Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_14 ID=scaffold_14-JGI_221_v2.0
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: 2042280
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64439 characters in sequence are not A, C, G, or T
File 6 of 7
Found at i:1477580 original size:37 final size:37
Alignment explanation
Indices: 1477502--1477595 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
1477492 GAACATTTAG
* * * * *
1477502 TAGAATTAATAGATATTGGTCATTTTAGCATATTTAG
1 TAGAATTAGTAGATATTGCTCATTTTAGCACATTCAA
1477539 TAGAATTAGTAGATATTGCTCATTTGT-GCACATTCAA
1 TAGAATTAGTAGATATTGCTCATTT-TAGCACATTCAA
* *
1477576 TAGAATCAGTGGATATTGCT
1 TAGAATTAGTAGATATTGCT
1477596 TGTTACAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
37 48 0.98
38 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (37 bp):
TAGAATTAGTAGATATTGCTCATTTTAGCACATTCAA
Found at i:1485253 original size:16 final size:16
Alignment explanation
Indices: 1485227--1485263 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1485217 GGATTTTCTC
1485227 AAAAA-TAAAAG-TAA
1 AAAAATTAAAAGTTAA
1485241 AATAAATTAAAAGTTAA
1 AA-AAATTAAAAGTTAA
1485258 AAAAAT
1 AAAAAT
1485264 CTTAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 3 0.15
16 10 0.50
17 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AAAAATTAAAAGTTAA
Found at i:1490577 original size:24 final size:23
Alignment explanation
Indices: 1490511--1490587 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 23
1490501 AGATATGTTT
* *
1490511 TCAAATGCAATTCAGATACAGAT
1 TCAAATGCAATTCAAATACAGAG
**
1490534 TCAAATATAATCTCAAATACAGAG
1 TCAAATGCAAT-TCAAATACAGAG
* * * *
1490558 TCATATGCAATATCACATACAAAA
1 TCAAATGCAAT-TCAAATACAGAG
1490582 TCAAAT
1 TCAAAT
1490588 CCTACCCCCA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 9 0.22
24 32 0.78
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (23 bp):
TCAAATGCAATTCAAATACAGAG
Found at i:1491808 original size:12 final size:12
Alignment explanation
Indices: 1491791--1491818 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1491781 AAGTGGACGT
1491791 GAAACAAAATGA
1 GAAACAAAATGA
1491803 GAAACAAAATGA
1 GAAACAAAATGA
1491815 GAAA
1 GAAA
1491819 AATGAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (12 bp):
GAAACAAAATGA
Found at i:1494956 original size:18 final size:18
Alignment explanation
Indices: 1494933--1494968 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1494923 TATACTAAAG
1494933 TTTTAATATTATAATAAT
1 TTTTAATATTATAATAAT
*
1494951 TTTTAATATTATATTAAT
1 TTTTAATATTATAATAAT
1494969 ACCAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAATATTATAATAAT
Found at i:1499262 original size:9 final size:9
Alignment explanation
Indices: 1499245--1499329 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
1499235 GTAGTGATTC
1499245 AATTCGGTT
1 AATTCGGTT
*
1499254 AATTTGGTT
1 AATTCGGTT
*
1499263 AATTCGGGT
1 AATTCGGTT
1499272 AATTCGGTT
1 AATTCGGTT
*
1499281 AATTCGGGT
1 AATTCGGTT
1499290 AA-TCTGGTT
1 AATTC-GGTT
*
1499299 AATCCGGTT
1 AATTCGGTT
*
1499308 AATTCGGGT
1 AATTCGGTT
1499317 AATTCGGTT
1 AATTCGGTT
1499326 AATT
1 AATT
1499330 TTTAACCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
8 2 0.03
9 61 0.95
10 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1501475 original size:35 final size:35
Alignment explanation
Indices: 1501429--1501512 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 35
1501419 GTTTGGTTGG
**
1501429 AAATGATCTACTGGGTCTACGAAGCGGCATCATGA
1 AAATGATCTACTGACTCTACGAAGCGGCATCATGA
* *
1501464 AAATGATCTACTGACTCTACGGAGCGGCATCATGG
1 AAATGATCTACTGACTCTACGAAGCGGCATCATGA
1501499 AAATGATCTACTGA
1 AAATGATCTACTGA
1501513 ATCTTGACCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (35 bp):
AAATGATCTACTGACTCTACGAAGCGGCATCATGA
Found at i:1501770 original size:30 final size:31
Alignment explanation
Indices: 1501734--1501803 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1501724 AGTAGTAATT
1501734 TAAAATTATATT-ACAAAAAATCAAATTAAA
1 TAAAATTATATTAACAAAAAATCAAATTAAA
*
1501764 -ATAAATTA-ATTAAACCAAAAATCAAATTAAA
1 TA-AAATTATATT-AACAAAAAATCAAATTAAA
1501795 TAAAATTAT
1 TAAAATTAT
1501804 CTAAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 4 0.12
30 6 0.18
31 23 0.68
32 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (31 bp):
TAAAATTATATTAACAAAAAATCAAATTAAA
Found at i:1501814 original size:30 final size:29
Alignment explanation
Indices: 1501734--1501815 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 29
1501724 AGTAGTAATT
* *
1501734 TAAAATTATATTACAAAAAATCAAATTAAA
1 TAAAATTAT-TAAAAAAAAATCAAATTAAA
*
1501764 -ATAAATTAATTAAACCAAAAATCAAATTAAA
1 TA-AAATT-ATTAAA-AAAAAATCAAATTAAA
1501795 TAAAATTATCTAAAAAAAAAT
1 TAAAATTAT-TAAAAAAAAAT
1501816 GTCCAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 1 0.02
30 15 0.35
31 26 0.60
32 1 0.02
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (29 bp):
TAAAATTATTAAAAAAAAATCAAATTAAA
Found at i:1502460 original size:18 final size:19
Alignment explanation
Indices: 1502412--1502463 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1502402 CTTTTAGAAA
1502412 TATATCGATACCTACTGAATT
1 TATATCGATACC-A-TGAATT
* *
1502433 T-TATCAATACCAT-ATTT
1 TATATCGATACCATGAATT
1502450 TATATCGATACCAT
1 TATATCGATACCAT
1502464 TTCTTCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
19 1 0.04
20 9 0.33
21 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATCGATACCATGAATT
Found at i:1512130 original size:21 final size:21
Alignment explanation
Indices: 1512104--1512147 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1512094 TATTTAAGAA
1512104 ATTTTTATTA-AATTATATATT
1 ATTTTTA-TAGAATTATATATT
*
1512125 ATTTTTATAGTATTATATATT
1 ATTTTTATAGAATTATATATT
1512146 AT
1 AT
1512148 GATTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATAGAATTATATATT
Found at i:1512469 original size:45 final size:44
Alignment explanation
Indices: 1512381--1512473 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 44
1512371 ATTACGACAT
1512381 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
1512425 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
1512470 CATT
1 CATT
1512474 ACAGCTCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:1512476 original size:16 final size:16
Alignment explanation
Indices: 1512455--1512494 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1512445 TTGAATTACT
1512455 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
*
1512471 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCC
1512487 ATTACAGT
1 ATTACAGT
1512495 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:1518157 original size:18 final size:18
Alignment explanation
Indices: 1518104--1518157 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
1518094 AAAATAAAAA
*
1518104 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAAATGAAT
* * *
1518122 AACGATTTGTAAATGAAT
1 AATGTTTTGAAAATGAAT
*
1518140 AATGTTTTGAAAACGAAT
1 AATGTTTTGAAAATGAAT
1518158 GACACAATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.37
Consensus pattern (18 bp):
AATGTTTTGAAAATGAAT
Found at i:1519113 original size:344 final size:344
Alignment explanation
Indices: 1518486--1519129 Score: 1144
Period size: 344 Copynumber: 1.9 Consensus size: 344
1518476 TGGTAAAACT
1518486 GATAAACACTGGTAGACACTGCGTCGTACGAAAACAAACTCTGAACTACTAAAACTATTTCCATA
1 GATAAACACTGGTAGACACTGCGTCGTACGAAAACAAACTCTGAACTACTAAAACTATTTCCATA
* *
1518551 AAACATCTGCTAATAACTATTGAACTGTAAACTGATTCATAAAACTTTTAATACATATAAGCACT
66 AAACATCTGCTAATAACTATTAAACTGTAAACTGATTCATAAAACTTTTAATACAGATAAGCACT
*
1518616 ACTAGACGATGAGCGCACGAGGTACTCGGGGACGGGGTACTAGAGGCCGAGGTAGAGGCCATAGA
131 ACTAGACGATGAGCGCACGAGGTACTCGCGGACGGGGTACTAGAGGCCGAGGTAGAGGCCATAGA
1518681 GGGGCTCGAGCTGAGTCCTCTTCACTGGGCAGTATGCCAAATCTAGACAATAGCGAGACGCCAGT
196 GGGGCTCGAGCTGAGTCCTCTTCACTGGGCAGTATGCCAAATCTAGACAATAGCGAGACGCCAGT
* ** *
1518746 GTCTCCTGTCACTGAGACTGGGTCACGTGATCGAGCGACTGGGGAAACACTCAGGTTAGTGTATA
261 GTCGCCTGTCACTGAGACTGGGTCACACGACCGAGCGACTGGGGAAACACTCAGGTTAGTGTATA
1518811 ATGATACTGTAATAAAATC
326 ATGATACTGTAATAAAATC
* * *
1518830 GATAAACACTGGTAGACATTGCGTTGTACGAAAACAAACTCTGAACTACTAAAACTGTTTCCATA
1 GATAAACACTGGTAGACACTGCGTCGTACGAAAACAAACTCTGAACTACTAAAACTATTTCCATA
1518895 AAACATCTGCTAATAACTATTAAACTGTAAACTGATTCATAAAACTTTTAATACAGATAAGCACT
66 AAACATCTGCTAATAACTATTAAACTGTAAACTGATTCATAAAACTTTTAATACAGATAAGCACT
* * *
1518960 ACTAGACGATGAGCGCATGAGGTACTCGCGGACGGGGTACTAGAGGCCGAGGTAGAGGTCGTAGA
131 ACTAGACGATGAGCGCACGAGGTACTCGCGGACGGGGTACTAGAGGCCGAGGTAGAGGCCATAGA
* * *
1519025 GGGGCTCGAGCTGAGTCCTCTTCACTGGGGAGTATGCCAAATCTAGACACTAGCGAGATGCCAGT
196 GGGGCTCGAGCTGAGTCCTCTTCACTGGGCAGTATGCCAAATCTAGACAATAGCGAGACGCCAGT
1519090 GTCGCCTGTCACTGAGACTGGGTCACACGACCGAGCGACT
261 GTCGCCTGTCACTGAGACTGGGTCACACGACCGAGCGACT
1519130 AGGAACGATG
Statistics
Matches: 284, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
344 284 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (344 bp):
GATAAACACTGGTAGACACTGCGTCGTACGAAAACAAACTCTGAACTACTAAAACTATTTCCATA
AAACATCTGCTAATAACTATTAAACTGTAAACTGATTCATAAAACTTTTAATACAGATAAGCACT
ACTAGACGATGAGCGCACGAGGTACTCGCGGACGGGGTACTAGAGGCCGAGGTAGAGGCCATAGA
GGGGCTCGAGCTGAGTCCTCTTCACTGGGCAGTATGCCAAATCTAGACAATAGCGAGACGCCAGT
GTCGCCTGTCACTGAGACTGGGTCACACGACCGAGCGACTGGGGAAACACTCAGGTTAGTGTATA
ATGATACTGTAATAAAATC
Found at i:1524428 original size:120 final size:120
Alignment explanation
Indices: 1524215--1524449 Score: 425
Period size: 120 Copynumber: 2.0 Consensus size: 120
1524205 CCAAGGTTGA
1524215 AACGTGAGGTTACTAATTTTGTGGGCAGATGTCTACTTGCCAGCAAGTTAAGTCTGAGCATCAGT
1 AACGTGAGGTTACTAATTTTGTGGGCAGATGTCTACTTGCCAGCAAGTTAAGTCTGAGCATCAGT
* *
1524280 TACCTTCGAGTTTGCTGCAGTCGGTTAAGATTCCTCTTTGGAAATAGGAACGCGT
66 TACCTTCGAGTTTACTGCAGCCGGTTAAGATTCCTCTTTGGAAATAGGAACGCGT
*
1524335 AACGTGAGGTTACTAATTTTGTGGGCAGATGTCTACTTGCCAGCAGGTTAAGTCTGAGCATCAGT
1 AACGTGAGGTTACTAATTTTGTGGGCAGATGTCTACTTGCCAGCAAGTTAAGTCTGAGCATCAGT
* *
1524400 TACCTTCGGGTTTACTGCAGCCGGTTAAGATTCCTCTTTGGAAATGGGAA
66 TACCTTCGAGTTTACTGCAGCCGGTTAAGATTCCTCTTTGGAAATAGGAA
1524450 TGCATAACTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (120 bp):
AACGTGAGGTTACTAATTTTGTGGGCAGATGTCTACTTGCCAGCAAGTTAAGTCTGAGCATCAGT
TACCTTCGAGTTTACTGCAGCCGGTTAAGATTCCTCTTTGGAAATAGGAACGCGT
Found at i:1533025 original size:50 final size:50
Alignment explanation
Indices: 1532924--1533108 Score: 208
Period size: 50 Copynumber: 3.6 Consensus size: 50
1532914 GGCATGAGAC
* *
1532924 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATGGG---TACTGA-G--ATGAGAGGT
*
1532980 CCCACGTAAGACCATGTCTGGGACATGGCATTGGTACTGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATGGGTACTGAGATGAGAGGT
* * * * * **
1533030 CCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAATT
1 CCCACGTAAGACCATGTCTGGGACATGGCATGGGTACTGAGATGAGAGGT
* *
1533080 CTCATGTAAGACCATGTCTGGGACATGGC
1 CCCACGTAAGACCATGTCTGGGACATGGC
1533109 TTTGGCATGT
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
50 76 0.67
52 1 0.01
53 5 0.04
56 32 0.28
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATGGGTACTGAGATGAGAGGT
Found at i:1533343 original size:20 final size:20
Alignment explanation
Indices: 1533318--1533356 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1533308 TGAGTTATTT
1533318 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
1533338 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
1533357 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:1545143 original size:43 final size:41
Alignment explanation
Indices: 1544988--1545144 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 41
1544978 TGTGATATCG
* * *
1544988 TGTAAGACCACGTCTGGGACGTTGGCATCAATTTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCTATTT--GA-TTACA
* * * *
1545032 TGTAAGACCATGTCTGGGACATTGGCGTCATATATAATTACA
1 TGTAAGACCACGTCTGGGACATTGGCATC-TATTTGATTACA
* * *
1545074 TGTAAGACC-CTGTCTAGGCCAGTGGCATCGTTATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATC--TATTTGATTACA
1545117 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
1545145 TGTACGAGCC
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 27 0.30
43 34 0.37
44 27 0.30
45 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACATTGGCATCTATTTGATTACA
Found at i:1550006 original size:24 final size:24
Alignment explanation
Indices: 1549961--1550007 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1549951 TATATATACC
1549961 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
1549985 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
1550008 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:1555695 original size:20 final size:21
Alignment explanation
Indices: 1555663--1555701 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1555653 TATTATTAAC
1555663 ATAATTTTATAA-TAAAATAA
1 ATAATTTTATAATTAAAATAA
1555683 ATAATATTT-TAATTAAAAT
1 ATAAT-TTTATAATTAAAAT
1555702 TTATTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTTTATAATTAAAATAA
Found at i:1566189 original size:12 final size:12
Alignment explanation
Indices: 1566172--1566197 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1566162 TGAGTTGCAT
1566172 GGCCTAACACAC
1 GGCCTAACACAC
1566184 GGCCTAACACAC
1 GGCCTAACACAC
1566196 GG
1 GG
1566198 GCATGTGGAG
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:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (12 bp):
GGCCTAACACAC
Found at i:1569241 original size:28 final size:28
Alignment explanation
Indices: 1569201--1569267 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
1569191 ATCGTTGCTC
1569201 ACACGAGCTGTGGGTC-GAAATGTAAGCT
1 ACACGAGCTGTGGGTCAG-AATGTAAGCT
1569229 ACACGAGCTGTGGGTCAGAATGTAAGCT
1 ACACGAGCTGTGGGTCAGAATGTAAGCT
1569257 ACACGATGCTG
1 ACACGA-GCTG
1569268 CTCACACGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
28 32 0.86
29 5 0.14
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.21
Consensus pattern (28 bp):
ACACGAGCTGTGGGTCAGAATGTAAGCT
Found at i:1575022 original size:81 final size:80
Alignment explanation
Indices: 1574883--1575037 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 80
1574873 CAGAGTACAA
1574883 GAGAATAAAGATCTCCTTCTTCCCCAAGAAAAACCTAAGCATTAGCCTAGTCTCATTCTCATTCT
1 GAGAATAAAGATCTCCTTCTTCCCCAAGAAAAACCTAAGCATTAGCCTAGTCTCATTCTCATTCT
*
1574948 CTTTCTCTTGCTTTT
66 CCTTCTCTTGCTTTT
* * ** *
1574963 GAGACTAAAGATCTCCTTCTTCCTCAAGAAAAAACCTAAGGGTTAGCCTAGTCTCATTCTTATTC
1 GAGAATAAAGATCTCCTTCTTCCCCAAG-AAAAACCTAAGCATTAGCCTAGTCTCATTCTCATTC
1575028 TCCTTCTCTT
65 TCCTTCTCTT
1575038 TCTTCTTCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 26 0.38
81 42 0.62
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.35
Consensus pattern (80 bp):
GAGAATAAAGATCTCCTTCTTCCCCAAGAAAAACCTAAGCATTAGCCTAGTCTCATTCTCATTCT
CCTTCTCTTGCTTTT
Found at i:1576667 original size:25 final size:25
Alignment explanation
Indices: 1576633--1576686 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1576623 ATCTCCTTTA
1576633 CATAAAAACAAAT-TACTTTATGACT
1 CATAAAAACAAATATACTTT-TGACT
1576658 CATAAAAACAAATATACTTTTGACT
1 CATAAAAACAAATATACTTTTGACT
1576683 CATA
1 CATA
1576687 CTTTTATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (25 bp):
CATAAAAACAAATATACTTTTGACT
Found at i:1579583 original size:20 final size:20
Alignment explanation
Indices: 1579566--1579608 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1579556 TTTCATATAG
*
1579566 TATCATAACTTATCATATCA
1 TATCATAACATATCATATCA
*
1579586 TATCATAACATATCATGTCA
1 TATCATAACATATCATATCA
1579606 TAT
1 TAT
1579609 AATGTCCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (20 bp):
TATCATAACATATCATATCA
Found at i:1579586 original size:5 final size:5
Alignment explanation
Indices: 1579566--1579608 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
1579556 TTTCATATAG
* * * *
1579566 TATCA TAACT TATCA TATCA TATCA TAACA TATCA TGTCA TAT
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TAT
1579609 AATGTCCTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (5 bp):
TATCA
Found at i:1579849 original size:20 final size:21
Alignment explanation
Indices: 1579826--1579864 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1579816 CCCACCCAAT
*
1579826 GCATATATA-AAATCACATTA
1 GCATACATACAAATCACATTA
*
1579846 GCATACATACATATCACAT
1 GCATACATACAAATCACAT
1579865 AGGTTGTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (21 bp):
GCATACATACAAATCACATTA
Found at i:1589445 original size:57 final size:57
Alignment explanation
Indices: 1589376--1589490 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
1589366 CATGTGAAGC
** *
1589376 TTAGTGTATGTACTATGTAATGTATGGTTTTAGCTATGGTTGATGTTATTTAGTTGA
1 TTAGTGTATGTACTAAATAATGTATGGTTTTAGCTATAGTTGATGTTATTTAGTTGA
** * *
1589433 TTAGTGTATGTACTAAATGGTGTGTGGTTTTCGCTATAGTTGATGTTATTTAGTTGA
1 TTAGTGTATGTACTAAATAATGTATGGTTTTAGCTATAGTTGATGTTATTTAGTTGA
1589490 T
1 T
1589491 GATTTCAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.22, C:0.04, G:0.25, T:0.49
Consensus pattern (57 bp):
TTAGTGTATGTACTAAATAATGTATGGTTTTAGCTATAGTTGATGTTATTTAGTTGA
Found at i:1599829 original size:47 final size:47
Alignment explanation
Indices: 1599775--1599868 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1599765 TATATCCCCA
1599775 CATAGAGTGTAGGGTTGGATGGAGATGATGTGTAGAGGCTGGATGGG
1 CATAGAGTGTAGGGTTGGATGGAGATGATGTGTAGAGGCTGGATGGG
*
1599822 CATAGAGTGTAGGGTTGGATGGAGATGGTGTGTAGAGGCTGGATGGG
1 CATAGAGTGTAGGGTTGGATGGAGATGATGTGTAGAGGCTGGATGGG
1599869 TAGGATTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.22, C:0.04, G:0.48, T:0.26
Consensus pattern (47 bp):
CATAGAGTGTAGGGTTGGATGGAGATGATGTGTAGAGGCTGGATGGG
Found at i:1599854 original size:23 final size:24
Alignment explanation
Indices: 1599781--1599867 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
1599771 CCCACATAGA
* *
1599781 GTGTAG-GGTTGGATGGAGATGAT
1 GTGTAGAGGCTGGATGGAGATGGT
* *
1599804 GTGTAGAGGCTGGATGG-GCATAGA
1 GTGTAGAGGCTGGATGGAG-ATGGT
*
1599828 GTGTAG-GGTTGGATGGAGATGGT
1 GTGTAGAGGCTGGATGGAGATGGT
1599851 GTGTAGAGGCTGGATGG
1 GTGTAGAGGCTGGATGG
1599868 GTAGGATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 25 0.48
24 27 0.52
ACGTcount: A:0.21, C:0.03, G:0.49, T:0.26
Consensus pattern (24 bp):
GTGTAGAGGCTGGATGGAGATGGT
Found at i:1600412 original size:18 final size:18
Alignment explanation
Indices: 1600383--1600445 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
1600373 AAGAAAACAT
*
1600383 TTTGAAATTGAATAACGA
1 TTTGAAAATGAATAACGA
* * *
1600401 TTTGTAAATGAATAATGT
1 TTTGAAAATGAATAACGA
*
1600419 TTTGAAAATGAACAACATGA
1 TTTGAAAATGAATAAC--GA
1600439 TTTGAAA
1 TTTGAAA
1600446 TTAACATAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 27 0.77
20 8 0.23
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
TTTGAAAATGAATAACGA
Found at i:1601592 original size:232 final size:235
Alignment explanation
Indices: 1601151--1601613 Score: 530
Period size: 232 Copynumber: 2.0 Consensus size: 235
1601141 AGAGTAACAA
* * **
1601151 ATTATATATTAATTATTATCAGATATTATTGTATATTATTCTAGTTGAAATATGCTCTAAGGCCC
1 ATTATATATTAATCATTATCAGATATTATTGTATATTATACTAGTACAAATATGCTCTAAGGCCC
* * *
1601216 TATACATTTTCTACATTTAAAAATTAGCCCTCCTATATTATATAATATTATACCGTATCATTTAG
66 TATACATTTTCTACATTTAAAAATTAGCCCTCCTATATTATATAATATTAAACCGTATCATTAAC
* * * * *
1601281 TATATAATATATTAAAAGGTTGTATATATATGTATCAATGATTAGACATTATAATATCATGTACT
131 TATACAATATATTAAAAGGTTGTATATATATGCACCAATGATTAAACATTATAATATCATGTAAT
* * *
1601346 ACTATATCTTTTATTATATTTTATA-ATATAATAGTTGTAC
196 ACTATATATTTTATTATAATCTATATA-ATAATAGTTGTAC
* * * *
1601386 ATTATATATTAATCATTATCATATATTATTGTTTATTATTATACTGGTACAAATATGCTTTAAGT
1 ATTATATATTAATCATTATCAGATATTATTG--TA-TATTATACTAGTACAAATATGCTCTAAGG
* * * * * * *
1601451 TCTTATACTTTTTGTTCATTTAAAAGTTAGCCCTCCTACTA-TAT-T-ATA-TAAAGC-TAT-AT
63 CCCTATACATTTTCTACATTTAAAAATTAGCCCTCCTA-TATTATATAATATTAAACCGTATCAT
* * * *
1601510 TAACTCATACAATATCTTAATA-GTT-TATATATATGCACCGATGATTAAATATTATAATATCAT
127 TAACT-ATACAATATATTAAAAGGTTGTATATATATGCACCAATGATTAAACATTATAATATCAT
*
1601573 GTAATATTATATATTTTATTATAATCTATATAATAATAGTT
191 GTAATACTATATATTTTATTATAATCTATATAATAATAGTT
1601614 ATATATGTAT
Statistics
Matches: 191, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
232 67 0.35
233 9 0.05
234 16 0.08
235 33 0.17
236 3 0.02
237 3 0.02
238 58 0.30
239 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (235 bp):
ATTATATATTAATCATTATCAGATATTATTGTATATTATACTAGTACAAATATGCTCTAAGGCCC
TATACATTTTCTACATTTAAAAATTAGCCCTCCTATATTATATAATATTAAACCGTATCATTAAC
TATACAATATATTAAAAGGTTGTATATATATGCACCAATGATTAAACATTATAATATCATGTAAT
ACTATATATTTTATTATAATCTATATAATAATAGTTGTAC
Found at i:1601929 original size:7 final size:7
Alignment explanation
Indices: 1601919--1602034 Score: 99
Period size: 7 Copynumber: 16.6 Consensus size: 7
1601909 AATCCTATAG
1601919 TCTCAAT
1 TCTCAAT
1601926 TCTCAAT
1 TCTCAAT
*
1601933 TTTCAAT
1 TCTCAAT
* *
1601940 CCTTAAT
1 TCTCAAT
*
1601947 TTTCAAT
1 TCTCAAT
*
1601954 TTTCAAT
1 TCTCAAT
*
1601961 TCTGAA-
1 TCTCAAT
1601967 TCTTCAAT
1 TC-TCAAT
*
1601975 GCTCAAT
1 TCTCAAT
1601982 TCTCAAT
1 TCTCAAT
**
1601989 AATCAAT
1 TCTCAAT
*
1601996 CCTCAAT
1 TCTCAAT
*
1602003 TCTTAAT
1 TCTCAAT
* *
1602010 TCTTAAA
1 TCTCAAT
1602017 TCTCAAT
1 TCTCAAT
1602024 TCTCAAT
1 TCTCAAT
1602031 TCTC
1 TCTC
1602035 TTTTAAATCT
Statistics
Matches: 86, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
6 2 0.02
7 83 0.97
8 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.44
Consensus pattern (7 bp):
TCTCAAT
Found at i:1610860 original size:14 final size:14
Alignment explanation
Indices: 1610841--1610878 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1610831 ATAGTAGTAC
1610841 ATTATATATTAATT
1 ATTATATATTAATT
*
1610855 ATTATATATTATTT
1 ATTATATATTAATT
*
1610869 TTTAT-TATTA
1 ATTATATATTA
1610879 TATTGGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATATATTAATT
Found at i:1619567 original size:23 final size:23
Alignment explanation
Indices: 1619493--1619567 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
1619483 AGTATTATTG
1619493 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
1619516 TTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1619539 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1619562 ACCAGT
1 ATCAGT
1619568 AAGGAACTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1622185 original size:23 final size:23
Alignment explanation
Indices: 1622154--1622229 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
1622144 AAAGTTATTG
1622154 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1622177 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1622200 ATCAGTGGTAACTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1622223 ACCAGTG
1 ATCAGTG
1622230 AGACACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1624590 original size:29 final size:29
Alignment explanation
Indices: 1624556--1624611 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1624546 CAGTTATTTC
*
1624556 TTTGGTGAACTATGTTCGCATATGTGTGT
1 TTTGGTGAACTATGTTCGCAAATGTGTGT
*
1624585 TTTGGTGAACTATGTTCGTAAATGTGT
1 TTTGGTGAACTATGTTCGCAAATGTGT
1624612 CTATTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.09, G:0.27, T:0.45
Consensus pattern (29 bp):
TTTGGTGAACTATGTTCGCAAATGTGTGT
Found at i:1630982 original size:27 final size:27
Alignment explanation
Indices: 1630942--1631092 Score: 106
Period size: 27 Copynumber: 5.3 Consensus size: 27
1630932 GGCTTGGGCC
**
1630942 GTAAAATTATCGAAATACCTTCGAAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* *
1630969 GTAAAATTAACGAAATACCCCCGATGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* * *
1630996 GTAAAATTATCAAAATACCCACGATACCCTTAATTG
1 GTAAAATTATCGAAATA--C-C----CCC-GAA-GG
* *
1631032 GTAAAATTAGCGAAATACCCTC-AATGG
1 GTAAAATTATCGAAATACCCCCGAA-GG
* *
1631059 GTAAAATTATCGAAATACCTCCGATGG
1 GTAAAATTATCGAAATACCCCCGAAGG
1631086 GTAAAAT
1 GTAAAAT
1631093 GACTGTAATG
Statistics
Matches: 97, Mismatches: 17, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
27 70 0.72
28 1 0.01
29 3 0.03
30 1 0.01
33 1 0.01
34 4 0.04
35 1 0.01
36 16 0.16
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCCCGAAGG
Found at i:1631023 original size:36 final size:36
Alignment explanation
Indices: 1630983--1631051 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
1630973 AATTAACGAA
* *
1630983 ATACCCCCGATGGGTAAAATTATCAAAATACCCACG
1 ATACCCCCAATGGGTAAAATTAGCAAAATACCCACG
** * *
1631019 ATACCCTTAATTGGTAAAATTAGCGAAATACCC
1 ATACCCCCAATGGGTAAAATTAGCAAAATACCC
1631052 TCAATGGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (36 bp):
ATACCCCCAATGGGTAAAATTAGCAAAATACCCACG
Found at i:1631140 original size:26 final size:27
Alignment explanation
Indices: 1631084--1631255 Score: 183
Period size: 27 Copynumber: 6.5 Consensus size: 27
1631074 TACCTCCGAT
1631084 GGGTAAAATGACTGTAATGCCCCTGTA
1 GGGTAAAATGACTGTAATGCCCCTGTA
1631111 GGGTAAAATGACTGTAATG-CCCTGTA
1 GGGTAAAATGACTGTAATGCCCCTGTA
*
1631137 GGGTAAAATGACCGTAATGCCCCTGTA
1 GGGTAAAATGACTGTAATGCCCCTGTA
* * **
1631164 GGTTAAAATGACCGTAATGCCCC-ACA
1 GGGTAAAATGACTGTAATGCCCCTGTA
* *
1631190 GGGCT-AAATGA-TCGAAATACCCCTGTA
1 GGG-TAAAATGACT-GTAATGCCCCTGTA
* * * * *
1631217 AGGTTAAATGACCGTAATGTCCCTGGA
1 GGGTAAAATGACTGTAATGCCCCTGTA
1631244 GGGT-AAATGACT
1 GGGTAAAATGACT
1631256 ATTTTGCCCC
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
26 50 0.41
27 71 0.59
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (27 bp):
GGGTAAAATGACTGTAATGCCCCTGTA
Found at i:1631146 original size:53 final size:52
Alignment explanation
Indices: 1631084--1631255 Score: 193
Period size: 53 Copynumber: 3.2 Consensus size: 52
1631074 TACCTCCGAT
* *
1631084 GGGTAAAATGACTGTAATGCCCCTGTAGGGTAAAATGACTGTAATGCCCTGTA
1 GGGT-AAATGACTGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCTGCA
* * **
1631137 GGGTAAAATGACCGTAATGCCCCTGTAGGTTAAAATGACCGTAATGCCCCACA
1 GGGT-AAATGACTGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCTGCA
* * * * *
1631190 GGGCTAAATGA-TCGAAATACCCCTGTAAGGTTAAATGACCGTAATGTCCCTGGA
1 GGG-TAAATGACT-GTAATGCCCCTGTAGGGTAAAATGACCGTAATG-CCCTGCA
1631244 GGGTAAATGACT
1 GGGTAAATGACT
1631256 ATTTTGCCCC
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
53 91 0.91
54 9 0.09
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (52 bp):
GGGTAAATGACTGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCTGCA
Found at i:1631327 original size:24 final size:24
Alignment explanation
Indices: 1631300--1631357 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1631290 CGTGATGTAA
1631300 ATGACT-AGTTTGTTTACGATTAGT
1 ATGACTGA-TTTGTTTACGATTAGT
** *
1631324 ATGACTGATTTGTTTGTGATTTGT
1 ATGACTGATTTGTTTACGATTAGT
1631348 ATGACTGATT
1 ATGACTGATT
1631358 CTGAGCATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (24 bp):
ATGACTGATTTGTTTACGATTAGT
Found at i:1631604 original size:31 final size:32
Alignment explanation
Indices: 1631526--1631604 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
1631516 TTTGTTGCGA
* *
1631526 TGCTACTGATGG-TTGTGTTCCAATCATATCAC
1 TGCTACTAATGGCTT-TGTGCCAATCATATCAC
*
1631558 TGCTACTAATGGCTTTGTGCCAATCATATTAC
1 TGCTACTAATGGCTTTGTGCCAATCATATCAC
*
1631590 TG-TACTTATGGCTTT
1 TGCTACTAATGGCTTT
1631605 TAGCCATTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 12 0.29
32 28 0.67
33 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (32 bp):
TGCTACTAATGGCTTTGTGCCAATCATATCAC
Found at i:1631620 original size:22 final size:22
Alignment explanation
Indices: 1631595--1631659 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
1631585 ATTACTGTAC
1631595 TTATGGCTTTTAGCCATTCTGT
1 TTATGGCTTTTAGCCATTCTGT
* * * *
1631617 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTTTTAGCCATTCTGT
* *
1631639 TTACGGCTCTTAGCCATTCTG
1 TTATGGCTTTTAGCCATTCTG
1631660 GTTACTAGCA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (22 bp):
TTATGGCTTTTAGCCATTCTGT
Found at i:1632361 original size:18 final size:18
Alignment explanation
Indices: 1632330--1632371 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1632320 AAAAATAAGG
*
1632330 TTTT-AAAGGTAATAACT
1 TTTTAAAAGGGAATAACT
*
1632347 TTTTAAAAGGGAATAGCT
1 TTTTAAAAGGGAATAACT
1632365 TTTTAAA
1 TTTTAAA
1632372 CCACGATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (18 bp):
TTTTAAAAGGGAATAACT
Found at i:1637656 original size:62 final size:62
Alignment explanation
Indices: 1637566--1637685 Score: 188
Period size: 62 Copynumber: 1.9 Consensus size: 62
1637556 GTACCTGGCC
1637566 GTGTGGCTTTGTACCACAAACAGTGAGTTACACAGCCTAAGCACACGCCCGTGTCCCTGGTT
1 GTGTGGCTTTGTACCACAAACAGTGAGTTACACAGCCTAAGCACACGCCCGTGTCCCTGGTT
* * **
1637628 GTGTGG-TCTTGTACCACAAACTGTGAGTTACACGGCCTGGGCACACGCCCGTGTCCCT
1 GTGTGGCT-TTGTACCACAAACAGTGAGTTACACAGCCTAAGCACACGCCCGTGTCCCT
1637686 TACCAGTGTG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.24
Consensus pattern (62 bp):
GTGTGGCTTTGTACCACAAACAGTGAGTTACACAGCCTAAGCACACGCCCGTGTCCCTGGTT
Found at i:1638462 original size:173 final size:173
Alignment explanation
Indices: 1638163--1638481 Score: 462
Period size: 173 Copynumber: 1.8 Consensus size: 173
1638153 CATGTCCCTT
* * * * *
1638163 ACCCGTGCGAACTCTGCACTAATATGGCCACACACAGCCTAGACACAGGACCATGTGCCTTGCCT
1 ACCCGTCCCAACTCTGCACTAATATGGCCACACACAGCCTAGACACACGACCATGTACCTTGCCC
* * * *
1638228 GTGTGGCCCCAAATTGATGAACAGTGAGTTACATGGCCAACCACACGGCTTGGGCACACGCCCGT
66 GTGTGGCCCCAAATTGATGAACAGTAAGTTACACGGCCAACCACACGGCCTGGGAACACGCCCGT
**
1638293 GTCCCTGGCCGTGTGGTCTTGTACCATAAACAGTGAGGTACAC
131 GTAACTGGCCGTGTGGTCTTGTACCATAAACAGTGAGGTACAC
* ** *
1638336 ACCCGTCCCAACTCTGCTCTAATATGGCCACACA-AGGCCTAGACACACCG-CTGTGTACCTTTC
1 ACCCGTCCCAACTCTGCACTAATATGGCCACACACA-GCCTAGACACA-CGACCATGTACCTTGC
*
1638399 CCGTGTGGCCTCAAATTGATGAACAGTAAGTTACACGGCCAACCACACGGCCTGGGAACACGCCC
64 CCGTGTGGCCCCAAATTGATGAACAGTAAGTTACACGGCCAACCACACGGCCTGGGAACACGCCC
1638464 GTGTAACTGGCCGTGTGG
129 GTGTAACTGGCCGTGTGG
1638482 CCTCAGCAGC
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
172 1 0.01
173 126 0.98
174 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (173 bp):
ACCCGTCCCAACTCTGCACTAATATGGCCACACACAGCCTAGACACACGACCATGTACCTTGCCC
GTGTGGCCCCAAATTGATGAACAGTAAGTTACACGGCCAACCACACGGCCTGGGAACACGCCCGT
GTAACTGGCCGTGTGGTCTTGTACCATAAACAGTGAGGTACAC
Found at i:1645395 original size:61 final size:61
Alignment explanation
Indices: 1645289--1645447 Score: 171
Period size: 61 Copynumber: 2.6 Consensus size: 61
1645279 TCCCTGCCTA
* * * * * *
1645289 TGTGACTCACACGGCCTGGGTATACTCCCATGTCCCTACCGTGTGG-CTTTGTACCACAAA-
1 TGTGAGTCACACGGCCTGGGCACACGCCCGTGTCCCTACCATGTGGTC-TTGTACCACAAAC
* *
1645349 TAGTGAGTCACACAGCCTGGGCACAC-CCCGTGTCCCTAGCTATGTGGTCTTGTACCACAAAC
1 T-GTGAGTCACACGGCCTGGGCACACGCCCGTGTCCCTA-CCATGTGGTCTTGTACCACAAAC
* * *
1645411 TGCGAGTTACACGGCCTGGGCACACGTCCGTGTCCCT
1 TGTGAGTCACACGGCCTGGGCACACGCCCGTGTCCCT
1645448 TACCCGTGCG
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
60 12 0.14
61 59 0.71
62 12 0.14
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (61 bp):
TGTGAGTCACACGGCCTGGGCACACGCCCGTGTCCCTACCATGTGGTCTTGTACCACAAAC
Found at i:1648557 original size:13 final size:13
Alignment explanation
Indices: 1648541--1648584 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1648531 TTCGTAAAAC
1648541 CATTTCATTTAAA
1 CATTTCATTTAAA
*
1648554 CATTTCATCTT-AC
1 CATTTCAT-TTAAA
*
1648567 CATTTCATTTACA
1 CATTTCATTTAAA
1648580 CATTT
1 CATTT
1648585 AACACAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (13 bp):
CATTTCATTTAAA
Found at i:1658483 original size:12 final size:13
Alignment explanation
Indices: 1658466--1658494 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1658456 CTCATACATG
1658466 AATAAATAAA-GC
1 AATAAATAAATGC
1658478 AATAAATAAATGC
1 AATAAATAAATGC
1658491 AATA
1 AATA
1658495 GTTATAGCCC
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:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:1663397 original size:82 final size:82
Alignment explanation
Indices: 1663260--1663427 Score: 336
Period size: 82 Copynumber: 2.0 Consensus size: 82
1663250 ACCATCGAGC
1663260 TCACCAAAATGTGAAATTCATCGATTGGCACATTCACAGAACCTTATAATTGGCCATATCTAATA
1 TCACCAAAATGTGAAATTCATCGATTGGCACATTCACAGAACCTTATAATTGGCCATATCTAATA
1663325 CCTTACTCCCACGTAAT
66 CCTTACTCCCACGTAAT
1663342 TCACCAAAATGTGAAATTCATCGATTGGCACATTCACAGAACCTTATAATTGGCCATATCTAATA
1 TCACCAAAATGTGAAATTCATCGATTGGCACATTCACAGAACCTTATAATTGGCCATATCTAATA
1663407 CCTTACTCCCACGTAAT
66 CCTTACTCCCACGTAAT
1663424 TCAC
1 TCAC
1663428 TCTAAGCATC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (82 bp):
TCACCAAAATGTGAAATTCATCGATTGGCACATTCACAGAACCTTATAATTGGCCATATCTAATA
CCTTACTCCCACGTAAT
Found at i:1664599 original size:41 final size:41
Alignment explanation
Indices: 1664512--1664835 Score: 341
Period size: 41 Copynumber: 7.9 Consensus size: 41
1664502 CTTTCGGGGA
* * * * * *
1664512 TTTAGCAGCG-TTTTAATAAAGAGCCACTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
1664552 TTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAATGCTTAGGGC
1 TTTAGCGGCGTTTTTGAG-AAAGCGCCGCTAATGCTCAGGGC
* * * * * *
1664593 TATAGCGGTGTTTTTGAGGAGGCGCCGCTAATGCTCGGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * **
1664634 TTTAGCGGCATTTTTGAGGAGGCGCCGCTAATGCTTGGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
1664675 TTTAGCGGCGTTTTTGAGGAAA-CGTCGCTAATGCTC-GTGGC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTCAG-GGC
* * * *
1664716 TTTAACGACATTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* *
1664757 TTTAGCGGCGTTTTTTGAGAAAGCACCACTAATGCTCAGGGC
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
1664799 TTTAGCGGCGTTTTTTGAGAAAGCGTCGCTAATGCTC
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGCTAATGCTC
1664836 TATTTTTAGC
Statistics
Matches: 238, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.06
41 158 0.66
42 66 0.28
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:1664844 original size:41 final size:41
Alignment explanation
Indices: 1664529--1664874 Score: 276
Period size: 41 Copynumber: 8.4 Consensus size: 41
1664519 GCGTTTTAAT
* * * *
1664529 AAAGAGCCACTAATGCTCAGGGATTTAGCGGCGTTTTTGGA-
1 AAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTTGAG
* * *
1664570 AAAGCGCCGCTAATGCTTAGGGCTATAGCGGTG-TTTTTGAG
1 AAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTTGAG
* * * * *
1664611 GAGGCGCCGCTAATGCTCGGGGATTTAGCGGC-ATTTTTGAG
1 AAAGCGCCGCTAATGCTC-AGGCTTTAGCGGCGTTTTTTGAG
* * **
1664652 GAGGCGCCGCTAATGCTTGGGGCTTTAGCGGCG-TTTTTGAGG
1 AAAGCGCCGCTAATGC-TCAGGCTTTAGCGGCGTTTTTTGA-G
* * * * *
1664694 AAA-CGTCGCTAATGCTCGTGGCTTTAACGAC-ATTTTTGAG
1 AAAGCGCCGCTAATGCTC-AGGCTTTAGCGGCGTTTTTTGAG
*
1664734 AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTTGAG
1 AAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTTGAG
* *
1664776 AAAGCACCACTAATGCTCAGGGCTTTAGCGGCGTTTTTTGAG
1 AAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTTGAG
* ** * * *
1664818 AAAGCGTCGCTAATGCTCTA-TTTTTAGCGGCATTTTCT-AA
1 AAAGCGCCGCTAATGCTC-AGGCTTTAGCGGCGTTTTTTGAG
*
1664858 AAAGCGCCACTAATGCT
1 AAAGCGCCGCTAATGCT
1664875 TAGGGATTTA
Statistics
Matches: 251, Mismatches: 42, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
40 27 0.11
41 158 0.63
42 65 0.26
43 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCTCAGGCTTTAGCGGCGTTTTTTGAG
Found at i:1665926 original size:35 final size:35
Alignment explanation
Indices: 1665876--1665991 Score: 99
Period size: 35 Copynumber: 3.3 Consensus size: 35
1665866 CTCCGATGGT
* * *
1665876 TTAGGGATTATGGTTTATGATTTATGGTTTAAAGG
1 TTAGGGTTTAAGGTTTAAGATTTATGGTTTAAAGG
** *
1665911 TTAGGGTTTAAGGTTTAAGGGTTATGGGTTAAAGG
1 TTAGGGTTTAAGGTTTAAGATTTATGGTTTAAAGG
* * * * * *
1665946 TTAGGGGTTAGGGGTTAGGGATTTATGTTTTATAA-T
1 TTAGGGTTTAAGGTTTA-AGATTTATGGTTTA-AAGG
1665982 TTAGGGTTTA
1 TTAGGGTTTA
1665992 TGGGATAGGG
Statistics
Matches: 63, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
35 43 0.68
36 18 0.29
37 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (35 bp):
TTAGGGTTTAAGGTTTAAGATTTATGGTTTAAAGG
Found at i:1665939 original size:7 final size:7
Alignment explanation
Indices: 1665909--1665965 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
1665899 ATGGTTTAAA
1665909 GGTTAGG
1 GGTTAGG
* *
1665916 GTTTAAG
1 GGTTAGG
* *
1665923 GTTTAAG
1 GGTTAGG
*
1665930 GGTTATG
1 GGTTAGG
**
1665937 GGTTAAA
1 GGTTAGG
1665944 GGTTAGG
1 GGTTAGG
1665951 GGTTAGG
1 GGTTAGG
1665958 GGTTAGG
1 GGTTAGG
1665965 G
1 G
1665966 ATTTATGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (7 bp):
GGTTAGG
Found at i:1665962 original size:21 final size:21
Alignment explanation
Indices: 1665901--1665958 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1665891 TATGATTTAT
* *
1665901 GGTTTAAAGGTTAGGGTTTAA
1 GGTTTAAGGGTTAGGGTTAAA
1665922 GGTTTAAGGGTTATGGGTTAAA
1 GGTTTAAGGGTTA-GGGTTAAA
*
1665944 GG-TTAGGGGTTAGGG
1 GGTTTAAGGGTTAGGG
1665959 GTTAGGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 21 0.64
22 9 0.27
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (21 bp):
GGTTTAAGGGTTAGGGTTAAA
Found at i:1665991 original size:7 final size:7
Alignment explanation
Indices: 1665981--1666034 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
1665971 TGTTTTATAA
1665981 TTTAGGG
1 TTTAGGG
1665988 TTTATGGG
1 TTTA-GGG
*
1665996 -ATAGGGG
1 TTTA-GGG
*
1666003 TTAAGGG
1 TTTAGGG
*
1666010 TTAAGGG
1 TTTAGGG
1666017 TTTAGGG
1 TTTAGGG
1666024 TTTAGGG
1 TTTAGGG
1666031 TTTA
1 TTTA
1666035 AGTTAATTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 36 0.90
8 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:1670916 original size:43 final size:43
Alignment explanation
Indices: 1670850--1671145 Score: 405
Period size: 43 Copynumber: 6.9 Consensus size: 43
1670840 AAGGTTTGTT
*
1670850 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTCGAG
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
* * *
1670893 CTATAGCGGCGTTTATGGAAAAAGTGCCGTTAAAGGTCTCGAG
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
* *
1670936 CTATAGCGGCGTTTGTGGAAAAAGTGTCGCTAAAGGTCTCGAG
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
* * *
1670979 CTATAGCAGCGTTT-TCGGAAAAAGCGCCGCTAAAGGTCTTGAT
1 CTATAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTCTCGAG
* * * *
1671022 CTATAGCGGCGTTTGTGGGAAAAGCGCCGATAAAGGTCTTGAT
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
* * * *
1671065 CTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGAT
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
* *
1671108 CTATAGCGGCGTTTGTGGAGAAAGCGCCGCCAAAGGTC
1 CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTC
1671146 CTGATCTATA
Statistics
Matches: 230, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
42 1 0.00
43 228 0.99
44 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (43 bp):
CTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTCGAG
Found at i:1671045 original size:129 final size:129
Alignment explanation
Indices: 1670829--1671166 Score: 455
Period size: 129 Copynumber: 2.6 Consensus size: 129
1670819 TTTTTGCGAG
* * * *
1670829 AAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTCGAG
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGAT
* *
1670893 CTATAGCGGCGTTTATGGAAAAAGTGCCGTTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
66 CTATAGCGGCGTTTATGGAAAAAGCGCCGATAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
* * * *
1670957 AAGTGTCGCTAAAGGTCTCGAGCTATAGCAGCGTTT-TCGGAAAAAGCGCCGCTAAAGGTCTTGA
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTCTTGA
* * * * *
1671021 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGATAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
65 TCTATAGCGGCGTTTATGGAAAAAGCGCCGATAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
** * * *
1671086 AAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAGAAAGCGCCGCCAAAGGTCCTGAT
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGAT
**
1671151 CTATAGTAGCGTTTAT
66 CTATAGCGGCGTTTAT
1671167 TTCTAAAAAC
Statistics
Matches: 180, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
128 16 0.09
129 163 0.91
130 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (129 bp):
AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGAT
CTATAGCGGCGTTTATGGAAAAAGCGCCGATAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
Found at i:1671151 original size:43 final size:42
Alignment explanation
Indices: 1670815--1671156 Score: 370
Period size: 43 Copynumber: 8.0 Consensus size: 42
1670805 TGTTTTTAGT
* * * *
1670815 GGCGTTTTTGCGAG-AAGCGTCGCTAAAGGTTTGTTCTATAGC
1 GGCGTTTGTG-GAGAAAGCGCCGCTAAAGGTCTGATCTATAGC
*
1670857 GGCGTTTGTGG-GAAAAGCGCCGCTAAAGGTCTCGAGCTATAGC
1 GGCGTTTGTGGAG-AAAGCGCCGCTAAAGGTCT-GATCTATAGC
* * * * *
1670900 GGCGTTTATGGAAAAAGTGCCGTTAAAGGTCTCGAGCTATAGC
1 GGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCT-GATCTATAGC
* * * *
1670943 GGCGTTTGTGGAAAAAGTGTCGCTAAAGGTCTCGAGCTATAGC
1 GGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCT-GATCTATAGC
* *
1670986 AGCGTTT-TCGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGT-GGAGAAAGCGCCGCTAAAGGTC-TGATCTATAGC
*
1671029 GGCGTTTGTGG-GAAAAGCGCCGATAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGAG-AAAGCGCCGCTAAAGGTC-TGATCTATAGC
*
1671072 GGCGTTTGTGG-GAAAAGCACCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGAG-AAAGCGCCGCTAAAGGTC-TGATCTATAGC
*
1671115 GGCGTTTGTGGAGAAAGCGCCGCCAAAGGTCCTGATCTATAG
1 GGCGTTTGTGGAGAAAGCGCCGCTAAAGGT-CTGATCTATAG
1671157 TAGCGTTTAT
Statistics
Matches: 267, Mismatches: 23, Indels: 19
0.86 0.07 0.06
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 26 0.10
43 235 0.88
44 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (42 bp):
GGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTGATCTATAGC
Found at i:1671396 original size:5 final size:5
Alignment explanation
Indices: 1671386--1671424 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
1671376 CTAACTCTCC
1671386 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1671425 TTAATAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:1671566 original size:30 final size:31
Alignment explanation
Indices: 1671508--1671581 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
1671498 TATATGATAA
*
1671508 TAATAGTTATAGATGTATTAATATTTTTA-G
1 TAATAGTTATATATGTATTAATATTTTTATG
1671538 TAATAGTTATATAT-TA-TAATACTATTTTATG
1 TAATAGTTATATATGTATTAATA-T-TTTTATG
* *
1671569 TATTAGTAATATA
1 TAATAGTTATATA
1671582 CTAATTTCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 5 0.13
29 3 0.08
30 18 0.47
31 12 0.32
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.50
Consensus pattern (31 bp):
TAATAGTTATATATGTATTAATATTTTTATG
Found at i:1671788 original size:21 final size:21
Alignment explanation
Indices: 1671764--1671816 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1671754 ATTTGCCCGG
*
1671764 CCCATTACCCAGTAAACTTAA
1 CCCATTACCCAATAAACTTAA
1671785 CCCATTACCCAATAAACTTAA
1 CCCATTACCCAATAAACTTAA
1671806 CCCATTACCCA
1 CCCATTACCCA
1671817 CCTAAACACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.23
Consensus pattern (21 bp):
CCCATTACCCAATAAACTTAA
Found at i:1672191 original size:4 final size:4
Alignment explanation
Indices: 1672182--1672211 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1672172 ACAAAGGTGC
1672182 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1672212 CAAAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1672363 original size:9 final size:8
Alignment explanation
Indices: 1672344--1672378 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1672334 AACCGAAGGG
1672344 TTTTCTTT
1 TTTTCTTT
1672352 TTTTCTTT
1 TTTTCTTT
*
1672360 TTTTCTTC
1 TTTTCTTT
*
1672368 TATTCTTT
1 TTTTCTTT
1672376 TTT
1 TTT
1672379 GACTTTTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1677108 original size:23 final size:23
Alignment explanation
Indices: 1677076--1677131 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1677066 AGTCAAAATG
* * *
1677076 AAAATGAAAAAAATAAAAAATAA
1 AAAATAAAAAAAAGAAAAAAGAA
*
1677099 AAAATAAAAAAAAGAAAGAAGAA
1 AAAATAAAAAAAAGAAAAAAGAA
*
1677122 AAAATCAAAA
1 AAAATAAAAA
1677132 TCAAGATCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAATAAAAAAAAGAAAAAAGAA
Found at i:1677110 original size:8 final size:7
Alignment explanation
Indices: 1677083--1677109 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1677073 ATGAAAATGA
1677083 AAAAAAT
1 AAAAAAT
1677090 AAAAAAT
1 AAAAAAT
1677097 AAAAAAT
1 AAAAAAT
1677104 AAAAAA
1 AAAAAA
1677110 AAGAAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1677127 original size:70 final size:72
Alignment explanation
Indices: 1677042--1677176 Score: 174
Period size: 70 Copynumber: 1.9 Consensus size: 72
1677032 CAAAAAATGG
* *
1677042 AAGAAAAAGAAAAATCAAAGTCAA-AGTCAAAATGAAAA-TGA-AAAAA-ATA-AAAAAT-AAAA
1 AAGAAAAAGAAAAATCAAAATCAAGA-TCAAAAT-AAAACTGAGAAAAAGAAAGAAAAATGAAAA
1677101 AATAAAAAA
64 AATAAAAAA
1677110 AAGAAAGAAGAAAAAATCAAAATCAAGATCAAAATAAAACTGAGAAAAAGAAAGAAAAATGAAAA
1 AAGAAA-AAG-AAAAATCAAAATCAAGATCAAAATAAAACTGAGAAAAAGAAAGAAAAATGAAAA
1677175 AA
64 AA
1677177 GGAGAAATCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
68 6 0.11
69 7 0.12
70 24 0.42
71 6 0.11
72 2 0.04
73 6 0.11
74 6 0.11
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.10
Consensus pattern (72 bp):
AAGAAAAAGAAAAATCAAAATCAAGATCAAAATAAAACTGAGAAAAAGAAAGAAAAATGAAAAAA
TAAAAAA
Found at i:1677970 original size:7 final size:7
Alignment explanation
Indices: 1677958--1678011 Score: 76
Period size: 7 Copynumber: 8.0 Consensus size: 7
1677948 CTGAGTCAAA
1677958 AAAAATG
1 AAAAATG
1677965 AAAAATG
1 AAAAATG
1677972 AAAAATG
1 AAAAATG
* *
1677979 -AGAATT
1 AAAAATG
1677985 AAAAATG
1 AAAAATG
1677992 AAAAATG
1 AAAAATG
1677999 -AAAATG
1 AAAAATG
1678005 AAAAATG
1 AAAAATG
1678012 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 10 0.24
7 31 0.76
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.17
Consensus pattern (7 bp):
AAAAATG
Found at i:1677988 original size:13 final size:13
Alignment explanation
Indices: 1677959--1678011 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
1677949 TGAGTCAAAA
1677959 AAAATGAAAAATG
1 AAAATGAAAAATG
* * *
1677972 AAAAATGAGAATTA
1 -AAAATGAAAAATG
1677986 AAAATGAAAAATG
1 AAAATGAAAAATG
1677999 AAAATGAAAAATG
1 AAAATGAAAAATG
1678012 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:1677990 original size:20 final size:20
Alignment explanation
Indices: 1677959--1678011 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1677949 TGAGTCAAAA
1677959 AAAATGAAAAATGAAAAATG
1 AAAATGAAAAATGAAAAATG
* *
1677979 AGAATTAAAAATGAAAAATG
1 AAAATGAAAAATGAAAAATG
1677999 AAAATGAAAAATG
1 AAAATGAAAAATG
1678012 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (20 bp):
AAAATGAAAAATGAAAAATG
Found at i:1679365 original size:86 final size:86
Alignment explanation
Indices: 1679215--1679948 Score: 1053
Period size: 86 Copynumber: 8.5 Consensus size: 86
1679205 CAGATTAGTG
* * * * *
1679215 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGTGAAACAGATTGAAAACAAAACATTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCA
*
1679280 TCGGTGGTCA-TGGAGCTGGTTA
65 TCGGTTG-CAGTGGAGCTGGTTA
* *
1679302 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGGGAAGCAGATCGAAAACAAAGTATTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
1679367 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* *
1679388 AAGAAGCAGATCTTGCCTTCCTGCGCTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
*
1679453 CGGTTGCAGTGGAGCTGGCTA
66 CGGTTGCAGTGGAGCTGGTTA
* * *
1679474 AAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAATAAAGTATTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
* *
1679539 CAGTTGCAGTGGAACTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* *
1679560 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
*
1679625 CGGTTGCAGTGGAGCTGGCTA
66 CGGTTGCAGTGGAGCTGGTTA
* * * *
1679646 AAAAAGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGTAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
1679711 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* *
1679732 AAGAAGTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACATTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
* *
1679797 CGGTTGCAATAGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* * * *
1679818 AAGAAGCAGATCTTGCCTTCCTGCCTTAACAGCGAAGCAGATCGAAAACAAAACCTTACCTCTC-
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTC-CA
* * * *
1679882 TCGATTGTAGTGGAGCGGGTTG
65 TCGGTTGCAGTGGAGCTGGTTA
* ** *
1679904 AAGACAACAGATCTTGCCTTCCTAAGTTGACA--GAAGCAGATCGAA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
1679949 GTAACCATAG
Statistics
Matches: 588, Mismatches: 56, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
85 15 0.03
86 546 0.93
87 27 0.05
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (86 bp):
AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCCAT
CGGTTGCAGTGGAGCTGGTTA
Found at i:1680501 original size:201 final size:202
Alignment explanation
Indices: 1679960--1681358 Score: 1700
Period size: 201 Copynumber: 7.0 Consensus size: 202
1679950 TAACCATAGT
* * * * *
1679960 TTGCAATTTAAAAGATTGAGGCCACAACGGCGAATCTTACTTTCTCAAGTGGTGCAGCGGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACAG
* *
1680025 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TTAAGAAGATTGAAGCTACAAC
66 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAA-AAGATTGAAGCCACAAC
* * * * * * *
1680089 AGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
130 GGCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTT
1680153 CCCTGACA
195 CCCTGACA
* * * * *
1680161 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-ATTGCAGCGGAACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGA-TGCAGCGGAACA
* * *
1680224 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TTAAGAAGATTGAAGCTACCA
65 GATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAA-AAGATTGAAGCCACAA
* * * * * *
1680288 CAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACT
129 CGGCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACT
1680352 TCCCTGACA
194 TCCCTGACA
* * * *
1680361 TTGCAATTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-ATTGCAGCGGAAC
1 TTGCAATTT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGA-TGCAGCGGAAC
*
1680424 AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCATAA
64 AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAA
* * * *
1680489 CGGTGAATCTTAC-TT-CTCAGGCGATACAGCGGAACAGATTGAAGCTACGACGGTGAATCTCAC
129 CGGCGAATCTTACTTTCCT-AGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTAC
1680552 TT-CCTCGACA
193 TTCCCT-GACA
* * * *
1680562 TTGCAATTTTAAAAGATTAAAGCCGCAATGGCGAATCTTA-TTTCCCAGGCGATGCAGCGGAATA
1 TTGCAA-TTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACA
*
1680626 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
65 GATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
* * *
1680691 GGCGAATCTTA-TTTCCCAGGCGATGCAGCGGAACAGATTGAAGTTACGACGGCGAATCTTGCTT
130 GGCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTAC-T
1680755 TCCC-GACA
194 TCCCTGACA
* ** *
1680763 TTGCAATTTAAAATATTGAAGCCACAACGGTAAATCTTAC-TTCCCAGGCGATGCAGTGGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACAG
* *
1680827 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCAACATTGCAATTTAAAAGATTGAAGCCACAACG
66 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACG
* * ** * * *
1680892 GTGAATCTTACTTTCC-AGGCGATACAGCGGAACAGATTGAAGCTATAACAGCGGATCTTGCTTC
131 GCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTTC
*
1680956 CCCGACA
196 CCTGACA
*
1680963 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACAG
* * * * * * * * *
1681027 ATTGAAGCTACGACGGTGAATCTCACTTTCTCGGCATTGCAA-TT-----ATTAAAGCCACAACG
66 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACG
* *
1681086 GCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTTACTT-
131 GCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTTC
*
1681149 CCTCAACA
196 CCT-GACA
* *
1681157 TTGTAATTTAAAAAGATTGAAGCTACAACGGCGAATCTTA-TTTCCCAGGCGATGCAGCGGAACA
1 TTGCAATTT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACA
* * * * *
1681221 GATTGAAGCTACGACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
65 GATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
* * * **** * * *
1681286 GGCGAATCTTACTTCCCT-GGCGGTGTAATACAATAGATTGAAGCTACGACGGCGAATCTAATTT
130 GGCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTT
*
1681350 CCCCGACA
195 CCCTGACA
1681358 T
1 T
1681359 CGCAGTTAAA
Statistics
Matches: 1064, Mismatches: 106, Indels: 56
0.87 0.09 0.05
Matches are distributed among these distances:
193 6 0.01
194 75 0.07
195 89 0.08
196 2 0.00
199 9 0.01
200 426 0.40
201 439 0.41
202 16 0.02
203 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (202 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACAG
ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACG
GCGAATCTTACTTTCCTAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTTC
CCTGACA
Found at i:1681374 original size:50 final size:50
Alignment explanation
Indices: 1680020--1681374 Score: 814
Period size: 50 Copynumber: 27.2 Consensus size: 50
1680010 GGTGCAGCGG
* * * *
1680020 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
* * * * **
1680070 AGA-AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CGTTGCAGTGG
1 A-ACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTA
* * * *
1680120 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
* * * * ***
1680170 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTA
* * * *
1680220 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
* * * * * **
1680270 AGA-AGATTGAAGCTACCACAGCGGATCTTACTTTCCTAG-CGTTGCAGTGG
1 A-ACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTA
* * *
1680320 AACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGC-AGTTA
* * * * ***
1680371 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTA
* * * *
1680421 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGC-AGTTA
* * * * * * ***
1680472 AA-AGATTGAAGCCATAACGGTGAATCTTACTTCTCAGGCGA-TACAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * *
1680521 AACAGATTGAAGCTACGACGGTGAATCTCACTTCCTC-GACATTGCAATTTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCC-CAGACATTGC-A-GTTA
* ** * * * ***
1680573 AA-AGATTAAAGCCGCAATGGCGAATCTTATTTCCCAGGCGA-TGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * * * *
1680622 AATAGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGC-AGTTA
* * * ***
1680673 AA-AGATTGAAGCCACAACGGCGAATCTTATTTCCCAGGCGA-TGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * *
1680722 AACAGATTGAAGTTACGACGGCGAATCTTGCTTTCCC-GACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGC-AGTTA
* * ** * **
1680773 AA-ATATTGAAGCCACAACGGTAAATCTTACTTCCCAGGCGA-TGCAGTGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * *
1680822 AACAGATTGAAGCTACAACAGCGGATCTTGCTTCCCCA-ACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTT-CCCAGACATTGC-AGTTA
* * * * * ***
1680873 AA-AGATTGAAGCCACAACGGTGAATCTTACTTTCCAGGCGA-TACAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * * * *
1680922 AACAGATTGAAGCTATAACAGCGGATCTTGCTTCCCCGACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGC-AGTTA
* * * ***
1680973 AA-AGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGA-TGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * * * *
1681022 AACAGATTGAAGCTACGACGGTGAATCTCACTTTCTC-GGCATTGCAATT-
1 AACAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTA
* * * ***
1681071 -----ATTAAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * *
1681116 AACAGATTGAAGCTACGACGGTGAATCTTACTTCCTCA-ACATTGTAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCC-CAGACATTG-CAGTTA
* * * ***
1681167 AAAAGATTGAAGCTACAACGGCGAATCTTATTTCCCAGGCGA-TGCAGCGG
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGAC-ATTGCAGTTA
* * * * *
1681217 AACAGATTGAAGCTACGACGGTGAATCTTGCTTCCCCGACATTGCAATTTA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGC-AGTTA
* * * ** * *
1681268 AA-AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTA-ATA
1 AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
* * * * * *
1681316 CAATAGATTGAAGCTACGACGGCGAATCTAATTTCCCCGACATCGCAGTTA
1 -AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
1681367 AACAGATT
1 AACAGATT
1681375 AGAGATGGCA
Statistics
Matches: 985, Mismatches: 257, Indels: 126
0.72 0.19 0.09
Matches are distributed among these distances:
43 4 0.00
44 28 0.03
45 1 0.00
48 2 0.00
49 59 0.06
50 721 0.73
51 161 0.16
52 9 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
AACAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACATTGCAGTTA
Found at i:1681374 original size:100 final size:100
Alignment explanation
Indices: 1679960--1681358 Score: 1665
Period size: 100 Copynumber: 14.0 Consensus size: 100
1679950 TAACCATAGT
* * * * *
1679960 TTGCAATTTAAAAGATTGAGGCCACAACGGCGAATCTTACTTTCTCAAGTGGTGCAGCGGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
* *
1680025 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 ATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * * * *
1680061 TTGCAA-TTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACA
1 TTGCAATTTAA-AAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACA
* *
1680124 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * * *
1680161 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-ATTGCAGCGGAACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGA-TGCAGCGGAACA
* *
1680224 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * * * * *
1680261 TTGCAA-TTAAGAAGATTGAAGCTACCACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACA
1 TTGCAATTTAA-AAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACA
*
1680324 GATTGAAGCTACAACAGCGAATCTTACTTCCCTGACA
64 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * *
1680361 TTGCAATTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-ATTGCAGCGGAAC
1 TTGCAATTT-AAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGA-TGCAGCGGAAC
*
1680424 AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
63 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * *
1680462 TTGCAATTTAAAAGATTGAAGCCATAACGGTGAATCTTACTTCTCAGGCGATACAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * * *
1680527 TTGAAGCTACGACGGTGAATCTCACTTCCTCGACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * * *
1680562 TTGCAATTTTAAAAGATTAAAGCCGCAATGGCGAATCTTATTTCCCAGGCGATGCAGCGGAATAG
1 TTGCAA-TTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAG
* *
1680627 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
65 ATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
*
1680663 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * * *
1680728 TTGAAGTTACGACGGCGAATCTTGCTTTCCCGACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* ** *
1680763 TTGCAATTTAAAATATTGAAGCCACAACGGTAAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * *
1680828 TTGAAGCTACAACAGCGGATCTTGCTTCCCCAACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * *
1680863 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCAGGCGATACAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * *
1680928 TTGAAGCTATAACAGCGGATCTTGCTTCCCCGACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
*
1680963 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * * * * *
1681028 TTGAAGCTACGACGGTGAATCTCACTTTCTCGGCA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
*
1681063 TTGCAA-TT-----ATTAAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * * *
1681122 TTGAAGCTACGACGGTGAATCTTACTTCCTCAACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * *
1681157 TTGTAATTTAAAAAGATTGAAGCTACAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAG
* * * *
1681222 ATTGAAGCTACGACGGTGAATCTTGCTTCCCCGACA
65 ATTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
* * * **** *
1681258 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAATACAATAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * *
1681323 TTGAAGCTACGACGGCGAATCTAATTTCCCCGACA
66 TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
1681358 T
1 T
1681359 CGCAGTTAAA
Statistics
Matches: 1161, Mismatches: 119, Indels: 37
0.88 0.09 0.03
Matches are distributed among these distances:
94 85 0.07
95 2 0.00
99 9 0.01
100 757 0.65
101 306 0.26
102 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (100 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACAGCGAATCTTACTTCCCCGACA
Found at i:1681491 original size:44 final size:43
Alignment explanation
Indices: 1681390--1681619 Score: 163
Period size: 44 Copynumber: 5.4 Consensus size: 43
1681380 TGGCAGACGT
* * * *
1681390 TATCTCTCTGAAGTTGCAGTAGAGCAGATC---G-CATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-CAAAGAAAT-CAATCC
* *
1681431 TATCTCGCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGAC-AAAGAAATCAATCC
* * * *
1681475 TATCTCCCTGAAGTTGCAGTGGAGCGGATCAAA-ACCA-CAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-CAAAGA-AATCA-ATCC
* * ** * * *
1681519 TATCTCTCTGAAGTTGCAGTAGAGTA-A-ATCG-TATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAGAAAT-CAATCC
1681560 TATCTCCCTGAAGTTGCAGTAGAGCAGACGAAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGAC-AAAGAAATCAATCC
*
1681604 TATCTCTCTGAAGTTG
1 TATCTCCCTGAAGTTG
1681620 TTACGAAGAA
Statistics
Matches: 149, Mismatches: 25, Indels: 27
0.74 0.12 0.13
Matches are distributed among these distances:
40 2 0.01
41 54 0.36
42 3 0.02
43 4 0.03
44 81 0.54
45 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAGAAATCAATCC
Found at i:1681658 original size:129 final size:129
Alignment explanation
Indices: 1681391--1681632 Score: 351
Period size: 129 Copynumber: 1.9 Consensus size: 129
1681381 GGCAGACGTT
* * * *
1681391 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCGCTGAAGTTGCAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGC
* * ** **
1681456 AGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTT
66 AGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCGAAGAAGATCAAAACCACAGATCAG
*
1681520 ATCTCTCTGAAGTTGCAGTAGAGTAAATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGC
* *
1681585 AGACGAAAGAAATCAATCCTATCTCTCTGAAGTTGTTA-CGAAGAAGAT
66 AGACGAAAGAAATCAATCCTATCTCCCTGAAGTTG-CAGCGAAGAAGAT
1681633 TGAAGCTACA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
129 100 0.99
130 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (129 bp):
ATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGC
AGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCGAAGAAGATCAAAACCACAGATCAG
Found at i:1681886 original size:21 final size:21
Alignment explanation
Indices: 1681850--1681901 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1681840 ATTTACCCGG
1681850 CCCATTACCC-ATAAACTTAA
1 CCCATTACCCAATAAACTTAA
1681870 CCCATTACCCAATAAACTTAA
1 CCCATTACCCAATAAACTTAA
1681891 CCCATTACCCA
1 CCCATTACCCA
1681902 CCTAAACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCATTACCCAATAAACTTAA
Found at i:1682447 original size:9 final size:8
Alignment explanation
Indices: 1682428--1682462 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1682418 AACCGAAGGG
1682428 TTTTCTTT
1 TTTTCTTT
1682436 TTTTCTTT
1 TTTTCTTT
*
1682444 TTTTCTTC
1 TTTTCTTT
*
1682452 TATTCTTT
1 TTTTCTTT
1682460 TTT
1 TTT
1682463 GACTTTTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1682733 original size:37 final size:38
Alignment explanation
Indices: 1682692--1682766 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1682682 GAAAGAAAAA
1682692 TAAAATTT-AAAAAAAAAATTGGTTTTATAAAGGGTTG
1 TAAAATTTAAAAAAAAAAATTGGTTTTATAAAGGGTTG
1682729 TAAAATTTAAAAAAAAAAATTGGTTTTATAAAGGGTTG
1 TAAAATTTAAAAAAAAAAATTGGTTTTATAAAGGGTTG
1682767 AAACGGCGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (38 bp):
TAAAATTTAAAAAAAAAAATTGGTTTTATAAAGGGTTG
Found at i:1686006 original size:3 final size:3
Alignment explanation
Indices: 1685998--1686030 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1685988 AAATGTAAGA
1685998 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1686031 AGCCTTTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1686678 original size:16 final size:15
Alignment explanation
Indices: 1686659--1686696 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1686649 TTAAGTACTA
1686659 TTCTTTTTCTTTCTTT
1 TTCTTTTTCTTT-TTT
1686675 TTCTTTTTCTTTTTT
1 TTCTTTTTCTTTTTT
1686690 TT-TTTTT
1 TTCTTTTT
1686697 GAGATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 12 0.55
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTCTTTTTCTTTTTT
Found at i:1687114 original size:31 final size:31
Alignment explanation
Indices: 1687057--1687177 Score: 143
Period size: 31 Copynumber: 3.8 Consensus size: 31
1687047 TAAAATTTTA
* *
1687057 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATGATAAATAATATTTAAATAATTT
* *
1687088 AATATAATGATAAATGATATTAAAATAATTT
1 AATATAATGATAAATAATATTTAAATAATTT
* * *
1687119 AACATAACGATACATAAAATATTTAAATAATTT
1 AATATAATGATA-A-ATAATATTTAAATAATTT
* *
1687152 AATATAATGATAAATAAAATATAAAT
1 AATATAATGATAAATAATATTTAAAT
1687178 TAATCTATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
31 47 0.64
32 2 0.03
33 25 0.34
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (31 bp):
AATATAATGATAAATAATATTTAAATAATTT
Found at i:1688029 original size:16 final size:16
Alignment explanation
Indices: 1688008--1688061 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
1687998 TTTGGTTCGC
1688008 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
1688024 TGTAATAGAATAGAGT
1 TGTAATGGAATAGAGG
*
1688040 TATAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1688056 CGTAAT
1 TGTAAT
1688062 AGTAATTCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1688136 original size:44 final size:45
Alignment explanation
Indices: 1688043--1688136 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 45
1688033 ATAGAGTTAT
*
1688043 AATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTGAATGG
*
1688088 AATGGAATAGAGGCGTAATAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1688132 AATGG
1 AATGG
1688137 TGTTGTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTGAATGG
Found at i:1688434 original size:16 final size:18
Alignment explanation
Indices: 1688417--1688570 Score: 67
Period size: 18 Copynumber: 8.9 Consensus size: 18
1688407 TTATTATTAA
1688417 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
**
1688435 ATATAATTTAATAAATTT
1 ATATAATTTAATAAAAAT
* ****
1688453 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
1688472 ATATGAATTTAAT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
1688490 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* *
1688506 ATATAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
1688525 A-ATTA-TT-AT-TAAA-
1 ATATAATTTAATAAAAAT
1688538 -TATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
1688555 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
1688571 TTCTTAATAT
Statistics
Matches: 98, Mismatches: 24, Indels: 28
0.65 0.16 0.19
Matches are distributed among these distances:
13 3 0.03
14 5 0.05
15 5 0.05
16 11 0.11
17 14 0.14
18 39 0.40
19 15 0.15
20 3 0.03
21 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:1688464 original size:120 final size:120
Alignment explanation
Indices: 1688267--1688873 Score: 1033
Period size: 120 Copynumber: 5.1 Consensus size: 120
1688257 ATAAATAATT
* *
1688267 TAAAATATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
**
1688332 TCTTAATATTAAATATTCTTATATGAATTTTTTAAAATCATAATATATAATACTA
66 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
* *
1688387 TAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAATT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
*
1688452 TCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTA
66 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
*
1688507 TATAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
*
1688572 TCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
66 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
* *
1688627 TAAAATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATGTAATTTAATAAA
1 TAAAATATAATTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAA
*
1688692 ATTCTTAATGTTAAATATTC-T-TA-GAATTTACTAAAATCATAATATATAATACTA
64 ATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
* *
1688746 TAAAATATAATTTAAATTAATTATTTTTAAATATAATTTAATAAAAA-ATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
*
1688810 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATTTAATACTA
66 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
1688865 TAAAATATA
1 TAAAATATA
1688874 TAATACTATA
Statistics
Matches: 462, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
116 33 0.07
117 19 0.04
118 2 0.00
119 96 0.21
120 259 0.56
121 1 0.00
122 52 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
Found at i:1688673 original size:16 final size:17
Alignment explanation
Indices: 1688654--1688692 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1688644 TAATTATTAT
*
1688654 TAAAAATA-TAATTTAG
1 TAAAAATAGTAATTTAA
1688670 TAAAAATATGTAATTTAA
1 TAAAAATA-GTAATTTAA
1688688 TAAAA
1 TAAAA
1688693 TTCTTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
TAAAAATAGTAATTTAA
Found at i:1688796 original size:17 final size:17
Alignment explanation
Indices: 1688774--1688808 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1688764 AATTATTTTT
1688774 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
1688791 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
1688808 A
1 A
1688809 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:1688886 original size:15 final size:15
Alignment explanation
Indices: 1688849--1688896 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
1688839 TACTAAAATC
*
1688849 ATAATATTTAATACT
1 ATAATATATAATACT
1688864 ATAAAATATATAATACT
1 AT--AATATATAATACT
1688881 ATAATATATAATACT
1 ATAATATATAATACT
1688896 A
1 A
1688897 GAAAGATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 16 0.53
17 14 0.47
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATATAATACT
Found at i:1691041 original size:18 final size:19
Alignment explanation
Indices: 1691001--1691042 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1690991 GCCGATACAA
* *
1691001 AAAAATCAAAGATGAAGAG
1 AAAAATCAAAGATAAAGAC
*
1691020 AAAAATCAAAGA-AAATAC
1 AAAAATCAAAGATAAAGAC
1691038 AAAAA
1 AAAAA
1691043 AAAAAGATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAATCAAAGATAAAGAC
Found at i:1691607 original size:24 final size:23
Alignment explanation
Indices: 1691556--1691608 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1691546 TGAAATTAAA
1691556 ATATATAAAATTTAAAAATAGTT
1 ATATATAAAATTTAAAAATAGTT
*
1691579 A-ATATATAAATTTATAAATA-TAT
1 ATATATA-AAATTTAAAAATAGT-T
1691602 ATATATA
1 ATATATA
1691609 CTAGCTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.23
23 15 0.58
24 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATATAAAATTTAAAAATAGTT
Found at i:1694182 original size:152 final size:152
Alignment explanation
Indices: 1693985--1694289 Score: 610
Period size: 152 Copynumber: 2.0 Consensus size: 152
1693975 GGTAATGTCC
1693985 AATTTATAAATTGTTTTTATTTTCGTTGCTTAAAATAAAACCTATGAAAGTTTAGTGACCAACTA
1 AATTTATAAATTGTTTTTATTTTCGTTGCTTAAAATAAAACCTATGAAAGTTTAGTGACCAACTA
1694050 TGTTGTTTACCCTACTTATAATACATATAATAAAATGTACAAGCCCAATAATGCCCGGGCCCAAG
66 TGTTGTTTACCCTACTTATAATACATATAATAAAATGTACAAGCCCAATAATGCCCGGGCCCAAG
1694115 CAAATAAATAAGCCCAAATACT
131 CAAATAAATAAGCCCAAATACT
1694137 AATTTATAAATTGTTTTTATTTTCGTTGCTTAAAATAAAACCTATGAAAGTTTAGTGACCAACTA
1 AATTTATAAATTGTTTTTATTTTCGTTGCTTAAAATAAAACCTATGAAAGTTTAGTGACCAACTA
1694202 TGTTGTTTACCCTACTTATAATACATATAATAAAATGTACAAGCCCAATAATGCCCGGGCCCAAG
66 TGTTGTTTACCCTACTTATAATACATATAATAAAATGTACAAGCCCAATAATGCCCGGGCCCAAG
1694267 CAAATAAATAAGCCCAAATACT
131 CAAATAAATAAGCCCAAATACT
1694289 A
1 A
1694290 GACCCAACCT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 153 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (152 bp):
AATTTATAAATTGTTTTTATTTTCGTTGCTTAAAATAAAACCTATGAAAGTTTAGTGACCAACTA
TGTTGTTTACCCTACTTATAATACATATAATAAAATGTACAAGCCCAATAATGCCCGGGCCCAAG
CAAATAAATAAGCCCAAATACT
Found at i:1704026 original size:26 final size:27
Alignment explanation
Indices: 1703970--1704033 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
1703960 TTGAGCCAGT
* *
1703970 ATTCTTTTATTCTTTTTTCGAGTAATT
1 ATTCTTTTATTCTTTTTTCGACTAATC
1703997 ATTCTTTTATTCTTTTTT-G-CTACATC
1 ATTCTTTTATTCTTTTTTCGACTA-ATC
1704023 ATTC-TTTATTC
1 ATTCTTTTATTC
1704034 ATTTCATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 9 0.26
26 7 0.21
27 18 0.53
ACGTcount: A:0.17, C:0.16, G:0.05, T:0.62
Consensus pattern (27 bp):
ATTCTTTTATTCTTTTTTCGACTAATC
Found at i:1707587 original size:7 final size:8
Alignment explanation
Indices: 1707549--1707588 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1707539 TTCTTAAAAA
1707549 AAAAGAAG
1 AAAAGAAG
*
1707557 AAGA-AAG
1 AAAAGAAG
1707564 -AAAGAAG
1 AAAAGAAG
1707571 AAAAGAAG
1 AAAAGAAG
1707579 AAAAG-AG
1 AAAAGAAG
1707586 AAA
1 AAA
1707589 GGAGAGGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 2 0.07
7 11 0.39
8 15 0.54
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:1708862 original size:43 final size:42
Alignment explanation
Indices: 1708796--1709034 Score: 170
Period size: 43 Copynumber: 5.7 Consensus size: 42
1708786 CTGAAGATTT
*
1708796 AATCCTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACATGCG
1 AATCTTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACAT-CG
* * * * *
1708839 GATCTTATCTCTCTGAGGTTGCAG-AGAG-TAGA-TCACCTC-
1 AATCTTATCTCCCTGAGGTTGCAGTGGAGCT-GATTGACATCG
* * * * * **
1708878 AAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATTT
1 AA-TCTTATCTCCCTGAGGTTGCAGTGGAGCTGATTG-ACATCG
*
1708922 AATAC-TATCTCCCTGAGGTTGCAGTGGAGCGGATTGACATACG
1 AAT-CTTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACAT-CG
* * * * * *
1708965 GATCTTATCTCTCTGAGGTTGCAG-AGAGCAGA-TCACCTC-
1 AATCTTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACATCG
*
1709004 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AA-TCTTATCTCCCTGAGGTTGCAGTGGAGC
1709035 AGACTGAAGA
Statistics
Matches: 151, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 41 0.27
41 18 0.12
42 16 0.11
43 71 0.47
44 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (42 bp):
AATCTTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACATCG
Found at i:1709007 original size:126 final size:126
Alignment explanation
Indices: 1708782--1709147 Score: 552
Period size: 126 Copynumber: 2.9 Consensus size: 126
1708772 CCCCAGAGAA
* * *
1708782 CAGACTGAAGATTTAATCCTATCTCCCTGAGGTTGCAGTGGAGCTGATTGACATGCGGATCTTAT
1 CAGACTGAAGATTTAATACTATCTCCCTGAGGTTGCAGTGGAGCGGATTGACATACGGATCTTAT
*
1708847 CTCTCTGAGGTTGCAGAGAGTAGATCACCTCAAGTCTTATCTCCTTGAAGTTGCAGTGGAG
66 CTCTCTGAGGTTGCAGAGAGCAGATCACCTCAAGTCTTATCTCCTTGAAGTTGCAGTGGAG
1708908 CAGACTGAAGATTTAATACTATCTCCCTGAGGTTGCAGTGGAGCGGATTGACATACGGATCTTAT
1 CAGACTGAAGATTTAATACTATCTCCCTGAGGTTGCAGTGGAGCGGATTGACATACGGATCTTAT
*
1708973 CTCTCTGAGGTTGCAGAGAGCAGATCACCTCAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
66 CTCTCTGAGGTTGCAGAGAGCAGATCACCTCAAGTCTTATCTCCTTGAAGTTGCAGTGGAG
* * * * * * * * * *
1709034 CAGACTGAAGAATCAATTCTATCTCCCTGAAGTTGCAATGGAGTGGATTAAAATCACAGATTTTA
1 CAGACTGAAGATTTAATACTATCTCCCTGAGGTTGCAGTGGAGCGGATTGACAT-ACGGATCTTA
* * * *
1709099 TCTTTCTGAGGTTACAGAGAGCAGATCACATCAAGTCTTATTTCCTTGA
65 TCTCTCTGAGGTTGCAGAGAGCAGATCACCTCAAGTCTTATCTCCTTGA
1709148 GGTTACAATG
Statistics
Matches: 219, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
126 167 0.76
127 52 0.24
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (126 bp):
CAGACTGAAGATTTAATACTATCTCCCTGAGGTTGCAGTGGAGCGGATTGACATACGGATCTTAT
CTCTCTGAGGTTGCAGAGAGCAGATCACCTCAAGTCTTATCTCCTTGAAGTTGCAGTGGAG
Found at i:1709059 original size:43 final size:43
Alignment explanation
Indices: 1708876--1709076 Score: 155
Period size: 43 Copynumber: 4.7 Consensus size: 43
1708866 GTAGATCACC
* * *
1708876 TCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGAT
1 TCAATTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-AA
* * * * * *
1708920 TTAATAC-TATCTCCCTGAGGTTGCAGTGGAGCGGATTG-ACA
1 TCAATTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAA
* * * * * **
1708961 TACGGA-TCTTATCTCTCTGAGGTTGCAG-AGAGCAGA-T-CACC
1 T-C-AATTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAA
*
1709002 TCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA
1 TCAATTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-AA
*
1709046 TCAATTC-TATCTCCCTGAAGTTGCAATGGAG
1 TCAATTCTTATCTCCCTGAAGTTGCAGTGGAG
1709077 TGGATTAAAA
Statistics
Matches: 123, Mismatches: 25, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 21 0.17
41 12 0.10
42 9 0.07
43 70 0.57
44 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
TCAATTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAA
Found at i:1710766 original size:2 final size:2
Alignment explanation
Indices: 1710759--1710792 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1710749 CTTTATACTT
* *
1710759 TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1710793 CGTCGTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1712725 original size:3 final size:3
Alignment explanation
Indices: 1712717--1712759 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1712707 TTAGGTTTTG
1712717 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1712760 TTCAAATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1712943 original size:27 final size:26
Alignment explanation
Indices: 1712912--1712976 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
1712902 CGACTTACAA
* *
1712912 TTTTTTAGTAATTTTATATATTTTATGT
1 TTTTTTA-TAAATTTATAAATTTTA-GT
1712940 TTTTTTATAAATTTATAAATTTTAGT
1 TTTTTTATAAATTTATAAATTTTAGT
*
1712966 ATTTTTATAAA
1 TTTTTTATAAA
1712977 ACTTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.35
27 15 0.44
28 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (26 bp):
TTTTTTATAAATTTATAAATTTTAGT
Found at i:1712998 original size:23 final size:24
Alignment explanation
Indices: 1712960--1713006 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1712950 ATTTATAAAT
* *
1712960 TTTAGTATTTTTATAAAACTTTAA
1 TTTAGTATTTTAATAAAAATTTAA
1712984 TTTA-TATTTTAATAAAAATTTAA
1 TTTAGTATTTTAATAAAAATTTAA
1713007 AAATATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAGTATTTTAATAAAAATTTAA
Found at i:1713754 original size:34 final size:35
Alignment explanation
Indices: 1713695--1713761 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1713685 CAAACAATAG
* *
1713695 AAAATATTTTCTAGTAAATCGTTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1713730 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
1713762 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1714084 original size:11 final size:11
Alignment explanation
Indices: 1714053--1714089 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1714043 AAAGAAAGTA
1714053 AAATATATAA-
1 AAATATATAAT
*
1714063 AACTA-ATAAT
1 AAATATATAAT
1714073 AAATATATAAT
1 AAATATATAAT
1714084 AAATAT
1 AAATAT
1714090 GGACAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 4 0.17
10 8 0.35
11 11 0.48
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATATAAT
Found at i:1717220 original size:2 final size:2
Alignment explanation
Indices: 1717215--1717245 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1717205 TTTAATTAAG
1717215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1717246 GAGTTGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1726046 original size:42 final size:42
Alignment explanation
Indices: 1725934--1726092 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 42
1725924 AGCTCGTACA
* ** *
1725934 ATGCCAACGTCCCAGACGTGGTCTTACGTGTAATCAAATAACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCATAT-ACG
* * *
1725977 ACGCC-AC-TGCCCAAAACAGGGTCTTACACGTAATCATATACG
1 ATGCCAACGT-CCC-AGACATGGTCTTACACGTAATCATATACG
* *
1726019 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCAT-ATA-CG
* *
1726063 ATGCCAACATCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
1726093 AAAATCACAT
Statistics
Matches: 94, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 29 0.31
43 34 0.36
44 30 0.32
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCATATACG
Found at i:1726076 original size:44 final size:45
Alignment explanation
Indices: 1725996--1726098 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 45
1725986 CCCAAAACAG
* **
1725996 GGTCTTACACGT-AA--TCATATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAATCTCAAATACGATGCCAACATCCCAGACAT
*
1726038 GGTCTTACACGTAAATCTCAAAT-CGATGCCAACATCCCAGACGT
1 GGTCTTACACGTAAATCTCAAATACGATGCCAACATCCCAGACAT
*
1726082 GGTCTTACACGAAAATC
1 GGTCTTACACGTAAATC
1726099 ACATATCGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
42 12 0.23
43 2 0.04
44 34 0.64
45 5 0.09
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (45 bp):
GGTCTTACACGTAAATCTCAAATACGATGCCAACATCCCAGACAT
Found at i:1727194 original size:13 final size:13
Alignment explanation
Indices: 1727176--1727200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1727166 ACAAACGATA
1727176 AAATTTTCACACG
1 AAATTTTCACACG
1727189 AAATTTTCACAC
1 AAATTTTCACAC
1727201 ACATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:1727465 original size:42 final size:42
Alignment explanation
Indices: 1727405--1727489 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
1727395 TGGTGTAGGA
1727405 TGTTCATGCATGGAAGGTATCTAAGCGTGGGGGTATAACAAT
1 TGTTCATGCATGGAAGGTATCTAAGCGTGGGGGTATAACAAT
*
1727447 TGTTCATGCATGGGAGGTATCTAAGCGTGGGGGTATAACAAT
1 TGTTCATGCATGGAAGGTATCTAAGCGTGGGGGTATAACAAT
1727489 T
1 T
1727490 TCCCCTAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (42 bp):
TGTTCATGCATGGAAGGTATCTAAGCGTGGGGGTATAACAAT
Found at i:1732357 original size:28 final size:28
Alignment explanation
Indices: 1732325--1732421 Score: 122
Period size: 28 Copynumber: 3.5 Consensus size: 28
1732315 TAATAAGTTC
* * * *
1732325 CACACTTAGTGCTTAATAATCAAACTTG
1 CACACTTAGTGCTTTACAATTAAACTCG
* *
1732353 CACACTTAGTGATTTACCATTAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
* *
1732381 CACACGTAATGCTTTACAATTAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
1732409 CACACTTAGTGCT
1 CACACTTAGTGCT
1732422 AATCTCATTA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (28 bp):
CACACTTAGTGCTTTACAATTAAACTCG
Found at i:1746284 original size:21 final size:21
Alignment explanation
Indices: 1746260--1746326 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1746250 TTGTCAGTTG
1746260 CACACGGGCATGTCTCTCAGC
1 CACACGGGCATGTCTCTCAGC
* *
1746281 CACACGGTTACATG-C-CTCAGT
1 CACACGG--GCATGTCTCTCAGC
* * *
1746302 TACACGGGCGTGTCTTTCAGC
1 CACACGGGCATGTCTCTCAGC
1746323 CACA
1 CACA
1746327 TGGTTGTGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 25 0.74
22 1 0.03
23 4 0.12
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.22
Consensus pattern (21 bp):
CACACGGGCATGTCTCTCAGC
Found at i:1751289 original size:14 final size:16
Alignment explanation
Indices: 1751270--1751302 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1751260 AATAATATTT
1751270 TAAATTT-AT-CTAAA
1 TAAATTTCATACTAAA
1751284 TAAATTTCATACTAAA
1 TAAATTTCATACTAAA
1751300 TAA
1 TAA
1751303 GTTTGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 2 0.12
16 8 0.47
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTCATACTAAA
Found at i:1752171 original size:24 final size:21
Alignment explanation
Indices: 1752121--1752183 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1752111 AATAATTAGG
1752121 AATTAATTAAA-TAAAATTTTA
1 AATTAA-TAAATTAAAATTTTA
1752142 AATTAAATAGAATTAATAATTTTA
1 AATT-AATA-AATTAA-AATTTTA
**
1752166 GGTTAATAAATTAAAATT
1 AATTAATAAATTAAAATT
1752184 GAGTGTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 10 0.28
22 10 0.28
23 7 0.19
24 9 0.25
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AATTAATAAATTAAAATTTTA
Found at i:1753886 original size:23 final size:23
Alignment explanation
Indices: 1753860--1753905 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1753850 ATGAATATAT
*
1753860 AGTTGCTAATGTTGATGGTATTA
1 AGTTGCTAATGTTGATGGAATTA
* *
1753883 AGTTTCTAATTTTGATGGAATTA
1 AGTTGCTAATGTTGATGGAATTA
1753906 CCTCTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (23 bp):
AGTTGCTAATGTTGATGGAATTA
Found at i:1756011 original size:22 final size:22
Alignment explanation
Indices: 1755983--1756112 Score: 188
Period size: 22 Copynumber: 5.9 Consensus size: 22
1755973 TGTTGATAGT
*
1755983 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
1756005 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
1756027 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
1756049 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
1756071 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
1756093 ACGTACTAAGCTCTCATGTT
1 ACGTACTAAGCTCTCATGTT
1756113 AGTCTTCTTC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 97 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:1756280 original size:17 final size:17
Alignment explanation
Indices: 1756258--1756297 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
1756248 AATCAACCTT
1756258 CACCTCCGGCACCAATC
1 CACCTCCGGCACCAATC
*
1756275 CACCT-C--CACCGATC
1 CACCTCCGGCACCAATC
1756289 CACCTCCGG
1 CACCTCCGG
1756298 TCCTTCACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.63
15 1 0.05
16 1 0.05
17 5 0.26
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCTCCGGCACCAATC
Found at i:1757837 original size:8 final size:8
Alignment explanation
Indices: 1757824--1757850 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1757814 AAAAGTTATA
1757824 TGCAAAGT
1 TGCAAAGT
1757832 TGCAAAGT
1 TGCAAAGT
1757840 TGCAAAGT
1 TGCAAAGT
1757848 TGC
1 TGC
1757851 GGTTTCTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (8 bp):
TGCAAAGT
Found at i:1758728 original size:120 final size:120
Alignment explanation
Indices: 1758589--1759103 Score: 944
Period size: 120 Copynumber: 4.3 Consensus size: 120
1758579 TATATTTAGA
*
1758589 AAAATTATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTGTAATTTTAG
1 AAAA-TATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTATAATTTTAG
*
1758653 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATAATATATTTTAATT
64 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
1758710 AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1758775 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
*
1758830 AAAATATATTTAATAACAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
1 AAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTATAATTTTAGT
1758894 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
*
1758950 AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1759015 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
*
1759070 AAAATATATTTAATAATAATTATGTTAAAATATA
1 AAAATATATTTAATAATAATTATGTTAAATTATA
1759104 ATTAAATTAT
Statistics
Matches: 385, Mismatches: 6, Indels: 7
0.97 0.02 0.02
Matches are distributed among these distances:
119 2 0.01
120 375 0.97
121 8 0.02
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
Found at i:1758737 original size:15 final size:16
Alignment explanation
Indices: 1758693--1758729 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1758683 AATTTTATTA
1758693 AATAATATATTTTAATT
1 AATAATATA-TTTAATT
1758710 AA-AATATATTTAA-T
1 AATAATATATTTAATT
1758724 AATAAT
1 AATAAT
1758730 TATGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 8 0.42
16 6 0.32
17 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATATATTTAATT
Done.