Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 18 of 433
Found at i:4893901 original size:485 final size:486
Alignment explanation
Indices: 4892571--4894013 Score: 2741
Period size: 485 Copynumber: 3.0 Consensus size: 486
4892561 GTAACAATAT
4892571 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
1 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
** *
4892636 ACAAAACACAATAG-TTTTTTTTTTTGCAAATTAGGGTCGGGTCGGACCAAAAAA-CTTACTCGA
66 ACAAAATGCAATAGTTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCGA
*
4892699 GGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTTTATTTTT
131 GGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTTT
* * * *
4892764 ATCTAACCTCTCCCACTTTTTGAACAGGCTTTCGAATCGGGTCAAGTGACTCGACCCATGATCAT
196 ATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTCGACCCATGATCAT
4892829 TTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGAA
261 TTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGAA
*
4892894 AAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATAAAAGTGACAATAATATTTAAATTTTAAC
326 AAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAAC
*
4892959 ATTCATGGCGTAGCAAAACAAGCATGGTAGATTTGACAATATCCACTTATACTCCTTTGTCATCC
391 ATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATCC
4893024 CTATATATAGGTCAATTGACAGTAGAAACAA
456 CTATATATAGGTCAATTGACAGTAGAAACAA
4893055 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
1 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
4893120 ACAAAATGCAATAGTTTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCG
66 ACAAAATGCAATAG-TTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCG
4893185 AGGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTT
130 AGGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTT
4893250 TATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTCGACCCATGATCA
195 TATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTCGACCCATGATCA
4893315 TTTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGA
260 TTTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGA
4893380 AAAAGGAGTAGTG-TTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAA
325 AAAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAA
4893444 CATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATC
390 CATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATC
4893509 CCTATATATAGGTCAATTGACAGTAGAAACAA
455 CCTATATATAGGTCAATTGACAGTAGAAACAA
4893541 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
1 AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
4893606 ACAAAATGCAATAGTTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCGA
66 ACAAAATGCAATAGTTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCGA
4893671 GGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTTT
131 GGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTTT
*
4893736 ATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTTGACCCATGATCAT
196 ATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTCGACCCATGATCAT
*
4893801 TTTTACTTAGATGTCAATTACACATT-AAAAATATTATAAATAACTAATAAATAACAAATAGGAA
261 TTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGAA
4893865 AAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAAC
326 AAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAAC
4893930 ATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATCC
391 ATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATCC
4893995 CTATATATAGGTCAATTGA
456 CTATATATAGGTCAATTGA
4894014 AATACTCATA
Statistics
Matches: 943, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
484 127 0.13
485 341 0.36
486 264 0.28
487 211 0.22
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (486 bp):
AATAGCGGAATGACATCAAAGCAACAACAAACAGTAGAAACAACAGCAAAATAGTGGAAGCAACA
ACAAAATGCAATAGTTTTTTTTTTTTGCAAATTAGGGCCGGGTCGGACCAAAAAAGCTTACTCGA
GGCCCATCCCATTTAGAAAATGGGCTTCATTTTTTACCCAAGCCCATTTTCGAGTCTATATTTTT
ATCTAAACTCTCCCACTTTTTGAACAGACCTTCGAATCTGGTCAAGTGACTCGACCCATGATCAT
TTTTACTTAGATGTCAATTGCACATTAAAAAATATTATAAATAACTAATAAATAACAAATAGGAA
AAAGGAGTAGTGATTATAAGTTTATCCAAGATTCATGAAAGTGACAATAATATTTAAATTTTAAC
ATTCATGGCGTAGCAAAACAAGCATGATAGATTTGACAATATCCACTTATACTCCTTTGTCATCC
CTATATATAGGTCAATTGACAGTAGAAACAA
Found at i:4896111 original size:20 final size:22
Alignment explanation
Indices: 4896055--4896113 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
4896045 ATATTGCTTG
*
4896055 TTTTAAATTTATTTTATACTTTA
1 TTTTAAA-TCATTTTATACTTTA
* *
4896078 TTTTAAACCCTTTT-TAC-TTA
1 TTTTAAATCATTTTATACTTTA
*
4896098 TTTTAAATGATTTTAT
1 TTTTAAATCATTTTAT
4896114 TTATTTCAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 14 0.48
21 4 0.14
22 4 0.14
23 7 0.24
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAATCATTTTATACTTTA
Found at i:4896337 original size:26 final size:25
Alignment explanation
Indices: 4896291--4896339 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
4896281 ATCATTCTAA
*
4896291 AATTTGTTTACATCTTATTTATCTT
1 AATTTGTTTACACCTTATTTATCTT
* *
4896316 AATTTGCTTTATACCTTTTTTATC
1 AATTTG-TTTACACCTTATTTATC
4896340 GCTTAATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.59
Consensus pattern (25 bp):
AATTTGTTTACACCTTATTTATCTT
Found at i:4896822 original size:34 final size:34
Alignment explanation
Indices: 4896784--4896854 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
4896774 TCAAAAGACC
4896784 AACTTATTCTCGAGGGTCTGAAATGTTGTGTCCT
1 AACTTATTCTCGAGGGTCTGAAATGTTGTGTCCT
4896818 AACTTATTCTCGAGGGTCTGAAATGTTGTGTCCT
1 AACTTATTCTCGAGGGTCTGAAATGTTGTGTCCT
4896852 AAC
1 AAC
4896855 GTACTGGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (34 bp):
AACTTATTCTCGAGGGTCTGAAATGTTGTGTCCT
Found at i:4898075 original size:3 final size:3
Alignment explanation
Indices: 4898067--4898172 Score: 92
Period size: 3 Copynumber: 36.0 Consensus size: 3
4898057 AATGAAAACG
* *
4898067 ATA ATA ATA ATA ATA AT- ATAA ATA ATA ATA ATA GTA GTA A-A AT-
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
4898110 ATA ATA ATA CTA ATG ATA ATA ATA ATA GTC ATA ATA AGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
4898158 TTA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA
4898173 GTGATAATGG
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
2 6 0.07
3 74 0.90
4 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4898487 original size:14 final size:14
Alignment explanation
Indices: 4898470--4898496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4898460 TAATAGTGAT
4898470 AATAGTAATAATAC
1 AATAGTAATAATAC
4898484 AATAGTAATAATA
1 AATAGTAATAATA
4898497 ATAATAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:4898487 original size:23 final size:23
Alignment explanation
Indices: 4898456--4898505 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
4898446 AAAGAAAGAA
* * *
4898456 AATATAATAGTGATAATAGTAAT
1 AATACAATAGTAATAATAATAAT
4898479 AATACAATAGTAATAATAATAAT
1 AATACAATAGTAATAATAATAAT
4898502 AATA
1 AATA
4898506 GTGACATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (23 bp):
AATACAATAGTAATAATAATAAT
Found at i:4898710 original size:43 final size:43
Alignment explanation
Indices: 4898611--4898710 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
4898601 TTTATTGAAA
* **
4898611 AAAACGCCGCTAAAAGTCACGGCTTTTTAGCGGCGTTTGTGGT
1 AAAACACCGCTAAAAGTCACGGCTTTTTAGCGGCGTTTGTGCC
* * *
4898654 AAAAGCACTGCTAAAAGTCACGTC-TTTTAGCGGCGCTTT-TTCC
1 AAAA-CACCGCTAAAAGTCACGGCTTTTTAGCGGCG-TTTGTGCC
4898697 ACAAACACCGCTAA
1 A-AAACACCGCTAA
4898711 TTTTGGCAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
43 25 0.53
44 22 0.47
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAACACCGCTAAAAGTCACGGCTTTTTAGCGGCGTTTGTGCC
Found at i:4898798 original size:31 final size:31
Alignment explanation
Indices: 4898763--4898845 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
4898753 CTTCCTGCAT
* * *
4898763 TAAAATCCAACCAAATATAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* *
4898794 TAAAATGCAACCAAAAACAACAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
*
4898825 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
4898846 TTAATTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
31 27 0.61
33 17 0.39
ACGTcount: A:0.61, C:0.18, G:0.04, T:0.17
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:4904134 original size:9 final size:9
Alignment explanation
Indices: 4904120--4904247 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
4904110 ATGTATTAGT
4904120 TAAGTTATG
1 TAAGTTATG
4904129 TAAGTTGTTATG
1 TAA---GTTATG
*
4904141 TACGTTATG
1 TAAGTTATG
*
4904150 TGAGTTATG
1 TAAGTTATG
*
4904159 TAAATTATG
1 TAAGTTATG
4904168 TAAGTTATG
1 TAAGTTATG
*
4904177 TGAGTTATG
1 TAAGTTATG
4904186 TAAGTTGTTATG
1 TAA---GTTATG
*
4904198 TAAATTATG
1 TAAGTTATG
*
4904207 TAAGTTATA
1 TAAGTTATG
*
4904216 TGAGTTATG
1 TAAGTTATG
4904225 TAAGTTATG
1 TAAGTTATG
* *
4904234 TAATTTATT
1 TAAGTTATG
4904243 TAAGT
1 TAAGT
4904248 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:4904247 original size:57 final size:57
Alignment explanation
Indices: 4904120--4904247 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
4904110 ATGTATTAGT
** * *
4904120 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
4904177 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
4904234 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
4904248 AATGATCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:4904791 original size:241 final size:241
Alignment explanation
Indices: 4904368--4904802 Score: 870
Period size: 241 Copynumber: 1.8 Consensus size: 241
4904358 TGAATATAGT
4904368 AATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGC
1 AATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGC
4904433 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATA
66 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATA
4904498 AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAAT
131 AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAAT
4904563 ATTCAATAATAAATGAGCTCGATAGAACTTTTTTCAACTCTTTTTG
196 ATTCAATAATAAATGAGCTCGATAGAACTTTTTTCAACTCTTTTTG
4904609 AATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGC
1 AATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGC
4904674 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATA
66 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATA
4904739 AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAA
131 AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAA
4904803 ATTAATTCAT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 194 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (241 bp):
AATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGC
TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATA
AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAAT
ATTCAATAATAAATGAGCTCGATAGAACTTTTTTCAACTCTTTTTG
Found at i:4905161 original size:2 final size:2
Alignment explanation
Indices: 4905154--4905192 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4905144 ATACAATAAC
4905154 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
4905193 CAATTTGACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4908241 original size:46 final size:44
Alignment explanation
Indices: 4908174--4908261 Score: 158
Period size: 46 Copynumber: 2.0 Consensus size: 44
4908164 GGTGAAGCAC
4908174 TTACCACCGTCCATTTAACCATATAGACAGTAATATTTTAATCACA
1 TTACCACCGTCCATTTAACCATATAGA-AGTAATA-TTTAATCACA
4908220 TTACCACCGTCCATTTAACCATATAGAAGTAATATTTAATCA
1 TTACCACCGTCCATTTAACCATATAGAAGTAATATTTAATCA
4908262 TTAACATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 8 0.19
45 7 0.17
46 27 0.64
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (44 bp):
TTACCACCGTCCATTTAACCATATAGAAGTAATATTTAATCACA
Found at i:4910124 original size:18 final size:17
Alignment explanation
Indices: 4910101--4910135 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4910091 TTAAATTATT
4910101 TAATATATAAATAAAAAA
1 TAATATA-AAATAAAAAA
*
4910119 TAATATAAATTAAAAAA
1 TAATATAAAATAAAAAA
4910136 ATAAGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAATATAAAATAAAAAA
Found at i:4910309 original size:17 final size:17
Alignment explanation
Indices: 4910266--4910309 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4910256 GAAATCTAGA
* *
4910266 AAATTATTGAAATTTTG
1 AAATTATTTAAAATTTG
*
4910283 AAATCA-TTAAAATTTG
1 AAATTATTTAAAATTTG
4910299 AAATTATTTAA
1 AAATTATTTAA
4910310 GATGTATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
AAATTATTTAAAATTTG
Found at i:4910754 original size:8 final size:8
Alignment explanation
Indices: 4910710--4910760 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 8
4910700 CTAGCTTGAA
4910710 CCATAAA-
1 CCATAAAC
4910717 CCATAAA-
1 CCATAAAC
*
4910724 CCATAATC
1 CCATAAAC
*
4910732 CC-TAAAT
1 CCATAAAC
*
4910739 CCACAAAC
1 CCATAAAC
4910747 CCATAAAC
1 CCATAAAC
4910755 CCATAA
1 CCATAA
4910761 TATTCCCTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
7 18 0.50
8 18 0.50
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (8 bp):
CCATAAAC
Found at i:4910856 original size:16 final size:14
Alignment explanation
Indices: 4910825--4910862 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
4910815 TCATAATCAA
4910825 TAAACCATAAACCC
1 TAAACCATAAACCC
4910839 TAAACCATATATACCC
1 TAAACCATA-A-ACCC
4910855 TAAACCAT
1 TAAACCAT
4910863 GCATAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.41
15 1 0.05
16 12 0.55
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:4911115 original size:14 final size:13
Alignment explanation
Indices: 4911095--4911141 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
4911085 TGTGGCATTA
4911095 ATTTAGGGTTTAT
1 ATTTAGGGTTTAT
*
4911108 AGTTTAGGGTTTCAA
1 A-TTTAGGGTTT-AT
*
4911123 ATTTAAGGTTTAT
1 ATTTAGGGTTTAT
4911136 ATTTAG
1 ATTTAG
4911142 TTTATGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 7 0.25
14 19 0.68
15 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (13 bp):
ATTTAGGGTTTAT
Found at i:4911755 original size:41 final size:42
Alignment explanation
Indices: 4911662--4911759 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 42
4911652 AGTTTAGATT
*
4911662 TATAGCGGCGTTTTTCCAAAAAGCGCCGCTAAAACTTAAATC
1 TATAGCGGCGTTTTTCCAAAAAGCGCCACTAAAACTTAAATC
* *
4911704 TATTA-TGGCGTTTTT-CTAAAAGCGCCACTAAAACTTAAATC
1 TA-TAGCGGCGTTTTTCCAAAAAGCGCCACTAAAACTTAAATC
4911745 TATAGCGGCGTTTTT
1 TATAGCGGCGTTTTT
4911760 GAGGAAGCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 2 0.04
41 35 0.70
42 11 0.22
43 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (42 bp):
TATAGCGGCGTTTTTCCAAAAAGCGCCACTAAAACTTAAATC
Found at i:4912118 original size:3 final size:3
Alignment explanation
Indices: 4912110--4912612 Score: 170
Period size: 3 Copynumber: 163.7 Consensus size: 3
4912100 CTTGTAGTGT
* * ** *
4912110 TAA TAA TAA TAA TAA TAA TAGA AAA TAA TAG TACA TTGT TAA TATA CAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A -TAA TAA TA-A TAA
* * **
4912159 TAA TAA CAA TAA TAA TATA TAA AAA TAGGA -AA TAA TAA T-A TGG TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA--A TAA TAA TAA TAA TAA TAA
* * * * * *
4912205 -AA AAA TAA T-A TAT TAA AAA AAA TAA TAG TAG TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * * * *
4912252 TGA TAA TAA AAA TACA TAA TAA TAG TAA -AA CAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
4912297 TAA TAA TAA TAA TAA TAG TAG TAG TGA TAT TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
4912345 TAGA AAA TAA TAG TACA TTGA TAA T-A TACGA TAA TAA CAT TAA TAA
1 TA-A TAA TAA TAA TA-A -TAA TAA TAA TA--A TAA TAA TAA TAA TAA
* ** * *
4912391 TATA TAA AAA TAGGA -AA TAA TAA T-A TGG TAA -AA AAA TAA TACGT
1 TA-A TAA TAA TA--A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA--A
* * * * * * *
4912435 TAA CAA AAA TAA TAG TAG TAA TAA CAA TAA TTAA TGA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* * * * *
4912481 TATA GAA TAA TAG TAA -AA CAA TAA TAG TAA TGA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
4912526 TAA TAA TACA TTAA GTTA CAA TAG TAA -AG TAA TAA TAG TGA TAA TAA
1 TAA TAA TA-A -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4912573 TAA T-A TAT TAGA TAA TAA TAA -AA -AA TAA CAA GTAA TAA TA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
4912613 CTAGATTAAA
Statistics
Matches: 367, Mismatches: 95, Indels: 76
0.68 0.18 0.14
Matches are distributed among these distances:
2 25 0.07
3 297 0.81
4 34 0.09
5 11 0.03
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4912402 original size:22 final size:22
Alignment explanation
Indices: 4912359--4912402 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4912349 AAATAATAGT
* * *
4912359 ACATTGATAATATACGATAATA
1 ACATTAATAATATACAAAAATA
*
4912381 ACATTAATAATATATAAAAATA
1 ACATTAATAATATACAAAAATA
4912403 GGAAATAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (22 bp):
ACATTAATAATATACAAAAATA
Found at i:4912428 original size:16 final size:17
Alignment explanation
Indices: 4912409--4912448 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4912399 AATAGGAAAT
*
4912409 AATAATATGGTAA-AAA
1 AATAATACGGTAACAAA
*
4912425 AATAATACGTTAACAAA
1 AATAATACGGTAACAAA
4912442 AATAATA
1 AATAATA
4912449 GTAGTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (17 bp):
AATAATACGGTAACAAA
Found at i:4912492 original size:217 final size:217
Alignment explanation
Indices: 4912113--4912530 Score: 746
Period size: 217 Copynumber: 1.9 Consensus size: 217
4912103 GTAGTGTTAA
*
4912113 TAATAATAATAATAATAGAAAATAATAGTACATTGTTAATATACAATAATAACAATAATAATATA
1 TAATAATAATAATAATAGAAAATAATAGTACATTGATAATATACAATAATAACAATAATAATATA
* *
4912178 TAAAAATAGGAAATAATAATATGGTAAAAAAATAATATATTAAAAAAAATAATAGTAGTAATAAT
66 TAAAAATAGGAAATAATAATATGGTAAAAAAATAATACATTAAAAAAAATAATAGTAGTAATAAC
*
4912243 AATAATTAATGATAATAAAAATACATAATAATAGTAAAACAATAATAGTAATAATAATAATAATA
131 AATAATTAATGATAATAAAAATACAGAATAATAGTAAAACAATAATAGTAATAATAATAATAATA
4912308 ATAATAGTAGTAGTGATATTAG
196 ATAATAGTAGTAGTGATATTAG
* *
4912330 TAATAATAATAATAATAGAAAATAATAGTACATTGATAATATACGATAATAACATTAATAATATA
1 TAATAATAATAATAATAGAAAATAATAGTACATTGATAATATACAATAATAACAATAATAATATA
* *
4912395 TAAAAATAGGAAATAATAATATGGTAAAAAAATAATACGTTAACAAAAATAATAGTAGTAATAAC
66 TAAAAATAGGAAATAATAATATGGTAAAAAAATAATACATTAAAAAAAATAATAGTAGTAATAAC
* *
4912460 AATAATTAATGATAATAAAAATATAGAATAATAGTAAAACAATAATAGTAATGATAATAATAATA
131 AATAATTAATGATAATAAAAATACAGAATAATAGTAAAACAATAATAGTAATAATAATAATAATA
4912525 ATAATA
196 ATAATA
4912531 ATACATTAAG
Statistics
Matches: 191, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 191 1.00
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (217 bp):
TAATAATAATAATAATAGAAAATAATAGTACATTGATAATATACAATAATAACAATAATAATATA
TAAAAATAGGAAATAATAATATGGTAAAAAAATAATACATTAAAAAAAATAATAGTAGTAATAAC
AATAATTAATGATAATAAAAATACAGAATAATAGTAAAACAATAATAGTAATAATAATAATAATA
ATAATAGTAGTAGTGATATTAG
Found at i:4913295 original size:18 final size:17
Alignment explanation
Indices: 4913265--4913298 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4913255 TTTAAAAAAT
*
4913265 AAAAAAAATAAAATAAC
1 AAAAAAAAGAAAATAAC
4913282 AAAAAAAACGAAAATAA
1 AAAAAAAA-GAAAATAA
4913299 TAAACCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGAAAATAAC
Found at i:4913684 original size:22 final size:23
Alignment explanation
Indices: 4913650--4913696 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4913640 TTTTGGGTTA
*
4913650 GGCTAGGGTTGAAATTAGGTTTG
1 GGCTAGGGCTGAAATTAGGTTTG
*
4913673 GGCTA-GGCTGAAATTGGGTTTG
1 GGCTAGGGCTGAAATTAGGTTTG
4913695 GG
1 GG
4913697 TTAATGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.19, C:0.06, G:0.43, T:0.32
Consensus pattern (23 bp):
GGCTAGGGCTGAAATTAGGTTTG
Found at i:4914075 original size:45 final size:45
Alignment explanation
Indices: 4914013--4914173 Score: 207
Period size: 45 Copynumber: 3.6 Consensus size: 45
4914003 GTTGCTTTAA
* *
4914013 TCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAACTTCAG
*
4914058 TCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCTAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAACTTCAG
* * * * *
4914103 TCTGTTCCACTGCAACTTCAGGGAGACAAGACTAG-TGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAACTTCAG
* * * *
4914147 TCTACTCCGCTGAAACTTCAAGGAGAT
1 TCTGCTCCACTGCAACTTCAGGGAGAT
4914174 CTACTGTGGC
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 28 0.28
45 73 0.72
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAACTTCAG
Found at i:4914299 original size:44 final size:44
Alignment explanation
Indices: 4914235--4914567 Score: 221
Period size: 44 Copynumber: 7.6 Consensus size: 44
4914225 AATTTCCAGC
*
4914235 CTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
* * * ** ** ** *
4914279 CTGTTTCCCTATTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGA-T
* * * *
4914322 CTGTTACCCTACTACTTAAGGGTTTAAGGCCCCTCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
** * ** * ** *
4914366 CTGTTTTCCTACTACTTAGGAGG-TTAAGATCTAT-AAATTC-AGC
1 CTGTTACCCTACTGCTTAGG-GGTTTAAGGCCCATCACCTTCGA-T
*
4914409 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
* * * * * ** * ** * *
4914453 CTGTTTCCCTATTGTTTAGGGGGTT-AGGATCTGTAAATTTAG-C
1 CTGTTACCCTACTGCTTAGGGGTTTAAGG-CCCATCACCTTCGAT
*
4914496 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
* *
4914540 CTGTTTCCCTACTGCTTAGGGGGTTAAG
1 CTGTTACCCTACTGCTTAGGGGTTTAAG
4914568 ATCTGTAAAT
Statistics
Matches: 205, Mismatches: 73, Indels: 22
0.68 0.24 0.07
Matches are distributed among these distances:
42 4 0.02
43 86 0.42
44 111 0.54
45 4 0.02
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
Found at i:4914349 original size:43 final size:43
Alignment explanation
Indices: 4914279--4914610 Score: 184
Period size: 43 Copynumber: 7.7 Consensus size: 43
4914269 CACCTTCGAT
* * *
4914279 CTGTTTCCCTATTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTCAGC
* * * ** ** *** *
4914322 CTGTTACCCTACTACTTAAGGGTTTAAGGCCCCTCGCCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTAT-AAATTCAG-C
** * *
4914366 CTGTTTTCCTACTACTTAGGAGGTTAAGATCTATAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTCAGC
* ** * *** *
4914409 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTAT-AAATTCAG-C
* * * * * *
4914453 CTGTTTCCCTATTGTTTAGGGGGTTAGGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTCAGC
* ** * *** *
4914496 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTAT-AAATTCAG-C
* * *
4914540 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTCAGC
* *
4914583 CTGTTACCCTACTGCTTAAGGGTTTAAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAG
4914611 GCTAGTGAAT
Statistics
Matches: 200, Mismatches: 80, Indels: 18
0.67 0.27 0.06
Matches are distributed among these distances:
43 111 0.56
44 89 0.44
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTCAGC
Found at i:4914384 original size:87 final size:87
Alignment explanation
Indices: 4914222--4914612 Score: 620
Period size: 87 Copynumber: 4.5 Consensus size: 87
4914212 AGAAAAGAAT
* * *
4914222 TGTAATTTCCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCC
1 TGTAAATT-CAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCC
*
4914287 CTATTGCTTAGGGGGTTAAGATC
65 CTACTGCTTAGGGGGTTAAGATC
* * * *
4914310 TGTAAATTCAGCCTGTTACCCTACTACTTAAGGGTTTAAGGCCCCTCGCCTTCGATCTGTTTTCC
1 TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
* *
4914375 TACTACTTAGGAGGTTAAGATC
66 TACTGCTTAGGGGGTTAAGATC
*
4914397 TATAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
1 TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
* * *
4914462 TATTGTTTAGGGGGTTAGGATC
66 TACTGCTTAGGGGGTTAAGATC
*
4914484 TGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
1 TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
4914549 TACTGCTTAGGGGGTTAAGATC
66 TACTGCTTAGGGGGTTAAGATC
* *
4914571 TGTAAATTTAGCCTGTTACCCTACTGCTTAAGGGTTTAAGGC
1 TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
4914613 TAGTGAATTC
Statistics
Matches: 277, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
87 270 0.97
88 7 0.03
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (87 bp):
TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCCC
TACTGCTTAGGGGGTTAAGATC
Found at i:4923271 original size:44 final size:45
Alignment explanation
Indices: 4923181--4923309 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
4923171 GGACAGAACA
*
4923181 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
4923227 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
4923271 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4923310 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:4930664 original size:44 final size:45
Alignment explanation
Indices: 4930574--4930702 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
4930564 GACAGAACGA
*
4930574 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
4930620 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
4930664 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4930703 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:4936148 original size:12 final size:12
Alignment explanation
Indices: 4936128--4936167 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4936118 GAAATGATCG
*
4936128 AATACATAAGTA
1 AATAAATAAGTA
4936140 AATAAATAAGTA
1 AATAAATAAGTA
4936152 AATAAA-AA-TA
1 AATAAATAAGTA
4936162 AATAAA
1 AATAAA
4936168 ACATGGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
12 17 0.63
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (12 bp):
AATAAATAAGTA
Found at i:4936213 original size:3 final size:3
Alignment explanation
Indices: 4936205--4936361 Score: 94
Period size: 3 Copynumber: 54.3 Consensus size: 3
4936195 AACGAAAACG
* * *
4936205 ATA ATA ATA ATA ATA AT- ATAA ATA ATA ATA GTA GTA GTA A-A AT-
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
4936248 ATA ATA ATA CTA ATG ATA ATA ATA ATA GTC ATA ATA AGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** *
4936296 TTA GTA ATA ATA ATA ATG ATA ATG GGA ATA A-A A-A ATA ACA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
4936341 ATA AT- ATA ATG ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
4936362 AAGTAAAAGT
Statistics
Matches: 116, Mismatches: 31, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
2 14 0.12
3 100 0.86
4 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4936605 original size:3 final size:3
Alignment explanation
Indices: 4936599--4937173 Score: 258
Period size: 3 Copynumber: 188.3 Consensus size: 3
4936589 AGAAAAAAAA
* *
4936599 AAT AAT AAT GAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
4936647 AAT AGT GAC ATT AGT AAT AAT AAT AAT AAT AAT AGAA AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
** * * *
4936693 ACATT GTT AAT ATAC AAT AAT AAC AAT AAT AAT ATAT AAA AAT AGGA-
1 A-A-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A--AT
** * * ** * * *
4936740 AAT AAT AAT -AT GGT AAA AAA AAT AAT -AT GTT AAC AAA AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
4936786 AGT AAT AAT AAT AATT AAT GAT AAT AAA AAT ACAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* *
4936833 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * * *
4936881 AGT AGT AGT AGT AGT AGT GAT ATT AGT AAT AAT AAT AAT AGT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * *
4936928 GAT AAT -AT ACGAT AAT AAC ATT AAT AAT ATAT AAA AAT AGGA- AAT
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT A-AT AAT AAT A--AT AAT
** ** * * ** *
4936973 AAT AAT -AT GGT AA- AA- AAT AAT -AT GTT AAC AAA AAT AAT AGC AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
4937017 AAT AAC AA- AAT AATT AAT GAT AAT AAA AAT ACAT AAT AAT AGT AA-
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * *
4937062 AAC AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT ACATT AAGT TAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AA-T AAT AAT
* * * * *
4937110 AGT AA- AGT AAT AAT AGT GAT AAT AAT AAT -AT ATT AGAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
4937154 AAA AAT AAC AAGT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT A
4937174 CTAGATTAAA
Statistics
Matches: 435, Mismatches: 103, Indels: 68
0.72 0.17 0.11
Matches are distributed among these distances:
2 23 0.05
3 370 0.85
4 33 0.08
5 9 0.02
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4936765 original size:17 final size:17
Alignment explanation
Indices: 4936743--4936783 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4936733 AATAGGAAAT
4936743 AATAATATGGTAAAAAA
1 AATAATATGGTAAAAAA
* *
4936760 AATAATATGTTAACAAA
1 AATAATATGGTAAAAAA
4936777 AATAATA
1 AATAATA
4936784 GTAGTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (17 bp):
AATAATATGGTAAAAAA
Found at i:4938137 original size:24 final size:24
Alignment explanation
Indices: 4938103--4938149 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4938093 AGGTGCAACT
*
4938103 GGCGGTGGCAGGTGGCTGACAAGC
1 GGCGGTAGCAGGTGGCTGACAAGC
4938127 GGCGGTAGCAGGTGGCTGACAAG
1 GGCGGTAGCAGGTGGCTGACAAG
4938150 GCTAAGGCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.49, T:0.13
Consensus pattern (24 bp):
GGCGGTAGCAGGTGGCTGACAAGC
Found at i:4938249 original size:22 final size:23
Alignment explanation
Indices: 4938210--4938259 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
4938200 TGTTTTTGGG
* *
4938210 TTGGGCTAGGGTTGAAATTAGGT
1 TTGGGCTAGGGCTAAAATTAGGT
*
4938233 TTGGGCTA-GGCTAAAATTGGGT
1 TTGGGCTAGGGCTAAAATTAGGT
4938255 TTGGG
1 TTGGG
4938260 TTAATGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.20, C:0.06, G:0.40, T:0.34
Consensus pattern (23 bp):
TTGGGCTAGGGCTAAAATTAGGT
Found at i:4941611 original size:30 final size:31
Alignment explanation
Indices: 4941570--4941631 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
4941560 TTATGTTAAT
4941570 ATCATAAATTTATGTCTTAAAAATTATCTAC
1 ATCATAAATTTATGTCTTAAAAATTATCTAC
4941601 ATCA-AAATTTATGTCTTAAAAATTATCTAC
1 ATCATAAATTTATGTCTTAAAAATTATCTAC
4941631 A
1 A
4941632 GTCGATGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (31 bp):
ATCATAAATTTATGTCTTAAAAATTATCTAC
Found at i:4941626 original size:14 final size:14
Alignment explanation
Indices: 4941579--4941626 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4941569 TATCATAAAT
4941579 TTATGTCTTAAAAA
1 TTATGTCTTAAAAA
* * *
4941593 TTATCTACATCAAAAT
1 TTATGT-C-TTAAAAA
4941609 TTATGTCTTAAAAA
1 TTATGTCTTAAAAA
4941623 TTAT
1 TTAT
4941627 CTACAGTCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 14 0.54
15 2 0.08
16 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (14 bp):
TTATGTCTTAAAAA
Found at i:4944371 original size:6 final size:6
Alignment explanation
Indices: 4944364--4944424 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
4944354 CAAACCACAA
* * *
4944364 CAACAA CAACAG CATCAG C-A--G CAACAG CAACAG CAACAA CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
4944409 CAACAG CAACAG CAAC
1 CAACAG CAACAG CAAC
4944425 GGGAACATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
6 44 0.94
ACGTcount: A:0.51, C:0.34, G:0.13, T:0.02
Consensus pattern (6 bp):
CAACAG
Found at i:4944390 original size:15 final size:15
Alignment explanation
Indices: 4944370--4944424 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
4944360 ACAACAACAA
*
4944370 CAACAGCATCAGCAG
1 CAACAGCAACAGCAG
*
4944385 CAACAGCAACAGCAA
1 CAACAGCAACAGCAG
* * *
4944400 CAACAACAGCAACAG
1 CAACAGCAACAGCAG
4944415 CAACAGCAAC
1 CAACAGCAAC
4944425 GGGAACATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.49, C:0.35, G:0.15, T:0.02
Consensus pattern (15 bp):
CAACAGCAACAGCAG
Found at i:4945736 original size:3 final size:3
Alignment explanation
Indices: 4945728--4945753 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4945718 TCACTGTGGC
4945728 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
4945754 TTGGGGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:4946631 original size:29 final size:29
Alignment explanation
Indices: 4946575--4946644 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
4946565 TTTAATATCC
* * * *
4946575 TATATTTTTA-TATTTTTTAAATATTAAAT
1 TATAATTTTATTA-TTTTTAAAGAGTAAAG
4946604 TA-AATTATTATTATTTTTAAAGAGTAAAG
1 TATAATT-TTATTATTTTTAAAGAGTAAAG
4946633 TATAATTTTATT
1 TATAATTTTATT
4946645 GTTATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 3 0.09
29 25 0.74
30 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (29 bp):
TATAATTTTATTATTTTTAAAGAGTAAAG
Found at i:4949363 original size:23 final size:23
Alignment explanation
Indices: 4949337--4949385 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
4949327 AGAAGAATTA
* *
4949337 TCAAGTTTAAAGACTAAATCTTG
1 TCAAGTTTAAAAACTAAATATTG
4949360 TCAAGTTTAAAAACTAAATATTG
1 TCAAGTTTAAAAACTAAATATTG
4949383 TCA
1 TCA
4949386 TATTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (23 bp):
TCAAGTTTAAAAACTAAATATTG
Found at i:4950339 original size:42 final size:39
Alignment explanation
Indices: 4950287--4950367 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 39
4950277 TATTAAAAAG
*
4950287 TATTATATTAAAAACCACTACCATAAATATAATAAATATTTT
1 TATTATATTAAAAACCAC-A-AATAAATATAA-AAATATTTT
**
4950329 TATTATATTAAAAATTACAAATAAATATAAAAATATTTT
1 TATTATATTAAAAACCACAAATAAATATAAAAATATTTT
4950368 ATTGTAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 9 0.25
40 10 0.28
41 1 0.03
42 16 0.44
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (39 bp):
TATTATATTAAAAACCACAAATAAATATAAAAATATTTT
Found at i:4958574 original size:25 final size:25
Alignment explanation
Indices: 4958546--4958598 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4958536 ATATTATGTG
*
4958546 AAATAATGTATAGAATACA-ATATTA
1 AAAT-ATGTACAGAATACACATATTA
* *
4958571 AAATATTTACATAATACACATATTA
1 AAATATGTACAGAATACACATATTA
4958596 AAA
1 AAA
4958599 ATAACTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATATGTACAGAATACACATATTA
Found at i:4958609 original size:25 final size:24
Alignment explanation
Indices: 4958559--4958611 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
4958549 TAATGTATAG
**
4958559 AATACAATATTAAAATATTTACAT
1 AATACAATATTAAAATAACTACAT
4958583 AATACACATATTAAAAATAACTA-AT
1 AATACA-ATATT-AAAATAACTACAT
4958608 AATA
1 AATA
4958612 ATATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (24 bp):
AATACAATATTAAAATAACTACAT
Found at i:4959893 original size:16 final size:16
Alignment explanation
Indices: 4959872--4959903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4959862 TTTTGTGTAA
*
4959872 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
4959888 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
4959904 GTTATTGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:4961979 original size:23 final size:23
Alignment explanation
Indices: 4961953--4961996 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4961943 TACGCTTGCT
4961953 TTGACTATAACTATACTTGTAGC
1 TTGACTATAACTATACTTGTAGC
* *
4961976 TTGACTATAACTGTATTTGTA
1 TTGACTATAACTATACTTGTA
4961997 ACTGTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (23 bp):
TTGACTATAACTATACTTGTAGC
Found at i:4970323 original size:2 final size:2
Alignment explanation
Indices: 4970316--4970344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4970306 AATTAATGTT
4970316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4970345 TGACACAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4973438 original size:22 final size:22
Alignment explanation
Indices: 4973410--4973454 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4973400 AGCTACATGC
4973410 ATCTAATATAAGCACAAAACTT
1 ATCTAATATAAGCACAAAACTT
4973432 ATCTAATATAAGCACAAAACTT
1 ATCTAATATAAGCACAAAACTT
4973454 A
1 A
4973455 CTTTGTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (22 bp):
ATCTAATATAAGCACAAAACTT
Found at i:4979495 original size:35 final size:35
Alignment explanation
Indices: 4979354--4979483 Score: 233
Period size: 35 Copynumber: 3.7 Consensus size: 35
4979344 GTATGGATTT
4979354 GATAATACCATACCTACATTTCACAGCTCAGTATG
1 GATAATACCATACCTACATTTCACAGCTCAGTATG
*
4979389 GATAATACCATACCTACATTTCATAGCTCAGTATG
1 GATAATACCATACCTACATTTCACAGCTCAGTATG
*
4979424 GATAATACCATACCTACATTTCACAACTCAGTATG
1 GATAATACCATACCTACATTTCACAGCTCAGTATG
*
4979459 GATGATACCATACCTACATTTCACA
1 GATAATACCATACCTACATTTCACA
4979484 CTTTTCCATG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 91 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (35 bp):
GATAATACCATACCTACATTTCACAGCTCAGTATG
Found at i:4983540 original size:26 final size:26
Alignment explanation
Indices: 4983504--4983613 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
4983494 CATGAAATTC
*
4983504 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
4983530 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
4983556 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
4983582 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
4983608 TCATCA
1 TTATCA
4983614 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:4987227 original size:17 final size:17
Alignment explanation
Indices: 4987205--4987347 Score: 132
Period size: 17 Copynumber: 8.5 Consensus size: 17
4987195 ACGGCTATAC
4987205 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
** *
4987222 TTTATATGTGAGTTGTC
1 TTTATATGCAAGTTGTG
* *
4987239 TTTATATGTAAGTTATG
1 TTTATATGCAAGTTGTG
*
4987256 -TTATATGCAAGTTGTA
1 TTTATATGCAAGTTGTG
* * *
4987272 TGTATATGCGAGTTGTC
1 TTTATATGCAAGTTGTG
4987289 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
* *
4987306 -TTATATGCGAA-CTGAG
1 TTTATATGC-AAGTTGTG
*
4987322 TTTATCTGCAAGTTGAT-
1 TTTATATGCAAGTTG-TG
4987339 TTTATATGC
1 TTTATATGC
4987348 GAGCTATGCT
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
16 26 0.26
17 74 0.74
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (17 bp):
TTTATATGCAAGTTGTG
Found at i:4987265 original size:50 final size:50
Alignment explanation
Indices: 4987206--4987313 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
4987196 CGGCTATACT
* * * *
4987206 TTATATGCAAGTTGTGTTTATATGTGAGTTGTCTTTATATGTAAGTTATG
1 TTATATGCAAGTTGTATGTATATGCGAGTTGTCTTTATATGCAAGTTATG
*
4987256 TTATATGCAAGTTGTATGTATATGCGAGTTGTCTTTATATGCAAGTTGTG
1 TTATATGCAAGTTGTATGTATATGCGAGTTGTCTTTATATGCAAGTTATG
4987306 TTATATGC
1 TTATATGC
4987314 GAACTGAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.47
Consensus pattern (50 bp):
TTATATGCAAGTTGTATGTATATGCGAGTTGTCTTTATATGCAAGTTATG
Found at i:4987336 original size:50 final size:50
Alignment explanation
Indices: 4987206--4987347 Score: 137
Period size: 50 Copynumber: 2.8 Consensus size: 50
4987196 CGGCTATACT
* * * ** *
4987206 TTATATGCAAGTTGTGTTTATATGTGAGTTGTCTTTATATGTAAGTTATG
1 TTATATGCAAGCTGTATGTATATGCAAGTTGTCTTTATATGCAAGTTATG
* * *
4987256 TTATATGCAAGTTGTATGTATATGCGAGTTGTCTTTATATGCAAGTTGTG
1 TTATATGCAAGCTGTATGTATATGCAAGTTGTCTTTATATGCAAGTTATG
* *
4987306 TTATATGCGAA-CTG-AGTTTATCTGCAAGTTGAT-TTTATATGC
1 TTATATGC-AAGCTGTA-TGTATATGCAAGTTG-TCTTTATATGC
4987348 GAGCTATGCT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 76 0.95
51 3 0.04
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.46
Consensus pattern (50 bp):
TTATATGCAAGCTGTATGTATATGCAAGTTGTCTTTATATGCAAGTTATG
Found at i:4988914 original size:47 final size:47
Alignment explanation
Indices: 4988845--4988940 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
4988835 ATTTCCAAAA
*
4988845 GATAGATATATAAATGTAACTAACTGGACTAGCAGTACATCAAACAT
1 GATAGATATATAAATGTAACTAACTAGACTAGCAGTACATCAAACAT
4988892 GATAGATATATAAATGTAACTAACTAGACTAGCAGTACATCAAACAT
1 GATAGATATATAAATGTAACTAACTAGACTAGCAGTACATCAAACAT
4988939 GA
1 GA
4988941 CCCAAGTAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (47 bp):
GATAGATATATAAATGTAACTAACTAGACTAGCAGTACATCAAACAT
Found at i:4989145 original size:30 final size:30
Alignment explanation
Indices: 4989111--4989170 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4989101 ATACAAGTAC
4989111 TTCGTTACATGAATTTACTTACAATAGTGG
1 TTCGTTACATGAATTTACTTACAATAGTGG
4989141 TTCGTTACATGAATTTACTTACAATAGTGG
1 TTCGTTACATGAATTTACTTACAATAGTGG
4989171 AATTCATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (30 bp):
TTCGTTACATGAATTTACTTACAATAGTGG
Found at i:4995287 original size:50 final size:49
Alignment explanation
Indices: 4995221--4995318 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
4995211 TTTGGAATTC
* *
4995221 TGACTTCTGATATATAAAACATAAGGTAGAATACTTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATAC-ATTTGTTGGTAAAAT
* * *
4995271 TGACTTCTGGTGTATAAAACATAAGGAAGGATACATTTGTTGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTGTTGGTAAAA
4995319 AACTGACTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 13 0.30
50 30 0.70
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (49 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTGTTGGTAAAAT
Found at i:5003837 original size:24 final size:24
Alignment explanation
Indices: 5003810--5003861 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5003800 TGAGGGGATG
* *
5003810 TATTGAGAATCTTTGATTATTTGA
1 TATTGAGAATCTTTCATTATTTAA
5003834 TATTGAGAATCTTTCATTATTTAA
1 TATTGAGAATCTTTCATTATTTAA
5003858 TATT
1 TATT
5003862 ATTAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (24 bp):
TATTGAGAATCTTTCATTATTTAA
Found at i:5017761 original size:28 final size:27
Alignment explanation
Indices: 5017729--5017788 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
5017719 TATTCATATA
5017729 AATTATTTAACATAA-AATAAAAAATTTT
1 AATTATTTAA-A-AATAATAAAAAATTTT
**
5017757 AATTATTTAAAAATTTTAAAAAATTTT
1 AATTATTTAAAAATAATAAAAAATTTT
5017784 AATTA
1 AATTA
5017789 CCGAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 17 0.59
28 10 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTATTTAAAAATAATAAAAAATTTT
Found at i:5017852 original size:32 final size:33
Alignment explanation
Indices: 5017801--5017878 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
5017791 GAATTAATCG
* *
5017801 AATTAACTTAAAATTTTTAAAATT-TAA-AATTTA
1 AATTAAATT-AAATTTTT-AAATTCAAATAATTTA
5017834 AATTAAATTAAATTTTTAAATTCAAATAATTTA
1 AATTAAATTAAATTTTTAAATTCAAATAATTTA
*
5017867 AA-TAAATCAAAT
1 AATTAAATTAAAT
5017879 ACAAACTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 5 0.12
32 19 0.47
33 16 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTAAATTAAATTTTTAAATTCAAATAATTTA
Found at i:5017867 original size:23 final size:24
Alignment explanation
Indices: 5017816--5017869 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5017806 ACTTAAAATT
* *
5017816 TTTAAAATTTAAAATTTAAATTAA
1 TTTAAATTTTAAAATTCAAATTAA
* *
5017840 ATTAAATTTTTAAATTCAAA-TAA
1 TTTAAATTTTAAAATTCAAATTAA
5017863 TTTAAAT
1 TTTAAAT
5017870 AAATCAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAATTTTAAAATTCAAATTAA
Found at i:5017922 original size:7 final size:7
Alignment explanation
Indices: 5017912--5017945 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
5017902 TAAATTATAT
5017912 TCCCCAC
1 TCCCCAC
5017919 TCCCCAC
1 TCCCCAC
5017926 TCCCCAC
1 TCCCCAC
5017933 TCCCCAC
1 TCCCCAC
5017940 TCCCCA
1 TCCCCA
5017946 AGCCCAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.71, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCCAC
Found at i:5019502 original size:13 final size:14
Alignment explanation
Indices: 5019484--5019525 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5019474 TTTCAATTTT
5019484 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
5019497 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
5019512 ATTTTAAATAATAT
1 ATTTT-AATAATAT
5019526 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:5019510 original size:16 final size:16
Alignment explanation
Indices: 5019488--5019524 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5019478 AATTTTATTT
5019488 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5019505 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5019520 TAATA
1 TAATA
5019525 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5020867 original size:61 final size:61
Alignment explanation
Indices: 5020773--5020895 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
5020763 TCAGTTGTAA
5020773 AAAAAAAAAAAAAGAGAAAAAATATACGGAGATTGAATGCAAAGATCAGAGGTGATTTCAT
1 AAAAAAAAAAAAAGAGAAAAAATATACGGAGATTGAATGCAAAGATCAGAGGTGATTTCAT
5020834 AAAAAAAAAAAAAGAGAAAAAATATACGGAGATTGAATGCAAAGATCAGAGGTGATTTCAT
1 AAAAAAAAAAAAAGAGAAAAAATATACGGAGATTGAATGCAAAGATCAGAGGTGATTTCAT
5020895 A
1 A
5020896 CTTTTCTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (61 bp):
AAAAAAAAAAAAAGAGAAAAAATATACGGAGATTGAATGCAAAGATCAGAGGTGATTTCAT
Found at i:5022283 original size:13 final size:13
Alignment explanation
Indices: 5022265--5022289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5022255 GTTATTATTA
5022265 AACACATATTTAG
1 AACACATATTTAG
5022278 AACACATATTTA
1 AACACATATTTA
5022290 ATTTTTATTC
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:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
AACACATATTTAG
Found at i:5024417 original size:22 final size:21
Alignment explanation
Indices: 5024380--5024421 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5024370 TCTCGACAAT
5024380 AAAAATTATATTTTTATATTTC
1 AAAAATTATATTTTTA-ATTTC
5024402 AAAAATT-TATATTTTAATTT
1 AAAAATTATAT-TTTTAATTT
5024422 TAATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAAATTATATTTTTAATTTC
Found at i:5024571 original size:37 final size:37
Alignment explanation
Indices: 5024521--5024594 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5024511 GAGGTAGTGG
5024521 GTGCTAACCCTAAACCTCTCACATCAGCTAAATGGGA
1 GTGCTAACCCTAAACCTCTCACATCAGCTAAATGGGA
5024558 GTGCTAACCCTAAACCTCTCACATCAGCTAAATGGGA
1 GTGCTAACCCTAAACCTCTCACATCAGCTAAATGGGA
5024595 CTTTCTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (37 bp):
GTGCTAACCCTAAACCTCTCACATCAGCTAAATGGGA
Found at i:5031127 original size:18 final size:17
Alignment explanation
Indices: 5031104--5031146 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5031094 TTATATTTTT
5031104 TAAAAACATTAATTACT-A
1 TAAAAACATTAA-TA-TGA
*
5031122 TAAAAATATTAATATGA
1 TAAAAACATTAATATGA
5031139 TAAAAACA
1 TAAAAACA
5031147 ATTTCTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 10 0.45
18 11 0.50
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAAACATTAATATGA
Found at i:5033144 original size:9 final size:9
Alignment explanation
Indices: 5033132--5033188 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 9
5033122 TACATTGACC
5033132 ATTAAAAAT
1 ATTAAAAAT
5033141 ATTAAAAAATT
1 ATT-AAAAA-T
*
5033152 ATAAAAAAGT
1 ATTAAAAA-T
*
5033162 ATAAAAAAT
1 ATTAAAAAT
5033171 ATT--AAAT
1 ATTAAAAAT
5033178 ATTAAAAAT
1 ATTAAAAAT
5033187 AT
1 AT
5033189 ACAATCACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 7 0.17
9 12 0.29
10 19 0.46
11 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:5033158 original size:19 final size:18
Alignment explanation
Indices: 5033134--5033189 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
5033124 CATTGACCAT
5033134 TAAAAATATTAAAAAATTA
1 TAAAAATATTAAAAAA-TA
5033153 TAAAAA-AGTATAAAAAATA
1 TAAAAATA-T-TAAAAAATA
*
5033172 T-TAAATATT-AAAAATA
1 TAAAAATATTAAAAAATA
5033188 TA
1 TA
5033190 CAATCACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 8 0.25
17 1 0.03
18 5 0.16
19 11 0.34
20 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAATATTAAAAAATA
Found at i:5039562 original size:12 final size:12
Alignment explanation
Indices: 5039531--5039563 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
5039521 ATTGAGATAT
5039531 AAAAAATTTTAA
1 AAAAAATTTTAA
5039543 AAACAAATTTTAA
1 AAA-AAATTTTAA
5039556 AAAAAATT
1 AAAAAATT
5039564 AACCATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATTTTAA
Found at i:5040363 original size:3 final size:3
Alignment explanation
Indices: 5040324--5040352 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5040314 ACAAACCAAA
5040324 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5040353 CCCAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5053928 original size:45 final size:45
Alignment explanation
Indices: 5053866--5054057 Score: 138
Period size: 45 Copynumber: 4.3 Consensus size: 45
5053856 TGTCTCCTTG
* * *
5053866 AAGTTACAGTGGAGCAGATCGAAGACGACAAATCTTATCTTCCTG
1 AAGTTACAGTGAAGCAGATCGAAGACGACAAATCTTATCTCCCTA
** * * * *
5053911 AAGTTACAGTGAAGCAGATTTAAG-CCAC-CATCCTAGCTCCCTA
1 AAGTTACAGTGAAGCAGATCGAAGACGACAAATCTTATCTCCCTA
** * * * * ** * *
5053954 AAGTTGTAGTGTAGTAG-GCTGGAGATTACAGATCTTGTCTCCCTA
1 AAGTTACAGTGAAGCAGATC-GAAGACGACAAATCTTATCTCCCTA
* * * *
5053999 AAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTA
1 AAGTTACAGTGAAGCAGATCGAAGACGACAAATCTTATCTCCCTA
*
5054044 AAGTTGCAGTGAAG
1 AAGTTACAGTGAAG
5054058 TATATTTAAG
Statistics
Matches: 107, Mismatches: 36, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
43 25 0.23
44 5 0.05
45 76 0.71
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (45 bp):
AAGTTACAGTGAAGCAGATCGAAGACGACAAATCTTATCTCCCTA
Found at i:5054085 original size:133 final size:133
Alignment explanation
Indices: 5053850--5054498 Score: 872
Period size: 133 Copynumber: 4.9 Consensus size: 133
5053840 TTGGTTCTAC
* * * * *
5053850 AGATATTGTCTCCTTGAAGTTACAGTGGAGCAGATCGAAGACGACAAATCTTATCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTGAAGT
* * *
5053915 TACAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGTAGTAGGCTGGAGAT
66 TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
**
5053980 TAC
131 TGT
* * *
5053983 AGATCTTGTCTCCCTAAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTAAAGT
1 AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTGAAGT
* * * *
5054048 TGCAGTGAAGTATATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGAAGTGGGCTGAAGAT
66 TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
5054113 TGT
131 TGT
* * *
5054116 AGATCTTGTTTCCCTAAAGTTACAGTAGAGCAGATCGAAGACGGCGAATCTTGTC-TCTCTGAAG
1 AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTC-CTGAAG
* * * *
5054180 TTGCAGTGGAGCCGATTTAAGCCACCATCCTAACTTCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
65 TTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
5054245 TTGT
130 TTGT
* * *
5054249 AGATCTTGTTTTCCTGAAGTTGCAGTGGAGCAGATCGAAGATGG-AGAATCTTGTC-TCTCTGAA
1 AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCA-AATCTTGTCTTC-CTGAA
* * *
5054312 GTTGCAGTGGAGTAGATTTAAGCTACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
64 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
5054377 ATTGT
129 ATTGT
* * ** * * *
5054382 AGATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAACGGTGAATCTTATCTTCTTAAAGT
1 AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTGAAGT
* * * * *
5054447 TGCAGTGAAGCAGATTTAAGCCACTATCTTATCTCCCTGAAGTTGCAGTGGA
66 TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGA
5054499 ACAGATCGAA
Statistics
Matches: 460, Mismatches: 52, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
132 2 0.00
133 456 0.99
134 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (133 bp):
AGATCTTGTTTCCCTGAAGTTACAGTGGAGCAGATCGAAGACGGCAAATCTTGTCTTCCTGAAGT
TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
TGT
Found at i:5054269 original size:45 final size:43
Alignment explanation
Indices: 5054214--5054411 Score: 150
Period size: 45 Copynumber: 4.5 Consensus size: 43
5054204 CCATCCTAAC
* *
5054214 TTCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTT
1 TTCCTGAAGTTGCAGTGGAGTAGGCTGAAGA-TGTAGATCTTG-T
* * *
5054259 TTCCTGAAGTTGCAGTGGAGCA-GATCGAAGATGGAGAATCTTGT
1 TTCCTGAAGTTGCAGTGGAGTAGGCT-GAAGATGTAG-ATCTTGT
* ** * * * * *
5054303 CTCTCTGAAGTTGCAGTGGAGTAGATTTAAG--CTACCATCCTAGC
1 TTC-CTGAAGTTGCAGTGGAGTAGGCTGAAGATGTA-GAT-CTTGT
* * *
5054347 TCCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGT
1 TTCCTGAAGTTGCAGTGGAGTAGGCTGAAGA-TGTAGATCTTGT
5054391 TTCCCTGAAGTTGCAGTGGAG
1 TT-CCTGAAGTTGCAGTGGAG
5054412 CAGATCGAAA
Statistics
Matches: 114, Mismatches: 29, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
43 25 0.22
44 17 0.15
45 69 0.61
46 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (43 bp):
TTCCTGAAGTTGCAGTGGAGTAGGCTGAAGATGTAGATCTTGT
Found at i:5054433 original size:45 final size:45
Alignment explanation
Indices: 5054251--5054508 Score: 106
Period size: 45 Copynumber: 5.8 Consensus size: 45
5054241 AAGATTGTAG
* * *
5054251 ATCTTGTTTTCCTGAAGTTGCAGTGGAGCAGATCGAAGATGG-AGA
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAATGGTA-C
* * * ** *
5054296 ATCTTGTCTCTCTGAAGTTGCAGTGGAGTAGAT--TTAA-GCTACC
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAATGGTA-C
* * * * * * * * *
5054339 ATCCTAG-CTCCCTAAAGTTGTAGTGGAGTAG-GCTGAAGATTGTAG
1 AT-CTTGTTTCCCTGAAGTTGCAGTGGAGCAGATC-GAAAATGGTAC
*
5054384 ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAACGGTGA-
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAATGGT-AC
* * * * ** **
5054429 ATCTTATCTT-CTTAAAGTTGCAGTGAAGCAGAT--TTAA-GCCAC
1 ATCTTGT-TTCCCTGAAGTTGCAGTGGAGCAGATCGAAAATGGTAC
* * *
5054471 TATCTTATCTCCCTGAAGTTGCAGTGGAACAGATCGAA
1 -ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAA
5054509 GTTACAATCC
Statistics
Matches: 153, Mismatches: 45, Indels: 30
0.67 0.20 0.13
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 53 0.35
44 6 0.04
45 84 0.55
46 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
ATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAAATGGTAC
Found at i:5054575 original size:266 final size:266
Alignment explanation
Indices: 5053866--5054589 Score: 721
Period size: 266 Copynumber: 2.7 Consensus size: 266
5053856 TGTCTCCTTG
* * * * * *
5053866 AAGTTACAGTGGAGCAGATCGAAGACGACAAATCTTATCT-TCCTGAAGTTACAGTGAAGCAGAT
1 AAGTTACAGTAGAGCAGATCGAAAACGGCGAATCTTATCTCT-CTAAAGTTGCAGTGAAGCAGAT
* * * ** * *
5053930 TTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGTAGTAGGCTGGAGATTACAGATCTTGTCT-
65 TTAAGCCACCATCCTAACTCCCTAAAGTTGCAGTGGAACAGGCTGAAGATTACAGATCTT-CCTA
* * * * * *** * * ** * *
5053994 CCCTAAAGTTACAGTGGAGCAGATCGAAGACGGCA-AATCTTGTCT-TCCTAAAGTTGCAGTGAA
129 TCCTGAAGTTGCAATAGAGCAGATCGAA-AATACAGAACCATACCTCT-CTGAAGTTGCAGTGGA
* *
5054057 GTATATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGAAGTGGGCTGAAGATTGTAGATCT
192 GTAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGAAGTAGGCTGAAGATTGTAGATCT
5054122 TGTTTCCCTA
257 TGTTTCCCTA
* * * * *
5054132 AAGTTACAGTAGAGCAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGGAGCCGATT
1 AAGTTACAGTAGAGCAGATCGAAAACGGCGAATCTTATCTCTCTAAAGTTGCAGTGAAGCAGATT
* * ** ** ** *
5054197 TAAGCCACCATCCTAACTTCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTTTTC
66 TAAGCCACCATCCTAACTCCCTAAAGTTGCAGTGGAACAGGCTGAAGATTACAGATCTTCCTATC
* * * ** * * **
5054262 CTGAAGTTGCAGTGGAGCAGATCGAAGATGGAGAATCTTGTCTCTCTGAAGTTGCAGTGGAGTAG
131 CTGAAGTTGCAATAGAGCAGATCGAAAATACAGAACCATACCTCTCTGAAGTTGCAGTGGAGTAG
* *
5054327 ATTTAAGCTACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTT
196 ATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGAAGTAGGCTGAAGATTGTAGATCTTGTT
*
5054392 TCCCTG
261 TCCCTA
* * *
5054398 AAGTTGCAGTGGAGCAGATCGAAAACGGTGAATCTTATCT-TCTTAAAGTTGCAGTGAAGCAGAT
1 AAGTTACAGTAGAGCAGATCGAAAACGGCGAATCTTATCTCTC-TAAAGTTGCAGTGAAGCAGAT
* * * * *
5054462 TTAAGCCACTATCTTATCTCCCTGAAGTTGCAGTGGAACA-GATCGAAG-TTACA-ATCCTTACC
65 TTAAGCCACCATCCTAACTCCCTAAAGTTGCAGTGGAACAGGCT-GAAGATTACAGAT-CTT-CC
5054524 TAT-CTGAAGTTGCAATAGAGCAGGAT-GAAAATACACGAACCATACCTCTCTGAAGTTGCAGTG
127 TATCCTGAAGTTGCAATAGAGCA-GATCGAAAATACA-GAACCATACCTCTCTGAAGTTGCAGTG
5054587 GAG
190 GAG
5054590 CGTATTGAAG
Statistics
Matches: 388, Mismatches: 60, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
264 2 0.01
265 36 0.09
266 348 0.90
267 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (266 bp):
AAGTTACAGTAGAGCAGATCGAAAACGGCGAATCTTATCTCTCTAAAGTTGCAGTGAAGCAGATT
TAAGCCACCATCCTAACTCCCTAAAGTTGCAGTGGAACAGGCTGAAGATTACAGATCTTCCTATC
CTGAAGTTGCAATAGAGCAGATCGAAAATACAGAACCATACCTCTCTGAAGTTGCAGTGGAGTAG
ATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGAAGTAGGCTGAAGATTGTAGATCTTGTT
TCCCTA
Found at i:5055191 original size:18 final size:18
Alignment explanation
Indices: 5055158--5055193 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5055148 GCAAAAATTG
*
5055158 TATTTTTTTATTTCTTTT
1 TATTTTTTTATATCTTTT
*
5055176 TATTTTTTTCTATCTTTT
1 TATTTTTTTATATCTTTT
5055194 CGGCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (18 bp):
TATTTTTTTATATCTTTT
Found at i:5055383 original size:38 final size:37
Alignment explanation
Indices: 5055306--5055379 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
5055296 TTTCGAACGC
5055306 CATATGTTCTGCCTTTTTTTCTTCTGAAAATTGTTTT
1 CATATGTTCTGCCTTTTTTTCTTCTGAAAATTGTTTT
*
5055343 CATATGTTCTGCCTTTTTTTCTTCTGAAAATTATTTT
1 CATATGTTCTGCCTTTTTTTCTTCTGAAAATTGTTTT
5055380 TCATCTTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (37 bp):
CATATGTTCTGCCTTTTTTTCTTCTGAAAATTGTTTT
Found at i:5056109 original size:131 final size:131
Alignment explanation
Indices: 5055865--5056112 Score: 293
Period size: 131 Copynumber: 1.9 Consensus size: 131
5055855 CATTCTTTTA
* * * * * * *
5055865 AAAATCCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGT
1 AAAACCCTTCAAAACGAAGGCAATATTCAATATTTGGCAATTCGCGGAATCGTACCCTAACGTGC
** *
5055930 TGGGTTGCAATTTCTCGTTTGCTCAACGTAATCAAATGTCCCTTTAGAATTTCATTCATGTTTCC
66 TGGGTTGCAATTTCTCGTTTGCTCAAAATAATCAAATATCCCTTTAGAATTTCATTCATGTTTCC
5055995 T
131 T
* * * * *
5055996 AAAACCCTTCAAAACGAAGGTAATATTCAATGTTTGGTAATTCGGGGAATCGTACCCTATCGTGC
1 AAAACCCTTCAAAACGAAGGCAATATTCAATATTTGGCAATTCGCGGAATCGTACCCTAACGTGC
* ** *
5056061 TGGGTTGCGATTTC-CTGTTTG-TCCAAAATAATTGAATATTCCTTTAGAATTT
66 TGGGTTGCAATTTCTC-GTTTGCT-CAAAATAATCAAATATCCCTTTAGAATTT
5056113 TACTCATGCT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
130 2 0.02
131 94 0.98
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (131 bp):
AAAACCCTTCAAAACGAAGGCAATATTCAATATTTGGCAATTCGCGGAATCGTACCCTAACGTGC
TGGGTTGCAATTTCTCGTTTGCTCAAAATAATCAAATATCCCTTTAGAATTTCATTCATGTTTCC
T
Found at i:5061835 original size:43 final size:43
Alignment explanation
Indices: 5061787--5061924 Score: 206
Period size: 43 Copynumber: 3.2 Consensus size: 43
5061777 AAAAAACACT
*
5061787 GCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCTCACAAACGCC
1 GCTAAAGGTCATGGCCTTTAGAGGCGCTTTTCTCACAAACGCC
* *
5061830 GCTAAAGGTCATGGCCTTTAGTGGCGCTTTTAC-CACAAAAGCC
1 GCTAAAGGTCATGGCCTTTAGAGGCGCTTTT-CTCACAAACGCC
* * *
5061873 GTTAAAGGTCATGGCCTTTAGAGACGCTTTTCTCAAAAACGCC
1 GCTAAAGGTCATGGCCTTTAGAGGCGCTTTTCTCACAAACGCC
5061916 GCTAAAGGT
1 GCTAAAGGT
5061925 TATAAAATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.01
43 83 0.98
44 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (43 bp):
GCTAAAGGTCATGGCCTTTAGAGGCGCTTTTCTCACAAACGCC
Found at i:5062003 original size:36 final size:33
Alignment explanation
Indices: 5061925--5062004 Score: 81
Period size: 36 Copynumber: 2.3 Consensus size: 33
5061915 CGCTAAAGGT
* *
5061925 TATAAAATTAAAAAAAATAAAATATTATAAAGG
1 TATAAAAATAAAAAAAATAAAATATTATAAAGA
5061958 TCATGAAAAATATAAAAAAATAAAATTCATTATCAAA-A
1 T-AT-AAAAATA-AAAAAAATAAAA-T-ATTAT-AAAGA
5061996 TATAAAAAT
1 TATAAAAAT
5062005 TTTCTATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
33 1 0.03
34 2 0.05
35 6 0.15
36 18 0.46
37 3 0.08
38 6 0.15
39 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (33 bp):
TATAAAAATAAAAAAAATAAAATATTATAAAGA
Found at i:5066481 original size:9 final size:8
Alignment explanation
Indices: 5066425--5066460 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
5066415 AAATATAAAA
5066425 TTTTTAA-
1 TTTTTAAT
5066432 TTTTTAAT
1 TTTTTAAT
5066440 TTTTTAAT
1 TTTTTAAT
5066448 TTTTTAAT
1 TTTTTAAT
5066456 TTTTT
1 TTTTT
5066461 TAAATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTAAT
Found at i:5066485 original size:8 final size:8
Alignment explanation
Indices: 5066422--5066485 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
5066412 ATTAAATATA
5066422 AAATTTTT
1 AAATTTTT
5066430 -AATTTTT
1 AAATTTTT
*
5066437 AATTTTTT
1 AAATTTTT
*
5066445 AATTTTTT
1 AAATTTTT
*
5066453 AATTTTTTT
1 AA-ATTTTT
5066462 AAATATTTTT
1 -AA-ATTTTT
5066472 ATAATTTTT
1 A-AATTTTT
5066481 AAATT
1 AAATT
5066486 AACATATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
7 7 0.14
8 20 0.40
9 14 0.28
10 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
AAATTTTT
Found at i:5066801 original size:22 final size:22
Alignment explanation
Indices: 5066773--5066867 Score: 83
Period size: 21 Copynumber: 4.4 Consensus size: 22
5066763 GGGTTAGAGT
5066773 TTTAAGGGTTTATGATTTGAGA
1 TTTAAGGGTTTATGATTTGAGA
* * *
5066795 TTTAA-GGTTTAGGGTGTTGGGA
1 TTTAAGGGTTTATGAT-TTGAGA
* *
5066817 -TTAA-GGTTTATCATTTTTAG-
1 TTTAAGGGTTTATGA-TTTGAGA
5066837 TCTTAAGGGTTTATGATTTGAGA
1 T-TTAAGGGTTTATGATTTGAGA
5066860 TTT-AGGGT
1 TTTAAGGGT
5066868 CTGGTGTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
21 26 0.46
22 22 0.39
23 9 0.16
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.46
Consensus pattern (22 bp):
TTTAAGGGTTTATGATTTGAGA
Found at i:5066825 original size:65 final size:65
Alignment explanation
Indices: 5066730--5066863 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 65
5066720 GGGCTTGGGG
* * * * *
5066730 TTTAAGGATTGGGGTTTGGGTGTTAGGGTTTA-CGGGTTAGAGTTTTAAGGGTTTATGATTTGAG
1 TTTAAGGATTAGGGTTTGGGTATTAAGGTTTATC-AGTTAGAGTCTTAAGGGTTTATGATTTGAG
5066794 A
65 A
* * **
5066795 TTTAAGGTTTAGGGTGTTGGG-ATTAAGGTTTATCATTTTTAGTCTTAAGGGTTTATGATTTGAG
1 TTTAAGGATTAGGGT-TTGGGTATTAAGGTTTATCAGTTAGAGTCTTAAGGGTTTATGATTTGAG
5066859 A
65 A
5066860 TTTA
1 TTTA
5066864 GGGTCTGGTG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
65 52 0.90
66 6 0.10
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (65 bp):
TTTAAGGATTAGGGTTTGGGTATTAAGGTTTATCAGTTAGAGTCTTAAGGGTTTATGATTTGAGA
Found at i:5067684 original size:40 final size:40
Alignment explanation
Indices: 5067639--5067814 Score: 253
Period size: 40 Copynumber: 4.4 Consensus size: 40
5067629 AGAAAGCGCT
5067639 GCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCC
1 GCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCC
* *
5067679 GCTAATGCTCAGATCTTTAGCGGCACTTTCTTAAAAATGCC
1 GCTAATGCTC-GATCTTTAGCGGCGCTTTCTTAAAAACGCC
* * * *
5067720 GCTAGTCCTTGATCTTTAGTGGCGCTTTCTTAAAAACGCC
1 GCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCC
* *
5067760 GCTAATGCTCGATCTTTAGTGGCGCTTTCTAAAAAACGCC
1 GCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCC
* *
5067800 GCTAATACTCAATCT
1 GCTAATGCTCGATCT
5067815 ATTCGATTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 86 0.71
41 35 0.29
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (40 bp):
GCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCC
Found at i:5067744 original size:81 final size:80
Alignment explanation
Indices: 5067649--5067803 Score: 256
Period size: 81 Copynumber: 1.9 Consensus size: 80
5067639 GCTAATGCTC
*
5067649 GATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATCTTTAGCGGCACTTTCTTAAA
1 GATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTC-GATCTTTAGCGGCACTTTCTAAAA
*
5067714 AATGCCGCTAGTCCTT
65 AACGCCGCTAGTCCTT
* * *
5067730 GATCTTTAGTGGCGCTTTCTTAAAAACGCCGCTAATGCTCGATCTTTAGTGGCGCTTTCTAAAAA
1 GATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCGATCTTTAGCGGCACTTTCTAAAAA
5067795 ACGCCGCTA
66 ACGCCGCTA
5067804 ATACTCAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 30 0.43
81 39 0.57
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (80 bp):
GATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCGATCTTTAGCGGCACTTTCTAAAAA
ACGCCGCTAGTCCTT
Found at i:5071430 original size:15 final size:16
Alignment explanation
Indices: 5071407--5071446 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
5071397 TGAATTTATC
*
5071407 TAATAAATATAT-TTT
1 TAATTAATATATATTT
5071422 TAATTAATAT-TATTT
1 TAATTAATATATATTT
5071437 T-ATTAATATA
1 TAATTAATATA
5071447 CTAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTAATATATATTT
Found at i:5073508 original size:2 final size:2
Alignment explanation
Indices: 5073501--5073535 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5073491 GAGAAACACA
5073501 AT AT AT AT AT 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 AT AT AT AT AT A
5073536 CTACTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5075318 original size:31 final size:31
Alignment explanation
Indices: 5075280--5075341 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5075270 TTTTTTTGGG
* * *
5075280 TCTAATTTGATACATAAACTTGACACTTTTT
1 TCTAATTTCACACAGAAACTTGACACTTTTT
*
5075311 TCTAATTTCACACCGAAACTTGACACTTTTT
1 TCTAATTTCACACAGAAACTTGACACTTTTT
5075342 CTTAACTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (31 bp):
TCTAATTTCACACAGAAACTTGACACTTTTT
Found at i:5075602 original size:24 final size:23
Alignment explanation
Indices: 5075557--5075606 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
5075547 TATGTTTTTT
*
5075557 ATTTTATTTTATATGTTCAATTA
1 ATTTTATTTTATATATTCAATTA
* *
5075580 ATTTTAGTTTTATTTATTTAATTA
1 ATTTTA-TTTTATATATTCAATTA
5075604 ATT
1 ATT
5075607 GTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTATTTTATATATTCAATTA
Found at i:5077362 original size:22 final size:21
Alignment explanation
Indices: 5077322--5077362 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5077312 TAAAAAAAAT
* *
5077322 TACTATTTTTTGTTGTTTTAA
1 TACTATTTTTTATTATTTTAA
5077343 TACTATTTTTTTATTATTTT
1 TACTA-TTTTTTATTATTTT
5077363 CTCCCTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
TACTATTTTTTATTATTTTAA
Found at i:5078748 original size:17 final size:17
Alignment explanation
Indices: 5078726--5078761 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5078716 TTTGAAGGAG
5078726 GAAACAATGGCCACGAT
1 GAAACAATGGCCACGAT
5078743 GAAACAATGGCCACGAT
1 GAAACAATGGCCACGAT
5078760 GA
1 GA
5078762 TGACTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (17 bp):
GAAACAATGGCCACGAT
Found at i:5080945 original size:2 final size:2
Alignment explanation
Indices: 5080940--5080987 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
5080930 GCTACTGTCA
**
5080940 AT AT AT AT GC 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 AT AT
*
5080982 TT AT AT
1 AT AT AT
5080988 TAGTACAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5084582 original size:20 final size:19
Alignment explanation
Indices: 5084553--5084603 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5084543 ATATTTTATG
5084553 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATTAGATAT-T
*
5084572 ATTATTTTAATGAGATATT
1 ATTATTTTAATTAGATATT
5084591 -TTATTATTAATTA
1 ATTATT-TTAATTA
5084604 TTTAGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTATTTTAATTAGATATT
Found at i:5086541 original size:46 final size:46
Alignment explanation
Indices: 5086489--5086669 Score: 265
Period size: 46 Copynumber: 3.9 Consensus size: 46
5086479 GTGTACTCTA
* * *
5086489 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAGCC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
5086535 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
5086581 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * *
5086627 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGATACTATGGCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
5086670 TCATGTCAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 124 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:5088699 original size:2 final size:2
Alignment explanation
Indices: 5088692--5088721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5088682 GATTTACTTC
5088692 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
5088722 CAATAATATC
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):
AT
Found at i:5092548 original size:73 final size:74
Alignment explanation
Indices: 5092423--5092562 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 74
5092413 ATTGTCTCAG
* * * * *
5092423 GGTAAGTCACTTTTATAACCTTACCCTCAATTGGGAGTAGGCAATTGTTATCAATACCTTGTCAT
1 GGTAAGTCACTTTTATAACCTTACCATCAATTGGGAGAAAGAAATTGTTATCAATACCTTGCCAT
5092488 AACAAACAT
66 AACAAACAT
* ** *
5092497 GGTAGGTCAC-TTTATAACCTTACCATTGATTGGGGGAAAGAAATTGTTATCAATACCTTGCCAT
1 GGTAAGTCACTTTTATAACCTTACCATCAATTGGGAGAAAGAAATTGTTATCAATACCTTGCCAT
5092561 AA
66 AA
5092563 TAGACCTTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
73 48 0.84
74 9 0.16
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (74 bp):
GGTAAGTCACTTTTATAACCTTACCATCAATTGGGAGAAAGAAATTGTTATCAATACCTTGCCAT
AACAAACAT
Found at i:5093615 original size:23 final size:24
Alignment explanation
Indices: 5093576--5093620 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5093566 AGTAATTTTA
*
5093576 TATATTTTTATTTTTATGAAATAT
1 TATATTTTTATTATTATGAAATAT
5093600 TATA-TTTTATTATTATGAAAT
1 TATATTTTTATTATTATGAAAT
5093621 TACAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATATTTTTATTATTATGAAATAT
Found at i:5097759 original size:22 final size:20
Alignment explanation
Indices: 5097720--5097759 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5097710 CAAACCATAA
5097720 ATTAATCTTAGATTTAAATC
1 ATTAATCTTAGATTTAAATC
*
5097740 ATTAAGTCTTTGATATTAAA
1 ATTAA-TCTTAGAT-TTAAA
5097760 GATGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTAATCTTAGATTTAAATC
Found at i:5101090 original size:25 final size:25
Alignment explanation
Indices: 5101056--5101104 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5101046 AGAGGTATTA
*
5101056 TATTTGGAGTGTTTATGCTCGATTG
1 TATTTGGAGTGTCTATGCTCGATTG
5101081 TATTTGGAGTGTCTATGCTCGATT
1 TATTTGGAGTGTCTATGCTCGATT
5101105 TTAACACAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.10, G:0.27, T:0.47
Consensus pattern (25 bp):
TATTTGGAGTGTCTATGCTCGATTG
Found at i:5102511 original size:20 final size:20
Alignment explanation
Indices: 5102484--5102521 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5102474 TCAAGTTACA
*
5102484 ATTATATATAT-CAAAATCG
1 ATTATATAAATGCAAAATCG
5102503 ATTATTATAAATGCAAAAT
1 ATTA-TATAAATGCAAAAT
5102522 TGAATTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 6 0.38
21 6 0.38
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTATATAAATGCAAAATCG
Found at i:5109019 original size:12 final size:12
Alignment explanation
Indices: 5109002--5109027 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5108992 AAAATAGGGC
5109002 TTTAGCGGCGTT
1 TTTAGCGGCGTT
5109014 TTTAGCGGCGTT
1 TTTAGCGGCGTT
5109026 TT
1 TT
5109028 ATCAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:5109103 original size:41 final size:41
Alignment explanation
Indices: 5109060--5109383 Score: 490
Period size: 41 Copynumber: 7.9 Consensus size: 41
5109050 GTAAAACACA
* * *
5109060 GAGCAATAGCGGCG-TTTCTTGTTAAAATGCCGCTAAAAA-CA
1 GAGCAATAGCGGCGCTTTC--GGTAAAACGCCGCTAAAAACCG
* * *
5109101 GAGCAATAGAGGCGTTTTCGGTAAAACGCCGCTAAAAACTG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
* *
5109142 GAGAAATAGCGGTGCTTTCGGTAAAACGCCGCTAAAAACCG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
*
5109183 GAGAAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
5109224 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
*
5109265 GAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
* *
5109306 GAGAAATAGCGGCGCTTTCGGTAAAACGCCGCGAAAAACCG
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
* *
5109347 GAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
1 GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAA
5109384 GTCATATAAC
Statistics
Matches: 261, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
40 17 0.07
41 240 0.92
42 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.17
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCG
Found at i:5109469 original size:15 final size:16
Alignment explanation
Indices: 5109437--5109469 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5109427 ACTAATCTAT
*
5109437 AACCCCTAAAATACTA
1 AACCCCTAAAACACTA
5109453 AACCCCT-AAACACTA
1 AACCCCTAAAACACTA
5109468 AA
1 AA
5109470 ATATAACCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (16 bp):
AACCCCTAAAACACTA
Found at i:5110376 original size:19 final size:19
Alignment explanation
Indices: 5110348--5110409 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
5110338 ATTAGATTTA
5110348 AAAAACATTGATAAATAAAT
1 AAAAACATTGAT-AATAAAT
5110368 AAAAA-ATTGATAATAAAT
1 AAAAACATTGATAATAAAT
*
5110386 AAAAACATTGATAACAAAT
1 AAAAACATTGATAATAAAT
5110405 AAAAA
1 AAAAA
5110410 TGAAATACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 12 0.30
19 23 0.57
20 5 0.12
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAACATTGATAATAAAT
Found at i:5110454 original size:15 final size:15
Alignment explanation
Indices: 5110434--5110467 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5110424 AAAAATGAAA
*
5110434 TATGGGTTTATGGAT
1 TATGGGTTTAGGGAT
5110449 TATGGGTTTAGGGAT
1 TATGGGTTTAGGGAT
5110464 TATG
1 TATG
5110468 ATTTATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (15 bp):
TATGGGTTTAGGGAT
Found at i:5111057 original size:41 final size:40
Alignment explanation
Indices: 5111011--5111096 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
5111001 AAAAATTATA
* * * * *
5111011 AAAAAGTCAAATATTAGTGGCGTTTATGGTAAAAACGCCGC
1 AAAAAGT-AAACAATAGCGGCGTTTATGATAAAAACGCCAC
* *
5111052 AAAAAGTAAGCAATAGCGGCGTTTATTATAAAAACGCCAC
1 AAAAAGTAAACAATAGCGGCGTTTATGATAAAAACGCCAC
5111092 AAAAA
1 AAAAA
5111097 AATCAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 31 0.82
41 7 0.18
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (40 bp):
AAAAAGTAAACAATAGCGGCGTTTATGATAAAAACGCCAC
Found at i:5111592 original size:63 final size:62
Alignment explanation
Indices: 5111510--5111639 Score: 172
Period size: 63 Copynumber: 2.1 Consensus size: 62
5111500 CTTCCTTTAA
*
5111510 TTTTCAATCATCTTAAAATTTTAGA-AATTTTAATTTGGGTTTCTTATTTTCTATTTTATTAG
1 TTTTCAATCATCTTAAAATTTTAGATAATTTTAATTTGGGTTTCTTA-TTTCTATTATATTAG
* * ** **
5111572 TTTTCAATCGTCTTAGAAATTTTTGATTTTTTTTGTTTGGGTTTCTTATTTCTATTATATTAG
1 TTTTCAATCATCTTA-AAATTTTAGATAATTTTAATTTGGGTTTCTTATTTCTATTATATTAG
5111635 TTTTC
1 TTTTC
5111640 TAGTTTCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 14 0.24
63 28 0.47
64 17 0.29
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.59
Consensus pattern (62 bp):
TTTTCAATCATCTTAAAATTTTAGATAATTTTAATTTGGGTTTCTTATTTCTATTATATTAG
Found at i:5113638 original size:14 final size:14
Alignment explanation
Indices: 5113616--5113655 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
5113606 CAATATTCTT
5113616 GTAAAATATATGAA
1 GTAAAATATATGAA
*
5113630 GTAATATATATGAA
1 GTAAAATATATGAA
5113644 GTAAAATTATAT
1 GTAAAA-TATAT
5113656 TGTATACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (14 bp):
GTAAAATATATGAA
Found at i:5114026 original size:183 final size:183
Alignment explanation
Indices: 5113718--5114086 Score: 657
Period size: 183 Copynumber: 2.0 Consensus size: 183
5113708 GATATAGTTC
* *
5113718 CATGTGTCTATATTAGTGAATTAATGTTGTATATGTTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTCTATATTAGTGAATTAATGTTATATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
5113783 ACTATTGGTTCAACTGAAGCTGCCATTTAATCGTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCGTCGAATTAATATTTGGTACTGATATAGATAAA
5113848 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
* *
5113901 CATGTGTCTGTATTAGTGAATTAATGTTATATGTATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTCTATATTAGTGAATTAATGTTATATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
* * * *
5113966 GCTATTGGTTTAACTGAAGCTGCTATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCGTCGAATTAATATTTGGTACTGATATAGATAAA
*
5114031 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
5114084 CAT
1 CAT
5114087 CTGTTCTAGG
Statistics
Matches: 177, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 177 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (183 bp):
CATGTGTCTATATTAGTGAATTAATGTTATATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCGTCGAATTAATATTTGGTACTGATATAGATAAA
GTTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
Found at i:5114307 original size:15 final size:15
Alignment explanation
Indices: 5114287--5114315 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5114277 GGAGTAGACC
5114287 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
5114302 AGGTACGTTTTATT
1 AGGTACGTTTTATT
5114316 TCAAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:5115096 original size:24 final size:24
Alignment explanation
Indices: 5115069--5115136 Score: 111
Period size: 24 Copynumber: 2.8 Consensus size: 24
5115059 ATTATTATTG
*
5115069 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
5115093 AAATATTATTC-TCCGTTTTATCAC
1 AAATATTA-TCGTCCGTTTTATCAC
5115117 AAATATTATCGTCCGTTTTA
1 AAATATTATCGTCCGTTTTA
5115137 CCGTTTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:5115470 original size:9 final size:9
Alignment explanation
Indices: 5115458--5115578 Score: 118
Period size: 9 Copynumber: 13.6 Consensus size: 9
5115448 TATTTGATAT
*
5115458 CATAATTTA
1 CATAACTTA
5115467 CATAACTTA
1 CATAACTTA
* *
5115476 TATAACATA
1 CATAACTTA
*
5115485 TATAACTTA
1 CATAACTTA
5115494 CATAACTTA
1 CATAACTTA
* *
5115503 TATAACATA
1 CATAACTTA
5115512 CATAACTTA
1 CATAACTTA
* * *
5115521 TATAGCATA
1 CATAACTTA
5115530 CATAACTTA
1 CATAACTTA
*
5115539 TATAACTTA
1 CATAACTTA
* *
5115548 GATAA-ATA
1 CATAACTTA
*
5115556 TATAACTTA
1 CATAACTTA
5115565 CATAACTTA
1 CATAACTTA
5115574 CATAA
1 CATAA
5115579 TACTTAAATA
Statistics
Matches: 90, Mismatches: 21, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
8 6 0.07
9 84 0.93
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:5115480 original size:18 final size:18
Alignment explanation
Indices: 5115458--5115578 Score: 145
Period size: 18 Copynumber: 6.8 Consensus size: 18
5115448 TATTTGATAT
* *
5115458 CATAATTTACATAACTTA
1 CATAACTTATATAACTTA
* *
5115476 TATAACATATATAACTTA
1 CATAACTTATATAACTTA
*
5115494 CATAACTTATATAACATA
1 CATAACTTATATAACTTA
* *
5115512 CATAACTTATATAGCATA
1 CATAACTTATATAACTTA
5115530 CATAACTTATATAACTTA
1 CATAACTTATATAACTTA
* *
5115548 GATAA-ATATATAACTTA
1 CATAACTTATATAACTTA
*
5115565 CATAACTTACATAA
1 CATAACTTATATAA
5115579 TACTTAAATA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
17 15 0.17
18 72 0.83
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (18 bp):
CATAACTTATATAACTTA
Done.