Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_pilon, whole genome shotgun sequence
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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1476087 original size:12 final size:12
Alignment explanation
Indices: 1476072--1476113 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
1476062 TGTCTATTAT
1476072 TTTTAATTAAAA
1 TTTTAATTAAAA
*
1476084 TTTTATTTTAAAA
1 TTTTA-ATTAAAA
*
1476097 TTTTAAAT-AAA
1 TTTTAATTAAAA
1476108 TTTTAA
1 TTTTAA
1476114 AGATGTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 6 0.23
13 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAATTAAAA
Found at i:1478909 original size:58 final size:56
Alignment explanation
Indices: 1478746--1478945 Score: 197
Period size: 57 Copynumber: 3.5 Consensus size: 56
1478736 GAATATGTTA
* * * * *
1478746 TATGGGAATAAATGATAATTTGAATAATGTTATATGAAAAACTATGAGTA-TATGTT
1 TATGTGAATAAATGATAAATTGAGTAATGCTATATGAAATACTATGAGTATTAT-TT
* * *
1478802 CTATGTGAATAAATGATAAGTTGAGTAATTCGATATGAAATGA-TATGAGTAATTATTT
1 -TATGTGAATAAATGATAAATTGAGTAATGCTATATGAAAT-ACTATGAGT-ATTATTT
* * * *
1478860 TATGTGAATAAATAATAAATTTAGGTAATGCTATGTGAAATACTATGAGTATATGTTT
1 TATGTGAATAAATGATAAATTGA-GTAATGCTATATGAAATACTATGAGTAT-TATTT
* * *
1478918 TATGTAAACAAATGATAAATTGAATAAT
1 TATGTGAATAAATGATAAATTGAGTAAT
1478946 AATATGGGAA
Statistics
Matches: 118, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
57 67 0.57
58 48 0.41
59 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (56 bp):
TATGTGAATAAATGATAAATTGAGTAATGCTATATGAAATACTATGAGTATTATTT
Found at i:1479066 original size:23 final size:24
Alignment explanation
Indices: 1479036--1479086 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
1479026 AGGGTTTTGC
*
1479036 GTGGTCCTTCGGGAC-AATTCTAT
1 GTGGTCCTTCGGGACAAAATCTAT
1479059 GTGGTCCTTCGGGACAAAATCTAT
1 GTGGTCCTTCGGGACAAAATCTAT
1479083 GTGG
1 GTGG
1479087 CACTTCAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (24 bp):
GTGGTCCTTCGGGACAAAATCTAT
Found at i:1479092 original size:24 final size:24
Alignment explanation
Indices: 1479051--1479155 Score: 115
Period size: 24 Copynumber: 4.4 Consensus size: 24
1479041 CCTTCGGGAC
*
1479051 AATTCTATGTGGTC-CTTC-GGGACA
1 AATTCTACGTGG-CACTTCAGGG-CA
* * *
1479075 AAATCTATGTGGCACTTCAGTGCA
1 AATTCTACGTGGCACTTCAGGGCA
* *
1479099 TATTCTACGTGGCACTTCAGTGCA
1 AATTCTACGTGGCACTTCAGGGCA
*
1479123 AATTCTACGTGGCACTTCAGTGCA
1 AATTCTACGTGGCACTTCAGGGCA
1479147 AATTCTACG
1 AATTCTACG
1479156 CGGTATTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.01
24 70 0.96
25 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCAGGGCA
Found at i:1481755 original size:2 final size:2
Alignment explanation
Indices: 1481748--1481779 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1481738 TATGATGGGT
1481748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1481780 AAAGATTGTT
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):
TA
Found at i:1486846 original size:2 final size:2
Alignment explanation
Indices: 1486839--1486884 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1486829 TTAGTTCGAT
1486839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1486881 TA TA
1 TA TA
1486885 AGTTATAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1487118 original size:3 final size:3
Alignment explanation
Indices: 1487110--1487149 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1487100 CTGATCTTAT
1487110 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
1487150 AATAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1488429 original size:18 final size:17
Alignment explanation
Indices: 1488408--1488449 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1488398 TATTTTGGTC
1488408 ATTTTTTATTG-CCATTTT
1 ATTTTTTATTGTCC--TTT
1488426 ATTTTATTATTGTCCTTT
1 ATTTT-TTATTGTCCTTT
1488444 ATTTTT
1 ATTTTT
1488450 CAATACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 6 0.27
20 2 0.09
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (17 bp):
ATTTTTTATTGTCCTTT
Found at i:1491586 original size:20 final size:20
Alignment explanation
Indices: 1491563--1491606 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1491553 ACATTTGCAT
* *
1491563 TTTTTATGTTTTCATTTTCA
1 TTTTTATATTTTCATTTACA
1491583 TTTTTATATTTTCATTTACA
1 TTTTTATATTTTCATTTACA
1491603 TTTT
1 TTTT
1491607 CATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATATTTTCATTTACA
Found at i:1491600 original size:12 final size:13
Alignment explanation
Indices: 1491576--1491618 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
1491566 TTATGTTTTC
1491576 ATTTTCATTTTTAT
1 ATTTTCA-TTTTAT
*
1491590 ATTTTCA-TTTAC
1 ATTTTCATTTTAT
1491602 ATTTTCATTTTAT
1 ATTTTCATTTTAT
1491615 ATTT
1 ATTT
1491619 GCATCTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTCATTTTAT
Found at i:1491609 original size:26 final size:26
Alignment explanation
Indices: 1491545--1491618 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 26
1491535 ATTCGTATTT
*
1491545 TTTTCA-TTACATTTGCATTTTT-TA
1 TTTTCATTTACATTTTCATTTTTATA
*
1491569 -TGT--TTT-CATTTTCATTTTTATA
1 TTTTCATTTACATTTTCATTTTTATA
1491591 TTTTCATTTACATTTTCA-TTTTATA
1 TTTTCATTTACATTTTCATTTTTATA
1491616 TTT
1 TTT
1491619 GCATCTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
21 12 0.29
22 4 0.10
23 4 0.10
25 13 0.32
26 8 0.20
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTTCATTTACATTTTCATTTTTATA
Found at i:1493825 original size:72 final size:72
Alignment explanation
Indices: 1493683--1493826 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
1493673 ATACAATAAA
* * *
1493683 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGAATTTATGGATAATATTCAACTAGC
1 GCTTGAGTTATCCCCCTAAAACAATTGATTAATAGCCCCGAATTTATGGATAATATTCAACTAAC
1493748 CTGTTAT
66 CTGTTAT
* ** *
1493755 GCTTGAGTTATCCCCCTAAAACAATTGATTAATCGCCCCGGCTTTATGGATAATATTCAGCTAAC
1 GCTTGAGTTATCCCCCTAAAACAATTGATTAATAGCCCCGAATTTATGGATAATATTCAACTAAC
*
1493820 TTGTTAT
66 CTGTTAT
1493827 ACTATTATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAACAATTGATTAATAGCCCCGAATTTATGGATAATATTCAACTAAC
CTGTTAT
Found at i:1498206 original size:45 final size:45
Alignment explanation
Indices: 1498137--1498384 Score: 372
Period size: 45 Copynumber: 5.5 Consensus size: 45
1498127 TTTGCACATA
* * *
1498137 TGTAAGACCTTCAGTGCATA-ATGTTTTCAAAACCTTCGAGTCATC
1 TGTAAGACCTACAGTGCA-AGATGTTTTCAAAGCCTTCGGGTCATC
** *
1498182 CATAAGACCTACAGTGCAGGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
1498227 TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
* *
1498272 TGTAAGACCTATAGTGCAAGATGTTTTCAAAGCCTTCGGGCCATC
1 TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
** *
1498317 CATAAGACCTACAGTGCAGGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
*
1498362 TGTAAGACCTACAATGCAAGATG
1 TGTAAGACCTACAGTGCAAGATG
1498385 CTTACAACAA
Statistics
Matches: 182, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 182 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (45 bp):
TGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGTCATC
Found at i:1498380 original size:135 final size:135
Alignment explanation
Indices: 1498137--1498384 Score: 428
Period size: 135 Copynumber: 1.8 Consensus size: 135
1498127 TTTGCACATA
*
1498137 TGTAAGACCTTCAGTGCATAATGTTTTCAAAACCTTCGAGTCATCCATAAGACCTACAGTGCAGG
1 TGTAAGACCTTCAGTGCATAATGTTTTCAAAACCTTCGAGCCATCCATAAGACCTACAGTGCAGG
*
1498202 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGG
66 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAAGATGTTTTCAAAGCCTTCGGG
1498267 TCATC
131 TCATC
* *
1498272 TGTAAGACCTAT-AGTGCA-AGATGTTTTCAAAGCCTTCGGGCCATCCATAAGACCTACAGTGCA
1 TGTAAGACCT-TCAGTGCATA-ATGTTTTCAAAACCTTCGAGCCATCCATAAGACCTACAGTGCA
1498335 GGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAAGATG
64 GGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAAGATG
1498385 CTTACAACAA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
134 1 0.01
135 105 0.98
136 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (135 bp):
TGTAAGACCTTCAGTGCATAATGTTTTCAAAACCTTCGAGCCATCCATAAGACCTACAGTGCAGG
ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAAGATGTTTTCAAAGCCTTCGGG
TCATC
Found at i:1501477 original size:19 final size:19
Alignment explanation
Indices: 1501441--1501489 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1501431 CTATTCACTA
* *
1501441 TTACTATTCACTGTTACTG
1 TTACTATTCACAGGTACTG
* *
1501460 TTACTGTTCACAGGTACTT
1 TTACTATTCACAGGTACTG
1501479 TTCACTATTCA
1 TT-ACTATTCA
1501490 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (19 bp):
TTACTATTCACAGGTACTG
Found at i:1504816 original size:2 final size:2
Alignment explanation
Indices: 1504811--1504835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1504801 ATATATATAT
1504811 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1504836 TAATGATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1508030 original size:20 final size:20
Alignment explanation
Indices: 1507963--1508032 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
1507953 ATATCTAGAG
*
1507963 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATA-GATTTAA
* *
1507984 TAATATTGAATATTTA-ATTTCAA
1 TTA-ATT-AA-ATATAGATTT-AA
1508007 TTAATTAAATATAGATTTAA
1 TTAATTAAATATAGATTTAA
1508027 TTAATT
1 TTAATT
1508033 TGAAATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 12 0.31
21 8 0.21
22 9 0.23
23 6 0.15
24 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (20 bp):
TTAATTAAATATAGATTTAA
Found at i:1509779 original size:21 final size:21
Alignment explanation
Indices: 1509755--1509801 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1509745 AATATGTAAA
*
1509755 TCGCATTACGATTTTCCAAAT
1 TCGCATTACGATATTCCAAAT
* *
1509776 TCGCGTTGCGATATTCCAAAT
1 TCGCATTACGATATTCCAAAT
1509797 TCGCA
1 TCGCA
1509802 ACGCGATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (21 bp):
TCGCATTACGATATTCCAAAT
Found at i:1509825 original size:20 final size:20
Alignment explanation
Indices: 1509792--1509944 Score: 161
Period size: 20 Copynumber: 7.8 Consensus size: 20
1509782 TGCGATATTC
1509792 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
1509812 CAAGTTCTCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
1509832 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
1509852 CAAATTCGCAACGCGAAAAT
1 CAAATTCGCAACGCGATAGT
* **
1509872 CAAATTCGCAAC-TGATTTT
1 CAAATTCGCAACGCGATAGT
* *
1509891 CAAATTCGCAAC-TGA-ATTT
1 CAAATTCGCAACGCGATA-GT
*
1509910 CAAATTCGCAACGCGA-ATT
1 CAAATTCGCAACGCGATAGT
* *
1509929 TAATTTCGCAACGCGA
1 CAAATTCGCAACGCGA
1509945 ATTTAATTTC
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
19 48 0.41
20 69 0.59
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:1509937 original size:38 final size:39
Alignment explanation
Indices: 1509671--1509978 Score: 173
Period size: 40 Copynumber: 7.8 Consensus size: 39
1509661 AAATGACCAA
* * *
1509671 CAAATTCGCAACGCG-ATCTCAAATTCGCAATGCGAATTC
1 CAAATTCGCAACGCGAAT-TTAAATTCGCAACGCGAATTT
* * * *
1509710 CAATTTTGCAAC-CCAATTTCCAATTTCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAATTT--AAATTCGCAACGCGAAT-T-T
*** * *** *
1509752 -AAA-TCGCATTACGATTTTCCAAATTCGCGTTGCGATATTC
1 CAAATTCGCAACGCGAATTT--AAATTCGCAACGCGA-ATTT
* * * * *
1509792 CAAATTCGCAACGCGATAGTCAAGTTCTCAACGCG-ATAGT
1 CAAATTCGCAACGCGA-ATTTAAATTCGCAACGCGAAT-TT
* * **
1509832 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAAT
1 CAAATTCGCAACGCGA-ATTTAAATTCGCAACGCGAATTT
* * *
1509872 CAAATTCGCAAC-TGATTTTCAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT-AAATTCGCAACGCGAATTT
*
1509910 CAAATTCGCAACGCGAATTTAATTTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTTAAATTCGCAACGCGAATTT
* * *
1509949 -AATTTCGCAATGCGAATTTAATTTCGCAAC
1 CAAATTCGCAACGCGAATTTAAATTCGCAAC
1509979 AGGTTTTAGT
Statistics
Matches: 206, Mismatches: 48, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
38 57 0.28
39 38 0.18
40 65 0.32
41 35 0.17
42 10 0.05
43 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (39 bp):
CAAATTCGCAACGCGAATTTAAATTCGCAACGCGAATTT
Found at i:1509963 original size:19 final size:19
Alignment explanation
Indices: 1509836--1509978 Score: 128
Period size: 19 Copynumber: 7.4 Consensus size: 19
1509826 GATAGTCAAA
* * *
1509836 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGA-ATTTAAT
* * *
1509856 TTCGCAACGCGAAAATCAAA
1 TTCGCAACGCG-AATTTAAT
* * *
1509876 TTCGCAAC-TGATTTTCAAA
1 TTCGCAACGCGAATTT-AAT
* *
1509895 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATTT-AAT
1509914 TTCGCAACGCGAATTTAAT
1 TTCGCAACGCGAATTTAAT
1509933 TTCGCAACGCGAATTTAAT
1 TTCGCAACGCGAATTTAAT
*
1509952 TTCGCAATGCGAATTTAAT
1 TTCGCAACGCGAATTTAAT
1509971 TTCGCAAC
1 TTCGCAAC
1509979 AGGTTTTAGT
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
18 2 0.02
19 76 0.69
20 31 0.28
21 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (19 bp):
TTCGCAACGCGAATTTAAT
Found at i:1510745 original size:12 final size:12
Alignment explanation
Indices: 1510724--1510757 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1510714 ACCACATTTC
*
1510724 CAATACCAAACA
1 CAATATCAAACA
1510736 CAATATCAAACA
1 CAATATCAAACA
*
1510748 CAATCTCAAA
1 CAATATCAAA
1510758 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1514863 original size:24 final size:24
Alignment explanation
Indices: 1514762--1514870 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
1514752 GAATATTTTA
* * *
1514762 TTTGATTTCTTATTTGAATTATGT
1 TTTGATATCTGATCTGAATTATGT
* * *
1514786 TTTGACATCTGATCTGAAATCTGT
1 TTTGATATCTGATCTGAATTATGT
* * * * *
1514810 TCTGAT-TCCTAACCTGGATTCTGT
1 TTTGATAT-CTGATCTGAATTATGT
*
1514834 TCTGATATCTGATCTGAATTATGT
1 TTTGATATCTGATCTGAATTATGT
*
1514858 TTTGATTTCTGAT
1 TTTGATATCTGAT
1514871 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (24 bp):
TTTGATATCTGATCTGAATTATGT
Found at i:1515037 original size:2 final size:2
Alignment explanation
Indices: 1515030--1515072 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1515020 ACGGATGGGG
1515030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1515072 T
1 T
1515073 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1517578 original size:22 final size:22
Alignment explanation
Indices: 1517550--1517600 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1517540 GATGGAGATA
1517550 GACGGATTTCGTCAGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
*
1517572 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
1517594 GACGGAT
1 GACGGAT
1517601 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:1517846 original size:20 final size:20
Alignment explanation
Indices: 1517801--1517855 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1517791 TTACATATTC
*
1517801 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGTAAACT
* **
1517821 GGGTTGCGAAATTGTAATTT
1 GCGTTGCGAAATTGTAAACT
*
1517841 GCGTTGCGAATTTGT
1 GCGTTGCGAAATTGT
1517856 TGGTCATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.35
Consensus pattern (20 bp):
GCGTTGCGAAATTGTAAACT
Found at i:1525003 original size:22 final size:22
Alignment explanation
Indices: 1524977--1525021 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1524967 ACCGGATCGA
1524977 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
1524999 CCGACCCGACCCGGCCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
1525021 C
1 C
1525022 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.51, G:0.24, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:1529554 original size:30 final size:30
Alignment explanation
Indices: 1529494--1529589 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
1529484 CCCGAAGGAC
* *
1529494 CTATCCAGAGGTCACAAAGACCCT-GGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1529523 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1529553 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1529583 CTATCCA
1 CTATCCA
1529590 TATGTTCCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 22 0.35
30 40 0.65
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1529670 original size:32 final size:32
Alignment explanation
Indices: 1529581--1529676 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
1529571 GATCCTCGGT
* *
1529581 AACTATCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
1529612 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
1529644 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1529676 A
1 A
1529677 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 20 0.37
32 26 0.48
33 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:1530539 original size:21 final size:21
Alignment explanation
Indices: 1530509--1530553 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1530499 ATTGTGTCGT
* *
1530509 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1530530 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1530551 TTG
1 TTG
1530554 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1534098 original size:2 final size:2
Alignment explanation
Indices: 1534085--1534120 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1534075 TGCACCTTTC
*
1534085 AT AT AA 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
1534121 TTATCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1534433 original size:30 final size:30
Alignment explanation
Indices: 1534374--1534469 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
1534364 CCCGAAGGAC
* *
1534374 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1534403 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1534433 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1534463 CTATCCA
1 CTATCCA
1534470 TATGTTCCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 19 0.31
30 43 0.69
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1534550 original size:32 final size:32
Alignment explanation
Indices: 1534461--1534556 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
1534451 GATCCTCGGT
* *
1534461 AACTATCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
1534492 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
1534524 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1534556 A
1 A
1534557 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 20 0.37
32 26 0.48
33 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:1535418 original size:21 final size:21
Alignment explanation
Indices: 1535388--1535431 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1535378 ATTCTGTCGT
* *
1535388 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1535409 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1535430 TT
1 TT
1535432 TCCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1539519 original size:20 final size:20
Alignment explanation
Indices: 1539494--1539549 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1539484 GGCTGCTGGA
*
1539494 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG-TTTCG
1539514 AACCGGTTCTGACCGG-TTCG
1 AACCGGTT-TGACCGGTTTCG
1539534 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1539550 CTGACCCGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.31
20 16 0.50
21 6 0.19
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTCG
Found at i:1539530 original size:10 final size:10
Alignment explanation
Indices: 1539515--1539555 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1539505 CCGGTTTTCA
1539515 ACCGGTTCTG
1 ACCGGTTCTG
1539525 ACCGGTTC-G
1 ACCGGTTCTG
1539534 AACCGGTT-TG
1 -ACCGGTTCTG
1539544 ACCGG-TCTG
1 ACCGGTTCTG
1539553 ACC
1 ACC
1539556 CGACCGACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.04
9 11 0.39
10 16 0.57
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1539607 original size:17 final size:17
Alignment explanation
Indices: 1539559--1539609 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
1539549 TCTGACCCGA
*
1539559 CCGACCCGACCGTTAAC
1 CCGACCCGACCGTTGAC
1539576 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
1539593 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
1539610 TGTTGACCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:1544006 original size:14 final size:14
Alignment explanation
Indices: 1543965--1544019 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
1543955 TATAATTTTT
1543965 TATTTTAATAA-AA
1 TATTTTAATAATAA
*** *
1543978 TATAGCAATATTAA
1 TATTTTAATAATAA
*
1543992 TATTTTATTAATAA
1 TATTTTAATAATAA
1544006 TATTTTAATAATAA
1 TATTTTAATAATAA
1544020 ATAAAGTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
13 7 0.23
14 24 0.77
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:1553021 original size:31 final size:31
Alignment explanation
Indices: 1552983--1553050 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1552973 TAAGTGAAAA
* *
1552983 TAGTCCCTAATGTTATTGATCTATTCAATTT
1 TAGTCCCTAATATTATTGATCCATTCAATTT
* *
1553014 TAGTCCCTAGTATTATTGATCCGTTCAATTT
1 TAGTCCCTAATATTATTGATCCATTCAATTT
1553045 TAGTCC
1 TAGTCC
1553051 TCCAGCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (31 bp):
TAGTCCCTAATATTATTGATCCATTCAATTT
Found at i:1558125 original size:36 final size:36
Alignment explanation
Indices: 1558084--1558158 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
1558074 AGAAATCCTT
1558084 CAGTCATGGTGCTTCTGCTCCAGGACCTGGAAGAGG
1 CAGTCATGGTGCTTCTGCTCCAGGACCTGGAAGAGG
1558120 CAGTCATGGTGCTTCTGCTCCAGGACCTGGAAGAGG
1 CAGTCATGGTGCTTCTGCTCCAGGACCTGGAAGAGG
1558156 CAG
1 CAG
1558159 AGGTTCAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.21
Consensus pattern (36 bp):
CAGTCATGGTGCTTCTGCTCCAGGACCTGGAAGAGG
Found at i:1565710 original size:14 final size:14
Alignment explanation
Indices: 1565686--1565724 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1565676 TCTGTCTATA
*
1565686 TTGCAGAGATTT-T
1 TTGCAGGGATTTAT
1565699 TATGCAGGGATTTAT
1 T-TGCAGGGATTTAT
1565714 TTGCAGGGATT
1 TTGCAGGGATT
1565725 ACTTCCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (14 bp):
TTGCAGGGATTTAT
Found at i:1566190 original size:2 final size:2
Alignment explanation
Indices: 1566183--1566209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1566173 TAGGCCAAGT
1566183 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 T
1566210 TAAAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1567782 original size:22 final size:23
Alignment explanation
Indices: 1567743--1567792 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
1567733 CTACGAAAAT
1567743 ATTA-TATTATGTTATATTATTA
1 ATTATTATTATGTTATATTATTA
*
1567765 ATTATTATTAT-TTTTATTATTA
1 ATTATTATTATGTTATATTATTA
1567787 ATTATT
1 ATTATT
1567793 TTTTCTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTATTATTATGTTATATTATTA
Found at i:1567783 original size:19 final size:16
Alignment explanation
Indices: 1567765--1567795 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1567755 TATATTATTA
1567765 ATTATT-ATTATTTTT
1 ATTATTAATTATTTTT
1567780 ATTATTAATTATTTTT
1 ATTATTAATTATTTTT
1567796 TCTTACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTATTAATTATTTTT
Found at i:1569596 original size:30 final size:32
Alignment explanation
Indices: 1569534--1569606 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 32
1569524 TTGCATTTTG
*
1569534 ATTT-TCT-TTTTTATTATTTATTTCGTTATT
1 ATTTATCTATTTTTATTATTTATTTCATTATT
1569564 A-TTAT-TATTTTTATTAGTTTA-TTCATCT-TT
1 ATTTATCTATTTTTATTA-TTTATTTCAT-TATT
1569594 ATTTATCTATTTT
1 ATTTATCTATTTT
1569607 GTTTTATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
29 3 0.08
30 18 0.50
31 9 0.25
32 6 0.17
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.70
Consensus pattern (32 bp):
ATTTATCTATTTTTATTATTTATTTCATTATT
Found at i:1577433 original size:8 final size:8
Alignment explanation
Indices: 1577420--1577452 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1577410 GGCAAGAACA
1577420 CCCAAAAC
1 CCCAAAAC
1577428 CCCAAAAC
1 CCCAAAAC
1577436 CCCAAAAC
1 CCCAAAAC
1577444 CCCAAAAC
1 CCCAAAAC
1577452 C
1 C
1577453 TATTCCACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAC
Found at i:1583261 original size:32 final size:32
Alignment explanation
Indices: 1583191--1583266 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1583181 GCATCTTTGA
*
1583191 AGATTCAACATCAAATGTTGAGGCATTTTCGG
1 AGATTCAACATCAAATATTGAGGCATTTTCGG
* * * *
1583223 ATATTCAACATCGAATATTGGGGCATTTTTTGG
1 AGATTCAACATCAAATATTGAGGCA-TTTTCGG
1583256 -GATTCAACATC
1 AGATTCAACATC
1583267 CATATGTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 31 0.84
33 6 0.16
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGAGGCATTTTCGG
Found at i:1583617 original size:64 final size:64
Alignment explanation
Indices: 1583526--1583655 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
1583516 GGGGCGACTG
*
1583526 TCAACAAACAACTTTCCAGTTTTATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTCGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTCGAC
* * * * *
1583590 TCAACAAATAATTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTCGAC
1583654 TC
1 TC
1583656 GAAATAATAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTCGAC
Found at i:1583992 original size:124 final size:123
Alignment explanation
Indices: 1583864--1584331 Score: 535
Period size: 124 Copynumber: 3.8 Consensus size: 123
1583854 TTCAGAACCA
** * *
1583864 ATTTCAACTTCGTGGCGAAGGATATTCAAGCTAAGGCTCAACTTCACAACGAATGGGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* *
1583929 GGTTTCAACTTCACGACGAAGGGAATCGTGTTCACCAGTAACATTCATCTTCAGCTTGG
66 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAG-TTGG
** *
1583988 ATTTCATTTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* * *
1584053 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAACAACATTCATCTTTAGATTGA
66 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAG-TTGG
* * * *
1584112 ATTTTAACTTCACGACGAAGGATATCCAA-TTCGAGGCTCAACTTCGCAACGAATGGGCCATCCA
1 ATTTCAACTTCACGACGAAGGATATTCAAGTT-AAGGCTCAACTTCACAACGAATGGGCCATCCA
* * * * * *
1584176 CGATTTTAACTTCACAAAGAAGGGAATCGTACCCACCAGCAACATTCATCTTCAGTGTGG
65 CGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAGT-TGG
* * * ** * * * * * *
1584236 ATTTTAACTTCACAATGAAGGACGTCCAA-TTAAAAGCTCAATTTCACAGCGAAAGAGCCATCCA
1 ATTTCAACTTCACGACGAAGGATATTCAAGTT-AAGGCTCAACTTCACAACGAATGGGCCATCCA
** * **
1584300 CAATTTCAACTTCACGAGGAAGGCTATCGTGC
65 CGGTTTCAACTTCACGACGAAGGGAATCGTGC
1584332 CTGATGAAGT
Statistics
Matches: 294, Mismatches: 48, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
123 3 0.01
124 291 0.99
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (123 bp):
ATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAATGGGCCATCCAC
GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAGTTGG
Found at i:1584566 original size:36 final size:36
Alignment explanation
Indices: 1584511--1584914 Score: 448
Period size: 36 Copynumber: 11.2 Consensus size: 36
1584501 AATTTACTCA
* *
1584511 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1584548 AAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1584584 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1584620 AAACAAATTATGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1584656 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
1584692 AAACAAA------ATCT-TTGA-ATATGTTTTACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-G-TTTCCCTTG
* * **
1584721 AAACAAATTTCGTCTCTCTTGAGATAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
1584757 GAACTAAGTTTTGTATCTCTTGAGATAGTTTCTCTCG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
1584794 AAACAAATTTTGTCTTTGTCTCTCTTGATACAATTTCTCTTG
1 AAACAAA-----T-TTTGTCTCTCTTGAGACAGTTTCCCTTG
1584836 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
1584872 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1584908 AAACAAA
1 AAACAAA
1584915 ATCTTTGAAT
Statistics
Matches: 317, Mismatches: 32, Indels: 37
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.01
29 12 0.04
30 9 0.03
35 8 0.03
36 214 0.68
37 41 0.13
41 1 0.00
42 30 0.09
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1584831 original size:42 final size:42
Alignment explanation
Indices: 1584766--1584886 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 42
1584756 GGAACTAAGT
* *
1584766 TTTGTATCTCTTGAGATAGTTTCTCTCGAAACAAATTTTGTC
1 TTTGTATCTCTTGAGACAATTTCTCTCGAAACAAATTTTGTC
* * *
1584808 TTTGTCTCTCTTGATACAATTTCTCTTGAAACAAATTTTGTC
1 TTTGTATCTCTTGAGACAATTTCTCTCGAAACAAATTTTGTC
* * *
1584850 ------TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
1 TTTGTATCTCTTGAGACAATTTCTCTCGAAACAAATTTTGTC
1584886 T
1 T
1584887 CTCTTGAGAC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
36 33 0.47
42 37 0.53
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (42 bp):
TTTGTATCTCTTGAGACAATTTCTCTCGAAACAAATTTTGTC
Found at i:1584854 original size:21 final size:21
Alignment explanation
Indices: 1584829--1584898 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
1584819 TGATACAATT
1584829 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1584850 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
1584867 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
1584886 TCTCTTGAGACAA
1 TCTCTTGAAACAA
1584899 TTTCCCTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 3 0.08
18 4 0.11
19 3 0.08
20 1 0.03
21 19 0.50
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1584859 original size:78 final size:79
Alignment explanation
Indices: 1584732--1584886 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 79
1584722 AACAAATTTC
* * * * * * *
1584732 GTCTCTCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTATCTCTTGAGATAGTTTCTCTCGAAA
1 GTCTCTCTTGAGACAATTTCTCTTGAAACTAAATTTTGTATCTCTTGAGACAGTTTCCCTCGAAA
1584797 CAAATTTTGTCTTT
66 CAAATTTTGTCTTT
* * *
1584811 GTCTCTCTTGATACAATTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAATTTCTCTTGAAACTAAATTTTGTATCTCTTGAGACAGTTTCCCTCGAAA
1584875 CAAATTTTGTCT
66 CAAATTTTGTCT
1584887 CTCTTGAGAC
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 42 0.64
79 24 0.36
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (79 bp):
GTCTCTCTTGAGACAATTTCTCTTGAAACTAAATTTTGTATCTCTTGAGACAGTTTCCCTCGAAA
CAAATTTTGTCTTT
Found at i:1584879 original size:216 final size:210
Alignment explanation
Indices: 1584511--1584995 Score: 695
Period size: 216 Copynumber: 2.3 Consensus size: 210
1584501 AATTTACTCA
* * ** * *
1584511 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTAAGACAG
1 AAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
* *
1584575 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATGTCTCTCTT
65 TTTCCCTCGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTATGTCTCTCTT
* *
1584640 GAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
130 GAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAATCTTT
1584705 GAATATGTTTTACATT-
195 GAATATGTTTT-CATTG
* * *
1584721 AAACAAATTTCGTCTCTCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTATCTCTTGAGATAGT
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
* * * *
1584786 TTCTCTCGAAACAAATTTTGTCTTTGTCTCTCTTGATACAATTTCTCTTGAAACAAATTTTGTCT
66 TTCCCTCGAAACAAA-----T-TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTATGTCT
1584851 CTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAA
125 CTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAA
*
1584916 TCTTTGAATATGTTTTCCTTG
190 TCTTTGAATATGTTTTCATTG
* * *
1584937 AAACAAATTTCGTCTCCCTTGAGACAGTTTATTTCGGAACTAAGTTTTGTCTCTCTTGA
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
1584996 AACAAATTTT
Statistics
Matches: 244, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
209 28 0.11
210 40 0.16
215 4 0.02
216 172 0.70
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (210 bp):
AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
TTCCCTCGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTATGTCTCTCTTG
AGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAATCTTTG
AATATGTTTTCATTG
Found at i:1585011 original size:159 final size:160
Alignment explanation
Indices: 1584829--1585126 Score: 469
Period size: 159 Copynumber: 1.9 Consensus size: 160
1584819 TGATACAATT
*
1584829 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTG
1 TCTCTTGAAACAAA-TTT-TCTCTCTTGAGACAATTTCCCTTGAAACAAAATTTTGTCTCTCTTG
*
1584893 AGACAATTTCCCTTAAAACA-AAATCTTTGAATATGTTT-TCCTTGAAAC-AAATTTCGTCTCCC
64 AGACAATTTCCCTTAAAACACAAATCTTTGAATATGTTTCT-CTTGAAACAAAATTTCGCCTCCC
1584955 TTGAGACAGTTTATTTCGGAACTAAGTTTTGTC
128 TTGAGACAGTTTATTTCGGAACTAAGTTTTGTC
1584988 TCTCTTGAAACAAATTTTCTCTCTTGAGACAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAG
1 TCTCTTGAAACAAATTTTCTCTCTTGAGACAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAG
* * * * * *
1585053 ATAGTTTCTCTTGAAACACCAATCTTTGAATATGTTTCTCTTGAAACAAAATTTTGCCTCCCTTG
66 ACAATTTCCCTTAAAACACAAATCTTTGAATATGTTTCTCTTGAAACAAAATTTCGCCTCCCTTG
1585118 AGACAGTTT
131 AGACAGTTT
1585127 CTCTTGAAAC
Statistics
Matches: 127, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
157 27 0.21
158 36 0.28
159 39 0.31
160 25 0.20
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (160 bp):
TCTCTTGAAACAAATTTTCTCTCTTGAGACAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAG
ACAATTTCCCTTAAAACACAAATCTTTGAATATGTTTCTCTTGAAACAAAATTTCGCCTCCCTTG
AGACAGTTTATTTCGGAACTAAGTTTTGTC
Found at i:1585023 original size:17 final size:19
Alignment explanation
Indices: 1584986--1585051 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
1584976 CTAAGTTTTG
1584986 TCTCTCTTGAAACAAATTT
1 TCTCTCTTGAAACAAATTT
*
1585005 TCTCTCTTGAGAC-AA-TT
1 TCTCTCTTGAAACAAATTT
1585022 TC-C-CTTGAAACAAAATTTT
1 TCTCTCTTGAAAC-AAA-TTT
1585041 GTCTCTCTTGA
1 -TCTCTCTTGA
1585052 GATAGTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 6 0.16
18 2 0.05
19 14 0.37
20 2 0.05
21 1 0.03
22 5 0.13
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTCTCTTGAAACAAATTT
Found at i:1585029 original size:34 final size:36
Alignment explanation
Indices: 1584991--1585070 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 36
1584981 TTTTGTCTCT
1584991 CTTGAAACAAA-TTT-TCTCTCTTGAGACAATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
* * *
1585025 CTTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCC
1585062 CTTGAAACA
1 CTTGAAACA
1585071 CCAATCTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.20
35 3 0.08
36 4 0.10
37 25 0.62
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
Found at i:1585447 original size:81 final size:81
Alignment explanation
Indices: 1585181--1585449 Score: 315
Period size: 81 Copynumber: 3.3 Consensus size: 81
1585171 ACACCAAACT
* * * * * * * * *
1585181 TTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CGTCATTTACAACATAACTCAAGGCTAGAAGGG
1 TTCGAGTTCGACTCCACTCAGCTCAAAGGAACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGG
*
1585245 TTATCTGTCAACAAAGACC
66 CTATCTG-C--CAAAGACC
* ** *
1585264 TTCGAGTTCGACTCCACTCAACTCAAAGGAACCATCATTTGTGGCATAGCCCAAGGCAAGAAGGG
1 TTCGAGTTCGACTCCACTCAGCTCAAAGGAACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGG
1585329 CTATCTGCCAAAGACC
66 CTATCTGCCAAAGACC
* * * * *
1585345 TTCGAATTCGACTCCACTCAGCTCAAATGCATCATCATTTGCAGCATAGCTTAAGGCAAGAAGGG
1 TTCGAGTTCGACTCCACTCAGCTCAAAGGAACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGG
1585410 CTATCTGCCAAAGACC
66 CTATCTGCCAAAGACC
* *
1585426 TTCGAGTTCGATTCCATTCAGCTC
1 TTCGAGTTCGACTCCACTCAGCTC
1585450 GAGGGCATAT
Statistics
Matches: 159, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
81 101 0.64
83 27 0.17
84 31 0.19
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (81 bp):
TTCGAGTTCGACTCCACTCAGCTCAAAGGAACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGG
CTATCTGCCAAAGACC
Found at i:1585825 original size:19 final size:18
Alignment explanation
Indices: 1585801--1585839 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1585791 TTATGTTATA
1585801 TTATTAATT-ATTATTATTT
1 TTATT-ATTAATTATT-TTT
1585820 TTATTATTAATTATTTTT
1 TTATTATTAATTATTTTT
1585838 TT
1 TT
1585840 CTTACATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTATTAATTATTTTT
Found at i:1585834 original size:22 final size:23
Alignment explanation
Indices: 1585780--1585834 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
1585770 CTACAAAAAC
1585780 ATTATATTA-TATTATGTTATATT
1 ATTA-ATTATTATTATGTTATATT
*
1585803 ATTAATTATTATTAT-TTTTATT
1 ATTAATTATTATTATGTTATATT
1585825 ATTAATTATT
1 ATTAATTATT
1585835 TTTTTCTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTAATTATTATTATGTTATATT
Found at i:1585836 original size:15 final size:15
Alignment explanation
Indices: 1585807--1585837 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1585797 TATATTATTA
1585807 ATTATTATTATTTTT
1 ATTATTATTATTTTT
1585822 ATTATTAATTATTTTT
1 ATTATT-ATTATTTTT
1585838 TTCTTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTATTATTATTTTT
Found at i:1587744 original size:24 final size:23
Alignment explanation
Indices: 1587659--1587744 Score: 59
Period size: 24 Copynumber: 3.5 Consensus size: 23
1587649 TTTCTTTTTT
* *
1587659 TATTATTTATTTCG-TTTATTAT
1 TATTATTTATTTTGTTTTATTAC
1587681 TATTATTT-TTATTAGTTTTATTCATC
1 TATTATTTATT-TT-GTTTTATT-A-C
*
1587707 TTTATTTATCTATTTTGTTTTATTAC
1 --TA-TTATTTATTTTGTTTTATTAC
1587733 TATTATTATATT
1 TATTATT-TATT
1587745 AATATTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
21 2 0.04
22 9 0.18
23 5 0.10
24 12 0.24
25 1 0.02
26 1 0.02
27 1 0.02
28 10 0.20
29 7 0.14
30 2 0.04
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.67
Consensus pattern (23 bp):
TATTATTTATTTTGTTTTATTAC
Found at i:1596034 original size:28 final size:28
Alignment explanation
Indices: 1595994--1596050 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1595984 TGAATGAAAG
1595994 GTTTTTCACCTGAACTGTCCGATTCGAA
1 GTTTTTCACCTGAACTGTCCGATTCGAA
1596022 GTTTTTCACCTGAACTGTCCGATTCGAA
1 GTTTTTCACCTGAACTGTCCGATTCGAA
1596050 G
1 G
1596051 ATCCGGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (28 bp):
GTTTTTCACCTGAACTGTCCGATTCGAA
Found at i:1599050 original size:15 final size:15
Alignment explanation
Indices: 1599030--1599058 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1599020 TTTTTTAAGT
1599030 TATTTTATAAAATTG
1 TATTTTATAAAATTG
1599045 TATTTTATAAAATT
1 TATTTTATAAAATT
1599059 TTGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTTTATAAAATTG
Found at i:1602149 original size:36 final size:36
Alignment explanation
Indices: 1602103--1602306 Score: 347
Period size: 36 Copynumber: 5.7 Consensus size: 36
1602093 ATATGAAGTA
*
1602103 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTATGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
* *
1602139 TTAAGATTTTACTTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1602175 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
*
1602211 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTATGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
* *
1602247 ATAAGCTTTTACCTAAAGCTAAAGTTCATATTACAT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1602283 TTAAGCTTTTACCT-AAGCTAAAGT
1 TTAAGCTTTTACCTAAAGCTAAAGT
1602307 GGATGTAATT
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 10 0.06
36 148 0.94
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (36 bp):
TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
Found at i:1606284 original size:15 final size:16
Alignment explanation
Indices: 1606251--1606289 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1606241 TTTTGTATTT
1606251 AAAATATATCTAGATA
1 AAAATATATCTAGATA
*
1606267 AAAATATATCTATA-A
1 AAAATATATCTAGATA
1606282 AAAATATA
1 AAAATATA
1606290 GACAATAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATATATCTAGATA
Found at i:1614934 original size:5 final size:5
Alignment explanation
Indices: 1614924--1614974 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
1614914 ATTGGACCGA
*
1614924 AAAAT AAAAT AAAA- AGAAT -AAAT AAAAT AAAAT AAAAT GGAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT
1614974 A
1 A
1614975 CTAGTAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 6 0.15
5 29 0.73
7 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1614968 original size:22 final size:23
Alignment explanation
Indices: 1614924--1614974 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1614914 ATTGGACCGA
1614924 AAAATAAAATAAAAAGAATAAAT
1 AAAATAAAATAAAAAGAATAAAT
* *
1614947 AAAATAAAATAAAATGGA-AAAT
1 AAAATAAAATAAAAAGAATAAAT
1614969 AAAATA
1 AAAATA
1614975 CTAGTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAATAAAATAAAAAGAATAAAT
Found at i:1615083 original size:34 final size:35
Alignment explanation
Indices: 1615007--1615162 Score: 178
Period size: 35 Copynumber: 4.5 Consensus size: 35
1614997 ATTTTGAAAA
1615007 ATATGTTTTCCAAAAACCATTTTTAAAAAAAACTATATT
1 ATATGTTTT-CAAAAACCA-TTTT--AAAAAACTATATT
*
1615046 ATATGTTTTCAAAAACCATTGTAAAAAACTATATAT
1 ATATGTTTTCAAAAACCATTTTAAAAAACTATAT-T
* ** *
1615082 ATAAGTTTT-AAAAAATATTTTAAAAAATTATATT
1 ATATGTTTTCAAAAACCATTTTAAAAAACTATATT
*
1615116 ATATGTTTTCAAAAA-TATTTT-AAAAAC--TATT
1 ATATGTTTTCAAAAACCATTTTAAAAAACTATATT
1615147 ATATGTTTTCAAAAAC
1 ATATGTTTTCAAAAAC
1615163 TATATTATAT
Statistics
Matches: 106, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
31 19 0.18
33 5 0.05
34 15 0.14
35 37 0.35
36 9 0.08
37 3 0.03
38 9 0.08
39 9 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (35 bp):
ATATGTTTTCAAAAACCATTTTAAAAAACTATATT
Found at i:1615168 original size:34 final size:34
Alignment explanation
Indices: 1615007--1615168 Score: 140
Period size: 34 Copynumber: 4.6 Consensus size: 34
1614997 ATTTTGAAAA
1615007 ATATGTTTTCCAAAAACCAT-TTTTAAAAAAAACTATATT
1 ATATGTTTT-CAAAAA-CATATTTT--AAAAAAC--TATT
* *
1615046 ATATGTTTTCAAAAAC-CATTGTAAAAAACTATAT
1 ATATGTTTTCAAAAACATATTTTAAAAAACTAT-T
*
1615080 ATATAAGTTTT-AAAAA-ATATTTTAAAAAATTATATT
1 ATAT--GTTTTCAAAAACATATTTTAAAAAA--CTATT
1615116 ATATGTTTTC-AAAA-ATATTTT-AAAAACTATT
1 ATATGTTTTCAAAAACATATTTTAAAAAACTATT
1615147 ATATGTTTTCAAAAACTATATT
1 ATATGTTTTCAAAAAC-ATATT
1615169 ATATATGTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 27
0.76 0.04 0.19
Matches are distributed among these distances:
31 14 0.13
32 4 0.04
33 8 0.08
34 26 0.25
35 22 0.21
36 10 0.09
37 7 0.07
38 6 0.06
39 9 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (34 bp):
ATATGTTTTCAAAAACATATTTTAAAAAACTATT
Found at i:1615193 original size:38 final size:37
Alignment explanation
Indices: 1615149--1615261 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 37
1615139 AAACTATTAT
1615149 ATGTTTTCAAAAACTATATTATATATGTTTCCAAAAAAC
1 ATGTTTTCAAAAACTATA-TATATATGTTT-CAAAAAAC
*
1615188 A-GTTTTTAAGAAAACTATATATTATATGTTTTC-AAAAAC
1 ATG-TTTTCA-AAAACTATATA-TATATG-TTTCAAAAAAC
*
1615227 ATGTTTTCAAAAAATATACTATATAT-TTTCAAAAA
1 ATGTTTTCAAAAACTATA-TATATATGTTTCAAAAA
1615262 TTATATATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
36 4 0.06
37 4 0.06
38 14 0.22
39 22 0.34
40 17 0.27
41 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (37 bp):
ATGTTTTCAAAAACTATATATATATGTTTCAAAAAAC
Found at i:1615202 original size:40 final size:38
Alignment explanation
Indices: 1615149--1615261 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 38
1615139 AAACTATTAT
1615149 ATGTTTTC-AAAAACTATATTATATATGTTTCCAAAAAAC
1 ATGTTTTCAAAAAACTATA-TATATATGTTT-CAAAAAAC
*
1615188 A-GTTTTTAAGAAAACTATATATTATATGTTTTC-AAAAAC
1 ATGTTTTCAA-AAAACTATATA-TATATG-TTTCAAAAAAC
1615227 ATGTTTTCAAAAAA-TATACTATATAT-TTTCAAAAA
1 ATGTTTTCAAAAAACTATA-TATATATGTTTCAAAAA
1615262 TTATATATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
36 4 0.06
37 4 0.06
38 14 0.22
39 17 0.26
40 23 0.35
41 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (38 bp):
ATGTTTTCAAAAAACTATATATATATGTTTCAAAAAAC
Found at i:1615232 original size:14 final size:14
Alignment explanation
Indices: 1615213--1615239 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1615203 TATATATTAT
1615213 ATGTTTTCAAAAAC
1 ATGTTTTCAAAAAC
1615227 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
1615240 ATATACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
ATGTTTTCAAAAAC
Found at i:1615262 original size:21 final size:20
Alignment explanation
Indices: 1615230--1615270 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1615220 CAAAAACATG
1615230 TTTTCAAAAAATATACTATATA
1 TTTTCAAAAAAT-TA-TATATA
1615252 TTTTC-AAAAATTATATATA
1 TTTTCAAAAAATTATATATA
1615271 ATATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 6 0.32
22 5 0.26
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTCAAAAAATTATATATA
Found at i:1615276 original size:24 final size:22
Alignment explanation
Indices: 1615230--1615270 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1615220 CAAAAACATG
1615230 TTTTCAAAAAATATACTATATA
1 TTTTCAAAAAATATACTATATA
*
1615252 TTTTCAAAAATTATA-TATA
1 TTTTCAAAAAATATACTATA
1615271 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTCAAAAAATATACTATATA
Found at i:1615353 original size:2 final size:2
Alignment explanation
Indices: 1615346--1615392 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1615336 GGTGTCTACA
1615346 AT AT 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 AT AT
1615388 AT AT A
1 AT AT A
1615393 ATAATGGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1629125 original size:31 final size:31
Alignment explanation
Indices: 1629090--1629174 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
1629080 GGAGTACCTT
* *
1629090 GGGGCCTGAGAGCCTACCCAAGATAATTCTC
1 GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
* * *
1629121 GGGGCCACG-GAGGCTTACCCAAGAAAAATCTT
1 GGGGCC-TGAGA-GCCTACCCAAGAAAAATCTC
*
1629153 GGGGCCTCAGAGCCTACCCAAG
1 GGGGCCTGAGAGCCTACCCAAG
1629175 GGTCGCCTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.15
Consensus pattern (31 bp):
GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
Found at i:1632302 original size:15 final size:15
Alignment explanation
Indices: 1632282--1632313 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1632272 GCACTCAGTA
1632282 TCACTAAGCCAATCC
1 TCACTAAGCCAATCC
1632297 TCACTAAGCCAATCC
1 TCACTAAGCCAATCC
1632312 TC
1 TC
1632314 GGCCTCAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (15 bp):
TCACTAAGCCAATCC
Found at i:1634425 original size:21 final size:20
Alignment explanation
Indices: 1634401--1634439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1634391 GAGTCGGGTA
* *
1634401 AAACAGTTCTGGTTGGGTCTC
1 AAACA-TTCAGGTCGGGTCTC
1634422 AAACATTCAGGTCGGGTC
1 AAACATTCAGGTCGGGTC
1634440 AGGTCAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (20 bp):
AAACATTCAGGTCGGGTCTC
Found at i:1636887 original size:73 final size:71
Alignment explanation
Indices: 1636758--1636900 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 71
1636748 CAAGAGGGGA
* *
1636758 GAAGTATGGTTTGAAAAATCAATCGCTTAATGAAAATGGGGAGCTGAACATTTTCACATATTTTT
1 GAAGTATGGTTTGAAAAATCAATCGCTTAATGAAAAGGGGGAGCTGAACATTTTCACATATTTTC
1636823 CATCAT
66 CATCAT
* *
1636829 GAAGTATGGTTTGAAAAATTCAATCTCTTAATGAAAAAGGGGGAGTTGAACATTTTCACATATTT
1 GAAGTATGGTTTGAAAAA-TCAATCGCTTAATG-AAAAGGGGGAGCTGAACATTTTCACATATTT
1636894 TCCATCA
64 TCCATCA
1636901 ATTGATCTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 18 0.27
72 13 0.20
73 35 0.53
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (71 bp):
GAAGTATGGTTTGAAAAATCAATCGCTTAATGAAAAGGGGGAGCTGAACATTTTCACATATTTTC
CATCAT
Found at i:1638101 original size:15 final size:15
Alignment explanation
Indices: 1638069--1638097 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1638059 GCTAAGAAAA
1638069 CAATTATTCATCTTT
1 CAATTATTCATCTTT
1638084 CAATT-TTCATCTTT
1 CAATTATTCATCTTT
1638098 TCAAACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (15 bp):
CAATTATTCATCTTT
Found at i:1639486 original size:2 final size:2
Alignment explanation
Indices: 1639479--1639534 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1639469 CCCTTTTCAA
1639479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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 AT AT
1639520 -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1639535 TAGGTCAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1642237 original size:2 final size:2
Alignment explanation
Indices: 1642187--1642226 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1642177 CAAAGGTAAA
1642187 AT 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 AT
1642227 GTACTTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1643099 original size:113 final size:112
Alignment explanation
Indices: 1642896--1643120 Score: 441
Period size: 113 Copynumber: 2.0 Consensus size: 112
1642886 CTTGAAGAAC
1642896 ACATGAACACCGCCGTAAATTTCCAGATTCCGGTGACTTTGTCGCCTCGTCGTCGTCGTTGATCG
1 ACATGAACACCGCCGTAAATTTCCAGATTCCGGTGACTTTGTCGCCTCGTCGTCGTCGTTGATCG
1642961 GCGCTGGCCGTCGGTCATCAGCGGCAAAAGTTTTATTTTTTTTATTT
66 GCGCTGGCCGTCGGTCATCAGCGGCAAAAGTTTTATTTTTTTTATTT
1643008 ACATGAAACACCGCCGTAAATTTCCAGATTCCGGTGACTTTGTCGCCTCGTCGTCGTCGTTGATC
1 ACATG-AACACCGCCGTAAATTTCCAGATTCCGGTGACTTTGTCGCCTCGTCGTCGTCGTTGATC
1643073 GGCGCTGGCCGTCGGTCATCAGCGGCAAAAGTTTTATTTTTTTTATTT
65 GGCGCTGGCCGTCGGTCATCAGCGGCAAAAGTTTTATTTTTTTTATTT
1643121 TTTTCAAAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 5 0.04
113 107 0.96
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (112 bp):
ACATGAACACCGCCGTAAATTTCCAGATTCCGGTGACTTTGTCGCCTCGTCGTCGTCGTTGATCG
GCGCTGGCCGTCGGTCATCAGCGGCAAAAGTTTTATTTTTTTTATTT
Found at i:1644706 original size:18 final size:18
Alignment explanation
Indices: 1644683--1644718 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1644673 TATGATCAAG
1644683 TTGGCTTGTGATTTCCTT
1 TTGGCTTGTGATTTCCTT
1644701 TTGGCTTGTGATTTCCTT
1 TTGGCTTGTGATTTCCTT
1644719 CAACGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.22, T:0.56
Consensus pattern (18 bp):
TTGGCTTGTGATTTCCTT
Found at i:1645872 original size:35 final size:35
Alignment explanation
Indices: 1645826--1645892 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
1645816 ATAATTATAT
1645826 ATATATATAATATTAATAAATTTAATTTAAATTAA
1 ATATATATAATATTAATAAATTTAATTTAAATTAA
* *
1645861 ATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATAATATTAATAAATTTAATTTAAAT
1645893 ATATATACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATATATATAATATTAATAAATTTAATTTAAATTAA
Found at i:1645881 original size:15 final size:15
Alignment explanation
Indices: 1645857--1645899 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1645847 TTAATTTAAA
1645857 TTAAATATATATAAT
1 TTAAATATATATAAT
* *
1645872 ATT-TATATATTTAAT
1 -TTAAATATATATAAT
1645887 TTAAATATATATA
1 TTAAATATATATA
1645900 CTCGGCCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATATATATAAT
Found at i:1648883 original size:11 final size:10
Alignment explanation
Indices: 1648850--1648883 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1648840 ATCCAAATGC
1648850 AAATG-AAAT
1 AAATGAAAAT
1648859 AAATGAAAAT
1 AAATGAAAAT
1648869 AAATGAAACAT
1 AAATGAAA-AT
1648880 AAAT
1 AAAT
1648884 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.22
10 12 0.52
11 6 0.26
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (10 bp):
AAATGAAAAT
Found at i:1648949 original size:29 final size:29
Alignment explanation
Indices: 1648866--1648951 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
1648856 AATAAATGAA
*
1648866 AATAAATGAAACATA-AATATAA-AATATAT
1 AATAAAT-AAATATATAATATAATAATA-AT
* *
1648895 AA-ATAGAAATATATAATAT-ATAAATAAT
1 AATAAATAAATATATAATATAAT-AATAAT
1648923 AATAAATAAATATATAATATAATAATAAT
1 AATAAATAAATATATAATATAATAATAAT
1648952 TTTAAAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.15
28 11 0.23
29 27 0.57
30 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
AATAAATAAATATATAATATAATAATAAT
Found at i:1648951 original size:11 final size:12
Alignment explanation
Indices: 1648905--1648951 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
1648895 AAATAGAAAT
1648905 ATATAATATATA
1 ATATAATATATA
1648917 A-ATAATA-ATA
1 ATATAATATATA
1648927 A-ATAAATATATA
1 ATAT-AATATATA
1648939 ATATAATA-ATA
1 ATATAATATATA
1648950 AT
1 AT
1648952 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.19
11 15 0.47
12 9 0.28
13 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATAATATATA
Found at i:1648959 original size:26 final size:22
Alignment explanation
Indices: 1648887--1648950 Score: 87
Period size: 21 Copynumber: 2.9 Consensus size: 22
1648877 CATAAATATA
*
1648887 AAATATATAAATAGA-AATATAT
1 AAATATATAAATA-ATAATAAAT
1648909 -AATATATAAATAATAATAAAT
1 AAATATATAAATAATAATAAAT
1648930 AAATATATAATATAATAATAA
1 AAATATATAA-ATAATAATAA
1648951 TTTTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
20 1 0.03
21 18 0.47
22 9 0.24
23 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATATATAAATAATAATAAAT
Found at i:1651456 original size:281 final size:278
Alignment explanation
Indices: 1650931--1651484 Score: 1065
Period size: 281 Copynumber: 2.0 Consensus size: 278
1650921 TTAGCCTTTA
1650931 AATTATTAACATGAAGATATATATTGAAGCAGTTGCAGCTAGTATTTTAACCAATAAAGAATGAT
1 AATTATTAACATGAAGATATATATTGAAGCAGTTGCAGCTAGTATTTTAACCAATAAAGAATGAT
1650996 TTGTCAAATTGGTAACAATTGATTAAAAATGTCAGCATTCAGCAATAAGCTTGATGCTTAGATGA
66 TTGTCAAATTGGTAACAATTGATTAAAAATGTCAGCATTCAGCAATAAGCTTGATGCTTAGATGA
1651061 ATTTATCTTCATGTCTGAAGAAGCATAAGTTACAGGATGTTTTCATGCGTGTTTATATGCATTAT
131 ATTTATCTTCATGTCTGAAGAAGCATAAGTTACAGGATGTTTTCATGCGTGTTTATATGCATTAT
1651126 GCCATATATACTAGCCCATTTGACATTTGATAGGTTGAACGTTGAGTAATGTGGTCCTGAAAAGC
196 GCCATATATACTAGCCCATTTGACATTTGATAGGTTGAACGTTGAGTAATGTGGTCCTGAAAAGC
1651191 AATGCCTTTGCTCATTTG
261 AATGCCTTTGCTCATTTG
1651209 AATTATTAACATGGAAGATATATATTTGAAGCAGTTGCAGCTAGTATTTTAACCAATAAAGAATG
1 AATTATTAACAT-GAAGATATATA-TTGAAGCAGTTGCAGCTAGTATTTTAACCAATAAAGAATG
1651274 ATTTGTCAAATTGGTAACAAATTGATTAATAAATGTCAGCATTCAGCAATAAGCTTGATGCTTAG
64 ATTTGTCAAATTGGTAAC-AATTGATTAA-AAATGTCAGCATTCAGCAATAAGCTTGATGCTTAG
1651339 ATGAATTTATCTTCATGTCTGAAGAAG-ATAAGTTACAGGATGTTTTCATGCGTGTTTATATGCA
127 ATGAATTTATCTTCATGTCTGAAGAAGCATAAGTTACAGGATGTTTTCATGCGTGTTTATATGCA
1651403 TTATGCCATATATACTAGCCCATTTGACATTTGATAGGTTGAACGTTGAGTAATGTGGTCCTGAA
192 TTATGCCATATATACTAGCCCATTTGACATTTGATAGGTTGAACGTTGAGTAATGTGGTCCTGAA
1651468 AAGCAATGCCTTTGCTC
257 AAGCAATGCCTTTGCTC
1651485 TCATTTGATA
Statistics
Matches: 272, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
278 12 0.04
279 11 0.04
280 58 0.21
281 129 0.47
282 62 0.23
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (278 bp):
AATTATTAACATGAAGATATATATTGAAGCAGTTGCAGCTAGTATTTTAACCAATAAAGAATGAT
TTGTCAAATTGGTAACAATTGATTAAAAATGTCAGCATTCAGCAATAAGCTTGATGCTTAGATGA
ATTTATCTTCATGTCTGAAGAAGCATAAGTTACAGGATGTTTTCATGCGTGTTTATATGCATTAT
GCCATATATACTAGCCCATTTGACATTTGATAGGTTGAACGTTGAGTAATGTGGTCCTGAAAAGC
AATGCCTTTGCTCATTTG
Found at i:1654341 original size:17 final size:17
Alignment explanation
Indices: 1654294--1654343 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1654284 TGAAAATAGA
*
1654294 TTATGAATTCATATATT
1 TTATGAATTCATATTTT
**
1654311 TTAT-AATTTTTATTTT
1 TTATGAATTCATATTTT
*
1654327 TTTTGAATTCATATTTT
1 TTATGAATTCATATTTT
1654344 AAAATATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (17 bp):
TTATGAATTCATATTTT
Found at i:1657394 original size:2 final size:2
Alignment explanation
Indices: 1657387--1657461 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1657377 ACGAATACGA
1657387 AT AT 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 AT AT
1657429 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 A
1657462 ATGTGTTACA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1657925 original size:2 final size:2
Alignment explanation
Indices: 1657913--1657978 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
1657903 TTAACTTATC
1657913 AT AT A- 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 AT AT
1657954 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 A
1657979 GCGGCCGGCT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1666012 original size:20 final size:21
Alignment explanation
Indices: 1665970--1666012 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1665960 AGTAAAATTG
* * *
1665970 ATATTTGAAAACTTTGGAGTA
1 ATATTTGAAAACATTCGAATA
1665991 ATATTTG-AAACATTCGAATA
1 ATATTTGAAAACATTCGAATA
1666011 AT
1 AT
1666013 TGAATCGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATTTGAAAACATTCGAATA
Found at i:1666052 original size:19 final size:18
Alignment explanation
Indices: 1666015--1666053 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1666005 CGAATAATTG
*
1666015 AATCGAATATAAATTTTA
1 AATCGAATATAAATCTTA
1666033 AATCGAATATAAAATCTTA
1 AATCGAATAT-AAATCTTA
1666052 AA
1 AA
1666054 ATTACTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (18 bp):
AATCGAATATAAATCTTA
Found at i:1667827 original size:12 final size:13
Alignment explanation
Indices: 1667810--1667842 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1667800 AATGGGAAAA
*
1667810 TTTGAAAACT-AT
1 TTTGAAAACTAAG
1667822 TTTGAAAACTAAG
1 TTTGAAAACTAAG
1667835 TTTGAAAA
1 TTTGAAAA
1667843 ATTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTAAG
Found at i:1667952 original size:19 final size:20
Alignment explanation
Indices: 1667908--1667953 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1667898 AATCAAAAAC
1667908 ATTTTTTATTTCAAAAATTA
1 ATTTTTTATTTCAAAAATTA
*
1667928 ATTTTTT-TTTGAAAAA-TA
1 ATTTTTTATTTCAAAAATTA
1667946 ATGTTTTT
1 AT-TTTTT
1667954 GATAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTTTTTATTTCAAAAATTA
Found at i:1685938 original size:539 final size:537
Alignment explanation
Indices: 1684944--1685943 Score: 1403
Period size: 539 Copynumber: 1.9 Consensus size: 537
1684934 TGATACCAAT
* * * * *
1684944 TGTTGAGTTAATCGATCGAATGAATCGGCCAAGAGGGCGTGAATTGACAATTAAAATTTTGGTGG
1 TGTTGAGTTAATCGATCGAAGGAATAGACCAAGAGGGCGTGAATTGACAATAAAAATTTCGGTGG
* * *
1685009 AAGCTTTGACAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCAACTTTCTCAACCAA
66 AAGCTTTGACAGAAAATTGAAAATATTTACACAACAATTTAGAGTGGTTCAACTTTCTCAACCAA
*
1685074 AGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTT
131 AGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAAAAATTCACTAATTTGTCTTT
* *
1685139 CTTATGAGGACAAAGAGTAACCTTATAACTCCCTCAAGAATTATACCCCAAATTCTTGAGAACAC
196 CTTATCAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATACCCCAAATTCTTGAGAACAC
* * * *
1685204 ACTCTCTCAAAGAGAACTTACAAATTTTGCAAACTTACAGAAAAACCTTACAAAGTAGAATGTTT
261 ACTCTCTCAAAGAGAACATACAAAATTTCCAAACTTACAGAAAAACCTCACAAAGTAGAATGTTT
*
1685269 GCACAATTCTAGAAAAAAGAAAGAACACTCAAAGAATAATACAATTGAGCACAAAGTGTGTTCTT
326 GCACAATTCTAGAAAAAAGAAAGAACACTCAAAGAATAATACAATAGAGCACAAAGTGTGTTCTT
* * *** * * * *
1685334 GAGAGCAAAATGAATATTGAAAGGATTTTGGCTTGAATTGCTCAAACTTGAGTTTTGATGCTTTC
391 GAAAGCAAAATGAATATTGAAAGAAAAATGGCTTGAATTGCTCAAACATAAGTTTTAAGGCTTTC
1685399 TCTCTTGTTTCTATCTCAATTCTTGTGTAATTCTTTATCACCAATGGCTTCAAAACTTGTTTAAA
456 TC-CTTGTTTCTATCTCAATTCTTGTGTAATTCTTTATCACCAATGGCTTCAAAACTTGTTTAAA
1685464 TACACCTCAAATGAATTC
520 TACACCTCAAATGAATTC
* *
1685482 TGTTGAGTTAATCGATC-AACGGAATAGACCAAGAGGGGGTGAATTGGCAATAAAAATTTCGGTG
1 TGTTGAGTTAATCGATCGAA-GGAATAGACCAAGAGGGCGTGAATTGACAATAAAAATTTCGGTG
* * *
1685546 GTAGCTTTTTG-CAGAAAATTGAAAATATTTACACAATAATTTAGAGTGGTTCGACTTTCTCAAC
65 GAAGC--TTTGACAGAAAATTGAAAATATTTACACAACAATTTAGAGTGGTTCAACTTTCTCAAC
* *
1685610 CAAAGTCTACGTCTACTACCTTAGCTATCCGCACTAAGGATTTTCCAAAAAATTCACTAATTT-T
128 CAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC-AAAAATTCACTAATTTGT
* *
1685674 TTTTCTTTTCAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATACCCCAAATT-TT-AGA
192 CTTTCTTATCAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATACCCCAAATTCTTGAGA
* * *
1685737 GCACACTCTTTTTCAAAGAGAA-ATACACAAATTTCCAAACTTACA-AGAAAACCTCACAAGGTA
257 ACACACTC--TCTCAAAGAGAACATACA-AAATTTCCAAACTTACAGA-AAAACCTCACAAAGTA
* * * * *
1685800 GATTGTTTGCATAATTCTAGAACAAAGAAAGAACACTC-AAGGATAAATACAATAGAGCATAAA-
318 GAATGTTTGCACAATTCTAGAAAAAAGAAAGAACACTCAAAGAAT-AATACAATAGAGCACAAAG
*
1685863 TGGTGTTCTTGAAAGC-AAATGAATATTGAATGAAAAATGAGCTTGTAA-TGCTCAAACAATAAG
382 T-GTGTTCTTGAAAGCAAAATGAATATTGAAAGAAAAATG-GCTTG-AATTGCTCAAAC-ATAAG
1685926 -TTTAAGGCTTTCTCCTTG
443 TTTTAAGGCTTTCTCCTTG
1685944 GTTATCTCTT
Statistics
Matches: 406, Mismatches: 43, Indels: 26
0.85 0.09 0.05
Matches are distributed among these distances:
537 12 0.03
538 93 0.23
539 277 0.68
540 24 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (537 bp):
TGTTGAGTTAATCGATCGAAGGAATAGACCAAGAGGGCGTGAATTGACAATAAAAATTTCGGTGG
AAGCTTTGACAGAAAATTGAAAATATTTACACAACAATTTAGAGTGGTTCAACTTTCTCAACCAA
AGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAAAAATTCACTAATTTGTCTTT
CTTATCAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATACCCCAAATTCTTGAGAACAC
ACTCTCTCAAAGAGAACATACAAAATTTCCAAACTTACAGAAAAACCTCACAAAGTAGAATGTTT
GCACAATTCTAGAAAAAAGAAAGAACACTCAAAGAATAATACAATAGAGCACAAAGTGTGTTCTT
GAAAGCAAAATGAATATTGAAAGAAAAATGGCTTGAATTGCTCAAACATAAGTTTTAAGGCTTTC
TCCTTGTTTCTATCTCAATTCTTGTGTAATTCTTTATCACCAATGGCTTCAAAACTTGTTTAAAT
ACACCTCAAATGAATTC
Found at i:1693311 original size:19 final size:19
Alignment explanation
Indices: 1693287--1693331 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1693277 GGAACACTTA
1693287 GTGCATCGGTGCACCAAGT
1 GTGCATCGGTGCACCAAGT
1693306 GTGCATCGGTGCACCAAGT
1 GTGCATCGGTGCACCAAGT
1693325 GTGCATC
1 GTGCATC
1693332 AATGTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTGCACCAAGT
Found at i:1696168 original size:22 final size:21
Alignment explanation
Indices: 1696141--1696220 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
1696131 GCATGACCCT
*
1696141 GTGCATTGATGCACTTCAAGG
1 GTGCATCGATGCACTTCAAGG
* *
1696162 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCA-CTTCAAGG
*
1696184 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCAC-TTCAAGG
*
1696206 ATGCATCGATGCACT
1 GTGCATCGATGCACT
1696221 GTTAGGTGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 27 0.57
23 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGCACTTCAAGG
Found at i:1696197 original size:43 final size:42
Alignment explanation
Indices: 1696148--1696238 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 42
1696138 CCTGTGCATT
* *
1696148 GATGCAC-TTCAAGGCGTGCATCGGTGCACCT-TCATGGTGTATC
1 GATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGTATC
*
1696191 GATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGTATC
1 GATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGTATC
1696233 GATGCA
1 GATGCA
1696239 TGAAGCACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 16 0.37
43 20 0.47
44 7 0.16
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (42 bp):
GATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGTATC
Found at i:1696235 original size:20 final size:21
Alignment explanation
Indices: 1696148--1696238 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
1696138 CCTGTGCATT
*
1696148 GATGCAC-TTCAAGGCGTGCATC
1 GATGCACATTCAA-G-GTGTATC
* * *
1696170 GGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGTGTATC
*
1696191 GATGCACATTCAAGGATGCATC
1 GATGCACATTCAAGG-TGTATC
*
1696213 GATGCAC-TGT-TAGGTGTATC
1 GATGCACAT-TCAAGGTGTATC
1696233 GATGCA
1 GATGCA
1696239 TGAAGCACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
20 11 0.19
21 22 0.39
22 20 0.35
23 4 0.07
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
GATGCACATTCAAGGTGTATC
Found at i:1697843 original size:19 final size:19
Alignment explanation
Indices: 1697819--1697864 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1697809 TTCTTGAGTA
1697819 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
1697838 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
1697857 TAGCCTTG
1 TAGCCTTG
1697865 TTTCTCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGCCTTGAGCAACAAGTC
Found at i:1702154 original size:46 final size:45
Alignment explanation
Indices: 1702095--1702182 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
1702085 TTGAAAAAGC
* * *
1702095 CTGAGTGCATCGATGCATGGTCTTGTGCATTGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1702141 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1702183 ACATTCGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (45 bp):
CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
Found at i:1702745 original size:20 final size:20
Alignment explanation
Indices: 1702703--1702745 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1702693 TTATTTTCAT
* *
1702703 TTTTTAATTTTGAAATATCA
1 TTTTTAATTTTGAAAAATAA
1702723 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
1702743 TTT
1 TTT
1702746 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:1704750 original size:65 final size:65
Alignment explanation
Indices: 1704692--1704817 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
1704682 ACAAATTTGC
* *
1704692 TTCGATGTTTCAA-AATAGCTTG-GTGTGCATCAATGCATGGTGTGTGCATCGGTACACAAAATC
1 TTCGATGTTTCAATAAAAGCCTGAGTGT--ATCAATGCATGGTGTGTGCATCGGTACACAAAATC
1704755 AA
64 AA
* *
1704757 TTCGATGTTTCAATAAAATCCTGAGTGTATCGATGCATGGT-TGTGCATCGGTACACAAAAT
1 TTCGATGTTTCAATAAAAGCCTGAGTGTATCAATGCATGGTGTGTGCATCGGTACACAAAAT
1704818 GCATTTGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
64 20 0.36
65 25 0.45
66 6 0.11
67 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (65 bp):
TTCGATGTTTCAATAAAAGCCTGAGTGTATCAATGCATGGTGTGTGCATCGGTACACAAAATCAA
Found at i:1705338 original size:44 final size:43
Alignment explanation
Indices: 1705275--1705374 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
1705265 CATTCCAATG
* * * **
1705275 GTATCGATACTGGCAAAGGGGCATCGGTACTACTTTGTAGTGTA
1 GTATCGATACCGGCAAA-GGGCATCGATACTACTATGTAAAGTA
* * *
1705319 GTATCGATACCGTCCAAGGGTATCGATACTACTATGTAAAGTA
1 GTATCGATACCGGCAAAGGGCATCGATACTACTATGTAAAGTA
*
1705362 GTATCGGTACCGG
1 GTATCGATACCGG
1705375 TCATGGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
43 32 0.70
44 14 0.30
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GTATCGATACCGGCAAAGGGCATCGATACTACTATGTAAAGTA
Found at i:1705762 original size:19 final size:19
Alignment explanation
Indices: 1705724--1705763 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1705714 CGAATAATTG
* * *
1705724 AATCTAATATAATATTTTA
1 AATCAAATATAAAATCTTA
1705743 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
1705762 AA
1 AA
1705764 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:1706314 original size:15 final size:14
Alignment explanation
Indices: 1706275--1706316 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1706265 TTTATATGTG
*
1706275 TTAATTTTTTTAAT
1 TTAATTTCTTTAAT
*
1706289 TT-ATGTCTTTAAT
1 TTAATTTCTTTAAT
1706302 TTCAATTTCTTTAAT
1 TT-AATTTCTTTAAT
1706317 CTAGTCTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 2 0.09
15 10 0.43
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (14 bp):
TTAATTTCTTTAAT
Found at i:1706330 original size:28 final size:28
Alignment explanation
Indices: 1706277--1706331 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1706267 TATATGTGTT
* * *
1706277 AATTTTTTTAATTTATGTCTTTAATTTC
1 AATTTCTTTAATCTATGTCTTGAATTTC
1706305 AATTTCTTTAATCTA-GTCTTAGAATTT
1 AATTTCTTTAATCTATGTCTT-GAATTT
1706332 TACTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.58
Consensus pattern (28 bp):
AATTTCTTTAATCTATGTCTTGAATTTC
Found at i:1706365 original size:6 final size:6
Alignment explanation
Indices: 1706354--1706379 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1706344 TAAACCTTTT
1706354 GATTTA GATTTA GATTTA GATTTA GA
1 GATTTA GATTTA GATTTA GATTTA GA
1706380 ATATTTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (6 bp):
GATTTA
Found at i:1709750 original size:5 final size:5
Alignment explanation
Indices: 1709740--1709768 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1709730 AAAAAGGAAA
1709740 AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGAT
1709769 AGGAAGGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:1713547 original size:16 final size:14
Alignment explanation
Indices: 1713481--1713539 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
1713471 AAAAATATTG
1713481 AAAAAAATAAATAT
1 AAAAAAATAAATAT
*
1713495 AAAAAAATACTAAAAT
1 AAAAAAATA--AATAT
*
1713511 -AAAAATTAAAT-T
1 AAAAAAATAAATAT
1713523 ACCAAAAAATAAATAT
1 A--AAAAAATAAATAT
1713539 A
1 A
1713540 TATAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 9 0.26
15 17 0.49
16 6 0.17
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAAATAAATAT
Found at i:1713557 original size:27 final size:23
Alignment explanation
Indices: 1713527--1713583 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 23
1713517 TAAATTACCA
1713527 AAAAATAAATATATATAAAAAAGCTAT
1 AAAAATAAAT-TAT-TAAAAAA--TAT
1713554 AAAATGATAAATTATTAAAAAATAT
1 AAAA--ATAAATTATTAAAAAATAT
1713579 AAAAA
1 AAAAA
1713584 ATATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 1 0.04
25 7 0.25
27 11 0.39
28 3 0.11
29 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAAATAAATTATTAAAAAATAT
Found at i:1732493 original size:20 final size:22
Alignment explanation
Indices: 1732448--1732501 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1732438 AGTGCAAGAA
1732448 GAATCGATACCCCCTTGAAGGG
1 GAATCGATACCCCCTTGAAGGG
* *
1732470 GAATCGATTCCCCCTT-TA-GG
1 GAATCGATACCCCCTTGAAGGG
1732490 GAATCGATACCC
1 GAATCGATACCC
1732502 TCCACGGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 15 0.52
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (22 bp):
GAATCGATACCCCCTTGAAGGG
Found at i:1735075 original size:18 final size:20
Alignment explanation
Indices: 1735049--1735089 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1735039 AACCAGATTG
*
1735049 CCCAGA-GGGTACAGATACC
1 CCCAGAGGGGAACAGATACC
1735068 CCCA-AGGGGAACAGATACC
1 CCCAGAGGGGAACAGATACC
1735087 CCC
1 CCC
1735090 TGCTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.32, C:0.37, G:0.24, T:0.07
Consensus pattern (20 bp):
CCCAGAGGGGAACAGATACC
Found at i:1735151 original size:20 final size:20
Alignment explanation
Indices: 1735122--1735163 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1735112 AAATAGAATG
*
1735122 CCCAGAGGGTATAGATTCCC
1 CCCAGAGGGTACAGATTCCC
* *
1735142 CCCAGGGGGTACCGATTCCC
1 CCCAGAGGGTACAGATTCCC
1735162 CC
1 CC
1735164 TGTTTAACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (20 bp):
CCCAGAGGGTACAGATTCCC
Found at i:1735853 original size:20 final size:20
Alignment explanation
Indices: 1735805--1735853 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1735795 AATATTTATT
*
1735805 GCCAATTCACCCGCCTCTTG
1 GCCAATTCCCCCGCCTCTTG
1735825 GCCAATTCCCCCGCCTCTTG
1 GCCAATTCCCCCGCCTCTTG
1735845 GCCAATTCC
1 GCCAATTCC
1735854 ATCGATCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.47, G:0.14, T:0.24
Consensus pattern (20 bp):
GCCAATTCCCCCGCCTCTTG
Done.