Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002273.1 Hibiscus syriacus cultivar Beakdansim tig00004620_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 802197
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:181331 original size:21 final size:21
Alignment explanation
Indices: 181265--181331 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
181255 GTGAATTGGG
*
181265 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
181285 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
181307 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
181328 CTCT
1 CTCT
181332 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:181350 original size:42 final size:41
Alignment explanation
Indices: 181265--181387 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
181255 GTGAATTGGG
* * * * *
181265 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
181307 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
181349 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
181388 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:183418 original size:20 final size:19
Alignment explanation
Indices: 183387--183547 Score: 101
Period size: 20 Copynumber: 8.8 Consensus size: 19
183377 TCTTTTGGTT
183387 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
183406 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
183427 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
183446 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
183460 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** *
183476 -CCA-GACAATCGCAAC-A
1 GAAATGAAAATCGCAACGA
*
183492 CGAAATGAAAATCGCAACCGC
1 -GAAATGAAAATCGCAA-CGA
*
183513 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
183532 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
183548 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
14 17 0.15
15 1 0.01
16 5 0.05
17 3 0.03
18 1 0.01
19 36 0.32
20 46 0.41
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:183469 original size:33 final size:33
Alignment explanation
Indices: 183412--183510 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
183402 ACGAGATAAT
*
183412 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
183446 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
183479 GACAATCGCAACACGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
183511 GCGAAATGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:183506 original size:19 final size:19
Alignment explanation
Indices: 183482--183552 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
183472 GCGACCAGAC
*
183482 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
183501 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
183521 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
183540 AATCGCAATGCGA
1 AATCGCAACGCGA
183553 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:183581 original size:19 final size:19
Alignment explanation
Indices: 183548--183614 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
183538 AAAATCGCAA
**
183548 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
183567 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
183586 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
183606 TGCGATTTT
1 TGCGATTTT
183615 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:184153 original size:20 final size:20
Alignment explanation
Indices: 184128--184180 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
184118 GCGCTATGTA
184128 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
184148 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
184168 TATCTCGTTGCGA
1 AATCGCGTTGCGA
184181 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:184234 original size:20 final size:20
Alignment explanation
Indices: 184211--184282 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
184201 ATAGTAAGTA
*
184211 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
184231 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
184252 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
184272 TCGCATTGCGA
1 TCGCATTGCGA
184283 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:188722 original size:17 final size:17
Alignment explanation
Indices: 188693--188727 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
188683 TTTTGAAAAT
188693 AAATTGAAGAAAAATAA
1 AAATTGAAGAAAAATAA
188710 AAATGTGAA-AAAAATAA
1 AAAT-TGAAGAAAAATAA
188727 A
1 A
188728 GGCCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATTGAAGAAAAATAA
Found at i:190007 original size:11 final size:10
Alignment explanation
Indices: 189986--190045 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
189976 CTTTTTTTAA
189986 AAAAATAAAT
1 AAAAATAAAT
189996 AAAAATACAAT
1 AAAAATA-AAT
*
190007 AAAAATGAATT
1 AAAAAT-AAAT
*
190018 AAAAAATGAAT
1 -AAAAATAAAT
* *
190029 AAAATTCAAT
1 AAAAATAAAT
190039 AAAAATA
1 AAAAATA
190046 TGATGTAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 20 0.50
11 13 0.32
12 7 0.17
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:190043 original size:22 final size:22
Alignment explanation
Indices: 189986--190048 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
189976 CTTTTTTTAA
* * *
189986 AAAAATAAATAAAAATA-CAAT
1 AAAAATCAATAAAAAAATGAAT
* *
190007 AAAAATGAATTAAAAAATGAAT
1 AAAAATCAATAAAAAAATGAAT
* *
190029 AAAATTCAATAAAAATATGA
1 AAAAATCAATAAAAAAATGA
190049 TGTAAAGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (22 bp):
AAAAATCAATAAAAAAATGAAT
Found at i:190607 original size:11 final size:10
Alignment explanation
Indices: 190572--190635 Score: 67
Period size: 11 Copynumber: 6.1 Consensus size: 10
190562 TTAGCTTTAC
190572 ATTATATTTTT
1 ATTA-ATTTTT
190583 ATTGAA-TTTT
1 ATT-AATTTTT
190593 ATTAATTTTT
1 ATTAATTTTT
190603 AATTAATTTTT
1 -ATTAATTTTT
*
190614 ATTGCATTTTT
1 ATT-AATTTTT
*
190625 ATTTATTTTT
1 ATTAATTTTT
190635 A
1 A
190636 AAAAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
9 2 0.04
10 21 0.45
11 23 0.49
12 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (10 bp):
ATTAATTTTT
Found at i:190613 original size:21 final size:20
Alignment explanation
Indices: 190572--190635 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
190562 TTAGCTTTAC
190572 ATTATATTTTTATTGAA-TTTT
1 ATTA-ATTTTTATT-AATTTTT
190593 ATTAATTTTTAATTAATTTTT
1 ATTAATTTTT-ATTAATTTTT
* *
190614 ATTGCATTTTTATTTATTTTT
1 ATT-AATTTTTATTAATTTTT
190635 A
1 A
190636 AAAAAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.21
21 24 0.63
22 6 0.16
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (20 bp):
ATTAATTTTTATTAATTTTT
Found at i:190633 original size:32 final size:32
Alignment explanation
Indices: 190567--190636 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
190557 TATTTTTAGC
190567 TTTACATTATATTTTTATTGAATTTTATTAATT
1 TTTA-ATTATATTTTTATTGAATTTTATTAATT
* *
190600 TTTAATTA-ATTTTTATTGCATTTTTATTTATT
1 TTTAATTATATTTTTATTG-AATTTTATTAATT
190632 TTTAA
1 TTTAA
190637 AAAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 10 0.29
32 20 0.59
33 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (32 bp):
TTTAATTATATTTTTATTGAATTTTATTAATT
Found at i:190891 original size:14 final size:14
Alignment explanation
Indices: 190872--190914 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
190862 TAGTTTTTTA
190872 CACGTTTAAGAAGG
1 CACGTTTAAGAAGG
* *
190886 CACGTTGTAGGAGACG
1 CACGTT-TAAGA-AGG
190902 CACGTTTAAGAAG
1 CACGTTTAAGAAG
190915 AGCGCGCCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.30
15 8 0.35
16 8 0.35
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (14 bp):
CACGTTTAAGAAGG
Found at i:197349 original size:23 final size:22
Alignment explanation
Indices: 197296--197349 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
197286 TATTAAAACA
197296 TTTAA-AAATATATTTATACTT
1 TTTAATAAATATATTTATACTT
*
197317 TTTAAT-AATATA-TTATTTCTCT
1 TTTAATAAATATATTTA-TACT-T
197339 TTTAATAAATA
1 TTTAATAAATA
197350 AGTAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.11
21 14 0.50
22 7 0.25
23 4 0.14
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATAAATATATTTATACTT
Found at i:197445 original size:17 final size:17
Alignment explanation
Indices: 197412--197455 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
197402 ATTTTTATTA
*
197412 TTAAAAATAATAATAAT
1 TTAAAAATAACAATAAT
*
197429 TTAAAAATAACACTAAT
1 TTAAAAATAACAATAAT
*
197446 ATAAATAATA
1 TTAAA-AATA
197456 TTTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAATAACAATAAT
Found at i:197484 original size:19 final size:21
Alignment explanation
Indices: 197446--197490 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
197436 TAACACTAAT
197446 ATAA-ATAATATTTGATTAAA
1 ATAATATAATATTTGATTAAA
*
197466 TTAATATAATATTT-A-TAAA
1 ATAATATAATATTTGATTAAA
197485 ATAATA
1 ATAATA
197491 ATATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAATATAATATTTGATTAAA
Found at i:197501 original size:22 final size:24
Alignment explanation
Indices: 197462--197527 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
197452 AATATTTGAT
*
197462 TAAATTAATATAAT-ATTTATAAAA
1 TAAA-TAATATTATAATTTATAAAA
* *
197486 T-AATAATATT-TAATTTTTATAA
1 TAAATAATATTATAATTTATAAAA
*
197508 TAAATAATATTATTATTTAT
1 TAAATAATATTATAATTTAT
197528 TATATTTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 15 0.44
23 11 0.32
24 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATAATATTATAATTTATAAAA
Found at i:197517 original size:23 final size:24
Alignment explanation
Indices: 197472--197527 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
197462 TAAATTAATA
197472 TAATATTTATAAAATAATAATATT
1 TAATATTTATAAAATAATAATATT
* *
197496 TAATTTTTATAATA-AATAATA-T
1 TAATATTTATAAAATAATAATATT
*
197518 TATTATTTAT
1 TAATATTTAT
197528 TATATTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 7 0.25
24 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATTTATAAAATAATAATATT
Found at i:197855 original size:14 final size:14
Alignment explanation
Indices: 197822--197855 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
197812 ATATTTCTGG
*
197822 AAAATATTTTCCGA
1 AAAATGTTTTCCGA
*
197836 AAAATGTTTTCCGT
1 AAAATGTTTTCCGA
197850 AAAATG
1 AAAATG
197856 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Found at i:198199 original size:23 final size:23
Alignment explanation
Indices: 198150--198212 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
198140 GTGTTATATT
* **
198150 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
198173 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
198196 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
198213 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:198256 original size:26 final size:26
Alignment explanation
Indices: 198196--198283 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
198186 CTTTATTAAA
*
198196 ATATTATTTAAATATATAAATAATATTATT
1 ATATTA-TTAAATATA-AAAT--TTTTATT
*
198226 -CATTATTAAATATAAAATTTTTATT
1 ATATTATTAAATATAAAATTTTTATT
* *
198251 ATATTATTAAA-ATAAAAATATATATT
1 ATATTATTAAATAT-AAAATTTTTATT
198277 ATATTAT
1 ATATTAT
198284 ATATAATTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
25 8 0.16
26 26 0.51
27 4 0.08
28 9 0.18
29 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTATTAAATATAAAATTTTTATT
Found at i:198331 original size:34 final size:33
Alignment explanation
Indices: 198284--198364 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 33
198274 ATTATATTAT
198284 ATATAATTGATTATTTTATATAATATTAA-AAATATA
1 ATATAA-T-ATTATTTTATA-AATATTAATAAATA-A
198320 ATATAATATTA--TTATAAATATTAATAAATAA
1 ATATAATATTATTTTATAAATATTAATAAATAA
198351 ATA-AATATTATTTT
1 ATATAATATTATTTT
198365 GATGAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
30 7 0.17
31 12 0.29
32 12 0.29
34 4 0.10
35 1 0.02
36 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
ATATAATATTATTTTATAAATATTAATAAATAA
Found at i:198338 original size:22 final size:22
Alignment explanation
Indices: 198307--198349 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
198297 TTTTATATAA
198307 TATTAAAAATA-TAATATAATAT
1 TATTAAAAATATTAATA-AATAT
*
198329 TATTATAAATATTAATAAATA
1 TATTAAAAATATTAATAAATA
198350 AATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTAAAAATATTAATAAATAT
Found at i:198358 original size:30 final size:32
Alignment explanation
Indices: 198295--198362 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
198285 TATAATTGAT
198295 TATT-TTATATAATATTAAAAATATAATATAA
1 TATTATTATATAATATTAAAAATATAATATAA
198326 TATTATTATA-AATATTAATAAATA-AATA-AA
1 TATTATTATATAATATTAA-AAATATAATATAA
198356 TATTATT
1 TATTATT
198363 TTGATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 9 0.26
31 16 0.46
32 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TATTATTATATAATATTAAAAATATAATATAA
Found at i:198584 original size:42 final size:42
Alignment explanation
Indices: 198537--198653 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
198527 ATGAATTACA
*
198537 TTCCGAAAAACT-AATTACGTGAAACAAACAC-GGAAAACCATT
1 TTCCGAAAAA-TAAATTACGTGAAACAAACACAAGAAAA-CATT
* * * *
198579 TTCCGAAAAATGAATTACATAAAACAAACACAAGAAAATATT
1 TTCCGAAAAATAAATTACGTGAAACAAACACAAGAAAACATT
**
198621 TTCTAAAAAATAAATTACGTGAAACAAACACAA
1 TTCCGAAAAATAAATTACGTGAAACAAACACAA
198654 AAATTCAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 58 0.91
43 5 0.08
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.21
Consensus pattern (42 bp):
TTCCGAAAAATAAATTACGTGAAACAAACACAAGAAAACATT
Found at i:201475 original size:15 final size:15
Alignment explanation
Indices: 201457--201489 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
201447 TAAAAATTTT
201457 AATCATAATTTTTCA
1 AATCATAATTTTTCA
*
201472 AATCATAATTTTTTA
1 AATCATAATTTTTCA
201487 AAT
1 AAT
201490 AGTCCGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
AATCATAATTTTTCA
Found at i:221999 original size:22 final size:22
Alignment explanation
Indices: 221974--222027 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
221964 GAATCAGATT
221974 TAAAATATCACTAATAAAAAAC
1 TAAAATATCACTAATAAAAAAC
*
221996 TAAAATATCACTAATAAAAAAT
1 TAAAATATCACTAATAAAAAAC
222018 TAAAATATCA
1 TAAAATATCA
222028 AAGTATACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAATATCACTAATAAAAAAC
Found at i:224223 original size:16 final size:17
Alignment explanation
Indices: 224191--224224 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
224181 TTACTTTAGG
*
224191 TATCCGAAATTTTCGGA
1 TATCCGAAATATTCGGA
224208 TATCCGAAA-ATTCGGA
1 TATCCGAAATATTCGGA
224224 T
1 T
224225 CGGATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (17 bp):
TATCCGAAATATTCGGA
Found at i:224491 original size:25 final size:25
Alignment explanation
Indices: 224438--224492 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
224428 AGAGCGAATT
* * *
224438 TATAATATTTTAAGAGAGATAAATT
1 TATAAAATTTTAAGAGAAATAAATA
224463 TATAAAATTTTAAGAGTAAATAAAATA
1 TATAAAATTTTAAGAG-AAAT-AAATA
224490 TAT
1 TAT
224493 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.60
26 3 0.12
27 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (25 bp):
TATAAAATTTTAAGAGAAATAAATA
Found at i:228022 original size:60 final size:60
Alignment explanation
Indices: 227902--228054 Score: 166
Period size: 60 Copynumber: 2.6 Consensus size: 60
227892 ATTTGGATGG
* * * *
227902 ATTTG-GGATGAAATTGGAAGATTTAAAAGGTTT-AGGACTAATTTAGAATAATAATTATA
1 ATTTGAGGATGAAATTAGAATATTTAAAA-GTTTAAGGACAAATTTAGAATAATAATCATA
* * * **
227961 ATTTGAGGATGAAATTAAAATATTCAAAAGTTTAAGGACAAATTTAGAATTATTGTCATA
1 ATTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACAAATTTAGAATAATAATCATA
* * * *
228021 ATTTAAAGATGACATTAGAATGTTTAAAAGTTTA
1 ATTTGAGGATGAAATTAGAATATTTAAAAGTTTA
228055 GACACCTATT
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 9 0.12
60 68 0.88
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (60 bp):
ATTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACAAATTTAGAATAATAATCATA
Found at i:229957 original size:2 final size:2
Alignment explanation
Indices: 229950--229976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
229940 TTCCTCCCAG
229950 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
229977 GTGTTTTTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:232537 original size:2 final size:2
Alignment explanation
Indices: 232530--232589 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
232520 TCTGCTAATG
232530 TA TA TA 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
232572 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
232590 CATTGGTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:240239 original size:30 final size:30
Alignment explanation
Indices: 240180--240281 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
240170 CCCGAAAGAC
* *
240180 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
240209 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
240239 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
240269 CTGTCCATAGGTC
1 CTATCCAGAGGTC
240282 CCGAAGAACC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 19 0.28
30 48 0.72
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:240305 original size:31 final size:31
Alignment explanation
Indices: 240254--240331 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
240244 CAGAGGTCAT
*
240254 AAAGATCATCGGT-AACTGTCCATAGGTCCCG
1 AAAGA-CATAGGTAAACTGTCCATAGGTCCCG
* * *
240285 -AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAAG-ACATAGGTAAACTGTCCATAGGTCCCG
240316 AAAGACATAGGTAAAC
1 AAAGACATAGGTAAAC
240332 CCTCGACTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 8 0.21
31 28 0.72
32 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (31 bp):
AAAGACATAGGTAAACTGTCCATAGGTCCCG
Found at i:257337 original size:24 final size:24
Alignment explanation
Indices: 257310--257365 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
257300 GGCTCGATTT
257310 TCTTCCAATAGTCAGACCTTTTAA
1 TCTTCCAATAGTCAGACCTTTTAA
*
257334 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAATAGTCAGACCTTTTAA
*
257358 -ATTCCAAT
1 TCTTCCAAT
257366 TACTTACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (24 bp):
TCTTCCAATAGTCAGACCTTTTAA
Found at i:260174 original size:16 final size:17
Alignment explanation
Indices: 260153--260186 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
260143 TGAAGCTGCC
260153 TGCTGAGTTAATA-TGG
1 TGCTGAGTTAATAGTGG
260169 TGCTGAGTTAATAGTGG
1 TGCTGAGTTAATAGTGG
260186 T
1 T
260187 TTGTGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (17 bp):
TGCTGAGTTAATAGTGG
Found at i:266852 original size:21 final size:23
Alignment explanation
Indices: 266828--266882 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
266818 TTTATAGTCT
266828 ATTTTATAATATATT-TTT-TAA
1 ATTTTATAATATATTATTTGTAA
* *
266849 ATTTAATAAT-TATTATTTGTCA
1 ATTTTATAATATATTATTTGTAA
*
266871 ATTTTATTATAT
1 ATTTTATAATAT
266883 TTCATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 12 0.44
22 10 0.37
23 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTATAATATATTATTTGTAA
Found at i:267352 original size:38 final size:37
Alignment explanation
Indices: 267310--267417 Score: 159
Period size: 34 Copynumber: 2.9 Consensus size: 37
267300 TAATTATCTC
267310 AAAATTGTACATTTATTTTTAATTTTAATATTTTTAGA
1 AAAATT-TACATTTATTTTTAATTTTAATATTTTTAGA
*
267348 AAAA-TT--ATTTATTTTTATTTTTAATATTTTTAGA
1 AAAATTTACATTTATTTTTAATTTTAATATTTTTAGA
*
267382 AAAATTTTACATTTATTGTTAATTTTAATATTTTTA
1 AAAA-TTTACATTTATTTTTAATTTTAATATTTTTA
267418 TAAATTTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
34 31 0.49
36 3 0.05
37 1 0.02
38 28 0.44
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (37 bp):
AAAATTTACATTTATTTTTAATTTTAATATTTTTAGA
Found at i:269692 original size:17 final size:17
Alignment explanation
Indices: 269670--269705 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
269660 TTGTTTGGTC
269670 TTTATGCTTGCTTTAGT
1 TTTATGCTTGCTTTAGT
269687 TTTATGCTTGCTTTAGT
1 TTTATGCTTGCTTTAGT
269704 TT
1 TT
269706 CCTAACTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.61
Consensus pattern (17 bp):
TTTATGCTTGCTTTAGT
Found at i:282884 original size:75 final size:75
Alignment explanation
Indices: 282797--283020 Score: 362
Period size: 75 Copynumber: 3.0 Consensus size: 75
282787 ATTTCAAGAG
* *
282797 CCCCTAATACCGAAGACTGTGTTCTAGAGACTCAAAATGAATCTATATCTAAAAATGAGTTGTTT
1 CCCCTAATACCGAAGACTGTGTTCAAGAGACTCAACATGAATCTATATCTAAAAATGAGTTGTTT
282862 ATCTAGATAA
66 ATCTAGATAA
* *
282872 CCCCTAATACCGAAGACTGTGTTCCAGAGACTCAACATGAATCTATATCTAAAAATGAGTTATTT
1 CCCCTAATACCGAAGACTGTGTTCAAGAGACTCAACATGAATCTATATCTAAAAATGAGTTGTTT
282937 ATCTAGA-AA
66 ATCTAGATAA
* * *
282946 -ACCTGAATACTGAAGACTGTGTTCAAGAGACTCAACAGGAATCTATATCTAAAAATGAGTTGTT
1 CCCCT-AATACCGAAGACTGTGTTCAAGAGACTCAACATGAATCTATATCTAAAAATGAGTTGTT
283010 TATCTAGATAA
65 TATCTAGATAA
283021 TTTACCTTTA
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
73 3 0.02
74 65 0.47
75 71 0.51
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (75 bp):
CCCCTAATACCGAAGACTGTGTTCAAGAGACTCAACATGAATCTATATCTAAAAATGAGTTGTTT
ATCTAGATAA
Found at i:283355 original size:14 final size:14
Alignment explanation
Indices: 283336--283363 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
283326 CACAGACTCC
283336 GCATCAATCTATAT
1 GCATCAATCTATAT
283350 GCATCAATCTATAT
1 GCATCAATCTATAT
283364 CTAAAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
GCATCAATCTATAT
Found at i:284754 original size:24 final size:24
Alignment explanation
Indices: 284727--284775 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
284717 TTTAAAATAG
*
284727 AAAGTAATGGTATATAGATAATTT
1 AAAGTAATGGTACATAGATAATTT
284751 AAAGTAATGGTACATAGATAATTT
1 AAAGTAATGGTACATAGATAATTT
284775 A
1 A
284776 CCTTTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (24 bp):
AAAGTAATGGTACATAGATAATTT
Found at i:286986 original size:703 final size:707
Alignment explanation
Indices: 284764--287625 Score: 2924
Period size: 689 Copynumber: 4.0 Consensus size: 707
284754 GTAATGGTAC
* ** * * *
284764 ATAGATAATTTACCTTTACTTTGATAAAGAGTAATTCTCATCATGTAAATAGTTACATAGCATAT
1 ATAGATAATTTACCTTAACTTTG----A-AGTAAACCTCATCATGTAAATAATTACACATCATAT
* * * * *
284829 TA-GTTTTGCAGATAAAACATATA-CTATATCATACAAGTTATGT-CACTTGAATTTCTAAAAGT
61 TATG-TTTGCAGATAAAACATAAATC-ATATCATACAAATCATGTGCAC-TGAAATTGTAAAAGT
* *
284891 TTTCTAATTTATGCAACTTACAATAAGTAACAAATATTAGTAATGGAAGCAAAAGTCCTCGAGCA
123 TTT-T-ATTT-T--AACTTACAATAAATAACAAATATTAATAATGGAAGCAAAAGTCCTCGAGCA
* ** * * *
284956 CAAACACAAATTGTAGAAAAAGTATTTCAAAAATCAAAAAAATATTCTTCTTAAATTCAGGAA-C
183 CAAAGACAAGCTATAG-CAAAGT-TTTCAAAAATCAGAAAAATATTCTTCTTAAATTCAGGAAGC
* * *
285020 CCCTAATATTGAAAACCATTTTATAAAGACTCAACATTTTATATCTAAAATGGATAGCCAAGGTA
246 CCCTAATACTGAAAACCATTTTCTAAAGACTCAACATTCTATATCTAAAATGGATAGCCAAGGTA
* * * *
285085 TCAAGATAATTTTATTTTACCTTGATAGAGAGTAACTCTCATCATGTAAATAATTACACATATTG
311 TCAAGATAATTTTATTTTACCTCGATAGAGAGTAACCCTTATCATGTAAATAATTACTCATATTG
* * * * * *
285150 CTACTAGGGATAAAATGTATAGGTATCATACAGTTTACCTTTTCATCGATAAAAAGTAATATCAT
376 CTTCTATGAATAAAATGTATAGGTATCATACAGTTTACCTTTTTATCGATAAAGAGTAACATCAT
* * *
285215 TATGTAAATAGTTACACATTGTTTTTAGAGATAAAATGTATAGGTATCATAGAAA-CATGCAAAC
441 CATGTAAATAGTTACTCATTGTTTTTAGAGA-AAAATGTATAGGTATCATAGAAAGCATGCAAGC
* *
285279 TGAAGTTACAAAAGTTATTT-AATTTTAAGCAACTT-TTCAAGATTTAGTAATAGAAAAAAAGTT
505 TGAAGTTACAAAAGTTATTTGAA-TTTAAGCAACTTGTCCAGGATTTAGTAATAGAAAAAAA--T
* * *
285342 GATGATGAATGGAGATGAATGGAGACAAGATGTAGAAAAATACTTCAAAAATCAAAATAATATAC
567 --T-AT--A---A-ATCAATGGAGACAAGATGTAGCAAAATACTTCAAAAATCATAATAATATAC
* * * * *
285407 TTCTCAACTTTAAGAGCCCCTAA-AATTCAAAATCATATTCTAAAGAGTCGACATGAATCTATAT
623 TCCTCAACTTTAAGAGCCCCTAATGA-TCAAAACCATATTCCAAAGACTCGACATGAATCTATAT
285471 CTAAAATAGAAAATAACATTAT
687 CTAAAATA-AAAATAACATTAT
* * *
285493 ATAAATAATTTACCTTAACTTTGAAAAAGTGTAACCCTTATCATGTAAATAATTACAC--CATAT
1 ATAGATAATTTACCTTAACTTTG---AA--GTAAACCTCATCATGTAAATAATTACACATCATAT
** ** *
285556 TATGTTTGCAGATAAAACATAAATTGTATCATACAAATCATGTGC-CCAAAATTTATAAAAGTTT
61 TATGTTTGCAGATAAAACATAAATCATATCATACAAATCATGTGCACTGAAA-TTGTAAAAGTTT
* * ** * * *
285620 TTATTTTTATTTTTAACTTACAATAACAAATATTAGTAATAGAAGCAAAAGTCCTCAAGCACAAA
125 TTATTTTAACTTACAA--TA-AATAACAAATATTAATAATGGAAGCAAAAGTCCTCGAGCACAAA
* *
285685 GACAAGCTATAGCAAAGTGCTTCAAAAATCAGAAAAATATTCTTCTTAAATTCATG-AGCCCCTA
187 GACAAGCTATAGCAAAGT-TTTCAAAAATCAGAAAAATATTCTTCTTAAATTCAGGAAGCCCCTA
* * * * * *
285749 ATACTGAAAACCATTTTCTAAAAACTCAGCATTTTATATCTACAATGGGTAAGTCAAGGTATCAA
251 ATACTGAAAACCATTTTCTAAAGACTCAACATTCTATATCTAAAATGGAT-AGCCAAGGTATCAA
* * ** * * *
285814 AATAATTTTATTTTACCTAGATAGAGAGTAAGTCTCAATCATATAAATAGTTACTCATATTGCTT
315 GATAATTTTATTTTACCTCGATAGAGAGTAACCCT-TATCATGTAAATAATTACTCATATTGCTT
* * **
285879 CTAT-AGATAAAA--TATACGGATATCATATAGTTTACCTTTTTATCGATAGAGAGTAATGTCAT
379 CTATGA-ATAAAATGTATA-GG-TATCATACAGTTTACCTTTTTATCGATAAAGAGTAACATCAT
* *
285941 CAAGTAAATAGTTACTCATTGTTTTCAGAGAAAAAATGTATAGGTATCATAGAAAGCATGCAAGC
441 CATGTAAATAGTTACTCATTGTTTTTAGAG-AAAAATGTATAGGTATCATAGAAAGCATGCAAGC
* * *
286006 TGAAGTTACATAAA-TTATTTGATTTTAAGCAACTTG-CCAGGATATAGTAATAG--AAGAA--A
505 TGAAGTTACA-AAAGTTATTTGAATTTAAGCAACTTGTCCAGGATTTAGTAATAGAAAAAAATTA
* * *
286065 -AAA-CAATGGAGACAAGTTGTAGC-AAATACTTCAAAAATCATAATAATCTATTCCTCAACTTT
569 TAAATCAATGGAGACAAGATGTAGCAAAATACTTCAAAAATCATAATAATATACTCCTCAACTTT
* * * *
286127 TAGAGCCCCTAATGTTCAAAACCATATTCCAAAGACTCAACAAGAATCTATATCTAAAATAGAAA
634 AAGAGCCCCTAATGATCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAAT--AAA
*
286192 AACAACATTAT
697 AATAACATTAT
* * * *
286203 ATAGATAATTTATCTTAACTTTGATAAGGAGTAACACTCATCATCTAAATAACTACACATCATAT
1 ATAGATAATTTACCTTAACTTTG--AAGTA--AAC-CTCATCATGTAAATAATTACACATCATAT
* ** * * *
286268 TACGTTTAAAGATAAAACATAAATCATGTCATACAAATCATGTACACTGAAATTGTAAATG-TTT
61 TATGTTTGCAGATAAAACATAAATCATATCATACAAATCATGTGCACTGAAATTGTAAAAGTTTT
* * *
286332 TA-TTTAACTTACAATAAATAATAAATATTAATAATGGAAGCAAAAATCCTTGAGCACAAAGACA
126 TATTTTAACTTACAATAAATAACAAATATTAATAATGGAAGCAAAAGTCCTCGAGCACAAAGACA
* * * *
286396 AGCTATAGCAAAGTTCATCAAAAATCAGAAAAATATTCTACTTAAATTCA-GAAGCTCCTAATAT
191 AGCTATAGCAAAGTT-TTCAAAAATCAGAAAAATATTCTTCTTAAATTCAGGAAGCCCCTAATAC
* * *
286460 TGAAAACCATTTTCTAAAGACTCAACATTCTATATTTAAAATGGATAGCCGATGTATCAAGATAA
255 TGAAAACCATTTTCTAAAGACTCAACATTCTATATCTAAAATGGATAGCCAAGGTATCAAGATAA
* *
286525 TTTTATTTTACTTCGATAGAGAGTAACCCTTGTCATGTAAATAATTACTCATATTGCTTCTATGA
320 TTTTATTTTACCTCGATAGAGAGTAACCCTTATCATGTAAATAATTACTCATATTGCTTCTATGA
* *
286590 ATAAAATGTATAGGTATCATACAATTTACCTTTTTATCGATAAAGAGTAACATAATCATGTAAAT
385 ATAAAATGTATAGGTATCATACAGTTTACCTTTTTATCGATAAAGAGTAACATCATCATGTAAAT
* * * *
286655 AGTTATTCATTGTTTTTAGAG-AGAATGTATAGGTATCATAGAAAGTATGCAAGTTGAAGTTACA
450 AGTTACTCATTGTTTTTAGAGAAAAATGTATAGGTATCATAGAAAGCATGCAAGCTGAAGTTACA
* * ** *
286719 AATGTTATTTGAATTTAAGTAACTTGTGGA-GATTTAATAATAGAAGAAAAATCT-TACAATCAA
515 AAAGTTATTTGAATTTAAGCAACTTGTCCAGGATTTAGTAATAGAA-AAAAAT-TATA-AATCAA
** * *
286782 TTAAGACAAGATGTAGCAAAATACTTCAAAAGTCATAATAATATACTCCTCAACTTCAAGAGCCC
577 TGGAGACAAGATGTAGCAAAATACTTCAAAAATCATAATAATATACTCCTCAACTTTAAGAGCCC
* * * * * *
286847 CTAATGATCAAAATCATACTCCAAAGGCTCGACGTGAATCTATATCTAAAAT-AAAGTAATATTA
642 CTAATGATCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAAAAATAACATTA
286911 T
707 T
*
286912 ATAGATAATTTACCTTAACATTG-AGTAAACCTCATCATGTAAATAATTACACATCATATTATGT
1 ATAGATAATTTACCTTAACTTTGAAGTAAACCTCATCATGTAAATAATTACACATCATATTATGT
* * * *
286976 TTGCAGATAAAACATAAATCATATCATGCAAATCATGTGCATTGAATTTGTAAAAG--ATT-TTT
66 TTGCAGATAAAACATAAATCATATCATACAAATCATGTGCACTGAAATTGTAAAAGTTTTTATTT
* * * * *
287038 T-ACTT----TGAACTTAC----AGTAA-AA---AA-CAAAAGTCATCGACCA-ATAAGACAAGC
131 TAACTTACAAT-AAATAACAAATATTAATAATGGAAGCAAAAGTCCTCGAGCACA-AAGACAAGC
* * * * * * *
287088 CATAGCAAAATGTTTCAAAACTCAGAAAAATATTCTTTTTAAATTCAAG-AGTCCTTAATACTGA
194 TATAGCAAAGT-TTTCAAAAATCAGAAAAATATTCTTCTTAAATTCAGGAAGCCCCTAATACTGA
* * * * *
287152 AAACCATTTTCTAAAGACT-AATCATCCAATATCTAAAATGTG-TAGTCAATGTATCAAGGTAAT
258 AAACCATTTTCTAAAGACTCAA-CATTCTATATCTAAAATG-GATAGCCAAGGTATCAAGATAAT
* * * * * *
287215 TTTATTTTTCCTCGACAGAGAGTAATCCTTATCATGTAAATAGTTACTCATATTGTTTCTATGGA
321 TTTATTTTACCTCGATAGAGAGTAACCCTTATCATGTAAATAATTACTCATATTGCTTCTATGAA
* * * * * *
287280 TAAAATGCAGAGGTATCAAACAGTTGA-CTTTTTCATCAATAAAGAGTAACGTCATCATGTAAAT
386 TAAAATGTATAGGTATCATACAGTTTACCTTTTT-ATCGATAAAGAGTAACATCATCATGTAAAT
* * * *
287344 AGTTACTCAATGTTTTTAGAGAGAAAGTGTATAAGTATCATAGAAAGTATGCAAGCTGAAGTTAC
450 AGTTACTCATTGTTTTTAGAGA-AAAATGTATAGGTATCATAGAAAGCATGCAAGCTGAAGTTAC
** * * ** *
287409 AAAAGTTATTTG-ATTCTTTGCAATTTGT-CAGGATTTAGTAATAGAAAAAAATGCTCTTTATGA
514 AAAAGTTATTTGAATT-TAAGCAACTTGTCCAGGATTTAGTAATAGAAAAAAAT--TATAAATCA
* * * * * *
287472 ATGGAGACAAGTTGTAGTAAAATACTTAAAAAATCATAATAACATACTCCTCAACTTGAGGAGCC
576 ATGGAGACAAGATGTAGCAAAATACTTCAAAAATCATAATAATATACTCCTCAACTTTAAGAGCC
** * * * * * *
287537 TTTGATGTTTAAAACCATATTCCAAAGACTAGACATGAA--TATGTCTAAAATAGAAAGTAACAT
641 CCTAATGATCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATA-AAAATAACAT
287600 TAT
705 TAT
* * *
287603 ATATATAATTTACCATAATTTTG
1 ATAGATAATTTACCTTAACTTTG
287626 GGTAACCTTC
Statistics
Matches: 1804, Mismatches: 267, Indels: 162
0.81 0.12 0.07
Matches are distributed among these distances:
688 9 0.00
689 259 0.14
690 15 0.01
691 192 0.11
692 1 0.00
693 2 0.00
694 4 0.00
697 1 0.00
698 4 0.00
701 4 0.00
702 7 0.00
703 150 0.08
704 4 0.00
705 98 0.05
706 52 0.03
707 144 0.08
708 2 0.00
709 123 0.07
710 79 0.04
711 24 0.01
712 138 0.08
713 4 0.00
715 1 0.00
718 1 0.00
722 5 0.00
723 1 0.00
724 96 0.05
725 104 0.06
726 122 0.07
727 105 0.06
728 9 0.00
729 44 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (707 bp):
ATAGATAATTTACCTTAACTTTGAAGTAAACCTCATCATGTAAATAATTACACATCATATTATGT
TTGCAGATAAAACATAAATCATATCATACAAATCATGTGCACTGAAATTGTAAAAGTTTTTATTT
TAACTTACAATAAATAACAAATATTAATAATGGAAGCAAAAGTCCTCGAGCACAAAGACAAGCTA
TAGCAAAGTTTTCAAAAATCAGAAAAATATTCTTCTTAAATTCAGGAAGCCCCTAATACTGAAAA
CCATTTTCTAAAGACTCAACATTCTATATCTAAAATGGATAGCCAAGGTATCAAGATAATTTTAT
TTTACCTCGATAGAGAGTAACCCTTATCATGTAAATAATTACTCATATTGCTTCTATGAATAAAA
TGTATAGGTATCATACAGTTTACCTTTTTATCGATAAAGAGTAACATCATCATGTAAATAGTTAC
TCATTGTTTTTAGAGAAAAATGTATAGGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTT
ATTTGAATTTAAGCAACTTGTCCAGGATTTAGTAATAGAAAAAAATTATAAATCAATGGAGACAA
GATGTAGCAAAATACTTCAAAAATCATAATAATATACTCCTCAACTTTAAGAGCCCCTAATGATC
AAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAAAAATAACATTAT
Found at i:288380 original size:21 final size:21
Alignment explanation
Indices: 288338--288380 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
288328 TTTCTGGGCT
* *
288338 AGGGGAATCGATACCCATTCA
1 AGGGAAATCGATACCCACTCA
*
288359 AGGGAAATCGATACCCCCTCA
1 AGGGAAATCGATACCCACTCA
288380 A
1 A
288381 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (21 bp):
AGGGAAATCGATACCCACTCA
Found at i:289254 original size:103 final size:103
Alignment explanation
Indices: 288926--289246 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
288916 GTAGAGGGTC
*
288926 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
288991 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
289029 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
**
289094 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
289132 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
289197 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
289235 TATGTGGTCCTT
1 TATGTGGTCCTT
289247 ATGGACATTA
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:289296 original size:23 final size:23
Alignment explanation
Indices: 289263--289325 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
289253 ATTATTATAT
*
289263 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
* *
289286 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
289309 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
289326 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:291678 original size:9 final size:9
Alignment explanation
Indices: 291664--291691 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
291654 CTTAGCAAAT
291664 GTAATGTCA
1 GTAATGTCA
291673 GTAATGTCA
1 GTAATGTCA
291682 GTAATGTCA
1 GTAATGTCA
291691 G
1 G
291692 CTAAGAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (9 bp):
GTAATGTCA
Found at i:294917 original size:10 final size:10
Alignment explanation
Indices: 294902--294931 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
294892 TCCAGAGTCA
294902 TCTTCTTCTT
1 TCTTCTTCTT
294912 TCTTCTTCTT
1 TCTTCTTCTT
294922 TCTTCTTCTT
1 TCTTCTTCTT
294932 CATACATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:295462 original size:20 final size:20
Alignment explanation
Indices: 295437--295474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
295427 GAACGCTAGA
*
295437 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
295457 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
295475 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:296284 original size:103 final size:103
Alignment explanation
Indices: 295956--296272 Score: 607
Period size: 103 Copynumber: 3.1 Consensus size: 103
295946 GTAGAGGGTC
295956 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
296021 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
296059 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
296124 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
296162 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
296227 TTGATCATTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
296265 TATGTGGT
1 TATGTGGT
296273 TCTTATGGAC
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:296327 original size:23 final size:23
Alignment explanation
Indices: 296301--296355 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
296291 ATGACACTAC
*
296301 GGTGTAATTCTACGCGGCACTCT
1 GGTGCAATTCTACGCGGCACTCT
*
296324 GGTGCAATTCTACGTGGCACT-T
1 GGTGCAATTCTACGCGGCACTCT
296346 AGGTGCAATT
1 -GGTGCAATT
296356 ATATGAGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCT
Found at i:298393 original size:602 final size:600
Alignment explanation
Indices: 296946--300005 Score: 5351
Period size: 602 Copynumber: 5.1 Consensus size: 600
296936 GGTGTTACAT
* *
296946 TCATCGTGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGA
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
* * *
297011 TTCTAAACTCAGAAAAATATTATTTTTAAATTCAAGAGTCCTTAATACTGAAAACCATTTTCTAA
66 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
*
297076 AGACTAAACATTCAATATCTAAAATGTGTAGTCAAGATATCAAGGTAATTTTATTTTTCCTCGAC
131 AGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGAC
* * *
297141 AGAGAGTAATCCTCATCAAGTAAATAGTTACTCATATTGTATCTATGGATAAATTGCAGAGGTAT
196 AGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTAT
* * **
297206 CAAACATTTGACTTTTTCATCAATAAAGAGAAACACCATCATGTAAATAGTTACTCAATGTTTTT
261 CAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTTT
*
297271 AGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGTTGAAGTTACAAAAGTTATTTGATTCT
326 AGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATTCT
* ** *
297336 TAGCAATTTGTCAAGATTTAGTAATAG-AAAAAATGCTCTTTATGAATAGAGACAAGATGTAGTA
391 TAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAAACTCTTTATGAATGGAGACAAGATGTAGTA
* *
297400 AAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGATCCTTTGATGTTTAAAGCCATA
456 AAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCATA
*
297465 TTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGCAACATTATATATATAATTTACCTT
521 TTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATAATTTACCTT
*
297530 AATTTTGGGTAATCC
586 AATTTTGGGTAACCC
*
297545 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAAATAAAACATAAGTCATAGCAAAATGT
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
*
297610 TTCAAAACTCAAAAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTA
66 TTCAAAACTC-AGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTA
297675 AAGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGA
130 AAGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGA
* * * *
297740 CAGAGAGTAATCCTCATCATGTAAATAATTACTCTTATTGTTTCTATGGATAAAATGTAGATGTA
195 CAGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTA
* * *
297805 TCAAACAGTTGACTTTTTCATCAATAAAGAGTAGCGTTGA-CGTGTAAATAGTTACTCAATGTTT
260 TCAAACAGTTGACTTTTTCATCAATAAAGAGTAACG-TCATCATGTAAATAGTTACTCAATGTTT
* *
297869 TTAAAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAATTATTTGATT
324 TTAGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATT
297934 CTTAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAAACTCTTTATGAATGGAGACAAGATGTAG
389 CTTAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAAACTCTTTATGAATGGAGACAAGATGTAG
297999 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
454 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
298064 TATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATATAATTTA
519 TATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACA-T-TATATATATAATTTA
*
298129 CTTTAATTTTGGGTAACCC
582 CCTTAATTTTGGGTAACCC
298148 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
298213 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
66 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
* *
298278 AGACTAAACATTCAATATCTAAAATGCGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGAT
131 AGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGAC
*
298343 AGAGAGTAATCCTCATCATGTAAATAGTTACTCGTATTGTTTCTATGGATAAAATGCAGAGGTAT
196 AGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTAT
*
298408 CAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATATTTTT
261 CAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTTT
*
298473 AGAGAGAAAGTGTATAAGTATCATAGAAAGCAAGCAAGCTGAAGTTACAAAAGTTATTTGATTCT
326 AGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATTCT
* *
298538 TAGCAATTTGTCTGGATTTAGTAATAGAAAAAAAAACACTTTTTATGAATGGAGACAAGATGTAG
391 TAGCAATTTGTCAGGATTTAGTAATAG-AAAAAAAA-ACTCTTTATGAATGGAGACAAGATGTAG
298603 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
454 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
* *
298668 TATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATAGAATTTTCC
519 TATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATAATTTACC
298733 TTAATTTTGGGTAACCC
584 TTAATTTTGGGTAACCC
*
298750 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAACGT
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
298815 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
66 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
298880 AGACTAAACATTCAATATCTAAAATGTGTAGTC-AGTGTATCAAGGTAATTTTATTTTTCCTCGA
131 AGACTAAACATTCAATATCTAAAATGTGTAGTCAAG-GTATCAAGGTAATTTTATTTTTCCTCGA
298944 CAGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTA
195 CAGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTA
* * *
299009 TCAAACATTTGACTTTTTCATAAATAAAGAGTAACGTCATCATGTAAATAGTTATTCAATGTTTT
260 TCAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTT
299074 TAGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAA-TTATTTGATTC
325 TAGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATTC
299138 TTAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAACACTCTTTATGAATGGAGACAAGATGTAG
390 TTAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAA-ACTCTTTATGAATGGAGACAAGATGTAG
299203 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
454 TAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCA
* *
299268 TATTCCAAAGACTAGAAATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATAGTTTACC
519 TATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATAATTTACC
*
299333 TTAATTTTGGGTTACCC
584 TTAATTTTGGGTAACCC
*
299350 TCATCATGTAAATAATTACACATCAAATTATATTTGCAGATAAAACATAAGTCATAGCAAAATGT
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
* ** *
299415 TTCAAAACTCATAAAAATATTCTTTTTAAATTCAATAGT-C--AATATTGAAAACCATTTTCTAA
66 TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
* *
299477 AGACTAAACATTCAATATCTAAAATGTCTAGTCAAGGTATCAAGGTAATTTTATTTTCCCTCGAC
131 AGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGAC
* *
299542 AGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATACAAAGGTAT
196 AGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTAT
*
299607 CAAACAGTTAACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTTT
261 CAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTTT
* * * *
299672 AGATAGAAAGTGTATAACTATCATAGAAAGCATGCAAGATGAAGTTACAAAAGTTATTTGATTAT
326 AGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATTCT
* *
299737 TAGCAATTTGTCAGGATTTAGTAATAGAAAAAAACACTCTTTATGAATGGAGACAAGATGTACTA
391 TAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAAACTCTTTATGAATGGAGACAAGATGTAGTA
*
299802 AAATACTTCAAAAATCATAATAACATACTCCTCAACTTGTGGAGCCTTTGATGTTTAAAACCATA
456 AAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCATA
299867 TTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATATATAATTTA
521 TTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAAC---AT-TATATATATAATTTA
*
299932 CCTTAATTTTCGGTAACCC
582 CCTTAATTTTGGGTAACCC
299951 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCAT
1 TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCAT
300006 TTCATGTAAA
Statistics
Matches: 2350, Mismatches: 96, Indels: 28
0.95 0.04 0.01
Matches are distributed among these distances:
597 390 0.17
598 47 0.02
599 72 0.03
600 597 0.25
601 269 0.11
602 721 0.31
603 115 0.05
604 139 0.06
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (600 bp):
TCATCATGTAAATAATTACACATCAAATTATGTTTGCAGATAAAACATAAGTCATAGCAAAATGT
TTCAAAACTCAGAAAAATATTCTTTTTAAATTCAGGAGTCCTTAATACTGAAAACCATTTTCTAA
AGACTAAACATTCAATATCTAAAATGTGTAGTCAAGGTATCAAGGTAATTTTATTTTTCCTCGAC
AGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAAAATGCAGAGGTAT
CAAACAGTTGACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTTACTCAATGTTTTT
AGAGAGAAAGTGTATAAGTATCATAGAAAGCATGCAAGCTGAAGTTACAAAAGTTATTTGATTCT
TAGCAATTTGTCAGGATTTAGTAATAGAAAAAAAAACTCTTTATGAATGGAGACAAGATGTAGTA
AAATACTTCAAAAATCATAATAACATACTCCTCAACTTGAGGAGCCTTTGATGTTTAAAACCATA
TTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTATATATATAATTTACCTT
AATTTTGGGTAACCC
Found at i:300950 original size:709 final size:708
Alignment explanation
Indices: 299403--301989 Score: 3133
Period size: 714 Copynumber: 3.6 Consensus size: 708
299393 AACATAAGTC
* * ** * ** * *
299403 ATAGCAAAATGTTTCAAAACTCATAAAAATATTCTTTTTAAATTCAATAG---T-CAATATTGAA
1 ATAGCAAAGTGCTTCAAAACTCGGAAAAATATTCTTCTTAAATTCAGGAGCCCTATAATACTGAA
* * * * * *
299464 AACCATTTTCTAAAGACTAAACATTCAATATCTAAAATGTCTAGTCAAGGTATCAAGGTAATTTT
66 AACCATCTTCTAAAGACTCAACATTCTATATCTAAAATGTGTAGCCAAGGTATCAAGATAATTTT
* * * *
299529 ATTTTCCCTCGACAGAGAGTAATCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAA
131 ATTTTACCTCGATAGAAAGTAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAA
* * * * * ** * *
299594 AATACAAAGGTATCAAACAGTTAACTTTTTCATCAATAAAGAGTAACGTCATCATGTAAATAGTT
196 AATATATAGGTATCACACAATTTACCATTCCATCGATAAAGAGTAACGTCATCATGTAAATAGTT
* * * * * *
299659 ACTCAATGTTTTTAGATAGAAAGTGTATAACTATCATAGAAAGCATGCAAGATGAAGTTACAAAA
261 ACTC-AT-TTTTTTGAGAGAAAATGTATAAGTATCATAGAAAGCATGCAAGTTGAACTTACAAAA
* * * * *
299724 GTTATTTGATTATTAGCAATTTGTCAGGATTTAGTAATAGAAA-AAAACA-CTCTTTATGAATGG
324 GTTATTTGATTCTAAGCAACTTGTCAGGATTTAGTAATA-AAAGAAAA-AGCTCATTATGAATAG
** **
299787 AGACAAGATGTA-CTAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTGTGGAGCCTTT
387 AGACAAGATGTAGC-AAAATACTTCAAAAATCATAATAACATACTCCTCAACTTCAGGAGCCCCT
* * * *
299851 GATGTTTAAAACCATATTCCAAAGACTAGACATGAATCTATGTCTAAAATAGAAAGTAACATTAT
451 AATGTTCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAGAAAGTAAC---AT
* * *
299916 ATATATATATAATTTACCTTAATTTTCG-GTAACCCTCATCATGTAAATAATTACACATCAAATT
513 -TATATAGATAATTTACCTTAACTTT-GAGTAACCCTCATCATGTAAATAATTACACATCATATT
* * ** *
299980 ATGTTTGCAGATAAAACATAAGTCATTTCATGTAAAAAAATGTGCATTGAATTTGTAAAAAAATT
576 ATGTTTGCAGATAAAACATAAGTCATATCATG-CAAATCATGTGCACTGAATTTGTAAAAAAATT
* * *
300045 ATTTTTAACTTACATTAAGTAACAAATATTAGTAATAGAAGCAAATGTCCTCGAGTACAAAGACA
640 ATTTTTAACTTACAGTAAGTAACAAATATTAGTAATAGAAGCAAAAGTCCTCGAGCACAAAGACA
300110 AGCT
705 AGCT
** * *
300114 ATAGCAAAGTGCTTCAAAACTCAAAAAAATATTCTTCTTAAATTCAGGAGCCCCA-AATACTAAA
1 ATAGCAAAGTGCTTCAAAACTCGGAAAAATATTCTTCTTAAATTCAGGAGCCCTATAATACTGAA
* * * * *
300178 AACCATCTTCTAAACACTCAACCTTTTATATCTAAAATGTGTAGCCAAGGAATCAAAATAATTTT
66 AACCATCTTCTAAAGACTCAACATTCTATATCTAAAATGTGTAGCCAAGGTATCAAGATAATTTT
* * *
300243 ATTTTACCTCGATAGAAAGTAACCCTCATCATGTAAATATTTACTCATATTATTTATATGGATAA
131 ATTTTACCTCGATAGAAAGTAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAA
*
300308 AATATATAGGTATCACACAATTTACCATTCCATCGATAAAGAGTAATGTCATCATGTAAATAGTT
196 AATATATAGGTATCACACAATTTACCATTCCATCGATAAAGAGTAACGTCATCATGTAAATAGTT
* *
300373 ACTCATTTTTTTAGAGAGAAAATGTATAAATATCATAGAAAGCATGCAAGTTGAACTTACAAAAA
261 ACTCATTTTTTT-GAGAGAAAATGTATAAGTATCATAGAAAGCATGCAAGTTGAACTTACAAAAG
* * *
300438 TTATTTGATTCTAAGCAATTTTTCAGGATTTAGTAATAAAAGAAAAAGCTCATTATGAATGGAGA
325 TTATTTGATTCTAAGCAACTTGTCAGGATTTAGTAATAAAAGAAAAAGCTCATTATGAATAGAGA
*
300503 CAAGATGTAGCAAAATATTTCAAAAATCATAATAACATACTCCTCAACTTCAGGAGCCCCTAATG
390 CAAGATGTAGCAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTCAGGAGCCCCTAATG
* **
300568 TTCAAAACCTTATTCCAAAGACTCGACATGAATCTATATAAAAAATAGAAAGTAACATTATATAG
455 TTCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAGAAAGTAACATTATATAG
* *
300633 ATAATTTATCTTAACTTTGAGTAACCCTTATCATGTAAATAATTACACATCATATTATGTTTGCA
520 ATAATTTACCTTAACTTTGAGTAACCCTCATCATGTAAATAATTACACATCATATTATGTTTGCA
***
300698 GATAAAACATAAGTCATATCATGCAAATCATGTGCACTGAATTTGTAAAAGTTTTTATTTTTAAC
585 GATAAAACATAAGTCATATCATGCAAATCATGTGCACTGAATTTGTAAAA-AAATTATTTTTAAC
* * *
300763 TTACAGTAAGTAACAAATATTAGTAATAGAAGCAAAAGTCCTTGGGCGCAAAGACAAGCT
649 TTACAGTAAGTAACAAATATTAGTAATAGAAGCAAAAGTCCTCGAGCACAAAGACAAGCT
*** * * * *
300823 ATTTTAAAGTTCTTCAAAAATCGGAAAAATATTCTTCTAAAATTAAGGAG-CCTATAATACTGAA
1 ATAGCAAAGTGCTTCAAAACTCGGAAAAATATTCTTCTTAAATTCAGGAGCCCTATAATACTGAA
* * * * * *
300887 AACCATATTCTAAGGATTCAACATTCTATATATGAAATGGGTAGCCAAGGTA-CGAAGATAATTT
66 AACCATCTTCTAAAGACTCAACATTCTATATCTAAAATGTGTAGCCAAGGTATC-AAGATAATTT
*
300951 TATTTTACCTCGATA-AACAATAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGAT
130 TATTTTACCTCGATAGAA-AGTAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGAT
* * * * * * * *
301015 AAAATGTATAGGTATCATATAGTTTACCTTTTCATTGATAAAGAGTAACGTCATCATATAAATAG
194 AAAATATATAGGTATCACACAATTTACCATTCCATCGATAAAGAGTAACGTCATCATGTAAATAG
* * *
301080 TTACTCATTGGTTTTTGAGAGAAAACGTATAGGTATCATATAAAGCATGCAAGTTGAACTTACAA
259 TTACTCATT--TTTTTGAGAGAAAATGTATAAGTATCATAGAAAGCATGCAAGTTGAACTTACAA
* * * * *
301145 AACTTATTTGATTCTAAGCAACTTCTCGGGATTTAGTAA-AAGGAGAAAAAGCT-TTTCATGAAT
322 AAGTTATTTGATTCTAAGCAACTTGTCAGGATTTAGTAATAA-AAGAAAAAGCTCATT-ATGAAT
* * * *
301208 AGAGACAAAATGT-GACAAAATACTTCGAAAATCATAATAATATACTCCTCAACATCAGGAGCCC
385 AGAGACAAGATGTAG-CAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTCAGGAGCCC
* * *
301272 CTAATGTTCAAAACCATATTCCAAAGACTCGGCATGAATCCATATCTAAAATAGAAAGAAACATT
449 CTAATGTTCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAGAAAGTAACATT
* * * *
301337 ATATAGATAATTTACCATAACTTTGAGTAACCCTCATTATATAAATAATTACACATCATATTGTG
514 ATATAGATAATTTACCTTAACTTTGAGTAACCCTCATCATGTAAATAATTACACATCATATTATG
* * * ** *
301402 TTTGTAGAAAAAAAAACATAAATCATATCACACAAATCGTGTGCACTGAATTTGTAAAAAAAAAA
579 TTTGCAG---ATAAAACATAAGTCATATCATGCAAATCATGTGCACTGAATTTGT---AAAAAAA
* * *
301467 TTATTTCTAACTTACAGTATGTAACAAATCTTAGTAATA-AAGCAAAAGTCCTCGAGCACAAAGA
638 TTATTTTTAACTTACAGTAAGTAACAAATATTAGTAATAGAAGCAAAAGTCCTCGAGCACAAAGA
*
301531 AAAGCT
703 CAAGCT
301537 ATAGCAAAGTGCTTCAAAACTCTGG-AAAATATTCTTCTTAAATTCAGGAGCCCT-TAATACTGA
1 ATAGCAAAGTGCTTCAAAACTC-GGAAAAATATTCTTCTTAAATTCAGGAGCCCTATAATACTGA
* * *
301600 AAACCATCTTCTAAGGACTCAACATTCTATATCTAAAATATGTAGCCACGGTATCAAGATAATTT
65 AAACCATCTTCTAAAGACTCAACATTCTATATCTAAAATGTGTAGCCAAGGTATCAAGATAATTT
* * * * * *
301665 TATTTTACCTCAATATAGAGCAACCCTCATAATGTAAATAGTTACTCATATTGCTTCTATGGATA
130 TATTTTACCTCGATAGAAAGTAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATA
* * * ** *
301730 ATATGTATATGTATCACACAGTTTACATTTTGATAAGTTTACCTTTTGATTGATAAAGAGTAACG
195 AAATATATAGGTATCACAC-----A-A-TTT-ACCA--TT-CC-----ATCGATAAAGAGTAACG
* *
301795 TCATCATGTAAATAGTTACTCATTTTTTT-AGAGAAAATGTATTAGTATCATAAAAAGCATGCAA
244 TCATCATGTAAATAGTTACTCATTTTTTTGAGAGAAAATGTATAAGTATCATAGAAAGCATGCAA
* * * * * *
301859 GCTGAAGTTACAAAAGTTCTTTGATTCTATGCAACTTGTCAGGATTTAGTAATAGAAGAAAAAGT
309 GTTGAACTTACAAAAGTTATTTGATTCTAAGCAACTTGTCAGGATTTAGTAATAAAAGAAAAAGC
* * * * *
301924 TCACTATGAATATAGACAAGATGTAACAAAATACTTAAAAAAAATCATAATAAAATACTCCTCAA
374 TCATTATGAATAGAGACAAGATGTAGCAAAATACTT--CAAAAATCATAATAACATACTCCTCAA
301989 C
437 C
301990 ATACTGAAAA
Statistics
Matches: 1617, Mismatches: 210, Indels: 80
0.85 0.11 0.04
Matches are distributed among these distances:
708 30 0.02
709 379 0.23
710 278 0.17
711 49 0.03
712 9 0.01
713 250 0.15
714 383 0.24
715 43 0.03
716 4 0.00
719 1 0.00
721 3 0.00
722 1 0.00
724 2 0.00
725 1 0.00
727 112 0.07
728 7 0.00
729 25 0.02
730 40 0.02
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (708 bp):
ATAGCAAAGTGCTTCAAAACTCGGAAAAATATTCTTCTTAAATTCAGGAGCCCTATAATACTGAA
AACCATCTTCTAAAGACTCAACATTCTATATCTAAAATGTGTAGCCAAGGTATCAAGATAATTTT
ATTTTACCTCGATAGAAAGTAACCCTCATCATGTAAATAGTTACTCATATTGTTTCTATGGATAA
AATATATAGGTATCACACAATTTACCATTCCATCGATAAAGAGTAACGTCATCATGTAAATAGTT
ACTCATTTTTTTGAGAGAAAATGTATAAGTATCATAGAAAGCATGCAAGTTGAACTTACAAAAGT
TATTTGATTCTAAGCAACTTGTCAGGATTTAGTAATAAAAGAAAAAGCTCATTATGAATAGAGAC
AAGATGTAGCAAAATACTTCAAAAATCATAATAACATACTCCTCAACTTCAGGAGCCCCTAATGT
TCAAAACCATATTCCAAAGACTCGACATGAATCTATATCTAAAATAGAAAGTAACATTATATAGA
TAATTTACCTTAACTTTGAGTAACCCTCATCATGTAAATAATTACACATCATATTATGTTTGCAG
ATAAAACATAAGTCATATCATGCAAATCATGTGCACTGAATTTGTAAAAAAATTATTTTTAACTT
ACAGTAAGTAACAAATATTAGTAATAGAAGCAAAAGTCCTCGAGCACAAAGACAAGCT
Found at i:301770 original size:16 final size:16
Alignment explanation
Indices: 301749--301779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301739 TGTATCACAC
301749 AGTTTACATTTTGATA
1 AGTTTACATTTTGATA
*
301765 AGTTTACCTTTTGAT
1 AGTTTACATTTTGAT
301780 TGATAAAGAG
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:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (16 bp):
AGTTTACATTTTGATA
Found at i:304636 original size:18 final size:20
Alignment explanation
Indices: 304613--304656 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
304603 CTCACGTGAT
*
304613 AAAAATA-GTATTAGAT-TA
1 AAAAATATGTAATAGATGTA
*
304631 AAAAATATGTAATAGGTGTA
1 AAAAATATGTAATAGATGTA
304651 AAAAAT
1 AAAAAT
304657 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAAATATGTAATAGATGTA
Found at i:309020 original size:24 final size:24
Alignment explanation
Indices: 308988--309035 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
308978 ACACGTGGTT
308988 TAACTGATCTAGAAGAGTTGGGTC
1 TAACTGATCTAGAAGAGTTGGGTC
309012 TAACTGATCTAGAAGAGTTGGGTC
1 TAACTGATCTAGAAGAGTTGGGTC
309036 GAGCTGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (24 bp):
TAACTGATCTAGAAGAGTTGGGTC
Found at i:309477 original size:22 final size:22
Alignment explanation
Indices: 309452--309493 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
309442 GAAGTCAACA
309452 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
309474 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
309494 AGACAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:309524 original size:19 final size:20
Alignment explanation
Indices: 309502--309558 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
309492 TCAGACAAAT
309502 CAAACCGGTTC-AGACCGG-C
1 CAAACCGGTTCGA-ACCGGTC
*
309521 CAAAACGGTTCGAACCGGTC
1 CAAACCGGTTCGAACCGGTC
* *
309541 GAAACCGG-TCAAACCGGT
1 CAAACCGGTTCGAACCGGT
309559 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.30, C:0.32, G:0.26, T:0.12
Consensus pattern (20 bp):
CAAACCGGTTCGAACCGGTC
Found at i:309546 original size:10 final size:9
Alignment explanation
Indices: 309501--309558 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 9
309491 GTCAGACAAA
309501 TCAAACCGG
1 TCAAACCGG
*
309510 TTCAGACCGG
1 -TCAAACCGG
* *
309520 CCAAAACGG
1 TCAAACCGG
*
309529 TTCGAACCGG
1 -TCAAACCGG
309539 TCGAAACCGG
1 TC-AAACCGG
309549 TCAAACCGG
1 TCAAACCGG
309558 T
1 T
309559 TTCCAGCAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
9 16 0.42
10 22 0.58
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (9 bp):
TCAAACCGG
Found at i:316701 original size:5 final size:5
Alignment explanation
Indices: 316691--316759 Score: 70
Period size: 5 Copynumber: 13.8 Consensus size: 5
316681 AGAAGTCAAC
* * * *
316691 GGTCG GGTCG GATCG GGTCAAC GGTCA GGTCG GGTCG GGTC- GGTCG GGT-T
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
316741 GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
316760 AGGCCGGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 7 0.13
5 42 0.79
7 4 0.08
ACGTcount: A:0.06, C:0.20, G:0.52, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:316710 original size:22 final size:22
Alignment explanation
Indices: 316685--316731 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
316675 GTCAAAAGAA
*
316685 GTCAACGGTCGGGTCGGATCGG
1 GTCAACGGTCAGGTCGGATCGG
*
316707 GTCAACGGTCAGGTCGGGTCGG
1 GTCAACGGTCAGGTCGGATCGG
316729 GTC
1 GTC
316732 GGTCGGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCAGGTCGGATCGG
Found at i:316746 original size:18 final size:19
Alignment explanation
Indices: 316723--316758 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
316713 GGTCAGGTCG
316723 GGTCGGGTC-GGTCGGGTT
1 GGTCGGGTCGGGTCGGGTT
316741 GGTCGGGTCGGGTCGGGT
1 GGTCGGGTCGGGTCGGGT
316759 CAGGCCGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.58, T:0.25
Consensus pattern (19 bp):
GGTCGGGTCGGGTCGGGTT
Found at i:316811 original size:19 final size:20
Alignment explanation
Indices: 316780--316825 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
316770 AACTGGTTCG
*
316780 AACCGGTCAAAACC-AGTCGA
1 AACCGGTCAAAACCGA-TCAA
316800 AACCGGTC-AAACCGATCAA
1 AACCGGTCAAAACCGATCAA
316819 AACCGGT
1 AACCGGT
316826 TGAAAGCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (20 bp):
AACCGGTCAAAACCGATCAA
Found at i:316813 original size:29 final size:30
Alignment explanation
Indices: 316780--316845 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
316770 AACTGGTTCG
*
316780 AACCGGTCAAAACCAGTCGAAA-CCGGTCA
1 AACCGGTCAAAACCAGTCGAAAGCCAGTCA
* * *
316809 AACCGATCAAAACCGGTTGAAAGCCAGTCA
1 AACCGGTCAAAACCAGTCGAAAGCCAGTCA
*
316839 AATCGGT
1 AACCGGT
316846 TTCCAGCAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (30 bp):
AACCGGTCAAAACCAGTCGAAAGCCAGTCA
Found at i:324373 original size:12 final size:12
Alignment explanation
Indices: 324356--324407 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
324346 TTATATATAG
324356 ATATTAATTTTA
1 ATATTAATTTTA
324368 ATATTAATTTTTTA
1 ATATTAA--TTTTA
* *
324382 A-A-TAAATTAA
1 ATATTAATTTTA
324392 ATATTAATTTTA
1 ATATTAATTTTA
324404 ATAT
1 ATAT
324408 ATTTAGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 4 0.12
11 1 0.03
12 20 0.62
13 1 0.03
14 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATTAATTTTA
Found at i:325135 original size:31 final size:31
Alignment explanation
Indices: 325100--325159 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
325090 TAGTTGTATG
325100 AATTATTTAAATTTCAGTATT-ATAAAACTAA
1 AATTATTTAAATTTCAGTATTGA-AAAACTAA
325131 AATTATTTAAATTTCAGTATTGAAAAACT
1 AATTATTTAAATTTCAGTATTGAAAAACT
325160 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGAAAAACTAA
Found at i:350764 original size:30 final size:31
Alignment explanation
Indices: 350705--350765 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
350695 TTTAAATTTT
*
350705 AATAAAAATATTTTTTTAATAGTCAAATATTC
1 AATAAAAATATTTTTATAATAG-CAAATATTC
350737 AATAAAAATA-TTTTATAATTA-CAAATATT
1 AATAAAAATATTTTTATAA-TAGCAAATATT
350766 TACATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 12 0.44
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (31 bp):
AATAAAAATATTTTTATAATAGCAAATATTC
Found at i:352013 original size:6 final size:6
Alignment explanation
Indices: 352002--352031 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
351992 ATCAATTGTT
*
352002 ATCATA ATCATA ATCATA ATCAAA ATCATA
1 ATCATA ATCATA ATCATA ATCATA ATCATA
352032 TTATTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (6 bp):
ATCATA
Found at i:356278 original size:17 final size:21
Alignment explanation
Indices: 356251--356302 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
356241 AAAAATATAG
* *
356251 AATATATATATATTTAAATTA
1 AATATATATATATATAATTTA
356272 AATATATATATATATAATTTA
1 AATATATATATATATAATTTA
356293 AATATATATA
1 AATATATATA
356303 CCCGGCCCAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATATATATAATTTA
Found at i:356297 original size:15 final size:15
Alignment explanation
Indices: 356206--356302 Score: 60
Period size: 15 Copynumber: 6.6 Consensus size: 15
356196 ATTATTATAT
356206 ATATATATAATATT-A
1 ATATATATAAT-TTAA
* *
356221 ATAAATTTAATTTAA
1 ATATATATAATTTAA
* * * *
356236 ATTTAAAAAATATAGA
1 ATATATATAATTTA-A
356252 ATATATATATATTT-A
1 ATATATATA-ATTTAA
* *
356267 A-AT-TA-AATATAT
1 ATATATATAATTTAA
356279 ATATATATAATTTAA
1 ATATATATAATTTAA
356294 ATATATATA
1 ATATATATA
356303 CCCGGCCCAA
Statistics
Matches: 59, Mismatches: 16, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
11 3 0.05
12 2 0.03
13 4 0.07
14 6 0.10
15 34 0.58
16 7 0.12
17 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (15 bp):
ATATATATAATTTAA
Found at i:359958 original size:213 final size:211
Alignment explanation
Indices: 359166--360005 Score: 1210
Period size: 211 Copynumber: 4.0 Consensus size: 211
359156 ATAGATTTAG
* * *
359166 CTTAAATTTGCTCTTAGGTTGTGAGTTGATAGTTTATTCTTTCCAGAGAGACAAATGTAGTTATT
1 CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGACAAA--TAGTTA-T
* * * * *
359231 TTTTTTTGATGGAGATTGTACAAGCTTATTTCGTGATAGTGGGGCTACATCAGTGA-GTCACAAA
63 TTTTCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAGCAGTGAGGT-ACAAA
*
359295 CTATAT-GCCTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCA
127 CTATATGGCTTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCA
359359 AGAACATAAATTATTTTGTT
192 AGAACATAAATTATTTTGTT
* ** *
359379 CTTAAAATTGCTCTTAGG-TGTGAG-TGATAGCTTTTTCTTTCTAGAGAGACCTAGGTAATTATT
1 CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGA-C-AAATAGTTATT
* * *
359442 TTTCTTGCTGGAGATTGTAGAAGCTTATTTCATGATAGTGGGGATACAGCAATGAGTTACAAACT
64 TTTCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAGCAGTGAGGTACAAACT
* * * * *
359507 ATATGGCTTTAAGTTGAAATAAATTTTCCAGAGATGAAATTGATCTTGAACGCTTCTTGATCAAG
129 ATATGGCTTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCAAG
359572 AACATAAATTATTTTGTT
194 AACATAAATTATTTTGTT
* * *
359590 CATAAAACTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGATAAAT-GTTA-TTT
1 CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGACAAATAGTTATTTT
* * * *
359653 T-TTCCTGGAGACTGTACAAGCTTATTTCATGATAGTGGGAATACAGCAGTGAGTTACAAACTAT
66 TCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAGCAGTGAGGTACAAACTAT
* * *
359717 ATGGCTTTATGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTCGAATGCTGCTGATTGAGCGA
131 ATGGCTTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGC---TTGAGCAA
359782 GAACATAAATTATTTTGTT
193 GAACATAAATTATTTTGTT
*
359801 CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTGGAGAGACAAAT-GTTATTTT
1 CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGACAAATAGTTATTTT
* *
359865 TCTTGCTGGAGATTGTACAAGCTTATTTCGTGATAGTGGGGATACAACAGTGAGGTACAAACTAT
66 TCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAGCAGTGAGGTACAAACTAT
* * *
359930 ATTGCTTTAAGTTGAAATTAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGATCAAGAA
131 ATGGCTTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCAAGAA
359995 CATAAATTATT
196 CATAAATTATT
360006 AAAATGAAAT
Statistics
Matches: 559, Mismatches: 57, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
208 106 0.19
209 4 0.01
210 84 0.15
211 199 0.36
212 17 0.03
213 149 0.27
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (211 bp):
CTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGACAAATAGTTATTTT
TCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAGCAGTGAGGTACAAACTAT
ATGGCTTTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCAAGAA
CATAAATTATTTTGTT
Found at i:359961 original size:421 final size:421
Alignment explanation
Indices: 359174--360005 Score: 1264
Period size: 421 Copynumber: 2.0 Consensus size: 421
359164 AGCTTAAATT
* *
359174 TGCTCTTAGGTTGTGAGTTGATAGTTTATTCTTTCCAGAGAGACAAATGTAGTTATTTTTTTTTG
1 TGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCCAGAGAGACAAA-GTAGTTA--TTTTTTTC
* * ** *
359239 ATGGAGATTGTACAAGCTTATTTCGTGATAGTGGGGCTACATCAGTGAGTCACAAACTATATGCC
63 ATGGAGACTGTACAAGCTTATTTCATGATAGTGGGAATACAGCAGTGAGTCACAAACTATATGCC
*
359304 TTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTTGAATGCTGCTTGAGCAAGAACATAAA
128 TTAAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTCGAATGCTGCTTGAGCAAGAACATAAA
* **
359369 TTATTTTGTTCTTAAAATTGCTCTTAGGTGTGAGTGATAGCTTTTTCTTTCTAGAGAGACCTAGG
193 TTATTTTGTTCTTAAAATTGCTCTTAGGTGTGAGTGATAGCTTATTCTTTCTAGAGAGACCTAAA
* * *
359434 TAATTATTTTTCTTGCTGGAGATTGTAGAAGCTTATTTCATGATAGTGGGGATACAGCAATGAGT
258 TAATTATTTTTCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAACAATGAGG
* *
359499 TACAAACTATATGGCTTTAAGTTGAAATAAATTTTCCAGAGATGAAATTGATCTTGAACGCTTCT
323 TACAAACTATATGGCTTTAAGTTGAAATAAATTTTCCAGAGATGAAATTGAGCTTGAACGCTGCT
359564 TGATCAAGAACATAAATTATTTTGTTCATAAAAC
388 TGATCAAGAACATAAATTATTTTGTTCATAAAAC
* * *
359598 TGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTAGAGAGATAAA-T-GTTA-TTTTTTCCTG
1 TGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCCAGAGAGACAAAGTAGTTATTTTTTTCATG
* *
359660 GAGACTGTACAAGCTTATTTCATGATAGTGGGAATACAGCAGTGAGTTACAAACTATATGGCTTT
66 GAGACTGTACAAGCTTATTTCATGATAGTGGGAATACAGCAGTGAGTCACAAACTATAT-GCCTT
* *
359725 ATGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTCGAATGCTGCTGATTGAGCGAGAACATAA
130 AAGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTCGAATGCTGC---TTGAGCAAGAACATAA
*
359790 ATTATTTTGTTCTTAAAATTGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCTGGAGAGA-C-
192 ATTATTTTGTTCTTAAAATTGCTCTTAGG-TGTGAG-TGATAGCTTATTCTTTCTAGAGAGACCT
* * *
359853 AAAT-GTTATTTTTCTTGCTGGAGATTGTACAAGCTTATTTCGTGATAGTGGGGATACAACAGTG
255 AAATAATTATTTTTCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAACAATG
* *
359917 AGGTACAAACTATATTGCTTTAAGTTGAAATTAAA-TTTCCAGAGATGAAATTGAGCTTGAATGC
320 AGGTACAAACTATATGGCTTTAAGTTGAAA-TAAATTTTCCAGAGATGAAATTGAGCTTGAACGC
359981 TGCTTGATCAAGAACATAAATTATT
384 TGCTTGATCAAGAACATAAATTATT
360006 AAAATGAAAT
Statistics
Matches: 372, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
418 61 0.16
419 48 0.13
421 138 0.37
422 51 0.14
423 7 0.02
424 67 0.18
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (421 bp):
TGCTCTTAGGTTGTGAGTTGATAGCTTATTCTTTCCAGAGAGACAAAGTAGTTATTTTTTTCATG
GAGACTGTACAAGCTTATTTCATGATAGTGGGAATACAGCAGTGAGTCACAAACTATATGCCTTA
AGTTGAAATAAAATTTCCAGAGATGAAATTGAGCTCGAATGCTGCTTGAGCAAGAACATAAATTA
TTTTGTTCTTAAAATTGCTCTTAGGTGTGAGTGATAGCTTATTCTTTCTAGAGAGACCTAAATAA
TTATTTTTCTTGCTGGAGATTGTACAAGCTTATTTCATGATAGTGGGGATACAACAATGAGGTAC
AAACTATATGGCTTTAAGTTGAAATAAATTTTCCAGAGATGAAATTGAGCTTGAACGCTGCTTGA
TCAAGAACATAAATTATTTTGTTCATAAAAC
Found at i:364591 original size:21 final size:22
Alignment explanation
Indices: 364545--364591 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
364535 TTATGTTTCT
*
364545 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
364567 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
364587 TTGTT
1 TTGTT
364592 GGCTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:367080 original size:14 final size:14
Alignment explanation
Indices: 367061--367088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
367051 AGAAAATGGC
367061 TTCGACGAGCAGGA
1 TTCGACGAGCAGGA
367075 TTCGACGAGCAGGA
1 TTCGACGAGCAGGA
367089 CATTGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.36, T:0.14
Consensus pattern (14 bp):
TTCGACGAGCAGGA
Found at i:383447 original size:60 final size:60
Alignment explanation
Indices: 383335--383448 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
383325 ATTTGGGATA
* * * *
383335 AAATTGGAATGTTCAAAAGTTTAGGGACTAATTCAGAATGAAGGTCACAGTTTAGTGAAG
1 AAATTGAAATATTCAAAAGTTGAGGGACTAATTCAGAATGAAGATCACAGTTTAGTGAAG
* *
383395 AAATTGAAATATTCAAAAGATTGA-GGACTAATTTAGAATGACA-ATCATAGTTTA
1 AAATTGAAATATTCAAAAG-TTGAGGGACTAATTCAGAATGA-AGATCACAGTTTA
383449 TGGATGGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 42 0.91
61 4 0.09
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (60 bp):
AAATTGAAATATTCAAAAGTTGAGGGACTAATTCAGAATGAAGATCACAGTTTAGTGAAG
Found at i:386722 original size:20 final size:20
Alignment explanation
Indices: 386697--386734 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
386687 TTCGGTTCAC
*
386697 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAGTG
386717 GGAATAAAAGATTATCAG
1 GGAATAAAAGATTATCAG
386735 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (20 bp):
GGAATAAAAGATTATCAGTG
Found at i:386737 original size:18 final size:19
Alignment explanation
Indices: 386697--386740 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
386687 TTCGGTTCAC
*
386697 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAG-G
386717 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTATCAGG
386735 GGAATA
1 GGAATA
386741 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (19 bp):
GGAATAAAAGATTATCAGG
Found at i:388826 original size:22 final size:22
Alignment explanation
Indices: 388796--388839 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
388786 ACCACCTTTA
388796 ATTCTCCTTTAATTAAAAGTTTT
1 ATTCTCC-TTAATTAAAAGTTTT
388819 ATTC-CCTTAATTAAAAGTTTT
1 ATTCTCCTTAATTAAAAGTTTT
388840 GTAGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.71
22 2 0.10
23 4 0.19
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTCTCCTTAATTAAAAGTTTT
Found at i:393237 original size:17 final size:17
Alignment explanation
Indices: 393211--393258 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
393201 CGATATATAT
* *
393211 TTATTCTTAATTAATTA
1 TTATTTTTAATTAAGTA
*
393228 TTATTTTTAAATAAGTA
1 TTATTTTTAATTAAGTA
393245 TTATTTTATAATTA
1 TTATTTT-TAATTA
393259 TCTTAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATTTTTAATTAAGTA
Found at i:400242 original size:2 final size:2
Alignment explanation
Indices: 400235--400280 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
400225 GGAATTATTC
400235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400277 AT AT
1 AT AT
400281 TTGAAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:400358 original size:30 final size:29
Alignment explanation
Indices: 400323--400396 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
400313 TATTTTTTTG
* *
400323 AAAAATATCTAATATGATAGTTATACTTT
1 AAAAATATCTAATATGATACTCATACTTT
* *
400352 AAAAAATATGTAA-GTGATACTCATACTTT
1 -AAAAATATCTAATATGATACTCATACTTT
* *
400381 TAAAATATTTAATATG
1 AAAAATATCTAATATG
400397 GTACATTTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 10 0.28
29 15 0.42
30 11 0.31
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (29 bp):
AAAAATATCTAATATGATACTCATACTTT
Found at i:400680 original size:27 final size:27
Alignment explanation
Indices: 400650--400701 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
400640 GTAATTGGAT
* *
400650 ATTTTGTCAAAATACATGTACCACAAC
1 ATTTTCTCAAAATACAAGTACCACAAC
* *
400677 ATTTTCTCAAAGTACAAGTATCACA
1 ATTTTCTCAAAATACAAGTACCACA
400702 TTGGATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
ATTTTCTCAAAATACAAGTACCACAAC
Found at i:401323 original size:23 final size:25
Alignment explanation
Indices: 401293--401353 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
401283 AAAAATATTG
*
401293 AAAAAAATTAATA-T-TTAACTTTT
1 AAAAAAATTAATACTAATAACTTTT
**
401316 AAAAAAATTAATACTAATATTTTTT
1 AAAAAAATTAATACTAATAACTTTT
401341 AAAAAAATTAATA
1 AAAAAAATTAATA
401354 AAATTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 13 0.39
24 1 0.03
25 19 0.58
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAAAATTAATACTAATAACTTTT
Found at i:406198 original size:2 final size:2
Alignment explanation
Indices: 406191--406232 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
406181 AATTAACATG
406191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406233 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411087 original size:2 final size:2
Alignment explanation
Indices: 411080--411123 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
411070 TTTAATACAA
411080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
411122 AT
1 AT
411124 TTCTCCAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:418174 original size:21 final size:21
Alignment explanation
Indices: 418138--418179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
418128 TTGTCTTTAT
418138 ATTTTGTATTATATTAATGTC
1 ATTTTGTATTATATTAATGTC
*
418159 ATTTT-TATTATAATTATTGTC
1 ATTTTGTATTAT-ATTAATGTC
418180 GTAGTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTTTGTATTATATTAATGTC
Found at i:425723 original size:302 final size:302
Alignment explanation
Indices: 425176--425750 Score: 759
Period size: 302 Copynumber: 1.9 Consensus size: 302
425166 TTCTATCCCG
* * * * * *
425176 TTATTATGTTTTGGTCACTCATTTATTTTTTTAAAGTTATAACTAGTGTTATATTTTATTTTTGT
1 TTATTATGCTTTGATCACTCATTTATTTTTTTAAAGTTATAACCAGTGTTACATCTTATTTATGT
* * * *
425241 TTTATCATTCATCACTAAAAAATATATAAAATTATTGACGTGATAATTTTTTTTCAATGACGTGA
66 TTTATCATCCACCACTAAAAAATATATAAAACTATTGACGTGATAA-TTTTTTTCAATGACATGA
* ** ** * * * *
425306 TATTATTTTATGATGACATATTGGTATTACTATTAATTTTTTAATGGTGAATGATCAAAACGAAA
130 TATTATCTTAAAATGACATATCAGTATCACCATTAATTTTTTAATGATGAATGATAAAAACGAAA
*
425371 TAAAATTATAATTAAAAAATAATTAAATGATTAAAATGAAACCGTAAAAGTAAATGTATAACTTA
195 TAAAATTATAATTAAAAAATAATTAAATGACTAAAATGAAACCGTAAAAGTAAATGTATAAC-TA
425436 -ATATATAGTTTACTAAATATATTTAGTCATGCATCTATTTCCA
259 GATATATAGTTTACTAAATATATTTAGTCATGCATCTATTTCCA
* * * * *
425479 TTATTATGCTTTGATCGCTTATTTA-TTTTTTAAAGTTATATCCAGTGTTACGTCTTGTTTATGT
1 TTATTATGCTTTGATCACTCATTTATTTTTTTAAAGTTATAACCAGTGTTACATCTTATTTATGT
425543 TTTGATCATCCACCACTAAAAAATATATAAAACTATTGACGTGATAA-TTTTTT-AATGATACAT
66 TTT-ATCATCCACCACTAAAAAATATATAAAACTATTGACGTGATAATTTTTTTCAATG--ACAT
* *
425606 GATATTATCTTAAAATGACGTGTCAGTATCACCATTAATTTTTTAATGAT-AGATGATAAAAACG
128 GATATTATCTTAAAATGACATATCAGTATCACCATTAATTTTTTAATGATGA-ATGATAAAAACG
* * *
425670 AAATGAAAA-TATAATTTAAAAAA-AATTGAGTGACTAAAATGAAACCGTAAAAGTAAATGTATG
192 AAAT-AAAATTATAA-TTAAAAAATAATTAAATGACTAAAATGAAACCGTAAAAGTAAATGTATA
425733 ACTAGATATATAGTTTAC
255 ACTAGATATATAGTTTAC
425751 CTTTTGATAA
Statistics
Matches: 235, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
300 4 0.02
301 9 0.04
302 149 0.63
303 73 0.31
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (302 bp):
TTATTATGCTTTGATCACTCATTTATTTTTTTAAAGTTATAACCAGTGTTACATCTTATTTATGT
TTTATCATCCACCACTAAAAAATATATAAAACTATTGACGTGATAATTTTTTTCAATGACATGAT
ATTATCTTAAAATGACATATCAGTATCACCATTAATTTTTTAATGATGAATGATAAAAACGAAAT
AAAATTATAATTAAAAAATAATTAAATGACTAAAATGAAACCGTAAAAGTAAATGTATAACTAGA
TATATAGTTTACTAAATATATTTAGTCATGCATCTATTTCCA
Found at i:445576 original size:18 final size:19
Alignment explanation
Indices: 445553--445594 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
445543 CAGTAATCCT
445553 ATTCC-CTATTAATCTTAC
1 ATTCCACTATTAATCTTAC
*
445571 ATTCCCACTGTTAATCTTAC
1 ATT-CCACTATTAATCTTAC
445591 ATTC
1 ATTC
445595 TGTGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 15 0.71
ACGTcount: A:0.26, C:0.29, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTCCACTATTAATCTTAC
Found at i:448814 original size:30 final size:30
Alignment explanation
Indices: 448718--448818 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
448708 CAACTTTTGA
448718 TGATGATGGTGCTTGTGATGTTGCAACTTC
1 TGATGATGGTGCTTGTGATGTTGCAACTTC
* *
448748 TGGTGATGGTGTTTGTGATGTTGCAACTTC
1 TGATGATGGTGCTTGTGATGTTGCAACTTC
* * *
448778 TAATGATGGTGCTTGTGATGTTACAGCCTT-
1 TGATGATGGTGCTTGTGATGTTGCA-ACTTC
448808 TGATGATGGTG
1 TGATGATGGTG
448819 TAATCCTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 59 0.95
31 3 0.05
ACGTcount: A:0.17, C:0.11, G:0.32, T:0.41
Consensus pattern (30 bp):
TGATGATGGTGCTTGTGATGTTGCAACTTC
Found at i:453753 original size:31 final size:31
Alignment explanation
Indices: 453715--453901 Score: 315
Period size: 31 Copynumber: 6.0 Consensus size: 31
453705 AGGGTCGAGG
*
453715 GTTTACCTAAGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
453746 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
453777 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
453808 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
453839 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
453870 GATTACCT-TGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTAT-GTTCTTCGGGA-CATATGGACT
453901 G
1 G
453902 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
30 1 0.01
31 149 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:454389 original size:21 final size:21
Alignment explanation
Indices: 454364--454406 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
454354 AAAGAATATA
454364 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
454385 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
454406 T
1 T
454407 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:458155 original size:31 final size:31
Alignment explanation
Indices: 458117--458272 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
458107 AGGGTCGAGG
458117 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
458148 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
458179 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
458210 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
458241 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
458272 G
1 G
458273 GTCTTTTGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:458760 original size:21 final size:21
Alignment explanation
Indices: 458735--458777 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
458725 AAAGAATATA
458735 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
458756 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
458777 T
1 T
458778 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:461419 original size:39 final size:39
Alignment explanation
Indices: 461373--461455 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
461363 TTGTTTTAAG
* *
461373 AATAATAACATATAAATGAATAGTTTAGTAGGTTTTGGA
1 AATAATAAAATATAAATGAATAGTTTAATAGGTTTTGGA
461412 AATAATAAAATATAAATGAATAGTTTAATAGGTTTTGGA
1 AATAATAAAATATAAATGAATAGTTTAATAGGTTTTGGA
461451 AATAA
1 AATAA
461456 AGTCATTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.35
Consensus pattern (39 bp):
AATAATAAAATATAAATGAATAGTTTAATAGGTTTTGGA
Found at i:470372 original size:390 final size:390
Alignment explanation
Indices: 469646--470596 Score: 1456
Period size: 390 Copynumber: 2.4 Consensus size: 390
469636 AGAATCAATT
* *
469646 AAATCAACTCTGCAAGATGAAGATATGGTTTTGAATATACTAGAGTCTCCGCAAGTACATGAAGA
1 AAATCAACTCTGCAAGACGAAGATATGGTTTTGAATATACTAAAGTCTCCGCAAGTACATGAAGA
* * *
469711 AAAACAGATTCCCCAGCTTCTATCTACATTGAAACCAAGGGAAGAAACCGACAACAAGGAAAATG
66 AAAACAGATTCCCCAGCTTCTTTCTGCTTTGAAACCAAGGGAAGAAACCGA-AACAAGGAAAATG
*
469776 CAGCAACTGATGGATGTAATCATCACTATCTCGCTGGAAAGGTTGAGGATGCTGACTGTGAGAAA
130 CAGCAACTGATGGATGT-A--ATCACTATCTCGATGGAAAGGTTGAGGATGCTGACTGTGAGAAA
* * *
469841 CTATCAAGGAAAGACTATGGAAGCCAACACACACGTTTTTATTCTGTTTTTCTCTCAACGGAATC
192 CTATCAAGGAAAGACTATGGAAACCAACACACACGTTTTTATTCTGATTCTCTCTCAACGGAATC
** * *
469906 AGTCAACTCATCTTTGCCCATTGCCGAAGATGATAAAAGGATTCCAACCCCACACACTCTCCTTG
257 AGTCAACTCATCTTTGCCCATTGCCGAAGATGATAAAAGGAGCCCAACCCCAAACACTCTCCATG
** *
469971 CTCCCGCTGTGCTGTCTGAGTCCGAAAATTTAGATGGCTCAAGAGTTTCCACCCAGCCTCCCCTG
322 CTCCCGCTGTGCTGTCTGAGTCCGAAAATTTAGATAACTCAAGAGTTTCCACCCAGCCTCACCTG
470036 ATGG
387 ATGG
*
470040 -AATCAACTCTGCAAGACGAAGATATGGTTTTGAATATACCAAAGTCTCCGCAAGTACATGAAGA
1 AAATCAACTCTGCAAGACGAAGATATGGTTTTGAATATACTAAAGTCTCCGCAAGTACATGAAGA
470104 AAAACAGATTCCCCAGCTTCTTTCTGCTTTGAAACCAAGGGAAGAAACCGAAACCAAGGAAAATG
66 AAAACAGATTCCCCAGCTTCTTTCTGCTTTGAAACCAAGGGAAGAAACCGAAA-CAAGGAAAATG
*
470169 CAGCAACTGATGGATGTAATCACTATCTTGATGGAAAGGTTGAGGATGCTGAC-GATGAGAAACT
130 CAGCAACTGATGGATGTAATCACTATCTCGATGGAAAGGTTGAGGATGCTGACTG-TGAGAAACT
* *
470233 ATCAAGTAAAGACTATGGAAACCAACACACAGGTTTTTATTCTGATTCTCTCTCAACGGAATCAG
194 ATCAAGGAAAGACTATGGAAACCAACACACACGTTTTTATTCTGATTCTCTCTCAACGGAATCAG
* *
470298 TCAACTTATCTTTGCCCATTGCCGAAGATGATAAAAGGAGCCCAACCCCAAACTCTCTCCATGCT
259 TCAACTCATCTTTGCCCATTGCCGAAGATGATAAAAGGAGCCCAACCCCAAACACTCTCCATGCT
* * *
470363 CCTGCTGTGCTGTCTGAGTCCGAGAATTTAGATAACTCAAGAGTTTCCACCCAGCCTCAGCTGAT
324 CCCGCTGTGCTGTCTGAGTCCGAAAATTTAGATAACTCAAGAGTTTCCACCCAGCCTCACCTGAT
470428 GG
389 GG
*
470430 AATCAATTAAATCAACTCGCATGCAAGACGAAGATATGGTTTTGAATGTACTAAAGTCTCCGCAA
1 --------AAATCAACT--C-TGCAAGACGAAGATATGGTTTTGAATATACTAAAGTCTCCGCAA
* * *
470495 GTGCATGAAGAAAAACAGATTCCGCAGCTTCTTTCTGCTTTGAAACCAAGGGGAGAAACCGAAAA
55 GTACATGAAGAAAAACAGATTCCCCAGCTTCTTTCTGCTTTGAAACCAAGGGAAGAAACCG-AAA
*
470560 TAAGGAAAATGCAGCAACTGATGGATGTAATCACTAT
119 CAAGGAAAATGCAGCAACTGATGGATGTAATCACTAT
470597 GAGAAACTAT
Statistics
Matches: 511, Mismatches: 31, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
389 1 0.00
390 222 0.43
392 3 0.01
393 137 0.27
399 8 0.02
401 1 0.00
402 136 0.27
403 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (390 bp):
AAATCAACTCTGCAAGACGAAGATATGGTTTTGAATATACTAAAGTCTCCGCAAGTACATGAAGA
AAAACAGATTCCCCAGCTTCTTTCTGCTTTGAAACCAAGGGAAGAAACCGAAACAAGGAAAATGC
AGCAACTGATGGATGTAATCACTATCTCGATGGAAAGGTTGAGGATGCTGACTGTGAGAAACTAT
CAAGGAAAGACTATGGAAACCAACACACACGTTTTTATTCTGATTCTCTCTCAACGGAATCAGTC
AACTCATCTTTGCCCATTGCCGAAGATGATAAAAGGAGCCCAACCCCAAACACTCTCCATGCTCC
CGCTGTGCTGTCTGAGTCCGAAAATTTAGATAACTCAAGAGTTTCCACCCAGCCTCACCTGATGG
Found at i:476154 original size:31 final size:31
Alignment explanation
Indices: 476119--476182 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
476109 TAACTCTAAG
*
476119 TGATCATATCTTAATTAAATAAAA-ACAAAAA
1 TGATCAAATCTTAATTAAATAAAATA-AAAAA
*
476150 TGATCAAATTTTAATTAAATAAAATAAAAAA
1 TGATCAAATCTTAATTAAATAAAATAAAAAA
476181 TG
1 TG
476183 GTCTAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (31 bp):
TGATCAAATCTTAATTAAATAAAATAAAAAA
Found at i:476257 original size:3 final size:3
Alignment explanation
Indices: 476249--476339 Score: 159
Period size: 3 Copynumber: 31.0 Consensus size: 3
476239 AATAAAATCA
476249 ATC ATC ATC ATC ATC ATC AT- AT- ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
476295 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
476340 GTTTGGTTTT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 4 0.05
3 81 0.95
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:481321 original size:25 final size:25
Alignment explanation
Indices: 481278--481325 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
481268 ACTTTTTTAG
481278 TTTTATATTAAATAATTTTTATTTGA
1 TTTTATATTAAATAA-TTTTATTTGA
* *
481304 TTTT-TATTTAATAGTTTTATTT
1 TTTTATATTAAATAATTTTATTT
481326 TTTTATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTATATTAAATAATTTTATTTGA
Found at i:518292 original size:20 final size:21
Alignment explanation
Indices: 518246--518306 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
518236 ATGACCAACA
* *
518246 AATTCGCAACACAGAATTTC-A
1 AATTCGCAACGC-GAATTTCTG
*
518267 AATTCGCAACTCG-ATTTCTG
1 AATTCGCAACGCGAATTTCTG
518287 AATTCGCAACGCGAATTTCT
1 AATTCGCAACGCGAATTTCT
518307 TTTTCGCAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 17 0.49
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (21 bp):
AATTCGCAACGCGAATTTCTG
Found at i:518312 original size:20 final size:20
Alignment explanation
Indices: 518248--518384 Score: 100
Period size: 20 Copynumber: 6.8 Consensus size: 20
518238 GACCAACAAA
***
518248 TTCGCAACACAGAATTTCAAA
1 TTCGCAACAC-GAATTTCTTT
* **
518269 TTCGCAACTCG-ATTTCTGAA
1 TTCGCAACACGAATTTCT-TT
*
518289 TTCGCAACGCGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
*
518309 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTCTTT
* * **
518329 TTCGCAACAAGACTTTCTAA
1 TTCGCAACACGAATTTCTTT
*
518349 ATCGCAACACGAATTT-TGTT
1 TTCGCAACACGAATTTCT-TT
518369 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
518385 TAATTTCGTA
Statistics
Matches: 93, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
19 8 0.09
20 69 0.74
21 16 0.17
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
TTCGCAACACGAATTTCTTT
Found at i:518392 original size:60 final size:60
Alignment explanation
Indices: 518248--518392 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
518238 GACCAACAAA
* ** * *
518248 TTCGCAACACAGAATTTCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTT
1 TTCGCAACAC-GAATTTCAATTTCGCAACAAGATTTCTGAAATCGCAACACGAATTTCTTT
**
518309 TTCGCAACAC-AAGTTTCCTTTTCGCAACAAGACTTTCT-AAATCGCAACACGAATTT-TGTT
1 TTCGCAACACGAA-TTTCAATTTCGCAACAAGA-TTTCTGAAATCGCAACACGAATTTCT-TT
*
518369 TTCGCAACACGAATTTTAATTTCG
1 TTCGCAACACGAATTTCAATTTCG
518393 TAATAGCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
59 3 0.04
60 50 0.71
61 17 0.24
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (60 bp):
TTCGCAACACGAATTTCAATTTCGCAACAAGATTTCTGAAATCGCAACACGAATTTCTTT
Found at i:521668 original size:18 final size:18
Alignment explanation
Indices: 521645--521680 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
521635 AAGCAAAAGG
521645 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
521663 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
521681 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:523429 original size:21 final size:21
Alignment explanation
Indices: 523405--523505 Score: 141
Period size: 21 Copynumber: 4.8 Consensus size: 21
523395 AATGTGAATT
*
523405 GGCCTCTTGAACGGTGAGAGG
1 GGCCTCTTGAACGATGAGAGG
523426 GGCCTCTTGAACGATGAGAGG
1 GGCCTCTTGAACGATGAGAGG
* *
523447 GTCCTCTTGAATGATGAGAGG
1 GGCCTCTTGAACGATGAGAGG
* *
523468 GTCCTCTTGAATGAT-AGGAGG
1 GGCCTCTTGAACGATGA-GAGG
523489 GGCCTCTTGAACGATGA
1 GGCCTCTTGAACGATGA
523506 CAGGTGAATC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
GGCCTCTTGAACGATGAGAGG
Found at i:523933 original size:21 final size:21
Alignment explanation
Indices: 523909--523979 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
523899 ACCATTGTCG
523909 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
523930 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
* *
523951 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGTACCGACCTCA
523972 TCACGTAA
1 TCACGTAA
523980 CTCCCCTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:524173 original size:42 final size:42
Alignment explanation
Indices: 524094--524192 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 42
524084 GTGATGAAAT
* ** *
524094 AGGTGATGGCTCTCGTTGTGGAGATGTATAATCGGCTCGATA
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATA
* * * *
524136 AGGTGATGGCTCTGGGTGTCAAGCTGTAGAATTGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATA
* *
524178 AGGCGATGACTCTCG
1 AGGTGATGGCTCTCG
524193 AAGTGGGGGG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATA
Found at i:525980 original size:23 final size:24
Alignment explanation
Indices: 525945--525989 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
525935 AGGGTCGTCG
525945 GATATGGGGACGGATGTCGCCGGA
1 GATATGGGGACGGATGTCGCCGGA
525969 GATA-GGGGACGGATGTCGCCG
1 GATATGGGGACGGATGTCGCCG
525990 TAAAGAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.20, C:0.18, G:0.47, T:0.16
Consensus pattern (24 bp):
GATATGGGGACGGATGTCGCCGGA
Found at i:526162 original size:20 final size:20
Alignment explanation
Indices: 526137--526185 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
526127 TAAACGCTCT
*
526137 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
526157 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
526177 TTACGAATT
1 TTGCGAATT
526186 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:526209 original size:20 final size:20
Alignment explanation
Indices: 526184--526242 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
526174 GTGTTACGAA
*
526184 TTACAAATTCGCATTGCGAT
1 TTACAAATTCGCGTTGCGAT
**
526204 TTACAAATTCATGTTGCGAT
1 TTACAAATTCGCGTTGCGAT
* *
526224 TTACATATTTGCGTTGCGA
1 TTACAAATTCGCGTTGCGA
526243 ATTTCAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
TTACAAATTCGCGTTGCGAT
Found at i:526228 original size:40 final size:40
Alignment explanation
Indices: 526175--526250 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
526165 TTGACTTATG
526175 TGTTACGAATTACAAATTCGCATTGCG-ATTTACAAATTCA
1 TGTTACGAATTACAAATTCGCATTGCGAATTT-CAAATTCA
* * * * *
526215 TGTTGCGATTTACATATTTGCGTTGCGAATTTCAAA
1 TGTTACGAATTACAAATTCGCATTGCGAATTTCAAA
526251 ATTGAGTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 26 0.87
41 4 0.13
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (40 bp):
TGTTACGAATTACAAATTCGCATTGCGAATTTCAAATTCA
Found at i:529651 original size:14 final size:14
Alignment explanation
Indices: 529632--529658 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
529622 TAACTAGTCT
529632 TATTTTATAATTTA
1 TATTTTATAATTTA
529646 TATTTTATAATTT
1 TATTTTATAATTT
529659 TTTTGAGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATAATTTA
Found at i:531529 original size:7 final size:8
Alignment explanation
Indices: 531505--531531 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
531495 CCATTTTCTC
531505 TTCACTTT
1 TTCACTTT
531513 TTCACTTT
1 TTCACTTT
531521 TTCACTTT
1 TTCACTTT
531529 TTC
1 TTC
531532 CTAGTTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (8 bp):
TTCACTTT
Found at i:531982 original size:206 final size:208
Alignment explanation
Indices: 531599--532015 Score: 820
Period size: 206 Copynumber: 2.0 Consensus size: 208
531589 GGACTGTTTC
531599 CAATAATGGGACTTTGCCATGGAAAACCCATTGAAAACCAACAAAAGCAATCAAGGGACATCTCA
1 CAATAATGGGACTTTGCCATGGAAAACCCATTGAAAACCAACAAAAGCAATCAAGGGACATCTCA
531664 ATCCCAGGTGAAACCGATGCACCACAAAACTCCCACTCCACCAAGTCATCAAATTTACCATTTTA
66 ATCCCAGGTGAAACCGATGCACCACAAAACTCCCACTCCACCAAGTCATCAAATTTACCATTTTA
531729 CAGTCCTAGTCCATTGCCAAGCCTCTTCAAGACATCTCCAGCTATACCCAGCGTGAATTCCACTC
131 CAGTCCTAGTCCATTGCCAAGCCTCTTCAAGACATCTCCAGCTATACCCAGCGTGAATTCCACTC
531794 CTCTCCGCTTCTT
196 CTCTCCGCTTCTT
531807 CAATAATGGGACTTTGCCATGGAAAACCCATTGAAAACCAACAAAAGCAATCAAGGGACATCTCA
1 CAATAATGGGACTTTGCCATGGAAAACCCATTGAAAACCAACAAAAGCAATCAAGGGACATCTCA
531872 ATCCCAGGTGAAACCGATGCA-C-CAAAACTCCCACTCCACCAAGTCATCAAATTTACCATTTTA
66 ATCCCAGGTGAAACCGATGCACCACAAAACTCCCACTCCACCAAGTCATCAAATTTACCATTTTA
531935 CAGTCCTAGTCCATTGCCAAGCCTCTTCAAGACATCTCCAGCTATACCCAGCGTGAATTCCACTC
131 CAGTCCTAGTCCATTGCCAAGCCTCTTCAAGACATCTCCAGCTATACCCAGCGTGAATTCCACTC
532000 CTCTCCGCTTCTT
196 CTCTCCGCTTCTT
532013 CAA
1 CAA
532016 ACGTCCATTC
Statistics
Matches: 209, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 122 0.58
207 1 0.00
208 86 0.41
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23
Consensus pattern (208 bp):
CAATAATGGGACTTTGCCATGGAAAACCCATTGAAAACCAACAAAAGCAATCAAGGGACATCTCA
ATCCCAGGTGAAACCGATGCACCACAAAACTCCCACTCCACCAAGTCATCAAATTTACCATTTTA
CAGTCCTAGTCCATTGCCAAGCCTCTTCAAGACATCTCCAGCTATACCCAGCGTGAATTCCACTC
CTCTCCGCTTCTT
Found at i:534450 original size:2 final size:2
Alignment explanation
Indices: 534445--534474 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
534435 TCTCTCTCTC
534445 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
534475 TATCCGATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:538024 original size:2 final size:2
Alignment explanation
Indices: 538017--538046 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
538007 GTAAAACAAT
538017 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
538047 ATGTATACGA
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):
TA
Found at i:546835 original size:19 final size:21
Alignment explanation
Indices: 546811--546855 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
546801 TGGTACGTCA
*
546811 TATAAAATA-AT-TTTAAAAT
1 TATAAAATATATATTAAAAAT
546830 TAT-AAATATATATTAAAAAT
1 TATAAAATATATATTAAAAAT
546850 TATAAA
1 TATAAA
546856 TAAAGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 10 0.45
21 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAATATATATTAAAAAT
Found at i:549682 original size:20 final size:20
Alignment explanation
Indices: 549631--549682 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
549621 GATTTTGACC
549631 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
549651 ATCACAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
549671 ATCGCAACGCGA
1 ATCGCAATGCGA
549683 TAACACGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:549716 original size:61 final size:61
Alignment explanation
Indices: 549651--549784 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 61
549641 GAATATGTAA
* *
549651 ATCACAATGCGAATATGTA-AATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
1 ATCACAACGCGAATATG-ACAATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACT
* * * * * *
549712 ATCACAACGAGATTTTGACTATCGCAACGCGATAATATGTAATCGCAACGCGATTCTGACT
1 ATCACAACGCGAATATGACAATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACT
*
549773 ATCGCAACGCGA
1 ATCACAACGCGA
549785 TTCTGACTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 1 0.02
61 61 0.98
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCACAACGCGAATATGACAATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACT
Found at i:549725 original size:20 final size:20
Alignment explanation
Indices: 549692--549798 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
549682 ATAACACGTG
549692 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
549712 ATCACAACGAGATTTTGACT
1 ATCGCAACGCGATTCTGACT
*
549732 ATCGCAACGCGATAATATG--T
1 ATCGCAACGCGAT--TCTGACT
549752 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
549773 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
549793 AACGCA
1 ATCGCA
549799 TCACTGAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.04
20 54 0.73
21 14 0.19
22 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Done.