Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 32
Found at i:1633118 original size:21 final size:21
Alignment explanation
Indices: 1633089--1633141 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1633079 ATTCTGACTA
1633089 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1633110 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1633131 TCGCAATGCGA
1 TCGCATTGCGA
1633142 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1633156 original size:20 final size:20
Alignment explanation
Indices: 1633131--1633237 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
1633121 TTTTCCTAAT
1633131 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1633151 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1633172 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1633192 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1633212 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1633232 TCGCAA
1 TCGCAA
1633238 CGAGATTCTG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 59 0.79
21 15 0.20
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1633177 original size:41 final size:40
Alignment explanation
Indices: 1633131--1633239 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 40
1633121 TTTTCCTAAT
**
1633131 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
1633172 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
1633212 TCGCAATGCGAAT-CTGTAAATCGCAACG
1 TCGCAATGCGAATAC-GTAAATCGCAACG
1633240 AGATTCTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 29 0.48
41 30 0.50
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:1633255 original size:40 final size:39
Alignment explanation
Indices: 1633131--1633258 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 39
1633121 TTTTCCTAAT
*
1633131 TCGCAATGCGAATACGTAAATCGCAACGCGAATT-TGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGAG-ATTCT-G-AAA
* *
1633172 TCGCAATGCGATTACGTAAATCGCAATGCGA-ATAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAA--CGAGATTCTG-AAA
*
1633212 TCGCAATGCGAAT-CTGTAAATCGCAACGAGATTCTGACTA
1 TCGCAATGCGAATAC-GTAAATCGCAACGAGATTCTGA-AA
1633252 TCGCAAT
1 TCGCAAT
1633259 ACTGAATTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
38 3 0.04
39 5 0.07
40 36 0.49
41 27 0.37
43 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (39 bp):
TCGCAATGCGAATACGTAAATCGCAACGAGATTCTGAAA
Found at i:1634131 original size:24 final size:24
Alignment explanation
Indices: 1634099--1634152 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1634089 GTATTCGAAA
1634099 TTTGATCTTGACCAATACCCGGAC
1 TTTGATCTTGACCAATACCCGGAC
** * *
1634123 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGACCAATACCCGGAC
1634147 TTTGAT
1 TTTGAT
1634153 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGACCAATACCCGGAC
Found at i:1635187 original size:14 final size:14
Alignment explanation
Indices: 1635168--1635204 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1635158 CATCAATTAA
1635168 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1635182 ACAAATCATCTTTT
1 ACAAATCAACATTT
1635196 ACAAATCAA
1 ACAAATCAA
1635205 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1636607 original size:21 final size:21
Alignment explanation
Indices: 1636583--1636661 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
1636573 CAACGATGAC
1636583 AGTGGCCTCTTGAACGGTGGG
1 AGTGGCCTCTTGAACGGTGGG
* * **
1636604 AGTGGACTCTTG-AGGGATGAT
1 AGTGGCCTCTTGAACGG-TGGG
* *
1636625 AGGGGCCTCTTGAACGATAGGG
1 AGTGGCCTCTTGAACGGT-GGG
*
1636647 -GAGGCCTCTTGAACG
1 AGTGGCCTCTTGAACG
1636662 ATGACAGGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (21 bp):
AGTGGCCTCTTGAACGGTGGG
Found at i:1636656 original size:42 final size:42
Alignment explanation
Indices: 1636577--1636669 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1636567 CCTTTTCAAC
* * *
1636577 GATGACAGTGGCCTCTTGAACGGTGGGAGTGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1636619 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1636661 GATGACAGG
1 GATGACAGG
1636670 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1637198 original size:33 final size:33
Alignment explanation
Indices: 1637146--1637242 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 33
1637136 TCTGAAACTT
* * *
1637146 AAAAGCGCAACGTGAAAATGACTATCGCAACGAG
1 AAAATCGCAACG-GAAAATGACTATCGCAACAAC
* * **
1637180 AGAATCGCAATGCG-AAATGAAAATCGCAACAAC
1 AAAATCGCAACG-GAAAATGACTATCGCAACAAC
1637213 AAAATCGCAACGGAAAAATGACTATCGCAA
1 AAAATCGCAACGG-AAAATGACTATCGCAA
1637243 TGCGAATTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
32 1 0.02
33 25 0.51
34 23 0.47
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGGAAAATGACTATCGCAACAAC
Found at i:1637241 original size:20 final size:20
Alignment explanation
Indices: 1637216--1637267 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1637206 CAACAACAAA
1637216 ATCGCAACG-GAAAAATGACT
1 ATCGCAACGCG-AAAATGACT
* **
1637236 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1637256 ATCGCAACGCGA
1 ATCGCAACGCGA
1637268 TTCTCTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1637301 original size:20 final size:20
Alignment explanation
Indices: 1637276--1637439 Score: 216
Period size: 20 Copynumber: 8.5 Consensus size: 20
1637266 GATTCTCTCG
*
1637276 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
1637296 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1637316 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1637336 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1637356 TTGAGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1637376 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1637390 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
1637410 TTGCGATAGCCATTTTCTCA
1 TTGCGATAGTCATTTTCGCA
1637430 TTGCGATAGT
1 TTGCGATAGT
1637440 AAACTATTCT
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.05
16 6 0.05
18 6 0.05
19 4 0.03
20 105 0.82
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1637369 original size:60 final size:56
Alignment explanation
Indices: 1637269--1637439 Score: 222
Period size: 54 Copynumber: 3.0 Consensus size: 56
1637259 GCAACGCGAT
*
1637269 TCTCTCGTTGCGATAGTCAAATTT-GCATTGCGATAGTCATTTTCGCATTGCGATAG
1 TCTCTCGTTGCGATAGTC-ATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
* *
1637325 TCATTTTCGCATTGCGATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGCGAT--
1 TC--TCTCG--TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
* * *
1637383 TCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGCCATTTTCTCATTGCGATAG
1 TCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
1637439 T
1 T
1637440 AAACTATTCT
Statistics
Matches: 100, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
54 43 0.43
56 7 0.07
58 6 0.06
59 4 0.04
60 40 0.40
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (56 bp):
TCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
Found at i:1639333 original size:20 final size:20
Alignment explanation
Indices: 1639310--1639375 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1639300 CTGAAACTTT
*
1639310 AAATCACAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
1639330 AAATCGCAGCACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1639350 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
1639369 AAATCGC
1 AAATCGC
1639376 CTTGCGATTC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 11 0.29
20 27 0.71
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1639416 original size:20 final size:20
Alignment explanation
Indices: 1639391--1639437 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1639381 GATTCTATCG
1639391 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1639411 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1639431 TTGCGAT
1 TTGCGAT
1639438 TCACTCGTTG
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:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1640032 original size:20 final size:20
Alignment explanation
Indices: 1640007--1640078 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1639997 GCTATGTAAA
1640007 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
1640027 TCGCATTGCGAT--TTACGTAT
1 TCGCATTGCGATAGTCA-G-AT
1640047 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
1640067 TCGCATTGCGAT
1 TCGCATTGCGAT
1640079 TTACGTATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 40 0.87
21 1 0.02
22 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:1640062 original size:40 final size:40
Alignment explanation
Indices: 1640007--1640097 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
1639997 GCTATGTAAA
1640007 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
1640047 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
1640087 TCGCATTGCGA
1 TCGCATTGCGA
1640098 ATTAGGAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
Found at i:1640088 original size:20 final size:20
Alignment explanation
Indices: 1640025--1640097 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
1640015 CGATAGTCAG
1640025 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1640045 ATTCGCATTGCGATAGT-CAG-
1 ATTCGCATTGCGAT-TTAC-GT
1640065 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1640085 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1640098 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1640118 original size:21 final size:21
Alignment explanation
Indices: 1640094--1640139 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1640084 TATTCGCATT
1640094 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1640115 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1640136 GCGA
1 GCGA
1640140 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1645994 original size:19 final size:19
Alignment explanation
Indices: 1645970--1646010 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1645960 TACCATCAAA
*
1645970 TCTAATGTAAGTAGGATTT
1 TCTAATGTAAGTAGGACTT
1645989 TCTAATGTAAGTAGGACTT
1 TCTAATGTAAGTAGGACTT
1646008 TCT
1 TCT
1646011 CTACTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (19 bp):
TCTAATGTAAGTAGGACTT
Found at i:1649941 original size:14 final size:14
Alignment explanation
Indices: 1649922--1649988 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
1649912 GAAGCCTGAG
1649922 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
1649936 GAGCCGCTTGAGCTGAGCC
1 GAGCCG-TT----TGAGCC
*
1649955 GAGCCGTTTAAGCC
1 GAGCCGTTTGAGCC
*
1649969 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
1649983 GAGCCG
1 GAGCCG
1649989 AGCCGCCTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.19
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:1649954 original size:19 final size:19
Alignment explanation
Indices: 1649930--1649994 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1649920 AGGAGCCGTT
1649930 TGAGCCGAGCCGCTTGAGC
1 TGAGCCGAGCCGCTTGAGC
1649949 TGAGCCGAGCCG-TT----
1 TGAGCCGAGCCGCTTGAGC
* *
1649963 TAAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGCTTGAGC
1649982 TGAGCCGAGCCGC
1 TGAGCCGAGCCGC
1649995 CTAGATCGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 11 0.29
15 2 0.05
18 2 0.05
19 23 0.61
ACGTcount: A:0.17, C:0.31, G:0.35, T:0.17
Consensus pattern (19 bp):
TGAGCCGAGCCGCTTGAGC
Found at i:1649959 original size:33 final size:33
Alignment explanation
Indices: 1649922--1649993 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
1649912 GAAGCCTGAG
*
1649922 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTAAGCCGAGCCGCTTGAGCTGAGCC
*
1649955 GAGCCGTTTAAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTAAGCCGAGCCGCTTGAGCTGAGCC
1649988 GAGCCG
1 GAGCCG
1649994 CCTAGATCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.18
Consensus pattern (33 bp):
GAGCCGTTTAAGCCGAGCCGCTTGAGCTGAGCC
Found at i:1650005 original size:33 final size:33
Alignment explanation
Indices: 1649932--1650010 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1649922 GAGCCGTTTG
* **
1649932 AGCCGAGCCGCTTGAGCTGAGCCGAGCCGTTTA
1 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGCCTA
1649965 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGCCT-
1 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGCCTA
*
1649997 AGATCGAGCCGTTT
1 AG-CCGAGCCGTTT
1650011 ACTGTTGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.05
33 39 0.95
ACGTcount: A:0.18, C:0.30, G:0.33, T:0.19
Consensus pattern (33 bp):
AGCCGAGCCGTTTGAGCTGAGCCGAGCCGCCTA
Found at i:1651167 original size:18 final size:18
Alignment explanation
Indices: 1651141--1651175 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1651131 TCGAAAGGAC
*
1651141 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1651159 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1651176 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1654944 original size:19 final size:19
Alignment explanation
Indices: 1654920--1655002 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1654910 AGGAGCCGTT
*
1654920 TGAGCCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1654939 TGAGCCGAGCCGTTT-A--
1 TGAGCCGAGCCGTTTGAGC
1654955 --AGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
1654972 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
*
1654991 TGAGCCAAGCCG
1 TGAGCCGAGCCG
1655003 AGCCGCCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.29, G:0.35, T:0.18
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:1654949 original size:33 final size:33
Alignment explanation
Indices: 1654912--1654996 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
1654902 GAAGCCTGAG
1654912 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
* *
1654945 GAGCCGTTTAAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
1654978 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCC
1654997 AAGCCGAGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.20
Consensus pattern (33 bp):
GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
Found at i:1654996 original size:14 final size:14
Alignment explanation
Indices: 1654912--1654978 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
1654902 GAAGCCTGAG
1654912 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
1654926 GAGCCGCTTGAGCTGAGCC
1 GAGCCG-TT----TGAGCC
*
1654945 GAGCCGTTTAAGCC
1 GAGCCGTTTGAGCC
*
1654959 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
1654973 GAGCCG
1 GAGCCG
1654979 AGCCGTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.19
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:1656181 original size:18 final size:18
Alignment explanation
Indices: 1656155--1656189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1656145 TCGAAAGGAC
*
1656155 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1656173 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1656190 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1662327 original size:21 final size:23
Alignment explanation
Indices: 1662283--1662327 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
1662273 CATACTTGTC
*
1662283 TTCATGGTACATATTAAGATTAT
1 TTCATGGTACATATTAAGAGTAT
*
1662306 TTCATGG-A-ATATTAAGGGTAT
1 TTCATGGTACATATTAAGAGTAT
1662327 T
1 T
1662328 CGTAAAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (23 bp):
TTCATGGTACATATTAAGAGTAT
Found at i:1673874 original size:20 final size:21
Alignment explanation
Indices: 1673830--1673885 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1673820 CAGTTTCCAA
* *
1673830 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
1673851 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
1673871 ATTCGCAACGCGATT
1 ATTCGCAACGCGATT
1673886 TTGAAAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:1673914 original size:19 final size:19
Alignment explanation
Indices: 1673890--1673975 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
1673880 GCGATTTTGA
*
1673890 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
1673909 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
1673930 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
* *
1673953 AAAAAGTGTTGTGATAGTG
1 AAAATGTGTTGCGATAGTG
1673972 AAAA
1 AAAA
1673976 ATCCAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 32 0.57
20 1 0.02
21 1 0.02
22 8 0.14
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:1674396 original size:19 final size:19
Alignment explanation
Indices: 1674369--1674440 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1674359 CCAGTCGTTG
1674369 CGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
* ** *
1674388 CGAATTTGGAAAATCGTAA
1 CGAACTTGGACTATCGCAA
*
1674407 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
* *
1674428 CAAATTTGGACTA
1 CGAACTTGGACTA
1674441 ACGTAAATTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 25 0.64
21 14 0.36
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:1674472 original size:21 final size:21
Alignment explanation
Indices: 1674448--1674489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1674438 CTAACGTAAA
1674448 TTTGGAAAATCGCATTGCGAT
1 TTTGGAAAATCGCATTGCGAT
* **
1674469 TTTGTATTATCGCATTGCGAT
1 TTTGGAAAATCGCATTGCGAT
1674490 AGTCAGAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (21 bp):
TTTGGAAAATCGCATTGCGAT
Found at i:1674506 original size:20 final size:20
Alignment explanation
Indices: 1674477--1674590 Score: 158
Period size: 20 Copynumber: 5.7 Consensus size: 20
1674467 ATTTTGTATT
*
1674477 ATCGCATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
1674497 ATCGCGTTGCGATAGTTAGA
1 ATCGCGTTGCGATAGTCAGA
1674517 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
1674537 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
1674558 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
1674578 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1674591 CGTTGCGATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 13 0.16
22 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:1674618 original size:49 final size:50
Alignment explanation
Indices: 1674541--1674635 Score: 183
Period size: 49 Copynumber: 1.9 Consensus size: 50
1674531 GTCAGAATCG
1674541 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT
1 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT
1674591 CGTTGCGATTTTGT-TTATCGCGTTGCGATAGTCAGAATCGCGTTG
1 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTG
1674636 TGATTTACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 31 0.69
50 14 0.31
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (50 bp):
CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT
Found at i:1674679 original size:90 final size:90
Alignment explanation
Indices: 1674517--1674680 Score: 215
Period size: 90 Copynumber: 1.8 Consensus size: 90
1674507 GATAGTTAGA
** * *
1674517 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCG
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTCATATTATCGCATTGCGATAGTCAAAATCG
**
1674582 CGTTGCGATCGTTGCGATTTTGTTT
66 CAATGCGATCGTTGCGATTTTGTTT
* **
1674607 ATCGCGTTGCGATAGTCAGAATCGCGTTGTGATTTACATA-T-TCGCATTGCGATTTTCTAAAAT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTT-CATATTATCGCATTGCGATAGTC-AAAAT
1674670 CGCAATGCGAT
64 CGCAATGCGAT
1674681 AGTCAAAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 13 0.21
90 48 0.76
91 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (90 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTCATATTATCGCATTGCGATAGTCAAAATCG
CAATGCGATCGTTGCGATTTTGTTT
Found at i:1674679 original size:110 final size:110
Alignment explanation
Indices: 1674497--1674699 Score: 273
Period size: 110 Copynumber: 1.8 Consensus size: 110
1674487 GATAGTCAGA
* * * **
1674497 ATCGCGTTGCGATAGTTAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCG
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTCTAAAATCG
** *
1674562 CGTTGCGATAGTCAGAATCGCGTTGCGATCGTTGCGATTTTGTTT
66 CAATGCGATAGTCAAAATCGCGTTGCGATCGTTGCGATTTTGTTT
* * * *
1674607 ATCGCGTTGCGATAGTCAGAATCGCGTTGTGAT-TTACATATTCGCATTGCGATTTTCTAAAATC
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAATCGCATTGCGATTTTCTAAAATC
*
1674671 GCAATGCGATAGTCAAAATTGCGTTGCGA
65 GCAATGCGATAGTCAAAATCGCGTTGCGA
1674700 ATCTGGAAAC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 1 0.01
110 78 0.99
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (110 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTCTAAAATCG
CAATGCGATAGTCAAAATCGCGTTGCGATCGTTGCGATTTTGTTT
Found at i:1674749 original size:19 final size:19
Alignment explanation
Indices: 1674725--1674780 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1674715 TGCGATACTG
1674725 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
* *
1674744 GAGATCGTGTTGCGGTTTA
1 GAGATCGCGTTGCGATTTA
*
1674763 GAGATCGCATTGCGATTT
1 GAGATCGCGTTGCGATTT
1674781 TGTTGGTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:1688450 original size:5 final size:5
Alignment explanation
Indices: 1688440--1688464 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1688430 ACCGGTCATA
1688440 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
1688465 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1691080 original size:24 final size:24
Alignment explanation
Indices: 1690958--1691073 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
1690948 TTCGATTTGA
*
1690958 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1690982 ATTCTTATATGATATCTT-ACATGG
1 ATTCTGATATGATA-CTTGACATGG
* *
1691006 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
1691030 ATTCTGATTTGTTACTTGAC-TTG
1 ATTCTGATATGATACTTGACATGG
1691053 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
1691074 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 6 0.08
24 70 0.89
25 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1691090 original size:24 final size:24
Alignment explanation
Indices: 1690954--1691090 Score: 102
Period size: 24 Copynumber: 5.7 Consensus size: 24
1690944 GATTTTCGAT
* *
1690954 TTGAATTCTGATCTGATACTTGAC
1 TTGATTTCTGATTTGATACTTGAC
* * *
1690978 ATGGA-TTCTTATATGATATCTT-AC
1 -TTGATTTCTGATTTGATA-CTTGAC
* *
1691002 ATGGA-TTCTGATCTGATACTTGAC
1 -TTGATTTCTGATTTGATACTTGAC
*
1691026 TTGGA-TTCTGATTTGTTACTTGAC
1 TT-GATTTCTGATTTGATACTTGAC
*
1691050 TTGATTTCTGATATGATACTTGAC
1 TTGATTTCTGATTTGATACTTGAC
* * *
1691074 CTGATTTATGTTTTGAT
1 TTGATTTCTGATTTGAT
1691091 TTTTGATATA
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
23 6 0.06
24 82 0.87
25 6 0.06
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (24 bp):
TTGATTTCTGATTTGATACTTGAC
Found at i:1692617 original size:14 final size:14
Alignment explanation
Indices: 1692598--1692636 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1692588 TAATGGGGAG
1692598 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1692612 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1692626 GAATCTCTGCA
1 TAATCCCTGCA
1692637 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1695103 original size:112 final size:112
Alignment explanation
Indices: 1694961--1695185 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
1694951 CGCCCGTTGG
1694961 GTACGCGGAACACCAAAACCAATAATTTGTGTTGTGATGCACATGCCTCTTCAGGGAACACCTTA
1 GTACGCGGAACACCAAAACCAATAATTTGTGTTGTGATGCACATGCCTCTTCAGGGAACACCTTA
*
1695026 CAGTCAATGCAAGCCCATCGTTCTCAATTTCTAACCAAGATGTAGTC
66 CAGTCAATGCAAGCCCATCGTTCCCAATTTCTAACCAAGATGTAGTC
1695073 GTACGCGGAACACCAAAACCAATAATTTGTGTTGTGATGCACATGCCTCTTCAGGGAACACCTTA
1 GTACGCGGAACACCAAAACCAATAATTTGTGTTGTGATGCACATGCCTCTTCAGGGAACACCTTA
*
1695138 CAGTCAATGCAAGCCCATCGTTCCCGATTTCTAACCAAGATGTAGTC
66 CAGTCAATGCAAGCCCATCGTTCCCAATTTCTAACCAAGATGTAGTC
1695185 G
1 G
1695186 ATTTGGGTAC
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (112 bp):
GTACGCGGAACACCAAAACCAATAATTTGTGTTGTGATGCACATGCCTCTTCAGGGAACACCTTA
CAGTCAATGCAAGCCCATCGTTCCCAATTTCTAACCAAGATGTAGTC
Found at i:1697618 original size:13 final size:13
Alignment explanation
Indices: 1697600--1697633 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1697590 ACCCGACCCG
*
1697600 ACCCGACCTGTTT
1 ACCCGACCTGTTA
1697613 ACCCGACCTGTTA
1 ACCCGACCTGTTA
1697626 ACCCGACC
1 ACCCGACC
1697634 CGACCCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.21
Consensus pattern (13 bp):
ACCCGACCTGTTA
Found at i:1700172 original size:24 final size:24
Alignment explanation
Indices: 1700145--1700256 Score: 147
Period size: 24 Copynumber: 4.7 Consensus size: 24
1700135 ATTTGAAATA
*
1700145 TGATCTGATACTTGATATGGATTC
1 TGATCTGATACTTGACATGGATTC
1700169 TGATCTGATA-TATGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1700193 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
1700217 TGATCTGTTACTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
*
1700241 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1700257 CTGATTTATG
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1700279 original size:24 final size:24
Alignment explanation
Indices: 1700193--1700266 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
1700183 ACATGGATTC
* * *
1700193 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
1700217 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
1700241 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
1700265 TG
1 TG
1700267 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:1704039 original size:175 final size:175
Alignment explanation
Indices: 1703721--1704043 Score: 418
Period size: 175 Copynumber: 1.8 Consensus size: 175
1703711 GTACAAAAAG
** * * *
1703721 AAAATCATATAGTGACATGTTTTGTAACTATAAGCTATAATTATTATTATAAAAAAAGTTGTCAC
1 AAAATCATATAGTGACAAATTTTGTAACTATAAGCTATAATAATTATTAAAAAAAAAATTGTCAC
* * *
1703786 TACAAATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTGTCGTTATATATTTTAATTATAG
66 TACAAATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTGTAGTTATAAATTTTAACTATAG
1703851 TGATAAAATATATTGTCACAAAGATTTCCCTCCATTTTGCACCAA
131 TGATAAAATATATTGTCACAAAGATTTCCCTCCATTTTGCACCAA
* * *
1703896 AAAAGTCATATGGTGACAAATTTTGTAACTATAAGTTTTAATAATTATTACAAAAAAAACATTGT
1 AAAA-TCATATAGTGACAAATTTTGTAACTATAAGCTATAATAATTATTA-AAAAAAAA-ATTGT
* * * * * * *
1703961 CAC-A-AAATAGTGATATTCACG-TTTTCGTGACAAATTATATTTGTAGTTATAAATTTTAACTA
63 CACTACAAATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTGTAGTTATAAATTTTAACTA
**
1704023 TAGTGATAGTATATATTGTCA
128 TAGTGATAAAATATATTGTCA
1704044 TAACTATTTT
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
175 57 0.46
176 53 0.42
177 8 0.06
178 7 0.06
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (175 bp):
AAAATCATATAGTGACAAATTTTGTAACTATAAGCTATAATAATTATTAAAAAAAAAATTGTCAC
TACAAATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTGTAGTTATAAATTTTAACTATAG
TGATAAAATATATTGTCACAAAGATTTCCCTCCATTTTGCACCAA
Found at i:1708108 original size:31 final size:31
Alignment explanation
Indices: 1708073--1708134 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1708063 AGATAATTTC
* *
1708073 TGATAATTTATTTAGATAAAATAACAAATTA
1 TGATAATTTATATAGACAAAATAACAAATTA
* *
1708104 TGATAGTTTATATAGACAATATAACAAATTA
1 TGATAATTTATATAGACAAAATAACAAATTA
1708135 AATTTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (31 bp):
TGATAATTTATATAGACAAAATAACAAATTA
Found at i:1708560 original size:32 final size:32
Alignment explanation
Indices: 1708458--1708548 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 32
1708448 ATTTTTCATT
* * * **
1708458 ATAAAATATTATGACAAATAATATTTTTTCACA
1 ATAAAAAATTATAACAAA-ATTATTTAGTCACA
*
1708491 ATAAAAAATTGTAACAAAATTATTTAGTCACA
1 ATAAAAAATTATAACAAAATTATTTAGTCACA
* *
1708523 GTAAAAAGTTATAA-AAAA-TATTTAGT
1 ATAAAAAATTATAACAAAATTATTTAGT
1708549 GACGAAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 8 0.16
31 4 0.08
32 22 0.45
33 15 0.31
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (32 bp):
ATAAAAAATTATAACAAAATTATTTAGTCACA
Found at i:1710250 original size:75 final size:78
Alignment explanation
Indices: 1710127--1710281 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 78
1710117 ACTTTAATGC
1710127 ACTATAAATTTGTTTAGATTACTAAATAATATAAGATGTTTTCTACGTTCTAAATAATA-TAGAA
1 ACTATAAATTTGTTTAGATTACTAAATAATATAAGATGTTTTCTACGTTCTAAATAATATTAGAA
1710191 T-TAA-TATAATT
66 TATAATTATAATT
1710202 ACTATAAATTTGTTTAGATTACTAAATAATATAAGATGTTTTCTACGTTCTAAATAATATTAGAA
1 ACTATAAATTTGTTTAGATTACTAAATAATATAAGATGTTTTCTACGTTCTAAATAATATTAGAA
1710267 TATAATTTATAATT
66 TATAA-TTATAATT
1710281 A
1 A
1710282 GTTAAACTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
75 59 0.78
76 6 0.08
77 3 0.04
79 8 0.11
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (78 bp):
ACTATAAATTTGTTTAGATTACTAAATAATATAAGATGTTTTCTACGTTCTAAATAATATTAGAA
TATAATTATAATT
Found at i:1725073 original size:21 final size:21
Alignment explanation
Indices: 1725047--1725093 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1725037 CATTTATCCC
1725047 TAAACA-TTTAAAAAAAACCCA
1 TAAACATTTTAAAAAAAA-CCA
*
1725068 TAAACATTTTTAAAAAAACCA
1 TAAACATTTTAAAAAAAACCA
1725089 TAAAC
1 TAAAC
1725094 TATTATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACATTTTAAAAAAAACCA
Found at i:1726748 original size:14 final size:14
Alignment explanation
Indices: 1726729--1726757 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1726719 GTGAGAGCTC
1726729 AATCGATCCCCACA
1 AATCGATCCCCACA
1726743 AATCGATCCCCACA
1 AATCGATCCCCACA
1726757 A
1 A
1726758 TTTTCTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.41, G:0.07, T:0.14
Consensus pattern (14 bp):
AATCGATCCCCACA
Found at i:1727492 original size:13 final size:13
Alignment explanation
Indices: 1727474--1727506 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1727464 AGTTGGCTCA
1727474 TTTCATCTTTTCC
1 TTTCATCTTTTCC
1727487 TTTCATCTTTTCC
1 TTTCATCTTTTCC
1727500 TTTCATC
1 TTTCATC
1727507 CTTAGCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTCATCTTTTCC
Found at i:1730007 original size:73 final size:72
Alignment explanation
Indices: 1729922--1730097 Score: 185
Period size: 73 Copynumber: 2.4 Consensus size: 72
1729912 AATTTTAAAT
**
1729922 ATTGATATTTTTAAATATTAGAAAAGTT-AAAAATAAGACCGAAATTTAAAATATCGATACTCAT
1 ATTGATA-TTTTAAATATTAGAAAAGTTGAAAAA-AAGACAAAAATTTAAAATATCGATACTCAT
*
1729986 GCGGTAATG
64 GCGATAATG
* * * * * *
1729995 ATTGATACTTTTAAAAATTAAAAAAGTTGATAAAAAGATAAAAATTTAAAATATTGATACTTATG
1 ATTGATA-TTTTAAATATTAGAAAAGTTGAAAAAAAGACAAAAATTTAAAATATCGATACTCATG
**
1730060 CGATGTTG
65 CGATAATG
*
1730068 ATCGATATTTTCAAATATT-GAACAAGTTGA
1 ATTGATATTTT-AAATATTAGAA-AAGTTGA
1730098 TGGATATGGT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
72 6 0.07
73 75 0.88
74 4 0.05
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (72 bp):
ATTGATATTTTAAATATTAGAAAAGTTGAAAAAAAGACAAAAATTTAAAATATCGATACTCATGC
GATAATG
Found at i:1731416 original size:14 final size:13
Alignment explanation
Indices: 1731395--1731421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1731385 ATTTTTGTCT
1731395 TTTGAAAAATTAC
1 TTTGAAAAATTAC
1731408 TTTGAAAAATTAC
1 TTTGAAAAATTAC
1731421 T
1 T
1731422 CCCCCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGAAAAATTAC
Found at i:1740299 original size:107 final size:108
Alignment explanation
Indices: 1740115--1740308 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 108
1740105 CGCTACCTGT
* * * **
1740115 TATGTTGTCATGAAAAACATGTTTTATCTTACTTTTATATAATATAAATGGTTTCATACTTATAA
1 TATGTTATCATGAAAAACATGTCTTATCTTACTTTTATATAATATAAACGACTTCATACTTATAA
1740180 CTTAAACGATTAACA-TTTTAAAAAAAAAAAGGTGTTACCTAA
66 CTTAAACGATTAACAGTTTTAAAAAAAAAAAGGTGTTACCTAA
* *
1740222 TATGTTATCATGAAAAATATGTCTTGTCTTACTTTTA-ATTAATATAAACGACTTCATACTTATA
1 TATGTTATCATGAAAAACATGTCTTATCTTACTTTTATA-TAATATAAACGACTTCATACTTATA
** *
1740286 ACTTAAATTATTAATAGTTTTAA
65 ACTTAAACGATTAACAGTTTTAA
1740309 GGGTTATCTA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
106 1 0.01
107 68 0.91
108 6 0.08
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (108 bp):
TATGTTATCATGAAAAACATGTCTTATCTTACTTTTATATAATATAAACGACTTCATACTTATAA
CTTAAACGATTAACAGTTTTAAAAAAAAAAAGGTGTTACCTAA
Found at i:1740477 original size:100 final size:100
Alignment explanation
Indices: 1740240--1740587 Score: 339
Period size: 100 Copynumber: 3.5 Consensus size: 100
1740230 CATGAAAAAT
* * * ** * *
1740240 ATGTCTTGTCTTACTTTT-AATTAATATAAACGACTTCATACTTATAACTTAAATTATTAATA-G
1 ATGTTTTGTCTTACTTTTGCA-TAATATAAATGGTTTCATACTTATAACTTAAATGATTAATATT
* *
1740303 TTTTAAGG-GTTATC-TAGTACATTATCATAAGCAAT
65 TTTTAAGGCGATA-CATAGTACATTATCATAAGCAAC
* * * *
1740338 ATG--TTGTCTTAGTATTGCATAATATAAATGGTATCATACTTATTACTTAAATGATTAATATTT
1 ATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTCATACTTATAACTTAAATGATTAATATTT
1740401 TTTAAGGCGATACATAGTACATTATCATAAGCAAC
66 TTTAAGGCGATACATAGTACATTATCATAAGCAAC
* * * * * * *
1740436 ATGTTTTGTCTTACTTTTGTATAATATAAATGGTTTTATACTTATAATTTAAACGATTGACATTA
1 ATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTCATACTTATAACTTAAATGATTAATATTT
*** * * * * * *
1740501 AAAAAAGCGCTACATAGTGCGTTATCATGAGCAAG
66 TTTAAGGCGATACATAGTACATTATCATAAGCAAC
*** *
1740536 ATGTTTTGTCTTACTTTTGCATAATATAAACAATTTCATATTTATAACTTAA
1 ATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTCATACTTATAACTTAA
1740588 TTTGTTGACA
Statistics
Matches: 205, Mismatches: 39, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
96 46 0.22
97 10 0.05
98 29 0.14
100 120 0.59
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (100 bp):
ATGTTTTGTCTTACTTTTGCATAATATAAATGGTTTCATACTTATAACTTAAATGATTAATATTT
TTTAAGGCGATACATAGTACATTATCATAAGCAAC
Found at i:1740596 original size:100 final size:99
Alignment explanation
Indices: 1740411--1740705 Score: 317
Period size: 100 Copynumber: 3.0 Consensus size: 99
1740401 TTTAAGGCGA
* * * *
1740411 TACATAGTACATTATCATAAGCAACATGTTTTGTCTTACTTTTGTATAATATAAATGGTTTTATA
1 TACATAGTACGTTATCATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATA
*
1740476 CTTATAATTTAAACGATTGACATTAAAAAAAGCGC
66 CTTATAATTTAATCG-TTGACATTAAAAAAAGCGC
* * * **
1740511 TACATAGTGCGTTATCATGAGCAAGATGTTTTGTCTTACTTTTGCATAATATAAACAATTTCATA
1 TACATAGTACGTTATCATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATA
* * * * *
1740576 TTTATAACTTAATTTGTTGACA-TAAAAAAGGTGC
66 CTTATAATTTAA-TCGTTGACATTAAAAAAAGCGC
* * ** * *
1740610 TATC-TATTATGTTATCATGATAAACATGTTTTGT-TGTACTTTCGTATCATATAAACGGTTTCA
1 TA-CATAGTACGTTATCATGAGCAACATGTTTTGTCT-TACTTTTGTATAATATAAACGGTTTCA
* *
1740673 TACTTATAATTTAAATGGATGACATTAAAAAAA
64 TACTTATAATTT-AATCGTTGACATTAAAAAAA
1740706 CATTACTTAC
Statistics
Matches: 159, Mismatches: 31, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
98 1 0.01
99 75 0.47
100 82 0.52
101 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (99 bp):
TACATAGTACGTTATCATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATA
CTTATAATTTAATCGTTGACATTAAAAAAAGCGC
Found at i:1740723 original size:99 final size:99
Alignment explanation
Indices: 1740422--1740725 Score: 285
Period size: 99 Copynumber: 3.1 Consensus size: 99
1740412 ACATAGTACA
* * * *
1740422 TTATCATAAGCAACATGTTTTGTCTTACTTTTGTATAATATAAATGGTTTTATACTTATAATTTA
1 TTATCATGAGAAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATACTTATAATTTA
* * * *
1740487 AA-CGATTGACATTAAAAAAAGCGCTACATAGTGCG
66 AATCGA-TGACATTAAAAAAA-CGTTACTTACTACG
* * * ** * *
1740522 TTATCATGAGCAAGATGTTTTGTCTTACTTTTGCATAATATAAACAATTTCATATTTATAACTTA
1 TTATCATGAGAAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATACTTATAATTTA
* * * * * *
1740587 ATTTGTTGACA-T-AAAAAAGGTGCTA-TCTATTATG
66 AATCGATGACATTAAAAAAACGT--TACT-TACTACG
* * *
1740621 TTATCATGATAAACATGTTTTGT-TGTACTTTCGTATCATATAAACGGTTTCATACTTATAATTT
1 TTATCATGAGAAACATGTTTTGTCT-TACTTTTGTATAATATAAACGGTTTCATACTTATAATTT
* *
1740685 AAATGGATGACATTAAAAAAACATTACTTACTACG
65 AAATCGATGACATTAAAAAAACGTTACTTACTACG
1740720 TTATCA
1 TTATCA
1740726 CAGGCCTAAC
Statistics
Matches: 161, Mismatches: 35, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
97 1 0.01
98 7 0.04
99 81 0.50
100 64 0.40
101 8 0.05
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (99 bp):
TTATCATGAGAAACATGTTTTGTCTTACTTTTGTATAATATAAACGGTTTCATACTTATAATTTA
AATCGATGACATTAAAAAAACGTTACTTACTACG
Found at i:1741157 original size:77 final size:77
Alignment explanation
Indices: 1741028--1741475 Score: 418
Period size: 77 Copynumber: 5.8 Consensus size: 77
1741018 CTTTCAAATT
** * * *
1741028 TTTTA-TAATAGAAAA-ATTAACATTCTAGATTGCAACTTGCTTTCTTAGTGAACCATAACATTC
1 TTTTATTAATA-AAAATATTAACATTCTAGATCACAACCT-ATTTCTTAGTGAACCATGACATTC
* *
1741091 TTGTGTGTAACCCA
64 TTGGGTGCAACCCA
* * * **
1741105 TTTTATTAATAAAAATATTATCATTCTAGATCCCAACCTATTTATTAGTGAACCATGGTATTCTT
1 TTTTATTAATAAAAATATTAACATTCTAGATCACAACCTATTTCTTAGTGAACCATGACATTCTT
*** **
1741170 GGGCAAAAATCA
66 GGGTGCAACCCA
* * * * * ** *
1741182 TTTTATTGATAAAAATATCAATATT-TCAGATCGCAACTTATTTCTTAGTGAATTACGACATTCT
1 TTTTATTAATAAAAATATTAACATTCT-AGATCACAACCTATTTCTTAGTGAACCATGACATTCT
*
1741246 TGGGGGCAACCCA
65 TGGGTGCAACCCA
* * * * *
1741259 TTTTATTAATAAAAATATTAACATTCCATATCACAATCTATTTATTAGTAAACCATGACATTCTT
1 TTTTATTAATAAAAATATTAACATTCTAGATCACAACCTATTTCTTAGTGAACCATGACATTCTT
*
1741324 GGGTGCAACCTA
66 GGGTGCAACCCA
* * * * *
1741336 TTTTATTAATAATAAAAATTAGCATTC-CGTATCACAACCTATTTCTTAGTGAATCGTGACATTC
1 TTTTATTAATAA-AAATATTAACATTCTAG-ATCACAACCTATTTCTTAGTGAACCATGACATTC
*
1741400 TTGAGTGCAACCCA
64 TTGGGTGCAACCCA
* * * ** * *
1741414 TTTTATTAATAAAAATCTTAACATTATAGATCGCAAATTGTTTCTTAATGAACCATGACATT
1 TTTTATTAATAAAAATATTAACATTCTAGATCACAACCTATTTCTTAGTGAACCATGACATT
1741476 TTTAGGCACA
Statistics
Matches: 294, Mismatches: 70, Indels: 14
0.78 0.19 0.04
Matches are distributed among these distances:
76 1 0.00
77 203 0.69
78 90 0.31
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCTAGATCACAACCTATTTCTTAGTGAACCATGACATTCTT
GGGTGCAACCCA
Found at i:1741468 original size:155 final size:154
Alignment explanation
Indices: 1741068--1741475 Score: 437
Period size: 155 Copynumber: 2.6 Consensus size: 154
1741058 TGCAACTTGC
* * * * *
1741068 TTTCTTAGTGAACCATAACATTCTTGTGTGTAACCCATTTTATTAATAAAAATATTATCATTCTA
1 TTTCTTAGTGAATCATGACATTCTTGAGTGCAACCCATTTTATTAATAAAAATATTAACATTCTA
* ** ** * *
1741133 GATCCCAACCTATTTATTAGTGAACCATGGTATTCTTGGGCAAAAATCATTTTATTGATAAAAAT
66 GATCACAAATTATTTATTAGTGAACCATGACATTCTTGGGCAAAAATCATTTTATTAATAAAAAA
* * *
1741198 ATCAATATTTCAGATCGCAACTTA
131 ATCAACATTTCAGATCACAACCTA
* * * * *
1741222 TTTCTTAGTGAATTACGACATTCTTGGGGGCAACCCATTTTATTAATAAAAATATTAACATTCCA
1 TTTCTTAGTGAATCATGACATTCTTGAGTGCAACCCATTTTATTAATAAAAATATTAACATTCTA
* * **
1741287 TATCAC-AATCTATTTATTAGTAAACCATGACATTCTTGGGTGC-AACCT-ATTTTATTAATAAT
66 GATCACAAAT-TATTTATTAGTGAACCATGACATTCTT-GG-GCAAAAATCATTTTATTAATAA-
* * *
1741349 AAAAATTAGCA-TTCCGTATCACAACCTA
127 AAAAATCAACATTTCAG-ATCACAACCTA
* * *
1741377 TTTCTTAGTGAATCGTGACATTCTTGAGTGCAACCCATTTTATTAATAAAAATCTTAACATTATA
1 TTTCTTAGTGAATCATGACATTCTTGAGTGCAACCCATTTTATTAATAAAAATATTAACATTCTA
* * * *
1741442 GATCGCAAATTGTTTCTTAATGAACCATGACATT
66 GATCACAAATTATTTATTAGTGAACCATGACATT
1741476 TTTAGGCACA
Statistics
Matches: 208, Mismatches: 40, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
153 1 0.00
154 100 0.48
155 102 0.49
156 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (154 bp):
TTTCTTAGTGAATCATGACATTCTTGAGTGCAACCCATTTTATTAATAAAAATATTAACATTCTA
GATCACAAATTATTTATTAGTGAACCATGACATTCTTGGGCAAAAATCATTTTATTAATAAAAAA
ATCAACATTTCAGATCACAACCTA
Found at i:1758387 original size:18 final size:18
Alignment explanation
Indices: 1758366--1758405 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1758356 AAGAACCTAA
1758366 GTTGCAAGAGGATGAACT
1 GTTGCAAGAGGATGAACT
* *
1758384 GTTGGAGGAGGATGAACT
1 GTTGCAAGAGGATGAACT
1758402 GTTG
1 GTTG
1758406 GAGAAGGATG
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:0.28, C:0.07, G:0.40, T:0.25
Consensus pattern (18 bp):
GTTGCAAGAGGATGAACT
Found at i:1758406 original size:18 final size:18
Alignment explanation
Indices: 1758373--1758416 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1758363 TAAGTTGCAA
1758373 GAGGATGAACTGTTGGAG
1 GAGGATGAACTGTTGGAG
1758391 GAGGATGAACTGTTGGAG
1 GAGGATGAACTGTTGGAG
*
1758409 AAGGATGA
1 GAGGATGA
1758417 GAATGAGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.43, T:0.20
Consensus pattern (18 bp):
GAGGATGAACTGTTGGAG
Found at i:1765248 original size:17 final size:18
Alignment explanation
Indices: 1765215--1765249 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1765205 AATTACCCCT
1765215 AAATTAAACGACTAAAGTG
1 AAATTAAAC-ACTAAAGTG
1765234 AAATTAAAC-CTAAAGT
1 AAATTAAACACTAAAGT
1765250 AGAGGCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (18 bp):
AAATTAAACACTAAAGTG
Found at i:1775014 original size:21 final size:23
Alignment explanation
Indices: 1774988--1775030 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1774978 ACTTAAATTC
1774988 ATCAAA-AAGACAAAC-CAAAAA
1 ATCAAACAAGACAAACTCAAAAA
*
1775009 ATCAAACAAGCCAAACTCAAAA
1 ATCAAACAAGACAAACTCAAAA
1775031 TTCCAACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.65, C:0.23, G:0.05, T:0.07
Consensus pattern (23 bp):
ATCAAACAAGACAAACTCAAAAA
Found at i:1780964 original size:31 final size:31
Alignment explanation
Indices: 1780921--1780979 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1780911 TTAAGAACAC
* *
1780921 ATCTTAGGGCCGCAGGGCCTACCCAAGAATG
1 ATCTCAGGGCCGCAGAGCCTACCCAAGAATG
*
1780952 ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTCAGGGCCGCAGAGCCTACCCAAGA
1780980 GTCACATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
ATCTCAGGGCCGCAGAGCCTACCCAAGAATG
Found at i:1780979 original size:63 final size:63
Alignment explanation
Indices: 1780858--1780979 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
1780848 CTAAGGGAAT
* * ** * * *
1780858 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGTCTACTTAAGAACAC
1 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAC
*
1780921 ATCTTAGGGCC-GCAGGGCCTACCCAAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1780980 GTCACATTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (63 bp):
ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAC
Found at i:1783859 original size:18 final size:18
Alignment explanation
Indices: 1783836--1783878 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1783826 CGGTCAACGA
1783836 GTCGGGTCAACAGATCGG
1 GTCGGGTCAACAGATCGG
* * *
1783854 GTCGGGTCAACGGGTTGG
1 GTCGGGTCAACAGATCGG
1783872 GTCGGGT
1 GTCGGGT
1783879 TATGACCGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.21
Consensus pattern (18 bp):
GTCGGGTCAACAGATCGG
Found at i:1788162 original size:25 final size:25
Alignment explanation
Indices: 1788061--1788164 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 25
1788051 TAACGAGCAT
* * *
1788061 CATTTTTCAAAATTCTTTTATCAAA
1 CATTTTTCAAAAATCATTCATCAAA
* * * *
1788086 CATTCTTCAAAATTCTTTCATCAAG
1 CATTTTTCAAAAATCATTCATCAAA
* **
1788111 CATTTCTCAAAAAAAAAATTC-TCAAA
1 CATTTTTC--AAAAATCATTCATCAAA
*
1788137 CATTTTTCAAAAATCATTCATAAAA
1 CATTTTTCAAAAATCATTCATCAAA
1788162 CAT
1 CAT
1788165 GTTCCAAACT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
24 9 0.15
25 35 0.56
26 11 0.18
27 7 0.11
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (25 bp):
CATTTTTCAAAAATCATTCATCAAA
Found at i:1797986 original size:17 final size:17
Alignment explanation
Indices: 1797964--1798017 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
1797954 ATTCAAGTTT
1797964 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
1797981 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
1797998 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
1798015 GAG
1 GAG
1798018 CTCAAGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:1805033 original size:21 final size:21
Alignment explanation
Indices: 1805005--1805085 Score: 108
Period size: 22 Copynumber: 3.8 Consensus size: 21
1804995 TTTCTGGGCT
*
1805005 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCATTCA
* *
1805026 ATGGGAATCTATACCCATTCA
1 AGGGGAATCGATACCCATTCA
*
1805047 AGGGGGAATCGGTACCCATTCA
1 A-GGGGAATCGATACCCATTCA
1805069 GAGGGGAATCGATACCC
1 -AGGGGAATCGATACCC
1805086 CCTTAATCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.37
22 31 0.61
23 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (21 bp):
AGGGGAATCGATACCCATTCA
Found at i:1806469 original size:106 final size:106
Alignment explanation
Indices: 1806284--1806497 Score: 383
Period size: 106 Copynumber: 2.0 Consensus size: 106
1806274 TCAAGAGATA
1806284 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1806349 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
* * * *
1806390 TAAGCTAATGTATATCTGTGAATTTCATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
*
1806455 TGAATATGAAATCATATGAGAATTGATATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
1806496 TA
1 TA
1806498 CATGTATGTG
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (106 bp):
TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
Found at i:1806826 original size:105 final size:105
Alignment explanation
Indices: 1806638--1806847 Score: 287
Period size: 105 Copynumber: 2.0 Consensus size: 105
1806628 GAGTCGAGGG
*
1806638 TCTACGCGGTCTTTCGGGACATATAGGTATCTTATGGAACATCTATGAGGTCCTTTGAGACACGT
1 TCTACGCGGTCATTCGGGACATATAGGTATCTTATGGAACATCTATGAGGTCCTTTGAGACACGT
* *
1806703 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
* * * * * * *
1806743 TCTACGTGGTCATTCGGGACGTATATGTATTCTT-TGGAGCATGTATGAGGTCTTTTGAGACACT
1 TCTACGCGGTCATTCGGGACATATAGGTA-TCTTATGGAACATCTATGAGGTCCTTTGAGACACG
* * *
1806807 TACTTGATCCTTGGTATATGTATATGGTTCTTAAGGAATTT
65 TACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
1806848 ATATGTGGTC
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 87 0.96
106 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (105 bp):
TCTACGCGGTCATTCGGGACATATAGGTATCTTATGGAACATCTATGAGGTCCTTTGAGACACGT
ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
Found at i:1806922 original size:23 final size:24
Alignment explanation
Indices: 1806877--1806922 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1806867 AATCTTATAT
*
1806877 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTATACGC
*
1806901 GGCACTTCGGTGC-AATTATACG
1 GGCACTACGGTGCAAATTATACG
1806923 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTATACGC
Found at i:1813785 original size:19 final size:19
Alignment explanation
Indices: 1813734--1813787 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
1813724 CGAAACCGGT
*
1813734 TTTTTCGGTTCGGTTCAGG
1 TTTTTCGGTTCGGTTCGGG
*
1813753 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
1813770 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
1813788 TTCGGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.06, C:0.15, G:0.31, T:0.48
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:1814149 original size:20 final size:20
Alignment explanation
Indices: 1814124--1814172 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1814114 GTATGTGTTG
1814124 GTTGAATTTGTAGAAATTTC
1 GTTGAATTTGTAGAAATTTC
1814144 GTTGAATTTGTAGAAATTTC
1 GTTGAATTTGTAGAAATTTC
*
1814164 ATTGAATTT
1 GTTGAATTT
1814173 CTTTGTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (20 bp):
GTTGAATTTGTAGAAATTTC
Found at i:1818838 original size:45 final size:45
Alignment explanation
Indices: 1818768--1818958 Score: 242
Period size: 45 Copynumber: 4.1 Consensus size: 45
1818758 TTTATTTTCG
*
1818768 TTTTTCGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTCGAA-AAA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
* *
1818815 TTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGGTCCGT-
1 TTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGT--TTA
1818861 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTCGAA-AAA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
* * *
1818908 TTTTT-TAAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAAA-AAGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1818954 TTTTT
1 TTTTT
1818959 GTGAATAACA
Statistics
Matches: 129, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
45 58 0.45
46 24 0.19
47 17 0.13
48 30 0.23
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (45 bp):
TTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
Found at i:1818927 original size:93 final size:93
Alignment explanation
Indices: 1818768--1818948 Score: 317
Period size: 93 Copynumber: 1.9 Consensus size: 93
1818758 TTTATTTTCG
* *
1818768 TTTTTCGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCAAACAAGCATGC
1818833 GAACTAGATATCATGCGGTTAGGTCCGT
66 GAACTAGATATCATGCGGTTAGGTCCGT
* *
1818861 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTAAATAAGCATGC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCAAACAAGCATGC
*
1818926 GAATTAGATATCATGCGGTTAGG
66 GAACTAGATATCATGCGGTTAGG
1818949 ATTTCTTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (93 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCAAACAAGCATGC
GAACTAGATATCATGCGGTTAGGTCCGT
Found at i:1828604 original size:31 final size:32
Alignment explanation
Indices: 1828568--1828741 Score: 142
Period size: 32 Copynumber: 5.4 Consensus size: 32
1828558 TTCGCCTGAA
* *
1828568 AAGAAATGAAAAAAGAAAAAGA-AAAAAAAGG
1 AAGAAATGAAAAAAGAAAAAAATAAAAAAAAG
* *
1828599 GAGAAATGAAAAAATAAAAAAATAAAAAAAAG
1 AAGAAATGAAAAAAGAAAAAAATAAAAAAAAG
*
1828631 AAGAAATGAAAAAATG-AAAAAATATAAGAAAAG
1 AAGAAATGAAAAAA-GAAAAAAATA-AAAAAAAG
* * * *
1828664 AAAAAATGATGAAAATGAAAAGAA-AAAAAAATG
1 AAGAAATGA--AAAAAGAAAAAAATAAAAAAAAG
* * * **
1828697 AAAAAAAGAAGAAAAGAAAAAAATGATGAAAAG
1 AAGAAATGAA-AAAAGAAAAAAATAAAAAAAAG
1828730 AA-AAA-GAAAAAA
1 AAGAAATGAAAAAA
1828742 TGGAATAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
30 4 0.03
31 23 0.20
32 42 0.36
33 36 0.31
34 2 0.02
35 9 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (32 bp):
AAGAAATGAAAAAAGAAAAAAATAAAAAAAAG
Found at i:1828610 original size:16 final size:16
Alignment explanation
Indices: 1828568--1828734 Score: 88
Period size: 16 Copynumber: 10.8 Consensus size: 16
1828558 TTCGCCTGAA
1828568 AAGAAATG-AAAAAAG
1 AAGAAATGAAAAAAAG
1828583 AA-AAA-GAAAAAAAAGG
1 AAGAAATG-AAAAAAA-G
*
1828599 GAGAAATGAAAAAATA-
1 AAGAAATGAAAAAA-AG
* *
1828615 AAAAAATAAAAAAAAG
1 AAGAAATGAAAAAAAG
*
1828631 AAGAAATGAAAAAATG
1 AAGAAATGAAAAAAAG
* *
1828647 -A-AAA--AATATAAG
1 AAGAAATGAAAAAAAG
*
1828659 -A-AAA-GAAAAAATG
1 AAGAAATGAAAAAAAG
*
1828672 ATGAAAATGAAAAGAAA-
1 AAG-AAATGAAAA-AAAG
*
1828689 AAAAAATGAAAAAAAG
1 AAGAAATGAAAAAAAG
*
1828705 AAGAAAAGAAAAAAATG
1 AAGAAATGAAAAAAA-G
* *
1828722 ATGAAAAGAAAAA
1 AAGAAATGAAAAA
1828735 GAAAAAATGG
Statistics
Matches: 117, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
12 9 0.08
13 6 0.05
14 6 0.05
15 13 0.11
16 51 0.44
17 28 0.24
18 4 0.03
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (16 bp):
AAGAAATGAAAAAAAG
Found at i:1828619 original size:32 final size:32
Alignment explanation
Indices: 1828568--1828742 Score: 142
Period size: 33 Copynumber: 5.5 Consensus size: 32
1828558 TTCGCCTGAA
* * *
1828568 AAGAAATGAAAAAAGAAAAAGA-AAAAAAAGG
1 AAGAAATGAAAAAATAAAAAAATAAAAAAAAG
*
1828599 GAGAAATGAAAAAATAAAAAAATAAAAAAAAG
1 AAGAAATGAAAAAATAAAAAAATAAAAAAAAG
* *
1828631 AAGAAATGAAAAAATGAAAAAATATAAGAAAAG
1 AAGAAATGAAAAAATAAAAAAATA-AAAAAAAG
* * * *
1828664 AAAAAATGATGAAAATGAAAAGAA-AAAAAAATG
1 AAGAAATGA-AAAAAT-AAAAAAATAAAAAAAAG
* * * * **
1828697 AAAAAAAGAAGAAAAGAAAAAAATGATGAAAAG
1 AAGAAATGAA-AAAATAAAAAAATAAAAAAAAG
1828730 AA-AAA-GAAAAAAT
1 AAGAAATGAAAAAAT
1828743 GGAATAAAAG
Statistics
Matches: 116, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
30 4 0.03
31 22 0.19
32 39 0.34
33 40 0.34
34 6 0.05
35 5 0.04
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (32 bp):
AAGAAATGAAAAAATAAAAAAATAAAAAAAAG
Found at i:1828643 original size:25 final size:26
Alignment explanation
Indices: 1828643--1828722 Score: 53
Period size: 22 Copynumber: 3.2 Consensus size: 26
1828633 GAAATGAAAA
* * *
1828643 AATGAAAAAATATAAGAAAAGAAAAA
1 AATGAAAAAAAAGAAGAAATGAAAAA
**
1828669 ATGATGAAAATGAA-AAGAAA---AAAA
1 A--ATGAAAAAAAAGAAGAAATGAAAAA
*
1828693 AATG-AAAAAAAGAAGAAAAGAAAAA
1 AATGAAAAAAAAGAAGAAATGAAAAA
1828718 AATGA
1 AATGA
1828723 TGAAAAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
21 5 0.12
22 9 0.21
24 5 0.12
25 8 0.19
26 1 0.02
27 6 0.14
28 8 0.19
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (26 bp):
AATGAAAAAAAAGAAGAAATGAAAAA
Found at i:1828693 original size:50 final size:50
Alignment explanation
Indices: 1828565--1828741 Score: 174
Period size: 50 Copynumber: 3.6 Consensus size: 50
1828555 TATTTCGCCT
* * * * *
1828565 GAAAAGAAATGA-AAAAAGAAAAAG-AAAAAAAAGGGAGAAATGAA-AAAA
1 GAAAA-AAATGATGAAAAGAAAAAGAAAAAAAAATGAAAAAAAGAAGAAAA
* *
1828613 TAAAAAAAT-A--AAAA-AAAGAAGAAATGAAAAAATGAAAAAATATAAGAAAA
1 GAAAAAAATGATGAAAAGAAA-AAGAAA--AAAAAATGAAAAAA-AGAAGAAAA
1828663 G-AAAAAATGATGAAAATG-AAAAGAAAAAAAAATGAAAAAAAGAAGAAAA
1 GAAAAAAATGATGAAAA-GAAAAAGAAAAAAAAATGAAAAAAAGAAGAAAA
1828712 GAAAAAAATGATGAAAAGAAAAAGAAAAAA
1 GAAAAAAATGATGAAAAGAAAAAGAAAAAA
1828742 TGGAATAAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
44 3 0.03
45 7 0.06
46 3 0.03
47 4 0.04
48 15 0.14
49 19 0.18
50 45 0.42
52 10 0.09
53 2 0.02
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (50 bp):
GAAAAAAATGATGAAAAGAAAAAGAAAAAAAAATGAAAAAAAGAAGAAAA
Found at i:1828728 original size:25 final size:25
Alignment explanation
Indices: 1828565--1828741 Score: 131
Period size: 25 Copynumber: 7.3 Consensus size: 25
1828555 TATTTCGCCT
1828565 GAAAAGAAATGAA-AAAAG-A-AAAA
1 GAAAA-AAATGAAGAAAAGAAGAAAA
* * *
1828588 GAAAAAAAAGGGAGAAATGAA-AAAA
1 G-AAAAAAATGAAGAAAAGAAGAAAA
* * * *
1828613 TAAAAAAATAAAAAAAAGAAGAAAT
1 GAAAAAAATGAAGAAAAGAAGAAAA
* *
1828638 G-AAAAAATGAAAAAATATAAGAAAA
1 GAAAAAAATGAAGAAA-AGAAGAAAA
*
1828663 G-AAAAAATGATGAAAATGAA-AAGAA
1 GAAAAAAATGAAGAAAA-GAAGAA-AA
*
1828688 -AAAAAAATGAAAAAAAGAAGAAAA
1 GAAAAAAATGAAGAAAAGAAGAAAA
*
1828712 GAAAAAAATGATGAAAAG-A-AAAA
1 GAAAAAAATGAAGAAAAGAAGAAAA
1828735 GAAAAAA
1 GAAAAAA
1828742 TGGAATAAAA
Statistics
Matches: 123, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
23 17 0.14
24 44 0.36
25 62 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (25 bp):
GAAAAAAATGAAGAAAAGAAGAAAA
Found at i:1829811 original size:16 final size:17
Alignment explanation
Indices: 1829776--1829808 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1829766 GTTTCCCAGG
1829776 GATAGTTGAAGATTGAA
1 GATAGTTGAAGATTGAA
1829793 GATA-TTGAAGCATTGA
1 GATAGTTGAAG-ATTGA
1829809 GATGAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (17 bp):
GATAGTTGAAGATTGAA
Found at i:1830083 original size:37 final size:36
Alignment explanation
Indices: 1830029--1830100 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
1830019 AAACAGGTCA
*
1830029 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAACC
*
1830065 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGAAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGAAAAC
1830101 TCATTTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAACC
Found at i:1830292 original size:56 final size:55
Alignment explanation
Indices: 1830115--1830364 Score: 266
Period size: 55 Copynumber: 4.6 Consensus size: 55
1830105 TTTATGAAGA
* * *
1830115 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACATTTTA-TGAAGA---
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATTT
* *
1830166 TCGAGTCCTATACTCTCTGAAGGAATAGGGAACGGAC-C-TGTTTATTGAAGATTT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGT-TTTATTGAAGATTT
* *
1830220 TCTGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGT
1 TC-GAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATT-T
* * * ** *
1830277 TCAAGTCTTATACTCTCTGAACGAATAGAGAGTAGACACATTTTA-TGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATT-T
1830332 TCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 TCGAGTCTTATACTCT-CTGAAGGAATAGGGAGC
1830365 AGGCTCGTCA
Statistics
Matches: 172, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
49 1 0.01
50 5 0.03
51 41 0.24
54 3 0.02
55 68 0.40
56 49 0.28
57 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (55 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATTT
Found at i:1830352 original size:111 final size:109
Alignment explanation
Indices: 1830115--1830394 Score: 274
Period size: 111 Copynumber: 2.6 Consensus size: 109
1830105 TTTATGAAGA
* * * * *
1830115 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACATTTTA-TGAAGA---TCGAGTCCTA
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATTTTCAAGTCTTA
* * *
1830176 TACTCTCTGAAGGAATAGGGAACGGACCTGTTTATTGAAGATTT
66 TACTCTCTGAACGAATAGAGAACAGACCTGTTTATTGAAGATTT
* *
1830220 TCTGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCAAGTC
1 TC-GAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATT-TTCAAGTC
**
1830284 TTATACTCTCTGAACGAATAGAGAGTAGACACAT-TTTA-TGAAGATTGT
63 TTATACTCTCTGAACGAATAGAGAACAGAC-C-TGTTTATTGAAGATT-T
* **
1830332 TCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGG-CTCGTCAT-TTGAAGATTTTTCAAGTC
1 TCGAGTCTTATACTCT-CTGAAGGAATAGGGAGC-GGACACGTTTTATTGAAGA-TTTTCAAGTC
1830394 T
63 T
1830395 AATTTATCCT
Statistics
Matches: 145, Mismatches: 16, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
105 2 0.01
106 37 0.26
107 6 0.04
110 17 0.12
111 71 0.49
112 11 0.08
113 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (109 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATTGAAGATTTTCAAGTCTTA
TACTCTCTGAACGAATAGAGAACAGACCTGTTTATTGAAGATTT
Found at i:1830381 original size:55 final size:54
Alignment explanation
Indices: 1830118--1830394 Score: 189
Period size: 55 Copynumber: 5.1 Consensus size: 54
1830108 ATGAAGATCG
* * * * *
1830118 AGTCCTATACTCTCTGAAAGAATAGGGAGC-GGACACATTTTATGAAGA----TCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTTT-TGAAGATTGTTCA
* * * *
1830169 AGTCCTATACTCTCTGAAGGAATAGGGAAC-GG-ACCTGTTTATTGAAGATT-TTCTG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCA-C-GTTT-TTGAAGATTGTTC-A
*
1830224 AGT-TCTATACTCTCTGAAGGAATAGAGAGC-GGACCCGTTTTATTGAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGG-CACG-TTT-TTGAAGATTGTTCA
* * * * *
1830280 AGTCTTATACTCTCTGAACGAATAGAGAGTAGACACATTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTT-TGAAGATTGTTCA
* * * *
1830335 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGGCACGT-TTTTGAAGATTGTTCA
1830390 AGTCT
1 AGTCT
1830395 AATTTATCCT
Statistics
Matches: 186, Mismatches: 23, Indels: 30
0.78 0.10 0.13
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 39 0.21
52 1 0.01
54 4 0.02
55 91 0.49
56 44 0.24
57 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (54 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTTTGAAGATTGTTCA
Found at i:1833554 original size:19 final size:19
Alignment explanation
Indices: 1833532--1833580 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1833522 TCTCTCATTT
*
1833532 TTTATTTAAATTACTTTTA
1 TTTATTTAAATCACTTTTA
* *
1833551 TTTATTTTAATCGCTTTTA
1 TTTATTTAAATCACTTTTA
*
1833570 -CTATTTAAATC
1 TTTATTTAAATC
1833581 TTATACTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATTTAAATCACTTTTA
Found at i:1834253 original size:21 final size:22
Alignment explanation
Indices: 1834209--1834263 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1834199 TACTCGGGGT
*
1834209 AGTATCGATACCCCAGAATAGG
1 AGTATCGATACTCCAGAATAGG
* *
1834231 AGTATCGATACTCTA-ACTAGG
1 AGTATCGATACTCCAGAATAGG
1834252 AGTATCGATACT
1 AGTATCGATACT
1834264 ACCTAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
AGTATCGATACTCCAGAATAGG
Found at i:1834342 original size:20 final size:20
Alignment explanation
Indices: 1834317--1834375 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1834307 TTGTTGGTGG
* *
1834317 GTATCGATACTTAAGGGTCA
1 GTATCGATACTAAAGGGTAA
*
1834337 GTATCGATACTAAATGGTTAA
1 GTATCGATACTAAA-GGGTAA
* *
1834358 ATATCGATACTGAAGGGT
1 GTATCGATACTAAAGGGT
1834376 TCAACGGTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (20 bp):
GTATCGATACTAAAGGGTAA
Found at i:1834376 original size:21 final size:21
Alignment explanation
Indices: 1834318--1834376 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
1834308 TGTTGGTGGG
* * *
1834318 TATCGATACTTAAGGG-TCAG
1 TATCGATACTAAAGGGTTAAA
*
1834338 TATCGATACTAAATGGTTAAA
1 TATCGATACTAAAGGGTTAAA
*
1834359 TATCGATACTGAAGGGTT
1 TATCGATACTAAAGGGTT
1834377 CAACGGTACC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (21 bp):
TATCGATACTAAAGGGTTAAA
Found at i:1839461 original size:19 final size:18
Alignment explanation
Indices: 1839408--1839472 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
1839398 CAATTTAAAC
*
1839408 TATAATAAAAAAATATAAA
1 TATAAT-AAAAAATATAAT
*
1839427 AATACA-AATAAAATATAAT
1 TATA-ATAA-AAAATATAAT
**
1839446 TATAATAAAAATATATTTT
1 TATAATAAAAA-ATATAAT
1839465 TATAATAA
1 TATAATAA
1839473 CTCACTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.16
19 30 0.81
20 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAATAAAAAATATAAT
Found at i:1847752 original size:30 final size:34
Alignment explanation
Indices: 1847688--1847757 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 34
1847678 TACTCTGAAC
*
1847688 AATTTAAATTCTTATATATCGTTTATTTTTATTAA
1 AATTTAAATTCTTATATATC-TTTATTATTATTAA
1847723 AATTTAAATTC-T-TATAT-TTT-TTATTATTAA
1 AATTTAAATTCTTATATATCTTTATTATTATTAA
1847753 AATTT
1 AATTT
1847758 TACTGATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 14 0.41
31 3 0.09
33 5 0.15
34 1 0.03
35 11 0.32
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (34 bp):
AATTTAAATTCTTATATATCTTTATTATTATTAA
Found at i:1856425 original size:22 final size:22
Alignment explanation
Indices: 1856364--1856412 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1856354 ATGTGAAATT
*
1856364 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAATGACCTATGAATA
1856386 TGTCCCGAATGACCTATGAATA
1 TGTCCCGAATGACCTATGAATA
1856408 TGTCC
1 TGTCC
1856413 TGAAGTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (22 bp):
TGTCCCGAATGACCTATGAATA
Found at i:1859533 original size:65 final size:64
Alignment explanation
Indices: 1859435--1859590 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 64
1859425 ATAAGACCTA
* * * ***
1859435 GTGCATCGGTACACT-AAATACATTCGATGTTTCAA-AAGAGCCAGGAGTGTATCGATGCATGGT
1 GTGCATCGATACA-TAAAATGCATTCGATGTTTCAATAA-AACCAGGAGCACATCGATGCATGGT
1859498 CT
64 -T
* *
1859500 GTGCATCGATACATAAAATGCATTTGATGTTTCAATAAAATCAGGAGCACATCGATGCATGGTT
1 GTGCATCGATACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGCACATCGATGCATGGTT
*
1859564 GTGCATC-AGTACACAAAATGCATTCGA
1 GTGCATCGA-TACATAAAATGCATTCGA
1859591 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 25 0.32
65 50 0.64
66 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGATACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGCACATCGATGCATGGTT
Found at i:1859949 original size:13 final size:13
Alignment explanation
Indices: 1859931--1859963 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1859921 TAAGATTTTC
1859931 TTTGAAAATCATT
1 TTTGAAAATCATT
1859944 TTTG-AAATCATT
1 TTTGAAAATCATT
1859956 TTTGAAAA
1 TTTGAAAA
1859964 ATTACTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:1862403 original size:44 final size:44
Alignment explanation
Indices: 1862301--1862404 Score: 154
Period size: 44 Copynumber: 2.4 Consensus size: 44
1862291 TGCACTGCAG
* *
1862301 AGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTTCAT
1 AGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTTCAT
* * * *
1862345 AGTGTATCGATGCATATTTAAGGGATGCATCGGTACACTTTTAT
1 AGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTTCAT
1862389 AGTGTATCGATGCATA
1 AGTGTATCGATGCATA
1862405 GTGCTCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
AGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTTCAT
Found at i:1879646 original size:14 final size:14
Alignment explanation
Indices: 1879627--1879655 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1879617 TAGCAATATT
1879627 CTCCGCCCGAGGAG
1 CTCCGCCCGAGGAG
1879641 CTCCGCCCGAGGAG
1 CTCCGCCCGAGGAG
1879655 C
1 C
1879656 GTAAACCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.34, T:0.07
Consensus pattern (14 bp):
CTCCGCCCGAGGAG
Found at i:1879711 original size:21 final size:21
Alignment explanation
Indices: 1879685--1879728 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1879675 TTGTTAATAG
1879685 CTTCCTCTGGTACCTCCGGAA
1 CTTCCTCTGGTACCTCCGGAA
1879706 CTTCCTCTGGTACCTCCGGAA
1 CTTCCTCTGGTACCTCCGGAA
1879727 CT
1 CT
1879729 ACCGTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.39, G:0.18, T:0.30
Consensus pattern (21 bp):
CTTCCTCTGGTACCTCCGGAA
Found at i:1882389 original size:19 final size:19
Alignment explanation
Indices: 1882365--1882410 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1882355 TAATGTAAAA
1882365 ATAAAAATCTACTATTAAC
1 ATAAAAATCTACTATTAAC
* *
1882384 ATAAAACTCTACTATTTAC
1 ATAAAAATCTACTATTAAC
*
1882403 ATGAAAAT
1 ATAAAAAT
1882411 AATCTCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAAAATCTACTATTAAC
Found at i:1887747 original size:27 final size:26
Alignment explanation
Indices: 1887717--1887789 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
1887707 CTAGCTGAGC
1887717 CTTTGGATCATCACTCTCCATC-TCAAG
1 CTTTGGATC-TCACTCTCC-TCTTCAAG
* *
1887744 CTTTGGACTCCCATTCTCCTCTTCAAG
1 CTTTGGA-TCTCACTCTCCTCTTCAAG
*
1887771 CTTTTGATCTCGACTCTCC
1 CTTTGGATCTC-ACTCTCC
1887790 GTTTGCAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.13
27 31 0.82
28 2 0.05
ACGTcount: A:0.16, C:0.36, G:0.11, T:0.37
Consensus pattern (26 bp):
CTTTGGATCTCACTCTCCTCTTCAAG
Found at i:1887813 original size:642 final size:640
Alignment explanation
Indices: 1886839--1888148 Score: 1813
Period size: 642 Copynumber: 2.0 Consensus size: 640
1886829 ATTCGTATTT
*
1886839 TCTTCTTGTTTTGATCTCTGCAAATGTTCTCCGATCAGTGGTACCTCTGTTACCAAGGGCTTATC
1 TCTTCTTGTTTTGAGCTCTGCAAATGTTCTCCGATCAGTGGTACCTCTGTTACCAAGGGCTTATC
* *
1886904 TTCCACCAACATGTCACTTTCTTCAACTACTCCATGAACAGATGCAGCCACGAAATCACTAATAT
66 TTCCACCAACATGTCAATTTCTTCAACCACTCCATGAACAGATGCAGCCACGAAATCACTAATAT
* * *** * * * *
1886969 CATCTTTTAACTTCAACGTGCACTCATTCTCACTATCACCATGGTCCACTACATCTTCAACTTTC
131 CATCCTTAAACTTCAACCCACACTCAATCTCACCACCACCATGATCCACTACATCTTCAACTTTC
* *
1887034 TTATGCATGTTATCCTCTTGATTATCATTCACTAGCTGAGCCTTATGGTCATCACTCTCCTCCTC
196 TTATGCATGTCATCCTCTTGATTATCAGTCACTAGCTGAGCCTTATGGTCATCACTCTCCTCCTC
* * *
1887099 AAGCTTTGAACTCCCATTCTTCACTTCAAGATTTCGATCTGGACTCTCCATTTGCATGTTGGAAT
261 AAGCTTTGAACTCCCATTCTCCACTTCAAGATTTCGATCTCGACTCTCCATTTGCAAGTTGGAAT
* * *
1887164 TCACATTCTCTTCTTGTTTCAAGCTCTGCAAATGTTCTCCGGTCAGAGGTACTTCTGTTACCG-A
326 TCACATTCTCTTCTTGTTTCAAGCTATGCAAATGTTCTCCGATCAGAGGTACCTCTGTTACCGCA
*
1887228 GGCCTTATCATCCACCAACATGTCACTTTCTTCAAT-TACTCCATAACCAGAT-TCAGCCACACA
391 -GCCTTATCATCCACCAACATGCCACTTTCTTCAATCT-CTCCATAACCAGATGT-AGCCACACA
* * * * * *
1887291 ATCACTGATATCAT-TTTTAATTGTCAACTCACACTCCTTATTCTCACCACCAATA-CGATCCCC
453 ATCACTAATATCATCTTTAAACT-TCAACCCACACTCCTCATTCTCACCACCAACATC-ATCCCC
* * * * *
1887354 AATATCTTTAACATTCTTATGGATGTCATCCTGTTGATTCTCATTCTCTATCCGAGTCTTAGGAT
516 AACATCTTTAACATTCTTATGAATGTCATCCTCTTGATTCTCATTCTCTAGCCGAGCCTTAGGAT
* * *
1887419 CATC-ACTCTCCACTTCAAG-ATT-T-T-GACTCTCAGTTTGCATGTTGGACTTCACATTC
581 CA-CGACTCTCCACCTCAAGCATTATCTCGACTCTCAGTTTGCATGTTGGAATTCACAATC
*
1887475 TCTTCTTGTTTTGAGCTTTGCAAATGTTCTCCGATCAGTGGTACCTCTGTTACCACA-GGCTTAT
1 TCTTCTTGTTTTGAGCTCTGCAAATGTTCTCCGATCAGTGGTACCTCTGTTACCA-AGGGCTTAT
* * *
1887539 TTTCCGCC-ACAATGTCAATTTCTTCAACCACTCCATGACCAGATGCAGCCAC-ATAATCACTAA
65 CTTCCACCAAC-ATGTCAATTTCTTCAACCACTCCATGAACAGATGCAGCCACGA-AATCACTAA
*
1887602 TATCATCCTTAAACTTCAACCCACACCCCTTCTCAATCTCACCACCACCATGATCTACTACATCT
128 TATCATCCTTAAACTTCAACCCACA------CTCAATCTCACCACCACCATGATCCACTACATCT
* *
1887667 TCAACTTTCTTATGCATGTCATCCTCTTGATTCTCAGTCTCTAGCTGAGCCTT-TGGATCATCAC
187 TCAACTTTCTTATGCATGTCATCCTCTTGATTATCAGTCACTAGCTGAGCCTTATGG-TCATCAC
* * * * *
1887731 TCTCCAT-CTCAAGCTTTGGACTCCCATTCTCCTCTTCAAGCTTTTGATCTCGACTCTCCGTTTG
251 TCTCC-TCCTCAAGCTTTGAACTCCCATTCTCCACTTCAAGATTTCGATCTCGACTCTCCATTTG
* * *
1887795 CAAGTTGGAATTCACATTCTCTTCTTGTTTCGAGCTATGCAAATGTTCTCCGATCAGTGGTCCCT
315 CAAGTTGGAATTCACATTCTCTTCTTGTTTCAAGCTATGCAAATGTTCTCCGATCAGAGGTACCT
**
1887860 CTGTTACCGCAGCCTTATCATCCACCAACATGCCACTTTCTTCAATCTCTCCATGGCCAGATGTA
380 CTGTTACCGCAGCCTTATCATCCACCAACATGCCACTTTCTTCAATCTCTCCATAACCAGATGTA
1887925 GCCACACAATCACTAATATCATCTTTAAACTTCAACCCACACTCCTCATTCTCACCACCAACATC
445 GCCACACAATCACTAATATCATCTTTAAACTTCAACCCACACTCCTCATTCTCACCACCAACATC
* * *
1887990 ATCCCCTACATCTTTAACTTTCTTATGAATGTCGTCCTCTTGATTCTCATTCTCTAGCCGAGCCT
510 ATCCCCAACATCTTTAACATTCTTATGAATGTCATCCTCTTGATTCTCATTCTCTAGCCGAGCCT
* * *
1888055 TAGGATCACGTCTCTCCACCTCAGGCATTCGATCTCGACTCTCCGTTTGCATGTTGGAATTCACA
575 TAGGATCACGACTCTCCACCTCAAGCATT--ATCTCGACTCTCAGTTTGCATGTTGGAATTCACA
1888120 ATC
638 ATC
*
1888123 TCTTCTTGTTTCGAGCTCTGCAAATG
1 TCTTCTTGTTTTGAGCTCTGCAAATG
1888149 CTGTCCAGTC
Statistics
Matches: 591, Mismatches: 60, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
635 3 0.01
636 133 0.23
637 1 0.00
641 4 0.01
642 381 0.64
643 14 0.02
646 1 0.00
647 1 0.00
648 53 0.09
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (640 bp):
TCTTCTTGTTTTGAGCTCTGCAAATGTTCTCCGATCAGTGGTACCTCTGTTACCAAGGGCTTATC
TTCCACCAACATGTCAATTTCTTCAACCACTCCATGAACAGATGCAGCCACGAAATCACTAATAT
CATCCTTAAACTTCAACCCACACTCAATCTCACCACCACCATGATCCACTACATCTTCAACTTTC
TTATGCATGTCATCCTCTTGATTATCAGTCACTAGCTGAGCCTTATGGTCATCACTCTCCTCCTC
AAGCTTTGAACTCCCATTCTCCACTTCAAGATTTCGATCTCGACTCTCCATTTGCAAGTTGGAAT
TCACATTCTCTTCTTGTTTCAAGCTATGCAAATGTTCTCCGATCAGAGGTACCTCTGTTACCGCA
GCCTTATCATCCACCAACATGCCACTTTCTTCAATCTCTCCATAACCAGATGTAGCCACACAATC
ACTAATATCATCTTTAAACTTCAACCCACACTCCTCATTCTCACCACCAACATCATCCCCAACAT
CTTTAACATTCTTATGAATGTCATCCTCTTGATTCTCATTCTCTAGCCGAGCCTTAGGATCACGA
CTCTCCACCTCAAGCATTATCTCGACTCTCAGTTTGCATGTTGGAATTCACAATC
Found at i:1891713 original size:25 final size:25
Alignment explanation
Indices: 1891679--1891742 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
1891669 CCTCCAATCG
* *
1891679 AACACTTTTGTTTCACGTTAACCAT
1 AACAATTTTGGTTCACGTTAACCAT
*
1891704 AACAATTTTGGTTCTCGTTAACCAT
1 AACAATTTTGGTTCACGTTAACCAT
1891729 AACAATTTTGGTTC
1 AACAATTTTGGTTC
1891743 CATCGCTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (25 bp):
AACAATTTTGGTTCACGTTAACCAT
Found at i:1892646 original size:150 final size:147
Alignment explanation
Indices: 1892466--1892763 Score: 537
Period size: 150 Copynumber: 2.0 Consensus size: 147
1892456 CATTCTTTCA
1892466 ACTCATTATCGTCTGACTTTAACTTATTTGAAT-ATATAAAAATCCAAAAATACTTTCAAATGTC
1 ACTCATTATCGTCTGACTTTAACTTATTTGAATCATATAAAAATCC-AAAATACTTTCAAATGTC
1892530 TTC-ATTGCTCAAATCTATTATTCAAAGAAGCAATTGCCATATCTACCACAAACCAAAAAATAAT
65 TTCAATTGCTCAAATCTATTATTCAAAGAAGCAATTGCCATATCTACCAC-AACCAAAAAATAAT
1892594 TGACTCTAAATGACTCTTC
129 TGACTCTAAATGACTCTTC
1892613 ACTCATTATCGTCTAATGACTTTAACTTATTTGAATCATATAAAAATCCAAAATACTTTCAAATG
1 ACTCATTATCGTC---TGACTTTAACTTATTTGAATCATATAAAAATCCAAAATACTTTCAAATG
1892678 TCTTCAATTGCTCAAATCTATTATTCAAAGAAGCAATTGCCATATCTACCACAACCAAAAAATAA
63 TCTTCAATTGCTCAAATCTATTATTCAAAGAAGCAATTGCCATATCTACCACAACCAAAAAATAA
1892743 TTGACTCTAAATGACTCTTC
128 TTGACTCTAAATGACTCTTC
1892763 A
1 A
1892764 GGCGATTCAA
Statistics
Matches: 146, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
147 13 0.09
150 75 0.51
151 58 0.40
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (147 bp):
ACTCATTATCGTCTGACTTTAACTTATTTGAATCATATAAAAATCCAAAATACTTTCAAATGTCT
TCAATTGCTCAAATCTATTATTCAAAGAAGCAATTGCCATATCTACCACAACCAAAAAATAATTG
ACTCTAAATGACTCTTC
Found at i:1898107 original size:21 final size:21
Alignment explanation
Indices: 1898083--1898143 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1898073 AACTTTGAAA
1898083 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1898104 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1898118 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1898139 AAATG
1 AAATG
1898144 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1898174 original size:37 final size:37
Alignment explanation
Indices: 1898075--1898193 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1898065 TGGCAACCAA
1898075 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1898112 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1898147 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1898184 -GTTGAAAAAT
1 CTTTGAAAAAT
1898194 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1902744 original size:36 final size:37
Alignment explanation
Indices: 1902691--1902774 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
1902681 TGGCAACCAA
*
1902691 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAAATGTTT
*
1902728 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
1902765 -GTTGAAAAAT
1 CTTTGAAAAAT
1902775 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:1912336 original size:15 final size:16
Alignment explanation
Indices: 1912308--1912337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1912298 ATCGATTTAG
1912308 TTAAAATTTATTTTTT
1 TTAAAATTTATTTTTT
1912324 TTAAAATTT-TTTTT
1 TTAAAATTTATTTTT
1912338 ACTACGGGCA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAAAATTTATTTTTT
Found at i:1912367 original size:11 final size:12
Alignment explanation
Indices: 1912351--1912380 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1912341 ACGGGCAATC
1912351 AAAATAGAATTA
1 AAAATAGAATTA
1912363 AAATATAGAATTA
1 AAA-ATAGAATTA
1912376 AAAAT
1 AAAAT
1912381 GTTACAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (12 bp):
AAAATAGAATTA
Found at i:1923117 original size:24 final size:24
Alignment explanation
Indices: 1923085--1923133 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1923075 ATGTACTTTA
1923085 TTTTATATTTATATAATGATAGTG
1 TTTTATATTTATATAATGATAGTG
1923109 TTTTATATTTATATAATGATAGTG
1 TTTTATATTTATATAATGATAGTG
1923133 T
1 T
1923134 GATGAGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTTATATTTATATAATGATAGTG
Found at i:1923524 original size:66 final size:66
Alignment explanation
Indices: 1923441--1923566 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
1923431 TACGTCTTGT
1923441 TAAATACATACCGGATAAATATATTCATGATTATCATAAGTAAAATATAACGATGAACGACCAGG
1 TAAATACATACCGGATAAATATATTCATGATTATCATAAGTAAAATATAACGATGAACGACCAGG
1923506 C
66 C
* * * * *
1923507 TAAATACTTACCTGATAAATATATTCATGATTATTATAAGTAAAATATATCGGTGAACGA
1 TAAATACATACCGGATAAATATATTCATGATTATCATAAGTAAAATATAACGATGAACGA
1923567 TCGGTGATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (66 bp):
TAAATACATACCGGATAAATATATTCATGATTATCATAAGTAAAATATAACGATGAACGACCAGG
C
Found at i:1924244 original size:32 final size:32
Alignment explanation
Indices: 1924194--1924257 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1924184 ATGAATATAG
* * *
1924194 TAGACAAATTCATGTATCAATGTGAATGAAAA
1 TAGACAAATTAATATATCAACGTGAATGAAAA
*
1924226 TAGATAAATTAATATATCAACGTGAATGAAAA
1 TAGACAAATTAATATATCAACGTGAATGAAAA
1924258 AATATACAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (32 bp):
TAGACAAATTAATATATCAACGTGAATGAAAA
Found at i:1924562 original size:21 final size:20
Alignment explanation
Indices: 1924536--1924586 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1924526 ACAGTAACTG
*
1924536 TGAGATTGATTACTATGACGA
1 TGAGATTGA-TACTATAACGA
*
1924557 TGAGATTGCATACTATAACGG
1 TGAGATTG-ATACTATAACGA
*
1924578 TAAGATTGA
1 TGAGATTGA
1924587 AATCAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (20 bp):
TGAGATTGATACTATAACGA
Found at i:1930748 original size:12 final size:12
Alignment explanation
Indices: 1930731--1930757 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1930721 TGTTTTAATC
1930731 TTAAAATAAATT
1 TTAAAATAAATT
1930743 TTAAAATAAATT
1 TTAAAATAAATT
1930755 TTA
1 TTA
1930758 CAAAGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAATAAATT
Found at i:1932627 original size:13 final size:13
Alignment explanation
Indices: 1932600--1932645 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1932590 ATAAATTTTT
1932600 TTATTATATTATA
1 TTATTATATTATA
1932613 TTATT-TATTATTA
1 TTATTATATTA-TA
1932626 TTATTAT-TTAT-
1 TTATTATATTATA
1932637 TTATT-TATT
1 TTATTATATT
1932646 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 6 0.20
13 15 0.50
14 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:1932632 original size:16 final size:15
Alignment explanation
Indices: 1932606--1932650 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1932596 TTTTTTATTA
1932606 TATTATATTATTTAT
1 TATTATATTATTTAT
1932621 TATTATTATTATTTATT
1 TATTA-TATTATTTA-T
*
1932638 TATT-TATTTTTTA
1 TATTATATTATTTA
1932651 ATTTTACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 13 0.48
16 9 0.33
17 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATATTATTTAT
Found at i:1932654 original size:20 final size:20
Alignment explanation
Indices: 1932600--1932641 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1932590 ATAAATTTTT
1932600 TTATTA-TATTATATTATTTA
1 TTATTATTATTAT-TTATTTA
1932620 TTATTATTATTATTTATTTA
1 TTATTATTATTATTTATTTA
1932640 TT
1 TT
1932642 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTATTATTATTTATTTA
Found at i:1938345 original size:55 final size:56
Alignment explanation
Indices: 1938209--1938366 Score: 158
Period size: 55 Copynumber: 2.8 Consensus size: 56
1938199 TTCAAAGTCA
* ** * * *
1938209 ATTTCAACTTCACAGCGAAGGATATTAAACTCGAAGTGACACAATTTGTTTGAAATTGG
1 ATTTCAACTTCACGGCGAAGGATATCCAACTC-AA--AACACAACTTGTTTCAAATTGG
* * *
1938268 ATTTCAACTCCACGACGGAGGATATCCAACTCAAAAC-CAACTT-TTTCAAGATTGG
1 ATTTCAACTTCACGGCGAAGGATATCCAACTCAAAACACAACTTGTTTCAA-ATTGG
* * *
1938323 ATTTCAACTTCACGGCGAAGGATATCCAATTCAAAGCTCAACTT
1 ATTTCAACTTCACGGCGAAGGATATCCAACTCAAAACACAACTT
1938367 CACGGCGAAG
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
54 5 0.06
55 42 0.51
56 8 0.10
58 2 0.02
59 26 0.31
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (56 bp):
ATTTCAACTTCACGGCGAAGGATATCCAACTCAAAACACAACTTGTTTCAAATTGG
Done.