Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 16 of 205
Found at i:4958852 original size:371 final size:370
Alignment explanation
Indices: 4958166--4958909 Score: 1267
Period size: 371 Copynumber: 2.0 Consensus size: 370
4958156 ATAATAATTG
*
4958166 GAATTGTTAGTTCAAATCTCCGGTAAGAAAAATCTCGAACACACGAACGGAACTCAAACAGAAAA
1 GAATTGTTAGTTCAAATCTCCGGTAAGAAAAATCTCAAACACACGAACGGAACTCAAACAGAAAA
*
4958231 AGAAGAAATAGGACAAGGCTCCAAGGCGTGTATCAAGCTACTATCTTTAAGGTTATATTCGCCCC
66 AGAAGAAATAGGACAAGACTCCAAGGCGTGTATCAAGCTACTATCTTTAAGGTTATATTCGCCCC
*
4958296 CACCTATCTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTTGAGGATACAATGAAGCCAATG
131 CACCTATCTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGAGGATACAATGAAGCCAATG
* **
4958361 ACTATTTGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAGCAATGTATAACAAGAAACT
196 ACTATTTGCGTTTTGCACTAACGAGAATAGTCCACTACACACTGAGCAATGTATAACAAGAAACT
* *
4958426 CAATTTCTACAAAAGATTTCTGTAGTAATACTTTATAGAATAATCTAATAATATTAGAAAATAAA
261 CAATTTCTACAAAAGATTTCTGCAGTAATACTTTATAGAATAATCTAAAAATATTAGAAAATAAA
4958491 GGAAGGAAAGAAAGAATATAAGAATTTGTTGGTGTGTCTTCCAAAT
326 GGAAGGAAAGAAA-AATATAAGAATTTGTTGGTGTGTCTTCCAAAT
* * * * *
4958537 GAATTGTTAG-TCGAAATCTCGGGTGAGGAAAATCTCAAACACATGAACGGAACTCGAACAGAAA
1 GAATTGTTAGTTC-AAATCTCCGGTAAGAAAAATCTCAAACACACGAACGGAACTCAAACAGAAA
4958601 AAGAAGAAATAGGACAAGACTCCAAGGCGTGTATCAAG-TCACTATCTTTAAGGTTATATTCGCC
65 AAGAAGAAATAGGACAAGACTCCAAGGCGTGTATCAAGCT-ACTATCTTTAAGGTTATATTCGCC
* *
4958665 CCCACCTATCTTTGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGAGGATACAATGGAGCCAA
129 CCCACCTATCTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGAGGATACAATGAAGCCAA
4958730 TGACTATTTGCGTTTTGCACTAACGAGAATAGTCCACTACACACTGAGCAATGTATAACAAGAAA
194 TGACTATTTGCGTTTTGCACTAACGAGAATAGTCCACTACACACTGAGCAATGTATAACAAGAAA
* * *
4958795 CTCAATTTTTACAAATGATTTCTGCAGTAATACTTTATAGAATAATCTAAAAATATTAGAAAATG
259 CTCAATTTCTACAAAAGATTTCTGCAGTAATACTTTATAGAATAATCTAAAAATATTAGAAAATA
* *
4958860 AAGGAAGGAAAGAAAAATATTAGAATTTGTTGGTGTGTTTTCCAAAT
324 AAGGAAGGAAAGAAAAATATAAGAATTTGTTGGTGTGTCTTCCAAAT
4958907 GAA
1 GAA
4958910 ATCTCATTCC
Statistics
Matches: 351, Mismatches: 20, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
370 36 0.10
371 315 0.90
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (370 bp):
GAATTGTTAGTTCAAATCTCCGGTAAGAAAAATCTCAAACACACGAACGGAACTCAAACAGAAAA
AGAAGAAATAGGACAAGACTCCAAGGCGTGTATCAAGCTACTATCTTTAAGGTTATATTCGCCCC
CACCTATCTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGAGGATACAATGAAGCCAATG
ACTATTTGCGTTTTGCACTAACGAGAATAGTCCACTACACACTGAGCAATGTATAACAAGAAACT
CAATTTCTACAAAAGATTTCTGCAGTAATACTTTATAGAATAATCTAAAAATATTAGAAAATAAA
GGAAGGAAAGAAAAATATAAGAATTTGTTGGTGTGTCTTCCAAAT
Found at i:4965321 original size:12 final size:12
Alignment explanation
Indices: 4965304--4965329 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4965294 GAATTCTTTC
4965304 AATTTGGTCCAA
1 AATTTGGTCCAA
4965316 AATTTGGTCCAA
1 AATTTGGTCCAA
4965328 AA
1 AA
4965330 GTGATTTTTC
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (12 bp):
AATTTGGTCCAA
Found at i:4967090 original size:91 final size:89
Alignment explanation
Indices: 4966936--4967117 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 89
4966926 TTGAATCAAA
** **
4966936 TGAAAATCTAATCAATCAAAGAAAACAATTTGGAAGATTACATTAGGGTAGAAAGAGGTTAAATC
1 TGAAAATCTAATCAATCAAAG-AAACAATTTAAAAGATTACATTAACGTAGAAAGAGGTTAAATC
*
4967001 ATTCAATTCAATCTCGTAAGTGAAG
65 ATTCAATTCAATCTCGTAAGTAAAG
*
4967026 TGAAAATCTAATCAATCAAAG-AACAATTTAAACTTATATTACATTAACGTAGAAAGAGGTTAAA
1 TGAAAATCTAATCAATCAAAGAAACAATTTAAA---AGATTACATTAACGTAGAAAGAGGTTAAA
*
4967090 TCATTCAATTCAATCTTGTAAGTAAAG
63 TCATTCAATTCAATCTCGTAAGTAAAG
4967117 T
1 T
4967118 TTCTCTCTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
88 9 0.11
90 21 0.26
91 52 0.63
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (89 bp):
TGAAAATCTAATCAATCAAAGAAACAATTTAAAAGATTACATTAACGTAGAAAGAGGTTAAATCA
TTCAATTCAATCTCGTAAGTAAAG
Found at i:4969368 original size:21 final size:22
Alignment explanation
Indices: 4969336--4969399 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
4969326 AATGATAAAT
* **
4969336 TTGAGATTTTATAGGGAATTAC
1 TTGAGTTTTTATAGGGAAAAAC
*
4969358 TTGA-TTTTTATAGAGAAAAAC
1 TTGAGTTTTTATAGGGAAAAAC
4969379 TTGAGTTTTTATAGGGAAAAA
1 TTGAGTTTTTATAGGGAAAAA
4969400 TTATTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (22 bp):
TTGAGTTTTTATAGGGAAAAAC
Found at i:4980791 original size:3 final size:3
Alignment explanation
Indices: 4980783--4980824 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
4980773 AATATAAATG
*
4980783 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4980825 TAAAGAGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4982464 original size:132 final size:131
Alignment explanation
Indices: 4982281--4982878 Score: 883
Period size: 132 Copynumber: 4.5 Consensus size: 131
4982271 GAGATAGGAA
* * * * *
4982281 TACTGGCTTCAATGTACTCCACGGTAACCTCAGTGAGGTAAAATCTGCCATCTTCGATCTACTCC
1 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCT-C
* ** * * * * *
4982346 ACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG-GGATAG
65 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAG-TAG
*
4982410 AGT
129 AAT
** *
4982413 TACTGGCTTCAATGTACTCTGCTGTAACCACAAGGAGGTAAAATCTGCCATCTTTGATCTGCGTC
1 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGC-TC
* * *
4982478 ACTATTGTTTAGGGAGACAAGATCTGAGATCTTTAATCTATTCTGCTGCTGTCCAGGGAAGTAGA
65 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGA
4982543 AT
130 AT
4982545 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCGTC
1 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGC-TC
* *
4982610 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTTAATCTATTCTGCTGCTGTCCAGGGAAGTAGA
65 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGA
4982675 AT
130 AT
* *
4982677 TACTGGCTCCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGTCATCTTTGATCTGCTCC
1 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCT-C
* *
4982742 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGTTGCTATCCAGGGAAGTAGA
65 ACTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGA
4982807 AT
130 AT
* *
4982809 TACTGGCTTCAATGTACTCCACTGTAACCACCGGGAGGTAAAATCTTCCATCTTTGATCTGCTTC
1 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGC-TC
4982874 ACTAT
65 ACTAT
4982879 CAATGCAGAA
Statistics
Matches: 428, Mismatches: 34, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.00
132 424 0.99
133 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (131 bp):
TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCA
CTATTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAA
T
Found at i:4984149 original size:14 final size:14
Alignment explanation
Indices: 4984130--4984172 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
4984120 CCTTGGCCTC
4984130 TCCATTTTACTTTT
1 TCCATTTTACTTTT
*
4984144 TCCATTTTTCATTTT
1 TCCATTTTAC-TTTT
4984159 TCC-TTTTCACTTTT
1 TCCATTTT-ACTTTT
4984173 CATTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (14 bp):
TCCATTTTACTTTT
Found at i:4984156 original size:21 final size:20
Alignment explanation
Indices: 4984132--4984178 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4984122 TTGGCCTCTC
* *
4984132 CATTTTACTTTTTCCATTTTT
1 CATTTTACCTTTT-CACTTTT
*
4984153 CATTTTTCCTTTTCACTTTT
1 CATTTTACCTTTTCACTTTT
4984173 CATTTT
1 CATTTT
4984179 TTCATTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (20 bp):
CATTTTACCTTTTCACTTTT
Found at i:4984179 original size:7 final size:7
Alignment explanation
Indices: 4984140--4984195 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
4984130 TCCATTTTAC
4984140 TTTTTCCA
1 TTTTT-CA
4984148 TTTTTCA
1 TTTTTCA
4984155 TTTTTC-
1 TTTTTCA
*
4984161 CTTTTCA
1 TTTTTCA
*
4984168 CTTTTCA
1 TTTTTCA
4984175 TTTTTTCA
1 -TTTTTCA
*
4984183 TTTCATCA
1 TTT-TTCA
4984191 TTTTT
1 TTTTT
4984196 AATGACTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
6 5 0.12
7 19 0.46
8 17 0.41
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTTCA
Found at i:4984186 original size:20 final size:20
Alignment explanation
Indices: 4984149--4984187 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4984139 CTTTTTCCAT
*
4984149 TTTTCATTTTTCCTTTTCAC
1 TTTTCATTTTTCCATTTCAC
*
4984169 TTTTCATTTTTTCATTTCA
1 TTTTCATTTTTCCATTTCA
4984188 TCATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCATTTTTCCATTTCAC
Found at i:4987054 original size:19 final size:20
Alignment explanation
Indices: 4987030--4987069 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4987020 AACTGTGTTT
* *
4987030 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
4987049 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
4987069 A
1 A
4987070 TGCTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:4993034 original size:22 final size:21
Alignment explanation
Indices: 4993000--4993048 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
4992990 AATTTTATCG
4993000 TTTTAAATAAAAATTATTTAAT
1 TTTTAAATAAAAATT-TTTAAT
* *
4993022 TTTTAGATTAAAATTTTT-AT
1 TTTTAAATAAAAATTTTTAAT
*
4993042 TTATAAA
1 TTTTAAA
4993049 GGAGTTAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 3 0.13
22 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTAAATAAAAATTTTTAAT
Found at i:4995072 original size:17 final size:17
Alignment explanation
Indices: 4995036--4995072 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4995026 TACTATTTGT
*
4995036 CACAAAAATAATTGTAC
1 CACAAAAATAAGTGTAC
*
4995053 CACAAAAATAAGTGTGC
1 CACAAAAATAAGTGTAC
4995070 CAC
1 CAC
4995073 TTAAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.19
Consensus pattern (17 bp):
CACAAAAATAAGTGTAC
Found at i:4996358 original size:24 final size:23
Alignment explanation
Indices: 4996329--4996391 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
4996319 GTAGTTAAAA
4996329 AAATTTATTTAAAATTAAATTGA-T
1 AAATTTATTTAAAATTAAA--GACT
* *
4996353 AAATTT-TATAAATTTTAAAGACT
1 AAATTTATTTAAA-ATTAAAGACT
*
4996376 AAATTTATTGAAAATT
1 AAATTTATTTAAAATT
4996392 TTAAAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 15 0.48
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
AAATTTATTTAAAATTAAAGACT
Found at i:5009700 original size:17 final size:17
Alignment explanation
Indices: 5009678--5009713 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5009668 AGTCTTTAGC
5009678 TTCATTGATCTTCTGGA
1 TTCATTGATCTTCTGGA
5009695 TTCATTGATCTTCTGGA
1 TTCATTGATCTTCTGGA
5009712 TT
1 TT
5009714 TTGTCAATCT
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:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (17 bp):
TTCATTGATCTTCTGGA
Found at i:5012050 original size:2 final size:2
Alignment explanation
Indices: 5012043--5012069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5012033 CTACTTTCAT
5012043 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5012070 ATGTACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5016914 original size:3 final size:3
Alignment explanation
Indices: 5016906--5016939 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5016896 AGCAATCCAA
5016906 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
5016940 GTTGCCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5023957 original size:21 final size:22
Alignment explanation
Indices: 5023898--5023957 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
5023888 CAGAAGCAAT
*
5023898 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
*
5023920 A-ACGACACACT-TGGTGCCT-A
1 ATACGACACA-TATAGTGCCTGA
5023940 ATACGACACATATAGTGC
1 ATACGACACATATAGTGC
5023958 TTGATCGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
22 2 0.06
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:5024445 original size:17 final size:18
Alignment explanation
Indices: 5024413--5024446 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5024403 TGAATTTTTA
*
5024413 TTCAATTTCTATCTTAAT
1 TTCAATTTCAATCTTAAT
5024431 TTCAATTT-AATCTTAA
1 TTCAATTTCAATCTTAA
5024447 CTAAATTCAC
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:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (18 bp):
TTCAATTTCAATCTTAAT
Found at i:5025076 original size:3 final size:3
Alignment explanation
Indices: 5025068--5025099 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5025058 AATTTATTTG
5025068 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5025100 TACAACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5025124 original size:13 final size:13
Alignment explanation
Indices: 5025106--5025130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5025096 TAATTACAAC
5025106 AATAATTTAATAT
1 AATAATTTAATAT
5025119 AATAATTTAATA
1 AATAATTTAATA
5025131 ATTAAATATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTTAATAT
Found at i:5025241 original size:14 final size:17
Alignment explanation
Indices: 5025222--5025259 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
5025212 ATTTATTTCT
5025222 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
5025236 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
5025253 TAATATA
1 TAATATA
5025260 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:5025277 original size:11 final size:11
Alignment explanation
Indices: 5025239--5025277 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5025229 ATATTTATAA
5025239 TATAATTAATT
1 TATAATTAATT
*
5025250 TAATAATATACTT
1 T-ATAAT-TAATT
5025263 TATAATTAATT
1 TATAATTAATT
5025274 TATA
1 TATA
5025278 TATTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:5026278 original size:22 final size:22
Alignment explanation
Indices: 5026253--5026295 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5026243 ATATCAATAA
*
5026253 ATTATTAAATATATATTTTTAT
1 ATTAATAAATATATATTTTTAT
*
5026275 ATTAATAATTATATATTTTTA
1 ATTAATAAATATATATTTTTA
5026296 CAATTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATAAATATATATTTTTAT
Found at i:5031158 original size:21 final size:21
Alignment explanation
Indices: 5031133--5031176 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5031123 ATTGGGCTGT
* *
5031133 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
5031154 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
5031175 TA
1 TA
5031177 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:5041070 original size:24 final size:24
Alignment explanation
Indices: 5041034--5041084 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5041024 TGGCACTACG
*
5041034 AATGTAAATGATGAACTGACGGAA
1 AATGTAAAGGATGAACTGACGGAA
* *
5041058 AATGTAAAGGATGAATTGACGGCA
1 AATGTAAAGGATGAACTGACGGAA
5041082 AAT
1 AAT
5041085 TACCCAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.22
Consensus pattern (24 bp):
AATGTAAAGGATGAACTGACGGAA
Found at i:5045059 original size:21 final size:21
Alignment explanation
Indices: 5045031--5045086 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
5045021 AACAGCAGTG
* *
5045031 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTATA
* *
5045052 GTGGTGAGATTGGATACTATA
1 GCGGTGAGATTAGATACTATA
*
5045073 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
5045087 AACAATGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:5047181 original size:14 final size:14
Alignment explanation
Indices: 5047162--5047191 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5047152 TCTCTCTCTC
*
5047162 AACAAAAATTTCAA
1 AACAAAAAGTTCAA
5047176 AACAAAAAGTTCAA
1 AACAAAAAGTTCAA
5047190 AA
1 AA
5047192 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (14 bp):
AACAAAAAGTTCAA
Found at i:5048190 original size:23 final size:23
Alignment explanation
Indices: 5048160--5048221 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
5048150 GGCTCGACCC
* *
5048160 TTTTTTAATTAAAATTTAAATTA
1 TTTTTTAATTAAAATTAAAACTA
5048183 TTTTTTAA-TAAAATTAAAACTA
1 TTTTTTAATTAAAATTAAAACTA
* *
5048205 ATTGTT-ATTAAAATTAA
1 TTTTTTAATTAAAATTAA
5048222 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 25 0.74
23 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTTTAATTAAAATTAAAACTA
Found at i:5048234 original size:16 final size:16
Alignment explanation
Indices: 5048197--5048236 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5048187 TTAATAAAAT
* *
5048197 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5048213 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5048229 TAAAATTA
1 TAAAATTA
5048237 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5048326 original size:9 final size:9
Alignment explanation
Indices: 5048309--5048361 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
5048299 ATTATCAAAT
5048309 TATTAATTG
1 TATTAATTG
*
5048318 TAGTAATTG
1 TATTAATTG
5048327 TATTAATTG
1 TATTAATTG
5048336 --TTAATTG
1 TATTAATTG
*
5048343 AATTAATTG
1 TATTAATTG
5048352 TATTAATTG
1 TATTAATTG
5048361 T
1 T
5048362 TGTAACAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
7 7 0.18
9 32 0.82
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (9 bp):
TATTAATTG
Found at i:5048339 original size:25 final size:25
Alignment explanation
Indices: 5048306--5048362 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
5048296 AAAATTATCA
* *
5048306 AATTATTAATTGTAGTAATTGTATT
1 AATTGTTAATTGAAGTAATTGTATT
*
5048331 AATTGTTAATTGAATTAATTGTATT
1 AATTGTTAATTGAAGTAATTGTATT
5048356 AATTGTT
1 AATTGTT
5048363 GTAACAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (25 bp):
AATTGTTAATTGAAGTAATTGTATT
Found at i:5048432 original size:68 final size:69
Alignment explanation
Indices: 5048348--5048493 Score: 249
Period size: 68 Copynumber: 2.1 Consensus size: 69
5048338 AATTGAATTA
* *
5048348 ATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
1 ATTGTATTAATGGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTAT
5048413 TATT
66 TATT
*
5048417 -TTGTATTAATGGTTGTAACAAAATCTAGCATTTGATTAGTAAAACAAACTTGATGTTTTATTAT
1 ATTGTATTAATGGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTAT
5048481 TATT
66 TATT
*
5048485 ATTTTATTA
1 ATTGTATTA
5048494 TTATTATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 65 0.90
69 7 0.10
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (69 bp):
ATTGTATTAATGGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTAT
TATT
Found at i:5048491 original size:14 final size:14
Alignment explanation
Indices: 5048472--5048503 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5048462 AAACTTGATG
5048472 TTTTATTATTATTA
1 TTTTATTATTATTA
5048486 TTTTATTATTATTA
1 TTTTATTATTATTA
5048500 TTTT
1 TTTT
5048504 GTAACAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:5059682 original size:3 final size:3
Alignment explanation
Indices: 5059674--5059706 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5059664 TGTAAGTAAA
5059674 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
5059707 AAACCGTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:5067814 original size:28 final size:28
Alignment explanation
Indices: 5067783--5067836 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
5067773 GAAAAAAAAC
5067783 TTAACTAAAAATGGTAAATTACACAGTA
1 TTAACTAAAAATGGTAAATTACACAGTA
5067811 TTAACTAAAAATGGTAAATTACACAG
1 TTAACTAAAAATGGTAAATTACACAG
5067837 CATGTTCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (28 bp):
TTAACTAAAAATGGTAAATTACACAGTA
Found at i:5072263 original size:19 final size:18
Alignment explanation
Indices: 5072236--5072283 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
5072226 TTATATATTC
5072236 TTTAGAATTTTTTTAAAAA
1 TTTA-AATTTTTTTAAAAA
5072255 TTTATAATTTTTTTAAAAA
1 TTTA-AATTTTTTTAAAAA
*
5072274 TATAAATTTT
1 TTTAAATTTT
5072284 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTTTTTAAAAA
Found at i:5072311 original size:19 final size:20
Alignment explanation
Indices: 5072289--5072331 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
5072279 ATTTTATAAT
*
5072289 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
*
5072308 -TTTTAAAAATTATTTTGTA
1 TTTTTAAAAATTATTTTGAA
5072327 TTTTT
1 TTTTT
5072332 TTAGAGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:5072317 original size:18 final size:19
Alignment explanation
Indices: 5072290--5072330 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5072280 TTTTATAATT
*
5072290 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
5072308 TTTTAAAAATTATTTTGTA
1 TTTTAAAAATTATTTTGAA
5072327 TTTT
1 TTTT
5072331 TTTAGAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:5081605 original size:22 final size:22
Alignment explanation
Indices: 5081579--5081622 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5081569 TAACAAGTTT
5081579 AATT-AATTAATATAAGTTATCA
1 AATTAAATTAAT-TAAGTTATCA
*
5081601 AATTAAATTAATTAATTTATCA
1 AATTAAATTAATTAAGTTATCA
5081623 TGAGTTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAATTAATTAAGTTATCA
Found at i:5081636 original size:32 final size:31
Alignment explanation
Indices: 5081577--5081653 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
5081567 TCTAACAAGT
*
5081577 TTAATTAATTAATATAAGTTATCAAATTAAA
1 TTAATTAATTTATATAAGTTATCAAATTAAA
* *
5081608 TTAATTAATTTATCATGAGTTA-CTAAATTCAA
1 TTAATTAATTTAT-ATAAGTTATC-AAATTAAA
* *
5081640 GTAATCAATTTATA
1 TTAATTAATTTATA
5081654 AGTTTACGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 14 0.36
32 25 0.64
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (31 bp):
TTAATTAATTTATATAAGTTATCAAATTAAA
Found at i:5082080 original size:19 final size:20
Alignment explanation
Indices: 5082043--5082080 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5082033 TGATTTTTAA
5082043 TAATAAAATGATGAATTTTT
1 TAATAAAATGATGAATTTTT
*
5082063 TAATAAAAT-ATTAATTTT
1 TAATAAAATGATGAATTTT
5082081 ATTTTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATAAAATGATGAATTTTT
Found at i:5086326 original size:3 final size:3
Alignment explanation
Indices: 5086318--5086350 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5086308 TTAACAGTAA
*
5086318 AAG AAG AAG AAG AAG -AG AAT AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5086351 GATGTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:5087226 original size:18 final size:18
Alignment explanation
Indices: 5087199--5087291 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
5087189 TACGACCGTT
5087199 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5087217 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5087235 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5087253 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5087271 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
5087289 TAC
1 TAC
5087292 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:5097480 original size:7 final size:7
Alignment explanation
Indices: 5097470--5097494 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5097460 AGGTTTAATG
5097470 TTTAAAA
1 TTTAAAA
5097477 TTTAAAA
1 TTTAAAA
5097484 TTTAAAA
1 TTTAAAA
5097491 TTTA
1 TTTA
5097495 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:5100172 original size:17 final size:16
Alignment explanation
Indices: 5100141--5100184 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
5100131 GATTTATTTA
5100141 ATAATATAATATCATT
1 ATAATATAATATCATT
*
5100157 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
5100174 AATTATATAAT
1 -ATAATATAAT
5100185 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:5105404 original size:30 final size:29
Alignment explanation
Indices: 5105370--5105426 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
5105360 TTATCAAATA
5105370 AATAAA-ATCTTTTAATATAATAATTTAATC
1 AATAAATATCTTTTAAT-TAA-AATTTAATC
* *
5105400 AATAAATTTCTTTTACTTAAAATTTAA
1 AATAAATATCTTTTAATTAAAATTTAA
5105427 GAAAATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATATCTTTTAATTAAAATTTAATC
Found at i:5106733 original size:23 final size:24
Alignment explanation
Indices: 5106688--5106734 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5106678 TTTGTTATTA
* *
5106688 TTTTAAATTTATTATTGATAAAAT
1 TTTTAAATATATTATTGAAAAAAT
*
5106712 TTTTAAATATA-TATTTAAAAAAT
1 TTTTAAATATATTATTGAAAAAAT
5106735 CGAATTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTTAAATATATTATTGAAAAAAT
Found at i:5108777 original size:4 final size:4
Alignment explanation
Indices: 5108768--5108795 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5108758 AACCAAAATT
5108768 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
5108796 ATAAGCGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:5131011 original size:8 final size:8
Alignment explanation
Indices: 5130998--5131022 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5130988 GAGACATGAT
5130998 AAAGACAA
1 AAAGACAA
5131006 AAAGACAA
1 AAAGACAA
5131014 AAAGACAA
1 AAAGACAA
5131022 A
1 A
5131023 GATTTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGACAA
Found at i:5132943 original size:11 final size:11
Alignment explanation
Indices: 5132936--5132977 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
5132926 TTGTTTTCTC
5132936 ACTATTTTGCT
1 ACTATTTTGCT
*
5132947 ACTATTTTACT
1 ACTATTTTGCT
* *
5132958 ATTATGTTGCT
1 ACTATTTTGCT
5132969 ACTATTTTG
1 ACTATTTTG
5132978 TTGTTATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (11 bp):
ACTATTTTGCT
Found at i:5133396 original size:24 final size:25
Alignment explanation
Indices: 5133356--5133402 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
5133346 TAATGGATTT
*
5133356 ATTTACACTTAATAAGTGAAATTGA
1 ATTTACACTTAATAAGTAAAATTGA
5133381 ATTT-CACTT-ATCAAGTAAAATT
1 ATTTACACTTAAT-AAGTAAAATT
5133403 TTGATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.70
25 4 0.20
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (25 bp):
ATTTACACTTAATAAGTAAAATTGA
Found at i:5133560 original size:93 final size:93
Alignment explanation
Indices: 5133456--5133644 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 93
5133446 AAATATGAAT
5133456 ATAATTATCTTATTTAATTCAATAATCAATTTGTTAAAATATTAGTATTTATAAAAATGTGACCG
1 ATAATTATCTTATTTAATTCAATAATCAATTTGTTAAAATATTAGTATTTATAAAAATGTGACCG
*
5133521 TTTAATTTATTTATAATTAAATTTTTTA
66 TTTAATTTATTTATAATTAAAATTTTTA
5133549 ATAATTATCTTATTTAATTCAATAATCAATTTGTTAAAATATTAGTATTTATAAAAATGTGACCG
1 ATAATTATCTTATTTAATTCAATAATCAATTTGTTAAAATATTAGTATTTATAAAAATGTGACCG
5133614 TTTAATTTATTTATAATTAAAATTTTTA
66 TTTAATTTATTTATAATTAAAATTTTTA
5133642 ATA
1 ATA
5133645 TTCAAATAAG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (93 bp):
ATAATTATCTTATTTAATTCAATAATCAATTTGTTAAAATATTAGTATTTATAAAAATGTGACCG
TTTAATTTATTTATAATTAAAATTTTTA
Found at i:5136472 original size:75 final size:74
Alignment explanation
Indices: 5136336--5136474 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 74
5136326 CTCATGTTGA
* * *
5136336 GGCTTGAACTTTTTTTAGTCCAATGTAAGCCCTGAACTTGACAATTATCCCTAGGTTGAGGCTTA
1 GGCTTAAACTTTTTTTAGTCCAATGTAAGCCCTGAACTTAACAATTATCCCTA-GTCGAGGCTTA
5136401 AAGTAGGTAG
65 AAGTAGGTAG
* * *
5136411 GGCTTAAACTTTTTTTTGTCCAA-GTTAGTCCCTGAGCTTAACAATTATTCCCATA-TCGAGGCT
1 GGCTTAAACTTTTTTTAGTCCAATGTAAG-CCCTGAACTTAACAATTA-TCCC-TAGTCGAGGCT
5136474 T
63 T
5136475 GAACTTTAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
74 4 0.07
75 45 0.82
76 4 0.07
77 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (74 bp):
GGCTTAAACTTTTTTTAGTCCAATGTAAGCCCTGAACTTAACAATTATCCCTAGTCGAGGCTTAA
AGTAGGTAG
Found at i:5136733 original size:64 final size:61
Alignment explanation
Indices: 5136574--5136766 Score: 190
Period size: 64 Copynumber: 3.1 Consensus size: 61
5136564 TAACTTTGAC
* *
5136574 AAAAAAAAGTACAAGCCCCAATGTTAGGATAATTGTCAAGCCTAAGGCTAATTTAGACAAA
1 AAAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGGCTAACTTAGACAAA
* * * * ** * * * ** *
5136635 AAAAGAGAGTATAAACCGTAATGTGACAACAATTGTCACA-TTTAACGTCTAACTTAGACAACA
1 AAAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCA-AGCCTAA-GGCTAACTTAGACAA-A
* *
5136698 ACAAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAGGGCCTAATTTAGACAAA
1 A-AAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGG-CTAACTTAGACAAA
5136761 AAAAAA
1 AAAAAA
5136767 TTATAAACCC
Statistics
Matches: 98, Mismatches: 28, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
61 31 0.32
62 19 0.19
63 6 0.06
64 42 0.43
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (61 bp):
AAAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGGCTAACTTAGACAAA
Found at i:5136827 original size:125 final size:121
Alignment explanation
Indices: 5136575--5136821 Score: 342
Period size: 125 Copynumber: 2.0 Consensus size: 121
5136565 AACTTTGACA
*
5136575 AAAAAAAGTACAAGCCCCAATGTTAGGATAATTGTCAAGCCTAAGGCTAATTTAGACAAAAAAAG
1 AAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGGCTAATTTAGACAAAAAAAG
* * *
5136640 AGAGTATAAACCGTAATGTGACAACAATTGTCACATTTAACGTCTAACTTAGACAACAAC
66 AGAGTATAAACC---A-CTGACAACAATTGTCACATTTAAAGTCTAACTTAGACAAAAAC
*
5136700 AAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAGGGCCTAATTTAGACAAAAAAA
1 AAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGG-CTAATTTAGACAAAAAAA
* *
5136765 -A-ATTATAAACC-CTGAGAACAATTGTCA-ATTTTAAAGTCTAACTTAGACAAAAA-
65 GAGAGTATAAACCACTGACAACAATTGTCACA-TTTAAAGTCTAACTTAGACAAAAAC
5136818 AAAA
1 AAAA
5136822 CACAAATTCT
Statistics
Matches: 113, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
118 5 0.04
119 36 0.32
124 9 0.08
125 45 0.40
126 18 0.16
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.23
Consensus pattern (121 bp):
AAAAAAAGTACAAGCCCCAATGTTAGAATAATTGTCAAGCCTAAGGCTAATTTAGACAAAAAAAG
AGAGTATAAACCACTGACAACAATTGTCACATTTAAAGTCTAACTTAGACAAAAAC
Found at i:5137227 original size:18 final size:17
Alignment explanation
Indices: 5137204--5137257 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
5137194 AAATTAGAAA
5137204 AAATTTATAATAAATAAT
1 AAATTT-TAATAAATAAT
* *
5137222 AAATTTTAGAAAAATTATT
1 AAATTTTA-ATAAA-TAAT
5137241 AAATTTTAATAAA-AAT
1 AAATTTTAATAAATAAT
5137257 A
1 A
5137258 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 14 0.47
19 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTTAATAAATAAT
Found at i:5137254 original size:19 final size:18
Alignment explanation
Indices: 5137204--5137254 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
5137194 AAATTAGAAA
5137204 AAATTTATAAT-AAATAAT
1 AAATTT-TAATAAAATAAT
*
5137222 AAATTTTAGA-AAAATTATT
1 AAATTTTA-ATAAAA-TAAT
5137241 AAATTTTAATAAAA
1 AAATTTTAATAAAA
5137255 ATATAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 15 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTTTAATAAAATAAT
Found at i:5137273 original size:44 final size:46
Alignment explanation
Indices: 5137213--5137311 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 46
5137203 AAAATTTATA
* *
5137213 ATAAATAATAAATTTTA-GAAAAATTATTAAA-TTTTAATAAAAAT-
1 ATAAAAAATAAATTTTATGAAAAATTA-GAAATTTTTAATAAAAATC
* *
5137257 ATAAAAAATAAATTTTATTAAAAATTAGAAATTTTTTATAAAAATC
1 ATAAAAAATAAATTTTATGAAAAATTAGAAATTTTTAATAAAAATC
5137303 ATAAAAAAT
1 ATAAAAAAT
5137312 TTAACGACCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 19 0.40
45 20 0.42
46 9 0.19
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (46 bp):
ATAAAAAATAAATTTTATGAAAAATTAGAAATTTTTAATAAAAATC
Found at i:5137505 original size:21 final size:21
Alignment explanation
Indices: 5137479--5137523 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5137469 AAAATTTATA
* *
5137479 TTTCTTTAC-ATTTTGTATAAT
1 TTTC-TTACGATTTTATAAAAT
5137500 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
5137521 TTT
1 TTT
5137524 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:5137634 original size:17 final size:18
Alignment explanation
Indices: 5137587--5137642 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 18
5137577 AATGTACAAT
* *
5137587 TTTTTATATAATTATTACGA
1 TTTTTATATATTTTTTA--A
5137607 TTTTTATATATTTTTTAA
1 TTTTTATATATTTTTTAA
5137625 TTTTTA-ATATTTTTTAA
1 TTTTTATATATTTTTTAA
5137642 T
1 T
5137643 AAATGCATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.35
18 7 0.21
20 15 0.44
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTATATATTTTTTAA
Found at i:5137761 original size:88 final size:89
Alignment explanation
Indices: 5137651--5137822 Score: 226
Period size: 88 Copynumber: 1.9 Consensus size: 89
5137641 ATAAATGCAT
* **
5137651 GGGCTTAATTGTTTTTTATGAAAA-AGTTTGAGGATCTTTTTGATACT-TTTTGAAAGTTTAAGT
1 GGGCTTAATTGTTTTTTATGAAAAGA-TTTGAGGATCTTTTTGATA-TATTTTAAAAACTTAAGT
*
5137714 A-CTCAATTGAGTGCAAAAAAGTAAG
64 ACCTAAATTGAGTGCAAAAAAGTAAG
* *
5137739 GGGCTTGATTGCTTTTTT-TGAAAAGATTTGAGGGTCTTTTTGATATATTTTAAAAACTTAAGTA
1 GGGCTTAATTG-TTTTTTATGAAAAGATTTGAGGATCTTTTTGATATATTTTAAAAACTTAAGTA
*
5137803 CCTAAATTGAGTGTAAAAAA
65 CCTAAATTGAGTGCAAAAAA
5137823 AATATTTTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
87 1 0.01
88 48 0.66
89 24 0.33
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (89 bp):
GGGCTTAATTGTTTTTTATGAAAAGATTTGAGGATCTTTTTGATATATTTTAAAAACTTAAGTAC
CTAAATTGAGTGCAAAAAAGTAAG
Found at i:5151455 original size:17 final size:18
Alignment explanation
Indices: 5151433--5151466 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5151423 ACTCGGTAGC
5151433 TTTTTTATTTT-ATTTTA
1 TTTTTTATTTTAATTTTA
5151450 TTTTTTATTTTAATTTT
1 TTTTTTATTTTAATTTT
5151467 CTAATAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTATTTTAATTTTA
Found at i:5153780 original size:18 final size:18
Alignment explanation
Indices: 5153739--5153780 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5153729 CAAAGATATT
* *
5153739 ATTTTTATATTTATTTTA
1 ATTTTAATATTTATTTAA
5153757 ATTTTAATATTT-TTTAA
1 ATTTTAATATTTATTTAA
5153774 ATATTTA
1 AT-TTTA
5153781 TTAACTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAATATTTATTTAA
Found at i:5157992 original size:19 final size:21
Alignment explanation
Indices: 5157968--5158012 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5157958 ACATCGTTTT
*
5157968 CAGAAGC-CCGAAG-GCTAAA
1 CAGAAGCACAGAAGTGCTAAA
*
5157987 CAGAAGCACATAAGTGCTAAA
1 CAGAAGCACAGAAGTGCTAAA
5158008 CAGAA
1 CAGAA
5158013 ACTTATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (21 bp):
CAGAAGCACAGAAGTGCTAAA
Found at i:5158051 original size:21 final size:21
Alignment explanation
Indices: 5157981--5158082 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 21
5157971 AAGCCCGAAG
* * * *
5157981 GCTAAACAGAAGCACATAAGT
1 GCTAAACGGAAACTCATAAGA
* *
5158002 GCTAAACAGAAACTTATAA-A
1 GCTAAACGGAAACTCATAAGA
* * *
5158022 GGTTGAACGGAAGCTCATAAGA
1 -GCTAAACGGAAACTCATAAGA
* * *
5158044 GCTAAACGGAAACCCATTAGG
1 GCTAAACGGAAACTCATAAGA
*
5158065 GTTAAACGGAAACTCATA
1 GCTAAACGGAAACTCATA
5158083 TGAGTTAATA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 60 0.98
22 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (21 bp):
GCTAAACGGAAACTCATAAGA
Found at i:5158073 original size:42 final size:42
Alignment explanation
Indices: 5157978--5158082 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
5157968 CAGAAGCCCG
* * * * **
5157978 AAGGCTAAACAGAAGCACATAAGTGCTAAACAGAAACTTATA
1 AAGGTTAAACGGAAGCTCATAAGAGCTAAACAGAAACCCATA
* * *
5158020 AAGGTTGAACGGAAGCTCATAAGAGCTAAACGGAAACCCATT
1 AAGGTTAAACGGAAGCTCATAAGAGCTAAACAGAAACCCATA
* *
5158062 AGGGTTAAACGGAAACTCATA
1 AAGGTTAAACGGAAGCTCATA
5158083 TGAGTTAATA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AAGGTTAAACGGAAGCTCATAAGAGCTAAACAGAAACCCATA
Found at i:5158089 original size:21 final size:21
Alignment explanation
Indices: 5158027--5158090 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
5158017 ATAAAGGTTG
* * *
5158027 AACGGAAGCTCATAAGAGCTA
1 AACGGAAACTCATATGAGTTA
* *
5158048 AACGGAAACCCAT-TAGGGTTA
1 AACGGAAACTCATAT-GAGTTA
5158069 AACGGAAACTCATATGAGTTA
1 AACGGAAACTCATATGAGTTA
5158090 A
1 A
5158091 TAGAAGCTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (21 bp):
AACGGAAACTCATATGAGTTA
Found at i:5158204 original size:24 final size:24
Alignment explanation
Indices: 5158177--5158238 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
5158167 ATTTGCCGTT
5158177 AATTCATCCTTTGCATTTA-TCGTC
1 AATTCATCCTTTGCATTTACT-GTC
5158201 AATTCATCCTTTGCATTTACTGTC
1 AATTCATCCTTTGCATTTACTGTC
*
5158225 AATTCATTCTTTGC
1 AATTCATCCTTTGC
5158239 CACAGAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
AATTCATCCTTTGCATTTACTGTC
Found at i:5181190 original size:8 final size:9
Alignment explanation
Indices: 5181173--5181268 Score: 54
Period size: 9 Copynumber: 10.1 Consensus size: 9
5181163 TTTATTTTAT
5181173 TTTTTAAAA
1 TTTTTAAAA
5181182 TTTTTAAATA
1 TTTTTAAA-A
*
5181192 CTTTTTTTAAA
1 --TTTTTAAAA
**
5181203 TTTTTTTAA
1 TTTTTAAAA
*
5181212 TTTTAAAAA
1 TTTTTAAAA
5181221 TATTTTAAAAA
1 T-TTTT-AAAA
5181232 TACTTTT--AA
1 T--TTTTAAAA
*
5181241 TTTTT-TAA
1 TTTTTAAAA
5181249 TTTTTAAATA
1 TTTTTAAA-A
5181259 TTTTTAAAA
1 TTTTTAAAA
5181268 T
1 T
5181269 AAATTTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
7 4 0.06
8 7 0.10
9 29 0.41
10 13 0.19
11 6 0.09
12 11 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:5181238 original size:12 final size:11
Alignment explanation
Indices: 5181211--5181240 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
5181201 AATTTTTTTA
5181211 ATTTTAAAAAT
1 ATTTTAAAAAT
5181222 ATTTTAAAAAT
1 ATTTTAAAAAT
5181233 ACTTTTAA
1 A-TTTTAA
5181241 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:5181375 original size:20 final size:21
Alignment explanation
Indices: 5181336--5181379 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5181326 AGAGGCCGGG
*
5181336 CCGGGCTTATAAATTTTTTTC
1 CCGGGCCTATAAATTTTTTTC
*
5181357 CCGGGCCTATGAA-TTTTTTC
1 CCGGGCCTATAAATTTTTTTC
5181377 CCG
1 CCG
5181380 AGCCAGGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
CCGGGCCTATAAATTTTTTTC
Found at i:5183200 original size:29 final size:30
Alignment explanation
Indices: 5183156--5183223 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
5183146 TTTAATTTTT
5183156 ATGTATAAAATCACACA-AAATCAAAATTC
1 ATGTATAAAATCACACATAAATCAAAATTC
* * *
5183185 ATGTATAACATTACACATTGAATCAAAATTC
1 ATGTATAAAATCACACA-TAAATCAAAATTC
5183216 ATGTATAA
1 ATGTATAA
5183224 TTTTAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (30 bp):
ATGTATAAAATCACACATAAATCAAAATTC
Found at i:5185811 original size:26 final size:26
Alignment explanation
Indices: 5185756--5185812 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
5185746 GCATTATAAA
*
5185756 ATATATAAAAATATATGTATACAAGG
1 ATATATAAAAATATAAGTATACAAGG
*
5185782 ATATATAAATAA-ATAAGATATA-AAGT
1 ATATATAAA-AATATAAG-TATACAAGG
5185808 ATATA
1 ATATA
5185813 GATATGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (26 bp):
ATATATAAAAATATAAGTATACAAGG
Found at i:5187637 original size:129 final size:129
Alignment explanation
Indices: 5187495--5188151 Score: 1057
Period size: 129 Copynumber: 5.1 Consensus size: 129
5187485 CACTGCAACG
* * * * * **
5187495 TCAGGGAGATAAGACTTGATACGATCTACTCCACTATAACTTCAGAGAGATAAGATTTTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
* * *
5187560 TAATTCGCTCCACTGTAATCTCAGGGAGATAGAATTACTAGCTTCAATCTACTCCGCTGTAATC
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
* * *
5187624 TCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
* *
5187689 TAATCCGCTACACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTGTAATC
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
* * *
5187753 TCAAGAAGATAAGACCTAATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
* *
5187818 TAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATC
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
* * *
5187882 TCAGGGAGATAAAACCTGATACGATCCACTTTACTGTCACTTC--AGAGATAAGATCTTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
*
5187945 TAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
* *
5188009 TCAGGGAGATAAGACCTGACACGATCCACTCTACTGTCACTTCAAAGAGATAAGATCCTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
5188074 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
*
5188138 TCAAGGAGATAAGA
1 TCAGGGAGATAAGA
5188152 TTTGAGATTC
Statistics
Matches: 491, Mismatches: 35, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
127 120 0.24
129 371 0.76
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (129 bp):
TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
Found at i:5187718 original size:44 final size:43
Alignment explanation
Indices: 5187523--5188152 Score: 239
Period size: 44 Copynumber: 14.7 Consensus size: 43
5187513 ATACGATCTA
* * ** * *
5187523 CTCCACTATAA-CTTCAGAGAGATAAGATTTTTTATTTTAATTCG
1 CTCCACTGTAATC-TCAGGGAGATAAGA-TCATTATTTCAATCCG
* * * **
5187567 CTCCACTGTAATCTCAGGGAGAT-AGAATTACTAGCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAG-ATCATTA-TTTCAATCCG
* * * * * **
5187611 CTCCGCTGTAATCTCAGGGAGATAAGA-CCTGA-TACGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTATTTCAATCCG
* * *
5187652 CTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCA-TTATTTCAATCCG
* * * * * *
5187696 CTACACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTA-TTTCAATCCG
* * * * * * * *
5187740 CTCCGCTGTAATCTCAAGAAGATAAGA-C-CTAATACGATCCA
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTATTTCAATCCG
* * * * *
5187781 CTCTACTGTCA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CATTATTTCAATCCG
* * * * * *
5187825 CTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTA-TTTCAATCCG
* * * * * * * *
5187869 CTCCGCTATAATCTCAGGGAGATAA-AACCTGA-TACGATCCA
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTATTTCAATCCG
** * * *
5187910 CTTTACTGTCA-CTTCA--GAGATAAGATCTTTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATC-ATTATTTCAATCCG
* * * * * *
5187952 CTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTA-TTTCAATCCG
* * * ** * *
5187996 CTCCGCTGTAATCTCAGGGAGATAAGA-CCTGA-CACGATCCA
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTATTTCAATCCG
* * ** * *
5188037 CTCTACTGTCA-CTTCAAAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CATTATTTCAATCCG
* * * * *
5188081 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCATTA-TTTCAATCCG
* *
5188125 CTCCGCTGTAATCTCAAGGAGATAAGAT
1 CTCCACTGTAATCTCAGGGAGATAAGAT
5188153 TTGAGATTCT
Statistics
Matches: 414, Mismatches: 142, Indels: 60
0.67 0.23 0.10
Matches are distributed among these distances:
39 7 0.02
40 6 0.01
41 93 0.22
42 20 0.05
43 25 0.06
44 258 0.62
45 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCATTATTTCAATCCG
Found at i:5188060 original size:256 final size:257
Alignment explanation
Indices: 5187495--5188149 Score: 1062
Period size: 256 Copynumber: 2.5 Consensus size: 257
5187485 CACTGCAACG
* * * * * **
5187495 TCAGGGAGATAAGACTTGATACGATCTACTCCACTATAACTTCAGAGAGATAAGATTTTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
* * *
5187560 TAATTCGCTCCACTGTAATCTCAGGGAGATAGAATTACTAGCTTCAATCTACTCCGCTGTAATCT
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
* *
5187625 CAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTT
131 CAGGGAGATAAAACCTGATACGATCCACTCTACTGTAACTTCA-AGAGATAAGATCATTTATTTT
5187690 AATCCGCTACACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTGTAATC
195 AATCCGCTACACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTGTAATC
* * *
5187753 TCAAGAAGATAAGACCTAATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
* *
5187818 TAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCT
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
* * *
5187883 CAGGGAGATAAAACCTGATACGATCCACTTTACTGTCACTTC-AGAGATAAGATCTTTTATTTTA
131 CAGGGAGATAAAACCTGATACGATCCACTCTACTGTAACTTCAAGAGATAAGATCATTTATTTTA
*
5187947 ATCCGCT-CTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
196 ATCCGCTAC-ACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTGTAATC
* *
5188009 TCAGGGAGATAAGACCTGACACGATCCACTCTACTGTCACTTCAAAGAGATAAGATCCTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
5188074 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
66 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
*
5188139 CAAGGAGATAA
131 CAGGGAGATAA
5188150 GATTTGAGAT
Statistics
Matches: 367, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
255 1 0.00
256 213 0.58
258 153 0.42
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (257 bp):
TCAGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTT
TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
CAGGGAGATAAAACCTGATACGATCCACTCTACTGTAACTTCAAGAGATAAGATCATTTATTTTA
ATCCGCTACACTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTGTAATC
Found at i:5200623 original size:26 final size:26
Alignment explanation
Indices: 5200568--5200624 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
5200558 GCATTATAAA
*
5200568 ATATATAAAAATATATGTATACAAGG
1 ATATATAAAAATATAAGTATACAAGG
*
5200594 ATATATAAATAA-ATAAGATATA-AAGT
1 ATATATAAA-AATATAAG-TATACAAGG
5200620 ATATA
1 ATATA
5200625 GATATGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (26 bp):
ATATATAAAAATATAAGTATACAAGG
Found at i:5201016 original size:21 final size:21
Alignment explanation
Indices: 5200992--5201033 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5200982 TAATAAGGCA
*
5200992 AATAATAAAAATAAAAGTAAT
1 AATAATAAAAATAAAACTAAT
* *
5201013 AATAATGATAATAAAACTAAT
1 AATAATAAAAATAAAACTAAT
5201034 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (21 bp):
AATAATAAAAATAAAACTAAT
Found at i:5202470 original size:37 final size:37
Alignment explanation
Indices: 5202418--5202488 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
5202408 ACACAAAAAA
*
5202418 TATTTTAAAAATAAAAAATAAAAAA-ATATTTTTAAAG
1 TATTTTAAAAAT-AAAAATAAAAAATATATATTTAAAG
*
5202455 TATTTTAAAATTAAAAATAAAAAATATATATTTA
1 TATTTTAAAAATAAAAATAAAAAATATATATTTA
5202489 TTATATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (37 bp):
TATTTTAAAAATAAAAATAAAAAATATATATTTAAAG
Found at i:5202472 original size:36 final size:38
Alignment explanation
Indices: 5202418--5202488 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
5202408 ACACAAAAAA
*
5202418 TATTTTAAAAATAAAAAATAAAAAA-ATATTTTTAAAG
1 TATTTTAAAAATAAAAAATAAAAAATATATATTTAAAG
*
5202455 TATTTT-AAAATTAAAAATAAAAAATATATATTTA
1 TATTTTAAAAATAAAAAATAAAAAATATATATTTA
5202489 TTATATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (38 bp):
TATTTTAAAAATAAAAAATAAAAAATATATATTTAAAG
Found at i:5202769 original size:19 final size:19
Alignment explanation
Indices: 5202747--5202802 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
5202737 TGAATTTTAA
*
5202747 TAAAAAACTATAAAAATAT
1 TAAAAAATTATAAAAATAT
5202766 T-AAAAATTAT-AAAATCAT
1 TAAAAAATTATAAAAAT-AT
* *
5202784 AAAAAAATTATAAATATAT
1 TAAAAAATTATAAAAATAT
5202803 AGAAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.16
18 10 0.32
19 12 0.39
20 4 0.13
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAAATTATAAAAATAT
Found at i:5202788 original size:27 final size:26
Alignment explanation
Indices: 5202756--5202853 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 26
5202746 ATAAAAAACT
*
5202756 ATAAAAATATTAAAAATTATAAAATC
1 ATAAAAAAATTAAAAATTATAAAATC
*
5202782 ATAAAAAAATTATAAATATATAGAAAT-
1 ATAAAAAAATTAAAAAT-TATA-AAATC
* *
5202809 ATAAAAAAATTATAAATTTTATAAAGTC
1 ATAAAAAAATTA-AAA-ATTATAAAATC
* *
5202837 GTAAAAAATATAAAAAA
1 ATAAAAAA-ATTAAAAA
5202854 GTAAAGAGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
26 15 0.26
27 19 0.33
28 20 0.34
29 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAAAAAAATTAAAAATTATAAAATC
Found at i:5203089 original size:10 final size:10
Alignment explanation
Indices: 5203076--5203209 Score: 64
Period size: 10 Copynumber: 13.4 Consensus size: 10
5203066 TTTTTATGCA
5203076 TTTTATAATT
1 TTTTATAATT
*
5203086 TTTTAATGA-T
1 TTTT-ATAATT
**
5203096 TTTTATAAAA
1 TTTTATAATT
* *
5203106 TTTTACATTT
1 TTTTATAATT
5203116 TTTTATAATT
1 TTTTATAATT
*
5203126 TTTTATGA-T
1 TTTTATAATT
5203135 TTTTATAAATTT
1 TTTTAT-AA-TT
*
5203147 ATTTTCTAATT
1 -TTTTATAATT
* *
5203158 TTTAATAA-A
1 TTTTATAATT
5203167 TTTTATATATT
1 TTTTATA-ATT
*
5203178 TTCTATTAA--
1 TTTTA-TAATT
**
5203187 AATT-TAATT
1 TTTTATAATT
5203196 TTTTATAATT
1 TTTTATAATT
5203206 TTTT
1 TTTT
5203210 TGCCACATGT
Statistics
Matches: 89, Mismatches: 23, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
7 3 0.03
9 19 0.21
10 47 0.53
11 10 0.11
12 5 0.06
13 5 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5203110 original size:39 final size:37
Alignment explanation
Indices: 5203076--5203209 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 37
5203066 TTTTTATGCA
5203076 TTTTATAATTTTTTAATGATTTTTATAAAATTTTACATTT
1 TTTTATAATTTTTT-ATGATTTTTATAAAATTTTACA--T
5203116 TTTTATAATTTTTTATGATTTTTATAAATTTATTTT-CTAAT
1 TTTTATAATTTTTTATGATTTTTATAAA---ATTTTAC--AT
*
5203157 TTTTAATAAATTTTATAT-ATTTTCTATTAAAA-TTTA-ATT
1 TTTT-AT-AATTTTTTATGATTTT-TA-TAAAATTTTACA-T
5203196 TTTTATAATTTTTT
1 TTTTATAATTTTTT
5203210 TGCCACATGT
Statistics
Matches: 81, Mismatches: 2, Indels: 25
0.75 0.02 0.23
Matches are distributed among these distances:
37 7 0.09
38 3 0.04
39 19 0.23
40 17 0.21
41 7 0.09
42 12 0.15
43 12 0.15
44 4 0.05
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (37 bp):
TTTTATAATTTTTTATGATTTTTATAAAATTTTACAT
Found at i:5203138 original size:29 final size:27
Alignment explanation
Indices: 5203066--5203139 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 27
5203056 TTAAAGGTCC
*
5203066 TTTTTATGCATTTTATAATTTTTTAATGA
1 TTTTTATG-ATTTT-TAATTTTTTAATAA
* * *
5203095 TTTTTATAAAATTTTACATTTTTTTATAA
1 TTTTTAT-GATTTTTA-ATTTTTTAATAA
5203124 TTTTTTATGATTTTTA
1 -TTTTTATGATTTTTA
5203140 TAAATTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 2 0.06
29 27 0.75
30 7 0.19
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTATGATTTTTAATTTTTTAATAA
Found at i:5203145 original size:20 final size:20
Alignment explanation
Indices: 5203066--5203179 Score: 85
Period size: 20 Copynumber: 5.7 Consensus size: 20
5203056 TTAAAGGTCC
5203066 TTTTTATGCA-TTTTAT-AAT
1 TTTTTATG-ATTTTTATAAAT
5203085 TTTTTAATGATTTTTATAAA-
1 TTTTT-ATGATTTTTATAAAT
* * *
5203105 ATTTTA-CATTTTTTTATAAT
1 TTTTTATGATTTTTATA-AAT
5203125 TTTTTATGATTTTTATAAATT
1 TTTTTATGATTTTTATAAA-T
* *
5203146 TATTTTCTAATTTTTAATAAAT
1 T-TTTTATGATTTTT-ATAAAT
*
5203168 TTTATAT-ATTTT
1 TTTTTATGATTTT
5203180 CTATTAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
18 8 0.11
19 9 0.12
20 25 0.33
21 16 0.21
22 13 0.17
23 5 0.07
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTATGATTTTTATAAAT
Found at i:5203159 original size:32 final size:31
Alignment explanation
Indices: 5203075--5203179 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 31
5203065 CTTTTTATGC
* *
5203075 ATTTTAT-AATTTTTTAATGATTTTT-ATAA
1 ATTTTATAAATTTTTTTATAATTTTTAATAA
* * * *
5203104 AATTT-TACATTTTTTTATAATTTTTTATGA
1 ATTTTATAAATTTTTTTATAATTTTTAATAA
* *
5203134 TTTTTATAAATTTATTTTCTAATTTTTAATAA
1 ATTTTATAAATTT-TTTTATAATTTTTAATAA
*
5203166 ATTTTATATATTTT
1 ATTTTATAAATTTT
5203180 CTATTAAAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
28 1 0.02
29 19 0.32
30 6 0.10
31 7 0.12
32 26 0.44
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (31 bp):
ATTTTATAAATTTTTTTATAATTTTTAATAA
Found at i:5203436 original size:88 final size:86
Alignment explanation
Indices: 5203306--5203579 Score: 322
Period size: 88 Copynumber: 3.1 Consensus size: 86
5203296 TAATGGTCAA
** *
5203306 AGGGCATTTTTGATGCA-TTTGACTGTTCAAATACCCAATTGAGTGCCAAAAAAAA-GAGCTTAA
1 AGGGCATTTTTGATGCATTTTGAAAGTTCAAGTA-CCAATTGAGTGCCAAAAAAAAGGAGCTTAA
5203369 TTGCTTTTTTTTTGAAAAAGTTTG
65 TTGC--TTTTTTTGAAAAAGTTTG
* * *
5203393 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACGCAATTGAGTGCAAAATAAAAAGGGGCTTA
1 AGGGCATTTTTGATGCATTTTGAAAGTTCAAGTAC-CAATTGAGTGCCAAA-AAAAAGGAGCTTA
* *
5203458 ATTACTATTTTTGAAAAAGTTTG
64 ATTGCTTTTTTTGAAAAAGTTTG
* * * * *
5203481 ACGGCATTTTTTATGCATCTTGAAAGTTCAAGTACCTAATTGTGTG-CAAAAAAAGGTAGGAACT
1 AGGGCATTTTTGATGCATTTTGAAAGTTCAAGTACC-AATTGAGTGCCAAAAAAA---AGGAGCT
5203545 TAATTGCTTTTTTTGAAAAAGTTTG
62 TAATTGCTTTTTTTGAAAAAGTTTG
5203570 AGGGC-TTTTT
1 AGGGCATTTTT
5203580 ACACCCTTAA
Statistics
Matches: 160, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
86 4 0.03
87 21 0.13
88 88 0.55
89 37 0.23
90 10 0.06
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (86 bp):
AGGGCATTTTTGATGCATTTTGAAAGTTCAAGTACCAATTGAGTGCCAAAAAAAAGGAGCTTAAT
TGCTTTTTTTGAAAAAGTTTG
Found at i:5205612 original size:6 final size:6
Alignment explanation
Indices: 5205601--5205651 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
5205591 TCATCTCCAG
5205601 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
5205649 ATA
1 ATA
5205652 TACACATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:5206654 original size:101 final size:102
Alignment explanation
Indices: 5206442--5206654 Score: 257
Period size: 101 Copynumber: 2.1 Consensus size: 102
5206432 TTGACAGTAG
* * * * * *
5206442 CTTATAAATCTTTGGTAATGTCAGCTCACTCATATGTGCTCAGACGTACTTTAGAATCATAATTC
1 CTTATAAATCTCTGGTAAAGTCAACACACTCA-ATGCGCTCAGACATACTTTAGAATCATAATTC
* * * *
5206507 AATTTGGAAGTTTATCTTCTAACAAGGACTTTGGATGT
65 AATTTGGAAGTTTATCTTCCAACAACGACATAGGATGT
* *
5206545 CTTTTAAATCTCTGGTAAAGTCAACACACTC-ATGCGCTCAGACATGCTTTAGAATCATAATTCA
1 CTTATAAATCTCTGGTAAAGTCAACACACTCAATGCGCTCAGACATACTTTAGAATCATAATTCA
* ** * *
5206609 ATTTTGAAGTTTATCTTCCAATGACGACATAGTATTT
66 ATTTGGAAGTTTATCTTCCAACAACGACATAGGATGT
5206646 CTTATAAAT
1 CTTATAAAT
5206655 TCTACTCTTC
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 66 0.72
103 26 0.28
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (102 bp):
CTTATAAATCTCTGGTAAAGTCAACACACTCAATGCGCTCAGACATACTTTAGAATCATAATTCA
ATTTGGAAGTTTATCTTCCAACAACGACATAGGATGT
Found at i:5210088 original size:21 final size:21
Alignment explanation
Indices: 5210062--5210105 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5210052 AATTTAATAA
5210062 TAGGTATGGATGG-AATCTGAT
1 TAGGTATGGATGGTAA-CTGAT
5210083 TAGGTATGGATGGTAACTGAT
1 TAGGTATGGATGGTAACTGAT
5210104 TA
1 TA
5210106 CATAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.34
Consensus pattern (21 bp):
TAGGTATGGATGGTAACTGAT
Found at i:5220570 original size:16 final size:17
Alignment explanation
Indices: 5220549--5220582 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5220539 TATAGAATTC
5220549 AATAAA-ATATTAAAAA
1 AATAAATATATTAAAAA
*
5220565 AATAAATATTTTAAAAA
1 AATAAATATATTAAAAA
5220582 A
1 A
5220583 TATATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAATATATTAAAAA
Found at i:5223671 original size:11 final size:11
Alignment explanation
Indices: 5223655--5223681 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5223645 AAGAGATATT
5223655 TTATTATTTTA
1 TTATTATTTTA
5223666 TTATTATTTTA
1 TTATTATTTTA
5223677 TTATT
1 TTATT
5223682 GTATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:5229350 original size:76 final size:77
Alignment explanation
Indices: 5229145--5229361 Score: 210
Period size: 76 Copynumber: 2.8 Consensus size: 77
5229135 GTTTAGTTAT
* * *
5229145 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTCTTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACT-ATATTATTATTA--GTTA-TTAT
5229210 TAGGATTAGTAAAAACCC
62 T--GATTAGTAAAAACCC
* *** * * * *
5229228 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTATATTATTGTTAGTTATTATT-T
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATATTATTATTAGTTATTATTGA
*
5229291 TTAGT-AAAATCC
65 TTAGTAAAAACCC
5229303 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTATTA-TTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTT-AGTAAAAAACTA-TATTATTATTAGTTATT
5229362 GTGTTAGTAA
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
75 29 0.26
76 31 0.28
79 5 0.04
80 4 0.04
82 29 0.26
83 14 0.12
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.51
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATATTATTATTAGTTATTATTGAT
TAGTAAAAACCC
Found at i:5232282 original size:15 final size:15
Alignment explanation
Indices: 5232262--5232290 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5232252 ATGTGTAATT
5232262 ATAATTAAATTTATA
1 ATAATTAAATTTATA
5232277 ATAATTAAATTTAT
1 ATAATTAAATTTAT
5232291 GCAGGTATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAAATTTATA
Found at i:5232402 original size:15 final size:15
Alignment explanation
Indices: 5232382--5232410 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5232372 ATGTGTAATT
5232382 ATAATTAAATTTATA
1 ATAATTAAATTTATA
5232397 ATAATTAAATTTAT
1 ATAATTAAATTTAT
5232411 GCAGGTATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAAATTTATA
Found at i:5232405 original size:120 final size:120
Alignment explanation
Indices: 5232192--5232550 Score: 700
Period size: 120 Copynumber: 3.0 Consensus size: 120
5232182 CTCAGCGAAA
5232192 CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
1 CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
5232257 TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAAG
66 TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAAG
5232312 CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
1 CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
5232377 TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAAG
66 TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAAG
*
5232432 CTATCATGTTGGACAATCGTCAAGATCGGGTCGGAATTGAGCTTATGCTGTAAAATTGTTATGTG
1 CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
*
5232497 TAATTATAATTAAATTTATAATAATTAAATTTATGCTGGTATGTGAATGACCAA
66 TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAA
5232551 TTCCATAGTA
Statistics
Matches: 237, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 237 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (120 bp):
CTATCATGTTGGACAATCGTCAAGATCGGGTCAGAATTGAGCTTATGCTGTAAAATTGTTATGTG
TAATTATAATTAAATTTATAATAATTAAATTTATGCAGGTATGTGAATGACCAAG
Found at i:5232522 original size:15 final size:15
Alignment explanation
Indices: 5232502--5232530 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5232492 ATGTGTAATT
5232502 ATAATTAAATTTATA
1 ATAATTAAATTTATA
5232517 ATAATTAAATTTAT
1 ATAATTAAATTTAT
5232531 GCTGGTATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAAATTTATA
Found at i:5233189 original size:156 final size:157
Alignment explanation
Indices: 5232900--5233352 Score: 706
Period size: 156 Copynumber: 2.9 Consensus size: 157
5232890 ACTTCAAAAC
5232900 AAATTTAGT-AAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGGATTTTATTACCT
1 AAATTTA-TAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGGATTTTATTA-CT
* *
5232964 TT--A-AAAAATATACTATTTT-TTAATTTTATTATTTTACATTATTTTAGTACATTATATTTGA
64 TTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATATTTGA
*
5233025 AATATATTAATTTAGTGTGTTTTTTAAAT-
128 AATGTATTAATTTAGTGTGTTTTTTAAATA
* *
5233054 AAATTTATAAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCC-GATATTTATTACTT
1 AAATTTATAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGGAT-TTTATTACTT
* * *
5233118 TCAATAAAAACATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTAAAA
65 TCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAA
*
5233183 TGTATTAATTTACTGTGTTTTTTAAATA
130 TGTATTAATTTAGTGTGTTTTTTAAATA
*
5233211 AAATTT-TAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCTGATTTTATTACTTT
1 AAATTTATAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGGATTTTATTACTTT
* *
5233275 CAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTAGATTATCTTTGAAAT
66 CAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAAT
5233340 GTATTAATTTAGT
131 GTATTAATTTAGT
5233353 AAAAAATATT
Statistics
Matches: 275, Mismatches: 16, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
153 8 0.03
154 53 0.19
155 1 0.00
156 203 0.74
157 10 0.04
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (157 bp):
AAATTTATAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGGATTTTATTACTTT
CAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAAT
GTATTAATTTAGTGTGTTTTTTAAATA
Found at i:5233467 original size:131 final size:133
Alignment explanation
Indices: 5233228--5233483 Score: 381
Period size: 131 Copynumber: 1.9 Consensus size: 133
5233218 AAAAAAACCC
* * *
5233228 TTATTTCGGCCCTTTATTCGTATTTTTTTCCCTGATTTTATTACTTTCAATAAAAATATATTATT
1 TTATTTCGGCCATTTATTCGTATTTTTTTCCCAGATTTTATCACTTTCAATAAAAATATATTATT
* * * *
5233293 TTCGTATTTTATTATTTTACATTATTTTAGTAGATTATCTTTGAAATGTATTAATTTAGTAAAAA
66 CTCATATTTTATTATTTTACATTATTTAAGTACATTATCTTTGAAATGTATTAATTTAGTAAAAA
5233358 ATA
131 ATA
* * * *
5233361 TTATTTCGGCTATTTGTTCGTATTTTTTTTCCAGATTTTCTCACTTTC-A-AAAAATATATTATT
1 TTATTTCGGCCATTTATTCGTATTTTTTTCCCAGATTTTATCACTTTCAATAAAAATATATTATT
* *
5233424 CTCATATTTTATTATTTTACATTCTTTAAGTACATTATGTTTGAAATGTATTAATTTAGT
66 CTCATATTTTATTATTTTACATTATTTAAGTACATTATCTTTGAAATGTATTAATTTAGT
5233484 GTGTTTTTTA
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 68 0.62
132 1 0.01
133 41 0.37
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (133 bp):
TTATTTCGGCCATTTATTCGTATTTTTTTCCCAGATTTTATCACTTTCAATAAAAATATATTATT
CTCATATTTTATTATTTTACATTATTTAAGTACATTATCTTTGAAATGTATTAATTTAGTAAAAA
ATA
Found at i:5234241 original size:41 final size:40
Alignment explanation
Indices: 5234155--5234241 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
5234145 CCGAATATAA
*
5234155 TAAAT-ATATTTTTTAATTTTTTAATTTTAAAAATACTTT
1 TAAATAATATTTTTTAATTTTTTAATTTTAAAAATAATTT
* * * *
5234194 TAAAATAATTTTTTTTATTTTTTTTATTTTTAAAATAAATTT
1 T-AAATAATATTTTTTAATTTTTTAATTTTAAAAAT-AATTT
5234236 TAAATA
1 TAAATA
5234242 TTTATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 4 0.10
41 30 0.75
42 5 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (40 bp):
TAAATAATATTTTTTAATTTTTTAATTTTAAAAATAATTT
Found at i:5234905 original size:11 final size:11
Alignment explanation
Indices: 5234868--5234956 Score: 72
Period size: 11 Copynumber: 8.0 Consensus size: 11
5234858 CATTGCTTTG
*
5234868 TTATCATTTTA
1 TTATTATTTTA
* *
5234879 TTATTATATTG
1 TTATTATTTTA
*
5234890 CTATTATTTTA
1 TTATTATTTTA
*
5234901 TTATTATTTGA
1 TTATTATTTTA
* *
5234912 ATATTA-TATA
1 TTATTATTTTA
5234922 TTTATTATTTTA
1 -TTATTATTTTA
*
5234934 TTATTAATTTTG
1 TTATT-ATTTTA
*
5234946 TTACTATTTTA
1 TTATTATTTTA
5234957 GATATATTTG
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
10 2 0.03
11 45 0.76
12 12 0.20
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:5238883 original size:17 final size:17
Alignment explanation
Indices: 5238863--5238913 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
5238853 TAGAAGTTCT
5238863 AATAATTAAATATTTAA
1 AATAATTAAATATTTAA
*
5238880 AATAATTAAATTATAATTAT
1 AATAATTAAA-TAT--TTAA
*
5238900 AATAATTAATTATT
1 AATAATTAAATATT
5238914 GAATAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 11 0.38
18 3 0.10
19 3 0.10
20 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATTAAATATTTAA
Found at i:5238903 original size:20 final size:18
Alignment explanation
Indices: 5238862--5238913 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
5238852 ATAGAAGTTC
5238862 TAATAATTAAA-TATTTA
1 TAATAATTAAATTATTTA
*
5238879 AAATAATTAAATTATAATTA
1 TAATAATTAAATTAT--TTA
5238899 TAATAATT-AATTATT
1 TAATAATTAAATTATT
5238914 GAATAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 11 0.37
18 3 0.10
19 6 0.20
20 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAATTAAATTATTTA
Found at i:5242410 original size:29 final size:29
Alignment explanation
Indices: 5242368--5242443 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
5242358 TTACTTTAAG
* *
5242368 TTACATTTTGGTCACTTATGTTTAAAATA
1 TTACGTTTTAGTCACTTATGTTTAAAATA
5242397 TTACGTTTTAGTCACTTATGTTTAAAATA
1 TTACGTTTTAGTCACTTATGTTTAAAATA
5242426 TTACGTTTTAGTCACTTA
1 TTACGTTTTAGTCACTTA
5242444 CGTTATACTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (29 bp):
TTACGTTTTAGTCACTTATGTTTAAAATA
Found at i:5242444 original size:15 final size:15
Alignment explanation
Indices: 5242397--5242447 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
5242387 GTTTAAAATA
5242397 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
* * *
5242412 TTATGTTTAAAAT-A-
1 TTACGTTT-TAGTCAC
5242426 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
5242441 TTACGTT
1 TTACGTT
5242448 ATACTGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:5242691 original size:27 final size:26
Alignment explanation
Indices: 5242640--5242692 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
5242630 ACTCTCTCTT
*
5242640 TTTCTCTTTATTTTCCATTATCTTCTG
1 TTTCTCTTTATTTTCCA-TACCTTCTG
5242667 TTTCTCCTTCTATTTTCC-TACCTTCT
1 TTTCT-CTT-TATTTTCCATACCTTCT
5242693 CCATGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 3 0.13
29 8 0.35
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCTCTTTATTTTCCATACCTTCTG
Found at i:5246266 original size:16 final size:16
Alignment explanation
Indices: 5246245--5246286 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5246235 TTTTTTTTGC
*
5246245 AAATATATTTATTTTT
1 AAATATATTTATTTTA
*
5246261 AAATAT-TAATATTTTA
1 AAATATAT-TTATTTTA
5246277 AAATATATTT
1 AAATATATTT
5246287 TTATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATATTTATTTTA
Found at i:5248862 original size:52 final size:52
Alignment explanation
Indices: 5248784--5248882 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
5248774 TGGCTTAGCC
5248784 AATACACCCCTAATCGGTGGGCCCCACCTAATACCTCTTTAACACGTAAGCT
1 AATACACCCCTAATCGGTGGGCCCCACCTAATACCTCTTTAACACGTAAGCT
* *
5248836 AATACACCCTTAATCGGTGGGCCCCACTTAATACCTCTTTAACACGT
1 AATACACCCCTAATCGGTGGGCCCCACCTAATACCTCTTTAACACGT
5248883 CGTTTGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.25
Consensus pattern (52 bp):
AATACACCCCTAATCGGTGGGCCCCACCTAATACCTCTTTAACACGTAAGCT
Found at i:5252225 original size:16 final size:16
Alignment explanation
Indices: 5252204--5252271 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
5252194 GATTTGCTAT
5252204 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5252220 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5252236 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
5252252 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
5252268 TACA
1 TACA
5252272 GTGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5259089 original size:36 final size:36
Alignment explanation
Indices: 5259048--5259116 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
5259038 TTTTTTAAAC
* *
5259048 TTCTAATTGAATTTTTAAAATATTAATATTGTAATG
1 TTCTAATTGAATTATAAAAATATTAATATTGTAATG
*
5259084 TTCTAATTGAATTATAAAAATATTAGTATTGTA
1 TTCTAATTGAATTATAAAAATATTAATATTGTA
5259117 TTAATCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.48
Consensus pattern (36 bp):
TTCTAATTGAATTATAAAAATATTAATATTGTAATG
Found at i:5266265 original size:40 final size:40
Alignment explanation
Indices: 5266220--5266532 Score: 274
Period size: 40 Copynumber: 7.7 Consensus size: 40
5266210 GTTTTAGTCT
*
5266220 GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCC
* * * *
5266260 ACTCCACTACTGCTTAGGG-GAATAAGATCTGTGGTTCTG-TCT
1 GCTCCACTACTGCTTAGGGAG-ATAAGA-C--TGGATGTGATCC
* * * * * *
5266302 GCTCCACTATTGCTTGGGGAGATAAGACTTGAAGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCC
* * *
5266342 GCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGTGATCC
* * *
5266384 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCC
* * *
5266424 GCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGTGATCC
* * * **
5266466 GCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCC
*
5266506 GCTCCACTATTGCTTAGGGAGATAAGA
1 GCTCCACTACTGCTTAGGGAGATAAGA
5266533 TCTGTGGTTT
Statistics
Matches: 219, Mismatches: 40, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
39 12 0.05
40 108 0.49
41 6 0.03
42 79 0.36
43 14 0.06
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCC
Found at i:5266304 original size:82 final size:82
Alignment explanation
Indices: 5266201--5266543 Score: 508
Period size: 82 Copynumber: 4.2 Consensus size: 82
5266191 CACGGGGATG
* * * * **
5266201 AGATTTGTGGTTTTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCTACTCCA
1 AGATCTGTGGTTTT-GTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCA
*
5266266 CTACTGCTTAGGG-GAATA
65 CTATTGCTTAGGGAG-ATA
* * * * * *
5266284 AGATCTGTGGTTCTGTCTGCTCCACTATTGCTTGGGGAGATAAGACTTGAAGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5266349 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
*
5266366 AGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5266431 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
* * *
5266448 AGATCTGTGGTTTTGTCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCCGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5266513 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
5266530 AGATCTGTGGTTTT
1 AGATCTGTGGTTTT
5266544 CACTCTATTC
Statistics
Matches: 241, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
82 228 0.95
83 13 0.05
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (82 bp):
AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
TATTGCTTAGGGAGATA
Found at i:5266808 original size:44 final size:45
Alignment explanation
Indices: 5266648--5267024 Score: 322
Period size: 44 Copynumber: 8.5 Consensus size: 45
5266638 GCTTCGCTGC
* * * * * *
5266648 CCAATACAGGAAGGCAAGATCTGCAATCCTCAATCTA-TTCCACTGT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT-CACT-A
* * * *
5266694 CAAATACAGG--GACAAGATCTGCTTTCTTCGATCTACTTCACCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * *
5266737 CCAGTATGGGAAGACAAGATCTG-TATCTTGGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * *
5266780 TCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-G
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * * *
5266824 CCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * *
5266869 CCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * *
5266912 CCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCAC-G
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * * *
5266956 CCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
*
5267001 CCAATATGGGAAGACAAGATCTGC
1 CCAATATAGGAAGACAAGATCTGC
5267025 ATCNNNNNNN
Statistics
Matches: 260, Mismatches: 62, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
43 48 0.18
44 146 0.56
45 57 0.22
46 9 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (45 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
Found at i:5266886 original size:132 final size:132
Alignment explanation
Indices: 5266704--5267027 Score: 567
Period size: 132 Copynumber: 2.5 Consensus size: 132
5266694 CAAATACAGG
* * * * * *
5266704 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGA
* *
5266769 TCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGACCTGCTACCTTCGATCTACTTCACGCCAATACATG
5266834 AA
131 AA
5266836 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGA
*
5266901 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGACCTGCTACCTTCGATCTACTTCACGCCAATACATG
5266966 AA
131 AA
5266968 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
5267028 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 183 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (132 bp):
GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGA
TCCACTTCCTACCAATATAGGAAGATAGGACCTGCTACCTTCGATCTACTTCACGCCAATACATG
AA
Found at i:5274535 original size:17 final size:17
Alignment explanation
Indices: 5274509--5274549 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5274499 GCCCCGTTAA
*
5274509 ATATGTAATGGATAATC
1 ATATGCAATGGATAATC
5274526 ATATGCAATGGATAATC
1 ATATGCAATGGATAATC
5274543 ATATGCA
1 ATATGCA
5274550 CGTATCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (17 bp):
ATATGCAATGGATAATC
Found at i:5275783 original size:3 final size:3
Alignment explanation
Indices: 5275775--5275838 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
5275765 ATGTTATGTC
*
5275775 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5275823 TAA TAG CAA TAA TAA T
1 TAA TAA TAA TAA TAA T
5275839 GTAAATATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5275928 original size:3 final size:3
Alignment explanation
Indices: 5275917--5276156 Score: 52
Period size: 3 Copynumber: 80.7 Consensus size: 3
5275907 TGATGATAGC
* * * * * *
5275917 AAT AGT AAT AAT -GT AAT AAT AA- AGT AAA AAA AAT AAT AGT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * *
5275965 AAT AAG AAT AAT AAT AGT -AT ATT AAT AAC AAT AAT AGAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * * * * *
5276010 GAC GA- AAT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AGT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
* * * * *
5276054 AAC AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * ** *
5276099 AAT AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AAT AGC AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5276146 AA- AATT AAT AA
1 AAT AA-T AAT AA
5276157 ATAAATATAA
Statistics
Matches: 170, Mismatches: 47, Indels: 40
0.66 0.18 0.16
Matches are distributed among these distances:
2 14 0.08
3 142 0.84
4 11 0.06
5 3 0.02
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:5275974 original size:23 final size:23
Alignment explanation
Indices: 5275948--5276001 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5275938 AAGTAAAAAA
*
5275948 AATAATAGTAATACATTAATAAG
1 AATAATAGTAATACATTAATAAC
* * *
5275971 AATAATAATAGTATATTAATAAC
1 AATAATAGTAATACATTAATAAC
5275994 AATAATAG
1 AATAATAG
5276002 AAAATAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
AATAATAGTAATACATTAATAAC
Done.