Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold152
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: 2945013
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 9 of 18
Found at i:1457792 original size:132 final size:132
Alignment explanation
Indices: 1457627--1457879 Score: 337
Period size: 132 Copynumber: 1.9 Consensus size: 132
1457617 CTAAAAGGTG
*** * * * *
1457627 CCACCAACTTGTGTGGGCTTTAGAAGGGTTGCCACCGACTTTTATGGGGTTTGGGAGGGTTGCCA
1 CCACCAACTTGTACAGGCTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTGGAAAGGTTGCCA
* ** * *
1457692 CCGACTTGTATGGGCTTTGGAAGGGTTACC-ACCGACTTATGTGGGCTTTAGAAAGGTAAAAGAG
66 CCGACTTATATGGGCTTTAAAAGGGTT-CCAACCAACATATGTGGGCTTTAGAAAGGTAAAAGAG
1457756 TTA
130 TTA
* * *
1457759 CCACCAACTTGTACAGGCTTTGGAAGGGTTGCCATCGACTTGTGTGGGCTTTGGAAAGGTTGCCA
1 CCACCAACTTGTACAGGCTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTGGAAAGGTTGCCA
* *
1457824 CCGACTTATGTGGGCTTTAAAAGGGTTCCAACCAACATGTGTGGGCTTTAGAAAGG
66 CCGACTTATATGGGCTTTAAAAGGGTTCCAACCAACATATGTGGGCTTTAGAAAGG
1457880 GGTGCCACAG
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
131 2 0.02
132 101 0.98
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (132 bp):
CCACCAACTTGTACAGGCTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTGGAAAGGTTGCCA
CCGACTTATATGGGCTTTAAAAGGGTTCCAACCAACATATGTGGGCTTTAGAAAGGTAAAAGAGT
TA
Found at i:1457956 original size:29 final size:29
Alignment explanation
Indices: 1457879--1457961 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 29
1457869 CTTTAGAAAG
* *
1457879 GGGTGCCACAGAGTTATTGACTTTAAGAA
1 GGGTGCCACTGAGTTATGGACTTTAAGAA
* * *
1457908 GAGATGCCACTAAGTCATGGACTTTAAGAA
1 G-GGTGCCACTGAGTTATGGACTTTAAGAA
1457938 GGGTGCCACTGAGTTATGGACTTT
1 GGGTGCCACTGAGTTATGGACTTT
1457962 TGAAAAAAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 21 0.47
30 24 0.53
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (29 bp):
GGGTGCCACTGAGTTATGGACTTTAAGAA
Found at i:1464038 original size:25 final size:25
Alignment explanation
Indices: 1463988--1464040 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
1463978 AGATTTTGAA
1463988 GAAAAGTGAGGTTGGAGTATCCCCTC
1 GAAAAGTGAGGTTGGAGTAT-CCCTC
*
1464014 GAAAGAGTGGGGTTGGAGTAT-CCTC
1 GAAA-AGTGAGGTTGGAGTATCCCTC
1464039 GA
1 GA
1464041 CAATCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 4 0.16
27 15 0.60
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (25 bp):
GAAAAGTGAGGTTGGAGTATCCCTC
Found at i:1465515 original size:44 final size:44
Alignment explanation
Indices: 1465475--1466272 Score: 544
Period size: 44 Copynumber: 18.3 Consensus size: 44
1465465 TTTGACCAAA
* *
1465475 GTGGTAACCATGCGTCAAATTAAAATGAAAAGAATCTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* * * * * * *
1465519 GTGGTAACCATACGTCAGACCGAAATGAGAAGAGTTTGACCAGA
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* *
1465563 GTGGTAACCATACGTCAAA-CAGGAA-GAAAATG-ATCTGACTAGG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAA-GAATCTGACCAGG
* * * * *
1465606 GTGGTAACCATACGTCATATCGAAAT-AAGAAGAGTTTGACCACG
1 GTGGTAACCATACGTCAAATCAAAATGAA-AAGAATCTGACCAGG
* * * *
1465650 GTGGTAACCATATGTC-AAGCAAGATGAAAAGAATCTGA-TAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* * ** * *
1465692 TTGGTAACCATACGTCATATTGAAAT-AAGAAGAGTTTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAA-AAGAATCTGACCAGG
* * *
1465736 GTGGTAACCATATGTCAAA-CATGAATGAAAA-AAACTTGACCAGG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAAGAATC-TGACCAGG
* ** *
1465780 GTGGTAACCATACGTCAAGT-AGGATAAAAAGAATCTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* * *
1465823 GTGGTAACCATACGTCAAA-CTGAAATGAGAAA-AGTTTGACCAGG
1 GTGGTAACCATACGTCAAATC-AAAATGA-AAAGAATCTGACCAGG
* *
1465867 GTGGTAACCATACGTCAAA-CATGAATGAAAAGAA-CTTGACTAGG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAAGAATC-TGACCAGG
* * * * * * * *
1465911 GTGGTAACCATACATTAGACCGAAATGAGAAGAGTTTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* *
1465955 GTGGTAACCATACATCAAA-CATGAATGAAAAGAA-CTTGACCAGG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAAGAATC-TGACCAGG
* * * * * * * *
1465999 GTGGTAACCATACAAT-AGACCGAAATGAGAAGAGTTTGACCAAG
1 GTGGTAACCATAC-GTCAAATCAAAATGAAAAGAATCTGACCAGG
* *
1466043 GTGGTAACCATACGTCAAA-CATGAATGAAAA-AAACTTGACCAGG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAAGAATC-TGACCAGG
* * ** * * * *
1466087 GTGGTAACCATACATC-AAGCAGGATAAAAAGAATCTAACTAAG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* * ** * * *
1466130 GTGGTAACCATATGTCAGATTGAAATGAGAAGAGTTTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
* * * *
1466174 GTGGTAACCATACGTCAAA-CATGAATAAAAAGACT-TGACCAAG
1 GTGGTAACCATACGTCAAATCA-AAATGAAAAGAATCTGACCAGG
* * * **
1466217 GTGGTAACCGTACATC-AAGCAGGATGAAAAGAATCTGACCAGG
1 GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
*
1466260 GAGGTAACCATAC
1 GTGGTAACCATAC
1466273 ATCGACCAAA
Statistics
Matches: 577, Mismatches: 140, Indels: 75
0.73 0.18 0.09
Matches are distributed among these distances:
42 30 0.05
43 170 0.29
44 368 0.64
45 9 0.02
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (44 bp):
GTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGG
Found at i:1465618 original size:87 final size:87
Alignment explanation
Indices: 1465423--1466272 Score: 654
Period size: 88 Copynumber: 9.7 Consensus size: 87
1465413 GTAAATTGTT
* * * * * **
1465423 TGACCAAGGTGGTAACCATATGTTAAACAGGAA-G-GAAGCAGATTTGACCAAAGTGGTAACCAT
1 TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAG-A-ATTTGACCAGGGTGGTAACCAT
* * *
1465486 GCGTCAAATTA-AAATGAAAAGAATC
64 ACGTCAAA-CAGGAATGAAAAG-ATC
* * * *
1465511 TGACCAGGGTGGTAACCATACGTCAGACCGAAATGAGAAGAGTTTGACCAGAGTGGTAACCATAC
1 TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAGAATTTGACCAGGGTGGTAACCATAC
1465576 GTCAAACAGGAA-GAAAATGATC
66 GTCAAACAGGAATGAAAA-GATC
* * * * *
1465598 TGACTAGGGTGGTAACCATACGTCATA-TCGAAATAAGAAGAGTTTGACCACGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAACT-GAAATGAGAAGAATTTGACCAGGGTGGTAACCATA
* * *
1465662 TGTCAAGCAAG-ATGAAAAGAATC
65 CGTCAAACAGGAATGAAAAG-ATC
* * * * * * *
1465685 TGA-TAGGTTGGTAACCATACGTCATATTGAAATAAGAAGAGTTTGACCAGGGTGGTAACCATAT
1 TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAGAATTTGACCAGGGTGGTAACCATAC
* * *
1465749 GTCAAACATGAATGAAAAAAAC
66 GTCAAACAGGAATGAAAAGATC
* * * * *
1465771 TTGACCAGGGTGGTAACCATACGTC-AAGT-AGGATAAAAAGAATCTGACCAGGGTGGTAACCAT
1 -TGACCAGGGTGGTAACCATACGTCAAACTGA-AATGAGAAGAATTTGACCAGGGTGGTAACCAT
* * *
1465834 ACGTCAAACTGAAATGAGAAA-AGTT
64 ACGTCAAACAGGAATGA-AAAGA-TC
* * *
1465859 TGACCAGGGTGGTAACCATACGTCAAACATG-AATGAAAAGAACTTGACTAGGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAAC-TGAAATGAGAAGAATTTGACCAGGGTGGTAACCATA
* * * * * * *
1465923 CATTAGACCGAAATGAGAAGAGTT
65 CGTCAAACAGGAATGAAAAGA-TC
* * *
1465947 TGACCAGGGTGGTAACCATACATCAAACATG-AATGAAAAGAACTTGACCAGGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAAC-TGAAATGAGAAGAATTTGACCAGGGTGGTAACCATA
* * * * * *
1466011 CAAT-AGACCGAAATGAGAAGAGTT
65 C-GTCAAACAGGAATGAAAAGA-TC
* * * *
1466035 TGACCAAGGTGGTAACCATACGTCAAACATG-AATGAAAAAAACTTGACCAGGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAAC-TGAAATGAGAAGAATTTGACCAGGGTGGTAACCATA
* * *
1466099 CATCAAGCAGG-ATAAAAAGAATC
65 CGTCAAACAGGAATGAAAAG-ATC
* * * * * * *
1466122 TAACTAAGGTGGTAACCATATGTCAGATTGAAATGAGAAGAGTTTGACCAGGGTGGTAACCATAC
1 TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAGAATTTGACCAGGGTGGTAACCATAC
* *
1466187 GTCAAACATGAATAAAAAGA-C
66 GTCAAACAGGAATGAAAAGATC
* * * * * * * * *
1466208 TTGACCAAGGTGGTAACCGTACATCAAGCAG-GATGAAAAGAATCTGACCAGGGAGGTAACCATA
1 -TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAGAATTTGACCAGGGTGGTAACCATA
1466272 C
65 C
1466273 ATCGACCAAA
Statistics
Matches: 649, Mismatches: 89, Indels: 50
0.82 0.11 0.06
Matches are distributed among these distances:
86 102 0.16
87 257 0.40
88 281 0.43
89 5 0.01
90 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (87 bp):
TGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAGAATTTGACCAGGGTGGTAACCATAC
GTCAAACAGGAATGAAAAGATC
Found at i:1466347 original size:307 final size:307
Alignment explanation
Indices: 1465420--1466275 Score: 913
Period size: 307 Copynumber: 2.8 Consensus size: 307
1465410 AATGTAAATT
* * * * ** * * **
1465420 GTTTGACCAAGGTGGTAACCATATGTTAAACAGGAAGGAAGCAGATTTGACCAAAGTGGTAACCA
1 GTTTGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
* * ** ** * * * * *
1465485 TGCGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGACCGAAATGAGAA
66 TACATC-AAGCAGGATAAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACTGAAATGAGAA
* * * * * * * *
1465550 GAGTTTGACCAGAGTGGTAACCATACGTCAAACAGGAAGAAAATGATC-TGACTAGGGTGGTAAC
130 AAGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATAAAAAGAACTTGACCAAGGTGGTAAC
* * * * * * * ** * *
1465614 CATACGTCATATC-GAAAT-AAGAAGAGTTTGACCACGGTGGTAACCATATGTCAAGCA-AGATG
195 CATACATAAGA-CAGAAATGAA-AAGAATCTGACCAGGGAGGTAACCATACATCAAACATAAATG
* * ** * * ** *
1465676 AAAAGAA-TCTGA-TAGGTTGGTAACCATAC-GTCATATTGAAATAAGAAGA
258 AAAAGAACT-TGACCAGGGTCCTAACCATACAAT-AGAACGAAATGAGAAGA
* *
1465725 GTTTGACCAGGGTGGTAACCATATGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
1 GTTTGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
* * * *
1465790 TACGTCAAGTAGGATAAAAAGAATCTGACCAGGGTGGTAACCATACGTCAAACTGAAATGAGAAA
66 TACATCAAGCAGGATAAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACTGAAATGAGAAA
* * *
1465855 AGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATGAAAAGAACTTGACTAGGGTGGTAACC
131 AGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATAAAAAGAACTTGACCAAGGTGGTAACC
* * * * * * *
1465920 ATACATTAGACCGAAATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACATGAATGAAA
196 ATACATAAGACAGAAATGAAAAGAATCTGACCAGGGAGGTAACCATACATCAAACATAAATGAAA
** *
1465985 AGAACTTGACCAGGGTGGTAACCATACAATAGACCGAAATGAGAAGA
261 AGAACTTGACCAGGGTCCTAACCATACAATAGAACGAAATGAGAAGA
1466032 GTTTGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
1 GTTTGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
* * * * *
1466097 TACATCAAGCAGGATAAAAAGAATCTAACTAAGGTGGTAACCATATGTCAGATTGAAATGAGAAG
66 TACATCAAGCAGGATAAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACTGAAATGAGAAA
1466162 AGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATAAAAAG-ACTTGACCAAGGTGGTAACC
131 AGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATAAAAAGAACTTGACCAAGGTGGTAACC
* *
1466226 GTACATCAAG-CAG-GATGAAAAGAATCTGACCAGGGAGGTAACCATACATC
196 ATACAT-AAGACAGAAATGAAAAGAATCTGACCAGGGAGGTAACCATACATC
1466276 GACCAAAATG
Statistics
Matches: 480, Mismatches: 63, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
304 94 0.20
305 153 0.32
306 39 0.08
307 193 0.40
308 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (307 bp):
GTTTGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAAAACTTGACCAGGGTGGTAACCA
TACATCAAGCAGGATAAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACTGAAATGAGAAA
AGTTTGACCAGGGTGGTAACCATACGTCAAACATGAATAAAAAGAACTTGACCAAGGTGGTAACC
ATACATAAGACAGAAATGAAAAGAATCTGACCAGGGAGGTAACCATACATCAAACATAAATGAAA
AGAACTTGACCAGGGTCCTAACCATACAATAGAACGAAATGAGAAGA
Found at i:1466412 original size:35 final size:36
Alignment explanation
Indices: 1466358--1466441 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
1466348 GATCCAATCA
** *
1466358 AATGATCGTGAAAAGAGTTTAACTAGGTACAGCCAAAT
1 AATGAT-G-GAAAAGAGTTTAACTAGAAACAGCCAAAC
* *
1466396 AATGATGGAAAA-AGTTTGACTAGAAACAGCTAAAC
1 AATGATGGAAAAGAGTTTAACTAGAAACAGCCAAAC
1466431 AATGATGGAAA
1 AATGATGGAAA
1466442 GATTTGATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 29 0.71
36 5 0.12
37 1 0.02
38 6 0.15
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.21
Consensus pattern (36 bp):
AATGATGGAAAAGAGTTTAACTAGAAACAGCCAAAC
Found at i:1466794 original size:88 final size:88
Alignment explanation
Indices: 1466668--1466835 Score: 261
Period size: 88 Copynumber: 1.9 Consensus size: 88
1466658 TCAAGATATC
*
1466668 CTTGCCCTAGGAAAATTAGGCTTTGTGATGCATTAATACCATCCAGTGGTTGGA-TGAAGTGGAT
1 CTTGCCCTAGGAAAATTAGGCTTTGTGATGCATCAATACCATCCAGTGGTT-GATTGAAG-GGAT
*
1466732 ATGATT-GGGAATGTGTGGCTCCCG
64 ATGATTAGGAAATGTGTGGCTCCCG
*
1466756 CTTGCCCTAAGG-AAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGATTGAAGGGATA
1 CTTGCCCT-AGGAAAATTAGGCTTTGTGATGCATCAATACCATCCAGTGGTTGATTGAAGGGATA
1466820 TGATTAGGAAATGTGT
65 TGATTAGGAAATGTGT
1466836 TTTCCTTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
87 12 0.16
88 59 0.80
89 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (88 bp):
CTTGCCCTAGGAAAATTAGGCTTTGTGATGCATCAATACCATCCAGTGGTTGATTGAAGGGATAT
GATTAGGAAATGTGTGGCTCCCG
Found at i:1467933 original size:13 final size:13
Alignment explanation
Indices: 1467915--1467939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1467905 ACCAAGAACA
1467915 TGTATCGATACAT
1 TGTATCGATACAT
1467928 TGTATCGATACA
1 TGTATCGATACA
1467940 AAGCAATATG
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:1468602 original size:13 final size:13
Alignment explanation
Indices: 1468584--1468610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1468574 CCTTTTTTAT
1468584 TTCAAAAATAATC
1 TTCAAAAATAATC
1468597 TTCAAAAATAATC
1 TTCAAAAATAATC
1468610 T
1 T
1468611 CCCTTTTTAT
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:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TTCAAAAATAATC
Found at i:1476565 original size:13 final size:13
Alignment explanation
Indices: 1476547--1476574 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1476537 ACATTTCACC
1476547 TTGTATCGATACA
1 TTGTATCGATACA
1476560 TTGTATCGATACA
1 TTGTATCGATACA
1476573 TT
1 TT
1476575 TCACCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1476570 original size:33 final size:33
Alignment explanation
Indices: 1476528--1476592 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1476518 TTGGGCTTAA
*
1476528 TGTATCGATACATTTCACCTTGTATCGATACAT
1 TGTATCGATACATTTCACCATGTATCGATACAT
*
1476561 TGTATCGATACATTTCACCATGTGTCGATACA
1 TGTATCGATACATTTCACCATGTATCGATACA
1476593 ATCTATCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATTTCACCATGTATCGATACAT
Found at i:1476605 original size:33 final size:33
Alignment explanation
Indices: 1476530--1476605 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
1476520 GGGCTTAATG
* * *
1476530 TATCGATACATTTCACCTTGTATCGATACATTG
1 TATCGATACATTTCACCATGTATCGATACAATC
*
1476563 TATCGATACATTTCACCATGTGTCGATACAATC
1 TATCGATACATTTCACCATGTATCGATACAATC
*
1476596 TATCAATACA
1 TATCGATACA
1476606 CTATATCGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (33 bp):
TATCGATACATTTCACCATGTATCGATACAATC
Found at i:1476689 original size:19 final size:20
Alignment explanation
Indices: 1476644--1476716 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1476634 CTGCCAGTTT
**
1476644 CATGTATCGATACAATTC-A
1 CATGTATCGATACAAAGCAA
*
1476663 CTATGTATCGATACCAAG-AA
1 C-ATGTATCGATACAAAGCAA
1476683 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAGCAA
* *
1476703 TATGTATCAATACA
1 CATGTATCGATACA
1476717 TCTAGGTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:1478110 original size:8 final size:8
Alignment explanation
Indices: 1478080--1478145 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
1478070 TAAAGCTTCA
1478080 TTTTTTTCC
1 TTTTTTT-C
*
1478089 ATTTTTTC
1 TTTTTTTC
**
1478097 GCTTTTTC
1 TTTTTTTC
1478105 TTTTTTTC
1 TTTTTTTC
*
1478113 TTTCCTTTC
1 TTT-TTTTC
1478122 TTTTTTTC
1 TTTTTTTC
*
1478130 TTTCCTTTC
1 TTT-TTTTC
1478139 TTTTTTT
1 TTTTTTT
1478146 TTATCATGCT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
8 26 0.57
9 20 0.43
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1478121 original size:17 final size:17
Alignment explanation
Indices: 1478101--1478145 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
1478091 TTTTTCGCTT
1478101 TTTCTTTTTTTCTTTCC
1 TTTCTTTTTTTCTTTCC
1478118 TTTCTTTTTTTCTTTCC
1 TTTCTTTTTTTCTTTCC
1478135 TTTCTTTTTTT
1 TTTCTTTTTTT
1478146 TTATCATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTTTCTTTCC
Found at i:1478434 original size:27 final size:27
Alignment explanation
Indices: 1478397--1478457 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1478387 TTATTTCCTC
1478397 TTTTT-TTTC-TTTTCATGCTTTTCT-TT
1 TTTTTCTTTCTTTTTC-T-CTTTTCTATT
*
1478423 TTTTTCTTTCTTTTTCTCTTTTTTATT
1 TTTTTCTTTCTTTTTCTCTTTTCTATT
1478450 TTTTTCTT
1 TTTTTCTT
1478458 ATTTAGAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 5 0.16
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (27 bp):
TTTTTCTTTCTTTTTCTCTTTTCTATT
Found at i:1482249 original size:155 final size:154
Alignment explanation
Indices: 1482029--1482412 Score: 412
Period size: 155 Copynumber: 2.5 Consensus size: 154
1482019 TAAGCTTTAA
* * * *
1482029 AAAAAATTATGAAAATACCCTTAGGGATACCTTCAACGTAAAAGTACCTGATACCCTTAAAGGAC
1 AAAAAATTATGAAAATACCCTAAGAGATACCTTCAACATAAAAGTACCTAATACCCTTAAAGGAC
* * * * * * *
1482094 TTAAAAGGGATTATAGATGGGATGCACCTATCCTTAACATGTACCTTCGGCAAAAAAGCAG-ACC
66 TTAAAAAGGATGATAGATGAGATGAACCTATCCTAAACATCTACCTTCAGCAAAAAAG-AGAACC
* * * *
1482158 TAGTGATAACTTAAGACTCGGTTCT
130 CAGTGACAACTTAAGACTCGATTAT
* * *
1482183 AAAAAATTACGAAAATACTTCTAAGAGATACCTTCGACATAAAAGTACCTAATACCCTTAAAGGA
1 AAAAAATTATGAAAATAC-CCTAAGAGATACCTTCAACATAAAAGTACCTAATACCCTTAAAGGA
* * * *
1482248 CTTAAAAAGGATGATAGATGAGATTAACCTATCCTAAATATCTACCTTCAGCATAAAAGTGAACC
65 CTTAAAAAGGATGATAGATGAGATGAACCTATCCTAAACATCTACCTTCAGCAAAAAAGAGAACC
*
1482313 CAGTGACAACTTAGGACTCGATTAT
130 CAGTGACAACTTAAGACTCGATTAT
* * * * * ** * * * *
1482338 GAAAAATTATGAAAATGCCCCTAGGGGATATCTTCGTCGTAGAAGTGCCTGATATCCC-TAAAGG
1 AAAAAATTATGAAAAT-ACCCTAAGAGATACCTTCAACATAAAAGTACCTAATA-CCCTTAAAGG
1482402 ACTTAAAAAGG
64 ACTTAAAAAGG
1482413 GTTACAAAAT
Statistics
Matches: 191, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
154 18 0.09
155 169 0.88
156 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (154 bp):
AAAAAATTATGAAAATACCCTAAGAGATACCTTCAACATAAAAGTACCTAATACCCTTAAAGGAC
TTAAAAAGGATGATAGATGAGATGAACCTATCCTAAACATCTACCTTCAGCAAAAAAGAGAACCC
AGTGACAACTTAAGACTCGATTAT
Found at i:1483160 original size:161 final size:166
Alignment explanation
Indices: 1482934--1483399 Score: 502
Period size: 161 Copynumber: 2.8 Consensus size: 166
1482924 TCATAATTTT
* * * ** * *
1482934 TATTTAATTTAAT-TTTTTTATTTCCCAAAAAAATTATTTTATACCTTAATGGAAAACCCAAAAG
1 TATTTATTTTATTATTTTTTATTT-TCAAAAATTTTA-TTCATACCTTAATGG-AAGCCCAAAAG
* * **
1482998 ATACGAAAAGTTTTAAAAATTTTCATACGTCCACGGATTCCCATGGGAATATTAGAAATTTTGAA
63 ATATGAAAAGTTTTAAATATTTTCATACCCCCACGGATTCCCATGGGAATATTAGAAATTTTGAA
1483063 AAATTTAGGTGATAATTTTTATTGGATG-AA-AA-A-GA
128 AAATTTAGGTGATAATTTTTATTGGATGAAAGAATATGA
1483098 -A-TTATTTT-TTATTTTTTATTTTCAAAAATTTTATTCCATACCTTAATGGAAGCCCAAAAAGA
1 TATTTATTTTATTATTTTTTATTTTCAAAAATTTTATT-CATACCTTAATGGAAGCCC-AAAAGA
* * * * * *
1483160 TATGAAAAATTTTAAATA-TTTCTATACCCCCATGGATACCCATAGGAATATGAGAAATTTTAAA
64 TATGAAAAGTTTTAAATATTTTC-ATACCCCCACGGATTCCCATGGGAATATTAGAAATTTTGAA
*
1483224 AAATTTAGGTGATAATTTTTATTGGATGAAAAGGAATTATTTA
128 AAATTTAGGTGATAATTTTTATTGGATG-AAA-GAA-TA-TGA
* * *
1483267 TTATTTTATTTTATTATTTTTTATTTTCAAAAATTTCATTCGTACCTTCATGGAAGCCCGAAAAG
1 -TA-TTTATTTTATTATTTTTTATTTTCAAAAATTTTATTCATACCTTAATGGAAGCCC-AAAAG
* * * *
1483332 ATATAAAAAGTTTTAAATATTTTTATACCCCCACGGATAT-CCATGAGAATATTAGAAATATATG
63 ATATGAAAAGTTTTAAATATTTTCATACCCCCACGGAT-TCCCATGGGAATATTAGAAAT-TTTG
1483396 AAAA
126 AAAA
1483400 TTATTAGTAA
Statistics
Matches: 250, Mismatches: 32, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
160 11 0.04
161 105 0.42
162 16 0.06
163 3 0.01
165 2 0.01
167 1 0.00
169 1 0.00
171 1 0.00
173 75 0.30
174 35 0.14
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (166 bp):
TATTTATTTTATTATTTTTTATTTTCAAAAATTTTATTCATACCTTAATGGAAGCCCAAAAGATA
TGAAAAGTTTTAAATATTTTCATACCCCCACGGATTCCCATGGGAATATTAGAAATTTTGAAAAA
TTTAGGTGATAATTTTTATTGGATGAAAGAATATGA
Found at i:1485178 original size:320 final size:320
Alignment explanation
Indices: 1484801--1485710 Score: 1193
Period size: 319 Copynumber: 2.8 Consensus size: 320
1484791 TTTTTAGGAG
* *
1484801 AAAGAAAAATTTTAAGGAAAAAAAATCAAAATTCATGAAAATGAATGAATTTTTGAAAACTGAAT
1 AAAGAAAAATTTTAAGG--AAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAAT
* * *
1484866 TAATATGAAATAAATAATAATATTTTATGAATTGTAAAAATCAAAAACCAAGAAAAATCCACCTA
64 TAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCC-CCT-
* *
1484931 AAAAAATTTGCAGAGTAGAAAACTTCATATTTCAAAAAAAGATAAATTTCAAGGAAAAAATTCAA
127 AAAAAATTT-CAGAGTAGAAAACTTCGTATTTAAAAAAAAGA-AAATTTCAAGGAAAAAATTCAA
* * *
1484996 AATTTATGGGAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGATAATATTTTATG
190 AATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATG
*
1485061 AATTTT-AAAAT-AA-AAAAATCTCT-CGAAAAAATTTACAGAGTAGAAAACTCCGTATTTCGAA
255 AATTTTAAAAATAAATAAAAATCCCTCCGAAAAAATTTACAGAGTAGAAAACTCCGTATTTCGAA
1485122 A
320 A
* * *
1485123 AAAGAAAAATTTCAAGGAAAAATTCAAAATTTATGAAAATGATTGAATTTTTGAAAACTAAATTA
1 AAAGAAAAATTTTAAGGAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATTA
***
1485188 ATATGAAATAAATAATAATATTTGATGAATTTTAAAAAT-AAAAAACAAGAAAAATCCCC-CCGA
66 ATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCCCCTAAAA
* * ***
1485251 AA----A-AGTATAAAACTTTGTATTTTGGAAAAAGAAAAATTTCAAGGAAAAAATTCAAAATTT
131 AATTTCAGAGTAGAAAACTTCGTATTTAAAAAAAAG-AAAATTTCAAGGAAAAAATTCAAAATTT
** *
1485311 ATGGAAACAAATGAATTTTTAAAAACTGAAA-TAATATGAAATAAATAATAATATTTGATGAATT
195 ATGGAAATGAATGAATTTTTGAAAACT-AAATTAATATGAAATAAATAATAATATTTGATGAATT
* * *
1485375 TTAAAAATAAAAAAAATAAAAATCCCTCCGAAAAAGTTTATAGAGTAGAAAACTTCGTATTTCGA
259 TTAAAAAT-----AAATAAAAATCCCTCCGAAAAAATTTACAGAGTAGAAAACTCCGTATTTCGA
1485440 AA
319 AA
**
1485442 AAA-AGGGAATTTTAAGGAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATT
1 AAAGA-AAAATTTTAAGGAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATT
* *
1485506 AATGTGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAATAAGAAAAATCCCCTTGA
65 AATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCCCC-T-A
* * * *
1485571 AAAATTTTCGGAGTAGAAAAC-TCTGTATTTTGAAAAAAAAGAGAATTTCAAGAAAAAAATTCAA
128 AAAAATTTCAGAGTAGAAAACTTC-GTA-TTT-AAAAAAAAGAAAATTTCAAGGAAAAAATTCAA
* *
1485635 AATTTTTGGAAATGAATGAATTTTTG-AAACTGAATTAATATGAAATAAATAATAATATTTGATG
190 AATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATG
*
1485699 AATTTTCAAAAT
255 AATTTTAAAAAT
1485711 TTTAAACCCA
Statistics
Matches: 511, Mismatches: 52, Indels: 44
0.84 0.09 0.07
Matches are distributed among these distances:
310 105 0.21
311 10 0.02
316 3 0.01
317 2 0.00
318 12 0.02
319 149 0.29
320 100 0.20
322 16 0.03
323 2 0.00
327 3 0.01
328 57 0.11
329 46 0.09
330 6 0.01
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (320 bp):
AAAGAAAAATTTTAAGGAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATTA
ATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCCCCTAAAA
AATTTCAGAGTAGAAAACTTCGTATTTAAAAAAAAGAAAATTTCAAGGAAAAAATTCAAAATTTA
TGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATGAATTTT
AAAAATAAATAAAAATCCCTCCGAAAAAATTTACAGAGTAGAAAACTCCGTATTTCGAAA
Found at i:1485490 original size:18 final size:19
Alignment explanation
Indices: 1485469--1485504 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1485459 AAAAATTCAA
1485469 AATTTATGAAAA-TGAATG
1 AATTTATGAAAACTGAATG
*
1485487 AATTTTTGAAAACTGAAT
1 AATTTATGAAAACTGAAT
1485505 TAATGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTATGAAAACTGAATG
Found at i:1485658 original size:18 final size:18
Alignment explanation
Indices: 1485635--1485669 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1485625 AAAAATTCAA
1485635 AATTTTTGGAAA-TGAATG
1 AATTTTT-GAAACTGAATG
1485653 AATTTTTGAAACTGAAT
1 AATTTTTGAAACTGAAT
1485670 TAATATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (18 bp):
AATTTTTGAAACTGAATG
Found at i:1485740 original size:165 final size:162
Alignment explanation
Indices: 1484819--1485772 Score: 885
Period size: 166 Copynumber: 5.9 Consensus size: 162
1484809 ATTTTAAGGA
* * *
1484819 AAAAAAATCAAAATTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
1 AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTAATATGAAATAAATAAT
* * * * * ** * *
1484884 AATATTTTATGAATTGTAAAAATCAAAAACCAA-GAAAAATCCACCTAAAAAAATTTGCAGAGTA
65 AATATTTGATGAATT-TTAAAATTAAAAA-AAATG-AAAATCC-TCTCGAAAAATTTTCGGAGTA
* * *
1484948 GAAAACT-T-CATATTT-CAAAAAAAGATAAATTTCAAGG
126 GAAAACTCTGTAT-TTTGAAAAAAAAGA-GAATTTCAA-G
* * *
1484985 AAAAAATTCAAAATTTATGGGAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGAT
1 AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTAATATGAAATAAATAAT
* * *
1485050 AATATTTTATGAATTTTAAAA-T-----AAA--AAAAT-CTCTCGAAAAAATTTACAGAGTAGAA
65 AATATTTGATGAATTTTAAAATTAAAAAAAATGAAAATCCTCTCG-AAAAATTTTCGGAGTAGAA
* *
1485106 AACTCCGTATTTCGAAAAAAGAA-A-AATTTCAAG
129 AACTCTGTATTTTGAAAAAA-AAGAGAATTTCAAG
* * * *
1485139 GAAAAATTCAAAATTTATGAAAATGATTGAATTTTTGAAAACTAAATTAATATGAAATAAATAAT
1 AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTAATATGAAATAAATAAT
* * * *
1485204 AATATTTGATGAATTTTAAAAATAAAAAACAA-GAAAAATCCCCCCG-AAAA-------AGTATA
65 AATATTTGATGAATTTTAAAATTAAAAAA-AATG-AAAATCCTCTCGAAAAATTTTCGGAGTAGA
* *
1485260 AAACTTTGTATTTTGGAAAAAGAA-A-AATTTCAAGG
128 AAACTCTGTATTTT-GAAAAAAAAGAGAATTTCAA-G
** * *
1485295 AAAAAATTCAAAATTTATGGAAACAAATGAATTTTTAAAAACTGAAATAATATGAAATAAATAAT
1 AAAAAATTCAAAATTTATGGAAATGAATGAATTTTT-GAAACTGAATTAATATGAAATAAATAAT
* * *
1485360 AATATTTGATGAATTTTAAAAATAAAAAAAATAAAAATCC-CTCCGAAAAAGTTTAT-AGAGTAG
65 AATATTTGATGAATTTTAAAATTAAAAAAAATGAAAATCCTCT-CGAAAAA-TTT-TCGGAGTAG
* * *
1485423 AAAACT-TCGTATTTCG-AAAAAAAGGGAATTTTAAG
127 AAAACTCT-GTATTTTGAAAAAAAAGAGAATTTCAAG
* * *
1485458 GAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATTAATGTGAAATAAATAAT
1 AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTAATATGAAATAAATAAT
* * *
1485523 AATATTTGATGAATTTTAAAAATCAAAAAATAA-GAAAAATCCCCTTGAAAAATTTTCGGAGTAG
65 AATATTTGATGAATTTT-AAAATTAAAAAA-AATG-AAAATCCTCTCGAAAAATTTTCGGAGTAG
1485587 AAAACTCTGTATTTTGAAAAAAAAGAGAATTTCAAG
127 AAAACTCTGTATTTTGAAAAAAAAGAGAATTTCAAG
*
1485623 AAAAAAATTCAAAATTTTTGGAAATGAATGAATTTTTGAAACTGAATTAATATGAAATAAATAAT
1 -AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAACTGAATTAATATGAAATAAATAAT
* *** *
1485688 AATATTTGATGAATTTTCAAAATTTTAAACCCATGAAAA-CCTTCTCGAAAAATTTTACGGAGAA
65 AATATTTGATGAATTTT-AAAA-TTAAAAAAAATGAAAATCC-TCTCGAAAAATTTT-CGGAGTA
* *
1485752 AAAAAC-CTTGTAATTTGAAAA
126 GAAAACTC-TGTATTTTGAAAA
1485773 CTGGAGGAAT
Statistics
Matches: 667, Mismatches: 75, Indels: 92
0.80 0.09 0.11
Matches are distributed among these distances:
154 84 0.13
155 70 0.10
156 103 0.15
157 8 0.01
158 4 0.01
160 1 0.00
161 2 0.00
162 10 0.01
163 83 0.12
164 61 0.09
165 103 0.15
166 138 0.21
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (162 bp):
AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAACTGAATTAATATGAAATAAATAATA
ATATTTGATGAATTTTAAAATTAAAAAAAATGAAAATCCTCTCGAAAAATTTTCGGAGTAGAAAA
CTCTGTATTTTGAAAAAAAAGAGAATTTCAAG
Found at i:1487817 original size:3 final size:3
Alignment explanation
Indices: 1487801--1487865 Score: 57
Period size: 3 Copynumber: 22.0 Consensus size: 3
1487791 ACTTAATATG
*
1487801 AAT AAT AA- AA- AAT AAT AAT AAT AAA AAT AAAT AAT AAAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT
*
1487845 ACAT AA- AAT AAT AAC AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT
1487866 TAATTAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 8 0.15
3 35 0.67
4 9 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1487819 original size:13 final size:13
Alignment explanation
Indices: 1487801--1487864 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
1487791 ACTTAATATG
1487801 AATAATAAAAAAT
1 AATAATAAAAAAT
1487814 AATAATAATAAAAAT
1 AATAAT-A-AAAAAT
*
1487829 AAATAATAAATAAT
1 -AATAATAAAAAAT
1487843 -ATACATAAAATAAT
1 AATA-ATAAAA-AAT
*
1487857 AACAATAA
1 AATAATAA
1487865 TTAATTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.07
13 11 0.26
14 13 0.31
15 9 0.21
16 6 0.14
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:1487850 original size:16 final size:14
Alignment explanation
Indices: 1487795--1487850 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
1487785 CAGTTTACTT
1487795 AATATGAATAATAAAA
1 AATAT-AATAAT-AAA
1487811 AATAATAATAATAAA
1 AAT-ATAATAATAAA
1487826 AATA-AATAATAAA
1 AATATAATAATAAA
1487839 TAATATACATAA
1 -AATATA-ATAA
1487851 AATAATAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.25
14 5 0.14
15 7 0.19
16 13 0.36
17 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AATATAATAATAAA
Found at i:1487863 original size:20 final size:20
Alignment explanation
Indices: 1487809--1487864 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1487799 TGAATAATAA
1487809 AAAATAATAATAATAAAAAT
1 AAAATAATAATAATAAAAAT
* *
1487829 -AAATAATAAATAATATACAT
1 AAAATAAT-AATAATAAAAAT
*
1487849 AAAATAATAACAATAA
1 AAAATAATAATAATAA
1487865 TTAATTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.23
20 16 0.53
21 7 0.23
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATAATAATAATAAAAAT
Found at i:1491958 original size:13 final size:13
Alignment explanation
Indices: 1491940--1491965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1491930 ACAATTTTTG
1491940 TGTATCGATACAT
1 TGTATCGATACAT
1491953 TGTATCGATACAT
1 TGTATCGATACAT
1491966 ACTTTCTGTA
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:1491962 original size:32 final size:32
Alignment explanation
Indices: 1491921--1491983 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1491911 TACAAGCCAA
* *
1491921 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
1491953 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
1491984 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:1492030 original size:21 final size:21
Alignment explanation
Indices: 1492004--1492079 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1491994 CTGCCAAGAA
*
1492004 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1492025 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1492045 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1492066 ATGTATCGATACAT
1 ATGTATCGATACAT
1492080 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1492050 original size:20 final size:20
Alignment explanation
Indices: 1492025--1492097 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1492015 CATCTTTTTT
1492025 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1492045 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1492066 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1492086 ATGTATCGATAC
1 ATGTATCGATAC
1492098 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1492061 original size:41 final size:41
Alignment explanation
Indices: 1492004--1492097 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1491994 CTGCCAAGAA
*
1492004 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1492045 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1492086 ATGTATCGATAC
1 ATGTATCGATAC
1492098 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1493743 original size:13 final size:13
Alignment explanation
Indices: 1493725--1493749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1493715 ACTGAAGCAA
1493725 TGTATCGATACAT
1 TGTATCGATACAT
1493738 TGTATCGATACA
1 TGTATCGATACA
1493750 ATCTGGAAAA
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:1497295 original size:13 final size:13
Alignment explanation
Indices: 1497277--1497302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1497267 ACAATTTTTG
1497277 TGTATCGATACAT
1 TGTATCGATACAT
1497290 TGTATCGATACAT
1 TGTATCGATACAT
1497303 ACTTTCTGTA
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:1497299 original size:32 final size:32
Alignment explanation
Indices: 1497258--1497320 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1497248 TACAAGCCAA
* *
1497258 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
1497290 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
1497321 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:1497367 original size:21 final size:21
Alignment explanation
Indices: 1497341--1497416 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1497331 CTGCCAAGAA
*
1497341 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1497362 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1497382 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1497403 ATGTATCGATACAT
1 ATGTATCGATACAT
1497417 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1497387 original size:20 final size:20
Alignment explanation
Indices: 1497362--1497434 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1497352 CATCTTTTTT
1497362 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1497382 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1497403 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1497423 ATGTATCGATAC
1 ATGTATCGATAC
1497435 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1497398 original size:41 final size:41
Alignment explanation
Indices: 1497341--1497434 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1497331 CTGCCAAGAA
*
1497341 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1497382 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1497423 ATGTATCGATAC
1 ATGTATCGATAC
1497435 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1499626 original size:13 final size:13
Alignment explanation
Indices: 1499608--1499634 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1499598 ACATTATGCT
1499608 TTGTATCGATACA
1 TTGTATCGATACA
1499621 TTGTATCGATACA
1 TTGTATCGATACA
1499634 T
1 T
1499635 GTTCATTGTA
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:1499720 original size:13 final size:13
Alignment explanation
Indices: 1499702--1499726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1499692 TACATGGTAC
1499702 ATTGTATCGATAT
1 ATTGTATCGATAT
1499715 ATTGTATCGATA
1 ATTGTATCGATA
1499727 CATGATGAAT
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:1499725 original size:33 final size:33
Alignment explanation
Indices: 1499683--1499751 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1499673 CTACCACAGT
* *
1499683 TTGTATCGATACATGGT-ACATTGTATCGATATA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
1499716 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1499749 TTG
1 TTG
1499752 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:1501479 original size:13 final size:14
Alignment explanation
Indices: 1501461--1501493 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
1501451 ATGGATTTTT
1501461 AGAAAAAGAA-AAA
1 AGAAAAAGAAGAAA
1501474 AG-AAAAGAAGAAA
1 AGAAAAAGAAGAAA
1501487 AGAAAAA
1 AGAAAAA
1501494 TTCAGATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 7 0.39
14 4 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAGAAA
Found at i:1503595 original size:73 final size:73
Alignment explanation
Indices: 1503513--1503659 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
1503503 TGCCTCTTTA
*
1503513 CTATTTTTTGCATTTGCACCTAATAATTCGCAGATTAAGAGCTGTGCAGGATATTGGACATTATT
1 CTATTTTTTGCATTTGCACCTAATAATTCACAGATTAAGAGCTGTGCAGGATATTGGACATTATT
1503578 CAATATAT
66 CAATATAT
1503586 CTATTTTTTGCATTTGCACCTAATAATTCACAGATTAAGAGCTGTGCAGGATATTGGACATTATT
1 CTATTTTTTGCATTTGCACCTAATAATTCACAGATTAAGAGCTGTGCAGGATATTGGACATTATT
1503651 CAATATAT
66 CAATATAT
1503659 C
1 C
1503660 AGCTTTCTCA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (73 bp):
CTATTTTTTGCATTTGCACCTAATAATTCACAGATTAAGAGCTGTGCAGGATATTGGACATTATT
CAATATAT
Found at i:1504291 original size:42 final size:41
Alignment explanation
Indices: 1504220--1504461 Score: 150
Period size: 42 Copynumber: 5.8 Consensus size: 41
1504210 AACTTTCTCA
* * *
1504220 AGTCTACTTGTCGGCTTTGACCTTGGAGACTTTCTTAGCTTC
1 AGTCTGCTTGTCGGCTTTGACC-TAGAGACTTTCTTACCTTC
* ** ** *
1504262 AGTCTGCTTGTCAGCTTTGATCCTAGAGACTGCCCAATC-TC
1 AGTCTGCTTGTCGGCTTTGA-CCTAGAGACTTTCTTACCTTC
*
1504303 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTT-TCTACCTTC
1 -AGTCTGCTTGTCGGCTTTGA-CCTAGAGACTTTCT-TACCTTC
* * * * ** * *
1504346 AGTCTGCCTATTGGCTTTGACCTTTGAGACTACCTCATC-TC
1 AGTCTGCTTGTCGGCTTTGACC-TAGAGACTTTCTTACCTTC
* * *
1504387 AAGTCTGCCTATTGGCTTTGACCTTAGAGACTTTCTTACC-TC
1 -AGTCTGCTTGTCGGCTTTGACC-TAGAGACTTTCTTACCTTC
* * *
1504429 AAGTCTACCTGTCGACTTTGACCCTAGAGACTT
1 -AGTCTGCTTGTCGGCTTTGA-CCTAGAGACTT
1504462 GACCCTAGAG
Statistics
Matches: 160, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
41 6 0.04
42 147 0.92
43 7 0.04
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.36
Consensus pattern (41 bp):
AGTCTGCTTGTCGGCTTTGACCTAGAGACTTTCTTACCTTC
Found at i:1504363 original size:84 final size:83
Alignment explanation
Indices: 1504215--1505102 Score: 345
Period size: 84 Copynumber: 10.4 Consensus size: 83
1504205 TTTTTAACTT
* * * * * *
1504215 TCTCAAGTCTACTTGTCGGCTTTGACCTTGGAGACTTTCTTAGCTTCAGTCTGCTTGTCAGCTTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTT
*
1504280 GATCCTAGAGACTGCC-CAA
66 GA-CCTAGAGACTACCTC-A
* * *
1504299 TCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTT-TCTACCTTCAGTCTGCCTATTGGCTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCT-TACCTTCAGTCTGCCTGTCGGCTT
*
1504363 TGACCTTTGAGACTACCTCA
65 TGACC-TAGAGACTACCTCA
* * * *
1504383 TCTCAAGTCTGCCTATTGGCTTTGACCTTAGAGACTTTCTTACC-TCAAGTCTACCTGTCGACTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
1504447 TGACCCTAGAGACTTGACC-C-
65 TGA-CCTAGAGAC-T-ACCTCA
** * * ** * * ** ** * ** *
1504467 T-AGAGACTTTCTTACCTCAAGTCTACCTATCGA-CTTTGACCCTAGAGACTT-TCTTACCCTCA
1 TCTCA-A--GTC-TGCCT---GTC-GGCT-TTGACCTTAGAGACT---TTCTTACCTT-CAGTCT
** * * * * *
1504529 GTTTGCCAG--TCGACTTTGACCTTGGAGACTACC-CA
53 GCCTGTCGGCTTTGAC-CT-A--G---AGACTACCTCA
* ** *** * *
1504564 TCTTAAGTCTGCCTGTCAACTTTGACCCCGGAGACTTT-TCTACC-TCAAGTCTGCCTATCGACT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCT-TACCTTC-AGTCTGCCTGTCGGCT
* * *
1504627 TTAACCTTGGAGACTTTCCT-A
64 TTGACC-TAGAGAC-TACCTCA
* * * * * * ** * * * *
1504648 CCTTC-AGTTTGTCTGTCGACTTTGACTTTGGAGACTGCCTCATC-TCAAATCTGCATGTCGGCT
1 TC-TCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCT
* ** *
1504711 TTGACCTTAGACACTTTCTTA
64 TTGACC-TAGAGACTACCTCA
* * * * * * *
1504732 CCACAATTCTGCTTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTT-AGTCTGCGTGTCGACTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTA-CCTTCAGTCTGCCTGTCGGCTT
*
1504796 TGACCTTAGAGACTGCCTCA
65 TGACC-TAGAGACTACCTCA
* * * * * * * *
1504816 TCTCAAGTATGCCTGTTGACTTTGACCCTGGAGACTTGCCTACCTTCAGTCTGCTTGTCGGCTTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTT
*
1504881 GACCCTAGAGACTGCCTCA
66 GA-CCTAGAGACTACCTCA
* * * * * * *
1504900 CCTCAAGTCTGCCTGTCGGCTTTAACCTTGGAGACTTTCCTACCTTCAGTCTACCTATCAGCTTT
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTT
* *
1504965 GACCCTGGATACTACCTCA
66 GA-CCTAGAGACTACCTCA
* * *
1504984 TCTCTAGTCTGCCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTT-AGTCTGTCTGTCGGCT
1 TCTCAAGTCTG-CCTGTCGGCTTTGACCTTAGAGACTTTCTTA-CCTTCAGTCTGCCTGTCGGCT
* ** *
1505048 TTGACCCTGGAGACTTTCTTA
64 TTGA-CCTAGAGACTACCTCA
* ** * *
1505069 CCTTTAGTCTGCCTGTCGACTTTGACCTTGGAGA
1 TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGA
1505103 AAACAATTGG
Statistics
Matches: 596, Mismatches: 158, Indels: 100
0.70 0.19 0.12
Matches are distributed among these distances:
83 19 0.03
84 411 0.69
85 76 0.13
86 12 0.02
87 11 0.02
88 1 0.00
89 7 0.01
90 9 0.02
91 13 0.02
92 7 0.01
93 2 0.00
94 13 0.02
95 3 0.01
96 4 0.01
97 3 0.01
98 5 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (83 bp):
TCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTT
GACCTAGAGACTACCTCA
Found at i:1504465 original size:14 final size:14
Alignment explanation
Indices: 1504446--1504475 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1504436 CCTGTCGACT
1504446 TTGACCCTAGAGAC
1 TTGACCCTAGAGAC
1504460 TTGACCCTAGAGAC
1 TTGACCCTAGAGAC
1504474 TT
1 TT
1504476 TCTTACCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (14 bp):
TTGACCCTAGAGAC
Found at i:1504471 original size:56 final size:56
Alignment explanation
Indices: 1504404--1504517 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
1504394 CCTATTGGCT
* *
1504404 TTGACCTTAGAGACTTTCTTACCTCAAGTCTACCTGTCGACTTTGACCCTAGAGAC
1 TTGACCCTAGAGACTTTCTTACCTCAAGTCTACCTATCGACTTTGACCCTAGAGAC
1504460 TTGACCCTAGAGACTTTCTTACCTCAAGTCTACCTATCGACTTTGACCCTAGAGAC
1 TTGACCCTAGAGACTTTCTTACCTCAAGTCTACCTATCGACTTTGACCCTAGAGAC
1504516 TT
1 TT
1504518 TCTTACCCTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (56 bp):
TTGACCCTAGAGACTTTCTTACCTCAAGTCTACCTATCGACTTTGACCCTAGAGAC
Found at i:1504501 original size:27 final size:27
Alignment explanation
Indices: 1504415--1504503 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
1504405 TGACCTTAGA
*
1504415 GACTTTCTTACCTCAAGTCTACCTGTC
1 GACTTTCTTACCTCAAGTCTACCTATC
* * **
1504442 GAC-TT-TGACC-CTAGAGACTTGACCCTAGA
1 GACTTTCTTACCTC-A-AGTC-T-A-CCTATC
1504471 GACTTTCTTACCTCAAGTCTACCTATC
1 GACTTTCTTACCTCAAGTCTACCTATC
1504498 GACTTT
1 GACTTT
1504504 GACCCTAGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
24 1 0.02
25 5 0.11
26 5 0.11
27 14 0.31
28 2 0.04
29 7 0.16
30 5 0.11
31 5 0.11
32 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.34
Consensus pattern (27 bp):
GACTTTCTTACCTCAAGTCTACCTATC
Found at i:1504506 original size:42 final size:42
Alignment explanation
Indices: 1504460--1505102 Score: 469
Period size: 42 Copynumber: 15.3 Consensus size: 42
1504450 CCCTAGAGAC
* * * *
1504460 TTGACCCTAGAGACTTTCTTACCTCAAGTCTACCTATCGACT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
* * * *
1504502 TTGACCCTAGAGACTTTCTTACCCTC-AGTTTGCCAGTCGACT
1 TTGACCTTGGAGACTTTCTTA-CCTCAAGTCTGCCTGTCGACT
* ** * * *
1504544 TTGACCTTGGAGAC-TACCCATCTTAAGTCTGCCTGTCAACT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
** *
1504585 TTGACCCCGGAGACTTT-TCTACCTCAAGTCTGCCTATCGACT
1 TTGACCTTGGAGACTTTCT-TACCTCAAGTCTGCCTGTCGACT
* * * *
1504627 TTAACCTTGGAGACTTTCCTACCTTC-AGTTTGTCTGTCGACT
1 TTGACCTTGGAGACTTTCTTACC-TCAAGTCTGCCTGTCGACT
* ** * * * * *
1504669 TTGACTTTGGAGACTGCCTCATCTCAAATCTGCATGTCGGCT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
* * * * * *
1504711 TTGACCTTAGACACTTTCTTACCACAATTCTGCTTGTCGGCT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
* *
1504753 TTGACCTTGGAGACTTTCTTACC-CTTAGTCTGCGTGTCGACT
1 TTGACCTTGGAGACTTTCTTACCTC-AAGTCTGCCTGTCGACT
* ** * * * *
1504795 TTGACCTTAGAGACTGCCTCATCTCAAGTATGCCTGTTGACT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
* * * * *
1504837 TTGACCCTGGAGACTTGCCTACCTTC-AGTCTGCTTGTCGGCT
1 TTGACCTTGGAGACTTTCTTACC-TCAAGTCTGCCTGTCGACT
* * ** * *
1504879 TTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
* * * *
1504921 TTAACCTTGGAGACTTTCCTACCTTC-AGTCTACCTATC-AGCT
1 TTGACCTTGGAGACTTTCTTACC-TCAAGTCTGCCTGTCGA-CT
* * ** * * *
1504963 TTGACCCTGGATACTACCTCATCTCTAGTCTGCCCTGTC-AGCT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTG-CCTGTCGA-CT
* * * *
1505006 TTGACCTTAGAGACTTTCTTACC-CTTAGTCTGTCTGTCGGCT
1 TTGACCTTGGAGACTTTCTTACCTC-AAGTCTGCCTGTCGACT
* **
1505048 TTGACCCTGGAGACTTTCTTACCTTTAGTCTGCCTGTCGACT
1 TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
1505090 TTGACCTTGGAGA
1 TTGACCTTGGAGA
1505103 AAACAATTGG
Statistics
Matches: 464, Mismatches: 119, Indels: 36
0.75 0.19 0.06
Matches are distributed among these distances:
40 2 0.00
41 35 0.08
42 384 0.83
43 43 0.09
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (42 bp):
TTGACCTTGGAGACTTTCTTACCTCAAGTCTGCCTGTCGACT
Found at i:1513155 original size:19 final size:20
Alignment explanation
Indices: 1513131--1513185 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1513121 GTATCGATAT
*
1513131 ATTGTATCAATACATGCTC-
1 ATTGTATCGATACATGCTCA
*
1513150 ATTGTATCGATACATACTCA
1 ATTGTATCGATACATGCTCA
1513170 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1513186 AAACCTGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGCTCA
Found at i:1516195 original size:13 final size:13
Alignment explanation
Indices: 1516177--1516203 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1516167 ATATTATGCT
1516177 TTGTATCGATACA
1 TTGTATCGATACA
1516190 TTGTATCGATACA
1 TTGTATCGATACA
1516203 T
1 T
1516204 GCTCATTGTA
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:1516233 original size:20 final size:19
Alignment explanation
Indices: 1516187--1516249 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1516177 TTGTATCGAT
1516187 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
1516206 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
* *
1516225 ACAATTGTATCAATATATG-
1 AC-ATTGTATCGATACATGC
1516244 ACATTG
1 ACATTG
1516250 GCAGTAGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 4 0.11
19 20 0.53
20 14 0.37
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1524338 original size:20 final size:19
Alignment explanation
Indices: 1524288--1524344 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1524278 TTGTATCGAT
1524288 ACATTATATCGATACATGC
1 ACATTATATCGATACATGC
* * *
1524307 TCATTGTATCGATACATGG
1 ACATTATATCGATACATGC
1524326 ACAATTATATCGATACATG
1 AC-ATTATATCGATACATG
1524345 AGATTGCCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
ACATTATATCGATACATGC
Found at i:1524455 original size:13 final size:13
Alignment explanation
Indices: 1524398--1524455 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1524388 GGACAATGTG
1524398 TCGATACATTGTA
1 TCGATACATTGTA
*
1524411 TCAATACATTGTA
1 TCGATACATTGTA
1524424 TCGATACA-TG-A
1 TCGATACATTGTA
1524435 T-GA-A-ATTGTA
1 TCGATACATTGTA
*
1524445 TCGATAAATTG
1 TCGATACATTG
1524456 CTTATAACGG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 4 0.11
11 4 0.11
12 3 0.08
13 23 0.61
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (13 bp):
TCGATACATTGTA
Found at i:1525450 original size:20 final size:20
Alignment explanation
Indices: 1525425--1525476 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1525415 TACAAGCCAA
**
1525425 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
1525445 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
*
1525464 TGTCTCGATACAA
1 TGTATCGATACAA
1525477 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:1527563 original size:21 final size:20
Alignment explanation
Indices: 1527534--1527576 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1527524 GACTAGTGTG
*
1527534 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
* *
1527555 GGGAGTGCCGGTCGTGACCT
1 GGGACTGCCGGTCGCGACCT
1527575 GG
1 GG
1527577 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1528017 original size:13 final size:13
Alignment explanation
Indices: 1527999--1528037 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1527989 ATAATCCTCC
* *
1527999 TGTATCAATACAG
1 TGTATCGATACAA
1528012 TGTATCGATACAA
1 TGTATCGATACAA
1528025 TGTATCGATACAA
1 TGTATCGATACAA
1528038 AAAAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1530117 original size:15 final size:15
Alignment explanation
Indices: 1530097--1530127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1530087 ATTTCGTTTG
*
1530097 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1530112 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1530127 G
1 G
1530128 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:1534201 original size:13 final size:13
Alignment explanation
Indices: 1534183--1534208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1534173 CAATTTTTTG
1534183 TGTATCGATACAT
1 TGTATCGATACAT
1534196 TGTATCGATACAT
1 TGTATCGATACAT
1534209 ACTTTGTGTA
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:1534220 original size:32 final size:33
Alignment explanation
Indices: 1534163--1534226 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1534153 TACAAGCTAA
**
1534163 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1534196 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1534227 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1535107 original size:2 final size:2
Alignment explanation
Indices: 1535100--1535137 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1535090 TTGAGCTTTC
1535100 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1535138 TCTTAAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1543365 original size:13 final size:13
Alignment explanation
Indices: 1543347--1543372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1543337 CAATTTTTGG
1543347 TGTATCGATACAT
1 TGTATCGATACAT
1543360 TGTATCGATACAT
1 TGTATCGATACAT
1543373 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:1543384 original size:32 final size:33
Alignment explanation
Indices: 1543327--1543390 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1543317 TACAAGCCAA
**
1543327 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1543360 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1543391 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1543397 original size:19 final size:18
Alignment explanation
Indices: 1543327--1543397 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1543317 TACAAGCCAA
1543327 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1543347 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1543360 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1543379 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1543398 CTACTGTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1543761 original size:2 final size:2
Alignment explanation
Indices: 1543754--1543785 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1543744 AGATCCTAAC
1543754 AT AT AT 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 AT AT AT
1543786 GCGCATGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1545423 original size:58 final size:60
Alignment explanation
Indices: 1545330--1545456 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 60
1545320 CTATTTACCC
* *
1545330 AATTAAACCATAGAAGTACTATTTTTATCTAATT-AACTCCTCAAAGTACTATTTTTGTAT
1 AATTAAACCATAGAAGTACTATTATTATCCAATTAAAC-CCTCAAAGTACTATTTTTGTAT
* * *
1545390 AATTAAACCATA-AAGTACTA-TATTGTCCAATTAAACCCTTAAAGTACTATTTTTGTCT
1 AATTAAACCATAGAAGTACTATTATTATCCAATTAAACCCTCAAAGTACTATTTTTGTAT
1545448 AATTAAACC
1 AATTAAACC
1545457 CTTAAAACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 38 0.62
59 11 0.18
60 12 0.20
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (60 bp):
AATTAAACCATAGAAGTACTATTATTATCCAATTAAACCCTCAAAGTACTATTTTTGTAT
Found at i:1545457 original size:30 final size:30
Alignment explanation
Indices: 1545330--1545462 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
1545320 CTATTTACCC
* *
1545330 AATTAAA-CCATAGAAGTACTATTTTTATCT
1 AATTAAACCCTTA-AAGTACTATTTTTGTCT
* *
1545360 AATT-AACTCCTCAAAGTACTATTTTTGTAT
1 AATTAAAC-CCTTAAAGTACTATTTTTGTCT
* * *
1545390 AATTAAA-CCATAAAGTACTA-TATTGTCC
1 AATTAAACCCTTAAAGTACTATTTTTGTCT
1545418 AATTAAACCCTTAAAGTACTATTTTTGTCT
1 AATTAAACCCTTAAAGTACTATTTTTGTCT
1545448 AATTAAACCCTTAAA
1 AATTAAACCCTTAAA
1545463 ACTTTTTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
28 12 0.14
29 25 0.29
30 44 0.51
31 5 0.06
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTAAACCCTTAAAGTACTATTTTTGTCT
Found at i:1549874 original size:13 final size:13
Alignment explanation
Indices: 1549856--1549881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1549846 CACTCCCAGA
1549856 TGTATCGATACAT
1 TGTATCGATACAT
1549869 TGTATCGATACAT
1 TGTATCGATACAT
1549882 GCTCATTGTA
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:1549890 original size:19 final size:19
Alignment explanation
Indices: 1549865--1549921 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1549855 ATGTATCGAT
1549865 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
1549884 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
1549903 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1549922 AAACTGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1549911 original size:20 final size:20
Alignment explanation
Indices: 1549867--1550003 Score: 88
Period size: 20 Copynumber: 6.8 Consensus size: 20
1549857 GTATCGATAC
**
1549867 ATTGTATCGATACATGCTC-
1 ATTGTATCGATACATGGACA
1549886 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1549906 ATTGTATCGATACAT-GA-A
1 ATTGTATCGATACATGGACA
* * * * *
1549924 ACTGACAGTAGCTACCCTAT-CACTA
1 ATTG-TA-TCGATA--C-ATGGAC-A
*
1549949 TTTGTATCGATACATGGGACA
1 ATTGTATCGATACAT-GGACA
1549970 A-TGTATCGATACATGGGACA
1 ATTGTATCGATACAT-GGACA
1549990 A-TGTATCGATACAT
1 ATTGTATCGATACAT
1550004 TGTATCGATA
Statistics
Matches: 94, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.04
19 20 0.21
20 54 0.57
21 2 0.02
22 3 0.03
23 7 0.07
24 1 0.01
25 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:1550009 original size:13 final size:13
Alignment explanation
Indices: 1549991--1550016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1549981 CATGGGACAA
1549991 TGTATCGATACAT
1 TGTATCGATACAT
1550004 TGTATCGATACAT
1 TGTATCGATACAT
1550017 AAGGAAATTG
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:1550034 original size:34 final size:33
Alignment explanation
Indices: 1549971--1550039 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
1549961 CATGGGACAA
*
1549971 TGTATCGATACATGGGACAATGTATCGATACAT
1 TGTATCGATACATAGGACAATGTATCGATACAT
1550004 TGTATCGATACATAAGGA-AATTGTATCGATACAT
1 TGTATCGATACAT-AGGACAA-TGTATCGATACAT
1550038 TG
1 TG
1550040 CTTGTAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 15 0.45
34 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGACAATGTATCGATACAT
Found at i:1558610 original size:32 final size:33
Alignment explanation
Indices: 1558549--1558613 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1558539 ACACTCCCAG
*
1558549 ATGTATCGATACATACTGCTTTGTATCGATACA
1 ATGTATCGATACATACTGCATTGTATCGATACA
* *
1558582 ATGTATCGATACGTGCT-CATTGTATCGATACA
1 ATGTATCGATACATACTGCATTGTATCGATACA
1558614 TGGATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACATACTGCATTGTATCGATACA
Found at i:1558703 original size:13 final size:13
Alignment explanation
Indices: 1558685--1558710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1558675 CATGGGACAA
1558685 TGTATCGATACAT
1 TGTATCGATACAT
1558698 TGTATCGATACAT
1 TGTATCGATACAT
1558711 AAGGAAATTG
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:1558706 original size:33 final size:34
Alignment explanation
Indices: 1558664--1558732 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
1558654 CTATCACTAT
* *
1558664 TTGTATCGATACAT-GGGACAA-TGTATCGATACA
1 TTGTATCGATACATAAGGA-AATTGTATCCATACA
1558697 TTGTATCGATACATAAGGAAATTGTATCCATACA
1 TTGTATCGATACATAAGGAAATTGTATCCATACA
1558731 TT
1 TT
1558733 ACTTATAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (34 bp):
TTGTATCGATACATAAGGAAATTGTATCCATACA
Found at i:1566180 original size:3 final size:3
Alignment explanation
Indices: 1566166--1566195 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1566156 AAATATGAAG
*
1566166 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1566196 AGCAGGCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1567239 original size:24 final size:24
Alignment explanation
Indices: 1567206--1567284 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
1567196 TGACTATTTC
*
1567206 TTTTATGTAAAAAAGTAGTTTTTG
1 TTTTAAGTAAAAAAGTAGTTTTTG
* * *
1567230 TTTTACGTAAGAAAAG-GGATTTT-
1 TTTTAAGTAA-AAAAGTAGTTTTTG
1567253 TTTTAAGTGAAAAATAGGTAGTTTTTG
1 TTTTAAGT-AAAAA-A-GTAGTTTTTG
1567280 TTTTA
1 TTTTA
1567285 GAAAATTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
23 10 0.23
24 17 0.40
25 6 0.14
26 5 0.12
27 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (24 bp):
TTTTAAGTAAAAAAGTAGTTTTTG
Found at i:1567581 original size:2 final size:2
Alignment explanation
Indices: 1567574--1567608 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1567564 TGCTAGCTTA
1567574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1567609 CTAGAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1568522 original size:2 final size:2
Alignment explanation
Indices: 1568515--1568545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1568505 GAACATGATT
1568515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1568546 TACTTAGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1569204 original size:16 final size:16
Alignment explanation
Indices: 1569185--1569346 Score: 74
Period size: 16 Copynumber: 10.1 Consensus size: 16
1569175 CGAACTTGAA
*
1569185 CCCGAACTCGAATAAG
1 CCCGAACCCGAATAAG
1569201 CCCGAACCCGAATAAG
1 CCCGAACCCGAATAAG
* * * *
1569217 CCCAAATCTGAAAAAG
1 CCCGAACCCGAATAAG
* * **
1569233 CTCAAACCCGAACGAG
1 CCCGAACCCGAATAAG
* * * *
1569249 CTCGAGCCCAAATGAG
1 CCCGAACCCGAATAAG
* *
1569265 CCCGAACCCAAATGAG
1 CCCGAACCCGAATAAG
* * **
1569281 TCCAAACCTTAA-AGAG
1 CCCGAACCCGAATA-AG
* **
1569297 CCCGAACCCGGACGAG
1 CCCGAACCCGAATAAG
* **
1569313 CCCGAACCCGGACGAG
1 CCCGAACCCGAATAAG
*
1569329 CCCGAACCCGAATGAG
1 CCCGAACCCGAATAAG
1569345 CC
1 CC
1569347 TAAACTTGAA
Statistics
Matches: 115, Mismatches: 29, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
16 115 1.00
ACGTcount: A:0.35, C:0.36, G:0.21, T:0.08
Consensus pattern (16 bp):
CCCGAACCCGAATAAG
Found at i:1569273 original size:64 final size:64
Alignment explanation
Indices: 1569199--1569356 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 64
1569189 AACTCGAATA
* * * * * *
1569199 AGCCCGAACCCGAATAAGCCCAAATCTGAAAAAGCTCAAACCCGAACGAGCTCGAGCCCAAATG
1 AGCCCGAACCCGAATGAGCCCAAACCTGAAAAAGCCCAAACCCGAACGAGCCCGAACCCAAACG
* * * * * * **
1569263 AGCCCGAACCCAAATGAGTCCAAACCTTAAAGAGCCCGAACCCGGACGAGCCCGAACCCGGACG
1 AGCCCGAACCCGAATGAGCCCAAACCTGAAAAAGCCCAAACCCGAACGAGCCCGAACCCAAACG
* *
1569327 AGCCCGAACCCGAATGAGCCTAAACTTGAA
1 AGCCCGAACCCGAATGAGCCCAAACCTGAA
1569357 CCTGCCTAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.36, C:0.34, G:0.21, T:0.09
Consensus pattern (64 bp):
AGCCCGAACCCGAATGAGCCCAAACCTGAAAAAGCCCAAACCCGAACGAGCCCGAACCCAAACG
Found at i:1569346 original size:32 final size:32
Alignment explanation
Indices: 1569199--1569351 Score: 110
Period size: 32 Copynumber: 4.8 Consensus size: 32
1569189 AACTCGAATA
* * * *
1569199 AGCCCGAACCCGAATAAGCCCAAATCTGAAAA
1 AGCCCGAACCCGAATGAGCCCAAACCCGAAAG
* * * * * *
1569231 AGCTCAAACCCGAACGAGCTCGAGCCC-AAATG
1 AGCCCGAACCCGAATGAGCCCAAACCCGAAA-G
* * **
1569263 AGCCCGAACCCAAATGAGTCCAAACCTTAAAG
1 AGCCCGAACCCGAATGAGCCCAAACCCGAAAG
* * * * *
1569295 AGCCCGAACCCGGACGAGCCCGAACCCGGACG
1 AGCCCGAACCCGAATGAGCCCAAACCCGAAAG
*
1569327 AGCCCGAACCCGAATGAGCCTAAAC
1 AGCCCGAACCCGAATGAGCCCAAAC
1569352 TTGAACCTGC
Statistics
Matches: 87, Mismatches: 32, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
31 3 0.03
32 81 0.93
33 3 0.03
ACGTcount: A:0.36, C:0.35, G:0.21, T:0.08
Consensus pattern (32 bp):
AGCCCGAACCCGAATGAGCCCAAACCCGAAAG
Found at i:1581494 original size:156 final size:156
Alignment explanation
Indices: 1581311--1581604 Score: 401
Period size: 156 Copynumber: 1.9 Consensus size: 156
1581301 CTTCAAAAAA
* * *
1581311 TTGGAAACTACTTTCCTAAATGGTTTAGGAAGTATTACATACTAAATGATTTGTATAAATTAAGA
1 TTGGAAACAACTTTCCTAAATGGTTTAGGAAATATGACATACTAAATGATTTGTATAAATTAAGA
* * * * *
1581376 CAAAGTTGTC-AAAAGTTAGATAATGTTCTAATTAAGATAAACAACCTAACAGTTAGATAAAGTC
66 CAAAGTTATCTAAAAGTTAGAAAATGTCCTAATTAAGACAAACAACCTAAAAGTTAGATAAAGTC
1581440 CAATTTAATGTCTTAAAATGTTGTTT
131 CAATTTAATGTCTTAAAATGTTGTTT
* * * * *
1581466 TTGGAAAACAACTTTCCTAAATGGTTTAGGAAATATGATATGCTAAATGGTTTGTCTGAATTAAG
1 TTGG-AAACAACTTTCCTAAATGGTTTAGGAAATATGACATACTAAATGATTTGTATAAATTAAG
* * * * *
1581531 ATAAAGTTATCTAAAAGTTAGAAAATGTCCTATTTAAGACATACAACCTAAAAGTTAGGTAATGT
65 ACAAAGTTATCTAAAAGTTAGAAAATGTCCTAATTAAGACAAACAACCTAAAAGTTAGATAAAGT
*
1581596 CTAATTTAA
130 CCAATTTAA
1581605 AACAGCTTCC
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
155 4 0.03
156 61 0.52
157 53 0.45
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (156 bp):
TTGGAAACAACTTTCCTAAATGGTTTAGGAAATATGACATACTAAATGATTTGTATAAATTAAGA
CAAAGTTATCTAAAAGTTAGAAAATGTCCTAATTAAGACAAACAACCTAAAAGTTAGATAAAGTC
CAATTTAATGTCTTAAAATGTTGTTT
Found at i:1582398 original size:16 final size:16
Alignment explanation
Indices: 1582377--1582409 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1582367 TCCAATCATA
1582377 AGAGAATCGTTGGGCT
1 AGAGAATCGTTGGGCT
1582393 AGAGAATCGTTGGGCT
1 AGAGAATCGTTGGGCT
1582409 A
1 A
1582410 TCCCAAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.24
Consensus pattern (16 bp):
AGAGAATCGTTGGGCT
Found at i:1584630 original size:156 final size:156
Alignment explanation
Indices: 1584454--1584774 Score: 389
Period size: 156 Copynumber: 2.1 Consensus size: 156
1584444 ATGTCTTTGG
*
1584454 GGTATACCTTTAACATGAAAGTATCCTGGTAATCC-TAATA-GACACTAAAATGATCATAAATTG
1 GGTATACCTTTAACATGAAAGTATCCTGGTAA-CCTTAA-AGGACACTAAAATGATCATAAATAG
* * * * ** * * *
1584517 GACGAACTTATCCTAAATGCATACATTCAGCATAAAAGTATCTCGGTGATAGCCTAGGACTCTAT
64 GACAAACCTATCCTAAATGCATACATTCAGCATAAAAGCATCCCAATGACAACCTAGGACTCGAT
*
1584582 TTTACA-AAAATTATGAAAATACCCTTAA
129 ATTA-AGAAAATTATGAAAATACCCTTAA
* * *
1584610 GGTATACTTTTGACATGAAAGTATCCTGGTAACCTTAAAGGACATTAAAATGATCATAAATAGGA
1 GGTATACCTTTAACATGAAAGTATCCTGGTAACCTTAAAGGACACTAAAATGATCATAAATAGGA
* * * * *
1584675 TAAACCTATCCTAAATGTATACCTTCGGCATGAAAGCATCCCAATGACAACCTAGGACTCGATAT
66 CAAACCTATCCTAAATGCATACATTCAGCATAAAAGCATCCCAATGACAACCTAGGACTCGATAT
* * *
1584740 TAAGAAAATTATGAAAAAACACTT-G
131 TAAGAAAATTATGAAAATACCCTTAA
1584765 GGTATACCTT
1 GGTATACCTT
1584775 CGATGTGAAA
Statistics
Matches: 139, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
155 13 0.09
156 126 0.91
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (156 bp):
GGTATACCTTTAACATGAAAGTATCCTGGTAACCTTAAAGGACACTAAAATGATCATAAATAGGA
CAAACCTATCCTAAATGCATACATTCAGCATAAAAGCATCCCAATGACAACCTAGGACTCGATAT
TAAGAAAATTATGAAAATACCCTTAA
Found at i:1585179 original size:163 final size:163
Alignment explanation
Indices: 1585010--1585401 Score: 671
Period size: 163 Copynumber: 2.4 Consensus size: 163
1585000 TGACTAAGAT
1585010 GATGATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAATTTCATTTCA
1 GATGATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAATTTCATTTCA
1585075 TACCCGATAGAAAATCGAGAGGATATGAAAAGTTTTAAAAGTTTTTATACCCTTATGGAAGACTA
66 TACCCGATAGAAAATCGAGAGGATATGAAAAGTTTTAAAAGTTTTTATACCCTTATGGAAGACTA
*
1585140 TAGGAATAATAAATTTTTTTAAAAAATGACTAA
131 TAGGAATAATAAAATTTTTTAAAAAATGACTAA
1585173 GATGATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAATTTCATTTCA
1 GATGATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAATTTCATTTCA
1585238 TACCCGATAGAAAATCGAGAGGATATGAAAAGTTTTAAAAGTTTTTATACCCTTATGGAAGACTA
66 TACCCGATAGAAAATCGAGAGGATATGAAAAGTTTTAAAAGTTTTTATACCCTTATGGAAGACTA
1585303 TAGGAATAATAAAATTTTTTAAAAAATGACTAA
131 TAGGAATAATAAAATTTTTTAAAAAATGACTAA
* ** * *
1585336 GATAGCTATTTTTTTTAAAAAACC-AAATTTGCTATTTAGTCCCTAAATTTTTA-AAAGTTTTCA
1 GAT-G--ATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAA--TTTCA
1585399 TTT
61 TTT
1585402 TAGTCTCTAC
Statistics
Matches: 218, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
163 165 0.76
164 4 0.02
165 28 0.13
166 21 0.10
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (163 bp):
GATGATTTTTCTTCTAAATCCTAAATTTGCTATTTAGTCCCTAAACTTTTACAAATTTCATTTCA
TACCCGATAGAAAATCGAGAGGATATGAAAAGTTTTAAAAGTTTTTATACCCTTATGGAAGACTA
TAGGAATAATAAAATTTTTTAAAAAATGACTAA
Found at i:1586515 original size:3 final size:3
Alignment explanation
Indices: 1586507--1586535 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1586497 TTTCTTTTCC
1586507 ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1586536 TTTTATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1586527 original size:14 final size:14
Alignment explanation
Indices: 1586508--1586542 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1586498 TTCTTTTCCA
1586508 TTATTATTATTATT
1 TTATTATTATTATT
1586522 TTATTATTATTATT
1 TTATTATTATTATT
1586536 TT-TTATT
1 TTATTATT
1586543 TGATTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:1587226 original size:153 final size:154
Alignment explanation
Indices: 1586900--1587378 Score: 447
Period size: 154 Copynumber: 3.2 Consensus size: 154
1586890 ATAAACAAAT
* * * *
1586900 TTAAT-AAAAATATTTGATA-AATTTTAAAAATTTTAAAC-TAAAAAAAATCCA-ACCAAAAAAA
1 TTAATCAATAATATTTGA-AGAATTTTAAAAATTATAAACAT-AGAAAAAT-CATACCGAAAAAA
* * * * ** * * *
1586961 TTTACGGATTAGAAAACTT-GTTTCTTGGTATCA-AAAAAATTATAAAACTCATAAAATAAATTG
63 TTTATGAAGTAGAAAACTTCGTATCTCAGTAACAGAAAAAATTCTAAAAATCATAAAATAAATTG
* *
1587024 AA-TTTTCAAAATTGA-TT----T-AA
128 AATTTTTCAAAACTAATTTAAGATAAA
* * *
1587044 -T-ATGAGTAATATTTGAATAATTTTAAAAATTATAAACATAGAAAAATTC-TACCGAAAAAATT
1 TTAATCAATAATATTTGAAGAATTTTAAAAATTATAAACATAGAAAAA-TCATACCGAAAAAATT
* ** *
1587106 TATGTAGTAGAAAAC-TCTGTATCTTGGTAGC-GAAAAAATT-TCAAAAATCATAAAATAAATTG
65 TATGAAGTAGAAAACTTC-GTATCTCAGTAACAGAAAAAATTCT-AAAAATCATAAAATAAATTG
* *
1587168 AATTTTTCAAAACTGATTTCAGATAAA
128 AATTTTTCAAAACTAATTTAAGATAAA
* * * *
1587195 TTAATCAATAATATTTGAAGAATTTTTAAAATTATAAACTTAGAAAAATCATTCTGAAAAAATTT
1 TTAATCAATAATATTTGAAGAATTTTAAAAATTATAAACATAGAAAAATCATACCGAAAAAATTT
* ** *
1587260 ATGAAGTAGAAAACTTCGTTTCTCAGTAACAGAAAAAATTCTAAAGCTTATAAAATAAATTGAAT
66 ATGAAGTAGAAAACTTCGTATCTCAGTAACAGAAAAAATTCTAAAAATCATAAAATAAATTGAAT
* *
1587325 TTTTCAAAACTAATTTAATATGAA
131 TTTTCAAAACTAATTTAAGATAAA
* *
1587349 TTAATCAATAATAATTGAAGAATTTGAAAA
1 TTAATCAATAATATTTGAAGAATTTTAAAA
1587379 TTAAAAATTT
Statistics
Matches: 279, Mismatches: 34, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
142 4 0.01
143 60 0.22
144 42 0.15
145 12 0.04
146 2 0.01
150 1 0.00
151 2 0.01
152 3 0.01
153 74 0.27
154 78 0.28
155 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (154 bp):
TTAATCAATAATATTTGAAGAATTTTAAAAATTATAAACATAGAAAAATCATACCGAAAAAATTT
ATGAAGTAGAAAACTTCGTATCTCAGTAACAGAAAAAATTCTAAAAATCATAAAATAAATTGAAT
TTTTCAAAACTAATTTAAGATAAA
Found at i:1587367 original size:154 final size:152
Alignment explanation
Indices: 1586919--1587394 Score: 503
Period size: 153 Copynumber: 3.2 Consensus size: 152
1586909 ATATTTGATA
* * * * * * * * *
1586919 AATTTTAAAAATTTTAAACTAAAAAAAATCCAACCAAAAAAATTTACGGATTAGAAAACTT-GTT
1 AATTTTAAAAATTATAAACTTAGAAAAATTCTACCGAAAAAATTTATGAAGTAGAAAACTTCGTT
* *
1586983 TCTTGGTATCA-AAAAAATTATAAAACTCATAAAATAAATTGAA-TTTTCAAAATTGATTTAATA
66 TCTTGGTAACAGAAAAAATT-TAAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAATA
* *
1587046 TG----AGT-AAT-AT-TTGAAT
130 TGAATTAATCAATAATATTGAAG
* *
1587062 AATTTTAAAAATTATAAACATAGAAAAATTCTACCGAAAAAATTTATGTAGTAGAAAAC-TCTGT
1 AATTTTAAAAATTATAAACTTAGAAAAATTCTACCGAAAAAATTTATGAAGTAGAAAACTTC-GT
* * * * *
1587126 ATCTTGGTAGC-GAAAAAATTTCAAAAATCATAAAATAAATTGAATTTTTCAAAACTGATTTCAG
65 TTCTTGGTAACAGAAAAAATTT-AAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAAT
*
1587190 ATAAATTAATCAATAATATTTGAAG
129 ATGAATTAATCAATAATA-TTGAAG
* * *
1587215 AATTTTTAAAATTATAAACTTAGAAAAA-TCATTCTGAAAAAATTTATGAAGTAGAAAACTTCGT
1 AATTTTAAAAATTATAAACTTAGAAAAATTC-TACCGAAAAAATTTATGAAGTAGAAAACTTCGT
** * * *
1587279 TTCTCAGTAACAGAAAAAATTCTAAAGCTTATAAAATAAATTGAATTTTTCAAAACTAATTTAAT
65 TTCTTGGTAACAGAAAAAATT-TAAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAAT
1587344 ATGAATTAATCAATAATAATTGAAG
129 ATGAATTAATCAATAAT-ATTGAAG
* * *
1587369 AA-TTTGAAAATTAAAAATTTAGAAAA
1 AATTTTAAAAATTATAAACTTAGAAAA
1587395 TCCTACTGGA
Statistics
Matches: 277, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
142 1 0.00
143 50 0.18
144 40 0.14
145 18 0.06
149 2 0.01
150 3 0.01
151 2 0.01
152 2 0.01
153 86 0.31
154 71 0.26
155 2 0.01
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.34
Consensus pattern (152 bp):
AATTTTAAAAATTATAAACTTAGAAAAATTCTACCGAAAAAATTTATGAAGTAGAAAACTTCGTT
TCTTGGTAACAGAAAAAATTTAAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAATAT
GAATTAATCAATAATATTGAAG
Found at i:1587469 original size:154 final size:154
Alignment explanation
Indices: 1587155--1587462 Score: 347
Period size: 154 Copynumber: 2.0 Consensus size: 154
1587145 TTCAAAAATC
* * *
1587155 ATAAAATAAATTGAATTTTTCAAAACTGATTTCAGATAAATTAATCAATAATATTTGAAGAATTT
1 ATAAAATAAATTGAATTTTTCAAAACTAATTTAAGATAAATTAATCAATAATAATTGAAGAATTT
* * * * *
1587220 TTAAAATTATAAACTTAGAAAAATCATTCTGAAAAAATTTATGAAGTAGAAAACTTCGTTTCTCA
66 TGAAAATTAAAAACTTAGAAAAATCATACTGAAAAAATTTACGAAGTAGAAAACTTCGTTTCTAA
** * ***
1587285 GTAACAGAAAAAATTCTAAAGCTT
131 AAAAAAGAAAAAATTCTAAAGAAA
* *
1587309 ATAAAATAAATTGAATTTTTCAAAACTAATTTAATATGAATTAATCAATAATAATTGAAGAA-TT
1 ATAAAATAAATTGAATTTTTCAAAACTAATTTAAGATAAATTAATCAATAATAATTGAAGAATTT
* * * * * * *
1587373 TGAAAATTAAAAATTTAG-AAAATCCTACTGGAGAAATTTACGGAGTA-AGAAACTTTGTATTTT
66 TGAAAATTAAAAACTTAGAAAAATCATACTGAAAAAATTTACGAAGTAGA-AAACTTCGT-TTCT
1587436 AAAAAAAAG-AAAAA-TCTAAAAGAAA
129 AAAAAAAAGAAAAAATTCT-AAAGAAA
1587461 AT
1 AT
1587463 GCAAAATTAA
Statistics
Matches: 128, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
151 4 0.03
152 42 0.33
153 25 0.20
154 57 0.45
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (154 bp):
ATAAAATAAATTGAATTTTTCAAAACTAATTTAAGATAAATTAATCAATAATAATTGAAGAATTT
TGAAAATTAAAAACTTAGAAAAATCATACTGAAAAAATTTACGAAGTAGAAAACTTCGTTTCTAA
AAAAAAGAAAAAATTCTAAAGAAA
Found at i:1588648 original size:43 final size:43
Alignment explanation
Indices: 1588568--1588836 Score: 254
Period size: 43 Copynumber: 6.3 Consensus size: 43
1588558 CCAACAAGTT
* * * *
1588568 AGTTAGAAA-GTATTGGTCGAGACGAAACCATACAAACCAACA
1 AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
* *
1588610 AGTTAGAAAGGTGTTGGCCGGGACAAAACCATACAAACCAACA
1 AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
* * * * * **
1588653 AGTTTGAAAGGTGTGGGTCGGGAGGAAACCATACGTACCAATG
1 AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
* * * * * *
1588696 AGTTATAAGGGTATTGGTCGGGACGAAACCATACGTACCAACG
1 AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
* * * * *
1588739 AGTTAG-AAGGATGTTGGCCTGGATGAAACCATACGTAGCAATA
1 AGTTAGAAAGG-TGTTGGCCGGGACGAAACCATACGAACCAACA
* * * * *
1588782 AGTTAGAAGGGTGTTGGCCAGGACAAAACCATTCGAACCAAAA
1 AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
1588825 AGTTAGAAAGGT
1 AGTTAGAAAGGT
1588837 ATTGACCGAT
Statistics
Matches: 186, Mismatches: 38, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
42 12 0.06
43 171 0.92
44 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (43 bp):
AGTTAGAAAGGTGTTGGCCGGGACGAAACCATACGAACCAACA
Found at i:1588700 original size:86 final size:86
Alignment explanation
Indices: 1588540--1588908 Score: 290
Period size: 86 Copynumber: 4.2 Consensus size: 86
1588530 GATGCTAGTT
* * * * * * * **
1588540 GGGACAAAACTAAATGAACCAACAAGTTAGTTAGAAAGTATTGGTCGAGACGAAACCATACAAAC
1 GGGACAAAACCATACGAACCAACAAGTTAG--A-AAGGTGTGGGTCGGGACGAAACCATACGTAC
* *
1588605 CAACAAGTTAGAAAGGTGTTGGCC
63 CAATAAGTTAGAAGGGTGTTGGCC
* * *
1588629 GGGACAAAACCATACAAACCAACAAGTTTGAAAGGTGTGGGTCGGGAGGAAACCATACGTACCAA
1 GGGACAAAACCATACGAACCAACAAGTTAGAAAGGTGTGGGTCGGGACGAAACCATACGTACCAA
* * * *
1588694 TGAGTTATAAGGGTATTGGTC
66 TAAGTTAGAAGGGTGTTGGCC
* * * * * * * *
1588715 GGGACGAAACCATACGTACCAACGAGTTAG-AAGGATGTTGGCCTGGATGAAACCATACGTAGCA
1 GGGACAAAACCATACGAACCAACAAGTTAGAAAGG-TGTGGGTCGGGACGAAACCATACGTACCA
1588779 ATAAGTTAGAAGGGTGTTGGCC
65 ATAAGTTAGAAGGGTGTTGGCC
* * * * * ** *
1588801 AGGACAAAACCATTCGAACCAAAAAGTTAGAAAGGTATTGACCGATGTTGATACGAAACCATATG
1 GGGACAAAACCATACGAACCAACAAGTTAGAAAGGT-GTG---G--GTCGGGACGAAACCATACG
* * * *
1588866 TACCAATGAGTTAGAAGGATATTGGCT
60 TACCAATAAGTTAGAAGGGTGTTGGCC
*
1588893 GGGATAAAACCATACG
1 GGGACAAAACCATACG
1588909 CGCCTGTAGA
Statistics
Matches: 217, Mismatches: 55, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
85 4 0.02
86 134 0.62
87 6 0.03
89 25 0.12
90 1 0.00
92 47 0.22
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (86 bp):
GGGACAAAACCATACGAACCAACAAGTTAGAAAGGTGTGGGTCGGGACGAAACCATACGTACCAA
TAAGTTAGAAGGGTGTTGGCC
Found at i:1588811 original size:129 final size:129
Alignment explanation
Indices: 1588568--1588908 Score: 328
Period size: 129 Copynumber: 2.6 Consensus size: 129
1588558 CCAACAAGTT
* ** * *
1588568 AGTTAGAAA-GTATTGGTCGAGACGAAACCATACAAACCAACAAGTTAGAAAGG-TGTTGGCCGG
1 AGTTAGAAAGGTATTGGTCGGGACGAAACCATACGTACCAACGAGTTAG-AAGGATGTTGGCCTG
* * * * * ** * **
1588631 GACAAAACCATACAAACCAACAAGTTTGAAAGGTGTGGGTCGGGAGGAAACCATACGTACCAATG
65 GATAAAACCATACGAACCAACAAGTTAGAAAGGTGTGGGCCAGGACAAAACCATACGAACCAAAA
* *
1588696 AGTTATAAGGGTATTGGTCGGGACGAAACCATACGTACCAACGAGTTAGAAGGATGTTGGCCTGG
1 AGTTAGAAAGGTATTGGTCGGGACGAAACCATACGTACCAACGAGTTAGAAGGATGTTGGCCTGG
* * * * * * *
1588761 ATGAAACCATACGTAGCAATAAGTTAGAAGGGTGTTGGCCAGGACAAAACCATTCGAACCAAAA
66 ATAAAACCATACGAACCAACAAGTTAGAAAGGTGTGGGCCAGGACAAAACCATACGAACCAAAA
** * * *
1588825 AGTTAGAAAGGTATTGACCGATGTTGATACGAAACCATATGTACCAATGAGTTAGAAGGATATTG
1 AGTTAGAAAGGTATTGGTCG--G--G--ACGAAACCATACGTACCAACGAGTTAGAAGGATGTTG
1588890 G-CTGGGATAAAACCATACG
60 GCCT-GGATAAAACCATACG
1588909 CGCCTGTAGA
Statistics
Matches: 172, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
128 11 0.06
129 108 0.63
131 1 0.01
133 1 0.01
134 2 0.01
135 49 0.28
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (129 bp):
AGTTAGAAAGGTATTGGTCGGGACGAAACCATACGTACCAACGAGTTAGAAGGATGTTGGCCTGG
ATAAAACCATACGAACCAACAAGTTAGAAAGGTGTGGGCCAGGACAAAACCATACGAACCAAAA
Found at i:1589499 original size:51 final size:51
Alignment explanation
Indices: 1589423--1589560 Score: 249
Period size: 51 Copynumber: 2.7 Consensus size: 51
1589413 AAAAGTACCT
* *
1589423 AGATGTATCGATACATTTTTCAATGTATCGATACATTTTGTCTTTTTAGCC
1 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCCTTTTAGCC
1589474 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCCTTTTAGCC
1 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCCTTTTAGCC
*
1589525 AAATGTATCGATACATTTTTCAATGTATCGATACAT
1 AGATGTATCGATACATTTTTCAATGTATCGATACAT
1589561 CTAGTTAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (51 bp):
AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCCTTTTAGCC
Found at i:1589501 original size:20 final size:20
Alignment explanation
Indices: 1589476--1589560 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1589466 TTTTAGCCAG
1589476 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1589496 ATGTATCGATACATTCTGTCCTTTTAGCCAA
1 ATGTATCGATACA-----T--TTTT---C-A
1589527 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1589547 ATGTATCGATACAT
1 ATGTATCGATACAT
1589561 CTAGTTAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
20 28 0.52
21 1 0.02
24 4 0.07
25 1 0.02
26 1 0.02
27 4 0.07
30 1 0.02
31 14 0.26
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1594921 original size:96 final size:95
Alignment explanation
Indices: 1594791--1595089 Score: 447
Period size: 96 Copynumber: 3.1 Consensus size: 95
1594781 TTTATTCACT
* * ***
1594791 GGGATACTCCAACCCATTCTTTCGAGGGGATACTCTAACCTTATTTTCAAAATTGTCAATATTTA
1 GGGATACTCCACCCCATTCTTTCGAGGGGATACTCCAACCCCGTTTTCAAAATTGTCAATATTTA
*
1594856 AATCTTATTTTGCCTAATTTATTATTATTG
66 AATCTTATTTTGCCTAATTTATTATTATTA
*
1594886 GGGATACTCTCACCCCATTCTTTTGAAGGGG-TACTCCAACCCCGTTTTCAAAATTGTCAATATT
1 GGGATACTC-CACCCCATTCTTTCG-AGGGGATACTCCAACCCCGTTTTCAAAATTGTCAATATT
*
1594950 TAAATCTTATTTTGCCTAATTTATTATCATTA
64 TAAATCTTATTTTGCCTAATTTATTATTATTA
*
1594982 GGGATACTCCAACCCCATTCTTTCGAGGGGATACTCCAACCCCGTTTTCAAAATTTTCAATATTT
1 GGGATACTCC-ACCCCATTCTTTCGAGGGGATACTCCAACCCCGTTTTCAAAATTGTCAATATTT
* * *
1595047 AGATCTTATTTTGCCTAATTTATCATTCATCA
65 AAATCTTATTTTGCCTAATTTATTATT-ATTA
1595079 GGGATACTCCA
1 GGGATACTCCA
1595090 ATCCTATTTT
Statistics
Matches: 185, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
95 15 0.08
96 152 0.82
97 18 0.10
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (95 bp):
GGGATACTCCACCCCATTCTTTCGAGGGGATACTCCAACCCCGTTTTCAAAATTGTCAATATTTA
AATCTTATTTTGCCTAATTTATTATTATTA
Found at i:1595142 original size:97 final size:97
Alignment explanation
Indices: 1594782--1595145 Score: 431
Period size: 96 Copynumber: 3.8 Consensus size: 97
1594772 ATATCAAATT
* * * ***
1594782 TTATTCACT-GGGATACTCCAA-CCCATTCTTTC-GAGGGGATACTCTAACCTTATTTTCAAAAT
1 TTATTCATTAGGGATACTCCAACCCCATTCTTTCTGAAGGGATACTCCAACCCCGTTTTCAAAAT
*
1594844 TGTCAATATTTAAATCTTATTTTGCCTAATTTA
66 T-TTAATATTTAAATCTTATTTTGCCTAATTTA
* *
1594877 TTATT-ATTGGGGATACTCTC-ACCCCATTCTTT-TGAAGGGGTACTCCAACCCCGTTTTCAAAA
1 TTATTCATTAGGGATACTC-CAACCCCATTCTTTCTGAAGGGATACTCCAACCCCGTTTTCAAAA
*
1594939 TTGTCAATATTTAAATCTTATTTTGCCTAATTTA
65 TT-TTAATATTTAAATCTTATTTTGCCTAATTTA
*
1594973 TTA-TCATTAGGGATACTCCAACCCCATTCTTTC-GAGGGGATACTCCAACCCCGTTTTCAAAAT
1 TTATTCATTAGGGATACTCCAACCCCATTCTTTCTGAAGGGATACTCCAACCCCGTTTTCAAAAT
*
1595036 TTTCAATATTTAGATCTTATTTTGCCTAATTTA
66 TTT-AATATTTAAATCTTATTTTGCCTAATTTA
* * * * * * * * *
1595069 TCATTCATCAGGGATACTCCAATCCTATT-TTTCTGAAAGGATACTCCAACTCCATTTTTAAAGT
1 TTATTCATTAGGGATACTCCAACCCCATTCTTTCTGAAGGGATACTCCAACCCCGTTTTCAAAAT
1595133 TATTAATATTTAA
66 T-TTAATATTTAA
1595146 GCCTTGTTTT
Statistics
Matches: 235, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
94 2 0.01
95 18 0.08
96 158 0.67
97 55 0.23
98 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (97 bp):
TTATTCATTAGGGATACTCCAACCCCATTCTTTCTGAAGGGATACTCCAACCCCGTTTTCAAAAT
TTTAATATTTAAATCTTATTTTGCCTAATTTA
Found at i:1597836 original size:90 final size:90
Alignment explanation
Indices: 1597678--1597864 Score: 338
Period size: 90 Copynumber: 2.1 Consensus size: 90
1597668 GAAAGGGCCA
* *
1597678 AGTCTACTGGATTTACTACAAAGCCTTGCAACCCCCTCCGTTTATGAAAAGATTAATGCAAATTC
1 AGTC-ACTGGATTTACTACAAAGCCCTGCAACCCCCTCCGTTCATGAAAAGATTAATGCAAATTC
1597743 TTGGGGCCAGGGAAACATGGGCCAAT
65 TTGGGGCCAGGGAAACATGGGCCAAT
1597769 AGTCACTGGATTTACTACAAAGCCCTGCAACCCCCTCCGTTCATGAAAAGATTAATGCAAATTCT
1 AGTCACTGGATTTACTACAAAGCCCTGCAACCCCCTCCGTTCATGAAAAGATTAATGCAAATTCT
*
1597834 TGGGGCCAGGGAAACATGGGCCGAT
66 TGGGGCCAGGGAAACATGGGCCAAT
1597859 AGTCAC
1 AGTCAC
1597865 GTTAAGTTAA
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 89 0.96
91 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (90 bp):
AGTCACTGGATTTACTACAAAGCCCTGCAACCCCCTCCGTTCATGAAAAGATTAATGCAAATTCT
TGGGGCCAGGGAAACATGGGCCAAT
Found at i:1609513 original size:158 final size:157
Alignment explanation
Indices: 1609312--1609599 Score: 425
Period size: 158 Copynumber: 1.8 Consensus size: 157
1609302 CATTCGGTAA
* *
1609312 TTTCTTCATCCTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGTACCTTCATCATCTTG
1 TTTCTTCATCCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTTG
** * * *
1609377 AAGACCAATATCGTTGGCTGTGAATTAGCATATTAGCATTTTTTATCATCTTCAGAGTCTAATGT
66 AAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCA-AGTCTAATGT
1609442 CACTAGCCCTAAATCAGCATATTAGCAT
130 CACTAGCCCTAAATCAGCATATTAGCAT
* ** *
1609470 TTTCTTCAT-CTCTAAGTCTAATATCGTTGGCCTTGAATCAGCACATTGGTACCTTCACCATTTT
1 TTTCTTCATCCT-TAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTT
* * *
1609534 TAAGACCAATATCACTGGCCGTGAATCAGCATATTGGCATTTTTTATCATATTTAAGTCTAATGT
65 GAAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCAAGTCTAATGT
1609599 C
130 C
1609600 GTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
157 13 0.11
158 102 0.89
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (157 bp):
TTTCTTCATCCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTTG
AAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCAAGTCTAATGTC
ACTAGCCCTAAATCAGCATATTAGCAT
Found at i:1609662 original size:158 final size:158
Alignment explanation
Indices: 1609312--1609670 Score: 407
Period size: 158 Copynumber: 2.3 Consensus size: 158
1609302 CATTCGGTAA
* * * *
1609312 TTTCTTCATCCTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGTACCTTCATCATCTTG
1 TTTCATCATCTTTAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTTG
** * * *
1609377 AAGACCAATATCGTTGGCTGTGAATTAGCATATTAGCATTTTTTATCATCTTCAGAGTCTAATGT
66 AAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCAGAGTCTAATGT
*
1609442 CACTAGCCCTAAATCAGCATATTAGCAT
131 CACTAGCCCTAAATCAGCACATTAGCAT
* * * ** * *
1609470 TTTCTTCATCTCTAAGTCTAATATCGTTGGCCTTGAATCAGCACATTGGTACCTTCACCATTTTT
1 TTTCATCATCTTTAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTTG
* *
1609535 AAGACCAATATCACTGGCCGTGAATCAGCATATTGGCATTTTTTATCATATTTA-AGTCTAATGT
66 AAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCAGAGTCTAATGT
** * ** * * *
1609599 CGTTGGCTTTGAATCATCACATTTGGCAT
131 CACTAGCCCTAAATCAGCACA-TTAGCAT
* ** *
1609628 TCTT-ATCATCTTTAAGTCTAATGGCACTACCCTTGAATTAGCA
1 T-TTCATCATCTTTAAGTCTAATGTCACTGGCCTTGAATCAGCA
1609671 TATTTGGCAT
Statistics
Matches: 165, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
157 23 0.14
158 140 0.85
159 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (158 bp):
TTTCATCATCTTTAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGTACCTTCACCATCTTG
AAGACCAATATCACTGGCCGTGAATCAGCATATTAGCATTTTTTATCATATTCAGAGTCTAATGT
CACTAGCCCTAAATCAGCACATTAGCAT
Found at i:1610439 original size:20 final size:20
Alignment explanation
Indices: 1610399--1610450 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
1610389 CAATAATTTT
1610399 TATCGATACAATAAGGTAATG
1 TATCGATAC-ATAAGGTAATG
1610420 TATCGATACATAA-GTGAATG
1 TATCGATACATAAGGT-AATG
*
1610440 TATTGATACAT
1 TATCGATACAT
1610451 GCCTAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 9 0.31
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TATCGATACATAAGGTAATG
Found at i:1612192 original size:96 final size:96
Alignment explanation
Indices: 1612056--1612230 Score: 298
Period size: 96 Copynumber: 1.8 Consensus size: 96
1612046 CTTCCGAGGG
* *
1612056 GATACTCCAACCCAGTTTTTAAAATTATCAATATTTAAATCTTATTTTGCGTAATTTATCATCAT
1 GATACTCCAACCCAGTTTTCAAAATTATCAATATTTAAATCTTATTTTGCCTAATTTATCATCAT
1612121 TAGGGATACTCCAATCCTATTCTTTAAAAGA
66 TAGGGATACTCCAATCCTATTCTTTAAAAGA
* *
1612152 GATACTCCAACCCCA-TTTTCCAAATTGTCAATATTTAAATCTTATTTTGCCTAATTTATCATCA
1 GATACTCCAA-CCCAGTTTTCAAAATTATCAATATTTAAATCTTATTTTGCCTAATTTATCATCA
1612216 TTAGGGATACTCCAA
65 TTAGGGATACTCCAA
1612231 CCCCATTTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
96 70 0.95
97 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (96 bp):
GATACTCCAACCCAGTTTTCAAAATTATCAATATTTAAATCTTATTTTGCCTAATTTATCATCAT
TAGGGATACTCCAATCCTATTCTTTAAAAGA
Found at i:1612277 original size:68 final size:69
Alignment explanation
Indices: 1612151--1612336 Score: 232
Period size: 68 Copynumber: 2.7 Consensus size: 69
1612141 TCTTTAAAAG
* *
1612151 AGATACTCCAACCCCATTTTCCAAATTGTCAATATTTAAATCTTATTTTGCCTAATTTATCA-TC
1 AGATACTCCAACCCCATTTTCAAAATTGTCAATACTTAAATCTTATTTTGCCTAATTTATCATTC
1612215 ATTA
66 ATTA
* * *
1612219 GGGATACTCCAACCCCATTTTCAAAATTG-CAATACTTAAATCTTATTTTGCTTGATTTATCATT
1 -AGATACTCCAACCCCATTTTCAAAATTGTCAATACTTAAATCTTATTTTGCCTAATTTATCATT
*
1612283 TATTA
65 CATTA
* * ** * * *
1612288 AGATACTCTAACCCCATTTTTAATGTTGTCAATATTTAAACCTTGTTTT
1 AGATACTCCAACCCCATTTTCAAAATTGTCAATACTTAAATCTTATTTT
1612337 TGCTCAAGTC
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
68 53 0.52
69 48 0.48
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (69 bp):
AGATACTCCAACCCCATTTTCAAAATTGTCAATACTTAAATCTTATTTTGCCTAATTTATCATTC
ATTA
Found at i:1612284 original size:96 final size:94
Alignment explanation
Indices: 1612028--1612244 Score: 258
Period size: 96 Copynumber: 2.3 Consensus size: 94
1612018 TAATTGTCAA
** * * * ** *
1612028 GGATACTCCAACCCCATTCTTCCGAGGGGATACTCCAA-CCCAGTTTTTAAAATTATCAATATTT
1 GGATACTCCAACCCCATTCTTCAAAAGAGATACTCAAACCCCA--TTTT-CCATTGTCAATATTT
*
1612092 AAATCTTATTTTGCGTAATTTATCATCATTAG
63 AAATCTTATTTTGCCTAATTTATCATCATTAG
* * * *
1612124 GGATACTCCAATCCTATTCTTTAAAAGAGATACTCCAACCCCATTTTCCAAATTGTCAATATTTA
1 GGATACTCCAACCCCATTCTTCAAAAGAGATACTCAAACCCCATTTTCC--ATTGTCAATATTTA
1612189 AATCTTATTTTGCCTAATTTATCATCATTAG
64 AATCTTATTTTGCCTAATTTATCATCATTAG
1612220 GGATACTCCAACCCCATT-TTCAAAA
1 GGATACTCCAACCCCATTCTTCAAAA
1612245 TTGCAATACT
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
95 10 0.10
96 90 0.87
97 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (94 bp):
GGATACTCCAACCCCATTCTTCAAAAGAGATACTCAAACCCCATTTTCCATTGTCAATATTTAAA
TCTTATTTTGCCTAATTTATCATCATTAG
Found at i:1614004 original size:13 final size:13
Alignment explanation
Indices: 1613986--1614011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1613976 TACAGCAAGT
1613986 ATGTATCGATACA
1 ATGTATCGATACA
1613999 ATGTATCGATACA
1 ATGTATCGATACA
1614012 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:1617524 original size:13 final size:13
Alignment explanation
Indices: 1617506--1617530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1617496 TTTTCCAGAT
1617506 TGTATCGATACAA
1 TGTATCGATACAA
1617519 TGTATCGATACA
1 TGTATCGATACA
1617531 TTGCTTCAGT
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:1619560 original size:13 final size:13
Alignment explanation
Indices: 1619542--1619567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1619532 TACAGCAAGT
1619542 ATGTATCGATACA
1 ATGTATCGATACA
1619555 ATGTATCGATACA
1 ATGTATCGATACA
1619568 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:1622751 original size:78 final size:78
Alignment explanation
Indices: 1622640--1622922 Score: 245
Period size: 79 Copynumber: 3.6 Consensus size: 78
1622630 GTGAAGACAG
* * * * *
1622640 GGTTGAAGTATCCCTAATGGTGGAAAA-CTGATATTTGAGAAATAAAATCGAGGTG-GGAG-ATC
1 GGTTAAAGTATCCCTGATGGTGAAAAATC-GATATTTTAGAAATAAAA-CGAGG-GCAGAGTATC
* *
1622702 CCCTTGGAAATAAGGA
63 CCCTCGGAAATAACGA
* * *
1622718 GGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTAGAGACAAAACTAGGGCTAGAGTATCCC
1 GGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTAGAAATAAAACGAGGGC-AGAGTATCCC
1622783 CTCGGAAATAACGA
65 CTCGGAAATAACGA
* * * * *
1622797 GGTCAGAA-TATCTCC-GATGGTGAAAAATCGATGTTTTAGAAATATAACTAGGGTTAGAGTATC
1 GGTTA-AAGTATC-CCTGATGGTGAAAAATCGATATTTTAGAAATAAAACGAGGG-CAGAGTATC
* *
1622860 CCCTCGAAAATAA-TA
63 CCCTCGGAAATAACGA
** * * * *
1622875 GGGTTTGAGTATCTCTAATGGTGAAAAATCGGTGTTTTAGAAATAAAA
1 -GGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTAGAAATAAAA
1622923 ATGGGGTTGA
Statistics
Matches: 170, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
76 1 0.01
77 4 0.02
78 45 0.26
79 116 0.68
80 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (78 bp):
GGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTAGAAATAAAACGAGGGCAGAGTATCCCC
TCGGAAATAACGA
Found at i:1622930 original size:79 final size:79
Alignment explanation
Indices: 1622699--1622940 Score: 263
Period size: 79 Copynumber: 3.1 Consensus size: 79
1622689 GAGGTGGGAG
* * * * * * * * *
1622699 ATCCCCTTGGAAATAAGGAGGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTAGAGACAAA
1 ATCCCCTCGAAAATAAAGAGGTCAGAGTATCTCTGATGGTGAAAAATCGATGTTTTAGAAATAAA
*
1622764 ACTAGGGCTAGAGT
66 ACTAGGGTTAGAGT
* * * * *
1622778 ATCCCCTCGGAAATAACGAGGTCAGAATATCTCCGATGGTGAAAAATCGATGTTTTAGAAATATA
1 ATCCCCTCGAAAATAAAGAGGTCAGAGTATCTCTGATGGTGAAAAATCGATGTTTTAGAAATAAA
1622843 ACTAGGGTTAGAGT
66 ACTAGGGTTAGAGT
** * *
1622857 ATCCCCTCGAAAATAATAG-GGTTTGAGTATCTCTAATGGTGAAAAATCGGTGTTTTAGAAATAA
1 ATCCCCTCGAAAATAA-AGAGGTCAGAGTATCTCTGATGGTGAAAAATCGATGTTTTAGAAATAA
* *
1622921 AAATGGGGTT-GAAGT
65 AACTAGGGTTAG-AGT
1622936 ATCCC
1 ATCCC
1622941 TAATGGTGGA
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
78 1 0.01
79 136 0.99
80 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (79 bp):
ATCCCCTCGAAAATAAAGAGGTCAGAGTATCTCTGATGGTGAAAAATCGATGTTTTAGAAATAAA
ACTAGGGTTAGAGT
Found at i:1622944 original size:51 final size:51
Alignment explanation
Indices: 1622882--1622991 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 51
1622872 ATAGGGTTTG
* *
1622882 AGTATCTCTAATGGTGAAAAATCGGTGTTTTAGAAATAAAAAT-GGGGTTGA
1 AGTATCCCTAATGGTGAAAAATCGATGTTTTAGAAA-AAAAATCGGGGTTGA
* *
1622933 AGTATCCCTAATGGTGGAAAATCGATGTTTTAGAAACAAAATCGGGGTTGA
1 AGTATCCCTAATGGTGAAAAATCGATGTTTTAGAAAAAAAATCGGGGTTGA
1622984 AGTATCCC
1 AGTATCCC
1622992 CTCAGAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 5 0.09
51 49 0.91
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTATCCCTAATGGTGAAAAATCGATGTTTTAGAAAAAAAATCGGGGTTGA
Found at i:1625408 original size:20 final size:21
Alignment explanation
Indices: 1625380--1625434 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1625370 TTAAAAACCC
1625380 AAAATGTATCGATAC-AATA-
1 AAAATGTATCGATACAAATAG
*
1625399 AAACATGTATTGATACAAATAG
1 AAA-ATGTATCGATACAAATAG
*
1625421 TAAATGTATCGATA
1 AAAATGTATCGATA
1625435 TATTTACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 14 0.47
22 2 0.07
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (21 bp):
AAAATGTATCGATACAAATAG
Found at i:1627579 original size:25 final size:25
Alignment explanation
Indices: 1627536--1627586 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1627526 GGGTTTTTTT
*
1627536 AATTAAAATTGGATTTTTAAAAAAA
1 AATTAAAATTGGATATTTAAAAAAA
*
1627561 AATTAAAATT-GATAATTTAAATAAA
1 AATTAAAATTGGAT-ATTTAAAAAAA
1627586 A
1 A
1627587 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AATTAAAATTGGATATTTAAAAAAA
Found at i:1630992 original size:20 final size:20
Alignment explanation
Indices: 1630967--1631131 Score: 120
Period size: 20 Copynumber: 7.8 Consensus size: 20
1630957 AAAAAGACAA
1630967 AATGTATCGATACATTGAAC
1 AATGTATCGATACATTGAAC
* **
1630987 AATGTATTGATATGGTT-ATAC
1 AATGTATCGATA-CATTGA-AC
*
1631008 -ATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAC
*
1631027 AATGTATCGATACATCTAGTAAAAAGATAG
1 AATGTATCGATACA--T--T-----GA-AC
*
1631057 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAC
*
1631077 AATGTATCGATACATTCATAC
1 AATGTATCGATACATTGA-AC
*
1631098 -ATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAC
1631117 AATGTATCGATACAT
1 AATGTATCGATACAT
1631132 CTGGGTAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
19 4 0.03
20 85 0.73
21 7 0.06
22 1 0.01
24 1 0.01
26 1 0.01
28 1 0.01
29 2 0.02
30 15 0.13
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAC
Found at i:1631101 original size:90 final size:91
Alignment explanation
Indices: 1630916--1631142 Score: 341
Period size: 90 Copynumber: 2.5 Consensus size: 91
1630906 TTTTAACTAG
*
1630916 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAAGACAAAATGTATCGATACA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGG-TAAAAAGACAAAATGTATCGATACA
* **
1630981 TTGAACAATGTATTGATATGGTTATAC
65 TTGAACAATGTATCGATATCATTATAC
* * *
1631008 ATGTATCGATACATTGAAAAATGTATCGATACATCT-AGTAAAAAGATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
*
1631072 TGAAGAATGTATCGATA-CATTCATAC
66 TGAACAATGTATCGATATCATT-ATAC
*
1631098 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1631143 TGTGACTTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
89 2 0.02
90 77 0.63
91 8 0.07
92 36 0.29
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
TGAACAATGTATCGATATCATTATAC
Found at i:1633131 original size:116 final size:116
Alignment explanation
Indices: 1632973--1633197 Score: 292
Period size: 116 Copynumber: 1.9 Consensus size: 116
1632963 GGCCCAACAC
** * * *
1632973 AATTAAATAAAATAGGCCTTGAATAAATTAATCAAATATGCACGTAGG-CCTTGTTTTATCTAAT
1 AATTAAATAAAATAGGCCTCAAATAAAATAATCAAATATGCACGTAGGACC-TATTCTATCTAAT
* *
1633037 ATATGTATTTTTATAAGGCTCAAGCTTAAATTAAATAATTTATGACCTAATAT
65 ATATAT-TTTTTATAAGACTCAAGCTTAAATTAAATAATTTATGACCTAATAT
* * *
1633090 AATTAAATAAAATTGGCC-CAAATAAAATAATTAAATATGCACGTTGGACCTATTCTATCTAATA
1 AATTAAATAAAATAGGCCTCAAATAAAATAATCAAATATGCACGTAGGACCTATTCTATCTAATA
** * *
1633154 TATATTTTTTATAAGACTTGATCTTACATTAAATAATTTATGAC
66 TATATTTTTTATAAGACTCAAGCTTAAATTAAATAATTTATGAC
1633198 TTTATCTTAG
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
115 34 0.37
116 40 0.43
117 19 0.20
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (116 bp):
AATTAAATAAAATAGGCCTCAAATAAAATAATCAAATATGCACGTAGGACCTATTCTATCTAATA
TATATTTTTTATAAGACTCAAGCTTAAATTAAATAATTTATGACCTAATAT
Found at i:1643894 original size:20 final size:20
Alignment explanation
Indices: 1643869--1643960 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
1643859 TTACCCAGAC
*
1643869 GTATCGATACATT-TTGCATT
1 GTATCGATACATTGCT-CATT
1643889 GTATCGATACATTGCTCATT
1 GTATCGATACATTGCTCATT
1643909 GTATCGATACATTGCTCATT
1 GTATCGATACATTGCTCATT
* *
1643929 GTAT-GATACATT-TTACAAT
1 GTATCGATACATTGCT-CATT
1643948 GTATCGATACATT
1 GTATCGATACATT
1643961 CAGGCATTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.02
19 15 0.23
20 49 0.74
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
GTATCGATACATTGCTCATT
Found at i:1643951 original size:39 final size:40
Alignment explanation
Indices: 1643869--1643961 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 40
1643859 TTACCCAGAC
* *
1643869 GTATCGATACATTTTGCATTGTATCGATACATTGCTCATT
1 GTATCGATACATTCTGCATTGTATCGATACATTGCTCAAT
*
1643909 GTATCGATACATTGCT-CATTGTAT-GATACATT-TTACAAT
1 GTATCGATACATT-CTGCATTGTATCGATACATTGCT-CAAT
1643948 GTATCGATACATTC
1 GTATCGATACATTC
1643962 AGGCATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.04
39 24 0.50
40 21 0.44
41 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (40 bp):
GTATCGATACATTCTGCATTGTATCGATACATTGCTCAAT
Found at i:1646187 original size:28 final size:27
Alignment explanation
Indices: 1646137--1646204 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1646127 TTCACAACTG
*
1646137 GGGATACTCCAACCCTGTCATTTCATCA
1 GGGATACTCCAACCCCGTCATTT-ATCA
* * *
1646165 GGGATACTCCAACCCCGTTATTTTTGA
1 GGGATACTCCAACCCCGTCATTTATCA
1646192 GAGGATACTCCAA
1 G-GGATACTCCAA
1646205 ACCCAGCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 3 0.09
28 32 0.91
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTCATTTATCA
Found at i:1646305 original size:28 final size:28
Alignment explanation
Indices: 1646259--1646319 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1646249 GGTACTCTAG
1646259 CCCCGTTATTTCATCGGGGACACTCCAA
1 CCCCGTTATTTCATCGGGGACACTCCAA
* *
1646287 CCCCGTTATTTCAGT-GGGGATAGTCCAA
1 CCCCGTTATTTCA-TCGGGGACACTCCAA
1646315 CCCCG
1 CCCCG
1646320 ACTTTATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.20, C:0.34, G:0.21, T:0.25
Consensus pattern (28 bp):
CCCCGTTATTTCATCGGGGACACTCCAA
Done.