Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 191 of 356
Found at i:62221042 original size:15 final size:15
Alignment explanation
Indices: 62221024--62221056 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62221014 TTAAAATCAA
62221024 TATTTTTACAACATC
1 TATTTTTACAACATC
*
62221039 TATTTTTACAATATC
1 TATTTTTACAACATC
62221054 TAT
1 TAT
62221057 ATTTCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTTACAACATC
Found at i:62225459 original size:21 final size:22
Alignment explanation
Indices: 62225430--62225473 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
62225420 CTTCAATTTT
*
62225430 GAAATAAAAAAAT-AAATTAAA
1 GAAACAAAAAAATAAAATTAAA
62225451 GAAACAAAAAAATGAAAATTAAA
1 GAAACAAAAAAAT-AAAATTAAA
62225474 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (22 bp):
GAAACAAAAAAATAAAATTAAA
Found at i:62229177 original size:16 final size:16
Alignment explanation
Indices: 62229128--62229178 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
62229118 GGGGTGCCAT
62229128 ATTTAAAATTTTATAA
1 ATTTAAAATTTTATAA
* *
62229144 ATTT-TACTTTTACT-A
1 ATTTAAAATTTTA-TAA
62229159 ATTTAAAATTTTATAA
1 ATTTAAAATTTTATAA
62229175 ATTT
1 ATTT
62229179 TAAAGGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAAATTTTATAA
Found at i:62232709 original size:16 final size:16
Alignment explanation
Indices: 62232681--62232720 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
62232671 GTAAATGAAT
*
62232681 TTAAACTTAAAAAATAA
1 TTAAAATTAAAAAA-AA
62232698 TTAAAATTAAAAAAAA
1 TTAAAATTAAAAAAAA
62232714 TTAAAAT
1 TTAAAAT
62232721 CCCTAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAATTAAAAAAAA
Found at i:62233892 original size:82 final size:82
Alignment explanation
Indices: 62233771--62233978 Score: 310
Period size: 82 Copynumber: 2.5 Consensus size: 82
62233761 GTATACATTG
* * * *
62233771 TTCAAAAAATCATTTCAAAAAAACAAACAAAATACGTTATACTAACGAAATGATGATATAGCAGT
1 TTCAAAAAATCATTTC-AAAAAACAAACAAAATATGTTATACTAACAAAATGATCATATAGAAGT
62233836 AAGATGTTAACCAACCAT
65 AAGATGTTAACCAACCAT
* * *
62233854 TTCAATAAATCATTTCAAAAAACAAACAAAATATGTTATGCTAACAAAATGATCCTATAGAAGTA
1 TTCAAAAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCATATAGAAGTA
*
62233919 AGATTTTAACCAACCAT
66 AGATGTTAACCAACCAT
*
62233936 TTCAACAAATCATTTCAAAAATACAAACAAAATATGTTA-ACTA
1 TTCAAAAAATCATTTCAAAAA-ACAAACAAAATATGTTATACTA
62233979 TCTCAATTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
82 82 0.72
83 32 0.28
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.26
Consensus pattern (82 bp):
TTCAAAAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCATATAGAAGTA
AGATGTTAACCAACCAT
Found at i:62234318 original size:159 final size:156
Alignment explanation
Indices: 62234052--62234509 Score: 473
Period size: 159 Copynumber: 2.9 Consensus size: 156
62234042 ATGCCATCCT
* * * * * * *
62234052 TTTTTG-GCTTGTAGTTCTCATACTCGTACTAGACTGAGAA-C--AAAAATTAAAACCCAAATTT
1 TTTTTGAGCTTCTAGTTCTCGTACTAGTACCAGACT-AAAACCAAAAAAATCAGAACCCAAA-TT
* *
62234113 AGATTTAAATAATT-TGGAATTGACATTAAAAAAATGTTTACAATATACCTGTGATCCAGTTCTG
64 AGATTTAAAT-ATTCT-GAATTGACATT-AAAAAGTGTTTACAATATACCTGTGATCCAGTTGTG
*
62234177 TTAGGCTGAATGCATGGTGTTTTGTTGTT-C
126 TTAGGCTGAATGCATGGTGTTATGTTGTTAC
* * * *
62234207 TTTTTTTAGCTTCTAGTTCGT-GTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCCAAAT
1 -TTTTTGAGCTTCTAGTTC-TCGTACTAGTACCAGACTAAAACCAAAAAAATCAGAA-CCCAAAT
* * * * *
62234271 TAGATTAAAATATTACTGAATTGACATTAAAATAGTGTATACGATATACCTATGATCCAGTTGTA
63 TAGATTTAAATATT-CTGAATTGACATTAAAA-AGTGTTTACAATATACCTGTGATCCAGTTGTG
*
62234336 TTAGGCTAAATGCATGGTGTTATGTTGTTAC
126 TTAGGCTGAATGCATGGTGTTATGTTGTTAC
* * *
62234367 TTTTTGGGCTTCTAGTTCTCGTACTAGTACCAGACTAAAACCAAAAAAATCAGAATCCAAATAAG
1 TTTTTGAGCTTCTAGTTCTCGTACTAGTACCAGACTAAAACCAAAAAAATCAGAACCCAAATTAG
* ** * * *
62234432 ATTTTAATATTTCAAAATTGACAATGAAAAAGTGTTTACAATATACCTGGGCTCCTA-TTGTGTT
66 ATTTAAATA-TTCTGAATTGAC-ATTAAAAAGTGTTTACAATATACCTGTGATCC-AGTTGTGTT
*
62234496 AGGTTGAATGCATG
128 AGGCTGAATGCATG
62234510 ATCCTTTGTT
Statistics
Matches: 251, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
156 7 0.03
157 25 0.10
158 70 0.28
159 141 0.56
160 8 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (156 bp):
TTTTTGAGCTTCTAGTTCTCGTACTAGTACCAGACTAAAACCAAAAAAATCAGAACCCAAATTAG
ATTTAAATATTCTGAATTGACATTAAAAAGTGTTTACAATATACCTGTGATCCAGTTGTGTTAGG
CTGAATGCATGGTGTTATGTTGTTAC
Found at i:62236293 original size:181 final size:181
Alignment explanation
Indices: 62235989--62236353 Score: 676
Period size: 181 Copynumber: 2.0 Consensus size: 181
62235979 TTTGGATGGT
* *
62235989 CCCCAATAGTAGCTTCAAAATGTTTTGTAATAACTTTTACATTGACCATTTTGTTTCTAAAACTA
1 CCCCAATAATAGCTTCAAAATGTTCTGTAATAACTTTTACATTGACCATTTTGTTTCTAAAACTA
*
62236054 ACACAATAGACGTGCTCATCATGAAAACTTTTCACCTGTGTGCATCTGGCCATGTTACTGTAACT
66 ACACAATAGACGTGCTCATCATGAAAACTTTTCACCTGTGTGCATCTGGCCATGTTACTGCAACT
62236119 TGAAAATATTCTCCATTTACACTTTTTTTGATGCAATGCATTTAACTCTAA
131 TGAAAATATTCTCCATTTACACTTTTTTTGATGCAATGCATTTAACTCTAA
62236170 CCCCAATAATAGCTTCAAAATGTTCTGTAATAACTTTTACATTGACCATTTTGTTTCTAAAACTA
1 CCCCAATAATAGCTTCAAAATGTTCTGTAATAACTTTTACATTGACCATTTTGTTTCTAAAACTA
* * *
62236235 ACACAATAGATGTGCTTATCATGAAAACTTTTCACCTGTGTGTATCTGGCCATGTTACTGCAACT
66 ACACAATAGACGTGCTCATCATGAAAACTTTTCACCTGTGTGCATCTGGCCATGTTACTGCAACT
62236300 TGAAAATATTCTCCATTTACACTTTTTTTGATGCAATGCATTTAACTCTAA
131 TGAAAATATTCTCCATTTACACTTTTTTTGATGCAATGCATTTAACTCTAA
62236351 CCC
1 CCC
62236354 TATTTGGTTC
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 178 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (181 bp):
CCCCAATAATAGCTTCAAAATGTTCTGTAATAACTTTTACATTGACCATTTTGTTTCTAAAACTA
ACACAATAGACGTGCTCATCATGAAAACTTTTCACCTGTGTGCATCTGGCCATGTTACTGCAACT
TGAAAATATTCTCCATTTACACTTTTTTTGATGCAATGCATTTAACTCTAA
Found at i:62253541 original size:16 final size:16
Alignment explanation
Indices: 62253522--62253556 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
62253512 ATATGAATCA
*
62253522 ATTTCTATATATATAT
1 ATTTATATATATATAT
*
62253538 ATTTATTTATATATAT
1 ATTTATATATATATAT
62253554 ATT
1 ATT
62253557 AAATGTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTATATATATATAT
Found at i:62264127 original size:98 final size:98
Alignment explanation
Indices: 62264019--62264229 Score: 298
Period size: 98 Copynumber: 2.2 Consensus size: 98
62264009 CGTCTTTTAA
* * *
62264019 AAATTATTTTTTTAGGAACTACTGTAGAAAAAGAGCATCCACGTAGGAATTTTTTTCAGTAATTT
1 AAATTATTTTTTTAGGAACTACTGTAGAAAAAAAGCATCCACGTAGGAACTTTTTTCAGTAAATT
* * *
62264084 TGTTGACAGTGCATCCTGCTTGAAGCTTTTTTG
66 TGCTGACAGTGCATACTGCTTGAAGCATTTTTG
* * * * *
62264117 AAATTATTTTTTCAGGAACTACTGTAGAAAAAAAGCGTCCATGTTGGAGCTTTTTTCAGTAAATT
1 AAATTATTTTTTTAGGAACTACTGTAGAAAAAAAGCATCCACGTAGGAACTTTTTTCAGTAAATT
62264182 TGCTGACAGTGCATACTGCTTGAAGCATTTTTG
66 TGCTGACAGTGCATACTGCTTGAAGCATTTTTG
*
62264215 ACATT-TTCTTTTTAG
1 AAATTATT-TTTTTAG
62264230 AACCGTCTTC
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 2 0.02
98 97 0.98
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (98 bp):
AAATTATTTTTTTAGGAACTACTGTAGAAAAAAAGCATCCACGTAGGAACTTTTTTCAGTAAATT
TGCTGACAGTGCATACTGCTTGAAGCATTTTTG
Found at i:62264148 original size:127 final size:127
Alignment explanation
Indices: 62263904--62264131 Score: 325
Period size: 126 Copynumber: 1.8 Consensus size: 127
62263894 TAAGGCCAAA
** * * *
62263904 TAGGAACTACTGTAGAAAAAGAGGGTCCACGTGGGAACTTTTTTTAGTAATTTTTTCTGATAGTG
1 TAGGAACTACTGTAGAAAAAGAGCATCCACGTAGGAACTTTTTTTAGTAATTTTGTCTGACAGTG
* * * **
62263969 CATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCATAATCGTCTTTTAAAAATTATTTTTT
66 CATCCTGCTTGAAGCGTTTTTGAAACTATTTTTTCAGAATCGTCTTAGAAAAATTATTTTTT
62264031 TAGGAACTACTGTAGAAAAAGAGCATCCACGTAGGAA-TTTTTTTCAGTAATTTTGT-TGACAGT
1 TAGGAACTACTGTAGAAAAAGAGCATCCACGTAGGAACTTTTTTT-AGTAATTTTGTCTGACAGT
* *
62264094 GCATCCTGCTTGAAGCTTTTTTGAAATTATTTTTTCAG
65 GCATCCTGCTTGAAGCGTTTTTGAAACTATTTTTTCAG
62264132 GAACTACTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
126 46 0.51
127 44 0.49
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (127 bp):
TAGGAACTACTGTAGAAAAAGAGCATCCACGTAGGAACTTTTTTTAGTAATTTTGTCTGACAGTG
CATCCTGCTTGAAGCGTTTTTGAAACTATTTTTTCAGAATCGTCTTAGAAAAATTATTTTTT
Found at i:62265607 original size:40 final size:42
Alignment explanation
Indices: 62265537--62265617 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 42
62265527 AAGACAAAAA
62265537 TATTATTTTCTCTTATATATATATTTTTAAGTGTATATGACG
1 TATTATTTTCTCTTATATATATATTTTTAAGTGTATATGACG
*
62265579 TATTATTTTCTC-T-TATATATATTTTTAAGTTTATATGAC
1 TATTATTTTCTCTTATATATATATTTTTAAGTGTATATGAC
62265618 ATGACAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 25 0.66
41 1 0.03
42 12 0.32
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (42 bp):
TATTATTTTCTCTTATATATATATTTTTAAGTGTATATGACG
Found at i:62266164 original size:26 final size:25
Alignment explanation
Indices: 62266129--62266191 Score: 99
Period size: 26 Copynumber: 2.5 Consensus size: 25
62266119 ATAATTTAAG
* *
62266129 ATAAATAATATTTATGTTTATGATA
1 ATAAATAATATTTATATTTATAATA
62266154 ACTAAATAATATTTATATTTATAATA
1 A-TAAATAATATTTATATTTATAATA
62266180 ATAAATAATATT
1 ATAAATAATATT
62266192 ATTTATCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 12 0.34
26 23 0.66
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (25 bp):
ATAAATAATATTTATATTTATAATA
Found at i:62266208 original size:28 final size:27
Alignment explanation
Indices: 62266129--62266209 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 27
62266119 ATAATTTAAG
* *
62266129 ATAAAT-A-ATATTTATGTTTATGATA
1 ATAAATAATATATTTATATTTAAGATA
62266154 ACTAAAT-A-ATATTTATATTTATA-ATA
1 A-TAAATAATATATTTATATTTA-AGATA
*
62266180 ATAAATAATATTATTTATCTTTAAGATA
1 ATAAATAATA-TATTTATATTTAAGATA
62266208 AT
1 AT
62266210 TTTATATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 6 0.13
26 23 0.49
27 2 0.04
28 16 0.34
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (27 bp):
ATAAATAATATATTTATATTTAAGATA
Found at i:62266214 original size:21 final size:21
Alignment explanation
Indices: 62266184--62266223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62266174 ATAATAATAA
*
62266184 ATAATATTATTTATCTTTAAG
1 ATAATATTATATATCTTTAAG
* *
62266205 ATAATTTTATATATTTTTA
1 ATAATATTATATATCTTTA
62266224 TTTTCTTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
ATAATATTATATATCTTTAAG
Found at i:62266288 original size:20 final size:20
Alignment explanation
Indices: 62266236--62266288 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
62266226 TTCTTACATA
* **
62266236 AAAATTTACGTAAATTTTTC
1 AAAATTTACTTAACCTTTTC
*
62266256 AAAATTTATTTAACCTTTTC
1 AAAATTTACTTAACCTTTTC
62266276 -AAATTTCACTTAA
1 AAAATTT-ACTTAA
62266289 GATTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTACTTAACCTTTTC
Found at i:62266595 original size:12 final size:12
Alignment explanation
Indices: 62266578--62266611 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
62266568 CGGCCCACCC
62266578 ATATTAATTTTT
1 ATATTAATTTTT
*
62266590 ATATTATTTTTT
1 ATATTAATTTTT
62266602 ATA-TAATTTT
1 ATATTAATTTT
62266612 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:62266769 original size:30 final size:29
Alignment explanation
Indices: 62266733--62266791 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
62266723 CAACTTAACA
62266733 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAA-AAAATT
* *
62266763 AGCAAATGTCTTTAAAATAATAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAATT
62266792 TAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (29 bp):
AGCAAATGCCTCTAAAATAATAAAAAATT
Found at i:62266878 original size:19 final size:20
Alignment explanation
Indices: 62266835--62266878 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
62266825 CAATAACAAC
* *
62266835 AAAATAGTAGTACATAATAGT
1 AAAATAGTAG-ACAAAATAGG
62266856 AAAATAGTAG-CAAAATAGG
1 AAAATAGTAGACAAAATAGG
62266875 AAAA
1 AAAA
62266879 AAATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATAGTAGACAAAATAGG
Found at i:62267196 original size:7 final size:7
Alignment explanation
Indices: 62267184--62267234 Score: 102
Period size: 7 Copynumber: 7.3 Consensus size: 7
62267174 CGTAATATAT
62267184 ATATCAC
1 ATATCAC
62267191 ATATCAC
1 ATATCAC
62267198 ATATCAC
1 ATATCAC
62267205 ATATCAC
1 ATATCAC
62267212 ATATCAC
1 ATATCAC
62267219 ATATCAC
1 ATATCAC
62267226 ATATCAC
1 ATATCAC
62267233 AT
1 AT
62267235 CCTTAACTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.29
Consensus pattern (7 bp):
ATATCAC
Found at i:62269068 original size:52 final size:52
Alignment explanation
Indices: 62269011--62269248 Score: 297
Period size: 52 Copynumber: 4.7 Consensus size: 52
62269001 ACCTAAAATA
* * * *
62269011 TTATGAATGCAACAAAACAAACAATTAAGCATAATTAAAAACACCACTTAAT
1 TTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAACACAACTTAAT
* * *
62269063 TTATGAATGCAACTAAACAATTAATGAAGCATAAATAAAAACACAACTTTAT
1 TTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAACACAACTTAAT
* * *
62269115 TTATGAATGCATCAAAGCAATCAATGAAACATAAATAAAAACA-AGAC----T
1 TTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAACACA-ACTTAAT
* *
62269163 TTATGAATGCAACAAAACAATCAATGAAGTATAAATAAAAACACAACTTTAT
1 TTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAACACAACTTAAT
* * *
62269215 TTATGAATGAAACAAAACAAACAATGAAACATAA
1 TTATGAATGCAACAAAACAATCAATGAAGCATAA
62269249 GTTGGAAACA
Statistics
Matches: 160, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
48 42 0.26
49 1 0.01
51 1 0.01
52 116 0.73
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.23
Consensus pattern (52 bp):
TTATGAATGCAACAAAACAATCAATGAAGCATAAATAAAAACACAACTTAAT
Found at i:62269189 original size:100 final size:100
Alignment explanation
Indices: 62269011--62269248 Score: 323
Period size: 100 Copynumber: 2.3 Consensus size: 100
62269001 ACCTAAAATA
* * * * * *
62269011 TTATGAATGCAACAAAACAAACAATTAAGCATAATTAAAAACACCACTTAATTTATGAATGCAAC
1 TTATGAATGAAACAAAACAAACAATGAAACATAAATAAAAACA--A--GACTTTATGAATGCAAC
* *
62269076 TAAACAATTAATGAAGCATAAATAAAAACACAACTTTAT
62 AAAACAATCAATGAAGCATAAATAAAAACACAACTTTAT
* * * *
62269115 TTATGAATGCATCAAAGCAATCAATGAAACATAAATAAAAACAAGACTTTATGAATGCAACAAAA
1 TTATGAATGAAACAAAACAAACAATGAAACATAAATAAAAACAAGACTTTATGAATGCAACAAAA
*
62269180 CAATCAATGAAGTATAAATAAAAACACAACTTTAT
66 CAATCAATGAAGCATAAATAAAAACACAACTTTAT
62269215 TTATGAATGAAACAAAACAAACAATGAAACATAA
1 TTATGAATGAAACAAAACAAACAATGAAACATAA
62269249 GTTGGAAACA
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
100 81 0.68
102 1 0.01
104 37 0.31
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.23
Consensus pattern (100 bp):
TTATGAATGAAACAAAACAAACAATGAAACATAAATAAAAACAAGACTTTATGAATGCAACAAAA
CAATCAATGAAGCATAAATAAAAACACAACTTTAT
Found at i:62274321 original size:21 final size:21
Alignment explanation
Indices: 62274284--62274347 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
62274274 TTATACAATA
*
62274284 TGAAACAAAATTTAGTGTATAC
1 TGAAAC-AAATTAAGTGTATAC
62274306 TGAAACAAATTAAGTGTATAC
1 TGAAACAAATTAAGTGTATAC
*
62274327 TGAAACAAGTTAAGTGT-TAC
1 TGAAACAAATTAAGTGTATAC
62274347 T
1 T
62274348 AATTTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.10
21 30 0.75
22 6 0.15
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (21 bp):
TGAAACAAATTAAGTGTATAC
Found at i:62279252 original size:25 final size:23
Alignment explanation
Indices: 62279211--62279272 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
62279201 TAGAAAATAA
62279211 AAAT-AAAAGATTATATATATGTTC
1 AAATAAAAAGATTATATATA--TTC
* *
62279235 AAATAAAAAGGTTGTATATATTC
1 AAATAAAAAGATTATATATATTC
62279258 AAATAAAAAGATTAT
1 AAATAAAAAGATTAT
62279273 GTTAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 16 0.48
24 4 0.12
25 13 0.39
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (23 bp):
AAATAAAAAGATTATATATATTC
Found at i:62286413 original size:6 final size:6
Alignment explanation
Indices: 62286381--62286411 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
62286371 CCCAATTAAG
*
62286381 AATAAA AATAAA AATAAA AATAAA ACTAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
62286412 CTCAAATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:62297359 original size:96 final size:94
Alignment explanation
Indices: 62297187--62297402 Score: 283
Period size: 95 Copynumber: 2.3 Consensus size: 94
62297177 TTTTTTTCAT
* * * * * *
62297187 TTAATTCGATACTTGAACTTTCAAAATGCATCAAAAAGGCTCTCAAGTTTTTTCAAAAAAAAATT
1 TTAATTCGATACTTGAACTGTCAAAATACATCAAAAAAGCCCTCAAGCTTTTTCAAAAAAAAAAT
62297252 AAGCCATTGCTTCTCTTTTTTTTTTTGCGC
66 AAGCCATTGCTTCT-TTTTTTTTTTTGCGC
* *
62297282 TTAATTTGGTACTTGAACTGTCAAAATACATCAAAAAAGCCCTCAAGCTTTTTCAAAAAAAAAAA
1 TTAATTCGATACTTGAACTGTCAAAATACATCAAAAAAGCCCTCAAGCTTTTTC-AAAAAAAAAA
62297347 TAAGCTC-TTGCTTCTTTTTTTTTTTTGCGC
65 TAAGC-CATTGCTTCTTTTTTTTTTTTGCGC
* * *
62297377 TCAATT-GAATACTTAAAATGTCAAAA
1 TTAATTCG-ATACTTGAACTGTCAAAA
62297403 GGCTATTTGA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
94 1 0.01
95 82 0.77
96 22 0.21
97 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (94 bp):
TTAATTCGATACTTGAACTGTCAAAATACATCAAAAAAGCCCTCAAGCTTTTTCAAAAAAAAAAT
AAGCCATTGCTTCTTTTTTTTTTTTGCGC
Found at i:62297879 original size:11 final size:9
Alignment explanation
Indices: 62297778--62297940 Score: 67
Period size: 10 Copynumber: 18.0 Consensus size: 9
62297768 CTTTGGTACG
62297778 ATAATTTTT
1 ATAATTTTT
*
62297787 ATATTTTTTT
1 ATA-ATTTTT
62297797 ATGAA-TTTT
1 AT-AATTTTT
62297806 AT-ATTTCTT
1 ATAATTT-TT
62297815 -TACATTTGTT
1 ATA-ATTT-TT
62297825 ATAACTTTTT
1 ATAA-TTTTT
* *
62297835 TTACAATTTT
1 ATA-ATTTTT
*
62297845 AT--GTTTT
1 ATAATTTTT
*
62297852 ACAATTTTT
1 ATAATTTTT
62297861 ATAATTTTT
1 ATAATTTTT
*
62297870 AATAAATTTT
1 -ATAATTTTT
62297880 A-AATTTTT
1 ATAATTTTT
*
62297888 -TTATTTTT
1 ATAATTTTT
* *
62297896 ATTAAAATTTA
1 A-T-AATTTTT
*
62297907 ATAACTTTT
1 ATAATTTTT
62297916 ATTAATTTTT
1 A-TAATTTTT
62297926 AT--TTTTT
1 ATAATTTTT
62297933 AT-ATTTTT
1 ATAATTTTT
62297941 TTGCCACTCA
Statistics
Matches: 117, Mismatches: 19, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
7 13 0.11
8 20 0.17
9 31 0.26
10 41 0.35
11 12 0.10
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:62297893 original size:26 final size:27
Alignment explanation
Indices: 62297848--62297926 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
62297838 CAATTTTATG
62297848 TTTTACAATTTTTATAATTTTTAATAAA
1 TTTTA-AATTTTTATAATTTTTAATAAA
* *
62297876 TTTTAAATTTTT-TTATTTTTATTAAAA
1 TTTTAAATTTTTATAATTTTTAAT-AAA
* *
62297903 TTTAATAACTTTTATTAATTTTTA
1 TTTTA-AATTTTTA-TAATTTTTA
62297927 TTTTTTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 9 0.21
27 14 0.33
28 11 0.26
30 8 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTAAATTTTTATAATTTTTAATAAA
Found at i:62301310 original size:28 final size:28
Alignment explanation
Indices: 62301270--62301324 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
62301260 CCGATTTGCT
62301270 CCCTCCGTTTATTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
62301298 CCCTCTGTTTATTTTCTTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCTTTTCT
62301325 ACCGATTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.04, C:0.27, G:0.05, T:0.64
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:62301345 original size:38 final size:39
Alignment explanation
Indices: 62301298--62301371 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
62301288 TTCTTTTCTG
*
62301298 CCCTCTGTTTATTTTC-TTTTCTTTTCTACCGATTTGCT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
* * * *
62301336 CCCTTTGTTTCTTCTCATTTTCTTTTTTGCCGATTT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTT
62301372 TTGAGTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 13 0.43
39 17 0.57
ACGTcount: A:0.07, C:0.26, G:0.08, T:0.59
Consensus pattern (39 bp):
CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
Found at i:62304584 original size:16 final size:16
Alignment explanation
Indices: 62304541--62304575 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
62304531 TGGTTCCTTA
*
62304541 TTAATTATAA-TATAT
1 TTAATAATAATTATAT
62304556 TTAATAATAATTATAT
1 TTAATAATAATTATAT
62304572 TTAA
1 TTAA
62304576 ATATGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATAATAATTATAT
Found at i:62304706 original size:18 final size:17
Alignment explanation
Indices: 62304678--62304712 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62304668 ATTATTAAGA
*
62304678 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62304695 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62304713 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:62304969 original size:16 final size:16
Alignment explanation
Indices: 62304948--62305031 Score: 141
Period size: 16 Copynumber: 5.2 Consensus size: 16
62304938 GATTTGCTAT
62304948 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62304964 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
62304980 TATACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
62304996 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
62305012 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62305028 TACA
1 TACA
62305032 GCGAACCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:62306615 original size:18 final size:18
Alignment explanation
Indices: 62306592--62306645 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
62306582 CATACAACGT
*
62306592 GATTCATGATTGTCAAGG
1 GATTCATGATCGTCAAGG
62306610 GATTCATGATCGTCAAGG
1 GATTCATGATCGTCAAGG
62306628 GATTCATGATCGTCAAGG
1 GATTCATGATCGTCAAGG
62306646 ATTTATGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (18 bp):
GATTCATGATCGTCAAGG
Found at i:62306972 original size:16 final size:14
Alignment explanation
Indices: 62306933--62306975 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
62306923 AATATAAGTG
62306933 GAATGGGATATCTC
1 GAATGGGATATCTC
*
62306947 GAATTGGGATATCTTTT
1 GAA-TGGGATATC--TC
62306964 GAATGGGATATC
1 GAATGGGATATC
62306976 CCTTATCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 9 0.36
17 4 0.16
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (14 bp):
GAATGGGATATCTC
Found at i:62307050 original size:21 final size:21
Alignment explanation
Indices: 62307018--62307057 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
62307008 TTCAATAACG
62307018 TAAAAAATTTGAACCAGACAC
1 TAAAAAATTTGAACCAGACAC
62307039 TAAAACAA-TTGAACCAGAC
1 TAAAA-AATTTGAACCAGAC
62307058 TGTAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.17
Consensus pattern (21 bp):
TAAAAAATTTGAACCAGACAC
Found at i:62309110 original size:21 final size:21
Alignment explanation
Indices: 62309086--62309127 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62309076 CTAAACCGAA
62309086 CACTAAAACAACC-GAATCGGG
1 CACTAAAA-AACCTGAATCGGG
*
62309107 CACTAAAAATCCTGAATCGGG
1 CACTAAAAAACCTGAATCGGG
62309128 ATGGAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (21 bp):
CACTAAAAAACCTGAATCGGG
Found at i:62312711 original size:26 final size:26
Alignment explanation
Indices: 62312682--62312765 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
62312672 TGATACAAAT
*
62312682 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
62312708 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
62312734 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
62312760 TGATAA
1 TGATAA
62312766 GAATTTCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:62319453 original size:25 final size:25
Alignment explanation
Indices: 62319410--62319492 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
62319400 CAACTTGCAT
* * *
62319410 GAGCTTACCATTATCCAGCTCGGAG
1 GAGCTTACTAATATTCAGCTCGGAG
* * ** *
62319435 GAGCTTATTAATGTTCAGCTCACAT
1 GAGCTTACTAATATTCAGCTCGGAG
* * *
62319460 GAGCTTGCTATTATTTAGCTCGGAG
1 GAGCTTACTAATATTCAGCTCGGAG
62319485 GAGCTTAC
1 GAGCTTAC
62319493 GGTTATCACT
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTACTAATATTCAGCTCGGAG
Found at i:62326634 original size:2 final size:2
Alignment explanation
Indices: 62326629--62326659 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62326619 AAAAAGATAA
62326629 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
62326660 AACAAATGGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62328022 original size:15 final size:15
Alignment explanation
Indices: 62328004--62328032 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62327994 AGCAAATTAC
62328004 ACATAAATAAATAGA
1 ACATAAATAAATAGA
62328019 ACATAAATAAATAG
1 ACATAAATAAATAG
62328033 TCAAACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
ACATAAATAAATAGA
Found at i:62331218 original size:21 final size:21
Alignment explanation
Indices: 62331194--62331233 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
62331184 AAAAACAACG
62331194 TAGTTTT-ACCTTTTAACTTAA
1 TAGTTTTGA-CTTTTAACTTAA
62331215 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
62331234 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:62336065 original size:28 final size:28
Alignment explanation
Indices: 62336025--62336086 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
62336015 CTTGCTCGAT
*
62336025 TTTAATTGAAATAGTAAAAAAATAAAAA
1 TTTAATTGAAATAATAAAAAAATAAAAA
** * *
62336053 TTTAATTTTAATAATAAAAATATATAAA
1 TTTAATTGAAATAATAAAAAAATAAAAA
62336081 TATTAA
1 T-TTAA
62336087 ACATAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTAATTGAAATAATAAAAAAATAAAAA
Found at i:62341094 original size:53 final size:53
Alignment explanation
Indices: 62341013--62341158 Score: 213
Period size: 53 Copynumber: 2.7 Consensus size: 53
62341003 CTTACACGGT
* *
62341013 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
62341068 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
**
62341121 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
62341159 AACTGGCGCA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:62345026 original size:12 final size:12
Alignment explanation
Indices: 62345009--62345033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62344999 ATGTAAGTGA
62345009 TCTTGATGATTT
1 TCTTGATGATTT
62345021 TCTTGATGATTT
1 TCTTGATGATTT
62345033 T
1 T
62345034 TACATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:62345804 original size:47 final size:45
Alignment explanation
Indices: 62345692--62345819 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 45
62345682 TCACTTGTGT
* **
62345692 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCATATTACG
1 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGACATAAGACG
* *
62345737 GAAGCTAATGTAAGACCATGTTTGGGACATGGCATCGGTAC-TAAGACG
1 G-TGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGG-ACATAAGACG
* *
62345785 AGTGCTAGTGTAAGACATGTCTAGGACATGCATCG
1 -GTGCTAGTGTAAGACATGTTTGGGACATGCATCG
62345820 ACTTCGAGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 17 0.25
47 26 0.38
48 23 0.33
49 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (45 bp):
GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGACATAAGACG
Found at i:62345844 original size:46 final size:48
Alignment explanation
Indices: 62345745--62345960 Score: 198
Period size: 47 Copynumber: 4.6 Consensus size: 48
62345735 CGGAAGCTAA
* ** *
62345745 TGTAAGACCATGTTTGGGACATGGCATCGGTACTAAGACGA-GT--GCTAG
1 TGTAAGACCATGTCTGGGACATGGCATC-G-ACTTCGA-GATGTAAGCCAG
* *
62345793 TGTAAGA-CATGTCTAGGACAT-GCATCGACTTCGAGATGTAAGCCAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGATGTAAGCCAG
* * * *
62345839 TGTAAGA-CATGTCTGGGACAT-ACATCGGCTACGAGATG-ATAGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGATGTA-AGCCAG
* * * *
62345885 TGTAAGACCATGTTTGGGATATGGCATCGACTT-GAGATATGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGATGTAAGCCAG
*
62345932 TGTAAGACCATGTCTGAGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
62345961 GTACCTTACC
Statistics
Matches: 138, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.01
44 7 0.05
45 2 0.01
46 53 0.38
47 60 0.43
48 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGATGTAAGCCAG
Found at i:62352634 original size:12 final size:12
Alignment explanation
Indices: 62352617--62352641 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62352607 ATGTAAGTGA
62352617 TCTTGATGATTT
1 TCTTGATGATTT
62352629 TCTTGATGATTT
1 TCTTGATGATTT
62352641 T
1 T
62352642 TACATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:62353356 original size:46 final size:46
Alignment explanation
Indices: 62353303--62353523 Score: 161
Period size: 46 Copynumber: 4.7 Consensus size: 46
62353293 TTGTGTGTGC
*
62353303 TAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGGAAGA
1 TAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATGGAAGA
* *
62353349 TAGTGTAAGACCATGTCTGGGACGTGGCATTGA-CAC-TGA--GACGAGTA
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCACATGATGGA--AG-A
* * * *
62353396 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTAAGC
1 -TAGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATGATGGAAGA
* * * * *
62353443 CAGTGTAAGACATGTCTGGGACATTCATCGGCTA-AGAGAT-GATAG-
1 TAGTGTAAGACATGTCTGGGACATGCATCGACCACA-TGATGGA-AGA
*
62353488 TCTGTGTAAGACCATGTCTGGGACATGGCATCGACC
1 T-AGTGTAAGA-CATGTCTGGGACAT-GCATCGACC
62353524 TGAGATATGA
Statistics
Matches: 139, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 62 0.45
47 46 0.33
48 26 0.19
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATGGAAGA
Found at i:62353529 original size:47 final size:45
Alignment explanation
Indices: 62353304--62353567 Score: 207
Period size: 47 Copynumber: 5.6 Consensus size: 45
62353294 TGTGTGTGCT
** *
62353304 AGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGGA-AGAT-
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTGA-GAT-GATAG-TC
* * * *
62353350 AGTGTAAGACCATGTCTGGGACGTGGCATTGACACTGAGACGAGTACT-
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-CTGAGATGA-TAGTC
* *
62353398 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCT-GAGATGAT-AGTC
* *
62353444 AGTGTAAGACATGTCTGGGACATTCATCG-GCTAAGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCT--GAGATGATAGTC
* *
62353490 TGTGTAAGACCATGTCTGGGACATGGCATCGACCTGAGAT-ATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTGAGATGAT-AGTC
* *
62353537 AGTGTAAGGCCATGTCTGGGATATGGCATCG
1 AGTGTAA-GACATGTCTGGGACAT-GCATCG
62353568 GCACCTTATC
Statistics
Matches: 179, Mismatches: 24, Indels: 29
0.77 0.10 0.12
Matches are distributed among these distances:
44 1 0.01
45 5 0.03
46 67 0.37
47 77 0.43
48 24 0.13
49 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCTGAGATGATAGTC
Found at i:62355298 original size:25 final size:25
Alignment explanation
Indices: 62355264--62355312 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
62355254 CGATTGATTC
62355264 GAAACTTTGCTTACAAAACAAACAA
1 GAAACTTTGCTTACAAAACAAACAA
62355289 GAAACTTTGCTTACAAAACAAACA
1 GAAACTTTGCTTACAAAACAAACA
62355313 CATTACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.08, T:0.20
Consensus pattern (25 bp):
GAAACTTTGCTTACAAAACAAACAA
Found at i:62355322 original size:29 final size:26
Alignment explanation
Indices: 62355265--62355337 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 26
62355255 GATTGATTCG
*
62355265 AAACTTTGCTTACAAAAC-AAACAAG
1 AAACTTTGCTTACAAAACAAAACAAC
62355290 AAACTTTGCTTACAAAACAAACACATTAC
1 AAACTTTGCTTACAAAACAAA-ACA--AC
62355319 AAACTCTT-CTTA-AAAACAA
1 AAACT-TTGCTTACAAAACAA
62355338 CTTTGAACAC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 18 0.43
26 2 0.05
27 3 0.07
28 7 0.17
29 10 0.24
30 2 0.05
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.23
Consensus pattern (26 bp):
AAACTTTGCTTACAAAACAAAACAAC
Found at i:62360035 original size:40 final size:40
Alignment explanation
Indices: 62359937--62360239 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
62359927 TCCTCGTTCA
* * * * *
62359937 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
62359976 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
62360016 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62360056 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62360096 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
62360136 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
62360176 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
62360216 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
62360240 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:62378271 original size:37 final size:37
Alignment explanation
Indices: 62378220--62378299 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
62378210 CTTATTACGA
* * *
62378220 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
* *
62378257 GGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
62378294 AGTCTT
1 AGTCTT
62378300 TAAAGCTCGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
Found at i:62378686 original size:49 final size:47
Alignment explanation
Indices: 62378418--62378920 Score: 848
Period size: 47 Copynumber: 10.6 Consensus size: 47
62378408 CCCTTCGGGA
* * * * * *
62378418 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
62378465 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378512 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378559 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378606 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378653 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378702 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378751 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378800 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378847 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
62378894 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
62378921 ACCAACCCTT
Statistics
Matches: 442, Mismatches: 10, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
46 36 0.08
47 218 0.49
48 50 0.11
49 138 0.31
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:62379218 original size:40 final size:40
Alignment explanation
Indices: 62379145--62379327 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
62379135 GCTACTCGTT
62379145 CAAATGCCTTCGGGA--TAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
62379183 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
62379223 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
62379262 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
62379303 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
62379328 CATCATTCGA
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 17 0.13
39 33 0.26
40 63 0.50
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:62379267 original size:79 final size:81
Alignment explanation
Indices: 62379145--62379327 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
62379135 GCTACTCGTT
* *
62379145 CAAATGCCTTCGGG-ATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
62379207 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
62379223 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
62379287 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
62379303 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
62379328 CATCATTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 17 0.19
79 54 0.59
80 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:62382957 original size:44 final size:44
Alignment explanation
Indices: 62382894--62382982 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
62382884 TTTTACTAAA
62382894 AAGGACGCGTCATTTGCCAATAACCTCGACAGTGAAAGAAACAT
1 AAGGACGCGTCATTTGCCAATAACCTCGACAGTGAAAGAAACAT
* **
62382938 AAGGACGCGTCATTTGCCAATAACCTTGATTGTGAAAGAAACAT
1 AAGGACGCGTCATTTGCCAATAACCTCGACAGTGAAAGAAACAT
62382982 A
1 A
62382983 CTTTCACCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (44 bp):
AAGGACGCGTCATTTGCCAATAACCTCGACAGTGAAAGAAACAT
Found at i:62389511 original size:27 final size:27
Alignment explanation
Indices: 62389446--62389622 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
62389436 ATATTGAGCC
* * * *
62389446 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
62389473 -GCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62389499 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
62389527 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
62389554 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
62389581 CGCACACTTAGTGCAACATAGTCATAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62389608 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
62389623 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.17
27 83 0.64
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:62390187 original size:13 final size:13
Alignment explanation
Indices: 62390169--62390193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62390159 TACTAAATTT
62390169 TCATGGATTCAAG
1 TCATGGATTCAAG
62390182 TCATGGATTCAA
1 TCATGGATTCAA
62390194 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:62390967 original size:19 final size:21
Alignment explanation
Indices: 62390945--62390987 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62390935 TTTATTCATC
*
62390945 CTTCTTTT-TTTT-TAATTCA
1 CTTCTTTTATTTTCTAATCCA
62390964 CTTCTTTTATTTTCTAATCCA
1 CTTCTTTTATTTTCTAATCCA
62390985 CTT
1 CTT
62390988 ACCAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
21 9 0.43
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTCTTTTATTTTCTAATCCA
Found at i:62397499 original size:27 final size:27
Alignment explanation
Indices: 62397469--62397646 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
62397459 ATATTGAGCC
* *
62397469 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
62397496 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
62397523 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
62397551 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
62397578 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
62397605 CGCACACTTAGTGCAACATAGTCATA-T
1 CGCACACTTAGTGCTACATAATCA-ACT
62397632 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
62397647 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:62397608 original size:82 final size:81
Alignment explanation
Indices: 62397490--62397645 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
62397480 TGCTATATAA
* *
62397490 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
62397555 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
62397572 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
62397636 CACTTAGTGC
65 CACTTAGTGC
62397646 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:62398212 original size:13 final size:13
Alignment explanation
Indices: 62398194--62398218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62398184 TACTAAATTT
62398194 TCATGGATTCAAG
1 TCATGGATTCAAG
62398207 TCATGGATTCAA
1 TCATGGATTCAA
62398219 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:62399015 original size:21 final size:20
Alignment explanation
Indices: 62398974--62399016 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
62398964 TATTCATCCT
* *
62398974 TTCTTTTCTTTTTAATTCAC
1 TTCTTTTATTTTTAATCCAC
62398994 TTCTTTTATTTTCTAATCCAC
1 TTCTTTTATTTT-TAATCCAC
62399015 TT
1 TT
62399017 ACCAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (20 bp):
TTCTTTTATTTTTAATCCAC
Found at i:62402380 original size:14 final size:15
Alignment explanation
Indices: 62402350--62402384 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
62402340 TTGATTATTA
*
62402350 TGATGAGATATTGTG
1 TGATGAGACATTGTG
62402365 TGATGAGACA-TGTG
1 TGATGAGACATTGTG
62402379 TGATGA
1 TGATGA
62402385 TTATTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (15 bp):
TGATGAGACATTGTG
Found at i:62403044 original size:18 final size:19
Alignment explanation
Indices: 62403017--62403054 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
62403007 ATAATTAAAC
* *
62403017 ATAAATAAATGAAAT-GAA
1 ATAAAGAAATAAAATAGAA
62403035 ATAAAGAAATAAAATAGAA
1 ATAAAGAAATAAAATAGAA
62403054 A
1 A
62403055 AAGAATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (19 bp):
ATAAAGAAATAAAATAGAA
Found at i:62403085 original size:7 final size:7
Alignment explanation
Indices: 62403075--62403106 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
62403065 AAGAAACGAA
62403075 AAAGGGG
1 AAAGGGG
62403082 AAAGGGG
1 AAAGGGG
62403089 AAAGGGG
1 AAAGGGG
62403096 AAAGGGG
1 AAAGGGG
62403103 AAAG
1 AAAG
62403107 AAAGAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (7 bp):
AAAGGGG
Found at i:62403085 original size:21 final size:21
Alignment explanation
Indices: 62403061--62403108 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
62403051 GAAAAAGAAT
62403061 AAAGAAGAAACGAAAAAGGGG
1 AAAGAAGAAACGAAAAAGGGG
** * **
62403082 AAAGGGGAAAGGGGAAAGGGG
1 AAAGAAGAAACGAAAAAGGGG
62403103 AAAGAA
1 AAAGAA
62403109 AGAAGGAAAG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAACGAAAAAGGGG
Found at i:62405644 original size:30 final size:30
Alignment explanation
Indices: 62405603--62405659 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
62405593 AAATTCACAT
* *
62405603 CTTTGGTAAAATGACCATTTTGCCCCTTGA
1 CTTTGGCAAAATGACCATTTTACCCCTTGA
62405633 CTTTGGCAAAATGACCATTTTACCCCT
1 CTTTGGCAAAATGACCATTTTACCCCT
62405660 ATGCTCGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTTGA
Found at i:62411159 original size:48 final size:48
Alignment explanation
Indices: 62411095--62411493 Score: 285
Period size: 48 Copynumber: 8.0 Consensus size: 48
62411085 TGTACAAGAT
* * * *
62411095 AAATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGTAATATGTATG
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
62411143 AAATATGTATATGTGGTAAAGCCGAATGTCTAATGTG--A-A-GTATG
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * * *
62411187 AGATATGTATATATGGTCAAGCTGAATGGCTAATGTGAAATATGTATG
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
62411235 AGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTATG
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * * * * *
62411283 AGATAATGTGAAATAT-GT-ATG-AGATAT-G-TATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAAT-ATGT-ATATGTGGTAAAGCCGA-ATGGCTA-ATGT-G-AAA----TAT-G-T-A--TG
* * *
62411341 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAACGGCTAGTGTGAAATATATATG
1 AAATATG-----------TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
62411400 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATG
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
62411448 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
62411494 GGAGATGTGT
Statistics
Matches: 286, Mismatches: 30, Indels: 70
0.74 0.08 0.18
Matches are distributed among these distances:
44 37 0.13
45 1 0.00
46 4 0.01
47 8 0.03
48 176 0.62
49 9 0.03
50 4 0.01
53 2 0.01
54 1 0.00
55 1 0.00
56 1 0.00
57 3 0.01
58 5 0.02
59 8 0.03
61 1 0.00
62 1 0.00
64 2 0.01
67 4 0.01
68 6 0.02
69 4 0.01
70 6 0.02
71 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
AAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:62411229 original size:92 final size:92
Alignment explanation
Indices: 62411108--62411278 Score: 270
Period size: 92 Copynumber: 1.9 Consensus size: 92
62411098 TATATATGTG
* * *
62411108 TGGTAAAGCCGAATGGCTAGTGTGTAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGTC
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGC
*
62411173 TAATGTGAAGTATGAGATATGTATATA
66 TAATGTGAAATATGAGATATGTATATA
* * * *
62411200 TGGTCAAGCTGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGC
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGC
62411265 TAATGTGAAATATG
66 TAATGTGAAATATG
62411279 TATGAGATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 71 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (92 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGC
TAATGTGAAATATGAGATATGTATATA
Found at i:62411290 original size:21 final size:21
Alignment explanation
Indices: 62411265--62411308 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
62411255 GTCGAATGGC
62411265 TAATGTGAAATATGTATGAGA
1 TAATGTGAAATATGTATGAGA
62411286 TAATGTGAAATATGTATGAGA
1 TAATGTGAAATATGTATGAGA
62411307 TA
1 TA
62411309 TGTATATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (21 bp):
TAATGTGAAATATGTATGAGA
Found at i:62411298 original size:69 final size:69
Alignment explanation
Indices: 62411217--62411356 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
62411207 GCTGAATGGC
*
62411217 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTAT
1 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
62411282 GAGA
66 GAGA
62411286 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
62411351 GAGA
66 GAGA
62411355 TA
1 TA
62411357 TGTATATGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (69 bp):
TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
GAGA
Found at i:62411365 original size:117 final size:117
Alignment explanation
Indices: 62411182--62411404 Score: 383
Period size: 117 Copynumber: 1.9 Consensus size: 117
62411172 CTAATGTGAA
* *
62411182 GTATGAGATATGTATATATGGTCAAGCTGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
1 GTATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
* * *
62411247 GTGGTAAAGTCGAATGGCTAATGTGAAATATGTATGAGATAATGTGAAATAT
66 GTGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATAATGTGAAATAT
*
62411299 GTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
1 GTATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
*
62411364 GTGGTAAAGCCGAACGGCTAGTGTGAAATATATATGAGATA
66 GTGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATA
62411405 TGTATATGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (117 bp):
GTATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
GTGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATAATGTGAAATAT
Found at i:62411415 original size:165 final size:161
Alignment explanation
Indices: 62411128--62411452 Score: 515
Period size: 165 Copynumber: 2.0 Consensus size: 161
62411118 GAATGGCTAG
* *
62411128 TGTGTAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGTCTAATGTGAAGTATGAGATAT
1 TGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAGTATGAGATAT
* * * * *
62411193 GTATATATGGTCAAGCTGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTC
66 GTATATATGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCC
62411258 GAATGGCTAATGTGAAATATGTATGAGATAA
131 GAATGGCTAATGTGAAATATGTATGAGATAA
*
62411289 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 TGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGCTAATGTG--A-A-GTATGAG
* *
62411354 ATATGTATATGTGGTAAAGCCGAACGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAA
62 ATATGTATATATGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
*
62411419 AGCCGAATGGCTAGTGTGAAATATGTATGAGATA
127 AGCCGAATGGCTAATGTGAAATATGTATGAGATA
62411453 TGTATATGTG
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
161 49 0.33
163 1 0.01
164 1 0.01
165 98 0.66
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (161 bp):
TGTGAAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAGTATGAGATAT
GTATATATGGTAAAGCCGAACGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCC
GAATGGCTAATGTGAAATATGTATGAGATAA
Found at i:62411476 original size:213 final size:209
Alignment explanation
Indices: 62411097--62411499 Score: 626
Period size: 213 Copynumber: 1.9 Consensus size: 209
62411087 TACAAGATAA
* * *
62411097 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGTAATATGTATGAAATATGTATATGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAA
* * * * *
62411162 AGCCGAATGTCTAATGTGAAGTATGAGATATGTATATATGGTCAAGCTGAATGGCTAATGTGAAA
66 AGCCGAACGGCTAATGTGAAATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAA
* *
62411227 TATGTATGAGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTATGAGATAATGT
131 TATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAGATAATGT
62411292 GAAATATGTATGAG
196 GAAATATGTATGAG
* *
62411306 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAA
* * *
62411371 AGCCGAACGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
66 AGCCGAACGGCTAATGTG--A-A-ATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGT
*
62411436 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
127 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAGAT
62411500 GTGTGTATAT
Statistics
Matches: 174, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
209 75 0.43
211 1 0.01
212 1 0.01
213 97 0.56
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (209 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAAATATGTATATGTGGTAA
AGCCGAACGGCTAATGTGAAATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAA
TATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAGATAATGT
GAAATATGTATGAG
Found at i:62411499 original size:48 final size:48
Alignment explanation
Indices: 62411289--62411499 Score: 386
Period size: 48 Copynumber: 4.4 Consensus size: 48
62411279 TATGAGATAA
*
62411289 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAA
1 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
*
62411337 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAACGGCTAG
1 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
*
62411385 TGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
1 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
62411433 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
1 TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
*
62411481 TGTGAAATATGTAGGAGAT
1 TGTGAAATATGTATGAGAT
62411500 GTGTGTATAT
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 157 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
Found at i:62411690 original size:37 final size:37
Alignment explanation
Indices: 62411640--62411742 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
62411630 GGAAATATAT
62411640 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
62411677 TCCGGGTAAGACCCGATGACTACGTGTTGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
62411714 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
62411743 GGACTATTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:62413126 original size:40 final size:40
Alignment explanation
Indices: 62413028--62413398 Score: 645
Period size: 40 Copynumber: 9.3 Consensus size: 40
62413018 GAGTTATATA
*
62413028 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
62413068 TAT-CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
62413107 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
62413147 TATCCGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
62413187 TATCCGGGCTAAGCTCCGAAAAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
62413227 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
62413267 TATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
62413307 TATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
62413347 TATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
62413387 TATCCGGGCTAA
1 TATCCGGGCTAA
62413399 ACCTCGAAGG
Statistics
Matches: 317, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 38 0.12
40 279 0.88
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
Found at i:62413470 original size:28 final size:27
Alignment explanation
Indices: 62413430--62413586 Score: 134
Period size: 28 Copynumber: 5.6 Consensus size: 27
62413420 GAGTTATGAG
* * *
62413430 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
* * * * *
62413458 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
*
62413486 GGCACTATGTGTGCGAGTTCTTCAATCAA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
62413515 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
62413543 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
62413572 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
62413587 AATCAGTCAG
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
28 56 0.55
29 46 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:62413493 original size:29 final size:27
Alignment explanation
Indices: 62413458--62413559 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 27
62413448 CTTCAACCGA
*
62413458 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTA-TTGAG
* * * * *
62413487 GCACTATGTGTGCGAGTTCTTCAATCAA
1 GCACTATGTGTGCGAGATCGT-ATTGAG
*
62413515 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGT-ATTGAG
62413544 GCACTATGTGTGCGAG
1 GCACTATGTGTGCGAG
62413560 TTCTTTAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
28 19 0.33
29 39 0.67
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (27 bp):
GCACTATGTGTGCGAGATCGTATTGAG
Found at i:62413518 original size:57 final size:57
Alignment explanation
Indices: 62413426--62413593 Score: 237
Period size: 57 Copynumber: 2.9 Consensus size: 57
62413416 GCTGGAGTTA
* * * * *
62413426 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* **
62413483 TGAGGCACTATGTGTGCGAGTTCTTCAATCAAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* * *
62413540 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
62413594 CAGTGGGCAC
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 97 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:62417193 original size:48 final size:48
Alignment explanation
Indices: 62417122--62417411 Score: 490
Period size: 48 Copynumber: 6.0 Consensus size: 48
62417112 CAAGATAAAT
* *
62417122 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
62417170 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
62417218 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
62417266 ATATGTATATGTGGTAAAGCCGAACGGCTAGTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
62417314 ATATGTATATGTGGTAACGCCGAACGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
62417362 ATATGTATATGTGGTAACGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
62417410 AT
1 AT
62417412 GTGTGTATAT
Statistics
Matches: 232, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 232 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:62417602 original size:37 final size:37
Alignment explanation
Indices: 62417552--62417691 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
62417542 GGAAATATAT
*
62417552 TCCGGGTAAGACCCGATGACTACGTGTGCAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
62417589 TCCGGGTAAGACCCGATGGCTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
62417626 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
62417663 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
62417692 GGACTATTCG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:62423939 original size:55 final size:55
Alignment explanation
Indices: 62423838--62423972 Score: 171
Period size: 55 Copynumber: 2.5 Consensus size: 55
62423828 TTAGCCCTTA
* * * ** *
62423838 GCCCGTGTGCAACACTAACTTTAAAACATGGCCATGATGCACGCCCGTGTGTCCT
1 GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCCT
* * *
62423893 GCCCGTGTACAACATTGACTTTAAAACACGGCTATGACACATGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCCT
* *
62423948 ACCCATGTACAACACTGACTTTAAA
1 GCCCGTGTACAACACTGACTTTAAA
62423973 TTTTAAGTGC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCCT
Found at i:62424797 original size:49 final size:45
Alignment explanation
Indices: 62424723--62424941 Score: 210
Period size: 49 Copynumber: 4.6 Consensus size: 45
62424713 GATATGTTGT
*
62424723 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATTGAGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCATC-TT-AGGC
* * * *
62424772 TGATGTCATGTCCCAGACATGGTCTTATACTAGCTCTCGTCTATACGTGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCATCT-TA-G-GC
* *
62424822 TGATGCATGTCCCAGACATGTCTTACACCAGC-A-CAACTCTTA-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTATC-A-TCTTAGGC
* * *
62424866 CGATGCGTGTCCCAGACACGTCTTACACTAGCTATCATCGTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTATCATC-T-TAGGC
62424913 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
62424942 GGTACACAAG
Statistics
Matches: 143, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
44 32 0.22
45 3 0.02
46 3 0.02
47 31 0.22
48 16 0.11
49 51 0.36
50 7 0.05
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTATCATCTTAGGC
Found at i:62428657 original size:18 final size:19
Alignment explanation
Indices: 62428634--62428669 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62428624 ATTAAACATA
*
62428634 AAATAAATGAAAT-GAAAT
1 AAATAAATAAAATAGAAAT
62428652 AAATAAATAAAATAGAAA
1 AAATAAATAAAATAGAAA
62428670 AAGAATAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AAATAAATAAAATAGAAAT
Found at i:62432190 original size:27 final size:27
Alignment explanation
Indices: 62432160--62432337 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
62432150 ATATTGAGTC
* * * *
62432160 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
62432187 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62432214 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
62432242 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
62432269 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
62432296 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62432323 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
62432338 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:62432299 original size:82 final size:81
Alignment explanation
Indices: 62432181--62432336 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
62432171 TGCTATATAA
* *
62432181 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
62432246 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
62432263 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
62432327 CACTTAGTGC
65 CACTTAGTGC
62432337 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:62461100 original size:43 final size:43
Alignment explanation
Indices: 62461052--62461198 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
62461042 ATCGAGATGT
* *
62461052 GATTACATGTAAGACCATGTTTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * * * *
62461095 GATTACGTGTAAAACCATGTCTAGTACATTGCCATCGTATTGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * ** * *
62461138 GATTTCGTGTAAGACTTTGTCTGGGATAGTGGCATCG-ATATGTA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TG-A
*
62461182 -TTTACATGTAAGACCAT
1 GATTACATGTAAGACCAT
62461199 ATTTGGGATA
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
42 2 0.03
43 77 0.97
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:62463220 original size:4 final size:4
Alignment explanation
Indices: 62463211--62463252 Score: 66
Period size: 4 Copynumber: 10.0 Consensus size: 4
62463201 CTTAAACCTT
62463211 TTTA TTTA TTTA TTTA TTTA TTTCA TTTCA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTT-A TTTA TTTA TTTA
62463253 CAAGACAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 28 0.76
5 9 0.24
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:62468178 original size:25 final size:25
Alignment explanation
Indices: 62468114--62468202 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
62468104 CATATAATAA
* * * * *
62468114 GAAGCTCATGTGAGTTATATATTGG
1 GAAGCTCAAGAGAGCTAAATATCGG
** *
62468139 GAAGCTCTTGCGAGCTAAATATCGG
1 GAAGCTCAAGAGAGCTAAATATCGG
**
62468164 GAAGCTCAAGAGAGCT-GTTAATCGG
1 GAAGCTCAAGAGAGCTAAAT-ATCGG
62468189 GAAGCTCAAGAGAG
1 GAAGCTCAAGAGAG
62468203 TCGTGGTGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 1 0.02
25 52 0.98
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (25 bp):
GAAGCTCAAGAGAGCTAAATATCGG
Found at i:62469630 original size:40 final size:40
Alignment explanation
Indices: 62469586--62469847 Score: 315
Period size: 39 Copynumber: 6.7 Consensus size: 40
62469576 GCTCCTCGTT
* *
62469586 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
62469626 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
62469666 CAAATGCCTTTGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
62469705 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
62469744 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
62469783 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
62469824 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
62469848 CATCATTCAA
Statistics
Matches: 200, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 124 0.62
40 64 0.32
41 10 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:62469802 original size:118 final size:121
Alignment explanation
Indices: 62469586--62469847 Score: 328
Period size: 118 Copynumber: 2.2 Consensus size: 121
62469576 GCTCCTCGTT
* *
62469586 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* * *
62469650 GATTTAGTAACTCGCACAAATGCCTTTGGGCTTAGCCCGGA-ATTAGT-A-TCTCGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATATT-GTCACT-TAGCA
* *
62469705 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCC-
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* * *
62469766 GAAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCA
66 G-AATTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGATATTGTCACTTAGCA
62469824 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
62469848 CATCATTCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
116 1 0.01
117 41 0.33
118 59 0.47
119 24 0.19
120 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (121 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
GAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATATTGTCACTTAGCA
Found at i:62473995 original size:17 final size:17
Alignment explanation
Indices: 62473967--62473999 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62473957 GGTGGTTGAT
62473967 GGTGGATGAGAAGTGAAC
1 GGTGGATGAGAA-TGAAC
62473985 GGTGG-TGAGAATGAA
1 GGTGGATGAGAATGAA
62474000 AGAAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTGGATGAGAATGAAC
Found at i:62482534 original size:19 final size:19
Alignment explanation
Indices: 62482510--62482547 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
62482500 TTATATGATG
62482510 TTTGAATTGAATATTTGAA
1 TTTGAATTGAATATTTGAA
62482529 TTTGAATTGAATATTTGAA
1 TTTGAATTGAATATTTGAA
62482548 AAGGATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTGAATTGAATATTTGAA
Found at i:62488191 original size:17 final size:17
Alignment explanation
Indices: 62488169--62488216 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
62488159 GGGCCAAATA
62488169 GGCCGTGTCCTTCACAC
1 GGCCGTGTCCTTCACAC
*
62488186 GGCCGTGTGC-T---A-
1 GGCCGTGTCCTTCACAC
62488198 GGCCGTGTCCTTCACAC
1 GGCCGTGTCCTTCACAC
62488215 GG
1 GG
62488217 TTGAGACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
12 9 0.38
13 2 0.08
16 2 0.08
17 11 0.46
ACGTcount: A:0.10, C:0.35, G:0.31, T:0.23
Consensus pattern (17 bp):
GGCCGTGTCCTTCACAC
Found at i:62490329 original size:40 final size:40
Alignment explanation
Indices: 62490246--62490524 Score: 375
Period size: 40 Copynumber: 7.0 Consensus size: 40
62490236 TTGAATGCTG
* * * * * *
62490246 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
62490286 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
62490326 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
62490366 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
62490406 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
62490446 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
62490486 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
62490525 ANNNNNNNNN
Statistics
Matches: 219, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 13 0.06
40 198 0.90
41 8 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:62501846 original size:79 final size:78
Alignment explanation
Indices: 62501746--62501968 Score: 249
Period size: 79 Copynumber: 2.8 Consensus size: 78
62501736 GCTCCTCGTT
* *
62501746 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
62501811 ATTTAGTAACTTGCA
64 AATTAGTAACTCGCA
*
62501826 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
62501889 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * *
62501904 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACA-TAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-A-ATTCGCACAAATGCCTTCGGGACTTAGCCC
62501966 GGA
62 GGA
62501969 CATCATTCAA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
78 46 0.37
79 57 0.46
80 20 0.16
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:62501866 original size:39 final size:40
Alignment explanation
Indices: 62501746--62501968 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
62501736 GCTCCTCGTT
* *
62501746 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
62501786 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
62501826 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
62501865 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
62501904 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CATAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
62501945 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
62501969 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 63 0.38
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:62505293 original size:15 final size:17
Alignment explanation
Indices: 62505273--62505306 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
62505263 TATATTATTA
62505273 AAAATTG-AAT-AAGTT
1 AAAATTGTAATGAAGTT
62505288 AAAATTGTAATGAAGTT
1 AAAATTGTAATGAAGTT
62505305 AA
1 AA
62505307 CATTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
AAAATTGTAATGAAGTT
Found at i:62510733 original size:21 final size:20
Alignment explanation
Indices: 62510709--62510760 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
62510699 TTATGCCACA
*
62510709 TCAGTATTCTTATCTTGAATT
1 TCAGTATT-TTATCCTGAATT
*
62510730 TCAGGATTTTATCCTGAATT
1 TCAGTATTTTATCCTGAATT
62510750 TCAGTATTTTA
1 TCAGTATTTTA
62510761 ATTTGGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (20 bp):
TCAGTATTTTATCCTGAATT
Found at i:62522391 original size:40 final size:40
Alignment explanation
Indices: 62522354--62522538 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
62522344 GCTACTCGTT
*
62522354 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
62522394 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
62522434 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
62522473 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
62522514 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
62522539 CATCATTGAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:62522471 original size:79 final size:81
Alignment explanation
Indices: 62522354--62522536 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
62522344 GCTACTCGTT
* ** *
62522354 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
62522418 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
62522434 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
62522497 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
62522514 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
62522537 GACATCATTG
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 32 0.36
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:62525599 original size:17 final size:16
Alignment explanation
Indices: 62525538--62525600 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
62525528 GTTCATTTAC
*
62525538 TTATTTATATATATATA
1 TTATTTATTTAT-TATA
* *
62525555 TTATTCATTTA-TATT
1 TTATTTATTTATTATA
*
62525570 TTATTTTAATTATTATA
1 TTA-TTTATTTATTATA
62525587 TTCATTTATTTATT
1 TT-ATTTATTTATT
62525601 GTTCTTTCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 23 0.64
18 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTATTTATTATA
Found at i:62525633 original size:28 final size:28
Alignment explanation
Indices: 62525602--62525667 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
62525592 TTATTTATTG
62525602 TTCTTTCATTTCTTTTTAAATTTTTACT
1 TTCTTTCATTTCTTTTTAAATTTTTACT
62525630 TTCTTTCATTTCTTTTTAAATTTTTACT
1 TTCTTTCATTTCTTTTTAAATTTTTACT
62525658 TTCTTTCATT
1 TTCTTTCATT
62525668 GATTATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (28 bp):
TTCTTTCATTTCTTTTTAAATTTTTACT
Found at i:62526546 original size:28 final size:28
Alignment explanation
Indices: 62526506--62526560 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
62526496 GCGTTATGAG
*
62526506 GGTGCTAACCCTTCCTCGTACGTAACTA
1 GGTGCTAACCCTTCCTCGTAAGTAACTA
*
62526534 GGTGCTAACCCTTCCTTGTAAGTAACT
1 GGTGCTAACCCTTCCTCGTAAGTAACT
62526561 GACTTCCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (28 bp):
GGTGCTAACCCTTCCTCGTAAGTAACTA
Found at i:62531354 original size:34 final size:34
Alignment explanation
Indices: 62531316--62531383 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
62531306 GTTTCAGAGG
62531316 AAAGACCCGAAAGGATGAGGAACTACTATGAGTT
1 AAAGACCCGAAAGGATGAGGAACTACTATGAGTT
* *
62531350 AAAGACCCGAAAGGATGAGGAACTATTGTGAGTT
1 AAAGACCCGAAAGGATGAGGAACTACTATGAGTT
62531384 CCATGTGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (34 bp):
AAAGACCCGAAAGGATGAGGAACTACTATGAGTT
Found at i:62532678 original size:51 final size:51
Alignment explanation
Indices: 62532611--62532818 Score: 317
Period size: 51 Copynumber: 4.1 Consensus size: 51
62532601 TCACATTTAC
* *
62532611 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGTTACTACTTATCACTTGT
1 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
62532662 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
1 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
* * * * *
62532713 CACTTGTCACTAATCAGATAAGTGTAGTTGAAGCTGCCACTTATCACTTGT
1 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
* * * *
62532764 CACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCGCTTATCACTTGT
1 CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
62532815 CACT
1 CACT
62532819 GATCAGAAAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 145 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
Found at i:62534483 original size:89 final size:89
Alignment explanation
Indices: 62534363--62534541 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
62534353 GCCCAAATAG
*
62534363 ACCTTAGGTCTATTTTCCTTTTAAACCCTCTTTCTTTTATCATTTAAGCTATTTAATCATTTCCC
1 ACCTTAGGTCTAGTTTCCTTTTAAACCCTCTTTCTTTTATCATTTAAGCTATTTAATCATTTCCC
62534428 ATAATTTTACATTTGTTACAATTT
66 ATAATTTTACATTTGTTACAATTT
62534452 ACCTTAGGTCTAGTTTCCTTTTAAACCCTCTTTCTTTTATCATTTAAGCTATTTAATCATTTCCC
1 ACCTTAGGTCTAGTTTCCTTTTAAACCCTCTTTCTTTTATCATTTAAGCTATTTAATCATTTCCC
62534517 ATAATTTTACATTTGTTACAATTT
66 ATAATTTTACATTTGTTACAATTT
62534541 A
1 A
62534542 GTCTTTTTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (89 bp):
ACCTTAGGTCTAGTTTCCTTTTAAACCCTCTTTCTTTTATCATTTAAGCTATTTAATCATTTCCC
ATAATTTTACATTTGTTACAATTT
Found at i:62539238 original size:14 final size:14
Alignment explanation
Indices: 62539219--62539245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62539209 TATCAAAAAA
62539219 ATAATTAAGAACAC
1 ATAATTAAGAACAC
62539233 ATAATTAAGAACA
1 ATAATTAAGAACA
62539246 AGTCAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:62547932 original size:24 final size:23
Alignment explanation
Indices: 62547900--62548005 Score: 79
Period size: 24 Copynumber: 4.4 Consensus size: 23
62547890 ACTCATTCGG
*
62547900 ACACATAGTGCCGCATTTCCTCGC
1 ACACATAGTGCCGCATAT-CTCGC
***
62547924 ACACATAGTGCTATATAATCTCGC
1 ACACATAGTGCCGCAT-ATCTCGC
* * *
62547948 ACACATAGTGCCATGTAGT-TTTTGC
1 ACACATAGTGCC--GCA-TATCTCGC
*
62547973 ACACATAGTGCCGCATAACCTCGC
1 ACACATAGTGCCGCAT-ATCTCGC
62547997 ACACATAGT
1 ACACATAGT
62548006 ACTGAAATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
22 1 0.02
23 2 0.03
24 41 0.64
25 17 0.27
26 2 0.03
27 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (23 bp):
ACACATAGTGCCGCATATCTCGC
Found at i:62552222 original size:7 final size:7
Alignment explanation
Indices: 62552210--62552235 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62552200 ATCACATTTA
62552210 TCACTTG
1 TCACTTG
62552217 TCACTTG
1 TCACTTG
62552224 TCACTTG
1 TCACTTG
62552231 TCACT
1 TCACT
62552236 AATCAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.12, T:0.42
Consensus pattern (7 bp):
TCACTTG
Found at i:62552287 original size:51 final size:51
Alignment explanation
Indices: 62552211--62552374 Score: 216
Period size: 51 Copynumber: 3.4 Consensus size: 51
62552201 TCACATTTAT
* *
62552211 CACTTGTCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTAC
* *
62552262 CACTTATCACTTGTCACTTGTCACTAGTCAGATAAGTGTAGCTGAAGTTAC
1 CACTTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTAC
* *
62552313 CACTTATCACTTGTCAC-TG------ATCAGATAATTGTAGCTGAGGCTAC
1 CACTTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTAC
*
62552357 CGCTTATCACTTGTCACT
1 CACTTATCACTTGTCACT
62552375 GATTAGAAGT
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
44 37 0.36
50 2 0.02
51 64 0.62
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (51 bp):
CACTTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTAC
Found at i:62552317 original size:44 final size:44
Alignment explanation
Indices: 62552218--62552374 Score: 163
Period size: 44 Copynumber: 3.4 Consensus size: 44
62552208 TATCACTTGT
* * * *
62552218 CACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTAGTCAGATAAGTGTAGCTGAAGTTAC
62552262 CACTTATCACTTGTCACTTGTCACTAGTCAGATAAGTGTAGCTGAAGTTAC
1 CAC-T-T-A----TCACTTGTCACTAGTCAGATAAGTGTAGCTGAAGTTAC
* * *
62552313 CACTTATCACTTGTCACT-GATCAGATAATTGTAGCTGAGGCTAC
1 CACTTATCACTTGTCACTAG-TCAGATAAGTGTAGCTGAAGTTAC
*
62552357 CGCTTATCACTTGTCACT
1 CACTTATCACTTGTCACT
62552375 GATTAGAAGT
Statistics
Matches: 97, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 53 0.55
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 38 0.39
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTAGTCAGATAAGTGTAGCTGAAGTTAC
Found at i:62561115 original size:46 final size:46
Alignment explanation
Indices: 62561063--62561505 Score: 564
Period size: 46 Copynumber: 9.6 Consensus size: 46
62561053 GCTTTCTGAA
* * *
62561063 ATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
62561109 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
62561155 ATGAAATTTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
62561201 ATGAAATGTGTAAGACCATGGTTGAAAGATAACATGGCAACATGAA
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
62561247 ATGAAATGTGTAAGACCATGGTGGAAAGATACCACGGTAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
62561293 ATGAAATGAACAAGACCATGGTTGAAAAATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
62561339 GGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * *
62561385 GGGAAATGAATAGGACCATGGTTGAAAGATACTATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
62561431 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGTAACATGA-
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
62561476 TTGGAATTGAGTAAGACCATAGTTGAAAGA
1 AT-GAAATGAGTAAGACCATGGTTGAAAGA
62561506 CACTATGACA
Statistics
Matches: 353, Mismatches: 43, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 352 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:62563826 original size:40 final size:40
Alignment explanation
Indices: 62563733--62563952 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
62563723 ACCCAAGTAT
* * ** * *
62563733 CTTCAGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
62563771 CTTCGGGTCATAGCCCGGATATGGTCACTAGCACAAATGT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
62563811 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCAAAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
62563851 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
62563891 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
*
62563931 CTTCGGGACTTAGCCCAGATAT
1 CTTCGGGACTTAGCCCGGATAT
62563953 CATTCGAATA
Statistics
Matches: 147, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
38 9 0.06
39 19 0.13
40 115 0.78
41 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:62571885 original size:40 final size:40
Alignment explanation
Indices: 62571831--62572014 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
62571821 TTCGCACAAG
* *
62571831 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
*
62571871 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
62571911 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
62571951 GCCTTC-GGATCTTAGTCCAGATATAGTCACTAGCATAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAAT
62571991 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
62572015 CATTCGAATA
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.94
41 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:62575279 original size:44 final size:44
Alignment explanation
Indices: 62575168--62575559 Score: 318
Period size: 44 Copynumber: 8.8 Consensus size: 44
62575158 ATAATCGTGG
* * * * *
62575168 CAAATCTTATCTCCTTAAAGTTGCAGTTGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * * *
62575212 GTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * * * *
62575257 TAAACCTTATCTCCCTGAAGTTGTAATGAAGCA-AGTTAAAAATAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGAT--A
* * **
62575303 CAAATCTTCTCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * * * * *
62575347 TAAACCTAATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * *
62575391 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * *
62575435 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * * *
62575479 GCAAATCTTATCTCTCTGAAGTTGTAGTAGAACAGATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
* * * * * *
62575524 TAAACCTTATTTCTCTGAAGTTGCAATGGAGAAGAT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
62575560 GGAAGTGAAA
Statistics
Matches: 276, Mismatches: 66, Indels: 11
0.78 0.19 0.03
Matches are distributed among these distances:
43 1 0.00
44 172 0.62
45 70 0.25
46 32 0.12
47 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA
Found at i:62575409 original size:134 final size:135
Alignment explanation
Indices: 62575168--62575551 Score: 371
Period size: 133 Copynumber: 2.9 Consensus size: 135
62575158 ATAATCGTGG
* * * * * * * *
62575168 CAAATCTTATCTCCTTAAAGTTGCAGTTGAGCAGACTGAAGATAGTAGATCTTATCTCTCTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGACAGTAAACCTAATCTCCCTGAAG
* *
62575233 TTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGTAATGAAGCAAGTTAAAA
66 TTGCAGTAGAACAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGTAATGAAGCAAGTTAAAA
62575298 ATAAA
131 ATAAA
* * *
62575303 CAAATCTTCTCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-TAAACCTAATCTCCCTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGACAGTAAACCTAATCTCCCTGAAG
* * * * ** * * * * *
62575367 TTGCAGTGGAACAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG-TAGATT-GA
66 TTGCAGTAGAACAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGTAATGAAGCAAG-TTAAA
* *
62575430 AGT-TA
130 AATAAA
* * * * * * * * *
62575435 CAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGACAGTAAACCTAATCTCCCTGAAG
* * * * *
62575500 TTGTAGTAGAACAGATTAAAGCTATAAACCTTATTTCTCTGAAGTTGCAATG
66 TTGCAGTAGAACAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGTAATG
62575552 GAGAAGATGG
Statistics
Matches: 198, Mismatches: 49, Indels: 6
0.78 0.19 0.02
Matches are distributed among these distances:
132 37 0.19
133 62 0.31
134 62 0.31
135 37 0.19
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (135 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGACAGTAAACCTAATCTCCCTGAAG
TTGCAGTAGAACAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGTAATGAAGCAAGTTAAAA
ATAAA
Done.