Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold282
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: 1446459
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 4 of 10
Found at i:477643 original size:104 final size:104
Alignment explanation
Indices: 477463--477986 Score: 850
Period size: 104 Copynumber: 5.1 Consensus size: 104
477453 AATAGGTATT
*
477463 TGTATCGATACATTATGGTTGACTTAAGTTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
1 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
*
477528 TCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
66 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
* * * *
477567 TGTATCAATATATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCTTAAATGTATCGATACACA
1 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
477632 CCCAGATGTATCGATACATTATGCTTTGTATCGATA-CA
66 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
* * * *
477670 TG----GACA-ATTGT-ATCGACTTAAGCTAC-AAGGTCAAAATCCTTGAATGTATCGATACACA
1 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
477728 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
66 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
477767 TGTATCGATACATTATGGTTGACTTAAGCTAC-AAGGTCAAAATCCTTGAATGTATCGATACACA
1 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
*
477831 CCCAGATGTATTGATACATTATGCTTTGTATCGATACCA
66 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
* *
477870 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCTTGAATGTATTGATACACA
1 TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
*
477935 CCCAGATGTATCGATACATTATGCTTTGTATCGATACAA
66 CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
*
477974 TGTATTGATACAT
1 TGTATCGATACAT
477987 GTTCATTGTA
Statistics
Matches: 389, Mismatches: 23, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
96 66 0.17
97 17 0.04
98 4 0.01
99 2 0.01
101 3 0.01
102 4 0.01
103 119 0.31
104 174 0.45
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (104 bp):
TGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAATCCTTGAATGTATCGATACACA
CCCAGATGTATCGATACATTATGCTTTGTATCGATACCA
Found at i:477839 original size:103 final size:103
Alignment explanation
Indices: 477684--477986 Score: 552
Period size: 103 Copynumber: 2.9 Consensus size: 103
477674 CAATTGTATC
477684 GACTTAAGCTACAAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATCGATACATTA
1 GACTTAAGCTACAAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATCGATACATTA
477749 TGCTTTGTATCGATACCATGTATCGATACATTATGGTT
66 TGCTTTGTATCGATACCATGTATCGATACATTATGGTT
*
477787 GACTTAAGCTACAAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATTGATACATTA
1 GACTTAAGCTACAAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATCGATACATTA
477852 TGCTTTGTATCGATACCATGTATCGATACATTATGGTT
66 TGCTTTGTATCGATACCATGTATCGATACATTATGGTT
* *
477890 GACTTAAGCTACAAAGGTCAAAACCCTTGAATGTATTGATACACACCCAGATGTATCGATACATT
1 GACTTAAGCTAC-AAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATCGATACATT
* *
477955 ATGCTTTGTATCGATACAATGTATTGATACAT
65 ATGCTTTGTATCGATACCATGTATCGATACAT
477987 GTTCATTGTA
Statistics
Matches: 193, Mismatches: 6, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
103 114 0.59
104 79 0.41
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (103 bp):
GACTTAAGCTACAAGGTCAAAATCCTTGAATGTATCGATACACACCCAGATGTATCGATACATTA
TGCTTTGTATCGATACCATGTATCGATACATTATGGTT
Found at i:477984 original size:33 final size:32
Alignment explanation
Indices: 477940--478004 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
477930 ACACACCCAG
*
477940 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
*
477973 ATGTATTGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
478005 TGGACAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:478016 original size:20 final size:20
Alignment explanation
Indices: 477970--478022 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
477960 TTGTATCGAT
* *
477970 ACAA-TGTATTGATACATGT
1 ACAATTGTATCGATACATGG
*
477989 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
478008 ACAATTGTATCGATA
1 ACAATTGTATCGATA
478023 AATGAAACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:478422 original size:13 final size:13
Alignment explanation
Indices: 478404--478428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
478394 CATAAAATGT
478404 TGTATCGATACAA
1 TGTATCGATACAA
478417 TGTATCGATACA
1 TGTATCGATACA
478429 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:478426 original size:33 final size:33
Alignment explanation
Indices: 478384--478453 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
478374 TTCAACGATT
478384 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
478417 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
478450 TGTA
1 TGTA
478454 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:478513 original size:13 final size:13
Alignment explanation
Indices: 478495--478519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
478485 ATTACTCACA
478495 TGTATCGATACAT
1 TGTATCGATACAT
478508 TGTATCGATACA
1 TGTATCGATACA
478520 CTGATCTTTG
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:478584 original size:52 final size:52
Alignment explanation
Indices: 478528--478648 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
478518 CACTGATCTT
*
478528 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
478580 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
478632 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
478649 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:484287 original size:51 final size:52
Alignment explanation
Indices: 484169--484307 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 52
484159 ATTTGCCTGC
**
484169 ATGTATCGATACGTTGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
* * **
484221 ATGCATTGATACAATGAAGAATGTATCGATACATTTGGGTC-AAAACTTAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
* * *
484272 ATGTATCAATACAATGAAAAATGTATAGATACATTT
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT
484308 TCATTCTATA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 39 0.51
52 37 0.49
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
Found at i:486626 original size:9 final size:9
Alignment explanation
Indices: 486612--486680 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
486602 TGCAGCTGAA
486612 TTTTTTTTC
1 TTTTTTTTC
486621 -TTTTTTTC
1 TTTTTTTTC
486629 TTATGTATTTT-
1 TT-T-T-TTTTC
486640 TTGTTTTTTC
1 TT-TTTTTTC
* *
486650 CTTTTCTTC
1 TTTTTTTTC
*
486659 TTTTTGTTC
1 TTTTTTTTC
486668 TTTTTTTT-
1 TTTTTTTTC
486676 TTTTT
1 TTTTT
486681 GAAATTCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 13 0.27
9 25 0.51
10 3 0.06
11 4 0.08
12 4 0.08
ACGTcount: A:0.03, C:0.10, G:0.04, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:486677 original size:30 final size:28
Alignment explanation
Indices: 486612--486679 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
486602 TGCAGCTGAA
*
486612 TTTTTTTTCTTTTTTTCTTATGTATTTT
1 TTTTTTTTCTTTTCTTCTTATGTATTTT
* *
486640 TTGTTTTTTCCTTTTCTTCTTTTTGTTCTTTT
1 TT-TTTTTT-CTTTTCTTC-TTATG-TATTTT
486672 TTTTTTTT
1 TTTTTTTT
486680 TGAAATTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 6 0.18
30 8 0.24
31 10 0.30
32 7 0.21
ACGTcount: A:0.03, C:0.10, G:0.04, T:0.82
Consensus pattern (28 bp):
TTTTTTTTCTTTTCTTCTTATGTATTTT
Found at i:488032 original size:50 final size:50
Alignment explanation
Indices: 487957--488087 Score: 174
Period size: 50 Copynumber: 2.6 Consensus size: 50
487947 ACAAGTTGTG
* * * *
487957 TCGATACATTCCTCATTGTATCGATACATTTTGTGTTTTACCTAGATGTA
1 TCGATACATTTCTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTA
* *
488007 TCGATACATTTTTCATTGTATCGATATATTCTGGGTTTTACCCAGATGTA
1 TCGATACATTTCTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTA
* *
488057 TC-AGTACATATCTCAATGTATCGATACATTC
1 TCGA-TACATTTCTCATTGTATCGATACATTC
488088 AAGCATTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 69 0.99
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (50 bp):
TCGATACATTTCTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTA
Found at i:490184 original size:79 final size:79
Alignment explanation
Indices: 490044--490488 Score: 484
Period size: 79 Copynumber: 5.6 Consensus size: 79
490034 CATCGATGTT
* * * * *
490044 TTTATTTCCAAAACACCAATTTTTCACTATCGAGGATACTCTAACCCTGTTA-TTTCTGAGGGGA
1 TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTATTTTC-GAGGGGA
*
490108 TACTCCAA-CCTCAAC
65 TACTCCAACCCT-GAC
* * * * *
490123 TTTATTTCAAAAATATCAATTTTTCACAATCAAGGATACTCCAACCCCGTCATTTTCGAGGGGAT
1 TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGAT
*
490188 ACTCCAACCCTGGC
66 ACTCCAACCCTGAC
* * * * * * * *
490202 CTTATTTCTAAAACATCGATTTTCCACAATCGTGGATACTCCAACCCCATTATTTTCGATGAGAT
1 TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGAT
* *
490267 ACTCTAACCCTGAT
66 ACTCCAACCCTGAC
* * *
490281 TTTATTTCCAAAACACCCATTTTCCACCATCGAGGATACTCCAACCCCGTTA-TTTCTGAGGGGA
1 TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTATTTTC-GAGGGGA
* *
490345 TACTCCAACCCCGAT
65 TACTCCAACCCTGAC
* * * * *
490360 TTTATTTCTAAAACACCCATTTGT-CACCATCGAGGATACTCCAATCCCGTTATTTCCGAGGGGA
1 TTTATTTCAAAAACACCAATTT-TCCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
490424 TACTCCACCCCCTGAC
65 TACTCCA-ACCCTGAC
* * * *
490440 TTTATTTCAAAAACATCGATTTTCCATAATCGGGGATACTCCAACCCCG
1 TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCG
490489 ATTTTATTTC
Statistics
Matches: 311, Mismatches: 48, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
78 4 0.01
79 251 0.81
80 56 0.18
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (79 bp):
TTTATTTCAAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGAT
ACTCCAACCCTGAC
Found at i:490508 original size:51 final size:51
Alignment explanation
Indices: 490419--490539 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
490409 TTATTTCCGA
* *
490419 GGGGATACTCCACCCCCTGACTTTATTTCAAAAACATCGATTTTCCATAATC
1 GGGGATACTCCAACCCC-GACTTTATTTCAAAAACATCGATTTTCCACAATC
* * * *
490471 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTCCACCATT
1 GGGGATACTCCAACCCCGACTTTATTTCAAAAACATCGATTTTCCACAATC
*
490522 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
490540 TTATTTTTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 46 0.74
52 16 0.26
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCAAAAACATCGATTTTCCACAATC
Found at i:494669 original size:73 final size:73
Alignment explanation
Indices: 494549--494692 Score: 270
Period size: 73 Copynumber: 2.0 Consensus size: 73
494539 CCAAATCGAT
* *
494549 GATCTAAGAAGGGATTTCGAGCAATGAAAACATGAATGGCTGTAAACAGTTGACCTTGCACACCA
1 GATCTAAGAAGGGATTTCGAGCAATGAAAACAAGAATGGCTGCAAACAGTTGACCTTGCACACCA
494614 GGACTAAA
66 GGACTAAA
494622 GATCTAAGAAGGGATTTCGAGCAATGAAAACAAGAATGGCTGCAAACAGTTGACCTTGCACACCA
1 GATCTAAGAAGGGATTTCGAGCAATGAAAACAAGAATGGCTGCAAACAGTTGACCTTGCACACCA
494687 GGACTA
66 GGACTA
494693 TCAAGGCCAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (73 bp):
GATCTAAGAAGGGATTTCGAGCAATGAAAACAAGAATGGCTGCAAACAGTTGACCTTGCACACCA
GGACTAAA
Found at i:499533 original size:33 final size:33
Alignment explanation
Indices: 499496--499562 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
499486 TTCAACGATT
499496 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
499529 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
499562 T
1 T
499563 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:499534 original size:13 final size:13
Alignment explanation
Indices: 499516--499540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
499506 CATAAAATGT
499516 TGTATCGATACAA
1 TGTATCGATACAA
499529 TGTATCGATACA
1 TGTATCGATACA
499541 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:499632 original size:13 final size:13
Alignment explanation
Indices: 499614--499638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
499604 ATTACTCACA
499614 TGTATCGATACAT
1 TGTATCGATACAT
499627 TGTATCGATACA
1 TGTATCGATACA
499639 CTGATCTTTG
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:499740 original size:52 final size:52
Alignment explanation
Indices: 499647--499774 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
499637 CACTGATCTT
*
499647 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
499698 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
499750 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
499775 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:507038 original size:12 final size:12
Alignment explanation
Indices: 507021--507053 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
507011 ACCTACTCTT
507021 CAAAAAAAAAAA
1 CAAAAAAAAAAA
507033 CAAAAAAAAAAA
1 CAAAAAAAAAAA
507045 -AAGAAAAAA
1 CAA-AAAAAA
507054 CCCCTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 18 0.90
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:507041 original size:14 final size:14
Alignment explanation
Indices: 507022--507053 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
507012 CCTACTCTTC
507022 AAAAAAAAAAACAA
1 AAAAAAAAAAACAA
*
507036 AAAAAAAAAAAGAA
1 AAAAAAAAAAACAA
507050 AAAA
1 AAAA
507054 CCCCTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAACAA
Found at i:508031 original size:30 final size:31
Alignment explanation
Indices: 507995--508076 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
507985 ATACCTTTTT
507995 AAAGTCCACGACTCAGTGGCATTTTGTC-TC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
508025 AAAGTCCACGACTCAGTGGCATTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* * *
508056 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
508077 CCTTGTTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTTC
Found at i:508099 original size:33 final size:33
Alignment explanation
Indices: 508025--508512 Score: 498
Period size: 33 Copynumber: 14.9 Consensus size: 33
508015 ATTTTGTCTC
* * * *
508025 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
*
508056 AAAGCCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAAGCCCACAACTCCGTGGCA-CTTTTTCCTTTT
*
508090 -AAGTCCACAACTCCGTGGCAC-----CCTTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
* * *
508117 AAAGCCCACAATTCTGTGGCACTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCT-TTT
*
508151 -AAGTCCACAACTCCGTGGCAC-----CCTTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
* * *
508178 AAAGCCCACAATTCTGTGGCACTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCT-TTT
* *
508212 -AAGTCCACAACTCCGTGGCAC-----CCGTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
*
508239 -AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCA-CTTTTTCCTTTT
*
508272 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
508305 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCA--CTTTTT-CCTTTT
*
508341 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
508375 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCA--CTTTTT-CCTTTT
508411 CAAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
1 -AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
508445 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCA--CTTTTT-CCTTTT
*
508481 -AAGTCCACAACTCCGTGGCATCTTTTTTCCTT
1 AAAGCCCACAACTCCGTGGCA-C-TTTTTCCTT
508513 CCCAAAGCCC
Statistics
Matches: 389, Mismatches: 32, Indels: 69
0.79 0.07 0.14
Matches are distributed among these distances:
27 31 0.08
28 40 0.10
31 18 0.05
32 1 0.00
33 141 0.36
34 46 0.12
35 54 0.14
36 16 0.04
37 42 0.11
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
Found at i:508118 original size:61 final size:62
Alignment explanation
Indices: 508053--508500 Score: 503
Period size: 61 Copynumber: 6.9 Consensus size: 62
508043 GCATTTTTTC
*
508053 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCAC-CCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCCT
* * *
508114 TTTAAAGCCCACAATTCTGTGGCA-CTTTTTCATCTTTAAGTCCACAACTCCGTGGCAC-CCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACTCCT
* * * *
508175 TTTAAAGCCCACAATTCTGTGGCA-CTTTTTCATCTTTAAGTCCACAACTCCGTGGCAC-CCG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACTCCT
* * *
508236 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCAC----TC
508300 CT
61 CT
*
508302 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGTCCACAACTCCGTGGCAC---
*
508367 TTTCT
59 -TCCT
*
508372 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGTCCACAACTCCGTGGCAC---
508437 TTCCT
59 -TCCT
508442 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGTCCACAACTCCGTGGCA
508501 TCTTTTTTCC
Statistics
Matches: 361, Mismatches: 14, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
60 28 0.08
61 140 0.39
66 4 0.01
67 21 0.06
68 25 0.07
69 5 0.01
70 138 0.38
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCCT
Found at i:508247 original size:27 final size:26
Alignment explanation
Indices: 508208--508260 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
508198 ACTTTTTCAT
*
508208 CTTTAAGTCCACAACTCCGTGGCACC
1 CTTTAAGCCCACAACTCCGTGGCACC
508234 CGTTTAAGCCCACAACTCCGTGGCACC
1 C-TTTAAGCCCACAACTCCGTGGCACC
508261 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.21
Consensus pattern (26 bp):
CTTTAAGCCCACAACTCCGTGGCACC
Found at i:508357 original size:70 final size:66
Alignment explanation
Indices: 508026--508512 Score: 546
Period size: 70 Copynumber: 7.5 Consensus size: 66
508016 TTTTGTCTCA
* * * *
508026 AAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTT
1 AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
508089 T
66 T
* * *
508090 AAGTCCACAACTCCGTGGCAC-----CCTTTTAAAGCCCACAATTCTGTGGCA-CTTTTTCATCT
1 AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-T
508149 TT
65 TT
* * *
508151 AAGTCCACAACTCCGTGGCAC-----CCTTTTAAAGCCCACAATTCTGTGGCA-CTTTTTCATCT
1 AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-T
508210 TT
65 TT
* *
508212 AAGTCCACAACTCCGTGGCAC-----CCGTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
508271 T
66 T
* *
508272 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 -AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CC
508337 TTTT
63 TTTT
* *
508341 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 --AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
508406 CTTTT
62 CTTTT
*
508411 CAAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 --AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
508476 CTTTT
62 CTTTT
508481 AAGTCCACAACTCCGTGGCATCTTTTTTCCTT
1 AAGTCCACAACTCCGTGGCA-C-TTTTTCCTT
508513 CCCAAAGCCC
Statistics
Matches: 390, Mismatches: 17, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
60 29 0.07
61 140 0.36
64 18 0.05
66 4 0.01
67 21 0.05
68 25 0.06
69 6 0.02
70 147 0.38
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (66 bp):
AAGTCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
T
Found at i:508692 original size:49 final size:49
Alignment explanation
Indices: 508579--509495 Score: 1251
Period size: 49 Copynumber: 18.7 Consensus size: 49
508569 GCAACCCCTC
* *
508579 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
508627 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
508676 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC-T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
508727 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
508776 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
508825 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
508874 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-CCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
508922 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
508971 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC-T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
509022 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
509071 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
509120 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
509169 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
509218 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
509267 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
509316 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
509365 TAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
509408 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
509460 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
509496 ACATCCTTTT
Statistics
Matches: 758, Mismatches: 92, Indels: 34
0.86 0.10 0.04
Matches are distributed among these distances:
43 38 0.05
45 1 0.00
48 88 0.12
49 505 0.67
50 1 0.00
51 82 0.11
52 43 0.06
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:509120 original size:295 final size:295
Alignment explanation
Indices: 508579--509495 Score: 1474
Period size: 295 Copynumber: 3.1 Consensus size: 295
508569 GCAACCCCTC
*
508579 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTG
508644 GCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
66 GCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
*
508709 TTGGCACCTTTTCCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
131 TTGGCACCTTTTCCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
*
508774 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
196 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAG
508839 CTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
261 CTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
* * * *
508874 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCCACCATTAAGTCCAATGTAGCTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTG
508939 GCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
66 GCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
509004 TTGGCACCTTTTCCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
131 TTGGCACCTTTTCCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
509069 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAG
196 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAG
* * *
509134 CTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
261 CTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
* * *
509169 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CCTCATCTTTAAGTCCAATGTAGCT
* * *
509234 GGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
65 GGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
**
509299 ATTGGCA--TCAT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
130 ATTGGCACCTTTTCCATC-TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * *
509361 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGG---CA-C--CTTTAAGTCCAATAT
194 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
* * *
509420 AGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
259 AGCTGGCCTTGACTCAGCACATTGGCACC-TTT--ATCTT
* *
509460 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
509496 ACATCCTTTT
Statistics
Matches: 580, Mismatches: 37, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
288 40 0.07
289 2 0.00
290 1 0.00
291 37 0.06
293 4 0.01
294 85 0.15
295 321 0.55
296 90 0.16
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (295 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTG
GCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
TTGGCACCTTTTCCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAG
CTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
Found at i:509429 original size:22 final size:22
Alignment explanation
Indices: 509361--509429 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
509351 GGCACCTTCA
*
509361 CCTTTAAGTCCAATGTAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * * *
509383 CCTTGAA-T-CAACACA-TTGG
1 CCTTTAAGTCCAATATAGCTGG
509402 CACCTTTAAGTCCAATATAGCTGG
1 --CCTTTAAGTCCAATATAGCTGG
509426 CCTT
1 CCTT
509430 GAATCAGCAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.21
22 11 0.33
23 5 0.15
24 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:509541 original size:56 final size:52
Alignment explanation
Indices: 509405--509543 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
509395 ACATTGGCAC
* *
509405 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
* * *
509457 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTC--CAT
* * * *
509513 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
509544 ACATATTGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 37 0.51
53 2 0.03
54 5 0.07
56 28 0.39
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
Found at i:510410 original size:13 final size:13
Alignment explanation
Indices: 510392--510416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
510382 CATAAAATGT
510392 TGTATCGATACAA
1 TGTATCGATACAA
510405 TGTATCGATACA
1 TGTATCGATACA
510417 TATTTTTTGT
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:510432 original size:32 final size:33
Alignment explanation
Indices: 510372--510437 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
510362 TTCAACGATT
510372 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
510405 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
510437 T
1 T
510438 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:510502 original size:13 final size:13
Alignment explanation
Indices: 510484--510508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
510474 ATTACTCACA
510484 TGTATCGATACAT
1 TGTATCGATACAT
510497 TGTATCGATACA
1 TGTATCGATACA
510509 CTGATCTTTG
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:510610 original size:52 final size:52
Alignment explanation
Indices: 510517--510644 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
510507 CACTGATCTT
*
510517 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
510568 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
510620 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
510645 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:514953 original size:28 final size:28
Alignment explanation
Indices: 514902--514972 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
514892 TTTTCACATT
*
514902 GGGGATACTCCAACCTCGTCATTTCTGA
1 GGGGATACTCTAACCTCGTCATTTCTGA
* *
514930 GGGGATACTCTAAGCC-CGTTATTTTTGA
1 GGGGATACTCTAA-CCTCGTCATTTCTGA
514958 GGGGATACTCTAACC
1 GGGGATACTCTAACC
514973 CTGACCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (28 bp):
GGGGATACTCTAACCTCGTCATTTCTGA
Found at i:515013 original size:106 final size:105
Alignment explanation
Indices: 514825--515050 Score: 267
Period size: 106 Copynumber: 2.1 Consensus size: 105
514815 TTCCACCATC
* * *
514825 GAGGATACTCCAACCTCGTTATTTCCGAGGGATACTCCAACCCTGACTTTATTTCTAAAATATTA
1 GAGGATACTCCAACCTCGTTATTTCCGAGGGATACTCCAACCCTGACCTTATTTCTAAAACATCA
* * * * *
514890 ATTTTTCACATTGGGGATACTCCAACCTCGTCATTTCTGA
66 ATTTTTCACAATCGGGATACTCAAACCCCATCATTTCTGA
* * ** *
514930 GGGGATACTCTAAGCC-CGTTATTTTTGAGGGGATACTCTAACCCTGACCTTATTTCTAAAACAT
1 GAGGATACTCCAA-CCTCGTTATTTCCGA-GGGATACTCCAACCCTGACCTTATTTCTAAAACAT
* * *
514994 CGA-TTTTCAACAATCGGGATACTCAAACCCCATTATTTTTGA
64 CAATTTTTC-ACAATCGGGATACTCAAACCCCATCATTTCTGA
515036 GAGGATACTCCAACC
1 GAGGATACTCCAACC
515051 CTGATTTTAT
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
105 28 0.28
106 72 0.72
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (105 bp):
GAGGATACTCCAACCTCGTTATTTCCGAGGGATACTCCAACCCTGACCTTATTTCTAAAACATCA
ATTTTTCACAATCGGGATACTCAAACCCCATCATTTCTGA
Found at i:515127 original size:79 final size:79
Alignment explanation
Indices: 514932--515346 Score: 460
Period size: 78 Copynumber: 5.3 Consensus size: 79
514922 ATTTCTGAGG
* * * ** *
514932 GGATACTCTAAGCCCGTTATTTTTGAGGGGATACTCTAACCCTGACCTTATTTCTAAAACATCGA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACATCGA
* *
514997 TTTTCAACAATCG-
66 TTTTCCACCATCGA
* * * * *
515010 GGATACTCAAACCCCATTATTTTTGAGAGGATACTCCAACCCTGATTTTATTTCCAAAACACCCA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACATCGA
*
515075 TTTTCTACCATCGA
66 TTTTCCACCATCGA
* * *
515089 GGATACTCCAACCCCGTTATTTTGGAGGGGATACTCCAACCCT-ATTTTATTTCCAAAACACCCA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACATCGA
515153 TTTTCCACCATCGA
66 TTTTCCACCATCGA
* * * ** * *
515167 GGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCACCCCTGGCTTTATTTCTAAAACATTGA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACATCGA
** **
515232 TTTTTTATAATCGA
66 TTTTCCACCATCGA
* * * * * *
515246 GGATACTCGAATCTCGTTATTTTCGAGGGGATACACCAA-CCTCGATTTTATTTCCAAAATATCG
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCT-GATTTTATTTCCAAAACATCG
*
515310 ATTTTCCACCAT-TA
65 ATTTTCCACCATCGA
*
515324 GGGATACTCTAACCCCGTTATTT
1 -GGATACTCCAACCCCGTTATTT
515347 CTGAAGAGGT
Statistics
Matches: 281, Mismatches: 52, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
78 143 0.51
79 138 0.49
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACATCGA
TTTTCCACCATCGA
Found at i:515171 original size:157 final size:157
Alignment explanation
Indices: 514932--515360 Score: 486
Period size: 157 Copynumber: 2.7 Consensus size: 157
514922 ATTTCTGAGG
* * * * ** *
514932 GGATACTCTAAGCCCGTTATTTTTGAGGGGATACTCTAACCCTGACCTTATTTCTAAAACATCGA
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCT-ATTTTATTTCCAAAACATCGA
* * * * *
514997 TTTTCAACAATCG-GGATACTCAAACCCCATTATTTTTGAGAGGATACTCCAACCCTGATTTTAT
65 TTTTCCACCATCGAGGATACTCAAACCCCGTTATTTCTGAGAGGATACTCCAACCCTGACTTTAT
*
515061 TTCCAAAACACCCATTTTCTACCATCGA
130 TTCCAAAACACCCATTTTCTACAATCGA
* * *
515089 GGATACTCCAACCCCGTTATTTTGGAGGGGATACTCCAACCCTATTTTATTTCCAAAACACCCAT
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTATTTTATTTCCAAAACATCGAT
* * * * *
515154 TTTCCACCATCGAGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCACCCCTGGCTTTATT
66 TTTCCACCATCGAGGATACTCAAACCCCGTTATTTCTGAGAGGATACTCCAACCCTGACTTTATT
* *** * *
515219 TCTAAAACATTGATTTTTTATAATCGA
131 TCCAAAACACCCATTTTCTACAATCGA
* * * * * *
515246 GGATACTCGAATCTCGTTATTTTCGAGGGGATACACCAACCTCGATTTTATTTCCAAAATATCGA
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACC-CTATTTTATTTCCAAAACATCGA
* *
515311 TTTTCCACCAT-TAGGGATACTCTAACCCCGTTATTTCTGAAGAGG-TACTC
65 TTTTCCACCATCGA-GGATACTCAAACCCCGTTATTTCTG-AGAGGATACTC
515361 TGAGCCCGTT
Statistics
Matches: 229, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
156 27 0.12
157 140 0.61
158 58 0.25
159 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (157 bp):
GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTATTTTATTTCCAAAACATCGAT
TTTCCACCATCGAGGATACTCAAACCCCGTTATTTCTGAGAGGATACTCCAACCCTGACTTTATT
TCCAAAACACCCATTTTCTACAATCGA
Found at i:516773 original size:12 final size:12
Alignment explanation
Indices: 516758--516790 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
516748 ACCATCAAAG
516758 ATGATGAAGATA
1 ATGATGAAGATA
*
516770 ATGATGATGATA
1 ATGATGAAGATA
516782 ATGATGAAG
1 ATGATGAAG
516791 TTGACTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (12 bp):
ATGATGAAGATA
Found at i:517441 original size:55 final size:55
Alignment explanation
Indices: 517352--517553 Score: 244
Period size: 55 Copynumber: 3.5 Consensus size: 55
517342 GGGACGAATT
*
517352 TGGCGCCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * * *
517407 TGGCACCTTTCAGTCCTTAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
517462 TGGCACCTTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTTAAAGCCCACACAAGTTGG
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TTTC-----AAAGCCCACACAAGTTGG
*
517524 TGGCA-CTTCCTAGTCCTCAAAGAGCAGGAC
1 TGGCACCTTTC-AGTCCTCAAAGAGCAGGAC
517554 ACTCTCTCCT
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
55 79 0.63
57 3 0.02
61 3 0.02
62 41 0.33
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (55 bp):
TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
Found at i:517634 original size:55 final size:55
Alignment explanation
Indices: 517569--517755 Score: 234
Period size: 55 Copynumber: 3.3 Consensus size: 55
517559 CTCCTTTCAC
*
517569 CCTTT-AGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
517623 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
517678 CCTTTTAGTCCTCAAAGAGCAGGACACCTTTTACTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCC-TTT-C-----AAAGCCCACACAAGTTGGTGGCA
*
517740 -CTTCCCAGTCCTCAAA
1 CCTT-TCAGTCCTCAAA
517756 CACCAAGATG
Statistics
Matches: 115, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
54 5 0.04
55 72 0.63
56 3 0.03
61 3 0.03
62 32 0.28
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:517708 original size:26 final size:26
Alignment explanation
Indices: 517621--517710 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
517611 AAGTTGGTGG
*
517621 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTTAGTCCTCAAAGAGCAGGA
* * * * **
517647 CGCCTTTTAAAGCCCACATAAGTTGGTGG-
1 CACCTTTT--AGTCCTCA-AAG-AGCAGGA
517676 CACCTTTTAGTCCTCAAAGAGCAGGA
1 CACCTTTTAGTCCTCAAAGAGCAGGA
517702 CACCTTTTA
1 CACCTTTTA
517711 CTTTTTAAAG
Statistics
Matches: 46, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.39
27 6 0.13
28 6 0.13
29 10 0.22
30 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (26 bp):
CACCTTTTAGTCCTCAAAGAGCAGGA
Found at i:517727 original size:211 final size:211
Alignment explanation
Indices: 517357--518200 Score: 1079
Period size: 211 Copynumber: 3.9 Consensus size: 211
517347 GAATTTGGCG
517357 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * * *
517422 CTTAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TTAGTCCTCAAAGAG
66 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAG
* * *
517486 TAGGACACCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAG
130 CAGGACACC-TTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAG
517551 GACACTCTCTCCTTTCAC
194 GACACTCTCTCCTTTCAC
*
517569 CCTTT-AGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
517633 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTGGTGGCACCTT-TTAGTCCTCAAAGAG
66 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAG
* * * *
517697 CAGGACACCTTTTACTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAACACCAA
130 CAGGACACCTTCT-CTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAG
**
517762 GATGCTCTCTCCTTTCAC
194 GACACTCTCTCCTTTCAC
* * * * *
517780 CATTT-AGTCCTCAAGGAGTATGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * * *
517844 CTCAAAAAACACGACGCCTTTTAAAGCCCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGC
66 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
* * * *
517909 AGGACGCCTTCTCTTTTTAAAGCCCACACAAATTTGTGGCTCTTCCCAGTCCTCAAAGAGCAGGA
131 AGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA
* * *
517974 CGCCTTTCAAAGCCCACATAAGTTGGTGGCA-
196 C-AC--TC---TCTC-C-----TT--T--CAC
* * * ** *
518005 TCTTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTTTTAGT
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTTCAGT
*
518070 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
65 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
* * *
518135 CAGGACACCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCACTTCCTA-TCCTCAAAGAGCAGG
130 CAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
518199 AC
195 AC
518201 GCCTTCTCCT
Statistics
Matches: 555, Mismatches: 57, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
210 54 0.10
211 313 0.56
212 5 0.01
213 2 0.00
216 2 0.00
217 1 0.00
222 2 0.00
224 1 0.00
225 3 0.01
226 64 0.12
227 108 0.19
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (211 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
AGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA
CACTCTCTCCTTTCAC
Found at i:517827 original size:156 final size:149
Alignment explanation
Indices: 517621--517904 Score: 381
Period size: 156 Copynumber: 1.9 Consensus size: 149
517611 AAGTTGGTGG
* * *
517621 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCAG
* * * *
517686 TCCTCAAAGAGCAGGACACCTTTTACTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCC
66 TCCTCAAAAAACACGAC-CC-----C-TTTTAAAGCCCACACAAGTTGATGGCACTTCCCAGTCC
517751 TCAAACACCAAGATGCTCTCTCCTTT
124 TCAAACACCAAGATGCTCTCTCCTTT
* * *
517777 CACCATTT-AGTCCTCAAGGAGTATGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCA
1 CACC-TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCA
* *
517841 GTCCTCAAAAAACACGACGCCTTTTAAAGCCCACACAAGTTGATGGCACTTCCTAGTCCTCAAA
65 GTCCTCAAAAAACACGACCCCTTTTAAAGCCCACACAAGTTGATGGCACTTCCCAGTCCTCAAA
517905 GAGCAGGACG
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
149 41 0.36
150 1 0.01
155 1 0.01
156 69 0.60
157 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (149 bp):
CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCAG
TCCTCAAAAAACACGACCCCTTTTAAAGCCCACACAAGTTGATGGCACTTCCCAGTCCTCAAACA
CCAAGATGCTCTCTCCTTT
Found at i:517932 original size:61 final size:60
Alignment explanation
Indices: 517806--518257 Score: 464
Period size: 55 Copynumber: 7.8 Consensus size: 60
517796 AGTATGACGC
* * * * * *
517806 CTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTC-AGTCCTCAAAAAACACGACG----C-
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
*
517861 CTTTTAAAGCCCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
517921 CTTTTTAAAGCCCACACAAATTTGTGGCTCTTCCCAGTCCTCAAAGAGCAGGACGCCTT-T
1 C-TTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
517981 C----AAAGCCCACATAAGTTGGTGGCATCTTTC-AGTCCTCAAAGAGTAGGACGCCTT-T
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * **
518036 C----AAAGCCCACCCAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGACG----C-
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
* *
518088 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
*
518148 CCTTTTAAAACCCACACAAGTTGGTGGCACTTCCTA-TCCTCAAAGAGCAGGACGCCTTCT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
518208 CCTTTTAAAGCCCACACAAGTTGGTGTCACTTCTTAGTCCTTAGAGAGCA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCA
518258 AAACACTTTC
Statistics
Matches: 339, Mismatches: 37, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
52 1 0.00
54 4 0.01
55 132 0.39
56 45 0.13
59 2 0.01
60 59 0.17
61 96 0.28
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (60 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT
Found at i:518190 original size:171 final size:172
Alignment explanation
Indices: 517805--518257 Score: 501
Period size: 171 Copynumber: 2.6 Consensus size: 172
517795 GAGTATGACG
* * * *
517805 CCTTTCAAAGCCCACAAAAGTTGGTGGCACCTTTCAGTCCTCAAAAAACACGACGCCTTTTAAAG
1 CCTTT-AAAGCCCACAAAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAG
517870 CCCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCA
65 CCCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGCAGGACG-C--CTCTTTTTAAAGCCCA
* * *
517935 CACAAATTTGTGGCTCTTCCCAGTCCTCAAAGAGCAGGACGCCTTT
127 CACAAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTT
* * *
517981 -C---AAAGCCCACATAAGTTGGTGGCATCTTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGC
1 CCTTTAAAGCCCACAAAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
* * * **
518042 CCACCCAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGACG-C-C-TTTTAAAGCCCACAC
66 CCACACAAGTTGATGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCCTCTTTTTAAAGCCCACAC
*
518104 AAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCT
130 AAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTT-T
* * *
518148 CCTTTTAAAACCCACACAAGTTGGTGGCA-CTTCCTA-TCCTCAAAGAGCAGGACGCCTTCTCCT
1 CC-TTTAAAGCCCACAAAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTT-T-C-
* * * * *
518211 TTTAAAGCCCACACAAGTTGGTGTCACTTCTTAGTCCTTAGAGAGCA
61 ---AAAGCCCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGCA
518258 AAACACTTTC
Statistics
Matches: 237, Mismatches: 26, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
166 53 0.22
167 2 0.01
168 2 0.01
171 94 0.40
172 46 0.19
173 1 0.00
175 1 0.00
176 17 0.07
177 21 0.09
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (172 bp):
CCTTTAAAGCCCACAAAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
CCACACAAGTTGATGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTCTTTTTAAAGCCCACACA
AATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTT
Found at i:518325 original size:326 final size:324
Alignment explanation
Indices: 517957--518575 Score: 847
Period size: 326 Copynumber: 1.9 Consensus size: 324
517947 GCTCTTCCCA
* * * *
517957 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCATCTTTCAGTCCTCAAAG
1 GTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGCCCTCAAAG
* * * *
518022 AG-TAGGACGCCTTTCAAAG-CCCACCCAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGA
66 AGCTA-GACGCCTTTCAAAGCCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGA
518085 CGCC-T-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCT
130 CGCCTTCTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACA------
*
518148 CCTTTTAAAACCCACACAAGTTGGTGGCA-CTTCCTA-TCCTCAAAGAGCAGGACGCCTTCTCCT
189 CCTTTTAAAACCCACACAAGTTGGTGGCACCTTCC-AGTCCCCAAAGAGCAGGACGCCTT-TCCT
*
518211 TTT-AAAGCCCACACAAGTTGGTGTCACTTCTTAGTCCTTAGAGAGCAAAACACTTTCTCCTTTC
252 TTTCAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTTAGAGAGCAAAACACTTTCTCCTTTC
518275 ACCTTTTG
317 ACCTTTTG
518283 GTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGCCCTCAAAG
1 GTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGCCCTCAAAG
* *
518348 AGCTAGACGCCTTTTAAAGCCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAAGAC
66 AGCTAGACGCCTTTCAAAGCCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGAC
* **** *
518413 GCCTTTCCCTTTAAAGCCCACACAAGTTGGTGGCATTTTTTGGTCCTCAAAGAGTAGGACACCTT
131 GCC-TT--CTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTT
* * * *
518478 TTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGTAGGATGCCTTTTCTTTTCAA
193 TTAAAACCCACACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGCAGGACGCCTTTCCTTTTCAA
* * * *
518543 AGCCTACACGAGTTTGTGGCACTTTTTAGTCCT
258 AGCCCACACAAGTTGGTGGCACTTCTTAGTCCT
518576 CAAAAAGCAG
Statistics
Matches: 257, Mismatches: 26, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
326 111 0.43
327 99 0.39
329 1 0.00
332 46 0.18
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (324 bp):
GTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGCCCTCAAAG
AGCTAGACGCCTTTCAAAGCCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGAC
GCCTTCTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTTTA
AAACCCACACAAGTTGGTGGCACCTTCCAGTCCCCAAAGAGCAGGACGCCTTTCCTTTTCAAAGC
CCACACAAGTTGGTGGCACTTCTTAGTCCTTAGAGAGCAAAACACTTTCTCCTTTCACCTTTTG
Found at i:518522 original size:55 final size:55
Alignment explanation
Indices: 518283--518534 Score: 263
Period size: 55 Copynumber: 4.5 Consensus size: 55
518273 TCACCTTTTG
* * *
518283 GTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGTAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
* * *
518338 GCCCTCAAAGAGCT-AGACGCCTTTTAAAGCCCCACACAAGTTGGTGGCACTTTTCTA
1 GTCCTCAAAGAG-TAAGACGCCTTTTAAAG-CCCACACAAGTTGGTGGCAC-CTTCCA
* * ** ***
518395 GTCCTTAAAGAGCAAGACGCCTTTCCCTTTAAAGCCCACACAAGTTGGTGGCATTTTTTG
1 GTCCTCAAAGAGTAAGACGCC--T---TTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
* *
518455 GTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
1 GTCCTCAAAGAGTAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
* * *
518510 GTCCCCAAAGAGTAGGATGCCTTTT
1 GTCCTCAAAGAGTAAGACGCCTTTT
518535 CTTTTCAAAG
Statistics
Matches: 164, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
55 75 0.46
56 20 0.12
57 20 0.12
58 1 0.01
59 1 0.01
60 21 0.13
61 19 0.12
62 7 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
GTCCTCAAAGAGTAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
Found at i:518569 original size:116 final size:118
Alignment explanation
Indices: 518302--518595 Score: 371
Period size: 116 Copynumber: 2.5 Consensus size: 118
518292 GAGCAAGACG
* * *
518302 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGCCCTCAAAGAGCTA-GACGCCTTTTAAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAG-TAGGACGCCTTTTAAA
* * **
518366 GCCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAAGACGCCTTTC
65 GCCCCACACAAGTTGGTGGCACTCTTCCAGTCCCCAAAGAGCAAGACGCCTTTC
* * *
518420 CCTTT-AAAGCCCACACAAGTTGGTGGCATTTTTTGGTCCTCAAAGAGTAGGACACCTTTTAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGACGCCTTTTAAAG
* * * *
518484 -CCCACACAAGTTGGTGGCAC-CTTCCAGTCCCCAAAGAGTAGGATGCCTTTT
66 CCCCACACAAGTTGGTGGCACTCTTCCAGTCCCCAAAGAGCAAGACGCCTTTC
* * * * * *
518535 CTTTTCAAAGCCTACACGAGTTTGTGGCACTTTTTAGTCCTCAAAAAGCAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGACGCCTTTT
518596 CCTTTTCTCC
Statistics
Matches: 151, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
115 27 0.18
116 69 0.46
117 50 0.33
118 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (118 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGACGCCTTTTAAAG
CCCCACACAAGTTGGTGGCACTCTTCCAGTCCCCAAAGAGCAAGACGCCTTTC
Found at i:519401 original size:21 final size:21
Alignment explanation
Indices: 519377--519432 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
519367 TTTTTGCCAA
519377 AATGTATCGATACATGCCCTT
1 AATGTATCGATACATGCCCTT
519398 AATGTATCGATACATGCCCTT
1 AATGTATCGATACATGCCCTT
519419 AATGTATCGATACA
1 AATGTATCGATACA
519433 AGGCCCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACATGCCCTT
Found at i:519505 original size:13 final size:13
Alignment explanation
Indices: 519487--519516 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
519477 ATACATTATT
519487 CATTGTATCGATA
1 CATTGTATCGATA
519500 CATTGTATCGATA
1 CATTGTATCGATA
519513 CATT
1 CATT
519517 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:519559 original size:20 final size:20
Alignment explanation
Indices: 519534--519585 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
519524 TACCCAAATG
*
519534 TATCGATACATT-TTGCATTA
1 TATCGATACATTACT-CATTA
*
519554 TATCGATACATTACTCATTG
1 TATCGATACATTACTCATTA
519574 TATCGATACATT
1 TATCGATACATT
519586 CAGGCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTACTCATTA
Found at i:521944 original size:51 final size:51
Alignment explanation
Indices: 521884--522103 Score: 273
Period size: 51 Copynumber: 4.3 Consensus size: 51
521874 ATTTTTTATC
** * * *
521884 TCGGGGATACTTTAACCCCGGTTTTATTTCCACAACA-TCAATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACT-AATTTTCCATAA
* * *
521935 TCAGAGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTCCATAA
521986 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTCCATAA
* * * * ** *
522037 TTGGGGATACTCTAACTCTGATTTTATTTTCAAAACA-TCAATTTTTTACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACT-AATTTTCCATAA
522088 TCGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
522104 CCCGGTATTT
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
50 1 0.01
51 145 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTCCATAA
Found at i:522127 original size:28 final size:28
Alignment explanation
Indices: 522087--522142 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
522077 ATTTTTTACA
522087 ATCGGGGATACTCCAACCCCGGTATTTC
1 ATCGGGGATACTCCAACCCCGGTATTTC
* *
522115 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGGTATTTC
522143 TGCGAGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGGTATTTC
Found at i:522234 original size:51 final size:51
Alignment explanation
Indices: 522164--522417 Score: 255
Period size: 51 Copynumber: 5.0 Consensus size: 51
522154 CTAATCCCGA
* * *
522164 CCTTATTTATAAAGCATTGATTTTCCACAATCGAGGATACTCCAACCCCAG
1 CCTTATTTCTAAATCATTGATTTTCCACAATCGGGGATACTCCAACCCCAG
* * * * * *
522215 CTTTATTCCTAAAAT-ATTGATTTTTCATAATCGGGGATACTCCAACCTCGG
1 CCTTATTTCT-AAATCATTGATTTTCCACAATCGGGGATACTCCAACCCCAG
* * * *
522266 CTTTATTTCTAAAAT-ATT-AATTTCTCACAATCGGGGATACTTCAACCCCGG
1 CCTTATTTCT-AAATCATTGATTTTC-CACAATCGGGGATACTCCAACCCCAG
** * **
522317 CCTTATTTCTAAATCACCGA-TTTCTCACAATCGGGGATACTTCAACCCTTG
1 CCTTATTTCTAAATCATTGATTTTC-CACAATCGGGGATACTCCAACCCCAG
* * *
522368 CCTTATTTCTAAATCATCGATTTTTCACAATCGAGGATACTCCAACCCCA
1 CCTTATTTCTAAATCATTGATTTTCCACAATCGGGGATACTCCAACCCCA
522418 TTATTTTCGA
Statistics
Matches: 172, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 8 0.05
51 157 0.91
52 7 0.04
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
CCTTATTTCTAAATCATTGATTTTCCACAATCGGGGATACTCCAACCCCAG
Found at i:522491 original size:51 final size:51
Alignment explanation
Indices: 522428--522547 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
522418 TTATTTTCGA
* *
522428 GGGGATACTCCAACCTCGATTTTATTTTCAAAATACCGATTTT-TCATAATT
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCT-ATAATC
* *
522479 GGGGATACTCCAACCCCGATTTTATTTTCAGAATATCGATTTTCTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATC
**
522530 AAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
522548 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
51 61 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATC
Found at i:530463 original size:32 final size:33
Alignment explanation
Indices: 530422--530485 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
530412 CTTTTCAAGG
* *
530422 TGTATCGATACTATG-AACATGTATTGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
530454 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
530486 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:533190 original size:20 final size:20
Alignment explanation
Indices: 533165--533205 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
533155 GTTTTTGTAG
*
533165 ATATATCGATACATTATTCA
1 ATATATCGATACATCATTCA
533185 ATATATCGATACATCATTCA
1 ATATATCGATACATCATTCA
533205 A
1 A
533206 GATCGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (20 bp):
ATATATCGATACATCATTCA
Found at i:535028 original size:15 final size:15
Alignment explanation
Indices: 535008--535036 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
534998 TATTTTTTTC
535008 AAAGAATACAAAAAA
1 AAAGAATACAAAAAA
535023 AAAGAATACAAAAA
1 AAAGAATACAAAAA
535037 GAGAAAAAAA
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:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAGAATACAAAAAA
Found at i:535818 original size:12 final size:11
Alignment explanation
Indices: 535796--535871 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
535786 AGAGAAAGAA
*
535796 GAGAGAGGAGG
1 GAGATAGGAGG
535807 GATGATAGGAGG
1 GA-GATAGGAGG
*
535819 AGAGACAGGA--
1 -GAGATAGGAGG
*
535829 GAGATAGTA--
1 GAGATAGGAGG
535838 GAGATAGGAGG
1 GAGATAGGAGG
535849 GATGATAGGAGG
1 GA-GATAGGAGG
*
535861 AGAGACAGGAG
1 -GAGATAGGAG
535872 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:535828 original size:24 final size:24
Alignment explanation
Indices: 535795--535880 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
535785 AAGAGAAAGA
*
535795 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
535819 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
535837 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
535861 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
535881 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:535847 original size:42 final size:42
Alignment explanation
Indices: 535786--535904 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
535776 TAGCCCTCAA
* *
535786 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
535828 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
535870 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
535905 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:541591 original size:20 final size:20
Alignment explanation
Indices: 541565--541635 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
541555 TGCCAGTTTT
541565 ATGTATCGATACTTTTCAAG
1 ATGTATCGATACTTTTCAAG
*
541585 GTGTATCGATACTTTTCAAG
1 ATGTATCGATACTTTTCAAG
* * *
541605 ATGTATCGATAC-TATGAAC
1 ATGTATCGATACTTTTCAAG
541624 ATGTATCGATAC
1 ATGTATCGATAC
541636 AATGTATCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACTTTTCAAG
Found at i:541642 original size:13 final size:13
Alignment explanation
Indices: 541624--541648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541614 TACTATGAAC
541624 ATGTATCGATACA
1 ATGTATCGATACA
541637 ATGTATCGATAC
1 ATGTATCGATAC
541649 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:541646 original size:32 final size:33
Alignment explanation
Indices: 541605--541669 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
541595 ACTTTTCAAG
*
541605 ATGTATCGATACTATG-AACATGTATCGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
*
541637 ATGTATCGATACTAAGCAATATGTATCGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
541670 TCTAGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACTAAGCAACATGTATCGATACA
Found at i:542002 original size:28 final size:29
Alignment explanation
Indices: 541968--542049 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
541958 AAGACAGTTC
*
541968 TAGTGTTTTAGTTGACTTTTGATTC-TTT
1 TAGTGTTTTAGTTGACTTTTAATTCATTT
* *
541996 TAGTGTTTTAGTTAACTTTTAATACATTT
1 TAGTGTTTTAGTTGACTTTTAATTCATTT
*
542025 TTGTGTTTTAGTTGACTTTTAATTC
1 TAGTGTTTTAGTTGACTTTTAATTC
542050 CTTATCTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 22 0.47
29 25 0.53
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.59
Consensus pattern (29 bp):
TAGTGTTTTAGTTGACTTTTAATTCATTT
Found at i:547098 original size:29 final size:29
Alignment explanation
Indices: 547053--547133 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
547043 GAAAGTTTTG
*
547053 GTATTTTAGTTGACTTTTGATTCCCTTTA
1 GTATTTTAGTTGACTTTTAATTCCCTTTA
* * * *
547082 GTGTTTTAGTTGACTTTTAATTTCTTTTT
1 GTATTTTAGTTGACTTTTAATTCCCTTTA
*
547111 GTATTTTAGTTAACTTTTAATTC
1 GTATTTTAGTTGACTTTTAATTC
547134 TTTAACTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59
Consensus pattern (29 bp):
GTATTTTAGTTGACTTTTAATTCCCTTTA
Found at i:550325 original size:11 final size:11
Alignment explanation
Indices: 550292--550327 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
550282 TTATGAAAAT
550292 TTATT-TACAA
1 TTATTATACAA
*
550302 TAATTATACAA
1 TTATTATACAA
550313 TTATTATACAA
1 TTATTATACAA
550324 TTAT
1 TTAT
550328 ATTAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTATACAA
Found at i:550331 original size:24 final size:23
Alignment explanation
Indices: 550292--550347 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
550282 TTATGAAAAT
550292 TTATT-TACAA-TAATT-ATACAA
1 TTATTATACAATTAATTAATA-AA
*
550313 TTATTATACAATTATATTAATAAT
1 TTATTATACAATTA-ATTAATAAA
550337 TTATTAT-CAAT
1 TTATTATACAAT
550348 AAAAGCAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.17
22 5 0.17
23 6 0.20
24 11 0.37
25 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTATACAATTAATTAATAAA
Found at i:552760 original size:15 final size:15
Alignment explanation
Indices: 552717--552771 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
552707 AAATTATTGT
552717 ATAATTTT-ATATTTA
1 ATAATTTTAAT-TTTA
*
552732 TATAAGTATTAATTTTTA
1 -ATAA-TTTTAA-TTTTA
552750 A-AATTTTAATTTTA
1 ATAATTTTAATTTTA
552764 ATAATTTT
1 ATAATTTT
552772 GTCACTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.18
15 11 0.33
16 6 0.18
17 4 0.12
18 5 0.15
19 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
ATAATTTTAATTTTA
Found at i:553404 original size:16 final size:17
Alignment explanation
Indices: 553378--553421 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
553368 TCCGAATCCA
*
553378 AAAAT-ATTCAAACTC-
1 AAAATAATTCAAAATCG
*
553393 ATAATAATTCAAAATCG
1 AAAATAATTCAAAATCG
553410 AAAATAATTCAA
1 AAAATAATTCAA
553422 TTTGAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 11 0.46
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATAATTCAAAATCG
Found at i:554211 original size:18 final size:19
Alignment explanation
Indices: 554177--554212 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
554167 TTATAGATTT
554177 TATTTTATATATATTTAAA
1 TATTTTATATATATTTAAA
*
554196 TATTTTA-ATCTATTTAA
1 TATTTTATATATATTTAA
554213 TTGAATCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTATATATATTTAAA
Found at i:554509 original size:16 final size:16
Alignment explanation
Indices: 554488--554519 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
554478 TTTTCTTACC
554488 ATCATAAAGGAATAAA
1 ATCATAAAGGAATAAA
554504 ATCATAAAGGAATAAA
1 ATCATAAAGGAATAAA
554520 GGGCTGGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
ATCATAAAGGAATAAA
Found at i:554700 original size:31 final size:31
Alignment explanation
Indices: 554665--554726 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
554655 GAATAGACAG
554665 TATTAATGAATTTAAGCTTGATTTGGATTCC
1 TATTAATGAATTTAAGCTTGATTTGGATTCC
554696 TATTAATGAATTTAAGCTTGATTTGGATTCC
1 TATTAATGAATTTAAGCTTGATTTGGATTCC
554727 AATGCGCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (31 bp):
TATTAATGAATTTAAGCTTGATTTGGATTCC
Found at i:554803 original size:13 final size:13
Alignment explanation
Indices: 554785--554813 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
554775 TATCACACCC
554785 AGCGTTCTAAAAT
1 AGCGTTCTAAAAT
554798 AGCGTTCTAAAAT
1 AGCGTTCTAAAAT
554811 AGC
1 AGC
554814 AGGTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (13 bp):
AGCGTTCTAAAAT
Found at i:556097 original size:36 final size:36
Alignment explanation
Indices: 556050--556118 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
556040 CCTCTCAATA
*
556050 CGATTAATCAAAAACCATCCGAATTAACTGATAATG
1 CGATTAATCAAAAACCATCAGAATTAACTGATAATG
556086 CGATTAATCAAAAACCATCAGAATTAACTGATA
1 CGATTAATCAAAAACCATCAGAATTAACTGATA
556119 TTACTTCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (36 bp):
CGATTAATCAAAAACCATCAGAATTAACTGATAATG
Found at i:566727 original size:89 final size:89
Alignment explanation
Indices: 566607--567108 Score: 501
Period size: 89 Copynumber: 5.7 Consensus size: 89
566597 TGATACGATA
* * * * *
566607 AAAAATATTTAACTAATATTTAATAAATTTCTTGGAACTTC-AAAGATGTGACAGATGTATGTGA
1 AAAAATATTTGACTAATACTTAATAAATTTCTTAGAAC-CCGAAAGATGTGACAGATGCATGTGA
*
566671 GTATCAGATTTCTTCTGACATGATCG
65 GTATCAGATTTCTTCTGACACGA-CG
* ** * *
566697 -AAAATATTTGACTAATACCTGTTAAATTTCTTA-AAACC---ATATGAT-A-A-ATGCATGTGA
1 AAAAATATTTGACTAATACTTAATAAATTTCTTAGAACCCGAAAGATG-TGACAGATGCATGTGA
* * * *
566754 ATATCAAATCAT-TTGTGACACGAC-
65 GTATCAGAT-TTCTTCTGACACGACG
* * * * *
566778 AGAAAATATTTGACTAATACTTAATAAATTTTTTAGAACTCGAAAGATATGATAGACGCATGT-A
1 A-AAAATATTTGACTAATACTTAATAAATTTCTTAGAACCCGAAAGATGTGACAGATGCATGTGA
*
566842 GGTATCAGATTCCTTCTGACACGACG
65 -GTATCAGATTTCTTCTGACACGACG
* * * *
566868 AAAAATATTTGACTAATACCTAATAAATTTCTTAGAACCCGAAAGATGTGACATATGCAAGTGGG
1 AAAAATATTTGACTAATACTTAATAAATTTCTTAGAACCCGAAAGATGTGACAGATGCATGTGAG
* * *
566933 TATCAGA-TTCTTTCTAACCCAACG
66 TATCAGATTTC-TTCTGACACGACG
* * *
566957 AAAAATATTTGACTAATACTTAATAAATTTCTTGGAACCCGAAAGATGTGACAAATGCATATGAG
1 AAAAATATTTGACTAATACTTAATAAATTTCTTAGAACCCGAAAGATGTGACAGATGCATGTGAG
* * * *
567022 TATCAGATTCCTTCTAATACGATG
66 TATCAGATTTCTTCTGACACGACG
* *
567046 AAAAATATTTGACTAATGCTTAATAAATTTCTT-GAAACCCGAAAGATGTAACAGATGCATGTG
1 AAAAATATTTGACTAATACTTAATAAATTTCTTAG-AACCCGAAAGATGTGACAGATGCATGTG
567109 GGCATCAGCT
Statistics
Matches: 337, Mismatches: 57, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
82 1 0.00
83 54 0.16
84 5 0.01
85 5 0.01
86 2 0.01
87 5 0.01
88 7 0.02
89 255 0.76
90 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (89 bp):
AAAAATATTTGACTAATACTTAATAAATTTCTTAGAACCCGAAAGATGTGACAGATGCATGTGAG
TATCAGATTTCTTCTGACACGACG
Found at i:567027 original size:178 final size:176
Alignment explanation
Indices: 566607--567116 Score: 565
Period size: 178 Copynumber: 2.9 Consensus size: 176
566597 TGATACGATA
* * *
566607 AAAAATATTTAACTAATATTTAATAAATTTCTTGGAACTTC-AAAGATGTGACAGATGTATGTGA
1 AAAAATATTTGACTAATACTTAATAAATTTCTTGGAAC-TCGAAAGATGTGACAGATGCATGTGA
* * ** *
566671 GTATCAGATTTCTTCTGACATGATCG-AAAATATTTGACTAATACCTGTTAAATTTCTTA-AAAC
65 GTATCAGATTCCTTCTGACACGA-CGAAAAATATTTGACTAATACCTAATAAATTTCTTAGAACC
* ** * * *
566734 C---ATATGATA-AATGCATGTGAATATCA-AATCATTTGTGACACGAC
129 CGAAAGATG-TACAATGCATGTGGGTATCAGAATCATTTCTAACACAAC
* * * * *
566778 AGAAAATATTTGACTAATACTTAATAAATTTTTTAGAACTCGAAAGATATGATAGACGCATGT-A
1 A-AAAATATTTGACTAATACTTAATAAATTTCTTGGAACTCGAAAGATGTGACAGATGCATGTGA
566842 GGTATCAGATTCCTTCTGACACGACGAAAAATATTTGACTAATACCTAATAAATTTCTTAGAACC
65 -GTATCAGATTCCTTCTGACACGACGAAAAATATTTGACTAATACCTAATAAATTTCTTAGAACC
* * *
566907 CGAAAGATGTGACATATGCAAGTGGGTATCAGATTC-TTTCTAACCCAAC
129 CGAAAGATGT-ACA-ATGCATGTGGGTATCAGAATCATTTCTAACACAAC
* * *
566956 GAAAAATATTTGACTAATACTTAATAAATTTCTTGGAACCCGAAAGATGTGACAAATGCATATGA
1 -AAAAATATTTGACTAATACTTAATAAATTTCTTGGAACTCGAAAGATGTGACAGATGCATGTGA
* * * * *
567021 GTATCAGATTCCTTCTAATACGATGAAAAATATTTGACTAATGCTTAATAAATTTCTT-GAAACC
65 GTATCAGATTCCTTCTGACACGACGAAAAATATTTGACTAATACCTAATAAATTTCTTAG-AACC
*
567085 CGAAAGATGTAACAGATGCATGTGGGCATCAG
129 CGAAAGATGT-ACA-ATGCATGTGGGTATCAG
567117 CTTCCTATTT
Statistics
Matches: 285, Mismatches: 39, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
171 6 0.02
172 102 0.36
173 4 0.01
175 1 0.00
176 5 0.02
177 2 0.01
178 160 0.56
179 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (176 bp):
AAAAATATTTGACTAATACTTAATAAATTTCTTGGAACTCGAAAGATGTGACAGATGCATGTGAG
TATCAGATTCCTTCTGACACGACGAAAAATATTTGACTAATACCTAATAAATTTCTTAGAACCCG
AAAGATGTACAATGCATGTGGGTATCAGAATCATTTCTAACACAAC
Found at i:570270 original size:233 final size:233
Alignment explanation
Indices: 569863--570331 Score: 814
Period size: 233 Copynumber: 2.0 Consensus size: 233
569853 AAGTCATGAC
569863 TATTGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAACCAGAAAATATTTGAAAAATC
1 TATTGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAACCAGAAAATATTTGAAAAATC
* * *
569928 GTAAACAAGTTTTATTCACTCAAAAACTCTTTAAAAACATGTTCTAAGTAATTTTCTATTAATGG
66 GTAAACAAGTTTTATTCACTCAAAAACTCTCTAAAAACATGTTCTAAGCAATTTTCTATCAATGG
** *
569993 AAGTTTTTAGAATTATAATCAAATGTTTTTGAACCTTAATTTAAATGTTTTTAAGGCAAAAATAC
131 AAGTTTTTAGAATTATAAAAAAATGTTTTTGAACCTTAATTTAAATGTTTTTAAGACAAAAATAC
*
570058 TTCAAAGTATCGATGCATAGGTATTTGTATCGATACAT
196 TTCAAAGTATCGATACATAGGTATTTGTATCGATACAT
*
570096 TATTGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAACC-GAAAAATGTTTGAAAAAT
1 TATTGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAACCAG-AAAATATTTGAAAAAT
* *
570160 CGTAAACAAGTTTTATTCACTCATAAACTCTCTAAAAACGTGTTCTAAGCAATTTTCTATCAATG
65 CGTAAACAAGTTTTATTCACTCAAAAACTCTCTAAAAACATGTTCTAAGCAATTTTCTATCAATG
* *
570225 GAAGTTTTTAGAGTTATAAAAAAATGTTTTTGAACTTTAATTTAAATGTTTTTAAGACAAAAATA
130 GAAGTTTTTAGAATTATAAAAAAATGTTTTTGAACCTTAATTTAAATGTTTTTAAGACAAAAATA
570290 CTTCAAAGTATCGATACATAGGTATTTGTATCGATACAT
195 CTTCAAAGTATCGATACATAGGTATTTGTATCGATACAT
570329 TAT
1 TAT
570332 GGTTGACTTA
Statistics
Matches: 223, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
232 1 0.00
233 222 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (233 bp):
TATTGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAACCAGAAAATATTTGAAAAATC
GTAAACAAGTTTTATTCACTCAAAAACTCTCTAAAAACATGTTCTAAGCAATTTTCTATCAATGG
AAGTTTTTAGAATTATAAAAAAATGTTTTTGAACCTTAATTTAAATGTTTTTAAGACAAAAATAC
TTCAAAGTATCGATACATAGGTATTTGTATCGATACAT
Found at i:578267 original size:115 final size:113
Alignment explanation
Indices: 578082--578437 Score: 396
Period size: 115 Copynumber: 3.1 Consensus size: 113
578072 GACGCCTTTT
* * * **
578082 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGTAGAACGCCTTCGCCTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG-CTTTTCCTTT
* *
578147 CAAAGCCCACACAAGTTGGTGGCACTATTCAGTCCTCAAAAAGCAGGACG
65 TAAAGCCCACACAAGTTGGTGGCACT-TTCAGTCCTCAAAGAGCAGGACG
*
578197 CCTTTTAAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG-CTTTTCCTTT
* *
578262 TAAAGCCCACACAAGTTGGTGGCACTTTTCAGTTCTCAAAGAGCAGGATG
65 TAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGACG
* * *
578312 CTTTCTTTTTGCAAAGCCCACACAAG-TCGGTGGCACTTTTCAATCCTCAAAGAGCA-GATGC-T
1 C---C-TTTT--AAAGCCCACACAAGCT-GGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCTT
* * * *
578374 TTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTTCCAATCCTCAAAGGGCAGGACG
58 TTCCTTTT--AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACG
578432 CCTTTT
1 CCTTTT
578438 CTTTTCAAAG
Statistics
Matches: 208, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
115 103 0.50
116 5 0.02
117 1 0.00
118 1 0.00
119 12 0.06
120 40 0.19
121 29 0.14
122 17 0.08
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (113 bp):
CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTCCTTTT
AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACG
Found at i:578328 original size:61 final size:60
Alignment explanation
Indices: 578055--578485 Score: 436
Period size: 61 Copynumber: 7.2 Consensus size: 60
578045 TTAGCCCTTC
* * * * *
578055 CAGTCCTCAAAAAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACG-C-TTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
* * * ** *
578116 -AGTCCTCAAAGAGTAGAACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCACTATT
1 CAGTCCTCAAAGAGCAGGACGCTTTC-TTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
* * * *
578176 CAGTCCTCAAAAAGCAGGACGC---C-TTTT-AAAGCCCACATAAGCTGGTGGCAC-CTT
1 CAGTCCTCAAAGAGCAGGACGCTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
*
578230 CAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACG-C-TTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
* * *
578291 CAGTTCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTCGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACGCTTTCTTTTT-CAAAGCCCACACAAGTTGGTGGCACTTTT
* * * *
578352 CAATCCTCAAAGAGCA-GATGCTTTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTTC
1 CAGTCCTCAAAGAGCAGGACGCTTTCTTTTT-CAAAGCCCACACAAGTTGGTGGCACTTTT
* * * * *
578411 CAATCCTCAAAGGGCAGGACGCCTTT-TCTTTTCAAAGCCTACACGAGTTGGTGGCATTTTT
1 CAGTCCTCAAAGAGCAGGACG-CTTTCT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
*
578472 CAGTTCTCAAAGAG
1 CAGTCCTCAAAGAG
578486 TAAGACACAC
Statistics
Matches: 317, Mismatches: 37, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
54 22 0.07
55 23 0.07
56 3 0.01
58 4 0.01
59 49 0.15
60 99 0.31
61 117 0.37
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (60 bp):
CAGTCCTCAAAGAGCAGGACGCTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
Found at i:578669 original size:35 final size:33
Alignment explanation
Indices: 578592--578662 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 33
578582 TTTCGTTTTC
578592 CTTTTTTTCCTTTATCCTCGAAAAGCAGGACGTA
1 CTTTTTTTCCTTTATCCTCGAAAAGCAGGAC-TA
*
578626 CTTTTTTTCACTTTGTCCTC-AACAAGCAGGA-TA
1 CTTTTTTTC-CTTTATCCTCGAA-AAGCAGGACTA
578659 CTTT
1 CTTT
578663 CCTTTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.18
34 11 0.32
35 17 0.50
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (33 bp):
CTTTTTTTCCTTTATCCTCGAAAAGCAGGACTA
Found at i:579060 original size:13 final size:13
Alignment explanation
Indices: 579042--579098 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
579032 CATAAAGTGT
579042 TGTATCGATACAA
1 TGTATCGATACAA
579055 TGTATCGATACATAA
1 TGTATCGATAC--AA
579070 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
579087 TGTATCGATACA
1 TGTATCGATACA
579099 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:579077 original size:32 final size:32
Alignment explanation
Indices: 579022--579119 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
579012 TTCAACGATT
579022 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
579055 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
579087 TGTATCGATACATAAGTTTTGTACCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
579119 T
1 T
579120 ATAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:579079 original size:19 final size:18
Alignment explanation
Indices: 579020--579117 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
579010 ATTTCAACGA
579020 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
579039 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
579055 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
579071 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
579087 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
579103 TTTTGTACCGATACA
1 -TTTGTATCGATACA
579118 ATATAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:579178 original size:13 final size:13
Alignment explanation
Indices: 579160--579184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579150 ATTACTCAAA
579160 TGTATCGATACAT
1 TGTATCGATACAT
579173 TGTATCGATACA
1 TGTATCGATACA
579185 CTGATCTTTG
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:579238 original size:52 final size:52
Alignment explanation
Indices: 579193--579321 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
579183 CACTGATCTT
*
579193 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
579245 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGAGACACTATGAAA
1 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
579297 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGTAGGCAAATTT
579322 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:581401 original size:13 final size:13
Alignment explanation
Indices: 581383--581407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
581373 CATAAAATGT
581383 TGTATCGATACAA
1 TGTATCGATACAA
581396 TGTATCGATACA
1 TGTATCGATACA
581408 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:581405 original size:33 final size:33
Alignment explanation
Indices: 581363--581432 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
581353 TTCAACGATT
581363 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
581396 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
581429 TGTA
1 TGTA
581433 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:581491 original size:13 final size:13
Alignment explanation
Indices: 581473--581500 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
581463 ATTACTCACA
581473 TGTATCGATACAT
1 TGTATCGATACAT
581486 TGTATCGATACAT
1 TGTATCGATACAT
581499 TG
1 TG
581501 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:581551 original size:52 final size:50
Alignment explanation
Indices: 581486--581626 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 50
581476 ATCGATACAT
*
581486 TGTATCGATACATTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
581538 TGTATTGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
581590 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACATTATT--ATGTATCGATACATGCAG
581627 ATAAATTTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (50 bp):
TGTATCGATACATTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:581634 original size:52 final size:52
Alignment explanation
Indices: 581506--581626 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
581496 CATTGATCTT
* *
581506 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
581558 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
581610 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
581627 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:585787 original size:10 final size:10
Alignment explanation
Indices: 585772--585798 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
585762 TGCTAACTAA
585772 GTTTTTGTTT
1 GTTTTTGTTT
585782 GTTTTTGTTT
1 GTTTTTGTTT
585792 GTTTTTG
1 GTTTTTG
585799 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:595494 original size:1 final size:1
Alignment explanation
Indices: 595488--595673 Score: 66
Period size: 1 Copynumber: 186.0 Consensus size: 1
595478 GGCGTCCTCC
** ** ** ** ** **
595488 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** ** *** ** ** **
595553 AAAAAAAAAAAAAACGAAAAAATGAAAAACCGAAAAAAAAAACCAAAAAATGAAAAACCAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * * * *
595618 AAAAAAAACAAAAGGAAAAAAAACAACAAAAAATAATAAAAAAACAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
595674 GGGGGTCCGG
Statistics
Matches: 137, Mismatches: 48, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 137 1.00
ACGTcount: A:0.82, C:0.10, G:0.05, T:0.03
Consensus pattern (1 bp):
A
Found at i:595531 original size:34 final size:34
Alignment explanation
Indices: 595488--595625 Score: 209
Period size: 34 Copynumber: 4.3 Consensus size: 34
595478 GGCGTCCTCC
595488 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
1 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
595522 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
1 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
595556 AAAAAAAAAAACG-AAAAAATGAAAAACC-----
1 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
* *
595584 GAAAAAAAAAAC-CAAAAAATGAAAAACCAAAAA
1 AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
595617 AAAAAAAAA
1 AAAAAAAAA
595626 CAAAAGGAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 13
0.86 0.02 0.12
Matches are distributed among these distances:
28 26 0.27
33 23 0.24
34 47 0.49
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (34 bp):
AAAAAAAAAAACGAAAAAAATGAAAAACCAAAAA
Found at i:595622 original size:28 final size:28
Alignment explanation
Indices: 595556--595622 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
595546 AAACCAAAAA
*
595556 AAAAAAAAAAACGAAAAAATGAAAAACC
1 AAAAAAAAAAACCAAAAAATGAAAAACC
*
595584 GAAAAAAAAAACCAAAAAATGAAAAACC
1 AAAAAAAAAAACCAAAAAATGAAAAACC
595612 AAAAAAAAAAA
1 AAAAAAAAAAA
595623 AAACAAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.81, C:0.10, G:0.06, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAAACCAAAAAATGAAAAACC
Found at i:595650 original size:95 final size:95
Alignment explanation
Indices: 595489--595662 Score: 244
Period size: 95 Copynumber: 1.8 Consensus size: 95
595479 GCGTCCTCCA
* *
595489 AAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAA
1 AAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAAAGAAAAAAA-GAAAAACAAAA
595554 AAAAAAAAAAAAACGAAAAAATGAAAAACCG
65 AAAAAAAAAAAAACGAAAAAATGAAAAACCG
* * *
595585 AAAAAAAAAAC-CAAAAAATGAAAAACCAAAAAAAAAAAAAACAAAAGGAAAAAA-AACAACAAA
1 AAAAAAAAAACGAAAAAAATGAAAAACC-AAAAAAAAAAAAA-AAAAGAAAAAAAGAAAAACAAA
* *
595648 AAATAATAAAAAAAC
64 AAAAAAAAAAAAAAC
595663 AAACAAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 35 0.51
96 24 0.35
97 10 0.14
ACGTcount: A:0.81, C:0.10, G:0.06, T:0.03
Consensus pattern (95 bp):
AAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAACAAAAA
AAAAAAAAAAAACGAAAAAATGAAAAACCG
Found at i:597169 original size:30 final size:29
Alignment explanation
Indices: 597114--597563 Score: 335
Period size: 30 Copynumber: 15.3 Consensus size: 29
597104 TCACCCTTCA
* *
597114 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
597143 AAAGCCCACAAGTCGGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
597172 GAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
597200 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
597230 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
597259 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
597289 TTTTGTAAGCTCACAACTCTA-TAGCA-CTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCATCT-TTTTC
* * *
597323 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
597350 AAGAGACCACAAGTCAGTGGCATATTTTTC
1 AA-AGCCCACAAGTCAGTGGCATCTTTTTC
* * *
597380 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
597409 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
597438 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
597468 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
597497 AAAGCCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
597524 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
597554 AAAGCCCACA
1 AAAGCCCACA
597564 CAAGTCGGTG
Statistics
Matches: 339, Mismatches: 59, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.00
27 60 0.18
28 50 0.15
29 59 0.17
30 145 0.43
31 2 0.01
33 2 0.01
34 5 0.01
35 15 0.04
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:597215 original size:27 final size:27
Alignment explanation
Indices: 597173--597225 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
597163 ATTTTTTTCG
*
597173 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
597200 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
597226 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:597428 original size:88 final size:86
Alignment explanation
Indices: 597323--597579 Score: 372
Period size: 88 Copynumber: 2.9 Consensus size: 86
597313 CACTCTTTTC
*
597323 AGCCCACAAGTTAGTGGCACCCTTTTCAAGAGACCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAA-AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
597388 ACAAGTCAGTGGCAACCTTTAAA
64 ACAAGTCAGTGGCAACCTTTAAA
597411 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
597476 ACAAGTCAGTGGCAACCTTTAAA
64 ACAAGTCAGTGGCAACCTTTAAA
* * * *** *
597499 AGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCAC
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAG-CC-C
*
597563 ACAAGTCGGTGGCAACC
64 ACAAGTCAGTGGCAACC
597580 CTTCTAAGCC
Statistics
Matches: 156, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
85 29 0.19
86 5 0.03
87 18 0.12
88 102 0.65
89 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (86 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCAC
AAGTCAGTGGCAACCTTTAAA
Found at i:597442 original size:58 final size:59
Alignment explanation
Indices: 597110--597579 Score: 340
Period size: 58 Copynumber: 8.0 Consensus size: 59
597100 TTCATCACCC
* *** * ***
597110 TTCAAAAGTCCACAAGTCAGTGGCATTTTTTTC-AAAGCCCACAAGTCGGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* * * *
597169 TTCGAAAGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * * * * *
597226 TTCCGAAGCCCACAAGTCGGTGGCA-TCTTTTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * * * * *
597286 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTC---AGCCCACAAGTTAGTGGCACCCTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
* * ***
597347 TTCAAGAGACCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * **
597406 TT-AAAAGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
*
597465 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
597521 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCGGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAG-CC-CACAAGTCAGTGGCAACC
597580 CTTCTAAGCC
Statistics
Matches: 329, Mismatches: 59, Indels: 46
0.76 0.14 0.11
Matches are distributed among these distances:
55 22 0.07
56 8 0.02
57 68 0.21
58 73 0.22
59 67 0.20
60 48 0.15
61 5 0.02
62 15 0.05
63 1 0.00
64 15 0.05
65 7 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:597697 original size:49 final size:48
Alignment explanation
Indices: 597580--597697 Score: 146
Period size: 49 Copynumber: 2.4 Consensus size: 48
597570 GGTGGCAACC
* *
597580 CTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTAT
1 CTTC-AAG-CCAATATCGCTGGCCTTGAATCACCACATTGGCACCTTTAT
* * *
597630 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
1 CTTCAAG-CCAATATCGCTGGCCTTGAATCACCACATTGGCACCTTTAT
*
597679 CTTCGAGCCTAATATCGCT
1 CTTCAAGCC-AATATCGCT
597698 AGCAGCATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.03
49 53 0.91
50 3 0.05
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (48 bp):
CTTCAAGCCAATATCGCTGGCCTTGAATCACCACATTGGCACCTTTAT
Found at i:598434 original size:13 final size:13
Alignment explanation
Indices: 598416--598440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
598406 CATAAAATGT
598416 TGTATCGATACAA
1 TGTATCGATACAA
598429 TGTATCGATACA
1 TGTATCGATACA
598441 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:598438 original size:33 final size:33
Alignment explanation
Indices: 598396--598465 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
598386 TTCAACGATT
598396 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
598429 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
598462 TGTA
1 TGTA
598466 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:598524 original size:13 final size:13
Alignment explanation
Indices: 598506--598533 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
598496 ATTACTCACA
598506 TGTATCGATACAT
1 TGTATCGATACAT
598519 TGTATCGATACAT
1 TGTATCGATACAT
598532 TG
1 TG
598534 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:598584 original size:52 final size:50
Alignment explanation
Indices: 598519--598659 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 50
598509 ATCGATACAT
*
598519 TGTATCGATACATTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
598571 TGTATTGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
598623 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACATTATT--ATGTATCGATACATGCAG
598660 ATAAATTTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (50 bp):
TGTATCGATACATTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:598667 original size:52 final size:52
Alignment explanation
Indices: 598539--598659 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
598529 CATTGATCTT
* *
598539 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
598591 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
598643 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
598660 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:602193 original size:501 final size:502
Alignment explanation
Indices: 601223--602225 Score: 1749
Period size: 501 Copynumber: 2.0 Consensus size: 502
601213 TCTCTCCGGG
* * * *
601223 GCGCATATGAGATGAAAACGATTTTCAGAAACCTAGATTTCTTTTTACACAAAATTCACACATTC
1 GCGCATATGAGATGAAAACAATTTCCAGAAACCTAGATTTATTTTCACACAAAATTCACACATTC
* * *
601288 AAAGGGGATCATATCATAATAATGATAAATCGAAATCAATGCAACCAATATCGAGTCAAAACGTT
66 AAAAGGGATCATATCAAAATAATGATAAATCGAAATCAATGCAACCAATATCGAGTCAAAACATT
* * * *
601353 GCTAGTAAGGTACCGATTTCGGGCGTCGCGAGGAGGTTTGTACCTCTTTGTGCGTAACCAACTCC
131 GCTAGTAAGGTACCAATTTCGGGCGTCGCAAGGAGGTTCGTACCTCTTTGCGCGTAACCAACTCC
*
601418 CGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCGATGTTTTGAGTTTCGTAACT
196 CGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCAATGTTTTGAGTTTCGTAACT
601483 CAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGGTGGCGACTCCAAA
261 CAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGGTGGCGACTCCAAA
601548 ATCTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCC
326 ATCTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCC
* * * * * *
601613 CCTTTTAATCAACATATTTCCCATCATGCCATAGAAATTCCCAATCGCGAGGGATATTAAGTCGA
391 CCCTTTAATCAACATACTTCCCACCATGCCACAAAAATTCCCAATCACGAGGGATATTAAGTCGA
601678 GCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
456 GCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
* **
601725 GCGCATATGAGATGAAAACAATTTCCA-AAACCTAGATTTATTTTCATACAAAATTCATGCATTC
1 GCGCATATGAGATGAAAACAATTTCCAGAAACCTAGATTTATTTTCACACAAAATTCACACATTC
601789 AAAAGGGATCATATCAAAATAATGATAAATCGAAATCAATGCAACCAATATCGAGTCAAAACATT
66 AAAAGGGATCATATCAAAATAATGATAAATCGAAATCAATGCAACCAATATCGAGTCAAAACATT
*
601854 GCTAGTAAGGTACCAATTTTGGGCGTCGCAAGGAGGTTCGTACCTCTTTGCGCGTAACCAACTCC
131 GCTAGTAAGGTACCAATTTCGGGCGTCGCAAGGAGGTTCGTACCTCTTTGCGCGTAACCAACTCC
*
601919 CGAACCCAACCGGCGAATCTCTAAAGTACGCAGACCACGGGATCAATGTTTTGAGTTTCGTAACT
196 CGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCAATGTTTTGAGTTTCGTAACT
*
601984 CAAGACATAGGTTTCAATAGGCATCCGATGATGCCTAGCCCGAAATGATCGGTGGCGACTCCAAA
261 CAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGGTGGCGACTCCAAA
*
602049 ATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCC
326 ATCTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCC
*
602114 CCCTTTAATCAACATACTTCCCACCATGCCACAAAAA-TCTCCAATCATGAGGGATATTAAGTCG
391 CCCTTTAATCAACATACTTCCCACCATGCCACAAAAATTC-CCAATCACGAGGGATATTAAGTCG
602178 AGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
455 AGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
602226 CTCAAAAAGT
Statistics
Matches: 474, Mismatches: 26, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
500 2 0.00
501 447 0.94
502 25 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (502 bp):
GCGCATATGAGATGAAAACAATTTCCAGAAACCTAGATTTATTTTCACACAAAATTCACACATTC
AAAAGGGATCATATCAAAATAATGATAAATCGAAATCAATGCAACCAATATCGAGTCAAAACATT
GCTAGTAAGGTACCAATTTCGGGCGTCGCAAGGAGGTTCGTACCTCTTTGCGCGTAACCAACTCC
CGAACCCAACCGACGAATCTCTAAAGTACGCAGACCACGGGATCAATGTTTTGAGTTTCGTAACT
CAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGGTGGCGACTCCAAA
ATCTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCC
CCCTTTAATCAACATACTTCCCACCATGCCACAAAAATTCCCAATCACGAGGGATATTAAGTCGA
GCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
Found at i:602916 original size:20 final size:20
Alignment explanation
Indices: 602891--602944 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
602881 GCCAAGGAAA
*
602891 TGTATCGATACAT-TATTCAT
1 TGTATCGATACATCGA-TCAT
*
602911 TGTATCGATACATCGATCTT
1 TGTATCGATACATCGATCAT
602931 TGTATCGATACATC
1 TGTATCGATACATC
602945 TAGGAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATCGATCAT
Found at i:602987 original size:20 final size:20
Alignment explanation
Indices: 602960--603016 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
602950 AGTTTACCCA
*
602960 AATGTATCGATACATTTTGC
1 AATGTATCGATACATTTTAC
*
602980 ATTGTATCGATACATTTTAC
1 AATGTATCGATACATTTTAC
603000 AATGTATCGATACATTT
1 AATGTATCGATACATTT
603017 AGGCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTAC
Found at i:603006 original size:71 final size:71
Alignment explanation
Indices: 602888--603019 Score: 187
Period size: 71 Copynumber: 1.9 Consensus size: 71
602878 ACTGCCAAGG
**
602888 AAATGTATCGATACATTATTCATTGTATCGATACATCGATCTTTGTATCGATACATCTAGGAAGT
1 AAATGTATCGATACATTATTCATTGTATCGATACATCGATCAATGTATCGATACATCTAGGAAGT
602953 TTACCC
66 TTACCC
** *
602959 AAATGTATCGATACATT-TTGCATTGTATCGATACAT-TTTACAATGTATCGATACATTTAGG
1 AAATGTATCGATACATTATT-CATTGTATCGATACATCGAT-CAATGTATCGATACATCTAGG
603020 CACTTTTGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 3 0.06
71 51 0.94
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (71 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATCGATCAATGTATCGATACATCTAGGAAGT
TTACCC
Found at i:605466 original size:51 final size:51
Alignment explanation
Indices: 605391--605511 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
605381 GTTATTTTCG
* * *
605391 AGGGGATACTCTAGCCCCGGTTTTATTTCTAAAATACCAATTTTCCACAAT
1 AGGGGATACTCCAGCCCCGATTTTATTTCTAAAACACCAATTTTCCACAAT
* * * * * * *
605442 TGGGGATACTCCATCTCCGATTTTATTTTTAGAACACCAATTTTTCATAAT
1 AGGGGATACTCCAGCCCCGATTTTATTTCTAAAACACCAATTTTCCACAAT
*
605493 AGGGGATACTCCAACCCCG
1 AGGGGATACTCCAGCCCCG
605512 TTATTTTCTA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
AGGGGATACTCCAGCCCCGATTTTATTTCTAAAACACCAATTTTCCACAAT
Found at i:605526 original size:79 final size:79
Alignment explanation
Indices: 605443--605749 Score: 316
Period size: 79 Copynumber: 3.9 Consensus size: 79
605433 TTCCACAATT
* * *
605443 GGGGATACTCCATCTCCGATTTTATTTTTAGAACACCAATTTTTCATAATAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAGAACACCAATTTTTCATAATAGGGGATACTCCAAC
*
605508 CCCGTTATTTTCTA
66 CCCGTTATTTTCAA
* *** * * * * *
605522 GGGGATACTTCAACCCCGGCCTTATTTCTA-AATCATCGATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAGAA-CACCAATTTTTCATAATAGGGGATACTCCAA
605586 CCCCGTTATTTTCAA
65 CCCCGTTATTTTCAA
* * * * *
605601 GGAGATACTCTAACCCCGATTTCATTT-TCAAAATACCAATTTTT-ATAATTA-GGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AGAACACCAATTTTTCATAA-TAGGGGATACTCCA
** * *
605663 ACCTTGTTATTTCCGA
64 ACCCCGTTATTTTCAA
* * * *
605679 GAGGATACTCCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAGAACACCAATTTTTCATAATAGGGGATACTCCAAC
*
605744 CTCGTT
66 CCCGTT
605750 GTTATCTCCA
Statistics
Matches: 181, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
78 63 0.35
79 116 0.64
80 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAGAACACCAATTTTTCATAATAGGGGATACTCCAAC
CCCGTTATTTTCAA
Found at i:605736 original size:157 final size:158
Alignment explanation
Indices: 605458--605749 Score: 365
Period size: 157 Copynumber: 1.9 Consensus size: 158
605448 TACTCCATCT
* * * * *
605458 CCGATTTTATTTTTAGAACACCAATTTTTCATAATAGGGGATACTCCAACCCCGTTATTTTCTAG
1 CCGATTTCATTTTCAAAACACCAATTTTTCATAATAGGGGATACTCCAACCCCGTTATTTCCGAG
* * * * * *
605523 GGGATACTTCAACCCCGGCCTTATTTCTAAATCATCGATTTTTCACAATCGAGGATACTCCAACC
66 AGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTCCACAATCGAGGATACTCCAACC
605588 CCGTTATTTTCAAGGAGATACTCTAACC
131 CCGTTATTTTCAAGGAGATACTCTAACC
* **
605616 CCGATTTCATTTTCAAAATACCAATTTTT-ATAATTA-GGGATACTCCAACCTTGTTATTTCCGA
1 CCGATTTCATTTTCAAAACACCAATTTTTCATAA-TAGGGGATACTCCAACCCCGTTATTTCCGA
** * * *
605679 GAGGATACTCCAACCCCGATTTTATTTCTGGAA-CACCAATTTTCCATAATCGGGGATACTCCAA
65 GAGGATACTCCAACCCCGACCTTATTTCT-AAATCACCAATTTTCCACAATCGAGGATACTCCAA
*
605743 CCTCGTT
129 CCCCGTT
605750 GTTATCTCCA
Statistics
Matches: 112, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
157 83 0.74
158 29 0.26
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (158 bp):
CCGATTTCATTTTCAAAACACCAATTTTTCATAATAGGGGATACTCCAACCCCGTTATTTCCGAG
AGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTCCACAATCGAGGATACTCCAACC
CCGTTATTTTCAAGGAGATACTCTAACC
Found at i:609993 original size:30 final size:30
Alignment explanation
Indices: 609959--610036 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
609949 ATAAAGTGAT
* *
609959 TTTTGATGATTTGTTTTGTTGT-TGAATGAA
1 TTTTGATG-TTTATTATGTTGTGTGAATGAA
609989 TTTTGATGTTTATTATGTTGTGTGAATG-A
1 TTTTGATGTTTATTATGTTGTGTGAATGAA
610018 TTTATGCATGTTTA-TATGT
1 TTT-TG-ATGTTTATTATGT
610037 ATTAGGGTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 15 0.35
30 21 0.49
31 7 0.16
ACGTcount: A:0.21, C:0.01, G:0.22, T:0.56
Consensus pattern (30 bp):
TTTTGATGTTTATTATGTTGTGTGAATGAA
Found at i:622230 original size:29 final size:29
Alignment explanation
Indices: 622188--622405 Score: 224
Period size: 29 Copynumber: 7.5 Consensus size: 29
622178 TTCCTCACCC
*
622188 TTCAAAAGCCCACAAGTCAGTGGTATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
*
622217 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTT
* *
622247 TTCCAAAGCCTACAAGTCAGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* * * *
622276 TTCCAAAGCCCATAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
622306 TTCCAAAGCCCACAAGTCAATGGTATCTC
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* *
622335 TTCAAAAGCCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* ** * *
622363 TTCAAAAGCACACAAGTTGGT-GCAACCCT
1 TTCAAAAGCCCACAAGTCAGTGGC-ATCTT
622392 TTCAAAAGCCCACA
1 TTCAAAAGCCCACA
622406 CAAATTGGTG
Statistics
Matches: 160, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.01
28 21 0.13
29 87 0.54
30 50 0.31
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTT
Found at i:622263 original size:59 final size:59
Alignment explanation
Indices: 622192--622364 Score: 274
Period size: 59 Copynumber: 2.9 Consensus size: 59
622182 TCACCCTTCA
622192 AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * * * *
622251 AAAGCCTACAAGTCAGTGGCATCTTTTCCAAAGCCCATAAGTTAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
622310 AAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTT
622365 CAAAAGCACA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 101 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (59 bp):
AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
Found at i:622418 original size:118 final size:117
Alignment explanation
Indices: 622192--622405 Score: 281
Period size: 118 Copynumber: 1.8 Consensus size: 117
622182 TCACCCTTCA
* * * *
622192 AAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCC
1 AAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCC
* * * * *
622257 TACAAGTCAGTGGCATCTTTTCCAAAGCCCATAAGTTAGTGGCACCCTTTTCC
65 TACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATTAGTGGCACCCTTTTCC
622310 AAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCAC
1 AAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGC-C
**
622374 -ACAAGTTGGT-GCAACCCTTTCAAAAGCCCACA
65 TACAAGTCAGTGGC-ACCCTTTCAAAAGCCCACA
622406 CAAATTGGTG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
115 2 0.02
116 31 0.37
117 1 0.01
118 50 0.60
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (117 bp):
AAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCT
ACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATTAGTGGCACCCTTTTCC
Found at i:622482 original size:49 final size:47
Alignment explanation
Indices: 622414--622698 Score: 327
Period size: 43 Copynumber: 6.0 Consensus size: 47
622404 CACAAATTGG
* * *
622414 TGGCATCTTCT-TCTAAGTCCAATATAGCTGGCCTTGAGTCAGCATAT
1 TGGCA-CTTCTCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
*
622461 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCA-CTTC-TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* *
622510 TGGCA---C-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAA
1 TGGCACTTCTCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
*
622553 TGGCAACTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGC-ACTTC-TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
*
622602 TGGCA---C-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1 TGGCACTTCTCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* *
622645 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCA-C--TT-C-TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
622697 TG
1 TG
622699 ACATCCTTTT
Statistics
Matches: 205, Mismatches: 16, Indels: 29
0.82 0.06 0.12
Matches are distributed among these distances:
43 78 0.38
44 1 0.00
45 2 0.01
47 10 0.05
48 2 0.01
49 75 0.37
50 1 0.00
52 36 0.18
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (47 bp):
TGGCACTTCTCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
Found at i:622584 original size:92 final size:92
Alignment explanation
Indices: 622427--622707 Score: 472
Period size: 92 Copynumber: 3.0 Consensus size: 92
622417 CATCTTCTTC
*
622427 TAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
622492 GGCCTTGAATCAGCACATTGGCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTT
* * *
622519 TAAGTCCAATATAGCTGGCCTTGAATCAGCATAATGGCAACTTCTTCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
622584 GGCCTTGAATCAGCACATTGGCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTT
*
622611 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTA
*
622676 GCTGGCCTTGAATCAGCACATTGACATCCTT
63 GCTGGCCTTGAATCAGCACATTGGCA-CCTT
622707 T
1 T
622708 TTCTCATCTT
Statistics
Matches: 176, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
92 127 0.72
94 2 0.01
95 42 0.24
96 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTT
Done.