Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold27
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: 2789374
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 115785 characters in sequence are not A, C, G, or T
File 8 of 16
Found at i:1318660 original size:94 final size:94
Alignment explanation
Indices: 1318383--1318723 Score: 393
Period size: 94 Copynumber: 3.6 Consensus size: 94
1318373 GACACCTTCT
* * *
1318383 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGACGTTCTC-TCAT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTTC-T
* *
1318447 TTCACCTTTTAGTCC-CTAAAGAGTAGGACA
65 TTCACCTTTTAGTCCTC-AAAGAGCAGGACG
* * **
1318477 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTCC-AGTCCTCAAAGGGCATAACGCTCT-TTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTT-CT
1318540 TTCACCTTTTAGTCCTCAAAGAGCAGGACG
65 TTCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * *
1318570 CCTTTTAAAGCCCACACAAATTGGTGGCACTTCCTAATCCTCAAATAGTAGGACGCTCTCTTCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTTCTT
* *
1318635 TTACCCTTTAGTCCTCAAAGAGCAGGACG
66 TCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * *
1318664 CATTTTTCTTTTAAAGCCCACACGAGCTGGTGGCACCTTCTTAGTCCTCAAAGAGTAGGA
1 C------CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA
1318724 TGCCTTTTCC
Statistics
Matches: 211, Mismatches: 24, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
93 79 0.37
94 84 0.40
95 2 0.01
100 25 0.12
101 21 0.10
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (94 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTTCTT
TCACCTTTTAGTCCTCAAAGAGCAGGACG
Found at i:1318743 original size:62 final size:62
Alignment explanation
Indices: 1318641--1319047 Score: 475
Period size: 62 Copynumber: 6.6 Consensus size: 62
1318631 TCTTTTACCC
* * * *
1318641 TTTAGTCCTCAAAGAGCAGGACGCATTTTTCTTTT-AAAGCCCACACGAGCTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * *
1318702 TCTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTT-GAAGCCCACACAAGTTGGTGGCATCT
1 T-TTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * * *
1318764 TTCTGGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGTA-CT
1 TT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* *
1318826 CTGTAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTCGAAGCCCACACAAGTTGGTGGCACCT
1 -TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * * *
1318888 TTCTAATCCTTAAAGAGCAGGACACCTTTT-TTTTTACAAAGCCTACACAAGTTGGTGGCACCT
1 TT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-CAAAGCCCACACAAGTTGGTGGCACCT
* * * ** **
1318951 TTTAGTCATCAAAGAGCATGACACCTTTT-CTTTTCAAAGCCCACATGAGTTGGTGGCAGTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
*
1319012 TTTAGTCCACAAAGAGCAGGACGCCTTTTCCTTTTC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTC
1319048 TCCTTTGCCT
Statistics
Matches: 295, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
61 75 0.25
62 171 0.58
63 49 0.17
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
Found at i:1319207 original size:41 final size:41
Alignment explanation
Indices: 1319075--1319402 Score: 190
Period size: 41 Copynumber: 7.9 Consensus size: 41
1319065 CGGGACGCCT
** *
1319075 TTTCCTTTTCTCCTTTGCCCTCAAAGAGCATGACACA-TTTCA
1 TTTCCTTTT-TCCTTTATCCTCAAAGAGCAGGACACACTTT-A
* * *
1319117 TTTCCTTCTTTTCCCTTTTGTCCTCAAAGAACAGG----A-TTTT
1 TTTCC-T-TTTT-CC-TTTATCCTCAAAGAGCAGGACACACTTTA
* *
1319157 TTTCTTTTTTCCTTTATCCTCAAGGAGCAGGACACACTTTA
1 TTTCCTTTTTCCTTTATCCTCAAAGAGCAGGACACACTTTA
* * * **
1319198 TTTCCTTTTTTTTCCTTCTAGTTCTCAAACACCAGGATGCACTTTA
1 TTTCC---TTTTTCCTT-TA-TCCTCAAAGAGCAGGACACACTTTA
* * * * *
1319244 TTCTCCTTTTTCCTTTGTCCTTAAAAAGCGGGACA-AATTTAA
1 TT-TCCTTTTTCCTTTATCCTCAAAGAGCAGGACACACTTT-A
* * * * ** *
1319286 TTTCCTTTTTCCTTTGTCTTCAAAGGGCATGATGCATTTTA
1 TTTCCTTTTTCCTTTATCCTCAAAGAGCAGGACACACTTTA
* *
1319327 TTTCCTTTTTCCTTTGTCCTC-AAGTAGCAGGACCCA-TTTCA
1 TTTCCTTTTTCCTTTATCCTCAAAG-AGCAGGACACACTTT-A
*
1319368 TTCTCC-TTTTCCTTAATCCTCAAAGAGCAGGACAC
1 TT-TCCTTTTTCCTTTATCCTCAAAGAGCAGGACAC
1319403 CCCTTCCATT
Statistics
Matches: 223, Mismatches: 42, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
36 16 0.07
37 2 0.01
38 4 0.02
39 1 0.00
40 11 0.05
41 92 0.41
42 29 0.13
43 3 0.01
44 23 0.10
45 18 0.08
46 21 0.09
47 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (41 bp):
TTTCCTTTTTCCTTTATCCTCAAAGAGCAGGACACACTTTA
Found at i:1320010 original size:13 final size:13
Alignment explanation
Indices: 1319992--1320016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319982 TTATTTATTA
1319992 TATCGATACATTG
1 TATCGATACATTG
1320005 TATCGATACATT
1 TATCGATACATT
1320017 CTGGGTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1322447 original size:50 final size:50
Alignment explanation
Indices: 1322343--1322473 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
1322333 AAATTTTTAG
* * **
1322343 ATTTTTCATCTCGGAGATACTCTAACTCCGACTTTATTTCTAAAATATTG
1 ATTTTTCATCTCGGAGATACTCTAACCCCGACTTTATTTCTAAAACATCA
* *
1322393 ATTTTTCATCTCGGGGATACTCTAACCCCGGA-TTTGTTTC-ACAAACATCA
1 ATTTTTCATCTCGGAGATACTCTAACCCC-GACTTTATTTCTA-AAACATCA
* * *
1322443 ATTTTTCATAATCGAAGATACTCTAATCCCG
1 ATTTTTCAT-CTCGGAGATACTCTAACCCCG
1322474 TTATTTTTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 49 0.72
51 18 0.26
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (50 bp):
ATTTTTCATCTCGGAGATACTCTAACCCCGACTTTATTTCTAAAACATCA
Found at i:1322526 original size:79 final size:78
Alignment explanation
Indices: 1322459--1322873 Score: 358
Period size: 79 Copynumber: 5.2 Consensus size: 78
1322449 CATAATCGAA
* **
1322459 GATACTCTAATCCCGTTATTTTTGAGGGGATACTCCAACCCC-AGCCTTATTTTTAAAGCTTTGA
1 GATACTCCAA-CCCGTTATTTTCAAGGGGATACTCCAACCCCGA-CCTTATTTTTAAAGCTTTGA
1322523 TTTTCCACAATCGGG
64 TTTTCCACAATCGGG
* * ** * * *
1322538 GATACTCCAACTCCGTTATTTTCAAGGGGATACTCTAACCCTGATTTTATTTTCAAAACGTTGA-
1 GATACTCCAAC-CCGTTATTTTCAAGGGGATACTCCAACCCCGACCTTATTTTTAAAGCTTTGAT
* *
1322602 TTTCCTATAATCTGG
65 TTTCC-ACAATCGGG
* * * * *
1322617 GATGCTCCAACCCTGTTATTTCCAAGGGGATACTTCAACCCCGACCTTATTTCTAAAGCTTCGAT
1 GATACTCCAACCC-GTTATTTTCAAGGGGATACTCCAACCCCGACCTTATTTTTAAAGCTTTGAT
1322682 TTTCCACAATCGGG
65 TTTCCACAATCGGG
* * ** *
1322696 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTTTAAAAAGC--CG
1 GATACTCCAA-CCCGTTATTTTCAAGGGGATACTCCAACCCCGACCTTATTTTT--AAAGCTTTG
* *
1322759 A-TTTCCTATAATCAGG
63 ATTTTCC-ACAATCGGG
* * * ** * * *
1322775 GATGCTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTCTAGAA-CATCGA
1 GATACTCCAACCC-GTTATTTTCAAGGGGATACTCCAACCCCGACCTTATTTTTA-AAGCTTTGA
*
1322839 TTTTCCA-TATCAGGG
64 TTTTCCACAATC-GGG
*
1322854 GATACTCCAGCCCCGTTATT
1 GATACTCCA-ACCCGTTATT
1322874 ATCCTCAAAA
Statistics
Matches: 276, Mismatches: 44, Indels: 32
0.78 0.12 0.09
Matches are distributed among these distances:
77 2 0.01
78 21 0.08
79 231 0.84
80 17 0.06
81 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (78 bp):
GATACTCCAACCCGTTATTTTCAAGGGGATACTCCAACCCCGACCTTATTTTTAAAGCTTTGATT
TTCCACAATCGGG
Found at i:1322693 original size:158 final size:158
Alignment explanation
Indices: 1322483--1322873 Score: 563
Period size: 158 Copynumber: 2.5 Consensus size: 158
1322473 GTTATTTTTG
* *
1322483 AGGGGATACTCCAACCCC-AGCCTTATTTTTAAAGCTTTGATTTTCCACAATCGGGGATACTCCA
1 AGGGGATACTCCAACCCCGA-CCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCA
* * * **
1322547 ACTCCGTTATTTTCAAGGGGATACTCTAACCCTGATTTTATTTTCAAAACGTTGATTTCCTATAA
65 ACCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAAAGCCGATTTCCTATAA
*
1322612 TCTGGGATGCTCCAACCCTGTTATTTCCA
130 TCAGGGATGCTCCAACCCTGTTATTTCCA
*
1322641 AGGGGATACTTCAACCCCGACCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGACCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCAA
* *
1322706 CCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTTTAAAAAGCCGATTTCCTATAAT
66 CCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAAAGCCGATTTCCTATAAT
* *
1322771 CAGGGATGCTCCAACCCTGTTATTTTCG
131 CAGGGATGCTCCAACCCTGTTATTTCCA
* ** * *
1322799 AGGGGATACTCCAACCTCGATTTTATTTCTAGAA-CATCGATTTTCCA-TATCAGGGGATACTCC
1 AGGGGATACTCCAACCCCGACCTTATTTCTA-AAGCTTCGATTTTCCACAATC-GGGGATACTCC
*
1322862 AGCCCCGTTATT
64 AACCCCGTTATT
1322874 ATCCTCAAAA
Statistics
Matches: 210, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
157 3 0.01
158 204 0.97
159 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (158 bp):
AGGGGATACTCCAACCCCGACCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCAA
CCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAAAGCCGATTTCCTATAAT
CAGGGATGCTCCAACCCTGTTATTTCCA
Found at i:1324682 original size:29 final size:31
Alignment explanation
Indices: 1324616--1324685 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 31
1324606 GGTCAACATG
1324616 TAATTTTGAAAAATTTAAGGGGGTCAAAGCA
1 TAATTTTGAAAAATTTAAGGGGGTCAAAGCA
* * *
1324647 TAA-TTTGAAAAGTTT-A-GGGGTCCACGCA
1 TAATTTTGAAAAATTTAAGGGGGTCAAAGCA
1324675 TAATTTTGAAA
1 TAATTTTGAAA
1324686 TGTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.37
29 8 0.23
30 11 0.31
31 3 0.09
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (31 bp):
TAATTTTGAAAAATTTAAGGGGGTCAAAGCA
Found at i:1324723 original size:44 final size:43
Alignment explanation
Indices: 1324646--1324729 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
1324636 GGGTCAAAGC
*
1324646 ATAATTTGAAAAGTTTAGGGGTCCACGCATAATTTTGAAATGT
1 ATAATTTGAAAAGTTTAGGGGTCAACGCATAATTTTGAAATGT
* * **
1324689 ATAATTTTGAAAAGTTTGGGGGTCAATGTGTAATTTTGAAA
1 ATAA-TTTGAAAAGTTTAGGGGTCAACGCATAATTTTGAAA
1324730 AGTTCATGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 4 0.11
44 31 0.89
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.37
Consensus pattern (43 bp):
ATAATTTGAAAAGTTTAGGGGTCAACGCATAATTTTGAAATGT
Found at i:1324726 original size:29 final size:29
Alignment explanation
Indices: 1324684--1324796 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
1324674 ATAATTTTGA
* *
1324684 AATGTATAATTTTGAAAAGTTTGGGGGTC
1 AATGTGTAATTTTGAAAAGTTTAGGGGTC
* * *
1324713 AATGTGTAATTTTGAAAAGTTCATGAGTC
1 AATGTGTAATTTTGAAAAGTTTAGGGGTC
* * *
1324742 AAAGTGTAATTTAGGAAAA-TTTAGAGGTC
1 AATGTGTAATTT-TGAAAAGTTTAGGGGTC
* *
1324771 AGTGTGTAATTTTAAAAAGTTTAGGG
1 AATGTGTAATTTTGAAAAGTTTAGGG
1324797 ACTTAATACC
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
28 4 0.06
29 57 0.86
30 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AATGTGTAATTTTGAAAAGTTTAGGGGTC
Found at i:1332549 original size:52 final size:52
Alignment explanation
Indices: 1332400--1332528 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1332390 CGAAATATGA
*
1332400 AAATTTGCCTGCATGTATCGATACATTTTATAGTATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
1332452 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1332504 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1332529 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1332612 original size:32 final size:33
Alignment explanation
Indices: 1332571--1332635 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1332561 TAGCTTAAAT
1332571 TGTATCGATACAAAAC-TTATGTATCAATACAA
1 TGTATCGATACAAAACTTTATGTATCAATACAA
* *
1332603 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCAATACAA
1332636 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCAATACAA
Found at i:1333381 original size:52 final size:52
Alignment explanation
Indices: 1333265--1333451 Score: 211
Period size: 49 Copynumber: 3.6 Consensus size: 52
1333255 ACCAATACAT
* * * * *
1333265 TGATTCACGGCCAACGATATTGG-GTTCAAAGATGAGAAAAAGGATGTCAATGTGC
1 TGATTCAAGGCCAGCTATATTGGACTT-AAAGATG-G-AAAAGG-TGTCAATATGC
* * *
1333320 AGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGTCAATATGC
1 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGTCAATATGC
* *
1333372 TGATTCAAGGCCAGCTATATTGGACTTAAAGA---ACAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGTCAATATGC
*
1333421 TGATTCAAGGCTAGCTATATTGGACTTAAAG
1 TGATTCAAGGCCAGCTATATTGGACTTAAAG
1333452 GTGCCAATGT
Statistics
Matches: 117, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 45 0.38
52 39 0.33
53 6 0.05
54 1 0.01
55 24 0.21
56 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
TGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGTCAATATGC
Found at i:1333429 original size:49 final size:48
Alignment explanation
Indices: 1333302--1333497 Score: 213
Period size: 49 Copynumber: 4.0 Consensus size: 48
1333292 AAAGATGAGA
* * * * *
1333302 AAAAGGATGTCAATGTGCAGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G
*
1333355 AAAAGGTGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
*
1333403 AACAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT----
1 AA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
1333448 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAG
1333496 AA
1 AA
1333498 GATGCCACGA
Statistics
Matches: 127, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
43 39 0.31
44 1 0.01
48 3 0.02
49 41 0.32
50 1 0.01
51 2 0.02
52 34 0.27
53 6 0.05
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (48 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Found at i:1333467 original size:43 final size:43
Alignment explanation
Indices: 1333356--1333491 Score: 182
Period size: 43 Copynumber: 3.0 Consensus size: 43
1333346 TAAAGATGGA
*
1333356 AAAGGTGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1333399 AAAGAACAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1333448 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1333491 A
1 A
1333492 GAAGAAGATG
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
43 40 0.49
44 1 0.01
48 1 0.01
49 40 0.49
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1333473 original size:21 final size:20
Alignment explanation
Indices: 1333405--1333473 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
1333395 ACTTAAAGAA
1333405 CAAGGTGCCAATATGCTGATT
1 CAAGGTGCCAAT-TGCTGATT
*
1333426 CAAGGCTAGCTATATTG--GACTT
1 CAAGG-T-GCCA-ATTGCTGA-TT
*
1333448 AAAGGTGCCAATGTGCTGATT
1 CAAGGTGCCAAT-TGCTGATT
1333469 CAAGG
1 CAAGG
1333474 CCAGCGATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 14 0.38
22 9 0.24
23 5 0.14
24 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
CAAGGTGCCAATTGCTGATT
Found at i:1333734 original size:30 final size:29
Alignment explanation
Indices: 1333554--1333944 Score: 570
Period size: 29 Copynumber: 13.4 Consensus size: 29
1333544 TGGGCTTTGG
* *
1333554 ACTGACTTGTGGGCTTTGAAAAAGATGCT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
1333583 ACTGACTTGTGGGCTTTGGAAAAGATGCC
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
* * *
1333612 ATTGACTTGTGGGATTTGGAAAAGATGCT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
*
1333641 ACTGACTTGT-GGCTTTGGAAAAGATGCT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
*
1333669 ACTGACTTGTGGGCTTTGGAAAAGATGCT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
*
1333698 ACTGACTTGTGGGCTTTGGAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGGAAAA-GATGCC
* *
1333728 ACTGACTTGTGGGCTTTGAAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGGAAAA-GATGCC
*
1333758 ACTGACTTGTGGGCTTTGGAAAAAGGTGCC
1 ACTGACTTGTGGGCTTTGG-AAAAGATGCC
*
1333788 ACTGACTTGTGGGCTTTGGAAAAGATGCT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
* * *
1333817 ACTGACTTGTGGGCTTTTG-AAGGTTGCC
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
*
1333845 ACTGACTTGTGGGCTTTGGAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGGAAAA-GATGCC
*
1333875 ACTGACTTGTGGGCTTTGGAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGGAAAA-GATGCC
1333905 ACTGACTTGTGGGCTTTGGAAAAGATGCC
1 ACTGACTTGTGGGCTTTGGAAAAGATGCC
1333934 ACTGACTTGTG
1 ACTGACTTGTG
1333945 AGGAAAATCC
Statistics
Matches: 336, Mismatches: 21, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
28 51 0.15
29 147 0.44
30 134 0.40
31 4 0.01
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (29 bp):
ACTGACTTGTGGGCTTTGGAAAAGATGCC
Found at i:1333876 original size:117 final size:118
Alignment explanation
Indices: 1333554--1333944 Score: 619
Period size: 117 Copynumber: 3.3 Consensus size: 118
1333544 TGGGCTTTGG
* * *
1333554 ACTGACTTGTGGGCTTTGAAAAAGATGCTACTGACTTGTGGGCTTTGGAAAAGATGCCATTGACT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
* * * * *
1333619 TGTGGGATTTGGAAAA-GATGCTACTGACTTGT-GGCTTTGG-AAAAGATGCT
66 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCC
*
1333669 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGAC
1 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTGG-AAAGGATGCCACTGAC
*
1333734 TTGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCC
65 TTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCC
* *
1333788 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
*
1333852 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCC
66 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCC
*
1333905 ACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTG
1 ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTG
1333945 AGGAAAATCC
Statistics
Matches: 257, Mismatches: 15, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
115 47 0.18
116 28 0.11
117 119 0.46
118 8 0.03
119 55 0.21
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (118 bp):
ACTGACTTGTGGGCTTTGGAAAAGATGCTACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCC
Found at i:1335377 original size:1 final size:1
Alignment explanation
Indices: 1335373--1335451 Score: 59
Period size: 1 Copynumber: 79.0 Consensus size: 1
1335363 CTTTTTGTTG
* * * * * * * * *
1335373 TTTTTTTTTGTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTTGTTTTTTTTGTTTATTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1335438 GTTTTTGTTTTTTT
1 TTTTTTTTTTTTTT
1335452 GCGGAGGACG
Statistics
Matches: 56, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.01, C:0.00, G:0.13, T:0.86
Consensus pattern (1 bp):
T
Found at i:1335396 original size:21 final size:19
Alignment explanation
Indices: 1335364--1335451 Score: 95
Period size: 21 Copynumber: 4.3 Consensus size: 19
1335354 ATCCGGACCC
*
1335364 TTTTTGTTGTTTTTTTTTGT
1 TTTTTTTTG-TTTTTTTTGT
*
1335384 TTTGTTTTTGTTTTTGTTTTT
1 TTT-TTTTTGTTTTT-TTTGT
1335405 GTTTTTTTTGTTTTTTTTGTT
1 -TTTTTTTTGTTTTTTTTG-T
*
1335426 TATTTTTTTGTTGTTTTTGT
1 T-TTTTTTTGTTTTTTTTGT
1335446 TTTTTT
1 TTTTTT
1335452 GCGGAGGACG
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
19 5 0.08
20 14 0.24
21 37 0.63
22 3 0.05
ACGTcount: A:0.01, C:0.00, G:0.14, T:0.85
Consensus pattern (19 bp):
TTTTTTTTGTTTTTTTTGT
Found at i:1335400 original size:30 final size:28
Alignment explanation
Indices: 1335364--1335451 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 28
1335354 ATCCGGACCC
1335364 TTTTTGTTGTTTTTTTTTGTTTTGTTTTT
1 TTTTTGTT-TTTTTTTTTGTTTTGTTTTT
*
1335393 GTTTTTG-TTTTTGTTTT-TTTTGTTTTT
1 -TTTTTGTTTTTTTTTTTGTTTTGTTTTT
*
1335420 TTTGTT-TATTTTTTTGTTGTTTTTGTTTTT
1 TTT-TTGT-TTTTTTTTTTG-TTTTGTTTTT
1335450 TT
1 TT
1335452 GCGGAGGACG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.06
27 12 0.24
28 16 0.32
29 1 0.02
30 18 0.36
ACGTcount: A:0.01, C:0.00, G:0.14, T:0.85
Consensus pattern (28 bp):
TTTTTGTTTTTTTTTTTGTTTTGTTTTT
Found at i:1335413 original size:45 final size:45
Alignment explanation
Indices: 1335364--1335449 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
1335354 ATCCGGACCC
*
1335364 TTTTTGTTGTTTTTT-TTTGTTTTGTTT-TTGTTTTTGTTTTTGTTT
1 TTTTTGTT-TTTTTTGTTTATTTT-TTTGTTGTTTTTGTTTTTGTTT
1335409 TTTTTGTTTTTTTTGTTTATTTTTTTGTTGTTTTTGTTTTT
1 TTTTTGTTTTTTTTGTTTATTTTTTTGTTGTTTTTGTTTTT
1335450 TTGCGGAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
44 9 0.24
45 29 0.76
ACGTcount: A:0.01, C:0.00, G:0.14, T:0.85
Consensus pattern (45 bp):
TTTTTGTTTTTTTTGTTTATTTTTTTGTTGTTTTTGTTTTTGTTT
Found at i:1349423 original size:52 final size:52
Alignment explanation
Indices: 1349272--1349402 Score: 219
Period size: 52 Copynumber: 2.5 Consensus size: 52
1349262 CCCAAAATAT
*
1349272 GAAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
1 GAAAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
*
1349324 GAAAATTTG-TCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCT-TGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
*
1349376 GCAAATTTGCTTGCATGTATCGATACA
1 GAAAATTTGCTTGCATGTATCGATACA
1349403 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
52 73 0.99
53 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (52 bp):
GAAAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
Found at i:1349473 original size:19 final size:20
Alignment explanation
Indices: 1349445--1349497 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1349435 TAGCTTAAAT
1349445 TGTATCGATACAAAAC-TTA
1 TGTATCGATACAAAACTTTA
* *
1349464 TGTATTGATACAACACTTTA
1 TGTATCGATACAAAACTTTA
1349484 TGTATCGATACAAA
1 TGTATCGATACAAA
1349498 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAAAACTTTA
Found at i:1356385 original size:50 final size:50
Alignment explanation
Indices: 1356304--1356448 Score: 220
Period size: 50 Copynumber: 2.9 Consensus size: 50
1356294 AAAAGTCACA
* * *
1356304 TTTTTACCCACATGTATCAATACATTTTTCAATGTATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATACA-TTTTCAATGTATCGATACATTCTATC
*
1356355 -TTTTACCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATC
1 TTTTTACCCAGATGTATCGATACATT-TTCAATGTATCGATACATTCTATC
*
1356405 TTTTTACCCAGATATATCGATACATTTTCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTCAATGTATCGATACAT
1356449 CTACTTAAAG
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
49 2 0.02
50 61 0.71
51 23 0.27
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (50 bp):
TTTTTACCCAGATGTATCGATACATTTTCAATGTATCGATACATTCTATC
Found at i:1358562 original size:33 final size:33
Alignment explanation
Indices: 1358519--1358588 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1358509 TTCAACGATT
1358519 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
* *** *
1358552 TGTATTGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1358585 TGTA
1 TGTA
1358589 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1358647 original size:13 final size:13
Alignment explanation
Indices: 1358629--1358653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1358619 ATTACTCACA
1358629 TGTATCGATACAT
1 TGTATCGATACAT
1358642 TGTATCGATACA
1 TGTATCGATACA
1358654 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1358718 original size:52 final size:52
Alignment explanation
Indices: 1358662--1358786 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1358652 CACTGATCTT
*
1358662 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1358714 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1358766 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1358787 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1365981 original size:1 final size:1
Alignment explanation
Indices: 1365975--1366026 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1365965 GTTCCTTTCT
* * * * * *
1365975 AAAAAAAAAACAAAACAAAAAAAAGAAAAAAAAAGAAAAGAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1366027 CAGAAAAGCT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1365996 original size:15 final size:14
Alignment explanation
Indices: 1365975--1366026 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1365965 GTTCCTTTCT
1365975 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
* *
1365989 ACAAAAAAAAGAAA
1 AAAAAAAAAACAAA
*
1366003 AAAAAAGAAAAGAAA
1 AAAAAA-AAAACAAA
1366018 AAAACAAAA
1 AAAA-AAAA
1366027 CAGAAAAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 17 0.52
15 14 0.42
16 2 0.06
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:1366008 original size:24 final size:24
Alignment explanation
Indices: 1365976--1366021 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1365966 TTCCTTTCTA
1365976 AAAAAAAAACAAAACAAAAAAAAG
1 AAAAAAAAACAAAACAAAAAAAAG
* *
1366000 AAAAAAAAAGAAAAGAAAAAAA
1 AAAAAAAAACAAAACAAAAAAA
1366022 CAAAACAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAAAACAAAAAAAAG
Found at i:1366031 original size:15 final size:14
Alignment explanation
Indices: 1365975--1366033 Score: 68
Period size: 13 Copynumber: 4.2 Consensus size: 14
1365965 GTTCCTTTCT
1365975 AAAAAAAAAACA-A
1 AAAAAAAAAACAGA
*
1365988 AACAAAAAAA-AGA
1 AAAAAAAAAACAGA
*
1366001 AAAAAAAAGAAAAGA
1 AAAAAAAA-AACAGA
1366016 AAAAAACAAAACAGA
1 AAAAAA-AAAACAGA
1366031 AAA
1 AAA
1366034 GCTCGATAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 1 0.03
13 17 0.44
14 2 0.05
15 17 0.44
16 2 0.05
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAGA
Found at i:1367066 original size:30 final size:31
Alignment explanation
Indices: 1367029--1367113 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 31
1367019 CAAATACCTT
1367029 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
*
1367060 -TCAAAGTCCACGACTCAGTGGCATTTTTTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
* * * *
1367090 TTTAAAGCCCACAACTCTGTGGCA
1 TTCAAAGTCCACGACTCAGTGGCA
1367114 CACTTTTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (31 bp):
TTCAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:1367205 original size:34 final size:34
Alignment explanation
Indices: 1367090--1367557 Score: 414
Period size: 34 Copynumber: 13.9 Consensus size: 34
1367080 GCATTTTTTC
*
1367090 TTTAAAGCCCACAACTCTGTGGCACACTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
** * *
1367125 TTTAAAGCCCACAACTTTGTGGCATTCTTTTGCCCTT
1 TTTAAAGCCCACAACTCCGTGGCA-CCTTTT--TCTT
*
1367162 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* **
1367196 TTTACAGCCCACAACTTTGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
1367233 TTTAAAGCCCACAACTCCGTGGCACC---TTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
1367264 TTCAAAGCCCACAACTCCGTGGCACC-----C-T
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * * *
1367292 TTT-AAGTCCACGACTACGTGGCA-CTCTTTTC-C
1 TTTAAAGCCCACAACTCCGTGGCACCT-TTTTCTT
* *
1367324 TTTAAAGCCCACAACTACGTGGCA-CTCTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCACCT-TTTTCTT
* *
1367358 TCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
* *
1367392 TCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
* *
1367426 TCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
* *
1367460 TCT-AAGCCCACAACTCCGTGGCACTCTTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-C-TTTTT-CTT
* *
1367496 TTTAAAGCCCACAACTCCATGGCACCTTGTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * *
1367530 TTT-AAGTCCACAACTTCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT
1367558 CACCCTTTCT
Statistics
Matches: 379, Mismatches: 35, Indels: 40
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.00
27 17 0.04
28 3 0.01
29 1 0.00
31 28 0.07
32 4 0.01
33 67 0.18
34 132 0.35
35 45 0.12
36 12 0.03
37 69 0.18
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
Found at i:1367208 original size:71 final size:69
Alignment explanation
Indices: 1367093--1367577 Score: 472
Period size: 68 Copynumber: 7.1 Consensus size: 69
1367083 TTTTTTCTTT
* ** *
1367093 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACAACTTTGTGGCATTCTTTTGC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT-AAGCCCACAACTCCGTGGCACTCTTTT-C
1367158 CCTTTTC
63 CCTTTTC
**
1367165 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCACAACTTTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA-AGCCCACAACTCCGTGGCACTC-TTTTCC
*
1367230 CTTTTT
64 CTTTTC
*
1367236 AAAGCCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCA-------CCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-TAAGCCCACAACTCCGTGGCACTCTTTTCCC
1367291 TTTT-
65 TTTTC
* * * * * *
1367295 -AAGTCCACGACTACGTGGCA-CTCTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTT-CC
1 AAAGCCCACAACTCCGTGGCACCT-TTTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCC
1367357 --TTC
65 TTTTC
* * * *
1367360 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCC
1367425 --TTC
65 TTTTC
* * *
1367428 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAGCCCACAACTCCGTGGCACTC--TTTTC
1367493 CCTTTT-
63 CCTTTTC
* * * *
1367499 AAAGCCCACAACTCCATGGCACCTTGTTCTTTTTAAGTCCACAACTTCGTGGCA-TC-TTTCACC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTC-CC
*
1367562 CTTTC
65 TTTTC
1367567 TAAAGCCCACA
1 -AAAGCCCACA
1367578 CAAGTCGGTG
Statistics
Matches: 361, Mismatches: 26, Indels: 55
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.00
58 17 0.05
60 27 0.07
61 6 0.02
64 2 0.01
66 23 0.06
67 39 0.11
68 89 0.25
69 13 0.04
70 34 0.09
71 83 0.23
72 27 0.07
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (69 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCCT
TTTC
Found at i:1367602 original size:33 final size:33
Alignment explanation
Indices: 1367561--1367731 Score: 267
Period size: 33 Copynumber: 5.2 Consensus size: 33
1367551 CATCTTTCAC
1367561 CCTT-TCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1367593 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1367626 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
1367659 CCTTCCTCTAAAGCCCACACAAGTTGGTGGCAATC
1 CCTT-CTCTAAAGCCCACACAAGTCGGTGGCAA-A
*
1367694 CCTTC-CTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1367726 CCTTCT
1 CCTTCT
1367732 AAGCCCAATA
Statistics
Matches: 130, Mismatches: 3, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
32 14 0.11
33 80 0.62
34 32 0.25
35 4 0.03
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:1367651 original size:67 final size:67
Alignment explanation
Indices: 1367559--1367731 Score: 289
Period size: 67 Copynumber: 2.6 Consensus size: 67
1367549 GGCATCTTTC
1367559 ACCCTT-TCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
1367623 AA
66 AA
*
1367625 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AACCTTCCTCTAAAGCCCACACAAGTTGGTGG
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTT-CTCTAAAGCCCACACAAGTCGGTGG
1367689 CAA
65 CAA
* *
1367692 TCCCTTC-CTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCT
1367732 AAGCCCAATA
Statistics
Matches: 101, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
66 38 0.38
67 63 0.62
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (67 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
AA
Found at i:1367847 original size:49 final size:49
Alignment explanation
Indices: 1367731--1368792 Score: 932
Period size: 49 Copynumber: 21.7 Consensus size: 49
1367721 GCAACCCTTC
* * * * *
1367731 TAAGCCCAATATAGCTGGCCTTGAATTAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
* *
1367783 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1367832 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1367881 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1367930 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1367979 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1368028 TAAGACCAATATAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1368077 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
1368120 TAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1368169 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CA-C-T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
1368210 TGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1368259 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * *
1368302 TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1368351 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-TCATCTT
* * * * * * ** * * *
1368406 TAAGCCCAATATCGTTGGTCGTGAATCAATATATTGGCATCTTTATCACTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT--CTT
* * * * * * * * *
1368457 T---TCTC-ATCTTCATCTTTAAGTCCAATGTAGCTGGC-C-TTGAATCAGCACATTGGCACCTT
1 TAAGTC-CAAT-GT-AGC--T--GGCC-TTGAATC-AGCACATTG-----GCACCTT--CATCTT
* * * * * * *
1368516 GAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATTTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1368565 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1368614 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1368662 TAAGTCCAATGTACCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1368705 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
1368757 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1368793 ACATCCTTTT
Statistics
Matches: 820, Mismatches: 129, Indels: 122
0.77 0.12 0.11
Matches are distributed among these distances:
41 34 0.04
42 3 0.00
43 111 0.14
45 3 0.00
47 4 0.00
48 48 0.06
49 456 0.56
50 7 0.01
51 8 0.01
52 71 0.09
54 9 0.01
55 43 0.05
56 6 0.01
58 1 0.00
59 8 0.01
60 1 0.00
61 3 0.00
62 4 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1368182 original size:92 final size:91
Alignment explanation
Indices: 1368025--1368395 Score: 593
Period size: 92 Copynumber: 4.0 Consensus size: 91
1368015 GCACATTTAT
* * * * *
1368025 CTTTAAGACCAATATAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAG-CCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
1368090 GCTGGCCTTGACTCAGCACATTGGCAC
65 GCTGGCCTTGAATCAGCACATTGGCAC
1368117 CTTTAAGCCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGCC-GATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1368182 GCTGGCCTTGAATCAGCACATTGGCA-
65 GCTGGCCTTGAATCAGCACATTGGCAC
* *
1368208 C-TTGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAG-CCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1368272 GCTGGCCTTGAATCAGCACATTGGCAC
65 GCTGGCCTTGAATCAGCACATTGGCAC
*
1368299 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAG-CCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
1368364 GCTGGCCTTGAATCAGCACATTGACATC
65 GCTGGCCTTGAATCAGCACATTGGCA-C
1368392 CTTT
1 CTTT
1368396 TTCTCATCTT
Statistics
Matches: 261, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
90 84 0.32
91 6 0.02
92 166 0.64
93 5 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (91 bp):
CTTTAAGCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:1368243 original size:22 final size:21
Alignment explanation
Indices: 1368182--1368243 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
1368172 GTCCAATGTA
*
1368182 GCTGGCCTTGAATCAGCACAT
1 GCTGGCCTTGAATCAGCATAT
*
1368203 --TGGCACTTGAGTC--CAATAT
1 GCTGGC-CTTGAATCAGC-ATAT
1368222 CGCTGGCCTTGAATCAGCATAT
1 -GCTGGCCTTGAATCAGCATAT
1368244 TGGCATCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 13
0.66 0.06 0.28
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 7 0.23
21 7 0.23
22 8 0.26
23 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (21 bp):
GCTGGCCTTGAATCAGCATAT
Found at i:1368535 original size:43 final size:43
Alignment explanation
Indices: 1368470--1368748 Score: 324
Period size: 43 Copynumber: 6.1 Consensus size: 43
1368460 TCATCTTCAT
1368470 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
1368513 CTTGAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
*
1368557 ATCATTTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTC
1 --C---TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C
1368609 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
1368659 CTTTAAGTCCAATGTACCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1368702 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1368745 CTTT
1 CTTT
1368749 TCCATCTTTA
Statistics
Matches: 207, Mismatches: 15, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
43 84 0.41
44 1 0.00
46 1 0.00
48 39 0.19
49 74 0.36
50 1 0.00
52 5 0.02
54 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1369594 original size:13 final size:13
Alignment explanation
Indices: 1369576--1369600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1369566 CATAAAATGT
1369576 TGTATCGATACAA
1 TGTATCGATACAA
1369589 TGTATCGATACA
1 TGTATCGATACA
1369601 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1369598 original size:33 final size:33
Alignment explanation
Indices: 1369556--1369625 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1369546 TTCAACGATT
1369556 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1369589 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1369622 TGTA
1 TGTA
1369626 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1369684 original size:13 final size:13
Alignment explanation
Indices: 1369666--1369690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1369656 ATTACTCACA
1369666 TGTATCGATACAT
1 TGTATCGATACAT
1369679 TGTATCGATACA
1 TGTATCGATACA
1369691 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1369755 original size:52 final size:52
Alignment explanation
Indices: 1369699--1369823 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1369689 CACTGATCTT
* * *
1369699 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1369751 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1369803 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAAGCAA
1369824 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1374132 original size:19 final size:20
Alignment explanation
Indices: 1374088--1374135 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1374078 CATCCAAATG
* * *
1374088 TATCGATACATTATGCTTTG
1 TATCGATACATGATGCATTA
1374108 TATCGATACATGAT-CATTA
1 TATCGATACATGATGCATTA
1374127 TATCGATAC
1 TATCGATAC
1374136 TTACACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATGATGCATTA
Found at i:1382471 original size:20 final size:21
Alignment explanation
Indices: 1382424--1382478 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1382414 AATCCCAATG
**
1382424 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACATCTTCA
*
1382445 GCATGTATCGATACAT-TTCA
1 ACATGTATCGATACATCTTCA
1382465 ACATGTATCGATAC
1 ACATGTATCGATAC
1382479 TTTGAATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (21 bp):
ACATGTATCGATACATCTTCA
Found at i:1384943 original size:13 final size:13
Alignment explanation
Indices: 1384925--1384963 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1384915 ATAATCCCCC
*
1384925 TGTATCGATACAG
1 TGTATCGATACAA
1384938 TGTATCGATACAA
1 TGTATCGATACAA
1384951 TGTATCGATACAA
1 TGTATCGATACAA
1384964 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1387061 original size:15 final size:15
Alignment explanation
Indices: 1387041--1387071 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1387031 ATTTCGTTTG
*
1387041 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1387056 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1387071 G
1 G
1387072 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1391158 original size:13 final size:13
Alignment explanation
Indices: 1391140--1391165 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1391130 AATTTTTTGG
1391140 TGTATCGATACAT
1 TGTATCGATACAT
1391153 TGTATCGATACAT
1 TGTATCGATACAT
1391166 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1391259 original size:20 final size:21
Alignment explanation
Indices: 1391213--1391267 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1391203 AATCCCAATG
***
1391213 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACATCTGCA
1391234 ACATGTATCGATACAT-TGCA
1 ACATGTATCGATACATCTGCA
1391254 ACATGTATCGATAC
1 ACATGTATCGATAC
1391268 TTTGAATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
ACATGTATCGATACATCTGCA
Found at i:1392948 original size:20 final size:20
Alignment explanation
Indices: 1392925--1392975 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1392915 CATCCAAATG
1392925 TATCGATACATTATGCTTTA
1 TATCGATACATTATGCTTTA
*
1392945 TATCGATACATTATGCTTTG
1 TATCGATACATTATGCTTTA
1392965 TATCGATACAT
1 TATCGATACAT
1392976 GATCATTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
TATCGATACATTATGCTTTA
Found at i:1393257 original size:14 final size:14
Alignment explanation
Indices: 1393238--1393268 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1393228 GCTACAAACA
1393238 CAATCATTCAACCT
1 CAATCATTCAACCT
1393252 CAATCATTCAACCT
1 CAATCATTCAACCT
1393266 CAA
1 CAA
1393269 ATGAGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (14 bp):
CAATCATTCAACCT
Found at i:1395371 original size:20 final size:20
Alignment explanation
Indices: 1395346--1395398 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1395336 GTTGGGTATA
*
1395346 ATGTATCGATACAAT-TCTT
1 ATGTATCGATACAATATCCT
1395365 CATGTATCGATACAATATCCT
1 -ATGTATCGATACAATATCCT
1395386 ATGTATCGATACA
1 ATGTATCGATACA
1395399 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATATCCT
Found at i:1395453 original size:20 final size:20
Alignment explanation
Indices: 1395427--1395481 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1395417 CTATCAGTTT
1395427 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* * *
1395447 TATGTATCAAAACAA-TGAG
1 CATGTATCGATACAATTGAG
1395466 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1395482 ATATCGATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:1395470 original size:19 final size:20
Alignment explanation
Indices: 1395427--1395473 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1395417 CTATCAGTTT
* *
1395427 CATGTATCGATACAATTGAG
1 CATGTATCAAAACAATTGAG
*
1395447 TATGTATCAAAACAA-TGAG
1 CATGTATCAAAACAATTGAG
1395466 CATGTATC
1 CATGTATC
1395474 GATACAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCAAAACAATTGAG
Found at i:1396778 original size:78 final size:79
Alignment explanation
Indices: 1396696--1397161 Score: 424
Period size: 79 Copynumber: 5.9 Consensus size: 79
1396686 ATAAAAATGG
* * * *
1396696 GGTTGTAGTATCTCCTCAAAAATAATGGGGTTGGAGTAT-CCCGATGGT-AGAAAATTGGTGTTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGA-AAAATCGGTGTTT
* *
1396759 TGGAAATAAAACTGA
65 TAGAAATAAAACCGA
* * ** * * * * * * *
1396774 GGTTGGAATGTCCCCTCTGAAATAACGAGGTTGGAATATCCTCGGTGATAAAAAATCAGTGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTT
* *
1396839 GGAAATAAAAACGA
66 AGAAATAAAACCGA
* * * * ** * *
1396853 TGTTGGAGTATCCCTTTAAAAATAACAGGGTTGGAGTATCCCTAATTGTGAAAAATAGGTG-TTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTT
* ** *
1396917 AAAAATAAAAGAGG
66 AGAAATAAAACCGA
* ** * * *
1396931 GGTTGGAGTGTCATCTCCAAAATAACGGGGTT--CGTATCCCCGATGGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTT
1396994 AGAAATAAAAGCCGA
66 AGAAATAAAA-CCGA
* * * * * *
1397009 -GTTGGAGTATCCCCTAAAAAATAACGAGGTTGGAGAATCCCCAATGGT-AGAAAATCGATATTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGA-AAAATCGGTGTTT
*
1397072 TATAAATAAAACCGA
65 TAGAAATAAAACCGA
* * * *
1397087 GGTTAGAGTCTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTTTTTT
1 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTT
1397152 AGAAATAAAA
66 AGAAATAAAA
1397162 ACATCAATGA
Statistics
Matches: 300, Mismatches: 79, Indels: 17
0.76 0.20 0.04
Matches are distributed among these distances:
76 21 0.07
77 37 0.12
78 72 0.24
79 168 0.56
80 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTT
AGAAATAAAACCGA
Found at i:1396935 original size:157 final size:152
Alignment explanation
Indices: 1396678--1397163 Score: 384
Period size: 157 Copynumber: 3.1 Consensus size: 152
1396668 AAATTTAATA
* * * * * * *
1396678 TTTTGGAGATAAAAATGGGGTTGTAGTATCTCCTCAAAAATAATGGGGTTGGAGTATCCCGATGG
1 TTTTGGAAATAAAAA-CGAGTTGGAGTATC-CCTAAAAAATAA-CGGGTTGGAGTATCCCAATGG
* ** * * ** *
1396743 TAGAAAATTGGTGTTTTGGAAATAAAACTGAGGTTGGAATGTCCCCTCTGAAATAACGAGGTTGG
63 TAGAAAATAGGTGTTTTAAAAATAAAACAGAGGTTGGAATGTCACCTCCAAAATAACGAGGTTCG
* *
1396808 AATATCCTCGGTGATAAAAAATC-AGTG
128 --TATCCCCGATGATAAAAAATCGA-TG
* *
1396835 TTTTGGAAATAAAAACGATGTTGGAGTATCCCTTTAAAAATAACAGGGTTGGAGTATCCCTAATT
1 TTTTGGAAATAAAAACGA-GTTGGAGTATCCC-TAAAAAATAAC-GGGTTGGAGTATCCC-AATG
* * * * *
1396900 GT-GAAAAATAGGTG-TTTAAAAATAAAAGAGGGGTTGGAGTGTCATCTCCAAAATAACGGGGTT
62 GTAG-AAAATAGGTGTTTTAAAAATAAAACAGAGGTTGGAATGTCACCTCCAAAATAACGAGGTT
* *
1396963 CGTATCCCCGATGGTGAAAAATCGATG
126 CGTATCCCCGATGATAAAAAATCGATG
* * *
1396990 TTTTAGAAATAAAAGCCGAGTTGGAGTATCCCCTAAAAAATAACGAGGTTGGAGAATCCCCAATG
1 TTTTGGAAATAAAA-ACGAGTTGGAGTAT-CCCTAAAAAATAACG-GGTTGGAGTAT-CCCAATG
* * * * * * * * * * *
1397055 GTAGAAAATCGATATTTTATAAATAAAACCGAGGTTAGAGTCTCCCCTCGAAAATAACGGGGTTG
62 GTAGAAAATAGGTGTTTTAAAAATAAAACAGAGGTTGGAATGTCACCTCCAAAATAACGAGGTT-
* * * * *
1397120 GAGTATCCCCGATGGTGAAAAATCGGTT
126 -CGTATCCCCGATGATAAAAAATCGATG
*
1397148 TTTTAGAAATAAAAAC
1 TTTTGGAAATAAAAAC
1397164 ATCAATGAAA
Statistics
Matches: 269, Mismatches: 46, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
154 1 0.00
155 74 0.28
156 54 0.20
157 89 0.33
158 51 0.19
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (152 bp):
TTTTGGAAATAAAAACGAGTTGGAGTATCCCTAAAAAATAACGGGTTGGAGTATCCCAATGGTAG
AAAATAGGTGTTTTAAAAATAAAACAGAGGTTGGAATGTCACCTCCAAAATAACGAGGTTCGTAT
CCCCGATGATAAAAAATCGATG
Found at i:1397040 original size:155 final size:157
Alignment explanation
Indices: 1396697--1397163 Score: 401
Period size: 155 Copynumber: 3.0 Consensus size: 157
1396687 TAAAAATGGG
* * * ** * * * *
1396697 GTTGTAGTATCTCCTCAAAAATAATGGGGTTGGAGTAT-CCCGATGGTAGAAAATTGGT-GTTTT
1 GTTGGAGTATCCCCTAAAAAATAACAGGGTTGGAGAATCCCCAATGGTAGAAAATAGATAG-TTT
** * * * * * ** * * * * * *
1396760 GGAAATAAAACTGAGGTTGGAATGTCCCCTCTGAAATAACGAGGTTGGAATATCCTCGGTGATAA
65 AAAAATAAAACAGAGGTTAGAGTCTCACCTCCAAAATAACGGGGTT-GAGTATCCCCGATGGTGA
*
1396825 AAAATC-AGTGTTTTGGAAATAAAAACGAT
129 AAAATCGA-TGTTTTAGAAATAAAAACGAT
* * * * * *
1396854 GTTGGAGTATCCCTTTAAAAATAACAGGGTTGGAGTATCCCTAATTGT-GAAAAATAGGT-GTTT
1 GTTGGAGTATCCCCTAAAAAATAACAGGGTTGGAGAATCCCCAATGGTAG-AAAATAGATAGTTT
* * * * * *
1396917 AAAAATAAAAGAGGGGTTGGAGTGTCATCTCCAAAATAACGGGGTT-CGTATCCCCGATGGTGAA
65 AAAAATAAAACAGAGGTTAGAGTCTCACCTCCAAAATAACGGGGTTGAGTATCCCCGATGGTGAA
*
1396981 AAATCGATGTTTTAGAAATAAAAGCCGA-
130 AAATCGATGTTTTAGAAATAAAA-ACGAT
* *
1397009 GTTGGAGTATCCCCTAAAAAATAAC-GAGGTTGGAGAATCCCCAATGGTAGAAAATCGATATTTT
1 GTTGGAGTATCCCCTAAAAAATAACAG-GGTTGGAGAATCCCCAATGGTAGAAAATAGATAGTTT
* * * *
1397073 ATAAATAAAACCGAGGTTAGAGTCTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGA
65 AAAAATAAAACAGAGGTTAGAGTCTCACCTCCAAAATAACGGGGTT-GAGTATCCCCGATGGTGA
* *
1397138 AAAATCGGTTTTTTAGAAATAAAAAC
129 AAAATCGATGTTTTAGAAATAAAAAC
1397164 ATCAATGAAA
Statistics
Matches: 251, Mismatches: 50, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
154 1 0.00
155 80 0.32
156 45 0.18
157 72 0.29
158 53 0.21
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (157 bp):
GTTGGAGTATCCCCTAAAAAATAACAGGGTTGGAGAATCCCCAATGGTAGAAAATAGATAGTTTA
AAAATAAAACAGAGGTTAGAGTCTCACCTCCAAAATAACGGGGTTGAGTATCCCCGATGGTGAAA
AATCGATGTTTTAGAAATAAAAACGAT
Found at i:1399594 original size:50 final size:49
Alignment explanation
Indices: 1399510--1399604 Score: 118
Period size: 50 Copynumber: 1.9 Consensus size: 49
1399500 CAACAATGCA
** * *
1399510 TGAATGTATCGATACGTTGAGAAATATATCGATACATCTGGGTAAAACCT
1 TGAATGTATCGATACAATAAAAAATATATCGATACAT-TGGGTAAAACCT
* * *
1399560 TGAATGTATCGATACAATAAAAAATGTATTGATACATTTGGTAAA
1 TGAATGTATCGATACAATAAAAAATATATCGATACATTGGGTAAA
1399605 TGTATCGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 7 0.18
50 31 0.82
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (49 bp):
TGAATGTATCGATACAATAAAAAATATATCGATACATTGGGTAAAACCT
Found at i:1400247 original size:77 final size:77
Alignment explanation
Indices: 1400137--1400300 Score: 202
Period size: 77 Copynumber: 2.1 Consensus size: 77
1400127 CTTTAAGGGC
* * *
1400137 AAAGGAAAATGAGTACATTCTGCACTTCAAGGACAACAAAAAAAGGAGAATGAAATAGGTCCTGC
1 AAAGGAAAAAGAGTACATCCTACACTTCAAGGACAACAAAAAAAGGAGAATGAAATAGGTCCTGC
* *
1400202 TCTTTAAAGATA
66 TCCTTAAAGACA
* * * *** *
1400214 AAAGGAAAAAGAGTACGTCCTACTCTTCGAGGACAATGGAAAAAGGAGAATGAAATGGGTCCTGC
1 AAAGGAAAAAGAGTACATCCTACACTTCAAGGACAACAAAAAAAGGAGAATGAAATAGGTCCTGC
*
1400279 TCCTTAAGGACA
66 TCCTTAAAGACA
*
1400291 AAAGAAAAAA
1 AAAGGAAAAA
1400301 AAAAGAAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (77 bp):
AAAGGAAAAAGAGTACATCCTACACTTCAAGGACAACAAAAAAAGGAGAATGAAATAGGTCCTGC
TCCTTAAAGACA
Found at i:1400405 original size:42 final size:42
Alignment explanation
Indices: 1400367--1400750 Score: 365
Period size: 42 Copynumber: 9.1 Consensus size: 42
1400357 TACTCTTCGG
*
1400367 GGACAAAGGAAAAAAGGAAATGAAGTGCATCTTGCTCTTTGA
1 GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
*
1400409 GGACAAAGGGAAAAAAAAGAAAATGAAGTGCATCCTGCTCTTTGA
1 GGACAAA-GG--AAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
** **
1400454 GGACAAAGGGAAAATAAGGAAATGAAGTGTGTCCTATTCTTTTGA
1 GGACAAA-GGAAAA-AAGGAAATGAAGTGCATCCTGCTC-TTTGA
* * * *
1400499 GGACAAAAGAGAAAAGGAAATAAAGTGCATCCTCCTCTTTGA
1 GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
* * **
1400541 GGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTGCTCTTTGA
1 GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
* *
1400583 GGACAAAGGAGAAAAA-GAAATGTAGTGTGCAT--TGCTCTTTTA
1 GGACAAAGGA-AAAAAGGAAATG-A-AGTGCATCCTGCTCTTTGA
* * * *
1400625 TGGGA-AAA-AAAGAAAAGGAAATAAAGTGCATCCTACTTTTTGA
1 --GGACAAAGGAA-AAAAGGAAATGAAGTGCATCCTGCTCTTTGA
* * **
1400668 GGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTGCTCTTTGA
1 GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
*
1400710 GGACAAAGGAAAAAA-G-AA--AA-TGCGTCCTGCTCTTTGA
1 GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
1400747 GGAC
1 GGAC
1400751 TAAAATGTGC
Statistics
Matches: 288, Mismatches: 38, Indels: 37
0.79 0.10 0.10
Matches are distributed among these distances:
37 20 0.07
38 2 0.01
40 2 0.01
41 11 0.04
42 124 0.43
43 46 0.16
44 30 0.10
45 53 0.18
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.22
Consensus pattern (42 bp):
GGACAAAGGAAAAAAGGAAATGAAGTGCATCCTGCTCTTTGA
Found at i:1400695 original size:85 final size:86
Alignment explanation
Indices: 1400436--1400716 Score: 299
Period size: 85 Copynumber: 3.3 Consensus size: 86
1400426 AGAAAATGAA
* * * *
1400436 GTGCATCCTGCTCTTTGAGGACAAAGGGAAA-ATAAGGAAATGAAGTGTGTCCTATTCTTTTGAG
1 GTGCATCCTCCTCTTTGAGGACAAA---AAAGAAAAGGAAATAAAGTGTGTCCTACT-TTTTGAG
*
1400500 GACAAAAGAGAAAAGGAAATAAA--
62 GACAAAGGAGAAAAGGAAATAAAGT
** * *
1400523 GTGCATCCTCCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTGCTCTTTGAGGACA
1 GTGCATCCTCCTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTGTGTCCTACTTTTTGAGGACA
* **
1400588 AAGGAGAAAAAGAAATGTAGT
66 AAGGAGAAAAGGAAATAAAGT
* * **
1400609 GTGCAT--TGCTCTTTTATGGGA-AAAAAAGAAAAGGAAATAAAGTGCATCCTACTTTTTGAGGA
1 GTGCATCCTCCTCTTTGA--GGACAAAAAAGAAAAGGAAATAAAGTGTGTCCTACTTTTTGAGGA
1400671 CAAAGGAGAAAAGGAAATAAAGT
64 CAAAGGAGAAAAGGAAATAAAGT
*
1400694 GTG--TCCTGCTCTTTGAGGACAAA
1 GTGCATCCTCCTCTTTGAGGACAAA
1400717 GGAAAAAAGA
Statistics
Matches: 162, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
83 4 0.02
84 37 0.23
85 88 0.54
86 9 0.06
87 24 0.15
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (86 bp):
GTGCATCCTCCTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTGTGTCCTACTTTTTGAGGACA
AAGGAGAAAAGGAAATAAAGT
Found at i:1400731 original size:127 final size:126
Alignment explanation
Indices: 1400378--1400728 Score: 458
Period size: 127 Copynumber: 2.7 Consensus size: 126
1400368 GACAAAGGAA
* * * * * * **
1400378 AAAAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAGGGAAAAAAAAGAAAATGAAGTGCATC
1 AAAAGGAAATAAAGTGCATCCTACTCTTTGAGGACAAA-GG--AGAAAAGGAAATAAAGTGTGTC
* *
1400443 CTGCTCTTTGAGGACAAAGGGAAAATAAGGAAATGAAGTGTGTCCTATTCTTTTGAGGACAAAAG
63 CTGCTCTTTGAGGACAAA-GGAAAA-AA-GAAATGAAGTGTGTCATATTCTTTTGAGGACAAAAA
1400508 AG
125 AG
*
1400510 AAAAGGAAATAAAGTGCATCCTCCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTG
1 AAAAGGAAATAAAGTGCATCCTACTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTG
*
1400575 CTCTTTGAGGACAAAGGAGAAAAAGAAATGTAGTGTG-CAT-TGCTCTTTT-ATGGGA-AAAAAA
66 CTCTTTGAGGACAAAGGA-AAAAAGAAATGAAGTGTGTCATAT--TCTTTTGA--GGACAAAAAA
1400636 G
126 G
*
1400637 AAAAGGAAATAAAGTGCATCCTACTTTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTG
1 AAAAGGAAATAAAGTGCATCCTACTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTG
1400702 CTCTTTGAGGACAAAGGAAAAAAGAAA
66 CTCTTTGAGGACAAAGGAAAAAAGAAA
1400729 ATGCGTCCTG
Statistics
Matches: 201, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
125 1 0.00
126 12 0.06
127 105 0.52
128 8 0.04
129 38 0.19
131 2 0.01
132 35 0.17
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (126 bp):
AAAAGGAAATAAAGTGCATCCTACTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTG
CTCTTTGAGGACAAAGGAAAAAAGAAATGAAGTGTGTCATATTCTTTTGAGGACAAAAAAG
Found at i:1400816 original size:62 final size:62
Alignment explanation
Indices: 1400720--1400854 Score: 182
Period size: 62 Copynumber: 2.2 Consensus size: 62
1400710 GGACAAAGGA
* * * * * *
1400720 AAAAAG-AAAATGCGTCCTGCTCTTTGAGGACTAAAATGTGCCACTAACTCATGTGGGCTTT
1 AAAAAGAAAAAAGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGAGCTTG
* *
1400781 AAAAAGAAAAAAGCATCCTGTTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGAGCTTG
1 AAAAAGAAAAAAGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGAGCTTG
*
1400843 GAAAAGAAAAAA
1 AAAAAGAAAAAA
1400855 ACGTGCCACC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
61 6 0.09
62 58 0.91
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (62 bp):
AAAAAGAAAAAAGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGAGCTTG
Found at i:1400875 original size:100 final size:100
Alignment explanation
Indices: 1400752--1400953 Score: 296
Period size: 100 Copynumber: 2.0 Consensus size: 100
1400742 TTTGAGGACT
* * * *
1400752 AAAATGTGCCACTAACTCATGTGGGCTTTAAAAAGAAAAAAGCATCCTGTTCTTTGAGGACTAAA
1 AAAACGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAAGCATCCTGCTCTTTAAGGACTAAA
*
1400817 GGGTGCCACCAACTCATGTGAGCTTGGAAAAGAAA
66 GGGTGCCACCAACTCATATGAGCTTGGAAAAGAAA
* * * *
1400852 AAAACGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATTCTGCTCTTTAAGGACTAAA
1 AAAACGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAAGCATCCTGCTCTTTAAGGACTAAA
* * *
1400917 GGGTGCCACCAACTCGTATGGGCTTTGAAAAGAAA
66 GGGTGCCACCAACTCATATGAGCTTGGAAAAGAAA
1400952 AA
1 AA
1400954 GGCATCCTAC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (100 bp):
AAAACGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAAGCATCCTGCTCTTTAAGGACTAAA
GGGTGCCACCAACTCATATGAGCTTGGAAAAGAAA
Found at i:1400885 original size:38 final size:38
Alignment explanation
Indices: 1400819--1400891 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1400809 GGACTAAAGG
1400819 GTGCCACCAACTCATGTGAGCTTGGAAAAGAAAAAAAC
1 GTGCCACCAACTCATGTGAGCTTGGAAAAGAAAAAAAC
* * *
1400857 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
1 GTGCCACCAACTCATGTGAGCTTGGAAAAGAAAAA
1400892 GGCATTCTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (38 bp):
GTGCCACCAACTCATGTGAGCTTGGAAAAGAAAAAAAC
Found at i:1400954 original size:62 final size:62
Alignment explanation
Indices: 1400857--1401198 Score: 438
Period size: 62 Copynumber: 5.5 Consensus size: 62
1400847 AGAAAAAAAC
* *
1400857 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATTCTGCTCTTTAAGGACTAAAGG
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
* * * *
1400919 GTGCCACCAACTCGTATGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTAAGGATTAAAGG
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
* * * *
1400981 GT-CCACCAATTCGTGTAGGCTTTGAAAAGAAAAAAGCGTCCTGCTCTTTGAGGACTAAAGG
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
* * * * *
1401042 GTGCCACTAACTTGTATGGGCTTTCAAAAGGAAAAA-GCGTCCTGCTCTTTAAGGACTAAAGA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
* * * * ** * *
1401104 GTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGTGTCCTATTCTTTGAGGACTAAAGC
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
*
1401166 ATGCCACCAACTCGTGTGGGCTTTGAAAA-AAAA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAA
1401199 GGTGTCATAT
Statistics
Matches: 242, Mismatches: 35, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
61 63 0.26
62 173 0.71
63 6 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (62 bp):
GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTAAGGACTAAAGG
Found at i:1401090 original size:123 final size:124
Alignment explanation
Indices: 1400857--1401198 Score: 465
Period size: 123 Copynumber: 2.8 Consensus size: 124
1400847 AGAAAAAAAC
* * * *
1400857 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATTCTGCTCTTTAAGGACTAAAGGGTG
1 GTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG
* *
1400922 CCACCAACTCGTATGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTAAGGATTAAAGG
66 CCACCAACTCGTATGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTAAGGACTAAAGA
* *
1400981 GT-CCACCAATTCGTGTAGGCTTTGAAAAGAAAAAAGCGTCCTGCTCTTTGAGGACTAAAGGGTG
1 GTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG
* * * * *
1401045 CCACTAACTTGTATGGGCTTTCAAAAGGAAAAA-GCGTCCTGCTCTTTAAGGACTAAAGA
66 CCACCAACTCGTATGGGCTTTGAAAA-GAAAAAGGCATCCTACTCTTTAAGGACTAAAGA
* * * ** **
1401104 GTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGTGTCCTATTCTTTGAGGACTAAAGCATG
1 GTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG
*
1401169 CCACCAACTCGTGTGGGCTTTGAAAA-AAAA
66 CCACCAACTCGTATGGGCTTTGAAAAGAAAA
1401199 GGTGTCATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
122 4 0.02
123 103 0.54
124 83 0.44
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (124 bp):
GTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG
CCACCAACTCGTATGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTAAGGACTAAAGA
Found at i:1405075 original size:79 final size:78
Alignment explanation
Indices: 1404992--1405459 Score: 417
Period size: 79 Copynumber: 5.9 Consensus size: 78
1404982 AAAAATGGGA
** * * * *
1404992 TTAGAGTATCCTTTCAAAAATAATAGGGTTGGAGTATCCCCGATGGT-AGAAAATCGGTGTTTT-
1 TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCGATGGTGA-AAAATCAGTATTTTA
1405055 GAAAATAAAACTGAGG
65 G-AAATAAAAC-GAGG
* *** * * ** *
1405071 TTAGAGTATCTCCTTTGAAATAATAGGGTTGGAGTATCCTCGGTAATGAAAAATTAGTATTTTAG
1 TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCGATGGTGAAAAATCAGTATTTTAG
1405136 AAATAAAATCGAGG
66 AAATAAAA-CGAGG
* * * * * * *
1405150 TTGGGGTATCCCCTCAAAAATAACGGGGTTGGAGTATCC-CAGATTGTGGAAAATCATTGTTTTA
1 TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTC-GATGGTGAAAAATCAGTATTTTA
*
1405214 TAAATAAAAGCG-GTG
65 GAAATAAAA-CGAG-G
* * * * * *
1405229 TTAGAATGTCCCCTCAGAAATTACAGGGTTGGAGTATCCTCGATGGTAAAAAATCTA-TGTTTTA
1 TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCGATGGTGAAAAATC-AGTATTTTA
1405293 GAAATAAAAGCGAGG
65 GAAATAAAA-CGAGG
* * * * * * *
1405308 TTGGAGTATCTCCTCGAAAATAACGGGGTTGAAGTATCCTCGATGGTGAAAAATCAATATTTTGG
1 TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCGATGGTGAAAAATCAGTATTTTAG
*
1405373 AAATAAAACCAGGG
66 AAATAAAACGA-GG
* * * * *
1405387 TTGGAGTATCCCTTCGAAAATAAC-GAGGTTGGAGTATCTTCGATGGTGAAAAATCGGTATTTTA
1 TTAGAGTATCCCCTCAAAAATAACAG-GGTTGGAGTATCCTCGATGGTGAAAAATCAGTATTTTA
1405451 GAAATAAAA
65 GAAATAAAA
1405460 ACATCAATGA
Statistics
Matches: 317, Mismatches: 61, Indels: 22
0.79 0.15 0.05
Matches are distributed among these distances:
78 6 0.02
79 305 0.96
80 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
TTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCGATGGTGAAAAATCAGTATTTTAG
AAATAAAACGAGG
Found at i:1405187 original size:158 final size:154
Alignment explanation
Indices: 1404995--1405459 Score: 468
Period size: 158 Copynumber: 2.9 Consensus size: 154
1404985 AATGGGATTA
** ** **
1404995 GAGTATCCTTTCAAAAATAATAGGGTTGGAGTATCCCCGATGGTAGAAAATCGGTGTTTTGAAAA
1 GAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGT-GAAAATCAATGTTTTGAAAA
* * **
1405060 TAAAACTGAGGTTAGAGTATCTCCTTTGAAATAATAGGGTTGGAGTATCCTCGGTAATGAAAAAT
65 TAAAAC-GAGGTTAGAGTATC-CCTTAGAAATAA-AGGGTTGGAGTATCCTCGATGGTGAAAAAT
*
1405125 TAGTATTTTAGAAATAAAATCGAGGTTG
127 TAGTATTTTAGAAATAAAAGCGAGGTTG
* * * *
1405153 GGGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCAGATTGTGGAAAATCATTGTTTT-ATAA
1 GAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGT-GAAAATCAATGTTTTGA-AA
* * * * *
1405217 ATAAAAGCG-GTGTTAGAATGTCCCCTCAGAAATTACAGGGTTGGAGTATCCTCGATGGTAAAAA
64 ATAAAA-CGAG-GTTAGAGTAT-CCCTTAGAAA-TAAAGGGTTGGAGTATCCTCGATGGTGAAAA
*
1405281 ATCTA-TGTTTTAGAAATAAAAGCGAGGTTG
125 AT-TAGTATTTTAGAAATAAAAGCGAGGTTG
* * * * * *
1405311 GAGTATCTCCTCGAAAATAACGGGGTTGAAGTATCCTCGATGGTGAAAAATCAATATTTTGGAAA
1 GAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTG-AAAATCAATGTTTTGAAAA
* * * * *
1405376 TAAAACCAGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCTTCGATGGTGAAAAAT
65 TAAAACGA-GGTTAGAGTATCCCTTAG-AAATAAAG-GGTTGGAGTATCCTCGATGGTGAAAAAT
**
1405441 CGGTATTTTAGAAATAAAA
127 TAGTATTTTAGAAATAAAA
1405460 ACATCAATGA
Statistics
Matches: 250, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
157 12 0.05
158 231 0.92
159 7 0.03
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (154 bp):
GAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAATCAATGTTTTGAAAAT
AAAACGAGGTTAGAGTATCCCTTAGAAATAAAGGGTTGGAGTATCCTCGATGGTGAAAAATTAGT
ATTTTAGAAATAAAAGCGAGGTTG
Found at i:1405458 original size:237 final size:237
Alignment explanation
Indices: 1405016--1405459 Score: 565
Period size: 237 Copynumber: 1.9 Consensus size: 237
1405006 CAAAAATAAT
* *
1405016 AGGGTTGGAGTATCCCCGATGGTAGAAAATCGGTGTTTTGAAAATAAAACTGAGGTTAGAGTATC
1 AGGGTTGGAGTATCCCCGATGGTAAAAAATCGATGTTTTGAAAATAAAACTGAGGTTAGAGTATC
* * * * * * *
1405081 TCCTTTGAAATAATAGGGTTGGAGTATCCTCGGTAATGAAAAATTAGTATTTTAGAAATAAAATC
66 TCCTTCGAAATAACAGGGTTGAAGTATCCTCGATAATGAAAAATCAATATTTTAGAAATAAAACC
* * * * * *
1405146 GAGGTTGGGGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCAGATTGTGGAAAATCATTGTT
131 GAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCAGATGGTGAAAAATCAGTATT
*
1405211 TTATAAATAAAAGCGGTGTTAGAATGTCCCCTCAGAAATTAC
196 TTAGAAATAAAAGCGGTGTTAGAATGTCCCCTCAGAAATTAC
* * *
1405253 AGGGTTGGAGTATCCTCGATGGTAAAAAATCTATGTTTT-AGAAATAAAAGC-GAGGTTGGAGTA
1 AGGGTTGGAGTATCCCCGATGGTAAAAAATCGATGTTTTGA-AAATAAAA-CTGAGGTTAGAGTA
* ** *
1405316 TCTCC-TCGAAAATAACGGGGTTGAAGTATCCTCGATGGTGAAAAATCAATATTTTGGAAATAAA
64 TCTCCTTCG-AAATAACAGGGTTGAAGTATCCTCGATAATGAAAAATCAATATTTTAGAAATAAA
* * * *
1405380 ACC-AGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCTTC-GATGGTGAAAAATCG
128 ACCGA-GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATC-CCAGATGGTGAAAAATCA
1405443 GTATTTTAGAAATAAAA
191 GTATTTTAGAAATAAAA
1405460 ACATCAATGA
Statistics
Matches: 175, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
236 4 0.02
237 169 0.97
238 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (237 bp):
AGGGTTGGAGTATCCCCGATGGTAAAAAATCGATGTTTTGAAAATAAAACTGAGGTTAGAGTATC
TCCTTCGAAATAACAGGGTTGAAGTATCCTCGATAATGAAAAATCAATATTTTAGAAATAAAACC
GAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCAGATGGTGAAAAATCAGTATT
TTAGAAATAAAAGCGGTGTTAGAATGTCCCCTCAGAAATTAC
Found at i:1407794 original size:20 final size:20
Alignment explanation
Indices: 1407769--1407823 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1407759 AAAATGCCTG
1407769 AATGTATCGATACATTGAGA
1 AATGTATCGATACATTGAGA
1407789 AATGTATCGATACATTGAGA
1 AATGTATCGATACATTGAGA
*
1407809 AATGTATCAATACAT
1 AATGTATCGATACAT
1407824 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAGA
Found at i:1407862 original size:20 final size:20
Alignment explanation
Indices: 1407837--1407894 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1407827 GGTAAAACCC
1407837 AGAATGTATCGATACAATAA
1 AGAATGTATCGATACAATAA
* **
1407857 AGAATGTATTGATAC-ATCT
1 AGAATGTATCGATACAATAA
1407876 AGTAAATGTATCGATACAA
1 AG--AATGTATCGATACAA
1407895 ATTGTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.13
20 14 0.45
21 12 0.39
22 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATACAATAA
Found at i:1407901 original size:21 final size:21
Alignment explanation
Indices: 1407839--1407902 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1407829 TAAAACCCAG
*
1407839 AATGTATCGATAC-AATA-AA
1 AATGTATCGATACAAATAGTA
* **
1407858 GAATGTATTGATACATCTAGTA
1 -AATGTATCGATACAAATAGTA
*
1407880 AATGTATCGATACAAATTGTA
1 AATGTATCGATACAAATAGTA
1407901 AA
1 AA
1407903 AATTTTAAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 12 0.35
21 21 0.62
22 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAAATAGTA
Found at i:1409717 original size:52 final size:52
Alignment explanation
Indices: 1409643--1409804 Score: 209
Period size: 52 Copynumber: 3.1 Consensus size: 52
1409633 TTCTCCCTCA
* * *
1409643 CAACCCCGTTTTTACTTTTAAAAATATTAAATTTTCCAACTTCGAGGATACTT
1 CAACCCTG-TTTTACTTTTAAAAATATCAAATTTTCCATCTTCGAGGATACTT
** * *
1409696 CAACCCTGTTTTACTCCTAAAAATATCAAATTTTCCATCTTCGGGGATACTC
1 CAACCCTGTTTTACTTTTAAAAATATCAAATTTTCCATCTTCGAGGATACTT
* * *
1409748 CAATCCAT-TTTTACTTTTAAAAATATCAAATTTTCCATCTACAAGGATACTT
1 CAA-CCCTGTTTTACTTTTAAAAATATCAAATTTTCCATCTTCGAGGATACTT
1409800 CAACC
1 CAACC
1409805 TCATCACTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.87
53 10 0.11
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (52 bp):
CAACCCTGTTTTACTTTTAAAAATATCAAATTTTCCATCTTCGAGGATACTT
Found at i:1411072 original size:97 final size:97
Alignment explanation
Indices: 1410954--1411266 Score: 409
Period size: 97 Copynumber: 3.2 Consensus size: 97
1410944 AAATTTATTT
* ** * *
1410954 ATCGAGGATAC-TCTAACCCCATTCTTTCAAAAGGATACTCCAATCTCGTTTTTAAACTTGTCAA
1 ATCGAGGATACTTC-AACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTCAA
* *
1411018 GATTTAAATCTTGTTTTTAACTAAATTATCATT
65 GATTTAAATCTTGTTTTTACCTAAATTATCATC
* *
1411051 ATTGAGGATACTTCAACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTTAAG
1 ATCGAGGATACTTCAACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTCAAG
* * * *
1411116 ATTTAAAACATGTTTTTGCCTAAATTGTCATC
66 ATTTAAATCTTGTTTTTACCTAAATTATCATC
* * * *
1411148 ATTGAGG-TA-TTCCAACCCTATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAA
1 ATCGAGGATACTT-CAACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTCAA
1411211 GATTTAAATCTT-TTTTTACCTAAATTATCATC
65 GATTTAAATCTTGTTTTTACCTAAATTATCATC
* *
1411243 ATCGGGGATACTCCAACCCCATTC
1 ATCGAGGATACTTCAACCCCATTC
1411267 CTCTAAGGGG
Statistics
Matches: 187, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
95 25 0.13
96 71 0.38
97 89 0.48
98 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (97 bp):
ATCGAGGATACTTCAACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTCAAG
ATTTAAATCTTGTTTTTACCTAAATTATCATC
Found at i:1411206 original size:96 final size:96
Alignment explanation
Indices: 1410957--1411295 Score: 385
Period size: 96 Copynumber: 3.5 Consensus size: 96
1410947 TTTATTTATC
* * ** ** * * *
1410957 GAGGATACTCTAACCCCATTCTTTCAAAAGGATACTCCAATCTCGTTTTTAAACTTGTCAAGATT
1 GAGGATATTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGATT
* *
1411022 TAAATCTTGTTTTTAACTAAATTATCATTATT
66 TAAATC-TGTTTTTACCTAAATTATCATCATT
* * *
1411054 GAGGATACTT-CAACCCCATTCTTTCGAGGGGATACTCCAATCCCATTTTTAAACTTGTTAAGAT
1 GAGGATA-TTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGAT
* * *
1411118 TTAAAACATGTTTTTGCCTAAATTGTCATCATT
65 TTAAATC-TGTTTTTACCTAAATTATCATCATT
*
1411151 GAGG-TATTCCAACCCTATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGATT
1 GAGGATATTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGATT
* *
1411215 TAAATCTTTTTTTACCTAAATTATCATCATC
66 TAAATCTGTTTTTACCTAAATTATCATCATT
* * * * * * * *
1411246 GGGGATACTCCAACCCCATTCCTCTAAGGGGATACTTCAGCCTCATTTTT
1 GAGGATATTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTTT
1411296 CAACCAAAAA
Statistics
Matches: 207, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
95 26 0.13
96 95 0.46
97 85 0.41
98 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (96 bp):
GAGGATATTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGATT
TAAATCTGTTTTTACCTAAATTATCATCATT
Found at i:1414044 original size:69 final size:70
Alignment explanation
Indices: 1413970--1414122 Score: 193
Period size: 70 Copynumber: 2.2 Consensus size: 70
1413960 GGGGAATGGG
* * *
1413970 GTTGGAGTGTCCTCAACT-ATGATAATTTAAGCAAAAATAAGA-TTAAAGTTTGATGAGTTTAAA
1 GTTGGAGTATCCCCAA-TAATGATAATTTAAGCAAAAATAAGATTTAAAGTTTGATAAGTTTAAA
1414033 AGTAGA
65 AGTAGA
* * * *
1414039 GTTGGAGTATCCCCGATAATGATAATTTAGGCAAAAATAATATTTAAATTTTGATAAGTTTAAAA
1 GTTGGAGTATCCCCAATAATGATAATTTAAGCAAAAATAAGATTTAAAGTTTGATAAGTTTAAAA
** *
1414104 GCGGG
66 GTAGA
1414109 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1414123 TCGGAATAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
68 1 0.01
69 35 0.49
70 36 0.50
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (70 bp):
GTTGGAGTATCCCCAATAATGATAATTTAAGCAAAAATAAGATTTAAAGTTTGATAAGTTTAAAA
GTAGA
Found at i:1414115 original size:70 final size:69
Alignment explanation
Indices: 1413988--1414122 Score: 198
Period size: 70 Copynumber: 1.9 Consensus size: 69
1413978 GTCCTCAACT
* *
1413988 ATGATAATTTAAGCAAAAATAAGATTAAAGTTTGATGAGTTTAAAAGTAGAGTTGGAGTATCCCC
1 ATGATAATTTAAGCAAAAATAAGATTAAAGTTTGATAAGTTTAAAAGCAGAGTTGGAGTATCCCC
1414053 GATA
66 GATA
* * * * *
1414057 ATGATAATTTAGGCAAAAATAATATTTAAATTTTGATAAGTTTAAAAGCGGGGTTGGAGTATCCC
1 ATGATAATTTAAGCAAAAATAAGA-TTAAAGTTTGATAAGTTTAAAAGCAGAGTTGGAGTATCCC
1414122 C
65 C
1414123 TCGGAATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
69 22 0.38
70 36 0.62
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (69 bp):
ATGATAATTTAAGCAAAAATAAGATTAAAGTTTGATAAGTTTAAAAGCAGAGTTGGAGTATCCCC
GATA
Found at i:1416364 original size:20 final size:19
Alignment explanation
Indices: 1416316--1416374 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1416306 AAAAACCCAG
1416316 AATGTATCGATACAATTGTAA
1 AATGTATCGATAC-ATT-TAA
*
1416337 ACATGTATCGATACATTTAGT
1 A-ATGTATCGATACATTTA-A
*
1416358 AATGTATCAATACATTT
1 AATGTATCGATACATTT
1416375 CCTTGGTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 17 0.50
21 5 0.15
22 12 0.35
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (19 bp):
AATGTATCGATACATTTAA
Found at i:1416431 original size:11 final size:11
Alignment explanation
Indices: 1416415--1416447 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1416405 AATACATTGT
1416415 ATCGATACAAA
1 ATCGATACAAA
1416426 ATCGATACAAA
1 ATCGATACAAA
1416437 ATCGATACAAA
1 ATCGATACAAA
1416448 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (11 bp):
ATCGATACAAA
Found at i:1419310 original size:20 final size:20
Alignment explanation
Indices: 1419285--1419338 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1419275 AAAACCCTTA
1419285 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
1419305 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
1419325 AAAGTATCGATACA
1 AAAGTATCGATACA
1419339 TGTTGCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAGTATCGATACACAATTC
Found at i:1419437 original size:13 final size:13
Alignment explanation
Indices: 1419419--1419444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1419409 TACACCAAGT
1419419 ATGTATCGATACA
1 ATGTATCGATACA
1419432 ATGTATCGATACA
1 ATGTATCGATACA
1419445 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1419442 original size:32 final size:33
Alignment explanation
Indices: 1419401--1419464 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1419391 TAGCCAAACT
* **
1419401 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1419433 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1419465 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1421693 original size:21 final size:21
Alignment explanation
Indices: 1421660--1421704 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1421650 TTGCAAGTTG
*
1421660 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1421682 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1421702 AAA
1 AAA
1421705 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1425622 original size:20 final size:20
Alignment explanation
Indices: 1425552--1425630 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1425542 ATGTCCAAAA
*
1425552 TGTATCGATACATGTTT-CT
1 TGTATCGATACATTTTTCCT
**
1425571 GTGTATCGATACATTTGGAAATTCAA
1 -TGTATCGATACATTT-----TTCCT
1425597 TGTATCGATACATTTTTCCT
1 TGTATCGATACATTTTTCCT
1425617 TGTATCGATACATT
1 TGTATCGATACATT
1425631 GTATCGATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 31 0.65
25 17 0.35
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTTCCT
Found at i:1425634 original size:13 final size:13
Alignment explanation
Indices: 1425616--1425641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1425606 ACATTTTTCC
1425616 TTGTATCGATACA
1 TTGTATCGATACA
1425629 TTGTATCGATACA
1 TTGTATCGATACA
1425642 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1425805 original size:20 final size:20
Alignment explanation
Indices: 1425762--1425807 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1425752 AAATCTTTTG
1425762 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1425783 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1425803 CAAAA
1 CAAAA
1425808 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1428104 original size:20 final size:20
Alignment explanation
Indices: 1428079--1428132 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1428069 AAAACCCTTA
1428079 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
1428099 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
1428119 AAAGTATCGATACA
1 AAAGTATCGATACA
1428133 TGTTGCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAGTATCGATACACAATTC
Found at i:1428231 original size:13 final size:13
Alignment explanation
Indices: 1428213--1428238 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1428203 TACACCAAGT
1428213 ATGTATCGATACA
1 ATGTATCGATACA
1428226 ATGTATCGATACA
1 ATGTATCGATACA
1428239 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1428236 original size:32 final size:33
Alignment explanation
Indices: 1428195--1428258 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1428185 TAGCCAAACT
* **
1428195 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1428227 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1428259 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1429831 original size:18 final size:19
Alignment explanation
Indices: 1429787--1429837 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1429777 CATCAATGTA
1429787 AAATCTTTGAATTCATAGTG
1 AAATCTTTGAATTCATA-TG
1429807 AAATCTTTGAATTCAT-TG
1 AAATCTTTGAATTCATATG
* *
1429825 AACTCTTTTAATT
1 AAATCTTTGAATT
1429838 TTACTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
AAATCTTTGAATTCATATG
Found at i:1431198 original size:17 final size:18
Alignment explanation
Indices: 1431176--1431210 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1431166 ATTATAAAAA
1431176 TATTTATATATAT-TTAT
1 TATTTATATATATATTAT
*
1431193 TATTTATCTATATATTAT
1 TATTTATATATATATTAT
1431211 CTTATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATATATATATTAT
Found at i:1431217 original size:20 final size:19
Alignment explanation
Indices: 1431182--1431221 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1431172 AAAATATTTA
1431182 TATATATTTATTATTTATC
1 TATATATTTATTATTTATC
*
1431201 TATATATTATCTTATTTATC
1 TATATATT-TATTATTTATC
1431221 T
1 T
1431222 TTTTTATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATTTATTATTTATC
Found at i:1431271 original size:5 final size:5
Alignment explanation
Indices: 1431261--1431287 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1431251 GTTACTATTT
1431261 TTCTA TTCTA TTCTA TTCTA TTCTA TT
1 TTCTA TTCTA TTCTA TTCTA TTCTA TT
1431288 TGATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.63
Consensus pattern (5 bp):
TTCTA
Found at i:1438910 original size:24 final size:26
Alignment explanation
Indices: 1438883--1438932 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1438873 TCAAAAATTT
1438883 ATTCAT-CG-GGGACACTCCAACCCC
1 ATTCATCCGAGGGACACTCCAACCCC
*
1438907 ATTCCTCCGAGGGACACTCCAACCCC
1 ATTCATCCGAGGGACACTCCAACCCC
1438933 GTTTTCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 2 0.09
26 16 0.70
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (26 bp):
ATTCATCCGAGGGACACTCCAACCCC
Found at i:1441414 original size:26 final size:25
Alignment explanation
Indices: 1441360--1441419 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1441350 TCTTTATTTT
**
1441360 TTAATTT-TTTTAAAATAATGATAA
1 TTAATTTATTTTAAAATAAAAATAA
*
1441384 TTAATTTATTTTTAAATAAAAATAA
1 TTAATTTATTTTAAAATAAAAATAA
*
1441409 TATAATATATT
1 T-TAATTTATT
1441420 AATATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 7 0.23
25 15 0.50
26 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAATTTATTTTAAAATAAAAATAA
Found at i:1441665 original size:16 final size:17
Alignment explanation
Indices: 1441627--1441685 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
1441617 AATAATAATT
*
1441627 AAAAATAATTTTATAATTA
1 AAAAAT-ATTTTA-AAATA
1441646 AAAAATA-TTTAAAATA
1 AAAAATATTTTAAAATA
*
1441662 AAAAA-ATTTTAAAAAA
1 AAAAATATTTTAAAATA
1441678 TAAAAATA
1 -AAAAATA
1441686 AATAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 1 0.03
16 17 0.49
17 9 0.26
18 2 0.06
19 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATATTTTAAAATA
Found at i:1441676 original size:17 final size:16
Alignment explanation
Indices: 1441626--1441684 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
1441616 TAATAATAAT
*
1441626 TAAAAATAATTTTATAA
1 TAAAAA-AATTTTAAAA
*
1441643 TTAAAAAATATTTAAAA
1 TAAAAAAAT-TTTAAAA
1441660 TAAAAAAATTTTAAAA
1 TAAAAAAATTTTAAAA
1441676 -AATAAAAAT
1 TAA-AAAAAT
1441685 AAATAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.05
16 16 0.43
17 19 0.51
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAAATTTTAAAA
Found at i:1441780 original size:24 final size:24
Alignment explanation
Indices: 1441739--1441805 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
1441729 TAAATAATAC
* *
1441739 TTAAAAAATTTATTTTATATTAAATT
1 TTAAAAAAATTA--TTATATTAAAAT
1441765 TTAAAAAAATTATTAT-TTAAAAT
1 TTAAAAAAATTATTATATTAAAAT
* *
1441788 CTAAGTAAAATTATTATA
1 TTAA-AAAAATTATTATA
1441806 GATATCTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.26
24 15 0.43
26 11 0.31
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TTAAAAAAATTATTATATTAAAAT
Found at i:1447778 original size:22 final size:21
Alignment explanation
Indices: 1447753--1447815 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1447743 ATATATGATA
*
1447753 ATAATTGAATGTACATATAAC
1 ATAACTGAATGTACATATAAC
* * *
1447774 TATAACAGCATGTACATATGAC
1 -ATAACTGAATGTACATATAAC
*
1447796 ATCAACTGAATGTATATATA
1 AT-AACTGAATGTACATATA
1447816 GTAAAAATCA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (21 bp):
ATAACTGAATGTACATATAAC
Found at i:1448237 original size:2 final size:2
Alignment explanation
Indices: 1448230--1448255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1448220 TCTAATTTGA
1448230 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1448256 GACTACATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448441 original size:22 final size:22
Alignment explanation
Indices: 1448394--1448446 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1448384 ATAAAAGAAT
*
1448394 ATGTTCATGTGACTATAACAAC
1 ATGTTCATATGACTATAACAAC
* *
1448416 ATGTTTATATGACTTTAACTAA-
1 ATGTTCATATGACTATAAC-AAC
1448438 ATG-TCATAT
1 ATGTTCATAT
1448447 AGTAAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (22 bp):
ATGTTCATATGACTATAACAAC
Found at i:1448639 original size:22 final size:22
Alignment explanation
Indices: 1448591--1448639 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1448581 ATATATATAT
* * *
1448591 ATATGACTATATCTGAATGTAC
1 ATATAACTATAACTAAATGTAC
* *
1448613 TTATAACTATAACTAAATGTTC
1 ATATAACTATAACTAAATGTAC
1448635 ATATA
1 ATATA
1448640 GTAAAAATGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
ATATAACTATAACTAAATGTAC
Found at i:1449233 original size:22 final size:22
Alignment explanation
Indices: 1449208--1449250 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1449198 AATAAAATTG
*
1449208 AATGTATATATGA-TTATAACTC
1 AATGTAAATATGACTT-TAACTC
1449230 AATGTAAATATGACTTTAACT
1 AATGTAAATATGACTTTAACT
1449251 AAACCAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
AATGTAAATATGACTTTAACTC
Found at i:1449377 original size:44 final size:45
Alignment explanation
Indices: 1449327--1449481 Score: 131
Period size: 50 Copynumber: 3.4 Consensus size: 45
1449317 TATTTTTAGT
* *
1449327 TTTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATG
1 TTTTTAATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATA
* * **
1449372 TTTTTAATTTTTATTTTTTAAAATAGTAATTTGATATTTAATATTAGTTA
1 TTTTTAA---TTA-TTTTT-AAATAGTAATTTGAGATTTAATATAAAATA
* * *
1449422 TTTTTAATT-TTTTAAAATAATAATTTG-GTATTTAATAT-ATATA
1 TTTTTAATTATTTTTAAATAGTAATTTGAG-ATTTAATATAAAATA
*
1449465 -TTTTAA-AATTTTTAAAT
1 TTTTTAATTATTTTTAAAT
1449482 TAGCGATAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
42 14 0.16
43 3 0.03
44 21 0.23
45 10 0.11
47 2 0.02
48 3 0.03
49 5 0.06
50 32 0.36
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (45 bp):
TTTTTAATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATA
Found at i:1449405 original size:50 final size:51
Alignment explanation
Indices: 1449328--1449433 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 51
1449318 ATTTTTAGTT
* *
1449328 TTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATGTTTTTAA
1 TTTTTATTATTTTAAAATAGTAATTTGAGATTTAATATAAAATATTTTTAA
* * **
1449379 TTTTTATT-TTTTAAAATAGTAATTTGATATTTAATATTAGTTATTTTTAA
1 TTTTTATTATTTTAAAATAGTAATTTGAGATTTAATATAAAATATTTTTAA
1449429 TTTTT
1 TTTTT
1449434 TAAAATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 41 0.84
51 8 0.16
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (51 bp):
TTTTTATTATTTTAAAATAGTAATTTGAGATTTAATATAAAATATTTTTAA
Found at i:1449467 original size:43 final size:43
Alignment explanation
Indices: 1449378--1449480 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 43
1449368 AATGTTTTTA
*
1449378 ATTTTT-ATTTTTTAAAATAGTAATTTGATATTTAATATTAGTT
1 ATTTTTAATTTTTTAAAATAATAATTTGATATTTAATATTAG-T
*
1449421 ATTTTTAATTTTTTAAAATAATAATTTGGTATTTAATATATA-T
1 ATTTTTAATTTTTTAAAATAATAATTTGATATTTAATAT-TAGT
* *
1449464 ATTTTAAAATTTTTAAA
1 ATTTTTAATTTTTTAAA
1449481 TTAGCGATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
43 22 0.41
44 30 0.56
45 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (43 bp):
ATTTTTAATTTTTTAAAATAATAATTTGATATTTAATATTAGT
Found at i:1450366 original size:20 final size:19
Alignment explanation
Indices: 1450320--1450376 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1450310 TTGTATCGAT
* *
1450320 ACATTGTATCGATATATGT
1 ACATTGTATCGATACATGG
*
1450339 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1450358 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1450377 AAACTGACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1450444 original size:13 final size:13
Alignment explanation
Indices: 1450422--1450451 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1450412 GATACATGGC
*
1450422 ACATTGTATCGAT
1 ACATTATATCGAT
1450435 ACATTATATCGAT
1 ACATTATATCGAT
1450448 ACAT
1 ACAT
1450452 GATAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:1450450 original size:33 final size:33
Alignment explanation
Indices: 1450408--1450473 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1450398 CCACTGTTTG
* *
1450408 TATCGATACATGGCACATTGTATCGATACATTA
1 TATCGATACATGACAAATTGTATCGATACATTA
*
1450441 TATCGATACATGATAAATTGTATCGATACATTA
1 TATCGATACATGACAAATTGTATCGATACATTA
1450474 CTTTAAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
TATCGATACATGACAAATTGTATCGATACATTA
Found at i:1450455 original size:20 final size:20
Alignment explanation
Indices: 1450432--1450471 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1450422 ACATTGTATC
*
1450432 GATACATTATATCGATACAT
1 GATAAATTATATCGATACAT
*
1450452 GATAAATTGTATCGATACAT
1 GATAAATTATATCGATACAT
1450472 TACTTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
GATAAATTATATCGATACAT
Found at i:1452078 original size:3 final size:3
Alignment explanation
Indices: 1452063--1452093 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1452053 AACCATCAAA
*
1452063 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1452094 GTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1457147 original size:21 final size:22
Alignment explanation
Indices: 1457123--1457172 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1457113 ATCAAATCTT
* *
1457123 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1457144 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1457166 --TCAAAAT
1 CTTCAAAAT
1457173 CATAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1458945 original size:24 final size:22
Alignment explanation
Indices: 1458909--1458955 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
1458899 TCTTTAACTG
1458909 TTTATCAACGGGAATAAATTTTTT
1 TTTATCAACGGG-A-AAATTTTTT
1458933 TTTATCGAA-GGGAAAATTTTTT
1 TTTATC-AACGGGAAAATTTTTT
1458955 T
1 T
1458956 AACGAGAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.45
23 1 0.05
24 9 0.41
25 2 0.09
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (22 bp):
TTTATCAACGGGAAAATTTTTT
Found at i:1460094 original size:13 final size:13
Alignment explanation
Indices: 1460076--1460102 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1460066 ACATTATGCT
1460076 TTGTATCGATACA
1 TTGTATCGATACA
1460089 TTGTATCGATACA
1 TTGTATCGATACA
1460102 T
1 T
1460103 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1460134 original size:20 final size:20
Alignment explanation
Indices: 1460088--1460142 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1460078 GTATCGATAC
* **
1460088 ATTGTATCGATACATGTTCA
1 ATTGTATCGATGCATGGACA
1460108 A-TGTATCGATGCATGGACA
1 ATTGTATCGATGCATGGACA
1460127 ATTGTATCGATGCATG
1 ATTGTATCGATGCATG
1460143 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATGCATGGACA
Found at i:1460197 original size:20 final size:18
Alignment explanation
Indices: 1460172--1460223 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 18
1460162 TACCACAGTT
1460172 TGTATCGATACATTGTACAA
1 TGTATCGATACATTG-A-AA
*
1460192 TGTATCGATACA-TGAAC
1 TGTATCGATACATTGAAA
1460209 TGTATCGATACATTG
1 TGTATCGATACATTG
1460224 CTTGTAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.43
18 3 0.10
19 2 0.07
20 12 0.40
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATTGAAA
Found at i:1460229 original size:17 final size:18
Alignment explanation
Indices: 1460171--1460229 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
1460161 CTACCACAGT
1460171 TTGTATCGATACATTGTAC
1 TTGTATCGATACATTG-AC
*
1460190 AATGTATCGATACA-TGAAC
1 -TTGTATCGATACATTG-AC
1460209 -TGTATCGATACATTG-C
1 TTGTATCGATACATTGAC
1460225 TTGTA
1 TTGTA
1460230 ATGGCTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 16 0.46
18 2 0.06
19 4 0.11
20 12 0.34
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACATTGAC
Done.