Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold419
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1725835
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 213561 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1536167 original size:42 final size:42
Alignment explanation
Indices: 1536098--1536178 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
1536088 TTTCTATTAA
* *
1536098 TTATGTCGACATGCAAGATGAACATGTTGACATGCAAGATAG
1 TTATGTCAACATGCAACATGAACATGTTGACATGCAAGATAG
1536140 TTATGTCAACATGCAACAT-AACTATGTTGACATGCAAGA
1 TTATGTCAACATGCAACATGAAC-ATGTTGACATGCAAGA
1536179 AAACTGCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 33 0.92
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (42 bp):
TTATGTCAACATGCAACATGAACATGTTGACATGCAAGATAG
Found at i:1536183 original size:21 final size:21
Alignment explanation
Indices: 1536099--1536183 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
1536089 TTCTATTAAT
1536099 TATGTCGACATGCAAGATGAAC
1 TATGTCGACATGCAAGAT-AAC
* **
1536121 -ATGTTGACATGCAAGATAGT
1 TATGTCGACATGCAAGATAAC
* *
1536141 TATGTCAACATGCAACATAAC
1 TATGTCGACATGCAAGATAAC
* *
1536162 TATGTTGACATGCAAGAAAAC
1 TATGTCGACATGCAAGATAAC
1536183 T
1 T
1536184 GCAGTCAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 49 0.98
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
TATGTCGACATGCAAGATAAC
Found at i:1536281 original size:21 final size:21
Alignment explanation
Indices: 1536257--1536359 Score: 127
Period size: 21 Copynumber: 4.9 Consensus size: 21
1536247 ATACACTTCC
1536257 TATTGATGTCAACATGCAACT
1 TATTGATGTCAACATGCAACT
* *
1536278 TATTTATGTTAACATGCAACT
1 TATTGATGTCAACATGCAACT
* *
1536299 TCTTGATGTCGACATGCAACT
1 TATTGATGTCAACATGCAACT
* *
1536320 TATTTATGTCGACATGCAACT
1 TATTGATGTCAACATGCAACT
*
1536341 TAGTT-ATGTTAACATGCAA
1 TA-TTGATGTCAACATGCAA
1536360 GATAAATATG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
21 69 0.97
22 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
TATTGATGTCAACATGCAACT
Found at i:1536340 original size:63 final size:63
Alignment explanation
Indices: 1536257--1536418 Score: 209
Period size: 63 Copynumber: 2.6 Consensus size: 63
1536247 ATACACTTCC
* * * * *** * *
1536257 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAA-CTTCTTGATGTCGACATGCAACT
1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAAT-ATGTCGACATGAAACA
*
1536320 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTTGACATGAAACA
1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTCGACATGAAACA
*
1536383 TATTTATGTCGACATGCAACTTAGTTATGTTGACAT
1 TATTTATGTCGACATGCAACTTAGTTATGTTAACAT
1536419 ACAGCTTATA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 85 0.98
64 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (63 bp):
TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTCGACATGAAACA
Found at i:1536390 original size:21 final size:21
Alignment explanation
Indices: 1536268--1536427 Score: 167
Period size: 21 Copynumber: 7.6 Consensus size: 21
1536258 ATTGATGTCA
*
1536268 ACATGCAACTTATTTATGTTA
1 ACATGCAACTTATTTATGTTG
* * *
1536289 ACATGCAACTTCTTGATGTCG
1 ACATGCAACTTATTTATGTTG
*
1536310 ACATGCAACTTATTTATGTCG
1 ACATGCAACTTATTTATGTTG
* *
1536331 ACATGCAACTTAGTTATGTTA
1 ACATGCAACTTATTTATGTTG
** **
1536352 ACATGCAAGATAAATATGTTG
1 ACATGCAACTTATTTATGTTG
* * *
1536373 ACATGAAACATATTTATGTCG
1 ACATGCAACTTATTTATGTTG
*
1536394 ACATGCAACTTAGTTATGTTG
1 ACATGCAACTTATTTATGTTG
* *
1536415 ACATACAGCTTAT
1 ACATGCAACTTAT
1536428 AAGTTGCATG
Statistics
Matches: 113, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 113 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (21 bp):
ACATGCAACTTATTTATGTTG
Found at i:1536478 original size:21 final size:21
Alignment explanation
Indices: 1536454--1536544 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
1536444 TATTTATCTC
* **
1536454 GCATGTCAACATACGTAAGTT
1 GCATGTCGACATAAATAAGTT
*
1536475 GCATGTTGACATAAATAAGTT
1 GCATGTCGACATAAATAAGTT
*
1536496 GCATCTCGACATAAATAAGTT
1 GCATGTCGACATAAATAAGTT
* *
1536517 GCATGTTGACATAAATAATTT
1 GCATGTCGACATAAATAAGTT
1536538 GCATGTC
1 GCATGTC
1536545 AGCATATTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (21 bp):
GCATGTCGACATAAATAAGTT
Found at i:1536550 original size:21 final size:22
Alignment explanation
Indices: 1536426--1536550 Score: 109
Period size: 21 Copynumber: 6.0 Consensus size: 22
1536416 CATACAGCTT
*
1536426 ATAAGTTGCATGTCAG-CATAT
1 ATAAGTTGCATGTCAGACATAA
* ** * *
1536447 TTATCTCGCATGTCA-ACATAC
1 ATAAGTTGCATGTCAGACATAA
* *
1536468 GTAAGTTGCATGT-TGACATAA
1 ATAAGTTGCATGTCAGACATAA
*
1536489 ATAAGTTGCATCTC-GACATAA
1 ATAAGTTGCATGTCAGACATAA
*
1536510 ATAAGTTGCATGT-TGACATAA
1 ATAAGTTGCATGTCAGACATAA
*
1536531 ATAATTTGCATGTCAG-CATA
1 ATAAGTTGCATGTCAGACATA
1536551 TTTATCTTGC
Statistics
Matches: 83, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
21 82 0.99
22 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (22 bp):
ATAAGTTGCATGTCAGACATAA
Found at i:1536561 original size:42 final size:42
Alignment explanation
Indices: 1536473--1536567 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
1536463 CATACGTAAG
*
1536473 TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAG
1 TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAC
* * ** *
1536515 TTGCATGTTGACATAAATAATTTGCATGTC-AGCATATTTATC
1 TTGCATGTTGACATAAATAAGTTGCATCTCGA-CATAAATAAC
1536557 TTGCATGTTGA
1 TTGCATGTTGA
1536568 TTTATGTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 45 0.98
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAC
Found at i:1561464 original size:19 final size:19
Alignment explanation
Indices: 1561437--1561473 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1561427 ATAGAATTGA
*
1561437 CATTGCAGATAGCATTTGT
1 CATTACAGATAGCATTTGT
1561456 CATTACAGATAGCATTTG
1 CATTACAGATAGCATTTG
1561474 CATGTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (19 bp):
CATTACAGATAGCATTTGT
Found at i:1562078 original size:13 final size:12
Alignment explanation
Indices: 1562060--1562106 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
1562050 ACTAAACTCC
1562060 GGGTTTACTTTTT
1 GGGTTTAC-TTTT
*
1562073 GGGTTTAC-TTG
1 GGGTTTACTTTT
*
1562084 GGGTTTACTCTT
1 GGGTTTACTTTT
1562096 -GGTTTACTTTT
1 GGGTTTACTTTT
1562107 TGAAAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 20 0.69
12 1 0.03
13 8 0.28
ACGTcount: A:0.09, C:0.11, G:0.26, T:0.55
Consensus pattern (12 bp):
GGGTTTACTTTT
Found at i:1565397 original size:2 final size:2
Alignment explanation
Indices: 1565390--1565434 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1565380 TTAACATATA
1565390 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1565432 CT C
1 CT C
1565435 ATATATACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1567827 original size:34 final size:34
Alignment explanation
Indices: 1567784--1568023 Score: 268
Period size: 34 Copynumber: 7.0 Consensus size: 34
1567774 ACTCTTTGAG
* * *
1567784 GAAGTCTGGTTATACATATACTTGGAATTCTGTC
1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT
** *
1567818 GAAGTCTGGTTGCACATGTACTTGGGTTTCTGTT
1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT
* ** *
1567852 GATGTCTGGTTATATGTGTACTTTGATTTCTGTT
1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT
* *
1567886 GAAGTCTGGTTATAC-TGGTACTTGGACTTCAGTT
1 GAAGTCTGGTTATACAT-GTACTTGGATTTCTGTT
*
1567920 GAAGTCTGGTTACACATGTACTTTGG-TTTCTGTT
1 GAAGTCTGGTTATACATGTAC-TTGGATTTCTGTT
** *
1567954 GAAGTCTGGTTATATGTGTACTTTGATTTCTGTT
1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT
** *
1567988 GAAGTCTGGTTATACATAAAGATTGGATTTCTGTT
1 GAAGTCTGGTTATACATGTA-CTTGGATTTCTGTT
1568023 G
1 G
1568024 TATTTTGTGA
Statistics
Matches: 170, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
33 4 0.02
34 148 0.87
35 18 0.11
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (34 bp):
GAAGTCTGGTTATACATGTACTTGGATTTCTGTT
Found at i:1567911 original size:102 final size:102
Alignment explanation
Indices: 1567784--1568005 Score: 365
Period size: 102 Copynumber: 2.2 Consensus size: 102
1567774 ACTCTTTGAG
* *
1567784 GAAGTCTGGTTATACATATACTTGGAATTCTGTCGAAGTCTGGTTGCACATGTACTTGGGTTTCT
1 GAAGTCTGGTTATACATATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTCT
*
1567849 GTTGATGTCTGGTTATATGTGTACTTTGATTTCTGTT
66 GTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT
* * * *
1567886 GAAGTCTGGTTATAC-TGGTACTTGGACTTCAGTTGAAGTCTGGTTACACATGTACTTTGGTTTC
1 GAAGTCTGGTTATACAT-ATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTC
1567950 TGTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT
65 TGTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT
1567988 GAAGTCTGGTTATACATA
1 GAAGTCTGGTTATACATA
1568006 AAGATTGGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 1 0.01
102 108 0.98
103 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (102 bp):
GAAGTCTGGTTATACATATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTCT
GTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT
Found at i:1567963 original size:17 final size:17
Alignment explanation
Indices: 1567943--1567998 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1567933 ACATGTACTT
1567943 TGGTTTCTGTTGAAGTC
1 TGGTTTCTGTTGAAGTC
* * * *
1567960 TGGTTATATG-TGTACTT
1 TGGTT-TCTGTTGAAGTC
*
1567977 TGATTTCTGTTGAAGTC
1 TGGTTTCTGTTGAAGTC
1567994 TGGTT
1 TGGTT
1567999 ATACATAAAG
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.14, C:0.09, G:0.27, T:0.50
Consensus pattern (17 bp):
TGGTTTCTGTTGAAGTC
Found at i:1570562 original size:2 final size:2
Alignment explanation
Indices: 1570557--1570611 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1570547 GTAATATATG
1570557 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1570599 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
1570612 GCAGCTCCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1571826 original size:27 final size:28
Alignment explanation
Indices: 1571796--1571855 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1571786 TTATGCTCTT
*
1571796 AATTTTCATCA-TTTGTTCCATGCAGTA
1 AATTTTCATCAGTTTGTTCCATGAAGTA
* *
1571823 AA-TTTCTTCAGTTTGTTCCGTGAAGTA
1 AATTTTCATCAGTTTGTTCCATGAAGTA
1571850 AATTTT
1 AATTTT
1571856 ATTCAATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.25
27 18 0.64
28 3 0.11
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (28 bp):
AATTTTCATCAGTTTGTTCCATGAAGTA
Found at i:1572038 original size:4 final size:4
Alignment explanation
Indices: 1572023--1572068 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
1572013 ATCACCCGTT
*
1572023 GTCC GT-C GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
1572069 TGTAAACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.46, G:0.26, T:0.28
Consensus pattern (4 bp):
GTCC
Found at i:1572069 original size:12 final size:12
Alignment explanation
Indices: 1572018--1572071 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
1572008 TTCTGATCAC
1572018 CCGT-TGTCCGT
1 CCGTCTGTCCGT
*
1572029 -CGTCCGTCCGT
1 CCGTCTGTCCGT
*
1572040 CCGTCCGTCCGT
1 CCGTCTGTCCGT
1572052 CCGTCTGTCCGT
1 CCGTCTGTCCGT
1572064 CCGTCTGT
1 CCGTCTGT
1572072 AAACTTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
10 3 0.08
11 6 0.15
12 30 0.77
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (12 bp):
CCGTCTGTCCGT
Found at i:1574570 original size:16 final size:17
Alignment explanation
Indices: 1574551--1574584 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1574541 CGTCACAATA
1574551 TACT-GGCGAGAAATGG
1 TACTCGGCGAGAAATGG
1574567 TACTCGGCGAGAAATGG
1 TACTCGGCGAGAAATGG
1574584 T
1 T
1574585 CGCACTCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (17 bp):
TACTCGGCGAGAAATGG
Found at i:1575489 original size:2 final size:2
Alignment explanation
Indices: 1575484--1575547 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1575474 TTAGTCTCTC
1575484 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1575526 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
1575548 CAAATGTAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1578607 original size:2 final size:2
Alignment explanation
Indices: 1578600--1578654 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1578590 GCAATTATAC
1578600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1578642 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1578655 ATTCTTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1579812 original size:2 final size:2
Alignment explanation
Indices: 1579805--1579859 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1579795 GCAATTATAC
1579805 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1579847 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1579860 ATTCTTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1583356 original size:2 final size:2
Alignment explanation
Indices: 1583349--1583402 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1583339 ATGTAAGTGT
1583349 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1583391 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1583403 ATTTTCACCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1583757 original size:2 final size:2
Alignment explanation
Indices: 1583750--1583807 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1583740 TTTTCCTTAA
1583750 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1583792 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
1583808 GGGGAACTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1586205 original size:2 final size:2
Alignment explanation
Indices: 1586198--1586253 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1586188 CCTAGTAATA
1586198 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1586240 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1586254 CAAGAGTTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1588605 original size:19 final size:19
Alignment explanation
Indices: 1588573--1588615 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1588563 AGTTTTAACC
*
1588573 AGTTTTAACCGGATATATT
1 AGTTTTAACCGGATATACT
** *
1588592 AGTTTTAATTGGATGTACT
1 AGTTTTAACCGGATATACT
1588611 AGTTT
1 AGTTT
1588616 ACAGTTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (19 bp):
AGTTTTAACCGGATATACT
Found at i:1589029 original size:30 final size:30
Alignment explanation
Indices: 1588995--1589129 Score: 209
Period size: 30 Copynumber: 4.5 Consensus size: 30
1588985 AATACGTTGC
*
1588995 CGGTCCAATAGATCACAGTCTATTGACCGG
1 CGGTCCAATAGATCACACTCTATTGACCGG
1589025 CGGTCCAATAGATCACACTCTATTGACCGG
1 CGGTCCAATAGATCACACTCTATTGACCGG
1589055 CGGTCCAATAGATCACACTCTATTGACCGG
1 CGGTCCAATAGATCACACTCTATTGACCGG
* * *
1589085 CGGTCTAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCACACTCTATTGACCGG
**
1589115 CAAT-CAATAGATCAC
1 CGGTCCAATAGATCAC
1589130 TTTCAAACCT
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
29 9 0.09
30 88 0.91
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (30 bp):
CGGTCCAATAGATCACACTCTATTGACCGG
Found at i:1593515 original size:21 final size:21
Alignment explanation
Indices: 1593458--1593517 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1593448 TGTAGCTATG
* *
1593458 TTGCATGTTGACATAATTATC
1 TTGCATGTCGACATATTTATC
*
1593479 TTGCATGTCAACATATTTATC
1 TTGCATGTCGACATATTTATC
1593500 TTGCATGTCGACATATTT
1 TTGCATGTCGACATATTT
1593518 GATAGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (21 bp):
TTGCATGTCGACATATTTATC
Found at i:1595300 original size:19 final size:19
Alignment explanation
Indices: 1595276--1595313 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1595266 TCAAACGGTA
*
1595276 TCAGGGTGAGTGTCGTCTG
1 TCAGGGTAAGTGTCGTCTG
1595295 TCAGGGTAAGTGTCGTCTG
1 TCAGGGTAAGTGTCGTCTG
1595314 CCATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.39, T:0.32
Consensus pattern (19 bp):
TCAGGGTAAGTGTCGTCTG
Found at i:1595361 original size:14 final size:14
Alignment explanation
Indices: 1595342--1595370 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1595332 CAACAAGAAC
1595342 GTCTATCTTTCCTA
1 GTCTATCTTTCCTA
1595356 GTCTATCTTTCCTA
1 GTCTATCTTTCCTA
1595370 G
1 G
1595371 AGTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.10, T:0.48
Consensus pattern (14 bp):
GTCTATCTTTCCTA
Found at i:1597712 original size:15 final size:15
Alignment explanation
Indices: 1597692--1597725 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1597682 ATAGATTTTG
1597692 ATATTTTATACCAAA
1 ATATTTTATACCAAA
1597707 ATATTTTATACCAAA
1 ATATTTTATACCAAA
1597722 ATAT
1 ATAT
1597726 AAACGAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTTTATACCAAA
Found at i:1599022 original size:2 final size:2
Alignment explanation
Indices: 1599015--1599069 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1599005 TTCAAGTGAG
1599015 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1599057 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
1599070 CGCTAAATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1600814 original size:17 final size:17
Alignment explanation
Indices: 1600788--1600826 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1600778 TTTATTACAC
*
1600788 TTTTTTAAAACTGCAAA
1 TTTTTAAAAACTGCAAA
* *
1600805 TTTTTAAAAATTTCAAA
1 TTTTTAAAAACTGCAAA
1600822 TTTTT
1 TTTTT
1600827 CATTGTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTTAAAAACTGCAAA
Found at i:1635820 original size:2 final size:2
Alignment explanation
Indices: 1635813--1635851 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1635803 AGACTGAAAA
1635813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1635852 TTTAATGTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1641313 original size:11 final size:11
Alignment explanation
Indices: 1641297--1641322 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1641287 GTATTGATCA
1641297 ACATCGTGTCT
1 ACATCGTGTCT
1641308 ACATCGTGTCT
1 ACATCGTGTCT
1641319 ACAT
1 ACAT
1641323 TGTACCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (11 bp):
ACATCGTGTCT
Found at i:1646252 original size:2 final size:2
Alignment explanation
Indices: 1646247--1646323 Score: 122
Period size: 2 Copynumber: 38.5 Consensus size: 2
1646237 ATATATGGAA
1646247 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TA- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG
1646289 AG AG AG AG AG AG TA- AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG A
1646324 TGGTTAAGGA
Statistics
Matches: 71, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.03
2 67 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1648076 original size:152 final size:152
Alignment explanation
Indices: 1647893--1648183 Score: 510
Period size: 152 Copynumber: 1.9 Consensus size: 152
1647883 AATAAATACG
* *
1647893 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATATTTACCATCTTTGGTGTAGCTCTCAG
1 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG
* *
1647958 GTCCATGATTGTAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT
66 GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT
*
1648023 TAAATCAAATAAATACGAGTAA
131 AAAATCAAATAAATACGAGTAA
*
1648045 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTGAG
1 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG
* *
1648110 GTCCATAATTGAAGACTGGATCTGGTGCTGTCAAAAAACATGTTTTAGTTAATAACATATCTTTT
66 GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT
1648175 AAAATCAAA
131 AAAATCAAA
1648184 ATTACAAAGC
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 131 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (152 bp):
ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG
GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT
AAAATCAAATAAATACGAGTAA
Found at i:1654999 original size:7 final size:7
Alignment explanation
Indices: 1654975--1655041 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
1654965 TTTAGATATT
1654975 GAATCTC
1 GAATCTC
* *
1654982 CAATTTC
1 GAATCTC
1654989 GAATCTC
1 GAATCTC
1654996 GAATCTC
1 GAATCTC
* *
1655003 GTATTTC
1 GAATCTC
1655010 GAATCTC
1 GAATCTC
* *
1655017 GTATTTC
1 GAATCTC
1655024 GAATCTC
1 GAATCTC
1655031 GAATCTC
1 GAATCTC
1655038 GAAT
1 GAAT
1655042 GATCCTTCTC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:1655000 original size:21 final size:21
Alignment explanation
Indices: 1654975--1655041 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
1654965 TTTAGATATT
*
1654975 GAATCTCCAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1654996 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
1655017 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
1655038 GAAT
1 GAAT
1655042 GATCCTTCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1659730 original size:21 final size:21
Alignment explanation
Indices: 1659706--1659749 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1659696 TTGGTCTTTA
1659706 TTTAACTAGACTGTTGGAATC
1 TTTAACTAGACTGTTGGAATC
1659727 TTTAACTAGACTGTTGGAATC
1 TTTAACTAGACTGTTGGAATC
1659748 TT
1 TT
1659750 ATTGTTGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
TTTAACTAGACTGTTGGAATC
Found at i:1660608 original size:2 final size:2
Alignment explanation
Indices: 1660601--1660653 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1660591 ACGATTTAAG
1660601 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1660643 GA GA GA GA GA G
1 GA GA GA GA GA G
1660654 TATAAAATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1663185 original size:2 final size:2
Alignment explanation
Indices: 1663178--1663213 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1663168 AAGATGATAT
1663178 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1663214 TTTACATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1663229 original size:4 final size:4
Alignment explanation
Indices: 1663222--1663319 Score: 178
Period size: 4 Copynumber: 24.5 Consensus size: 4
1663212 GATTTACATG
1663222 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
* *
1663270 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TCGA TCGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1663318 TA
1 TA
1663320 TTTGTTAGTA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 92 1.00
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:1665715 original size:2 final size:2
Alignment explanation
Indices: 1665708--1665742 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1665698 AGAAGCAAGG
* *
1665708 GA GA GA GA GA GA GA GT GA AA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1665743 GGGGGGTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1668600 original size:2 final size:2
Alignment explanation
Indices: 1668593--1668644 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1668583 CTCTAGCTAC
*
1668593 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1668635 GA GA GA GA GA
1 GA GA GA GA GA
1668645 ACCCAGAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1672507 original size:2 final size:2
Alignment explanation
Indices: 1672500--1672566 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1672490 NNNNNNNNNG
1672500 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1672542 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1672567 GCAAATAATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1677294 original size:57 final size:57
Alignment explanation
Indices: 1677117--1677294 Score: 216
Period size: 57 Copynumber: 3.1 Consensus size: 57
1677107 TGCAAAGACA
* * * *
1677117 GATAGTGATAGTGTGCACAATGCACCAGAGCACCAAGCTGTGCTAACTGCATTGACT
1 GATAGTGATAGTGTCCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT
* * * ** *
1677174 GATAGTAACAATGTGCCA-AATACATCAGATTACCAAGCTGTGCTAACTGCAATGAGT
1 GATAGTGATAGTGT-CCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT
* *
1677231 GATAGTGATAGTGTCCACAATACATCAAAGCAACC-AGCTGTGCTAACTGCCTTGAGT
1 GATAGTGATAGTGTCCACAATACATCAGAGC-ACCAAGCTGTGCTAACTGCATTGAGT
1677288 GATAGTG
1 GATAGTG
1677295 TGCTCAATAC
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
56 3 0.03
57 92 0.92
58 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (57 bp):
GATAGTGATAGTGTCCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT
Found at i:1686345 original size:2 final size:2
Alignment explanation
Indices: 1686338--1686402 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1686328 AGTATCAATT
1686338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1686380 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1686403 GTGTGCTACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1688103 original size:2 final size:2
Alignment explanation
Indices: 1688096--1688149 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1688086 CATGTACAAC
1688096 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1688138 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1688150 CGATATTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1693195 original size:2 final size:2
Alignment explanation
Indices: 1693188--1693264 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1693178 NNNNNNNNNN
1693188 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1693230 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1693265 TGCATACATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1713203 original size:159 final size:160
Alignment explanation
Indices: 1712904--1713241 Score: 502
Period size: 160 Copynumber: 2.1 Consensus size: 160
1712894 AACATCCAGA
* *
1712904 AAGAAAATGAGCGGAAACTGCACACAACTGGAATTTTCTAAGTCCAAAGGCCATAACTCTGTCAA
1 AAGAAAATGAGCGGAAACTGCAAACAACTGGAATTTTCTAAGTCCAAAGGCAATAACTCTGTCAA
* *
1712969 AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATGATAAACCTGTATACTA
66 AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATACCA
*
1713034 AATTTTATTTCAA-ATGTTCATCCTCTGCG
131 AATTTCATTTCAATATGTTCATCCTCTGCG
* *
1713063 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACGTCC-AAGGACAATAACTCTGTC
1 AAGAAAATGAGCGGAAACTGCAAACAACTGGAA-TTTTCTAAGTCCAAAGG-CAATAACTCTGTC
* * ** * *
1713127 GAAAATGGCTCGATCGTGCCCAATATTGAACTTGACCTAGATATTATCATAAT-AACCTGTATAC
64 AAAAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATAC
*
1713191 CAAATTTCATTTCAATATGTTCATCCTCTGCT
129 CAAATTTCATTTCAATATGTTCATCCTCTGCG
*
1713223 AAGAAAATGAACGGAAACT
1 AAGAAAATGAGCGGAAACT
1713242 TATGGTGGAC
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
159 59 0.37
160 102 0.63
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (160 bp):
AAGAAAATGAGCGGAAACTGCAAACAACTGGAATTTTCTAAGTCCAAAGGCAATAACTCTGTCAA
AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATACCA
AATTTCATTTCAATATGTTCATCCTCTGCG
Found at i:1713404 original size:49 final size:49
Alignment explanation
Indices: 1713327--1713994 Score: 698
Period size: 49 Copynumber: 13.6 Consensus size: 49
1713317 TAATTACAGG
* * * * * *
1713327 TACATGTATTTACCACGTGCTGTATGATACAGGTGAAACACATACATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * *
1713376 TACAGGTATTTACTATGTGTTGTATGATAGAGGTGAGATACATGCACGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * *
1713425 TACATGTATTTACTATGTGTTGTATGATAGAGGTGAGATACATGCATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * * * * *
1713474 TACAGGTATCTA-TAACATGCTGTATGATACAGGTGAAACACATACATAA
1 TACAGGTATTTACT-ACGTGTTGTATGATACAGGTGAGATACATGCATGA
* *
1713523 TACAGGTATTTACTACGTGTTGTATGATACTGGTGAGATACATGCACGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * * * *
1713572 TACAGTTATTTACTATGTGTTGTATGATACAGGTGAAACACATACATAA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* *
1713621 TACAGGTATTTACTACGTGTTGTATGATACTGGTGAGATACATGCACGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * *
1713670 TACAGTTATTTACTATGTGTTGTATGATACAAGTGAGACACATGCATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * * *
1713719 TACAGGTATTTACCACCTGCTGTATGATTCAGGTGAGATACATGGATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* ** *
1713768 TACAGGTATTTACTACATGCTACTATGATACAGG-GCAATGACACAGTG--TGA
1 TACAGGTATTTACTACGTG-TTGTATGATACAGGTG--A-GATACA-TGCATGA
* * ** * * * *
1713819 TACAGCTGTTTACTAAATGTTGTATGATATAGGTGAGAAATATGTATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * *
1713868 TACAGGAATTTACAACATGTTGTATGATACAGATGAGATACATGCATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
* * * * *
1713917 TACAGGTAATAACTACGTGTTGTATGATACAGGTGCGTTATAT-CTATGA
1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGC-ATGA
*
1713966 TACAGGTATTTACTATGTGTTGTATGATA
1 TACAGGTATTTACTACGTGTTGTATGATA
1713995 AAGGACAATG
Statistics
Matches: 510, Mismatches: 98, Indels: 22
0.81 0.16 0.03
Matches are distributed among these distances:
47 2 0.00
48 6 0.01
49 452 0.89
50 22 0.04
51 21 0.04
52 5 0.01
53 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (49 bp):
TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA
Found at i:1724030 original size:55 final size:55
Alignment explanation
Indices: 1723964--1724255 Score: 318
Period size: 55 Copynumber: 5.5 Consensus size: 55
1723954 AACCCTAGAC
* *
1723964 TAGAGTGGCCCGACTGACTAGCAACTGGCATGCTGTACCCTAAAATCTGACAGAT
1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
* * * * *
1724019 TAGAGTGGCCCGACTGACAAACTACTGGCGTGCTGTACCCTAGACTCTGACAGAC
1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
*
1724074 TAGAGTGACCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
* * *
1724129 TAGAGTGGCCCGACTGACTAACTACTGACAG-GCTGTAGCCT---A---GAC----
1 TAGAGTGGCCCGACTGACTAGCTACTGGC-GTGCTGTACCCTAAAATCTGACAGAT
* ** * * * * * *
1724174 TAGAGTGACTTGACTGAATAACTACTGACGTGCTGTAGCCTAGAATCTGACATAT
1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
1724229 TAGAGTGGCCCGACTGACTAGCTACTG
1 TAGAGTGGCCCGACTGACTAGCTACTG
1724256 ACGTAGCATA
Statistics
Matches: 199, Mismatches: 26, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
44 1 0.01
45 35 0.18
48 1 0.01
49 3 0.02
51 3 0.02
52 1 0.01
55 154 0.77
56 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (55 bp):
TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT
Found at i:1724243 original size:100 final size:100
Alignment explanation
Indices: 1724070--1724257 Score: 295
Period size: 100 Copynumber: 1.9 Consensus size: 100
1724060 AGACTCTGAC
* * *
1724070 AGACTAGAGTGACCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGATTAGAGT
1 AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT
1724135 GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT
66 GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT
** * * *
1724170 AGACTAGAGTGACTTGACTGAATAACTACTGACGTGCTGTAGCCTAGAATCTGACATATTAGAGT
1 AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT
*
1724235 GGCCCGACTGACTAGCTACTGAC
66 GGCCCGACTGACTAACTACTGAC
1724258 GTAGCATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (100 bp):
AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT
GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT
Found at i:1725136 original size:30 final size:30
Alignment explanation
Indices: 1725100--1725181 Score: 155
Period size: 30 Copynumber: 2.7 Consensus size: 30
1725090 CCTAAACACA
1725100 TGATATCTGGTCCTACTACACATGATATCC
1 TGATATCTGGTCCTACTACACATGATATCC
*
1725130 TGATATCTGGTCCAACTACACATGATATCC
1 TGATATCTGGTCCTACTACACATGATATCC
1725160 TGATATCTGGTCCTACTACACA
1 TGATATCTGGTCCTACTACACA
1725182 GGATCTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (30 bp):
TGATATCTGGTCCTACTACACATGATATCC
Done.