Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1648865 original size:20 final size:20
Alignment explanation
Indices: 1648836--1648882 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1648826 AATGCAAAAT
* *
1648836 TAGTACCGATACTGCTATAG
1 TAGTATCGATACTGCTAAAG
1648856 TAGTATCGATACTGCTAAAG
1 TAGTATCGATACTGCTAAAG
*
1648876 TAATATC
1 TAGTATC
1648883 AAGTCAAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (20 bp):
TAGTATCGATACTGCTAAAG
Found at i:1652201 original size:20 final size:20
Alignment explanation
Indices: 1652176--1652226 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1652166 TATTGTATTG
*
1652176 TATGAACAGTACCGATACTA
1 TATGAACAGTACCAATACTA
* *
1652196 TATGAATAGTACCAATACTG
1 TATGAACAGTACCAATACTA
*
1652216 TGTGAACAGTA
1 TATGAACAGTA
1652227 ATGAACAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (20 bp):
TATGAACAGTACCAATACTA
Found at i:1657043 original size:134 final size:134
Alignment explanation
Indices: 1656859--1657116 Score: 358
Period size: 134 Copynumber: 1.9 Consensus size: 134
1656849 TTGATCTGTT
* * * **
1656859 TCTTTTTTGGGTAGTCAAATCAATTTTGAAAGACGAGTATGTTTCACTCTTCTTTCAGGGAGATA
1 TCTTTTTTGGGTACTCAAATCAATTTTGAAAGACGAGTATGCTCCACTCTTCTTTCAAAGAGATA
* * *
1656924 AGACTCGAGAAATCTTTGGAAGACGGGTCCT-CTCCACTCTTCTTTCAGGGAGATAAGACGATAT
66 AGACTCGAAAAATCTTTGGAAGACGGGT-CTGCTCCACTATTCTTTCAAGGAGATAAGACGATAT
1656988 ATTCC
130 ATTCC
** *
1656993 TCTTTTTTGGGTACTCAGGTCAATTTTGGAAA-ACGAGTCTGCTCCACTCTTCTTTCAAAGAGAT
1 TCTTTTTTGGGTACTCAAATCAATTTT-GAAAGACGAGTATGCTCCACTCTTCTTTCAAAGAGAT
* * *
1657057 AAGACTCGAAAAATCTTTTGAAGACGGGTCTGCTCCATTATTCTTTTAAGGAGATAAGAC
65 AAGACTCGAAAAATCTTTGGAAGACGGGTCTGCTCCACTATTCTTTCAAGGAGATAAGAC
1657117 TCGAGAAATC
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 2 0.02
134 102 0.94
135 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (134 bp):
TCTTTTTTGGGTACTCAAATCAATTTTGAAAGACGAGTATGCTCCACTCTTCTTTCAAAGAGATA
AGACTCGAAAAATCTTTGGAAGACGGGTCTGCTCCACTATTCTTTCAAGGAGATAAGACGATATA
TTCC
Found at i:1657101 original size:55 final size:55
Alignment explanation
Indices: 1657016--1657235 Score: 230
Period size: 55 Copynumber: 4.0 Consensus size: 55
1657006 CTCAGGTCAA
* * *
1657016 TTTTGGAAAACGAGTCTGCTCCACTCTTCTTTCAAAGAGATAAGACTCGAAAAATC
1 TTTT-GAAAACGGGTCTGCTCCACTATTCTTTCAAAGAGATAAGACTCGAGAAATC
* * * *
1657072 TTTTGAAGACGGGTCTGCTCCATTATTCTTTTAAGGAGATAAGACTCGAGAAATC
1 TTTTGAAAACGGGTCTGCTCCACTATTCTTTCAAAGAGATAAGACTCGAGAAATC
* * * * * *
1657127 TTTGGAAAATGGGTCTACTTCACTA-TCTTTCAGAGAGATAAAACTCGAGAAATC
1 TTTTGAAAACGGGTCTGCTCCACTATTCTTTCAAAGAGATAAGACTCGAGAAATC
* * ** *
1657181 -TTTGAAAAACAGGTCTGCTCCACTCTTCTTTCAGGGAGATATA-ACTCAAGAAATC
1 TTTTG-AAAACGGGTCTGCTCCACTATTCTTTCAAAGAGATA-AGACTCGAGAAATC
1657236 AGAAAGATTG
Statistics
Matches: 136, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
53 3 0.02
54 40 0.29
55 88 0.65
56 5 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
TTTTGAAAACGGGTCTGCTCCACTATTCTTTCAAAGAGATAAGACTCGAGAAATC
Found at i:1657349 original size:63 final size:63
Alignment explanation
Indices: 1657270--1657440 Score: 181
Period size: 62 Copynumber: 2.7 Consensus size: 63
1657260 GGAAATCAAT
* *
1657270 GATAACAAA-AGTTGACTTTTCTTCATAAAG-AAGTCAATGATTTGACTCTATTGGGGAGTCAGG
1 GATAACAAAGA-TTGACTTTTCTTCATAAAGAAAGTCAAGGA-TTGACTCTACTGGGGAGTCAGG
** *
1657333 GATAACAAAGATTGACTTCTT-TTCA-CGAGAAAGTCAAGGATTGACTCTGCTGGGGAGTCAGG
1 GATAACAAAGATTGACTT-TTCTTCATAAAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* * * * * *
1657395 AATAACAAAGGTTGACTTCTCTTCAT-GAGGAAGCCAAGGATTGACT
1 GATAACAAAGATTGACTTTTCTTCATAAAGAAAGTCAAGGATTGACT
1657441 ATAGGAAATA
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
61 1 0.01
62 60 0.65
63 29 0.31
64 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (63 bp):
GATAACAAAGATTGACTTTTCTTCATAAAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
Found at i:1657400 original size:62 final size:62
Alignment explanation
Indices: 1657300--1657440 Score: 192
Period size: 62 Copynumber: 2.3 Consensus size: 62
1657290 CTTCATAAAG
* * * *
1657300 AAGTCAATGATTTGACTCTATTGGGGAGTCAGGGATAACAAAGATTGACTTCTTTTCACGAGA
1 AAGTCAAGGA-TTGACTCTACTGGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGA
* * * *
1657363 AAGTCAAGGATTGACTCTGCTGGGGAGTCAGGAATAACAAAGGTTGACTTCTCTTCATGAGG
1 AAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGA
*
1657425 AAGCCAAGGATTGACT
1 AAGTCAAGGATTGACT
1657441 ATAGGAAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
62 60 0.87
63 9 0.13
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (62 bp):
AAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGA
Found at i:1659296 original size:17 final size:16
Alignment explanation
Indices: 1659242--1659296 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
1659232 ATTTAATTTA
*
1659242 TTTTTTCTCATTT-TTC
1 TTTTTTCT-TTTTCTTC
1659258 TTTTTTCTTTTTCTCTC
1 TTTTTTCTTTTTCT-TC
*
1659275 ATTTTTCTTTCTTCTTC
1 TTTTTTCTTT-TTCTTC
1659292 TTTTT
1 TTTTT
1659297 ATCTCTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 3 0.09
16 9 0.27
17 17 0.52
18 4 0.12
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTC
Found at i:1661243 original size:190 final size:194
Alignment explanation
Indices: 1660918--1661301 Score: 731
Period size: 190 Copynumber: 2.0 Consensus size: 194
1660908 TATATCTAGC
*
1660918 GTGAATACAAGATAATATATGTTCAAAGATTCTCTTTAAAAATGAATGTTTATACTCTTATATAC
1 GTGAATACAAGATAATATATGTTCAAAGATTCTCTTTAAAAATGAATGTTCATACTCTTATATAC
1660983 GATGTGCTCGAACTCGGGACCTCCAATGATAACAACAAATTCCTTAACTACTAAAGTCGTTTGGT
66 GATGTGCTCGAACTCGGGACCTCCAATGATAACAACAAATTCCTTAACTACTAAAGTCGTTTGGT
1661048 TCGTATTTATACCCCTACATATCTTTTGACAATGAACGCTCATACTATCA-ATATCA-TTGTCT
131 TCGTATTTATACCCCTACATATCTTTTGACAATGAACGCTCATACTATCATATATCATTTGTCT
1661110 GTGAATACAAGAT-A-ATATGTTCAAAGATTCTCTTTAAAAATGAATGTTCATACTCTTATATAC
1 GTGAATACAAGATAATATATGTTCAAAGATTCTCTTTAAAAATGAATGTTCATACTCTTATATAC
1661173 GATGTGCTCGAACTCGGGACCTCCAATGATAACAACAAATTCCTTAACTACTAAAGTCGTTTGGT
66 GATGTGCTCGAACTCGGGACCTCCAATGATAACAACAAATTCCTTAACTACTAAAGTCGTTTGGT
1661238 TCGTATTTATACCCCTACATATCTTTTGACAATGAACGCTCATACTATCATATATCATTTGTCT
131 TCGTATTTATACCCCTACATATCTTTTGACAATGAACGCTCATACTATCATATATCATTTGTCT
1661302 CTGACTTTAA
Statistics
Matches: 189, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
190 163 0.86
191 7 0.04
192 19 0.10
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (194 bp):
GTGAATACAAGATAATATATGTTCAAAGATTCTCTTTAAAAATGAATGTTCATACTCTTATATAC
GATGTGCTCGAACTCGGGACCTCCAATGATAACAACAAATTCCTTAACTACTAAAGTCGTTTGGT
TCGTATTTATACCCCTACATATCTTTTGACAATGAACGCTCATACTATCATATATCATTTGTCT
Found at i:1672662 original size:23 final size:23
Alignment explanation
Indices: 1672636--1672725 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
1672626 AACTGGTAAA
*
1672636 CGTGAACGTTAAATGAACACGTT
1 CGTGAACATTAAATGAACACGTT
*
1672659 CGTGAACGTTAAATGAACACGTT
1 CGTGAACATTAAATGAACACGTT
* * * *
1672682 CGTGAACATATTAACGAATATGTT
1 CGTGAACAT-TAAATGAACACGTT
*
1672706 CGCGAACATTAAATGAACAC
1 CGTGAACATTAAATGAACAC
1672726 ATTCACGAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 38 0.68
24 18 0.32
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (23 bp):
CGTGAACATTAAATGAACACGTT
Found at i:1672736 original size:23 final size:23
Alignment explanation
Indices: 1672639--1672742 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
1672629 TGGTAAACGT
* *
1672639 GAACGTTAAATGAACACGTTCGT
1 GAACATTAAATGAACACGTTCGC
* *
1672662 GAACGTTAAATGAACACGTTCGT
1 GAACATTAAATGAACACGTTCGC
* * * *
1672685 GAACATATTAACGAATATGTTCGC
1 GAACAT-TAAATGAACACGTTCGC
* *
1672709 GAACATTAAATGAACACATTCAC
1 GAACATTAAATGAACACGTTCGC
*
1672732 GAACAATAAAT
1 GAACATTAAAT
1672743 AAACGAACAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 49 0.73
24 18 0.27
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (23 bp):
GAACATTAAATGAACACGTTCGC
Found at i:1672772 original size:30 final size:32
Alignment explanation
Indices: 1672718--1672781 Score: 96
Period size: 30 Copynumber: 2.0 Consensus size: 32
1672708 CGAACATTAA
1672718 ATGAACACATTCACGAACAATAAATAAACGAAC
1 ATGAACACATTCAC-AACAATAAATAAACGAAC
*
1672751 ATGAACACCTTCA-AA-AATAAATAAACGAAC
1 ATGAACACATTCACAACAATAAATAAACGAAC
1672781 A
1 A
1672782 CGAATACGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.53
31 2 0.07
33 12 0.40
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (32 bp):
ATGAACACATTCACAACAATAAATAAACGAAC
Found at i:1673399 original size:88 final size:89
Alignment explanation
Indices: 1673295--1673471 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 89
1673285 CTTAAAATAA
1673295 GTGTTGTTATAAAACCAAAATAAACAAATTGTCAAGCACCAACTTGCTGCGGTGTCTTGAACAGA
1 GTGTTGTTATAAAACCAAAATAAACAAATTGTCAAGCACCAACTTGCTGCGGTGTCTTGAACAGA
1673360 AAGTTAAGTAAGAATC-CATGTCC
66 AAGTTAAGTAAGAATCTCATGTCC
1673383 GTGTTGTTATAAAACCAAAATAAACAAATTGTCAAGCACCAACTTGCTGCGGTGTCTTGAACAGA
1 GTGTTGTTATAAAACCAAAATAAACAAATTGTCAAGCACCAACTTGCTGCGGTGTCTTGAACAGA
1673448 AAGTTAAGTAAGAATCTCATGTCC
66 AAGTTAAGTAAGAATCTCATGTCC
1673472 TTTTCCAGAT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 81 0.92
89 7 0.08
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (89 bp):
GTGTTGTTATAAAACCAAAATAAACAAATTGTCAAGCACCAACTTGCTGCGGTGTCTTGAACAGA
AAGTTAAGTAAGAATCTCATGTCC
Found at i:1674384 original size:126 final size:126
Alignment explanation
Indices: 1674225--1675472 Score: 983
Period size: 126 Copynumber: 10.1 Consensus size: 126
1674215 TGAGTGAAAT
* * * * ** *
1674225 CGATGAAGATACAAGCTCGTCAATGAAAGGAGGAGGCGGAAATGTCGATCAGGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * *
1674290 CTAGAAATGACATGGTCGAAAGCATAGAATCAAAGATACCTATTGAAGAAACGAGCAAAAT
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * *
1674351 CGATGAAGACACAACCTTGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGCTTCTAGTGTTT
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * * *
1674416 ATGAAAATGACATAGTTGAAAGCATAGAATCGAAGAGACCCATTAAAGAAACGAGCGAAAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * *
1674477 CAATAAAAATACAAGCTCGTTAAC-AAA--AGGAGACAAAAATATCGATAAAGATTCTAGTATTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * * * **
1674539 ATGGAAATGACGTGGTTCAAAACATAGAATCAAAGAGATCTATTGAAGATACAAGTGAAAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * * * * *
1674600 CAATGAAAACACAAACTTGATAACAAAAGGAGAAAGCGAAAATGTCGATCAAGATTTTAGTTTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* ** * * * * *
1674665 ATGGAAATTATGTGGTTGAAAGCATAGAATCGAATAGACCCATTCAAGAAACGAGCGAAAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * * *
1674726 CAATGAAAATACGAGCCCATTAACGAAAGGAGGCGGAAAAAATGTTGATCAAGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * * *
1674791 ATGGAAAGGACATGGTTGAAAGTATAGAATCGAAGAAACCTATTGAAGAAACAAGCGAAAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * *
1674852 CGATGAGAATACAAGCTCGTTAACGAAAGAAGAAGACAAAAATGTTGATGAAGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * * * *
1674917 ATGGAAGTGACATAGTTGAAAGCATAGAATCAAAGAAATCTATTGAAGTAACGAGCGATAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* ** * * * * * *
1674978 CTACAAAAACACAAGCTCATTAACGAAAGGAAGAGGGAAAAATATTGACCAAGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * *** * *
1675043 ATGGGAATGGCATGGTTGAAAGCGTAGAATTGGAGAAACCCATTGAAG--A--A--AAAAC
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * *
1675098 TGATGAAAACACAAACTCGTCAATGAAAGGAGGA-G-----A---CAATCAAGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * * * * * * * *
1675154 ATGGAACTTACAAGGTTGAAATCGTAGAATCGAAGATACCTATTGAAGATACGAGAAAAAT
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * *
1675215 CGATGAATACACAAGCTTGATAATGAAAGGAGG-CG-AAAATAT-T-GATCAAGGTTCTAGGGTT
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAA-ATGTCGATCAAGATTCTAGTGTT
* ** * * * ** * *
1675276 GAGGGAAATGACATTATTGAAAGCGTAGAATCAAAGTGATCTACAGAAGAAATGAGCAAAAT
65 GATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
* * * * * * ** * * *
1675338 TGACGAAAACATAAGCTTGATAATGAAAGGAGGAGATAAACATATCGATCGAGATTCTAGTGTTG
1 CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
* * * ** *
1675403 ATGAAAATGACATGATTGAAAGCATATAATCAAAGAGACCTATTGAAGAAACGATAAAAAA
66 ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
1675464 CGATGAAAA
1 CGATGAAAA
1675473 TATAAACTTG
Statistics
Matches: 886, Mismatches: 215, Indels: 42
0.78 0.19 0.04
Matches are distributed among these distances:
111 55 0.06
113 1 0.00
114 1 0.00
115 1 0.00
117 32 0.04
119 1 0.00
120 28 0.03
122 2 0.00
123 187 0.21
124 6 0.01
125 7 0.01
126 565 0.64
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (126 bp):
CGATGAAAACACAAGCTCGTTAACGAAAGGAGGAGGCAAAAATGTCGATCAAGATTCTAGTGTTG
ATGGAAATGACATGGTTGAAAGCATAGAATCAAAGAGACCTATTGAAGAAACGAGCAAAAC
Found at i:1674938 original size:252 final size:250
Alignment explanation
Indices: 1674255--1675456 Score: 948
Period size: 249 Copynumber: 4.9 Consensus size: 250
1674245 CAATGAAAGG
* * * * * *
1674255 AGGAGGCGG--AAATGTCGATCAGGATTCTAGTGTTGCTAGAAATGACATGGTCGAAAGCATAGA
1 AGGAGGCGGAAAAATATCGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGCATAGA
* * * * *
1674318 ATCAAAGATACCTATTGAAGAAACGAGCAAAATCGATGAAGACACAACCTTGTTAACGAAAGGAG
66 ATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATGAA-ACACAAACTTGTTAACGAAAGGAG
* * * * *
1674383 GAGGCAAAAATGTCGATCAAGCTTCTAGTGTTTATGAAAATGACATAGTTGAAAGCATAGAATCG
130 AAGACAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATAGTTGAAAGCATAGAATCG
* *
1674448 AAGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGCTCGTTAACAAA
195 AAGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGCTCATTAACGAA
* * * * * * *
1674504 AGGAGAC--AAAAATATCGATAAAGATTCTAGTATTGATGGAAATGACGTGGTTCAAAACATAGA
1 AGGAGGCGGAAAAATATCGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGCATAGA
* * * * * * *
1674567 ATCAAAGAGATCTATTGAAGATACAAGTGAAACCAATGAAAACACAAACTTGATAACAAAAGGAG
66 ATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATG-AAACACAAACTTGTTAACGAAAGGAG
* * * * ** *
1674632 AA-AGCGAAAATGTCGATCAAGATTTTAGTTTTGATGGAAATTATGTGGTTGAAAGCATAGAATC
130 AAGA-CAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATAGTTGAAAGCATAGAATC
* * * * *
1674696 GAATAGACCCATTCAAGAAACGAGCGAAACCAATGAAAATACGAGCCCATTAACGAA
194 GAAGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGCTCATTAACGAA
* * *
1674753 AGGAGGCGGAAAAAATGTTGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGTATAG
1 AGGAGGCGG-AAAAATATCGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGCATAG
* * * * *
1674818 AATCGAAGAAACCTATTGAAGAAACAAGCGAAACCGATGAGAATACAAGCTCGTTAACGAAAGAA
65 AATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATGA-AACACAAACTTGTTAACGAAAGGA
* * *
1674883 GAAGACAAAAATGTTGATGAAGATTCTAGTGTTGATGGAAGTGACATAGTTGAAAGCATAGAATC
129 GAAGACAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATAGTTGAAAGCATAGAATC
* * * * * * * * * *
1674948 AAAGAAATCTATTGAAGTAACGAGCGATACCTACAAAAACACAAGCTCATTAACGAA
194 GAAGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGCTCATTAACGAA
* * * *
1675005 AGGAAGAG-GGAAAAATATTGACCAAGATTCTAGTGTTGATGGGAATGG-CATGGTTGAAAGCGT
1 AGG-AG-GCGGAAAAATATCGATCAAGATTCTAGTGTTGAT-GGAAAGGACATGGTTGAAAGCAT
*** * * * * *
1675068 AGAATTGGAGAAACCCATTGAAG--A-AA---AAACTGATGAAAACACAAACTCGTCAATGAAAG
63 AGAATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATG-AAACACAAACTTGTTAACGAAAG
* * * * *
1675127 GAGGAGAC----A-----ATCAAGATTCTAGTGTTGATGGAACTTACA-AGGTTGAAATCGTAGA
127 GAGAAGACAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATA-GTTGAAAGCATAGA
* * * * ** * * * * * * *
1675182 ATCGAAGATACCTATTGAAGATACGAGAAAAATCGATGAATACACAAGCTTGA-TAATGAA
191 ATCGAAGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGC-TCATTAACGAA
* * * * * ** *
1675242 AGGAGGC-G-AAAATATTGATCAAGGTTCTAGGGTTGAGGGAAATGACATTATTGAAAGCGTAGA
1 AGGAGGCGGAAAAATATCGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGCATAGA
** * ** ** * ** * * *
1675305 ATCAAAGTGATCTACAGAAGAAATGAGCAAAATTGACGAAA-ACATAAGCTTGATAATGAAAGGA
66 ATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATGAAACACA-AA-CTTGTTAACGAAAGGA
* * * * * * *
1675369 GGAGATAAACATATCGATCGAGATTCTAGTGTTGATGAAAATGACAT-GATTGAAAGCATATAAT
129 GAAGACAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATAG-TTGAAAGCATAGAAT
* * *
1675433 CAAAGAGACCTATTGAAGAAACGA
193 CGAAGAGACCCATTAAAGAAACGA
1675457 TAAAAAACGA
Statistics
Matches: 761, Mismatches: 156, Indels: 72
0.77 0.16 0.07
Matches are distributed among these distances:
233 5 0.01
234 52 0.07
235 2 0.00
236 4 0.01
237 85 0.11
238 5 0.01
239 5 0.01
240 25 0.03
242 1 0.00
244 1 0.00
246 32 0.04
247 1 0.00
248 1 0.00
249 269 0.35
250 3 0.00
251 1 0.00
252 257 0.34
253 11 0.01
254 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (250 bp):
AGGAGGCGGAAAAATATCGATCAAGATTCTAGTGTTGATGGAAAGGACATGGTTGAAAGCATAGA
ATCAAAGAAACCTATTGAAGAAACAAGCGAAACCGATGAAACACAAACTTGTTAACGAAAGGAGA
AGACAAAAATGTCGATCAAGATTCTAGTGTTGATGGAAATGACATAGTTGAAAGCATAGAATCGA
AGAGACCCATTAAAGAAACGAGCGAAACCAATAAAAATACAAGCTCATTAACGAA
Found at i:1675488 original size:126 final size:123
Alignment explanation
Indices: 1675136--1675488 Score: 382
Period size: 123 Copynumber: 2.8 Consensus size: 123
1675126 GGAGGAGACA
* * * * * * *
1675136 ATCAAGATTCTAGTGTTGATGGAACTTACAAGGTTGAAATCGTAGAATCGAAGATACCTATTGAA
1 ATCAAGATTCTAGTGTTGATGGAAATGACATGATTGAAAGCGTAGAATCAAAGAGACCTATTGAA
* * * * *
1675201 GATACGAGAAAAATCGATGAATACACAAGCTTGATAATGAAAGGAGGCGAAAATATTG
66 GAAACGAGAAAAATCGATGAAAACATAAGCTTGATAATGAAAGGAGGAGAAAATATCG
* * * * * * **
1675259 ATCAAGGTTCTAGGGTTGAGGGAAATGACATTATTGAAAGCGTAGAATCAAAGTGATCTACAGAA
1 ATCAAGATTCTAGTGTTGATGGAAATGACATGATTGAAAGCGTAGAATCAAAGAGACCTATTGAA
* * * *
1675324 GAAATGAGCAAAATTGACGAAAACATAAGCTTGATAATGAAAGGAGGAGATAAACATATCG
66 GAAACGAGAAAAATCGATGAAAACATAAGCTTGATAATGAAAGGAGGAG--AAA-ATATCG
* * * *
1675385 ATCGAGATTCTAGTGTTGATGAAAATGACATGATTGAAAGCATATAATCAAAGAGACCTATTGAA
1 ATCAAGATTCTAGTGTTGATGGAAATGACATGATTGAAAGCGTAGAATCAAAGAGACCTATTGAA
* * * * *
1675450 GAAACGATAAAAAACGATGAAAATATAAACTTGTTAATG
66 GAAACGAGAAAAATCGATGAAAACATAAGCTTGATAATG
1675489 GAAGAAGAAA
Statistics
Matches: 182, Mismatches: 45, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
123 91 0.50
125 3 0.02
126 88 0.48
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (123 bp):
ATCAAGATTCTAGTGTTGATGGAAATGACATGATTGAAAGCGTAGAATCAAAGAGACCTATTGAA
GAAACGAGAAAAATCGATGAAAACATAAGCTTGATAATGAAAGGAGGAGAAAATATCG
Found at i:1675731 original size:41 final size:42
Alignment explanation
Indices: 1675649--1675732 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1675639 GTAGACGAAA
1675649 ATACCTTGGGGGACAAGAAACAAGTAGAAAATGCAAAAGAAG
1 ATACCTTGGGGGACAAGAAACAAGTAGAAAATGCAAAAGAAG
*
1675691 ATACCTTGGTGGACAAGAAACAAG-AGAAAATGCAAAAGAAG
1 ATACCTTGGGGGACAAGAAACAAGTAGAAAATGCAAAAGAAG
1675732 A
1 A
1675733 AACTTCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 18 0.44
42 23 0.56
ACGTcount: A:0.51, C:0.12, G:0.25, T:0.12
Consensus pattern (42 bp):
ATACCTTGGGGGACAAGAAACAAGTAGAAAATGCAAAAGAAG
Found at i:1684099 original size:21 final size:22
Alignment explanation
Indices: 1684044--1684102 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1684034 AAACCATTCA
* *
1684044 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGATTCCCCCTTGG
1684066 GGGGGAATCGATTCCCCCTTGG
1 GGGGGAATCGATTCCCCCTTGG
1684088 GGGGGAAT-GATTCCC
1 GGGGGAATCGATTCCC
1684103 TCTAAGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 7 0.20
22 28 0.80
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCCTTGG
Found at i:1687445 original size:20 final size:20
Alignment explanation
Indices: 1687420--1687459 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1687410 AATTGGCAAG
1687420 TACCGGAGGTGCTTTCCTAT
1 TACCGGAGGTGCTTTCCTAT
1687440 TACCGGAGGTGCTTTCCTAT
1 TACCGGAGGTGCTTTCCTAT
1687460 CTAATTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
TACCGGAGGTGCTTTCCTAT
Found at i:1690474 original size:22 final size:21
Alignment explanation
Indices: 1690432--1690471 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1690422 AAGTTTGTTT
*
1690432 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1690453 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1690472 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1695662 original size:41 final size:40
Alignment explanation
Indices: 1695600--1695684 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
1695590 ACCAACGGTG
* * *
1695600 CTGAACGTTGGTACACTAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACTAATGTACCAAAGCTAAACTGA-AA
1695641 CTGAACATTGATACA-TGAATGTACCAAAGCTAAACTGAAA
1 CTGAACATTGATACACT-AATGTACCAAAGCTAAACTGAAA
1695681 CTGA
1 CTGA
1695685 TAAAAATTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 7 0.17
41 33 0.82
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (40 bp):
CTGAACATTGATACACTAATGTACCAAAGCTAAACTGAAA
Found at i:1695805 original size:18 final size:18
Alignment explanation
Indices: 1695782--1695869 Score: 83
Period size: 18 Copynumber: 5.0 Consensus size: 18
1695772 TATTAATATG
*
1695782 TATCTGATAAATGTAAAA
1 TATCTGATAACTGTAAAA
* * * *
1695800 TATCTGAT-ATTTTTAAT
1 TATCTGATAACTGTAAAA
*
1695817 TATATGATAACTGT-AAA
1 TATCTGATAACTGTAAAA
1695834 TCATCTGATAACTGTAAAA
1 T-ATCTGATAACTGTAAAA
*
1695853 TATCAGATAACTG-AAAA
1 TATCTGATAACTGTAAAA
1695870 CCATCATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
17 19 0.33
18 34 0.60
19 4 0.07
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (18 bp):
TATCTGATAACTGTAAAA
Found at i:1695875 original size:18 final size:17
Alignment explanation
Indices: 1695822--1695880 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1695812 TTAATTATAT
* *
1695822 GATAACTGTAAATCATCT
1 GATAACTG-AAAACATCA
*
1695840 GATAACTGTAAAATATCA
1 GATAACTG-AAAACATCA
1695858 GATAACTGAAAACCATCA
1 GATAACTGAAAA-CATCA
*
1695876 TATAA
1 GATAA
1695881 TTGTAAACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 4 0.11
18 31 0.89
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (17 bp):
GATAACTGAAAACATCA
Found at i:1696094 original size:3 final size:3
Alignment explanation
Indices: 1696086--1696131 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1696076 ACTTTAGCAC
1696086 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1696132 AATCAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1703725 original size:18 final size:18
Alignment explanation
Indices: 1703702--1703790 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
1703692 TATTAATATG
1703702 TATCTGATAACTGTAAAA
1 TATCTGATAACTGTAAAA
1703720 TATCTGATAACTGT-AAA
1 TATCTGATAACTGTAAAA
*
1703737 TCATCTAATAACTGTAAAA
1 T-ATCTGATAACTGTAAAA
*
1703756 TATCTTATAACTG-AAAA
1 TATCTGATAACTGTAAAA
* *
1703773 TCATTTGATAATTGTAAA
1 T-ATCTGATAACTGTAAA
1703791 CATTTAGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
17 9 0.15
18 46 0.74
19 7 0.11
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
TATCTGATAACTGTAAAA
Found at i:1703749 original size:36 final size:36
Alignment explanation
Indices: 1703703--1703790 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
1703693 ATTAATATGT
*
1703703 ATCTGATAACTGTAAAATATCTGATAACTGTAAATC
1 ATCTGATAACTGTAAAATATCTGATAACTGAAAATC
* *
1703739 ATCTAATAACTGTAAAATATCTTATAACTGAAAATC
1 ATCTGATAACTGTAAAATATCTGATAACTGAAAATC
* *
1703775 ATTTGATAATTGTAAA
1 ATCTGATAACTGTAAA
1703791 CATTTAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (36 bp):
ATCTGATAACTGTAAAATATCTGATAACTGAAAATC
Found at i:1703999 original size:3 final size:3
Alignment explanation
Indices: 1703991--1704060 Score: 131
Period size: 3 Copynumber: 23.0 Consensus size: 3
1703981 CTTTAACACT
1703991 TTA TTA 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 TTA TTA
1704037 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1704061 AATAAAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1709126 original size:30 final size:30
Alignment explanation
Indices: 1709090--1709155 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1709080 GAAAACATAT
* *
1709090 ACAGCTTGGTGGAGCATTTTTGGA-AGACAA
1 ACAGCTTGGTGGAGCA-TTTGGGAGACACAA
1709120 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1709150 ACAGCT
1 ACAGCT
1709156 CACAAGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
ACAGCTTGGTGGAGCATTTGGGAGACACAA
Found at i:1709857 original size:2 final size:2
Alignment explanation
Indices: 1709850--1709885 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1709840 ACATATCACC
1709850 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
1709886 TCCGCTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712642 original size:30 final size:30
Alignment explanation
Indices: 1712606--1712671 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1712596 GAAAACATAT
* *
1712606 ACAGCTTGGTGGAGCATTTTTGGA-AGACAA
1 ACAGCTTGGTGGAGCA-TTTGGGAGACACAA
1712636 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
1712666 ACAGCT
1 ACAGCT
1712672 CACAAGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
ACAGCTTGGTGGAGCATTTGGGAGACACAA
Found at i:1715301 original size:72 final size:70
Alignment explanation
Indices: 1715111--1715338 Score: 207
Period size: 72 Copynumber: 3.2 Consensus size: 70
1715101 TCTGATCGGT
* * * * *
1715111 AAGTATCGATACTTTTCCACAAGTATAGATATTTTCGAATTT-TAAAAA-ATGGAAAATAAAAAA
1 AAGTATCAATACTTTTCCACAAATATA-ATAATTTCAAATTTATAAAAACATGAAAAATAAAAAA
1715174 GCTGCA
65 GCTGCA
* * * * *
1715180 AAGTATCAATACTTATCCACAAATATTTATACTTCCAAATTTTAAAAAAACATGAAAAAT-AAAA
1 AAGTATCAATACTTTTCCACAAATA-TAATAATTTCAAA-TTTATAAAAACATGAAAAATAAAAA
1715244 AGACTGCA
64 AG-CTGCA
* * *
1715252 AAGTTTCAATATTTTTCCACAAATATCAATAATTTCAAATTTACTAAAAATCAT-AGAAAATGAA
1 AAGTATCAATACTTTTCCACAAATAT-AATAATTTCAAATTTA-TAAAAA-CATGA-AAAATAAA
* *
1715316 AAGGATGC-
62 AAAGCTGCA
1715324 AAGTATCAA-ACTTTT
1 AAGTATCAATACTTTT
1715339 TTTTAAATAA
Statistics
Matches: 129, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
69 30 0.23
70 4 0.03
71 21 0.16
72 58 0.45
73 11 0.09
74 5 0.04
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (70 bp):
AAGTATCAATACTTTTCCACAAATATAATAATTTCAAATTTATAAAAACATGAAAAATAAAAAAG
CTGCA
Found at i:1716210 original size:20 final size:21
Alignment explanation
Indices: 1716172--1716211 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1716162 AGTAAGAAAC
1716172 TTGAAAATATACTAGTAAATG
1 TTGAAAATATACTAGTAAATG
*
1716193 TTGAAAAT-TACTATTAAAT
1 TTGAAAATATACTAGTAAAT
1716212 ATAAAGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
TTGAAAATATACTAGTAAATG
Found at i:1716943 original size:3 final size:3
Alignment explanation
Indices: 1716935--1717065 Score: 190
Period size: 3 Copynumber: 43.7 Consensus size: 3
1716925 GTAACCTAAA
* * * *
1716935 AAT AAT AAT AAT AAA AAT ATT AAT AAT AGT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1716983 AAT AAT AAT AAT GAT GAT GAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1717031 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1717066 ACAATTAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1717466 original size:100 final size:99
Alignment explanation
Indices: 1717280--1717584 Score: 414
Period size: 100 Copynumber: 3.0 Consensus size: 99
1717270 ATAGTGCAAT
* * **
1717280 AATAGTTACAACTTAACCAATTAAAATAAAATAGGAG-AACCTATTACGTTAAACTAGCTACAAA
1 AATATTTACAACTTAACCAGTTAAAATAAAATAGGAGCAACCTATTACGTTAAACTAGCTACTGA
*
1717344 TTTGTTTAAAGGTATAAAAATAATGTAAACGGTAA
66 TTTGTTTAAA-GTATAATAATAATGTAAACGGTAA
* * * *
1717379 AATATTTACAACTTAACCAGTTAAAATAAAATAGGCGCAACATATTACATTAAATTAGCTACTGA
1 AATATTTACAACTTAACCAGTTAAAATAAAATAGGAGCAACCTATTACGTTAAACTAGCTACTGA
*
1717444 TTTGTTTAAATGTATAATAATAATGTAAACGATAA
66 TTTGTTTAAA-GTATAATAATAATGTAAACGGTAA
* * *
1717479 AATATTTACAATTTAACCTGTTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACCTG
1 AATATTTACAACTTAACCAGTTAAAATAAAATAGGAGCAACCTATTACGTTAAACTAGCTA-CTG
* * *
1717544 TTTTTGTTTATAGATATAATAATAATGTAAACAGTAA
65 -ATTTGTTTAAAG-TATAATAATAATGTAAACGGTAA
1717581 AATA
1 AATA
1717585 AAATAGGTGC
Statistics
Matches: 181, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
99 34 0.19
100 109 0.60
101 4 0.02
102 34 0.19
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (99 bp):
AATATTTACAACTTAACCAGTTAAAATAAAATAGGAGCAACCTATTACGTTAAACTAGCTACTGA
TTTGTTTAAAGTATAATAATAATGTAAACGGTAA
Found at i:1717593 original size:78 final size:76
Alignment explanation
Indices: 1717500--1717660 Score: 241
Period size: 78 Copynumber: 2.1 Consensus size: 76
1717490 TTTAACCTGT
* * *
1717500 TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACCTGTTTTTGTTTATAGATATAATA
1 TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA-CAG-GTTTGTTTAAAGATATAATA
1717565 ATAATGTAAACAG
64 ATAATGTAAACAG
* * *
1717578 TAAAATAAAATAGGTGCTACCTATTATGTTAAACTAGCTACAGGTTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACAGGTTTGTTTAAAGATATAATAAT
*
1717643 AATGTAAACGG
66 AATGTAAACAG
1717654 TAAAATA
1 TAAAATA
1717661 TTTACAACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
76 36 0.47
77 2 0.03
78 38 0.50
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (76 bp):
TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACAGGTTTGTTTAAAGATATAATAAT
AATGTAAACAG
Found at i:1717641 original size:178 final size:174
Alignment explanation
Indices: 1717391--1717931 Score: 678
Period size: 171 Copynumber: 3.1 Consensus size: 174
1717381 TATTTACAAC
* * * * * * * *
1717391 TTAACCAGTTAAAATAAAATAGGCGCAACATATTACATTAAATTAGCTACTGATTTGTTTAAATG
1 TTAAACAG-TAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTACAGGTTTGTTTAAAGG
* *
1717456 TATAATAATAATGTAAACGATAAAATATTTACAATTTAACCTGTTAAAATAAAATAGGTGCAACC
65 TATAATAATAATGTAAACGGTAAAATATTTACAATTTAACCGGTTAAAATAAAATAGGTGCAACC
* * *
1717521 TATTACGTTAAACTAGCTACCTGTTTTTGTTTATAGATATAATAATAA
130 TATTACGTTAAACTAACTATC-G-ATTTGTTTA-AGATATAATAATAA
* *
1717569 TGTAAACAGTAAAATAAAATAGGTGCTACCTATTATGTTAAACTAGCTACAGGTTTGTTTAAAGG
1 T-TAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTACAGGTTTGTTTAAAGG
* * *
1717634 TATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGCGCAACA
65 TATAATAATAATGTAAACGGTAAAATATTTACAATTTAACCGGTTAAAATAAAATAGGTGCAACC
* * ** *
1717699 TAATACGTTAAACTAACTATCGATCTGTTTAA-AGGT-ATAACAA
130 TATTACGTTAAACTAACTATCGATTTGTTTAAGATATAATAATAA
* *
1717742 -TAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATTA-GTTTGTTTAAAGG
1 TTAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTA-CAGGTTTGTTTAAAGG
* * * *
1717805 TATAATAATAATATAAACGGTAAAATATTTACAATTTAACAGGTTAAAATAAAATAAGCT-CTAC
65 TATAATAATAATGTAAACGGTAAAATATTTACAATTTAACCGGTTAAAATAAAAT-AGGTGCAAC
* * *
1717869 CTATTACGTTAAACTACCTATCGGTTTGTTTAAAGATATAATACTAA
129 CTATTACGTTAAACTAACTATCGATTTGTTT-AAGATATAATAATAA
1717916 TATAAACAGTAAAATA
1 T-TAAACAGTAAAATA
1717932 TTTACAACTT
Statistics
Matches: 313, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
171 138 0.44
172 5 0.02
173 8 0.03
174 7 0.02
175 1 0.00
176 21 0.07
177 1 0.00
178 126 0.40
179 6 0.02
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (174 bp):
TTAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTACAGGTTTGTTTAAAGGT
ATAATAATAATGTAAACGGTAAAATATTTACAATTTAACCGGTTAAAATAAAATAGGTGCAACCT
ATTACGTTAAACTAACTATCGATTTGTTTAAGATATAATAATAA
Found at i:1717758 original size:100 final size:99
Alignment explanation
Indices: 1717578--1717760 Score: 217
Period size: 100 Copynumber: 1.8 Consensus size: 99
1717568 ATGTAAACAG
* * * * * * * * *
1717578 TAAAATAAAATAGGTGCTACCTATTATGTTAAACTAGCTACAGGTTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTACAGATCTGTTTAAAGGTATAACAAT
* *
1717643 AATGTAAACGGTAAAATATTTACAACTTAACCGGT
66 AAAGTAAAC-ATAAAATATTTACAACTTAACCGGT
1717678 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTATC-GATCTGTTTAAAGGTATAACAA
1 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTA-CAGATCTGTTTAAAGGTATAACAA
1717742 TAAACAGTAAA-ATAAAATA
65 T-AA-AGTAAACATAAAATA
1717761 GGCGCTACCT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
100 61 0.88
101 3 0.04
102 5 0.07
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (99 bp):
TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTACAGATCTGTTTAAAGGTATAACAAT
AAAGTAAACATAAAATATTTACAACTTAACCGGT
Found at i:1717831 original size:71 final size:71
Alignment explanation
Indices: 1717678--1717815 Score: 197
Period size: 71 Copynumber: 1.9 Consensus size: 71
1717668 CTTAACCGGT
*
1717678 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTATCGATCTGTTTAAAGGTATAACAAT
1 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTATAGATCTGTTTAAAGGTATAACAAT
1717743 AAACAG
66 AAACAG
* * * * * *
1717749 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATTAG-TTTGTTTAAAGGTATAATAA
1 TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTA-TAGATCTGTTTAAAGGTATAACAA
1717813 TAA
65 TAA
1717816 TATAAACGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 57 0.97
72 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (71 bp):
TAAAATAAAATAGGCGCAACATAATACGTTAAACTAACTATAGATCTGTTTAAAGGTATAACAAT
AAACAG
Found at i:1717857 original size:100 final size:100
Alignment explanation
Indices: 1717749--1718044 Score: 403
Period size: 100 Copynumber: 3.0 Consensus size: 100
1717739 CAATAAACAG
* * **
1717749 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTATCTATTAGTTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAGGTATAATAAT
*
1717814 AATATAAACGGTAAAATATTTACAATTTAACAGGT
66 AATATAAACGGTAAAATATTTACAACTTAACAGGT
* * * *
1717849 TAAAATAAAATAAGCTCTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAGATATAATACT
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAGGTATAATAAT
* *
1717914 AATATAAACAGTAAAATATTTACAACTTAACCGGT
66 AATATAAACGGTAAAATATTTACAACTTAACAGGT
* * ** * * *
1717949 TAAAATAAAATAGACATTGTCTATTACGTTAAACTACCTACCGGATTATTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAGGTATAATAAT
* * *
1718014 AATGTAAACGATAAAATATTTACAAGTTAAC
66 AATATAAACGGTAAAATATTTACAACTTAAC
1718045 CATTTAAAAT
Statistics
Matches: 171, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 171 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (100 bp):
TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAGGTATAATAAT
AATATAAACGGTAAAATATTTACAACTTAACAGGT
Found at i:1718957 original size:107 final size:106
Alignment explanation
Indices: 1718695--1719262 Score: 692
Period size: 107 Copynumber: 5.3 Consensus size: 106
1718685 ATGTTTATTT
* * * * * *
1718695 ATAACAAAATAAATATTTAACCTATTTTGTTATCTTGAGATTTCGAACGTCCCATCAGCTTAACC
1 ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAA-GTCCCATCAGCTTAAAC
* *
1718760 TTTAGTAACATTTTTTAGGCGCTACCTAATATGTTAATAATATTA
65 TTTGGTAACA--TTTTAGGCGCTACCTAATATGTTGATAATA-TA
* * * * * * *
1718805 ATAAAAAAAATAAGTAATTGACTTATTTTATTATTGTGAGATTTCTAAGATTCCGTCAGCTTAAA
1 AT-AACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAAG-TCCCATCAGCTTAAA
1718870 CTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATA
64 CTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATA
1718913 ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAA-TGCCACATCAGCTTAAA
1 ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAAGT-CC-CATCAGCTTAAA
* *
1718977 CTTTGGTAACATTTTAGGCACTATCTAATATGTTGATAATATA
64 CTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATA
* *
1719020 ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAATGCCCCATCAGCTTAACC
1 ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAA-GTCCCATCAGCTTAAAC
* *
1719085 TTTGGTAACATTTTAGGCGCTACCTAATATGTTAATAGTATA
65 TTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATA
* * * * * *
1719127 ATAAAAAAATAATTAATTAATC-TATTTTGTTATCATTG-GATTTCTAAGGCCCATCAGATCAAA
1 ATAACAAAATAAGTAATTAA-CATATTTTGTTATC-GTGAGATTTCTAAGTCCCATCAGCTTAAA
* * * *
1719190 TTTTGATAAACATATTAGGCGCTACCTAATATGTTGATAAAATTA
64 CTTTGGT-AACATTTTAGGCGCTACCTAATATGTTGATAATA-TA
* * *
1719235 ATAACAAAATAAGTTATTTACTTATTTT
1 ATAACAAAATAAGTAATTAACATATTTT
1719263 CTTACCGTTT
Statistics
Matches: 401, Mismatches: 46, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.00
106 18 0.04
107 259 0.65
108 33 0.08
109 29 0.07
110 3 0.01
111 58 0.14
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (106 bp):
ATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAGATTTCTAAGTCCCATCAGCTTAAACT
TTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATA
Found at i:1721690 original size:20 final size:22
Alignment explanation
Indices: 1721653--1721700 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
1721643 AATTAAATCC
1721653 ATATTTTTATTGAATAAAAATA
1 ATATTTTTATTGAATAAAAATA
*
1721675 ATATTTTT-TT-AATAAATATA
1 ATATTTTTATTGAATAAAAATA
*
1721695 TTATTT
1 ATATTT
1721701 CGGGTCGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATTTTTATTGAATAAAAATA
Found at i:1729105 original size:2 final size:2
Alignment explanation
Indices: 1729100--1729126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1729090 TAATAACAAT
1729100 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
1729127 TGTATGTAAA
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:1729795 original size:3 final size:3
Alignment explanation
Indices: 1729787--1729822 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1729777 TAGTGTATGA
*
1729787 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1729823 CAATTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1730376 original size:19 final size:19
Alignment explanation
Indices: 1730344--1730381 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1730334 ACCTGAACTG
1730344 AAATAATATATTTATTTAA
1 AAATAATATATTTATTTAA
* *
1730363 AAATATTATTTTTATTTAA
1 AAATAATATATTTATTTAA
1730382 TAAAAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATAATATATTTATTTAA
Found at i:1733335 original size:18 final size:17
Alignment explanation
Indices: 1733312--1733351 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1733302 CACATTTCTT
1733312 AATATTAAAAAATAAATA
1 AATATTAAAAAA-AAATA
* *
1733330 AATATTAATAAAACATA
1 AATATTAAAAAAAAATA
1733347 AATAT
1 AATAT
1733352 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATTAAAAAAAAATA
Found at i:1733355 original size:2 final size:2
Alignment explanation
Indices: 1733348--1733376 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1733338 TAAAACATAA
1733348 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 A
1733377 ATTTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1733407 original size:18 final size:18
Alignment explanation
Indices: 1733384--1733442 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
1733374 ATAATTTATA
1733384 AAAATAAAATATTTATTT
1 AAAATAAAATATTTATTT
* *
1733402 AAAATAATATATATAATTTAT
1 AAAATAAAATAT-TTA-TT-T
1733423 AAAAGTAAAATATTTATTT
1 AAAA-TAAAATATTTATTT
1733442 A
1 A
1733443 TTAAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 11 0.33
19 4 0.12
20 4 0.12
21 7 0.21
22 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATAAAATATTTATTT
Found at i:1733451 original size:44 final size:40
Alignment explanation
Indices: 1733320--1733442 Score: 142
Period size: 40 Copynumber: 3.0 Consensus size: 40
1733310 TTAATATTAA
* * * *
1733320 AAAATAA-ATAAAT-ATTAATAAAACATAAATATATATATAT
1 AAAATAATATATATAATTTATAAAA-ATAAA-ATATTTATTT
*
1733360 ATATATATATATATATAATTTATAAAAATAAAATATTTATTT
1 A-AAATA-ATATATATAATTTATAAAAATAAAATATTTATTT
*
1733402 AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAATAATATATATAATTTATAAAAATAAAATATTTATTT
1733442 A
1 A
1733443 TTAAAAATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
40 35 0.49
41 8 0.11
42 10 0.14
43 10 0.14
44 9 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (40 bp):
AAAATAATATATATAATTTATAAAAATAAAATATTTATTT
Found at i:1734947 original size:3 final size:3
Alignment explanation
Indices: 1734939--1735019 Score: 74
Period size: 3 Copynumber: 27.0 Consensus size: 3
1734929 CTGTAATATG
* * * * *
1734939 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1734984 TAA TAA TAA TTA TAA CAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1735020 AACGAGCAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1734979 original size:30 final size:30
Alignment explanation
Indices: 1734939--1735019 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1734929 CTGTAATATG
*
1734939 TAATAATAATATTTATTAATAA-AAATATAA
1 TAATAATAATAATTA-TAATAATAAATATAA
* *
1734969 TAATAGTAATAATTATAATAATAATTATAA
1 TAATAATAATAATTATAATAATAAATATAA
* * *
1734999 CAATTATAATAATAATAATAA
1 TAATAATAATAATTATAATAA
1735020 AACGAGCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 6 0.14
30 37 0.86
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
TAATAATAATAATTATAATAATAAATATAA
Found at i:1735603 original size:118 final size:117
Alignment explanation
Indices: 1735388--1735704 Score: 332
Period size: 118 Copynumber: 2.6 Consensus size: 117
1735378 GAATTAATGC
* *
1735388 AAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAA------CTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * *
1735453 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCAAGCAA
60 GAACTTTC-TCTAGAAATAGCTCTGCTGATCTATCTCCTTCT-GAAATAGAGTCAAGCAA
1735512 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
* * * ** *
1735577 TCTCTAGAAA-AGTTGGTGTTGATCTATCTCCTTCTGTCATAGAGTCATGCAA
66 TCTCTAGAAATAGCT-CTGCTGATCTATCTCCTTCTGAAATAGAGTCAAGCAA
* * *
1735629 AAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCATGTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC--C-TC---TTCAGATAAGTTCTTCTCATTAT
1735694 GAACTTTCTCT
60 GAACTTTCTCT
1735705 GGCAACGCTG
Statistics
Matches: 168, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
117 47 0.28
118 54 0.32
119 4 0.02
120 2 0.01
123 33 0.20
124 28 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (117 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
TCTCTAGAAATAGCTCTGCTGATCTATCTCCTTCTGAAATAGAGTCAAGCAA
Found at i:1735717 original size:117 final size:117
Alignment explanation
Indices: 1735388--1735810 Score: 341
Period size: 112 Copynumber: 3.6 Consensus size: 117
1735378 GAATTAATGC
* * *
1735388 AAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CT-TTCAGATAAGTTCTTCTCATTAT
* * * * *
1735453 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCAAGCAA
64 GAACTTTC-TCTGG-AA-AG--C-GCTGATCTATCTCCTTCTGGAAATAGAGTCAAGCAA
1735512 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC--C-TC-TTCAGATAAGTTCTTCTCATTATGA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCAGATAAGTTCTTCTCATTATGA
* * * ** *
1735573 ACTTTCTCTAGAAAAGTTGGTGTTGATCTATCTCCTTCT-GTCATAGAGTCATGCAA
66 ACTTTCTCT-GGAAA----GCGCTGATCTATCTCCTTCTGGAAATAGAGTCAAGCAA
* * *
1735629 AAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCATGTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-T-TTCAGATAAGTTCTTCTCATTAT
* * *** ** **
1735694 GAACTTTCTCTGGCAA-CGCTGATCCATCGGGTGAT-G-AAT----TTGAGCAA
64 GAACTTTCTCTGGAAAGCGCTGATCTATCTCCTTCTGGAAATAGAGTCAAGCAA
* * *
1735741 AAGGTTGAACAAGTTCCTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CT-TTCAGATAAGTTCTTCTCATTAT
1735806 GAACT
64 GAACT
1735811 CTTTAGGAAA
Statistics
Matches: 248, Mismatches: 38, Indels: 38
0.77 0.12 0.12
Matches are distributed among these distances:
112 66 0.27
113 1 0.00
116 2 0.01
117 57 0.23
118 44 0.18
119 5 0.02
120 3 0.01
121 2 0.01
122 4 0.02
123 33 0.13
124 31 0.12
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (117 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCAGATAAGTTCTTCTCATTATGA
ACTTTCTCTGGAAAGCGCTGATCTATCTCCTTCTGGAAATAGAGTCAAGCAA
Found at i:1735999 original size:73 final size:72
Alignment explanation
Indices: 1735871--1736105 Score: 353
Period size: 73 Copynumber: 3.2 Consensus size: 72
1735861 GAGGTCTTAT
* *
1735871 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAACGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAA-GCTCCCGAAGGCTT
1735936 TTTGAAAA
65 TTTGAAAA
1735944 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCGAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATC-AAAAGCTCCCGAAGGCTT
*
1736009 TTTGAGAA
65 TTTGAAAA
* *
1736017 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTTAAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGA-GGCTTT---AAGATC-AAAAGCTCCCGAAG
1736082 GCTTTTTGAAAA
61 GCTTTTTGAAAA
*
1736094 CATCCTGCACTG
1 CATCATGCACTG
1736106 CAGGGCGTAC
Statistics
Matches: 149, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
73 99 0.66
74 9 0.06
77 41 0.28
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (72 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAGCTCCCGAAGGCTTT
TTGAAAA
Found at i:1736812 original size:22 final size:22
Alignment explanation
Indices: 1736784--1736834 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1736774 GATAAAGCTT
1736784 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTCGAAAAGAGAATCTA
* **
1736806 TCATCTTTGACGAGAGAATCTA
1 TCATCTTCGAAAAGAGAATCTA
1736828 TCATCTT
1 TCATCTT
1736835 TGAAGAGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTCGAAAAGAGAATCTA
Found at i:1736835 original size:22 final size:22
Alignment explanation
Indices: 1736796--1736837 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1736786 ATCTTCGAAA
1736796 AGAGAATCTATCATCTTTGACG
1 AGAGAATCTATCATCTTTGACG
1736818 AGAGAATCTATCATCTTTGA
1 AGAGAATCTATCATCTTTGA
1736838 AGAGTGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (22 bp):
AGAGAATCTATCATCTTTGACG
Found at i:1740283 original size:32 final size:32
Alignment explanation
Indices: 1740242--1740303 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1740232 GAAGAAATGA
*
1740242 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
1740274 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
1740304 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:1740840 original size:9 final size:8
Alignment explanation
Indices: 1740800--1740838 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
1740790 CTTGGTTCAA
1740800 TTTTTTCC
1 TTTTTTCC
1740808 TTTTTTCC
1 TTTTTTCC
*
1740816 TTTTTCCC
1 TTTTTTCC
1740824 TTTTTTTCC
1 -TTTTTTCC
1740833 TTTTTT
1 TTTTTT
1740839 TCAAGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1743558 original size:12 final size:13
Alignment explanation
Indices: 1743534--1743562 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1743524 AAAATGAAAA
1743534 AAATGCAAAATGT
1 AAATGCAAAATGT
1743547 AAATGC-AAATGT
1 AAATGCAAAATGT
1743559 AAAT
1 AAAT
1743563 ACGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:1745786 original size:20 final size:18
Alignment explanation
Indices: 1745749--1745791 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1745739 CTCATTTCTT
*
1745749 AATATTAAAAAATAAATA
1 AATATTAAAAAACAAATA
1745767 AATATTAATAAAACATAATA
1 AATATTAA-AAAACA-AATA
*
1745787 TATAT
1 AATAT
1745792 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTAAAAAACAAATA
Found at i:1745836 original size:19 final size:19
Alignment explanation
Indices: 1745812--1745873 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
1745802 ATATAATTTA
1745812 TAAAAATAAAATATTTATT
1 TAAAAATAAAATATTTATT
* *
1745831 TAAAAATAATATATATAATT
1 TAAAAATAAAATAT-TTATT
1745851 TATAAAAGTAAAATATTTATT
1 TA-AAAA-TAAAATATTTATT
1745872 TA
1 TA
1745874 TTAAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.36
20 6 0.17
21 10 0.28
22 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAATAAAATATTTATT
Found at i:1745878 original size:22 final size:20
Alignment explanation
Indices: 1745807--1745879 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
1745797 TATATATATA
1745807 ATTTATAAAAATAAAATATTT
1 ATTTAT-AAAATAAAATATTT
* *
1745828 ATTTA-AAAATAATATATATA
1 ATTTATAAAATAAAATAT-TT
1745848 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAA-TAAAATATTT
1745869 ATTTATTAAAA
1 ATTTA-TAAAA
1745880 ATATCAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.25
20 6 0.14
21 15 0.34
22 12 0.27
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATAAAATATTT
Found at i:1747812 original size:3 final size:3
Alignment explanation
Indices: 1747804--1747893 Score: 74
Period size: 3 Copynumber: 30.0 Consensus size: 3
1747794 CAGTAATATG
* * * * *
1747804 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1747849 TAA TAA TAA TTA TAA CAA TTA TAA TAA TAA AAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1747894 AACGGGCAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
2 2 0.03
3 63 0.94
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1747844 original size:30 final size:30
Alignment explanation
Indices: 1747804--1747893 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
1747794 CAGTAATATG
*
1747804 TAATAATAATATTTATTAATAA-AAATATAA
1 TAATAATAATAATTA-TAATAATAAATATAA
* *
1747834 TAATAGTAATAATTATAATAATAATTATAA
1 TAATAATAATAATTATAATAATAAATATAA
* * * * *
1747864 CAATTATAATAATAAAAATAATAAAAATAA
1 TAATAATAATAATTATAATAATAAATATAA
1747894 AACGGGCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
29 6 0.12
30 43 0.88
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
TAATAATAATAATTATAATAATAAATATAA
Found at i:1752833 original size:42 final size:42
Alignment explanation
Indices: 1752774--1752857 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1752764 CGTAAACTCT
*
1752774 CTCTTAGGCGGTATTTGTTTTTGCAGAGGTAAAAGGTCTGCA
1 CTCTTAGGCGGTATTTGTTTTTGCAGAAGTAAAAGGTCTGCA
* *
1752816 CTCTTAGGTGGTGTTTGTTTTTGCAGAAGTAAAAGGTCTGCA
1 CTCTTAGGCGGTATTTGTTTTTGCAGAAGTAAAAGGTCTGCA
1752858 GTCTGCAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (42 bp):
CTCTTAGGCGGTATTTGTTTTTGCAGAAGTAAAAGGTCTGCA
Found at i:1753186 original size:31 final size:31
Alignment explanation
Indices: 1753150--1753208 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1753140 AACTTAAAAG
* *
1753150 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1753181 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1753209 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1753807 original size:13 final size:13
Alignment explanation
Indices: 1753789--1753813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1753779 TATAATTATA
1753789 AAAATATTTTTAG
1 AAAATATTTTTAG
1753802 AAAATATTTTTA
1 AAAATATTTTTA
1753814 AATTTATCAA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAAATATTTTTAG
Found at i:1754085 original size:20 final size:19
Alignment explanation
Indices: 1754037--1754085 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1754027 AACTTAAATC
*
1754037 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
1754057 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
1754075 AAAATAATTTA
1 AAAATAATTTA
1754086 TATGATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:1754131 original size:14 final size:14
Alignment explanation
Indices: 1754114--1754162 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1754104 ATATATAATA
1754114 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
1754128 TAATATT---TAAT
1 TAATATTAAAAAAT
*
1754139 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
1754152 TAATATTAAAA
1 TAATATTAAAA
1754163 TTAATATCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:1754133 original size:26 final size:24
Alignment explanation
Indices: 1754104--1754167 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
1754094 AAAATTAAAT
1754104 ATATATAATATAATATTAAAAAATTA
1 ATATATAAT-TAAT-TTAAAAAATTA
* *
1754130 ATATTTAATTTATTTAAAAAATTA
1 ATATATAATTAATTTAAAAAATTA
*
1754154 ATATTAAAATTAAT
1 ATA-TATAATTAAT
1754168 ATCTCTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.44
25 10 0.31
26 8 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATAATTAATTTAAAAAATTA
Found at i:1755483 original size:21 final size:21
Alignment explanation
Indices: 1755451--1755540 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 21
1755441 AAGACATTTC
*
1755451 GATGAAAGGACTTAACCTTTT
1 GATGAAAAGACTTAACCTTTT
* **
1755472 GATTAAAAGACTTCTCCTTTT
1 GATGAAAAGACTTAACCTTTT
* * * *
1755493 TATGAAAGGGCTTAACCTTGT
1 GATGAAAAGACTTAACCTTTT
* * * *
1755514 CATGAAAGGATTTAATCTTTT
1 GATGAAAAGACTTAACCTTTT
*
1755535 CATGAA
1 GATGAA
1755541 GAAAATTGTT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (21 bp):
GATGAAAAGACTTAACCTTTT
Found at i:1758397 original size:3 final size:3
Alignment explanation
Indices: 1758389--1758461 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
1758379 ATCTGAGATG
1758389 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1758437 ATA ATA ACA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1758462 ATATTATTAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1758846 original size:26 final size:24
Alignment explanation
Indices: 1758807--1758856 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1758797 TTGTCAATTG
1758807 TGTGTTGTAACTTATGTAACTTATGT
1 TGTGTTGTAACTTA--TAACTTATGT
**
1758833 TGTGTTGTGTCTTATAACTTATGT
1 TGTGTTGTAACTTATAACTTATGT
1758857 CTAATTGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (24 bp):
TGTGTTGTAACTTATAACTTATGT
Found at i:1758987 original size:21 final size:21
Alignment explanation
Indices: 1758961--1759007 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1758951 ACATCTTGTG
* *
1758961 ATGAAAGGGCTTAACCTTTTC
1 ATGAAAAGACTTAACCTTTTC
* *
1758982 ATGAAAAGATTTAATCTTTTC
1 ATGAAAAGACTTAACCTTTTC
1759003 ATGAA
1 ATGAA
1759008 GAGAATTGTT
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:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
ATGAAAAGACTTAACCTTTTC
Found at i:1759933 original size:22 final size:22
Alignment explanation
Indices: 1759890--1759934 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1759880 AGGAAATATT
* *
1759890 AAATTTTAAAAATATTATATAA
1 AAATTTTAAAAATATAAAATAA
1759912 AAATGTTTAAAAA-ATAAAATAA
1 AAAT-TTTAAAAATATAAAATAA
1759934 A
1 A
1759935 TGAAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATTTTAAAAATATAAAATAA
Found at i:1760064 original size:14 final size:13
Alignment explanation
Indices: 1760047--1760076 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1760037 AAGAAGTGGG
1760047 AAAATAAAAATAAA
1 AAAAT-AAAATAAA
1760061 AAAATAAAATAAA
1 AAAATAAAATAAA
1760074 AAA
1 AAA
1760077 GTGTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:1760092 original size:5 final size:5
Alignment explanation
Indices: 1759996--1760074 Score: 54
Period size: 5 Copynumber: 14.8 Consensus size: 5
1759986 GTTAAAAGAG
* * *
1759996 AAAAT AAAAAT AAAAC AAAAC AAAAT AAAAT AAAAT AAAAA AAGAAGT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AA-T
1760044 GGGAAAAT AAAA- ATAAA- AAAAT AAAAT AAAA
1 ---AAAAT AAAAT A-AAAT AAAAT AAAAT AAAA
1760075 AAGTGTTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.06
5 46 0.74
6 7 0.11
8 1 0.02
9 2 0.03
10 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:1760162 original size:18 final size:18
Alignment explanation
Indices: 1760141--1760180 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1760131 GTTGTTATTA
*
1760141 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1760159 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1760177 AAAT
1 AAAT
1760181 GAATAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1761701 original size:123 final size:123
Alignment explanation
Indices: 1761481--1761752 Score: 368
Period size: 123 Copynumber: 2.2 Consensus size: 123
1761471 TTTGGGTACG
* *
1761481 ATATCCTTCGTTGTGAAGTCGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCGTTGTGAAGTTGAAATCGTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTG
* * * * * *
1761546 GATATCCTTCATTGTGAAGTTGAAATCCAATCTTGTAAATTGAATT-TCTTTGAGATTA
66 GATATCCTTCATTATGAAGTTGAAATCAAATCTAGAAAATTGAATTGGC-TCGAGATTA
* * *
1761604 ATATCTTTCATTGTGAAGTTGAAATTGT-GGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATT
1 ATATCCTTCGTTGTGAAGTTGAAATCGTAGG-TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATT
* * * *
1761668 GGATGTCCTTCGTTATGAAGTTGAAATCAAATCTAGAAAATTGCATTGGCTCGAGTTTA
65 GGATATCCTTCATTATGAAGTTGAAATCAAATCTAGAAAATTGAATTGGCTCGAGATTA
*
1761727 ATATCCTTCGTTATGAAGTTGAAATC
1 ATATCCTTCGTTGTGAAGTTGAAATC
1761753 CAATCTAGAA
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
122 2 0.02
123 125 0.98
124 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (123 bp):
ATATCCTTCGTTGTGAAGTTGAAATCGTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTG
GATATCCTTCATTATGAAGTTGAAATCAAATCTAGAAAATTGAATTGGCTCGAGATTA
Found at i:1761761 original size:57 final size:56
Alignment explanation
Indices: 1761673--1761804 Score: 228
Period size: 57 Copynumber: 2.3 Consensus size: 56
1761663 GAATTGGATG
1761673 TCCTTCGTTATGAAGTTGAAATCAAATCTAGAAAATTGCATTGGCTCGAGTTTAATA
1 TCCTTCGTTATGAAGTTGAAATCAAATCTAGAAAATTGCATTGGCTCGAGTTTAA-A
* *
1761730 TCCTTCGTTATGAAGTTGAAATCCAATCTAGAAAATTGCATTGGCTGGAGTTTAAA
1 TCCTTCGTTATGAAGTTGAAATCAAATCTAGAAAATTGCATTGGCTCGAGTTTAAA
*
1761786 TCCTTCGTTGTGAAGTTGA
1 TCCTTCGTTATGAAGTTGA
1761805 CATTGACTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
56 19 0.26
57 53 0.74
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (56 bp):
TCCTTCGTTATGAAGTTGAAATCAAATCTAGAAAATTGCATTGGCTCGAGTTTAAA
Found at i:1763029 original size:85 final size:80
Alignment explanation
Indices: 1762900--1763058 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 80
1762890 GATTTTTTTC
*
1762900 TTTTCTTTTTTCATGGAACAAGAGTGATACGAGATCTCAAGTCTCGATAAGGGTGTGGAAAGAGA
1 TTTTCTTTTTTCATGGAACAAGAGTGATACAAGATCTCAAGTCTCGATAAGGGTGT-G---GAGA
1762965 GGAAAAATAAAAAGAATTA
62 GGAAAAATAAAAAGAATTA
** * *
1762984 TTTTCTTTTTTTTGTGGAACAAGAGTGATACAAGATCTCATGTCTCGGTAAGGGTGTGGAGAGGA
1 TTTTC-TTTTTTCATGGAACAAGAGTGATACAAGATCTCAAGTCTCGATAAGGGTGTGGAGAGGA
1763049 AAAATAAAAA
65 AAAATAAAAA
1763059 AAAGGTTTCG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 17 0.25
84 6 0.09
85 46 0.67
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (80 bp):
TTTTCTTTTTTCATGGAACAAGAGTGATACAAGATCTCAAGTCTCGATAAGGGTGTGGAGAGGAA
AAATAAAAAGAATTA
Found at i:1767607 original size:26 final size:26
Alignment explanation
Indices: 1767578--1767634 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1767568 CCTTACAAAT
1767578 GTAAATAAAGAAATTAAAGTGCTTAA
1 GTAAATAAAGAAATTAAAGTGCTTAA
1767604 GTAAATAAAGAAATTAAAGTGCTTAA
1 GTAAATAAAGAAATTAAAGTGCTTAA
1767630 GTAAA
1 GTAAA
1767635 AAAAAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (26 bp):
GTAAATAAAGAAATTAAAGTGCTTAA
Found at i:1769368 original size:59 final size:59
Alignment explanation
Indices: 1769276--1769399 Score: 248
Period size: 59 Copynumber: 2.1 Consensus size: 59
1769266 TTGGTACCAA
1769276 TTTTCATCTATTTGGTCCATCAGTGAAATTTTGAGTTCCAAGTTCTTCTCATTATGAAC
1 TTTTCATCTATTTGGTCCATCAGTGAAATTTTGAGTTCCAAGTTCTTCTCATTATGAAC
1769335 TTTTCATCTATTTGGTCCATCAGTGAAATTTTGAGTTCCAAGTTCTTCTCATTATGAAC
1 TTTTCATCTATTTGGTCCATCAGTGAAATTTTGAGTTCCAAGTTCTTCTCATTATGAAC
1769394 TTTTCA
1 TTTTCA
1769400 CTCTTCTGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (59 bp):
TTTTCATCTATTTGGTCCATCAGTGAAATTTTGAGTTCCAAGTTCTTCTCATTATGAAC
Found at i:1769744 original size:139 final size:138
Alignment explanation
Indices: 1769467--1770255 Score: 653
Period size: 139 Copynumber: 5.7 Consensus size: 138
1769457 ACTCCTTCTC
* * * *
1769467 TGATAGAATCGAGCAACAGGTTGAAATAAGTTCTTCTCATTATGAACTTATTCTCTCTCT-TCAG
1 TGAT-GAATCGAGCTATAGGTTG-AACAAGTTCTTCTCATTATGAACTTCTTCTC-C-CTATCAG
* * *
1769531 -TCGAGTTCTTCTCATTATGAAC-CATCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTG
62 AT-GAGTTCTTCTCATTATGAACTC-TCCACTGGAAAGGTTGATCCCTCAAGTGAGGTGTT-CTG
* *
1769594 ACTCAAATCCATATG
124 ATTCAACTCCATATG
* * * * *
1769609 TGATGAATCGAGCTA-AGATTAAACAAGTTCTTCTCATTATGAACTTTTTCTCCCATATCGGACG
1 TGATGAATCGAGCTATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC-TATCAGATG
* *
1769673 AGTTCTTCTCATTATGAACTCTCAACTGGAAAGGATGATCCCTCAAGTGAGGTGTTACTGATTCA
65 AGTTCTTCTCATTATGAACTCTCCACTGGAAAGGTTGATCCCTCAAGTGAGGTGTT-CTGATTCA
1769738 ACTCCATATG
129 ACTCCATATG
* * * * * *
1769748 CGATGAACCAAGTTA-AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATA
1 TGATGAATCGAGCTATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-ATCAGATG
* * * *
1769812 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCACTGATTCG
65 AGTTCTTCTCATTATGAACTCTCCACTGGAAAGGTTGATCCCTCAAGTGAGGTGT-TCTGATTCA
1769877 A----A-ATG
129 ACTCCATATG
* * * * * *
1769882 CCG-TGAATCGAG-TGATAGGTCGAATAAGTTCTTCTTATTATGAACTTTTTCTCCCTTTTTTCA
1 -TGATGAATCGAGCT-ATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC---TATCA
* * * * * * * * ** *
1769945 GATGAGTTATTCTAATTATGAACTATCTATTTG-AAGAGTTAATCCCTTAAGCAAGGCG-TC-G-
61 GATGAGTTCTTCTCATTATGAACTCTCCACTGGAAAG-GTTGATCCCTCAAGTGAGGTGTTCTGA
* * * *
1770006 CT-AATTCGAAATG
125 TTCAACTCCATATG
* * * * * * *
1770019 TCATAAATCGAGCGATAGGTTGAACGAGCTCTTCTTATTATGAACTTCTTCTCCCTTTGTCAGAT
1 TGATGAATCGAGCTATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC--TATCAGAT
* * ** * * *
1770084 GAGTTTTTCTCATTATGAACTCTCCGCTGGAAATATTGATCCCTCGAATTAAGTGTGGT-TGATT
64 GAGTTCTTCTCATTATGAACTCTCCACTGGAAAGGTTGATCCCTC-AAGTGAG-GTGTTCTGATT
1770148 CAACTCCATATG
127 CAACTCCATATG
* * *
1770160 TGATGAATCGAGCTA-AAGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATG
1 TGATGAATCGAGCTATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-ATCAGATG
* *
1770224 AGTTATTGTCATTATGAACTCTCCACTGGAAA
65 AGTTCTTCTCATTATGAACTCTCCACTGGAAA
1770256 TATTGATTTG
Statistics
Matches: 523, Mismatches: 96, Indels: 59
0.77 0.14 0.09
Matches are distributed among these distances:
132 1 0.00
133 2 0.00
134 12 0.02
135 39 0.07
136 43 0.08
137 98 0.19
138 7 0.01
139 247 0.47
140 40 0.08
141 30 0.06
142 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (138 bp):
TGATGAATCGAGCTATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTATCAGATGA
GTTCTTCTCATTATGAACTCTCCACTGGAAAGGTTGATCCCTCAAGTGAGGTGTTCTGATTCAAC
TCCATATG
Found at i:1771670 original size:144 final size:144
Alignment explanation
Indices: 1771368--1771711 Score: 494
Period size: 144 Copynumber: 2.4 Consensus size: 144
1771358 AAGACTTACT
* * *
1771368 GATGGCCTGAAGGACTTATGCTGATTTGAAGTGTTGTGAATCGAGCAATAGGAAATGTTAACCCC
1 GATGGCCTGAAGGACTTAAGCTGATTCGAAGTG-TGTGAATCGAGCAATATGAAATGTTAACCCC
** * *
1771433 TCTGGTGGGGCATTAGTGATTCGAAGTGTTGTGAATCGAGCAAAAGAATTGTTGAAAACATCCTG
65 TCTGGTGGGGCATTAGTGATTCGAAGTGTTGTGAATAAAGCAAAAGAAATGTTGAAAACATCCTA
1771498 CCCGAAGGTCTTATG
130 CCCGAAGGTCTTATG
* * *
1771513 GATAG-CTCGAAGGACTTAAGTTTATTCGAAGTGTGTGAATCGAGCAATATGAAATGTTAACCCC
1 GATGGCCT-GAAGGACTTAAGCTGATTCGAAGTGTGTGAATCGAGCAATATGAAATGTTAACCCC
* * * *
1771577 TCTGGTGGGGCGTT-GCTGATTCTAAGTGTTGTGAATAAAGTAAAGGAAATGTTGAAAACATCCT
65 TCTGGTGGGGCATTAG-TGATTCGAAGTGTTGTGAATAAAGCAAAAGAAATGTTGAAAACATCCT
*
1771641 ACCTGAAGGTCTTATG
129 ACCCGAAGGTCTTATG
* *
1771657 GATGGCCTAAAGGACTTAAGCTGCTTCGAAGTGTGTGAATCGAGCAATATGAAAT
1 GATGGCCTGAAGGACTTAAGCTGATTCGAAGTGTGTGAATCGAGCAATATGAAAT
1771712 ATTGAAAACT
Statistics
Matches: 176, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
143 1 0.01
144 148 0.84
145 27 0.15
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (144 bp):
GATGGCCTGAAGGACTTAAGCTGATTCGAAGTGTGTGAATCGAGCAATATGAAATGTTAACCCCT
CTGGTGGGGCATTAGTGATTCGAAGTGTTGTGAATAAAGCAAAAGAAATGTTGAAAACATCCTAC
CCGAAGGTCTTATG
Found at i:1771769 original size:84 final size:83
Alignment explanation
Indices: 1771591--1771842 Score: 306
Period size: 84 Copynumber: 3.0 Consensus size: 83
1771581 GTGGGGCGTT
* ** * * * **
1771591 GCTGATTCTAAGTGTTGTGAATAAAGTAAAGGAAATGTTGAAAACATCCTACCTGAAGGTCTTAT
1 GCTGATTCGAAGTG-TGTGAATCGAGCAAAGGAAATATTGAAAACATCCGACCCAAAGGTCTTAT
**
1771656 GGATGGCCTAAAGGACTTAA
65 GG-TGGCCCGAAGGACTTAA
* * * * *
1771676 GCTGCTTCGAAGTGTGTGAATCGAGCAATATGAAATATTGAAAACTTCTGACCCTAAGGTCTTAT
1 GCTGATTCGAAGTGTGTGAATCGAGCAA-AGGAAATATTGAAAACATCCGACCCAAAGGTCTTAT
1771741 GGTGGCCCGAAGGACTTAA
65 GGTGGCCCGAAGGACTTAA
* *
1771760 GCTGATTCGAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACATCCGGCCCAAAGGTCTTATA
1 GCTGATTCGAAGTGTGTGAATCGAGCAAAGGAAATATTGAAAACATCCGACCCAAAGGTCTTAT-
*
1771825 GATGGCCCGAAGGACTTA
65 GGTGGCCCGAAGGACTTA
1771843 TCATATTGCT
Statistics
Matches: 143, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
83 30 0.21
84 70 0.49
85 43 0.30
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (83 bp):
GCTGATTCGAAGTGTGTGAATCGAGCAAAGGAAATATTGAAAACATCCGACCCAAAGGTCTTATG
GTGGCCCGAAGGACTTAA
Found at i:1771876 original size:41 final size:42
Alignment explanation
Indices: 1771819--1771905 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
1771809 GCCCAAAGGT
* * *
1771819 CTTATAGATGGCCCGAAGGACTT-ATCAT-ATTGCTCGAAAGA
1 CTTATAAATGACCCGAAGGACTTAATCATCA-TACTCGAAAGA
*
1771860 CTTATAAATGACCCGAAGGATTTAATCATCATACTCGAAAGA
1 CTTATAAATGACCCGAAGGACTTAATCATCATACTCGAAAGA
1771902 CTTA
1 CTTA
1771906 CTGATGGCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 20 0.50
42 19 0.47
43 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (42 bp):
CTTATAAATGACCCGAAGGACTTAATCATCATACTCGAAAGA
Found at i:1771917 original size:42 final size:41
Alignment explanation
Indices: 1771819--1771925 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
1771809 GCCCAAAGGT
*
1771819 CTTATAGATGGCCCGAAGGACTTATCATATTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATATTACTCGAAAGA
* * *
1771860 CTTATAAATGACCCGAAGGATTTAATCATCA-TACTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCAT-ATTACTCGAAAGA
*
1771902 CTTACT-GATGGCCCGAAAGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
1771926 CTTATCAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
41 21 0.38
42 32 0.58
43 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATATTACTCGAAAGA
Found at i:1772212 original size:53 final size:52
Alignment explanation
Indices: 1772026--1772212 Score: 205
Period size: 52 Copynumber: 3.6 Consensus size: 52
1772016 TGAAAATCAT
* * * ** *
1772026 CATCAAGAAACCCTTGAAAATCAAGCTTAGTTTC-CAAAAACTCATTTGAAAA
1 CATCAAGAAACCCCT-AAAATCAGGCTTAGATTCTTTAAAATTCATTTGAAAA
* * * *
1772078 CATCAAGAAATCCCTAATAATTATGCTTAAATTCTTTAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAA-AATCAGGCTTAGATTCTTTAAAATTCATTTGAAAA
* * * *
1772131 CATTAAGAAACCCCTAAAATTAGGCTTAGCTTCTTTTAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAATCAGGCTTAGATTCTTTAAAATTCATTTGAAAA
*
1772183 CATCGAGAAACCCCTGAAAATCAGGCTTAG
1 CATCAAGAAACCCCT-AAAATCAGGCTTAG
1772213 TTTATAAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 2 0.02
52 69 0.61
53 43 0.38
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (52 bp):
CATCAAGAAACCCCTAAAATCAGGCTTAGATTCTTTAAAATTCATTTGAAAA
Found at i:1772282 original size:40 final size:38
Alignment explanation
Indices: 1772237--1772371 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 38
1772227 TTTTCGAGTG
1772237 AAACAATCTCAAGCGAGATAAAATCTTCTGGTTTTAAGAA
1 AAACAATCTCAAGCGAGATAAAAT-TTCTGGTTTTAAG-A
* * * *
1772277 AAACAATCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGA
1 AAACAATCTCAAGCGAGATAAAATTTCTGGTTTTAA--GA
** *
1772317 AAACTGTCTCAAGCGAGAT-GAA-TT-TGGTTTTAAGA
1 AAACAATCTCAAGCGAGATAAAATTTCTGGTTTTAAGA
* *
1772352 AAACCATCTCAAGTGAGATA
1 AAACAATCTCAAGCGAGATA
1772372 CATTTTTTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
35 18 0.23
37 7 0.09
38 2 0.03
39 12 0.15
40 38 0.49
41 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (38 bp):
AAACAATCTCAAGCGAGATAAAATTTCTGGTTTTAAGA
Found at i:1772367 original size:75 final size:72
Alignment explanation
Indices: 1772265--1772406 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 72
1772255 TAAAATCTTC
*
1772265 TGGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTGTCTCAAG
1 TGGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATTT-TT-TTTCAAGGG-AAACTGTCTCAAG
*
1772330 CGAGATGAATT
62 AGAGATGAATT
* * *
1772341 TGGTTTTAAG-AAAACCATCTCAAGTGAGATACATTTTTTTTCAAGGGAAACTGTCTCCAGAGAG
1 TGGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTTTTCAAGGGAAACTGTCTCAAGAGAG
1772405 AT
66 AT
1772407 AAAATTTGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 17 0.28
72 9 0.15
73 2 0.03
74 5 0.08
75 18 0.30
76 10 0.16
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (72 bp):
TGGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTTTTCAAGGGAAACTGTCTCAAGAGAG
ATGAATT
Found at i:1772419 original size:36 final size:36
Alignment explanation
Indices: 1772304--1772427 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
1772294 ATAAAATTTC
* *
1772304 TTGTTTCAAGGGAAAACTGTCTCAAGCGAGAT-GAAT
1 TTGTTTCAAGGG-AAACTGTCTCAAGAGAGATAAAAT
* * ** * * *
1772340 TTGGTTTTAA-GAAAACCATCTCAAGTGAGATACATT
1 TT-GTTTCAAGGGAAACTGTCTCAAGAGAGATAAAAT
* *
1772376 TTTTTTCAAGGGAAACTGTCTCCAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAAT
1772412 TTGTTTCAAGGGAAAC
1 TTGTTTCAAGGGAAAC
1772428 GATGTCAAAG
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
35 21 0.31
36 41 0.60
37 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAAT
Found at i:1772756 original size:37 final size:37
Alignment explanation
Indices: 1772711--1772913 Score: 184
Period size: 37 Copynumber: 5.8 Consensus size: 37
1772701 AAAGAAAGTA
* *
1772711 TCTCAAGTGAGACGAAATTTGTTTTGAGAGAAAAATG
1 TCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAATG
*
1772748 TCTCAAGTGAGATAAAATTTGTTTTTAAGA-AAAAA--
1 TCTCAAGTGAGATGAAATTTG-TTTTAAGAGAAAAATG
* *
1772783 ---CAACT---TTGAAATTTGTGTTCTGAAG-G-AAAATG
1 TCTCAAGTGAGATGAAATTTGT-TT-T-AAGAGAAAAATG
*
1772815 TCTCAAGTGAGATG-AGTTT-TTTTAAGAGAAAAATG
1 TCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAATG
*
1772850 TCTCAAGTGAGAAGAAATTTGTTTTAAGAGAAAAATG
1 TCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAATG
* *
1772887 TATCAAGTGAGAT--AATTTTTTTTAAGA
1 TCTCAAGTGAGATGAAATTTGTTTTAAGA
1772914 AAACAATATC
Statistics
Matches: 135, Mismatches: 14, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
28 1 0.01
29 10 0.07
30 5 0.04
31 3 0.02
32 4 0.03
33 3 0.02
34 2 0.01
35 38 0.28
36 5 0.04
37 55 0.41
38 9 0.07
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (37 bp):
TCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAATG
Found at i:1772849 original size:102 final size:101
Alignment explanation
Indices: 1772606--1772884 Score: 330
Period size: 102 Copynumber: 2.7 Consensus size: 101
1772596 ATTTTGGGAG
* * * *
1772606 AATGTCTCAAGCGAGACGATGTTTATTTTGAGAG-AAATTGTCTCAAGCGAGACAAAATTTGGTT
1 AATGTCTCAAGTGAGACGA-GTTTATTTTGAGAGAAAAATGTCTCAAGTGAGA-AAAATTTGTTT
* * *
1772670 CAAG-TAAAATAACTTTGAAATTTGTGCTCCGAAAGAA
64 TAAGAAAAAACAACTTTGAAATTTGTGCTCCGAAAGAA
* * * *
1772707 AGTATCTCAAGTGAGACGAAATTTGTTTTGAGAGAAAAATGTCTCAAGTGAGATAAAATTTGTTT
1 AATGTCTCAAGTGAGACG-AGTTTATTTTGAGAGAAAAATGTCTCAAGTGAGA-AAAATTTG-TT
* * *
1772772 TTAAGAAAAAACAACTTTGAAATTTGTGTTCTGAAGGAA
63 TTAAGAAAAAACAACTTTGAAATTTGTGCTCCGAAAGAA
* *
1772811 AATGTCTCAAGTGAGATGAGTTT-TTTTAAGAGAAAAATGTCTCAAGTGAGAAGAAATTTGTTTT
1 AATGTCTCAAGTGAGACGAGTTTATTTTGAGAGAAAAATGTCTCAAGTGAGAA-AAATTTGTTTT
1772875 AAGAGAAAAA
65 AAGA-AAAAA
1772885 TGTATCAAGT
Statistics
Matches: 152, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
101 36 0.24
102 64 0.42
103 9 0.06
104 43 0.28
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (101 bp):
AATGTCTCAAGTGAGACGAGTTTATTTTGAGAGAAAAATGTCTCAAGTGAGAAAAATTTGTTTTA
AGAAAAAACAACTTTGAAATTTGTGCTCCGAAAGAA
Found at i:1772853 original size:35 final size:35
Alignment explanation
Indices: 1772809--1772955 Score: 154
Period size: 35 Copynumber: 4.1 Consensus size: 35
1772799 GTTCTGAAGG
*
1772809 AAAATGTCTCAAGTGAGATGAGTTTTTTTAAGAGA
1 AAAATGTCTCAAGTGAGATGAATTTTTTTAAGAGA
*
1772844 AAAATGTCTCAAGTGAGAAGAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAGATG-AATTT-TTTTAAGAGA
*
1772881 AAAATGTATCAAGTGAGAT-AATTTTTTTTAAGA-A
1 AAAATGTCTCAAGTGAGATGAA-TTTTTTTAAGAGA
* * * *
1772915 AACAATATCTCTAGCGAGACGACATTTTGTTTAGAGAGA
1 AA-AATGTCTCAAGTGAGATGA-ATTTT-TTTA-AGAGA
1772954 AA
1 AA
1772956 CAACACTCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
34 3 0.03
35 41 0.44
36 12 0.13
37 32 0.34
38 3 0.03
39 3 0.03
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (35 bp):
AAAATGTCTCAAGTGAGATGAATTTTTTTAAGAGA
Found at i:1772898 original size:18 final size:18
Alignment explanation
Indices: 1772840--1772898 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1772830 GTTTTTTTAA
*
1772840 GAGAAAAATGTCTCAAGT
1 GAGAAAAATGTATCAAGT
* *
1772858 GAGAAGAAATTTGTTTTAA--
1 GAGAA-AAA--TGTATCAAGT
1772877 GAGAAAAATGTATCAAGT
1 GAGAAAAATGTATCAAGT
1772895 GAGA
1 GAGA
1772899 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 6 0.19
18 12 0.38
19 8 0.25
21 6 0.19
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.25
Consensus pattern (18 bp):
GAGAAAAATGTATCAAGT
Found at i:1775317 original size:20 final size:20
Alignment explanation
Indices: 1775289--1775326 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1775279 CTATGTATAG
*
1775289 ATGCTAATGCAAAGATGCTC
1 ATGCAAATGCAAAGATGCTC
1775309 ATGCAAATGCAAAGATGC
1 ATGCAAATGCAAAGATGC
1775327 AAAAATGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
ATGCAAATGCAAAGATGCTC
Found at i:1775344 original size:22 final size:22
Alignment explanation
Indices: 1775314--1775374 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
1775304 TGCTCATGCA
1775314 AATGCAAAGATGCAAAAATGGG
1 AATGCAAAGATGCAAAAATGGG
*
1775336 AATGTAAAGATGCAAAAATGGG
1 AATGCAAAGATGCAAAAATGGG
*
1775358 AATGCAAAAATGCAAAA
1 AATGCAAAGATGCAAAA
1775375 TGTAAAATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (22 bp):
AATGCAAAGATGCAAAAATGGG
Found at i:1779383 original size:21 final size:21
Alignment explanation
Indices: 1779330--1779383 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
1779320 GTAAGTTTAA
*
1779330 AGATTTGC-AAATCAAAATCG
1 AGATTTGCAAAATAAAAATCG
1779350 ATGATTTAG-AAAATAAAAATTC-
1 A-GATTT-GCAAAATAAAAA-TCG
1779372 AGATTTGCAAAA
1 AGATTTGCAAAA
1779384 CTTACTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
20 2 0.07
21 14 0.50
22 10 0.36
23 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (21 bp):
AGATTTGCAAAATAAAAATCG
Found at i:1783158 original size:23 final size:20
Alignment explanation
Indices: 1783088--1783185 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 20
1783078 CCATAAACAA
*
1783088 GTATCGATACCCCCTTGCTAG-
1 GTATCGATA-CCCCTTGAT-GT
** * *
1783109 GTATCGATACTGCTTCAACGT
1 GTATCGATACCCCTT-GATGT
1783130 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-C-TTG-ATGT
*
1783153 GTATCGATACCCCTTGATGG
1 GTATCGATACCCCTTGATGT
*
1783173 GTACCGATACCCC
1 GTATCGATACCCC
1783186 CTGTCGGGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
20 20 0.33
21 22 0.36
22 2 0.03
23 17 0.28
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCCTTGATGT
Found at i:1783182 original size:20 final size:22
Alignment explanation
Indices: 1783134--1783185 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
1783124 CAACGTGTAT
* *
1783134 CGATACCCTCTTTGAATGTGTAT
1 CGATACCC-CTTTGAATGGGTAC
1783157 CGATACCCC-TTG-ATGGGTAC
1 CGATACCCCTTTGAATGGGTAC
1783177 CGATACCCC
1 CGATACCCC
1783186 CTGTCGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
21 3 0.11
22 1 0.04
23 8 0.30
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (22 bp):
CGATACCCCTTTGAATGGGTAC
Found at i:1783614 original size:17 final size:16
Alignment explanation
Indices: 1783581--1783630 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1783571 TCGAAATAGA
1783581 AAATTATTTTGTTTTT
1 AAATTATTTTGTTTTT
1783597 AAATTGATTTT-TTATTT
1 AAATT-ATTTTGTT-TTT
*
1783614 -AATTATGTTGTTTTT
1 AAATTATTTTGTTTTT
1783629 AA
1 AA
1783631 TGAAAACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (16 bp):
AAATTATTTTGTTTTT
Found at i:1785630 original size:28 final size:27
Alignment explanation
Indices: 1785599--1785652 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
1785589 TATTCGATCC
1785599 AATTAATCAAATATCACATATTACTCCA
1 AATTAATCAAATATCA-ATATTACTCCA
** * *
1785627 AATTTTTCAAATGTCAATTTTACTCC
1 AATTAATCAAATATCAATATTACTCC
1785653 TTACTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (27 bp):
AATTAATCAAATATCAATATTACTCCA
Found at i:1790356 original size:5 final size:5
Alignment explanation
Indices: 1790346--1790388 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
1790336 ACGTTAGATT
*
1790346 ATAAA ATAAA ATAAA TATCAA ATAAA ATTAAA ATTAAA ATAAA
1 ATAAA ATAAA ATAAA -ATAAA ATAAA A-TAAA A-TAAA ATAAA
1790389 TCAAAAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 19 0.56
6 15 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (5 bp):
ATAAA
Found at i:1790379 original size:11 final size:10
Alignment explanation
Indices: 1790346--1790388 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
1790336 ACGTTAGATT
1790346 ATAAAATAAA
1 ATAAAATAAA
*
1790356 ATAAATATCAA
1 ATAAA-ATAAA
1790367 ATAAAATTAAA
1 ATAAAA-TAAA
1790378 ATTAAAATAAA
1 A-TAAAATAAA
1790389 TCAAAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 6 0.21
11 17 0.61
12 5 0.18
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:1790389 original size:16 final size:17
Alignment explanation
Indices: 1790345--1790394 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
1790335 AACGTTAGAT
*
1790345 TATAAAATAAAAT-AAA
1 TATAAAATAAATTAAAA
*
1790361 TATCAAATAAAATTAAAA
1 TATAAAAT-AAATTAAAA
*
1790379 T-TAAAATAAATCAAAA
1 TATAAAATAAATTAAAA
1790395 GAATGAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.54
17 9 0.32
18 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (17 bp):
TATAAAATAAATTAAAA
Found at i:1791245 original size:12 final size:13
Alignment explanation
Indices: 1791228--1791256 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1791218 AAAACAAAGA
1791228 TAAAATAATAT-T
1 TAAAATAATATCT
1791240 TAAAATAATATCT
1 TAAAATAATATCT
1791253 TAAA
1 TAAA
1791257 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:1792238 original size:2 final size:2
Alignment explanation
Indices: 1792226--1792256 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1792216 AAATTATAAA
1792226 AT AT A- 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
1792257 TAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1792425 original size:30 final size:31
Alignment explanation
Indices: 1792385--1792449 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1792375 AAAAGTGAAG
1792385 AAATAATCATT-AATTTTATT-AATTATTATA
1 AAATAATCATTAAATTTTATTAAATTATTA-A
*
1792415 AAATCATCATTAAATTTTATTAAATTATTAA
1 AAATAATCATTAAATTTTATTAAATTATTAA
1792446 AAAT
1 AAAT
1792450 TATAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 10 0.31
31 14 0.44
32 8 0.25
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATAATCATTAAATTTTATTAAATTATTAA
Found at i:1805126 original size:22 final size:23
Alignment explanation
Indices: 1805078--1805127 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
1805068 CGTTTCTTTC
*
1805078 ATTT-TTCTTTTTGAGTGCTTGA
1 ATTTCTTCTTTTTGAGTGCTTCA
1805100 A-TTCTTC-TTTTGAGTGCTTCA
1 ATTTCTTCTTTTTGAGTGCTTCA
1805121 ATTTCTT
1 ATTTCTT
1805128 TGCTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (23 bp):
ATTTCTTCTTTTTGAGTGCTTCA
Found at i:1815365 original size:21 final size:21
Alignment explanation
Indices: 1815339--1815398 Score: 111
Period size: 21 Copynumber: 2.8 Consensus size: 21
1815329 CACTGTTGAT
1815339 TACATATGATGTTATCAGGAA
1 TACATATGATGTTATCAGGAA
1815360 TACATATGATGTTATCAGGAA
1 TACATATGATGTTATCAGGAA
1815381 TACATATGATGTTTATCA
1 TACATATGATG-TTATCA
1815399 TAAAAGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (21 bp):
TACATATGATGTTATCAGGAA
Found at i:1816656 original size:12 final size:12
Alignment explanation
Indices: 1816639--1816664 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1816629 ATTAGACATG
1816639 GAGTTAAATGAA
1 GAGTTAAATGAA
1816651 GAGTTAAATGAA
1 GAGTTAAATGAA
1816663 GA
1 GA
1816665 TAGAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (12 bp):
GAGTTAAATGAA
Found at i:1823851 original size:18 final size:18
Alignment explanation
Indices: 1823828--1823864 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1823818 ACCAGAGAGT
*
1823828 ATACAAATTACATGTGGC
1 ATACAAAGTACATGTGGC
1823846 ATACAAAGTACATGTGGC
1 ATACAAAGTACATGTGGC
1823864 A
1 A
1823865 GCATGGGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (18 bp):
ATACAAAGTACATGTGGC
Found at i:1826761 original size:10 final size:10
Alignment explanation
Indices: 1826746--1826770 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1826736 TGCACAATAT
1826746 TTTAGTTGCA
1 TTTAGTTGCA
1826756 TTTAGTTGCA
1 TTTAGTTGCA
1826766 TTTAG
1 TTTAG
1826771 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:1844220 original size:21 final size:22
Alignment explanation
Indices: 1844171--1844221 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1844161 TCGATGGTTT
* * *
1844171 TATGTGGTCTTTGGGGACAAACC
1 TATGTGGTCCTTCGAGACAAA-C
1844194 TATGTGGTCCTTCGAGACAAA-
1 TATGTGGTCCTTCGAGACAAAC
1844215 TATGTGG
1 TATGTGG
1844222 CACTTTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (22 bp):
TATGTGGTCCTTCGAGACAAAC
Found at i:1855162 original size:12 final size:11
Alignment explanation
Indices: 1855143--1855174 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1855133 ACTCCCCAAT
1855143 GAAAAAAAAAA
1 GAAAAAAAAAA
1855154 GAGAAAAAAAAA
1 GA-AAAAAAAAA
1855166 GAAAAAAAA
1 GAAAAAAAA
1855175 GTTGATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:1862267 original size:24 final size:24
Alignment explanation
Indices: 1862223--1862272 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1862213 ATAAAGAACC
*
1862223 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1862247 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1862271 AA
1 AA
1862273 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1872703 original size:24 final size:24
Alignment explanation
Indices: 1872659--1872708 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1872649 ATAAAGAACC
*
1872659 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1872683 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1872707 AA
1 AA
1872709 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1873788 original size:54 final size:54
Alignment explanation
Indices: 1873603--1873801 Score: 260
Period size: 54 Copynumber: 3.7 Consensus size: 54
1873593 TCGATACGGT
* * * * *
1873603 AATTCACAAACTCATTATGAATTACATATGG-TGCA-ATCACAGTGCCAATACGGA
1 AATTCATAAACTAATTATGAATTTCTTA-GGTTGCACA-CACAGTGCCAATACGAA
*
1873657 AATTCATAAACTAATTATGAA-TTCTTTAGGTTGCACACATAGTGCCAATACGAA
1 AATTCATAAACTAATTATGAATTTC-TTAGGTTGCACACACAGTGCCAATACGAA
* * *
1873711 AATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAATGCCAATACGAA
1 AATTCATAAACTAATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGAA
*
1873765 AATTCATAAACTAATTTTGAATTTCTTAGGTTGCACA
1 AATTCATAAACTAATTATGAATTTCTTAGGTTGCACA
1873802 TATAGCCTTG
Statistics
Matches: 128, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 4 0.03
54 120 0.94
55 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
AATTCATAAACTAATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGAA
Found at i:1874094 original size:22 final size:22
Alignment explanation
Indices: 1874060--1874118 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
1874050 GTACCCCTCT
*
1874060 TATGGTATCGATACTTCTATAC
1 TATGGTATTGATACTTCTATAC
* *
1874082 TATTGTATTGATATTTCTATAC
1 TATGGTATTGATACTTCTATAC
*
1874104 TATGGTACTGATACT
1 TATGGTATTGATACT
1874119 CCCTTTCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (22 bp):
TATGGTATTGATACTTCTATAC
Found at i:1877351 original size:23 final size:23
Alignment explanation
Indices: 1877305--1877364 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1877295 GTTCTATTGT
*
1877305 GTCCTTCAGGA-AAAACTATGTG
1 GTCCTTCAGGATAAAACTATATG
* *
1877327 GTCCTTCGGGATAAACCTATATG
1 GTCCTTCAGGATAAAACTATATG
1877350 GTCCTTCAGGATAAA
1 GTCCTTCAGGATAAA
1877365 TATGTAGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
GTCCTTCAGGATAAAACTATATG
Found at i:1878875 original size:15 final size:16
Alignment explanation
Indices: 1878857--1878886 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1878847 AATAATTTAA
1878857 AATAG-AAATTAAAAT
1 AATAGAAAATTAAAAT
1878872 AATAGAAAATTAAAA
1 AATAGAAAATTAAAA
1878887 GGGAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (16 bp):
AATAGAAAATTAAAAT
Done.