Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_pilon, whole genome shotgun sequence
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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1851410 original size:29 final size:29
Alignment explanation
Indices: 1851377--1851440 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
1851367 ATAAATATTG
1851377 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1851406 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1851435 GGGGAC
1 GGGGAC
1851441 CTAAATGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (29 bp):
GGGGACTGTATTGCAAGTTTTAAAAGTTA
Found at i:1851449 original size:29 final size:29
Alignment explanation
Indices: 1851377--1851451 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1851367 ATAAATATTG
* *
1851377 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGAAATGCAAGTTTTAAAAGTTA
* *
1851406 GGGGACTGTATTGCAAGTTTTAAAAGTTA
1 GGGGACTGAAATGCAAGTTTTAAAAGTTA
1851435 GGGGACCT-AAATGCAAG
1 GGGGA-CTGAAATGCAAG
1851452 CTTCAGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (29 bp):
GGGGACTGAAATGCAAGTTTTAAAAGTTA
Found at i:1860504 original size:66 final size:66
Alignment explanation
Indices: 1860397--1860521 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
1860387 CGGGAACTCG
* * *
1860397 AACGAGTCGACTATTACCGAGGGACGTGGGAAAGAAACTGTACCCACCAACCCGAAGAAGAGCAC
1 AACGAGTCAACTATTACCGAGGAACGTGGGAAAGAAACTGTACCCACCAACCAGAAGAAGAGCAC
1860462 C
66 C
* * *
1860463 AACGAGTCAACTATTACTGAGGAACGTGGGAGAGAAGCTGTACCCACCAACCAGAAGAA
1 AACGAGTCAACTATTACCGAGGAACGTGGGAAAGAAACTGTACCCACCAACCAGAAGAA
1860522 AAAAAGGGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.38, C:0.25, G:0.26, T:0.12
Consensus pattern (66 bp):
AACGAGTCAACTATTACCGAGGAACGTGGGAAAGAAACTGTACCCACCAACCAGAAGAAGAGCAC
C
Found at i:1866525 original size:30 final size:30
Alignment explanation
Indices: 1866491--1866564 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 30
1866481 TGTTTGTTCC
1866491 ATTTTAGTTCTTTAACTTTCTA-TTTTT-ACT
1 ATTTTAG-TCTTTAACTTT-TAGTTTTTCACT
* * * *
1866521 ATTTTTGATCTTAAAGTTTTAGTTTTTCTCT
1 ATTTTAG-TCTTTAACTTTTAGTTTTTCACT
1866552 ATTTTAGTCTTTA
1 ATTTTAGTCTTTA
1866565 TAAATTTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
29 2 0.06
30 25 0.71
31 8 0.23
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (30 bp):
ATTTTAGTCTTTAACTTTTAGTTTTTCACT
Found at i:1870532 original size:16 final size:16
Alignment explanation
Indices: 1870511--1870544 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1870501 ACACCTTCAT
1870511 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1870527 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1870543 TT
1 TT
1870545 TCTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.24
Consensus pattern (16 bp):
TTCAACCGCTACACGC
Found at i:1870686 original size:2 final size:2
Alignment explanation
Indices: 1870679--1870708 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1870669 GTTTTAGGCC
1870679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1870709 TGATATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1876797 original size:31 final size:29
Alignment explanation
Indices: 1876774--1876829 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1876764 TAACCGTACT
1876774 TAATCCAACATTTTATTAGTATAACCGAG
1 TAATCCAACATTTTATTAGTATAACCGAG
* **
1876803 TCATCTTACATTTTATTAGTATAACCG
1 TAATCCAACATTTTATTAGTATAACCG
1876830 GGATCATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
TAATCCAACATTTTATTAGTATAACCGAG
Found at i:1879862 original size:13 final size:13
Alignment explanation
Indices: 1879846--1879895 Score: 75
Period size: 12 Copynumber: 3.8 Consensus size: 13
1879836 GAAAAAAGGT
1879846 TTTTTTAAAATAA
1 TTTTTTAAAATAA
1879859 -TTTTTAAAATAA
1 TTTTTTAAAATAA
*
1879871 TTTTTTAAAAATAG
1 TTTTTT-AAAATAA
1879885 TTTTTTAAAAT
1 TTTTTTAAAAT
1879896 GATATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.35
13 10 0.29
14 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAATAA
Found at i:1882158 original size:16 final size:16
Alignment explanation
Indices: 1882137--1882170 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1882127 ACACCTTCAT
1882137 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1882153 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1882169 TT
1 TT
1882171 TCTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.24
Consensus pattern (16 bp):
TTCAACCGCTACACGC
Found at i:1882309 original size:2 final size:2
Alignment explanation
Indices: 1882302--1882336 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1882292 GTTTTAGGCC
1882302 AT AT AT 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 AT AT AT
1882337 TGAACATCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1884076 original size:17 final size:18
Alignment explanation
Indices: 1884040--1884077 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1884030 AAAGAAACTG
1884040 TAAGTCATTCAATAAAAC
1 TAAGTCATTCAATAAAAC
1884058 TAAGTC-TTCAA-AAATAC
1 TAAGTCATTCAATAAA-AC
1884075 TAA
1 TAA
1884078 TATCAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 10 0.53
18 6 0.32
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAGTCATTCAATAAAAC
Found at i:1887943 original size:13 final size:12
Alignment explanation
Indices: 1887911--1887950 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1887901 GATTTAAAAA
*
1887911 AAATAATTTTTT
1 AAATATTTTTTT
*
1887923 AAA-GTTTTTTT
1 AAATATTTTTTT
1887934 AAATATTTTTTT
1 AAATATTTTTTT
1887946 AAATA
1 AAATA
1887951 CTATAAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:1889110 original size:155 final size:153
Alignment explanation
Indices: 1888811--1889128 Score: 507
Period size: 155 Copynumber: 2.0 Consensus size: 153
1888801 ATGGGAGTTG
*
1888811 CTTCTGCTGCATTTTTGCCGGTGGTGATTCTTCGGGGGGGGGGGGGGGGTAGCGAATCAGGTGTA
1 CTTCTGCTGCATTTTTGCCGGTGGTGATTCTTC---GGGGGGGGGGGGGTAGAGAATCAGGTGTA
1888876 TGTTATCCATTGTGGAGAACCTCGACGTCTTGATAACGTTAGGATTGTTTTAGGGAAAGGATAAT
63 TGTTATCCATTGTGGAGAACCTCGACGTCTTGATAACGTTAGGATTGTTTTAGGGAAAGGATAAT
1888941 CAGCCCATAAAAAAAGACCACC-TTTT
128 CAGCCCAT-AAAAAAGACCACCTTTTT
1888967 CTTCTGCTGCATTTTTGCCGGTGGTGATTCTTC-GGGGGGGGGGGGT-GAGAATCAGGTGTAATG
1 CTTCTGCTGCATTTTTGCCGGTGGTGATTCTTCGGGGGGGGGGGGGTAGAGAATCAGGTGT-A--
1889030 CTGTTATCCATTGTGGAGAACCTCGACGTCTTGATAACGTTAGGATTGTTTTAGGGAAAGGATAT
63 -TGTTATCCATTGTGGAGAACCTCGACGTCTTGATAACGTTAGGATTGTTTTAGGGAAAGG--AT
1889095 AATCAGCCCATAAAAAAAGACCACCTTTTT
125 AATCAGCCCAT-AAAAAAGACCACCTTTTT
1889125 CTTC
1 CTTC
1889129 GTTACTGGGG
Statistics
Matches: 154, Mismatches: 1, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
151 12 0.08
152 14 0.09
155 60 0.39
156 33 0.21
157 27 0.18
158 8 0.05
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (153 bp):
CTTCTGCTGCATTTTTGCCGGTGGTGATTCTTCGGGGGGGGGGGGGTAGAGAATCAGGTGTATGT
TATCCATTGTGGAGAACCTCGACGTCTTGATAACGTTAGGATTGTTTTAGGGAAAGGATAATCAG
CCCATAAAAAAGACCACCTTTTT
Found at i:1891554 original size:14 final size:13
Alignment explanation
Indices: 1891537--1891586 Score: 75
Period size: 12 Copynumber: 3.8 Consensus size: 13
1891527 AAAAAAAGGG
1891537 TTTTTTAAAATAA
1 TTTTTTAAAATAA
1891550 -TTTTTAAAATAA
1 TTTTTTAAAATAA
*
1891562 TTTTTTAAAAATAG
1 TTTTTT-AAAATAA
1891576 TTTTTTAAAAT
1 TTTTTTAAAAT
1891587 GATATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.35
13 10 0.29
14 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAATAA
Found at i:1893849 original size:16 final size:16
Alignment explanation
Indices: 1893828--1893861 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1893818 ACACCTTCAT
1893828 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1893844 TTCAACCGCTACACGC
1 TTCAACCGCTACACGC
1893860 TT
1 TT
1893862 TCTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.24
Consensus pattern (16 bp):
TTCAACCGCTACACGC
Found at i:1894002 original size:2 final size:2
Alignment explanation
Indices: 1893995--1894028 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1893985 GTTTTAGGCC
1893995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1894029 TGAACATCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1900130 original size:31 final size:29
Alignment explanation
Indices: 1900107--1900162 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1900097 TAACCGTACT
1900107 TAATCCAACATTTTATTAGTATAACCGAG
1 TAATCCAACATTTTATTAGTATAACCGAG
* **
1900136 TCATCTTACATTTTATTAGTATAACCG
1 TAATCCAACATTTTATTAGTATAACCG
1900163 GGATCATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
TAATCCAACATTTTATTAGTATAACCGAG
Found at i:1946627 original size:607 final size:600
Alignment explanation
Indices: 1944947--1946763 Score: 2898
Period size: 604 Copynumber: 3.0 Consensus size: 600
1944937 CTCTAAACAC
* * * * * * *
1944947 CGACCAATAGTCAATCTCTCACCGACCACATCTCTTTGCCTAAACCAGAAGGGATAAATTTTCAA
1 CGACCAACAGTAAATCTCTCACCGACTACATCTTTTTTCC-AAACCAGAAGGGATGAATTGTCAA
* * * *
1945012 TGACTGAC-ACC-AAATTATTCCCATAAAAAATAACTATTTAGTCGAACGTTTATGATATTTTTA
65 TGATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAAC----ATGATATTTTTA
1945075 TCATTATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAATCACTTATTTCG
126 TCATTATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAATCACTTATTTCG
1945140 TGTAAAAAATTCAACAGCTAAATATATATTAATAAAATTATTTTTTTACTCATGAAAACCAGTGT
191 TGTAAAAAATTCAACAGCTAAATATATATTAATAAAATTATTTTTTTACTCATGAAAACCAGTGT
1945205 ATCTTATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCAAA
256 ATCTTATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCAAA
1945270 TTAAATAAAAATTGACAACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTTTCT
321 TTAAATAAAAATTGACAACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTTTCT
1945335 TCTATGTTTTCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTT
386 TCTATG---TCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTT
1945400 TAGTGAAAAGGAAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAATAAA-AAAAAA
448 TAGTGAAAA-GAAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAATAAATAAAAAA
*
1945464 TACTAATCAACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAATTTGAGC
512 TACTAATCAACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAGTTTGAGC
1945529 ACCAGTAACTGCAAGAGTGATTGA
577 ACCAGTAACTGCAAGAGTGATTGA
* *
1945553 CGACCAACAGTAAATCTCTCACCGACTACATCTTTTTGTCCAAACTAGAAGAGATGAATTGTCAA
1 CGACCAACAGTAAATCTCTCACCGACTACATCTTTTT-TCCAAACCAGAAGGGATGAATTGTCAA
1945618 TGATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAACATGATATTTTTATCAT
65 TGATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAACATGATATTTTTATCAT
1945683 TATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAATCACTTATTTCGTGTA
130 TATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAATCACTTATTTCGTGTA
1945748 AAAAATTCAACAGCTAAATATATATTAATAAAATTATTTTTTTACTCATGAAAACCAGTGTATCT
195 AAAAATTCAACAGCTAAATATATATTAATAAAATTATTTTTTTACTCATGAAAACCAGTGTATCT
1945813 TATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCAAATTAA
260 TATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCAAATTAA
1945878 ATAAAAATTGACAACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTTTCTTCTA
325 ATAAAAATTGACAACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTTTCTTCTA
1945943 TGTTTTCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTTTAGT
390 TG---TCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTTTAGT
1946008 GAAAAGGAAAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAATAAAATAAAAAATA
452 GAAAA-G-AAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAAT-AAATAAAAAATA
1946073 CTAATCAACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAGTTTGAGCAC
514 CTAATCAACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAGTTTGAGCAC
1946138 CAGTAACTGCAAGAGTGATTGA
579 CAGTAACTGCAAGAGTGATTGA
1946160 CGACCAACAGTAAATCTCTCACCGACTACATCTTTTTATCCAAACCAGAAGGGATGAATTGTCAA
1 CGACCAACAGTAAATCTCTCACCGACTACATCTTTTT-TCCAAACCAGAAGGGATGAATTGTCAA
*
1946225 TAATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAACATGATATTTTTATCAT
65 TGATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAACATGATATTTTTATCAT
* * *
1946290 TATTTCTTTTTCGATATATGACAAAAATTTAATAATATTAAATTTTTAAGT-ACTTATTTCGTGT
130 TATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAA-TCACTTATTTCGTGT
*
1946354 AAAAAATTCAACAACTAAATATATATTAATAAAATTATTACTTTTTTTTACTCATGAAAACCAGT
194 AAAAAATTCAACAGCTAAATATATATTAAT-AAA--ATTA--TTTTTTTACTCATGAAAACCAGT
* * * * *
1946419 GTATCTTATTAAATGATAAAACCTTAGCAATTGGCCCTCCCAAATTATTGGAATGGACCCTCCCA
254 GTATCTTATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCA
* * * * *
1946484 AATTAAAGAGAAATTGACGCACTGATAAGACAAAGATGATATTTTGGGACTTCTGCTCTAACCTT
319 AATTAAATAAAAATTGAC-AACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTT
*
1946549 TCTTCTATG-C-TTTTTCCCCATAATTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTT
383 TCTTCTATGTCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTT
* * * *
1946612 TAGTGAAAAG--AAAAAAA-AATATAAAGTTGGCATGAACTGAGTCTTAAAAATCTAAATAAATA
448 TAGTGAAAAGAAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAA--TAAATAAAAA
* * ** * * * * * *
1946674 GTA-TAAACCAACTTACCTTAATGGTTAAAGGAATAAATATTGTTTCTAGAGATCACGGGTTTGA
511 ATACT-AATCAACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAGTTTGA
* * *
1946738 GCACCAGCAACTGTAAGGGTGATTGA
575 GCACCAGTAACTGCAAGAGTGATTGA
1946764 GTGTTCATTG
Statistics
Matches: 1145, Mismatches: 50, Indels: 34
0.93 0.04 0.03
Matches are distributed among these distances:
603 31 0.03
604 438 0.38
605 45 0.04
606 63 0.06
607 314 0.27
608 98 0.09
609 1 0.00
610 4 0.00
612 99 0.09
613 52 0.05
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (600 bp):
CGACCAACAGTAAATCTCTCACCGACTACATCTTTTTTCCAAACCAGAAGGGATGAATTGTCAAT
GATTGACTACCAAAATTATTCCCATCAATAATAACTATTTAGTCAAACATGATATTTTTATCATT
ATTTCTTTATAGATATATGACAAAAATTTAATAATATTAATTTTTTAATCACTTATTTCGTGTAA
AAAATTCAACAGCTAAATATATATTAATAAAATTATTTTTTTACTCATGAAAACCAGTGTATCTT
ATTAAATGATAAAACCGTAGCAATTGACCCTTCCAAATTAATGGAATGAACCCTCCCAAATTAAA
TAAAAATTGACAACTGACAAGACAAAGATGATATTTTTGGACTTCTGCTCTAACCTTTCTTCTAT
GTCTTTTTTCCCCATATTTTTAAAACTTATGAAATTGGTTATTATTTGGTATTCGTTTAGTGAAA
AGAAAAAAAAAGAATATAACGTTGGCATGACCTGAGTCCTAAAAATAAATAAAAAATACTAATCA
ACTTATTTTAATGATTAAAGGAATCAATGTTGTTTCTAGAGGTAACGAGTTTGAGCACCAGTAAC
TGCAAGAGTGATTGA
Found at i:1947560 original size:3 final size:3
Alignment explanation
Indices: 1947552--1947592 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1947542 ACGTTTAGCT
1947552 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1947593 TTGGTATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1950369 original size:12 final size:12
Alignment explanation
Indices: 1950354--1950456 Score: 66
Period size: 12 Copynumber: 8.6 Consensus size: 12
1950344 CTATTTTGAT
1950354 TTCTGATCTGAA
1 TTCTGATCTGAA
* *
1950366 TTCTGTTCTGAT
1 TTCTGATCTGAA
* *
1950378 TTCTGATATGGA
1 TTCTGATCTGAA
* *
1950390 TTATGTTCTG-A
1 TTCTGATCTGAA
*
1950401 TGTCTGATCTGGA
1 T-TCTGATCTGAA
* *
1950414 TTTTGTTCTG-A
1 TTCTGATCTGAA
1950425 TGTCTGATCTGAA
1 T-TCTGATCTGAA
* * *
1950438 TTCTGTTTTGAT
1 TTCTGATCTGAA
1950450 TTCTGAT
1 TTCTGAT
1950457 ATCTCCGTTT
Statistics
Matches: 68, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
11 4 0.06
12 60 0.88
13 4 0.06
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (12 bp):
TTCTGATCTGAA
Found at i:1950381 original size:24 final size:24
Alignment explanation
Indices: 1950324--1950456 Score: 149
Period size: 24 Copynumber: 5.5 Consensus size: 24
1950314 GAATATTTTA
** * *
1950324 TCTGATTTCCAATTTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
*
1950348 TTTGATTTCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
1950372 TCTGATTTCTGATATGGATTATGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
1950396 TCTGATGTCTGATCTGGATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1950420 TCTGATGTCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1950444 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1950457 ATCTCCGTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1951613 original size:18 final size:18
Alignment explanation
Indices: 1951590--1951635 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1951580 CACAGAATGT
*
1951590 ATAGGATTACCGGTGGGA
1 ATAGGATTACCGGCGGGA
*
1951608 ATAGGATTACCGGCGTGA
1 ATAGGATTACCGGCGGGA
*
1951626 ATAAGATTAC
1 ATAGGATTAC
1951636 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (18 bp):
ATAGGATTACCGGCGGGA
Found at i:1952934 original size:60 final size:60
Alignment explanation
Indices: 1952841--1952953 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1952831 AGTCAGTGAC
* ** * * *
1952841 CATTTTGTAACTTTTGGTAGTTGAGGGACTCAACAAAGCAACTCCTTATAACCGGGAGAT
1 CATTTTCTAACTTTTAATAGTTCAGGGACTCAACAAAACAACTCCCTATAACCGGGAGAT
*
1952901 CATTTTCTAACTTTTAATAG-TCAGGTGACTCAACAAAATAACTCCCTATAACC
1 CATTTTCTAACTTTTAATAGTTCAGG-GACTCAACAAAACAACTCCCTATAACC
1952954 AAGGGACCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.09
60 41 0.91
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (60 bp):
CATTTTCTAACTTTTAATAGTTCAGGGACTCAACAAAACAACTCCCTATAACCGGGAGAT
Found at i:1959501 original size:226 final size:226
Alignment explanation
Indices: 1959103--1959560 Score: 909
Period size: 226 Copynumber: 2.0 Consensus size: 226
1959093 TCAATGTCTG
1959103 GAAA-TTGACGATGGACACTAAGATTTCTTCATCCTCCAATCTCCATGATCCATCTTTCGATGGG
1 GAAAGTTGACGATGGACACTAAGATTTCTTCATCCTCCAATCTCCATGATCCATCTTTCGATGGG
1959167 CCTGAAACTAACTATGTTGGTCAACCCATCATTTTCATTGGTCCACTATTCAGATTGGTCGTCAA
66 CCTGAAACTAACTATGTTGGTCAACCCATCATTTTCATTGGTCCACTATTCAGATTGGTCGTCAA
1959232 TCCACCAAGCTATGCCACGTCAGCCCGTCTGTAAAGTTTTTAACGGGTACTAAAATAAAATAAAA
131 TCCACCAAGCTATGCCACGTCAGCCCGTCTGTAAAGTTTTTAACGGGTACTAAAATAAAATAAAA
1959297 ACTAAACGTTAGGTATAATTTTAAAAGAAAT
196 ACTAAACGTTAGGTATAATTTTAAAAGAAAT
1959328 GAAAGTTGACGATGGACACTAAGATTTCTTCATCCTCCAATCTCCATGATCCATCTTTCGATGGG
1 GAAAGTTGACGATGGACACTAAGATTTCTTCATCCTCCAATCTCCATGATCCATCTTTCGATGGG
1959393 CCTGAAACTAACTATGTTGGTCAACCCATCATTTTCATTGGTCCACTATTCAGATTGGTCGTCAA
66 CCTGAAACTAACTATGTTGGTCAACCCATCATTTTCATTGGTCCACTATTCAGATTGGTCGTCAA
1959458 TCCACCAAGCTATGCCACGTCAGCCCGTCTGTAAAGTTTTTAACGGGTACTAAAATAAAATAAAA
131 TCCACCAAGCTATGCCACGTCAGCCCGTCTGTAAAGTTTTTAACGGGTACTAAAATAAAATAAAA
1959523 ACTAAACGTTAGGTATAATTTTAAAAGAAAT
196 ACTAAACGTTAGGTATAATTTTAAAAGAAAT
1959554 GAAAGTT
1 GAAAGTT
1959561 TAGATACTAA
Statistics
Matches: 232, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
225 4 0.02
226 228 0.98
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (226 bp):
GAAAGTTGACGATGGACACTAAGATTTCTTCATCCTCCAATCTCCATGATCCATCTTTCGATGGG
CCTGAAACTAACTATGTTGGTCAACCCATCATTTTCATTGGTCCACTATTCAGATTGGTCGTCAA
TCCACCAAGCTATGCCACGTCAGCCCGTCTGTAAAGTTTTTAACGGGTACTAAAATAAAATAAAA
ACTAAACGTTAGGTATAATTTTAAAAGAAAT
Found at i:1962050 original size:7 final size:7
Alignment explanation
Indices: 1962038--1962063 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1962028 AAATTGTTAT
1962038 CTCTTCA
1 CTCTTCA
1962045 CTCTTCA
1 CTCTTCA
1962052 CTCTTCA
1 CTCTTCA
1962059 CTCTT
1 CTCTT
1962064 GTGATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.46
Consensus pattern (7 bp):
CTCTTCA
Found at i:1962653 original size:17 final size:17
Alignment explanation
Indices: 1962621--1962658 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1962611 CAAAGTTTTC
*
1962621 TTAAATTAATTAAATT-
1 TTAAATTAACTAAATTA
1962637 TTAAATATAACTAAATTA
1 TTAAAT-TAACTAAATTA
1962655 TTAA
1 TTAA
1962659 GTAAATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATTAACTAAATTA
Found at i:1962756 original size:31 final size:30
Alignment explanation
Indices: 1962702--1962760 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
1962692 AGCGATAATA
1962702 TCAACACCGTAAAATATTATAAATTATTACG
1 TCAACACCGTAAAATATTATAAA-TATTACG
*
1962733 TCAACACCGTAAACTATCT-TAAATATTA
1 TCAACACCGTAAAATAT-TATAAATATTA
1962761 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 20 0.77
32 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (30 bp):
TCAACACCGTAAAATATTATAAATATTACG
Found at i:1964337 original size:33 final size:34
Alignment explanation
Indices: 1964278--1964344 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
1964268 GACTGAATAA
*
1964278 TAGTAAAAATAATCCAAGTCATCATTTTGATTAC
1 TAGTAAAAAAAATCCAAGTCATCATTTTGATTAC
* *
1964312 TAGTAAAAAAAAT-TAATTCATCATTTTGATTAC
1 TAGTAAAAAAAATCCAAGTCATCATTTTGATTAC
1964345 AATAGTTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.60
34 12 0.40
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.37
Consensus pattern (34 bp):
TAGTAAAAAAAATCCAAGTCATCATTTTGATTAC
Found at i:1969149 original size:64 final size:63
Alignment explanation
Indices: 1969033--1969173 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
1969023 CATATTCAAT
* * * *
1969033 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTA
* * * * *
1969096 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCAAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCAAAGGCAATTAGTGCATCGATGCATAGGTA
1969160 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1969174 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTA
Found at i:1969206 original size:20 final size:22
Alignment explanation
Indices: 1969161--1969218 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1969151 GCATGGGTAG
1969161 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1969185 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1969205 TGCATCGATGCACT
1 TGCATCGATGCACT
1969219 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1972320 original size:33 final size:33
Alignment explanation
Indices: 1972282--1972358 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
1972272 CTTCTTGCAA
1972282 TCTGGTATGCTAAGATACCCGAAAGAACCATTG
1 TCTGGTATGCTAAGATACCCGAAAGAACCATTG
1972315 TCTGGTATGCTAAGATACCCGAAAGAACCATTG
1 TCTGGTATGCTAAGATACCCGAAAGAACCATTG
*
1972348 TCTGGTTTGCT
1 TCTGGTATGCT
1972359 GATAACCCGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (33 bp):
TCTGGTATGCTAAGATACCCGAAAGAACCATTG
Found at i:1981649 original size:105 final size:104
Alignment explanation
Indices: 1981506--1981698 Score: 246
Period size: 105 Copynumber: 1.8 Consensus size: 104
1981496 AATGTTTTGC
* * *
1981506 TTGATGCATATTGCAAGGAGGAGATGATTTCTGAAGCTGTAGATACCATTGGCATA-ATGAGAAA
1 TTGATGCACATTGCAAGGAGGAGATCATTTCTGAAGCTGAAGATACCATT-G-ATACATGAGAAA
* *
1981570 GCAAGGCATTGAGCCTGATGTTGTCACGTATAGTATATTGG
64 GAAAGGCATTGAGCCTAATGTTGTCACGTATAGTATATTGG
* ****
1981611 TTGATGCACATTGCAAGGAAGG-GATCATTTTTGAAGCTGAAGATGTTGTTGATACGATGAGAAA
1 TTGATGCACATTGCAAGG-AGGAGATCATTTCTGAAGCTGAAGATACCATTGATAC-ATGAGAAA
1981675 GAAAGGCATTGAGCCTAATGTTGT
64 GAAAGGCATTGAGCCTAATGTTGT
1981699 TACCTATAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
103 3 0.04
104 1 0.01
105 68 0.91
106 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (104 bp):
TTGATGCACATTGCAAGGAGGAGATCATTTCTGAAGCTGAAGATACCATTGATACATGAGAAAGA
AAGGCATTGAGCCTAATGTTGTCACGTATAGTATATTGG
Found at i:1984841 original size:5 final size:5
Alignment explanation
Indices: 1984831--1984873 Score: 77
Period size: 5 Copynumber: 8.4 Consensus size: 5
1984821 AATATATCTT
1984831 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATGTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TA
1984874 CTTGTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:1991680 original size:59 final size:60
Alignment explanation
Indices: 1991563--1991695 Score: 180
Period size: 59 Copynumber: 2.2 Consensus size: 60
1991553 ATCAAGTGGT
*
1991563 CATTTTGTAACTTTTAATAGTCGATGAACTCAACAAAACAATTCCCTATAGTCGAGGGAC
1 CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAATTCCCTATAGTCGAGGGAC
* * * **
1991623 CATTTTGTAACTTTTAATAGTCG-GGAACTCAACAAAGCATTTTCCTATAGTTTAGGGAC
1 CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAATTCCCTATAGTCGAGGGAC
*
1991682 TATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
1991696 ACCCATTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 39 0.60
60 26 0.40
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAATTCCCTATAGTCGAGGGAC
Found at i:1995703 original size:38 final size:40
Alignment explanation
Indices: 1995656--1995732 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
1995646 TCCAAAACCC
1995656 ATATAATATATATTTTTAAAAAT-ATTTT-AAAATTATATT
1 ATATAATATATA-TTTTAAAAATGATTTTCAAAATTATATT
*
1995695 ATAT-ATATATATTTTAAAAATGTTTTTCAAAATTATAT
1 ATATAATATATATTTTAAAAATGATTTTCAAAATTATAT
1995733 AGTTTTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 10 0.29
38 11 0.31
39 14 0.40
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (40 bp):
ATATAATATATATTTTAAAAATGATTTTCAAAATTATATT
Found at i:1995730 original size:34 final size:33
Alignment explanation
Indices: 1995661--1995802 Score: 114
Period size: 34 Copynumber: 4.2 Consensus size: 33
1995651 AACCCATATA
* ** *
1995661 ATATATATTTTTAAAAATATTTTAAAATTATATTAT
1 ATATATATTTTTAAAAATGTTTTTCAA--A-ACTAT
1995697 ATATATATATTTTAAAAATGTTTTTCAAAA-T-T
1 ATATATAT-TTTTAAAAATGTTTTTCAAAACTAT
* *
1995729 ATATA-GTTTTCAAAAATGTTTTT-AAAACTAT
1 ATATATATTTTTAAAAATGTTTTTCAAAACTAT
* *
1995760 ATATTATATGTTTTCAAAATG-ATTTCAAAACTAT
1 ATA-TATAT-TTTTAAAAATGTTTTTCAAAACTAT
1995794 ATAATATAT
1 AT-ATATAT
1995803 ATATACGTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
29 4 0.04
30 16 0.18
31 5 0.06
32 8 0.09
33 5 0.06
34 25 0.28
35 2 0.02
36 8 0.09
37 16 0.18
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (33 bp):
ATATATATTTTTAAAAATGTTTTTCAAAACTAT
Found at i:1995732 original size:30 final size:28
Alignment explanation
Indices: 1995700--1995764 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
1995690 ATATTATATA
*
1995700 TATATATTTT-AAAAATGTTTTTCAAAAT
1 TATATATTTTCAAAAATGTTTTT-AAAAC
1995728 TATATAGTTTTCAAAAATGTTTTTAAAAC
1 TATATA-TTTTCAAAAATGTTTTTAAAAC
1995757 TATATATT
1 TATATATT
1995765 ATATGTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.24
29 14 0.41
30 12 0.35
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (28 bp):
TATATATTTTCAAAAATGTTTTTAAAAC
Found at i:1995825 original size:104 final size:101
Alignment explanation
Indices: 1995664--1995916 Score: 314
Period size: 104 Copynumber: 2.4 Consensus size: 101
1995654 CCATATAATA
* * * * *
1995664 TATATTTTTAAAAAT-ATTTTAAAATTATATTATATATATATATTTTAAAAATGTTTTTCAAAA-
1 TATATTTTTCAAAATGATTTAAAAACTATATAATATATATATATTTTAAAAATGTTTTTAAAAAC
*
1995727 T-TATATAGTTTTCAAAAATGTTTTTAAAACTATATAT
66 TATATATA-TTTTC-AAAATGTTTTAAAAACTATATAT
* *
1995764 TATATGTTTTCAAAATGATTTCAAAACTATATAATATATATATACGTTTTCAAAATGTTTTTAAA
1 TATAT-TTTTCAAAATGATTTAAAAACTATATAATATATATATA--TTTTAAAAATGTTTTTAAA
1995829 AACTATATATATTTTCAAAATGTTTTAAAAACTATATAT
63 AACTATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
1995868 TATATTTATTTTCAAAATGTTTTAAAAACTATAATATATATATATATAT
1 TATA--T-TTTTCAAAATGATTTAAAAACTAT-ATA-ATATATATATAT
1995917 ATATATTTCC
Statistics
Matches: 133, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
100 5 0.04
101 9 0.07
102 24 0.18
104 45 0.34
105 6 0.05
106 30 0.23
107 3 0.02
108 11 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (101 bp):
TATATTTTTCAAAATGATTTAAAAACTATATAATATATATATATTTTAAAAATGTTTTTAAAAAC
TATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:1995837 original size:36 final size:34
Alignment explanation
Indices: 1995728--1995909 Score: 171
Period size: 36 Copynumber: 5.2 Consensus size: 34
1995718 TTTTCAAAAT
*
1995728 TATATAGTTTTCAAAAATGTTTTTAAAACTATATA
1 TATATAGTTTTC-AAAATGTTTTAAAAACTATATA
* *
1995763 T-TATATGTTTTCAAAATGATTTCAAAACTATATAATATA
1 TATATA-GTTTTCAAAATG-TTTTAAAA--A-CT-ATATA
1995802 TATATACGTTTTCAAAATGTTTTTAAAAAC----TA
1 TATATA-GTTTTCAAAATG-TTTTAAAAACTATATA
1995834 TATATA-TTTTCAAAATGTTTTAAAAACTATATA
1 TATATAGTTTTCAAAATGTTTTAAAAACTATATA
1995867 TTATATTTA-TTTTCAAAATGTTTTAAAAACTATAATA
1 -TATA--TAGTTTTCAAAATGTTTTAAAAACTAT-ATA
1995904 TATATA
1 TATATA
1995910 TATATATATA
Statistics
Matches: 125, Mismatches: 7, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
29 10 0.08
30 11 0.09
32 8 0.06
33 2 0.02
34 16 0.13
35 13 0.10
36 30 0.24
37 4 0.03
38 2 0.02
39 6 0.05
40 23 0.18
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATAGTTTTCAAAATGTTTTAAAAACTATATA
Found at i:1995864 original size:29 final size:31
Alignment explanation
Indices: 1995800--1995867 Score: 113
Period size: 29 Copynumber: 2.2 Consensus size: 31
1995790 CTATATAATA
1995800 TATATATACGTTTTCAAAATGTTTTTAAAAAC
1 TATATATAC-TTTTCAAAATGTTTTTAAAAAC
1995832 TATATATA-TTTTCAAAATG-TTTTAAAAAC
1 TATATATACTTTTCAAAATGTTTTTAAAAAC
1995861 TATATAT
1 TATATAT
1995868 TATATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 17 0.47
30 11 0.31
32 8 0.22
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (31 bp):
TATATATACTTTTCAAAATGTTTTTAAAAAC
Found at i:1995945 original size:49 final size:45
Alignment explanation
Indices: 1995861--1995962 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 45
1995851 TTTTAAAAAC
* *
1995861 TATATATTATATTTATTTTCAAAATGTTTTAAAAACTATAATAT-A
1 TATATATTATATATATTTCCAAAATGTTTTAAAAACTAT-ATATGA
*
1995906 TATATATATATATATATTTCCAAAAAATCGTTTTCAAAACTATATATGA
1 TATATAT-TATATATATTTCC--AAAAT-GTTTTAAAAACTATATATGA
1995955 TATATATT
1 TATATATT
1995963 TTAAAAACGT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
45 7 0.14
46 11 0.22
48 10 0.20
49 21 0.43
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (45 bp):
TATATATTATATATATTTCCAAAATGTTTTAAAAACTATATATGA
Found at i:1995975 original size:85 final size:82
Alignment explanation
Indices: 1995832--1995994 Score: 220
Period size: 85 Copynumber: 2.0 Consensus size: 82
1995822 TTTTAAAAAC
* * * * *
1995832 TATATATATTTTCAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTCCAAAATGTTTTAAAAACTATATATGATATATATTTTAAAAACGTTTTAAAAAC
1995897 TATAAT-ATATATATATA
66 TAT-ATGATATATATATA
* *
1995914 TATATATATTTCCAAAAAATCGTTTTCAAAACTATATATGATATATATTTTAAAAACGTTTTCAA
1 TATATATATTTCC--AAAAT-GTTTTAAAAACTATATATGATATATATTTTAAAAACGTTTTAAA
1995979 AACTATATGATATATA
63 AACTATATGATATATA
1995995 CATTTTCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
82 12 0.17
84 7 0.10
85 51 0.73
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (82 bp):
TATATATATTTCCAAAATGTTTTAAAAACTATATATGATATATATTTTAAAAACGTTTTAAAAAC
TATATGATATATATATA
Found at i:1996000 original size:36 final size:37
Alignment explanation
Indices: 1995908--1996055 Score: 126
Period size: 36 Copynumber: 4.0 Consensus size: 37
1995898 ATAATATATA
* *
1995908 TATATAT-ATATATATTTCCAAAAAATCGTTTTCAAAAC
1 TATATATGATATACATTTTC-AAAAA-CGTTTTCAAAAC
*
1995946 TATATATGATATATATTTT-AAAAACGTTTTCAAAAC
1 TATATATGATATACATTTTCAAAAACGTTTTCAAAAC
* * *
1995982 TATATGAT-ATATACATTTTCAAAAACCATTTTCTGGAAAT
1 TATAT-ATGATATACATTTTCAAAAA-CGTTTTC--AAAAC
* * *
1996022 TATATATTATAT-CA-TTTCAAAAGCATTTTCAAAA
1 TATATATGATATACATTTTCAAAAACGTTTTCAAAA
1996056 AATGATGTTA
Statistics
Matches: 96, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
35 3 0.03
36 27 0.28
37 19 0.20
38 21 0.22
39 14 0.15
40 12 0.12
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (37 bp):
TATATATGATATACATTTTCAAAAACGTTTTCAAAAC
Found at i:1997405 original size:27 final size:27
Alignment explanation
Indices: 1997374--1997428 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1997364 TTATGGCCTT
1997374 ATTCTATCTATGTATAAAATATGATAA
1 ATTCTATCTATGTATAAAATATGATAA
1997401 ATTCTATCTATGTATAAAATATGATAA
1 ATTCTATCTATGTATAAAATATGATAA
1997428 A
1 A
1997429 GGCCAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (27 bp):
ATTCTATCTATGTATAAAATATGATAA
Found at i:1999374 original size:20 final size:20
Alignment explanation
Indices: 1999349--1999394 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1999339 TTTGGGCTTC
1999349 ATCAGCCGACAGATACAACA
1 ATCAGCCGACAGATACAACA
*
1999369 ATCAGCCGATAGATACAACA
1 ATCAGCCGACAGATACAACA
1999389 ATCAGC
1 ATCAGC
1999395 AACTGTAGAT
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:0.43, C:0.28, G:0.15, T:0.13
Consensus pattern (20 bp):
ATCAGCCGACAGATACAACA
Found at i:2006079 original size:16 final size:16
Alignment explanation
Indices: 2006058--2006091 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2006048 AAAAGGAAGA
2006058 AAGCGTGTAGCAGTTG
1 AAGCGTGTAGCAGTTG
2006074 AAGCGTGTAGCAGTTG
1 AAGCGTGTAGCAGTTG
2006090 AA
1 AA
2006092 ATGAAGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.35, T:0.24
Consensus pattern (16 bp):
AAGCGTGTAGCAGTTG
Found at i:2006369 original size:29 final size:29
Alignment explanation
Indices: 2006337--2006395 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2006327 GATGACATGA
2006337 ATTATTTTATTATTTTTTCATAAAAAATG
1 ATTATTTTATTATTTTTTCATAAAAAATG
2006366 ATTATTTTATTATTTTTTCATAAAAAATG
1 ATTATTTTATTATTTTTTCATAAAAAATG
2006395 A
1 A
2006396 CATATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATTATTTTATTATTTTTTCATAAAAAATG
Found at i:2006406 original size:28 final size:29
Alignment explanation
Indices: 2006333--2006408 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 29
2006323 CAATGATGAC
2006333 ATGAATTATTTTATTATTTTTTCATAAAAA
1 ATGAA-TATTTTATTATTTTTTCATAAAAA
*
2006363 ATGATTATTTTATTATTTTTTCATAAAAA
1 ATGAATATTTTATTATTTTTTCATAAAAA
2006392 ATGACATATTTTTATTA
1 ATGA-ATA-TTTTATTA
2006409 ATATTTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
29 28 0.67
30 6 0.14
31 8 0.19
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
ATGAATATTTTATTATTTTTTCATAAAAA
Found at i:2006800 original size:20 final size:21
Alignment explanation
Indices: 2006767--2006806 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2006757 TTAAAACCCT
2006767 AAATTAATGGTTTAAAGTTAA
1 AAATTAATGGTTTAAAGTTAA
*
2006788 AAATTAA-GGTTTAAGGTTA
1 AAATTAATGGTTTAAAGTTA
2006807 GGGTTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
AAATTAATGGTTTAAAGTTAA
Found at i:2007373 original size:20 final size:20
Alignment explanation
Indices: 2007348--2007701 Score: 217
Period size: 20 Copynumber: 17.4 Consensus size: 20
2007338 GATTTTCCAG
**
2007348 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
* * *
2007368 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * * *
2007388 TATCGCAACGAGTACCCGTAAA
1 AATCGCAACGCGAATCCG--AA
* * *
2007410 AATCGCAACACGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
2007430 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
2007451 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
2007471 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* *
2007491 AATCGCAACGCGATTCTGAA
1 AATCGCAACGCGAATCCGAA
* **
2007511 TATCGCAACGAAAATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* *
2007532 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
2007552 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
2007572 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
** * *
2007593 AATCGCAACAAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
* *
2007613 AATCGCAACGAGAAT-CTATA
1 AATCGCAACGCGAATCCGA-A
** *
2007633 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGAA
*** *
2007653 AATCGCAACAATAATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
2007673 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
2007693 AATCGCAAC
1 AATCGCAAC
2007702 ACTGAAATTT
Statistics
Matches: 264, Mismatches: 61, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
20 201 0.76
21 48 0.18
22 15 0.06
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:2007491 original size:61 final size:61
Alignment explanation
Indices: 2007389--2007701 Score: 300
Period size: 61 Copynumber: 5.1 Consensus size: 61
2007379 GATTCTGACT
* * * *
2007389 ATCGCAACGAGTACCCGTAAAAATCGCAACACGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATCCGT-AAAATCGCAACAAGAATCCGTAAATCGCAACGACAAT-CGTAAA
* * * * * * *
2007452 ATCGCAATGCGTATCCGT-AAATCGCAACGAGAATACGTAAATCGCAACG-CGATTC-TGAAT
1 ATCGCAACGAGAATCCGTAAAATCGCAACAAGAATCCGTAAATCGCAACGAC-AATCGT-AAA
* ** * *
2007512 ATCGCAACGAAAATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACG-CGTATCCGT-AA
1 ATCGCAACGAGAATCCGTAAAATCGCAACAAGAATCCGTAAATCGCAACGAC-AAT-CGTAAA
* * *
2007573 ATCGCAACGAGAATACGTAAAATCGCAACAAGAATCTGTAAATCGCAACGAGAATC-TATAA
1 ATCGCAACGAGAATCCGTAAAATCGCAACAAGAATCCGTAAATCGCAACGACAATCGTA-AA
* * *
2007634 ATCGCAACGATAATCCGT-AAATCGCAACAATAATCCGTAAATCGCAACGAGAATCTGT-AA
1 ATCGCAACGAGAATCCGTAAAATCGCAACAAGAATCCGTAAATCGCAACGACAATC-GTAAA
2007694 ATCGCAAC
1 ATCGCAAC
2007702 ACTGAAATTT
Statistics
Matches: 209, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
59 2 0.01
60 64 0.31
61 125 0.60
62 2 0.01
63 16 0.08
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
ATCGCAACGAGAATCCGTAAAATCGCAACAAGAATCCGTAAATCGCAACGACAATCGTAAA
Found at i:2007533 original size:81 final size:82
Alignment explanation
Indices: 2007389--2007701 Score: 309
Period size: 81 Copynumber: 3.9 Consensus size: 82
2007379 GATTCTGACT
* * * * * *
2007389 ATCGCAACGAGTACCCGTAAAAATCGCAAC-ACGTATCCGT-AAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATCCGT--AAATCGCAACGA-GAATACGTAAAATCGCAACGAAAATCCGTAAA
*
2007452 ATCGCAATGCGTATCCGTAA
63 ATCGCAACGCGTATCCGTAA
* * * *
2007472 ATCGCAACGAGAATACGTAAATCGCAACGCG-ATTC-TGAATATCGCAACGAAAATCCGTAAAAT
1 ATCGCAACGAGAATCCGTAAATCGCAACGAGAATACGT-AAAATCGCAACGAAAATCCGTAAAAT
2007535 CGCAACGCGTATCCGTAA
65 CGCAACGCGTATCCGTAA
* * *
2007553 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAATCGCAAC-AAGAATCTGT-AAAT
1 ATCGCAACGAGAATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGAA-AATCCGTAAAAT
* * **
2007616 CGCAACGAGAATCTATAA
65 CGCAACGCGTATCCGTAA
* * * * * *
2007634 ATCGCAACGATAATCCGTAAATCGCAACAATAATCCGT-AAATCGCAACGAGAATCTGT-AAATC
1 ATCGCAACGAGAATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGAAAATCCGTAAAATC
2007697 GCAAC
66 GCAAC
2007702 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 30 0.15
81 130 0.66
82 19 0.10
83 16 0.08
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (82 bp):
ATCGCAACGAGAATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGAAAATCCGTAAAATC
GCAACGCGTATCCGTAA
Found at i:2007565 original size:101 final size:100
Alignment explanation
Indices: 2007423--2007702 Score: 347
Period size: 101 Copynumber: 2.8 Consensus size: 100
2007413 CGCAACACGT
* * *
2007423 ATCCGT-AAATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCGCAACGAGAATA
1 ATCCGTAAAATCGCAACG-CTATCCGT-AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATA
** *
2007487 CGTAAATCGCAACGCGATTCTG-AATATCGCAACGAAA
64 CGTAAATCGCAACAAGAATCTGTAA-ATCGCAACGAAA
2007524 ATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATAC
1 ATCCGTAAAATCGCAACGC-TATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATAC
*
2007589 GTAAAATCGCAACAAGAATCTGTAAATCGCAACGAGA
65 GT-AAATCGCAACAAGAATCTGTAAATCGCAACGAAA
* **
2007626 AT-C-TATAAATCGCAACGATAATCCGTAAATCGCAAC-AATAATCCGTAAATCGCAACGAGAAT
1 ATCCGTA-AAATCGCAACGCT-ATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAAT
2007688 -CTGTAAATCGCAACA
63 AC-GTAAATCGCAACA
2007703 CTGAAATTTT
Statistics
Matches: 161, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
100 16 0.10
101 98 0.61
102 45 0.28
103 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (100 bp):
ATCCGTAAAATCGCAACGCTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACG
TAAATCGCAACAAGAATCTGTAAATCGCAACGAAA
Found at i:2008537 original size:24 final size:24
Alignment explanation
Indices: 2008510--2008563 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2008500 GTATTCGAAA
2008510 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2008534 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2008558 TTTGAT
1 TTTGAT
2008564 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2008771 original size:12 final size:12
Alignment explanation
Indices: 2008756--2008785 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2008746 AACAGAAGGA
2008756 GAAGAATTCCCC
1 GAAGAATTCCCC
2008768 GAAGAATTCCCC
1 GAAGAATTCCCC
2008780 GAAGAA
1 GAAGAA
2008786 GAGAAAAAGA
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:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (12 bp):
GAAGAATTCCCC
Found at i:2011160 original size:33 final size:33
Alignment explanation
Indices: 2011090--2011290 Score: 186
Period size: 33 Copynumber: 5.8 Consensus size: 33
2011080 CTTAATGACT
* * *
2011090 ATCGCAACGCGAAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
* * *
2011124 ATCGCAATGCGAAATGAAAATCGTAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
2011157 ATCGCAACGCGAATATGAATATCGCAACGCGGAAATTA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
*
2011195 CTATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2011230 ATCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
2011263 ATCGCAATGCAAAATTAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2011291 CGAATTTAGT
Statistics
Matches: 138, Mismatches: 22, Indels: 15
0.79 0.13 0.09
Matches are distributed among these distances:
33 85 0.62
34 21 0.15
35 1 0.01
36 4 0.03
37 3 0.02
38 1 0.01
39 12 0.09
40 11 0.08
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2011175 original size:20 final size:19
Alignment explanation
Indices: 2011123--2011257 Score: 83
Period size: 19 Copynumber: 7.5 Consensus size: 19
2011113 GCAACGAGAG
*
2011123 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2011142 AATCGTAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
2011156 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* * *
2011176 TATCGCAACGCGGAAATTAC
1 AATCGCAACGC-GAAATGAA
* * *
2011196 TATCGTAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2011215 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
2011229 AATCGTAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2011248 AATCGCAACG
1 AATCGCAACG
2011258 AGGGAATCGC
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
14 20 0.23
15 1 0.01
16 4 0.05
17 4 0.05
18 1 0.01
19 29 0.33
20 26 0.30
21 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2011491 original size:14 final size:14
Alignment explanation
Indices: 2011472--2011508 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2011462 CATCAATTAA
2011472 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2011486 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2011500 ACAAATCAA
1 ACAAATCAA
2011509 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2013039 original size:14 final size:14
Alignment explanation
Indices: 2013020--2013076 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2013010 TGGAAATGAA
2013020 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2013034 AATCGCAACACGAAATGAA
1 AATCGC-A-ACG--A-GAG
2013053 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2013067 AATCGCAACG
1 AATCGCAACG
2013077 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2013052 original size:33 final size:33
Alignment explanation
Indices: 2013012--2013095 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
2013002 TCGCAACGTG
2013012 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
*
2013045 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
2013078 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
2013096 CGAAATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACAC
Found at i:2013117 original size:19 final size:19
Alignment explanation
Indices: 2012972--2013117 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
2012962 TCTTTTGGTT
*
2012972 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
2012991 GAGAATGACTATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
2013012 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
2013029 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
2013045 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2013062 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2013078 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2013097 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2013116 GA
1 GA
2013118 TTCTCTCGTT
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.19
15 2 0.02
16 4 0.04
17 3 0.03
18 2 0.02
19 45 0.43
20 26 0.25
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2013144 original size:21 final size:21
Alignment explanation
Indices: 2013118--2013209 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 21
2013108 CGCAATGCGA
2013118 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
2013139 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
2013160 TT-TCGCGTT--GA----GA-
1 TTCTCTCGTTGCGATTTTCAT
2013173 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2013194 TTCTCTCGTTACGATT
1 TTCTCTCGTTGCGATT
2013210 CTTCTGCAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.04
14 7 0.12
16 2 0.04
18 2 0.04
20 7 0.12
21 36 0.64
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2013770 original size:20 final size:20
Alignment explanation
Indices: 2013745--2013940 Score: 207
Period size: 20 Copynumber: 9.6 Consensus size: 20
2013735 CTTTAAAAAT
*
2013745 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
2013765 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2013785 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2013806 CGCGTTGCGATTTTACGGATT
1 CGCGTTGCGA-TTTACGGATA
* * *
2013827 CTCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2013847 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2013867 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2013887 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2013908 CGCGTTGCGATTTTTACGGGTA
1 CGCGTTGCGA--TTTACGGATA
*
2013930 CTCGTTGCGAT
1 CGCGTTGCGAT
2013941 AGTCAGAATC
Statistics
Matches: 150, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
20 81 0.54
21 51 0.34
22 18 0.12
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2013806 original size:41 final size:41
Alignment explanation
Indices: 2013745--2013940 Score: 211
Period size: 41 Copynumber: 4.8 Consensus size: 41
2013735 CTTTAAAAAT
* *
2013745 CGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
* *
2013785 TGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATT
1 CG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
* * * *
2013827 CTCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
* *
2013867 CGCGTTGCGATTTTACGTAT-TGTCGTTGCGA-TTTACGGATA
1 CGCGTTGCGA-TTTACGGATACG-CGTTGCGATTTTACGGATA
* *
2013908 CGCGTTGCGATTTTTACGGGTACTCGTTGCGAT
1 CGCGTTGCGA--TTTACGGATACGCGTTGCGAT
2013941 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
40 19 0.14
41 98 0.74
42 16 0.12
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
Found at i:2013841 original size:61 final size:61
Alignment explanation
Indices: 2013745--2013940 Score: 252
Period size: 61 Copynumber: 3.2 Consensus size: 61
2013735 CTTTAAAAAT
* * *
2013745 CGCGTTGCGA-TTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGA-TTTACGTATTGTCGTTGCGATTTACGGATA
*
2013806 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
* * * * *
2013867 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG-CGTTGCGATTTTTACGGGTA
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTAT-TGTCGTTGCGA--TTTACGGATA
*
2013930 CTCGTTGCGAT
1 CGCGTTGCGAT
2013941 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
61 84 0.70
62 17 0.14
63 19 0.16
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
Found at i:2013996 original size:102 final size:101
Alignment explanation
Indices: 2013742--2014001 Score: 341
Period size: 102 Copynumber: 2.5 Consensus size: 101
2013732 GCGCTTTAAA
2013742 AATCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTA-AGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
* *
2013807 GCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGT
65 GCGTTGCGATTTTACGGATACTCGTTGCGATTCACGT
* * *
2013844 ATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTA-AGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
2013909 GCGTTGCGATTTTTACGGGTACTCGTTGCGATAGTCA-G-
65 GCGTTGCGA-TTTTACGGATACTCGTTGCGAT--TCACGT
* *
2013947 AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCG-CGTTGCGATT
1 AATCGCGTTGCGATTTA-A-GATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATT
2014002 CTGTAAAATC
Statistics
Matches: 141, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
102 86 0.61
103 51 0.36
104 2 0.01
105 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (101 bp):
AATCGCGTTGCGATTTAAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
CGTTGCGATTTTACGGATACTCGTTGCGATTCACGT
Found at i:2014050 original size:21 final size:20
Alignment explanation
Indices: 2013744--2014064 Score: 103
Period size: 20 Copynumber: 15.7 Consensus size: 20
2013734 GCTTTAAAAA
* *
2013744 TCGCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTTCAAAT
* **
2013764 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CAAAT
* **
2013785 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTTCAAAT
* **
2013805 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGATTTT-CAAAT
* * **
2013826 TCTCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCAAAT
* * **
2013846 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCAAAT
* **
2013866 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CAAAT
* **
2013887 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTTCAAAT
* ***
2013907 ACGCGTTGCGATTTTTACGGGT
1 TCGCGTTGCGA-TTTT-CAAAT
* * **
2013929 ACTCGTTGCGATAGTCAGAA-
1 TCGCGTTGCGATTTTCA-AAT
**
2013949 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCAAAT
*
2013969 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAT
*
2013989 TCGCGTTGCGATTCTGT-AAAA
1 TCGCGTTGCGATT-T-TCAAAT
** * *
2014010 TCGCAATGCGATAGTACAAAT
1 TCGCGTTGCGAT-TTTCAAAT
*
2014031 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTT-CAAAT
*
2014052 ACGCGTTGCGATT
1 TCGCGTTGCGATT
2014065 CTTGAAACTG
Statistics
Matches: 234, Mismatches: 49, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.00
20 120 0.51
21 98 0.42
22 15 0.06
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAT
Found at i:2017531 original size:28 final size:28
Alignment explanation
Indices: 2017495--2017548 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2017485 ATTTTTCCAT
*
2017495 TATTAT-AAAGTATAGAAAATATTAAATA
1 TATTATAAAAATATA-AAAATATTAAATA
* *
2017523 TATTTTAAAAATATAAAAATTTTAAA
1 TATTATAAAAATATAAAAATATTAAA
2017549 CTCGTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
TATTATAAAAATATAAAAATATTAAATA
Found at i:2017594 original size:2 final size:2
Alignment explanation
Indices: 2017587--2017613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2017577 CTATAATTTA
2017587 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 A
2017614 AATGAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2026748 original size:24 final size:24
Alignment explanation
Indices: 2026654--2026760 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
2026644 ATATTTTATC
* *
2026654 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * *
2026678 TGACATCTGATCTGAAATCTGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * * *
2026702 TGAT-TCCTAACCTGGATTCTGTTC
1 TGATAT-CTGATCTGAATTATGTTT
2026726 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
*
2026750 TGATTTCTGAT
1 TGATATCTGAT
2026761 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:2028167 original size:6 final size:6
Alignment explanation
Indices: 2028151--2028193 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
2028141 AATTAAAATT
2028151 CTCACC C-CACC CTCACC CTCACC CTCACC CTCACC C-CACC CTC
1 CTCACC CTCACC CTCACC CTCACC CTCACC CTCACC CTCACC CTC
2028194 GATGACAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.16, C:0.70, G:0.00, T:0.14
Consensus pattern (6 bp):
CTCACC
Found at i:2029233 original size:3 final size:3
Alignment explanation
Indices: 2029225--2029266 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
2029215 AACGACACAG
* * *
2029225 CAA CAA CAA CAA CAG CAA CAG CAA CAA CAA CAA TAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2029267 AACCCAATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.31, G:0.05, T:0.02
Consensus pattern (3 bp):
CAA
Found at i:2029501 original size:14 final size:14
Alignment explanation
Indices: 2029482--2029519 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
2029472 AATTGGCAGT
2029482 AATCCCTGCAAATA
1 AATCCCTGCAAATA
2029496 AATCCCTGCAAATA
1 AATCCCTGCAAATA
*
2029510 AATCTCTGCA
1 AATCCCTGCA
2029520 TATAGACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (14 bp):
AATCCCTGCAAATA
Found at i:2030336 original size:31 final size:31
Alignment explanation
Indices: 2030301--2030371 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2030291 AACATATGTA
* *
2030301 ATATCATTACTTTCAAAAAGTGACATGTGAC
1 ATATCATCAATTTCAAAAAGTGACATGTGAC
* **
2030332 ATATCATCAATTTCAACACTTGACATGTGAC
1 ATATCATCAATTTCAAAAAGTGACATGTGAC
*
2030363 ATATGATCA
1 ATATCATCA
2030372 TTTTGAACAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (31 bp):
ATATCATCAATTTCAAAAAGTGACATGTGAC
Found at i:2030381 original size:31 final size:31
Alignment explanation
Indices: 2030321--2030387 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2030311 TTTCAAAAAG
*
2030321 TGACATGTGACATATCATCAATTTCAACACT
1 TGACATGTGACATATCATCAATTTCAACACA
* * *
2030352 TGACATGTGACATATGATCATTTTGAACACA
1 TGACATGTGACATATCATCAATTTCAACACA
2030383 TGACA
1 TGACA
2030388 CTCTTTTGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (31 bp):
TGACATGTGACATATCATCAATTTCAACACA
Found at i:2036761 original size:35 final size:34
Alignment explanation
Indices: 2036722--2036833 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
2036712 AACTTTGAAA
2036722 AAAATGGTTTTCAAAGTTTGGTAAATGCTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATG-TTCTTTG
*
2036757 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATG-TTCTTTG
* * *
2036792 AAAAATAGTTTTTCAAAATTTGGTAGATGTT-TGTTG
1 -AAAAT-GGTTTTCAAAGTTTGGTAAATGTTCT-TTG
2036828 AAAATG
1 AAAATG
2036834 ATAATAGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.01
35 39 0.57
36 10 0.15
37 18 0.26
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTCTTTG
Found at i:2041199 original size:21 final size:21
Alignment explanation
Indices: 2041175--2041235 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2041165 ACTTTGAAAA
2041175 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2041196 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
2041210 AAATGGTTTTCAAAGATTGGT
1 AAATGGTTTTCAAAGTTTGGT
2041231 AAATG
1 AAATG
2041236 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 3 0.10
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2041281 original size:36 final size:36
Alignment explanation
Indices: 2041173--2041286 Score: 160
Period size: 35 Copynumber: 3.2 Consensus size: 36
2041163 CAACTTTGAA
2041173 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
2041209 -AAAATGGTTTTCAAAGATTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * * *
2041244 AAAAATAGTTTTTCAATGTTTGGTAGATGTTT-GTTG
1 AAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
2041280 AAAAATG
1 AAAAATG
2041287 ATAATGGAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
35 35 0.50
36 14 0.20
37 21 0.30
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.43
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:2043444 original size:23 final size:21
Alignment explanation
Indices: 2043401--2043444 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2043391 TTTTTTGTAA
*
2043401 TTTAAAATAAATTATGATTTT
1 TTTAAAATAAATAATGATTTT
2043422 TTTATAAATATAATAATG-TTTT
1 TTTA-AAATA-AATAATGATTTT
2043444 T
1 T
2043445 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAAATAAATAATGATTTT
Found at i:2043750 original size:19 final size:19
Alignment explanation
Indices: 2043726--2043774 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2043716 AGACCCAAAA
*
2043726 TTTTTTACTTCACTTATTT
1 TTTTTTACCTCACTTATTT
2043745 TTTTTTACCTCACTTA-TT
1 TTTTTTACCTCACTTATTT
2043763 TTTTTTACCTCA
1 TTTTTTACCTCA
2043775 TAAACATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTACCTCACTTATTT
Found at i:2048293 original size:16 final size:16
Alignment explanation
Indices: 2048272--2048305 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2048262 AAAAGGAAGA
2048272 AAGCGTGTAGCAGTTG
1 AAGCGTGTAGCAGTTG
2048288 AAGCGTGTAGCAGTTG
1 AAGCGTGTAGCAGTTG
2048304 AA
1 AA
2048306 ATGAAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.35, T:0.24
Consensus pattern (16 bp):
AAGCGTGTAGCAGTTG
Found at i:2048605 original size:30 final size:31
Alignment explanation
Indices: 2048533--2048611 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 31
2048523 TCACTCAATG
2048533 ATGACATGAATTTTATTATTTTTTTCATAAAAA
1 ATGACAT--ATTTTATTATTTTTTTCATAAAAA
*
2048566 ATGA-TTATTTTATTA-TTTTTTCATAAAAA
1 ATGACATATTTTATTATTTTTTTCATAAAAA
2048595 ATGACATATTTTTATTA
1 ATGACATA-TTTTATTA
2048612 ATATTTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 18 0.43
30 11 0.26
31 8 0.19
32 1 0.02
33 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (31 bp):
ATGACATATTTTATTATTTTTTTCATAAAAA
Found at i:2049558 original size:20 final size:20
Alignment explanation
Indices: 2049533--2049867 Score: 203
Period size: 20 Copynumber: 16.4 Consensus size: 20
2049523 GATTTTCCAG
* *
2049533 AATCGCAACGCGAATATGAA
1 AATCGCAACGAGAATCTGAA
* * *
2049553 AATCGCAACGTGATTCTGAC
1 AATCGCAACGAGAATCTGAA
* ** *
2049573 TATCGCAACGAGTACCCGTAAA
1 AATCGCAACGAG-AATC-TGAA
* * *
2049595 AATCGCAAC-ACGTATCCGTA
1 AATCGCAACGA-GAATCTGAA
*
2049615 AATCGCAACGACAATAC-GTAA
1 AATCGCAACGAGAAT-CTG-AA
* * * * *
2049636 AATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATCTGAA
*
2049656 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGAGAAT-CTGAA
* *
2049676 AATCGCAACGCGATTCTGAA
1 AATCGCAACGAGAATCTGAA
* *
2049696 TATCGCAACGAGAATCCGTAAA
1 AATCGCAACGAGAAT-C-TGAA
* * *
2049718 AATCGCAAC-ACGTATCCGTA
1 AATCGCAACGA-GAATCTGAA
2049738 AATCGCAACGAGAATAC-GTAA
1 AATCGCAACGAGAAT-CTG-AA
* *
2049759 AATCGCAACAAGAATCTGTA
1 AATCGCAACGAGAATCTGAA
*
2049779 AATCGCAACGAGAATCTGTA
1 AATCGCAACGAGAATCTGAA
* * *
2049799 AATCGCAACGATAATCCGTA
1 AATCGCAACGAGAATCTGAA
* * * *
2049819 AATCGCAACAATAATCCGTA
1 AATCGCAACGAGAATCTGAA
*
2049839 AATCGCAACGAGAATCTGTA
1 AATCGCAACGAGAATCTGAA
2049859 AATCGCAAC
1 AATCGCAAC
2049868 ACTGAAATTT
Statistics
Matches: 248, Mismatches: 51, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.00
20 181 0.73
21 41 0.17
22 25 0.10
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGAGAATCTGAA
Found at i:2049660 original size:123 final size:123
Alignment explanation
Indices: 2049533--2049808 Score: 426
Period size: 123 Copynumber: 2.2 Consensus size: 123
2049523 GATTTTCCAG
* * * * *
2049533 AATCGCAACGCGAATATGAAAATCGCAACGTGATTCTGACTATCGCAACGAGTACCCGTAAAAAT
1 AATCGCAACGAGAATATGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAACCCGTAAAAAT
*** *
2049598 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTA
66 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
* *
2049656 AATCGCAACGAGAATACGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAAT
1 AATCGCAACGAGAATATGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAACCCGTAAAAAT
* *
2049721 CGCAACACGTATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACAAGAATCTGTA
66 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
*
2049779 AATCGCAACGAGAATCTGTAAATCGCAACG
1 AATCGCAACGAGAATATGTAAATCGCAACG
2049809 ATAATCCGTA
Statistics
Matches: 138, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 138 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (123 bp):
AATCGCAACGAGAATATGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAACCCGTAAAAAT
CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
Found at i:2049824 original size:123 final size:123
Alignment explanation
Indices: 2049533--2049867 Score: 401
Period size: 123 Copynumber: 2.7 Consensus size: 123
2049523 GATTTTCCAG
* * * * * * * * *
2049533 AATCGCAACGCGAATATGAAAATCGCAACGTGATTCTGACTATCGCAACGAGTACCCGTAAAAAT
1 AATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGAATATCGCAACGAGAATCCGTAAAAAT
*** *
2049598 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTA
66 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
* * *
2049656 AATCGCAACGAGAATACGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAAT
1 AATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGAATATCGCAACGAGAATCCGTAAAAAT
* *
2049721 CGCAACACGTATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACAAGAATCTGTA
66 CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
* * *
2049779 AATCGCAACGAGAAT-CTGTAAATCGCAACGATAATCCGTAA-ATCGCAACAATAATCCGT--AA
1 AATCGCAACGAGAATAC-GTAAATCGCAACGAGAATCCG-AATATCGCAACGAGAATCCGTAAAA
* *
2049840 ATCGCAACGA-GAATCTGTAAATCGCAAC
64 ATCGCAAC-ACGTATCCGTAAATCGCAAC
2049868 ACTGAAATTT
Statistics
Matches: 188, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
121 26 0.14
122 2 0.01
123 158 0.84
124 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (123 bp):
AATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGAATATCGCAACGAGAATCCGTAAAAAT
CGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACAAGAATCCGTA
Found at i:2049868 original size:40 final size:41
Alignment explanation
Indices: 2049533--2049867 Score: 310
Period size: 40 Copynumber: 8.2 Consensus size: 41
2049523 GATTTTCCAG
* * * * *
2049533 AATCGCAACGCGAATATG-AAAATCGCAACGTGATTCTG-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
* * ** *
2049572 CTATCGCAACGAGTACCCGTAAAAATCGCAAC-ACGTATCCGTA
1 -AATCGCAACGAGAATACGT-AAAATCGCAACGA-GAATCCGTA
* * * *
2049615 AATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
* * *
2049656 AATCGCAACGAGAATACGT-AAATCGCAACGCGATTCTG-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
* *
2049695 ATATCGCAACGAGAATCCGTAAAAATCGCAAC-ACGTATCCGTA
1 A-ATCGCAACGAGAATACGT-AAAATCGCAACGA-GAATCCGTA
* *
2049738 AATCGCAACGAGAATACGTAAAATCGCAACAAGAATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
*
2049779 AATCGCAACGAGAAT-CTGT-AAATCGCAACGATAATCCGTA
1 AATCGCAACGAGAATAC-GTAAAATCGCAACGAGAATCCGTA
* * * *
2049819 AATCGCAACAATAATCCGT-AAATCGCAACGAGAATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
2049859 AATCGCAAC
1 AATCGCAAC
2049868 ACTGAAATTT
Statistics
Matches: 245, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.01
40 106 0.43
41 73 0.30
42 61 0.25
43 3 0.01
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGAGAATCCGTA
Found at i:2050694 original size:24 final size:23
Alignment explanation
Indices: 2050666--2050719 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
2050656 AGTATTCGAA
2050666 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
*
2050689 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
2050713 ATTTGAT
1 ATTTGAT
2050720 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:2053183 original size:33 final size:33
Alignment explanation
Indices: 2053113--2053313 Score: 195
Period size: 33 Copynumber: 5.8 Consensus size: 33
2053103 CTTAATGACT
* * *
2053113 ATCGCAACGCGAAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
* * *
2053147 ATCGCAATGCGAAATGAAAATCGTAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
2053180 ATCGCAACGCGAATATGAATATCGCAACGCGGAAATTA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
*
2053218 CTATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2053253 ATCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2053286 ATCGCAATGCAAAATTAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2053314 CGAATTTAGT
Statistics
Matches: 139, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
33 86 0.62
34 21 0.15
35 1 0.01
36 4 0.03
37 3 0.02
38 1 0.01
39 12 0.09
40 11 0.08
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2053198 original size:20 final size:19
Alignment explanation
Indices: 2053146--2053280 Score: 83
Period size: 19 Copynumber: 7.5 Consensus size: 19
2053136 GCAACGAGAG
*
2053146 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2053165 AATCGTAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
2053179 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* * *
2053199 TATCGCAACGCGGAAATTAC
1 AATCGCAACGC-GAAATGAA
* * *
2053219 TATCGTAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2053238 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
2053252 AATCGTAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2053271 AATCGCAACG
1 AATCGCAACG
2053281 AGGGAATCGC
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
14 20 0.23
15 1 0.01
16 4 0.05
17 4 0.05
18 1 0.01
19 29 0.33
20 26 0.30
21 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2053335 original size:19 final size:19
Alignment explanation
Indices: 2053313--2053354 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2053303 AAATCGCAAC
*
2053313 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCATT
*
2053332 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
2053351 GCGA
1 GCGA
2053355 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:2053355 original size:19 final size:19
Alignment explanation
Indices: 2053323--2053388 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
2053313 GCGAATTTAG
*
2053323 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
2053342 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
* * *
2053358 TCTCG--TTGCAATTTTTA
1 TTTCGCATTGCGATTTTCA
2053375 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2053389 AGTCATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 5 0.14
16 6 0.17
17 7 0.19
19 18 0.50
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:2053510 original size:13 final size:14
Alignment explanation
Indices: 2053494--2053529 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2053484 CATCAATTAA
2053494 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
2053507 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2053521 ACAAATCAA
1 ACAAATCAA
2053530 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2055055 original size:14 final size:14
Alignment explanation
Indices: 2055036--2055092 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2055026 TGGAAATGAA
2055036 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2055050 AATCGCAACACGAAATGAA
1 AATCGC-A-ACG--A-GAG
2055069 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2055083 AATCGCAACG
1 AATCGCAACG
2055093 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2055068 original size:33 final size:33
Alignment explanation
Indices: 2055028--2055111 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
2055018 TCGCAACGTG
2055028 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
*
2055061 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
2055094 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
2055112 CGAAATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACAC
Found at i:2055133 original size:19 final size:19
Alignment explanation
Indices: 2054988--2055133 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
2054978 TCTTTTGGTT
* *
2054988 GAAATGAAAATCGTAACGA
1 GAAATGAAAATCGCAACGC
** *
2055007 GAGAATGACTATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
2055028 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
2055045 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
2055061 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2055078 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2055094 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2055113 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2055132 GA
1 GA
2055134 TTCTCTCGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
15 2 0.02
16 4 0.04
17 3 0.03
18 2 0.02
19 45 0.44
20 25 0.24
21 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2055160 original size:21 final size:21
Alignment explanation
Indices: 2055134--2055225 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 21
2055124 CGCAATGCGA
2055134 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
2055155 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
2055176 TT-TCGCGTT--GA----GA-
1 TTCTCTCGTTGCGATTTTCAT
2055189 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2055210 TTCTCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
2055226 CTTCTGCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.04
14 7 0.12
16 2 0.04
18 2 0.04
20 7 0.12
21 37 0.65
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2055194 original size:34 final size:35
Alignment explanation
Indices: 2055155--2055227 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
2055145 CGATTTTCAT
2055155 TTCTCTCGTTGCGATAGTCATTT-TCGCGTTGAGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
** * *
2055189 TTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
2055224 TTCT
1 TTCT
2055228 TCTGCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 21 0.62
35 13 0.38
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (35 bp):
TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
Found at i:2055786 original size:20 final size:20
Alignment explanation
Indices: 2055761--2055936 Score: 203
Period size: 20 Copynumber: 8.7 Consensus size: 20
2055751 CTTTAAAAAT
*
2055761 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
2055781 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2055801 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2055822 CGCGTTGCGATTTTACGGATT
1 CGCGTTGCGA-TTTACGGATA
* * *
2055843 CTCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2055863 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2055883 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2055903 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
2055924 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2055937 TTACGGGTGC
Statistics
Matches: 134, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
20 83 0.62
21 51 0.38
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2055822 original size:41 final size:41
Alignment explanation
Indices: 2055763--2055936 Score: 201
Period size: 41 Copynumber: 4.3 Consensus size: 41
2055753 TTAAAAATCG
* * *
2055763 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
2055804 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
* * * * *
2055845 CGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
* * * *
2055885 CGTTGCGATTTTACGTAT-TGTCGTTGCGA-TTTACGGATACG
1 CGTTGCGA-TTTACGGATACG-CGTTGCGATTTTACGGATTCT
2055926 CGTTGCGATTT
1 CGTTGCGATTT
2055937 TTACGGGTGC
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 21 0.17
41 100 0.83
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
Found at i:2055857 original size:61 final size:61
Alignment explanation
Indices: 2055761--2055936 Score: 248
Period size: 61 Copynumber: 2.9 Consensus size: 61
2055751 CTTTAAAAAT
* * *
2055761 CGCGTTGCGA-TTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGA-TTTACGTATTGTCGTTGCGATTTACGGATA
*
2055822 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
* * * *
2055883 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG-CGTTGCGATTT
1 CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTAT-TGTCGTTGCGATTT
2055937 TTACGGGTGC
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
61 87 0.84
62 17 0.16
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
Found at i:2055937 original size:41 final size:41
Alignment explanation
Indices: 2055761--2055956 Score: 195
Period size: 41 Copynumber: 4.8 Consensus size: 41
2055751 CTTTAAAAAT
* * *
2055761 CGCGTTGCGA-TTTACAG-ATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTAC-GTATTCTCGTTGCGA-TTTACGGATA
* * * * *
2055801 TGTCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGGATT
1 CG-CGTTGCGATTTTACGTATTCTCGTTGCGA-TTTACGGATA
*
2055843 CTCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
2055883 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
** *
2055924 CGCGTTGCGATTTTTACGGGTGCTCGTTGCGAT
1 CGCGTTGCGA-TTTTACGTATTCTCGTTGCGAT
2055957 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
40 20 0.15
41 99 0.72
42 18 0.13
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:2055988 original size:20 final size:20
Alignment explanation
Indices: 2055965--2056017 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2055955 ATAGTCAGAA
*
2055965 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2055985 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
2056005 TCGCGTTGTGATT
1 TCGCGTTGCGATT
2056018 CTGTAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2056012 original size:102 final size:101
Alignment explanation
Indices: 2055758--2055999 Score: 337
Period size: 102 Copynumber: 2.4 Consensus size: 101
2055748 GCGCTTTAAA
2055758 AATCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTA-AGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
* *
2055823 GCGTTGCGATTTTACGGATTCTCGTTGCGATTTACGT
65 GCGTTGCGATTTTACGGATGCTCGTTGCGATTCACGT
* * *
2055860 ATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTA-AGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
2055925 GCGTTGCGATTTTTACGGGTGCTCGTTGCGATAGTCA-G-
65 GCGTTGCGA-TTTTACGGATGCTCGTTGCGAT--TCACGT
*
2055963 AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTA-A-GATACGCGTTGCGATTTT
2056000 CATATTCGCG
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
102 71 0.57
103 50 0.40
104 2 0.02
105 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (101 bp):
AATCGCGTTGCGATTTAAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
CGTTGCGATTTTACGGATGCTCGTTGCGATTCACGT
Found at i:2059544 original size:16 final size:18
Alignment explanation
Indices: 2059510--2059546 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2059500 TAAAGTATAG
2059510 AAAATATAAATATATTTT
1 AAAATATAAATATATTTT
2059528 AAAATATAAA-A-ATTTT
1 AAAATATAAATATATTTT
2059544 AAA
1 AAA
2059547 CTCGTTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATAAATATATTTT
Found at i:2059618 original size:15 final size:14
Alignment explanation
Indices: 2059609--2059641 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2059599 ATATATAATG
2059609 AACTATTATAT-TC
1 AACTATTATATATC
2059622 AACTATTATATATTC
1 AACTATTATATA-TC
2059637 AACTA
1 AACTA
2059642 AATGATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
15 7 0.39
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (14 bp):
AACTATTATATATC
Found at i:2076333 original size:9 final size:8
Alignment explanation
Indices: 2076321--2076400 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 8
2076311 AATATTTTAT
2076321 ATATAATTA
1 ATATAA-TA
*
2076330 ATATAAAAA
1 ATAT-AATA
2076339 ATATAA-A
1 ATATAATA
*
2076346 ATATTATA
1 ATATAATA
2076354 TATATAATTA
1 -ATATAA-TA
*
2076364 ATATAAAA
1 ATATAATA
2076372 ATATAA-A
1 ATATAATA
*
2076379 ATATTAT-
1 ATATAATA
2076386 ATAT-ATA
1 ATATAATA
2076393 TATATAAT
1 -ATATAAT
2076401 CGGGGCGGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
6 2 0.03
7 16 0.28
8 14 0.24
9 22 0.38
10 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:2076349 original size:25 final size:26
Alignment explanation
Indices: 2076321--2076382 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
2076311 AATATTTTAT
2076321 ATATAAT-TAATATAAAAAATAT-AAA
1 ATATAATAT-ATATAAAAAATATAAAA
* **
2076346 ATATTATATATATAATTAATATAAAA
1 ATATAATATATATAAAAAATATAAAA
*
2076372 ATATAAAATAT
1 ATATAATATAT
2076383 TATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATAATATATATAAAAAATATAAAA
Found at i:2076377 original size:33 final size:34
Alignment explanation
Indices: 2076309--2076392 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
2076299 CTCGAACCCG
*
2076309 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
2076343 AAAATATTATATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
2076376 AAAATATTATATATATA
1 AAAATATTATATATATA
2076393 TATATAATCG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 25 0.51
34 24 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:2077875 original size:2 final size:2
Alignment explanation
Indices: 2077868--2077899 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2077858 TCAGGTACTG
2077868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2077900 GCGTGTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2083729 original size:34 final size:34
Alignment explanation
Indices: 2083686--2083752 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2083676 TCTTAATCGT
2083686 TCGAACATTAACAGATCCAACGGCCTATAAAAAA
1 TCGAACATTAACAGATCCAACGGCCTATAAAAAA
* *
2083720 TCGATCATTAATAGATCCAACGGCCTATAAAAA
1 TCGAACATTAACAGATCCAACGGCCTATAAAAA
2083753 GCGGTGACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (34 bp):
TCGAACATTAACAGATCCAACGGCCTATAAAAAA
Found at i:2084360 original size:23 final size:25
Alignment explanation
Indices: 2084323--2084375 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
2084313 AATAAATCTG
2084323 TTTATATGACACGTTTTCATATGTC
1 TTTATATGACACGTTTTCATATGTC
*
2084348 TTTATA-G-CACGTTTTCATCTGTC
1 TTTATATGACACGTTTTCATATGTC
2084371 TTTAT
1 TTTAT
2084376 GATATGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (25 bp):
TTTATATGACACGTTTTCATATGTC
Found at i:2084384 original size:23 final size:23
Alignment explanation
Indices: 2084318--2084386 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
2084308 TTTTCAATAA
2084318 ATCTGT-TTATATGACACGTTTTC
1 ATCTGTCTT-TATGACACGTTTTC
*
2084341 ATATGTCTTTAT-AGCACGTTTTC
1 ATCTGTCTTTATGA-CACGTTTTC
* *
2084364 ATCTGTCTTTATGATATGTTTTC
1 ATCTGTCTTTATGACACGTTTTC
2084387 TTATGCCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 35 0.90
24 3 0.08
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (23 bp):
ATCTGTCTTTATGACACGTTTTC
Found at i:2085111 original size:35 final size:35
Alignment explanation
Indices: 2085071--2085187 Score: 216
Period size: 35 Copynumber: 3.3 Consensus size: 35
2085061 AGGGTGGACA
*
2085071 AAATAATTAAAATCTTGGGATGCTCAATTCAAATT
1 AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
2085106 AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
1 AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
2085141 AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
1 AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
2085176 AAATAATGTAAA
1 AAATAAT-TAAA
2085188 TTTATATTTA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
35 76 0.95
36 4 0.05
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (35 bp):
AAATAATTAAAATCTTGGGGTGCTCAATTCAAATT
Found at i:2110652 original size:25 final size:25
Alignment explanation
Indices: 2110624--2110682 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
2110614 TTTTGAGAAA
* *
2110624 TTATAAAATTTAGTTTTTTTTAAAT
1 TTATAAAATTTAGTGTTTTTCAAAT
**
2110649 TTAT-AAATTTAGTGTTTTTCATTT
1 TTATAAAATTTAGTGTTTTTCAAAT
2110673 TTATAAAATT
1 TTATAAAATT
2110683 AATATTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (25 bp):
TTATAAAATTTAGTGTTTTTCAAAT
Found at i:2112736 original size:31 final size:27
Alignment explanation
Indices: 2112696--2112751 Score: 76
Period size: 31 Copynumber: 1.9 Consensus size: 27
2112686 CTTTTTTGCC
2112696 CTAAAATAAAATGATAATGACTAAAATATT
1 CTAAAATAAAATGA-AA-GAC-AAAATATT
2112726 CTAAATATAAAATGAAAGACAAAATA
1 CTAAA-ATAAAATGAAAGACAAAATA
2112752 ATCATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 3 0.12
30 7 0.28
31 9 0.36
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (27 bp):
CTAAAATAAAATGAAAGACAAAATATT
Found at i:2114361 original size:31 final size:30
Alignment explanation
Indices: 2114313--2114381 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 30
2114303 AAATCTTTTT
2114313 TATATATTACGTTTTATTA-TATATATA-TA
1 TATATATTACGTTTTATTATTAT-TATACTA
*
2114342 TATATATTATTGTTATTATTATTATTATACGTA
1 TATATATTA-CGTT-TTATTATTATTATAC-TA
2114375 TATATAT
1 TATATAT
2114382 GTATGTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 9 0.26
30 3 0.09
31 10 0.29
32 3 0.09
33 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (30 bp):
TATATATTACGTTTTATTATTATTATACTA
Found at i:2114964 original size:2 final size:2
Alignment explanation
Indices: 2114957--2114984 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2114947 CATATTCTAC
2114957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2114985 TTTTTTATTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2116212 original size:10 final size:10
Alignment explanation
Indices: 2116199--2116232 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2116189 TTTTATTACC
2116199 ATTTATTTTT
1 ATTTATTTTT
2116209 ATTTATTTTT
1 ATTTATTTTT
* *
2116219 ATCTATTTCT
1 ATTTATTTTT
2116229 ATTT
1 ATTT
2116233 TACTAACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Done.