Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 126 of 150
Found at i:38199866 original size:13 final size:13
Alignment explanation
Indices: 38199850--38199874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38199840 TCATTTGACT
38199850 GAGAGATTTGTTG
1 GAGAGATTTGTTG
38199863 GAGAGATTTGTT
1 GAGAGATTTGTT
38199875 TTCAAAATTT
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:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (13 bp):
GAGAGATTTGTTG
Found at i:38200498 original size:15 final size:16
Alignment explanation
Indices: 38200471--38200502 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38200461 AAAAACCATA
38200471 AGCCCGAGCCCGGCCC
1 AGCCCGAGCCCGGCCC
38200487 AGCCCG-GCCCGGCCC
1 AGCCCGAGCCCGGCCC
38200502 A
1 A
38200503 TTTTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.12, C:0.56, G:0.31, T:0.00
Consensus pattern (16 bp):
AGCCCGAGCCCGGCCC
Found at i:38200543 original size:21 final size:22
Alignment explanation
Indices: 38200505--38200560 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
38200495 CCGGCCCATT
* **
38200505 TTTTAATAAATATCAAAAATTTA
1 TTTTAA-AAATATAAAAAAAGTA
38200528 TTTTAAAAAT-TAAAAAAAGTA
1 TTTTAAAAATATAAAAAAAGTA
38200549 TTTTAAAAATAT
1 TTTTAAAAATAT
38200561 TTTTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTAAAAATATAAAAAAAGTA
Found at i:38200561 original size:11 final size:11
Alignment explanation
Indices: 38200541--38200660 Score: 85
Period size: 11 Copynumber: 11.4 Consensus size: 11
38200531 TAAAAATTAA
38200541 AAAAAGTATTTT
1 AAAAA-TATTTT
38200553 AAAAATATTTT
1 AAAAATATTTT
*
38200564 TAAAATATTTT
1 AAAAATATTTT
*
38200575 --AAA-A-TTA
1 AAAAATATTTT
* *
38200582 AAAAAAATTTA
1 AAAAATATTTT
38200593 AAAAAGTATTTT
1 AAAAA-TATTTT
38200605 AAAAATATTTT
1 AAAAATATTTT
*
38200616 --AAA-A-TTA
1 AAAAATATTTT
* **
38200623 AAAAATAATAA
1 AAAAATATTTT
38200634 AAAAATTATTTT
1 AAAAA-TATTTT
38200646 AAAAATATTTT
1 AAAAATATTTT
38200657 AAAA
1 AAAA
38200661 TTTAAAAAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 12 0.13
10 2 0.02
11 47 0.53
12 22 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:38200603 original size:41 final size:41
Alignment explanation
Indices: 38200526--38200669 Score: 186
Period size: 41 Copynumber: 3.5 Consensus size: 41
38200516 ATCAAAAATT
* *
38200526 TATTTTAAAAATTAAAAAAAGTATTT-TAAAAATATTTTTAAAA
1 TATTTT-AAAATTAAAAAAA--ATTTAAAAAAATATTTTAAAAA
*
38200569 TATTTTAAAATTAAAAAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTTAAAAAAATATTTTAAAAA
38200610 TATTTTAAAATTAAAAAATAA--TAAAAAAATTATTTTAAAAA
1 TATTTTAAAATTAAAAAA-AATTTAAAAAAA-TATTTTAAAAA
*
38200651 TATTTTAAAATTTAAAAAA
1 TATTTTAAAATTAAAAAAA
38200670 TAAATATATT
Statistics
Matches: 93, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
40 12 0.13
41 60 0.65
42 15 0.16
43 6 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAAATATTTTAAAAA
Found at i:38200624 original size:30 final size:31
Alignment explanation
Indices: 38200585--38200649 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
38200575 AAAATTAAAA
* **
38200585 AAAATTTAAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTTAAAAAA-TAATAAAAAAATTATTTT
38200616 AAAA-TTAAAAAATAATAAAAAAATTATTTT
1 AAAATTTAAAAAATAATAAAAAAATTATTTT
38200646 AAAA
1 AAAA
38200650 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.27
30 18 0.60
31 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAATTTAAAAAATAATAAAAAAATTATTTT
Found at i:38200637 original size:52 final size:52
Alignment explanation
Indices: 38200532--38200660 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 52
38200522 AATTTATTTT
* **
38200532 AAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTTTAAAATTAAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATATTAAAAAATTAAA
38200584 AAAAATTTAAAAAAGTATTTTAAAAATA-TTTT-AAA-ATTAAAAAATAATAAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATATTAAAAAAT--TAAA
*
38200635 AAAATTATTTTAAAAA-TATTTTAAAA
1 AAAA--ATTTAAAAAAGTATTTTAAAA
38200661 TTTAAAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
49 8 0.12
50 3 0.04
51 12 0.17
52 37 0.54
53 9 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (52 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATATTAAAAAATTAAA
Found at i:38204134 original size:43 final size:44
Alignment explanation
Indices: 38204075--38204187 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
38204065 CAATGCCTAC
* *
38204075 GTCCCAGACGAGGTCTTACATC-T-AATC-AAATATCGATGCCACT
1 GTCCCAGACGTGGTCTTACA-CGTAAATCTAAAT-TCGATGCCAAT
* *
38204118 GTCCTAGACAG-GGTCTTACACGTAAATCTCAATTCGATGCCAAT
1 GTCCCAGAC-GTGGTCTTACACGTAAATCTAAATTCGATGCCAAT
38204162 GTCCCAGACGTGGTCTTACACG-AAAT
1 GTCCCAGACGTGGTCTTACACGTAAAT
38204188 AACATATCGG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
42 1 0.02
43 23 0.38
44 34 0.56
45 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (44 bp):
GTCCCAGACGTGGTCTTACACGTAAATCTAAATTCGATGCCAAT
Found at i:38205320 original size:13 final size:13
Alignment explanation
Indices: 38205302--38205326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38205292 ACAAACGATA
38205302 AAATTTTCACACG
1 AAATTTTCACACG
38205315 AAATTTTCACAC
1 AAATTTTCACAC
38205327 ACATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:38221080 original size:13 final size:13
Alignment explanation
Indices: 38221062--38221087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38221052 CTTGCAGGGG
38221062 TATGATATTATTT
1 TATGATATTATTT
38221075 TATGATATTATTT
1 TATGATATTATTT
38221088 GTCTTGTTGC
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATGATATTATTT
Found at i:38226761 original size:23 final size:23
Alignment explanation
Indices: 38226731--38226780 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
38226721 ACCATTTGAT
38226731 AATTATTGAAACGACTGACAAGA
1 AATTATTGAAACGACTGACAAGA
38226754 AATTATTGAAACGACTGACAAGA
1 AATTATTGAAACGACTGACAAGA
38226777 AATT
1 AATT
38226781 TCTTACTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (23 bp):
AATTATTGAAACGACTGACAAGA
Found at i:38229225 original size:30 final size:30
Alignment explanation
Indices: 38229191--38229280 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 30
38229181 CATTTGGTCC
38229191 TTAATACTTACATATTTTATCAATTTGATA
1 TTAATACTTACATATTTTATCAATTTGATA
* * * * *
38229221 TTAATTC-TAAATAATTTAATAAATTTAACTA
1 TTAATACTTACAT-ATTTTATCAATTTGA-TA
* * * *
38229252 TTCATATTTACAAATTCTATCAATTTGAT
1 TTAATACTTACATATTTTATCAATTTGAT
38229281 CCTCAAACTT
Statistics
Matches: 43, Mismatches: 14, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
29 4 0.09
30 19 0.44
31 17 0.40
32 3 0.07
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAATACTTACATATTTTATCAATTTGATA
Found at i:38234106 original size:16 final size:16
Alignment explanation
Indices: 38234085--38234125 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38234075 AAAATATCTA
*
38234085 AATTTATAATTATTTG
1 AATTTAAAATTATTTG
*
38234101 AATTTAAAATTATTTA
1 AATTTAAAATTATTTG
38234117 AACTTTAAA
1 AA-TTTAAA
38234126 GTTGAATTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
AATTTAAAATTATTTG
Found at i:38234366 original size:2 final size:2
Alignment explanation
Indices: 38234359--38234383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38234349 CAATTGAGAA
38234359 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 A
38234384 AATAAATTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38249965 original size:3 final size:3
Alignment explanation
Indices: 38249957--38249990 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
38249947 ATAGGCGTAT
* *
38249957 ATA ATA ATA ATA ATA ATA TTA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38249991 ATAGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38251749 original size:45 final size:44
Alignment explanation
Indices: 38251611--38251839 Score: 221
Period size: 45 Copynumber: 5.1 Consensus size: 44
38251601 CGCCATCTTC
* * *
38251611 GATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAA
1 GATCTGTTTTCTTCGATCTACTTC-CCACCAGTATGGGAAGACAA
* * * * * ***
38251656 TATCTGTTGTATTTGATCTACTTCACACC-GATACATGAAGACAA
1 GATCTGTTTTCTTCGATCTACTTCCCACCAG-TATGGGAAGACAA
* *
38251700 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGATAA
1 GATCTGTTTTCTTCGATCTACTTC-CCACCAGTATGGGAAGACAA
* * ***
38251745 GATCTGGTATTT-TT-GATCTACTTCTCGCCAGTACATGAAGACAA
1 GATCT-GT-TTTCTTCGATCTACTTCCCACCAGTATGGGAAGACAA
38251789 GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGTTTTCTTCGATCTACTTC-CCACCAGTATGGGAAGACAA
38251834 GATCTG
1 GATCTG
38251840 CTGCTTTTCA
Statistics
Matches: 143, Mismatches: 33, Indels: 16
0.74 0.17 0.08
Matches are distributed among these distances:
42 3 0.02
43 5 0.03
44 61 0.43
45 66 0.46
46 5 0.03
47 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
GATCTGTTTTCTTCGATCTACTTCCCACCAGTATGGGAAGACAA
Found at i:38251762 original size:89 final size:89
Alignment explanation
Indices: 38251611--38251839 Score: 334
Period size: 89 Copynumber: 2.6 Consensus size: 89
38251601 CGCCATCTTC
* * * * * * *
38251611 GATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGTTGTATTTGATCTA
1 GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATATTTGATCTA
38251676 CTTCACACC-GATACATGAAGACAA
66 CTTCACACCAG-TACATGAAGACAA
* * *
38251700 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGATAAGATCTGGTATTTTTGATCTA
1 GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATATTTGATCTA
* *
38251765 CTTCTCGCCAGTACATGAAGACAA
66 CTTCACACCAGTACATGAAGACAA
38251789 GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
1 GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
38251840 CTGCTTTTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 124 0.99
90 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (89 bp):
GATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATATTTGATCTA
CTTCACACCAGTACATGAAGACAA
Found at i:38252628 original size:44 final size:44
Alignment explanation
Indices: 38252577--38252747 Score: 182
Period size: 44 Copynumber: 3.9 Consensus size: 44
38252567 CCTGTTTCGC
** *
38252577 CACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTTCA
1 CACCAGTACAGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
* * * * * **
38252621 CGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCTGTTTCA
1 CACCAGTACAGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
** *
38252665 CCACCAGTATGGGAAAACAAGATCTGTTATCTTTGATCTACTTCA
1 -CACCAGTACAGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
* *
38252710 CACCAGTACATGAAGACAAGATCTGCTT-TCTTCGATCT
1 CACCAGTACAGGAAGACAAGATCTG-TTATCTTTGATCT
38252748 GGGTTCGGTC
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 64 0.64
45 36 0.36
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
CACCAGTACAGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
Found at i:38252719 original size:89 final size:89
Alignment explanation
Indices: 38252568--38252748 Score: 308
Period size: 89 Copynumber: 2.0 Consensus size: 89
38252558 CGTCTATTCC
* * *
38252568 CTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTTCACGCCAGTACATG
1 CTGTTTCACCACCAGTATGGGAAAACAAGATCTGTTACCTTTGATCTACTTCACACCAGTACATG
*
38252633 AAGACAAGATCTATTTTCTTCGAT
66 AAGACAAGATCTACTTTCTTCGAT
*
38252657 CTGTTTCACCACCAGTATGGGAAAACAAGATCTGTTATCTTTGATCTACTTCACACCAGTACATG
1 CTGTTTCACCACCAGTATGGGAAAACAAGATCTGTTACCTTTGATCTACTTCACACCAGTACATG
*
38252722 AAGACAAGATCTGCTTTCTTCGAT
66 AAGACAAGATCTACTTTCTTCGAT
38252746 CTG
1 CTG
38252749 GGTTCGGTCC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (89 bp):
CTGTTTCACCACCAGTATGGGAAAACAAGATCTGTTACCTTTGATCTACTTCACACCAGTACATG
AAGACAAGATCTACTTTCTTCGAT
Found at i:38253728 original size:3 final size:3
Alignment explanation
Indices: 38253720--38253773 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
38253710 TTTATTACTG
*
38253720 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
38253765 CTA TTA TTA
1 TTA TTA TTA
38253774 ACGTATATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.93
4 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:38257110 original size:20 final size:20
Alignment explanation
Indices: 38257085--38257123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38257075 TCATCTCATA
*
38257085 CATCGCATCATATGTATTAG
1 CATCGCATCATATGCATTAG
*
38257105 CATCGCATTATATGCATTA
1 CATCGCATCATATGCATTA
38257124 TAGACCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
CATCGCATCATATGCATTAG
Found at i:38259990 original size:3 final size:3
Alignment explanation
Indices: 38259982--38260015 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
38259972 ATAGGCGTAT
* *
38259982 ATA ATA ATA ATA ATA ATA TTA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38260016 ATAGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38261749 original size:44 final size:43
Alignment explanation
Indices: 38261681--38262016 Score: 242
Period size: 44 Copynumber: 7.6 Consensus size: 43
38261671 CAGTATGGGG
* * * *
38261681 AGACAATATCTGTTGTATTTGATCTACTTCACGCC-GATACATGA
1 AGACAAGATCTGTTATCTTCGATCTACTTCAC-CCAG-TACATGA
* * * * ***
38261725 AGACAAGATATGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGA
1 AGACAAGATCTGTTATCTTCGATCTACTTC-AC-CCAGTACATGA
* * *
38261770 AGACAAGATCTGGTATCTTTGATCTACTGCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTCGATCTACTTCAC-CCAGTACATGA
* * ** * ****
38261814 AGACAAGATTTGTTTTCTTCGATCTGGTTCGCCACCAGTTTGGGA
1 AGACAAGATCTGTTATCTTCGATCTACTTC-AC-CCAGTACATGA
* * *
38261859 ATACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTCGATCTACTTCAC-CCAGTACATGA
* * * ***
38261903 AGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGA
1 AGACAAGATCTGTTATCTTCGATCTACTTC-AC-CCAGTACATGA
* * *
38261948 AGATAAGATCTGGTATCTTTGATCTACTTCACTCCAGTACATGA
1 AGACAAGATCTGTTATCTTCGATCTACTTCAC-CCAGTACATGA
*
38261992 AGACAAGATCTGTTCTCTTCGATCT
1 AGACAAGATCTGTTATCTTCGATCT
38262017 GTTACGCCAC
Statistics
Matches: 216, Mismatches: 72, Indels: 8
0.73 0.24 0.03
Matches are distributed among these distances:
44 119 0.55
45 96 0.44
46 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
AGACAAGATCTGTTATCTTCGATCTACTTCACCCAGTACATGA
Found at i:38261774 original size:45 final size:45
Alignment explanation
Indices: 38261723--38262048 Score: 302
Period size: 45 Copynumber: 7.3 Consensus size: 45
38261713 GCCGATACAT
* *
38261723 GAAGACAAGATATGTTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
* * * * ***
38261768 GAAGACAAGATCTGGTATCTTTGATCTAC-T-GCACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGC-CACCAGTATGG
* * * *
38261812 GAAGACAAGATTTGTTTTCTTCGATCTGGTTCGCCACCAGTTTGG
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
* * * * * * ***
38261857 GAATACAAGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
*
38261901 GAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
* * * * * * ***
38261946 GAAGATAAGATCTGGTATCTTTGATCTACTTC-ACTCCAGTACAT
1 GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
*
38261990 GAAGACAAGATCTGTTCTCTTCGATCTG-TTACGCCACCAGTATGG
1 GAAGACAAGATCTGTTATCTTCGATCTGCTT-CGCCACCAGTATGG
38262035 GAAGACAAGATCTG
1 GAAGACAAGATCTG
38262049 CTGCTTTTTA
Statistics
Matches: 212, Mismatches: 63, Indels: 12
0.74 0.22 0.04
Matches are distributed among these distances:
43 4 0.02
44 95 0.45
45 111 0.52
46 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (45 bp):
GAAGACAAGATCTGTTATCTTCGATCTGCTTCGCCACCAGTATGG
Found at i:38261803 original size:89 final size:89
Alignment explanation
Indices: 38261642--38262048 Score: 620
Period size: 89 Copynumber: 4.6 Consensus size: 89
38261632 TGCCATCTTC
* * * * * * * * *
38261642 GATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGTTGTATTTGATCTA
1 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
38261707 CTTCACGCC-GATACATGAAGACAA
66 CTTCACGCCAG-TACATGAAGACAA
*
38261731 GATATGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
1 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
*
38261796 CTGCACGCCAGTACATGAAGACAA
66 CTTCACGCCAGTACATGAAGACAA
* * * *
38261820 GATTTGTTTTCTTCGATCTGGTTCGCCACCAGTTTGGGAATACAAGATCTGGTATCTTTGATCTA
1 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
38261885 CTTCACGCCAGTACATGAAGACAA
66 CTTCACGCCAGTACATGAAGACAA
*
38261909 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGATAAGATCTGGTATCTTTGATCTA
1 GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
*
38261974 CTTCACTCCAGTACATGAAGACAA
66 CTTCACGCCAGTACATGAAGACAA
*
38261998 GATCTGTTCTCTTCGATCTG-TTACGCCACCAGTATGGGAAGACAAGATCTG
1 GATCTGTTTTCTTCGATCTGCTT-CGCCACCAGTATGGGAAGACAAGATCTG
38262049 CTGCTTTTTA
Statistics
Matches: 292, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
88 2 0.01
89 289 0.99
90 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (89 bp):
GATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTA
CTTCACGCCAGTACATGAAGACAA
Found at i:38270161 original size:20 final size:20
Alignment explanation
Indices: 38270136--38270175 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38270126 TAAAGGTCTA
38270136 TAATGCATATAATGCGATGC
1 TAATGCATATAATGCGATGC
* *
38270156 TAATGCATATGATGTGATGC
1 TAATGCATATAATGCGATGC
38270176 ATGAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:38274226 original size:3 final size:3
Alignment explanation
Indices: 38274218--38274251 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
38274208 ATAGGCGTAT
* *
38274218 ATA ATA ATA ATA ATA ATA TTA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38274252 ATAGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38283459 original size:12 final size:12
Alignment explanation
Indices: 38283442--38283479 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
38283432 TATAATTTAT
38283442 AAAAATTAATAA
1 AAAAATTAATAA
*
38283454 AAAAATT-TTAA
1 AAAAATTAATAA
38283465 AAAAATTAATAA
1 AAAAATTAATAA
38283477 AAA
1 AAA
38283480 CTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATTAATAA
Found at i:38283467 original size:22 final size:21
Alignment explanation
Indices: 38283437--38283492 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
38283427 CCACGTATAA
38283437 TTTATAAAAATTAATAAAAAAAT
1 TTTA-AAAAATTAAT-AAAAAAT
*
38283460 TTTAAAAAAATTAATAAAAACT
1 TTT-AAAAAATTAATAAAAAAT
38283482 TTTAAAAAATT
1 TTTAAAAAATT
38283493 TATTCATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 8 0.26
22 9 0.29
23 13 0.42
24 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAAAAAATTAATAAAAAAT
Found at i:38283468 original size:23 final size:22
Alignment explanation
Indices: 38283437--38283490 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
38283427 CCACGTATAA
*
38283437 TTTATAAAAATTAATAAAAAAAT
1 TTTAAAAAAATTAAT-AAAAAAT
*
38283460 TTTAAAAAAATTAATAAAAACT
1 TTTAAAAAAATTAATAAAAAAT
38283482 TTTAAAAAA
1 TTTAAAAAA
38283491 TTTATTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAAAAATTAATAAAAAAT
Found at i:38284440 original size:21 final size:21
Alignment explanation
Indices: 38284411--38284450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38284401 TCGGGCTTCA
38284411 ACTCAGCCTGATTGATGGAAT
1 ACTCAGCCTGATTGATGGAAT
* *
38284432 ACTCGGCCTGATTGTTGGA
1 ACTCAGCCTGATTGATGGA
38284451 TAAGTCTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (21 bp):
ACTCAGCCTGATTGATGGAAT
Found at i:38285598 original size:15 final size:16
Alignment explanation
Indices: 38285563--38285601 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
38285553 TGAAAAAAAT
*
38285563 ATTTAAAATGATTCAA
1 ATTTAAAATGAATCAA
*
38285579 ATTTAAAAT-AATCTA
1 ATTTAAAATGAATCAA
38285594 ATTTAAAA
1 ATTTAAAA
38285602 AGCTTGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTTAAAATGAATCAA
Found at i:38286010 original size:18 final size:18
Alignment explanation
Indices: 38285987--38286043 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
38285977 TTAAAAGTCT
38285987 AAAAAATATATATATTTA
1 AAAAAATATATATATTTA
* *
38286005 AAAAAATATATTTGATTAA
1 AAAAAATATATAT-ATTTA
*
38286024 AAATAAAAATATATATTTA
1 AAA-AAATATATATATTTA
38286043 A
1 A
38286044 TATATAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.38
19 12 0.38
20 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAAATATATATATTTA
Found at i:38286038 original size:42 final size:39
Alignment explanation
Indices: 38285929--38286039 Score: 98
Period size: 42 Copynumber: 2.7 Consensus size: 39
38285919 CCCGGCCCAC
* * * *
38285929 ATTTGATTAAAAATAAAAAAAATAAAAATATTTAATATATA
1 ATTTGATTAAAAAT--AAAAAATATATATATTTAAAAAATA
* *
38285970 ATTCGGATTAAAAGTCTAAAAAATATATATATTTAAAAAAATA
1 ATT-TGATTAAAA--ATAAAAAATATATATATTT-AAAAAATA
38286013 TATTTGATTAAAAAT-AAAAATATATAT
1 -ATTTGATTAAAAATAAAAAATATATAT
38286040 TTAATATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
40 12 0.21
41 4 0.07
42 23 0.40
43 14 0.25
44 4 0.07
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (39 bp):
ATTTGATTAAAAATAAAAAATATATATATTTAAAAAATA
Found at i:38290229 original size:25 final size:24
Alignment explanation
Indices: 38290179--38290229 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
38290169 TTTATTAAAG
**
38290179 ATAATCTTAAATTTCATAAATTAA
1 ATAATCTTAAATTTCATAAAGAAA
* *
38290203 ATAATTCTTTAATTTTATAAAGAAA
1 ATAA-TCTTAAATTTCATAAAGAAA
38290228 AT
1 AT
38290230 GATGATGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATCTTAAATTTCATAAAGAAA
Found at i:38294577 original size:24 final size:25
Alignment explanation
Indices: 38294545--38294591 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
38294535 AAATCAAACT
38294545 TAATCACTTTAA-TATTAAATTAATA
1 TAATCAC-TTAAGTATTAAATTAATA
*
38294570 TAAT-ACTTAAGTATTAGATTAA
1 TAATCACTTAAGTATTAAATTAA
38294592 ATTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (25 bp):
TAATCACTTAAGTATTAAATTAATA
Found at i:38296683 original size:19 final size:21
Alignment explanation
Indices: 38296661--38296706 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
38296651 TAATTAAAAC
38296661 AACTAAATA-A-GATTAATTA
1 AACTAAATACATGATTAATTA
*
38296680 AACTATATACATGATTAATTA
1 AACTAAATACATGATTAATTA
*
38296701 AGCTAA
1 AACTAA
38296707 TCGTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTAAATACATGATTAATTA
Found at i:38299154 original size:33 final size:32
Alignment explanation
Indices: 38299110--38299256 Score: 87
Period size: 33 Copynumber: 4.4 Consensus size: 32
38299100 TGATGATTAT
*
38299110 ATGTAAAACCATAGCTGGGCTATGACATTCTG
1 ATGTAAGACCATAGCTGGGCTATGACATTCTG
* * * * * *
38299142 ATGATAAGACCATAACTGGGTTACGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGACATTCTG
* * * * * * *
38299175 AACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGCTGGGCTATGACA-T-TCT-G
* * *
38299211 ATGTAATACCATAGCTGGGCTATGGCATTCTA
1 ATGTAAGACCATAGCTGGGCTATGACATTCTG
38299243 ATGATAAGACCATA
1 ATG-TAAGACCATA
38299257 ATTGAGTTAT
Statistics
Matches: 80, Mismatches: 29, Indels: 11
0.67 0.24 0.09
Matches are distributed among these distances:
32 6 0.08
33 49 0.61
34 3 0.04
35 22 0.28
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGACATTCTG
Found at i:38299326 original size:24 final size:24
Alignment explanation
Indices: 38299274--38299326 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
38299264 TATGGCACTA
* *
38299274 CAAATGTAAAGGATGGATTTACAG
1 CAAATGTAAAGGATGAATTGACAG
* *
38299298 AAAATGTAAAGGATGAATTGACGG
1 CAAATGTAAAGGATGAATTGACAG
38299322 CAAAT
1 CAAAT
38299327 TACCCAAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.23
Consensus pattern (24 bp):
CAAATGTAAAGGATGAATTGACAG
Found at i:38300202 original size:28 final size:28
Alignment explanation
Indices: 38300170--38300231 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
38300160 TTAATGATGG
* *
38300170 CTTATATGT-AGTGTGTTGAGTTTAGTCA
1 CTTAT-TGTGAGTGTGTTAAGTTTAATCA
* *
38300198 CTTATTTTGGGTGTGTTAAGTTTAATCA
1 CTTATTGTGAGTGTGTTAAGTTTAATCA
38300226 CTTATT
1 CTTATT
38300232 TTGGCTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (28 bp):
CTTATTGTGAGTGTGTTAAGTTTAATCA
Found at i:38300232 original size:28 final size:28
Alignment explanation
Indices: 38300180--38300235 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
38300170 CTTATATGTA
* *
38300180 GTGTGTTGAGTTTAGTCACTTATTTTGG
1 GTGTGTTAAGTTTAATCACTTATTTTGG
38300208 GTGTGTTAAGTTTAATCACTTATTTTGG
1 GTGTGTTAAGTTTAATCACTTATTTTGG
38300236 CTTATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (28 bp):
GTGTGTTAAGTTTAATCACTTATTTTGG
Found at i:38314859 original size:24 final size:24
Alignment explanation
Indices: 38314832--38314878 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
38314822 ATTGAAATAG
38314832 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
38314856 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
38314879 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:38317807 original size:25 final size:27
Alignment explanation
Indices: 38317779--38317840 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
38317769 GTGTTGTATG
* *
38317779 TTTCAAATATATGTATA-A-TCAGCAT
1 TTTCAAATATATATATACAGTCAACAT
*
38317804 TTTCAAATAATATATATACAGTCAATAT
1 TTTCAAAT-ATATATATACAGTCAACAT
38317832 TTTCAAATA
1 TTTCAAATA
38317841 AGGCTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 8 0.26
26 8 0.26
27 2 0.06
28 13 0.42
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (27 bp):
TTTCAAATATATATATACAGTCAACAT
Found at i:38320823 original size:28 final size:28
Alignment explanation
Indices: 38320785--38320849 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
38320775 TTTTTTATAT
38320785 TTTTTATAATTTAATAATTTTT-AA-ATGAA
1 TTTTTA-AATTT--TAATTTTTGAATATGAA
* *
38320814 TTTTTAAATTTTTATTTTTGAATTTGAA
1 TTTTTAAATTTTAATTTTTGAATATGAA
38320842 TTTTTAAA
1 TTTTTAAA
38320850 AAAATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 7 0.22
27 2 0.06
28 17 0.53
29 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTTTAAATTTTAATTTTTGAATATGAA
Found at i:38320832 original size:14 final size:14
Alignment explanation
Indices: 38320800--38320849 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
38320790 ATAATTTAAT
38320800 AATTTTTAAA--TG
1 AATTTTTAAATTTG
*
38320812 AATTTTTAAATTTT
1 AATTTTTAAATTTG
* *
38320826 TATTTTTGAATTTG
1 AATTTTTAAATTTG
38320840 AATTTTTAAA
1 AATTTTTAAA
38320850 AAAATATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 10 0.33
14 20 0.67
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
AATTTTTAAATTTG
Found at i:38321072 original size:14 final size:14
Alignment explanation
Indices: 38321053--38321083 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38321043 AGCAGGACTC
*
38321053 AAAATATCAAAATT
1 AAAATATAAAAATT
38321067 AAAATATAAAAATT
1 AAAATATAAAAATT
38321081 AAA
1 AAA
38321084 TTTGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:38322560 original size:46 final size:46
Alignment explanation
Indices: 38322493--38322594 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
38322483 ACTACTAATT
* **
38322493 TGTAATATTAGTTATGCACTTGGACGATATTGTAGTTAACATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTAACATGTGG
*
38322539 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTAACATGTGG
*
38322585 TGTACTACTA
1 TGTAATACTA
38322595 ATTTGTAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTAACATGTGG
Found at i:38329929 original size:46 final size:46
Alignment explanation
Indices: 38329861--38330137 Score: 439
Period size: 46 Copynumber: 6.0 Consensus size: 46
38329851 CATGGCAAAG
* *
38329861 TGTGAAACGTAGGTATGATATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
38329907 TGTGAAAAGTAGGTATGGTATTTC-GATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAG-TGAAGAAAACCATACTGAGT
*
38329953 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
38329999 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACGATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
38330045 TGTGAAAAGTAGGTATGATGTTTCAGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
38330091 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGCAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
38330137 T
1 T
38330138 ATAGTAATGT
Statistics
Matches: 213, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.00
46 212 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:38331501 original size:268 final size:267
Alignment explanation
Indices: 38330980--38331518 Score: 1006
Period size: 268 Copynumber: 2.0 Consensus size: 267
38330970 GAAATTGATT
*
38330980 TGTACTCAATAATATTACGGGCATCATTTGTACCCTCCCTTGAAGCATCACCGAAAAAGATGCAT
1 TGTACTCAATAATATTACGGACATCATTTGTACCCTCCCTTGAAGCATCACCGAAAAAGATGCAT
38331045 TCATCTGCAAAAAGCAGATGATTAACTGCAAAACTTCCACTACCAATTTAGGCCCCCTCATCAAC
66 TCATCTGCAAAAAGCAGATGATTAACTGCAAAACTTCCACTACCAATTTAGGCCCCCTCATCAAC
*
38331110 CTTGATGACTTGGCCTCATTCAGTAGTGTCAAGAACCACTTTGCATAGGTAAGAAACATGTAAGG
131 CTTGATGACTTGGCCTCATTCAGTAGTGTCAAGAACCACTTTGCATAGGTAAGAAACAGGTAAGG
* *
38331175 ACTTAATGGATCCCCCTACCGTAGTCCTTTTGATGGTAGAAACTGATCACTAAGTTTTTCATTAA
196 ACTTAATGGATCCCCCTACCGTAGTCCTTTTGATGGCAGAAACCGATCACTAAGTTTTTCATTAA
38331240 TACCCAC
261 TACCCAC
38331247 TGTACTCAATAATATTACGGACATCATTTGTACCCTCCCTTGAAGCATCACCGAAAAAGATGCAT
1 TGTACTCAATAATATTACGGACATCATTTGTACCCTCCCTTGAAGCATCACCGAAAAAGATGCAT
*
38331312 TCATCTGCAAAAAGCAGATGATTAACTGCAAAACTTCCACTGCCAATTTAGGCCCCCCTCATCAA
66 TCATCTGCAAAAAGCAGATGATTAACTGCAAAACTTCCACTACCAATTTAGG-CCCCCTCATCAA
* *
38331377 CCTTGATGACTTGGCCTCATTCAGTAGTGTCGAGAACCCCTTTGCATAGGTAAGAAACAGGTAAG
130 CCTTGATGACTTGGCCTCATTCAGTAGTGTCAAGAACCACTTTGCATAGGTAAGAAACAGGTAAG
38331442 GACTTAATGGATCCCCCTACCGTAGTCCTTTTGATGGCAGAAACCGATCACTAAGTTTTTCATTA
195 GACTTAATGGATCCCCCTACCGTAGTCCTTTTGATGGCAGAAACCGATCACTAAGTTTTTCATTA
38331507 ATACCCAC
260 ATACCCAC
38331515 TGTA
1 TGTA
38331519 TAGCAGATCG
Statistics
Matches: 264, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
267 115 0.44
268 149 0.56
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (267 bp):
TGTACTCAATAATATTACGGACATCATTTGTACCCTCCCTTGAAGCATCACCGAAAAAGATGCAT
TCATCTGCAAAAAGCAGATGATTAACTGCAAAACTTCCACTACCAATTTAGGCCCCCTCATCAAC
CTTGATGACTTGGCCTCATTCAGTAGTGTCAAGAACCACTTTGCATAGGTAAGAAACAGGTAAGG
ACTTAATGGATCCCCCTACCGTAGTCCTTTTGATGGCAGAAACCGATCACTAAGTTTTTCATTAA
TACCCAC
Found at i:38333090 original size:27 final size:27
Alignment explanation
Indices: 38333052--38333104 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
38333042 TTTCGGACTT
*
38333052 GAAATCAAATGATTTAAAGTGTATTTA
1 GAAATAAAATGATTTAAAGTGTATTTA
38333079 GAAATAAAATGATTTAAAGTGTATTT
1 GAAATAAAATGATTTAAAGTGTATTT
38333105 CGAAGCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (27 bp):
GAAATAAAATGATTTAAAGTGTATTTA
Found at i:38345478 original size:22 final size:22
Alignment explanation
Indices: 38345453--38345494 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38345443 GCCTAAGATA
38345453 TAAATTGGATTGAAA-TGAGTAT
1 TAAATTGGATT-AAATTGAGTAT
*
38345475 TAAATTGTATTAAATTGAGT
1 TAAATTGGATTAAATTGAGT
38345495 TAATTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
TAAATTGGATTAAATTGAGTAT
Found at i:38355964 original size:42 final size:41
Alignment explanation
Indices: 38355918--38356019 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 41
38355908 GGGTCACACT
*
38355918 ACAACACCACCTACCAATCTTC-CTACTCCTATGGA-CCCTATC
1 ACAACACCACC-ACCAATCTTCTC-ACTCCTATGGATCCC-ACC
*
38355960 ACAACACCACCCACCAATCTTCTCATTCCTATGGATCCCACC
1 ACAACACCA-CCACCAATCTTCTCACTCCTATGGATCCCACC
*
38356002 ACAATACCATCCACCAAT
1 ACAACACCA-CCACCAAT
38356020 TTAACGTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
42 47 0.89
43 6 0.11
ACGTcount: A:0.31, C:0.43, G:0.04, T:0.22
Consensus pattern (41 bp):
ACAACACCACCACCAATCTTCTCACTCCTATGGATCCCACC
Found at i:38362426 original size:47 final size:47
Alignment explanation
Indices: 38362372--38362464 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
38362362 ATAAGCTTAA
38362372 AATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGAATATAC
1 AATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGAATATAC
*
38362419 AATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGATTATA
1 AATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGAATATA
38362465 AACCAGAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.55, C:0.12, G:0.13, T:0.20
Consensus pattern (47 bp):
AATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGAATATAC
Found at i:38362446 original size:26 final size:26
Alignment explanation
Indices: 38362372--38362446 Score: 63
Period size: 26 Copynumber: 3.1 Consensus size: 26
38362362 ATAAGCTTAA
38362372 AATTTCAGATATAAAAAAGAAGCAAC
1 AATTTCAGATATAAAAAAGAAGCAAC
* ** *
38362398 -A----AGGTATAAACCAGAA-TATAC
1 AATTTCAGATATAAAAAAGAAGCA-AC
38362419 AATTTCAGATATAAAAAAGAAGCAAC
1 AATTTCAGATATAAAAAAGAAGCAAC
38362445 AA
1 AA
38362447 GGTATAAACC
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
25 1 0.03
26 16 0.47
27 1 0.03
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (26 bp):
AATTTCAGATATAAAAAAGAAGCAAC
Found at i:38362466 original size:12 final size:12
Alignment explanation
Indices: 38362449--38362478 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38362439 AGCAACAAGG
*
38362449 TATAAACCAGAT
1 TATAAACCAGAA
38362461 TATAAACCAGAA
1 TATAAACCAGAA
38362473 TATAAA
1 TATAAA
38362479 ATTTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (12 bp):
TATAAACCAGAA
Found at i:38362474 original size:59 final size:59
Alignment explanation
Indices: 38362402--38362525 Score: 230
Period size: 59 Copynumber: 2.1 Consensus size: 59
38362392 AGCAACAAGG
* *
38362402 TATAAACCAGAATATACAATTTCAGATATAAAAAAGAAGCAACAAGGTATAAACCAGAT
1 TATAAACCAGAATATAAAATTTCAAATATAAAAAAGAAGCAACAAGGTATAAACCAGAT
38362461 TATAAACCAGAATATAAAATTTCAAATATAAAAAAGAAGCAACAAGGTATAAACCAGAT
1 TATAAACCAGAATATAAAATTTCAAATATAAAAAAGAAGCAACAAGGTATAAACCAGAT
38362520 TATAAA
1 TATAAA
38362526 ATTTAAGATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.21
Consensus pattern (59 bp):
TATAAACCAGAATATAAAATTTCAAATATAAAAAAGAAGCAACAAGGTATAAACCAGAT
Found at i:38362681 original size:14 final size:14
Alignment explanation
Indices: 38362662--38362688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38362652 AAATGGAACT
38362662 GTAAGGCAACAACA
1 GTAAGGCAACAACA
38362676 GTAAGGCAACAAC
1 GTAAGGCAACAAC
38362689 GACAGATTAT
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:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GTAAGGCAACAACA
Found at i:38362715 original size:59 final size:59
Alignment explanation
Indices: 38362645--38362822 Score: 356
Period size: 59 Copynumber: 3.0 Consensus size: 59
38362635 CTTTTGAACG
38362645 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
1 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
38362704 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
1 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
38362763 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
1 ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
38362822 A
1 A
38362823 GGTTTTGAAC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 119 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (59 bp):
ACTAAACAAATGGAACTGTAAGGCAACAACAGTAAGGCAACAACGACAGATTATAAACA
Found at i:38362738 original size:14 final size:14
Alignment explanation
Indices: 38362721--38362747 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38362711 AAATGGAACT
38362721 GTAAGGCAACAACA
1 GTAAGGCAACAACA
38362735 GTAAGGCAACAAC
1 GTAAGGCAACAAC
38362748 GACAGATTAT
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:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GTAAGGCAACAACA
Found at i:38362797 original size:14 final size:14
Alignment explanation
Indices: 38362780--38362806 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38362770 AAATGGAACT
38362780 GTAAGGCAACAACA
1 GTAAGGCAACAACA
38362794 GTAAGGCAACAAC
1 GTAAGGCAACAAC
38362807 GACAGATTAT
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:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GTAAGGCAACAACA
Found at i:38363745 original size:17 final size:17
Alignment explanation
Indices: 38363705--38363749 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
38363695 TCTTAATCAC
38363705 ATTAATATTAAATTAAT
1 ATTAATATTAAATTAAT
* *
38363722 ATAAATATTAGATTAA-
1 ATTAATATTAAATTAAT
38363738 ATTTAATATTAA
1 A-TTAATATTAA
38363750 CTCTTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTAATATTAAATTAAT
Found at i:38363850 original size:25 final size:25
Alignment explanation
Indices: 38363796--38363850 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
38363786 AAACACTAAA
*
38363796 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
38363821 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
38363845 TATTAA
1 T-TTAA
38363851 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:38365988 original size:7 final size:7
Alignment explanation
Indices: 38365978--38366014 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
38365968 TTATTATTTA
38365978 TTAAATT
1 TTAAATT
38365985 TTAAATT
1 TTAAATT
38365992 TTAAATT
1 TTAAATT
38365999 TTAAATT
1 TTAAATT
38366006 TTAAATT
1 TTAAATT
38366013 TT
1 TT
38366015 CAAGTGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTAAATT
Found at i:38366024 original size:21 final size:21
Alignment explanation
Indices: 38365979--38366024 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
38365969 TATTATTTAT
* *
38365979 TAAATTTTAAATTTTAAATTT
1 TAAATTTTAAATTTTAAAGTG
*
38366000 TAAATTTTAAATTTTCAAGTG
1 TAAATTTTAAATTTTAAAGTG
38366021 TAAA
1 TAAA
38366025 GTTAAGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
TAAATTTTAAATTTTAAAGTG
Found at i:38366907 original size:15 final size:16
Alignment explanation
Indices: 38366887--38366920 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38366877 TTTCAAGAAT
*
38366887 AACCA-TGTTTTGAAC
1 AACCATTGTTTGGAAC
38366902 AACCATTGTTTGGAAC
1 AACCATTGTTTGGAAC
38366918 AAC
1 AAC
38366921 TTGTATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (16 bp):
AACCATTGTTTGGAAC
Found at i:38368235 original size:15 final size:15
Alignment explanation
Indices: 38368194--38368240 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
38368184 TAACAAAGAG
38368194 TGACCAAAATATAAA
1 TGACCAAAATATAAA
* *
38368209 CGATCTAAAATATAAA
1 TGA-CCAAAATATAAA
*
38368225 TGACCAAAATAAAAA
1 TGACCAAAATATAAA
38368240 T
1 T
38368241 TATCTAAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (15 bp):
TGACCAAAATATAAA
Found at i:38380830 original size:16 final size:16
Alignment explanation
Indices: 38380809--38380841 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38380799 TTAACAAAAG
38380809 GGTTATGAGAATCTGA
1 GGTTATGAGAATCTGA
38380825 GGTTATGAGAATCTGA
1 GGTTATGAGAATCTGA
38380841 G
1 G
38380842 CTAGTAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.30
Consensus pattern (16 bp):
GGTTATGAGAATCTGA
Found at i:38386414 original size:105 final size:105
Alignment explanation
Indices: 38386229--38386438 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
38386219 AAAAAACCCT
38386229 TAGTTTCATTCGAAGTACTCATGGGATGGCAAAGTTTTAAGGAGAAAAGGGAAAGTGGTAGTTGG
1 TAGTTTCATTCGAAGTACTCATGGGATGGCAAAGTTTTAAGGAGAAAAGGGAAAGTGGTAGTTGG
*
38386294 TCAGGATTTAGAACTGAGAATGAAACTTTTTGACTTATTC
66 TCAGGATTTAAAACTGAGAATGAAACTTTTTGACTTATTC
38386334 TAGTTTCATTCGAAGTACTCATGGGATGGCAAAGTTTTAAGGAGAAAAGGGAAAGTGGTAGTTGG
1 TAGTTTCATTCGAAGTACTCATGGGATGGCAAAGTTTTAAGGAGAAAAGGGAAAGTGGTAGTTGG
38386399 TCAGGATTTAAAACTGAGAATGAAACTTTTTGACTTATTC
66 TCAGGATTTAAAACTGAGAATGAAACTTTTTGACTTATTC
38386439 CACAGTGAAG
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (105 bp):
TAGTTTCATTCGAAGTACTCATGGGATGGCAAAGTTTTAAGGAGAAAAGGGAAAGTGGTAGTTGG
TCAGGATTTAAAACTGAGAATGAAACTTTTTGACTTATTC
Found at i:38398407 original size:42 final size:41
Alignment explanation
Indices: 38398338--38398422 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
38398328 ATTTTGGGGC
* *
38398338 CGATTTCCATTCGACCGAACATAAGCTTCCCAGCCTGTTGA
1 CGATTCCCATTCGACCGAACACAAGCTTCCCAGCCTGTTGA
* * *
38398379 CGATTCCCATTCGAACCGAACCCAAGCTTTCTAGCCTGTTGA
1 CGATTCCCATTCG-ACCGAACACAAGCTTCCCAGCCTGTTGA
38398421 CG
1 CG
38398423 TGAAGTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 12 0.32
42 26 0.68
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.26
Consensus pattern (41 bp):
CGATTCCCATTCGACCGAACACAAGCTTCCCAGCCTGTTGA
Found at i:38407830 original size:17 final size:16
Alignment explanation
Indices: 38407795--38407843 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
38407785 TTCATATTTG
* *
38407795 ATTTTTTTT-AGATTA
1 ATTTTTTTTAAAAATA
38407810 ATTTTTATTTAAAAATA
1 ATTTTT-TTTAAAAATA
*
38407827 ATTTTTTTTAAATATA
1 ATTTTTTTTAAAAATA
38407843 A
1 A
38407844 CACACTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 13 0.45
17 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTTTTTTAAAAATA
Found at i:38408109 original size:6 final size:6
Alignment explanation
Indices: 38408098--38408125 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38408088 TTAGTGATTT
38408098 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
38408126 ATTTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:38414869 original size:17 final size:17
Alignment explanation
Indices: 38414843--38414879 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
38414833 TGATAAACTG
*
38414843 AAAAATTAAGTGTCGAA
1 AAAAAATAAGTGTCGAA
*
38414860 AAAAAATAAGTGTTGAA
1 AAAAAATAAGTGTCGAA
38414877 AAA
1 AAA
38414880 TTAAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.16, T:0.22
Consensus pattern (17 bp):
AAAAAATAAGTGTCGAA
Found at i:38414893 original size:14 final size:15
Alignment explanation
Indices: 38414872--38414906 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38414862 AAAATAAGTG
*
38414872 TTGAAAAATTAAATA
1 TTGAAAATTTAAATA
*
38414887 TTGAAAATTTAAGTA
1 TTGAAAATTTAAATA
38414902 TTGAA
1 TTGAA
38414907 TTTAAGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (15 bp):
TTGAAAATTTAAATA
Found at i:38421688 original size:13 final size:12
Alignment explanation
Indices: 38421644--38421766 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
38421634 AAAAACGAAA
* *
38421644 TGATTAAAAATT
1 TGATGAAAAACT
* *
38421656 TGATGGAAAATT
1 TGATGAAAAACT
*
38421668 TTATGAAAAGACT
1 TGATGAAAA-ACT
38421681 TGATGAAAAACT
1 TGATGAAAAACT
*
38421693 T--TAAAAGGAACT
1 TGATGAAA--AACT
* *
38421705 TGCTGCAAAACT
1 TGATGAAAAACT
*
38421717 TGATAAAAAACT
1 TGATGAAAAACT
*
38421729 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
38421744 TGATAAAAGAACT
1 TGATGAAA-AACT
*
38421757 AGATGAAAAA
1 TGATGAAAAA
38421767 TACTTGAAGA
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
10 4 0.05
12 47 0.55
13 21 0.24
14 4 0.05
15 10 0.12
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:38421726 original size:12 final size:12
Alignment explanation
Indices: 38421711--38421773 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
38421701 AACTTGCTGC
38421711 AAAACTTGATAA
1 AAAACTTGATAA
*
38421723 AAAACTTGGTAATTA
1 AAAACTT-G--ATAA
38421738 AAAACTTGATAA
1 AAAACTTGATAA
*
38421750 AAGAACTAGATGAA
1 AA-AACTTGAT-AA
38421764 AAATACTTGA
1 AAA-ACTTGA
38421774 AGAAAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 12 0.29
13 9 0.22
14 10 0.24
15 10 0.24
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (12 bp):
AAAACTTGATAA
Found at i:38421784 original size:18 final size:18
Alignment explanation
Indices: 38421761--38421798 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38421751 AGAACTAGAT
*
38421761 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
38421779 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
38421797 GA
1 GA
38421799 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:38426120 original size:27 final size:27
Alignment explanation
Indices: 38426089--38426160 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
38426079 CCCGATTATA
*
38426089 GGCTCTTCGTGAGCTTCCTGTTAAATT
1 GGCTCTTTGTGAGCTTCCTGTTAAATT
38426116 GGCTCTTTGTGAGCTTCCTGTTAAATT
1 GGCTCTTTGTGAGCTTCCTGTTAAATT
38426143 GGCTCTTTGTGAGCTTCC
1 GGCTCTTTGTGAGCTTCC
38426161 CGATAGTGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (27 bp):
GGCTCTTTGTGAGCTTCCTGTTAAATT
Found at i:38426286 original size:24 final size:24
Alignment explanation
Indices: 38426215--38426286 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
38426205 TCCCGTTATG
* * *
38426215 TGGCTCTTCGTGAGCTTCCCGA-TA
1 TGGCTCTT-ATGAGCTTCTCTATTA
* *
38426239 TGGTTCTTTATGAACTTACT-TATTA
1 TGGCTC-TTATGAGCTT-CTCTATTA
38426264 TGGCTCTTATGAGCTTCTCTATT
1 TGGCTCTTATGAGCTTCTCTATT
38426287 TATATATCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
23 2 0.05
24 25 0.68
25 10 0.27
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (24 bp):
TGGCTCTTATGAGCTTCTCTATTA
Found at i:38430132 original size:27 final size:27
Alignment explanation
Indices: 38430094--38430149 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
38430084 TATTAACTTA
38430094 ATTAATCACTAATCATCTTTTTAGTGC
1 ATTAATCACTAATCATCTTTTTAGTGC
38430121 ATTAATCACTAATCATCTTTTTAGTGC
1 ATTAATCACTAATCATCTTTTTAGTGC
38430148 AT
1 AT
38430150 AACCCATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (27 bp):
ATTAATCACTAATCATCTTTTTAGTGC
Found at i:38430477 original size:5 final size:5
Alignment explanation
Indices: 38430467--38430502 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
38430457 TTGAAAAAGT
38430467 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
38430503 GTTTAATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:38431679 original size:2 final size:2
Alignment explanation
Indices: 38431672--38431712 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38431662 CCATTACTCT
38431672 TA TA 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 TA TA T
38431713 TAGATTCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38436158 original size:2 final size:2
Alignment explanation
Indices: 38436147--38436175 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38436137 TAAATATGTA
38436147 AT AT -T 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
38436176 GCGTGTGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38448904 original size:46 final size:45
Alignment explanation
Indices: 38448851--38448989 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 45
38448841 ACAATGCTAT
* *
38448851 AACTCAGTATGGTTTCCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTT-CTTCACTGAAACACCATACCTACTTTTCAC
*
38448897 AACTCAGTATGGTTTTCTTCGCTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
38448943 AACTCAGTATAGCTTTATTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTAT-GGTTTCTTCACTGAAACACCATACCTACTTTTCAC
38448989 A
1 A
38448990 GTTTTCCATG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
46 81 0.95
47 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (45 bp):
AACTCAGTATGGTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:38449758 original size:17 final size:17
Alignment explanation
Indices: 38449736--38449783 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
38449726 AAATTCTTTT
38449736 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
38449753 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
38449770 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
38449784 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:38449944 original size:21 final size:21
Alignment explanation
Indices: 38449904--38450068 Score: 79
Period size: 21 Copynumber: 8.0 Consensus size: 21
38449894 TTACATTTTT
*
38449904 AGAAGCTCA-AA-AGCTGAAC
1 AGAAGCTCATAAGAGCTAAAC
*
38449923 AGAAGCTCATGAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
* * * * *
38449944 AAAAAC-CTATAAGGGTTGAAC
1 AGAAGCTC-ATAAGAGCTAAAC
* **
38449965 GGAAGCTTGTAAGAGCTAAA-
1 AGAAGCTCATAAGAGCTAAAC
* * * *
38449985 AAAAACTCATAAGGGTTAAAC
1 AGAAGCTCATAAGAGCTAAAC
* *
38450006 AGAAGCTCGAT-AGAGTTGAAC
1 AGAAGCTC-ATAAGAGCTAAAC
* * * *
38450027 GGAAACTCATATGAGTTAAAC
1 AGAAGCTCATAAGAGCTAAAC
* *
38450048 AAAAGCTCATGAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
38450069 GAAAAGTAAA
Statistics
Matches: 102, Mismatches: 37, Indels: 12
0.68 0.25 0.08
Matches are distributed among these distances:
19 9 0.09
20 17 0.17
21 74 0.73
22 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTAAAC
Found at i:38450001 original size:41 final size:42
Alignment explanation
Indices: 38449920--38450012 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 42
38449910 TCAAAAGCTG
** * *
38449920 AACAGAAGCTCATGAGAGCTAAACAAAAACCTATAAGGGTTG
1 AACAGAAGCTTGTAAGAGCTAAACAAAAACCTATAAGGGTTA
*
38449962 AACGGAAGCTTGTAAGAGCTAAA-AAAAA-CTCATAAGGGTTA
1 AACAGAAGCTTGTAAGAGCTAAACAAAAACCT-ATAAGGGTTA
38450003 AACAGAAGCT
1 AACAGAAGCT
38450013 CGATAGAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.05
41 23 0.52
42 19 0.43
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTTGTAAGAGCTAAACAAAAACCTATAAGGGTTA
Found at i:38459358 original size:30 final size:29
Alignment explanation
Indices: 38459294--38459376 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 29
38459284 CAAAAGATAC
38459294 AAATTACATTTTAGCCCCTGAA-CTTTTCAA
1 AAATTACATTTTA-CCCCT-AATCTTTTCAA
* *
38459324 AAATTACATTTTGACCCCTAATTTTTTTATA
1 AAATTACATTTT-ACCCCTAATCTTTTCA-A
* *
38459355 AATTTACATCTTAACCCCTAAT
1 AAATTACAT-TTTACCCCTAAT
38459377 AACTTGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 2 0.04
30 22 0.49
31 19 0.42
32 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTACCCCTAATCTTTTCAA
Found at i:38459820 original size:22 final size:22
Alignment explanation
Indices: 38459792--38459844 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
38459782 CCAAGAAGTA
*
38459792 AAAAAAAGAAAAAACAGC-AAGG
1 AAAAAAAGAAAAAA-AACAAAGG
38459814 AAAAAAAGAAAAAAAACAAAGG
1 AAAAAAAGAAAAAAAACAAAGG
38459836 AAAAAAAGA
1 AAAAAAAGA
38459845 GAAGAAAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAACAAAGG
Found at i:38459957 original size:4 final size:4
Alignment explanation
Indices: 38459940--38459999 Score: 59
Period size: 4 Copynumber: 14.8 Consensus size: 4
38459930 CTGAACGGGG
* * *
38459940 AAGA AAGA AGGA AAGAA AAAA AAGA AAGA AAGA AAGA AGGGA AA-A AAGA
1 AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA
*
38459989 AAAA AAGA AAG
1 AAGA AAGA AAG
38460000 GGGGAAGAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 3 0.07
4 36 0.80
5 6 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:38460310 original size:13 final size:13
Alignment explanation
Indices: 38460292--38460326 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
38460282 TCTGAAACAA
38460292 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
38460305 AAAAAGAGAAAAG
1 AAAAAGAAAAAAG
38460318 AAAAA-AAAA
1 AAAAAGAAAA
38460327 CAAAAAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:38460331 original size:15 final size:15
Alignment explanation
Indices: 38460290--38460332 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38460280 AATCTGAAAC
38460290 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
38460305 AAAAAGAGAAAAGAA-
1 AAAAAAAGAAAA-AAG
*
38460320 AAAAAAACAAAAA
1 AAAAAAAGAAAAA
38460333 GGCCCCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.88
16 2 0.08
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:38460331 original size:23 final size:23
Alignment explanation
Indices: 38460290--38460333 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
38460280 AATCTGAAAC
*
38460290 AAAAAAAGAAAAAAGAAAAAGAG
1 AAAAAAAGAAAAAACAAAAAGAG
38460313 AAAAGAAA-AAAAAACAAAAAG
1 AAAA-AAAGAAAAAACAAAAAG
38460334 GCCCCAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAACAAAAAGAG
Found at i:38460332 original size:7 final size:7
Alignment explanation
Indices: 38460291--38460323 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
38460281 ATCTGAAACA
38460291 AAAAAAG
1 AAAAAAG
38460298 AAAAAAG
1 AAAAAAG
38460305 -AAAAAG
1 AAAAAAG
*
38460311 AGAAAAG
1 AAAAAAG
38460318 AAAAAA
1 AAAAAA
38460324 AAACAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:38460780 original size:18 final size:18
Alignment explanation
Indices: 38460759--38461161 Score: 303
Period size: 18 Copynumber: 22.7 Consensus size: 18
38460749 TCTCATGTTT
38460759 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
38460777 AAAAAATTCTCGTG-TTT-
1 -AAAAATTTTCGTGTTTTC
*
38460794 AAAAATTTTCGTGTTTTTA
1 AAAAATTTTCGTG-TTTTC
38460813 AAAAATTTTCGTG-TTT-
1 AAAAATTTTCGTGTTTTC
38460829 AAAAATTTTCGTGTTTAT-
1 AAAAATTTTCGTGTTT-TC
38460847 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
** *
38460864 AAAAATCCTAGTGTTTTCC
1 AAAAATTTTCGTGTTTT-C
* ***
38460883 AAAAAAATTTCCGTGATTAAA
1 --AAAAATTTTCGTG-TTTTC
*
38460904 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
38460922 CAAAATTTCCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
38460939 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
*
38460957 AAAAATTATCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
38460975 AAAAATTATCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
38460993 AACAATTCTCGCG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
38461010 ATAAATTTTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
* ** *
38461027 -AAATTTTTTTTGCTTTTTA
1 AAAAATTTTCGTG--TTTTC
*
38461046 AAAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
38461063 AAAAATTGTCATGTTTTA
1 AAAAATTTTCGTGTTTTC
* *
38461081 AAAAAATTTCCTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
38461098 TAAAATTTTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
* *
38461115 AAAAATTCTAGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
38461133 AAAAATTCTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
*
38461150 AAAAACTTTCGT
1 AAAAATTTTCGT
38461162 TTTGTTTAAA
Statistics
Matches: 304, Mismatches: 60, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
16 33 0.11
17 97 0.32
18 118 0.39
19 37 0.12
20 8 0.03
21 9 0.03
22 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:38460786 original size:35 final size:36
Alignment explanation
Indices: 38460740--38461220 Score: 323
Period size: 35 Copynumber: 13.5 Consensus size: 36
38460730 TAAGAAAAAA
*
38460740 TCAAAAAATTCTCATGTTT-AAAAATTTTCGTGTTT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
38460775 TCAAAAAATTCTCGTGTTT-AAAAATTTTCGTGTTT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
* *
38460810 TTAAAAAATTTTCGTGTTT-AAAAATTTTCGTG-TT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
* ** *
38460844 T-ATAAAAATTTTCGTGTTTCAAAAATCCTAGTGTTT
1 TCA-AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
** *
38460880 TCCAAAAAAATT-TCCGTGATTAAAAAAAATTCTCGTGTTT
1 T-C-AAAAAATTCT-CGTG-TT-TCAAAAATTTTCGTGTTT
* * *
38460920 TCCAAAATTTC-CGTGTTTCAAAAATTTTCATGTTT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
* *
38460955 TC-AAAAATTATCGTGTTTTCAAAAATTATCGTGTTT
1 TCAAAAAATTCTCGTG-TTTCAAAAATTTTCGTGTTT
* * * *
38460991 TC-AACAATTCTCGCGTTTCATAAATTTTCGTATTT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
*** * * * * *
38461026 T-AAATTTTTTTTGCTTTTTAAAAAATTCTCGTG-TT
1 TCAAAAAATTCTCG-TGTTTCAAAAATTTTCGTGTTT
* * * * *
38461061 TC-AAAAATTGTCATGTTTTAAAAAAATTTCCTG-TT
1 TCAAAAAATTCTCGTG-TTTCAAAAATTTTCGTGTTT
* * * * *
38461096 TC-TAAAATTTTCGTGTTTTAAAAATTCTAGTGTTT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
* * *
38461131 TC-AAAAATTCTCGTGTTTAAAAAACTTTCGTTTTGT
1 TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTT-T
* * *
38461167 TTAAAAAATT-ACGTGCTTC-AAAATTCTT-GTGTTT
1 TCAAAAAATTCTCGTGTTTCAAAAATT-TTCGTGTTT
* *
38461201 TAAAAAAAATCATCGTGTTT
1 TCAAAAAATTC-TCGTGTTT
38461221 TAATCGGATC
Statistics
Matches: 352, Mismatches: 72, Indels: 43
0.75 0.15 0.09
Matches are distributed among these distances:
33 1 0.00
34 47 0.13
35 192 0.55
36 64 0.18
37 12 0.03
38 17 0.05
39 4 0.01
40 15 0.04
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (36 bp):
TCAAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTT
Found at i:38461654 original size:9 final size:9
Alignment explanation
Indices: 38461640--38461664 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38461630 GCATGTTGTT
38461640 AAAATTTTC
1 AAAATTTTC
38461649 AAAATTTTC
1 AAAATTTTC
38461658 AAAATTT
1 AAAATTT
38461665 CTTGTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTC
Found at i:38472078 original size:15 final size:17
Alignment explanation
Indices: 38472060--38472105 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
38472050 TATTATGCCT
38472060 AAAAAAAC-A-AAACAA
1 AAAAAAACAAGAAACAA
38472075 AAAAAAACAAGAAACAA
1 AAAAAAACAAGAAACAA
38472092 AAAAGAAA-AAGAAA
1 AAAA-AAACAAGAAA
38472106 AAGCAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 16 0.57
18 3 0.11
ACGTcount: A:0.85, C:0.09, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAGAAACAA
Found at i:38473083 original size:75 final size:74
Alignment explanation
Indices: 38472956--38473611 Score: 567
Period size: 75 Copynumber: 8.7 Consensus size: 74
38472946 CAAGAAATAT
*** * * * *
38472956 TTTTCAATTTCTGTTTAAAAAAAAATCAAATTATAATGCAAGAGGTGAGTTGAGCCTTGGGCACA
1 TTTTCAATTTCTGTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACA
**
38473021 TGCCAAGGTA
65 TGCTGAGGTA
* * * * **
38473031 TTTCTCAATTTCTGTTTTTCAAAAATCAACTTACAATGCGAGAAGTGAGTTGAGCCTCAGGC-CA
1 TTT-TCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACA
*
38473095 CGCTGAGGTA
65 TGCTGAGGTA
* *
38473105 TTTTCAATTTCTGCTTTTCAAAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG-CA
38473170 C--GCTGAGGTA
63 CATGCTGAGGTA
* * *
38473180 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGGCA
38473245 CATGCTGAGGTA
63 CATGCTGAGGTA
* * * * *
38473257 TATTTTAATTTCTATTTTCCAAAAAATCAACTTATATTGCGAGAGGTAAGTTGA-CTCTTGGGTC
1 T-TTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-CTTGGG-C
** *
38473321 ACAAACTGAGGTTTTTT
62 ACATGCTGAGG----TA
* **
38473338 TTCTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGA----A-CCTAAGGCTAC
1 TT-TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGC-AC
** **
38473398 ACACCAAGGTA
64 ATGCTGAGGTA
* * *** * *
38473409 TTTTTAATTTCTTTTTTTTTTAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGCTATA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGC-ACA
**
38473474 CACTGAGGTA
65 TGCTGAGGTA
* * *
38473484 TTTTTAATTTCTGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGGTCATA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG-CACA
38473549 TGCTGAGGTA
65 TGCTGAGGTA
* ** * *
38473559 TTTTTCAATTTCTATTTTTCAAAGCTCAACTCATAATT-TGAGAAGTGAGTTGA
1 -TTTTCAATTTCTGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
38473612 ACTTTGGATC
Statistics
Matches: 483, Mismatches: 72, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
70 38 0.08
71 3 0.01
73 15 0.03
74 18 0.04
75 227 0.47
76 68 0.14
77 57 0.12
78 15 0.03
80 27 0.06
81 15 0.03
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (74 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACAT
GCTGAGGTA
Found at i:38473670 original size:14 final size:14
Alignment explanation
Indices: 38473653--38473679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38473643 TTCAGGCTTT
38473653 CAAAAAAATATAAA
1 CAAAAAAATATAAA
38473667 CAAAAAAATATAA
1 CAAAAAAATATAA
38473680 TAATTTTAGA
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (14 bp):
CAAAAAAATATAAA
Found at i:38473973 original size:30 final size:32
Alignment explanation
Indices: 38473938--38474019 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 32
38473928 CAAAAAATAC
38473938 AAATTACATTTTAGCCCCTAAAC-TTTTT-AA
1 AAATTACATTTTAGCCCCTAAACATTTTTCAA
* * *
38473968 AAATTACATTTT-GACCCTTAACATTTTTCTA
1 AAATTACATTTTAGCCCCTAAACATTTTTCAA
* * *
38473999 AATTTACATCTTAACCCCTAA
1 AAATTACATTTTAGCCCCTAA
38474020 TAATTTGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 8 0.20
30 17 0.41
31 11 0.27
32 5 0.12
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.40
Consensus pattern (32 bp):
AAATTACATTTTAGCCCCTAAACATTTTTCAA
Found at i:38474456 original size:25 final size:26
Alignment explanation
Indices: 38474428--38474486 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
38474418 ACCAAGAAGT
*
38474428 AAAAAA-AAAAAAAACAAC-AAGGAA
1 AAAAAAGAAAAAAAAAAACAAAGGAA
*
38474452 AAAAAAGGAAAAAAAAAACAAAGGAA
1 AAAAAAGAAAAAAAAAAACAAAGGAA
38474478 AAAAAAGAA
1 AAAAAAGAA
38474487 GAAATGGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 6 0.20
25 10 0.33
26 14 0.47
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAAAAAACAAAGGAA
Found at i:38474457 original size:26 final size:25
Alignment explanation
Indices: 38474428--38474486 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
38474418 ACCAAGAAGT
*
38474428 AAAAAAA-AAAAAAACAAC-AAGGA
1 AAAAAAAGAAAAAAAAAACAAAGGA
38474451 AAAAAAAGGAAAAAAAAAACAAAGGA
1 AAAAAAA-GAAAAAAAAAACAAAGGA
38474477 AAAAAAAGAA
1 AAAAAAAGAA
38474487 GAAATGGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 7 0.22
25 13 0.41
26 12 0.38
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAAAACAAAGGA
Found at i:38474490 original size:28 final size:28
Alignment explanation
Indices: 38474432--38474484 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
38474422 AGAAGTAAAA
38474432 AAAAAAAAAACAACAAGGAAAAAAAAGG
1 AAAAAAAAAACAACAAGGAAAAAAAAGG
38474460 AAAAAAAAAAC-A-AAGGAAAAAAAAG
1 AAAAAAAAAACAACAAGGAAAAAAAAG
38474485 AAGAAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.52
27 1 0.04
28 11 0.44
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAACAACAAGGAAAAAAAAGG
Found at i:38474596 original size:12 final size:12
Alignment explanation
Indices: 38474579--38474608 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38474569 CTGAACGGGG
38474579 AAGAAAAAAAGA
1 AAGAAAAAAAGA
38474591 AAGAAAAAAAGA
1 AAGAAAAAAAGA
38474603 AA-AAAA
1 AAGAAAA
38474609 GAAGGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:38474607 original size:19 final size:20
Alignment explanation
Indices: 38474579--38474632 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
38474569 CTGAACGGGG
38474579 AAGAAAAAAAGAAAGAAAAA
1 AAGAAAAAAAGAAAGAAAAA
* *
38474599 AAGAAAAAAAGAAGGGAAAA
1 AAGAAAAAAAGAAAGAAAAA
38474619 AAG-AAAAAAGAAAG
1 AAGAAAAAAAGAAAG
38474633 GGGGAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAGAAAGAAAAA
Found at i:38475596 original size:72 final size:72
Alignment explanation
Indices: 38475451--38475598 Score: 174
Period size: 71 Copynumber: 2.1 Consensus size: 72
38475441 TCTTGGGTTT
* * **
38475451 AAAATTTTCTTGTTTTCAAAAAAATTTTCGTGTCTAAAAGTTTTCATGTTTTCAAAAAAAAATTC
1 AAAATTTTCGTGTTTTCAAAAAAATTTTCGTGTCTAAAAATCCTCATGTTTTCAAAAAAAAATTC
*
38475516 GTGTTTA
66 GTGATTA
* * * * *
38475523 AAAATTTTCGTG-TTTC-CAAAAATTTTCGTGTTTAAAAAATCCTCGTGTTTTCCAAAAAAATTT
1 AAAATTTTCGTGTTTTCAAAAAAATTTTCGTGTCT-AAAAATCCTCATGTTTTCAAAAAAAAATT
38475586 CCGTGATTA
65 -CGTGATTA
38475595 AAAA
1 AAAA
38475599 CAATTCTAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
70 15 0.23
71 27 0.42
72 22 0.34
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (72 bp):
AAAATTTTCGTGTTTTCAAAAAAATTTTCGTGTCTAAAAATCCTCATGTTTTCAAAAAAAAATTC
GTGATTA
Found at i:38475620 original size:37 final size:36
Alignment explanation
Indices: 38475535--38475629 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 36
38475525 AATTTTCGTG
* * *
38475535 TTTCCAAAAATTTTCGTGTTTAAAAAATCCTCGTGT
1 TTTCCAAAAATTTCCGTGTTAAAAAAATCCTAGTGT
*
38475571 TTTCCAAAAAAATTTCCGTGATTAAAAACAATTCTAGTGT
1 TTTCC--AAAAATTTCCGTG-TTAAAAA-AATCCTAGTGT
38475611 TTTCC-AAAATTTCCGTGTT
1 TTTCCAAAAATTTCCGTGTT
38475630 TCAAAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 7 0.14
37 12 0.24
38 12 0.24
39 6 0.12
40 14 0.27
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (36 bp):
TTTCCAAAAATTTCCGTGTTAAAAAAATCCTAGTGT
Found at i:38475674 original size:53 final size:52
Alignment explanation
Indices: 38475451--38475854 Score: 203
Period size: 53 Copynumber: 7.5 Consensus size: 52
38475441 TCTTGGGTTT
* * * *
38475451 AAAATTTTCTTGTTTTCAAAAAAATTTTCGTGTCT-AAAAGTTTTC-ATGTTTTCAAA
1 AAAATTTTCGTG-TTTC--AAAAATTTTCGTGTTTCAAAAATTGTCGA-GTTTTC--A
** * * *
38475507 AAAAAATTCGTGTTT-AAAAATTTTCGTGTTTCCAAAAATTTTCGTG-TTTAA
1 AAAATTTTCGTGTTTCAAAAATTTTCGTGTTT-CAAAAATTGTCGAGTTTTCA
** * ** * * * *
38475558 AAAATCCTCGTGTTTTCCAAAAAAATTTCCGTGATTAAAAACAATTCTAGTGTTTTCC
1 AAAATTTTCGTG-TTT-C--AAAAATTTTCGTG-TTTCAAA-AATTGTCGAGTTTTCA
* *
38475616 AAAATTTCCGTGTTTCAAAAATTTTCATGTTTTCAAAAATTGTCGAGTTTTCA
1 AAAATTTTCGTGTTTCAAAAATTTTCGTG-TTTCAAAAATTGTCGAGTTTTCA
* * * * *
38475669 AAAATTTTCGTGTTTTCAACAATTCTCGCGTTTCACAAATTTTCGTA-TTTT-A
1 AAAATTTTCGTG-TTTCAAAAATTTTCGTGTTTCAAAAATTGTCG-AGTTTTCA
** * * * * * * *
38475721 AATTTTTTTGTTTTTTTAAAAAATTCTCGTGTTTCAAAAATTGTTGTGTTTTTAA
1 AAAATTTTCG--TGTTTCAAAAATTTTCGTGTTTCAAAAATTGTCGAG-TTTTCA
* * * * *
38475776 AAAATTTTCGTGTTTCTAAAA-TTTCTGTGTTTTAAAAATTCTAGTGTTTTCA
1 AAAATTTTCGTGTTTCAAAAATTTTC-GTGTTTCAAAAATTGTCGAGTTTTCA
* *
38475828 AAAATTATCGTGTTT-AAAAACTTTCGT
1 AAAATTTTCGTGTTTCAAAAATTTTCGT
38475855 TTTTTTAAAA
Statistics
Matches: 268, Mismatches: 60, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
51 16 0.06
52 52 0.19
53 94 0.35
54 45 0.17
55 11 0.04
56 25 0.09
57 13 0.05
58 12 0.04
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (52 bp):
AAAATTTTCGTGTTTCAAAAATTTTCGTGTTTCAAAAATTGTCGAGTTTTCA
Found at i:38475901 original size:18 final size:18
Alignment explanation
Indices: 38475415--38475866 Score: 215
Period size: 18 Copynumber: 25.3 Consensus size: 18
38475405 AGAAAAAATC
*
38475415 AAAAAATTCTCGTGTTTT
1 AAAAAATTTTCGTGTTTT
*
38475433 CAAAAAATTCTT-G-GGTTT
1 -AAAAAATT-TTCGTGTTTT
*
38475451 --AAAATTTTCTTGTTTT
1 AAAAAATTTTCGTGTTTT
*
38475467 CAAAAAAATTTTCGTG-TCT
1 --AAAAAATTTTCGTGTTTT
* *
38475486 -AAAAGTTTTCATGTTTT
1 AAAAAATTTTCGTGTTTT
**
38475503 CAAAAAAAAATTCGTG-TTT
1 --AAAAAATTTTCGTGTTTT
*
38475522 -AAAAATTTTCGTGTTTC
1 AAAAAATTTTCGTGTTTT
*
38475539 CAAAAATTTTCGTG-TTT
1 AAAAAATTTTCGTGTTTT
**
38475556 AAAAAATCCTCGTGTTTT
1 AAAAAATTTTCGTGTTTT
* * *
38475574 CCAAAAAAATTTCCGTGATTA
1 ---AAAAAATTTTCGTGTTTT
* *
38475595 AAAACAATTCTAGTGTTTT
1 AAAA-AATTTTCGTGTTTT
** *
38475614 CCAAAATTTCCGTG-TTT
1 AAAAAATTTTCGTGTTTT
* *
38475631 CAAAAATTTTCATGTTTT
1 AAAAAATTTTCGTGTTTT
* * *
38475649 CAAAAATTGTCGAGTTTT
1 AAAAAATTTTCGTGTTTT
*
38475667 CAAAAATTTTCGTGTTTT
1 AAAAAATTTTCGTGTTTT
* * * *
38475685 CAACAATTCTCGCG-TTT
1 AAAAAATTTTCGTGTTTT
* * *
38475702 CACAAATTTTCGTATTTT
1 AAAAAATTTTCGTGTTTT
** * *
38475720 -AAATTTTTTTGTTTTTTT
1 AAAAAATTTTCG-TGTTTT
*
38475738 AAAAAATTCTCGTG-TTT
1 AAAAAATTTTCGTGTTTT
*
38475755 CAAAAATTGTT-GTGTTTTT
1 AAAAAATT-TTCGTG-TTTT
38475774 AAAAAATTTTCGTGTTTCT
1 AAAAAATTTTCGTGTTT-T
38475793 --AAAA-TTTCTGTGTTTT
1 AAAAAATTTTC-GTGTTTT
* *
38475809 -AAAAATTCTAGTGTTTT
1 AAAAAATTTTCGTGTTTT
* *
38475826 CAAAAATTATCGTG-TTT
1 AAAAAATTTTCGTGTTTT
* *
38475843 -AAAAACTTTCGTTTTTTT
1 AAAAAATTTTCG-TGTTTT
38475861 AAAAAA
1 AAAAAA
38475867 AAATTTGTGC
Statistics
Matches: 328, Mismatches: 71, Indels: 68
0.70 0.15 0.15
Matches are distributed among these distances:
14 2 0.01
15 6 0.02
16 40 0.12
17 88 0.27
18 107 0.33
19 51 0.16
20 21 0.06
21 13 0.04
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAAATTTTCGTGTTTT
Found at i:38483802 original size:25 final size:25
Alignment explanation
Indices: 38483774--38483842 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
38483764 CCCAATTTAT
*
38483774 GGCTCTTTAGAGCTTTCCGATTAAA
1 GGCTCTTTAGAGCTTCCCGATTAAA
* *
38483799 GGCTTTTTCATGAGCTTCCCGATTAAT
1 GGCTCTTT-A-GAGCTTCCCGATTAAA
*
38483826 GGCTCTTTTGAGCTTCC
1 GGCTCTTTAGAGCTTCC
38483843 TAATATTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 15 0.41
26 1 0.03
27 21 0.57
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
GGCTCTTTAGAGCTTCCCGATTAAA
Found at i:38491632 original size:3 final size:3
Alignment explanation
Indices: 38491618--38491661 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
38491608 TACAAAGCGG
* * * *
38491618 TAA TAG TAA TAA TAA TAA CAA TAG TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
38491662 CACTACACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:38491642 original size:18 final size:18
Alignment explanation
Indices: 38491619--38491653 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
38491609 ACAAAGCGGT
38491619 AATAGTAATAATAATAAC
1 AATAGTAATAATAATAAC
38491637 AATAGTAATAATAATAA
1 AATAGTAATAATAATAA
38491654 TAACAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
AATAGTAATAATAATAAC
Found at i:38491951 original size:42 final size:42
Alignment explanation
Indices: 38491793--38492045 Score: 316
Period size: 42 Copynumber: 6.0 Consensus size: 42
38491783 GGTGCTTACA
*
38491793 GAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTG
*
38491836 GAAAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
*
38491879 GAAAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * * *
38491921 GGAAAAAACGCTGCTAAAGAAT-ATGATCTTTAGCGGCGTTTAG
1 GAAAAAAACGCCGCTAAAG-ATCATGTTCTTTAGCGGCGCTT-G
* * *
38491964 G-AAAAAATGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG
* *
38492005 GTAAAAAACGCCGCTAAA-AGTAATGTTCTTTAGCGGCGCTT
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTT
38492046 CATCTACAAA
Statistics
Matches: 190, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 103 0.54
43 83 0.44
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (42 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
Found at i:38492075 original size:43 final size:41
Alignment explanation
Indices: 38491798--38492102 Score: 186
Period size: 43 Copynumber: 7.2 Consensus size: 41
38491788 TTACAGAAAA
* * * *
38491798 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT-TGGAAAA
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAT---TAC
* * ** *
38491841 AAACGCCGCT-AATGATCATGTTCTTTAGCGGCGCTTAGGAAAA
1 AAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTA--TTAC
* * *** *
38491884 AAACGCCGCT-AATGATCATGTTCTTTAGCGGCGCTTGGGAAA
1 AAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTT-ATTAC
* * * * ** *
38491926 AAACGCTGCT-AAAGAATATGATCTTTAGCGGCGTTTAGGAAA
1 AAACGCCGCTAAAAGTA-ATGTTCTTTAGCGGCGCTTA-TTAC
* * * * *
38491968 AAATGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGTAAA
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-ATTAC
38492010 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-AT-TAC
* *
38492053 AAACGCCGCTAAAAGTAGTGTTCTTTCGCGGCGCTTATTTCAC
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTA-TT-AC
38492096 AAACGCC
1 AAACGCC
38492103 ACTATATGAT
Statistics
Matches: 223, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
42 103 0.46
43 120 0.54
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTATTAC
Found at i:38492086 original size:85 final size:83
Alignment explanation
Indices: 38491792--38492088 Score: 337
Period size: 85 Copynumber: 3.5 Consensus size: 83
38491782 CGGTGCTTAC
* *
38491792 AGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTGGAAAAAAACGCCGCTAATGAT
1 AGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGC-TTGGAAAAAAACGCCGCTAAAG-T
*
38491857 CATGTTCTTTAGCGGCGCTT
64 AATGTTCTTTAGCGGCGCTT
* * * *
38491877 AGGAAAAAAACGCCGCT-AATGATCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCTGCTAAAGA
1 A-GAAAAAAACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGCTTGGAAAAAAACGCCGCTAAAGT
* *
38491941 ATATGATCTTTAGCGGCGTTT
64 A-ATGTTCTTTAGCGGCGCTT
* * * * *
38491962 AGGAAAAAATGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGTAAAAAACGCCGCTAAAAGTA
1 AGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTGGAAAAAAACGCCGCT-AAAGTA
38492027 ATGTTCTTTAGCGGCGCTT
65 ATGTTCTTTAGCGGCGCTT
*** * *
38492046 CATCTACAAACGCCGCTAAAAGT-AGTGTTCTTTCGCGGCGCTT
1 -AGAAAAAAACGCCGCTAAAAGTCA-TGTTCTTTAGCGGCGCTT
38492089 ATTTCACAAA
Statistics
Matches: 180, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
84 64 0.36
85 82 0.46
86 34 0.19
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (83 bp):
AGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTGGAAAAAAACGCCGCTAAAGTAA
TGTTCTTTAGCGGCGCTT
Found at i:38492528 original size:66 final size:66
Alignment explanation
Indices: 38492458--38492588 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
38492448 TTTGCTCTGC
* * *
38492458 TCTGCTTCTCTCGATG-TCGCATCTGCTTGAAGTCGTAGCTGTAGTTGTTCATATTTCTTTTGAA
1 TCTGCTTCTCTCGATGCT-GCATCTGCTTGAAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAA
38492522 CA
65 CA
* * * * * *
38492524 TCTGCTTCTCTCGCTGCTGCCTCTGTTTTAAGTTGTTGCTGAAGTTCTTCATATTTCCTTTGAAC
1 TCTGCTTCTCTCGATGCTGCATCTGCTTGAAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAAC
38492589 CTCAAATGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (66 bp):
TCTGCTTCTCTCGATGCTGCATCTGCTTGAAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAAC
A
Found at i:38498007 original size:9 final size:9
Alignment explanation
Indices: 38497972--38498675 Score: 460
Period size: 9 Copynumber: 77.0 Consensus size: 9
38497962 TTAAACAATA
38497972 ATGTAAGTT
1 ATGTAAGTT
*
38497981 A-GGAAGGTT
1 ATGTAA-GTT
38497990 ATGT-A-TT
1 ATGTAAGTT
38497997 ATGTAAGTT
1 ATGTAAGTT
*
38498006 ATGAAAGTT
1 ATGTAAGTT
*
38498015 ATGTAATTT
1 ATGTAAGTT
38498024 ATGTAAGTT
1 ATGTAAGTT
38498033 ATGTAAGTT
1 ATGTAAGTT
38498042 ATGTAAGTT
1 ATGTAAGTT
* *
38498051 ATTTAATTT
1 ATGTAAGTT
38498060 ATGTAAGTT
1 ATGTAAGTT
*
38498069 ATGTAAGAT
1 ATGTAAGTT
38498078 ATGTAAGTT
1 ATGTAAGTT
* *
38498087 ATATAATTT
1 ATGTAAGTT
38498096 ATGTAAGCAATT
1 ATGTAAG---TT
* *
38498108 -TAGAAAAAATT
1 AT-G--TAAGTT
38498119 ATGTAAGTT
1 ATGTAAGTT
38498128 ATGTACTAAGTT
1 ATG---TAAGTT
38498140 ATGT-A-TT
1 ATGTAAGTT
* *
38498147 ATGTAAATA
1 ATGTAAGTT
*
38498156 ATTTAAGTT
1 ATGTAAGTT
*
38498165 A-GGAAGGTT
1 ATGTAA-GTT
38498174 ATGT-A-TT
1 ATGTAAGTT
38498181 ATGTAAGTT
1 ATGTAAGTT
* *
38498190 ATTTAATTT
1 ATGTAAGTT
38498199 ATGTAAGTT
1 ATGTAAGTT
*
38498208 ATGTAAGAT
1 ATGTAAGTT
38498217 ATGTAAGTT
1 ATGTAAGTT
* *
38498226 ATATAATTT
1 ATGTAAGTT
38498235 ATGTAAGCAATT
1 ATGTAAG---TT
* *
38498247 -TAGAAAAAATT
1 AT-G--TAAGTT
38498258 ATGTAAGTT
1 ATGTAAGTT
38498267 ATGTACTAAGTT
1 ATG---TAAGTT
38498279 ATGT-A-TT
1 ATGTAAGTT
* *
38498286 ATGTAAATA
1 ATGTAAGTT
*
38498295 ATTTAAGTT
1 ATGTAAGTT
*
38498304 A-GGAAGGTT
1 ATGTAA-GTT
38498313 ATGT-A-TT
1 ATGTAAGTT
38498320 ATGTAAGTT
1 ATGTAAGTT
*
38498329 ATTTAAGTT
1 ATGTAAGTT
38498338 ATGTAAGTT
1 ATGTAAGTT
*
38498347 ATTTAAGTT
1 ATGTAAGTT
* *
38498356 ATTTAATTT
1 ATGTAAGTT
38498365 ATGTAAGTT
1 ATGTAAGTT
38498374 ATGTAAGTT
1 ATGTAAGTT
38498383 ATGTAAGTT
1 ATGTAAGTT
*
38498392 ATTTAAGTT
1 ATGTAAGTT
38498401 ATGTAAGTT
1 ATGTAAGTT
* *
38498410 ATATAATTT
1 ATGTAAGTT
**
38498419 ATGTAAGCA
1 ATGTAAGTT
* ***
38498428 ATTTAGAAAAA
1 ATGT--AAGTT
*
38498439 AT-TAATTT
1 ATGTAAGTT
38498447 ATGTAAGCAATT
1 ATGTAAG---TT
* *
38498459 -TAGAAAAAATT
1 AT-G--TAAGTT
38498470 ATGTAAGTT
1 ATGTAAGTT
38498479 ATGTACTAAGTT
1 ATG---TAAGTT
38498491 ATGT-A-TT
1 ATGTAAGTT
* *
38498498 ATGTAAATA
1 ATGTAAGTT
38498507 ATGTAAGTT
1 ATGTAAGTT
* *
38498516 AGGAAAGTT
1 ATGTAAGTT
38498525 ATGT-A-TT
1 ATGTAAGTT
38498532 ATGTAAGTT
1 ATGTAAGTT
*
38498541 ATTTAAGTT
1 ATGTAAGTT
38498550 ATGTAAGTT
1 ATGTAAGTT
38498559 ATGTAAGTT
1 ATGTAAGTT
* *
38498568 ATTTAATTT
1 ATGTAAGTT
38498577 ATGTAAGTT
1 ATGTAAGTT
*
38498586 ATGTAAATT
1 ATGTAAGTT
* *
38498595 ATTTAATTT
1 ATGTAAGTT
*
38498604 ATGTAATTT
1 ATGTAAGTT
38498613 ATGTAAGTT
1 ATGTAAGTT
38498622 ATGTAAGTT
1 ATGTAAGTT
* *
38498631 ATTTAATTT
1 ATGTAAGTT
38498640 ATGTAAGTT
1 ATGTAAGTT
*
38498649 ATGTAATTT
1 ATGTAAGTT
*
38498658 ATATAAGTT
1 ATGTAAGTT
*
38498667 ATGCAAGTT
1 ATGTAAGTT
38498676 TATATATAAG
Statistics
Matches: 542, Mismatches: 100, Indels: 106
0.72 0.13 0.14
Matches are distributed among these distances:
7 42 0.08
8 22 0.04
9 412 0.76
10 4 0.01
11 17 0.03
12 39 0.07
14 6 0.01
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:38498194 original size:139 final size:139
Alignment explanation
Indices: 38498030--38498380 Score: 621
Period size: 139 Copynumber: 2.5 Consensus size: 139
38498020 ATTTATGTAA
38498030 GTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATT
1 GTTATGT-A-TTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATT
38498095 TATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAATAATTT
64 TATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAATAATTT
38498160 AAGTTAGGAAG
129 AAGTTAGGAAG
38498171 GTTATGTATTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATTTA
1 GTTATGTATTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATTTA
38498236 TGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAATAATTTAA
66 TGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAATAATTTAA
38498301 GTTAGGAAG
131 GTTAGGAAG
* * * * * * *
38498310 GTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATTTAAGTTATTTAATTTATGTAAGTTA
1 GTTATGTATTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATTTA
38498375 TGTAAG
66 TGTAAG
38498381 TTATGTAAGT
Statistics
Matches: 203, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
139 195 0.96
140 1 0.00
141 7 0.03
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (139 bp):
GTTATGTATTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATGTAAGTTATATAATTTA
TGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAATAATTTAA
GTTAGGAAG
Found at i:38498453 original size:28 final size:28
Alignment explanation
Indices: 38498413--38498470 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
38498403 GTAAGTTATA
38498413 TAATTTATGTAAGCAATTTAGAAAAAAT
1 TAATTTATGTAAGCAATTTAGAAAAAAT
38498441 TAATTTATGTAAGCAATTTAGAAAAAAT
1 TAATTTATGTAAGCAATTTAGAAAAAAT
38498469 TA
1 TA
38498471 TGTAAGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.36
Consensus pattern (28 bp):
TAATTTATGTAAGCAATTTAGAAAAAAT
Found at i:38498478 original size:212 final size:212
Alignment explanation
Indices: 38498229--38498632 Score: 718
Period size: 212 Copynumber: 1.9 Consensus size: 212
38498219 GTAAGTTATA
38498229 TAATTTATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAAT
1 TAATTTATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAAT
* * *
38498294 AATTTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATTTAAGTTATT
66 AATGTAAGTTAGGAAAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATT
* * *
38498359 TAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAAGTTATGTAAGTTATATAATTTATGTA
131 TAATTTATGTAAGTTATGTAAATTATGTAAGTTATGTAAGTTATGTAAGTTATATAAGTTATGTA
38498424 AGCAATTTAGAAAAAAT
196 AGCAATTTAGAAAAAAT
38498441 TAATTTATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAAT
1 TAATTTATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAAT
38498506 AATGTAAGTTAGGAAAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATT
66 AATGTAAGTTAGGAAAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATT
* * * *
38498571 TAATTTATGTAAGTTATGTAAATTATTTAATTTATGTAATTTATGTAAGTTATGTAAGTTAT
131 TAATTTATGTAAGTTATGTAAATTATGTAAGTTATGTAAGTTATGTAAGTTATATAAGTTAT
38498633 TTAATTTATG
Statistics
Matches: 182, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
212 182 1.00
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (212 bp):
TAATTTATGTAAGCAATTTAGAAAAAATTATGTAAGTTATGTACTAAGTTATGTATTATGTAAAT
AATGTAAGTTAGGAAAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATT
TAATTTATGTAAGTTATGTAAATTATGTAAGTTATGTAAGTTATGTAAGTTATATAAGTTATGTA
AGCAATTTAGAAAAAAT
Done.