Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 198 of 226
Found at i:59499303 original size:20 final size:19
Alignment explanation
Indices: 59499280--59499318 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
59499270 TCTATATTAT
59499280 TATATTATTAATATTATTTA
1 TATATTATTAATA-TATTTA
59499300 TATATTATTAATATATTTA
1 TATATTATTAATATATTTA
59499319 ATTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTATTAATATATTTA
Found at i:59499304 original size:11 final size:11
Alignment explanation
Indices: 59499280--59499329 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
59499270 TCTATATTAT
59499280 TATATTA-TTA
1 TATATTATTTA
59499290 -ATATTATTTA
1 TATATTATTTA
*
59499300 TATATTATTAA
1 TATATTATTTA
59499311 TATATTTAATTTA
1 TATA-TT-ATTTA
59499324 TATATT
1 TATATT
59499330 TAAATGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 6 0.18
10 3 0.09
11 13 0.38
12 4 0.12
13 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTATTTA
Found at i:59499329 original size:13 final size:13
Alignment explanation
Indices: 59499295--59499332 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
59499285 TATTAATATT
59499295 ATTTATATA-TT-
1 ATTTATATATTTA
*
59499306 ATTAATATATTTA
1 ATTTATATATTTA
59499319 ATTTATATATTTA
1 ATTTATATATTTA
59499332 A
1 A
59499333 ATGATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTATATATTTA
Found at i:59499344 original size:24 final size:24
Alignment explanation
Indices: 59499295--59499344 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
59499285 TATTAATATT
* **
59499295 ATTTATATATTATTAATATATTTA
1 ATTTATATATTATAAATATAAATA
59499319 ATTTATATATT-TAAATGATAAATA
1 ATTTATATATTATAAAT-ATAAATA
59499343 AT
1 AT
59499345 AAAATAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTATATATTATAAATATAAATA
Found at i:59499357 original size:15 final size:15
Alignment explanation
Indices: 59499339--59499367 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59499329 TTAAATGATA
59499339 AATAATAAAATAAAC
1 AATAATAAAATAAAC
59499354 AATAATAAAATAAA
1 AATAATAAAATAAA
59499368 AAACTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAATAAAATAAAC
Found at i:59499748 original size:15 final size:16
Alignment explanation
Indices: 59499723--59499755 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
59499713 GCCGAGGCGG
*
59499723 GCCCTTGCCCTGCCCT
1 GCCCTTGCCCTGCACT
59499739 GCCC-TGCCCTGCACT
1 GCCCTTGCCCTGCACT
59499754 GC
1 GC
59499756 ACAGCACTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.03, C:0.55, G:0.21, T:0.21
Consensus pattern (16 bp):
GCCCTTGCCCTGCACT
Found at i:59503149 original size:22 final size:22
Alignment explanation
Indices: 59503107--59503149 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59503097 TGCCGTTGTT
*
59503107 TTGCTACCATTTTGCTATTTTA
1 TTGCTACCATTTTGATATTTTA
* *
59503129 TTGCTACTATTTTGATGTTTT
1 TTGCTACCATTTTGATATTTT
59503150 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTGATATTTTA
Found at i:59503610 original size:30 final size:31
Alignment explanation
Indices: 59503558--59503617 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
59503548 TAAGTTTTTA
59503558 TACTTTTCATAAATTTAAAATTTA-GTCCATT
1 TACTTTTCA-AAATTTAAAATTTAGGTCCATT
59503589 TACTTTTC-AAATTTCAAAATTTAGGTCCA
1 TACTTTTCAAAATTT-AAAATTTAGGTCCA
59503618 ACTATTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 6 0.22
30 8 0.30
31 13 0.48
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (31 bp):
TACTTTTCAAAATTTAAAATTTAGGTCCATT
Found at i:59508665 original size:19 final size:19
Alignment explanation
Indices: 59508627--59508665 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59508617 TTAATTAAAT
*
59508627 AAAAGAAATAAAAGATAGA
1 AAAAGAAATAAAAGACAGA
59508646 AAAAGAGAATAAAA-ACAGA
1 AAAAGA-AATAAAAGACAGA
59508665 A
1 A
59508666 TAGCAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAGAAATAAAAGACAGA
Found at i:59508721 original size:26 final size:27
Alignment explanation
Indices: 59508670--59508726 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
59508660 ACAGAATAGC
* *
59508670 AAAACGAAAATAGGGTAGAAAGGAAAG
1 AAAAAGAAAATAGGGAAGAAAGGAAAG
59508697 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAATAGGGAA-GAAAGGAAAG
59508723 AAAA
1 AAAA
59508727 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAATAGGGAAGAAAGGAAAG
Found at i:59509752 original size:41 final size:37
Alignment explanation
Indices: 59509704--59509806 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 37
59509694 TCGAACTTGA
59509704 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
59509744 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
59509782 GCCGATGAGACACTGGGTGTCAACT
1 GTCGATGAGACACTGGGTGTCAACT
59509807 ATTGCTTCGA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 19 0.39
38 11 0.22
40 2 0.04
41 17 0.35
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:59527585 original size:3 final size:3
Alignment explanation
Indices: 59527577--59527616 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
59527567 TGCCAAAATC
59527577 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
59527617 TTTTGCATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:59530459 original size:26 final size:26
Alignment explanation
Indices: 59530430--59530480 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
59530420 ATTGTCATAC
59530430 AAGAGAATTTAAAACAGTGTTGTACT
1 AAGAGAATTTAAAACAGTGTTGTACT
59530456 AAGAGAATTTAAAACAGTGTTGTAC
1 AAGAGAATTTAAAACAGTGTTGTAC
59530481 AAGCTTGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (26 bp):
AAGAGAATTTAAAACAGTGTTGTACT
Found at i:59531840 original size:7 final size:7
Alignment explanation
Indices: 59531828--59531852 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59531818 AGATACACGA
59531828 GAAATGG
1 GAAATGG
59531835 GAAATGG
1 GAAATGG
59531842 GAAATGG
1 GAAATGG
59531849 GAAA
1 GAAA
59531853 CGCGAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (7 bp):
GAAATGG
Found at i:59531859 original size:14 final size:14
Alignment explanation
Indices: 59531828--59531861 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
59531818 AGATACACGA
* *
59531828 GAAATGGGAAATGG
1 GAAATGGGAAACGC
59531842 GAAATGGGAAACGC
1 GAAATGGGAAACGC
59531856 GAAATG
1 GAAATG
59531862 TAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.38, T:0.12
Consensus pattern (14 bp):
GAAATGGGAAACGC
Found at i:59544421 original size:19 final size:18
Alignment explanation
Indices: 59544377--59544421 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
59544367 TTTTTTTTAT
*
59544377 AATGC-TTTTGTCTCAAA
1 AATGCTTTTTGTCCCAAA
*
59544394 AGTGCTTTTTGTCCCAAA
1 AATGCTTTTTGTCCCAAA
59544412 AATGCTTTTT
1 AATGCTTTTT
59544422 CGAAGCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (18 bp):
AATGCTTTTTGTCCCAAA
Found at i:59544828 original size:143 final size:140
Alignment explanation
Indices: 59544487--59544859 Score: 434
Period size: 139 Copynumber: 2.6 Consensus size: 140
59544477 TCCCATCTTT
* * * *
59544487 ACCAGGCATATATCCTGCCTCCTCCATATGTGGAATAAGCAACTCTACAACCCCATTTGATCATT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
* * * *
59544552 TTCAGTAATTCAATTCCGTTTCTT-ATGCTTCTCTTCTCTTCAAGTCCCACTTTCAAGATCATGT
66 TTCAGTAATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGT
**
59544616 ATCAATGTAA
131 ATCAATCAAA
* * * *
59544626 ACCAGGCATTTACCCTGTTTCTTCCATATGTAGAACAAGCAACT-TAACAACCCCATTTGATCAT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCT-ACAACCCCATTTGATCAT
* * * *
59544690 ATTCAGTACCTT-ACTTTAGTTTCTTCA-GCTTCTCTCCT-TTGAAGGCCTA-TCTTCAAGATCA
65 ATTCAGTA-ATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACT-TTCAAGATCA
59544751 TGTATCAAACAATCAAA
128 TGTAT----CAATCAAA
* * *
59544768 ACCAGGCATGTATCCTAGCTTCTTCCATATTTAGAATAAGCAACTCTATAACCCCATTTGATCAT
1 ACCAGGCATATATCCT-GCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCAT
*
59544833 GTTCAGTAATTCACTTCAGTTTCTTCA
65 ATTCAGTAATTCACTTCAGTTTCTTCA
59544860 AATCCCAACT
Statistics
Matches: 196, Mismatches: 27, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
137 1 0.01
138 24 0.12
139 82 0.42
140 3 0.02
142 22 0.11
143 63 0.32
144 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (140 bp):
ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
TTCAGTAATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGT
ATCAATCAAA
Found at i:59548475 original size:18 final size:18
Alignment explanation
Indices: 59548402--59548476 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
59548392 TACGACCGTT
59548402 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
59548420 T-CTGGTACTATTCACGTA
1 TAC-GGTACTATTCACGTA
* *
59548438 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
59548456 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
59548474 TAC
1 TAC
59548477 AGTAGTTGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 1 0.02
18 49 0.98
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:59553907 original size:42 final size:42
Alignment explanation
Indices: 59553859--59554230 Score: 390
Period size: 42 Copynumber: 8.5 Consensus size: 42
59553849 AGCCCCACAG
59553859 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* * *
59553901 TTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* **
59553943 TTAATCCCACCTCCATTAGGATTTATATAAGCATATCTTTTTAAATTTTCAT
1 TTAATCCCACCTCAATTAGG----AT-T-----TATCTTTTTAGCTTTTCAT
* * *
59553995 TTAATCTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* *
59554037 TTAATCCCAACTCAATTAGGATTTATGTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
*
59554079 TTAATCCCA-C-C-ATTGAGGATTTATGTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATT-AGGATTTATCTTTTTAGCTTTTCAT
* * *
59554119 TTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGTTTTTCTT
1 TTAATCCCACCTCAATT---AGGATTTATCTTTTTAGCTTTTCAT
* * *
59554164 TTAATCCCACCTCAATTAGGAGGACTTATGTTTTTAGTTTTTCAT
1 TTAATCCCACCTCAATT---AGGATTTATCTTTTTAGCTTTTCAT
* *
59554209 TTAATCCCGCCTGAATTAGGAT
1 TTAATCCCACCTCAATTAGGAT
59554231 ACTTCTGTTC
Statistics
Matches: 288, Mismatches: 26, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.01
40 35 0.12
41 2 0.01
42 124 0.43
43 3 0.01
45 82 0.28
46 2 0.01
47 2 0.01
48 2 0.01
52 33 0.11
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.47
Consensus pattern (42 bp):
TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
Found at i:59554043 original size:94 final size:94
Alignment explanation
Indices: 59553882--59554062 Score: 274
Period size: 94 Copynumber: 1.9 Consensus size: 94
59553872 AATTAGGATT
** * *
59553882 TATCTTTTTAGCTTTTCATTTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTTTTAA
1 TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
* *
59553947 TCCCACCTCCATTAGGATTTATATAAGCA
66 TCCCAACTCAATTAGGATTTATATAAGCA
* *
59553976 TATCTTTTTAAATTTTCATTTAAT-CTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCATTTA
1 TATCTTTTTAAATTTTCATTTAATCCT-ACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTA
59554040 ATCCCAACTCAATTAGGATTTAT
65 ATCCCAACTCAATTAGGATTTAT
59554063 GTTTTTAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 2 0.03
94 76 0.97
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (94 bp):
TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
TCCCAACTCAATTAGGATTTATATAAGCA
Found at i:59554122 original size:136 final size:134
Alignment explanation
Indices: 59553859--59554216 Score: 378
Period size: 136 Copynumber: 2.7 Consensus size: 134
59553849 AGCCCCACAG
* * *
59553859 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCATTTAATCCTACCTCAATTAGGATT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
* *
59553924 TATCATTTTAGCTTTTCTTTTAATCCCACCTCCATTAGGATTTATATAAGCATATCTTTTTAAAT
66 TATCATTTTAGCTTTTCATTTAATCCCA-C-CCATTAGGATTTATATAAGCATATCTATTTAAAT
59553989 TTTCAT
129 TTTCAT
* *
59553995 TTAATCTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCATTTAATCCCAACTCAATTAGGATT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
** **
59554060 TATGTTTTTAGCTTTTCATTTAATCCCA-CCATTGAGGA-TT-TAT--G----T-T-TTTAGCTT
66 TATCATTTTAGCTTTTCATTTAATCCCACCCATT-AGGATTTATATAAGCATATCTATTTAAATT
59554114 TTCAT
130 TTCAT
** * * *
59554119 TTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGTTTTTCTTTTAATCCCACCTCAATTAGG
1 TTAATCCCACCTCAATT---AGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATT---
* ** *
59554184 AGGACTTATGTTTTTAGTTTTTCATTTAATCCC
60 AGGATTTATCATTTTAGCTTTTCATTTAATCCC
59554217 GCCTGAATTA
Statistics
Matches: 198, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
124 27 0.14
125 1 0.01
126 1 0.01
127 38 0.19
130 32 0.16
132 3 0.02
133 7 0.04
134 4 0.02
136 85 0.43
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (134 bp):
TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
TATCATTTTAGCTTTTCATTTAATCCCACCCATTAGGATTTATATAAGCATATCTATTTAAATTT
TCAT
Found at i:59554161 original size:45 final size:43
Alignment explanation
Indices: 59553988--59554230 Score: 318
Period size: 45 Copynumber: 5.7 Consensus size: 43
59553978 TCTTTTTAAA
* **
59553988 TTTTCATTTAATCTCACCTCAATT-AGGATTTACCTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
* *
59554030 TTTTCATTTAATCCCAACTCAATT-AGGATTTATGTTTTTAGC
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
*
59554072 TTTTCATTTAATCCCA-C-C-ATTGAGGATTTATGTTTTTAGC
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
59554112 TTTTCATTTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATT--GAGGATTTATGTTTTTAGT
* *
59554157 TTTTCTTTTAATCCCACCTCAATTAGGAGGACTTATGTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATT--GAGGATTTATGTTTTTAGT
* *
59554202 TTTTCATTTAATCCCGCCTGAATT-AGGAT
1 TTTTCATTTAATCCCACCTCAATTGAGGAT
59554231 ACTTCTGTTC
Statistics
Matches: 183, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
39 3 0.02
40 35 0.19
41 2 0.01
42 58 0.32
43 3 0.02
45 82 0.45
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (43 bp):
TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
Found at i:59556701 original size:23 final size:22
Alignment explanation
Indices: 59556659--59556701 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
59556649 ATTTTAACAA
*
59556659 AAATTTAATTATTAAAATATAT
1 AAATTTAATTATAAAAATATAT
59556681 AAATATTAA-TATAAAAGATAT
1 AAAT-TTAATTATAAAA-ATAT
59556702 TCTTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:59559833 original size:43 final size:42
Alignment explanation
Indices: 59559708--59559877 Score: 241
Period size: 42 Copynumber: 4.0 Consensus size: 42
59559698 ATGTCACCCG
*
59559708 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTC
1 AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* *
59559750 AATTAAGATTTATCTTTTTAGCTTTTCATTTAATCCCACCTC
1 AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* *
59559792 AATTAGGATTTATCTTTTTATTTTTTTCATTTAATCCCACCTA
1 AATTAGGATTTATCTTTTTA-GTTTTTCATTTAATCCCACCTC
* *
59559835 AATTAGGAGGATTTATGTTTTTAGTTTTTCATTTAATCTCACC
1 AATT---AGGATTTATCTTTTTAGTTTTTCATTTAATCCCACC
59559878 GAATCAATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 58 0.51
43 23 0.20
45 18 0.16
46 15 0.13
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (42 bp):
AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
Found at i:59559888 original size:85 final size:83
Alignment explanation
Indices: 59559714--59559877 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 83
59559704 CCCGAATTAG
*
59559714 GATTTATCTTTTTATTTTTTCATTTAATCCCACCTCAATTAAGATTTATCTTTTTAGCTTTTCAT
1 GATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAAGATTTATCTTTTTAGCTTTTCAT
*
59559779 TTAATCCCACCTCAATTA
66 TTAATCCCACCTCAATCA
* *
59559797 GGATTTATCTTTTTATTTTTTTCATTTAATCCCACCTAAATTAGGAGGATTTATGTTTTTAGTTT
1 -GATTTATCTTTTTA-TTTTTTCATTTAATCCCACCTAAATTA--A-GATTTATCTTTTTAGCTT
*
59559862 TTCATTTAATCTCACC
61 TTCATTTAATCCCACC
59559878 GAATCAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
84 14 0.19
85 26 0.36
87 1 0.01
88 31 0.43
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (83 bp):
GATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAAGATTTATCTTTTTAGCTTTTCAT
TTAATCCCACCTCAATCA
Found at i:59565383 original size:19 final size:19
Alignment explanation
Indices: 59565359--59565397 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
59565349 TATTATTAAT
*
59565359 ACATTTATAATTATAATAA
1 ACATTTATAATTAAAATAA
*
59565378 ACATTTATTATTAAAATAA
1 ACATTTATAATTAAAATAA
59565397 A
1 A
59565398 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTATAATTAAAATAA
Found at i:59565643 original size:17 final size:18
Alignment explanation
Indices: 59565613--59565648 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
59565603 TAAATTTACC
59565613 AGGAACTCTTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
59565631 AGGAACT-TTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
59565648 A
1 A
59565649 ATAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (18 bp):
AGGAACTCTTTTTTGAAG
Found at i:59568625 original size:21 final size:22
Alignment explanation
Indices: 59568588--59568631 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
59568578 TTCGTATTTT
59568588 ACAAATTAAATACAAAA-TAAA
1 ACAAATTAAATACAAAATTAAA
*
59568609 ACAAATTAAA-ATTAAAATTAAA
1 ACAAATTAAATA-CAAAATTAAA
59568631 A
1 A
59568632 TTATTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATTAAATACAAAATTAAA
Found at i:59577398 original size:18 final size:19
Alignment explanation
Indices: 59577370--59577407 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
59577360 TACTAAGAAA
59577370 AATTCAAAATAAAAAAAAT
1 AATTCAAAATAAAAAAAAT
*
59577389 AATT-AAAATAAACAAAAT
1 AATTCAAAATAAAAAAAAT
59577407 A
1 A
59577408 TAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AATTCAAAATAAAAAAAAT
Found at i:59582335 original size:6 final size:6
Alignment explanation
Indices: 59582324--59582372 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
59582314 TCTATTTATT
*
59582324 TATGTA TATGTA TATGCA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
59582372 T
1 T
59582373 CTATCCTGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (6 bp):
TATGTA
Found at i:59583422 original size:11 final size:11
Alignment explanation
Indices: 59583406--59583430 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59583396 AATAAAATAA
59583406 AATAATTATAT
1 AATAATTATAT
59583417 AATAATTATAT
1 AATAATTATAT
59583428 AAT
1 AAT
59583431 TAAAAATAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTATAT
Found at i:59589239 original size:16 final size:17
Alignment explanation
Indices: 59589218--59589263 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
59589208 GGTAAATAGT
59589218 TAAAATAATTTAAAT-A
1 TAAAATAATTTAAATCA
* *
59589234 TAAAATAATTAAAATCT
1 TAAAATAATTTAAATCA
*
59589251 TAAAATGATTTAA
1 TAAAATAATTTAA
59589264 TTATGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAATAATTTAAATCA
Found at i:59590216 original size:40 final size:41
Alignment explanation
Indices: 59590128--59590218 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
59590118 CATTTTTCCC
* **
59590128 GAAATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAG
1 GAAATCGCGTCCACGTCAGCGCGATG-CAGGCTACGTGGAAG
*
59590170 GAAATCGCGTCCACGTCAGCGCGA-G-ATGCTAACGTGGAAG
1 GAAATCGCGTCCACGTCAGCGCGATGCAGGCT-ACGTGGAAG
59590210 GAAATCGCG
1 GAAATCGCG
59590219 CTCTCAAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 3 0.07
40 16 0.36
41 1 0.02
42 24 0.55
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.16
Consensus pattern (41 bp):
GAAATCGCGTCCACGTCAGCGCGATGCAGGCTACGTGGAAG
Found at i:59591707 original size:17 final size:17
Alignment explanation
Indices: 59591685--59591718 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59591675 ATGTAATTTT
59591685 ATTATTAAATTTTTAAA
1 ATTATTAAATTTTTAAA
59591702 ATTATTAAATTTTTAAA
1 ATTATTAAATTTTTAAA
59591719 GGGTTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTAAATTTTTAAA
Found at i:59597207 original size:21 final size:21
Alignment explanation
Indices: 59597166--59597209 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59597156 CGAACCTAAT
*
59597166 TAAATAAAAAGGATAATTAAA
1 TAAATAAAAAGGATAAATAAA
*
59597187 TAAAT-AAAATGATACAATAAA
1 TAAATAAAAAGGATA-AATAAA
59597208 TA
1 TA
59597210 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAATAAAAAGGATAAATAAA
Found at i:59597908 original size:5 final size:5
Alignment explanation
Indices: 59597898--59597924 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59597888 TTTTGTCCCG
59597898 GGCCC GGCCC GGCCC GGCCC GGCCC GG
1 GGCCC GGCCC GGCCC GGCCC GGCCC GG
59597925 ATCTAATTAA
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:0.00, C:0.56, G:0.44, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:59597998 original size:20 final size:21
Alignment explanation
Indices: 59597973--59598021 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
59597963 ATTACATTTA
59597973 CATTTCCCAATTCCC-CTCCC
1 CATTTCCCAATTCCCACTCCC
* * *
59597993 CATTTCCCATTTCCCATTTCC
1 CATTTCCCAATTCCCACTCCC
59598014 CATTTCCC
1 CATTTCCC
59598022 GACCCCGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.14, C:0.49, G:0.00, T:0.37
Consensus pattern (21 bp):
CATTTCCCAATTCCCACTCCC
Found at i:59598001 original size:7 final size:7
Alignment explanation
Indices: 59597973--59598021 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
59597963 ATTACATTTA
59597973 CATTTCC
1 CATTTCC
*
59597980 CAATTCC
1 CATTTCC
* *
59597987 C-CTCCC
1 CATTTCC
59597993 CATTTCC
1 CATTTCC
59598000 CATTTCC
1 CATTTCC
59598007 CATTTCC
1 CATTTCC
59598014 CATTTCC
1 CATTTCC
59598021 C
1 C
59598022 GACCCCGTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
6 4 0.11
7 32 0.89
ACGTcount: A:0.14, C:0.49, G:0.00, T:0.37
Consensus pattern (7 bp):
CATTTCC
Found at i:59599313 original size:23 final size:23
Alignment explanation
Indices: 59599287--59599341 Score: 92
Period size: 25 Copynumber: 2.3 Consensus size: 23
59599277 TTGATATATG
59599287 TATATGTTAGTTTCGAATATGTA
1 TATATGTTAGTTTCGAATATGTA
59599310 TATATGTATTAGTTTCGAATATGTA
1 TATATG--TTAGTTTCGAATATGTA
59599335 TATATGT
1 TATATGT
59599342 ACATGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.23
25 23 0.77
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (23 bp):
TATATGTTAGTTTCGAATATGTA
Found at i:59599327 original size:25 final size:25
Alignment explanation
Indices: 59599293--59599342 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
59599283 TATGTATATG
59599293 TTAGTTTCGAATATGTATATATGTA
1 TTAGTTTCGAATATGTATATATGTA
59599318 TTAGTTTCGAATATGTATATATGTA
1 TTAGTTTCGAATATGTATATATGTA
59599343 CATGTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
TTAGTTTCGAATATGTATATATGTA
Found at i:59600119 original size:13 final size:13
Alignment explanation
Indices: 59600101--59600222 Score: 119
Period size: 13 Copynumber: 9.7 Consensus size: 13
59600091 ATTTTTAATG
59600101 TAATATACTGTTT
1 TAATATACTGTTT
*
59600114 TAATATACTGTTA
1 TAATATACTGTTT
*
59600127 TAA-A-A-T-TTG
1 TAATATACTGTTT
**
59600136 TAATATTTTGTTT
1 TAATATACTGTTT
59600149 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
59600163 AAATATATTGTTT
1 TAATATACTGTTT
*
59600176 TAATATAATGTTT
1 TAATATACTGTTT
59600189 TAATATACTGTTT
1 TAATATACTGTTT
* *
59600202 TAATATATTGTTA
1 TAATATACTGTTT
59600215 TAA-ATACT
1 TAATATACT
59600223 ACACCTTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 1 0.01
12 6 0.07
13 65 0.72
14 11 0.12
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:59600138 original size:35 final size:37
Alignment explanation
Indices: 59600099--59600212 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 37
59600089 TAATTTTTAA
*
59600099 TGTAATATACTGTTTTAATATACTGTTATAAA-AT-T
1 TGTAATATAATGTTTTAATATACTGTTATAAATATAT
**
59600134 TGTAATATTTTGTTTTAATATACTGTTATAAATATAT
1 TGTAATATAATGTTTTAATATACTGTTATAAATATAT
*
59600171 TGTTTTAATATAATGTTTTAATATACTGTT-TTAATATAT
1 TG---TAATATAATGTTTTAATATACTGTTATAAATATAT
59600210 TGT
1 TGT
59600213 TATAAATACT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
35 30 0.43
36 3 0.04
37 3 0.04
39 10 0.14
40 23 0.33
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (37 bp):
TGTAATATAATGTTTTAATATACTGTTATAAATATAT
Found at i:59600310 original size:81 final size:81
Alignment explanation
Indices: 59600212--59600372 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
59600202 TAATATATTG
*
59600212 TTATAAATACTACACCTTAATTTTTGA-TATAATATACTGTTTTAATATACTATTATAAAATTTG
1 TTATAAATACTACACCTTAATTATT-ATTATAATATACTGTTTTAATATACTATTATAAAATTTG
*
59600276 TAATATACTGTTATAAC
65 TAATATAATGTTATAAC
* * *
59600293 TTATAAATACTACACCTTAATTATTATTGTAATATACTGTTTTAATATATTGTTATAAAATTTGT
1 TTATAAATACTACACCTTAATTATTATTATAATATACTGTTTTAATATACTATTATAAAATTTGT
59600358 AATATAATGTTATAA
66 AATATAATGTTATAA
59600373 ATATAATATT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 1 0.01
81 73 0.99
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (81 bp):
TTATAAATACTACACCTTAATTATTATTATAATATACTGTTTTAATATACTATTATAAAATTTGT
AATATAATGTTATAAC
Found at i:59601473 original size:24 final size:25
Alignment explanation
Indices: 59601428--59601482 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
59601418 TGTTAAATAT
59601428 ATATATTTGATTAAAAAATAAAAAA
1 ATATATTTGATTAAAAAATAAAAAA
*
59601453 ATATATTTGATT-AAAAATAAAAAT
1 ATATATTTGATTAAAAAATAAAAAA
59601477 ATATAT
1 ATATAT
59601483 ATTTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATTTGATTAAAAAATAAAAAA
Found at i:59601488 original size:22 final size:23
Alignment explanation
Indices: 59601441--59601488 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
59601431 TATTTGATTA
*
59601441 AAAAATAAAAAAATATATTTGATT
1 AAAAATAAAAAAATATATAT-ATT
*
59601465 AAAAATAAAAATATATATAT-TT
1 AAAAATAAAAAAATATATATATT
59601487 AA
1 AA
59601489 TATATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
24 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATAAAAAAATATATATATT
Found at i:59602455 original size:3 final size:3
Alignment explanation
Indices: 59602447--59602471 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59602437 TCTATGCAGA
59602447 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
59602472 CAAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:59607470 original size:31 final size:31
Alignment explanation
Indices: 59607404--59607470 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
59607394 AACAGTCTAG
** * * *
59607404 TGACTTAAATAAAAACTTTTGAATATTTTAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
59607435 TGACTTAAATAAAAACTTTCAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
59607466 TGACT
1 TGACT
59607471 AACTTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAA
Found at i:59607751 original size:6 final size:6
Alignment explanation
Indices: 59607740--59607765 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59607730 TCAATAAAAA
59607740 GCCTCG GCCTCG GCCTCG GCCTCG GC
1 GCCTCG GCCTCG GCCTCG GCCTCG GC
59607766 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.35, T:0.15
Consensus pattern (6 bp):
GCCTCG
Found at i:59611657 original size:39 final size:41
Alignment explanation
Indices: 59611614--59611694 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 41
59611604 CGAATATAAT
*
59611614 AAATATATATTTTTA-ATTTTTAATTTT-AAAATACTTTTA
1 AAATAAATATTTTTATATTTTTAATTTTAAAAATACTTTTA
* * * *
59611653 AAATAAATTTTTTTATTTTTTTTATTTTAAAAATATTTTTA
1 AAATAAATATTTTTATATTTTTAATTTTAAAAATACTTTTA
59611694 A
1 A
59611695 TGTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.37
40 10 0.29
41 12 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (41 bp):
AAATAAATATTTTTATATTTTTAATTTTAAAAATACTTTTA
Found at i:59613026 original size:36 final size:36
Alignment explanation
Indices: 59612977--59613048 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
59612967 CCAACTATAC
**
59612977 TCATTTTTGTAGGTTAATAGTAGAACAATGCTTTTA
1 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
59613013 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
1 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
59613049 ACAAGTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (36 bp):
TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
Found at i:59627860 original size:48 final size:48
Alignment explanation
Indices: 59627797--59627893 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
59627787 CTTCCTAAAA
59627797 GTGTTTTTTTTTTTCCAAAAGCACTTTTGAGAAACATTCCTAAACTAT
1 GTGTTTTTTTTTTTCCAAAAGCACTTTTGAGAAACATTCCTAAACTAT
59627845 GTGTTTTTTTTTTTCCAAAAGCACTTTTGAGAAACATTCCTAAACTAT
1 GTGTTTTTTTTTTTCCAAAAGCACTTTTGAGAAACATTCCTAAACTAT
59627893 G
1 G
59627894 ACCAAATGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.43
Consensus pattern (48 bp):
GTGTTTTTTTTTTTCCAAAAGCACTTTTGAGAAACATTCCTAAACTAT
Found at i:59628185 original size:28 final size:28
Alignment explanation
Indices: 59628149--59628203 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
59628139 AATTTATTGC
* * *
59628149 ATTGTAGTGACATCTAATAATGCATAAG
1 ATTGCAGTGACATCAAATAATACATAAG
* *
59628177 ATTGCAGTGGCATGAAATAATACATAA
1 ATTGCAGTGACATCAAATAATACATAA
59628204 AGTAGTGTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (28 bp):
ATTGCAGTGACATCAAATAATACATAAG
Found at i:59628384 original size:5 final size:6
Alignment explanation
Indices: 59628366--59628393 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
59628356 TTTGTCTATA
59628366 TTATTT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTAT
59628394 GTAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:59633747 original size:13 final size:13
Alignment explanation
Indices: 59633729--59633764 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
59633719 GTACAGTATG
59633729 ATAAAAATTTCGT
1 ATAAAAATTTCGT
59633742 ATAAAAATTTCGT
1 ATAAAAATTTCGT
59633755 -TAAGAAATTT
1 ATAA-AAATTT
59633765 TACCGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (13 bp):
ATAAAAATTTCGT
Found at i:59634053 original size:25 final size:25
Alignment explanation
Indices: 59634018--59634075 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
59634008 TATATATTAA
*
59634018 ATATATATTTTATTTTTAATAAAAT
1 ATATATTTTTTATTTTTAATAAAAT
59634043 ATATATTTTTTATTTTTAATAAAAT
1 ATATATTTTTTATTTTTAATAAAAT
59634068 ATATATTT
1 ATATATTT
59634076 AATATGGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATATTTTTTATTTTTAATAAAAT
Found at i:59635317 original size:25 final size:25
Alignment explanation
Indices: 59635289--59635354 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
59635279 CTGATATTTA
*
59635289 GCTCTCACGAGCTTCCCAATTAATG
1 GCTCTCATGAGCTTCCCAATTAATG
* * *
59635314 GCTCTCTTGAGCTTCCCGATTTATG
1 GCTCTCATGAGCTTCCCAATTAATG
*
59635339 GCTCACATGAGCTTCC
1 GCTCTCATGAGCTTCC
59635355 TGATGTACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCAATTAATG
Found at i:59635388 original size:25 final size:24
Alignment explanation
Indices: 59635340--59635430 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 24
59635330 CGATTTATGG
*
59635340 CTCACATGAGCTTC-CTGATGTACAA
1 CTCACATGAGCTTCTC-G-TTTACAA
*** *
59635365 CTCGGTTGAGCTTCTCGTTATACAG
1 CTCACATGAGCTTCTCGTT-TACAA
*
59635390 CTCACATGAGCTTCTCGTTTACATG
1 CTCACATGAGCTTCTCGTTTACA-A
*
59635415 CTCATATGAGCATTCT
1 CTCACATGAGC-TTCT
59635431 TGAATATGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
24 5 0.09
25 43 0.81
26 5 0.09
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (24 bp):
CTCACATGAGCTTCTCGTTTACAA
Found at i:59648062 original size:30 final size:31
Alignment explanation
Indices: 59648008--59648067 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
59647998 AAACCTTTTA
*
59648008 TTTTCCCCCAAAATTTTTACTCTC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCTCTTCCCAC
* **
59648038 TTTTCCCCTAAAACTTTTGTTCTCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCTCTTCCCA
59648068 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.37, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCTCTTCCCAC
Found at i:59648179 original size:16 final size:16
Alignment explanation
Indices: 59648160--59648199 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
59648150 CTTTCCCTCT
59648160 AACTTTTATTCCCCAA
1 AACTTTTATTCCCCAA
* * *
59648176 AACTTTTTTTTCCCTA
1 AACTTTTATTCCCCAA
59648192 AACTTTTA
1 AACTTTTA
59648200 CTTCTCACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (16 bp):
AACTTTTATTCCCCAA
Found at i:59650756 original size:18 final size:18
Alignment explanation
Indices: 59650735--59650792 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
59650725 AAATTTATTA
59650735 TTTTATAAAATTTTAATT
1 TTTTATAAAATTTTAATT
* *
59650753 TTTTATATATTTTTAGAGTT
1 TTTTATAAAATTTTA-A-TT
59650773 TTTT-T-AAATTTATAATT
1 TTTTATAAAATTT-TAATT
59650790 TTT
1 TTT
59650793 GTTTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 5 0.15
18 18 0.55
19 4 0.12
20 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTATAAAATTTTAATT
Found at i:59650838 original size:18 final size:20
Alignment explanation
Indices: 59650800--59650837 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59650790 TTTGTTTAAA
*
59650800 ATAAAAATTTTAGAATTTTT
1 ATAAATATTTTAGAATTTTT
59650820 ATAAATATTTT-GAATTTT
1 ATAAATATTTTAGAATTTT
59650838 AAAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAGAATTTTT
Found at i:59650843 original size:18 final size:18
Alignment explanation
Indices: 59650801--59650844 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
59650791 TTGTTTAAAA
59650801 TAAAAATTTTAGAATTTT
1 TAAAAATTTTAGAATTTT
59650819 TATAAATATTTT-GAA-TTT
1 TA-AAA-ATTTTAGAATTTT
59650837 TAAAAATT
1 TAAAAATT
59650845 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 7 0.29
19 6 0.25
20 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TAAAAATTTTAGAATTTT
Found at i:59650856 original size:19 final size:18
Alignment explanation
Indices: 59650814--59650856 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
59650804 AAATTTTAGA
* *
59650814 ATTTTTATAAATATTTTG
1 ATTTTTAAAAATACTTTG
*
59650832 AATTTTAAAAATTACTTTG
1 ATTTTTAAAAA-TACTTTG
59650851 ATTTTT
1 ATTTTT
59650857 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTTTAAAAATACTTTG
Found at i:59655276 original size:24 final size:24
Alignment explanation
Indices: 59655244--59655290 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
59655234 GACAAAAAAA
59655244 AATGTTGTATGTAAATAAATGATG
1 AATGTTGTATGTAAATAAATGATG
*
59655268 AATGTTGTATTTAAATAAATGAT
1 AATGTTGTATGTAAATAAATGAT
59655291 CTCGGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (24 bp):
AATGTTGTATGTAAATAAATGATG
Found at i:59658154 original size:12 final size:12
Alignment explanation
Indices: 59658134--59658174 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
59658124 GCCAGAACCA
*
59658134 GAGCTGGAGCTG
1 GAGCCGGAGCTG
*
59658146 GAGCCGGAGCCG
1 GAGCCGGAGCTG
*
59658158 GATCCGGAGCTG
1 GAGCCGGAGCTG
59658170 GAGCC
1 GAGCC
59658175 ACTGCTTCAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.27, G:0.46, T:0.10
Consensus pattern (12 bp):
GAGCCGGAGCTG
Found at i:59659317 original size:11 final size:10
Alignment explanation
Indices: 59659270--59659317 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
59659260 AAAAAATTAG
*
59659270 GGAAAAAAGA
1 GGAAAGAAGA
59659280 GGGAAAGAAGA
1 -GGAAAGAAGA
*
59659291 GGAAAGATGA
1 GGAAAGAAGA
59659301 -GAAAGAAGAA
1 GGAAAGAAG-A
59659311 GGAAAGA
1 GGAAAGA
59659318 TATGCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 7 0.22
10 10 0.31
11 15 0.47
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (10 bp):
GGAAAGAAGA
Found at i:59663740 original size:228 final size:233
Alignment explanation
Indices: 59663326--59663751 Score: 535
Period size: 228 Copynumber: 1.8 Consensus size: 233
59663316 GGAGGGGCAG
* *
59663326 AGTGCTTGTGAAACACAGCCAAAAGAAAAAGGAGGAGGGGGGGAAGGGGACGAAGCATAGAAATC
1 AGTGCTTGAGAAACACAGCCAAAAGAAAAA-GAGGAGGGAGGGAA-GGGA-G-AGCATAGAAATC
* *
59663391 ACCTACGTTGCTGGGGCTCTTCATTTTTGTTGAAGCATGTGTCCAGACACTCATATGAGACACAC
62 ACCTACGTTGCTGGGGCTCTTCAGTTTTGTTGAAGCATGCGTCCAGACACTCATATGAGACACAC
** * * * *
59663456 GTATACTAGATATGACCTCCAATGAGTCTCCAGATGCATGAAAAAACTTAAAAAAGACTAATCAT
127 AAATACAAGATATAACCTCCAATGACTCTCCAAATGCATGAAAAAACTTAAAAAAGACTAATCAT
59663521 ACCTATATTGTACACATACCCGACACTCACACCTGAGCTGTC
192 ACCTATATTGTACACATACCCGACACTCACACCTGAGCTGTC
*
59663563 AGTGCTTGAGAAACACAGCC-AAA-AAAAA-AGGAGGGAGGGAA-GG-G-GCATAGTAATCACCT
1 AGTGCTTGAGAAACACAGCCAAAAGAAAAAGAGGAGGGAGGGAAGGGAGAGCATAGAAATCACCT
* * * * * * *
59663622 ATGTTGCTTGTGCTCTTCAGTTTTGTTGAAGTATAGGCGTCTA-ACACTCGTGTTG-GACACACA
66 ACGTTGCTGGGGCTCTTCAGTTTTGTTGAAGCAT--GCGTCCAGACACTCAT-ATGAGACACACA
* * * *
59663685 AATACAATATATAACCTTCAATTACTCTCCAAATGCATGAAAAAACTTGAAAAAGACTAATCATA
128 AATACAAGATATAACCTCCAATGACTCTCCAAATGCATGAAAAAACTTAAAAAAGACTAATCATA
59663750 CC
193 CC
59663752 CGTATCCTAC
Statistics
Matches: 164, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
227 43 0.26
228 72 0.44
229 8 0.05
231 2 0.01
233 12 0.07
235 5 0.03
236 3 0.02
237 19 0.12
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (233 bp):
AGTGCTTGAGAAACACAGCCAAAAGAAAAAGAGGAGGGAGGGAAGGGAGAGCATAGAAATCACCT
ACGTTGCTGGGGCTCTTCAGTTTTGTTGAAGCATGCGTCCAGACACTCATATGAGACACACAAAT
ACAAGATATAACCTCCAATGACTCTCCAAATGCATGAAAAAACTTAAAAAAGACTAATCATACCT
ATATTGTACACATACCCGACACTCACACCTGAGCTGTC
Found at i:59665709 original size:21 final size:21
Alignment explanation
Indices: 59665671--59665710 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
59665661 CCCCGAACCC
*
59665671 GTTTAAGGTTCGAGGTTCAGT
1 GTTTAAGGTTCGAAGTTCAGT
* *
59665692 GTTTAATGTTTGAAGTTCA
1 GTTTAAGGTTCGAAGTTCA
59665711 TGATTCAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (21 bp):
GTTTAAGGTTCGAAGTTCAGT
Found at i:59666297 original size:24 final size:26
Alignment explanation
Indices: 59666250--59666297 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
59666240 ATGATTATAA
* *
59666250 TAAAATATTTAGTATTTTATAAATCC
1 TAAAATATTTAGTATTATAAAAATCC
59666276 TAAAA-ATTTA-TATTATAAAAAT
1 TAAAATATTTAGTATTATAAAAAT
59666298 AATTTGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 5 0.25
26 5 0.25
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAATATTTAGTATTATAAAAATCC
Found at i:59666589 original size:18 final size:19
Alignment explanation
Indices: 59666566--59666606 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
59666556 TAAAACCTTG
59666566 TTTTTTAAAGGTTATA-TA
1 TTTTTTAAAGGTTATATTA
**
59666584 TTTTTTAAATTTTATATTA
1 TTTTTTAAAGGTTATATTA
59666603 TTTT
1 TTTT
59666607 GACTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTAAAGGTTATATTA
Found at i:59667582 original size:43 final size:43
Alignment explanation
Indices: 59667521--59667608 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
59667511 TCGTAATAAG
* *
59667521 ATTACCGAAATATAAGATTATAGTGGAATGTAAGATTATCTCA
1 ATTACCGAAATATAAGATTATAATGGAATATAAGATTATCTCA
*
59667564 ATTACCTAAATATAAGATTATAATGGAATATAAGATTATCTCA
1 ATTACCGAAATATAAGATTATAATGGAATATAAGATTATCTCA
59667607 AT
1 AT
59667609 GTAAGATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
ATTACCGAAATATAAGATTATAATGGAATATAAGATTATCTCA
Found at i:59668724 original size:17 final size:17
Alignment explanation
Indices: 59668693--59668726 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59668683 CATGGTAAAT
* *
59668693 AATAAAAAGTTAACAAA
1 AATAAAAAATAAACAAA
59668710 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
59668727 CAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:59669041 original size:19 final size:21
Alignment explanation
Indices: 59669003--59669044 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
59668993 GTATAAATAT
*
59669003 TATATAGTATATGTATATAAA
1 TATATAGTATATGTAAATAAA
59669024 TATATAG-ATAT-TAAATAAA
1 TATATAGTATATGTAAATAAA
59669043 TA
1 TA
59669045 AAAAGCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TATATAGTATATGTAAATAAA
Found at i:59671016 original size:46 final size:44
Alignment explanation
Indices: 59670911--59671241 Score: 181
Period size: 44 Copynumber: 7.6 Consensus size: 44
59670901 ATTTTAATCC
* * * *
59670911 GCTCCATTGTAA-CTTCAGGGAGATAGGAT-AG-TGTCTTCGATCT
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCTGAT-TCTTTGATCT
* *
59670954 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTG--ATTCTTTGATCT
* * *
59671000 GTTCCACTGTAATCTCAGAGGA-ATAAGACCTGA---TGTGATCT
1 GCTCCACTGTAATCTCAG-GGAGATAAGATCTGATTCTTTGATCT
** * * * * *
59671041 TTTCTACTGTAA-CTTCAGAGAGAT-AG----GATCCTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCTGATTCTTTGATCT
* * *
59671080 GCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGA-T-TCTTTGATCT
* * * * **
59671124 GCTCCGCTGTAATCTCAGGGATATAAGATCT-CTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAT-TCTTTGATCT
* * * *
59671168 GCTCCACTGTTACCTTAGGGAGATAAGATCTGAAATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTG--ATTCTTTGATCT
*
59671214 GTTCCACTGTAATCTCAGGGAGATAAGA
1 GCTCCACTGTAATCTCAGGGAGATAAGA
59671242 CCTGTATAAT
Statistics
Matches: 215, Mismatches: 51, Indels: 41
0.70 0.17 0.13
Matches are distributed among these distances:
36 2 0.01
39 21 0.10
40 7 0.03
41 22 0.10
42 1 0.00
43 25 0.12
44 68 0.32
45 1 0.00
46 63 0.29
47 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCTGATTCTTTGATCT
Found at i:59683287 original size:16 final size:17
Alignment explanation
Indices: 59683257--59683289 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59683247 CATGGTAAAT
*
59683257 AATAAAAAGTTAACAAA
1 AATAAAAAGTAAACAAA
59683274 AATAAAAA-TAAACAAA
1 AATAAAAAGTAAACAAA
59683290 CAAGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AATAAAAAGTAAACAAA
Found at i:59683604 original size:19 final size:21
Alignment explanation
Indices: 59683566--59683607 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
59683556 GTATAAATAT
*
59683566 TATATAGTATATGTATATAAA
1 TATATAGTATATGTAAATAAA
59683587 TATATAG-ATAT-TAAATAAA
1 TATATAGTATATGTAAATAAA
59683606 TA
1 TA
59683608 AAAAGCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TATATAGTATATGTAAATAAA
Found at i:59689390 original size:32 final size:32
Alignment explanation
Indices: 59689354--59689419 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
59689344 TTTAGTGTAG
*
59689354 ATATGGCCTTAAGGTGAATCAATGGGTCACTC
1 ATATGGCCTTAAGATGAATCAATGGGTCACTC
*
59689386 ATATGGCCTTAAGATGAATCAATGGGTTACTC
1 ATATGGCCTTAAGATGAATCAATGGGTCACTC
59689418 AT
1 AT
59689420 TTTGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (32 bp):
ATATGGCCTTAAGATGAATCAATGGGTCACTC
Found at i:59693231 original size:31 final size:29
Alignment explanation
Indices: 59693164--59693232 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
59693154 AACATAACGT
** *
59693164 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATGACAAACAA
* *
59693193 GATTGACTAAAATGTAACATGAGACAAACAA
1 AAGTGACTAAAATGTAACAT--GACAAACAA
59693224 AAGTGACTA
1 AAGTGACTA
59693233 TTTTGATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 18 0.58
31 13 0.42
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGACAAACAA
Found at i:59697324 original size:63 final size:63
Alignment explanation
Indices: 59697231--59697351 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
59697221 CCTTCATGAG
* * * * *
59697231 AAGCGGTCCGGTACTCAAATCCTTAGCTTTGGCTTCAGTATGCTCAGGTTCTTCCTCCGCAAC
1 AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCCGCAAC
*
59697294 AAGCGGTCTGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCC
1 AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCC
59697352 ACGGGAAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.30
Consensus pattern (63 bp):
AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCCGCAAC
Found at i:59704820 original size:22 final size:22
Alignment explanation
Indices: 59704771--59704814 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59704761 TTTTTTGAAG
*
59704771 AATATTTATATTATTTTAATTT
1 AATATTTATAATATTTTAATTT
*
59704793 AATATTTTTAATATTTT-ATTT
1 AATATTTATAATATTTTAATTT
59704814 A
1 A
59704815 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATAATATTTTAATTT
Found at i:59705592 original size:16 final size:16
Alignment explanation
Indices: 59705571--59705603 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59705561 CGACCCACCC
59705571 ATATTAATTTTT-TATA
1 ATATT-ATTTTTATATA
59705587 ATATTATTTTTATATA
1 ATATTATTTTTATATA
59705603 A
1 A
59705604 AAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATTTTTATATA
Found at i:59714030 original size:17 final size:16
Alignment explanation
Indices: 59714008--59714055 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
59713998 ATAATTTTAA
59714008 AATATAATTTAAAATTG
1 AATATAATTT-AAATTG
59714025 AATATAATTT-AA-T-
1 AATATAATTTAAATTG
59714038 AATATAATTTAAATTG
1 AATATAATTTAAATTG
59714054 AA
1 AA
59714056 CGATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 3 0.11
16 2 0.07
17 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATATAATTTAAATTG
Found at i:59714062 original size:30 final size:29
Alignment explanation
Indices: 59713996--59714062 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 29
59713986 ATGAACCGAT
59713996 AGATAATTTTAAAATATAATTTAAAATTGA
1 AGATAA-TTTAAAATATAATTTAAAATTGA
*
59714026 ATATAATTTAATAATATAATTT-AAATTGA
1 AGATAATTTAA-AATATAATTTAAAATTGA
59714055 ACGATAAT
1 A-GATAAT
59714063 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
AGATAATTTAAAATATAATTTAAAATTGA
Found at i:59717449 original size:15 final size:16
Alignment explanation
Indices: 59717429--59717459 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59717419 ACATGTGTAA
59717429 TATTTTT-ATATAATT
1 TATTTTTAATATAATT
59717444 TATTTTTAATATAATT
1 TATTTTTAATATAATT
59717460 ATTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATATAATT
Found at i:59739594 original size:14 final size:13
Alignment explanation
Indices: 59739560--59739607 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
59739550 ATCAATCAAA
59739560 TTTATTGAAAATT
1 TTTATTGAAAATT
*
59739573 TTTGTTGAAAATT
1 TTTATTGAAAATT
59739586 TTTATTTG-AAA--
1 TTTA-TTGAAAATT
59739597 TTTATTGAAAA
1 TTTATTGAAAA
59739608 AAATAACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 18 0.58
14 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (13 bp):
TTTATTGAAAATT
Found at i:59740502 original size:23 final size:23
Alignment explanation
Indices: 59740476--59740531 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
59740466 CTTGTATCAG
59740476 TTTAGTTTAAATTCATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
*
59740499 TTTAGTTTAAATTTATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
59740522 TTATA-TTTAA
1 TT-TAGTTTAA
59740532 TTTTTTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTAGTTTAAATTCATTTTATCT
Found at i:59743863 original size:22 final size:23
Alignment explanation
Indices: 59743810--59743864 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
59743800 ACAATTCAAT
59743810 AATATAAATAATATAAAATGTGA
1 AATATAAATAATATAAAATGTGA
*
59743833 AAT-TTAATAATAT-AAATAGT-A
1 AATATAAATAATATAAAAT-GTGA
*
59743854 TATATAAATAA
1 AATATAAATAA
59743865 AATTATTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.26
22 17 0.63
23 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (23 bp):
AATATAAATAATATAAAATGTGA
Found at i:59744365 original size:9 final size:9
Alignment explanation
Indices: 59744351--59744387 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
59744341 TATAGTTTGA
59744351 TATTCGAAT
1 TATTCGAAT
59744360 TATTCGAAT
1 TATTCGAAT
*
59744369 TATTCGAGT
1 TATTCGAAT
59744378 TATTCGAAT
1 TATTCGAAT
59744387 T
1 T
59744388 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:59744458 original size:9 final size:9
Alignment explanation
Indices: 59744441--59744471 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
59744431 TCGAGTTGAT
59744441 TCGAATAAC
1 TCGAATAAC
*
59744450 TCGATTAAC
1 TCGAATAAC
59744459 TCGAATAAC
1 TCGAATAAC
59744468 TCGA
1 TCGA
59744472 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:59756301 original size:5 final size:5
Alignment explanation
Indices: 59756288--59756325 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
59756278 AACATTAACC
*
59756288 TATAC TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
59756326 GCTTCCTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:59757347 original size:27 final size:23
Alignment explanation
Indices: 59757295--59757340 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
59757285 AACTTTAACA
59757295 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
59757318 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
59757341 GGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACCTTGTTTAGAAGGACTGAT
Found at i:59760518 original size:10 final size:10
Alignment explanation
Indices: 59760504--59760537 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
59760494 AGGTATGGTT
*
59760504 TGTATTGTAT
1 TGTATTGTAG
59760514 TGTATTGTAG
1 TGTATTGTAG
*
59760524 TCTATTGTAG
1 TGTATTGTAG
59760534 TGTA
1 TGTA
59760538 ATCTATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (10 bp):
TGTATTGTAG
Found at i:59767620 original size:3 final size:3
Alignment explanation
Indices: 59767612--59767645 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
59767602 ACAATTAGAG
*
59767612 AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
59767646 AATGAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:59775427 original size:22 final size:24
Alignment explanation
Indices: 59775402--59775446 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
59775392 AGGGATGTGC
59775402 TATTA-CATTTT-TTATTTTTTCT
1 TATTATCATTTTCTTATTTTTTCT
* *
59775424 TATTATTATTTTCTTTTTTTTTC
1 TATTATCATTTTCTTATTTTTTC
59775447 AAAATTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTATCATTTTCTTATTTTTTCT
Found at i:59777106 original size:15 final size:16
Alignment explanation
Indices: 59777088--59777122 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
59777078 TGGGTTCCAA
59777088 AATTTGGTTTT-AAAG
1 AATTTGGTTTTCAAAG
59777103 AA-TTGGTTTTCAAAG
1 AATTTGGTTTTCAAAG
59777118 AATTT
1 AATTT
59777123 TAAACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 8 0.44
16 2 0.11
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (16 bp):
AATTTGGTTTTCAAAG
Found at i:59777370 original size:16 final size:17
Alignment explanation
Indices: 59777351--59777388 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
59777341 AATATTAAAA
59777351 CTAATG-CATAAAACTT
1 CTAATGACATAAAACTT
*
59777367 CTAATGTAGATAAAACTT
1 CTAATG-ACATAAAACTT
59777385 CTAA
1 CTAA
59777389 GTCACAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (17 bp):
CTAATGACATAAAACTT
Found at i:59778042 original size:21 final size:21
Alignment explanation
Indices: 59778011--59778065 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
59778001 GGTGGTGTCG
* * *
59778011 AAGTATAAGAGATATGTATCG
1 AAGTATGAGAGATATATATCA
* *
59778032 GAGTATGAGAGATGTATATCA
1 AAGTATGAGAGATATATATCA
59778053 AAGTATGAGAGAT
1 AAGTATGAGAGAT
59778066 GTGTTAGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGTATGAGAGATATATATCA
Found at i:59783809 original size:26 final size:26
Alignment explanation
Indices: 59783780--59783833 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
59783770 TCACTTTCAT
*
59783780 GTGACATCGTCAAATAGGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
59783806 GTGACATCGTCAAATACGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
59783832 GT
1 GT
59783834 CTAGGCCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (26 bp):
GTGACATCGTCAAATACGACCATAAA
Found at i:59784821 original size:7 final size:7
Alignment explanation
Indices: 59784809--59784846 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
59784799 GAATAATACG
*
59784809 AAAATAT
1 AAAATTT
*
59784816 AAAA-TA
1 AAAATTT
59784822 AAAATTT
1 AAAATTT
59784829 AAAATTT
1 AAAATTT
59784836 AAAATTT
1 AAAATTT
59784843 AAAA
1 AAAA
59784847 GAGGATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTT
Found at i:59790534 original size:86 final size:86
Alignment explanation
Indices: 59790444--59790624 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
59790434 AATATAATTG
59790444 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
59790509 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
59790530 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
59790595 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
59790616 TAATT-TTAT
1 TAATTATTAT
59790625 GTGGAGAGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (86 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
TGTTAAGTATTAATGTTGATA
Found at i:59790766 original size:51 final size:50
Alignment explanation
Indices: 59790691--59790793 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 50
59790681 TATACGTAAA
59790691 AATTATCATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAAC
1 AATTATCATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAAC
59790741 AATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
1 AATTAT-CATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
59790792 AA
1 AA
59790794 GTAATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 7 0.14
51 44 0.86
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (50 bp):
AATTATCATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
Found at i:59790802 original size:33 final size:34
Alignment explanation
Indices: 59790739--59790849 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 34
59790729 CATTAAACCA
* *
59790739 ACAATTATACATACACCAACAATGT-TTTTTAGGG
1 ACAATTATACATAAACCAACAA-GTAATTTTAGGG
59790773 ACAA-TA-ACATTAAACCAACAAGTAATTTTA-GG
1 ACAATTATACA-TAAACCAACAAGTAATTTTAGGG
* * *
59790805 TCAATTATACATACACCAACAATTAATTTTA-GG
1 ACAATTATACATAAACCAACAAGTAATTTTAGGG
*
59790838 TCAATTATACAT
1 ACAATTATACAT
59790850 GCTTTATAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.15
33 51 0.75
34 7 0.10
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (34 bp):
ACAATTATACATAAACCAACAAGTAATTTTAGGG
Found at i:59793992 original size:18 final size:17
Alignment explanation
Indices: 59793964--59793998 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59793954 ATTATTAAGA
*
59793964 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59793981 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59793999 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59794158 original size:121 final size:120
Alignment explanation
Indices: 59793873--59794256 Score: 716
Period size: 120 Copynumber: 3.2 Consensus size: 120
59793863 TTTTCAAGTT
*
59793873 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
59793938 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
59793993 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
59794058 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTTTATTAAATTATATATTTTAATTAAA
59794114 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
59794179 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
59794234 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
59794257 TAAATATGAT
Statistics
Matches: 256, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 2 0.01
120 137 0.54
121 115 0.45
122 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:59794233 original size:18 final size:17
Alignment explanation
Indices: 59794205--59794239 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59794195 ATTATTAAGA
*
59794205 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59794222 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59794240 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59794453 original size:44 final size:45
Alignment explanation
Indices: 59794403--59794493 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
59794393 ACCTCTATTC
* * *
59794403 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
59794447 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
59794492 CA
1 CA
59794494 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:59794495 original size:16 final size:16
Alignment explanation
Indices: 59794474--59794542 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
59794464 GATTAGCTAT
59794474 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
59794490 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
59794507 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
59794523 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
59794539 TACA
1 TACA
59794543 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:59794516 original size:33 final size:32
Alignment explanation
Indices: 59794474--59794542 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
59794464 GATTAGCTAT
59794474 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
59794507 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
59794539 TACA
1 TACA
59794543 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:59796261 original size:24 final size:23
Alignment explanation
Indices: 59796216--59796262 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
59796206 AAGCAATACT
*
59796216 ACATGCATAAGTAAGACTAAAAA
1 ACATGCATAAGAAAGACTAAAAA
59796239 ACATGCCATAAGAAGAGAC-AAAAA
1 ACATG-CATAAGAA-AGACTAAAAA
59796263 CGTCTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
ACATGCATAAGAAAGACTAAAAA
Found at i:59796643 original size:21 final size:21
Alignment explanation
Indices: 59796617--59796676 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
59796607 TTCTTCTCTG
59796617 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCACTGCAGC
* * * *
59796638 CTCTGCTGCTCTCATTGCTGC
1 CTCTGCTTCCCTCACTGCAGC
* *
59796659 CTCTGCTTTCCTCGCTGC
1 CTCTGCTTCCCTCACTGC
59796677 TGCATCAGCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.43, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTGCAGC
Found at i:59796677 original size:21 final size:21
Alignment explanation
Indices: 59796617--59796688 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
59796607 TTCTTCTCTG
* *
59796617 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTTCCTCACTGCTGC
* *
59796638 CTCTGC-TGCTCTCATTGCTGC
1 CTCTGCTTTC-CTCACTGCTGC
*
59796659 CTCTGCTTTCCTCGCTGCTGC
1 CTCTGCTTTCCTCACTGCTGC
* *
59796680 ATCAGCTTT
1 CTCTGCTTT
59796689 AAGTTGTAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.07, C:0.40, G:0.17, T:0.36
Consensus pattern (21 bp):
CTCTGCTTTCCTCACTGCTGC
Found at i:59796792 original size:87 final size:87
Alignment explanation
Indices: 59796653--59796840 Score: 304
Period size: 87 Copynumber: 2.2 Consensus size: 87
59796643 CTGCTCTCAT
* * * * *
59796653 TGCTGCCTCTGCTTTCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTTATATTTTC
1 TGCTGCCTCTGCTTCCCTCACCGCTGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTTC
59796718 TTTGAACCTCAGCTTCTCTCGA
66 TTTGAACCTCAGCTTCTCTCGA
**
59796740 TGCTGCCTCTGCTTCCCTCACCGCTGCATTTGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTTC
1 TGCTGCCTCTGCTTCCCTCACCGCTGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTTC
*
59796805 TTTGAACCTTAGCTTCTCTCGA
66 TTTGAACCTCAGCTTCTCTCGA
59796827 TGCTGCCTCTGCTT
1 TGCTGCCTCTGCTT
59796841 TAAGTTGAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (87 bp):
TGCTGCCTCTGCTTCCCTCACCGCTGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTTC
TTTGAACCTCAGCTTCTCTCGA
Found at i:59798730 original size:41 final size:40
Alignment explanation
Indices: 59798571--59798729 Score: 151
Period size: 41 Copynumber: 3.9 Consensus size: 40
59798561 GCACTTTCAC
** * *
59798571 AAAAACGCAGCTAAAACCCCGAGCTTTAGCGGCGCCTTTCT
1 AAAAACGCCTCTAAAACCCCGAGCATTAGCGGCG-CTTTTT
* * * * *
59798612 AAAAATGCCGCTAAAACCCCGAACATTAGCGGCGCTTAATA
1 AAAAACGCCTCTAAAACCCCGAGCATTAGCGGCGCTT-TTT
* *
59798653 AAAAACG-CTGCTAAAACCCTGAGCATTGGCGGCGCTATTTT
1 AAAAACGCCT-CTAAAACCCCGAGCATTAGCGGCGCT-TTTT
*
59798694 AAAAACGCCTTTAAAACCCAC-AGCATTAGCGGCGCT
1 AAAAACGCCTCTAAAACCC-CGAGCATTAGCGGCGCT
59798730 ACTCCAGAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
40 4 0.04
41 89 0.93
42 3 0.03
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (40 bp):
AAAAACGCCTCTAAAACCCCGAGCATTAGCGGCGCTTTTT
Found at i:59798741 original size:41 final size:41
Alignment explanation
Indices: 59798664--59798743 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
59798654 AAAACGCTGC
** * * **
59798664 TAAAACCCTGAGCATTGGCGGCGCTATTTTAAAAACGCCTT
1 TAAAACCCACAGCATTAGCGGCGCTACTCCAAAAACGCCTT
*
59798705 TAAAACCCACAGCATTAGCGGCGCTACTCCAGAAACGCC
1 TAAAACCCACAGCATTAGCGGCGCTACTCCAAAAACGCC
59798744 ACTAAAGCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (41 bp):
TAAAACCCACAGCATTAGCGGCGCTACTCCAAAAACGCCTT
Found at i:59798742 original size:82 final size:82
Alignment explanation
Indices: 59798571--59798729 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 82
59798561 GCACTTTCAC
* *
59798571 AAAAACGCAGCTAAAACCCCGAGCTTTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCCCGAAC
1 AAAAACGCAGCTAAAACCCCGAGCATTAGCGGCGCCTTTCTAAAAACGCCGCTAAAACCCCGAAC
59798636 ATTAGCGGCGCTTAATA
66 ATTAGCGGCGCTTAATA
* * * * **
59798653 AAAAACGCTGCTAAAACCCTGAGCATTGGCGGCG-CTATTTTAAAAACGCCTTTAAAACCCAC-A
1 AAAAACGCAGCTAAAACCCCGAGCATTAGCGGCGCCT-TTCTAAAAACGCCGCTAAAACCC-CGA
*
59798716 GCATTAGCGGCGCT
64 ACATTAGCGGCGCT
59798730 ACTCCAGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
81 2 0.03
82 63 0.95
83 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (82 bp):
AAAAACGCAGCTAAAACCCCGAGCATTAGCGGCGCCTTTCTAAAAACGCCGCTAAAACCCCGAAC
ATTAGCGGCGCTTAATA
Found at i:59799027 original size:37 final size:37
Alignment explanation
Indices: 59798983--59799057 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
59798973 AGTTAGGGGG
59798983 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
* *
59799020 TTTAGAAGATGATGAACATGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
59799057 T
1 T
59799058 CTTATTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.27
Consensus pattern (37 bp):
TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
Found at i:59804359 original size:21 final size:21
Alignment explanation
Indices: 59804329--59804368 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59804319 CCTCAATGCA
*
59804329 ATTGGGTCATTGCGAGATGAC
1 ATTGGGTCATTACGAGATGAC
*
59804350 ATTGGTTCATTACGAGATG
1 ATTGGGTCATTACGAGATG
59804369 TAGTTAGTGG
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:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGGGTCATTACGAGATGAC
Found at i:59808761 original size:26 final size:26
Alignment explanation
Indices: 59808677--59808770 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
59808667 CGTAAAAATC
* *
59808677 TAAAATAAATAATATACGTAAAACAGTT
1 TAAAATAAATAATATA--TGAAACAATT
*
59808705 TAAGAT-AA-AATA-ATAGAAAGCAATT
1 TAAAATAAATAATATAT-GAAA-CAATT
**
59808730 CGAAATAAATAATATATGAAACAATT
1 TAAAATAAATAATATATGAAACAATT
**
59808756 TAAAATTGATAATAT
1 TAAAATAAATAATAT
59808771 CAAACAGTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 8 0.16
26 22 0.43
27 10 0.20
28 7 0.14
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (26 bp):
TAAAATAAATAATATATGAAACAATT
Found at i:59809611 original size:14 final size:15
Alignment explanation
Indices: 59809592--59809622 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59809582 ATTATTTAGT
59809592 ATAAAAG-GAAAAAA
1 ATAAAAGAGAAAAAA
59809606 ATAAAAGAGAAAAAA
1 ATAAAAGAGAAAAAA
59809621 AT
1 AT
59809623 CGAACAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
ATAAAAGAGAAAAAA
Found at i:59829275 original size:13 final size:14
Alignment explanation
Indices: 59829237--59829282 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
59829227 ACCACCTATA
59829237 AAAAATAA-AAATTT
1 AAAAATAATAAA-TT
59829251 AATAAA-AATAAA-T
1 AA-AAATAATAAATT
59829264 AAAAATAATAAATT
1 AAAAATAATAAATT
59829278 AAAAA
1 AAAAA
59829283 ACAATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 9 0.32
14 10 0.36
15 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATAATAAATT
Done.