Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:436359 original size:22 final size:22
Alignment explanation
Indices: 436343--436385 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
436333 AATTTATTAG
*
436343 TATGGATTTATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
436365 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
436386 TAATTTATTA
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:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:436422 original size:22 final size:22
Alignment explanation
Indices: 436397--436439 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
436387 AATTTATTAG
436397 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
436419 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
436440 TAATTTATTA
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:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:436447 original size:14 final size:14
Alignment explanation
Indices: 436428--436513 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
436418 ATATGGATTG
436428 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
436442 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
436460 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
436474 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
436492 ATTTATTTTAAATA
1 ATTTATTTTAAATA
436506 ATTTATTT
1 ATTTATTT
436514 GTATGGATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 27 0.50
15 2 0.04
16 4 0.07
17 2 0.04
18 19 0.35
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:436607 original size:18 final size:17
Alignment explanation
Indices: 436442--436610 Score: 62
Period size: 18 Copynumber: 10.4 Consensus size: 17
436432 ATTTTAAATA
436442 ATTTATTAGTATGAATTG
1 ATTTATT-GTATGAATTG
* *
436460 ATTTATT-T-T-AAATA
1 ATTTATTGTATGAATTG
*
436474 ATTTATTAGTATGGATTG
1 ATTTATT-GTATGAATTG
* *
436492 ATTTATT-T-T-AAATA
1 ATTTATTGTATGAATTG
*
436506 ATTTATTTGTATGGATTG
1 ATTTA-TTGTATGAATTG
* *
436524 ATTTATTTTA-AAATATGG
1 ATTTATTGTATGAAT-T-G
* *
436542 ATTAATT-TAT-TATTG
1 ATTTATTGTATGAATTG
436557 ---TAGTTGTATGAATTG
1 ATTTA-TTGTATGAATTG
* *
436572 ATTTATT-T-T-AAATA
1 ATTTATTGTATGAATTG
436586 ATTTATTAGTATGAATTG
1 ATTTATT-GTATGAATTG
436604 ATTTATT
1 ATTTATT
436611 TTAAATTATG
Statistics
Matches: 108, Mismatches: 22, Indels: 42
0.63 0.13 0.24
Matches are distributed among these distances:
12 1 0.01
13 2 0.02
14 30 0.28
15 10 0.09
16 9 0.08
17 14 0.13
18 42 0.39
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (17 bp):
ATTTATTGTATGAATTG
Found at i:436620 original size:22 final size:22
Alignment explanation
Indices: 436595--436638 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
436585 AATTTATTAG
436595 TATGAATTGATTTATTTTAAAT
1 TATGAATTGATTTATTTTAAAT
*
436617 TATGGATTGATTTATTTTAAAT
1 TATGAATTGATTTATTTTAAAT
436639 AATTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAT
Found at i:436645 original size:14 final size:14
Alignment explanation
Indices: 436626--436678 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
436616 TTATGGATTG
436626 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
436640 ATTTATTATTATGGATTG
1 ATTTATT-TTA---AATA
436658 ATTTATTTTAAATA
1 ATTTATTTTAAATA
436672 ATTTATT
1 ATTTATT
436679 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 3 0.10
17 3 0.10
18 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:436777 original size:22 final size:22
Alignment explanation
Indices: 436761--436803 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
436751 AATTTATTAG
436761 TATGGATTAATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
*
436783 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
436804 TAATTTATTA
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:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:436815 original size:166 final size:166
Alignment explanation
Indices: 435809--436813 Score: 1599
Period size: 166 Copynumber: 6.0 Consensus size: 166
435799 TATTTTAAAA
435809 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
435874 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
* *
435939 AAAATATGGATTTATTTATTTTAAATAATTTATTAT
131 AAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
435975 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAATATGGAT
436040 TGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA
62 TGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA
436105 TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
127 TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
436145 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
436210 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
436275 AAAATATGGATTGATTTATTTTAAATAATTTATTAG
131 AAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
436311 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* * * * *
436376 TTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAA
66 TTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAA
* * * *
436439 ATAATTTA--TT--AGTATGAATTGATTTATTTTAAATAATTTATTAG
119 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
436483 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
436548 TTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
* *
436613 AAATTATGGATTGATTTATTTTAAATAATTTATTAT
131 AAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
436649 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
436714 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
436779 AAAATATGGATTGATTTATTTTAAATAATTTATTA
131 AAAATATGGATTGATTTATTTTAAATAATTTATTA
436814 TTGTAGTTGT
Statistics
Matches: 779, Mismatches: 38, Indels: 44
0.90 0.04 0.05
Matches are distributed among these distances:
161 3 0.00
162 14 0.02
164 2 0.00
165 5 0.01
166 438 0.56
167 3 0.00
168 4 0.01
169 1 0.00
170 166 0.21
171 2 0.00
172 118 0.15
173 5 0.01
174 2 0.00
176 13 0.02
177 3 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (166 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:436863 original size:31 final size:31
Alignment explanation
Indices: 436828--436886 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
436818 AGTTGTATGG
* *
436828 ATTATTTAAATTTCAA-TATTGTAAAACTAAA
1 ATTATTTAAATCT-AAGTATTGCAAAACTAAA
436859 ATTATTTAAATCTAAGTATTGCAAAACT
1 ATTATTTAAATCTAAGTATTGCAAAACT
436887 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTAAGTATTGCAAAACTAAA
Found at i:442918 original size:79 final size:79
Alignment explanation
Indices: 442832--442989 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
442822 AGTTAATAAC
442832 ACCTTAGCCATGGGCCATACTAACACAATTACTCCAACACGTGACATTCAAATACTGTAACTTTA
1 ACCTTAGCCATGGGCCATACTAACACAATTACTCCAACACGTGACATTCAAATACTGTAACTTTA
442897 ATCTTAGAACCCTT
66 ATCTTAGAACCCTT
* *
442911 ACCTTAGCCATGGGCCATGCTAACACAATTACTCCAACACGTGACATTCAAATACTGTAACTTTG
1 ACCTTAGCCATGGGCCATACTAACACAATTACTCCAACACGTGACATTCAAATACTGTAACTTTA
*
442976 ATCTTAGAATCCTT
66 ATCTTAGAACCCTT
442990 GCTTAAATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (79 bp):
ACCTTAGCCATGGGCCATACTAACACAATTACTCCAACACGTGACATTCAAATACTGTAACTTTA
ATCTTAGAACCCTT
Found at i:450486 original size:20 final size:20
Alignment explanation
Indices: 450463--450631 Score: 112
Period size: 20 Copynumber: 8.4 Consensus size: 20
450453 GTTTCTGCAA
*
450463 TCGCAACGCGAATTTCTTTT
1 TCGCAACACGAATTTCTTTT
* * ***
450483 TCGCAACGCGATTTTCCAAAT
1 TCGCAACACGAATTT-CTTTT
* **
450504 TCGCAACTCG-ATTTCTGAAT
1 TCGCAACACGAATTTCT-TTT
*
450524 TCGCAACGCGAATTTCTTTT
1 TCGCAACACGAATTTCTTTT
*
450544 TCGCAACAC-AAGTTTCCTTT
1 TCGCAACACGAA-TTTCTTTT
* * **
450564 TCGCAACAAGATTTTCTAAT
1 TCGCAACACGAATTTCTTTT
*
450584 TCGCAACATGAATTT-TGTTT
1 TCGCAACACGAATTTCT-TTT
*
450604 TCGCAACACGAATTT-TAATT
1 TCGCAACACGAATTTCT-TTT
450624 TCGCAACA
1 TCGCAACA
450632 GCTTTTATTT
Statistics
Matches: 119, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.03
20 97 0.82
21 18 0.15
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TCGCAACACGAATTTCTTTT
Found at i:450507 original size:61 final size:62
Alignment explanation
Indices: 450421--450619 Score: 223
Period size: 61 Copynumber: 3.3 Consensus size: 62
450411 TCGCAACACA
*
450421 TCGCAACGCGAATTTTTCAAATTCGCAACTC-AGTTTCTGCAA-TCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTTCCAAATTCGCAACTCGA-TTTCTG-AATTCGCAACGCGAATTTCTTTT
450483 TCGCAACGCG-ATTTTCCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTTCCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTT
* * ** ** **
450544 TCGCAACAC-AAGTTTCC-TTTTCGCAACAAGATTTTCT-AATTCGCAACATGAATTT-TGTTT
1 TCGCAACGCGAATTTTCCAAATTCGCAACTCGA-TTTCTGAATTCGCAACGCGAATTTCT-TTT
*
450604 TCGCAACACGAATTTT
1 TCGCAACGCGAATTTT
450620 AATTTCGCAA
Statistics
Matches: 121, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
59 1 0.01
60 40 0.33
61 69 0.57
62 11 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (62 bp):
TCGCAACGCGAATTTTCCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTT
Found at i:450626 original size:60 final size:60
Alignment explanation
Indices: 450421--450631 Score: 191
Period size: 60 Copynumber: 3.5 Consensus size: 60
450411 TCGCAACACA
* * *
450421 TCGCAACGCGAATTTTTCAAATTCGCAACTCAG-TTTCTGCAA-TCGCAACGCGAATTTCTTTT
1 TCGCAACACGAA-TTTT-AATTTCGCAAC-AAGATTTCTG-AATTCGCAACGCGAATTTCTTTT
* * **
450483 TCGCAACGCG-ATTTTCCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTT
1 TCGCAACACGAATTTT--AATTTCGCAACAAGATTTCTGAATTCGCAACGCGAATTTCTTTT
*** **
450544 TCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTCT-AATTCGCAACATGAATTT-TGTTT
1 TCGCAACACGAA-TTTTAATTTCGCAACAAGA-TTTCTGAATTCGCAACGCGAATTTCT-TTT
450604 TCGCAACACGAATTTTAATTTCGCAACA
1 TCGCAACACGAATTTTAATTTCGCAACA
450632 GCTTTTATTT
Statistics
Matches: 127, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
59 1 0.01
60 58 0.46
61 55 0.43
62 13 0.10
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (60 bp):
TCGCAACACGAATTTTAATTTCGCAACAAGATTTCTGAATTCGCAACGCGAATTTCTTTT
Found at i:450643 original size:18 final size:20
Alignment explanation
Indices: 450523--450650 Score: 104
Period size: 20 Copynumber: 6.5 Consensus size: 20
450513 GATTTCTGAA
*
450523 TTCGCAACGCGAATTTCT-TT
1 TTCGCAACACGAATTT-TATT
**
450543 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTTATT
* * *
450563 TTCGCAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTTAT-T
* *
450583 TTCGCAACATGAATTTTGTT
1 TTCGCAACACGAATTTTATT
*
450603 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTATT
*
450623 TTCGCAACA-G-CTTTTATT
1 TTCGCAACACGAATTTTATT
450641 TTCGCAACAC
1 TTCGCAACAC
450651 AAATATTTTG
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
18 15 0.17
19 8 0.09
20 60 0.67
21 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTATT
Found at i:450807 original size:14 final size:15
Alignment explanation
Indices: 450788--450825 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
450778 TCCCCATCTC
450788 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
450802 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
450818 TAATTTTT
1 TAATTTTT
450826 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:451451 original size:12 final size:12
Alignment explanation
Indices: 451417--451449 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
451407 ACCACATTTT
*
451417 CAATACCAAACA
1 CAATATCAAACA
451429 CAATATCAAACA
1 CAATATCAAACA
451441 CAAT-TCAAA
1 CAATATCAAA
451450 ACCCACAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:451811 original size:3 final size:3
Alignment explanation
Indices: 451803--451833 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
451793 ATATAACCTT
*
451803 GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
451834 TCCCCGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:455689 original size:21 final size:21
Alignment explanation
Indices: 455663--455739 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
455653 ATGAATTGAG
* *
455663 CTCTTGAACGGTGGGAGCGAC
1 CTCTTGAACGATGGGAGGGAC
*
455684 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGGGAC
*
455705 CTCTTGAACGATGAGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
*
455726 CTCTTGAGCGATGG
1 CTCTTGAACGATGG
455740 CAAGTGAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGAC
Found at i:456358 original size:42 final size:42
Alignment explanation
Indices: 456311--456409 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
456301 GTGATGGAAT
* * * *
456311 AGGTGATGGCTCTTGGTGTGGAGGTATATAATCGGCTCAATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCAATC
* *
456353 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCAATC
456395 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
456410 AAGTGGGGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCAATC
Found at i:457896 original size:20 final size:20
Alignment explanation
Indices: 457871--457909 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
457861 TCGTGTTGCG
*
457871 ATTTTCGTTTTACGAATTTC
1 ATTTTCGTGTTACGAATTTC
*
457891 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTACGAATTT
457910 AAGTTTCAAA
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:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTACGAATTTC
Found at i:457916 original size:20 final size:20
Alignment explanation
Indices: 457873--457916 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
457863 GTGTTGCGAT
* * *
457873 TTTCGTTTTACGAATTTCAT
1 TTTCGTGTTACGAATTTAAG
*
457893 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTACGAATTTAAG
457913 TTTC
1 TTTC
457917 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGAATTTAAG
Found at i:458418 original size:20 final size:20
Alignment explanation
Indices: 458395--458440 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
458385 AAAATTCGCT
*
458395 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTATG
*
458415 TTGCGAATTTGATTTCTATG
1 TTGCGAATTTGACTTCTATG
458435 TTGCGA
1 TTGCGA
458441 TTTACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTATG
Found at i:458457 original size:20 final size:21
Alignment explanation
Indices: 458434--458545 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 21
458424 TGATTTCTAT
458434 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTTACAAATTCGC
* *
458454 GTTGCGAATTT-CAGATTCGT
1 GTTGCGAATTTACAAATTCGC
* * *
458474 TTTGC-TATTTACATATTCGC
1 GTTGCGAATTTACAAATTCGC
* **
458494 GTTACGAATTTGGAAATTCGC
1 GTTGCGAATTTACAAATTCGC
* *
458515 GTTGCGGAA--AAGAAATTCGC
1 GTTGC-GAATTTACAAATTCGC
*
458535 ATTGCGAATTT
1 GTTGCGAATTT
458546 GGAATATGTG
Statistics
Matches: 69, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
19 7 0.10
20 40 0.58
21 19 0.28
22 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (21 bp):
GTTGCGAATTTACAAATTCGC
Found at i:458458 original size:40 final size:38
Alignment explanation
Indices: 458414--458505 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 38
458404 TGACTTCTGT
458414 GTTGCGAATTTGATTTC-TATGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGA-TTCGT-T-TTGCGATTTACAAATTCGC
* *
458454 GTTGCGAATTTCAGATTCGTTTTGCTATTTACATATTCGC
1 GTTGCGAATTT--GATTCGTTTTGCGATTTACAAATTCGC
*
458494 GTTACGAATTTG
1 GTTGCGAATTTG
458506 GAAATTCGCG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 1 0.02
40 38 0.83
41 4 0.09
42 3 0.07
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (38 bp):
GTTGCGAATTTGATTCGTTTTGCGATTTACAAATTCGC
Found at i:464399 original size:40 final size:40
Alignment explanation
Indices: 464355--464452 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 40
464345 TGTCGTTACA
464355 ACAAACTCCGCAATAGAAAGTAATTTAGCGGCGTTTTCAT
1 ACAAACTCCGCAATAGAAAGTAATTTAGCGGCGTTTTCAT
* **** * *
464395 ACAAACGT-TGCAATATTTTGGTATTTTAGCGGCGTTTTTAT
1 ACAAAC-TCCGCAATA-GAAAGTAATTTAGCGGCGTTTTCAT
*
464436 ACAAACGCCGCAATAGA
1 ACAAACTCCGCAATAGA
464453 TTAATTTATA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
40 12 0.27
41 32 0.73
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (40 bp):
ACAAACTCCGCAATAGAAAGTAATTTAGCGGCGTTTTCAT
Found at i:464907 original size:16 final size:16
Alignment explanation
Indices: 464886--464919 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
464876 GTATATAATT
464886 TAAATTTAATAA-AAAA
1 TAAATTTAA-AATAAAA
464902 TAAATTTAAAATAAAA
1 TAAATTTAAAATAAAA
464918 TA
1 TA
464920 TTAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATTTAAAATAAAA
Found at i:467231 original size:55 final size:55
Alignment explanation
Indices: 467138--467245 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
467128 TACAGGGTGT
* *
467138 TACTTTGTTGAATCTCTCGACTATTAAAAGTTATAAAATGGTTTCCCGACTATGC
1 TACTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGGTTACCCGACTATGC
* *
467193 TACTTTGTTGAGTCTCTCGACTATTAAAATTTACAAAATGGTTACCCGACTAT
1 TACTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGGTTACCCGACTAT
467246 TTATATGTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (55 bp):
TACTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGGTTACCCGACTATGC
Found at i:471883 original size:230 final size:230
Alignment explanation
Indices: 471450--471890 Score: 584
Period size: 230 Copynumber: 1.9 Consensus size: 230
471440 GAAATGAGAT
* * *
471450 AAAAAACAATGAGTTAATCTCAGTATTTGATTTTCCTCAATCCAATGGTCCAAAAAAGGTGTAAA
1 AAAAAACAATGAGTTAATCTCAGCATTTGATTTTCCTCAATCCAACGATCCAAAAAAGGTGTAAA
* * * * *
471515 ACCCTTAGTTTTACATTGGGTATAGGTGGATCCTAACCTTATTAATGAGACAGGATCCGTTCACA
66 ACCCTTAGTTTTACAGTGAGTATAAGTGGATCCT-ACCCTATTAAAGAGACAGGATCCGTTCACA
* * * *
471580 CCCAGTGTAAAACTAAGAGTTTTACACCTTTTTAGGACCATTAGAAGAGATAAATCAAAGGCTGA
130 CCCAATGTAAAACTAAGAGTTTTACACCTTTTTAGGACCACTAGAAGAGAGAAATCAAAGGATGA
471645 GATTAACAGTAAGAAAGGAGAATATATTCACTAGAG
195 GATTAACAGTAAGAAAGGAGAATATATTCACTAGAG
* *
471681 AAAAAACAA-GAAGTTAATCTCAGCCA-TTGA-TTTCCTTCAATCCAACGATGCTAAAAAGGTGT
1 AAAAAACAATG-AGTTAATCTCAG-CATTTGATTTTCC-TCAATCCAACGATCCAAAAAAGGTGT
* * * * * *
471743 AAAACTCTTAAGTTTTACAGTGAGTGTAAGTGGATCCT-CCCTATTAAAGGGATAGGATTCGTTT
63 AAAACCCTT-AGTTTTACAGTGAGTATAAGTGGATCCTACCCTATTAAAGAGACAGGATCCGTTC
* * * *
471807 ACACCCAATTTAAAACTAAGAGTTTTACACCTTTTTAGGACCACTGGATGAGAGAAATTAAAGGA
127 ACACCCAATGTAAAACTAAGAGTTTTACACCTTTTTAGGACCACTAGAAGAGAGAAATCAAAGGA
*
471872 TGAGATTAACAGTAGGAAA
192 TGAGATTAACAGTAAGAAA
471891 TAAGCAGATA
Statistics
Matches: 181, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
230 101 0.56
231 55 0.30
232 25 0.14
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (230 bp):
AAAAAACAATGAGTTAATCTCAGCATTTGATTTTCCTCAATCCAACGATCCAAAAAAGGTGTAAA
ACCCTTAGTTTTACAGTGAGTATAAGTGGATCCTACCCTATTAAAGAGACAGGATCCGTTCACAC
CCAATGTAAAACTAAGAGTTTTACACCTTTTTAGGACCACTAGAAGAGAGAAATCAAAGGATGAG
ATTAACAGTAAGAAAGGAGAATATATTCACTAGAG
Found at i:476268 original size:19 final size:19
Alignment explanation
Indices: 476252--476291 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
476242 TATTAATTTG
476252 TTTTAAA-AATTTTAATTA
1 TTTTAAACAATTTTAATTA
*
476270 TTTTAAACAA-TTTATTTA
1 TTTTAAACAATTTTAATTA
476288 TTTT
1 TTTT
476292 TTTAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAACAATTTTAATTA
Found at i:476403 original size:19 final size:19
Alignment explanation
Indices: 476379--476424 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
476369 TTGTTTATTT
476379 ATTTATTTAATTATTTCGA
1 ATTTATTTAATTATTTCGA
** *
476398 ATTTATTTGTTTGTTTCGA
1 ATTTATTTAATTATTTCGA
*
476417 AATTATTT
1 ATTTATTT
476425 GTTTATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (19 bp):
ATTTATTTAATTATTTCGA
Found at i:476405 original size:4 final size:4
Alignment explanation
Indices: 476311--476394 Score: 62
Period size: 4 Copynumber: 20.8 Consensus size: 4
476301 TTTGTTCGAT
* * * * **
476311 TTTA TTTA TTTA TGTA TTTA TTTCGA ATTA ATTA TTCA TTTA TTT- TGAA
1 TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA TTTA
* * *
476360 TTTA TTTA CTTG TTTA TTTA TTTA TTTA ATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
476395 CGAATTTATT
Statistics
Matches: 61, Mismatches: 16, Indels: 6
0.73 0.19 0.07
Matches are distributed among these distances:
3 1 0.02
4 57 0.93
6 3 0.05
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:476425 original size:19 final size:19
Alignment explanation
Indices: 476392--476428 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
476382 TATTTAATTA
*
476392 TTTCGAATTTATTTGTTTG
1 TTTCGAAATTATTTGTTTG
476411 TTTCGAAATTATTTGTTT
1 TTTCGAAATTATTTGTTT
476429 ATTTGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (19 bp):
TTTCGAAATTATTTGTTTG
Found at i:478523 original size:29 final size:28
Alignment explanation
Indices: 478490--478547 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
478480 ATTAGTTGTT
478490 TACATTTATAATTTTTTAGTT-ATTCGAAC
1 TACATTT-TAATTTTTTAGTTAATT-GAAC
**
478519 TACATTTTCTTTTTTTAGTTAATTGAAC
1 TACATTTTAATTTTTTAGTTAATTGAAC
478547 T
1 T
478548 TCTTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (28 bp):
TACATTTTAATTTTTTAGTTAATTGAAC
Found at i:478553 original size:27 final size:28
Alignment explanation
Indices: 478501--478561 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
478491 ACATTTATAA
478501 TTTTTTAGTTATTCGAACTACATTTTCT
1 TTTTTTAGTTATTCGAACTACATTTTCT
* *
478529 TTTTTTAGTTAATT-GAACTTCTTTTTCT
1 TTTTTTAGTT-ATTCGAACTACATTTTCT
478557 TTTTT
1 TTTTT
478562 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTTTAGTTATTCGAACTACATTTTCT
Found at i:478655 original size:17 final size:17
Alignment explanation
Indices: 478603--478655 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
478593 TAGTTTTTTT
478603 TTAATTTGTTTAAATTA
1 TTAATTTGTTTAAATTA
***
478620 TTAATCAACTTTAAATTA
1 TTAAT-TTGTTTAAATTA
*
478638 TTAATTTGTTTAAGTTA
1 TTAATTTGTTTAAATTA
478655 T
1 T
478656 CATTGAACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.55
Consensus pattern (17 bp):
TTAATTTGTTTAAATTA
Found at i:492293 original size:12 final size:12
Alignment explanation
Indices: 492270--492304 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
492260 ATAATGAGAT
*
492270 AAAAATTAAATA
1 AAAAAATAAATA
*
492282 AACAAATAAATA
1 AAAAAATAAATA
492294 AAAAAATAAAT
1 AAAAAATAAAT
492305 TGGGATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:494585 original size:197 final size:197
Alignment explanation
Indices: 494250--494643 Score: 743
Period size: 197 Copynumber: 2.0 Consensus size: 197
494240 AGTCTCGATA
*
494250 TGCATTGTGATTAAAAGTTCTATAATATCCTAATTAGTCCGGCACACTCAATTCAAACAATGATC
1 TGCATTGTGATTAAAAGTTCTATAATATCCTAATTAGTCCGGCACACTCAATTCAAACAATGAGC
494315 AAGAAAGAAAATGTATGCTCGTGGATCAAATCTCAAAAGAAAAATTTATATGCACTGAGTCAAGT
66 AAGAAAGAAAATGTATGCTCGTGGATCAAATCTCAAAAGAAAAATTTATATGCACTGAGTCAAGT
* *
494380 TCATCTCTATCGACAAAAACATGAAATATCAATATTCAACAAAAAATTCACCAACTTTACAAATC
131 TCATCTCTATCGACAAAAACATGAAATATCAATACTCAACAAAAAATTCACCAACTATACAAATC
494445 AC
196 AC
494447 TGCATTGTGATTAAAAGTTCTATAATATCCTAATTAGTCCGGCACACTCAATTCAAACAATGAGC
1 TGCATTGTGATTAAAAGTTCTATAATATCCTAATTAGTCCGGCACACTCAATTCAAACAATGAGC
494512 AAGAAAGAAAATGTATGCTCGTGGATCAAATCTCAAAAGAAAAATTTATATGCACTGAGTCAAGT
66 AAGAAAGAAAATGTATGCTCGTGGATCAAATCTCAAAAGAAAAATTTATATGCACTGAGTCAAGT
* *
494577 TCATCTCTATCGACAAAAGCATGAAATATCAATACTCAACAAAAAATTCACCAGCTATACAAATC
131 TCATCTCTATCGACAAAAACATGAAATATCAATACTCAACAAAAAATTCACCAACTATACAAATC
494642 AC
196 AC
494644 CAATCATGCA
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
197 192 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (197 bp):
TGCATTGTGATTAAAAGTTCTATAATATCCTAATTAGTCCGGCACACTCAATTCAAACAATGAGC
AAGAAAGAAAATGTATGCTCGTGGATCAAATCTCAAAAGAAAAATTTATATGCACTGAGTCAAGT
TCATCTCTATCGACAAAAACATGAAATATCAATACTCAACAAAAAATTCACCAACTATACAAATC
AC
Found at i:494992 original size:5 final size:5
Alignment explanation
Indices: 494982--495031 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
494972 TGTTCAGAGA
***
494982 AAAAT AAAAT AAAAT AAAACAT CTGAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT -AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
495032 TGGAATGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 32 0.86
6 3 0.08
7 2 0.05
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:499102 original size:57 final size:57
Alignment explanation
Indices: 499039--499285 Score: 314
Period size: 57 Copynumber: 4.3 Consensus size: 57
499029 CACTTATCAT
* * * * *
499039 TCCATCATCCATTGCTATTAAGCCAACCATTAATCCATCTAACACTTCTATTACACT
1 TCCATCATCCACTGCTATTACGCCAACCATTAATCCATCTCACACTTCTATTTCACC
* *
499096 TCCATCATCCACTGCTATTACGCCAACCATTAATTCATCTCACACTTCTATTCCACC
1 TCCATCATCCACTGCTATTACGCCAACCATTAATCCATCTCACACTTCTATTTCACC
* * * * * *
499153 TCCATCATCTACGGCTATTACGCCTATCATTCATCCATTTCACACTTCTATTTCACC
1 TCCATCATCCACTGCTATTACGCCAACCATTAATCCATCTCACACTTCTATTTCACC
* * * * * *
499210 TCTATCATCAACTACTATTACGCCCACCATTAATCCATCTTACACTTTTATTTCACC
1 TCCATCATCCACTGCTATTACGCCAACCATTAATCCATCTCACACTTCTATTTCACC
*
499267 TCCATCATCCACTACTATT
1 TCCATCATCCACTGCTATT
499286 TCATCCACCA
Statistics
Matches: 164, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 164 1.00
ACGTcount: A:0.27, C:0.35, G:0.03, T:0.35
Consensus pattern (57 bp):
TCCATCATCCACTGCTATTACGCCAACCATTAATCCATCTCACACTTCTATTTCACC
Found at i:499279 original size:24 final size:24
Alignment explanation
Indices: 499243--499288 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
499233 CCACCATTAA
* **
499243 TCCATCTTACACTTTTATTTCACC
1 TCCATCATACACTACTATTTCACC
*
499267 TCCATCATCCACTACTATTTCA
1 TCCATCATACACTACTATTTCA
499289 TCCACCATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (24 bp):
TCCATCATACACTACTATTTCACC
Found at i:501840 original size:26 final size:26
Alignment explanation
Indices: 501810--501864 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
501800 TAAATCTGAT
* *
501810 GCCCCTATATGTTGCTCTGGGCCGTC
1 GCCCCTACATGCTGCTCTGGGCCGTC
501836 GCCCCTACATGCTGCTCTGGGCCGTC
1 GCCCCTACATGCTGCTCTGGGCCGTC
501862 GCC
1 GCC
501865 AATCTGACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.07, C:0.40, G:0.27, T:0.25
Consensus pattern (26 bp):
GCCCCTACATGCTGCTCTGGGCCGTC
Found at i:503037 original size:12 final size:13
Alignment explanation
Indices: 503005--503029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502995 TCTCTTATAT
503005 TTTAGATTTTTTC
1 TTTAGATTTTTTC
503018 TTTAGATTTTTT
1 TTTAGATTTTTT
503030 TATTGATTAT
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:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTAGATTTTTTC
Found at i:504184 original size:23 final size:23
Alignment explanation
Indices: 504158--504206 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
504148 ATTCAAAAAA
* *
504158 ACATAAGAAAATGTGTTATAAAG
1 ACATAAGAAAACGTGTCATAAAG
* *
504181 ACATATGAAAACGTGTCATATAG
1 ACATAAGAAAACGTGTCATAAAG
504204 ACA
1 ACA
504207 GACTTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (23 bp):
ACATAAGAAAACGTGTCATAAAG
Found at i:513362 original size:3 final size:3
Alignment explanation
Indices: 513354--513388 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
513344 AATATCTTAT
* *
513354 TTA TTA TTA TTC TTA TTC TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
513389 GAAGCTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:518412 original size:24 final size:24
Alignment explanation
Indices: 518380--518459 Score: 160
Period size: 24 Copynumber: 3.3 Consensus size: 24
518370 CTATTCTTTC
518380 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
518404 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
518428 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
518452 GCTTCAAT
1 GCTTCAAT
518460 CGAACTTCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:518720 original size:30 final size:30
Alignment explanation
Indices: 518684--518749 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
518674 AGTGAATCGG
* *
518684 CGGTTCAAACCGGTTTTGCCGATTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
** *
518714 CGGTTCACCCCGATTTTCCCGGTTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
518744 CGGTTC
1 CGGTTC
518750 TTCCGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCCCGATTTTCAGC
Found at i:518757 original size:20 final size:20
Alignment explanation
Indices: 518732--518770 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
518722 CCCGATTTTC
518732 CCGGTT-TTCAGCCGGTTCTT
1 CCGGTTCTTCA-CCGGTTCTT
*
518752 CCGGTTCTTTACCGGTTCT
1 CCGGTTCTTCACCGGTTCT
518771 GTGCTAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.05, C:0.31, G:0.23, T:0.41
Consensus pattern (20 bp):
CCGGTTCTTCACCGGTTCTT
Found at i:519273 original size:2 final size:2
Alignment explanation
Indices: 519268--519292 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
519258 TTTTTAATAA
519268 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 A
519293 ATTCTAAAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:519491 original size:39 final size:39
Alignment explanation
Indices: 519441--519515 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
519431 TTTTAAAAAT
*
519441 AATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTTAA
1 AATTTAAAATGTT-ATGGTAGAAA-AATTTAAGAAATTTAA
*
519480 AATTTAAAATGTTATGGTAGCAAAATTTAAGAAATT
1 AATTTAAAATGTTATGGTAGAAAAATTTAAGAAATT
519516 AGGATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.06
39 27 0.84
40 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTAAAATGTTATGGTAGAAAAATTTAAGAAATTTAA
Found at i:519530 original size:39 final size:38
Alignment explanation
Indices: 519441--519546 Score: 99
Period size: 39 Copynumber: 2.7 Consensus size: 38
519431 TTTTAAAAAT
519441 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTTAA
1 AATTTAGAATGTT-ATGTGAAATAATTTAAGAAATTTAA
* * *
519480 AATTTAAAATGTTATGGTAGCAA-AATTTAAGAAA-TTAGG
1 AATTTAGAATGTTAT-GT-GAAATAATTTAAGAAATTTA-A
* * *
519519 ATTTTAGAATGTTAGAGTGAAATTATTT
1 AATTTAGAATGTTA-TGTGAAATAATTT
519547 GAAAACTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 8 0.15
39 43 0.80
40 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.16, T:0.39
Consensus pattern (38 bp):
AATTTAGAATGTTATGTGAAATAATTTAAGAAATTTAA
Found at i:521700 original size:13 final size:13
Alignment explanation
Indices: 521658--521693 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
521648 CTATGACGCG
* *
521658 CATTTATAACACA
1 CATTTATGACATA
521671 CATTTATGACATA
1 CATTTATGACATA
521684 CATTTATGAC
1 CATTTATGAC
521694 GTTCATTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (13 bp):
CATTTATGACATA
Found at i:521862 original size:2 final size:2
Alignment explanation
Indices: 521855--521888 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
521845 TTTCGTAAAT
521855 TA TA TA TA TA TA TA TA TA TA TCA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
521889 AGCAATCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:526176 original size:18 final size:21
Alignment explanation
Indices: 526139--526181 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
526129 AGATAAAACG
526139 TAAAAATTAACATAAAAACAT
1 TAAAAATTAACATAAAAACAT
526160 TAAAAA-TAA-AT-AAAACAT
1 TAAAAATTAACATAAAAACAT
526178 TAAA
1 TAAA
526182 CTTTCAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
19 2 0.09
20 3 0.14
21 6 0.27
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAATTAACATAAAAACAT
Found at i:528377 original size:20 final size:22
Alignment explanation
Indices: 528352--528391 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
528342 ATTGGTTGAA
528352 AATTA-TTAAAA-AATTAATAT
1 AATTATTTAAAATAATTAATAT
528372 AATTATTTAAAATAATTAAT
1 AATTATTTAAAATAATTAAT
528392 TTTTGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTATTTAAAATAATTAATAT
Found at i:530683 original size:29 final size:31
Alignment explanation
Indices: 530634--530696 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
530624 TTTTTGGTCC
*
530634 CTAAACTTTTACAAAATTTATACTTTAGCCA
1 CTAAACTTTTACAAAACTTATACTTTAGCCA
* *
530665 CTAAAC-TTT-CAAAACTTATATTTTAGTCA
1 CTAAACTTTTACAAAACTTATACTTTAGCCA
530694 CTA
1 CTA
530697 CCAAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 3 0.10
31 6 0.21
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (31 bp):
CTAAACTTTTACAAAACTTATACTTTAGCCA
Found at i:531022 original size:21 final size:21
Alignment explanation
Indices: 530997--531049 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
530987 TTGTAATGAC
530997 AGTATCAATACCCCTTCAAGG
1 AGTATCAATACCCCTTCAAGG
531018 AGTATCAATACCCCTTCAAGG
1 AGTATCAATACCCCTTCAAGG
531039 AGTATCAATAC
1 AGTATCAATAC
531050 TTAGGGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (21 bp):
AGTATCAATACCCCTTCAAGG
Found at i:533292 original size:17 final size:18
Alignment explanation
Indices: 533270--533303 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
533260 CCAAAGTCGA
533270 TATTTT-ATTTTGAAAAC
1 TATTTTGATTTTGAAAAC
533287 TATTTTGATTTTGAAAA
1 TATTTTGATTTTGAAAA
533304 ATAAGCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (18 bp):
TATTTTGATTTTGAAAAC
Found at i:534577 original size:18 final size:18
Alignment explanation
Indices: 534556--534594 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
534546 TCTCTTTTGC
534556 TTTCGAACAACT-TCTTTT
1 TTTCGAACAACTAT-TTTT
*
534574 TTTCGAACTACTATTTTT
1 TTTCGAACAACTATTTTT
534592 TTT
1 TTT
534595 ATTCAACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTCGAACAACTATTTTT
Found at i:537551 original size:10 final size:10
Alignment explanation
Indices: 537533--537568 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
537523 AATGCTTGAC
*
537533 AAAACAAAAA
1 AAAATAAAAA
537543 AAAATAAAAA
1 AAAATAAAAA
*
537553 AAAATAAATA
1 AAAATAAAAA
537563 AAAATA
1 AAAATA
537569 TAGCAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:544983 original size:21 final size:21
Alignment explanation
Indices: 544929--544983 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
544919 CTCTACTTGC
* *
544929 AGTATTGATACCATAGGGTCA
1 AGTATCGATACCCTAGGGTCA
544950 AGTATCGATACCCTAGGGTCA
1 AGTATCGATACCCTAGGGTCA
544971 AGTATCGATACCC
1 AGTATCGATACCC
544984 CTATGAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
AGTATCGATACCCTAGGGTCA
Found at i:545330 original size:18 final size:20
Alignment explanation
Indices: 545293--545335 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
545283 GGTCTTAATG
545293 TATCATAAAACACCTTATTTA
1 TATCATAAAACA-CTTATTTA
545314 TATC-TAAAACA-TTATTTA
1 TATCATAAAACACTTATTTA
545332 -ATCA
1 TATCA
545336 AGAAATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 7 0.33
20 7 0.33
21 4 0.19
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (20 bp):
TATCATAAAACACTTATTTA
Found at i:545666 original size:23 final size:23
Alignment explanation
Indices: 545635--545682 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
545625 TTGGAACTTG
* *
545635 GAGAGGAAAAAAGAT-ATGAAAAT
1 GAGAAGAAAAAA-ATGAAGAAAAT
545658 GAGAAGAAAAAAATGAAGAAAAT
1 GAGAAGAAAAAAATGAAGAAAAT
545681 GA
1 GA
545683 AGAGAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (23 bp):
GAGAAGAAAAAAATGAAGAAAAT
Found at i:555429 original size:25 final size:21
Alignment explanation
Indices: 555376--555428 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
555366 TAGCCTTCAC
555376 AACAAACTAACAAATCATCCA
1 AACAAACTAACAAATCATCCA
555397 AACAAACTAACAAATCATCCA
1 AACAAACTAACAAATCATCCA
*
555418 AGCAAACTAAC
1 AACAAACTAAC
555429 TGCTAGCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.57, C:0.28, G:0.02, T:0.13
Consensus pattern (21 bp):
AACAAACTAACAAATCATCCA
Found at i:555761 original size:71 final size:72
Alignment explanation
Indices: 555678--555819 Score: 205
Period size: 71 Copynumber: 2.0 Consensus size: 72
555668 ATTGAATTAG
* * *
555678 ATATTAACCATTAGATTAACTTGTCAAGATCCATATTATTAA-AGGTTAATAATACTTGATGGAT
1 ATATTAACCATTAGATTAACTTGTCAAGATCCACATTATTAAGAGGTTAATAATACTTAATGCAT
555742 GAGTGAC
66 GAGTGAC
* * ** *
555749 ATATTAATCATTAGATTAACTTGTCAAGCTTTACATTATTAAGAGGTTAATAATAGTTAATGCAT
1 ATATTAACCATTAGATTAACTTGTCAAGATCCACATTATTAAGAGGTTAATAATACTTAATGCAT
555814 GAGTGA
66 GAGTGA
555820 TAAAAACATT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
71 37 0.60
72 25 0.40
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (72 bp):
ATATTAACCATTAGATTAACTTGTCAAGATCCACATTATTAAGAGGTTAATAATACTTAATGCAT
GAGTGAC
Found at i:560152 original size:30 final size:32
Alignment explanation
Indices: 560112--560206 Score: 140
Period size: 33 Copynumber: 3.0 Consensus size: 32
560102 CAATGTGTAC
* *
560112 AAGTTAGCCACC-A-AATATGAAATTTCCAAT
1 AAGTTGGCCACCAACAAGATGAAATTTCCAAT
560142 AAGTTGGCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTGGCCACCAA-CAAGATGAAATTTCCAAT
560175 AAGTTGGCCACCAACCAAGATGAAATTTCCAA
1 AAGTTGGCCACCAA-CAAGATGAAATTTCCAA
560207 CTTGTCAACA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 11 0.18
31 1 0.02
33 48 0.80
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (32 bp):
AAGTTGGCCACCAACAAGATGAAATTTCCAAT
Found at i:560170 original size:33 final size:33
Alignment explanation
Indices: 560128--560206 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
560118 GCCACCAAAT
560128 ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
1 ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
560161 ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
1 ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
560194 ATGAAATTTCCAA
1 ATGAAATTTCCAA
560207 CTTGTCAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (33 bp):
ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
Found at i:567290 original size:21 final size:21
Alignment explanation
Indices: 567266--567326 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
567256 CAAACTTTAC
567266 CAAACTTTGGAAAACATTTTT
1 CAAACTTTGGAAAACATTTTT
**
567287 CAAA-----G-AAACATTTAC
1 CAAACTTTGGAAAACATTTTT
*
567302 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGGAAAACATTTTT
567323 CAAA
1 CAAA
567327 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 12 0.41
16 1 0.03
21 16 0.55
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (21 bp):
CAAACTTTGGAAAACATTTTT
Found at i:567308 original size:36 final size:35
Alignment explanation
Indices: 567257--567327 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
567247 AACATCTACC
*
567257 AAACTTTACCAAACTTTGGAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
567292 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
567328 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:571891 original size:36 final size:35
Alignment explanation
Indices: 571846--571916 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
571836 AACATCTACC
571846 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
*
571881 AAACATTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
571917 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:572021 original size:34 final size:34
Alignment explanation
Indices: 571973--572043 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
571963 AGGCTTCGTT
* *
571973 ATGCTTAGTTTTCTAAACCCAAGTCCTCCCT-GTG
1 ATGCATAGTTTTCTAAACCCAAGCCCT-CCTGGTG
572007 ATGCATAGTTTTCTAAACCCAAGCCCTCCTGGTG
1 ATGCATAGTTTTCTAAACCCAAGCCCTCCTGGTG
572041 ATG
1 ATG
572044 TTGGTGAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 3 0.09
34 31 0.91
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (34 bp):
ATGCATAGTTTTCTAAACCCAAGCCCTCCTGGTG
Found at i:574413 original size:17 final size:18
Alignment explanation
Indices: 574380--574419 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
574370 TATCACGGTT
*
574380 GGAGAAGGAAGACGAGTG
1 GGAGAAGGAAGAAGAGTG
574398 GGAGAA-GAAGAAGAGTG
1 GGAGAAGGAAGAAGAGTG
*
574415 AGAGA
1 GGAGA
574420 TGAGTATCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.45, C:0.03, G:0.47, T:0.05
Consensus pattern (18 bp):
GGAGAAGGAAGAAGAGTG
Found at i:582878 original size:30 final size:30
Alignment explanation
Indices: 582838--582906 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
582828 AGGATAGAGT
*
582838 CAATAACCTGGACAAAATGATCGCAAATAA
1 CAATATCCTGGACAAAATGATCGCAAATAA
582868 CAATATCCTGGACAAAATGATCGCAAATAA
1 CAATATCCTGGACAAAATGATCGCAAATAA
*
582898 CCATATCCT
1 CAATATCCT
582907 CACCATCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (30 bp):
CAATATCCTGGACAAAATGATCGCAAATAA
Found at i:587706 original size:21 final size:21
Alignment explanation
Indices: 587680--587719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
587670 AGACAAGTAG
* *
587680 TACTCCACAGCAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
587701 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
587720 TTTCAGTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:590398 original size:2 final size:2
Alignment explanation
Indices: 590391--590425 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
590381 ACCTCTACAG
* *
590391 TA TA TA TA TA TA TA TG TA TG 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
590426 GTTAAATGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:590415 original size:20 final size:20
Alignment explanation
Indices: 590390--590427 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
590380 CACCTCTACA
590390 GTATATATATATATATGTAT
1 GTATATATATATATATGTAT
590410 GTATATATATATATATGT
1 GTATATATATATATATGT
590428 TAAATGACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
GTATATATATATATATGTAT
Found at i:591346 original size:36 final size:35
Alignment explanation
Indices: 591265--591404 Score: 190
Period size: 36 Copynumber: 3.9 Consensus size: 35
591255 AGATGAACAA
* *
591265 TTGAATCGAAAGTGCTGACGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* * *
591300 TTGAATCGAAAGTGCCGGTGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
*
591336 TTGAATCGAAAGTGCCGATGCTTACTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* *
591371 TTTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
591405 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
35 30 0.33
36 61 0.67
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
Found at i:591402 original size:72 final size:71
Alignment explanation
Indices: 591265--591409 Score: 236
Period size: 72 Copynumber: 2.0 Consensus size: 71
591255 AGATGAACAA
* * *
591265 TTGAATCGAAAGTGCTGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGGTGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGACGCTTACTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
591330 TTCTTC
66 TTCTTC
* *
591336 TTGAATCGAAAGTGCCGATGCTTACTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGACGCTTACTTCCGTTCAC-TTGAATCGAAAGTGCCGATGCTTCCTTTC
591401 GTTCTTC
65 GTTCTTC
591408 TT
1 TT
591410 ATTCACCTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 32 0.47
72 36 0.53
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGACGCTTACTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
TTCTTC
Found at i:604636 original size:29 final size:29
Alignment explanation
Indices: 604624--604901 Score: 202
Period size: 29 Copynumber: 9.7 Consensus size: 29
604614 AGATACAATT
*
604624 TTTTTAGAATTTACCATAAAGGATAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* * *
604653 TTTTTGGAATGTATAATAAAGGATAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAAC
*
604682 TTTTTAGATTTTACAATAAAGGATAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAAC
** * * * * ***
604711 TTAATGGAATTTATAATAAACGA-CATTT
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* *
604739 TTTTTGGAATTTACAATAAAGGACAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* * * *
604768 TTATTAGAATATACAATAAAAGACAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* * * * *
604797 TTATTGGGATTTACAATAAAGTACAAAA-
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* * * *
604825 GTTTTGGAATTTACAATTAAGGACAAAA-
1 TTTTTAGAATTTACAATAAAGGATAAAAC
* * ** *
604853 TGTTTTATAAATTACAATAAAATATTAAAC
1 T-TTTTAGAATTTACAATAAAGGATAAAAC
* *
604883 TTTTTATAAATTACAATAA
1 TTTTTAGAATTTACAATAA
604902 TTGTATTTCT
Statistics
Matches: 197, Mismatches: 49, Indels: 6
0.78 0.19 0.02
Matches are distributed among these distances:
28 43 0.22
29 153 0.78
30 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (29 bp):
TTTTTAGAATTTACAATAAAGGATAAAAC
Found at i:604701 original size:58 final size:58
Alignment explanation
Indices: 604624--604901 Score: 229
Period size: 57 Copynumber: 4.8 Consensus size: 58
604614 AGATACAATT
* * * *
604624 TTTTTAGAATTTACCATAAAGGATAAAACTTTTTGGAATGTATAATAAAGGATAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAAAGGACAAAAC
* ** * * ***
604682 TTTTTAGATTTTACAATAAAGGATAAAACTTAATGGAATTTATAATAAACGAC-ATTT
1 TTTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAAAGGACAAAAC
* * * * * *
604739 TTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAATATACAATAAAAGACAAAAC
1 TTTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAAAGGACAAAAC
* * * * * * *
604797 TTATTGGGATTTACAATAAAGTACAAAA-GTTTTGGAATTTACAATTAAGGACAAAA-
1 TTTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAAAGGACAAAAC
* * ** * ** *
604853 TGTTTTATAAATTACAATAAAATATTAAACTTTTTATAAATTACAATAA
1 T-TTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAA
604902 TTGTATTTCT
Statistics
Matches: 174, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
56 1 0.01
57 87 0.50
58 86 0.49
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (58 bp):
TTTTTAGAATTTACAATAAAGGATAAAACTTTTTGGAATTTACAATAAAGGACAAAAC
Found at i:604760 original size:86 final size:86
Alignment explanation
Indices: 604630--604852 Score: 250
Period size: 86 Copynumber: 2.6 Consensus size: 86
604620 AATTTTTTTA
* * * * * * * * *
604630 GAATTTACCATAAAGGATAAAACTTTTTGGAATGTATAATAAAGGATAAAACTTTTTAGATTTTA
1 GAATTTACAATAAAGTACAAAA-TTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAATATA
* *
604695 CAATAAAGGATAAAACTTAATG
65 CAATAAAAGACAAAACTTAATG
* ***
604717 GAATTTATAATAAACG-ACATTTTTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAATATA
1 GAATTTACAATAAA-GTACAAAATTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAATATA
*
604781 CAATAAAAGACAAAACTTATTG
65 CAATAAAAGACAAAACTTAATG
* * *
604803 GGATTTACAATAAAGTACAAAAGTTTTGGAATTTACAATTAAGGACAAAA
1 GAATTTACAATAAAGTACAAAATTTTTGGAATTTACAATAAAGGACAAAA
604853 TGTTTTATAA
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
85 1 0.01
86 96 0.86
87 14 0.12
88 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (86 bp):
GAATTTACAATAAAGTACAAAATTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAATATAC
AATAAAAGACAAAACTTAATG
Found at i:604897 original size:86 final size:86
Alignment explanation
Indices: 604627--604901 Score: 196
Period size: 86 Copynumber: 3.2 Consensus size: 86
604617 TACAATTTTT
* * * * * * * * * * *
604627 TTAGAATTTACCATAAAGGATAAAACTTTTTGGAATGTATAATAAAGGATAAAACTTTTTAGATT
1 TTAGAAATTACAATAAAGTACAAAA-GTTTTGGAATTTACAATAAAGGACAAAACTTATTAAAAT
* * *
604692 TTACAATAAAGGATAAAACTTA
65 ATACAATAAAAGACAAAACTTA
* * * * **** *
604714 ATGGAATTTATAATAAACG-ACATTTTTTTTGGAATTTACAATAAAGGACAAAACTTATTAGAAT
1 TTAGAAATTACAATAAA-GTACAAAAGTTTTGGAATTTACAATAAAGGACAAAACTTATTAAAAT
604778 ATACAATAAAAGACAAAACTTA
65 ATACAATAAAAGACAAAACTTA
* * * * *
604800 TTGGGATTTACAATAAAGTACAAAAGTTTTGGAATTTACAATTAAGGACAAAA-TGTTTTATAAA
1 TTAGAAATTACAATAAAGTACAAAAGTTTTGGAATTTACAATAAAGGACAAAACT-TATTA-AAA
* ** *
604864 T-TACAATAAAATATTAAACTTT
64 TATACAATAAAAGACAAAACTTA
*
604886 TTATAAATTACAATAA
1 TTAGAAATTACAATAA
604902 TTGTATTTCT
Statistics
Matches: 150, Mismatches: 34, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
85 2 0.01
86 129 0.86
87 18 0.12
88 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (86 bp):
TTAGAAATTACAATAAAGTACAAAAGTTTTGGAATTTACAATAAAGGACAAAACTTATTAAAATA
TACAATAAAAGACAAAACTTA
Found at i:605714 original size:42 final size:42
Alignment explanation
Indices: 605655--605765 Score: 179
Period size: 42 Copynumber: 2.6 Consensus size: 42
605645 AAGTCGGAAC
605655 CAAGTCATATCAGTTCGGGTCAATTTTAGGTTGATTTGGCAT
1 CAAGTCATATCAGTTCGGGTCAATTTTAGGTTGATTTGGCAT
605697 CAAGTCATATCAGTTCGGGTCAATTTTAGGTTGATTTGGCAT
1 CAAGTCATATCAGTTCGGGTCAATTTTAGGTTGATTTGGCAT
* *
605739 CAAGTTCAGT-TCAGGTCGGGTTAATTT
1 CAAG-TCA-TATCAGTTCGGGTCAATTT
605766 CAGTTCCGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
42 46 0.71
43 18 0.28
44 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (42 bp):
CAAGTCATATCAGTTCGGGTCAATTTTAGGTTGATTTGGCAT
Found at i:609327 original size:42 final size:42
Alignment explanation
Indices: 609281--609392 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
609271 TAAAAACGCT
609281 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACACC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACACC
* * * * **
609323 GCAATAGAGTGGTAAAT-TAGCGGCGTTTATACCACAAATGCC
1 GCAATAGAGTTG-ACATATAGCGGCGTTTTTACAACAAACACC
* * *
609365 GCAATATA-TTAACATATAGTGGCGTTTT
1 GCAATAGAGTTGACATATAGCGGCGTTTT
609393 AGCCAAAACG
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
40 3 0.05
41 11 0.20
42 39 0.70
43 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (42 bp):
GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACACC
Found at i:609430 original size:41 final size:40
Alignment explanation
Indices: 609298--609432 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 40
609288 AGTTGACATA
* * *
609298 TAGCGGCGTTTTTACAACAAACACCGCAATAGAGTGGTAAAT
1 TAGCGGCG-TTTTACCACAAACGCCGCAATA-AATGGTAAAT
* *
609340 TAGCGGCGTTTATACCACAAATGCCGCAATATAT--TAACAT
1 TAGCGGCGTTT-TACCACAAACGCCGCAATAAATGGTAA-AT
*
609380 ATAGTGGCGTTTTAGCCA-AAACGCCGCAATAAATCGGTAAAT
1 -TAGCGGCGTTTTA-CCACAAACGCCGCAATAAAT-GGTAAAT
609422 TAGCGGCGTTT
1 TAGCGGCGTTT
609433 ATGGTAAACG
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
39 3 0.04
40 18 0.23
41 27 0.35
42 26 0.34
43 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (40 bp):
TAGCGGCGTTTTACCACAAACGCCGCAATAAATGGTAAAT
Found at i:609512 original size:82 final size:82
Alignment explanation
Indices: 609335--609596 Score: 182
Period size: 82 Copynumber: 3.2 Consensus size: 82
609325 AATAGAGTGG
* * * * * *
609335 TAAATTAGCGGCGTTTATACCACAAATGCCGCAATA-TATTAA-CATATAGTGGC-GTTTTAGCC
1 TAAA-TAGTGGCGTTTATA-GACAAACGCCGAAATAGTATTAATCA-ATAGTGGCATTTTTA-CA
** ***
609397 AAAACGCCGCAATA-AATCGG
62 AAAACGCCGCAATAGTTTTAA
* **
609417 TAAATTAGCGGCGTTTAT-GGTAAACGCCGAAATAG-ATTACA-CATATAGTGGCATTTATT-CT
1 TAAA-TAGTGGCGTTTATAGACAAACGCCGAAATAGTATTA-ATCA-ATAGTGGCATTT-TTAC-
* *
609478 TAAAACGCCGTAATA-TTTATAA
61 AAAAACGCCGCAATAGTTT-TAA
* * * *
609500 TAAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAA
1 TAAATAGTGGCGTTTATAGACAAACGCCGAAATAGTATTAATCAATAGTGGCATTTTTACAAAAA
609565 CGCCGCAATAGTTTTAA
66 CGCCGCAATAGTTTTAA
*
609582 TCAATAGTGGCGTTT
1 TAAATAGTGGCGTTT
609597 TTTTAACAAA
Statistics
Matches: 146, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
80 15 0.10
81 13 0.09
82 77 0.53
83 36 0.25
84 5 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (82 bp):
TAAATAGTGGCGTTTATAGACAAACGCCGAAATAGTATTAATCAATAGTGGCATTTTTACAAAAA
CGCCGCAATAGTTTTAA
Found at i:609534 original size:83 final size:82
Alignment explanation
Indices: 609438--609632 Score: 206
Period size: 83 Copynumber: 2.4 Consensus size: 82
609428 CGTTTATGGT
* * *
609438 AAACGCCGAAATAG-ATTACA-CATATAGTGGCATTTATT-CTTAAAACGCCGTAATA-TTTATA
1 AAACGCCGCAATAGTATTA-ATCA-ATAGTGGCATTT-TTAC-AAAAACGCCGCAATAGTTT-TA
609499 ATAAATAGTGGCG-TTTTTAGAC
61 ATAAATAGTGGCGTTTTTTA-AC
* * *
609521 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAACGCCGCAATAGTTTTAATCAA
1 AAACGCCGCAATAGTATTAATCAATAGTGGCATTTTTACAAAAACGCCGCAATAGTTTTAATAAA
609586 TAGTGGCGTTTTTTTAAC
66 TAGTGGCG-TTTTTTAAC
*
609604 AAACGCCACAATA--ATGTAATCAATAGTGG
1 AAACGCCGCAATAGTAT-TAATCAATAGTGG
609633 TGTTTTTTGT
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
81 1 0.01
82 42 0.43
83 43 0.44
84 11 0.11
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (82 bp):
AAACGCCGCAATAGTATTAATCAATAGTGGCATTTTTACAAAAACGCCGCAATAGTTTTAATAAA
TAGTGGCGTTTTTTAAC
Found at i:609547 original size:41 final size:40
Alignment explanation
Indices: 609480--609639 Score: 189
Period size: 41 Copynumber: 3.9 Consensus size: 40
609470 TTTATTCTTA
* * *
609480 AAACGCCGTAATA-TTTATAATAAATAGTGGCGTTTTTAGAC
1 AAACGCCGCAATAGTGT-TAATCAATAGTGGCGTTTTTA-AC
*
609521 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTACAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTA-AC
*
609562 AAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTTAAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCG--TTTTTAAC
* * *
609604 AAACGCCACAATAATG-TAATCAATAGTGGTGTTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
609640 TGTATAAACG
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
39 5 0.05
41 78 0.74
42 16 0.15
43 6 0.06
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAAC
Found at i:609649 original size:41 final size:41
Alignment explanation
Indices: 609497--609655 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 41
609487 GTAATATTTA
* * *
609497 TAATAAATAGTGGCGTTTTTAG-ACAAACGCCGCAATAGTG
1 TAATCAATAGTGGCGTTTTTTGTACAAACGCCGCAATAATG
** * * *
609537 TTAATCAATAGTGGCG-TTTTTACAAAAACGCCGCAATAGTTT
1 -TAATCAATAGTGGCGTTTTTTGTACAAACGCCGCAATA-ATG
*
609579 TAATCAATAGTGGCGTTTTTT-TAACAAACGCCACAATAATG
1 TAATCAATAGTGGCGTTTTTTGT-ACAAACGCCGCAATAATG
* * *
609620 TAATCAATAGTGGTGTTTTTTGTATAAACGTCGCAA
1 TAATCAATAGTGGCGTTTTTTGTACAAACGCCGCAA
609656 AATATTAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
40 4 0.04
41 74 0.76
42 20 0.20
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (41 bp):
TAATCAATAGTGGCGTTTTTTGTACAAACGCCGCAATAATG
Found at i:609655 original size:83 final size:82
Alignment explanation
Indices: 609479--609639 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 82
609469 ATTTATTCTT
* * *
609479 AAAACGCCGTAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCA
1 AAAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
609544 ATAGTGGCGTTTTTACA
66 ATAGTGGCGTTTTTACA
*
609561 AAAACGCCGCAATAGTTT-TAATCAATAGTGGCGTTTTTTTA-ACAAACGCCACAATAATG-TAA
1 AAAACGCCGCAATA-TTTATAATAAATAGTGGCG--TTTTTAGACAAACGCCACAATAATGTTAA
*
609623 TCAATAGTGGTGTTTTT
63 TCAATAGTGGCGTTTTT
609640 TGTATAAACG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
82 46 0.65
83 19 0.27
84 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (82 bp):
AAAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
ATAGTGGCGTTTTTACA
Found at i:609672 original size:83 final size:82
Alignment explanation
Indices: 609479--609672 Score: 193
Period size: 83 Copynumber: 2.4 Consensus size: 82
609469 ATTTATTCTT
* * *
609479 AAAACGCCGTAAT-AT-TTATAATAAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAAT
1 AAAACGCCGCAATAATATTA-AAT-AATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAAT
609542 CAATAGTGGCGTTTTTACA
64 CAATAGTGGCGTTTTTACA
* *
609561 AAAACGCCGCAATAGT-TTTAATCAATAGTGGCGTTTTTTTA-ACAAACGCCACAATAATG-TAA
1 AAAACGCCGCAATAATATTAAAT-AATAGTGGCG--TTTTTAGACAAACGCCACAATAATGTTAA
* **
609623 TCAATAGTGGTGTTTTTTGTA
63 TCAATAGTGGCG-TTTTTACA
* *
609644 TAAACGTCGCAA-AATATTAAATATATAGT
1 AAAACGCCGCAATAATATTAAATA-ATAGT
609673 CCTCTTTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
82 42 0.45
83 45 0.48
84 6 0.06
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (82 bp):
AAAACGCCGCAATAATATTAAATAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
ATAGTGGCGTTTTTACA
Found at i:610272 original size:42 final size:42
Alignment explanation
Indices: 610207--610573 Score: 494
Period size: 42 Copynumber: 8.8 Consensus size: 42
610197 TTGTATCCAA
* *
610207 AAACGCCGCTATAAACTC-TACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * * * * * * *
610248 AAACGACTCTAAAGACACGTACTTTAGTAGCATTTT-TATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
610289 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
610330 AAACGCCGCTATAGACTCTTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
610372 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * *
610414 AAACGCTGCTA-ATGACTCGAACTTTAGTGGCGTTTT-TATAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTTTGAATAC
*
610455 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
*
610497 AAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
*
610539 AAACGCTGCTA-ATGACTCGTACTTTAGTGGCGTTT
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT
610574 ATATTTACAA
Statistics
Matches: 285, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
41 120 0.42
42 165 0.58
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
Found at i:610321 original size:83 final size:82
Alignment explanation
Indices: 610207--610573 Score: 479
Period size: 83 Copynumber: 4.4 Consensus size: 82
610197 TTGTATCCAA
* * * *
610207 AAACGCCGCTATAAACTC-TACTTTAGTGGCGTTTTGAATGCAAACGACTCTAAAGACACGTACT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACG-CGCTAAAGACTCGTACT
* * *
610271 TTAGTAGCATTTTTATAT
65 TTAGTGGCGTTTTTATAC
* * * *
610289 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TATACAAACGCCGCTATAGACTCTTACT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACG-CGCTAAAGACTCGTACT
* *
610353 TTAGTGGCGTTTTGAATGC
65 TTAGTGGCGTTTT-TATAC
* *
610372 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGAACT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGC-GCTAAAGACTCGTACT
610437 TTAGTGGCGTTTTTATAC
65 TTAGTGGCGTTTTTATAC
* *
610455 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGCAAACGTCGCTATAGACTCGTACT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACG-CGCTAAAGACTCGTACT
*
610520 TTAGTGGCGTTTTGAATAC
65 TTAGTGGCGTTTT-TATAC
*
610539 AAACGCTGCTA-ATGACTCGTACTTTAGTGGCGTTT
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT
610574 ATATTTACAA
Statistics
Matches: 250, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
82 48 0.19
83 131 0.52
84 71 0.28
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (82 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCGCTAAAGACTCGTACTT
TAGTGGCGTTTTTATAC
Found at i:610466 original size:125 final size:124
Alignment explanation
Indices: 610207--610573 Score: 576
Period size: 125 Copynumber: 3.0 Consensus size: 124
610197 TTGTATCCAA
* * * *
610207 AAACGCCGCTATAAACTCTACTTTAGTGGCGTTTTGAATGCAAACGACTCTAAAGACACGTACTT
1 AAACGCCGCTATAGACTCTACTTTAGTGGCGTTTTGAATGCAAACGACGCTATAGACTCGTACTT
* * * * * *
610272 TAGTAGCATTTT-TATATAAACGCCGCT-ATAGACTAGTACTTTAGTGGCGTTTTTATAC
66 TAGTGGCGTTTTGAATACAAACGCTGCTAAT-GACTCGTACTTTAGTGGCGTTTTTATAC
*
610330 AAACGCCGCTATAGACTCTTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
1 AAACGCCGCTATAGACTC-TACTTTAGTGGCGTTTTGAATGCAAACGACGCTATAGACTCGTACT
*
610395 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGAACTTTAGTGGCGTTTTTATAC
65 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTTTTATAC
*
610455 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGCAAACGTCGCTATAGACTCGTACT
1 AAACGCCGCTATAGACTC-TACTTTAGTGGCGTTTTGAATGCAAACGACGCTATAGACTCGTACT
610520 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTT
65 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTT
610574 ATATTTACAA
Statistics
Matches: 226, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
123 17 0.08
124 53 0.23
125 154 0.68
126 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (124 bp):
AAACGCCGCTATAGACTCTACTTTAGTGGCGTTTTGAATGCAAACGACGCTATAGACTCGTACTT
TAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:613462 original size:3 final size:3
Alignment explanation
Indices: 613454--613530 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
613444 TATAGCTTTC
613454 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
613502 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
613531 GATGATGATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:615662 original size:129 final size:129
Alignment explanation
Indices: 615515--615768 Score: 352
Period size: 129 Copynumber: 2.0 Consensus size: 129
615505 ACGCTTGTTT
* * *
615515 GAAAAACGCCGCTAAACAACAACACCTATTGCGACGTTTGTGGGAAAAACGCCGCTAAACAACGA
1 GAAAAACGCCGCTAAACAACAACACCTATTGCGACATTTGTAGGAAAAACGCCGCTAAACAACAA
615580 CACCTATTGCGGCG-TTTGT-AAGCCAAACGCCGCTAAATATCAAT-ACCTACTGCGGCGTTTGT
66 CACCTATTGCGGCGTTTTGTCAA--CAAACGCCGCTAAATATC-ATCACCTACTGCGGCGTTTGT
615642 GG
128 GG
* * * * *
615644 GAAAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTAGGACAAACGCCGCTAAATAGCAA
1 GAAAAACGCCGCTAAACAACAACACCTATTGCGACATTTGTAGGAAAAACGCCGCTAAACAACAA
* * * *
615709 CACCTATTGCGGCGTTTTTTCAACAAACGCCGCTATATATCGTCACCTATTGCGGCGTTT
66 CACCTATTGCGGCGTTTTGTCAACAAACGCCGCTAAATATCATCACCTACTGCGGCGTTT
615769 TTCGTTAACA
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 1 0.01
129 103 0.94
130 4 0.04
131 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (129 bp):
GAAAAACGCCGCTAAACAACAACACCTATTGCGACATTTGTAGGAAAAACGCCGCTAAACAACAA
CACCTATTGCGGCGTTTTGTCAACAAACGCCGCTAAATATCATCACCTACTGCGGCGTTTGTGG
Found at i:615720 original size:43 final size:43
Alignment explanation
Indices: 615518--615768 Score: 277
Period size: 43 Copynumber: 5.8 Consensus size: 43
615508 CTTGTTTGAA
* * *
615518 AAACGCCGCTAAACAACAACACCTATTGCGACGTTTGTGGGAA
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
* * *
615561 AAACGCCGCTAAACAACGACACCTATTGCGGCGTTTGTAAGCC
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
* * * * * *
615604 AAACGCCGCTAAATATCAATACCTACTGCGGCGTTTGTGGGAA
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
* *
615647 AAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTAGGAC
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
* * * ***
615690 AAACGCCGCTAAATAGCAACACCTATTGCGGCGTTTTTTCAAC
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
* * * **
615733 AAACGCCGCTATATATCGTCACCTATTGCGGCGTTT
1 AAACGCCGCTAAACAACAACACCTATTGCGGCGTTT
615769 TTCGTTAACA
Statistics
Matches: 175, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 175 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAACAACAACACCTATTGCGGCGTTTGTAGGAC
Found at i:615737 original size:86 final size:86
Alignment explanation
Indices: 615518--615770 Score: 328
Period size: 86 Copynumber: 2.9 Consensus size: 86
615508 CTTGTTTGAA
* *
615518 AAACGCCGCTAAACAACAACACCTATTGCGACGTTTGTGGGAAAAACGCCGCTAAACAACGACAC
1 AAACGCCGCTAAATAACAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAACAACGACAC
* *
615583 CTATTGCGGCGTTTGTAAGCC
66 CTATTGCGGCGTTTTTAAGAC
* * * *
615604 AAACGCCGCTAAATATCAATACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACAACAACAC
1 AAACGCCGCTAAATAACAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAACAACGACAC
* *
615669 CTATTGCGGCATTTTTAGGAC
66 CTATTGCGGCGTTTTTAAGAC
* *** * * * *
615690 AAACGCCGCTAAATAGCAACACCTATTGCGGCGTTT-TTTCAACAAACGCCGCTATATATCGTCA
1 AAACGCCGCTAAATAACAACACCTATTGCGGCGTTTGTGGGAA-AAACGCCGCTAAACAACGACA
615754 CCTATTGCGGCGTTTTT
65 CCTATTGCGGCGTTTTT
615771 CGTTAACAAA
Statistics
Matches: 144, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
85 3 0.02
86 141 0.98
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAATAACAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAACAACGACAC
CTATTGCGGCGTTTTTAAGAC
Found at i:615769 original size:43 final size:43
Alignment explanation
Indices: 615430--615770 Score: 255
Period size: 43 Copynumber: 7.9 Consensus size: 43
615420 GTTTTTTACC
* * * * *
615430 ACAAACGCCGCTAAATATCATA-ACATGTAGCGGCG-TTTTCGA
1 ACAAACGCCGCTAAATAACA-ACACCTATTGCGGCGTTTTTTGA
* * ** * * * *
615472 TAAAAATGCCGCTAAATCTCAACGCTTATTGCGACGCTTGTTTGA
1 -ACAAACGCCGCTAAATAACAACACCTATTGCGGCG-TTTTTTGA
* * **
615517 A-AAACGCCGCTAAACAACAACACCTATTGCGACGTTTGTGGGA
1 ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTT-TTTGA
* * *
615560 A-AAACGCCGCTAAACAACGACACCTATTGCGGCG-TTTGT-A
1 ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTGA
* * * **
615600 AGCCAAACGCCGCTAAATATCAATACCTACTGCGGCGTTTGTGGGA
1 A--CAAACGCCGCTAAATAACAACACCTATTGCGGCGTTT-TTTGA
* * * *
615646 A-AAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTAGG
1 ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTGA
* *
615688 ACAAACGCCGCTAAATAGCAACACCTATTGCGGCGTTTTTTCA
1 ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTGA
* * **
615731 ACAAACGCCGCTATATATCGTCACCTATTGCGGCGTTTTT
1 ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTT
615771 CGTTAACAAA
Statistics
Matches: 241, Mismatches: 46, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 8 0.03
43 217 0.90
44 3 0.01
45 7 0.03
46 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
ACAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTGA
Found at i:619024 original size:27 final size:27
Alignment explanation
Indices: 618989--619042 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
618979 TAGGTGTTCT
* *
618989 TGAATTTTTAAAATTATTTCAAGTTTA
1 TGAAATTTTAAAACTATTTCAAGTTTA
619016 TGAAATTTTAAAACTATTTCAAGTTTA
1 TGAAATTTTAAAACTATTTCAAGTTTA
619043 AATTTTGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (27 bp):
TGAAATTTTAAAACTATTTCAAGTTTA
Found at i:626741 original size:15 final size:15
Alignment explanation
Indices: 626698--626747 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
626688 GTCAGCGGTC
626698 AACGGGTCGGGTCAA
1 AACGGGTCGGGTCAA
* *
626713 CAGGTCGAGTCGGGTCAA
1 -A--ACGGGTCGGGTCAA
626731 AACGGGTCGGGTCAA
1 AACGGGTCGGGTCAA
626746 AA
1 AA
626748 TTGGGTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 14 0.50
16 1 0.04
17 1 0.04
18 12 0.43
ACGTcount: A:0.28, C:0.20, G:0.38, T:0.14
Consensus pattern (15 bp):
AACGGGTCGGGTCAA
Found at i:635799 original size:24 final size:24
Alignment explanation
Indices: 635768--635862 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
635758 AAAAATAATT
*
635768 CAGGTCAAGTATCAGATTAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
** * *
635792 CATTTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
635816 CAGGTCAAATATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * * *
635840 CAAGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
635863 TCAAATCGAA
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:635861 original size:48 final size:48
Alignment explanation
Indices: 635768--635862 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
635758 AAAAATAATT
* * ** *
635768 CAGGTCAAGTATCAGATTAGAATCCATTTCAAGTAACATATCAGAATC
1 CAGGTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAACAGAATC
* *
635816 CAGGTCAAATATCAGATCAGAATCCAAGTCAGGTATCATAACAGAAT
1 CAGGTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAACAGAAT
635863 TCAAATCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (48 bp):
CAGGTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAACAGAATC
Found at i:649577 original size:24 final size:24
Alignment explanation
Indices: 649521--649595 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
649511 TATATAAAAA
* * *
649521 ATCAAAACATAATTCAGGTAAAGT
1 ATCAAATCAAAATTCAGGTCAAGT
*
649545 ATCATATCAAAATTCAGGTCAAGT
1 ATCAAATCAAAATTCAGGTCAAGT
* * * *
649569 ATCAAATCAGAATCCATGTCAGGT
1 ATCAAATCAAAATTCAGGTCAAGT
649593 ATC
1 ATC
649596 GTAACTGAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCAAATCAAAATTCAGGTCAAGT
Found at i:655711 original size:16 final size:18
Alignment explanation
Indices: 655680--655713 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
655670 GGTTAATTTT
655680 TTTTGATAAGAATGAAGA
1 TTTTGATAAGAATGAAGA
655698 TTTT-ATAA-AATGAAGA
1 TTTTGATAAGAATGAAGA
655714 GTCGAAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (18 bp):
TTTTGATAAGAATGAAGA
Found at i:661294 original size:24 final size:24
Alignment explanation
Indices: 661267--661349 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
661257 AATAATTCAG
*
661267 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
661291 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
661315 GTCAAATATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
661339 GTCATGTATCA
1 GTCAAGTATCA
661350 TAATAGAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:661325 original size:48 final size:48
Alignment explanation
Indices: 661267--661376 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
661257 AATAATTCAG
* *
661267 GTCAAGTATCAGATCAGAATCCATGTCAAGTAACAT-ATCAGAATCCAA
1 GTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAAT-AGAATCCAA
* * *
661315 GTCAAATATCAGATCAGAATCCAAGTCATGTATCATAATAGAATTCAA
1 GTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAATAGAATCCAA
*
661363 ATCGAAA-ATCAGAT
1 GTC-AAATATCAGAT
661377 AAAATATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
48 49 0.91
49 5 0.09
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (48 bp):
GTCAAATATCAGATCAGAATCCAAGTCAAGTAACATAATAGAATCCAA
Found at i:662802 original size:13 final size:13
Alignment explanation
Indices: 662781--662817 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
662771 CAGTTGGCTT
662781 GGCTCGGCTCAGC
1 GGCTCGGCTCAGC
* *
662794 GGCTTGGCTCAGT
1 GGCTCGGCTCAGC
662807 GGCTCGGCTCA
1 GGCTCGGCTCA
662818 ACTGCTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.08, C:0.32, G:0.38, T:0.22
Consensus pattern (13 bp):
GGCTCGGCTCAGC
Found at i:669635 original size:24 final size:24
Alignment explanation
Indices: 669608--669682 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
669598 TATATCAAAA
* *
669608 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
669632 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
669656 ATCAAATCAGAATCCATGTCAGGT
1 ATCAAAACAAAATCCAGGTCAAGT
669680 ATC
1 ATC
669683 GTAACAGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:672285 original size:10 final size:11
Alignment explanation
Indices: 672263--672292 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
672253 AATCAACGTG
672263 AATCAACGAAA
1 AATCAACGAAA
672274 AATCAACGAAA
1 AATCAACGAAA
672285 AATCAACG
1 AATCAACG
672293 GAGATTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (11 bp):
AATCAACGAAA
Found at i:673074 original size:2 final size:2
Alignment explanation
Indices: 673067--673098 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
673057 TTAATTATTA
673067 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
673099 TTAAAAAATA
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:674215 original size:16 final size:18
Alignment explanation
Indices: 674184--674217 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
674174 GTTAATTATT
674184 TTTTGATAAGAATGAAGA
1 TTTTGATAAGAATGAAGA
674202 TTTT-ATAA-AATGAAGA
1 TTTTGATAAGAATGAAGA
674218 GTCGAAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (18 bp):
TTTTGATAAGAATGAAGA
Found at i:674503 original size:19 final size:19
Alignment explanation
Indices: 674481--674517 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
674471 CAATCAACGC
674481 ATACAGAGACAACAAAAGT
1 ATACAGAGACAACAAAAGT
* *
674500 ATACGGAGACAATAAAAG
1 ATACAGAGACAACAAAAG
674518 CATTTCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.19, T:0.11
Consensus pattern (19 bp):
ATACAGAGACAACAAAAGT
Found at i:680138 original size:2 final size:2
Alignment explanation
Indices: 680133--680167 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
680123 TTAATTATTA
680133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
680168 ATAAATAAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:680259 original size:24 final size:25
Alignment explanation
Indices: 680198--680259 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
680188 TATACCCCTC
680198 AATTAAAAAAT-TTTGTTTATGGAA
1 AATTAAAAAATATTTGTTTATGGAA
680222 AATTAAAAAA-ATTTGTTTATGGAA
1 AATTAAAAAATATTTGTTTATGGAA
680246 AA-TAAAAAATATTT
1 AATTAAAAAATATTT
680260 TAACCCCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.19
24 29 0.81
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (25 bp):
AATTAAAAAATATTTGTTTATGGAA
Found at i:680865 original size:50 final size:50
Alignment explanation
Indices: 680790--680893 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
680780 GTTAAAATGG
* *
680790 CTTAAGGGCTTGTTACTTAGCTTGGGTGTTCATCATCTCAAGGTTATTCC
1 CTTAAGGGCGTGTTACTTAGCTTGGGTGTTCACCATCTCAAGGTTATTCC
680840 CTTAAGGGCGTGTTACTTAGCTTGGGTGTTCACCATCTCAAGGTTATTCC
1 CTTAAGGGCGTGTTACTTAGCTTGGGTGTTCACCATCTCAAGGTTATTCC
680890 CTTA
1 CTTA
680894 TTTTGTGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.38
Consensus pattern (50 bp):
CTTAAGGGCGTGTTACTTAGCTTGGGTGTTCACCATCTCAAGGTTATTCC
Found at i:687304 original size:24 final size:24
Alignment explanation
Indices: 687254--687328 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
687244 AATTGATATA
* * * * *
687254 TCAAAAATCAAAACATAATTCAAG
1 TCAAATATCAAATCAAAATCCAGG
*
687278 TCAAATATCATATCAAAATCCAGG
1 TCAAATATCAAATCAAAATCCAGG
* * *
687302 TCAAGTATCAAATCAGAATCCATG
1 TCAAATATCAAATCAAAATCCAGG
687326 TCA
1 TCA
687329 GGTATCGTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (24 bp):
TCAAATATCAAATCAAAATCCAGG
Found at i:687333 original size:24 final size:24
Alignment explanation
Indices: 687277--687334 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
687267 CATAATTCAA
* *
687277 GTCAAATATCATATCAAAATCCAG
1 GTCAAGTATCAAATCAAAATCCAG
* *
687301 GTCAAGTATCAAATCAGAATCCAT
1 GTCAAGTATCAAATCAAAATCCAG
*
687325 GTCAGGTATC
1 GTCAAGTATC
687335 GTAACAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAAATCAAAATCCAG
Found at i:693363 original size:23 final size:23
Alignment explanation
Indices: 693337--693384 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
693327 TTAAAGTACA
*
693337 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
693360 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
693383 AT
1 AT
693385 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:693885 original size:21 final size:20
Alignment explanation
Indices: 693855--693908 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
693845 GATAGATACT
*
693855 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
693876 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
693899 TTACATTATA
1 TTACATTATA
693909 TAAGCGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:693896 original size:23 final size:23
Alignment explanation
Indices: 693870--693932 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
693860 ATATAACCAT
693870 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
693893 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
693916 TACCTATTACATCATAT
1 TACCTATTACATTATAT
693933 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Done.