Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 142 of 204
Found at i:42848063 original size:3 final size:3
Alignment explanation
Indices: 42848055--42848099 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
42848045 TCAAGAACAA
42848055 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42848100 GAAAAGACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42849083 original size:19 final size:21
Alignment explanation
Indices: 42849048--42849144 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
42849038 AATCATATAT
42849048 TCTAAGATTGAATATATCATA
1 TCTAAGATTGAATATATCATA
42849069 TCTAAGATTGAATATATCATA
1 TCTAAGATTGAATATATCATA
*
42849090 TCTAAGAATGAATATATCATA
1 TCTAAGATTGAATATATCATA
*
42849111 TCTAAGATTG--CATATCATA
1 TCTAAGATTGAATATATCATA
*
42849130 TCTAAGATTGCATAT
1 TCTAAGATTGAATAT
42849145 CCTTGAAGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.26
21 52 0.74
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (21 bp):
TCTAAGATTGAATATATCATA
Found at i:42863957 original size:25 final size:25
Alignment explanation
Indices: 42863923--42863975 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
42863913 TCAACAAAGC
42863923 ACAAAGGTTTACCAAAATCTATTTA
1 ACAAAGGTTTACCAAAATCTATTTA
42863948 ACAAAGGTTTACCAAAATCTATTTA
1 ACAAAGGTTTACCAAAATCTATTTA
42863973 ACA
1 ACA
42863976 TAAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (25 bp):
ACAAAGGTTTACCAAAATCTATTTA
Found at i:42864995 original size:21 final size:22
Alignment explanation
Indices: 42864971--42865018 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
42864961 GAAGATGAGG
42864971 AAAAGG-AAAGGAG-AGAGAAAA
1 AAAAGGAAAAGGAGAAG-GAAAA
42864992 AAAAGGAAAAAGGAGAAGGAAAA
1 AAAAGG-AAAAGGAGAAGGAAAA
42865015 AAAA
1 AAAA
42865019 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.25
23 16 0.67
24 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAAGGAAAAGGAGAAGGAAAA
Found at i:42865024 original size:23 final size:23
Alignment explanation
Indices: 42864977--42865025 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
42864967 GAGGAAAAGG
*
42864977 AAAGGAGAGAGAAAAAAAAGGAA
1 AAAGGAGAGAGAAAAAAAAGAAA
*
42865000 AAAGGAGA-AGGAAAAAAAATAAA
1 AAAGGAGAGA-GAAAAAAAAGAAA
42865023 AAA
1 AAA
42865026 TAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (23 bp):
AAAGGAGAGAGAAAAAAAAGAAA
Found at i:42874316 original size:20 final size:20
Alignment explanation
Indices: 42874291--42874330 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42874281 TTGTACGGGA
* *
42874291 TCGCACTTCGGTGTCTCTGT
1 TCGCACTTCAGTGCCTCTGT
42874311 TCGCACTTCAGTGCCTCTGT
1 TCGCACTTCAGTGCCTCTGT
42874331 ATTTGCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.33, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCACTTCAGTGCCTCTGT
Found at i:42886409 original size:22 final size:22
Alignment explanation
Indices: 42886376--42886418 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42886366 ATATTTGTTC
42886376 AATTCTAATTTGAATTCTTGGT
1 AATTCTAATTTGAATTCTTGGT
*
42886398 AATT-TAAGTTTGATTTCTTGG
1 AATTCTAA-TTTGAATTCTTGG
42886419 ACATAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (22 bp):
AATTCTAATTTGAATTCTTGGT
Found at i:42896187 original size:41 final size:41
Alignment explanation
Indices: 42896130--42896210 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
42896120 GACAAGTCTG
*
42896130 TGCAAGATTGAAGAAATGAAAAAGATGGTAGAAGAATTGGT
1 TGCAAGATTGAAGAAATGAAAAAGATGATAGAAGAATTGGT
*
42896171 TGCAAGATTGAAGAAATGAAAAAGATTATAGAAGAATTGG
1 TGCAAGATTGAAGAAATGAAAAAGATGATAGAAGAATTGG
42896211 AGTACGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.22
Consensus pattern (41 bp):
TGCAAGATTGAAGAAATGAAAAAGATGATAGAAGAATTGGT
Found at i:42905434 original size:38 final size:38
Alignment explanation
Indices: 42905383--42905503 Score: 161
Period size: 38 Copynumber: 3.0 Consensus size: 38
42905373 CTTATCTCCC
42905383 TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
1 TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
42905421 TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
1 TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
* * *
42905459 TCTCCCTGAGATTACAGCGAAGCAGATTGTAGCTAGTAATCCTA
1 ------TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
42905503 T
1 T
42905504 TTCCCTGAGA
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
38 39 0.53
44 35 0.47
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (38 bp):
TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTA
Found at i:42905484 original size:44 final size:44
Alignment explanation
Indices: 42905370--42905530 Score: 226
Period size: 44 Copynumber: 3.8 Consensus size: 44
42905360 GAAGATGGTG
*
42905370 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
42905414 AATCCTA------TGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
* * *
42905452 AATCCTATCTCCCTGAGATTACAGCGAAGCAGATTGTAGCTAGT
1 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
* *
42905496 AATCCTATTTCCCTGAGATTACAGTGGAGCAGATT
1 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATT
42905531 AAAATAAAGG
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
38 38 0.37
44 66 0.63
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
Found at i:42905698 original size:301 final size:301
Alignment explanation
Indices: 42905151--42905722 Score: 912
Period size: 301 Copynumber: 1.9 Consensus size: 301
42905141 AAAGATGGTG
* * *
42905151 AATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCCAGTAATCCTATTTCTCTGAGATTA
1 AATCCTATCTCCCTGAGATTACAGCGAAGCAAATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
* * *
42905216 CAATGGAGCGGATTAAAATTAAGGATCTTATCTCTCTAAAGTTATAGTAGAGTAGATCGCATCAG
66 CAATGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
* * * * * * *
42905281 GTCTTATTTCCCTAAGATTACAGTGGAATACACCGAAGAGTTCCAGATCTTGTTTCCCTGAGCAA
131 GTCTTATCTCCCTAAGATTACAGTGGAATACAACGAAGAATTCCAAATCTTATCTCCCTAAGCAA
* *
42905346 TAGCGAAGCAGATCGAAGATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCC
196 TAGCGAAGCAGATCAAAAATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCC
42905411 AGTAATCCTATGAGATTACAGCGGAGCAGATTGAAGCCAGT
261 AGTAATCCTATGAGATTACAGCGGAGCAGATTGAAGCCAGT
* * *
42905452 AATCCTATCTCCCTGAGATTACAGCGAAGCAGATTGTAGCTAGTAATCCTATTTCCCTGAGATTA
1 AATCCTATCTCCCTGAGATTACAGCGAAGCAAATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
* *
42905517 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAATGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
* *
42905582 GTCTTATCTCCCTGAGATTACAGTGGAATAGAACGAAGAATTCCAAATCTTATCTCCCTAAGCAA
131 GTCTTATCTCCCTAAGATTACAGTGGAATACAACGAAGAATTCCAAATCTTATCTCCCTAAGCAA
* *
42905647 TAGTGGAGCTA-ATCAAAAATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC
196 TAGCGAAGC-AGATCAAAAATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC
42905711 CAGTAATCCTAT
260 CAGTAATCCTAT
42905723 TTCCCTGAAA
Statistics
Matches: 246, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
301 245 1.00
302 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (301 bp):
AATCCTATCTCCCTGAGATTACAGCGAAGCAAATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
CAATGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTAAGATTACAGTGGAATACAACGAAGAATTCCAAATCTTATCTCCCTAAGCAA
TAGCGAAGCAGATCAAAAATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCC
AGTAATCCTATGAGATTACAGCGGAGCAGATTGAAGCCAGT
Found at i:42905901 original size:219 final size:219
Alignment explanation
Indices: 42905421--42905924 Score: 726
Period size: 219 Copynumber: 2.3 Consensus size: 219
42905411 AGTAATCCTA
* *
42905421 TGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGCGAAGCAGAT
1 TGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAGAT
* * * *
42905486 TGTAGCTAGTAATCCTATTTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTC
66 TGAAGCCAGTAATCCTATTTCCCTGAAATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTC
*
42905551 TCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGAAC
131 TCTGAAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGAAC
*
42905616 GAAGAATTCCAAATCTTATCTCCC
196 GAAGAATTCCAAATCTTATCGCCC
* * * ** ** * *
42905640 TAAGCA--ATAGTGGAGCTA-ATCAAAAATGGTGAATCTTATCTCCCTGAGATTACAGCGGAGCA
1 TGAG-ATTACAGCGGAGC-AGATTGAAGCTAGT-AATCCTATCTCCCTGAGATTACAGCGGAGCA
42905702 GATTGAAGCCAGTAATCCTATTTCCCTGAAATTACAGTGGAACAGATTAAAATAAAGGATCTTAT
63 GATTGAAGCCAGTAATCCTATTTCCCTGAAATTACAGTGGAACAGATTAAAATAAAGGATCTTAT
* *
42905767 CTCTCTGAAGTTACAATAGATTAGATCGCGTCAGGTCTTATCTCCCTGAGATTACAGTGGAATAG
128 CTCTCTGAAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAG
* * *
42905832 ACCGAAGAATTTCAGATCTTATCGCCC
193 AACGAAGAATTCCAAATCTTATCGCCC
* * * *
42905859 TGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGAT
1 TGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAGAT
42905924 T
66 T
42905925 AAAATAAAGG
Statistics
Matches: 244, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
218 15 0.06
219 214 0.88
220 15 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (219 bp):
TGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAGAT
TGAAGCCAGTAATCCTATTTCCCTGAAATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTC
TCTGAAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGAAC
GAAGAATTCCAAATCTTATCGCCC
Found at i:42907984 original size:17 final size:19
Alignment explanation
Indices: 42907964--42907998 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42907954 ATTTTAATAT
42907964 ATGTA-TAT-ATTTATAAA
1 ATGTATTATAATTTATAAA
42907981 ATGTATTATAATTTATAA
1 ATGTATTATAATTTATAA
42907999 TTTATACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (19 bp):
ATGTATTATAATTTATAAA
Found at i:42910964 original size:20 final size:20
Alignment explanation
Indices: 42910923--42910971 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
42910913 ATATACATAT
*
42910923 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
42910942 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
42910962 ATATCAATAA
1 ATATAAATAA
42910972 GGCTAGTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:42912645 original size:128 final size:128
Alignment explanation
Indices: 42912427--42912699 Score: 415
Period size: 128 Copynumber: 2.1 Consensus size: 128
42912417 ATAAGATTTA
* **
42912427 TGGCTTAAATCTGTTTCCCTACTCTTGAAGATAAGATTCGTTATCTCCGATCTGCTCCGCTACTG
1 TGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCATCTCCGATCTGCTCCGCTACTG
* * *
42912492 CTTAGGGAGATAAGATCTGTGATTTCCAACCTATTCCACTGTTGACC-AGGTAGATAGGACT-T
66 CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAAGG-AGATAGGACTAT
* * *
42912554 GTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACT
1 -TGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCATCTCCGATCTGCTCCGCTACT
42912619 GCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAAGGAGATAGGACTAT
65 GCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAAGGAGATAGGACTAT
**
42912683 TGGCTTCGATCTGCTTC
1 TGGCTTAAATCTGCTTC
42912700 ACTGTCGATG
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
128 128 0.97
129 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
TGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCATCTCCGATCTGCTCCGCTACTG
CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAAGGAGATAGGACTAT
Found at i:42912804 original size:88 final size:88
Alignment explanation
Indices: 42912686--42913385 Score: 990
Period size: 88 Copynumber: 8.0 Consensus size: 88
42912676 GGACTATTGG
* * * *
42912686 CTTCGATCTGCTTCACTGTCGATGCAGGAAGACAAGACCTGCTATCTTCAATCTGCTCCATTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
42912751 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
** * * *
42912774 CTTCGATCTGCTTCGTTGTAGATGCAGGAAGGCAAGATCTGCTTTCTTCAACCTACTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
42912839 ACCGAGGAAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * *
42912862 CTTCAATCTGCCTCACTATCGATGCAGGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
42912927 ACCAAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
42912950 CTTCGATCTGCTTCACTGTC-AGTACAGGAAGGCAAGATCTGCTATCTTCAACTTGCTCCACTAC
1 CTTCGATCTGCTTCACTGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
42913014 AACCGAAGGAGGCAAGGCTTGTGT
65 AACCGAGGGAGGCAAGGCTTGTGT
* * *
42913038 CTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGACCTGCTATCTTCAACCTGCTCCACTACG
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
42913103 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * * *
42913126 CTTCAATCTGCTTCACTGTCGATGCAGGAAGGTAAGGTCTACTATCTTCAACCTGCTCCACTACG
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
42913191 ACCAAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
42913214 CTTCAATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTTCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
* * *
42913279 ACCAATGGAGGTAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * * * * ** *
42913302 CTTCGATCTGCTTC-GTCATCAATGCAGAAATGCCAGATCTATTATCTTCAATCTGCTCCACTAC
1 CTTCGATCTGCTTCACT-GTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
42913366 AATCGAGGGAGGCAAGGCTT
65 AACCGAGGGAGGCAAGGCTT
42913386 TGTGATTTCA
Statistics
Matches: 545, Mismatches: 64, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
87 2 0.00
88 542 0.99
89 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCGAGGGAGGCAAGGCTTGTGT
Found at i:42912847 original size:44 final size:44
Alignment explanation
Indices: 42912799--42913281 Score: 228
Period size: 44 Copynumber: 11.0 Consensus size: 44
42912789 TTGTAGATGC
* *
42912799 AGGAAGGCAAGATCTGCTTTCTTCAACCTACTCCACTACAACCG
1 AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
* * * * *
42912843 AGGAAGGCAAG-GCTTG-TGTCTTCAATCTGC-CTCACTATCGA-TG
1 AGGAAGGCAAGATC-TGCTATCTTCAACCTGCTC-CACTA-CAACCG
* *
42912886 CAGGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTACAACCA
1 -AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
* * * * * * *
42912931 AGGGAGGCAAG-GCTTG-TGTCTTCGATCTGCTTCACTGTCAGTA-C-
1 AGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACT-ACA--ACCG
*
42912975 AGGAAGGCAAGATCTGCTATCTTCAACTTGCTCCACTACAACCG
1 AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
* * * * * * * * *
42913019 AAGG-AGGCAAG-GCTTG-TGTCTTCGATCTGCTTCGCTGTCGA-TG
1 -AGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACT-ACAACCG
* *
42913062 CAGGAAGGCAAGACCTGCTATCTTCAACCTGCTCCACTACGACCG
1 -AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
* * * * * * * *
42913107 AGGGAGGCAAG-GCTTG-TGTCTTCAATCTGCTTCACTGTCGA-TG
1 AGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACT-ACAACCG
* * * * *
42913150 CAGGAAGGTAAGGTCTACTATCTTCAACCTGCTCCACTACGACCA
1 -AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
* * * * * * * *
42913195 AGGGAGGCAAG-GCTTG-TGTCTTCAATCTGCTTCACTGTCGA-TG
1 AGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACT-ACAACCG
*
42913238 CAGGAAGGCAAGATCTGCTATCTTCAACCTTCTCCACTACAACC
1 -AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
42913282 AATGGAGGTA
Statistics
Matches: 320, Mismatches: 84, Indels: 69
0.68 0.18 0.15
Matches are distributed among these distances:
42 2 0.01
43 92 0.29
44 134 0.42
45 90 0.28
46 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (44 bp):
AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCG
Found at i:42915547 original size:7 final size:7
Alignment explanation
Indices: 42915535--42915582 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
42915525 TAACCTCTCC
42915535 TTTTTCT
1 TTTTTCT
42915542 TTTTTCT
1 TTTTTCT
42915549 TTTTTCT
1 TTTTTCT
42915556 TTTTTCT
1 TTTTTCT
*
42915563 TTTTTTT
1 TTTTTCT
42915570 ATTTTTCAT
1 -TTTTTC-T
42915579 TTTT
1 TTTT
42915583 GATTTGGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 27 0.73
8 9 0.24
9 1 0.03
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:42919649 original size:500 final size:500
Alignment explanation
Indices: 42918708--42919654 Score: 1894
Period size: 500 Copynumber: 1.9 Consensus size: 500
42918698 TGTTTGGCTC
42918708 TAAAGTCAAGGTACCCGAACCAGCAGATTCCTCGTTCTTCACCCATTATAGGCTTATACAGACCA
1 TAAAGTCAAGGTACCCGAACCAGCAGATTCCTCGTTCTTCACCCATTATAGGCTTATACAGACCA
42918773 AGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAATCTCACGAAGACATAG
66 AGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAATCTCACGAAGACATAG
42918838 GTACGAATGTATTCTGAAAGTGATCCACTATCCTGCACAGAGGTGAAAACCTCACGAAGGAGTAG
131 GTACGAATGTATTCTGAAAGTGATCCACTATCCTGCACAGAGGTGAAAACCTCACGAAGGAGTAG
42918903 CTTCTCACTCCCACTTAAAAGGGTAAGACTAAGCAGTCTTTATGCAATATGATGCCAAGATATAA
196 CTTCTCACTCCCACTTAAAAGGGTAAGACTAAGCAGTCTTTATGCAATATGATGCCAAGATATAA
42918968 AATTTAATTTACAGTAATCATTCAAACAAATACGAAGGGAGGATCATAATTTTTCAAATCAAATT
261 AATTTAATTTACAGTAATCATTCAAACAAATACGAAGGGAGGATCATAATTTTTCAAATCAAATT
42919033 TTCAATTTTCGACAATAAGACAAAAAATAATCAATTTTACGGCCTGACTCTCTAAAGGTCCCTAG
326 TTCAATTTTCGACAATAAGACAAAAAATAATCAATTTTACGGCCTGACTCTCTAAAGGTCCCTAG
42919098 TGGAGTCGTCAAGCTCTCGAAACCACCATTTTGAAAAACAAAAATTTAGTAGTCGACTTATTAAA
391 TGGAGTCGTCAAGCTCTCGAAACCACCATTTTGAAAAACAAAAATTTAGTAGTCGACTTATTAAA
42919163 AATGAAAATTGAAGTCGCCACCAATCTTTTATTGAGAAAATAGGT
456 AATGAAAATTGAAGTCGCCACCAATCTTTTATTGAGAAAATAGGT
42919208 TAAAGTCAAGGTACCCGAACCAGCAGATTCCTCGTTCTTCACCCATTATAGGCTTATACAGACCA
1 TAAAGTCAAGGTACCCGAACCAGCAGATTCCTCGTTCTTCACCCATTATAGGCTTATACAGACCA
42919273 AGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAATCTCACGAAGACATAG
66 AGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAATCTCACGAAGACATAG
42919338 GTACGAATGTATTCTGAAAGTGATCCACTATCCTGCACAGAGGTGAAAACCTCACGAAGGAGTAG
131 GTACGAATGTATTCTGAAAGTGATCCACTATCCTGCACAGAGGTGAAAACCTCACGAAGGAGTAG
42919403 CTTCTCACTCCCACTTAAAAGGGTAAGACTAAGCAGTCTTTATGCAATATGATGCCAAGATATAA
196 CTTCTCACTCCCACTTAAAAGGGTAAGACTAAGCAGTCTTTATGCAATATGATGCCAAGATATAA
42919468 AATTTAATTTACAGTAATCATTCAAACAAATACGAAGGGAGGATCATAATTTTTCAAATCAAATT
261 AATTTAATTTACAGTAATCATTCAAACAAATACGAAGGGAGGATCATAATTTTTCAAATCAAATT
42919533 TTCAATTTTCGACAATAAGACAAAAAATAATCAATTTTACGGCCTGACTCTCTAAAGGTCCCTAG
326 TTCAATTTTCGACAATAAGACAAAAAATAATCAATTTTACGGCCTGACTCTCTAAAGGTCCCTAG
42919598 TGGAGTCGTCAAGCTCTCGAAACCACCATTTTGAAAAACAAAAATTTAGTAGTCGAC
391 TGGAGTCGTCAAGCTCTCGAAACCACCATTTTGAAAAACAAAAATTTAGTAGTCGAC
42919655 GTCTGCGAAT
Statistics
Matches: 447, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
500 447 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (500 bp):
TAAAGTCAAGGTACCCGAACCAGCAGATTCCTCGTTCTTCACCCATTATAGGCTTATACAGACCA
AGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAATCTCACGAAGACATAG
GTACGAATGTATTCTGAAAGTGATCCACTATCCTGCACAGAGGTGAAAACCTCACGAAGGAGTAG
CTTCTCACTCCCACTTAAAAGGGTAAGACTAAGCAGTCTTTATGCAATATGATGCCAAGATATAA
AATTTAATTTACAGTAATCATTCAAACAAATACGAAGGGAGGATCATAATTTTTCAAATCAAATT
TTCAATTTTCGACAATAAGACAAAAAATAATCAATTTTACGGCCTGACTCTCTAAAGGTCCCTAG
TGGAGTCGTCAAGCTCTCGAAACCACCATTTTGAAAAACAAAAATTTAGTAGTCGACTTATTAAA
AATGAAAATTGAAGTCGCCACCAATCTTTTATTGAGAAAATAGGT
Found at i:42920762 original size:40 final size:40
Alignment explanation
Indices: 42920673--42920768 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 40
42920663 GCGTTTGGAT
** * *
42920673 GAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTCTA
1 GAAAACGCCGCTAAA-AAAGAGCATTAGCAGCGATTTTCTA
*
42920714 -AAAACGCCGCTAAAAAAGAGCATTAGCAGC-ATTTTTTA
1 GAAAACGCCGCTAAAAAAGAGCATTAGCAGCGATTTTCTA
42920752 GAAAAGCGCCGC-AAAAA
1 GAAAA-CGCCGCTAAAAA
42920769 CCTAAGCCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
38 6 0.12
39 22 0.46
40 20 0.42
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (40 bp):
GAAAACGCCGCTAAAAAAGAGCATTAGCAGCGATTTTCTA
Found at i:42920856 original size:41 final size:41
Alignment explanation
Indices: 42920799--42920993 Score: 264
Period size: 41 Copynumber: 4.7 Consensus size: 41
42920789 ACCTTTCGGG
* * * *
42920799 GCTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGTTTAGA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* *
42920840 GCTTTAGCGGCGTTTTTGGAGAATCGCCGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* * *
42920881 GCTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATTCTTAGA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
*
42920922 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATACTCAGA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* **
42920963 TCTTTAGCGGCGTTTTTTAAAAAAGCGCCGC
1 GCTTTAGCGGCG-TTTTTGGAAAAGCGCCGC
42920994 AAAAACATTT
Statistics
Matches: 136, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 120 0.88
42 16 0.12
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
Found at i:42920936 original size:82 final size:82
Alignment explanation
Indices: 42920799--42920993 Score: 293
Period size: 82 Copynumber: 2.4 Consensus size: 82
42920789 ACCTTTCGGG
* * *
42920799 GCTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGTTTAGAGCTTTAGCGGCGTTTTTGGAGAAT
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGTTTAGAGCTTTAGCGGCGTTTTTGGAAAAG
*
42920864 CGCCGCTAATGCTCAGA
66 CGCCGCTAATACTCAGA
* *
42920881 GCTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAAT-TCTTAGAGCTTTAGCGGCGTTTTTGGAAAA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGT-TTAGAGCTTTAGCGGCGTTTTTGGAAAA
42920945 GCGCCGCTAATACTCAGA
65 GCGCCGCTAATACTCAGA
* *
42920963 TCTTTAGCGGCGTTTTTTAAAAAAGCGCCGC
1 GCTTTAGCGGCG-TTTTTGAAAAAGCGCCGC
42920994 AAAAACATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 85 0.84
83 15 0.15
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (82 bp):
GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGTTTAGAGCTTTAGCGGCGTTTTTGGAAAAG
CGCCGCTAATACTCAGA
Found at i:42921166 original size:35 final size:35
Alignment explanation
Indices: 42921125--42921196 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
42921115 TAATTTGTTT
42921125 ATTTATAAAAAAACATAGAAAAATATTTGTTAAAA
1 ATTTATAAAAAAACATAGAAAAATATTTGTTAAAA
42921160 ATTTATAAAAAAACATAGAAAAATATTTGTTAAAA
1 ATTTATAAAAAAACATAGAAAAATATTTGTTAAAA
42921195 AT
1 AT
42921197 GGAAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.32
Consensus pattern (35 bp):
ATTTATAAAAAAACATAGAAAAATATTTGTTAAAA
Found at i:42921371 original size:14 final size:14
Alignment explanation
Indices: 42921352--42921400 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
42921342 CATTATAGTT
* *
42921352 TATGGTTTAATATA
1 TATGGTTTAGTGTA
*
42921366 TATGGTTTAGGGTA
1 TATGGTTTAGTGTA
42921380 TATGGTTTAGTGTA
1 TATGGTTTAGTGTA
42921394 TATGGTT
1 TATGGTT
42921401 AATTTAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGTGTA
Found at i:42921626 original size:7 final size:7
Alignment explanation
Indices: 42921614--42921672 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
42921604 TAAATAATGT
42921614 TTAGGGG
1 TTAGGGG
42921621 TTAGGGG
1 TTAGGGG
42921628 TTAGGGG
1 TTAGGGG
* **
42921635 CTAGTAG
1 TTAGGGG
42921642 TTAGGGG
1 TTAGGGG
42921649 TTAGGGG
1 TTAGGGG
42921656 TTAGGGG
1 TTAGGGG
*
42921663 TTAGAGG
1 TTAGGGG
42921670 TTA
1 TTA
42921673 AGAGTTAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.19, C:0.02, G:0.49, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:42922475 original size:22 final size:22
Alignment explanation
Indices: 42922432--42922476 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42922422 TTATTCCAAA
* *
42922432 TGAAATATTTTTACGGCGTTTT
1 TGAAATATTTTTACGACATTTT
42922454 TGAAATATTTTTACGACATTTT
1 TGAAATATTTTTACGACATTTT
42922476 T
1 T
42922477 ATGAAAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (22 bp):
TGAAATATTTTTACGACATTTT
Found at i:42924734 original size:18 final size:18
Alignment explanation
Indices: 42924711--42924746 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42924701 TATTTTTCAT
*
42924711 TTGCTTCAATTTCTATGC
1 TTGCTTCAATTTCCATGC
42924729 TTGCTTCAATTTCCATGC
1 TTGCTTCAATTTCCATGC
42924747 CTTACAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (18 bp):
TTGCTTCAATTTCCATGC
Found at i:42926681 original size:43 final size:42
Alignment explanation
Indices: 42926612--42926818 Score: 168
Period size: 43 Copynumber: 4.9 Consensus size: 42
42926602 AAGTCATGTT
* *
42926612 TTTAGCGGCGTTTGT-GAAAAAGCGTCGCTAAAGGTCAT-TC
1 TTTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATATC
* *** **
42926652 TTCATAGTGCCGTTTGTGGTTGAAGCGTCGAAAAAGGTCATGATC
1 TT--TAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGTCAT-ATC
* *
42926697 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGTCAT-ATC
* * * ** * *
42926740 TTCAGCGGCATTTGTGGGAAAAGAATCACTAAAGGTC-TCTGCC
1 TTTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATAT--C
* *
42926783 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
1 TTTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGT
42926819 AAAAAAAACG
Statistics
Matches: 132, Mismatches: 28, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
40 2 0.02
41 1 0.01
42 12 0.09
43 113 0.86
45 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (42 bp):
TTTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATATC
Found at i:42926756 original size:86 final size:84
Alignment explanation
Indices: 42926600--42926818 Score: 230
Period size: 86 Copynumber: 2.6 Consensus size: 84
42926590 AATTTTTTTT
* * * *
42926600 AAAA-GTCATGTTTTTAGCGGCGTTTGT-GAAAAAGCGTCGCTAAAGGTCATTCTTCATAGTGCC
1 AAAAGGTCATGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATTCTTCA-AGCGCC
* *** **
42926663 GTTTGTGGTTGAAGCGTCGA-
65 ATTTGTGGGAAAAGAATC-AC
42926683 AAAAGGTCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTC-AGCG
1 AAAAGGTCATG-TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT--TCTTCAAGCG
*
42926747 GCATTTGTGGGAAAAGAATCAC
63 CCATTTGTGGGAAAAGAATCAC
* * *
42926769 TAAAGGTCTCTGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
1 AAAAGGTC-ATGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
42926819 AAAAAAAACG
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
83 4 0.03
84 6 0.05
85 17 0.15
86 81 0.70
87 2 0.02
88 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (84 bp):
AAAAGGTCATGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATTCTTCAAGCGCCA
TTTGTGGGAAAAGAATCAC
Found at i:42927083 original size:20 final size:20
Alignment explanation
Indices: 42927042--42927090 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
42927032 ATATACATAT
*
42927042 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
42927061 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
42927081 ATATCAATAA
1 ATATAAATAA
42927091 GGCTAGTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:42929710 original size:20 final size:20
Alignment explanation
Indices: 42929685--42929731 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
42929675 CAATTAAGTG
42929685 CTTTTATTGGATTTTCAAAA
1 CTTTTATTGGATTTTCAAAA
*
42929705 CTTTTATTGGATTTTCAAAT
1 CTTTTATTGGATTTTCAAAA
42929725 CTTTTAT
1 CTTTTAT
42929732 CTAATAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (20 bp):
CTTTTATTGGATTTTCAAAA
Found at i:42932550 original size:37 final size:37
Alignment explanation
Indices: 42932506--42932585 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
42932496 CCTTCTATTG
42932506 ATTTTTTTTGAATTTTAAAAAA-TATATA-ATTTTTAT
1 ATTTTTTTTGAATTTTAAAAAATTATATATA-TTTTAT
* *
42932542 ATGTTTTTTTGAATTTTGAAAAGTTATATATATTTTAT
1 AT-TTTTTTTGAATTTTAAAAAATTATATATATTTTAT
42932580 ATTTTT
1 ATTTTT
42932586 AAAAAAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 2 0.05
37 22 0.56
38 14 0.36
39 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (37 bp):
ATTTTTTTTGAATTTTAAAAAATTATATATATTTTAT
Found at i:42932654 original size:25 final size:26
Alignment explanation
Indices: 42932596--42932655 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
42932586 AAAAAAATTG
**
42932596 TTATAAATTTTATGTAGTTTTTTAAT
1 TTATAAATTTTACCTAGTTTTTTAAT
* *
42932622 TTAAAAATTTTACCTA-TTTTTTATT
1 TTATAAATTTTACCTAGTTTTTTAAT
*
42932647 TTTTAAATT
1 TTATAAATT
42932656 ATAATTTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (26 bp):
TTATAAATTTTACCTAGTTTTTTAAT
Found at i:42933982 original size:29 final size:29
Alignment explanation
Indices: 42933950--42934027 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
42933940 ATGTTTAATA
*
42933950 TGGTACTTCTACTTTGAAAATATCCAATG
1 TGGTACTTCTAATTTGAAAATATCCAATG
* * *
42933979 TGGTACTTGTAATTTGGAAATGTCCAATG
1 TGGTACTTCTAATTTGAAAATATCCAATG
* *
42934008 TAGTACTTGTAATTTAGAAA
1 TGGTACTTCTAATTT-GAAA
42934028 TGTTCAATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 39 0.93
30 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (29 bp):
TGGTACTTCTAATTTGAAAATATCCAATG
Found at i:42934028 original size:29 final size:29
Alignment explanation
Indices: 42933967--42934037 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
42933957 TCTACTTTGA
* * *
42933967 AAATATCCAATGTGGTACTTGTAATTTGG
1 AAATGTCCAATGTAGTACTTGTAATTTAG
42933996 AAATGTCCAATGTAGTACTTGTAATTTAG
1 AAATGTCCAATGTAGTACTTGTAATTTAG
*
42934025 AAATGTTCAATGT
1 AAATGTCCAATGT
42934038 GATAACTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (29 bp):
AAATGTCCAATGTAGTACTTGTAATTTAG
Found at i:42946061 original size:6 final size:6
Alignment explanation
Indices: 42946050--42946094 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
42946040 CACAAGTTTT
* *
42946050 AGCCTC AGCCTC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGC
1 AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGC
42946095 AGTAGTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.60, G:0.18, T:0.04
Consensus pattern (6 bp):
AGCCCC
Found at i:42959469 original size:40 final size:40
Alignment explanation
Indices: 42959418--42959552 Score: 193
Period size: 40 Copynumber: 3.4 Consensus size: 40
42959408 GTTTGGACAA
*
42959418 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATG
* *
42959458 AAAAGCGCCGCTAAAGATCGAGCATTAGCGGCGTTTTAAG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATG
* * *
42959498 GAAAGCGCCGCTAAAAAT-TAGTATTAGCGGCGTTTTATG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATG
*
42959537 AAATGCGCCGC-AAAAA
1 AAAAGCGCCGCTAAAAA
42959553 CCTAAGCCCA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 5 0.06
39 27 0.32
40 53 0.62
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATG
Found at i:42959647 original size:41 final size:41
Alignment explanation
Indices: 42959592--42959742 Score: 232
Period size: 41 Copynumber: 3.7 Consensus size: 41
42959582 CTTTCGGGGC
* * *
42959592 TTTAGCAGCGTTTTT-GAGAAAGCGCCGCTAATGCTCAGCGC
1 TTTAGCGGCGTTTTTGGA-AAAGCGCCGCTAATGCTCAGGGA
*
42959633 TTTAACGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGA
*
42959674 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTTAGGGA
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGA
*
42959715 TTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGC
42959743 AAAAACATTT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 100 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGGA
Found at i:42961405 original size:23 final size:21
Alignment explanation
Indices: 42961363--42961405 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42961353 CCCTTCCCTC
*
42961363 CAAAACCCAAATTCCTTCAAG
1 CAAAACCCAAACTCCTTCAAG
42961384 CAAAACCCAAACCCTCCTTCAA
1 CAAAACCCAAA--CTCCTTCAA
42961406 ATTATCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAAACCCAAACTCCTTCAAG
Found at i:42964698 original size:43 final size:43
Alignment explanation
Indices: 42964607--42964890 Score: 295
Period size: 43 Copynumber: 6.7 Consensus size: 43
42964597 TATTTTTAGT
* * * * **
42964607 GGCGTTTTTGTGAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * * *
42964649 GGCGTTTATGGGAAAAGTGTCGCTAAAGGTATCGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * * * *
42964692 GACGTTTGTGGAAAAAGTGCGGCTAAAGGT-TGTGACCTACAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGAGCTATAGC
* * *
42964735 GGCGTTTGTGGGAAAAGCGCCGCCAAAGCTCTTGAGCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * *
42964778 GGCGTTTCTGGGAAAAGCGCCGCTAAATGTCTTGATCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *
42964821 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
42964864 GGCGTTTTTGGG-AAAGCGCCGCTAAAG
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAG
42964891 TTAGCGACGC
Statistics
Matches: 202, Mismatches: 37, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
42 42 0.21
43 159 0.79
44 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
Found at i:42964876 original size:129 final size:128
Alignment explanation
Indices: 42964607--42964890 Score: 329
Period size: 129 Copynumber: 2.2 Consensus size: 128
42964597 TATTTTTAGT
* * * * ** * *
42964607 GGCGTTTTTGTGAGAAGCGTCGCTAAAGGTTTGTTCTATAGCGGCGTTTATGGGAAAAGTGTCGC
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAGCTTTGAGCTATAGCGGCGTTTATGGGAAAAGCGCCGC
* * *
42964672 TAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGTGCGGCTAAAGGTTGTGACCTACAGC
66 TAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGCGCCGCTAAAGGTTGCGACCTACAGC
* * * *
42964735 GGCGTTTGTGGGAAAAGCGCCGCCAAAGCTCTTGAGCTATAGTGGCGTTTCTGGGAAAAGCGCCG
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAGCT-TTGAGCTATAGCGGCGTTTATGGGAAAAGCGCCG
* * * * * * * *
42964800 CTAAATGTCTTGATCTATAGTGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCT-CGAGCTATAGC
65 CTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGCGCCGCTAAAGGT-TGCGACCTACAGC
42964864 GGCGTTTTTGGG-AAAGCGCCGCTAAAG
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAG
42964891 TTAGCGACGC
Statistics
Matches: 129, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
128 38 0.29
129 90 0.70
130 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (128 bp):
GGCGTTTTTGGGAAAAGCGCCGCTAAAGCTTTGAGCTATAGCGGCGTTTATGGGAAAAGCGCCGC
TAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGCGCCGCTAAAGGTTGCGACCTACAGC
Found at i:42964997 original size:22 final size:21
Alignment explanation
Indices: 42964961--42965004 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
42964951 TTAGCGGTGA
* *
42964961 TAAAAAACGCTGCTAAAGGCC
1 TAAAAAACGCCGCTAAAAGCC
42964982 TAAAAAAGCGCCGCTAAAAGCC
1 TAAAAAA-CGCCGCTAAAAGCC
42965004 T
1 T
42965005 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAGCC
Found at i:42967216 original size:34 final size:34
Alignment explanation
Indices: 42967154--42967218 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
42967144 TAATTCTTAT
* *
42967154 TGATACTGAAATGGGCTTAAGCCTAAACTGATAC
1 TGATACTGAAATAGGCTTAAGCCCAAACTGATAC
*
42967188 TGATACTGAAA-AGGCTTAGGCCCCAAACTGA
1 TGATACTGAAATAGGCTTAAG-CCCAAACTGA
42967219 GATTATCTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (34 bp):
TGATACTGAAATAGGCTTAAGCCCAAACTGATAC
Found at i:42967457 original size:55 final size:55
Alignment explanation
Indices: 42967391--42967506 Score: 205
Period size: 55 Copynumber: 2.1 Consensus size: 55
42967381 CTTAATTAAA
*
42967391 ATTTTGATTCTATTTTGGGGGTATTTTATTGTAATTATGGCCTCTTTGGATTTTT
1 ATTTTGATTCTATTTTAGGGGTATTTTATTGTAATTATGGCCTCTTTGGATTTTT
*
42967446 ATTTTGATTCTATTTTAGGGGTATTTTATTGTAATTATGGCTTCTTTGGATTTTT
1 ATTTTGATTCTATTTTAGGGGTATTTTATTGTAATTATGGCCTCTTTGGATTTTT
42967501 ACTTTT
1 A-TTTT
42967507 AATTTGGGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 54 0.93
56 4 0.07
ACGTcount: A:0.17, C:0.07, G:0.18, T:0.58
Consensus pattern (55 bp):
ATTTTGATTCTATTTTAGGGGTATTTTATTGTAATTATGGCCTCTTTGGATTTTT
Found at i:42967673 original size:18 final size:18
Alignment explanation
Indices: 42967638--42967675 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42967628 ACAATACGTG
*
42967638 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATAAATA
42967656 ACGTTTTGAAAGA-AAATA
1 ACGTTTTGAAA-ATAAATA
42967674 AC
1 AC
42967676 TGTTGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
ACGTTTTGAAAATAAATA
Found at i:42970890 original size:3 final size:3
Alignment explanation
Indices: 42970882--42970916 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
42970872 AAATATTTGG
*
42970882 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42970917 CAATATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:42972662 original size:44 final size:43
Alignment explanation
Indices: 42972612--42972723 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 43
42972602 AATCTGACCT
* * *
42972612 ACTGCAACTTCAGAGGTATAGGATTCATCA-TTTTAATCCGCTCC
1 ACTGCAACTTCAGAGG-ATAGGATTAAT-AGCTTCAATCCGCTCC
* *
42972656 ACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGAG-GATAGGATTAATAGCTTCAATCCGCTCC
*
42972700 GCTGCAACTTCAGAGAGATAGGAT
1 ACTGCAACTTCAGAG-GATAGGAT
42972724 CTGCTATCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 57 0.97
45 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (43 bp):
ACTGCAACTTCAGAGGATAGGATTAATAGCTTCAATCCGCTCC
Found at i:42973758 original size:29 final size:30
Alignment explanation
Indices: 42973721--42973777 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42973711 TCCGAGCCTT
*
42973721 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
42973750 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
42973778 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:42974008 original size:13 final size:13
Alignment explanation
Indices: 42973990--42974020 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42973980 TTCCAGAAAC
42973990 TATGAATTTATTT
1 TATGAATTTATTT
42974003 TATGAATTTATTT
1 TATGAATTTATTT
*
42974016 GATGA
1 TATGA
42974021 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:42974190 original size:50 final size:50
Alignment explanation
Indices: 42974115--42974224 Score: 220
Period size: 50 Copynumber: 2.2 Consensus size: 50
42974105 ATTTGGGTAA
42974115 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
42974165 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
42974215 AGAGGTCCCA
1 AGAGGTCCCA
42974225 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:42978151 original size:16 final size:16
Alignment explanation
Indices: 42978130--42978164 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42978120 CCTTTTAATG
* *
42978130 AAATGCCATGTAGTCA
1 AAATGCAATGCAGTCA
42978146 AAATGCAATGCAGTCA
1 AAATGCAATGCAGTCA
42978162 AAA
1 AAA
42978165 CAAAACAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATGCAATGCAGTCA
Found at i:42979263 original size:109 final size:109
Alignment explanation
Indices: 42979073--42979731 Score: 1090
Period size: 109 Copynumber: 6.1 Consensus size: 109
42979063 AAGATTTAGG
* * * *
42979073 AGGATATTTGGCTACTTGGTCGAACGAG--AAATCGAAACCTAGCACACTAAGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
42979136 AAATTTCCAAACGTAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
*
42979180 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
42979245 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
42979289 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCGGCATATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
42979354 AAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * * *
42979398 AGGATATTTGGCTATTTGGTTGAACAAGAAAAATCGAAACCCAGCATATTAGGGCACATTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
42979463 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * *
42979507 AGGATATTTGGCTATTTGGTTGGACGAGAAAAATCGAAACCCAGCACATTACGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
42979572 GAATTTCCAAACGCAAAACATTGCCTTATTTTCAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
42979616 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACG-TTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
42979680 GAATTTCCAAACGCAAAACATTGCTTTATTTTGAAATCTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
*
42979724 AGAATATT
1 AGGATATT
42979732 AGTATGCGTA
Statistics
Matches: 521, Mismatches: 29, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
107 27 0.05
108 54 0.10
109 440 0.84
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:42990714 original size:102 final size:102
Alignment explanation
Indices: 42990537--42990766 Score: 354
Period size: 102 Copynumber: 2.3 Consensus size: 102
42990527 GATGAACACA
* * **
42990537 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACATATATCGATAAATAATGAACACATGTGTAGTACTAAG
* *
42990602 TGAAGACTACTATGTGTACCGAGAAGTTTTGGTCACG
66 TGAAGACTACTATGTGTACCGAAAAGCTTTGGTCACG
* *
42990639 TGTGTAGTACTGTGTGAAGGCTACTACATATA-CAGATAAATGATGAACACATGTGTAGTACTAA
1 TGTGTAGTACTATGTGAAGGCTACTACATATATC-GATAAATAATGAACACATGTGTAGTACTAA
*
42990703 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
65 GTGAAGACTACTATGTGTACCGAAAAGCTTTGGTCACG
*
42990741 TGTGTAGTACTATGTGAAGCCTACTA
1 TGTGTAGTACTATGTGAAGGCTACTA
42990767 TGTGAAGGCT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 115 0.99
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTATGTGAAGGCTACTACATATATCGATAAATAATGAACACATGTGTAGTACTAAG
TGAAGACTACTATGTGTACCGAAAAGCTTTGGTCACG
Found at i:42990767 original size:51 final size:51
Alignment explanation
Indices: 42990533--42990770 Score: 255
Period size: 51 Copynumber: 4.7 Consensus size: 51
42990523 TATCGATGAA
* *
42990533 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATGGT
* * * * **
42990584 CACATGTGTAGTACTAAGTGAAGACTACTATGTGTACCGAGAAGTTTTGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATGGT
* * ** * * * **
42990635 CACGTGTGTAGTACTGTGTGAAGGCTACTACATATACAGATAAATGATGAA
1 CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATGGT
* *
42990686 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAA--TAATGGT
* *
42990737 CACGTGTGTAGTACTATGTGAAGCCTACTATGTG
1 CACATGTGTAGTACTATGTGAAGGCTACTATGTG
42990771 AAGGCTACTA
Statistics
Matches: 150, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
50 3 0.02
51 146 0.97
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATGGT
Found at i:42990788 original size:14 final size:14
Alignment explanation
Indices: 42990748--42990791 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
42990738 ACGTGTGTAG
*
42990748 TACTATGTGAAGCC
1 TACTATGTGAAGGC
42990762 TACTATGTGAAGGC
1 TACTATGTGAAGGC
42990776 TACTATGTGAAGGC
1 TACTATGTGAAGGC
42990790 TA
1 TA
42990792 TTACGTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (14 bp):
TACTATGTGAAGGC
Found at i:42995079 original size:5 final size:5
Alignment explanation
Indices: 42995069--42995096 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42995059 GTTAATTCTC
42995069 ATGAT ATGAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATG
42995097 GTCGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:42997220 original size:41 final size:41
Alignment explanation
Indices: 42997175--42997315 Score: 228
Period size: 41 Copynumber: 3.4 Consensus size: 41
42997165 TGATTCAATA
* * *
42997175 CACCGGCATTAAACCTGCTACACGTAAGGTCTAAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
* *
42997216 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
*
42997257 CACCAGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
42997298 CACCGGCATTAAGCCTGC
1 CACCGGCATTAAGCCTGC
42997316 AGGCACAAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
Found at i:42997266 original size:82 final size:81
Alignment explanation
Indices: 42997175--42997332 Score: 244
Period size: 82 Copynumber: 1.9 Consensus size: 81
42997165 TGATTCAATA
* *
42997175 CACCGGCATTAAACCTGCTACACGTAAGGTCTAAAATATTTCACCGGCATTAAGCCTGCTAGACA
1 CACCAGCATTAAACCTGCTACACGTAAAGTCTAAAATATTTCACCGGCATTAAGCCTGC-AGACA
* *
42997240 TAAAGTCTGAAATATTT
65 CAAAGCCTGAAATATTT
* * *
42997257 CACCAGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTTCACCGGCATTAAGCCTGCAGGCAC
1 CACCAGCATTAAACCTGCTACACGTAAAGTCTAAAATATTTCACCGGCATTAAGCCTGCAGACAC
42997322 AAAGCCTGAAA
66 AAAGCCTGAAA
42997333 ATCTCATATA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 14 0.20
82 55 0.80
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (81 bp):
CACCAGCATTAAACCTGCTACACGTAAAGTCTAAAATATTTCACCGGCATTAAGCCTGCAGACAC
AAAGCCTGAAATATTT
Found at i:42997334 original size:41 final size:42
Alignment explanation
Indices: 42997175--42997334 Score: 211
Period size: 41 Copynumber: 3.9 Consensus size: 42
42997165 TGATTCAATA
* * * *
42997175 CACCGGCATTAAACCTGCTACACGTAAGGTCT-AAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAAATATTT
42997216 CACCGGCATTAAGCCTGCTAGACATAAAGTCTG-AAATATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAAATATTT
* *
42997257 CACCAGCATTAAGCCTGCTAGACGTAAAGTCT-AAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAAATATTT
* * *
42997298 CACCGGCATTAAGCCTGC-AGGCACAAAGCCTGAAAAT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAAAT
42997335 CTCATATACA
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 9 0.09
41 96 0.91
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAAATATTT
Found at i:42997555 original size:65 final size:65
Alignment explanation
Indices: 42997483--42997606 Score: 189
Period size: 65 Copynumber: 1.9 Consensus size: 65
42997473 ACTTTAACTT
42997483 CAGCTCAA-AGAATTTGTAA-CTAATATTCAAACCACATATGTATATAAAATTCATACATTAAAA
1 CAGCTCAAGA-AATTTGTAACCT-ATATTCAAACCACATATGTATATAAAATTCATACATTAAAA
42997546 TC
64 TC
** *
42997548 CAGCTCAAGAAATTTGTAACCTATATTTGAACCACATATGTATATAAAATTTATACATT
1 CAGCTCAAGAAATTTGTAACCTATATTCAAACCACATATGTATATAAAATTCATACATT
42997607 GAATTCAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
65 51 0.94
66 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (65 bp):
CAGCTCAAGAAATTTGTAACCTATATTCAAACCACATATGTATATAAAATTCATACATTAAAATC
Found at i:43000544 original size:3 final size:3
Alignment explanation
Indices: 43000536--43000587 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
43000526 TAATATCTCC
*
43000536 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43000584 ATT A
1 ATT A
43000588 GTTGTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43003113 original size:15 final size:15
Alignment explanation
Indices: 43003093--43003122 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43003083 TCTCTAGGCA
*
43003093 TTCATTTCATGCATT
1 TTCATTACATGCATT
43003108 TTCATTACATGCATT
1 TTCATTACATGCATT
43003123 AAAGTCCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCATTACATGCATT
Found at i:43005620 original size:7 final size:7
Alignment explanation
Indices: 43005608--43005659 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
43005598 CAAAAAAATG
43005608 TGAAAAA
1 TGAAAAA
43005615 TGAAAAA
1 TGAAAAA
43005622 TGAAAACA
1 TGAAAA-A
*
43005630 --AAGAA
1 TGAAAAA
43005635 TGAAAAA
1 TGAAAAA
43005642 TGAAAAA
1 TGAAAAA
43005649 -GTAAAAA
1 TG-AAAAA
43005656 TGAA
1 TGAA
43005660 GAGGCTAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 31 0.82
8 2 0.05
ACGTcount: A:0.69, C:0.02, G:0.15, T:0.13
Consensus pattern (7 bp):
TGAAAAA
Found at i:43007209 original size:50 final size:50
Alignment explanation
Indices: 43007151--43007509 Score: 274
Period size: 50 Copynumber: 7.2 Consensus size: 50
43007141 GCAGTGGAAC
* * * * * *
43007151 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTACAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * ** *
43007201 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAA
* * * *
43007251 AGATTAACGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** * ** *
43007301 AGATTAAAGCTACCACAGCGAATCTTACTT-CTCAAGCGGTGTAGTGGAAT
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGA-CATTGCAGTTAAAA
* * *
43007351 AGATTAACGCCACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** * ** *
43007401 AGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** *
43007451 AGATTGAAGCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
43007501 AGATTAAAG
1 AGATTAAAG
43007510 TTACGAGTTA
Statistics
Matches: 231, Mismatches: 72, Indels: 12
0.73 0.23 0.04
Matches are distributed among these distances:
49 8 0.03
50 214 0.93
51 9 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:43007296 original size:100 final size:100
Alignment explanation
Indices: 43007140--43007509 Score: 526
Period size: 100 Copynumber: 3.7 Consensus size: 100
43007130 CCCCTGAGGT
* * * *
43007140 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTACAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGAT
* *
43007205 TAAAGCTACAACAGCGAATCTTACTCCCCAGGCGA
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
* *
43007240 TGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGAT
* * *
43007305 TAAAGCTACCACAGCGAATCTTACTTCTCAAGCGG
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
* * * * *
43007340 TGTAGTGGAATAGATTAACGCCACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGAT
43007405 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
* * * * * *
43007440 TGTAGTGGAACAGATTGAA-GCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAACAGA
1 TGCAGTGGAACAGATT-AACGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGA
43007504 TTAAAG
65 TTAAAG
43007510 TTACGAGTTA
Statistics
Matches: 241, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 239 0.99
101 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
Found at i:43009055 original size:3 final size:3
Alignment explanation
Indices: 43008991--43009038 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
43008981 TAATATCTCC
43008991 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43009039 TTACTTAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43028282 original size:46 final size:46
Alignment explanation
Indices: 43028215--43028307 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
43028205 AGATTGATTC
* * *
43028215 ATGCCTCTTTCTTTCCTTTTCCTTTTAATTTCGGCCAAAGTGGGAA
1 ATGCCTCTTTCTTTCCCTTTCCTTTTAAATTCAGCCAAAGTGGGAA
43028261 ATGCCTCTTTCTTTCCCTTTCCTTTTAAATTCAGCCAAAGTGGGAA
1 ATGCCTCTTTCTTTCCCTTTCCTTTTAAATTCAGCCAAAGTGGGAA
43028307 A
1 A
43028308 ATGGCAGGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (46 bp):
ATGCCTCTTTCTTTCCCTTTCCTTTTAAATTCAGCCAAAGTGGGAA
Found at i:43028867 original size:22 final size:22
Alignment explanation
Indices: 43028810--43028879 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 22
43028800 TAAACATGCG
* **
43028810 AACCCTATATATGTTACATGTG
1 AACCCTATATATGTTATATGAA
**
43028832 AATTCTATACATATGTTATATGAA
1 AACCCTAT--ATATGTTATATGAA
43028856 AACCCTATATATGATATATATGAA
1 AACCCTATATATG-T-TATATGAA
43028880 CCATTGTACA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
22 11 0.30
23 1 0.03
24 25 0.68
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
AACCCTATATATGTTATATGAA
Found at i:43030814 original size:55 final size:55
Alignment explanation
Indices: 43030730--43030835 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 55
43030720 GATAGTCCTT
43030730 CAAAATAAACGATGTGACCCAAAACCGATCTTCTTAAGAATAAGCTAAATACCTC
1 CAAAATAAACGATGTGACCCAAAACCGATCTTCTTAAGAATAAGCTAAATACCTC
*
43030785 CAAAATAAACGATGTGACCCATAACCGATCTTCTTAAGAATAAGCTAAATA
1 CAAAATAAACGATGTGACCCAAAACCGATCTTCTTAAGAATAAGCTAAATA
43030836 GCCAGATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (55 bp):
CAAAATAAACGATGTGACCCAAAACCGATCTTCTTAAGAATAAGCTAAATACCTC
Found at i:43031327 original size:31 final size:31
Alignment explanation
Indices: 43031284--43031346 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
43031274 TCGTCACACA
43031284 TGTCTCTCGAGAAGCACAATATTAAAAAGCC
1 TGTCTCTCGAGAAGCACAATATTAAAAAGCC
**
43031315 TGTCTC-CTGAGAAGTGCAATATTAAAAAGCC
1 TGTCTCTC-GAGAAGCACAATATTAAAAAGCC
43031346 T
1 T
43031347 CAAGTCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (31 bp):
TGTCTCTCGAGAAGCACAATATTAAAAAGCC
Found at i:43034378 original size:30 final size:30
Alignment explanation
Indices: 43034342--43034403 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
43034332 CCACACTTAC
43034342 AAGTGTGATGTCCTATACGGTCGCACAAAT
1 AAGTGTGATGTCCTATACGGTCGCACAAAT
43034372 AAGTGTGATGTCCTATACGGTCGCACAAAT
1 AAGTGTGATGTCCTATACGGTCGCACAAAT
43034402 AA
1 AA
43034404 TAAAAAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (30 bp):
AAGTGTGATGTCCTATACGGTCGCACAAAT
Found at i:43036707 original size:51 final size:52
Alignment explanation
Indices: 43036631--43036730 Score: 175
Period size: 51 Copynumber: 1.9 Consensus size: 52
43036621 ATATAAATAA
43036631 AATTATTAATATATAGATTTAGGGA-TTTTTTGGATGATTTTAATTTTTGAT
1 AATTATTAATATATAGATTTAGGGATTTTTTTGGATGATTTTAATTTTTGAT
* *
43036682 AATTATTACTATATAGGTTTAGGGATTTTTTTGGATGATTTTAATTTTT
1 AATTATTAATATATAGATTTAGGGATTTTTTTGGATGATTTTAATTTTT
43036731 TATTTGAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 23 0.50
52 23 0.50
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (52 bp):
AATTATTAATATATAGATTTAGGGATTTTTTTGGATGATTTTAATTTTTGAT
Found at i:43037506 original size:14 final size:15
Alignment explanation
Indices: 43037479--43037507 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43037469 TTATATTCTA
43037479 TATATGTATCATTAT
1 TATATGTATCATTAT
43037494 TATATGT-TCATTAT
1 TATATGTATCATTAT
43037508 GCTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
TATATGTATCATTAT
Found at i:43042895 original size:46 final size:46
Alignment explanation
Indices: 43042842--43043148 Score: 344
Period size: 46 Copynumber: 6.6 Consensus size: 46
43042832 TTTGAGTACT
* * *
43042842 TCTGATCAAGTGACAAAGTGATAAGCGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
43042888 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
43042940 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
43042986 TCTGATCAAGTGAC--------AAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
43043024 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
43043076 TCTGATCAA-TAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGT-GACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
43043122 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
43043149 GCTACACTTA
Statistics
Matches: 226, Mismatches: 13, Indels: 44
0.80 0.05 0.16
Matches are distributed among these distances:
38 37 0.16
46 112 0.50
51 1 0.00
52 76 0.34
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:43042972 original size:98 final size:95
Alignment explanation
Indices: 43042842--43043148 Score: 338
Period size: 98 Copynumber: 3.3 Consensus size: 95
43042832 TTTGAGTACT
* * *
43042842 TCTGATCAAGTGACAAAGTGATAAGCGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-A--G
*
43042907 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
63 AAAAGTGATAAGTGATAGCTTCGGCTACACTTA
43042940 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAGAAA
43043000 ------AAGTGATAGCTTCGGCTACACTTA
66 AGTGATAAGTGATAGCTTCGGCTACACTTA
* *
43043024 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAA-T--
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
**
43043086 -AGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
60 CAGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
43043122 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
43043149 GCTACACTTA
Statistics
Matches: 182, Mismatches: 9, Indels: 42
0.78 0.04 0.18
Matches are distributed among these distances:
84 37 0.20
89 1 0.01
90 39 0.21
92 13 0.07
98 92 0.51
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (95 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAGAAA
AGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:43043006 original size:38 final size:38
Alignment explanation
Indices: 43042955--43043043 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
43042945 TCAAGTGACA
*
43042955 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
1 AAGTGACAAGTGATAGCTTCAGCTACACTTATCTGATC
*
43042993 AAGTGACAAGTGATAGCTTCGGCTACACTTATCTGATC
1 AAGTGACAAGTGATAGCTTCAGCTACACTTATCTGATC
43043031 AAGTGACAAGTGA
1 AAGTGACAAGTGA
43043044 AAAGTGATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (38 bp):
AAGTGACAAGTGATAGCTTCAGCTACACTTATCTGATC
Found at i:43043056 original size:52 final size:52
Alignment explanation
Indices: 43042993--43043148 Score: 191
Period size: 52 Copynumber: 3.1 Consensus size: 52
43042983 TTATCTGATC
*
43042993 AAGTGACAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAA
*
43043045 AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAA-T----A--GACA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-A
** * *
43043091 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGAT
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTGAA
43043144 AAGTG
1 AAGTG
43043149 GCTACACTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
45 2 0.02
46 38 0.43
47 1 0.01
51 1 0.01
52 39 0.44
53 5 0.06
54 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAA
Found at i:43043096 original size:136 final size:135
Alignment explanation
Indices: 43042878--43043296 Score: 525
Period size: 136 Copynumber: 3.3 Consensus size: 135
43042868 GGTAGCTTTA
43042878 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
*
43042943 GATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTGAT
66 GATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
43043007 -AGCTTCG
131 AAG--T-G
43043014 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
*
43043079 GATCAA-TAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGA
66 GATCAAGT-GACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
43043143 TAAGTG
130 TAAGTG
* * *
43043149 GCTACACTTATCTGATCAA--GA-AA---CAAA-T--TGA-T-A-AG--T-GGCTACACTTATCT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
** *
43043199 GATCAAGAAACAAAGTGATAA--G-T-G-----GCTACACTTATCTGATCAAGAAACAAAGTGAT
66 GATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
43043255 AAGTG
131 AAGTG
*
43043260 GCTACACTTATCTGATC-AGTGACAAGTGATAAGTGAT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGAT
43043297 CATACGTAAG
Statistics
Matches: 260, Mismatches: 10, Indels: 43
0.83 0.03 0.14
Matches are distributed among these distances:
110 1 0.00
111 53 0.20
112 2 0.01
113 2 0.01
116 3 0.01
117 2 0.01
118 1 0.00
119 1 0.00
120 31 0.12
121 1 0.00
123 2 0.01
124 1 0.00
125 1 0.00
126 2 0.01
128 1 0.00
129 3 0.01
132 2 0.01
133 2 0.01
135 21 0.08
136 119 0.46
137 7 0.03
138 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (135 bp):
GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
GATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
AAGTG
Found at i:43043156 original size:37 final size:37
Alignment explanation
Indices: 43043112--43043294 Score: 316
Period size: 37 Copynumber: 5.0 Consensus size: 37
43043102 GATAGCTTTA
*
43043112 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
43043149 GCTACACTTATCTGATCAAGAAACAAATTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
43043186 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
43043223 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
43043260 GCTACACTTATCTGATC-AGTGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
43043295 ATCATACGTA
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
35 12 0.09
36 4 0.03
37 125 0.89
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:43048048 original size:26 final size:25
Alignment explanation
Indices: 43048019--43048067 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
43048009 GCCTTAATCA
43048019 ATTTATTCATACAACTACTTTTAGGC
1 ATTTA-TCATACAACTACTTTTAGGC
* * *
43048045 ATTTATGATTCAACTATTTTTAG
1 ATTTATCATACAACTACTTTTAG
43048068 TCCTATATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (25 bp):
ATTTATCATACAACTACTTTTAGGC
Found at i:43050435 original size:11 final size:11
Alignment explanation
Indices: 43050403--43050428 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43050393 TAATTCGACA
43050403 AAAAATTATTT
1 AAAAATTATTT
43050414 AAAAATTATTT
1 AAAAATTATTT
43050425 AAAA
1 AAAA
43050429 TTCATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATTATTT
Found at i:43065854 original size:12 final size:13
Alignment explanation
Indices: 43065833--43065860 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43065823 TTTTACTTTT
43065833 AAAACAAAAAAAA
1 AAAACAAAAAAAA
43065846 AAAACAAAAAAAA
1 AAAACAAAAAAAA
43065859 AA
1 AA
43065861 TCAAGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:43066214 original size:19 final size:19
Alignment explanation
Indices: 43066192--43066255 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
43066182 TAAAGATCAA
*
43066192 TAAAAATTATAAAAATAAT
1 TAAAAATTATAAAAAAAAT
*
43066211 T--AAATTTTAATAAAAAAT
1 TAAAAATTATAA-AAAAAAT
*
43066229 ATAAAAATTAGAAAAAAAAT
1 -TAAAAATTATAAAAAAAAT
43066249 TAGAAAA
1 TA-AAAA
43066256 AAATTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 8 0.22
18 6 0.17
19 4 0.11
20 11 0.31
21 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAAATTATAAAAAAAAT
Found at i:43066248 original size:12 final size:12
Alignment explanation
Indices: 43066231--43066258 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43066221 TAAAAAATAT
43066231 AAAAATTAGAAA
1 AAAAATTAGAAA
43066243 AAAAATTAGAAA
1 AAAAATTAGAAA
43066255 AAAA
1 AAAA
43066259 TTATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAATTAGAAA
Found at i:43066255 original size:11 final size:11
Alignment explanation
Indices: 43066231--43066266 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
43066221 TAAAAAATAT
43066231 AAAAATTAGAAA
1 AAAAATTAG-AA
43066243 AAAAATTAGAA
1 AAAAATTAGAA
*
43066254 AAAAATTATAA
1 AAAAATTAGAA
43066265 AA
1 AA
43066267 TATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:43066358 original size:13 final size:13
Alignment explanation
Indices: 43066340--43066364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43066330 AAGAAATATA
43066340 AAATTTATAAAAT
1 AAATTTATAAAAT
43066353 AAATTTATAAAA
1 AAATTTATAAAA
43066365 CTTATCGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTTATAAAAT
Found at i:43066563 original size:21 final size:21
Alignment explanation
Indices: 43066538--43066603 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
43066528 TTAAAGGATC
43066538 TTTTTGATGCA-TTTTATAATT
1 TTTTTGATG-ATTTTTATAATT
* *
43066559 TTTTTTATGATTTTTATAAAAT
1 TTTTTGATGATTTTTAT-AATT
***
43066581 TTTACAAT-ATTTTTATAATT
1 TTTTTGATGATTTTTATAATT
43066601 TTT
1 TTT
43066604 ACGATTTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 7 0.19
21 22 0.59
22 8 0.22
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTGATGATTTTTATAATT
Found at i:43066906 original size:30 final size:30
Alignment explanation
Indices: 43066872--43066931 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
43066862 AATAAATATT
43066872 GCAAAATTATTTCAAAAATGAGGAAATAGC
1 GCAAAATTATTTCAAAAATGAGGAAATAGC
43066902 GCAAAATTATTTCAAAAATGAGGAAATAGC
1 GCAAAATTATTTCAAAAATGAGGAAATAGC
43066932 TTAATGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (30 bp):
GCAAAATTATTTCAAAAATGAGGAAATAGC
Found at i:43069879 original size:29 final size:29
Alignment explanation
Indices: 43069816--43069881 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
43069806 ACAATTAATT
*
43069816 TTTTTCTATTTTTTAATAAAATTTAAATA
1 TTTTTATATTTTTTAATAAAATTTAAATA
* *
43069845 TGTTTATATTTTTTATTAAAATTT-AATAA
1 TTTTTATATTTTTTAATAAAATTTAAAT-A
43069874 TTTTTATA
1 TTTTTATA
43069882 ACTTTCATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTATATTTTTTAATAAAATTTAAATA
Found at i:43070194 original size:95 final size:92
Alignment explanation
Indices: 43070017--43070336 Score: 300
Period size: 90 Copynumber: 3.5 Consensus size: 92
43070007 TTAATGAGCC
* * * * **
43070017 TTTTTGATACATTTT-ACAGTTCAAGTACCTAATTGAGTGTAAAAAAATCAG-GGG-CTTAA--A
1 TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGAGGGACTTAATTA
* * * *
43070077 TTTTTGTTTTTGAAAAAATTTGAGGGCT
66 TTTTT-TTTTTGAAAAAGTTTGATGACA
*
43070105 TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTACAAAAGAAAAAAGTAGGGACTTAAT
1 TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAA-AAAAAAG-AGGGACTTAAT
*
43070170 TACTTTTTTTTTTGAAAAAGTTTGATGACC
64 TA-TTTTTTTTTTGAAAAAGTTTGATGACA
* * * ** *
43070200 TTTTTAATGCATTTTGAAAGTTCAAGCAATCAATTGAGTGC--AAAAAAAAGCAAGGACTTAATT
1 TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAG-AGGGACTTAATT
* * *
43070263 -GTTTTTTTTTGAAAAAGTTTAATGTCA
65 ATTTTTTTTTTGAAAAAGTTTGATGACA
* * * *
43070290 TTTTTGATACAATTTAAAAGTTTAAATA-CCAATTGAGTG-AAAAAAAA
1 TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAA
43070337 GAGTTTAATT
Statistics
Matches: 191, Mismatches: 31, Indels: 18
0.80 0.13 0.08
Matches are distributed among these distances:
88 14 0.07
89 35 0.18
90 55 0.29
92 21 0.11
93 7 0.04
95 54 0.28
96 5 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (92 bp):
TTTTTAATACATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGAGGGACTTAATTA
TTTTTTTTTTGAAAAAGTTTGATGACA
Found at i:43076454 original size:16 final size:16
Alignment explanation
Indices: 43076429--43076465 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
43076419 TGAAATGGTA
43076429 AAATTGATGATGTTTT
1 AAATTGATGATGTTTT
*
43076445 AAATTTATGATGTTTT
1 AAATTGATGATGTTTT
43076461 AAATT
1 AAATT
43076466 ATCTGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
AAATTGATGATGTTTT
Found at i:43091368 original size:21 final size:21
Alignment explanation
Indices: 43091344--43091390 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
43091334 CCTTGCCCGT
*
43091344 ATGGCCCACAAAGCTTGGCTC
1 ATGGCCCACAAAGCCTGGCTC
**
43091365 ATGGCCCACACGGCCTGGCTC
1 ATGGCCCACAAAGCCTGGCTC
43091386 ATGGC
1 ATGGC
43091391 TTACACGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.17
Consensus pattern (21 bp):
ATGGCCCACAAAGCCTGGCTC
Found at i:43094963 original size:15 final size:15
Alignment explanation
Indices: 43094945--43094975 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43094935 TTTCTTCTTG
43094945 AGTGGTGGTTTTAGT
1 AGTGGTGGTTTTAGT
43094960 AGTGGTGGTTTTAGT
1 AGTGGTGGTTTTAGT
43094975 A
1 A
43094976 TTGACTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (15 bp):
AGTGGTGGTTTTAGT
Found at i:43097374 original size:5 final size:5
Alignment explanation
Indices: 43097364--43097391 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43097354 TTTAATTGAA
43097364 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
43097392 AAACAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:43098998 original size:21 final size:21
Alignment explanation
Indices: 43098959--43098998 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43098949 GAAAAATTAT
*
43098959 AAAATTAAAAAAATCAAAATC
1 AAAATTAAAAAAATAAAAATC
*
43098980 AAAATTAAAAATATAAAAA
1 AAAATTAAAAAAATAAAAA
43098999 GTTGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATTAAAAAAATAAAAATC
Found at i:43099244 original size:19 final size:19
Alignment explanation
Indices: 43099193--43099244 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
43099183 ATTTGACATA
**
43099193 ACACATTT-TTAAATGGAC
1 ACACATTTATTAAATCAAC
*
43099211 -CACTTTTATTAAAATCAAC
1 ACACATTTATT-AAATCAAC
43099230 ACACATTTATTAAAT
1 ACACATTTATTAAAT
43099245 TCATTAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.22
18 2 0.07
19 10 0.37
20 9 0.33
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (19 bp):
ACACATTTATTAAATCAAC
Found at i:43101659 original size:18 final size:18
Alignment explanation
Indices: 43101636--43101682 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
43101626 CAATCGATCT
* *
43101636 AATTTAAAAATTATTAAA
1 AATTTAAAAAATAATAAA
43101654 AATTTAAAAAATAATAAA
1 AATTTAAAAAATAATAAA
*
43101672 AA-ATAAAAAAT
1 AATTTAAAAAAT
43101683 CCGATTCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTTAAAAAATAATAAA
Found at i:43101665 original size:19 final size:18
Alignment explanation
Indices: 43101636--43101675 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
43101626 CAATCGATCT
* *
43101636 AATTTAAAAATTATTAAA
1 AATTTAAAAATAATAAAA
43101654 AATTTAAAAAATAATAAAA
1 AATTT-AAAAATAATAAAA
43101673 AAT
1 AAT
43101676 AAAAAATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTAAAAATAATAAAA
Found at i:43103917 original size:6 final size:6
Alignment explanation
Indices: 43103906--43103938 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43103896 TGTCAAGGAT
*
43103906 AGGGGA AGGGGA AGGGGA AGGGGA AGGGAA AGG
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGG
43103939 AAAAGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:43103944 original size:18 final size:18
Alignment explanation
Indices: 43103906--43103944 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43103896 TGTCAAGGAT
* **
43103906 AGGGGAAGGGGAAGGGGA
1 AGGGGAAGGGAAAGGAAA
43103924 AGGGGAAGGGAAAGGAAA
1 AGGGGAAGGGAAAGGAAA
43103942 AGG
1 AGG
43103945 AAAATTTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
AGGGGAAGGGAAAGGAAA
Found at i:43113106 original size:28 final size:26
Alignment explanation
Indices: 43113049--43113100 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
43113039 TTTTAGTTAA
*
43113049 TTATTTAAAAAAGAGATATGATTTTCG
1 TTATTTAAAAAAAAGATA-GATTTTCG
43113076 TTATTTAAAAAAAAGATCA-ATTTTC
1 TTATTTAAAAAAAAGAT-AGATTTTC
43113101 AAGTTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 16 0.70
28 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (26 bp):
TTATTTAAAAAAAAGATAGATTTTCG
Found at i:43125569 original size:73 final size:73
Alignment explanation
Indices: 43125450--43125598 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 73
43125440 TGAATATTGC
43125450 TTCACTGTTTCTTCTTCCTTTAATTTTAAATTTTTAAAGTCCCTTCTCAAATTCAGTAGTTGCTA
1 TTCACTGTTTCTTCTTCCTTTAATTTTAAATTTTTAAAGTCCCTTCTCAAATTCAGTAGTTGCTA
43125515 TTGTCTCG
66 TTGTCTCG
*
43125523 TTCACTGTTTCTTCTTCCTTTAATTTTAAATTTTTAAAGTCCCTTCTCAAATTCAGTAGTTGCTG
1 TTCACTGTTTCTTCTTCCTTTAATTTTAAATTTTTAAAGTCCCTTCTCAAATTCAGTAGTTGCTA
43125588 TTGTCTCG
66 TTGTCTCG
43125596 TTC
1 TTC
43125599 TTTCAGTCCC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (73 bp):
TTCACTGTTTCTTCTTCCTTTAATTTTAAATTTTTAAAGTCCCTTCTCAAATTCAGTAGTTGCTA
TTGTCTCG
Found at i:43125979 original size:30 final size:30
Alignment explanation
Indices: 43125943--43126003 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
43125933 TGTTGGAACT
43125943 AAGAATGCAAGATGAATTAAGTTAACAGAG
1 AAGAATGCAAGATGAATTAAGTTAACAGAG
*
43125973 AAGAATGCAATATGAATTAAGTTAACAGAG
1 AAGAATGCAAGATGAATTAAGTTAACAGAG
43126003 A
1 A
43126004 CTTGAGCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (30 bp):
AAGAATGCAAGATGAATTAAGTTAACAGAG
Found at i:43132743 original size:44 final size:44
Alignment explanation
Indices: 43132679--43132855 Score: 228
Period size: 44 Copynumber: 4.0 Consensus size: 44
43132669 AGGAAAGTAA
* * * *
43132679 GATTCGCAATTTTTAACCTATTCCACTGCTAACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* *
43132723 GATTCACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAT
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * *
43132767 GATTCACAATCCTCAGCCTATTCCATTGCTGACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * * * *
43132811 GATTCACAATCTTTAGCCTATTCCATTGTTGTCCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
43132855 G
1 G
43132856 GTTGGGGTTA
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 118 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
Found at i:43132969 original size:43 final size:43
Alignment explanation
Indices: 43132916--43133057 Score: 133
Period size: 44 Copynumber: 3.3 Consensus size: 43
43132906 TATTTTTAAC
43132916 CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
* * *** * * * * * *
43132959 CTGCTTCGCTGTTAGTGCAGGAAGGCAAGATCTGCTAT-TTTGAAC
1 CTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCTTCG-AT
*
43133004 CTACTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
*
43133047 CTGCTTCGCTG
1 CTGCTCCGCTG
43133058 TTGGTGCAAG
Statistics
Matches: 70, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 25 0.36
44 30 0.43
45 15 0.21
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (43 bp):
CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
Found at i:43132985 original size:44 final size:44
Alignment explanation
Indices: 43132932--43133075 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
43132922 CGCTGCAACC
*
43132932 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTAGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTAGTG
* * * * * * * * ***
43132976 CAGGAAGGCAAGATCTGCTAT-TTTGAACCTACTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCG-ATCTGCTTCGCTGTTAGTG
* *
43133020 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTAGTG
*
43133064 CAAGAAGGCAAG
1 CAGGAAGGCAAG
43133076 ATCTGCTATT
Statistics
Matches: 69, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
43 15 0.22
44 39 0.57
45 15 0.22
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTAGTG
Found at i:43132992 original size:88 final size:88
Alignment explanation
Indices: 43132866--43133519 Score: 819
Period size: 88 Copynumber: 7.4 Consensus size: 88
43132856 GTTGGGGTTA
*
43132866 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
43132931 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * *
43132954 TCGATCTGCTTCGCTGTTAGTGCAGGAAGGCAAGATCTGCTATTTTGAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
43133019 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
** *
43133042 TCGATCTGCTTCGCTGTTGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
43133107 CTAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * * * * *
43133130 TCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCGCTGCCAT
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
43133195 CGAGAGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * ** * * * *
43133218 TCAATCTGCTTCACTGTTAGTATAGGAAGGCAAGATTTGCTATCTTTAACCTGCTTCGCTGCCAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
43133283 CGAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* ** * * ** * * *
43133306 TCGATCTAC-TC-CACT-ACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTGCTCTGCTGCA
1 TCGATCTGCTTCGCTGTCAGTGC--AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCA
*
43133368 ACCCAGGGAGGCAAGGCTGGTGTCT
64 ACCCAGGGAGGCAAGGCTAGTGTCT
* * * **
43133393 TTGATCTGCTTCGCTGCCGGTATAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
43133458 CTAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * *
43133481 TCGATCTACTTCACTGTCGGTGTAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTG
43133520 TTATCTTCAC
Statistics
Matches: 493, Mismatches: 68, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
85 2 0.00
86 2 0.00
87 62 0.13
88 425 0.86
89 1 0.00
90 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTAGTGTCT
Found at i:43133274 original size:45 final size:45
Alignment explanation
Indices: 43133135--43133274 Score: 135
Period size: 45 Copynumber: 3.2 Consensus size: 45
43133125 TGTCTTCAAT
43133135 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
1 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
* * * ** * * * *
43133180 CTGCTCCGCTGCCA-T-C-GAGAGAGGCAAGGCTAG-TGTCTTCAAT
1 CTGCTTCACTGTCAGTACAG-GA-AGGCAAGATTTGCTATCTTTAAC
* *
43133223 CTGCTTCACTGTTAGTATAGGAAGGCAAGATTTGCTATCTTTAAC
1 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
43133268 CTGCTTC
1 CTGCTTC
43133275 GCTGCCACCG
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
42 1 0.01
43 20 0.29
44 20 0.29
45 27 0.39
46 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (45 bp):
CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
Found at i:43133463 original size:351 final size:352
Alignment explanation
Indices: 43132889--43133526 Score: 967
Period size: 351 Copynumber: 1.8 Consensus size: 352
43132879 CTGTCGGTGC
* *
43132889 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCT
1 AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
* ** * * * *
43132954 TCGATCTGCTTCGCTGTTAGTGCAGGAAGGCAAGATCTGCTATTTTGAACCTACTCCGCTGCAAC
66 TCGATCTACTTCGCTACTACTGCAGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCAAC
** *
43133019 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTGCAAGAAGGCAAGATCTGCTA
131 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAAGAAGGCAAGATCTGCTA
*
43133084 TTTTTAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTTCACTGTCA
196 TTTTTAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCAATCTACTTCACTGTCA
*
43133149 GTACAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTAGT
261 GTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTAGT
43133214 GTCTTCAATCTGCTTCACTGTTAGTAT
326 GTCTTCAATCTGCTTCACTGTTAGTAT
* * * *
43133241 AGGAAGGCAAGATTTGCTATCTTTAACCTGCTTCGCTGCCACCGAGGGAGGCAAGGCTAGTGTCT
1 AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
* * * *
43133306 TCGATCTAC-TC-C-ACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTGCTCTGCTGCA
66 TCGATCTACTTCGCTACTACTGC--AGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCA
* * *
43133368 ACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGGTATAGGAAGGCAAGATCTGC
129 ACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAAGAAGGCAAGATCTGC
*
43133433 TATTTTTAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCGATCTACTTCACTGT
194 TATTTTTAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCAATCTACTTCACTGT
* ** *
43133498 CGGTGTAGGAAGGCAAGATCTGTTATCTT
259 CAGTACAGGAAGGCAAGATCTGCTATCTT
43133527 CACTGATCTG
Statistics
Matches: 254, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
349 5 0.02
350 1 0.00
351 181 0.71
352 67 0.26
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (352 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
TCGATCTACTTCGCTACTACTGCAGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAAGAAGGCAAGATCTGCTA
TTTTTAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCAATCTACTTCACTGTCA
GTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTAGT
GTCTTCAATCTGCTTCACTGTTAGTAT
Found at i:43153913 original size:19 final size:18
Alignment explanation
Indices: 43153878--43153913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43153868 TCTTACTACA
*
43153878 GTTTTCAGTTTCACTATT
1 GTTTTCAGTTACACTATT
43153896 GTTTTCAGTATACACTAT
1 GTTTTCAGT-TACACTAT
43153914 CTACAGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (18 bp):
GTTTTCAGTTACACTATT
Found at i:43159889 original size:2 final size:2
Alignment explanation
Indices: 43159882--43159922 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43159872 CACCAACTTA
43159882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43159923 AACATAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43160309 original size:18 final size:21
Alignment explanation
Indices: 43160280--43160337 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 21
43160270 AAAAATAATA
43160280 AAAATAATTTTT-AAAATTC-
1 AAAATAATTTTTAAAAATTCT
43160299 AAAAT-ATTTTTAAAAATTCT
1 AAAATAATTTTTAAAAATTCT
43160319 AAAATTTATATTTTTAAAA
1 AAAA--TA-ATTTTTAAAA
43160338 TGTATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 4 0.12
22 1 0.03
24 10 0.30
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATAATTTTTAAAAATTCT
Found at i:43169138 original size:29 final size:30
Alignment explanation
Indices: 43169106--43169172 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
43169096 GAAAAATGCC
*
43169106 TCAATTGAACCCTCA-A-TAATGAAAATAA
1 TCAATTGAACCCTCATATTAATAAAAATAA
**
43169134 TTCAATTGGCCCCTCATATTAATAAAAATAA
1 -TCAATTGAACCCTCATATTAATAAAAATAA
43169165 TCAATTGA
1 TCAATTGA
43169173 CCAATTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.41
30 8 0.25
31 11 0.34
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (30 bp):
TCAATTGAACCCTCATATTAATAAAAATAA
Found at i:43177190 original size:21 final size:22
Alignment explanation
Indices: 43177161--43177201 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
43177151 AATAAAGTTT
*
43177161 TATAGTATGTGTGTATGGTATA
1 TATAGTATGAGTGTATGGTATA
*
43177183 TATA-TATGAGTGTGTGGTA
1 TATAGTATGAGTGTATGGTA
43177202 ATTTAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (22 bp):
TATAGTATGAGTGTATGGTATA
Found at i:43183058 original size:21 final size:22
Alignment explanation
Indices: 43183023--43183075 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
43183013 ATTTGATCTG
43183023 AAAAGAAGAAA---AAAATAGT
1 AAAAGAAGAAATTGAAAATAGT
*
43183042 AATA-AAGAAATTGAAAATAGT
1 AAAAGAAGAAATTGAAAATAGT
43183063 AAAAGAAGAAATT
1 AAAAGAAGAAATT
43183076 TGAGATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
21 11 0.39
22 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (22 bp):
AAAAGAAGAAATTGAAAATAGT
Found at i:43185107 original size:17 final size:16
Alignment explanation
Indices: 43185078--43185120 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
43185068 ATAAAAAATT
*
43185078 TTAAAAATAATATTAA
1 TTAAAAATTATATTAA
*
43185094 CTTAATAATTATATTAA
1 -TTAAAAATTATATTAA
43185111 TTAAAAATTA
1 TTAAAAATTA
43185121 AATAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAAATTATATTAA
Found at i:43186838 original size:2 final size:2
Alignment explanation
Indices: 43186831--43186858 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43186821 TTGTTGTGAA
43186831 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43186859 TCTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:43197975 original size:22 final size:20
Alignment explanation
Indices: 43197924--43197976 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
43197914 GCACACAAAC
*
43197924 AAACATACAAATAAATGAAA
1 AAACATAAAAATAAATGAAA
*
43197944 AATA-ACAAAAATAACTATGAAA
1 AA-ACATAAAAATAA--ATGAAA
43197966 AAACATAAAAA
1 AAACATAAAAA
43197977 AATTTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 10 0.38
21 2 0.08
22 14 0.54
ACGTcount: A:0.72, C:0.09, G:0.04, T:0.15
Consensus pattern (20 bp):
AAACATAAAAATAAATGAAA
Found at i:43198229 original size:23 final size:24
Alignment explanation
Indices: 43198203--43198255 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
43198193 ATAAATTTTT
43198203 TTAAAAGA-TAAAAATCCAAAAAA
1 TTAAAAGATTAAAAATCCAAAAAA
* * *
43198226 TTAAAA-ATTACAAGTCCCAAAAA
1 TTAAAAGATTAAAAATCCAAAAAA
43198249 TTAAAAG
1 TTAAAAG
43198256 TTCCAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (24 bp):
TTAAAAGATTAAAAATCCAAAAAA
Found at i:43198247 original size:16 final size:16
Alignment explanation
Indices: 43198228--43198262 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43198218 CCAAAAAATT
*
43198228 AAAAATTACAAGTCCC
1 AAAAATTAAAAGTCCC
*
43198244 AAAAATTAAAAGTTCC
1 AAAAATTAAAAGTCCC
43198260 AAA
1 AAA
43198263 GTTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAATTAAAAGTCCC
Done.