Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 97 of 182
Found at i:31728027 original size:87 final size:88
Alignment explanation
Indices: 31727909--31728076 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 88
31727899 GTTATTAAAA
* * * * *
31727909 GCCTTTATGGTTGATCTTTGTTATTGGAAGCCTTTGTGGTTGATCTATGTTATTGGAAGCCTTCA
1 GCCTCTATGGCTGATCTTTGTTATTGAAAGCCTTCGTGGTTGATCTATGTTATTGGAAACCTTCA
31727974 TGGCT-ATCTCTATTAAATGAAT
66 TGGCTGATCTCTATTAAATGAAT
* * * *
31727996 GCCTCTATGGCTGGTCTTTGTTATTGAAAGCCTTCGTGGTTGATCTTTGTTATTGGAAATCTTCG
1 GCCTCTATGGCTGATCTTTGTTATTGAAAGCCTTCGTGGTTGATCTATGTTATTGGAAACCTTCA
*
31728061 TGGTTGATCTCTATTA
66 TGGCTGATCTCTATTA
31728077 TAGGACGCCT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
87 60 0.86
88 10 0.14
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (88 bp):
GCCTCTATGGCTGATCTTTGTTATTGAAAGCCTTCGTGGTTGATCTATGTTATTGGAAACCTTCA
TGGCTGATCTCTATTAAATGAAT
Found at i:31728059 original size:29 final size:28
Alignment explanation
Indices: 31727890--31728070 Score: 123
Period size: 29 Copynumber: 6.2 Consensus size: 28
31727880 GCCTTTGTGA
* *
31727890 TTGATCTTTGTTATTAAAAGCCTTTATGG
1 TTGATCTTTGTTATTGAAA-CCTTCATGG
* **
31727919 TTGATCTTTGTTATTGGAAGCCTTTGTGG
1 TTGATCTTTGTTATT-GAAACCTTCATGG
* *
31727948 TTGATCTATGTTATTGGAAGCCTTCATGG
1 TTGATCTTTGTTATT-GAAACCTTCATGG
* * * * *
31727977 CT-ATCTCTATTAAATGAATGCC-TCTATGG
1 TTGATCTTTGTT-ATTGAA-ACCTTC-ATGG
* * *
31728006 CTGGTCTTTGTTATTGAAAGCCTTCGTGG
1 TTGATCTTTGTTATTGAAA-CCTTCATGG
* *
31728035 TTGATCTTTGTTATTGGAAATCTTCGTGG
1 TTGATCTTTGTTATT-GAAACCTTCATGG
31728064 TTGATCT
1 TTGATCT
31728071 CTATTATAGG
Statistics
Matches: 125, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
28 12 0.10
29 99 0.79
30 14 0.11
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.45
Consensus pattern (28 bp):
TTGATCTTTGTTATTGAAACCTTCATGG
Found at i:31728098 original size:116 final size:116
Alignment explanation
Indices: 31727894--31728117 Score: 331
Period size: 116 Copynumber: 1.9 Consensus size: 116
31727884 TTGTGATTGA
* * * *
31727894 TCTTTGTTATTAAAAGCCTTTATGGTTGATCTTTGTTATTGGAAGCCTTTGTGGTTGATCTATGT
1 TCTTTGTTATTAAAAGCCTTCATGGTTGATCTTTGTTATTGGAAACCTTCGTGGTTGATCTATAT
* *
31727959 TATTGGAAGCCTTCATGGCTATCTCTATTAAATGAATGCCTCTATGGCTGG
66 TATAGGAAGCCTTCATAGCTATCTCTATTAAATGAATGCCTCTATGGCTGG
* * * *
31728010 TCTTTGTTATTGAAAGCCTTCGTGGTTGATCTTTGTTATTGGAAATCTTCGTGGTTGATCTCTAT
1 TCTTTGTTATTAAAAGCCTTCATGGTTGATCTTTGTTATTGGAAACCTTCGTGGTTGATCTATAT
* * *
31728075 TATAGGACGCCTTCATAGCTATCTCTGTTAAATGACTGCCTCT
66 TATAGGAAGCCTTCATAGCTATCTCTATTAAATGAATGCCTCT
31728118 GTGGAAAACT
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.43
Consensus pattern (116 bp):
TCTTTGTTATTAAAAGCCTTCATGGTTGATCTTTGTTATTGGAAACCTTCGTGGTTGATCTATAT
TATAGGAAGCCTTCATAGCTATCTCTATTAAATGAATGCCTCTATGGCTGG
Found at i:31728182 original size:22 final size:22
Alignment explanation
Indices: 31728157--31728199 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31728147 TGACGAGATG
*
31728157 TGAAAGCCTTTATGGCGATCTA
1 TGAAAACCTTTATGGCGATCTA
* *
31728179 TGAAAACCTTTGTGGCTATCT
1 TGAAAACCTTTATGGCGATCT
31728200 TTTTTTAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (22 bp):
TGAAAACCTTTATGGCGATCTA
Found at i:31728273 original size:26 final size:26
Alignment explanation
Indices: 31728243--31728301 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
31728233 AAAGGGCACA
* *
31728243 TTCATGGCGTAGTCTGAAGAACTACC
1 TTCATGGCATAGTCTAAAGAACTACC
* *
31728269 TTCATGGCATAGTTTAAAGAATTACC
1 TTCATGGCATAGTCTAAAGAACTACC
31728295 TTCATGG
1 TTCATGG
31728302 AAAATCCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (26 bp):
TTCATGGCATAGTCTAAAGAACTACC
Found at i:31740503 original size:47 final size:47
Alignment explanation
Indices: 31740452--31740604 Score: 150
Period size: 47 Copynumber: 3.3 Consensus size: 47
31740442 GTGGAAGATA
*
31740452 TGACAGTTTATCAGCAAAAGTGGTGGCATGTCCACAATATTATAAAG
1 TGACAGTTTATCAGCAAAAGTGGTGGCATGTCCACAATATTATTAAG
** * * *
31740499 TGACAGTTTATTTGCAAAATTGGTGG-ATTTTCCACAATATT-TCTAGG
1 TGACAGTTTATCAGCAAAAGTGGTGGCA-TGTCCACAATATTAT-TAAG
** * * *
31740546 TGGTAGTATAACATCAAAAGTGGTGGC-TAGTCCACAATATTATTAAG
1 TGACAGTTTATCAGCAAAAGTGGTGGCAT-GTCCACAATATTATTAAG
*
31740593 TGGCAGTTTATC
1 TGACAGTTTATC
31740605 TACATTACTA
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
46 3 0.04
47 78 0.95
48 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (47 bp):
TGACAGTTTATCAGCAAAAGTGGTGGCATGTCCACAATATTATTAAG
Found at i:31744902 original size:52 final size:52
Alignment explanation
Indices: 31744768--31744962 Score: 230
Period size: 52 Copynumber: 3.8 Consensus size: 52
31744758 CCGTAAATGG
* **
31744768 AAGAGATCCGATGACTCTATGTCATCGTGAGTATATGAATCCTTTTTGGATT
1 AAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
31744820 -AGAGGTCCAATGACTCTATGTCATCGTGAGTATATGAATCCCTTACGGATT
1 AAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAATCCTTTACGGATT
** * * * *
31744871 AAGAGGTCCGATGACTCCGTGTTATCATGAGTATATGTATCCTTTGCGGATT
1 AAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAATCCTTTACGGATT
** * * * *
31744923 GTGAGGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 AAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAAT
31744963 GAAGTGAAAT
Statistics
Matches: 120, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
51 46 0.38
52 74 0.62
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (52 bp):
AAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:31752061 original size:52 final size:51
Alignment explanation
Indices: 31751931--31752068 Score: 197
Period size: 51 Copynumber: 2.7 Consensus size: 51
31751921 CGTAAATGGA
* * *
31751931 AGAGGTTCGATGACTTTTTGTCATCGTGAGTATATGAATCCTTTTCGGATT
1 AGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTGCGGATT
* *
31751982 AGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAAT-CTCTTGCGGATT
1 AGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTGCGGATT
*
31752033 ATGAGGTTCGATGGCTATGTGTCATCGTGAGTATAT
1 A-GAGGTTCGATGACTATGTGTCATCGTGAGTATAT
31752069 AAATGAAGTG
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 2 0.03
51 45 0.58
52 31 0.40
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (51 bp):
AGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTGCGGATT
Found at i:31765566 original size:18 final size:18
Alignment explanation
Indices: 31765543--31765579 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31765533 CTTGTCACTT
31765543 TATTACTTGATATGATTG
1 TATTACTTGATATGATTG
31765561 TATTACTTGATATGATTG
1 TATTACTTGATATGATTG
31765579 T
1 T
31765580 GTACACTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (18 bp):
TATTACTTGATATGATTG
Found at i:31771052 original size:34 final size:34
Alignment explanation
Indices: 31770978--31771056 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
31770968 CATGTATCAA
* * *
31770978 AGTTAATTGATTCATGTAACAAAAAGAAAGAGGT
1 AGTTAATTGGTTCATGTAACAAAAAGAAAAAAGT
*
31771012 AATTAATTGGTTCATGTAACCAAAAAGAAAAAAG-
1 AGTTAATTGGTTCATGTAA-CAAAAAGAAAAAAGT
31771046 AGTTAA-TGGTT
1 AGTTAATTGGTT
31771057 TCAAAATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.13
34 22 0.56
35 12 0.31
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (34 bp):
AGTTAATTGGTTCATGTAACAAAAAGAAAAAAGT
Found at i:31779149 original size:14 final size:14
Alignment explanation
Indices: 31779102--31779183 Score: 71
Period size: 14 Copynumber: 5.9 Consensus size: 14
31779092 CCCGAAAAAA
* *
31779102 GTCAACGATCAA-A
1 GTCAACGGTCAACT
*
31779115 GTCAACGGTTAA-T
1 GTCAACGGTCAACT
31779128 GATCAACGGTCAACT
1 G-TCAACGGTCAACT
*
31779143 GTTAACGGTCAA-T
1 GTCAACGGTCAACT
*
31779156 GGTCAATGGTCAACT
1 -GTCAACGGTCAACT
*
31779171 GCCAACGGTCAAC
1 GTCAACGGTCAAC
31779184 AGATTGGGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 12 0.21
14 41 0.73
15 3 0.05
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (14 bp):
GTCAACGGTCAACT
Found at i:31779156 original size:28 final size:28
Alignment explanation
Indices: 31779117--31779182 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
31779107 CGATCAAAGT
* *
31779117 CAACGGTTAATGATCAACGGTCAACTGT
1 CAACGGTCAATGATCAACGGTCAACTGC
* * *
31779145 TAACGGTCAATGGTCAATGGTCAACTGC
1 CAACGGTCAATGATCAACGGTCAACTGC
31779173 CAACGGTCAA
1 CAACGGTCAA
31779183 CAGATTGGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
CAACGGTCAATGATCAACGGTCAACTGC
Found at i:31779183 original size:7 final size:7
Alignment explanation
Indices: 31779102--31779183 Score: 58
Period size: 7 Copynumber: 11.9 Consensus size: 7
31779092 CCCGAAAAAA
31779102 GTCAACG
1 GTCAACG
* *
31779109 ATCAA-A
1 GTCAACG
31779115 GTCAACG
1 GTCAACG
* *
31779122 GTTAATG
1 GTCAACG
*
31779129 ATCAACG
1 GTCAACG
*
31779136 GTCAACT
1 GTCAACG
*
31779143 GTTAACG
1 GTCAACG
*
31779150 GTCAATG
1 GTCAACG
*
31779157 GTCAATG
1 GTCAACG
*
31779164 GTCAACT
1 GTCAACG
*
31779171 GCCAACG
1 GTCAACG
31779178 GTCAAC
1 GTCAAC
31779184 AGATTGGGCT
Statistics
Matches: 54, Mismatches: 20, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
6 4 0.07
7 50 0.93
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (7 bp):
GTCAACG
Found at i:31786240 original size:13 final size:13
Alignment explanation
Indices: 31786222--31786262 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
31786212 TTTCCTAGAA
31786222 AAAGTCAACGATC
1 AAAGTCAACGATC
* *
31786235 AAAGTCAACAATT
1 AAAGTCAACGATC
31786248 AAAGTCAACGATC
1 AAAGTCAACGATC
31786261 AA
1 AA
31786263 CGATTAATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:31786276 original size:21 final size:20
Alignment explanation
Indices: 31786239--31786284 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
31786229 ACGATCAAAG
31786239 TCAACAATTAAAGTCAACGA
1 TCAACAATTAAAGTCAACGA
*
31786259 TCAACGATTAATAGTCAACGA
1 TCAACAATTAA-AGTCAACGA
31786280 TCAAC
1 TCAAC
31786285 TGTCAACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (20 bp):
TCAACAATTAAAGTCAACGA
Found at i:31786278 original size:14 final size:14
Alignment explanation
Indices: 31786259--31786298 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
31786249 AAGTCAACGA
*
31786259 TCAACGATTAA-TAG
1 TCAACGATCAACT-G
31786273 TCAACGATCAACTG
1 TCAACGATCAACTG
31786287 TCAACGATCAAC
1 TCAACGATCAAC
31786299 AGATTAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (14 bp):
TCAACGATCAACTG
Found at i:31788467 original size:27 final size:27
Alignment explanation
Indices: 31788429--31788483 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
31788419 AACGCATTAG
31788429 GAAAGAGTAGCCTTTACGATGAAATAT
1 GAAAGAGTAGCCTTTACGATGAAATAT
* * *
31788456 GAAATAGTAGCCTTTGCGATGAATTAT
1 GAAAGAGTAGCCTTTACGATGAAATAT
31788483 G
1 G
31788484 TAGGAATAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (27 bp):
GAAAGAGTAGCCTTTACGATGAAATAT
Found at i:31788493 original size:27 final size:27
Alignment explanation
Indices: 31788429--31788495 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
31788419 AACGCATTAG
*
31788429 GAAAGAGTAGCCTTTACGATGAAATAT
1 GAAAGAATAGCCTTTACGATGAAATAT
* * * *
31788456 GAAATAGTAGCCTTTGCGATGAATTAT
1 GAAAGAATAGCCTTTACGATGAAATAT
* *
31788483 GTAGGAATAGCCT
1 GAAAGAATAGCCT
31788496 CTATGGCGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (27 bp):
GAAAGAATAGCCTTTACGATGAAATAT
Found at i:31805524 original size:74 final size:75
Alignment explanation
Indices: 31805376--31805525 Score: 230
Period size: 74 Copynumber: 2.0 Consensus size: 75
31805366 ATAGAAATTA
* * **
31805376 ATATTCTTTTGGAAAGAATTTAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATTAGG
1 ATATTCTTTTGGAAAGAATGTAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCCATTAAGAAGG
*
31805441 GAATAATCCT
66 AAATAATCCT
* *
31805451 ATATTCTTTTGGAACGAATGTAATTCCTTTTTCTAA-TTTCCATTTGTCTTCTCCATTAAGAAGG
1 ATATTCTTTTGGAAAGAATGTAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCCATTAAGAAGG
31805515 AAATAATCCT
66 AAATAATCCT
31805525 A
1 A
31805526 CTTTTCCTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 34 0.50
75 34 0.50
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATGTAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCCATTAAGAAGG
AAATAATCCT
Found at i:31818764 original size:57 final size:57
Alignment explanation
Indices: 31818671--31818784 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
31818661 TTCAAGCTCT
*
31818671 TTTGGAAATGTGTATATCTTAACGGCTGTTTACTATGTCTCGAAGTGGATCGAGGCA
1 TTTGGAAATGTGTATATCTTAACAGCTGTTTACTATGTCTCGAAGTGGATCGAGGCA
* *
31818728 TTTGGAAATGTGTATATCTTAACAGTTGTTTCCTATGTCTCGAAGTGGATCGAGGCA
1 TTTGGAAATGTGTATATCTTAACAGCTGTTTACTATGTCTCGAAGTGGATCGAGGCA
31818785 ATTACAGTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (57 bp):
TTTGGAAATGTGTATATCTTAACAGCTGTTTACTATGTCTCGAAGTGGATCGAGGCA
Found at i:31831143 original size:21 final size:21
Alignment explanation
Indices: 31831101--31831144 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31831091 GGTTGGTTCA
* *
31831101 AAGGACAAGAAGAAGTAGCAC
1 AAGGACAAGAAGAAGAAACAC
31831122 AAGGACAAGAA-AAGAAAACAC
1 AAGGACAAGAAGAAG-AAACAC
31831143 AA
1 AA
31831145 AGAGGAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.61, C:0.14, G:0.23, T:0.02
Consensus pattern (21 bp):
AAGGACAAGAAGAAGAAACAC
Found at i:31836140 original size:21 final size:23
Alignment explanation
Indices: 31836114--31836161 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
31836104 ATAGCAAACA
31836114 TTTTTTTC-TTTTCTC-TTTTAT
1 TTTTTTTCTTTTTCTCATTTTAT
*
31836135 TTTTTTTCTTTTTCTCATTTTCT
1 TTTTTTTCTTTTTCTCATTTTAT
31836158 TTTT
1 TTTT
31836162 CTAAGTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTCATTTTAT
Found at i:31846810 original size:18 final size:17
Alignment explanation
Indices: 31846789--31846833 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
31846779 AGAGAAGGGT
31846789 GAAGAAAAAGAAGAAGAA
1 GAAGAAAAAGAAGAAG-A
* *
31846807 GAAGGAAAGGAAGAAGA
1 GAAGAAAAAGAAGAAGA
31846824 GAAGGAAAAA
1 GAA-GAAAAA
31846834 ATTGAACCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAAAAAGAAGAAGA
Found at i:31849380 original size:4 final size:4
Alignment explanation
Indices: 31849371--31849428 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
31849361 AAACCAAATT
* * *
31849371 TAAA TAAA TAAA TAAA TATA TGAA -AAA TAAA -CAA -AAA TAAA TTAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA
31849417 TAAA TAAA TAAA
1 TAAA TAAA TAAA
31849429 AATCGTATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 6 0.13
4 35 0.78
5 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:31892421 original size:9 final size:9
Alignment explanation
Indices: 31892407--31892432 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31892397 CAATATTTGG
31892407 TTTCTTGAT
1 TTTCTTGAT
31892416 TTTCTTGAT
1 TTTCTTGAT
31892425 TTTCTTGA
1 TTTCTTGA
31892433 AAACAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (9 bp):
TTTCTTGAT
Found at i:31900639 original size:20 final size:20
Alignment explanation
Indices: 31900614--31900668 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
31900604 TAATATCGTG
**
31900614 GTATCGATAATTTTATACGA
1 GTATCGATAATTTTATAAAA
*
31900634 GTATCGATATTTTTATAAAA
1 GTATCGATAATTTTATAAAA
31900654 GTATCGATAATTTTA
1 GTATCGATAATTTTA
31900669 AAACAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (20 bp):
GTATCGATAATTTTATAAAA
Found at i:31903993 original size:16 final size:16
Alignment explanation
Indices: 31903972--31904006 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31903962 ATTTTTTTTT
31903972 CACGTGGACACTGCTA
1 CACGTGGACACTGCTA
31903988 CACGTGGACACTGCTA
1 CACGTGGACACTGCTA
31904004 CAC
1 CAC
31904007 ATGCACCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (16 bp):
CACGTGGACACTGCTA
Found at i:31909700 original size:20 final size:20
Alignment explanation
Indices: 31909675--31909720 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31909665 TATTTTTATG
31909675 ATGATTAGAAACATAATTAC
1 ATGATTAGAAACATAATTAC
* ***
31909695 ATGATTTGAGTGATAATTAC
1 ATGATTAGAAACATAATTAC
31909715 ATGATT
1 ATGATT
31909721 TTTTAGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGATTAGAAACATAATTAC
Found at i:31912152 original size:20 final size:20
Alignment explanation
Indices: 31912122--31912180 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
31912112 TTTGTAGTGT
* * *
31912122 TAAAATGATTTTGTCTTGGC
1 TAAAATCATTTTGACTTGAC
* *
31912142 TGAAATCATTTTGACTTGAT
1 TAAAATCATTTTGACTTGAC
*
31912162 TAAAATCATTTTAACTTGA
1 TAAAATCATTTTGACTTGA
31912181 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (20 bp):
TAAAATCATTTTGACTTGAC
Found at i:31912181 original size:20 final size:20
Alignment explanation
Indices: 31912144--31912182 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31912134 GTCTTGGCTG
*
31912144 AAATCATTTTGACTTGATTA
1 AAATCATTTTAACTTGATTA
31912164 AAATCATTTTAACTTGATT
1 AAATCATTTTAACTTGATT
31912183 TTAAAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (20 bp):
AAATCATTTTAACTTGATTA
Found at i:31921766 original size:40 final size:40
Alignment explanation
Indices: 31921711--31921869 Score: 160
Period size: 40 Copynumber: 4.0 Consensus size: 40
31921701 CACTGATCAA
* *
31921711 CATCCAATCTTTTACCCTAAGCAGAGGGTAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
31921751 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
*** * ** * * *
31921791 ATCATTTGATCTCTTACCCCGACCATTA-GGTAAATTGAAG-C
1 --CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGAC
* *
31921832 AATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
31921870 CTACCATCTC
Statistics
Matches: 93, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
38 1 0.01
39 25 0.27
40 38 0.41
41 1 0.01
42 27 0.29
43 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
Found at i:31923836 original size:15 final size:16
Alignment explanation
Indices: 31923812--31923844 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31923802 TATTAATTTA
*
31923812 TTTATTTATTTT-CAT
1 TTTATATATTTTACAT
31923827 TTTATATATTTTACAT
1 TTTATATATTTTACAT
31923843 TT
1 TT
31923845 GATTCTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATATATTTTACAT
Found at i:31923900 original size:20 final size:21
Alignment explanation
Indices: 31923877--31923916 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31923867 TGTTATGTGA
*
31923877 TTTATCCAT-TTGTTTATTAT
1 TTTAGCCATATTGTTTATTAT
*
31923897 TTTAGCCATATTTTTTATTA
1 TTTAGCCATATTGTTTATTA
31923917 AATGCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAGCCATATTGTTTATTAT
Found at i:31931223 original size:20 final size:20
Alignment explanation
Indices: 31931198--31931235 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31931188 CAACATAGTT
*
31931198 TGCAAAAATCACACACGATC
1 TGCAAAAAACACACACGATC
31931218 TGCAAAAAACACACACGA
1 TGCAAAAAACACACACGA
31931236 CTGTGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.11, T:0.11
Consensus pattern (20 bp):
TGCAAAAAACACACACGATC
Found at i:31935683 original size:71 final size:71
Alignment explanation
Indices: 31935567--31935841 Score: 381
Period size: 71 Copynumber: 3.9 Consensus size: 71
31935557 TTTCACATAT
* * * *
31935567 AGTGACTCACGATGCTGTAGAGAATCCGTAACAAATGTAGGATCTCAGCCATCGGACCAATTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATCGGACCAATTTCA
*
31935632 CTTTGC
66 CTTTAC
* * * * *
31935638 AGTGACTCACGATACTGTAAAGAATCAGCAACAAATGCAAGATCTCAATCATCGAACCAATTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATCGGACCAATTTCA
31935703 CTTTAC
66 CTTTAC
* * *
31935709 AGTGACTCATGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATTGGACCAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATCGGACCAATTTCA
31935774 CTTTAC
66 CTTTAC
* * * * *
31935780 AATGACTCACGATGCTATAGAGAATCCGCAACAAATGCAGGATCTCAGGCATCAGA-CAATTT
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATCGGACCAATTT
31935842 TCTATCTTTG
Statistics
Matches: 178, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
70 5 0.03
71 173 0.97
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (71 bp):
AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGTCATCGGACCAATTTCA
CTTTAC
Found at i:31944120 original size:92 final size:92
Alignment explanation
Indices: 31944024--31944200 Score: 236
Period size: 92 Copynumber: 1.9 Consensus size: 92
31944014 GTAAAAAGTT
* *
31944024 CTCAAATTTTTTCAAAACAAAAAAATTAAGTCCC-T-CCTATTTT-CTCACTCAATT-GAGCACT
1 CTCAAACTTCTTCAAAA-AAAAAAATTAAG-CCCTTGCCTATTTTCCTCACTCAATTAG-GCACT
31944085 TGAACTTTCAAAATGCATAAAAAAAAAAGCC
63 TGAACTTTCAAAAT-CATAAAAAAAAAAGCC
** *
31944116 CTCAAACTTCTTCAAAAAAAGCAATTAAGCCCTTGCCTATTTTCCTCACTCAATTAGGTACTTGA
1 CTCAAACTTCTTCAAAAAAAAAAATTAAGCCCTTGCCTATTTTCCTCACTCAATTAGGCACTTGA
*
31944181 ACTTTCAAAATCATCAAAAA
66 ACTTTCAAAATCATAAAAAA
31944201 GACCCTCAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
90 3 0.04
91 11 0.15
92 31 0.41
93 29 0.39
94 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (92 bp):
CTCAAACTTCTTCAAAAAAAAAAATTAAGCCCTTGCCTATTTTCCTCACTCAATTAGGCACTTGA
ACTTTCAAAATCATAAAAAAAAAAGCC
Found at i:31944191 original size:93 final size:87
Alignment explanation
Indices: 31944032--31944239 Score: 233
Period size: 93 Copynumber: 2.3 Consensus size: 87
31944022 TTCTCAAATT
**
31944032 TTTTCAAAACAAAAAAATTAAGTCCC-T-CCTATTTTCTCACTCAATTGAGCACTTGAACTTTCA
1 TTTTCAAAA-AAAGCAATTAAG-CCCTTGCCTATTTTCTCACTCAATTGAGCACTTGAACTTTCA
*
31944095 AAATGCATAAAAAAAAAAGCCCTCAAAC
64 AAAT-CAT--AAAAAAAA-CCCTCAAAA
*
31944123 TTCTTCAAAAAAAGCAATTAAGCCCTTGCCTATTTTCCTCACTCAATT-AGGTACTTGAACTTTC
1 TT-TTCAAAAAAAGCAATTAAGCCCTTGCCTATTTT-CTCACTCAATTGA-GCACTTGAACTTTC
* *
31944187 AAAATCATCAAAAAGACCCTCAAAA
63 AAAATCATAAAAAAAACCCTCAAAA
** *
31944212 TTTTTTAAAAAAGCAATTAAGCCGTTGC
1 TTTTCAAAAAAAGCAATTAAGCCCTTGC
31944240 TCTTATTAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 13
0.82 0.07 0.10
Matches are distributed among these distances:
88 23 0.22
89 10 0.10
90 9 0.09
91 13 0.13
92 19 0.18
93 29 0.28
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (87 bp):
TTTTCAAAAAAAGCAATTAAGCCCTTGCCTATTTTCTCACTCAATTGAGCACTTGAACTTTCAAA
ATCATAAAAAAAACCCTCAAAA
Found at i:31944618 original size:10 final size:10
Alignment explanation
Indices: 31944605--31944667 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
31944595 CTTTTATAAA
31944605 TTTTTACAA-
1 TTTTTACAAT
31944614 TTTTTACAAT
1 TTTTTACAAT
*
31944624 TTTTTACGA-
1 TTTTTACAAT
*
31944633 TTTTTA-TAT
1 TTTTTACAAT
31944642 TTTTT-CTAAT
1 TTTTTAC-AAT
* *
31944652 TTTTAATAAT
1 TTTTTACAAT
31944662 TTTTTA
1 TTTTTA
31944668 TTACCATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.02
9 20 0.47
10 22 0.51
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTTACAAT
Found at i:31944626 original size:8 final size:9
Alignment explanation
Indices: 31944603--31944656 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
31944593 AACTTTTATA
31944603 AATTTTTAC
1 AATTTTTAC
31944612 AATTTTTAC
1 AATTTTTAC
31944621 AATTTTTTAC
1 AA-TTTTTAC
*
31944631 GATTTTTA-
1 AATTTTTAC
* *
31944639 TATTTTTTC
1 AATTTTTAC
31944648 TAATTTTTA
1 -AATTTTTA
31944657 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
8 6 0.16
9 17 0.46
10 14 0.38
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (9 bp):
AATTTTTAC
Found at i:31944627 original size:19 final size:18
Alignment explanation
Indices: 31944596--31944667 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 18
31944586 GTACTATAAC
31944596 TTTTATAAA-TTTTTACAA
1 TTTT-TAAATTTTTTACAA
*
31944614 TTTTTACAATTTTTTACGA
1 TTTTTA-AATTTTTTACAA
*
31944633 TTTTTATATTTTTT-CTAA
1 TTTTTAAATTTTTTAC-AA
31944651 TTTTTAATAATTTTTTA
1 TTTTT-A-AATTTTTTA
31944668 TTACCATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.07
18 19 0.43
19 15 0.34
20 7 0.16
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTTAAATTTTTTACAA
Found at i:31944826 original size:90 final size:88
Alignment explanation
Indices: 31944745--31944917 Score: 211
Period size: 89 Copynumber: 2.0 Consensus size: 88
31944735 CTTAATTATT
** * ** * *
31944745 TTTTTTTGAAAAAATTTGAGGATTTTTTTTATGCATTTTAAAAGTTCAAGTACCCAATTAAGTGT
1 TTTTTTTGAAAAAATTTGAGGACCTTTTTGATAAATTTTAAAAGTTCAAGTACCCAAATAAGTAT
*
31944810 AAAAAAAAGTAGGGGCTTAATTGC
66 -AAAAAAAGGAGGGGCTTAATTGC
** * * * *
31944834 TTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATAAATTTTGAAAGTTTAAGTACCCAAATGAGTAT
1 TTTTTTTGAAAAAATTTGAGGACCTTTTTGATAAATTTTAAAAGTTCAAGTACCCAAATAAGTAT
31944899 AAAAAAAGGAGGGGCTTAA
66 AAAAAAAGGAGGGGCTTAA
31944918 ATGCACTTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
88 18 0.26
89 52 0.74
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (88 bp):
TTTTTTTGAAAAAATTTGAGGACCTTTTTGATAAATTTTAAAAGTTCAAGTACCCAAATAAGTAT
AAAAAAAGGAGGGGCTTAATTGC
Found at i:31944862 original size:89 final size:86
Alignment explanation
Indices: 31944779--31944948 Score: 216
Period size: 89 Copynumber: 1.9 Consensus size: 86
31944769 TTTTTTATGC
* * * *
31944779 ATTTTAAAAGTTCAAGTACCCAATTAAGTGTAAAAAAAAGTAGGGGCTTAATTGCTTTTTTTGAA
1 ATTTTAAAAGTTCAAGTACCCAAATAAGTAT-AAAAAAAGGAGGGGCTTAAATGCTTTTTTTGAA
31944844 AAGGTTTGAGGGCCTTTTTGATAA
65 AA-GTTTGAGGG-CTTTTTGATAA
* * * **
31944868 ATTTTGAAAGTTTAAGTACCCAAATGAGTATAAAAAAAGGAGGGGCTTAAATGC-ACTTTTGAGA
1 ATTTTAAAAGTTCAAGTACCCAAATAAGTATAAAAAAAGGAGGGGCTTAAATGCTTTTTTTGA-A
31944932 AAGTTTGAGGGCTTTTT
65 AAGTTTGAGGGCTTTTT
31944949 ACACACTTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
86 6 0.08
87 15 0.21
88 24 0.34
89 26 0.37
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (86 bp):
ATTTTAAAAGTTCAAGTACCCAAATAAGTATAAAAAAAGGAGGGGCTTAAATGCTTTTTTTGAAA
AGTTTGAGGGCTTTTTGATAA
Found at i:31958809 original size:6 final size:6
Alignment explanation
Indices: 31958798--31958837 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
31958788 TAGTTTGTGA
31958798 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTT
31958838 ATAATAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (6 bp):
TTTTGG
Found at i:31960698 original size:21 final size:21
Alignment explanation
Indices: 31960674--31960715 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31960664 TAGTTTCGTA
*
31960674 TTAAAATTTGGTTAGGTAATT
1 TTAAAATTTGGATAGGTAATT
* *
31960695 TTAACATTTGGATAGTTAATT
1 TTAAAATTTGGATAGGTAATT
31960716 AAGAAAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (21 bp):
TTAAAATTTGGATAGGTAATT
Found at i:31961504 original size:18 final size:18
Alignment explanation
Indices: 31961481--31961516 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31961471 ACTCTGTTTT
31961481 TGGCTCGAAAGAGCGATA
1 TGGCTCGAAAGAGCGATA
31961499 TGGCTCGAAAGAGCGATA
1 TGGCTCGAAAGAGCGATA
31961517 CTCTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (18 bp):
TGGCTCGAAAGAGCGATA
Found at i:31961539 original size:27 final size:27
Alignment explanation
Indices: 31961499--31961574 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
31961489 AAGAGCGATA
*
31961499 TGGCTCGAAAGAGCGATACTCTATTTC
1 TGGCTCGAATGAGCGATACTCTATTTC
*
31961526 TGGCTCGAATGAGCGATACTCTATTTT
1 TGGCTCGAATGAGCGATACTCTATTTC
* *
31961553 TGG-TCCGAATGACCAATACTCT
1 TGGCT-CGAATGAGCGATACTCT
31961575 GTACATGGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (27 bp):
TGGCTCGAATGAGCGATACTCTATTTC
Found at i:31961583 original size:27 final size:27
Alignment explanation
Indices: 31961553--31961618 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
31961543 ACTCTATTTT
*
31961553 TGGTCCGAATGA-CCAATACTCTGTACA
1 TGGTCCGAATGAGCC-ACACTCTGTACA
* * *
31961580 TGGTTCAAATGAGCCACACTCTGTACT
1 TGGTCCGAATGAGCCACACTCTGTACA
31961607 TGG-CTCGAATGA
1 TGGTC-CGAATGA
31961619 ATAATATTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (27 bp):
TGGTCCGAATGAGCCACACTCTGTACA
Found at i:31965140 original size:28 final size:28
Alignment explanation
Indices: 31965101--31965181 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 28
31965091 CACAATCTAC
*
31965101 AAAATCCTACACAGCCTATCAGTCTGCA
1 AAAATCCCACACAGCCTATCAGTCTGCA
* *
31965129 AAAATCCCACACAGCCTACCACAAATTCTGCA
1 AAAATCCCACACAGCCTA--TC--AGTCTGCA
*
31965161 AAAATCCCACACGGCCTATCA
1 AAAATCCCACACAGCCTATCA
31965182 CACAATTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 18 0.41
30 2 0.05
32 24 0.55
ACGTcount: A:0.38, C:0.36, G:0.09, T:0.17
Consensus pattern (28 bp):
AAAATCCCACACAGCCTATCAGTCTGCA
Found at i:31965164 original size:32 final size:30
Alignment explanation
Indices: 31965125--31965299 Score: 181
Period size: 32 Copynumber: 5.6 Consensus size: 30
31965115 CCTATCAGTC
31965125 TGCAAAAATCCCACACAGCCTACCACAAATT
1 TGCAAAAATCCCACAC-GCCTACCACAAATT
*
31965156 CTGCAAAAATCCCACACGGCCTATCACACAATT
1 -TGCAAAAATCCCACAC-GCCTACCACA-AATT
* * * * *
31965189 TGTAAAAATCCCACACGACTTATCACATAGTC
1 TGCAAAAATCCCACACG-CCTACCACA-AATT
*
31965221 TGTAAAAATCCCACACAGCCTACCACACAATT
1 TGCAAAAATCCCACAC-GCCTACCACA-AATT
*
31965253 TGCAAAAATCACACACGACCTACCAC-AATT
1 TGCAAAAATCCCACACG-CCTACCACAAATT
*
31965283 TGCAAAAATTCCACACG
1 TGCAAAAATCCCACACG
31965300 ATCGGATGTC
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
30 19 0.15
31 2 0.02
32 97 0.79
33 5 0.04
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.19
Consensus pattern (30 bp):
TGCAAAAATCCCACACGCCTACCACAAATT
Found at i:31965228 original size:64 final size:64
Alignment explanation
Indices: 31965125--31965298 Score: 219
Period size: 64 Copynumber: 2.8 Consensus size: 64
31965115 CCTATCAGTC
* * *
31965125 TGCAAAAATCCCACAC-AGCCTACCACAAATTCTGCAAAAATCCCACACGGCCTATCACACAATT
1 TGCAAAAATCCCACACGA-CCTACCACAAAGTCTGCAAAAATCCCACACAGCCTACCACACAATT
* * * * *
31965189 TGTAAAAATCCCACACGACTTATCACATAGTCTGTAAAAATCCCACACAGCCTACCACACAATT
1 TGCAAAAATCCCACACGACCTACCACAAAGTCTGCAAAAATCCCACACAGCCTACCACACAATT
* * *
31965253 TGCAAAAATCACACACGACCTACCAC-AA-TTTGCAAAAATTCCACAC
1 TGCAAAAATCCCACACGACCTACCACAAAGTCTGCAAAAATCCCACAC
31965299 GATCGGATGT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 15 0.16
63 1 0.01
64 76 0.82
65 1 0.01
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.19
Consensus pattern (64 bp):
TGCAAAAATCCCACACGACCTACCACAAAGTCTGCAAAAATCCCACACAGCCTACCACACAATT
Found at i:31965243 original size:96 final size:94
Alignment explanation
Indices: 31965121--31965300 Score: 281
Period size: 96 Copynumber: 1.9 Consensus size: 94
31965111 ACAGCCTATC
* *
31965121 AGTCTGCAAAAATCCCACACAGCCTACCACA-AATTCTGCAAAAATCCCACACGGCCTATCACAC
1 AGTCTGCAAAAATCCCACACAGCCTACCACACAATT-TGCAAAAATCACACACGACCTA-C-CAC
*
31965185 AATTTGTAAAAATCCCACACGACTTATCACAT
63 AATTTGCAAAAATCCCACACGACTTATCACAT
*
31965217 AGTCTGTAAAAATCCCACACAGCCTACCACACAATTTGCAAAAATCACACACGACCTACCACAAT
1 AGTCTGCAAAAATCCCACACAGCCTACCACACAATTTGCAAAAATCACACACGACCTACCACAAT
*
31965282 TTGCAAAAATTCCACACGA
66 TTGCAAAAATCCCACACGA
31965301 TCGGATGTCT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
94 23 0.29
95 1 0.01
96 50 0.64
97 4 0.05
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.19
Consensus pattern (94 bp):
AGTCTGCAAAAATCCCACACAGCCTACCACACAATTTGCAAAAATCACACACGACCTACCACAAT
TTGCAAAAATCCCACACGACTTATCACAT
Found at i:31966266 original size:18 final size:18
Alignment explanation
Indices: 31966245--31966286 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
31966235 TTTGCACTTC
31966245 TGGTCTTTTTG-TTTCTGT
1 TGGT-TTTTTGCTTTCTGT
*
31966263 TGGTTTTTTGCTTTCTTT
1 TGGTTTTTTGCTTTCTGT
31966281 TGGTTT
1 TGGTTT
31966287 GCTGTGGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.00, C:0.10, G:0.21, T:0.69
Consensus pattern (18 bp):
TGGTTTTTTGCTTTCTGT
Found at i:31985702 original size:15 final size:15
Alignment explanation
Indices: 31985682--31985763 Score: 101
Period size: 15 Copynumber: 5.5 Consensus size: 15
31985672 CTTAAGAACA
* *
31985682 AAATCGTGAAATCTC
1 AAATCATGAAATCCC
*
31985697 AAATCGTGAAATCCC
1 AAATCATGAAATCCC
*
31985712 TAATCATGAAATCCC
1 AAATCATGAAATCCC
31985727 AAATCATGAAATCCC
1 AAATCATGAAATCCC
* *
31985742 TAATCATGAAATTCC
1 AAATCATGAAATCCC
*
31985757 TAATCAT
1 AAATCAT
31985764 TCTAATTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (15 bp):
AAATCATGAAATCCC
Found at i:31985724 original size:30 final size:30
Alignment explanation
Indices: 31985683--31985763 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
31985673 TTAAGAACAA
* * *
31985683 AATCGTGAAATCTCAAATCGTGAAATCCCT
1 AATCATGAAATCCCAAATCATGAAATCCCT
31985713 AATCATGAAATCCCAAATCATGAAATCCCT
1 AATCATGAAATCCCAAATCATGAAATCCCT
* *
31985743 AATCATGAAATTCCTAATCAT
1 AATCATGAAATCCCAAATCAT
31985764 TCTAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (30 bp):
AATCATGAAATCCCAAATCATGAAATCCCT
Found at i:31989597 original size:51 final size:51
Alignment explanation
Indices: 31989516--31989648 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 51
31989506 ATTTTCATTA
* ** **
31989516 GCAAAATCAGCAGCATATTGATCAGCAACATTATCCACTCCATCTGATGTT
1 GCAAAATCAGCAACATATCCATCAATAACATTATCCACTCCATCTGATGTT
* * **
31989567 GCAAAATTAGCATCATATCCATCAATAACATTATCTTCTCCATCTGATGTT
1 GCAAAATCAGCAACATATCCATCAATAACATTATCCACTCCATCTGATGTT
* *
31989618 GCAAAATCAGCAACATATTCATCAGTAACAT
1 GCAAAATCAGCAACATATCCATCAATAACAT
31989649 CTTCACTATA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (51 bp):
GCAAAATCAGCAACATATCCATCAATAACATTATCCACTCCATCTGATGTT
Found at i:31989722 original size:33 final size:33
Alignment explanation
Indices: 31989680--31989837 Score: 126
Period size: 33 Copynumber: 4.8 Consensus size: 33
31989670 TAACAATAGA
*
31989680 CCCTCCTACATCACCCTCCACATCAGATTTTAC
1 CCCTCCTACATCACCCTCCACATCAGATTCTAC
* * * *
31989713 CCCTCCTACATCACCTTCCTCAACAGCTTCTAC
1 CCCTCCTACATCACCCTCCACATCAGATTCTAC
* * *
31989746 CCTTTCC-AGATCA-CCTTCACCATCAGATTCTAC
1 CC-CTCCTACATCACCCTCCA-CATCAGATTCTAC
* * * * *
31989779 CCCTTC-ATCATCTCCCTCCCCATCA-ACTCCTGC
1 CCCTCCTA-CATCACCCTCCACATCAGA-TTCTAC
31989812 CCCTCCTACATCACCCTCCTACATCA
1 CCCTCCTACATCACCCTCC-ACATCA
31989838 CCCTCCCCAT
Statistics
Matches: 95, Mismatches: 23, Indels: 13
0.73 0.18 0.10
Matches are distributed among these distances:
32 7 0.07
33 75 0.79
34 13 0.14
ACGTcount: A:0.22, C:0.48, G:0.03, T:0.27
Consensus pattern (33 bp):
CCCTCCTACATCACCCTCCACATCAGATTCTAC
Found at i:31989830 original size:13 final size:13
Alignment explanation
Indices: 31989812--31989843 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
31989802 CAACTCCTGC
31989812 CCCTCCTACATCA
1 CCCTCCTACATCA
31989825 CCCTCCTACATCA
1 CCCTCCTACATCA
31989838 CCCTCC
1 CCCTCC
31989844 CCATCAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCTCCTACATCA
Found at i:31989870 original size:33 final size:35
Alignment explanation
Indices: 31989833--31989913 Score: 121
Period size: 33 Copynumber: 2.3 Consensus size: 35
31989823 CACCCTCCTA
31989833 CATCACCCTCCCCATCAACTTCTA-CC-CCTTCAT
1 CATCACCCTCCCCATCAACTTCTACCCACCTTCAT
* *
31989866 CATCACCTTCCCCATCAACTTTTACCCATCCTTCAT
1 CATCACCCTCCCCATCAACTTCTACCCA-CCTTCAT
31989902 CATCACCCTCCC
1 CATCACCCTCCC
31989914 TAGAAGTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 22 0.52
34 2 0.05
36 18 0.43
ACGTcount: A:0.21, C:0.51, G:0.00, T:0.28
Consensus pattern (35 bp):
CATCACCCTCCCCATCAACTTCTACCCACCTTCAT
Found at i:31989903 original size:79 final size:79
Alignment explanation
Indices: 31989755--31989912 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 79
31989745 CCCTTTCCAG
* * * *
31989755 ATCACCTTCACCATCAGATTCTACCCCTTCATCATCTCCCTCCCCATCAACTCCTGCCCCTCCTA
1 ATCACCCTCACCATCAGATTCTACCCCTTCATCATCACCCTCCCCATCAACTCCTACCCATCCTA
31989820 CATCACCCTCCTAC
66 CATCACCCTCCTAC
* * **
31989834 ATCACCCTCCCCATCA-ACTTCTACCCCTTCATCATCACCTTCCCCATCAACTTTTACCCATCCT
1 ATCACCCTCACCATCAGA-TTCTACCCCTTCATCATCACCCTCCCCATCAACTCCTACCCATCC-
31989898 TCATCATCACCCTCC
64 T-A-CATCACCCTCC
31989913 CTAGAAGTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 53 0.79
80 1 0.01
81 1 0.01
82 11 0.16
ACGTcount: A:0.21, C:0.50, G:0.01, T:0.28
Consensus pattern (79 bp):
ATCACCCTCACCATCAGATTCTACCCCTTCATCATCACCCTCCCCATCAACTCCTACCCATCCTA
CATCACCCTCCTAC
Found at i:31990822 original size:17 final size:16
Alignment explanation
Indices: 31990793--31990852 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
31990783 TGTTGAAGCT
*
31990793 TTTTAGGGA-TTTAATG
1 TTTT-GGGATTTTAATA
31990809 TTTTGAGGATTTTAATA
1 TTTTG-GGATTTTAATA
*
31990826 TTTAGGGATTTTAATA
1 TTTTGGGATTTTAATA
31990842 TTTTAGGGATT
1 TTTT-GGGATT
31990853 CAAATAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 1 0.03
16 21 0.55
17 16 0.42
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.52
Consensus pattern (16 bp):
TTTTGGGATTTTAATA
Found at i:31990834 original size:16 final size:16
Alignment explanation
Indices: 31990794--31990852 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
31990784 GTTGAAGCTT
*
31990794 TTTAGGGA-TTTAATG
1 TTTAGGGATTTTAATA
*
31990809 TTTTGAGGATTTTAATA
1 TTTAG-GGATTTTAATA
31990826 TTTAGGGATTTTAATA
1 TTTAGGGATTTTAATA
31990842 TTTTAGGGATT
1 -TTTAGGGATT
31990853 CAAATAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 4 0.11
16 14 0.37
17 20 0.53
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (16 bp):
TTTAGGGATTTTAATA
Found at i:31995702 original size:46 final size:46
Alignment explanation
Indices: 31995630--31995731 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
31995620 TATTACAAAT
* * **
31995630 TAGTAGTACACCACATGATAAATACAATATTTTCCAAGTGCATAAC
1 TAGTATTACACCACATGATAAATACAACATCGTCCAAGTGCATAAC
* *
31995676 TAGTATTACACTACATGATAACTACAACATCGTCCAAGTGCATAAC
1 TAGTATTACACCACATGATAAATACAACATCGTCCAAGTGCATAAC
*
31995722 TAATATTACA
1 TAGTATTACA
31995732 AATTAGTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (46 bp):
TAGTATTACACCACATGATAAATACAACATCGTCCAAGTGCATAAC
Found at i:32004175 original size:2 final size:2
Alignment explanation
Indices: 32004168--32004195 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32004158 TTTACCATTA
32004168 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
32004196 GAGAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32005299 original size:25 final size:25
Alignment explanation
Indices: 32005262--32005327 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
32005252 ATACTAGTTA
32005262 AACTCTATCTGGGCTCGAAAGAGCT
1 AACTCTATCTGGGCTCGAAAGAGCT
* * *
32005287 AACTCTGTTTGGGCTCGTAAGAGCT
1 AACTCTATCTGGGCTCGAAAGAGCT
*
32005312 AAC-CTTATCTAGGCTC
1 AACTC-TATCTGGGCTC
32005328 ATATGAGCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (25 bp):
AACTCTATCTGGGCTCGAAAGAGCT
Found at i:32012770 original size:18 final size:18
Alignment explanation
Indices: 32012747--32012791 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
32012737 ACCAGATAAT
**
32012747 ATGCGATCACATGACCAG
1 ATGCGATCACAAAACCAG
*
32012765 ATGCGATCACAAAATCAG
1 ATGCGATCACAAAACCAG
32012783 ATGCGATCA
1 ATGCGATCA
32012792 TATAACAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (18 bp):
ATGCGATCACAAAACCAG
Found at i:32025648 original size:16 final size:17
Alignment explanation
Indices: 32025624--32025669 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
32025614 TGGCAATATA
32025624 TTTTT-TTCTTTTTTTC
1 TTTTTCTTCTTTTTTTC
*
32025640 -TTTTCTTC-TTCTTTC
1 TTTTTCTTCTTTTTTTC
32025655 TTTTTCTATCTTTTT
1 TTTTTCT-TCTTTTT
32025670 GTGAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 2 0.08
18 3 0.12
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTTC
Found at i:32026295 original size:18 final size:17
Alignment explanation
Indices: 32026265--32026303 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
32026255 AAATGTACTA
*
32026265 ACAAATGAAATGCAGTG
1 ACAAATGAAATGCAATG
32026282 ACAAATGAAAATGCAATG
1 ACAAATG-AAATGCAATG
32026300 ACAA
1 ACAA
32026304 CTAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.54, C:0.13, G:0.18, T:0.15
Consensus pattern (17 bp):
ACAAATGAAATGCAATG
Found at i:32027365 original size:17 final size:19
Alignment explanation
Indices: 32027330--32027367 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
32027320 AGTGTCTGAT
*
32027330 TTCTCCTTTTTCTTCCTTC
1 TTCTCCTTTTCCTTCCTTC
32027349 TTCT-CTTTTCCTT-CTTC
1 TTCTCCTTTTCCTTCCTTC
32027366 TT
1 TT
32027368 GGGTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
TTCTCCTTTTCCTTCCTTC
Found at i:32027621 original size:115 final size:115
Alignment explanation
Indices: 32027419--32027638 Score: 413
Period size: 115 Copynumber: 1.9 Consensus size: 115
32027409 TTCTTTCTAT
*
32027419 TGAGATATCATTAATGGGGCCCTTATTATCTAACACTTCCTCACCATCACGAGGAACAATCCTAT
1 TGAGATATCATTAATAGGGCCCTTATTATCTAACACTTCCTCACCATCACGAGGAACAATCCTAT
32027484 TTTGTTTACAAAGTCACATTACTAAAGAAGGAAAGGGTAACACTTCCTAC
66 TTTGTTTACAAAGTCACATTACTAAAGAAGGAAAGGGTAACACTTCCTAC
* *
32027534 TGAGATATCATTAATAGGGCCCTTGTTGTCTAACACTTCCTCACCATCACGAGGAACAATCCTAT
1 TGAGATATCATTAATAGGGCCCTTATTATCTAACACTTCCTCACCATCACGAGGAACAATCCTAT
32027599 TTTGTTTACAAAGTCACATTACTAAAGAAGGAAAGGGTAA
66 TTTGTTTACAAAGTCACATTACTAAAGAAGGAAAGGGTAA
32027639 TATACATGTT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 102 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (115 bp):
TGAGATATCATTAATAGGGCCCTTATTATCTAACACTTCCTCACCATCACGAGGAACAATCCTAT
TTTGTTTACAAAGTCACATTACTAAAGAAGGAAAGGGTAACACTTCCTAC
Found at i:32041203 original size:358 final size:358
Alignment explanation
Indices: 32040545--32041260 Score: 1306
Period size: 358 Copynumber: 2.0 Consensus size: 358
32040535 CACCGAAAGG
32040545 TAAGATTTCTATGAGATGCTGCAAAGTACTATTAGAAAGAATCATACCTGTTCAAAGTATAAACT
1 TAAGATTTCTATGAGATGCTGCAAAGTACTATTAGAAAGAATCATACCTGTTCAAAGTATAAACT
32040610 GACAATATTATTCGTCACTGTGTTCTTGAAGAAGAAATGCTTTCTATCTTAAAGCATTGTCATGA
66 GACAATATTATTCGTCACTGTGTTCTTGAAGAAGAAATGCTTTCTATCTTAAAGCATTGTCATGA
32040675 TGCCCCTTATGGAGGTCATTTTGGAGGTGTTAGGACTGCTGCAAAGGTCCTTCAATCGAGAGTTT
131 TGCCCCTTATGGAGGTCATTTTGGAGGTGTTAGGACTGCTGCAAAGGTCCTTCAATCGAGAGTTT
* *
32040740 ATTGGTCATCATTGTTTCGAAACTCTCACAATTTCGTTCAACAATGCGATAAATGTCAGCGCACT
196 ATTGGCCATCATTATTTCGAAACTCTCACAATTTCGTTCAACAATGCGATAAATGTCAGCGCACT
32040805 AGATCTATATCTCGACGCAACGAGATGCTGCAACAGCATATAATGGAAGTTGAACTTTTCTACGT
261 AGATCTATATCTCGACGCAACGAGATGCTGCAACAGCATATAATGGAAGTTGAACTTTTCTACGT
*
32040870 CTAGGGTATGGATTTCATGAGACCGTTTCCCAA
326 CTAGGGTATGGATTTCATGAGACCATTTCCCAA
** *
32040903 TAAGATTTCTATGAGATGCTGCAAAGTACTATTAGAAAGAATCATACCTGTTCAAAGTATGCATT
1 TAAGATTTCTATGAGATGCTGCAAAGTACTATTAGAAAGAATCATACCTGTTCAAAGTATAAACT
32040968 GACAATATTATTCGTCACTGTGTTCTTGAAGAAGAAATGCTTTCTATCTTAAAGCATTGTCATGA
66 GACAATATTATTCGTCACTGTGTTCTTGAAGAAGAAATGCTTTCTATCTTAAAGCATTGTCATGA
* *
32041033 TGCCCCTTATGGAGGTCATTTTGGTGGTGTTAGGACTGCTGCAAAGGTCCTTCAATCGAGATTTT
131 TGCCCCTTATGGAGGTCATTTTGGAGGTGTTAGGACTGCTGCAAAGGTCCTTCAATCGAGAGTTT
*
32041098 ATTGGCCATCATTATTTCGAAACTCTCACAATTTCGTTCAACAATGCGATAAATGTCAGTGCACT
196 ATTGGCCATCATTATTTCGAAACTCTCACAATTTCGTTCAACAATGCGATAAATGTCAGCGCACT
* * * *
32041163 AGATCTATATCTTGACGCAACGAGATGCTGCAATAGCATATTATGGAAGTTGAGCTTTTCTACGT
261 AGATCTATATCTCGACGCAACGAGATGCTGCAACAGCATATAATGGAAGTTGAACTTTTCTACGT
*
32041228 CTGGGGTATGGATTTCATGAGACCATTTCCCAA
326 CTAGGGTATGGATTTCATGAGACCATTTCCCAA
32041261 CTCTTGGAAA
Statistics
Matches: 344, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
358 344 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (358 bp):
TAAGATTTCTATGAGATGCTGCAAAGTACTATTAGAAAGAATCATACCTGTTCAAAGTATAAACT
GACAATATTATTCGTCACTGTGTTCTTGAAGAAGAAATGCTTTCTATCTTAAAGCATTGTCATGA
TGCCCCTTATGGAGGTCATTTTGGAGGTGTTAGGACTGCTGCAAAGGTCCTTCAATCGAGAGTTT
ATTGGCCATCATTATTTCGAAACTCTCACAATTTCGTTCAACAATGCGATAAATGTCAGCGCACT
AGATCTATATCTCGACGCAACGAGATGCTGCAACAGCATATAATGGAAGTTGAACTTTTCTACGT
CTAGGGTATGGATTTCATGAGACCATTTCCCAA
Found at i:32046018 original size:18 final size:17
Alignment explanation
Indices: 32045981--32046022 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
32045971 TCCCTTAGTC
32045981 AAAA-AAAAAGAGAAAG
1 AAAAGAAAAAGAGAAAG
*
32045997 -AAAGAAAAAGGGAAAAG
1 AAAAGAAAAAGAG-AAAG
32046014 AAAAGAAAA
1 AAAAGAAAA
32046023 GAAAAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 7 0.32
17 4 0.18
18 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAGAAAG
Found at i:32055281 original size:16 final size:18
Alignment explanation
Indices: 32055241--32055278 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
32055231 CACGTCAGCA
*
32055241 AAAAAATAATTATTTTTT
1 AAAATATAATTATTTTTT
32055259 AAAATATAATT-TTTTTT
1 AAAATATAATTATTTTTT
32055276 AAA
1 AAA
32055279 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATATAATTATTTTTT
Found at i:32055362 original size:14 final size:14
Alignment explanation
Indices: 32055343--32055380 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
32055333 TCTGTTCTCC
32055343 TTCCTCTTCTTATT
1 TTCCTCTTCTTATT
32055357 TTCCTCTTCTTATT
1 TTCCTCTTCTTATT
*
32055371 TGCCTCTTCT
1 TTCCTCTTCT
32055381 AGATAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.32, G:0.03, T:0.61
Consensus pattern (14 bp):
TTCCTCTTCTTATT
Found at i:32056161 original size:12 final size:11
Alignment explanation
Indices: 32056140--32056165 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32056130 TTATATTTAA
32056140 AAAATATTTTT
1 AAAATATTTTT
32056151 AAAATATTTTT
1 AAAATATTTTT
32056162 AAAA
1 AAAA
32056166 AAATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:32056176 original size:17 final size:18
Alignment explanation
Indices: 32056154--32056195 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
32056144 TATTTTTAAA
32056154 ATATTTTTAAAAA-AATT
1 ATATTTTTAAAAATAATT
*
32056171 ATATTTTAAAAAATAATT
1 ATATTTTTAAAAATAATT
32056189 A-ATTTTT
1 ATATTTTT
32056196 TGCTGACGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTTTAAAAATAATT
Found at i:32056190 original size:27 final size:25
Alignment explanation
Indices: 32056138--32056190 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
32056128 TTTTATATTT
* **
32056138 AAAAAATATTTTTAAAATATTTTTA
1 AAAAAATATTTTTAAAAAATAATTA
32056163 AAAAAATTATATTTTAAAAAATAATTA
1 AAAAAA-TAT-TTTTAAAAAATAATTA
32056190 A
1 A
32056191 TTTTTTGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAAAATATTTTTAAAAAATAATTA
Found at i:32056195 original size:18 final size:15
Alignment explanation
Indices: 32056151--32056183 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
32056141 AAATATTTTT
32056151 AAAA-TATTTTTAAA
1 AAAATTATTTTTAAA
32056165 AAAATTATATTTTAAA
1 AAAATTAT-TTTTAAA
32056181 AAA
1 AAA
32056184 TAATTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 3 0.18
16 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATTTTTAAA
Found at i:32059723 original size:25 final size:26
Alignment explanation
Indices: 32059682--32059732 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
32059672 GTATTTTTTA
* *
32059682 TATTTTATATAAAAAATTTTTGAATAT
1 TATTTTATAT-AAAAATCTTTAAATAT
32059709 TATTTTATAT-AAAATCTTTAAATA
1 TATTTTATATAAAAATCTTTAAATA
32059733 AAACAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
27 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTTTATATAAAAATCTTTAAATAT
Found at i:32061195 original size:17 final size:18
Alignment explanation
Indices: 32061155--32061197 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
32061145 ATAGAAATAC
32061155 ATAAACAAATCAAGAAAAT
1 ATAAA-AAATCAAGAAAAT
32061174 ATAAAAAAT-AA-AAAATT
1 ATAAAAAATCAAGAAAA-T
32061191 ATAAAAA
1 ATAAAAA
32061198 TGGAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
18 4 0.17
19 5 0.22
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
ATAAAAAATCAAGAAAAT
Found at i:32061257 original size:29 final size:30
Alignment explanation
Indices: 32061184--32061257 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
32061174 ATAAAAAATA
* *
32061184 AAAAATTATAAAAATGGAAAAAATATATTT
1 AAAAATTATAAAATTGCAAAAAATATATTT
*
32061214 AAAATTTTATAAAATTGCAAAAAATA-ATTT
1 AAAA-ATTATAAAATTGCAAAAAATATATTT
*
32061244 AAAAAGTATAAAAT
1 AAAAATTATAAAAT
32061258 GAAAATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 8 0.21
30 12 0.32
31 18 0.47
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAAATTATAAAATTGCAAAAAATATATTT
Found at i:32061267 original size:29 final size:29
Alignment explanation
Indices: 32061184--32061267 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
32061174 ATAAAAAATA
*
32061184 AAAAATTATAAAAATGGAAAAAATATATTT
1 AAAAATTAT-AAAATGAAAAAAATATATTT
* *
32061214 AAAATTTTATAAAATTGCAAAAAATA-ATTT
1 AAAA-ATTATAAAA-TGAAAAAAATATATTT
*
32061244 AAAAAGTATAAAATGAAAATAAAT
1 AAAAATTATAAAATGAAAA-AAAT
32061268 GAAAAAGTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 5 0.11
29 11 0.24
30 16 0.35
31 14 0.30
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTATAAAATGAAAAAAATATATTT
Found at i:32061306 original size:18 final size:17
Alignment explanation
Indices: 32061283--32061323 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
32061273 AGTGATTAGT
*
32061283 TTTTAATTTATATATATA
1 TTTTAATTTATATA-AAA
32061301 TTTTAATTTATATAAAA
1 TTTTAATTTATATAAAA
32061318 TTTTAA
1 TTTTAA
32061324 ATAACTGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATTTATATAAAA
Found at i:32072400 original size:303 final size:303
Alignment explanation
Indices: 32071853--32072462 Score: 1121
Period size: 303 Copynumber: 2.0 Consensus size: 303
32071843 AAAGGGGGAG
32071853 AATAGGGAACAATACAATGTGCCAAACTATTTTCATGTTTAGTAACCTCTTTTCTACTTAATTAT
1 AATAGGGAACAATACAATGTGCCAAACTATTTTCATGTTTAGTAACCTCTTTTCTACTTAATTAT
**
32071918 GCTTTGAAAATCATACCTATCCTAAGCCACAAACATTACAAGCCGAAAAGTCCTATGTGACCTAA
66 GCTTTGAAAATCATACCTATCCTAAGCCACAAACATTACAAGCCGAAAAACCCTATGTGACCTAA
*
32071983 ACAACTCTATGTAGGGATAGATGTGGAAATTGCATAATCTCATTATAATTATCTGTATTGTACTA
131 ACAACTCTATGCAGGGATAGATGTGGAAATTGCATAATCTCATTATAATTATCTGTATTGTACTA
32072048 GGATGATCAAAATACTTATGTTAGGCAATGATGGAGTTATATCAACAAGACTTTAATATTCATAT
196 GGATGATCAAAATACTTATGTTAGGCAATGATGGAGTTATATCAACAAGACTTTAATATTCATAT
* * *
32072113 TTCTTGTAACTTACTGATTGAAGGATTCATATGGAAACAACCT
261 TTCTTGTAACTTACTGATTGAAGGACTCATACGAAAACAACCT
32072156 AATAGGGAACAATACAATGTGCCAAACTATTTTCATGTTTAGTAACCTCTTTTCTACTTAATTAT
1 AATAGGGAACAATACAATGTGCCAAACTATTTTCATGTTTAGTAACCTCTTTTCTACTTAATTAT
* *
32072221 GCTTTGAAAATCATACCTGTCCTAAGCCATAAACATTACAAGCCGAAAAACCCTATGTGACCTAA
66 GCTTTGAAAATCATACCTATCCTAAGCCACAAACATTACAAGCCGAAAAACCCTATGTGACCTAA
*
32072286 ACAACTCTATGCATGGATAGATGTGGAAATTGCATAATCTCATTATAATTATCTGTATTGTACTA
131 ACAACTCTATGCAGGGATAGATGTGGAAATTGCATAATCTCATTATAATTATCTGTATTGTACTA
*
32072351 GGATGATCAAAATACTTATGTTAGGCAATGATGGAGTTATATCAACAAGACTTTAATTTTCATAT
196 GGATGATCAAAATACTTATGTTAGGCAATGATGGAGTTATATCAACAAGACTTTAATATTCATAT
*
32072416 TTCTTGTAACTTACTGATTGAAGGACTCATACGAAAACGACCT
261 TTCTTGTAACTTACTGATTGAAGGACTCATACGAAAACAACCT
32072459 AATA
1 AATA
32072463 TCCCCAAAGT
Statistics
Matches: 296, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 296 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (303 bp):
AATAGGGAACAATACAATGTGCCAAACTATTTTCATGTTTAGTAACCTCTTTTCTACTTAATTAT
GCTTTGAAAATCATACCTATCCTAAGCCACAAACATTACAAGCCGAAAAACCCTATGTGACCTAA
ACAACTCTATGCAGGGATAGATGTGGAAATTGCATAATCTCATTATAATTATCTGTATTGTACTA
GGATGATCAAAATACTTATGTTAGGCAATGATGGAGTTATATCAACAAGACTTTAATATTCATAT
TTCTTGTAACTTACTGATTGAAGGACTCATACGAAAACAACCT
Found at i:32078219 original size:20 final size:21
Alignment explanation
Indices: 32078179--32078241 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
32078169 ATTTTGAAAC
*
32078179 AATTTTAAAATCAAGTTAAAAT
1 AATTTTAAAA-CAAGTCAAAAT
*
32078201 GATTTT-AAACAAGTCAAAAT
1 AATTTTAAAACAAGTCAAAAT
* *
32078221 AATTTTCAAACAAGTCGAAAT
1 AATTTTAAAACAAGTCAAAAT
32078242 TAGCTTTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 15 0.42
21 16 0.44
22 5 0.14
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (21 bp):
AATTTTAAAACAAGTCAAAAT
Found at i:32082050 original size:16 final size:16
Alignment explanation
Indices: 32082026--32082063 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
32082016 ATAATAATTG
32082026 ATTGATATGAATTGGT
1 ATTGATATGAATTGGT
* *
32082042 ATTGGTATGAATTTGT
1 ATTGATATGAATTGGT
32082058 ATTGAT
1 ATTGAT
32082064 GTTAAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (16 bp):
ATTGATATGAATTGGT
Found at i:32091936 original size:16 final size:16
Alignment explanation
Indices: 32091909--32091951 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
32091899 TATTTTTTCT
*
32091909 TTTCTCTTTTCTTCTTC
1 TTTCT-TTTTCTTATTC
32091926 TTTCTTTTTCTTATTC
1 TTTCTTTTTCTTATTC
*
32091942 ATTCATTTTT
1 TTTC-TTTTT
32091952 TATAAATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTTTTTCTTATTC
Found at i:32093421 original size:20 final size:19
Alignment explanation
Indices: 32093388--32093425 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
32093378 AAGTGAAACA
32093388 AATTAGTAAAAAAAATAAG
1 AATTAGTAAAAAAAATAAG
*
32093407 AATTAAGTAAGAAAAATAA
1 AATT-AGTAAAAAAAATAA
32093426 TTGCTACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AATTAGTAAAAAAAATAAG
Found at i:32105333 original size:26 final size:26
Alignment explanation
Indices: 32105304--32105353 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
32105294 TAAGAGCTTT
* *
32105304 ATTCTGTTTAGGCTCGAATGAGCTGA
1 ATTCTGTCTAGGCTCAAATGAGCTGA
*
32105330 ATTCTGTCTGGGCTCAAATGAGCT
1 ATTCTGTCTAGGCTCAAATGAGCT
32105354 AAACTTTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (26 bp):
ATTCTGTCTAGGCTCAAATGAGCTGA
Found at i:32105363 original size:26 final size:26
Alignment explanation
Indices: 32105314--32105534 Score: 223
Period size: 26 Copynumber: 8.6 Consensus size: 26
32105304 ATTCTGTTTA
* *
32105314 GGCTCGAATGAGCTGAATTCTGTCTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* *
32105340 GGCTCAAATGAGCTAAACTTTGTCTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* * *
32105366 GGCTAGTATGAGCTAAACTC--T-AG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* *
32105389 GGCTCGAATAAGCTAAACTTTGTCTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* ** *
32105415 GACTCTTATGAGCTAAACTCTGTTTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* *
32105441 GGCTCGAATAAGCTAAACTCTGTTTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* *
32105467 GGCTCGTATGAGCTAAACTCTATCTG
1 GGCTCGAATGAGCTAAACTCTGTCTG
* * *
32105493 GGCTTGTATGAGCTAAACTCTATCCTG
1 GGCTCGAATGAGCTAAACTCTGT-CTG
*
32105520 GGCTCGAAAGAGCTA
1 GGCTCGAATGAGCTA
32105535 CTTTTATGTA
Statistics
Matches: 159, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
23 17 0.11
24 1 0.01
25 1 0.01
26 125 0.79
27 15 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (26 bp):
GGCTCGAATGAGCTAAACTCTGTCTG
Found at i:32108448 original size:27 final size:27
Alignment explanation
Indices: 32108410--32108468 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
32108400 GTTGGGTTGG
*
32108410 CTAGTGTGTTTGGCGAGCT-GGTGGTCA
1 CTAGTGCGTTTGGCGAGCTAGG-GGTCA
* *
32108437 CTAGTGCGTTTGGTGAGCTAGGGTTCA
1 CTAGTGCGTTTGGCGAGCTAGGGGTCA
32108464 CTAGT
1 CTAGT
32108469 CAAGTTGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.14, C:0.15, G:0.37, T:0.34
Consensus pattern (27 bp):
CTAGTGCGTTTGGCGAGCTAGGGGTCA
Found at i:32113341 original size:192 final size:192
Alignment explanation
Indices: 32113014--32113400 Score: 747
Period size: 192 Copynumber: 2.0 Consensus size: 192
32113004 AGGGAATTTT
32113014 GGCATTGGGTTCCTGCTCAAGCCGCGCAATATGGTGACAATAGCATTATTCCATGCTCTAGTATA
1 GGCATTGGGTTCCTGCTCAAGCCGCGCAATATGGTGACAATAGCATTATTCCATGCTCTAGTATA
32113079 TGCATAGAATAAATTCCGTATGAATTGCATCTCCTCCACTGTGCCGACAAGTTTGATTTTTCTGG
66 TGCATAGAATAAATTCCGTATGAATTGCATCTCCTCCACTGTGCCGACAAGTTTGATTTTTCTGG
32113144 TACTTATCCTATCGACAAATTTTTCAATCTCATCAAGTTTCCTCGAAATTTGAGGGTCTGTG
131 TACTTATCCTATCGACAAATTTTTCAATCTCATCAAGTTTCCTCGAAATTTGAGGGTCTGTG
*
32113206 GGCATTGGGTTCCTGCTCAAGCCGCGTAATATGGTGACAATAGCATTATTCCATGCTCTAGTATA
1 GGCATTGGGTTCCTGCTCAAGCCGCGCAATATGGTGACAATAGCATTATTCCATGCTCTAGTATA
*
32113271 TGCATAGAATAAATTTCGTATGAATTGCATCTCCTCCACTGTGCCGACAAGTTTGATTTTTCTGG
66 TGCATAGAATAAATTCCGTATGAATTGCATCTCCTCCACTGTGCCGACAAGTTTGATTTTTCTGG
*
32113336 TACTTATCCTATCGACAAATTTTTCAATTTCATCAAGTTTCCTCGAAATTTGAGGGTCTGTG
131 TACTTATCCTATCGACAAATTTTTCAATCTCATCAAGTTTCCTCGAAATTTGAGGGTCTGTG
32113398 GGC
1 GGC
32113401 GCATGGTTCT
Statistics
Matches: 192, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 192 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (192 bp):
GGCATTGGGTTCCTGCTCAAGCCGCGCAATATGGTGACAATAGCATTATTCCATGCTCTAGTATA
TGCATAGAATAAATTCCGTATGAATTGCATCTCCTCCACTGTGCCGACAAGTTTGATTTTTCTGG
TACTTATCCTATCGACAAATTTTTCAATCTCATCAAGTTTCCTCGAAATTTGAGGGTCTGTG
Found at i:32123736 original size:19 final size:19
Alignment explanation
Indices: 32123712--32123763 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
32123702 ATCAAAAACA
*
32123712 AACTACTAAAACTTCATAC
1 AACTACCAAAACTTCATAC
* *
32123731 AACTACCGAAACTTTATAC
1 AACTACCAAAACTTCATAC
*
32123750 AACTACCGAAACTT
1 AACTACCAAAACTT
32123764 AGAATCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.44, C:0.27, G:0.04, T:0.25
Consensus pattern (19 bp):
AACTACCAAAACTTCATAC
Found at i:32124859 original size:16 final size:16
Alignment explanation
Indices: 32124840--32124873 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32124830 AAATATATAT
* *
32124840 ATGTTTATATATTCAA
1 ATGTATATATAATCAA
32124856 ATGTATATATAATCAA
1 ATGTATATATAATCAA
32124872 AT
1 AT
32124874 TTATTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
ATGTATATATAATCAA
Found at i:32127057 original size:9 final size:9
Alignment explanation
Indices: 32127043--32127092 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
32127033 TATATATATA
32127043 TTTTTCTTT
1 TTTTTCTTT
32127052 TTTTTCTTT
1 TTTTTCTTT
32127061 TTTTATCTATTT
1 TTTT-TC--TTT
32127073 TTCTTTCTTT
1 TT-TTTCTTT
*
32127083 CTTTTCTTT
1 TTTTTCTTT
32127092 T
1 T
32127093 ATGCGACTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 20 0.57
10 6 0.17
12 7 0.20
13 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:32132964 original size:3 final size:3
Alignment explanation
Indices: 32132946--32133019 Score: 103
Period size: 3 Copynumber: 24.7 Consensus size: 3
32132936 AGGTCAAACC
* * *
32132946 TCA TCA TAA TCT TCA TCA TCA TCA TCA TCA TCA TCA TCC TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* *
32132994 TCC TCA TCC TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
32133020 TTCAATATCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:32137808 original size:84 final size:84
Alignment explanation
Indices: 32137649--32137809 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 84
32137639 CAGGAATGTG
* * *
32137649 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAGTTTAGAGCATGAG
1 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAATTTAAAGCATGAA
*
32137714 GAAGCAGAAGCAAGTTCAA
66 GAACCAGAAGCAAGTTCAA
* * * *
32137733 ATAAAATTGCCAAAGGTGTCACTGAGGACAATGAAACTGAATG-GATTTTGAATTTAAAGCATGA
1 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA-GAGAATTCGAATTTAAAGCATGA
*
32137797 AGAACCCGAAGCA
65 AGAACCAGAAGCA
32137810 CAATCAAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 66 0.99
85 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (84 bp):
ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAATTTAAAGCATGAA
GAACCAGAAGCAAGTTCAA
Found at i:32143112 original size:28 final size:28
Alignment explanation
Indices: 32143071--32143195 Score: 117
Period size: 28 Copynumber: 4.5 Consensus size: 28
32143061 AGGACACACT
* *
32143071 TTTGTGGTTGACTCTATTAAAGGAAGTC
1 TTTGTGGTTAACTCTATTAAAGGAAGCC
* **
32143099 TTTGTGGCTAACTCTATTAAAGGAAGAAA
1 TTTGTGGTTAACTCTATTAAAGGAAG-CC
* * *
32143128 TTT-TTGTTGACTCTATTAAAGGTAGCC
1 TTTGTGGTTAACTCTATTAAAGGAAGCC
* * * *
32143155 TTTGTGGCTAAATTTGTTAAAGGAAGCC
1 TTTGTGGTTAACTCTATTAAAGGAAGCC
*
32143183 ATTGTGGTTAACT
1 TTTGTGGTTAACT
32143196 ATGAAAGGAC
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
27 3 0.04
28 69 0.92
29 3 0.04
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (28 bp):
TTTGTGGTTAACTCTATTAAAGGAAGCC
Found at i:32151917 original size:14 final size:14
Alignment explanation
Indices: 32151898--32151927 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32151888 TTAAAAATCC
32151898 TTGAAATAACTTTA
1 TTGAAATAACTTTA
32151912 TTGAAATAACTTTA
1 TTGAAATAACTTTA
32151926 TT
1 TT
32151928 TTTGACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTGAAATAACTTTA
Found at i:32154265 original size:24 final size:24
Alignment explanation
Indices: 32154237--32154296 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
32154227 ATTCACGAAC
* *
32154237 AAGCTCATTTATTGGCTTGTTTAT
1 AAGCTCATTTATTGACTCGTTTAT
*
32154261 AAGCTCGTTTATTGACTCGTTTAT
1 AAGCTCATTTATTGACTCGTTTAT
32154285 AA-CTCATTTATT
1 AAGCTCATTTATT
32154297 TATTAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (24 bp):
AAGCTCATTTATTGACTCGTTTAT
Found at i:32154435 original size:23 final size:23
Alignment explanation
Indices: 32154392--32154437 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
32154382 ACATTGTTCG
*
32154392 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATGAAATTAAA
32154415 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
32154438 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:32158304 original size:49 final size:50
Alignment explanation
Indices: 32158240--32158335 Score: 158
Period size: 49 Copynumber: 1.9 Consensus size: 50
32158230 TTCGGATCAT
* *
32158240 AATTTATAACTATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
1 AATTTATAACCATTACTCCAAACAATTCGTAACAAAAATTATTATATGTA
*
32158290 AATTT-TAACCATTACTCCAAACAATTCGTAACAAAAATTGTTATAT
1 AATTTATAACCATTACTCCAAACAATTCGTAACAAAAATTATTATAT
32158336 AAAACTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
49 38 0.88
50 5 0.12
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (50 bp):
AATTTATAACCATTACTCCAAACAATTCGTAACAAAAATTATTATATGTA
Found at i:32160199 original size:23 final size:23
Alignment explanation
Indices: 32160171--32160230 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
32160161 TTTTCATTTC
32160171 ATAAAATATTAACATATTT-TT-AT
1 ATAAAAT-TTAACAT-TTTATTGAT
32160194 ATAAAACTTTAACATTTTATTGAT
1 ATAAAA-TTTAACATTTTATTGAT
*
32160218 ATAATATCTTAAC
1 ATAAAAT-TTAAC
32160231 TAAAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 3 0.09
23 16 0.50
24 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTTAACATTTTATTGAT
Found at i:32169151 original size:13 final size:13
Alignment explanation
Indices: 32169133--32169164 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
32169123 ACTGCAGAAC
32169133 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
32169146 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
32169159 AAAGAA
1 AAAGAA
32169165 GGAAGAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:32169160 original size:17 final size:17
Alignment explanation
Indices: 32169133--32169178 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
32169123 ACTGCAGAAC
32169133 AAAGAAAAGAAAGAAAGA
1 AAAG-AAAGAAAGAAAGA
*
32169151 AAAGAAAGAAAGAAGGA
1 AAAGAAAGAAAGAAAGA
*
32169168 AGAAGGAAGAA
1 A-AAGAAAGAA
32169179 GGAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAGA
Found at i:32169380 original size:4 final size:4
Alignment explanation
Indices: 32169358--32169401 Score: 61
Period size: 4 Copynumber: 10.5 Consensus size: 4
32169348 TTTTATTAGT
*
32169358 AAAG AAAC AAAG AAAAG AAAG AAAG AAAG AAAAG AAAG AAAG AA
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AA
32169402 GGAAGAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:32169399 original size:17 final size:17
Alignment explanation
Indices: 32169358--32169415 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
32169348 TTTTATTAGT
*
32169358 AAAGAAACAAAGAAAAG
1 AAAGAAAGAAAGAAAAG
32169375 AAAGAAAGAAAGAAAAG
1 AAAGAAAGAAAGAAAAG
*
32169392 AAAGAAAGAAGGAAGAAG
1 AAAGAAAGAAAGAA-AAG
*
32169410 GAAGAA
1 AAAGAA
32169416 GGAGAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
17 29 0.78
18 8 0.22
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAAG
Found at i:32169401 original size:13 final size:13
Alignment explanation
Indices: 32169358--32169398 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
32169348 TTTTATTAGT
*
32169358 AAAGAAACAAAGA
1 AAAGAAAGAAAGA
32169371 AAAGAAAGAAAG-
1 AAAGAAAGAAAGA
32169383 AAAGAAAAGAAAGA
1 AAAG-AAAGAAAGA
32169397 AA
1 AA
32169399 GAAGGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 4 0.16
13 19 0.76
14 2 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:32169541 original size:237 final size:238
Alignment explanation
Indices: 32169133--32169595 Score: 892
Period size: 237 Copynumber: 1.9 Consensus size: 238
32169123 ACTGCAGAAC
32169133 AAAGAAAAGAAAGAAAGAAAAGAAAGAAAGAAGGAAGAAGGAAGAAGGAGAAAAAAATAGTGTAT
1 AAAGAAAAGAAAGAAAGAAAAGAAAGAAAGAAGGAAGAAGGAAGAAGGAGAAAAAAATAGTGTAT
*
32169198 TTATTTTTAAAATATTTTAATTTATTAATTAGTAATAGTAATTTTAATTTTATTATTTAATGTGA
66 TTATTTTTAAAATATTTTAATTTATTAATTAATAATAGTAATTTTAATTTTATTATTTAATGTGA
32169263 TTGATTTGTTATTGTAATTTTATTTGTTTAGTAGGTTGGTTAAAAAAGTAAAAGATTAAAAGAAA
131 TTGATTTGTTATTGTAATTTTATTTGTTTAGTAGGTTGGTTAAAAAAGTAAAAGATTAAAAGAAA
32169328 AGAAGAAAGATAAATTTGGTTTTTATTAGTAAAGAAACAAAGA
196 AGAAGAAAGATAAATTTGGTTTTTATTAGTAAAGAAACAAAGA
*
32169371 AAAG-AAAGAAAGAAAGAAAAGAAAGAAAGAAGGAAGAAGGAAGAAGGAGAAAAAAGTAGTGTAT
1 AAAGAAAAGAAAGAAAGAAAAGAAAGAAAGAAGGAAGAAGGAAGAAGGAGAAAAAAATAGTGTAT
*
32169435 TTATTTTTAAAATATTTTAATTTATTAATTAATAGTAGTAATTTTAATTTTATTATTTAATGTGA
66 TTATTTTTAAAATATTTTAATTTATTAATTAATAATAGTAATTTTAATTTTATTATTTAATGTGA
32169500 TTGATTTGTTATTGTAATTTTATTTGTTTAGTAGGTTGGTTAAAAAAGTAAAAGATTAAAAGAAA
131 TTGATTTGTTATTGTAATTTTATTTGTTTAGTAGGTTGGTTAAAAAAGTAAAAGATTAAAAGAAA
32169565 AGAAGAAAGATAAATTTGGTTTTTATTAGTA
196 AGAAGAAAGATAAATTTGGTTTTTATTAGTA
32169596 TTTATTATTT
Statistics
Matches: 222, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
237 218 0.98
238 4 0.02
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (238 bp):
AAAGAAAAGAAAGAAAGAAAAGAAAGAAAGAAGGAAGAAGGAAGAAGGAGAAAAAAATAGTGTAT
TTATTTTTAAAATATTTTAATTTATTAATTAATAATAGTAATTTTAATTTTATTATTTAATGTGA
TTGATTTGTTATTGTAATTTTATTTGTTTAGTAGGTTGGTTAAAAAAGTAAAAGATTAAAAGAAA
AGAAGAAAGATAAATTTGGTTTTTATTAGTAAAGAAACAAAGA
Found at i:32170194 original size:16 final size:16
Alignment explanation
Indices: 32170149--32170198 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
32170139 TAAACCTAGC
*
32170149 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
32170165 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
32170179 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
32170195 TAAT
1 TAAT
32170199 ATCTCCATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:32170265 original size:30 final size:30
Alignment explanation
Indices: 32170231--32170325 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
32170221 AAATGGTACA
32170231 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
* * * *
32170261 AAAT-AATGA--TGTGTGGATACCATTTTGGT
1 AAATAAAT-ATTTATTTTG-TACCATTTTAGT
* *
32170290 ATATAAATATTTATTTTGTATCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
32170320 AAATAA
1 AAATAA
32170326 CTTATTTTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.08
29 18 0.37
30 23 0.47
31 4 0.08
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:32171581 original size:43 final size:42
Alignment explanation
Indices: 32171499--32171591 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 42
32171489 ATTAACATGT
*
32171499 TAAATTATATTACTTGAATCGTGTTAATATAGTTGCATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATAGTTGCATGTTA
* * * *
32171541 CTAAATTATATTACTTTACTCTTATTAATAT-TTTGACATGTTA
1 -TAAATTATATTACTTGAATCGTATTAATATAGTTG-CATGTTA
*
32171584 TTAATTAT
1 TAAATTAT
32171592 GCAGTTCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 10 0.23
43 33 0.77
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (42 bp):
TAAATTATATTACTTGAATCGTATTAATATAGTTGCATGTTA
Found at i:32172521 original size:29 final size:29
Alignment explanation
Indices: 32172465--32172535 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
32172455 ATTTCATACT
32172465 TTTAAACCCTAAACCCGACACTTTAAACC
1 TTTAAACCCTAAACCCGACACTTTAAACC
* * *
32172494 TTTAAATCCTAAACCCTA-ATTTTAAAACC
1 TTTAAACCCTAAACCCGACACTTT-AAACC
*
32172523 -TTAAACCTTAAAC
1 TTTAAACCCTAAAC
32172536 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.30
Consensus pattern (29 bp):
TTTAAACCCTAAACCCGACACTTTAAACC
Found at i:32172549 original size:28 final size:29
Alignment explanation
Indices: 32172518--32172574 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
32172508 CCTAATTTTA
*
32172518 AAACCTTAAACCTTAAACTT-AAAATTAT
1 AAACCCTAAACCTTAAACTTAAAAATTAT
*
32172546 AAACCCTAAACCTTAAATTTAAAAATTAT
1 AAACCCTAAACCTTAAACTTAAAAATTAT
32172575 TAATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.32
Consensus pattern (29 bp):
AAACCCTAAACCTTAAACTTAAAAATTAT
Found at i:32174716 original size:12 final size:12
Alignment explanation
Indices: 32174699--32174723 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32174689 CAATATGTGT
32174699 AATTGGATTTTC
1 AATTGGATTTTC
32174711 AATTGGATTTTC
1 AATTGGATTTTC
32174723 A
1 A
32174724 TCGTCATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
AATTGGATTTTC
Found at i:32174962 original size:24 final size:24
Alignment explanation
Indices: 32174934--32174980 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
32174924 CACCATACAC
32174934 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATCTTCATTTTCTACT
32174958 GGAGTTGGATCTTCATTTTCTAC
1 GGAGTTGGATCTTCATTTTCTAC
32174981 AAGTTCCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:32175448 original size:4 final size:4
Alignment explanation
Indices: 32175441--32175474 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
32175431 TCCTTCTTCC
32175441 TTCT TTCTT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTCT T
32175475 CTTCTGCCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:32175453 original size:16 final size:15
Alignment explanation
Indices: 32175434--32175477 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
32175424 CTTTCTCTCC
32175434 TTCTTCCTTCTTTCTT
1 TTCTTCCTTCTTTC-T
*
32175450 TTCTTTCTTTCTTTCT
1 TTC-TTCCTTCTTTCT
*
32175466 TTCTTTCTTCTT
1 TTCTTCCTTCTT
32175478 CTGCCCGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTCCTTCTTTCT
Found at i:32176812 original size:28 final size:27
Alignment explanation
Indices: 32176768--32176898 Score: 88
Period size: 28 Copynumber: 4.7 Consensus size: 27
32176758 AATGAACTCA
*
32176768 TTTTTTTT-AATTGTTAAAGATCAAAT
1 TTTTTTTTCAATTTTTAAAGATCAAAT
* * *
32176794 TTTTTTTATCAATTTTTAAGGGTTTTAATAAT
1 TTTTTTT-TCAATTTTTAA-AG--ATCA-AAT
*
32176826 TTTTTTTT-AATTTTTAAGGATTC-AAT
1 TTTTTTTTCAATTTTTAAAGA-TCAAAT
* * *
32176852 TTTTTTTACTAATTTTTAAAAGCTTAAAT
1 TTTTTTTTC-AATTTTT-AAAGATCAAAT
*
32176881 TTTTTTTTCAACTTTTAA
1 TTTTTTTTCAATTTTTAA
32176899 GAAATTTAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 21
0.71 0.10 0.18
Matches are distributed among these distances:
26 17 0.21
27 3 0.04
28 23 0.28
29 17 0.21
30 9 0.11
31 3 0.04
32 10 0.12
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (27 bp):
TTTTTTTTCAATTTTTAAAGATCAAAT
Found at i:32176868 original size:29 final size:26
Alignment explanation
Indices: 32176768--32176898 Score: 75
Period size: 29 Copynumber: 4.6 Consensus size: 26
32176758 AATGAACTCA
*
32176768 TTTTTTTTAATTGTT-AAAGATCAAAT
1 TTTTTTTTAATT-TTAAAAGATTAAAT
** *
32176794 TTTTTTTATCAATTTTTAAGGGTTTTAATAAT
1 TTTTTTT-T-AA-TTTTAAAAG-ATT-A-AAT
* * *
32176826 TTTTTTTTAATTTTTAAGGATTCAAT
1 TTTTTTTTAATTTTAAAAGATTAAAT
*
32176852 TTTTTTTACTAATTTTTAAAAGCTTAAAT
1 TTTTTTT--TAA-TTTTAAAAGATTAAAT
32176881 TTTTTTTTCAACTTTTAA
1 TTTTTTTT-AA-TTTTAA
32176899 GAAATTTAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
26 17 0.21
27 2 0.02
28 17 0.21
29 30 0.37
30 3 0.04
31 2 0.02
32 10 0.12
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (26 bp):
TTTTTTTTAATTTTAAAAGATTAAAT
Found at i:32176887 original size:58 final size:58
Alignment explanation
Indices: 32176768--32176888 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 58
32176758 AATGAACTCA
** * *
32176768 TTTTTTTTAATTGTTAAAGATCAAATTTTTTTTATCAATTTTTAAGGGTTTTAATAAT
1 TTTTTTTTAATTGTTAAAGATCAAATTTTTTTTATCAATTTTTAAAAGCTTAAATAAT
* *
32176826 TTTTTTTTAATTTTTAAGGATTC-AATTTTTTTTA-CTAATTTTTAAAAGCTTAAAT--T
1 TTTTTTTTAATTGTTAAAGA-TCAAATTTTTTTTATC-AATTTTTAAAAGCTTAAATAAT
32176882 TTTTTTT
1 TTTTTTT
32176889 CAACTTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
56 8 0.15
57 1 0.02
58 44 0.80
59 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (58 bp):
TTTTTTTTAATTGTTAAAGATCAAATTTTTTTTATCAATTTTTAAAAGCTTAAATAAT
Done.