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 11 of 182
Found at i:4275828 original size:27 final size:28
Alignment explanation
Indices: 4275762--4275829 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 28
4275752 TGTATATCAA
* * * * *
4275762 ATTTAATGTAAATTAAAATTTTATAATT
1 ATTTAATATATATAAAAACTTTATAATC
* *
4275790 ATTTATTTTATATAAAAACTTT-TAATC
1 ATTTAATATATATAAAAACTTTATAATC
4275817 ATTTAATATATAT
1 ATTTAATATATAT
4275830 TAATACAGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTAATATATATAAAAACTTTATAATC
Found at i:4293473 original size:3 final size:3
Alignment explanation
Indices: 4293465--4293522 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
4293455 ATTGGAGGAA
* * * *
4293465 CTG CTG CTG CTG TTG CTG CTG CTG CTG TTG TTG CTG TTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
4293513 CTG CTG CTG C
1 CTG CTG CTG C
4293523 AAAAGCATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.28, G:0.33, T:0.40
Consensus pattern (3 bp):
CTG
Found at i:4301959 original size:18 final size:19
Alignment explanation
Indices: 4301932--4301986 Score: 87
Period size: 18 Copynumber: 3.0 Consensus size: 19
4301922 CTCATCTCCT
4301932 TTAA-TTTTTCTCATTTAA
1 TTAATTTTTTCTCATTTAA
4301950 TT-ATTTTTTCTCATTTAA
1 TTAATTTTTTCTCATTTAA
*
4301968 TTAATCTTTTCTCATTTAA
1 TTAATTTTTTCTCATTTAA
4301987 AAATTTGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 1 0.03
18 18 0.53
19 15 0.44
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTTTTTCTCATTTAA
Found at i:4302573 original size:18 final size:17
Alignment explanation
Indices: 4302529--4302587 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
4302519 AATTAATTTG
* *
4302529 TAATTCAAATATTTATTG
1 TAATTTAAATATTT-TTA
4302547 TAGATTTAAATATTTTTA
1 TA-ATTTAAATATTTTTA
4302565 TTAATTTAAATATTTTTA
1 -TAATTTAAATATTTTTA
4302583 TAATT
1 TAATT
4302588 ATTATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.14
18 19 0.51
19 13 0.35
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (17 bp):
TAATTTAAATATTTTTA
Found at i:4303964 original size:14 final size:14
Alignment explanation
Indices: 4303932--4303965 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4303922 TTTTAAATAT
4303932 TTTTTATTTTTAAA
1 TTTTTATTTTTAAA
* *
4303946 GTTTTATTTTTGAA
1 TTTTTATTTTTAAA
4303960 TTTTTA
1 TTTTTA
4303966 AGAATCAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTATTTTTAAA
Found at i:4304653 original size:22 final size:22
Alignment explanation
Indices: 4304628--4304672 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4304618 TCTTCTTTGC
*
4304628 TTCAGATCT-TTTCATTTTTGTT
1 TTCAGATATATTTC-TTTTTGTT
*
4304650 TTCAGGTATATTTCTTTTTGTT
1 TTCAGATATATTTCTTTTTGTT
4304672 T
1 T
4304673 CCGAGTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.64
Consensus pattern (22 bp):
TTCAGATATATTTCTTTTTGTT
Found at i:4304685 original size:23 final size:22
Alignment explanation
Indices: 4304637--4304689 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
4304627 CTTCAGATCT
* *
4304637 TTTCATTTTTGTTTTCAGGTATA
1 TTTC-TTTTTGTTTCCAGGTAGA
*
4304660 TTTCTTTTTGTTTCCGAGTTAGA
1 TTTCTTTTTGTTTCC-AGGTAGA
4304683 TTTCTTT
1 TTTCTTT
4304690 GATTTTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.62
Consensus pattern (22 bp):
TTTCTTTTTGTTTCCAGGTAGA
Found at i:4305854 original size:72 final size:72
Alignment explanation
Indices: 4305760--4305992 Score: 439
Period size: 72 Copynumber: 3.2 Consensus size: 72
4305750 AACGCTCAGC
*
4305760 TGATCCGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
4305825 GCTTTGA
66 GCTTTGA
4305832 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
4305897 GCTTTGA
66 GCTTTGA
* *
4305904 TGATCAGGTGAAAAAGAAGAGTTCAAATGACGATTCCCCGAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
4305969 GCTTTGA
66 GCTTTGA
4305976 TGATCAGGTGAAAAAGA
1 TGATCAGGTGAAAAAGA
4305993 GCTCAAATGA
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 158 1.00
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (72 bp):
TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
GCTTTGA
Found at i:4313818 original size:2 final size:2
Alignment explanation
Indices: 4313811--4313835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4313801 AAAGAAAAGA
4313811 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4313836 AAACCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4316157 original size:2 final size:2
Alignment explanation
Indices: 4316150--4316178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4316140 ATTTTAATAA
4316150 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 A
4316179 AAGGATGTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4328751 original size:16 final size:17
Alignment explanation
Indices: 4328720--4328753 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
4328710 TTTAAAAATG
4328720 GTTCCTTTCCTGGCAATT
1 GTTCCTTT-CTGGCAATT
4328738 GTTCCTTT-TGGCAATT
1 GTTCCTTTCTGGCAATT
4328754 TTTATATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (17 bp):
GTTCCTTTCTGGCAATT
Found at i:4333056 original size:17 final size:18
Alignment explanation
Indices: 4333034--4333067 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4333024 ACAATATTTT
4333034 TTAAAAA-TATTTTTGAG
1 TTAAAAATTATTTTTGAG
4333051 TTAAAAATTATTTTTGA
1 TTAAAAATTATTTTTGA
4333068 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTAAAAATTATTTTTGAG
Found at i:4333136 original size:17 final size:18
Alignment explanation
Indices: 4333114--4333148 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4333104 AAATATTTTT
*
4333114 CCAAAA-TATTTTTGAAA
1 CCAAAAGTAATTTTGAAA
4333131 CCAAAAGTAATTTTGAAA
1 CCAAAAGTAATTTTGAAA
4333149 AATTCAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (18 bp):
CCAAAAGTAATTTTGAAA
Found at i:4333214 original size:17 final size:17
Alignment explanation
Indices: 4333172--4333216 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
4333162 TTTGTTTAGT
* *
4333172 AATATTTTTATCTCAAA
1 AATATTTTTGTCCCAAA
*
4333189 AGTACTTTTTGTCCCAAA
1 AATA-TTTTTGTCCCAAA
4333207 AATATTTTTG
1 AATATTTTTG
4333217 AGAAGTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (17 bp):
AATATTTTTGTCCCAAA
Found at i:4337653 original size:21 final size:22
Alignment explanation
Indices: 4337627--4337669 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4337617 AGCACAAAAA
*
4337627 AATGTTTTTTTTTTGTT-TTTT
1 AATGTTATTTTTTTGTTGTTTT
4337648 AATGTTATTTTTTTGTTGTTTT
1 AATGTTATTTTTTTGTTGTTTT
4337670 CTCCCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (22 bp):
AATGTTATTTTTTTGTTGTTTT
Found at i:4337785 original size:30 final size:30
Alignment explanation
Indices: 4337751--4337812 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
4337741 ACTTATTTTA
*
4337751 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
*
4337781 TTGTTAATTTTGTTACTATTTTAGATGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
4337811 TT
1 TT
4337813 ATTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGGCAT
Found at i:4339467 original size:18 final size:19
Alignment explanation
Indices: 4339444--4339486 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4339434 GAATAAAATT
4339444 TTAATTAAATAAATTT-AA
1 TTAATTAAATAAATTTAAA
* *
4339462 TTAATT-GATAATTTTAAA
1 TTAATTAAATAAATTTAAA
4339480 TTAATTA
1 TTAATTA
4339487 CAATTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATTAAATAAATTTAAA
Found at i:4339685 original size:31 final size:28
Alignment explanation
Indices: 4339617--4339671 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4339607 AACGATAACG
*
4339617 TAAGTGACTAAAATGTAAATTTCAAACA
1 TAAGTGACTAAAATGTAAATCTCAAACA
*
4339645 TAAGTGACTAAAATGTAAA-CTGAAACA
1 TAAGTGACTAAAATGTAAATCTCAAACA
4339672 AATAAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (28 bp):
TAAGTGACTAAAATGTAAATCTCAAACA
Found at i:4344148 original size:22 final size:22
Alignment explanation
Indices: 4344120--4344164 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4344110 TTATGCTGAT
*
4344120 TCATAGAGCTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
4344142 TCATAGAACTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
4344164 T
1 T
4344165 TTGTTTTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.33
Consensus pattern (22 bp):
TCATAGAACTGATTTGTAGGGA
Found at i:4352065 original size:35 final size:35
Alignment explanation
Indices: 4352019--4352097 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
4352009 TATTTTATAC
* *
4352019 TTAATTTTTATGGTGCTTTATGATTATCCTGCCCA
1 TTAATTTTTATGGTGCATTATGATTACCCTGCCCA
*
4352054 TTAATTTTTATGTTGCATTATGATTACCCTGCCCA
1 TTAATTTTTATGGTGCATTATGATTACCCTGCCCA
4352089 TTAATTTTT
1 TTAATTTTT
4352098 TTCATGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (35 bp):
TTAATTTTTATGGTGCATTATGATTACCCTGCCCA
Found at i:4353290 original size:2 final size:2
Alignment explanation
Indices: 4353283--4353307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4353273 GTTTCATTTT
4353283 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 T
4353308 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4357967 original size:16 final size:14
Alignment explanation
Indices: 4357932--4357971 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
4357922 GTTTTCATGG
4357932 TTAATTTAATAAAAA
1 TTAA-TTAATAAAAA
4357947 TTAATTAATAAAATTA
1 TTAATTAATAAAA--A
4357963 TTAATTAAT
1 TTAATTAAT
4357972 TAAGAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATTAATAAAAA
Found at i:4362599 original size:147 final size:147
Alignment explanation
Indices: 4362390--4362688 Score: 598
Period size: 147 Copynumber: 2.0 Consensus size: 147
4362380 ATTTATCAGA
4362390 AATGGGGATTACTCTTTCTAGAAATTCTTAATTGCCTGTTGGGAAGCCAGAATTGGGTGAAAGAA
1 AATGGGGATTACTCTTTCTAGAAATTCTTAATTGCCTGTTGGGAAGCCAGAATTGGGTGAAAGAA
4362455 TTTGGATTCAAATTATTTGTTTGGATATCCAATACAAAAATAGATTTGGATTTGAGTAAATTCAA
66 TTTGGATTCAAATTATTTGTTTGGATATCCAATACAAAAATAGATTTGGATTTGAGTAAATTCAA
4362520 TTTTAAGTGATAAATTT
131 TTTTAAGTGATAAATTT
4362537 AATGGGGATTACTCTTTCTAGAAATTCTTAATTGCCTGTTGGGAAGCCAGAATTGGGTGAAAGAA
1 AATGGGGATTACTCTTTCTAGAAATTCTTAATTGCCTGTTGGGAAGCCAGAATTGGGTGAAAGAA
4362602 TTTGGATTCAAATTATTTGTTTGGATATCCAATACAAAAATAGATTTGGATTTGAGTAAATTCAA
66 TTTGGATTCAAATTATTTGTTTGGATATCCAATACAAAAATAGATTTGGATTTGAGTAAATTCAA
4362667 TTTTAAGTGATAAATTT
131 TTTTAAGTGATAAATTT
4362684 AATGG
1 AATGG
4362689 CAAAAGATTT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 152 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (147 bp):
AATGGGGATTACTCTTTCTAGAAATTCTTAATTGCCTGTTGGGAAGCCAGAATTGGGTGAAAGAA
TTTGGATTCAAATTATTTGTTTGGATATCCAATACAAAAATAGATTTGGATTTGAGTAAATTCAA
TTTTAAGTGATAAATTT
Found at i:4365682 original size:241 final size:241
Alignment explanation
Indices: 4365259--4365741 Score: 912
Period size: 241 Copynumber: 2.0 Consensus size: 241
4365249 TCGTGGGGGG
*
4365259 ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTAAA
1 ACTGTGAGTAGCGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTAAA
*
4365324 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
66 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTCAGGATGGGAACCTCATAATAATTTTTGACA
*
4365389 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
131 ATGGCTCCAAATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
4365454 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
196 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
*
4365500 ACTGTGAGTAGCGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
1 ACTGTGAGTAGCGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTAAA
4365565 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTCAGGATGGGAACCTCATAATAATTTTTGACA
66 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTCAGGATGGGAACCTCATAATAATTTTTGACA
4365630 ATGGCTCCAAATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
131 ATGGCTCCAAATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
* *
4365695 ATTGAAGTAATGCCATAACAGCAACTTGAGTTACTAGTAGCTACAA
196 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
4365741 A
1 A
4365742 TACTGGATTT
Statistics
Matches: 236, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 236 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (241 bp):
ACTGTGAGTAGCGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTAAA
ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTCAGGATGGGAACCTCATAATAATTTTTGACA
ATGGCTCCAAATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
Found at i:4371289 original size:15 final size:15
Alignment explanation
Indices: 4371269--4371309 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
4371259 ACTTCAACAC
4371269 ATTTTTTTAAGAAT-T
1 ATTTTTTTAA-AATAT
4371284 A-TTTTTTAAAATAT
1 ATTTTTTTAAAATAT
4371298 ATGTTTTTTAAA
1 AT-TTTTTTAAA
4371310 TTGATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 10 0.43
15 1 0.04
16 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (15 bp):
ATTTTTTTAAAATAT
Found at i:4374820 original size:15 final size:16
Alignment explanation
Indices: 4374790--4374832 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4374780 TAATAAAAAT
4374790 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
4374807 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
4374822 ATAATTT-TTAT
1 ATAATTTATTAT
4374833 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 16 0.67
16 4 0.17
17 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:4374821 original size:24 final size:24
Alignment explanation
Indices: 4374789--4374834 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4374779 ATAATAAAAA
*
4374789 TATAATTTTATTATTTTAATAATT
1 TATAATTTTATAATTTTAATAATT
* *
4374813 TATATTTTTATAATTTTTATAA
1 TATAATTTTATAATTTTAATAA
4374835 AATAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATAATTTTATAATTTTAATAATT
Found at i:4374849 original size:24 final size:23
Alignment explanation
Indices: 4374822--4374872 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4374812 TTATATTTTT
*
4374822 ATAATTTTTATAAAATAAAATAAA
1 ATAATTATTATAAAA-AAAATAAA
**
4374846 ATAATTATTATTTAAAAAATAAA
1 ATAATTATTATAAAAAAAATAAA
4374869 ATAA
1 ATAA
4374873 AATTTTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATTATTATAAAAAAAATAAA
Found at i:4381776 original size:12 final size:12
Alignment explanation
Indices: 4381754--4381782 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4381744 CGAATGACCT
4381754 TAAAA-TAATAA
1 TAAAATTAATAA
4381765 TAAAATTAATAA
1 TAAAATTAATAA
4381777 TAAAAT
1 TAAAAT
4381783 AAAGAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:4385644 original size:51 final size:50
Alignment explanation
Indices: 4385539--4385645 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 50
4385529 AAATTTTCTG
* * * * *
4385539 AAATTTTAATTAGGCCTCTCAAATTTTTGAAAATTATTATTAAACCTTTG
1 AAATTTCAATTAGACCTCTCAAATTTTTGAAAATTATTATAAAACCTCTA
*
4385589 AAATTTCAATTAGA-CTCTTCAAATTTTTTGTAAATT-TTCATAAAACCTCTA
1 AAATTTCAATTAGACCTC-TCAAA-TTTTTGAAAATTATT-ATAAAACCTCTA
4385640 AAATTT
1 AAATTT
4385646 TGAAAGTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
49 3 0.06
50 19 0.40
51 26 0.54
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (50 bp):
AAATTTCAATTAGACCTCTCAAATTTTTGAAAATTATTATAAAACCTCTA
Found at i:4385917 original size:19 final size:19
Alignment explanation
Indices: 4385893--4385932 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4385883 CTGAGAACTG
4385893 AATAGTTAAGCAATATTAT
1 AATAGTTAAGCAATATTAT
4385912 AATAGTTAAGCAATATTAT
1 AATAGTTAAGCAATATTAT
4385931 AA
1 AA
4385933 CAACCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (19 bp):
AATAGTTAAGCAATATTAT
Found at i:4397345 original size:20 final size:21
Alignment explanation
Indices: 4397320--4397361 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4397310 AAAAAAAATC
4397320 AAATTCAA-ATGAAATTGTTG
1 AAATTCAAGATGAAATTGTTG
4397340 AAATTCAAGATGAAATTGTTG
1 AAATTCAAGATGAAATTGTTG
4397361 A
1 A
4397362 TGTGGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATTCAAGATGAAATTGTTG
Found at i:4414395 original size:21 final size:19
Alignment explanation
Indices: 4414358--4414396 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4414348 TTTTAAAAAA
*
4414358 TATAAAATTTGATTTTTTT
1 TATAAAATTTGAATTTTTT
4414377 TATAAATATTTTGAATTTTT
1 TATAAA-A-TTTGAATTTTT
4414397 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATAAAATTTGAATTTTTT
Found at i:4416452 original size:18 final size:18
Alignment explanation
Indices: 4416429--4416466 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4416419 TTTTTTAAAA
4416429 TATAAAT-TTTGAAATTTT
1 TATAAATATTTG-AATTTT
4416447 TATAAATAGTTTGAATTTT
1 TATAAATA-TTTGAATTTT
4416466 T
1 T
4416467 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:4416485 original size:9 final size:9
Alignment explanation
Indices: 4416460--4416486 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4416450 AAATAGTTTG
4416460 AATTTTTTT
1 AATTTTTTT
4416469 AATTTTTTT
1 AATTTTTTT
4416478 AATTTTTTT
1 AATTTTTTT
4416487 GTAATTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
AATTTTTTT
Found at i:4418754 original size:23 final size:22
Alignment explanation
Indices: 4418700--4418755 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
4418690 AAATTTTATT
*
4418700 ATATTTAAAAAATTAACCAATA
1 ATATTAAAAAAATTAACCAATA
* *
4418722 CTTTTCAAAAAAATTAACCAATAA
1 ATATT-AAAAAAATTAACCAAT-A
4418746 ATATTAAAAA
1 ATATTAAAAA
4418756 TTTATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
ATATTAAAAAAATTAACCAATA
Found at i:4419294 original size:17 final size:17
Alignment explanation
Indices: 4419272--4419313 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
4419262 CTCTCTTGAC
*
4419272 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
4419289 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
4419306 CTTGTAAC
1 CTT-TAAC
4419314 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:4419297 original size:24 final size:24
Alignment explanation
Indices: 4419249--4419299 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
4419239 TAAATGAATG
*
4419249 TTTAACATTTCATCTCTCTTGACC
1 TTTAACATTTCATCTCTCTTAACC
*
4419273 TTTAACCTTTCATCT-TCTTTAACC
1 TTTAACATTTCATCTCTC-TTAACC
4419297 TTT
1 TTT
4419300 CATATTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.20, C:0.27, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTAACATTTCATCTCTCTTAACC
Found at i:4426484 original size:29 final size:30
Alignment explanation
Indices: 4426441--4426521 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
4426431 AAATTGGATC
*
4426441 AAATCAAATTTTCATGTATAAAATTACACA-
1 AAATCAAA-ATTCATGTATAAAATTACACAT
* *
4426471 AAATCAAAATTCATGTATACAATTGCACATT
1 AAATCAAAATTCATGTATAAAATTACACA-T
*
4426502 AAATCATAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
4426522 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 18 0.41
30 8 0.18
31 18 0.41
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTACACAT
Found at i:4428019 original size:14 final size:14
Alignment explanation
Indices: 4427990--4428030 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
4427980 AACTTTTTAA
4427990 ATATATATATA-T-
1 ATATATATATATTC
4428002 ATATATATATATTC
1 ATATATATATATTC
* *
4428016 ATATGTATATTTTC
1 ATATATATATATTC
4428030 A
1 A
4428031 AAGTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 13 0.52
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATATATATATTC
Found at i:4441007 original size:17 final size:15
Alignment explanation
Indices: 4440965--4441007 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4440955 TTGTTTGAAA
*
4440965 TTTATATTTATATTT
1 TTTATATTTTTATTT
*
4440980 TTTATAATTTTATTT
1 TTTATATTTTTATTT
4440995 TATTCATATTTTT
1 T-TT-ATATTTTT
4441008 CCTAGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
16 2 0.09
17 7 0.30
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATATTTTTATTT
Found at i:4441061 original size:2 final size:2
Alignment explanation
Indices: 4441056--4441100 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4441046 ATTTTTTAAT
4441056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4441098 TA T
1 TA T
4441101 GAGATTTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4446118 original size:16 final size:16
Alignment explanation
Indices: 4446097--4446132 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4446087 AATCCATATA
4446097 TTTACAACATCCATTT
1 TTTACAACATCCATTT
* *
4446113 TTTACAATATTCATTT
1 TTTACAACATCCATTT
4446129 TTTA
1 TTTA
4446133 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTACAACATCCATTT
Found at i:4446810 original size:20 final size:19
Alignment explanation
Indices: 4446787--4446846 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
4446777 TCATATCAGC
4446787 AAATTATTTTAAAATTATCA
1 AAATTATTTTAAAATTAT-A
*
4446807 AAATTATTTTTTTAAA-TATA
1 AAATTA--TTTTAAAATTATA
*
4446827 AAACTATTTTAAAATTATA
1 AAATTATTTTAAAATTATA
4446846 A
1 A
4446847 TAATCATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 7 0.21
19 5 0.15
20 12 0.35
21 3 0.09
22 7 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTATTTTAAAATTATA
Found at i:4450439 original size:31 final size:30
Alignment explanation
Indices: 4450403--4450476 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
4450393 TTAATGACTC
*
4450403 AATAATTAAAATATTAAAATATATTAATTA-A
1 AATAATTAAAATATTAAAAT-T-TTAAATATA
4450434 AATAATTAAAATA-TAAAATTTTAAATATA
1 AATAATTAAAATATTAAAATTTTAAATATA
*
4450463 AATAACTAAAATAT
1 AATAATTAAAATAT
4450477 AATCTGAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 6 0.15
29 14 0.36
30 6 0.15
31 13 0.33
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
AATAATTAAAATATTAAAATTTTAAATATA
Found at i:4450441 original size:23 final size:22
Alignment explanation
Indices: 4450405--4450448 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
4450395 AATGACTCAA
4450405 TAATTAAAATATTAAAATATAT
1 TAATTAAAATATTAAAATATAT
4450427 TAATTAAAATAATTAAAATATA
1 TAATTAAAAT-ATTAAAATATA
4450449 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATTAAAATATTAAAATATAT
Found at i:4450460 original size:23 final size:23
Alignment explanation
Indices: 4450406--4450453 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
4450396 ATGACTCAAT
*
4450406 AATTAAAAT-ATTAAAATATATT
1 AATTAAAATAATTAAAATATATA
4450428 AATTAAAATAATTAAAATATA-A
1 AATTAAAATAATTAAAATATATA
4450450 AATT
1 AATT
4450454 TTAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTAAAATAATTAAAATATATA
Found at i:4450474 original size:15 final size:15
Alignment explanation
Indices: 4450403--4450478 Score: 68
Period size: 14 Copynumber: 5.1 Consensus size: 15
4450393 TTAATGACTC
4450403 AATAATTAAAATATTAA
1 AATAATTAAAATA-T-A
*
4450420 AATATATT-AATTA-A
1 AATA-ATTAAAATATA
4450434 AATAATTAAAATATA
1 AATAATTAAAATATA
* *
4450449 AA-ATTTTAAATATA
1 AATAATTAAAATATA
*
4450463 AATAACTAAAATATA
1 AATAATTAAAATATA
4450478 A
1 A
4450479 TCTGAGTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 3 0.06
14 21 0.44
15 13 0.27
17 8 0.17
18 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATTAAAATATA
Found at i:4453010 original size:16 final size:16
Alignment explanation
Indices: 4452971--4453011 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4452961 GTTATAAAAA
4452971 TATAATTTTATTATTT
1 TATAATTTTATTATTT
4452987 TA-ATATTTTA-TATCTT
1 TATA-ATTTTATTAT-TT
4453003 TATAATTTT
1 TATAATTTT
4453012 TAAAAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.18
16 17 0.77
17 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATAATTTTATTATTT
Found at i:4455743 original size:19 final size:19
Alignment explanation
Indices: 4455719--4455758 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4455709 GCAACTTTTT
4455719 ATTTCCACTACCATAGTCC
1 ATTTCCACTACCATAGTCC
4455738 ATTTCCACTACCATAGTCC
1 ATTTCCACTACCATAGTCC
4455757 AT
1 AT
4455759 AAAGCTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTTCCACTACCATAGTCC
Found at i:4462308 original size:16 final size:16
Alignment explanation
Indices: 4462265--4462310 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
4462255 GTTAATTCGG
* * *
4462265 TAATTATTTGCTAACA
1 TAATTGTTTGCCAAAA
4462281 TAATTG-TTGCCAAAA
1 TAATTGTTTGCCAAAA
4462296 TAATTGTTTGCCAAA
1 TAATTGTTTGCCAAA
4462311 GAAATCTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (16 bp):
TAATTGTTTGCCAAAA
Found at i:4462684 original size:6 final size:6
Alignment explanation
Indices: 4462676--4462714 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4462666 AACTCTCGCT
* * *
4462676 CTCTTT CTCTTT CCCTTG CTCTTG CTCTTG CTCTTG CTC
1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTC
4462715 CACCGTCCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.38, G:0.10, T:0.51
Consensus pattern (6 bp):
CTCTTG
Found at i:4465243 original size:24 final size:25
Alignment explanation
Indices: 4465189--4465246 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
4465179 AATTTTAAAA
*
4465189 AAAATTATTAAATCATTTAAAAGTT
1 AAAATTATTAAATCATTAAAAAGTT
** * *
4465214 TTAATT-TTAAATTATTAAAATGTT
1 AAAATTATTAAATCATTAAAAAGTT
4465238 AAAATTATT
1 AAAATTATT
4465247 GTTATACGGT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
AAAATTATTAAATCATTAAAAAGTT
Found at i:4465584 original size:28 final size:28
Alignment explanation
Indices: 4465518--4465584 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
4465508 AAATAAACCA
4465518 TTTTGAATATTTTAATAATTTAATTGAAAT
1 TTTTGAA-A-TTTAATAATTTAATTGAAAT
* * *
4465548 TTTTAAAATTTAATAATTT-TTTGTAATT
1 TTTTGAAATTTAATAATTTAATTG-AAAT
4465576 TTTTGAAAT
1 TTTTGAAAT
4465585 AAAGTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.09
28 22 0.69
29 1 0.03
30 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTTGAAATTTAATAATTTAATTGAAAT
Found at i:4473029 original size:25 final size:26
Alignment explanation
Indices: 4472990--4473039 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
4472980 TGTACAATCT
*
4472990 ATATTGAAATAAATATTAAATTTATA
1 ATATTCAAATAAATATTAAATTTATA
4473016 ATATTCAAA-AAATATTAAATTTAT
1 ATATTCAAATAAATATTAAATTTAT
4473040 GTATATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATTCAAATAAATATTAAATTTATA
Found at i:4473045 original size:26 final size:26
Alignment explanation
Indices: 4472989--4473051 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
4472979 ATGTACAATC
*
4472989 TATATTGAAATAAATATTAAATTTAT
1 TATATTCAAATAAATATTAAATTTAT
*
4473015 AATATTCAAA-AAATATTAAATTTAT
1 TATATTCAAATAAATATTAAATTTAT
*
4473040 GTATATACAAAT
1 -TATATTCAAAT
4473052 CTTTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (26 bp):
TATATTCAAATAAATATTAAATTTAT
Found at i:4473660 original size:22 final size:24
Alignment explanation
Indices: 4473617--4473666 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
4473607 ATTGATTCAC
* *
4473617 AAATAAAGTAATATTTTTTAACA-
1 AAATAAAATAATATTTTATAACAT
4473640 AAATAAAATAATA-TTTATAACAT
1 AAATAAAATAATATTTTATAACAT
4473663 AAAT
1 AAAT
4473667 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATAAAATAATATTTTATAACAT
Found at i:4481477 original size:20 final size:20
Alignment explanation
Indices: 4481452--4481517 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
4481442 TATCTAAATA
4481452 TTGGTAAATCTTTAGATATT
1 TTGGTAAATCTTTAGATATT
* *
4481472 TTGGTAAAGT-TTTAGAAATA
1 TTGGTAAA-TCTTTAGATATT
*
4481492 TTGGTAAATCCTTAGATATT
1 TTGGTAAATCTTTAGATATT
4481512 TTGGTA
1 TTGGTA
4481518 GAAGCTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
TTGGTAAATCTTTAGATATT
Found at i:4481491 original size:40 final size:42
Alignment explanation
Indices: 4481447--4481526 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 42
4481437 CAAAATATCT
*
4481447 AAATATTGGTAAATCTTTAGATATTTTGGTA-AAG-TTTTAG
1 AAATATTGGTAAATCCTTAGATATTTTGGTAGAAGCTTTTAG
4481487 AAATATTGGTAAATCCTTAGATATTTTGGTAGAAGCTTTT
1 AAATATTGGTAAATCCTTAGATATTTTGGTAGAAGCTTTT
4481527 CCTAAGCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 30 0.81
41 3 0.08
42 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (42 bp):
AAATATTGGTAAATCCTTAGATATTTTGGTAGAAGCTTTTAG
Found at i:4491645 original size:29 final size:29
Alignment explanation
Indices: 4491582--4491647 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
4491572 AAAATTTTAA
*
4491582 TTTAATAATGATAAAATTGTATTTTAACCC
1 TTTAA-AATGATAAAATTGTAATTTAACCC
* * *
4491612 CTTAAAATGATAATAATT-TAATTTAATCT
1 TTTAAAATGATAA-AATTGTAATTTAACCC
4491641 TTTAAAA
1 TTTAAAA
4491648 AATATAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTAAAATGATAAAATTGTAATTTAACCC
Found at i:4493834 original size:21 final size:21
Alignment explanation
Indices: 4493782--4493834 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
4493772 AAATATATAT
* *
4493782 AATATATCAAATATACTTAAA
1 AATATAACAAATAAACTTAAA
*
4493803 AATATTA-AAATAAACATTAAA
1 AATATAACAAATAAAC-TTAAA
4493824 AATA-AACAAAT
1 AATATAACAAAT
4493835 TTAAAATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
AATATAACAAATAAACTTAAA
Found at i:4494774 original size:9 final size:9
Alignment explanation
Indices: 4494760--4494786 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4494750 TTAGGGAAAT
4494760 GAGGAGGGA
1 GAGGAGGGA
4494769 GAGGAGGGA
1 GAGGAGGGA
4494778 GAGGAGGGA
1 GAGGAGGGA
4494787 TTGAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (9 bp):
GAGGAGGGA
Found at i:4504760 original size:17 final size:18
Alignment explanation
Indices: 4504726--4504761 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4504716 TGTTTTTCAG
*
4504726 AAATATTTTTGGGTTAAA
1 AAATATTTTTGAGTTAAA
4504744 AAATATTTTTGAG-TAAA
1 AAATATTTTTGAGTTAAA
4504761 A
1 A
4504762 GTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (18 bp):
AAATATTTTTGAGTTAAA
Found at i:4510189 original size:21 final size:20
Alignment explanation
Indices: 4510147--4510189 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4510137 AAAATTATTT
*
4510147 AATTTTTTTATAATTTATAA
1 AATTTTTTTATAATTTAAAA
4510167 AATTTTATTT-TAACTTTAAAA
1 AATTTT-TTTATAA-TTTAAAA
4510188 AA
1 AA
4510190 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTTTTATAATTTAAAA
Found at i:4510204 original size:29 final size:29
Alignment explanation
Indices: 4510165--4510230 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
4510155 TATAATTTAT
*
4510165 AAAATTTTATTTTAA-CTTTAAAAAAAATA
1 AAAATATTA-TTTAATCTTTAAAAAAAATA
* *
4510194 AAAATATTATTTAATTTTTTAAAAAATATA
1 AAAATATTATTTAA-TCTTTAAAAAAAATA
4510224 AAAATAT
1 AAAATAT
4510231 AAACTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 8 0.25
30 19 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATATTATTTAATCTTTAAAAAAAATA
Found at i:4516751 original size:28 final size:27
Alignment explanation
Indices: 4516706--4516759 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
4516696 TAAGATAACT
*
4516706 ATATAAAAATTTTCAATAAATAAAAAAA
1 ATATAAAAATTTTAAAT-AATAAAAAAA
*
4516734 ATAT-AAAATTATTAAATATTAAAAAA
1 ATATAAAAATT-TTAAATAATAAAAAA
4516760 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
ATATAAAAATTTTAAATAATAAAAAAA
Found at i:4517619 original size:14 final size:15
Alignment explanation
Indices: 4517597--4517635 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4517587 GTATATTAGC
*
4517597 AAAATAATATTAATT
1 AAAATAATATTAAAT
4517612 AAAA-AATATTAAAT
1 AAAATAATATTAAAT
*
4517626 AAAATCATAT
1 AAAATAATAT
4517636 AGTACTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATATTAAAT
Found at i:4521928 original size:17 final size:16
Alignment explanation
Indices: 4521906--4521954 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
4521896 CATTGTTTTT
*
4521906 TAAAAATATTTTTGAGA
1 TAAAAATATTTTT-AAA
*
4521923 TAAAAATATTGTTAAA
1 TAAAAATATTTTTAAA
4521939 T-AAAATATTTTTAAA
1 TAAAAATATTTTTAAA
4521954 T
1 T
4521955 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.48
16 3 0.10
17 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TAAAAATATTTTTAAA
Found at i:4546573 original size:13 final size:13
Alignment explanation
Indices: 4546555--4546579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4546545 GGATTTAGAT
4546555 TAAATTTTAAATC
1 TAAATTTTAAATC
4546568 TAAATTTTAAAT
1 TAAATTTTAAAT
4546580 TGGATTAAAT
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:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTTAAATC
Found at i:4556502 original size:93 final size:93
Alignment explanation
Indices: 4556155--4556491 Score: 505
Period size: 93 Copynumber: 3.6 Consensus size: 93
4556145 GACGTCCTTG
* * * * ** * *
4556155 CTCTTTATCACTCTCGTGTTTGCTGCCCTTGGACTCCATTGAAGCACCTCTCTCTTGTTGATG-C
1 CTCTTCATCACTCTCGTG-TT-C-GGCCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTC
* *
4556219 TCAGCAGCAGCAGCATAACTCCGTCGTCCTTT
63 -CAGCAGCAGCGGCATAACTCCGTCGTCTTTT
* *
4556251 CTCTTTATCACTCTCGTGTTCGGTCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTCCAG
1 CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTCCAG
*
4556316 CGGCAGCGGCATAACTCCGTCGTCTTTT
66 CAGCAGCGGCATAACTCCGTCGTCTTTT
4556344 CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTCCAG
1 CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTCCAG
4556409 CAGCAGCGGCATAACTCCGTCGTCTTTT
66 CAGCAGCGGCATAACTCCGTCGTCTTTT
*
4556437 CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAGTACCTCTCTCCTGT
1 CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAATACCTCTCTCCTGT
4556492 CCAGCTCCAG
Statistics
Matches: 225, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
93 203 0.90
94 2 0.01
95 2 0.01
96 18 0.08
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.33
Consensus pattern (93 bp):
CTCTTCATCACTCTCGTGTTCGGCCTTAGACGCCATTGAAATACCTCTCTCCTGTGGATGTCCAG
CAGCAGCGGCATAACTCCGTCGTCTTTT
Found at i:4567960 original size:22 final size:22
Alignment explanation
Indices: 4567925--4567966 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4567915 TAAATTAAGT
*
4567925 AAATATTTAAATATATTTCTTA
1 AAATATATAAATATATTTCTTA
* *
4567947 AAATATATATATATTTTTCT
1 AAATATATAAATATATTTCT
4567967 ATAGTACATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATATAAATATATTTCTTA
Found at i:4570776 original size:81 final size:81
Alignment explanation
Indices: 4570620--4570782 Score: 184
Period size: 81 Copynumber: 2.0 Consensus size: 81
4570610 ATCAGAGTAA
* ** * * * * * * *
4570620 TAACATAATCATAGTAAAGGTATTCACCGTTGCAAGTATAGTTTAGATTTGAATCGCGTTAGTCA
1 TAACATAATCATAATAAAAATATTCACCATTGCAAATATAATTGAGATCTAAATCGCGTTAATCA
*
4570685 TATTACTATTAAGAAT
66 TATTACTATTAAAAAT
4570701 TAACATAATCATAATAAAAATATTCACCATTGCAAATATAATCTGA-ATCTAAATCGCGTTAATC
1 TAACATAATCATAATAAAAATATTCACCATTGCAAATATAAT-TGAGATCTAAATCGCGTTAATC
* * *
4570765 GTTTTATTATTAAAAAT
65 ATATTACTATTAAAAAT
4570782 T
1 T
4570783 TAACTTCACT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 65 0.97
82 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (81 bp):
TAACATAATCATAATAAAAATATTCACCATTGCAAATATAATTGAGATCTAAATCGCGTTAATCA
TATTACTATTAAAAAT
Found at i:4575198 original size:23 final size:23
Alignment explanation
Indices: 4575170--4575335 Score: 125
Period size: 23 Copynumber: 7.4 Consensus size: 23
4575160 AGTGCTGGGT
*
4575170 AACAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
4575193 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
4575212 -ACTGAGAG--CACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
4575232 ATCAGAGAGCACACGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
4575256 TAACAAAGAGCACA-AGACGTGCTA
1 -AACAGAGAGCACACA-AAGTGCTA
**
4575280 AACAGAGAGCACACACTGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
**
4575303 CTCAGAGAGCACACACAA-TGCTA
1 AACAGAGAGCACACA-AAGTGCTA
*
4575326 ACCAGAGAGC
1 AACAGAGAGC
4575336 GCGCTAGTGT
Statistics
Matches: 112, Mismatches: 19, Indels: 24
0.72 0.12 0.15
Matches are distributed among these distances:
16 6 0.05
18 8 0.07
19 1 0.01
20 1 0.01
21 6 0.05
23 70 0.62
24 3 0.03
25 17 0.15
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:4576074 original size:13 final size:13
Alignment explanation
Indices: 4576056--4576082 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4576046 ACCATTTCTT
4576056 CCATATGAAACTA
1 CCATATGAAACTA
4576069 CCATATGAAACTA
1 CCATATGAAACTA
4576082 C
1 C
4576083 ATTCAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (13 bp):
CCATATGAAACTA
Found at i:4576883 original size:18 final size:18
Alignment explanation
Indices: 4576857--4576892 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4576847 TTTTCTATCA
*
4576857 ATTTCTCTTTATAAAAAT
1 ATTTCTCTTAATAAAAAT
*
4576875 ATTTTTCTTAATAAAAAT
1 ATTTCTCTTAATAAAAAT
4576893 GGTAAAATTG
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:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTCTCTTAATAAAAAT
Found at i:4580109 original size:25 final size:23
Alignment explanation
Indices: 4580029--4580108 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
4580019 CACTAGCGCA
*
4580029 CCCTCTGTTTAGCACGTTT-CGTG
1 CCCTCTGTTTAGCAC-TTTGTGTG
* *
4580052 CCCTCTGTTCAGCACTGTGTGTG
1 CCCTCTGTTTAGCACTTTGTGTG
4580075 CCCTCTGTTATTAGCACTTTGTGTG
1 CCCTCTG-T-TTAGCACTTTGTGTG
4580100 CCCTCTGTT
1 CCCTCTGTT
4580109 AAGTACTTCG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.04
23 25 0.51
24 2 0.04
25 20 0.41
ACGTcount: A:0.09, C:0.30, G:0.21, T:0.40
Consensus pattern (23 bp):
CCCTCTGTTTAGCACTTTGTGTG
Found at i:4585158 original size:22 final size:23
Alignment explanation
Indices: 4585133--4585178 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
4585123 GAATGTATCG
4585133 AAGTACT-TAACAAAGGGCACAT
1 AAGTACTGTAACAAAGGGCACAT
*
4585155 AAGTGCTGGGTAACAAAGGGCACA
1 AAGTACT--GTAACAAAGGGCACA
4585179 CAAAGTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
25 14 0.70
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.15
Consensus pattern (23 bp):
AAGTACTGTAACAAAGGGCACAT
Found at i:4585201 original size:23 final size:23
Alignment explanation
Indices: 4585171--4585248 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
4585161 TGGGTAACAA
4585171 AGGGCACACAAAGTGCTAATCAG
1 AGGGCACACAAAGTGCTAATCAG
* *
4585194 AGGGCACACGAAGTGCTAATAATAG
1 AGGGCACACAAAGTGCTAAT--CAG
* *
4585219 AGGGCATACACAGTGCTGAA-CAG
1 AGGGCACACAAAGTGCT-AATCAG
4585242 AGGGCAC
1 AGGGCAC
4585249 GAAATGTACT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 27 0.60
25 16 0.36
26 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.29, T:0.13
Consensus pattern (23 bp):
AGGGCACACAAAGTGCTAATCAG
Found at i:4587841 original size:17 final size:18
Alignment explanation
Indices: 4587819--4587852 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4587809 TGTTAAAAAC
*
4587819 AACTAAT-TTTTATTTAA
1 AACTAATATTATATTTAA
4587836 AACTAATATTATATTTA
1 AACTAATATTATATTTA
4587853 TAAGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AACTAATATTATATTTAA
Found at i:4589750 original size:89 final size:88
Alignment explanation
Indices: 4589595--4589771 Score: 273
Period size: 89 Copynumber: 2.0 Consensus size: 88
4589585 GAAGAAAAAG
* *
4589595 GATAGGTATGAAAAAAATCTAGGGTCCCCTTTAAAGTGAAGGACGAAAATAATCACAATTAGCAA
1 GATAGGCATGAAAAAAATCTAGGGTCCCCTTTAAAGTGAAGGACGAAAATAATCACAATTAACAA
* *
4589660 GGTATCCTTACTGCTTTGCAGAT
66 GGTAACCTTACTGCATTGCAGAT
** * *
4589683 GATAGGCATGAAAAAAAATCTAGGGTTTCCTTTTAAGTGAAGGATGAAAATAATCACAATTAACA
1 GATAGGCATG-AAAAAAATCTAGGGTCCCCTTTAAAGTGAAGGACGAAAATAATCACAATTAACA
4589748 AGGTAACCTTACTGCATTGCAGAT
65 AGGTAACCTTACTGCATTGCAGAT
4589772 AATCTTTTTG
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 9 0.11
89 71 0.89
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (88 bp):
GATAGGCATGAAAAAAATCTAGGGTCCCCTTTAAAGTGAAGGACGAAAATAATCACAATTAACAA
GGTAACCTTACTGCATTGCAGAT
Found at i:4595053 original size:16 final size:17
Alignment explanation
Indices: 4595027--4595059 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4595017 TTAAAAAAAA
4595027 TTTATAGAATTTATAAT
1 TTTATAGAATTTATAAT
*
4595044 TTTATA-AATTTTTAAT
1 TTTATAGAATTTATAAT
4595060 AAATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTATAGAATTTATAAT
Found at i:4595063 original size:11 final size:10
Alignment explanation
Indices: 4595043--4595088 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
4595033 GAATTTATAA
4595043 TTTTATAAAT
1 TTTTATAAAT
4595053 TTTTAATAAA-
1 TTTT-ATAAAT
*
4595063 TTATATAAAT
1 TTTTATAAAT
*
4595073 TCTT-TAAAT
1 TTTTATAAAT
4595082 TTTTATA
1 TTTTATA
4595089 TAATAATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 13 0.45
10 11 0.38
11 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:4595069 original size:20 final size:21
Alignment explanation
Indices: 4595041--4595079 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4595031 TAGAATTTAT
*
4595041 AATTTTATAAATT-TTTAATA
1 AATTATATAAATTCTTTAATA
4595061 AATTATATAAATTCTTTAA
1 AATTATATAAATTCTTTAA
4595080 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATATAAATTCTTTAATA
Found at i:4600985 original size:13 final size:13
Alignment explanation
Indices: 4600967--4600991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4600957 TTCACTCTTG
4600967 CCCTTGCTCCAAT
1 CCCTTGCTCCAAT
4600980 CCCTTGCTCCAA
1 CCCTTGCTCCAA
4600992 CCTTCAAATC
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:0.16, C:0.48, G:0.08, T:0.28
Consensus pattern (13 bp):
CCCTTGCTCCAAT
Found at i:4605085 original size:17 final size:17
Alignment explanation
Indices: 4605063--4605099 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4605053 ACCTATATCT
4605063 TTATAATTTTTAAAGGA
1 TTATAATTTTTAAAGGA
*
4605080 TTATAATTTTTAAATGA
1 TTATAATTTTTAAAGGA
4605097 TTA
1 TTA
4605100 AATCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TTATAATTTTTAAAGGA
Found at i:4605496 original size:29 final size:29
Alignment explanation
Indices: 4605442--4605523 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
4605432 AAAATTTGAT
* *
4605442 AAAATCAAAATTTCATGTATAAAATTATAC
1 AAAATC-AAAGTTCATGTATAAAATTACAC
* * *
4605472 AAAATCAAAGTTCACGTATACAATTGCAC
1 AAAATCAAAGTTCATGTATAAAATTACAC
4605501 ATTAAATCAAAGTTCATGTATAA
1 A--AAATCAAAGTTCATGTATAA
4605524 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 19 0.44
30 6 0.14
31 18 0.42
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAATCAAAGTTCATGTATAAAATTACAC
Found at i:4620941 original size:24 final size:22
Alignment explanation
Indices: 4620902--4620951 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
4620892 AAAATTATTG
4620902 TTATTTTTTTACTGTTTTACAA
1 TTATTTTTTTACTGTTTTACAA
*
4620924 TTATTATTTTTCATTGTTTTACAA
1 TTATT-TTTTT-ACTGTTTTACAA
4620948 TTAT
1 TTAT
4620952 CTCGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.20
23 5 0.20
24 15 0.60
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATTTTTTTACTGTTTTACAA
Found at i:4637270 original size:31 final size:31
Alignment explanation
Indices: 4637214--4637308 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 31
4637204 GACGGAAATC
* *
4637214 ATATTAATAATATTATTTATGTTTTTTTAATT
1 ATATTAATAATATT-TTAATATTTTTTTAATT
*
4637246 AT-TTAATAATATTTTAATAATTTTTTTTA-T
1 ATATTAATAATATTTTAAT-ATTTTTTTAATT
4637276 ATCATTAATATATAATTTTAATA-TTTTTTAATT
1 AT-ATTAATA-AT-ATTTTAATATTTTTTTAATT
4637309 TAAAATTCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
30 7 0.13
31 19 0.36
32 15 0.28
33 4 0.08
34 8 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (31 bp):
ATATTAATAATATTTTAATATTTTTTTAATT
Found at i:4637302 original size:33 final size:32
Alignment explanation
Indices: 4637210--4637304 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 32
4637200 AAGGGACGGA
4637210 AATCATATTAATAATATTATT--T-ATGTTTTTTT
1 AATCAT-TTAATAATATT-TTAATAAT-TTTTTTT
*
4637242 AATTATTTAATAATATTTTAATAATTTTTTTT
1 AATCATTTAATAATATTTTAATAATTTTTTTT
4637274 ATATCA-TTAATATATAATTTTAAT-ATTTTTT
1 A-ATCATTTAATA-AT-ATTTTAATAATTTTTT
4637305 AATTTAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
30 2 0.04
31 11 0.20
32 20 0.36
33 14 0.25
34 8 0.15
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (32 bp):
AATCATTTAATAATATTTTAATAATTTTTTTT
Found at i:4638467 original size:20 final size:21
Alignment explanation
Indices: 4638442--4638481 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4638432 CATCGTCCGA
*
4638442 TTTTCTTTTTCTTTT-TTTGC
1 TTTTCTATTTCTTTTCTTTGC
*
4638462 TTTTCTATTTGTTTTCTTTG
1 TTTTCTATTTCTTTTCTTTG
4638482 TTTCCGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTCTATTTCTTTTCTTTGC
Found at i:4641617 original size:83 final size:83
Alignment explanation
Indices: 4641476--4641698 Score: 367
Period size: 83 Copynumber: 2.7 Consensus size: 83
4641466 AGATATATGG
**
4641476 ATAGAGTAAGAGCTGTCAACTAAGTTTTCTTGGGATTTAGTTATCCTAGTCATGACATAAAGTCA
1 ATAGAGTAAGAGCCATC-A-TAAGTTTTCTTGGGATTTAGTTATCCTAGTCATGACATAAAGTCA
*
4641541 TAAAATATTGGCAAATGTCA
64 AAAAATATTGGCAAATGTCA
4641561 ATAGAGTAAGAGCCATCATAAGTTTTCTTGGGATTTAGTTATCCTAGTCATGACATAAAGTCAAA
1 ATAGAGTAAGAGCCATCATAAGTTTTCTTGGGATTTAGTTATCCTAGTCATGACATAAAGTCAAA
4641626 AAATATTGGCAAATGTCA
66 AAATATTGGCAAATGTCA
* *
4641644 ATAGAGTAAGAGCCATCATAAGTTTTCCTGGGATTTAGTTA-CACTAGTCACGACA
1 ATAGAGTAAGAGCCATCATAAGTTTTCTTGGGATTTAGTTATC-CTAGTCATGACA
4641699 ATCAAGATAC
Statistics
Matches: 132, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
82 1 0.01
83 115 0.87
84 1 0.01
85 15 0.11
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (83 bp):
ATAGAGTAAGAGCCATCATAAGTTTTCTTGGGATTTAGTTATCCTAGTCATGACATAAAGTCAAA
AAATATTGGCAAATGTCA
Found at i:4646179 original size:19 final size:20
Alignment explanation
Indices: 4646148--4646210 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
4646138 TATTTAATAG
* *
4646148 TAATA-TAATTATTTTTATT
1 TAATATTAAGTATTATTATT
* *
4646167 TAATATTAA-TATTAATGTT
1 TAATATTAAGTATTATTATT
4646186 TAAT-TTAAGT-TTATTATT
1 TAATATTAAGTATTATTATT
4646204 TAATATT
1 TAATATT
4646211 TTAGAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 14 0.39
19 19 0.53
20 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TAATATTAAGTATTATTATT
Found at i:4646527 original size:92 final size:92
Alignment explanation
Indices: 4646396--4646581 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
4646386 TTTTATTTTA
4646396 AATGACTAAAGTAAAAAAAAAAGATAGTTGATTGAGAGTATACCCTTTAAAACAAAGCAGCAGTT
1 AATGACTAAAGTAAAAAAAAAAGATAGTTGATTGAGAGTATACCCTTTAAAACAAAGCAGCAGTT
4646461 TAAAATAAAGTTTTCTAACTCCTTAAG
66 TAAAATAAAGTTTTCTAACTCCTTAAG
*
4646488 AATGACTAAAGTAAAAAAAAATGATAGTTGATTGAGAGTATACCCTTTAAAACAAAGCAGCAGTT
1 AATGACTAAAGTAAAAAAAAAAGATAGTTGATTGAGAGTATACCCTTTAAAACAAAGCAGCAGTT
4646553 TAAAATAAAGTTTTCTAACTCCTTAAG
66 TAAAATAAAGTTTTCTAACTCCTTAAG
4646580 AA
1 AA
4646582 GATCCAACTG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (92 bp):
AATGACTAAAGTAAAAAAAAAAGATAGTTGATTGAGAGTATACCCTTTAAAACAAAGCAGCAGTT
TAAAATAAAGTTTTCTAACTCCTTAAG
Found at i:4660714 original size:22 final size:22
Alignment explanation
Indices: 4660688--4660729 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4660678 ATTATTGAAA
4660688 TAAAACA-CTATTATCAAAAAAT
1 TAAAACATCTATTAT-AAAAAAT
*
4660710 TAAAATATCTATTATAAAAA
1 TAAAACATCTATTATAAAAA
4660730 TTACTTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAACATCTATTATAAAAAAT
Found at i:4662866 original size:4 final size:4
Alignment explanation
Indices: 4662857--4662891 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
4662847 AAGGCCTCAA
*
4662857 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
4662892 TACAGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:4669643 original size:31 final size:31
Alignment explanation
Indices: 4669598--4669660 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
4669588 ATATTATTAA
4669598 CATATTTATTTGGTATAATAAA-ATCATTTTT
1 CATATTTATTTGGTA-AATAAATATCATTTTT
* *
4669629 CATATTT-TTCTGGTAATTAAATATCTTTTTT
1 CATATTTATT-TGGTAAATAAATATCATTTTT
4669660 C
1 C
4669661 CCAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (31 bp):
CATATTTATTTGGTAAATAAATATCATTTTT
Found at i:4671349 original size:70 final size:70
Alignment explanation
Indices: 4671236--4671376 Score: 255
Period size: 70 Copynumber: 2.0 Consensus size: 70
4671226 AACAAAAATA
* *
4671236 ATCGAATATACCCTAAACCCGTATTTTATCAAAATGATATGTGAACAGTGATGCCGTCTCTTAAC
1 ATCGAATATACCCTAAACCCATATTTTACCAAAATGATATGTGAACAGTGATGCCGTCTCTTAAC
4671301 TAGGC
66 TAGGC
*
4671306 ATCGAGTATACCCTAAACCCATATTTTACCAAAATGATATGTGAACAGTGATGCCGTCTCTTAAC
1 ATCGAATATACCCTAAACCCATATTTTACCAAAATGATATGTGAACAGTGATGCCGTCTCTTAAC
4671371 TAGGC
66 TAGGC
4671376 A
1 A
4671377 CCATCAATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (70 bp):
ATCGAATATACCCTAAACCCATATTTTACCAAAATGATATGTGAACAGTGATGCCGTCTCTTAAC
TAGGC
Found at i:4671666 original size:16 final size:16
Alignment explanation
Indices: 4671641--4671675 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4671631 TTAGTTTAAA
4671641 GTTTTATTTA-AAATT
1 GTTTTATTTATAAATT
4671656 GTTTATATTTATAAATT
1 GTTT-TATTTATAAATT
4671673 GTT
1 GTT
4671676 AGTTGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (16 bp):
GTTTTATTTATAAATT
Found at i:4672275 original size:40 final size:40
Alignment explanation
Indices: 4672231--4672306 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
4672221 AAGTAAAAGT
* *
4672231 TAAAATTTTCTGTTTTTAAAAAAATATTTTTGAAAAAAAA
1 TAAAAATTTCTGTTTCTAAAAAAATATTTTTGAAAAAAAA
*
4672271 TAAAAATTTCTGTTTCTAAAAAAATATTTTTTAAAA
1 TAAAAATTTCTGTTTCTAAAAAAATATTTTTGAAAA
4672307 GCATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (40 bp):
TAAAAATTTCTGTTTCTAAAAAAATATTTTTGAAAAAAAA
Found at i:4675042 original size:24 final size:24
Alignment explanation
Indices: 4674972--4675133 Score: 144
Period size: 24 Copynumber: 6.5 Consensus size: 24
4674962 GACGAAGCTC
*
4674972 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
4674996 TCGTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
* *
4675023 CTGCTGCCGCCGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
4675047 ACGTTGATGCTGCTGAAGCTCCAGCTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
* * *
4675074 CTGATGTCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4675098 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
4675122 ATGCTGCTGCTG
1 CTGCTGCCGCTG
4675134 TTGTAGTTCC
Statistics
Matches: 111, Mismatches: 21, Indels: 11
0.78 0.15 0.08
Matches are distributed among these distances:
24 68 0.61
25 2 0.02
26 2 0.02
27 39 0.35
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:4675052 original size:51 final size:51
Alignment explanation
Indices: 4674972--4675133 Score: 177
Period size: 51 Copynumber: 3.2 Consensus size: 51
4674962 GACGAAGCTC
* * * *
4674972 CTGCTGCCGCTGAAGTTCCAACTGTCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* *
4675023 CTGCTGCCGCCGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAGCTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* * ** * *
4675074 CTGATGTCGCTGAAGCTCCAATTG-C--TGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* *
4675122 ATGCTGCTGCTG
1 CTGCTGCCGCTG
4675134 TTGTAGTTCC
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
48 28 0.30
50 1 0.01
51 64 0.69
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (51 bp):
CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
Found at i:4683856 original size:24 final size:24
Alignment explanation
Indices: 4683786--4684134 Score: 511
Period size: 24 Copynumber: 14.3 Consensus size: 24
4683776 GACGAAGCTC
*
4683786 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
4683810 TCGTTGATGCTGCTGAA-CTTCCAACTG
1 -C--TGCTGCCGCTGAAGC-TCCAACTG
*
4683837 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
4683861 ATGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4683885 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
4683909 CTGCTGCCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
4683933 CTGCTGCCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4683957 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4683981 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4684005 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4684029 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4684053 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
4684077 CTGCTGCCGCTGAAGCTCCAACTGATG
1 CTGCTGCCGCTGAAGCTCCAAC---TG
* * *
4684104 CTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
4684128 CCGCTGC
1 CTGCTGC
4684135 TGCTCAAATT
Statistics
Matches: 298, Mismatches: 19, Indels: 15
0.90 0.06 0.05
Matches are distributed among these distances:
24 255 0.86
25 2 0.01
26 1 0.00
27 40 0.13
ACGTcount: A:0.17, C:0.34, G:0.25, T:0.23
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:4687941 original size:6 final size:6
Alignment explanation
Indices: 4687930--4687955 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4687920 TAAGAGAACG
4687930 AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AA
4687956 GGAAATGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:4697239 original size:31 final size:29
Alignment explanation
Indices: 4697139--4697241 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 29
4697129 ACGATATTAA
*
4697139 AAATATAATTTTATTA-TTTTAATAG-TT
1 AAATATAATTTTATTATTTTTAAAAGATT
* *
4697166 ---TATATTTTTATAATTTTTAAAAGATT
1 AAATATAATTTTATTATTTTTAAAAGATT
* *
4697192 AAATCAAAATTTTATTATTTTTAAATGATT
1 AAAT-ATAATTTTATTATTTTTAAAAGATT
*
4697222 CAAAATATACTTTTATTATT
1 --AAATATAATTTTATTATT
4697242 ACTAATTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
24 11 0.19
25 8 0.14
26 2 0.03
29 1 0.02
30 21 0.36
31 12 0.20
32 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
AAATATAATTTTATTATTTTTAAAAGATT
Found at i:4704467 original size:25 final size:25
Alignment explanation
Indices: 4704404--4704467 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
4704394 TAAATATTTT
* *
4704404 TATATTTATAATTTCATTTTTATAAA
1 TATATTTAT-ATTACATTATTATAAA
*
4704430 TATATCTCA-ATTACATTCATT-TAAA
1 TATAT-TTATATTACATT-ATTATAAA
4704455 TATATTTATATTA
1 TATATTTATATTA
4704468 TATGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 2 0.06
25 20 0.65
26 7 0.23
27 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATTTATATTACATTATTATAAA
Found at i:4704520 original size:13 final size:14
Alignment explanation
Indices: 4704502--4704534 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4704492 ATTAATTAGG
4704502 TTTAATAACT-TAA
1 TTTAATAACTATAA
*
4704515 TTTAATAACTATAT
1 TTTAATAACTATAA
4704529 TTTAAT
1 TTTAAT
4704535 TTTAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATAACTATAA
Found at i:4704874 original size:25 final size:25
Alignment explanation
Indices: 4704840--4704888 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4704830 ATAATTTAAT
4704840 TTAGCTTAATTCATTAGAAAATTTTG
1 TTAGCTTAATTCATT-GAAAATTTTG
* *
4704866 TTAG-TTAATTTATTTAAAATTTT
1 TTAGCTTAATTCATTGAAAATTTT
4704889 TATTGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 9 0.43
26 4 0.19
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (25 bp):
TTAGCTTAATTCATTGAAAATTTTG
Found at i:4705883 original size:14 final size:13
Alignment explanation
Indices: 4705855--4705879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4705845 AGTTTGGACA
4705855 AAAATATAGGCTG
1 AAAATATAGGCTG
4705868 AAAATATAGGCT
1 AAAATATAGGCT
4705880 TGAACAAAAA
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:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
AAAATATAGGCTG
Found at i:4709425 original size:2 final size:2
Alignment explanation
Indices: 4709418--4709445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4709408 TGGATGATTA
4709418 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
4709446 TCATTAAGCA
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:4719437 original size:21 final size:21
Alignment explanation
Indices: 4719408--4719450 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4719398 ATAAACAATA
*
4719408 TAATAGTTTTGTCTTTTAATT
1 TAATAGTTTTGACTTTTAATT
*
4719429 TAATGGTTTTGACTTTTAATT
1 TAATAGTTTTGACTTTTAATT
4719450 T
1 T
4719451 TAGAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (21 bp):
TAATAGTTTTGACTTTTAATT
Found at i:4719946 original size:2 final size:2
Alignment explanation
Indices: 4719939--4719970 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4719929 AAAAATAACT
4719939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4719971 AAATTAACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4721057 original size:44 final size:44
Alignment explanation
Indices: 4720972--4721057 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
4720962 GTCTTTTTAA
* *
4720972 AATTTGTTGAGAAACATTTGTTTCAATGTTTTCAATTTATTTTC
1 AATTTGTTGAGAAACATATGTTTCAATGTTTTCAATGTATTTTC
* * *
4721016 AATTTGTTTG-GAAACATATGTTTTAATGTTTTTAGTGTATTT
1 AATTTG-TTGAGAAACATATGTTTCAATGTTTTCAATGTATTT
4721058 GATATATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (44 bp):
AATTTGTTGAGAAACATATGTTTCAATGTTTTCAATGTATTTTC
Found at i:4724349 original size:11 final size:11
Alignment explanation
Indices: 4724333--4724360 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4724323 GTCTTTTAAT
4724333 TTATTTAAATA
1 TTATTTAAATA
4724344 TTATTTAAATA
1 TTATTTAAATA
4724355 TTATTT
1 TTATTT
4724361 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTAAATA
Found at i:4724577 original size:21 final size:20
Alignment explanation
Indices: 4724526--4724577 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4724516 TTTTTTACCT
* *
4724526 TAAACTCTAAATTTAAATCC
1 TAAATTCTAAATTTAAACCC
4724546 TAAATAT-TAAATCTTAAACCC
1 TAAAT-TCTAAAT-TTAAACCC
4724567 TAAATTCTAAA
1 TAAATTCTAAA
4724578 CTCATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATTCTAAATTTAAACCC
Found at i:4724723 original size:28 final size:30
Alignment explanation
Indices: 4724682--4724755 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
4724672 ATTTAAAATA
*
4724682 AAAAAATTACTAAAATTA-TATAATGAT-A-T
1 AAAAAA-TATTAAAATTATTATAAT-ATAATT
*
4724711 AAAAAATATTAAAA-TATTATTATATAATT
1 AAAAAATATTAAAATTATTATAATATAATT
4724740 AAAAAATATATAAAAT
1 AAAAAATAT-TAAAAT
4724756 AACATAACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.11
28 13 0.34
29 16 0.42
30 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAAAATATTAAAATTATTATAATATAATT
Found at i:4725784 original size:30 final size:30
Alignment explanation
Indices: 4725728--4725786 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4725718 ATACATAATT
* *
4725728 TATATTTATTATGAAACCTATGATTGAGTC
1 TATATTTATTATGAAACATATAATTGAGTC
*
4725758 TATATTTATTAT-AAATCATTTAATTGAGT
1 TATATTTATTATGAAA-CATATAATTGAGT
4725787 TGATGTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (30 bp):
TATATTTATTATGAAACATATAATTGAGTC
Found at i:4726462 original size:11 final size:12
Alignment explanation
Indices: 4726440--4726464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4726430 TATAAAGAAA
4726440 TTGGATTTTTTT
1 TTGGATTTTTTT
4726452 TTGGATTTTTTT
1 TTGGATTTTTTT
4726464 T
1 T
4726465 AAACAAGGAA
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:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (12 bp):
TTGGATTTTTTT
Found at i:4744257 original size:18 final size:18
Alignment explanation
Indices: 4744234--4744276 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4744224 TAATAGATTT
*
4744234 TTAATTAAATGAATTT-AA
1 TTAATTAAA-AAATTTAAA
4744252 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
4744270 TTAATTA
1 TTAATTA
4744277 CATCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:4750668 original size:18 final size:20
Alignment explanation
Indices: 4750645--4750683 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
4750635 AATTATTATT
4750645 TATATTAATTT-TTAA-AAA
1 TATATTAATTTATTAATAAA
*
4750663 TATATTTATTTATTAATAAA
1 TATATTAATTTATTAATAAA
4750683 T
1 T
4750684 TAAGTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTAATTTATTAATAAA
Found at i:4751185 original size:15 final size:16
Alignment explanation
Indices: 4751155--4751193 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
4751145 TAATAAAAAT
4751155 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
4751172 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
4751187 ATAATTT
1 ATAATTT
4751194 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Done.