Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 2 of 173
Found at i:373439 original size:19 final size:18
Alignment explanation
Indices: 373409--373447 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
373399 ACATAAAGAA
373409 TTATTTTTTATTCTATTT
1 TTATTTTTTATTCTATTT
*
373427 TTATTTTTGTATTTTATTT
1 TTATTTTT-TATTCTATTT
373446 TT
1 TT
373448 TCTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTATTTTTTATTCTATTT
Found at i:374119 original size:22 final size:21
Alignment explanation
Indices: 374086--374134 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
374076 CCCTAAACTA
*
374086 TAAATCCTTAGCTCTAAACCCC
1 TAAATCCTTAGCCCT-AACCCC
374108 TAAA-CCTCTAGCCCTAACCCC
1 TAAATCCT-TAGCCCTAACCCC
374129 TAAATC
1 TAAATC
374135 TTAAATCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.33, C:0.39, G:0.04, T:0.24
Consensus pattern (21 bp):
TAAATCCTTAGCCCTAACCCC
Found at i:374290 original size:15 final size:16
Alignment explanation
Indices: 374264--374297 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
374254 CTATACCTCT
374264 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
374280 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
374295 AAC
1 AAC
374298 ACCATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:374643 original size:41 final size:41
Alignment explanation
Indices: 374584--374696 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
374574 AAAAAAAAAT
* * **
374584 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTTAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
* *
374625 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
374666 ATTAGCGGCGCTTCTT-AAGAAACGCCGCTAA
1 ATTAGCGGCGCTTCTTCAA-AAACGCCGCTAA
374697 GGGCCCCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
40 2 0.03
41 62 0.97
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
Found at i:374792 original size:38 final size:39
Alignment explanation
Indices: 374738--374812 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
374728 TGGCTTAGGC
*
374738 TTTTTGCGGCGATTTTCAGAAAA-CGCCGCTATTGCTAA
1 TTTTTGCGGCGATTTTCAGAAAAGCGCCGCTAATGCTAA
*
374776 TTTTTAGCGGCG-TTTTCTGAAAAGCGCCGCTAATGCT
1 TTTTT-GCGGCGATTTTCAGAAAAGCGCCGCTAATGCT
374813 CTACCTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (39 bp):
TTTTTGCGGCGATTTTCAGAAAAGCGCCGCTAATGCTAA
Found at i:374886 original size:41 final size:41
Alignment explanation
Indices: 374757--374889 Score: 123
Period size: 40 Copynumber: 3.3 Consensus size: 41
374747 CGATTTTCAG
* * *
374757 AAAA-CGCCGCTATTGCT-AATTTTTAGCGGCGTTTTCTG-
1 AAAAGCGCCGCTAATGCTCAATTTTTAGTGGCGTTTTTTGT
* ** * *
374795 AAAAGCGCCGCTAATGCTCTACCTTTAGTGGTG-TTTTTAT
1 AAAAGCGCCGCTAATGCTCAATTTTTAGTGGCGTTTTTTGT
* *
374835 AAAAGTGCCGCTAATGCTCGATTTTTAGTGGCGTTTTTTGT
1 AAAAGCGCCGCTAATGCTCAATTTTTAGTGGCGTTTTTTGT
*
374876 CCAAA-CGCCGCTAA
1 -AAAAGCGCCGCTAA
374890 AAATGCCGCT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
38 4 0.05
39 16 0.22
40 37 0.50
41 14 0.19
42 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTCAATTTTTAGTGGCGTTTTTTGT
Found at i:375337 original size:32 final size:32
Alignment explanation
Indices: 375259--375337 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
375249 ACTTACACGC
* *
375259 TCGTGTGGCCCACACGACCTAATTGGCTCAGA
1 TCGTGTGGCCCACACAACCCAATTGGCTCAGA
* *
375291 TCGTGCGACCCACACAACCCAATTGGC-CTAGA
1 TCGTGTGGCCCACACAACCCAATTGGCTC-AGA
*
375323 TCGTGTGGCTCACAC
1 TCGTGTGGCCCACAC
375338 GGCCTGTCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (32 bp):
TCGTGTGGCCCACACAACCCAATTGGCTCAGA
Found at i:377533 original size:9 final size:9
Alignment explanation
Indices: 377514--377577 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
377504 AATGTAGTTC
377514 AAAATATTAT
1 AAAA-ATTAT
377524 AAAAATTAT
1 AAAAATTAT
* *
377533 AAAATTTTT
1 AAAAATTAT
** *
377542 AACATGTTGT
1 AA-AAATTAT
377552 AAAAATTAT
1 AAAAATTAT
377561 -AAAATTAT
1 AAAAATTAT
377569 AAAAATTAT
1 AAAAATTAT
377578 CGATAATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
8 8 0.18
9 26 0.59
10 10 0.23
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (9 bp):
AAAAATTAT
Found at i:377652 original size:21 final size:20
Alignment explanation
Indices: 377599--377649 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
377589 AAAAAAATTC
377599 TAACAAAACA-T-TAAAATA
1 TAACAAAACATTATAAAATA
* *
377617 TGAATAAAATATTATAAAATA
1 T-AACAAAACATTATAAAATA
377638 TAACAAAACATT
1 TAACAAAACATT
377650 TATCCACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 7 0.27
20 10 0.38
21 8 0.31
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (20 bp):
TAACAAAACATTATAAAATA
Found at i:378237 original size:17 final size:17
Alignment explanation
Indices: 378163--378241 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
378153 TGAATTAGTT
*
378163 TTAAATTTAAT-TTATA
1 TTAAATTTAATCATATA
*
378179 TTCTAATTTAATGGCATAT-
1 TT-AAATTTAAT--CATATA
* * *
378198 TAAATATTTAAATCTTATT
1 TTAA-ATTT-AATCATATA
378217 TTAAATTTAATCATATA
1 TTAAATTTAATCATATA
378234 TTAAATTT
1 TTAAATTT
378242 TGAGATAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.04
17 23 0.48
18 9 0.19
19 8 0.17
20 6 0.12
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTAATCATATA
Found at i:378263 original size:21 final size:21
Alignment explanation
Indices: 378229--378277 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
378219 AAATTTAATC
* *
378229 ATATATTAAATTTTGAGATAA
1 ATATATTAAATTTTAAAATAA
**
378250 ATATATTACTTTTTAAAATAA
1 ATATATTAAATTTTAAAATAA
*
378271 AAATATT
1 ATATATT
378278 GATATAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
ATATATTAAATTTTAAAATAA
Found at i:385385 original size:27 final size:28
Alignment explanation
Indices: 385337--385392 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
385327 AAAAATTGAA
*
385337 GTAAAAAAAGTTACGTTAATTTTATAGAT
1 GTAAAAAAAGTTAC-TTAATTTAATAGAT
385366 GTAAAATAAAGTTA-TT-ATTTAATAGAT
1 GTAAAA-AAAGTTACTTAATTTAATAGAT
385393 CTCTAAGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 10 0.40
28 2 0.08
29 6 0.24
30 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (28 bp):
GTAAAAAAAGTTACTTAATTTAATAGAT
Found at i:394607 original size:35 final size:34
Alignment explanation
Indices: 394566--394658 Score: 88
Period size: 33 Copynumber: 2.8 Consensus size: 34
394556 TCGTATTTGT
*
394566 AAATTTTATTGTGTTAATTATAATTATATTTA-A
1 AAATTTTATTGTGTTAATTATAATTATATGTATA
* *
394599 AATTATTTTAATT-T-TTAA--ATATTTAATATGTATC
1 AA--ATTTT-ATTGTGTTAATTATAATT-ATATGTATA
394633 AAATTTTATTGTGTTAATTATAATTA
1 AAATTTTATTGTGTTAATTATAATTA
394659 CATATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
31 3 0.06
32 11 0.23
33 12 0.26
34 7 0.15
35 11 0.23
36 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (34 bp):
AAATTTTATTGTGTTAATTATAATTATATGTATA
Found at i:395048 original size:27 final size:27
Alignment explanation
Indices: 395017--395077 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
395007 TAAATCCAAC
*
395017 AAAAAGAG-GGATTAAATTTCTAGAA-AT
1 AAAAAGAGAAGATTAAATTT-TA-AATAT
395044 AAAAATG-GAAGATTAAATTTTAAATAT
1 AAAAA-GAGAAGATTAAATTTTAAATAT
395071 AAAAAGA
1 AAAAAGA
395078 ATATAGGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 3 0.10
27 15 0.52
28 11 0.38
ACGTcount: A:0.57, C:0.02, G:0.15, T:0.26
Consensus pattern (27 bp):
AAAAAGAGAAGATTAAATTTTAAATAT
Found at i:395601 original size:13 final size:12
Alignment explanation
Indices: 395571--395607 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
395561 AGTAATTTTA
395571 ATTAAGTTTAAT
1 ATTAAGTTTAAT
*
395583 AGTAAGTTCTAAT
1 ATTAAGTT-TAAT
395596 ATTAAGTTTAAT
1 ATTAAGTTTAAT
395608 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (12 bp):
ATTAAGTTTAAT
Found at i:397595 original size:86 final size:86
Alignment explanation
Indices: 397445--397700 Score: 318
Period size: 86 Copynumber: 3.0 Consensus size: 86
397435 AGATAAAAAC
* ** *
397445 ATTTGTAATTACTGCCACTTGTTGTGAGTGCACAACATGGTTGCAGATTAAACAAACTGCCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
397510 AGTTTTGTGGACAAGCCACGT
66 AGTTTTGTGGACAAGCCACGT
** * * * * *
397531 ATTTGCAATTACTATCACTTGTTGTAAGTTCACAACATATTTTCAAATTAAACAAATTGTCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
* *
397596 GGTTTTGTGGGCAAGCCACGT
66 AGTTTTGTGGACAAGCCACGT
* * * *
397617 ATTTACAGTTAATGCCACTTGTGGTGAGTGCACAACATATTTGCAGATTAAAC-AATCTGCCACT
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAT-TGCCACT
*
397681 -AGATTTTATGGACAAGCCAC
65 GAG-TTTTGTGGACAAGCCAC
397701 CACTTGTATG
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
85 4 0.03
86 137 0.97
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (86 bp):
ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
AGTTTTGTGGACAAGCCACGT
Found at i:405153 original size:18 final size:17
Alignment explanation
Indices: 405106--405160 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
405096 AAAATAAAAA
405106 AAAACATTAAAAA-TATT
1 AAAA-ATTAAAAATTATT
* * *
405123 ATAACTTATAAATTTATT
1 AAAAATTA-AAAATTATT
405141 AAAAATTAAAAA-TATT
1 AAAAATTAAAAATTATT
405157 AAAA
1 AAAA
405161 TTGACATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 9 0.30
18 10 0.33
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATTAAAAATTATT
Found at i:405210 original size:23 final size:24
Alignment explanation
Indices: 405168--405215 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
405158 AAATTGACAT
405168 AAACTTATAAAAATTATATAAAAA
1 AAACTTATAAAAATTATATAAAAA
405192 AAACTTATAAAACATTATA-AAAAA
1 AAACTTATAAAA-ATTATATAAAAA
405216 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
AAACTTATAAAAATTATATAAAAA
Found at i:405240 original size:18 final size:17
Alignment explanation
Indices: 405190--405257 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
405180 ATTATATAAA
405190 AAAAACTTATAAAACATTAT
1 AAAAAC-TATAAAAC--TAT
* * *
405210 AAAAAATATTAAAAATCT
1 AAAAACTA-TAAAACTAT
405228 AAAAATCTATAAAACTAT
1 AAAAA-CTATAAAACTAT
405246 -AAAACTATAAAA
1 AAAAACTATAAAA
405258 AATTTATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 8 0.20
17 4 0.10
18 14 0.35
19 4 0.10
20 10 0.25
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAACTATAAAACTAT
Found at i:405306 original size:10 final size:10
Alignment explanation
Indices: 405255--405372 Score: 50
Period size: 10 Copynumber: 11.6 Consensus size: 10
405245 TAAAACTATA
405255 AAAAATTTAT
1 AAAAATTTAT
*
405265 -AAAATTAATT
1 AAAAATTTA-T
*
405275 AAACATATT-T
1 AAAAAT-TTAT
405285 -AAAATATT-T
1 AAAAAT-TTAT
405294 AAAAATTTAT
1 AAAAATTTAT
** *
405304 AAAAACGTGT
1 AAAAATTTAT
405314 AAAAATTCT-T
1 AAAAATT-TAT
*
405324 AAAAACTTAT
1 AAAAATTTAT
*
405334 AAAAATTCATT
1 AAAAATTTA-T
*
405345 AAAAATATA-
1 AAAAATTTAT
405354 AAAACATTTTATT
1 AAAA-A-TTTA-T
405367 AAAAAT
1 AAAAAT
405373 CATAAGAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
9 22 0.27
10 36 0.44
11 17 0.21
12 2 0.02
13 4 0.05
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:405308 original size:20 final size:20
Alignment explanation
Indices: 405255--405352 Score: 60
Period size: 20 Copynumber: 4.9 Consensus size: 20
405245 TAAAACTATA
* *
405255 AAAAATTTATAAAATTAATT
1 AAAAATTTATAAAAATATTT
*
405275 AAACATATT-T-AAAATATTT
1 AAAAAT-TTATAAAAATATTT
** *
405294 AAAAATTTATAAAAACGTGT
1 AAAAATTTATAAAAATATTT
*
405314 AAAAATTCT-TAAAAACT-TAT
1 AAAAATT-TATAAAAA-TATTT
*
405334 AAAAATTCATTAAAAATAT
1 AAAAATTTA-TAAAAATAT
405353 AAAAACATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 35 0.58
21 10 0.17
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTTATAAAAATATTT
Found at i:405357 original size:20 final size:20
Alignment explanation
Indices: 405314--405377 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 20
405304 AAAAACGTGT
405314 AAAAATTC-TTAAAAACT-TA
1 AAAAATTCATTAAAAA-TATA
405333 TAAAAATTCATTAAAAATATA
1 -AAAAATTCATTAAAAATATA
*
405354 AAAACATTTTATTAAAAATCATA
1 AAAA-A-TTCATTAAAAAT-ATA
405377 A
1 A
405378 GAATAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 13 0.34
21 10 0.26
22 11 0.29
23 4 0.11
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCATTAAAAATATA
Found at i:405933 original size:15 final size:15
Alignment explanation
Indices: 405913--405943 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
405903 GTTCACCATC
405913 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
405928 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
405943 G
1 G
405944 TTCAAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (15 bp):
GCACTGTGACCTGAA
Found at i:407843 original size:12 final size:12
Alignment explanation
Indices: 407826--407866 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
407816 ATGAGAGTCA
407826 ATTTTGATAAAT
1 ATTTTGATAAAT
407838 ATTTTGATAAAT
1 ATTTTGATAAAT
407850 A-TTT-ATAAAT
1 ATTTTGATAAAT
407860 ATTTTGA
1 ATTTTGA
407867 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 6 0.22
12 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
ATTTTGATAAAT
Found at i:407876 original size:20 final size:20
Alignment explanation
Indices: 407827--407893 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
407817 TGAGAGTCAA
* *
407827 TTTTGATAAATATTTTGATAAA
1 TTTTTATAAATATTTTG--AAT
*
407849 TATTTATAAATATTTTGAAT
1 TTTTTATAAATATTTTGAAT
** *
407869 TTTTTATATTTATTTTAAAT
1 TTTTTATAAATATTTTGAAT
407889 TTTTT
1 TTTTT
407894 TTGTAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 23 0.61
22 15 0.39
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTATAAATATTTTGAAT
Found at i:410586 original size:11 final size:11
Alignment explanation
Indices: 410555--410598 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
410545 TAATAATAAC
*
410555 AAAATAGTAGT
1 AAAATAATAGT
*
410566 AATATAATAGT
1 AAAATAATAGT
*
410577 AAAATAATAGC
1 AAAATAATAGT
*
410588 AAAACAATAGT
1 AAAATAATAGT
410599 GAAACATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:422262 original size:17 final size:17
Alignment explanation
Indices: 422228--422273 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
422218 TTGCATTCTT
* *
422228 ATATT-TTTAAATTGAC
1 ATATTATTTGAATTAAC
*
422244 ATTTTATTTGAATTAAC
1 ATATTATTTGAATTAAC
422261 ATATTATTTGAAT
1 ATATTATTTGAAT
422274 AGGTGAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (17 bp):
ATATTATTTGAATTAAC
Found at i:426779 original size:20 final size:20
Alignment explanation
Indices: 426754--426793 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
426744 CCAAAAATGA
*
426754 TTTCTGGAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
*
426774 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATAATTTACT
426794 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:426871 original size:33 final size:32
Alignment explanation
Indices: 426784--426869 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
426774 TTTCTGAAAA
*
426784 ATGATTTACTGAAAATATTTTCTGATGTTTGG
1 ATGATTTCCTGAAAATATTTTCTGATGTTTGG
* * *
426816 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGATGTTTGG
426849 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
426870 TCAGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 24 0.55
34 3 0.07
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGATGTTTGG
Found at i:429256 original size:16 final size:16
Alignment explanation
Indices: 429235--429265 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
429225 AAATGATCAG
429235 TAACTACAGAAAATTT
1 TAACTACAGAAAATTT
429251 TAACTACAGAAAATT
1 TAACTACAGAAAATT
429266 ATAGCAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TAACTACAGAAAATTT
Found at i:432267 original size:12 final size:13
Alignment explanation
Indices: 432244--432272 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
432234 TACAAAATCA
432244 AAATTCACATATT
1 AAATTCACATATT
432257 AAATT-ACATATT
1 AAATTCACATATT
432269 AAAT
1 AAAT
432273 CAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTCACATATT
Found at i:439020 original size:21 final size:21
Alignment explanation
Indices: 439003--439074 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
438993 ACCAAAAATT
439003 TATTTTAAAAATTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAG
**
439024 TATTTTAAAAATATTTTAAAAA-
1 TATTTT-AAAA-ATTAAAAAAAG
*
439046 TGTTTT-AAAATT--AAAAAG
1 TATTTTAAAAATTAAAAAAAG
439064 TATTTTAAAAA
1 TATTTTAAAAA
439075 CATTTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 7 0.16
20 3 0.07
21 6 0.14
22 9 0.21
23 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TATTTTAAAAATTAAAAAAAG
Found at i:439055 original size:10 final size:11
Alignment explanation
Indices: 439018--439084 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
439008 TAAAAATTAA
439018 AAAAAGTATTTT
1 AAAAA-TATTTT
439030 AAAAATATTTT
1 AAAAATATTTT
*
439041 AAAAATGTTTT
1 AAAAATATTTT
439052 --AAA-A--TT
1 AAAAATATTTT
439058 AAAAAGTATTTT
1 AAAAA-TATTTT
*
439070 AAAAACATTTT
1 AAAAATATTTT
439081 AAAA
1 AAAA
439085 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
6 2 0.04
8 3 0.07
9 3 0.07
10 1 0.02
11 25 0.54
12 12 0.26
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:439061 original size:17 final size:18
Alignment explanation
Indices: 439039--439073 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
439029 TAAAAATATT
*
439039 TTAAAAA-TGTTTTAAAA
1 TTAAAAAGTATTTTAAAA
439056 TTAAAAAGTATTTTAAAA
1 TTAAAAAGTATTTTAAAA
439074 ACATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TTAAAAAGTATTTTAAAA
Found at i:439071 original size:29 final size:28
Alignment explanation
Indices: 439028--439091 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 28
439018 AAAAAGTATT
**
439028 TTAAAAATATTTTAAAAATGTTTTAAAA
1 TTAAAAATATTTTAAAAACATTTTAAAA
439056 TTAAAAAGTATTTTAAAAACATTTTAAAA
1 TTAAAAA-TATTTTAAAAACATTTTAAAA
439085 TTAAAAA
1 TTAAAAA
439092 AAATCACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (28 bp):
TTAAAAATATTTTAAAAACATTTTAAAA
Found at i:439216 original size:38 final size:39
Alignment explanation
Indices: 439156--439241 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
439146 AATTTATTTT
* ***
439156 AAAAATTAAAAAAAGTATTTTTAAAATGT-TTTAAAATTA
1 AAAAATAAAAAAAAGTATTTTTAAAA-GTAAAAAAAATTA
*
439195 AAAAATAAAAAAAATTA-TTTTAAAAGTAAAAAAAATTA
1 AAAAATAAAAAAAAGTATTTTTAAAAGTAAAAAAAATTA
439233 AAAAATAAA
1 AAAAATAAA
439242 TATATTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 2 0.05
38 24 0.59
39 15 0.37
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (39 bp):
AAAAATAAAAAAAAGTATTTTTAAAAGTAAAAAAAATTA
Found at i:443500 original size:28 final size:28
Alignment explanation
Indices: 443431--443500 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
443421 ATGTTTGACA
*
443431 AACCCCTATGGTAAACTCGTATTTAGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
* *
443459 AACCCCTATAGTGAACTCGTATTTGGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
*
443487 AACCCCTAGGGTGA
1 AACCCCTATGGTGA
443501 TCACAAGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (28 bp):
AACCCCTATGGTGAACTCGTATTTAGCG
Found at i:443568 original size:25 final size:26
Alignment explanation
Indices: 443527--443587 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
443517 CTTATGTTGA
* *
443527 ACTACTATGGCGTACCC-TATGGAGG
1 ACTACTATGGCGAACCCTTAAGGAGG
* *
443552 ACTACTATGGTGAACCCTTAAGGAGT
1 ACTACTATGGCGAACCCTTAAGGAGG
*
443578 ACTCCTATGG
1 ACTACTATGG
443588 AAAACCCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
ACTACTATGGCGAACCCTTAAGGAGG
Found at i:449852 original size:21 final size:21
Alignment explanation
Indices: 449821--449876 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
449811 TCTTTACCTT
* *
449821 AAACCCCAAACTTAGAATCTC
1 AAACCCTAAACTTAGAATATC
* *
449842 GAACCTTAAACCTT-GAATATC
1 AAACCCTAAA-CTTAGAATATC
449863 AAACCCTAAACTTA
1 AAACCCTAAACTTA
449877 AAGCCAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.43, C:0.29, G:0.05, T:0.23
Consensus pattern (21 bp):
AAACCCTAAACTTAGAATATC
Found at i:451761 original size:18 final size:19
Alignment explanation
Indices: 451722--451772 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
451712 ATTACAAAGA
* *
451722 AAAAATTAAAATATTTTTT
1 AAAATTTAAAATATTTTAT
451741 AAAATTTAAAATA-TTTAT
1 AAAATTTAAAATATTTTAT
451759 AAAAGTTCTAAAAT
1 AAAA-TT-TAAAAT
451773 TCAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 14 0.50
20 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATTTAAAATATTTTAT
Found at i:457546 original size:21 final size:21
Alignment explanation
Indices: 457520--457656 Score: 85
Period size: 21 Copynumber: 6.5 Consensus size: 21
457510 TTGAAGGTTG
*
457520 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
457541 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* * *
457562 AACGGAAGCTCTTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
457583 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
457604 AATAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
** * * *
457625 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
457646 AACAGAAGCTC
1 AACAGAAGCTC
457657 GTGAGATCTA
Statistics
Matches: 81, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:457562 original size:42 final size:42
Alignment explanation
Indices: 457515--457674 Score: 158
Period size: 42 Copynumber: 3.8 Consensus size: 42
457505 GAAGCTTGAA
* *
457515 GGTTGAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * *
457557 GGTTGAACGGAAGCTCTTAAGAGCTGAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * ** * *
457599 GGTTAAATAGAAGCTCAAAAGAGCTGAATGGAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * * *
457641 AGTTAAACAGAAGCTCGTGAGATCTAAACGGAAA
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAA
457675 GTAAACACGA
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
Found at i:483442 original size:18 final size:19
Alignment explanation
Indices: 483421--483461 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
483411 TGTTGTTACT
483421 ATTTTATA-ATTAATTAAA
1 ATTTTATATATTAATTAAA
*
483439 ATTTTATATTTTTAATTAAA
1 ATTTTATA-TATTAATTAAA
483459 ATT
1 ATT
483462 ATTGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATATATTAATTAAA
Found at i:500142 original size:11 final size:11
Alignment explanation
Indices: 500126--500151 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
500116 TATTTTTTTA
500126 TTTTAAAATAC
1 TTTTAAAATAC
500137 TTTTAAAATAC
1 TTTTAAAATAC
500148 TTTT
1 TTTT
500152 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:500172 original size:31 final size:31
Alignment explanation
Indices: 500137--500209 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 31
500127 TTTAAAATAC
500137 TTTTAAAATACTTTTTTTAAATTT-T-TTTTAAT
1 TTTTAAAATA-TTTTTTT--ATTTCTGTTTTAAT
*
500169 TTTAAAAATATTTTTTTATTTCTGTTTTAAT
1 TTTTAAAATATTTTTTTATTTCTGTTTTAAT
500200 TTTTAAAATA
1 TTTTAAAATA
500210 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.11
30 1 0.03
31 23 0.62
32 9 0.24
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (31 bp):
TTTTAAAATATTTTTTTATTTCTGTTTTAAT
Found at i:509287 original size:39 final size:40
Alignment explanation
Indices: 509243--509333 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
509233 TGAATTATAG
* * *
509243 AATACTGGATATTGTTTTG-AGTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGTTATGTA-TAATGCAGTGAATTGTGAA
*
509282 AATACTGAATATTGTTATGTATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
*
509322 ATTACTGCAATA
1 AATACTG-AATA
509334 CTGTGAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 21 0.48
40 19 0.43
41 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (40 bp):
AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
Found at i:509590 original size:45 final size:45
Alignment explanation
Indices: 509516--509664 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 45
509506 ATGTGCCGAC
** *
509516 TACTGTTACTGTTA-ATTTTCTGCACTTTGTGTGTCAAATATTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
* * ** * *
509560 TACTGTTACGGTTACCGATTTGGCACTTTGTGTGTCTAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
** * **
509605 TACCATTACTATTACAGATTCAGCACTTTGTGTGTTGAATATTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
509650 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
509665 TGCTACCATT
Statistics
Matches: 83, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
44 13 0.16
45 70 0.84
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
Found at i:511171 original size:30 final size:28
Alignment explanation
Indices: 511127--511200 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
511117 ATTTTATAAA
* * *
511127 ATTTTTTA-ATTTTTAATAAATTTAAAAT
1 ATTTTTAATATTTTTAATAAAATT-TAAT
*
511155 ATTTTTAAATATTTTTATTAAAATTTAAT
1 ATTTTT-AATATTTTTAATAAAATTTAAT
*
511184 ATTTTTTATATTTTTAA
1 ATTTTTAATATTTTTAA
511201 ATTTTTATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 15 0.39
29 10 0.26
30 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTAATATTTTTAATAAAATTTAAT
Found at i:515599 original size:18 final size:18
Alignment explanation
Indices: 515576--515611 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
515566 AAAGAAAATT
*
515576 ATCTTTGATTACATACTC
1 ATCTTTAATTACATACTC
515594 ATCTTTAATTACATACTC
1 ATCTTTAATTACATACTC
515612 TGTGTGTAAA
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:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
ATCTTTAATTACATACTC
Found at i:516301 original size:15 final size:15
Alignment explanation
Indices: 516283--516314 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
516273 TAGAAAATAG
*
516283 AATATTATAATATTA
1 AATATTAAAATATTA
516298 AATATTAAAATATTA
1 AATATTAAAATATTA
516313 AA
1 AA
516315 AAATACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATTAAAATATTA
Found at i:516307 original size:28 final size:26
Alignment explanation
Indices: 516247--516309 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
516237 AATTAGGTTC
516247 ATTAAAATAAAACATTAAATTTAAAT
1 ATTAAAATAAAACATTAAATTTAAAT
* * *
516273 -TAGAAAATAGAATATTATAATATTAAAT
1 AT-TAAAATAAAACATTA-AAT-TTAAAT
516301 ATTAAAATA
1 ATTAAAATA
516310 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 1 0.03
26 12 0.41
27 3 0.10
28 12 0.41
29 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (26 bp):
ATTAAAATAAAACATTAAATTTAAAT
Found at i:516315 original size:8 final size:8
Alignment explanation
Indices: 516283--516315 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
516273 TAGAAAATAG
*
516283 AATATTAT
1 AATATTAA
516291 AATATT-A
1 AATATTAA
516298 AATATTAA
1 AATATTAA
516306 AATATTAA
1 AATATTAA
516314 AA
1 AA
516316 AATACTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATTAA
Found at i:516362 original size:21 final size:21
Alignment explanation
Indices: 516328--516373 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
516318 TACTTAAACT
* *
516328 TTGATAGATTGTTGATCGATG
1 TTGATAGATCGTTGATCGACG
*
516349 TTGATTGATCGTTGATCGACG
1 TTGATAGATCGTTGATCGACG
516370 TTGA
1 TTGA
516374 CTAGCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (21 bp):
TTGATAGATCGTTGATCGACG
Found at i:516484 original size:20 final size:20
Alignment explanation
Indices: 516461--516501 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
516451 ATTATATTGA
516461 TTAAAAA-TATAAAAAATAAT
1 TTAAAAAGT-TAAAAAATAAT
*
516481 TTAAAAAGTTTAAAAATAAT
1 TTAAAAAGTTAAAAAATAAT
516501 T
1 T
516502 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAAAGTTAAAAAATAAT
Found at i:516532 original size:15 final size:15
Alignment explanation
Indices: 516509--516555 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
516499 ATTATATTTT
516509 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
*
516524 TATATAATTCTAAAA
1 TATAAAATTCTAAAA
* *
516539 TTTAAAATTTTAAAA
1 TATAAAATTCTAAAA
516554 TA
1 TA
516556 ATATATACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:516779 original size:21 final size:19
Alignment explanation
Indices: 516743--516785 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
516733 ATTTTAATAA
*
516743 TTTTTTATAATTTATATGT
1 TTTTTTATAATTTATATAT
*
516762 TTTTTTCTAGATTATATATAT
1 TTTTTTATA-ATT-TATATAT
516783 TTT
1 TTT
516786 AATTTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTATAATTTATATAT
Found at i:524505 original size:15 final size:14
Alignment explanation
Indices: 524482--524524 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
524472 AATTTATTTA
524482 TTAAAATAAAAATT
1 TTAAAATAAAAATT
524496 TTATAAATAAAACAATT
1 TTA-AAAT-AAA-AATT
524513 TTAAAA-AAAAAT
1 TTAAAATAAAAAT
524525 CCACAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.12
14 6 0.23
15 4 0.15
16 6 0.23
17 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATAAAAATT
Found at i:534233 original size:22 final size:22
Alignment explanation
Indices: 534186--534237 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
534176 CTAAAAATGT
* *
534186 AATTTCATCATTTTAATAGTAT
1 AATTTTATCATTTTAATAGTAA
*
534208 AATTTTATCATTATTAAT-TTAA
1 AATTTTATCATT-TTAATAGTAA
534230 AATTTTAT
1 AATTTTAT
534238 AAATTATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
AATTTTATCATTTTAATAGTAA
Found at i:538588 original size:31 final size:31
Alignment explanation
Indices: 538553--538615 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
538543 ATAAAATTCT
538553 TTTGCATAAACACAAAAAGGACTGGCATATG
1 TTTGCATAAACACAAAAAGGACTGGCATATG
*
538584 TTTGCATAAACACAAAAAGGACTGTCATATG
1 TTTGCATAAACACAAAAAGGACTGGCATATG
538615 T
1 T
538616 AAGAGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (31 bp):
TTTGCATAAACACAAAAAGGACTGGCATATG
Found at i:545136 original size:13 final size:13
Alignment explanation
Indices: 545118--545143 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
545108 CAGATGTTCA
545118 TTTAGATTTGTGT
1 TTTAGATTTGTGT
545131 TTTAGATTTGTGT
1 TTTAGATTTGTGT
545144 GACAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TTTAGATTTGTGT
Found at i:550048 original size:23 final size:26
Alignment explanation
Indices: 550022--550069 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
550012 TTGAAATTTT
*
550022 AAAA-TTATTAAAA-AA-TTATAAAC
1 AAAATTTATAAAAATAAGTTATAAAC
550045 AAAATTTATAAAAATAAGTTATAAA
1 AAAATTTATAAAAATAAGTTATAAA
550070 GATTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 8 0.38
25 2 0.10
26 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATTTATAAAAATAAGTTATAAAC
Found at i:550210 original size:9 final size:9
Alignment explanation
Indices: 550186--550266 Score: 65
Period size: 9 Copynumber: 8.1 Consensus size: 9
550176 TAATAAAAGA
550186 TTATAA-TT
1 TTATAATTT
*
550194 TTAAAATTT
1 TTATAATTT
550203 TTATAATTTTTT
1 TTATAA---TTT
550215 CTTATAAATTT
1 -TTAT-AATTT
550226 TGTCTATAATTT
1 T-T--ATAATTT
550238 TTATAATTT
1 TTATAATTT
550247 TTATAATTT
1 TTATAATTT
550256 TTAATAATTT
1 TT-ATAATTT
550266 T
1 T
550267 AAAAATTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
8 5 0.08
9 25 0.41
10 9 0.15
11 5 0.08
12 9 0.15
13 6 0.10
14 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:550267 original size:9 final size:9
Alignment explanation
Indices: 550231--550274 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
550221 AATTTTGTCT
*
550231 ATAATTTTT
1 ATAATTTTA
*
550240 ATAATTTTT
1 ATAATTTTA
550249 ATAATTTTTA
1 ATAA-TTTTA
550259 ATAATTTTA
1 ATAATTTTA
*
550268 AAAATTT
1 ATAATTT
550275 AAAAGGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATAATTTTA
Found at i:550273 original size:19 final size:18
Alignment explanation
Indices: 550233--550274 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
550223 TTTTGTCTAT
* *
550233 AATTTTTATAATTTTTAT
1 AATTTTTATAATTTTAAA
550251 AATTTTTAATAATTTTAAA
1 AATTTTT-ATAATTTTAAA
550270 AATTT
1 AATTT
550275 AAAAGGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTTATAATTTTAAA
Found at i:552050 original size:14 final size:14
Alignment explanation
Indices: 552027--552063 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
552017 AAAATTATCG
552027 ATTAAA-ATTTAAT
1 ATTAAATATTTAAT
552040 ATTAAATATTTAAT
1 ATTAAATATTTAAT
552054 A-TAAATATTT
1 ATTAAATATTT
552064 GTTAAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAAATATTTAAT
Found at i:563676 original size:33 final size:34
Alignment explanation
Indices: 563639--563704 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
563629 AGCTTCAAGA
*
563639 TTTTCA-TTAATGACTTGTTCCTTTATTCAACCT
1 TTTTCATTTAATGACTTGTTACTTTATTCAACCT
* *
563672 TTTTCATTTAATGCCTTGTTATTTTATTCAACC
1 TTTTCATTTAATGACTTGTTACTTTATTCAACC
563705 ATAAGTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (34 bp):
TTTTCATTTAATGACTTGTTACTTTATTCAACCT
Found at i:567379 original size:22 final size:23
Alignment explanation
Indices: 567351--567396 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
567341 TTTACATGGG
567351 TAAAAAAAT-GATAATAA-AATAA
1 TAAAAAAATAG-TAATAAGAATAA
*
567373 TAAAAAAGTAGTAATAAGAATAA
1 TAAAAAAATAGTAATAAGAATAA
567396 T
1 T
567397 TTTTAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (23 bp):
TAAAAAAATAGTAATAAGAATAA
Found at i:567829 original size:25 final size:25
Alignment explanation
Indices: 567797--567848 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
567787 GGGAAATTAT
567797 CCCGACTATATTACATGCGCCATTC
1 CCCGACTATATTACATGCGCCATTC
567822 CCCGACTATATTACATGCGCCATTC
1 CCCGACTATATTACATGCGCCATTC
567847 CC
1 CC
567849 TTTGTGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (25 bp):
CCCGACTATATTACATGCGCCATTC
Found at i:573086 original size:39 final size:38
Alignment explanation
Indices: 572969--573097 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 38
572959 GATCCGATTG
* *
572969 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGAG-ATTT-TTTTTTTGAAAACACGAAAATTTTA
* * * *
573009 AGACA-TA-ATATTTTTTTT-AAAACA--AAAATTTATG
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTT-TA
573043 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTT-A
*
573082 AAACACCGAAATTTTT
1 AAACA-CGAGATTTTT
573098 GAAAACAAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
33 6 0.09
34 5 0.07
35 7 0.10
36 16 0.23
37 9 0.13
38 1 0.01
39 13 0.19
40 13 0.19
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (38 bp):
AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTA
Found at i:573104 original size:35 final size:35
Alignment explanation
Indices: 573058--573219 Score: 161
Period size: 35 Copynumber: 4.7 Consensus size: 35
573048 CGAGATTTTT
**
573058 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
573093 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
573128 ATTTTGAAAACACG-AAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
**
573162 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * *
573195 TTTTTAGAAGACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
573220 GAAAATGGAT
Statistics
Matches: 103, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
32 3 0.03
33 26 0.25
34 22 0.21
35 41 0.40
36 11 0.11
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:573178 original size:16 final size:17
Alignment explanation
Indices: 573058--573219 Score: 150
Period size: 17 Copynumber: 9.4 Consensus size: 17
573048 CGAGATTTTT
573058 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
**
573076 TTTTCAAAACACCG-AAA
1 TTTTTGAAACA-CGAAAA
* **
573093 TTTTTGAAAACAAGAGGA
1 TTTTTG-AAACACGAAAA
*
573111 TTTTTGAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
573128 ATTTTGAAAACACG-AAA
1 TTTTTG-AAACACGAAAA
*
573145 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGAAAA
573162 TTTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
*
573178 TTTTTGAAACACAAAAA
1 TTTTTGAAACACGAAAA
*
573195 TTTTTAGAAGACACTAAAA
1 TTTTT-GAA-ACACGAAAA
*
573214 ATTTTG
1 TTTTTG
573220 GAAAATGGAT
Statistics
Matches: 118, Mismatches: 18, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
16 22 0.19
17 56 0.47
18 28 0.24
19 12 0.10
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:573435 original size:20 final size:19
Alignment explanation
Indices: 573397--573443 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
573387 GAATATATTT
573397 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
573417 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
573436 -TTTTGAAA
1 TTTTTGAAA
573444 AATAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:573818 original size:8 final size:7
Alignment explanation
Indices: 573807--573890 Score: 78
Period size: 7 Copynumber: 11.0 Consensus size: 7
573797 AACTCTCTTT
573807 TTTTCTTC
1 TTTT-TTC
573815 TTTTTTCC
1 TTTTTT-C
573823 TTTTTTCC
1 TTTTTT-C
573831 TTTTTTTC
1 -TTTTTTC
*
573839 TCTTTTC
1 TTTTTTC
*
573846 TTTTTTT
1 TTTTTTC
573853 TTTCTTTC
1 TTT-TTTC
573861 TTTTTTTC
1 -TTTTTTC
573869 TTTTTTC
1 TTTTTTC
*
573876 TTTCTCTC
1 TTT-TTTC
573884 TTTTTTC
1 TTTTTTC
573891 CTGGCCTGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
7 29 0.45
8 27 0.42
9 9 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:573834 original size:7 final size:8
Alignment explanation
Indices: 573814--573892 Score: 60
Period size: 8 Copynumber: 10.2 Consensus size: 8
573804 TTTTTTTCTT
573814 CTTTTTTC
1 CTTTTTTC
573822 CTTTTTTC
1 CTTTTTTC
*
573830 CTTTTTTT
1 CTTTTTTC
*
573838 CTCTTTT-
1 CTTTTTTC
573845 CTTTTTT-
1 CTTTTTTC
*
573852 -TTTTCTTT
1 CTTTT-TTC
*
573860 CTTTTTTT
1 CTTTTTTC
573868 CTTTTTT-
1 CTTTTTTC
*
573875 C-TTTCTC
1 CTTTTTTC
573882 TCTTTTTTC
1 -CTTTTTTC
573891 CT
1 CT
573893 GGCCTGCTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
6 8 0.13
7 9 0.15
8 34 0.57
9 9 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
CTTTTTTC
Found at i:573848 original size:15 final size:15
Alignment explanation
Indices: 573807--573890 Score: 98
Period size: 15 Copynumber: 5.5 Consensus size: 15
573797 AACTCTCTTT
*
573807 TTTTCTTCTTTTTTCC
1 TTTT-TTCTTTTTTTC
573823 TTTTTTCCTTTTTTTC
1 TTTTTT-CTTTTTTTC
*
573839 TCTTTTCTTTTTTT-
1 TTTTTTCTTTTTTTC
573853 TTTCTTTCTTTTTTTC
1 TTT-TTTCTTTTTTTC
* *
573869 TTTTTTCTTTCTCTC
1 TTTTTTCTTTTTTTC
573884 TTTTTTC
1 TTTTTTC
573891 CTGGCCTGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.03
15 38 0.63
16 20 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:573867 original size:23 final size:23
Alignment explanation
Indices: 573804--573889 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
573794 TGAAACTCTC
*
573804 TTTTTTTC-TTCTTTTTTCCTTT
1 TTTTTTTCTTTCTTTTTTTCTTT
*
573826 TTTCCTTTT-TTTC-TCTTTTCTTT
1 TTT--TTTTCTTTCTTTTTTTCTTT
573849 TTTTTTTCTTTCTTTTTTTCTTT
1 TTTTTTTCTTTCTTTTTTTCTTT
* *
573872 TTTCTTTCTCTCTTTTTT
1 TTTTTTTCTTTCTTTTTT
573890 CCTGGCCTGC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
21 4 0.07
22 7 0.13
23 36 0.67
24 7 0.13
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTCTTTCTTTTTTTCTTT
Found at i:573876 original size:19 final size:18
Alignment explanation
Indices: 573802--573880 Score: 86
Period size: 19 Copynumber: 4.2 Consensus size: 18
573792 ATTGAAACTC
573802 TCTTTTTTTCTTCTTTTTT
1 TCTTTTTTTCTT-TTTTTT
* * *
573821 CCTTTTTTCCTTTTTTTC
1 TCTTTTTTTCTTTTTTTT
*
573839 TCTTTTCTTTTTTTTTTCTT
1 TCTTTT-TTTCTTTTTT-TT
573859 TCTTTTTTTCTTTTTTCTT
1 TCTTTTTTTCTTTTTT-TT
573878 TCT
1 TCT
573881 CTCTTTTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.20
19 33 0.66
20 7 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTCTTTTTTTT
Found at i:573890 original size:45 final size:45
Alignment explanation
Indices: 573804--573890 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
573794 TGAAACTCTC
* *
573804 TTTTTTTCTTCTTTTTTCCTTTTTTCCTTTTTTTCTCTTTTCTTT
1 TTTTTTTCTTCTTTTTTCCTTTTTTCCTTTCTCTCTCTTTTCTTT
* *
573849 TTTTTTTCTTTCTTTTTTTCTTTTTT-CTTTCTCTCTTTTTTC
1 TTTTTTTC-TTCTTTTTTCCTTTTTTCCTTTCTCTCTCTTTTC
573891 CTGGCCTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 21 0.57
46 16 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (45 bp):
TTTTTTTCTTCTTTTTTCCTTTTTTCCTTTCTCTCTCTTTTCTTT
Found at i:574025 original size:15 final size:15
Alignment explanation
Indices: 574002--574041 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
573992 GTTGTTTTTC
574002 TTTTTTTTGGGC-CT
1 TTTTTTTTGGGCGCT
574016 TTTCTTTTTGGGCTGCT
1 TTT-TTTTTGGGC-GCT
574033 TTTTTTTTG
1 TTTTTTTTG
574042 CTTTGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.13
15 9 0.39
16 6 0.26
17 5 0.22
ACGTcount: A:0.00, C:0.12, G:0.20, T:0.68
Consensus pattern (15 bp):
TTTTTTTTGGGCGCT
Found at i:574089 original size:34 final size:33
Alignment explanation
Indices: 574020--574091 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
574010 GGGCCTTTTC
* * *
574020 TTTTTGGGCTGCTTTTTTTTTGCTTTGGTTTTTT
1 TTTTTGGGCTGATTTCTTTTT-CTTTGGTTGTTT
574054 TTTTTGGGCTGATTTGCTTTTT-TTTGTGTTGTTT
1 TTTTTGGGCTGATTT-CTTTTTCTTTG-GTTGTTT
574088 TTTT
1 TTTT
574092 AATTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 4 0.12
34 24 0.73
35 5 0.15
ACGTcount: A:0.01, C:0.07, G:0.21, T:0.71
Consensus pattern (33 bp):
TTTTTGGGCTGATTTCTTTTTCTTTGGTTGTTT
Found at i:574210 original size:3 final size:3
Alignment explanation
Indices: 574204--574238 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
574194 TTTTTTTTCT
574204 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC T
574239 CCTACACGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:574649 original size:30 final size:30
Alignment explanation
Indices: 574594--574710 Score: 130
Period size: 30 Copynumber: 3.9 Consensus size: 30
574584 TGTAATTTTT
* *
574594 AGAAAATTTA-GGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGGTCAAAATGAAATTTAA
* * *
574623 TGAAAATTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAATTTAGGGGTCAAAATGAAATTTAA
* *
574653 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAGGGGTCAAAATGAAATTTAA
* *
574682 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAGGGGTCAAAATGAAATTT
574711 TTATTTTTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 14 0.19
30 58 0.81
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAGGGGTCAAAATGAAATTTAA
Found at i:575168 original size:54 final size:55
Alignment explanation
Indices: 574982--575199 Score: 333
Period size: 54 Copynumber: 4.1 Consensus size: 55
574972 CACGTGAGCC
* * *
574982 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG-AA
575037 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAA
*
575088 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
575142 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
575197 AAG
1 AAG
575200 TAGAAATTGA
Statistics
Matches: 151, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 53 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
Found at i:575197 original size:14 final size:14
Alignment explanation
Indices: 575178--575212 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
575168 GAGTTGATTT
575178 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
*
575192 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
575206 TTGAAAA
1 TTGAAAA
575213 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:575444 original size:85 final size:87
Alignment explanation
Indices: 575300--575547 Score: 281
Period size: 85 Copynumber: 2.8 Consensus size: 87
575290 AATAGAAATT
* * * * * *
575300 AAAAACAGAATTTGAAAAGACATCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-AGTAGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
575365 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
575387 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCAGTAGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
575450 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
575476 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCA-GT-AGCCTGAGGCTCAACTCACCTCTTGCAATATGA
575540 GTTGATTT
64 GTTGATTT
575548 TTGAAAAACA
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 31 0.23
88 3 0.02
89 31 0.23
91 33 0.24
93 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCAGTAGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:575493 original size:15 final size:16
Alignment explanation
Indices: 575460--575493 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
575450 TTGATTTTTG
* *
575460 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
575476 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
575492 AA
1 AA
575494 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:575535 original size:91 final size:88
Alignment explanation
Indices: 575300--575554 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 88
575290 AATAGAAATT
* * * *
575300 AAAAACAGAATTTGAAAAGACATCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
575365 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
575387 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
575450 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
575476 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
575540 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
575555 ACAAAAATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 31 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:575872 original size:191 final size:192
Alignment explanation
Indices: 575512--576314 Score: 1540
Period size: 191 Copynumber: 4.2 Consensus size: 192
575502 CATGTGAGCC
** *
575512 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
575577 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
575641 AACTCATTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
575704 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
575769 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
575834 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
575895 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA-GCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
575959 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
576024 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
576086 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
576151 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
576216 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
576278 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
576315 CCTTGGAAAG
Statistics
Matches: 604, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
190 106 0.18
191 253 0.42
192 245 0.41
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:584523 original size:17 final size:17
Alignment explanation
Indices: 584497--584640 Score: 130
Period size: 17 Copynumber: 8.4 Consensus size: 17
584487 CGTGATTTTT
584497 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
584515 TTTTCAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
* **
584532 TTTTTGAAAACAAGAGGA
1 TTTTT-AAAACACGAAAA
* *
584550 TTTTTGAAATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
584568 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
584585 TTTTTGAAACACGGAAA
1 TTTTTAAAACACGAAAA
*
584602 TTTTTGAAA-ACGAAAA
1 TTTTTAAAACACGAAAA
* *
584618 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
584635 TTTTTA
1 TTTTTA
584641 GAATACACTA
Statistics
Matches: 102, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
16 15 0.15
17 57 0.56
18 30 0.29
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:584525 original size:39 final size:38
Alignment explanation
Indices: 584408--584526 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 38
584398 GATCCGATTG
* * *
584408 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGTG-ATTT-TTTTTTTGAAAACACGAAAATTTTA
* * * *
584448 AGACA--TAATATTTTTTTT-AAAACA--AAAATTTATG
1 AAACACGTGATTTTTTTTTTGAAAACACGAAAATTT-TA
584482 AAACACGTGATTTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGTGATTTTTTTTTTGAAAACACGAAAATTTT-A
584521 AAACAC
1 AAACAC
584527 CGAAATTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
33 6 0.10
34 5 0.08
35 6 0.10
36 17 0.28
37 9 0.15
38 1 0.02
39 13 0.21
40 4 0.07
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (38 bp):
AAACACGTGATTTTTTTTTTGAAAACACGAAAATTTTA
Found at i:584543 original size:35 final size:35
Alignment explanation
Indices: 584497--584659 Score: 170
Period size: 35 Copynumber: 4.7 Consensus size: 35
584487 CGTGATTTTT
**
584497 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
584532 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
584567 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
**
584602 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * *
584635 TTTTTAGAATACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
584660 GAAAATGGAT
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
33 27 0.26
34 6 0.06
35 60 0.57
36 12 0.11
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:584875 original size:20 final size:19
Alignment explanation
Indices: 584837--584883 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
584827 AATATATTTT
584837 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
584857 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
584876 -TTTTGAAA
1 TTTTTGAAA
584884 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:585264 original size:8 final size:8
Alignment explanation
Indices: 585253--585332 Score: 67
Period size: 8 Copynumber: 10.2 Consensus size: 8
585243 TTTTTTTCTT
585253 CTTTTTTC
1 CTTTTTTC
585261 CTTTTTTC
1 CTTTTTTC
*
585269 CTTTTTTT
1 CTTTTTTC
*
585277 CTCTTTT-
1 CTTTTTTC
*
585284 CTTTTTTT
1 CTTTTTTC
*
585292 CTTCTTT-
1 CTTTTTTC
*
585299 CTTTTTTT
1 CTTTTTTC
585307 CTTTTTT-
1 CTTTTTTC
*
585314 CTTTCTCTC
1 CTTT-TTTC
*
585323 TTTTTTTC
1 CTTTTTTC
585331 CT
1 CT
585333 GGCCTGCTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
7 16 0.27
8 40 0.68
9 3 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (8 bp):
CTTTTTTC
Found at i:585294 original size:39 final size:37
Alignment explanation
Indices: 585238--585330 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 37
585228 CGAATTGAAA
*
585238 CTCTTTT-TTTTTCTTCTTTTTTCCTTTTTTCCTTTTTTT
1 CTCTTTTCTTTTT-TTCTTCTTT-CTTTTTTCC-TTTTTT
*
585277 CTCTTTTCTTTTTTTCTTCTTTCTTTTTTTCTTTTTT
1 CTCTTTTCTTTTTTTCTTCTTTCTTTTTTCCTTTTTT
585314 CT-TTCTCTCTTTTTTTC
1 CTCTT-T-TCTTTTTTTC
585331 CTGGCCTGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
36 2 0.04
37 9 0.18
38 18 0.37
39 15 0.31
40 5 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (37 bp):
CTCTTTTCTTTTTTTCTTCTTTCTTTTTTCCTTTTTT
Found at i:585315 original size:15 final size:15
Alignment explanation
Indices: 585241--585328 Score: 106
Period size: 15 Copynumber: 5.9 Consensus size: 15
585231 ATTGAAACTC
*
585241 TTTTTT-TTTCTTCT
1 TTTTTTCTTTTTTCT
*
585255 TTTTTCCTTTTTTCCT
1 TTTTTTCTTTTTT-CT
*
585271 TTTTTTCTCTTTTCT
1 TTTTTTCTTTTTTCT
*
585286 TTTTTTCTTCTTTCT
1 TTTTTTCTTTTTTCT
585301 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
* *
585316 TTCTCTCTTTTTT
1 TTTTTTCTTTTTT
585329 TCCTGGCCTG
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
14 5 0.08
15 45 0.71
16 13 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:585319 original size:23 final size:22
Alignment explanation
Indices: 585239--585330 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 22
585229 GAATTGAAAC
585239 TCTTTTTTTTTC-TTCTTTTTT
1 TCTTTTTTTTTCTTTCTTTTTT
* * *
585260 CCTTTTTTCCTTTTTTTC-TCTTT
1 TCTTTTTT--TTTCTTTCTTTTTT
585283 TCTTTTTTTCTTCTTTCTTTTTT
1 TCTTTTTTT-TTCTTTCTTTTTT
*
585306 TCTTTTTTCTTTCTCTCTTTTTT
1 TCTTTTTT-TTTCTTTCTTTTTT
585329 TC
1 TC
585331 CTGGCCTGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
21 8 0.14
22 6 0.10
23 40 0.69
24 4 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TCTTTTTTTTTCTTTCTTTTTT
Found at i:585460 original size:14 final size:15
Alignment explanation
Indices: 585443--585481 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
585433 GCTGTTTTTT
585443 CTTTTTTTTTGGGC-
1 CTTTTTTTTTGGGCA
585457 CTTTTCTTTTTGGGCTA
1 CTTTT-TTTTTGGGC-A
585474 CTTTTTTT
1 CTTTTTTT
585482 GCTTTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 3 0.14
17 5 0.23
ACGTcount: A:0.03, C:0.15, G:0.15, T:0.67
Consensus pattern (15 bp):
CTTTTTTTTTGGGCA
Found at i:585639 original size:9 final size:9
Alignment explanation
Indices: 585625--585653 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
585615 GATTGTTAAA
585625 TTTTTTTCT
1 TTTTTTTCT
585634 TTTTTTTCT
1 TTTTTTTCT
585643 TTTTTTTCT
1 TTTTTTTCT
585652 TT
1 TT
585654 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:585658 original size:3 final size:3
Alignment explanation
Indices: 585652--585685 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
585642 TTTTTTTTCT
585652 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
585686 CCTCCTCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:585789 original size:10 final size:10
Alignment explanation
Indices: 585754--585803 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
585744 ACGCTGGTAC
585754 TCTT-TCTTT
1 TCTTCTCTTT
* *
585763 TCTTCTCCTC
1 TCTTCTCTTT
585773 T-TTCTCTTT
1 TCTTCTCTTT
585782 TCTTCTCTTT
1 TCTTCTCTTT
*
585792 TCTTCTTTTT
1 TCTTCTCTTT
585802 TC
1 TC
585804 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:585801 original size:19 final size:19
Alignment explanation
Indices: 585758--585800 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
585748 TGGTACTCTT
585758 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
585777 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
585794 TTCTTTT
1 -TCTTTT
585801 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:586014 original size:29 final size:29
Alignment explanation
Indices: 585981--586097 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
585971 TGTAATTTTT
*
585981 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
586010 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
586040 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
586069 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
586098 TTATTTTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:586036 original size:30 final size:30
Alignment explanation
Indices: 585996--586097 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
585986 ATTTAGGATT
*
585996 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
586026 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
586056 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
586086 AAAATGCAATTT
1 AAAATGAAATTT
586098 TTATTTTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:586118 original size:14 final size:16
Alignment explanation
Indices: 586093--586127 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
586083 GTCAAAATGC
586093 AATTTTTATTTTT-AA
1 AATTTTTATTTTTGAA
586108 AATTTTT-TTTTTGAA
1 AATTTTTATTTTTGAA
586123 AATTT
1 AATTT
586128 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
AATTTTTATTTTTGAA
Found at i:588035 original size:30 final size:30
Alignment explanation
Indices: 587990--588081 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 30
587980 AAATATTATT
587990 TTTATTTAATTTAATA-ACA-TATTTTTTTA
1 TTTATTTAATTTAATATA-ATTATTTTTTTA
*
588019 TTTATTTATTTTTAATATAATTATTTTTTTAA
1 TTTATTTA-ATTTAATATAATTATTTTTTT-A
* * ** *
588051 CTCATGAAACTTTAATATAATTATATTTTTA
1 TTTATTTAA-TTTAATATAATTATTTTTTTA
588082 CAATACTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 8 0.16
30 8 0.16
31 11 0.22
32 24 0.47
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTATTTAATTTAATATAATTATTTTTTTA
Found at i:592591 original size:50 final size:50
Alignment explanation
Indices: 592467--592715 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
592457 GATAATAACA
* * ** * *
592467 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
592518 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
592568 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
592618 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
592673 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
592716 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:592645 original size:100 final size:104
Alignment explanation
Indices: 592466--592715 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
592456 TGATAATAAC
**
592466 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
592531 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
592568 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
592631 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
592673 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
592716 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:592831 original size:13 final size:13
Alignment explanation
Indices: 592810--592841 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
592800 GCTTGGATCA
*
592810 TCATCAAATAAAT
1 TCATAAAATAAAT
592823 TCATAAAATAAAT
1 TCATAAAATAAAT
592836 TCATAA
1 TCATAA
592842 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:593088 original size:30 final size:30
Alignment explanation
Indices: 593053--593110 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
593043 CCTCGACTCT
*
593053 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
593083 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
593111 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:596390 original size:29 final size:29
Alignment explanation
Indices: 596349--596404 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
596339 TATATAATTA
596349 ATTTTAATGTTTATAATA-TAAAAATAAAT
1 ATTTTAATGTTTA-AATAGTAAAAATAAAT
*
596378 ATTTTATAT-TTTAAATAGTGAAAATAA
1 ATTTTA-ATGTTTAAATAGTAAAAATAA
596405 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 18 0.75
30 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTTAATGTTTAAATAGTAAAAATAAAT
Found at i:611529 original size:18 final size:17
Alignment explanation
Indices: 611503--611540 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
611493 TATTTACGTA
611503 AAATTTT-AATTTTTACT
1 AAATTTTAAATTTTTA-T
611520 AAATTATTAAATTTTTAT
1 AAATT-TTAAATTTTTAT
611538 AAA
1 AAA
611541 AATAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTTTAAATTTTTAT
Found at i:615843 original size:15 final size:15
Alignment explanation
Indices: 615823--615851 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
615813 TAAACCCAAC
615823 AGAAGCAGCAGCAGA
1 AGAAGCAGCAGCAGA
615838 AGAAGCAGCAGCAG
1 AGAAGCAGCAGCAG
615852 CGTTGAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.34, T:0.00
Consensus pattern (15 bp):
AGAAGCAGCAGCAGA
Found at i:616694 original size:28 final size:27
Alignment explanation
Indices: 616663--616733 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
616653 CTATTTTAGA
616663 ATATTTTTAAAATTTTAACTTTTTTTAT
1 ATATTTTTAAAATTTTAA-TTTTTTTAT
* *
616691 ATATTTCTAAAATTTTTTAATTTTTTTTT
1 ATATTTTTAAAA--TTTTAATTTTTTTAT
* *
616720 ATAATTTAAAAATT
1 ATATTTTTAAAATT
616734 GGAATTTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.06
28 11 0.31
29 17 0.47
30 6 0.17
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTTTTAAAATTTTAATTTTTTTAT
Found at i:618365 original size:31 final size:31
Alignment explanation
Indices: 618327--618387 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
618317 TTAGTTAATA
*
618327 ATATTTTATATCA-TTCTTATTTTGATCACTC
1 ATATTTTAGATCATTTC-TATTTTGATCACTC
* *
618358 ATATTTTAGATCGTTTCTATTTTGGTCACT
1 ATATTTTAGATCATTTCTATTTTGATCACT
618388 TCCTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (31 bp):
ATATTTTAGATCATTTCTATTTTGATCACTC
Found at i:620891 original size:23 final size:22
Alignment explanation
Indices: 620839--620891 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
620829 TCCACGTCTT
*
620839 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
620861 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
620884 TTTCTTTT
1 TTTCTTTT
620892 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:623199 original size:6 final size:6
Alignment explanation
Indices: 623188--623213 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
623178 ATAAATAAAT
623188 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
623214 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:637099 original size:12 final size:14
Alignment explanation
Indices: 637072--637106 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
637062 ATAGAAGTTA
637072 TATATTATAGTTTT
1 TATATTATAGTTTT
637086 TATATTA-A-TTTT
1 TATATTATAGTTTT
637098 TATATTATA
1 TATATTATA
637107 AATAGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.55
13 2 0.10
14 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATATTATAGTTTT
Found at i:641288 original size:77 final size:77
Alignment explanation
Indices: 641082--641305 Score: 324
Period size: 76 Copynumber: 2.9 Consensus size: 77
641072 CTTTGGAAAT
* * * * *
641082 TTAAATACCTAAATTATACATCATATTAGGACCAAATCCTTTTAAGGTAAACTTCAATCTACATG
1 TTAAATACCTATATTATTCATCATATTAGGGCCAAATCCTTTTAAAGTAAACTCCAATCTACATG
* *
641147 ATAGAAGAAAAT
66 ATAGAAAAAAAA
** * *
641159 TTAAATATTTATAGTATTCATCATA-TAGGGCCAAACCCTTTTAAAGTAAACTCCAATCTACATG
1 TTAAATACCTATATTATTCATCATATTAGGGCCAAATCCTTTTAAAGTAAACTCCAATCTACATG
641223 ATAGAAAAAAAA
66 ATAGAAAAAAAA
* *
641235 TTAAATACCTATATTATTCATCATATTAGGGCCATATCCTTTTAAAGTGAACTCCAATCTACATG
1 TTAAATACCTATATTATTCATCATATTAGGGCCAAATCCTTTTAAAGTAAACTCCAATCTACATG
641300 ATAGAA
66 ATAGAA
641306 CAGAATAAAA
Statistics
Matches: 129, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
76 67 0.52
77 62 0.48
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (77 bp):
TTAAATACCTATATTATTCATCATATTAGGGCCAAATCCTTTTAAAGTAAACTCCAATCTACATG
ATAGAAAAAAAA
Found at i:642997 original size:26 final size:24
Alignment explanation
Indices: 642948--642999 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
642938 TTTATTTGCA
642948 ATTTTTTAAAATTTAAATACTTTTT
1 ATTTTTTAAAATTTAAATA-TTTTT
*
642973 ATTTTTATAAAATTCTACA-ATTTTT
1 ATTTTT-TAAAATT-TAAATATTTTT
642998 AT
1 AT
643000 ATCTTATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 13 0.54
26 8 0.33
27 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTTTAAAATTTAAATATTTTT
Found at i:643039 original size:22 final size:24
Alignment explanation
Indices: 642995--643043 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
642985 TTCTACAATT
*
642995 TTTATATCTTATGATTTTTTAAAA
1 TTTATATCTTATGATATTTTAAAA
643019 TTTATAT-TTAT-ATATTTTAAAA
1 TTTATATCTTATGATATTTTAAAA
643041 TTT
1 TTT
643044 TAAAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.54
23 4 0.17
24 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTATATCTTATGATATTTTAAAA
Done.