Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 3 of 74
Found at i:306705 original size:26 final size:25
Alignment explanation
Indices: 306676--306726 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
306666 TCGGAAATAA
*
306676 TTTTTTAGAAATTTTTGGCGAAATTT
1 TTTTTTAGAAATTTCTGG-GAAATTT
*
306702 TTTTTTGGAAATTTCTGGGAAATTT
1 TTTTTTAGAAATTTCTGGGAAATTT
306727 CCAGATTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (25 bp):
TTTTTTAGAAATTTCTGGGAAATTT
Found at i:306791 original size:31 final size:32
Alignment explanation
Indices: 306736--306797 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
306726 TCCAGATTCT
*
306736 GGCAAAAATTTCGGTAACATTTGAA-TTTTTC
1 GGCAAAAATTTCGGTAACACTTGAAGTTTTTC
*
306767 GGCAATAATTTCGGTGAAC-CTTGAAGTTTTT
1 GGCAAAAATTTCGGT-AACACTTGAAGTTTTT
306798 GGTGACCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (32 bp):
GGCAAAAATTTCGGTAACACTTGAAGTTTTTC
Found at i:307229 original size:23 final size:23
Alignment explanation
Indices: 307198--307250 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
307188 TTTTTTGAAA
*
307198 ATTTTTTTTATTTTC-ATTTATTT
1 ATTTATTTT-TTTTCTATTTATTT
* *
307221 GTTTATTTTTTTTCTATTTTTTT
1 ATTTATTTTTTTTCTATTTATTT
307244 ATTTATT
1 ATTTATT
307251 AGATTAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (23 bp):
ATTTATTTTTTTTCTATTTATTT
Found at i:307347 original size:20 final size:18
Alignment explanation
Indices: 307290--307354 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 18
307280 TTATCTTATT
307290 TTTATTTTTGTTTCACTTTTC
1 TTTA-TTTT-TTT-ACTTTTC
*
307311 TTTATTTTTTT--TCTTC
1 TTTATTTTTTTACTTTTC
307327 TTTATTTACTTTTACTTTTC
1 TTTATTT--TTTTACTTTTC
*
307347 TTTGTTTT
1 TTTATTTT
307355 ATATTCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
16 11 0.30
18 5 0.14
19 3 0.08
20 14 0.38
21 4 0.11
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTATTTTTTTACTTTTC
Found at i:307611 original size:59 final size:58
Alignment explanation
Indices: 307374--307709 Score: 482
Period size: 58 Copynumber: 5.7 Consensus size: 58
307364 AAATAAAAAT
*
307374 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTT-
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAA-TTTC
* *
307433 AAAAAAAATTATCTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATTTC
1 AAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* *
307492 -AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* *
307550 AAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAATCAAAGTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAA-TTTC
*
307609 AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTC
1 -AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTC
*
307669 -AAAAAAATAATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAAT-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
307710 TCCTACACAA
Statistics
Matches: 252, Mismatches: 16, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
57 42 0.17
58 60 0.24
59 56 0.22
60 52 0.21
61 38 0.15
62 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:308450 original size:53 final size:53
Alignment explanation
Indices: 308312--308462 Score: 162
Period size: 54 Copynumber: 2.8 Consensus size: 53
308302 AGACAAAAAA
* * *
308312 AATAAA-AAAAATATTTCTAAATTGACCCAAATTGTGAAAAATTTAGAAATCT
1 AATAAATAAAAATATTTATAAATTGGCCCAAATGGTGAAAAATTTAGAAATCT
* * * * *
308364 AATAAATAAATAAAATTTATAAATAGGCCCAAATGGTGAAAATTTTAGGAATTT
1 AATAAATAAA-AATATTTATAAATTGGCCCAAATGGTGAAAAATTTAGAAATCT
* * *
308418 AA-AAATAGAAAATATTTTTAATTTGGCTCAAATGGTGAAATAATT
1 AATAAATA-AAAATATTTATAAATTGGCCCAAATGGTGAAA-AATT
308463 AGATATATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
52 6 0.07
53 33 0.41
54 42 0.52
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (53 bp):
AATAAATAAAAATATTTATAAATTGGCCCAAATGGTGAAAAATTTAGAAATCT
Found at i:310317 original size:15 final size:15
Alignment explanation
Indices: 310297--310327 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
310287 TTCAATTACA
310297 ATTAAAAAATAATTG
1 ATTAAAAAATAATTG
310312 ATTAAAAAATAATTG
1 ATTAAAAAATAATTG
310327 A
1 A
310328 AAGTAAATTA
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:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATTAAAAAATAATTG
Found at i:311698 original size:30 final size:30
Alignment explanation
Indices: 311664--311754 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
311654 AAAAAACCTG
* * *
311664 AACCTGAAAAGCCCAAGGAGCCTGAGAAGA
1 AACCTGAAAAGCCTAAAGAGCCTGAAAAGA
*
311694 AACCTGAAAAGCCTAAAGAACCTGAAAAGA
1 AACCTGAAAAGCCTAAAGAGCCTGAAAAGA
* *
311724 AACCTGAGAAGCCTAAAGAGCCCGAAAAGA
1 AACCTGAAAAGCCTAAAGAGCCTGAAAAGA
311754 A
1 A
311755 GCCGGAGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.08
Consensus pattern (30 bp):
AACCTGAAAAGCCTAAAGAGCCTGAAAAGA
Found at i:311746 original size:69 final size:68
Alignment explanation
Indices: 311602--311730 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 68
311592 CACCACCTCC
* * *
311602 AAAA-CCCAAGGAGCCTGAGAAGAAACCTGAAAAGGCTAATGAACAGGAGAAGAAAAAACCTGAA
1 AAAAGCCCAAGGAGCCTGAGAAGAAACCTGAAAAGCCTAAAGAACA-CAGAAGAAAAAACCTGAA
311666 CCTG
65 CCTG
* *
311670 AAAAGCCCAAGGAGCCTGAGAAGAAACCTGAAAAGCCTAAAGAAC-CTGAA-AAGAAACCTGA
1 AAAAGCCCAAGGAGCCTGAGAAGAAACCTGAAAAGCCTAAAGAACACAGAAGAAAAAACCTGA
311731 GAAGCCTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
66 10 0.18
67 3 0.05
68 4 0.07
69 38 0.69
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (68 bp):
AAAAGCCCAAGGAGCCTGAGAAGAAACCTGAAAAGCCTAAAGAACACAGAAGAAAAAACCTGAAC
CTG
Found at i:311763 original size:30 final size:30
Alignment explanation
Indices: 311690--311774 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
311680 GGAGCCTGAG
* * *
311690 AAGAAACCTGAAAAGCCTAAAGAACCTGAA
1 AAGAAACCGGAGAAGCCTAAAGAACCCGAA
* *
311720 AAGAAACCTGAGAAGCCTAAAGAGCCCGAA
1 AAGAAACCGGAGAAGCCTAAAGAACCCGAA
* * *
311750 AAGAAGCCGGAGAAACCAAAAGAAC
1 AAGAAACCGGAGAAGCCTAAAGAAC
311775 AGGAAAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.52, C:0.21, G:0.21, T:0.06
Consensus pattern (30 bp):
AAGAAACCGGAGAAGCCTAAAGAACCCGAA
Found at i:311781 original size:60 final size:60
Alignment explanation
Indices: 311664--311781 Score: 130
Period size: 60 Copynumber: 2.0 Consensus size: 60
311654 AAAAAACCTG
* * * * * **
311664 AACCTGAAAAGCCCAAGGAGCCTGAGAAGAAACCTGAAAAGCCTAAAGAACCTGAAAAGA
1 AACCTGAAAAGCCCAAAGAGCCCGAAAAGAAACCGGAAAAGCCAAAAGAACAGGAAAAGA
* * *
311724 AACCTGAGAAGCCTAAAGAGCCCGAAAAGAAGCCGGAGAAA-CCAAAAGAACAGGAAAA
1 AACCTGAAAAGCCCAAAGAGCCCGAAAAGAAACCGGA-AAAGCCAAAAGAACAGGAAAA
311782 ATCACCTCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.50, C:0.21, G:0.23, T:0.06
Consensus pattern (60 bp):
AACCTGAAAAGCCCAAAGAGCCCGAAAAGAAACCGGAAAAGCCAAAAGAACAGGAAAAGA
Found at i:313184 original size:99 final size:99
Alignment explanation
Indices: 313013--313206 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 99
313003 ACATTGGTGG
* *
313013 ACCACCACCGCCAGTTGTCAATCCTGGGTTTTGTTGCACGGATTGTTGTCATGGACGTAGTGGGG
1 ACCACCACCGCCAATTGTCAATCCTGGGTTTTGTTGCACGGATTGTTATCATGGACGTAGTGGGG
313078 GCCCTTGCTACATTGGTGGACCACCACCACCACC
66 GCCCTTGCTACATTGGTGGACCACCACCACCACC
* * * * *
313112 ACCACCACCGCTAATTTTCATTCCTGGGTTTTGTTGCACGGATTGTTATCATGGACGTGGTGGGT
1 ACCACCACCGCCAATTGTCAATCCTGGGTTTTGTTGCACGGATTGTTATCATGGACGTAGTGGGG
*
313177 GCCCTTGCTACATTGGTGGACCACCCCCAC
66 GCCCTTGCTACATTGGTGGACCACCACCAC
313207 GCCCTTGCTA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.28
Consensus pattern (99 bp):
ACCACCACCGCCAATTGTCAATCCTGGGTTTTGTTGCACGGATTGTTATCATGGACGTAGTGGGG
GCCCTTGCTACATTGGTGGACCACCACCACCACC
Found at i:316484 original size:24 final size:24
Alignment explanation
Indices: 316457--316519 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
316447 TCAAACCACC
* *
316457 ACCACCACCGCCACCTACACCAAA
1 ACCATCACCACCACCTACACCAAA
316481 ACCATCACCACCACCTACACCAAA
1 ACCATCACCACCACCTACACCAAA
316505 ACCATCACCACCACC
1 ACCATCACCACCACC
316520 GTCGCGGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.54, G:0.02, T:0.06
Consensus pattern (24 bp):
ACCATCACCACCACCTACACCAAA
Found at i:316615 original size:3 final size:3
Alignment explanation
Indices: 316607--316636 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
316597 ACATTGGTGG
316607 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
316637 GCTAATTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:318110 original size:2 final size:2
Alignment explanation
Indices: 318103--318134 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
318093 GTTGCATCGA
318103 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
318135 GCGCGCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:318170 original size:2 final size:2
Alignment explanation
Indices: 318163--318196 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
318153 TTTCCTGACG
318163 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
318197 GCGCGCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:318198 original size:62 final size:62
Alignment explanation
Indices: 318103--318227 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
318093 GTTGCATCGA
318103 ATATATATATATATATATATATATATATATATGCGCGCATGATATTATTCTTTCCTGACGAT
1 ATATATATATATATATATATATATATATATATGCGCGCATGATATTATTCTTTCCTGACGAT
318165 ATATATATATATATATATATATATATATATATGCGCGCATGATATTATTCTTTCCTGACGAT
1 ATATATATATATATATATATATATATATATATGCGCGCATGATATTATTCTTTCCTGACGAT
318227 A
1 A
318228 ACCTGCAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (62 bp):
ATATATATATATATATATATATATATATATATGCGCGCATGATATTATTCTTTCCTGACGAT
Found at i:323710 original size:2 final size:2
Alignment explanation
Indices: 323703--323748 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
323693 TTGAGTATCA
323703 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
323745 AG AG
1 AG AG
323749 TTACTGGTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:328247 original size:2 final size:2
Alignment explanation
Indices: 328240--328274 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
328230 TATTCTCGTG
328240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
328275 GTATTGACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:337798 original size:23 final size:23
Alignment explanation
Indices: 337748--337804 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
337738 AAAAATGAAT
* * *
337748 GATAAATCAAATTAAAAATAAAA
1 GATAAATCAGATGAAAAACAAAA
* *
337771 AATAAATCAGATGAAAAACCAAA
1 GATAAATCAGATGAAAAACAAAA
337794 GATAAAT-AGAT
1 GATAAATCAGAT
337805 AATTAACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (23 bp):
GATAAATCAGATGAAAAACAAAA
Found at i:337852 original size:15 final size:15
Alignment explanation
Indices: 337822--337859 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
337812 AAAAAAATTC
337822 AAAAAAT-AATAAAT
1 AAAAAATAAATAAAT
* *
337836 AATAAATAAATACAT
1 AAAAAATAAATAAAT
337851 AAAAAATAA
1 AAAAAATAA
337860 TTGAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:341299 original size:2 final size:2
Alignment explanation
Indices: 341294--341326 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
341284 TTCGCATGTA
341294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
341327 CACGTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:341817 original size:23 final size:25
Alignment explanation
Indices: 341790--341835 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
341780 GAATTTTTTA
341790 TTAAAAATGAATAA-AT-AAAAATT
1 TTAAAAATGAATAATATGAAAAATT
*
341813 TTAAAAATTAATAATATGAAAAA
1 TTAAAAATGAATAATATGAAAAA
341836 ATAACTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAAATGAATAATATGAAAAATT
Found at i:341950 original size:11 final size:11
Alignment explanation
Indices: 341888--341956 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
341878 TATTTAACGA
*
341888 TAAAATTTTGT
1 TAAAATTTTAT
*
341899 TAATATTATTAT
1 TAAAATT-TTAT
341911 TAAAAATATTTATT
1 T-AAAAT-TTTA-T
*
341925 TCACAAA-TATAT
1 T-A-AAATTTTAT
341937 TAAAATTTTAT
1 TAAAATTTTAT
341948 TAAAATTTT
1 TAAAATTTT
341957 CATGCTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
10 3 0.07
11 20 0.43
12 6 0.13
13 10 0.22
14 4 0.09
15 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (11 bp):
TAAAATTTTAT
Found at i:342010 original size:13 final size:13
Alignment explanation
Indices: 341980--342023 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
341970 TATGATGAAA
341980 AATTTTAATTTATC
1 AATTTTAATTT-TC
*
341994 AATTTTGATTTTC
1 AATTTTAATTTTC
342007 AATTTTAATTTT-
1 AATTTTAATTTTC
342019 AATTT
1 AATTT
342024 ACTCATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 5 0.18
13 13 0.46
14 10 0.36
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (13 bp):
AATTTTAATTTTC
Found at i:342016 original size:6 final size:6
Alignment explanation
Indices: 341980--342023 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
341970 TATGATGAAA
*
341980 AATTTT AATTTAT CAATTTT GATTTT CAATTTT AATTTT AATTT
1 AATTTT AATTT-T -AATTTT AATTTT -AATTTT AATTTT AATTT
342024 ACTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 21 0.64
7 7 0.21
8 5 0.15
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:343428 original size:17 final size:17
Alignment explanation
Indices: 343396--343428 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
343386 TAGGGCTTAA
343396 TTTATTATTTATTTATG
1 TTTATTATTTATTTATG
343413 TTTA-TATTTATATTAT
1 TTTATTATTTAT-TTAT
343429 AAGTGGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTATTTATTTATG
Found at i:343933 original size:16 final size:15
Alignment explanation
Indices: 343914--343944 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
343904 TTTACATTAA
343914 TTTATATTTATATATT
1 TTTATATTTA-ATATT
343930 TTTATATTTAATATT
1 TTTATATTTAATATT
343945 ATCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATATTTAATATT
Found at i:343951 original size:16 final size:16
Alignment explanation
Indices: 343916--343953 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
343906 TACATTAATT
*
343916 TATATTTATATATTTT
1 TATATTTATATATTTC
343932 TATATTTA-ATATTATC
1 TATATTTATATATT-TC
343948 TATATT
1 TATATT
343954 AATTGTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTATATATTTC
Found at i:352132 original size:12 final size:12
Alignment explanation
Indices: 352086--352132 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
352076 ATTTATTATC
352086 AATTAAT-TTTA
1 AATTAATATTTA
352097 AATTTAATATTT-
1 AA-TTAATATTTA
352109 AATATAATATTTA
1 AAT-TAATATTTA
*
352122 AATTAAGATTT
1 AATTAATATTT
352133 TTTTTCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.10
12 22 0.71
13 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
AATTAATATTTA
Found at i:352565 original size:19 final size:18
Alignment explanation
Indices: 352541--352634 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 18
352531 TTAAGATTTT
352541 TTTTAGAATTTTTGAAAAA
1 TTTTAGAATTTTT-AAAAA
**
352560 TTTTAGAATATTTTAAATT
1 TTTTAGAAT-TTTTAAAAA
* *
352579 TTTTAAGAAAAATTTTAAAAT
1 TTTT-AG--AATTTTTAAAAA
352600 TTTTAGAATATTTTAAAATA
1 TTTTAGAAT-TTTTAAAA-A
*
352620 TTTTAGATTTTTTAA
1 TTTTAGAATTTTTAA
352635 TTTTTTTTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 30 0.48
20 16 0.26
21 12 0.19
22 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTTAGAATTTTTAAAAA
Found at i:352624 original size:10 final size:10
Alignment explanation
Indices: 352541--352624 Score: 68
Period size: 10 Copynumber: 8.5 Consensus size: 10
352531 TTAAGATTTT
*
352541 TTTTAGAAT-
1 TTTTAAAATA
352550 TTTTGAAAA-A
1 TTTT-AAAATA
*
352560 TTTTAGAATA
1 TTTTAAAATA
*
352570 TTTT-AAATT
1 TTTTAAAATA
*
352579 TTTTAAGAAAAA
1 TTTT-A-AAATA
352591 TTTTAAAAT-
1 TTTTAAAATA
*
352600 TTTTAGAATA
1 TTTTAAAATA
352610 TTTTAAAATA
1 TTTTAAAATA
352620 TTTTA
1 TTTTA
352625 GATTTTTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
9 22 0.37
10 29 0.49
11 1 0.02
12 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:352642 original size:19 final size:21
Alignment explanation
Indices: 352599--352659 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
352589 AATTTTAAAA
*
352599 TTTTTAGAATATTTTA-AA-AT
1 TTTTTAGAAT-TTTTATAATTT
*
352619 ATTTTAG-ATTTTT-TAATTT
1 TTTTTAGAATTTTTATAATTT
352638 TTTTTAGAAATTTTTATAATTT
1 TTTTTAG-AATTTTTATAATTT
352660 AAAAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 6 0.18
19 9 0.27
20 6 0.18
21 6 0.18
22 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTAGAATTTTTATAATTT
Found at i:352658 original size:9 final size:9
Alignment explanation
Indices: 352517--352659 Score: 61
Period size: 10 Copynumber: 14.6 Consensus size: 9
352507 GATTTTTTTT
*
352517 AATTTTAAA
1 AATTTTTAA
352526 AATTTTTAA
1 AATTTTTAA
* *
352535 GATTTTTTTTAG
1 -A--ATTTTTAA
352547 AATTTTTGAA
1 AATTTTT-AA
* *
352557 AAATTTTAG
1 AATTTTTAA
352566 AATATTTTAA
1 AAT-TTTTAA
*
352576 ATTTTTTAAGAA
1 AATTTTT---AA
*
352588 AAATTTTAA
1 AATTTTTAA
*
352597 AATTTTTAG
1 AATTTTTAA
352606 AATATTTTAA
1 AAT-TTTTAA
*
352616 AATATTTTAG
1 AAT-TTTTAA
*
352626 ATTTTTTAA
1 AATTTTTAA
**
352635 TTTTTTTTAGA
1 -AATTTTTA-A
*
352646 AATTTTTAT
1 AATTTTTAA
352655 AATTT
1 AATTT
352660 AAAAAAAATT
Statistics
Matches: 101, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
9 42 0.42
10 44 0.44
11 2 0.02
12 13 0.13
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:352687 original size:11 final size:11
Alignment explanation
Indices: 352673--352721 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
352663 AAAAATTCAT
352673 TTTTTTTAGAA
1 TTTTTTTAGAA
*
352684 -TTTTTTAAAA
1 TTTTTTTAGAA
* *
352694 CTTTTTTAGAT
1 TTTTTTTAGAA
352705 TTTTTTTAGAA
1 TTTTTTTAGAA
352716 TTTTTT
1 TTTTTT
352722 AATACTGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (11 bp):
TTTTTTTAGAA
Found at i:353158 original size:35 final size:36
Alignment explanation
Indices: 353106--353176 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
353096 AACTTAATTT
*
353106 TTTTATATTTTATTTTTTTCAAACCAAAATTTATAA
1 TTTTATACTTTATTTTTTTCAAACCAAAATTTATAA
353142 TTTTATACTTTA-TTTTTTCAAACCAAAATTTATAA
1 TTTTATACTTTATTTTTTTCAAACCAAAATTTATAA
353177 GTATTTCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (36 bp):
TTTTATACTTTATTTTTTTCAAACCAAAATTTATAA
Found at i:353219 original size:17 final size:17
Alignment explanation
Indices: 353197--353230 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
353187 CCTTTTCAAG
353197 AAAACAATTATACTCAT
1 AAAACAATTATACTCAT
353214 AAAACAATTATACTCAT
1 AAAACAATTATACTCAT
353231 TTTATGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAACAATTATACTCAT
Found at i:357946 original size:2 final size:2
Alignment explanation
Indices: 357941--357965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
357931 ATATATATAT
357941 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
357966 AACCTGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:358324 original size:24 final size:24
Alignment explanation
Indices: 358297--358347 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
358287 AATAATTATT
*
358297 ATTATTATAATTGTA-ATTAAAAAA
1 ATTATTATAATT-AAGATTAAAAAA
358321 ATTATTATAATTAAGATTAAAAAA
1 ATTATTATAATTAAGATTAAAAAA
358345 ATT
1 ATT
358348 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTATTATAATTAAGATTAAAAAA
Found at i:360327 original size:21 final size:21
Alignment explanation
Indices: 360301--360341 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
360291 TAATACATCT
360301 AGAATACAACCCCTATGAACA
1 AGAATACAACCCCTATGAACA
*
360322 AGAATACAACCGCTATGAAC
1 AGAATACAACCCCTATGAAC
360342 TGAGATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (21 bp):
AGAATACAACCCCTATGAACA
Found at i:363974 original size:3 final size:3
Alignment explanation
Indices: 363966--363993 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
363956 TTCTTAAATC
363966 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
363994 CATGTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:372792 original size:3 final size:3
Alignment explanation
Indices: 372786--372810 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
372776 CACCACCACC
372786 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
372811 TCTAAGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:376175 original size:24 final size:26
Alignment explanation
Indices: 376148--376208 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
376138 ATATAATTTT
376148 TTATTTTATTAAATTT-AT-ATATAA
1 TTATTTTATTAAATTTAATCATATAA
* *
376172 TTATTATTA-TAATTTTAAATCATATTA
1 TTATT-TTATTAAATTT-AATCATATAA
376199 TTATTTTATT
1 TTATTTTATT
376209 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 11 0.37
25 3 0.10
26 5 0.17
27 11 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATTAAATTTAATCATATAA
Found at i:380482 original size:20 final size:20
Alignment explanation
Indices: 380453--380491 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
380443 AATTTTCATT
380453 AATTGGTTGATCATAGGTAA
1 AATTGGTTGATCATAGGTAA
*
380473 AATTGTTTGATCATAGGTA
1 AATTGGTTGATCATAGGTA
380492 TTTAATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (20 bp):
AATTGGTTGATCATAGGTAA
Found at i:384157 original size:13 final size:13
Alignment explanation
Indices: 384139--384163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
384129 ACTATCAATT
384139 GATGCCTACAAAG
1 GATGCCTACAAAG
384152 GATGCCTACAAA
1 GATGCCTACAAA
384164 TTCAAACATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (13 bp):
GATGCCTACAAAG
Found at i:391168 original size:30 final size:30
Alignment explanation
Indices: 391132--391192 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
391122 TCTTGTAAAT
391132 TTGTAGAAAATGAGCCTAGCTTTCTTTTAA
1 TTGTAGAAAATGAGCCTAGCTTTCTTTTAA
*
391162 TTGTAGAAAATGAGCTTAGCTTTCTTTTAA
1 TTGTAGAAAATGAGCCTAGCTTTCTTTTAA
391192 T
1 T
391193 AGCGGTAGGC
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:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (30 bp):
TTGTAGAAAATGAGCCTAGCTTTCTTTTAA
Found at i:391929 original size:20 final size:19
Alignment explanation
Indices: 391902--391945 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
391892 GATAAAACTA
*
391902 AAATAAAATTTACA-TTATT
1 AAATAAAAATTA-ATTTATT
391921 AAATCAAAAATTAATTTATT
1 AAAT-AAAAATTAATTTATT
391941 AAATA
1 AAATA
391946 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAAAAATTAATTTATT
Found at i:408741 original size:1 final size:1
Alignment explanation
Indices: 408703--408733 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
408693 TGAGCTTGAG
408703 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
408734 CATTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:424798 original size:17 final size:18
Alignment explanation
Indices: 424759--424799 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
424749 ACACTTATCC
*
424759 ATAATTCATGTATGAAAA
1 ATAATTCATATATGAAAA
424777 ATAATTCATATA-GAAAA
1 ATAATTCATATATGAAAA
*
424794 TTAATT
1 ATAATT
424800 TGCCTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (18 bp):
ATAATTCATATATGAAAA
Found at i:426134 original size:16 final size:14
Alignment explanation
Indices: 426076--426123 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
426066 TATAATTATA
*
426076 ATTAAAAAAATTTT
1 ATTAAATAAATTTT
* *
426090 AATAAA-AATTTTAT
1 ATTAAATAAATTT-T
426104 ATTAAATAAATTTT
1 ATTAAATAAATTTT
426118 ATTAAA
1 ATTAAA
426124 ATTAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 5 0.18
14 18 0.64
15 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATAAATTTT
Found at i:426135 original size:27 final size:26
Alignment explanation
Indices: 426063--426137 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
426053 TAATAATTAG
* * *
426063 TATTATAATTATAATTAAAAAAATTT
1 TATTAAAATTATATTTAAATAAATTT
* *
426089 TAATAAAAATTTTATATTAAATAAATTT
1 T-ATTAAAATTATAT-TTAAATAAATTT
426117 TATTAAAATTAATATTTAAAT
1 TATTAAAATT-ATATTTAAAT
426138 TTAATTAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.03
27 23 0.59
28 15 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTAAAATTATATTTAAATAAATTT
Found at i:426137 original size:23 final size:25
Alignment explanation
Indices: 426110--426155 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
426100 TTATATTAAA
*
426110 TAAATTTTATTAA-AAT-TAATATT
1 TAAATTTAATTAATAATATAATATT
426133 TAAATTTAATTAATAATATAATA
1 TAAATTTAATTAATAATATAATA
426156 AATTTAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 3 0.15
25 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATTTAATTAATAATATAATATT
Found at i:426450 original size:2 final size:2
Alignment explanation
Indices: 426443--426482 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
426433 TATAGCATAA
426443 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
426483 CCAACACACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432315 original size:4 final size:4
Alignment explanation
Indices: 432306--432385 Score: 142
Period size: 4 Copynumber: 20.0 Consensus size: 4
432296 TAATCTACTC
* *
432306 ACAT ACAT ACAT ACGT ACAT ACAT ACAT ACGT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
432354 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
432386 GTACGCACAC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:435318 original size:18 final size:20
Alignment explanation
Indices: 435279--435317 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
435269 TTTATTTTTA
*
435279 TATATTATTTTAATAAATTT
1 TATATTATTTAAATAAATTT
435299 TATA-TATTTAAATAAATTT
1 TATATTATTTAAATAAATTT
435318 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTATTTAAATAAATTT
Found at i:435363 original size:17 final size:18
Alignment explanation
Indices: 435343--435381 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
435333 ATTTTTATTT
*
435343 TATAAAAATTTA-AATAA
1 TATAAAAATTAATAATAA
435360 TATAAAAATTAATAATAA
1 TATAAAAATTAATAATAA
435378 TATA
1 TATA
435382 TAATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAAAATTAATAATAA
Found at i:436300 original size:5 final size:5
Alignment explanation
Indices: 436290--436321 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
436280 ACTCATTTGT
436290 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
436322 CCATTGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:438155 original size:35 final size:34
Alignment explanation
Indices: 438113--438181 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
438103 TTTACCAAAT
438113 ATATTTTTTAAAAAACAAATAATAAAAAATAAAAA
1 ATATTTTTTAAAAAACAAA-AATAAAAAATAAAAA
* **
438148 ATATTTTTTAGAAAATGAAAATAAAAAATAAAAA
1 ATATTTTTTAAAAAACAAAAATAAAAAATAAAAA
438182 TAAAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (34 bp):
ATATTTTTTAAAAAACAAAAATAAAAAATAAAAA
Found at i:438181 original size:13 final size:13
Alignment explanation
Indices: 438159--438188 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
438149 TATTTTTTAG
*
438159 AAAATGAAAATAA
1 AAAATAAAAATAA
438172 AAAATAAAAATAA
1 AAAATAAAAATAA
438185 AAAA
1 AAAA
438189 CATTGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:439996 original size:15 final size:15
Alignment explanation
Indices: 439976--440007 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
439966 GTTATACACT
439976 TGGTTCACCTTTCTC
1 TGGTTCACCTTTCTC
439991 TGGTTCACCTTTCTC
1 TGGTTCACCTTTCTC
440006 TG
1 TG
440008 TGCCAACGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.16, T:0.47
Consensus pattern (15 bp):
TGGTTCACCTTTCTC
Found at i:443805 original size:2 final size:2
Alignment explanation
Indices: 443798--443833 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
443788 AACAAGCAAA
443798 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
443834 TCTAAGATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:443852 original size:29 final size:29
Alignment explanation
Indices: 443820--443889 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
443810 AGAGAGAGAG
443820 AGAGAGAGAGGAGATCTAAGATGAAAAGA
1 AGAGAGAGAGGAGATCTAAGATGAAAAGA
*
443849 AGAGAGAGAGGAGATCTGAGATGAAAAGA
1 AGAGAGAGAGGAGATCTAAGATGAAAAGA
*
443878 AGAGAGAAAGGA
1 AGAGAGAGAGGA
443890 AGGCTTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.51, C:0.03, G:0.37, T:0.09
Consensus pattern (29 bp):
AGAGAGAGAGGAGATCTAAGATGAAAAGA
Found at i:448315 original size:2 final size:2
Alignment explanation
Indices: 448308--448348 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
448298 ATTGGAAGAA
448308 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
448349 TGAAGAGAAT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:451603 original size:2 final size:2
Alignment explanation
Indices: 451596--451621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
451586 TTGTCATAAA
451596 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
451622 CATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:453988 original size:3 final size:3
Alignment explanation
Indices: 453973--454014 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
453963 ATGATGCCGT
*
453973 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
454015 ATCGGTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:454279 original size:2 final size:2
Alignment explanation
Indices: 454272--454301 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
454262 TAATTATTAC
454272 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
454302 GACAACTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457779 original size:10 final size:10
Alignment explanation
Indices: 457764--457831 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
457754 AAAAGAAACG
457764 TCTCTCTCTT
1 TCTCTCTCTT
457774 TCTCTCTCTT
1 TCTCTCTCTT
457784 TCTCTCTC-T
1 TCTCTCTCTT
*
457793 ACT-TCTCTT
1 TCTCTCTCTT
* *
457802 CCTC-CTGCCCT
1 TCTCTCT--CTT
*
457813 GCTCTCTCTT
1 TCTCTCTCTT
457823 TCTCTCTCT
1 TCTCTCTCT
457832 ACCCGTCTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 4 0.09
9 8 0.17
10 28 0.60
11 5 0.11
12 2 0.04
ACGTcount: A:0.01, C:0.44, G:0.03, T:0.51
Consensus pattern (10 bp):
TCTCTCTCTT
Found at i:459740 original size:99 final size:101
Alignment explanation
Indices: 459563--459762 Score: 350
Period size: 99 Copynumber: 2.0 Consensus size: 101
459553 GCTTCAAAGT
* *
459563 ATGATTCTTTTCATGTTTAATGATGCATTTTTCGTGATTTAGACTTATCTTTGCCATGTGTATGG
1 ATGATTCTTTTCATGTTTAATGATGCATTTTTCCTGATTTAGACTTATCTTTGCCATGTGTACGG
*
459628 TTGCAGGAGCAAGCTAGAAAAGCATTAG-AAGTGCA
66 TTGCAGGAACAAGCTAGAAAAGCATTAGAAAGTGCA
459663 ATGATTCTTTTCATGTTTAATGATGCA-TTTTCCTGATTTAGACTTATCTTTGCCATGTGTACGG
1 ATGATTCTTTTCATGTTTAATGATGCATTTTTCCTGATTTAGACTTATCTTTGCCATGTGTACGG
*
459727 TTGCAGGAACAAGCTGGAAAAGCATTAGAAAGTGCA
66 TTGCAGGAACAAGCTAGAAAAGCATTAGAAAGTGCA
459763 CTTGGCGGAA
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 61 0.64
100 34 0.36
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (101 bp):
ATGATTCTTTTCATGTTTAATGATGCATTTTTCCTGATTTAGACTTATCTTTGCCATGTGTACGG
TTGCAGGAACAAGCTAGAAAAGCATTAGAAAGTGCA
Found at i:462834 original size:6 final size:6
Alignment explanation
Indices: 462823--462854 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
462813 TTTGTTCATA
462823 TTTCAG TTTCAG TTTCAG TTTCAG TTTCAG TT
1 TTTCAG TTTCAG TTTCAG TTTCAG TTTCAG TT
462855 CTTTTCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTCAG
Found at i:516181 original size:10 final size:10
Alignment explanation
Indices: 516168--516194 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
516158 AATTATAATT
516168 TAAAATTATA
1 TAAAATTATA
516178 TAAAATTATA
1 TAAAATTATA
516188 TAAAATT
1 TAAAATT
516195 TATGTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAAATTATA
Found at i:529999 original size:15 final size:14
Alignment explanation
Indices: 529985--530025 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
529975 CAAAAATAAT
529985 TTAATTTAATTTAA
1 TTAATTTAATTTAA
*
529999 TTAATTCAATTTTAA
1 TTAATTTAA-TTTAA
*
530014 ATAATTTAATTT
1 TTAATTTAATTT
530026 GAAATTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTTAATTTAA
Found at i:530030 original size:15 final size:14
Alignment explanation
Indices: 529986--530030 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
529976 AAAAATAATT
*
529986 TAATTTAATTTAAT
1 TAATTTAATTTAAA
*
530000 TAATTCAATTTTAAA
1 TAATTTAA-TTTAAA
530015 TAATTTAATTTGAAA
1 TAATTTAATTT-AAA
530030 T
1 T
530031 TAATCAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
TAATTTAATTTAAA
Found at i:535094 original size:17 final size:18
Alignment explanation
Indices: 535069--535102 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
535059 CAAAATATAA
535069 ATAAGTAATTT-TTAATT
1 ATAAGTAATTTATTAATT
*
535086 ATAATTAATTTATTAAT
1 ATAAGTAATTTATTAAT
535103 AGAATTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATAAGTAATTTATTAATT
Found at i:537662 original size:2 final size:2
Alignment explanation
Indices: 537655--537683 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
537645 ACGTACTTTC
537655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
537684 ATCTAGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546147 original size:2 final size:2
Alignment explanation
Indices: 546140--546184 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
546130 GTTAAAAATA
546140 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT
546182 CT C
1 CT C
546185 CATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:546191 original size:2 final size:2
Alignment explanation
Indices: 546186--546221 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
546176 CTCTCTCTCC
546186 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
546222 GTCATCGCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:547811 original size:3 final size:3
Alignment explanation
Indices: 547805--547842 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
547795 CTTCTTGTTG
547805 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
547843 CTTTCCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:548526 original size:8 final size:7
Alignment explanation
Indices: 548498--548584 Score: 51
Period size: 7 Copynumber: 12.6 Consensus size: 7
548488 AATCGCAGGT
548498 TTTTTTA
1 TTTTTTA
548505 -TTTTTA
1 TTTTTTA
548511 --TTTTA
1 TTTTTTA
548516 TTTTTTGA
1 TTTTTT-A
548524 --TTTTA
1 TTTTTTA
*
548529 ATTTTTA
1 TTTTTTA
548536 TTTATTTTA
1 -TT-TTTTA
548545 TATTTTTA
1 T-TTTTTA
548553 GTTTTTT-
1 -TTTTTTA
*
548560 TGTTTTA
1 TTTTTTA
**
548567 TTTTCAA
1 TTTTTTA
548574 TTTTTTA
1 TTTTTTA
548581 TTTT
1 TTTT
548585 ATTTTACTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
5 6 0.10
6 15 0.24
7 22 0.35
8 13 0.21
9 7 0.11
ACGTcount: A:0.17, C:0.01, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:548560 original size:17 final size:16
Alignment explanation
Indices: 548507--548552 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
548497 TTTTTTTATT
548507 TTTATTTT-A-TTTT-
1 TTTATTTTAATTTTTA
*
548520 TTGATTTTAATTTTTA
1 TTTATTTTAATTTTTA
548536 TTTATTTTATATTTTTA
1 TTTATTTTA-ATTTTTA
548553 GTTTTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 1 0.04
15 4 0.15
16 8 0.30
17 7 0.26
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTTTAATTTTTA
Found at i:548600 original size:56 final size:58
Alignment explanation
Indices: 548496--548606 Score: 133
Period size: 57 Copynumber: 1.9 Consensus size: 58
548486 CCAATCGCAG
* * *
548496 GTTTTTTTATTTTTATTTTATTTTTTGATTTTAATTTTTATTTATTTTA-TATTTTTA
1 GTTTTTTTAGTTTTATTTTATTTTTTGATTTTAATTTTTACTGATTTTATTATTTTTA
548553 GTTTTTTT-GTTTTATTTTCAATTTTTT-ATTTT-A-TTTTACTGATTTTTATTATTT
1 GTTTTTTTAGTTTTATTTT--ATTTTTTGATTTTAATTTTTACTGA-TTTTATTATTT
548607 ATTAAATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
55 7 0.15
56 15 0.32
57 18 0.38
58 7 0.15
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.76
Consensus pattern (58 bp):
GTTTTTTTAGTTTTATTTTATTTTTTGATTTTAATTTTTACTGATTTTATTATTTTTA
Found at i:548606 original size:57 final size:57
Alignment explanation
Indices: 548496--548607 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 57
548486 CCAATCGCAG
* * *
548496 GTTTTTTTATTTTTATTTTATTTTTTGATTTTAATTTTTATTTATTTTATATTTTTA
1 GTTTTTTTAGTTTTATTTTATTTTTTGATTTTAATTTTTACTGATTTTATATTTTTA
548553 GTTTTTTT-GTTTTATTTTCAATTTTTT-ATTTT-A-TTTTACTGATTTT-TATTATTTA
1 GTTTTTTTAGTTTTATTTT--ATTTTTTGATTTTAATTTTTACTGATTTTATATT-TTTA
548608 TTAAATATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
54 4 0.08
55 15 0.31
56 10 0.20
57 13 0.27
58 7 0.14
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (57 bp):
GTTTTTTTAGTTTTATTTTATTTTTTGATTTTAATTTTTACTGATTTTATATTTTTA
Found at i:552813 original size:20 final size:21
Alignment explanation
Indices: 552790--552829 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
552780 TGGTTCAACG
*
552790 AGAAAATTGGTAG-TTAAAAA
1 AGAAAATTGATAGTTTAAAAA
552810 AGAAAATTGATAGTTTAAAA
1 AGAAAATTGATAGTTTAAAA
552830 TGAAGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AGAAAATTGATAGTTTAAAAA
Found at i:553510 original size:22 final size:22
Alignment explanation
Indices: 553482--553528 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
553472 CTCAATTGTA
553482 AAGATTTATTTGATAGTGGATT
1 AAGATTTATTTGATAGTGGATT
553504 AAGATTTATTTGATAGTGGATT
1 AAGATTTATTTGATAGTGGATT
553526 AAG
1 AAG
553529 TTTGGAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (22 bp):
AAGATTTATTTGATAGTGGATT
Found at i:554830 original size:25 final size:25
Alignment explanation
Indices: 554796--554846 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
554786 CTATGGTAGT
554796 AATGATTCATTGAAAGTGTACAAGA
1 AATGATTCATTGAAAGTGTACAAGA
554821 AATGATTCATTGAAAGTGTACAAGA
1 AATGATTCATTGAAAGTGTACAAGA
554846 A
1 A
554847 TGGTAGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (25 bp):
AATGATTCATTGAAAGTGTACAAGA
Found at i:567781 original size:2 final size:2
Alignment explanation
Indices: 567774--567798 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
567764 GAAAAGCAAA
567774 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
567799 TTAAGCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:580328 original size:2 final size:2
Alignment explanation
Indices: 580321--580346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
580311 CCATATTGTA
580321 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
580347 GGCCACCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:583362 original size:14 final size:14
Alignment explanation
Indices: 583343--583381 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
583333 TTGATTTGAT
583343 TTAATTTTTTAAAA
1 TTAATTTTTTAAAA
583357 TTAATTTTTTTTAAAA
1 TTAA--TTTTTTAAAA
583373 TTAAATTTT
1 TT-AATTTT
583382 AGATTAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 4 0.18
16 12 0.55
17 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTTTTAAAA
Found at i:583367 original size:17 final size:17
Alignment explanation
Indices: 583347--583381 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
583337 TTTGATTTAA
583347 TTTTTTAAAATT-AATT
1 TTTTTTAAAATTAAATT
583363 TTTTTTAAAATTAAATT
1 TTTTTTAAAATTAAATT
583380 TT
1 TT
583382 AGATTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTTAAAATTAAATT
Found at i:583499 original size:19 final size:18
Alignment explanation
Indices: 583470--583516 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
583460 TTATTTAATT
583470 ATATATTTATATTAAAAATA
1 ATAT-TTTATATTAAAAA-A
**
583490 ATATTTTATATTTTAAAA
1 ATATTTTATATTAAAAAA
583508 ATATTTTAT
1 ATATTTTAT
583517 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 11 0.44
20 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTATATTAAAAAA
Found at i:583507 original size:20 final size:19
Alignment explanation
Indices: 583470--583526 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
583460 TTATTTAATT
*
583470 ATATATTTATA-TTAAAAATA
1 ATAT-TTTATATTTTAAAA-A
583490 ATATTTTATATTTT-AAAA
1 ATATTTTATATTTTAAAAA
583508 ATATTTTATTAATTTTAAA
1 ATATTTTA-T-ATTTTAAA
583527 TTAAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.28
19 10 0.31
20 11 0.34
21 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTATATTTTAAAAA
Found at i:583507 original size:21 final size:20
Alignment explanation
Indices: 583481--583526 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
583471 TATATTTATA
583481 TTAAAAATAATATT-TTATATT
1 TTAAAAAT-ATATTATTA-ATT
*
583502 TTAAAAATATTTTATTAATT
1 TTAAAAATATATTATTAATT
583522 TTAAA
1 TTAAA
583527 TTAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAAAATATATTATTAATT
Found at i:583553 original size:26 final size:25
Alignment explanation
Indices: 583502--583558 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
583492 ATTTTATATT
* * * *
583502 TTAAAAATATTTTATTAATTTTAAA
1 TTAAATATAATTTATTAATATCAAA
583527 TTAAATATAATTTATATAATATCAAA
1 TTAAATATAATTTAT-TAATATCAAA
*
583553 TCAAAT
1 TTAAAT
583559 TTAAATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAATATAATTTATTAATATCAAA
Found at i:583616 original size:39 final size:41
Alignment explanation
Indices: 583550--583626 Score: 97
Period size: 39 Copynumber: 1.9 Consensus size: 41
583540 ATATAATATC
583550 AAATCAAATTTAAATATAAAAAAATAAA-A-AAATATTTTT
1 AAATCAAATTTAAATATAAAAAAATAAATATAAATATTTTT
* **
583589 AAATCAAA-TTAAATTTAAATATTATAAATATAAATATT
1 AAATCAAATTTAAATATAAA-AAAATAAATATAAATATT
583627 GAATTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 10 0.31
39 14 0.44
40 1 0.03
41 7 0.22
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (41 bp):
AAATCAAATTTAAATATAAAAAAATAAATATAAATATTTTT
Found at i:609043 original size:49 final size:49
Alignment explanation
Indices: 608990--609086 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
608980 TGAAAATTAT
*
608990 CGTAGTAATTAGTTTCAAGTCTTAAAATTTAGATAAATTTAAAATAAGA
1 CGTAGTAATTAGTTTCAAGCCTTAAAATTTAGATAAATTTAAAATAAGA
*
609039 CGTAGTAATTAGTTTCAGGCCTTAAAATTTAGATAAATTTAAAATAAG
1 CGTAGTAATTAGTTTCAAGCCTTAAAATTTAGATAAATTTAAAATAAG
609087 GCATCGTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (49 bp):
CGTAGTAATTAGTTTCAAGCCTTAAAATTTAGATAAATTTAAAATAAGA
Found at i:611307 original size:19 final size:18
Alignment explanation
Indices: 611266--611301 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
611256 TAAAAATAAA
*
611266 AAATTAATAAATTAAATC
1 AAATTAATAAATAAAATC
611284 AAATTAAATAAATAAAAT
1 AAATT-AATAAATAAAAT
611302 TTAATTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTAATAAATAAAATC
Found at i:611363 original size:23 final size:24
Alignment explanation
Indices: 611323--611367 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
611313 TGAATTAAAT
* *
611323 TATATAAAAATTCTATTCAAATAA
1 TATAAAAAAATTCAATTCAAATAA
611347 TATAAAAAAATT-AATTCAAAT
1 TATAAAAAAATTCAATTCAAAT
611368 TTAAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
TATAAAAAAATTCAATTCAAATAA
Found at i:613480 original size:13 final size:13
Alignment explanation
Indices: 613461--613500 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
613451 ATTTATTTAA
613461 ATATATTAAAATT
1 ATATATTAAAATT
* *
613474 TTATATTAAAATA
1 ATATATTAAAATT
*
613487 ATATATAAAAATT
1 ATATATTAAAATT
613500 A
1 A
613501 AAAATTAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:613506 original size:33 final size:31
Alignment explanation
Indices: 613426--613503 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
613416 TTTTTATAAA
* *
613426 ATAAAAATTATAATTTTATATCAAAATTTAT
1 ATAAAAATTAAAATTTTATATCAAAATATAT
* *
613457 TTAAATATATTAAAATTTTATATTAAAATAATAT
1 ATAAA-A-ATTAAAATTTTATATCAAAAT-ATAT
613491 ATAAAAATTAAAA
1 ATAAAAATTAAAA
613504 ATTAAAGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 4 0.10
32 8 0.21
33 20 0.51
34 7 0.18
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAAAAATTAAAATTTTATATCAAAATATAT
Found at i:613507 original size:26 final size:26
Alignment explanation
Indices: 613460--613509 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
613450 AATTTATTTA
* ** *
613460 AATATATTAAAATTTTATATTAAAAT
1 AATATATAAAAATTAAAAATTAAAAT
613486 AATATATAAAAATTAAAAATTAAA
1 AATATATAAAAATTAAAAATTAAA
613510 GACCGATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATATAAAAATTAAAAATTAAAAT
Found at i:616213 original size:17 final size:19
Alignment explanation
Indices: 616186--616222 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
616176 ACAATATGCT
616186 ACTTTTATAAAT-ATTTTA
1 ACTTTTATAAATAATTTTA
616204 ACTTTT-TAAATAATTTTA
1 ACTTTTATAAATAATTTTA
616222 A
1 A
616223 AATTGATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ACTTTTATAAATAATTTTA
Found at i:617041 original size:46 final size:46
Alignment explanation
Indices: 616991--617118 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 46
616981 ATAAAAATTA
*
616991 AGCTTATTTTTATATATTAATCAAATCTAATTGAGTGAGCTCGAGT
1 AGCTTATTTTTATATATTAATCAAATCTAATCGAGTGAGCTCGAGT
* * *
617037 AGCTTATTTTTACATATTAATCAAATTTAATCGAATGAGCTCGAGT
1 AGCTTATTTTTATATATTAATCAAATCTAATCGAGTGAGCTCGAGT
** *
617083 AATTTATTTTTATATATTAATCAAGTCTAATCGAGT
1 AGCTTATTTTTATATATTAATCAAATCTAATCGAGT
617119 CGAATTTGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (46 bp):
AGCTTATTTTTATATATTAATCAAATCTAATCGAGTGAGCTCGAGT
Found at i:628805 original size:17 final size:17
Alignment explanation
Indices: 628770--628805 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
628760 TAATAATCTA
*
628770 AAATACGATACAAACAT
1 AAATACGATACAAAAAT
*
628787 AAATACGATATAAAAAT
1 AAATACGATACAAAAAT
628804 AA
1 AA
628806 GACACGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (17 bp):
AAATACGATACAAAAAT
Found at i:634709 original size:18 final size:18
Alignment explanation
Indices: 634667--634712 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
634657 AAATTGAATC
*
634667 AAATTATATATTTTTATT
1 AAATTTTATATTTTTATT
*
634685 AATTTTTATATTTTT-TT
1 AAATTTTATATTTTTATT
634702 AAAATTTTATA
1 -AAATTTTATA
634713 AAATAAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AAATTTTATATTTTTATT
Found at i:634824 original size:19 final size:19
Alignment explanation
Indices: 634792--634852 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
634782 AAATATAAAT
634792 ATAAAATTTAAAATTTAATAA
1 ATAAAA-TT-AAATTTAATAA
* *
634813 ATTAAATTAAATTAAATAA
1 ATAAAATTAAATTTAATAA
*
634832 ATAAAATTTAATTTGAATAA
1 ATAAAATTAAATTT-AATAA
634852 A
1 A
634853 ACCAATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 21 0.62
20 8 0.24
21 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATTAAATTTAATAA
Found at i:636340 original size:2 final size:2
Alignment explanation
Indices: 636335--636378 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
636325 TAATTCACAC
* * *
636335 AT AT AT AA AT AT -T TT AT AT AG 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
636376 AT A
1 AT A
636379 AATTTGAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:641473 original size:27 final size:27
Alignment explanation
Indices: 641443--641499 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
641433 GATGTTTTGG
*
641443 TTGGTAATATGATGTTGGGTTGTAACA
1 TTGGTAATATGATGTTGAGTTGTAACA
*
641470 TTGGTAATATGATGTTTAGTTGTAACA
1 TTGGTAATATGATGTTGAGTTGTAACA
641497 TTG
1 TTG
641500 AAATTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (27 bp):
TTGGTAATATGATGTTGAGTTGTAACA
Found at i:648099 original size:20 final size:20
Alignment explanation
Indices: 648060--648096 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
648050 TTATACATCA
648060 AATATTATAATTAAATAATT
1 AATATTATAATTAAATAATT
*
648080 AATATT-TATTTAAATAA
1 AATATTATAATTAAATAA
648097 ATTTGCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTATAATTAAATAATT
Found at i:648976 original size:3 final size:3
Alignment explanation
Indices: 648970--649003 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
648960 CCTCCACTTT
*
648970 CAC CAC CGC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
649004 TCCTCCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.68, G:0.03, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:649343 original size:18 final size:18
Alignment explanation
Indices: 649320--649360 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
649310 ATAACCACTG
649320 CCACCTCCACCACC-CTCT
1 CCACCTCCACCACCTC-CT
649338 CCACCTCCACCACCTCCT
1 CCACCTCCACCACCTCCT
649356 CCACC
1 CCACC
649361 AGTCTCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.17, C:0.68, G:0.00, T:0.15
Consensus pattern (18 bp):
CCACCTCCACCACCTCCT
Found at i:652437 original size:12 final size:12
Alignment explanation
Indices: 652422--652455 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
652412 CCACCTCCAA
652422 ATCCTCCACCAT
1 ATCCTCCACCAT
*
652434 ATCCTCCGCCAT
1 ATCCTCCACCAT
*
652446 ATCCACCACC
1 ATCCTCCACC
652456 GAATGAGCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.53, G:0.03, T:0.21
Consensus pattern (12 bp):
ATCCTCCACCAT
Found at i:678336 original size:27 final size:28
Alignment explanation
Indices: 678301--678359 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
678291 GAAGAACAGA
*
678301 AAAAAACAAAAGAATAAAGAA-AAATAG
1 AAAAAACAAAAGAATAAAGAATAAAAAG
678328 AAAAAACAAAAGAATAAAGAATAAAAAG
1 AAAAAACAAAAGAATAAAGAATAAAAAG
678356 AAAA
1 AAAA
678360 TGATATCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (28 bp):
AAAAAACAAAAGAATAAAGAATAAAAAG
Found at i:678353 original size:15 final size:14
Alignment explanation
Indices: 678308--678353 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
678298 AGAAAAAAAC
678308 AAAAGAATAAAGAA
1 AAAAGAATAAAGAA
*
678322 AAATAGAA-AAA-AC
1 AAA-AGAATAAAGAA
678335 AAAAGAATAAAGAA
1 AAAAGAATAAAGAA
678349 TAAAA
1 -AAAA
678354 AGAAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 4 0.15
13 7 0.27
14 7 0.27
15 8 0.31
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAAGAATAAAGAA
Found at i:702154 original size:52 final size:52
Alignment explanation
Indices: 702049--702155 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
702039 AAAAGCAATG
* * * *
702049 AAGTAGGAATTAAGGAACAACAAACAGACAAACTGATAAAGTAGTGCCTCCC
1 AAGTAGGAATTAAGGAACAACAAACAGACAAACTCATAAAGCAATGCCCCCC
* *
702101 AAGTAGGAATTAAGGAACAACATACAGACAAACTCATGAAGCAATGCCCCCC
1 AAGTAGGAATTAAGGAACAACAAACAGACAAACTCATAAAGCAATGCCCCCC
702153 AAG
1 AAG
702156 CCCCAGCTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (52 bp):
AAGTAGGAATTAAGGAACAACAAACAGACAAACTCATAAAGCAATGCCCCCC
Found at i:704624 original size:46 final size:45
Alignment explanation
Indices: 704567--704659 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
704557 GAAGAAGTAA
*
704567 ATGGGATTACATGTTTCCAACTTAAAAAAGGTAAACAAACCTCTTT
1 ATGGGAATACATGTTTCCAACTT-AAAAAGGTAAACAAACCTCTTT
* *
704613 ATGGGAATACATGTTTCCAACTTTAAAATGTAAACAAACCTCTTT
1 ATGGGAATACATGTTTCCAACTTAAAAAGGTAAACAAACCTCTTT
704658 AT
1 AT
704660 TGGGTGCATG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 22 0.50
46 22 0.50
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (45 bp):
ATGGGAATACATGTTTCCAACTTAAAAAGGTAAACAAACCTCTTT
Found at i:709315 original size:29 final size:28
Alignment explanation
Indices: 709283--709393 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 28
709273 AAAATTTTTG
709283 TATATATTTATATTAATTATGTATATTTA
1 TATATATTTATATTAATTATGT-TATTTA
* *
709312 TATATACTCGTATTACTTACATCTAT-TTATATA
1 TATATA-T-TTA-TA-TTA-AT-TATGTTATTTA
*
709345 TATATATTTATATTATTTATGTTTATTTA
1 TATATATTTATATTAATTATG-TTATTTA
* *
709374 TATCATATTTAAATAAATTA
1 TAT-ATATTTATATTAATTA
709394 ATTATATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
27 3 0.05
28 1 0.02
29 18 0.28
30 16 0.25
31 4 0.06
32 3 0.05
33 14 0.22
34 3 0.05
35 3 0.05
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (28 bp):
TATATATTTATATTAATTATGTTATTTA
Found at i:709412 original size:62 final size:62
Alignment explanation
Indices: 709284--709413 Score: 138
Period size: 62 Copynumber: 2.1 Consensus size: 62
709274 AAATTTTTGT
** * * * *
709284 ATATATTTATATTAATTATGTATATTTATATATACTCGTATTACTTACATCTATTTATATAT
1 ATATATTTATATTAATTATGTATATTTATATATACTCAAATAAATTACATCTATATATATAA
* * * *
709346 ATATATTTATATTATTTATGTTTATTTATATCATATTTAAATAAATTA-AT-TATATATATTAA
1 ATATATTTATATTAATTATGTATATTTATAT-ATACTCAAATAAATTACATCTATATATA-TAA
709408 ATATAT
1 ATATAT
709414 CATATTGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
61 7 0.12
62 39 0.70
63 10 0.18
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (62 bp):
ATATATTTATATTAATTATGTATATTTATATATACTCAAATAAATTACATCTATATATATAA
Found at i:709488 original size:18 final size:18
Alignment explanation
Indices: 709458--709509 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
709448 GTATCGTATT
*
709458 TATA-TTTAAAATTTAAA
1 TATATTTTATAATTTAAA
*
709475 TATATTTTATAATTTATA
1 TATATTTTATAATTTAAA
*
709493 T-TATATTTATATTTTAA
1 TATAT-TTTATAATTTAA
709510 TAATTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTTATAATTTAAA
Found at i:709503 original size:25 final size:26
Alignment explanation
Indices: 709475--709530 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
709465 AAAATTTAAA
*
709475 TATATTTT-ATAATTTATATTA-TATT
1 TATATTTTAATAATTTA-ATTATTATA
709500 TATATTTTAATAATTTAATTATTATA
1 TATATTTTAATAATTTAATTATTATA
709526 TATAT
1 TATAT
709531 CAAATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATATTTTAATAATTTAATTATTATA
Found at i:709619 original size:61 final size:61
Alignment explanation
Indices: 709554--709672 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
709544 AAATATGATA
709554 AAAAAAATAAATTATTTGATCTATATAGGATAATATGAAACCTTGAAATCTACGTCAATTT
1 AAAAAAATAAATTATTTGATCTATATAGGATAATATGAAACCTTGAAATCTACGTCAATTT
*
709615 AAAAAGATAAATTATTTGATCTATATAGGATAATATGAAACCTTGAAATCTACGTCAA
1 AAAAAAATAAATTATTTGATCTATATAGGATAATATGAAACCTTGAAATCTACGTCAA
709673 GTTACCACCC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (61 bp):
AAAAAAATAAATTATTTGATCTATATAGGATAATATGAAACCTTGAAATCTACGTCAATTT
Found at i:710923 original size:24 final size:22
Alignment explanation
Indices: 710883--710937 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
710873 GATTGTTGTC
710883 TATTACTATATGTTTATTATGATA
1 TATTACT-TATGTTTATTATG-TA
* *
710907 TATTACTTATGTGTTATTGTGTT
1 TATTACTTATGT-TTATTATGTA
710930 TATTACTT
1 TATTACTT
710938 CAAGCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.58
Consensus pattern (22 bp):
TATTACTTATGTTTATTATGTA
Done.