Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:155298 original size:2 final size:2
Alignment explanation
Indices: 155286--155335 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
155276 TGACAGGTGA
*
155286 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155328 AT AT AT AT
1 AT AT AT AT
155336 GATAACAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:156279 original size:21 final size:21
Alignment explanation
Indices: 156246--156302 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
156236 GGTTCTACGC
156246 GGTCCTTCAGGACATATATGT
1 GGTCCTTCAGGACATATATGT
* * *
156267 GGTCATTCGGGACATCTATGT
1 GGTCCTTCAGGACATATATGT
156288 GGTCCTTCAGGACAT
1 GGTCCTTCAGGACAT
156303 TTCTACGTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (21 bp):
GGTCCTTCAGGACATATATGT
Found at i:158900 original size:23 final size:23
Alignment explanation
Indices: 158865--158940 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
158855 GAATTAAGGG
*
158865 TTCTACGCTGTCTTTC-AGGACAA
1 TTCTACGCGGTCTTTCGA-GACAA
*
158888 TTCTATGCGGTCTTTCGAGACAA
1 TTCTACGCGGTCTTTCGAGACAA
* * *
158911 TTCTACGTGGTCCTTCGAGACAT
1 TTCTACGCGGTCTTTCGAGACAA
158934 TTCTACG
1 TTCTACG
158941 TGGCACTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 45 0.98
24 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCTTTCGAGACAA
Found at i:160703 original size:44 final size:44
Alignment explanation
Indices: 160640--160730 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
160630 GATTTGAGCA
160640 ATTATGTATGTAGGGTGTGTGTGTTTTGTCAATGATTAAGAAAG
1 ATTATGTATGTAGGGTGTGTGTGTTTTGTCAATGATTAAGAAAG
160684 ATTATGTATGTAGGGTGTGTGTGTTTTGTCAATGATTAAGAAAG
1 ATTATGTATGTAGGGTGTGTGTGTTTTGTCAATGATTAAGAAAG
160728 ATT
1 ATT
160731 CTGAACAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (44 bp):
ATTATGTATGTAGGGTGTGTGTGTTTTGTCAATGATTAAGAAAG
Found at i:161572 original size:2 final size:2
Alignment explanation
Indices: 161565--161616 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
161555 TTTGTCTGCA
* * * *
161565 AT AT AT AT AT AT AT AT AC AT AT AT AT CAA AT AT AT AT AA AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
161608 A- AT AT AT AT
1 AT AT AT AT AT
161617 TGTAAGTAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.03
2 38 0.95
3 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:180205 original size:30 final size:30
Alignment explanation
Indices: 180169--180230 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
180159 ATCTTACGTT
180169 AGTCCATGTGCGCATTGAAAACGTCTGTCG
1 AGTCCATGTGCGCATTGAAAACGTCTGTCG
180199 AGTCCATGTGCGCATTGAAAACGTCTGTCG
1 AGTCCATGTGCGCATTGAAAACGTCTGTCG
180229 AG
1 AG
180231 GTATTCGCTG
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:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (30 bp):
AGTCCATGTGCGCATTGAAAACGTCTGTCG
Found at i:182314 original size:2 final size:2
Alignment explanation
Indices: 182305--182343 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
182295 ATCACACATT
182305 TA TA -A TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
182344 TTAGTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:183554 original size:24 final size:24
Alignment explanation
Indices: 183517--183567 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
183507 TTTTGTTGTG
*
183517 TATATATGTATATTTTTATTAATT
1 TATATATGTATATTTTAATTAATT
*
183541 TATATATAGT-TATTTTAATTATTT
1 TATATAT-GTATATTTTAATTAATT
183565 TAT
1 TAT
183568 TTGATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TATATATGTATATTTTAATTAATT
Found at i:194455 original size:34 final size:30
Alignment explanation
Indices: 194417--194485 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
194407 TTGATATAAC
194417 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
194451 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
194480 AATTTA
1 AATTTA
194486 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:194497 original size:29 final size:30
Alignment explanation
Indices: 194426--194485 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
194416 CAATTTAAGG
194426 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
194457 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
194486 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:194591 original size:21 final size:21
Alignment explanation
Indices: 194565--194659 Score: 115
Period size: 21 Copynumber: 4.5 Consensus size: 21
194555 AGGGTGTCAA
194565 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
194586 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
194607 AGTGCATCCATGCACCTACACT--
1 AGTGCATCCATGCACC--C-CTGC
* *
194629 AGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCCTGC
194649 AGTGCATCCAT
1 AGTGCATCCAT
194660 ACACTCAAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 10 0.16
21 36 0.56
22 13 0.20
23 1 0.02
24 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:194729 original size:21 final size:21
Alignment explanation
Indices: 194684--194746 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
194674 AATGCAATTA
***
194684 GTGCATCGATGCATC-ATTTT
1 GTGCATCGATGCATCAAGGCT
194704 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
194725 GTGCATCGATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
194746 G
1 G
194747 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:196048 original size:19 final size:20
Alignment explanation
Indices: 196024--196071 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
196014 AATGATTTTC
*
196024 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
196043 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
196063 TTTTGAAAA
1 TTTTGAAAA
196072 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:197355 original size:34 final size:30
Alignment explanation
Indices: 197317--197385 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
197307 TTGATATAAC
197317 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
197351 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
197380 AATTTA
1 AATTTA
197386 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:197396 original size:29 final size:30
Alignment explanation
Indices: 197326--197385 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
197316 CAATTTAAGG
197326 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
197357 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
197386 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:197491 original size:21 final size:21
Alignment explanation
Indices: 197465--197605 Score: 180
Period size: 21 Copynumber: 6.7 Consensus size: 21
197455 AGGGTGTCAA
197465 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
197486 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
197507 AATGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
197528 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
197549 AGTGCATTCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* * *
197570 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTGC
197591 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
197606 TCAAACACCG
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.04
20 13 0.12
21 73 0.70
22 12 0.11
23 3 0.03
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:197652 original size:21 final size:21
Alignment explanation
Indices: 197626--197668 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
197616 AATGCAATTA
197626 GTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCA-CGAAGGCT
197647 GTGCATCGATGCACGAAGGCT
1 GTGCATCGATGCACGAAGGCT
197668 G
1 G
197669 CAACGACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (21 bp):
GTGCATCGATGCACGAAGGCT
Found at i:197800 original size:20 final size:22
Alignment explanation
Indices: 197762--197801 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
197752 TTTGAGTAGA
197762 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
197784 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
197802 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:198653 original size:106 final size:106
Alignment explanation
Indices: 198512--198814 Score: 464
Period size: 106 Copynumber: 2.9 Consensus size: 106
198502 AAACACAAGT
* * ** *
198512 TCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTTC
1 TCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTC
*
198577 AACTTCACAACGAAGGATATTAGACTCGAGATAGCACAAAC
66 AACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAAC
198618 TCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTC
1 TCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTC
*
198683 AACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAGC
66 AACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAAC
* * * * *
198724 TCAACTTCACAGCGAAGGGGTGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTC
1 TCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTC
* *
198789 AACTTCACGAC-AGAGGATATTGGACT
66 AACTTCACAACGA-AGGATATTAGACT
198815 TGGAGCAATA
Statistics
Matches: 182, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
105 1 0.01
106 181 0.99
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTC
AACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAAC
Found at i:207654 original size:113 final size:113
Alignment explanation
Indices: 207526--207752 Score: 436
Period size: 113 Copynumber: 2.0 Consensus size: 113
207516 AGTGAAGTTC
207526 TACCAATTTCAATTTTGCAGAGAAATGAGAGGCTACATTTTTGTATTGTTTTGTTCTGAATATTC
1 TACCAATTTCAATTTTGCAGAGAAATGAGAGGCTACATTTTTGTATTGTTTTGTTCTGAATATTC
* *
207591 ATATAGCTTACATTCAGTGACTTCAATTTACCTTCCAAACTCTATATT
66 ATATAGCTTAAATTCAGTGACTTAAATTTACCTTCCAAACTCTATATT
207639 TACCAATTTCAATTTTGCAGAGAAATGAGAGGCTACATTTTTGTATTGTTTTGTTCTGAATATTC
1 TACCAATTTCAATTTTGCAGAGAAATGAGAGGCTACATTTTTGTATTGTTTTGTTCTGAATATTC
207704 ATATAGCTTAAATTCAGTGACTTAAATTTACCTTCCAAACTCTATATT
66 ATATAGCTTAAATTCAGTGACTTAAATTTACCTTCCAAACTCTATATT
207752 T
1 T
207753 TCCTAGTGAA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (113 bp):
TACCAATTTCAATTTTGCAGAGAAATGAGAGGCTACATTTTTGTATTGTTTTGTTCTGAATATTC
ATATAGCTTAAATTCAGTGACTTAAATTTACCTTCCAAACTCTATATT
Found at i:214254 original size:22 final size:22
Alignment explanation
Indices: 214226--214270 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
214216 TAGTGATGTA
214226 TGTTGTTTAATGGAAATAAGAC
1 TGTTGTTTAATGGAAATAAGAC
214248 TGTTGTTTAATGGAAATAAGAC
1 TGTTGTTTAATGGAAATAAGAC
214270 T
1 T
214271 TTTGACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (22 bp):
TGTTGTTTAATGGAAATAAGAC
Found at i:216410 original size:24 final size:24
Alignment explanation
Indices: 216378--216455 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
216368 GAAACTGCTG
*
216378 CGTAGAATATTCACTGAAGTGCCA
1 CGTAGAATATGCACTGAAGTGCCA
216402 CGTAGAATATGCACTGAAGTGCCA
1 CGTAGAATATGCACTGAAGTGCCA
216426 CGTAGAATATGCACTGAAGTGCCA
1 CGTAGAATATGCACTGAAGTGCCA
*
216450 CATAGA
1 CGTAGA
216456 TTTGTCCAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (24 bp):
CGTAGAATATGCACTGAAGTGCCA
Found at i:221370 original size:11 final size:11
Alignment explanation
Indices: 221354--221385 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
221344 AGTTTTCTAT
221354 TTTGTTGATTA
1 TTTGTTGATTA
221365 TTTGTTGATTA
1 TTTGTTGATTA
221376 TTTGTTGATT
1 TTTGTTGATT
221386 TAAAGTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.66
Consensus pattern (11 bp):
TTTGTTGATTA
Found at i:222553 original size:29 final size:28
Alignment explanation
Indices: 222489--222547 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
222479 CATGCACATG
222489 TGATACATGTTACATGATATGAATCTATA
1 TGATACATGTTACATGATATGAA-CTATA
*
222518 TGATACATGTTATATGATATGAGA-TATA
1 TGATACATGTTACATGATATGA-ACTATA
222546 TG
1 TG
222548 TTTACACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 21 0.75
30 1 0.04
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (28 bp):
TGATACATGTTACATGATATGAACTATA
Found at i:223094 original size:17 final size:19
Alignment explanation
Indices: 223060--223097 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
223050 ATATGATTAT
223060 ATGATAAAAGGTATTAATG
1 ATGATAAAAGGTATTAATG
*
223079 ATGATAATAGG-A-TAATG
1 ATGATAAAAGGTATTAATG
223096 AT
1 AT
223098 AAGGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (19 bp):
ATGATAAAAGGTATTAATG
Found at i:223539 original size:21 final size:21
Alignment explanation
Indices: 223515--223558 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
223505 TACGGAAGTA
* *
223515 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAAGGTATCGATACC
223536 CTGTAGCAAGGTATCGATACC
1 CTGTAGCAAGGTATCGATACC
223557 CT
1 CT
223559 AGCAGCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
CTGTAGCAAGGTATCGATACC
Found at i:229403 original size:22 final size:22
Alignment explanation
Indices: 229369--229412 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
229359 TAACATTTGG
229369 TACTATTCACGGTATTGATCAT
1 TACTATTCACGGTATTGATCAT
* * *
229391 TACTGTTCTCGGTATTGTTCAT
1 TACTATTCACGGTATTGATCAT
229413 ACCATATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (22 bp):
TACTATTCACGGTATTGATCAT
Found at i:230189 original size:51 final size:51
Alignment explanation
Indices: 230127--230241 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
230117 AGAATTAGAT
*** * *
230127 TTATTATTTTATTAAGAATTAAGG-TAGCCTTAAAACATTATCTTTAATTTA
1 TTATTATTTTATTAAGAATT-AGGATAAAATCAAAACATTATCTCTAATTTA
* * *
230178 TTATTATTTTATTATGAATTAGGATAAAATCATAAGATTATCTCTAATTTA
1 TTATTATTTTATTAAGAATTAGGATAAAATCAAAACATTATCTCTAATTTA
230229 TTATTATTTTATT
1 TTATTATTTTATT
230242 CATTAGTTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 3 0.05
51 52 0.95
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (51 bp):
TTATTATTTTATTAAGAATTAGGATAAAATCAAAACATTATCTCTAATTTA
Found at i:232636 original size:60 final size:60
Alignment explanation
Indices: 232565--232689 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
232555 TTTTATTCTG
* *
232565 TTTTGGTCACTCAACTTTTTTTTGTTTCGAAAGCATACCTAATTTTACGTTTT-AGTTTCA
1 TTTTGGTCACTCAACTATTTTTTGTTTCGAAAGCATACCTAACTTTACGTTTTGA-TTTCA
* *
232625 TTTTGGTCACTCAACTATTTTTTGTTTCGAAAGCATATCTAACTTTATGTTTTGATTTCA
1 TTTTGGTCACTCAACTATTTTTTGTTTCGAAAGCATACCTAACTTTACGTTTTGATTTCA
232685 TTTTG
1 TTTTG
232690 ATTACTCACC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (60 bp):
TTTTGGTCACTCAACTATTTTTTGTTTCGAAAGCATACCTAACTTTACGTTTTGATTTCA
Found at i:233256 original size:22 final size:22
Alignment explanation
Indices: 233199--233257 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
233189 ACGCGATTCT
*
233199 GACTATCGCATTACGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
233221 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
233242 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
233258 ATATATAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:233271 original size:20 final size:20
Alignment explanation
Indices: 233246--233297 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
233236 TTTTCCGACT
233246 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATATAA
*
233266 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATATAA
233286 ATCGCAATGCGA
1 ATCGCAATGCGA
233298 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATATAA
Found at i:233309 original size:20 final size:20
Alignment explanation
Indices: 233286--233333 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
233276 GAATATGTAA
*
233286 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
233306 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
233326 GTCGCAAC
1 ATCGCAAC
233334 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:236481 original size:6 final size:6
Alignment explanation
Indices: 236470--236503 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
236460 AGAAAAAGGC
**
236470 AATCAA AATCAA AATCGC AATCAA AATCAA AATC
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATC
236504 CCAATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (6 bp):
AATCAA
Found at i:236489 original size:18 final size:18
Alignment explanation
Indices: 236468--236510 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
236458 CAAGAAAAAG
236468 GCAATCAAAATCAAAATC
1 GCAATCAAAATCAAAATC
236486 GCAATCAAAATCAAAATC
1 GCAATCAAAATCAAAATC
*
236504 CCAATCA
1 GCAATCA
236511 CAACCGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.26, G:0.05, T:0.16
Consensus pattern (18 bp):
GCAATCAAAATCAAAATC
Found at i:236826 original size:140 final size:140
Alignment explanation
Indices: 236570--236835 Score: 523
Period size: 140 Copynumber: 1.9 Consensus size: 140
236560 AAACGTTGTA
236570 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
236635 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGACTAT
236700 TATGTGTATT
131 TATGTGTATT
236710 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
236775 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGA
236836 TTATCGCAAC
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACGCGAATTTGACTAT
TATGTGTATT
Found at i:236865 original size:34 final size:37
Alignment explanation
Indices: 236822--236916 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
236812 TTGAATATCA
* *
236822 CAACGCGAATTTGATTATCGCAAC-TC-A-AAAATCG
1 CAACGCGAATTTGACTATCGCAACAACGAGAAAATCG
*
236856 CAACGCGAATTTGACTATCACAACAACGAGAAAATCG
1 CAACGCGAATTTGACTATCGCAACAACGAGAAAATCG
* * *
236893 CAAAGCGTATTAGACTATCGCAAC
1 CAACGCGAATTTGACTATCGCAAC
236917 GCGAATTGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 22 0.43
35 1 0.02
36 1 0.02
37 27 0.53
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (37 bp):
CAACGCGAATTTGACTATCGCAACAACGAGAAAATCG
Found at i:236932 original size:19 final size:20
Alignment explanation
Indices: 236889--236932 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
236879 CAACGAGAAA
*
236889 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
236909 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
236928 TTCGC
1 ATCGC
236933 GTTGTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:236977 original size:20 final size:20
Alignment explanation
Indices: 236922--236979 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
236912 GCAACGCGAA
* *
236922 TTGACTTTCGCGTTGTGATT
1 TTGACTTTAGCGTTGCGATT
* * *
236942 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
236962 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
236980 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:239145 original size:18 final size:19
Alignment explanation
Indices: 239122--239208 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 19
239112 GAAACTTAAA
*
239122 ATCGCAACACG-AATGACT
1 ATCGCAACGCGAAATGACT
239140 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
239160 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
239180 ATCACAACGC-AAATTTGACT
1 ATCGCAACGCGAAA--TGACT
239200 ATCGCAACG
1 ATCGCAACG
239209 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
18 13 0.21
20 49 0.79
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:239158 original size:20 final size:20
Alignment explanation
Indices: 239133--239208 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
239123 TCGCAACACG
239133 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
239153 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
239173 AATGACTATCACAACGC-AA
1 AATGACTATCGCAACGCGAA
*
239192 ATTTGACTATCGCAACG
1 A-ATGACTATCGCAACG
239209 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 3 0.06
20 49 0.94
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:239259 original size:20 final size:20
Alignment explanation
Indices: 239234--239299 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
239224 GATTCTTTCA
239234 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
239254 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
239274 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCG
239294 TTGCGA
1 TTGCGA
239300 AAGTAAACTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:239470 original size:18 final size:18
Alignment explanation
Indices: 239447--239496 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
239437 TTTACTAAGC
239447 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
239465 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
239483 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
239497 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:241253 original size:20 final size:20
Alignment explanation
Indices: 241230--241297 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
241220 TCTGAAACTT
*
241230 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
**
241250 AAAATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
241270 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
241289 AAAATCGCA
1 AAAATCGCA
241298 TTGCGATTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 7 0.18
20 32 0.82
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:241710 original size:22 final size:22
Alignment explanation
Indices: 241683--241725 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
241673 GAGATAGACG
241683 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
*
241705 GATTTCGTCGGAGATGGGGAC
1 GATTTCGCCGGAGATGGGGAC
241726 GAATGTCGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:241926 original size:20 final size:20
Alignment explanation
Indices: 241901--241956 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
241891 GCTTTGAAAA
241901 TCGCATTGCGATAGTCATAC
1 TCGCATTGCGATAGTCATAC
* *
241921 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CATAC
*
241941 TCGCATTGCTATAGTC
1 TCGCATTGCGATAGTC
241957 GAAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATAC
Found at i:249933 original size:33 final size:33
Alignment explanation
Indices: 249891--249958 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
249881 TATAAAAAAC
249891 TTCCAAATATTTGGCAGTGAATGTTACCTAATA
1 TTCCAAATATTTGGCAGTGAATGTTACCTAATA
249924 TTCCAAATATTTGGCAGTGAATGTTACCTAATA
1 TTCCAAATATTTGGCAGTGAATGTTACCTAATA
249957 TT
1 TT
249959 TTTAACCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (33 bp):
TTCCAAATATTTGGCAGTGAATGTTACCTAATA
Found at i:250795 original size:38 final size:38
Alignment explanation
Indices: 250711--250787 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
250701 GTTCGGGTCA
250711 GGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAGTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCG
* *
250748 GGTCGGGTTTTTTTAAGTTTGATATTCGGTTCG-GTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCG
250785 GGT
1 GGT
250788 TCTGGTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 14 0.38
38 23 0.62
ACGTcount: A:0.12, C:0.10, G:0.36, T:0.42
Consensus pattern (38 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCG
Found at i:251010 original size:36 final size:37
Alignment explanation
Indices: 250959--251028 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
250949 TTTTGTTCGG
250959 GTCGGGTC-GGTTTTTTAAGTCTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTCTGATATTCGGGTCGA
* *
250995 GTCGGGTCGGGTTTTTTAAGTGTGATATTTGGGT
1 GTCGGGTCGGGTTTTTTAAGTCTGATATTCGGGT
251029 AGGATCGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.41
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTCTGATATTCGGGTCGA
Found at i:251152 original size:256 final size:257
Alignment explanation
Indices: 250480--251338 Score: 1243
Period size: 256 Copynumber: 3.4 Consensus size: 257
250470 CTTTATTTTC
* * * * *
250480 GTCGGGTCGGATCGGGTTTTTTTACA-TGTGATATTCGGGTCGGGTCGAGTCAGGTTTGGGTTTA
1 GTCGAGTCGGGTCGGGTTTTTTTA-AGTGTGATATTCGGGT-AGGTCGGGTCAGGTTCGGGTTTA
250544 GGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTG
64 GGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTG
*
250609 TTTTTATTAAATAAAAATAATTTTTTATTATTTC--G--GGTCGGGTCGGATTTCTAATTCATAT
129 TTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGTCGGGTCGAATTTCTAATTCATAT
250670 ATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCAGGTCGGGTTTTTTAAGTGTGATAT
194 ATT---GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-GGTC-GGTTTTTTAAGTGTGATAT
250735 TCGG
254 TCGG
* * *
250739 GTCGAGTCGGGTCGGGTTTTTTTAAGTTTGATATTC-GGT---TC-GGTCGGGTTCTGGTTTAGG
1 GTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTAGGTCGGGTCAGGTTCGGGTTTAGG
* * *
250799 GTGAAAAAAACCGGACCAACCCGAAAATATATATAA-TCTGGTCGGGTTGGATTAAGTCACTGTT
66 GTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTT
250863 TTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGAGTCGGGTCGAATTTCTAATTCATATA
131 TTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCG-GTCGGGTCGAATTTCTAATTCATATA
*
250928 -T-TCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGTTTTTTAAGTCTGATATTCGG
195 TTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-GGTCGGTTTTTTAAGTGTGATATTCGG
*
250990 GTCGAGTCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTAGGATCGGGTCAGGTTCGGGTTTAG
1 GTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTAGG-TCGGGTCAGGTTCGGGTTTAG
* *
251054 GGTGAAAAAAA-CGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGCCACTGT
65 GGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGT
* *
251118 TTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTGAATTTCTAATTCATAT
130 TTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTC-GGTCGGGTCGAATTTCTAATTCATAT
*
251183 ATTTGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-G--GGTTTTTTAAGTGTGACATTC
194 A-TT--GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGTCGGTTTTTTAAGTGTGATATTC
251245 GG
256 GG
* * *
251247 GTCGAGTTGGGTCGGGTTTTTCTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAG
1 GTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGT-AGGTCGGGTCAGGTTCGGGTTTAG
*
251312 GGT-AAAAAAACCGAACCGACCCGAAAA
65 GGTGAAAAAAACCGGACCGACCCGAAAA
251339 AAAAATATAA
Statistics
Matches: 548, Mismatches: 30, Indels: 45
0.88 0.05 0.07
Matches are distributed among these distances:
250 17 0.03
251 41 0.07
252 95 0.17
253 50 0.09
254 3 0.01
255 26 0.05
256 115 0.21
257 69 0.13
258 64 0.12
259 35 0.06
261 33 0.06
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (257 bp):
GTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTAGGTCGGGTCAGGTTCGGGTTTAGG
GTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTT
TTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGTCGGGTCGAATTTCTAATTCATATAT
TGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGTCGGTTTTTTAAGTGTGATATTCGG
Found at i:251283 original size:38 final size:37
Alignment explanation
Indices: 251216--251302 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 37
251206 TTTATTTTGT
251216 TCGGGTCGGGTTTTTTAAGTGTGACATTCGGGTC-GAG
1 TCGGGTCGGGTTTTTTAAGTGTGACATTCGGGTCAG-G
* *
251253 TTGGGTCGGGTTTTTCTAAGTGTGATATTCGGGTCAGG
1 TCGGGTCGGGTTTTT-TAAGTGTGACATTCGGGTCAGG
251291 TCGGGTCGGGTT
1 TCGGGTCGGGTT
251303 CGGGTTTAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 14 0.31
38 30 0.67
39 1 0.02
ACGTcount: A:0.11, C:0.13, G:0.39, T:0.37
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGACATTCGGGTCAGG
Found at i:251905 original size:16 final size:17
Alignment explanation
Indices: 251880--251924 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
251870 TATGGAATTG
251880 GATTCCAATTCC-TACA
1 GATTCCAATTCCTTACA
*
251896 GATTCTAATTCCTTTACA
1 GATTCCAATTCC-TTACA
251914 GATTCCAATTC
1 GATTCCAATTC
251925 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (17 bp):
GATTCCAATTCCTTACA
Found at i:252246 original size:19 final size:19
Alignment explanation
Indices: 252224--252267 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
252214 AATTTTGAAT
252224 TATTTTTTAACTTAAAAGC
1 TATTTTTTAACTTAAAAGC
252243 TATTTTTTAACTTAAAAGC
1 TATTTTTTAACTTAAAAGC
*
252262 CATTTT
1 TATTTT
252268 ATTTTAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
TATTTTTTAACTTAAAAGC
Found at i:254694 original size:16 final size:15
Alignment explanation
Indices: 254662--254709 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
254652 ACGAGAGATT
254662 AGAGAAGTAGAGAGA
1 AGAGAAGTAGAGAGA
*
254677 AGAGAACGTAG-GAGG
1 AGAGAA-GTAGAGAGA
254692 A-AGAAGTAGAGA-A
1 AGAGAAGTAGAGAGA
254705 AGAGA
1 AGAGA
254710 TGAAGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 10 0.36
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
AGAGAAGTAGAGAGA
Found at i:258231 original size:16 final size:15
Alignment explanation
Indices: 258199--258246 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
258189 ACGAGAGATT
258199 AGAGAAGTAGAGAGA
1 AGAGAAGTAGAGAGA
*
258214 AGAGAACGTAG-GAGG
1 AGAGAA-GTAGAGAGA
258229 A-AGAAGTAGAGA-A
1 AGAGAAGTAGAGAGA
258242 AGAGA
1 AGAGA
258247 TGAAGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 10 0.36
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
AGAGAAGTAGAGAGA
Found at i:260215 original size:48 final size:48
Alignment explanation
Indices: 260141--260522 Score: 486
Period size: 48 Copynumber: 8.0 Consensus size: 48
260131 ACTCTACAGG
* * * *
260141 ATCAACAAGATAAGTTTTACTGGTTTGAATAACATTGTGTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * *
260189 ATTAACAAGAGAACCTTTT-CTGGTTTGAATAACATTGTGTGCTTCTTC
1 ATCAACAAGAGAA-CTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * * *
260237 GTCAGA-AAGAGAACTTTTACTGGTTTTAATAACATTGATTGCTTCTTC
1 ATCA-ACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * * * *
260285 ACCAACTAGAGAACTTTTACTGGCCTGAATTACATTTTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * *
260333 ATCAACAAGAGAACTTTTACAGGTCTGAACAACACTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
*
260381 ATCAACAAGAGAACTTTTACTGGTCTGAATAGCATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * *
260429 ATCAACATGAGAACTTTTACTTGTCTGAATAACATTATTTG---CTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* *
260474 ATCAACAAGAGAACTTTTAGTGGTCTGAACAACATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
260522 A
1 A
260523 GAGGGTAACT
Statistics
Matches: 289, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
45 40 0.14
47 6 0.02
48 238 0.82
49 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (48 bp):
ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
Found at i:262363 original size:16 final size:16
Alignment explanation
Indices: 262338--262370 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
262328 TAATAAATAA
262338 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
262354 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
262370 A
1 A
262371 TAAACGTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:263510 original size:14 final size:14
Alignment explanation
Indices: 263451--263510 Score: 83
Period size: 14 Copynumber: 4.6 Consensus size: 14
263441 GATTGGGTTA
*
263451 AACATAAATGAACG
1 AACATAACTGAACG
263465 AACAT-A---AACG
1 AACATAACTGAACG
263475 AACATAACTGAACG
1 AACATAACTGAACG
263489 AACATAACTGAACG
1 AACATAACTGAACG
263503 AACATAAC
1 AACATAAC
263511 AAAACGTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.21
11 1 0.02
13 1 0.02
14 31 0.74
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.13
Consensus pattern (14 bp):
AACATAACTGAACG
Found at i:263516 original size:14 final size:14
Alignment explanation
Indices: 263465--263516 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
263455 TAAATGAACG
263465 AACATAAACGAACAT
1 AACA-AAACGAACAT
**
263480 AACTGAACGAACAT
1 AACAAAACGAACAT
**
263494 AACTGAACGAACAT
1 AACAAAACGAACAT
263508 AACAAAACG
1 AACAAAACG
263517 TTCACGAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
14 30 0.91
15 3 0.09
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (14 bp):
AACAAAACGAACAT
Found at i:265061 original size:28 final size:28
Alignment explanation
Indices: 265030--265124 Score: 172
Period size: 28 Copynumber: 3.4 Consensus size: 28
265020 TGCAATGCTT
265030 AGGCTCAAGCATTTGCAAGTAACCATGG
1 AGGCTCAAGCATTTGCAAGTAACCATGG
265058 AGGCTCAAGCATTTGCAAGTAACCATGG
1 AGGCTCAAGCATTTGCAAGTAACCATGG
*
265086 AGGCTCAAGCATTTGCATGTAACCATGG
1 AGGCTCAAGCATTTGCAAGTAACCATGG
*
265114 AGGCACAAGCA
1 AGGCTCAAGCA
265125 ACACTAGGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (28 bp):
AGGCTCAAGCATTTGCAAGTAACCATGG
Found at i:266746 original size:32 final size:34
Alignment explanation
Indices: 266705--266777 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
266695 ACACATATAT
266705 AATAAATAAATAAATA-AA-A-AGAAGAAAATAAA
1 AATAAATAAATAAATACAATATA-AAGAAAATAAA
266737 AATAAATAAATAAATACAATATAAAGAAAATAAA
1 AATAAATAAATAAATACAATATAAAGAAAATAAA
*
266771 AACAAAT
1 AATAAAT
266778 GGAATGAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 16 0.43
33 2 0.05
34 18 0.49
35 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (34 bp):
AATAAATAAATAAATACAATATAAAGAAAATAAA
Found at i:266860 original size:4 final size:4
Alignment explanation
Indices: 266851--266941 Score: 62
Period size: 4 Copynumber: 22.8 Consensus size: 4
266841 ATTTAAAGAG
* * * *
266851 AAAT AAAT AAAT AAAT AAAT ATAT ATAT -TAT AATAT TAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT AAAT
* * * *
266900 AAAT AAAT -AA- AAAT AATAT ATAT ATAT ATAT ACAT AAAT AAA
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAA
266942 ATACCTAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
3 7 0.09
4 58 0.78
5 9 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (4 bp):
AAAT
Found at i:266884 original size:44 final size:44
Alignment explanation
Indices: 266822--266929 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 44
266812 AAATAATAGT
*
266822 AAAAATA-ATATATAATAATATT-TAAAGAGAAATAAATAAATAA
1 AAAAATATATATATTATAATATTATAAA-AGAAATAAATAAATAA
* *
266865 ATAAATATATATATTATAATATTAATAAAATAAATAAATAAATAA
1 AAAAATATATATATTATAATATT-ATAAAAGAAATAAATAAATAA
266910 AAATAATATATATATATATA
1 AAA-AATATATATAT-TATA
266930 TACATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
43 6 0.11
44 14 0.25
45 17 0.30
46 15 0.27
47 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (44 bp):
AAAAATATATATATTATAATATTATAAAAGAAATAAATAAATAA
Found at i:266937 original size:44 final size:43
Alignment explanation
Indices: 266812--266941 Score: 135
Period size: 45 Copynumber: 3.0 Consensus size: 43
266802 AATAAAAAGG
* *
266812 AAATAATAGTAAAAATAATATATA-ATA-ATAT-TTAAAGAGAAAT
1 AAATAA-A-TAAAAATAATATATATATATATATAATAAA-ATAAAT
*
266855 AAATAAATAAATA-AATATATATATTATAATATTAATAAAATAAAT
1 AAATAAATAAAAATAATATATATA-TAT-ATA-TAATAAAATAAAT
266900 AAATAAATAAAAATAATATATATATATATATACAT-AAATAAA
1 AAATAAATAAAAATAATATATATATATATATA-ATAAAATAAA
266942 ATACCTAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
40 8 0.11
41 6 0.08
42 3 0.04
43 15 0.20
44 8 0.11
45 21 0.28
46 14 0.19
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (43 bp):
AAATAAATAAAAATAATATATATATATATATAATAAAATAAAT
Found at i:266958 original size:48 final size:46
Alignment explanation
Indices: 266824--266944 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 46
266814 ATAATAGTAA
* * *
266824 AAATA-ATATATAATAATAT-TTAAAGAGAAATAAATAAAT--AAAT
1 AAATATATATATTATAATATAATAAA-ATAAATAAATAAATAAAAAT
266867 AAATATATATATTATAATATTAATAAAATAAATAAATAAATAAAAAT
1 AAATATATATATTATAATA-TAATAAAATAAATAAATAAATAAAAAT
266914 AATATATATATATATATACATA-AATAAAATA
1 AA-ATATATATAT-TATA-ATATAATAAAATA
266945 CCTAATAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
43 5 0.07
44 12 0.18
45 14 0.21
46 4 0.06
47 6 0.09
48 19 0.28
49 4 0.06
50 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (46 bp):
AAATATATATATTATAATATAATAAAATAAATAAATAAATAAAAAT
Found at i:270012 original size:6 final size:5
Alignment explanation
Indices: 269976--270005 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
269966 ACACACCTTA
269976 TTTTC TTTTC TTTTC TTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
270006 TCATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:270015 original size:10 final size:11
Alignment explanation
Indices: 269975--270018 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
269965 AACACACCTT
269975 ATTTTCTTTTC
1 ATTTTCTTTTC
269986 -TTTTCTTTTC
1 ATTTTCTTTTC
*
269996 TTTTTCTTTTTC
1 ATTTTC-TTTTC
270008 ATTTT-TTTTC
1 ATTTTCTTTTC
270018 A
1 A
270019 ATTTAGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 16 0.53
11 5 0.17
12 9 0.30
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (11 bp):
ATTTTCTTTTC
Found at i:270015 original size:16 final size:15
Alignment explanation
Indices: 269975--270017 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
269965 AACACACCTT
269975 ATTTTCTTTTCTTTTC
1 ATTTT-TTTTCTTTTC
*
269991 TTTTCTTTTTCTTTTTC
1 ATTT-TTTTTC-TTTTC
270008 ATTTTTTTTC
1 ATTTTTTTTC
270018 AATTTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTTTTCTTTTC
Found at i:280462 original size:39 final size:38
Alignment explanation
Indices: 280419--280498 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
280409 ACACATATAT
*
280419 AATAAATAAATAAATAAAACCA-AGAAGAAAATAAAAATA
1 AATAAATAAATAAATAAAA-CATA-AAGAAAATAAAAACA
* *
280458 AATAAATAAATAAATACAATATAAAGAAAATAAAAACA
1 AATAAATAAATAAATAAAACATAAAGAAAATAAAAACA
280496 AAT
1 AAT
280499 GGAATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 18 0.49
39 19 0.51
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (38 bp):
AATAAATAAATAAATAAAACATAAAGAAAATAAAAACA
Found at i:280465 original size:35 final size:38
Alignment explanation
Indices: 280419--280498 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 38
280409 ACACATATAT
* *
280419 AATAAATAAATAAATAAA-ACCA-A-GAAGAAAATAAA
1 AATAAATAAATAAATAAATACAATATAAAGAAAATAAA
280454 AATAAATAAATAAATAAATACAATATAAAGAAAATAAA
1 AATAAATAAATAAATAAATACAATATAAAGAAAATAAA
*
280492 AACAAAT
1 AATAAAT
280499 GGAATGAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 18 0.46
36 3 0.08
37 1 0.03
38 17 0.44
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (38 bp):
AATAAATAAATAAATAAATACAATATAAAGAAAATAAA
Found at i:280566 original size:23 final size:23
Alignment explanation
Indices: 280532--280585 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
280522 ATAAAAAGGA
* * *
280532 AATAATA-GTAAAAATAATATAT
1 AATAATATTTAAAAAGAAAATAT
280554 AATAATATTTAAAAAGAAAATAT
1 AATAATATTTAAAAAGAAAATAT
280577 -ATATATATT
1 AATA-ATATT
280586 AGAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAATATTTAAAAAGAAAATAT
Found at i:280592 original size:31 final size:29
Alignment explanation
Indices: 280541--280620 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
280531 AAATAATAGT
*
280541 AAAA-ATAATATATAATAATATTTAAAAAG
1 AAAATATAATATATAAGAATA-TTAAAAAG
* *
280570 AAAATATATATATATTAGAATATTAATAAG
1 AAAATATA-ATATATAAGAATATTAAAAAG
* *
280600 ACAAATA-AATAAATAAAAATA
1 A-AAATATAATATATAAGAATA
280621 ATATATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 14 0.33
30 12 0.29
31 16 0.38
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATATAATATATAAGAATATTAAAAAG
Found at i:282412 original size:42 final size:42
Alignment explanation
Indices: 282353--282463 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 42
282343 GGGAGAAGGC
282353 AAAGCCATGGAATTTAATAATTAAAGCACTATAGAATAAGAA
1 AAAGCCATGGAATTTAATAATTAAAGCACTATAGAATAAGAA
* * *
282395 AAAGCCATGAAATTTAATAATTAAAGCACTATGGAATAAGAC
1 AAAGCCATGGAATTTAATAATTAAAGCACTATAGAATAAGAA
* *
282437 AAAGCCATGGACTTTAACAATTAAAGC
1 AAAGCCATGGAATTTAATAATTAAAGC
282464 TTTATAATAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (42 bp):
AAAGCCATGGAATTTAATAATTAAAGCACTATAGAATAAGAA
Found at i:282421 original size:22 final size:22
Alignment explanation
Indices: 282353--282421 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
282343 GGGAGAAGGC
*
282353 AAAGCCATGGAATTTAATAATT
1 AAAGCCATGAAATTTAATAATT
*
282375 AAAGCACTAT-AGAA--TAAGAA--
1 AAAGC-C-ATGA-AATTTAATAATT
282395 AAAGCCATGAAATTTAATAATT
1 AAAGCCATGAAATTTAATAATT
282417 AAAGC
1 AAAGC
282422 ACTATGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 16
0.65 0.05 0.29
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 10 0.28
22 15 0.42
23 1 0.03
24 4 0.11
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (22 bp):
AAAGCCATGAAATTTAATAATT
Found at i:284453 original size:106 final size:106
Alignment explanation
Indices: 284232--284490 Score: 313
Period size: 106 Copynumber: 2.4 Consensus size: 106
284222 CGTAAGTAAG
* * * * *
284232 TTGTATTGT-TCCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAAT
1 TTGTATTGTCT-CAAGTCCAATATCATCCGCCGTGAAGTTGAAATTAGCTCTGAAACTGGGAAAT
*
284296 TATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
65 TATTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAAC
* * *
284338 TTGTATTGTCTCAAGTCCAATATCATTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATT
1 TTGTATTGTCTCAAGTCCAATATCATCCGCCGTGAAGTTGAAATTAGCTCTGAAACTGGGAAATT
* * *
284403 GTTTGTTGACAACTAGTCGTCCCTTCATTGTGAAGTTGAAC
66 ATTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAAC
* * * * * *
284444 TTGTGTTGTCTTAAATGTCACGATATCCTCCGTCGTGGAGTTGAAAT
1 TTGTATTGTC-TCAA-GTC-CAATATCATCCGCCGTGAAGTTGAAAT
284491 CGGGGATGGC
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
106 101 0.78
107 4 0.03
108 3 0.02
109 21 0.16
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (106 bp):
TTGTATTGTCTCAAGTCCAATATCATCCGCCGTGAAGTTGAAATTAGCTCTGAAACTGGGAAATT
ATTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAAC
Found at i:285002 original size:72 final size:75
Alignment explanation
Indices: 284880--285021 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 75
284870 AAAAATAGTC
* * * *
284880 TTGAGTGAAATGAAATGCATTCTTTCTAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTTA
1 TTGAGTGAAATGAAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAAGTC-TGTTTTA
284944 AGAAAAACAATT
65 A-AAAAACAATT
*
284956 TTGAGTGAAAT-AAAT-C-TTATTTCAAGT-AAAACAGTATCAAGTGAGACAAAGTCTGTTTTAA
1 TTGAGTGAAATGAAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAAGTCTGTTTTAA
285017 AAAAA
66 AAAAA
285022 GTAATCTCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
71 5 0.08
72 28 0.47
73 11 0.18
74 1 0.02
75 4 0.07
76 11 0.18
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (75 bp):
TTGAGTGAAATGAAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAAGTCTGTTTTAA
AAAAACAATT
Found at i:285035 original size:72 final size:75
Alignment explanation
Indices: 284883--285040 Score: 164
Period size: 72 Copynumber: 2.1 Consensus size: 75
284873 AATAGTCTTG
* * * *
284883 AGTGAAATGAAATGCATTCTTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGAA
1 AGTGAAAT-AAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAATCTTGTTTTAAGAA
* **
284948 AAACAATTTTG
65 AAACAATCTCA
*
284959 AGTGAAATAAAT-C-TTATTTCAAGT-AAAACAGTATCAAGTGAGACAAAGTC-TGTTTTAA-AA
1 AGTGAAATAAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAA-TCTTGTTTTAAGAA
*
285019 AAAGTAATCTCA
65 AAA-CAATCTCA
*
285031 AGTGAGATAA
1 AGTGAAATAA
285041 TCATCTGCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
71 5 0.07
72 41 0.59
73 11 0.16
74 1 0.01
75 4 0.06
76 8 0.11
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.29
Consensus pattern (75 bp):
AGTGAAATAAATGCATTATTTCAAGTGAAAACAGTATCAAGCGAGACAAATCTTGTTTTAAGAAA
AACAATCTCA
Found at i:285832 original size:22 final size:22
Alignment explanation
Indices: 285806--285882 Score: 154
Period size: 22 Copynumber: 3.5 Consensus size: 22
285796 TCGTGTTTGG
285806 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
285828 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
285850 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
285872 TCAAAGGTTTG
1 TCAAAGGTTTG
285883 ATAGGGTAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:286511 original size:17 final size:16
Alignment explanation
Indices: 286489--286528 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
286479 TCTTTTTCCC
286489 TTTTTCTTTTTGATTCT
1 TTTTTCTTTTTG-TTCT
*
286506 TTTTTCCTTTTGTTCT
1 TTTTTCTTTTTGTTCT
*
286522 TGTTTCT
1 TTTTTCT
286529 CATGTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.03, C:0.15, G:0.07, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTGTTCT
Found at i:288526 original size:5 final size:5
Alignment explanation
Indices: 288516--288553 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
288506 GCAAGTGATG
288516 AAAAT AAAAT AAAAT AAAAT AAAAT AAAGAT GAAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT A
288554 GTTAGTGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 24 0.77
6 4 0.13
7 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:288536 original size:15 final size:17
Alignment explanation
Indices: 288512--288553 Score: 70
Period size: 15 Copynumber: 2.6 Consensus size: 17
288502 TGATGCAAGT
288512 GATGAAAATAAAATAAA
1 GATGAAAATAAAATAAA
288529 -AT-AAAATAAAATAAA
1 GATGAAAATAAAATAAA
288544 GATGAAAATA
1 GATGAAAATA
288554 GTTAGTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.57
16 4 0.17
17 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (17 bp):
GATGAAAATAAAATAAA
Found at i:289866 original size:24 final size:24
Alignment explanation
Indices: 289838--289910 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
289828 AGGCAAAGCC
289838 ATGGAATTTAATAATTAAAGCACT
1 ATGGAATTTAATAATTAAAGCACT
*
289862 ATGGAA--TAAGAA--AAAGC-C-
1 ATGGAATTTAATAATTAAAGCACT
*
289880 ATGAAATTTAATAATTAAAGCACT
1 ATGGAATTTAATAATTAAAGCACT
289904 ATGGAAT
1 ATGGAAT
289911 AAGACAAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
18 5 0.13
19 1 0.03
20 10 0.26
22 10 0.26
23 1 0.03
24 12 0.31
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.27
Consensus pattern (24 bp):
ATGGAATTTAATAATTAAAGCACT
Found at i:289891 original size:42 final size:42
Alignment explanation
Indices: 289832--289942 Score: 186
Period size: 42 Copynumber: 2.6 Consensus size: 42
289822 GGGAGAAGGC
289832 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
* *
289874 AAAGCCATGAAATTTAATAATTAAAGCACTATGGAATAAGAC
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
* *
289916 AAAGCCATGGACTTTAAAAATTAAAGC
1 AAAGCCATGGAATTTAATAATTAAAGC
289943 TTTATAATAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (42 bp):
AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
Found at i:289900 original size:22 final size:22
Alignment explanation
Indices: 289832--289942 Score: 76
Period size: 22 Copynumber: 5.2 Consensus size: 22
289822 GGGAGAAGGC
289832 AAAGCCATGGAATTTAATAATT
1 AAAGCCATGGAATTTAATAATT
*
289854 AAAGCACTATGGAA--TAAGAA--
1 AAAGC-C-ATGGAATTTAATAATT
*
289874 AAAGCCATGAAATTTAATAATT
1 AAAGCCATGGAATTTAATAATT
* *
289896 AAAGCACTATGGAA--TAA-GA-C
1 AAAGC-C-ATGGAATTTAATAATT
* *
289916 AAAGCCATGGACTTTAAAAATT
1 AAAGCCATGGAATTTAATAATT
289938 AAAGC
1 AAAGC
289943 TTTATAATAG
Statistics
Matches: 68, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
18 10 0.15
19 2 0.03
20 18 0.26
21 2 0.03
22 23 0.34
23 2 0.03
24 11 0.16
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (22 bp):
AAAGCCATGGAATTTAATAATT
Found at i:295768 original size:56 final size:56
Alignment explanation
Indices: 295707--295812 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 56
295697 AGTTTGAAAA
** *
295707 AAATATTTTAATTTAAAATGTTAATTTACAATTAATTGAATTAAAATATGAGACTT
1 AAATATTTTAATCCAAAATGTTAATTTACAATTAATTGAACTAAAATATGAGACTT
* * *
295763 AAATATTTTAATCCAAAATGTTAATTTATAGTTAGTTGAACTAAAATATG
1 AAATATTTTAATCCAAAATGTTAATTTACAATTAATTGAACTAAAATATG
295813 GGATTCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (56 bp):
AAATATTTTAATCCAAAATGTTAATTTACAATTAATTGAACTAAAATATGAGACTT
Found at i:297021 original size:22 final size:20
Alignment explanation
Indices: 296986--297047 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
296976 AAAAGATGAT
*
296986 TTTTACCCTAAAATAAAATG
1 TTTTAACCTAAAATAAAATG
* *
297006 TTTTAGTATCTAAAATAACA--
1 TTTTA--ACCTAAAATAAAATG
297026 TTTTAACCTAAAATAAAATG
1 TTTTAACCTAAAATAAAATG
297046 TT
1 TT
297048 GAAACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 11 0.33
20 12 0.36
22 10 0.30
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTTAACCTAAAATAAAATG
Found at i:299826 original size:66 final size:66
Alignment explanation
Indices: 299720--299870 Score: 248
Period size: 66 Copynumber: 2.3 Consensus size: 66
299710 TGAAAGCGAC
* *
299720 GTCTTCGTGAGAATTTATTATCCGTGTCAAACCTAGCAAGTAGCTTCTGGGGTTCACATGTCTTA
1 GTCTTCGTGAGAATTTATTATCCGTGCCAAACCTAGCAAGTAGCTTCCGGGGTTCACATGTCTTA
299785 T
66 T
* * *
299786 GTCTTCATGAGAATTTATTATCCGTGCCAGACCTAGCAAGTAGCTTCCGGGGTTCATATGTCTTA
1 GTCTTCGTGAGAATTTATTATCCGTGCCAAACCTAGCAAGTAGCTTCCGGGGTTCACATGTCTTA
299851 T
66 T
*
299852 GTCTTCGTGAGGATTTATT
1 GTCTTCGTGAGAATTTATT
299871 CTCCATGTGA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (66 bp):
GTCTTCGTGAGAATTTATTATCCGTGCCAAACCTAGCAAGTAGCTTCCGGGGTTCACATGTCTTA
T
Found at i:304123 original size:74 final size:74
Alignment explanation
Indices: 304037--304423 Score: 614
Period size: 74 Copynumber: 5.2 Consensus size: 74
304027 AAAAGATCAG
* * * * *
304037 AAATTTTTTCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCATCTCGCTTGATACAATTTTAA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
304102 CTTGAAACA
66 CTTGAAACA
** * *
304111 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACCCCGTCACACTTGAGACAGTTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
304176 CTTGAAACA
66 CTTGAAACA
* * *
304185 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCACTTGAGACAGTTTTCT
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
304250 CTTGAAACA
66 CTTGAAACA
* * *
304259 AAA-TTTATCTCACTCTAGAGAGTTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGACAGTTTTC
1 AAATTTTATCTCACTCGAGATAG-TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
304323 ACTTGAAACA
65 ACTTGAAACA
*
304333 AAATTTTATCTCACTCGAGATAGTTTTTCTTATAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
304398 CTTGAAACA
66 CTTGAAACA
304407 AAATTTTATCTCACTCG
1 AAATTTTATCTCACTCG
304424 TGTAGATGCT
Statistics
Matches: 289, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
73 17 0.06
74 255 0.88
75 17 0.06
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (74 bp):
AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCA
CTTGAAACA
Found at i:309783 original size:15 final size:14
Alignment explanation
Indices: 309758--309845 Score: 65
Period size: 15 Copynumber: 5.9 Consensus size: 14
309748 AAGAAGAAAT
309758 AAAAGAGAAAATGAA
1 AAAAGA-AAAATGAA
309773 AAAATGAAAAA--AA
1 AAAA-GAAAAATGAA
*
309786 TAATAATAAAAATGAGA
1 -AA-AAGAAAAATGA-A
*
309803 AGAAGAAAAA-GAA
1 AAAAGAAAAATGAA
309816 GAAAAGAAAAATGAGGA
1 -AAAAGAAAAATGA--A
309833 AAAAGAAAAATGA
1 AAAAGAAAAATGA
309846 TGGAAAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.05
14 18 0.31
15 19 0.32
16 17 0.29
17 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAAGAAAAATGAA
Found at i:309786 original size:29 final size:28
Alignment explanation
Indices: 309754--309842 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
309744 CTTGAAGAAG
309754 AAATAAAAGAGAAAATGA-AAAAATGAAAA
1 AAATAAAAGA-AAAATGAGAAAAA-GAAAA
* *
309783 AAATAATAATAAAAATGAGAAGAAGAAAA
1 AAATAA-AAGAAAAATGAGAAAAAGAAAA
*
309812 AGAAGAAAAGAAAAATGAGGAAAAAGAAAA
1 A-AATAAAAGAAAAATGA-GAAAAAGAAAA
309842 A
1 A
309843 TGATGGAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 29 0.57
30 22 0.43
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (28 bp):
AAATAAAAGAAAAATGAGAAAAAGAAAA
Found at i:309842 original size:17 final size:16
Alignment explanation
Indices: 309793--309853 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
309783 AAATAATAAT
*
309793 AAAAATGA-GAAGAAG
1 AAAAATGAGGAAAAAG
*
309808 AAAAA-GAAG-AAAAG
1 AAAAATGAGGAAAAAG
309822 AAAAATGAGGAAAAAG
1 AAAAATGAGGAAAAAG
309838 AAAAATGATGGAAAAA
1 AAAAATGA-GGAAAAA
309854 AGAGAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.28
15 9 0.22
16 13 0.32
17 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (16 bp):
AAAAATGAGGAAAAAG
Found at i:309855 original size:18 final size:18
Alignment explanation
Indices: 309817--309870 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
309807 GAAAAAGAAG
309817 AAAAGAAAAATGA-GG-A
1 AAAAGAAAAATGATGGAA
309833 AAAAGAAAAATGATGGAA
1 AAAAGAAAAATGATGGAA
*
309851 AAAAGAGAAA-GAATGGAA
1 AAAAGAAAAATG-ATGGAA
309869 AA
1 AA
309871 TGGAAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 13 0.38
17 3 0.09
18 18 0.53
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAATGATGGAA
Found at i:311370 original size:55 final size:54
Alignment explanation
Indices: 311300--311592 Score: 367
Period size: 55 Copynumber: 5.4 Consensus size: 54
311290 GATTGAGTCA
* *
311300 TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTC
1 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTCGAGTTC
*
311355 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGGTCGAGTTC
1 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGTTCGAGTTC
*
311410 TATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTTC
1 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTCGAGTTC
* ** * * * *
311465 TATACTATCTGAAGGAATAGAGAGCATACGCATTTTATGAAAATTGTTTGAGTTC
1 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGTTCGAGTTC
* * *
311520 TATACTCCCTGAACGG-ATAGGGAGC-GACCCGTTTATTGAAGATTGATCGAG-TC
1 TATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTCGAGTTC
*
311573 TTATACTCCCTGAAGGAATA
1 -TATACTCTCTGAAGGAATA
311593 AGGAGCAGAC
Statistics
Matches: 210, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
53 4 0.02
54 36 0.17
55 167 0.80
56 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (54 bp):
TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTTGAAGATTGTTCGAGTTC
Found at i:311428 original size:110 final size:110
Alignment explanation
Indices: 311300--311603 Score: 418
Period size: 110 Copynumber: 2.8 Consensus size: 110
311290 GATTGAGTCA
311300 TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCT
1 TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCT
* * *
311365 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGGTCGAGTTC
66 GAAGGAATAGAGAGCAGACCCATTTTATGAAAATTGGTCGAGTTC
* * *
311410 TATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTTCTATACTATCT
1 TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCT
* * * *
311475 GAAGGAATAGAGAGCATACGCATTTTATGAAAATTGTTTGAGTTC
66 GAAGGAATAGAGAGCAGACCCATTTTATGAAAATTGGTCGAGTTC
* * * * *
311520 TATACTCCCTGAACGG-ATAGGGAGC-GACCCGTTTATTGAAGATTGATCGAG-TCTTATACTCC
1 TATACTCTCTGAA-GGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTC-TATACTCT
311582 CTGAAGGAATA-AGGAGCAGACC
64 CTGAAGGAATAGA-GAGCAGACC
311604 TGTCATTCAA
Statistics
Matches: 172, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
108 3 0.02
109 47 0.27
110 120 0.70
111 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (110 bp):
TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCT
GAAGGAATAGAGAGCAGACCCATTTTATGAAAATTGGTCGAGTTC
Found at i:314337 original size:61 final size:62
Alignment explanation
Indices: 314264--314612 Score: 216
Period size: 74 Copynumber: 5.1 Consensus size: 62
314254 AATCGTTTCG
* * *
314264 ACAACTCGAGATAGTTTTTCTTAAAACAAACTTTGT-TCCGCTTGAGACA-ATTTCACTTGAA
1 ACAACTCAAGATAGTTTTTCTTAAAACAAACTTCGTCT-CGCTTAAGACAGATTTCACTTGAA
* * *
314325 ACAACTCAAGATAGTTTTTCTTAAAATAAACTTCGTCTTGCTTAAGACAGTTTTCACTTGAA
1 ACAACTCAAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGATTTCACTTGAA
* * * *
314387 ACAAAATTTTATCTCACTCGAGTTAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTT
1 AC---A----A-CTCA----AGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGATT
*
314452 TCACTTAAA
54 TCACTTGAA
*
314461 ACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGTTT
1 AC---A----A-CTCA----AGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGATT
314526 TCACTTGAA
54 TCACTTGAA
* * *
314535 ACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGACAGTTT
1 AC---A----A-CTCA----AGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGATT
314600 TCACTTGAA
54 TCACTTGAA
314609 ACAA
1 ACAA
314613 AATTTTATCT
Statistics
Matches: 256, Mismatches: 18, Indels: 22
0.86 0.06 0.07
Matches are distributed among these distances:
61 42 0.16
62 14 0.05
65 1 0.00
67 1 0.00
69 1 0.00
70 4 0.02
71 1 0.00
74 192 0.75
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (62 bp):
ACAACTCAAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGATTTCACTTGAA
Found at i:314457 original size:74 final size:74
Alignment explanation
Indices: 314328--314797 Score: 694
Period size: 74 Copynumber: 6.4 Consensus size: 74
314318 ACTTGAAACA
* * * *
314328 ACTCAAGATAGTTTTTCTTAAAATAAACTTCGTCTTGCTTAAGACAGTTTTCACTTGAAACAAAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
314393 TTTTATCTC
66 TTTTATCTC
* * *
314402 ACTCGAGTTAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCACTTAAAACAAAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
314467 TTTTATCTC
66 TTTTATCTC
*
314476 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTAAGACAGTTTTCACTTGAAACAAAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
314541 TTTTATCTC
66 TTTTATCTC
*
314550 ACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
314615 TTTTATCTC
66 TTTTATCTC
* * *
314624 ACTCGAGATAGTTTTTCTTAAAACAAACTTTGTATTGCTTGAGACAGTTTTCACTTGAAACAAAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
314689 TTTTATCTC
66 TTTTATCTC
* * ** * * *
314698 ACTTGAGATTGTTTTTCTTAAAACAAACTTTTTCTCGGTTGAGACAGTTTTC-CCTCAAA-ATAA
1 ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACA-AA
*
314761 ATTTTATTTC
65 ATTTTATCTC
** *
314771 AC-CTGAGATAGTTCCTCTTGAAACAAA
1 ACTC-GAGATAGTTTTTCTTAAAACAAA
314798 TTTATTTTCA
Statistics
Matches: 365, Mismatches: 29, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
72 1 0.00
73 37 0.10
74 327 0.90
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (74 bp):
ACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACTTGAAACAAAA
TTTTATCTC
Found at i:315193 original size:43 final size:44
Alignment explanation
Indices: 315117--315226 Score: 107
Period size: 43 Copynumber: 2.5 Consensus size: 44
315107 TACTCAATCT
* * * * *
315117 TTCACATAAGGAGTTTGATCAGT-AACAACCTTTCACTTGATTC
1 TTCACAGAAGGAGTTGGATCAATGAACAACCTTTCACATGATTA
* * *
315160 TTCACAGAAGGAGTTGGATCAATGAA-AATCTTTCGCATGGTTA
1 TTCACAGAAGGAGTTGGATCAATGAACAACCTTTCACATGATTA
* * *
315203 TTCATAGAATGAGTTGAATCAATG
1 TTCACAGAAGGAGTTGGATCAATG
315227 TCAATCTGGT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 53 0.96
44 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (44 bp):
TTCACAGAAGGAGTTGGATCAATGAACAACCTTTCACATGATTA
Found at i:316092 original size:23 final size:23
Alignment explanation
Indices: 316058--316154 Score: 115
Period size: 23 Copynumber: 4.2 Consensus size: 23
316048 AGAATATACA
316058 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* *
316081 CCAAAAGACCACATAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
316104 CCGAAGGACCGCGTAGATATGTC
1 CCGAAGGACCACATAGAAATGTC
* *
316127 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAAATGTC
316150 CCGAA
1 CCGAA
316155 TGACTGCGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 1 0.02
23 62 0.98
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:316128 original size:46 final size:46
Alignment explanation
Indices: 316071--316167 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
316061 AAGTGCCACA
316071 TAGAAATGTCCCAAAAGACCACATAGAAATGTCCCGAAGGACCGCG
1 TAGAAATGTCCCAAAAGACCACATAGAAATGTCCCGAAGGACCGCG
* * * * * * *
316117 TAGATATGTCCCGAAGGACCACGTAGAATTGTCCCGAATGACTGCG
1 TAGAAATGTCCCAAAAGACCACATAGAAATGTCCCGAAGGACCGCG
316163 TAGAA
1 TAGAA
316168 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (46 bp):
TAGAAATGTCCCAAAAGACCACATAGAAATGTCCCGAAGGACCGCG
Found at i:316164 original size:23 final size:23
Alignment explanation
Indices: 316071--316167 Score: 97
Period size: 23 Copynumber: 4.2 Consensus size: 23
316061 AAGTGCCACA
* * * * *
316071 TAGAAATGTCCCAAAAGACCACA
1 TAGAATTGTCCCGAAGGACCGCG
*
316094 TAGAAATGTCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
*
316117 TAG-ATATGTCCCGAAGGACCACG
1 TAGAAT-TGTCCCGAAGGACCGCG
* *
316140 TAGAATTGTCCCGAATGACTGCG
1 TAGAATTGTCCCGAAGGACCGCG
316163 TAGAA
1 TAGAA
316168 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 1 0.02
23 60 0.95
24 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Found at i:319218 original size:30 final size:30
Alignment explanation
Indices: 319147--319224 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
319137 CACGAACTTA
319147 AAAGATTAAAATAG-AAAAACCAGAAATTT
1 AAAGATTAAAATAGCAAAAACCAGAAATTT
**
319176 AAAG--TACCAAATAGCAAAAA-CAGAGGTTT
1 AAAGATTA--AAATAGCAAAAACCAGAAATTT
*
319205 GAAAGATTAAAATAACAAAA
1 -AAAGATTAAAATAGCAAAA
319225 CAATCCTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
27 2 0.05
29 17 0.43
30 19 0.47
32 2 0.05
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (30 bp):
AAAGATTAAAATAGCAAAAACCAGAAATTT
Found at i:319855 original size:3 final size:3
Alignment explanation
Indices: 319847--319915 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
319837 TTAGGTTAGG
* * * *
319847 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TATA TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
319893 CAA CAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
319916 TTTTTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 57 0.97
4 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:320601 original size:134 final size:133
Alignment explanation
Indices: 320114--320599 Score: 373
Period size: 134 Copynumber: 3.7 Consensus size: 133
320104 TGGTCGTCTA
* * * ** *
320114 AGGGTTGACACAGCTCCTACATGATGAGGATATATGGTCAGGG-GATGACAC--TTCTCATACGT
1 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC-GGGAGATGACACGATTC-C-TACGT
* **** * *
320176 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGAT
63 GATGAGGACAGATTGGCCATCTTTAGGAA--GTGATAACACGGTTCCTACGTGATGAGGACGGCT
** *
320241 GACTATCAA
126 GGTTATC-T
* * * * * * * *
320250 AGGGGTGACACGGCTCCTACGTGATGAGGAGATTTGGTCGGGTGAGGAAACGGTTTCTACGCGAT
1 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGAGATGACACGATTCCTACGTGAT
* ** * * * * * *
320315 AAGGAC-GACAGGTCATCTATA-G--GTGATAACATGGTTCCTATGTAATGAGGACGACTGGTTA
66 GAGGACAGATTGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
320376 TCT
131 TCT
* * * * * * * * *
320379 -GGGGTGAAACGGTTCCTACGCGATAAGGACGACTGGTCGGGGGATGACACGACTCATACGTGAT
1 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGAGATGACACGATTCCTACGTGAT
* * * * *
320443 GA--AGAGTTCTGGTCATCTTTAGGGAATGTGATAACACGGTTCCTACGCGATGATGACGGCTGG
66 GAGGACAGAT-TGGCCATCTTTA-GGAA-GTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
320506 TTATCT
128 TTATCT
**
320512 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGAGATGACACGATTCCTACGTGAT
1 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGAGATGACACGATTCCTACGTGAT
320577 GAGGACAG-TTGGCCATCTTTAGG
66 GAGGACAGATTGGCCATCTTTAGG
320600 GATAATGGTT
Statistics
Matches: 269, Mismatches: 68, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
126 1 0.00
127 1 0.00
128 59 0.22
130 34 0.13
133 38 0.14
134 67 0.25
135 13 0.05
136 53 0.20
137 1 0.00
138 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (133 bp):
AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGAGATGACACGATTCCTACGTGAT
GAGGACAGATTGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
TCT
Found at i:321312 original size:133 final size:137
Alignment explanation
Indices: 321053--321327 Score: 432
Period size: 133 Copynumber: 2.0 Consensus size: 137
321043 ATTTTTCAAA
* * *
321053 AGAAATTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATTTCAAAGGTGATTAGCTTTG
1 AGAAATTATCTCAAGAGAGACAAAATTGGTTTAAAGAGAAACAATTTCAAAGGTGATCAGCTTTG
* *
321118 TTTTATATGAAACAAACTCAAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATT
66 TTTCATATGAAACAAACTCAAAAATTTATATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATT
321183 TGTTTTG
131 TGTTTTG
* *
321190 AGAAATTGTCTC-A-AGAGAC-AACTTGGTTTAAAGAGAAACAATTTCAAAGGTGATCAGCTTTG
1 AGAAATTATCTCAAGAGAGACAAAATTGGTTTAAAGAGAAACAATTTCAAAGGTGATCAGCTTTG
* *
321252 TTTCATGTGAAAC-AACTCAAAAATTTATATCTCAAAGGAAAAATGTCTCAAGCGATACGAAATT
66 TTTCATATGAAACAAACTCAAAAATTTATATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATT
*
321316 TGTTTTT
131 TGTTTTG
321323 AGAAA
1 AGAAA
321328 AACACCATCA
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
133 60 0.47
134 50 0.39
135 6 0.05
136 1 0.01
137 11 0.09
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (137 bp):
AGAAATTATCTCAAGAGAGACAAAATTGGTTTAAAGAGAAACAATTTCAAAGGTGATCAGCTTTG
TTTCATATGAAACAAACTCAAAAATTTATATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATT
TGTTTTG
Found at i:327975 original size:3 final size:3
Alignment explanation
Indices: 327969--328012 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
327959 GTAGTAGTAG
327969 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
328013 TTTTTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:332224 original size:280 final size:280
Alignment explanation
Indices: 331723--332284 Score: 1124
Period size: 280 Copynumber: 2.0 Consensus size: 280
331713 ATGTTAGGTC
331723 TTTTGACCCTTTCCTTTGTCAAATTGCCTATGACAGTGGCAACGCTCAATGACCAACATATTAAA
1 TTTTGACCCTTTCCTTTGTCAAATTGCCTATGACAGTGGCAACGCTCAATGACCAACATATTAAA
331788 GATTTATTTAAAACTAAAAGAGAAAAAAAGTTAAATTTTATCTATTTACTTGTAAAAAGCTTTGA
66 GATTTATTTAAAACTAAAAGAGAAAAAAAGTTAAATTTTATCTATTTACTTGTAAAAAGCTTTGA
331853 TTATAGTACATTTCTTCTATACTTTCATAACAAAGGGTAAAACAATAGTAATAAAGGAACCTACA
131 TTATAGTACATTTCTTCTATACTTTCATAACAAAGGGTAAAACAATAGTAATAAAGGAACCTACA
331918 ATGTGGTATTATTCTCTCTCCTTTATCTGATCAAAAGTCGACAAGTGCATCACCCATCTTTTCCA
196 ATGTGGTATTATTCTCTCTCCTTTATCTGATCAAAAGTCGACAAGTGCATCACCCATCTTTTCCA
331983 TTCATCCCTATCAATCCCAA
261 TTCATCCCTATCAATCCCAA
332003 TTTTGACCCTTTCCTTTGTCAAATTGCCTATGACAGTGGCAACGCTCAATGACCAACATATTAAA
1 TTTTGACCCTTTCCTTTGTCAAATTGCCTATGACAGTGGCAACGCTCAATGACCAACATATTAAA
332068 GATTTATTTAAAACTAAAAGAGAAAAAAAGTTAAATTTTATCTATTTACTTGTAAAAAGCTTTGA
66 GATTTATTTAAAACTAAAAGAGAAAAAAAGTTAAATTTTATCTATTTACTTGTAAAAAGCTTTGA
332133 TTATAGTACATTTCTTCTATACTTTCATAACAAAGGGTAAAACAATAGTAATAAAGGAACCTACA
131 TTATAGTACATTTCTTCTATACTTTCATAACAAAGGGTAAAACAATAGTAATAAAGGAACCTACA
332198 ATGTGGTATTATTCTCTCTCCTTTATCTGATCAAAAGTCGACAAGTGCATCACCCATCTTTTCCA
196 ATGTGGTATTATTCTCTCTCCTTTATCTGATCAAAAGTCGACAAGTGCATCACCCATCTTTTCCA
332263 TTCATCCCTATCAATCCCAA
261 TTCATCCCTATCAATCCCAA
332283 TT
1 TT
332285 CCTTCTCACC
Statistics
Matches: 282, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
280 282 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (280 bp):
TTTTGACCCTTTCCTTTGTCAAATTGCCTATGACAGTGGCAACGCTCAATGACCAACATATTAAA
GATTTATTTAAAACTAAAAGAGAAAAAAAGTTAAATTTTATCTATTTACTTGTAAAAAGCTTTGA
TTATAGTACATTTCTTCTATACTTTCATAACAAAGGGTAAAACAATAGTAATAAAGGAACCTACA
ATGTGGTATTATTCTCTCTCCTTTATCTGATCAAAAGTCGACAAGTGCATCACCCATCTTTTCCA
TTCATCCCTATCAATCCCAA
Found at i:333992 original size:2 final size:2
Alignment explanation
Indices: 333985--334031 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
333975 TAAAAGAGTA
333985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334027 AT AT A
1 AT AT A
334032 AACTCTCTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:334370 original size:20 final size:19
Alignment explanation
Indices: 334324--334372 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
334314 ATGACCAACA
* * *
334324 AATTCGCAACGCGATCTCG
1 AATTCGTAACGCGAACTCC
334343 AATTCGTAACGCGAACTCC
1 AATTCGTAACGCGAACTCC
334362 AATTTCGTAAC
1 AA-TTCGTAAC
334373 ACAGCTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (19 bp):
AATTCGTAACGCGAACTCC
Found at i:334424 original size:20 final size:20
Alignment explanation
Indices: 334322--334460 Score: 122
Period size: 20 Copynumber: 7.0 Consensus size: 20
334312 AAATGACCAA
334322 CAAATTCGCAACGCG-A-TC
1 CAAATTCGCAACGCGAATTC
* * *
334340 TCGAATTCGTAACGCGAACTC
1 -CAAATTCGCAACGCGAATTC
* * * *
334361 CAATTTCGTAACAC-AGCTTC
1 CAAATTCGCAACGCGA-ATTC
* *
334381 CAAATTCGCAACTCGATTTTC
1 CAAATTCGCAACGCGA-ATTC
* *
334402 CAAAATCGCAACACGAATTC
1 CAAATTCGCAACGCGAATTC
*
334422 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACGCGAATTC
334442 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
334461 TTAATTTCGC
Statistics
Matches: 97, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.14
20 63 0.65
21 20 0.21
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTC
Found at i:335446 original size:24 final size:24
Alignment explanation
Indices: 335419--335472 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
335409 GTATTCAAAA
335419 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
335443 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
335467 TTTGAT
1 TTTGAT
335473 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:335664 original size:12 final size:12
Alignment explanation
Indices: 335647--335671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
335637 ATATAACCCT
335647 GAAGAAGAAAAA
1 GAAGAAGAAAAA
335659 GAAGAAGAAAAA
1 GAAGAAGAAAAA
335671 G
1 G
335672 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:338047 original size:29 final size:29
Alignment explanation
Indices: 337997--338052 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
337987 CGATTTTTTG
337997 TTGCGATTGTTGCAAAAGTCAAATTCGCA
1 TTGCGATTGTTGCAAAAGTCAAATTCGCA
** *
338026 TTGCGATTGTTGTGAAATTCAAATTCG
1 TTGCGATTGTTGCAAAAGTCAAATTCG
338053 AAACGCGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (29 bp):
TTGCGATTGTTGCAAAAGTCAAATTCGCA
Found at i:338060 original size:29 final size:29
Alignment explanation
Indices: 337999--338060 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
337989 ATTTTTTGTT
* **
337999 GCGATTGTTGCAAAAGTCAAATTCGCATT
1 GCGATTGTTGCAAAAGTCAAATTCGAAAC
** *
338028 GCGATTGTTGTGAAATTCAAATTCGAAAC
1 GCGATTGTTGCAAAAGTCAAATTCGAAAC
338057 GCGA
1 GCGA
338061 AAATCAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (29 bp):
GCGATTGTTGCAAAAGTCAAATTCGAAAC
Found at i:338067 original size:20 final size:20
Alignment explanation
Indices: 338039--338077 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
338029 CGATTGTTGT
*
338039 GAAATTCAAATTCGAAACGC
1 GAAAATCAAATTCGAAACGC
*
338059 GAAAATCAAATTCGCAACG
1 GAAAATCAAATTCGAAACG
338078 TAAAAATCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (20 bp):
GAAAATCAAATTCGAAACGC
Found at i:338083 original size:20 final size:20
Alignment explanation
Indices: 338044--338085 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
338034 GTTGTGAAAT
*
338044 TCAAATTCGAAACGCGAAAA
1 TCAAATTCGAAACGCAAAAA
* *
338064 TCAAATTCGCAACGTAAAAA
1 TCAAATTCGAAACGCAAAAA
338084 TC
1 TC
338086 GCAACGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (20 bp):
TCAAATTCGAAACGCAAAAA
Found at i:339649 original size:21 final size:21
Alignment explanation
Indices: 339619--339736 Score: 146
Period size: 21 Copynumber: 5.6 Consensus size: 21
339609 GTGAATCGGG
* * *
339619 CTCTTAAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
**
339640 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
339661 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
339682 CTTTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
339703 CTCTTGAACGATAGGATGGGC
1 CTCTTGAACGATGGGAGGGGC
339724 CTCTTGAACGATG
1 CTCTTGAACGATG
339737 ACAGATGAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:339678 original size:42 final size:41
Alignment explanation
Indices: 339619--339740 Score: 172
Period size: 42 Copynumber: 2.9 Consensus size: 41
339609 GTGAATCGGG
*
339619 CTCTTAAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGGGC
* *
339661 CTCTTGAACGGTGGGAGGGGCCTTTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGGGC
* *
339703 CTCTTGAACGATAGGATGGGCCTCTTGAACGATGACAG
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAG
339741 ATGAATCAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 68 0.96
43 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGGGC
Found at i:340171 original size:21 final size:21
Alignment explanation
Indices: 340147--340187 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
340137 ATCGTGACGT
*
340147 AAAGTACCAACCTCATCACGC
1 AAAGCACCAACCTCATCACGC
**
340168 AAAGCACTGACCTCATCACG
1 AAAGCACCAACCTCATCACG
340188 TAACTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAGCACCAACCTCATCACGC
Found at i:341772 original size:19 final size:19
Alignment explanation
Indices: 341721--341774 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
341711 AGTAGTTTCT
*
341721 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
341741 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
341761 GAAACTAAAATCGC
1 GAAACTAAAATCGC
341775 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:342156 original size:22 final size:22
Alignment explanation
Indices: 342131--342176 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
342121 GATGGAGATA
342131 GACGGATTTCGCCGCAGATGGG
1 GACGGATTTCGCCGCAGATGGG
* *
342153 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGCAGATGGG
342175 GA
1 GA
342177 TGTATGTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGCAGATGGG
Found at i:342985 original size:21 final size:21
Alignment explanation
Indices: 342959--343000 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
342949 CCAGAATGGG
*
342959 GGGAATCGGCACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
*
342980 GGGAATCGATACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
343001 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (21 bp):
GGGAATCGACACCCCTTCATA
Done.