Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
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: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 20
Found at i:479612 original size:20 final size:21
Alignment explanation
Indices: 479588--479645 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
479578 AACATTTACT
479588 ATTATAATTAAATATTTT-AA
1 ATTATAATTAAATATTTTAAA
* * *
479608 TTTATTAGTATAAATTTTTTAAA
1 ATTA-TAAT-TAAATATTTTAAA
479631 ATT-TAATTAAATATT
1 ATTATAATTAAATATT
479646 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
20 10 0.34
21 6 0.21
22 9 0.31
23 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTATAATTAAATATTTTAAA
Found at i:479731 original size:19 final size:19
Alignment explanation
Indices: 479701--479747 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
479691 TGAATTTTTA
479701 AAATTTAA-TTAATTTCTT
1 AAATTTAATTTAATTTCTT
*
479719 AAATTTAATTTAATTTTTT
1 AAATTTAATTTAATTTCTT
479738 AATATTTAAT
1 AA-ATTTAAT
479748 ATTTTCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATTTAATTTAATTTCTT
Found at i:480093 original size:2 final size:2
Alignment explanation
Indices: 480056--480081 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
480046 TATTGTATTA
480056 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
480082 CTTCAATATA
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:484567 original size:13 final size:13
Alignment explanation
Indices: 484549--484573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484539 ATTACTCAAA
484549 TGTATCGATACAT
1 TGTATCGATACAT
484562 TGTATCGATACA
1 TGTATCGATACA
484574 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:484675 original size:52 final size:52
Alignment explanation
Indices: 484582--484705 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
484572 CACTGATCTT
*
484582 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
484633 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
484685 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
484706 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:489549 original size:23 final size:22
Alignment explanation
Indices: 489507--489572 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
489497 AATAAGAGAG
* *
489507 TTTTAAATAATTTTTTTTAATT
1 TTTTAAATAATTGTTATTAATT
*
489529 TTTTCAAATAATTGTTATTAAAATA
1 TTTT-AAATAATTGTTATT--AATT
* *
489554 TTTTAAAAAATTATTATTA
1 TTTTAAATAATTGTTATTA
489573 TTATTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 5 0.14
23 12 0.33
24 12 0.33
25 7 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAAATAATTGTTATTAATT
Found at i:489571 original size:3 final size:3
Alignment explanation
Indices: 489563--489612 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
489553 ATTTTAAAAA
489563 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
489611 AT
1 AT
489613 GTTGGCTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:494943 original size:2 final size:2
Alignment explanation
Indices: 494936--494972 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
494926 TCTCTTGTTG
*
494936 TC TC TC TC TC TC TC TC TT 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 T
494973 TATTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:495033 original size:49 final size:49
Alignment explanation
Indices: 494961--495062 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
494951 CTTTCTCTCT
494961 CTCTCTCTCTCTTATTTTCTTTCCATAGCTTAGTTTAATCTCTCTCAAC
1 CTCTCTCTCTCTTATTTTCTTTCCATAGCTTAGTTTAATCTCTCTCAAC
*
495010 CTCTCTCTCTCTTATTTTTTTTCCATAGCTTAGTTTAATCTCTCTCAAC
1 CTCTCTCTCTCTTATTTTCTTTCCATAGCTTAGTTTAATCTCTCTCAAC
495059 CTCT
1 CTCT
495063 TTCTTAATAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.16, C:0.30, G:0.04, T:0.50
Consensus pattern (49 bp):
CTCTCTCTCTCTTATTTTCTTTCCATAGCTTAGTTTAATCTCTCTCAAC
Found at i:496871 original size:2 final size:2
Alignment explanation
Indices: 496864--496888 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
496854 TTTTATGTAT
496864 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
496889 TCCATTTAAA
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:496946 original size:2 final size:2
Alignment explanation
Indices: 496939--496968 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
496929 GGAGCAATGT
496939 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
496969 ATAAATCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:497188 original size:14 final size:15
Alignment explanation
Indices: 497169--497197 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
497159 TAACAATCGA
497169 AAAGTTATT-TTAAT
1 AAAGTTATTATTAAT
497183 AAAGTTATTATTAAT
1 AAAGTTATTATTAAT
497198 TTATCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAAGTTATTATTAAT
Found at i:497530 original size:36 final size:36
Alignment explanation
Indices: 497465--497542 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
497455 AAACACCGCC
* * * *
497465 AAATTTGTCAAAAAAATGGTGTCGGTAAAGTTCGCT
1 AAATTTGTCAAAAAAATAGTGCCGCTAAAGTTCACT
* *
497501 AAATTTGTCGAAAACATAGTGCCGCTAAAGTTCACT
1 AAATTTGTCAAAAAAATAGTGCCGCTAAAGTTCACT
497537 AAATTT
1 AAATTT
497543 AGATGTGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (36 bp):
AAATTTGTCAAAAAAATAGTGCCGCTAAAGTTCACT
Found at i:498340 original size:2 final size:2
Alignment explanation
Indices: 498333--498357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
498323 ATAGTTTGTC
498333 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
498358 TAGAATTTAT
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:498540 original size:23 final size:23
Alignment explanation
Indices: 498513--498562 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
498503 TTTAAATACT
*
498513 TTAATTTTATTTTATTATTAATA
1 TTAATTTAATTTTATTATTAATA
* *
498536 TTAATTTAATTTTTTTATTAATT
1 TTAATTTAATTTTATTATTAATA
498559 TTAA
1 TTAA
498563 ACTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTAATTTAATTTTATTATTAATA
Found at i:501263 original size:17 final size:17
Alignment explanation
Indices: 501241--501273 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
501231 TTTTATTTTC
501241 ATGAAAGCATGCATGAA
1 ATGAAAGCATGCATGAA
*
501258 ATGAAAGTATGCATGA
1 ATGAAAGCATGCATGA
501274 GACGTATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (17 bp):
ATGAAAGCATGCATGAA
Found at i:501345 original size:33 final size:33
Alignment explanation
Indices: 501303--501373 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
501293 AATGCAATGC
501303 ATTTCTTTATTTTTGGCCAAGTTTGTTTATTCA
1 ATTTCTTTATTTTTGGCCAAGTTTGTTTATTCA
*
501336 ATTTCTTTATTTTTTGCCAAGTTTGTTTATTCA
1 ATTTCTTTATTTTTGGCCAAGTTTGTTTATTCA
501369 ATTTC
1 ATTTC
501374 ATGCATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (33 bp):
ATTTCTTTATTTTTGGCCAAGTTTGTTTATTCA
Found at i:501509 original size:21 final size:20
Alignment explanation
Indices: 501483--501523 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
501473 TTCGATTTCT
*
501483 TTTTTAAAATTTTTATTTTTA
1 TTTTTAAAATTATT-TTTTTA
501504 TTTTTAAAATTATTTTTTTA
1 TTTTTAAAATTATTTTTTTA
501524 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAAAATTATTTTTTTA
Found at i:501581 original size:14 final size:14
Alignment explanation
Indices: 501564--501590 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
501554 ATTATTATTG
501564 TTATTATATTTTTA
1 TTATTATATTTTTA
501578 TTATTATATTTTT
1 TTATTATATTTTT
501591 TATTTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATATTTTTA
Found at i:501593 original size:23 final size:22
Alignment explanation
Indices: 501554--501598 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
501544 TAATTAACTA
501554 ATTATTATTGTTATTATATTTTT
1 ATTATTATTGTTATTAT-TTTTT
*
501577 ATTATTATAT-TTTTTATTTTTT
1 ATTATTAT-TGTTATTATTTTTT
501599 GTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 14 0.70
24 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTATTATTGTTATTATTTTTT
Found at i:502908 original size:33 final size:33
Alignment explanation
Indices: 502851--502915 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
502841 CGTTAGAAGC
*
502851 AATGTATCGACACAATTCATCATGTATCGATAT
1 AATGTATCGACACAATTCACCATGTATCGATAT
* *
502884 AATGTATCGATACAATAT-ACCATGTGTCGATA
1 AATGTATCGACACAAT-TCACCATGTATCGATA
502916 CAAACAGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
AATGTATCGACACAATTCACCATGTATCGATAT
Found at i:502971 original size:19 final size:19
Alignment explanation
Indices: 502946--502994 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
502936 ACTTCTAGTT
502946 TCATGTATCGATA-AATTG-
1 TCATGTATCGATATAA-TGA
502964 TCCATGTATCGATATAATGA
1 T-CATGTATCGATATAATGA
502984 TCATGTATCGA
1 TCATGTATCGA
502995 CACAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 24 0.86
20 3 0.11
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (19 bp):
TCATGTATCGATATAATGA
Found at i:508814 original size:13 final size:13
Alignment explanation
Indices: 508796--508822 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
508786 ACATTATGCT
508796 TTGTATCGATACA
1 TTGTATCGATACA
508809 TTGTATCGATACA
1 TTGTATCGATACA
508822 T
1 T
508823 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:508928 original size:33 final size:33
Alignment explanation
Indices: 508872--508940 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
508862 CTACCACTGT
*
508872 TTGTATCGATACATGGTACATTGTATCAATAAA
1 TTGTATCGATACATGATACATTGTATCAATAAA
* *
508905 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACATTGTATCAATAAA
508938 TTG
1 TTG
508941 CTTGTTACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATACATTGTATCAATAAA
Found at i:509003 original size:20 final size:19
Alignment explanation
Indices: 508978--509064 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 19
508968 TTTAAATCAA
*
508978 TGTATCGATACATTATGAAT
1 TGTATCGATACATGAT-AAT
*
508998 TGTATCGATACATGGTACAT
1 TGTATCGATACATGATA-AT
509018 TGTATC---A-AT-A-AAT
1 TGTATCGATACATGATAAT
509031 TGTATCGATACATGATGAAT
1 TGTATCGATACATGAT-AAT
509051 TGTATCGATACATG
1 TGTATCGATACATG
509065 GCTACGGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
13 8 0.14
14 1 0.02
16 3 0.05
17 3 0.05
18 1 0.02
19 1 0.02
20 39 0.70
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:517143 original size:20 final size:20
Alignment explanation
Indices: 517115--517189 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
517105 TTTTACCTTG
517115 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
517135 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
517155 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
517175 ATGTATCGATACATT
1 ATGTATCGATACATT
517190 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:517182 original size:40 final size:39
Alignment explanation
Indices: 517115--517192 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
517105 TTTTACCTTG
* *
517115 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
517155 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
517193 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:521893 original size:20 final size:20
Alignment explanation
Indices: 521838--521894 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
521828 GTGTCGATTG
* *
521838 CTTTTGC-TTTTTCTTCTCT
1 CTTTTGCTTTTTTTTTCTCC
**
521857 CTTTTG-TTTTCAATTTCTCC
1 CTTTTGCTTTT-TTTTTCTCC
521877 CTTTTGCTTTTTTTTTCT
1 CTTTTGCTTTTTTTTTCT
521895 TTTATTCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 4 0.14
ACGTcount: A:0.04, C:0.23, G:0.05, T:0.68
Consensus pattern (20 bp):
CTTTTGCTTTTTTTTTCTCC
Found at i:522514 original size:17 final size:17
Alignment explanation
Indices: 522492--522584 Score: 97
Period size: 17 Copynumber: 5.8 Consensus size: 17
522482 CATTTGCATG
522492 AAAGCATGCATGAAGTA
1 AAAGCATGCATGAAGTA
* *
522509 AAAGCATGCATGAAATG
1 AAAGCATGCATGAAGTA
*
522526 AAAGAATGCAT---G--
1 AAAGCATGCATGAAGTA
*
522538 AAAGTATGCATGAAGTA
1 AAAGCATGCATGAAGTA
* *
522555 AAAGCATGCATGAAATG
1 AAAGCATGCATGAAGTA
522572 AAAGCATGCATGA
1 AAAGCATGCATGA
522585 CACGTATGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.16
15 1 0.02
17 52 0.83
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (17 bp):
AAAGCATGCATGAAGTA
Found at i:522536 original size:46 final size:46
Alignment explanation
Indices: 522486--522584 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
522476 GCATTTCATT
522486 TGCATGAAAGCATGCATGAAGTAAAAGCATGCATGAAATGAAAGAA
1 TGCATGAAAGCATGCATGAAGTAAAAGCATGCATGAAATGAAAGAA
* *
522532 TGCATGAAAGTATGCATGAAGTAAAAGCATGCATGAAATGAAAGCA
1 TGCATGAAAGCATGCATGAAGTAAAAGCATGCATGAAATGAAAGAA
522578 TGCATGA
1 TGCATGA
522585 CACGTATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.19
Consensus pattern (46 bp):
TGCATGAAAGCATGCATGAAGTAAAAGCATGCATGAAATGAAAGAA
Found at i:522541 original size:29 final size:29
Alignment explanation
Indices: 522509--522569 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
522499 GCATGAAGTA
*
522509 AAAGCATGCATGAAATGAAAGAATGCATG
1 AAAGCATGCATGAAATAAAAGAATGCATG
* * *
522538 AAAGTATGCATGAAGTAAAAGCATGCATG
1 AAAGCATGCATGAAATAAAAGAATGCATG
522567 AAA
1 AAA
522570 TGAAAGCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.23, T:0.18
Consensus pattern (29 bp):
AAAGCATGCATGAAATAAAAGAATGCATG
Found at i:522801 original size:31 final size:30
Alignment explanation
Indices: 522760--522819 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
522750 ATTCGATCTC
* * *
522760 TTTTTAAAAAAATTTATTTTTATTTTTTAAA
1 TTTTTAAAAAAAATTA-ATTAATTTTTTAAA
*
522791 TTTTTTAAAAAAATTAATTAATTTTTTAA
1 TTTTTAAAAAAAATTAATTAATTTTTTAA
522820 TTAACTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTAAAAAAAATTAATTAATTTTTTAAA
Found at i:522854 original size:14 final size:14
Alignment explanation
Indices: 522837--522896 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
522827 ATTATTATTG
522837 TTATTATATTTTTA
1 TTATTATATTTTTA
*
522851 TTATCATA-TTTTA
1 TTATTATATTTTTA
*
522864 TT-TTTTATTTTTTA
1 TTATTATA-TTTTTA
*
522878 TT-TTTTATTTTT-
1 TTATTATATTTTTA
522890 TTATTAT
1 TTATTAT
522897 TTATGTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 5 0.13
13 15 0.38
14 19 0.49
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTATATTTTTA
Found at i:522875 original size:8 final size:7
Alignment explanation
Indices: 522859--522900 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
522849 TATTATCATA
522859 TTTTATT
1 TTTTATT
522866 TTTTATT
1 TTTTATT
522873 TTTTATT
1 TTTTATT
522880 TTTTATTT
1 TTTTA-TT
522888 TTTTATT
1 TTTTATT
*
522895 ATTTAT
1 TTTTAT
522901 GTTAAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:522889 original size:15 final size:15
Alignment explanation
Indices: 522859--522900 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
522849 TATTATCATA
522859 TTTTATTTTTTA-TT
1 TTTTATTTTTTATTT
522873 TTTTATTTTTTATTT
1 TTTTATTTTTTATTT
*
522888 TTTTATTATTTAT
1 TTTTATTTTTTAT
522901 GTTAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTTTTTATTT
Found at i:524361 original size:22 final size:22
Alignment explanation
Indices: 524321--524363 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
524311 ATTAAGATAT
* * *
524321 TATTTTTATATTTATATTTATA
1 TATTTTTATAATAAAATTTATA
524343 TATTTTTATAATAAAATTTAT
1 TATTTTTATAATAAAATTTAT
524364 TTTTTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATAATAAAATTTATA
Found at i:524371 original size:17 final size:18
Alignment explanation
Indices: 524343--524376 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
524333 TATATTTATA
524343 TATTTTTATAATAAAATT
1 TATTTTTATAATAAAATT
524361 TATTTTT-TAATAAAAT
1 TATTTTTATAATAAAAT
524377 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTATAATAAAATT
Found at i:524445 original size:10 final size:10
Alignment explanation
Indices: 524379--524450 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
524369 AATAAAATAA
524379 TAATTTAAAT
1 TAATTTAAAT
* *
524389 TAAATCAAAT
1 TAATTTAAAT
*
524399 TATTTTAAAT
1 TAATTTAAAT
* **
524409 TTATAAAAAT
1 TAATTTAAAT
*
524419 TTATTTATAATT
1 TAATTTA-AA-T
524431 TAATTTAAAT
1 TAATTTAAAT
524441 TAA-TTAAAT
1 TAATTTAAAT
524450 T
1 T
524451 TATCAAATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
9 7 0.15
10 30 0.62
11 4 0.08
12 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:526063 original size:19 final size:18
Alignment explanation
Indices: 526023--526081 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
526013 AAATACATAT
*
526023 TATTAAA-TATTTATTTAT
1 TATTAAATTATTT-TTTAA
526041 TATTAAATTATATTTTTAA
1 TATTAAATTAT-TTTTTAA
* *
526060 TATTTAATTTTTTTTTTAA
1 TA-TTAAATTATTTTTTAA
526079 TAT
1 TAT
526082 AATTGGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 8 0.23
19 18 0.51
20 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTAAATTATTTTTTAA
Found at i:527170 original size:18 final size:18
Alignment explanation
Indices: 527147--527205 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
527137 ATATTTGATG
527147 AAAATTTTTAATAAAATT
1 AAAATTTTTAATAAAATT
* ***
527165 AAAA-TTCTATATTTGA-T
1 AAAATTTTTA-ATAAAATT
*
527182 AAATTTTTTAATAAAATT
1 AAAATTTTTAATAAAATT
527200 AAAATT
1 AAAATT
527206 ATTACTTATA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AAAATTTTTAATAAAATT
Found at i:527197 original size:35 final size:36
Alignment explanation
Indices: 527136--527205 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
527126 ATTAAATAAA
527136 TATATTTGATGAAAATTTTTAATAAAATTAAAATTC
1 TATATTTGATGAAAATTTTTAATAAAATTAAAATTC
*
527172 TATATTTGAT-AAATTTTTTAATAAAATTAAAATT
1 TATATTTGATGAAAATTTTTAATAAAATTAAAATT
527206 ATTACTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATTTGATGAAAATTTTTAATAAAATTAAAATTC
Found at i:527491 original size:26 final size:25
Alignment explanation
Indices: 527438--527504 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 25
527428 ATTTATAAAA
*
527438 ATTTATATTATATAAATTTTGATGT
1 ATTTATATTATATAAATTTTGATAT
*
527463 ATTTATATATATATTAATATTTTAATAT
1 ATTTATAT-TATA-TAA-ATTTTGATAT
*
527491 TTTTAATATTATAT
1 ATTT-ATATTATAT
527505 CTATATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 8 0.23
26 4 0.11
27 4 0.11
28 15 0.43
29 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTTATATTATATAAATTTTGATAT
Found at i:528006 original size:8 final size:8
Alignment explanation
Indices: 527993--528019 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
527983 GGCCCTTTAA
527993 TTTCTCTC
1 TTTCTCTC
528001 TTTCTCTC
1 TTTCTCTC
528009 TTTCTCTC
1 TTTCTCTC
528017 TTT
1 TTT
528020 TCTTCTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCTCTC
Found at i:534356 original size:30 final size:30
Alignment explanation
Indices: 534320--534377 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
534310 AAACTCGATA
* *
534320 AACTCGAGTGTTAAATCTAATTGACTCATT
1 AACTCGAGTATTAAATCCAATTGACTCATT
*
534350 AACTCGAGTATTATATCCAATTGACTCA
1 AACTCGAGTATTAAATCCAATTGACTCA
534378 ACCCAAAATG
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:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (30 bp):
AACTCGAGTATTAAATCCAATTGACTCATT
Found at i:534721 original size:27 final size:27
Alignment explanation
Indices: 534689--534743 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
534679 ACATGCACAC
*
534689 TGAATGAATGATTAGTAAATTTGCATG
1 TGAATGAATGATTAATAAATTTGCATG
534716 TGAATGAATGATTAATAAATTTGCATG
1 TGAATGAATGATTAATAAATTTGCATG
534743 T
1 T
534744 AAATCCAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (27 bp):
TGAATGAATGATTAATAAATTTGCATG
Found at i:541221 original size:27 final size:25
Alignment explanation
Indices: 541174--541223 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
541164 TGTTTCTTCA
**
541174 AATATTTATTTAATTGTTTAATTTT
1 AATATTTATTTAATTAATTAATTTT
541199 AATATTTATTTTTAATTAATTAATT
1 AATATTTA--TTTAATTAATTAATT
541224 ATTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
27 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
AATATTTATTTAATTAATTAATTTT
Found at i:541326 original size:31 final size:30
Alignment explanation
Indices: 541291--541391 Score: 68
Period size: 31 Copynumber: 3.4 Consensus size: 30
541281 TAAATTATCT
*
541291 AAAATTAAAATTAAGTGTCAAAATTCAATC
1 AAAAATAAAATTAAGTGTCAAAATTCAATC
* * *
541321 AAAAATAACATTTTAGTG-AAATAATTCAATC
1 AAAAATAA-AATTAAGTGTCAA-AATTCAATC
* *
541352 --AAAT-AAATTAGAATATCAAAATTCAAT-
1 AAAAATAAAATTA-AGTGTCAAAATTCAATC
541379 AACAAATTAAAAT
1 AA-AAA-TAAAAT
541392 ATAACTAGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
27 3 0.06
28 11 0.21
29 6 0.11
30 12 0.23
31 17 0.32
32 4 0.08
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAAATAAAATTAAGTGTCAAAATTCAATC
Found at i:542874 original size:20 final size:20
Alignment explanation
Indices: 542851--542923 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
542841 ACAATTCAAA
542851 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
542871 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
542892 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
542912 GTATCGATACAT
1 GTATCGATACAT
542924 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:542895 original size:21 final size:21
Alignment explanation
Indices: 542869--542944 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
542859 ACATGTTGCA
542869 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
542890 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
542910 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
542931 ATGTATCGATACAT
1 ATGTATCGATACAT
542945 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:542902 original size:41 final size:41
Alignment explanation
Indices: 542851--542944 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
542841 ACAATTCAAA
*
542851 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
542892 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
542933 GTATCGATACAT
1 GTATCGATACAT
542945 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:543001 original size:13 final size:13
Alignment explanation
Indices: 542983--543008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
542973 TACAGCAAGT
542983 ATGTATCGATACA
1 ATGTATCGATACA
542996 ATGTATCGATACA
1 ATGTATCGATACA
543009 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:546848 original size:15 final size:15
Alignment explanation
Indices: 546828--546858 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
546818 TAAAAATGTC
*
546828 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
546843 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
546858 C
1 C
546859 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:548951 original size:20 final size:21
Alignment explanation
Indices: 548872--548950 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
548862 AATGTCCAAA
*
548872 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
548892 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
548917 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
548937 TTGTATCGATACAT
1 ATGTATCGATACAT
548951 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:548955 original size:13 final size:13
Alignment explanation
Indices: 548937--548975 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
548927 ACATTTTTCT
548937 TTGTATCGATACA
1 TTGTATCGATACA
548950 TTGTATCGATACA
1 TTGTATCGATACA
*
548963 CTGTATCGATACA
1 TTGTATCGATACA
548976 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:550805 original size:33 final size:33
Alignment explanation
Indices: 550768--550830 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
550758 AATTTTGATA
550768 TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
*
550801 TGAATTATTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
550831 AATAAACGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (33 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
Found at i:551474 original size:20 final size:20
Alignment explanation
Indices: 551451--551523 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
551441 ACAATTCAAA
551451 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
551471 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
551492 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
551512 GTATCGATACAT
1 GTATCGATACAT
551524 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:551495 original size:21 final size:21
Alignment explanation
Indices: 551469--551544 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
551459 ACATGTTGCA
551469 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
551490 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
551510 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
551531 ATGTATCGATACAT
1 ATGTATCGATACAT
551545 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:551502 original size:41 final size:41
Alignment explanation
Indices: 551451--551544 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
551441 ACAATTCAAA
*
551451 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
551492 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
551533 GTATCGATACAT
1 GTATCGATACAT
551545 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:551601 original size:13 final size:13
Alignment explanation
Indices: 551583--551608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
551573 TACAGCAAGT
551583 ATGTATCGATACA
1 ATGTATCGATACA
551596 ATGTATCGATACA
1 ATGTATCGATACA
551609 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:552420 original size:16 final size:16
Alignment explanation
Indices: 552384--552429 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
552374 AATTTGAGTA
* *
552384 TTAAATTT-AATTAAT
1 TTAAATTTAAAATAAC
552399 TTAAATTTAAAATAAC
1 TTAAATTTAAAATAAC
552415 TTAAATTTAAAATAA
1 TTAAATTTAAAATAA
552430 TTCAAACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAAATAAC
Found at i:552907 original size:11 final size:11
Alignment explanation
Indices: 552885--552914 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
552875 CGTAAAAAAT
552885 TATAAA-ATAA
1 TATAAATATAA
552895 TATAAATATAA
1 TATAAATATAA
552906 TATAAATAT
1 TATAAATAT
552915 TTAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:553101 original size:19 final size:20
Alignment explanation
Indices: 553057--553104 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
553047 TAAAATTATT
553057 ATTTAAT-TATAAAATATAA
1 ATTTAATATATAAAATATAA
553076 ATATTAATATA-AAAATA-ATA
1 AT-TTAATATATAAAATATA-A
553096 ATTTAATAT
1 ATTTAATAT
553105 TTTATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 10 0.38
20 14 0.54
21 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAATATATAAAATATAA
Found at i:553111 original size:30 final size:32
Alignment explanation
Indices: 553077--553142 Score: 100
Period size: 30 Copynumber: 2.1 Consensus size: 32
553067 AAAATATAAA
553077 TATTAATATAAAAATAATAATTT-AA-TATTT
1 TATTAATATAAAAATAATAATTTAAATTATTT
* *
553107 TATTAATTTTAAAATAATAATTTAAATTATTT
1 TATTAATATAAAAATAATAATTTAAATTATTT
553139 TATT
1 TATT
553143 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 21 0.66
31 2 0.06
32 9 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTAATATAAAAATAATAATTTAAATTATTT
Found at i:557010 original size:13 final size:13
Alignment explanation
Indices: 556992--557018 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
556982 ACATTACTTA
556992 AATGTATCGATAC
1 AATGTATCGATAC
557005 AATGTATCGATAC
1 AATGTATCGATAC
557018 A
1 A
557019 CTGATCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:557185 original size:22 final size:21
Alignment explanation
Indices: 557160--557205 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
557150 TTAAAATTAT
*
557160 ATTTATTAAATTTTTAATATAA
1 ATTTATTAAATATTTAATA-AA
*
557182 ATTTATTAAATATTTGATAAA
1 ATTTATTAAATATTTAATAAA
557203 ATT
1 ATT
557206 GAACCAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTATTAAATATTTAATAAA
Found at i:569031 original size:28 final size:29
Alignment explanation
Indices: 568970--569033 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
568960 GGTCTTGAGG
*
568970 TGGTGGGGTTCGGGTAATGAGTTAGTGGCT
1 TGGT-GGGTTCGGGTAATGAGGTAGTGGCT
569000 TGGTGGGTT-GGGTAATTG-GGTAGCTGGC-
1 TGGTGGGTTCGGGTAA-TGAGGTAG-TGGCT
569028 TGGTGG
1 TGGTGG
569034 TGAGTTGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 16 0.52
29 11 0.35
30 4 0.13
ACGTcount: A:0.11, C:0.06, G:0.50, T:0.33
Consensus pattern (29 bp):
TGGTGGGTTCGGGTAATGAGGTAGTGGCT
Found at i:571172 original size:24 final size:25
Alignment explanation
Indices: 571127--571173 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
571117 TTTTTGAAAT
* *
571127 AATTGTAAATTTATTTTATATTTCA
1 AATTGTAAATTAATTTGATATTTCA
*
571152 AATTG-AAATTAATTTGGTATTT
1 AATTGTAAATTAATTTGATATTT
571174 TCAGTAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (25 bp):
AATTGTAAATTAATTTGATATTTCA
Found at i:571513 original size:15 final size:15
Alignment explanation
Indices: 571493--571522 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
571483 TCTTCTACTA
571493 TAATTTATTTATATT
1 TAATTTATTTATATT
571508 TAATTTATTTATATT
1 TAATTTATTTATATT
571523 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTATTTATATT
Found at i:572402 original size:40 final size:37
Alignment explanation
Indices: 572358--572497 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 37
572348 TTTAAAAAAT
*
572358 AATAAAAATTTTAAAAATAAAAATCATAAAAAATCTATAA
1 AATAAAAATTCTAAAAATAAAAAT-ATAAAAAAT-T-TAA
572398 AATAAAAA-TCTATAAAATAATAAATATATTATAAAATTTTAA
1 AATAAAAATTCTA-AAAATAA-AAATATA--A-AAAA-TTTAA
* *
572440 AACATAAAATTCAAAAAATTATAAAAT-TATAAAAATTTAA
1 AATA-AAAATTCTAAAAA-TA-AAAATATA-AAAAATTTAA
572480 AATAAAAATT-TAGAAAAT
1 AATAAAAATTCTA-AAAAT
572498 TAGAAAAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 24
0.74 0.04 0.21
Matches are distributed among these distances:
38 2 0.02
39 13 0.15
40 26 0.31
41 8 0.10
42 9 0.11
43 15 0.18
44 10 0.12
45 1 0.01
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.31
Consensus pattern (37 bp):
AATAAAAATTCTAAAAATAAAAATATAAAAAATTTAA
Found at i:572404 original size:15 final size:15
Alignment explanation
Indices: 572386--572422 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
572376 AAAAATCATA
572386 AAAAATCTATAAAAT
1 AAAAATCTATAAAAT
572401 AAAAATCTATAAAAT
1 AAAAATCTATAAAAT
572416 AATAAAT
1 AA-AAAT
572423 ATATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATCTATAAAAT
Found at i:572406 original size:25 final size:24
Alignment explanation
Indices: 572352--572414 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
572342 TAGAATTTTA
* * *
572352 AAAAATAATAAAAATTTTAAAAAT
1 AAAAATCATAAAAAATCTAAAAAT
572376 AAAAATCATAAAAAATCTATAAAAT
1 AAAAATCATAAAAAATCTA-AAAAT
572401 AAAAATCTATAAAA
1 AAAAATC-ATAAAA
572415 TAATAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 16 0.47
25 12 0.35
26 6 0.18
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATCATAAAAAATCTAAAAAT
Found at i:572474 original size:9 final size:9
Alignment explanation
Indices: 572352--572620 Score: 56
Period size: 9 Copynumber: 31.4 Consensus size: 9
572342 TAGAATTTTA
*
572352 AAAAATAAT
1 AAAAATTAT
572361 AAAAATT-T
1 AAAAATTAT
*
572369 TAAAA--AT
1 AAAAATTAT
*
572376 AAAAATCAT
1 AAAAATTAT
* *
572385 AAAAAATCT
1 AAAAATTAT
*
572394 ATAAA--AT
1 AAAAATTAT
572401 AAAAATCTAT
1 AAAAAT-TAT
*
572411 -AAAATAAT
1 AAAAATTAT
572419 AAATATATTAT
1 AAA-A-ATTAT
572430 -AAAATT-T
1 AAAAATTAT
* *
572437 TAAAA-CAT
1 AAAAATTAT
572445 -AAAATTCA-
1 AAAAATT-AT
572453 AAAAATTAT
1 AAAAATTAT
572462 -AAAATTAT
1 AAAAATTAT
572470 AAAAATT-T
1 AAAAATTAT
572478 --AAA--AT
1 AAAAATTAT
572483 AAAAATT-T
1 AAAAATTAT
*
572491 AGAAAATTAGA
1 A-AAAATTA-T
572502 AAAAATTAT
1 AAAAATTAT
**
572511 GAAAAGCCTAT
1 -AAAA-ATTAT
* *
572522 -GAACTTCA-
1 AAAAATT-AT
572530 AAAAACTTAT
1 AAAAA-TTAT
*
572540 AAAAAGTA-
1 AAAAATTAT
*
572548 AAAGAAATAT
1 AAA-AATTAT
572558 -AAAA--AT
1 AAAAATTAT
572564 AAAAATT-T
1 AAAAATTAT
572572 AGAAAATTAT
1 A-AAAATTAT
572582 -AAAA-TAT
1 AAAAATTAT
572589 ATAAAATT-T
1 A-AAAATTAT
572598 AAAAATTATTT
1 AAAAATTA--T
572609 AAAAATT-T
1 AAAAATTAT
572617 AAAA
1 AAAA
572621 TAAAAATAAA
Statistics
Matches: 194, Mismatches: 23, Indels: 87
0.64 0.08 0.29
Matches are distributed among these distances:
5 1 0.01
6 5 0.03
7 25 0.13
8 51 0.26
9 71 0.37
10 25 0.13
11 16 0.08
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:572585 original size:17 final size:16
Alignment explanation
Indices: 572552--572601 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
572542 AAAGTAAAAG
*
572552 AAATATA-AAAA-TAA
1 AAATATAGAAAATTTA
*
572566 AAATTTAGAAAATTATA
1 AAATATAGAAAATT-TA
*
572583 AAATATATAAAATTTA
1 AAATATAGAAAATTTA
572599 AAA
1 AAA
572602 ATTATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 6 0.21
15 4 0.14
16 6 0.21
17 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATATAGAAAATTTA
Found at i:572620 original size:18 final size:18
Alignment explanation
Indices: 572568--572621 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
572558 AAAAATAAAA
572568 ATTTAGAAAATTATAAAA-T
1 ATTTA-AAAATT-TAAAATT
*
572587 ATAT-AAAATTTAAAAATT
1 ATTTAAAAATTT-AAAATT
572605 ATTTAAAAATTTAAAAT
1 ATTTAAAAATTTAAAAT
572622 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 9 0.30
19 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTTAAAAATTTAAAATT
Found at i:572630 original size:37 final size:38
Alignment explanation
Indices: 572568--572642 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
572558 AAAAATAAAA
*
572568 ATTTAGAAAATTATAAAATATATAAAATT-TAAAAATT
1 ATTTAGAAAATTATAAAATAAATAAAATTGTAAAAATT
*
572605 ATTTA-AAAATT-TAAAATAAAAATAAAATTGTGAAAATT
1 ATTTAGAAAATTATAAAAT--AAATAAAATTGTAAAAATT
572643 GCAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.18
36 6 0.18
37 14 0.42
38 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (38 bp):
ATTTAGAAAATTATAAAATAAATAAAATTGTAAAAATT
Found at i:572674 original size:14 final size:16
Alignment explanation
Indices: 572646--572678 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
572636 GAAAATTGCA
572646 AAAAAATATAGAAAAG
1 AAAAAATATAGAAAAG
572662 AAAAAAT-TA-AAAAG
1 AAAAAATATAGAAAAG
572676 AAA
1 AAA
572679 TTATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAATATAGAAAAG
Found at i:572741 original size:18 final size:19
Alignment explanation
Indices: 572718--572773 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
572708 ATAAAAATCT
*
572718 ATAAAATTAAAAAATAAGA
1 ATAAAATTAAAAAATAAAA
572737 A-AAAATT-AAAAATAAAA
1 ATAAAATTAAAAAATAAAA
*
572754 ATAAAAAT-AAAAATAAAA
1 ATAAAATTAAAAAATAAAA
572772 AT
1 AT
572774 TCATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 10 0.29
18 23 0.68
19 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
ATAAAATTAAAAAATAAAA
Found at i:572747 original size:6 final size:6
Alignment explanation
Indices: 572727--572773 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
572717 TATAAAATTA
* *
572727 AAAAAT AAGAA- AAAATT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
572774 TCATAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:572860 original size:10 final size:9
Alignment explanation
Indices: 572829--573086 Score: 76
Period size: 9 Copynumber: 29.3 Consensus size: 9
572819 TGATAAAAAA
572829 TTTATGAATT
1 TTTAT-AATT
*
572839 TTT-TACAAT
1 TTTATA-ATT
572848 TTTATATATT
1 TTTATA-ATT
572858 TTTATAATT
1 TTTATAATT
*
572867 TTT-GAA-T
1 TTTATAATT
572874 TTT-T-A-T
1 TTTATAATT
*
572880 TTT-TAGTT
1 TTTATAATT
572888 TTTATAAATT
1 TTTAT-AATT
572898 TTT-TGAA-T
1 TTTAT-AATT
*
572906 TTGATAATTT
1 TTTATAA-TT
*
572916 TTTGTAATT
1 TTTATAATT
572925 TTT-TGAATTT
1 TTTAT-AA-TT
* *
572935 TATTTTTATT
1 T-TTATAATT
572945 TTTA-AATT
1 TTTATAATT
572953 TTTAATAA-T
1 TTT-ATAATT
*
572962 TTT-TAA-C
1 TTTATAATT
572969 TTTATAGATT
1 TTTATA-ATT
*
572979 TTTA-AACT
1 TTTATAATT
572987 TTTATAAGTT
1 TTTATAA-TT
*
572997 TTT-GAATT
1 TTTATAATT
573005 TTTACT--TT
1 TTTA-TAATT
*
573013 TTAATAATTT
1 TTTATAA-TT
573023 TTTAATAATT
1 TTT-ATAATT
573033 TTTATAATT
1 TTTATAATT
*
573042 TTT-TTA-T
1 TTTATAATT
*
573049 TTT-TCATT
1 TTTATAATT
573057 TTTA-AATTT
1 TTTATAA-TT
*
573066 TTTAAAATT
1 TTTATAATT
573075 TTT-TGAATT
1 TTTAT-AATT
573084 TTT
1 TTT
573087 TCTTTTTTCC
Statistics
Matches: 191, Mismatches: 26, Indels: 63
0.68 0.09 0.22
Matches are distributed among these distances:
6 6 0.03
7 17 0.09
8 44 0.23
9 64 0.34
10 52 0.27
11 7 0.04
12 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:572924 original size:58 final size:57
Alignment explanation
Indices: 572829--572955 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 57
572819 TGATAAAAAA
* *
572829 TTTATGAATTTTTTACAATTTTATATATTTTTATAA-TTTTTGAATTTTTATTTTTAGTT
1 TTTATAAATTTTTTACAATTTGATATATTTTTATAATTTTTTGAA-TTTTATTTTTA--T
* *
572888 TTTATAAATTTTTT-GAATTTGATA-ATTTTTTGTAATTTTTTGAATTTTATTTTTAT
1 TTTATAAATTTTTTACAATTTGATATA-TTTTTATAATTTTTTGAATTTTATTTTTAT
572944 TTT-TAAATTTTT
1 TTTATAAATTTTT
572956 AATAATTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
55 9 0.15
56 4 0.06
57 1 0.02
58 27 0.44
59 21 0.34
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.67
Consensus pattern (57 bp):
TTTATAAATTTTTTACAATTTGATATATTTTTATAATTTTTTGAATTTTATTTTTAT
Found at i:572953 original size:8 final size:8
Alignment explanation
Indices: 572942--573077 Score: 69
Period size: 8 Copynumber: 15.8 Consensus size: 8
572932 TTTTATTTTT
572942 ATTTTTAA
1 ATTTTTAA
572950 ATTTTTAATA
1 ATTTTT-A-A
572960 ATTTTTAA
1 ATTTTTAA
* * *
572968 CTTTATAG
1 ATTTTTAA
572976 ATTTTTAA
1 ATTTTTAA
572984 ACTTTTATAA
1 A-TTTT-TAA
* *
572994 GTTTTTGA
1 ATTTTTAA
573002 ATTTTT-A
1 ATTTTTAA
*
573009 CTTTTTAATA
1 ATTTTT-A-A
573019 ATTTTTTAATA
1 A-TTTTT-A-A
573030 ATTTTTATA
1 ATTTTTA-A
**
573039 ATTTTTTT
1 ATTTTTAA
*
573047 ATTTTT-C
1 ATTTTTAA
573054 ATTTTTAA
1 ATTTTTAA
573062 ATTTTTTAAA
1 A-TTTTT-AA
573072 ATTTTT
1 ATTTTT
573078 TGAATTTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
7 12 0.12
8 32 0.31
9 29 0.28
10 19 0.19
11 10 0.10
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (8 bp):
ATTTTTAA
Found at i:573026 original size:11 final size:11
Alignment explanation
Indices: 573010--573045 Score: 58
Period size: 10 Copynumber: 3.5 Consensus size: 11
573000 GAATTTTTAC
573010 TTTTTAATAAT
1 TTTTTAATAAT
573021 TTTTTAATAA-
1 TTTTTAATAAT
573031 TTTTT-ATAAT
1 TTTTTAATAAT
573041 TTTTT
1 TTTTT
573046 TATTTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.17
10 10 0.42
11 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:573087 original size:9 final size:9
Alignment explanation
Indices: 572886--573087 Score: 50
Period size: 10 Copynumber: 22.7 Consensus size: 9
572876 TTATTTTTAG
572886 TTTTTATAAA
1 TTTTT-TAAA
*
572896 TTTTTTGAA
1 TTTTTTAAA
**
572905 TTTGAT-AA
1 TTTTTTAAA
*
572913 TTTTTTGTAA
1 TTTTTT-AAA
*
572923 TTTTTTGAA
1 TTTTTTAAA
**
572932 TTTTATT-TT
1 TTTT-TTAAA
572941 TATTTTTAAA
1 T-TTTTTAAA
572951 -TTTTTAATA
1 TTTTTTAA-A
*
572960 ATTTTT-AA
1 TTTTTTAAA
* * *
572968 CTTTATAGA
1 TTTTTTAAA
572977 -TTTTTAAA
1 TTTTTTAAA
*
572985 -CTTTTATAA
1 TTTTTTA-AA
* *
572994 GTTTTTGAA
1 TTTTTTAAA
*
573003 -TTTTT-AC
1 TTTTTTAAA
*
573010 TTTTTAATAA
1 TTTTTTA-AA
573020 TTTTTTAATA
1 TTTTTTAA-A
*
573030 ATTTTTATAA
1 TTTTTTA-AA
*
573040 TTTTTT-TA
1 TTTTTTAAA
*
573048 -TTTTT-CA
1 TTTTTTAAA
573055 -TTTTTAAA
1 TTTTTTAAA
573063 TTTTTTAAAA
1 TTTTTT-AAA
*
573073 TTTTTTGAA
1 TTTTTTAAA
573082 TTTTTT
1 TTTTTT
573088 CTTTTTTCCT
Statistics
Matches: 146, Mismatches: 28, Indels: 37
0.69 0.13 0.18
Matches are distributed among these distances:
7 12 0.08
8 40 0.27
9 37 0.25
10 56 0.38
11 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:576310 original size:18 final size:18
Alignment explanation
Indices: 576287--576323 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
576277 AGATTATAAT
*
576287 TTATACTCATTGCAAACA
1 TTATACTCATTGAAAACA
*
576305 TTATACTCTTTGAAAACA
1 TTATACTCATTGAAAACA
576323 T
1 T
576324 GTTGAGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (18 bp):
TTATACTCATTGAAAACA
Found at i:580180 original size:97 final size:97
Alignment explanation
Indices: 580061--580280 Score: 289
Period size: 97 Copynumber: 2.3 Consensus size: 97
580051 TAAAAAATAA
* ** **
580061 GGTTGGAGTATCCTCTCAGAGGAATGGGGTT-AGAGTGTCCCCGATGATGACAATTTAAATAAGA
1 GGTTGGAGTATCCCCTTGGAGGAATAAGGTTGA-AGTGTCCCCGATGATGACAATTTAAATAAGA
*
580125 ATAAGATTTAAACTTTGACGCATTTTAAAGCGG
65 ATAAGATTTAAACTTTGACGCATTTAAAAGCGG
* * * * *
580158 GGTTAGAGTATCCCCTTGGAGGAATAAGGTTGAAGTGTCCCCGTTGGTGACAATTTAAGTGAGAA
1 GGTTGGAGTATCCCCTTGGAGGAATAAGGTTGAAGTGTCCCCGATGATGACAATTTAAATAAGAA
* * **
580223 TATGATTTAAACTTTGATGTGTTTAAAAGCGG
66 TAAGATTTAAACTTTGACGCATTTAAAAGCGG
580255 GGTTGGAGTATCCCCTTGGAGGAATA
1 GGTTGGAGTATCCCCTTGGAGGAATA
580281 GGATTGGAGT
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 105 0.99
98 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (97 bp):
GGTTGGAGTATCCCCTTGGAGGAATAAGGTTGAAGTGTCCCCGATGATGACAATTTAAATAAGAA
TAAGATTTAAACTTTGACGCATTTAAAAGCGG
Found at i:580310 original size:97 final size:97
Alignment explanation
Indices: 580107--580310 Score: 232
Period size: 97 Copynumber: 2.1 Consensus size: 97
580097 GTCCCCGATG
* *
580107 ATGACAATTTAAATAAGAATAAGATTTAAACTTTGACGCATTTTAAAGCGGGGTTAGAGTATCCC
1 ATGAAAATTTAAATAAGAATAAGATTTAAACTTTGACGCATTTAAAAGCGGGGTTAGAGTATCCC
* **
580172 CTTGGAGGAATAAGGTTGAAGTGTCCCCGTTG
66 CTTGGAGGAATAAGGTTGAAGTATCCCCGTAA
* * * * * * ** *
580204 GTGACAATTTAAGTGAGAATATGATTTAAACTTTGATGTGTTTAAAAGCGGGGTTGGAGTATCCC
1 ATGAAAATTTAAATAAGAATAAGATTTAAACTTTGACGCATTTAAAAGCGGGGTTAGAGTATCCC
* *
580269 CTTGGAGGAAT-AGGATTGGAGTATCCTCGATAA
66 CTTGGAGGAATAAGG-TTGAAGTATCCCCG-TAA
580302 AT-AAAATTT
1 ATGAAAATTT
580311 TGATTTTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
96 3 0.03
97 84 0.94
98 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (97 bp):
ATGAAAATTTAAATAAGAATAAGATTTAAACTTTGACGCATTTAAAAGCGGGGTTAGAGTATCCC
CTTGGAGGAATAAGGTTGAAGTATCCCCGTAA
Found at i:580545 original size:97 final size:97
Alignment explanation
Indices: 580377--580568 Score: 246
Period size: 97 Copynumber: 2.0 Consensus size: 97
580367 TCCTCAATGA
* * * *
580377 TGACAATTTAAGTGAGAATAAGATTCAAACTTTGATGCGTTTTAAAGCGGAGTTAGATTATCCCT
1 TGACAATTTAAGTGAGAATAAGATTCAAACTTTGATGCGTTTAAAAGAGGAGTTAGAGTATCCCC
* *
580442 TTGGAGGAA-CGGGATTGAAGTATCCCCGATGG
66 TCGGAGGAATAGGG-TTGAAGTATCCCCGATGG
* * *
580474 TGACAATTTAAGTGAGAATAAGATTTAAACTTT-AGTGTGTTTAAAAGTAGG-GTTGGAGTATCC
1 TGACAATTTAAGTGAGAATAAGATTCAAACTTTGA-TGCGTTTAAAAG-AGGAGTTAGAGTATCC
*
580537 CCTCGGAGGAATAGGGTTGGAGTATCCCCGAT
64 CCTCGGAGGAATAGGGTTGAAGTATCCCCGAT
580569 AAGTAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 1 0.01
97 76 0.93
98 5 0.06
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (97 bp):
TGACAATTTAAGTGAGAATAAGATTCAAACTTTGATGCGTTTAAAAGAGGAGTTAGAGTATCCCC
TCGGAGGAATAGGGTTGAAGTATCCCCGATGG
Found at i:580578 original size:269 final size:267
Alignment explanation
Indices: 580088--580624 Score: 808
Period size: 269 Copynumber: 2.0 Consensus size: 267
580078 AGAGGAATGG
* *
580088 GGTTAGAGTGTCCCCGATGATGACAATTTAAATAAGAATAAGATTTAAACTTTGACGCATTTTAA
1 GGTTAGAGTGTCCCCAATGATGACAATTTAAATAAGAATAAGATTCAAACTTTGACGCATTTTAA
* * *
580153 AGCGGGGTTAGAGTATCCCCTTGGAGGAATAAGGTTGAAGTGTCCCCGTTGGTGACAATTTAAGT
66 AGCGGAGTTAGAGTATCCCCTTGGAGGAATAAGGTTGAAGTATCCCCGATGGTGACAATTTAAGT
* * *
580218 GAGAATATGATTTAAACTTTGATGTGTTTAAAAGCGGGGTTGGAGTATCCCCTTGGAGGAATAGG
131 GAGAATAAGATTTAAACTTTGATGTGTTTAAAAGCAGGGTTGGAGTATCCCCTCGGAGGAATAGG
* *
580283 ATTGGAGTATCCTCGATAAATAAAATTTTGATTTTTTTATAAAGAAAATTAATGTGAACGAGGAT
196 ATTGGAGTATCCCCGATAAATAAAATTTT-AATTTTTTAT-AAGAAAATTAATGTGAACGAGGAT
580348 GGTAATGAT
259 GGTAATGAT
* * * * * *
580357 GGTTGGAGTGTCCTCAATGATGACAATTTAAGTGAGAATAAGATTCAAACTTTGATGCGTTTTAA
1 GGTTAGAGTGTCCCCAATGATGACAATTTAAATAAGAATAAGATTCAAACTTTGACGCATTTTAA
* * **
580422 AGCGGAGTTAGATTATCCCTTTGGAGGAA-CGGGATTGAAGTATCCCCGATGGTGACAATTTAAG
66 AGCGGAGTTAGAGTATCCCCTTGGAGGAATAAGG-TTGAAGTATCCCCGATGGTGACAATTTAAG
*
580486 TGAGAATAAGATTTAAACTTT-AGTGTGTTTAAAAGTAGGGTTGGAGTATCCCCTCGGAGGAATA
130 TGAGAATAAGATTTAAACTTTGA-TGTGTTTAAAAGCAGGGTTGGAGTATCCCCTCGGAGGAATA
* * *
580550 GGGTTGGAGTATCCCCGATAAGTAAAATTTTAATTTTTTATAAGAAAATTAATGTGAATGAGGAT
194 GGATTGGAGTATCCCCGATAAATAAAATTTTAATTTTTTATAAGAAAATTAATGTGAACGAGGAT
580615 GGTAATGAT
259 GGTAATGAT
580624 G
1 G
580625 TAAAAGTATT
Statistics
Matches: 242, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
267 33 0.14
268 12 0.05
269 197 0.81
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (267 bp):
GGTTAGAGTGTCCCCAATGATGACAATTTAAATAAGAATAAGATTCAAACTTTGACGCATTTTAA
AGCGGAGTTAGAGTATCCCCTTGGAGGAATAAGGTTGAAGTATCCCCGATGGTGACAATTTAAGT
GAGAATAAGATTTAAACTTTGATGTGTTTAAAAGCAGGGTTGGAGTATCCCCTCGGAGGAATAGG
ATTGGAGTATCCCCGATAAATAAAATTTTAATTTTTTATAAGAAAATTAATGTGAACGAGGATGG
TAATGAT
Found at i:582228 original size:13 final size:12
Alignment explanation
Indices: 582201--582238 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
582191 TTTGTTTCTA
*
582201 TTTCTTCTTTAT
1 TTTCTTCTTTTT
582213 TTTCTCTCTTTTT
1 TTTCT-TCTTTTT
582226 TTT-TTCTTTTT
1 TTTCTTCTTTTT
582237 TT
1 TT
582239 AGTTGAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 9 0.38
12 6 0.25
13 9 0.38
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:582939 original size:165 final size:165
Alignment explanation
Indices: 582762--583108 Score: 360
Period size: 165 Copynumber: 2.1 Consensus size: 165
582752 TAAAATTTTC
* * * ** *
582762 AAAACTGAATTAATAGGAGTTC-ATGACATTATTAGATGAATTCTAAAATTTTTAAATTGAAAAA
1 AAAACTGAATTAATAGGA-ATCAATGACAGTATTAGATGAATTCTAAAAATTAAAAAATG-AAAA
* * * *
582826 AAATC-CTTCCAAAAAAA-TTACGGAGAAGAAAACTCAGTTTTTTCAAAAAAAAGAGATTTTCAA
64 AAATCTCTT-CAAAAAAATTTACGGAGAAGAAAACACAG-TATTTCAAAAAAAAAAGAATTTCAA
** *
582889 AG-AAAAATTCAAAACTCATAAAAATGAATGAATTTTGG
127 AGAAAAAATAAAAAACTCATAAAAAGGAATGAATTTTGG
* * ** * * * *
582927 AAAATTGAATTAATATGAATCAAATGATGGTGTTTGATGAATTTTAAAAATTAAAAAATGAGAAA
1 AAAACTGAATTAATAGGAATC-AATGACAGTATTAGATGAATTCTAAAAATTAAAAAATGAAAAA
** *
582992 AATCTCTTCAAAAAAATTTACGGAGTTGAAAACACCGTATTTCAAAAAAAAAAGAATTTCAAAGA
65 AATCTCTTCAAAAAAATTTACGGAGAAGAAAACACAGTATTTCAAAAAAAAAAGAATTTCAAAG-
* **
583057 AAAAAATAAAAAACTCATGAAAAGGAATGAATTTTTA
129 AAAAAATAAAAAACTCATAAAAAGGAATGAATTTTGG
*
583094 AAAACTGAATAAATA
1 AAAACTGAATTAATA
583109 TGAAATAAAT
Statistics
Matches: 147, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
164 2 0.01
165 56 0.38
166 46 0.31
167 43 0.29
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (165 bp):
AAAACTGAATTAATAGGAATCAATGACAGTATTAGATGAATTCTAAAAATTAAAAAATGAAAAAA
ATCTCTTCAAAAAAATTTACGGAGAAGAAAACACAGTATTTCAAAAAAAAAAGAATTTCAAAGAA
AAAATAAAAAACTCATAAAAAGGAATGAATTTTGG
Found at i:583802 original size:32 final size:31
Alignment explanation
Indices: 583733--583816 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
583723 TAGGTGCTAC
**
583733 CAACTTGTGTGGGCTTTGACTAGGGTGCCAT
1 CAACTTGTGTGGGCTTTGAAAAGGGTGCCAT
*
583764 CAACTTGTGTGGGCTTTAAAAAGGGTTGCCA-
1 CAACTTGTGTGGGCTTTGAAAAGGG-TGCCAT
*
583795 CTGAC-T-TGTGGGCTTTGAAAAG
1 C-AACTTGTGTGGGCTTTGAAAAG
583817 TGGCTATTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.33
31 24 0.52
32 7 0.15
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (31 bp):
CAACTTGTGTGGGCTTTGAAAAGGGTGCCAT
Found at i:584007 original size:85 final size:84
Alignment explanation
Indices: 583771--584175 Score: 433
Period size: 85 Copynumber: 4.8 Consensus size: 84
583761 CATCAACTTG
* * * * * * *
583771 TGTGGGCTTTAAAAAGGGTTGCCACTGACTTGTGGGCTTTGAAAAG-TGGCTATTGGCTTGTTGG
1 TGTGGGCTTTGAAAA--GATGCCACTGACTTGTGGACTTTGAAAAGAT-GCCACTGACTTGTGGG
*
583835 CTTTTGAAAGG-TGCCACAGACT
63 C-TTTGAAAGGATGCCACTGACT
* * * * * * *
583857 TGTTGGTTTTG-AAAGGTGCCATTGACTTGTAGG-CTTTG-AAAGGTGCCACTAACATGTGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGT-GGACTTTGAAAAGATGCCACTGACTTGTGGGCT
*
583919 TTGAAAGGATGCCACTGATT
65 TTGAAAGGATGCCACTGACT
* * *
583939 TATGGGCTTTGAAAAGATGCCACTGACTTGTGGACTTTTGAAAGGATGCCACTGACTTGTGGGAT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGAC-TTTGAAAAGATGCCACTGACTTGTGGGCT
584004 TTGAAAGGATGCCACTGACT
65 TTGAAAGGATGCCACTGACT
* *
584024 TGTGGACTTTGAAAAGATGCCACTGACTTGTGGACTTTGAAAAGATGCTACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACTTGTGGGCTT
*
584089 TGAAAGGATGCCACTGATT
66 TGAAAGGATGCCACTGACT
* * * * * * * *
584108 TGTGAGCTTTAAAAAAGATGTCACTGACTCGTGGGCTTTAAAAAAGATGCCACTGACTTATGAGC
1 TGTGGGCTTT-GAAAAGATGCCACTGACTTGTGGACTTT-GAAAAGATGCCACTGACTTGTGGGC
584173 TTT
64 TTT
584176 AAAAAGAGTC
Statistics
Matches: 270, Mismatches: 40, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
81 9 0.03
82 34 0.13
83 38 0.14
84 59 0.22
85 98 0.36
86 32 0.12
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (84 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACTTGTGGGCTT
TGAAAGGATGCCACTGACT
Found at i:584111 original size:28 final size:28
Alignment explanation
Indices: 583771--584175 Score: 413
Period size: 28 Copynumber: 14.4 Consensus size: 28
583761 CATCAACTTG
* *
583771 TGTGGGCTTTAAAAAGGGTTGCCACTGACT
1 TGTGGGCTTT-GAAA-GGATGCCACTGACT
* * * *
583801 TGTGGGCTTTGAAAAG-TGGCTATTGGCT
1 TGTGGGCTTTGAAAGGAT-GCCACTGACT
* *
583829 TGTTGGCTTTTGAAAGG-TGCCACAGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* * *
583857 TGTTGGTTTTGAAAGG-TGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
583884 TGTAGGCTTTGAAAGG-TGCCACTAACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
583911 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
583939 TATGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
583967 TGTGGACTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
*
583996 TGTGGGATTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
584024 TGTGGACTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
584052 TGTGGACTTTGAAAAGATGCTACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
584080 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
584108 TGTGAGCTTTAAAAAAGATGTCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
584137 CGTGGGCTTTAAAAAAGATGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* *
584166 TATGAGCTTT
1 TGTGGGCTTT
584176 AAAAAGAGTC
Statistics
Matches: 320, Mismatches: 50, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
27 56 0.17
28 170 0.53
29 84 0.26
30 10 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:585487 original size:15 final size:14
Alignment explanation
Indices: 585467--585502 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
585457 TAGACCCTTC
585467 TTTTTTGTTTGTTT
1 TTTTTTGTTTGTTT
*
585481 GTTTTTTTTTTGTTT
1 -TTTTTTGTTTGTTT
585496 TTTTTTG
1 TTTTTTG
585503 GGTATTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTTGTTTGTTT
Found at i:595415 original size:13 final size:13
Alignment explanation
Indices: 595397--595423 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
595387 TATTACTCAA
595397 TGTATCGATACAT
1 TGTATCGATACAT
595410 TGTATCGATACAT
1 TGTATCGATACAT
595423 T
1 T
595424 TGATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:607230 original size:22 final size:23
Alignment explanation
Indices: 607205--607265 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
607195 GCGTCCTTCG
* *
607205 CAAAGAAAAAAAGAAG-AAAAAA
1 CAAAAAAAAAAAAAAGAAAAAAA
607227 CAAACAAACAAAAAAAAAGAAAAAAA
1 C-AA-AAA-AAAAAAAAAGAAAAAAA
*
607253 CAAACAAAAAAAA
1 CAAAAAAAAAAAA
607266 CAAACAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.03
23 9 0.28
24 4 0.12
25 11 0.34
26 7 0.22
ACGTcount: A:0.84, C:0.10, G:0.07, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAAAAAAAGAAAAAAA
Found at i:607233 original size:4 final size:4
Alignment explanation
Indices: 607224--607291 Score: 56
Period size: 4 Copynumber: 17.8 Consensus size: 4
607214 AAAGAAGAAA
* * *
607224 AAAC AAAC AAAC AAA- AAA- AAAG AAAA AAAC AAAC AAAAA AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC -AAAC AAAC AAAC
607271 AAAC AGAA- AAA- AAAC -AAC AAA
1 AAAC A-AAC AAAC AAAC AAAC AAA
607292 AAGGGTCCGG
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
3 14 0.25
4 36 0.65
5 5 0.09
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:607240 original size:26 final size:25
Alignment explanation
Indices: 607205--607265 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
607195 GCGTCCTTCG
607205 CAAAGAAAAAAAGAAG-AAAAAACAAA
1 CAAA-AAAAAAA-AAGAAAAAAACAAA
607231 CAAACAAAAAAAAAGAAAAAAACAAA
1 CAAA-AAAAAAAAAGAAAAAAACAAA
607257 CAAAAAAAA
1 CAAAAAAAA
607266 CAAACAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.84, C:0.10, G:0.07, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAAAAAGAAAAAAACAAA
Found at i:607243 original size:17 final size:18
Alignment explanation
Indices: 607222--607291 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
607212 AAAAAGAAGA
*
607222 AAAAACAAACAAACAAAA
1 AAAAACAAACAAACAAAC
* *
607240 AAAAAGAAAAAAACAAAC
1 AAAAACAAACAAACAAAC
607258 AAAAA-AAACAAACAAAC
1 AAAAACAAACAAACAAAC
*
607275 AGAAAAAAAAC-AACAAA
1 A-AAAACAAACAAACAAA
607292 AAGGGTCCGG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.26
18 30 0.65
19 4 0.09
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAACAAACAAACAAAC
Found at i:607279 original size:31 final size:30
Alignment explanation
Indices: 607210--607293 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
607200 CTTCGCAAAG
* *
607210 AAAAAAAG-AAGAAAAAAC-AAACAAACAA
1 AAAAAAAGAAAAAAAAAACAAAAAAAACAA
607238 AAAAAAAGAAAAAAACAAACAAAAAAAACAA
1 AAAAAAAGAAAAAAA-AAACAAAAAAAACAA
* *
607269 ACAAACAGAAAAAAAACAACAAAAA
1 AAAAAAAGAAAAAAAA-AACAAAAA
607294 GGGTCCGGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.17
29 5 0.10
30 5 0.10
31 30 0.62
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (30 bp):
AAAAAAAGAAAAAAAAAACAAAAAAAACAA
Found at i:607283 original size:22 final size:21
Alignment explanation
Indices: 607221--607291 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 21
607211 AAAAAAGAAG
607221 AAAAAACAAACAAAC-AAAAA
1 AAAAAACAAACAAACAAAAAA
* *
607241 AAAAGA-AAA-AAACAAACAA
1 AAAAAACAAACAAACAAAAAA
607260 AAAAAACAAACAAACAGAAAAA
1 AAAAAACAAACAAACA-AAAAA
*
607282 AAACAACAAA
1 AAAAAACAAA
607292 AAGGGTCCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 4 0.10
19 12 0.29
20 8 0.19
21 5 0.12
22 13 0.31
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (21 bp):
AAAAAACAAACAAACAAAAAA
Found at i:607551 original size:39 final size:39
Alignment explanation
Indices: 607507--607585 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
607497 CTAAAAAGCA
607507 TTCATGTCACAGTTACCAAAGGCGTCTTTCGTCTAAAAT
1 TTCATGTCACAGTTACCAAAGGCGTCTTTCGTCTAAAAT
607546 TTCATGTCACAGTTACCAAAGGCGTCTTTCGTCTAAAAT
1 TTCATGTCACAGTTACCAAAGGCGTCTTTCGTCTAAAAT
607585 T
1 T
607586 AATCCTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (39 bp):
TTCATGTCACAGTTACCAAAGGCGTCTTTCGTCTAAAAT
Found at i:608831 original size:28 final size:28
Alignment explanation
Indices: 608762--608999 Score: 255
Period size: 28 Copynumber: 8.5 Consensus size: 28
608752 TCACCATTTT
* *
608762 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCC
608791 AAAGCCCACAAGTCAGTGGCAACCTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTCC
* *
608819 AAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCC
* * * *
608847 AAAGCCCATAAGTCAGTGGCATCTTTTCT
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCC
* * *
608876 AAAGCCCACAAATCAGTGGCAATCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCC
* * *
608904 AAAGCGCACAAGTCAGTGGCACCCCTTTC
1 AAAGCCCACAAGTCAGTGGCA-ACCTTCC
* * *
608933 AAA-CCCACAAGTCAGTGGTATCCTTTC
1 AAAGCCCACAAGTCAGTGGCAACCTTCC
* *
608960 AAAG-CCACAAGTGAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCC
*
608987 AAAGCACACAAGT
1 AAAGCCCACAAGT
609000 TGATGCAACC
Statistics
Matches: 177, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
27 31 0.18
28 96 0.54
29 50 0.28
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCC
Found at i:608880 original size:57 final size:56
Alignment explanation
Indices: 608761--609025 Score: 245
Period size: 57 Copynumber: 4.7 Consensus size: 56
608751 CTCACCATTT
* * * *
608761 TAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTC
1 TAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCAACTTTC
* * * *
608818 CAAAGCCCATAAGTCAGTGGCAACCTTCAAAAGCCCATAAGTCAGTGGCATCTTTTC
1 TAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAAC-TTTC
* * * *
608875 TAAAGCCCACAAATCAGTGGCAATCTTCAAAAGCGCACAAGTCAGTGGCACCCCTTTC
1 TAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCA--ACTTTC
* * * *
608933 -AAA-CCCACAAGTCAGTGGTATCCTTTC-AAAG-CCACAAGTGAGTGGCAACCTTC
1 TAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCAACTTTC
* * *
608986 AAAAGCACACAAGT-TGAT-GCAACCCTTTCAAAAGCCCACA
1 TAAAGCCCACAAGTCAG-TGGCAA-CC-TTCAAAAGCCCACA
609026 CAAGTTGGTG
Statistics
Matches: 171, Mismatches: 27, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
53 4 0.02
54 6 0.04
55 29 0.17
56 48 0.28
57 79 0.46
58 4 0.02
59 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (56 bp):
TAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACTTTC
Found at i:608908 original size:85 final size:85
Alignment explanation
Indices: 608753--608999 Score: 322
Period size: 85 Copynumber: 2.9 Consensus size: 85
608743 AGACATTCCT
*
608753 CACCATTTTAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTC
1 CACC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTT-CAAAGCCCACAAGTCAGTGGCAACCTTC
* *
608818 CAAAGCCCATAAGTCAGTGGCA
64 AAAAGCCCACAAGTCAGTGGCA
* * *
608840 -ACC-TTCAAAAGCCCATAAGTCAGTGGCATCTTTTCTAAAGCCCACAAATCAGTGGCAATCTTC
1 CACCTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTC
*
608903 AAAAGCGCACAAGTCAGTGGCA
64 AAAAGCCCACAAGTCAGTGGCA
* * * *
608925 CCCCTTTCAAA-CCCACAAGTCAGTGGTATCCTTTCAAAG-CCACAAGTGAGTGGCAACCTTCAA
1 CACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAA
*
608988 AAGCACACAAGT
66 AAGCCCACAAGT
609000 TGATGCAACC
Statistics
Matches: 141, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
83 32 0.23
84 7 0.05
85 91 0.65
86 8 0.06
87 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.21
Consensus pattern (85 bp):
CACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAA
AAGCCCACAAGTCAGTGGCA
Found at i:609012 original size:28 final size:30
Alignment explanation
Indices: 608762--609037 Score: 131
Period size: 28 Copynumber: 9.7 Consensus size: 30
608752 TCACCATTTT
* * * * *
608762 AAAGCCCACAAG-TCAGTGGCATCTTTTCC
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
* * *
608791 AAAGCCCACAAG-TCAGTGGCAACC-TTCC
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
* * *
608819 AAAGCCCATAAG-TCAGTGGCAACC-TTCA
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
* * * * * *
608847 AAAGCCCATAAG-TCAGTGGCATCTTTTCT
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
* * * *
608876 AAAGCCCACAA-ATCAGTGGCAATC-TTCA
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
* * *
608904 AAAGCGCACAAG-TCAGTGGCACCCCTTTC-
1 AAAGCACACAAGTTGAGTGGCA-ACCTTTCA
* * * *
608933 AAA-CCCACAAG-TCAGTGGTATCCTTTC-
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
608960 AAAGC-CACAAG-TGAGTGGCAACC-TTCA
1 AAAGCACACAAGTTGAGTGGCAACCTTTCA
608987 AAAGCACACAAGTTGA-T-GCAACCCTTTCA
1 AAAGCACACAAGTTGAGTGGCAA-CCTTTCA
609016 AAAGCCCACACAAGTTG-GTGGC
1 AAAG--CACACAAGTTGAGTGGC
609038 GTCTTCTTCT
Statistics
Matches: 211, Mismatches: 21, Indels: 27
0.81 0.08 0.10
Matches are distributed among these distances:
26 3 0.01
27 33 0.16
28 99 0.47
29 59 0.28
30 3 0.01
31 12 0.06
32 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (30 bp):
AAAGCACACAAGTTGAGTGGCAACCTTTCA
Found at i:609173 original size:22 final size:21
Alignment explanation
Indices: 609107--609173 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
609097 AAAACCAAAA
609107 ATCGCTGGCCTTGAATCAGCAT
1 ATCG-TGGCCTTGAATCAGCAT
* *** *
609129 ATTGACACCTTGAAGTCCG-AT
1 ATCGTGGCCTTGAA-TCAGCAT
609150 ATCGTTGGCCTTGAATCAGCAT
1 ATCG-TGGCCTTGAATCAGCAT
609172 AT
1 AT
609174 TGGCACCGGC
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (21 bp):
ATCGTGGCCTTGAATCAGCAT
Found at i:609340 original size:39 final size:39
Alignment explanation
Indices: 609277--609353 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
609267 CCTTGTCTTT
* *
609277 AAGTCCAATGTCGCTGACCTTGAATCAGCACATTGGCAC
1 AAGTCCAATATCGCTGACCGTGAATCAGCACATTGGCAC
* * *
609316 AAGTCCAATATCGTTGGCCGTGAATCAGCATATTGGCA
1 AAGTCCAATATCGCTGACCGTGAATCAGCACATTGGCA
609354 TCTTTATCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (39 bp):
AAGTCCAATATCGCTGACCGTGAATCAGCACATTGGCAC
Found at i:609340 original size:87 final size:88
Alignment explanation
Indices: 609051--609353 Score: 317
Period size: 87 Copynumber: 3.4 Consensus size: 88
609041 TTCTTCTAAA
* * ** * *** *
609051 TCCAATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCAAAAATCGCTGGC
1 TCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-GGATCTTTAAGACCAATGTTCGCTGAC
* *
609116 CTTGAATCAGCATATTGACACCTTGAAG
65 CTTGAATCAGCACATTGGCA-C---AAG
*
609144 TCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCGGCATCTTTAAGACCAATGTTC-CTGAC
1 TCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCGG-ATCTTTAAGACCAATGTTCGCTGAC
* *
609208 CTTGAATCAACACATTGGCATAAG
65 CTTGAATCAGCACATTGGCACAAG
* * * * * *
609232 CCCAATATCGCTGGCTTTGAAT-AGGCGTATTGGCACCTTG-TCTTTAAGTCCAATG-TCGCTGA
1 TCCAATATCGTTGGCCTTGAATCA-GCATATTGGCACC-GGATCTTTAAGACCAATGTTCGCTGA
609294 CCTTGAATCAGCACATTGGCACAAG
64 CCTTGAATCAGCACATTGGCACAAG
*
609319 TCCAATATCGTTGGCCGTGAATCAGCATATTGGCA
1 TCCAATATCGTTGGCCTTGAATCAGCATATTGGCA
609354 TCTTTATCAC
Statistics
Matches: 177, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
86 2 0.01
87 70 0.40
88 34 0.19
89 1 0.01
92 21 0.12
93 49 0.28
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (88 bp):
TCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCGGATCTTTAAGACCAATGTTCGCTGACC
TTGAATCAGCACATTGGCACAAG
Found at i:610178 original size:21 final size:20
Alignment explanation
Indices: 610148--610186 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
610138 TCACATTTTG
610148 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
610168 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
610187 AGGTCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:610337 original size:13 final size:13
Alignment explanation
Indices: 610319--610345 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
610309 CATTACTCAA
610319 TGTATCGATACAT
1 TGTATCGATACAT
610332 TGTATCGATACAT
1 TGTATCGATACAT
610345 T
1 T
610346 TGATCTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:615595 original size:97 final size:97
Alignment explanation
Indices: 615479--615708 Score: 329
Period size: 97 Copynumber: 2.4 Consensus size: 97
615469 TGAAAAATGG
* *
615479 GGTTAGAGTATCCCTTCGGAGGAATGGGGTTGGAGTGTC-CTCGATGATGACAATTTAAGTGAGA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCTC-CGATGATGACAATTTAAGTGAGA
615543 ATAAGATTTAAACTTTGATGCGTTTTAAAA-CAA
65 ATAAGATTTAAACTTTGATGCG-TTTAAAAGCAA
* *
615576 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCTCCGATGGTGACAATTTAAGTGAGAA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCTCCGATGATGACAATTTAAGTGAGAA
* ***
615641 TAAGATTTAAACTTTGATGTGTTTAAAAGTGG
66 TAAGATTTAAACTTTGATGCGTTTAAAAGCAA
* **
615673 GGTTGGAGTATCCCCTTGGAGGAATACGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGT
615709 ATTCCTGATA
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
96 7 0.06
97 111 0.93
98 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.30
Consensus pattern (97 bp):
GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCTCCGATGATGACAATTTAAGTGAGAA
TAAGATTTAAACTTTGATGCGTTTAAAAGCAA
Found at i:615996 original size:97 final size:97
Alignment explanation
Indices: 615793--615981 Score: 229
Period size: 97 Copynumber: 1.9 Consensus size: 97
615783 GTCCCTGATG
* ** * *
615793 ATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCTTTTTAAAGCGAGGTTGGAGTATCCT
1 ATGAAAATTTAAGTGAGAATAAGATTTAAACTTTGATGCTTTCAAAAGCGAGGTTGAAGTATCCC
* * *
615858 CTCGGAGGAATAGGGTTAAAGTGTCCCATATG
66 CTCGGAGGAATAGGCTTAAAGTATCCCATATA
* * *
615890 GTGACAATTTAAGTGAGAATAAGATTTAAACTTTGATG-TGTTCAAAAGTG-GAGTTGAAGTATC
1 ATGAAAATTTAAGTGAGAATAAGATTTAAACTTTGATGCT-TTCAAAAGCGAG-GTTGAAGTATC
**
615953 CCCTCGGAGGAATAGGCTTGGAGTATCCC
64 CCCTCGGAGGAATAGGCTTAAAGTATCCC
615982 CGATAAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 2 0.03
97 78 0.98
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (97 bp):
ATGAAAATTTAAGTGAGAATAAGATTTAAACTTTGATGCTTTCAAAAGCGAGGTTGAAGTATCCC
CTCGGAGGAATAGGCTTAAAGTATCCCATATA
Found at i:616006 original size:268 final size:269
Alignment explanation
Indices: 615508--616044 Score: 850
Period size: 268 Copynumber: 2.0 Consensus size: 269
615498 AGGAATGGGG
*
615508 TTGGAGTGTCCTCGATGATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCGTTTTAAAA
1 TTGGAGAGTCCTCGATGATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCGTTTTAAAA
* *
615573 CAAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCTCCGATGGTGACAATTTAAGTGA
66 CAAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTAAAGTGTCTCCGATGGTGACAATTTAAGTGA
* * * *
615638 GAATAAGATTTAAACTTTGATGTGTTTAAAAGTGGGGTTGGAGTATCCCCTTGGAGGAATACGGT
131 GAATAAGATTTAAACTTTGATGTGTTCAAAAGTGGAGTTGAAGTATCCCCTCGGAGGAATACGGT
* * *
615703 TGGAGTATTCCTGATAAATAAAATTTTGATTTTTTTAT-AAGAAAATTGATGTGAACAAGGATGG
196 TGGAGTATCCCCGATAAATAAAATTTTGATTTTTTTATAAAGAAAATTAATGTGAACAAGGATGG
*
615767 TGATGATGT
261 TAATGATGT
*
615776 TTGGAGAGTCC-CTGATGATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCTTTTTAAA
1 TTGGAGAGTCCTC-GATGATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCGTTTTAAA
* * * *
615840 GCGAGGTTGGAGTATCCTCTCGGAGGAATAGGGTTAAAGTGTC-CCATATGGTGACAATTTAAGT
65 ACAAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTAAAGTGTCTCC-GATGGTGACAATTTAAGT
615904 GAGAATAAGATTTAAACTTTGATGTGTTCAAAAGTGGAGTTGAAGTATCCCCTCGGAGGAATA-G
129 GAGAATAAGATTTAAACTTTGATGTGTTCAAAAGTGGAGTTGAAGTATCCCCTCGGAGGAATACG
*
615968 GCTTGGAGTATCCCCGATAAATAAAATTTT-AGTTTTTTTATAAAGAAAATTAATGTGAACGAGG
194 G-TTGGAGTATCCCCGATAAATAAAATTTTGA-TTTTTTTATAAAGAAAATTAATGTGAACAAGG
616032 ATGGTAATGATGT
257 ATGGTAATGATGT
616045 AAAAGTATTT
Statistics
Matches: 247, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
267 6 0.02
268 209 0.85
269 32 0.13
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.33
Consensus pattern (269 bp):
TTGGAGAGTCCTCGATGATGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCGTTTTAAAA
CAAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTAAAGTGTCTCCGATGGTGACAATTTAAGTGA
GAATAAGATTTAAACTTTGATGTGTTCAAAAGTGGAGTTGAAGTATCCCCTCGGAGGAATACGGT
TGGAGTATCCCCGATAAATAAAATTTTGATTTTTTTATAAAGAAAATTAATGTGAACAAGGATGG
TAATGATGT
Found at i:617417 original size:15 final size:15
Alignment explanation
Indices: 617397--617426 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
617387 GATCATTTGA
*
617397 AAAAATAATAATAAT
1 AAAAATAAAAATAAT
617412 AAAAATAAAAATAAT
1 AAAAATAAAAATAAT
617427 CATGGGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:618358 original size:12 final size:13
Alignment explanation
Indices: 618329--618361 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
618319 AACTCGGTAT
618329 TTTCAAAAAAAAA
1 TTTCAAAAAAAAA
*
618342 TTTCAAAGAAAAA
1 TTTCAAAAAAAAA
618355 -TTCAAAA
1 TTTCAAAA
618362 CTCATGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (13 bp):
TTTCAAAAAAAAA
Found at i:635994 original size:1 final size:1
Alignment explanation
Indices: 635990--636044 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
635980 TTCTTTTTTC
* * * * * *
635990 AAAAACAAACAAAAAAACAAAAAAAAAACAAAAAAACAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
636045 GAGAATCTGC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:636014 original size:11 final size:11
Alignment explanation
Indices: 635990--636044 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
635980 TTCTTTTTTC
635990 AAAAACAAACAA
1 AAAAACAAA-AA
636002 AAAAACAAAAA
1 AAAAACAAAAA
636013 AAAAAC---AA
1 AAAAACAAAAA
636021 AAAAACAAAAA
1 AAAAACAAAAA
*
636032 AAAAAGAAAAA
1 AAAAACAAAAA
636043 AA
1 AA
636045 GAGAATCTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 8 0.21
11 22 0.56
12 9 0.23
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:636018 original size:19 final size:19
Alignment explanation
Indices: 635990--636044 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
635980 TTCTTTTTTC
*
635990 AAAAACAAACAAAAAAACA
1 AAAAAAAAACAAAAAAACA
636009 AAAAAAAAACAAAAAAACA
1 AAAAAAAAACAAAAAAACA
*
636028 AAAAAAAAAGAAAAAAA
1 AAAAAAAAACAAAAAAA
636045 GAGAATCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAACA
Found at i:636948 original size:36 final size:36
Alignment explanation
Indices: 636908--636980 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
636898 TTGATGAGAG
636908 ATAAACCAGTAAGGAGCACAAGCTGCATTTCCTGTA
1 ATAAACCAGTAAGGAGCACAAGCTGCATTTCCTGTA
636944 ATAAACCAGTAAGGAGCACAAGCTGCATTTCCTGTA
1 ATAAACCAGTAAGGAGCACAAGCTGCATTTCCTGTA
636980 A
1 A
636981 GTATCCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (36 bp):
ATAAACCAGTAAGGAGCACAAGCTGCATTTCCTGTA
Done.