Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008167.1 Hibiscus syriacus cultivar Beakdansim tig00110748_pilon, whole genome shotgun sequence
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: 1661898
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 5
Found at i:259690 original size:14 final size:14
Alignment explanation
Indices: 259671--259697 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
259661 CTTCCCGGTT
259671 CGAGGCCATCCGAC
1 CGAGGCCATCCGAC
259685 CGAGGCCATCCGA
1 CGAGGCCATCCGA
259698 GAGCATCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.30, T:0.07
Consensus pattern (14 bp):
CGAGGCCATCCGAC
Found at i:259704 original size:10 final size:10
Alignment explanation
Indices: 259684--259717 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
259674 GGCCATCCGA
259684 CCGAGGCCAT
1 CCGAGGCCAT
259694 CCGAGAG-CAT
1 CCGAG-GCCAT
259704 CCGAGGCCAT
1 CCGAGGCCAT
259714 CCGA
1 CCGA
259718 ACTAGCTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:259742 original size:33 final size:33
Alignment explanation
Indices: 259671--259775 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
259661 CTTCCCGGTT
* * * *
259671 CGAGGCCATCCGACCGAGGCCATCCGAGAGCATC
1 CGAGGCCATCCGAACGA-GCTATGCGAGGGCATC
*
259705 CGAGGCCATCCGAACTAGCTATGCGAGGGCATC
1 CGAGGCCATCCGAACGAGCTATGCGAGGGCATC
* * * *
259738 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
1 CGAGGCCATCCGAACGAGCTATGCGAGGGCATC
259771 CGAGG
1 CGAGG
259776 GAAGCCGAGC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 46 0.75
34 15 0.25
ACGTcount: A:0.25, C:0.30, G:0.34, T:0.10
Consensus pattern (33 bp):
CGAGGCCATCCGAACGAGCTATGCGAGGGCATC
Found at i:259776 original size:33 final size:33
Alignment explanation
Indices: 259702--259788 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
259692 ATCCGAGAGC
* * * * *
259702 ATCCGAGGCCATCCGAACTAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
259735 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
259768 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
259789 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.26, C:0.26, G:0.37, T:0.10
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:259825 original size:29 final size:29
Alignment explanation
Indices: 259792--259847 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
259782 GAGCGAGGGT
259792 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
259821 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
259848 TGTGTTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.30, G:0.39, T:0.11
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:259960 original size:29 final size:29
Alignment explanation
Indices: 259918--259974 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
259908 GAGCAAGGGT
259918 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
259947 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
259975 GACCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:261790 original size:135 final size:137
Alignment explanation
Indices: 261636--261995 Score: 392
Period size: 135 Copynumber: 2.6 Consensus size: 137
261626 CCCTAACCTT
* * * ***
261636 TTTAATTTAGGTGATTTTTTTATTTGATC-CT-CATATTTATGCTTGAGGTTCCATTTTAATTAT
1 TTTAATTTAGGAGAATTTTTAATTTGATCGCTGC-T-TTTATGCCCAAGGTTCCATTTTAATTAT
*
261699 TCGAT-T-CAATAATTTGTTAAAATTG-ACGATTAATAATTAGAGCCTT-AATTTAGTTTAATTT
64 TCGATCTGC--TAATTTGATAAAATTGTACGATTAATAATTAGAGCCTTCAATTTAGTTTAATTT
261760 CACTTTAGTCC
127 CACTTTAGTCC
* *
261771 TTTAATTTAGGAGAATTTTTAATTTGATCGTTGCTTTTATGCCCAAGGTTCTATTTTAATTATTC
1 TTTAATTTAGGAGAATTTTTAATTTGATCGCTGCTTTTATGCCCAAGGTTCCATTTTAATTATTC
* * *
261836 GATCTGCTAATTTGATAAAATTGTTTAGGATTAATAATTAGAGTCTTCATTTTAGTTTAATTTCA
66 GATCTGCTAATTTGATAAAATTG--TACGATTAATAATTAGAGCCTTCAATTTAGTTTAATTTCA
* *
261901 CTTTATTTC
129 CTTTAGTCC
** * * ** *
261910 TTTAATTTAGGAGAATTTTTGGTTGGGTCATTGCTTTTATGCCCAAGGTTCCA-TTTAATTAGTC
1 TTTAATTTAGGAGAATTTTTAATTTGATCGCTGCTTTTATGCCCAAGGTTCCATTTTAATTATTC
* ** *
261974 GATTTAATAATTTGCTAAAATT
66 GATCTGCTAATTTGATAAAATT
261996 TATTAGGTTT
Statistics
Matches: 192, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
135 70 0.36
136 3 0.02
137 2 0.01
138 47 0.24
139 70 0.36
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.48
Consensus pattern (137 bp):
TTTAATTTAGGAGAATTTTTAATTTGATCGCTGCTTTTATGCCCAAGGTTCCATTTTAATTATTC
GATCTGCTAATTTGATAAAATTGTACGATTAATAATTAGAGCCTTCAATTTAGTTTAATTTCACT
TTAGTCC
Found at i:262033 original size:139 final size:138
Alignment explanation
Indices: 261681--262026 Score: 434
Period size: 139 Copynumber: 2.5 Consensus size: 138
261671 TTTATGCTTG
* * * *
261681 AGGTTCCATTTTAATTATTCGATTCAATAATTTGTTAAAA--TTGACGATTAATAATTAGAGCCT
1 AGGTTCCATTTTAATTATTCGATTTAATAATTTGATAAAATTTTTAGGATTAATAATTAGAGCC-
* *
261744 TA-A-TTTAGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATCGTTGCTT
65 TACATTTTAGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAATTGGATCATTGCTT
261807 TTATGCCCA
130 TTATGCCCA
* * ** *
261816 AGGTTCTATTTTAATTATTCGATCTGCTAATTTGATAAAATTGTTTAGGATTAATAATTAGAGTC
1 AGGTTCCATTTTAATTATTCGATTTAATAATTTGATAAAATT-TTTAGGATTAATAATTAGAGCC
* * * ** *
261881 TTCATTTTAGTTTAATTTCACTTTATTTCTTTAATTTAGGAGAATTTTTGGTTGGGTCATTGCTT
65 TACATTTTAGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAATTGGATCATTGCTT
261946 TTATGCCCA
130 TTATGCCCA
* * *
261955 AGGTTCCA-TTTAATTAGTCGATTTAATAATTTGCTAAAATTTATTAGGTTTTAAT-ATTAGAGC
1 AGGTTCCATTTTAATTATTCGATTTAATAATTTGATAAAATTT-TTAGG-ATTAATAATTAGAGC
262018 CTACATTTT
64 CTACATTTT
262027 GGGTTTAGTC
Statistics
Matches: 178, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
135 34 0.19
137 2 0.01
138 68 0.38
139 74 0.42
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.47
Consensus pattern (138 bp):
AGGTTCCATTTTAATTATTCGATTTAATAATTTGATAAAATTTTTAGGATTAATAATTAGAGCCT
ACATTTTAGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAATTGGATCATTGCTTT
TATGCCCA
Found at i:263029 original size:22 final size:21
Alignment explanation
Indices: 262978--263051 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 21
262968 TGCAGAAATG
*
262978 GTATCGATACTGTA-ATAG-A
1 GTATCGATACTATAGATAGAA
262997 GTATC-AGTACTATAGTATAGAA
1 GTATCGA-TACTATAG-ATAGAA
*
263019 GTATCGATACTA-AGAGA-AA
1 GTATCGATACTATAGATAGAA
263038 GGTATCGATACTAT
1 -GTATCGATACTAT
263052 GGATCCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 14 0.30
21 6 0.13
22 11 0.24
23 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (21 bp):
GTATCGATACTATAGATAGAA
Found at i:263524 original size:54 final size:54
Alignment explanation
Indices: 263465--263574 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
263455 TACCGAATGA
* *
263465 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
*
263519 CACTATGTGTGCAACTTAAGAAATTCTTAATGAGTTTATGAATTTCCGTATGGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
263573 CA
1 CA
263575 TTGGGTGTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (54 bp):
CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
Found at i:268789 original size:56 final size:56
Alignment explanation
Indices: 268669--269005 Score: 453
Period size: 56 Copynumber: 6.0 Consensus size: 56
268659 CTCACTACCA
* * * *
268669 ATACGGAAATTCATATACTTATTATGAATTTCTTA-ATTTTGCACATAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
268724 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACCCAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
268780 ATACGGAAATTCAAAAACTCAATATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
268836 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCAAATAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
** *
268892 ATAAAGAAATTCATAAACACACACATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCAT--A-A-ACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * * *
268952 ATATGGAAATTCATAAACTCATTATG-TTTTTTTTGTATTTGCACACATAGTGCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCC
269006 ATTTTGTAAT
Statistics
Matches: 250, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
55 55 0.22
56 142 0.57
57 1 0.00
58 2 0.01
59 1 0.00
60 49 0.20
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
Found at i:275694 original size:56 final size:56
Alignment explanation
Indices: 275601--275970 Score: 564
Period size: 56 Copynumber: 6.6 Consensus size: 56
275591 TTATATACAT
* * * *
275601 ATTATGAATTTCTTA-ATTTTGCACATAAAGTTCCCATACGGAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
* * *
275656 ATTGTGAATTTCTTAGTTTTTGCACACAAAGTGTCCATACAAAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
*
275712 ATTATGAATTTCTTAGTTTTTGCACACAAAGTCCCCATACGAAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
* * *
275768 ATTATTAATTTCTTAGTTTTTGTACACAAAGTGTCCATACGAAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
* *
275824 ATTATGAATTTGTTAGTTTTTGCACATAAAGTGCCCATAC-AGAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA-AAATTCATAAACTC
*
275880 ATTATGAATTTATTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
* * *
275936 ATTATGAATTTCTTTGTTTTTGTACACAGAGTGCC
1 ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCC
275971 ATTTGGTAAT
Statistics
Matches: 286, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
55 15 0.05
56 270 0.94
57 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (56 bp):
ATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTC
Found at i:279200 original size:54 final size:54
Alignment explanation
Indices: 279136--279318 Score: 294
Period size: 54 Copynumber: 3.4 Consensus size: 54
279126 GATTACCAAA
*
279136 TGGCACTATGTGTGCTACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
1 TGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
*
279190 TGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTTGTAT
1 TGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
* * * *
279244 TGGCACTATGTGTGCAACTTAATAAATTCATAATGAGTCTCTGAATTTCCGTAT
1 TGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
* *
279298 TGGTACTACGTGTGCAACTTA
1 TGGCACTATGTGTGCAACTTA
279319 TTTTCGCATT
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (54 bp):
TGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
Found at i:279395 original size:84 final size:84
Alignment explanation
Indices: 279242--279398 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
279232 GAATTTTTGT
* * * * *
279242 ATTGGCACTATGTGTGCAACTTAATAAATTCATAATGAGTCTCTGAATTTCCGTATTGGTACTAC
1 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTCTATGAATTTCCGTATGGGCACTAC
279307 GTGTGCAACTTATTTTCGC
66 GTGTGCAACTTATTTTCGC
* * **
279326 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTGG
1 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTCTATGAATTTCCGTATGGGCACTAC
279391 GTGTGCAA
66 GTGTGCAA
279399 ATTACTTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (84 bp):
ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTCTATGAATTTCCGTATGGGCACTAC
GTGTGCAACTTATTTTCGC
Found at i:279436 original size:138 final size:138
Alignment explanation
Indices: 279188--279438 Score: 369
Period size: 138 Copynumber: 1.8 Consensus size: 138
279178 GAATTTCTGT
* * * *
279188 ATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACTAT
1 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTAG
* * * *
279253 GTGTGCAACTTAATAAATTCATAATGAGTCTCTGAATTTCCGTATTGGTACTACGTGTGCAACTT
66 GTGTGCAAATTAATAAATTCATAATAAATCTCTGAATTACCGTATTGGTACTACGTGTGCAACTT
279318 ATTTTCGC
131 ATTTTCGC
*
279326 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTGG
1 ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTAG
* * * *
279391 GTGTGCAAATTACTTAAATT-ATAGTAAATTTGTGAATTACCGTATTGG
66 GTGTGCAAATTA-ATAAATTCATAATAAATCTCTGAATTACCGTATTGG
279439 CACTGCAAGT
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
138 93 0.94
139 6 0.06
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (138 bp):
ATTGGCAATATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTAG
GTGTGCAAATTAATAAATTCATAATAAATCTCTGAATTACCGTATTGGTACTACGTGTGCAACTT
ATTTTCGC
Found at i:283844 original size:16 final size:16
Alignment explanation
Indices: 283806--283836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
283796 TTGATCTGAA
*
283806 ACCCAAACCATACCCG
1 ACCCAAACAATACCCG
283822 ACCCAAACAATACCC
1 ACCCAAACAATACCC
283837 TATCCAAAAT
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:0.42, C:0.48, G:0.03, T:0.06
Consensus pattern (16 bp):
ACCCAAACAATACCCG
Found at i:287919 original size:22 final size:22
Alignment explanation
Indices: 287891--287937 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
287881 AAGAAGGGCT
287891 TACAATTCTGATATCGACTTCC
1 TACAATTCTGATATCGACTTCC
287913 TACAATTCTGATATCGACTTCC
1 TACAATTCTGATATCGACTTCC
287935 TAC
1 TAC
287938 TTTAGGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (22 bp):
TACAATTCTGATATCGACTTCC
Found at i:293611 original size:32 final size:32
Alignment explanation
Indices: 293575--293663 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
293565 TGACTCAATT
* *
293575 CAAAAATTAACCGATCCGACATTGACCCGACC
1 CAAAAATTAATCGATCCGATATTGACCCGACC
*
293607 C-AAAATCTAATCGATCCGATATTAACCCGACC
1 CAAAAAT-TAATCGATCCGATATTGACCCGACC
* *
293639 CAAAAGTCAATCGATCCGATATTGA
1 CAAAAATTAATCGATCCGATATTGA
293664 TTATAACAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.10
32 40 0.82
33 4 0.08
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.20
Consensus pattern (32 bp):
CAAAAATTAATCGATCCGATATTGACCCGACC
Found at i:295359 original size:2 final size:2
Alignment explanation
Indices: 295352--295388 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
295342 TAATTGAATG
295352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
295389 ATTTATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:297759 original size:30 final size:30
Alignment explanation
Indices: 297715--297868 Score: 106
Period size: 30 Copynumber: 5.2 Consensus size: 30
297705 TGGCTTAAAC
*
297715 TAAA-ATATTTTATTCTTATCTTAACTTAT
1 TAAATATATTATATTCTTATCTTAACTTAT
* * *
297744 TACATA-AGTTATATTCTTAACTTAAATTAT
1 TAAATATA-TTATATTCTTATCTTAACTTAT
* * *
297774 T-AA-ATATTCTATTCTTACCTTAAATTAT
1 TAAATATATTATATTCTTATCTTAACTTAT
*
297802 TAAATATAATTA-ATTC-TATTTTAACTTA-
1 TAAATAT-ATTATATTCTTATCTTAACTTAT
* * * *
297830 AAACATATCTTTTTATTCTTATCTTAGCTTAT
1 TAA-ATAT-ATTATATTCTTATCTTAACTTAT
*
297862 AAAATAT
1 TAAATAT
297869 TTTTATTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
28 24 0.24
29 23 0.23
30 31 0.32
31 17 0.17
32 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (30 bp):
TAAATATATTATATTCTTATCTTAACTTAT
Found at i:297795 original size:28 final size:28
Alignment explanation
Indices: 297717--297808 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
297707 GCTTAAACTA
* * *
297717 AAATATTTTATTCTTATCTTAACTTATT
1 AAATATTATATTCTTAACTTAAATTATT
*
297745 ACATAAGTTATATTCTTAACTTAAATTATT
1 AAAT-A-TTATATTCTTAACTTAAATTATT
* *
297775 AAATATTCTATTCTTACCTTAAATTATT
1 AAATATTATATTCTTAACTTAAATTATT
297803 AAATAT
1 AAATAT
297809 AATTAATTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 30 0.55
29 2 0.04
30 23 0.42
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (28 bp):
AAATATTATATTCTTAACTTAAATTATT
Found at i:297899 original size:24 final size:26
Alignment explanation
Indices: 297860--297926 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 26
297850 ATCTTAGCTT
297860 ATAAAATAT-TTTTATTTTAAC-TAC
1 ATAAAATATATTTTATTTTAACTTAC
* *
297884 A-AAAATATATTTTATTTTATCTTAT
1 ATAAAATATATTTTATTTTAACTTAC
297909 ATAAAATATA-TTTATTTT
1 ATAAAATATATTTTATTTT
297927 TATCCCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 7 0.18
24 12 0.32
25 11 0.29
26 8 0.21
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
ATAAAATATATTTTATTTTAACTTAC
Found at i:297914 original size:49 final size:52
Alignment explanation
Indices: 297818--297926 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 52
297808 TAATTAATTC
* * *
297818 TATTTTAACTTAAAACATATCTTTTTATTCTTATCTTAGCTTATAAAATATTTT
1 TATTTTAACTTAAAAAATATCATTTTATTCTTATCTTA-C-TATAAAATATATT
297872 TATTTTAAC-TACAAAAATAT-ATTTTATT-TTATCTTA-TATAAAATATATT
1 TATTTTAACTTA-AAAAATATCATTTTATTCTTATCTTACTATAAAATATATT
297921 TATTTT
1 TATTTT
297927 TATCCCAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 18 0.35
52 8 0.16
53 9 0.18
54 16 0.31
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (52 bp):
TATTTTAACTTAAAAAATATCATTTTATTCTTATCTTACTATAAAATATATT
Found at i:297927 original size:26 final size:26
Alignment explanation
Indices: 297841--297930 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
297831 AACATATCTT
* *
297841 TTTATTCTTATCTTAGCTTATAAAATATT
1 TTTATTTTTATCTTA---TATAAAATATA
* *
297870 TTTA-TTTTAAC-TACA-AAAATATA
1 TTTATTTTTATCTTATATAAAATATA
297893 TTT-TATTTTATCTTATATAAAATATA
1 TTTAT-TTTTATCTTATATAAAATATA
297919 TTTATTTTTATC
1 TTTATTTTTATC
297931 CCAAATTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 10 0.20
24 7 0.14
25 3 0.06
26 18 0.36
27 3 0.06
28 5 0.10
29 4 0.08
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTATTTTTATCTTATATAAAATATA
Found at i:298044 original size:27 final size:27
Alignment explanation
Indices: 297977--298074 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
297967 TTAAGTCAAG
* * *
297977 ATAAGAATAAATTATTTTTTAATTTAAG
1 ATAAGAATAAAATA-TTTTTAAATTAAA
* * *
298005 ATAACATTCAAATATTTTTAAATTAAA
1 ATAAGAATAAAATATTTTTAAATTAAA
** *
298032 ATAAGAATAAAATAGATTTTTAGGTTACA
1 ATAAGAATAAAAT--ATTTTTAAATTAAA
298061 A-AAGAATAAAATAT
1 ATAAGAATAAAATAT
298075 ATTTGATAGG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.04
27 21 0.38
28 21 0.38
29 12 0.21
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (27 bp):
ATAAGAATAAAATATTTTTAAATTAAA
Found at i:298051 original size:29 final size:28
Alignment explanation
Indices: 298018--298078 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
298008 ACATTCAAAT
298018 ATTTTTAAATTAAAATAAGAATAAAATAG
1 ATTTTTAAATTAAAA-AAGAATAAAATAG
** * *
298047 ATTTTTAGGTTACAAAAGAATAAAATAT
1 ATTTTTAAATTAAAAAAGAATAAAATAG
298075 ATTT
1 ATTT
298079 GATAGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (28 bp):
ATTTTTAAATTAAAAAAGAATAAAATAG
Found at i:333849 original size:28 final size:28
Alignment explanation
Indices: 333816--333875 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
333806 ATTGGAATTA
*
333816 TAAAATTACACCTGAAGGGTAAAATGA-C
1 TAAAA-TACACCTAAAGGGTAAAATGACC
* * *
333844 TAAAATGCCCCTAAAGTGTAAAATGACC
1 TAAAATACACCTAAAGGGTAAAATGACC
333872 TAAA
1 TAAA
333876 GTACCTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (28 bp):
TAAAATACACCTAAAGGGTAAAATGACC
Found at i:333885 original size:28 final size:27
Alignment explanation
Indices: 333816--333886 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
333806 ATTGGAATTA
* * *
333816 TAAAATTACACCTGAAGGGTAAAATGAC
1 TAAAA-TACCCCTAAAGTGTAAAATGAC
*
333844 TAAAATGCCCCTAAAGTGTAAAATGACC
1 TAAAATACCCCTAAAGTGTAAAATGA-C
* *
333872 TAAAGTACCTCTAAA
1 TAAAATACCCCTAAA
333887 CCCATGAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 17 0.49
28 18 0.51
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (27 bp):
TAAAATACCCCTAAAGTGTAAAATGAC
Found at i:364315 original size:14 final size:12
Alignment explanation
Indices: 364287--364362 Score: 68
Period size: 12 Copynumber: 6.3 Consensus size: 12
364277 TCAAAACCTG
364287 TATACTATATTA
1 TATACTATATTA
364299 TATATCTATATT-
1 TATA-CTATATTA
* *
364311 TATATGTATTTTA
1 TATA-CTATATTA
*
364324 AATACTATATTA
1 TATACTATATTA
364336 TATA-TATATTCA
1 TATACTATATT-A
*
364348 -AAACTATATTA
1 TATACTATATTA
364359 TATA
1 TATA
364363 TTTATTTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 9 0.18
12 32 0.63
13 10 0.20
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (12 bp):
TATACTATATTA
Found at i:364353 original size:23 final size:24
Alignment explanation
Indices: 364287--364368 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 24
364277 TCAAAACCTG
*
364287 TATACTATATT-ATATATCTATATT-
1 TATA-TATATTCAAATA-CTATATTA
* *
364311 TATATGTATTTTAAATACTATATTA
1 TATATATA-TTCAAATACTATATTA
364336 TATATATATTCAAA-ACTATATTA
1 TATATATATTCAAATACTATATTA
*
364359 TATATTTATT
1 TATATATATT
364369 TTTCCAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 21 0.42
24 18 0.36
25 11 0.22
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (24 bp):
TATATATATTCAAATACTATATTA
Found at i:364855 original size:55 final size:55
Alignment explanation
Indices: 364725--365223 Score: 597
Period size: 55 Copynumber: 9.1 Consensus size: 55
364715 TCAGATCAAT
* * * * *
364725 TTTGGAAGATGGCTCTGCTCCACTATTCTTTCAAGGGAGATCAGACTCAAGAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTC-AGGGAGATAAGACTCAAAAAATC
** * ** * *
364781 TTTAAAAGA-GAGGCCTGCTCCACTCTTCTTTCAAAGAGATAAGACTCGAAAAATA
1 TTTGGAAGACG-GGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
**
364836 TTTGGAAGACGGGTCTGCTCCACTAATCTTTCAGGGAGATAAGACTCAAAAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* *
364891 ATTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAACTC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* *
364946 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGATATAAGACTCGAAAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* * * * * * *
365001 TTTGGAAGACGAGTTTACTCCACTATTCTTTCAGAGAGATAAGACTTAAAAAATA
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* * *
365056 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCATGGAGATAAAACTCCAAAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* * * * * * *
365111 CTTGGAAGACCGGTTTCCTCCACTCTTCTTTCAGAGAGATAAAACTAAAAAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
* * * * *
365166 TTTGGAAGATGTGTCTGCTCTACTCTTCTTTCATGGAGA-ATAGACTCGAAAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATA-AGACTCAAAAAATC
365221 TTT
1 TTT
365224 TGATCCACTT
Statistics
Matches: 373, Mismatches: 67, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
54 1 0.00
55 346 0.93
56 26 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (55 bp):
TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCAAAAAATC
Found at i:366075 original size:45 final size:44
Alignment explanation
Indices: 365982--366252 Score: 215
Period size: 45 Copynumber: 6.0 Consensus size: 44
365972 TACAAACAGG
* * * * * *
365982 TTGACTCCTCTATACAAGAAAGTCAAAAATCACAACATTGAAAGA
1 TTGACTTCTCT-TACGAGAAAGTCAATAATGACAACACTAAAAGA
* * *
366027 TTGATTTCTCTATAAGAGAAAGTCAATAATGACAACACTAAAATA
1 TTGACTTCTCT-TACGAGAAAGTCAATAATGACAACACTAAAAGA
* * * * * *
366072 TTGACTCCTCTTCCCGAGAAAGTAAAAAATGTCATCACTAAAAGA
1 TTGACTTCTCTT-ACGAGAAAGTCAATAATGACAACACTAAAAGA
* * *
366117 TCGAC-TCATCTTCTCGAGAAAGTTAATGAA-GACAACACTAAAAGA
1 TTGACTTC-TCTT-ACGAGAAAGTCAAT-AATGACAACACTAAAAGA
* * ** * *
366162 TTGACTTATCTCCACGAGAAAGTCAATAACAACACCACTAAAAGG
1 TTGACTTCTCT-TACGAGAAAGTCAATAATGACAACACTAAAAGA
* *
366207 TTGACTTCTCTTTACGAGAAAGTCAAGAATGACATCACT-AAAGA
1 TTGACTTCTC-TTACGAGAAAGTCAATAATGACAACACTAAAAGA
366251 TT
1 TT
366253 AACTATTCCT
Statistics
Matches: 179, Mismatches: 40, Indels: 15
0.76 0.17 0.06
Matches are distributed among these distances:
44 10 0.06
45 165 0.92
46 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (44 bp):
TTGACTTCTCTTACGAGAAAGTCAATAATGACAACACTAAAAGA
Found at i:378760 original size:77 final size:79
Alignment explanation
Indices: 378671--378821 Score: 184
Period size: 77 Copynumber: 1.9 Consensus size: 79
378661 AAATTAATAA
*
378671 TTAAAATATTATTCAATTAAATCAAATTAAATAT-ACATT-AAAGACTTATAATCTAAATTACAA
1 TTAAAATATTATTCAATTAAATCAAATTAAATATCA-ATTAAAAGACTTATAATCTAAAATACAA
378734 TC-TTTAATGTTTAT
65 TCTTTTAATGTTTAT
* ** * * * *
378748 TTAAAA-ACTTATTTAATTATTTCAAATTATATATCAATTAAAAGAGTTGTAATCTAAAATACAT
1 TTAAAATA-TTATTCAATTAAATCAAATTAAATATCAATTAAAAGACTTATAATCTAAAATACAA
378812 TCTTTTAATG
65 TCTTTTAATG
378822 CTTACTTACT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
76 1 0.02
77 31 0.50
78 23 0.37
79 7 0.11
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (79 bp):
TTAAAATATTATTCAATTAAATCAAATTAAATATCAATTAAAAGACTTATAATCTAAAATACAAT
CTTTTAATGTTTAT
Found at i:384090 original size:15 final size:13
Alignment explanation
Indices: 384054--384096 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
384044 CACATAATAT
384054 AAATAA-AATGAA
1 AAATAATAATGAA
*
384066 AAATAGTAATGATA
1 AAATAATAATGA-A
384080 ATAATAATAATGAA
1 A-AATAATAATGAA
384094 AAA
1 AAA
384097 ACGTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.19
13 7 0.27
14 4 0.15
15 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (13 bp):
AAATAATAATGAA
Found at i:384113 original size:2 final size:2
Alignment explanation
Indices: 384108--384139 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
384098 CGTATAAAAC
384108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
384140 AATGTCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:384261 original size:29 final size:28
Alignment explanation
Indices: 384229--384322 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 28
384219 ATATATATTC
*
384229 AAAACTATATTATATATCTATTTTTTTTA
1 AAAACTATATTATATAT-TATTTTTTATA
* * *
384258 AAAACTATATTCTATATT-TGTTTTCTA
1 AAAACTATATTATATATTATTTTTTATA
384285 AAAACTATA-TACTATA-TATATTTTTATA
1 AAAACTATATTA-TATATTAT-TTTTTATA
384313 AAAACTATAT
1 AAAACTATAT
384323 GCTATAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
26 2 0.04
27 21 0.38
28 16 0.29
29 16 0.29
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (28 bp):
AAAACTATATTATATATTATTTTTTATA
Found at i:384289 original size:27 final size:28
Alignment explanation
Indices: 384229--384328 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
384219 ATATATATTC
* * *
384229 AAAACTATATTATATATCTATTTTTTTTA
1 AAAACTATATTCTATATATA-TTTTTATA
*
384258 AAAACTATATTCTATAT-T-TGTTTTCTA
1 AAAACTATATTCTATATATAT-TTTTATA
*
384285 AAAACTATATACTATATATATTTTTATA
1 AAAACTATATTCTATATATATTTTTATA
*
384313 AAAACTATATGCTATA
1 AAAACTATATTCTATA
384329 AAAACACGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 22 0.35
28 23 0.37
29 17 0.27
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAACTATATTCTATATATATTTTTATA
Found at i:401375 original size:30 final size:30
Alignment explanation
Indices: 401339--401399 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
401329 GAAGAATATG
*
401339 AACAGTCCTTAAATTTATATGATAACAATC
1 AACAGTCCTTAAATTTAGATGATAACAATC
401369 AACAGTCCTTAAATTTAGATGATAACAATC
1 AACAGTCCTTAAATTTAGATGATAACAATC
401399 A
1 A
401400 GCTTTGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (30 bp):
AACAGTCCTTAAATTTAGATGATAACAATC
Found at i:401827 original size:17 final size:17
Alignment explanation
Indices: 401802--401854 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
401792 AATTAAGAGT
401802 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
401819 TATTTTAATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
401836 TAGTTTAATTAGTGAAC
1 TAGTTTAATAAATGAAC
401853 TA
1 TA
401855 CTTCCCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:405872 original size:24 final size:23
Alignment explanation
Indices: 405841--405885 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
405831 AATTGACTCG
405841 TATGCTTCTATGGTATACTTTTT
1 TATGCTTCTATGGTATACTTTTT
*
405864 TATGACTTCTATGGTTTACTTT
1 TATG-CTTCTATGGTATACTTT
405886 AAAGTGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (23 bp):
TATGCTTCTATGGTATACTTTTT
Found at i:406258 original size:207 final size:207
Alignment explanation
Indices: 405903--406316 Score: 828
Period size: 207 Copynumber: 2.0 Consensus size: 207
405893 GTGAAATTGT
405903 ATTTGATTGTATATGGATTACTCTGATGACTAATACGATGTTTTGATATTTGAATCAAACTATCT
1 ATTTGATTGTATATGGATTACTCTGATGACTAATACGATGTTTTGATATTTGAATCAAACTATCT
405968 TGATTTGGTATCGAGTGTCATAGAACATTTTCTAATTGATGTTCTAGAGTAGTATGCCAGGTTTG
66 TGATTTGGTATCGAGTGTCATAGAACATTTTCTAATTGATGTTCTAGAGTAGTATGCCAGGTTTG
406033 ATGGTTTGGTTAGAGGAAAATATTATTTTTTTAAAAATCACAAAACCAATAATATATTAACACAT
131 ATGGTTTGGTTAGAGGAAAATATTATTTTTTTAAAAATCACAAAACCAATAATATATTAACACAT
406098 GTCGTGATCGGG
196 GTCGTGATCGGG
406110 ATTTGATTGTATATGGATTACTCTGATGACTAATACGATGTTTTGATATTTGAATCAAACTATCT
1 ATTTGATTGTATATGGATTACTCTGATGACTAATACGATGTTTTGATATTTGAATCAAACTATCT
406175 TGATTTGGTATCGAGTGTCATAGAACATTTTCTAATTGATGTTCTAGAGTAGTATGCCAGGTTTG
66 TGATTTGGTATCGAGTGTCATAGAACATTTTCTAATTGATGTTCTAGAGTAGTATGCCAGGTTTG
406240 ATGGTTTGGTTAGAGGAAAATATTATTTTTTTAAAAATCACAAAACCAATAATATATTAACACAT
131 ATGGTTTGGTTAGAGGAAAATATTATTTTTTTAAAAATCACAAAACCAATAATATATTAACACAT
406305 GTCGTGATCGGG
196 GTCGTGATCGGG
406317 TTGAATTATT
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 207 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (207 bp):
ATTTGATTGTATATGGATTACTCTGATGACTAATACGATGTTTTGATATTTGAATCAAACTATCT
TGATTTGGTATCGAGTGTCATAGAACATTTTCTAATTGATGTTCTAGAGTAGTATGCCAGGTTTG
ATGGTTTGGTTAGAGGAAAATATTATTTTTTTAAAAATCACAAAACCAATAATATATTAACACAT
GTCGTGATCGGG
Found at i:406882 original size:24 final size:24
Alignment explanation
Indices: 406832--406884 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
406822 CATGGGTCTT
* *
406832 GGCGGTGGTGGCTTCAGATGTGGA
1 GGCGGTGGTGGCTTCAGAGGCGGA
*
406856 GGCGGTGGTGGCTTCAGAGGCGTA
1 GGCGGTGGTGGCTTCAGAGGCGGA
406880 GGCGG
1 GGCGG
406885 AGGTCAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.15, G:0.53, T:0.21
Consensus pattern (24 bp):
GGCGGTGGTGGCTTCAGAGGCGGA
Found at i:414565 original size:198 final size:198
Alignment explanation
Indices: 414227--414619 Score: 524
Period size: 198 Copynumber: 2.0 Consensus size: 198
414217 CTTTTTACTG
* * **
414227 TGACTAAATAATTTTATTATAATTAGTTATTGTGAAAGAATATTATTTGTCACACTTTTTTATAA
1 TGACTAAATAATTTTATTACAATTAGTTATTGTAAAAGAATATTATTTGTCACAAATTTTTATAA
* * *
414292 TGAGAAATTAATATTTATTATAAATTGTTATTTTTATTAAATAAATTTGTCACAAATTTTTATTT
66 TGAGAAATTAATATTTATTATAAATTATTATTTTGATTAAATAAATTTCTCACAAATTTTTATTT
* * * * *
414357 TGACAAAATATTAG-GACGAAATTAATTTGCCATAACTTTTTCCTTTGACTAAATTTAACT-TGT
131 TGACAAAATATT-GTGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATTT-ACTATGT
414420 TATTT
194 TATTT
* * * *
414425 TGACTAAATCATTTTGTTACAATTTGTTATTTTAAAAGAATATTACTTT-TCACAAATTTTTA-A
1 TGACTAAATAATTTTATTACAATTAGTTATTGTAAAAGAATATTA-TTTGTCACAAATTTTTATA
* * *
414488 GATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTCTCAGAATTTTTTAT
65 -ATGAGAAATTAATATTTATTATAAATTATTATTTTGATTAAATAAATTTCTCACAAATTTTTAT
* * *
414553 TTTTACAAAATATTGTGACAAAATAAATTTGAGATAAATTTTTATTTTGACTAAATTTACTATGT
129 TTTGACAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATTTACTATGT
414618 TA
194 TA
414620 AAAACAAAAA
Statistics
Matches: 169, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
197 5 0.03
198 161 0.95
199 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (198 bp):
TGACTAAATAATTTTATTACAATTAGTTATTGTAAAAGAATATTATTTGTCACAAATTTTTATAA
TGAGAAATTAATATTTATTATAAATTATTATTTTGATTAAATAAATTTCTCACAAATTTTTATTT
TGACAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATTTACTATGTTA
TTT
Found at i:419979 original size:20 final size:20
Alignment explanation
Indices: 419954--419996 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
419944 TATATTGGGC
* *
419954 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
419974 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
419994 TAT
1 TAT
419997 GGAATAATGG
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:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:420025 original size:23 final size:23
Alignment explanation
Indices: 419999--420071 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
419989 ATGGTTATGG
419999 AATAATGGCAAGTGTATTGGTAA
1 AATAATGGCAAGTGTATTGGTAA
** *
420022 AATAAGCTTACGAGCT-TA-TGG--A
1 AATAA--TGGCAAG-TGTATTGGTAA
420044 AATAATGGCAAGTGTATTGGTAA
1 AATAATGGCAAGTGTATTGGTAA
420067 AATAA
1 AATAA
420072 GCTTACGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.16
21 3 0.08
22 6 0.16
23 11 0.30
24 3 0.08
25 6 0.16
26 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (23 bp):
AATAATGGCAAGTGTATTGGTAA
Found at i:420056 original size:45 final size:45
Alignment explanation
Indices: 419993--420178 Score: 243
Period size: 45 Copynumber: 4.1 Consensus size: 45
419983 TGGTATATGG
*
419993 TTATGG-AATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
*
420037 TTATGGAAATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
420082 TTATAGAACA-AATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
1 TTATGGAA-ATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
* * * *
420127 TTAT-GATATTAAATGGTAAGTATATTGGTAAAATAAACTTACGAGA
1 TTATGGA-AAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
420173 TTATGG
1 TTATGG
420179 GATAAATGGT
Statistics
Matches: 128, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
44 8 0.06
45 82 0.64
46 37 0.29
47 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
TTATGGAAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:420186 original size:91 final size:90
Alignment explanation
Indices: 419993--420191 Score: 267
Period size: 91 Copynumber: 2.2 Consensus size: 90
419983 TGGTATATGG
* * *
419993 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGAAATAATGGCAAGT
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAAATAATGGCAAGT
* * *
420057 GTATTGGTAAAATAAGCTTACGAGC
66 ATATTGGTAAAATAAACTTACGAGA
* * * *
420082 TTATAGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTAT-GATATTAAATGGTAA
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGA-AAT-AATGGCAA
420146 GTATATTGGTAAAATAAACTTACGAGA
64 GTATATTGGTAAAATAAACTTACGAGA
*
420173 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
420192 AGATTTTATA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
89 9 0.10
90 38 0.40
91 47 0.50
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (90 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAAATAATGGCAAGT
ATATTGGTAAAATAAACTTACGAGA
Found at i:422026 original size:417 final size:411
Alignment explanation
Indices: 421113--421923 Score: 1028
Period size: 415 Copynumber: 2.0 Consensus size: 411
421103 TTTTGCACAA
* * * ** * * * *
421113 AAAAATAGGCAAAAATGTTTCTGATAGTATAATTT-TTCATAATGATTAAAATATGTAACTGCAA
1 AAAAATAGACAGAAATGGTTCTGATAAAATAATTTATTAATAATGATTAAAATATATAAATACAA
* * *
421177 AAATAATTAATTATAAAAAACTTGAATTTTATTATCTAATTTGATAATTTTTTATAACAATAACT
66 AAATAATTAATTACAAAAAACTTAAATTTTATTATCTAATGTGATAATTTTTTATAACAATAACT
* **
421242 ATAAATTATAATTACAAAACCTATCAATATAACTTTTGAAACAAAAAGTGGAGAGAAAATATTTA
131 ATAAATTATAATTACAAAAACTATCAATATAACTTTTGAAACAAAAAGT-GAGAGAAAATAGCTA
* * * * *
421307 TCATAATATATGTAATCACTATAATTAAAATTTATAATTACAAGTATAATTTGTCACAAAAATAT
195 TCACAATATATGTAATCACTATAACTAAAATTTATAACTACAAATATAATTTGTCACAAAAACAT
421372 GAATACCATTATTTTTTTGTAACAATATATTTTTGTAATAATTATAAACACTTATAATTACAAAA
260 GAATACCATTATTTTTTTGTAACAATATATTTTTGTAATAATTATAAACACTTATAATTACAAAA
* * *
421437 ATTGTTACTATATGATTTTTTTGGCGTAAAAAAATATAGAGGAAAATCTTTATGACAATATATTT
325 ATTGTCAATATATGATTTTTTTGGC--AAAAAAATATAGAGGAAAA-CTATATGACAATATATTT
* ***
421502 TGTTACTATATAACATTTTTGACACT
387 TGTCAC-ATATAACATTTAAAACACT
** * *
421528 AAAAATAGGGAGAAATGGTTCTGATAATATAATTTTTTAATAATGATTAAAATATATAAATACAA
1 AAAAATAGACAGAAATGGTTCTGATAAAATAATTTATTAATAATGATTAAAATATATAAATACAA
* *
421593 AAATAATTAATTACAAAAAACTTAAATTTTATTATTTGATGTGATAATTTTTTATATAACAATAA
66 AAATAATTAATTACAAAAAACTTAAATTTTATTATCTAATGTGATAA-TTTTT-TATAACAATAA
* * *
421658 CTATAAATTATAATTATAAAAATTGTCAATATAACTTTTGAAACAAAAAAGT-AGAGAAAATAGC
129 CTATAAATTATAATTACAAAAACTATCAATATAACTTTTGAAAC-AAAAAGTGAGAGAAAATAGC
* *
421722 TATGACAATATATG-ATATCACTATAGCTAAAATTTATAACTACAAATATAATTTGTCTA-AAAA
193 TATCACAATATATGTA-ATCACTATAACTAAAATTTATAACTACAAATATAATTTGTC-ACAAAA
* * ** * *
421785 ACGTGAATATCATTA-TTTTTTGTGGCAATAT-TTTTTGTAATAATTATTAACACTTATAGTTAC
256 ACATGAATACCATTATTTTTTTGTAACAATATATTTTTGTAATAATTATAAACACTTATAATTAC
* * * *
421848 AAAATTTGTCAATATATGATTTTTTTGAGC-AAATAATATGGAGGAAAA-TATGTGACAATATAT
321 AAAAATTGTCAATATATGATTTTTTTG-GCAAAAAAATATAGAGGAAAACTATATGACAATATAT
421911 TTTGTCAC-TATAA
385 TTTGTCACATATAA
421924 TTAAAACATA
Statistics
Matches: 349, Mismatches: 40, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
409 5 0.01
411 20 0.06
413 16 0.05
415 85 0.24
416 84 0.24
417 80 0.23
418 52 0.15
419 7 0.02
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (411 bp):
AAAAATAGACAGAAATGGTTCTGATAAAATAATTTATTAATAATGATTAAAATATATAAATACAA
AAATAATTAATTACAAAAAACTTAAATTTTATTATCTAATGTGATAATTTTTTATAACAATAACT
ATAAATTATAATTACAAAAACTATCAATATAACTTTTGAAACAAAAAGTGAGAGAAAATAGCTAT
CACAATATATGTAATCACTATAACTAAAATTTATAACTACAAATATAATTTGTCACAAAAACATG
AATACCATTATTTTTTTGTAACAATATATTTTTGTAATAATTATAAACACTTATAATTACAAAAA
TTGTCAATATATGATTTTTTTGGCAAAAAAATATAGAGGAAAACTATATGACAATATATTTTGTC
ACATATAACATTTAAAACACT
Found at i:423923 original size:25 final size:22
Alignment explanation
Indices: 423894--423939 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
423884 CTTTTAACCC
423894 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
423919 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
423940 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:426389 original size:44 final size:44
Alignment explanation
Indices: 426270--426394 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
426260 AATAAAATCC
426270 CTTACCATTATTCCATAAGCTCGTAAGC-TATTTTAAAAAAATA
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAAAAAAATA
*** *
426313 CTTACCATTTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCA--TT--ATTCCATAAGCTCGTAAGCTTATTTTAAAAAAATA
* *
426361 CTTGCCATTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
426395 ATATGCTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
43 7 0.10
44 24 0.34
45 2 0.03
46 2 0.03
47 19 0.27
48 17 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAAAAAAATA
Found at i:431953 original size:6 final size:6
Alignment explanation
Indices: 431942--431972 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
431932 ACACTTATAT
431942 CATGAC CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
431973 TATGGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:433819 original size:44 final size:45
Alignment explanation
Indices: 433692--433824 Score: 187
Period size: 47 Copynumber: 2.9 Consensus size: 45
433682 AAAATAATAT
433692 AAAATACCTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAAC
1 AAAATA-CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAAC
*
433738 AAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACC
1 AAAATACTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAAC
* * * *
433785 CATATACTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 AAAATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
433825 ATATGCTTAC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
44 24 0.30
45 10 0.12
46 8 0.10
47 38 0.47
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (45 bp):
AAAATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAAC
Found at i:441235 original size:44 final size:45
Alignment explanation
Indices: 441115--441240 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
441105 TATAAAATCC
441115 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
441160 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
441207 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
441241 ATATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:441469 original size:59 final size:58
Alignment explanation
Indices: 441334--441470 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 58
441324 ATAAGCACCG
* * ** *
441334 TAGTGCTATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTAGTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* ** *
441393 AAGTACAGTCACGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
*
441452 TAGTGTATTCCCAAATATG
1 TAGTGTA-TCCCGAATATG
441471 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:445510 original size:26 final size:26
Alignment explanation
Indices: 445453--445510 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
445443 TCGCTTGCAA
*
445453 TTTTTTGAAATTTTAGCTTTTTTTTC
1 TTTTTTGAAATTTTAGCCTTTTTTTC
* ** * *
445479 TGTTTTGATTTTTTTGCCTTTTTTTG
1 TTTTTTGAAATTTTAGCCTTTTTTTC
445505 TTTTTT
1 TTTTTT
445511 TTGAAAAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.09, C:0.07, G:0.10, T:0.74
Consensus pattern (26 bp):
TTTTTTGAAATTTTAGCCTTTTTTTC
Found at i:449818 original size:45 final size:45
Alignment explanation
Indices: 449729--450064 Score: 389
Period size: 45 Copynumber: 7.4 Consensus size: 45
449719 ATTCATGTTT
* * * * *
449729 ATAATGCA-CCATTATGCATTTTCAATTATAGCGTACTTTTATGCCG
1 ATAATGCACCCA-TATGCATTTTC-ATTTTGGCATCCTTTCATGCCG
* * * *
449775 ATAATGCACACATATGCA-TTTCAGCTATAGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTTCA-TTTTGGCATCCTTTCATGCCG
449820 ATAATGCACCCATATGCATTATTC-TTTTGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATT-TTCATTTTGGCATCCTTTCATGCCG
*
449865 ATAATGCACCCATATGCATTATTC-TTTTGTCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATT-TTCATTTTGGCATCCTTTCATGCCG
* *
449910 ATAATGCACCCATTTGCATTATTC-TTTTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATT-TTCATTTTGGCATCCTTTCATGCCG
* *
449955 ATAATGCACCCATATGTATTATTC-TTTTGACATCCTTTCATGCCG
1 ATAATGCACCCATATGCATT-TTCATTTTGGCATCCTTTCATGCCG
** * *
450000 ATAATGCACCTGTATGCATTATTC-TTTTGGCATTCTTTCATGCCA
1 ATAATGCACCCATATGCATT-TTCATTTTGGCATCCTTTCATGCCG
450045 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
450065 ATTCGTTTGT
Statistics
Matches: 261, Mismatches: 25, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
44 1 0.00
45 240 0.92
46 15 0.06
47 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTTCATTTTGGCATCCTTTCATGCCG
Found at i:450065 original size:45 final size:45
Alignment explanation
Indices: 449764--450073 Score: 453
Period size: 45 Copynumber: 6.9 Consensus size: 45
449754 TTATAGCGTA
* * * * *
449764 CTTTTATGCCGATAATGCACACATATGCA-T-TTCAGCTATAGCATC
1 CTTTCATGCCGATAATGCACCCATATGCATTATTC--TTTTGGCATC
449809 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
*
449854 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGTCATC
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
*
449899 CTTTCATGCCGATAATGCACCCATTTGCATTATTCTTTTGGCATC
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
* * *
449944 CTTTCATGCCAATAATGCACCCATATGTATTATTCTTTTGACATC
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
** *
449989 CTTTCATGCCGATAATGCACCTGTATGCATTATTCTTTTGGCATT
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
* *
450034 CTTTCATGCCAATAATGCACCCATATGCATTATTCGTTTG
1 CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTG
450074 TTATTTCATT
Statistics
Matches: 241, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
45 237 0.98
46 1 0.00
47 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (45 bp):
CTTTCATGCCGATAATGCACCCATATGCATTATTCTTTTGGCATC
Found at i:450523 original size:22 final size:19
Alignment explanation
Indices: 450491--450552 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
450481 GTAACAATAC
*
450491 CCCTACCATGGTATCGATA
1 CCCTACTATGGTATCGATA
*
450510 CTACCATACTATGGTACCGATA
1 C--CC-TACTATGGTATCGATA
*
450532 CCCTCCTATGGTATCGATA
1 CCCTACTATGGTATCGATA
450551 CC
1 CC
450553 ATTTTTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 17 0.47
20 2 0.06
21 2 0.06
22 15 0.42
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (19 bp):
CCCTACTATGGTATCGATA
Found at i:450604 original size:20 final size:21
Alignment explanation
Indices: 450579--450626 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
450569 TTAAAATTGC
*
450579 ATCGATACCT-TCCCTTTGGT
1 ATCGATACCTCCCCCTTTGGT
450599 ATCGATA-CTCCCCCTTTGGT
1 ATCGATACCTCCCCCTTTGGT
*
450619 ATAGATAC
1 ATCGATAC
450627 TGACTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCGATACCTCCCCCTTTGGT
Found at i:450627 original size:20 final size:20
Alignment explanation
Indices: 450590--450627 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
450580 TCGATACCTT
*
450590 CCCTTTGGTATCGATACTCC
1 CCCTTTGGTATAGATACTCC
450610 CCCTTTGGTATAGATACT
1 CCCTTTGGTATAGATACT
450628 GACTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (20 bp):
CCCTTTGGTATAGATACTCC
Found at i:458396 original size:32 final size:32
Alignment explanation
Indices: 458360--458515 Score: 154
Period size: 32 Copynumber: 4.9 Consensus size: 32
458350 ACTCCTTTGT
* * * *
458360 ATTATCTGAATGCAATATTGACTCTGCTATGC
1 ATTATCTGAATGCAACACTGACTCTACTGTGC
**
458392 ATTATCCAAATGCAACAGC-GACTCTACTGT-C
1 ATTATCTGAATGCAACA-CTGACTCTACTGTGC
* *
458423 AATTATCTGAATGCAACACTGACTTTACTGTAC
1 -ATTATCTGAATGCAACACTGACTCTACTGTGC
* * *
458456 ATTATTTGAATGCAACACTGACTCTGCTGTGT
1 ATTATCTGAATGCAACACTGACTCTACTGTGC
* * *
458488 ATGATCTGAATGCAACATTGACACTACT
1 ATTATCTGAATGCAACACTGACTCTACT
458516 ATTCAACACA
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
31 2 0.02
32 98 0.97
33 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (32 bp):
ATTATCTGAATGCAACACTGACTCTACTGTGC
Found at i:458432 original size:64 final size:64
Alignment explanation
Indices: 458360--458517 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 64
458350 ACTCCTTTGT
* * *
458360 ATTATCTGAATGCAATATTGACTCTGCTATGCATTATCCAAATGCAACAGC-GACTCTACTGTCA
1 ATTATCTGAATGCAACATTGACTCTACTATACATTATCCAAATGCAACA-CTGACTCTACTGTCA
* * * *** * **
458424 ATTATCTGAATGCAACACTGACTTTACTGTACATTATTTGAATGCAACACTGACTCTGCTGTGT
1 ATTATCTGAATGCAACATTGACTCTACTATACATTATCCAAATGCAACACTGACTCTACTGTCA
* *
458488 ATGATCTGAATGCAACATTGACACTACTAT
1 ATTATCTGAATGCAACATTGACTCTACTAT
458518 TCAACACACA
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
63 1 0.01
64 75 0.99
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (64 bp):
ATTATCTGAATGCAACATTGACTCTACTATACATTATCCAAATGCAACACTGACTCTACTGTCA
Found at i:462822 original size:90 final size:88
Alignment explanation
Indices: 462670--462839 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
462660 ACACACCCAT
462670 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTACTTCAAATTAATTAAATCTATATTTA
1 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTACTTCAAATTAATTAAATCTATATTTA
*
462735 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
* * *
462759 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAACCAAGTTACCCTAATCATATTAGGG-TTTTATTACTTCAAATTAATTAAATCTATATTT
462824 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
462840 ATATTCGAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 36 0.47
90 40 0.53
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (88 bp):
TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTACTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:463340 original size:90 final size:89
Alignment explanation
Indices: 463219--463381 Score: 272
Period size: 90 Copynumber: 1.8 Consensus size: 89
463209 TAATCCCGAA
* * *
463219 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAT-CCTAATATGAT
*
463284 TAGGGTAACTTGGATATATGAGGAT
65 TACGGTAACTTGGATATATGAGGAT
*
463309 TATTAAATTCCAATTAATTAAATATAGATTTATTTAATTTGAAATAATAAAATCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTAATATGATT
463374 ACGGTAAC
66 ACGGTAAC
463382 ATGGCTAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 19 0.28
90 49 0.72
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTAATATGATT
ACGGTAACTTGGATATATGAGGAT
Found at i:470142 original size:90 final size:89
Alignment explanation
Indices: 470031--470198 Score: 300
Period size: 90 Copynumber: 1.9 Consensus size: 89
470021 CTGAAAATTT
*
470031 AATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGATTAGGG
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCCAATATGATTAGGG
470096 TAACTTGGATATAAGAGGATTATTA
65 TAACTTGGATATAAGAGGATTATTA
*
470121 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGT
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCCAATATGATTAGGGT
*
470186 AAGTTGGATATAA
66 AACTTGGATATAA
470199 AAAGGTGTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 29 0.39
90 46 0.61
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (89 bp):
AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCCAATATGATTAGGGT
AACTTGGATATAAGAGGATTATTA
Found at i:475214 original size:90 final size:89
Alignment explanation
Indices: 475093--475265 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 89
475083 TAATCCCGAA
* * *
475093 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCC-AATATGA
1 TATTAAATTCCAATTAATTAAACATAGATTTAATTAATTTGAAATAATAAAA-C-CCTAATATGA
475157 TTAGGGTAACTTGGATATAAGAGGAT
64 TTAGGGTAACTTGGATATAAGAGGAT
* *
475183 TATTAAATTCCAATTAATTAAACATATATTTATTTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAACATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
* *
475248 AGGGTAAGTTGGCTATAA
66 AGGGTAACTTGGATATAA
475266 AAAGGTGTGT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
88 2 0.03
89 26 0.35
90 47 0.63
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAACATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:481004 original size:17 final size:18
Alignment explanation
Indices: 480972--481007 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
480962 TAGGATAAGG
480972 TAGAAAGGAATAGAAGAAA
1 TAGAAAGG-ATAGAAGAAA
480991 TAGAAAGG-TAGAAGAAA
1 TAGAAAGGATAGAAGAAA
481008 AGATTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (18 bp):
TAGAAAGGATAGAAGAAA
Found at i:488938 original size:26 final size:26
Alignment explanation
Indices: 488860--488943 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
488850 AGTTTGGTTG
* *
488860 TAATAAAGATAAGAAAAGGAAGATG-AT
1 TAATAAAGATAA-AAAATGAA-ATGAAA
* * *
488887 TAATAAAG--GAAGAAT-AAATGAGA
1 TAATAAAGATAAAAAATGAAATGAAA
488910 TAATAAAGATAAAAAATGAAATGAAA
1 TAATAAAGATAAAAAATGAAATGAAA
*
488936 TAAAAAAG
1 TAATAAAG
488944 GGATAGAGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
22 3 0.07
23 10 0.23
24 3 0.07
25 6 0.14
26 14 0.32
27 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (26 bp):
TAATAAAGATAAAAAATGAAATGAAA
Found at i:489007 original size:17 final size:18
Alignment explanation
Indices: 488976--489009 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
488966 GATGGTCTTG
*
488976 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
488994 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
489010 TGTTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:493117 original size:28 final size:27
Alignment explanation
Indices: 493068--493127 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
493058 TTGCTTTCTC
493068 TTTT-TGAATTTCTTTTTCTTTTCTTA
1 TTTTCTGAATTTCTTTTTCTTTTCTTA
* *
493094 TTTTCTGAATTTTCTTCTTT-TTTTTTTC
1 TTTTCTGAA-TTTCTT-TTTCTTTTCTTA
493122 TTTTCT
1 TTTTCT
493128 TTTTGCACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 4 0.14
28 18 0.62
29 3 0.10
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTCTGAATTTCTTTTTCTTTTCTTA
Found at i:493474 original size:17 final size:18
Alignment explanation
Indices: 493443--493476 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
493433 GATGGTATTG
*
493443 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
493461 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
493477 TGGTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:498881 original size:20 final size:20
Alignment explanation
Indices: 498855--498907 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
498845 TCTAAGGTGG
*
498855 GTAGTATTGATACTCTACATT
1 GTAGTATCGATACTCTAC-TT
498876 -TAGTATCGATACTCTACTT
1 GTAGTATCGATACTCTACTT
*
498895 GTAGTATCAATAC
1 GTAGTATCGATAC
498908 CCTAGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
GTAGTATCGATACTCTACTT
Found at i:499741 original size:21 final size:21
Alignment explanation
Indices: 499717--499770 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
499707 TTTTATGGCT
*
499717 AGTTGGGCCCAAATCCAACCC
1 AGTTGAGCCCAAATCCAACCC
499738 AGTTGAGCCCAAATCCAACCC
1 AGTTGAGCCCAAATCCAACCC
499759 AGTTGAGCCCAA
1 AGTTGAGCCCAA
499771 CAACTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.15
Consensus pattern (21 bp):
AGTTGAGCCCAAATCCAACCC
Found at i:509129 original size:29 final size:29
Alignment explanation
Indices: 509087--509144 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
509077 TAAGGAAATG
509087 TGTTAGGCTATTTTATAGCCTAGTTTCTT
1 TGTTAGGCTATTTTATAGCCTAGTTTCTT
509116 TGTTAGGCTATTTTATAGCCTAGTTTCTT
1 TGTTAGGCTATTTTATAGCCTAGTTTCTT
509145 CCTTGTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (29 bp):
TGTTAGGCTATTTTATAGCCTAGTTTCTT
Found at i:510914 original size:28 final size:29
Alignment explanation
Indices: 510883--510947 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
510873 GGTTGAATTA
510883 TTGATCTTTATTTTTGG-GAA-TTTATAAT
1 TTGAT-TTTATTTTTGGAGAATTTTATAAT
*
510911 TTGA-TTT-TTTTTGGATAATTTTTATAAT
1 TTGATTTTATTTTTGGAGAA-TTTTATAAT
510939 TTGATTTTA
1 TTGATTTTA
510948 CAAGGTGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
25 7 0.23
26 5 0.16
28 16 0.52
29 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.62
Consensus pattern (29 bp):
TTGATTTTATTTTTGGAGAATTTTATAAT
Found at i:514058 original size:20 final size:21
Alignment explanation
Indices: 514033--514072 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
514023 TGCATTTTTC
*
514033 ATAAAAATGATC-ATCCCTTT
1 ATAAAAAAGATCGATCCCTTT
514053 ATAAAAAAGATCGATCCCTT
1 ATAAAAAAGATCGATCCCTT
514073 AAGGAATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAAAAAAGATCGATCCCTTT
Found at i:525423 original size:30 final size:30
Alignment explanation
Indices: 525371--525462 Score: 166
Period size: 30 Copynumber: 3.0 Consensus size: 30
525361 ATTTGACTTA
525371 TGGAAGATGATAAGGTTTAGGTGTGTTGGTT
1 TGGAAGATGATAAGG-TTAGGTGTGTTGGTT
525402 TGGAAGATGATAAGGTTAGGTGTGTTGGTT
1 TGGAAGATGATAAGGTTAGGTGTGTTGGTT
*
525432 TGGAAGATGATAAGGTTAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTAGGTGTGTTGGTT
525462 T
1 T
525463 AATGGTAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 45 0.75
31 15 0.25
ACGTcount: A:0.23, C:0.01, G:0.38, T:0.38
Consensus pattern (30 bp):
TGGAAGATGATAAGGTTAGGTGTGTTGGTT
Found at i:526793 original size:24 final size:25
Alignment explanation
Indices: 526748--526797 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
526738 TGCATAACAT
526748 TGTACATAGATGTTTTTATACATCA
1 TGTACATAGATGTTTTTATACATCA
*
526773 TGTATATAGATG-TTTTATACATCA
1 TGTACATAGATGTTTTTATACATCA
526797 T
1 T
526798 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (25 bp):
TGTACATAGATGTTTTTATACATCA
Found at i:544787 original size:14 final size:14
Alignment explanation
Indices: 544768--544795 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
544758 GAGTTGACTC
544768 AAATAATTTAAATT
1 AAATAATTTAAATT
544782 AAATAATTTAAATT
1 AAATAATTTAAATT
544796 TTAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATAATTTAAATT
Found at i:545502 original size:18 final size:18
Alignment explanation
Indices: 545481--545541 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
545471 GTGGATGTGA
*
545481 AATAAATAAGCAAAAAAT
1 AATAAATAAACAAAAAAT
*
545499 AATAAATAAACAAAAAACA
1 AATAAATAAACAAAAAA-T
545518 AATAAA-AAACATAAAAAAT
1 AATAAATAAAC--AAAAAAT
545537 AATAA
1 AATAA
545542 GAACTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 20 0.54
19 11 0.30
20 6 0.16
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.15
Consensus pattern (18 bp):
AATAAATAAACAAAAAAT
Found at i:545540 original size:19 final size:19
Alignment explanation
Indices: 545481--545541 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
545471 GTGGATGTGA
*
545481 AATAAATAAGC-AAAAAAT
1 AATAAATAAACAAAAAAAT
545499 AATAAATAAACAAAAAACA-
1 AATAAATAAACAAAAAA-AT
545518 AATAAA-AAACATAAAAAAT
1 AATAAATAAACA-AAAAAAT
545537 AATAA
1 AATAA
545542 GAACTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 16 0.42
19 21 0.55
20 1 0.03
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.15
Consensus pattern (19 bp):
AATAAATAAACAAAAAAAT
Found at i:547791 original size:36 final size:35
Alignment explanation
Indices: 547685--547887 Score: 129
Period size: 36 Copynumber: 5.6 Consensus size: 35
547675 CAAGGAAAAA
* * * *
547685 TATCTGAAGTGAGACAAAATTTGTTTTA-AAATGAAC
1 TATCTCAAGTGAGACAAAATTTATTTGAGAGA--AAC
* * * *
547721 TATCTTAAGTAAGATAAAAATTTTATTTTGAGAGAAAT
1 TATCTCAAGTGAGA-CAAAA-TTTA-TTTGAGAGAAAC
* * *
547759 TGTCTCAAGCGAGACAAAATTTATTTGAAGAGACAC
1 TATCTCAAGTGAGACAAAATTTATTTG-AGAGAAAC
* *** *
547795 TATCTCAAGTGAGATAAAACAAATTTGAGGGAAAC
1 TATCTCAAGTGAGACAAAATTTATTTGAGAGAAAC
* * * * * *
547830 TGTCTCGAGTGAGACGAGATTTGTTTCAAGAGAAAC
1 TATCTCAAGTGAGACAAAATTTATTT-GAGAGAAAC
*
547866 TATCTCAAGTGAGATAAAATTT
1 TATCTCAAGTGAGACAAAATTT
547888 TCATTTCAAG
Statistics
Matches: 123, Mismatches: 38, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
35 27 0.22
36 67 0.54
37 8 0.07
38 15 0.12
39 4 0.03
40 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (35 bp):
TATCTCAAGTGAGACAAAATTTATTTGAGAGAAAC
Found at i:547861 original size:71 final size:71
Alignment explanation
Indices: 547747--547884 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 71
547737 AAAATTTTAT
* * *
547747 TTTGAGAGAAATTGTCTCAAGCGAGACAAAATTTATTTGAAGAGACACTATCTCAAGTGAGATAA
1 TTTGAGAGAAACTGTCTCAAGCGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGTGAGATAA
547812 AACAAA
66 AACAAA
* * * * * *
547818 TTTGAGGGAAACTGTCTCGAGTGAGACGAGATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAA
1 TTTGAGAGAAACTGTCTCAAGCGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGTGAGATAA
547883 AA
66 AA
547885 TTTTCATTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (71 bp):
TTTGAGAGAAACTGTCTCAAGCGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGTGAGATAA
AACAAA
Found at i:547932 original size:74 final size:73
Alignment explanation
Indices: 547627--547939 Score: 269
Period size: 74 Copynumber: 4.3 Consensus size: 73
547617 CGAGTGAGGT
* * * *
547627 AAAATTTGTTTCAAGA-AAATCTACCTCAAGT-AGATAAAATTTTTATTTCAAGGAAAAATATCT
1 AAAATTTGTTTCAAGAGAAA-CTATCTCAAGTGAGATAAAA-TTTTATTTCAAGGGAAACTGTC-
547690 G-AAGTGAGAC
63 GCAAGTGAGAC
* * * * ** * * *
547700 AAAATTTGTTTTAAAATG-AACTATCTTAAGTAAGATAAAAATTTTATTTTGAGAGAAATTGTCT
1 AAAATTTGTTTCAAGA-GAAACTATCTCAAGTGAGAT-AAAATTTTATTTCAAGGGAAACTGTCG
*
547764 CAAGCGAGAC
64 CAAGTGAGAC
* * * *** * * *
547774 AAAATTTATTTGAAGAGACACTATCTCAAGTGAGATAAAA-CAAATTT-GAGGGAAACTGTCTCG
1 AAAATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTATTTCAAGGGAAACTGTCGCA
547837 AGTGAGAC
66 AGTGAGAC
* *
547845 GAGATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTCATTTCAAGGGAAACTGTCGC
1 AAAATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTT-ATTTCAAGGGAAACTGTCGC
*
547910 AAGTGAGAT
65 AAGTGAGAC
* * *
547919 GAAATATGTTTCAAGATAAAC
1 AAAATTTGTTTCAAGAGAAAC
547940 AGTCTTAAGC
Statistics
Matches: 191, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
71 55 0.29
72 4 0.02
73 32 0.17
74 96 0.50
75 4 0.02
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (73 bp):
AAAATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTATTTCAAGGGAAACTGTCGCA
AGTGAGAC
Found at i:547962 original size:74 final size:74
Alignment explanation
Indices: 547822--547962 Score: 167
Period size: 74 Copynumber: 1.9 Consensus size: 74
547812 AACAAATTTG
* * * * ** *
547822 AGGGAAACTGTCTCGAGTGAGACGAGATTTGTTTCAAGAGAAACTATCTCAAGTGAGATAAAATT
1 AGGGAAACTGTCGCAAGTGAGACGAAATATGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATT
547887 TTCATTTCA
66 TTCATTTCA
* * * *
547896 AGGGAAACTGTCGCAAGTGAGATGAAATATGTTTCAAGATAAAC-AGTCTTAAGCAAGACAAGAT
1 AGGGAAACTGTCGCAAGTGAGACGAAATATGTTTCAAGAGAAACTA-TCTCAAGCAAGACAAAAT
547960 TTT
65 TTT
547963 TTAAGAGAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 1 0.02
74 54 0.98
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (74 bp):
AGGGAAACTGTCGCAAGTGAGACGAAATATGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATT
TTCATTTCA
Found at i:550574 original size:47 final size:45
Alignment explanation
Indices: 550506--550677 Score: 197
Period size: 47 Copynumber: 3.8 Consensus size: 45
550496 ATAAAATCTT
*
550506 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAAAATAC
*
550551 TTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTA-TACAAAATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACT--AAAATAC
* * ** *
550599 TTACCATTTAATCTCATAAGCTTGTAAGCTTATTTTACCCATATAC
1 TTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACTAAAATAC
*
550645 TTGCCA-TTATTCCA-AATGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAA-GCTCGTAAGCTTATTT
550678 GTATGCTTAC
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
43 2 0.02
44 17 0.16
45 14 0.13
46 14 0.13
47 46 0.42
48 16 0.15
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAAAATAC
Found at i:556861 original size:59 final size:59
Alignment explanation
Indices: 556762--556890 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
556752 CAGTAAGCTG
** * *
556762 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
* * * *
556821 CATATTCGGGACTATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
*
556880 CATACTCGGGA
1 CATATTCGGGA
556891 TTGCATTACG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:574016 original size:141 final size:144
Alignment explanation
Indices: 573463--574041 Score: 610
Period size: 143 Copynumber: 4.1 Consensus size: 144
573453 TCCATTTTAT
* * * * * * *
573463 TGACATAAAATTTTCAGTGCCCAATAACTTTACTTAAGAAACTTTTTAGTAATATATTAATTCAT
1 TGACAGAAACTTTTCAGTGCCCAATAACTTCACTTTAGAAAATTTTTAGTGATATATTAACTCAT
* * * * *
573528 TTC-AGAAACTTTTCAATAGTTATATATCA-TATCATTTTAGAAAAA-TGTCCATTTCTCATAGG
66 TTCAAGAAACTTTTCAGTAGTGATATATCACT-TCATTTCATAAAAACTGTCCATTTCTCATAGA
*
573590 CTATTTAATGCACAA
130 CCATTTAATGCACAA
* * * * * * *
573605 TGACA-AGAACTTTTTAGTTCCCAATAATTTCACTTCAG-AAACTTTGAGTTATATATTAACTCA
1 TGACAGA-AACTTTTCAGTGCCCAATAACTTCACTTTAGAAAATTTTTAGTGATATATTAACTCA
* * *
573668 TTTCAGAAAAATTTTTCAGTAGTGATATATCACTTCATTTCATAAAAAC-ATCCATTTCTCATAG
65 TTTCA-AGAAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAAACTGTCCATTTCTCATAG
*
573732 -CACATTTAATGCACAC
129 AC-CATTTAATGCACAA
* * * * **
573748 TGATAGAAACTTTTCAGTGCCCAATAA-TATTACTTTAGAAAGTTTTTAGTGGTATAGCAACTCA
1 TGACAGAAACTTTTCAGTGCCCAATAACT-TCACTTTAGAAAATTTTTAGTGATATATTAACTCA
* * *
573812 TTTCAAGAAAATTTTCAGTAGTGATATATCATTTCATTTCATAAAAA-TGTCAATTTCTCATAGA
65 TTTCAAGAAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAAACTGTCCATTTCTCATAGA
*
573876 CCATTTAATGCACGA
130 CCATTTAATGCACAA
* * * *
573891 TGACA-AAAGTTTTCAGTGCCCAATAACTTCACTTTAGAAAAATTTTAGTGATATATAAATTCAT
1 TGACAGAAACTTTTCAGTGCCCAATAACTTCACTTTAGAAAATTTTTAGTGATATATTAACTCAT
* *
573955 TT-AAGAAACTCTTCAGTAGTGTTATATCACTTCA-TT-ATAGAAAAGCT-TCCATTTCTCATAG
66 TTCAAGAAACTTTTCAGTAGTGATATATCACTTCATTTCATA-AAAA-CTGTCCATTTCTCATAG
* *
574016 ACAATTTAATGCTCAA
129 ACCATTTAATGCACAA
*
574032 TGACATAAAC
1 TGACAGAAAC
574042 CTTTATGTGA
Statistics
Matches: 364, Mismatches: 57, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
139 3 0.01
140 6 0.02
141 84 0.23
142 87 0.24
143 158 0.43
144 26 0.07
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (144 bp):
TGACAGAAACTTTTCAGTGCCCAATAACTTCACTTTAGAAAATTTTTAGTGATATATTAACTCAT
TTCAAGAAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAAACTGTCCATTTCTCATAGAC
CATTTAATGCACAA
Found at i:576660 original size:21 final size:21
Alignment explanation
Indices: 576634--576673 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
576624 AAACAATTGG
576634 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
576655 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
576674 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:583908 original size:21 final size:23
Alignment explanation
Indices: 583885--583927 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
583875 GACATAACTC
*
583885 AAAATCCAAAAG-AAATTTCTCA
1 AAAATCAAAAAGAAAATTTCTCA
*
583907 AAAATTAAAAAGAAAATTTCT
1 AAAATCAAAAAGAAAATTTCT
583928 ATTACCTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.26
Consensus pattern (23 bp):
AAAATCAAAAAGAAAATTTCTCA
Found at i:587890 original size:80 final size:81
Alignment explanation
Indices: 587535--588065 Score: 619
Period size: 81 Copynumber: 6.6 Consensus size: 81
587525 AACTTGCAAG
* * * * * * * *
587535 ATTGACACCTTTCTATCC-AATACACTGTTAGACCATTAATATTTTACTTAAAGTTATTTAACCT
1 ATTGACACCTTTCTA-CCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATATTTAACCT
* * *
587599 TTCATCTAATTGGAATA
65 TTCATCTAACTAGCATA
* * * *
587616 ATTGACACCTTTC-AGCCAAATACACATCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCT
1 ATTGACACCTTTCTA-CCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATATTTAACCT
*
587680 TTCATCTAA-TTGACATA
65 TTCATCTAACTAG-CATA
* * * * *
587697 ATTGACACTTTTCTGCCAAATGCACAACTAGGC-ATTAATCTTTTACTAAAAAAGTATTTAACCT
1 ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGA-TATTTAACCT
*
587761 TTCATCTAACTGGCATA
65 TTCATCTAACTAGCATA
* * * **
587778 ATTAACAACTTTCTCCCAAATGCACAAATAGGCTATTAATCTTTTACTCAAAGATATTTAACCTT
1 ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATATTTAACCTT
**
587843 TCATCT-ACTAGTGTA
66 TCATCTAACTAGCATA
* *
587858 ATTGACACCTTTCTACCAAATGCATAGCTAGGCTATTAATCTTTTACTCAAATG-TATTAAACCT
1 ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAA-GATATTTAACCT
587922 TTCATCTAACTAGCATA
65 TTCATCTAACTAGCATA
* * * *
587939 ATTGACA-CTTTCTACCAAATACAAAG-TAGGCTATTAATCTATTACTCAAAGGTATTTAACCTT
1 ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATATTTAACCTT
*
588002 TCATCTAACTAACATA
66 TCATCTAACTAGCATA
* *
588018 ATTGACACCTTTCTGCCAAATGCACATCTAGGCTATTAATCTTTTACT
1 ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACT
588066 TTGGATTAGT
Statistics
Matches: 392, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
78 1 0.00
79 55 0.14
80 122 0.31
81 194 0.49
82 20 0.05
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (81 bp):
ATTGACACCTTTCTACCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATATTTAACCTT
TCATCTAACTAGCATA
Found at i:588793 original size:21 final size:21
Alignment explanation
Indices: 588768--588843 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
588758 CCTATCTTGG
*
588768 TATCGATACTACTTGCATAAG
1 TATCGATACTACTTGCATAAC
588789 TATCGATACTACTTGCATAAC
1 TATCGATACTACTTGCATAAC
588810 TATCGATACTACTTGCATAAC
1 TATCGATACTACTTGCATAAC
588831 TATCGATACTACT
1 TATCGATACTACT
588844 CAACTAATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (21 bp):
TATCGATACTACTTGCATAAC
Found at i:590452 original size:19 final size:20
Alignment explanation
Indices: 590409--590459 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
590399 GAAACCCCTT
* **
590409 TGAAAATACATGATTTTTGA
1 TGAAAATACATGAATTTAAA
590429 TGAAAATACAT-AATTTAAA
1 TGAAAATACATGAATTTAAA
590448 TGAAAATACATG
1 TGAAAATACATG
590460 TTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGAATTTAAA
Found at i:593400 original size:4 final size:4
Alignment explanation
Indices: 593391--593430 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
593381 AGTGCTTTAA
*
593391 CTTT CTTT CTTT CTTT CTTT CTTT TTTCT CTTT C-TT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTTT CTTT CTTT
593431 TGGAGTGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:607749 original size:56 final size:56
Alignment explanation
Indices: 607679--607789 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
607669 GGATAACTTA
*
607679 GCATGTACACATCTTTATAATTGATGCACATTGTTATTTAAATATGTTAAGCATGT
1 GCATGTACACATCTTTATAATTGATGCACATTGGTATTTAAATATGTTAAGCATGT
* *
607735 GCATGTACATATCTTTATAATTGATGCACATTGGTATTTAAGTATGTTAAGCATG
1 GCATGTACACATCTTTATAATTGATGCACATTGGTATTTAAATATGTTAAGCATG
607790 CTATAATAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (56 bp):
GCATGTACACATCTTTATAATTGATGCACATTGGTATTTAAATATGTTAAGCATGT
Found at i:619758 original size:16 final size:16
Alignment explanation
Indices: 619737--619767 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
619727 TTGATAACAA
*
619737 TTGTTGTAGGAAAATT
1 TTGTTGAAGGAAAATT
619753 TTGTTGAAGGAAAAT
1 TTGTTGAAGGAAAAT
619768 ATTTCTCCCA
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:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (16 bp):
TTGTTGAAGGAAAATT
Found at i:627948 original size:5 final size:5
Alignment explanation
Indices: 627940--627972 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
627930 AAAAAAAATA
627940 AATTT AATTT AATTT AATTT AATTT AACTTT AA
1 AATTT AATTT AATTT AATTT AATTT AA-TTT AA
627973 GGAAATGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:631162 original size:18 final size:19
Alignment explanation
Indices: 631120--631162 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
631110 CCTACTGGAA
631120 TATCGATACTCTACCGTTGG
1 TATCGATACTC-ACCGTTGG
631140 TATCGATACTC-CC-TTGAG
1 TATCGATACTCACCGTTG-G
631158 TATCG
1 TATCG
631163 TTACCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
20 11 0.50
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (19 bp):
TATCGATACTCACCGTTGG
Found at i:638849 original size:17 final size:16
Alignment explanation
Indices: 638822--638863 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
638812 GTAGCTTGAT
638822 TAGGTAG-TTAGCTAGG
1 TAGGTAGTTTAGCTA-G
638838 TAGGTAGTTTAGCTAG
1 TAGGTAGTTTAGCTAG
638854 TGAGGTAGTT
1 T-AGGTAGTT
638864 GAGGTAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.24, C:0.05, G:0.36, T:0.36
Consensus pattern (16 bp):
TAGGTAGTTTAGCTAG
Found at i:640608 original size:41 final size:39
Alignment explanation
Indices: 640548--640654 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 39
640538 CAGCATGTAC
*
640548 TAATTCACAATTTGATTCAAGTCAATAA-AGAAAACATGAAA
1 TAATTCACAA-TTGATTCAATTCAATAATAGAAAA-A-GAAA
* * *
640589 TAGTTCACAATTCGATTCAATTCAATAATGGAAAAAGCAA
1 TAATTCACAATT-GATTCAATTCAATAATAGAAAAAGAAA
640629 TAATTCACAATATGATTCAATTCAAT
1 TAATTCACAAT-TGATTCAATTCAAT
640655 CATGTCATCA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 28 0.48
41 25 0.43
42 5 0.09
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (39 bp):
TAATTCACAATTGATTCAATTCAATAATAGAAAAAGAAA
Found at i:640679 original size:41 final size:41
Alignment explanation
Indices: 640625--640714 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
640615 AATGGAAAAA
*
640625 GCAATAATTCACAATATGATTCAATTCAATCA-TGTCATCAT
1 GCAATAATACACAATATGATTCAATTCAATCATTGTCAT-AT
* * *
640666 GCAATAATACACAATTTGATTCAATTTAATCATTGTCGTAT
1 GCAATAATACACAATATGATTCAATTCAATCATTGTCATAT
640707 GCAATAAT
1 GCAATAAT
640715 TCACCATTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 39 0.89
42 5 0.11
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (41 bp):
GCAATAATACACAATATGATTCAATTCAATCATTGTCATAT
Found at i:654798 original size:15 final size:15
Alignment explanation
Indices: 654778--654815 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
654768 CTGCCATAAC
*
654778 ACTCACCATATTG-CA
1 ACTCACC-TATGGCCA
654793 ACTCACCTATGGCCA
1 ACTCACCTATGGCCA
654808 ACTCACCT
1 ACTCACCT
654816 CCAGCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.29, C:0.39, G:0.08, T:0.24
Consensus pattern (15 bp):
ACTCACCTATGGCCA
Found at i:657266 original size:23 final size:24
Alignment explanation
Indices: 657239--657297 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
657229 AATCCAGCAC
657239 AGAAAATCAAAGCACTC-AAAAGA
1 AGAAAATCAAAGCACTCAAAAAGA
*
657262 AGAAAATTC-CAGCACTCAAAAAGA
1 AGAAAA-TCAAAGCACTCAAAAAGA
657286 AGAAAATCAAAG
1 AGAAAATCAAAG
657298 AAAAGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.10
Consensus pattern (24 bp):
AGAAAATCAAAGCACTCAAAAAGA
Found at i:661670 original size:25 final size:25
Alignment explanation
Indices: 661636--661689 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
661626 AGCATGATGG
661636 ACGCAAGGTAACCTTGATGCCATTA
1 ACGCAAGGTAACCTTGATGCCATTA
*
661661 ACGCAAGGTAACCTTGATGCCATTG
1 ACGCAAGGTAACCTTGATGCCATTA
661686 ACGC
1 ACGC
661690 CAAAAGAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (25 bp):
ACGCAAGGTAACCTTGATGCCATTA
Found at i:663854 original size:20 final size:20
Alignment explanation
Indices: 663829--663883 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 20
663819 GAAACCCCTT
663829 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
663849 TGAAAATACATGA--TTTAA
1 TGAAAATACATGATTTTTAA
*
663867 TGAAAGTACAT-ATTTTT
1 TGAAAATACATGATTTTT
663884 GTGATATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.03
18 15 0.47
19 3 0.09
20 13 0.41
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:664624 original size:30 final size:30
Alignment explanation
Indices: 664583--664658 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
664573 AAGGAGCTTC
*
664583 AACTTAACTGGAGGAGCTAGCATGTTGCTA
1 AACTTAGCTGGAGGAGCTAGCATGTTGCTA
*
664613 AACTTAGCTGGATGAGCTAGCATGTTGCTA
1 AACTTAGCTGGAGGAGCTAGCATGTTGCTA
664643 AACTTAGCTGGAGGAG
1 AACTTAGCTGGAGGAG
664659 AGCTTTGGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (30 bp):
AACTTAGCTGGAGGAGCTAGCATGTTGCTA
Found at i:664788 original size:16 final size:16
Alignment explanation
Indices: 664767--664799 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
664757 TTTAAATTGA
664767 TTGTGGTGATAGAAGG
1 TTGTGGTGATAGAAGG
664783 TTGTGGTGATAGAAGG
1 TTGTGGTGATAGAAGG
664799 T
1 T
664800 CCTAAACACA
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:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (16 bp):
TTGTGGTGATAGAAGG
Found at i:665460 original size:17 final size:16
Alignment explanation
Indices: 665434--665469 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
665424 AATAAGGGTG
665434 AAGAACATGTTACTTC
1 AAGAACATGTTACTTC
665450 AAGAGACATGTTACTTC
1 AAGA-ACATGTTACTTC
665467 AAG
1 AAG
665470 TTGAAGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (16 bp):
AAGAACATGTTACTTC
Found at i:667474 original size:20 final size:19
Alignment explanation
Indices: 667427--667477 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
667417 CGGCCAAGAG
*
667427 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
**
667446 CGGGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
667466 CATGTATTTTCA
1 CATGTATTTTCA
667478 ATGGGATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:668815 original size:27 final size:27
Alignment explanation
Indices: 668777--668829 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
668767 CACCACAAGG
*
668777 GACCAAGAATCATTTCCTCTCCCATTA
1 GACCAAGAATCATTTCCTCTACCATTA
*
668804 GACCAAGCATCATTTCCTCTACCATT
1 GACCAAGAATCATTTCCTCTACCATT
668830 TGGCGCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (27 bp):
GACCAAGAATCATTTCCTCTACCATTA
Found at i:669569 original size:27 final size:25
Alignment explanation
Indices: 669539--669595 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
669529 AATCAGCAAA
669539 AAAATTGAAGCACTCCAAAAGAAGAAG
1 AAAATTGAAGCACT-CAAAA-AAGAAG
*
669566 AAAAATGAAGCACTCAAAAAAGAAG
1 AAAATTGAAGCACTCAAAAAAGAAG
669591 AAAAT
1 AAAAT
669596 AAAAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.36
26 5 0.18
27 13 0.46
ACGTcount: A:0.61, C:0.12, G:0.16, T:0.11
Consensus pattern (25 bp):
AAAATTGAAGCACTCAAAAAAGAAG
Found at i:669594 original size:25 final size:28
Alignment explanation
Indices: 669538--669594 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 28
669528 AAATCAGCAA
669538 AAAAATTGAAGCACTCCAAAAGAAGAAG
1 AAAAATTGAAGCACTCCAAAAGAAGAAG
669566 AAAAA-TGAAGCACT-CAAAA-AAGAAG
1 AAAAATTGAAGCACTCCAAAAGAAGAAG
669591 AAAA
1 AAAA
669595 TAAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 10 0.34
26 5 0.17
27 9 0.31
28 5 0.17
ACGTcount: A:0.63, C:0.12, G:0.16, T:0.09
Consensus pattern (28 bp):
AAAAATTGAAGCACTCCAAAAGAAGAAG
Found at i:671973 original size:21 final size:21
Alignment explanation
Indices: 671947--671995 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
671937 AAGTACATGG
671947 AAGCTCATGAAACACTAAGGA
1 AAGCTCATGAAACACTAAGGA
*
671968 AAGCTCATGGAACACTAAGGA
1 AAGCTCATGAAACACTAAGGA
671989 AAGCTCA
1 AAGCTCA
671996 ACTCAGCTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (21 bp):
AAGCTCATGAAACACTAAGGA
Found at i:690576 original size:9 final size:9
Alignment explanation
Indices: 690564--690593 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
690554 GTTCTTCAAC
690564 TTCTTTTCT
1 TTCTTTTCT
690573 TTCTTTTCTT
1 TTCTTTTC-T
690583 TTCTTTTCT
1 TTCTTTTCT
690592 TT
1 TT
690594 TTCTTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:690577 original size:4 final size:5
Alignment explanation
Indices: 690564--690599 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
690554 GTTCTTCAAC
690564 TTCTT TTC-T TTCTT TTCTT TTCTT TTCTTT TTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TTCTT T
690600 GAGTGCCGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:693742 original size:25 final size:26
Alignment explanation
Indices: 693713--693761 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
693703 TGGCGCCTAA
* *
693713 ATGATC-CATGCAAGGCGCATGGGGG
1 ATGATCACATGCAAAGCACATGGGGG
*
693738 ATGATCATATGCAAAGCACATGGG
1 ATGATCACATGCAAAGCACATGGG
693762 TGTTCTAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.31, C:0.18, G:0.33, T:0.18
Consensus pattern (26 bp):
ATGATCACATGCAAAGCACATGGGGG
Found at i:704881 original size:19 final size:20
Alignment explanation
Indices: 704842--704892 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
704832 GAAATCCCTT
*
704842 TGAAAATACATGAGTTTTAA
1 TGAAAATACATGAGCTTTAA
*
704862 TGAAAATATATGA-CTTTAA
1 TGAAAATACATGAGCTTTAA
704881 TGAAAATACATG
1 TGAAAATACATG
704893 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGAGCTTTAA
Found at i:725326 original size:44 final size:45
Alignment explanation
Indices: 725207--725331 Score: 173
Period size: 44 Copynumber: 2.8 Consensus size: 45
725197 TATAAAATCC
725207 CTTACCATTTATTCCATAAGCTCGTAAG-TTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
725251 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
725298 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
725332 ATATGCTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
44 34 0.47
46 20 0.27
47 19 0.26
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:730831 original size:6 final size:6
Alignment explanation
Indices: 730820--730844 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
730810 ACACTTATAT
730820 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
730845 TATGGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:732667 original size:44 final size:45
Alignment explanation
Indices: 732548--732673 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
732538 TATAAAATCC
* *
732548 CTTACCATTTATTCCATAAGCTCGCAAGCTTAATTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
732593 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
732640 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
732674 ATATGCTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 36 0.50
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Done.