Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 6 of 141
Found at i:1478934 original size:81 final size:81
Alignment explanation
Indices: 1478755--1479068 Score: 339
Period size: 81 Copynumber: 3.9 Consensus size: 81
1478745 ACCTTTCGGG
* * * * * * *
1478755 GCTTTAGCGGCGCTTTTAAAGAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAG
1 GCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTAAA-AAG
* *
1478820 CGTCGCTAATGCTCAGA
65 CGCCGCTAATGCTCAAA
* * *
1478837 GCTTTAGCGGCATTTTTGAAGAAGCGCTGCTAATGTTCGGGGTTTTAGCGGCGTTTTTAAAAAGC
1 GCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTAAAAAGC
1478902 GCCGC-AACTGCTCAAA
66 GCCGCTAA-TGCTCAAA
* * * * **
1478918 GCTTTAGCGCCGTTTTT-AAGGAAGCGCCACTAATACTCGAGGTTTTAGCGGCGTTTTTGGAAAG
1 GCTTTAGCGGCGTTTTTGAA-GAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTAAAAAG
***
1478982 CGCCGCTAATGCTCGTG
65 CGCCGCTAATGCTCAAA
* * *
1478999 GTTTTAGCGGCGTTTTTTGAA-AAGCGCCGTTAATGCTC-GGGATTTAGCGGCGTTTTTGAAAAA
1 GCTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTT-AAAAA
1479062 GCGCCGC
64 GCGCCGC
1479069 AAAAACATTT
Statistics
Matches: 193, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
80 21 0.11
81 112 0.58
82 58 0.30
83 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (81 bp):
GCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTAAAAAGC
GCCGCTAATGCTCAAA
Found at i:1478967 original size:122 final size:121
Alignment explanation
Indices: 1478749--1479027 Score: 355
Period size: 122 Copynumber: 2.3 Consensus size: 121
1478739 TTTGTAACCT
* * * * *
1478749 TTCGGGGCTTTAGCGGCGCTTTTAAAGAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTA
1 TTCGGGGTTTTAGCGGCGTTTTTAAA-AAGCGCCGCAACTGCTCAAAGCTTTAGCAGCGTTTTTA
* * * *
1478814 AAGAAGCGTCGCTAATGCTCAGAGCTTTAGCGGCATTTTTGAAGAAGCGCTGCTAATG
65 AAGAAGCGCCACTAATACTCAGAGCTTTAGCGGCATTTTTGAA-AAGCGCCGCTAATG
1478872 TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCAACTGCTCAAAGCTTTAGC-GCCGTTTTTA
1 TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCAACTGCTCAAAGCTTTAGCAG-CGTTTTTA
* * * *
1478936 AGGAAGCGCCACTAATACTC-GAGGTTTTAGCGGCGTTTTTGGAAAGCGCCGCTAATG
65 AAGAAGCGCCACTAATACTCAGA-GCTTTAGCGGCATTTTTGAAAAGCGCCGCTAATG
* * *
1478993 CTCGTGGTTTTAGCGGCGTTTTTTGAAAAGCGCCG
1 TTCGGGGTTTTAGCGGCG-TTTTTAAAAAGCGCCG
1479028 TTAATGCTCG
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
121 32 0.23
122 81 0.59
123 24 0.18
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (121 bp):
TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCAACTGCTCAAAGCTTTAGCAGCGTTTTTAA
AGAAGCGCCACTAATACTCAGAGCTTTAGCGGCATTTTTGAAAAGCGCCGCTAATG
Found at i:1479036 original size:122 final size:121
Alignment explanation
Indices: 1478750--1479066 Score: 347
Period size: 122 Copynumber: 2.6 Consensus size: 121
1478740 TTGTAACCTT
* * * *
1478750 TCGGGGCTTTAGCGGCGCTTTTAAAGAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAA
1 TCGGGGTTTTAGCGGCGTTTTTAAA-AAGCGCCG-TAATGCTCAAAGCTTTAGCAGCGTTTTTAA
* * * * *
1478815 AGAAGCGTCGCTAATGCTCAGAGCTTTAGCGGCATTTTTGAAGAAGCGCTGCTAATGT
64 AGAAGCGCCACTAATACTCAGAGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
*
1478873 TCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCAACTGCTCAAAGCTTTAGC-GCCGTTTTTAA
1 TCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGTAA-TGCTCAAAGCTTTAGCAG-CGTTTTTAA
* * * *
1478937 GGAAGCGCCACTAATACTC-GAGGTTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATGC
64 AGAAGCGCCACTAATACTCAGA-GCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
* * ** * *
1478994 TCGTGGTTTTAGCGGCGTTTTTTGAAAAGCGCCGTTAATGCTC-GGGATTTAGCGGCGTTTTTGA
1 TCGGGGTTTTAGCGGCG-TTTTTAAAAAGCGCCG-TAATGCTCAAAGCTTTAGCAGCGTTTTT-A
1479058 AA-AAGCGCC
63 AAGAAGCGCC
1479067 GCAAAAACAT
Statistics
Matches: 166, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
121 54 0.33
122 87 0.52
123 25 0.15
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (121 bp):
TCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGTAATGCTCAAAGCTTTAGCAGCGTTTTTAAAG
AAGCGCCACTAATACTCAGAGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
Found at i:1479232 original size:71 final size:71
Alignment explanation
Indices: 1479144--1479301 Score: 316
Period size: 71 Copynumber: 2.2 Consensus size: 71
1479134 TTTTTAATTG
1479144 AATATTTGTTAAAAATAGATAAATTTGAAATAATGACACGTAGAAATAATTTAAAGTAAAAAACA
1 AATATTTGTTAAAAATAGATAAATTTGAAATAATGACACGTAGAAATAATTTAAAGTAAAAAACA
1479209 TAGAAA
66 TAGAAA
1479215 AATATTTGTTAAAAATAGATAAATTTGAAATAATGACACGTAGAAATAATTTAAAGTAAAAAACA
1 AATATTTGTTAAAAATAGATAAATTTGAAATAATGACACGTAGAAATAATTTAAAGTAAAAAACA
1479280 TAGAAA
66 TAGAAA
1479286 AATATTTGTTAAAAAT
1 AATATTTGTTAAAAAT
1479302 GAAAAAAAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 87 1.00
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (71 bp):
AATATTTGTTAAAAATAGATAAATTTGAAATAATGACACGTAGAAATAATTTAAAGTAAAAAACA
TAGAAA
Found at i:1479626 original size:21 final size:21
Alignment explanation
Indices: 1479602--1479652 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1479592 GGTTGTAATT
* *
1479602 TAAGATTTATGGGTTAGGGGC
1 TAAGAGTTATGGGTTAGAGGC
* *
1479623 TAAGGGTTATGGGTTAGAGGT
1 TAAGAGTTATGGGTTAGAGGC
1479644 TAAGAGTTA
1 TAAGAGTTA
1479653 GGGATTTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.33
Consensus pattern (21 bp):
TAAGAGTTATGGGTTAGAGGC
Found at i:1479758 original size:7 final size:7
Alignment explanation
Indices: 1479746--1479809 Score: 60
Period size: 7 Copynumber: 9.3 Consensus size: 7
1479736 AGGGGTTGAA
1479746 GTTAGGG
1 GTTAGGG
1479753 GTTAGGG
1 GTTAGGG
**
1479760 GTT-GAA
1 GTTAGGG
1479766 GTTAGGG
1 GTTAGGG
1479773 GTTAGGG
1 GTTAGGG
*
1479780 GTTGGGG
1 GTTAGGG
1479787 GTT-GGAG
1 GTTAGG-G
*
1479794 GTTGGGG
1 GTTAGGG
*
1479801 GTTAAGG
1 GTTAGGG
1479808 GT
1 GT
1479810 CGAGTTAGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 6 0.13
7 39 0.83
8 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.56, T:0.30
Consensus pattern (7 bp):
GTTAGGG
Found at i:1479759 original size:20 final size:20
Alignment explanation
Indices: 1479734--1479783 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1479724 TAAATAAGGT
1479734 TTAGGGGTTGAAGTTAGGGG
1 TTAGGGGTTGAAGTTAGGGG
1479754 TTAGGGGTTGAAGTTAGGGG
1 TTAGGGGTTGAAGTTAGGGG
1479774 TTAGGGGTTG
1 TTAGGGGTTG
1479784 GGGGTTGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (20 bp):
TTAGGGGTTGAAGTTAGGGG
Found at i:1479927 original size:21 final size:21
Alignment explanation
Indices: 1479889--1479945 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1479879 TTAGTGGTTA
* * *
1479889 ATTAGTGGTTTGGGGTTAGAG
1 ATTAGAGGTTTAGAGTTAGAG
*
1479910 ATTAGAGGTTTAGAGTTAGTG
1 ATTAGAGGTTTAGAGTTAGAG
1479931 ATTTA-AGGTTTAGAG
1 A-TTAGAGGTTTAGAG
1479946 ATTCGGGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (21 bp):
ATTAGAGGTTTAGAGTTAGAG
Found at i:1482048 original size:4 final size:4
Alignment explanation
Indices: 1482039--1482065 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1482029 TAATAATGAG
1482039 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1482066 CTAAGTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1484549 original size:7 final size:7
Alignment explanation
Indices: 1484537--1484578 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
1484527 ATGTGAATTT
1484537 GATATTA
1 GATATTA
1484544 GATATTA
1 GATATTA
*
1484551 GATATTT
1 GATATTA
*
1484558 GGTATT-
1 GATATTA
1484564 GATATTA
1 GATATTA
1484571 GATATTA
1 GATATTA
1484578 G
1 G
1484579 GCTGTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:1484569 original size:20 final size:21
Alignment explanation
Indices: 1484533--1484576 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1484523 TTTGATGTGA
1484533 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
1484554 ATTTGGTATT-GATATTAGAT
1 ATTTGATATTAGATATTAGAT
1484574 ATT
1 ATT
1484577 AGGCTGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:1484627 original size:90 final size:90
Alignment explanation
Indices: 1484523--1484757 Score: 452
Period size: 90 Copynumber: 2.6 Consensus size: 90
1484513 AATATATATA
*
1484523 TTTGATGTGAATTTGATATTAGATATTAGATATTTGGTATTGATATTAGATATTAGGCTGTGATT
1 TTTGATGTGAATTTGATATTACATATTAGATATTTGGTATTGATATTAGATATTAGGCTGTGATT
1484588 AAATGTTTGCTACTGTCAAATGTTC
66 AAATGTTTGCTACTGTCAAATGTTC
*
1484613 TTTGATGTGAATTTGATAATACATATTAGATATTTGGTATTGATATTAGATATTAGGCTGTGATT
1 TTTGATGTGAATTTGATATTACATATTAGATATTTGGTATTGATATTAGATATTAGGCTGTGATT
1484678 AAATGTTTGCTACTGTCAAATGTTC
66 AAATGTTTGCTACTGTCAAATGTTC
1484703 TTTGATGTGAATTTGATATTACATATTAGATATTTGGTATTGATATTAGATATTA
1 TTTGATGTGAATTTGATATTACATATTAGATATTTGGTATTGATATTAGATATTA
1484758 TATATGGTTT
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 142 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (90 bp):
TTTGATGTGAATTTGATATTACATATTAGATATTTGGTATTGATATTAGATATTAGGCTGTGATT
AAATGTTTGCTACTGTCAAATGTTC
Found at i:1485023 original size:7 final size:7
Alignment explanation
Indices: 1485011--1485052 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
1485001 ATATGAATTT
1485011 GATATTA
1 GATATTA
1485018 GATATTA
1 GATATTA
*
1485025 GATATTT
1 GATATTA
*
1485032 GGTATT-
1 GATATTA
1485038 GATATTA
1 GATATTA
1485045 GATATTA
1 GATATTA
1485052 G
1 G
1485053 GGTTTAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:1485043 original size:20 final size:21
Alignment explanation
Indices: 1485007--1485050 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1484997 TTTGATATGA
1485007 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
1485028 ATTTGGTATT-GATATTAGAT
1 ATTTGATATTAGATATTAGAT
1485048 ATT
1 ATT
1485051 AGGGTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:1485356 original size:9 final size:9
Alignment explanation
Indices: 1485326--1485713 Score: 248
Period size: 9 Copynumber: 46.2 Consensus size: 9
1485316 AACTTATTAA
*
1485326 TACATAACC
1 TACATAACT
1485335 TACATAA--
1 TACATAACT
*
1485342 GACATAACT
1 TACATAACT
*
1485351 TCCATAACT
1 TACATAACT
1485360 TACATAA--
1 TACATAACT
* *
1485367 TACAAAATT
1 TACATAACT
*
1485376 TATATAACT
1 TACATAACT
*
1485385 TATATAA--
1 TACATAACT
*
1485392 GAC--AACT
1 TACATAACT
*
1485399 TACATAATT
1 TACATAACT
*
1485408 TACTTAA--
1 TACATAACT
1485415 TACATAACT
1 TACATAACT
**
1485424 TACAT-GTT
1 TACATAACT
1485432 TACATAA--
1 TACATAACT
*
1485439 TATATAACT
1 TACATAACT
*
1485448 TACATAACC
1 TACATAACT
1485457 TACATAA--
1 TACATAACT
*
1485464 GACATAACT
1 TACATAACT
*
1485473 TCCATAACT
1 TACATAACT
*
1485482 TTCATAA--
1 TACATAACT
* *
1485489 TACACAATT
1 TACATAACT
1485498 TACATAACT
1 TACATAACT
*
1485507 TAAATAACT
1 TACATAACT
1485516 TACATAAC-
1 TACATAACT
*
1485524 T-CACAACT
1 TACATAACT
1485532 TACATAACT
1 TACATAACT
1485541 TACATAACT
1 TACATAACT
1485550 TACATAAC-
1 TACATAACT
*
1485558 T-CACAACT
1 TACATAACT
1485566 TACATAACT
1 TACATAACT
1485575 TA-ATTACACT
1 TACA-TA-ACT
*
1485585 ATACACAACT
1 -TACATAACT
* *
1485595 TACGTAACA
1 TACATAACT
1485604 TACATAA--
1 TACATAACT
1485611 TACATAACT
1 TACATAACT
1485620 TACATAACT
1 TACATAACT
1485629 TACATAA--
1 TACATAACT
1485636 TACATAACT
1 TACATAACT
1485645 TA-ATTTAA--
1 TACA--TAACT
*
1485653 TACACAACT
1 TACATAACT
*
1485662 TACATAGCT
1 TACATAACT
1485671 TACATAA--
1 TACATAACT
1485678 TACATAACT
1 TACATAACT
1485687 TACATAACT
1 TACATAACT
*
1485696 TATATAA--
1 TACATAACT
1485703 TACATAACT
1 TACATAACT
1485712 TA
1 TA
1485714 TATGATTTAC
Statistics
Matches: 296, Mismatches: 45, Indels: 76
0.71 0.11 0.18
Matches are distributed among these distances:
5 2 0.01
7 77 0.26
8 14 0.05
9 190 0.64
10 9 0.03
11 3 0.01
12 1 0.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:1485363 original size:25 final size:25
Alignment explanation
Indices: 1485326--1485734 Score: 334
Period size: 25 Copynumber: 16.9 Consensus size: 25
1485316 AACTTATTAA
* *
1485326 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * *
1485351 TCCATAACTTACATAATACAAAATT
1 TACATAACTTACATAATACATAACT
* * *
1485376 TATATAACTTATATAAGAC--AACT
1 TACATAACTTACATAATACATAACT
* *
1485399 TACATAATTTACTTAATACATAACT
1 TACATAACTTACATAATACATAACT
** *
1485424 TACAT-GTTTACATAATATATAACT
1 TACATAACTTACATAATACATAACT
* *
1485448 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
1485473 TCCATAACTTTCATAATACACAATT
1 TACATAACTTACATAATACATAACT
*
1485498 TACATAACTTAAATAACTTACATAAC-
1 TACATAACTTACATAA--TACATAACT
*
1485524 T-CACAACTTACATAACTTACATAACT
1 TACATAACTTACATAA--TACATAACT
* *
1485550 TACATAACTCACA-ACTTACATAACT
1 TACATAACTTACATA-ATACATAACT
* *
1485575 TA-ATTAC--AC-T-ATACACAACT
1 TACATAACTTACATAATACATAACT
* *
1485595 TACGTAACATACATAATACATAACT
1 TACATAACTTACATAATACATAACT
1485620 TACATAACTTACATAATACATAAC-
1 TACATAACTTACATAATACATAACT
*
1485644 T---TAA-TT---TAATACACAACT
1 TACATAACTTACATAATACATAACT
*
1485662 TACATAGCTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
*
1485687 TACATAACTTATATAATACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
1485712 TATATGATTTACTTAATACATAA
1 TACATAACTTACATAATACATAA
1485735 ATATATATCA
Statistics
Matches: 305, Mismatches: 57, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
17 10 0.03
18 1 0.00
20 12 0.04
21 8 0.03
22 4 0.01
23 19 0.06
24 27 0.09
25 206 0.68
26 3 0.01
27 15 0.05
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:1485503 original size:34 final size:34
Alignment explanation
Indices: 1485393--1485713 Score: 202
Period size: 34 Copynumber: 9.8 Consensus size: 34
1485383 CTTATATAAG
* * *
1485393 ACAACTTACATAATTTACTTAA--TACATAACTT
1 ACAACTTACATAACTTACATAACTTACATAACTC
** *
1485425 ACATGTTTACATAA--TATATAACTTACATAAC-C
1 ACA-ACTTACATAACTTACATAACTTACATAACTC
** * *
1485457 TACATA-AGACATAACTTCCATAACTTTCATAA-TAC
1 -ACA-ACTTACATAACTTACATAACTTACATAACT-C
* *
1485492 ACAATTTACATAACTTAAATAACTTACATAACTC
1 ACAACTTACATAACTTACATAACTTACATAACTC
1485526 ACAACTTACATAACTTACATAACTTACATAACTC
1 ACAACTTACATAACTTACATAACTTACATAACTC
*
1485560 ACAACTTACATAACTTA-ATTAC--AC-T-A-TAC
1 ACAACTTACATAACTTACATAACTTACATAACT-C
* *
1485589 ACAACTTACGTAACATACATAA--TACATAACTTAC
1 ACAACTTACATAACTTACATAACTTACATAAC-T-C
*
1485623 ATAACTTACATAA--TACATAACTTA-ATTTAA-TAC
1 ACAACTTACATAACTTACATAACTTACA--TAACT-C
*
1485656 ACAACTTACATAGCTTACATAA--TACATAACTTAC
1 ACAACTTACATAACTTACATAACTTACATAAC-T-C
* *
1485690 ATAACTTATATAA--TACATAACTTA
1 ACAACTTACATAACTTACATAACTTA
1485714 TATGATTTAC
Statistics
Matches: 232, Mismatches: 29, Indels: 54
0.74 0.09 0.17
Matches are distributed among these distances:
28 1 0.00
29 17 0.07
30 6 0.03
31 8 0.03
32 27 0.12
33 42 0.18
34 119 0.51
35 12 0.05
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (34 bp):
ACAACTTACATAACTTACATAACTTACATAACTC
Found at i:1485662 original size:42 final size:42
Alignment explanation
Indices: 1485608--1485688 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
1485598 GTAACATACA
*
1485608 TAATACATAACTTACATAACTTACATAATACATAACTTAATT
1 TAATACACAACTTACATAACTTACATAATACATAACTTAATT
*
1485650 TAATACACAACTTACATAGCTTACATAATACATAACTTA
1 TAATACACAACTTACATAACTTACATAATACATAACTTA
1485689 CATAACTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (42 bp):
TAATACACAACTTACATAACTTACATAATACATAACTTAATT
Found at i:1485716 original size:16 final size:16
Alignment explanation
Indices: 1485308--1485713 Score: 170
Period size: 16 Copynumber: 24.9 Consensus size: 16
1485298 TTTAAATTTT
*
1485308 TAATACATAACTTA-T
1 TAATACATAACTTACA
*
1485323 TAATACATAACCTACA
1 TAATACATAACTTACA
* *
1485339 TAAGACATAACTTCCA
1 TAATACATAACTTACA
1485355 TAACTTACATAA--TACA
1 TAA--TACATAACTTACA
* * *
1485371 AAATTTATATAACTTATA
1 TAA--TACATAACTTACA
*
1485389 TAAGAC--AACTTACA
1 TAATACATAACTTACA
*
1485403 TAATTTACTTAA--TACA
1 TAA--TACATAACTTACA
**
1485419 TAACTTACAT-GTTTACA
1 TAA--TACATAACTTACA
*
1485436 TAATATATAACTTACA
1 TAATACATAACTTACA
*
1485452 TAACCTACATAA--GACA
1 TAA--TACATAACTTACA
* *
1485468 TAACTTCCATAACTTTCA
1 TAA--TACATAACTTACA
* *
1485486 TAATACACAATTTACA
1 TAATACATAACTTACA
*
1485502 TAACTTAAATAACTTACA
1 TAA--TACATAACTTACA
*
1485520 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
1485536 TAACTTACATAACTTACA
1 TAA--TACATAACTTACA
*
1485554 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
*
1485570 T-A-ACTTAA-TTACA
1 TAATACATAACTTACA
* *
1485583 CT-ATACACAACTTACG
1 -TAATACATAACTTACA
1485599 TAACATACATAA--TACA
1 T-A-ATACATAACTTACA
1485615 TAACTTACATAACTTACA
1 TAA--TACATAACTTACA
1485633 TAATACATAACTTA-A
1 TAATACATAACTTACA
*
1485648 TTTAATACACAACTTACA
1 --TAATACATAACTTACA
*
1485666 TAGCTTACATAA--TACA
1 TA--ATACATAACTTACA
*
1485682 TAACTTACATAACTTATA
1 TAA--TACATAACTTACA
1485700 TAATACATAACTTA
1 TAATACATAACTTA
1485714 TATGATTTAC
Statistics
Matches: 297, Mismatches: 54, Indels: 79
0.69 0.13 0.18
Matches are distributed among these distances:
13 5 0.02
14 16 0.05
15 25 0.08
16 151 0.51
17 23 0.08
18 77 0.26
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (16 bp):
TAATACATAACTTACA
Found at i:1487051 original size:21 final size:21
Alignment explanation
Indices: 1487026--1487106 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
1487016 AGAGGTGGCG
*
1487026 GCGAGGGAAGCAGAGGCGGCA
1 GCGAGGGAAGCAGAGGCAGCA
* **
1487047 ACGAGGGAAGCAGAGGCAATA
1 GCGAGGGAAGCAGAGGCAGCA
* * *
1487068 GCGAGAGAAGCAGACGCTGCA
1 GCGAGGGAAGCAGAGGCAGCA
1487089 GCGAGGGAAGCAG-GGCAG
1 GCGAGGGAAGCAGAGGCAG
1487107 AGCAAAAAGT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.33, C:0.19, G:0.46, T:0.02
Consensus pattern (21 bp):
GCGAGGGAAGCAGAGGCAGCA
Found at i:1487078 original size:42 final size:41
Alignment explanation
Indices: 1487026--1487105 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
1487016 AGAGGTGGCG
* *
1487026 GCGAGGGAAGCAGAGGCGGCAACGAGGGAAGCAGAGGCAATA
1 GCGAGAGAAGCAGACGCGGCAACGAGGGAAGCAG-GGCAATA
* *
1487068 GCGAGAGAAGCAGACGCTGCAGCGAGGGAAGCAGGGCA
1 GCGAGAGAAGCAGACGCGGCAACGAGGGAAGCAGGGCA
1487106 GAGCAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.34, C:0.19, G:0.45, T:0.03
Consensus pattern (41 bp):
GCGAGAGAAGCAGACGCGGCAACGAGGGAAGCAGGGCAATA
Found at i:1487513 original size:43 final size:43
Alignment explanation
Indices: 1487450--1487617 Score: 194
Period size: 43 Copynumber: 3.9 Consensus size: 43
1487440 TCATTACCTT
* * *** *
1487450 TAGCGGCATTTGTGGGAAAAGCGCTATTAAAGGTCATGATTTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATTTA
* * *
1487493 TAGCGGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATG-TTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATT-TA
* *
1487536 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATTTA
* * *
1487579 TAGCAGCGTTTGTGGAAAAAGAGCCGCTAAAGGTCATGA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGA
1487618 CCTTTAGAGG
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.02
43 102 0.97
44 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATTTA
Found at i:1487523 original size:86 final size:86
Alignment explanation
Indices: 1487411--1487632 Score: 257
Period size: 86 Copynumber: 2.6 Consensus size: 86
1487401 CAAAATTAGT
* * * * * *
1487411 GGCGTTTTTAAAAAAAACGCCACTAAAACTCATTACCTTTAGCGGCATTTGTGGGAAAAGCGCTA
1 GGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATTACCTTTAGCGGCATTTGTGGGAAAAGCGCCA
* * *
1487476 TTAAAGGTCATGATTTATAGC
66 CTAAAAGTCATGATCTATAGC
* *
1487497 GGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATGT-TCTTTAGCGGCGTTTGTGGGAAAAGCGCC
1 GGCGTTTATAGAAAAAGCGCCGCTAAAAGTCAT-TACCTTTAGCGGCATTTGTGGGAAAAGCGCC
*
1487561 GCTAAAAGTCATGATCTATAGC
65 ACTAAAAGTCATGATCTATAGC
* * * * * * *
1487583 AGCGTTTGTGGAAAAAGAGCCGCTAAAGGTCATGACCTTTAGAGGCATTT
1 GGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATTACCTTTAGCGGCATTT
1487633 ATTTTTAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
86 112 0.99
87 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (86 bp):
GGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATTACCTTTAGCGGCATTTGTGGGAAAAGCGCCA
CTAAAAGTCATGATCTATAGC
Found at i:1489510 original size:35 final size:35
Alignment explanation
Indices: 1489411--1489511 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 35
1489401 CTCTGTTTGA
* * *
1489411 TGTGTTTCGGAGGGATTAGCTCTTTTAAGCATTGG
1 TGTGTTTCGGAGGGATTAGCTCTTATGAGCAATGG
** *
1489446 TGTGTTTCGGTTGGACTAGCTCTTATGAGCAATGG
1 TGTGTTTCGGAGGGATTAGCTCTTATGAGCAATGG
* * * *
1489481 TGTGTTTTGGAGGGATTGGCTCATGTGAGCA
1 TGTGTTTCGGAGGGATTAGCTCTTATGAGCA
1489512 TCTAGTGTGT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.17, C:0.12, G:0.34, T:0.38
Consensus pattern (35 bp):
TGTGTTTCGGAGGGATTAGCTCTTATGAGCAATGG
Found at i:1505811 original size:44 final size:44
Alignment explanation
Indices: 1505740--1506302 Score: 793
Period size: 44 Copynumber: 12.8 Consensus size: 44
1505730 GATTAAGCCA
* * *
1505740 CAAGTCCTATCTCCCTGACCAGTAGCGGAATAGGTTGAAAATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * * * *
1505784 TATGTCCTATTTCCCAGACCAGCAGCGGAATAGGTGGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* *
1505828 CAAGTCCTATGTCCCTGACCAACAGTGGAATAGGTTGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * * *
1505872 TAGGTCTTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
1505916 CAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * *
1505960 TAGGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
1506004 CAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * *
1506048 TAGGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
1506092 CAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * *
1506136 TAGGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
1506180 CAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTG
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * * *
1506224 TAGGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
1506268 CAAGTCCTATCTCCCTGACCAACAGTGGAATAGGT
1 CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1506303 GGAAAATTAG
Statistics
Matches: 455, Mismatches: 64, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 455 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
CAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
Found at i:1505847 original size:88 final size:88
Alignment explanation
Indices: 1505739--1506302 Score: 1020
Period size: 88 Copynumber: 6.4 Consensus size: 88
1505729 AGATTAAGCC
** * * * * *
1505739 ACAAGTCCTATCTCCCTGACCAGTAGCGGAATAGGTTGAAAATTGTATGTCCTATTTCCCAGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
* *
1505804 AGCAGCGGAATAGGTGGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
* * *
1505827 GCAAGTCCTATGTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCTTATGTCCCTGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1505892 AGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
1505915 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1505980 AGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
1506003 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1506068 AGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
1506091 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1506156 AGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
1506179 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
1506244 AGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTTGAAGATT
1506267 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGT
1 ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGT
1506303 GGAAAATTAG
Statistics
Matches: 461, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 461 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (88 bp):
ACAAGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAGGTCCTATGTCCCTGACC
AGCAGTGGAATAGGTTGAAGATT
Found at i:1510969 original size:21 final size:21
Alignment explanation
Indices: 1510923--1510969 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1510913 AATCTAAGTT
**
1510923 TTTCCTATAAAAACCCAGGTA
1 TTTCCTATAAAAACCCAGACA
*
1510944 ATTCCTAT-AAAACCTCAGACA
1 TTTCCTATAAAAACC-CAGACA
1510965 TTTCC
1 TTTCC
1510970 CTCTTATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (21 bp):
TTTCCTATAAAAACCCAGACA
Found at i:1511002 original size:19 final size:19
Alignment explanation
Indices: 1510980--1511017 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1510970 CTCTTATTAA
1510980 GACAAACCTAAAATTAATT
1 GACAAACCTAAAATTAATT
1510999 GACAAACCTAAAATTAATT
1 GACAAACCTAAAATTAATT
1511018 CAGGGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (19 bp):
GACAAACCTAAAATTAATT
Found at i:1511099 original size:20 final size:20
Alignment explanation
Indices: 1511060--1511099 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1511050 ACATAAATTG
*
1511060 GTTTTTCTATAAAAATTCAA
1 GTTTTTCTATAAAAACTCAA
1511080 GTTTTTCGTAT-AAAACTCAA
1 GTTTTTC-TATAAAAACTCAA
1511100 CTAGTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (20 bp):
GTTTTTCTATAAAAACTCAA
Found at i:1512113 original size:9 final size:9
Alignment explanation
Indices: 1512099--1512129 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
1512089 CTCGACACAT
1512099 CAAAATAAA
1 CAAAATAAA
1512108 CAAAATAAA
1 CAAAATAAA
1512117 CAAAATAAA
1 CAAAATAAA
1512126 CAAA
1 CAAA
1512130 GGCCCGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (9 bp):
CAAAATAAA
Found at i:1518478 original size:19 final size:19
Alignment explanation
Indices: 1518429--1518477 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1518419 TTTCTTTTCA
1518429 CTTTCTTTTTTCAAGTTTT
1 CTTTCTTTTTTCAAGTTTT
* *
1518448 CTTTCTTTTTTCCATTTTT
1 CTTTCTTTTTTCAAGTTTT
1518467 CTTTTCTTTTT
1 C-TTTCTTTTT
1518478 CTCTCATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (19 bp):
CTTTCTTTTTTCAAGTTTT
Found at i:1520985 original size:23 final size:23
Alignment explanation
Indices: 1520952--1521018 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1520942 TTGGTTTGGG
* * *
1520952 TTTGGAACGAAATGCTAATGTAA
1 TTTGGTACGAAATGCAAATGGAA
* *
1520975 TTTGGTGCGAAATGGAAATGGAA
1 TTTGGTACGAAATGCAAATGGAA
*
1520998 TTTGGTACGAAATGGAAATGG
1 TTTGGTACGAAATGCAAATGG
1521019 TTCAAAAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (23 bp):
TTTGGTACGAAATGCAAATGGAA
Found at i:1521796 original size:31 final size:31
Alignment explanation
Indices: 1521761--1521826 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1521751 TCATGCATGC
** *
1521761 ACCTTGCTAAATGAATCTTCACATTCGGCTA
1 ACCTTGCTAAATGAATCCCCACATTCGGCCA
*
1521792 ACCTTGTTAAATGAATCCCCACATTCGGCCA
1 ACCTTGCTAAATGAATCCCCACATTCGGCCA
1521823 ACCT
1 ACCT
1521827 ACATAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.29
Consensus pattern (31 bp):
ACCTTGCTAAATGAATCCCCACATTCGGCCA
Found at i:1521834 original size:31 final size:31
Alignment explanation
Indices: 1521768--1521834 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
1521758 TGCACCTTGC
** * ***
1521768 TAAATGAATCTTCACATTCGGCTAACCTTGT
1 TAAATGAATCCCCACATTCGGCCAACCTACA
1521799 TAAATGAATCCCCACATTCGGCCAACCTACA
1 TAAATGAATCCCCACATTCGGCCAACCTACA
1521830 TAAAT
1 TAAAT
1521835 AGGATGAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (31 bp):
TAAATGAATCCCCACATTCGGCCAACCTACA
Found at i:1522159 original size:30 final size:30
Alignment explanation
Indices: 1522101--1522159 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1522091 TTGTAAATGT
*
1522101 TTGAGCTGAAATTGAACTAGTTCAAGCTCA
1 TTGAGCTGAAATTGAACTAATTCAAGCTCA
*
1522131 TTGAGCTGAAATTGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATTGAA-CTAATTCAAGCTC
1522160 GTAATAGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (30 bp):
TTGAGCTGAAATTGAACTAATTCAAGCTCA
Found at i:1522845 original size:18 final size:18
Alignment explanation
Indices: 1522822--1522863 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
1522812 CTCATAAATA
1522822 TGAAATAATGAAATATAC-
1 TGAAATAATGAAATA-ACT
1522840 TGAAATAATGAAATAACT
1 TGAAATAATGAAATAACT
1522858 TGAAAT
1 TGAAAT
1522864 TCAATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (18 bp):
TGAAATAATGAAATAACT
Found at i:1522863 original size:10 final size:8
Alignment explanation
Indices: 1522817--1522855 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
1522807 AACAACTCAT
1522817 AAAT-ATG
1 AAATAATG
1522824 AAATAATG
1 AAATAATG
1522832 AAATATACTG
1 AAATA-A-TG
1522842 AAATAATG
1 AAATAATG
1522850 AAATAA
1 AAATAA
1522856 CTTGAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.14
8 16 0.55
9 2 0.07
10 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (8 bp):
AAATAATG
Found at i:1525646 original size:17 final size:17
Alignment explanation
Indices: 1525624--1525660 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1525614 AATCAATATT
1525624 CACTAAGACGATTGTAC
1 CACTAAGACGATTGTAC
1525641 CACTAAGACGATTGTAC
1 CACTAAGACGATTGTAC
1525658 CAC
1 CAC
1525661 ATCTGTCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (17 bp):
CACTAAGACGATTGTAC
Found at i:1526219 original size:35 final size:35
Alignment explanation
Indices: 1526188--1526286 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 35
1526178 ACTTATTGAT
*
1526188 ATTCTGATTCACATGTTAAGCATGCTATTATTCTG
1 ATTCTGATTCACATGTTAAGCATGCCATTATTCTG
* **
1526223 ATTATGATTTGCATGTTAAGCATGCCATTATTCTG
1 ATTCTGATTCACATGTTAAGCATGCCATTATTCTG
* * *
1526258 ATTCTGATTCTCATGTTAAACATGTCATT
1 ATTCTGATTCACATGTTAAGCATGCCATT
1526287 GTGTTAAGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (35 bp):
ATTCTGATTCACATGTTAAGCATGCCATTATTCTG
Found at i:1528263 original size:21 final size:21
Alignment explanation
Indices: 1528234--1528282 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1528224 GCCCGTGTGG
*
1528234 CCCACACGGCCTAGCTCAAAA
1 CCCACACGGCCTAGCCCAAAA
* *
1528255 CCCATACGGCCTGGCCCAAAA
1 CCCACACGGCCTAGCCCAAAA
1528276 CCCACAC
1 CCCACAC
1528283 ACCCGTGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.47, G:0.14, T:0.08
Consensus pattern (21 bp):
CCCACACGGCCTAGCCCAAAA
Found at i:1528467 original size:29 final size:29
Alignment explanation
Indices: 1528425--1528483 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1528415 GGCCACATGC
1528425 CCTTGTGGTGCAGACAGACACACCTGGTA
1 CCTTGTGGTGCAGACAGACACACCTGGTA
1528454 CCTTGTGGTGCAGACAGACACACCTGGTA
1 CCTTGTGGTGCAGACAGACACACCTGGTA
1528483 C
1 C
1528484 AGTTTTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (29 bp):
CCTTGTGGTGCAGACAGACACACCTGGTA
Found at i:1530983 original size:9 final size:9
Alignment explanation
Indices: 1530969--1531002 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1530959 AAAATATAAA
1530969 CCAAAAAGT
1 CCAAAAAGT
1530978 CCAAAAAGT
1 CCAAAAAGT
* *
1530987 CCAGAGAGT
1 CCAAAAAGT
1530996 CCAAAAA
1 CCAAAAA
1531003 ATACAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.24, G:0.15, T:0.09
Consensus pattern (9 bp):
CCAAAAAGT
Found at i:1536750 original size:20 final size:20
Alignment explanation
Indices: 1536725--1536762 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536715 CATTTAAGTG
*
1536725 AATATCTATGAAGCTTAGTA
1 AATATCTATGAAACTTAGTA
*
1536745 AATATCTTTGAAACTTAG
1 AATATCTATGAAACTTAG
1536763 ATGAAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
AATATCTATGAAACTTAGTA
Found at i:1539049 original size:29 final size:29
Alignment explanation
Indices: 1539012--1539067 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1539002 TATATCAGCC
1539012 CATACA-TTTCACAATTTCTCATATTTAACA
1 CATACATTTTCA-AATTTCTCA-ATTTAACA
*
1539042 CATA-ATTTTCATATTTCTCAATTTAA
1 CATACATTTTCAAATTTCTCAATTTAA
1539068 TCCCTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.45
Consensus pattern (29 bp):
CATACATTTTCAAATTTCTCAATTTAACA
Found at i:1541312 original size:27 final size:28
Alignment explanation
Indices: 1541282--1541341 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1541272 GACATCAAAA
*
1541282 ATAGTCT-GACGAGACATTAAACACGGG
1 ATAGTCTCAACGAGACATTAAACACGGG
*
1541309 ATAG-CTCAATGAGACATTAAACACGGG
1 ATAGTCTCAACGAGACATTAAACACGGG
*
1541336 GTAGTC
1 ATAGTC
1541342 CTAAAGGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 25 0.89
28 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (28 bp):
ATAGTCTCAACGAGACATTAAACACGGG
Found at i:1541383 original size:27 final size:27
Alignment explanation
Indices: 1541326--1541383 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1541316 AATGAGACAT
* * *
1541326 TAAACACGGGGTAGTCCTAAAGGATGT
1 TAAACACGAGGTAGTCCTAAAGGACGA
*
1541353 TAAACACGAGGTAGT-CTGATAGGACGA
1 TAAACACGAGGTAGTCCT-AAAGGACGA
1541380 TAAA
1 TAAA
1541384 TACAAGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (27 bp):
TAAACACGAGGTAGTCCTAAAGGACGA
Found at i:1544563 original size:23 final size:23
Alignment explanation
Indices: 1544519--1544568 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1544509 AGATAGATTG
* *
1544519 TAGTAACAACAAAGATAAGAGAA
1 TAGTAACAAAAAAAATAAGAGAA
*
1544542 TAGTAAGAAAAAAAATATGAGAGAA
1 TAGTAACAAAAAAAATA--AGAGAA
1544567 TA
1 TA
1544569 TAAGACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (23 bp):
TAGTAACAAAAAAAATAAGAGAA
Found at i:1548141 original size:36 final size:35
Alignment explanation
Indices: 1548088--1548156 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
1548078 TTCTTTTTTT
1548088 TGGGGGGGGGGGAGAGTAAACTCGTGACCCAGGGG
1 TGGGGGGGGGGGAGAGTAAACTCGTGACCCAGGGG
* *
1548123 TGGGGGGGCGGGGGGAGTAAACTCGTGACTCAGG
1 TGGGGGGG-GGGGAGAGTAAACTCGTGACCCAGG
1548157 TGACTGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.19, C:0.14, G:0.54, T:0.13
Consensus pattern (35 bp):
TGGGGGGGGGGGAGAGTAAACTCGTGACCCAGGGG
Found at i:1553785 original size:21 final size:20
Alignment explanation
Indices: 1553759--1553813 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
1553749 TTTTACACTA
1553759 TTGTGGATAAACCACTCATCG
1 TTGTGGATAAACCACTC-TCG
**
1553780 TTGTGGACGAACCA--CTCG
1 TTGTGGATAAACCACTCTCG
1553798 TTGTGGATAAACCACT
1 TTGTGGATAAACCACT
1553814 AGTAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 15 0.54
19 1 0.04
21 12 0.43
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
TTGTGGATAAACCACTCTCG
Found at i:1553972 original size:21 final size:22
Alignment explanation
Indices: 1553929--1553973 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1553919 GCTAGTACGA
*
1553929 TGTGGTTAAACCACTCAAACGG
1 TGTGGATAAACCACTCAAACGG
1553951 TGTGGATAAACCACTC-AACGG
1 TGTGGATAAACCACTCAAACGG
1553972 TG
1 TG
1553974 CAAATAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (22 bp):
TGTGGATAAACCACTCAAACGG
Found at i:1553980 original size:21 final size:22
Alignment explanation
Indices: 1553935--1553982 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1553925 ACGATGTGGT
***
1553935 TAAACCACTCAAACGGTGTGGA
1 TAAACCACTCAAACGGTGCAAA
1553957 TAAACCACTC-AACGGTGCAAA
1 TAAACCACTCAAACGGTGCAAA
1553978 TAAAC
1 TAAAC
1553983 TGCTCAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (22 bp):
TAAACCACTCAAACGGTGCAAA
Found at i:1554129 original size:34 final size:34
Alignment explanation
Indices: 1554091--1554155 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1554081 CCCTATGGAA
* *
1554091 GCAATCATTATGCTTATAATAGTTTGATTCAGTG
1 GCAATCATTATGCTTATAATAGATTCATTCAGTG
*
1554125 GCAATTATTATGCTTATAATAGATTCATTCA
1 GCAATCATTATGCTTATAATAGATTCATTCA
1554156 ATAACAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (34 bp):
GCAATCATTATGCTTATAATAGATTCATTCAGTG
Found at i:1555511 original size:19 final size:21
Alignment explanation
Indices: 1555473--1555511 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1555463 ATTATATATT
*
1555473 AAATATATATTATTTTTAATC
1 AAATATATATTATTTGTAATC
1555494 AAATATATA-TA-TTGTAAT
1 AAATATATATTATTTGTAAT
1555512 ATGCCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
AAATATATATTATTTGTAATC
Found at i:1555829 original size:34 final size:34
Alignment explanation
Indices: 1555784--1555850 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1555774 ATGGCCCAAC
1555784 GCCGCCAAACACAACCAGAAACCCTAGCATCATT
1 GCCGCCAAACACAACCAGAAACCCTAGCATCATT
*
1555818 GCCGCCCAACACAACCAGAAACCCTAGCATCAT
1 GCCGCCAAACACAACCAGAAACCCTAGCATCAT
1555851 AGTCCCAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.40, G:0.12, T:0.10
Consensus pattern (34 bp):
GCCGCCAAACACAACCAGAAACCCTAGCATCATT
Found at i:1556379 original size:12 final size:12
Alignment explanation
Indices: 1556362--1556387 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1556352 GTTTTGCTAT
1556362 TAAGCATATATA
1 TAAGCATATATA
1556374 TAAGCATATATA
1 TAAGCATATATA
1556386 TA
1 TA
1556388 TAATAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (12 bp):
TAAGCATATATA
Found at i:1561058 original size:6 final size:6
Alignment explanation
Indices: 1561049--1561144 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
1561039 GAAAAAGAAA
* * * *
1561049 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAATGAA AAAATC AAAAT-
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT--C AAAATC AAAATC
* * * * *
1561098 AAAA-- AAAATAA AAAATAA AAAATA AAAATC AAGATC AAAATG AAAAT
1 AAAATC AAAAT-C AAAAT-C AAAATC AAAATC AAAATC AAAATC AAAAT
1561145 AAGAAAAAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
4 4 0.05
5 4 0.05
6 51 0.67
7 12 0.16
8 5 0.07
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:1561096 original size:7 final size:7
Alignment explanation
Indices: 1561079--1561125 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
1561069 AATGAAAATG
1561079 AAAATGAA
1 AAAAT-AA
1561087 AAAATCAA
1 AAAAT-AA
1561095 AATAA-AA
1 AA-AATAA
1561102 AAAATAA
1 AAAATAA
1561109 AAAATAA
1 AAAATAA
1561116 AAAATAA
1 AAAATAA
1561123 AAA
1 AAA
1561126 TCAAGATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
6 2 0.06
7 23 0.64
8 9 0.25
9 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:1561101 original size:12 final size:12
Alignment explanation
Indices: 1561048--1561146 Score: 69
Period size: 12 Copynumber: 8.2 Consensus size: 12
1561038 AGAAAAAGAA
1561048 AAAAATCAAAAT
1 AAAAATCAAAAT
* *
1561060 CAAAGTCAAAAT
1 AAAAATCAAAAT
* *
1561072 GAAAATGAAAAT
1 AAAAATCAAAAT
1561084 GAAAAAATCAAAAT
1 --AAAAATCAAAAT
1561098 -AAAA--AAAAT
1 AAAAATCAAAAT
*
1561107 AAAAAATAAAAAAT
1 -AAAAAT-CAAAAT
*
1561121 AAAAATCAAGAT
1 AAAAATCAAAAT
* *
1561133 CAAAATGAAAAT
1 AAAAATCAAAAT
1561145 AA
1 AA
1561147 GAAAAAGAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
9 5 0.07
11 8 0.12
12 33 0.49
13 6 0.09
14 15 0.22
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:1561182 original size:44 final size:43
Alignment explanation
Indices: 1561109--1561212 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
1561099 AAAAAAATAA
* * *
1561109 AAAATAAAAAATAAAAATCAAGATCAAAATGAAAATAAGAAAAAG
1 AAAAGAAAAAAGAAAAATCAAGATCAAAATCAAAAT--GAAAAAG
* * * *
1561154 -AAAGAAAAAAGAGAAATCTAGATGAAAATCAGAATGAAAAAG
1 AAAAGAAAAAAGAAAAATCAAGATCAAAATCAAAATGAAAAAG
1561196 AAAAAGAAAAAAGAAAA
1 -AAAAGAAAAAAGAAAA
1561213 GGAGAGGCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 7 0.14
44 42 0.86
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (43 bp):
AAAAGAAAAAAGAAAAATCAAGATCAAAATCAAAATGAAAAAG
Found at i:1563360 original size:43 final size:43
Alignment explanation
Indices: 1563283--1563411 Score: 206
Period size: 43 Copynumber: 3.0 Consensus size: 43
1563273 TCAGTGAATA
* *
1563283 CGGCGGATCTTATCTT-CCCAGGAGTGGGGAAACAGATCTAAG
1 CGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG
1563325 CGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG
1 CGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG
* * *
1563368 CGGTGAATCTTATTTTCCCCAGGAGTAGGGAAACAGATTTAAG
1 CGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG
1563411 C
1 C
1563412 CACAAGTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 15 0.19
43 66 0.81
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (43 bp):
CGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG
Found at i:1563685 original size:44 final size:43
Alignment explanation
Indices: 1563592--1563696 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 43
1563582 GAAGCAAATA
* * *
1563592 TTATCTCCCTGAAGTTACTGTGGAGCAGATTGAAGCCGATAATC
1 TTATCTCCCTGAAGTT-GTGTGGAGCAGATTAAAGCCAATAATC
* * *
1563636 CTATCTCCCTCAAGTTGTAGTGGAGCAGATTAAAG-TAATAGATC
1 TTATCTCCCTGAAGTTGT-GTGGAGCAGATTAAAGCCAATA-ATC
*
1563680 TTATCTCTCTGAAGTTG
1 TTATCTCCCTGAAGTTG
1563697 CAGTAGAGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGTGTGGAGCAGATTAAAGCCAATAATC
Found at i:1566542 original size:11 final size:11
Alignment explanation
Indices: 1566525--1566563 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
1566515 TTTTTAATCA
1566525 AATATATATTT
1 AATATATATTT
*
1566536 TATATATATTT
1 AATATATATTT
1566547 AATATATATTT
1 AATATATATTT
1566558 AATATA
1 AATATA
1566564 GGCCAGGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATATATATTT
Found at i:1567940 original size:21 final size:20
Alignment explanation
Indices: 1567904--1567970 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1567894 TCTCTCTCAA
*
1567904 AAAATATTATAAAAAAAATTC
1 AAAATATT-TATAAAAAATTC
**
1567925 AAAATAACTTT-TAAAATTTTC
1 AAAAT-A-TTTATAAAAAATTC
*
1567946 AAAATATTTATAAAAAAATC
1 AAAATATTTATAAAAAATTC
1567966 AAAAT
1 AAAAT
1567971 TTAAATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.08
20 13 0.35
21 17 0.46
22 2 0.05
23 2 0.05
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATATTTATAAAAAATTC
Found at i:1582642 original size:20 final size:20
Alignment explanation
Indices: 1582617--1582682 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1582607 ATAAATGAGT
1582617 AAATTTCTAGAATTTCAGCA
1 AAATTTCTAGAATTTCAGCA
*
1582637 AAATTTCTAGAATTTCAACA
1 AAATTTCTAGAATTTCAGCA
* *
1582657 TAATTTCTAAAATTTCAGCA
1 AAATTTCTAGAATTTCAGCA
*
1582677 TAATTT
1 AAATTT
1582683 TTCAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATTTCTAGAATTTCAGCA
Found at i:1590231 original size:86 final size:85
Alignment explanation
Indices: 1590070--1590233 Score: 247
Period size: 86 Copynumber: 1.9 Consensus size: 85
1590060 TTGCAATTTT
* * * *
1590070 TGCCACTTGTTGTGGGTACACAACATATTTGCAGATTAAACAAACTACCACTTGGTTCATGATCG
1 TGCCACTTGTTGTGAGTACACAACATATTTGCAGATTAAACAAACTACCACTTGATTCATAATCA
*
1590135 AACCATATATTTGCAGTTAC
66 AACCACATATTTGCAGTTAC
* * *
1590155 TGCCACTTGTTGTGAGTGCACAATATATTTGACGGATTAAACAAACTACCACTTGATTCATAATC
1 TGCCACTTGTTGTGAGTACACAACATATTTG-CAGATTAAACAAACTACCACTTGATTCATAATC
1590220 AAACCACATATTTG
65 AAACCACATATTTG
1590234 TGGATTAAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 28 0.40
86 42 0.60
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (85 bp):
TGCCACTTGTTGTGAGTACACAACATATTTGCAGATTAAACAAACTACCACTTGATTCATAATCA
AACCACATATTTGCAGTTAC
Found at i:1591842 original size:22 final size:22
Alignment explanation
Indices: 1591817--1591858 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1591807 TATTTATAGG
1591817 TGAGTATAAAGCTAAAGGATAT
1 TGAGTATAAAGCTAAAGGATAT
1591839 TGAGTATAAAGCTAAAGGAT
1 TGAGTATAAAGCTAAAGGAT
1591859 GACTCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (22 bp):
TGAGTATAAAGCTAAAGGATAT
Found at i:1595560 original size:41 final size:39
Alignment explanation
Indices: 1595477--1595560 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
1595467 GCACAATATA
* ***
1595477 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAAAAAT
*
1595516 ATATAAAAAGCATATATAAATATATGTATGTCACAAAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAAAAA-T
1595557 ATAT
1 ATAT
1595561 TCATTTATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 30 0.79
40 3 0.08
41 5 0.13
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAAAAAT
Found at i:1597680 original size:22 final size:22
Alignment explanation
Indices: 1597632--1597699 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
1597622 TCTTTCATAT
*
1597632 AAATTTTAAATAAATAATTATT
1 AAATTTTAAATAAATAATTATA
* *
1597654 AAATTTTAAGT-AATATTTATA
1 AAATTTTAAATAAATAATTATA
*
1597675 AGAA--TTAGAT-AA-AATTATA
1 A-AATTTTAAATAAATAATTATA
1597694 AAATTT
1 AAATTT
1597700 AGTTTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 2 0.05
19 7 0.19
20 7 0.19
21 9 0.24
22 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATTTTAAATAAATAATTATA
Found at i:1597716 original size:18 final size:19
Alignment explanation
Indices: 1597697--1597741 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1597687 AATTATAAAA
1597697 TTTAGTTTTT-TATTTCAAT
1 TTTA-TTTTTGTATTTCAAT
* *
1597716 TTTATTTTTGTATTTTATT
1 TTTATTTTTGTATTTCAAT
1597735 TTTATTT
1 TTTATTT
1597742 CTTATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTATTTTTGTATTTCAAT
Found at i:1597892 original size:14 final size:15
Alignment explanation
Indices: 1597873--1597905 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1597863 CTTAAACCAG
1597873 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
1597887 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1597902 AATC
1 AATC
1597906 TATACGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:1598532 original size:122 final size:123
Alignment explanation
Indices: 1598303--1598582 Score: 348
Period size: 122 Copynumber: 2.3 Consensus size: 123
1598293 AAATGTTTTT
* * * * * **
1598303 GCGGCGCTTTTTCAGAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCTTTTTTAAAAAAGCCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCACCTTTACAAAAAAGCCGC
* * * * * * *
1598368 TAAATCCCCTAGCAGTAGCGGCGCTTTTTCAAAAACGTCGCTAAATCCCTGAGCATTA
66 TAAAGCCCCGAGCAGTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
1598426 GCGGTGCTTTTTCAAAAACGCCGCTAAAGCCCCG-GCATTAGCGGCACCTTTACAAAAACGCCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCACCTTTACAAAAAAGCCGC
* * *
1598490 TAAAGCCTCGAGCATTAGCGACGC-TTTCCAAAAAATGCCGCTAAAGCCCCGAGCATTA
66 TAAAGCCCCGAGCAGTAGCGACGCTTTTCC-AAAAACGCCGCTAAAGCCCCGAGCATTA
* *
1598548 GGGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGA
1598583 AAGGTAAAAA
Statistics
Matches: 133, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
121 4 0.03
122 99 0.74
123 30 0.23
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (123 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCACCTTTACAAAAAAGCCGC
TAAAGCCCCGAGCAGTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:1598576 original size:41 final size:41
Alignment explanation
Indices: 1598303--1598582 Score: 348
Period size: 41 Copynumber: 6.9 Consensus size: 41
1598293 AAATGTTTTT
* * *
1598303 GCGGCGCTTTTTCAGAAACGCCGCTAAATCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * * *
1598344 GCGGCGCTTTTTTAAAAAAGCCGCTAAATCCCCTAGCAGTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * *
1598385 GCGGCGCTTTTTCAAAAACGTCGCTAAATCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
*
1598426 GCGGTGCTTTTTCAAAAACGCCGCTAAAGCCCCG-GCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
1598466 GCGGCACCTTTACAAAAACGCCGCTAAAGCCTCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * *
1598507 GCGACGC-TTTCCAAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTC-AAAAACGCCGCTAAAGCCCCGAGCATTA
* *
1598548 GGGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGA
1598583 AAGGTAAAAA
Statistics
Matches: 207, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
40 39 0.19
41 163 0.79
42 5 0.02
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:1598701 original size:40 final size:40
Alignment explanation
Indices: 1598626--1598701 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
1598616 TTTTTAGAGG
* *
1598626 AAAGCGCCGCTAATGCTCGATCTTTAGCTGCGTTTTACGT
1 AAAGCGCCACTAATGCTCGATCTTTAGCGGCGTTTTACGT
* * *
1598666 AAAGTGCCACTAATGCTCGATTTTTAGCGGTGTTTT
1 AAAGCGCCACTAATGCTCGATCTTTAGCGGCGTTTT
1598702 TTGTCTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (40 bp):
AAAGCGCCACTAATGCTCGATCTTTAGCGGCGTTTTACGT
Found at i:1599876 original size:7 final size:8
Alignment explanation
Indices: 1599831--1599881 Score: 66
Period size: 8 Copynumber: 6.0 Consensus size: 8
1599821 GATATTATAA
1599831 AAAATTAT
1 AAAATTAT
1599839 AAAATTAT
1 AAAATTAT
*
1599847 AAAACTAT
1 AAAATTAT
1599855 AAACATTATT
1 AAA-ATTA-T
1599865 AAAATTAT
1 AAAATTAT
1599873 AAATATTAT
1 AAA-ATTAT
1599882 TAATTGATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
8 22 0.58
9 12 0.32
10 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:1599882 original size:18 final size:18
Alignment explanation
Indices: 1599808--1599884 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
1599798 TTTTAAAGCC
1599808 TAAACATTATTAAGATATTAT
1 TAAA-ATTA-TAA-ATATTAT
*
1599829 AAAAAATTATAAA-ATTA-
1 -TAAAATTATAAATATTAT
* *
1599846 TAAAACTATAAACATTAT
1 TAAAATTATAAATATTAT
1599864 TAAAATTATAAATATTAT
1 TAAAATTATAAATATTAT
1599882 TAA
1 TAA
1599885 TTGATTATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 10 0.21
17 4 0.08
18 23 0.48
19 1 0.02
20 3 0.06
21 4 0.08
22 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (18 bp):
TAAAATTATAAATATTAT
Found at i:1599972 original size:22 final size:21
Alignment explanation
Indices: 1599924--1599993 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
1599914 TAAATGTTAG
*
1599924 AAAAATTT-TAGAAATTATATAA
1 AAAAATTTATA-AAATT-TATTA
*
1599946 AAAAATGTTATAAAATTTATTTT
1 AAAAAT-TTATAAAATTTA-TTA
*
1599969 AAAAATTTATAAATTTTATTA
1 AAAAATTTATAAAATTTATTA
1599990 AAAA
1 AAAA
1599994 TATTAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 6 0.15
22 19 0.46
23 14 0.34
24 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAAATTTATAAAATTTATTA
Found at i:1599984 original size:21 final size:21
Alignment explanation
Indices: 1599946--1600010 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1599936 AATTATATAA
* *
1599946 AAAAATGTTATAAAATTTATTTT
1 AAAAATATTAT-AAATTT-TATT
1599969 AAAAAT-TTATAAATTTTATT
1 AAAAATATTATAAATTTTATT
*
1599989 AAAAATATTAAAAATTGTTATT
1 AAAAATATTATAAATT-TTATT
1600011 TTGAAGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 9 0.24
21 14 0.37
22 9 0.24
23 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
AAAAATATTATAAATTTTATT
Found at i:1603537 original size:44 final size:44
Alignment explanation
Indices: 1603488--1603592 Score: 192
Period size: 44 Copynumber: 2.4 Consensus size: 44
1603478 AAGACTTATA
1603488 TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTGCTT
*
1603532 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTGCTT
*
1603576 TCTTCGATCTACTCCAC
1 TCTTTGATCTACTCCAC
1603593 CACCAGTATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTGCTT
Found at i:1603853 original size:44 final size:44
Alignment explanation
Indices: 1603792--1603940 Score: 163
Period size: 44 Copynumber: 3.4 Consensus size: 44
1603782 AAGACAGAAC
* *
1603792 CTACTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGAT
1 CTACTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
* * * * *** *
1603836 CTATTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGAT
1 CTACTTTCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGAT
* * **
1603881 TTGCTACCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
1 CTACTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
1603925 CTACTTTCTTTGATCT
1 CTACTTTCTTTGATCT
1603941 GCTTTGCCAC
Statistics
Matches: 78, Mismatches: 26, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
44 47 0.60
45 31 0.40
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (44 bp):
CTACTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
Found at i:1603918 original size:133 final size:132
Alignment explanation
Indices: 1603493--1603940 Score: 332
Period size: 133 Copynumber: 3.4 Consensus size: 132
1603483 TTATATCTTT
* * * *
1603493 GATCTACTCCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACA
1 GATCTACTCCACGCCAGTACAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACA
* * * * **
1603558 TGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGATAGAATTACTGGCT
66 TGAAGACAAGATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGGAGAAAGATTTGCTACCT
1603623 TC
131 TC
* * * * * * ** * * * * ** *
1603625 AATATACTCCACTGCAACTTCAGGGAGGTAAAATCC-ACCATCTTTGATCTGCTCCACTACTGCT
1 GATCTACTCCAC-GCCAGTACAGGAAGACAAGA-CCTACTATCTTTGATCTACTTCACGCCAG-T
* * * * ** * * * * *
1603689 -TAGGGAGGCAAGATCTGTAATCTTCAATCTACTTCGCCACCAGTATGGGAAGATAAGATATG-T
63 ACATGAAGACAAGATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGGAGA-AAGATTTGCT
**
1603752 ATATTC
127 ACCTTC
* * * *
1603758 GATCCACTTTGCTAC-CGA-TATAGGAAGAC-AGAACCTACTATCTTTGATCTACTTCACGCCAG
1 GATCTAC--T-CCACGCCAGTACAGGAAGACAAG-ACCTACTATCTTTGATCTACTTCACGCCAG
* *
1603820 TACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATTTGC
62 TACATGAAGACAAGATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGGAGA-AAGATTTGC
*
1603885 TACCTTT
126 TACCTTC
* * * *
1603892 GATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCT
1 GATCTACTCCACGCCAGTACAGGAAGACAAGACCTACTATCTTTGATCT
1603941 GCTTTGCCAC
Statistics
Matches: 223, Mismatches: 79, Indels: 27
0.68 0.24 0.08
Matches are distributed among these distances:
131 2 0.01
132 17 0.08
133 180 0.81
134 20 0.09
135 1 0.00
136 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (132 bp):
GATCTACTCCACGCCAGTACAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACA
TGAAGACAAGATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGGAGAAAGATTTGCTACCT
TC
Found at i:1603951 original size:89 final size:89
Alignment explanation
Indices: 1603799--1603974 Score: 262
Period size: 89 Copynumber: 2.0 Consensus size: 89
1603789 AACCTACTAT
* *
1603799 CTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCA
* *
1603864 GTATGGGGAGACAAGATTTGCTAC
66 GTATGGGAAGACAAGATCTGCTAC
* * *** *
1603888 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTTGCCACCG
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCA
1603953 GTATGGGAAGACAAGATCTGCT
66 GTATGGGAAGACAAGATCTGCT
1603975 GCTTTTCAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (89 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCA
GTATGGGAAGACAAGATCTGCTAC
Found at i:1608510 original size:67 final size:67
Alignment explanation
Indices: 1608434--1608568 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
1608424 ATTCAAAATA
* *
1608434 ACCGCTCTTATGGAAAGAAAGATTTGCTCCAAAAATGACTGCAAACATGAATTTTATTAAAATAA
1 ACCGCTCTTATGGAAAGAAAGATTTGCTCCAAAAATGACTACAAACATGAACTTTATTAAAATAA
1608499 CG
66 CG
* *
1608501 ACCGCTCTTATGGAAAGAAATATTTGTTCCAAAAATGACTACAAACATGAACTTTATTAAAATAA
1 ACCGCTCTTATGGAAAGAAAGATTTGCTCCAAAAATGACTACAAACATGAACTTTATTAAAATAA
1608566 CG
66 CG
1608568 A
1 A
1608569 ATTTTTGGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (67 bp):
ACCGCTCTTATGGAAAGAAAGATTTGCTCCAAAAATGACTACAAACATGAACTTTATTAAAATAA
CG
Found at i:1609366 original size:51 final size:51
Alignment explanation
Indices: 1609290--1609387 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
1609280 ACCAGCTTCA
1609290 GTTTTTGATGTAACGATGACGGTACCGCACCTGCTGAACGAATCCATAGAC
1 GTTTTTGATGTAACGATGACGGTACCGCACCTGCTGAACGAATCCATAGAC
*
1609341 GTTTTTGATGTAACGATGACGGTACCGTACCTGCTGAACGAATCCAT
1 GTTTTTGATGTAACGATGACGGTACCGCACCTGCTGAACGAATCCAT
1609388 GGCCTTCCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (51 bp):
GTTTTTGATGTAACGATGACGGTACCGCACCTGCTGAACGAATCCATAGAC
Found at i:1612186 original size:20 final size:20
Alignment explanation
Indices: 1612161--1612200 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1612151 TAAAGGTCTT
1612161 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
1612181 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
1612201 ATGAGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:1616653 original size:20 final size:18
Alignment explanation
Indices: 1616609--1616692 Score: 55
Period size: 20 Copynumber: 4.4 Consensus size: 18
1616599 TAATTATTTG
* *
1616609 TAAAATTTAATTTCAATA
1 TAAAATTAAATTTAAATA
1616627 TATAAATTAAATATTAAATA
1 TA-AAATTAAAT-TTAAATA
1616647 TTAAAATT--ATTTAAAATA
1 -TAAAATTAAATTT-AAATA
*
1616665 TAACCATTACAAATTTAAATA
1 TAA-AATT--AAATTTAAATA
*
1616686 TATAATT
1 TAAAATT
1616693 TTATATATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
17 5 0.10
18 12 0.23
19 8 0.15
20 14 0.27
21 9 0.17
22 4 0.08
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTAAATTTAAATA
Found at i:1617021 original size:41 final size:41
Alignment explanation
Indices: 1616929--1617039 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
1616919 CGTTTGGACA
* *
1616929 AAAAACGCCGCAAAATA-TCTAACAGTAGCAGCGTTTTTCTC
1 AAAAACGCCGCAAAA-AGTCTAACAGTAGCAGCGTTTATCAC
* * * * *
1616970 ATAAATGCCGCAAAAAGTCTAACAGTAGCGGCGTTTATGAG
1 AAAAACGCCGCAAAAAGTCTAACAGTAGCAGCGTTTATCAC
* *
1617011 AAAAACGCCGCAAAAAGTCAAACATTAGC
1 AAAAACGCCGCAAAAAGTCTAACAGTAGC
1617040 TCCTTGTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.02
41 57 0.98
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCAAAAAGTCTAACAGTAGCAGCGTTTATCAC
Found at i:1622718 original size:40 final size:40
Alignment explanation
Indices: 1622646--1622896 Score: 319
Period size: 40 Copynumber: 6.3 Consensus size: 40
1622636 ATTTGAATGA
* *
1622646 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
1622686 TATCTGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
1622726 TATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
1622766 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * *
1622806 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * * * * *
1622846 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
1622886 TATCC-GGCTAA
1 TATCCGGGCTAA
1622897 ATTCCGAAGA
Statistics
Matches: 192, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
39 7 0.04
40 182 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:1626209 original size:43 final size:43
Alignment explanation
Indices: 1626148--1626307 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 43
1626138 CCTTGGTCGA
*
1626148 GGAAAGCGCCGCTAAAGGTCATGTTTTATAGTGGCGTTTATGG
1 GGAAAGCACCGCTAAAGGTCATGTTTTATAGTGGCGTTTATGG
* * *
1626191 GGAAAGCACCGTTAAAGGTCATGTTCTT-TAGCGGCGTTTGTGG
1 GGAAAGCACCGCTAAAGGTCATGTT-TTATAGTGGCGTTTATGG
* * *** *
1626234 GAAAAGCGCCGCTAAAGGTCATGTTTTATAGTGATATTTTTGTG
1 GGAAAGCACCGCTAAAGGTCATGTTTTATAGTGGCGTTTATG-G
* *
1626278 AGAAA-CACCGCTAAAGGTCATGTTCTATAG
1 GGAAAGCACCGCTAAAGGTCATGTTTTATAG
1626308 CGGCATTTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.02
43 90 0.92
44 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (43 bp):
GGAAAGCACCGCTAAAGGTCATGTTTTATAGTGGCGTTTATGG
Found at i:1626295 original size:86 final size:86
Alignment explanation
Indices: 1626150--1626311 Score: 245
Period size: 86 Copynumber: 1.9 Consensus size: 86
1626140 TTGGTCGAGG
* * * *
1626150 AAAGCGCCGCTAAAGGTCATGTTTTATAGTGGCGTTTATGGGGAAAGCACCGTTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTTTTATAGTGACATTTATGGAGAAAGCACCGCTAAAGGTCATGT
*
1626215 TCTTTAGCGGCGTTTGTGGGA
66 TCTATAGCGGCGTTTGTGGGA
* *
1626236 AAAGCGCCGCTAAAGGTCATGTTTTATAGTGATATTTTTGTGAGAAA-CACCGCTAAAGGTCATG
1 AAAGCGCCGCTAAAGGTCATGTTTTATAGTGACATTTATG-GAGAAAGCACCGCTAAAGGTCATG
1626300 TTCTATAGCGGC
65 TTCTATAGCGGC
1626312 ATTTTTCCAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 63 0.93
87 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGGTCATGTTTTATAGTGACATTTATGGAGAAAGCACCGCTAAAGGTCATGT
TCTATAGCGGCGTTTGTGGGA
Found at i:1630350 original size:31 final size:31
Alignment explanation
Indices: 1630313--1630381 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1630303 AAAAAAGAAA
*
1630313 TCATTTTAGGCACTGTGGTAAAAAACTATTT
1 TCATTTTACGCACTGTGGTAAAAAACTATTT
* * * * *
1630344 TCATTTTACGTATTGTTGTTAAAAATTATTT
1 TCATTTTACGCACTGTGGTAAAAAACTATTT
1630375 TCATTTT
1 TCATTTT
1630382 GATCACCCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (31 bp):
TCATTTTACGCACTGTGGTAAAAAACTATTT
Found at i:1631039 original size:19 final size:20
Alignment explanation
Indices: 1631017--1631057 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1631007 AAAAAAAACT
*
1631017 AAAATTAATTCAAAA-ATAA
1 AAAATAAATTCAAAAGATAA
1631036 AAAATAAATTCAAAAGATAA
1 AAAATAAATTCAAAAGATAA
1631056 AA
1 AA
1631058 TAAGTGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAATTCAAAAGATAA
Found at i:1631058 original size:18 final size:17
Alignment explanation
Indices: 1631010--1631060 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
1631000 TTTTACTAAA
*
1631010 AAAAACTAAAATTAATTC
1 AAAAA-TAAAATAAATTC
1631028 AAAAATAAAAAATAAATTC
1 AAAAAT--AAAATAAATTC
1631047 AAAAGATAAAATAA
1 AAAA-ATAAAATAA
1631061 GTGACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 14 0.48
20 2 0.07
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAATAAAATAAATTC
Found at i:1633483 original size:19 final size:18
Alignment explanation
Indices: 1633450--1633497 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1633440 AGTTGAGAGA
**
1633450 TGAGAGAATGATGAACGAG
1 TGAG-GAATGATGAAAAAG
1633469 TGAGGAATGATTGAAAAAG
1 TGAGGAATGA-TGAAAAAG
*
1633488 TGAGAAATGA
1 TGAGGAATGA
1633498 ACTCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (18 bp):
TGAGGAATGATGAAAAAG
Found at i:1651461 original size:44 final size:43
Alignment explanation
Indices: 1651351--1651466 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
1651341 AGCTTGTACA
* * * *
1651351 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAAACATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAACATCG
* *
1651394 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGT-AATC-AAACATCG
**
1651438 ATGCCAATGTCTTAGACGTGGTCTT-CACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
1651467 ATAACTCATA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
43 30 0.50
44 28 0.47
45 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAACATCG
Found at i:1655993 original size:41 final size:41
Alignment explanation
Indices: 1655933--1656042 Score: 211
Period size: 41 Copynumber: 2.7 Consensus size: 41
1655923 NNNNNNNNNN
*
1655933 TTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGA
1 TTCAGATCACCGGCTCTTAGCCTGCTAGGTTTATAACCTGA
1655974 TTCAGATCACCGGCTCTTAGCCTGCTAGGTTTATAACCTGA
1 TTCAGATCACCGGCTCTTAGCCTGCTAGGTTTATAACCTGA
1656015 TTCAGATCACCGGCTCTTAGCCTGCTAG
1 TTCAGATCACCGGCTCTTAGCCTGCTAG
1656043 ACTTAAAGTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCAGATCACCGGCTCTTAGCCTGCTAGGTTTATAACCTGA
Found at i:1661954 original size:82 final size:83
Alignment explanation
Indices: 1661854--1662093 Score: 346
Period size: 82 Copynumber: 2.9 Consensus size: 83
1661844 TTTAACATAT
*
1661854 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTA-ATCACCGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAGTTCACCGGCACTTAGCCTGCTAGG
1661918 TTTATAACCTGATTCAGA
66 TTTATAACCTGATTCAGA
* *
1661936 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTC-AGTTCACCGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAGTTCACCGGCACTTAGCCTGCTAGG
1662000 TTTATAACCTGATTCAGA
66 TTTATAACCTGATTCAGA
* * * * * *
1662018 TCACCGGCTCTTAGCCTGCTAGACTTAAAGTCTGAAT-TATTTCACCGGC-CTTAAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAGTTCACCGGCACTT-AGCCTGCTAG
1662081 GTTT-TAAACCTGA
65 GTTTAT-AACCTGA
1662094 AAATTTCAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
81 5 0.03
82 138 0.97
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (83 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAGTTCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAGA
Found at i:1662066 original size:41 final size:41
Alignment explanation
Indices: 1661854--1662039 Score: 320
Period size: 41 Copynumber: 4.5 Consensus size: 41
1661844 TTTAACATAT
* *
1661854 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTC-AGA
1661895 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
1661936 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1661977 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
1662018 TCACCGGCTCTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
1662040 ACTTAAAGTC
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
40 1 0.01
41 138 0.99
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:1662075 original size:123 final size:123
Alignment explanation
Indices: 1661853--1662093 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 123
1661843 ATTTAACATA
* *
1661853 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCTAATCACCGGCACTTAGCCTGCTAGA
*
1661918 TTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGG-TTTATAACCTGATTCAG
66 CTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTTA-AACCTGATTCAG
* *
1661976 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTC-AGATCACCGGCTCTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCTA-ATCACCGGCACTTAGCCTGCTAG
* **
1662040 ACTTA-AAGTCTGAATT-ATTTCACCGGC-CTTAAGCCTGCTAGGTTTTAAACCTGA
65 ACTTATAA-CCTG-ATTCAGATCACCGGCACTT-AGCCTGCTAGGTTTTAAACCTGA
1662094 AAATTTCAAT
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
122 6 0.06
123 92 0.88
124 7 0.07
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (123 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCTAATCACCGGCACTTAGCCTGCTAGA
CTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTTAAACCTGATTCAG
Found at i:1666324 original size:20 final size:18
Alignment explanation
Indices: 1666277--1666383 Score: 53
Period size: 20 Copynumber: 5.8 Consensus size: 18
1666267 CAAGATAAAC
1666277 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
*
1666294 ATGAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
1666314 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
1666333 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
1666350 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
1666370 ATTAAAATAATATT
1 ATTAAATTAATATT
1666384 AATTCTAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
16 1 0.01
17 14 0.21
18 9 0.13
19 21 0.31
20 23 0.34
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1666371 original size:37 final size:36
Alignment explanation
Indices: 1666309--1666386 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 36
1666299 GATAATCACT
*
1666309 TTAATATTAAATTAATAAAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
1666346 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
1666382 TTAAT
1 TTAAT
1666387 TCTAGAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:1667755 original size:28 final size:28
Alignment explanation
Indices: 1667676--1667801 Score: 144
Period size: 28 Copynumber: 4.4 Consensus size: 28
1667666 ATACAATATG
* * * *
1667676 CAGTAACAGTCTGGGCCTGAGCCCTATT
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
1667704 CAGTAACAGTACAGTGTGGCCTTAGCCCGATA
1 CAGTAACAGT---GTG-GGCCTTAGCCCAATA
* *
1667736 CAGTAATAGTGTGGGCCTTAGCCTAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
1667764 CAGTAACAGTGTGGACCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
1667792 CAGTAACAGT
1 CAGTAACAGT
1667802 ATAGTGCAGT
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
28 58 0.69
29 3 0.04
31 2 0.02
32 21 0.25
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:1667769 original size:60 final size:56
Alignment explanation
Indices: 1667676--1667801 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 56
1667666 ATACAATATG
* * *
1667676 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAACAGTACAGTGTGGCCTTAGCCCGATA
1 CAGTAACAGTCTGGGCCTGAGCCCTATACAGTAACAGT---GTG-GACCTTAGCCCAATA
* * *
1667736 CAGTAATAGTGTGGGCCTTAG-CCTAATACAGTAACAGTGTGGACCTTAGCCCAATA
1 CAGTAACAGTCTGGGCCTGAGCCCT-ATACAGTAACAGTGTGGACCTTAGCCCAATA
1667792 CAGTAACAGT
1 CAGTAACAGT
1667802 ATAGTGCAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 22 0.38
57 3 0.05
59 3 0.05
60 30 0.52
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (56 bp):
CAGTAACAGTCTGGGCCTGAGCCCTATACAGTAACAGTGTGGACCTTAGCCCAATA
Found at i:1668727 original size:15 final size:15
Alignment explanation
Indices: 1668703--1668734 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1668693 TATGCATGTA
*
1668703 AAATATAAAAGACAT
1 AAATACAAAAGACAT
1668718 AAATACAAAAGACAT
1 AAATACAAAAGACAT
1668733 AA
1 AA
1668735 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:1673573 original size:72 final size:71
Alignment explanation
Indices: 1673448--1673587 Score: 217
Period size: 72 Copynumber: 2.0 Consensus size: 71
1673438 TGCTTTGGGT
* *
1673448 AATGGAACTTAGATACTGTCGCACCCAAGGCCAATGTGGATGTTCCCAAGCCCAAGAAGTTCAAG
1 AATGGAACTTAGATACTATCGCACCCAAGGCCAATGTGAATGTTCCCAAGCCCAAGAAGTTCAAG
1673513 GGAGGC
66 GGAGGC
* * * *
1673519 AATGGAAGGTTAGATACTATCGCACCCAAGGCTAGTGTGAATGTTCCCAAGCCCAAGGAGTTCAA
1 AATGGAA-CTTAGATACTATCGCACCCAAGGCCAATGTGAATGTTCCCAAGCCCAAGAAGTTCAA
1673584 GGGA
65 GGGA
1673588 ATAAGGTCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 7 0.11
72 55 0.89
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (71 bp):
AATGGAACTTAGATACTATCGCACCCAAGGCCAATGTGAATGTTCCCAAGCCCAAGAAGTTCAAG
GGAGGC
Found at i:1674096 original size:15 final size:15
Alignment explanation
Indices: 1674076--1674106 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1674066 TATGATTTTG
1674076 TGGTTGGATTAAGTT
1 TGGTTGGATTAAGTT
1674091 TGGTTGGATTAAGTT
1 TGGTTGGATTAAGTT
1674106 T
1 T
1674107 CCTTGATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (15 bp):
TGGTTGGATTAAGTT
Found at i:1674354 original size:100 final size:100
Alignment explanation
Indices: 1674181--1674581 Score: 748
Period size: 100 Copynumber: 4.0 Consensus size: 100
1674171 CAATGCATGG
*
1674181 TGAGAATGACAAGGAACAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1674246 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
66 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
1674281 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1674346 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
66 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
1674381 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
1674446 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
66 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
*
1674481 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTTCTAAAGGA
1 TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
* * * *
1674546 GTACGTAGAGATAAAGTCTCCTATTTAGCTACATT
66 ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
1674581 T
1 T
1674582 AAGATCAAAA
Statistics
Matches: 295, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 295 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (100 bp):
TGAGAATGACAAGGAAGAGAAACATGGAGGGAAAAACATTGTTGACAATCCAATTTGCTAAAGGA
ATACATAGAGATGAAGTCTCCTATTTAGCCACATT
Found at i:1679144 original size:17 final size:18
Alignment explanation
Indices: 1679105--1679148 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1679095 ATGAAATTAG
*
1679105 AATTTGATTGAGAAAAAT
1 AATTTAATTGAGAAAAAT
*
1679123 AATTTAATTGAG-AAATT
1 AATTTAATTGAGAAAAAT
1679140 AATTTAATT
1 AATTTAATT
1679149 AATTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
AATTTAATTGAGAAAAAT
Found at i:1684259 original size:17 final size:18
Alignment explanation
Indices: 1684237--1684270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1684227 AAAAAGTTGT
1684237 TATAAG-GTTAGATAAAC
1 TATAAGTGTTAGATAAAC
*
1684254 TATAAGTGTTGGATAAA
1 TATAAGTGTTAGATAAA
1684271 AGTCTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
TATAAGTGTTAGATAAAC
Found at i:1688164 original size:2 final size:2
Alignment explanation
Indices: 1688157--1688203 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1688147 TCTCATTCTC
1688157 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
1688199 AG AG A
1 AG AG A
1688204 CGTATATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1693426 original size:22 final size:22
Alignment explanation
Indices: 1693398--1693442 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1693388 AGGGGGAGTG
1693398 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
1693420 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
1693442 T
1 T
1693443 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:1695219 original size:9 final size:9
Alignment explanation
Indices: 1695214--1695247 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1695204 TTTATAATTT
1695214 GAATAACTC
1 GAATAACTC
1695223 GAATAACTC
1 GAATAACTC
* *
1695232 GAATAATTT
1 GAATAACTC
1695241 GAATAAC
1 GAATAAC
1695248 AGATGAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
GAATAACTC
Found at i:1695347 original size:19 final size:19
Alignment explanation
Indices: 1695325--1695386 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
1695315 AAAATTACAA
1695325 AAAAAATCAAAATAATTTT
1 AAAAAATCAAAATAATTTT
1695344 AAAAAATTCAAAATAATTTT
1 AAAAAA-TCAAAATAATTTT
* *
1695364 TAAAATTCAAAAT-ATTTAT
1 AAAAAATCAAAATAATTT-T
1695383 AAAA
1 AAAA
1695387 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 17 0.45
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATCAAAATAATTTT
Found at i:1695349 original size:20 final size:20
Alignment explanation
Indices: 1695324--1695386 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
1695314 AAAAATTACA
*
1695324 AAAAAAATCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
1695344 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
1695364 -TAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
1695383 AAAA
1 AAAA
1695387 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 13 0.34
20 21 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:1695398 original size:18 final size:17
Alignment explanation
Indices: 1695341--1695398 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
1695331 TCAAAATAAT
*
1695341 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTC-AAA-AA
*
1695360 TTTTTAAAATTCAAAATA
1 TTTATAAAATTCAAAA-A
*
1695378 TTTATAAAAGTTCTAAAA
1 TTTATAAAA-TTCAAAAA
1695396 TTT
1 TTT
1695399 GCATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 16 0.48
19 16 0.48
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTATAAAATTCAAAAA
Found at i:1695805 original size:21 final size:21
Alignment explanation
Indices: 1695779--1695818 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1695769 ACCTTATCTA
*
1695779 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
1695800 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
1695819 CATTGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:1711294 original size:16 final size:16
Alignment explanation
Indices: 1711263--1711307 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1711253 AAACATCATA
1711263 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
1711277 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
1711293 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
1711308 CCCAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:1711305 original size:17 final size:16
Alignment explanation
Indices: 1711261--1711307 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1711251 ATAAACATCA
1711261 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
1711276 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
1711292 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
1711308 CCCAATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:1713428 original size:27 final size:27
Alignment explanation
Indices: 1713398--1713455 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1713388 TTCAGAGCTT
1713398 GCCATACGTACTATTCCTTCAAAGTTC
1 GCCATACGTACTATTCCTTCAAAGTTC
* *
1713425 GCCATACGTACTATTCCTTCAATGTTT
1 GCCATACGTACTATTCCTTCAAAGTTC
1713452 GCCA
1 GCCA
1713456 CACATATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.34
Consensus pattern (27 bp):
GCCATACGTACTATTCCTTCAAAGTTC
Found at i:1713467 original size:27 final size:27
Alignment explanation
Indices: 1713387--1713515 Score: 91
Period size: 27 Copynumber: 4.8 Consensus size: 27
1713377 AGAACATTTT
* * * *
1713387 CTTCAGAGCTTGCCATACGTACTATTC
1 CTTCAAAGTTTGCCACACATACTATTC
* * *
1713414 CTTCAAAGTTCGCCATACGTACTATTC
1 CTTCAAAGTTTGCCACACATACTATTC
*
1713441 CTTCAATGTTTGCCACACATA-TCATTC
1 CTTCAAAGTTTGCCACACATACT-ATTC
* * * * *
1713468 CTTCGAGGTTTGTCACACTTACAATT-
1 CTTCAAAGTTTGCCACACATACTATTC
* * *
1713494 CTTCAGAGTTAGCCATACATAC
1 CTTCAAAGTTTGCCACACATAC
1713516 ATTTCTTGCG
Statistics
Matches: 81, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
26 16 0.20
27 65 0.80
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (27 bp):
CTTCAAAGTTTGCCACACATACTATTC
Found at i:1713514 original size:53 final size:53
Alignment explanation
Indices: 1713385--1713698 Score: 171
Period size: 54 Copynumber: 6.1 Consensus size: 53
1713375 GCAGAACATT
* * * * * * *
1713385 TTCTTCAGAGCTT-GCCATACGTA-CTATTCCTTCAAAGTTCGCCATACGTACTA
1 TTCTTCAGAG-TTAGCCATACATATC-ATTCCTTCGAGGTTTGTCATACTTACAA
* * *
1713438 TTCCTTCA-ATGTTTGCCACACATATCATTCCTTCGAGGTTTGTCACACTTACAA
1 TT-CTTCAGA-GTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * **
1713492 TTCTTCAGAGTTAGCCATACATA-CATTTCTT-G-CG---G--A-AC--A-GT
1 TTCTTCAGAGTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * * * * * *
1713533 TTATTCAGAGCTT-GCCATACGTA-CTATTCCTTCAAAGTTTGCCATACGTACTA
1 TTCTTCAGAG-TTAGCCATACATATC-ATTCCTTCGAGGTTTGTCATACTTACAA
* * *
1713586 TTCCTTCA-ATGTTCGCCACACATATCATTCCTTCGAGGTTTATCATACTTACAA
1 TT-CTTCAGA-GTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * *
1713640 TTCTTCAGAGTTAGCCATACATATCATT-CTTCTAGGGTTGGTCATACTTACCA
1 TTCTTCAGAGTTAGCCATACATATCATTCCTTCGA-GGTTTGTCATACTTACAA
1713693 TTCTTC
1 TTCTTC
1713699 TCATTCAAGG
Statistics
Matches: 200, Mismatches: 37, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
41 19 0.09
42 9 0.05
44 3 0.01
45 1 0.00
47 2 0.01
49 1 0.00
50 3 0.01
51 1 0.00
52 13 0.06
53 70 0.35
54 76 0.38
55 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (53 bp):
TTCTTCAGAGTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
Done.