Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 3 of 56
Found at i:333283 original size:15 final size:15
Alignment explanation
Indices: 333263--333293 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
333253 ACCACGGCCT
333263 CCACCTCTTCCACCG
1 CCACCTCTTCCACCG
333278 CCACCTCTTCCACCG
1 CCACCTCTTCCACCG
333293 C
1 C
333294 GCTCTCCTCC
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:0.13, C:0.61, G:0.06, T:0.19
Consensus pattern (15 bp):
CCACCTCTTCCACCG
Found at i:333543 original size:21 final size:21
Alignment explanation
Indices: 333519--333576 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 21
333509 CTCTGCCGCC
333519 ACCACGACCGCCTCCACCATA
1 ACCACGACCGCCTCCACCATA
* *
333540 A-C-C-ACTGCCTCCTCCATA
1 ACCACGACCGCCTCCACCATA
*
333558 ACCACCG-CCGCCGCCACCA
1 ACCA-CGACCGCCTCCACCA
333577 CCAGCACCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
18 14 0.50
19 2 0.07
20 1 0.04
21 11 0.39
ACGTcount: A:0.24, C:0.55, G:0.10, T:0.10
Consensus pattern (21 bp):
ACCACGACCGCCTCCACCATA
Found at i:333551 original size:18 final size:18
Alignment explanation
Indices: 333528--333562 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
333518 CACCACGACC
333528 GCCTCCACCATAACCACT
1 GCCTCCACCATAACCACT
*
333546 GCCTCCTCCATAACCAC
1 GCCTCCACCATAACCAC
333563 CGCCGCCGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (18 bp):
GCCTCCACCATAACCACT
Found at i:337082 original size:2 final size:2
Alignment explanation
Indices: 337075--337139 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
337065 TTAGCTTGTT
* * *
337075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
337117 TA TA TA TA CA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
337140 GTCGGTGCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:337268 original size:2 final size:2
Alignment explanation
Indices: 337261--337321 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
337251 TTAGCTTGTT
* *
337261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
337303 TA TA CA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA T
337322 GTCGGTGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:337472 original size:182 final size:183
Alignment explanation
Indices: 337061--337456 Score: 749
Period size: 182 Copynumber: 2.2 Consensus size: 183
337051 TGATTGGATT
337061 CTTGTTAGCTTGTTTATATATATATATATATATATATATATATATATATACACACATATATATAC
1 CTTGTTAGCTTG--TATATATATATATATATATATATATATATATATATA-ACACATATATATAC
337126 ATATATATACATATGTCGGTGCATTGTTAAGCACTAAGACTGAAGTTCATGTAAGCTGTGCACAT
63 ATATATATACATATGTCGGTGCATTGTTAAGCACTAAGACTGAAGTTCATGTAAGCTGTGCACAT
337191 AAGTAGTGTTTGAATCAGAATGTGGACATTGATAAATTACTTATATATCATGACAA
128 AAGTAGTGTTTGAATCAGAATGTGGACATTGATAAATTACTTATATATCATGACAA
*
337247 CTTGTTAGCTTGTTTATATATATATATATATATATATATATATATAT-ACACATATATATACATA
1 CTTGTTAGCTTGTATATATATATATATATATATATATATATATATATAACACATATATATACATA
337311 TATATACATATGTCGGTGCATTGTTAAGCACTAAGACTGAAGTTCATGTAAGCTGTGCACATAAG
66 TATATACATATGTCGGTGCATTGTTAAGCACTAAGACTGAAGTTCATGTAAGCTGTGCACATAAG
337376 TAGTGTTTGAATCAGAATGTGGACATTGATAAATTACTTATATATCATGACAA
131 TAGTGTTTGAATCAGAATGTGGACATTGATAAATTACTTATATATCATGACAA
337429 CTTGTTAGCTTGTATATATATATATATA
1 CTTGTTAGCTTGTATATATATATATATA
337457 CACACACATA
Statistics
Matches: 208, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 162 0.78
184 34 0.16
186 12 0.06
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (183 bp):
CTTGTTAGCTTGTATATATATATATATATATATATATATATATATATAACACATATATATACATA
TATATACATATGTCGGTGCATTGTTAAGCACTAAGACTGAAGTTCATGTAAGCTGTGCACATAAG
TAGTGTTTGAATCAGAATGTGGACATTGATAAATTACTTATATATCATGACAA
Found at i:340003 original size:25 final size:24
Alignment explanation
Indices: 339975--340030 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
339965 TAATAAAATG
*
339975 ATAAAATTTAATATAATATCAATAT
1 ATAAAATTT-ATATAATATCAATAC
* *
340000 AT-AAATTTATATATTATTAATAC
1 ATAAAATTTATATAATATCAATAC
340023 ATCAAAAT
1 AT-AAAAT
340031 AAATGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.54
24 6 0.23
25 6 0.23
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAAATTTATATAATATCAATAC
Found at i:340173 original size:1 final size:1
Alignment explanation
Indices: 340158--340191 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
340148 TAGGACACTG
* *
340158 CCCCTCCCCCGCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
340192 GTGTTAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.94, G:0.03, T:0.03
Consensus pattern (1 bp):
C
Found at i:341610 original size:16 final size:17
Alignment explanation
Indices: 341573--341609 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
341563 AAGTATTTAA
341573 TAAAATATTTTATATTT
1 TAAAATATTTTATATTT
341590 TAAAATA-TTTAT-TTT
1 TAAAATATTTTATATTT
341605 TAAAA
1 TAAAA
341610 AAAACTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 5 0.25
17 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAAATATTTTATATTT
Found at i:341611 original size:17 final size:19
Alignment explanation
Indices: 341568--341611 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
341558 TTATAAAGTA
341568 TTTAATAAAATATTTTATAT
1 TTTAA-AAAATATTTTATAT
341588 TTT--AAAATA-TTTAT-T
1 TTTAAAAAATATTTTATAT
341603 TTTAAAAAA
1 TTTAAAAAA
341612 AACTAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.18
16 5 0.23
17 10 0.45
20 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAAAAATATTTTATAT
Found at i:342786 original size:2 final size:2
Alignment explanation
Indices: 342781--342810 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
342771 TATATACTTG
342781 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
342811 TTATTAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:345067 original size:18 final size:19
Alignment explanation
Indices: 345044--345080 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
345034 AGAATGAAAT
345044 TATTTATTTAA-ATTTAAA
1 TATTTATTTAATATTTAAA
345062 TATTTATTTAATATTTAAA
1 TATTTATTTAATATTTAAA
345081 AGTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTATTTAATATTTAAA
Found at i:345123 original size:18 final size:19
Alignment explanation
Indices: 345089--345125 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
345079 AAAGTTTTTT
345089 ATAAAATTAATTTTAAAAA
1 ATAAAATTAATTTTAAAAA
345108 ATAAAATTAA-TTTAAAAA
1 ATAAAATTAATTTTAAAAA
345126 TTAATTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATTAATTTTAAAAA
Found at i:345921 original size:2 final size:2
Alignment explanation
Indices: 345916--345943 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
345906 TCTCGAATGA
345916 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
345944 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:345948 original size:2 final size:2
Alignment explanation
Indices: 345943--345980 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
345933 TCTCTCTCTC
345943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
345981 AGTGCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:348069 original size:22 final size:23
Alignment explanation
Indices: 348023--348069 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
348013 CAAAATTTAA
*
348023 ATATTACATAAATATATAAATTT
1 ATATAACATAAATATATAAATTT
*
348046 ATATAACATAAAT-TATTAATTT
1 ATATAACATAAATATATAAATTT
348068 AT
1 AT
348070 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATAACATAAATATATAAATTT
Found at i:348092 original size:27 final size:28
Alignment explanation
Indices: 348053--348107 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
348043 TTTATATAAC
348053 ATAAATTATTAAT-TTATTAAAAT-TTAT
1 ATAAATTATTAATATT-TTAAAATATTAT
348080 ATAAA-TATATAATATTTTAAAATATTAT
1 ATAAATTAT-TAATATTTTAAAATATTAT
348108 TGCTTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 3 0.12
27 16 0.64
28 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
ATAAATTATTAATATTTTAAAATATTAT
Found at i:348879 original size:2 final size:2
Alignment explanation
Indices: 348867--348900 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
348857 TTGTATCAGA
* *
348867 AT AT AT CT AT AT AT AC 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
348901 TCAAGGGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:349372 original size:2 final size:2
Alignment explanation
Indices: 349367--349415 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
349357 AATAAAACAC
*
349367 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
349409 AG AG AG A
1 AG AG AG A
349416 TTTGAGCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:350428 original size:3 final size:3
Alignment explanation
Indices: 350422--350453 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
350412 TTATATCCAC
350422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
350454 GCATCATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:370020 original size:2 final size:2
Alignment explanation
Indices: 370013--370041 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
370003 TTTCATAGCA
370013 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
370042 TGGCTTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:378862 original size:13 final size:14
Alignment explanation
Indices: 378841--378873 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
378831 TAATCCACCT
378841 ATAAAATTAAA-AA
1 ATAAAATTAAATAA
*
378854 ATAATATTAAATAA
1 ATAAAATTAAATAA
378868 ATAAAA
1 ATAAAA
378874 AAATAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATTAAATAA
Found at i:385422 original size:2 final size:2
Alignment explanation
Indices: 385415--385448 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
385405 CATTTCCATG
385415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
385449 TTGTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:390350 original size:23 final size:23
Alignment explanation
Indices: 390324--390367 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
390314 AAATACAATA
* *
390324 AAAATATAATATTATTTAAAATT
1 AAAATATAATATGATATAAAATT
390347 AAAATATAATATGATATAAAA
1 AAAATATAATATGATATAAAA
390368 AAATTATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATATAATATGATATAAAATT
Found at i:390384 original size:21 final size:20
Alignment explanation
Indices: 390347--390387 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
390337 ATTTAAAATT
* *
390347 AAAATATAATATGATATAAA
1 AAAATATAACATAATATAAA
390367 AAAATTATAACATAATATAAA
1 AAAA-TATAACATAATATAAA
390388 GATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATATAACATAATATAAA
Found at i:390418 original size:33 final size:32
Alignment explanation
Indices: 390378--390451 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
390368 AAATTATAAC
390378 ATAATATAAAGATA-T-AAATACGTTAAAATTTAT
1 ATAATATAAA-ATATTAAAATA--TTAAAATTTAT
*
390411 ATAATATAAATTATTAAAATATTAAAATTTAT
1 ATAATATAAAATATTAAAATATTAAAATTTAT
390443 ATAA-ATAAA
1 ATAATATAAA
390452 TAATAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 5 0.13
32 17 0.45
33 11 0.29
34 5 0.13
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (32 bp):
ATAATATAAAATATTAAAATATTAAAATTTAT
Found at i:390448 original size:18 final size:18
Alignment explanation
Indices: 390389--390449 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
390379 TAATATAAAG
390389 ATATAAATACGTTAAAATTT
1 ATATAAATA--TTAAAATTT
390409 ATAT-AATA-T-AAA-TT
1 ATATAAATATTAAAATTT
390423 AT-TAAAATATTAAAATTT
1 ATAT-AAATATTAAAATTT
390441 ATATAAATA
1 ATATAAATA
390450 AATAATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 7 0.20
16 2 0.06
17 3 0.09
18 9 0.26
19 5 0.14
20 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATAAATATTAAAATTT
Found at i:404684 original size:3 final size:3
Alignment explanation
Indices: 404676--404717 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
404666 ACTCGAATAA
404676 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
404718 GGTTTATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:404975 original size:5 final size:5
Alignment explanation
Indices: 404965--404994 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
404955 GAAGGCTCCA
404965 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
404995 GGGTGAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:411694 original size:29 final size:29
Alignment explanation
Indices: 411661--411718 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
411651 AGTTAAAATA
411661 TAAATAAATTATCAAAATATTATTATTTT
1 TAAATAAATTATCAAAATATTATTATTTT
* * * *
411690 TAAATTATTTATCAAATTATTATTGTTTT
1 TAAATAAATTATCAAAATATTATTATTTT
411719 GATCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (29 bp):
TAAATAAATTATCAAAATATTATTATTTT
Found at i:413614 original size:2 final size:2
Alignment explanation
Indices: 413607--413639 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
413597 TAGGCTTGAG
413607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
413640 TCACAAAGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:414368 original size:2 final size:2
Alignment explanation
Indices: 414358--414391 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
414348 ATTTATTTTT
* *
414358 TA TA CA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414392 AATGTCGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:414809 original size:14 final size:14
Alignment explanation
Indices: 414790--414824 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
414780 TTTGTTATTT
* *
414790 TATATTATTTAGAA
1 TATATTATTAAAAA
414804 TATATTATTAAAAA
1 TATATTATTAAAAA
414818 TATATTA
1 TATATTA
414825 AAATTAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATTATTAAAAA
Found at i:416407 original size:2 final size:2
Alignment explanation
Indices: 416400--416431 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
416390 AAATTTCGTC
416400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416432 CGTACCCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416593 original size:2 final size:2
Alignment explanation
Indices: 416588--416625 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
416578 GATATGTGTG
416588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
416626 GCATGTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:422010 original size:2 final size:2
Alignment explanation
Indices: 422003--422039 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
421993 CTACCTTGGT
422003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
422040 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:422811 original size:21 final size:21
Alignment explanation
Indices: 422787--422833 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
422777 TGAATCGAAA
422787 TATAAATTTGAT-TTATTTATT
1 TATAAATTTGATCTTA-TTATT
*
422808 TAT-AATTTTATCTTATTATT
1 TATAAATTTGATCTTATTATT
422828 TA-AAAT
1 TATAAAT
422834 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATAAATTTGATCTTATTATT
Found at i:422872 original size:16 final size:16
Alignment explanation
Indices: 422840--422870 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
422830 AAATATTAAA
422840 AATAATTTTATTATTT
1 AATAATTTTATTATTT
422856 AATAATTTTA-TATTT
1 AATAATTTTATTATTT
422871 TATATTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATAATTTTATTATTT
Found at i:422934 original size:13 final size:13
Alignment explanation
Indices: 422916--422943 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
422906 TATAAAACCT
422916 TAAACAAAATTCA
1 TAAACAAAATTCA
422929 TAAACAAAATTCA
1 TAAACAAAATTCA
422942 TA
1 TA
422944 CAAAGTCCCA
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:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAACAAAATTCA
Found at i:427987 original size:16 final size:16
Alignment explanation
Indices: 427961--428003 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
427951 TCGATTGACT
427961 TAAACTTAAAATGAATC
1 TAAACTTAAAATG-ATC
427978 TAAA-TTAAAATGATC
1 TAAACTTAAAATGATC
427993 TAAACTTAAAA
1 TAAACTTAAAA
428004 AAATTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (16 bp):
TAAACTTAAAATGATC
Found at i:427997 original size:32 final size:31
Alignment explanation
Indices: 427960--428052 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
427950 TTCGATTGAC
* *
427960 TTAAACTTAAAATGAATCTAAATTAAAATGA
1 TTAAACTTAAAATGAATCAAAATAAAAATGA
* * *
427991 TCTAAACTTAAAA-AAATTCGAAATCAAAATGA
1 T-TAAACTTAAAATGAA-TCAAAATAAAAATGA
* *
428023 TTCAAACGTAAAATGACTCAAAATAAAAAT
1 TT-AAACTTAAAATGAATCAAAATAAAAAT
428053 AAAATAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
31 4 0.08
32 45 0.90
33 1 0.02
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (31 bp):
TTAAACTTAAAATGAATCAAAATAAAAATGA
Found at i:431179 original size:2 final size:2
Alignment explanation
Indices: 431172--431208 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
431162 GCAACAACAG
431172 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
431209 ATTTCTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:432825 original size:17 final size:17
Alignment explanation
Indices: 432803--432836 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
432793 CATTAATGTG
432803 GAAAGTGAATTGTATCT
1 GAAAGTGAATTGTATCT
*
432820 GAAAGTGATTTGTATCT
1 GAAAGTGAATTGTATCT
432837 CACAAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (17 bp):
GAAAGTGAATTGTATCT
Found at i:436954 original size:82 final size:82
Alignment explanation
Indices: 436863--437027 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
436853 AATACATACC
436863 ATAACATCCAAAACTCAATTGCCTCCCAATTTAAAATCAAATACGAGGGATTACTAGATTTAACA
1 ATAACATCCAAAACTCAATTGCCTCCCAATTTAAAATCAAATACGAGGGATTACTAGATTTAACA
436928 ACACCAAGAAATTAAAT
66 ACACCAAGAAATTAAAT
*
436945 ATAACATCCAAAACTCAATTGCCTCCCAATTTAAAATCAAATATGAGGGATTACTAGATTTAACA
1 ATAACATCCAAAACTCAATTGCCTCCCAATTTAAAATCAAATACGAGGGATTACTAGATTTAACA
437010 ACACCAAGAAATTAAAT
66 ACACCAAGAAATTAAAT
437027 A
1 A
437028 CTCATTTAGT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (82 bp):
ATAACATCCAAAACTCAATTGCCTCCCAATTTAAAATCAAATACGAGGGATTACTAGATTTAACA
ACACCAAGAAATTAAAT
Found at i:441151 original size:32 final size:29
Alignment explanation
Indices: 441115--441188 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 29
441105 ATATAAATAT
441115 TTTTTTTATTATT-AAATATATTATATGTT-
1 TTTTTTTATTATTAAAAT-TATTATAT-TTA
441144 TTATTTTTATATATTTAAAATTATTATATTTA
1 TT-TTTTTAT-TA-TTAAAATTATTATATTTA
441176 TTTTTTTATTATT
1 TTTTTTTATTATT
441189 TTTTGATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
29 4 0.10
30 9 0.22
31 11 0.28
32 12 0.30
33 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTTTTTATTATTAAAATTATTATATTTA
Found at i:441167 original size:29 final size:31
Alignment explanation
Indices: 441111--441189 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 31
441101 GTGTATATAA
*
441111 ATATTT-TTTTTAT-TATTAAATATATTA-T
1 ATATTTATTTTTATATATTTAATATATTATT
*
441139 ATGTTTTATTTTTATATATTTAA-A-ATTATT
1 AT-ATTTATTTTTATATATTTAATATATTATT
*
441169 ATATTTATTTTTTTATTATTT
1 ATATTTATTTTTATA-TATTT
441190 TTTGATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 2 0.05
29 18 0.43
30 16 0.38
31 6 0.14
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (31 bp):
ATATTTATTTTTATATATTTAATATATTATT
Found at i:441672 original size:6 final size:6
Alignment explanation
Indices: 441655--441684 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
441645 AATTGAATTA
441655 ATTTTAT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTT-T ATTTTT ATTTTT ATTTTT ATTTT
441685 GTTTATAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:445665 original size:21 final size:20
Alignment explanation
Indices: 445641--445679 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
445631 ATTTCTGGTG
*
445641 CTTTCCCTTCCAAGTCCAACC
1 CTTTCCCATCCAA-TCCAACC
*
445662 CTTTGCCATCCAATCCAA
1 CTTTCCCATCCAATCCAA
445680 GAGTTAGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.44, G:0.05, T:0.28
Consensus pattern (20 bp):
CTTTCCCATCCAATCCAACC
Found at i:449701 original size:6 final size:6
Alignment explanation
Indices: 449690--449729 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
449680 TCTGGATTTT
*
449690 GGGGG- GGGGG- GGGGG- GGGAGA GGGGGA GGGGGA GGGGGA G
1 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA G
449730 AGGTGGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.12, C:0.00, G:0.88, T:0.00
Consensus pattern (6 bp):
GGGGGA
Found at i:449714 original size:14 final size:13
Alignment explanation
Indices: 449690--449732 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
449680 TCTGGATTTT
* *
449690 GGGGGGGGGGGGG
1 GGGGGAGGGGGGA
449703 GGGGGAGAGGGGGA
1 GGGGGAG-GGGGGA
449717 GGGGGAGGGGGAGA
1 GGGGGAGGGGG-GA
449731 GG
1 GG
449733 TGGTTGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (13 bp):
GGGGGAGGGGGGA
Found at i:449720 original size:20 final size:20
Alignment explanation
Indices: 449691--449732 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
449681 CTGGATTTTG
* *
449691 GGGGGGGGGGGGGGGGGAGA
1 GGGGGAGGGGGAGGGGGAGA
449711 GGGGGAGGGGGAGGGGGAGA
1 GGGGGAGGGGGAGGGGGAGA
449731 GG
1 GG
449733 TGGTTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (20 bp):
GGGGGAGGGGGAGGGGGAGA
Found at i:450357 original size:16 final size:17
Alignment explanation
Indices: 450327--450359 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
450317 GGCACATCAC
450327 TCTTTGGCAGCAATGTT
1 TCTTTGGCAGCAATGTT
*
450344 TCTTT-GCAGTAATGTT
1 TCTTTGGCAGCAATGTT
450360 AATTGGCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (17 bp):
TCTTTGGCAGCAATGTT
Found at i:454912 original size:2 final size:2
Alignment explanation
Indices: 454907--454941 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
454897 CACAAAAAAC
454907 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 A
454942 CAATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:461610 original size:15 final size:15
Alignment explanation
Indices: 461588--461627 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
461578 AAGATTACTG
461588 TTTAAAATTAAATTT
1 TTTAAAATTAAATTT
461603 TATT-AAA-TAAATTT
1 T-TTAAAATTAAATTT
461617 TTTAAAATTAA
1 TTTAAAATTAA
461628 TTGTCCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 11 0.50
15 7 0.32
16 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATTAAATTT
Found at i:462832 original size:17 final size:18
Alignment explanation
Indices: 462810--462856 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
462800 AGGTGTCATC
462810 TCAAAATTATTAT-AATA
1 TCAAAATTATTATGAATA
462827 TCAAAA-TATATATGAATA
1 TCAAAATTAT-TATGAATA
462845 T-AAAATATATTA
1 TCAAAAT-TATTA
462857 AAAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 7 0.27
19 3 0.12
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
TCAAAATTATTATGAATA
Found at i:462869 original size:16 final size:17
Alignment explanation
Indices: 462848--462886 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
462838 ATGAATATAA
462848 AATATATTAAAA-ATAT
1 AATATATTAAAACATAT
*
462864 AATATAATAAAACATAT
1 AATATATTAAAACATAT
462881 AA-ATAT
1 AATATAT
462887 CAAATGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATATTAAAACATAT
Found at i:463516 original size:2 final size:2
Alignment explanation
Indices: 463509--463563 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
463499 AACGCATTAA
463509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463551 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
463564 AACATATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:465071 original size:25 final size:25
Alignment explanation
Indices: 465024--465072 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
465014 AATGATGAAC
* **
465024 TTAAACTTAACTGAATTGGTTCATT
1 TTAAACTTAACTCAATTAATTCATT
465049 TTAAACTTAACTCAATTAATTCAT
1 TTAAACTTAACTCAATTAATTCAT
465073 GCTGTGATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (25 bp):
TTAAACTTAACTCAATTAATTCATT
Found at i:468979 original size:26 final size:26
Alignment explanation
Indices: 468943--468994 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
468933 TTCCTTTAAT
468943 TAATTTTTTGCCACTACCACAATCAC
1 TAATTTTTTGCCACTACCACAATCAC
468969 TAATTTTTTGCCACTACCACAATCAC
1 TAATTTTTTGCCACTACCACAATCAC
468995 CAGAAAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.35
Consensus pattern (26 bp):
TAATTTTTTGCCACTACCACAATCAC
Found at i:469068 original size:29 final size:29
Alignment explanation
Indices: 469036--469145 Score: 139
Period size: 32 Copynumber: 3.6 Consensus size: 29
469026 CCAGAGAGCT
469036 ATTAATTACGTTTAAATTCCACCAGAACC
1 ATTAATTACGTTTAAATTCCACCAGAACC
* *
469065 ATTAACTACGTTTAAATTCCACCAAGAGAGCT
1 ATTAATTACGTTTAAATTCCACC-AGA-A-CC
*
469097 ATTAATTACGTTTAAATTCCACCAGGGAGCC
1 ATTAATTACGTTTAAATTCCACCA--GAACC
*
469128 ATTAATTAGGTTTAAATT
1 ATTAATTACGTTTAAATT
469146 TTACTCCAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
29 22 0.31
30 3 0.04
31 20 0.29
32 23 0.33
33 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (29 bp):
ATTAATTACGTTTAAATTCCACCAGAACC
Found at i:469100 original size:61 final size:62
Alignment explanation
Indices: 469028--469145 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 62
469018 CCAGATAACC
469028 AGAGAGCTATTAATTACGTTTAAATTCCACCA-GAACCATTAACTACGTTTAAATTCCACCA
1 AGAGAGCTATTAATTACGTTTAAATTCCACCAGGAACCATTAACTACGTTTAAATTCCACCA
* * *
469089 AGAGAGCTATTAATTACGTTTAAATTCCACCAGGGAGCCATTAATTAGGTTTAAATT
1 AGAGAGCTATTAATTACGTTTAAATTCCACCA-GGAACCATTAACTACGTTTAAATT
469146 TTACTCCAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 32 0.62
63 20 0.38
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (62 bp):
AGAGAGCTATTAATTACGTTTAAATTCCACCAGGAACCATTAACTACGTTTAAATTCCACCA
Found at i:469107 original size:32 final size:31
Alignment explanation
Indices: 469025--469145 Score: 174
Period size: 31 Copynumber: 3.9 Consensus size: 31
469015 CCACCAGATA
*
469025 ACCAGAGAGCTATTAATTACGTTTAAATTCC
1 ACCAGAGAGCCATTAATTACGTTTAAATTCC
*
469056 ACCAGA-A-CCATTAACTACGTTTAAATTCC
1 ACCAGAGAGCCATTAATTACGTTTAAATTCC
*
469085 ACCAAGAGAGCTATTAATTACGTTTAAATTCC
1 ACC-AGAGAGCCATTAATTACGTTTAAATTCC
* *
469117 ACCAGGGAGCCATTAATTAGGTTTAAATT
1 ACCAGAGAGCCATTAATTACGTTTAAATT
469146 TTACTCCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
29 23 0.29
30 4 0.05
31 30 0.38
32 23 0.29
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (31 bp):
ACCAGAGAGCCATTAATTACGTTTAAATTCC
Found at i:469224 original size:16 final size:16
Alignment explanation
Indices: 469188--469218 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
469178 GGGTTCTGAC
*
469188 GTCAGACTTTATATAA
1 GTCAGACTTAATATAA
469204 GTCAGACTTAATATA
1 GTCAGACTTAATATA
469219 GATCAGGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
GTCAGACTTAATATAA
Found at i:472945 original size:2 final size:2
Alignment explanation
Indices: 472938--472966 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
472928 TTTCCATATA
472938 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
472967 CCCAGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:475706 original size:2 final size:2
Alignment explanation
Indices: 475694--475724 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
475684 ATCCAAATAC
*
475694 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
475725 TGTTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:481750 original size:18 final size:19
Alignment explanation
Indices: 481723--481759 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
481713 AGTTAATGCT
*
481723 TAAAA-TTTTTATTTTTTA
1 TAAAAGTTTTGATTTTTTA
481741 TAAAAGTTTTGATTTTTTA
1 TAAAAGTTTTGATTTTTTA
481760 ATAATTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TAAAAGTTTTGATTTTTTA
Found at i:481907 original size:7 final size:7
Alignment explanation
Indices: 481879--481943 Score: 50
Period size: 7 Copynumber: 9.9 Consensus size: 7
481869 TAATGAGATA
481879 TTAAT-T
1 TTAATAT
481885 TTAATAT
1 TTAATAT
*
481892 TT-TTAT
1 TTAATAT
481898 TTAATAT
1 TTAATAT
481905 TT-ATA-
1 TTAATAT
481910 TT-ATAT
1 TTAATAT
*
481916 TTAAAAT
1 TTAATAT
*
481923 TATAAAAT
1 T-TAATAT
*
481931 TTAAAAT
1 TTAATAT
481938 TTAATA
1 TTAATA
481944 AAATATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
5 5 0.10
6 15 0.30
7 23 0.46
8 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TTAATAT
Found at i:482003 original size:19 final size:20
Alignment explanation
Indices: 481976--482026 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
481966 TGATAATAAT
481976 AATAATTA-TAA-ATTTATTA
1 AATAATTATTAATATTT-TTA
*
481995 AATATTTATTAATATTTTTA
1 AATAATTATTAATATTTTTA
* *
482015 AAAAATAATTAA
1 AATAATTATTAA
482027 ATTAAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 15 0.58
21 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTATTAATATTTTTA
Found at i:482555 original size:20 final size:20
Alignment explanation
Indices: 482527--482564 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
482517 CGAATATATA
482527 TATTATATATATCTATATTT
1 TATTATATATATCTATATTT
* *
482547 TATTTTATATATTTATAT
1 TATTATATATATCTATAT
482565 GTGTGACTTA
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:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATATATATCTATATTT
Found at i:483107 original size:20 final size:20
Alignment explanation
Indices: 483082--483133 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
483072 CTTCAGCAGA
* *
483082 GAAAGAAAAAGATAAA-AATG
1 GAAAGAAAAA-AAAAAGAAAG
483102 GAAAGAAAAAAAAAAGAAAG
1 GAAAGAAAAAAAAAAGAAAG
483122 GAAAGAAAAAAA
1 GAAAGAAAAAAA
483134 CATTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (20 bp):
GAAAGAAAAAAAAAAGAAAG
Found at i:483184 original size:9 final size:9
Alignment explanation
Indices: 483172--483205 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
483162 TTTTTATTTA
483172 AAATATTAT
1 AAATATTAT
483181 AAAT-TTAT
1 AAATATTAT
483189 ATAATATTAT
1 A-AATATTAT
483199 AAATATT
1 AAATATT
483206 TTTTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AAATATTAT
Found at i:483435 original size:27 final size:28
Alignment explanation
Indices: 483378--483436 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
483368 CGTATTGTAT
* * *
483378 TTATTTTATTTTTTGTATTATGTTTTAA
1 TTATTTTATTATTTATATTATGTTATAA
483406 TTATTTT-TTATTTATATTATGTTCAT-A
1 TTATTTTATTATTTATATTATGTT-ATAA
483433 TTAT
1 TTAT
483437 GTCTCAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (28 bp):
TTATTTTATTATTTATATTATGTTATAA
Found at i:484173 original size:17 final size:16
Alignment explanation
Indices: 484146--484179 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
484136 TCAGTTACAT
*
484146 AAAATTTTAAATTATA
1 AAAATTTTAAATAATA
484162 AAAATATTTAAATAATA
1 AAAAT-TTTAAATAATA
484179 A
1 A
484180 TCATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAATAATA
Found at i:484601 original size:10 final size:10
Alignment explanation
Indices: 484572--484601 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
484562 AACCTTCTCA
*
484572 TTCCTTCCTC
1 TTCCTTCCTT
484582 TTCCTTCCTT
1 TTCCTTCCTT
484592 TTCCTTCCTT
1 TTCCTTCCTT
484602 CTAAGTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
TTCCTTCCTT
Found at i:492002 original size:2 final size:2
Alignment explanation
Indices: 491995--492019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
491985 TAATTAACTA
491995 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
492020 TTATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:493042 original size:15 final size:16
Alignment explanation
Indices: 493011--493050 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
493001 GTGTTGTCTC
493011 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
493027 AAAAAGAAA-AAGAAG
1 AAAAAGAAAGAAAAAG
*
493042 AAAACGAAA
1 AAAAAGAAA
493051 TGTGATCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:497673 original size:3 final size:3
Alignment explanation
Indices: 497661--497709 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
497651 TAATCAAATA
*
497661 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
497708 AT
1 AT
497710 ATGCTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:499526 original size:7 final size:8
Alignment explanation
Indices: 499488--499536 Score: 50
Period size: 7 Copynumber: 6.2 Consensus size: 8
499478 TTTTTAAAAA
499488 TAATA-TT
1 TAATATTT
499495 TAATAATTT
1 TAAT-ATTT
499504 TAA-ATTT
1 TAATATTT
499511 TAA-ATTT
1 TAATATTT
499518 TAATATTT
1 TAATATTT
*
499526 ATAATTTTT
1 -TAATATTT
499535 TA
1 TA
499537 TTTTTTATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 18 0.49
8 7 0.19
9 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TAATATTT
Found at i:500893 original size:18 final size:17
Alignment explanation
Indices: 500870--500955 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 17
500860 AAAATAATTA
*
500870 AAATATTATATAAAATAT
1 AAATATAATA-AAAATAT
500888 AAATATAATAAAAATAT
1 AAATATAATAAAAATAT
*
500905 ATGAATATATTAAAATTTATAT
1 A--AATATAATAAAA---ATAT
* * *
500927 AAATAT-ATAATATTTT
1 AAATATAATAAAAATAT
*
500943 AATTATAATAAAA
1 AAATATAATAAAA
500956 TTTTAATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.13
17 13 0.24
18 9 0.17
19 15 0.28
20 5 0.09
22 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
AAATATAATAAAAATAT
Found at i:500895 original size:13 final size:12
Alignment explanation
Indices: 500858--500939 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 12
500848 TATCTATTTA
*
500858 AAAAAATAAT-T
1 AAAATATAATAT
*
500869 AAAATATTATAT
1 AAAATATAATAT
500881 AAAATATAAATAT
1 AAAATAT-AATAT
500894 AATAA-A-AATAT
1 AA-AATATAATAT
*
500905 ATGAATAT-AT-T
1 A-AAATATAATAT
*
500916 AAAAT-TTATAT
1 AAAATATAATAT
500927 AAATATATAATAT
1 AAA-ATATAATAT
500940 TTTAATTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
9 1 0.02
10 5 0.09
11 22 0.40
12 13 0.24
13 12 0.22
14 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:500930 original size:10 final size:10
Alignment explanation
Indices: 500884--500935 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
500874 ATTATATAAA
500884 ATATAAATAT
1 ATATAAATAT
*
500894 A-ATAAAAAT
1 ATATAAATAT
*
500903 ATATGAATAT
1 ATATAAATAT
*
500913 AT-TAAAATTT
1 ATAT-AAATAT
500923 ATATAAATAT
1 ATATAAATAT
500933 ATA
1 ATA
500936 ATATTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 9 0.27
10 23 0.70
11 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATATAAATAT
Found at i:500958 original size:17 final size:16
Alignment explanation
Indices: 500879--500966 Score: 59
Period size: 17 Copynumber: 5.1 Consensus size: 16
500869 AAAATATTAT
* *
500879 ATAAAATATAAATATA
1 ATAAAATTTTAATATA
*
500895 ATAAAAATATATGAATATA
1 AT-AAAAT-T-TTAATATA
* *
500914 TTAAAATTTATATAAATA
1 ATAAAATTT-TA-ATATA
*
500932 TATAATATTTTAATTATA
1 -ATAAAATTTTAA-TATA
500950 ATAAAATTTTAATATA
1 ATAAAATTTTAATATA
500966 A
1 A
500967 ATATATAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
16 8 0.14
17 19 0.34
18 14 0.25
19 15 0.27
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATAAAATTTTAATATA
Found at i:500973 original size:38 final size:36
Alignment explanation
Indices: 500884--500982 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 36
500874 ATTATATAAA
* *
500884 ATATAAATATAATAAAAATATATGAA-TATATTAAAATTT
1 ATATAAATAT-AT--AAAT-TATTAATTATAATAAAATTT
500923 ATATAAATATATAATATT-TTAATTATAATAAAATTTT
1 ATATAAATATATAA-ATTATTAATTATAATAAAA-TTT
500960 AATATAAATATATAAATTATTAA
1 -ATATAAATATATAAATTATTAA
500983 ACTTATTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
35 3 0.06
36 12 0.23
37 8 0.15
38 20 0.38
39 10 0.19
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
ATATAAATATATAAATTATTAATTATAATAAAATTT
Found at i:501259 original size:5 final size:5
Alignment explanation
Indices: 501249--501273 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
501239 TGCTTGTGAG
501249 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
501274 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:501594 original size:21 final size:21
Alignment explanation
Indices: 501560--501599 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
501550 GCGGTGATAA
**
501560 TAAGATTAGTTATTGTAATCG
1 TAAGATTAAATATTGTAATCG
*
501581 TAAGATTAAATATTTTAAT
1 TAAGATTAAATATTGTAAT
501600 GAGATTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
TAAGATTAAATATTGTAATCG
Found at i:501755 original size:35 final size:35
Alignment explanation
Indices: 501712--501868 Score: 149
Period size: 35 Copynumber: 4.4 Consensus size: 35
501702 TGTATTTATG
501712 TAAAAAATAATAAAAAATATATTTATATTAAATAA
1 TAAAAAATAATAAAAAATATATTTATATTAAATAA
* *
501747 TAAAAAATAA-ATAAAAATATATTTATGTTGAATAA
1 TAAAAAATAATA-AAAAATATATTTATATTAAATAA
* * *
501782 TAATTAAAA-ATTAATAAATTATATTTATATTTAATAA
1 TAA--AAAATAATAA-AAAATATATTTATATTAAATAA
* * * * *
501819 TATAAATTACT-AGAATTATATTTATATTAAATAA
1 TAAAAAATAATAAAAAATATATTTATATTAAATAA
*
501853 TAAAAATATATTAAAA
1 TAAAAA-ATAATAAAA
501869 TTGAAAAATT
Statistics
Matches: 99, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
34 26 0.26
35 41 0.41
36 6 0.06
37 26 0.26
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (35 bp):
TAAAAAATAATAAAAAATATATTTATATTAAATAA
Found at i:501836 original size:34 final size:33
Alignment explanation
Indices: 501729--501859 Score: 145
Period size: 34 Copynumber: 3.8 Consensus size: 33
501719 TAATAAAAAA
* *
501729 TATATTTATATTAAATAATAAAAAATAAATAAAAA
1 TATATTTATATTAAATAAT-AAAAATTAAT-AAAT
*
501764 TATATTTATGTTGAATAATAATTAAAAATTAATAAAT
1 TATATTTATATT--A-AATAA-TAAAAATTAATAAAT
* * *
501801 TATATTTATATTTAATAATATAAATTACTAGAAT
1 TATATTTATATTAAATAATAAAAATTAATA-AAT
501835 TATATTTATATTAAATAATAAAAAT
1 TATATTTATATTAAATAATAAAAAT
501860 ATATTAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
33 10 0.12
34 31 0.38
35 11 0.13
37 15 0.18
38 14 0.17
39 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (33 bp):
TATATTTATATTAAATAATAAAAATTAATAAAT
Found at i:503569 original size:17 final size:17
Alignment explanation
Indices: 503549--503588 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
503539 AAAAAATTAA
503549 ATATATTCATATTAAAT
1 ATATATTCATATTAAAT
* *
503566 ATATATTTATATTTAAT
1 ATATATTCATATTAAAT
503583 AT-TATT
1 ATATATT
503589 AAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTCATATTAAAT
Found at i:503605 original size:17 final size:16
Alignment explanation
Indices: 503544--503607 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
503534 ATTTAAAAAA
*
503544 ATTAAATATAT-TCAT
1 ATTAAATATATATTAT
503559 ATTAAATATATATTTAT
1 ATTAAATATATA-TTAT
503576 ATT---TA-ATA-T-T
1 ATTAAATATATATTAT
503586 ATTAAATATATATTAAT
1 ATTAAATATATATT-AT
503603 ATTAA
1 ATTAA
503608 GGTGTCCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 16
0.70 0.02 0.29
Matches are distributed among these distances:
10 4 0.10
11 1 0.03
13 5 0.13
14 5 0.13
15 12 0.31
17 12 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATATATATTAT
Found at i:505073 original size:8 final size:8
Alignment explanation
Indices: 505045--505088 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
505035 AGGAAGTGAG
*
505045 ATATATAT
1 ATATGTAT
*
505053 ATATATAT
1 ATATGTAT
505061 ATATGTAT
1 ATATGTAT
505069 ATATGTAT
1 ATATGTAT
* *
505077 GTACGTAT
1 ATATGTAT
505085 ATAT
1 ATAT
505089 AGAAAGAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (8 bp):
ATATGTAT
Found at i:505077 original size:12 final size:12
Alignment explanation
Indices: 505045--505089 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
505035 AGGAAGTGAG
*
505045 ATATATATATAT
1 ATATATATGTAT
505057 ATATATATGTAT
1 ATATATATGTAT
*
505069 ATATGTATGTACGT
1 ATATATATGTA--T
505083 ATATATA
1 ATATATA
505090 GAAAGAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 21 0.75
14 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:507377 original size:15 final size:17
Alignment explanation
Indices: 507340--507383 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
507330 ACATGAGGCA
507340 AGCAAAAGAAAGAAAGT
1 AGCAAAAGAAAGAAAGT
507357 AG-AAAA-AAAGAAAG-
1 AGCAAAAGAAAGAAAGT
507371 AGCAAAAGGAAAG
1 AGCAAAA-GAAAG
507384 TTAATGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 4 0.17
17 6 0.25
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.02
Consensus pattern (17 bp):
AGCAAAAGAAAGAAAGT
Found at i:515784 original size:2 final size:2
Alignment explanation
Indices: 515779--515811 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
515769 ACACACACAC
515779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
515812 TTAATTTTCC
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:517235 original size:2 final size:2
Alignment explanation
Indices: 517228--517258 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
517218 CACATGTGAA
517228 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 A
517259 GTTTACATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:522329 original size:23 final size:24
Alignment explanation
Indices: 522302--522348 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
522292 TATGTCTTTA
* *
522302 TATTAAACATATTATA-TTATATT
1 TATTAAAAATATCATATTTATATT
522325 TATTAAAAATATCATATTTATATT
1 TATTAAAAATATCATATTTATATT
522349 ATTTTATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAAAAATATCATATTTATATT
Found at i:523170 original size:26 final size:26
Alignment explanation
Indices: 523113--523170 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
523103 TTTTAATTTA
*
523113 ATTACTTTTAATTTTCTTTTGTGAATG
1 ATTA-TTTTAATTTTATTTTGTGAATG
* *
523140 CTTATTTT-ATTTTATTTTGTTATATG
1 ATTATTTTAATTTTATTTTGTGA-ATG
523166 ATTAT
1 ATTAT
523171 GATCTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.46
26 11 0.42
27 3 0.12
ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64
Consensus pattern (26 bp):
ATTATTTTAATTTTATTTTGTGAATG
Found at i:523279 original size:2 final size:2
Alignment explanation
Indices: 523274--523303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
523264 GTGTACGCGC
523274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
523304 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526021 original size:2 final size:2
Alignment explanation
Indices: 526014--526038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
526004 GATACGCCAT
526014 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
526039 CCTTTGCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:531660 original size:2 final size:2
Alignment explanation
Indices: 531653--531678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
531643 TTTTAGATAA
531653 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
531679 CCGCAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533875 original size:2 final size:2
Alignment explanation
Indices: 533868--533905 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
533858 TTGAACTCTA
533868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
533906 GATCAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:543443 original size:12 final size:13
Alignment explanation
Indices: 543420--543448 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
543410 TGAAATTTAG
543420 AAAAATATATATT
1 AAAAATATATATT
543433 AAAAATA-ATATT
1 AAAAATATATATT
543445 AAAA
1 AAAA
543449 TTATGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATATATT
Found at i:551047 original size:2 final size:2
Alignment explanation
Indices: 551040--551069 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
551030 CTTAGGAAAA
551040 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
551070 GGAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:552640 original size:17 final size:16
Alignment explanation
Indices: 552618--552674 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
552608 TAATTTTTAA
552618 TATATTTATA-TACTAAT
1 TATATTTATATTA-T-AT
552635 TATATTTATATTATAT
1 TATATTTATATTATAT
*
552651 TATATTT-TAAT-TAT
1 TATATTTATATTATAT
552665 T-TATTTATAT
1 TATATTTATAT
552675 CGTAATACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.14
14 6 0.17
15 3 0.08
16 9 0.25
17 11 0.31
18 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:552653 original size:27 final size:29
Alignment explanation
Indices: 552618--552674 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
552608 TAATTTTTAA
552618 TATATTTATATACTAATTA-TATTTATAT
1 TATATTTATATACTAATTATTATTTATAT
**
552646 TATA-TTATATTTTAATTATTTATTTATAT
1 TATATTTATATACTAATTA-TTATTTATAT
552675 CGTAATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 4 0.16
29 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TATATTTATATACTAATTATTATTTATAT
Found at i:557561 original size:21 final size:21
Alignment explanation
Indices: 557535--557583 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
557525 AACCCGAATT
* *
557535 TGGATACATGTCTGGTTACCC
1 TGGATACATGCCGGGTTACCC
*
557556 TGGATACATGCCGGGTTATCC
1 TGGATACATGCCGGGTTACCC
557577 TGGATAC
1 TGGATAC
557584 GGGCACCCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
TGGATACATGCCGGGTTACCC
Found at i:563474 original size:42 final size:42
Alignment explanation
Indices: 563426--563509 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
563416 CTGAAGTATG
563426 AATTAAGCTTCTTATAAAGCA-CAAATTGCTCAATCCTTTCAT
1 AATTAAGCTTCTTATAAAGCAGC-AATTGCTCAATCCTTTCAT
563468 AATTAAGCTTCTTATAAAGCAGCAATTGCTCAATCCTTTCAT
1 AATTAAGCTTCTTATAAAGCAGCAATTGCTCAATCCTTTCAT
563510 GCAATGCCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (42 bp):
AATTAAGCTTCTTATAAAGCAGCAATTGCTCAATCCTTTCAT
Found at i:573663 original size:2 final size:2
Alignment explanation
Indices: 573656--573685 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
573646 AGAAAAAGCA
*
573656 AT AT AT AT AC 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
573686 TTATGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:575453 original size:6 final size:6
Alignment explanation
Indices: 575444--575480 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
575434 TTTTATATGT
* *
575444 CGGCAA CGGCAA CGGCGA CGGCGA CGGCAA CGGCAA C
1 CGGCAA CGGCAA CGGCAA CGGCAA CGGCAA CGGCAA C
575481 ACATCACTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (6 bp):
CGGCAA
Found at i:576874 original size:22 final size:22
Alignment explanation
Indices: 576849--576893 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
576839 GGGTGTGTGT
*
576849 GTGTGTGTCTGTGAGAGAAAGA
1 GTGTGTGTCTGAGAGAGAAAGA
* *
576871 GTGTGTGTGTGAGAGAGAGAGA
1 GTGTGTGTCTGAGAGAGAAAGA
576893 G
1 G
576894 AGAGAGAGAG
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:0.27, C:0.02, G:0.47, T:0.24
Consensus pattern (22 bp):
GTGTGTGTCTGAGAGAGAAAGA
Found at i:576876 original size:20 final size:20
Alignment explanation
Indices: 576851--576891 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
576841 GTGTGTGTGT
576851 GTGTGTCTGTGAGAGAAAGA
1 GTGTGTCTGTGAGAGAAAGA
* *
576871 GTGTGTGTGTGAGAGAGAGA
1 GTGTGTCTGTGAGAGAAAGA
576891 G
1 G
576892 AGAGAGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.46, T:0.24
Consensus pattern (20 bp):
GTGTGTCTGTGAGAGAAAGA
Found at i:576886 original size:2 final size:2
Alignment explanation
Indices: 576881--576940 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
576871 GTGTGTGTGT
*
576881 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
576923 GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
576941 CCTGAGATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:576888 original size:24 final size:24
Alignment explanation
Indices: 576847--576895 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
576837 GTGGGTGTGT
* *
576847 GTGTGTGTGTCTGTGAGAGAAAGA
1 GTGTGTGTGTCAGAGAGAGAAAGA
* *
576871 GTGTGTGTGTGAGAGAGAGAGAGA
1 GTGTGTGTGTCAGAGAGAGAAAGA
576895 G
1 G
576896 AGAGAGAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.47, T:0.24
Consensus pattern (24 bp):
GTGTGTGTGTCAGAGAGAGAAAGA
Found at i:581045 original size:21 final size:21
Alignment explanation
Indices: 581021--581060 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
581011 ATTACTGAAA
581021 ATTTAA-ATATTTAATTAATTT
1 ATTTAATATA-TTAATTAATTT
*
581042 ATTTATTATATTAATTAAT
1 ATTTAATATATTAATTAAT
581061 GATTCAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAATATATTAATTAATTT
Found at i:581850 original size:20 final size:21
Alignment explanation
Indices: 581804--581851 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
581794 ATAATTACTC
**
581804 TAAAAT-TATAATCATAATCT
1 TAAAATATATAATCATAATAA
*
581824 TATAATATATAAT-ATAATAA
1 TAAAATATATAATCATAATAA
581844 TAAAATAT
1 TAAAATAT
581852 TTATTTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATATATAATCATAATAA
Found at i:581973 original size:18 final size:19
Alignment explanation
Indices: 581939--581981 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
581929 AACATTTTAC
*
581939 TTATAAATTAAATAAATA-
1 TTATAAATTAAAAAAATAT
581957 TTATAAA-TAATAAAAATAT
1 TTATAAATTAA-AAAAATAT
581976 TTATAA
1 TTATAA
581982 TGAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATAAATTAAAAAAATAT
Found at i:582966 original size:2 final size:2
Alignment explanation
Indices: 582954--582992 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
582944 AAAACGCTTT
* *
582954 TC TC TC GC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
582993 GTGCAACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.46, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:591161 original size:33 final size:33
Alignment explanation
Indices: 591086--591149 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
591076 ATTATATTAA
* *
591086 TATAATATAAATAAATAAATATTTTTAAAATTT
1 TATAATATAAATAATTAAATATTATTAAAATTT
591119 TATAATATAAATAATTAAA-A-TATTAAAATTT
1 TATAATATAAATAATTAAATATTATTAAAATTT
591150 ATGTAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 10 0.34
32 1 0.03
33 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TATAATATAAATAATTAAATATTATTAAAATTT
Found at i:591418 original size:28 final size:30
Alignment explanation
Indices: 591376--591439 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
591366 TTCAAATTTT
591376 TATATTTTACATAAAAATTATT-AAAAT-AAA
1 TATATTTTA-ATAAAAA-TATTAAAAATAAAA
*
591406 TATATTTT-ATAAATATATTAAAAATAAAA
1 TATATTTTAATAAAAATATTAAAAATAAAA
591435 TATAT
1 TATAT
591440 GATAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 4 0.13
28 11 0.35
29 8 0.26
30 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
TATATTTTAATAAAAATATTAAAAATAAAA
Found at i:591444 original size:27 final size:26
Alignment explanation
Indices: 591390--591444 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
591380 TTTTACATAA
* *
591390 AAATTATTAAAATAAATATATTTTAT
1 AAATTATTAAAATAAATATATATGAT
591416 AAATATATTAAAAATAAA-ATATATGAT
1 AAAT-TATT-AAAATAAATATATATGAT
591443 AA
1 AA
591445 TTTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 13 0.52
28 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATTATTAAAATAAATATATATGAT
Found at i:591850 original size:18 final size:17
Alignment explanation
Indices: 591817--591862 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
591807 TAATTCGTGT
*
591817 AATTATATTATTTTTAA
1 AATTATATTATGTTTAA
591834 AATTATAATTATGTTTAA
1 AATTAT-ATTATGTTTAA
591852 AGTATTATATT
1 A--ATTATATT
591863 TTTATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 11 0.44
19 3 0.12
20 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTATATTATGTTTAA
Done.