Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000910.1 Hibiscus syriacus cultivar Beakdansim tig00001809_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: 95025
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2859 original size:30 final size:30
Alignment explanation
Indices: 2823--2897 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2813 TTAATTAATT
* *
2823 AATTAAAGGAGTAAAATA-ACAAAAACATAA
1 AATTAAAGGACTAAAATAGA-AAAAACAGAA
* *
2853 AATTAAATGACTAAAATAGAAATAACAGAA
1 AATTAAAGGACTAAAATAGAAAAAACAGAA
*
2883 AATTAAAGGGCTAAA
1 AATTAAAGGACTAAA
2898 CCACAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.19
Consensus pattern (30 bp):
AATTAAAGGACTAAAATAGAAAAAACAGAA
Found at i:2906 original size:30 final size:30
Alignment explanation
Indices: 2823--2906 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
2813 TTAATTAATT
* * *
2823 AATTAAAGGAGTAAAATAACAAA-AACATAA
1 AATTAAAGGACTAAAA-CACAAATAACAGAA
* * *
2853 AATTAAATGACTAAAATAGAAATAACAGAA
1 AATTAAAGGACTAAAACACAAATAACAGAA
* *
2883 AATTAAAGGGCTAAACCACAAATA
1 AATTAAAGGACTAAAACACAAATA
2907 TAAAAAACAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 4 0.09
30 39 0.91
ACGTcount: A:0.62, C:0.10, G:0.11, T:0.18
Consensus pattern (30 bp):
AATTAAAGGACTAAAACACAAATAACAGAA
Found at i:3485 original size:3 final size:3
Alignment explanation
Indices: 3477--3508 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3467 TACAAAAATG
*
3477 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3509 TTATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6079 original size:23 final size:23
Alignment explanation
Indices: 6053--6097 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6043 AAGTACTCAA
6053 ATTTAAAGCTAAATTAGTTAAAC
1 ATTTAAAGCTAAATTAGTTAAAC
*
6076 ATTTAAAGGTAAATTAGTTAAA
1 ATTTAAAGCTAAATTAGTTAAA
6098 ATAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (23 bp):
ATTTAAAGCTAAATTAGTTAAAC
Found at i:12694 original size:20 final size:20
Alignment explanation
Indices: 12665--12711 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
12655 TTTGCCTTAG
*
12665 CACTGCCCCTACTGCGTAGT
1 CACTGGCCCTACTGCGTAGT
*
12685 CACTGGCCCTACTGTGTAGT
1 CACTGGCCCTACTGCGTAGT
12705 CACTGGC
1 CACTGGC
12712 ATCACACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (20 bp):
CACTGGCCCTACTGCGTAGT
Found at i:19982 original size:16 final size:16
Alignment explanation
Indices: 19934--19972 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19924 GTATTATGCC
* *
19934 TATTTAATTTAATAATT
1 TATTTAA-TTAGTTATT
19951 TATTTAATTAGTTATT
1 TATTTAATTAGTTATT
19967 TATTTA
1 TATTTA
19973 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTAATTAGTTATT
Found at i:28333 original size:102 final size:102
Alignment explanation
Indices: 28172--28362 Score: 242
Period size: 102 Copynumber: 1.9 Consensus size: 102
28162 TTTTGGAAGG
* * * * *
28172 TTTATCCTCAAAGAAGCGCTTTAGTCTGGTTGATAGGTCTAAGATGTTGTCATGTAGACAAACCT
1 TTTATCCTCAAAGAAGCGCTTTAGTCTGGTTGATAGGTCTAAAATATTATCACGAAGACAAA-CT
* *
28237 TT-ATCCTATGTGATAGAAATAGATGTCCTTTAAAAGA
65 TTCATACTATGTGACAGAAATAGATGTCCTTTAAAAGA
* * * *
28274 TTTATCCTCAAAGAAGCGCCTTTATTTTGG-TGATGGGTCTAAAATATTATCACGAAGACATACT
1 TTTATCCTCAAAGAAGCG-CTTTAGTCTGGTTGATAGGTCTAAAATATTATCACGAAGACAAACT
*
28338 TTCATATTATGTGACAGAAATAGAT
65 TTCATACTATGTGACAGAAATAGAT
28363 ATTATTATAA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
101 4 0.05
102 62 0.83
103 9 0.12
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (102 bp):
TTTATCCTCAAAGAAGCGCTTTAGTCTGGTTGATAGGTCTAAAATATTATCACGAAGACAAACTT
TCATACTATGTGACAGAAATAGATGTCCTTTAAAAGA
Found at i:32036 original size:21 final size:21
Alignment explanation
Indices: 32010--32053 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32000 AGTTGAAGTT
*
32010 ACTGTAGCAATGCATCGGTAC
1 ACTGTAGCAATGCATCGATAC
* *
32031 ACTGTAGTAGTGCATCGATAC
1 ACTGTAGCAATGCATCGATAC
32052 AC
1 AC
32054 ACTTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATAC
Found at i:33024 original size:24 final size:25
Alignment explanation
Indices: 32971--33043 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 25
32961 ACAATCTTAT
*
32971 ATGGCACTACGGTGC-ATTTCTACG
1 ATGGCACTTCGGTGCAATTTCTACG
32995 AT-GCACTTCGGTGCAATTTCTAC-
1 ATGGCACTTCGGTGCAATTTCTACG
* *
33018 ATGGCACTTCGGTGAAATTTATACG
1 ATGGCACTTCGGTGCAATTTCTACG
33043 A
1 A
33044 GTTGTGGTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 13 0.30
24 29 0.67
25 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (25 bp):
ATGGCACTTCGGTGCAATTTCTACG
Found at i:37381 original size:18 final size:16
Alignment explanation
Indices: 37339--37381 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
37329 GTCAAACTTT
37339 AAAAGAAGAAGGAAGA
1 AAAAGAAGAAGGAAGA
37355 AGAATAGAAGAAGGTGAAGA
1 A-AA-AGAAGAA-G-GAAGA
37375 AAAAGAA
1 AAAAGAA
37382 AGTTGGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 2 0.09
18 11 0.48
19 3 0.13
20 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (16 bp):
AAAAGAAGAAGGAAGA
Found at i:38992 original size:44 final size:43
Alignment explanation
Indices: 38887--38992 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 43
38877 AATAAGGTAT
38887 CGATATTGGTACCGATACTAATATGTAAAAAACACTACAATAC
1 CGATATTGGTACCGATACTAATATGTAAAAAACACTACAATAC
* * * * * *
38930 TGATACTAGTATCGATACTAATGTGTAAAAATACACTGA-AGTAC
1 CGATATTGGTACCGATACTAATATGTAAAAA-ACACT-ACAATAC
38974 CGATATTGGTACCGATACT
1 CGATATTGGTACCGATACT
38993 TCCTTTAAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
43 26 0.51
44 24 0.47
45 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (43 bp):
CGATATTGGTACCGATACTAATATGTAAAAAACACTACAATAC
Found at i:40334 original size:18 final size:16
Alignment explanation
Indices: 40292--40334 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
40282 GTCAAACTTT
40292 AAAAGAAGAAGGAAGA
1 AAAAGAAGAAGGAAGA
40308 AGAACAGAAGAAGGTGAAGA
1 A-AA-AGAAGAA-G-GAAGA
40328 AAAAGAA
1 AAAAGAA
40335 AGTGGGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 2 0.09
18 11 0.48
19 3 0.13
20 6 0.26
ACGTcount: A:0.65, C:0.02, G:0.30, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAGGAAGA
Found at i:43050 original size:242 final size:241
Alignment explanation
Indices: 42625--43087 Score: 716
Period size: 242 Copynumber: 1.9 Consensus size: 241
42615 ATCTAGAGAG
* *
42625 GATATGCAAGAACAAACACAAGAATATCTTGAGAAGCATATTCAAGAGGAATGAGAAGTATCATG
1 GATATGCAAGAACAAACACAAGAACATCTTGAGAAGCATATTCAAGAGGAAAGAGAAGTATCATG
* * *
42690 CCCAAGGGAGTACAACAATGTCAAGGATGGTGAGAATTTAAGTGATTCATCCAAAGGGGTAACTA
66 CCCAAAGGAGTACAACAATGTCAAGGATGGTGAGAATTTAAGCGATCCATCCAAAGGGGTAACTA
* *
42755 CTAGATCTTCTCTTAGAAATATTTATATTTTTTTGCATATATCTCATGCATAGATATTAAGAATA
131 CTAGATCATCTCTTAGAAATATTTATATTTTTTT-CATATATCTCATGCATAGAGATTAAGAATA
42820 TCAAAGAAACATTAAAAGATAAATTTGGTAAACCAACATCTAAATAA
195 TCAAAGAAACATTAAAAGATAAATTTGGTAAACCAACATCTAAATAA
* * *
42867 GATATGCAAGAACAAACACAAGAAGCA-CTTGAGGAGCTTATTCAAGAGGAAAGTGAAGTATCAT
1 GATATGCAAGAACAAACACAAGAA-CATCTTGAGAAGCATATTCAAGAGGAAAGAGAAGTATCAT
* * * *
42931 GCCCAAAGGAGTACAACTATGTCAAGGATGGTGAGATTTTAGGCGATCCATCTAAAGGGGTAACT
65 GCCCAAAGGAGTACAACAATGTCAAGGATGGTGAGAATTTAAGCGATCCATCCAAAGGGGTAACT
*
42996 ACTAGATCATCTCTTAGAAATACTTGTA-ATTTGTTTT-ATATATCTCATGCATAGAGCTTAAGA
130 ACTAGATCATCTCTTAGAAATA-TT-TATATTT-TTTTCATATATCTCATGCATAGAGATTAAGA
*
43059 ATATCAAAGAAACATTAAAAGATGAATTT
192 ATATCAAAGAAACATTAAAAGATAAATTT
43088 TGGATATTGG
Statistics
Matches: 201, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
242 188 0.94
243 7 0.03
244 6 0.03
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (241 bp):
GATATGCAAGAACAAACACAAGAACATCTTGAGAAGCATATTCAAGAGGAAAGAGAAGTATCATG
CCCAAAGGAGTACAACAATGTCAAGGATGGTGAGAATTTAAGCGATCCATCCAAAGGGGTAACTA
CTAGATCATCTCTTAGAAATATTTATATTTTTTTCATATATCTCATGCATAGAGATTAAGAATAT
CAAAGAAACATTAAAAGATAAATTTGGTAAACCAACATCTAAATAA
Found at i:43107 original size:27 final size:27
Alignment explanation
Indices: 43077--43137 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
43067 GAAACATTAA
43077 AAGATGAATTTTGGATATTGGCTATGC
1 AAGATGAATTTTGGATATTGGCTATGC
43104 AAGATGAATTTTGGATATTGGCTATGC
1 AAGATGAATTTTGGATATTGGCTATGC
43131 AAGATGA
1 AAGATGA
43138 GTTAAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (27 bp):
AAGATGAATTTTGGATATTGGCTATGC
Found at i:45605 original size:45 final size:45
Alignment explanation
Indices: 45556--45802 Score: 269
Period size: 45 Copynumber: 5.6 Consensus size: 45
45546 TATTTTTCTT
*
45556 TTGATAATGCACCCATATGCATTTCAATTATAGTATACTTTTCAG
1 TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAG
** *
45601 TTGAT-ATG----GGT-T-CATTTCAACTATAATATACTTTTCAG
1 TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAG
* * * ** *
45639 TTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTCTG
1 TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAG
* *
45684 TTGACAATGCACCCATATGCATTTCAACTATTGTATACTTTT-ATG
1 TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCA-G
* * * *
45729 TTGATAATGTACCCATATACATTTCAACTATCGTATA-TTTCTCTG
1 TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTT-TCAG
45774 TTGATAATGCACCCATATGCATTTCAACT
1 TTGATAATGCACCCATATGCATTTCAACT
45803 CTGGCATCCT
Statistics
Matches: 168, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
38 29 0.17
39 4 0.02
40 1 0.01
43 1 0.01
44 7 0.04
45 126 0.75
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (45 bp):
TTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAG
Found at i:45826 original size:90 final size:90
Alignment explanation
Indices: 45642--45841 Score: 249
Period size: 90 Copynumber: 2.2 Consensus size: 90
45632 TTTTCAGTTG
*
45642 ATAATGTACCCATATACATTTCAACTCTAACATACTTTTCTGTTGACAATGCACCCATATGCATT
1 ATAATGTACCCATATACATTTCAACTATAACATACTTTTCTGTTGACAATGCACCCATATGCATT
* * * ***
45707 TCAACTATTGTATACTTTTATGTTG
66 TCAACTATGGCATACTTTCATGCCA
*** *
45732 ATAATGTACCCATATACATTTCAACTATCGTATA-TTTCTCTGTTGATAATGCACCCATATGCAT
1 ATAATGTACCCATATACATTTCAACTATAACATACTTT-TCTGTTGACAATGCACCCATATGCAT
* *
45796 TTCAACTCTGGCATCCTTTCATGCCA
65 TTCAACTATGGCATACTTTCATGCCA
* *
45822 ATAATGCACCCATATGCATT
1 ATAATGTACCCATATACATT
45842 ATTGTTTTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
89 3 0.03
90 91 0.97
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (90 bp):
ATAATGTACCCATATACATTTCAACTATAACATACTTTTCTGTTGACAATGCACCCATATGCATT
TCAACTATGGCATACTTTCATGCCA
Found at i:45828 original size:135 final size:128
Alignment explanation
Indices: 45559--45841 Score: 311
Period size: 135 Copynumber: 2.2 Consensus size: 128
45549 TTTTCTTTTG
* **
45559 ATAATGCACCCATATGCATTTCAATTATAGTATACTTTTCAGTTGATATGGGTTCATTTCAACTA
1 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAGTTGATATGCATTCATTTCAACTA
* * ***
45624 TAATATACTTTTCAGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTCTGTTG
66 TAATATACTTTTCAGTTGATAATGCACCCATATACATTTCAACTCTAACATACCTTTCTGCCA
* *
45687 ACAATGCACCCATATGCATTTCAACTATTGTATACTTTT-ATGTTGATAATGTACCCATATACAT
1 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCA-GTTGAT-ATG----CAT-T-CAT
** * * **
45751 TTCAACTATCGTATA-TTTCTCTGTTGATAATGCACCCATATGCATTTCAACTCTGGCAT-CCTT
58 TTCAACTATAATATACTTT-TCAGTTGATAATGCACCCATATACATTTCAACTCTAACATACCTT
45814 TCATGCCA
122 TC-TGCCA
45822 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
45842 ATTGTTTTAT
Statistics
Matches: 128, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
127 1 0.01
128 42 0.33
129 3 0.02
133 1 0.01
134 9 0.07
135 72 0.56
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (128 bp):
ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCAGTTGATATGCATTCATTTCAACTA
TAATATACTTTTCAGTTGATAATGCACCCATATACATTTCAACTCTAACATACCTTTCTGCCA
Found at i:46299 original size:20 final size:20
Alignment explanation
Indices: 46271--46325 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
46261 TGGCCCTTCA
46271 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
* *
46291 GTATTGATACTACTCTACTATG
1 GTATCGATAC--CCCTACTATG
46313 GTATCGATACCCC
1 GTATCGATACCCC
46326 CTACCAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.38
22 18 0.62
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:48107 original size:20 final size:20
Alignment explanation
Indices: 48082--48120 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48072 TTATCATCCT
48082 TACAATACAAATATTATTCA
1 TACAATACAAATATTATTCA
**
48102 TACAATACTGATATTATTC
1 TACAATACAAATATTATTC
48121 TTTTAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (20 bp):
TACAATACAAATATTATTCA
Found at i:48736 original size:2 final size:2
Alignment explanation
Indices: 48729--48764 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48719 TTTTTGTACA
48729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48765 TTCTACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51008 original size:32 final size:31
Alignment explanation
Indices: 50941--51010 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
50931 CATATGATAT
** *
50941 CGATACTAATATGTAAAAAACACTGTAGTAC
1 CGATACTAATATGTAAAAAACACTAAAGTAA
* *
50972 CGATATTAATGTGTAAAAATACACTAAAGTAA
1 CGATACTAATATGTAAAAA-ACACTAAAGTAA
51004 CGATACT
1 CGATACT
51011 GGTACCGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (31 bp):
CGATACTAATATGTAAAAAACACTAAAGTAA
Found at i:51143 original size:31 final size:32
Alignment explanation
Indices: 51080--51147 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
51070 TGATACTCTC
* *
51080 GGAGTATCAATACTGGTATCTATAATCTAAGT
1 GGAGTACCAATAATGGTATCTATAATCTAAGT
*
51112 GGAGTACCAATAATGGTATC-ATACTCTAAGT
1 GGAGTACCAATAATGGTATCTATAATCTAAGT
51143 GGAGT
1 GGAGT
51148 GTCGATACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (32 bp):
GGAGTACCAATAATGGTATCTATAATCTAAGT
Found at i:64972 original size:39 final size:39
Alignment explanation
Indices: 64918--64997 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
64908 AATAAAAAGA
64918 GGTAATGAAGAACCAAAAACAGCATCTAGAGACGACCTT
1 GGTAATGAAGAACCAAAAACAGCATCTAGAGACGACCTT
** *
64957 GGTAATGAAGAACCAAAGGCAGCATCTGGAGACGACCTT
1 GGTAATGAAGAACCAAAAACAGCATCTAGAGACGACCTT
64996 GG
1 GG
64998 AACGGAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (39 bp):
GGTAATGAAGAACCAAAAACAGCATCTAGAGACGACCTT
Found at i:67581 original size:110 final size:111
Alignment explanation
Indices: 67387--67607 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 111
67377 ATTACAAAAA
* *
67387 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
67452 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
67498 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
67562 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
67608 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 71 0.67
111 35 0.33
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:73352 original size:3 final size:3
Alignment explanation
Indices: 73336--73412 Score: 79
Period size: 3 Copynumber: 25.7 Consensus size: 3
73326 TTTGGGCTTG
* *
73336 TAA TAA TATT TAA TAA TAA T-A TAAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
73382 TAA TTA T-A TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
73413 TTTAAATGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:73770 original size:124 final size:121
Alignment explanation
Indices: 73546--73830 Score: 366
Period size: 124 Copynumber: 2.4 Consensus size: 121
73536 ATGTTGAATA
* * *
73546 AATTCTTCTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGAC
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
* * * *
73610 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTT-ATTATG
66 CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTT-TTCATTATG
* *
73666 AACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGC
1 AA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGC
* * * *
73730 TAATCTATCTGCTTCTGTGATAGAATTATACAAAAGGTTGAACAAGCTCTTTTCATTGTG
62 TAACCTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
73790 AA--CTTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
73831 CTTCTTCTTC
Statistics
Matches: 146, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
120 37 0.25
121 17 0.12
122 33 0.23
123 2 0.01
124 57 0.39
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.42
Consensus pattern (121 bp):
AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
Found at i:73829 original size:36 final size:36
Alignment explanation
Indices: 73777--73866 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
73767 TTGAACAAGC
* *
73777 TCTTTTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
73813 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
73849 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
73867 TCTCTGGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:73862 original size:16 final size:16
Alignment explanation
Indices: 73807--73862 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
73797 TCTTCTTCAG
73807 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
*
73823 ATGAACTTCTTCTTC-TT
1 ATG-AGTTCTTC-TCATT
73840 CAGATGAGTTCTTCTCATT
1 ---ATGAGTTCTTCTCATT
73859 ATGA
1 ATGA
73863 ACTTTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:73943 original size:17 final size:17
Alignment explanation
Indices: 73921--74009 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
73911 GTTGAACAAA
*
73921 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
* *
73938 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAC
73955 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
73972 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
73991 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
74008 TT
1 TT
74010 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 27 0.48
18 9 0.16
19 14 0.25
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:73964 original size:34 final size:36
Alignment explanation
Indices: 73921--74012 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
73911 GTTGAACAAA
73921 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
73955 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
73991 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
74013 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:73972 original size:143 final size:145
Alignment explanation
Indices: 73759--74124 Score: 583
Period size: 143 Copynumber: 2.5 Consensus size: 145
73749 ATAGAATTAT
* * * *
73759 ACAAAAGGTTGAACAAGCTCTTTTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
*
73824 TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATC
66 TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
73889 AAGTGATGGATTTGA
131 AAGTGATGGATTTGA
*
73904 ACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAGTTCTTCTCATTA
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
73967 TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
66 TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
*
74032 AAGTGATGGTTTTGA
131 AAGTGATGGATTTGA
*
74047 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGAT---GAGTTCTT
74112 CTCATTATGAACT
59 CTCATTATGAACT
74125 CTACCTGGCA
Statistics
Matches: 203, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
143 131 0.65
144 1 0.00
145 36 0.18
146 5 0.02
147 1 0.00
148 1 0.00
149 7 0.03
152 21 0.10
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (145 bp):
ACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
AAGTGATGGATTTGA
Found at i:74155 original size:116 final size:113
Alignment explanation
Indices: 73953--74501 Score: 696
Period size: 116 Copynumber: 4.8 Consensus size: 113
73943 CTTTCAGATG
*
73953 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
* * * * **
74013 CTGGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACA
65 CTGGCAATGCTGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACA
74062 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCT
* * *
74127 ACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACA
63 ACCTGGCAATGCTGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACA
* ** *
74178 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATTTGTTCTTCTCATTATGAACT-TTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
* * * ** * *
74242 CTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACA
65 CTGGCAATGCTGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACA
* * * *
74291 AATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCATATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCT
* * *
74356 ACATGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
63 ACCTGGCAATGCTGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACA
* *
74407 AGTTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
**
74472 TGGCAATGCTGATCCATTGAATGATGGATT
66 TGGCAATGCTGATCCATCAAATGATGGATT
74502 TAAATCTTTG
Statistics
Matches: 378, Mismatches: 49, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
109 18 0.05
112 8 0.02
113 156 0.41
114 1 0.00
115 1 0.00
116 190 0.50
117 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
TGGCAATGCTGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACA
Found at i:74502 original size:229 final size:228
Alignment explanation
Indices: 73953--74466 Score: 881
Period size: 229 Copynumber: 2.3 Consensus size: 228
73943 CTTTCAGATG
73953 AGTTCTTCTCATTATGAACTTC-T-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 AGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* *
74015 GGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAGTTCTTCTCATTATGAA
66 GGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
*
74080 CTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCC
131 CTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCC
*
74145 ATCAAATGATGAATTCAAACAAAAGGTTGAACA
196 ATCAAATGATGAATTCAAACAAAAAGTTGAACA
* **
74178 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATTTGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
74243 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
65 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* * *
74308 ATTTCTTCTTTCTTCTTCATATGACGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATC
130 ACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATC
74373 CATCAAATGATGAATTCAAACAAAAAGTTGAACA
195 CATCAAATGATGAATTCAAACAAAAAGTTGAACA
74407 AGTTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACTTCTT-CTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
74467 CGACCTGGCA
Statistics
Matches: 269, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
225 21 0.08
226 1 0.00
228 1 0.00
229 245 0.91
230 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (228 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
GGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCC
ATCAAATGATGAATTCAAACAAAAAGTTGAACA
Found at i:74984 original size:22 final size:22
Alignment explanation
Indices: 74906--74982 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
74896 GATAAAGCTT
*
74906 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
74928 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
74950 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
74972 TCATCTTTGAA
1 TCATCTTTGAA
74983 GAATGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:77665 original size:114 final size:114
Alignment explanation
Indices: 77418--77639 Score: 342
Period size: 114 Copynumber: 2.0 Consensus size: 114
77408 GATCATGCAG
* * *
77418 TTCATCTTTC-AATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCT-AATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAG
*
77482 AACACTTTCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
* * *
77532 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATTAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
77597 ACACTTCCAGAAGATGCTATTGGG-C-TCGTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTACTATGA
77640 GAATGTGGCA
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 2 0.02
113 16 0.16
114 77 0.78
115 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
Found at i:79893 original size:5 final size:5
Alignment explanation
Indices: 79883--79932 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
79873 GATTCAATTT
* * * *
79883 TTTTC TTTTC TTTTC TTTTT TTTTG TTTTG TTTTG TTTTG TTTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG -TTTTG TTTT
79933 TCTTCTTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:80245 original size:2 final size:2
Alignment explanation
Indices: 80238--80310 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
80228 ACAACAAAGG
80238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80280 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 A
80311 AGGATAAATG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84542 original size:23 final size:25
Alignment explanation
Indices: 84515--84573 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 25
84505 TCTAACAAAC
84515 AAATAAAATAAAAAT-ATAATA-AT
1 AAATAAAATAAAAATAATAATATAT
84538 AAATAAAATAAAAATAATAATATAT
1 AAATAAAATAAAAATAATAATATAT
84563 AAA-AATAATAA
1 AAATAA-AATAA
84574 GTAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 15 0.45
24 8 0.24
25 10 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (25 bp):
AAATAAAATAAAAATAATAATATAT
Found at i:84566 original size:16 final size:14
Alignment explanation
Indices: 84515--84584 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 14
84505 TCTAACAAAC
84515 AAAT-AAAATAA-A
1 AAATAAAAATAATA
*
84527 AATATAATAATAAATA
1 AA-ATAAAAAT-AATA
84543 AAATAAAAATAATA
1 AAATAAAAATAATA
84557 ATATATAAAAATAATA
1 A-A-ATAAAAATAATA
84573 AGTAATAAAAAT
1 A--AATAAAAAT
84585 TTGAAAGAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 9 0.18
15 10 0.20
16 24 0.49
17 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:86797 original size:12 final size:11
Alignment explanation
Indices: 86707--86805 Score: 88
Period size: 12 Copynumber: 9.3 Consensus size: 11
86697 TTTGGGCTTG
86707 TAATAAT-ATT
1 TAATAATAATT
86717 TAATAATAATAT
1 TAATAATAAT-T
*
86729 TAATAATAA-A
1 TAATAATAATT
86739 TAATAAT-ATT
1 TAATAATAATT
86749 AATAATAATAATT
1 --TAATAATAATT
86762 ATAATAATAA--
1 -TAATAATAATT
86772 TAATAATAA--
1 TAATAATAATT
86781 TAATAATAATT
1 TAATAATAATT
86792 TAAATAAT-ATT
1 T-AATAATAATT
86803 TAA
1 TAA
86806 ATGAAAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
9 19 0.24
10 16 0.21
11 7 0.09
12 33 0.42
13 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAATAATT
Found at i:86800 original size:3 final size:3
Alignment explanation
Indices: 86707--86790 Score: 114
Period size: 3 Copynumber: 27.3 Consensus size: 3
86697 TTTGGGCTTG
* * *
86707 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
86754 TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
86791 TTAAATAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
3 66 0.93
4 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:87216 original size:121 final size:120
Alignment explanation
Indices: 86936--87219 Score: 333
Period size: 121 Copynumber: 2.3 Consensus size: 120
86926 GTTGAATAAA
* * *
86936 TTCTTCTCTTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGACCTA
1 TTCTT-TC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAACCTA
* * * * * *
87001 TTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTC
64 TCTACTTATGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTCTTATTATGAA--TC
* * *
87060 TTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGCTAATCT
1 TTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGCTAACCT
* *
87124 ATCTACTTATGTGATAGAATTATACAAAAAGGTTGAACAAGCTCTT-TTCATTGTGAA-C
63 ATCTACTTATGTGATAGAATCATAC-AAAAGGTTGAACAAGCTCTTCTT-ATTATGAATC
87182 TTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
87220 CTTCTTCTTC
Statistics
Matches: 141, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
121 40 0.28
122 36 0.26
123 2 0.01
124 37 0.26
125 26 0.18
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (120 bp):
TTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAACCTATC
TACTTATGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTCTTATTATGAATC
Found at i:87218 original size:36 final size:36
Alignment explanation
Indices: 87166--87255 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
87156 TTGAACAAGC
* *
87166 TCTTTTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
87202 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
87238 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
87256 TCTCTGGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:87251 original size:16 final size:16
Alignment explanation
Indices: 87196--87251 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
87186 TCTTCTTCAG
87196 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
*
87212 ATGAACTTCTTCTTC-TT
1 ATG-AGTTCTTC-TCATT
87229 CAGATGAGTTCTTCTCATT
1 ---ATGAGTTCTTCTCATT
87248 ATGA
1 ATGA
87252 ACTTTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:87332 original size:17 final size:17
Alignment explanation
Indices: 87310--87398 Score: 69
Period size: 17 Copynumber: 5.1 Consensus size: 17
87300 GTTGAACAAA
*
87310 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
*
87327 TTCTTCTTTCA-TATG-AG
1 TTCTTC--TCATTATGAAC
87344 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
87361 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
87380 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
87397 TT
1 TT
87399 TCTCTGGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
15 3 0.05
16 4 0.07
17 27 0.47
18 10 0.17
19 14 0.24
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:87353 original size:34 final size:36
Alignment explanation
Indices: 87310--87401 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
87300 GTTGAACAAA
*
87310 TTCTTCTCATTATGAATTTCTTC-T-TTCATATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
87344 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
87380 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
87402 CTGGAAAAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 25 0.48
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.51
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:87365 original size:143 final size:143
Alignment explanation
Indices: 87150--87477 Score: 548
Period size: 143 Copynumber: 2.3 Consensus size: 143
87140 GAATTATACA
* * *
87150 AAAAGGTTGAACAAGCTCTTTTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATG
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-T-TTCAGATGAGTTCTTCTCATTATG
**
87215 AACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATTTATCAA
64 AACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
87280 GTGATGGATTTGAAC
129 GTGATGGATTTGAAC
* * *
87295 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCATATGAGTTCTTCTCATTATGAA
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCAGATGAGTTCTTCTCATTATGAA
87360 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
66 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
*
87425 GATGGTTTTGAAC
131 GATGGATTTGAAC
*
87438 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
87478 CCTTCTTCAG
Statistics
Matches: 171, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
143 137 0.80
144 1 0.01
145 33 0.19
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (143 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCAGATGAGTTCTTCTCATTATGAA
CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
GATGGATTTGAAC
Found at i:87762 original size:222 final size:225
Alignment explanation
Indices: 87344--87847 Score: 829
Period size: 224 Copynumber: 2.2 Consensus size: 225
87334 TTCATATGAG
87344 TTCTTCTCATTATGAACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* *
87408 AAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
*
87473 TTCTTCCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCA
131 TTCTTCCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCCATCA
*
87538 AATGATGAATTCAAACAAAAGGTTGAACAAA
196 AATGATGAATTCAAACAAAAAGTTGAAC-AA
**
87569 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATTTGTTC-T-TCATTATGAACTTTCTCTGGAA
1 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* * *
87632 AAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT-ATTATGAATTTC
66 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
* *
87696 TTCTT-CTTCTTTAGATGACGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCCATCA
131 TTCTTCCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCCATCA
*
87760 AATGATGAATTCAAACAAAAAGTTGAACAG
196 AATGATGAATTCAAACAAAAAGTTGAACAA
87790 TTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTC-T--TCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
87848 CGACTGGCAA
Statistics
Matches: 259, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
221 21 0.08
222 84 0.32
223 16 0.06
224 87 0.34
225 24 0.09
226 27 0.10
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (225 bp):
TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCCATCA
AATGATGAATTCAAACAAAAAGTTGAACAA
Found at i:88362 original size:22 final size:22
Alignment explanation
Indices: 88284--88360 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
88274 GATAAAGCTT
*
88284 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
88306 TCATCTTTAAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
88328 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
88350 TCATCTTTGAA
1 TCATCTTTGAA
88361 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:93219 original size:10 final size:10
Alignment explanation
Indices: 93204--93248 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
93194 CTTGATTCAA
93204 TTTTTTCTTT
1 TTTTTTCTTT
*
93214 TTTTTTGTTT
1 TTTTTTCTTT
93224 TGTTTTGT-TTT
1 T-TTTT-TCTTT
93235 TTTTTTCTTT
1 TTTTTTCTTT
93245 TTTT
1 TTTT
93249 CTTTCTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 1 0.03
10 21 0.68
11 8 0.26
12 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:93550 original size:2 final size:2
Alignment explanation
Indices: 93543--93580 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
93533 ACAACAAAGG
93543 AT AT AT AT AT AT -T 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 AT A
93581 AAAGGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.