Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 26 of 378
Found at i:6374166 original size:53 final size:52
Alignment explanation
Indices: 6374108--6374395 Score: 213
Period size: 53 Copynumber: 5.5 Consensus size: 52
6374098 AAAAAAATTA
6374108 GTGCTGGCCTGTCAATGGCCGGCACCAGTATGAAAAAAAAATCAATTTTTTTT
1 GTGCTGGCCTGTCAATGGCCGGCACCAGTATG-AAAAAAAATCAATTTTTTTT
** * * **
6374161 GTGCTGGCCTGTCAATGGTTGGTACCAAGTACGGCAAAAAATCAATTTTTTTT
1 GTGCTGGCCTGTCAATGGCCGGCACC-AGTATGAAAAAAAATCAATTTTTTTT
* * *
6374214 GTGCTGGCCTGTCAATGGCCGTCACTAGATATG-----AGAT---TTTTTTTT
1 GTGCTGGCCTGTCAATGGCCGGCACCAG-TATGAAAAAAAATCAATTTTTTTT
* * * * * *
6374259 -T-TTTGCAT-TCTAATGGCCAGCAACAGT-TCGAAAAAAAAAAATTCAAATTTTTTTG
1 GTGCTGGCCTGTC-AATGGCCGGCACCAGTAT-G---AAAAAAAA-TC-AATTTTTTTT
* *
6374314 GTGCTGGCCTGTCAATGGCCGGCACCAGGTACGAAAAAAATTCAAATTTTTTTT
1 GTGCTGGCCTGTCAATGGCCGGCACCA-GTATGAAAAAAAATC-AATTTTTTTT
* *
6374368 ATGCTGGCCTGTCAATGGCCGGCTCCAG
1 GTGCTGGCCTGTCAATGGCCGGCACCAG
6374396 GTACGAGATT
Statistics
Matches: 181, Mismatches: 32, Indels: 44
0.70 0.12 0.17
Matches are distributed among these distances:
41 1 0.01
42 4 0.02
43 15 0.08
44 1 0.01
45 8 0.04
48 3 0.02
50 2 0.01
51 1 0.01
52 2 0.01
53 66 0.36
54 42 0.23
55 14 0.08
56 1 0.01
57 16 0.09
58 5 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (52 bp):
GTGCTGGCCTGTCAATGGCCGGCACCAGTATGAAAAAAAATCAATTTTTTTT
Found at i:6374318 original size:153 final size:153
Alignment explanation
Indices: 6374121--6374498 Score: 430
Period size: 152 Copynumber: 2.5 Consensus size: 153
6374111 CTGGCCTGTC
* * * ** *
6374121 AATGGCCGGCACCAGTATGAAAAAAAAA-TC-AATTTTTTTTGTGCTGGCCTGTCAATGGTTGGT
1 AATGGCCAGCAACAGTACGAAAAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGC
* * * * *
6374184 ACCAAGTACGGCAAAAAA-TC-AATTTTTTTTGTGCTGGCCTGTCAATGGCCGTCACTAGATATG
66 ACCAAGTAC-GAAAAAAATTCAAATTTTTTTTATGCTGGCCTGTCAATGGCCGGCACCAGATACG
*
6374247 AGATTTT-TTTTTTTTTGCATTCT
130 AGATTTTAATTTTTTTTGCATTCT
* *
6374270 AATGGCCAGCAACAGTTCGAAAAAAAAAAATTCAAATTTTTTTGGTGCTGGCCTGTCAATGGCCG
1 AATGGCCAGCAACAGTACG--AAAAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCG
* * *
6374335 GCACCAGGTACGAAAAAAATTCAAATTTTTTTTATGCTGGCCTGTCAATGGCCGGCTCCAGGTAC
64 GCACCAAGTACGAAAAAAATTCAAATTTTTTTTATGCTGGCCTGTCAATGGCCGGCACCAGATAC
*
6374400 GAGATTTTAAATTTTTTTTGCCTTCT
129 GAGATTTT-AATTTTTTTTGCATTCT
* * * * * * *
6374426 AATTGTCGGCACCAGTACG--AAAAAAATTCAATTTTTTTTTGTGCTAGCCTATCAATGGCC-GC
1 AATGGCCAGCAACAGTACGAAAAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGC
*
6374488 ACCAGGTACGA
66 ACCAAGTACGA
6374499 GTATTTAAAA
Statistics
Matches: 194, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
149 15 0.08
151 22 0.11
152 46 0.24
153 39 0.20
154 44 0.23
156 28 0.14
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (153 bp):
AATGGCCAGCAACAGTACGAAAAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGC
ACCAAGTACGAAAAAAATTCAAATTTTTTTTATGCTGGCCTGTCAATGGCCGGCACCAGATACGA
GATTTTAATTTTTTTTGCATTCT
Found at i:6374355 original size:54 final size:54
Alignment explanation
Indices: 6374293--6374498 Score: 220
Period size: 54 Copynumber: 4.0 Consensus size: 54
6374283 AGTTCGAAAA
*
6374293 AAAAAAATTCAAATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGGTACG
1 AAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGCACCAGGTACG
* *
6374347 AAAAAAATTCAAATTTTTTTTATGCTGGCCTGTCAATGGCCGGCTCCAGGTACG
1 AAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGCACCAGGTACG
* * * * *
6374401 ---AGATTTTAAA--TTTTTT-T--T-GCCT-TCTAATTGTCGGCACCA-GTACG
1 AAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTC-AATGGCCGGCACCAGGTACG
* * *
6374445 AAAAAAATTCAATTTTTTTTTGTGCTAGCCTATCAATGGCC-GCACCAGGTACG
1 AAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGCACCAGGTACG
6374498 A
1 A
6374499 GTATTTAAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
44 7 0.06
45 15 0.12
46 1 0.01
47 6 0.05
48 1 0.01
49 12 0.10
50 1 0.01
51 7 0.06
52 7 0.06
53 15 0.12
54 53 0.42
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
AAAAAAATTCAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGCACCAGGTACG
Found at i:6375180 original size:13 final size:14
Alignment explanation
Indices: 6375162--6375191 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6375152 ATTTAGCTCA
6375162 TTTATATTAAAT-T
1 TTTATATTAAATGT
6375175 TTTATATTAAATGT
1 TTTATATTAAATGT
6375189 TTT
1 TTT
6375192 TATGTTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTATATTAAATGT
Found at i:6376245 original size:16 final size:16
Alignment explanation
Indices: 6376224--6376256 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6376214 TAATATCACA
6376224 TATTTAGAAAAGAGAG
1 TATTTAGAAAAGAGAG
6376240 TATTTAGAAAAGAGAG
1 TATTTAGAAAAGAGAG
6376256 T
1 T
6376257 CATATCCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (16 bp):
TATTTAGAAAAGAGAG
Found at i:6388825 original size:31 final size:31
Alignment explanation
Indices: 6388790--6388850 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
6388780 CTTGTCATTT
6388790 GTAGCTGAAGCTACCACTATTCACTGATCAG
1 GTAGCTGAAGCTACCACTATTCACTGATCAG
* * *
6388821 GTAGCTGGAGCTACCATTTTTCACTGATCA
1 GTAGCTGAAGCTACCACTATTCACTGATCA
6388851 AATTACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (31 bp):
GTAGCTGAAGCTACCACTATTCACTGATCAG
Found at i:6389000 original size:35 final size:35
Alignment explanation
Indices: 6388944--6389257 Score: 292
Period size: 35 Copynumber: 9.0 Consensus size: 35
6388934 TTTCCTCATT
*
6388944 AAAATACCATACCTACGTTTCACAACTCGGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
* * ** *
6388979 AAAACACCATACCTACTTTTCA-TGCTCGGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
* * ** *
6389013 ACAATACCATTCCTATATTTCATAACTCAGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
*** * * * *
6389048 GCGATGCCATACCTACGTATCATAGCTCAGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
** ** * *
6389083 ACGACGCCATACCTACGTTTCATAGCTC-GATATGG
1 AAAATACCATACCTACGTTTCACAACTCAG-TATGG
*
6389118 -AAATACCATACCTACGTTTCACAGCTCAGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
** *
6389152 TTAATACCATACCTATGTTTCACAACTCAGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
** *
6389187 CTAATACCATACCTACGTTTCACAACTCGGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
** *
6389222 TTAATACCATACCTACATTTCACAACTCAGTATGG
1 AAAATACCATACCTACGTTTCACAACTCAGTATGG
6389257 A
1 A
6389258 CCAACCACGG
Statistics
Matches: 237, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
34 55 0.23
35 182 0.77
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (35 bp):
AAAATACCATACCTACGTTTCACAACTCAGTATGG
Found at i:6389138 original size:104 final size:104
Alignment explanation
Indices: 6388946--6389256 Score: 374
Period size: 104 Copynumber: 3.0 Consensus size: 104
6388936 TCCTCATTAA
* * *
6388946 AATACCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCAT-GCTCGGTA
1 AATACCATACCTACGTTTCACAACTCAGTATGGACAACACCATACCTACGTTTCATAGCTCGGTA
* * *
6389010 TGGACAATACCATTCCTATATTTCATAACTCAGTATGGGC
66 TGGA-AATACCATACCTACATTTCACAACTCAGTATGGGC
* * * * * * * *
6389050 GATGCCATACCTACGTATCATAGCTCAGTATGGACGACGCCATACCTACGTTTCATAGCTCGATA
1 AATACCATACCTACGTTTCACAACTCAGTATGGACAACACCATACCTACGTTTCATAGCTCGGTA
* * **
6389115 TGGAAATACCATACCTACGTTTCACAGCTCAGTATGGTT
66 TGGAAATACCATACCTACATTTCACAACTCAGTATGGGC
* * * *
6389154 AATACCATACCTATGTTTCACAACTCAGTATGG-CTAATACCATACCTACGTTTCACAACTCGGT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAC-AACACCATACCTACGTTTCATAGCTCGGT
*
6389218 ATGGTTAATACCATACCTACATTTCACAACTCAGTATGG
65 ATGG-AAATACCATACCTACATTTCACAACTCAGTATGG
6389257 ACCAACCACG
Statistics
Matches: 171, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
103 1 0.01
104 128 0.75
105 42 0.25
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (104 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGACAACACCATACCTACGTTTCATAGCTCGGTA
TGGAAATACCATACCTACATTTCACAACTCAGTATGGGC
Found at i:6389167 original size:139 final size:139
Alignment explanation
Indices: 6388950--6389257 Score: 352
Period size: 139 Copynumber: 2.2 Consensus size: 139
6388940 CATTAAAATA
* * * *
6388950 CCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCATGCTCGGTATGGAC
1 CCATACCTACGTTTCACAACTCGATATGGAAAACACCATACCTACGTTTCAAGCTCAGTATGGAC
* * * *
6389015 AATACCATTCCTATATTTCATAACTCAGTATGGGC-GATGCCATACCTACGTATCATAGCTCAGT
66 AATACCATACCTATATTTCACAACTCAGTAT-GGCTAATACCATACCTACGTATCATAGCTCAGT
6389079 ATGGACGACG
130 ATGGACGACG
* * * *
6389089 CCATACCTACGTTTCATAGCTCGATATGG-AAATACCATACCTACGTTTCACAGCTCAGTATGGT
1 CCATACCTACGTTTCACAACTCGATATGGAAAACACCATACCTACGTTTCA-AGCTCAGTATGGA
* * * * * *
6389153 TAATACCATACCTATGTTTCACAACTCAGTATGGCTAATACCATACCTACGTTTCACAACTCGGT
65 CAATACCATACCTATATTTCACAACTCAGTATGGCTAATACCATACCTACGTATCATAGCTCAGT
*** **
6389218 ATGGTTAATA
130 ATGGACGACG
*
6389228 CCATACCTACATTTCACAACTC-AGTATGGA
1 CCATACCTACGTTTCACAACTCGA-TATGGA
6389258 CCAACCACGG
Statistics
Matches: 139, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
138 23 0.17
139 116 0.83
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (139 bp):
CCATACCTACGTTTCACAACTCGATATGGAAAACACCATACCTACGTTTCAAGCTCAGTATGGAC
AATACCATACCTATATTTCACAACTCAGTATGGCTAATACCATACCTACGTATCATAGCTCAGTA
TGGACGACG
Found at i:6393669 original size:2 final size:2
Alignment explanation
Indices: 6393662--6393696 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6393652 ATATTCTATT
6393662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6393697 GGGGGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6393931 original size:2 final size:2
Alignment explanation
Indices: 6393924--6393950 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6393914 AGCTTTGGTC
6393924 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 A
6393951 ATGCCCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6396902 original size:17 final size:18
Alignment explanation
Indices: 6396880--6396918 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6396870 TAAAAATTAT
6396880 AAAATTTAT-ATTTTTTA
1 AAAATTTATAATTTTTTA
*
6396897 AAAATTTTTAATTTTTTA
1 AAAATTTATAATTTTTTA
6396915 AAAA
1 AAAA
6396919 AATTAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATTTATAATTTTTTA
Found at i:6407302 original size:5 final size:5
Alignment explanation
Indices: 6407292--6407319 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6407282 CTTTCCATCC
6407292 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
6407320 GCAAAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:6408095 original size:24 final size:23
Alignment explanation
Indices: 6408042--6408095 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
6408032 TGGGATGTAG
*
6408042 TCGATTAACTTGAAATTTTTTAA
1 TCGATTAACTTAAAATTTTTTAA
* *
6408065 TCTGATTAATTTAAAATTTTTTCAC
1 TC-GATTAACTTAAAATTTTTT-AA
6408090 TCGATT
1 TCGATT
6408096 CGATCAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 21 0.81
25 3 0.12
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.50
Consensus pattern (23 bp):
TCGATTAACTTAAAATTTTTTAA
Found at i:6410979 original size:12 final size:12
Alignment explanation
Indices: 6410964--6410995 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6410954 TATATTTCAT
*
6410964 TATTATTTTTAA
1 TATTATTATTAA
6410976 TATTATTATTAA
1 TATTATTATTAA
6410988 TATTATTA
1 TATTATTA
6410996 GATGTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:6411119 original size:23 final size:23
Alignment explanation
Indices: 6411078--6411137 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
6411068 GTATATAAGT
6411078 TTTTTATATTA-TATT--TTATACA
1 TTTTTATA-TACTATTAGTTATA-A
* *
6411100 TTTTTA-ATATTATTAGTTATAT
1 TTTTTATATACTATTAGTTATAA
6411122 TTTTTATATACTATTA
1 TTTTTATATACTATTA
6411138 CATGTATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 12 0.38
23 13 0.41
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTATATACTATTAGTTATAA
Found at i:6411188 original size:21 final size:21
Alignment explanation
Indices: 6411140--6411188 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6411130 TACTATTACA
* *
6411140 TGTATACTTCTAATATTATAT
1 TGTATATTTCTAATATCATAT
*
6411161 TGCATATTTCTAATATCATCAT
1 TGTATATTTCTAATATCAT-AT
6411183 T-TATAT
1 TGTATAT
6411189 ATATATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (21 bp):
TGTATATTTCTAATATCATAT
Found at i:6412407 original size:15 final size:15
Alignment explanation
Indices: 6412376--6412409 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6412366 TATTTGGTTG
6412376 TTTTTTAGTTTTCAA
1 TTTTTTAGTTTTCAA
6412391 TTTTTATAGTTTT-AA
1 TTTTT-TAGTTTTCAA
6412406 TTTT
1 TTTT
6412410 GGTTTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTTTAGTTTTCAA
Found at i:6423802 original size:159 final size:160
Alignment explanation
Indices: 6423513--6423894 Score: 705
Period size: 159 Copynumber: 2.4 Consensus size: 160
6423503 TTGTTTTTTC
* *
6423513 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
6423578 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
6423643 GACACGTT-GGGTAATTTCAATTTATGTTT
131 GACACGTTGGGGTAATTTCAATTTATGTTT
6423672 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
6423737 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
6423802 GACACGTTGGGGTAATTTCAATTTATGTTT
131 GACACGTTGGGGTAATTTCAATTTATGTTT
* *
6423832 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTC-GGGCACGCTGAGGTAATTTCAATT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATT
6423895 CCTATTAAAT
Statistics
Matches: 217, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
159 158 0.73
160 59 0.27
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (160 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
GACACGTTGGGGTAATTTCAATTTATGTTT
Found at i:6423926 original size:73 final size:69
Alignment explanation
Indices: 6423763--6424011 Score: 232
Period size: 73 Copynumber: 3.5 Consensus size: 69
6423753 GTTTTCCAAG
* * * *
6423763 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTAATTTCAATTTAT
1 AAAATCA-CTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTAATTTCAATTTAT
*
6423828 GTTTCA
64 GTATCA
* *
6423834 AAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGCACGCTGAGGTAATTTCAATTCCTA
1 AAAATC-ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTAATTTCAATT--TA
*
6423899 T-TAAATCT
63 TGT--ATCA
* * *
6423907 AAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCT
1 AAAATC-ACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GGCACGCTGAGGTAATTTC-AATT-T
*
6423972 ATCT-TCA
62 ATGTATCA
* * * *
6423979 AAAGTCAATTCATATTACGAGAGGTGAATTGAG
1 AAAATC-ACTCATATTGCGAGAGGTGAGTTGAG
6424012 TCTTTTAATT
Statistics
Matches: 150, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
70 20 0.13
71 34 0.23
72 34 0.23
73 36 0.24
74 21 0.14
75 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (69 bp):
AAAATCACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTAATTTCAATTTATGT
ATCA
Found at i:6424011 original size:72 final size:69
Alignment explanation
Indices: 6423763--6424011 Score: 239
Period size: 71 Copynumber: 3.5 Consensus size: 69
6423753 GTTTTCCAAG
* * * * ** **
6423763 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTAAGGTAATTTCAATTCCT
*
6423828 GTTTC
65 ATTTC
* * *
6423833 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGCACGCTGAGGTAATTTCAATTCCT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTAAGGTAATTTCAATTCCT
6423898 ATTAAATC
65 ATT---TC
* * *
6423906 TAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATT-
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GGCACGCTAAGGTAATTTC-AATTC
6423970 CTATCTTC
63 CTAT-TTC
* * *
6423978 AAAAGTCAATTCATATTACGAGAGGTGAATTGAG
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAG
6424012 TCTTTTAATT
Statistics
Matches: 150, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
70 23 0.15
71 38 0.25
72 27 0.18
73 36 0.24
74 21 0.14
75 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTAAGGTAATTTCAATTCCTA
TTTC
Found at i:6424140 original size:68 final size:68
Alignment explanation
Indices: 6424060--6424233 Score: 321
Period size: 68 Copynumber: 2.5 Consensus size: 68
6424050 TTCAAAGATC
*
6424060 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCATTTTTCGAAATCTACTTTTCAAATT
1 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTAATTTTCATTTTTCGAAATCTACTTTTCAAATT
6424125 ATT
66 ATT
*
6424128 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTTCGAAATCTACTTTTCAAATT
1 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTAATTTTCATTTTTCGAAATCTACTTTTCAAATT
6424193 ATT
66 ATT
6424196 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTTAATTT
1 AACTCATGTTGCGAGAGGTGAGTTGAGCC-TTTAATTT
6424234 CTACTTTTAA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
68 95 0.92
69 8 0.08
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (68 bp):
AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTAATTTTCATTTTTCGAAATCTACTTTTCAAATT
ATT
Found at i:6424242 original size:13 final size:13
Alignment explanation
Indices: 6424224--6424249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6424214 TGAGTTGAGC
6424224 CTTTTAATTTCTA
1 CTTTTAATTTCTA
6424237 CTTTTAATTTCTA
1 CTTTTAATTTCTA
6424250 TGTTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTTAATTTCTA
Found at i:6426233 original size:12 final size:12
Alignment explanation
Indices: 6426218--6426249 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6426208 TATATTTCAT
*
6426218 TATTATTTTTAA
1 TATTATTATTAA
6426230 TATTATTATTAA
1 TATTATTATTAA
6426242 TATTATTA
1 TATTATTA
6426250 GATGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:6426372 original size:23 final size:23
Alignment explanation
Indices: 6426325--6426390 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 23
6426315 TTGTTATGTA
6426325 TATAAGTTTTTATATTA-TATT--T
1 TATAA-TTTTTATA-TACTATTAGT
*
6426347 TATACATTTTTA-ATATTATTAGT
1 TATA-ATTTTTATATACTATTAGT
*
6426370 TATATTTTTTATATACTATTA
1 TATAATTTTTATATACTATTA
6426391 CATGTATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 16 0.43
23 14 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (23 bp):
TATAATTTTTATATACTATTAGT
Found at i:6426441 original size:21 final size:21
Alignment explanation
Indices: 6426393--6426441 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6426383 TACTATTACA
* *
6426393 TGTATACTTCTAATATTATAT
1 TGTATATTTCTAATATCATAT
*
6426414 TGCATATTTCTAATATCATCAT
1 TGTATATTTCTAATATCAT-AT
6426436 T-TATAT
1 TGTATAT
6426442 ATATATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (21 bp):
TGTATATTTCTAATATCATAT
Found at i:6428394 original size:18 final size:18
Alignment explanation
Indices: 6428364--6428418 Score: 87
Period size: 17 Copynumber: 3.2 Consensus size: 18
6428354 CATGATCCGA
6428364 TTGAAAA-ACGAAAATTT
1 TTGAAAACACGAAAATTT
*
6428381 TTTAAAACACGAAAA-TT
1 TTGAAAACACGAAAATTT
6428398 TTGAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
6428416 TTG
1 TTG
6428419 GGATCCGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:6428992 original size:26 final size:27
Alignment explanation
Indices: 6428949--6429002 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
6428939 TATGTATACC
*
6428949 AAATAATACATAATAATACT-AAAATA
1 AAATAATACATAACAATACTGAAAATA
*
6428975 AAATAATA-AGTAACAATAGTGAAAATA
1 AAATAATACA-TAACAATACTGAAAATA
6429002 A
1 A
6429003 TAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAATAATACATAACAATACTGAAAATA
Found at i:6429037 original size:18 final size:17
Alignment explanation
Indices: 6429011--6429064 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
6429001 AATAAGCATA
6429011 ATAATAAATATAATGATAT
1 ATAA-AAATATAAT-ATAT
*
6429030 ATAAAAATAATACTATAT
1 ATAAAAAT-ATAATATAT
*
6429048 ATAAAAGTAT-ATATAT
1 ATAAAAATATAATATAT
6429064 A
1 A
6429065 CGTACAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 15 0.48
19 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAAATATAATATAT
Found at i:6430210 original size:10 final size:10
Alignment explanation
Indices: 6430195--6430219 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6430185 TTAAATAATT
6430195 AAAATTAAGA
1 AAAATTAAGA
6430205 AAAATTAAGA
1 AAAATTAAGA
6430215 AAAAT
1 AAAAT
6430220 ATATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAATTAAGA
Found at i:6433398 original size:58 final size:57
Alignment explanation
Indices: 6433280--6433431 Score: 175
Period size: 58 Copynumber: 2.7 Consensus size: 57
6433270 AATAGTTATG
* * *
6433280 ATTTT-TT-AATT-TATATAATAATAATTATATTAAGAATTTTATTAAATTATATATT
1 ATTTTATTAAATTATATTTAATAATAATTATATTAA-AATATGATTAAATTATATATT
* * * *
6433335 ATTTTATTAAGTTATATTTAATAATAATTATGTTAAAATATGGTTAAATTATTTATT
1 ATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATT
* * *
6433392 ATTTTTATTAAATTATTTTTAATAGTAATTTTATTAAAAT
1 A-TTTTATTAAATTATATTTAATAATAATTATATTAAAAT
6433432 TTAATAACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 5 0.06
56 2 0.02
57 21 0.26
58 53 0.65
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (57 bp):
ATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATT
Found at i:6433614 original size:16 final size:16
Alignment explanation
Indices: 6433593--6433647 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
6433583 TGAATTACTG
6433593 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTTC
6433609 ATTACAGCTCTA-TTC
1 ATTACAGCTCTATTTC
*
6433624 AATTACAGC-CTTATTCC
1 -ATTACAGCTC-TATTTC
6433641 ATTACAG
1 ATTACAG
6433648 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 4 0.11
16 29 0.83
17 2 0.06
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:6438300 original size:19 final size:19
Alignment explanation
Indices: 6438276--6438316 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6438266 TATGTCATTC
6438276 CTATTAGCTGGCCTGGCAA
1 CTATTAGCTGGCCTGGCAA
6438295 CTATTAGCTGGCCTGGCAA
1 CTATTAGCTGGCCTGGCAA
6438314 CTA
1 CTA
6438317 AGTCTCAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
CTATTAGCTGGCCTGGCAA
Found at i:6438401 original size:65 final size:65
Alignment explanation
Indices: 6438319--6438441 Score: 228
Period size: 65 Copynumber: 1.9 Consensus size: 65
6438309 GGCAACTAAG
*
6438319 TCTCAAGTTTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTACTTCCAACAGCTAGC
1 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTACTTCCAACAGCTAGC
*
6438384 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAAC
1 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTACTTCCAAC
6438442 CTTGTTGAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (65 bp):
TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTACTTCCAACAGCTAGC
Found at i:6442419 original size:10 final size:10
Alignment explanation
Indices: 6442400--6442459 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
6442390 TTAAATTTTA
6442400 AAAGATAAAT
1 AAAGATAAAT
6442410 ACAA-ATAAAT
1 A-AAGATAAAT
*
6442420 AAAGATAATT
1 AAAGATAAAT
*
6442430 AAATATAAAT
1 AAAGATAAAT
6442440 AAAGATAAAT
1 AAAGATAAAT
6442450 GAAA-ATAAAT
1 -AAAGATAAAT
6442460 CCTAAAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.05
10 36 0.84
11 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:6442423 original size:20 final size:19
Alignment explanation
Indices: 6442400--6442459 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 19
6442390 TTAAATTTTA
6442400 AAAGATAAATACAAATAAAT
1 AAAGATAAATA-AAATAAAT
*
6442420 AAAGATAATTAAATATAAAT
1 AAAGATAAATAAA-ATAAAT
6442440 AAAGATAAATGAAAATAAAT
1 AAAGATAAAT-AAAATAAAT
6442460 CCTAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 31 0.86
21 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:6443229 original size:95 final size:96
Alignment explanation
Indices: 6443100--6443277 Score: 286
Period size: 95 Copynumber: 1.9 Consensus size: 96
6443090 TATTTATTTA
* * *
6443100 TTTATTTTTGCTTAAGAATATATTGAATCTTTTGACGTGAAGAGAGATGACAACCAAGCACCCCA
1 TTTATTTTTGCTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAACCAAGCACCCCA
*
6443165 CCCTGGTTACTCAGCCCATTATACTCCTAAT
66 CCCCGGTTACTCAGCCCATTATACTCCTAAT
* * *
6443196 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATTACAGCCAAGCACCTCA
1 TTTATTTTTGCTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAACCAAGCACCCCA
6443260 CCCCGGTTACTCAGCCCA
66 CCCCGGTTACTCAGCCCA
6443278 ACACATTCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
95 66 0.88
96 9 0.12
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (96 bp):
TTTATTTTTGCTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAACCAAGCACCCCA
CCCCGGTTACTCAGCCCATTATACTCCTAAT
Found at i:6444417 original size:5 final size:5
Alignment explanation
Indices: 6444407--6444489 Score: 53
Period size: 5 Copynumber: 15.6 Consensus size: 5
6444397 ATTAATATCC
* * *
6444407 AAATA AAATA AAGTA ATAA-A ATAATA AATTAA AAATA AATTAA AAATTAA
1 AAATA AAATA AAATA A-AATA A-AATA AAAT-A AAATA AAAT-A AAA-T-A
*
6444457 AAATA AAGATA AAA-A GAATA AAATA AAATA AAA
1 AAATA AA-ATA AAATA AAATA AAATA AAATA AAA
6444490 ATGGGTTACC
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
4 3 0.05
5 38 0.60
6 16 0.25
7 6 0.10
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:6444430 original size:18 final size:16
Alignment explanation
Indices: 6444407--6444491 Score: 68
Period size: 16 Copynumber: 5.2 Consensus size: 16
6444397 ATTAATATCC
*
6444407 AAATAAAATAAAGTAA
1 AAATAAAATAAAATAA
* *
6444423 TAAA-ATAATAAATTAA
1 -AAATAAAATAAAATAA
*
6444439 AAATAAATTAAAAATTAA
1 AAATAAAAT-AAAA-TAA
6444457 AAATAAAGAT-AAA-AA
1 AAATAAA-ATAAAATAA
*
6444472 GAATAAAATAAAATAA
1 AAATAAAATAAAATAA
6444488 AAAT
1 AAAT
6444492 GGGTTACCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.04
15 14 0.26
16 18 0.33
17 9 0.17
18 10 0.19
19 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:6444445 original size:11 final size:11
Alignment explanation
Indices: 6444429--6444453 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6444419 GTAATAAAAT
6444429 AATAAATTAAA
1 AATAAATTAAA
6444440 AATAAATTAAA
1 AATAAATTAAA
6444451 AAT
1 AAT
6444454 TAAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:6444445 original size:19 final size:18
Alignment explanation
Indices: 6444421--6444491 Score: 88
Period size: 19 Copynumber: 3.8 Consensus size: 18
6444411 AAAATAAAGT
6444421 AATAAAATAATAAATTAAA
1 AATAAAATAA-AAATTAAA
*
6444440 AATAAATTAAAAATTAAA
1 AATAAAATAAAAATTAAA
**
6444458 AATAAAGATAAAAAGAATAA
1 AATAAA-ATAAAAATTA-AA
6444478 AATAAAATAAAAAT
1 AATAAAATAAAAAT
6444492 GGGTTACCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
18 14 0.31
19 23 0.51
20 8 0.18
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AATAAAATAAAAATTAAA
Found at i:6444468 original size:6 final size:6
Alignment explanation
Indices: 6444407--6444491 Score: 52
Period size: 6 Copynumber: 13.7 Consensus size: 6
6444397 ATTAATATCC
*
6444407 AAAT-A AAATAA AGTAAT-A AAATAA TAAATTAA AAAT-A AATTAA AAATTAA
1 AAATAA AAATAA A--AATAA AAATAA -AAA-TAA AAATAA AAATAA AAA-TAA
* *
6444457 AAATAA AGATAA AAAGAA TAAA-ATA AAATAA AAAT
1 AAATAA AAATAA AAATAA -AAATA-A AAATAA AAAT
6444492 GGGTTACCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
5 11 0.17
6 28 0.44
7 19 0.30
8 6 0.09
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:6447490 original size:50 final size:50
Alignment explanation
Indices: 6447414--6447739 Score: 519
Period size: 50 Copynumber: 6.5 Consensus size: 50
6447404 CCATGGCAAC
* * * *
6447414 AAGTGATAAGTGATAGTTTCGACTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
6447464 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
6447513 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
6447563 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
6447613 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
6447663 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
6447714 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
6447740 CTGATCAATG
Statistics
Matches: 259, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
49 48 0.19
50 188 0.73
51 23 0.09
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:6447757 original size:31 final size:31
Alignment explanation
Indices: 6447719--6447777 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
6447709 ATGGCAAGTA
6447719 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
6447750 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
6447778 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:6447785 original size:46 final size:46
Alignment explanation
Indices: 6447732--6447823 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
6447722 AGTGGTAGCT
* *
6447732 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
6447778 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
6447824 GCGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:6451725 original size:10 final size:10
Alignment explanation
Indices: 6451698--6451735 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
6451688 TTAAATTCTA
*
6451698 AAAGATAAAT
1 AAAGATAATT
6451708 ACAA-ATAATT
1 A-AAGATAATT
6451718 AAAGATAATT
1 AAAGATAATT
6451728 AAAGATAA
1 AAAGATAA
6451736 ATGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAATT
Found at i:6462321 original size:17 final size:18
Alignment explanation
Indices: 6462285--6462324 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6462275 CTTCTAAGAC
*
6462285 GCACTTTTGGGACAAAAA
1 GCACTTTTGAGACAAAAA
*
6462303 GCACTTTTGAGA-TAAAA
1 GCACTTTTGAGACAAAAA
6462320 GCACT
1 GCACT
6462325 CCTAAACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (18 bp):
GCACTTTTGAGACAAAAA
Found at i:6463779 original size:2 final size:2
Alignment explanation
Indices: 6463772--6463796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6463762 AATAGAAAAC
6463772 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6463797 TGCAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6466803 original size:31 final size:31
Alignment explanation
Indices: 6466735--6466803 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6466725 GATTAGCCCT
*** *
6466735 TAAACTTAGCAATTGTTCCTATATTGGGGGC
1 TAAACTTAGCAATTGTTCCTATATCAAGGCC
*
6466766 TGAACTTAGCAATTGTTCCTATATCAAGGCC
1 TAAACTTAGCAATTGTTCCTATATCAAGGCC
6466797 TAAACTT
1 TAAACTT
6466804 TGGGTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (31 bp):
TAAACTTAGCAATTGTTCCTATATCAAGGCC
Found at i:6469865 original size:22 final size:22
Alignment explanation
Indices: 6469821--6469872 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6469811 TTATTTTTTA
* **
6469821 AAATATTTTATGATATTTTAAT
1 AAATTTTTTATGATATTGAAAT
*
6469843 AAATTTTTTATGTTATTGAAAT
1 AAATTTTTTATGATATTGAAAT
6469865 ATAATTTT
1 A-AATTTT
6469873 GCTATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
AAATTTTTTATGATATTGAAAT
Found at i:6469865 original size:40 final size:42
Alignment explanation
Indices: 6469777--6469866 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 42
6469767 TATATTCGGA
* * *
6469777 GAAATTATTTTATGAACTATTTTCATCATATTATTTATTTTTT
1 GAAA-TATTTTATGAACTATTTTAATCAAATTATTTATTTATT
* *
6469820 AAAATATTTTATG-A-TATTTTAAT-AAATTTTTTATGTTATT
1 GAAATATTTTATGAACTATTTTAATCAAATTATTTAT-TTATT
6469860 GAAATAT
1 GAAATAT
6469867 AATTTTGCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
39 9 0.22
40 18 0.45
41 1 0.03
42 9 0.22
43 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (42 bp):
GAAATATTTTATGAACTATTTTAATCAAATTATTTATTTATT
Found at i:6470992 original size:7 final size:7
Alignment explanation
Indices: 6470956--6470994 Score: 57
Period size: 6 Copynumber: 6.0 Consensus size: 7
6470946 GCTTTCCCTT
6470956 AAAAG-A
1 AAAAGAA
6470962 AAAAGAA
1 AAAAGAA
6470969 AAAA-AA
1 AAAAGAA
6470975 AAAA-AA
1 AAAAGAA
6470981 AAAAGAA
1 AAAAGAA
6470988 AAAAGAA
1 AAAAGAA
6470995 CACTATCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.55
7 14 0.45
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:6491960 original size:21 final size:21
Alignment explanation
Indices: 6491914--6491960 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6491904 TAGTTAAATG
*
6491914 TTTAAAAAGTTATTAAAATAT
1 TTTAAAAAGTTACTAAAATAT
* *
6491935 GTTAAAAA-TATACTAAAATTT
1 TTTAAAAAGT-TACTAAAATAT
6491956 TTTAA
1 TTTAA
6491961 TTAAAAATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTAAAAAGTTACTAAAATAT
Found at i:6492565 original size:16 final size:18
Alignment explanation
Indices: 6492523--6492560 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
6492513 TTTTTTAAAT
6492523 TTAAAA-AATATTAAAAA
1 TTAAAATAATATTAAAAA
6492540 TTAAAATAATA-TAAAAA
1 TTAAAATAATATTAAAAA
6492557 TTAA
1 TTAA
6492561 TTAATTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAATAATATTAAAAA
Found at i:6494680 original size:2 final size:2
Alignment explanation
Indices: 6494675--6494703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6494665 ACTTTTTTTA
6494675 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 A
6494704 AGTCATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6495431 original size:4 final size:4
Alignment explanation
Indices: 6495422--6495461 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
6495412 GTAAGGGCAG
*
6495422 CATA CATA CATA CATA CATA CATA CATA CATA CATT CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
6495462 TATATGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:6497586 original size:24 final size:24
Alignment explanation
Indices: 6497563--6497607 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6497553 ATATTTAATA
*
6497563 ATAAATGTTGT-ATAATATAAAAT
1 ATAAATATTGTAATAATATAAAAT
*
6497586 ATAAATATTTTAATAATATAAA
1 ATAAATATTGTAATAATATAAA
6497608 TAAGAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATAAATATTGTAATAATATAAAAT
Found at i:6498031 original size:13 final size:13
Alignment explanation
Indices: 6498013--6498037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6498003 TACAATCATC
6498013 TTGACACAAAAAA
1 TTGACACAAAAAA
6498026 TTGACACAAAAA
1 TTGACACAAAAA
6498038 GAAAAACAGT
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (13 bp):
TTGACACAAAAAA
Found at i:6498086 original size:14 final size:14
Alignment explanation
Indices: 6498062--6498100 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6498052 CAAAGAAAAC
6498062 AATCTATTTTTTAGA
1 AATCTATTTTTT-GA
6498077 AATC-ATTTTTTGA
1 AATCTATTTTTTGA
*
6498090 AAGCTATTTTT
1 AATCTATTTTT
6498101 AATGAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (14 bp):
AATCTATTTTTTGA
Found at i:6515129 original size:41 final size:41
Alignment explanation
Indices: 6515083--6515165 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
6515073 TTCAACCTAA
6515083 ACTTTGACATTTTTATCCTCAAATATATAAACTATGAACTC
1 ACTTTGACATTTTTATCCTCAAATATATAAACTATGAACTC
6515124 ACTTTGACATTTTTATCCTCAAATATATAAACTATGAACTC
1 ACTTTGACATTTTTATCCTCAAATATATAAACTATGAACTC
6515165 A
1 A
6515166 TTAATTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (41 bp):
ACTTTGACATTTTTATCCTCAAATATATAAACTATGAACTC
Found at i:6516536 original size:16 final size:16
Alignment explanation
Indices: 6516517--6516563 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
6516507 ATTTAGGTTC
6516517 TTTATAATTTATAAAA
1 TTTATAATTTATAAAA
6516533 TTTATAATTTATAAAA
1 TTTATAATTTATAAAA
*
6516549 TTT-TAAATTA-AAAA
1 TTTATAATTTATAAAA
6516563 T
1 T
6516564 AGTAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 19 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATAATTTATAAAA
Found at i:6516617 original size:30 final size:30
Alignment explanation
Indices: 6516556--6516634 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
6516546 AAATTTTAAA
* *
6516556 TTAAAAATAGTAAAATTATACTTTGACCCT
1 TTAAAAATAATAAAATTATACTTTAACCCT
* *
6516586 TTAAAAATAATAAAATTTTGA-TTTAATCCT
1 TTAAAAATAATAAAATTAT-ACTTTAACCCT
* *
6516616 TT-AAAATTATAAAAATATA
1 TTAAAAATAATAAAATTATA
6516635 AACTATTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 13 0.32
30 26 0.63
31 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATACTTTAACCCT
Found at i:6532470 original size:2 final size:2
Alignment explanation
Indices: 6532463--6532489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6532453 TTTATTAAAT
6532463 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6532490 GAACTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6533229 original size:26 final size:27
Alignment explanation
Indices: 6533191--6533246 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
6533181 TGATTAAATG
*
6533191 TATTCAATCATTACGAAATAAA-AAAAA
1 TATTCAATAATTA-GAAATAAATAAAAA
* *
6533218 TATT-AATAATTATAAATAAATAACAA
1 TATTCAATAATTAGAAATAAATAAAAA
6533244 TAT
1 TAT
6533247 AAAAATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.28
26 14 0.56
27 4 0.16
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (27 bp):
TATTCAATAATTAGAAATAAATAAAAA
Found at i:6536118 original size:8 final size:8
Alignment explanation
Indices: 6536105--6536134 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6536095 AAGTACCCAA
6536105 ATATATTT
1 ATATATTT
*
6536113 ATATATAT
1 ATATATTT
6536121 ATATATTT
1 ATATATTT
6536129 ATATAT
1 ATATAT
6536135 AAGTATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATATTT
Found at i:6536142 original size:16 final size:16
Alignment explanation
Indices: 6536105--6536135 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6536095 AAGTACCCAA
6536105 ATATATTTATATATAT
1 ATATATTTATATATAT
6536121 ATATATTTATATATA
1 ATATATTTATATATA
6536136 AGTATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTTATATATAT
Found at i:6536154 original size:14 final size:14
Alignment explanation
Indices: 6536137--6536168 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6536127 TTATATATAA
6536137 GTATATGTATGCAT
1 GTATATGTATGCAT
*
6536151 GTATATGTATGTAT
1 GTATATGTATGCAT
6536165 GTAT
1 GTAT
6536169 GTAGGGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (14 bp):
GTATATGTATGCAT
Found at i:6540082 original size:2 final size:2
Alignment explanation
Indices: 6540075--6540107 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6540065 GACTTTACAT
6540075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6540108 TCTAAATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6542363 original size:19 final size:20
Alignment explanation
Indices: 6542318--6542374 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
6542308 TATAACTCAA
6542318 CAATTGAAACAACAAATACG
1 CAATTGAAACAACAAATACG
6542338 CAATTGAAACAACAAATACG
1 CAATTGAAACAACAAATACG
*
6542358 -AATTGAACCAACAAATA
1 CAATTGAAACAACAAATA
6542375 TTTACAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.56, C:0.19, G:0.09, T:0.16
Consensus pattern (20 bp):
CAATTGAAACAACAAATACG
Found at i:6548801 original size:2 final size:2
Alignment explanation
Indices: 6548789--6548834 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
6548779 TGAATGCTTT
*
6548789 TA TA CA TA TA 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
6548831 TA TA
1 TA TA
6548835 AATTTAACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6554588 original size:2 final size:2
Alignment explanation
Indices: 6554577--6554616 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
6554567 ACTAAAATGT
6554577 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6554617 CCTATAAATA
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:6559962 original size:38 final size:38
Alignment explanation
Indices: 6559906--6559983 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
6559896 TCTAGCCATT
*
6559906 TAAACATTTGTACCTAAATTGCTTGGACAACTTGAATC
1 TAAACATTTATACCTAAATTGCTTGGACAACTTGAATC
*
6559944 TAAACATTTATACTTAAATTGCTTGGACAACTTGAATC
1 TAAACATTTATACCTAAATTGCTTGGACAACTTGAATC
6559982 TA
1 TA
6559984 TCATGTTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (38 bp):
TAAACATTTATACCTAAATTGCTTGGACAACTTGAATC
Found at i:6560816 original size:26 final size:25
Alignment explanation
Indices: 6560787--6560850 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
6560777 TTATAGATTA
**
6560787 TTAATTTAAATTTTATTATTAAATAT
1 TTAATTTAAATTTTAAGATTAAA-AT
*
6560813 TTAATTCAAATATTTAAGATTAAAAT
1 TTAATTTAAAT-TTTAAGATTAAAAT
6560839 TT-ATTATAAATT
1 TTAATT-TAAATT
6560851 AAATTTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.12
26 18 0.56
27 10 0.31
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAATTTAAATTTTAAGATTAAAAT
Found at i:6562332 original size:53 final size:53
Alignment explanation
Indices: 6562258--6562408 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
6562248 CTTACACGGT
* * *
6562258 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATTACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
6562313 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
6562366 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
6562409 GCGCACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:6563969 original size:40 final size:37
Alignment explanation
Indices: 6563868--6563995 Score: 165
Period size: 35 Copynumber: 3.5 Consensus size: 37
6563858 CATGGCAAAG
6563868 TGTGAAATGTAGGTATGG--TATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
*
6563903 TGTGAAATGTAGGTATGGTAT-T-ATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
*
6563938 TGTGAACTGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-TATC--ATCCATACTGAGT
**
6563978 TAAGAAATGTAGGTATGG
1 TGTGAAATGTAGGTATGG
6563996 CATTTCCCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
35 49 0.61
36 2 0.03
37 2 0.03
40 27 0.34
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
Found at i:6564006 original size:35 final size:35
Alignment explanation
Indices: 6563871--6564015 Score: 148
Period size: 35 Copynumber: 4.0 Consensus size: 35
6563861 GGCAAAGTGT
* **
6563871 GAAATGTAGGTATGGTATCATCCATACTGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACTGAGTTAA
* **
6563906 GAAATGTAGGTATGGTATTATCCATACTGAGCTGT
1 GAAATGTAGGTATGGTATTATCCATACTGAGTTAA
*
6563941 GAACTGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTA-T-T---ATCCATACTGAGTTAA
* *
6563981 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTAT-CCATACTGAGTTAA
6564016 AATGTGACAG
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
34 1 0.01
35 62 0.65
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.29
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACTGAGTTAA
Found at i:6564006 original size:75 final size:70
Alignment explanation
Indices: 6563868--6564007 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 70
6563858 CATGGCAAAG
** *
6563868 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATAC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTAAGAAATGTAGGTATGGCATTATCCATAC
6563933 TGAGC
66 TGAGC
*
6563938 TGTGAACTGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTAAGAAATGTAGGTATGGCATTAT-
6564002 CCATAC
60 CCATAC
6564008 CGAGTTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
70 17 0.28
73 4 0.07
74 1 0.02
75 38 0.63
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (70 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTAAGAAATGTAGGTATGGCATTATCCATAC
TGAGC
Found at i:6565070 original size:40 final size:40
Alignment explanation
Indices: 6564942--6565072 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
6564932 TAAGCTGGAA
* * *
6564942 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * *
6564982 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TG
* *
6565022 ATTCTATCCAGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
6565062 ATTATATCCGG
1 ATTATATCCGG
6565073 TTATATTCCG
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 70 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:6572467 original size:139 final size:136
Alignment explanation
Indices: 6572210--6572607 Score: 370
Period size: 139 Copynumber: 2.8 Consensus size: 136
6572200 TCGAAACATC
* * ***
6572210 TTAACAATGCATACATAGATGCATTAAAAACTTGCATCAGTTCCTAAACT-CGAAAGAAAGA-GG
1 TTAACAAAGCACACATAGATGCATT-AAAACTCATATCAGTTCCTAAACTACGAAAGAAA-ACGG
* * * * * * *
6572273 AAACCAAATGATACACAAGTATACTCATTAATAAAATTAAATTCACAAGACAAAGA-AAGGCTAG
64 AAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAACAAAGAGAA-GCTAA
* *
6572337 TCGAGACACC
128 TCAAGACA-A
* * * *
6572347 TTAACAAGGTACACATAGATGCATTAGAAACTCATATCCGTTCCTAAACTTACCAAAGAAAACGG
1 TTAACAAAGCACACATAGATGCATTA-AAACTCATATCAGTTCCTAAAC-TACGAAAGAAAACGG
* *
6572412 AAATCAAAAGACACATAAGTATACTTATTAATAAAAATAAATTCACAAAAGAAAGAGAAGCTAAT
64 AAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAACAAAGAGAAGCTAAT
6572477 CAAGACAA
129 CAAGACAA
* ** * *
6572485 TTTACAAAGCATGCATAGATGCATTAAAAGCTCATATCGGTTCCTAAACACACGAAAGAAAGCAA
1 TTAACAAAGCACACATAGATGCATTAAAA-CTCATATCAGTTCCTAAAC-TAC----GAAAG--A
** * * *
6572550 AAAGCAAAAATCAAAGGGCACACAAGTATACTTATTAATAAAAATAAATTCATAAAAC
58 AAA-CGGAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAAC
6572608 CTCTCTATCC
Statistics
Matches: 213, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
136 1 0.00
137 43 0.20
138 43 0.20
139 69 0.32
140 2 0.01
142 4 0.02
144 4 0.02
145 47 0.22
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (136 bp):
TTAACAAAGCACACATAGATGCATTAAAACTCATATCAGTTCCTAAACTACGAAAGAAAACGGAA
ATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAACAAAGAGAAGCTAATCA
AGACAA
Found at i:6572836 original size:23 final size:23
Alignment explanation
Indices: 6572806--6572876 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 23
6572796 TATTACCGTT
6572806 ATTTAAAAAAACAATACATTCAA
1 ATTTAAAAAAACAATACATTCAA
** *
6572829 ATTT---AAAATTAT-CATT--T
1 ATTTAAAAAAACAATACATTCAA
6572846 ATTTAAAAAAACAATACATTCAA
1 ATTTAAAAAAACAATACATTCAA
6572869 ATTTAAAA
1 ATTTAAAA
6572877 TTATCATTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 4 0.11
19 4 0.11
20 12 0.33
21 4 0.11
23 12 0.33
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTTAAAAAAACAATACATTCAA
Found at i:6572883 original size:40 final size:40
Alignment explanation
Indices: 6572804--6572884 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
6572794 TTTATTACCG
6572804 TTATTTAAAAAAACAATACATTCAAATTTAAAATTATCAT
1 TTATTTAAAAAAACAATACATTCAAATTTAAAATTATCAT
6572844 TTATTTAAAAAAACAATACATTCAAATTTAAAATTATCAT
1 TTATTTAAAAAAACAATACATTCAAATTTAAAATTATCAT
6572884 T
1 T
6572885 CTCTTTTGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (40 bp):
TTATTTAAAAAAACAATACATTCAAATTTAAAATTATCAT
Found at i:6575985 original size:22 final size:22
Alignment explanation
Indices: 6575957--6575998 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6575947 TATAATTTAT
6575957 TTTTTAATTATTAAAA-TAATCA
1 TTTTTAA-TATTAAAACTAATCA
6575979 TTTTTAATATTAAAACTAAT
1 TTTTTAATATTAAAACTAAT
6575999 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTAATATTAAAACTAATCA
Found at i:6576414 original size:30 final size:30
Alignment explanation
Indices: 6576365--6576430 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
6576355 GTTAGGATAA
* * *
6576365 AAAATTTAAAATTCGAAAAGTTCAA-AATT
1 AAAATTTAAAATTCAAAAAGTACAATAACT
*
6576394 AAAATTTATCAATTCAAAAAGTACAATAACT
1 AAAATTTA-AAATTCAAAAAGTACAATAACT
6576425 AAAATT
1 AAAATT
6576431 GACCAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.26
30 14 0.45
31 9 0.29
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAATTTAAAATTCAAAAAGTACAATAACT
Found at i:6577794 original size:3 final size:3
Alignment explanation
Indices: 6577781--6577866 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
6577771 GAGGGCATAT
6577781 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
6577825 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6577867 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:6577805 original size:12 final size:12
Alignment explanation
Indices: 6577781--6577863 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
6577771 GAGGGCATAT
6577781 ATAATAT-AATA
1 ATAATATAAATA
6577792 ATAATATAAATA
1 ATAATATAAATA
6577804 ATAATATATACATGA
1 ATAATATA-A-AT-A
6577819 GA-AATA-ATAATA
1 -ATAATATA-AATA
6577831 ATAATATAAATA
1 ATAATATAAATA
* *
6577843 ATAGTAAAAATA
1 ATAATATAAATA
*
6577855 ATAAAATAA
1 ATAATATAA
6577864 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:6577825 original size:21 final size:18
Alignment explanation
Indices: 6577786--6577866 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
6577776 CATATATAAT
*
6577786 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
6577804 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
6577825 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
6577843 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
6577860 ATAATAA
1 ATAATAA
6577867 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:6577854 original size:27 final size:27
Alignment explanation
Indices: 6577781--6577867 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
6577771 GAGGGCATAT
* *
6577781 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
6577807 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
6577831 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
6577858 A-AATAATAAA
1 ATAAT-ATAAA
6577868 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:6578238 original size:22 final size:21
Alignment explanation
Indices: 6578197--6578243 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6578187 CTTCTTTCCA
*
6578197 AAAAAACAAAAAAACACCTCT
1 AAAAAACAAAAAAACACCTCC
*
6578218 AAAAAACAAAAAAACCTCCTCC
1 AAAAAACAAAAAAA-CACCTCC
6578240 AAAA
1 AAAA
6578244 CAAAGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.66, C:0.26, G:0.00, T:0.09
Consensus pattern (21 bp):
AAAAAACAAAAAAACACCTCC
Found at i:6578740 original size:8 final size:9
Alignment explanation
Indices: 6578725--6578749 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6578715 ATATTATTAT
6578725 ATTAAAAAA
1 ATTAAAAAA
6578734 ATTAAAAAA
1 ATTAAAAAA
6578743 ATTAAAA
1 ATTAAAA
6578750 TGGATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:6591783 original size:26 final size:26
Alignment explanation
Indices: 6591754--6591809 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
6591744 ACACATAAGC
6591754 TAATAGCTAACCTTACGGAATGACCA
1 TAATAGCTAACCTTACGGAATGACCA
* *
6591780 TAATAGCTAAGCTTATGGAATGACCA
1 TAATAGCTAACCTTACGGAATGACCA
6591806 TAAT
1 TAAT
6591810 CTGATGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (26 bp):
TAATAGCTAACCTTACGGAATGACCA
Found at i:6598221 original size:14 final size:15
Alignment explanation
Indices: 6598202--6598231 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6598192 TTAAAATAAT
6598202 ATAAAATTAT-ATTA
1 ATAAAATTATAATTA
6598216 ATAAAATTATAATTA
1 ATAAAATTATAATTA
6598231 A
1 A
6598232 AAACAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTATAATTA
Found at i:6598229 original size:20 final size:20
Alignment explanation
Indices: 6598184--6598230 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
6598174 ATTGTGGAGA
6598184 ATAATTATTTAAAATAATAT
1 ATAATTATTTAAAATAATAT
*
6598204 AAAATTATATTAATAA-AAT-T
1 ATAATTAT-TTAA-AATAATAT
6598224 ATAATTA
1 ATAATTA
6598231 AAAACAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 7 0.30
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTATTTAAAATAATAT
Found at i:6598677 original size:17 final size:16
Alignment explanation
Indices: 6598651--6598689 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
6598641 ATAAATTATT
6598651 AAAAATTTAAAAA-AA
1 AAAAATTTAAAAATAA
6598666 CAAAAATATTAAAAATAA
1 -AAAAAT-TTAAAAATAA
6598684 AAAAAT
1 AAAAAT
6598690 CTAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:6601933 original size:16 final size:16
Alignment explanation
Indices: 6601914--6601949 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6601904 CTTTTCCCCC
6601914 CTCTCCTTCCTCCCTT
1 CTCTCCTTCCTCCCTT
* *
6601930 CTCTCTTTTCTCCCTT
1 CTCTCCTTCCTCCCTT
6601946 CTCT
1 CTCT
6601950 TTCTTCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (16 bp):
CTCTCCTTCCTCCCTT
Found at i:6602441 original size:20 final size:21
Alignment explanation
Indices: 6602399--6602443 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6602389 TTTTGTTGTT
*
6602399 TATTCTTATTTTCTTATTAAA
1 TATTCTTATTATCTTATTAAA
6602420 TATTCTTATTAT-TTA-TATAA
1 TATTCTTATTATCTTATTA-AA
6602440 TATT
1 TATT
6602444 AGTGCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 11 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTCTTATTATCTTATTAAA
Found at i:6602477 original size:3 final size:3
Alignment explanation
Indices: 6602449--6602520 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
6602439 ATATTAGTGC
* * * * *
6602449 TAT TAC TAT TAC TAT TGT TCT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6602497 TAT TAT TAT TAT TAT TAT GTAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TA
6602521 GTTTATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:6602753 original size:15 final size:15
Alignment explanation
Indices: 6602720--6602758 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6602710 TTTAATGTCG
*
6602720 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
6602736 TATTATATATTTTCA
1 TATTATATATTTTAA
6602751 TATTATAT
1 TATTATAT
6602759 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:6609606 original size:75 final size:72
Alignment explanation
Indices: 6609406--6609855 Score: 574
Period size: 75 Copynumber: 6.2 Consensus size: 72
6609396 TATTTTGATG
* ***
6609406 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGTGCGC
1 TTTCAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
6609471 TGAGGTAT
65 TGAGGTAT
* *
6609479 TTTCAATTTAT-TTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
6609543 GAGGTAT
66 GAGGTAT
6609550 TTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
6609615 GCTGAGGTAA
63 GCTGAGGTAT
* * * *
6609625 TTTCAATTTATG-TTT-----GTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
6609684 GAGGTAT
66 GAGGTAT
*
6609691 TTTCAATTTCTGCTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTCTG-TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
6609756 CTGAGGTAA
64 CTGAGGTAT
* * **
6609765 TTTCAATTTATGTTTTTCAAAAATCAACTCATATAGTAAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* * *
6609829 TGTTGAGGTCT
62 CGCTGAGGTAT
6609840 TTTCAATTTCTGTTTT
1 TTTCAATTTCTGTTTT
6609856 TCAATTTCTG
Statistics
Matches: 331, Mismatches: 31, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
66 58 0.18
68 2 0.01
71 62 0.19
72 5 0.02
73 53 0.16
74 66 0.20
75 85 0.26
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (72 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTAT
Found at i:6609682 original size:66 final size:66
Alignment explanation
Indices: 6609574--6609784 Score: 296
Period size: 66 Copynumber: 3.1 Consensus size: 66
6609564 TTTCAAAAAA
6609574 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
6609639 T
66 T
* * * * *
6609640 GTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATG-T
6609705 CTT
65 -TT
6609708 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 ------ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
6609773 TATGTTT
60 TATGTTT
*
6609780 TTCAA
1 ATCAA
6609785 AAATCAACTC
Statistics
Matches: 126, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
66 62 0.49
67 1 0.01
68 2 0.02
72 2 0.02
73 1 0.01
74 58 0.46
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (66 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
T
Found at i:6609848 original size:215 final size:211
Alignment explanation
Indices: 6609429--6609820 Score: 624
Period size: 215 Copynumber: 1.8 Consensus size: 211
6609419 TTGTCAAAAA
* ** *
6609429 TCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGTGCGCTGAGGTATTTTCAATTTATTTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTATTCTT
* *
6609494 CAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
66 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* * *
6609559 CTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
131 ATGCTTTTC-AAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
6609624 ATTTCAATTTATGTTTG
195 ATTTCAATTTATGTTTG
* *
6609641 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTGCTC
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT--TC
6609706 TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
64 TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
* *
6609771 TTTATGTTTTTC-AAAAATCAACTCATATAGTAAGAGGTGAGTTGAGCCTC
128 TTTATGCTTTTCAAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTC
6609821 GGCTCACATG
Statistics
Matches: 164, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
212 56 0.34
213 35 0.21
214 4 0.02
215 69 0.42
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (211 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTATTCTT
CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
ATGCTTTTCAAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
TTTCAATTTATGTTTG
Found at i:6609858 original size:14 final size:14
Alignment explanation
Indices: 6609839--6609873 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6609829 TGTTGAGGTC
6609839 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
6609853 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
*
6609867 CTTTCAA
1 TTTTCAA
6609874 AAAAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:6609950 original size:15 final size:14
Alignment explanation
Indices: 6609929--6609963 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
6609919 GCTGAGGTAA
6609929 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
*
6609943 TCTTCAATTTTTGTT
1 T-TTCAATTTCTGTT
6609958 TTTCAA
1 TTTCAA
6609964 AAATCAGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTCAATTTCTGTT
Found at i:6610079 original size:90 final size:90
Alignment explanation
Indices: 6609765--6610092 Score: 387
Period size: 90 Copynumber: 3.7 Consensus size: 90
6609755 GCTGAGGTAA
*** * ** *
6609765 TTTCAATTTATGTTTTTCAAAAATCAACTCATATAGTAAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACA
* *
6609829 TGTTGAGGTCTTTTCAATTTCTGTT
66 TGTCGAGGTATTTTCAATTTCTGTT
* *
6609854 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCA-GG--A
1 TTTCAATTTATG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCA
*
6609916 CATG-CTGAGGTAATTTCAATTTCTGTT
64 CATGTC-GAGGTATTTTCAATTTCTGTT
* *** *
6609943 TCTTCAATTTTTGTTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCAC
1 T-TTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCAC
** *
6610008 ATGTCGAGGTATTTTCAAAATCTGCT
65 ATGTCGAGGTATTTTCAATTTCTGTT
* *
6610034 TTTCAAATTAAGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
6610093 ACACGCTGAG
Statistics
Matches: 201, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
88 40 0.20
89 38 0.19
90 61 0.30
91 61 0.30
92 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (90 bp):
TTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACA
TGTCGAGGTATTTTCAATTTCTGTT
Found at i:6610095 original size:178 final size:178
Alignment explanation
Indices: 6609766--6610121 Score: 534
Period size: 178 Copynumber: 2.0 Consensus size: 178
6609756 CTGAGGTAAT
*
6609766 TTCAATTTATGTTTTTCAAAAATCAACTCATATAGTAAGAGGTGAGTTGAGCCTCGGCTCACATG
1 TTCAATTTATGTTTTTCAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTCGGCTCACATG
* * ** * * **
6609831 TTGAGGTCTTTTCAATTTCTGTTTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAG
66 TCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG-CTTTCAAAAAAATCAACTCATATTACGAG
* *
6609896 AGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCTGTTTC
130 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTC
* * * * *
6609945 TTCAATTTTTGTTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTCACAT
1 TTCAATTTATGTTTTTCAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTC-GGCTCACAT
*
6610010 GTCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG-TTTCAAAAAAATCAACTCATATTGCGAG
65 GTCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTACGAG
6610074 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTT
130 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTT
6610122 GTCAACTCAT
Statistics
Matches: 159, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
178 73 0.46
179 50 0.31
180 36 0.23
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (178 bp):
TTCAATTTATGTTTTTCAAAAATCAACTCATATAGCAAGAGGTGAGTTGAGCCTCGGCTCACATG
TCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTACGAGA
GGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTC
Found at i:6610164 original size:66 final size:66
Alignment explanation
Indices: 6610056--6610303 Score: 280
Period size: 66 Copynumber: 3.5 Consensus size: 66
6610046 TTTCAAAAAA
6610056 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
6610121 T
66 T
* * * *
6610122 GTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTACT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-TT-TA-T
* *
6610187 CTTCAAAAAA
63 GTT------T
6610197 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATG--
6610262 TTT
64 TTT
* *
6610265 CAAAAATCAACTCATATAGTGAGAGGTGAGTTGAGCCTC
1 -----ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
6610304 GGCTCACATG
Statistics
Matches: 152, Mismatches: 14, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
66 53 0.35
67 2 0.01
68 2 0.01
69 3 0.02
72 1 0.01
73 34 0.22
74 4 0.03
75 53 0.35
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (66 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTT
T
Found at i:6610319 original size:75 final size:72
Alignment explanation
Indices: 6610052--6610342 Score: 296
Period size: 75 Copynumber: 4.0 Consensus size: 72
6610042 TAAGTTTCAA
*
6610052 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACA-GCTGAGGTATTTTCAATTT
*
6610116 ATG--TTT-
64 CTGTTTTTC
*
6610122 ----GTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC-GCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC--GGCACAGCTGAGGTATTTTCAATTT
** *
6610182 CTACTCTTC
64 CTGTTTTTC
*
6610191 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAAT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACA-GCTGAGGTATTTTCAAT
*
6610255 TTATGTTTTTC
62 TTCTGTTTTTC
* * * * *
6610266 AAAAATCAACTCATATAGTGAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTCTTTTCAACT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACA-GCTGAGGTATTTTCAATT
6610331 TCTGTTTTTC
63 TCTGTTTTTC
6610341 AA
1 AA
6610343 TTTCTGTCTT
Statistics
Matches: 184, Mismatches: 21, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
66 52 0.28
67 2 0.01
68 4 0.02
72 2 0.01
73 38 0.21
74 2 0.01
75 84 0.46
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACAGCTGAGGTATTTTCAATTTCT
GTTTTTC
Found at i:6610341 original size:14 final size:14
Alignment explanation
Indices: 6610322--6610356 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6610312 TGTTGAGGTC
6610322 TTTTCAACTTCTGT
1 TTTTCAACTTCTGT
*
6610336 TTTTCAATTTCTGT
1 TTTTCAACTTCTGT
*
6610350 CTTTCAA
1 TTTTCAA
6610357 AAAAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAACTTCTGT
Found at i:6610434 original size:16 final size:16
Alignment explanation
Indices: 6610413--6610443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6610403 CTGAGGTAAT
*
6610413 TTCAATTTCTGTTTTC
1 TTCAATTTATGTTTTC
6610429 TTCAATTTATGTTTT
1 TTCAATTTATGTTTT
6610444 TCAAAAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
TTCAATTTATGTTTTC
Found at i:6610462 original size:89 final size:87
Alignment explanation
Indices: 6610248--6610478 Score: 286
Period size: 89 Copynumber: 2.6 Consensus size: 87
6610238 GCTGAGGTAA
*
6610248 TTTCAATTTATGTTTTTCAAAAATCAACTCATA-TAGTGAGAGGTGAGTTGAGCCTCGGCTCACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTA-CGAGAGGTGAGTTGAGCCTCGG--CACA
* **
6610312 TGTTGAGGTCTTTTCAACTTCTGTT
63 TGCTGAGGTAATTTCAACTTCTGTT
* *
6610337 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGG-ACA
1 TTTCAATTTATGTTTTTC--AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-GGCACA
*
6610401 TGCTGAGGTAATTTCAATTTCTGTTT
63 TGCTGAGGTAATTTCAACTTCTG-TT
* * *
6610427 TCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGGGGTGGGTTGA
1 T-TTCAATTTATGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGA
6610479 ACCTTTTAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
89 68 0.55
90 3 0.02
91 49 0.40
92 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (87 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGCACATGC
TGAGGTAATTTCAACTTCTGTT
Found at i:6610589 original size:14 final size:13
Alignment explanation
Indices: 6610556--6610585 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6610546 TGCTGAGGTA
*
6610556 TTTTCAATTTTTG
1 TTTTCAATTTATG
6610569 TTTTCAATTTATG
1 TTTTCAATTTATG
6610582 TTTT
1 TTTT
6610586 TCAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:6610676 original size:145 final size:143
Alignment explanation
Indices: 6610336--6610963 Score: 851
Period size: 143 Copynumber: 4.4 Consensus size: 143
6610326 CAACTTCTGT
* *
6610336 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTT-AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
6610401 TGCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCG
63 TGCTGAGGTAATTTCAATTTCTGTGTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCG
* *
6610466 AGGGGTGGGTTGAACC
128 AGAGGTGAGTTGAACC
* * *
6610482 TTTTAATTTCTACTTTTTC-AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGTCTCAGGTCACA
1 TTTTAATTTCT-GTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
*
6610546 TGCTGAGGTATTTTCAATTT-T-TGTT-TTCAATTTATGTTTTTCAAAAAATCAACTCATATTGC
63 TGCTGAGGTAATTTCAATTTCTGTGTTCTTCAATTTATGTTTTTC-AAAAATCAACTCATATTGC
*
6610608 GAGAGGTGAGTTGAGCC
127 GAGAGGTGAGTTGAACC
* *
6610625 TTTTAATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAT
1 TTTTAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
* *
6610690 GCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAATTCATATTGCGA
64 GCTGAGGTAATTTCAATTTCTGTGTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGA
*
6610755 GGGGT-AGGTTGAACC
129 GAGGTGA-GTTGAACC
* * *
6610770 TTTTAATTTCTACTTTTTC-AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGTCTCAGGTCACA
1 TTTTAATTTCT-GTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
*
6610834 TGCTGAGGTATTTTCAATTT-T-TGTT-TTCAATTTATGTTTTTCAAAAAATCAACTCATATTGC
63 TGCTGAGGTAATTTCAATTTCTGTGTTCTTCAATTTATGTTTTTC-AAAAATCAACTCATATTGC
*
6610896 GAGAGGTGAGTTGAGCC
127 GAGAGGTGAGTTGAACC
* * * *
6610913 TTTTAATTCCTGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGGGTTGA
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
6610964 ACCTTTTAAT
Statistics
Matches: 429, Mismatches: 36, Indels: 37
0.85 0.07 0.07
Matches are distributed among these distances:
142 46 0.11
143 214 0.50
144 5 0.01
145 132 0.31
146 32 0.07
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.39
Consensus pattern (143 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
TGAGGTAATTTCAATTTCTGTGTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAACC
Found at i:6610722 original size:16 final size:16
Alignment explanation
Indices: 6610701--6610731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6610691 CTGAGGTAAT
*
6610701 TTCAATTTCTGTTTTC
1 TTCAATTTATGTTTTC
6610717 TTCAATTTATGTTTT
1 TTCAATTTATGTTTT
6610732 TCAAAAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
TTCAATTTATGTTTTC
Found at i:6610867 original size:288 final size:288
Alignment explanation
Indices: 6610336--6610963 Score: 1161
Period size: 288 Copynumber: 2.2 Consensus size: 288
6610326 CAACTTCTGT
* *
6610336 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTT-AATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACA
6610401 TGCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCG
65 TGCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCG
*
6610466 AGGGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTT
130 AGGGGTAGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTT
6610531 GAGTCTCAGGTCACATGCTGAGGTATTTTCAATTTTTGTTTTCAATTTATGTTTTTCAAAAAATC
195 GAGTCTCAGGTCACATGCTGAGGTATTTTCAATTTTTGTTTTCAATTTATGTTTTTCAAAAAATC
6610596 AACTCATATTGCGAGAGGTGAGTTGAGCC
260 AACTCATATTGCGAGAGGTGAGTTGAGCC
6610625 TTTTAATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAT
1 TTTTAATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAT
*
6610690 GCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAATTCATATTGCGA
66 GCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGA
6610755 GGGGTAGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTG
131 GGGGTAGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTG
6610820 AGTCTCAGGTCACATGCTGAGGTATTTTCAATTTTTGTTTTCAATTTATGTTTTTCAAAAAATCA
196 AGTCTCAGGTCACATGCTGAGGTATTTTCAATTTTTGTTTTCAATTTATGTTTTTCAAAAAATCA
6610885 ACTCATATTGCGAGAGGTGAGTTGAGCC
261 ACTCATATTGCGAGAGGTGAGTTGAGCC
* * * *
6610913 TTTTAATTCCTGTTTTTC--AAAAATTAATTCATATTGCGAGAGGTGGGTTGA
1 TTTTAATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGA
6610964 ACCTTTTAAT
Statistics
Matches: 331, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
286 29 0.09
288 298 0.90
289 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.39
Consensus pattern (288 bp):
TTTTAATTCCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAT
GCTGAGGTAATTTCAATTTCTGTTTTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGA
GGGGTAGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTG
AGTCTCAGGTCACATGCTGAGGTATTTTCAATTTTTGTTTTCAATTTATGTTTTTCAAAAAATCA
ACTCATATTGCGAGAGGTGAGTTGAGCC
Found at i:6610877 original size:14 final size:13
Alignment explanation
Indices: 6610844--6610873 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6610834 TGCTGAGGTA
*
6610844 TTTTCAATTTTTG
1 TTTTCAATTTATG
6610857 TTTTCAATTTATG
1 TTTTCAATTTATG
6610870 TTTT
1 TTTT
6610874 TCAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:6610951 original size:54 final size:54
Alignment explanation
Indices: 6610868--6611021 Score: 245
Period size: 54 Copynumber: 2.8 Consensus size: 54
6610858 TTTCAATTTA
* *
6610868 TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCC
1 TGTTTTTC-AAAAATTAATTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCC
* * *
6610923 TGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTC
1 TGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCC
*
6610977 TGTTTTTCAAAAATTAATTCGTATTGCGAGAGGTGAGTTGAGCCT
1 TGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGAGTTGAGCCT
6611022 AGGGTCACAT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 83 0.91
55 8 0.09
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (54 bp):
TGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCC
Found at i:6610964 original size:197 final size:197
Alignment explanation
Indices: 6610726--6611111 Score: 548
Period size: 197 Copynumber: 2.0 Consensus size: 197
6610716 CTTCAATTTA
*
6610726 TGTTTTTCAAAAATCAATTCATATTGCGAGGGGTAGGTTGAACCTTTTAATTTCTACTTTTTC-A
1 TGTTTTTCAAAAATCAATTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCT-CTTTTTCAA
* * **
6610790 AAATCAGCTCATATTGCGAGAGGTGAGTTGAGTCTCA-GGTCACATG-CTGAGGTATTTTCAATT
65 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGGTCACATGTC-GAGGTATTTTCAAAA
* * * * *
6610853 TTTG-TTTTCAATTTATGTTTTTCAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTT
128 TCTGCTTTTCAAATTAAG--TTTCAAAAAGATCAACTCACATTGCGAGAAGTGAGTTGAGCCTTT
6610916 TAATTCC
191 TAATTCC
* * *
6610923 TGTTTTTCAAAAATTAATTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAA
1 TGTTTTTCAAAAATCAATTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTCTTTTTCAAA
* * *
6610988 AATTAATTCGTATTGCGAGAGGTGAGTTGAGCCTAGGGTCACATGTCGAGGTATTTTCAAAATCT
66 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGGTCACATGTCGAGGTATTTTCAAAATCT
6611053 GCTTTTCAAATTAAGTTTCAAAAAGATCAACTCACATTGCGAGAAGTGAGTTGAGCCTT
131 GCTTTTCAAATTAAGTTTCAAAAAGATCAACTCACATTGCGAGAAGTGAGTTGAGCCTT
6611112 AGCTCATGTG
Statistics
Matches: 168, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
196 16 0.10
197 140 0.83
198 12 0.07
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (197 bp):
TGTTTTTCAAAAATCAATTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTCTTTTTCAAA
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGGTCACATGTCGAGGTATTTTCAAAATCT
GCTTTTCAAATTAAGTTTCAAAAAGATCAACTCACATTGCGAGAAGTGAGTTGAGCCTTTTAATT
CC
Found at i:6612553 original size:16 final size:17
Alignment explanation
Indices: 6612511--6612554 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
6612501 CCTTTTCCCC
6612511 CTCTTCTTCCTCCCTTCT
1 CTCTTCTT-CTCCCTTCT
6612529 CTCTT-TTCTCCCTTCT
1 CTCTTCTTCTCCCTTCT
6612545 CT-TTCTTCTC
1 CTCTTCTTCTC
6612555 TTTTTCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 16 0.64
17 2 0.08
18 5 0.20
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
CTCTTCTTCTCCCTTCT
Found at i:6613025 original size:3 final size:3
Alignment explanation
Indices: 6612995--6613126 Score: 122
Period size: 3 Copynumber: 43.0 Consensus size: 3
6612985 TTTTTGTTGT
* * * *
6612995 TTA TTC TTA TT- TTC TTA TTAA ATA TTA TTA TTA TTTA TATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA T-TA TTA TTA
* * * * * * *
6613042 GTG CTA TTA CTA TTA CTA TTG TTC TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6613090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
6613127 GTTTATGTTT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
2 2 0.02
3 93 0.89
4 10 0.10
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:6613359 original size:15 final size:15
Alignment explanation
Indices: 6613326--6613364 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6613316 TTTAATGTCG
*
6613326 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
6613342 TATTATATATTTTCA
1 TATTATATATTTTAA
6613357 TATTATAT
1 TATTATAT
6613365 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:6616528 original size:21 final size:21
Alignment explanation
Indices: 6616502--6616542 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6616492 ATCTGCTCAA
* *
6616502 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6616523 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6616543 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Done.