Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold433
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: 558157
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 7244 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:273465 original size:34 final size:34
Alignment explanation
Indices: 273380--273466 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
273370 TCCTATATTT
*
273380 TAATTTAAAATTTTTAA-TATTTATAAAATTTTA
1 TAATATAAAATTTTTAATTATTTATAAAATTTTA
* ** *
273413 TGATATATATTTTATTTAATTTTTTA-AAAATTTATA
1 TAATATA-AAATT-TTTAATTATTTATAAAATTT-TA
273449 TAATATAAAATTTTTAAT
1 TAATATAAAATTTTTAAT
273467 AAATATTCGA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
33 5 0.12
34 9 0.21
35 15 0.36
36 13 0.31
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TAATATAAAATTTTTAATTATTTATAAAATTTTA
Found at i:274348 original size:29 final size:27
Alignment explanation
Indices: 274316--274379 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
274306 GTTCGACTTA
274316 ATTTAAATTAAAATTTATTTAATAAAAAT
1 ATTTAAATTAAAATTTATTT--TAAAAAT
* * *
274345 ATTTTATTTAAATTTTATTTTAAAAAT
1 ATTTAAATTAAAATTTATTTTAAAAAT
*
274372 ATATAAAT
1 ATTTAAAT
274380 ATTAATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 12 0.41
29 17 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTAAATTAAAATTTATTTTAAAAAT
Found at i:274761 original size:21 final size:22
Alignment explanation
Indices: 274741--274782 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
274731 TTTATAATTA
274741 ATTTTAA-ATAAAAATA-TATT
1 ATTTTAATATAAAAATACTATT
*
274761 ATTTTAATATATAAATACTATT
1 ATTTTAATATAAAAATACTATT
274783 CCAAACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAATATAAAAATACTATT
Found at i:275348 original size:16 final size:16
Alignment explanation
Indices: 275321--275364 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
275311 AGAAAATATT
275321 AAATAA-TTAAATTTA
1 AAATAATTTAAATTTA
*
275336 AAATAATTTAAATTTG
1 AAATAATTTAAATTTA
*
275352 AAATAATATAAAT
1 AAATAATTTAAAT
275365 CTGACAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:277118 original size:32 final size:32
Alignment explanation
Indices: 277082--277151 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
277072 AATAATATTA
*
277082 ATATAATATAAATATATAAAT-TTTTAAAATTT
1 ATATAATATAAAT-TATAAATATATTAAAATTT
*
277114 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTATAAATATATTAAAATTT
277146 ATATAA
1 ATATAA
277152 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATTAAAATTT
Found at i:277147 original size:18 final size:18
Alignment explanation
Indices: 277062--277156 Score: 53
Period size: 18 Copynumber: 5.5 Consensus size: 18
277052 TAACACAAAA
*
277062 TAATATA-TAAAATAATAT
1 TAATATATTAAAAT-TTAT
* *
277080 TAATATAATATAAATATAT
1 TAATATATTA-AAATTTAT
* *
277099 AAAT-TTTTAAAATTTA-
1 TAATATATTAAAATTTAT
277115 T-ATA-A-TATAAA-TTAT
1 TAATATATTA-AAATTTAT
277130 TAATATATTAAAATTTAT
1 TAATATATTAAAATTTAT
277148 ATAA-ATATT
1 -TAATATATT
277157 TTAAATAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 5 0.08
15 6 0.10
16 3 0.05
17 10 0.16
18 21 0.34
19 12 0.20
20 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATTAAAATTTAT
Found at i:277488 original size:17 final size:17
Alignment explanation
Indices: 277460--277520 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
277450 TATGTCATAT
277460 TTATTAATTATAAATTTA
1 TTATT-ATTATAAATTTA
277478 TTATTATTATAAA-TTA
1 TTATTATTATAAATTTA
* * *
277494 TTTATAATTTTATATTTA
1 -TTATTATTATAAATTTA
277512 TTA-TATTAT
1 TTATTATTAT
277521 TAGTATGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 7 0.19
17 21 0.58
18 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATTATAAATTTA
Found at i:277500 original size:28 final size:28
Alignment explanation
Indices: 277462--277516 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
277452 TGTCATATTT
277462 ATTAATTATAAATTTAT-TATTATTATAA
1 ATTAATTATAAATTTATAT-TTATTATAA
* *
277490 ATTATTTATAATTTTATATTTATTATA
1 ATTAATTATAAATTTATATTTATTATA
277517 TTATTAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTAATTATAAATTTATATTTATTATAA
Found at i:279092 original size:2 final size:2
Alignment explanation
Indices: 279085--279120 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
279075 ATCTTTAGTG
279085 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
279121 CATGCTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:279795 original size:15 final size:15
Alignment explanation
Indices: 279768--279815 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
279758 TTTTAAGTAC
279768 TTAAAAT-TTTATTT
1 TTAAAATATTTATTT
279782 TTAAAATATTTATTT
1 TTAAAATATTTATTT
* * *
279797 ATTAGATTAATTATTT
1 -TTAAAATATTTATTT
279813 TTA
1 TTA
279816 CGAAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 7 0.24
15 10 0.34
16 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTAAAATATTTATTT
Found at i:280989 original size:2 final size:2
Alignment explanation
Indices: 280982--281020 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
280972 AGAGAACATA
280982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
281021 ATTAGGGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:281999 original size:11 final size:11
Alignment explanation
Indices: 281983--282037 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 11
281973 GATATAATTT
281983 TATAATATAAA
1 TATAATATAAA
281994 TATAATAT-AA
1 TATAATATAAA
282004 TATAA-A-AAA
1 TATAATATAAA
282013 TA-AA-ATAAA
1 TATAATATAAA
282022 TATAATATAAA
1 TATAATATAAA
282033 TATAA
1 TATAA
282038 AAATATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 3 0.08
9 10 0.25
10 9 0.22
11 18 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAATATAAA
Found at i:282020 original size:28 final size:29
Alignment explanation
Indices: 281984--282040 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
281974 ATATAATTTT
*
281984 ATAATATAAATATAATAT-AATATAAAAA
1 ATAAAATAAATATAATATAAATATAAAAA
282012 ATAAAATAAATATAATATAAATATAAAAA
1 ATAAAATAAATATAATATAAATATAAAAA
282041 TATATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (29 bp):
ATAAAATAAATATAATATAAATATAAAAA
Found at i:282050 original size:28 final size:26
Alignment explanation
Indices: 281986--282053 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 26
281976 ATAATTTTAT
281986 AATAT-AAATATAATATAATATAAAA
1 AATATAAAATATAATATAATATAAAA
*
282011 AATAAAATAAATATAATATAAATATAAAA
1 AAT-ATA-AAATATAATAT-AATATAAAA
282040 ATATATAAAATATA
1 A-ATATAAAATATA
282054 TTATTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
28 18 0.50
29 12 0.33
30 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AATATAAAATATAATATAATATAAAA
Found at i:282054 original size:11 final size:11
Alignment explanation
Indices: 281986--282051 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
281976 ATAATTTTAT
281986 AATAT-AAATA
1 AATATAAAATA
*
281996 TAATATAATATAA
1 -AATATAAAAT-A
*
282009 AAAATAAAATA
1 AATATAAAATA
*
282020 AATATAATATA
1 AATATAAAATA
282031 AATATAAAA-A
1 AATATAAAATA
*
282041 TATATAAAATA
1 AATATAAAATA
282052 TATTATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
10 9 0.20
11 24 0.53
12 11 0.24
13 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATATAAAATA
Found at i:282455 original size:22 final size:22
Alignment explanation
Indices: 282430--282474 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
282420 TAATTATACG
*
282430 ATATAAAAATTATTAAAATATA
1 ATATAAAAATTAATAAAATATA
* *
282452 ATATAAAATTTAATAAGATATA
1 ATATAAAAATTAATAAAATATA
282474 A
1 A
282475 AAATATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATAAAAATTAATAAAATATA
Found at i:286049 original size:102 final size:102
Alignment explanation
Indices: 285873--286076 Score: 345
Period size: 102 Copynumber: 2.0 Consensus size: 102
285863 ACTAAAAGTA
*
285873 ACATAGTTGACAACAGAACTGTTACTCTACAAGGGGATAGTACTACTAATGCAGCAACCATTCTC
1 ACATACTTGACAACAGAACTGTTACTCTACAAGGGGATAGTACTACTAATGCAGCAACCATTCTC
*
285938 TGATTTTGCTCCTTGTGCATGCTTGGCTTTATAAAGC
66 TGATTTTGCTCCTTGTGCATGCTTGACTTTATAAAGC
* * * *
285975 ACATACTTGACAACAGAACTGTTACTCTACGAGGGGATGGTACTACTAATGCGGTAACCATTCTC
1 ACATACTTGACAACAGAACTGTTACTCTACAAGGGGATAGTACTACTAATGCAGCAACCATTCTC
*
286040 TGATTTTGCTCCTTGTGCATGCTTGATTTTATAAAGC
66 TGATTTTGCTCCTTGTGCATGCTTGACTTTATAAAGC
286077 TAAAAGCTAT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (102 bp):
ACATACTTGACAACAGAACTGTTACTCTACAAGGGGATAGTACTACTAATGCAGCAACCATTCTC
TGATTTTGCTCCTTGTGCATGCTTGACTTTATAAAGC
Found at i:290969 original size:5 final size:5
Alignment explanation
Indices: 290955--290988 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
290945 TTTAACAATG
*
290955 AATTT AATTT GATTT AATTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
290989 AACACAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:292254 original size:26 final size:24
Alignment explanation
Indices: 292207--292270 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
292197 GACACTATTT
* *
292207 TTTAATTAATTATTTAAAAAATTA
1 TTTAATTAATTTTTTAAAAAATAA
292231 TTTAATTAATTTTATTAAATAAATAA
1 TTTAATTAATTTT-TTAAA-AAATAA
*
292257 TTTAATTACTTTTT
1 TTTAATTAATTTTT
292271 AATTAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.34
25 6 0.17
26 17 0.49
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAATTAATTTTTTAAAAAATAA
Found at i:292326 original size:24 final size:23
Alignment explanation
Indices: 292292--292336 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
292282 ATTTTATAAA
*
292292 AAATATAAATATTTTATATTAAGT
1 AAATATAAATATATTAT-TTAAGT
*
292316 AAATATTAATATATTATTTAA
1 AAATATAAATATATTATTTAA
292337 TATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATATAAATATATTATTTAAGT
Found at i:292327 original size:30 final size:31
Alignment explanation
Indices: 292293--292367 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 31
292283 TTTTATAAAA
292293 AATATAAATATTTTATA-TTAAGTAAA-TATT
1 AATATAAATATTTTATATTTAAGTAAATTA-T
* * * *
292323 AATAT-ATTATTTAATATTTAATTTAATTAT
1 AATATAAATATTTTATATTTAAGTAAATTAT
292353 AATATATAATATTTT
1 AATATA-AATATTTT
292368 TAAAAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
29 9 0.26
30 18 0.51
31 2 0.06
32 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
AATATAAATATTTTATATTTAAGTAAATTAT
Found at i:292362 original size:25 final size:25
Alignment explanation
Indices: 292321--292396 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 25
292311 TAAGTAAATA
* *
292321 TTAA-TATATTATTTAATATTTAAT
1 TTAATTATAATATATAATATTTAAT
292345 TTAATTATAATATATAATA-TT--T
1 TTAATTATAATATATAATATTTAAT
**
292367 TTAAAAATAAT-TAT-ATATTTAAT
1 TTAATTATAATATATAATATTTAAT
292390 TT-ATTAT
1 TTAATTAT
292397 GTATCTGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 3 0.07
21 5 0.12
22 13 0.31
23 3 0.07
24 6 0.14
25 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATTATAATATATAATATTTAAT
Found at i:292480 original size:35 final size:37
Alignment explanation
Indices: 292408--292481 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
292398 TATCTGATTA
*
292408 AATATTAAGTATTATATTAATATTTATTTAATAATAAT
1 AATATTAAGTATTATA-TAATATTTATTAAATAATAAT
* *
292446 AATATTAAGTATT-TA-AATTTTTATTAAATTATAAT
1 AATATTAAGTATTATATAATATTTATTAAATAATAAT
292481 A
1 A
292482 TAAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 18 0.55
37 2 0.06
38 13 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (37 bp):
AATATTAAGTATTATATAATATTTATTAAATAATAAT
Found at i:292494 original size:35 final size:35
Alignment explanation
Indices: 292404--292500 Score: 83
Period size: 35 Copynumber: 2.8 Consensus size: 35
292394 TATGTATCTG
* * * *
292404 ATTA-AATATTAAGTATTATATT-AATATTTATTTA
1 ATTATAATATAAATTATTAT-TTAAATTTTTATTAA
* * *
292438 ATAATAATA-ATATTAAGTATTTAAATTTTTATTAA
1 ATTATAATATAAATT-ATTATTTAAATTTTTATTAA
292473 ATTATAATATAAATTATTATTTTAAATT
1 ATTATAATATAAATTATTA-TTTAAATT
292501 AAATTTTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
34 7 0.15
35 29 0.60
36 12 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (35 bp):
ATTATAATATAAATTATTATTTAAATTTTTATTAA
Found at i:293326 original size:32 final size:31
Alignment explanation
Indices: 293261--293331 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
293251 ATTTTTTTAA
* * * *
293261 ATTTTTTTATTTAAATTTAATTAATAAATTT
1 ATTTTATTATTTAAATTAAAATAATAAAATT
*
293292 ATTTTATTATTTAAATTAAAAATGATAAAATT
1 ATTTTATTATTTAAATT-AAAATAATAAAATT
293324 ATTGTTAT
1 ATT-TTAT
293332 ATTAATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 16 0.48
32 13 0.39
33 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTATTATTTAAATTAAAATAATAAAATT
Found at i:294302 original size:30 final size:29
Alignment explanation
Indices: 294245--294302 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
294235 AACAATCTTC
* * *
294245 ATAAATTATATTTTTTAATTTATTTTTTT
1 ATAAATTATATTTTTAAACTTAATTTTTT
294274 ATAAATTCATATTTTTAAACTTAATTTTT
1 ATAAATT-ATATTTTTAAACTTAATTTTT
294303 GGTCTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
ATAAATTATATTTTTAAACTTAATTTTTT
Found at i:296268 original size:20 final size:21
Alignment explanation
Indices: 296243--296282 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
296233 AAACTGATTA
296243 ATTTTAATATT-AATTTAATT
1 ATTTTAATATTAAATTTAATT
*
296263 ATTTTAATTTTAAATTTAAT
1 ATTTTAATATTAAATTTAAT
296283 ATTAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTAATATTAAATTTAATT
Found at i:296285 original size:20 final size:21
Alignment explanation
Indices: 296243--296296 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
296233 AAACTGATTA
*
296243 ATTTTAATATT-AATTTAATT
1 ATTTTAATTTTAAATTTAATT
296263 ATTTTAATTTTAAATTTAA-T
1 ATTTTAATTTTAAATTTAATT
*
296283 ATTAATAATTTTAA
1 ATT-TTAATTTTAA
296297 TATTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTAATTTTAAATTTAATT
Found at i:296291 original size:21 final size:20
Alignment explanation
Indices: 296247--296309 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
296237 TGATTAATTT
* *
296247 TAATATTAATTTAATTATT-T
1 TAATTTTAATTTAA-TATTAA
296267 TAATTTTAAATTTAATATTAA
1 TAATTTT-AATTTAATATTAA
*
296288 TAATTTTAATATTAAAATTAA
1 TAATTTTAAT-TTAATATTAA
296309 T
1 T
296310 TAAATTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 13 0.35
21 24 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTTAATTTAATATTAA
Found at i:296295 original size:27 final size:26
Alignment explanation
Indices: 296240--296331 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
296230 ATTAAACTGA
*
296240 TTAATTTT-AATATTAATTTAATTATT
1 TTAATTTTAAAT-TTAATTTAATAATT
296266 TTAATTTTAAATTTAATATTAATAATT
1 TTAATTTTAAATTTAAT-TTAATAATT
* * *
296293 TTAATATTAAAATTAATTAAATTAATTT
1 TTAATTTTAAATTTAATTTAA-TAA-TT
296321 TTAA-TTTAAAT
1 TTAATTTTAAAT
296332 AAATTAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
26 16 0.29
27 34 0.61
28 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAATTTTAAATTTAATTTAATAATT
Found at i:296317 original size:21 final size:21
Alignment explanation
Indices: 296293--296342 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
296283 ATTAATAATT
*
296293 TTAATATTAAAATTAATTAAA
1 TTAATATTAAAATTAAATAAA
* * *
296314 TTAATTTTTAATTTAAATAAA
1 TTAATATTAAAATTAAATAAA
296335 TTAA-ATTA
1 TTAATATTA
296343 CCGCACTTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATATTAAAATTAAATAAA
Found at i:296338 original size:26 final size:29
Alignment explanation
Indices: 296273--296342 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 29
296263 ATTTTAATTT
296273 TAAATTTAATATTAATAATTTTAATATTAAAA
1 TAAA-TTAA-ATTAAT-ATTTTAATATTAAAA
*
296305 TTAATTAAATTAAT-TTTTAAT-TT-AAA
1 TAAATTAAATTAATATTTTAATATTAAAA
296331 TAAATTAAATTA
1 TAAATTAAATTA
296343 CCGCACTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 14 0.39
27 2 0.06
28 7 0.19
30 6 0.17
31 4 0.11
32 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAATTAAATTAATATTTTAATATTAAAA
Found at i:297291 original size:24 final size:24
Alignment explanation
Indices: 297259--297304 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
297249 ATGTTCATAT
297259 TTATAATAA-AAAATTTATTAAAAA
1 TTATAATAATAAAATTT-TTAAAAA
* *
297283 TTATTATAATATAATTTTTAAA
1 TTATAATAATAAAATTTTTAAA
297305 TTATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATAATAATAAAATTTTTAAAAA
Found at i:297422 original size:23 final size:22
Alignment explanation
Indices: 297386--297441 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
297376 TTTTATTTAA
*
297386 ATTTAATTATAAAATATAAAAAT
1 ATTT-ATTAAAAAATATAAAAAT
* *
297409 ATTTATATAAAAAATTTTAAAAT
1 ATTTAT-TAAAAAATATAAAAAT
*
297432 TTTTATTAAA
1 ATTTATTAAA
297442 TATGAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTATTAAAAAATATAAAAAT
Found at i:297979 original size:21 final size:19
Alignment explanation
Indices: 297953--298008 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 19
297943 AATAATATTT
297953 ATAAAATTAATATTTTAATAA
1 ATAAAATTAATA-TTTAAT-A
297974 ATAAAATATTAA-ATTTAATA
1 AT-AAA-ATTAATATTTAATA
*
297994 ATATAATTAAT-TTTA
1 ATAAAATTAATATTTA
298009 TCATGCATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 9 0.29
19 2 0.06
20 3 0.10
21 8 0.26
22 4 0.13
23 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATTAATATTTAATA
Found at i:299087 original size:2 final size:2
Alignment explanation
Indices: 299075--299107 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
299065 ATAGCAAAGA
299075 AT AT A- 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
299108 GAGTTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:299253 original size:2 final size:2
Alignment explanation
Indices: 299246--299273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
299236 ATTTTTATTC
299246 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
299274 TTGATTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301182 original size:23 final size:24
Alignment explanation
Indices: 301127--301185 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
301117 TATATTTAAA
301127 TTTCATTTATAACTTCTAAATTTT
1 TTTCATTTATAACTTCTAAATTTT
*
301151 TTTCATTTATAACTTCTGAA-TTT
1 TTTCATTTATAACTTCTAAATTTT
*
301174 TTTCTTTTATAA
1 TTTCATTTATAA
301186 AATAAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTCATTTATAACTTCTAAATTTT
Found at i:301639 original size:22 final size:21
Alignment explanation
Indices: 301614--301681 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
301604 TTTAATTATT
301614 ATTTAATAATAAAAATAATTAA
1 ATTTAAT-ATAAAAATAATTAA
301636 ATTTAAT-TATAAAAT-ATATAA
1 ATTTAATATA-AAAATAAT-TAA
*
301657 ATATTAATATAAAAA-AATTTA
1 AT-TTAATATAAAAATAATTAA
301678 ATTT
1 ATTT
301682 GATTGATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
20 6 0.15
21 14 0.35
22 18 0.45
23 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAATATAAAAATAATTAA
Found at i:302033 original size:18 final size:18
Alignment explanation
Indices: 301991--302063 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 18
301981 TATAAATGTA
*
301991 TTTAAAAAATTTT-ATA-
1 TTTAATAAATTTTGATAT
302007 TTTATATAAATTTTGATAT
1 TTTA-ATAAATTTTGATAT
302026 TTTAAT-AATTTATAGAT-T
1 TTTAATAAATTT-T-GATAT
* *
302044 TTGAA-AAATTTTTATAT
1 TTTAATAAATTTTGATAT
302061 TTT
1 TTT
302064 TATCATATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 6 0.13
17 17 0.37
18 16 0.35
19 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAATAAATTTTGATAT
Found at i:303168 original size:21 final size:20
Alignment explanation
Indices: 303142--303182 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
303132 TATCTTTCTA
*
303142 TTTTTCTCTTTAATTTTTTAT
1 TTTTTCACTTT-ATTTTTTAT
*
303163 TTTTTCACTTTCTTTTTTAT
1 TTTTTCACTTTATTTTTTAT
303183 CCTATCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCACTTTATTTTTTAT
Found at i:303574 original size:16 final size:17
Alignment explanation
Indices: 303553--303589 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
303543 AAAATATATA
303553 TTTTCTTTCT-TTTT-AT
1 TTTTCTTT-TATTTTAAT
303569 TTTTCTTTTATTTTAAT
1 TTTTCTTTTATTTTAAT
303586 TTTT
1 TTTT
303590 TATCTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 12 0.63
17 6 0.32
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTATTTTAAT
Found at i:304416 original size:2 final size:2
Alignment explanation
Indices: 304409--304442 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
304399 TTTTTAGTGG
*
304409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
304443 GAGGCAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:305455 original size:22 final size:23
Alignment explanation
Indices: 305430--305480 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
305420 ATTTTATTTT
*
305430 TAAATATAATT-ATATAAAAAAA
1 TAAATATAATTAAAATAAAAAAA
* *
305452 TAAAAATGATTAAAATAAAAAAA
1 TAAATATAATTAAAATAAAAAAA
*
305475 TTAATA
1 TAAATA
305481 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAATATAATTAAAATAAAAAAA
Found at i:309382 original size:19 final size:19
Alignment explanation
Indices: 309346--309382 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
309336 CTTACTCAAT
*
309346 TTTTTATTTATATATAATA
1 TTTTTATTTAAATATAATA
*
309365 TTTTTATTTAAATTTAAT
1 TTTTTATTTAAATATAAT
309383 TATAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATTTAAATATAATA
Found at i:309709 original size:8 final size:9
Alignment explanation
Indices: 309696--309733 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
309686 GAATTGAAAG
309696 TTTATATA-
1 TTTATATAT
309704 TTTATATAT
1 TTTATATAT
309713 TTTATTATAT
1 TTTA-TATAT
*
309723 TTTAAATAT
1 TTTATATAT
309732 TT
1 TT
309734 ATTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
10 9 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTATATAT
Found at i:309745 original size:38 final size:37
Alignment explanation
Indices: 309700--309798 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 37
309690 TGAAAGTTTA
*
309700 TATATTTATATATTTTATTATATTTTAAAT-ATT-TAT
1 TATATTTATA-ATTTTTTTATATTTTAAATAATTATAT
*
309736 TAATAATTTATAATTTTTTTAAATATTTAAATAATTATAT
1 T-AT-ATTTATAATTTTTTTATAT-TTTAAATAATTATAT
309776 TATATTT-TAAATTTTTTTATATT
1 TATATTTAT-AATTTTTTTATATT
309799 ATCTAATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
36 1 0.02
37 14 0.26
38 30 0.56
39 5 0.09
40 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (37 bp):
TATATTTATAATTTTTTTATATTTTAAATAATTATAT
Found at i:310171 original size:15 final size:15
Alignment explanation
Indices: 310151--310237 Score: 52
Period size: 15 Copynumber: 5.5 Consensus size: 15
310141 TATAAATATT
310151 ATAAAATTTATTATA
1 ATAAAATTTATTATA
*
310166 ATAAAAATTATTACATA
1 ATAAAATTTATT--ATA
* *
310183 TAAAAAATTTATATAAA
1 -ATAAAATTTAT-TATA
310200 TATAAAATATT-TTA-A
1 -ATAAAAT-TTATTATA
* *
310215 ATATAATTATAATATA
1 ATAAAATT-TATTATA
310231 ATAAAAT
1 ATAAAAT
310238 ATATAAATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.02
14 7 0.12
15 14 0.25
16 9 0.16
17 13 0.23
18 11 0.20
19 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTTATTATA
Found at i:310190 original size:17 final size:17
Alignment explanation
Indices: 310133--310220 Score: 65
Period size: 19 Copynumber: 5.0 Consensus size: 17
310123 AATATAATAT
310133 AAAATTAATATAAATATTATA
1 AAAATT-AT-TAAATA-TA-A
* *
310154 AAATTTATTATA-AT-A
1 AAAATTATTAAATATAA
*
310169 AAAATTATTACATATAA
1 AAAATTATTAAATATAA
310186 AAAATTTATATAAATATAA
1 AAAA-TTAT-TAAATATAA
*
310205 AATATT-TTAAATATAA
1 AAAATTATTAAATATAA
310221 TTATAATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
15 11 0.19
16 11 0.19
17 7 0.12
18 7 0.12
19 14 0.25
20 2 0.04
21 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTATTAAATATAA
Found at i:310513 original size:19 final size:19
Alignment explanation
Indices: 310462--310506 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
310452 TGATTAATTT
310462 AATCAGTTATTAATTAATAA
1 AATCA-TTATTAATTAATAA
*
310482 AATCATTAATAATTAATAA
1 AATCATTATTAATTAATAA
310501 AA-CATT
1 AATCATT
310507 TGTTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (19 bp):
AATCATTATTAATTAATAA
Found at i:312412 original size:19 final size:18
Alignment explanation
Indices: 312327--312412 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
312317 TAAAAACTTA
*
312327 TATTATATTTATATATTT
1 TATTATATTTATAAATTT
312345 TATTATATTTA-AAATATT
1 TATTATATTTATAAAT-TT
**
312363 TATTAATAATTCGTAAATTTT
1 TATT-AT-ATTTATAAA-TTT
** *
312384 TAAAATATTTATATAATTA
1 TATTATATTTATA-AATTT
312403 TATTATATTT
1 TATTATATTT
312413 TAATTTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
17 3 0.06
18 17 0.33
19 17 0.33
20 7 0.13
21 7 0.13
22 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
TATTATATTTATAAATTT
Found at i:312413 original size:30 final size:30
Alignment explanation
Indices: 312331--312413 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
312321 AACTTATATT
*
312331 ATATTTATAT-ATTTTATTATA--TTTAAA
1 ATATTTATATAATTATATTATATTTTTAAA
* *
312358 ATATTTAT-TAATAAT-TCGTAAATTTTTAAA
1 ATATTTATATAATTATAT--TATATTTTTAAA
312388 ATATTTATATAATTATATTATATTTT
1 ATATTTATATAATTATATTATATTTT
312414 AATTTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
26 2 0.05
27 11 0.25
28 3 0.07
30 21 0.48
31 6 0.14
32 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATTTATATAATTATATTATATTTTTAAA
Found at i:312597 original size:15 final size:15
Alignment explanation
Indices: 312577--312624 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
312567 TATAAAATTT
312577 TAAAATTTATTATAA
1 TAAAATTTATTATAA
312592 TAAAATTATTATGTATAA
1 TAAAA-T-TTAT-TATAA
312610 -AAAATTTA-TATAA
1 TAAAATTTATTATAA
312623 TA
1 TA
312625 TAAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 8 0.28
16 2 0.07
17 8 0.28
18 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATTTATTATAA
Found at i:312618 original size:18 final size:17
Alignment explanation
Indices: 312583--312660 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 17
312573 ATTTTAAAAT
312583 TTATTATAATAAAATTA
1 TTATTATAATAAAATTA
312600 TTATGTATAA-AAAA-T-
1 TTAT-TATAATAAAATTA
*
312615 TTA-TATAATATAAAATA
1 TTATTATAATA-AAATTA
*
312632 TT-TTA-AATATAATTA
1 TTATTATAATAAAATTA
* *
312647 -TAATATAATCAAAT
1 TTATTATAATAAAAT
312661 ATATAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
13 5 0.10
14 2 0.04
15 12 0.25
16 12 0.25
17 12 0.25
18 5 0.10
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTATTATAATAAAATTA
Found at i:313839 original size:31 final size:32
Alignment explanation
Indices: 313801--313862 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
313791 GGTTAACCTG
313801 AATTATTAT-TTAAATATT-AATAAAAATATCA
1 AATTATTATATTAAAT-TTAAATAAAAATATCA
313832 AATTATTATAATTAAATTTAAATAAAAATAT
1 AATTATTAT-ATTAAATTTAAATAAAAATAT
313863 TTTTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 9 0.32
32 2 0.07
33 17 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (32 bp):
AATTATTATATTAAATTTAAATAAAAATATCA
Found at i:314453 original size:19 final size:20
Alignment explanation
Indices: 314415--314453 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
314405 ATTTTACTCA
*
314415 ATTTATTATTTATATATAAT
1 ATTTATTATTTAAATATAAT
*
314435 ATTT-TTATTTAAATTTAAT
1 ATTTATTATTTAAATATAAT
314454 TATAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATTATTTAAATATAAT
Found at i:314812 original size:18 final size:19
Alignment explanation
Indices: 314777--314818 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
314767 GAATTGAAAG
314777 TTTATAAATTTATATTATA
1 TTTATAAATTTATATTATA
*
314796 TTTATATATTT-TATTATA
1 TTTATAAATTTATATTATA
314814 TTTAT
1 TTTAT
314819 TAATAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATAAATTTATATTATA
Found at i:315202 original size:22 final size:23
Alignment explanation
Indices: 315177--315235 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
315167 AAATTTGAAA
*
315177 AAAATATGATATAAAAAAAAT-T
1 AAAATATAATATAAAAAAAATAT
* *
315199 AAAATATAATATAAATATAATAT
1 AAAATATAATATAAAAAAAATAT
315222 AAAAT-TAATATAAA
1 AAAATATAATATAAA
315236 TATTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATATAATATAAAAAAAATAT
Found at i:315216 original size:11 final size:11
Alignment explanation
Indices: 315178--315238 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
315168 AATTTGAAAA
*
315178 AAATATGATAT
1 AAATATAATAT
* *
315189 AAAAAAAAT-T
1 AAATATAATAT
315199 AAAATATAATAT
1 -AAATATAATAT
315211 AAATATAATAT
1 AAATATAATAT
315222 AAA-ATTAATAT
1 AAATA-TAATAT
315233 AAATAT
1 AAATAT
315239 TATAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 2 0.05
11 37 0.90
12 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:315231 original size:16 final size:16
Alignment explanation
Indices: 315201--315296 Score: 52
Period size: 16 Copynumber: 5.6 Consensus size: 16
315191 AAAAAATTAA
* *
315201 AATATAATATAAATAT
1 AATATAAAATTAATAT
315217 AATATAAAATTAATAT
1 AATATAAAATTAATAT
*
315233 AAATATTATAAAATTTATTAT
1 --A-A-TATAAAA-TTAATAT
*
315254 AATA-AAAATTATTACGT
1 AATATAAAATTAATA--T
* *
315271 -ATAAAAAATTTATAT
1 AATATAAAATTAATAT
315286 AAATATAAAAT
1 -AATATAAAAT
315297 ATTTTAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.11
16 21 0.33
17 19 0.30
18 2 0.03
19 2 0.03
20 7 0.11
21 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
AATATAAAATTAATAT
Found at i:315237 original size:33 final size:32
Alignment explanation
Indices: 315177--315264 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
315167 AAATTTGAAA
*
315177 AAAATATGATATAAAAAAAATTAAAATATAAT
1 AAAATATAATATAAAAAAAATTAAAATATAAT
** *
315209 ATAAATATAATATAAAATTAA-TATAAATATTAT
1 A-AAATATAATATAAAAAAAATTA-AAATATAAT
* * *
315242 AAAATTTATTATAATAAAAATTA
1 AAAATATAATATAAAAAAAATTA
315265 TTACGTATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
32 17 0.39
33 27 0.61
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (32 bp):
AAAATATAATATAAAAAAAATTAAAATATAAT
Found at i:315257 original size:20 final size:20
Alignment explanation
Indices: 315198--315247 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
315188 TAAAAAAAAT
315198 TAAAATATAATATAAATATAATA
1 TAAAAT-TAATATAAATAT--TA
315221 TAAAATTAATATAAATATTA
1 TAAAATTAATATAAATATTA
315241 TAAAATT
1 TAAAATT
315248 TATTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.33
22 12 0.44
23 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATTAATATAAATATTA
Found at i:315295 original size:17 final size:17
Alignment explanation
Indices: 315213--315296 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 17
315203 TATAATATAA
*
315213 ATAT-AATATAAAATTA
1 ATATAAATATAAAATTT
315229 ATATAAATATTATAAAATTT
1 ATAT-AA-A-TATAAAATTT
315249 AT-TATAATA-AAAA-TT
1 ATATA-AATATAAAATTT
* *
315264 AT-TACGTATAAAAAATTT
1 ATATA--AATATAAAATTT
315282 ATATAAATATAAAAT
1 ATATAAATATAAAAT
315297 ATTTTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
15 6 0.11
16 11 0.20
17 14 0.26
18 7 0.13
19 5 0.09
20 11 0.20
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:315617 original size:8 final size:8
Alignment explanation
Indices: 315597--315643 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
315587 AAAATATTTG
315597 TTAATAT-
1 TTAATATA
315604 TTAATATA
1 TTAATATA
315612 TTAATATA
1 TTAATATA
315620 TGT-ATATA
1 T-TAATATA
315628 TTTAAATATA
1 -TT-AATATA
315638 TTAATA
1 TTAATA
315644 AAATAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.20
8 19 0.54
9 4 0.11
10 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (8 bp):
TTAATATA
Found at i:315823 original size:31 final size:28
Alignment explanation
Indices: 315752--315824 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 28
315742 TTTGATCGAT
*
315752 TTGATTAATTTAATTATTATTATTAAAA
1 TTGATTAATTTAATCATTATTATTAAAA
* * *
315780 TTAATTATTTTAATCCATTTTTATATCAAAA
1 TTGATTAATTTAAT-CATTATTAT-T-AAAA
315811 TTGATTAATTTAAT
1 TTGATTAATTTAAT
315825 TTTCCATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 12 0.33
29 7 0.19
30 1 0.03
31 16 0.44
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (28 bp):
TTGATTAATTTAATCATTATTATTAAAA
Found at i:316306 original size:3 final size:3
Alignment explanation
Indices: 316300--316335 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
316290 TTAATTTTAA
* *
316300 AAT AAT AAT AAT AAT AAT AAG AAT AAG AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
316336 GTCCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:317230 original size:16 final size:17
Alignment explanation
Indices: 317190--317246 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
317180 ACTATGCAAT
* *
317190 TTTAATAATAAATAAACA
1 TTTAATAA-GAATAAATA
* *
317208 TTAAATATG-ATAAATA
1 TTTAATAAGAATAAATA
*
317224 TTTAATAAGAATATATA
1 TTTAATAAGAATAAATA
317241 TTTAAT
1 TTTAAT
317247 CAAGTTATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.42
17 12 0.39
18 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAATAAGAATAAATA
Found at i:317878 original size:25 final size:26
Alignment explanation
Indices: 317848--317897 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
317838 TCATATCTCA
*
317848 AATTCTGACCTAAATAAAAA-ATTTG
1 AATTCTGACCTAAACAAAAATATTTG
* *
317873 AATTCTGGCCTGAACAAAAATATTT
1 AATTCTGACCTAAACAAAAATATTT
317898 AATAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (26 bp):
AATTCTGACCTAAACAAAAATATTTG
Found at i:318421 original size:16 final size:17
Alignment explanation
Indices: 318381--318437 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
318371 ACTATGCAAT
* *
318381 TTTAATAATAAATAAACA
1 TTTAATAA-GAATAAATA
* *
318399 TTAAATATG-ATAAATA
1 TTTAATAAGAATAAATA
*
318415 TTTAATAAGAATATATA
1 TTTAATAAGAATAAATA
318432 TTTAAT
1 TTTAAT
318438 CAAGTTATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.42
17 12 0.39
18 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAATAAGAATAAATA
Found at i:319069 original size:25 final size:26
Alignment explanation
Indices: 319039--319088 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
319029 TCATATCTCA
*
319039 AATTCTGACCTAAATAAAAA-ATTTG
1 AATTCTGACCTAAACAAAAATATTTG
* *
319064 AATTCTGGCCTGAACAAAAATATTT
1 AATTCTGACCTAAACAAAAATATTT
319089 AATAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (26 bp):
AATTCTGACCTAAACAAAAATATTTG
Found at i:319611 original size:16 final size:17
Alignment explanation
Indices: 319571--319627 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
319561 ACTATGCAAT
* *
319571 TTTAATAATAAATAAACA
1 TTTAATAA-GAATAAATA
* *
319589 TTAAATATG-ATAAATA
1 TTTAATAAGAATAAATA
*
319605 TTTAATAAGAATATATA
1 TTTAATAAGAATAAATA
319622 TTTAAT
1 TTTAAT
319628 CAAGTTATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.42
17 12 0.39
18 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAATAAGAATAAATA
Found at i:321262 original size:17 final size:16
Alignment explanation
Indices: 321237--321270 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
321227 TTAACGTATC
*
321237 AAAATTTATATAAATAT
1 AAAAATTATA-AAATAT
321254 AAAAATTATAAAATAT
1 AAAAATTATAAAATAT
321270 A
1 A
321271 CAAACATAAC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATTATAAAATAT
Found at i:322861 original size:17 final size:19
Alignment explanation
Indices: 322825--322861 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
322815 AGAGAGCTAT
322825 GTCCTATTAAGTTGTTTAA
1 GTCCTATTAAGTTGTTTAA
*
322844 GTCC-ATTAGGTT-TTTAA
1 GTCCTATTAAGTTGTTTAA
322861 G
1 G
322862 AATGTCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (19 bp):
GTCCTATTAAGTTGTTTAA
Found at i:331860 original size:6 final size:6
Alignment explanation
Indices: 331846--331885 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
331836 TCAGTCCCTA
*
331846 AAATCG AAATTG AAATTG AAATTG AAATTG AAATTG AAAT
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAAT
331886 CACATTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (6 bp):
AAATTG
Found at i:332557 original size:32 final size:30
Alignment explanation
Indices: 332498--332560 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
332488 GTTGTTGCTA
332498 TTTAATTAGGTTTTTATTTTTATTTTTAAT
1 TTTAATTAGGTTTTTATTTTTATTTTTAAT
*
332528 TTTAATTGAGTTTTATTATTTTT-TATTTTAAT
1 TTTAATT-AGGTTT-TTATTTTTAT-TTTTAAT
332560 T
1 T
332561 AAAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.24
31 6 0.21
32 16 0.55
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (30 bp):
TTTAATTAGGTTTTTATTTTTATTTTTAAT
Found at i:332644 original size:43 final size:42
Alignment explanation
Indices: 332596--332690 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
332586 TTTTGATGAG
332596 TTTTTAATTTAAA-TTTAAATAGGTTTAAAT-TTATATTTATATT
1 TTTTTAATTTAAATTTTAAATA-GTTTAAATATTA-ATTTA-ATT
* *
332639 TTTTTAA-ATAAATTTTAAATATTTTAAATATTAATTTAATT
1 TTTTTAATTTAAATTTTAAATAGTTTAAATATTAATTTAATT
* *
332680 ATTTAAATTTA
1 TTTTTAATTTA
332691 TTTAATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
41 8 0.18
42 18 0.41
43 18 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (42 bp):
TTTTTAATTTAAATTTTAAATAGTTTAAATATTAATTTAATT
Found at i:332653 original size:42 final size:43
Alignment explanation
Indices: 332596--332676 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
332586 TTTTGATGAG
*
332596 TTTTTAATTTAAA-TTTAAATAGGTTTAAAT-TTATATTTATATT
1 TTTTTAATATAAATTTTAAATA-GTTTAAATATTA-ATTTATATT
*
332639 TTTTTAA-ATAAATTTTAAATATTTTAAATATTAATTTA
1 TTTTTAATATAAATTTTAAATAGTTTAAATATTAATTTA
332677 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 16 0.47
43 18 0.53
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (43 bp):
TTTTTAATATAAATTTTAAATAGTTTAAATATTAATTTATATT
Found at i:332701 original size:20 final size:20
Alignment explanation
Indices: 332661--332697 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
332651 TTTTAAATAT
332661 TTTAAATATTAATTTAATTA
1 TTTAAATATTAATTTAATTA
332681 TTTAAAT-TT-ATTTAATT
1 TTTAAATATTAATTTAATT
332698 TTATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATATTAATTTAATTA
Found at i:338438 original size:20 final size:20
Alignment explanation
Indices: 338394--338431 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
338384 AAATCATATA
*
338394 AACGAAAGGAAGAATGATGG
1 AACGCAAGGAAGAATGATGG
338414 AACGCAAGGAA-AATGATG
1 AACGCAAGGAAGAATGATG
338432 AGTACGCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.08, G:0.32, T:0.11
Consensus pattern (20 bp):
AACGCAAGGAAGAATGATGG
Found at i:338552 original size:24 final size:22
Alignment explanation
Indices: 338498--338552 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
338488 CAGCACTTAA
*
338498 AATAGATTTATTTAAATTATTTT
1 AATA-ATTAATTTAAATTATTTT
*
338521 -ATATTTAATTTAAATTAATATTT
1 AATAATTAATTTAAATT-AT-TTT
338544 AATAATTAA
1 AATAATTAA
338553 AAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 11 0.42
22 5 0.19
23 3 0.12
24 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATTAATTTAAATTATTTT
Found at i:338589 original size:35 final size:36
Alignment explanation
Indices: 338521--338590 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
338511 AAATTATTTT
*
338521 ATATTTAATTTAAATTAATATTTAATAATTAAAAAA
1 ATATTTAATTTAAATTAATATATAATAATTAAAAAA
338557 ATATTT-ATTTAAATTTAAT-TATAA-AATATAAAAA
1 ATATTTAATTTAAA-TTAATATATAATAAT-TAAAAA
338591 TTTAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 3 0.10
35 17 0.55
36 11 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
ATATTTAATTTAAATTAATATATAATAATTAAAAAA
Found at i:339101 original size:13 final size:13
Alignment explanation
Indices: 339083--339110 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
339073 TTAAAAAATT
339083 ATTTATTTTTTAA
1 ATTTATTTTTTAA
339096 ATTTATTTTTTAA
1 ATTTATTTTTTAA
339109 AT
1 AT
339111 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTATTTTTTAA
Found at i:339567 original size:23 final size:24
Alignment explanation
Indices: 339513--339568 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
339503 AAAGTTAAAA
339513 ATTTAT-ATTATTATTTATATAAT
1 ATTTATAATTATTATTTATATAAT
*
339536 A-TTAAAATTA-T-TTTATATTAAT
1 ATTTATAATTATTATTTATA-TAAT
339558 ATTTATAATTA
1 ATTTATAATTA
339569 AATTTAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTATAATTATTATTTATATAAT
Found at i:339573 original size:12 final size:12
Alignment explanation
Indices: 339513--339574 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
339503 AAAGTTAAAA
*
339513 ATTTATATTATT
1 ATTTATATTAAT
339525 ATTTATA-TAAT
1 ATTTATATTAAT
* *
339536 ATTAAAATT-AT
1 ATTTATATTAAT
339547 -TTTATATTAAT
1 ATTTATATTAAT
339558 ATTTATAATTAA-
1 ATTTAT-ATTAAT
339570 ATTTA
1 ATTTA
339575 AAGATAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 6 0.15
11 12 0.29
12 18 0.44
13 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATTAAT
Found at i:339907 original size:20 final size:20
Alignment explanation
Indices: 339882--339922 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
339872 TATATGTAGA
* *
339882 TTTTTTGAAAAGTACATAAT
1 TTTTTTAAAAAATACATAAT
*
339902 TTTTTTAAAAAATATATAAT
1 TTTTTTAAAAAATACATAAT
339922 T
1 T
339923 CTTAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTTTAAAAAATACATAAT
Found at i:340442 original size:22 final size:22
Alignment explanation
Indices: 340417--340470 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
340407 TTAATAATTA
*
340417 AAAAATATTTAAAT-TTAGTTAT
1 AAAAATATTTAAATATTA-ATAT
340439 AAAAATATTTAAATATTAATAT
1 AAAAATATTTAAATATTAATAT
*
340461 CAAAATATTT
1 AAAAATATTT
340471 TATATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAATATTTAAATATTAATAT
Found at i:342216 original size:24 final size:24
Alignment explanation
Indices: 342189--342239 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
342179 TAAAAATATT
* * * *
342189 TTTAATTTTTTATTTAAGTTTGAA
1 TTTAATTTATTATGTAAATTTAAA
342213 TTTAATTTATTATGTAAATTTAAA
1 TTTAATTTATTATGTAAATTTAAA
342237 TTT
1 TTT
342240 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTAATTTATTATGTAAATTTAAA
Found at i:342234 original size:18 final size:18
Alignment explanation
Indices: 342211--342253 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
342201 TTTAAGTTTG
342211 AATTTAATTTATTATGT-A
1 AATTTAATTT-TTATGTAA
*
342229 AATTTAAATTTTTATTTAA
1 AATTT-AATTTTTATGTAA
342248 AATTTA
1 AATTTA
342254 TTAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTAATTTTTATGTAA
Found at i:342250 original size:19 final size:19
Alignment explanation
Indices: 342211--342253 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
342201 TTTAAGTTTG
342211 AATTT-AATTTATTATGTA
1 AATTTAAATTTATTATGTA
*
342229 AATTTAAATTT-TTATTTAA
1 AATTTAAATTTATTATGT-A
342248 AATTTA
1 AATTTA
342254 TTAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTAAATTTATTATGTA
Found at i:344295 original size:2 final size:2
Alignment explanation
Indices: 344288--344325 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
344278 TTTTGAAGCC
* *
344288 AG AG AG AG AG AG AG AC AG AG AG AG AG AG TG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
344326 GGAATGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:344932 original size:22 final size:22
Alignment explanation
Indices: 344907--344959 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
344897 TTAAACTAAA
*
344907 TTAAATTTATCAAAATATTAAC
1 TTAAATTTATAAAAATATTAAC
*
344929 TTAAATTCATAAAAATATTAAC
1 TTAAATTTATAAAAATATTAAC
344951 TTAAATTTA
1 TTAAATTTA
344960 ATCTTTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATTTATAAAAATATTAAC
Found at i:345334 original size:30 final size:30
Alignment explanation
Indices: 345269--345334 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
345259 ATAATTTTTT
*
345269 TAATTATTTAAAAATAATTTTAATATTAAA
1 TAATTATTTAAAAATAATTTTAATAATAAA
*
345299 TAATTATTT-AATATAATTTATAATTAATAAA
1 TAATTATTTAAAAATAATTT-TAA-TAATAAA
345330 -AATTA
1 TAATTA
345335 CGTATTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.28
30 17 0.53
31 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATTATTTAAAAATAATTTTAATAATAAA
Found at i:345449 original size:20 final size:20
Alignment explanation
Indices: 345413--345450 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
345403 AAATATAAAA
**
345413 TTAATTTTTTATTAATTTAT
1 TTAATTTTTTAAAAATTTAT
345433 TTAATTTTTTAAAAATTT
1 TTAATTTTTTAAAAATTT
345451 TTATAGTTAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAATTTTTTAAAAATTTAT
Found at i:345719 original size:17 final size:17
Alignment explanation
Indices: 345697--345739 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
345687 TTTTCTTCAA
345697 ATATTCATAACATACAT
1 ATATTCATAACATACAT
* *
345714 ATATTCA-AATATAGAT
1 ATATTCATAACATACAT
345730 ATCATTCATA
1 AT-ATTCATA
345740 TGAAACTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
17 12 0.55
18 1 0.05
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (17 bp):
ATATTCATAACATACAT
Found at i:345739 original size:25 final size:25
Alignment explanation
Indices: 345692--345740 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
345682 TATATTTTTC
*
345692 TTCAAATATTCATAACATACATATA
1 TTCAAATATACATAACATACATATA
* * *
345717 TTCAAATATAGATATCATTCATAT
1 TTCAAATATACATAACATACATAT
345741 GAAACTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (25 bp):
TTCAAATATACATAACATACATATA
Found at i:346017 original size:18 final size:18
Alignment explanation
Indices: 345994--346039 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
345984 TTAGATATGA
345994 ATATGTTTAATCTTTTAT
1 ATATGTTTAATCTTTTAT
*
346012 ATATGTTTAATTTTTTAT
1 ATATGTTTAATCTTTTAT
*
346030 ATATATTTAA
1 ATATGTTTAA
346040 AAGATCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
ATATGTTTAATCTTTTAT
Found at i:349098 original size:13 final size:13
Alignment explanation
Indices: 349077--349106 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
349067 ATATTCGAAT
*
349077 ATATTGAATATAA
1 ATATCGAATATAA
349090 ATATCGAATATAA
1 ATATCGAATATAA
349103 ATAT
1 ATAT
349107 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATCGAATATAA
Found at i:352104 original size:20 final size:20
Alignment explanation
Indices: 352064--352113 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
352054 AGATTGTTTA
352064 ATTAAA-AAA-AATTTAAAT
1 ATTAAATAAATAATTTAAAT
352082 ATTAAATTAAATAATTT-AAT
1 ATTAAA-TAAATAATTTAAAT
352102 ATTAAATAAATA
1 ATTAAATAAATA
352114 TTAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 12 0.41
21 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAAATAAATAATTTAAAT
Found at i:352107 original size:15 final size:14
Alignment explanation
Indices: 352083--352126 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
352073 AATTTAAATA
352083 TTAAATTAAATAAT
1 TTAAATTAAATAAT
352097 TTAATATTAAATAAAT
1 TTAA-ATTAAAT-AAT
*
352113 ATTAAATTTAATAA
1 -TTAAATTAAATAA
352127 AATTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 9 0.35
17 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAATTAAATAAT
Found at i:352135 original size:26 final size:29
Alignment explanation
Indices: 352077--352137 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
352067 AAAAAAAATT
352077 TAAATATTAAATTAAATAATTTAATATTAAA
1 TAAATATTAAATTAAATAA--TAATATTAAA
*
352108 TAAATATTAAATTTAATAA-AAT-TT-AA
1 TAAATATTAAATTAAATAATAATATTAAA
352134 TAAA
1 TAAA
352138 AAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 3 0.10
31 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATATTAAATTAAATAATAATATTAAA
Found at i:352239 original size:25 final size:26
Alignment explanation
Indices: 352184--352250 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 26
352174 ATAAATTTAA
*
352184 AAAATTAAATATTTAAATATCATTATAT
1 AAAA-TAAAT-TTAAAATATCATTATAT
352212 AAAATAAATTTAAAATATCCA-TAT-T
1 AAAATAAATTTAAAATAT-CATTATAT
352237 AAAA-ATAATTTAAA
1 AAAATA-AATTTAAA
352251 CTCGATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 1 0.03
25 13 0.36
26 11 0.31
27 7 0.19
28 4 0.11
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATAAATTTAAAATATCATTATAT
Found at i:352277 original size:20 final size:20
Alignment explanation
Indices: 352252--352289 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
352242 TAATTTAAAC
*
352252 TCGATTTTTTATCAATTTCA
1 TCGATTTTTCATCAATTTCA
352272 TCGATTTTTCATCAATTT
1 TCGATTTTTCATCAATTT
352290 TCAAAACTAT
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:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (20 bp):
TCGATTTTTCATCAATTTCA
Found at i:353365 original size:15 final size:14
Alignment explanation
Indices: 353316--353367 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
353306 CAATGATTTT
*
353316 TAAAAAATTTTAAA
1 TAAAAAAATTTAAA
*
353330 TAAAAATA-TTAAA
1 TAAAAAAATTTAAA
353343 TTTAAAAAAATTTAAA
1 --TAAAAAAATTTAAA
353359 TAAAAAAAT
1 TAAAAAAAT
353368 ATATTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.16
14 15 0.47
15 7 0.22
16 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAAAAATTTAAA
Found at i:353471 original size:25 final size:25
Alignment explanation
Indices: 353417--353471 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
353407 TCATTTTTTT
*
353417 AATTATGTAATATATTATTTATATA
1 AATTATGTAATATATTATTTATAAA
* *
353442 TATTATGTAATTTA-TATTTTATAAA
1 AATTATGTAATATATTA-TTTATAAA
353467 AATTA
1 AATTA
353472 AATATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
AATTATGTAATATATTATTTATAAA
Found at i:353498 original size:39 final size:39
Alignment explanation
Indices: 353455--353568 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 39
353445 TATGTAATTT
353455 ATATTTTATAAAAATTAAATATATAA-TATTATAATTTAA
1 ATATTTTATAAAAATTAAATATA-AATTATTATAATTTAA
*
353494 ATA---T-TAAAAA-TATAT-TAAATTATT-TATATTTAA
1 ATATTTTATAAAAATTAAATATAAATTATTATA-ATTTAA
* * *
353527 A-ATTTAATAAAAATTAAATATAAAATTATTAAAAATTAA
1 ATATTTTATAAAAATTAAATAT-AAATTATTATAATTTAA
353566 ATA
1 ATA
353569 AAAATTATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
32 5 0.08
33 13 0.22
34 4 0.07
35 6 0.10
36 7 0.12
37 4 0.07
38 1 0.02
39 17 0.29
40 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (39 bp):
ATATTTTATAAAAATTAAATATAAATTATTATAATTTAA
Found at i:353541 original size:11 final size:11
Alignment explanation
Indices: 353525--353575 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
353515 ATTTATATTT
*
353525 AAAATTTAATA
1 AAAATTAAATA
353536 AAAATTAAATA
1 AAAATTAAATA
*
353547 TAAAATT-ATTA
1 -AAAATTAAATA
353558 AAAATTAAATA
1 AAAATTAAATA
353569 AAAATTA
1 AAAATTA
353576 TATTTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.17
11 23 0.66
12 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTAAATA
Found at i:353661 original size:14 final size:13
Alignment explanation
Indices: 353628--353669 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
353618 ATAAAATTAA
*
353628 AAATAATTATTTT
1 AAATAATTATATT
*
353641 AAATTA-TATA-T
1 AAATAATTATATT
353652 AAATAATTATATT
1 AAATAATTATATT
353665 AAATA
1 AAATA
353670 TTAATAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.25
12 7 0.29
13 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATAATTATATT
Found at i:353942 original size:16 final size:15
Alignment explanation
Indices: 353919--353949 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
353909 TTAATTTAAA
353919 ATTTTATATTAATAT
1 ATTTTATATTAATAT
353934 ATTTGTATATTAATAT
1 ATTT-TATATTAATAT
353950 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTTTATATTAATAT
Found at i:354011 original size:20 final size:20
Alignment explanation
Indices: 353988--354061 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
353978 TTATAATTAA
353988 TAATTTAAATAAAATAAAAT
1 TAATTTAAATAAAATAAAAT
*
354008 TAATTTAAAATATAAA-AAATT
1 TAATTT-AAATA-AAATAAAAT
* * * *
354029 TTATTTAAATTTAATTAATAT
1 TAATTTAAA-TAAAATAAAAT
*
354050 AAATTTAAATAA
1 TAATTTAAATAA
354062 TAATTATAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
20 13 0.32
21 25 0.61
22 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTTAAATAAAATAAAAT
Found at i:354054 original size:15 final size:15
Alignment explanation
Indices: 354034--354063 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
354024 AAATTTTATT
*
354034 TAAATTTAATTAATA
1 TAAATTTAAATAATA
354049 TAAATTTAAATAATA
1 TAAATTTAAATAATA
354064 ATTATAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTTAAATAATA
Found at i:354145 original size:25 final size:26
Alignment explanation
Indices: 354101--354168 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
354091 TTAATAATTT
*
354101 TAATATTTT-TTATTATTAATATCATAA
1 TAATATTTTATTATAATT-A-ATCATAA
*
354128 TTAATATTTTATTATAATTAATTATAA
1 -TAATATTTTATTATAATTAATCATAA
354155 TAATA-TTTATTATA
1 TAATATTTTATTATA
354169 TTTATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.24
26 5 0.14
27 6 0.16
28 10 0.27
29 7 0.19
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATATTTTATTATAATTAATCATAA
Found at i:354168 original size:15 final size:15
Alignment explanation
Indices: 354141--354184 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
354131 ATATTTTATT
354141 ATAATTAATTATAATA
1 ATAATT-ATTATAATA
* * *
354157 ATATTTATTATATTT
1 ATAATTATTATAATA
354172 ATAATTATTATAA
1 ATAATTATTATAA
354185 ATATGAGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTATTATAATA
Found at i:355466 original size:24 final size:24
Alignment explanation
Indices: 355436--355486 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
355426 TCACTTAGAA
355436 AAATTTTTAAAAAAAT-TAAAAAAT
1 AAATTTTTAAAAAAATAT-AAAAAT
*
355460 AAATTTTTAAATAAATATAAAAAT
1 AAATTTTTAAAAAAATATAAAAAT
355484 AAA
1 AAA
355487 GTATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATTTTTAAAAAAATATAAAAAT
Found at i:356023 original size:19 final size:19
Alignment explanation
Indices: 355996--356042 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
355986 TTATAATTAA
355996 ATTTAAATT-AAAATATATT
1 ATTTAAATTAAAAAT-TATT
*
356015 ATTTTAATTAAAAATTATT
1 ATTTAAATTAAAAATTATT
356034 ATTTCAAAT
1 ATTT-AAAT
356043 CGAGTCCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAATTAAAAATTATT
Found at i:356265 original size:23 final size:23
Alignment explanation
Indices: 356235--356280 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
356225 CTAGTTTTAG
* *
356235 AGATTCGATTTTTAACATCTAAA
1 AGATTCGATTTCTAACACCTAAA
356258 AGATTCGATTTCTAACACCTAAA
1 AGATTCGATTTCTAACACCTAAA
356281 GTATATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
AGATTCGATTTCTAACACCTAAA
Found at i:356519 original size:14 final size:14
Alignment explanation
Indices: 356500--356540 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
356490 TATATTACTA
356500 TTTAAAATAATATT
1 TTTAAAATAATATT
356514 TTTAAAAT--TATT
1 TTTAAAATAATATT
* *
356526 TTTATATTAATATT
1 TTTAAAATAATATT
356540 T
1 T
356541 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAAATAATATT
Found at i:356777 original size:14 final size:16
Alignment explanation
Indices: 356747--356778 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
356737 ATATTAAGAG
356747 AATAAACAATAATATT
1 AATAAACAATAATATT
356763 AATAAA-AAT-ATATT
1 AATAAACAATAATATT
356777 AA
1 AA
356779 AAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAACAATAATATT
Found at i:356787 original size:21 final size:20
Alignment explanation
Indices: 356763--356816 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
356753 CAATAATATT
356763 AATAAAAATATATTAAAAATA
1 AATAAAAATAT-TTAAAAATA
*
356784 AATAATAAT-TTTAAAAATA
1 AATAAAAATATTTAAAAATA
356803 AA-AATAAATATTTA
1 AATAA-AAATATTTA
356817 TCAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 5 0.17
21 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAAATATTTAAAAATA
Found at i:356799 original size:30 final size:34
Alignment explanation
Indices: 356736--356802 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
356726 AGCAAATTGT
356736 TATATTAAGAGAATAAACAATAATATTAATAAAAA
1 TATATTAAGAGAATAAACAATAATATT-ATAAAAA
*
356771 TATATTAA-A-AATAAATAATAAT-TT-TAAAAA
1 TATATTAAGAGAATAAACAATAATATTATAAAAA
356801 TA
1 TA
356803 AAAATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 8 0.26
32 2 0.06
33 12 0.39
34 1 0.03
35 8 0.26
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (34 bp):
TATATTAAGAGAATAAACAATAATATTATAAAAA
Found at i:357202 original size:29 final size:28
Alignment explanation
Indices: 357166--357222 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
357156 ATTATTTTTA
357166 TTTTAATA-TTTATATATTTATT-ATTAAT
1 TTTTAATATTTTAT-TA-TTATTAATTAAT
357194 TTTTAAATATTTTATTATTATTAATTAAT
1 TTTT-AATATTTTATTATTATTAATTAAT
357223 AATTTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 9 0.35
29 12 0.46
30 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTAATATTTTATTATTATTAATTAAT
Done.