Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold241
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1040028
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 103832 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:830867 original size:353 final size:352
Alignment explanation
Indices: 830298--831042 Score: 960
Period size: 353 Copynumber: 2.1 Consensus size: 352
830288 ACTTGAAAGA
* * ** *
830298 CTTGGATGCTGAATCTGAGTTCTAAATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGGT
1 CTTGGATGCTGAATCTGAGCTATAGGTTTCAGATGCT-GAGGAGGTTAAGGTTGTTAGACCAGGT
*
830363 TAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCAGGTCCGTACTTCACC
65 TAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTGCAGGTCCGTACTTCACC
* * * * *
830428 AAACTTGCATGGATGATGTGTCTTATGATACTGATGGACCAGACAGGCTTGAGTGCTGAATCTGA
130 AAACTTCCATGGATGATGCGTCTAATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGA
* * ***
830493 GCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGG
195 GCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGAAACAGG
* * * * *
830558 TGCCCTTTGATAGCA-ATATCTAAGTTACTGCTGGTCCGT-ACTTCACCAAACTTGCATTGATGG
260 TGCCCTCTGAT-G-ATATATCTAAGTTACTACTGGTCC-TAACTACACCAAACTTCCATGGATGG
* *
830621 TGTGTCTTATGATACTGATGCACCAGGCAGG
322 TGCGTCTTATGATACTGATGCACCAGACAGG
* * * * * *
830652 CTTGGATGCTGAATCTGAGCTATAGGCTACAGATGCTGAGTAGGTTAAGGTTTTTAGAGCTGGTT
1 CTTGGATGCTGAATCTGAGCTATAGGTTTCAGATGCTGAGGAGGTTAAGGTTGTTAGACCAGGTT
* * **
830717 AAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATTATATCTTAGTTACTTCTTGTCC-TAACTTCA
66 AAAGTTTTTGTTGCAGGTGCCCTCTGATAGCA--ATATCTAAGTTACTGCAGGTCCGT-ACTTCA
* * *
830779 CCAGACTTCCATTGATGGTGCGTCTAATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCT
128 CCAAACTTCCATGGATGATGCGTCTAATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCT
* *
830844 GAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTATAGCTGGTTAAAGTTTTTGAAACA
193 GAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGAAACA
* * * *
830909 GGTGCCCTCTGATGATTATATCTTAGTTATTACTTGTCCTAACTACACCAGACTTCCATGGATGG
258 GGTGCCCTCTGATGA-TATATCTAAGTTACTACTGGTCCTAACTACACCAAACTTCCATGGATGG
* *
830974 TGCGTCTTATGATACTGATGCACCTGACTGG
322 TGCGTCTTATGATACTGATGCACCAGACAGG
* * *
831005 CTTGAATGCTGAGTCTGAGCCATAGGTTTCAGATGCTG
1 CTTGGATGCTGAATCTGAGCTATAGGTTTCAGATGCTG
831043 GATATGTTTA
Statistics
Matches: 336, Mismatches: 49, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
351 2 0.01
352 4 0.01
353 299 0.89
354 31 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (352 bp):
CTTGGATGCTGAATCTGAGCTATAGGTTTCAGATGCTGAGGAGGTTAAGGTTGTTAGACCAGGTT
AAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTGCAGGTCCGTACTTCACCA
AACTTCCATGGATGATGCGTCTAATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAG
CCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGAAACAGGT
GCCCTCTGATGATATATCTAAGTTACTACTGGTCCTAACTACACCAAACTTCCATGGATGGTGCG
TCTTATGATACTGATGCACCAGACAGG
Found at i:832454 original size:15 final size:15
Alignment explanation
Indices: 832434--832468 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
832424 ATATTCTATA
*
832434 ATATTGTATCATACG
1 ATATTGTATAATACG
*
832449 ATATTGTATAATATG
1 ATATTGTATAATACG
832464 ATATT
1 ATATT
832469 AGTTTCTGGA
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:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (15 bp):
ATATTGTATAATACG
Found at i:832779 original size:220 final size:219
Alignment explanation
Indices: 832511--832951 Score: 864
Period size: 220 Copynumber: 2.0 Consensus size: 219
832501 ACTGTTTAAA
832511 ATGATACTGTAATATTATATAATATCGTATCATACGATATATTGTATAATATGATATTGGTTTAT
1 ATGATACTGTAATATTATATAATATCGTATCATACGATATATTGTATAATATGATATTGGTTTAT
832576 AATATAATATATTATCACATCACATGAAATTGTATTGTATGATATTGTAAAATATATTATTGTAT
66 AATATAATATATTATCACATCACATGAAATTGTATTGTATGATATTGTAAAATATATTATTGTAT
832641 CATATGATACAATATGTATAATATAATGTTGTATTATATATTTTACTTTATCACATAATATTGTA
131 CATATGATACAATATGTATAATATAATGTTGTATTATATATTTTACTTTATCACATAATATTGTA
*
832706 TCATTTGATTTGATACAATGTTGT
196 TCATTTGATATGATACAATGTTGT
832730 NATGATACTGTAATATTATATAATATCGTATCATACGATATATTGTATAATATGATATTGGTTTA
1 -ATGATACTGTAATATTATATAATATCGTATCATACGATATATTGTATAATATGATATTGGTTTA
832795 TAATATAATATATTATCACATCACATGAAATTGTATTGTATGATATTGTAAAATATATTATTGTA
65 TAATATAATATATTATCACATCACATGAAATTGTATTGTATGATATTGTAAAATATATTATTGTA
832860 TCATATGATACAATATGTATAATATAATGTTGTATTATATATTTTACTTTATCACATAATATTGT
130 TCATATGATACAATATGTATAATATAATGTTGTATTATATATTTTACTTTATCACATAATATTGT
832925 ATCATTTGATATGATACAATGTTGT
195 ATCATTTGATATGATACAATGTTGT
832950 AT
1 AT
832952 CAAATTATAT
Statistics
Matches: 220, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
219 2 0.01
220 218 0.99
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (219 bp):
ATGATACTGTAATATTATATAATATCGTATCATACGATATATTGTATAATATGATATTGGTTTAT
AATATAATATATTATCACATCACATGAAATTGTATTGTATGATATTGTAAAATATATTATTGTAT
CATATGATACAATATGTATAATATAATGTTGTATTATATATTTTACTTTATCACATAATATTGTA
TCATTTGATATGATACAATGTTGT
Found at i:833030 original size:10 final size:10
Alignment explanation
Indices: 833002--833040 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
832992 TTCAAAAATG
*
833002 ATACAACATC
1 ATACAATATC
833012 ATACAATATC
1 ATACAATATC
* *
833022 ATACTATATT
1 ATACAATATC
833032 ATACAATAT
1 ATACAATAT
833041 AATATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (10 bp):
ATACAATATC
Found at i:833433 original size:16 final size:15
Alignment explanation
Indices: 833403--833447 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
833393 ATTTAATATG
833403 ATAAAGGTG-GTCTC
1 ATAAAGGTGAGTCTC
833417 ATAAAGGTGAAGTCTC
1 ATAAAGGTG-AGTCTC
*
833433 ATAAGGGTGATGTCT
1 ATAAAGGTGA-GTCT
833448 TGTCTCGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 17 0.63
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (15 bp):
ATAAAGGTGAGTCTC
Found at i:847100 original size:33 final size:33
Alignment explanation
Indices: 847056--847143 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
847046 ATTCTGTGTC
* *
847056 GAAAACGTGTATTGACGTATTTCGTGCCATGCT
1 GAAAACTTGTATTGACGTATTTCGTGCCATGCA
*
847089 GAAAAGTTGTATTGACGTATTTCGTGCCATGCA
1 GAAAACTTGTATTGACGTATTTCGTGCCATGCA
*
847122 GAAAACTTGTATTTACGTATTT
1 GAAAACTTGTATTGACGTATTT
847144 TGTAACCACA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (33 bp):
GAAAACTTGTATTGACGTATTTCGTGCCATGCA
Found at i:855708 original size:22 final size:22
Alignment explanation
Indices: 855683--855731 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
855673 AGCAATGGTA
*
855683 CGATAATGCAATGACAATGAAG
1 CGATAATGCAACGACAATGAAG
* *
855705 CGATGATGCGACGACAATGAAG
1 CGATAATGCAACGACAATGAAG
855727 CGATA
1 CGATA
855732 GCGCAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (22 bp):
CGATAATGCAACGACAATGAAG
Found at i:864437 original size:18 final size:18
Alignment explanation
Indices: 864414--864452 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
864404 AGTAGTTTCG
*
864414 TCACCACAATCATCATCA
1 TCACCACAATCATCAACA
* *
864432 TCACCACTATCGTCAACA
1 TCACCACAATCATCAACA
864450 TCA
1 TCA
864453 TCAACTACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.38, G:0.03, T:0.23
Consensus pattern (18 bp):
TCACCACAATCATCAACA
Found at i:864617 original size:23 final size:23
Alignment explanation
Indices: 864585--864661 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
864575 ATCATCGTCG
*
864585 TCGTCATCATCACCATAACATCA
1 TCGTCGTCATCACCATAACATCA
*
864608 TCGTCGTCATCAACATGAACATCGCA
1 TCGTCGTCATCACCAT-AACAT--CA
*
864634 TCGTCATCGACATCACCATAACATCA
1 TCG---TCGTCATCACCATAACATCA
864660 TC
1 TC
864662 ATCTTCTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 14 0.32
24 5 0.11
26 9 0.20
28 5 0.11
29 11 0.25
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (23 bp):
TCGTCGTCATCACCATAACATCA
Found at i:864635 original size:29 final size:28
Alignment explanation
Indices: 864574--864664 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
864564 ACATGACCAT
* * * *
864574 CATCATCGTCGTCGTCATCATCACCATAA
1 CATCATCGTCGTCATCAACAT-AACATCA
*
864603 CATCATCGTCGTCATCAACATGAACATCG
1 CATCATCGTCGTCATCAACAT-AACATCA
* * * *
864632 CATCGTCATCGACATCACCATAACATCA
1 CATCATCGTCGTCATCAACATAACATCA
864660 TCATC
1 -CATC
864665 TTCTCAACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
28 6 0.12
29 44 0.88
ACGTcount: A:0.31, C:0.34, G:0.10, T:0.25
Consensus pattern (28 bp):
CATCATCGTCGTCATCAACATAACATCA
Found at i:867632 original size:2 final size:2
Alignment explanation
Indices: 867627--867676 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
867617 CAATTTTTTA
867627 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
867669 AG AG AG AG
1 AG AG AG AG
867677 GCGTTTCCGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:873912 original size:21 final size:21
Alignment explanation
Indices: 873882--874020 Score: 125
Period size: 21 Copynumber: 6.6 Consensus size: 21
873872 ACGGTTTCGT
* *
873882 GTTAATTCGCGAAAGTTATGC
1 GTTAAATCGCGAAAGTTACGC
*
873903 GTTAAATCGCGAAAGTAACGC
1 GTTAAATCGCGAAAGTTACGC
* *
873924 ATTATATCGCGAAAGTTACGC
1 GTTAAATCGCGAAAGTTACGC
* * * * *
873945 GTTTATTTGCGAAACTTACAC
1 GTTAAATCGCGAAAGTTACGC
* *
873966 GTTATATCGCGAAAGTTTCGC
1 GTTAAATCGCGAAAGTTACGC
* * * *
873987 GTTTATTTGCGAAACTTACGC
1 GTTAAATCGCGAAAGTTACGC
*
874008 GTTATATCGCGAA
1 GTTAAATCGCGAA
874021 TTTTTCGCGT
Statistics
Matches: 88, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (21 bp):
GTTAAATCGCGAAAGTTACGC
Found at i:873947 original size:42 final size:42
Alignment explanation
Indices: 873888--874034 Score: 186
Period size: 42 Copynumber: 3.5 Consensus size: 42
873878 TCGTGTTAAT
* * * * * * *
873888 TCGCGAAAGTTATGCGTTAAATCGCGAAAGTAACGCATTATA
1 TCGCGAAAGTTACGCGTTTATTTGCGAAACTTACGCGTTATA
*
873930 TCGCGAAAGTTACGCGTTTATTTGCGAAACTTACACGTTATA
1 TCGCGAAAGTTACGCGTTTATTTGCGAAACTTACGCGTTATA
*
873972 TCGCGAAAGTTTCGCGTTTATTTGCGAAACTTACGCGTTATA
1 TCGCGAAAGTTACGCGTTTATTTGCGAAACTTACGCGTTATA
** *
874014 TCGCGAATTTTTCGCGTTTAT
1 TCGCGAAAGTTACGCGTTTAT
874035 CGAAAACAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (42 bp):
TCGCGAAAGTTACGCGTTTATTTGCGAAACTTACGCGTTATA
Found at i:874029 original size:21 final size:20
Alignment explanation
Indices: 873928--874036 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 20
873918 TAACGCATTA
* *
873928 TATCGCGAAAGTTACGCGTT
1 TATCGCGAAACTTTCGCGTT
* * *
873948 TATTTGCGAAACTTACACGTT
1 TA-TCGCGAAACTTTCGCGTT
*
873969 ATATCGCGAAAGTTTCGCGTT
1 -TATCGCGAAACTTTCGCGTT
* *
873990 TATTTGCGAAACTTACGCGTT
1 TA-TCGCGAAACTTTCGCGTT
**
874011 ATATCGCGAATTTTTCGCGTT
1 -TATCGCGAAACTTTCGCGTT
874032 TATCG
1 TATCG
874037 AAAACAATAT
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
20 9 0.13
21 58 0.82
22 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
TATCGCGAAACTTTCGCGTT
Found at i:875578 original size:2 final size:2
Alignment explanation
Indices: 875571--875611 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
875561 GGAAAAGATA
875571 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
875612 GATTTATTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:877716 original size:38 final size:38
Alignment explanation
Indices: 877668--877815 Score: 269
Period size: 38 Copynumber: 3.9 Consensus size: 38
877658 TAACGTTTCG
* *
877668 GTCCGTTATTATTCAAATGAATATGTGGACAGGCCTCC
1 GTCCTTTATTATTCAAATGAATATGTGGACAGGTCTCC
877706 GTCCTTTATTATTCAAATGAATATGTGGACAGGTCTCC
1 GTCCTTTATTATTCAAATGAATATGTGGACAGGTCTCC
*
877744 GTCCTTCATTATTCAAATGAATATGTGGACAGGTCTCC
1 GTCCTTTATTATTCAAATGAATATGTGGACAGGTCTCC
877782 GTCCTTTATTATTCAAATGAATATGTGGACAGGT
1 GTCCTTTATTATTCAAATGAATATGTGGACAGGT
877816 TTATCTGTTT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 106 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (38 bp):
GTCCTTTATTATTCAAATGAATATGTGGACAGGTCTCC
Found at i:878544 original size:14 final size:14
Alignment explanation
Indices: 878525--878553 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
878515 ACGCGAAGCG
878525 TCCCAAACAGGCAC
1 TCCCAAACAGGCAC
878539 TCCCAAACAGGCAC
1 TCCCAAACAGGCAC
878553 T
1 T
878554 ATTTATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.41, G:0.14, T:0.10
Consensus pattern (14 bp):
TCCCAAACAGGCAC
Found at i:885263 original size:18 final size:18
Alignment explanation
Indices: 885240--885324 Score: 100
Period size: 18 Copynumber: 4.6 Consensus size: 18
885230 TTTATAGACA
885240 CTCTCTCTTTCTCTCTCT
1 CTCTCTCTTTCTCTCTCT
885258 CTCTCTCTCTCTCTCTCTCT
1 CTCTCTCT-T-TCTCTCTCT
**
885278 CTCTCTCTCCCTCTCTCT
1 CTCTCTCTTTCTCTCTCT
*
885296 CTCTCTCGTTAC-CTCTCT
1 CTCTCTC-TTTCTCTCTCT
*
885314 ATCTCTCTTTC
1 CTCTCTCTTTC
885325 CTGCCAATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
17 3 0.05
18 35 0.60
19 3 0.05
20 17 0.29
ACGTcount: A:0.02, C:0.47, G:0.01, T:0.49
Consensus pattern (18 bp):
CTCTCTCTTTCTCTCTCT
Found at i:885321 original size:2 final size:2
Alignment explanation
Indices: 885240--885302 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
885230 TTTATAGACA
*
885240 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
885282 CT CT CC CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
885303 GTTACCTCTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:894878 original size:21 final size:20
Alignment explanation
Indices: 894854--894910 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
894844 TTTGCATATA
894854 GACATAATTATCGTACATGTT
1 GACATAATTATC-TACATGTT
* *
894875 GACATACATTTTCTGCATGTT
1 GACATA-ATTATCTACATGTT
*
894896 GACCTAATTAATCTA
1 GACATAATT-ATCTA
894911 TCTTACATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.10
21 21 0.72
22 5 0.17
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
GACATAATTATCTACATGTT
Found at i:912663 original size:2 final size:2
Alignment explanation
Indices: 912656--912683 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
912646 ATAATTTTAT
912656 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
912684 AGGGGGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:931156 original size:4 final size:4
Alignment explanation
Indices: 931147--931202 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
931137 TACCCTTGTG
** * * * *
931147 TGTC TGTC TGTC TGTC CATC CGTC CGTC CGTC CGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
931195 TGTC TGTC
1 TGTC TGTC
931203 CGTCCGTAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.02, C:0.34, G:0.23, T:0.41
Consensus pattern (4 bp):
TGTC
Found at i:931195 original size:12 final size:12
Alignment explanation
Indices: 931147--931206 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
931137 TACCCTTGTG
*
931147 TGTCTGTCTGTC
1 TGTCTGTCCGTC
**
931159 TGTCCATCCGTC
1 TGTCTGTCCGTC
* *
931171 CGTCCGTCCGTC
1 TGTCTGTCCGTC
*
931183 TGTCTGTCTGTC
1 TGTCTGTCCGTC
931195 TGTCTGTCCGTC
1 TGTCTGTCCGTC
931207 CGTAACAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.02, C:0.35, G:0.23, T:0.40
Consensus pattern (12 bp):
TGTCTGTCCGTC
Found at i:931624 original size:166 final size:167
Alignment explanation
Indices: 931233--931836 Score: 989
Period size: 167 Copynumber: 3.6 Consensus size: 167
931223 GTCGCATTTA
* * *
931233 TCTCAACAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAATATTTGTAT-AGGCATGCCATA
931297 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
931362 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* *
931400 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAATATTTGTATAGGCATGCCATAT
* * *
931465 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAATTGACGACTTTGATTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * *
931530 TT-GCCAAAATTTTCAAACAAATTTCCATCAAAGAAT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
*
931566 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAATATTTGTAT-AGGCATGCCATA
* *
931630 TTGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
*
931695 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* *
931733 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTCACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAATATTTGTATAGGCATGCCATAT
* **
931798 CGTGGGATATATTTCTGTACCAATCGGGTGTCAACTTCC
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCC
931837 AAAATTTTCA
Statistics
Matches: 402, Mismatches: 31, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
165 1 0.00
166 153 0.38
167 246 0.61
168 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAATATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
Found at i:931821 original size:333 final size:333
Alignment explanation
Indices: 931233--931836 Score: 1091
Period size: 333 Copynumber: 1.8 Consensus size: 333
931223 GTCGCATTTA
* *
931233 TCTCAACAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAACAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
931298 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
931363 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCAACTGTTTATCGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTT
* *
931428 GAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
196 GAAATTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCAGA
931493 CGTCAACTTCCTGTTAATTGACGACTTTGATTATTTTTTGCCAAAATTTTCAAACAAATTTCCAT
261 CGTCAACTTCCTGTTAATTGACGACTTTGATTATTTTTTGCCAAAATTTTCAAACAAATTTCCAT
931558 CAAAGAAT
326 CAAAGAAT
*
931566 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
1 TCTCAACAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
* *
931631 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* *
931696 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTT
* *
931761 GAAATTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGG
196 GAAATTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCAGA
*
931826 TGTCAACTTCC
261 CGTCAACTTCC
931837 AAAATTTTCA
Statistics
Matches: 258, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
333 258 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (333 bp):
TCTCAACAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTT
GAAATTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCAGA
CGTCAACTTCCTGTTAATTGACGACTTTGATTATTTTTTGCCAAAATTTTCAAACAAATTTCCAT
CAAAGAAT
Found at i:931871 original size:135 final size:135
Alignment explanation
Indices: 931700--931971 Score: 535
Period size: 135 Copynumber: 2.0 Consensus size: 135
931690 TATTTTTTAA
*
931700 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAA
931765 TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
66 TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
931830 AACTT
131 AACTT
931835 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAA
931900 TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
66 TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
931965 AACTT
131 AACTT
931970 CC
1 CC
931972 TGTTAAATGA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (135 bp):
CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAA
TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
AACTT
Found at i:932109 original size:166 final size:166
Alignment explanation
Indices: 931835--932494 Score: 1054
Period size: 166 Copynumber: 4.0 Consensus size: 166
931825 GTGTCAACTT
*
931835 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
* * * * **
931900 TTTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTC
66 TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
931965 AACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG
131 AACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG
*
932001 CCAAAATTTTCAAACCAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
* * * *
932066 TTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTATCACTCGGACGTC
66 TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
* * *
932131 AACTTCCTGTTAAATAATGACTTTGTTTATTTTTTG
131 AACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG
* * *
932167 ACAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCAATTTATCGGAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
* * *
932232 TTTTTACACAGTGTTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
66 TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
*
932297 ATCTTCCTGTTAAATGA-GTACTTTGTTTA-TTTTAG
131 AACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAG
932332 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
1 CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
* *
932397 TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGATGCC
66 TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
* * *
932462 AGCTTTCTGTTAAATGTCGACTTTGTTTATTTT
131 AACTTCCTGTTAAATGACGACTTTGTTTATTTT
932495 GCATATTCAC
Statistics
Matches: 451, Mismatches: 40, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
165 152 0.34
166 299 0.66
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
CCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAA
TTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTC
AACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG
Found at i:932487 original size:331 final size:332
Alignment explanation
Indices: 931836--932494 Score: 1090
Period size: 331 Copynumber: 2.0 Consensus size: 332
931826 TGTCAACTTC
*
931836 CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAAT
1 CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACAATTTATCGCAGATGCTTGAAAT
**
931901 TTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGGTGTCA
66 TTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGACGTCA
*
931966 ACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACCAATTTTCGTCAAAG
131 ACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAG
*
932031 ATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCA
196 ATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCA
* * * *
932096 TATTGTGGGATATATTTTTGTATCACTCGGACGTCAACTTCCTGTTAAATAATGACTTTGTTTAT
261 TATTGTGGGATATATTTCTGTACCAATCGGACGCCAACTTCCTGTTAAATAATGACTTTGTTTAT
932161 TTTTTGA
326 TTTTTGA
* *
932168 CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCAATTTATCGGAGATGCTTGAAAT
1 CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACAATTTATCGCAGATGCTTGAAAT
* * * * *
932233 TTTTACACAGTGTTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGTCA
66 TTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGACGTCA
*
932298 TCTTCCTGTTAAATGA-GTACTTTGTTTA-TTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAA
131 ACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAA
932361 GATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCC
195 GATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCC
* * * *
932426 ATATTGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAAT-GTCGACTTTGTTT
260 ATATTGTGGGATATATTTCTGTACCAATCGGACGCCAACTTCCTGTTAAATAAT-GACTTTGTTT
932490 ATTTT
324 ATTTT
932495 GCATATTCAC
Statistics
Matches: 304, Mismatches: 21, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
330 1 0.00
331 158 0.52
332 145 0.48
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (332 bp):
CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACAATTTATCGCAGATGCTTGAAAT
TTTCACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCGGACGTCA
ACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAG
ATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCA
TATTGTGGGATATATTTCTGTACCAATCGGACGCCAACTTCCTGTTAAATAATGACTTTGTTTAT
TTTTTGA
Found at i:936589 original size:37 final size:37
Alignment explanation
Indices: 936533--936720 Score: 286
Period size: 37 Copynumber: 5.1 Consensus size: 37
936523 GTACTTGCAT
* * *
936533 AATCAGCAAGAAAACGAATCAAACACACTTCAAGGAA
1 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
* * **
936570 GATCATCAAGAAAACGAATCAAACGCTTCTCAAGTAA
1 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
* *
936607 AATCACCATGAAAACGAATCAAACGCACCTCAAGTAA
1 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
936644 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
1 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
*
936681 AATCAGCATGAAAACGAATCAAACGCACCTCAAGTAA
1 AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
936718 AAT
1 AAT
936721 GCAGTTTACC
Statistics
Matches: 136, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.50, C:0.23, G:0.13, T:0.14
Consensus pattern (37 bp):
AATCAGCAAGAAAACGAATCAAACGCACCTCAAGTAA
Found at i:954206 original size:25 final size:25
Alignment explanation
Indices: 954172--954249 Score: 129
Period size: 25 Copynumber: 3.0 Consensus size: 25
954162 CTTAATCTTC
954172 AGTAATCAGGGACGTATATACTAAG
1 AGTAATCAGGGACGTATATACTAAG
954197 AGTAATCAGGGACGTATATAGTACTAAG
1 AGTAATCAGGGACG--TATA-TACTAAG
954225 AGTAATCAGGGACGTATATACTAAG
1 AGTAATCAGGGACGTATATACTAAG
954250 TAAATACGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
25 21 0.42
26 4 0.08
27 4 0.08
28 21 0.42
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (25 bp):
AGTAATCAGGGACGTATATACTAAG
Found at i:954230 original size:28 final size:27
Alignment explanation
Indices: 954172--954244 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 27
954162 CTTAATCTTC
954172 AGTAATCAGGGACG--TATATACTAAG
1 AGTAATCAGGGACGTATATATACTAAG
954197 AGTAATCAGGGACGTATATAGTACTAAG
1 AGTAATCAGGGACGTATATA-TACTAAG
954225 AGTAATCAGGGACGTATATA
1 AGTAATCAGGGACGTATATA
954245 CTAAGTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
25 14 0.31
27 4 0.09
28 27 0.60
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (27 bp):
AGTAATCAGGGACGTATATATACTAAG
Found at i:958457 original size:12 final size:12
Alignment explanation
Indices: 958440--958469 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
958430 CCCTGTTTCT
958440 ACCACTCTTCCC
1 ACCACTCTTCCC
958452 ACCACTCTTCCC
1 ACCACTCTTCCC
958464 ACCACT
1 ACCACT
958470 ACCACCCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (12 bp):
ACCACTCTTCCC
Found at i:958481 original size:18 final size:18
Alignment explanation
Indices: 958460--958495 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
958450 CCACCACTCT
958460 TCCCACCACTACCACCCC
1 TCCCACCACTACCACCCC
958478 TCCCACCACTACCACCCC
1 TCCCACCACTACCACCCC
958496 CACGCCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.67, G:0.00, T:0.11
Consensus pattern (18 bp):
TCCCACCACTACCACCCC
Found at i:958856 original size:44 final size:44
Alignment explanation
Indices: 958806--959513 Score: 922
Period size: 44 Copynumber: 17.0 Consensus size: 44
958796 GAATCACGCG
958806 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
* *
958850 AATCAGTGATCTACTGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
958894 AATCAGTGAT-C-CA--C----TGTCATTTGTGTTAGTTGTTAA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
958930 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTC-
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
958973 AATCAGTGAT-C-CA--C----TGTCATTTGTGTTCGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959009 AATCAGTGAT-C-CA--C----TGTCATTTGTGTTCGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959045 AATCAGTGAT-C-CA--CA----GTCATTTGTGTTAGTTGTTAA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
* *
959081 AATCAGTGATCCACAGTCATTGTGTCATTTGTTTTAGTTGTTAA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
* * *
959125 AATCAGTGATCCACTGTCATTGCGTCATTTGTGTTTGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
* * *
959169 AATCAGTGATCCCCTGTCAATGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959213 AATCAGTGAT-C-CA--C----TGTCATTTGTGTTAATTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
959249 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
959293 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959337 AATCAGTGATCCACTGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959381 AATCAGTGATCCACTGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
*
959425 AATCAGTGATCCACTGTCATTGTGTCATTTGTGTTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
* * * * *
959469 AATCAGTGATCAACGGTCATTATGTCATTTTTATTAGTTGTTCA
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
959513 A
1 A
959514 GACGGACCAA
Statistics
Matches: 610, Mismatches: 28, Indels: 52
0.88 0.04 0.08
Matches are distributed among these distances:
35 20 0.03
36 141 0.23
37 3 0.00
38 6 0.01
39 1 0.00
40 6 0.01
41 2 0.00
42 3 0.00
43 11 0.02
44 417 0.68
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (44 bp):
AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
Found at i:959231 original size:124 final size:122
Alignment explanation
Indices: 958806--959489 Score: 807
Period size: 124 Copynumber: 5.5 Consensus size: 122
958796 GAATCACGCG
*
958806 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCTACTGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
*
958871 GTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCA---C--T-GTCATTTGTGTTAGTTGTTAA
66 -TG-----T-T-TTAGTTGTTCAAATCAGTGATCCACGTCATTGGTCATTTGTGTTAGTTGTTCA
958930 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTC-AATCAGTGATCCACTGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
* * *
958994 TGTGTTCGTTGTTCAAATCAGTGATCCA---C--T-GTCATTTGTGTTCGTTGTTCA
66 TGTTTTAGTTGTTCAAATCAGTGATCCACGTCATTGGTCATTTGTGTTAGTTGTTCA
*
959045 AATCAGTGAT-C-CA--CA----GTCATTTGTGTTAGTTGTTAAAATCAGTGATCCACAGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGAT-C-CA--C---
* *
959102 GTGTCATTTGTTTTAGTTGTTAAAATCAGTGATCCACTGTCATTGCGTCATTTGTGTTTGTTGTT
59 -TGTCATTTGTTTTAGTTGTTCAAATCAGTGATCCAC-GTCATTG-GTCATTTGTGTTAGTTGTT
959167 CA
121 CA
* * *
959169 AATCAGTGATCCCCTGTCAATGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
* *
959234 TGTGTTAATTGTTCAAATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCA
66 TGTTTTAGTTGTTCAAATCAGTGATCCAC-GTCATTG-GTCATTTGTGTTAGTTGTTCA
959293 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
959358 GTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATTGTGTCATTTGTGTTAGTTGTT
66 -TG-----T-T-TTAGTTGTTCAAATCAGTGATCCAC-GTCATTG-GTCATTTGTGTTAGTTGTT
959423 CA
121 CA
* * *
959425 AATCAGTGATCCACTGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCAACGGTCATT
1 AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
959490 ATGTCATTTT
Statistics
Matches: 500, Mismatches: 27, Indels: 58
0.85 0.05 0.10
Matches are distributed among these distances:
107 19 0.04
108 10 0.02
109 1 0.00
110 2 0.00
111 2 0.00
112 1 0.00
113 2 0.00
114 1 0.00
115 54 0.11
116 32 0.06
117 1 0.00
120 1 0.00
122 3 0.01
123 20 0.04
124 195 0.39
125 3 0.01
126 1 0.00
128 3 0.01
130 3 0.01
131 1 0.00
132 145 0.29
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (122 bp):
AATCAGTGATCCACAGTCATTGTGTCATTTGTGTTAGTTGTTCAAATCAGTGATCCACTGTCATT
TGTTTTAGTTGTTCAAATCAGTGATCCACGTCATTGGTCATTTGTGTTAGTTGTTCA
Found at i:962423 original size:28 final size:28
Alignment explanation
Indices: 962390--962446 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
962380 AAGGAATTTA
*
962390 TGTTAAACCTAAAGCTAGATATGTTATT
1 TGTTAAACCTAAAGCTAGATATATTATT
**
962418 TGTTAAACCTTTAGCTAGATATATTATT
1 TGTTAAACCTAAAGCTAGATATATTATT
962446 T
1 T
962447 TTGCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (28 bp):
TGTTAAACCTAAAGCTAGATATATTATT
Found at i:964492 original size:13 final size:12
Alignment explanation
Indices: 964473--964515 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 12
964463 TTGTTTGGGG
*
964473 GTTTTTTGTTTT
1 GTTTTTTTTTTT
964485 GTTTTTTTTGTTT
1 GTTTTTTTT-TTT
964498 GTTTTTTTTTTT
1 GTTTTTTTTTTT
964510 -TTTTTT
1 GTTTTTT
964516 GCACCTATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 6 0.21
12 11 0.38
13 12 0.41
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:964494 original size:25 final size:23
Alignment explanation
Indices: 964466--964515 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
964456 TTTTCATTTG
964466 TTTGGGGGTTTTTTGTTTTGTTTTT
1 TTTGGGGGTTTTTT-TTTT-TTTTT
***
964491 TTTGTTTGTTTTTTTTTTTTTTT
1 TTTGGGGGTTTTTTTTTTTTTTT
964514 TT
1 TT
964516 GCACCTATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (23 bp):
TTTGGGGGTTTTTTTTTTTTTTT
Found at i:964500 original size:18 final size:18
Alignment explanation
Indices: 964477--964516 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
964467 TTGGGGGTTT
964477 TTTGTTTTGTTTTTTTTG
1 TTTGTTTTGTTTTTTTTG
* *
964495 TTTGTTTTTTTTTTTTTT
1 TTTGTTTTGTTTTTTTTG
964513 TTTG
1 TTTG
964517 CACCTATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTGTTTTGTTTTTTTTG
Found at i:966008 original size:22 final size:22
Alignment explanation
Indices: 965978--966069 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 22
965968 GTATCACTTC
*
965978 TTCGCCTTCGCAACCTCGCACT
1 TTCGTCTTCGCAACCTCGCACT
* * *
966000 TTCGTCTTCGCATCTTCGCGC-
1 TTCGTCTTCGCAACCTCGCACT
*
966021 TTCGTCGTCGC-ACCTTCGCACT
1 TTCGTCTTCGCAACC-TCGCACT
* *
966043 TTCGCCTTCGCAACTTCGCACT
1 TTCGTCTTCGCAACCTCGCACT
*
966065 CTCGT
1 TTCGT
966070 GTCTTCGCCC
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.28
22 36 0.67
23 2 0.04
ACGTcount: A:0.10, C:0.41, G:0.16, T:0.33
Consensus pattern (22 bp):
TTCGTCTTCGCAACCTCGCACT
Found at i:970475 original size:2 final size:2
Alignment explanation
Indices: 970468--970509 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
970458 GGGCATTTAT
970468 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
970510 AGAGAGACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:970712 original size:16 final size:16
Alignment explanation
Indices: 970689--970729 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
970679 TCAGTTCGTT
*
970689 TGTCCATCCATCTATCC
1 TGTCCATCCATCCAT-C
970706 T-TCCATCCATCCATC
1 TGTCCATCCATCCATC
970721 TGTCCATCC
1 TGTCCATCC
970730 TACATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.17, C:0.44, G:0.05, T:0.34
Consensus pattern (16 bp):
TGTCCATCCATCCATC
Found at i:971248 original size:2 final size:2
Alignment explanation
Indices: 971243--971279 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
971233 ACATTGTGTG
*
971243 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
971280 TTTACTGTGA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:971668 original size:2 final size:2
Alignment explanation
Indices: 971661--971712 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
971651 TTATGGAAAT
971661 GA GA GA GA GA GA GA GA GA GA GA GA -A TGA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA
971703 GA GA GA GA GA
1 GA GA GA GA GA
971713 AATCCAAGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:973761 original size:166 final size:166
Alignment explanation
Indices: 973503--974404 Score: 1316
Period size: 166 Copynumber: 5.5 Consensus size: 166
973493 ACAATGGGGG
* * * *
973503 GGGGGGTCGAAGTTTTACATAGGAATATATACAGTATATCTTTAAAAATCTTCTTCTCAGAAACT
1 GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* * *
973568 AATCAGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAGATTCATAGTTATGA
66 AATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGA
973633 AAATCATGACCCCCTGGGGTAGGGTGGGGCCACAAT
131 AAATCATGACCCCCTGGGGTAGGGTGGGGCCACAAT
* * * * *
973669 GGGGGATCGAAGTTTTACATAGGAATATATACAGTATATCTTTAAAAATCTGCTTCTCAGAAACA
1 GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* *
973734 AATCAGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGA
66 AATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGA
*
973799 AAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT
131 AAATCATGACCCCCTGGGGTAGGGTGGGGCCACAAT
*
973835 GGGGGATCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
1 GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
*
973900 AATCAGCC-GGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTG
66 AATCAGCCAGG-AAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTG
* * *
973964 AAAATAAT-AACCCCTGGGGGTAGGTTGGGGCCACAAT
130 AAAATCATGACCCCCT-GGGGTAGGGTGGGGCCACAAT
* *
974001 GGGGGATCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
1 GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
* * * *
974066 AATTAGCCAGGAAAGCTGGCACTTGTGTGGAAGCATCCTCAAGTAGTGTAGATTCAAATTTGTGA
66 AATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGA
* *
974131 AAATCATGA-CCCCTGGGGATAGGTTTGGGCCACAAT
131 AAATCATGACCCCCTGGGG-TAGGGTGGGGCCACAAT
* * * *
974167 GGGAGG-TCGATA-TTTTACATAGGAATAAACAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAA
1 GGG-GGATCGA-AGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAA
* * * *
974230 CTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTTGTGTAGATTCAAGGTTGT
64 CTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGT
* * *
974295 GAAAATCATGATCCTCAGGGGTAGGGTGGGGCCACAAT
129 GAAAATCATGACCCCCTGGGGTAGGGTGGGGCCACAAT
* * * *
974333 GGGGGGTCAAAGTTTAACAAAGGAATATATAGGGTAAATCTTTAAAAA---TCTTCTCAGAAACT
1 GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
974395 AATCAGCCAG
66 AATCAGCCAG
974405 ATGATTCTTT
Statistics
Matches: 673, Mismatches: 53, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
163 23 0.03
165 14 0.02
166 623 0.93
167 13 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (166 bp):
GGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
AATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGA
AAATCATGACCCCCTGGGGTAGGGTGGGGCCACAAT
Found at i:974795 original size:16 final size:16
Alignment explanation
Indices: 974758--974804 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
974748 TTTAATATGA
*
974758 TAAAGGTG--GTCTCA
1 TAAAGGTGAAGTCTCG
974772 TAAAGGTGAAGTCTCG
1 TAAAGGTGAAGTCTCG
* *
974788 TAAGGGTGATGTCTCG
1 TAAAGGTGAAGTCTCG
974804 T
1 T
974805 CTCGGTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 8 0.29
16 20 0.71
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.30
Consensus pattern (16 bp):
TAAAGGTGAAGTCTCG
Found at i:976417 original size:4 final size:4
Alignment explanation
Indices: 976408--976432 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
976398 ATTGAAATGC
976408 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
976433 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:976437 original size:2 final size:2
Alignment explanation
Indices: 976430--976462 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
976420 AAATAAATAA
976430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
976463 AAGATCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:979124 original size:59 final size:58
Alignment explanation
Indices: 979033--979144 Score: 197
Period size: 59 Copynumber: 1.9 Consensus size: 58
979023 GTGCAAAGTA
*
979033 ATGATTATGATTAAAGCATAACATGGTAGATCTTTAATTAGGAGCATCAAATTTTTTT
1 ATGATTATGATTAAAGCATAAAATGGTAGATCTTTAATTAGGAGCATCAAATTTTTTT
*
979091 ATGATTTATGATTAAAGCATAAAATGTTAGATCTTTAATTAGGAGCATCAAATT
1 ATGA-TTATGATTAAAGCATAAAATGGTAGATCTTTAATTAGGAGCATCAAATT
979145 GTTATATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
58 4 0.08
59 47 0.92
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (58 bp):
ATGATTATGATTAAAGCATAAAATGGTAGATCTTTAATTAGGAGCATCAAATTTTTTT
Found at i:979148 original size:29 final size:29
Alignment explanation
Indices: 979059--979148 Score: 87
Period size: 28 Copynumber: 3.1 Consensus size: 29
979049 CATAACATGG
*
979059 TAGATCTTTAATTAGGAGCATCAAATTTTTT
1 TAGATCTTTAATTAGGAGCATCAAA--TTGT
* * *
979090 TATGAT-TTATGATTA-AAGCAT-AAAATGT
1 TA-GATCTT-TAATTAGGAGCATCAAATTGT
979118 TAGATCTTTAATTAGGAGCATCAAATTGT
1 TAGATCTTTAATTAGGAGCATCAAATTGT
979147 TA
1 TA
979149 TATATTTCTC
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
27 8 0.17
28 11 0.23
29 8 0.17
30 3 0.06
31 9 0.19
32 8 0.17
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (29 bp):
TAGATCTTTAATTAGGAGCATCAAATTGT
Found at i:979808 original size:16 final size:16
Alignment explanation
Indices: 979787--979818 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
979777 TAAGCAAGAT
*
979787 TATATTTTATATGTTA
1 TATATTATATATGTTA
979803 TATATTATATATGTTA
1 TATATTATATATGTTA
979819 ATTATCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TATATTATATATGTTA
Found at i:984075 original size:21 final size:21
Alignment explanation
Indices: 984051--984111 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
984041 TGTAGCAATC
984051 CTATCCTATCCTATCGTGCAT
1 CTATCCTATCCTATCGTGCAT
* * * *
984072 CTATACTGT-ATAATCGTGCGT
1 CTATCCTATCCT-ATCGTGCAT
984093 -TAATCCTATCCTATCGTGC
1 CT-ATCCTATCCTATCGTGC
984112 CTGTATACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (21 bp):
CTATCCTATCCTATCGTGCAT
Found at i:984100 original size:42 final size:42
Alignment explanation
Indices: 984053--984148 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
984043 TAGCAATCCT
984053 ATCCTATCCTATCGTGCATCTATACTGTAT-AATCGTGCGTTA
1 ATCCTATCCTATCGTGCATCTATACTGT-TCAATCGTGCGTTA
* * *
984095 ATCCTATCCTATCGTGCCTGTATACTGTTCTATCGTGCGTTA
1 ATCCTATCCTATCGTGCATCTATACTGTTCAATCGTGCGTTA
*
984137 ACCCTATCCTAT
1 ATCCTATCCTAT
984149 AGTCATACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (42 bp):
ATCCTATCCTATCGTGCATCTATACTGTTCAATCGTGCGTTA
Found at i:984148 original size:21 final size:20
Alignment explanation
Indices: 984084--984148 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
984074 ATACTGTATA
984084 ATCGTGCGTTAATCCTATCCT
1 ATCGTGCGTTAA-CCTATCCT
* * *
984105 ATCGTGCCTGTATA-CTGTTCT
1 ATCGTGCGT-TA-ACCTATCCT
984126 ATCGTGCGTTAACCCTATCCT
1 ATCGTGCGTTAA-CCTATCCT
984147 AT
1 AT
984149 AGTCATACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 28 0.82
22 2 0.06
23 1 0.03
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (20 bp):
ATCGTGCGTTAACCTATCCT
Found at i:985204 original size:8 final size:8
Alignment explanation
Indices: 985184--985229 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
985174 ATCACATTTT
985184 GTCTGT-C
1 GTCTGTCC
* *
985191 GTCCGTCT
1 GTCTGTCC
*
985199 GTCCGTCC
1 GTCTGTCC
985207 GTCTGTCC
1 GTCTGTCC
985215 GTCTGTCC
1 GTCTGTCC
985223 GTCTGTC
1 GTCTGTC
985230 TGTCCGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
7 5 0.15
8 29 0.85
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (8 bp):
GTCTGTCC
Found at i:985207 original size:12 final size:12
Alignment explanation
Indices: 985184--985236 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
985174 ATCACATTTT
985184 GTCTGT-CGTCC
1 GTCTGTCCGTCC
985195 GTCTGTCCGTCC
1 GTCTGTCCGTCC
985207 GTC--T--GTCC
1 GTCTGTCCGTCC
*
985215 GTCTGTCCGTCT
1 GTCTGTCCGTCC
985227 GTCTGTCCGT
1 GTCTGTCCGT
985237 AAACTTTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
8 7 0.19
10 2 0.06
11 6 0.17
12 21 0.58
ACGTcount: A:0.00, C:0.36, G:0.26, T:0.38
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:985216 original size:20 final size:20
Alignment explanation
Indices: 985191--985236 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
985181 TTTGTCTGTC
985191 GTCCGTCTGTCCGTCCGTCT
1 GTCCGTCTGTCCGTCCGTCT
*
985211 GTCCGTCTGTCCGTCTGTCT
1 GTCCGTCTGTCCGTCCGTCT
985231 GTCCGT
1 GTCCGT
985237 AAACTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (20 bp):
GTCCGTCTGTCCGTCCGTCT
Found at i:985810 original size:166 final size:166
Alignment explanation
Indices: 985406--986626 Score: 1632
Period size: 166 Copynumber: 7.2 Consensus size: 166
985396 AGAAATTTTC
**
985406 AAAAATCTTCTTCTCA-AGAAC-AAGAAAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTAA-TCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* **
985469 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGG
985534 GTCGAAGTTTT-CATAGGAATATATAGAGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
985571 AAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAATGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
985636 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGTGTAGGGTGGGGCCACAATGGGTGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
985701 CGAAGTTTTACATAGGAATATATAGAATAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
985737 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
985802 TAGTGTAGATTCAAAATTGTGAAAATCATAACCCCTGGGGTTAGGTTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
985867 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
985903 AAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
985968 TAGTGAAGATTCAAAGTTGTGAAAATCATGACCGACCCCCGGGGGTAGGGTGGGGCCACAATGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCAT----GACCCCTGGGGGTAGGGTGGGGCCACAATGGG
* *
986033 GGGTCGAAGTTTTACATAAGAATATATAGAATAAATCTTT
127 GGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
986073 AAAAATCTTTTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** * * *
986138 TAGTGTAGATTCAAAGTTGGGAAAAGAATGATCCCTGGGGGTAGGG-GGAGGCCCCATTGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGG-GGCCACAAT------
*
986202 GGGGGGT-GTTAAAATTTTACATAGGAATATATAGAGTAAATCTTT
124 GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
986247 AAAAATCTTCTTCACAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** * * * *
986312 TAGTGTAGATTCAAAGTTGGGAAAAGAATTATCCCTGGGGGTAGGG-GGAGGCCCCATTGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGG-GGCCACAAT------
*
986376 GGGGGGT-GTTAAAATTTTACATAGGAATATATAGAGTAAATCTTT
124 GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * *
986421 AAAAATCTTCTTCACAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG-GGAAGTATCCTAAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
986485 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGAGGCCAC-ATGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAAT-------
**
986549 GGGGGGGGGGTTAAAGTTTTACATAGGAATATATATAGAGTAAATCTTT
124 ----GGGGGGTCGAAGTTTTACATAGG-A-ATATATAGAGTAAATCTTT
986598 AAAAATCTTCTTCTCAGAAACTAATCAGC
1 AAAAATCTTCTTCTCAGAAACTAATCAGC
986627 AAGATGATTC
Statistics
Matches: 973, Mismatches: 57, Indels: 40
0.91 0.05 0.04
Matches are distributed among these distances:
165 130 0.13
166 296 0.30
170 153 0.16
171 1 0.00
172 8 0.01
173 59 0.06
174 252 0.26
175 13 0.01
176 1 0.00
177 60 0.06
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:986125 original size:336 final size:335
Alignment explanation
Indices: 985406--986626 Score: 1626
Period size: 336 Copynumber: 3.6 Consensus size: 335
985396 AGAAATTTTC
**
985406 AAAAATCTTCTTCTCA-AGAAC-AAGAAAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTAA-TCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * **
985469 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAAT-GGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCTGGGGGTAGGGTGGGGCCACAATGGGGG
985533 GGTCGAAGTTTT-CATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAAC
129 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAAC
*
985597 AGCCAGGAATGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
194 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* *
985662 CAT--GACCCCCGGGTGTAGGGTGGGGCCACAATGGGTGGTCGAAGTTTTACATAGGAATATATA
259 CATGAGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATA
985725 GAATAAATCTTT
324 GAATAAATCTTT
985737 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
985802 TAGTGTAGATTCAAAATTGTGAAAATCATAACCCCTGGGGTTAGGTTGGGGCCACAAT-GGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGG
985866 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAACAG
131 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAACAG
* *
985931 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGGTAGTGAAGATTCAAAGTTGTGAAAATCA
196 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
*
985996 TGACCGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAAGAATATATA
261 TGA--GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATA
986061 GAATAAATCTTT
324 GAATAAATCTTT
*
986073 AAAAATCTTTTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** * * * *
986138 TAGTGTAGATTCAAAGTTGGGAAAAGAATGATCCCTGGGGGTAGGG-GGAGGCCCCATTGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCTGGGGGTAGGGTGG-GGCCACAAT-----G
* *
986202 GGGGGGT-GTTAAAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAA
125 GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAA
*
986266 ACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTG
187 ACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTG
* ** * * * * * *
986331 GGAAAAGAAT--TATCCCTGGGGGTAGGG-GGAGGCCCCATTGGGGGGGGGGGGT-GTTAAAATT
252 TGAAAATCATGAGACCCCCGGGGGTAGGGTGG-GGCCACAAT------GGGGGGTCG---AAGTT
*
986392 TTACATAGGAATATATAGAGTAAATCTTT
307 TTACATAGGAATATATAGAATAAATCTTT
* * *
986421 AAAAATCTTCTTCACAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG-GGAAGTATCCTAAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
986485 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGAGGCCAC-ATGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCTGGGGGTAGGGTGGGGCCACAAT-------
**
986549 GGGGGGGGGGTTAAAGTTTTACATAGGAATATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
124 ---GGGGGGGTCGAAGTTTTACATAGG-A-ATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
*
986614 GAAACTAATCAGC
184 GAAACTAAACAGC
986627 AAGATGATTC
Statistics
Matches: 798, Mismatches: 56, Indels: 52
0.88 0.06 0.06
Matches are distributed among these distances:
331 125 0.16
332 120 0.15
335 2 0.00
336 178 0.22
339 2 0.00
340 21 0.03
341 1 0.00
342 7 0.01
344 120 0.15
345 1 0.00
346 8 0.01
347 60 0.08
348 79 0.10
349 13 0.02
350 1 0.00
351 60 0.08
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (335 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGG
TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAACAG
CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
TGAGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGA
ATAAATCTTT
Found at i:986530 original size:173 final size:174
Alignment explanation
Indices: 986042--986626 Score: 974
Period size: 174 Copynumber: 3.3 Consensus size: 174
986032 GGGGTCGAAG
* * * *
986042 TTTTACATAAGAATATATAGAATAAATCTTTAAAAATCTTTTTCTCAGAAACTAATCAGCCAGGA
1 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
986107 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATGATCC
66 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATGATCC
986172 CTGGGGGTAGGGGGAGGCCCCATTGGGGGGGGGGGGTGTTAAAA
131 CTGGGGGTAGGGGGAGGCCCCATTGGGGGGGGGGGGTGTTAAAA
986216 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
1 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
*
986281 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATTATCC
66 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATGATCC
986346 CTGGGGGTAGGGGGAGGCCCCATTGGGGGGGGGGGGTGTTAAAA
131 CTGGGGGTAGGGGGAGGCCCCATTGGGGGGGGGGGGTGTTAAAA
986390 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
1 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
* * * ** *
986455 AAGCTGAAACTTGTG-GGAAGTATCCTAAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCC
66 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATGATCC
* * * * *
986519 CTGGGGGTAGGGTGAGGCCACATGGGGGGGGGGGGGGGGGTTAAAG
131 CTGGGGGTAGGGGGAGGCCCCAT--TGGGGGGGGGGGGTGTTAAAA
*
986565 TTTTACATAGGAATATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
1 TTTTACATAGG-A-ATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGC
986627 AAGATGATTC
Statistics
Matches: 389, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
173 63 0.16
174 249 0.64
175 29 0.07
176 1 0.00
177 47 0.12
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (174 bp):
TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCACAGAAACTAATCAGCCAGGA
AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGGGAAAAGAATGATCC
CTGGGGGTAGGGGGAGGCCCCATTGGGGGGGGGGGGTGTTAAAA
Found at i:990200 original size:167 final size:166
Alignment explanation
Indices: 989761--990347 Score: 980
Period size: 166 Copynumber: 3.5 Consensus size: 166
989751 TTTAGGGGGC
*
989761 ATGTCTTTAAAAATCTTCTTCTCAAGAA-CACTGCACCAGAAATGGCAATATTTACACAAAAGCT
1 ATGT-TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCT
989825 TGTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAG
65 TGTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAG
989890 GCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
130 GCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
*
989927 ATGTTTAAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
989992 GTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAGG
66 GTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAGG
990057 CGGGGTTCAAAGTTTAACATAGAACA-ACATATGGAAA
131 CGGGGTTCAAAGTTTAACATAGAA-ATACATA-GGAAA
* * *
990094 ATGTTTTAAAAATGTTGTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAACTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
* * *
990159 GTATATATAGTGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGACCAAAACTGGGACCCCAGG
66 GTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAGG
*
990224 CGGGGTTCAAAGTTTAACATAGAAATACATAGGAAC
131 CGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
* * * * ** *
990260 ATTTTTTAAAAATTTTCTTCTCAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
*
990325 GTATATATAGTGAAGATTGTAAA
66 GTATATATAGTGAAGATTCTAAA
990348 AATCGTGACC
Statistics
Matches: 397, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
165 22 0.06
166 217 0.55
167 158 0.40
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (166 bp):
ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
GTATATATAGTGAAGATTCTAAATTGTAAAAATCCTGACCCTCGGACCAAAACTGGGGCCCCAGG
CGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
Found at i:996385 original size:2 final size:2
Alignment explanation
Indices: 996378--996441 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
996368 GGGGTGCATG
996378 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
996420 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
996442 TCAAAAAGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1009165 original size:18 final size:17
Alignment explanation
Indices: 1009142--1009185 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1009132 AAGTAAATGT
*
1009142 ATGTTATACATGTTTGTG
1 ATGTTATA-ATGTTTCTG
1009160 ATGTTAATAATGTTTCTG
1 ATGTT-ATAATGTTTCTG
*
1009178 TTGTTATA
1 ATGTTATA
1009186 GTGGTGTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (17 bp):
ATGTTATAATGTTTCTG
Found at i:1017145 original size:1 final size:1
Alignment explanation
Indices: 1017139--1017170 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
1017129 TTGTGACAAG
1017139 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1017171 ACACACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1024963 original size:13 final size:13
Alignment explanation
Indices: 1024945--1024971 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1024935 AGAAACCGTA
1024945 GAATAACAATAGG
1 GAATAACAATAGG
1024958 GAATAACAATAGG
1 GAATAACAATAGG
1024971 G
1 G
1024972 TCTTCCGTTG
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:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (13 bp):
GAATAACAATAGG
Found at i:1029761 original size:2 final size:2
Alignment explanation
Indices: 1029754--1029792 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1029744 GAAAATAATT
1029754 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1029793 GTGTGTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1031076 original size:21 final size:21
Alignment explanation
Indices: 1031052--1031102 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1031042 ACAGCCTCTT
1031052 ATGCAAAATCAACAGA-CAACG
1 ATGCAAAA-CAACAGATCAACG
* *
1031073 ATGCAAAACAACCGATCACCG
1 ATGCAAAACAACAGATCAACG
1031094 ATGCAAAAC
1 ATGCAAAAC
1031103 CGAAAGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.49, C:0.27, G:0.14, T:0.10
Consensus pattern (21 bp):
ATGCAAAACAACAGATCAACG
Found at i:1032461 original size:21 final size:21
Alignment explanation
Indices: 1032432--1032502 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1032422 GTCGATAAAT
1032432 ATGCAAGATAAATATGTTGAC
1 ATGCAAGATAAATATGTTGAC
* ** **
1032453 ATGCGAGATAGTTATGTCAAC
1 ATGCAAGATAAATATGTTGAC
* *
1032474 ATGCAACATAACTATGTTGAC
1 ATGCAAGATAAATATGTTGAC
1032495 ATGCAAGA
1 ATGCAAGA
1032503 AAACTGCAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
ATGCAAGATAAATATGTTGAC
Found at i:1032616 original size:21 final size:21
Alignment explanation
Indices: 1032581--1032688 Score: 126
Period size: 21 Copynumber: 5.1 Consensus size: 21
1032571 ATACGCTACC
* *
1032581 TATTGATGTCCACATGCAACT
1 TATTTATGTCGACATGCAACT
* **
1032602 TATCTATGTTAACATGCAACT
1 TATTTATGTCGACATGCAACT
*
1032623 TCTTTATGTCGACATGCAACT
1 TATTTATGTCGACATGCAACT
1032644 TATTTATGTCGACATGCAACT
1 TATTTATGTCGACATGCAACT
* * * *
1032665 GAGTTATGTTGACATACAACT
1 TATTTATGTCGACATGCAACT
1032686 TAT
1 TAT
1032689 AAGTTGCATT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (21 bp):
TATTTATGTCGACATGCAACT
Found at i:1032739 original size:21 final size:21
Alignment explanation
Indices: 1032687--1032897 Score: 178
Period size: 21 Copynumber: 10.0 Consensus size: 21
1032677 CATACAACTT
*
1032687 ATAAGTTGCATTTCAACAT-A
1 ATAAGTTGCATGTCAACATAA
* * * *
1032707 TTTATTTCGCATGTAAACATAA
1 ATAAGTT-GCATGTCAACATAA
*
1032729 CTAAGTTGCATGTCAACAT-A
1 ATAAGTTGCATGTCAACATAA
* * *
1032749 TTCA-TCTCGCTTGTCAACATAA
1 ATAAGT-T-GCATGTCAACATAA
* **
1032771 GTAAGTTGCATGTTGACATAA
1 ATAAGTTGCATGTCAACATAA
*
1032792 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
*
1032813 ATAAGTTACATGTCAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
1032834 ATAAGTTGCATATCAGCA-AA
1 ATAAGTTGCATGTCAACATAA
** *
1032854 TATATTTTGCATGTTAACATAA
1 -ATAAGTTGCATGTCAACATAA
*
1032876 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
1032897 A
1 A
1032898 AAGGTAGCAT
Statistics
Matches: 150, Mismatches: 33, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
19 1 0.01
20 10 0.07
21 127 0.85
22 11 0.07
23 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:1033005 original size:21 final size:21
Alignment explanation
Indices: 1032980--1033065 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
1032970 TATCTGATTG
*
1032980 TAATTTTCTTGCATGTCAACA
1 TAATTATCTTGCATGTCAACA
* **
1033001 TAATTATGTTGCATGTTTACA
1 TAATTATCTTGCATGTCAACA
1033022 TAATTATCTTGCATGTCAACA
1 TAATTATCTTGCATGTCAACA
** *
1033043 TGTTTATCTTGCATGTCGACA
1 TAATTATCTTGCATGTCAACA
1033064 TA
1 TA
1033066 TTTGATAGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (21 bp):
TAATTATCTTGCATGTCAACA
Found at i:1034601 original size:146 final size:146
Alignment explanation
Indices: 1034092--1034660 Score: 687
Period size: 146 Copynumber: 3.9 Consensus size: 146
1034082 TTTTAAACAA
* * * *
1034092 TGACCTTGAACTT-CCTCAATTGACCTTGGGTCAAGGTCATGACACACCCTCAGGTTATAAGCAA
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* *** * * *
1034156 T-TTTGATGTGAATTAAGAACTTTTTATACTTT-TCCATTAGAAAGATATGGACCGGACATGAAT
65 TCTTTG-TGTGAAGTAAGAACTTCCAAT-GTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
**
1034219 TTTGCAC-TTTTCAGCCAG
128 TTTGCACTTTTTTTGCCAG
* * *
1034237 TGACTTTGACCTAGCCAAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * * *
1034302 CTTTTTGTGAACTAAGAACTTACAATGTTTCTCCATAAGAAAGATATTGACCGCACACAAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
* *
1034367 TCACTTTTTTTTTCCAG
131 GCAC-TTTTTTTGCCAG
* *** * * * *
1034384 TGACCTTGACCTTGCCCAAATGACTTTTATTCAAGGTCATGACACATCCTTACGTCATAAGAAAA
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * **
1034449 CTTTGTGTAAAGTAAAAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACGTGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
1034514 GCACTTTTTTTGCCAG
131 GCACTTTTTTTGCCAG
* * * *
1034530 TGACCTTGGCCTTGCCCGAATGACCTTGGGTCAAGGTCATGACACGCCCTTAGGTCATGAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
1034595 CATTGTGTGAAGTAAGAACTTCTAATGTTTCTCAATAAGAAAGATATGGACCGGACACGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
1034660 G
131 G
1034661 AACAGACGGT
Statistics
Matches: 355, Mismatches: 64, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
144 3 0.01
145 104 0.29
146 128 0.36
147 120 0.34
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
GCACTTTTTTTGCCAG
Found at i:1036385 original size:2 final size:2
Alignment explanation
Indices: 1036378--1036436 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1036368 CTTGGAGGAT
1036378 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1036420 TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
1036437 TTTGTTTCAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1038145 original size:1 final size:1
Alignment explanation
Indices: 1038139--1038203 Score: 130
Period size: 1 Copynumber: 65.0 Consensus size: 1
1038129 TATTTAAATA
1038139 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1038204 GAAGGTAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1038148 original size:31 final size:33
Alignment explanation
Indices: 1038088--1038157 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
1038078 GAAAAAATGA
1038088 TTTCCCTTATTGAAATATTATTTTCTTTTTTTT
1 TTTCCCTTATTGAAATATTATTTTCTTTTTTTT
* * *
1038121 TTNTCCCTTATTTAAATATTTTTTTTTTTTTTTT
1 TT-TCCCTTATTGAAATATTATTTTCTTTTTTTT
1038155 TTT
1 TTT
1038158 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.71
Consensus pattern (33 bp):
TTTCCCTTATTGAAATATTATTTTCTTTTTTTT
Found at i:1039188 original size:19 final size:20
Alignment explanation
Indices: 1039152--1039191 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1039142 TTTTTGTATA
1039152 TTATATTTTATATCCATTGC
1 TTATATTTTATATCCATTGC
*
1039172 TTATATTTTA-GTCCATTGC
1 TTATATTTTATATCCATTGC
1039191 T
1 T
1039192 GAATCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (20 bp):
TTATATTTTATATCCATTGC
Found at i:1040011 original size:20 final size:20
Alignment explanation
Indices: 1039982--1040019 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1039972 GCAATGTATT
*
1039982 TTGCGTTTAAACGCAAAAGA
1 TTGCGATTAAACGCAAAAGA
1040002 TTGCGATTAAACGCAAAA
1 TTGCGATTAAACGCAAAA
1040020 AGTATTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGCGATTAAACGCAAAAGA
Done.