Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 124 of 125
Found at i:39213861 original size:175 final size:171
Alignment explanation
Indices: 39213505--39213862 Score: 497
Period size: 175 Copynumber: 2.1 Consensus size: 171
39213495 TTTTTCCTCT
* * *
39213505 TTTTG-TTGAATATGAATTACATGGCTTAAAGATCTTGTTTCTGTTTAATGTGTTGTGATTTTTT
1 TTTTGATTGAATATGAATTACATGGCTTAAAGATCTTGTTTCTATTTAATGTATGGTGATTTTTT
* **
39213569 CTGGGTTTTGCTTGTCTTGATTGAATATGCATTACAAGGAGTTAAAATCGTGTTTTTTTTTTAAA
66 CTGGGTCTTGCTTGTCTTGATTGAATATGCATTACAAGGAGTTAAAATCAAGTTTTTTTTTTAAA
*
39213634 AATTTAAAGTCTGTTATGATACTTTTTCTGGGTTTTGCTTG
131 AATTTAAAGTCTGTGATGATACTTTTTCTGGGTTTTGCTTG
* * * *
39213675 TTTTGATTGAATATGCATTACTTGGACTTAAAGATCTTGTTTTTATTTTATGTATGGTGATATTT
1 TTTTGATTGAATATGAATTACATGG-CTTAAAGATCTTGTTTCTATTTAATGTATGGTG--ATTT
* * *
39213740 TTTCTGGGTCTTGCTTGTTTTGATTGAATATGCATTACATGGTGTTAAAGATCAAGTTTTTTTTA
63 TTTCTGGGTCTTGCTTGTCTTGATTGAATATGCATTACAAGGAGTTAAA-ATCAAGTTTTTTTT-
* *
39213805 TT-TAAATTTAAAGTCTGTGATGATATTTTTTCTGGGTTTTGCTTG
126 TTAAAAATTTAAAGTCTGTGATGATACTTTTTCTGGGTTTTGCTTG
39213850 -TTTGAATTGAATA
1 TTTTG-ATTGAATA
39213863 CTGTTAGGTA
Statistics
Matches: 165, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
170 5 0.03
171 17 0.10
172 28 0.17
174 53 0.32
175 60 0.36
176 2 0.01
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.51
Consensus pattern (171 bp):
TTTTGATTGAATATGAATTACATGGCTTAAAGATCTTGTTTCTATTTAATGTATGGTGATTTTTT
CTGGGTCTTGCTTGTCTTGATTGAATATGCATTACAAGGAGTTAAAATCAAGTTTTTTTTTTAAA
AATTTAAAGTCTGTGATGATACTTTTTCTGGGTTTTGCTTG
Found at i:39218429 original size:92 final size:92
Alignment explanation
Indices: 39218272--39218463 Score: 357
Period size: 92 Copynumber: 2.1 Consensus size: 92
39218262 CACTTGTTAA
*
39218272 TTATATTCGAGTTAAAACGCTTAGGTAAATTCTTCTTTAAAATCCTCCTTCCTACAACGAGAAAA
1 TTATATTCGAATTAAAACGCTTAGGTAAATTCTTCTTTAAAATCCTCCTTCCTACAACGAGAAAA
39218337 GATGTTAAAAATATATAATTCAAGTCC
66 GATGTTAAAAATATATAATTCAAGTCC
* *
39218364 TTATATTCGAATTAAAACGCTTAGGTAAATTTTTCTTTAAAATCCTCCTTCTTACAACGAGAAAA
1 TTATATTCGAATTAAAACGCTTAGGTAAATTCTTCTTTAAAATCCTCCTTCCTACAACGAGAAAA
39218429 GATGTTAAAAATATATAATTCAAGTCC
66 GATGTTAAAAATATATAATTCAAGTCC
39218456 TTATATTC
1 TTATATTC
39218464 TTAGTGCACA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 97 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (92 bp):
TTATATTCGAATTAAAACGCTTAGGTAAATTCTTCTTTAAAATCCTCCTTCCTACAACGAGAAAA
GATGTTAAAAATATATAATTCAAGTCC
Found at i:39219613 original size:3 final size:3
Alignment explanation
Indices: 39219605--39219648 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39219595 CATGATTGAA
39219605 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39219649 AGGTGTGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39221996 original size:51 final size:51
Alignment explanation
Indices: 39221879--39221998 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 51
39221869 TATATAAGTG
* * * *
39221879 TTGACAGGATGTGCATATATTGTAGGTTAAATTTGTTAAATCATGACTAAA
1 TTGACAGGATGTGTAAATATTGTAGGTTAAATTTGTTAAATCAAGACCAAA
** * * * *
39221930 TTGAGGGGATATGTAAATGTTGTGGGTTAAATTTGTTAATTCAAGACCAAA
1 TTGACAGGATGTGTAAATATTGTAGGTTAAATTTGTTAAATCAAGACCAAA
*
39221981 TTGACAGAATGTGTAAAT
1 TTGACAGGATGTGTAAAT
39221999 TTTGAGAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.36
Consensus pattern (51 bp):
TTGACAGGATGTGTAAATATTGTAGGTTAAATTTGTTAAATCAAGACCAAA
Found at i:39225738 original size:132 final size:134
Alignment explanation
Indices: 39225509--39225756 Score: 315
Period size: 132 Copynumber: 1.9 Consensus size: 134
39225499 CAGAACAAAT
* * * ** *
39225509 ATCCATACGAAAAACAAAAGCATCAAAGCTAAGAGCATTCACCTGCTACAAATTCTTCAAGCTAT
1 ATCCATACAAAAAACAAAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTACAAGC-AT
* * * **
39225574 ATAAATACACTTACCAAATGCAAACAATAAAAGCTTTACTGTAAAGCACGAGAACCTTCAAAAAA
65 ATAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGAGAACCTTCAAAAAA
39225639 AAAAA
130 AAAAA
*
39225644 ATCCATACAAAAAACACAAA-CTTCAAAG-TAAGAGCATCCAACTGAAACAAATTC-ACAAAGC-
1 ATCCATACAAAAAACA-AAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTAC-AAGCA
**
39225705 TATAAATACACTAATGAAACGCAAACAACAAAAGCTTTACCATAAAGCACGA
64 TATAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGA
39225757 ACCGGTAACA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
132 45 0.46
133 1 0.01
134 26 0.27
135 22 0.23
136 3 0.03
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.18
Consensus pattern (134 bp):
ATCCATACAAAAAACAAAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTACAAGCATA
TAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGAGAACCTTCAAAAAAA
AAAA
Found at i:39226142 original size:125 final size:126
Alignment explanation
Indices: 39225891--39226152 Score: 359
Period size: 125 Copynumber: 2.1 Consensus size: 126
39225881 CAAATAACAG
* * * *
39225891 AAACTTCAAACTAAGAGCACCCAACCGAAACAAATTCTTGAAGCTATAAATACACTAATGAAATG
1 AAACATCAAGCTAAGAGCACCCAACCGAAACAAATTCATGAAGCTATAAATAAACTAATGAAATG
* *
39225956 CAAACAACGAAAGCTTTACCGTAAAGCAAAAATCATAACATGGTCCACTTCGGGGG-GAAA
66 CAAACAACGAAAGCTTTACCGTAAAGCAAAAATCATAACACGGTCCACTTCGGGGGAAAAA
* * * * *
39226016 AAACATCAAGCTAAGAGCATCCAACCGAAACATATTCATGTAGCTATAAGTAAACTGATGAAATG
1 AAACATCAAGCTAAGAGCACCCAACCGAAACAAATTCATGAAGCTATAAATAAACTAATGAAATG
* *
39226081 CAAACAA-TACAAGCTTTTACCGTAAAGCACAAATCATAACACGGTCCACTTC-GGGGAAAAA
66 CAAACAACGA-AAGC-TTTACCGTAAAGCAAAAATCATAACACGGTCCACTTCGGGGGAAAAA
39226142 ACAACATCAAG
1 A-AACATCAAG
39226153 AAATGCAAAC
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
124 1 0.01
125 71 0.59
126 39 0.32
127 9 0.08
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.19
Consensus pattern (126 bp):
AAACATCAAGCTAAGAGCACCCAACCGAAACAAATTCATGAAGCTATAAATAAACTAATGAAATG
CAAACAACGAAAGCTTTACCGTAAAGCAAAAATCATAACACGGTCCACTTCGGGGGAAAAA
Found at i:39227622 original size:15 final size:16
Alignment explanation
Indices: 39227602--39227631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39227592 TGATAGATTA
39227602 ATGTA-TAATTTTATC
1 ATGTATTAATTTTATC
39227617 ATGTATTAATTTTAT
1 ATGTATTAATTTTAT
39227632 GATTTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (16 bp):
ATGTATTAATTTTATC
Found at i:39230593 original size:18 final size:18
Alignment explanation
Indices: 39230570--39230609 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
39230560 GTATGTTAAA
39230570 TATTTCACTATTAATATT
1 TATTTCACTATTAATATT
39230588 TATTTCACTATTAATATT
1 TATTTCACTATTAATATT
39230606 TATT
1 TATT
39230610 ATGTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTCACTATTAATATT
Found at i:39238896 original size:31 final size:29
Alignment explanation
Indices: 39238858--39238927 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
39238848 ATATCAAAGC
39238858 TATATATGAACTTTGATCCAATGTGCAATAT
1 TATATATGAACTTTGAT--AATGTGCAATAT
* ** *
39238889 TATATATGAATTTTGATTTTGTGCAATTT
1 TATATATGAACTTTGATAATGTGCAATAT
39238918 TATATATGAA
1 TATATATGAA
39238928 GTTTTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (29 bp):
TATATATGAACTTTGATAATGTGCAATAT
Found at i:39238911 original size:29 final size:30
Alignment explanation
Indices: 39238879--39238937 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
39238869 TTTGATCCAA
39238879 TGTGCAATATTATATATGAA-TTTTGATTT
1 TGTGCAATATTATATATGAAGTTTTGATTT
* *
39238908 TGTGCAATTTTATATATGAAGTTTTTATTT
1 TGTGCAATATTATATATGAAGTTTTGATTT
39238938 GATTCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (30 bp):
TGTGCAATATTATATATGAAGTTTTGATTT
Found at i:39244442 original size:29 final size:28
Alignment explanation
Indices: 39244412--39244571 Score: 101
Period size: 29 Copynumber: 5.5 Consensus size: 28
39244402 ATCGGGATTA
39244412 AAAATGGAATTTTAAAAGATTCGAGGGT
1 AAAATGGAATTTTAAAAGATTCGAGGGT
* **
39244440 AAAATCGCAATTTTTGGTGAA-ATT-G-GGGTT
1 AAAAT-GGAA-TTTT--AAAAGATTCGAGGG-T
*
39244470 AAAAATGGAATTTTAAAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGAGGGT
* ** * *
39244499 AAAATGGTAATTTTCAGTGAAATCGAGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGAGGGT
* * *
39244529 AAAAATGGAATTTTAGAAGCTTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGAGGGT
39244558 AAAATGGTAATTTT
1 AAAATGG-AATTTT
39244572 TGGTGAAATC
Statistics
Matches: 99, Mismatches: 20, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
27 2 0.02
28 22 0.22
29 32 0.32
30 26 0.26
31 15 0.15
32 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTAAAAGATTCGAGGGT
Found at i:39244473 original size:59 final size:59
Alignment explanation
Indices: 39244375--39244836 Score: 649
Period size: 59 Copynumber: 7.9 Consensus size: 59
39244365 TATGGATACC
* * * * * *
39244375 CGGGGGCAAAATAGTAATTTT-GGTGTAATCGGGATTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * * * * *
39244433 CGAGGGTAAAATCGCAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
39244492 CGGGGGTAAAATGGTAATTTTCAGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* **
39244551 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACAGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * *
39244610 CAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
39244669 CGGGGGTAAGATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
** *
39244728 TAGGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * *
39244787 TGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-TCAAAATGTAATTTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT
39244837 TGTAAAGTTT
Statistics
Matches: 364, Mismatches: 39, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
58 30 0.08
59 334 0.92
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:39244850 original size:30 final size:30
Alignment explanation
Indices: 39244816--39244895 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
39244806 TTCGGTGAAA
* *
39244816 TCGGGGTCAAAATGTAATTTTTGTAAAGTT
1 TCGGGGTCAAAATGTAATTTTGGGAAAGTT
*
39244846 TCGGGGTCAAAATATAATTTTGGGAAAGTT
1 TCGGGGTCAAAATGTAATTTTGGGAAAGTT
*
39244876 TTGGGGTCAAAATGTAATTT
1 TCGGGGTCAAAATGTAATTT
39244896 CTGGACAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (30 bp):
TCGGGGTCAAAATGTAATTTTGGGAAAGTT
Found at i:39245180 original size:162 final size:162
Alignment explanation
Indices: 39244993--39245306 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 162
39244983 ATTTGAAAAT
*
39244993 CTTGAAAAAATTTTGGATCAATTTTGTAATT-AAATAAAAGTCGATTTAAGGATTAAATTAAAAC
1 CTTGAAAAAATTTTGGACCAATTTTGTAATTAAAAT-AAAGTCGATTTAAGGATTAAATTAAAAC
* *
39245057 AAATTAAAAATAAAAAGGACTAAATGTAGAAATAATCAAAAAAATGACACGTGGCAACCTCTGGT
65 AAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCAAAAAAATGACACGTGGCAACCTCTGGC
*
39245122 GCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
130 ACAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * * **
39245155 CTTG-AAAAATTATTGGGCCAATTTTGTATTTAAAATAAAGTTGATTTTGGGATTAAATTAAAAC
1 CTTGAAAAAATT-TTGGACCAATTTTGTAATTAAAATAAAGTCGATTTAAGGATTAAATTAAAAC
* * * * *
39245219 AAATTAAAAATGAAAAGGACTAAATGCATAAATAATCCAATACATGACACGTGGCAACCTCTGGC
65 AAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCAAAAAAATGACACGTGGCAACCTCTGGC
39245284 ACAGTCAAACAGTCAAAGGACTA
130 ACAGTCAAACAGTCAAAGGACTA
39245307 AATCATAAAC
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 7 0.05
162 125 0.92
163 4 0.03
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (162 bp):
CTTGAAAAAATTTTGGACCAATTTTGTAATTAAAATAAAGTCGATTTAAGGATTAAATTAAAACA
AATTAAAAATAAAAAGGACTAAATGCAGAAATAATCAAAAAAATGACACGTGGCAACCTCTGGCA
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:39246926 original size:17 final size:16
Alignment explanation
Indices: 39246883--39246975 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 16
39246873 CTTTCCTTTT
39246883 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
39246900 TTAAATTTTAAATTAAA
1 TTAAA-TTTAAATTAAA
39246917 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
39246935 TTGAATTTAAAGTAAA
1 TTAAATTTAAATTAAA
*
39246951 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
39246968 TTTAATTT
1 TTAAATTT
39246976 TCAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 36 0.56
18 18 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:39246929 original size:6 final size:6
Alignment explanation
Indices: 39246900--39246972 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
39246890 TATAATAATA
* *
39246900 TTAAATT TTAAA- TTAAAT TCAAAT TTAAAT TTAAA- TTGAAT TTAAA-
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
39246946 GTAAAT TTAAGA- TTAAA- ATAAAT TTAA
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAA
39246973 TTTTCAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
5 18 0.34
6 29 0.55
7 6 0.11
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:39246941 original size:11 final size:11
Alignment explanation
Indices: 39246899--39246975 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
39246889 TTATAATAAT
39246899 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
39246911 ATTAAATTCAA
1 ATTAAATTTAA
39246922 ATTTAAATTTAA
1 A-TTAAATTTAA
*
39246934 ATTGAATTTAA
1 ATTAAATTTAA
*
39246945 AGTAAATTTAA
1 ATTAAATTTAA
*
39246956 GATTAAA-ATAA
1 -ATTAAATTTAA
*
39246967 ATTTAATTT
1 ATTAAATTT
39246976 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:39247157 original size:32 final size:32
Alignment explanation
Indices: 39247111--39247173 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
39247101 ATTAATCAGT
* * *
39247111 ATGAGTTATCAAAATTAATTAATTAATTTATC
1 ATGAGTTATCAAAATCAAGTAATCAATTTATC
* *
39247143 ATGAGTTGTTAAAATCAAGTAATCAATTTAT
1 ATGAGTTATCAAAATCAAGTAATCAATTTAT
39247174 AAGTTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (32 bp):
ATGAGTTATCAAAATCAAGTAATCAATTTATC
Found at i:39259417 original size:31 final size:29
Alignment explanation
Indices: 39259345--39259426 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
39259335 AATGTGTAAT
*
39259345 TGTATACATG-AACTTTAATTTGGTGCAA
1 TGTATACTTGAAACTTTAATTTGGTGCAA
* *
39259373 T-TATACATGTGAAACTCTAATTGTGGTTCAAA
1 TGTATAC-T-TGAAACTTTAATT-TGGTGC-AA
39259405 TGTATACTTGAAACTTTAATTT
1 TGTATACTTGAAACTTTAATTT
39259427 TAATTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 5 0.11
28 1 0.02
29 2 0.05
30 10 0.23
31 17 0.39
32 4 0.09
33 5 0.11
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (29 bp):
TGTATACTTGAAACTTTAATTTGGTGCAA
Found at i:39261840 original size:204 final size:204
Alignment explanation
Indices: 39261401--39262018 Score: 1137
Period size: 204 Copynumber: 3.0 Consensus size: 204
39261391 AAGCAAATAG
39261401 ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCTGAAATAA
1 ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCTGAAATAA
* *
39261466 AAGCAATGGTGTTTTTTCCAGTATACATGCACGCATCTATATGTTTATATATATGTGTGCATTAA
66 AAGCAATGGTGTTTTTTCCAGTACACATGCACACATCTATATGTTTATATATA--TGTGCATTAA
*
39261531 GATGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCATTGTTTGGTGCTGAG
129 GATGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAG
39261596 ACAAAAGTTGC
194 ACAAAAGTTGC
*
39261607 ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCCGAAATAA
1 ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCTGAAATAA
39261672 AAGCAATGGTGTTTTTTCCAGTACACATGCACACATCTATATGTTTATATATATGTGCATTAAGA
66 AAGCAATGGTGTTTTTTCCAGTACACATGCACACATCTATATGTTTATATATATGTGCATTAAGA
*
39261737 AGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGAC
131 TGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGAC
39261802 AAAAGTTGC
196 AAAAGTTGC
* *
39261811 ATCAACCTGTTTCTGCACATACTAGAAAATTAGATTGTATGTCTTCATTCTACATGCTGAAATAA
1 ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCTGAAATAA
* *
39261876 AAGCAATGGTGTTTTTTCCAGTACACATGCACCCATCTATATGCTTATATATATGTGCATTAAGA
66 AAGCAATGGTGTTTTTTCCAGTACACATGCACACATCTATATGTTTATATATATGTGCATTAAGA
39261941 TGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGAC
131 TGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGAC
39262006 AAAAGTTGC
196 AAAAGTTGC
39262015 ATCA
1 ATCA
39262019 GCAAATAGAT
Statistics
Matches: 401, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
204 286 0.71
206 115 0.29
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (204 bp):
ATCAACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCTGAAATAA
AAGCAATGGTGTTTTTTCCAGTACACATGCACACATCTATATGTTTATATATATGTGCATTAAGA
TGAAACATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGAC
AAAAGTTGC
Found at i:39262948 original size:313 final size:310
Alignment explanation
Indices: 39262374--39262992 Score: 1008
Period size: 313 Copynumber: 2.0 Consensus size: 310
39262364 GAGATAATTT
39262374 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTGTTTAAACATGTTAC
1 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTG-TTAAACATGTTAC
* *
39262439 AGTAATAGAGGTTGAACTTCAATAATCAAGTTATTATGCATGGTGAAACACGAATCACCGTATAG
65 AGTAATAGAGCTTGAACTTCAATAATCAAGTTATTATGCATGGTGAAACACGAATCACCATATAG
* *
39262504 AATAAATGGATTCACAATAGTGATATGATTCCTAGAACCAAACATGGCATGTAGTGTATAATAAC
130 AATAAATGGATTCACAATAGTGATACGATTCCTAGAACCAAACATGGCATGCAGTGTATAATAAC
* *
39262569 CCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCTTTTTGGAA
195 CCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGTGGAA
39262634 TTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGCGGCTTCACGTTGGCA
260 TTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGCGGCTTCACGTTGGCA
* ***
39262685 TTTTTT-GGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTG-TGAGTGTGTTTAA
1 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTGTTAAACATG-TT--
* *
39262748 ACATGCTATTAGAGCTTGAACTTCCATAATCAAGTTATTATGCATGGTGAAACACGAATCACCAT
63 ACA-G-TAATAGAGCTTGAACTTCAATAATCAAGTTATTATGCATGGTGAAACACGAATCACCAT
* * *
39262813 ATAGAATAAATGGATTCACGATGGTGCTACGATTCCTAGAACCAAACATGGCATGCAGTGTATAA
126 ATAGAATAAATGGATTCACAATAGTGATACGATTCCTAGAACCAAACATGGCATGCAGTGTATAA
*
39262878 TAACCCTGGAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGT
191 TAACCCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGT
* *
39262943 GGAATTTGCTTGGCTCTCACTTGCAGTACTCCCTTGGCGTGGCTTCACGT
256 GGAATTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGCGGCTTCACGT
39262993 AGGTATCTTT
Statistics
Matches: 285, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
308 4 0.01
309 2 0.01
310 44 0.15
311 9 0.03
312 1 0.00
313 225 0.79
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (310 bp):
TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTGTTAAACATGTTACA
GTAATAGAGCTTGAACTTCAATAATCAAGTTATTATGCATGGTGAAACACGAATCACCATATAGA
ATAAATGGATTCACAATAGTGATACGATTCCTAGAACCAAACATGGCATGCAGTGTATAATAACC
CTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGTGGAAT
TTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGCGGCTTCACGTTGGCA
Found at i:39268106 original size:22 final size:23
Alignment explanation
Indices: 39268051--39268110 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
39268041 TTAAGTACCA
39268051 AAAAAAATAAAAAAATTTAAAAAC
1 AAAAAAA-AAAAAAATTTAAAAAC
* * * *
39268075 TAACATAAAAAAAATTT-AAAGC
1 AAAAAAAAAAAAAATTTAAAAAC
39268097 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
39268111 GCAAACTCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 15 0.52
23 10 0.34
24 4 0.14
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (23 bp):
AAAAAAAAAAAAAATTTAAAAAC
Found at i:39270325 original size:17 final size:17
Alignment explanation
Indices: 39270292--39270324 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39270282 AATTCAATTG
39270292 ATATATTTAAATATTTT
1 ATATATTTAAATATTTT
39270309 ATATA-TTAAATATTTT
1 ATATATTTAAATATTTT
39270325 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTAAATATTTT
Found at i:39270343 original size:12 final size:13
Alignment explanation
Indices: 39270316--39270343 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39270306 TTTATATATT
39270316 AAATATTTTTTAA
1 AAATATTTTTTAA
39270329 AAATATTTTTTAA
1 AAATATTTTTTAA
39270342 AA
1 AA
39270344 CGAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:39273083 original size:25 final size:25
Alignment explanation
Indices: 39273049--39273098 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39273039 TTTGTTTCCT
39273049 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
*
39273074 TTCCTTCTTCAAAAATTTGCTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
39273099 AACAGATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (25 bp):
TTCCTTCTTCAAAAATTTACTGTTA
Found at i:39273171 original size:27 final size:27
Alignment explanation
Indices: 39273133--39273193 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
39273123 GCATTGACAA
39273133 AGGCACCACTAGTGCCGCCTACCCAGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
**
39273160 AGGCACCACTAGTGCCGCCTACCTGGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
39273187 AGGCACC
1 AGGCACC
39273194 TCTTGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.15
Consensus pattern (27 bp):
AGGCACCACTAGTGCCGCCTACCCAGT
Found at i:39273416 original size:20 final size:23
Alignment explanation
Indices: 39273393--39273433 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
39273383 ATTTAATTTA
39273393 ATTTTTT-TA-AATT-TTATAAT
1 ATTTTTTCTACAATTCTTATAAT
39273413 ATTTTTTCTACAATTCTTATA
1 ATTTTTTCTACAATTCTTATA
39273434 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTCTACAATTCTTATAAT
Found at i:39274394 original size:16 final size:16
Alignment explanation
Indices: 39274368--39274405 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
39274358 TCAATTAGTC
39274368 CAAAAAA-ATTTATAT
1 CAAAAAATATTTATAT
*
39274383 CAAAAAATATTTTTAT
1 CAAAAAATATTTATAT
39274399 -AAAAAAT
1 CAAAAAAT
39274406 TCAATTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAAAAATATTTATAT
Found at i:39275118 original size:22 final size:24
Alignment explanation
Indices: 39275075--39275124 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
39275065 TAAATAATAA
*
39275075 AAAATTATATTATTTTAATATT-T
1 AAAATTATATTATATTAATATTGT
* *
39275098 AAAATT-TTTTATATTATTATTGT
1 AAAATTATATTATATTAATATTGT
39275121 AAAA
1 AAAA
39275125 AATCCACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AAAATTATATTATATTAATATTGT
Found at i:39282076 original size:22 final size:24
Alignment explanation
Indices: 39282048--39282091 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
39282038 AATTTCGTCA
39282048 ATTTTAATTTG-TAT-TCAAAAAC
1 ATTTTAATTTGTTATATCAAAAAC
39282070 ATTTTAATTTGTTATATCAAAA
1 ATTTTAATTTGTTATATCAAAA
39282092 TATTTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 3 0.15
24 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTTTAATTTGTTATATCAAAAAC
Found at i:39282661 original size:18 final size:18
Alignment explanation
Indices: 39282638--39282680 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39282628 GAATAGGTTT
39282638 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
39282656 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39282674 TTAATTA
1 TTAATTA
39282681 CGGCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39283643 original size:27 final size:27
Alignment explanation
Indices: 39283613--39283665 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39283603 CATTATAAGA
39283613 ATAAAGTGATTAAATTAAACCAAATCT
1 ATAAAGTGATTAAATTAAACCAAATCT
*
39283640 ATAATGTGATTAAATTAAACCAAATC
1 ATAAAGTGATTAAATTAAACCAAATC
39283666 AAGAGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (27 bp):
ATAAAGTGATTAAATTAAACCAAATCT
Found at i:39285184 original size:2 final size:2
Alignment explanation
Indices: 39285177--39285206 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39285167 GTAATATTTA
39285177 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
39285207 TAAGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39288740 original size:36 final size:36
Alignment explanation
Indices: 39288700--39288806 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 36
39288690 TATTGTTAGA
39288700 GTTAGTGGTAGTTAGCAATTAGCAGAAGTTAAGTCT
1 GTTAGTGGTAGTTAGCAATTAGCAGAAGTTAAGTCT
* ** *
39288736 GTTA---GTA-TTAGC--TAAGTCAGTTG-TATAG-CA
1 GTTAGTGGTAGTTAGCAATTAG-CAGAAGTTA-AGTCT
39288766 GTTAGTGGTAGTTAG-AAGTTAGCAGAAGTTAAGTCT
1 GTTAGTGGTAGTTAGCAA-TTAGCAGAAGTTAAGTCT
39288802 GTTAG
1 GTTAG
39288807 GTAAGAGACC
Statistics
Matches: 52, Mismatches: 8, Indels: 22
0.63 0.10 0.27
Matches are distributed among these distances:
30 10 0.19
31 6 0.12
32 5 0.10
33 6 0.12
34 4 0.08
35 6 0.12
36 15 0.29
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (36 bp):
GTTAGTGGTAGTTAGCAATTAGCAGAAGTTAAGTCT
Found at i:39306024 original size:11 final size:11
Alignment explanation
Indices: 39306008--39306040 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
39305998 TTCGGACTTA
39306008 AAACTGAAGAT
1 AAACTGAAGAT
39306019 AAACTGAAGAT
1 AAACTGAAGAT
39306030 AAACTGAAGAT
1 AAACTGAAGAT
39306041 TAAAAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (11 bp):
AAACTGAAGAT
Found at i:39306282 original size:21 final size:20
Alignment explanation
Indices: 39306258--39306296 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39306248 TAAAAGTATC
*
39306258 GTGGAAATATTTGTATTAAGA
1 GTGGAAATAATTG-ATTAAGA
*
39306279 GTGGAGATAATTGATTAA
1 GTGGAAATAATTGATTAA
39306297 TTTCTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (20 bp):
GTGGAAATAATTGATTAAGA
Found at i:39306370 original size:20 final size:20
Alignment explanation
Indices: 39306345--39306398 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
39306335 GTTAAACATT
39306345 ATTAATTTTTATTTTTAAAA
1 ATTAATTTTTATTTTTAAAA
39306365 ATTAATTTTTATTTTTAAAA
1 ATTAATTTTTATTTTTAAAA
39306385 ATTAATTTTTATTT
1 ATTAATTTTTATTT
39306399 AATAGCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTAATTTTTATTTTTAAAA
Found at i:39312959 original size:21 final size:23
Alignment explanation
Indices: 39312934--39312975 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39312924 TTGTATAAGA
39312934 AAATTTAA-T-TTTTATTTTTAG
1 AAATTTAATTCTTTTATTTTTAG
39312955 AAATTTAATTCTTTTATTTTT
1 AAATTTAATTCTTTTATTTTT
39312976 TTGAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
AAATTTAATTCTTTTATTTTTAG
Found at i:39319225 original size:17 final size:17
Alignment explanation
Indices: 39319205--39319238 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39319195 TTGTATTATG
*
39319205 CTTTATCTACTTGCTTT
1 CTTTATCTAATTGCTTT
*
39319222 CTTTATGTAATTGCTTT
1 CTTTATCTAATTGCTTT
39319239 GTATGACTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.59
Consensus pattern (17 bp):
CTTTATCTAATTGCTTT
Found at i:39321124 original size:21 final size:22
Alignment explanation
Indices: 39321100--39321141 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
39321090 TGATGTAGTG
*
39321100 AATTTTTTATAA-TTAAAAAAT
1 AATTTATTATAACTTAAAAAAT
39321121 AATTTATTATAACTTAAAAAA
1 AATTTATTATAACTTAAAAAA
39321142 ATAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTATTATAACTTAAAAAAT
Found at i:39321757 original size:58 final size:58
Alignment explanation
Indices: 39321649--39321764 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 58
39321639 ATCAACAAAT
* * *
39321649 TAAACCAAAATATTTTTAGACCCAAATATAATTTTATTCTTCAAAAACACTTATAAAC
1 TAAACCAAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAAAACACTCATAAAC
* ** * *
39321707 TAAACCCAAATATTTTTAAACTTAACTATAATTTTATTCCT-AAATGACACTCATAAAC
1 TAAACCAAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAA-AACACTCATAAAC
39321765 AACTTCTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 3 0.06
58 46 0.94
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (58 bp):
TAAACCAAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAAAACACTCATAAAC
Found at i:39323170 original size:39 final size:38
Alignment explanation
Indices: 39323095--39323170 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 38
39323085 TATTCATCAT
*
39323095 AATTTAAATTTATATATTTCCTATATCATAAAATTAACG
1 AATTTAAATTTATATATTT-CTATATAATAAAATTAACG
*
39323134 AATTTAAGTTTATATATTT-TATATAATATAATATTAA
1 AATTTAAATTTATATATTTCTATATAATA-AA-ATTAA
39323171 TAAATTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 8 0.24
38 2 0.06
39 23 0.70
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
AATTTAAATTTATATATTTCTATATAATAAAATTAACG
Found at i:39323177 original size:39 final size:38
Alignment explanation
Indices: 39323095--39323183 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
39323085 TATTCATCAT
* * *
39323095 AATTTAAATTTATATATTTCCTATATCATAAAATTAACG
1 AATTTAAGTTTATATATTT-CTATATAATAAAATTAACA
*
39323134 AATTTAAGTTTATATATTT-TATATAATATAATATTAATA
1 AATTTAAGTTTATATATTTCTATATAATA-AA-ATTAACA
*
39323173 AATTTGAGTTT
1 AATTTAAGTTT
39323184 TTTAATCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 8 0.19
38 2 0.05
39 33 0.77
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (38 bp):
AATTTAAGTTTATATATTTCTATATAATAAAATTAACA
Found at i:39326224 original size:31 final size:30
Alignment explanation
Indices: 39326188--39326245 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
39326178 TTTTATAATT
* *
39326188 TAAAATTATATTTTAATCTTTTCAAAAACAA
1 TAAAATTATAATTTAATCTCTT-AAAAACAA
*
39326219 TAAAATTTTAATTTAATCTCTTAAAAA
1 TAAAATTATAATTTAATCTCTTAAAAA
39326246 TTACAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (30 bp):
TAAAATTATAATTTAATCTCTTAAAAACAA
Found at i:39329592 original size:22 final size:22
Alignment explanation
Indices: 39329567--39329611 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39329557 CATAATGATA
*
39329567 TATATATATAATATATTT-TTAT
1 TATATA-ATAACATATTTATTAT
*
39329589 TATATAATTACATATTTATTAT
1 TATATAATAACATATTTATTAT
39329611 T
1 T
39329612 TTATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATAATAACATATTTATTAT
Found at i:39329608 original size:19 final size:18
Alignment explanation
Indices: 39329571--39329610 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39329561 ATGATATATA
* *
39329571 TATATAATATATTTTTAT
1 TATATAATACATATTTAT
39329589 TATATAATTACATATTTAT
1 TATATAA-TACATATTTAT
39329608 TAT
1 TAT
39329611 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAATACATATTTAT
Found at i:39329651 original size:13 final size:13
Alignment explanation
Indices: 39329633--39329657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39329623 TAAAAGAGTT
39329633 ATTAATTAAAAAC
1 ATTAATTAAAAAC
39329646 ATTAATTAAAAA
1 ATTAATTAAAAA
39329658 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:39342669 original size:23 final size:23
Alignment explanation
Indices: 39342643--39342686 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
39342633 TTAATAAAAA
39342643 TATTATAAT-TATATTATAATTGT
1 TATT-TAATATATATTATAATTGT
* *
39342666 TATTTTATATATTTTATAATT
1 TATTTAATATATATTATAATT
39342687 AAATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTTAATATATATTATAATTGT
Found at i:39342697 original size:27 final size:28
Alignment explanation
Indices: 39342674--39342726 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
39342664 GTTATTTTAT
*
39342674 ATATTTTA-TAATTAAATTTAATTTAAA
1 ATATTTTATTAATTAAATTGAATTTAAA
* *
39342701 ATTTTTTATTATTTAAATTGAATTTA
1 ATATTTTATTAATTAAATTGAATTTA
39342727 GATCGAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATATTTTATTAATTAAATTGAATTTAAA
Found at i:39344254 original size:57 final size:57
Alignment explanation
Indices: 39344193--39344308 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
39344183 GGTTCGTGAC
* *
39344193 TATAACTTCTAATAGGTAACAATGTTACTTTTAAGATTTATGTTCGAGGTTCATAAT
1 TATAACTTCTAATAGGTAACAATGTTACCTTCAAGATTTATGTTCGAGGTTCATAAT
39344250 TATAACTTCTAATAGGTAACAATGTTACCTTCAAGATTTATGTTCGAGGTTCATAAT
1 TATAACTTCTAATAGGTAACAATGTTACCTTCAAGATTTATGTTCGAGGTTCATAAT
39344307 TA
1 TA
39344309 CTTCTCTTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (57 bp):
TATAACTTCTAATAGGTAACAATGTTACCTTCAAGATTTATGTTCGAGGTTCATAAT
Found at i:39348231 original size:61 final size:61
Alignment explanation
Indices: 39348156--39348310 Score: 258
Period size: 61 Copynumber: 2.6 Consensus size: 61
39348146 CGTAAATGCA
39348156 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATAAAATGAATCCTATTACGGATT
1 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATAAAATGAATCCTATTACGGATT
* *
39348217 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTATGGATT
1 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATAAAATGAATCCTATTACGGATT
* * *
39348278 -ATAGGTCCGATGACTCTGTGTCATCGTAAGTAT
1 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTAT
39348311 CAAACGCGAA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 30 0.34
61 59 0.66
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (61 bp):
AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATAAAATGAATCCTATTACGGATT
Found at i:39355830 original size:25 final size:25
Alignment explanation
Indices: 39355796--39355845 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39355786 TGATGCATGG
39355796 GCTGTCTTATTAACTACAATAATTA
1 GCTGTCTTATTAACTACAATAATTA
*
39355821 GCTGTCTTATTGACTACAATAATTA
1 GCTGTCTTATTAACTACAATAATTA
39355846 ATAATAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
GCTGTCTTATTAACTACAATAATTA
Found at i:39357006 original size:5 final size:5
Alignment explanation
Indices: 39356996--39357026 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
39356986 AAGAGTATTA
39356996 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT C
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT C
39357027 ATCTTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCCT
Found at i:39377408 original size:29 final size:30
Alignment explanation
Indices: 39377363--39377424 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
39377353 TAATAAAAAT
*
39377363 AAAATTATATTTTATC-TTTAAAAATAATA
1 AAAATTATATTTAATCTTTTAAAAATAATA
* *
39377392 AAAATT-TGATTTAATCTTTTAAACATTATA
1 AAAATTAT-ATTTAATCTTTTAAAAATAATA
39377422 AAA
1 AAA
39377425 GATAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 13 0.46
30 14 0.50
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAATTATATTTAATCTTTTAAAAATAATA
Found at i:39381448 original size:30 final size:29
Alignment explanation
Indices: 39381414--39381504 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
39381404 CACGATCTGG
* * *
39381414 CACATGACCGTGTGCTCAGCTCGTGTGGCT
1 CACATGACTGTGTG-TCAACCCGTGTGGCT
* * *
39381444 CACATGGCTGTGTGTCCATCCCATGTGGCT
1 CACATGACTGTGTGT-CAACCCGTGTGGCT
39381474 CACATGACTGTGTGTCTAACCCGTGTGGCT
1 CACATGACTGTGTGTC-AACCCGTGTGGCT
39381504 C
1 C
39381505 TTAAAATATG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.04
30 49 0.96
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.29
Consensus pattern (29 bp):
CACATGACTGTGTGTCAACCCGTGTGGCT
Found at i:39386904 original size:26 final size:28
Alignment explanation
Indices: 39386875--39386926 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
39386865 GTATTTTAAC
39386875 AAAAATTATAAAT-TT-TTTAA-AAAAGG
1 AAAAATTA-AAATATTATTTAATAAAAGG
39386901 AAAAATTAAAATATTATTTAATAAAA
1 AAAAATTAAAATATTATTTAATAAAA
39386927 TTAGAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 5 0.22
28 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATTAAAATATTATTTAATAAAAGG
Found at i:39394664 original size:30 final size:30
Alignment explanation
Indices: 39394630--39394686 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
39394620 TGCATTTCCA
*
39394630 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
1 TTCTGCTGCAGAATTTGAGGAGCCAAAATG
*
39394660 TTCTGGTGCAGAATTTGAGGAGCCAAA
1 TTCTGCTGCAGAATTTGAGGAGCCAAA
39394687 GGATACAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TTCTGCTGCAGAATTTGAGGAGCCAAAATG
Found at i:39399340 original size:2 final size:2
Alignment explanation
Indices: 39399333--39399390 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
39399323 TAATTCTAAA
39399333 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39399375 AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG A
39399391 AACTGGAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39402504 original size:2 final size:2
Alignment explanation
Indices: 39402491--39402530 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
39402481 ATATACAAAT
39402491 TA TA TA -A T- 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 TA TA TA TA TA
39402531 AGGAATTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39409020 original size:18 final size:18
Alignment explanation
Indices: 39408997--39409033 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39408987 AGTTCATTTC
39408997 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
39409015 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
39409033 T
1 T
39409034 AGATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:39411920 original size:13 final size:13
Alignment explanation
Indices: 39411902--39411929 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39411892 TGAAAATTCG
39411902 TTAATGGTACATT
1 TTAATGGTACATT
39411915 TTAATGGTACATT
1 TTAATGGTACATT
39411928 TT
1 TT
39411930 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:39414071 original size:21 final size:20
Alignment explanation
Indices: 39414038--39414077 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39414028 TATATTATAA
39414038 AAATATTAAAATTGATAAAAT
1 AAATATTAAAATT-ATAAAAT
**
39414059 AAATATTTTAATTATAAAA
1 AAATATTAAAATTATAAAA
39414078 ATTCGTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTAAAATTATAAAAT
Found at i:39418853 original size:18 final size:18
Alignment explanation
Indices: 39418830--39418867 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39418820 TTATTTCTAT
39418830 TTAGTAAGAATGAATTTC
1 TTAGTAAGAATGAATTTC
39418848 TTAGTAAGAATGAATTTC
1 TTAGTAAGAATGAATTTC
39418866 TT
1 TT
39418868 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
TTAGTAAGAATGAATTTC
Found at i:39420737 original size:18 final size:18
Alignment explanation
Indices: 39420714--39420750 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39420704 AGTTCATTTC
39420714 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
39420732 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
39420750 T
1 T
39420751 AGATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:39423637 original size:13 final size:13
Alignment explanation
Indices: 39423619--39423646 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39423609 TGAAAATTCG
39423619 TTAATGGTACATT
1 TTAATGGTACATT
39423632 TTAATGGTACATT
1 TTAATGGTACATT
39423645 TT
1 TT
39423647 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:39425788 original size:21 final size:20
Alignment explanation
Indices: 39425755--39425794 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39425745 TATATTATAA
39425755 AAATATTAAAATTGATAAAAT
1 AAATATTAAAATT-ATAAAAT
**
39425776 AAATATTTTAATTATAAAA
1 AAATATTAAAATTATAAAA
39425795 ATTCGTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTAAAATTATAAAAT
Found at i:39430571 original size:18 final size:18
Alignment explanation
Indices: 39430548--39430585 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39430538 TTATTTCTAT
39430548 TTAGTAAGAATGAATTTC
1 TTAGTAAGAATGAATTTC
39430566 TTAGTAAGAATGAATTTC
1 TTAGTAAGAATGAATTTC
39430584 TT
1 TT
39430586 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
TTAGTAAGAATGAATTTC
Found at i:39431417 original size:55 final size:55
Alignment explanation
Indices: 39431358--39431467 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
39431348 TTCTTTGATA
39431358 CATTCAAAGGAGAAAAAGGATGAAGGTTGATACATGTATTGAGAATTTTGATGTT
1 CATTCAAAGGAGAAAAAGGATGAAGGTTGATACATGTATTGAGAATTTTGATGTT
39431413 CATTCAAAGGAGAAAAAGGATGAAGGTTGATACATGTATTGAGAATTTTGATGTT
1 CATTCAAAGGAGAAAAAGGATGAAGGTTGATACATGTATTGAGAATTTTGATGTT
39431468 GATGCAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (55 bp):
CATTCAAAGGAGAAAAAGGATGAAGGTTGATACATGTATTGAGAATTTTGATGTT
Found at i:39441191 original size:119 final size:120
Alignment explanation
Indices: 39441037--39441276 Score: 410
Period size: 119 Copynumber: 2.0 Consensus size: 120
39441027 TGTCAATTTA
*
39441037 AAGGCAATTTTTTTTATTAACAGAACAACAGATAACAGTTAGTTAACTATGTTGAAAATATATTA
1 AAGGCAATTTTTTTTATTAACAGAACAACAAATAACAGTTAGTTAACTATGTTGAAAATATATTA
*
39441102 CTGCAAAACAAAATCGTTAGCCTTGACAGAAAAATAAACTGAGTGTAAATAAAAT
66 CTGCAAAACAAAATCGTTAGCCTTGACAGAAAAATAAACTGAGTATAAATAAAAT
* *
39441157 AAGGCAA-TTTTTTTATTAATAGAACAACAAATAACAGTTAGTTAACTATGTTGGAAATATATTA
1 AAGGCAATTTTTTTTATTAACAGAACAACAAATAACAGTTAGTTAACTATGTTGAAAATATATTA
* * *
39441221 CTGCGAATCAAAATCGTTAGCGTTGACAGAAAAATAAACTGAGTATAAATAAAAT
66 CTGCAAAACAAAATCGTTAGCCTTGACAGAAAAATAAACTGAGTATAAATAAAAT
39441276 A
1 A
39441277 GCAATCACTG
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 106 0.94
120 7 0.06
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (120 bp):
AAGGCAATTTTTTTTATTAACAGAACAACAAATAACAGTTAGTTAACTATGTTGAAAATATATTA
CTGCAAAACAAAATCGTTAGCCTTGACAGAAAAATAAACTGAGTATAAATAAAAT
Found at i:39446183 original size:25 final size:24
Alignment explanation
Indices: 39446133--39446201 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
39446123 CTATTCTACC
39446133 AATTATATT-AATTTTTAAATGTA-AA
1 AATTA-ATTCAATTTTT-AAT-TACAA
*
39446158 ATTTAATTCAATTTTTAATTACAA
1 AATTAATTCAATTTTTAATTACAA
* *
39446182 AATTAATTTATTTTTTAATT
1 AATTAATTCAATTTTTAATT
39446202 TAATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 2 0.05
24 25 0.66
25 11 0.29
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTAATTCAATTTTTAATTACAA
Found at i:39457294 original size:24 final size:24
Alignment explanation
Indices: 39457246--39457302 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
39457236 TATGGTATAA
39457246 TGATATTTATATTTTTTTATCAATT
1 TGATATTTATATTTTTTTA-CAATT
39457271 TGATATTTA-ATTTTTAGTTA-AATT
1 TGATATTTATATTTTT--TTACAATT
39457295 TGACTATT
1 TGA-TATT
39457303 AACGATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 13 0.45
25 13 0.45
26 3 0.10
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (24 bp):
TGATATTTATATTTTTTTACAATT
Found at i:39461857 original size:5 final size:5
Alignment explanation
Indices: 39461847--39461873 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39461837 CAACACAAAT
39461847 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
39461874 CTATCCACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:39475996 original size:34 final size:34
Alignment explanation
Indices: 39475953--39476017 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
39475943 TTCATCTCTT
39475953 TTGACTTTTAACCTTCCATC-TTCTTTAACCTCCC
1 TTGACTTTTAACCTTCCATCTTTC-TTAACCTCCC
*
39475987 TTGACTTTTAACCTTTCATCTTTCTTAACCT
1 TTGACTTTTAACCTTCCATCTTTCTTAACCT
39476018 TTTATATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.18, C:0.31, G:0.03, T:0.48
Consensus pattern (34 bp):
TTGACTTTTAACCTTCCATCTTTCTTAACCTCCC
Found at i:39480073 original size:28 final size:28
Alignment explanation
Indices: 39480033--39480090 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
39480023 CGCTCACAAG
39480033 ACACTTGGTATTGATTATGAAGAGACAT
1 ACACTTGGTATTGATTATGAAGAGACAT
39480061 ACACTTGGTATTGATTATGAAGAGACAT
1 ACACTTGGTATTGATTATGAAGAGACAT
39480089 AC
1 AC
39480091 TCTCCTGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (28 bp):
ACACTTGGTATTGATTATGAAGAGACAT
Found at i:39483668 original size:16 final size:16
Alignment explanation
Indices: 39483647--39483678 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39483637 GTTTCAATGT
39483647 TGATTGAAGGTAGAAC
1 TGATTGAAGGTAGAAC
*
39483663 TGATTGAAGGTGGAAC
1 TGATTGAAGGTAGAAC
39483679 ATTTTGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (16 bp):
TGATTGAAGGTAGAAC
Found at i:39489018 original size:20 final size:20
Alignment explanation
Indices: 39488995--39489033 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39488985 TATATATAAT
*
39488995 TACATGATGA-ATTTTTTTAC
1 TACAT-ATGACATTATTTTAC
39489015 TACATATGACATTATTTTA
1 TACATATGACATTATTTTA
39489034 TGATTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TACATATGACATTATTTTAC
Found at i:39497190 original size:24 final size:24
Alignment explanation
Indices: 39497163--39497227 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
39497153 TCATTAATAT
*
39497163 TGTTTGTGAACATGTTCGATTATA
1 TGTTTATGAACATGTTCGATTATA
39497187 TGTTTATGAACATGTTCGATTA-A
1 TGTTTATGAACATGTTCGATTATA
*
39497210 -GTTAAATGAACATGTTCG
1 TGTT-TATGAACATGTTCG
39497228 TGAATATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.08
23 14 0.37
24 21 0.55
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (24 bp):
TGTTTATGAACATGTTCGATTATA
Found at i:39497237 original size:23 final size:23
Alignment explanation
Indices: 39497169--39497238 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
39497159 ATATTGTTTG
* * **
39497169 TGAACATGTTCGATTATATGTTTA
1 TGAACATGTTCGATGAAAT-TAAA
* *
39497193 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
39497216 TGAACATGTTCG-TGAATATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
39497239 CAAACGAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.08
23 19 0.49
24 17 0.44
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:39508608 original size:17 final size:17
Alignment explanation
Indices: 39508577--39508651 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 17
39508567 CATGTTTTTT
39508577 TAAAACTATTT-AATATA
1 TAAAA-TATTTAAATATA
*
39508594 TAAAATATTTAAATAGA
1 TAAAATATTTAAATATA
* *
39508611 TCAAATTAATTAAAT-TA
1 T-AAAATATTTAAATATA
*
39508628 -AATAAT-TTCAAATATA
1 TAA-AATATTTAAATATA
39508644 -AAAATATT
1 TAAAATATT
39508652 AATTGATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 10 0.22
16 13 0.28
17 12 0.26
18 11 0.24
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAAATATTTAAATATA
Found at i:39519714 original size:23 final size:23
Alignment explanation
Indices: 39519649--39519714 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
39519639 CAAAGTAAGA
* *
39519649 AGTAACTGTTGTTAACTGAT-A-
1 AGTAACTGCTGATAACTGATAAC
* *
39519670 A-TAACTGCTAATAAC-AACTAAC
1 AGTAACTGCTGATAACTGA-TAAC
39519692 AGTAACTGCTGATAACTGATAAC
1 AGTAACTGCTGATAACTGATAAC
39519715 TAATAAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.03
20 12 0.35
21 2 0.06
22 1 0.03
23 17 0.50
24 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (23 bp):
AGTAACTGCTGATAACTGATAAC
Found at i:39527981 original size:19 final size:20
Alignment explanation
Indices: 39527945--39527982 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
39527935 TTAAAATATG
*
39527945 TTTTAATTAAACATATTTAA
1 TTTTAATTAAACAAATTTAA
*
39527965 TTTT-ATTAAATAAATTTA
1 TTTTAATTAAACAAATTTA
39527983 TTAATGCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTAATTAAACAAATTTAA
Found at i:39542759 original size:22 final size:20
Alignment explanation
Indices: 39542714--39542766 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
39542704 ATAATTATAT
*
39542714 TTATTTTTTTAAATTAAGAG
1 TTATTTTTTTAAATTAAGAA
*
39542734 TTATTTTTTTAAACTTCATGAA
1 TTATTTTTTTAAA-TT-AAGAA
*
39542756 TTATTTATTTA
1 TTATTTTTTTA
39542767 TTTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
22 13 0.46
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (20 bp):
TTATTTTTTTAAATTAAGAA
Found at i:39558815 original size:39 final size:38
Alignment explanation
Indices: 39558743--39558822 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
39558733 ATTTATTGAA
*
39558743 TTTTTTGTAATTTGAAATATTTTTCTAGTTTTTTTAATT
1 TTTTTTGTAATTTGAAATATTTTTCTAG-TTTTTGAATT
*
39558782 TTTTTTGTAATTTTATAA-ATTTGTTACTA-TTTTTGAATT
1 TTTTTTGTAATTTGA-AATATTT-TT-CTAGTTTTTGAATT
39558821 TT
1 TT
39558823 ATATATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 29 0.81
40 4 0.11
41 3 0.08
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (38 bp):
TTTTTTGTAATTTGAAATATTTTTCTAGTTTTTGAATT
Found at i:39561032 original size:191 final size:193
Alignment explanation
Indices: 39560654--39561038 Score: 675
Period size: 191 Copynumber: 2.0 Consensus size: 193
39560644 TTCAATGCAC
* *
39560654 AAGTTTCCATTTGCGCTGTCCTTATTCAGAAAGACCACCCTAGGGAACCATCTAGATTAAAGACT
1 AAGTTTCCATTTGCGCTGTCCTCATTCAAAAAGACCACCCTAGGGAACCATCTAGATTAAAGACT
39560719 TAAGACACCAGCTAAAACGAATTTGAATGATGTCCGATGAAAATGCTTTATATAATAAAGTGTAT
66 TAAGACACCAGCTAAAACGAATTTGAA-GATGTCCGATGAAAATGCTTTATATAATAAAGTGTAT
39560784 AAAGAGATGGCACCTCATAATACACACCACGTATAGAATACAAAAAGAAATAAACATGTGGTAG
130 AAAGAGATGGCACCTCATAATACACACCACGTATAGAATACAAAAAGAAATAAACATGTGGTAG
*
39560848 AAGTTTCCATTTGCGCTGTCCTCATTCAAAAAGACCACCCTAGGGAACCATCTAGATTGAAGACT
1 AAGTTTCCATTTGCGCTGTCCTCATTCAAAAAGACCACCCTAGGGAACCATCTAGATTAAAGACT
* * *
39560913 TAAGACACCAGCTACAACGAATTTG-A-ATGTCTGATGAAAATGCTTTATTTAATAAAGTGTATA
66 TAAGACACCAGCTAAAACGAATTTGAAGATGTCCGATGAAAATGCTTTATATAATAAAGTGTATA
* *
39560976 AAGAGATGGCACCTGATAATACACACCTCGTATAGAATACAAAAAGAAATAAACATGTGGTAG
131 AAGAGATGGCACCTCATAATACACACCACGTATAGAATACAAAAAGAAATAAACATGTGGTAG
39561039 GATCAGAGTT
Statistics
Matches: 183, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
191 96 0.52
193 1 0.01
194 86 0.47
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (193 bp):
AAGTTTCCATTTGCGCTGTCCTCATTCAAAAAGACCACCCTAGGGAACCATCTAGATTAAAGACT
TAAGACACCAGCTAAAACGAATTTGAAGATGTCCGATGAAAATGCTTTATATAATAAAGTGTATA
AAGAGATGGCACCTCATAATACACACCACGTATAGAATACAAAAAGAAATAAACATGTGGTAG
Found at i:39569183 original size:15 final size:15
Alignment explanation
Indices: 39569165--39569193 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39569155 TTCTTCCTCC
39569165 TCCTCCTCTTCGTCG
1 TCCTCCTCTTCGTCG
39569180 TCCTCCTCTTCGTC
1 TCCTCCTCTTCGTC
39569194 TGCTTCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.48, G:0.10, T:0.41
Consensus pattern (15 bp):
TCCTCCTCTTCGTCG
Found at i:39569742 original size:23 final size:23
Alignment explanation
Indices: 39569712--39569761 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
39569702 AAAATTTGAT
* *
39569712 ATTTTTTTTAATTTGGTACCTAA
1 ATTTTTTTCAATTTAGTACCTAA
*
39569735 ATTTTTTTCAATTTAGTATCTAA
1 ATTTTTTTCAATTTAGTACCTAA
39569758 ATTT
1 ATTT
39569762 GACATTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTTTTTTCAATTTAGTACCTAA
Found at i:39570866 original size:12 final size:12
Alignment explanation
Indices: 39570849--39570873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39570839 GTGCGGAAGG
39570849 AAAAAAATGAAA
1 AAAAAAATGAAA
39570861 AAAAAAATGAAA
1 AAAAAAATGAAA
39570873 A
1 A
39570874 CCCCTTGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:39575176 original size:27 final size:27
Alignment explanation
Indices: 39575146--39575206 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
39575136 AAAACGGGAC
*
39575146 TTTTGGATAC-CGGGGGCAAAATGGTAA
1 TTTTGGACACACGGGGGC-AAATGGTAA
*
39575173 TTTTGGACGCACGGGGGCAAATGGTAA
1 TTTTGGACACACGGGGGCAAATGGTAA
39575200 TGTTTGG
1 T-TTTGG
39575207 TGAAATCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.28
Consensus pattern (27 bp):
TTTTGGACACACGGGGGCAAATGGTAA
Found at i:39575278 original size:59 final size:59
Alignment explanation
Indices: 39575184--39575496 Score: 409
Period size: 59 Copynumber: 5.4 Consensus size: 59
39575174 TTTGGACGCA
* *
39575184 CGGGGGC-AAATGGTAATGTTTGGTGAAATCGGGGTTAAAAATGGAATATTGGAAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
** ** * *
39575242 CGGGGGCAAAATGGTAATTTTTTATGAAATTAGGGTTAATAATGGAATTTTGAAAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
39575301 C-GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
** * * * *
39575359 TAGGGGTAAAATGGTAACTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGAAAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * *
39575418 -TGGGGCTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGGAAGTT
1 CGGGGGC-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
*
39575477 CGGGGG-TAAATGGTAATTTT
1 CGGGGGCAAAATGGTAATTTT
39575497 CGGACAGTCT
Statistics
Matches: 223, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
58 75 0.34
59 144 0.65
60 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (59 bp):
CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:39575291 original size:30 final size:30
Alignment explanation
Indices: 39575249--39575458 Score: 120
Period size: 30 Copynumber: 7.1 Consensus size: 30
39575239 GTTCGGGGGC
*
39575249 AAAATGGTAATTTTTTATGAAATTAGGGTT
1 AAAATGGTAATTTTTGATGAAATTAGGGTT
* *
39575279 AATAATGG-AA-TTTTGA--AAAGTTCGGGGT
1 AA-AATGGTAATTTTTGATGAAA-TTAGGGTT
**
39575307 AAAATGGTAATTTTTGATGAAATCGGGGTT
1 AAAATGGTAATTTTTGATGAAATTAGGGTT
*
39575337 AAAAATGG-AA-TTTTG--GAAAGTTTAGGGGT
1 -AAAATGGTAATTTTTGATGAAA--TTAGGGTT
* * ***
39575366 AAAATGGTAACTTTTGGTGAAACCGGGGTT
1 AAAATGGTAATTTTTGATGAAATTAGGGTT
* *
39575396 AAAAATGG-AA-TTTTGA--AAAGTTTGGGGCT
1 -AAAATGGTAATTTTTGATGAAA--TTAGGGTT
* **
39575425 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTTGATGAAATTAGGGTT
39575455 AAAA
1 AAAA
39575459 ATGAAATTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
27 15 0.11
28 24 0.17
29 35 0.25
30 37 0.26
31 22 0.16
32 7 0.05
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGATGAAATTAGGGTT
Found at i:39575371 original size:117 final size:118
Alignment explanation
Indices: 39575191--39575496 Score: 454
Period size: 117 Copynumber: 2.6 Consensus size: 118
39575181 GCACGGGGGC
* * *
39575191 AAATGGTAATGTTTGGTGAAATCGGGGTTAAAAATGGAATATTGGAAAGTTCGGGGGCAAAATGG
1 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG
* ** *
39575256 TAATTTTTTATGAAATTAGGGTTAATAATGGAATTTTGAAAAGTTCGGGG-TA
66 TAATTTTTGATGAAACCAGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGCTA
* **
39575308 AAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGG
1 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG
* * * *
39575373 TAACTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGAAAAGTTTGGGGCTA
66 TAATTTTTGATGAAACCAGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGCTA
* *
39575426 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGGAAGTTCGGGGGT-AAATGG
1 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG
39575490 TAATTTT
66 TAATTTT
39575497 CGGACAGTCT
Statistics
Matches: 168, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
117 113 0.67
118 55 0.33
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (118 bp):
AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG
TAATTTTTGATGAAACCAGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGCTA
Found at i:39575467 original size:30 final size:30
Alignment explanation
Indices: 39575191--39575468 Score: 142
Period size: 29 Copynumber: 9.4 Consensus size: 30
39575181 GCACGGGGGC
*
39575191 AAATGGTAATGTTTGGTGAAATCGGGGTTAA
1 AAATGG-AATTTTTGGTGAAATCGGGGTTAA
* **
39575222 AAATGGAA-TATT-G-GAAAGTTCGGGG-GCA
1 AAATGGAATTTTTGGTGAAA--TCGGGGTTAA
** **
39575250 AAATGGTAATTTTTTATGAAATTAGGGTTAA
1 AAATGG-AATTTTTGGTGAAATCGGGGTTAA
* *
39575281 TAATGGAA-TTTT-G-AAAAGTTCGGGG-T-A
1 AAATGGAATTTTTGGTGAAA--TCGGGGTTAA
*
39575308 AAATGGTAATTTTTGATGAAATCGGGGTTAA
1 AAATGG-AATTTTTGGTGAAATCGGGGTTAA
*
39575339 AAATGGAA-TTTT-G-GAAAGTTTAGGGG-T-A
1 AAATGGAATTTTTGGTGAAA---TCGGGGTTAA
* *
39575367 AAATGGTAACTTTTGGTGAAACCGGGGTTAA
1 AAATGG-AATTTTTGGTGAAATCGGGGTTAA
* * *
39575398 AAATGGAA-TTTT-G-AAAAGTTTGGGGCT-A
1 AAATGGAATTTTTGGTGAAA--TCGGGGTTAA
39575426 AAATGGTAATTTTTGGTGAAATCGGGGTTAA
1 AAATGG-AATTTTTGGTGAAATCGGGGTTAA
*
39575457 AAATGAAATTTT
1 AAATGGAATTTT
39575469 GGGAAGTTCG
Statistics
Matches: 186, Mismatches: 30, Indels: 63
0.67 0.11 0.23
Matches are distributed among these distances:
27 20 0.11
28 26 0.14
29 50 0.27
30 42 0.23
31 37 0.20
32 11 0.06
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (30 bp):
AAATGGAATTTTTGGTGAAATCGGGGTTAA
Found at i:39575483 original size:30 final size:29
Alignment explanation
Indices: 39575329--39575486 Score: 92
Period size: 29 Copynumber: 5.4 Consensus size: 29
39575319 TTTGATGAAA
* *
39575329 TCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 TCGGGGTTAAAAATGAAATTTTGGGAAG-T
* * *
39575359 TAGGGG-T-AAAATGGTAACTTTTGGTGAA-A
1 TCGGGGTTAAAAAT-G-AAATTTTGG-GAAGT
* * **
39575388 CCGGGGTTAAAAATGGAATTTTGAAAAGT
1 TCGGGGTTAAAAATGAAATTTTGGGAAGT
* * * *
39575417 TTGGGGCT-AAAATGGTAATTTTTGGTGAA-A
1 TCGGGGTTAAAAAT-G-AAATTTTGG-GAAGT
39575447 TCGGGGTTAAAAATGAAATTTTGGGAAGT
1 TCGGGGTTAAAAATGAAATTTTGGGAAGT
*
39575476 TCGGGGGTAAA
1 TCGGGGTTAAA
39575487 TGGTAATTTT
Statistics
Matches: 92, Mismatches: 25, Indels: 23
0.66 0.18 0.16
Matches are distributed among these distances:
28 15 0.16
29 36 0.39
30 27 0.29
31 14 0.15
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (29 bp):
TCGGGGTTAAAAATGAAATTTTGGGAAGT
Found at i:39576486 original size:3 final size:3
Alignment explanation
Indices: 39576473--39576512 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
39576463 TTATAAATAT
* *
39576473 TTA TTA TTTA TTA TTA TTA TAA TTA TTA TTA ATA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39576513 ATAATATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39576511 original size:9 final size:9
Alignment explanation
Indices: 39576462--39576520 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
39576452 AATGATATTA
*
39576462 ATTATAAAT
1 ATTATTAAT
39576471 ATTTATT-AT
1 A-TTATTAAT
*
39576480 -TTATTATT
1 ATTATTAAT
39576488 ATTA-TAATT
1 ATTATTAA-T
39576497 ATTATTAAT
1 ATTATTAAT
39576506 ATTATTAAT
1 ATTATTAAT
*
39576515 AATATT
1 ATTATT
39576521 CAAAGAGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.12
8 3 0.07
9 26 0.63
10 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTATTAAT
Found at i:39577297 original size:6 final size:6
Alignment explanation
Indices: 39577288--39577392 Score: 64
Period size: 6 Copynumber: 18.0 Consensus size: 6
39577278 TTAATATTAT
*
39577288 TTTAAA TTT-AA -TTAAA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
39577332 TCAGTAAG TTTAAA TTTAAGA --TAAA TTTAAAA ATT-AA TTTAAA ATT-AA
1 T--TTAAA TTTAAA TTTAA-A TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
39577380 TTTAAA CTTTAAA
1 TTTAAA -TTTAAA
39577393 AAATCAAAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
4 3 0.04
5 24 0.31
6 34 0.44
7 12 0.16
8 4 0.05
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:39577301 original size:15 final size:15
Alignment explanation
Indices: 39577289--39577330 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
39577279 TAATATTATT
39577289 TTAAATTTAATTAAA
1 TTAAATTTAATTAAA
39577304 TTAAATTTAAATTTAAA
1 TTAAATTT-AA-TTAAA
*
39577321 ATAAATTTAA
1 TTAAATTTAA
39577331 ATCAGTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 4 0.17
17 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTAATTAAA
Found at i:39577315 original size:11 final size:11
Alignment explanation
Indices: 39577289--39577332 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
39577279 TAATATTATT
39577289 TTAAATTT-AA
1 TTAAATTTAAA
39577299 TTAAA-TTAAA
1 TTAAATTTAAA
39577309 TTTAAATTTAAA
1 -TTAAATTTAAA
*
39577321 ATAAATTTAAA
1 TTAAATTTAAA
39577332 T
1 T
39577333 CAGTAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 7 0.24
11 15 0.52
12 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:39577391 original size:12 final size:11
Alignment explanation
Indices: 39577344--39577385 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
39577334 AGTAAGTTTA
* *
39577344 AATTTAAGATA
1 AATTTAAAATT
39577355 AATTTAAAAATT
1 AATTT-AAAATT
39577367 AATTTAAAATT
1 AATTTAAAATT
39577378 AATTTAAA
1 AATTTAAA
39577386 CTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:39578547 original size:21 final size:21
Alignment explanation
Indices: 39578516--39578568 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
39578506 ATGCCCTATT
*
39578516 AAATATAAAAACATAAACTTAA
1 AAAT-TAAAAACATAAAATTAA
*
39578538 AAATTAAAAACATAAAATTCA
1 AAATTAAAAACATAAAATTAA
*
39578559 CAATTAAAAA
1 AAATTAAAAA
39578569 TTAAATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATTAAAAACATAAAATTAA
Found at i:39581964 original size:21 final size:21
Alignment explanation
Indices: 39581938--39581992 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
39581928 CATCCATACA
39581938 TTTTTTTATCATTTT-TTAAT
1 TTTTTTTATCATTTTATTAAT
*
39581958 TTTTTTTCTCATTTTATTAAT
1 TTTTTTTATCATTTTATTAAT
**
39581979 TACTTTTA-CATTTT
1 TTTTTTTATCATTTT
39581993 TCTTAGGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTTATCATTTTATTAAT
Found at i:39585498 original size:31 final size:31
Alignment explanation
Indices: 39585460--39585518 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
39585450 TAATTTCTTC
*
39585460 CTAACCATATCATCTTATTTCACATTTTATA
1 CTAACCATATCATCTTACTTCACATTTTATA
39585491 CTAACCATATCATCTTACTTCACATTTT
1 CTAACCATATCATCTTACTTCACATTTT
39585519 TATGGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (31 bp):
CTAACCATATCATCTTACTTCACATTTTATA
Found at i:39588331 original size:82 final size:80
Alignment explanation
Indices: 39588232--39588397 Score: 260
Period size: 82 Copynumber: 2.0 Consensus size: 80
39588222 AGAAGAAACT
*
39588232 GATTCTTCTGAAATATCGGCCTATATTGAAGATTTGAAGAGATTAAGTAAGTTTTCAGAACTGTA
1 GATTCTTCTGAAATATCGGCCTATATTGAAGATTTGAAGAGATTAAGT--GTTTTCAGAACTATA
39588297 CTTTATGCATGTCAACA
64 CTTTATGCATGTCAACA
* *
39588314 GATTCTTCTGAAATATCGGCCTATATTGAAGATTTGAAGAGATTAAGTTTTTTGAGAACTATACT
1 GATTCTTCTGAAATATCGGCCTATATTGAAGATTTGAAGAGATTAAGTGTTTTCAGAACTATACT
* * *
39588379 TTTTGCATTTGAACA
66 TTATGCATGTCAACA
39588394 GATT
1 GATT
39588398 TAAAAAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 30 0.38
82 48 0.62
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (80 bp):
GATTCTTCTGAAATATCGGCCTATATTGAAGATTTGAAGAGATTAAGTGTTTTCAGAACTATACT
TTATGCATGTCAACA
Found at i:39589390 original size:66 final size:65
Alignment explanation
Indices: 39589305--39589435 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 65
39589295 TAACAACGGA
* * * *
39589305 TTATGTCTTCAGCTCTTTTTAGATTAATTAATGATGTCTTACTCTCAAGTCTTAAAGTTTGCATT
1 TTATGTCTCCAGCTCTTTTTAGATCAATTAATGATGTCTTACACT-AAGTCTTAAAGTCTGCATT
39589370 C
65 C
* * *
39589371 TTATGTCTCCTGCTCTTTTTAGATCAATTAGTTATGTCTTACACTAAGTCTTAAAGTCTGCATTC
1 TTATGTCTCCAGCTCTTTTTAGATCAATTAATGATGTCTTACACTAAGTCTTAAAGTCTGCATTC
39589436 CTTCATTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
65 19 0.33
66 39 0.67
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (65 bp):
TTATGTCTCCAGCTCTTTTTAGATCAATTAATGATGTCTTACACTAAGTCTTAAAGTCTGCATTC
Found at i:39589486 original size:21 final size:21
Alignment explanation
Indices: 39589461--39589507 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39589451 TGGAGTTTGA
*
39589461 GGTTTGAGGGTTGAAGG-TTAG
1 GGTTTGA-GATTGAAGGTTTAG
*
39589482 GGTTTGAGATTTAAGGTTTAG
1 GGTTTGAGATTGAAGGTTTAG
39589503 GGTTT
1 GGTTT
39589508 AAAGGTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
GGTTTGAGATTGAAGGTTTAG
Found at i:39589499 original size:35 final size:35
Alignment explanation
Indices: 39589460--39589542 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
39589450 TTGGAGTTTG
* *
39589460 AGGTTTGAGGG-TTGAAGGTTAGGGTTTGAGATTTA
1 AGGTTT-AGGGTTTAAAGGTTAGAGTTTGAGATTTA
* *
39589495 AGGTTTAGGGTTTAAAGGTTAGAGTTTGGGGTTTA
1 AGGTTTAGGGTTTAAAGGTTAGAGTTTGAGATTTA
* *
39589530 AGGGTTAGAGTTT
1 AGGTTTAGGGTTT
39589543 GGGGTTGGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 4 0.10
35 37 0.90
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (35 bp):
AGGTTTAGGGTTTAAAGGTTAGAGTTTGAGATTTA
Found at i:39589521 original size:21 final size:21
Alignment explanation
Indices: 39589497--39589548 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
39589487 GAGATTTAAG
*
39589497 GTTTAGGGTTTAAAGGTTAGA
1 GTTTGGGGTTTAAAGGTTAGA
*
39589518 GTTTGGGGTTTAAGGGTTAGA
1 GTTTGGGGTTTAAAGGTTAGA
39589539 GTTTGGGGTT
1 GTTTGGGGTT
39589549 GGGGTTGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
GTTTGGGGTTTAAAGGTTAGA
Found at i:39592010 original size:17 final size:16
Alignment explanation
Indices: 39591990--39592021 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
39591980 AATTTTGTGC
39591990 AAATTTAAATTTAAAAT
1 AAATTT-AATTTAAAAT
39592007 AAATTTAATTTAAAA
1 AAATTTAATTTAAAA
39592022 CCAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Found at i:39592027 original size:17 final size:16
Alignment explanation
Indices: 39591989--39592030 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
39591979 AAATTTTGTG
39591989 CAAATTTAAATTTAAAA
1 CAAATTT-AATTTAAAA
*
39592006 TAAATTTAATTTAAAA
1 CAAATTTAATTTAAAA
39592022 CCAAATTTA
1 -CAAATTTA
39592031 TCTTATTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (16 bp):
CAAATTTAATTTAAAA
Found at i:39592264 original size:21 final size:21
Alignment explanation
Indices: 39592224--39592266 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39592214 TAATTGCTTC
**
39592224 ACTGTTAACTCAAAGTTATCT
1 ACTGTTAACTCAAAACTATCT
39592245 ACTGTTAACTCAAAACTATCT
1 ACTGTTAACTCAAAACTATCT
39592266 A
1 A
39592267 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (21 bp):
ACTGTTAACTCAAAACTATCT
Found at i:39594033 original size:24 final size:24
Alignment explanation
Indices: 39593979--39594033 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
39593969 TGAATTTTAA
*
39593979 TATTTATATTTTTTAAATCCATCC
1 TATTTTTATTTTTTAAATCCATCC
* *
39594003 T-TATTTATTTTTTAAATTCCAT-G
1 TATTTTTATTTTTTAAA-TCCATCC
39594026 TATTTTTA
1 TATTTTTA
39594034 AAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTTTTATTTTTTAAATCCATCC
Found at i:39595757 original size:14 final size:14
Alignment explanation
Indices: 39595718--39595757 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
39595708 TTTGAAAATT
39595718 TGAAA-TATAAAGA
1 TGAAAGTATAAAGA
39595731 TGAAAGTTATAAAGA
1 TGAAAG-TATAAAGA
39595746 TGAAAGTATAAA
1 TGAAAGTATAAA
39595758 CTTAGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.20
14 6 0.24
15 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.25
Consensus pattern (14 bp):
TGAAAGTATAAAGA
Found at i:39596620 original size:126 final size:126
Alignment explanation
Indices: 39596482--39596724 Score: 432
Period size: 126 Copynumber: 1.9 Consensus size: 126
39596472 AACTAAGTTC
* * *
39596482 ATTTCCTAAGAGAGATGACCTTGAAGATGATAGTTGGAAAAGATGTGAAAGTTTGAAATTTTGCA
1 ATTTCCTAAGAGAAATGACCTTGAAGATGATAGTTGGAAAAGATGCGAAAGTTTGAAATTTTACA
*
39596547 AAAGGAAGATTATGCGCTTTTTATGCGTAGTATTTATCGTATGATTGATAAATTTTTTTTA
66 AAAGGAAGATTATGCGCTTTCTATGCGTAGTATTTATCGTATGATTGATAAATTTTTTTTA
* *
39596608 ATTTCCTAAGAGAAATGAGCTTGAAGATGATAGTTGGAAAAGATGCGAAAGTTTGAAATTTTACT
1 ATTTCCTAAGAGAAATGACCTTGAAGATGATAGTTGGAAAAGATGCGAAAGTTTGAAATTTTACA
39596673 AAAGGAAGATTATGCGCTTTCTATGCGTAGTATTTATCGTATGATTGATAAA
66 AAAGGAAGATTATGCGCTTTCTATGCGTAGTATTTATCGTATGATTGATAAA
39596725 AAAATTTTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.36
Consensus pattern (126 bp):
ATTTCCTAAGAGAAATGACCTTGAAGATGATAGTTGGAAAAGATGCGAAAGTTTGAAATTTTACA
AAAGGAAGATTATGCGCTTTCTATGCGTAGTATTTATCGTATGATTGATAAATTTTTTTTA
Found at i:39597997 original size:170 final size:171
Alignment explanation
Indices: 39597710--39598051 Score: 569
Period size: 170 Copynumber: 2.0 Consensus size: 171
39597700 TTTTAACAAA
*
39597710 ATAAAACTCATACATTTATAAGGAATAAACTTAAAACAGGAACATTAAAAGCTGCTTCCGTGAAA
1 ATAAAACTCATACATTTATAAGGAATAAACTTAAAACAAGAACATTAAAAGCTGCTTCCGTGAAA
* * *
39597775 TTATTATTTATTATATTCATTTTTGGGCAAGTGGACTTTAGTATGGTATTTAAATGATTTATTTT
66 TTAATATTTATTATATTCATTTTTGGGCAAGTGAACTTTAGTATGATATTTAAATGATTTATTTT
*
39597840 GAATTATTTATGA-TTTTTTTTTTGCAAAATGTTTTGCAAT
131 AAATTATTTATGATTTTTTTTTTTGCAAAATGTTTTGCAAT
* * *
39597880 ATAAAACTCATGCATTTATAAGGGATAAACTTAAAACAAGAATATTAAAAGCTGCTTCCGTGAAA
1 ATAAAACTCATACATTTATAAGGAATAAACTTAAAACAAGAACATTAAAAGCTGCTTCCGTGAAA
**
39597945 TTAATATTTATTATATTCATTTTTGGGCACTTGAACTTTAGTATGATATTTAAATGATTTATTTT
66 TTAATATTTATTATATTCATTTTTGGGCAAGTGAACTTTAGTATGATATTTAAATGATTTATTTT
*
39598010 AAATTATTTATTATTTTTTTTTTTTGCAAAATGTTTTGCAAT
131 AAATTATTTATGA-TTTTTTTTTTTGCAAAATGTTTTGCAAT
39598052 CGATCTAATT
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
170 132 0.83
172 27 0.17
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (171 bp):
ATAAAACTCATACATTTATAAGGAATAAACTTAAAACAAGAACATTAAAAGCTGCTTCCGTGAAA
TTAATATTTATTATATTCATTTTTGGGCAAGTGAACTTTAGTATGATATTTAAATGATTTATTTT
AAATTATTTATGATTTTTTTTTTTGCAAAATGTTTTGCAAT
Found at i:39601258 original size:116 final size:115
Alignment explanation
Indices: 39600991--39601267 Score: 385
Period size: 115 Copynumber: 2.4 Consensus size: 115
39600981 ATTAACAACG
* * * *
39600991 CAATAATTAAAATAAAATTTTGAAGTCATGTCGGAGTAATTCACATAAAAGTATTAAAAAAATAT
1 CAATAATTGAAATAAAATTTTGAAGTCATGTCGGATTAATTCATAAAAAAGTATTAAAAAAATAT
* * *
39601056 GTAGAAAATAAATAATAAAATGATAATTTTAATTAAATAAAAAAGTAACA
66 GTAGAAAATAAATAATAAAATGATAACTTAAATTAAATAAAAAAATAACA
* * **
39601106 CAATAATTGAAATAAAATTTTAAATTCATGTCGGATTAATTCATAAAAAAGTATTCGCAAAAATA
1 CAATAATTGAAATAAAATTTTGAAGTCATGTCGGATTAATTCATAAAAAAGTATT-AAAAAAATA
*
39601171 TGTAG-AAATAAATAATAAAATGGTAACTTAAATTAAATAAAAAAAATAACA
65 TGTAGAAAATAAATAATAAAATGATAACTTAAATTAAAT-AAAAAAATAACA
* * * *
39601222 CAATAATTGAAATAAAATTTTGTAGTCATATGGGATTAACTCATAA
1 CAATAATTGAAATAAAATTTTGAAGTCATGTCGGATTAATTCATAA
39601268 GAAGTTAAAT
Statistics
Matches: 142, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
115 79 0.56
116 63 0.44
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.30
Consensus pattern (115 bp):
CAATAATTGAAATAAAATTTTGAAGTCATGTCGGATTAATTCATAAAAAAGTATTAAAAAAATAT
GTAGAAAATAAATAATAAAATGATAACTTAAATTAAATAAAAAAATAACA
Found at i:39601517 original size:21 final size:21
Alignment explanation
Indices: 39601474--39601666 Score: 83
Period size: 21 Copynumber: 9.0 Consensus size: 21
39601464 TTGAAGGTAG
* *
39601474 GGGTTTGGGGCTC--GGTTTA
1 GGGTTTGGGGTTCGGGGTTTC
39601493 GGGTTTGGGGTTCGGGGTTTC
1 GGGTTTGGGGTTCGGGGTTTC
* *
39601514 GGGTTTTGGGTCTCGGGTCTCGAGTCTC
1 GGGTTTGGGGT-TC-GG----G-GTTTC
* * *
39601542 GGGTCTCGGGTCTC-GGGTCTC
1 GGGTTTGGGGT-TCGGGGTTTC
* * *
39601563 GGGTCTCGGG-TCTGGGGTCTC
1 GGGTTTGGGGTTC-GGGGTTTC
* * *
39601584 GGGTCTGGGG-TCTGGGGTCTG
1 GGGTTTGGGGTTC-GGGGTTTC
* *
39601605 GGGTTTGGGGTTTGGGGTTTG
1 GGGTTTGGGGTTCGGGGTTTC
* *
39601626 GGGTTTGGGGTT-AGGGTTTA
1 GGGTTTGGGGTTCGGGGTTTC
*
39601646 GGGTTTTAGGGTTCGGGGTTT
1 GGG-TTTGGGGTTCGGGGTTT
39601667 TAGGTTTTTA
Statistics
Matches: 145, Mismatches: 15, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.10
20 9 0.06
21 92 0.63
22 10 0.07
23 2 0.01
26 1 0.01
27 1 0.01
28 16 0.11
ACGTcount: A:0.03, C:0.13, G:0.49, T:0.36
Consensus pattern (21 bp):
GGGTTTGGGGTTCGGGGTTTC
Found at i:39601524 original size:14 final size:14
Alignment explanation
Indices: 39601506--39601636 Score: 136
Period size: 14 Copynumber: 9.4 Consensus size: 14
39601496 TTTGGGGTTC
* *
39601506 GGGGTTTCGGGTTT
1 GGGGTCTCGGGTCT
*
39601520 TGGGTCTCGGGTCT
1 GGGGTCTCGGGTCT
* *
39601534 CGAGTCTCGGGTCT
1 GGGGTCTCGGGTCT
*
39601548 CGGGTCTCGGGTCT
1 GGGGTCTCGGGTCT
*
39601562 CGGGTCTCGGGTCT
1 GGGGTCTCGGGTCT
39601576 GGGGTCTCGGGTCT
1 GGGGTCTCGGGTCT
*
39601590 GGGGTCTGGGGTCT
1 GGGGTCTCGGGTCT
* * *
39601604 GGGGTTTGGGGTTT
1 GGGGTCTCGGGTCT
* * *
39601618 GGGGTTTGGGGTTT
1 GGGGTCTCGGGTCT
39601632 GGGGT
1 GGGGT
39601637 TAGGGTTTAG
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 107 1.00
ACGTcount: A:0.01, C:0.16, G:0.50, T:0.34
Consensus pattern (14 bp):
GGGGTCTCGGGTCT
Found at i:39601531 original size:7 final size:7
Alignment explanation
Indices: 39601507--39601608 Score: 132
Period size: 7 Copynumber: 14.6 Consensus size: 7
39601497 TTGGGGTTCG
*
39601507 GGGTTTC
1 GGGTCTC
* *
39601514 GGGTTTT
1 GGGTCTC
39601521 GGGTCTC
1 GGGTCTC
39601528 GGGTCTC
1 GGGTCTC
*
39601535 GAGTCTC
1 GGGTCTC
39601542 GGGTCTC
1 GGGTCTC
39601549 GGGTCTC
1 GGGTCTC
39601556 GGGTCTC
1 GGGTCTC
39601563 GGGTCTC
1 GGGTCTC
*
39601570 GGGTCTG
1 GGGTCTC
39601577 GGGTCTC
1 GGGTCTC
*
39601584 GGGTCTG
1 GGGTCTC
*
39601591 GGGTCTG
1 GGGTCTC
*
39601598 GGGTCTG
1 GGGTCTC
39601605 GGGT
1 GGGT
39601609 TTGGGGTTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 87 1.00
ACGTcount: A:0.01, C:0.21, G:0.47, T:0.31
Consensus pattern (7 bp):
GGGTCTC
Found at i:39601613 original size:7 final size:7
Alignment explanation
Indices: 39601605--39601727 Score: 65
Period size: 7 Copynumber: 17.7 Consensus size: 7
39601595 CTGGGGTCTG
*
39601605 GGGTTTG
1 GGGTTTA
*
39601612 GGGTTTG
1 GGGTTTA
*
39601619 GGGTTTG
1 GGGTTTA
39601626 GGGTTT-
1 GGGTTTA
*
39601632 GGGGTTA
1 GGGTTTA
39601639 GGGTTTA
1 GGGTTTA
39601646 GGGTTTTA
1 GGG-TTTA
**
39601654 GGGTTCG
1 GGGTTTA
39601661 GGGTTTTA
1 GGG-TTTA
*
39601669 GGTTTTTA
1 GG-GTTTA
*
39601677 -GG-TTG
1 GGGTTTA
* *
39601682 GGGGTTG
1 GGGTTTA
39601689 GGGTTTA
1 GGGTTTA
*
39601696 GGGTTTG
1 GGGTTTA
*
39601703 GGGTTTG
1 GGGTTTA
*
39601710 GGGGTT-
1 GGGTTTA
*
39601716 GGGTCTA
1 GGGTTTA
39601723 GGGTT
1 GGGTT
39601728 GGGGCTCGGG
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
5 2 0.02
6 11 0.12
7 65 0.70
8 15 0.16
ACGTcount: A:0.06, C:0.02, G:0.51, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:39601637 original size:14 final size:14
Alignment explanation
Indices: 39601570--39602670 Score: 801
Period size: 14 Copynumber: 78.9 Consensus size: 14
39601560 CTCGGGTCTC
* * *
39601570 GGGTCTGGGGTCTC
1 GGGTTTGGGGTTTA
* * *
39601584 GGGTCTGGGGTCTG
1 GGGTTTGGGGTTTA
* *
39601598 GGGTCTGGGGTTTG
1 GGGTTTGGGGTTTA
*
39601612 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTA
39601626 GGGTTTGGGG-TTA
1 GGGTTTGGGGTTTA
*
39601639 GGGTTTAGGGTTTTA
1 GGGTTT-GGGGTTTA
*
39601654 GGGTTCGGGGTTTTA
1 GGGTTTGGGG-TTTA
* ** *
39601669 GGTTTTTAGG-TTG
1 GGGTTTGGGGTTTA
*
39601682 GGGGTTGGGGTTTA
1 GGGTTTGGGGTTTA
*
39601696 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTA
* *
39601710 GGGGTT-GGGTCTA
1 GGGTTTGGGGTTTA
* **
39601723 GGG-TTGGGGCTCG
1 GGGTTTGGGGTTTA
* * * **
39601736 GGGCTCGGGGCTCG
1 GGGTTTGGGGTTTA
* * * **
39601750 GGGCTCGGGGCTCG
1 GGGTTTGGGGTTTA
* * * **
39601764 GGGCTCGGGGCTCG
1 GGGTTTGGGGTTTA
*
39601778 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39601792 GGGTTTAGGGTTTTA
1 GGGTTT-GGGGTTTA
* * *
39601807 GGGTCTGGGGTCTG
1 GGGTTTGGGGTTTA
* * **
39601821 GGGTCTGGGGCTCG
1 GGGTTTGGGGTTTA
* * * *
39601835 GGGCTCGGGG-CTC
1 GGGTTTGGGGTTTA
* * * *
39601848 GGTGCTCGGGG-CTC
1 GG-GTTTGGGGTTTA
* * *
39601862 GGGTTTAGGGTCTG
1 GGGTTTGGGGTTTA
* * *
39601876 GGGTCTGGGGTCTG
1 GGGTTTGGGGTTTA
*
39601890 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTA
*
39601904 GGGTTTGGGG-TTC
1 GGGTTTGGGGTTTA
* *
39601917 GGGGTTCGGGTTTA
1 GGGTTTGGGGTTTA
* *
39601931 GGGTTTAGGGTTTG
1 GGGTTTGGGGTTTA
*
39601945 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTA
*
39601959 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTA
*
39601973 GGGTTTGGGGTTTT
1 GGGTTTGGGGTTTA
* *
39601987 GGGTTTCGGGTTTCG
1 GGGTTTGGGGTTT-A
* **
39602002 GGGTTCGGGGTTCG
1 GGGTTTGGGGTTTA
* **
39602016 GGGTTCGGGGTTCG
1 GGGTTTGGGGTTTA
* **
39602030 GGGTTCGGGGTTCG
1 GGGTTTGGGGTTTA
* **
39602044 GGGTTCGGGGTTCG
1 GGGTTTGGGGTTTA
* *
39602058 GGGTTTCGGGTTTC
1 GGGTTTGGGGTTTA
* *
39602072 GGGTTTCGGGTTTC
1 GGGTTTGGGGTTTA
* *
39602086 GGGTTTCGGGTTTC
1 GGGTTTGGGGTTTA
* *
39602100 GGGTTTCGGGTTTC
1 GGGTTTGGGGTTTA
* *
39602114 GGGTTTCGGGTTTG
1 GGGTTTGGGGTTTA
* *
39602128 GGGTTTCGGG-TTC
1 GGGTTTGGGGTTTA
*
39602141 GGGCTTGGGGTTTA
1 GGGTTTGGGGTTTA
*
39602155 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602169 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602183 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602197 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602211 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602225 GGGTTTAGGGTTTTA
1 GGGTTT-GGGGTTTA
*
39602240 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602254 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602268 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602282 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602296 -GGTTT-AGGTTTA
1 GGGTTTGGGGTTTA
*
39602308 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602322 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602336 GGG-TTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602349 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602363 GGGTTT-TGGTTTA
1 GGGTTTGGGGTTTA
*
39602376 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602390 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602404 GGGTTTAGGG-TTA
1 GGGTTTGGGGTTTA
*
39602417 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602431 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602445 GGGTTT-AGGTTTA
1 GGGTTTGGGGTTTA
39602458 GGGTTTAGGAGGGTTTA
1 GGGTTT--G-GGGTTTA
*
39602475 GGGTTT-AGGTTTA
1 GGGTTTGGGGTTTA
*
39602488 GGGTTTAGGGTTTTA
1 GGGTTT-GGGGTTTA
*
39602503 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602517 GGGTTTAGGGTTTTA
1 GGGTTT-GGGGTTTA
*
39602532 GGGTTTTAGGGTTTA
1 GGG-TTTGGGGTTTA
*
39602547 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602561 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602575 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602589 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602603 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602617 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602631 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602645 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTA
*
39602659 GGGTTTAGGGTT
1 GGGTTTGGGGTT
Statistics
Matches: 961, Mismatches: 100, Indels: 52
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.01
13 129 0.13
14 729 0.76
15 80 0.08
16 3 0.00
17 12 0.01
ACGTcount: A:0.08, C:0.06, G:0.47, T:0.39
Consensus pattern (14 bp):
GGGTTTGGGGTTTA
Done.