Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold84
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: 2025335
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 30794 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1323392 original size:19 final size:20
Alignment explanation
Indices: 1323360--1323398 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1323350 ATTTTCAACC
1323360 TTTAATTTTGAAATT-ATTT
1 TTTAATTTTGAAATTCATTT
1323379 TTTATATTTT-AAATTCATTT
1 TTTA-ATTTTGAAATTCATTT
1323399 CCTCAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTAATTTTGAAATTCATTT
Found at i:1324943 original size:79 final size:79
Alignment explanation
Indices: 1324807--1324954 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 79
1324797 AGATAACAAC
* * *
1324807 GGGGCTGGAGTATCCCCGATTATAGAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGTATC
1 GGGGCTGGAGTATCCCCGATTATAGAAAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTATC
1324872 CCCGTGAAAATAAT
66 CCCGTGAAAATAAT
* * * ** *
1324886 GGGGTTGGAGTATCCCCGATTAT-GAGAAATTAATATTTTAGAAATAAGGTCGGGGTTGAAGTAT
1 GGGGCTGGAGTATCCCCGATTATAGA-AAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTAT
1324950 CCCCG
65 CCCCG
1324955 ATTGTGAGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 2 0.03
79 57 0.97
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGGCTGGAGTATCCCCGATTATAGAAAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTATC
CCCGTGAAAATAAT
Found at i:1324952 original size:51 final size:51
Alignment explanation
Indices: 1324886--1325007 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
1324876 TGAAAATAAT
* * *
1324886 GGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAGGTC
1 GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCC
* * *
1324937 GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCC
1324988 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
1325008 GAAATAACGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:1324967 original size:130 final size:130
Alignment explanation
Indices: 1324776--1325083 Score: 363
Period size: 130 Copynumber: 2.4 Consensus size: 130
1324766 ACATCCCCCG
* * * *
1324776 ATGAGAAATTTAATATTTTGGAGATAACAA-CGGGGCTGGAGTATCCCCGATTATAGAAAATCGA
1 ATGAGAAA-TTAATATTTTAGAAATAA-AATCGGGGTTGGAGTATCCCCGATTATAGAAAATCAA
* * *
1324840 TGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCCG-TGAAAATAATGGGGTTGGAGTATCCCCG
64 TATTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATG-AAATAACGGGGTTGGAGTATCCCCG
1324904 ATT
128 ATT
** * *
1324907 ATGAGAAATTAATATTTTAGAAATAAGGTCGGGGTTGAAGTATCCCCGATTGT-GAGAAATCAAT
1 ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATAGA-AAATCAAT
** * * *
1324971 ATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCTCCGAT
65 ATTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCGAT
1325036 T
130 T
* ** *
1325037 GTG-GAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 ATGAGA-AATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1325084 TCGAAAATAA
Statistics
Matches: 150, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.03
130 136 0.91
131 10 0.07
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (130 bp):
ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATAGAAAATCAATA
TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCGATT
Found at i:1325019 original size:79 final size:77
Alignment explanation
Indices: 1324936--1325241 Score: 344
Period size: 79 Copynumber: 3.9 Consensus size: 77
1324926 GAAATAAGGT
* * * *
1324936 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1325001 CCCCGATGAAATAA
66 CCCC--TGAAATAA
* * * * *** *
1325015 CGGGGTTGGAGTATCTCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1325080 CCCCTCGAAAATAA
66 CCCCT-G-AAATAA
* * * *
1325094 CGGGGTTGGAGTATCCCCAATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1325159 CCCCTCGGAAATAA
66 CCCCT--GAAATAA
* ** * * *
1325173 CGGGGTT-AGAGTATCCCTGATTGTGAAAAATCGGTGTTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGA-AGTATCCCCGATTGTGAAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTA
1325237 TCCCC
65 TCCCC
1325242 AATTAAGAAA
Statistics
Matches: 192, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
77 1 0.01
78 1 0.01
79 189 0.98
80 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (77 bp):
CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTGAAATAA
Found at i:1325177 original size:158 final size:158
Alignment explanation
Indices: 1324936--1325241 Score: 443
Period size: 158 Copynumber: 1.9 Consensus size: 158
1324926 GAAATAAGGT
* * * * *
1324936 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
* * * * *
1325001 CCCCGATGAAATAACGGGGTTGGAGTATCTCC-GATTGTGGAGAATTGGTGTTTTAGAAATAAAA
66 CCCCGAGGAAATAACGGGGTTAGAGTATC-CCTGATTGTGAAAAATCGGTGTTTTAGAAATAAAA
*
1325065 TCGGGGTTGGAGTATCCCCTCGAAAATAA
130 TCGGAGTTGGAGTATCCCCTCGAAAATAA
* * *
1325094 CGGGGTTGGAGTATCCCCAATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
** *
1325159 CCCCTCGGAAATAACGGGGTTAGAGTATCCCTGATTGTGAAAAATCGGTGTTTTGGAAATAAAAT
66 CCCCGAGGAAATAACGGGGTTAGAGTATCCCTGATTGTGAAAAATCGGTGTTTTAGAAATAAAAT
1325224 CGGAGTTGGAGTATCCCC
131 CGGAGTTGGAGTATCCCC
1325242 AATTAAGAAA
Statistics
Matches: 130, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
157 2 0.02
158 128 0.98
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (158 bp):
CGGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCGAGGAAATAACGGGGTTAGAGTATCCCTGATTGTGAAAAATCGGTGTTTTAGAAATAAAAT
CGGAGTTGGAGTATCCCCTCGAAAATAA
Found at i:1327131 original size:441 final size:442
Alignment explanation
Indices: 1326273--1327143 Score: 1464
Period size: 441 Copynumber: 2.0 Consensus size: 442
1326263 AAGCCTTAAC
* *
1326273 TTCATGTTATTCTCCATGTATGGGAGGTAGCATGAGTTTGGCTTGGGGATGTCTTTAAAATCTGA
1 TTCATGTTATTCTCCATGTATGGGAGGTAGCATGAGCTTGGCTTGGGGATGTCCTTAAAATCTGA
* * * *
1326338 TTTTGGCACGCAAATAAGCATCTTGGCACAAACAACATGCCACAAACACAACATATGTCATGGAG
66 TTTTGGCACACAAATAAGCATCTTGGCACAAACAACATGCCACAAACACAACATATGCCATGAAA
*
1326403 GACAGAAATGCTTGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAAAAAATGAGCAAATGCA
131 GACAGAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAAAAAA-GAGCAAATGCA
1326468 TGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAACATTTTTATTTCATGGAACCTAT
195 TGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAACATTTTTATTTCATGGAACCTAT
1326533 CAAGCTATTAATCATGCATGAACATGCTCAAGATGGTTGAAATGACATCCAAATATGAGATGAAG
260 CAAGCTATTAATCATGCATGAACATGCTCAAGATGGTTGAAATGACATCCAAATATGAGATGAAG
*
1326598 ATGTGAATATGGAAGGAATGAACAAAGGATGCAAAAACAAGGGCTATTAGGGTGATGAAAATGCA
325 ATGTGAATATGGAAGGAATGAACAAAGGATGCAAAAACAAGGGCTATCAGGGTGATGAAAATGCA
* *
1326663 AACAAAACCAAGGAATAACAAAGTCCTAAACTACCACAAACAAGGGCCATAAG
390 AACAAAACCAAGGAACAAAAAAGTCCTAAACTACCACAAACAAGGGCCATAAG
1326716 TTCATGTTATTCTCCATGTATGGGAGGTAGCATGAGCTTGGCTTGGGGATGTCCTTAAAATCTTG
1 TTCATGTTATTCTCCATGTATGGGAGGTAGCATGAGCTTGGCTTGGGGATGTCCTTAAAATC-TG
* *
1326781 -TTTTGGCACACAAATGAGCATCTTGGCACAAACAACAT-TCAGCAAACACAACATATGCCATGA
65 ATTTTGGCACACAAATAAGCATCTTGGCACAAACAACATGCCA-CAAACACAACATATGCCATGA
* *
1326844 AAGATAGAAATGCATGAACCAAGATGACATTTTTATGGGAGGAAAAGAAAAAGAAA-AGCAAATG
129 AAGACAGAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAAA-AAAGAGCAAATG
*
1326908 CATGGTGATGGCAAGATATCATCAAGATAAACATGTT-AAAAAACATTTTTATTTTATGGAACCT
193 CATGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAACATTTTTATTTCATGGAACCT
* *
1326972 ATCTAGCTATTAATCATGCATGAACATGCTCAAGATGTGTTGAAATGACATTC-AATATGAGATG
258 ATCAAGCTATTAATCATGCATGAACATGCTCAAGATG-GTTGAAATGACATCCAAATATGAGATG
* * * * *
1327036 AAGATGTGAATATGGGAGGAATGAACAAAGGATGCAAAAACAGGGGCTGTCATGGTGATGAAGAT
322 AAGATGTGAATATGGAAGGAATGAACAAAGGATGCAAAAACAAGGGCTATCAGGGTGATGAAAAT
1327101 GCAAACAAAACCAAGGAACAAAAAAGTCCTAAACTACCACAAA
387 GCAAACAAAACCAAGGAACAAAAAAGTCCTAAACTACCACAAA
1327144 ACAAAAACCA
Statistics
Matches: 402, Mismatches: 22, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
441 173 0.43
442 61 0.15
443 163 0.41
444 5 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (442 bp):
TTCATGTTATTCTCCATGTATGGGAGGTAGCATGAGCTTGGCTTGGGGATGTCCTTAAAATCTGA
TTTTGGCACACAAATAAGCATCTTGGCACAAACAACATGCCACAAACACAACATATGCCATGAAA
GACAGAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAAAAAAGAGCAAATGCAT
GGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAACATTTTTATTTCATGGAACCTATC
AAGCTATTAATCATGCATGAACATGCTCAAGATGGTTGAAATGACATCCAAATATGAGATGAAGA
TGTGAATATGGAAGGAATGAACAAAGGATGCAAAAACAAGGGCTATCAGGGTGATGAAAATGCAA
ACAAAACCAAGGAACAAAAAAGTCCTAAACTACCACAAACAAGGGCCATAAG
Found at i:1329099 original size:55 final size:55
Alignment explanation
Indices: 1328955--1329950 Score: 948
Period size: 55 Copynumber: 17.3 Consensus size: 55
1328945 ATAATGTGCA
*
1328955 TCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATGCG
1 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AAA-G----GCG
* * ** * *
1329016 TCTTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1329071 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
1329126 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTT-AAGAGGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
1329181 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGACATTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGCG
* **
1329243 T-CTGGCTCTTTGAGGACTAGAAAATGCCACCGACCCGTGTGGGCTTTGAAAGGCG
1 TCCT-GCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1329298 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
1329353 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGCG
*
1329415 TCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
1329470 TCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGAGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1329524 TCTTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGCG
* * * *
1329586 TCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAAGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1329641 TCCTGCTCTTTGAAGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCG
1 TCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
** * * * *
1329702 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGACTTTAAAAGGAAAATGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* *
1329762 TCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * * * *
1329817 TCCTACTCTTTCAAGACTGGGAAGTGCCACCAACTTGTGTGGGTTTTAAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
* ** * * * *
1329878 TCATGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1329932 TCCTGTTCTTTGAGGACTA
1 TCCTGCTCTTTGAGGACTA
1329951 AAGGGTGAAG
Statistics
Matches: 792, Mismatches: 96, Indels: 100
0.80 0.10 0.10
Matches are distributed among these distances:
54 76 0.10
55 367 0.46
56 15 0.02
59 3 0.00
60 74 0.09
61 121 0.15
62 129 0.16
63 7 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1329267 original size:172 final size:171
Alignment explanation
Indices: 1328955--1329929 Score: 1274
Period size: 172 Copynumber: 5.6 Consensus size: 171
1328945 ATAATGTGCA
* * * *
1328955 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATGCGTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT--AAA-G--AGGCGTCC
** *
1329019 TGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTT-----G-AAAGGTGTCCTGCT
60 TGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGTGTCCTGCT
* * *
1329078 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
124 CTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
* * *
1329126 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTT-AAGAGGCATCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
*
1329190 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGACATTTAAAAAGAAAAGGTGT-CTGGCTCTTT
66 TTGAGGACT-GAAAATGCCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGGTGTCCT-GCTCTTT
*
1329254 GAGGACTAGAAAATGCCACCGACCCGTGTGGGCTTTGAAAGGCG
128 GAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
1329298 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
1329362 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTGTCCTGCTCTTTG
66 TTGAGGACT-GAAAATGCCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGGTGTCCTGCTCTTTG
*
1329427 AGGACTAGAAAATGCCACCGACTTGTGTGGGCTTTGAAAGGCG
129 AGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
* * *
1329470 TCCTGCTCTTTGAGGACTGG-AAGTGCCACCAACTTGTGTGAGCTTTAAA-AGGCGTCTTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
1329533 TTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTGTCCTGCTCTTT
66 TTGAGGACTGAAAA--TGCCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGGTGTCCTGCTCTTT
* *
1329597 GAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAAGCA
128 GAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
* * *
1329641 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGTCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAG----AGGCGTCCT
** * * * *
1329706 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGACTTTAAAAGGAAAATGTGTCCTGCTCT
61 GCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGTGTCCTGCTCT
1329771 TTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
126 TTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
* * * * * * *
1329817 TCCTACTCTTTCAAGACTGGGAAGTGCCACCAACTTGTGTGGGTTTTAAAAGAAAAAGGCGTCAT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAG----AGGCGTCCT
** *
1329882 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAG
61 GCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAG
1329930 CATCCTGTTC
Statistics
Matches: 731, Mismatches: 52, Indels: 37
0.89 0.06 0.05
Matches are distributed among these distances:
165 42 0.06
166 3 0.00
167 1 0.00
168 2 0.00
169 4 0.01
171 195 0.27
172 267 0.37
173 5 0.01
176 171 0.23
177 18 0.02
178 21 0.03
179 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (171 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
TTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGTGTCCTGCTCTTTGAG
GACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGGCG
Found at i:1329289 original size:117 final size:113
Alignment explanation
Indices: 1328952--1329927 Score: 909
Period size: 117 Copynumber: 8.5 Consensus size: 113
1328942 AAAATAATGT
* * *
1328952 GCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATGCG
1 GCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAA-GAAAGGTG
** * *
1329016 TCTTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAG
63 TC-TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
** *
1329068 GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG---GCGT-CC
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAG-GTGTC
* * *
1329129 TACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTAAGAG
65 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* *
1329178 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGACATTTAAAAAGAAAAGGTG
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGC-TTT-AAAAG-AAAGGTG
* * ** *
1329243 TCTGGCTCTTTGAGGACTAGAAAATGCCACCGACCCGTGTGGGCTTTGAAAG
63 TCT-GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
1329295 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--AAG--AGGCGTCC
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGTGT-C
1329356 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAG
65 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGC-TTT------AAAAG
** * *
1329412 GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTTGTGTGGGCTTT----GAAAGGCGTCC
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGTGT-C
* *
1329473 TGCTCTTTGAGGACTGG-AAGTGCCACCAACTTGTGTGAGCTTTAAAAG
65 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
1329521 GCGTCTTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGT
1 GCATCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGC-TTT-AAAAG-AAAGGT
* * *
1329585 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAA-
62 GT-CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG
* * *
1329638 GCATCCTGCTCTTTGAAGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCG
1 GCATCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAG--AAAGGTG
** * *
1329702 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGACTTTAAAAG
63 T-CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
1329753 GAAAATGTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTT----GAAAG
1 G--CA----TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
* * * * * * *
1329814 GCGTCCTACTCTTTCAAGACTGGGAAGTGCCACCAACTTGTGTGGGTTTTAAAAGAAAAAG
60 GTGT-CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------AAAAG
* * ** *
1329875 GCGTCATGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAA
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
1329928 AGCATCCTGT
Statistics
Matches: 726, Mismatches: 82, Indels: 101
0.80 0.09 0.11
Matches are distributed among these distances:
108 3 0.00
109 44 0.06
110 129 0.18
111 9 0.01
112 6 0.01
113 3 0.00
114 5 0.01
115 83 0.11
116 161 0.22
117 227 0.31
118 7 0.01
121 42 0.06
122 7 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (113 bp):
GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGTGTCT
GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:1330043 original size:94 final size:94
Alignment explanation
Indices: 1329883--1330142 Score: 380
Period size: 94 Copynumber: 2.8 Consensus size: 94
1329873 AGGCGTCATG
* * *
1329883 CTCTTTGAGGACT--GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGCATCCTGTTCTTTGAG
1 CTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTCTTTGAG
* *
1329946 GACTAAAGGGTGAAGGGAGAGAGTGTCCTA
65 GACTAAAGGGTGAAAGGAGAGAGCGTCCTA
* * *
1329976 CTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCTTGCTCTTTGAGG
1 CTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTCTTTGAGG
* * *
1330041 ACTAAAGGGTGAAAGGAGAGGGCGTCTTG
66 ACTAAAGGGTGAAAGGAGAGAGCGTCCTA
* *
1330070 CTCTTTGAGGACTAGGAAGTGCCCCCAACTTGTGTGGGCTTTAAAAGGCGTCCTATTCTTTGAGG
1 CTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTCTTTGAGG
1330135 ACTAAAGG
66 ACTAAAGG
1330143 TGCCACCAAC
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
93 13 0.09
94 133 0.89
95 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (94 bp):
CTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTCTTTGAGG
ACTAAAGGGTGAAAGGAGAGAGCGTCCTA
Found at i:1336138 original size:443 final size:443
Alignment explanation
Indices: 1335312--1336175 Score: 1719
Period size: 443 Copynumber: 2.0 Consensus size: 443
1335302 TTTGTAAGGT
1335312 TTGTCCTCCCTACTAGGTTTTGAGATTTTCTAAGGCTTGACCTCCTTAAATAGGTTTTGGTTACT
1 TTGTCCTCCCTACTAGGTTTTGAGATTTTCTAAGGCTTGACCTCCTTAAATAGGTTTTGGTTACT
1335377 GTAGGCTTTGGAAAGGTTTGCCACCAACTTGTGTGGACTTTTTGGGTGTTGCCAACTTGTGTAGA
66 GTAGGCTTTGGAAAGGTTTGCCACCAACTTGTGTGGACTTTTTGGGTGTTGCCAACTTGTGTAGA
*
1335442 CTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACTTTTTGAGGATAAAGGAAAAGAGAATGAA
131 CTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACTTTTTGAGGACAAAGGAAAAGAGAATGAA
1335507 ATAGGTCTTGCCTTTTGAGGACAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTGAGGACA
196 ATAGGTCTTGCCTTTTGAGGACAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTGAGGACA
1335572 AAGTTAAAAAGAGTACGTCTCGTTTTTCGAGGACAAAGGACATAGTGTCATGCATTTTAAGACCA
261 AAGTTAAAAAGAGTACGTCTCGTTTTTCGAGGACAAAGGACATAGTGTCATGCATTTTAAGACCA
1335637 TTTAAAAGTGAATTCGTCTCCACATATGTCCAATCCTCCACCTACTAGCTAGGCTTCAAGTTGTC
326 TTTAAAAGTGAATTCGTCTCCACATATGTCCAATCCTCCACCTACTAGCTAGGCTTCAAGTTGTC
1335702 GAAAATTGGTCCGGACAAAATGAGGTGTCTAAACAAGAGGTTTAGACAAGAGG
391 GAAAATTGGTCCGGACAAAATGAGGTGTCTAAACAAGAGGTTTAGACAAGAGG
1335755 TTGTCCTCCCTACTAGGTTTTGAGATTTTCTAAGGCTTGACCTCCTTAAATAGGTTTTGGTTACT
1 TTGTCCTCCCTACTAGGTTTTGAGATTTTCTAAGGCTTGACCTCCTTAAATAGGTTTTGGTTACT
1335820 GTAGGCTTTGGAAAGGTTTGCCACCAACTTGTGTGGACTTTTTGGGTGTTGCCAACTTGTGTAGA
66 GTAGGCTTTGGAAAGGTTTGCCACCAACTTGTGTGGACTTTTTGGGTGTTGCCAACTTGTGTAGA
1335885 CTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACTTTTTGAGGACAAAGGAAAAGAGAATGAA
131 CTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACTTTTTGAGGACAAAGGAAAAGAGAATGAA
1335950 ATAGGTCTTGCCTTTTGAGGACAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTGAGGACA
196 ATAGGTCTTGCCTTTTGAGGACAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTGAGGACA
1336015 AAGTTAAAAAGAGTACGTCTCGTTTTTCGAGGACAAAGGACATAGTGTCATGCATTTTAAGACCA
261 AAGTTAAAAAGAGTACGTCTCGTTTTTCGAGGACAAAGGACATAGTGTCATGCATTTTAAGACCA
1336080 TTTAAAAGTGAATTCGTCTCCACATATGTCCAATCCTCCACCTACTAGCTAGGCTTCAAGTTGTC
326 TTTAAAAGTGAATTCGTCTCCACATATGTCCAATCCTCCACCTACTAGCTAGGCTTCAAGTTGTC
1336145 GAAAATTGGTCCGGACAAAATGAGGTGTCTA
391 GAAAATTGGTCCGGACAAAATGAGGTGTCTA
1336176 CACATATAAT
Statistics
Matches: 420, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
443 420 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (443 bp):
TTGTCCTCCCTACTAGGTTTTGAGATTTTCTAAGGCTTGACCTCCTTAAATAGGTTTTGGTTACT
GTAGGCTTTGGAAAGGTTTGCCACCAACTTGTGTGGACTTTTTGGGTGTTGCCAACTTGTGTAGA
CTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACTTTTTGAGGACAAAGGAAAAGAGAATGAA
ATAGGTCTTGCCTTTTGAGGACAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTGAGGACA
AAGTTAAAAAGAGTACGTCTCGTTTTTCGAGGACAAAGGACATAGTGTCATGCATTTTAAGACCA
TTTAAAAGTGAATTCGTCTCCACATATGTCCAATCCTCCACCTACTAGCTAGGCTTCAAGTTGTC
GAAAATTGGTCCGGACAAAATGAGGTGTCTAAACAAGAGGTTTAGACAAGAGG
Found at i:1338654 original size:14 final size:14
Alignment explanation
Indices: 1338632--1338687 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
1338622 TTTTTAATGC
*
1338632 CATACTTAATATAA
1 CATATTTAATATAA
1338646 CATATTTAATATAA
1 CATATTTAATATAA
*
1338660 TA-ATCTTAATATAA
1 CATAT-TTAATATAA
*
1338674 CTTATTTAATATAA
1 CATATTTAATATAA
1338688 TAATGGTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.06
14 32 0.89
15 2 0.06
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (14 bp):
CATATTTAATATAA
Found at i:1338667 original size:28 final size:28
Alignment explanation
Indices: 1338636--1338691 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1338626 TAATGCCATA
1338636 CTTAATATAACATATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
*
1338664 CTTAATATAACTTATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
1338692 GGTAGATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (28 bp):
CTTAATATAACATATTTAATATAATAAT
Found at i:1339084 original size:19 final size:18
Alignment explanation
Indices: 1339047--1339084 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1339037 TTATCTTTTA
*
1339047 TGTATAATATTTTAATTT
1 TGTATAATATTTAAATTT
1339065 TGTATAATATTTAAAATTT
1 TGTATAATATTT-AAATTT
1339084 T
1 T
1339085 ATTTGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TGTATAATATTTAAATTT
Found at i:1341091 original size:24 final size:25
Alignment explanation
Indices: 1341045--1341094 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
1341035 TTTTATTTAA
1341045 ATTTATTATAATTGATAATAATAAT
1 ATTTATTATAATTGATAATAATAAT
*
1341070 ATTTATTAT-ATTTATAATAATAAT
1 ATTTATTATAATTGATAATAATAAT
1341094 A
1 A
1341095 AATATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTATTATAATTGATAATAATAAT
Found at i:1341103 original size:12 final size:12
Alignment explanation
Indices: 1341086--1341120 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1341076 TATATTTATA
1341086 ATAATAATAAAT
1 ATAATAATAAAT
*
1341098 ATAATAAAAAAT
1 ATAATAATAAAT
*
1341110 ATATTAATAAA
1 ATAATAATAAA
1341121 AAATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:1341128 original size:15 final size:15
Alignment explanation
Indices: 1341076--1341128 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
1341066 TAATATTTAT
*
1341076 TATATTTATAATAATAA
1 TATATTAATAA-AA-AA
*
1341093 TAAATATAATAAAAAA
1 TATAT-TAATAAAAAA
1341109 TATATTAATAAAAAA
1 TATATTAATAAAAAA
1341124 TATAT
1 TATAT
1341129 ATATCTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 15 0.47
16 6 0.19
17 6 0.19
18 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATTAATAAAAAA
Found at i:1343022 original size:28 final size:28
Alignment explanation
Indices: 1342991--1343058 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1342981 TATTTTCTTA
*
1342991 AGTCATATTCAA-AATTATTAAGTCTTGT
1 AGTCATATTCAATAATTATCAA-TCTTGT
*
1343019 AGTCATTATTCAAATAATTATCAATTTTGT
1 AGTCA-TATTC-AATAATTATCAATCTTGT
1343049 -GTCATATTCA
1 AGTCATATTCA
1343059 TTTTATGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 10 0.29
29 9 0.26
30 7 0.20
31 8 0.23
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (28 bp):
AGTCATATTCAATAATTATCAATCTTGT
Found at i:1344899 original size:97 final size:97
Alignment explanation
Indices: 1344558--1344899 Score: 443
Period size: 97 Copynumber: 3.5 Consensus size: 97
1344548 TTTTTGGTTG
* * * * * *
1344558 AAAAATGGGATTGGAGTATCCCCTTGGAGGAATGGGGTTGGAGTATTCCTGACGATGATAATTTA
1 AAAAATGGGATTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCCTGATGATGATAATTT-
** * *
1344623 GAAAAAAAAATAAGATTTAAGTCGTGACAAGTTT
65 -AAGCAAAAATAAGATTTAAATCTTGACAAGTTT
* * * * * * *
1344657 AAAAGTGGGATTGGAGTATCCTCTCAAAAAAATAGGGTTGGAGTATCCTTGATGATGATAATTTA
1 AAAAATGGGATTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCCTGATGATGATAATTTA
1344722 AGCAAAAATAAGATTTAAATCTTGACAAGTTT
66 AGCAAAAATAAGATTTAAATCTTGACAAGTTT
* * * *
1344754 CAAAACGGGGTTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCCGGATGATGATAATTTA
1 AAAAATGGGATTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCCTGATGATGATAATTTA
*
1344819 AGCAAAAATAAGATTTAAATCTTAACAAGTTT
66 AGCAAAAATAAGATTTAAATCTTGACAAGTTT
*
1344851 AAAAATGAGG-TTAGAGTATCCCCTCGGAAGAATGGGGTTGGAGTATCCC
1 AAAAATG-GGATTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCC
1344900 CGTGAATAAA
Statistics
Matches: 212, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
97 157 0.74
98 2 0.01
99 53 0.25
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (97 bp):
AAAAATGGGATTAGAGTATCCCCTCGAAAGAATGGGGTTGGAGTATCCCTGATGATGATAATTTA
AGCAAAAATAAGATTTAAATCTTGACAAGTTT
Found at i:1348533 original size:58 final size:56
Alignment explanation
Indices: 1348466--1348693 Score: 208
Period size: 58 Copynumber: 3.9 Consensus size: 56
1348456 AGGGACTTTT
* * * *
1348466 ATGTCATTTCATGCACTTTAATGTCATTTTAGTAATTTTCCATGATATAAGGATTATA
1 ATGTAATTTCATGCA-TTTAATGTCATTTTAGTAATTTGCCATG-TTTTAGGATTATA
** * * * * *
1348524 ATGTAATTTCATGCATTTTTTCATCATTTTAGTGATTTGCCATGTTTTATGACTATTT
1 ATGTAATTTCATGCATTTAAT-GTCATTTTAGTAATTTGCCATGTTTTAGGATTA-TA
* * * *
1348582 ATGTAATTTCATGTATTTTAGGATCATTTTAGTAATTTGCCATGTTTTAGGATATTTGA
1 ATGTAATTTCATGCATTTAATG-TCATTTTAGTAATTTGCCATGTTTTAGGAT-TAT-A
* *
1348641 A-GCAATTTCATGCATTTTAGA-GTCATTTTAGTAATTTGTCATGTTTTAGGATT
1 ATGTAATTTCATGCA-TTTA-ATGTCATTTTAGTAATTTGCCATGTTTTAGGATT
1348694 GTCGTAACGT
Statistics
Matches: 139, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
57 12 0.09
58 120 0.86
59 6 0.04
60 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (56 bp):
ATGTAATTTCATGCATTTAATGTCATTTTAGTAATTTGCCATGTTTTAGGATTATA
Found at i:1348581 original size:29 final size:28
Alignment explanation
Indices: 1348549--1348692 Score: 111
Period size: 29 Copynumber: 5.0 Consensus size: 28
1348539 TTTTTTCATC
* *
1348549 ATTTTAGTGATTTGCCATGTTTTATGACT
1 ATTTTAGTAATTTGCCATGTTTTAGGA-T
1348578 A-TTTATGTAATTT--CATGTATTTTAGGAT
1 ATTTTA-GTAATTTGCCATG--TTTTAGGAT
1348606 CATTTTAGTAATTTGCCATGTTTTAGGAT
1 -ATTTTAGTAATTTGCCATGTTTTAGGAT
* *
1348635 ATTTGAAGCAATTT--CATGCATTTTA-GAGT
1 ATTT-TAGTAATTTGCCATG--TTTTAGGA-T
*
1348664 CATTTTAGTAATTTGTCATGTTTTAGGAT
1 -ATTTTAGTAATTTGCCATGTTTTAGGAT
1348693 TGTCGTAACG
Statistics
Matches: 94, Mismatches: 6, Indels: 30
0.72 0.05 0.23
Matches are distributed among these distances:
27 8 0.09
28 11 0.12
29 57 0.61
30 10 0.11
31 8 0.09
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (28 bp):
ATTTTAGTAATTTGCCATGTTTTAGGAT
Found at i:1348591 original size:116 final size:115
Alignment explanation
Indices: 1348459--1348688 Score: 270
Period size: 116 Copynumber: 2.0 Consensus size: 115
1348449 TTGACTTAGG
* * *
1348459 GACTTTTATGTCATTTCATGCACTTTAATG-TCATTTTAGTAATTTTCCATGATATAAGGAT-TA
1 GACTTTTATGTAATTTCATGCA-TTTAAGGATCATTTTAGTAATTTGCCATG-TATAAGGATATA
* * *
1348522 T-AATGTAATTTCATGCATTTTTTCA-TCATTTTAGTGATTTGCCATGTTTTAT
64 TGAA-GCAATTTCATGCA-TTTTACAGTCATTTTAGTAATTTGCCATGTTTTAT
* * * * *
1348574 GACTATTTATGTAATTTCATGTATTTTAGGATCATTTTAGTAATTTGCCATGTTTTAGGATATTT
1 GACT-TTTATGTAATTTCATGCATTTAAGGATCATTTTAGTAATTTGCCATGTATAAGGATATAT
* *
1348639 GAAGCAATTTCATGCATTTTAGAGTCATTTTAGTAATTTGTCATGTTTTA
65 GAAGCAATTTCATGCATTTTACAGTCATTTTAGTAATTTGCCATGTTTTA
1348689 GGATTGTCGT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
115 21 0.22
116 74 0.76
117 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (115 bp):
GACTTTTATGTAATTTCATGCATTTAAGGATCATTTTAGTAATTTGCCATGTATAAGGATATATG
AAGCAATTTCATGCATTTTACAGTCATTTTAGTAATTTGCCATGTTTTAT
Found at i:1351001 original size:50 final size:51
Alignment explanation
Indices: 1350923--1351055 Score: 207
Period size: 51 Copynumber: 2.6 Consensus size: 51
1350913 TCATAATTTG
* *
1350923 TATCGATACATTT-TCATTGTATCAATACATTCTGGGTTTT-ACCTAGATA
1 TATCGATACATTTCTCATTGTATCAATACATTCTGGGTTTTAACCCAAATA
* *
1350972 TATTGATACATTTCTCATTGTATCGATACATTCTGGGTTTTAACCCAAATA
1 TATCGATACATTTCTCATTGTATCAATACATTCTGGGTTTTAACCCAAATA
*
1351023 TATCGATACATTTCTCAATGTATCAATACATTC
1 TATCGATACATTTCTCATTGTATCAATACATTC
1351056 AGGCATTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
49 12 0.16
50 26 0.35
51 37 0.49
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (51 bp):
TATCGATACATTTCTCATTGTATCAATACATTCTGGGTTTTAACCCAAATA
Found at i:1352746 original size:13 final size:13
Alignment explanation
Indices: 1352728--1352753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1352718 CAATTTTTTG
1352728 TGTATCGATACAT
1 TGTATCGATACAT
1352741 TGTATCGATACAT
1 TGTATCGATACAT
1352754 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1352768 original size:32 final size:33
Alignment explanation
Indices: 1352708--1352771 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1352698 TACAAGCCAA
** *
1352708 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1352741 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1352772 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1354694 original size:80 final size:79
Alignment explanation
Indices: 1354561--1354732 Score: 238
Period size: 80 Copynumber: 2.2 Consensus size: 79
1354551 CATTCATGTT
** * * *
1354561 TTTATTTCTAAAATACTGATTTTCCACCTTCGAGGATACTCCAACCCCGTTATTTTCGAAGGGGA
1 TTTATTTCTAAAATACCAACTTTCCACCTTCGAGGATACTCCAACCCCATTATTTTCG-AGAGGA
1354626 TACTCCAAACACGGC
65 TACTCCAAACACGGC
* *
1354641 TTTATTTTTAAAATACCAACTTTCCACCTTC-AGGGATACTCCAACCCCATTATTTTTGAGAGGA
1 TTTATTTCTAAAATACCAACTTTCCACCTTCGA-GGATACTCCAACCCCATTATTTTCGAGAGGA
* *
1354705 TACTCCAACCCCGGC
65 TACTCCAAACACGGC
1354720 TTTATTTCTAAAA
1 TTTATTTCTAAAA
1354733 CATTAATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 31 0.38
80 50 0.62
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (79 bp):
TTTATTTCTAAAATACCAACTTTCCACCTTCGAGGATACTCCAACCCCATTATTTTCGAGAGGAT
ACTCCAAACACGGC
Found at i:1354756 original size:79 final size:79
Alignment explanation
Indices: 1354561--1354765 Score: 259
Period size: 79 Copynumber: 2.6 Consensus size: 79
1354551 CATTCATGTT
* * *
1354561 TTTATTTCTAAAATACTGATTTTCCACCTTCGAGGATACTCCAACCCCGTTATTTTCGAAGGGGA
1 TTTATTTCTAAAATACTAATTTTCCACCTTCG-GGATACTCCAACCCCATTATTTTCGAAGAGGA
1354626 TACTCCAAACACGGC
65 TACTCCAAACACGGC
* * * *
1354641 TTTATTTTTAAAATACCAACTTTCCACCTTCAGGGATACTCCAACCCCATTATTTTTG-AGAGGA
1 TTTATTTCTAAAATACTAATTTTCCACCTTC-GGGATACTCCAACCCCATTATTTTCGAAGAGGA
* *
1354705 TACTCCAACCCCGGC
65 TACTCCAAACACGGC
* * * *
1354720 TTTATTTCTAAAACATTAATTTTTCACAATTCGGGATACTCCAACC
1 TTTATTTCTAAAATACTAATTTTCCAC-CTTCGGGATACTCCAACC
1354766 TCGATTTTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 53 0.50
80 53 0.50
81 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (79 bp):
TTTATTTCTAAAATACTAATTTTCCACCTTCGGGATACTCCAACCCCATTATTTTCGAAGAGGAT
ACTCCAAACACGGC
Found at i:1354762 original size:51 final size:51
Alignment explanation
Indices: 1354702--1354817 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
1354692 ATTTTTGAGA
*
1354702 GGATACTCCAACCCCGGCTTTATTTCTAAAACATTAATTTTTCACAATTCG
1 GGATACTCCAACCCCGACTTTATTTCTAAAACATTAATTTTTCACAATTCG
* * * * * * *
1354753 GGATACTCCAACCTCGATTTTATTTTTGAAATATTGATTTTTCACAATTGG
1 GGATACTCCAACCCCGACTTTATTTCTAAAACATTAATTTTTCACAATTCG
1354804 GGATACTCCAACCC
1 GGATACTCCAACCC
1354818 TATTATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (51 bp):
GGATACTCCAACCCCGACTTTATTTCTAAAACATTAATTTTTCACAATTCG
Found at i:1354835 original size:79 final size:79
Alignment explanation
Indices: 1354752--1355155 Score: 374
Period size: 79 Copynumber: 5.1 Consensus size: 79
1354742 TTCACAATTC
* * * *
1354752 GGGATACTCCAACCTCGATTTTATTTTTGAAATATTGATTTTTCACAATTGGGGATACTCCAACC
1 GGGATACTCCAACCTCGATTTTATTTCTAAAACATTGATTTTTCACAATCGGGGATACTCCAACC
*
1354817 CTATTATTTTTGAG
66 CTGTTATTTTTGAG
* * * * *
1354831 GGGATATTCCAACCTCGATTTTATTTCTAAAACATCGATTTTTCAAAATCGTGGATACTCTAA-C
1 GGGATACTCCAACCTCGATTTTATTTCTAAAACATTGATTTTTCACAATCGGGGATACTCCAACC
1354895 CTCGTTA-TTTTGAG
66 CT-GTTATTTTTGAG
* * * * ** *
1354909 GGGATACTCCAACCTTGGTTTTATTT-TCGAAACATTGATTTTTCACAGTCATGGATATTCCAA-
1 GGGATACTCCAACCTCGATTTTATTTCT-AAAACATTGATTTTTCACAATCGGGGATACTCCAAC
* *
1354972 TCTCGTTATTTTCGAG
65 CCT-GTTATTTTTGAG
* * *
1354988 GGGATACTCCAAACC-C-AGTTTTATTTCCAAAACATCGATTTTTTTCACAATTGGGGATACTCC
1 GGGATACTCC-AACCTCGA-TTTTATTTCTAAAACATTGA--TTTTTCACAATCGGGGATACTCC
* * *
1355051 AACCCCGTTATTTCTGAA
62 AACCCTGTTATTTTTGAG
* * * * ** *
1355069 GGAATACTCCAA-CTCTAGTTTTATTTCTAAAACATTAATTTTCCACCGTCAGGGATAC-CACAA
1 GGGATACTCCAACCTCGA-TTTTATTTCTAAAACATTGATTTTTCACAATCGGGGATACTC-CAA
*
1355132 CCCCGTTATTTTTGAG
64 CCCTGTTATTTTTGAG
1355148 GGGATACT
1 GGGATACT
1355156 TCAATCTTAT
Statistics
Matches: 264, Mismatches: 49, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
77 1 0.00
78 69 0.26
79 129 0.49
80 7 0.03
81 57 0.22
82 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (79 bp):
GGGATACTCCAACCTCGATTTTATTTCTAAAACATTGATTTTTCACAATCGGGGATACTCCAACC
CTGTTATTTTTGAG
Found at i:1357083 original size:27 final size:27
Alignment explanation
Indices: 1357045--1357164 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 27
1357035 GGGACGAATT
* *
1357045 CGTGGCATCCTTTTAAGTCCATAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
*
1357072 CGTGGCACCCTTTTAAGCCCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
*
1357099 TGTGGCATTCTTTTTCCTTTTAAGTCCACAACTC
1 CGTGGCA--C-----CCTTTTAAGTCCACAACTC
1357133 CGTGGCACCCTTTTAAGTCCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
1357160 CGTGG
1 CGTGG
1357165 TATCTTTCTC
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
27 54 0.68
29 1 0.01
32 1 0.01
34 24 0.30
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.32
Consensus pattern (27 bp):
CGTGGCACCCTTTTAAGTCCACAACTC
Found at i:1357146 original size:34 final size:34
Alignment explanation
Indices: 1357080--1357146 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1357070 TCCGTGGCAC
* **
1357080 CCTTTTAAGCCCACAACTCTGTGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACCCTTTTT
*
1357114 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACCCTTTT
1357147 AAGTCCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.33, G:0.12, T:0.37
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCACCCTTTTT
Found at i:1357179 original size:61 final size:61
Alignment explanation
Indices: 1357053--1357179 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
1357043 TTCGTGGCAT
* * *
1357053 CCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTC
* *
1357114 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGTA-TCTTTCTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATTCTTT-TC
1357175 CCTTT
1 CCTTT
1357180 AGGCCCACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 5 0.08
61 55 0.92
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (61 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTC
Found at i:1357217 original size:30 final size:30
Alignment explanation
Indices: 1357182--1357304 Score: 121
Period size: 29 Copynumber: 4.2 Consensus size: 30
1357172 CTCCCTTTAG
* *
1357182 GCCCACAAGTTAGTGGCATCCTTTTCAAAA
1 GCCCACAAGTCAGTGGCACCCTTTTCAAAA
* *
1357212 GCCCACAAGTCGGTGGCACCCCTTTC-AAA
1 GCCCACAAGTCAGTGGCACCCTTTTCAAAA
*
1357241 GCCCACAAGTCAGTGGCAACC--TTCAAAA
1 GCCCACAAGTCAGTGGCACCCTTTTCAAAA
* ** *
1357269 GCACACAAGTTGGT-GCAACCCTTTT-AGAA
1 GCCCACAAGTCAGTGGC-ACCCTTTTCAAAA
1357298 GCCCACA
1 GCCCACA
1357305 TAAGTTGGTC
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.06
28 17 0.22
29 31 0.40
30 24 0.31
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (30 bp):
GCCCACAAGTCAGTGGCACCCTTTTCAAAA
Found at i:1357276 original size:57 final size:58
Alignment explanation
Indices: 1357182--1357304 Score: 160
Period size: 57 Copynumber: 2.1 Consensus size: 58
1357172 CTCCCTTTAG
* * * *
1357182 GCCCACAAGTTAGTGGCATCCTTTTCAAAAGCCCACAAGTCGGTGGCACCCCTTTCA-AA
1 GCCCACAAGTCAGTGGCAACC-TTTCAAAAGCACACAAGTCGGT-GCAACCCTTTCAGAA
* *
1357241 GCCCACAAGTCAGTGGCAACC-TTCAAAAGCACACAAGTTGGTGCAACCCTTTTAGAA
1 GCCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCGGTGCAACCCTTTCAGAA
1357298 GCCCACA
1 GCCCACA
1357305 TAAGTTGGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
56 10 0.18
57 28 0.49
59 19 0.33
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (58 bp):
GCCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCGGTGCAACCCTTTCAGAA
Found at i:1357291 original size:28 final size:29
Alignment explanation
Indices: 1357182--1357291 Score: 109
Period size: 30 Copynumber: 3.8 Consensus size: 29
1357172 CTCCCTTTAG
** * *
1357182 GCCCACAAGTTAGTGGCATCCTTTTCAAAA
1 GCCCACAAGTCGGTGGCAACC-CTTCAAAA
*
1357212 GCCCACAAGTCGGTGGCACCCCTTTC-AAA
1 GCCCACAAGTCGGTGGCAACCC-TTCAAAA
*
1357241 GCCCACAAGTCAGTGGCAA-CCTTCAAAA
1 GCCCACAAGTCGGTGGCAACCCTTCAAAA
* *
1357269 GCACACAAGTTGGT-GCAACCCTT
1 GCCCACAAGTCGGTGGCAACCCTT
1357292 TTAGAAGCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.10
28 20 0.29
29 20 0.29
30 21 0.31
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (29 bp):
GCCCACAAGTCGGTGGCAACCCTTCAAAA
Found at i:1357434 original size:39 final size:39
Alignment explanation
Indices: 1357375--1357579 Score: 122
Period size: 48 Copynumber: 4.8 Consensus size: 39
1357365 CCTTTATCTC
* * *
1357375 TAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
* * *
1357414 TAAGCCCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTA
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGG---C--A
* *
1357458 TCTCTAAGACCAATATTGCTGGCCTTAAATCAGCATATTGGCA
1 ----TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
* *
1357501 CCTTGCCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
* * * *
1357549 CAAGCCCAATATCGTTGGCCTTGAATCAGCA
1 TAAGACCAATATCGCTGGCCTTAAATCAGCA
1357580 TATCGGCACC
Statistics
Matches: 134, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
39 58 0.43
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
48 72 0.54
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
Found at i:1357567 original size:135 final size:134
Alignment explanation
Indices: 1357324--1357685 Score: 526
Period size: 135 Copynumber: 2.7 Consensus size: 134
1357314 CGCGTCTTCT
* *
1357324 TCTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTCTAAGACCAATGTCG
1 TCTAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TT-CCTCTAAGACCAATGTCG
* * *
1357389 CTGGCCTTGAATTAGCACATTGGCATAAGCCCAATATCGTTGGCCTTAAATCAGCATATTGGCAC
64 CTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTAAATCAGCATATCGGCAC
1357454 CTTATC
129 CTTATC
*
1357460 TCTAAGACCAATATTGCTGGCCTTAAATCAGCATATTGGCACCTTGCCTCTAAGACCAATGTCGC
1 TCTAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT-CCTCTAAGACCAATGTCGC
*
1357525 TGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCAGCATATCGGCACC
65 TGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTAAATCAGCATATCGGCACC
*
1357590 TTGTC
130 TTATC
* * * * * * * *
1357595 TTTAAGACCAATGTCGCTGGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCG
1 TCTAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTC--CTCTAAGACCAATGTCG
*
1357660 CTGGCCTTGAATCAGCATATTGGCAC
64 CTGGCCTTGAATCAGCACATTGGCAC
1357686 CTTCGTCATC
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 1 0.00
135 124 0.60
136 80 0.39
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (134 bp):
TCTAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCCTCTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTAAATCAGCATATCGGCACCT
TATC
Found at i:1357717 original size:52 final size:52
Alignment explanation
Indices: 1357554--1358134 Score: 500
Period size: 52 Copynumber: 11.5 Consensus size: 52
1357544 TGGCACAAGC
* * * *
1357554 CCAATATCGTTGGCCTTGAATCAGCATATCGGCACCTT-G---TCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* *
1357602 CCAATGTCGCTGGCCTTGAATCAGTACATTGGCACC-T--TCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* *
1357651 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * *
1357703 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCAGCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * * * * *
1357752 TCGATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * * * *
1357804 CCAATGTCACTGGCCTTGAATTAGTACATTGGCA-C--CATCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * *
1357853 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * *
1357905 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCAGCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
* * * * * *** * * *
1357954 CCGATATCGTTGACCTTGAATCAGCATATTGGCATCTTTAACATTCCTCAA-C
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCA-TCTTTAAGT
* ** * *
1358006 CCAATGTCATTGGCCTTGAATCAGCACATTGGCATTCTTC-TCATCTTCAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCGTCATCTTTAAGT
* * * * * * **
1358058 CTAATGTCGCTGACCATGAATCAGCACATT-G-ACATTCTTTACATCTTTAAAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTC-GT-CATCTTTAAGT
* *
1358110 CCAATATCGTTGGCCGTGAATCAGC
1 CCAATATCGCTGGCCTTGAATCAGC
1358135 GTATTGGTCT
Statistics
Matches: 427, Mismatches: 85, Indels: 38
0.78 0.15 0.07
Matches are distributed among these distances:
47 1 0.00
48 31 0.07
49 165 0.39
50 3 0.01
51 9 0.02
52 210 0.49
53 8 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (52 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCGTCATCTTTAAGT
Found at i:1357732 original size:101 final size:101
Alignment explanation
Indices: 1357554--1358088 Score: 666
Period size: 101 Copynumber: 5.3 Consensus size: 101
1357544 TGGCACAAGC
* *
1357554 CCAATATCGTTGGCCTTGAATCAGCATATCGGCACCTT-G---TCTTTAAGACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
*
1357615 CCTTGAATCAGTACATTGGCACCTTCATCTTTAAGT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1357651 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
* *
1357716 CCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * * * *
1357752 TCGATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
* * *
1357817 CCTTGAATTAGTACATTGGCACCATCATCTTTAAGT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
1357853 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
* *
1357918 CCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * *** * * * **
1357954 CCGATATCGTTGACCTTGAATCAGCATATTGGCATCTTTAACATTCCTCAA-CCCAATGTCATTG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCA-TCTTTAAGACCAATGTCGCTG
* *
1358018 GCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGT
65 GCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTAAGT
* * * * *
1358058 CTAATGTCGCTGACCATGAATCAGCACATTG
1 CCAATATCGCTGGCCTTGAATCAGCATATTG
1358089 ACATTCTTTA
Statistics
Matches: 377, Mismatches: 53, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
97 36 0.10
98 1 0.00
101 299 0.79
102 5 0.01
103 1 0.00
104 35 0.09
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (101 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:1357939 original size:202 final size:198
Alignment explanation
Indices: 1357429--1358039 Score: 788
Period size: 202 Copynumber: 3.1 Consensus size: 198
1357419 CCAATATCGT
* * * * * * *
1357429 TGGCCTTAAATCAGCATATTGGCACCTTATCTCTAAGACCAATATTGCTGGCCTTAAATCAGCAT
1 TGGCCTTGAATCAGTACATTGGCACCTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCAT
* *
1357494 ATTGGCACCTT-G-C--CTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C--AA
66 ATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCA
** *
1357552 GC-CCAA-TATCG-T-T-G-GCCTTGAATCAGCATATCGGCACC-TTG--TCTTTAAGACCAATG
131 GCTTTAAGT-TCGATATCGTGCCTTGAATCAGCATATTGGCACCTTTGCATCTTTAAGACCAATG
*
1357608 TCGC
195 TCAC
*
1357612 TGGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGTACATTGGCACC-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
1357677 TATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTC
65 TATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTC
* *
1357742 AGCTTTAAGTTCGATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCA
130 AGCTTTAAGTTCGATATCG-T-GCCTTGAATCAGCATATTGGCACCTTTG-CATCTTTAAGACCA
1357807 ATGTCAC
192 ATGTCAC
*
1357814 TGGCCTTGAATTAGTACATTGGCACCATCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGTACATTGGCACC-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
1357879 TATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTC
65 TATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTC
* * * * * *
1357944 AGCTTTAAGTCCGATATCGTTGACCTTGAATCAGCATATTGGCATCTTTAACATTCCTCAA-CCC
130 AGCTTTAAGTTCGATATCG-TG-CCTTGAATCAGCATATTGGCACCTTT-GCA-TCTTTAAGACC
*
1358008 AATGTCAT
191 AATGTCAC
*
1358016 TGGCCTTGAATCAGCACATTGGCA
1 TGGCCTTGAATCAGTACATTGGCA
1358040 TTCTTCTCAT
Statistics
Matches: 375, Mismatches: 30, Indels: 27
0.87 0.07 0.06
Matches are distributed among these distances:
183 23 0.06
184 45 0.12
185 1 0.00
186 1 0.00
188 41 0.11
189 1 0.00
191 3 0.01
192 5 0.01
193 2 0.01
194 1 0.00
195 1 0.00
198 22 0.06
199 3 0.01
201 1 0.00
202 220 0.59
203 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (198 bp):
TGGCCTTGAATCAGTACATTGGCACCTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCAT
ATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCA
GCTTTAAGTTCGATATCGTGCCTTGAATCAGCATATTGGCACCTTTGCATCTTTAAGACCAATGT
CAC
Found at i:1368211 original size:28 final size:28
Alignment explanation
Indices: 1368168--1368222 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1368158 TCACTTTATA
*
1368168 ACTCTAGATGACGACCTATTTTGGGACT
1 ACTCTAGACGACGACCTATTTTGGGACT
*
1368196 ACTCTAGACGATGACCTATTTTGGGAC
1 ACTCTAGACGACGACCTATTTTGGGAC
1368223 CAATCTTTTG
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:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
ACTCTAGACGACGACCTATTTTGGGACT
Found at i:1368400 original size:111 final size:109
Alignment explanation
Indices: 1368196--1368644 Score: 399
Period size: 109 Copynumber: 4.1 Consensus size: 109
1368186 TTTTGGGACT
* * * * *
1368196 ACTCTAGACGATGACCTATTTTGGGACCAATCTTTTGGAGCCCAAATTTACGTAATTAGTGCCAA
1 ACTCTAGACGATGACC-ATTTCGGG-CCAATCTTTTAGTGCCCGAATTTACGTAATTAATGCCAA
* * * *
1368261 AAAAATGAATTATGTTATATAGAGGGCATTCGTACGCCGCTTTATG
64 AAAAATGAATTATCTTATGTAAAGGGCATTCGTACGCCGCTTTAAG
* * * *
1368307 GCTCTAGATGATGACCAATTCGGGTCCAATCTTTTAGTGCCCGAATTTACATAATTAATGCCAAA
1 ACTCTAGACGATGACCATTTCGGG-CCAATCTTTTAGTGCCCGAATTTACGTAATTAATGCCAAA
* * *
1368372 AAAATTGAATTATCCTATGTAAAGGGCATTCGTATGCCGTTTTACA-
65 AAAA-TGAATTATCTTATGTAAAGGGCATTCGTACGCCGCTTTA-AG
* ** * * * *
1368418 ACTTTAGACGATGATTTATTTCGAAGCCAATCTTTTTGTGCTCGAATATTATGTAATTAATG-C-
1 ACTCTAGACGATGA-CCATTTCG-GGCCAATCTTTTAGTGCCCGAAT-TTACGTAATTAATGCCA
*
1368481 -AAAAATGAATTGTCTTATGTAAAGGGCATTCGTACGCCGCTTTAAG
63 AAAAAATGAATTATCTTATGTAAAGGGCATTCGTACGCCGCTTTAAG
* ** * * * * *
1368527 ACTCTAGACGGTGATTTATTTCGAGGCCAGTCCTTTGGTGCCCAAATATTATGTAATTAATG-C-
1 ACTCTAGACGATGA-CCATTTCG-GGCCAATCTTTTAGTGCCCGAAT-TTACGTAATTAATGCCA
* * ** * * *
1368590 -AAAAATGAGTTATCTTATGTGAAGGGTGTTCATATGCCGCTTTACG
63 AAAAAATGAATTATCTTATGTAAAGGGCATTCGTACGCCGCTTTAAG
1368636 ACTCTAGAC
1 ACTCTAGAC
1368645 AGTTGTAGAC
Statistics
Matches: 284, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
108 1 0.00
109 137 0.48
110 50 0.18
111 58 0.20
112 25 0.09
113 13 0.05
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
ACTCTAGACGATGACCATTTCGGGCCAATCTTTTAGTGCCCGAATTTACGTAATTAATGCCAAAA
AAATGAATTATCTTATGTAAAGGGCATTCGTACGCCGCTTTAAG
Found at i:1370940 original size:27 final size:27
Alignment explanation
Indices: 1370902--1371028 Score: 148
Period size: 27 Copynumber: 4.6 Consensus size: 27
1370892 TAGAAATCCT
* *
1370902 CACCCTTTTAAGTCCATGACTCTGTGG
1 CACCCTTTTAAGCCCACGACTCTGTGG
*
1370929 CACCTTTTTAAGCCCACGACTCTGTGG
1 CACCCTTTTAAGCCCACGACTCTGTGG
*
1370956 CACCCTTTTAAGCCCATGACT-TCGTGG
1 CACCCTTTTAAGCCCACGACTCT-GTGG
* * *
1370983 CACCCTTTTAAGTCCGCGACTATGTGG
1 CACCCTTTTAAGCCCACGACTCTGTGG
*
1371010 CACCTTTTTCAAAGCCCAC
1 CACCCTTTT--AAGCCCAC
1371029 AAGTCAGTGG
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 77 0.91
28 1 0.01
29 6 0.07
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (27 bp):
CACCCTTTTAAGCCCACGACTCTGTGG
Found at i:1370984 original size:54 final size:54
Alignment explanation
Indices: 1370902--1371027 Score: 164
Period size: 54 Copynumber: 2.3 Consensus size: 54
1370892 TAGAAATCCT
* * *
1370902 CACCCTTTTAAGTCCATGACTCTGTGGCACCTTTTTAAGCCCACGACTCTGTGG
1 CACCCTTTTAAGCCCATGACTCTGTGGCACCCTTTTAAGCCCACGACTATGTGG
* *
1370956 CACCCTTTTAAGCCCATGACT-TCGTGGCACCCTTTTAAGTCCGCGACTATGTGG
1 CACCCTTTTAAGCCCATGACTCT-GTGGCACCCTTTTAAGCCCACGACTATGTGG
*
1371010 CACCTTTTTCAAAGCCCA
1 CACCCTTTT--AAGCCCA
1371028 CAAGTCAGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
53 1 0.02
54 55 0.87
56 7 0.11
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (54 bp):
CACCCTTTTAAGCCCATGACTCTGTGGCACCCTTTTAAGCCCACGACTATGTGG
Found at i:1371431 original size:52 final size:49
Alignment explanation
Indices: 1371047--1371436 Score: 287
Period size: 52 Copynumber: 7.7 Consensus size: 49
1371037 GGCCTTTACT
* *
1371047 TTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTGTCATC
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TC-T-TCATC
* * * * *
1371099 TTTAAGCCCAATATCGTTGGCTTTGAATCAGCATATTGGTATCTTCAATA
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTC-ATC
* * * *
1371149 TTCCTAAGCCTAACATCGCTGGCCTTGAATCAGCACATTGGTACCTTCATC
1 TT--TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * * * * * *
1371200 TTTAAGTCCAATGTCGTTGGCCTTGAATTAGCACATCGGCACCTTTATC
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * * * * * *
1371249 TTTAAGTCCGATATCGCTGGCCTTGAATCAACATATTGGCATTTTTAAC
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * * *
1371298 TTTCCTAAGCCCAATGTCACT-GCCTTGATTCAGCACATTAGCATTCTTCTTATC
1 -TT--TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TCTTC--ATC
* * * *** * * *
1371352 TTTAAGTCTAATGTCGCTAATCGTGAATCAACACATTGACATTCTTCGCATC
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TCTT--CATC
*
1371404 TTTAAGCCCAATATCGCTAGCCTTGAATCAGCA
1 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCA
1371437 AGTTAGCACC
Statistics
Matches: 267, Mismatches: 59, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
49 79 0.30
50 7 0.03
51 37 0.14
52 139 0.52
53 2 0.01
54 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
Found at i:1372278 original size:13 final size:13
Alignment explanation
Indices: 1372260--1372284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372250 TTAATAAATA
1372260 TATCGATACATTG
1 TATCGATACATTG
1372273 TATCGATACATT
1 TATCGATACATT
1372285 AATACTGAAT
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:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1375815 original size:20 final size:20
Alignment explanation
Indices: 1375790--1375834 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1375780 CCTTCGTGAG
1375790 TGTAAATTACCTATGTCTCT
1 TGTAAATTACCTATGTCTCT
1375810 TGTAAATTACCTATGTCTCT
1 TGTAAATTACCTATGTCTCT
1375830 TGTAA
1 TGTAA
1375835 GTAACTCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (20 bp):
TGTAAATTACCTATGTCTCT
Found at i:1377686 original size:20 final size:20
Alignment explanation
Indices: 1377661--1377735 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1377651 TGTTACCCAG
1377661 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1377681 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1377701 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1377721 ATGTATCGATACATT
1 ATGTATCGATACATT
1377736 CTATCTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1381692 original size:25 final size:24
Alignment explanation
Indices: 1381643--1381692 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
1381633 TATATTTATA
* *
1381643 TCATGTTTATATTTTTCGTGTTGT
1 TCATGTTTATATTTTTCCTGATGT
1381667 TCATGCTTTATTATTTTTCCT-ATGT
1 TCATG-TTTA-TATTTTTCCTGATGT
1381692 T
1 T
1381693 ATATTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 9 0.41
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (24 bp):
TCATGTTTATATTTTTCCTGATGT
Found at i:1383076 original size:2 final size:2
Alignment explanation
Indices: 1383069--1383095 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1383059 AAACTAATTT
1383069 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1383096 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1383100 original size:2 final size:2
Alignment explanation
Indices: 1383095--1383119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1383085 ACACACACAC
1383095 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1383120 AATTACTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1383330 original size:2 final size:2
Alignment explanation
Indices: 1383323--1383402 Score: 81
Period size: 2 Copynumber: 40.0 Consensus size: 2
1383313 TAACTTTAAA
** ** ** *
1383323 AT AT AT AT AT AT AT AT AT AT AT AT CC AT CC AT AT CC ACC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
1383365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1383403 TATTGGCTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1383981 original size:1 final size:1
Alignment explanation
Indices: 1383975--1384005 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1383965 CTCTCTCTCT
*
1383975 CCCCCCCCCCCCCCCCCCCCCCCCGCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1384006 ACTAAATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:1386141 original size:2 final size:2
Alignment explanation
Indices: 1386134--1386163 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1386124 GTTTTACTCC
1386134 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1386164 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1386211 original size:2 final size:2
Alignment explanation
Indices: 1386163--1386192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1386153 TCTCTCTCTC
1386163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1386193 GGCCATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1395357 original size:16 final size:15
Alignment explanation
Indices: 1395319--1395358 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1395309 AATTATTTTA
1395319 TATTATTTAAATGAT
1 TATTATTTAAATGAT
* *
1395334 TTTTATTTAATATTAT
1 TATTATTTAA-ATGAT
1395350 TATTATTTA
1 TATTATTTA
1395359 GTTATTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATTTAAATGAT
Found at i:1396073 original size:18 final size:18
Alignment explanation
Indices: 1396050--1396084 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1396040 CCTAAAGGTA
*
1396050 TAAAATTAATTTGTTATG
1 TAAAATTAATTTATTATG
1396068 TAAAATTAATTTATTAT
1 TAAAATTAATTTATTAT
1396085 ATAATTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TAAAATTAATTTATTATG
Found at i:1398087 original size:21 final size:21
Alignment explanation
Indices: 1398053--1398092 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1398043 TATTTTTATT
1398053 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1398074 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
1398093 ATTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1399659 original size:34 final size:34
Alignment explanation
Indices: 1399613--1399830 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
1399603 GTAAAAACCA
*
1399613 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1399647 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1399681 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1399715 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1399748 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1399782 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1399815 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1399831 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1399727 original size:68 final size:67
Alignment explanation
Indices: 1399611--1399830 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1399601 TGGTAAAAAC
* * *
1399611 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1399676 AT
66 AT
* * *
1399678 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1399743 AAT
65 AAT
* * * * * *
1399746 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1399811 AT
66 AT
1399813 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1399831 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1403923 original size:19 final size:19
Alignment explanation
Indices: 1403896--1403958 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1403886 TCACGTGTAC
* *
1403896 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1403915 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1403934 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1403953 AGTACC
1 AGTACC
1403959 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1404305 original size:34 final size:34
Alignment explanation
Indices: 1404259--1404474 Score: 269
Period size: 34 Copynumber: 6.4 Consensus size: 34
1404249 GTAAAAACCA
*
1404259 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1404293 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1404327 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1404361 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1404394 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
1404428 CTATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1404461 CCATTTAATCAACA
1 CCATTTAATCAACA
1404475 TATATATCAT
Statistics
Matches: 158, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
33 42 0.27
34 114 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1404373 original size:68 final size:67
Alignment explanation
Indices: 1404257--1404474 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
1404247 TGGTAAAAAC
* * *
1404257 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1404322 AT
66 AT
* * *
1404324 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1404389 AAT
65 AAT
* * * * * * *
1404392 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCTATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1404457 AT
66 AT
1404459 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1404475 TATATATCAT
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 72 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1405290 original size:29 final size:28
Alignment explanation
Indices: 1405257--1405317 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
1405247 ACTTGGGATG
*
1405257 TAATTAAAATATTAATAA-AAAATTATATT
1 TAATTAAAATATTAA-AATAAAATAAT-TT
*
1405286 TAATTTAAATATTAAAATAAAATAATTT
1 TAATTAAAATATTAAAATAAAATAATTT
1405314 TAAT
1 TAAT
1405318 AATATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATTAAAATATTAAAATAAAATAATTT
Found at i:1405614 original size:23 final size:23
Alignment explanation
Indices: 1405588--1405632 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1405578 AAATTAAAAT
* *
1405588 ATTTAATTATTTATTTAATATAA
1 ATTTAATTAATTATTAAATATAA
**
1405611 ATTTTTTTAATTATTAAATATA
1 ATTTAATTAATTATTAAATATA
1405633 TATTGAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTAATTAATTATTAAATATAA
Found at i:1406892 original size:2 final size:2
Alignment explanation
Indices: 1406887--1406927 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1406877 AAGAGGGGAA
* *
1406887 AG AG AG AG AC AG AG AT AG AG AG AG A- AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1406927 A
1 A
1406928 AAGAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.02, G:0.41, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1406919 original size:11 final size:11
Alignment explanation
Indices: 1406889--1406927 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1406879 GAGGGGAAAG
*
1406889 AGAGAGACAGA
1 AGAGAGAGAGA
*
1406900 GATAGAGAGAGA
1 -AGAGAGAGAGA
1406912 AGAGAGAGAGA
1 AGAGAGAGAGA
1406923 AGAGA
1 AGAGA
1406928 AAGAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.54, C:0.03, G:0.41, T:0.03
Consensus pattern (11 bp):
AGAGAGAGAGA
Found at i:1406928 original size:16 final size:15
Alignment explanation
Indices: 1406887--1406928 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1406877 AAGAGGGGAA
*
1406887 AGAGAGAGACAGAGAT
1 AGAGAGAGA-AGAGAG
1406903 AGAGAGAGAAGAGAG
1 AGAGAGAGAAGAGAG
1406918 AGAGAAGAGAA
1 AGAG-AGAGAA
1406929 AGAAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.55, C:0.02, G:0.40, T:0.02
Consensus pattern (15 bp):
AGAGAGAGAAGAGAG
Found at i:1407319 original size:18 final size:18
Alignment explanation
Indices: 1407296--1407335 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1407286 TTCAAGAAAG
*
1407296 AAAACAAAAAAATAAAAC
1 AAAACAAAAAAAGAAAAC
*
1407314 AAAACAAAAGAAGAAAAC
1 AAAACAAAAAAAGAAAAC
1407332 AAAA
1 AAAA
1407336 TCCTTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.10, G:0.05, T:0.03
Consensus pattern (18 bp):
AAAACAAAAAAAGAAAAC
Found at i:1408063 original size:18 final size:20
Alignment explanation
Indices: 1408035--1408076 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
1408025 GTTTTTATTA
1408035 TAATATGTTATTATAA-AAT
1 TAATATGTTATTATAATAAT
1408054 TAAT-TGTTATTATAATAAT
1 TAATATGTTATTATAATAAT
1408073 TAAT
1 TAAT
1408077 CATTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATATGTTATTATAATAAT
Found at i:1408072 original size:15 final size:15
Alignment explanation
Indices: 1408021--1408073 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1408011 CAAAACATGG
* *
1408021 AATTGTTTTTATTAT
1 AATTGTTATTATAAT
1408036 AATATGTTATTATAAAATT
1 AAT-TGTTATTAT--AA-T
1408055 AATTGTTATTATAAT
1 AATTGTTATTATAAT
1408070 AATT
1 AATT
1408074 AATCATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.25
16 10 0.31
18 10 0.31
19 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
AATTGTTATTATAAT
Found at i:1408082 original size:19 final size:18
Alignment explanation
Indices: 1408042--1408082 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1408032 TTATAATATG
**
1408042 TTATTATAAAATTAATTG
1 TTATTATAAAATTAATCA
1408060 TTATTATAATAATTAATCA
1 TTATTATAA-AATTAATCA
1408079 TTAT
1 TTAT
1408083 AATATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TTATTATAAAATTAATCA
Found at i:1411356 original size:8 final size:7
Alignment explanation
Indices: 1411282--1411354 Score: 65
Period size: 7 Copynumber: 9.6 Consensus size: 7
1411272 TTTTGTATAT
*
1411282 AAAATTA
1 AAAATAA
1411289 AAAATAA
1 AAAATAA
1411296 AAAATAA
1 AAAATAA
1411303 AAAATTGAA
1 AAAA-T-AA
*
1411312 AAATGAAAA
1 AAA--ATAA
1411321 AATAATCAA
1 AA-AAT-AA
*
1411330 AAAATCA
1 AAAATAA
1411337 AAAATAA
1 AAAATAA
1411344 AAAATAA
1 AAAATAA
1411351 AAAA
1 AAAA
1411355 ATTAATTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 35 0.64
8 5 0.09
9 13 0.24
10 1 0.02
11 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:1411669 original size:88 final size:88
Alignment explanation
Indices: 1411515--1411679 Score: 258
Period size: 88 Copynumber: 1.9 Consensus size: 88
1411505 AAAAAAAATC
* * * *
1411515 CATGCATTTCATACTTTCATGTGAAGCTTAAGAAACATTTCATGCATTGCATTCATTTCATTGTA
1 CATGCATTTCATACTTTCATGTAAAACTTAAAAAACATTTCATGCATTACATTCATTTCATTGTA
* *
1411580 TTGCTTTTATGCCTTCATGTATA
66 TTACTTTCATGCCTTCATGTATA
* *
1411603 CATGTATTTCATACTTTCATTTAAAACTTAAAAAACATTTCATGCATTACATTCATTTCATTGTA
1 CATGCATTTCATACTTTCATGTAAAACTTAAAAAACATTTCATGCATTACATTCATTTCATTGTA
1411668 TTACTTTCATGC
66 TTACTTTCATGC
1411680 ATGCATTTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (88 bp):
CATGCATTTCATACTTTCATGTAAAACTTAAAAAACATTTCATGCATTACATTCATTTCATTGTA
TTACTTTCATGCCTTCATGTATA
Found at i:1413389 original size:69 final size:66
Alignment explanation
Indices: 1413299--1413430 Score: 174
Period size: 69 Copynumber: 2.0 Consensus size: 66
1413289 ATTCTTCTAA
* * *
1413299 GGGGATACTTCAACTCCATTTTTAAACTTATCAAAATTTAAATATTATTTTGTCTAAATTATCAT
1 GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATATTA-TTT-TC-AAATTATCAT
1413364 TGTC
63 TGTC
** * *
1413368 GGGGATACTCCAACCCCATTTTTAAACTCATTGAAATTTAAGTCTTATTTTCAAATTATCATT
1 GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATATTATTTTCAAATTATCATT
1413431 ATTAGGGATA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
66 11 0.20
67 2 0.04
68 3 0.05
69 40 0.71
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.42
Consensus pattern (66 bp):
GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATATTATTTTCAAATTATCATTGT
C
Found at i:1414234 original size:13 final size:13
Alignment explanation
Indices: 1414216--1414241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1414206 AATTTTTTGG
1414216 TGTATCGATACAT
1 TGTATCGATACAT
1414229 TGTATCGATACAT
1 TGTATCGATACAT
1414242 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1415952 original size:21 final size:20
Alignment explanation
Indices: 1415923--1415965 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1415913 GGCTAGTGTG
*
1415923 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1415944 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1415964 GG
1 GG
1415966 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1416264 original size:21 final size:20
Alignment explanation
Indices: 1416240--1416286 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1416230 TTTGAAGCTG
1416240 ATTTTG-ATGAAAAACGAAGT
1 ATTTTGAATGAAAAAC-AAGT
*
1416260 AATTTGAAATGAAAAACAAGT
1 ATTTTG-AATGAAAAACAAGT
1416281 ATTTTG
1 ATTTTG
1416287 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (20 bp):
ATTTTGAATGAAAAACAAGT
Found at i:1416271 original size:22 final size:21
Alignment explanation
Indices: 1416246--1416286 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1416236 GCTGATTTTG
1416246 ATGAAAAACGAAGTAATTTGAA
1 ATGAAAAAC-AAGTAATTTGAA
*
1416268 ATGAAAAACAAGTATTTTG
1 ATGAAAAACAAGTAATTTG
1416287 CAAAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (21 bp):
ATGAAAAACAAGTAATTTGAA
Found at i:1416602 original size:13 final size:13
Alignment explanation
Indices: 1416584--1416623 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
1416574 AAAAACACAG
1416584 AATCATTCATCAA
1 AATCATTCATCAA
1416597 AATCATTCATTTCAA
1 AATCATTCA--TCAA
*
1416612 CATCATTCATCA
1 AATCATTCATCA
1416624 TAAAATCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (13 bp):
AATCATTCATCAA
Found at i:1416631 original size:15 final size:14
Alignment explanation
Indices: 1416584--1416631 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1416574 AAAAACACAG
1416584 AATCATTCATC-AA
1 AATCATTCATCTAA
*
1416597 AATCATTCATTTCAA
1 AATCATTCATCT-AA
*
1416612 CATCATTCATCATAA
1 AATCATTCATC-TAA
1416627 AATCA
1 AATCA
1416632 CAAAATCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.36
15 17 0.61
16 1 0.04
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (14 bp):
AATCATTCATCTAA
Found at i:1421074 original size:52 final size:52
Alignment explanation
Indices: 1420941--1421081 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
1420931 TGAAAAGTTA
1420941 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1420993 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
1421045 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
1421082 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1421088 original size:13 final size:13
Alignment explanation
Indices: 1421070--1421094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1421060 CAAAAATCAG
1421070 TGTATCGATACAA
1 TGTATCGATACAA
1421083 TGTATCGATACA
1 TGTATCGATACA
1421095 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1421179 original size:13 final size:13
Alignment explanation
Indices: 1421161--1421185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1421151 CAAAAAAATA
1421161 TGTATCGATACAT
1 TGTATCGATACAT
1421174 TGTATCGATACA
1 TGTATCGATACA
1421186 ACATTTTATG
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1421181 original size:33 final size:33
Alignment explanation
Indices: 1421139--1421205 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1421129 AGTAGCTTAA
1421139 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1421172 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1421205 A
1 A
1421206 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1421284 original size:21 final size:21
Alignment explanation
Indices: 1421243--1421284 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1421233 GTTGGGACCT
*
1421243 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1421264 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1421285 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1426277 original size:13 final size:13
Alignment explanation
Indices: 1426259--1426284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1426249 AATTTTTTGG
1426259 TGTATCGATACAT
1 TGTATCGATACAT
1426272 TGTATCGATACAT
1 TGTATCGATACAT
1426285 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1427936 original size:49 final size:49
Alignment explanation
Indices: 1427727--1428287 Score: 748
Period size: 49 Copynumber: 11.7 Consensus size: 49
1427717 AAAAGGATGT
* *
1427727 CAATGTACTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
1427779 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1427822 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1427870 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1427919 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1427967 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1428016 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1428059 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1428108 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1428151 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1428200 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
1428252 CAATATGCTGATTCAAGGCGAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1428288 GAAGGGTTGC
Statistics
Matches: 453, Mismatches: 33, Indels: 46
0.85 0.06 0.09
Matches are distributed among these distances:
43 116 0.26
45 2 0.00
47 2 0.00
48 95 0.21
49 170 0.38
52 68 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1428114 original size:92 final size:92
Alignment explanation
Indices: 1427771--1428238 Score: 687
Period size: 92 Copynumber: 5.0 Consensus size: 92
1427761 TAAAGATGGA
* * *
1427771 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
1427830 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTACATTGGACTT
1427857 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
*
1427922 TGTGCTGAGTCAAGGCCAGCTACATTGGACTT
61 TGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1427954 AAAGATGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCGA
1 --A-A--AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* *
1428019 TATGCTGATTCAAGGCCAGCTATATTGGACTT
61 TGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1428051 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* *
1428116 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTACATTGGACTT
*
1428143 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
1428208 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTACATTGGACTT
1428235 AAAG
1 AAAG
1428239 ATGGAAAAGG
Statistics
Matches: 352, Mismatches: 17, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
87 2 0.01
91 38 0.11
92 177 0.50
94 1 0.00
95 2 0.01
97 129 0.37
98 2 0.01
99 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGATTCAAGGCCAGCTACATTGGACTT
Found at i:1428331 original size:33 final size:35
Alignment explanation
Indices: 1428287--1428356 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
1428277 TATTGGGCTT
1428287 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
1428321 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
1428355 AG
1 AG
1428357 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:1428399 original size:34 final size:33
Alignment explanation
Indices: 1428361--1428923 Score: 500
Period size: 34 Copynumber: 16.9 Consensus size: 33
1428351 AGGAAGGGAG
* * *
1428361 AAAGATGCCACGGAGTTGTGGACTTGAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA-AGAA
1428395 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAG----AA
* *
1428433 AAAGGTGCCACGGAGTTGTGGAC-TTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA-A-GAA
*
1428467 AAA-AGTGCCACGGAGTTATGGGC-TTAAAAG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGAA
* ** *
1428497 ---GGTGCCATAGAGTTGTGGGC-TTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTA-AAAGAA
* *
1428527 AAAGAGTGCCACAGAGTTGTGGGC-TTAGAAGGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTA-AAAGAA
1428561 AAAGAGTGCCACGGAGTTGTGGGCTTT--AA-AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGAA
* *
1428592 AGAG-TGCCACGGAGTCGTGGGCTTTCAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGAA
* * *
1428625 GAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGAA
* * * *
1428659 GAAGGTGCCATGGAGCTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGAA
* *
1428693 GAAGGTGCCACGGAGTTGTGGGCTTT-AAAG--
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAAGAA
*
1428723 --AG-TGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT--AAA-AGAA
1428756 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAA-AGAA
*
1428791 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAA--GAA
*
1428827 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGAA
*
1428861 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGAA
*
1428895 AAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA
1428924 GAGTAGGATG
Statistics
Matches: 454, Mismatches: 38, Indels: 75
0.80 0.07 0.13
Matches are distributed among these distances:
27 38 0.08
28 5 0.01
29 20 0.04
30 2 0.00
31 7 0.02
32 8 0.02
33 29 0.06
34 224 0.49
35 40 0.09
36 16 0.04
37 58 0.13
38 7 0.02
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTTAAAAGAA
Found at i:1428416 original size:71 final size:68
Alignment explanation
Indices: 1428341--1428925 Score: 542
Period size: 71 Copynumber: 8.7 Consensus size: 68
1428331 CACCGACTTG
* * * * *
1428341 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTGAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTA-AAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTT-AAA-AGAAAAAGAGTGCCA
1428406 CGGAGT
63 CGGAGT
** *
1428412 TGTGGGCTTTAAAAGAAAAAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA-AGTGCC
1 TGTGGGCTTTAAAAG--GGAAAAAGGTGCCACGGAGTTGTGGGCTTAAA-A-GAAAAAGAGTGCC
1428476 ACGGAGT
62 ACGGAGT
* ** * *
1428483 TATGGGC-TTAAAA--G-----GGTGCCATAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACA
1 TGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTA-AAAGAAAAAGAGTGCCACG
1428540 GAGT
65 GAGT
* *
1428544 TGTGGGC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTT----TAAAAAGAGTGCCACG
1 TGTGGGCTTTAAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACG
1428603 GAGT
65 GAGT
* * * *
1428607 CGTGGGCTTTCAAAA--GAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAG-GTGCCA
1 TGTGGGCTTT-AAAAGGGAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGAAAAAGAGTGCCA
* *
1428669 TGGAGC
63 CGGAGT
* * *
1428675 TGTGGGCTTTAAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTT------TAAAGAGTGCCACGG
1 TGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
1428733 AGT
66 AGT
* *
1428736 CGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAG-GTGCC
1 TGTGGGCTTT-AAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAA-AGAAAAAGAGTGCC
1428800 ACGGAGT
62 ACGGAGT
*
1428807 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAG-GTGCCA
1 TGTGGGCTTT-AAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGAAAAAGAGTGCCA
1428871 CGGAGT
63 CGGAGT
* *
1428877 TGTGGGCTTTAAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGA
1 TGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGA
1428926 GTAGGATGCC
Statistics
Matches: 439, Mismatches: 42, Indels: 71
0.80 0.08 0.13
Matches are distributed among these distances:
60 9 0.02
61 62 0.14
62 7 0.02
63 49 0.11
64 29 0.07
65 5 0.01
66 7 0.02
67 25 0.06
68 70 0.16
69 9 0.02
70 39 0.09
71 93 0.21
72 35 0.08
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (68 bp):
TGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
AGT
Found at i:1428503 original size:27 final size:27
Alignment explanation
Indices: 1428471--1428524 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1428461 GATGAAAAAA
*
1428471 GTGCCACGGAGTTATGGGCTTAAAAGG
1 GTGCCACAGAGTTATGGGCTTAAAAGG
* * *
1428498 GTGCCATAGAGTTGTGGGCTTAGAAGG
1 GTGCCACAGAGTTATGGGCTTAAAAGG
1428525 AAAAAGAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.13, G:0.39, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAGTTATGGGCTTAAAAGG
Found at i:1428510 original size:61 final size:61
Alignment explanation
Indices: 1428431--1428558 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
1428421 TAAAAGAAAA
* * *
1428431 AAAAAGGTGCCACGGAGTTGTGGACTTA-AAGATGAAAAA-AGTGCCACGGAGTTATGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAGAAG--GAAAAAGAGTGCCACAGAGTTATGGGCTT
* * *
1428492 AAAAGGGTGCCATAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
*
1428553 AGAAGG
1 AAAAGG
1428559 AAAAAGAGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 6 0.10
61 49 0.84
62 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
Found at i:1428679 original size:131 final size:132
Alignment explanation
Indices: 1428361--1428920 Score: 592
Period size: 132 Copynumber: 4.2 Consensus size: 132
1428351 AGGAAGGGAG
* * * *
1428361 AAAGATGCCACGGAGTTGTGGAC-TTGAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACAGAGTTGTGGGCTTTGAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
* * * **
1428425 AGAAAAAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA-AGTGCCACGGAGTTATGGG
64 AG-GAAAAAGA-GTGCCACGGAGTTGTGGGCTT-----T-AAAAAGAGTGCCACGGAGTCGTGGG
1428489 C-TT-AAAAG--
121 CTTTAAAAAGAA
* * * * *
1428497 ---GGTGCCATAGAGTTGTGGGCTTAG-AAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTAGAA
1 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
*
1428557 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTCAAAA
65 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAA
1428622 GAA
130 GAA
* * * * *
1428625 GAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCATGGAGCTGTGGGCTTTAAAAA
1 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
*
1428690 GAAGAAG-GTGCCACGGAGTTGTGGGCTTT--AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAG
66 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTT-AAAA-
1428752 AGAA
129 AGAA
*
1428756 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAG-GTGCCACAGAGTTGTGGGCTTTGAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AA
* * *
1428820 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCT
63 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--AA-AAAGA-GTGCCACGGAGTCGTGGGCT
1428885 TTAAAAAGAA
123 TTAAAAAGAA
*
1428895 AAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAGGTGCCACAGAGTTGTGGGCTTT
1428921 AAAGAGTAGG
Statistics
Matches: 367, Mismatches: 33, Indels: 46
0.82 0.07 0.10
Matches are distributed among these distances:
123 5 0.01
124 19 0.05
125 2 0.01
126 5 0.01
129 47 0.13
130 9 0.02
131 76 0.21
132 94 0.26
133 22 0.06
134 8 0.02
135 21 0.06
138 22 0.06
139 8 0.02
140 8 0.02
141 21 0.06
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (132 bp):
AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAAG
AA
Found at i:1428809 original size:166 final size:163
Alignment explanation
Indices: 1428395--1428923 Score: 559
Period size: 166 Copynumber: 3.2 Consensus size: 163
1428385 TGAAAGGGAA
* *
1428395 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAAAGGTGCCACGGAGTTGTGGAC-TTA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG-AAAAAAGA-GTGCCACGGAGTTGTGGGCTTTA
* *
1428459 AAGATGAAAAAAGTGCCACGGAGTTATGGGC-TT---AA-AAG--GGTGCCATAGAGTTGTGGGC
64 AA-A-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCATAGAGTTGTGGGC
* * * *
1428517 -TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAGAAGGAA
127 TTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTT-------T
*
1428561 AAAGAGTGCCACGGAGTTGTGGGCTTT------AAAAAGAGTGCCACGGAGTCGTGGGCTTTCAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * * *
1428620 AAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCATGGAGCTGTGGGCTTT
65 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCATAGAGTTGTGGGCTTT
*
1428685 AAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
130 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
*
1428719 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGA-AAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* *
1428784 AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGG
64 AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTGCCATAGAGTTGTGG
1428849 GCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
125 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1428887 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 --AAAG----A-GTGCCACGGAGTTGTGGGCTTTAAA
1428924 GAGTAGGATG
Statistics
Matches: 310, Mismatches: 24, Indels: 50
0.81 0.06 0.13
Matches are distributed among these distances:
158 65 0.21
159 11 0.04
160 3 0.01
162 2 0.01
163 3 0.01
165 41 0.13
166 99 0.32
168 38 0.12
169 19 0.06
170 4 0.01
174 4 0.01
175 21 0.07
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (163 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCATAGAGTTGTGGGCTTTA
AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:1428883 original size:104 final size:107
Alignment explanation
Indices: 1428719--1428920 Score: 347
Period size: 104 Copynumber: 1.9 Consensus size: 107
1428709 TGTGGGCTTT
*
1428719 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACAGAGTCGTGGGCTTT-AAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
1428784 AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
65 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
*
1428827 AAAGAGTGCCACAGAGTTGTGGGCTTT-AAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
1 AAAGAGTGCCACAGAGTCGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1428889 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
66 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1428921 AAAGAGTAGG
Statistics
Matches: 91, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
104 55 0.60
105 8 0.09
106 3 0.03
108 25 0.27
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (107 bp):
AAAGAGTGCCACAGAGTCGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
Found at i:1428968 original size:31 final size:31
Alignment explanation
Indices: 1428932--1429014 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
1428922 AAGAGTAGGA
* *
1428932 TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1428963 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
1428994 TGCCACTGAGTCATGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1429015 TTTTTTTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:1430355 original size:8 final size:8
Alignment explanation
Indices: 1430344--1430406 Score: 76
Period size: 8 Copynumber: 7.9 Consensus size: 8
1430334 TTTTTGTGTT
1430344 TTTTTTTG
1 TTTTTTTG
1430352 TTTTTTTG
1 TTTTTTTG
1430360 TTTTTTT-
1 TTTTTTTG
*
1430367 TTTTTGTG
1 TTTTTTTG
1430375 TTTTTTTTG
1 -TTTTTTTG
*
1430384 TTTGTTTG
1 TTTTTTTG
1430392 TTTGTTTT-
1 TTT-TTTTG
1430400 TTTTTTT
1 TTTTTTT
1430407 TCATCACCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
7 10 0.21
8 28 0.58
9 10 0.21
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1430355 original size:23 final size:22
Alignment explanation
Indices: 1430329--1430405 Score: 102
Period size: 23 Copynumber: 3.5 Consensus size: 22
1430319 TGCCTTTGCA
1430329 TTTTTTTTTTGTGTTTTTTTTTG
1 TTTTTTTTTTGT-TTTTTTTTTG
*
1430352 TTTTTTTGTT-TTTTTTTTTTG
1 TTTTTTTTTTGTTTTTTTTTTG
* *
1430373 TGTTTTTTTTGTTTGTTTGTTTG
1 TTTTTTTTTTGTTT-TTTTTTTG
1430396 TTTTTTTTTT
1 TTTTTTTTTT
1430406 TTCATCACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 18 0.38
22 4 0.09
23 25 0.53
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (22 bp):
TTTTTTTTTTGTTTTTTTTTTG
Found at i:1430357 original size:21 final size:21
Alignment explanation
Indices: 1430331--1430403 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
1430321 CCTTTGCATT
1430331 TTTTTTTTGTGTTTTTTTTTG
1 TTTTTTTTGTGTTTTTTTTTG
*
1430352 -TTTTTTTGTTTTTTTTTTTTG
1 TTTTTTTTG-TGTTTTTTTTTG
1430373 TGTTTTTTT-TGTTTGTTTGTTTG
1 T-TTTTTTTGTGTTT-TTT-TTTG
1430396 TTTTTTTT
1 TTTTTTTT
1430404 TTTTCATCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.18
21 15 0.33
22 10 0.22
23 12 0.27
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (21 bp):
TTTTTTTTGTGTTTTTTTTTG
Found at i:1430369 original size:36 final size:36
Alignment explanation
Indices: 1430329--1430407 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
1430319 TGCCTTTGCA
*
1430329 TTTTTTTTT-TGTGTTTTTT-TTTGTTTTTTTGTTT
1 TTTTTTTTTGTGTGTTTTTTGTTTGTTTGTTTGTTT
*
1430363 TTTTTTTTTGTGTTTTTTTTGTTTGTTTGTTTGTTT
1 TTTTTTTTTGTGTGTTTTTTGTTTGTTTGTTTGTTT
1430399 TTTTTTTTT
1 TTTTTTTTT
1430408 CATCACCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 9 0.22
35 9 0.22
36 23 0.56
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (36 bp):
TTTTTTTTTGTGTGTTTTTTGTTTGTTTGTTTGTTT
Found at i:1430370 original size:32 final size:32
Alignment explanation
Indices: 1430329--1430404 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 32
1430319 TGCCTTTGCA
*
1430329 TTTTTTTTTTGTGTTTTTTTTTGTTTTTTTGTT
1 TTTTTTTTTTGTG-TTTTTTTTGTTTGTTTGTT
1430362 TTTTTTTTTTGTGTTTTTTTTGTTTGTTTGTT
1 TTTTTTTTTTGTGTTTTTTTTGTTTGTTTGTT
1430394 TGTTTTTTTTT
1 T-TTTTTTTTT
1430405 TTTCATCACC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 19 0.46
33 22 0.54
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (32 bp):
TTTTTTTTTTGTGTTTTTTTTGTTTGTTTGTT
Found at i:1430420 original size:1 final size:1
Alignment explanation
Indices: 1430329--1430407 Score: 68
Period size: 1 Copynumber: 79.0 Consensus size: 1
1430319 TGCCTTTGCA
* * * * * * * * *
1430329 TTTTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTTTGTGTTTTTTTTGTTTGTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1430394 TGTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
1430408 CATCACCTTT
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:1437414 original size:52 final size:52
Alignment explanation
Indices: 1437281--1437421 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
1437271 TGAAAAGTTA
1437281 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1437333 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
1437385 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
1437422 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1437428 original size:13 final size:13
Alignment explanation
Indices: 1437410--1437434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1437400 CAAAAATCAG
1437410 TGTATCGATACAA
1 TGTATCGATACAA
1437423 TGTATCGATACA
1 TGTATCGATACA
1437435 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1437518 original size:13 final size:13
Alignment explanation
Indices: 1437500--1437524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1437490 CAAAAAAATA
1437500 TGTATCGATACAT
1 TGTATCGATACAT
1437513 TGTATCGATACA
1 TGTATCGATACA
1437525 ACATTTTATG
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1437520 original size:33 final size:33
Alignment explanation
Indices: 1437478--1437544 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1437468 AGTAGCTTAA
1437478 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1437511 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1437544 A
1 A
1437545 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1437623 original size:21 final size:21
Alignment explanation
Indices: 1437582--1437623 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1437572 GTTGGGACCT
*
1437582 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1437603 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1437624 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1442617 original size:13 final size:13
Alignment explanation
Indices: 1442599--1442624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1442589 AATTTTTTGG
1442599 TGTATCGATACAT
1 TGTATCGATACAT
1442612 TGTATCGATACAT
1 TGTATCGATACAT
1442625 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1444080 original size:13 final size:13
Alignment explanation
Indices: 1444062--1444094 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1444052 ACATAAGTGT
1444062 TGTATCGATACAA
1 TGTATCGATACAA
1444075 TGTATCGATACAA
1 TGTATCGATACAA
1444088 TGTATCG
1 TGTATCG
1444095 CTACGAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1446318 original size:24 final size:24
Alignment explanation
Indices: 1446286--1446333 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1446276 TTCGAGTAAA
1446286 ACTCGTTTTCGAACTTCAATTAAT
1 ACTCGTTTTCGAACTTCAATTAAT
1446310 ACTCGTTTTCGAACTTCAATTAAT
1 ACTCGTTTTCGAACTTCAATTAAT
1446334 CAAAGAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (24 bp):
ACTCGTTTTCGAACTTCAATTAAT
Found at i:1447321 original size:202 final size:205
Alignment explanation
Indices: 1446963--1447368 Score: 619
Period size: 202 Copynumber: 2.0 Consensus size: 205
1446953 GATCATGCCT
*
1446963 AGCCCGAAATGATCGGTGGCGACTCCAAAATTTCGGTCATTTCGTAGTGACCATTGAAGATCAAT
1 AGCCCGAAATGATCGGTGGCGACTCCAAAATTTCGGTCATTTCGTAGTGACCATCGAAGATCAAT
*
1447028 TAGATGGGCGATTCATCTACCGATCTTCTCCCTTTAATCAACATACTTCCTATCATGCCATAGAA
66 TAGATAGGCGATTCATCTACCGATCTTCTCCCTTTAATCAACATACTTCCTATCATGCCATAGAA
*
1447093 ATCCCCAATCACGAGGGATATTAAGTCA-AGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCG
131 ATCCCCAATCACGAGGGATATTAAGTCAGA-CGCGCCTCATTTGCCCTATCGCCAGGGTCGAGCG
1447157 CACGTTACGAC
195 CACGTTACGAC
* * * * * **
1447168 AGCCCGAAATGATCGGTGGCG-TTCCAAATTTTCGGTCATTTCGTGGTGACCGTCGAGGATTGAT
1 AGCCCGAAATGATCGGTGGCGACTCCAAAATTTCGGTCATTTCGTAGTGACCATCGAAGATCAAT
*
1447232 TAGATAGGCGCTTCATCTACCGATCTTC-CCCTTTTTAA-C-ACATA-TCTCCTA-CATGCCATA
66 TAGATAGGCGATTCATCTACCGATCTTCTCCC--TTTAATCAACATACT-TCCTATCATGCCATA
*
1447292 GAAATCCCCAATCACGAGGGATATTAAGTCAGACGCGCCTTATTTGCCCTATCGCCAGGGTCGAG
128 GAAATCCCCAATCACGAGGGATATTAAGTCAGACGCGCCTCATTTGCCCTATCGCCAGGGTCGAG
1447357 CGCACGTTACGA
193 CGCACGTTACGA
1447369 TAGCTTGGCG
Statistics
Matches: 185, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
202 83 0.45
203 14 0.08
204 62 0.34
205 26 0.14
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (205 bp):
AGCCCGAAATGATCGGTGGCGACTCCAAAATTTCGGTCATTTCGTAGTGACCATCGAAGATCAAT
TAGATAGGCGATTCATCTACCGATCTTCTCCCTTTAATCAACATACTTCCTATCATGCCATAGAA
ATCCCCAATCACGAGGGATATTAAGTCAGACGCGCCTCATTTGCCCTATCGCCAGGGTCGAGCGC
ACGTTACGAC
Found at i:1451182 original size:13 final size:13
Alignment explanation
Indices: 1451164--1451191 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1451154 CAAAGATCAG
1451164 TGTATCGATACAA
1 TGTATCGATACAA
1451177 TGTATCGATACAA
1 TGTATCGATACAA
1451190 TG
1 TG
1451192 AGTAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1451185 original size:33 final size:33
Alignment explanation
Indices: 1451143--1451208 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1451133 ATTTGCTTGC
* *
1451143 ATGTGTCGATACAAAGA-TCAGTGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
*
1451176 ATGTATCGATACAATGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
1451209 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:1455819 original size:32 final size:32
Alignment explanation
Indices: 1455763--1455833 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1455753 TTCAATGATT
* *
1455763 TGTATCGATACATAAGTGCGGTATCGATATAA
1 TGTATCGATACATAAGTGCGGTATCGACACAA
***
1455795 TGTATCGATACATAAGTTTTGTATCGACACAA
1 TGTATCGATACATAAGTGCGGTATCGACACAA
1455827 TGTATCG
1 TGTATCG
1455834 CTACGAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGCGGTATCGACACAA
Found at i:1455896 original size:13 final size:13
Alignment explanation
Indices: 1455878--1455902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1455868 ATTACTCAAA
1455878 TATATCGATACAT
1 TATATCGATACAT
1455891 TATATCGATACA
1 TATATCGATACA
1455903 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:1455951 original size:53 final size:52
Alignment explanation
Indices: 1455919--1456040 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
1455909 TTTGTATCAA
1455919 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCG
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCG
** *
1455971 ATACATATAGGCAAATTTGCCCAGATGTATCCATACACTATGAAATGTATCG
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCG
1456023 ATACATGCAGGCAAATTT
1 ATACATGCAGGCAAATTT
1456041 TCATATTTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCG
Found at i:1469897 original size:9 final size:9
Alignment explanation
Indices: 1469880--1469940 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
1469870 TCCACAGAAA
1469880 AAAAAAAAC
1 AAAAAAAAC
*
1469889 AAAACAAAC
1 AAAAAAAAC
*
1469898 AAACAAAA-
1 AAAAAAAAC
* **
1469906 AAAAGAAGG
1 AAAAAAAAC
1469915 AAAAAAAAC
1 AAAAAAAAC
*
1469924 AAAAACAAC
1 AAAAAAAAC
1469933 AAAAAAAA
1 AAAAAAAA
1469941 GGGTTCGAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
8 5 0.12
9 35 0.88
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Done.