Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 16 of 27
Found at i:2583556 original size:33 final size:33
Alignment explanation
Indices: 2583519--2583585 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2583509 TAAAACCATC
*
2583519 ACTACTGAACCATAGCATCTTCTTTAAGCTAAA
1 ACTACTGAACAATAGCATCTTCTTTAAGCTAAA
2583552 ACTACTGAACAATAGCATCTTCTTTAAGCTAAA
1 ACTACTGAACAATAGCATCTTCTTTAAGCTAAA
2583585 A
1 A
2583586 AATATATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (33 bp):
ACTACTGAACAATAGCATCTTCTTTAAGCTAAA
Found at i:2585097 original size:4 final size:4
Alignment explanation
Indices: 2585088--2585128 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
2585078 TTCAGATGAA
* *
2585088 AAAG AAAG AAAG AAA- AAAA AAAG AAAG -AAG AAAA AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2585129 ATTTTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2585110 original size:15 final size:15
Alignment explanation
Indices: 2585086--2585128 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
2585076 ATTTCAGATG
*
2585086 AAAAAGAAAGAAAGA
1 AAAAAAAAAGAAAGA
2585101 AAAAAAAAAGAAAGA
1 AAAAAAAAAGAAAGA
*
2585116 AGAAAAAAAGAAA
1 AAAAAAAAAGAAA
2585129 ATTTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:2585110 original size:19 final size:18
Alignment explanation
Indices: 2585086--2585124 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 18
2585076 ATTTCAGATG
2585086 AAAAAGAAAGAAAGAAAAA
1 AAAAAGAAAG-AAGAAAAA
2585105 AAAAAGAAAGAAGAAAAA
1 AAAAAGAAAGAAGAAAAA
2585123 AA
1 AA
2585125 GAAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAGAAAAA
Found at i:2585157 original size:15 final size:15
Alignment explanation
Indices: 2585137--2585171 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2585127 AAATTTTATA
2585137 TATATTTTTAAATAT
1 TATATTTTTAAATAT
* *
2585152 TATATTTTTATATTT
1 TATATTTTTAAATAT
2585167 TATAT
1 TATAT
2585172 ATTAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATATTTTTAAATAT
Found at i:2585776 original size:11 final size:11
Alignment explanation
Indices: 2585755--2585809 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
2585745 TCGAATATTC
*
2585755 TTATCATGTTT
1 TTATTATGTTT
*
2585766 ATATTATGTTTT
1 TTATTATG-TTT
2585778 TTATTATGTTT
1 TTATTATGTTT
*
2585789 TAATTAT-TTT
1 TTATTATGTTT
2585799 TTATTTATGTT
1 TTA-TTATGTT
2585810 GTGTTCATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 5 0.14
11 19 0.53
12 12 0.33
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (11 bp):
TTATTATGTTT
Found at i:2586070 original size:8 final size:9
Alignment explanation
Indices: 2586042--2586097 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 9
2586032 TTAATAATTA
2586042 ATATTATAT
1 ATATTATAT
*
2586051 ATATTCTGAT
1 ATATTAT-AT
2586061 ATATT-TAT
1 ATATTATAT
2586069 ATATTTATGAT
1 ATA-TTAT-AT
2586080 ATATT-TAT
1 ATATTATAT
2586088 ATATT-TAT
1 ATATTATAT
2586096 AT
1 AT
2586098 TATCTTCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
8 17 0.40
9 10 0.24
10 10 0.24
11 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (9 bp):
ATATTATAT
Found at i:2586108 original size:19 final size:19
Alignment explanation
Indices: 2586045--2586095 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
2586035 ATAATTAATA
*
2586045 TTATATATATTCTGATATAT
1 TTATATAT-TTATGATATAT
2586065 TTATATATTTATGATATAT
1 TTATATATTTATGATATAT
2586084 TTATATATTTAT
1 TTATATATTTAT
2586096 ATTATCTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
TTATATATTTATGATATAT
Found at i:2586108 original size:27 final size:28
Alignment explanation
Indices: 2586042--2586113 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
2586032 TTAATAATTA
2586042 ATAT-TAT-ATATATTCTGATATATTTAT
1 ATATCTATCATATATT-TGATATATTTAT
* *
2586069 ATATTTATGATATATTT-ATATATTTAT
1 ATATCTATCATATATTTGATATATTTAT
2586096 ATTATCT-TCATATTATTT
1 A-TATCTATCATA-TATTT
2586114 TTTATATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 19 0.49
28 13 0.33
29 7 0.18
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATCTATCATATATTTGATATATTTAT
Found at i:2587538 original size:16 final size:16
Alignment explanation
Indices: 2587517--2587569 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
2587507 AATATATAAT
2587517 TTAAAATTTTAAAATA
1 TTAAAATTTTAAAATA
2587533 TTAAAATTTATATAAATA
1 TTAAAATTT-TA-AAATA
*
2587551 -TAAAATATTTTAAATA
1 TTAAAAT-TTTAAAATA
2587567 TTA
1 TTA
2587570 TTATAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.44
17 11 0.34
18 7 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATTTTAAAATA
Found at i:2587556 original size:17 final size:17
Alignment explanation
Indices: 2587508--2587556 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2587498 TACAATTCAA
*
2587508 ATATATAATTTAAAATTT
1 ATATA-AATATAAAATTT
2587526 -TA-AAATATTAAAATTT
1 ATATAAATA-TAAAATTT
2587542 ATATAAATATAAAAT
1 ATATAAATATAAAAT
2587557 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.11
16 9 0.33
17 10 0.37
18 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:2587556 original size:25 final size:24
Alignment explanation
Indices: 2587526--2587607 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 24
2587516 TTTAAAATTT
2587526 TAAAATATTAAAATTTATATAAATA
1 TAAAATATT-AAATTTATATAAATA
2587551 TAAAATATTTTAAATATTATTATAATATTA
1 TAAAATA--TTAAAT-TTA-TATAA-A-TA
2587581 TAAAATAATT-AATTTAATATAAATA
1 TAAAAT-ATTAAATTT-ATATAAATA
2587606 TA
1 TA
2587608 TGAATTATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
25 11 0.22
26 5 0.10
27 12 0.24
28 9 0.18
29 3 0.06
30 8 0.16
31 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATATTAAATTTATATAAATA
Found at i:2587669 original size:2 final size:2
Alignment explanation
Indices: 2587662--2587696 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2587652 ATCACTTTCA
2587662 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2587697 CAGGGGTTAT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2587803 original size:14 final size:13
Alignment explanation
Indices: 2587775--2587812 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2587765 ATTAAAAATT
2587775 TACTTAATTTTTA
1 TACTTAATTTTTA
*
2587788 TACTCAATTATTTA
1 TACTTAATT-TTTA
2587802 TACTTAATTTT
1 TACTTAATTTT
2587813 GAATTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (13 bp):
TACTTAATTTTTA
Found at i:2589384 original size:15 final size:16
Alignment explanation
Indices: 2589364--2589393 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2589354 ATTAAAATCT
2589364 TTTGATTTT-ATTTTG
1 TTTGATTTTAATTTTG
2589379 TTTGATTTTAATTTT
1 TTTGATTTTAATTTT
2589394 AAAACTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
TTTGATTTTAATTTTG
Found at i:2593564 original size:21 final size:20
Alignment explanation
Indices: 2593527--2593567 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2593517 AAATTAAACC
*
2593527 TTTTAATTATATTTTAATTT
1 TTTTAATTATATATTAATTT
*
2593547 TTTTAAATTTTATATTAATTT
1 TTTT-AATTATATATTAATTT
2593568 AAATGTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAATTATATATTAATTT
Found at i:2598849 original size:21 final size:21
Alignment explanation
Indices: 2598825--2598883 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
2598815 AAATTATTCT
*
2598825 TTTTATATTAATAATTATATA
1 TTTTATATTAATAATTAAATA
* *
2598846 TTTTATAATTAA-ATTTAAATT
1 TTTTAT-ATTAATAATTAAATA
2598867 TTTTATTATTAAATAAT
1 TTTTA-TATT-AATAAT
2598884 AATTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 20 0.67
22 8 0.27
23 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATATTAATAATTAAATA
Found at i:2600144 original size:2 final size:2
Alignment explanation
Indices: 2600137--2600163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2600127 ACCACCATAA
2600137 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2600164 ATTTCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2602471 original size:31 final size:32
Alignment explanation
Indices: 2602412--2602479 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
2602402 AATATGATAT
2602412 AAATATATAAATATTTAAAATTTATAATAAAA
1 AAATATATAAATATTTAAAATTTATAATAAAA
*
2602444 AAAT-TATTAATATATTAAAATTT-TAATAAAA
1 AAATATATAAATAT-TTAAAATTTATAATAAAA
*
2602475 TAATA
1 AAATA
2602480 AATTCAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATATATAAATATTTAAAATTTATAATAAAA
Found at i:2603046 original size:25 final size:24
Alignment explanation
Indices: 2602992--2603046 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
2602982 AGCTAGACCT
* *
2602992 GTTTGATTTATATATCAAATTTTG
1 GTTTTATTTATATATAAAATTTTG
** *
2603016 CCTTTATTTATATGTAAATATTTTG
1 GTTTTATTTATATATAAA-ATTTTG
2603041 GTTTTA
1 GTTTTA
2603047 ATAGTTAAAG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.56
Consensus pattern (24 bp):
GTTTTATTTATATATAAAATTTTG
Found at i:2603718 original size:29 final size:29
Alignment explanation
Indices: 2603683--2603744 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
2603673 TAGTAAACAA
2603683 AATATTTTAAT-TTATATGTTATTAAATT-T
1 AATATTTTAATATT-TAT-TTATTAAATTAT
*
2603712 AATATTTTAATATTTATTTTTTAAATTAT
1 AATATTTTAATATTTATTTATTAAATTAT
2603741 AATA
1 AATA
2603745 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.30
29 19 0.63
30 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
AATATTTTAATATTTATTTATTAAATTAT
Found at i:2603767 original size:21 final size:20
Alignment explanation
Indices: 2603738--2603802 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
2603728 TTTTTTAAAT
*
2603738 TATAATAAAAAAATAATTAA
1 TATATTAAAAAAATAATTAA
* *
2603758 TGATATT-AAAAATTATTTAA
1 T-ATATTAAAAAAATAATTAA
*
2603778 -ATATTAATAAAAT-ATTAA
1 TATATTAAAAAAATAATTAA
2603796 TATATTA
1 TATATTA
2603803 TGTGATATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 9 0.25
19 11 0.31
20 12 0.33
21 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TATATTAAAAAAATAATTAA
Found at i:2603800 original size:19 final size:18
Alignment explanation
Indices: 2603745--2603802 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
2603735 AATTATAATA
2603745 AAAAAATAATTAATGATATT
1 AAAAAAT-ATTAAT-ATATT
*
2603765 AAAAATTATTTAA-ATATT
1 AAAAAATA-TTAATATATT
2603783 AATAAAATATTAATATATT
1 AA-AAAATATTAATATATT
2603802 A
1 A
2603803 TGTGATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 11 0.33
19 12 0.36
20 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAAATATTAATATATT
Found at i:2603931 original size:20 final size:22
Alignment explanation
Indices: 2603891--2603931 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2603881 TTATATAATA
2603891 AAATAATATTTTATCAACATTC
1 AAATAATATTTTATCAACATTC
*
2603913 AAATAA-ATTTT-TTAACATT
1 AAATAATATTTTATCAACATT
2603932 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATAATATTTTATCAACATTC
Found at i:2609529 original size:32 final size:29
Alignment explanation
Indices: 2609493--2609558 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 29
2609483 TTTTTATAGT
*
2609493 ATATTTAAATTTTTATTATTTTAAAAAATAAA
1 ATATTT-AATTTTTA-TATTAT-AAAAATAAA
2609525 ATATTT-ATTTTTATATTATAAAAATAAA
1 ATATTTAATTTTTATATTATAAAAATAAA
2609553 A-ATTTA
1 ATATTTA
2609559 TTAAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.12
28 10 0.31
29 5 0.16
30 7 0.22
32 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATATTTAATTTTTATATTATAAAAATAAA
Found at i:2609546 original size:29 final size:28
Alignment explanation
Indices: 2609501--2609560 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
2609491 GTATATTTAA
*
2609501 ATTTTTATTATTTTAAAAAATAAAATATTT
1 ATTTTTATTATTAT-AAAAATAAAA-ATTT
2609531 ATTTTTA-TATTATAAAAATAAAAATTT
1 ATTTTTATTATTATAAAAATAAAAATTT
2609558 ATT
1 ATT
2609561 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.24
28 10 0.34
29 5 0.17
30 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTTTATTATTATAAAAATAAAAATTT
Found at i:2612786 original size:2 final size:2
Alignment explanation
Indices: 2612779--2612818 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2612769 TAATGAAAGC
* *
2612779 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2612819 TTGGACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2613044 original size:20 final size:20
Alignment explanation
Indices: 2613021--2613070 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2613011 TTTAATAGAC
2613021 ATTTTTATTTTTTATTATT-A
1 ATTTTTATTTTTTATT-TTAA
* *
2613041 ATTTTGAGTTTTTATTTTAA
1 ATTTTTATTTTTTATTTTAA
2613061 ATGTTTTATT
1 AT-TTTTATT
2613071 AAAAGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (20 bp):
ATTTTTATTTTTTATTTTAA
Found at i:2616388 original size:11 final size:11
Alignment explanation
Indices: 2616367--2616418 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
2616357 AAATTATAAA
2616367 ATATTTATA-T
1 ATATTTATATT
2616377 AT-TTT-TATT
1 ATATTTATATT
2616386 ATATTTATATT
1 ATATTTATATT
2616397 ATATTTAATATT
1 ATATTT-ATATT
2616409 ATA-TTATATT
1 ATATTTATATT
2616419 TTAATTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 10 0.26
11 12 0.32
12 8 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTATATT
Found at i:2616767 original size:14 final size:14
Alignment explanation
Indices: 2616744--2616802 Score: 57
Period size: 16 Copynumber: 4.0 Consensus size: 14
2616734 AAAAATTATG
*
2616744 AAAATTTAAAAATA
1 AAAATATAAAAATA
*
2616758 AAAATATAAATATAAA
1 AAAATATAAA-A-ATA
2616774 AAAATTATCAAAAATA
1 AAAA-TAT-AAAAATA
2616790 AAAATA-AAAAATA
1 AAAATATAAAAATA
2616803 TTAATATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.18
14 9 0.24
15 3 0.08
16 12 0.32
17 4 0.11
18 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATATAAAAATA
Found at i:2616768 original size:20 final size:19
Alignment explanation
Indices: 2616724--2616777 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
2616714 ATTATTTTTT
*
2616724 TAAATTT-AAAAAAAATTA
1 TAAATTTAAAAAAAAAATA
2616742 TGAAAATTTAAAAATAAAAATA
1 T--AAATTTAAAAA-AAAAATA
*
2616764 TAAATATAAAAAAA
1 TAAATTTAAAAAAA
2616778 TTATCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 2 0.07
20 16 0.53
21 4 0.13
22 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAATTTAAAAAAAAAATA
Found at i:2616786 original size:26 final size:25
Alignment explanation
Indices: 2616757--2616805 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
2616747 ATTTAAAAAT
2616757 AAAAATATAAATATAAAAAA-ATTATC
1 AAAAATA-AAA-ATAAAAAATATTATC
2616783 AAAAATAAAAATAAAAAATATTA
1 AAAAATAAAAATAAAAAATATTA
2616806 ATATTCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATAAAAATAAAAAATATTATC
Found at i:2616792 original size:18 final size:16
Alignment explanation
Indices: 2616744--2616879 Score: 56
Period size: 16 Copynumber: 8.7 Consensus size: 16
2616734 AAAAATTATG
*
2616744 AAAATTTAAAAAT--A
1 AAAATATAAAAATAAA
*
2616758 AAAATATAAATATAAA
1 AAAATATAAAAATAAA
2616774 AAAATTATCAAAAAT--A
1 AAAA-TAT-AAAAATAAA
2616790 AAAATA-AAAAAT--A
1 AAAATATAAAAATAAA
** ***
2616803 TTAATAT-TCTATAAA
1 AAAATATAAAAATAAA
*
2616818 ATAAA-ATAAAATTCAAA
1 A-AAATATAAAAAT-AAA
*
2616835 AAATATATAAAATTCAAA
1 AAA-ATATAAAAAT-AAA
*
2616853 AAATTATAAAAATAAA
1 AAAATATAAAAATAAA
*
2616869 AAATTATAAAA
1 AAAATATAAAA
2616880 TTTTGTAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
13 13 0.14
14 11 0.12
15 5 0.05
16 29 0.31
17 16 0.17
18 20 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATAAAAATAAA
Found at i:2616799 original size:25 final size:26
Alignment explanation
Indices: 2616757--2616805 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2616747 ATTTAAAAAT
*
2616757 AAAAATATAAATATAAAAAAATTATC
1 AAAAATAAAAATATAAAAAAATTATC
*
2616783 AAAAATAAAAATA-AAAAATATTA
1 AAAAATAAAAATATAAAAAAATTA
2616806 ATATTCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAAATAAAAATATAAAAAAATTATC
Found at i:2616800 original size:39 final size:39
Alignment explanation
Indices: 2616732--2616809 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
2616722 TTTAAATTTA
* *
2616732 AAAAAAATTATGAAAATTTAAAAATAAAAATATAAATAT
1 AAAAAAATTATCAAAATATAAAAATAAAAATATAAATAT
*
2616771 AAAAAAATTATCAAAA-ATAAAAATAAAAAATATTAATAT
1 AAAAAAATTATCAAAATATAAAAAT-AAAAATATAAATAT
2616810 TCTATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 7 0.20
39 28 0.80
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (39 bp):
AAAAAAATTATCAAAATATAAAAATAAAAATATAAATAT
Found at i:2616841 original size:26 final size:25
Alignment explanation
Indices: 2616757--2616872 Score: 69
Period size: 25 Copynumber: 4.5 Consensus size: 25
2616747 ATTTAAAAAT
*
2616757 AAAAATATAAATATAAAAAAATTATC-
1 AAAAATATAAA-ATAAAAAAAAT-TCA
*
2616783 AAAAATA-AAAATAAAAAATATT-A
1 AAAAATATAAAATAAAAAAAATTCA
***
2616806 ATATTCTATAAAATAAAATAAAATTCAA
1 A-AAAATATAAAATAAAA-AAAATTC-A
**
2616834 AAAATATATAAAATTCAAAAAATT-A
1 AAAA-ATATAAAATAAAAAAAATTCA
*
2616859 TAAAAATAAAAAAT
1 -AAAAATATAAAAT
2616873 TATAAAATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
23 2 0.03
24 12 0.17
25 21 0.30
26 16 0.23
27 7 0.10
28 12 0.17
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAATATAAAATAAAAAAAATTCA
Found at i:2616878 original size:61 final size:60
Alignment explanation
Indices: 2616812--2616931 Score: 143
Period size: 61 Copynumber: 2.0 Consensus size: 60
2616802 ATTAATATTC
**
2616812 TATAAAATAAAATAAAATTCA-AAAAATATATAAAATTCAAAAAATTATAAAAATAAAAAAT
1 TATAAAATAAAATAAAATT-ATAAAAATATAT-AAATTCAAAAAAAGATAAAAATAAAAAAT
**** *
2616873 TATAAAATTTTGTAAAATTATTAAAAATATATAAATTTAAAAAAAGATAAAAATAAAAA
1 TATAAAATAAAATAAAATTA-TAAAAATATATAAATTCAAAAAAAGATAAAAATAAAAA
2616932 TTAAATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.02
61 39 0.78
62 10 0.20
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (60 bp):
TATAAAATAAAATAAAATTATAAAAATATATAAATTCAAAAAAAGATAAAAATAAAAAAT
Found at i:2616951 original size:61 final size:61
Alignment explanation
Indices: 2616832--2616978 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 61
2616822 AATAAAATTC
* ** * ***
2616832 AAAAAATATATAAAATTCAAAAAATTATAAAAATAAAAAATTATAAAATTTTGTAAAATTAT
1 AAAAAATATAT-AAATTTAAAAAAAGATAAAAATAAAAAATTATAAAAATTCAAAAAATTAT
*
2616894 TAAAAATATATAAATTTAAAAAAAGATAAAAAT-AAAAATTA-AATTAAATTCAAAAAATTAT
1 AAAAAATATATAAATTTAAAAAAAGATAAAAATAAAAAATTATAA--AAATTCAAAAAATTAT
2616955 AAAAAATCCAT-TAAATTTAAAAAA
1 AAAAAAT--ATATAAATTTAAAAAA
2616979 TTATAATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.03
60 8 0.11
61 37 0.51
62 23 0.32
63 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (61 bp):
AAAAAATATATAAATTTAAAAAAAGATAAAAATAAAAAATTATAAAAATTCAAAAAATTAT
Found at i:2616956 original size:28 final size:28
Alignment explanation
Indices: 2616925--2616984 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2616915 AAAGATAAAA
*
2616925 ATAAAAATTAAATTAAATTCAAAAAATT
1 ATAAAAAATAAATTAAATTCAAAAAATT
** *
2616953 ATAAAAAATCCATTAAATTTAAAAAATT
1 ATAAAAAATAAATTAAATTCAAAAAATT
2616981 ATAA
1 ATAA
2616985 TTTTCAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAAAAAATAAATTAAATTCAAAAAATT
Found at i:2616995 original size:13 final size:13
Alignment explanation
Indices: 2616977--2617001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2616967 AAATTTAAAA
2616977 AATTATAATTTTC
1 AATTATAATTTTC
2616990 AATTATAATTTT
1 AATTATAATTTT
2617002 TTTCTATTTT
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:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTATAATTTTC
Found at i:2617018 original size:8 final size:8
Alignment explanation
Indices: 2617007--2617098 Score: 52
Period size: 8 Copynumber: 11.5 Consensus size: 8
2616997 ATTTTTTTCT
2617007 ATTTTATA
1 ATTTTATA
*
2617015 ATTTTTTGA
1 ATTTTAT-A
2617024 ATTTT-TA
1 ATTTTATA
*
2617031 TTTTTATA
1 ATTTTATA
2617039 A-TTTA-A
1 ATTTTATA
**
2617045 AACTTATGA
1 ATTTTAT-A
2617054 ATTTTAT-
1 ATTTTATA
2617061 -TTTTA-A
1 ATTTTATA
2617067 ATTTTTTATA
1 A--TTTTATA
2617077 ATTTTATA
1 ATTTTATA
2617085 GATTTTTATA
1 -A-TTTTATA
2617095 ATTT
1 ATTT
2617099 CTGAATTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
6 7 0.11
7 12 0.18
8 19 0.29
9 19 0.29
10 9 0.14
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (8 bp):
ATTTTATA
Found at i:2617162 original size:18 final size:19
Alignment explanation
Indices: 2617141--2617182 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2617131 AATTTTTAGT
2617141 TTTTTGGATTTTTA-T-AAA
1 TTTTT-GATTTTTATTAAAA
*
2617159 TTTTTTATTTTTATTAAAA
1 TTTTTGATTTTTATTAAAA
2617178 TTTTT
1 TTTTT
2617183 TAATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTGATTTTTATTAAAA
Found at i:2617164 original size:19 final size:19
Alignment explanation
Indices: 2617148--2617184 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2617138 AGTTTTTTGG
2617148 ATTTTTA-T-AAATTTTTT
1 ATTTTTATTAAAATTTTTT
2617165 ATTTTTATTAAAATTTTTT
1 ATTTTTATTAAAATTTTTT
2617184 A
1 A
2617185 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTATTAAAATTTTTT
Found at i:2617705 original size:24 final size:23
Alignment explanation
Indices: 2617643--2617706 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
2617633 AATTAATTAA
* *
2617643 TATATTATTTATAATAATAAAAT
1 TATATTATTTGTAATAACAAAAT
* **
2617666 TATACTAAACTGTAATAACAAAAT
1 TATA-TTATTTGTAATAACAAAAT
2617690 TATATTATTTGTTAATA
1 TATATTATTTG-TAATA
2617707 TATTATTTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
TATATTATTTGTAATAACAAAAT
Found at i:2623604 original size:2 final size:2
Alignment explanation
Indices: 2623597--2623631 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2623587 AGGTCTCCTT
2623597 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2623632 TTGTGTATAC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2626485 original size:2 final size:2
Alignment explanation
Indices: 2626478--2626504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2626468 CTCATCTTGC
2626478 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2626505 ACACACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2637099 original size:2 final size:2
Alignment explanation
Indices: 2637092--2637134 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2637082 GTGGGCTCAA
2637092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2637134 A
1 A
2637135 GTAGATTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2640854 original size:19 final size:19
Alignment explanation
Indices: 2640826--2640871 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2640816 CAACACAATT
2640826 ATAT-AATACGAATATATA
1 ATATGAATACGAATATATA
2640844 ATATGAATACGAATATATA
1 ATATGAATACGAATATATA
2640863 ATATGAATA
1 ATATGAATA
2640872 TGATACGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (19 bp):
ATATGAATACGAATATATA
Found at i:2643710 original size:5 final size:5
Alignment explanation
Indices: 2643702--2643728 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2643692 ATATCATATA
2643702 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
2643729 TTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2651411 original size:2 final size:2
Alignment explanation
Indices: 2651404--2651435 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2651394 ACATAAATAA
2651404 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
2651436 TGATAGTAGA
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:2653556 original size:34 final size:34
Alignment explanation
Indices: 2653485--2653703 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 34
2653475 TTAAGAATAT
** *
2653485 ATTGTTGATTAAAT-GGTGATTTGGTAATTTATC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * * *
2653518 ATTGTTGATTAAATGGGTGATTTGATGGTTTGCA
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2653552 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2653586 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2653620 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2653654 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTACC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
*
2653688 ATTATTGATTAAATGG
1 ATTGTTGATTAAATGG
2653704 TGGTTTTTAC
Statistics
Matches: 156, Mismatches: 27, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
33 17 0.11
34 138 0.88
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2653628 original size:102 final size:101
Alignment explanation
Indices: 2653485--2653703 Score: 312
Period size: 102 Copynumber: 2.2 Consensus size: 101
2653475 TTAAGAATAT
** * * * * *
2653485 ATTGTTGATTAAATGGTGATTTGGTAATTTATCATTGTTGATTAAATGGGTGATTTGATGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGATGGCTTA
2653550 CAATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CAATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
2653586 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGATGGCTT
* * *
2653651 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTACC
65 ACAATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
2653688 ATTATTGATTAAATGG
1 ATTGTTGATTAAATGG
2653704 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 88 0.85
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGATGGCTTA
CAATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2658181 original size:34 final size:34
Alignment explanation
Indices: 2658112--2658369 Score: 277
Period size: 34 Copynumber: 7.5 Consensus size: 34
2658102 AAGTGGGAGA
* *
2658112 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2658145 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2658179 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2658213 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2658247 ATTATTTTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ---A--TTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2658286 ATTATTGATTAAATGGGTGATTTGGTGGCTTATC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2658320 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2658354 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2658370 TGGTTTTTAC
Statistics
Matches: 193, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
33 17 0.09
34 140 0.73
35 1 0.01
36 1 0.01
37 1 0.01
39 33 0.17
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2658268 original size:39 final size:39
Alignment explanation
Indices: 2658180--2658291 Score: 162
Period size: 39 Copynumber: 3.0 Consensus size: 39
2658170 TGGTTTGCCA
* * *
2658180 TTGTTGACTAAATGGGAGATTTGGTAGCTTACC---A--
1 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
2658214 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
1 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
2658253 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
1 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
2658292 GATTAAATGG
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
34 30 0.43
37 1 0.01
39 39 0.56
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (39 bp):
TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATT
Found at i:2658299 original size:107 final size:107
Alignment explanation
Indices: 2658146--2658356 Score: 271
Period size: 107 Copynumber: 2.0 Consensus size: 107
2658136 TAGTTTACCA
* ** * * * *
2658146 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGCTTA
1 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGCTTA
*
2658211 CCATTGTTGATTAAATGAG-AAATTTGGTAGCTTACCATTATT
66 CCATTGTTGACTAAATG-GTAAATTTGGTAGCTTACCATTATT
* * *
2658253 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGCTTA
* * * *
2658318 TCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATT
66 CCATTGTTGACTAAATGGTAAATTTGGTAGCTTACCATT
2658357 GTTGATTAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
106 1 0.01
107 87 0.99
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (107 bp):
TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGCTTA
CCATTGTTGACTAAATGGTAAATTTGGTAGCTTACCATTATT
Found at i:2658330 original size:141 final size:140
Alignment explanation
Indices: 2658113--2658368 Score: 404
Period size: 141 Copynumber: 1.8 Consensus size: 140
2658103 AGTGGGAGAA
** * * * *
2658113 TTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
2658178 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCT
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCT
2658243 TACCATTATT
131 TACCATTATT
*
2658253 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * * *
2658318 TCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTGTTGATTAAATG
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATG
2658369 GTGGTTTTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
140 14 0.13
141 90 0.87
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (140 bp):
TTGTTGATTAAATGGAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCT
TACCATTATT
Found at i:2660789 original size:11 final size:11
Alignment explanation
Indices: 2660771--2660800 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2660761 CAACACAATT
2660771 ACATAATATGA
1 ACATAATATGA
*
2660782 ATATAATATGA
1 ACATAATATGA
2660793 ACATAATA
1 ACATAATA
2660801 AGAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ACATAATATGA
Found at i:2663547 original size:22 final size:22
Alignment explanation
Indices: 2663522--2663569 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2663512 ATTTAATTTA
2663522 TAAAATTATATAAAAATT-AAAT
1 TAAAATTATAT-AAAATTAAAAT
* * *
2663544 TAAATTTTTATAATATTAAAAT
1 TAAAATTATATAAAATTAAAAT
2663566 TAAA
1 TAAA
2663570 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATTATATAAAATTAAAAT
Found at i:2663596 original size:27 final size:27
Alignment explanation
Indices: 2663529--2663583 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2663519 TTATAAAATT
*
2663529 ATATAAAAATTAAATTAAATTTTTATA
1 ATATTAAAATTAAATTAAATTTTTATA
2663556 ATATTAAAATTAAATTAAATTTTT-TA
1 ATATTAAAATTAAATTAAATTTTTATA
2663582 AT
1 AT
2663584 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTAAAATTAAATTAAATTTTTATA
Found at i:2666175 original size:13 final size:13
Alignment explanation
Indices: 2666157--2666182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2666147 GACACCGAAA
2666157 ACATAGTAGTTGT
1 ACATAGTAGTTGT
2666170 ACATAGTAGTTGT
1 ACATAGTAGTTGT
2666183 GGAACATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
ACATAGTAGTTGT
Found at i:2670739 original size:19 final size:20
Alignment explanation
Indices: 2670715--2670758 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
2670705 ATTAAATATG
2670715 ATAAAAT-TATATATAAAAA-
1 ATAAAATATAT-TATAAAAAT
2670734 ATAAAATATATTATAAAAAT
1 ATAAAATATATTATAAAAAT
2670754 ATAAA
1 ATAAA
2670759 TTAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAATATATTATAAAAAT
Found at i:2671708 original size:17 final size:18
Alignment explanation
Indices: 2671681--2671717 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2671671 TATAATTTTT
2671681 ATAATTAAATTTAAA-TAA
1 ATAATTAAA-TTAAATTAA
2671699 ATAA-TAAATTAAATTAA
1 ATAATTAAATTAAATTAA
2671716 AT
1 AT
2671718 TTATTCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTAAATTAAATTAA
Found at i:2673468 original size:2 final size:2
Alignment explanation
Indices: 2673461--2673497 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2673451 ATAGAGGAGT
2673461 TA 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 TA T
2673498 GATGTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2673618 original size:20 final size:21
Alignment explanation
Indices: 2673580--2673622 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2673570 ATTTAAATTA
2673580 AAATAATTTTAAATATTAAAT
1 AAATAATTTTAAATATTAAAT
* *
2673601 AAAT-ATTTTTAATGTTAAAT
1 AAATAATTTTAAATATTAAAT
2673621 AA
1 AA
2673623 GTAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATAATTTTAAATATTAAAT
Found at i:2674134 original size:16 final size:16
Alignment explanation
Indices: 2674115--2674198 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
2674105 TTTAATAATT
2674115 TTAATA-TTATTTATTA
1 TTAATATTTA-TTATTA
*
2674131 TTAAAATTT-TTA--A
1 TTAATATTTATTATTA
* *
2674144 TTAAAATTTATTATAA
1 TTAATATTTATTATTA
2674160 TTAATTATTATATTATTTA
1 TTAA-TATT-TATTA-TTA
*
2674179 TT-ATATTTATAATTA
1 TTAATATTTATTATTA
2674194 -TAATA
1 TTAATA
2674199 AATATAATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.18
14 4 0.07
15 9 0.16
16 14 0.25
17 9 0.16
18 6 0.11
19 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATTTATTATTA
Found at i:2674179 original size:12 final size:12
Alignment explanation
Indices: 2674149--2674185 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
2674139 TTTAATTAAA
2674149 ATTTATTATAATT
1 ATTTATTAT-ATT
*
2674162 AATTATTATATT
1 ATTTATTATATT
2674174 ATTTATTATATT
1 ATTTATTATATT
2674186 TATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:2674746 original size:19 final size:19
Alignment explanation
Indices: 2674724--2674766 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2674714 ATAATTAAAT
*
2674724 TAAATAAATAT-AAATTATA
1 TAAA-AAATATAAAAATATA
*
2674743 TAAAAATTATAAAAATATA
1 TAAAAAATATAAAAATATA
2674762 TAAAA
1 TAAAA
2674767 TTAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAATATAAAAATATA
Found at i:2674749 original size:26 final size:29
Alignment explanation
Indices: 2674696--2674767 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
2674686 AATTTACGTG
2674696 AATAAATAATAAAATATGATAATTAAATTA-
1 AATAAAT-ATAAAATATGATAA-TAAATTAT
*
2674726 AATAAATATAAATTAT-ATAA-AAATTAT
1 AATAAATATAAAATATGATAATAAATTAT
*
2674753 AAAAATATATAAAAT
1 AATAA-ATATAAAAT
2674768 TAATGTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.16
27 4 0.11
28 12 0.32
29 8 0.22
30 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
AATAAATATAAAATATGATAATAAATTAT
Found at i:2674751 original size:11 final size:10
Alignment explanation
Indices: 2674725--2674766 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2674715 TAATTAAATT
*
2674725 AAATAAATATA
1 AAATATATA-A
*
2674736 AATTATATAA
1 AAATATATAA
2674746 AAAT-TATAA
1 AAATATATAA
2674755 AAATATATAA
1 AAATATATAA
2674765 AA
1 AA
2674767 TTAATGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.33
10 11 0.41
11 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:2675309 original size:2 final size:2
Alignment explanation
Indices: 2675267--2675296 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2675257 TCAAAATTCC
*
2675267 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2675297 TCTTCAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2676685 original size:2 final size:2
Alignment explanation
Indices: 2676678--2676702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2676668 GAGGCCATAA
2676678 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
2676703 ACCTCCTAAC
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:2677147 original size:15 final size:15
Alignment explanation
Indices: 2677123--2677170 Score: 80
Period size: 14 Copynumber: 3.2 Consensus size: 15
2677113 AAAAATAATA
2677123 TTTAATAATTTTAAAT
1 TTTAA-AATTTTAAAT
2677139 TTTAAAATTTTAAAT
1 TTTAAAATTTTAAAT
2677154 TTT-AAATTTTAAAT
1 TTTAAAATTTTAAAT
2677168 TTT
1 TTT
2677171 TTTGTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 14 0.44
15 13 0.41
16 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAAATTTTAAAT
Found at i:2677157 original size:22 final size:22
Alignment explanation
Indices: 2677129--2677171 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2677119 AATATTTAAT
2677129 AATTTTAAATTTTAAAATTTTA
1 AATTTTAAATTTTAAAATTTTA
*
2677151 AATTTTAAATTTTAAATTTTT
1 AATTTTAAATTTTAAAATTTT
2677172 TTGTGTAATG
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTTAAATTTTAAAATTTTA
Found at i:2677171 original size:8 final size:7
Alignment explanation
Indices: 2677129--2677170 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
2677119 AATATTTAAT
2677129 AATTTTA
1 AATTTTA
2677136 AATTTTAA
1 AATTTT-A
2677144 AATTTTA
1 AATTTTA
2677151 AATTTTA
1 AATTTTA
2677158 AATTTTA
1 AATTTTA
2677165 AATTTT
1 AATTTT
2677171 TTTGTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:2677607 original size:22 final size:22
Alignment explanation
Indices: 2677572--2677624 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2677562 TAAGTATTTG
*
2677572 ATTTAAAATTAATTTAAAACAT-A
1 ATTT-AAATAAATTT-AAACATAA
*
2677595 ATTTAAATAAATTTATACATAA
1 ATTTAAATAAATTTAAACATAA
2677617 ATTTAAAT
1 ATTTAAAT
2677625 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 18 0.67
23 4 0.15
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAAATAAATTTAAACATAA
Found at i:2679922 original size:2 final size:2
Alignment explanation
Indices: 2679915--2679942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2679905 AGGCCCATCG
2679915 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
2679943 ATGTCTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2680383 original size:16 final size:16
Alignment explanation
Indices: 2680362--2680398 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2680352 AAAATAATTT
**
2680362 AAAATTTAAAATTTAA
1 AAAATTTAAAAAATAA
2680378 AAAATTTAAAAAATAA
1 AAAATTTAAAAAATAA
2680394 AAAAT
1 AAAAT
2680399 AATATAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTTAAAAAATAA
Found at i:2680570 original size:24 final size:23
Alignment explanation
Indices: 2680523--2680581 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
2680513 TGATTTTGGG
*
2680523 TTAAATTTTTTAATATTTGCTTT
1 TTAAATTTTTTAATATTTGATTT
* * *
2680546 TCTAAATTTTTTCATTTTTTATTT
1 T-TAAATTTTTTAATATTTGATTT
*
2680570 TTAATTTTTTTA
1 TTAAATTTTTTA
2680582 TGATTCTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (23 bp):
TTAAATTTTTTAATATTTGATTT
Found at i:2680773 original size:12 final size:12
Alignment explanation
Indices: 2680756--2680801 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
2680746 GAATATTATT
2680756 ATATTATATTTA
1 ATATTATATTTA
2680768 ATATTATATTTTA
1 ATATTATA-TTTA
*
2680781 ATA--AT-TTTT
1 ATATTATATTTA
2680790 ATATTATATTTA
1 ATATTATATTTA
2680802 TAATAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 6 0.21
11 4 0.14
12 11 0.39
13 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:2680813 original size:22 final size:22
Alignment explanation
Indices: 2680768--2680814 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2680758 ATTATATTTA
*
2680768 ATATTATATTTTAATAATTTTT
1 ATATTATATTTTAATAATTGTT
2680790 ATATTATATTTATAATAA-TGTT
1 ATATTATATTT-TAATAATTGTT
2680812 ATA
1 ATA
2680815 GGATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTATATTTTAATAATTGTT
Found at i:2682747 original size:3 final size:3
Alignment explanation
Indices: 2682739--2682765 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2682729 CAAATCTAAC
2682739 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2682766 CTCTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2682986 original size:34 final size:33
Alignment explanation
Indices: 2682948--2683049 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 33
2682938 TAAATTAGAT
2682948 TTAAAATTAAAATTTTATTTATTTAAAATTTATA
1 TTAAAATTAAAATTTTA-TTATTTAAAATTTATA
* * *
2682982 TTAAATTTAAAAATTTTATTATTAAAAATATATA
1 TTAAAATT-AAAATTTTATTATTTAAAATTTATA
*
2683016 TTAAGATATTAAAA-ATTATT-TTTAAAACTTTATA
1 TTAA-A-ATTAAAATTTTATTATTTAAAA-TTTATA
2683050 ATTTATATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
33 6 0.11
34 35 0.61
35 14 0.25
36 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
TTAAAATTAAAATTTTATTATTTAAAATTTATA
Found at i:2682989 original size:22 final size:22
Alignment explanation
Indices: 2682934--2682990 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2682924 AGGTAGAACT
*
2682934 AAATTAAATTAGATTTAAAATTA
1 AAATTAAATT-TATTTAAAATTA
** *
2682957 AAATTTTATTTATTTAAAATTT
1 AAATTAAATTTATTTAAAATTA
*
2682979 ATATTAAATTTA
1 AAATTAAATTTA
2682991 AAAATTTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATTAAATTTATTTAAAATTA
Found at i:2683006 original size:21 final size:18
Alignment explanation
Indices: 2682948--2683057 Score: 68
Period size: 16 Copynumber: 6.1 Consensus size: 18
2682938 TAAATTAGAT
*
2682948 TTAAAATTAAAATTT-TA
1 TTAAATTTAAAATTTATA
*
2682965 TT-TATTTAAAATTTATA
1 TTAAATTTAAAATTTATA
2682982 TTAAATTTAAAAATTT-TA
1 TTAAATTT-AAAATTTATA
* *
2683000 TT--ATTAAAAATATATA
1 TTAAATTTAAAATTTATA
* *
2683016 TTAAGATATTAAAAATTATTT
1 TTAA-AT-TTAAAATTTA-TA
*
2683037 TTAAAACTTTATAATTTATA
1 TT-AAA-TTTAAAATTTATA
2683057 T
1 T
2683058 ATAACCATTA
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
15 6 0.09
16 17 0.24
17 6 0.09
18 8 0.11
19 9 0.13
20 9 0.13
21 12 0.17
22 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (18 bp):
TTAAATTTAAAATTTATA
Found at i:2683481 original size:19 final size:19
Alignment explanation
Indices: 2683431--2683487 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2683421 ACATCATATT
*
2683431 AAATATTTAATTTTAAAT-T
1 AAATATTTAA-TTTAAATAA
*
2683450 AATTA-TTAA--TAAATAA
1 AAATATTTAATTTAAATAA
2683466 AAATATTTAATTTAAATAA
1 AAATATTTAATTTAAATAA
2683485 AAA
1 AAA
2683488 CTCACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 5 0.16
16 4 0.13
17 4 0.13
18 4 0.13
19 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATTTAATTTAAATAA
Found at i:2686610 original size:9 final size:8
Alignment explanation
Indices: 2686583--2686624 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
2686573 AAAATTATTT
*
2686583 TATATATA
1 TATATAAA
2686591 TATATAAA
1 TATATAAA
*
2686599 TATATCAA
1 TATATAAA
2686607 -ATATAAA
1 TATATAAA
2686614 TAT-TAAA
1 TATATAAA
2686621 TATA
1 TATA
2686625 AATATGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 13 0.45
8 16 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:2686621 original size:13 final size:14
Alignment explanation
Indices: 2686584--2686634 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
2686574 AAATTATTTT
*
2686584 ATATATATATATAA
1 ATATATAAATATAA
2686598 ATATATCAAATATAA
1 ATATAT-AAATATAA
2686613 ATAT-TAAATATAA
1 ATATATAAATATAA
*
2686626 ATATGTAAA
1 ATATATAAA
2686635 AAAAAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.35
14 11 0.32
15 11 0.32
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
ATATATAAATATAA
Found at i:2688042 original size:21 final size:23
Alignment explanation
Indices: 2687991--2688048 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
2687981 TATGAGGACA
2687991 GTGGAGGAGGATATGCAGCTAGC
1 GTGGAGGAGGATATGCAGCTAGC
2688014 G-GAAGAGGAGGATATGCAGC-AG-
1 GTG--GAGGAGGATATGCAGCTAGC
2688036 GTGGAGGAGGATA
1 GTGGAGGAGGATA
2688049 CGTAGATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.31
22 2 0.06
23 4 0.12
24 16 0.50
ACGTcount: A:0.31, C:0.09, G:0.47, T:0.14
Consensus pattern (23 bp):
GTGGAGGAGGATATGCAGCTAGC
Found at i:2691344 original size:14 final size:14
Alignment explanation
Indices: 2691302--2691345 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2691292 TTAATTTTTA
*
2691302 TTAAATAATTAAAC
1 TTAAATAATTAAAT
* *
2691316 TTAATTAAATAAAT
1 TTAAATAATTAAAT
*
2691330 TTAAATAATTTAAT
1 TTAAATAATTAAAT
2691344 TT
1 TT
2691346 TTATTTCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATAATTAAAT
Found at i:2695014 original size:141 final size:142
Alignment explanation
Indices: 2694738--2695023 Score: 513
Period size: 141 Copynumber: 2.0 Consensus size: 142
2694728 ATGAGATGAA
2694738 TAGCGTAACTATCATTGTTCCAACTAGCCATTCAATAAACAATCGTAAAAACTAGAAAACCAGCC
1 TAGCGTAACTATCATTGTTCCAACTAGCCATTCAATAAACAATCGTAAAAACTAGAAAACCAG-C
*
2694803 AAAAAAAATTCTAGAAAATTCAACTATTTACCGATTGGTAAAGCTGGAAGGCCCTGCCACCAGCT
65 AAAAAAAATGCTAGAAAATTCAACTATTTACCGATTGGTAAAGCTGGAAGGCCCTGCCACCAGCT
2694868 TCAATGGCAACAC
130 TCAATGGCAACAC
2694881 TAGCGTAACTATCATTGTTCCAACTAGCCATTCAATAAACTAA-CGTAAAAACTAGAAAACCAG-
1 TAGCGTAACTATCATTGTTCCAACTAGCCATTCAATAAAC-AATCGTAAAAACTAGAAAACCAGC
* *
2694944 AAAATAAATGCTAGAAAATTCAACTATTTACCGATTGGTAAAGCTGGAAGGCTCTGCCACCAGCT
65 AAAAAAAATGCTAGAAAATTCAACTATTTACCGATTGGTAAAGCTGGAAGGCCCTGCCACCAGCT
2695009 TCAATGGCAACAC
130 TCAATGGCAACAC
2695022 TA
1 TA
2695024 ACTGGCTGAT
Statistics
Matches: 139, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
141 77 0.55
143 60 0.43
144 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (142 bp):
TAGCGTAACTATCATTGTTCCAACTAGCCATTCAATAAACAATCGTAAAAACTAGAAAACCAGCA
AAAAAAATGCTAGAAAATTCAACTATTTACCGATTGGTAAAGCTGGAAGGCCCTGCCACCAGCTT
CAATGGCAACAC
Found at i:2697813 original size:13 final size:13
Alignment explanation
Indices: 2697795--2697825 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2697785 TGAAGAAAAC
*
2697795 TTTTATTTTTATT
1 TTTTATTTTTATG
2697808 TTTTATTTTTATG
1 TTTTATTTTTATG
2697821 TTTTA
1 TTTTA
2697826 ACCAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTATG
Found at i:2702237 original size:25 final size:26
Alignment explanation
Indices: 2702200--2702254 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
2702190 TATGCAATTC
2702200 TTGAAAGCTGCATGAGCTTACTAGCG
1 TTGAAAGCTGCATGAGCTTACTAGCG
* *
2702226 TTGAAA-CTGCATGAGTTTACTAGTG
1 TTGAAAGCTGCATGAGCTTACTAGCG
2702251 TTGA
1 TTGA
2702255 GATTTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (26 bp):
TTGAAAGCTGCATGAGCTTACTAGCG
Found at i:2704747 original size:30 final size:31
Alignment explanation
Indices: 2704700--2704808 Score: 204
Period size: 30 Copynumber: 3.6 Consensus size: 31
2704690 TCAGAAGATT
2704700 AATTTGCATCAATGATAATTTCCTTTTCTTA
1 AATTTGCATCAATGATAATTTCCTTTTCTTA
2704731 AATTTGCATC-ATGATAATTTCCTTTTCTTA
1 AATTTGCATCAATGATAATTTCCTTTTCTTA
2704761 AATTTGCATC-ATGATAATTTCCTTTTCTTA
1 AATTTGCATCAATGATAATTTCCTTTTCTTA
2704791 AATTTGCATCAATGATAA
1 AATTTGCATCAATGATAA
2704809 ATCATTGAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
30 60 0.78
31 17 0.22
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (31 bp):
AATTTGCATCAATGATAATTTCCTTTTCTTA
Found at i:2706782 original size:205 final size:197
Alignment explanation
Indices: 2706429--2706836 Score: 642
Period size: 205 Copynumber: 2.0 Consensus size: 197
2706419 CTGGAAGGTG
*
2706429 ATTGATGACAATTTTCAGAAACTAGACAATGAGAAAGTGAGCATATATATAGATGTATTAATCTT
1 ATTGATGACAATTTTCAGAAACTAGACAATGAGAAAGTGAGCATATATATAGATGCATTAATCTT
*
2706494 TTAGCCAAGACTGTTAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTAAAAAGGTAAGGCC
66 TTAGCCAAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTAAAAAGGTAAGGCC
2706559 AGTTTTGTATGAGGTAACTTAGTTTATTTGATATTGGAAGAACC-TTTTTTCTAGAATAATGTTA
131 AGTTTTGTATGAGGTAAC---------TT-ATATTGGAAGAACCTTTTTTTCTAGAATAATGTTA
2706623 AATTGCTTATTA
186 AATTGCTTATTA
* *
2706635 ATTGATGACAATTTTCATAACCTAGACAATGAGAAAGTGAGCATATATATAGATGCATTAATCTT
1 ATTGATGACAATTTTCAGAAACTAGACAATGAGAAAGTGAGCATATATATAGATGCATTAATCTT
*
2706700 TTAGCC-AGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTATAAAGGTAAGGCC
66 TTAGCCAAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTAAAAAGGTAAGGCC
* *
2706764 AGTTTTGTATGGGGTAACTTATATTGGAGGAACCTTTTTTTCTAGAATAATGTTAAATTGCTTAT
131 AGTTTTGTATGAGGTAACTTATATTGGAAGAACCTTTTTTTCTAGAATAATGTTAAATTGCTTAT
2706829 TA
196 TA
2706831 A-TGATG
1 ATTGATG
2706837 CTCGGCTAAC
Statistics
Matches: 194, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
195 18 0.09
196 35 0.18
205 73 0.38
206 68 0.35
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (197 bp):
ATTGATGACAATTTTCAGAAACTAGACAATGAGAAAGTGAGCATATATATAGATGCATTAATCTT
TTAGCCAAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTAAAAAGGTAAGGCC
AGTTTTGTATGAGGTAACTTATATTGGAAGAACCTTTTTTTCTAGAATAATGTTAAATTGCTTAT
TA
Found at i:2707175 original size:277 final size:267
Alignment explanation
Indices: 2706691--2707234 Score: 829
Period size: 277 Copynumber: 2.0 Consensus size: 267
2706681 ATATAGATGC
2706691 ATTAATCTTTTAGCCAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTATAAAG
1 ATTAATCTTTTAGCCAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTATAAAG
* *
2706756 GTAAGGCCAGTTTTGTATGGGGTAACTTATATTGGAGGAACCTTTTTTTCTAGAATAATGTTAAA
66 ATAAGGCCAGTTTTGTATGGGGTAACTTATATTGGAGGAACCTTATTTTCTAGAATAATGTTAAA
* * * *
2706821 TTGCTTATTAATGATGCTCGGCTAACTTTTGAAAAAGCACATTATGAACTAATGTTTCTTGCTCA
131 TTGCTTATTAATGATGCTCAGCAAACTTTTGAAAAAACACATTATGAACTAATATTTCTTGCTCA
* *
2706886 AAAAAGAGATTCTTACAGGTCGAGACCCATCTCCAATGTTATCTTGGAATTTGCGCATTTGTCTT
196 AAAAAGAGATTCTTACAGGTCGAGACCCATCTCCAATGTTAACTTGGAATATGCGCATTTGTCTT
2706951 GAATGGT
261 GAATGGT
* * *
2706958 ATTAATCTTTTAGCCGGACTGTCAGAATGCTAGTTGCTATTGTTTATAGACTATGACTTATAAAG
1 ATTAATCTTTTAGCCAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTATAAAG
2707023 ATAAGGCCAGTTTTGTATGGGGTAACTTAGTTTATTTGCAATTGGAGGAACCTTATTTTCTAGAA
66 ATAAGGCCAGTTTTGTATGGGGTAAC-----TTA--T---ATTGGAGGAACCTTATTTTCTAGAA
* *
2707088 TAATGTTTAATTGCTTATTAATGATGCTCAGCAAACTTTTGAAAAAACACATTAT-AGAGTAATA
121 TAATGTTAAATTGCTTATTAATGATGCTCAGCAAACTTTTGAAAAAACACATTATGA-ACTAATA
** *
2707152 TTTCTTGCTCAAAAAAGAGATTCTTATGGGTCGAGACCCATCTGCAATGTTAACTTGGAATATGC
185 TTTCTTGCTCAAAAAAGAGATTCTTACAGGTCGAGACCCATCTCCAATGTTAACTTGGAATATGC
*
2707217 GCATTTGTCTTGGATGGT
250 GCATTTGTCTTGAATGGT
2707235 GGCAAGTGTC
Statistics
Matches: 249, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
267 87 0.35
272 3 0.01
274 1 0.00
276 1 0.00
277 157 0.63
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (267 bp):
ATTAATCTTTTAGCCAGACTGTCAGAATCCTAGTTGCTATTGTTTATAGACTAAGACTTATAAAG
ATAAGGCCAGTTTTGTATGGGGTAACTTATATTGGAGGAACCTTATTTTCTAGAATAATGTTAAA
TTGCTTATTAATGATGCTCAGCAAACTTTTGAAAAAACACATTATGAACTAATATTTCTTGCTCA
AAAAAGAGATTCTTACAGGTCGAGACCCATCTCCAATGTTAACTTGGAATATGCGCATTTGTCTT
GAATGGT
Found at i:2708485 original size:17 final size:17
Alignment explanation
Indices: 2708463--2708498 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2708453 AGAATATATA
2708463 TTTTTTAAGAGATAAAT
1 TTTTTTAAGAGATAAAT
* *
2708480 TTTTTTAATATATAAAT
1 TTTTTTAAGAGATAAAT
2708497 TT
1 TT
2708499 AGTTGGATAA
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:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTTTAAGAGATAAAT
Found at i:2709841 original size:17 final size:17
Alignment explanation
Indices: 2709808--2709839 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2709798 ATTAATATCA
2709808 TTTATATTTATTTAAAT
1 TTTATATTTATTTAAAT
2709825 TTTAT-TTTATTTAAA
1 TTTATATTTATTTAAA
2709840 ATATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATATTTATTTAAAT
Found at i:2709904 original size:10 final size:10
Alignment explanation
Indices: 2709807--2709907 Score: 62
Period size: 10 Copynumber: 9.9 Consensus size: 10
2709797 TATTAATATC
2709807 ATTTATATTT
1 ATTTATATTT
*
2709817 ATTTAAATTTT
1 ATTTATA-TTT
2709828 ATTT-TATTT
1 ATTTATATTT
** **
2709837 A-AAATATAA
1 ATTTATATTT
*
2709846 ATTTTAAATTTT
1 A-TTTATA-TTT
*
2709858 ATTTAGATTT
1 ATTTATATTT
2709868 ATTTATATTT
1 ATTTATATTT
** *
2709878 ATAAATAATTA
1 ATTTAT-ATTT
2709889 ATTTATATTT
1 ATTTATATTT
2709899 ATTTATATT
1 ATTTATATT
2709908 ATATATTTTT
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
9 8 0.12
10 35 0.53
11 21 0.32
12 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (10 bp):
ATTTATATTT
Found at i:2710148 original size:18 final size:18
Alignment explanation
Indices: 2710121--2710159 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2710111 CCAATTAAAT
2710121 TTTTAAATAA-ATTTTATA
1 TTTTAAATAATATTTT-TA
*
2710139 TTTTACATAATATTTTTA
1 TTTTAAATAATATTTTTA
2710157 TTT
1 TTT
2710160 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAAATAATATTTTTA
Found at i:2710887 original size:15 final size:15
Alignment explanation
Indices: 2710869--2710900 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2710859 AGAATGTCCA
2710869 CCACCACCACCACCT
1 CCACCACCACCACCT
*
2710884 CCACCACCACCGCCT
1 CCACCACCACCACCT
2710899 CC
1 CC
2710901 GCCTCCTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.69, G:0.03, T:0.06
Consensus pattern (15 bp):
CCACCACCACCACCT
Found at i:2710933 original size:39 final size:39
Alignment explanation
Indices: 2710890--2710972 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
2710880 ACCTCCACCA
*
2710890 CCACCGCCTCCGCCTCCTCCACCACCTAAACCTGAATGC
1 CCACCACCTCCGCCTCCTCCACCACCTAAACCTGAATGC
* *
2710929 CCACCACCTCCGCCTCCTCCACCGCCTAAACCTGAATGT
1 CCACCACCTCCGCCTCCTCCACCACCTAAACCTGAATGC
2710968 CCACC
1 CCACC
2710973 TCTATCACCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.20, C:0.54, G:0.10, T:0.16
Consensus pattern (39 bp):
CCACCACCTCCGCCTCCTCCACCACCTAAACCTGAATGC
Found at i:2711040 original size:72 final size:72
Alignment explanation
Indices: 2710944--2711092 Score: 235
Period size: 72 Copynumber: 2.1 Consensus size: 72
2710934 ACCTCCGCCT
* * *
2710944 CCTCCACCGCCTAAACCTGAATGTCCACCTCTATCACCGCCGCCACCACCGCCTCCACCTCCTCC
1 CCTCCACCGCCAAAACCTGAATGTCCACCTCTATCACCGCCGCCACCACCACCTCCACCTCCACC
2711009 ACCACCA
66 ACCACCA
* *
2711016 CCTCCACCGCCAAAACCTGTATGTCCACCTCTATCACCGCCGCCGCCACCACCTCCACCTCCACC
1 CCTCCACCGCCAAAACCTGAATGTCCACCTCTATCACCGCCGCCACCACCACCTCCACCTCCACC
* *
2711081 ACCTCCT
66 ACCACCA
2711088 CCTCC
1 CCTCC
2711093 TCCTCCTCCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.19, C:0.56, G:0.08, T:0.16
Consensus pattern (72 bp):
CCTCCACCGCCAAAACCTGAATGTCCACCTCTATCACCGCCGCCACCACCACCTCCACCTCCACC
ACCACCA
Found at i:2711073 original size:6 final size:6
Alignment explanation
Indices: 2711064--2711116 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
2711054 GCCGCCGCCA
* * * * * *
2711064 CCACCT CCACCT CCACCA CCTCCT CCTCCT CCTCCT CCACCA CCACCA
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
2711112 CCACC
1 CCACC
2711117 ACCTCCATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.17, C:0.68, G:0.00, T:0.15
Consensus pattern (6 bp):
CCACCT
Found at i:2711082 original size:9 final size:9
Alignment explanation
Indices: 2711070--2711123 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
2711060 GCCACCACCT
2711070 CCACCTCCA
1 CCACCTCCA
*
2711079 CCACCTCCT
1 CCACCTCCA
* *
2711088 CCTCCTCCT
1 CCACCTCCA
* *
2711097 CCTCCACCA
1 CCACCTCCA
*
2711106 CCACCACCA
1 CCACCTCCA
2711115 CCACCTCCA
1 CCACCTCCA
2711124 TGTACGTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.19, C:0.67, G:0.00, T:0.15
Consensus pattern (9 bp):
CCACCTCCA
Found at i:2713235 original size:21 final size:22
Alignment explanation
Indices: 2713209--2713250 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2713199 ATTATATCAT
2713209 TAAATTAAATA-AATATTTATA
1 TAAATTAAATATAATATTTATA
* *
2713230 TAAATTATATATTATATTTAT
1 TAAATTAAATATAATATTTAT
2713251 TCAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATTAAATATAATATTTATA
Found at i:2713835 original size:35 final size:35
Alignment explanation
Indices: 2713763--2713835 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
2713753 CTTTCACATT
* *
2713763 TTTTATATTTATTATATCATTTTAATATTTATTAA
1 TTTTATATTTATTATATCATTTTAATAATTATAAA
2713798 TTTTATATTT-TTATATCATATTTAA-AATTATCAAA
1 TTTTATATTTATTATATCAT-TTTAATAATTAT-AAA
2713833 TTT
1 TTT
2713836 ACTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (35 bp):
TTTTATATTTATTATATCATTTTAATAATTATAAA
Found at i:2716182 original size:28 final size:26
Alignment explanation
Indices: 2716135--2716187 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
2716125 GGTTTATTTA
2716135 AATTATTATTTAATAATAAAAATAAT
1 AATTATTATTTAATAATAAAAATAAT
2716161 AATT-TTATTTAAATTAATTAAAAATAA
1 AATTATTATTT-AA-TAA-TAAAAATAA
2716188 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 6 0.25
27 3 0.12
28 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTATTATTTAATAATAAAAATAAT
Found at i:2716201 original size:31 final size:31
Alignment explanation
Indices: 2716129--2716241 Score: 79
Period size: 34 Copynumber: 3.4 Consensus size: 31
2716119 CGAATTGGTT
* *
2716129 TATTTAAATTATTATTTAATAATAAAAATAATAATTT
1 TATTTAAATTA--A-TTAAAAATAAAAATAA-AA--A
2716166 TATTTAAATTAATTAAAAATAAAAATAAAAA
1 TATTTAAATTAATTAAAAATAAAAATAAAAA
* *
2716197 TATTTTAA-TAATATAATAAATTACAAGAT-AAAA
1 TATTTAAATTAAT-TAA-AAA-TA-AAAATAAAAA
2716230 T-TTTAAATTAAT
1 TATTTAAATTAAT
2716242 CTATCTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
30 4 0.06
31 10 0.15
32 8 0.12
33 13 0.20
34 19 0.29
35 1 0.02
37 11 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
TATTTAAATTAATTAAAAATAAAAATAAAAA
Found at i:2718517 original size:2 final size:2
Alignment explanation
Indices: 2718505--2718540 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2718495 GATTTGTCAA
2718505 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2718541 CATGTGCGCG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2720247 original size:2 final size:2
Alignment explanation
Indices: 2720240--2720266 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2720230 CAGCCTGTTT
2720240 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 T
2720267 GCGTGGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2720338 original size:15 final size:17
Alignment explanation
Indices: 2720301--2720341 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
2720291 ATTTAAAGAA
2720301 ATAATATTTAATTAATTT
1 ATAAT-TTTAATTAATTT
*
2720319 TTAATTTTAA-T-ATTT
1 ATAATTTTAATTAATTT
2720334 ATAATTTT
1 ATAATTTT
2720342 TTATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 5 0.24
18 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTAATTAATTT
Found at i:2720351 original size:23 final size:24
Alignment explanation
Indices: 2720302--2720348 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2720292 TTTAAAGAAA
2720302 TAATATTTAATTAATTTTTAATTT
1 TAATATTTAATTAATTTTTAATTT
*
2720326 TAATATTT-A-TAATTTTTTATTT
1 TAATATTTAATTAATTTTTAATTT
2720348 T
1 T
2720349 TAAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TAATATTTAATTAATTTTTAATTT
Found at i:2723568 original size:12 final size:11
Alignment explanation
Indices: 2723543--2723567 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2723533 GTCGCTGTTC
2723543 TTTCCTTTTTT
1 TTTCCTTTTTT
2723554 TTTCCTTTTTT
1 TTTCCTTTTTT
2723565 TTT
1 TTT
2723568 TTTTATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCCTTTTTT
Found at i:2724060 original size:17 final size:17
Alignment explanation
Indices: 2724037--2724078 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2724027 TAAATATTAA
* *
2724037 ATTTAAAAAATAATTTT
1 ATTTAAAAAAAAAATTT
*
2724054 TTTTAAAAAAAAAATTT
1 ATTTAAAAAAAAAATTT
2724071 ATTTAAAA
1 ATTTAAAA
2724079 TTACTTCAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAAAAAAAATTT
Found at i:2725911 original size:22 final size:24
Alignment explanation
Indices: 2725886--2725931 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2725876 AACATAATTT
*
2725886 AATTAAT-TTTTAT-AATTTTAAA
1 AATTAATATTTAATAAATTTTAAA
2725908 AATTAATATTTAATAAATTTTAAA
1 AATTAATATTTAATAAATTTTAAA
2725932 TTAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAATATTTAATAAATTTTAAA
Found at i:2725932 original size:22 final size:21
Alignment explanation
Indices: 2725886--2725935 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2725876 AACATAATTT
*
2725886 AATTAATTTTTATAATTTTAAA
1 AATTAATTTTAATAATTTT-AA
2725908 AATTAATATTTAATAAATTTT-A
1 AATTAAT-TTTAAT-AATTTTAA
2725930 AATTAA
1 AATTAA
2725936 AATATCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 14 0.56
23 5 0.20
24 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAATTTTAATAATTTTAA
Found at i:2727639 original size:14 final size:14
Alignment explanation
Indices: 2727620--2727654 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2727610 TTAAAATAAA
2727620 TATTTAAATATATT
1 TATTTAAATATATT
* *
2727634 TATTTAAATTTTTT
1 TATTTAAATATATT
2727648 TATTTAA
1 TATTTAA
2727655 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTAAATATATT
Found at i:2727748 original size:25 final size:24
Alignment explanation
Indices: 2727720--2727771 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
2727710 TTTATTATTA
*
2727720 ATTAAAAAAATTAATAAATTTATAT
1 ATTAAAAAAATTAA-AAATTTAAAT
** *
2727745 ATTAATCAAATTAAATATTTAAAT
1 ATTAAAAAAATTAAAAATTTAAAT
2727769 ATT
1 ATT
2727772 TAAATTCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTAAAAAAATTAAAAATTTAAAT
Found at i:2733016 original size:30 final size:30
Alignment explanation
Indices: 2732980--2733064 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
2732970 ATCTATTATT
*
2732980 AAATATTTTATTATATTTTAATTATTTTTA
1 AAATATTTTATTTTATTTTAATTATTTTTA
* * *
2733010 AAATATTTTAATTTTATTAT-ATAAATTTTA
1 AAATATTTT-ATTTTATTTTAATTATTTTTA
* *
2733040 AAA-AATGTATTTTATTTTAATTATT
1 AAATATTTTATTTTATTTTAATTATT
2733065 ATATTTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 9 0.20
29 7 0.16
30 20 0.45
31 8 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
AAATATTTTATTTTATTTTAATTATTTTTA
Found at i:2733027 original size:11 final size:11
Alignment explanation
Indices: 2732982--2733111 Score: 55
Period size: 10 Copynumber: 12.2 Consensus size: 11
2732972 CTATTATTAA
2732982 ATATTTT-ATT
1 ATATTTTAATT
2732992 ATATTTTAATT
1 ATATTTTAATT
*
2733003 AT-TTTTAA-A
1 ATATTTTAATT
2733012 ATATTTTAATT
1 ATATTTTAATT
* *
2733023 TTATTAT-A-T
1 ATATTTTAATT
*
2733032 AAATTTTAA--
1 ATATTTTAATT
* * *
2733041 AAAATGT-ATT
1 ATATTTTAATT
*
2733051 TTATTTTAATT
1 ATATTTTAATT
2733062 ATTATATTTAAATT
1 A-TAT-TTT-AATT
2733076 ATAATTTATAATT
1 AT-ATTT-TAATT
2733089 ATA-TTTAA-T
1 ATATTTTAATT
*
2733098 ATTATTATAATT
1 A-TATTTTAATT
2733110 AT
1 AT
2733112 GCAATAAATT
Statistics
Matches: 90, Mismatches: 15, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
8 1 0.01
9 14 0.16
10 29 0.32
11 20 0.22
12 6 0.07
13 12 0.13
14 8 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (11 bp):
ATATTTTAATT
Done.