15 0.27
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (10 bp):
TAAAATATTA
Done.