Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold80
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: 1499392
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 217494 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1406019 original size:34 final size:33
Alignment explanation
Indices: 1405958--1406024 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1405948 ATTTGCCTGC
*
1405958 ATGTATCGATACAAAGATTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
**
1405991 ATGTATCGATACATTTGAGTAATGTATCGATACA
1 ATGTATCGATACA-AAGAGTAATGTATCGATACA
1406025 TTTTTTGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:1406081 original size:33 final size:33
Alignment explanation
Indices: 1406044--1406110 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1406034 AGTAGCTTAA
1406044 ATTGTATCAATACAAAAAAATATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
* * ***
1406077 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
1406110 A
1 A
1406111 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCAATACAAAAAAATATGTATCGATAC
Found at i:1406084 original size:13 final size:13
Alignment explanation
Indices: 1406066--1406090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1406056 CAAAAAAATA
1406066 TGTATCGATACAT
1 TGTATCGATACAT
1406079 TGTATCGATACA
1 TGTATCGATACA
1406091 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1416279 original size:49 final size:49
Alignment explanation
Indices: 1416005--1416454 Score: 364
Period size: 52 Copynumber: 9.0 Consensus size: 49
1415995 AAGAGTGATA
* * ** * *
1416005 AAGGTGCCAATATGTTGATTC-AGGACCAGTGATATTGGGCTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGG-CCAGCAACATTGGACTTAAAGATG
* * ** * * * *
1416054 TAAAGAATGTCAATGTGCTGATTCGCGGTCAGCGACATTAGACTTGAAGATGAG
1 --AAG-GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGAT--G
* * * ** *
1416108 AAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGACGATA
1 AAG-GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT-AA-A-GATG
** * * * *
1416161 AAAATGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT-AAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
* * * *
1416209 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAATTAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
* * * *
1416258 AAGGTGCTAATGTACTGATTCAAGACCAACAACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
** * * * * *
1416307 ACAAAGGCACCGATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
1 ---AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
* * *
1416359 AAGGTGCCAATGTGCTAATTCAAGGCCAGCAACATTGGACTAAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
*
1416408 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGA
1416455 AGATGCCACC
Statistics
Matches: 320, Mismatches: 68, Indels: 24
0.78 0.17 0.06
Matches are distributed among these distances:
48 40 0.12
49 129 0.40
50 1 0.00
51 3 0.01
52 137 0.43
53 5 0.02
54 2 0.01
55 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (49 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
Found at i:1416428 original size:150 final size:149
Alignment explanation
Indices: 1416113--1416454 Score: 486
Period size: 150 Copynumber: 2.3 Consensus size: 149
1416103 ATGAGAAGAA
** * ** *
1416113 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGACGATAAAAATGCCAATATGTTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACGACAAAAACACCAATATGCTG
* * *
1416178 ATTCAAGGCCAGCGATATTGGACTTAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATA
66 ATTCAAGGCCAGCGATATTGGACTTAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACA
*
1416243 TTGGAATTAAAGGTGAAGG
131 TTGGAATAAAAGGTGAAGG
* * * * * ** *
1416262 TGCTAATGTACTGATTCAAGACCAACAACATTGGACTTAAAGATGACAAAGGCACCGATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACGACAAAAACACCAATATGCTG
*
1416327 ATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTAATTCAAGGCCAGCAAC
66 ATTCAAGGCCAGCGATATTGGACTT-AAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAAC
*
1416392 ATTGGACTAAAAGGTGAAGG
130 ATTGGAATAAAAGGTGAAGG
*
1416412 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGA
1416455 AGATGCCACC
Statistics
Matches: 167, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
149 76 0.46
150 91 0.54
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (149 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGACGACAAAAACACCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACA
TTGGAATAAAAGGTGAAGG
Found at i:1416458 original size:101 final size:100
Alignment explanation
Indices: 1416005--1416458 Score: 384
Period size: 101 Copynumber: 4.5 Consensus size: 100
1415995 AAGAGTGATA
* * * * * * *
1416005 AAGGTGCCAATATGTTGATTC-AGGACCAGTGATATTGGGCTTAAAGATG-TAAAGAATGTCAAT
1 AAGGTGCCAATATGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGAAGATAAAG-GTGCCAAT
** * * * *
1416068 GTGCTGATTCGCGGTCAGCGACATTAGACTTGAAGATGAG
64 GTGCTGATTCAAGGCCAGCAACATTGGAC-TAAAGAT--G
* * * ** * ** *
1416108 AAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGACGATAAAAATGCCAATA
1 AAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGATAAAGGTGCCAATG
* * * *
1416173 TGTTGATTCAAGGCCAGCGATATTGGACTTAAGATG
65 TGCTGATTCAAGGCCAGCAACATTGGACTAAAGATG
* * * * *
1416209 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAATTAAAG--G-TGAAGGTGCTAATGT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGATAAAGGTGCCAATGT
* * *
1416271 ACTGATTCAAGACCAACAACATTGGACTTAAAGATG
66 GCTGATTCAAGGCCAGCAACATTGGAC-TAAAGATG
** * *
1416307 ACAAAGGCACCGATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAGATAAAGGTGCCAA
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGATAAAGGTGCCAA
* *
1416369 TGTGCTAATTCAAGGCCAGCAACATTGGACTAAAAGGTG
63 TGTGCTGATTCAAGGCCAGCAACATTGGACT-AAAGATG
*
1416408 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAT
1416459 GCCACCAACT
Statistics
Matches: 283, Mismatches: 54, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
97 31 0.11
98 45 0.16
99 1 0.00
100 39 0.14
101 88 0.31
103 9 0.03
104 63 0.22
105 7 0.02
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (100 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGATAAAGGTGCCAATGT
GCTGATTCAAGGCCAGCAACATTGGACTAAAGATG
Found at i:1416530 original size:28 final size:26
Alignment explanation
Indices: 1416497--1416665 Score: 104
Period size: 28 Copynumber: 6.0 Consensus size: 26
1416487 GGTTGCACCA
1416497 ACTTGTGTGCCTTTGAAAGTTGCCACT
1 ACTTGTG-GCCTTTGAAAGTTGCCACT
* * **
1416524 ACCTTGTGGGCTTTGAAGGTTTTCACT
1 A-CTTGTGGCCTTTGAAAGTTGCCACT
* *
1416551 GACTTGTGGGCTTTTGAAGGTTGCCACT
1 -ACTTGT-GGCCTTTGAAAGTTGCCACT
* * *
1416579 AACTTGTGGGCTTTGAAAGGGGTGCCACCG
1 -ACTTGTGGCCTTTGAAA--GTTGCCA-CT
* * *
1416609 ACTTATGGGCTTTTGAAAAGATGCCACT
1 ACTTGT-GGCCTTTG-AAAGTTGCCACT
*
1416637 GACTTGTGGGCTTTGGAAAGGTTGCCACT
1 -ACTTGTGGCCTTT-GAAA-GTTGCCACT
1416666 GCCATGTAGG
Statistics
Matches: 108, Mismatches: 23, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
27 29 0.27
28 38 0.35
29 31 0.29
30 7 0.06
31 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (26 bp):
ACTTGTGGCCTTTGAAAGTTGCCACT
Found at i:1416617 original size:29 final size:29
Alignment explanation
Indices: 1416471--1416714 Score: 157
Period size: 29 Copynumber: 8.6 Consensus size: 29
1416461 CACCAACTTG
* * *
1416471 TGTGGGCTTTTGAAAAGGTTG-CACCAACT
1 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
* * *
1416500 TGTGTGCCTTTGAAA--GTTGCCA-CTACCT
1 TGTG-GGCTTTGAAAGGGGTGCCACCGA-CT
* ** *
1416528 TGTGGGCTTTG-AA-GGTTTTCACTGACT
1 TGTGGGCTTTGAAAGGGGTGCCACCGACT
* **
1416555 TGTGGGCTTTTG-AA-GGTTGCCACTAACT
1 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1416583 TGTGGGCTTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGGTGCCACCGACT
* * * *
1416612 TATGGGCTTTTGAAA-AGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
* * * *
1416641 TGTGGGCTTTGGAAA-GGTTGCCACTGCCA
1 TGTGGGCTTT-GAAAGGGGTGCCACCGACT
*
1416670 TGTAGGCTTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGGTGCCACCGACT
*
1416699 TGTGGGCTTTGGAAGG
1 TGTGGGCTTTGAAAGG
1416715 TGTGGAATGT
Statistics
Matches: 175, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 30 0.17
28 42 0.24
29 92 0.53
30 9 0.05
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTGAAAGGGGTGCCACCGACT
Found at i:1416647 original size:58 final size:56
Alignment explanation
Indices: 1416471--1416715 Score: 228
Period size: 58 Copynumber: 4.3 Consensus size: 56
1416461 CACCAACTTG
* * *
1416471 TGTGGGCTTTTGAAAAGGTTG-CACCAACTTGTGTGCCTTTGAAAGTTGCCACT-ACCT
1 TGTGGGC-TTTG-AAAGGTTGCCACCGACTTGTGGGCTTTTGAAAGTTGCCACTGA-CT
** * * *
1416528 TGTGGGCTTTG-AAGGTTTTCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGTTGCCACCGACTTGTGGGCTTTTGAAAGTTGCCACTGACT
* * *
1416583 TGTGGGCTTTGAAAGGGGTGCCACCGACTTATGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAA-GGTTGCCACCGACTTGTGGGCTTTTG-AAAGTTGCCACTGACT
* * * * * *
1416641 TGTGGGCTTTGGAAAGGTTGCCACTGCCATGTAGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTT-GAAAGGTTGCCACCGACTTGTGGGCTTTTGAAA--GTTGCCACTGACT
*
1416699 TGTGGGCTTTGGAAGGT
1 TGTGGGCTTTGAAAGGT
1416716 GTGGAATGTC
Statistics
Matches: 157, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
54 6 0.04
55 40 0.25
56 10 0.06
57 38 0.24
58 59 0.38
59 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.31
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGTTGCCACCGACTTGTGGGCTTTTGAAAGTTGCCACTGACT
Found at i:1416679 original size:87 final size:86
Alignment explanation
Indices: 1416547--1416708 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 86
1416537 TGAAGGTTTT
* * *
1416547 CACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACCGACT
1 CACTGACTTGTGGGCTTTGGAAGGTTGCCACTAACATGTAGGCTTTGAAAGGGGTGCCACCGACT
1416612 TATGGGCTTTTGAAAAGATGC
66 TATGGGCTTTTGAAAAGATGC
**
1416633 CACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGCCATGTAGGCTTTGAAAGGGGTGCCACCGAC
1 CACTGACTTGTGGGCTTTGG-AAGGTTGCCACTAACATGTAGGCTTTGAAAGGGGTGCCACCGAC
*
1416698 TTGTGGGCTTT
65 TTATGGGCTTT
1416709 GGAAGGTGTG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 19 0.28
87 50 0.72
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (86 bp):
CACTGACTTGTGGGCTTTGGAAGGTTGCCACTAACATGTAGGCTTTGAAAGGGGTGCCACCGACT
TATGGGCTTTTGAAAAGATGC
Found at i:1417116 original size:37 final size:37
Alignment explanation
Indices: 1417075--1417196 Score: 235
Period size: 37 Copynumber: 3.3 Consensus size: 37
1417065 GATGAAGCAT
1417075 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1417112 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
*
1417149 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAT
1 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1417186 AAATGCATCAT
1 AAATGCATCAT
1417197 TGTGGCATGA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 84 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (37 bp):
AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
Found at i:1432209 original size:20 final size:20
Alignment explanation
Indices: 1432184--1432309 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
1432174 ATTTGCCTGC
1432184 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
1432204 ATGTATCGATACATCTGGGTAAAATTCCTA
1 ATGTATCGATACAT-T--G---AA----TA
**
1432234 GATGTATCGATACAAAG-ATCA
1 -ATGTATCGATACATTGAAT-A
*
1432255 ATGTATTGATACATTGAATA
1 ATGTATCGATACATTGAATA
1432275 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
1432295 ATGTATTGATACATT
1 ATGTATCGATACATT
1432310 TCCTTGGTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
20 62 0.72
21 4 0.05
23 1 0.01
24 1 0.01
26 2 0.02
28 1 0.01
30 2 0.02
31 13 0.15
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:1432351 original size:13 final size:13
Alignment explanation
Indices: 1432335--1432361 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1432325 AGAGTAGCTT
1432335 TGTATCGATACAA
1 TGTATCGATACAA
1432348 TGTATCGATACAA
1 TGTATCGATACAA
1432361 T
1 T
1432362 ACTTATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1432371 original size:19 final size:20
Alignment explanation
Indices: 1432347--1432400 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
1432337 TATCGATACA
1432347 ATGTATCGATACAATACT-T
1 ATGTATCGATACAATACTGT
*
1432366 ATGTATCGATACATTTACTGT
1 ATGTATCGATACA-ATACTGT
*
1432387 TTGTATCGATACAA
1 ATGTATCGATACAA
1432401 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATACTGT
Found at i:1434634 original size:20 final size:21
Alignment explanation
Indices: 1434609--1434665 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
1434599 AAAAAAAGAC
*
1434609 AGAATGTATCGATACATTGA-
1 AGAATGTATCGATACATTCAT
1434629 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTCAT
*
1434650 A-CATGTATCGATACAT
1 AGAATGTATCGATACAT
1434666 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAT
Found at i:1439290 original size:155 final size:154
Alignment explanation
Indices: 1439027--1439627 Score: 606
Period size: 155 Copynumber: 3.9 Consensus size: 154
1439017 ATACTTTCAT
* ** * * *
1439027 GTCGAAGGTATACCTTA-AGAGCATTTTCATAATTTTTCTATAACTGAGTCCTAAGTTGTCACT-
1 GTCGAAGGTATCCCTTAGAG-GCATTTTTGTAATTTTT-TAAAAC-GAGTCTTAGGTTGTCACTA
** ** * * *
1439090 -GTCTGCTTTTATGTCAAAGGTGGCG--TTTAGGATAGGTTTATCCCATCTATTATCCTTTTTAA
63 GGTCCACTTTTATGTTGAAGATGG-GTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAA
** *
1439152 GTCCTTTAGGGGTATTGGGCATTTCTAA
127 GTCCTTTAGGGGTATCAGGCACTTCTAA
* ** *
1439180 GTCAAAAATATCCCCTAGAGGCATTTTTGTAATTTTTTAAAACCGAGTCTTAGGTTGTCACTAGG
1 GTCGAAGGTATCCCTTAGAGGCATTTTTGTAATTTTTTAAAA-CGAGTCTTAGGTTGTCACTAGG
*
1439245 TCCACTTTTATGTTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCC-TTTTATGTC
65 TCCACTTTTATGTTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * *
1439309 TTTTAGAGGTATCAGGTACTTCTAT
130 CTTTAGGGGTATCAGGCACTTCTAA
* * ** * *
1439334 GTCGAAGGTATCCCTTAGACGCATTTTCGTAATTCTTCCAAAATCGAGTCTTAAGTTGTCGCTAG
1 GTCGAAGGTATCCCTTAGAGGCATTTTTGTAATT-TTTTAAAA-CGAGTCTTAGGTTGTCACTA-
* * **
1439399 GGTCCACTTTTATGCTT-AAGGTGGGTATTTAGGATACGTTCATCTTATCTATAATCCTTTTTAA
63 GGTCCACTTTTATG-TTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAA
*
1439463 GTCCTCTAGGGGTATCAGGCACTTCTAA
127 GTCCTTTAGGGGTATCAGGCACTTCTAA
** * ** * * **
1439491 GTCGAAGGTATCAAATTA-AGGGTATTTTTGTAATTTTTTAAAATTAATCCTAGGTTGTTTCTAG
1 GTCGAAGGTATC-CCTTAGA-GGCATTTTTGTAATTTTTTAAAACGAGTCTTAGGTTGTCACTAG
* * * *
1439555 GTTCACTTTTATGATGAATATGGGTATTTAAGATAGGTTCATCCCATCTATAATCCTTTTTAAGT
64 GTCCACTTTTATGTTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGT
1439620 CCTTTAGG
129 CCTTTAGG
1439628 ACCACTGGGT
Statistics
Matches: 366, Mismatches: 69, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
152 20 0.05
153 29 0.08
154 75 0.20
155 115 0.31
156 63 0.17
157 49 0.13
158 15 0.04
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (154 bp):
GTCGAAGGTATCCCTTAGAGGCATTTTTGTAATTTTTTAAAACGAGTCTTAGGTTGTCACTAGGT
CCACTTTTATGTTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
TTTAGGGGTATCAGGCACTTCTAA
Found at i:1445994 original size:33 final size:32
Alignment explanation
Indices: 1445936--1445999 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1445926 CAATTCAGTG
* *
1445936 TGTATCGATACCAAGAACATGTATCGATACAA
1 TGTATCGAAACAAAGAACATGTATCGATACAA
*
1445968 TGTATCGAAACAAAGCAATATGTATCGATACA
1 TGTATCGAAACAAAG-AACATGTATCGATACA
1446000 TCTGGGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (32 bp):
TGTATCGAAACAAAGAACATGTATCGATACAA
Found at i:1451471 original size:19 final size:19
Alignment explanation
Indices: 1451416--1451474 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1451406 AATTCTTTAC
1451416 GTATCGATACAATGAACTT
1 GTATCGATACAATGAACTT
*
1451435 GTATC-A-A-TAT-AA--T
1 GTATCGATACAATGAACTT
1451448 GTATCGATACAATGAACTT
1 GTATCGATACAATGAACTT
1451467 GTATCGAT
1 GTATCGAT
1451475 TAATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 6 0.19
14 1 0.03
15 3 0.09
16 4 0.12
17 3 0.09
18 1 0.03
19 14 0.44
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (19 bp):
GTATCGATACAATGAACTT
Found at i:1451502 original size:32 final size:32
Alignment explanation
Indices: 1451416--1451507 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
1451406 AATTCTTTAC
*
1451416 GTATCGATACAATGAACTTGTATCAATATAAT
1 GTATCGATACAATGAACTTGTATCGATATAAT
1451448 GTATCGATACAATGAACTTGTATCGAT-TAAT
1 GTATCGATACAATGAACTTGTATCGATATAAT
*
1451479 GTATCGATACAAAGCAA-TATGTATCGATA
1 GTATCGATACAATG-AACT-TGTATCGATA
1451508 CTTATGGGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 18 0.33
32 37 0.67
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (32 bp):
GTATCGATACAATGAACTTGTATCGATATAAT
Found at i:1459811 original size:13 final size:13
Alignment explanation
Indices: 1459793--1459822 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1459783 ACATTTTACT
*
1459793 ATGTATCTATACA
1 ATGTATCAATACA
1459806 ATGTATCAATACA
1 ATGTATCAATACA
1459819 ATGT
1 ATGT
1459823 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1459926 original size:13 final size:13
Alignment explanation
Indices: 1459908--1459934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1459898 TATAATGAAC
1459908 ATGTATCGATACA
1 ATGTATCGATACA
1459921 ATGTATCGATACA
1 ATGTATCGATACA
1459934 A
1 A
1459935 ACCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1462305 original size:21 final size:21
Alignment explanation
Indices: 1462281--1462321 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1462271 TTCATCCGAG
* *
1462281 TCAACTTCTTCATCATCATTA
1 TCAACATCCTCATCATCATTA
1462302 TCAACATCCTCATCATCATT
1 TCAACATCCTCATCATCATT
1462322 GATGGTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (21 bp):
TCAACATCCTCATCATCATTA
Found at i:1465833 original size:154 final size:155
Alignment explanation
Indices: 1465588--1465892 Score: 375
Period size: 154 Copynumber: 2.0 Consensus size: 155
1465578 GTGCTTGACG
* * * *
1465588 CCCCTAAAAGACTTAAAAAGGATTATAGATGGGATGAACCTATCTTAAGTAGCCACATTCGACAT
1 CCCCTAAAAGACTTAAAAAGGATAAAAGATGGGATGAACCTATCCTAAATAGCCACATTCGACAT
* * * ** *
1465653 AAAAGTGAACCTAGTGATAATTTAGGACTCAGTTCT-AAAAAATATGAAAATG-CCTTTAGGGGA
66 AAAAGTGAACCCAATGACAACCTAGGACTCAGTTCTGAAAAAATATGAAAATGTCC-CTAGGGGA
* *
1465716 TACTTTCGACGTAGAAGTGCCTCGCA
130 TACATTCGACGTAAAAGTGCCTCGCA
* *
1465742 CCCCTAAAGGACTTAAAAAGG-TAAAAAGATGGGATGAACCTATCCTAAATA-CCTACCTTCGAC
1 CCCCTAAAAGACTTAAAAAGGAT-AAAAGATGGGATGAACCTATCCTAAATAGCC-ACATTCGAC
** ** *
1465805 ATAAAAGTGGTCCCAATGACAACCTAGGACTTGGTTTTGAAAAAATATGAAAATGTCCCTAGGGG
64 ATAAAAGTGAACCCAATGACAACCTAGGACTCAGTTCTGAAAAAATATGAAAATGTCCCTAGGGG
*
1465870 ATACATTCGATGTAAAAGTGCCT
129 ATACATTCGACGTAAAAGTGCCT
1465893 GATGACAACA
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
153 3 0.02
154 80 0.63
155 42 0.33
156 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (155 bp):
CCCCTAAAAGACTTAAAAAGGATAAAAGATGGGATGAACCTATCCTAAATAGCCACATTCGACAT
AAAAGTGAACCCAATGACAACCTAGGACTCAGTTCTGAAAAAATATGAAAATGTCCCTAGGGGAT
ACATTCGACGTAAAAGTGCCTCGCA
Found at i:1466775 original size:141 final size:142
Alignment explanation
Indices: 1466574--1466947 Score: 488
Period size: 141 Copynumber: 2.6 Consensus size: 142
1466564 AAAATCAGAG
* * * * *
1466574 GATACGAAAAGTTTTAAAAATTTCTACACCCT-TAC-AGAAAACCATAGGAATATTAAAAATTTT
1 GATACGAAATGTTTTGAAGATTTCTATA-CCTATACGA-AAAACCATAGGAATATTAGAAATTTT
* * **
1466637 GAGAAATTAAGATAATAATTTTGATTTAATTTTTAA-TTTTAA-AAAGTTCATTTTGTACCTTAA
64 GAGAAATTAAGATAATAATTTTTATTTAATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAA
1466700 TGGA-AAACCAAAAA
129 TGGAGAAA-CAAAAA
* *
1466714 GATATGAAATGTTTTGAAGATTTCTATACCTATACGAAAAAACCATAGGAATATTAGAAATTTGG
1 GATACGAAATGTTTTGAAGATTTCTATACCTATACG-AAAAACCATAGGAATATTAGAAATTTTG
*
1466779 AGAAATTAAGATAATAATTTTTATTTAATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAGT
65 AGAAATTAAGATAATAATTTTTATTTAATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAAT
* *
1466844 GGAGAAATATAAA
130 GGAGAAACAAAAA
* * * ** *
1466857 GATACGAAATGTTTTGAAGGTTTCTATACCTCTATGAAAAATTATAGGAATATTAGAAATCTTGA
1 GATACGAAATGTTTTGAAGATTTCTATACCTATACGAAAAACCATAGGAATATTAGAAATTTTGA
*
1466922 GATATTAAGATAATAATTTTTATTTA
66 GAAATTAAGATAATAATTTTTATTTA
1466948 GTGATAAAAT
Statistics
Matches: 205, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
139 3 0.01
140 26 0.13
141 59 0.29
142 57 0.28
143 57 0.28
144 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (142 bp):
GATACGAAATGTTTTGAAGATTTCTATACCTATACGAAAAACCATAGGAATATTAGAAATTTTGA
GAAATTAAGATAATAATTTTTATTTAATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATG
GAGAAACAAAAA
Found at i:1467877 original size:12 final size:11
Alignment explanation
Indices: 1467857--1467898 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
1467847 TATTTTTCTA
*
1467857 TTTTTTCT-TG
1 TTTTTTCTCTT
1467867 TTTTTTCTC-T
1 TTTTTTCTCTT
1467877 TTTTTTCTCTCT
1 TTTTTTCTCT-T
1467889 TTTTTTCTCT
1 TTTTTTCTCT
1467899 CCCCTTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:1467899 original size:12 final size:12
Alignment explanation
Indices: 1467862--1467899 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1467852 TTCTATTTTT
1467862 TCTTGTTTTT-TC
1 TCTT-TTTTTCTC
1467874 TCTTTTTTTCTC
1 TCTTTTTTTCTC
1467886 TCTTTTTTTCTC
1 TCTTTTTTTCTC
1467898 TC
1 TC
1467900 CCCTTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (12 bp):
TCTTTTTTTCTC
Found at i:1468052 original size:19 final size:19
Alignment explanation
Indices: 1468011--1468052 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1468001 TTTTCTTTTC
*
1468011 TTTTTATTTTTCATGACAT
1 TTTTTATTTTTCATGACAA
*
1468030 TTTTCTATTTTTTATG-CAA
1 TTTT-TATTTTTCATGACAA
1468049 TTTT
1 TTTT
1468053 ATGAGATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTTCATGACAA
Found at i:1469699 original size:18 final size:18
Alignment explanation
Indices: 1469676--1469714 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1469666 ATCATAATAT
*
1469676 ATTA-TTATACAAAATTAC
1 ATTATTTAT-CAAAATGAC
1469694 ATTATTTATCAAAATGAC
1 ATTATTTATCAAAATGAC
1469712 ATT
1 ATT
1469715 GAATAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATTTATCAAAATGAC
Found at i:1475530 original size:2 final size:2
Alignment explanation
Indices: 1475523--1475556 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1475513 CAATAGCATC
* *
1475523 AT AT AT AT AT AT AT AT AT AT AT AT GT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1475557 CGCATCATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1475872 original size:28 final size:28
Alignment explanation
Indices: 1475808--1475862 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1475798 CAAATGCCAC
*
1475808 CCTTTGTATTTGTTAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1475836 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1475863 ATTTTTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1475903 original size:24 final size:24
Alignment explanation
Indices: 1475844--1475912 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1475834 TTCCTTTGTA
* * *
1475844 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
1475870 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
1475894 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
1475913 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:1480450 original size:28 final size:28
Alignment explanation
Indices: 1480386--1480440 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1480376 CAAATGCCAC
*
1480386 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
1480414 CCTTTGTATTTGTCAAATATGGTAGTT
1 CCTTTGTATTTGTCAAATATGGTAGTT
1480441 ATTTTTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTAGTTT
Found at i:1480481 original size:24 final size:24
Alignment explanation
Indices: 1480445--1480490 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1480435 GTAGTTATTT
1480445 TTGTATGTAAAAAATGGTGGCTTG
1 TTGTATGTAAAAAATGGTGGCTTG
* * *
1480469 TTGTTTGTCAAAATTGGTGGCT
1 TTGTATGTAAAAAATGGTGGCT
1480491 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (24 bp):
TTGTATGTAAAAAATGGTGGCTTG
Found at i:1484417 original size:231 final size:229
Alignment explanation
Indices: 1483984--1484447 Score: 813
Period size: 231 Copynumber: 2.0 Consensus size: 229
1483974 CTGTCATTTG
*
1483984 TGATCTCTTTGTTATATTTTAAGACAAATTCTAAAAATGTCCTCGTATGTTTTAAAATTAAGTTT
1 TGATATCTTTGTTATATTTTAAGACAAATTCTAAAAATGTCCTCGTATGTTTTAAAATTAAGTTT
1484049 TATATTTGACACATGGACCGTTAGTGTCTTAGATTTTCACTACGTTCTTGTATTGAATAAATTAG
66 TATATTTGACACATGGACCGTTAGTGTCTTAGATTTTCACTACGTTCTTGTATTGAATAAATTAG
* * * *
1484114 ATTTTTAATCTTTAATTTGTGATCTCTTTATTGTTTCTTAAGGCTAAAATATTAAAAAAATCCTC
131 ATTTTTAATCTTTAATTCGTAATCTCTTTATTGTTTCTTAAAGCTAAAATACTAAAAAAATCCTC
*
1484179 GTATATTTTAAAATTATATTTATATTTAACGCAT
196 ATATATTTTAAAATTATATTTATATTTAACGCAT
1484213 TGATATCTTTGTTATATTTTAAGACTAAAATTCTAAAAAAT-TCCTCGTATGTTTTAAAATTAAG
1 TGATATCTTTGTTATATTTTAAGAC--AAATTCT-AAAAATGTCCTCGTATGTTTTAAAATTAAG
* *
1484277 TTTTATATTTGACGCATGGACCGTTTGTGTCTTAGATTTTCACTACGTTCTTGTATTGAATAAAT
63 TTTTATATTTGACACATGGACCGTTAGTGTCTTAGATTTTCACTACGTTCTTGTATTGAATAAAT
1484342 TAGATTTTTAATCTTTAATTCGTAATCTCTTTATTGTTTCTTAAAGCTAAAATACTAAAAAAATC
128 TAGATTTTTAATCTTTAATTCGTAATCTCTTTATTGTTTCTTAAAGCTAAAATACTAAAAAAATC
*
1484407 CTCATATATTTTAAAATTATATTTATATTTAATGCAT
193 CTCATATATTTTAAAATTATATTTATATTTAACGCAT
1484444 TGAT
1 TGAT
1484448 CATCCGTGAA
Statistics
Matches: 223, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
229 24 0.11
231 193 0.87
232 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (229 bp):
TGATATCTTTGTTATATTTTAAGACAAATTCTAAAAATGTCCTCGTATGTTTTAAAATTAAGTTT
TATATTTGACACATGGACCGTTAGTGTCTTAGATTTTCACTACGTTCTTGTATTGAATAAATTAG
ATTTTTAATCTTTAATTCGTAATCTCTTTATTGTTTCTTAAAGCTAAAATACTAAAAAAATCCTC
ATATATTTTAAAATTATATTTATATTTAACGCAT
Found at i:1484844 original size:165 final size:166
Alignment explanation
Indices: 1484570--1484872 Score: 391
Period size: 165 Copynumber: 1.8 Consensus size: 166
1484560 TTCAAGTGAG
* * *
1484570 CTAGATTTTCACTACTTTCTTAAATAAAATGAATTATACTGTAATCTGTAATTTGTGATATGTTG
1 CTAGATTTTCACTACTTTCTTAAATAAAATGAATTATACTCTAATCTATAATTTGTGATATCTTG
* * * *
1484635 TTATTTCTTAAGACTAGAGTACCAAAGAAATCCTTATATGTTTTAAAATTGTATTGATAT-TTT-
66 TTATTTCTTAAGACTAAAATACCAAAGAAATCATTATATGTTTTAAAATTGAATT-ATATATTTG
*
1484698 ATGTACTAACAATATATATCTAAACACTATTATTAAA
130 ATGCACTAACAATATATATCTAAACACTATTATTAAA
* * * *
1484735 CTAGATTTTCACTACTTTC-T-AATACTGAATGAATTAT-TTCCTAATCTATAATTTTTGATCTC
1 CTAGATTTTCACTACTTTCTTAAATA--AAATGAATTATACT-CTAATCTATAATTTGTGATATC
* * * *
1484797 TTGTTATTTCTTAAGGCTAAAATACTAAAGAAATCATTGTTTGTTTTAAAATTGAATTATATATT
63 TTGTTATTTCTTAAGACTAAAATACCAAAGAAATCATTATATGTTTTAAAATTGAATTATATATT
1484862 TGATGCACTAA
128 TGATGCACTAA
1484873 TTGAGTACAT
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
163 4 0.03
164 6 0.05
165 99 0.85
166 8 0.07
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (166 bp):
CTAGATTTTCACTACTTTCTTAAATAAAATGAATTATACTCTAATCTATAATTTGTGATATCTTG
TTATTTCTTAAGACTAAAATACCAAAGAAATCATTATATGTTTTAAAATTGAATTATATATTTGA
TGCACTAACAATATATATCTAAACACTATTATTAAA
Found at i:1486577 original size:21 final size:21
Alignment explanation
Indices: 1486552--1486592 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1486542 GCTTATAAGC
1486552 TTGGTG-AATAGTATAATTTTT
1 TTGGTGTAATA-TATAATTTTT
*
1486573 TTGGTGTAATATTTAATTTT
1 TTGGTGTAATATATAATTTT
1486593 AGAATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (21 bp):
TTGGTGTAATATATAATTTTT
Found at i:1490028 original size:37 final size:37
Alignment explanation
Indices: 1489987--1490092 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
1489977 TCAGTTTCAA
*
1489987 CCATGCCATCGATTAGAATAGTGGTTTTTGTTTTGAT
1 CCATGCCATCGATAAGAATAGTGGTTTTTGTTTTGAT
* *
1490024 CCATGCCATCGGTAAGAATAGTGATTTTTGTTTTGAT
1 CCATGCCATCGATAAGAATAGTGGTTTTTGTTTTGAT
* * *
1490061 CTATGCCACCGATAAGAATAATGGTTTTTGTT
1 CCATGCCATCGATAAGAATAGTGGTTTTTGTT
1490093 CTAAGCGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (37 bp):
CCATGCCATCGATAAGAATAGTGGTTTTTGTTTTGAT
Found at i:1491246 original size:33 final size:33
Alignment explanation
Indices: 1491209--1491275 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1491199 TTCAATGATT
1491209 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1491242 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1491275 T
1 T
1491276 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1491247 original size:13 final size:13
Alignment explanation
Indices: 1491229--1491253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1491219 CATAAAATGT
1491229 TGTATCGATACAA
1 TGTATCGATACAA
1491242 TGTATCGATACA
1 TGTATCGATACA
1491254 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1491334 original size:13 final size:13
Alignment explanation
Indices: 1491316--1491340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1491306 ATTACTCAAA
1491316 TGTATCGATACAT
1 TGTATCGATACAT
1491329 TGTATCGATACA
1 TGTATCGATACA
1491341 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1491405 original size:52 final size:52
Alignment explanation
Indices: 1491349--1491468 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
1491339 CACCGATCTT
* *
1491349 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
1491401 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
1491453 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1491469 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:1499347 original size:21 final size:21
Alignment explanation
Indices: 1499323--1499363 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1499313 ATAATGTTTT
*
1499323 GATACATTGCAAGCATGTATC
1 GATACATTACAAGCATGTATC
*
1499344 GATACATTATAAGCATGTAT
1 GATACATTACAAGCATGTAT
1499364 ATTACAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
GATACATTACAAGCATGTATC
Done.