Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 188 of 320
Found at i:62384332 original size:80 final size:81
Alignment explanation
Indices: 62384229--62384426 Score: 256
Period size: 80 Copynumber: 2.5 Consensus size: 81
62384219 AGGCTAAAAT
* * * *
62384229 GGTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTACAAATTGAGGGCATTTCAGTAATTTTAC
1 GGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACAAATTGAAGGCATTTCAGTAATTTTAC
62384294 -AATCGACGATATTTC
66 AAATCGACGATATTTC
* * *
62384309 GGTAATTTTATAAACCGGGGGTACTTTGGTAATTTTACAAGTTGAAGGTATTTCAGTAATTTTAC
1 GGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACAAATTGAAGGCATTTCAGTAATTTTAC
* *
62384374 AAATCGAGGGTATTTC
66 AAATCGACGATATTTC
* * **
62384390 AGTAATTTTACAAACTAAGGGTA-TTTCGGTAATTTTA
1 GGTAATTTTATAAACCGAGGGTACTTT-GGTAATTTTA
62384427 GTAAACTAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
80 61 0.60
81 41 0.40
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
GGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACAAATTGAAGGCATTTCAGTAATTTTAC
AAATCGACGATATTTC
Found at i:62386430 original size:40 final size:40
Alignment explanation
Indices: 62386328--62386554 Score: 334
Period size: 40 Copynumber: 5.7 Consensus size: 40
62386318 ATTTGGATGA
* * * *
62386328 AAAT-CGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACT
1 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
62386367 AGTTCCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
62386406 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
62386446 AAATCAGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
62386486 AAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
62386526 CTAA-CCGGGCTATGTCCCGAAGGCATTTG
1 -AAATCCGGGCTAAGTCCCGAAGGCATTTG
62386555 AGTGAGTAGC
Statistics
Matches: 171, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.20
40 134 0.78
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:62388877 original size:46 final size:45
Alignment explanation
Indices: 62388684--62389077 Score: 411
Period size: 45 Copynumber: 8.7 Consensus size: 45
62388674 TTCAATCGAG
** * *
62388684 TAAGACCATAGTTGAAAGATGCTATGGCATCATGATTC--AGATGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATCAT-A-TCAAAAATGAA
* ** *
62388729 TAATACCATAGTTGAAAGACACTATGGCATCATATTGGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATA-TCAAAAATGAA
* * * *
62388775 TAAGACCATAGTT-AGAGACACTATGGAATCCTATCAAAAATGGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAATGAA
*
62388819 TAAGGCCATAGTTGAAAGACACTATGGCATCATATCAAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-AAAAATGAA
* * *
62388865 TAAGACCATAGTTGAAAGACACTATTGCATCCTATCAAAAATGGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAATGAA
* * * * *
62388910 TAAGACTATATTTAAAAGACACTATGGCATTATATCAAAAACTGCA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAA-TGAA
* *
62388956 TAAGACTATGGTTGAAAGACACTATGGCATCATATCAAAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAA-TGAA
* * * * *
62389002 TAAGACCAT-GATTGAAAGATATTATGGCATCA-AGTCGAGAATAAA
1 TAAGACCATAG-TTGAAAGACACTATGGCATCATA-TCAAAAATGAA
* *
62389047 TAAGACCATGGTTGAAAGACACTGTGGCATC
1 TAAGACCATAGTTGAAAGACACTATGGCATC
62389078 CTTCAATCAT
Statistics
Matches: 295, Mismatches: 46, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
44 22 0.07
45 140 0.47
46 133 0.45
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAATGAA
Found at i:62388945 original size:91 final size:90
Alignment explanation
Indices: 62388684--62389083 Score: 409
Period size: 91 Copynumber: 4.4 Consensus size: 90
62388674 TTCAATCGAG
** * * *
62388684 TAAGACCATAGTTGAAAGATGCTATGGCATCATGATTC--AGAT-GAGTAATACCATAGTTGAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCCT-A-TCAAAAATGGA-TAAGACCATA-TTGAAA
*** *
62388746 GACACTATGGCATCATATTGGAAAGTGAA
62 GACACTATGGCATCATATCAAAAAATGAA
* * *
62388775 TAAGACCATAGTT-AGAGACACTATGGAATCCTATCAAAAATGGATAAGGCCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACACTATGGCATCCTATCAAAAATGGATAAGACCATA-TTGAAAGAC
62388839 ACTATGGCATCATATCAAAAAATGAA
65 ACTATGGCATCATATCAAAAAATGAA
* * *
62388865 TAAGACCATAGTTGAAAGACACTATTGCATCCTATCAAAAATGGATAAGACTATATTTAAAAGAC
1 TAAGACCATAGTTGAAAGACACTATGGCATCCTATCAAAAATGGATAAGACCATA-TTGAAAGAC
* * *
62388930 ACTATGGCATTATATCAAAAACTGCA
65 ACTATGGCATCATATCAAAAAATGAA
* * * *
62388956 TAAGACTATGGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCATGATTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCCTATCAAAAA-TGGATAAGACCAT-ATTGAAAGA
* * * * *
62389021 TATTATGGCATCA-AGTC-GAGAATAAA
64 CACTATGGCATCATA-TCAAAAAATGAA
* *
62389047 TAAGACCATGGTTGAAAGACACTGTGGCATCCT-TCAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCCTATCAA
62389084 TCATTACTAT
Statistics
Matches: 262, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
88 2 0.01
89 1 0.00
90 74 0.28
91 154 0.59
92 30 0.11
93 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (90 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCCTATCAAAAATGGATAAGACCATATTGAAAGACA
CTATGGCATCATATCAAAAAATGAA
Found at i:62389050 original size:137 final size:135
Alignment explanation
Indices: 62388684--62389077 Score: 395
Period size: 137 Copynumber: 2.9 Consensus size: 135
62388674 TTCAATCGAG
** * * *
62388684 TAAGACCATAGTTGAAAGATGCTATGGCATCATGATTC---AGATGAGTAATACCATAGTTGAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCAT-A-TCAAAAAATGAATAAGACCATAGTTGAAA
** * * * * *
62388746 GACACTATGGCAT-CATATTGGAAAGTGAATAAGACCATAGTTAGAGACACTATGGAATCCTATC
64 GACACTATGGCATCCA-A-TCAAAAATAAATAAGACCATAGTTAAAGACACTATGGCATCATATC
*
62388810 AAAAATGGA
127 AAAAATGCA
*
62388819 TAAGGCCATAGTTGAAAGACACTATGGCATCATATCAAAAAATGAATAAGACCATAGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAATGAATAAGACCATAGTTGAAAGA
* * ** * * *
62388884 CACTATTGCATCCTATCAAAAATGGATAAGACTATATTTAAAAGACACTATGGCATTATATCAAA
66 CACTATGGCATCCAATCAAAAATAAATAAGACCATAGTT-AAAGACACTATGGCATCATATCAAA
62388949 AACTGCA
130 AA-TGCA
* * *
62388956 TAAGACTATGGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCAT-GATTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAATGAATAAGACCATAG-TTGAAAG
* * * * * *
62389020 ATATTATGGCAT-CAAGTCGAGAATAAATAAGACCATGGTTGAAAGACACTGTGGCATC
65 ACACTATGGCATCCAA-TCAAAAATAAATAAGACCATAGTT-AAAGACACTATGGCATC
62389078 CTTCAATCAT
Statistics
Matches: 214, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
133 2 0.01
134 1 0.00
135 48 0.22
136 60 0.28
137 103 0.48
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (135 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAATGAATAAGACCATAGTTGAAAGA
CACTATGGCATCCAATCAAAAATAAATAAGACCATAGTTAAAGACACTATGGCATCATATCAAAA
ATGCA
Found at i:62399484 original size:21 final size:21
Alignment explanation
Indices: 62399459--62399511 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
62399449 GTTGTTGAGA
*
62399459 AGGAAGTTGCTGCTGCAGAAG
1 AGGAAGTTGCTGCTGAAGAAG
* * *
62399480 AGGAAGTTGTTGTTGAAGTAG
1 AGGAAGTTGCTGCTGAAGAAG
*
62399501 AAGAAGTTGCT
1 AGGAAGTTGCT
62399512 AAAACTGAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.36, T:0.26
Consensus pattern (21 bp):
AGGAAGTTGCTGCTGAAGAAG
Found at i:62401614 original size:7 final size:7
Alignment explanation
Indices: 62401602--62401638 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
62401592 CACATTTCTA
62401602 CTCATCC
1 CTCATCC
62401609 CTCATCC
1 CTCATCC
62401616 CTCATCC
1 CTCATCC
*
62401623 CTCATCA
1 CTCATCC
62401630 CTCATCC
1 CTCATCC
62401637 CT
1 CT
62401639 TATCATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.54, G:0.00, T:0.30
Consensus pattern (7 bp):
CTCATCC
Found at i:62401621 original size:14 final size:14
Alignment explanation
Indices: 62401601--62401649 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
62401591 TCACATTTCT
62401601 ACTCATCCCTCATC
1 ACTCATCCCTCATC
*
62401615 CCTCATCCCTCATC
1 ACTCATCCCTCATC
*
62401629 ACTCATCCCTTATC
1 ACTCATCCCTCATC
*
62401643 ATTCATC
1 ACTCATC
62401650 ACTCTCTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.33
Consensus pattern (14 bp):
ACTCATCCCTCATC
Found at i:62401648 original size:21 final size:21
Alignment explanation
Indices: 62401601--62401653 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
62401591 TCACATTTCT
*
62401601 ACTCATCCCTCATCCCTCATC
1 ACTCATCACTCATCCCTCATC
* *
62401622 CCTCATCACTCATCCCTTATC
1 ACTCATCACTCATCCCTCATC
*
62401643 ATTCATCACTC
1 ACTCATCACTC
62401654 TCTCCTCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.47, G:0.00, T:0.32
Consensus pattern (21 bp):
ACTCATCACTCATCCCTCATC
Found at i:62411433 original size:13 final size:13
Alignment explanation
Indices: 62411415--62411443 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
62411405 TTTAGTTTAA
62411415 TTAGTTAATTAGT
1 TTAGTTAATTAGT
62411428 TTAGTTAATTAGT
1 TTAGTTAATTAGT
62411441 TTA
1 TTA
62411444 ATGAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:62413287 original size:40 final size:40
Alignment explanation
Indices: 62413231--62413415 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
62413221 CGGATGATAA
* *
62413231 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * *
62413271 TCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * * *
62413311 CCGAGCTAAGTCTCGAAGGCATTTGTACGAGTTACTATAC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
62413351 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTTTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-TAAAT
62413391 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
62413416 AGCAAGTATC
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
40 124 0.98
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:62413429 original size:80 final size:80
Alignment explanation
Indices: 62413227--62413448 Score: 265
Period size: 80 Copynumber: 2.8 Consensus size: 80
62413217 TATTCGGATG
* * * * *
62413227 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CTAAATTCGGGCTATGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGT-ATCTATATCCGGGCTAAGTCCCGAAGGC
62413291 ATTTGTGCGAGTTATT
65 ATTTGTGCGAGTTATT
* * * * *
62413307 ATATCCGAGCTAAGTCTCGAAGGCATTTGTA-CGAGT-TACTATACCCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG-AGCAAGTAT-CTATATCCGGGCTAAGTCCCGAAGG
62413370 CATTTGTGCGAGTTACTT
64 CATTTGTGCGAGTTA-TT
* *
62413388 -TAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTATCTATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTATCTATATCCGGGCTAAGTCCCGAAGG
62413449 TACTTGGTTT
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
79 15 0.12
80 102 0.85
81 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTATCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTATT
Found at i:62424981 original size:23 final size:23
Alignment explanation
Indices: 62424951--62424997 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
62424941 GTTTATTTAA
62424951 TCATATTTTATTTGATAAGTTTT
1 TCATATTTTATTTGATAAGTTTT
62424974 TCATATTTTATTTGATAAGTTTT
1 TCATATTTTATTTGATAAGTTTT
62424997 T
1 T
62424998 TTTTCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (23 bp):
TCATATTTTATTTGATAAGTTTT
Found at i:62425148 original size:17 final size:18
Alignment explanation
Indices: 62425122--62425155 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
62425112 TTTTTGTTTA
62425122 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
62425139 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
62425156 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:62431041 original size:43 final size:42
Alignment explanation
Indices: 62430925--62431095 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 42
62430915 GTTATCGAGA
*
62430925 TGTGATTACATGTACGACCATGTCTGAGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTG-GACATTGGCATTGTAT
* *
62430968 TGAGATTACATATAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTAT
* * * * * *
62431011 TGTGATTTCGTGTAAGACCTTGTCTAGGACAGTAGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTAT
* * *
62431053 ATG-CATTGACATGTAAGACCATATCTAGGATA-TGGCATTGTAT
1 -TGTGATT-ACATGTAAGACCATGTCT-GGACATTGGCATTGTAT
62431096 GAGCTTTTGT
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 11 0.11
43 92 0.88
44 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
TGTGATTACATGTAAGACCATGTCTGGACATTGGCATTGTAT
Found at i:62434491 original size:45 final size:45
Alignment explanation
Indices: 62434426--62434837 Score: 189
Period size: 45 Copynumber: 9.1 Consensus size: 45
62434416 TAAGCAGGTT
** **
62434426 CATCATTATTCAAATGAGTAAGACCATAGCTGAAAGATGCTATGG
1 CATCATTATTCAAACAAGTAAGACCATAGCTGAAAGACACTATGG
* * **
62434471 CATCATTATTCAAACAAGTAATATCATAGCTGAAAGATGCTATGG
1 CATCATTATTCAAACAAGTAAGACCATAGCTGAAAGACACTATGG
* * ** *
62434516 CATCATGATTCAGATGAGTAAGACCATAGTTGAAAGACACTATGG
1 CATCATTATTCAAACAAGTAAGACCATAGCTGAAAGACACTATGG
*
62434561 CATCCA--A-TCGAAAACGAA-TAAGACCATAGTTGAAAGACACTATGG
1 CAT-CATTATTC--AAAC-AAGTAAGACCATAGCTGAAAGACACTATGG
* *
62434606 CATCA-TA-TCGGAAAGTATA-TAAGACCATAG-TTAAAGACACTATGG
1 CATCATTATTC--AAA-CA-AGTAAGACCATAGCTGAAAGACACTATGG
* * * * * * *
62434651 CAAC-CTA-CCGAAGATGGATAAGACCATAGTTGAAAGACAC-ATGG
1 CATCATTATTCAAACA-AG-TAAGACCATAGCTGAAAGACACTATGG
* * * *
62434695 CATCA-TA-TCGGAAAGTGAA-TAAGACTATAGTTGAAAGACAATAT-G
1 CATCATTATTC--AAA--CAAGTAAGACCATAGCTGAAAGACACTATGG
* * *
62434740 -A-CATTCTATCGAATATGAA-TAAGACCATAGTTGAAAGACACTATGG
1 CATCATTAT-TC-AA-A-CAAGTAAGACCATAGCTGAAAGACACTATGG
* * * *
62434786 CATCA-TATTGGAAA-ATGAATAAGACCATGGTTGAAAGACACTATGG
1 CATCATTATT-CAAACA--AGTAAGACCATAGCTGAAAGACACTATGG
62434832 CATCAT
1 CATCAT
62434838 ATCGGGAAGT
Statistics
Matches: 301, Mismatches: 37, Indels: 56
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.01
43 7 0.02
44 26 0.09
45 202 0.67
46 57 0.19
47 3 0.01
48 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (45 bp):
CATCATTATTCAAACAAGTAAGACCATAGCTGAAAGACACTATGG
Found at i:62434589 original size:90 final size:89
Alignment explanation
Indices: 62434426--62434927 Score: 441
Period size: 90 Copynumber: 5.6 Consensus size: 89
62434416 TAAGCAGGTT
* * **
62434426 CATCATTATTCAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCAT-CATTATTC-AAACA--
1 CATCA-TATTCAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCCA--A-TCGAAA-ATG
* * * * **
62434487 AGTAATATCATAGCTGAAAGATGCTATGG
61 AATAAGACCATAGTTGAAAGACACTATGG
* * *
62434516 CATCATGATTCAGATGAGTAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAACGAATA
1 CATCAT-ATTCAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAATGAATA
62434581 AGACCATAGTTGAAAGACACTATGG
65 AGACCATAGTTGAAAGACACTATGG
* * * * *
62434606 CATCATA-TCGGAAA-GTATATAAGACCATAGTT-AAAGACACTATGGCAACCTACCGAAGATGG
1 CATCATATTC--AAATG-A-ATAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAATGA
62434668 ATAAGACCATAGTTGAAAGACAC-ATGG
62 ATAAGACCATAGTTGAAAGACACTATGG
* * * * * *
62434695 CATCATA-TCGGAAAGTGAATAAGACTATAGTTGAAAGACAATATGACATTCTATCGAATATGAA
1 CATCATATTC--AAA-TGAATAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAATGAA
62434759 TAAGACCATAGTTGAAAGACACTATGG
63 TAAGACCATAGTTGAAAGACACTATGG
* * * *
62434786 CATCATATTGGAAAATGAATAAGACCATGGTTGAAAGACACTATGGCAT-CATATCGGGAAGTGA
1 CATCATATT--CAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCCA-ATC-GAAAATGA
* * *
62434850 ATAAGACCATGGTTGAAAGACATTATAG
62 ATAAGACCATAGTTGAAAGACACTATGG
* * * *
62434878 CATTA-AGTCGAGAATAAATAAGACCATGGTTGAAAGACACTATGGCATCC
1 CATCATATTC-A-AATGAATAAGACCATAGTTGAAAGACACTATGGCATCC
62434928 TTCAATCATT
Statistics
Matches: 349, Mismatches: 42, Indels: 40
0.81 0.10 0.09
Matches are distributed among these distances:
88 5 0.01
89 38 0.11
90 170 0.49
91 97 0.28
92 39 0.11
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (89 bp):
CATCATATTCAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAATGAATAA
GACCATAGTTGAAAGACACTATGG
Found at i:62434612 original size:24 final size:24
Alignment explanation
Indices: 62434540--62434612 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 24
62434530 TGAGTAAGAC
62434540 CATAGTTGAAAGACACTATGGCAT
1 CATAGTTGAAAGACACTATGGCAT
* * * *
62434564 CCA-A-TCGAAA-ACGAATA-AG-AC
1 -CATAGTTGAAAGAC-ACTATGGCAT
62434585 CATAGTTGAAAGACACTATGGCAT
1 CATAGTTGAAAGACACTATGGCAT
62434609 CATA
1 CATA
62434613 TCGGAAAGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 13
0.62 0.15 0.24
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 11 0.32
23 11 0.32
24 6 0.18
25 2 0.06
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (24 bp):
CATAGTTGAAAGACACTATGGCAT
Found at i:62434767 original size:180 final size:182
Alignment explanation
Indices: 62434534--62434927 Score: 496
Period size: 180 Copynumber: 2.2 Consensus size: 182
62434524 TTCAGATGAG
* *
62434534 TAAGACCATAGTTGAAAGACACTATGGCATCCAATCGAAAACGAATAAGACCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACAATATGACATCCAATCGAAAACGAATAAGACCATAGTTGAAAGAC
* *
62434599 ACTATGGCATCATATCGGAAAGT-ATATAAGACCATAGTT-AAAGACACTATGGCAACCTA-C-C
66 ACTATGGCATCATATCGGAAAATGA-ATAAGACCATAGTTGAAAGACACTATGGCAACATATCGC
*
62434660 GAAGATGGATAAGACCATAGTTGAAAGACACATGGCATCATATCGGAAAGTGAA
130 GAAG-TGAATAAGACCATAGTTGAAAGACACATGGCATCATATCGGAAAGTGAA
* * * * *
62434714 TAAGACTATAGTTGAAAGACAATATGACATTCTATCGAATATGAATAAGACCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACAATATGACATCCAATCGAAAACGAATAAGACCATAGTTGAAAGAC
* * * *
62434779 ACTATGGCATCATATTGGAAAATGAATAAGACCATGGTTGAAAGACACTATGGCATCATATCGGG
66 ACTATGGCATCATATCGGAAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATATCGCG
* * * * *
62434844 AAGTGAATAAGACCATGGTTGAAAGACATTATAGCATTA-AGTC-GAGAA-TAAA
131 AAGTGAATAAGACCATAGTTGAAAGACA-CATGGCATCATA-TCGGA-AAGTGAA
* * *
62434896 TAAGACCATGGTTGAAAGACACTATGGCATCC
1 TAAGACCATAGTTGAAAGACAATATGACATCC
62434928 TTCAATCATT
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
180 92 0.50
181 19 0.10
182 57 0.31
183 15 0.08
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (182 bp):
TAAGACCATAGTTGAAAGACAATATGACATCCAATCGAAAACGAATAAGACCATAGTTGAAAGAC
ACTATGGCATCATATCGGAAAATGAATAAGACCATAGTTGAAAGACACTATGGCAACATATCGCG
AAGTGAATAAGACCATAGTTGAAAGACACATGGCATCATATCGGAAAGTGAA
Found at i:62434922 original size:91 final size:91
Alignment explanation
Indices: 62434534--62434926 Score: 471
Period size: 91 Copynumber: 4.3 Consensus size: 91
62434524 TTCAGATGAG
* *
62434534 TAAGACCATAGTTGAAAGACACTATGGCATCCA-ATCGAAAACGAATAAGACCATAGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCAT-CATATCGGAAATGAATAAGACCATAGTTGAAAGA
*
62434598 CACTATGGCATCATATCGGAAAGTATA
65 CACTATGGCATCATATCGGAAAGTAAA
* * * *
62434625 TAAGACCATAGTT-AAAGACACTATGGCAACCTA-CCGAAGATGGATAAGACCATAGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCGGAA-ATGAATAAGACCATAGTTGAAAGA
*
62434688 CAC-ATGGCATCATATCGGAAAGTGAA
65 CACTATGGCATCATATCGGAAAGTAAA
* * *
62434714 TAAGACTATAGTTGAAAGACAATATGACATTC-TATC-GAATATGAATAAGACCATAGTTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCA-TCATATCGGAA-ATGAATAAGACCATAGTTGAAAG
* * *
62434777 ACACTATGGCATCATATTGGAAAATGAA
64 ACACTATGGCATCATATCGGAAAGTAAA
* * *
62434805 TAAGACCATGGTTGAAAGACACTATGGCATCATATCGGGAAGTGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-GGAAATGAATAAGACCATAGTTGAAAGA
* * *
62434870 CATTATAGCATTA-AGTC-GAGAA-TAAA
65 CACTATGGCATCATA-TCGGA-AAGTAAA
*
62434896 TAAGACCATGGTTGAAAGACACTATGGCATC
1 TAAGACCATAGTTGAAAGACACTATGGCATC
62434927 CTTCAATCAT
Statistics
Matches: 264, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
89 37 0.14
90 87 0.33
91 102 0.39
92 35 0.13
93 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (91 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCGGAAATGAATAAGACCATAGTTGAAAGAC
ACTATGGCATCATATCGGAAAGTAAA
Found at i:62438238 original size:5 final size:5
Alignment explanation
Indices: 62438228--62438252 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62438218 TTTTTCATGG
62438228 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
62438253 TTTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:62440477 original size:25 final size:25
Alignment explanation
Indices: 62440432--62440502 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
62440422 GAGGAAGTGC
*
62440432 AAAAGGGCTTTTGCCCCAGTTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTACCA
* *
62440458 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
62440483 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
62440503 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 33 0.80
26 8 0.20
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:62440515 original size:24 final size:24
Alignment explanation
Indices: 62440431--62440515 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 24
62440421 GGAGGAAGTG
*
62440431 CAAAAGGGCTTTTGCCCCAGTTTAC
1 CAAAAGGGC-TTTGCCCCAGTTTAT
*
62440456 CGAAAAGGGCTTTGCCCTAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
62440481 CAAAAAGGGCTTTGCCCCAG-TTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
*
62440505 TAAAAGAGGCT
1 CAAAAG-GGCT
62440516 AAGCCTCCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 32 0.60
26 8 0.15
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:62440757 original size:30 final size:31
Alignment explanation
Indices: 62440723--62440804 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
62440713 CGTTTACAGT
*
62440723 AAAGGCTTCGGCCTAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
62440753 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
62440784 AAAGGCTTTGGCCCAGT-ATAT
1 AAAGGCTTCGGCCCAGTGATAT
62440805 ATTGAGATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 24 0.52
31 22 0.48
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:62440788 original size:31 final size:30
Alignment explanation
Indices: 62440723--62440800 Score: 111
Period size: 31 Copynumber: 2.6 Consensus size: 30
62440713 CGTTTACAGT
* *
62440723 AAAGGCTTCGGCCTAGTGATATGATAATGA
1 AAAGGCTTCGGCCCAGTGACATGATAATGA
*
62440753 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATG-ATAATGA
*
62440784 AAAGGCTTTGGCCCAGT
1 AAAGGCTTCGGCCCAGT
62440801 ATATATTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGACATGATAATGA
Found at i:62444428 original size:50 final size:49
Alignment explanation
Indices: 62444312--62444487 Score: 185
Period size: 50 Copynumber: 3.5 Consensus size: 49
62444302 TTGGTACGCA
* * **
62444312 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* *
62444361 TAGTAGCCTGCACTTAGTATTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
* *** * *
62444411 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACG
62444462 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
62444488 TGCGACCTCA
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 28 0.26
50 40 0.37
51 36 0.34
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:62444486 original size:101 final size:99
Alignment explanation
Indices: 62444312--62444498 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 99
62444302 TTGGTACGCA
* * *
62444312 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
* *
62444377 GTATTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* * *
62444411 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
*
62444475 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
62444499 AATAAATCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 42 0.55
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:62446887 original size:71 final size:71
Alignment explanation
Indices: 62446771--62446913 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
62446761 AGAACATAAA
62446771 AAGGCCATAGCTTGGAAAATTTCTAACATTAAAGGAATCAACCCTTCTTTTTGCACCCACAAAAT
1 AAGGCCATAGCTTGGAAAATTTCTAACATTAAAGGAATCAACCCTTCTTTTTGCACCCACAAAAT
62446836 TTTGAT
66 TTTGAT
62446842 AAGGCCATAGCTTGGAAAATTTCTAACATTAAAGGAATCAACCCTTCTTTTTGCACCCACAAAAT
1 AAGGCCATAGCTTGGAAAATTTCTAACATTAAAGGAATCAACCCTTCTTTTTGCACCCACAAAAT
62446907 TTTGAT
66 TTTGAT
62446913 A
1 A
62446914 GAAGATGAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (71 bp):
AAGGCCATAGCTTGGAAAATTTCTAACATTAAAGGAATCAACCCTTCTTTTTGCACCCACAAAAT
TTTGAT
Found at i:62453910 original size:53 final size:52
Alignment explanation
Indices: 62453829--62453987 Score: 237
Period size: 53 Copynumber: 3.0 Consensus size: 52
62453819 TGGTTAAGTG
* * * *
62453829 CCCTAATGGGAACCTTTAAAAAGGAATTGACAGATTATTAAATCATACGCTT
1 CCCTAATGGGACCCTTGAAAAAGGAATTGACGGATTATTAAATCATACACTT
*
62453881 CTCTAATGGGCACCCTTGAAAAAGGAATTGACGGATTATTAAATCATACACTT
1 CCCTAATGGG-ACCCTTGAAAAAGGAATTGACGGATTATTAAATCATACACTT
* *
62453934 CCCTAATGGGTACGCTTGAAAAAGGAATTGACGGATTATTGAATCATACACTT
1 CCCTAATGGG-ACCCTTGAAAAAGGAATTGACGGATTATTAAATCATACACTT
62453987 C
1 C
62453988 GAGTGTACTA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 9 0.09
53 88 0.91
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
CCCTAATGGGACCCTTGAAAAAGGAATTGACGGATTATTAAATCATACACTT
Found at i:62454555 original size:12 final size:12
Alignment explanation
Indices: 62454538--62454567 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
62454528 TATGTGATAT
62454538 GTTATTGCTTAA
1 GTTATTGCTTAA
62454550 GTTATTGCTTAA
1 GTTATTGCTTAA
62454562 GTTATT
1 GTTATT
62454568 CCAAGGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (12 bp):
GTTATTGCTTAA
Found at i:62457588 original size:27 final size:27
Alignment explanation
Indices: 62457558--62457616 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
62457548 AAATAGGAGG
**
62457558 ATTAACACCTTGAACATTTGGATTATC
1 ATTAACACCAAGAACATTTGGATTATC
*
62457585 ATTAACACCAAGACCATTTGGATTATC
1 ATTAACACCAAGAACATTTGGATTATC
62457612 ATTAA
1 ATTAA
62457617 GACTAGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (27 bp):
ATTAACACCAAGAACATTTGGATTATC
Found at i:62458016 original size:14 final size:14
Alignment explanation
Indices: 62457997--62458023 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62457987 TAGATTAACG
62457997 TTATAACAAAGTTA
1 TTATAACAAAGTTA
62458011 TTATAACAAAGTT
1 TTATAACAAAGTT
62458024 CTCTTGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TTATAACAAAGTTA
Found at i:62458299 original size:344 final size:345
Alignment explanation
Indices: 62457671--62458345 Score: 1316
Period size: 344 Copynumber: 2.0 Consensus size: 345
62457661 TTCCTTCTTC
62457671 ACAAAGTTCTCTTGATCTCTGGATCAAAAGGATACTCATTGTTAGTAGGAATGCCTCTTCTCATG
1 ACAAAGTTCTCTTGATCTCTGGATCAAAAGGATACTCATTGTTAGTAGGAATGCCTCTTCTCATG
*
62457736 CACTGATGGTAAACCTATAGAAATCATATTAAATTGAGTTAGATAAAACTAATGGAATTATATAA
66 CACTGATGGCAAACCTATAGAAATCATATTAAATTGAGTTAGATAAAACTAATGGAATTATATAA
62457801 GAAAATAAAAAAAAAATCACCAAATTGCTGCTCTTCGGCAATGGCACCAAAAACTTGTCACGTGT
131 GAAAATAAAAAAAAAATCACCAAATTGCTGCTCTTCGGCAATGGCACCAAAAACTTGTCACGTGT
62457866 GAATATAATATGCGAATTGTGCAAGTATACATGCCGAATCAAGTAATAAAATGATAAGTGAGTAT
196 GAATATAATATGCGAATTGTGCAAGTATACATGCCGAATCAAGTAATAAAATGATAAGTGAGTAT
*
62457931 CATTCTCACGAGGATTAGATTGAGGCACAAAAGTGGTCAAGTTATTATAATAAAGTTAGATTAAC
261 CATTCTCACGAGGATTAGATTGAGGCACAAAAATGGTCAAGTTATTATAATAAAGTTAGATTAAC
62457996 GTTATAACAAAGTTATTATA
326 GTTATAACAAAGTTATTATA
62458016 ACAAAGTTCTCTTGATCTCTGGATCAAAAGGATACTCATTGTTAGTAGGAATGCCTCTTCTCATG
1 ACAAAGTTCTCTTGATCTCTGGATCAAAAGGATACTCATTGTTAGTAGGAATGCCTCTTCTCATG
62458081 CACTGATGGCAAACCTATAGAAATCATATTAAATTGAGTTAGATAAAACTAATGGAATTATATAA
66 CACTGATGGCAAACCTATAGAAATCATATTAAATTGAGTTAGATAAAACTAATGGAATTATATAA
*
62458146 GAAAAT-AAAACAAAATCACCAAATTGCTGCTCTTCGGCAATGGCACCAAAAACTTGTCACGTGT
131 GAAAATAAAAAAAAAATCACCAAATTGCTGCTCTTCGGCAATGGCACCAAAAACTTGTCACGTGT
62458210 GAATATAATATGCGAATTGTGCAAGTATACATGCCGAATCAAGTAATAAAATGATAAGTGAGTAT
196 GAATATAATATGCGAATTGTGCAAGTATACATGCCGAATCAAGTAATAAAATGATAAGTGAGTAT
62458275 CATTCTCACGAGGATTAGATTGAGGCACAAAAATGGTCAAGTTATTATAATAAAGTTAGATTAAC
261 CATTCTCACGAGGATTAGATTGAGGCACAAAAATGGTCAAGTTATTATAATAAAGTTAGATTAAC
62458340 GTTATA
326 GTTATA
62458346 GCGAAATAAT
Statistics
Matches: 327, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
344 192 0.59
345 135 0.41
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (345 bp):
ACAAAGTTCTCTTGATCTCTGGATCAAAAGGATACTCATTGTTAGTAGGAATGCCTCTTCTCATG
CACTGATGGCAAACCTATAGAAATCATATTAAATTGAGTTAGATAAAACTAATGGAATTATATAA
GAAAATAAAAAAAAAATCACCAAATTGCTGCTCTTCGGCAATGGCACCAAAAACTTGTCACGTGT
GAATATAATATGCGAATTGTGCAAGTATACATGCCGAATCAAGTAATAAAATGATAAGTGAGTAT
CATTCTCACGAGGATTAGATTGAGGCACAAAAATGGTCAAGTTATTATAATAAAGTTAGATTAAC
GTTATAACAAAGTTATTATA
Found at i:62459623 original size:22 final size:21
Alignment explanation
Indices: 62459583--62459624 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
62459573 CTCTTAAAAT
62459583 AGGGGCACACACCCATGTGGA
1 AGGGGCACACACCCATGTGGA
* *
62459604 AGGGGCGACACGCCCGTGTGG
1 AGGGGC-ACACACCCATGTGG
62459625 CCTTTTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.29, G:0.40, T:0.10
Consensus pattern (21 bp):
AGGGGCACACACCCATGTGGA
Found at i:62461142 original size:46 final size:46
Alignment explanation
Indices: 62461090--62461257 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 46
62461080 TATTTGGGCA
62461090 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
62461136 TCTGAACTCGTTGAGTTGAGTCTGAGTTC-GTGAAATGTAACTAG-GCAT-
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATG
* * *
62461184 TC-AAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
62461229 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTC
62461258 GCTTGTGGGC
Statistics
Matches: 96, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 54 0.56
47 26 0.27
48 4 0.04
49 4 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:62463799 original size:49 final size:48
Alignment explanation
Indices: 62463641--62463955 Score: 183
Period size: 49 Copynumber: 6.7 Consensus size: 48
62463631 AGGGTACGAT
* * * * *
62463641 GTCGACGCCATGTTCCAAACATTGTCTTACACTGGCTCTCAC-ATCTAA
1 GTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCACTATCTGA
* *
62463689 GTCGATGCCATGTCCTAGACAGGTCTTACACTAGCT-TC-C-ATACATCGA
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTAT-C-T-GA
* * *
62463737 GGCCAATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTTATCTGT
1 -GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAC-TATCTGA
* * * * * * * *
62463787 GTCGATGACATGTCCCAGAAAGGGCCTACACT-G-ACACAC-CTC-AA
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATCTGA
* * * ** *
62463831 GCCAATGCAATGTCCCAGACAGGTCTTACACTAAC-CT-AC-CTC-GA
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATCTGA
* * *
62463875 G-CTGATGCCATGTCCCAGATAGGTCTTACACTAGATCTCATCTAT-TG-
1 GTC-GATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCA-CTATCTGA
*
62463922 GTGCCGATGTCATGTCCCAGACAGGTCTTACACT
1 GT--CGATGCCATGTCCCAGACAGGTCTTACACT
62463956 AGCACATACA
Statistics
Matches: 207, Mismatches: 41, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
43 1 0.00
44 59 0.29
45 8 0.04
46 4 0.02
47 20 0.10
48 21 0.10
49 85 0.41
50 4 0.02
51 2 0.01
52 1 0.00
53 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATCTGA
Found at i:62463817 original size:98 final size:91
Alignment explanation
Indices: 62463664--62463862 Score: 227
Period size: 93 Copynumber: 2.1 Consensus size: 91
62463654 TCCAAACATT
* * * * * *
62463664 GTCTTACACTGGCTCTCACATCTAAGTCGATGCCATGTCCTAGACAGGTCTTACACTAGCTTCCA
1 GTCTTACACTGGCTCTCACATCTAAGTCGATGACATGTCCCAGAAAGGGCCTACACT-G---ACA
* * *
62463729 TACATCGAGGCCAATGCCATGTCCCAGACAG
62 CACATC-AAGCCAATGCAATGTCCCAGACAG
**
62463760 GTCTTACACTGGCTCTCACTTATCTGTGTCGATGACATGTCCCAGAAAGGGCCTACACTGACACA
1 GTCTTACACTGGCTCTCAC--ATCTAAGTCGATGACATGTCCCAGAAAGGGCCTACACTGACACA
*
62463825 CCTCAAGCCAATGCAATGTCCCAGACAG
64 CATCAAGCCAATGCAATGTCCCAGACAG
62463853 GTCTTACACT
1 GTCTTACACT
62463863 AACCTACCTC
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
93 32 0.36
94 6 0.07
96 19 0.21
97 1 0.01
98 31 0.35
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (91 bp):
GTCTTACACTGGCTCTCACATCTAAGTCGATGACATGTCCCAGAAAGGGCCTACACTGACACACA
TCAAGCCAATGCAATGTCCCAGACAG
Found at i:62463861 original size:44 final size:44
Alignment explanation
Indices: 62463796--62463907 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
62463786 TGTCGATGAC
* * *
62463796 ATGTCCCAGAAAGGGCCTACACTGACAC-ACCTCAAGCCAATGCA
1 ATGTCCCAGAAAGGTCTTACACTAAC-CTACCTCAAGCCAATGCA
* * ** *
62463840 ATGTCCCAGACAGGTCTTACACTAACCTACCTCGAGCTGATGCC
1 ATGTCCCAGAAAGGTCTTACACTAACCTACCTCAAGCCAATGCA
*
62463884 ATGTCCCAGATAGGTCTTACACTA
1 ATGTCCCAGAAAGGTCTTACACTA
62463908 GATCTCATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (44 bp):
ATGTCCCAGAAAGGTCTTACACTAACCTACCTCAAGCCAATGCA
Found at i:62470373 original size:28 final size:28
Alignment explanation
Indices: 62470360--62470431 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
62470350 TCGGGCCAGA
*
62470360 TGGGCGATATGAATGTGATTAGGCCTAG
1 TGGGCCATATGAATGTGATTAGGCCTAG
**
62470388 TGGGCCATATGAATAAGATT-GTGCCTAG
1 TGGGCCATATGAATGTGATTAG-GCCTAG
*
62470416 TGGGCCATATGCATGT
1 TGGGCCATATGAATGT
62470432 ATGTAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (28 bp):
TGGGCCATATGAATGTGATTAGGCCTAG
Found at i:62474221 original size:40 final size:39
Alignment explanation
Indices: 62474173--62474456 Score: 353
Period size: 40 Copynumber: 7.2 Consensus size: 39
62474163 GGACTAAGAT
62474173 CCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCC-GGCTAAGTC
* *
62474213 CCGAAGGCATTTGTACTAGTTACTATAACCGGACTAAGAT-
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGG-CTAAG-TC
62474253 CCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAA--C
1 CCGAAGGCATTTGTGCTAGTTACTATATCC-GGCTAAGTC
*
62474291 CCGAAGGCATTTGTGCTAGTTACTATAACCGGACTAAGAT-
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGG-CTAAG-TC
*
62474331 CCGAAGGCATTTGTGCTAGTTACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATC-CGGCTAAGTC
* *
62474371 CGGAAAGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCC-GGCTAAGTC
* * * *
62474411 CCGAAGCCATTTGT-CTGAGTTGCTATATCTGGCTAAATC
1 CCGAAGGCATTTGTGCT-AGTTACTATATCCGGCTAAGTC
*
62474450 CTGAAGG
1 CCGAAGG
62474457 TACTTGGGTT
Statistics
Matches: 214, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
37 2 0.01
38 33 0.15
39 18 0.08
40 156 0.73
41 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGCTAAGTC
Found at i:62474381 original size:118 final size:119
Alignment explanation
Indices: 62474173--62474437 Score: 369
Period size: 118 Copynumber: 2.2 Consensus size: 119
62474163 GGACTAAGAT
*
62474173 CCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCATTTGTACTAGTTACTA
1 CCGAAGGCATTTGTGCTAGTTACTATAACCAGGCTAAGTCCCGAAGGCATTTGTACTAGTTACTA
*
62474238 TAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAA-C
66 TAACCGGACTAAGATCCGAAAGCATTTGTGCTAGTTACTATATCCAGGCTAAGC
*
62474291 CCGAAGGCATTTGTGCTAGTTACTATAACC-GGACTAAGAT-CCGAAGGCATTTGTGCTAGTTAC
1 CCGAAGGCATTTGTGCTAGTTACTATAACCAGG-CTAAG-TCCCGAAGGCATTTGTACTAGTTAC
* * * *
62474354 TATATCTGGGCTAAG-TCCGGAAAGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
64 TATAACCGGACTAAGATCC-GAAAGCATTTGTGCTAGTTACTATATCCAGGCTAAG-C
* *
62474411 CCGAAGCCATTTGT-CTGAGTTGCTATA
1 CCGAAGGCATTTGTGCT-AGTTACTATA
62474438 TCTGGCTAAA
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
117 5 0.04
118 101 0.77
119 3 0.02
120 23 0.17
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (119 bp):
CCGAAGGCATTTGTGCTAGTTACTATAACCAGGCTAAGTCCCGAAGGCATTTGTACTAGTTACTA
TAACCGGACTAAGATCCGAAAGCATTTGTGCTAGTTACTATATCCAGGCTAAGC
Found at i:62474437 original size:80 final size:80
Alignment explanation
Indices: 62474157--62474456 Score: 430
Period size: 80 Copynumber: 3.8 Consensus size: 80
62474147 TATTCAGATG
*
62474157 ATAATCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
*
62474222 TTTGTACTAGTTACT
66 TTTGTGCTAGTTACT
62474237 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAA--CCCGAAGGCA
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
62474300 TTTGTGCTAGTTACT
66 TTTGTGCTAGTTACT
** * *
62474315 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCTGGGCTAAGTCCGGAAAGCA
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
62474380 TTTGTGCTAGTTACT
66 TTTGTGCTAGTTACT
* * * * * * *
62474395 ATATCCGGGCTAAG-TCCCGAAGCCATTTGT-CTGAGTTGCTATAT-CTGGCTAAATCCTGAAGG
1 ATAACCGGACTAAGAT-CCGAAGGCATTTGTGCT-AGTTACTATATCCAGGCTAAGTCCCGAAGG
62474457 TACTTGGGTT
Statistics
Matches: 201, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
78 75 0.37
79 16 0.08
80 110 0.55
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (80 bp):
ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
TTTGTGCTAGTTACT
Found at i:62493353 original size:40 final size:40
Alignment explanation
Indices: 62493274--62493503 Score: 322
Period size: 40 Copynumber: 5.8 Consensus size: 40
62493264 GGATATAGCT
* * *
62493274 ACTCGCTCAAATGCCTTC-GGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
62493313 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
62493353 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
62493393 ACTCGCACAATTGCCTTTGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
62493433 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
62493472 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
62493504 TTATCATCCA
Statistics
Matches: 173, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 49 0.28
40 122 0.71
41 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:62496821 original size:40 final size:39
Alignment explanation
Indices: 62496744--62496829 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
62496734 TAACGATTTA
**
62496744 TCGGCTAAAATGGCACTTAGGGTGCGGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGGGTGCAATTCGAAATAGCT
* *
62496783 TCGGCTAAAAGTGGCACTT-GGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGG-GTGCAATTCGAAATAGCT
*
62496823 TTGGCTA
1 TCGGCTA
62496830 TATATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 12 0.30
40 28 0.70
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGGGTGCAATTCGAAATAGCT
Found at i:62517784 original size:55 final size:55
Alignment explanation
Indices: 62517724--62517847 Score: 140
Period size: 55 Copynumber: 2.3 Consensus size: 55
62517714 AGCCTCTACC
* * * * *
62517724 AAAACAACACAGGCATACGGCATGCTCGTGTGGAAGAACCGTGGGCGAACCTGAT
1 AAAACAACACAGGCATACGACACGCCCGCGTGGAACAACCGTGGGCGAACCTGAT
* * * * *
62517779 AAAACAACACGGGCATTCGACACGCCCGCGTGGAACACCCGTGGTCGAACCTGTT
1 AAAACAACACAGGCATACGACACGCCCGCGTGGAACAACCGTGGGCGAACCTGAT
**
62517834 AAATTAACACAGGC
1 AAAACAACACAGGC
62517848 GTGGGGCTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.32, C:0.27, G:0.26, T:0.15
Consensus pattern (55 bp):
AAAACAACACAGGCATACGACACGCCCGCGTGGAACAACCGTGGGCGAACCTGAT
Found at i:62523623 original size:10 final size:10
Alignment explanation
Indices: 62523608--62523634 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
62523598 AGACAACAAT
62523608 ACCATGTAAG
1 ACCATGTAAG
62523618 ACCATGTAAG
1 ACCATGTAAG
62523628 ACCATGT
1 ACCATGT
62523635 TTGGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (10 bp):
ACCATGTAAG
Found at i:62523687 original size:47 final size:47
Alignment explanation
Indices: 62523618--62523726 Score: 182
Period size: 47 Copynumber: 2.3 Consensus size: 47
62523608 ACCATGTAAG
*
62523618 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGAT
1 ACCATGTAAGACCATGTTTGGAACATGGCATTTGCTAAGACAAGGAT
* *
62523665 ACCATGTAAGACCATGTTTGGAATATGGCATTTGCTAAGATAAGGAT
1 ACCATGTAAGACCATGTTTGGAACATGGCATTTGCTAAGACAAGGAT
*
62523712 ATCATGTAAGACCAT
1 ACCATGTAAGACCAT
62523727 TCCAAGGCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (47 bp):
ACCATGTAAGACCATGTTTGGAACATGGCATTTGCTAAGACAAGGAT
Found at i:62523834 original size:55 final size:54
Alignment explanation
Indices: 62523706--62523902 Score: 247
Period size: 55 Copynumber: 3.6 Consensus size: 54
62523696 TTGCTAAGAT
* * *
62523706 AAGGATATCATGTAAGACCAT-TCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGT-CAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
62523760 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGCTGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * * *
62523815 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
*
62523868 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
62523903 ATGGTAAGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
52 4 0.03
53 33 0.26
54 40 0.32
55 44 0.35
56 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:62527029 original size:45 final size:46
Alignment explanation
Indices: 62526976--62527096 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 46
62526966 TATGTGAGCT
* * * *
62526976 AGTGTAAGACCATCTCTGGGACATGGCATCGGCTTGATATGTG-TC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATA
*
62527021 AGTGTAAGACCATGTTTGGGACATGGCATCGACTCGATATGTGATTA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGA-TA
*
62527068 AATGTAAGACCATGTC-GGGACATTGGCAT
1 AGTGTAAGACCATGTCTGGGACA-TGGCAT
62527097 TGTATTGTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 39 0.59
46 6 0.09
47 21 0.32
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATA
Found at i:62527150 original size:43 final size:42
Alignment explanation
Indices: 62527054--62527165 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 42
62527044 TGGCATCGAC
*
62527054 TCGATATGTGATTAAATGTAAGACCATGTCGGGACATTGGCA
1 TCGATATGTGATTAAATGTAAGACCATGTCGGGACAGTGGCA
* *** * * *
62527096 TTG-TATTGTGATTTCGTGTAAGACCCTGTGTGGGATAGTGGCA
1 TCGATA-TGTGATTAAATGTAAGACCATGT-CGGGACAGTGGCA
*
62527139 TCGATATGTGA-TAACATGTAAAACCAT
1 TCGATATGTGATTAA-ATGTAAGACCAT
62527166 ATCTAGGATA
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
41 2 0.04
42 22 0.42
43 26 0.50
44 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (42 bp):
TCGATATGTGATTAAATGTAAGACCATGTCGGGACAGTGGCA
Found at i:62554352 original size:11 final size:11
Alignment explanation
Indices: 62554331--62554359 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62554321 ATTGTTCAAC
62554331 TATAA-AATAA
1 TATAATAATAA
62554341 TATAATAATAA
1 TATAATAATAA
62554352 TATAATAA
1 TATAATAA
62554360 ATAGTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TATAATAATAA
Found at i:62571400 original size:150 final size:150
Alignment explanation
Indices: 62571129--62571429 Score: 602
Period size: 150 Copynumber: 2.0 Consensus size: 150
62571119 TTTTGTTTAG
62571129 TGTCACATTGTTTTGGGACCAAATGTGTTGACTTGTTTTAGTAATTGACACCATTTTGTATTAGG
1 TGTCACATTGTTTTGGGACCAAATGTGTTGACTTGTTTTAGTAATTGACACCATTTTGTATTAGG
62571194 TCATGTAAAATGGCTAATGTTGAAGGTTGTTATATGAATACAAGAGGTTCTTTCATGAATGAGTA
66 TCATGTAAAATGGCTAATGTTGAAGGTTGTTATATGAATACAAGAGGTTCTTTCATGAATGAGTA
62571259 ATTCGTTGGTTGCTTCGATA
131 ATTCGTTGGTTGCTTCGATA
62571279 TGTCACATTGTTTTGGGACCAAATGTGTTGACTTGTTTTAGTAATTGACACCATTTTGTATTAGG
1 TGTCACATTGTTTTGGGACCAAATGTGTTGACTTGTTTTAGTAATTGACACCATTTTGTATTAGG
62571344 TCATGTAAAATGGCTAATGTTGAAGGTTGTTATATGAATACAAGAGGTTCTTTCATGAATGAGTA
66 TCATGTAAAATGGCTAATGTTGAAGGTTGTTATATGAATACAAGAGGTTCTTTCATGAATGAGTA
62571409 ATTCGTTGGTTGCTTCGATA
131 ATTCGTTGGTTGCTTCGATA
62571429 T
1 T
62571430 ATATATATAT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 151 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.40
Consensus pattern (150 bp):
TGTCACATTGTTTTGGGACCAAATGTGTTGACTTGTTTTAGTAATTGACACCATTTTGTATTAGG
TCATGTAAAATGGCTAATGTTGAAGGTTGTTATATGAATACAAGAGGTTCTTTCATGAATGAGTA
ATTCGTTGGTTGCTTCGATA
Found at i:62575556 original size:41 final size:40
Alignment explanation
Indices: 62575402--62575612 Score: 307
Period size: 40 Copynumber: 5.3 Consensus size: 40
62575392 TCCTCGTTCA
* * * ** *
62575402 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62575441 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62575481 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62575521 AATGCCTTCGGGACTTAACCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAA-CCCGGATTTAACAACTCGCACG
** * *
62575562 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
62575602 AAGGCCTTCGG
1 AATGCCTTCGG
62575613 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.21
40 86 0.54
41 40 0.25
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:62575563 original size:81 final size:79
Alignment explanation
Indices: 62575402--62575612 Score: 323
Period size: 81 Copynumber: 2.6 Consensus size: 79
62575392 TCCTCGTTCA
* * * *
62575402 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
62575467 TAACAACTCGCACG
66 TAACAACTCGCACG
**
62575481 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAA-CCCGGA
62575546 TTTAACAACTCGCACG
64 TTTAACAACTCGCACG
* *
62575562 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGG
62575613 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 33 0.28
80 18 0.15
81 68 0.57
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:62575655 original size:121 final size:119
Alignment explanation
Indices: 62575400--62575658 Score: 290
Period size: 121 Copynumber: 2.2 Consensus size: 119
62575390 GCTCCTCGTT
* * * **
62575400 CAAATGCCTTCGGGACAT-AGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAACCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGG
* * * *
62575464 ATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
65 ATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAACAACTAGCA
* *
62575519 CGAATGCCTTCGGGACTTAACCCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCG
1 C-AAAGCCTTCGGGACTTAACCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCG
** * ** *
62575584 GATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCA
64 GATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATA-ACAAC-TAGCA
62575641 CAAAGCCTTCGGGACTTA
1 CAAAGCCTTCGGGACTTA
62575659 GCCCGGACAG
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
119 13 0.11
120 23 0.20
121 74 0.64
122 6 0.05
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (119 bp):
CAAAGCCTTCGGGACTTAACCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAACAACTAGCA
Found at i:62575674 original size:41 final size:41
Alignment explanation
Indices: 62575597--62575674 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
62575587 TTAGTATCTC
* * *
62575597 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
62575638 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
62575675 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:62583446 original size:40 final size:40
Alignment explanation
Indices: 62583355--62583566 Score: 300
Period size: 40 Copynumber: 5.3 Consensus size: 40
62583345 TCCTCGTTCA
* * * ** *
62583355 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62583394 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62583434 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62583474 AATGCCTTCGGGACTTAACCCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAA--CCCGGATTTAACAACTCGCACG
** * *
62583516 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
62583556 AAGGCCTTCGG
1 AATGCCTTCGG
62583567 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 33 0.21
40 86 0.54
42 40 0.25
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:62583517 original size:82 final size:79
Alignment explanation
Indices: 62583355--62583566 Score: 316
Period size: 82 Copynumber: 2.6 Consensus size: 79
62583345 TCCTCGTTCA
* * * *
62583355 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
62583420 TAACAACTCGCACG
66 TAACAACTCGCACG
**
62583434 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCCCGG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAA--CCCGG
62583499 ATTTAACAACTCGCACG
63 ATTTAACAACTCGCACG
* *
62583516 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGG
62583567 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
79 33 0.28
80 18 0.15
82 68 0.57
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:62583611 original size:122 final size:121
Alignment explanation
Indices: 62583385--62583612 Score: 291
Period size: 122 Copynumber: 1.9 Consensus size: 121
62583375 CGGTTTTAGT
* *
62583385 AACTCACACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCACACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
* * *
62583450 AACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCCCGGATTTAAC
66 AACCCGGATATAACAACTAGCACGAAAGCCTTCGGGACTTAACCCCCGGATTTAAC
* ** *
62583506 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATC
1 AACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-C
** *
62583570 TTAGTCCGGATATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTA
64 TTAACCCGGATATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTA
62583613 GCCCGGACAG
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
121 11 0.12
122 74 0.81
123 6 0.07
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (121 bp):
AACTCACACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
AACCCGGATATAACAACTAGCACGAAAGCCTTCGGGACTTAACCCCCGGATTTAAC
Found at i:62583628 original size:41 final size:41
Alignment explanation
Indices: 62583551--62583628 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
62583541 TTAGTATCTC
* * *
62583551 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
62583592 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
62583629 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:62586065 original size:11 final size:11
Alignment explanation
Indices: 62586049--62586076 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
62586039 AACCGATTCA
62586049 TAATTTCACTC
1 TAATTTCACTC
62586060 TAATTTCACTC
1 TAATTTCACTC
62586071 TAATTT
1 TAATTT
62586077 AAAACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTCACTC
Found at i:62598161 original size:47 final size:46
Alignment explanation
Indices: 62598081--62598250 Score: 147
Period size: 46 Copynumber: 3.7 Consensus size: 46
62598071 AGGGTATAAT
* *
62598081 GCCGATACCATG-CCCTAGACATGGTCTTTCACTGGCTC-TCACGTTAA
1 GCCGATGCCATGTCCC-AGACATGGTCTTACACTGGCTCATCACG-T-A
* * * *
62598128 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCATGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACGTA
* *
62598174 GCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACATCTCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCACGTA
**
62598219 GGCAAATG-CATGTCCCAGACAT-GTCTTACACT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACT
62598251 AGTTCTCGTC
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
44 12 0.12
45 14 0.14
46 40 0.39
47 30 0.29
48 7 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACGTA
Found at i:62598292 original size:47 final size:46
Alignment explanation
Indices: 62598178--62598300 Score: 149
Period size: 46 Copynumber: 2.7 Consensus size: 46
62598168 CATGTAGCCG
* * *
62598178 ATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGAGGCAA
1 ATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCAAGGCAA
* * * *
62598224 ATGCATGTCCCAGACATGTCTTACACTAG-TTCTCGTCTCAATGCCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCTT-ACATCTCAAGGCAA
*
62598270 ATGCCATGTCCCAGACATGTCTTCCACTAGC
1 ATG-CATGTCCCAGACATGTCTTACACTAGC
62598301 ACGCAAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
45 2 0.03
46 39 0.59
47 25 0.38
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCAAGGCAA
Found at i:62609450 original size:16 final size:17
Alignment explanation
Indices: 62609429--62609461 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62609419 CACATTGAAC
62609429 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
62609445 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
62609462 CTTCTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:62610274 original size:27 final size:28
Alignment explanation
Indices: 62610236--62610349 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 28
62610226 CTATTCAGAA
* *
62610236 ATCAGTGTTAAT-TGGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCCATAGCCCAT
62610263 ATCAGTATTAATCTGGGCCATAGCCC-T
1 ATCAGTATTAATCTGGGCCATAGCCCAT
* *
62610290 ATTACAATATCAGAGCATACTGGGCC-TAGCCCAT
1 A-T-CAGTAT--TA--AT-CTGGGCCATAGCCCAT
* * *
62610324 ATCAGTATCATTCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCCATAGCCC
62610350 TATTACAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
27 20 0.29
28 20 0.29
29 5 0.07
30 1 0.01
31 1 0.01
32 5 0.07
33 9 0.13
34 9 0.13
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (28 bp):
ATCAGTATTAATCTGGGCCATAGCCCAT
Found at i:62611050 original size:8 final size:8
Alignment explanation
Indices: 62611036--62611075 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
62611026 TCACAAATGC
62611036 CGGCTTTT
1 CGGCTTTT
*
62611044 TGGCTTTT
1 CGGCTTTT
*
62611052 CGACTTTT
1 CGGCTTTT
*
62611060 TGGCTTTT
1 CGGCTTTT
62611068 CGGCTTTT
1 CGGCTTTT
62611076 ACCGATCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.55
Consensus pattern (8 bp):
CGGCTTTT
Found at i:62611060 original size:16 final size:16
Alignment explanation
Indices: 62611039--62611075 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
62611029 CAAATGCCGG
62611039 CTTTTTGGCTTTTCGA
1 CTTTTTGGCTTTTCGA
*
62611055 CTTTTTGGCTTTTCGG
1 CTTTTTGGCTTTTCGA
62611071 CTTTT
1 CTTTT
62611076 ACCGATCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.19, G:0.19, T:0.59
Consensus pattern (16 bp):
CTTTTTGGCTTTTCGA
Found at i:62612754 original size:15 final size:15
Alignment explanation
Indices: 62612717--62612745 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62612707 TTTTTCTATC
62612717 TAATAATAATAATTA
1 TAATAATAATAATTA
62612732 TAATAATAATAATT
1 TAATAATAATAATT
62612746 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:62631338 original size:51 final size:50
Alignment explanation
Indices: 62631210--62631404 Score: 232
Period size: 49 Copynumber: 3.9 Consensus size: 50
62631200 TAGACAAGGC
* * **
62631210 TATCTGGTCCGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAG-
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAGT
* * *
62631259 TATCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAAGT
* * * *
62631310 TATCGGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAA-T
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAGT
* * * *
62631359 TATCCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
62631405 TCACAATAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 78 0.63
50 7 0.06
51 38 0.31
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (50 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAGT
Found at i:62631392 original size:100 final size:100
Alignment explanation
Indices: 62631210--62631402 Score: 305
Period size: 100 Copynumber: 1.9 Consensus size: 100
62631200 TAGACAAGGC
* * * *
62631210 TATCTGGTCCGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAGTATCTGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAGTATCCGATACACGTAG
*
62631275 TAGCCTACACTTAGTACTACACATGTGATCGAAGT
66 TAGCCTACACTTAGTACTACACACGTGATCGAAGT
* * *
62631310 TATCGGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGATACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAGTATCCGATACACGTAG
*
62631375 TAGCCTGCACTTAGTACTACACACGTGA
66 TAGCCTACACTTAGTACTACACACGTGA
62631403 CCTCACAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAGTATCCGATACACGTAG
TAGCCTACACTTAGTACTACACACGTGATCGAAGT
Found at i:62631670 original size:27 final size:27
Alignment explanation
Indices: 62631630--62631683 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
62631620 AGGTACAACC
* *
62631630 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
62631657 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
62631684 TCATATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:62638345 original size:28 final size:28
Alignment explanation
Indices: 62638280--62638430 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
62638270 GAGATTGGCG
* * * *
62638280 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
62638309 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
62638337 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
62638365 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
62638393 CTAAGTGTGCTAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
62638420 CTGAGTGTGCG
1 CTAAGTGTGCG
62638431 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.20
28 75 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:62640516 original size:49 final size:49
Alignment explanation
Indices: 62640460--62640691 Score: 304
Period size: 49 Copynumber: 4.7 Consensus size: 49
62640450 CTGGTAGGAA
62640460 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATTCGG-TACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTA-TCGGATACACG
* ** *
62640509 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCGGATACACG
* * * * * *
62640559 TAGTAGCCTGCACTTAGCACTACACAAGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCGGATACACG
* *
62640610 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCGGATACACG
*
62640659 TAGTAGCCTGCATTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
62640692 TCACAATAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
49 76 0.49
50 43 0.28
51 37 0.24
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCGGATACACG
Found at i:62644568 original size:40 final size:39
Alignment explanation
Indices: 62644470--62644692 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
62644460 TCCTCGTTCA
* * * * *
62644470 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
62644509 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
62644548 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
62644588 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
62644628 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
62644669 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
62644693 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:62644692 original size:120 final size:119
Alignment explanation
Indices: 62644470--62644692 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
62644460 TCCTCGTTCA
* * * *
62644470 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
62644535 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
62644589 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
62644653 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
62644693 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:62652478 original size:40 final size:40
Alignment explanation
Indices: 62652380--62652642 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
62652370 TCCTCGTTCA
* * * * *
62652380 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
62652419 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62652459 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62652499 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
62652539 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
62652579 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
62652619 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
62652643 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:62657607 original size:16 final size:17
Alignment explanation
Indices: 62657588--62657620 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62657578 TGAATGCAAA
62657588 TAAAAC-TAAAGAAAAT
1 TAAAACATAAAGAAAAT
*
62657604 TAAAACATAATGAAAAT
1 TAAAACATAAAGAAAAT
62657621 GCTTGTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAAACATAAAGAAAAT
Found at i:62661757 original size:17 final size:17
Alignment explanation
Indices: 62661735--62661768 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62661725 GTTTGAACTC
62661735 TTTTATGATCTTACCTA
1 TTTTATGATCTTACCTA
62661752 TTTTATGATCTTACCTA
1 TTTTATGATCTTACCTA
62661769 AGCTAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTTATGATCTTACCTA
Found at i:62664591 original size:20 final size:20
Alignment explanation
Indices: 62664566--62664603 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
62664556 AAATGCTAAC
62664566 AGAGGCACCAAAGTGCAAAT
1 AGAGGCACCAAAGTGCAAAT
62664586 AGAGGCACCAAAGTGCAA
1 AGAGGCACCAAAGTGCAA
62664604 TCCCGTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.26, T:0.08
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAT
Found at i:62667237 original size:26 final size:25
Alignment explanation
Indices: 62667176--62667239 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
62667166 TTTCTGACAA
*
62667176 TTCTTTT-CTCT-TATTCTTTTCTC
1 TTCTTTTCCTCTATATTCTCTTCTC
* * *
62667199 CTCTTTTCATCTATTTTCTCTTCTTC
1 TTCTTTTCCTCTATATTCTCTTC-TC
62667225 TTCTTTTCCTCTATA
1 TTCTTTTCCTCTATA
62667240 GCCGAATCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 6 0.19
24 3 0.10
25 8 0.26
26 14 0.45
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTTCCTCTATATTCTCTTCTC
Found at i:62668393 original size:28 final size:28
Alignment explanation
Indices: 62668350--62668413 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
62668340 GGAGGAAGCA
**
62668350 TTCTGGTGGCTTTGCCACAAATATCTGT
1 TTCTGGTGGCCCTGCCACAAATATCTGT
*
62668378 TTCTGGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCCCTGCCACAAATATCTGT
*
62668406 ATCTGGTG
1 TTCTGGTG
62668414 ACTCTATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (28 bp):
TTCTGGTGGCCCTGCCACAAATATCTGT
Found at i:62668424 original size:28 final size:28
Alignment explanation
Indices: 62668364--62668426 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
62668354 GGTGGCTTTG
* * * *
62668364 CCACAAATATCTGTTTCTGGTGGCCCTG
1 CCACAATTATCTGTATCTGGTGACCCTA
*
62668392 CCACAATTATCTGTATCTGGTGACTCTA
1 CCACAATTATCTGTATCTGGTGACCCTA
*
62668420 TCACAAT
1 CCACAAT
62668427 ATTCGTTCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (28 bp):
CCACAATTATCTGTATCTGGTGACCCTA
Found at i:62673758 original size:24 final size:26
Alignment explanation
Indices: 62673718--62673765 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
62673708 TGTTGTTTGA
62673718 TAAAATGAAATTTTAAGTTATAAATT
1 TAAAATGAAATTTTAAGTTATAAATT
62673744 TAAAAT-AAA-TTTAAGTTATAAA
1 TAAAATGAAATTTTAAGTTATAAA
62673766 AAATAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.59
25 3 0.14
26 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (26 bp):
TAAAATGAAATTTTAAGTTATAAATT
Found at i:62673764 original size:13 final size:13
Alignment explanation
Indices: 62673729--62673765 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
62673719 AAAATGAAAT
62673729 TTTAAGTTATAAA
1 TTTAAGTTATAAA
*
62673742 TTTAA--AATAAA
1 TTTAAGTTATAAA
62673753 TTTAAGTTATAAA
1 TTTAAGTTATAAA
62673766 AAATAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (13 bp):
TTTAAGTTATAAA
Found at i:62680962 original size:43 final size:44
Alignment explanation
Indices: 62680870--62680962 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 44
62680860 ATGTTGTGGT
*
62680870 GTTTGTAGCTAGAAGCGCTGCAAAAGATCATGTTCTTCAGTGGC
1 GTTTGTAGCTAGAAGCGCTGCAAAAGATCATGTTCTTCAGCGGC
* * *
62680914 ATTTGTAG-TAGAAGCG-TCGCTAAAGCTCATGTTCTAT-AGCGGC
1 GTTTGTAGCTAGAAGCGCT-GCAAAAGATCATGTTCT-TCAGCGGC
62680957 GTTTGT
1 GTTTGT
62680963 GGAAAAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 1 0.02
43 33 0.79
44 8 0.19
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (44 bp):
GTTTGTAGCTAGAAGCGCTGCAAAAGATCATGTTCTTCAGCGGC
Found at i:62686082 original size:37 final size:36
Alignment explanation
Indices: 62686040--62686116 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 36
62686030 TTTAATCTTG
*
62686040 TTCTGTAGCTTATAGCACTCAGATTTAATATGTCCT
1 TTCTGTAGCTTATAGCACTCAGATTTAATATGCCCT
*
62686076 ATTCTGTAGCTTATAGCATTCAGATTTAATATGCCCT
1 -TTCTGTAGCTTATAGCACTCAGATTTAATATGCCCT
62686113 TTCT
1 TTCT
62686117 TCTTACAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.11
37 34 0.89
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (36 bp):
TTCTGTAGCTTATAGCACTCAGATTTAATATGCCCT
Found at i:62687046 original size:95 final size:96
Alignment explanation
Indices: 62686886--62687073 Score: 288
Period size: 95 Copynumber: 2.0 Consensus size: 96
62686876 GATACCAATA
* * * *
62686886 TGTGAAGAAATAAAATAAAATAAAATAAAGAATACACAGATTTTATGTGGAAACCCTTTCAGG-A
1 TGTGAAAAAATAAAATAAAATAAAATAAAGAACACACAGATTTTACGTGAAAACCCTTTCAGGAA
62686950 AAAAACCACGAGCAAAAGAGAAGAAAATATG
66 AAAAACCACGAGCAAAAGAGAAGAAAATATG
* *
62686981 TGTGAAAAAATGAAATAAAATAAAATAAAGAACACACAGATTTTACGTGAAAACCCTTTCGGGAA
1 TGTGAAAAAATAAAATAAAATAAAATAAAGAACACACAGATTTTACGTGAAAACCCTTTCAGGAA
* * *
62687046 AAAAACCACGGGCAGAGGAGAAGAAAAT
66 AAAAACCACGAGCAAAAGAGAAGAAAAT
62687074 TCAATATGTC
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 57 0.69
96 26 0.31
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (96 bp):
TGTGAAAAAATAAAATAAAATAAAATAAAGAACACACAGATTTTACGTGAAAACCCTTTCAGGAA
AAAAACCACGAGCAAAAGAGAAGAAAATATG
Found at i:62689419 original size:41 final size:41
Alignment explanation
Indices: 62689374--62689519 Score: 177
Period size: 41 Copynumber: 3.6 Consensus size: 41
62689364 CAGTGACATT
* * *
62689374 CAGGCTTTATGTCGATGAATTATATCAGGCTTATTGCCTAG
1 CAGGCTTTATGCCGATGTATTATTTCAGGCTTATTGCCTAG
*
62689415 CAGGC-TTATTGCCGATGTATTATTTCAAGCTTATTGCCTAG
1 CAGGCTTTA-TGCCGATGTATTATTTCAGGCTTATTGCCTAG
* * *
62689456 CAGGCTTTATGCCGGTGTATTATTTCAGGCCTATTGCATAG
1 CAGGCTTTATGCCGATGTATTATTTCAGGCTTATTGCCTAG
* * * *
62689497 TAGGCTCTGTGCCGGTGTATTAT
1 CAGGCTTTATGCCGATGTATTAT
62689520 ACTAGGCTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 3 0.03
41 86 0.93
42 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
CAGGCTTTATGCCGATGTATTATTTCAGGCTTATTGCCTAG
Found at i:62690548 original size:22 final size:22
Alignment explanation
Indices: 62690523--62690593 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
62690513 TAAAATGAAG
62690523 TTGTATATTTAGTATATGAGGT
1 TTGTATATTTAGTATATGAGGT
* * * *
62690545 TTGTGTA-TTCG--GATGAAG-
1 TTGTATATTTAGTATATGAGGT
62690563 TTGTATATTTAGTATATGAGGT
1 TTGTATATTTAGTATATGAGGT
*
62690585 TTGTGTATT
1 TTGTATATT
62690594 CGGATTGGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
18 6 0.17
19 8 0.22
21 8 0.22
22 14 0.39
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.49
Consensus pattern (22 bp):
TTGTATATTTAGTATATGAGGT
Found at i:62690561 original size:40 final size:40
Alignment explanation
Indices: 62690517--62690598 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
62690507 TTGTCATAAA
62690517 ATGAAGTTGTATATTTAGTATATGAGGTTTGTGTATTCGG
1 ATGAAGTTGTATATTTAGTATATGAGGTTTGTGTATTCGG
62690557 ATGAAGTTGTATATTTAGTATATGAGGTTTGTGTATTCGG
1 ATGAAGTTGTATATTTAGTATATGAGGTTTGTGTATTCGG
62690597 AT
1 AT
62690599 TGGTAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.45
Consensus pattern (40 bp):
ATGAAGTTGTATATTTAGTATATGAGGTTTGTGTATTCGG
Found at i:62692730 original size:24 final size:25
Alignment explanation
Indices: 62692677--62692730 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
62692667 TGGGAAAGAA
62692677 AAAAAAATAAGTTAGGGATTTGGGG
1 AAAAAAATAAGTTAGGGATTTGGGG
*
62692702 AAAAAACTAAGTTAGGGATTTGGGG
1 AAAAAAATAAGTTAGGGATTTGGGG
62692727 AAAA
1 AAAA
62692731 CGATTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (25 bp):
AAAAAAATAAGTTAGGGATTTGGGG
Found at i:62695182 original size:62 final size:59
Alignment explanation
Indices: 62695073--62695186 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 59
62695063 AATCACTTTA
* * * *
62695073 TTATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATACAAAATC
1 TTATTAAATTAATAAAATATTTATCAAGAGAAACATTAAATTAAATTTAATACAAAATC
*
62695132 TTATTAAATTAATAAAATATTTATCTACAAGAGAAGCATTAAATTAAATTTAATA
1 TTATTAAATTAATAAAATATTTA--T-CAAGAGAAACATTAAATTAAATTTAATA
62695187 TTAAGATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 22 0.47
61 1 0.02
62 24 0.51
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.39
Consensus pattern (59 bp):
TTATTAAATTAATAAAATATTTATCAAGAGAAACATTAAATTAAATTTAATACAAAATC
Found at i:62695216 original size:20 final size:18
Alignment explanation
Indices: 62695169--62695217 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
62695159 CAAGAGAAGC
62695169 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
62695186 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
62695206 ATTAAATTAATA
1 ATTAAATTAATA
62695218 AATTACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:62699063 original size:43 final size:43
Alignment explanation
Indices: 62698918--62699094 Score: 203
Period size: 43 Copynumber: 4.1 Consensus size: 43
62698908 AACATGCTAA
** * * * * **
62698918 ATAGAACATGACCTTTAGATGCACTTCTACCATAAACGCAACT
1 ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGCCGCT
* ** * *
62698961 ATAGAACATGACCTTTAGCGGCG-ATTCCCTACAAACGTCGCT
1 ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGCCGCT
*
62699003 ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAATGCCGCT
1 ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGCCGCT
* *
62699046 ATAGAACATGACATTTAGTGGCGCTTTTACTAAAAACGCCGCT
1 ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGCCGCT
62699089 ATAGAA
1 ATAGAA
62699095 TTGAGCTTTA
Statistics
Matches: 112, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 33 0.29
43 79 0.71
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
ATAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGCCGCT
Found at i:62703126 original size:50 final size:50
Alignment explanation
Indices: 62703002--62703239 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
62702992 AGTCGAAGCT
* * * *
62703002 ATCTGATACGCATAATAGCCTGCACTTAGTACTACACATGTGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * *
62703051 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAGGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * * *
62703101 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CC
* * * * * *
62703152 AT-TGAGTACGCATAGTAGCCTGCATTTAGTACTACACATGCGA-GTAAAC
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * *
62703201 AGTATGGTACATGTAGTAGCCTGCACTTAGTACTACACA
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
62703240 CGTGTACTTA
Statistics
Matches: 158, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
49 42 0.27
50 79 0.50
51 37 0.23
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
Found at i:62703217 original size:101 final size:99
Alignment explanation
Indices: 62703017--62703243 Score: 271
Period size: 101 Copynumber: 2.3 Consensus size: 99
62703007 ATACGCATAA
* *
62703017 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCTGGTACACGTAGTAGCCTGCACTTAGTA
1 TAGCCTGCACTTAGTACTACACACGTGACCAACAATCTGGTACACATAGTAGCCTGCACTTAGTA
* * * *
62703082 CTACACAGGTGACCTCACCATCTGATACACGTAG
66 CTACACAGGCGACCTAAACATATGATACACGTAG
* * *
62703116 TAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-AT-TGAGTACGCATAGTAGCCTGCATTT
1 TAGCCTGCACTTAGTACTACACACGTGA-CCAA--CAATCTG-GTACACATAGTAGCCTGCACTT
* * * *
62703179 AGTACTACACATGCGA-GTAAACAGTATGGTACATGTAG
62 AGTACTACACAGGCGACCTAAACA-TATGATACACGTAG
62703217 TAGCCTGCACTTAGTACTACACACGTG
1 TAGCCTGCACTTAGTACTACACACGTG
62703244 TACTTACAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
99 27 0.25
100 9 0.08
101 73 0.66
102 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (99 bp):
TAGCCTGCACTTAGTACTACACACGTGACCAACAATCTGGTACACATAGTAGCCTGCACTTAGTA
CTACACAGGCGACCTAAACATATGATACACGTAG
Found at i:62705191 original size:42 final size:42
Alignment explanation
Indices: 62705144--62705230 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
62705134 TACGCTCATA
*
62705144 TGTGAATCCGTGTGACACACACGACCAATAGACACGCCCGTG
1 TGTGAATCCGTGTGACACACACGACCAATAGACACACCCGTG
* *
62705186 TGTGAATCCGTGTGACACACATGGCCAATAGACACACCCGTG
1 TGTGAATCCGTGTGACACACACGACCAATAGACACACCCGTG
62705228 TGT
1 TGT
62705231 CTAAGCCGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.20
Consensus pattern (42 bp):
TGTGAATCCGTGTGACACACACGACCAATAGACACACCCGTG
Found at i:62706329 original size:23 final size:23
Alignment explanation
Indices: 62706245--62706330 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 23
62706235 GCTGATAAAT
*
62706245 AGTAAGCTC-TATTGAGC-AAAAC
1 AGTAAGCTCTTA-CGAGCTAAAAC
* * * *
62706267 AATAAGCTCTTTCGAGCTGAATC
1 AGTAAGCTCTTACGAGCTAAAAC
* ** *
62706290 GGTAAGCTCCAATGAGCTAAAAC
1 AGTAAGCTCTTACGAGCTAAAAC
62706313 AGTAAGCTCTTACGAGCT
1 AGTAAGCTCTTACGAGCT
62706331 GTGGTGAGTT
Statistics
Matches: 45, Mismatches: 17, Indels: 3
0.69 0.26 0.05
Matches are distributed among these distances:
22 12 0.27
23 33 0.73
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (23 bp):
AGTAAGCTCTTACGAGCTAAAAC
Found at i:62710562 original size:9 final size:9
Alignment explanation
Indices: 62710548--62710768 Score: 130
Period size: 9 Copynumber: 25.3 Consensus size: 9
62710538 TAAGTATAAT
62710548 TAAGTTATG
1 TAAGTTATG
62710557 TAAGTTATG
1 TAAGTTATG
62710566 TAAGTTATG
1 TAAGTTATG
62710575 TAAGTTATG
1 TAAGTTATG
* * *
62710584 ATATGATATA
1 -TAAGTTATG
* *
62710594 T-ATTTATA
1 TAAGTTATG
62710602 TAAGTTATG
1 TAAGTTATG
*
62710611 TAAGTAATG
1 TAAGTTATG
*
62710620 -ACATTTATG
1 TA-AGTTATG
*
62710629 -ATA-TGAT-
1 TA-AGTTATG
62710636 TATA-TTCATG
1 TA-AGTT-ATG
62710646 T-A-TTATG
1 TAAGTTATG
62710653 TAAGTTATG
1 TAAGTTATG
62710662 TAAGTTATG
1 TAAGTTATG
* * *
62710671 ATATGATATA
1 -TAAGTTATG
62710681 T-A-TATATG
1 TAAGT-TATG
62710689 TAAGTTATG
1 TAAGTTATG
62710698 TAAGTTATG
1 TAAGTTATG
*
62710707 TATGTTATG
1 TAAGTTATG
*
62710716 TGAGTTATG
1 TAAGTTATG
62710725 TAAGTTATG
1 TAAGTTATG
*
62710734 ATAA-TT-TA
1 -TAAGTTATG
*
62710742 T-A--TATT
1 TAAGTTATG
62710748 TAAGTTATG
1 TAAGTTATG
62710757 TAAGTTATG
1 TAAGTTATG
62710766 TAA
1 TAA
62710769 TTTTAAAGAA
Statistics
Matches: 168, Mismatches: 27, Indels: 34
0.73 0.12 0.15
Matches are distributed among these distances:
5 1 0.01
6 3 0.02
7 6 0.04
8 22 0.13
9 119 0.71
10 17 0.10
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:62710606 original size:36 final size:36
Alignment explanation
Indices: 62710561--62710768 Score: 149
Period size: 36 Copynumber: 5.5 Consensus size: 36
62710551 GTTATGTAAG
62710561 TTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGTAAGTTATGATATGATATATAT
*
62710597 TTATATAAGTTATGTAAGTAATGACATTTATGATATGATTATATTCAT
1 TTATGTAAGTTA--T--GTAA-G----TTATGATATGA-TATA-T-AT
*
62710645 GTATTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTA---TGTAAGTTATGTAAGTTATGATATGATATATAT
* * * *
62710684 ATATGTAAGTTATGTAAGTTATG-TATGTTATGTGAG
1 TTATGTAAGTTATGTAAGTTATGATATGATATAT-AT
* *
62710720 TTATGTAAGTTATGATAA-TT-T-ATAT-ATTTA-AG
1 TTATGTAAGTTATG-TAAGTTATGATATGATATATAT
62710752 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
62710769 TTTTAAAGAA
Statistics
Matches: 143, Mismatches: 11, Indels: 41
0.73 0.06 0.21
Matches are distributed among these distances:
31 3 0.02
32 16 0.11
34 2 0.01
35 12 0.08
36 47 0.33
37 3 0.02
38 1 0.01
39 4 0.03
40 5 0.03
41 5 0.03
42 11 0.08
45 11 0.08
46 5 0.03
47 5 0.03
48 4 0.03
49 1 0.01
51 8 0.06
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.47
Consensus pattern (36 bp):
TTATGTAAGTTATGTAAGTTATGATATGATATATAT
Found at i:62710608 original size:45 final size:45
Alignment explanation
Indices: 62710552--62710715 Score: 237
Period size: 45 Copynumber: 3.7 Consensus size: 45
62710542 TATAATTAAG
62710552 TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
* * *
62710597 TTATATAAGTTATGTAAGTAATG-ACATTTATGATATGAT-TATAT
1 TTATGTAAGTTATGTAAGTTATGTA-AGTTATGATATGATATATAT
*
62710641 TCATGT-A-TTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
* *
62710684 ATATGTAAGTTATGTAAGTTATGTATGTTATG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATG
62710716 TGAGTTATGT
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
42 26 0.25
43 11 0.11
44 11 0.11
45 56 0.54
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (45 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
Found at i:62710722 original size:63 final size:59
Alignment explanation
Indices: 62710648--62710767 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
62710638 TATTCATGTA
62710648 TTATGTAAGTTATGTAAGTTATGATATGATATATATATATGTAAGTTATGTAAGTTATGTATG
1 TTATGTAAGTTATGTAAGTTATGATA--AT-T-TATATATGTAAGTTATGTAAGTTATGTATG
* *
62710711 TTATGTGAGTTATGTAAGTTATGATAATTTATATATTTAAGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGATAATTTATATATGTAAGTTATGTAAGTTATGTA
62710768 ATTTTAAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 27 0.49
60 1 0.02
61 2 0.04
63 25 0.45
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (59 bp):
TTATGTAAGTTATGTAAGTTATGATAATTTATATATGTAAGTTATGTAAGTTATGTATG
Found at i:62712525 original size:19 final size:19
Alignment explanation
Indices: 62712498--62712537 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
62712488 TTGGGATTTT
* *
62712498 GATTTGGGGAAAATTTAGG
1 GATTAGGGGAAAATTGAGG
*
62712517 GATTAGGGGAGAATTGAGG
1 GATTAGGGGAAAATTGAGG
62712536 GA
1 GA
62712538 AATGGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (19 bp):
GATTAGGGGAAAATTGAGG
Found at i:62712829 original size:122 final size:123
Alignment explanation
Indices: 62712647--62712890 Score: 339
Period size: 122 Copynumber: 2.0 Consensus size: 123
62712637 GACCGTTGTA
* * * * * *
62712647 GTGTTTTTTAAAAAGTGACGCTAGTGCTGATATATTGTGGCATTTATAAGCTAGCGCCGCTAATT
1 GTGTTTTTAAAAAAGTGACACTAATACTGATATATTGCGGCATTTATAAGCTAGCACCGCTAATT
* * *
62712712 CCACTAAAGGGTCA-TCTAAAACAACGACGTTTTGATTCAATTAAAA-ATTTTTTTGCG
66 CCACTAAAGAGCCACT-TAAAACAACGACGTTTTCATTCAATTAAAACATTTTTTTGCG
* * **
62712769 GTGTTTTTAAAAAAGTGCCACTAATACTGATCTATTGCGGTGTTTATAAGCTAGCACCGCTAATT
1 GTGTTTTTAAAAAAGTGACACTAATACTGATATATTGCGGCATTTATAAGCTAGCACCGCTAATT
*
62712834 CCACTAAAGAGCCACTTAAAACGACGACGTTTTCATTCAATTAAAACATTTTTTTGC
66 CCACTAAAGAGCCACTTAAAACAACGACGTTTTCATTCAATTAAAACATTTTTTTGC
62712891 AGCATTTTGC
Statistics
Matches: 106, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
122 95 0.90
123 11 0.10
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (123 bp):
GTGTTTTTAAAAAAGTGACACTAATACTGATATATTGCGGCATTTATAAGCTAGCACCGCTAATT
CCACTAAAGAGCCACTTAAAACAACGACGTTTTCATTCAATTAAAACATTTTTTTGCG
Found at i:62713476 original size:7 final size:7
Alignment explanation
Indices: 62713449--62713491 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
62713439 CAAATTTTAT
62713449 CCCTAAA
1 CCCTAAA
* *
62713456 CCTTACA
1 CCCTAAA
*
62713463 CCTTAAA
1 CCCTAAA
62713470 CCCTAAA
1 CCCTAAA
62713477 CCCTAAA
1 CCCTAAA
*
62713484 CCATAAA
1 CCCTAAA
62713491 C
1 C
62713492 ATATACACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:62713490 original size:21 final size:21
Alignment explanation
Indices: 62713449--62713491 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62713439 CAAATTTTAT
* * *
62713449 CCCTAAACCTTACACCTTAAA
1 CCCTAAACCCTAAACCATAAA
62713470 CCCTAAACCCTAAACCATAAA
1 CCCTAAACCCTAAACCATAAA
62713491 C
1 C
62713492 ATATACACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (21 bp):
CCCTAAACCCTAAACCATAAA
Found at i:62713655 original size:12 final size:13
Alignment explanation
Indices: 62713625--62713657 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
62713615 ATCAAAATCT
62713625 CTAACCCTAAACC
1 CTAACCCTAAACC
*
62713638 CCAACCCT-AACC
1 CTAACCCTAAACC
62713650 CTAACCCT
1 CTAACCCT
62713658 TAAAACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (13 bp):
CTAACCCTAAACC
Found at i:62713711 original size:22 final size:22
Alignment explanation
Indices: 62713661--62713722 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
62713651 TAACCCTTAA
*
62713661 AACCAT-AAACACTAAGA-CCCT
1 AACCATAAAACACTAA-ACCCCC
*
62713682 AACTATAAAACACTAAACCCCC
1 AACCATAAAACACTAAACCCCC
* *
62713704 AACCATAAAATAATAAACC
1 AACCATAAAACACTAAACC
62713723 ATAACCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.53, C:0.31, G:0.02, T:0.15
Consensus pattern (22 bp):
AACCATAAAACACTAAACCCCC
Found at i:62713792 original size:15 final size:15
Alignment explanation
Indices: 62713759--62713797 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
62713749 ACTCAAATTA
*
62713759 CTAAA-CATTAAGCC
1 CTAAACCATAAAGCC
*
62713773 ATAAACCATAAAGCC
1 CTAAACCATAAAGCC
62713788 CTAAACCATA
1 CTAAACCATA
62713798 GACTTAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.18
Consensus pattern (15 bp):
CTAAACCATAAAGCC
Found at i:62713955 original size:41 final size:41
Alignment explanation
Indices: 62713861--62713972 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
62713851 GTATTTTTAT
** *
62713861 AACGCCGCTACTGCTTGACCTTTTGCGACG---TTATCTTA
1 AACGCCGCTACTGCTTGACCTTTTGCGGTGTTTTTATCATA
*
62713899 AATGCCGCTACTGCTTGACCTTTTGCGGTGTTTTTATCATA
1 AACGCCGCTACTGCTTGACCTTTTGCGGTGTTTTTATCATA
* * *
62713940 AACGCTGCTAATGCTTAACCTTTTGCGGTGTTT
1 AACGCCGCTACTGCTTGACCTTTTGCGGTGTTT
62713973 ATGACTGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 27 0.43
41 36 0.57
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (41 bp):
AACGCCGCTACTGCTTGACCTTTTGCGGTGTTTTTATCATA
Found at i:62724187 original size:104 final size:104
Alignment explanation
Indices: 62724032--62724500 Score: 528
Period size: 104 Copynumber: 4.5 Consensus size: 104
62724022 AAAAGAACTT
* * * * ** * * *
62724032 AGGTTGCGAGCGTAAATCAACTAACCTTTAATCATTAGATCAGAACATAGGT-CAGTGAATTGTT
1 AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGTCCA-TGAACTATT
* *
62724096 TCGAAGTTGCGAGCTTAACTCGGTTAACTCAAATAACTGG
65 TCGAAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGG
* * ** *
62724136 AGGTTACGAGCTTAACTCAACCAACCTTTAATCATCAGTTGGGAACGTAGGTCTGTGAGCTATTT
1 AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGTCCATGAACTATTT
* * * *
62724201 GGAAGTTGTGAGCTTAACTCGGCTAACTTAAATAACTGG
66 CGAAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGG
* ** * *
62724240 AGGTTGCGAGCTTAACTCAGCTAACCTTTAATCATCAACTGGGAACGTAGGTCCACGAGCTATTT
1 AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGTCCATGAACTATTT
* * *
62724305 CGGAGTTGTGAGCTTAACTCAGTTAACTCAAATAACTGG
66 CGAAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGG
* ** * *
62724344 AGGTTGCAAATTTAACTCAACTAACCTTTAATCATCAATTGGGAACGTAGGTCCA-CAAGCTATT
1 AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGTCCATGAA-CTATT
* * *
62724408 TCGGAGTTGCGGGCTTAACTCAGCTAACTCAAAATAATTGG
65 TCGAAGTTGCGAGCTTAACTCAGCTAACTC-AAATAACTGG
* * * * *
62724449 AGGTTACAAGCTTAACTTATCTAACCCTTAATCATCAGTTGGGAACGTAGGT
1 AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGT
62724501 GTAATGCCCC
Statistics
Matches: 313, Mismatches: 49, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
103 1 0.00
104 258 0.82
105 54 0.17
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (104 bp):
AGGTTGCGAGCTTAACTCAACTAACCTTTAATCATCAGTTGGGAACGTAGGTCCATGAACTATTT
CGAAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGG
Found at i:62724342 original size:208 final size:207
Alignment explanation
Indices: 62723983--62724500 Score: 583
Period size: 208 Copynumber: 2.5 Consensus size: 207
62723973 TTTAAATCAG
* * * * * * *
62723983 CGAGCTATTTGGAAGTTGTGATCTTAAATCAGTTAAGTTAAAAGAACT-TAGGTTGCGAGCGTAA
1 CGAGCTATTTGGAAGTTGTGAGCTTAACTCAGCTAACTT-AAATAACTGGAGGTTGCGAGCTTAA
* * ** * * * *
62724047 ATCAACTAACCTTTAATCATTAGATCAGAACATAGGTCAGTGAATTGTTTCGAAGTTGCGAGCTT
65 CTCAACTAACCTTTAATCATCA-ATGGGAACGTAGGTCAGCGAACTATTTCGAAGTTGCGAGCTT
* * * *
62724112 AACTCGGTTAACTCAAATAACTGGAGGTTACGAGCTTAACTCAACCAACCTTTAATCATCAGTTG
129 AACTCAGTTAACTCAAATAACTGGAGGTTACAAACTTAACTCAACCAACCTTTAATCATCAATTG
**
62724177 GGAACGTAGGTCTG
194 GGAACGTAGGTCCA
* *
62724191 TGAGCTATTTGGAAGTTGTGAGCTTAACTCGGCTAACTTAAATAACTGGAGGTTGCGAGCTTAAC
1 CGAGCTATTTGGAAGTTGTGAGCTTAACTCAGCTAACTTAAATAACTGGAGGTTGCGAGCTTAAC
* * * *
62724256 TCAGCTAACCTTTAATCATCAACTGGGAACGTAGGTCCA-CGAGCTATTTCGGAGTTGTGAGCTT
66 TCAACTAACCTTTAATCATCAA-TGGGAACGTAGGT-CAGCGAACTATTTCGAAGTTGCGAGCTT
* * *
62724320 AACTCAGTTAACTCAAATAACTGGAGGTTGCAAATTTAACTCAACTAACCTTTAATCATCAATTG
129 AACTCAGTTAACTCAAATAACTGGAGGTTACAAACTTAACTCAACCAACCTTTAATCATCAATTG
62724385 GGAACGTAGGTCCA
194 GGAACGTAGGTCCA
* * * * * * *
62724399 CAAGCTATTTCGG-AGTTGCGGGCTTAACTCAGCTAACTCAAAATAATTGGAGGTTACAAGCTTA
1 CGAGCTATTT-GGAAGTTGTGAGCTTAACTCAGCTAACT-TAAATAACTGGAGGTTGCGAGCTTA
* * * *
62724463 ACTTATCTAACCCTTAATCATCAGTTGGGAACGTAGGT
64 ACTCAACTAACCTTTAATCATCA-ATGGGAACGTAGGT
62724501 GTAATGCCCC
Statistics
Matches: 261, Mismatches: 43, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
207 8 0.03
208 195 0.75
209 58 0.22
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (207 bp):
CGAGCTATTTGGAAGTTGTGAGCTTAACTCAGCTAACTTAAATAACTGGAGGTTGCGAGCTTAAC
TCAACTAACCTTTAATCATCAATGGGAACGTAGGTCAGCGAACTATTTCGAAGTTGCGAGCTTAA
CTCAGTTAACTCAAATAACTGGAGGTTACAAACTTAACTCAACCAACCTTTAATCATCAATTGGG
AACGTAGGTCCA
Found at i:62726165 original size:43 final size:43
Alignment explanation
Indices: 62726098--62726264 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
62726088 AGCTCATACT
* * * *
62726098 ATGCC-ATGTCCCAGATATGATCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCA
* * * * * *
62726140 GTGCCAATGTCCCAGCCATGGTCTTACACGAAATCATATAACA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCA
62726183 ATGCCAATGTCCCA-ACCATGGTCTTACATGTAATCACA-ATACA
1 ATGCCAATGTCCCAGA-CATGGTCTTACATGTAATCACATAT-CA
*
62726226 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
62726265 CTCGGTAATT
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
42 5 0.05
43 97 0.94
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCA
Found at i:62728974 original size:42 final size:43
Alignment explanation
Indices: 62728837--62729030 Score: 250
Period size: 43 Copynumber: 4.6 Consensus size: 43
62728827 TTATGTAAAA
* * * * *
62728837 AAACGTCGTTAAAGAACATGACCGTTAGCGACGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
62728880 AAACGCTGCTAAAGAACATGGCCTTTAGCGGCAG-TTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGC-GCTTTTCCCAC
**
62728923 AAACGCCGCTAAAGAACATGATATTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
62728965 AAACGCCGCTAAAGAACTTGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
62729008 AAACGCCGCTATAGAACA-GACCT
1 AAACGCCGCTAAAGAACATGACCT
62729031 GGAAAAAACG
Statistics
Matches: 131, Mismatches: 17, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
42 44 0.34
43 86 0.66
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:62729003 original size:85 final size:86
Alignment explanation
Indices: 62728837--62729025 Score: 247
Period size: 85 Copynumber: 2.2 Consensus size: 86
62728827 TTATGTAAAA
* * * * *
62728837 AAACGTCGTTAAAGAACATGACCGTTAGCGACGCTTTTACCACAAACGCTGCTAAAGAACATGGC
1 AAACGCCGCTAAAGAACATGACAGTTAGCGACGCTTTTACCACAAACGCCGCTAAAGAACATGAC
62728902 CTTTAGCGGCAGTTTTCCCAC
66 CTTTAGCGGCAGTTTTCCCAC
* * * * *
62728923 AAACGCCGCTAAAGAACATGATATTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGAACTTGAC
1 AAACGCCGCTAAAGAACATGACAGTTAGCGACGCTTTTACCACAAACGCCGCTAAAGAACATGAC
*
62728987 CTTTAGTGGC-GCTTTTCCCAC
66 CTTTAGCGGCAG-TTTTCCCAC
*
62729008 AAACGCCGCTATAGAACA
1 AAACGCCGCTAAAGAACA
62729026 GACCTGGAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
84 1 0.01
85 61 0.68
86 28 0.31
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACAGTTAGCGACGCTTTTACCACAAACGCCGCTAAAGAACATGAC
CTTTAGCGGCAGTTTTCCCAC
Found at i:62729107 original size:22 final size:24
Alignment explanation
Indices: 62729080--62729123 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
62729070 ATATTTTAAT
62729080 TAAATAATAT-TTAT-TTTTATGA
1 TAAATAATATATTATGTTTTATGA
*
62729102 TAAATATTATATTATGTTTTAT
1 TAAATAATATATTATGTTTTAT
62729124 TTTTGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATAATATATTATGTTTTATGA
Found at i:62733745 original size:16 final size:16
Alignment explanation
Indices: 62733724--62733775 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
62733714 TTTGGTTCGC
*
62733724 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
62733740 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
62733756 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
62733772 TGTA
1 TGTA
62733776 ATAGCCAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:62734033 original size:18 final size:17
Alignment explanation
Indices: 62734012--62734046 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
62734002 TTATTATTTA
62734012 ATATATTTTAATTAAAAT
1 ATATATTTTAA-TAAAAT
62734030 ATATATTTTAATAAAAT
1 ATATATTTTAATAAAAT
62734047 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTTTAATAAAAT
Found at i:62734180 original size:18 final size:17
Alignment explanation
Indices: 62734159--62734193 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
62734149 TTATTATTAA
62734159 ATATATTTTAATTAAAAT
1 ATATATTTTAA-TAAAAT
62734177 ATATATTTTAATAAAAT
1 ATATATTTTAATAAAAT
62734194 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTTTAATAAAAT
Found at i:62734205 original size:147 final size:149
Alignment explanation
Indices: 62733931--62734205 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
62733921 ATGATTATTG
*
62733931 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
62733996 ACATAATTATTATTTAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAATTAGC
62734061 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
62734080 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
62734143 ACATAATTATTATTAAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAATTA
62734206 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Done.