Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 5 of 221
Found at i:1565005 original size:23 final size:24
Alignment explanation
Indices: 1564968--1565023 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 24
1564958 AAAGTATGTA
1564968 TTATAAAAAATTATAGTA-TATAAAT
1 TTAT-AAAAATTATA-TATTATAAAT
1564993 TTATAAAAA-TATATATTATAAAT
1 TTATAAAAATTATATATTATAAAT
1565016 TTATAAAA
1 TTATAAAA
1565024 TGTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.07
23 19 0.63
24 5 0.17
25 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TTATAAAAATTATATATTATAAAT
Found at i:1570696 original size:47 final size:47
Alignment explanation
Indices: 1570642--1570735 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
1570632 TCATGCATGT
1570642 AAATTTTTAAAATCGGTTCAATATCT-TCATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCT-ATCATATTGATCTAAAAAG
1570689 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
1570736 GTGTATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 45 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (47 bp):
AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
Found at i:1571882 original size:16 final size:16
Alignment explanation
Indices: 1571861--1571891 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1571851 AAAATCCTCA
1571861 ACTCTTTCATCGAATG
1 ACTCTTTCATCGAATG
1571877 ACTCTTTCATCGAAT
1 ACTCTTTCATCGAAT
1571892 AATATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.39
Consensus pattern (16 bp):
ACTCTTTCATCGAATG
Found at i:1573551 original size:16 final size:17
Alignment explanation
Indices: 1573519--1573551 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1573509 TAACCAAACA
1573519 TAAAACAAGAACACACAC
1 TAAAACAAG-ACACACAC
1573537 TAAAACAAG-CACACA
1 TAAAACAAGACACACA
1573552 AAGCAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.61, C:0.27, G:0.06, T:0.06
Consensus pattern (17 bp):
TAAAACAAGACACACAC
Found at i:1576713 original size:29 final size:29
Alignment explanation
Indices: 1576653--1576713 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1576643 GGCCTATTTC
** *
1576653 CCTAATTAATTTTAAAACGGGCCTAAATG
1 CCTAATTAATTAAAAAACGGGCCTAAAGG
*
1576682 CCTAATTAATTAAAAAAAC-GGCCTATAGG
1 CCTAATTAATT-AAAAAACGGGCCTAAAGG
1576711 CCT
1 CCT
1576714 TACTTTGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (29 bp):
CCTAATTAATTAAAAAACGGGCCTAAAGG
Found at i:1577173 original size:20 final size:22
Alignment explanation
Indices: 1577134--1577173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1577124 CAAAATTAAT
*
1577134 AAACTTTTATTATGAATTAGAC
1 AAACTTTAATTATGAATTAGAC
1577156 AAACTTTAATT-T-AATTAG
1 AAACTTTAATTATGAATTAG
1577174 TAGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (22 bp):
AAACTTTAATTATGAATTAGAC
Found at i:1581657 original size:30 final size:31
Alignment explanation
Indices: 1581594--1581660 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1581584 ATATGTTGAT
** *
1581594 AGTCCTTATACTTTGATAAAATTTGAGATTA
1 AGTCCTTATACTTTGATAAAATTAAAAATTA
1581625 AGTCCTTATA-TTT-ATAAAAGTTAAAAATTA
1 AGTCCTTATACTTTGATAAAA-TTAAAAATTA
1581655 AGTCCT
1 AGTCCT
1581661 CCTAGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 16 0.50
31 10 0.31
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
AGTCCTTATACTTTGATAAAATTAAAAATTA
Found at i:1584130 original size:9 final size:9
Alignment explanation
Indices: 1584112--1584158 Score: 85
Period size: 9 Copynumber: 5.2 Consensus size: 9
1584102 TTGAGTTTTC
1584112 TAATTCGAA
1 TAATTCGAA
*
1584121 TAACTCGAA
1 TAATTCGAA
1584130 TAATTCGAA
1 TAATTCGAA
1584139 TAATTCGAA
1 TAATTCGAA
1584148 TAATTCGAA
1 TAATTCGAA
1584157 TA
1 TA
1584159 TCAAAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (9 bp):
TAATTCGAA
Found at i:1584235 original size:21 final size:21
Alignment explanation
Indices: 1584194--1584236 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1584184 ACCCCAAACT
* *
1584194 CCCAAACCTTTTTACTTTTCC
1 CCCAAAACTTTTTACTCTTCC
1584215 CCCAAAAC-TTTTACTCCTTCC
1 CCCAAAACTTTTTACT-CTTCC
1584236 C
1 C
1584237 ACTTCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (21 bp):
CCCAAAACTTTTTACTCTTCC
Found at i:1586305 original size:12 final size:12
Alignment explanation
Indices: 1586281--1586316 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1586271 TGACCTGCCC
1586281 ATATTACTTTTTT
1 ATATTA-TTTTTT
1586294 ATATTATTTTTT
1 ATATTATTTTTT
*
1586306 ATATAATTTTT
1 ATATTATTTTT
1586317 AAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1586370 original size:25 final size:24
Alignment explanation
Indices: 1586342--1586389 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1586332 ATCAAAAATA
*
1586342 CCAAAAATATT-AAATTAAATATTTC
1 CCAAAAA-ATTGAAAATAAA-ATTTC
1586367 CCAAAAAATTGAAAATAAAATTT
1 CCAAAAAATTGAAAATAAAATTT
1586390 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
CCAAAAAATTGAAAATAAAATTTC
Found at i:1594355 original size:44 final size:44
Alignment explanation
Indices: 1594307--1594454 Score: 174
Period size: 44 Copynumber: 3.2 Consensus size: 44
1594297 CCGCTTGTCA
1594307 CTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTG-CCG
1 CTGATCAGATAAGTGTAGCTAA-GCTACCACTTATCACTTGTCCG
* *
1594351 CTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTG
1 CTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGTC-C--G
*
1594399 TCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCC-
1 ---CTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGTCCG
1594446 CTGATCAGA
1 CTGATCAGA
1594455 AGTACTCAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
44 44 0.49
45 3 0.03
46 1 0.01
48 1 0.01
50 1 0.01
51 39 0.44
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
CTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCCG
Found at i:1594414 original size:95 final size:94
Alignment explanation
Indices: 1594241--1594454 Score: 340
Period size: 95 Copynumber: 2.3 Consensus size: 94
1594231 TACGTATGAT
* * *
1594241 CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGCCGCTTGTC
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGCCACTTGTC
*
1594306 ACTGATCAGATAAGTGTAGCTAATGCTAC
66 ACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
1594335 CACTTATCACTTG-CCGCTGATCAGATAAGTGTAGCTGAAACTATCACTTATCACTTGTCACTTG
1 CACTTATCACTTGTCC-CTGATCAGATAAGTGTAGCT-AAACTACCACTTATCACTTGCCACTTG
*
1594399 TCACTGATTAGATAAGTGTAGCTAAAGCTAC
64 TCACTGATCAGATAAGTGTAGCTAAAGCTAC
1594430 CACTTATCACTTGTCCCTGATCAGA
1 CACTTATCACTTGTCCCTGATCAGA
1594455 AGTACTCAAA
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
93 2 0.02
94 32 0.29
95 74 0.67
96 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (94 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGCCACTTGTC
ACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1594442 original size:51 final size:50
Alignment explanation
Indices: 1594239--1594444 Score: 266
Period size: 51 Copynumber: 4.2 Consensus size: 50
1594229 CTTACGTATG
*
1594239 ATCACTTATCACTTGTCCTTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCC-TGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
1594289 ATCACTTGCCGCTTGTCACTGATCAGATAAGTGTAGCTAATGCTACCACTT
1 ATCACTTGTCACTTGTC-CTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
1594340 ATCACTTG-C-C--G--CTGATCAGATAAGTGTAGCTGAAA-CTATCACTT
1 ATCACTTGTCACTTGTCCTGATCAGATAAGTGTAGCT-AAAGCTACCACTT
*
1594384 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTC-CTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1594435 ATCACTTGTC
1 ATCACTTGTC
1594445 CCTGATCAGA
Statistics
Matches: 137, Mismatches: 8, Indels: 21
0.83 0.05 0.13
Matches are distributed among these distances:
44 36 0.26
45 3 0.02
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 37 0.27
51 57 0.42
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (50 bp):
ATCACTTGTCACTTGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:1598387 original size:31 final size:30
Alignment explanation
Indices: 1598290--1598391 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
1598280 AAAAACCATA
* *
1598290 AAGTTTAGGCCTTAATGTGGGAACAATTATC
1 AAGTTCAGGCCTCAATGT-GGAACAATTATC
* * * * *
1598321 AAGCTCAAGCCCCAATGTGGAAACAATCATT
1 AAGTTCAGGCCTCAATGTGG-AACAATTATC
*
1598352 AAGTTCAGGCCTCAATGTGAGAACAATTGTC
1 AAGTTCAGGCCTCAATGTG-GAACAATTATC
1598383 AAGTTCAGG
1 AAGTTCAGG
1598392 GATTAACTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (30 bp):
AAGTTCAGGCCTCAATGTGGAACAATTATC
Found at i:1601567 original size:29 final size:29
Alignment explanation
Indices: 1601517--1601573 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1601507 TCCAATCCTA
*
1601517 TGTACATGCATAATTACAAAATTCATGCT
1 TGTACATGCATAATTACAAAATACATGCT
* *
1601546 TGTACATGCGTTAA-TACCAAATACATGC
1 TGTACATGC-ATAATTACAAAATACATGC
1601574 ATCTAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (29 bp):
TGTACATGCATAATTACAAAATACATGCT
Found at i:1612701 original size:25 final size:21
Alignment explanation
Indices: 1612656--1612697 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1612646 TCTCTATAAT
1612656 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
1612677 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
1612698 AGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (21 bp):
CACTTCATCCTAAAAAAAGAA
Found at i:1613917 original size:24 final size:24
Alignment explanation
Indices: 1613884--1613963 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 24
1613874 TAAACATTAA
* **
1613884 AAAATGTTAAAAATTACTATATAT
1 AAAATTTTAAAAATTAAAATATAT
*
1613908 AAAATTTTAATAAATAAAAAATATAT
1 AAAATTTTAA-AAAT-TAAAATATAT
*
1613934 AACATTATTAAAAATTAAAATAATAT
1 AAAATT-TTAAAAATTAAAAT-ATAT
1613960 AAAA
1 AAAA
1613964 ATATTTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 9 0.20
25 9 0.20
26 23 0.51
27 4 0.09
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (24 bp):
AAAATTTTAAAAATTAAAATATAT
Found at i:1613931 original size:26 final size:27
Alignment explanation
Indices: 1613902--1613970 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
1613892 AAAAATTACT
1613902 ATATATAAAATTTTAATAAA-TAAAA-A
1 ATATATAAAATTTTAA-AAATTAAAATA
*
1613928 ATATATAACATTATTAAAAATTAAAATA
1 ATATATAAAATT-TTAAAAATTAAAATA
1613956 ATATA-AAAATATTTA
1 ATATATAAAAT-TTTA
1613971 TATTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 14 0.38
27 16 0.43
28 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATATAAAATTTTAAAAATTAAAATA
Found at i:1615128 original size:22 final size:23
Alignment explanation
Indices: 1615088--1615131 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1615078 AAGAATCCGA
*
1615088 AATTAAACTATATATTTTTACAAG
1 AATTAAAC-ATATAATTTTACAAG
1615112 AATTAAA-ATATAATTTTACA
1 AATTAAACATATAATTTTACA
1615132 GTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (23 bp):
AATTAAACATATAATTTTACAAG
Found at i:1616783 original size:8 final size:8
Alignment explanation
Indices: 1616770--1616797 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1616760 TGTTAAAAAA
1616770 ATATTATT
1 ATATTATT
1616778 ATATTATT
1 ATATTATT
1616786 ATATTATT
1 ATATTATT
1616794 ATAT
1 ATAT
1616798 GTATATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATTATT
Found at i:1617957 original size:25 final size:24
Alignment explanation
Indices: 1617890--1618021 Score: 153
Period size: 25 Copynumber: 5.5 Consensus size: 24
1617880 ACTTTAGCGC
*
1617890 GCTCTCTGATATTAGTACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1617914 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1617938 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
* ***
1617963 GCTCACTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* * *
1617988 ACTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
1618010 GCTCTCTG-TATT
1 GCTCTCTGATATT
1618022 TGTTCCGTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
22 17 0.18
23 2 0.02
24 35 0.38
25 39 0.42
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:1618854 original size:17 final size:17
Alignment explanation
Indices: 1618832--1618865 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1618822 ATGTGGCATG
*
1618832 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
1618849 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
1618866 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:1621113 original size:25 final size:24
Alignment explanation
Indices: 1621085--1621154 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1621075 GTTTTTTAAT
1621085 TTTTATAATATATCATATTAAATTA
1 TTTTATAATATATCATATTAAA-TA
*
1621110 TTTT-TACATAT-TACATATTATATA
1 TTTTATA-ATATAT-CATATTAAATA
*
1621134 ATTTATAATATAT-ATAATTAA
1 TTTTATAATATATCAT-ATTAA
1621155 TAGACTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 19 0.51
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATAATATATCATATTAAATA
Found at i:1622641 original size:30 final size:32
Alignment explanation
Indices: 1622589--1622666 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
1622579 CATTTTTTAA
1622589 TAAACATTAAAAATATTTTAAAAA-TAAAAAAT
1 TAAA-ATTAAAAATATTTTAAAAATTAAAAAAT
*
1622621 TAAAATTAAAAGTA-TTTAAAAATTAAAAAAT
1 TAAAATTAAAAATATTTTAAAAATTAAAAAAT
* *
1622652 AAAAATAAAAAATAT
1 TAAAATTAAAAATAT
1622667 ATATTTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.20
31 28 0.70
32 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (32 bp):
TAAAATTAAAAATATTTTAAAAATTAAAAAAT
Found at i:1622988 original size:24 final size:25
Alignment explanation
Indices: 1622912--1622989 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 25
1622902 GTCATCATCT
1622912 CAAAATTAAATAAA-AAAT-TATTA
1 CAAAATTAAATAAATAAATATATTA
* * *
1622935 -ATAAATTTAAATATATATATA-ATAA
1 CA-AAA-TTAAATAAATAAATATATTA
1622960 C-AAA-TAAATAAATAAATATATTA
1 CAAAATTAAATAAATAAATATATTA
1622983 CAAAATT
1 CAAAATT
1622990 TAAAAAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 13 0.32
23 7 0.17
24 14 0.34
25 7 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
CAAAATTAAATAAATAAATATATTA
Found at i:1635450 original size:30 final size:30
Alignment explanation
Indices: 1635416--1635473 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1635406 ACGCGTGTTA
1635416 TTATTAATTTTAAATACTATATTT-TATTAT
1 TTATTAATTTTAAATA-TATATTTATATTAT
*
1635446 TTATTATTTTTAAATATATATTTATATT
1 TTATTAATTTTAAATATATATTTATATT
1635474 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATTAATTTTAAATATATATTTATATTAT
Found at i:1635488 original size:20 final size:18
Alignment explanation
Indices: 1635449--1635484 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1635439 TTATTATTTA
*
1635449 TTATTTTTAAATATATAT
1 TTATTTTTAAATAAATAT
1635467 TTATATTTTAAATAAATA
1 TTAT-TTTTAAATAAATA
1635485 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTTTTAAATAAATAT
Found at i:1641449 original size:2 final size:2
Alignment explanation
Indices: 1641442--1641466 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1641432 AAGATGTTAC
1641442 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1641467 GAATTGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1643625 original size:26 final size:27
Alignment explanation
Indices: 1643596--1643648 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1643586 TCATTAGTTC
* *
1643596 AATTATCGGTTCAATCAATCT-ATATT
1 AATTATCAGATCAATCAATCTAATATT
*
1643622 AATTCTCAGATCAATCAATCTAATATT
1 AATTATCAGATCAATCAATCTAATATT
1643649 TCTCTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (27 bp):
AATTATCAGATCAATCAATCTAATATT
Found at i:1650176 original size:24 final size:23
Alignment explanation
Indices: 1650149--1650198 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1650139 TAATATATAT
*
1650149 AATATTATCTAAATTAATTTTTCA
1 AATATT-TCTAAATTAAATTTTCA
* *
1650173 AATATTTTTATATTAAATTTTCA
1 AATATTTCTAAATTAAATTTTCA
1650196 AAT
1 AAT
1650199 CAAATTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTCTAAATTAAATTTTCA
Found at i:1650992 original size:20 final size:20
Alignment explanation
Indices: 1650946--1650995 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1650936 TTACATCAGT
** *
1650946 TTTTTTTCTCTTGAATTTTA
1 TTTTTTTCAGTTGAATTTAA
* *
1650966 GTATTTTCAGTTGAATTTAA
1 TTTTTTTCAGTTGAATTTAA
1650986 TTTTTTTCAG
1 TTTTTTTCAG
1650996 GAAGAAAATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTTTCAGTTGAATTTAA
Found at i:1657793 original size:20 final size:19
Alignment explanation
Indices: 1657748--1657789 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1657738 TGAAAGAAAT
*
1657748 AAAA-ATTTAAAAATTATG
1 AAAATATTTAAAAAATATG
1657766 AAAATATTTAAAAAA-ATAG
1 AAAATATTTAAAAAATAT-G
1657785 AAAAT
1 AAAAT
1657790 TATTAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATATTTAAAAAATATG
Found at i:1657890 original size:20 final size:21
Alignment explanation
Indices: 1657853--1657892 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1657843 TAAAAATTGT
1657853 AAAACAAATTAAAAATATATG
1 AAAACAAATTAAAAATATATG
* *
1657874 AAAA-AAATTATATATATAT
1 AAAACAAATTAAAAATATAT
1657893 ATATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAACAAATTAAAAATATATG
Found at i:1658284 original size:19 final size:18
Alignment explanation
Indices: 1658256--1658297 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1658246 TGTTTTTGTT
* *
1658256 ATTTTAATATTTTTTGAA
1 ATTTTAATATATTTTAAA
1658274 ATTTTATATATATTTTAAA
1 ATTTTA-ATATATTTTAAA
1658293 ATTTT
1 ATTTT
1658298 GTACATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTAATATATTTTAAA
Found at i:1660052 original size:15 final size:16
Alignment explanation
Indices: 1660024--1660054 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1660014 ACCACTTTTT
1660024 TGGCCCGAGCCCGGCC
1 TGGCCCGAGCCCGGCC
1660040 TGGCCCG-GCCCGGCC
1 TGGCCCGAGCCCGGCC
1660055 CGATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.03, C:0.52, G:0.39, T:0.06
Consensus pattern (16 bp):
TGGCCCGAGCCCGGCC
Found at i:1660106 original size:19 final size:18
Alignment explanation
Indices: 1660074--1660195 Score: 113
Period size: 19 Copynumber: 6.6 Consensus size: 18
1660064 AAATATATTT
1660074 ATTTTAAAAT-TTTTTTA
1 ATTTTAAAATATTTTTTA
1660091 ATTTTAAAATATTTTTAAATA
1 ATTTTAAAATATTTTT---TA
* ****
1660112 CTTTTTTCTTATTTTTTA
1 ATTTTAAAATATTTTTTA
**
1660130 ATTTTAAAATGATTTTAAA
1 ATTTTAAAAT-ATTTTTTA
1660149 ATTTTAAAAT-TTTTTTA
1 ATTTTAAAATATTTTTTA
1660166 ATTTTAAAATATTTTTTA
1 ATTTTAAAATATTTTTTA
*
1660184 CTTTTTAAAATA
1 -ATTTTAAAATA
1660196 AATTTTTGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
17 25 0.30
18 19 0.23
19 26 0.31
21 13 0.16
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTAAAATATTTTTTA
Found at i:1666003 original size:24 final size:25
Alignment explanation
Indices: 1665957--1666008 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1665947 TAGAAATGAA
* *
1665957 AAATAAATTAATTTAGATAATATTT
1 AAATAAATTAATATAGATAATATAT
* *
1665982 AAATAATTTAATATA-ATTATATAT
1 AAATAAATTAATATAGATAATATAT
1666006 AAA
1 AAA
1666009 ATATACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATAAATTAATATAGATAATATAT
Found at i:1670436 original size:25 final size:25
Alignment explanation
Indices: 1670402--1670459 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1670392 ATCCATCTTT
1670402 CTTC-AATGGTGTTGCAGCTCCTGA
1 CTTCAAATGGTGTTGCAGCTCCTGA
1670426 CTTCAAATGGTGTTGCAGCTCCTGA
1 CTTCAAATGGTGTTGCAGCTCCTGA
1670451 CTTCAAATG
1 CTTCAAATG
1670460 CCTGACCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (25 bp):
CTTCAAATGGTGTTGCAGCTCCTGA
Found at i:1673670 original size:2 final size:2
Alignment explanation
Indices: 1673659--1673702 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1673649 TCAACACCAA
1673659 TC TC -C 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
1673700 TC T
1 TC T
1673703 ATTTTGTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1681176 original size:22 final size:21
Alignment explanation
Indices: 1681142--1681184 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1681132 CTTGAAATTT
* *
1681142 ATAAATTTTATTTTACTTAAAA
1 ATAAAATTAATTTTAC-TAAAA
1681164 ATAAAATTAATTTTACTAAAA
1 ATAAAATTAATTTTACTAAAA
1681185 TTTGAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATTAATTTTACTAAAA
Found at i:1688977 original size:13 final size:13
Alignment explanation
Indices: 1688959--1688985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1688949 TGTGAGATTC
1688959 ATCTATAATTGTG
1 ATCTATAATTGTG
1688972 ATCTATAATTGTG
1 ATCTATAATTGTG
1688985 A
1 A
1688986 ACAATATGCT
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:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATCTATAATTGTG
Found at i:1694410 original size:37 final size:37
Alignment explanation
Indices: 1694360--1694435 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
1694350 ATCATTCGGT
1694360 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
* * *
1694397 CTTGGAATCAAATTCCAGTTTAATAGTATCAATATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
1694434 CT
1 CT
1694436 ACACCAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (37 bp):
CTTGGAATCAAATTCCAATCTAATAGGATCAATATTC
Found at i:1696321 original size:12 final size:13
Alignment explanation
Indices: 1696304--1696333 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1696294 TCGAGGAAGG
1696304 AAGGGTGATAT-T
1 AAGGGTGATATAT
1696316 AAGGGTGATATAT
1 AAGGGTGATATAT
1696329 AAGGG
1 AAGGG
1696334 GCTTCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (13 bp):
AAGGGTGATATAT
Found at i:1701481 original size:21 final size:22
Alignment explanation
Indices: 1701452--1701498 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1701442 TAAAAGGAGT
*
1701452 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1701474 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1701495 GAGT
1 GAGT
1701499 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1707162 original size:21 final size:21
Alignment explanation
Indices: 1707136--1707176 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1707126 ATCTGCTCAA
* *
1707136 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1707157 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1707177 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1713248 original size:27 final size:27
Alignment explanation
Indices: 1713210--1713263 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1713200 TAGATTCTTC
**
1713210 CTAATATCTTCTACATGGAGTATATTG
1 CTAATATCTTCTACATAAAGTATATTG
*
1713237 CTAATATCTTCTGCATAAAGTATATTG
1 CTAATATCTTCTACATAAAGTATATTG
1713264 TTAAGGGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (27 bp):
CTAATATCTTCTACATAAAGTATATTG
Found at i:1714114 original size:17 final size:17
Alignment explanation
Indices: 1714092--1714125 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1714082 ATCCACTAAT
*
1714092 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1714109 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1714126 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1718754 original size:17 final size:17
Alignment explanation
Indices: 1718732--1718765 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1718722 ATCCACTAAT
*
1718732 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1718749 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1718766 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1723264 original size:24 final size:24
Alignment explanation
Indices: 1723236--1723288 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1723226 ATTCGTACGT
** *
1723236 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTAAACTAATAAATAC
*
1723260 TAAATATATTAAACTAATAAATAC
1 TAAATAAATTAAACTAATAAATAC
1723284 TAAAT
1 TAAAT
1723289 CTTTTAGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAATTAAACTAATAAATAC
Found at i:1724352 original size:22 final size:21
Alignment explanation
Indices: 1724286--1724355 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
1724276 TCATCCTAAA
*
1724286 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
1724307 CCAATACCCTAAACCAACCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
1724330 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
1724352 CCAA
1 CCAA
1724356 ATTTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 21 0.49
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Found at i:1738601 original size:23 final size:21
Alignment explanation
Indices: 1738566--1738635 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 21
1738556 TCATCCTAAA
*
1738566 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
*
1738587 CCAATACCCTAAACCAATCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
1738610 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
1738632 CCAA
1 CCAA
1738636 ATTTTAAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 14 0.34
22 7 0.17
23 20 0.49
ACGTcount: A:0.39, C:0.40, G:0.07, T:0.14
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Found at i:1752080 original size:44 final size:44
Alignment explanation
Indices: 1751905--1752564 Score: 473
Period size: 44 Copynumber: 15.2 Consensus size: 44
1751895 TGAAGTCATT
* * *
1751905 AAAGTAGATC-TGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * * * * *
1751948 ATATCAGATCCTATCTT-CTATATTGGTAG-GAAGTGGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAG
* * * * *
1751991 -ATGCAGATCTTGTCTTCCCATACTGGATGGCGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGG--CGTGAAGTAGATCGAAG
* *
1752036 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * * * * *
1752080 ATATCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAG
* * * *
1752124 -ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-AG
1 AAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAG
* *
1752167 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * ** *
1752211 ATA-CAG-TC-TATCTTCCTATATTGTAG-GAAGTGGATC-AAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * * *
1752250 -ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-AG
1 AAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAG
* *
1752293 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * * * ** * *
1752337 ATAGCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAG
1 AAAGCAGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAG
* * * *
1752381 -ATGCAGATCTTGTCTTCCCATATTGATG-GCGAAGTAGATCGCAG
1 AAAGCAGATCTTGTCTTCCTATATTG--GCGTGAAGTAGATCGAAG
* * *
1752425 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAG
1 AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
* * * * ** * *
1752469 ATAA-CAGGTCCTATCTTCCTATAAT-GATTGGAAGTGGATCGACG
1 A-AAGCAGATCTTGTCTTCCTATATTGGCGT-GAAGTAGATCGAAG
* * *
1752513 -ACGCAGATC-TGTCTTCCCATACTGTG-GTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAG
1752555 AAAGCAGATC
1 AAAGCAGATC
1752565 GACGATGGCG
Statistics
Matches: 474, Mismatches: 114, Indels: 58
0.73 0.18 0.09
Matches are distributed among these distances:
39 6 0.01
40 11 0.02
41 26 0.05
42 38 0.08
43 133 0.28
44 201 0.42
45 38 0.08
46 21 0.04
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (44 bp):
AAAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAG
Found at i:1752154 original size:132 final size:131
Alignment explanation
Indices: 1751905--1752564 Score: 1068
Period size: 132 Copynumber: 5.1 Consensus size: 131
1751895 TGAAGTCATT
*
1751905 AAAGTAGATC-TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTT-CTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
*
1751968 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGATGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG-TGGCGAAGTAGATCG
1752033 AAG
130 -AG
1752036 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
1752101 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
1752166 G
131 G
1752167 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA-CAG-T-CTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
1752229 TATT-GTAGGAAGTGGATC-AAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
1752292 G
131 G
* *
1752293 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
* * *
1752358 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
1752423 AG
130 AG
* * *
1752425 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
* * * * * * *
1752490 TAATGATTGGAAGTGGATCGACGACGCAGATC-TGTCTTCCCATACT-GTGGTGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-
1752553 AG
130 AG
1752555 AAAGCAGATC
1 AAAGCAGATC
1752565 GACGATGGCG
Statistics
Matches: 506, Mismatches: 15, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
126 93 0.18
127 17 0.03
128 16 0.03
129 16 0.03
130 42 0.08
131 114 0.23
132 157 0.31
133 51 0.10
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (131 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
G
Found at i:1753200 original size:22 final size:21
Alignment explanation
Indices: 1753134--1753203 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
1753124 TCATCCTAAA
*
1753134 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
1753155 CCAATACCCTAAACCAACCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
1753178 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
1753200 CCAA
1 CCAA
1753204 ATTTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 21 0.49
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Found at i:1769772 original size:27 final size:27
Alignment explanation
Indices: 1769735--1769796 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
1769725 TACTTTTTTT
1769735 TATA-TTTTTAT-AATT-AATAAAATAA
1 TATATTTTTTATAAATTGAATAAAA-AA
*
1769760 TATATTTTATTATAAAATTGAATTAAAAA
1 TATATTTT-TTAT-AAATTGAATAAAAAA
1769789 TATATTTT
1 TATATTTT
1769797 CCTAGTGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 4 0.13
29 14 0.45
30 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATTTTTTATAAATTGAATAAAAAA
Found at i:1770082 original size:38 final size:39
Alignment explanation
Indices: 1770031--1770104 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
1770021 CTACATCGGT
* * *
1770031 AAATAATTTAAAAATTATAA-AAAAATATTCATAAAAGAA
1 AAATAATTCAAAAAATAAAATAAAAAT-TTCATAAAAGAA
1770070 AAAT-ATTCAAAAAATAAAATAAAAATTTCATAAAA
1 AAATAATTCAAAAAATAAAATAAAAATTTCATAAAA
1770105 ATTCAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 21 0.68
39 10 0.32
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (39 bp):
AAATAATTCAAAAAATAAAATAAAAATTTCATAAAAGAA
Found at i:1770086 original size:22 final size:22
Alignment explanation
Indices: 1770061--1770106 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1770051 AAAAATATTC
1770061 ATAAAAGAAAAATATTCA-AAAA
1 ATAAAAGAAAAAT-TTCATAAAA
*
1770083 ATAAAATAAAAATTTCATAAAA
1 ATAAAAGAAAAATTTCATAAAA
1770105 AT
1 AT
1770107 TCAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAAAGAAAAATTTCATAAAA
Found at i:1770090 original size:16 final size:17
Alignment explanation
Indices: 1770051--1770088 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1770041 AAAATTATAA
1770051 AAAAATATTCATAAAAG
1 AAAAATATTCATAAAAG
* *
1770068 AAAAATATTCAAAAAAT
1 AAAAATATTCATAAAAG
1770085 AAAA
1 AAAA
1770089 TAAAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATATTCATAAAAG
Found at i:1776377 original size:304 final size:306
Alignment explanation
Indices: 1775826--1776417 Score: 1064
Period size: 304 Copynumber: 1.9 Consensus size: 306
1775816 GAACATACAA
* * *
1775826 AAACCAGGCCGACCGGATGGTGGCAAGTGGAGATCAAGCAAGGTAAAGGTCATGATTTATTTTTC
1 AAACCAGGCCGACCAGACGGTGGCAAGTGGAGATCAAGCAAGGTAAAGGTCAGGATTTATTTTTC
1775891 TAGATCTATTAGTGTACGGATGATTTTGGGTGATAAGAATTTTGATTCTGGATTAGGAGGATGGA
66 TAGATCTATTAGTGTACGGATGATTTTGGGTGATAAGAATTTTGATTCTGGATTAGGAGGATGGA
* * *
1775956 AGAACTGTGGGGGGATATTTCTTTTGGCCTGTCGAAGCTCCGTCCAATTGTGGGGGTGCCGTTGT
131 AGAACTGTGGGAGGATATTTCTTTTGGCCTGTCGAAGCTCCGTCCAATTGCGGCGGTGCCGTTGT
1776021 CGGAGTTCTCCATTCTTCTTCGGCCGTTAGAGAGAACCAAAGAATGAAAGAAAATAGTTTTAGAC
196 CGGAGTTCTCCATTCTTCTTCGGCCGTTAGAGAGAACCAAAGAATGAAAGAAAATAGTTTTAGAC
*
1776086 AGGAAAATCGAAAGCCAGAAGTTTATAGGAGATCAAGCACATACCG
261 AGGAAAATCGAAAGCCAGAAGTTCATAGGAGATCAAGCACATACCG
*
1776132 AAACCAGGCCGACCAGACGGTGGCAAGTGGAGATCAAGCAAGGTAAAGGTCAGGGTTTA-TTTTC
1 AAACCAGGCCGACCAGACGGTGGCAAGTGGAGATCAAGCAAGGTAAAGGTCAGGATTTATTTTTC
1776196 TAGATCTATTAGTGTACGGATGATTTTGGGTGATAA-AGATTTTGATTCTGGATTA-GAGGATGG
66 TAGATCTATTAGTGTACGGATGATTTTGGGTGATAAGA-ATTTTGATTCTGGATTAGGAGGATGG
*
1776259 AAGAACTGTGGGAGGATATTTCTTTTGGCCTGTCGAAGCTCCGTCCGATTGCGGCGGTGCCGTTG
130 AAGAACTGTGGGAGGATATTTCTTTTGGCCTGTCGAAGCTCCGTCCAATTGCGGCGGTGCCGTTG
1776324 TCGGAGTTCTCCATTCTTCTTCGGCCGTTAGAGAGAACCAAAGAATGAAAGAAAATAGTTTTAGA
195 TCGGAGTTCTCCATTCTTCTTCGGCCGTTAGAGAGAACCAAAGAATGAAAGAAAATAGTTTTAGA
*
1776389 CAGGAGAATCGAAAGCCAGAAGTTCATAG
260 CAGGAAAATCGAAAGCCAGAAGTTCATAG
1776418 AAGGGTTTCG
Statistics
Matches: 275, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
304 162 0.59
305 58 0.21
306 55 0.20
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (306 bp):
AAACCAGGCCGACCAGACGGTGGCAAGTGGAGATCAAGCAAGGTAAAGGTCAGGATTTATTTTTC
TAGATCTATTAGTGTACGGATGATTTTGGGTGATAAGAATTTTGATTCTGGATTAGGAGGATGGA
AGAACTGTGGGAGGATATTTCTTTTGGCCTGTCGAAGCTCCGTCCAATTGCGGCGGTGCCGTTGT
CGGAGTTCTCCATTCTTCTTCGGCCGTTAGAGAGAACCAAAGAATGAAAGAAAATAGTTTTAGAC
AGGAAAATCGAAAGCCAGAAGTTCATAGGAGATCAAGCACATACCG
Found at i:1776947 original size:12 final size:12
Alignment explanation
Indices: 1776930--1776955 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1776920 GCTTTGAACT
1776930 ACAGCCTGTGAC
1 ACAGCCTGTGAC
1776942 ACAGCCTGTGAC
1 ACAGCCTGTGAC
1776954 AC
1 AC
1776956 TAGGTGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (12 bp):
ACAGCCTGTGAC
Found at i:1777069 original size:15 final size:16
Alignment explanation
Indices: 1777049--1777083 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1777039 TCCCTGTAGT
1777049 TTTAAG-TTTATTTCA
1 TTTAAGTTTTATTTCA
1777064 TTTAAGTTTTTATTTCA
1 TTTAAG-TTTTATTTCA
1777081 TTT
1 TTT
1777084 TAGGGTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTAAGTTTTATTTCA
Found at i:1777783 original size:15 final size:15
Alignment explanation
Indices: 1777763--1777793 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1777753 CGTTACTCAC
1777763 TAAAAATCCAATTAA
1 TAAAAATCCAATTAA
1777778 TAAAAATCCAATTAA
1 TAAAAATCCAATTAA
1777793 T
1 T
1777794 GAATTAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATCCAATTAA
Found at i:1783364 original size:18 final size:18
Alignment explanation
Indices: 1783341--1783433 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
1783331 CCCAACTACT
*
1783341 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1783359 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
1783377 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
1783395 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
1783413 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1783431 GTA
1 GTA
1783434 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1783393 original size:36 final size:36
Alignment explanation
Indices: 1783341--1783433 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
1783331 CCCAACTACT
*
1783341 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
1783377 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
1783413 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
1783434 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:1784803 original size:38 final size:39
Alignment explanation
Indices: 1784726--1784803 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
1784716 GCAGATGGTG
* *
1784726 ACTTCTTTGTAGGTATATATCATAGTTTCCCATAAAATT
1 ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
* *
1784765 ACTTCTTTGTAGGTATATATCAT-GGTTCCCCCAGAATT
1 ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
1784803 A
1 A
1784804 GATAAGTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (39 bp):
ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
Found at i:1792918 original size:22 final size:24
Alignment explanation
Indices: 1792886--1792937 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
1792876 TTTATTATTG
*
1792886 ATTTTATAATATTTTA-AATGTAT
1 ATTTTATAATATTTTATAATATAT
1792909 ATTTTA-AATATTTTATAATATAT
1 ATTTTATAATATTTTATAATATAT
1792932 -TTTTAT
1 ATTTTAT
1792938 TCAAACGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTATAATATTTTATAATATAT
Found at i:1793063 original size:9 final size:10
Alignment explanation
Indices: 1793039--1793073 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1793029 GTTTATTATT
1793039 TATTTTATAA
1 TATTTTATAA
1793049 TATTTTA-AA
1 TATTTTATAA
*
1793058 TGTTTTATAA
1 TATTTTATAA
1793068 TATTTT
1 TATTTT
1793074 TATTCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TATTTTATAA
Found at i:1793114 original size:21 final size:20
Alignment explanation
Indices: 1793090--1793144 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1793080 AACGATTTTA
1793090 AAAAATATTATATTTAAAATT
1 AAAAATATTATATTT-AAATT
* * *
1793111 AAAAATAATAATATTTTATTT
1 AAAAAT-ATTATATTTAAATT
1793132 AGAAAATATTATA
1 A-AAAATATTATA
1793145 AGACATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAATATTATATTTAAATT
Found at i:1796070 original size:10 final size:10
Alignment explanation
Indices: 1796057--1796109 Score: 70
Period size: 10 Copynumber: 4.9 Consensus size: 10
1796047 TTTAAATGGA
1796057 AAAAAATTAT
1 AAAAAATTAT
1796067 AAAAAAATTAT
1 -AAAAAATTAT
1796078 AAAAAATTATTTT
1 AAAAAATTA---T
1796091 AAAAAATTAT
1 AAAAAATTAT
1796101 AAAAAATTA
1 AAAAAATTA
1796110 AAATAGGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 19 0.49
11 10 0.26
13 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:1796072 original size:11 final size:11
Alignment explanation
Indices: 1796056--1796106 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
1796046 TTTTAAATGG
1796056 AAAAAAATTAT
1 AAAAAAATTAT
1796067 AAAAAAATTAT
1 AAAAAAATTAT
1796078 -AAAAAATTATTT
1 AAAAAAATTA--T
*
1796090 TAAAAAATTAT
1 AAAAAAATTAT
1796101 AAAAAA
1 AAAAAA
1796107 TTAAAATAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.25
11 17 0.47
12 1 0.03
13 9 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:1797663 original size:24 final size:24
Alignment explanation
Indices: 1797636--1797687 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1797626 TTAGTAAGTC
*
1797636 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1797660 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1797684 AAAT
1 AAAT
1797688 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1799636 original size:24 final size:24
Alignment explanation
Indices: 1799609--1799660 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1799599 TTAGTAAGTC
* *
1799609 AAATAAACTATCCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1799633 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1799657 AAAT
1 AAAT
1799661 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1801455 original size:16 final size:15
Alignment explanation
Indices: 1801434--1801483 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
1801424 AAATAGTATT
1801434 AAAAATAAAATACCGA
1 AAAAATAAAATA-CGA
** *
1801450 AAAAATATATTTATGA
1 AAAAATA-AAATACGA
1801466 AAAAATAAAATACGA
1 AAAAATAAAATACGA
1801481 AAA
1 AAA
1801484 TAGTATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 8 0.30
16 16 0.59
17 3 0.11
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAATAAAATACGA
Found at i:1801472 original size:32 final size:32
Alignment explanation
Indices: 1801434--1801519 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 32
1801424 AAATAGTATT
1801434 AAAAATAAAATACCGAAAAAATATATTTA-TGA
1 AAAAATAAAATA-CGAAAAAATATATTTACTGA
*
1801466 AAAAATAAAATACGAAAATAGTATATTTACTGA
1 AAAAATAAAATACGAAAA-AATATATTTACTGA
* *
1801499 AAGTAATAAAATTCGAAAAAA
1 AA-AAATAAAATACGAAAAAA
1801520 AATACGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.13
32 21 0.45
33 6 0.13
34 14 0.30
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (32 bp):
AAAAATAAAATACGAAAAAATATATTTACTGA
Found at i:1801855 original size:156 final size:152
Alignment explanation
Indices: 1801465--1801896 Score: 577
Period size: 148 Copynumber: 2.9 Consensus size: 152
1801455 TATATTTATG
* **
1801465 AAAAAATAAAATACGAAAATAGTATATTTACTGAAAGTAATAAAAT-T--CGA-AAAAAAATACG
1 AAAAAATAAAATACGAAAATAGTATATTT-TTGAAAGTAATAAAATCTAAAAATAAAAAAATACG
*
1801526 AACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAAACACACTAAAATAATACAT
65 AACAAATGGCCAAAATAAGGGTTTTTCACTAAATTTATAT-AAAAAACACACTAAAATAATACAT
1801591 TTCAAACATATGTACTAAAATAAT
129 TTCAAACATATGTACTAAAATAAT
*
1801615 --AAAAT----T-CGAAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAAATAAGAAAAATAC
1 AAAAAATAAAATACGAAAATAGTATA-TTTTTGAAAGTAATAAAATCTAAAAATAA-AAAAATAC
**
1801673 GAACAAATGGCCAAAATAAAAGTTTTTCACTAAATTTATAT-AAAAA-ACACTAAAATAATACAT
64 GAACAAATGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATAATACAT
*
1801736 TTCAAACTTTATGTACTAAAATAATAT
129 TTCAAAC-ATATGTACTAAAAT-A-AT
1801763 AAAATAATAAAATACGAAAATAGTATAGTTTTTGAAAGTAATAAAATCTAAAAATAAAAAAATAC
1 AAAA-AATAAAATACGAAAATAGTATA-TTTTTGAAAGTAATAAAATCTAAAAATAAAAAAATAC
* *
1801828 GAACAAATGGCCAAAAT-AGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
64 GAACAAATGGCCAAAATAAGGG-TTTTTCACTAAATTTATAT-AAAAAACACACTAAAATAATAC
1801892 ATTTC
127 ATTTC
1801897 TCATTGTTTG
Statistics
Matches: 247, Mismatches: 14, Indels: 34
0.84 0.05 0.12
Matches are distributed among these distances:
143 28 0.11
144 4 0.02
145 24 0.10
146 19 0.08
147 3 0.01
148 53 0.21
150 2 0.01
151 3 0.01
154 2 0.01
155 44 0.18
156 41 0.17
157 5 0.02
158 19 0.08
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (152 bp):
AAAAAATAAAATACGAAAATAGTATATTTTTGAAAGTAATAAAATCTAAAAATAAAAAAATACGA
ACAAATGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATAATACATTT
CAAACATATGTACTAAAATAAT
Found at i:1803233 original size:10 final size:10
Alignment explanation
Indices: 1803220--1803270 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
1803210 TTTAAATGGA
1803220 AAAAAATTAT
1 AAAAAATTAT
1803230 AAAAAAATTA-
1 -AAAAAATTAT
*
1803240 AAAAATTATTTT
1 AAAAA--ATTAT
1803252 AAAAAATTAT
1 AAAAAATTAT
1803262 AAAAAATTA
1 AAAAAATTA
1803271 AAATAGGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 5 0.14
10 13 0.37
11 12 0.34
12 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:1803235 original size:11 final size:11
Alignment explanation
Indices: 1803219--1803267 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1803209 TTTTAAATGG
1803219 AAAAAAATTAT
1 AAAAAAATTAT
1803230 AAAAAAATTA-
1 AAAAAAATTAT
*
1803240 AAAAATTATT-T
1 AAAAA-AATTAT
*
1803251 TAAAAAATTAT
1 AAAAAAATTAT
1803262 AAAAAA
1 AAAAAA
1803268 TTAAAATAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:1803253 original size:13 final size:13
Alignment explanation
Indices: 1803237--1803261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1803227 TATAAAAAAA
1803237 TTAAAAAATTATT
1 TTAAAAAATTATT
1803250 TTAAAAAATTAT
1 TTAAAAAATTAT
1803262 AAAAAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAAAATTATT
Found at i:1804743 original size:19 final size:18
Alignment explanation
Indices: 1804700--1804745 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1804690 AAAGAGGAAG
1804700 AGAAAA-AAAAGAAAAAA
1 AGAAAAGAAAAGAAAAAA
**
1804717 AGGGAAGAAAAGGAAAAAA
1 AGAAAAGAAAA-GAAAAAA
1804736 AGAAAAGAAA
1 AGAAAAGAAA
1804746 TACTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAAAGAAAAAA
Found at i:1806932 original size:28 final size:27
Alignment explanation
Indices: 1806892--1806978 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 27
1806882 GAAATTAAAG
1806892 TATAAGGATTAAATCTCAAATTTAAGCA
1 TATAAGGATTAAAT-TCAAATTTAAGCA
* * * *
1806920 TATTAGGACTAAAATTGAAATTAAAG--
1 TATAAGGA-TTAAATTCAAATTTAAGCA
*
1806946 TATAAGAATTAAATTTCAAATTTAAGCA
1 TATAAGGATTAAA-TTCAAATTTAAGCA
1806974 TATAA
1 TATAA
1806979 AAAGGACTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
25 4 0.09
26 16 0.35
28 21 0.46
29 5 0.11
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.33
Consensus pattern (27 bp):
TATAAGGATTAAATTCAAATTTAAGCA
Found at i:1806966 original size:26 final size:26
Alignment explanation
Indices: 1806883--1806967 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
1806873 ATGATGCTAG
*
1806883 AAATTAAAGTATAAGGATTAAATCTC
1 AAATTAAAGTATAAGGATTAAATTTC
* * * * *
1806909 AAATTTAAGCATATTAGGACTAAAATTG
1 AAATTAAAG--TATAAGGATTAAATTTC
*
1806937 AAATTAAAGTATAAGAATTAAATTTC
1 AAATTAAAGTATAAGGATTAAATTTC
1806963 AAATT
1 AAATT
1806968 TAAGCATATA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
26 25 0.56
28 20 0.44
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.33
Consensus pattern (26 bp):
AAATTAAAGTATAAGGATTAAATTTC
Found at i:1808079 original size:14 final size:14
Alignment explanation
Indices: 1808060--1808088 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1808050 ATAAAATACT
1808060 ATAAAATACTATAA
1 ATAAAATACTATAA
1808074 ATAAAATACTATAA
1 ATAAAATACTATAA
1808088 A
1 A
1808089 GTTTACTACT
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:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAATACTATAA
Found at i:1808088 original size:10 final size:10
Alignment explanation
Indices: 1808050--1808074 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1808040 TTTAAATAAA
1808050 ATAAAATACT
1 ATAAAATACT
1808060 ATAAAATACT
1 ATAAAATACT
1808070 ATAAA
1 ATAAA
1808075 TAAAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATACT
Found at i:1812461 original size:21 final size:22
Alignment explanation
Indices: 1812432--1812478 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1812422 CAGAAGGAGT
*
1812432 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1812454 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1812475 GAGT
1 GAGT
1812479 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1831643 original size:30 final size:30
Alignment explanation
Indices: 1831609--1831665 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1831599 AGAAAATTCA
1831609 AATATTAAATTAAACATCAAAACTAAATTT
1 AATATTAAATTAAACATCAAAACTAAATTT
* *
1831639 AATATTAAATTAAATATTAAAACTAAA
1 AATATTAAATTAAACATCAAAACTAAA
1831666 CCAAATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (30 bp):
AATATTAAATTAAACATCAAAACTAAATTT
Found at i:1870736 original size:30 final size:30
Alignment explanation
Indices: 1870691--1870748 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1870681 CACGAGCTAG
* *
1870691 CACATGGGCATGTGTCCAGCCCGTGTGGCT
1 CACACGGGCATGTGTCCAACCCGTGTGGCT
*
1870721 CACACGGGCGTGTGTCCAACCCGTGTGG
1 CACACGGGCATGTGTCCAACCCGTGTGG
1870749 AAATGCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.21
Consensus pattern (30 bp):
CACACGGGCATGTGTCCAACCCGTGTGGCT
Found at i:1873963 original size:40 final size:40
Alignment explanation
Indices: 1873903--1874250 Score: 597
Period size: 40 Copynumber: 8.7 Consensus size: 40
1873893 GAGCATTGGA
*
1873903 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
1873943 ATATGTCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
1873983 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
1874023 ATATGTCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
1874063 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTCG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1874103 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
1874143 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
1874183 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
1874223 ATATGTCCGGGTTAAGACCTGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
1874251 ATGTGTTTGC
Statistics
Matches: 291, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 291 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:1880461 original size:17 final size:19
Alignment explanation
Indices: 1880401--1880477 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
1880391 AATCTTCGAG
*
1880401 GATATATAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
1880420 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
1880439 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
1880461 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
1880478 GATTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
19 29 0.58
20 3 0.06
22 8 0.16
23 10 0.20
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:1880490 original size:21 final size:23
Alignment explanation
Indices: 1880433--1880491 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1880423 ATGCAATCTT
*
1880433 AGATATG-ATATGTAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
1880455 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
1880477 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
1880492 ATACCCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.28
22 11 0.34
23 12 0.38
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.42
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:1880914 original size:3 final size:3
Alignment explanation
Indices: 1880906--1880945 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1880896 ATTGATTTTG
*
1880906 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
1880946 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1880919 original size:15 final size:15
Alignment explanation
Indices: 1880901--1880945 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1880891 ATTTTATTGA
*
1880901 TTTTGTTATTATTAT
1 TTTTATTATTATTAT
1880916 TTTTATTATTA-TAT
1 TTTTATTATTATTAT
*
1880930 TATATATTATTATTAT
1 T-TTTATTATTATTAT
1880946 ACCTACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 19 0.73
16 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:1880921 original size:12 final size:12
Alignment explanation
Indices: 1880892--1880943 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
1880882 TTTTAGTCTA
1880892 TTTTATTGATT-T
1 TTTTATT-ATTAT
*
1880904 TGTTATTATTAT
1 TTTTATTATTAT
1880916 TTTTATTATTAT
1 TTTTATTATTAT
1880928 ATTATATATTATTAT
1 -TT-T-TATTATTAT
1880943 T
1 T
1880944 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:1887280 original size:88 final size:88
Alignment explanation
Indices: 1887130--1887892 Score: 1085
Period size: 88 Copynumber: 8.7 Consensus size: 88
1887120 AGCAGATCAG
* * ** * * *
1887130 TAAAAATAACAGATTTTGCCTTCCTGCGTCGACAGCTAAGCAGATCAAAGACACCAGTCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1887195 CCCTGGGTTGCAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
1887218 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
1887283 CCCTGGGTTACAGCGGAGTAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* * *
1887306 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
1887371 CCCTGTGTTGCAGTGGAGCAAGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* * * *
1887394 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCTAAGCAGATCAAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
1887459 CACTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGC
* *
1887482 TAAAAATAGTAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
1887547 CCCTGGGTTACAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* ** *
1887570 TAAAATTAGCAGATCTTGCCTTCCTGCACCGACAATGAAGCAGATCGAAGTCACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
1887635 CCCTGGGTTGTAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* *
1887658 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGATACCAGCCTTTCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
1887723 CCTTGGGTTGTAGCGGAGTAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* * * * * **
1887746 TGAGAATAGAAGATCTTGCCTTCCTGCGCCGATAGCGAAATAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
1887811 CCTTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGC
* * * * * *
1887834 TAAAAATAACAGATCTTTCCTTCTTGCACCGACAGCGAAGCAGATTGATGACCCCAGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
1887893 CTATCTCCCT
Statistics
Matches: 596, Mismatches: 79, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 596 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGC
Found at i:1887955 original size:44 final size:44
Alignment explanation
Indices: 1887892--1888266 Score: 444
Period size: 44 Copynumber: 8.7 Consensus size: 44
1887882 TGACCCCAGC
* *
1887892 CCTATCTCCCTGGTCAACAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
** * * * * *
1887936 CCTATCTCCCTGAACAACAGTGAAATATGTTAAAGACTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
1887980 TCTATCT-CCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
1888023 TCTATCTCCCTGGGCAGCAGTGGAATAGGTTG-A-A----GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
1888061 CCTATCTCTCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
1888105 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
1888149 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA-AT
* *
1888193 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
1888237 CCTATCTCCCTGAG-CAGCAATGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
1888267 GGAAAATAGT
Statistics
Matches: 285, Mismatches: 36, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
38 32 0.11
39 1 0.00
40 1 0.00
42 1 0.00
43 37 0.13
44 211 0.74
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:1888152 original size:126 final size:126
Alignment explanation
Indices: 1887932--1888266 Score: 467
Period size: 126 Copynumber: 2.6 Consensus size: 126
1887922 TAAAGATTGT
* * * * * *
1887932 GAATCCTATCTCCCTGAACAACAGTGAAATATGTTAAAGACTGTGAATTCTATCT-CCTGGTCAG
1 GAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAG
*
1887996 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAA
66 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
*
1888057 GAATCCTATCTCTCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAG
1 GAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAG
1888122 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
66 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
* * * *
1888183 GATTGTAGGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCCT
1 GA----A--TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCT
* *
1888248 GAG-CAGCAATGGAGTAGGT
60 G-GTCAGCAGTGGAATAGGT
1888267 GGAAAATAGT
Statistics
Matches: 187, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
125 48 0.26
126 71 0.38
130 1 0.01
132 66 0.35
133 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (126 bp):
GAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAG
CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
Found at i:1888817 original size:45 final size:43
Alignment explanation
Indices: 1888572--1889030 Score: 194
Period size: 44 Copynumber: 10.6 Consensus size: 43
1888562 ATGACAAATT
* * * *
1888572 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTAA-AGTCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAATC-A-AGTC
* * * * **
1888616 CTATCTCCCTGAAGTTGCAGTGAAGC-GAATTAA-AACCTTGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-ACTAAGAATC-AAG-TC
* ** * * * *
1888660 TTATCTCTCTGAAGTTGCAG-AAAGCAGA-T-TGCATCTAGTT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAATCAAGTC
** *
1888700 TTATCTCCCTGAAGTTATAGTGGAGCAGAGTAAGTAATCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AATCAAGTC
* *
1888744 TTATC-CTCCTAAAGTTGCAAT-GAGGCAGACTGAAG-ATGGCGAA-TC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAT--C-AAGTC
*
1888789 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AA-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG--AATCAAGTC
* * * *
1888833 CTATCTCTCTGAGGTTGCAGTGGAGCAGATTAA-AATCACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAATCA-AG-TC
** * * * * * * *
1888877 TTATCTCTTTGAAGTTGTAGTAGAGTAGA-TCA-CATTAGGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAATCAAGTC
* *
1888918 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AATCAAGTC
* * * * * * *
1888963 TTATCCCCCTGAAATTGCAGTGGGGCATACTAAATAAACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAATCAAGTC
* * *
1889007 CTGTCTCCCT-AAGTTGTAGTGGAG
1 TTATCTCCCTGAAGTTGCAGTGGAG
1889031 TGGACTAGAG
Statistics
Matches: 314, Mismatches: 74, Indels: 55
0.71 0.17 0.12
Matches are distributed among these distances:
40 21 0.07
41 35 0.11
42 7 0.02
43 31 0.10
44 148 0.47
45 65 0.21
46 5 0.02
48 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAATCAAGTC
Found at i:1888821 original size:217 final size:219
Alignment explanation
Indices: 1888557--1889030 Score: 550
Period size: 217 Copynumber: 2.2 Consensus size: 219
1888547 TTCCTAACAT
* * * *
1888557 TGAAGATGACAAATTTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTCGATAATCCTATCT
1 TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCT
***
1888622 CCCTGAAGTTGCAGTGAAGC-GAATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAG-AAAGC
66 CCCTGAAGTTGCAGTGAAGCAG-ATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAAAGC
** * * * * *
1888685 AGATTGCATCTA-GTTTTATCTCCCTGAAGTTATAGTGGAGCAGAGT-AAGTAATCAAGTCTTAT
130 AGATCACAT-TAGGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
*
1888748 CCTCCT-AAAGTTGCAATGAGGCAGAC
194 CCCCCTGAAA-TTGCAATGAGGCAGAC
* *
1888774 TGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCT
1 TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCT
* * * * * * * *
1888839 CTCTGAGGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTTTGAAGTTGTAGTAGAGTA
66 CCCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAAAGCA
* *
1888904 GATCACATTAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTTTTATCC
131 GATCACATTAGGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCC
* * *
1888969 CCCTGAAATTGCAGTGGGGCATAC
196 CCCTGAAATTGCAATGAGGCAGAC
* * * *
1888993 T-AA-ATAAACAAATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 TGAAGAT-GACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
1889031 TGGACTAGAG
Statistics
Matches: 215, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
217 123 0.57
218 56 0.26
219 33 0.15
220 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (219 bp):
TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCT
CCCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAAAGCA
GATCACATTAGGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCC
CCCTGAAATTGCAATGAGGCAGAC
Found at i:1888882 original size:44 final size:43
Alignment explanation
Indices: 1888572--1888946 Score: 223
Period size: 44 Copynumber: 8.7 Consensus size: 43
1888562 ATGACAAATT
* *
1888572 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTCGATA-ATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-A-AGATC
* * * **
1888616 CTATCTCCCTGAAGTTGCAGTGAAGC-GAATTAAAACCTTGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAATC-AAGATC
* ** ** * *
1888660 TTATCTCTCTGAAGTTGCAG-AAAGCAGATT-GCATCTAG-TT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAAGATC
** *
1888700 TTATCTCCCTGAAGTTATAGTGGAGCAGAGTAAGTAATCAAG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCAAGATC
* * * * *
1888744 TTATC-CTCCTAAAGTTGCAAT-GAGGCAGACTGAAGATGGCGA-ATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CAAGATC
** *
1888789 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAA-GATC
* * *
1888833 CTATCTCTCTGAGGTTGCAGTGGAGCAGATTAAAATCACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCA-AGATC
** * * * * * * *
1888877 TTATCTCTTTGAAGTTGTAGTAGAGTAGA-TCACAT-TAGGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAAGATC
1888918 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
1888947 CTCAAGAAAG
Statistics
Matches: 251, Mismatches: 62, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
40 18 0.07
41 37 0.15
42 4 0.02
43 17 0.07
44 143 0.57
45 29 0.12
46 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAAGATC
Found at i:1889366 original size:21 final size:21
Alignment explanation
Indices: 1889341--1889384 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1889331 ATCTTCGAGG
1889341 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
1889362 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
1889383 AT
1 AT
1889385 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:1889390 original size:19 final size:19
Alignment explanation
Indices: 1889340--1889395 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
1889330 AATCTTCGAG
1889340 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1889359 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
1889380 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
1889396 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:1889402 original size:22 final size:23
Alignment explanation
Indices: 1889353--1889418 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1889343 ATGCAATCTT
*
1889353 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
1889374 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
1889396 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
1889419 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:1889431 original size:21 final size:23
Alignment explanation
Indices: 1889374--1889432 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1889364 ATGCAATCTT
*
1889374 AGATATG-ATATGTAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
1889396 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
1889418 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
1889433 ATACCCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.28
22 11 0.34
23 12 0.38
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.42
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:1889628 original size:21 final size:19
Alignment explanation
Indices: 1889591--1889629 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1889581 CTTACTGTTT
*
1889591 TTTTTTCCTTTTTCGATTA
1 TTTTTTACTTTTTCGATTA
1889610 TTTTTTACTTATTTACGATT
1 TTTTTTACTT-TTT-CGATT
1889630 TTAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTACTTTTTCGATTA
Found at i:1889849 original size:3 final size:3
Alignment explanation
Indices: 1889841--1889880 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1889831 GTTGATTTTG
1889841 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T
1889881 ACCTACGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1890252 original size:51 final size:52
Alignment explanation
Indices: 1890138--1890253 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 52
1890128 ATTTTCCACG
**
1890138 TTTT-TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
* * * * *
1890188 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATACTTATATATTTCATT-TTTTCATAAATGCATGAATATA
1890239 TTTTATATATATATA
1 TTTTATATATATATA
1890254 AGTTTTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 28 0.51
52 23 0.42
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (52 bp):
TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:1891832 original size:69 final size:69
Alignment explanation
Indices: 1891721--1891859 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
1891711 ATCAATAACT
1891721 TTCAAACTTAGGTAGTACTTCGGTCAAATAACCAAAGTCTCAAAAGATCTAATTTAGGAATTGAA
1 TTCAAACTTAGGTAGTACTTCGGTCAAATAACCAAAGTCTCAAAAGATCTAATTTAGGAATTGAA
1891786 AATA
66 AATA
1891790 TTCAAACTTAGGTAGTACTTCGGTCAAATAACCAAAGTCTCAAAAGATCTAATTTAGGAATTGAA
1 TTCAAACTTAGGTAGTACTTCGGTCAAATAACCAAAGTCTCAAAAGATCTAATTTAGGAATTGAA
1891855 AATA
66 AATA
1891859 T
1 T
1891860 GAGGTGGACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (69 bp):
TTCAAACTTAGGTAGTACTTCGGTCAAATAACCAAAGTCTCAAAAGATCTAATTTAGGAATTGAA
AATA
Found at i:1892719 original size:21 final size:19
Alignment explanation
Indices: 1892686--1892737 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
1892676 TCACGTCAAC
*
1892686 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTAAA
1892705 AAATAAATATTAAAAATT-AA
1 AAAT-AAT-TTAAAAATTAAA
1892725 AAA-AATTTAAAAA
1 AAATAATTTAAAAA
1892738 AATAACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 4 0.13
20 7 0.23
21 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATTTAAAAATTAAA
Found at i:1894783 original size:41 final size:40
Alignment explanation
Indices: 1894726--1894813 Score: 167
Period size: 41 Copynumber: 2.2 Consensus size: 40
1894716 ATGACTCCTT
1894726 AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1 AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1894766 AAAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1 -AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1894807 AAAGAAA
1 AAAGAAA
1894814 TCTTGCACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 7 0.15
41 40 0.85
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.16
Consensus pattern (40 bp):
AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
Found at i:1908305 original size:31 final size:31
Alignment explanation
Indices: 1908270--1908331 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1908260 GGTTAAGAAT
*
1908270 AAAATTT-TACCAACTTTTAAGGGACCTAAAA
1 AAAATTTCT-CCAACTTTTAAGGAACCTAAAA
1908301 AAAATTTCTCCAACTTTTAAGGAACCTAAAA
1 AAAATTTCTCCAACTTTTAAGGAACCTAAAA
1908332 CCCCATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (31 bp):
AAAATTTCTCCAACTTTTAAGGAACCTAAAA
Found at i:1908604 original size:16 final size:17
Alignment explanation
Indices: 1908583--1908620 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1908573 TCAAATATAA
* *
1908583 AAAAAAAT-TAATTTTT
1 AAAAAAATGTAAATGTT
1908599 AAAAAAATGTAAATGTT
1 AAAAAAATGTAAATGTT
1908616 AAAAA
1 AAAAA
1908621 CTAAATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAAAATGTAAATGTT
Found at i:1910032 original size:19 final size:19
Alignment explanation
Indices: 1909996--1910038 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1909986 ATTTTTATAA
*
1909996 AATTTTTATAATTTATTAT
1 AATTTTTATAATTTATTAC
*
1910015 AATTTTTA-ATTTTCATTAC
1 AATTTTTATAATTT-ATTAC
1910034 AATTT
1 AATTT
1910039 ATAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATAATTTATTAC
Found at i:1922800 original size:3 final size:3
Alignment explanation
Indices: 1922792--1922832 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1922782 GCTTTTCTAT
1922792 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1922833 TTTATTTTCA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1934535 original size:23 final size:24
Alignment explanation
Indices: 1934509--1934555 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1934499 GCAAGGCTCG
1934509 ATTCTAAAT-GATCGCATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
* *
1934532 ATTCTAAATGGGTCGGATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
1934556 TTATATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (24 bp):
ATTCTAAATGGATCGCATAATCTT
Found at i:1949421 original size:26 final size:26
Alignment explanation
Indices: 1949384--1949451 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
1949374 TGAGAGGACA
1949384 ACAAGG-GAAGCTCGTAGACCTAGCTC
1 ACAAGGAG-AGCTCGTAGACCTAGCTC
* * *
1949410 GCAA-GAGGAGCTCATAGATCTAGCTC
1 ACAAGGA-GAGCTCGTAGACCTAGCTC
1949436 ACAAGGAGAGCTCGTA
1 ACAAGGAGAGCTCGTA
1949452 TGAACCAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 30 0.88
27 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (26 bp):
ACAAGGAGAGCTCGTAGACCTAGCTC
Found at i:1951407 original size:17 final size:18
Alignment explanation
Indices: 1951372--1951408 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1951362 AGTATATTAC
1951372 TAATACATAATATAATAT
1 TAATACATAATATAATAT
*
1951390 TAATACAT-ATATAGTAT
1 TAATACATAATATAATAT
1951407 TA
1 TA
1951409 CATGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATACATAATATAATAT
Found at i:1954263 original size:16 final size:16
Alignment explanation
Indices: 1954230--1954263 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1954220 TGGTGATGTT
* *
1954230 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
1954246 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
1954262 AA
1 AA
1954264 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:1957081 original size:21 final size:21
Alignment explanation
Indices: 1957055--1957095 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1957045 AGACGAGCAA
* *
1957055 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1957076 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1957096 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1959034 original size:16 final size:16
Alignment explanation
Indices: 1959001--1959034 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1958991 GGAGATTGTT
* *
1959001 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
1959017 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
1959033 AA
1 AA
1959035 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:1960169 original size:10 final size:10
Alignment explanation
Indices: 1960154--1960178 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1960144 TGCATTACAT
1960154 ATTTACATAA
1 ATTTACATAA
1960164 ATTTACATAA
1 ATTTACATAA
1960174 ATTTA
1 ATTTA
1960179 AGATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTACATAA
Done.