Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 112 of 189
Found at i:31311278 original size:50 final size:50
Alignment explanation
Indices: 31311210--31311405 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 50
31311200 TTTTCTGTAC
* * **
31311210 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
31311260 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
31311310 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC------GG
*
31311369 TGTCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31311406 TATCATTCCC
Statistics
Matches: 119, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
50 82 0.69
53 1 0.01
59 36 0.30
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31316601 original size:28 final size:28
Alignment explanation
Indices: 31316562--31316712 Score: 209
Period size: 28 Copynumber: 5.4 Consensus size: 28
31316552 CTATTAAGTG
31316562 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
31316589 ACAGTAACAGTGTAGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
31316617 ATAGTAATAGTTTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
31316645 ACA-AAATCAGTGTGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
*
31316673 ACAG-AATCAGTGTGTGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
31316701 ACAGTAACAGTG
1 ACAGTAACAGTG
31316713 CAGTGCAATA
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
27 7 0.06
28 101 0.92
29 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:31316854 original size:26 final size:26
Alignment explanation
Indices: 31316811--31316861 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31316801 GCCAACACAC
* * *
31316811 CAATATCGCAGCAGAGCTGCCAGTAT
1 CAATATCGCAACAAAGCTACCAGTAT
*
31316837 CAATATCGCAATAAAGCTACCAGTA
1 CAATATCGCAACAAAGCTACCAGTA
31316862 ACAGTTATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (26 bp):
CAATATCGCAACAAAGCTACCAGTAT
Found at i:31317186 original size:81 final size:80
Alignment explanation
Indices: 31317074--31317408 Score: 340
Period size: 81 Copynumber: 4.1 Consensus size: 80
31317064 TGCCATAACA
31317074 GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCAGACATTTTACCC
1 GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCAGACATTTTACCC
*
31317139 TATGGGGGTATTTCG
66 TATAGGGGTATTTCG
* *
31317154 GTTATTTTACCCTATGAGGGTATTTC-AGTCATTTTACCCTAT-GAGGGTATTTCAGTCATTTTA
1 GTCATTTTACCCTATG-GGGTATTTCGA-TCATTTTACCCTATAG-GGGTATTTCAGACATTTTA
**
31317217 CCCTATAATGGTATTTCG
63 CCCTATAGGGGTATTTCG
* * * * *
31317235 GTCATTTTACCTTAAGAGGGTATTTCGATAATTTTACCCTTTAGGGATATTTCA-ATCATTTTAC
1 GTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCTATAGGGGTATTTCAGA-CATTTTAC
* *
31317299 CTTATAGGGATATTTCG
64 CCTATAGGGGTATTTCG
* * * * * **
31317316 ATCATTTTACGCTATGGTGGTCTTTCAATCATTTT-CATCTATTAGGGGTAAAAT-A-ACCATTT
1 GTCATTTTACCCTATGG-GGTATTTCGATCATTTTAC-CCTA-TAGGGGT-ATTTCAGA-CATTT
* * *
31317378 TACCATTTAGGGGTATTTTG
61 TACCCTATAGGGGTATTTCG
31317398 GTCATTTTACC
1 GTCATTTTACC
31317409 TATTTTAGGG
Statistics
Matches: 210, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
80 19 0.09
81 149 0.71
82 40 0.19
83 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (80 bp):
GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCAGACATTTTACCC
TATAGGGGTATTTCG
Found at i:31317341 original size:27 final size:26
Alignment explanation
Indices: 31317075--31317350 Score: 279
Period size: 27 Copynumber: 10.3 Consensus size: 26
31317065 GCCATAACAG
31317075 TCATTTTACCCTATGGGGTATTTCGA
1 TCATTTTACCCTATGGGGTATTTCGA
31317101 TCATTTTACCCTATAGGGGTATTTCAGA
1 TCATTTTACCCTAT-GGGGTATTTC-GA
*
31317129 -CATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGA
*
31317155 TTATTTTACCCTATGAGGGTATTTC-A
1 TCATTTTACCCTATG-GGGTATTTCGA
31317181 GTCATTTTACCCTATGAGGGTATTTC-A
1 -TCATTTTACCCTATG-GGGTATTTCGA
** *
31317208 GTCATTTTACCCTATAATGGTATTTCGG
1 -TCATTTTACCCTAT-GGGGTATTTCGA
* *
31317236 TCATTTTACCTTAAGAGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTCGA
* * * *
31317263 TAATTTTACCCTTTAGGGATATTTCAA
1 TCATTTTACCCTAT-GGGGTATTTCGA
* *
31317290 TCATTTTACCTTATAGGGATATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGA
* * *
31317317 TCATTTTACGCTATGGTGGTCTTTCAA
1 TCATTTTACCCTATGG-GGTATTTCGA
31317344 TCATTTT
1 TCATTTT
31317351 CATCTATTAG
Statistics
Matches: 212, Mismatches: 28, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.08
27 191 0.90
28 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (26 bp):
TCATTTTACCCTATGGGGTATTTCGA
Found at i:31319925 original size:49 final size:50
Alignment explanation
Indices: 31319863--31319987 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 50
31319853 GTCATTAAGA
* * * *
31319863 CTTACCGATTCTCAACTCGTATGAGTTTATCGATTT-CAACTCGTGAGAG
1 CTTACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAACTCATGAGAG
* *
31319912 CTTATCGATTCTCAGCTCGTACGAGCTTACCGATTTACAACTCATGAGAG
1 CTTACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAACTCATGAGAG
** *
31319962 CAAACCGATTCACAGCTCGTATGAGC
1 CTTACCGATTCTCAGCTCGTATGAGC
31319988 ATACATGTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 31 0.48
50 33 0.52
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (50 bp):
CTTACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAACTCATGAGAG
Found at i:31319937 original size:25 final size:24
Alignment explanation
Indices: 31319863--31319987 Score: 101
Period size: 25 Copynumber: 5.0 Consensus size: 24
31319853 GTCATTAAGA
31319863 CTTACCGATTCTCAACTCGTATGAG
1 CTTACCGATTCTCAACTCGTA-GAG
* *
31319888 TTTATCGATT-TCAACTCGTGAGAG
1 CTTACCGATTCTCAACTCGT-AGAG
* *
31319912 CTTATCGATTCTCAGCTCGTACGAG
1 CTTACCGATTCTCAACTCGTA-GAG
*
31319937 CTTACCGATT-TACAACTCATGAGAG
1 CTTACCGATTCT-CAACTCGT-AGAG
** * *
31319962 CAAACCGATTCACAGCTCGTATGAG
1 CTTACCGATTCTCAACTCGTA-GAG
31319987 C
1 C
31319988 ATACATGTAC
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
24 24 0.30
25 56 0.69
26 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (24 bp):
CTTACCGATTCTCAACTCGTAGAG
Found at i:31320196 original size:30 final size:31
Alignment explanation
Indices: 31320129--31320201 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
31320119 TTACAGGTAT
*
31320129 ATATATGAAATACATGGAAATGATATTACATG
1 ATATATGGAA-ACATGGAAATGATATTACATG
31320161 ATATATGGAAACAT-GAAATAGATGA-TACATG
1 ATATATGGAAACATGGAAAT-GAT-ATTACATG
31320192 -TATAT-GAAAC
1 ATATATGGAAAC
31320202 TTGCTTACTG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 5 0.13
30 10 0.26
31 13 0.34
32 10 0.26
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (31 bp):
ATATATGGAAACATGGAAATGATATTACATG
Found at i:31321633 original size:16 final size:16
Alignment explanation
Indices: 31321612--31321644 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31321602 TTTACTGTAT
31321612 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
31321628 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
31321644 T
1 T
31321645 AGCAAATCAA
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:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:31321898 original size:18 final size:17
Alignment explanation
Indices: 31321877--31321911 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31321867 TTATTATTAA
*
31321877 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31321895 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31321912 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31321997 original size:120 final size:120
Alignment explanation
Indices: 31321852--31322606 Score: 1296
Period size: 120 Copynumber: 6.3 Consensus size: 120
31321842 ATAATTTAAT
* *
31321852 TATATTTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
* * *
31321917 ATAATCAATACTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
31321972 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
*
31322037 ATAATCAATATTCTTATATGAATTTACTATAATTATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
31322092 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
*
31322157 ATAATCAATATTCTTATATGAATTTACTATAATTATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
31322212 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
31322277 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
31322332 TATAATTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
1 TATAATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
* * * *
31322396 AATATTAAATATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAA
65 AATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
* * * * *
31322452 TATATTTTAACATAATTATTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
* * * *
31322517 ATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
*
31322572 TATAATTTAAAATAATTATTATTAAATATAATTTT
1 TATAATTTAACATAATTATTATTAAATAT-ATTTT
31322607 TCTAAATATA
Statistics
Matches: 610, Mismatches: 22, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
119 2 0.00
120 602 0.99
121 6 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
Found at i:31322018 original size:18 final size:17
Alignment explanation
Indices: 31321995--31322031 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
31321985 AATTATTATT
31321995 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
31322011 AAATATATGATTTAATA
1 AAATATATGATTTAATA
31322028 AAAT
1 AAAT
31322032 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:31322138 original size:18 final size:17
Alignment explanation
Indices: 31322115--31322151 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
31322105 AATTATTATT
31322115 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
31322131 AAATATATGATTTAATA
1 AAATATATGATTTAATA
31322148 AAAT
1 AAAT
31322152 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:31322258 original size:18 final size:17
Alignment explanation
Indices: 31322235--31322271 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
31322225 AATTATTATT
31322235 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
31322251 AAATATATGATTTAATA
1 AAATATATGATTTAATA
31322268 AAAT
1 AAAT
31322272 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:31322378 original size:18 final size:17
Alignment explanation
Indices: 31322355--31322391 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
31322345 AATTATTATT
31322355 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
31322371 AAATATATGATTTAATA
1 AAATATATGATTTAATA
31322388 AAAT
1 AAAT
31322392 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:31323273 original size:19 final size:19
Alignment explanation
Indices: 31323249--31323286 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31323239 GTAAGTCTTC
31323249 AGCATCATTTACTATCTCA
1 AGCATCATTTACTATCTCA
31323268 AGCATCATTTACTATCTCA
1 AGCATCATTTACTATCTCA
31323287 CCTTTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (19 bp):
AGCATCATTTACTATCTCA
Found at i:31325181 original size:34 final size:34
Alignment explanation
Indices: 31325133--31325202 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
31325123 TGAGCAAAAT
*
31325133 GGAGAGATTAGAAATCGGTGGATTTCACCGATTA
1 GGAGAGATTAGAAATCGGTAGATTTCACCGATTA
*
31325167 GGAGGGATTAGAAATCGGTAGATTTCACCGATTA
1 GGAGAGATTAGAAATCGGTAGATTTCACCGATTA
31325201 GG
1 GG
31325203 TCAGTAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (34 bp):
GGAGAGATTAGAAATCGGTAGATTTCACCGATTA
Found at i:31327369 original size:23 final size:23
Alignment explanation
Indices: 31327338--31327383 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31327328 ATATAAGAGG
*
31327338 TAATTCCATCAAAATTAGAAACT
1 TAATACCATCAAAATTAGAAACT
* *
31327361 TAATACCATCAACATTAGCAACT
1 TAATACCATCAAAATTAGAAACT
31327384 ATATATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (23 bp):
TAATACCATCAAAATTAGAAACT
Found at i:31329174 original size:7 final size:7
Alignment explanation
Indices: 31329164--31329194 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31329154 AGATTATGGA
31329164 ATTAGGG
1 ATTAGGG
31329171 ATTAGGG
1 ATTAGGG
*
31329178 ATTATGG
1 ATTAGGG
31329185 ATTAGGG
1 ATTAGGG
31329192 ATT
1 ATT
31329195 CTAGTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (7 bp):
ATTAGGG
Found at i:31329186 original size:14 final size:14
Alignment explanation
Indices: 31329150--31329194 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
31329140 ATTTTAAGGT
* *
31329150 TTATAGATTATGGAA
1 TTATGGATTA-GGGA
*
31329165 TTAGGGATTAGGGA
1 TTATGGATTAGGGA
31329179 TTATGGATTAGGGA
1 TTATGGATTAGGGA
31329193 TT
1 TT
31329195 CTAGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (14 bp):
TTATGGATTAGGGA
Found at i:31329442 original size:83 final size:81
Alignment explanation
Indices: 31329291--31329443 Score: 209
Period size: 83 Copynumber: 1.9 Consensus size: 81
31329281 TAGGGCTTAA
* * *
31329291 GGTTTAGGTTAATTAGTATGTTTTAATCTATATTAAATAAGGTTTAGGGGTTAGGGGTTAGGGAT
1 GGTTTAGATTAATTAGTATGTTTTAATATATATTAAATAAGGTTTAGGGGTTAGGAGTTAGGGAT
31329356 TTGGGATAAGGTTTAG
66 TTGGGATAAGGTTTAG
* * * *
31329372 GGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTATGGGTTAGTAGTTAAGG
1 GGTTTAGATTAATTAGTATGTTTTAA--TATATATTAAATAAGGTTTAGGGGTTAGGAGTT-AGG
31329437 G-TTTGGG
63 GATTTGGG
31329444 TTTTGGGGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 23 0.37
83 35 0.56
84 4 0.06
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (81 bp):
GGTTTAGATTAATTAGTATGTTTTAATATATATTAAATAAGGTTTAGGGGTTAGGAGTTAGGGAT
TTGGGATAAGGTTTAG
Found at i:31333663 original size:43 final size:43
Alignment explanation
Indices: 31333615--31333842 Score: 208
Period size: 43 Copynumber: 5.3 Consensus size: 43
31333605 AGGTTATATT
* * * **
31333615 TTTAGCAGCGTTTTTTGCAAAAATGTTGCTAAAGGTCATGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * *
31333658 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * *
31333701 TTTAGC-GACGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAG-CGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * *
31333744 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * *
31333787 TTTAGCGGCGTTTGTGAG-AGAAGCGCTGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTG-GCAAAAACGCCGCTAAAGGTCATGGTC
*
31333830 TTTAGCGGCGTTT
1 TTTAGCAGCGTTT
31333843 TTTTCTAAAA
Statistics
Matches: 171, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
42 1 0.01
43 168 0.98
44 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
Found at i:31333760 original size:86 final size:86
Alignment explanation
Indices: 31333642--31333842 Score: 357
Period size: 86 Copynumber: 2.3 Consensus size: 86
31333632 CAAAAATGTT
*
31333642 GCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
1 GCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
*
31333707 GACGTTTGTGGGAGAAGCGCC
66 GACGTTTGTGAGAGAAGCGCC
*
31333728 GCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
1 GCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
* *
31333793 GGCGTTTGTGAGAGAAGCGCT
66 GACGTTTGTGAGAGAAGCGCC
31333814 GCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 GCTAAAGGTCTTGGTCTTTAGCGGCGTTT
31333843 TTTTCTAAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 110 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (86 bp):
GCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
GACGTTTGTGAGAGAAGCGCC
Found at i:31335398 original size:14 final size:16
Alignment explanation
Indices: 31335367--31335399 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31335357 TTTTACAAAC
31335367 TTATTTAGTATGAAAT
1 TTATTTAGTATGAAAT
31335383 TTATTTAG-AT-AAAT
1 TTATTTAGTATGAAAT
31335397 TTA
1 TTA
31335400 AAATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 2 0.12
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (16 bp):
TTATTTAGTATGAAAT
Found at i:31340403 original size:21 final size:21
Alignment explanation
Indices: 31340340--31340406 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
31340330 CACACAACTA
* *
31340340 TGTGGCTGAAAGACACGCCCG
1 TGTGGCTGAGAGACATGCCCG
** *
31340361 TGTAACTGAG-G-CATGTGACCG
1 TGTGGCTGAGAGACA--TGCCCG
31340382 TGTGGCTGAGAGACATGCCCG
1 TGTGGCTGAGAGACATGCCCG
31340403 TGTG
1 TGTG
31340407 CAACTGACAA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 28 0.82
22 1 0.03
23 2 0.06
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (21 bp):
TGTGGCTGAGAGACATGCCCG
Found at i:31353021 original size:28 final size:28
Alignment explanation
Indices: 31352982--31353078 Score: 122
Period size: 28 Copynumber: 3.5 Consensus size: 28
31352972 TAATGAGATT
*
31352982 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGTTTAATGGTAA
* *
31353010 AGCATTACGTGTGCGAGTTTAATGGTAA
1 AGCACTAAGTGTGCGAGTTTAATGGTAA
* * ** *
31353038 ATCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATGGTAA
31353066 AGCACTAAGTGTG
1 AGCACTAAGTGTG
31353079 GAACTTATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATGGTAA
Found at i:31358160 original size:42 final size:42
Alignment explanation
Indices: 31358101--31358185 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
31358091 AACTAGGGGA
*
31358101 AATTGTTATATCCCCACGCTTAGATACCTCCCATGCATGAAC
1 AATTGTTATACCCCCACGCTTAGATACCTCCCATGCATGAAC
*
31358143 AATTGTTATACCCCCACGCTTAGATACCTTCCATGCATGAAC
1 AATTGTTATACCCCCACGCTTAGATACCTCCCATGCATGAAC
31358185 A
1 A
31358186 TCCTACACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (42 bp):
AATTGTTATACCCCCACGCTTAGATACCTCCCATGCATGAAC
Found at i:31359690 original size:43 final size:42
Alignment explanation
Indices: 31359537--31359691 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 42
31359527 GATTTTCGTC
* *
31359537 TAAGACCACGTTTGGGATGTTGGCATCG-ATTTGAGATTTACGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGTATTT--GA-TTACGTG
* * *
31359581 TAAGACCATGTCTGGGACATTGGCATCGTATGTGATTACGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACGTG
* * *
31359623 TAAGACC-CTATTTTGGG-CAG-TGGCATCGTTATTTGATTACATG
1 TAAGACCAC--GTCTGGGAC-GTTGGCATCG-TATTTGATTACGTG
31359666 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
31359692 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
42 29 0.32
43 33 0.37
44 25 0.28
45 3 0.03
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (42 bp):
TAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACGTG
Found at i:31371837 original size:29 final size:29
Alignment explanation
Indices: 31371805--31371860 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
31371795 AAAGGCCATT
31371805 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
31371834 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
31371861 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:31373079 original size:23 final size:25
Alignment explanation
Indices: 31373041--31373088 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
31373031 AATAATATTT
*
31373041 TTAAATTTTTATTAAAAATA-TAAA
1 TTAAAGTTTTATTAAAAATACTAAA
31373065 TTAAAGTTTTA-TAAAAATACTAAA
1 TTAAAGTTTTATTAAAAATACTAAA
31373089 ATTTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAAGTTTTATTAAAAATACTAAA
Found at i:31373115 original size:27 final size:26
Alignment explanation
Indices: 31373072--31373136 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
31373062 AAATTAAAGT
* *
31373072 TTTATAAAAATACTAAAATTTATAAA
1 TTTATAAAAAAACTAAAATATATAAA
31373098 TTTATAAAAAAACATAAAATATATAAA
1 TTTATAAAAAAAC-TAAAATATATAAA
*
31373125 ATTACTAAAAAA
1 TTTA-TAAAAAA
31373137 TTGTAAGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.35
27 15 0.44
28 7 0.21
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
TTTATAAAAAAACTAAAATATATAAA
Found at i:31377434 original size:21 final size:21
Alignment explanation
Indices: 31377391--31377436 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
31377381 TTTTTTTTGG
* **
31377391 AAAAAAATAAAATTAGTTTTT
1 AAAAAAATAAAATGAGTGATT
*
31377412 AAAAAGATAAAATGAGTGATT
1 AAAAAAATAAAATGAGTGATT
31377433 AAAA
1 AAAA
31377437 TGAAAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (21 bp):
AAAAAAATAAAATGAGTGATT
Found at i:31378623 original size:20 final size:21
Alignment explanation
Indices: 31378575--31378623 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
31378565 AAGACGTGGT
* *
31378575 AAAAATAT-TTAAAATTATTT
1 AAAAATATATGAAAATTATTA
*
31378595 AAAATTATATGAAAATT-TTA
1 AAAAATATATGAAAATTATTA
31378615 AAAAATATA
1 AAAAATATA
31378624 AATTCTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATATATGAAAATTATTA
Found at i:31381862 original size:17 final size:17
Alignment explanation
Indices: 31381842--31381876 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31381832 ATATTAAGAA
31381842 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
31381859 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
31381876 T
1 T
31381877 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:31381993 original size:16 final size:17
Alignment explanation
Indices: 31381958--31381996 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
31381948 ACATTAAGAA
*
31381958 TTTTATTAAATTACATAT
1 TTTTACTAAATTA-ATAT
31381976 TTTTACTAAATT-ATAT
1 TTTTACTAAATTAATAT
31381992 TTTTA
1 TTTTA
31381997 ATAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTACTAAATTAATAT
Found at i:31382007 original size:18 final size:16
Alignment explanation
Indices: 31381958--31382000 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
31381948 ACATTAAGAA
*
31381958 TTTTATTAAATTACATAT
1 TTTTAATAAATT--ATAT
*
31381976 TTTTACTAAATTATAT
1 TTTTAATAAATTATAT
31381992 TTTTAATAA
1 TTTTAATAA
31382001 TAATTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
18 11 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATAAATTATAT
Found at i:31382174 original size:120 final size:120
Alignment explanation
Indices: 31381786--31382381 Score: 1011
Period size: 120 Copynumber: 5.0 Consensus size: 120
31381776 TTGATCTTTC
31381786 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * * *
31381851 ATTATAT-TTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATGTTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTAA
*
31381905 TAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAACATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * *
31381967 ATTACATATTTTTACTAAATTATATTTTTAATAATAATTATTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAAATTATATTTAA
*
31382024 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
31382089 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTAA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTAA
* *
31382144 TAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAAATTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
31382209 ATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTAA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTAA
*
31382264 TAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* *
31382329 ATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTT
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTT
31382382 TAAATTATTT
Statistics
Matches: 453, Mismatches: 18, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
116 36 0.08
117 15 0.03
119 90 0.20
120 260 0.57
122 52 0.11
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTAA
Found at i:31382216 original size:37 final size:37
Alignment explanation
Indices: 31382163--31382336 Score: 100
Period size: 38 Copynumber: 4.4 Consensus size: 37
31382153 ATATTATGAT
31382163 TTTATTAAATTCATATAAGAATATTTAATATTAAGAAA
1 TTTATTAAATT-ATATAAGAATATTTAATATTAAGAAA
**** * *
31382201 TTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATAAGAATATT---TAATA-TTAA-GA-AA
* ** * *
31382244 TTATGTTAAATTATAT-TTAATAGTATTATATATTATG-AT
1 TT-TATTAAATTATATAAGAATA-T-TTA-ATATTAAGAAA
** *
31382283 TTTAGAAAATTCATATAAGAATATTTAATATTAAGAAT
1 TTTATTAAATT-ATATAAGAATATTTAATATTAAGAAA
31382321 TTTATTAAATTATATA
1 TTTATTAAATTATATA
31382337 TTTTTATTAA
Statistics
Matches: 102, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
37 21 0.21
38 31 0.30
39 8 0.08
40 8 0.08
41 4 0.04
42 5 0.05
43 11 0.11
44 13 0.13
45 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (37 bp):
TTTATTAAATTATATAAGAATATTTAATATTAAGAAA
Found at i:31382599 original size:45 final size:44
Alignment explanation
Indices: 31382514--31382609 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
31382504 ATTACAACAT
* *
31382514 CATTCCATTCAACCAAACACAATAATACTATTACGTCTCTATTC
1 CATTACATTCAACCAAACACAATAATACTATTACGCCTCTATTC
*
31382558 CATTACATTCAACCAAACA-ATTGAATTACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAT-AA-TACTATTACGCCTCTATTC
31382603 CATTACA
1 CATTACA
31382610 GCTCTATTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 2 0.04
44 20 0.43
45 25 0.53
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAATAATACTATTACGCCTCTATTC
Found at i:31382614 original size:16 final size:16
Alignment explanation
Indices: 31382595--31382643 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
31382585 ACTATTACGC
31382595 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
* *
31382611 CTCTATTCTATTACAC
1 CTCTATTCCATTACAG
*
31382627 CTTTATTCCATTACAG
1 CTCTATTCCATTACAG
31382643 C
1 C
31382644 GAACCAAGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.04, T:0.41
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:31383510 original size:33 final size:33
Alignment explanation
Indices: 31383473--31383601 Score: 153
Period size: 31 Copynumber: 4.0 Consensus size: 33
31383463 AGATTAATTT
31383473 ATATTTTATTTATCATTATATTAAATTATTTAA
1 ATATTTTATTTATCATTATATTAAATTATTTAA
* *
31383506 ATATTTTATGTAT-AGTTATGTTAAATTATTTAA
1 ATATTTTATTTATCA-TTATATTAAATTATTTAA
*
31383539 ATA--TCATTTATCATTATATTAAATTATTT-A
1 ATATTTTATTTATCATTATATTAAATTATTTAA
* *
31383569 A-ATCTTATTTATTATTATATTTAAATT-TTTAA
1 ATATTTTATTTATCATTATA-TTAAATTATTTAA
31383601 A
1 A
31383602 AACATTTTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 13
0.81 0.07 0.13
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 37 0.45
32 11 0.13
33 32 0.39
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (33 bp):
ATATTTTATTTATCATTATATTAAATTATTTAA
Found at i:31384614 original size:3 final size:3
Alignment explanation
Indices: 31384606--31384662 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
31384596 GCCAAAGGCT
31384606 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31384654 ATA ATA ATA
1 ATA ATA ATA
31384663 TCTTACATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31386466 original size:30 final size:31
Alignment explanation
Indices: 31386423--31386490 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 31
31386413 TTAGTATACT
*
31386423 ACTAATACATAAAATAGTATT-ATA-ATATATA
1 ACTATTACATAAAA-A-TATTAATACATATATA
31386454 ACTATTAC-TAAAAATATTAATACATATATA
1 ACTATTACATAAAAATATTAATACATATATA
31386484 ACTATTA
1 ACTATTA
31386491 TTATCATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.12
29 4 0.12
30 19 0.56
31 7 0.21
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (31 bp):
ACTATTACATAAAAATATTAATACATATATA
Found at i:31386933 original size:43 final size:42
Alignment explanation
Indices: 31386863--31387118 Score: 282
Period size: 43 Copynumber: 6.0 Consensus size: 42
31386853 ATAAACGCTA
* * * *
31386863 CTATAGATCAGGACATTTAACGACGCTTTCTCCACAAACGCCG
1 CTATAGATCAAGACCTTTAGCGGCGCTTT-TCCACAAACGCCG
* *
31386906 CTATAGATCAAGACCTTTAGCAGCGCTTTTCTCACAAACACCG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTTC-CACAAACGCCG
*
31386949 CTATAGATCAAGACCTTTATCGGCGCTTTTTCCACAAACGCCG
1 CTATAGATCAAGACCTTTAGCGGCGC-TTTTCCACAAACGCCG
* * * **
31386992 CTATAGCTCGAGACCTTTAGCGGCACTTTTTCCATGAACGCCG
1 CTATAGATCAAGACCTTTAGCGGCGC-TTTTCCACAAACGCCG
* *
31387035 CTATAGCTCGAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCCG
* * *
31387078 CTATAGGA-CAA-ACCTTTAGCGACGCTTCTCGCAAAAACGCC
1 CTATA-GATCAAGACCTTTAGCGGCGCTTTTC-CACAAACGCC
31387119 ACTAAAAACA
Statistics
Matches: 185, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 31 0.17
43 147 0.79
44 6 0.03
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (42 bp):
CTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAACGCCG
Found at i:31392122 original size:21 final size:21
Alignment explanation
Indices: 31392113--31392159 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31392103 CATAACTCCT
31392113 AACCTTTAACCCCTAACCCTTA
1 AACCTTTAA-CCCTAACCCTTA
* *
31392135 AACCTTAAACCCTAACCTTTA
1 AACCTTTAACCCTAACCCTTA
31392156 AACC
1 AACC
31392160 ATAAATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCTTTAACCCTAACCCTTA
Found at i:31392135 original size:14 final size:14
Alignment explanation
Indices: 31392095--31392135 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
31392085 AAACATAAAT
*
31392095 CCCTAACCCATAAC
1 CCCTAACCCTTAAC
* *
31392109 TCCTAACCTTTAAC
1 CCCTAACCCTTAAC
31392123 CCCTAACCCTTAA
1 CCCTAACCCTTAA
31392136 ACCTTAAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:31392164 original size:21 final size:21
Alignment explanation
Indices: 31392123--31392164 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31392113 AACCTTTAAC
*
31392123 CCCTAACCCTTAAACCTTAAA
1 CCCTAACCCTTAAACCATAAA
*
31392144 CCCTAACCTTTAAACCATAAA
1 CCCTAACCCTTAAACCATAAA
31392165 TCATAAACCA
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:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCTAACCCTTAAACCATAAA
Found at i:31393452 original size:122 final size:122
Alignment explanation
Indices: 31393208--31393526 Score: 412
Period size: 122 Copynumber: 2.6 Consensus size: 122
31393198 CGCTTTCTAA
* * * *
31393208 AAAAACGCCGCTAAAGCCCTGAGCATTAGTGGCACTTTCTCAAAAAACGCTGCTAAAGCCCTGAG
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCT-AAAAAACGCCGCTAAAGCCCTGAG
* * * * *
31393273 CATTAGCGGCGCTTCTCAAAAATGCCGTTAAAGCCACAAGCATTAGCGGCGCTTCCTC
65 CATTAGCGGCGCTCCTCAAAAAAGCCGCTAAAGCCACAAGCATTAGCAGCGCCTCCTC
**
31393331 AAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCCTAAAAAACGCCGCTAAAGCCC-GAGC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTAAAAAACGCCGCTAAAGCCCTGAGC
* *
31393395 ATTAGCGGCGCCTCCTCAAAAAAGCCGCTAAATCC-CTGAGCATTAGCAGCGCCTCCTC
66 ATTAGCGGCG-CTCCTCAAAAAAGCCGCTAAAGCCAC-AAGCATTAGCAGCGCCTCCTC
* * *
31393453 AAAAACACCGCTATAGCCCTGAGCATTAGCGGCGCTTTTCC--AAAAACGCCGCTAAATCCCTGA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC--TTCCTAAAAAACGCCGCTAAAGCCCTGA
*
31393516 GCATTAACGGC
64 GCATTAGCGGC
31393527 TCTTTATTAA
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
121 15 0.09
122 106 0.62
123 47 0.27
124 4 0.02
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (122 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTAAAAAACGCCGCTAAAGCCCTGAGC
ATTAGCGGCGCTCCTCAAAAAAGCCGCTAAAGCCACAAGCATTAGCAGCGCCTCCTC
Found at i:31393539 original size:41 final size:41
Alignment explanation
Indices: 31393177--31393549 Score: 412
Period size: 41 Copynumber: 9.1 Consensus size: 41
31393167 TAAATTATTT
* * * * *
31393177 TAAATCCCTAAGCATTAGTGGCGCTTTCTAAAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCT-CAAAAACGCCGC
* * * *
31393219 TAAAGCCCTGAGCATTAGTGGCACTTTCTCAAAAAACGCTGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTC-AAAAACGCCGC
* *
31393261 TAAAGCCCTGAGCATTAGCGGCGCTT-CTCAAAAATGCCGT
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
*
31393301 TAAAGCCAC-AAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
1 TAAAGCC-CTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
** *
31393342 TAAAGCCCCAAGCATTAGCGGCGCTTCCTAAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
* *
31393383 TAAAGCCC-GAGCATTAGCGGCGCCTCCTCAAAAAAGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
* * * *
31393423 TAAATCCCTGAGCATTAGCAGCGCCTCCTCAAAAACACCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
* *
31393464 TATAGCCCTGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCT-CAAAAACGCCGC
* * * ** * *
31393505 TAAATCCCTGAGCATTAACGGCTCTTTATTAAAAACGCCAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
31393546 TAAA
1 TAAA
31393550 TCCCCGAAAG
Statistics
Matches: 289, Mismatches: 35, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
40 68 0.24
41 160 0.55
42 61 0.21
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
Found at i:31408411 original size:13 final size:13
Alignment explanation
Indices: 31408385--31408428 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
31408375 TAATTGTGTT
31408385 AAATGTGTAAATG
1 AAATGTGTAAATG
31408398 AAATG-GTAAGATG
1 AAATGTGTAA-ATG
*
31408411 AAATGTTTAAATG
1 AAATGTGTAAATG
31408424 AAATG
1 AAATG
31408429 GTTTTACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 21 0.75
14 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (13 bp):
AAATGTGTAAATG
Found at i:31408439 original size:26 final size:27
Alignment explanation
Indices: 31408385--31408453 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
31408375 TAATTGTGTT
* *
31408385 AAATGTGTAAATGAAATGGTAAGATG-
1 AAATGTTTAAATGAAATGGTAAGACGA
***
31408411 AAATGTTTAAATGAAATGGTTTTACGA
1 AAATGTTTAAATGAAATGGTAAGACGA
* *
31408438 AAATGCTTATATGAAA
1 AAATGTTTAAATGAAA
31408454 AAATATATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (27 bp):
AAATGTTTAAATGAAATGGTAAGACGA
Found at i:31411640 original size:61 final size:60
Alignment explanation
Indices: 31411523--31411681 Score: 169
Period size: 61 Copynumber: 2.6 Consensus size: 60
31411513 CGCACGGGTA
* * *
31411523 AGGGACACGGACGTGTGCCCAGGCTGTGTAACTCGCAGTTTGTGGTACAAGACCACATAGCC
1 AGGGACACGGA-GTGTGCCCAGGCTGTGTGAGTCACAGTTTGTGGTACAAGACCACA-AGCC
* * **
31411585 AGGGACACGGGGTGTGCCCAGGCTGTGTGAGTCACTA-TTTGTGGTACAA-AGCCACACGGT
1 AGGGACACGGAGTGTGCCCAGGCTGTGTGAGTCAC-AGTTTGTGGTACAAGA-CCACAAGCC
* * *
31411645 AGGGACATTGGAGTGTACCCAGGCCGTGTGAGTCACA
1 AGGGACA-CGGAGTGTGCCCAGGCTGTGTGAGTCACA
31411682 TGGGCAGGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
60 10 0.12
61 62 0.75
62 11 0.13
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (60 bp):
AGGGACACGGAGTGTGCCCAGGCTGTGTGAGTCACAGTTTGTGGTACAAGACCACAAGCC
Found at i:31412239 original size:9 final size:9
Alignment explanation
Indices: 31412225--31412314 Score: 117
Period size: 9 Copynumber: 9.6 Consensus size: 9
31412215 TTTGGTTAAA
31412225 AATTACCCG
1 AATTACCCG
31412234 AATTACCCG
1 AATTACCCG
31412243 AATTACCCG
1 AATTACCCG
31412252 AATTACCCG
1 AATTACCCG
* *
31412261 AAAATTACTCA
1 --AATTACCCG
31412272 AATTACCCG
1 AATTACCCG
*
31412281 AATTACTCG
1 AATTACCCG
31412290 AAAATTACCCG
1 --AATTACCCG
31412301 AATTACCCG
1 AATTACCCG
31412310 AATTA
1 AATTA
31412315 AATCACTACA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
9 56 0.79
11 15 0.21
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:31412268 original size:38 final size:39
Alignment explanation
Indices: 31412223--31412314 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 39
31412213 TTTTTGGTTA
31412223 AAAATTACCCGAATTACCCGAATTACCCG-AATTACCCG
1 AAAATTACCCGAATTACCCGAATTACCCGAAATTACCCG
* * *
31412261 AAAATTACTCAAATTACCCGAATTACTCGAAAATTACCCG
1 AAAATTACCCGAATTACCCGAATTACCCG-AAATTACCCG
31412301 --AATTACCCGAATTA
1 AAAATTACCCGAATTA
31412315 AATCACTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 38 0.81
40 9 0.19
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (39 bp):
AAAATTACCCGAATTACCCGAATTACCCGAAATTACCCG
Found at i:31412343 original size:17 final size:17
Alignment explanation
Indices: 31412310--31412417 Score: 67
Period size: 17 Copynumber: 6.1 Consensus size: 17
31412300 GAATTACCCG
*
31412310 AATT-AAATCACTACAT
1 AATTAAAATCATTACAT
*
31412326 AATTAAAAGCATTACAT
1 AATTAAAATCATTACAT
* *
31412343 AAATATTTAAATCACTACAT
1 --A-ATTAAAATCATTACAT
31412363 AATTAAAA-CTATTACAT
1 AATTAAAATC-ATTACAT
* ** *
31412380 AGTCTTTGAATCACTACAT
1 A--ATTAAAATCATTACAT
*
31412399 AATTAAAAACATTACAT
1 AATTAAAATCATTACAT
31412416 AA
1 AA
31412418 GTCTTGAATT
Statistics
Matches: 68, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
16 5 0.07
17 36 0.53
18 1 0.01
19 12 0.18
20 14 0.21
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (17 bp):
AATTAAAATCATTACAT
Found at i:31412358 original size:37 final size:37
Alignment explanation
Indices: 31412312--31412451 Score: 185
Period size: 37 Copynumber: 3.8 Consensus size: 37
31412302 ATTACCCGAA
* * *
31412312 TTAAATCACTACATAATTAAAAGCATTACATAAATAT
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
31412349 TTAAATCACTACATAATT-AAAACTATTACAT-AGTCT
1 TTAAATCACTACATAATTAAAAAC-ATTACATAAGTCT
*
31412385 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
* *
31412422 TGAATTAACACTACATAATTAAAAACATTA
1 TTAA--ATCACTACATAATTAAAAACATTA
31412452 ATTACAATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
36 31 0.34
37 37 0.41
39 23 0.25
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
TTAAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:31412363 original size:20 final size:19
Alignment explanation
Indices: 31412312--31412364 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
31412302 ATTACCCGAA
31412312 TTAAATCACTACAT--AAT
1 TTAAATCACTACATAAAAT
* * *
31412329 TAAAAGCATTACATAAATAT
1 TTAAATCACTACATAAA-AT
31412349 TTAAATCACTACATAA
1 TTAAATCACTACATAA
31412365 TTAAAACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (19 bp):
TTAAATCACTACATAAAAT
Found at i:31413688 original size:16 final size:16
Alignment explanation
Indices: 31413667--31413706 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31413657 GCCTAAGAGA
31413667 AAATTGGGCTAGATTT
1 AAATTGGGCTAGATTT
* *
31413683 AAATTGGGCTGGGTTT
1 AAATTGGGCTAGATTT
31413699 AAATTGGG
1 AAATTGGG
31413707 AGGGAGTAGG
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:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTAGATTT
Found at i:31420683 original size:173 final size:173
Alignment explanation
Indices: 31420392--31420710 Score: 460
Period size: 173 Copynumber: 1.8 Consensus size: 173
31420382 GCTACTGAGG
** * * * * *
31420392 CCACACGGCCAGTTACACGGGCGTGTTCCCAGGCCGTGTGGTTGGCCGTGTAACTTACTGTTCAT
1 CCACACGGCCAGGGACACGGGAGTGTGCCCAAGCCGTGTGGTTGGCCATGTAACTCACTGTTCAT
* * *
31420457 CAATTTGAGGCCACACGGGCAAGGTACACAGTAGTGTGTCTAGGCCTTGTGTGGCCATATTAGAG
66 CAATTTGAGGCCACACAGGCAAGGCACACAGTACTGTGTCTAGGCCTTGTGTGGCCATATTAGAG
31420522 CAGAGTTGGCACGGGTGTGTAACTGACTGTTTATGGTACAAGA
131 CAGAGTTGGCACGGGTGTGTAACTGACTGTTTATGGTACAAGA
31420565 CCACACGGCCAGGGACACGGGAGTGTGCCCAAGCCGTGTGGTTGGCCATGTAACTCACTGTTCAT
1 CCACACGGCCAGGGACACGGGAGTGTGCCCAAGCCGTGTGGTTGGCCATGTAACTCACTGTTCAT
* * * ** * *
31420630 CGATTTGGGGCCGCACAGGCAAGGCACATGGTCCTGTGTCTAGG-CTGTGTGTGGCCATATTAGT
66 CAATTTGAGGCCACACAGGCAAGGCACACAGTACTGTGTCTAGGCCT-TGTGTGGCCATATTAGA
*
31420694 GCAGAGTTTGCACGGGT
130 GCAGAGTTGGCACGGGT
31420711 AAGGGACACG
Statistics
Matches: 127, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
172 2 0.02
173 125 0.98
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (173 bp):
CCACACGGCCAGGGACACGGGAGTGTGCCCAAGCCGTGTGGTTGGCCATGTAACTCACTGTTCAT
CAATTTGAGGCCACACAGGCAAGGCACACAGTACTGTGTCTAGGCCTTGTGTGGCCATATTAGAG
CAGAGTTGGCACGGGTGTGTAACTGACTGTTTATGGTACAAGA
Found at i:31421262 original size:62 final size:62
Alignment explanation
Indices: 31421188--31421314 Score: 184
Period size: 62 Copynumber: 2.0 Consensus size: 62
31421178 CACACGGGTA
* *
31421188 AGGGACATGGGCGTGTGCCTAGGCCGTGTAACTCACAGTTTGTGGTAC-AAGACCACACAGCC
1 AGGGACACGGGCGTGTGCCTAGGACGTGTAACTCACAGTTTGTGGTACAAAG-CCACACAGCC
* * * *
31421250 AGGGACACGGGCGTGTGCTTAGGATGTGTAACTCACTGTTTGTGGTACAAAGCCACACGGCC
1 AGGGACACGGGCGTGTGCCTAGGACGTGTAACTCACAGTTTGTGGTACAAAGCCACACAGCC
31421312 AGG
1 AGG
31421315 TATATGGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.95
63 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (62 bp):
AGGGACACGGGCGTGTGCCTAGGACGTGTAACTCACAGTTTGTGGTACAAAGCCACACAGCC
Found at i:31426507 original size:17 final size:18
Alignment explanation
Indices: 31426470--31426510 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31426460 CTATCGTGGC
*
31426470 TTAAAAAGCTATTCCCTT
1 TTAAAAAGCTATTACCTT
*
31426488 TTAAAAAGTTATTACC-T
1 TTAAAAAGCTATTACCTT
31426505 TTAAAA
1 TTAAAA
31426511 CCTTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (18 bp):
TTAAAAAGCTATTACCTT
Found at i:31427224 original size:22 final size:22
Alignment explanation
Indices: 31427181--31427245 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
31427171 GGCTAGTAAC
* * *
31427181 CAGAATGGCTAAGAGCCGTAAA
1 CAGAATAGCTAAAAGCCATAAA
* * *
31427203 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTAAAAGCCATAAA
*
31427225 CAGAATGGCTAAAAGCCATAA
1 CAGAATAGCTAAAAGCCATAA
31427246 GTACAGTAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (22 bp):
CAGAATAGCTAAAAGCCATAAA
Found at i:31427271 original size:31 final size:32
Alignment explanation
Indices: 31427236--31427295 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
31427226 AGAATGGCTA
31427236 AAAGCCATAAGTA-CAGTAATATGATTGGCAC
1 AAAGCCATAAGTAGCAGTAATATGATTGGCAC
* *
31427267 AAAGCCATTAGTAGCAGTGATATGATTGG
1 AAAGCCATAAGTAGCAGTAATATGATTGG
31427296 AACACAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (32 bp):
AAAGCCATAAGTAGCAGTAATATGATTGGCAC
Found at i:31427312 original size:32 final size:31
Alignment explanation
Indices: 31427240--31427314 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
31427230 TGGCTAAAAG
*
31427240 CCATAAGTA-CAGTAATATGATTGGCACAAA
1 CCATCAGTAGCAGTAATATGATTGGCACAAA
* *
31427270 GCCATTAGTAGCAGTGATATGATTGGAACACAAA
1 -CCATCAGTAGCAGTAATATGATTGG--CACAAA
31427304 -CATCAGTAGCA
1 CCATCAGTAGCA
31427315 TCGCAACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 8 0.21
32 24 0.63
34 6 0.16
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (31 bp):
CCATCAGTAGCAGTAATATGATTGGCACAAA
Found at i:31427344 original size:26 final size:26
Alignment explanation
Indices: 31427314--31427367 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
31427304 CATCAGTAGC
31427314 ATCGCAACAAAGCTGCCAGCAACAGT
1 ATCGCAACAAAGCTGCCAGCAACAGT
** * *
31427340 ATCGCAGGAAAGCTGCTAGTAACAGT
1 ATCGCAACAAAGCTGCCAGCAACAGT
31427366 AT
1 AT
31427368 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTGCCAGCAACAGT
Found at i:31427413 original size:27 final size:28
Alignment explanation
Indices: 31427348--31427419 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 28
31427338 GTATCGCAGG
* *
31427348 AAAGCTGCTAGTAACAGTATATGTGGCC
1 AAAGCCGCCAGTAACAGTATATGTGGCC
**
31427376 AAA-CCATCAGTAACAGTGAT-TGTGG-C
1 AAAGCCGCCAGTAACAGT-ATATGTGGCC
31427402 AAAGCCGCCAGT-ACAGTA
1 AAAGCCGCCAGTAACAGTA
31427420 CTTCCTCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
25 1 0.03
26 9 0.25
27 21 0.58
28 5 0.14
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (28 bp):
AAAGCCGCCAGTAACAGTATATGTGGCC
Found at i:31427515 original size:24 final size:24
Alignment explanation
Indices: 31427483--31427540 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
31427473 CCATGCTCAG
31427483 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATACAAATCACAAACA
* **
31427507 AATCAGTCATACTAATCGTAAACA
1 AATCAGTCATACAAATCACAAACA
*
31427531 AACCAGTCAT
1 AATCAGTCAT
31427541 TTACATCACG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAAACA
Found at i:31427737 original size:53 final size:52
Alignment explanation
Indices: 31427585--31427742 Score: 183
Period size: 53 Copynumber: 3.0 Consensus size: 52
31427575 GGGTAAAATA
* * * *
31427585 GTCATTTACCCTCCAGAGGCATTACGGTC-ATTTAACCTTACAGGGGTATTTCG
1 GTCATTTACCCTACAG-GGCATTACGGTCAATTT-ACCCTACAGGGGCATTACG
* ** * *
31427638 ATCATTTATCCCTATGGGGCATTACGGTCATTTTAACCTACAGGGGCATTACG
1 GTCATTTA-CCCTACAGGGCATTACGGTCAATTTACCCTACAGGGGCATTACG
*
31427691 GTCATTTTACCCTACAGGGCATTACAGTCAATTTACCCTACAGGGGCATTAC
1 GTCA-TTTACCCTACAGGGCATTACGGTCAATTTACCCTACAGGGGCATTAC
31427743 AGTTATTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
53 75 0.86
54 12 0.14
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (52 bp):
GTCATTTACCCTACAGGGCATTACGGTCAATTTACCCTACAGGGGCATTACG
Found at i:31427750 original size:26 final size:26
Alignment explanation
Indices: 31427585--31427742 Score: 176
Period size: 27 Copynumber: 6.0 Consensus size: 26
31427575 GGGTAAAATA
* *
31427585 GTCATTTACCCTCCAGAGGCATTACG
1 GTCATTTACCCTACAGGGGCATTACG
* * *
31427611 GTCATTTAACCTTACAGGGGTATTTCG
1 GTCATTT-ACCCTACAGGGGCATTACG
* *
31427638 ATCATTTATCCCTA-TGGGGCATTACG
1 GTCATTTA-CCCTACAGGGGCATTACG
*
31427664 GTCATTTTAACCTACAGGGGCATTACG
1 GTCA-TTTACCCTACAGGGGCATTACG
*
31427691 GTCATTTTACCCTACA-GGGCATTACA
1 GTCA-TTTACCCTACAGGGGCATTACG
31427717 GTCAATTTACCCTACAGGGGCATTAC
1 GTC-ATTTACCCTACAGGGGCATTAC
31427743 AGTTATTTTA
Statistics
Matches: 111, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 47 0.42
27 64 0.58
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (26 bp):
GTCATTTACCCTACAGGGGCATTACG
Found at i:31427777 original size:27 final size:26
Alignment explanation
Indices: 31427747--31427808 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 26
31427737 CATTACAGTT
31427747 ATTTTACCCATCAGAGGTATTTCGATA
1 ATTTTACCCATC-GAGGTATTTCGATA
*
31427774 ATTTTACCCATTGAGGGTATTTCGATA
1 ATTTTACCCATCGA-GGTATTTCGATA
31427801 ATTTTACC
1 ATTTTACC
31427809 AATTAAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (26 bp):
ATTTTACCCATCGAGGTATTTCGATA
Found at i:31427817 original size:27 final size:27
Alignment explanation
Indices: 31427762--31427820 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
31427752 ACCCATCAGA
* *
31427762 GGTATTTCGATAATTTTACCCATTGAG
1 GGTATTTCGATAATTTTACCAATTAAG
31427789 GGTATTTCGATAATTTTACCAATTAAG
1 GGTATTTCGATAATTTTACCAATTAAG
31427816 GGTAT
1 GGTAT
31427821 CGAGGGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCAATTAAG
Found at i:31427849 original size:27 final size:27
Alignment explanation
Indices: 31427819--31427897 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
31427809 AATTAAGGGT
*
31427819 ATCGAGGGTATTTCGGTAATTTTACCC
1 ATCGAGGGTATTTCGATAATTTTACCC
*
31427846 ATCGAGAGTATTTCGATAATTTTACCC
1 ATCGAGGGTATTTCGATAATTTTACCC
* *
31427873 TTCGAAGGTATTTCGATAATTTTAC
1 ATCGAGGGTATTTCGATAATTTTAC
31427898 GGCCCAAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (27 bp):
ATCGAGGGTATTTCGATAATTTTACCC
Found at i:31434237 original size:29 final size:29
Alignment explanation
Indices: 31434196--31434251 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
31434186 AACTTAATAG
*
31434196 ACACATTTACGAACATAGTTCACCAAAAC
1 ACACATATACGAACATAGTTCACCAAAAC
*
31434225 ACACATATGCGAACATAGTTCACCAAA
1 ACACATATACGAACATAGTTCACCAAA
31434252 GAAATAACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.20
Consensus pattern (29 bp):
ACACATATACGAACATAGTTCACCAAAAC
Found at i:31436603 original size:23 final size:23
Alignment explanation
Indices: 31436577--31436652 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
31436567 ATAAGTGTCT
* *
31436577 CACTGGTATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31436600 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
31436623 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
31436646 CACTGAT
1 CACTGAT
31436653 CAATAACACT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:31439677 original size:23 final size:23
Alignment explanation
Indices: 31439651--31439726 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
31439641 ATAAGTGCCT
* *
31439651 CACTGGTATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31439674 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
31439697 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
31439720 CACTGAT
1 CACTGAT
31439727 CAATAACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:31457263 original size:7 final size:7
Alignment explanation
Indices: 31457251--31457359 Score: 78
Period size: 7 Copynumber: 15.6 Consensus size: 7
31457241 AGATTTAAAA
31457251 GAGAATT
1 GAGAATT
31457258 GAGAATT
1 GAGAATT
* *
31457265 AATAATT
1 GAGAATT
*
31457272 AAGAATT
1 GAGAATT
*
31457279 GAGGATT
1 GAGAATT
**
31457286 GATTATT
1 GAGAATT
31457293 GAGAATT
1 GAGAATT
31457300 GA-ACATT
1 GAGA-ATT
31457307 GA-AGATT
1 GAGA-ATT
*
31457314 TAGAATT
1 GAGAATT
*
31457321 GAAAATT
1 GAGAATT
*
31457328 GAAAATT
1 GAGAATT
* *
31457335 AAGGATT
1 GAGAATT
*
31457342 GAAAATT
1 GAGAATT
31457349 GAGAATT
1 GAGAATT
31457356 GAGA
1 GAGA
31457360 CTATAGGATT
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
6 1 0.01
7 78 0.98
8 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.31
Consensus pattern (7 bp):
GAGAATT
Found at i:31457278 original size:21 final size:21
Alignment explanation
Indices: 31457252--31457355 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
31457242 GATTTAAAAG
*
31457252 AGAATTGAGAATT-AATAATTA
1 AGAATTGAAAATTGAA-AATTA
** ** *
31457273 AGAATTGAGGATTGATTATTG
1 AGAATTGAAAATTGAAAATTA
* * *
31457294 AGAATTGAACATTGAAGATTT
1 AGAATTGAAAATTGAAAATTA
31457315 AGAATTGAAAATTGAAAATTA
1 AGAATTGAAAATTGAAAATTA
* *
31457336 AGGATTGAAAATTGAGAATT
1 AGAATTGAAAATTGAAAATT
31457356 GAGACTATAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
21 67 0.99
22 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.20, T:0.33
Consensus pattern (21 bp):
AGAATTGAAAATTGAAAATTA
Found at i:31458873 original size:18 final size:18
Alignment explanation
Indices: 31458850--31458898 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31458840 AATCGTGTCG
31458850 TTCATTTTCAAAACATTA
1 TTCATTTTCAAAACATTA
* * *
31458868 TTCATTTACAAATCGTTA
1 TTCATTTTCAAAACATTA
*
31458886 TTCAATTTCAAAA
1 TTCATTTTCAAAA
31458899 TGTTTTCTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (18 bp):
TTCATTTTCAAAACATTA
Found at i:31471555 original size:5 final size:5
Alignment explanation
Indices: 31471536--31471578 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
31471526 GTAGGACATT
* * * *
31471536 ATATG ACATG ATATG TTATG ATATG ATATG ATAAG TTATG ATA
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATA
31471579 CTATATGAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:31471586 original size:20 final size:20
Alignment explanation
Indices: 31471536--31471578 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
31471526 GTAGGACATT
* *
31471536 ATATGACATGATATGTTATG
1 ATATGATATGATAAGTTATG
31471556 ATATGATATGATAAGTTATG
1 ATATGATATGATAAGTTATG
31471576 ATA
1 ATA
31471579 CTATATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
ATATGATATGATAAGTTATG
Found at i:31474509 original size:26 final size:25
Alignment explanation
Indices: 31474459--31474512 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
31474449 GGTATAAAAG
31474459 TATGAGTCAAAAGTATATTTGTTTT
1 TATGAGTCAAAAGTATATTTGTTTT
*
31474484 TATGAGTCATAAAGTA-GTTTGTTTT
1 TATGAGTCA-AAAGTATATTTGTTTT
31474509 TATG
1 TATG
31474513 TAAAGGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.48
Consensus pattern (25 bp):
TATGAGTCAAAAGTATATTTGTTTT
Found at i:31489733 original size:32 final size:32
Alignment explanation
Indices: 31489697--31489757 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
31489687 GTACTATTTT
*
31489697 GGGTTTGTTTGATTGTCAGTAAAATATTTGTA
1 GGGTTTATTTGATTGTCAGTAAAATATTTGTA
31489729 GGGTTTATTTGATTGTCAGTAAAATATTT
1 GGGTTTATTTGATTGTCAGTAAAATATTT
31489758 TTCGTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (32 bp):
GGGTTTATTTGATTGTCAGTAAAATATTTGTA
Found at i:31495440 original size:20 final size:21
Alignment explanation
Indices: 31495403--31495441 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
31495393 AGAACAATAA
31495403 ATTTTAATTAAAATATTATTT
1 ATTTTAATTAAAATATTATTT
31495424 ATTTT-ATTATAAA-ATTAT
1 ATTTTAATTA-AAATATTAT
31495442 GTTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTAATTAAAATATTATTT
Found at i:31501122 original size:6 final size:6
Alignment explanation
Indices: 31501108--31501171 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
31501098 TTATAATGAT
* *
31501108 AAAAG- AAAAGA AAAAGA AAAATGGA AACAG- AGAAGCA AAAATGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAA--GA AAAAGA AAAAG-A AAAA-GA AAAAGA
*
31501158 AAAAGA GAAAGA AA
1 AAAAGA AAAAGA AA
31501172 GAAAGGAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
5 8 0.17
6 25 0.53
7 8 0.17
8 6 0.13
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:31501159 original size:25 final size:25
Alignment explanation
Indices: 31501108--31501166 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
31501098 TTATAATGAT
*
31501108 AAAAGAAAAG-AAAAAGAAAAATGGA
1 AAAAGAGAAGCAAAAAGAAAAA-GGA
*
31501133 AACAGAGAAGCAAAAATGAAAAA-GA
1 AAAAGAGAAGCAAAAA-GAAAAAGGA
31501158 AAAAGAGAA
1 AAAAGAGAA
31501167 AGAAAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 18 0.62
26 5 0.17
27 6 0.21
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.03
Consensus pattern (25 bp):
AAAAGAGAAGCAAAAAGAAAAAGGA
Found at i:31501426 original size:24 final size:24
Alignment explanation
Indices: 31501398--31501444 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31501388 ATTGAAATGG
31501398 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
31501422 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
31501445 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:31506311 original size:43 final size:42
Alignment explanation
Indices: 31506245--31506403 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 42
31506235 GGCTCATACA
*
31506245 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAAATAATG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAAT-ATG
* * * *
31506288 ATGCCACTGGCCCAGACAGGGTCTTACACGTAATTATATATG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATATG
* * *
31506330 ACGCCAATGTCTCAGACATGGTCTTACACGTAAATCTCAAAT-TG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGT-AA--TCAAATATG
*
31506374 ATGCCAACGTCCCA-A-ATGTGGTCTTACACG
1 ATGCCAATGTCCCAGACA-G-GGTCTTACACG
31506404 ATATCACATT
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 30 0.32
43 35 0.37
44 25 0.27
45 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATATG
Found at i:31506356 original size:42 final size:43
Alignment explanation
Indices: 31506247--31506362 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
31506237 CTCATACAAT
* * *
31506247 GCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATAATGAT
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCAAATAATGAC
* * * * *
31506290 GCCACTGGCCCAGACAGGGTCTTACACGTAATTATAT-ATGAC
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCAAATAATGAC
*
31506332 GCCAATGTCTCAGACATGGTCTTACACGTAA
1 GCCAATGTCCCAGACATGGTCTTACACGTAA
31506363 ATCTCAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 31 0.51
43 30 0.49
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACGTAATCAAATAATGAC
Found at i:31518468 original size:50 final size:50
Alignment explanation
Indices: 31518284--31518522 Score: 191
Period size: 50 Copynumber: 4.7 Consensus size: 50
31518274 TAATAACATG
* * *
31518284 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-TGTTTC--CT-GTATTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATCTCG-A-TA
* * * * * * * *
31518333 CAAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATCGCTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGATA
* *** *
31518383 CCCATGCCATGTCCCAGACATGGTCTTATGGGGGACTTCTCATCTCGGTA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGATA
* *
31518433 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTT-TCATAACCTCAATAA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCAT---CTCGAT-A
31518487 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
1 --CCAATGCCATGTCCCAGACATGGTCTTACATGGG
31518523 GTCTCATCCC
Statistics
Matches: 153, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
49 33 0.22
50 77 0.50
51 4 0.03
52 1 0.01
53 4 0.03
54 1 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGATA
Found at i:31527203 original size:120 final size:120
Alignment explanation
Indices: 31526998--31527229 Score: 437
Period size: 120 Copynumber: 1.9 Consensus size: 120
31526988 TAGTTACGCA
* *
31526998 TTCCCATTTCCAAAGAGGAATCTTAACCGGCTGCAGCAAACCCGAAGGTAACTGATGCTCAGACT
1 TTCCCATTTCCAAAGAGGAATCTTAACCGGCTACAGCAAACCCAAAGGTAACTGATGCTCAGACT
*
31527063 TAACCTGCTGGCAAGTAGACATCTGCCCACAAAATTAGTAACCTCACGTTACACG
66 TAACCTGCTAGCAAGTAGACATCTGCCCACAAAATTAGTAACCTCACGTTACACG
31527118 TTCCCATTTCCAAAGAGGAATCTTAACCGGCTACAGCAAACCCAAAGGTAACTGATGCTCAGACT
1 TTCCCATTTCCAAAGAGGAATCTTAACCGGCTACAGCAAACCCAAAGGTAACTGATGCTCAGACT
31527183 TAACCTGCTAGCAAGTAGACATCTGCCCACAAAATTAGTAACCTCAC
66 TAACCTGCTAGCAAGTAGACATCTGCCCACAAAATTAGTAACCTCAC
31527230 ATTTCAACCT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (120 bp):
TTCCCATTTCCAAAGAGGAATCTTAACCGGCTACAGCAAACCCAAAGGTAACTGATGCTCAGACT
TAACCTGCTAGCAAGTAGACATCTGCCCACAAAATTAGTAACCTCACGTTACACG
Found at i:31532954 original size:343 final size:344
Alignment explanation
Indices: 31532323--31532972 Score: 1045
Period size: 343 Copynumber: 1.9 Consensus size: 344
31532313 CATCGTTCCT
* *
31532323 AGTCGCTCGGTCGTGTGACCCAGTCTCAGTGACAAGCGACACTAGCGTCTCACTAGTGTCTAGAT
1 AGTCGCTCGATCATGTGACCCAGTCTCAGTGACAAGCGACACTAGCGTCTCACTAGTGTCTAGAT
* *
31532388 TTGGCATACTCTCCAGTGAAGAGGACTTAGCTCGAGCTCCTCTACGACCTCTACCTCGGCCTCTA
66 TTGGCATACTCTCCAGTGAAGAGGACTCAGCTCGAGCCCCTCTACGACCTCTACCTCGGCCTCTA
* * *
31532453 GTACCCTGTCCGCGAGTACCTCATGCGCTCATCGTCTAGTAGTGCTTATCTGTATTAAAAGTTTT
131 GTACCCCGTCCGCCAGTACCTCATGCGCTCATCGTCTAGTAGTGCTTATATGTATTAAAAGTTTT
*
31532518 ATGAATCAGATTACAGTTTAATAGTTATTAGCTGATGTTTTATGGAAACAGTTTTAGTAGTTCAG
196 ATGAATCAGATTACAGTTCAATAGTTATTAGCTGATGTTTTATGGAAACAGTTTTAGTAGTTCAG
*
31532583 AGTTTGTTTTCGTACAACGCAATGTCTACCAGTGTTTATCGATTTTATTACAGTATCATTATACA
261 AGTTTGTTTTCATACAACGCAATGTCTACCAGTGTTTATCGATTTTATTACAGTATCATTATACA
31532648 CTAACCTGACTGTTTCCCC
326 CTAACCTGACTGTTTCCCC
* * * *
31532667 AGTCGCTCGATCATGTGACCCAGTCTCAGTGACAGGCGACACTGGCGTCTCGCTATTGTCTAGAT
1 AGTCGCTCGATCATGTGACCCAGTCTCAGTGACAAGCGACACTAGCGTCTCACTAGTGTCTAGAT
* * * *
31532732 TTGGCATATTGC-CCAGTGAAGAGGACTCAGCTCGAGCCCCTCTATGGCCTTTACCTCGGCCTCT
66 TTGGCATACT-CTCCAGTGAAGAGGACTCAGCTCGAGCCCCTCTACGACCTCTACCTCGGCCTCT
* *
31532796 AGTACCCCGTCC-CCAGTACCTCGTGCGCTCATCGTCTAGTAGTGTTTATATGTATTAAAAGTTT
130 AGTACCCCGTCCGCCAGTACCTCATGCGCTCATCGTCTAGTAGTGCTTATATGTATTAAAAGTTT
* *
31532860 TATGAATCAGTTTACAGTTCAATAGTTATTAG-TAGATGTTTTATGGAAATAGTTTTAGTAGTTC
195 TATGAATCAGATTACAGTTCAATAGTTATTAGCT-GATGTTTTATGGAAACAGTTTTAGTAGTTC
* * *
31532924 AGAGTTTGTTTTCATACGACGCAGTGTCTACCAGTGTTTATCGGTTTTA
259 AGAGTTTGTTTTCATACAACGCAATGTCTACCAGTGTTTATCGATTTTA
31532973 CCACAGTAAC
Statistics
Matches: 280, Mismatches: 24, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
342 1 0.00
343 152 0.54
344 126 0.45
345 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (344 bp):
AGTCGCTCGATCATGTGACCCAGTCTCAGTGACAAGCGACACTAGCGTCTCACTAGTGTCTAGAT
TTGGCATACTCTCCAGTGAAGAGGACTCAGCTCGAGCCCCTCTACGACCTCTACCTCGGCCTCTA
GTACCCCGTCCGCCAGTACCTCATGCGCTCATCGTCTAGTAGTGCTTATATGTATTAAAAGTTTT
ATGAATCAGATTACAGTTCAATAGTTATTAGCTGATGTTTTATGGAAACAGTTTTAGTAGTTCAG
AGTTTGTTTTCATACAACGCAATGTCTACCAGTGTTTATCGATTTTATTACAGTATCATTATACA
CTAACCTGACTGTTTCCCC
Found at i:31533324 original size:18 final size:18
Alignment explanation
Indices: 31533300--31533347 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31533290 TGTCATTCCT
31533300 TTTCAAAACATTATTC-A
1 TTTCAAAACATTATTCAA
* *
31533317 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTCAA
31533336 TTTCAAAACATT
1 TTTCAAAACATT
31533348 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTCAAAACATTATTCAA
Found at i:31538973 original size:16 final size:16
Alignment explanation
Indices: 31538952--31538987 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31538942 TGGTTCGCTC
*
31538952 TAATGGAATAGAGCTG
1 TAATGGAATAGAACTG
31538968 TAATGGAATAGAACTG
1 TAATGGAATAGAACTG
31538984 TAAT
1 TAAT
31538988 AGTAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (16 bp):
TAATGGAATAGAACTG
Found at i:31539033 original size:45 final size:44
Alignment explanation
Indices: 31538969--31539061 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
31538959 ATAGAGCTGT
31538969 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
31539014 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
31539058 AATG
1 AATG
31539062 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:31549019 original size:18 final size:19
Alignment explanation
Indices: 31548996--31549047 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
31548986 AAATGAAGAA
31548996 ATGGTATCGATATAAAAT-
1 ATGGTATCGATATAAAATC
* *
31549014 ATGGTATTGATA-AAATTC
1 ATGGTATCGATATAAAATC
31549032 AGTAGGTATCGATATA
1 A-T-GGTATCGATATA
31549048 TTTCTAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
19 1 0.04
20 9 0.33
21 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (19 bp):
ATGGTATCGATATAAAATC
Found at i:31549997 original size:35 final size:35
Alignment explanation
Indices: 31549951--31550036 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 35
31549941 GTTCAAGATT
*
31549951 CAGTAGATCATTTCCATGATGCCACTCCGTAGAGC
1 CAGTAGATCATTTCCATGATGCCACTCCGTAGACC
* * *
31549986 CAGTAGATCATTTTCATGATGCCGCTTCGTAGACC
1 CAGTAGATCATTTCCATGATGCCACTCCGTAGACC
31550021 CAGTAGATCATTTCCA
1 CAGTAGATCATTTCCA
31550037 ACCAAACTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (35 bp):
CAGTAGATCATTTCCATGATGCCACTCCGTAGACC
Found at i:31551244 original size:25 final size:25
Alignment explanation
Indices: 31551216--31551263 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31551206 ATACCATTCA
*
31551216 ATAACAACAA-AATACAATACGTAGT
1 ATAA-AACAATAACACAATACGTAGT
*
31551241 ATAAATCAATAACACAATACGTA
1 ATAAAACAATAACACAATACGTA
31551264 CCATTGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.21
Consensus pattern (25 bp):
ATAAAACAATAACACAATACGTAGT
Found at i:31552138 original size:9 final size:9
Alignment explanation
Indices: 31552120--31552285 Score: 199
Period size: 9 Copynumber: 18.4 Consensus size: 9
31552110 TTTGGTTAAA
31552120 AATTAACCG
1 AATTAACCG
*
31552129 AATTACCCG
1 AATTAACCG
31552138 AATTAACCG
1 AATTAACCG
* *
31552147 GATTAATCG
1 AATTAACCG
*
31552156 AATTACCCG
1 AATTAACCG
31552165 AATTAACCG
1 AATTAACCG
31552174 AATT-ACCTG
1 AATTAACC-G
*
31552183 AATTAACCA
1 AATTAACCG
31552192 AATTAACCG
1 AATTAACCG
31552201 AATTAACCG
1 AATTAACCG
*
31552210 AATTACCCG
1 AATTAACCG
31552219 AATTAACCG
1 AATTAACCG
* *
31552228 GATTAATCG
1 AATTAACCG
* *
31552237 GATTACCCG
1 AATTAACCG
*
31552246 AATTAACTG
1 AATTAACCG
*
31552255 AATTACCCG
1 AATTAACCG
*
31552264 AATTAACCA
1 AATTAACCG
31552273 AATTAACCG
1 AATTAACCG
31552282 AATT
1 AATT
31552286 GAATCACTAC
Statistics
Matches: 131, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
8 3 0.02
9 125 0.95
10 3 0.02
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:31552427 original size:18 final size:18
Alignment explanation
Indices: 31552387--31552430 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31552377 AATTTTTATG
**
31552387 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
31552405 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
31552423 CTTGGGTT
1 ATTGGGTT
31552431 TGGATTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:31555920 original size:17 final size:17
Alignment explanation
Indices: 31555895--31555937 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
31555885 TTTATTTAAC
*
31555895 AATACTTTTATCTCAAA
1 AATATTTTTATCTCAAA
31555912 AATATTTTTTTATCTCAAA
1 AATA--TTTTTATCTCAAA
*
31555931 AGTATTT
1 AATATTT
31555938 CTTAAGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (17 bp):
AATATTTTTATCTCAAA
Found at i:31555924 original size:19 final size:19
Alignment explanation
Indices: 31555900--31555937 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31555890 TTAACAATAC
31555900 TTTTATCTCAAAAATATTT
1 TTTTATCTCAAAAATATTT
*
31555919 TTTTATCTCAAAAGTATTT
1 TTTTATCTCAAAAATATTT
31555938 CTTAAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTATCTCAAAAATATTT
Found at i:31556668 original size:19 final size:19
Alignment explanation
Indices: 31556641--31556677 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31556631 AAATTTTGGT
31556641 ATTAATATAATATTAAAAA
1 ATTAATATAATATTAAAAA
*
31556660 ATTATTATAATATTAAAA
1 ATTAATATAATATTAAAA
31556678 CTTTAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAATATAATATTAAAAA
Found at i:31556687 original size:19 final size:19
Alignment explanation
Indices: 31556641--31556687 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
31556631 AAATTTTGGT
*
31556641 ATTAATATAATATTAAAAA
1 ATTAGTATAATATTAAAAA
* *
31556660 ATTATTATAATATTAAAAC
1 ATTAGTATAATATTAAAAA
*
31556679 TTTAGTATA
1 ATTAGTATA
31556688 TCTTTTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTAGTATAATATTAAAAA
Found at i:31559774 original size:12 final size:12
Alignment explanation
Indices: 31559773--31559800 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31559763 TTTCCTCATT
31559773 TTTCTCATTTTG
1 TTTCTCATTTTG
31559785 TTTCTCATTTTG
1 TTTCTCATTTTG
31559797 TTTC
1 TTTC
31559801 ACGTCCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.18, G:0.07, T:0.68
Consensus pattern (12 bp):
TTTCTCATTTTG
Found at i:31561038 original size:24 final size:23
Alignment explanation
Indices: 31561006--31561075 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
31560996 GGGTAGGATT
*
31561006 TGATTCTGTATGTGATATTGCATA
1 TGATTCTGTATCTGA-ATTGCATA
* ** *
31561030 TGATTCTGTATTTGAGATTATATT
1 TGATTCTGTATCTGA-ATTGCATA
*
31561054 TGAATCTGTATCTGAATTGCAT
1 TGATTCTGTATCTGAATTGCAT
31561076 TTGAAAACGT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 5 0.14
24 32 0.86
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (23 bp):
TGATTCTGTATCTGAATTGCATA
Found at i:31574095 original size:37 final size:37
Alignment explanation
Indices: 31574026--31574155 Score: 127
Period size: 37 Copynumber: 3.5 Consensus size: 37
31574016 AAAAATGGAA
* * * ** *
31574026 TACTGATTTTACTGAATGTGTTGTAACAAGCAATATC
1 TACTAATTCTACTGAATGTGCTAAAACGAGCAATATC
* * *
31574063 TACTGATTCTATTGAATGTGC-ACAAATGAGCAATATC
1 TACTAATTCTACTGAATGTGCTA-AAACGAGCAATATC
* * *
31574100 TACTAACTCTACTAAATATGCTAAAACGAGCAATATC
1 TACTAATTCTACTGAATGTGCTAAAACGAGCAATATC
*
31574137 TATTAATTCTACTGAATGT
1 TACTAATTCTACTGAATGT
31574156 TCGCTCGAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
37 73 0.99
38 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (37 bp):
TACTAATTCTACTGAATGTGCTAAAACGAGCAATATC
Found at i:31579988 original size:30 final size:31
Alignment explanation
Indices: 31579925--31579989 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
31579915 CCCTGATATT
* *
31579925 ATTAAATTATCACAATAGTTAACACATCCCA
1 ATTAAATTACCACAATAGTTAACACATCACA
* *
31579956 ATTAAATTACCAC-ATAGTTAATATATCACA
1 ATTAAATTACCACAATAGTTAACACATCACA
31579986 ATTA
1 ATTA
31579990 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.32
Consensus pattern (31 bp):
ATTAAATTACCACAATAGTTAACACATCACA
Found at i:31581649 original size:16 final size:17
Alignment explanation
Indices: 31581628--31581663 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
31581618 GATTGATATA
31581628 TTTCTATTTTAT-TTAT
1 TTTCTATTTTATATTAT
31581644 TTTCTATTTTATATTAT
1 TTTCTATTTTATATTAT
31581661 TTT
1 TTT
31581664 TGCATTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTATTTTATATTAT
Found at i:31582466 original size:11 final size:11
Alignment explanation
Indices: 31582446--31582489 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
31582436 TAATAACATA
*
31582446 TATAATAATAT
1 TATAATAATAG
*
31582457 TATAAGAATAG
1 TATAATAATAG
31582468 TATAATAATAG
1 TATAATAATAG
*
31582479 ATAGAATAATA
1 -TATAATAATA
31582490 AAATAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (11 bp):
TATAATAATAG
Found at i:31587980 original size:21 final size:21
Alignment explanation
Indices: 31587956--31587996 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31587946 ATCTGCTCAA
* *
31587956 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
31587977 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
31587997 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:31594514 original size:13 final size:13
Alignment explanation
Indices: 31594496--31594520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31594486 CTATGATATA
31594496 AAACATAAGCAAC
1 AAACATAAGCAAC
31594509 AAACATAAGCAA
1 AAACATAAGCAA
31594521 ATTCATCTTA
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:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
AAACATAAGCAAC
Found at i:31599367 original size:2 final size:2
Alignment explanation
Indices: 31599362--31599415 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
31599352 AGTACATATG
* * * *
31599362 CT CT CT CT CT CT CT CT CT CT CT CC CT GT CT CT CT CA CT CT CA
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
31599404 CT CT CA CT CT CT
1 CT CT CT CT CT CT
31599416 TTTAAACATA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.06, C:0.50, G:0.02, T:0.43
Consensus pattern (2 bp):
CT
Found at i:31599379 original size:12 final size:12
Alignment explanation
Indices: 31599362--31599415 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
31599352 AGTACATATG
*
31599362 CTCTCTCTCTCT
1 CTCTCTCTCTCA
*
31599374 CTCTCTCTCTCC
1 CTCTCTCTCTCA
*
31599386 CTGTCTCTCTCA
1 CTCTCTCTCTCA
*
31599398 CTCTCACTCTCA
1 CTCTCTCTCTCA
31599410 CTCTCT
1 CTCTCT
31599416 TTTAAACATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.06, C:0.50, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCTCTCTCA
Found at i:31600336 original size:5 final size:5
Alignment explanation
Indices: 31600298--31600335 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
31600288 AAATGTCCTA
* *
31600298 AAAAT AAAAT AAAAT AAAAT AAAAT AAAGT AAAGT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
31600336 GACAAGATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:31606686 original size:151 final size:151
Alignment explanation
Indices: 31606499--31606790 Score: 530
Period size: 151 Copynumber: 1.9 Consensus size: 151
31606489 TAACTAAATG
*
31606499 ATTAACTAAGAAAATAAAAAGTAAAAATTCCAATGCATGATTTCAAAAAAATGAGTTTAATCAAT
1 ATTAACTAAGAAAATAAAAAGTAAAAATTCCAATGCACGATTTCAAAAAAATGAGTTTAATCAAT
* *
31606564 ATGATATAAATGTGCTAGATCAGTTTTATTCTTTAACTTAGAATAATTAAAGTTGTGTTCATGTT
66 ATGATATAAATGTGCTAGATCAATTTTATTCTTTAACTTAGAATAATTAAAGTTATGTTCATGTT
31606629 GTTATGAATAAACTAAGAATA
131 GTTATGAATAAACTAAGAATA
*
31606650 ATTAACTAAGAAAATAAAAAGTAAATATTCCAATGCACGATTTCAAAAAAATGAGTTTAATCAAT
1 ATTAACTAAGAAAATAAAAAGTAAAAATTCCAATGCACGATTTCAAAAAAATGAGTTTAATCAAT
* *
31606715 ATGATATAAATGTGTTAGATCAATTTTATTTTTTAACTTAGAATAATTAAAGTTATGTTCATGTT
66 ATGATATAAATGTGCTAGATCAATTTTATTCTTTAACTTAGAATAATTAAAGTTATGTTCATGTT
31606780 GTTATGAATAA
131 GTTATGAATAA
31606791 TTTCACAGCA
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
151 135 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (151 bp):
ATTAACTAAGAAAATAAAAAGTAAAAATTCCAATGCACGATTTCAAAAAAATGAGTTTAATCAAT
ATGATATAAATGTGCTAGATCAATTTTATTCTTTAACTTAGAATAATTAAAGTTATGTTCATGTT
GTTATGAATAAACTAAGAATA
Found at i:31608615 original size:119 final size:120
Alignment explanation
Indices: 31608433--31608655 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
31608423 TTCTCGTTCA
* *
31608433 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
31608498 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
31608553 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* * *
31608615 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
31608656 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:31608655 original size:40 final size:40
Alignment explanation
Indices: 31608431--31608655 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
31608421 GCTTCTCGTT
* *
31608431 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
31608471 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
31608511 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
31608551 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
31608590 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
31608631 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31608656 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 118 0.73
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:31622166 original size:80 final size:80
Alignment explanation
Indices: 31622066--31622234 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 80
31622056 CTCGTTCAAG
* * ** * *
31622066 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATTC-AATGCCTTCAGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCAGGACTTAACCCGGA-A
*
31622129 TTAAAAACTCGCACGAA
64 TTAAAAACTCGCACAAA
* * * *
31622146 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCAGGACTTAACCCGGAATT
*
31622211 AATAACTCGCACAAA
66 AAAAACTCGCACAAA
*
31622226 TACCTTCGG
1 TGCCTTCGG
31622235 ATCTTAGTCC
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
80 51 0.69
81 23 0.31
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCAGGACTTAACCCGGAATT
AAAAACTCGCACAAA
Found at i:31622247 original size:40 final size:40
Alignment explanation
Indices: 31622103--31622234 Score: 183
Period size: 40 Copynumber: 3.3 Consensus size: 40
31622093 TAACTCATTC
* * * *
31622103 AATGCCTTCAGGACTTAACCCGGATTTTAAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
31622144 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31622184 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31622224 AATACCTTCGG
1 AATGCCTTCGG
31622235 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 57 0.71
41 23 0.29
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:31622247 original size:80 final size:81
Alignment explanation
Indices: 31622106--31622287 Score: 203
Period size: 80 Copynumber: 2.3 Consensus size: 81
31622096 CTCATTCAAT
* * * *
31622106 GCCTTCAGGACTTAACCCGGATTTTAAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-
*
31622170 TAGT-A-TCTCGCACAAA
65 TAGTCACT-TAGCACAAA
* **
31622186 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTAAAAACTCGCACAAATACCTTCGGGA-CTTAACCCGGAT
31622249 ATAGTCACTTAGCACAAA
64 ATAGTCACTTAGCACAAA
* *
31622267 GCCTTCGAGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
31622288 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
79 3 0.03
80 53 0.61
81 30 0.34
82 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (81 bp):
GCCTTCGGGACTTAACCCGGATATTAAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATAT
AGTCACTTAGCACAAA
Done.