Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1154
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1159333
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 97731 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:867759 original size:204 final size:203
Alignment explanation
Indices: 867409--867815 Score: 805
Period size: 204 Copynumber: 2.0 Consensus size: 203
867399 CACGGATCTA
867409 AAACGATGACAAATATCGAAAAGGCAATATTGTGGGTGAAGGATGAATGTGTGCATGTAGTTTGT
1 AAACGATGACAAATATCGAAAAGGCAATATTGTGGGTGAAGGATGAATGTGTGCATGTAGTTTGT
867474 TTTCGAGGTTTATATTTGATACATGTAATTATATTTATCTCGATCAGTTTTGTTTGTTGTTTTGT
66 TTTCGAGGTTTATATTTGATACATGTAATTATATTTATCTCGATCAGTTTTGTTTGTTGTTTTGT
867539 TTTGTTTATTAAAAAGGGGAATAAAGAAAATGAGTAATTTCCAGGCACGTAGCATCGTTTTTGAA
131 TTTGTTTATTAAAAAGGGGAATAAAGAAAATGAGTAATTTCCAGGCACGTAGCATCGTTTTTGAA
867604 AGTGGGGG
196 AGTGGGGG
867612 NAAACGATGACAAATATCGAAAAGGCAATATTGTGGGTGAAGGATGAATGTGTGCATGTAGTTTG
1 -AAACGATGACAAATATCGAAAAGGCAATATTGTGGGTGAAGGATGAATGTGTGCATGTAGTTTG
867677 TTTTCGAGGTTTATATTTGATACATGTAATTATATTTATCTCGATCAGTTTTGTTTGTTGTTTTG
65 TTTTCGAGGTTTATATTTGATACATGTAATTATATTTATCTCGATCAGTTTTGTTTGTTGTTTTG
867742 TTTTGTTTATTAAAAAGGGGAATAAAGAAAATGAGTAATTTCCAGGCACGTAGCATCGTTTTTGA
130 TTTTGTTTATTAAAAAGGGGAATAAAGAAAATGAGTAATTTCCAGGCACGTAGCATCGTTTTTGA
867807 AAGTGGGGG
195 AAGTGGGGG
867816 GGGGGCAAAC
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 203 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (203 bp):
AAACGATGACAAATATCGAAAAGGCAATATTGTGGGTGAAGGATGAATGTGTGCATGTAGTTTGT
TTTCGAGGTTTATATTTGATACATGTAATTATATTTATCTCGATCAGTTTTGTTTGTTGTTTTGT
TTTGTTTATTAAAAAGGGGAATAAAGAAAATGAGTAATTTCCAGGCACGTAGCATCGTTTTTGAA
AGTGGGGG
Found at i:885730 original size:2 final size:2
Alignment explanation
Indices: 885723--885756 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
885713 TTATGATCTT
* *
885723 TC TC TC TC TC TC CC TC TC TC TC GC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
885757 ACACACACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.44
Consensus pattern (2 bp):
TC
Found at i:910393 original size:2 final size:2
Alignment explanation
Indices: 910386--910424 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
910376 CGGCCTTATG
*
910386 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
910425 GTTTGTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:911477 original size:2 final size:2
Alignment explanation
Indices: 911470--911513 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
911460 ACGGGAAGGC
*
911470 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
911512 AG
1 AG
911514 GGGGGCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:915216 original size:97 final size:97
Alignment explanation
Indices: 915050--915231 Score: 285
Period size: 97 Copynumber: 1.9 Consensus size: 97
915040 TTTGTTTAAG
* *
915050 TTAATTATCTCCCAAACCACGAGTCATTTTGATATACCCATTTAATTCTCAATATGTCCTTGGTT
1 TTAATTATCTCCCAAACCACGAGTCATTTTGATATACCCATTTAATTCTCAATATATCCGTGGTT
915115 AATTAAATTTTGATTTACATGTTTAAAGTAAA
66 AATTAAATTTTGATTTACATGTTTAAAGTAAA
* * ** *
915147 TTAATTATCTTCCAAACCACGAGTCGTTTTGATATACCGGTTTAGA-TCTCAATATATTCGTGGT
1 TTAATTATCTCCCAAACCACGAGTCATTTTGATATACCCATTTA-ATTCTCAATATATCCGTGGT
915211 TAATTAAATTTTGATTTACAT
65 TAATTAAATTTTGATTTACAT
915232 TATAATCAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 76 0.99
98 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (97 bp):
TTAATTATCTCCCAAACCACGAGTCATTTTGATATACCCATTTAATTCTCAATATATCCGTGGTT
AATTAAATTTTGATTTACATGTTTAAAGTAAA
Found at i:932754 original size:2 final size:2
Alignment explanation
Indices: 932747--932791 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
932737 GGAAAACATT
932747 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
932789 AG A
1 AG A
932792 TACAGACAGA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:934672 original size:147 final size:146
Alignment explanation
Indices: 934208--934854 Score: 827
Period size: 146 Copynumber: 4.5 Consensus size: 146
934198 TTAAACTGTT
* *
934208 GGTCAAAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCAT--G--AGATAAT-GA
1 GGTCATAAGCAATATTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
* * *
934267 CCAGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCAGACACAAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
*
934332 GGTCATGACACACCCTTT
129 GGTCATGACACACCCTTA
* * * * *
934350 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATACAATGTGTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* *
934415 AGACACGAATTTTTGTATTTTTTCTGCCAGTGACCTTG-CC-T----AAATGACCTTGGTTCAAG
66 AGACAC-AAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
934474 GTCATGACACACCCTTT
130 GTCATGACACACCCTTA
* *
934491 GGAT-TTAAGGAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGAC
1 GG-TCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGAC
* *
934555 CGGACACAAATTTTGTATTTTTTTCTGCCAGTGACATTGACCTTGCCCAAATGACCTTGGGTCAA
65 CAGACACAAATTTTGTA-TTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
*
934620 GGTCATGACACACCCTAA
129 GGTCATGACACACCCTTA
* * * ** * *
934638 GGTCATAAGCAATCTTTGTGTAAAGTAAAAACTTCCAATAATTCTACATAAGAACGATATGGACC
1 GGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* ** *
934703 GGACA-AGAATTTTGTATTCATTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAG
66 AGACACA-AATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
934767 GTCATGAGACACCCTTA
130 GTCATGACACACCCTTA
* * * *
934784 GGTTATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTGCATAAGAGAGATATGGACC
1 GGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
934849 AGACAC
66 AGACAC
934855 GATTGCACAG
Statistics
Matches: 440, Mismatches: 47, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
140 9 0.02
141 117 0.27
142 44 0.10
143 1 0.00
144 1 0.00
145 3 0.01
146 138 0.31
147 127 0.29
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (146 bp):
GGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
AGACACAAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTA
Found at i:934883 original size:12 final size:12
Alignment explanation
Indices: 934861--934894 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
934851 ACACGATTGC
*
934861 ACAGACAGACGG
1 ACAGACGGACGG
*
934873 ACAGAGGGACGG
1 ACAGACGGACGG
934885 ACAGACGGAC
1 ACAGACGGAC
934895 AAGGTGACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.38, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:941159 original size:12 final size:12
Alignment explanation
Indices: 941142--941167 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
941132 CCCCCAAAAA
941142 AAAAAAAAAATT
1 AAAAAAAAAATT
941154 AAAAAAAAAATT
1 AAAAAAAAAATT
941166 AA
1 AA
941168 GAATTTTTTT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:942166 original size:43 final size:43
Alignment explanation
Indices: 942100--942603 Score: 665
Period size: 43 Copynumber: 11.5 Consensus size: 43
942090 TATATGTCAT
* *
942100 TGATCAAATTATGGAATGATTTTCATTTT-ATCATTACTTTACA
1 TGATCAAATTATGAAATGATTTTC-TTTTCATCATTACTTTATA
*
942143 TGATTAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
942186 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
*
942229 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACATG
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTT--ATA
* * *
942274 TCAGATTAAATTAGGAAATGATTTTCATTTC-TACATTACTTTATA
1 T--GATCAAATTATGAAATGATTTTCTTTTCAT-CATTACTTTATA
* * *
942319 TGAACAAATTATGAAATGATTTTATTTTCATCATTACTTTTTA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
* * *
942362 TAATGAAATTATGAAATGATTTTCTTTTTATCATTACTTTATA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
* *
942405 TGATCAAATTATGAAATAATTTTCTATTT-ATCATTACTTTTCATG
1 TGATCAAATTATGAAATGATTTTCT-TTTCATCATTAC-TTT-ATA
* *
942450 TCAGATTAAATTATGAAATGATTTT-TATTTTATCATTACTTTATA
1 T--GATCAAATTATGAAATGATTTTCT-TTTCATCATTACTTTATA
* * *
942495 TGATCAAATTATGAAAAGACTTTCTTTTCATCATTACTTTAGA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
942538 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
* * *
942581 TGAGCAAATTGTGAACTGATTTT
1 TGATCAAATTATGAAATGATTTT
942604 TCTATAAACG
Statistics
Matches: 408, Mismatches: 39, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.01
43 313 0.77
44 8 0.02
45 12 0.03
46 9 0.02
47 62 0.15
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.48
Consensus pattern (43 bp):
TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
Found at i:942334 original size:133 final size:128
Alignment explanation
Indices: 942100--942604 Score: 658
Period size: 133 Copynumber: 3.9 Consensus size: 128
942090 TATATGTCAT
* *
942100 TGATCAAATTATGGAATGATTTTCATTTT-ATCATTACTTTACATGATTAAATTATGAAATGATT
1 TGATCAAATTATGAAATGATTTTC-TTTTCATCATTACTTTACATGATCAAATTATGAAATGATT
* *
942164 TTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTATA
65 TTCATTTCATCATTACTTTATATGAACAAATTATGAAATGATTTT-TTTTCATCATTACTTTATA
* *
942229 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACATGTCAGATTAAATTAGGAAATG
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACA--T--GATCAAATTATGAAATG
942294 ATTTTCATTTC-TACATTACTTTATATGAACAAATTATGAAATGATTTTATTTTCATCATTACTT
62 ATTTTCATTTCAT-CATTACTTTATATGAACAAATTATGAAATGATTTT-TTTTCATCATTACTT
*
942358 TTTA
125 TATA
* * * * *
942362 TAATGAAATTATGAAATGATTTTCTTTTTATCATTACTTTATATGATCAAATTATGAAATAATTT
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACATGATCAAATTATGAAATGATTT
* *
942427 TCTATTT-ATCATTACTTT-TCATGTCAGATTAAATTATGAAATGATTTTTATTTTATCATTACT
66 TC-ATTTCATCATTACTTTAT-ATG--A-A-CAAATTATGAAATGATTTTT-TTTCATCATTACT
942490 TTATA
124 TTATA
* * *
942495 TGATCAAATTATGAAAAGACTTTCTTTTCATCATTACTTTAGATGATCAAATTATGAAATGATTT
1 TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACATGATCAAATTATGAAATGATTT
* * * *
942560 TCTTTTCATCATTACTTTATATGAGCAAATTGTGAACTGATTTTT
66 TCATTTCATCATTACTTTATATGAACAAATTATGAAATGATTTTT
942605 CTATAAACGT
Statistics
Matches: 332, Mismatches: 28, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
128 5 0.02
129 86 0.26
130 5 0.02
131 4 0.01
132 6 0.02
133 225 0.68
134 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (128 bp):
TGATCAAATTATGAAATGATTTTCTTTTCATCATTACTTTACATGATCAAATTATGAAATGATTT
TCATTTCATCATTACTTTATATGAACAAATTATGAAATGATTTTTTTTCATCATTACTTTATA
Found at i:942408 original size:176 final size:176
Alignment explanation
Indices: 942086--942608 Score: 791
Period size: 176 Copynumber: 3.0 Consensus size: 176
942076 TCTAGTTATG
* * * *
942086 ACTTTATATGTCATTGATCAAATTATGG-AATGATTTTCATTTTATCATTACTTTACATGATTAA
1 ACTTTACATGTCA--GATTAAATTA-GGAAATGATTTTCATTTTATCATTACTTTATATGATCAA
942150 ATTATGAAATGATTTTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTC
63 ATTATGAAATGATTTTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTC
942215 ATCATTACTTTATATGATCAAATTATGAAATGATTTTCT-TTTCATCATT
128 ATCATTACTTTATATGATCAAATTATGAAATGATTTTCTATTT-ATCATT
*
942264 ACTTTACATGTCAGATTAAATTAGGAAATGATTTTCATTTCTA-CATTACTTTATATGAACAAAT
1 ACTTTACATGTCAGATTAAATTAGGAAATGATTTTCATTT-TATCATTACTTTATATGATCAAAT
* * * * *
942328 TATGAAATGATTTTATTTTCATCATTACTTTTTATAATGAAATTATGAAATGATTTTCTTTTTAT
65 TATGAAATGATTTTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTCAT
*
942393 CATTACTTTATATGATCAAATTATGAAATAATTTTCTATTTATCATT
130 CATTACTTTATATGATCAAATTATGAAATGATTTTCTATTTATCATT
* * *
942440 ACTTTTCATGTCAGATTAAATTATGAAATGATTTTTATTTTATCATTACTTTATATGATCAAATT
1 ACTTTACATGTCAGATTAAATTAGGAAATGATTTTCATTTTATCATTACTTTATATGATCAAATT
* * *
942505 ATGAAAAGACTTTCTTTTCATCATTACTTTAGATGATCAAATTATGAAATGATTTTCTTTTCATC
66 ATGAAATGATTTTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTCATC
* * *
942570 ATTACTTTATATGAGCAAATTGTGAACTGATTTTTCTAT
131 ATTACTTTATATGATCAAATTATGAAATGA-TTTTCTAT
942609 AAACGTTACT
Statistics
Matches: 313, Mismatches: 27, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
175 4 0.01
176 284 0.91
177 13 0.04
178 12 0.04
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (176 bp):
ACTTTACATGTCAGATTAAATTAGGAAATGATTTTCATTTTATCATTACTTTATATGATCAAATT
ATGAAATGATTTTCTTTTCATCATTACTTTATATGATCAAATTATGAAATGATTTTCTTTTCATC
ATTACTTTATATGATCAAATTATGAAATGATTTTCTATTTATCATT
Found at i:947034 original size:21 final size:21
Alignment explanation
Indices: 947008--947049 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
946998 CACTAAAACG
*
947008 CATGCAACGAATGCGAGAGCT
1 CATGCAACGAATGAGAGAGCT
*
947029 CATGCAACGTATGAGAGAGCT
1 CATGCAACGAATGAGAGAGCT
947050 TGTGCGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (21 bp):
CATGCAACGAATGAGAGAGCT
Found at i:951545 original size:26 final size:26
Alignment explanation
Indices: 951509--951568 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
951499 CTGCATAAAC
951509 ATCAACATATGGTTCAATGTTTCAAT
1 ATCAACATATGGTTCAATGTTTCAAT
951535 ATCAACATATGGTTCAATGTTTCAAT
1 ATCAACATATGGTTCAATGTTTCAAT
951561 ATCAACAT
1 ATCAACAT
951569 TTAAAAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (26 bp):
ATCAACATATGGTTCAATGTTTCAAT
Found at i:953432 original size:24 final size:24
Alignment explanation
Indices: 953391--953463 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
953381 AATATCCACA
* * *
953391 TTGTCTTTGGAAGCCTCATTCTGT
1 TTGTCTTGGGATGTCTCATTCTGT
*
953415 TTGTCTTGGGATGTCTCATTTTGT
1 TTGTCTTGGGATGTCTCATTCTGT
* * * *
953439 TTCTCTTGAGATGTTTCTTTCTGT
1 TTGTCTTGGGATGTCTCATTCTGT
953463 T
1 T
953464 CACCTCCCGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.10, C:0.16, G:0.21, T:0.53
Consensus pattern (24 bp):
TTGTCTTGGGATGTCTCATTCTGT
Found at i:959238 original size:16 final size:16
Alignment explanation
Indices: 959219--959249 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
959209 GTACACTGAC
959219 TATATTTACCCGACTA
1 TATATTTACCCGACTA
*
959235 TATATTTACCTGACT
1 TATATTTACCCGACT
959250 CATCTGACTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (16 bp):
TATATTTACCCGACTA
Found at i:965374 original size:20 final size:20
Alignment explanation
Indices: 965346--965384 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
965336 CTACAGTATA
965346 TGAACATTCACCAACTTACT
1 TGAACATTCACCAACTTACT
* *
965366 TGAATATTCACTAACTTAC
1 TGAACATTCACCAACTTAC
965385 ATGTAGTTTT
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:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (20 bp):
TGAACATTCACCAACTTACT
Found at i:973857 original size:12 final size:12
Alignment explanation
Indices: 973840--973864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
973830 TTACAATTCA
973840 AAAAAAAAAAAG
1 AAAAAAAAAAAG
973852 AAAAAAAAAAAG
1 AAAAAAAAAAAG
973864 A
1 A
973865 TTGCTATCCC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:984146 original size:1 final size:1
Alignment explanation
Indices: 984140--984164 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
984130 GCGGATTTAA
984140 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
984165 CCCCCCCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:988007 original size:2 final size:2
Alignment explanation
Indices: 988000--988060 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
987990 GTATTAATTT
988000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
988042 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
988061 TCGCAAATCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:991054 original size:1 final size:1
Alignment explanation
Indices: 991048--991085 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
991038 CCGTCTGTCC
991048 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
991086 ACAAATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:999139 original size:237 final size:236
Alignment explanation
Indices: 998724--999197 Score: 939
Period size: 237 Copynumber: 2.0 Consensus size: 236
998714 GTCATTGCTC
998724 AAATCCAAATGGGTTATATCTAGCTGGAACAAACGACAAATTTGGGCAAGGAATTAACTATGAAC
1 AAATCCAAATGGGTTATATCTAGCTGGAACAAACGACAAATTTGGGCAAGGAATTAACTATGAAC
998789 CGTGGTTAGGCTACTATTATTCCCTGAGAACCGTTCGTTTAATGGTAAGAAAAGTGGGTAAAAAA
66 CGTGGTTAGGCTACTATTATTCCCTGAGAACCGTTCGTTTAATGGTAAGAAAAGTGGGTAAAAAA
998854 ATATGATAGTAGTGACTTTGACATTGACCAATGCGCAGTAGCGTCAGATGACTGTGTAGAGAAAC
131 ATATGATAGTAGTGACTTTGACATTGACCAATGCGCAGTAGCGTCAGATGACTGTGTAGAGAAAC
998919 AATTTTAAATTTCTAACAGAAAATGAATCAAATATATATAT
196 AATTTTAAATTTCTAACAGAAAATGAATCAAATATATATAT
998960 NAAATCCAAATGGGTTATATCTAGCTGGAACAAACGACAAATTTGGGCAAGGAATTAACTATGAA
1 -AAATCCAAATGGGTTATATCTAGCTGGAACAAACGACAAATTTGGGCAAGGAATTAACTATGAA
999025 CCGTGGTTAGGCTACTATTATTCCCTGAGAACCGTTCGTTTAATGGTAAGAAAAGTGGGTAAAAA
65 CCGTGGTTAGGCTACTATTATTCCCTGAGAACCGTTCGTTTAATGGTAAGAAAAGTGGGTAAAAA
999090 AATATGATAGTAGTGACTTTGACATTGACCAATGCGCAGTAGCGTCAGATGACTGTGTAGAGAAA
130 AATATGATAGTAGTGACTTTGACATTGACCAATGCGCAGTAGCGTCAGATGACTGTGTAGAGAAA
999155 CAATTTTAAATTTCTAACAGAAAATGAATCAAATATATATAT
195 CAATTTTAAATTTCTAACAGAAAATGAATCAAATATATATAT
999197 A
1 A
999198 TATATATATA
Statistics
Matches: 237, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
236 1 0.00
237 236 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (236 bp):
AAATCCAAATGGGTTATATCTAGCTGGAACAAACGACAAATTTGGGCAAGGAATTAACTATGAAC
CGTGGTTAGGCTACTATTATTCCCTGAGAACCGTTCGTTTAATGGTAAGAAAAGTGGGTAAAAAA
ATATGATAGTAGTGACTTTGACATTGACCAATGCGCAGTAGCGTCAGATGACTGTGTAGAGAAAC
AATTTTAAATTTCTAACAGAAAATGAATCAAATATATATAT
Found at i:1003005 original size:66 final size:66
Alignment explanation
Indices: 1002881--1003010 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
1002871 GGACGAATCC
* * * * * * *
1002881 AGCAAATACACCATAAGCATATCAGGATATTCTGGAAATGTTGGTAATATGATTAATAATACTTT
1 AGCAAATACACAATAAGCATATCAAGATATTCTGGAAATGTTAGTAAGATCATAAATAACACTTT
1002946 A
66 A
* * *
1002947 AGCAAATCCACAATAGGCATATCAAGATATTTTGGAAATGTTAGTAAGATCATAAATAACACTT
1 AGCAAATACACAATAAGCATATCAAGATATTCTGGAAATGTTAGTAAGATCATAAATAACACTT
1003011 CCCTTATTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (66 bp):
AGCAAATACACAATAAGCATATCAAGATATTCTGGAAATGTTAGTAAGATCATAAATAACACTTT
A
Found at i:1005678 original size:1 final size:1
Alignment explanation
Indices: 1005667--1005703 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
1005657 ACTATTCAGG
*
1005667 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1005704 NGTAAAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1005735 original size:2 final size:2
Alignment explanation
Indices: 1005728--1005760 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1005718 ATTATTGTAC
1005728 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1005761 TAATTATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1022793 original size:66 final size:66
Alignment explanation
Indices: 1022661--1022794 Score: 189
Period size: 66 Copynumber: 2.0 Consensus size: 66
1022651 GATGGACGAA
* * * *
1022661 TCAAGCAAATACGCCATAAGCATATCAGGATATTCTGGAAATGTTGGTAATATGCTTAATATTAC
1 TCAAGCAAATACGCCATAAGCATATCAAGATATTCTAGAAATGTTGGTAATATGCTAAATAATAC
1022726 T
66 T
* * *
1022727 TCAAGTAAATCCGCCATAGGCATATCAAGATATTCTAGAAATGTTGGTAATAT-CATAAATAATA
1 TCAAGCAAATACGCCATAAGCATATCAAGATATTCTAGAAATGTTGGTAATATGC-TAAATAATA
1022791 CT
65 CT
1022793 TC
1 TC
1022795 CCTAACTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (66 bp):
TCAAGCAAATACGCCATAAGCATATCAAGATATTCTAGAAATGTTGGTAATATGCTAAATAATAC
T
Found at i:1024116 original size:3 final size:3
Alignment explanation
Indices: 1024108--1024133 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1024098 CGCCCCACCG
1024108 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1024134 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1030246 original size:42 final size:42
Alignment explanation
Indices: 1030199--1030282 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1030189 TCAGGGCCCG
* *
1030199 CCATGCTTGGCTGTAGCGACTCGATGGGCATTGGTTGCGTCC
1 CCATGCCTGACTGTAGCGACTCGATGGGCATTGGTTGCGTCC
* * *
1030241 CCATGCCTGACTGTATCGGCTCGATGGGCATTGGTTGTGTCC
1 CCATGCCTGACTGTAGCGACTCGATGGGCATTGGTTGCGTCC
1030283 GATTTTGGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.30
Consensus pattern (42 bp):
CCATGCCTGACTGTAGCGACTCGATGGGCATTGGTTGCGTCC
Found at i:1040075 original size:166 final size:166
Alignment explanation
Indices: 1039653--1040743 Score: 1251
Period size: 166 Copynumber: 6.5 Consensus size: 166
1039643 GTGATGATTT
** * * *
1039653 TCTACACTAATTGAGGATGCTTCCACACAAGTGTCAGATTTTCTGGCTGATTAGTTTCTGAGAAG
1 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
* * * *
1039718 AAGATTTTTAAAGA--T--T-TATATATTCCTTTGTTAAACTTTGA-CCCCCATTGTGGCCCTAC
66 AAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCGACCCCCCATTGTGGCCCCAC
* *
1039777 CCTACCCCCAGGGGTCATGATTTTCAAAACTTTGAA
131 CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * * *
1039813 TCTACACTACCTGAGTAGTGAGGATGCTTCCACACAAATTTCAGCTCTCCTGG-T-CTTATGGTT
1 TCTACACTACC-------TGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTA-GTTT
* * *
1039876 CATGAGAATAAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCAACCCCCCATGG
58 C-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCGACCCCCCATTG
** * *
1039941 TGGCCCCATTCTACCCCCGGGGGTTATGATTTTCACAACATTGAA
122 TGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* *
1039986 T-TAACACTACCTGAGGATGCTTCCACACAAGTTTTAGCTTTGCTGGCTGATTAGTTTCTGAGAA
1 TCT-ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAA
* * *
1040050 GAAGATTTTTAAAGATTTACTCTATATATTTC-TCTGTTAAACTTTGACCCCCCCCATTGGGGCC
65 GAAGATTTTTAAAGATTTACTCTATATA-TTCATATGTTAAACTTCGA--CCCCCCATTGTGGCC
1040114 CCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
127 CCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
** * * *
1040154 TCTACACTACCTGACGAGTGAGGATAATTCTACACAAGTTTCAGCTTTCCTGG-T-CTTATGGTT
1 TCTACACTA-C---C---TGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTA-GTTT
* * *
1040217 CATGAGAAGAAGATTTTTAAAGATTTACTCTGTATATTCATATG-TATAATTTCGACCCCTCCTT
58 C-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGTTA-AACTTCGACCCC-CCAT
* * * *
1040281 TGTGGCCCAAACCTACCCTCGGGGGGGTCATGATTTTCACAACTTTGTA
120 TGTGGCCCCACCCTACCC-C-CGGGGGTCATGATTTTCACAACTTTGAA
* * *
1040330 TCTACACTACCTGAGGATGTTTCCACAAAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAG
1 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
*
1040395 AAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTTGACCCCCCATTGTGGCCCCAC
66 AAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCGACCCCCCATTGTGGCCCCAC
* * * *
1040460 CCTACCCCTGGGGATCATGAGTTTCACAACTATGAA
131 CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* ** *
1040496 TCTACACTACCTGAGAATGCTTCCACACAAGTGCCAGCTGTCCTGGCTGATTAGTTTCTGAGAAG
1 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
* * * *
1040561 AAGATTTTTAAAGATTTACTCTATATATTCCTTTATAAAACTTCGACCCCCCATTGTGGCCCCAC
66 AAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCGACCCCCCATTGTGGCCCCAC
*
1040626 CCTACCCCCAGGGGTCATGATTTTCACAACTTTGAA
131 CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * * * *
1040662 TCTACACTAACTGAGGATGCTTTCACGCAAGTGTCAGCTTTCCTGGCT--TTATGGTTCATGAGA
1 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTA-GTTTC-TGAGA
*
1040725 AGATGATTTTTGAAA-ATTT
64 AGAAGATTTTT-AAAGATTT
1040744 CTCGAAAATT
Statistics
Matches: 791, Mismatches: 98, Indels: 78
0.82 0.10 0.08
Matches are distributed among these distances:
160 9 0.01
164 3 0.00
165 7 0.01
166 314 0.40
167 62 0.08
168 78 0.10
169 84 0.11
170 7 0.01
171 4 0.01
172 24 0.03
173 62 0.08
174 28 0.04
175 74 0.09
176 35 0.04
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (166 bp):
TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
AAGATTTTTAAAGATTTACTCTATATATTCATATGTTAAACTTCGACCCCCCATTGTGGCCCCAC
CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
Found at i:1042437 original size:20 final size:20
Alignment explanation
Indices: 1042386--1043743 Score: 766
Period size: 20 Copynumber: 67.0 Consensus size: 20
1042376 ACCCACACCG
* *
1042386 ACCCACACAGCGATCCACAT
1 ACCCACACACCGATCCACAA
* * * *
1042406 ATCCATATACCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1042426 ACCCACACACCGA-CGTACAA
1 ACCCACACACCGATC-CACAA
** *
1042446 ATTCACACACCTATCCA-AA
1 ACCCACACACCGATCCACAA
*
1042465 ATCCCACACACTGATCCACAA
1 A-CCCACACACCGATCCACAA
*** *
1042486 A-CCAC-CTTAGAACCACAA
1 ACCCACACACCGATCCACAA
* *
1042504 TCCCTAACACACCGATTCACAA
1 ACCC--ACACACCGATCCACAA
* *
1042526 ACCCACACATCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1042546 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
* *
1042566 ACCGACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
* * * *
1042586 TCCTACACAGAGCGATCAACAA
1 ACC--CACACACCGATCCACAA
* * *
1042608 ACCCATATACCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1042628 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
* *
1042648 ACCCACACACCGACCCAGAA
1 ACCCACACACCGATCCACAA
* *
1042668 ACCCTCACACCTATCCA-AA
1 ACCCACACACCGATCCACAA
*
1042687 ATCCCACACACTGATCCACAA
1 A-CCCACACACCGATCCACAA
** *
1042708 ACCCACTTA--GAACCACAA
1 ACCCACACACCGATCCACAA
* * *
1042726 TCCCTTATACACCGATCCAAAA
1 ACCC--ACACACCGATCCACAA
* *
1042748 ACCCACACATCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1042768 ACCCACACA-TGCATAGACCAACAA
1 ACCCACACACCG-AT---CC-ACAA
* * *
1042792 ACCCACAAACCAATACACAA
1 ACCCACACACCGATCCACAA
* * *
1042812 ACCGACACGCCGACCCACAA
1 ACCCACACACCGATCCACAA
* * *
1042832 TCCTACACAGAGCGATCCACAA
1 ACC--CACACACCGATCCACAA
* * * *
1042854 ACCCATATACCGACCCACAT
1 ACCCACACACCGATCCACAA
*
1042874 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
* *
1042894 ACCCACACACCTATTCA-AA
1 ACCCACACACCGATCCACAA
* *
1042913 ATCCCACACACTGATCAACAA
1 A-CCCACACACCGATCCACAA
** *
1042934 ACCCACTTTA---AACCACAA
1 ACCCAC-ACACCGATCCACAA
* *
1042952 TCCATAACACACCGATCCACAA
1 ACC--CACACACCGATCCACAA
* *
1042974 ACCCACACATCGACCCACAA
1 ACCCACACACCGATCCACAA
** *
1042994 ACCCACAC-CAAATACACAA
1 ACCCACACACCGATCCACAA
* * *
1043013 ACCGACACGCCGACCCACAA
1 ACCCACACACCGATCCACAA
* *
1043033 TCCTCCACACAGCGATCCACAA
1 -AC-CCACACACCGATCCACAA
* * *
1043055 ACCCATATACCGA-CTCACAT
1 ACCCACACACCGATC-CACAA
* * * * *
1043075 ATCCATATACCAACCCACAA
1 ACCCACACACCGATCCACAA
*
1043095 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1043115 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
* * *
1043135 ACCGACACGCCGACCCACAA
1 ACCCACACACCGATCCACAA
* **
1043155 TCCTCCACACAGTGATCCACAA
1 -AC-CCACACACCGATCCACAA
* *
1043177 ACCCATATACCGA-CTCACAA
1 ACCCACACACCGATC-CACAA
*
1043197 ACCCACACACCGA-CGTACAA
1 ACCCACACACCGATC-CACAA
** *
1043217 ATTCACACACCTATCCA-AA
1 ACCCACACACCGATCCACAA
*
1043236 ATCCCACACATCGATCCACAA
1 A-CCCACACACCGATCCACAA
** *
1043257 ACCCACTTA--GAACCACAA
1 ACCCACACACCGATCCACAA
* * * *
1043275 TCCTTAACACACCTATCCAAAA
1 ACC--CACACACCGATCCACAA
*
1043297 ACCCACACATCGATCCACAA
1 ACCCACACACCGATCCACAA
* * *
1043317 ACCCAAAGATGCATCGACCCACAA
1 ACCC--ACA--CACCGATCCACAA
*
1043341 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
* * * *
1043361 ACCGACACGCCGACCCATAA
1 ACCCACACACCGATCCACAA
* * *
1043381 TCCTACCCACAGCGATCCACAA
1 ACC--CACACACCGATCCACAA
* * *
1043403 ACCCATATACCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1043423 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1043443 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
** *
1043463 ATTCACACACCTATCCA-AA
1 ACCCACACACCGATCCACAA
**
1043482 ATCCCACACATTGATCCACAA
1 A-CCCACACACCGATCCACAA
** *
1043503 ACCCACTTA--GAACCACAA
1 ACCCACACACCGATCCACAA
* * * *
1043521 TCCTTAACACACCTATCCAAAA
1 ACC--CACACACCGATCCACAA
* *
1043543 ACCCACACATCGACCCACAA
1 ACCCACACACCGATCCACAA
*
1043563 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
* *
1043583 ACCAACA-AGCCGACCCACAA
1 ACCCACACA-CCGATCCACAA
* *
1043603 TCCTACACACAGCGATCCACAA
1 ACC--CACACACCGATCCACAA
* *
1043625 ACCCATATACCGA-CTCACAA
1 ACCCACACACCGATC-CACAA
*
1043645 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
*
1043665 ACCCACACACCGATACACAA
1 ACCCACACACCGATCCACAA
* * * *
1043685 ACTCACACATCGACCCATAA
1 ACCCACACACCGATCCACAA
*
1043705 ACCCACACACCGACCCACAA
1 ACCCACACACCGATCCACAA
* * *
1043725 ACCTATACACCGATACACA
1 ACCCACACACCGATCCACA
1043744 TACCGACACG
Statistics
Matches: 1002, Mismatches: 271, Indels: 130
0.71 0.19 0.09
Matches are distributed among these distances:
18 48 0.05
19 41 0.04
20 722 0.72
21 26 0.03
22 132 0.13
23 3 0.00
24 30 0.03
ACGTcount: A:0.40, C:0.44, G:0.06, T:0.10
Consensus pattern (20 bp):
ACCCACACACCGATCCACAA
Found at i:1042936 original size:226 final size:222
Alignment explanation
Indices: 1042386--1043125 Score: 848
Period size: 226 Copynumber: 3.3 Consensus size: 222
1042376 ACCCACACCG
* * ** **
1042386 ACCCACACAGCGATCCACATATCCATATACCGACCCACAAACCCACACACCGACGTACAAATTCA
1 ACCCACACAGCGATCCACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCA
1042451 CACACCTATCCAAAATCCCACACACTGATCCACAAA-CCACCTTAGAACCACAATCCCTAACACA
66 CACACCTATCCAAAATCCCACACACTGATCCACAAACCCA-CTTAGAACCACAATCCCTAACACA
* * * *
1042515 CCGATTCACAAACCCACACATCGACCCACAAACCCACACACCGATACACAAACCGACACACCGAC
130 CCGATCCACAAACCCACACATCGACCCACAAACCCACACACCGATACACAAACCCACAAACCAAC
* * * * *
1042580 CCACAATCCTACACAGAGCGATCAACAA
195 ACACAAACCGACACAGACCGACCAACAA
* * * * * * * *
1042608 ACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCACACACCGACCCAGAAACCCT
1 ACCCACACAGCGATCCACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCA
* *
1042673 CACACCTATCCAAAATCCCACACACTGATCCACAAACCCACTTAGAACCACAATCCCTTATACAC
66 CACACCTATCCAAAATCCCACACACTGATCCACAAACCCACTTAGAACCACAATCCCTAACACAC
* *
1042738 CGATCCAAAAACCCACACATCGACCCACAAACCCACACA-TGCATAGACCAACAAACCCACAAAC
131 CGATCCACAAACCCACACATCGACCCACAAACCCACACACCG-AT--A-C-ACAAACCCACAAAC
* *
1042802 CAATACACAAACCGACAC-G-CCGACCCACAA
191 CAACACACAAACCGACACAGACCGACCAACAA
* * *
1042832 TCCTACACAGAGCGATCCACAAACCCATATACCGACCCACATACCCACACACCGACCCACAAACC
1 ACC--CACACAGCGATCCACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACC
* * *
1042897 CACACACCTATTCAAAATCCCACACACTGATCAACAAACCCACTTTA-AACCACAATCCATAACA
64 CACACACCTATCCAAAATCCCACACACTGATCCACAAACCCAC-TTAGAACCACAATCCCTAACA
** * ** *
1042961 CACCGATCCACAAACCCACACATCGACCCACAAACCCACAC-CAAATACACAAACCGACACGCCG
128 CACCGATCCACAAACCCACACATCGACCCACAAACCCACACACCGATACACAAACCCACAAACCA
* * ** * *
1043025 ACCCACAATCCTCCACACAGCGATCC-ACAA
193 ACACACAAACCGACACAGACCGA-CCAACAA
* * * * * *
1043055 ACCCATATACCGA-CTCACATATCCATATACCAACCCACAAACCCACACACCGACCCACAAACCC
1 ACCCACACAGCGATC-CACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCC
1043119 ACACACC
65 ACACACC
1043126 GATACACAAA
Statistics
Matches: 438, Mismatches: 66, Indels: 29
0.82 0.12 0.05
Matches are distributed among these distances:
220 1 0.00
221 83 0.19
222 150 0.34
223 13 0.03
224 13 0.03
225 4 0.01
226 171 0.39
227 3 0.01
ACGTcount: A:0.40, C:0.44, G:0.06, T:0.10
Consensus pattern (222 bp):
ACCCACACAGCGATCCACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCA
CACACCTATCCAAAATCCCACACACTGATCCACAAACCCACTTAGAACCACAATCCCTAACACAC
CGATCCACAAACCCACACATCGACCCACAAACCCACACACCGATACACAAACCCACAAACCAACA
CACAAACCGACACAGACCGACCAACAA
Found at i:1043239 original size:82 final size:80
Alignment explanation
Indices: 1042510--1043721 Score: 568
Period size: 82 Copynumber: 14.9 Consensus size: 80
1042500 ACAATCCCTA
* * *
1042510 ACACACCGATTCACAAACCCACACATCGACCCACAAACCCACACACCGATACACAAACCGACACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
*
1042575 CCGACCCACAATCCTAC
66 CCGACCCAAAATCC--C
* * * * * ** *
1042592 ACAGAGCGATCAACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCACACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
1042657 CCGACCCAGAAA-CCC
66 CCGACCCA-AAATCCC
* * * * * ** * *
1042672 TCACACCTATCCA-AAATCCCACACACTGATCCACAAACCCACTTA--GA-ACCACAATCCCTTA
1 ACACATCGATCCACAAA-CCCACACACCGACCCACAAACCCACACACCGATA-CACAA-ACC-GA
* * *
1042733 TACACCGATCCAAAAACCC
62 CACACCGACCCAAAATCCC
* * * * *
1042752 ACACATCGACCCACAAACCCACACATGCATAGACCAACAAACCCACAAACCAATACACAAACCGA
1 ACACATCGATCCACAAACCCACACA--C--CGACCCACAAACCCACACACCGATACACAAACCGA
* *
1042817 CACGCCGACCCACAATCCTAC
62 CACACCGACCCAAAATCC--C
* * * * * ** *
1042838 ACAGAGCGATCCACAAACCCATATACCGACCCACATACCCACACACCGACCCACAAACCCACACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
* **
1042903 CCTATTCAAAATCCC
66 CCGACCCAAAATCCC
* ** * * * * *
1042918 ACACA-CTGATCAACAAACCCACTTTA---AACCACAATCCATAACACACCGATCCACAAACCCA
1 ACACATC-GATCCACAAACCCAC-ACACCGACCCACAAACC--CACACACCGATACACAAACCGA
*
1042979 CACATCGACCCACAAA-CCC
62 CACACCGACCCA-AAATCCC
* * * * * * * * *
1042998 ACAC--CAAATACACAAACCGACACGCCGACCCACAATCCTCCACACAGCGATCCACAAACCCAT
1 ACACATC-GATCCACAAACCCACACACCGACCCACAA-AC-CCACACACCGATACACAAACCGAC
* * *
1043061 ATACCGACTCACATAT-CC
63 ACACCGACCCA-AAATCCC
* * * * * *
1043079 ATATACCAACCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACG
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
*
1043144 CCGACCCACAATCCTCC
66 CCGACCCAAAAT-C-CC
* * * **
1043161 ACACAGT-GATCCACAAACCCATATACCGACTCACAAACCCACACACCGACGTACA-AATTC-AC
1 ACACA-TCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGA--TACACAAACCGAC
* *
1043223 ACACCTATCCAAAATCCC
63 ACACCGACCCAAAATCCC
** * * * * * * *
1043241 ACACATCGATCCACAAACCCACTTA--GAACCACAATCCTTAACACACCTATCCAAAAACCCACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACC--CACACACCGATACACAAACCGACA
* *
1043304 CATCGATCCACAAA-CCC
64 CACCGACCCA-AAATCCC
* * ** * * ** * * *
1043321 AAAGATGCATCGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCATAATCCTA
1 --ACA--CATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGA
* *
1043386 CCCACAGCGATCCACAAA-CCC
62 --CACACCGACCCA-AAATCCC
* * * * ** *
1043407 ATATACCGACCCACAAACCCACACACCGACCCACAAACCCACACACCGACCCACAAATTC-ACAC
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAA-CCGACAC
* *
1043471 ACCTATCCAAAATCCC
65 ACCGACCCAAAATCCC
* ** * * * * * * *
1043487 ACACATTGATCCACAAACCCACTTA--GAACCACAATCCTTAACACACCTATCCAAAAACCCACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACC--CACACACCGATACACAAACCGACA
*
1043550 CATCGACCCACAAA-CCC
64 CACCGACCCA-AAATCCC
* * * * * * * *
1043567 ACACACCGATACACAAACCAACA-AGCCGACCCACAATCCTACACACAGCGATCCACAAACCCAT
1 ACACATCGATCCACAAACCCACACA-CCGACCCACAAACC--CACACACCGATACACAAACCGAC
* *
1043631 ATACCGACTCACAAA-CCC
63 ACACCGACCCA-AAATCCC
* * ** * * ** * *
1043649 ACACACCGATACACAAACCCACACACCGATACACAAACTCACACATCGACCCATAAACCCACACA
1 ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
1043714 CCGACCCA
66 CCGACCCA
1043722 CAAACCTATA
Statistics
Matches: 867, Mismatches: 204, Indels: 120
0.73 0.17 0.10
Matches are distributed among these distances:
78 37 0.04
79 32 0.04
80 292 0.34
81 58 0.07
82 313 0.36
83 9 0.01
84 69 0.08
85 2 0.00
86 54 0.06
87 1 0.00
ACGTcount: A:0.40, C:0.44, G:0.06, T:0.10
Consensus pattern (80 bp):
ACACATCGATCCACAAACCCACACACCGACCCACAAACCCACACACCGATACACAAACCGACACA
CCGACCCAAAATCCC
Found at i:1043366 original size:226 final size:229
Alignment explanation
Indices: 1043105--1043567 Score: 682
Period size: 246 Copynumber: 2.0 Consensus size: 229
1043095 ACCCACACAC
*
1043105 CGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCACAATCCT-CCACACAGTG
1 CGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCACAATCCTACC-CACAGCG
* *
1043169 ATCCACAAACCCATATACCGACTCACAAACCCACACACCG-A-CG-TACAAATTCACACACCTAT
65 ATCCACAAACCCATATACCGACCCACAAACCCACACACCGCACCGCCACAAATTCACACACCTAT
1043231 CCAAAATCCCACACATCGATCCACAAACCCACTTAGAACCACAATCCTTAACACACCTATCCAAA
130 CCAAAATCCCACACATCGATCCACAAACCCACTTAGAACCACAATCCTTAACACACCTATCCAAA
*
1043296 AACCCACACATCGATCCACAAACCCAAAGATGCAT
195 AACCCACACATCGACCCACAAACCCAAAGATGCAT
*
1043331 CGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCATAATCCTACCCACAGCGA
1 CGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCACAATCCTACCCACAGCGA
1043396 TCCACAAACCCATATACCGACCCACAAACCCACACACCGACCCACAAACCCACACACCGACCCAC
66 TCCACAAACCCATATACCGACCCACAAACCCACACACCG---------------CACCG--CCAC
*
1043461 AAATTCACACACCTATCCAAAATCCCACACATTGATCCACAAACCCACTTAGAACCACAATCCTT
114 AAATTCACACACCTATCCAAAATCCCACACATCGATCCACAAACCCACTTAGAACCACAATCCTT
1043526 AACACACCTATCCAAAAACCCACACATCGACCCACAAACCCA
179 AACACACCTATCCAAAAACCCACACATCGACCCACAAACCCA
1043568 CACACCGATA
Statistics
Matches: 210, Mismatches: 6, Indels: 22
0.88 0.03 0.09
Matches are distributed among these distances:
226 98 0.47
227 2 0.01
242 1 0.00
243 2 0.01
246 107 0.51
ACGTcount: A:0.40, C:0.43, G:0.06, T:0.11
Consensus pattern (229 bp):
CGACCCACAAACCCACACACCGATACACAAACCGACACGCCGACCCACAATCCTACCCACAGCGA
TCCACAAACCCATATACCGACCCACAAACCCACACACCGCACCGCCACAAATTCACACACCTATC
CAAAATCCCACACATCGATCCACAAACCCACTTAGAACCACAATCCTTAACACACCTATCCAAAA
ACCCACACATCGACCCACAAACCCAAAGATGCAT
Found at i:1043438 original size:12 final size:12
Alignment explanation
Indices: 1043423--1043461 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1043413 CGACCCACAA
1043423 ACCCACACACCG
1 ACCCACACACCG
1043435 ACCCACA-A---
1 ACCCACACACCG
1043443 ACCCACACACCG
1 ACCCACACACCG
1043455 ACCCACA
1 ACCCACA
1043462 AATTCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.38, C:0.56, G:0.05, T:0.00
Consensus pattern (12 bp):
ACCCACACACCG
Found at i:1043839 original size:20 final size:20
Alignment explanation
Indices: 1043814--1043869 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1043804 CACACACATA
1043814 CCACAAACCTACACACTGAT
1 CCACAAACCTACACACTGAT
* *
1043834 CCACAAA-CTCACATATTGAT
1 CCACAAACCT-ACACACTGAT
**
1043854 ATACAAACCTACACAC
1 CCACAAACCTACACAC
1043870 CAATACAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.18
Consensus pattern (20 bp):
CCACAAACCTACACACTGAT
Found at i:1053789 original size:12 final size:12
Alignment explanation
Indices: 1053756--1053800 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1053746 TCCGTGCAAC
*
1053756 CAAAAAAAAAAA
1 CAAAAAAACAAA
* *
1053768 GAAAAGAACAAA
1 CAAAAAAACAAA
*
1053780 CAAACAAACAAA
1 CAAAAAAACAAA
1053792 CAAAAAAAC
1 CAAAAAAAC
1053801 TACTAAACTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (12 bp):
CAAAAAAACAAA
Found at i:1058247 original size:2 final size:2
Alignment explanation
Indices: 1058240--1058275 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1058230 TCTCATCTGC
1058240 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1058276 GTTCAGATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1060429 original size:19 final size:20
Alignment explanation
Indices: 1060401--1060449 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1060391 TACATGTATA
*
1060401 AATCAGTATCAGCCCTGCA-
1 AATCAATATCAGCCCTGCAG
* *
1060420 TATCAATATCAGTCCTGCAG
1 AATCAATATCAGCCCTGCAG
1060440 AATCAATATC
1 AATCAATATC
1060450 GGCTTTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (20 bp):
AATCAATATCAGCCCTGCAG
Found at i:1072756 original size:22 final size:23
Alignment explanation
Indices: 1072730--1072774 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1072720 AGAAAACTCC
1072730 ATAAGCAAATATGACG-TAATCA
1 ATAAGCAAATATGACGTTAATCA
1072752 ATAAGCAAATATGACGTTAATCA
1 ATAAGCAAATATGACGTTAATCA
1072775 TGCAGTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.24
Consensus pattern (23 bp):
ATAAGCAAATATGACGTTAATCA
Found at i:1075109 original size:22 final size:22
Alignment explanation
Indices: 1075084--1075134 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1075074 ATTTGGGTCC
* *
1075084 ACTCTGGGTTTACTTT-GCGTTT
1 ACTCGGGGTATACTTTAG-GTTT
1075106 ACTCGGGGTATACTTTAGGTTT
1 ACTCGGGGTATACTTTAGGTTT
1075128 ACTCGGG
1 ACTCGGG
1075135 AATTGCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (22 bp):
ACTCGGGGTATACTTTAGGTTT
Found at i:1093823 original size:92 final size:92
Alignment explanation
Indices: 1093652--1093824 Score: 215
Period size: 92 Copynumber: 1.9 Consensus size: 92
1093642 GATGTACACA
* * * **
1093652 ATATTGATACGATATCGATTTTACATTGTAAACATTGCCTATATTTCTTTGCCGTTTACATCAAC
1 ATATTGATACGATATCGATTTTACATCGTAAACATGGCCGATATTTCTTTAACGTTTACATCAAC
*
1093717 GACATTGTCGACATCGCAAAATTGACG
66 GACATTGTCAACATCGCAAAATTGACG
** * *
1093744 ATATTGA-ACAGATATCGATTTTACATCGTTGACATGGCCGATATTTTTTTTAACGTTTACATCG
1 ATATTGATAC-GATATCGATTTTACATCGTAAACATGGCCGATA-TTTCTTTAACGTTTACATCA
*
1093808 TCGACATTG-CAACATCG
64 ACGACATTGTCAACATCG
1093825 ACGATGTTGA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 2 0.03
92 42 0.62
93 24 0.35
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (92 bp):
ATATTGATACGATATCGATTTTACATCGTAAACATGGCCGATATTTCTTTAACGTTTACATCAAC
GACATTGTCAACATCGCAAAATTGACG
Found at i:1094021 original size:83 final size:83
Alignment explanation
Indices: 1093740--1094025 Score: 290
Period size: 83 Copynumber: 3.4 Consensus size: 83
1093730 TCGCAAAATT
* * * * * *
1093740 GACGATATTG-AACAGATATCGATTTTACATCGT-TGACATGGCCGATATTTTTTTTAACGTTTA
1 GACGATGTTGAAACA-ATATCAAATTTACATTGTCT-ACATCGCCGATA-TTTCTTTAACGTTTA
*
1093803 CATCGTCGACATTGCAACATC
63 CATCGTCGACATTGCAACGTC
* * * * * * * * * *
1093824 GACGATGTTGAATCGATATTGAGA-TAACATCGTCGACATTGCCGATATTTCTTAAACGTTAACA
1 GACGATGTTGAAACAATA-TCAAATTTACATTGTCTACATCGCCGATATTTCTTTAACGTTTACA
*
1093888 TCGTCGACATCGCAACGTC
65 TCGTCGACATTGCAACGTC
** * * *
1093907 GATAATGTTGAAACAATATCTAATTTTCATTGTCTACATCGCGGATATTTCTTTAACGTTTACAT
1 GACGATGTTGAAACAATATCAAATTTACATTGTCTACATCGCCGATATTTCTTTAACGTTTACAT
*
1093972 CGTCGACATTGCAATGTC
66 CGTCGACATTGCAACGTC
*
1093990 GACGATGTTGAACCAATATCAAATTTACATTGTCTA
1 GACGATGTTGAAACAATATCAAATTTACATTGTCTA
1094026 TATTGATGAA
Statistics
Matches: 161, Mismatches: 37, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
82 2 0.01
83 125 0.78
84 31 0.19
85 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (83 bp):
GACGATGTTGAAACAATATCAAATTTACATTGTCTACATCGCCGATATTTCTTTAACGTTTACAT
CGTCGACATTGCAACGTC
Found at i:1111335 original size:140 final size:139
Alignment explanation
Indices: 1111147--1111544 Score: 479
Period size: 131 Copynumber: 3.0 Consensus size: 139
1111137 TATTGTTGTT
* *
1111147 AAAGTCCCATAACTCCAACAAAAAGCATCGACCAATGCTGATTTTCGAACTTTACCAAAGTATTA
1 AAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTA-TA
*
1111212 GTGGTATGAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTAGGAATGAGAGCGCTT
65 GTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTAGGAATGAGAGCGCTT
1111277 ACAAGGTCAC
130 ACAAGGTCAC
*
1111287 AAAGTCCCATAACTCCAACAAAAAGTATCAACCAATGCTGATTTTCGAACTTGACCAAAGTAATA
1 AAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGT-ATA
*** * * * * *
1111352 GTGGTATAAACATTTGG--T--A-GGCATG-AGAGCGCTTACAAAA-----AAGTATGAGAGCGC
65 GTGGTATAAACATTTGGTATAAATTTAATGAAAATC-CGT-CAAAATTTGTAGGAATGAGAGCGC
*
1111406 TTACATGGTCAC
128 TTACAAGGTCAC
* *
1111418 ACAGTCCCATAACTCCAACCAAAAGTATCGACCAATGCTGATTTTCGAACTTGACC-----A-AG
1 AAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATAG
* * *
1111477 TGGTATAAACATATGGTATAAATTTAATGAAAATCCGTCAACATTTGTAGGCATGAGAGCGCTTA
66 TGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTAGGAATGAGAGCGCTTA
1111542 CAA
131 CAA
1111545 AAAGTGTGAC
Statistics
Matches: 217, Mismatches: 27, Indels: 35
0.78 0.10 0.13
Matches are distributed among these distances:
124 17 0.08
125 1 0.00
126 1 0.00
128 5 0.02
129 5 0.02
130 3 0.01
131 76 0.35
133 17 0.08
134 3 0.01
135 5 0.02
136 6 0.03
138 1 0.00
140 76 0.35
141 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (139 bp):
AAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATAG
TGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTAGGAATGAGAGCGCTTA
CAAGGTCAC
Found at i:1112460 original size:4 final size:4
Alignment explanation
Indices: 1112444--1112481 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
1112434 AACAAAAACA
*
1112444 CTTT CTTT ATTT CTTT CTTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT C
1112482 CAACTATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:1112467 original size:17 final size:17
Alignment explanation
Indices: 1112445--1112480 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1112435 ACAAAAACAC
1112445 TTTCTTTATTTCTTTCT
1 TTTCTTTATTTCTTTCT
*
1112462 TTTCTTTCTTTCTTTCT
1 TTTCTTTATTTCTTTCT
1112479 TT
1 TT
1112481 CCAACTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTATTTCTTTCT
Found at i:1118027 original size:180 final size:179
Alignment explanation
Indices: 1117526--1118075 Score: 834
Period size: 180 Copynumber: 3.0 Consensus size: 179
1117516 GTGAAATGGA
* * *
1117526 GTACCCTATATGCAACATTTTGCCAAAAAATGACAAAGTTCCAAAGC-AGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCC-AAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * * * *
1117590 TAATCAGAAATCAAAATCTTAACAATATGCACACCTCTGATGTACATGTATGTACAATTAATCTG
65 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGA--T--A--TATGTACAATTGATCTG
*
1117655 CAAAAGAACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
124 CAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
* * *
1117711 GTACCTTATATGCAATATTTTGACAAAAAGGACAAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
1 GTACCCTATATGCAATATTTTGCCAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
* * * * *
1117776 TATCGGTAATCAAAATTCTAGCAATATGCACACTTCTAATATAAGTACAATTGATCTGCAAAAGA
66 TATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGA
1117841 ACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
131 ACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
*
1117890 GTACCCTATATGCAATATTTTGCCAATAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAA
1 GTACCCTATATGCAATATTTTGCCAA-AAATGACAAAGTTCAAAAGCTGGTATTTTTTTC-ATAA
1117954 ATTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAA
64 ATTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAA
*
1118019 GAACAACTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGG
129 GAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
1118070 GTACCC
1 GTACCC
1118076 NNNNNNNNNN
Statistics
Matches: 335, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
179 101 0.30
180 143 0.43
181 1 0.00
183 1 0.00
184 20 0.06
185 69 0.21
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (179 bp):
GTACCCTATATGCAATATTTTGCCAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
TATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGA
ACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
Found at i:1125800 original size:21 final size:21
Alignment explanation
Indices: 1125774--1125870 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
1125764 TACACCATAG
1125774 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
1125795 CATAGCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
* *
1125816 CATAGCATACCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
*
1125837 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
1125857 CATAGAATCGCATT
1 CATAGCATAGCATT
1125871 CGTCATATCA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 15 0.23
21 51 0.77
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:1126058 original size:5 final size:5
Alignment explanation
Indices: 1126045--1126078 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1126035 GTTCAAATCT
* *
1126045 CATAG CATAC CATAG CATAG CATAG CATAC CATA
1 CATAG CATAG CATAG CATAG CATAG CATAG CATA
1126079 TCATTAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (5 bp):
CATAG
Found at i:1126060 original size:10 final size:10
Alignment explanation
Indices: 1126045--1126078 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1126035 GTTCAAATCT
1126045 CATAGCATAC
1 CATAGCATAC
*
1126055 CATAGCATAG
1 CATAGCATAC
1126065 CATAGCATAC
1 CATAGCATAC
1126075 CATA
1 CATA
1126079 TCATTAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:1126129 original size:21 final size:21
Alignment explanation
Indices: 1126105--1126181 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1126095 TTCTATTTCT
*
1126105 CATAGCATAGGATACAAATCG
1 CATAGCATAGCATACAAATCG
* *
1126126 CATAGCATACCATACAAATCT
1 CATAGCATAGCATACAAATCG
*
1126147 CATAGCATATCATTA-AAATCG
1 CATAGCATAGCA-TACAAATCG
*
1126168 CATACCATAGCATA
1 CATAGCATAGCATA
1126182 GCATTAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (21 bp):
CATAGCATAGCATACAAATCG
Found at i:1126153 original size:42 final size:42
Alignment explanation
Indices: 1126102--1126181 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1126092 CATTTCTATT
* *
1126102 TCTCATAGCATAGGA-TACAAATCGCATAGCATACCATACAAA
1 TCTCATAGCATAGCATTA-AAATCGCATACCATACCATACAAA
* *
1126144 TCTCATAGCATATCATTAAAATCGCATACCATAGCATA
1 TCTCATAGCATAGCATTAAAATCGCATACCATACCATA
1126182 GCATTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (42 bp):
TCTCATAGCATAGCATTAAAATCGCATACCATACCATACAAA
Found at i:1126758 original size:21 final size:18
Alignment explanation
Indices: 1126716--1126752 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1126706 GGAGATCACC
1126716 CCGCCGCGGTAAAAACGT
1 CCGCCGCGGTAAAAACGT
*
1126734 CCGCCGCGGTTAAAACGT
1 CCGCCGCGGTAAAAACGT
1126752 C
1 C
1126753 GACCGCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.27, T:0.14
Consensus pattern (18 bp):
CCGCCGCGGTAAAAACGT
Found at i:1128342 original size:75 final size:75
Alignment explanation
Indices: 1128215--1128468 Score: 436
Period size: 75 Copynumber: 3.4 Consensus size: 75
1128205 ACACACAGCT
* * * * *
1128215 GATAAACACAGTGGCTGAAGCCGATTTCCGGAATCACGCAACAACGATAGCGAATCCCTCAATAT
1 GATAAACATAGTTGCTGAAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCTCAATAT
1128280 GTTACAACTA
66 GTTACAACTA
*
1128290 GATAAACATAGTTGCTGAAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCTAAATAT
1 GATAAACATAGTTGCTGAAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCTCAATAT
1128355 GTTACAACTA
66 GTTACAACTA
* *
1128365 GATAAACATAGTTGCTGGAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCCCAATAT
1 GATAAACATAGTTGCTGAAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCTCAATAT
1128430 GTTACAACTA
66 GTTACAACTA
1128440 GATAAACATAGTTGCTGAAGCCGATTTCC
1 GATAAACATAGTTGCTGAAGCCGATTTCC
1128469 AAAATATACG
Statistics
Matches: 169, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 169 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (75 bp):
GATAAACATAGTTGCTGAAGCCGATTTCCGGAATCAAGCTACAACGAAAGCGAATCCCTCAATAT
GTTACAACTA
Found at i:1130279 original size:16 final size:16
Alignment explanation
Indices: 1130260--1130292 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1130250 CAAGAAATCT
1130260 TTACTTTTTGAAAAGG
1 TTACTTTTTGAAAAGG
1130276 TTACTTTTTGAAAAGG
1 TTACTTTTTGAAAAGG
1130292 T
1 T
1130293 ATTATTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TTACTTTTTGAAAAGG
Found at i:1136314 original size:2 final size:2
Alignment explanation
Indices: 1136307--1136346 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1136297 AAGCATGAAC
* * *
1136307 GA GA GA GA GA AA GA GA AA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1136347 TACAGTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1136327 original size:10 final size:10
Alignment explanation
Indices: 1136308--1136346 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1136298 AGCATGAACG
1136308 AGAGAGAGAA
1 AGAGAGAGAA
*
1136318 AGAGAAAGAA
1 AGAGAGAGAA
*
1136328 AGAGAGAGAG
1 AGAGAGAGAA
1136338 AGAGAGAGA
1 AGAGAGAGA
1136347 TACAGTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAA
Found at i:1137640 original size:2 final size:2
Alignment explanation
Indices: 1137633--1137662 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1137623 NNNNNNNNNN
1137633 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1137663 ATATACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1137714 original size:20 final size:20
Alignment explanation
Indices: 1137689--1138032 Score: 373
Period size: 20 Copynumber: 16.8 Consensus size: 20
1137679 TTTATAACTT
1137689 ATTCGTCCGAACAAATCCTA
1 ATTCGTCCGAACAAATCCTA
1137709 ATTCGTCCGAACAAATCCTA
1 ATTCGTCCGAACAAATCCTA
** *
1137729 ATTCGTCCGAACAAATAAGTT
1 ATTCGTCCGAACAAAT-CCTA
* *
1137750 ATTTGTCCGAACAAATATCTA
1 ATTCGTCCGAACAAAT-CCTA
*
1137771 ATTCGTCCGAACAAATAGCTA
1 ATTCGTCCGAACAAAT-CCTA
*
1137792 ATTCGTCCGAACAAATCCCA
1 ATTCGTCCGAACAAATCCTA
* * *
1137812 AATCGTCCGAACAAATTACTT
1 ATTCGTCCGAACAAA-TCCTA
* *
1137833 ATTTGTCCGAACAAATCATA
1 ATTCGTCCGAACAAATCCTA
* * *
1137853 ATTTGTCCGAACAAATAACTT
1 ATTCGTCCGAACAAAT-CCTA
*
1137874 ATTCGTCCGAACAAATCGTA
1 ATTCGTCCGAACAAATCCTA
*
1137894 ATTCGTCCGAACAAATCGTA
1 ATTCGTCCGAACAAATCCTA
* *
1137914 ATTCGTCCGAACAAATAACTT
1 ATTCGTCCGAACAAAT-CCTA
* **
1137935 ATTTGTCCGAACAAATATGTA
1 ATTCGTCCGAACAAAT-CCTA
* * *
1137956 ATTCGTCCAAACAAATAACTT
1 ATTCGTCCGAACAAAT-CCTA
*
1137977 ATTCGTCCGAACAAATCGTA
1 ATTCGTCCGAACAAATCCTA
*
1137997 ATTCGTCCGAACAAATCGTA
1 ATTCGTCCGAACAAATCCTA
1138017 ATTCGTCCGAACAAAT
1 ATTCGTCCGAACAAAT
1138033 AACTTGTTTG
Statistics
Matches: 277, Mismatches: 43, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
20 144 0.52
21 133 0.48
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
ATTCGTCCGAACAAATCCTA
Found at i:1137759 original size:21 final size:21
Alignment explanation
Indices: 1137682--1138052 Score: 388
Period size: 21 Copynumber: 18.0 Consensus size: 21
1137672 TACACTATTT
*
1137682 ATAACTTATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137703 AT-CCTAATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137723 AT-CCTAATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
* * *
1137743 ATAAGTTATTTGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137764 ATATCTAATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137785 ATAGCTAATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
* * *
1137806 AT-CCCAAATCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
* * *
1137826 ATTACTTATTTGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
* *
1137847 ATCA-TAATTTGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137867 ATAACTTATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
1137888 AT--CGTAATTCGTCCGAACAA
1 ATAAC-TAATTCGTCCGAACAA
1137908 AT--CGTAATTCGTCCGAACAA
1 ATAAC-TAATTCGTCCGAACAA
* *
1137928 ATAACTTATTTGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
** *
1137949 ATATGTAATTCGTCCAAACAA
1 ATAACTAATTCGTCCGAACAA
*
1137970 ATAACTTATTCGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
1137991 AT--CGTAATTCGTCCGAACAA
1 ATAAC-TAATTCGTCCGAACAA
1138011 AT--CGTAATTCGTCCGAACAA
1 ATAAC-TAATTCGTCCGAACAA
** *
1138031 ATAACTTGTTTGTCCGAACAA
1 ATAACTAATTCGTCCGAACAA
1138052 A
1 A
1138053 GAATTTTTTA
Statistics
Matches: 301, Mismatches: 40, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.49
21 150 0.50
22 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAACTAATTCGTCCGAACAA
Found at i:1137868 original size:103 final size:102
Alignment explanation
Indices: 1137689--1138052 Score: 543
Period size: 103 Copynumber: 3.5 Consensus size: 102
1137679 TTTATAACTT
* * * *
1137689 ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAAT-CCTAATTCGTCCGAACAAATAAGTTATT
1 ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAAT-AGTAATT
* * *
1137753 TGTCCGAACAAATATCTAATTCGTCCGAACAAATAGCTA
65 TGTCCGAACAAATAACTTATTCGTCCGAACAAATCG-TA
* * *
1137792 ATTCGTCCGAACAAATCCCAAATCGTCCGAACAAATTACTTATTTGTCCGAACAAATCA-TAATT
1 ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAAT-AGTAATT
1137856 TGTCCGAACAAATAACTTATTCGTCCGAACAAATCGTA
65 TGTCCGAACAAATAACTTATTCGTCCGAACAAATCGTA
*
1137894 ATTCGTCCGAACAAATCGTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAATATGTAATT
1 ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAATA-GTAATT
* *
1137959 CGTCCAAACAAATAACTTATTCGTCCGAACAAATCGTA
65 TGTCCGAACAAATAACTTATTCGTCCGAACAAATCGTA
* *
1137997 ATTCGTCCGAACAAATCGTAATTCGTCCGAACAAATAACTTGTTTGTCCGAACAAA
1 ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAA
1138053 GAATTTTTTA
Statistics
Matches: 241, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
101 1 0.00
102 55 0.23
103 167 0.69
104 18 0.07
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (102 bp):
ATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAACTTATTTGTCCGAACAAATAGTAATTT
GTCCGAACAAATAACTTATTCGTCCGAACAAATCGTA
Found at i:1138005 original size:185 final size:185
Alignment explanation
Indices: 1137682--1138052 Score: 575
Period size: 185 Copynumber: 2.0 Consensus size: 185
1137672 TACACTATTT
1137682 ATAACTTATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAA
1 ATAACTTATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAA
* * *
1137747 GTTATTTGTCCGAACAAATATCTAATTCGTCCGAACAAATAGCTAATTCGTCCGAACAAATCCCA
66 CTTATTTGTCCGAACAAATATCTAATTCGTCCAAACAAATAACTAATTCGTCCGAACAAATCCCA
* * *
1137812 AATCGTCCGAACAAATTAC-TTATTTGTCCGAACAAATCA-TAATTTGTCCGAACAA
131 AATCGTCCGAACAAA-T-CGTAATTCGTCCGAACAAATAACTAATTTGTCCGAACAA
* *
1137867 ATAACTTATTCGTCCGAACAAATCGTAATTCGTCCGAACAAATCGTAATTCGTCCGAACAAATAA
1 ATAACTTATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAA
* * **
1137932 CTTATTTGTCCGAACAAATATGTAATTCGTCCAAACAAATAACTTATTCGTCCGAACAAATCGTA
66 CTTATTTGTCCGAACAAATATCTAATTCGTCCAAACAAATAACTAATTCGTCCGAACAAATCCCA
* **
1137997 ATTCGTCCGAACAAATCGTAATTCGTCCGAACAAATAACTTGTTTGTCCGAACAA
131 AATCGTCCGAACAAATCGTAATTCGTCCGAACAAATAACTAATTTGTCCGAACAA
1138052 A
1 A
1138053 GAATTTTTTA
Statistics
Matches: 169, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
183 1 0.01
184 18 0.11
185 150 0.89
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (185 bp):
ATAACTTATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATCCTAATTCGTCCGAACAAATAA
CTTATTTGTCCGAACAAATATCTAATTCGTCCAAACAAATAACTAATTCGTCCGAACAAATCCCA
AATCGTCCGAACAAATCGTAATTCGTCCGAACAAATAACTAATTTGTCCGAACAA
Found at i:1148112 original size:2 final size:2
Alignment explanation
Indices: 1148105--1148143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1148095 ACTCTAAGTG
1148105 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1148144 AATAAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1148358 original size:16 final size:16
Alignment explanation
Indices: 1148320--1148358 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1148310 TAAACACTTC
*
1148320 AAAAAAGAAAAAAAAA
1 AAAAAATAAAAAAAAA
*
1148336 AAAAAATAAAAAATAA
1 AAAAAATAAAAAAAAA
1148352 AAAAAAT
1 AAAAAAT
1148359 GCTAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.08
Consensus pattern (16 bp):
AAAAAATAAAAAAAAA
Found at i:1148371 original size:2 final size:2
Alignment explanation
Indices: 1148366--1148417 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1148356 AATGCTAAAC
1148366 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1148408 TG TG TG TG TG
1 TG TG TG TG TG
1148418 GATTTGTAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1156346 original size:21 final size:20
Alignment explanation
Indices: 1156322--1156377 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
1156312 CGTGCAAGAT
1156322 ACGAACTGTACCGTTCACAAA
1 ACGAAC-GTACCGTTCACAAA
1156343 ACGAAACGTACCGTTCACAAA
1 ACG-AACGTACCGTTCACAAA
*
1156364 GCGAACCGTACCGT
1 ACGAA-CGTACCGT
1156378 GCAAAAAGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (20 bp):
ACGAACGTACCGTTCACAAA
Found at i:1156388 original size:21 final size:20
Alignment explanation
Indices: 1156305--1156384 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
1156295 AACGAACCGT
* *
1156305 ACCGTTCCGTGCAAGATACGA
1 ACCGTACCGTGCAA-AAACGA
* *
1156326 ACTGTACCGTTCACAAAACGA
1 ACCGTACCGTGCA-AAAACGA
* * *
1156347 AACGTACCGTTCACAAAGCGA
1 ACCGTACCGTGCA-AAAACGA
1156368 ACCGTACCGTGCAAAAA
1 ACCGTACCGTGCAAAAA
1156385 GCGAGCAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 3 0.06
21 44 0.92
22 1 0.02
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (20 bp):
ACCGTACCGTGCAAAAACGA
Found at i:1157727 original size:2 final size:2
Alignment explanation
Indices: 1157720--1157755 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1157710 CCCTCAGATT
1157720 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1157756 TTTGAGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.