Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 7 of 54
Found at i:3174864 original size:255 final size:254
Alignment explanation
Indices: 3174382--3174888 Score: 944
Period size: 255 Copynumber: 2.0 Consensus size: 254
3174372 ATAACAATTC
3174382 TTAATTCTATTAGGATAATATTCCTAATTATATTAGGATAAAGTTATTGTATTTGGCACTATAAA
1 TTAATTCTATTAGGATAATATTCCTAATTATATTAGGATAAAGTTATTGTATTTGGCACTATAAA
* *
3174447 AGGACCTTATGGGTTAAAGAATAATAATAACTTAAATTTAGAGAGAGTGATTTAGGTGTACGTGG
66 AAGACCCTATGGGTTAAAGAATAATAATAACTTAAATTTAGAGAGAGTGATTTAGGTGTACGTGG
3174512 CATAAGGGTTATGAGTTTGAGACTGTTCTTGTAATCTTCTGATTTTTTCTCTTAGTGGATTTTTC
131 CATAAGGGTTATGAGTTTGAGACTGTTCTTGTAATCTTCTGATTTTTTCTCTTAGTGGATTTTTC
*
3174577 TCTATTGTTGTGCCCGTGAATGTAGGCATCAAAATACCGAACCACGTAAATTCTTGTTT
196 TCTATTGTTGTGCCCGTGAATGTAGGCATCAAAAGACCGAACCACGTAAATTCTTGTTT
* *
3174636 TNTAATTCTATTAGGATAATATTCCTAATTATATTAGGATAAGGTTATTGTATTTGGCATTATAA
1 T-TAATTCTATTAGGATAATATTCCTAATTATATTAGGATAAAGTTATTGTATTTGGCACTATAA
3174701 AAAGACCCTATGGGTTAAAGAATAATAATAACTTAAATTTAGAGAGAGTGATTTAGGTGTACGTG
65 AAAGACCCTATGGGTTAAAGAATAATAATAACTTAAATTTAGAGAGAGTGATTTAGGTGTACGTG
3174766 GCATAAGGGTTATGAGTTTGAGACTGTTCTTGTAATCTTCTGA-TTTTTCTCTTAGTGGATTTTT
130 GCATAAGGGTTATGAGTTTGAGACTGTTCTTGTAATCTTCTGATTTTTTCTCTTAGTGGATTTTT
3174830 CTCTATTGTTGTGCCCGTGAATGTAGGTCATCAAAAGACCGAACCACGTAAATTCTTGT
195 CTCTATTGTTGTGCCCGTGAATGTAGG-CATCAAAAGACCGAACCACGTAAATTCTTGT
3174889 GTTCTTGTGA
Statistics
Matches: 246, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
254 49 0.20
255 197 0.80
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (254 bp):
TTAATTCTATTAGGATAATATTCCTAATTATATTAGGATAAAGTTATTGTATTTGGCACTATAAA
AAGACCCTATGGGTTAAAGAATAATAATAACTTAAATTTAGAGAGAGTGATTTAGGTGTACGTGG
CATAAGGGTTATGAGTTTGAGACTGTTCTTGTAATCTTCTGATTTTTTCTCTTAGTGGATTTTTC
TCTATTGTTGTGCCCGTGAATGTAGGCATCAAAAGACCGAACCACGTAAATTCTTGTTT
Found at i:3176129 original size:29 final size:28
Alignment explanation
Indices: 3176083--3176143 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
3176073 TTTTACTTTG
* *
3176083 TTCTCTTGTACCTGTTCAAT-TATGGTTT
1 TTCTCTTATACCTATTC-ATGTATGGTTT
*
3176111 CTTCTCTTATACTTATTCATGTATGGTTT
1 -TTCTCTTATACCTATTCATGTATGGTTT
3176140 TTCT
1 TTCT
3176144 TTGTTAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.15, C:0.18, G:0.11, T:0.56
Consensus pattern (28 bp):
TTCTCTTATACCTATTCATGTATGGTTT
Found at i:3187988 original size:33 final size:33
Alignment explanation
Indices: 3187946--3188008 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
3187936 GAAAGAAAAT
*
3187946 TAATCTTCTTCCCTCAATTGTATTAACAAGTAA
1 TAATCTTCTTCCCTCAATTATATTAACAAGTAA
3187979 TAATCTTCTTCCCTCAATTATATTAACAAG
1 TAATCTTCTTCCCTCAATTATATTAACAAG
3188009 ACCGCATGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (33 bp):
TAATCTTCTTCCCTCAATTATATTAACAAGTAA
Found at i:3191917 original size:74 final size:74
Alignment explanation
Indices: 3191796--3191942 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
3191786 GGAAAAGACT
3191796 AAAGGAAAGAGAAAGGTAAAAGAGGGAAGGTGAAGAAAATGGAGAGCAAACTTAAACTGATTCCA
1 AAAGGAAAGAGAAAGGTAAAAGAGGGAAGGTGAAGAAAATGGAGAGCAAACTTAAACTGATTCCA
3191861 AACCGGCCA
66 AACCGGCCA
3191870 AAAGGAAAGAGAAAGGTAAAAGAGGGAAGGTGAAGAAAATGGAGAGCAAACTTAAACTGATTCCA
1 AAAGGAAAGAGAAAGGTAAAAGAGGGAAGGTGAAGAAAATGGAGAGCAAACTTAAACTGATTCCA
3191935 AACCGGCC
66 AACCGGCC
3191943 CTTATCACTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.48, C:0.12, G:0.29, T:0.11
Consensus pattern (74 bp):
AAAGGAAAGAGAAAGGTAAAAGAGGGAAGGTGAAGAAAATGGAGAGCAAACTTAAACTGATTCCA
AACCGGCCA
Found at i:3201257 original size:29 final size:29
Alignment explanation
Indices: 3201209--3201288 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
3201199 AAAAGGTAAT
*
3201209 AGAAAAGAGGTGTACAAGAATAAGTACAAG
1 AGAAAA-AGCTGTACAAGAATAAGTACAAG
* * *
3201239 AGAAGAAGCTGTACGAGAATAGGTACAAG
1 AGAAAAAGCTGTACAAGAATAAGTACAAG
*
3201268 AGAAAAAGCTGTACATGAATA
1 AGAAAAAGCTGTACAAGAATA
3201289 GGTATATGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 38 0.88
30 5 0.12
ACGTcount: A:0.50, C:0.09, G:0.26, T:0.15
Consensus pattern (29 bp):
AGAAAAAGCTGTACAAGAATAAGTACAAG
Found at i:3201546 original size:35 final size:35
Alignment explanation
Indices: 3201507--3201586 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
3201497 CTACTTGTAT
* *
3201507 TAGTTGTTC-CTTATAGAGTAGTACTTTACTTATTC
1 TAGTTGTTCTCTTATA-AGTAATACTTCACTTATTC
* * *
3201542 TAGTTGTTCTGTTTTAAGTAATACTTCACTTGTTC
1 TAGTTGTTCTCTTATAAGTAATACTTCACTTATTC
3201577 TAGTTGTTCT
1 TAGTTGTTCT
3201587 GTGTGAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (35 bp):
TAGTTGTTCTCTTATAAGTAATACTTCACTTATTC
Found at i:3201605 original size:35 final size:35
Alignment explanation
Indices: 3201523--3201646 Score: 126
Period size: 35 Copynumber: 3.5 Consensus size: 35
3201513 TTCCTTATAG
* * *
3201523 AGTAGTACTTT-ACTTATTCTAGTTGTTCTGTTTTA
1 AGTAGTA-TTTCACTTGTTCTAGTTGTTCTGTGTGA
* *
3201558 AGTAATACTTCACTTGTTCTAGTTGTTCTGTGTGA
1 AGTAGTATTTCACTTGTTCTAGTTGTTCTGTGTGA
* * * *
3201593 ATTAGTGTTTCACTTGTT-TAAGTTATTCTGCGTGA
1 AGTAGTATTTCACTTGTTCT-AGTTGTTCTGTGTGA
*
3201628 AGTAGCATTTCACTTGTTC
1 AGTAGTATTTCACTTGTTC
3201647 AGGTTATTCT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
34 3 0.04
35 69 0.96
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (35 bp):
AGTAGTATTTCACTTGTTCTAGTTGTTCTGTGTGA
Found at i:3201653 original size:35 final size:34
Alignment explanation
Indices: 3201566--3201656 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 34
3201556 TAAGTAATAC
* * * **
3201566 TTCACTTGTTCTAGTTGTTCTGTGTGAATTAGTGT
1 TTCACTTGTTC-AGTTATTCTGCGTGAAGTAGCAT
*
3201601 TTCACTTGTTTAAGTTATTCTGCGTGAAGTAGCAT
1 TTCACTTG-TTCAGTTATTCTGCGTGAAGTAGCAT
3201636 TTCACTTGTTCAGGTTATTCT
1 TTCACTTGTTCA-GTTATTCT
3201657 CTGTACAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
34 3 0.06
35 42 0.89
36 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (34 bp):
TTCACTTGTTCAGTTATTCTGCGTGAAGTAGCAT
Found at i:3203762 original size:30 final size:29
Alignment explanation
Indices: 3203686--3203790 Score: 97
Period size: 30 Copynumber: 3.6 Consensus size: 29
3203676 TAAGAAAATT
* * *
3203686 TAAATAAGTCTTTATATTTTTATTATG-T
1 TAAATAAGTCTTTATACTTTTATTTTGAC
*
3203714 TCAATCAAG-CTCTTATACTTTTATTTTGAAC
1 TAAAT-AAGTCT-TTATACTTTTATTTTG-AC
*
3203745 TAAATAAGTCTTTATACTTTTATTTTGAG
1 TAAATAAGTCTTTATACTTTTATTTTGAC
**
3203774 TCAAATAAACCTTTATA
1 T-AAATAAGTCTTTATA
3203791 ACTAATAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
28 6 0.10
29 19 0.30
30 32 0.51
31 6 0.10
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (29 bp):
TAAATAAGTCTTTATACTTTTATTTTGAC
Found at i:3204653 original size:20 final size:20
Alignment explanation
Indices: 3204624--3204664 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3204614 AAAATATGAC
*
3204624 TTTAATATTACTTGT-TTCTT
1 TTTAAAATTAC-TGTCTTCTT
3204644 TTTAAAATTACTGTCTTCTT
1 TTTAAAATTACTGTCTTCTT
3204664 T
1 T
3204665 GACTTCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAAATTACTGTCTTCTT
Found at i:3212305 original size:21 final size:21
Alignment explanation
Indices: 3212255--3212306 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
3212245 TCGTTATAGT
*
3212255 GGTTTAGGGTTGAATGTTGAC
1 GGTTTAGGGTTGAATGTTGAA
* * *
3212276 TGTTGAGGGTT-TATGGTTGAA
1 GGTTTAGGGTTGAAT-GTTGAA
3212297 GGTTTAGGGT
1 GGTTTAGGGT
3212307 ATAAGTGATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (21 bp):
GGTTTAGGGTTGAATGTTGAA
Found at i:3214978 original size:36 final size:32
Alignment explanation
Indices: 3214924--3215009 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
3214914 AAAGAAATTA
* *
3214924 AAAT-AAAATATATAATATAAAAAATTATATTAAAG
1 AAATGAAAATA-A-AATATATAAAA-TATAAT-AAG
*
3214959 AAATGAAAATAAAATATATAAGATATAATAAG
1 AAATGAAAATAAAATATATAAAATATAATAAG
3214991 AAATGAAAATAAAATATAT
1 AAATGAAAATAAAATATAT
3215010 GAGATTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
32 22 0.47
33 5 0.11
34 9 0.19
35 5 0.11
36 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (32 bp):
AAATGAAAATAAAATATATAAAATATAATAAG
Found at i:3222093 original size:27 final size:27
Alignment explanation
Indices: 3222049--3222114 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
3222039 TCGAGATATT
* ***
3222049 ATTTAATCGATAAGTTAATAATTTATTA
1 ATTT-ATCAATAAGTTAATAAAAAATTA
3222077 ATTTATACAATAA-TTAATAAAAAATTA
1 ATTTAT-CAATAAGTTAATAAAAAATTA
3222104 ATTTATCAATA
1 ATTTATCAATA
3222115 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 5 0.15
27 19 0.58
28 9 0.27
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (27 bp):
ATTTATCAATAAGTTAATAAAAAATTA
Found at i:3222693 original size:16 final size:17
Alignment explanation
Indices: 3222649--3222694 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3222639 ACCAGTCAAA
3222649 AATATT-ATTTAATCATG
1 AATATTAATTT-ATCATG
* *
3222666 ATTATAAATTTATC-TG
1 AATATTAATTTATCATG
3222682 AATATTAATTTAT
1 AATATTAATTTAT
3222695 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
AATATTAATTTATCATG
Found at i:3232676 original size:34 final size:34
Alignment explanation
Indices: 3232624--3232737 Score: 106
Period size: 34 Copynumber: 3.4 Consensus size: 34
3232614 CGTTATAACG
** *
3232624 TTTAAAAGAAAATCAGTCAGTCTTATCTTAGCACA
1 TTTAAAAGAAAAAAAGTCAGT-TTATCTTAACACA
* * *
3232659 TTTAAAA-AAAAAAAGTCAGTTAATCTTATCATA
1 TTTAAAAGAAAAAAAGTCAGTTTATCTTAACACA
* * * *
3232692 TTTAAAATAAAAGTAA-TCAGTTTATCTCAACACC
1 TTTAAAAGAAAA-AAAGTCAGTTTATCTTAACACA
3232726 TTTAAAAGAAAA
1 TTTAAAAGAAAA
3232738 GGTAGAAAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
33 17 0.26
34 39 0.60
35 9 0.14
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (34 bp):
TTTAAAAGAAAAAAAGTCAGTTTATCTTAACACA
Found at i:3232695 original size:33 final size:34
Alignment explanation
Indices: 3232624--3232703 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
3232614 CGTTATAACG
** *
3232624 TTTAAAAGAAAATCAGTCAGTCTTATCTTAGCACA
1 TTTAAAA-AAAAAAAGTCAGTCTAATCTTAGCACA
* *
3232659 TTTAAAAAAAAAAAGTCAGT-TAATCTTATCATA
1 TTTAAAAAAAAAAAGTCAGTCTAATCTTAGCACA
*
3232692 TTTAAAATAAAA
1 TTTAAAAAAAAA
3232704 GTAATCAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 21 0.54
34 11 0.28
35 7 0.18
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (34 bp):
TTTAAAAAAAAAAAGTCAGTCTAATCTTAGCACA
Found at i:3235538 original size:27 final size:27
Alignment explanation
Indices: 3235508--3235600 Score: 75
Period size: 27 Copynumber: 3.6 Consensus size: 27
3235498 TCACAACATA
*
3235508 TAATTTTGATGTTATGTACTACTCCTT
1 TAATTTTGATATTATGTACTACTCCTT
* * * ****
3235535 TAATTTGGACATTATCTA--AC-AAAA
1 TAATTTTGATATTATGTACTACTCCTT
3235559 TAATTTTGATATTATGTACTACTCCTT
1 TAATTTTGATATTATGTACTACTCCTT
* *
3235586 TAATTTGGACATTAT
1 TAATTTTGATATTAT
3235601 CTAACAAAAT
Statistics
Matches: 46, Mismatches: 17, Indels: 6
0.67 0.25 0.09
Matches are distributed among these distances:
24 15 0.33
25 2 0.04
26 2 0.04
27 27 0.59
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (27 bp):
TAATTTTGATATTATGTACTACTCCTT
Found at i:3235568 original size:51 final size:51
Alignment explanation
Indices: 3235507--3235621 Score: 221
Period size: 51 Copynumber: 2.3 Consensus size: 51
3235497 ATCACAACAT
*
3235507 ATAATTTTGATGTTATGTACTACTCCTTTAATTTGGACATTATCTAACAAA
1 ATAATTTTGATATTATGTACTACTCCTTTAATTTGGACATTATCTAACAAA
3235558 ATAATTTTGATATTATGTACTACTCCTTTAATTTGGACATTATCTAACAAA
1 ATAATTTTGATATTATGTACTACTCCTTTAATTTGGACATTATCTAACAAA
3235609 ATAATTTTGATAT
1 ATAATTTTGATAT
3235622 GCATGCGACC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (51 bp):
ATAATTTTGATATTATGTACTACTCCTTTAATTTGGACATTATCTAACAAA
Found at i:3235572 original size:24 final size:24
Alignment explanation
Indices: 3235535--3235615 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
3235525 ACTACTCCTT
3235535 TAATTTGGACATTATCTAACAAAA
1 TAATTTGGACATTATCTAACAAAA
* * * ****
3235559 TAATTTTGATATTATGTACTACTCCTT
1 TAATTTGGACATTATCTA--AC-AAAA
3235586 TAATTTGGACATTATCTAACAAAA
1 TAATTTGGACATTATCTAACAAAA
3235610 TAATTT
1 TAATTT
3235616 TGATATGCAT
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
24 21 0.52
25 2 0.05
26 2 0.05
27 15 0.38
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (24 bp):
TAATTTGGACATTATCTAACAAAA
Found at i:3244436 original size:17 final size:16
Alignment explanation
Indices: 3244408--3244440 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3244398 CATACAATGA
3244408 TTAAATATATAAATAG
1 TTAAATATATAAATAG
3244424 TTAAATAATATAAATAG
1 TTAAAT-ATATAAATAG
3244441 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:3248627 original size:18 final size:16
Alignment explanation
Indices: 3248604--3248638 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
3248594 AAAAAGTTAT
3248604 ATTAAAAAATTAAAAAAA
1 ATTAAAAAA--AAAAAAA
3248622 ATTAAAAAAAAAAAAA
1 ATTAAAAAAAAAAAAA
3248638 A
1 A
3248639 GGGGGATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
ATTAAAAAAAAAAAAA
Found at i:3248633 original size:11 final size:10
Alignment explanation
Indices: 3248607--3248632 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3248597 AAGTTATATT
3248607 AAAAAATTAA
1 AAAAAATTAA
3248617 AAAAAATTAA
1 AAAAAATTAA
3248627 AAAAAA
1 AAAAAA
3248633 AAAAAAGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:3249675 original size:8 final size:8
Alignment explanation
Indices: 3249662--3249688 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3249652 TATTTTTTAA
3249662 AAAAAAAT
1 AAAAAAAT
3249670 AAAAAAAT
1 AAAAAAAT
3249678 AAAAAAAT
1 AAAAAAAT
3249686 AAA
1 AAA
3249689 TAANNNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3264226 original size:20 final size:20
Alignment explanation
Indices: 3264196--3264240 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3264186 TTATAACTTT
**
3264196 ACAAA-AGATAATGTTAAAA
1 ACAAATAGATAAAATTAAAA
3264215 ACAAATAGATAAAATTAAAA
1 ACAAATAGATAAAATTAAAA
3264235 A-AAATA
1 ACAAATA
3264241 AATAGCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
ACAAATAGATAAAATTAAAA
Found at i:3266533 original size:21 final size:21
Alignment explanation
Indices: 3266507--3266548 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3266497 TAACGTAAAA
3266507 GGGTTCACTAAGAACTCAGAT
1 GGGTTCACTAAGAACTCAGAT
3266528 GGGTTCACTAAGAACTCAGAT
1 GGGTTCACTAAGAACTCAGAT
3266549 TTTTATGACT
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:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGTTCACTAAGAACTCAGAT
Found at i:3306862 original size:13 final size:12
Alignment explanation
Indices: 3306838--3306921 Score: 50
Period size: 13 Copynumber: 7.0 Consensus size: 12
3306828 GCCATCCCGA
3306838 TTTTTT-TTTAT
1 TTTTTTATTTAT
3306849 TTTTTTATTCTAT
1 TTTTTTATT-TAT
*
3306862 TTATTTATTTA-
1 TTTTTTATTTAT
* *
3306873 -ATTTAATTTA-
1 TTTTTTATTTAT
* *
3306883 ATTTATATTTAT
1 TTTTTTATTTAT
3306895 TTTTATTATTATTAT
1 TTTT-TTA-T-TTAT
*
3306910 TTTTTAATTTAT
1 TTTTTTATTTAT
3306922 GTGTCTACAG
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 7 0.12
11 13 0.23
12 11 0.20
13 14 0.25
14 3 0.05
15 8 0.14
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:3306903 original size:15 final size:15
Alignment explanation
Indices: 3306850--3306913 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
3306840 TTTTTTTATT
*
3306850 TTTTTATTCTATTTA
1 TTTTTATTATATTTA
*
3306865 TTTAT-TTA-ATTTA
1 TTTTTATTATATTTA
* *
3306878 ATTTAATTTATATTTA
1 TTTTTA-TTATATTTA
3306894 TTTTTATTAT-TATTA
1 TTTTTATTATAT-TTA
3306909 TTTTT
1 TTTTT
3306914 TAATTTATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 7 0.18
14 3 0.08
15 19 0.50
16 9 0.24
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTATATTTA
Found at i:3329026 original size:15 final size:15
Alignment explanation
Indices: 3328996--3329025 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3328986 ATCGTCCTCC
3328996 TCTTTCCTTTCTTTT
1 TCTTTCCTTTCTTTT
3329011 TCTTT-CTTTCTTTT
1 TCTTTCCTTTCTTTT
3329025 T
1 T
3329026 TTTTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTTTCCTTTCTTTT
Found at i:3333036 original size:11 final size:10
Alignment explanation
Indices: 3333020--3333053 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3333010 CCTTTAGATA
3333020 TTTTTTTTAT
1 TTTTTTTTAT
3333030 TTTTTTTTAT
1 TTTTTTTTAT
* *
3333040 TTTCTTTTCT
1 TTTTTTTTAT
3333050 TTTT
1 TTTT
3333054 AGTGAATTGA
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:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:3337965 original size:22 final size:22
Alignment explanation
Indices: 3337937--3337978 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3337927 TAAAAGACCC
3337937 TTATGTCTGCTATGCTTTGCCA
1 TTATGTCTGCTATGCTTTGCCA
3337959 TTATGTCTGCTATGCTTTGC
1 TTATGTCTGCTATGCTTTGC
3337979 GTTAACCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (22 bp):
TTATGTCTGCTATGCTTTGCCA
Found at i:3338686 original size:28 final size:28
Alignment explanation
Indices: 3338654--3338709 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3338644 TTCAAGACAA
3338654 GCATGATAAGATATATGGACAAAGTTTT
1 GCATGATAAGATATATGGACAAAGTTTT
3338682 GCATGATAAGATATATGGACAAAGTTTT
1 GCATGATAAGATATATGGACAAAGTTTT
3338710 AACATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (28 bp):
GCATGATAAGATATATGGACAAAGTTTT
Found at i:3338718 original size:28 final size:28
Alignment explanation
Indices: 3338655--3338718 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
3338645 TCAAGACAAG
*
3338655 CATGATAAGATATATGGACAAAGTTTTG
1 CATGATAAGATATATGGACAAAGTTTTA
3338683 CATGATAAGATATATGGACAAAGTTTTAA
1 CATGATAAGATATATGGACAAAGTTTT-A
3338712 CAT-ATAA
1 CATGATAA
3338719 AATGGCTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (28 bp):
CATGATAAGATATATGGACAAAGTTTTA
Found at i:3345553 original size:11 final size:11
Alignment explanation
Indices: 3345537--3345579 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3345527 GCATATATGC
3345537 ATATATATAGT
1 ATATATATAGT
3345548 ATATATATAGT
1 ATATATATAGT
*
3345559 TTCAATATATA-T
1 AT--ATATATAGT
3345571 ATATATATA
1 ATATATATA
3345580 TTCCCTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.25
11 12 0.43
12 2 0.07
13 7 0.25
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (11 bp):
ATATATATAGT
Found at i:3345662 original size:10 final size:10
Alignment explanation
Indices: 3345647--3345680 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3345637 GATAAAAACA
*
3345647 ATATATATAT
1 ATATATATTT
3345657 ATATATATTT
1 ATATATATTT
*
3345667 ATTTATATTT
1 ATATATATTT
3345677 ATAT
1 ATAT
3345681 TTCCAGTTCC
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATATTT
Found at i:3345793 original size:2 final size:2
Alignment explanation
Indices: 3345786--3345836 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
3345776 GAATGAATGA
3345786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3345827 AT TT AT AT AT
1 AT AT AT AT AT
3345837 TTAGACAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3349098 original size:21 final size:20
Alignment explanation
Indices: 3349064--3349104 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3349054 GTTTTTAATT
3349064 TTAATTTTTCAATATATTTTA
1 TTAATTTTTCAATAT-TTTTA
3349085 TTAATATTTT-AATATTTTTA
1 TTAAT-TTTTCAATATTTTTA
3349105 AATATACGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATTTTTCAATATTTTTA
Found at i:3349973 original size:2 final size:2
Alignment explanation
Indices: 3349952--3350012 Score: 95
Period size: 2 Copynumber: 30.0 Consensus size: 2
3349942 AATACCAAAT
* *
3349952 TA TA CTA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3349995 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3350013 AAGAAGCCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3360965 original size:3 final size:3
Alignment explanation
Indices: 3360959--3360983 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3360949 AGTGATGATG
3360959 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3360984 AAAGTCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3370164 original size:2 final size:2
Alignment explanation
Indices: 3370159--3370186 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3370149 AAAAGAAAGT
3370159 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3370187 ATAAGAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3371261 original size:2 final size:2
Alignment explanation
Indices: 3371254--3371282 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3371244 GTTAGCTATC
3371254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3371283 TCAATTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3386975 original size:27 final size:27
Alignment explanation
Indices: 3386934--3386986 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3386924 ACTATGTCAT
* * * *
3386934 ATAATGAAAAGTTACGTGAATTTAAAC
1 ATAATAAAAAATTACATGAACTTAAAC
3386961 ATAATAAAAAATTACATGAACTTAAA
1 ATAATAAAAAATTACATGAACTTAAA
3386987 AATTATGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (27 bp):
ATAATAAAAAATTACATGAACTTAAAC
Found at i:3388846 original size:20 final size:20
Alignment explanation
Indices: 3388821--3388860 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3388811 TGTAATAGTG
3388821 CTTCAAATCGAAACAGCTGA
1 CTTCAAATCGAAACAGCTGA
*
3388841 CTTCAAATTGAAACAGCTGA
1 CTTCAAATCGAAACAGCTGA
3388861 TTCTGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CTTCAAATCGAAACAGCTGA
Found at i:3392006 original size:13 final size:13
Alignment explanation
Indices: 3391988--3392013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3391978 CAACAACTTT
3391988 AAAATACTAGAAA
1 AAAATACTAGAAA
3392001 AAAATACTAGAAA
1 AAAATACTAGAAA
3392014 TGAGTACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAATACTAGAAA
Found at i:3393131 original size:7 final size:7
Alignment explanation
Indices: 3393115--3393152 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
3393105 TTGGAAAGAA
3393115 GCAT-AT
1 GCATAAT
3393121 GCATAAT
1 GCATAAT
3393128 GCATAAT
1 GCATAAT
3393135 GCATAAT
1 GCATAAT
3393142 GCATAAT
1 GCATAAT
3393149 GCAT
1 GCAT
3393153 GCAAAATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (7 bp):
GCATAAT
Found at i:3398360 original size:44 final size:45
Alignment explanation
Indices: 3398296--3398408 Score: 147
Period size: 44 Copynumber: 2.5 Consensus size: 45
3398286 GGATCTCCTA
* * *
3398296 TATTAAGCTAACTAAAGTTATATAACGAGACTTATGTTAAAATTG
1 TATTAATCTAACTAAAGTTATATAACGAAACTTATATTAAAATTG
* * *
3398341 TATTAATCTAA-TAAAGTTATATAATGAAAGTTATATTAAAGTTG
1 TATTAATCTAACTAAAGTTATATAACGAAACTTATATTAAAATTG
* *
3398385 CATTAATCTAATTAAAGTTATATA
1 TATTAATCTAACTAAAGTTATATA
3398409 TTTTCTTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 38 0.63
45 22 0.37
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (45 bp):
TATTAATCTAACTAAAGTTATATAACGAAACTTATATTAAAATTG
Found at i:3422672 original size:22 final size:22
Alignment explanation
Indices: 3422640--3422695 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
3422630 TAATCACCGT
* *
3422640 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCACTAC
* *
3422662 GTGA-TTGGTTTTAGGCACTAC
1 GTGACTAGTTTTTAGGCACTAC
3422683 GTGACTAGTTTTT
1 GTGACTAGTTTTT
3422696 GTACATTGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCACTAC
Found at i:3422846 original size:26 final size:24
Alignment explanation
Indices: 3422730--3422950 Score: 176
Period size: 23 Copynumber: 9.4 Consensus size: 24
3422720 GCAACGCCTA
* *
3422730 AGTCACACAATGCCTTA-CGAACT
1 AGTCACGCAATGCCTTATCAAACT
* * *
3422753 AGTCACACAATGCCTTA-CTAACA
1 AGTCACGCAATGCCTTATCAAACT
* * *
3422776 AGTCACGCAATACCTTA-CTAACA
1 AGTCACGCAATGCCTTATCAAACT
3422799 AGTCACGCAATGCC-TATC-AACT
1 AGTCACGCAATGCCTTATCAAACT
3422821 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATC--AAACT
* *
3422847 AGTCACGCAATGCCTTATAAAAAATT
1 AGTCACGCAATGCCTTAT--CAAACT
* *
3422873 AGTCACGTAATG-C---TCAAAAT
1 AGTCACGCAATGCCTTATCAAACT
*
3422893 CAGTCACGCAATGCC-TAT-TAACT
1 -AGTCACGCAATGCCTTATCAAACT
*
3422916 AGTCACGCAATGCCTTATCAGAAAT
1 AGTCACGCAATGCCTTATCA-AACT
3422941 CAGTCACGCA
1 -AGTCACGCA
3422951 GTACTTAAAA
Statistics
Matches: 167, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
20 4 0.02
21 11 0.07
22 35 0.21
23 66 0.40
24 1 0.01
25 4 0.02
26 46 0.28
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (24 bp):
AGTCACGCAATGCCTTATCAAACT
Found at i:3422897 original size:21 final size:21
Alignment explanation
Indices: 3422867--3422906 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3422857 TGCCTTATAA
* *
3422867 AAAATTAGTCACGTAATGCTC
1 AAAATCAGTCACGCAATGCTC
3422888 AAAATCAGTCACGCAATGC
1 AAAATCAGTCACGCAATGC
3422907 CTATTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
AAAATCAGTCACGCAATGCTC
Found at i:3423596 original size:74 final size:74
Alignment explanation
Indices: 3423515--3423670 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
3423505 CATTGCTAAC
* * *
3423515 ATTGCTAACGTTTGTACCAAACTTGAAATTATGGAGAAAAAAATAATTAATAG-TCAATGAGTGA
1 ATTGCTAACATTTGTACAAAACTTGAAATTAT-GAGAAAAAAATAATTAATAGCT-AATGAGTCA
3423579 ATGCTAA-AAT
64 ATGCTAACAAT
* *
3423589 ATTGCTAACATTTGTACAAAACTTTAAATTATGAGAAAAAAATAATTAATAGCTAGTGAGTCAAT
1 ATTGCTAACATTTGTACAAAACTTGAAATTATGAGAAAAAAATAATTAATAGCTAATGAGTCAAT
3423654 GCTAACAAT
66 GCTAACAAT
3423663 ATTGCTAA
1 ATTGCTAA
3423671 TAAATGTACA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
73 34 0.45
74 41 0.55
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (74 bp):
ATTGCTAACATTTGTACAAAACTTGAAATTATGAGAAAAAAATAATTAATAGCTAATGAGTCAAT
GCTAACAAT
Found at i:3462556 original size:42 final size:42
Alignment explanation
Indices: 3462496--3462587 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
3462486 AGTCGTCGCA
*
3462496 CAAATTGTACATTCACTTTCCTTGAAGTTGTTTCACAGTAATG
1 CAAA-TGTAAATTCACTTTCCTTGAAGTTGTTTCACAGTAATG
*
3462539 CAAATGTAAATTCACTTTCCTTGAAGTTGTTTCACGGTAATG
1 CAAATGTAAATTCACTTTCCTTGAAGTTGTTTCACAGTAATG
3462581 CAAATGT
1 CAAATGT
3462588 GAATAGAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (42 bp):
CAAATGTAAATTCACTTTCCTTGAAGTTGTTTCACAGTAATG
Found at i:3463470 original size:24 final size:24
Alignment explanation
Indices: 3463443--3463492 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3463433 TATATCATTC
3463443 GTGATATAATCTGATGAATAACAG
1 GTGATATAATCTGATGAATAACAG
3463467 GTGATATAATCTGATGAATAACAG
1 GTGATATAATCTGATGAATAACAG
3463491 GT
1 GT
3463493 CATTGCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (24 bp):
GTGATATAATCTGATGAATAACAG
Found at i:3486171 original size:2 final size:2
Alignment explanation
Indices: 3486164--3486195 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3486154 TTTAAACATA
3486164 AT AT AT AT AT -T AT AT AT A- 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
3486196 TAGAGTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3486179 original size:9 final size:8
Alignment explanation
Indices: 3486164--3486195 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
3486154 TTTAAACATA
3486164 ATATATAT
1 ATATATAT
3486172 AT-TATAT
1 ATATATAT
3486179 ATA-ATAT
1 ATATATAT
3486186 ATATATAT
1 ATATATAT
3486194 AT
1 AT
3486196 TAGAGTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATAT
Found at i:3486184 original size:18 final size:17
Alignment explanation
Indices: 3486161--3486195 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
3486151 CCATTTAAAC
3486161 ATAATATATATATTATAT
1 ATAATATATATA-TATAT
3486179 ATAATATATATATATAT
1 ATAATATATATATATAT
3486196 TAGAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATATATATATATAT
Found at i:3489423 original size:34 final size:34
Alignment explanation
Indices: 3489371--3489441 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
3489361 CGACCCAAGT
3489371 CCAATCACCGGCCCAGCAACTTTTCGAACCTAAA
1 CCAATCACCGGCCCAGCAACTTTTCGAACCTAAA
* *
3489405 CCAATCACTGGCCTAGCAACTTTTCGAACCTAAA
1 CCAATCACCGGCCCAGCAACTTTTCGAACCTAAA
3489439 CCA
1 CCA
3489442 CATGGCCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.20
Consensus pattern (34 bp):
CCAATCACCGGCCCAGCAACTTTTCGAACCTAAA
Found at i:3495020 original size:74 final size:74
Alignment explanation
Indices: 3494942--3495083 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 74
3494932 ATAAATGGAA
* * * *
3494942 TAAATCTTATTAATAATTATAATAAAAAATATTTCAATGATCATTATTTGATTAATACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
3495007 TAATAGTTT
66 TAATAGTTT
* *
3495016 TAAATCTTACTAATAATTATAATTAAAAATATTTCAATGATCGTCATTTAATGAATACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
3495081 TAA
66 TAA
3495084 GCATAGATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACATTTA
TAATAGTTT
Found at i:3495229 original size:54 final size:53
Alignment explanation
Indices: 3495153--3495264 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 53
3495143 AAAAGTGATA
3495153 AAATGGAAATTTTTTTGAAAATTAGAGTTTATTTTCATCACAGATATGTGGTT
1 AAATGGAAATTTTTTTGAAAATTAGAGTTTATTTTCATCACAGATATGTGGTT
** *
3495206 AAATGNGAAATTTTTTTTTAAATTAGAGTTTATTTTCATTACAGATATGTGGTT
1 AAATG-GAAATTTTTTTGAAAATTAGAGTTTATTTTCATCACAGATATGTGGTT
3495260 AAATG
1 AAATG
3495265 CTTTGAGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.09
54 50 0.91
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.45
Consensus pattern (53 bp):
AAATGGAAATTTTTTTGAAAATTAGAGTTTATTTTCATCACAGATATGTGGTT
Found at i:3500666 original size:21 final size:21
Alignment explanation
Indices: 3500624--3500667 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3500614 TCGAATATTT
*
3500624 AGATCATTCACTTTTCTTTTA
1 AGATCATTCACTTTTCTCTTA
3500645 AGATCATTCACATTTTC-CTTA
1 AGATCATTCAC-TTTTCTCTTA
3500666 AG
1 AG
3500668 TTTCCGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (21 bp):
AGATCATTCACTTTTCTCTTA
Found at i:3506964 original size:11 final size:11
Alignment explanation
Indices: 3506948--3506972 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3506938 GCAACAAGCC
3506948 CTTCCTATAGG
1 CTTCCTATAGG
3506959 CTTCCTATAGG
1 CTTCCTATAGG
3506970 CTT
1 CTT
3506973 GCAAGTGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (11 bp):
CTTCCTATAGG
Found at i:3510231 original size:2 final size:2
Alignment explanation
Indices: 3510214--3510251 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3510204 TGTGAATCAA
* *
3510214 AT AT AT AA AT AA 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 AT AT
3510252 TACCCACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3512455 original size:3 final size:3
Alignment explanation
Indices: 3512449--3512477 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3512439 AGTAGTAGTA
3512449 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3512478 GAGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3512717 original size:33 final size:32
Alignment explanation
Indices: 3512680--3512745 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3512670 TTATGTTTAT
*
3512680 ATTAAAAAAGAGAAATTATTTAGCAAATGAGAA
1 ATTAAAAAAGA-AAAATATTTAGCAAATGAGAA
* * *
3512713 ATTAAGAGATAAAAATATTTAGCAAATGAGAA
1 ATTAAAAAAGAAAAATATTTAGCAAATGAGAA
3512745 A
1 A
3512746 GAGATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.58, C:0.03, G:0.15, T:0.24
Consensus pattern (32 bp):
ATTAAAAAAGAAAAATATTTAGCAAATGAGAA
Found at i:3512749 original size:28 final size:30
Alignment explanation
Indices: 3512696--3512757 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 30
3512686 AAAGAGAAAT
3512696 TATTTAGCAAATGAGAAATTAAGAGATAAAAA
1 TATTTAGCAAATGAG-AA-TAAGAGATAAAAA
*
3512728 TATTTAGCAAATGAG-A-AAGAGATGAAAA
1 TATTTAGCAAATGAGAATAAGAGATAAAAA
3512756 TA
1 TA
3512758 AACTCACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 13 0.45
30 1 0.03
32 15 0.52
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (30 bp):
TATTTAGCAAATGAGAATAAGAGATAAAAA
Found at i:3520455 original size:85 final size:84
Alignment explanation
Indices: 3520316--3520544 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 84
3520306 ATCGTTAAAA
* * *
3520316 TTAAATTAT-GGGAAAAAA-AA-TAATAGT-AGGTGAGACAATGCTGTAAGTCATTGCTAACATT
1 TTAAATTATGGGGAAAAAATAATTAATAGTCA-ATGAGTCAATGCTGCAAGTCATTGCTAACATT
* * *
3520377 GCTAACGTTTGCACCAAACT
65 CCGAACGTTTGAACCAAACT
*
3520397 TTAAATTATGGGGAAAAAATTAATTAATAGTCAATGAGTCAATGCTGCAAGTCGTTGCTAACATT
1 TTAAATTATGGGGAAAAAA-TAATTAATAGTCAATGAGTCAATGCTGCAAGTCATTGCTAACATT
3520462 CCGAACGTTTGAACCAAACT
65 CCGAACGTTTGAACCAAACT
* *
3520482 TTAAATTATGGGGAAAAAAATAATTAATAGTCAATGAGTCAATGCT-AAAAT-ATTGCTAACATT
1 TTAAATTATGGGG-AAAAAATAATTAATAGTCAATGAGTCAATGCTGCAAGTCATTGCTAACATT
3520545 TGTACAAAAC
Statistics
Matches: 132, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
81 9 0.07
82 9 0.07
83 11 0.08
84 5 0.04
85 91 0.69
86 7 0.05
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (84 bp):
TTAAATTATGGGGAAAAAATAATTAATAGTCAATGAGTCAATGCTGCAAGTCATTGCTAACATTC
CGAACGTTTGAACCAAACT
Found at i:3520593 original size:73 final size:75
Alignment explanation
Indices: 3520477--3520626 Score: 243
Period size: 74 Copynumber: 2.0 Consensus size: 75
3520467 CGTTTGAACC
*
3520477 AAACTTTAAATTATGGGGAAAAAAATAATTAATAGTCAATGAGTCAATGCTAA-AATATTGCTAA
1 AAACTTTAAATTATGGAGAAAAAAATAATTAATAGTCAATGAGTCAATGCTAACAATATTGCTAA
*
3520541 CATTTGTACA
66 CATATGTACA
*
3520551 AAACTTTAAATTAT-GAGAAAAAAATAATTAATAGAT-AGTGAGTCAATGCTAACAATATTGCTA
1 AAACTTTAAATTATGGAGAAAAAAATAATTAATAG-TCAATGAGTCAATGCTAACAATATTGCTA
3520614 ACATATGTACA
65 ACATATGTACA
3520625 AA
1 AA
3520627 TCTTATATAA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
73 34 0.48
74 37 0.52
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (75 bp):
AAACTTTAAATTATGGAGAAAAAAATAATTAATAGTCAATGAGTCAATGCTAACAATATTGCTAA
CATATGTACA
Found at i:3528623 original size:250 final size:249
Alignment explanation
Indices: 3528177--3528671 Score: 972
Period size: 250 Copynumber: 2.0 Consensus size: 249
3528167 TACAAACGTA
3528177 TCCTCTAGCATTAAGCATTGGAGATGACAAATCCTCCGTAATATTCCTACTGGTAGCTCTTTTAA
1 TCCTCTAGCATTAAGCATTGGAGATGACAAATCCTCCGTAATATTCCTACTGGTAGCTCTTTTAA
3528242 AGCCCATGACCTCATACGAAGATCTCTCAAGTTTTCTAACATCTCTATGCCATGAGGAACCTCTC
66 AGCCCATGACCTCATACGAAGATCTCTCAAGTTTTCTAACATCTCTATGCCATGAGGAACCTCTC
3528307 CAATTCCTGTACCCGAAAGGTCCAACTTTCTTAGTGATGTGAGCTCTACTAAGGAAGGCACATAT
131 CAATTCCTGTACCCGAAAGGTCCAACTTTCTTAGTGATGTGAGCTCTACTAAGGAAGGCACATAT
3528372 TTTAACTGGTTACAACAAAAGAGTATCAATGCATTGAGAGTTTTCAAGTTAGAG
196 TTTAACTGGTTACAACAAAAGAGTATCAATGCATTGAGAGTTTTCAAGTTAGAG
*
3528426 NTCCTGTAGCATTAAGCATTGGAGATGACAAATCCTCCGTAATATTCCTACTGGTAGCTCTTTTA
1 -TCCTCTAGCATTAAGCATTGGAGATGACAAATCCTCCGTAATATTCCTACTGGTAGCTCTTTTA
3528491 AAGCCCATGACCTCATACGAAGATCTCTCAAGTTTTCTAACATCTCTATGCCATGAGGAACCTCT
65 AAGCCCATGACCTCATACGAAGATCTCTCAAGTTTTCTAACATCTCTATGCCATGAGGAACCTCT
3528556 CCAATTCCTGTACCCGAAAGGTCCAACTTTCTTAGTGATGTGAGCTCTACTAAGGAAGGCACATA
130 CCAATTCCTGTACCCGAAAGGTCCAACTTTCTTAGTGATGTGAGCTCTACTAAGGAAGGCACATA
3528621 TTTTAACTGGTTACAACAAAAGAGTATCAATGCATTGAGAGTTTTCAAGTT
195 TTTTAACTGGTTACAACAAAAGAGTATCAATGCATTGAGAGTTTTCAAGTT
3528672 TGAGATCGAC
Statistics
Matches: 244, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 244 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (249 bp):
TCCTCTAGCATTAAGCATTGGAGATGACAAATCCTCCGTAATATTCCTACTGGTAGCTCTTTTAA
AGCCCATGACCTCATACGAAGATCTCTCAAGTTTTCTAACATCTCTATGCCATGAGGAACCTCTC
CAATTCCTGTACCCGAAAGGTCCAACTTTCTTAGTGATGTGAGCTCTACTAAGGAAGGCACATAT
TTTAACTGGTTACAACAAAAGAGTATCAATGCATTGAGAGTTTTCAAGTTAGAG
Found at i:3531856 original size:41 final size:42
Alignment explanation
Indices: 3531795--3531885 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
3531785 AGTCGTCGCA
* *
3531795 CAAATTGTACATTCACTTTCCTTGAAG-TGTTTCACAGTAATG
1 CAAA-TGTAAATTCACTTTCCTTGAAGTTGTTCCACAGTAATG
* *
3531837 CAAATGTAAATTCAGTTTCCTTGAAGTTGTTCCACGGTAATG
1 CAAATGTAAATTCACTTTCCTTGAAGTTGTTCCACAGTAATG
*
3531879 CACATGT
1 CAAATGT
3531886 GAATAGAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (42 bp):
CAAATGTAAATTCACTTTCCTTGAAGTTGTTCCACAGTAATG
Found at i:3550564 original size:16 final size:16
Alignment explanation
Indices: 3550545--3550579 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3550535 ATTCCACATA
3550545 CTCCAATTATTCCAAC
1 CTCCAATTATTCCAAC
3550561 CTCCAATTATTCCAAC
1 CTCCAATTATTCCAAC
3550577 CTC
1 CTC
3550580 ATCACCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (16 bp):
CTCCAATTATTCCAAC
Found at i:3564617 original size:61 final size:62
Alignment explanation
Indices: 3564516--3564643 Score: 195
Period size: 61 Copynumber: 2.1 Consensus size: 62
3564506 TTGTACAAAG
* * * *
3564516 CATTAAATTATGGGAAAAAAATAATTAATAGTCGGTGAGTCCATGCAGCAAGTCATCGCTAA
1 CATTGAATTATGGGAAAAAAATAATTAATAGTCAGTGAGTCAATGCAGCAACTCATCGCTAA
* *
3564578 CATTGAATTATGGGAAAAAAA-AATTAATAGTCAGTGAGTCAATGCTGCAACTCATTGCTAA
1 CATTGAATTATGGGAAAAAAATAATTAATAGTCAGTGAGTCAATGCAGCAACTCATCGCTAA
3564639 CATTG
1 CATTG
3564644 CTAACATTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 40 0.67
62 20 0.33
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (62 bp):
CATTGAATTATGGGAAAAAAATAATTAATAGTCAGTGAGTCAATGCAGCAACTCATCGCTAA
Found at i:3564665 original size:145 final size:146
Alignment explanation
Indices: 3564377--3564725 Score: 479
Period size: 145 Copynumber: 2.4 Consensus size: 146
3564367 AGATAATAAC
* * * * * *
3564377 TTATGAGAAAACAATGATTAATAGTTGGTTAGTCAATGCAGCACGTCATCGCTAACATTAAATTA
1 TTATGGGAAAAAAATAATTAATAGTCGGTAAGTCAATGCAGCAAGTCATCGCTAACATTAAATTA
* * *
3564442 CGGGAAAAAAATAATTAATAGTCAGTGATTAGATGCTGCAACTCATTGCTGATATTGCTAACATT
66 CGGGAAAAAAATAATTAATAGTCAGTGATCAGATGCTGCAACTCATTGCTAACATTGCTAACATT
*
3564507 TGTACAAAGCATTAAA
131 TGTACAAAACATTAAA
* * *
3564523 TTATGGGAAAAAAATAATTAATAGTCGGTGAGTCCATGCAGCAAGTCATCGCTAACATTGAATTA
1 TTATGGGAAAAAAATAATTAATAGTCGGTAAGTCAATGCAGCAAGTCATCGCTAACATTAAATTA
*
3564588 TGGGAAAAAAA-AATTAATAGTCAGTGAGTCA-ATGCTGCAACTCATTGCTAACATTGCTAACAT
66 CGGGAAAAAAATAATTAATAGTCAGTGA-TCAGATGCTGCAACTCATTGCTAACATTGCTAACAT
* *
3564651 TTGTCCAAAACATTAGA
130 TTGTACAAAACATTAAA
* * * *
3564668 TTACGGGAAAAAAATAATTAATAGTC-GTCAAGTCAATGCTGCAAATCATTGCTAACAT
1 TTATGGGAAAAAAATAATTAATAGTCGGT-AAGTCAATGCAGCAAGTCATCGCTAACAT
3564726 CAACTAATAG
Statistics
Matches: 180, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
144 2 0.01
145 109 0.61
146 69 0.38
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (146 bp):
TTATGGGAAAAAAATAATTAATAGTCGGTAAGTCAATGCAGCAAGTCATCGCTAACATTAAATTA
CGGGAAAAAAATAATTAATAGTCAGTGATCAGATGCTGCAACTCATTGCTAACATTGCTAACATT
TGTACAAAACATTAAA
Found at i:3564749 original size:44 final size:43
Alignment explanation
Indices: 3564698--3564892 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 43
3564688 ATAGTCGTCA
3564698 AGTCAATGCTGCAAATCATTGCTAACATCAACTAATAGTTAGTG
1 AGTCAATGCTGCAAATCATTGCTAACAT-AACTAATAGTTAGTG
* ** * *
3564742 AGTCAATGCTGCAAGTCATTGCTAACATTGCTAACA-TTTGT-
1 AGTCAATGCTGCAAATCATTGCTAACATAACTAATAGTTAGTG
** * * * ** * * *
3564783 A--CAAAACAT-TAAATTATGGAAAAAAATAATTAATAGTCA-TCG
1 AGTCAATGC-TGCAAATCATTG-CTAACATAACTAATAGTTAGT-G
*
3564825 AGTCAATGCTGCAAGTCATTGCTAACATCAACTAATAGTTAGTG
1 AGTCAATGCTGCAAATCATTGCTAACAT-AACTAATAGTTAGTG
3564869 AGTCAATGCT---AA-CATTGCTAACAT
1 AGTCAATGCTGCAAATCATTGCTAACAT
3564893 TTGTACAAAA
Statistics
Matches: 109, Mismatches: 32, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
39 10 0.09
40 22 0.20
41 3 0.03
42 5 0.05
43 10 0.09
44 58 0.53
45 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (43 bp):
AGTCAATGCTGCAAATCATTGCTAACATAACTAATAGTTAGTG
Found at i:3564864 original size:127 final size:127
Alignment explanation
Indices: 3564602--3565543 Score: 1407
Period size: 127 Copynumber: 7.7 Consensus size: 127
3564592 AAAAAAAAAT
* * * *
3564602 TAATAGTCAGTGAGTCAATGCTGCAACTCATTGCTAACATTGCTAACATTTGTCCAAAACATTAG
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
* * * * *
3564667 ATTACGGGAAAAAAATAATTAATAGTCGTCAAGTCAATGCTGCAAATCATTGCTAACATCAAC
66 ATTA-TGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
3564730 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
*
3564795 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAAC
66 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
3564857 TAATAGTTAGT--G---A-G-T-C-A---A-TGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
*
3564909 ATTAT-GAAAAACAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCCTTGCTAACATTAAC
66 ATTATGGAAAAA-AATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
3564971 TAATAGTTAGTGAGTCAATGCTGC-A---A--G-T--CATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
*
3565027 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAAC
66 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
* *
3565089 TAATAGTTTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
3565154 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
66 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
3565216 TAATAGTTAGT--G---A-G-T-C-A---A-TGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
* * *
3565268 ATTATGGGAAAAAAATAATTAATAGGCATCGAGTCAATGTTGCAAGTCATTGCTAACATCAAC
66 ATTAT-GGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
3565331 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
*
3565396 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAAC
66 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
* *
3565458 TAATAGTTTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
* *
3565523 ATTATGGGAAAAATTAATTAA
66 ATTATGGAAAAAAATAATTAA
3565544 AAGTTAGTGA
Statistics
Matches: 754, Mismatches: 27, Indels: 67
0.89 0.03 0.08
Matches are distributed among these distances:
113 6 0.01
114 137 0.18
115 67 0.09
116 1 0.00
117 1 0.00
118 105 0.14
119 10 0.01
120 5 0.01
121 5 0.01
122 7 0.01
123 1 0.00
124 2 0.00
125 3 0.00
127 300 0.40
128 104 0.14
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (127 bp):
TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAAC
Found at i:3564955 original size:114 final size:114
Alignment explanation
Indices: 3564755--3565498 Score: 1067
Period size: 114 Copynumber: 6.2 Consensus size: 114
3564745 CAATGCTGCA
*
3564755 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
1 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
*
3564820 CATCGAGTCAATGCTGCAAGTCATTGCTAACATCAACTAATAGTTAGTG
66 CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
3564869 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTAT-GAAAAACAATAATTAATAG
1 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAA-AATAATTAATAG
*
3564933 TCATCGAGTCAATGCTGCAAGTCCTTGCTAACATTAACTAATAGTTAGTG
65 TCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
3564983 AGTCAATGCTGCAAGTCATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAA
1 AGTCAATGCT--AA--CATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAA
*
3565048 TAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGTTTGTGAGTCAATG
62 TAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAG--T-T-AG----TG
*
3565109 CTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTA
1 -----AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTA
3565174 ATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
61 ATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
3565228 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGGAAAAAAATAATTAATAG
1 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTAT-GGAAAAAAATAATTAATAG
* * *
3565293 GCATCGAGTCAATGTTGCAAGTCATTGCTAACATCAACTAATAGTTAGTGAG
65 TCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGT--G
3565345 TCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAA
1 ---A-G-T-C-A---A-TGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAA
* *
3565410 TAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGTTTGTG
55 TAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
3565470 AGTCAATGCTCCAAGTCATTGCTAACATT
1 AGTCAATGCT--AA--CATTGCTAACATT
3565499 GCTAACATTT
Statistics
Matches: 577, Mismatches: 16, Indels: 70
0.87 0.02 0.11
Matches are distributed among these distances:
113 6 0.01
114 162 0.28
115 66 0.11
116 4 0.01
117 1 0.00
118 101 0.18
119 9 0.02
120 3 0.01
121 3 0.01
122 4 0.01
123 3 0.01
124 2 0.00
125 2 0.00
126 2 0.00
127 159 0.28
128 39 0.07
129 2 0.00
131 9 0.02
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (114 bp):
AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTG
Found at i:3565104 original size:359 final size:364
Alignment explanation
Indices: 3564602--3565543 Score: 1581
Period size: 359 Copynumber: 2.6 Consensus size: 364
3564592 AAAAAAAAAT
* * *
3564602 TAATAGTCAGTGAGTCAATGCTGCAACTCATTGCTAACATTGCTAACATTTGTCCAAAACATTAG
1 TAATAGTTAGTGAGTCAATGCTGCAA--CA-TGCT-ACATTGCTAACATTTGTACAAAACATTAA
* * * * * *
3564667 ATTACGGGAAAAAAATAATTAATAGTCGTCAAGTCAATGCTGCAAATCATTGCTAACATCAACTA
62 ATTA-TGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTA
* *
3564732 ATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAAT
126 ATAGTTTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAAT
3564797 TATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAACTAATA
191 TATGGAAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAACTAATA
3564862 GTTAGTGAGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTAT-GAAAAACAATAA
256 GTTAGTGAGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAA-AATAA
* * *
3564926 TTAATAGTCATCGAGTCAATGCTGCAAGTCCTTGCTAACATTAAC
320 TTAATAGGCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAAC
3564971 TAATAGTTAGTGAGTCAATGCTGC-A-A-G-T-CATTGCTAACATTTGTACAAAACATTAAATTA
1 TAATAGTTAGTGAGTCAATGCTGCAACATGCTACATTGCTAACATTTGTACAAAACATTAAATTA
3565031 TGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGT
66 TGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGT
3565096 TTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGG
131 TTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGG
*
3565161 AAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAG
196 AAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAACTAATAGTTAG
3565226 TGAGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGGAAAAAAATAATTAAT
261 TGAGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTAT-GGAAAAAAATAATTAAT
*
3565291 AGGCATCGAGTCAATGTTGCAAGTCATTGCTAACATCAAC
325 AGGCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAAC
3565331 TAATAGTTAGTGAGTCAATGCTGCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAA
1 TAATAGTTAGTGAGTCAATGCTGCAA--CA-TGCT-ACATTGCTAACATTTGTACAAAACATTAA
3565396 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAA
62 ATTATGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAA
3565461 TAGTTTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATT
127 TAGTTTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATT
* *
3565526 ATGGGAAAAATTAATTAA
192 ATGGAAAAAAATAATTAA
3565544 AAGTTAGTGA
Statistics
Matches: 544, Mismatches: 18, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
359 233 0.43
360 100 0.18
361 7 0.01
362 1 0.00
363 1 0.00
364 1 0.00
365 1 0.00
366 1 0.00
367 1 0.00
368 1 0.00
369 197 0.36
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (364 bp):
TAATAGTTAGTGAGTCAATGCTGCAACATGCTACATTGCTAACATTTGTACAAAACATTAAATTA
TGGAAAAAAATAATTAATAGTCATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGT
TTGTGAGTCAATGCTCCAAGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGG
AAAAAAATAATTAATAGTCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAACTAATAGTTAG
TGAGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATA
GGCATCGAGTCAATGCTGCAAGTCATTGCTAACATCAAC
Found at i:3565390 original size:242 final size:243
Alignment explanation
Indices: 3564869--3565498 Score: 1095
Period size: 242 Copynumber: 2.6 Consensus size: 243
3564859 ATAGTTAGTG
*
3564869 AGTCAATGCTAACATTGCTAACATTTGTACAAAACATTAAATTAT-GAAAAACAATAATTAATAG
1 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAA-AATAATTAATAG
*
3564933 TCATCGAGTCAATGCTGCAAGTCCTTGCTAACATTAACTAATAGTTAGTGAGTCAATGCTGCAAG
65 TCATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTGAGTCAATGCT-CAAG
*
3564998 TCATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGTCATCGAGTCAA
129 -CATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGGCATCGAGTCAA
* *
3565063 TACTGCAAGTCATTGCTAACATTAACTAATAGTTTGTGAGTCAATGCTCCA
193 TACTGCAAGTCATTGCTAACATCAACTAATAGTTAGTGAGTCAATGCTCCA
3565114 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
1 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
3565179 CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTGAGTCAATGCT-AA-CA
66 CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTGAGTCAATGCTCAAGCA
*
3565242 TTGCTAACATTTGTACAAAACATTAAATTATGGGAAAAAAATAATTAATAGGCATCGAGTCAATG
131 TTGCTAACATTTGTACAAAACATTAAATTAT-GGAAAAAAATAATTAATAGGCATCGAGTCAATA
* *
3565307 TTGCAAGTCATTGCTAACATCAACTAATAGTTAGTGAGTCAATGCTGCA
195 CTGCAAGTCATTGCTAACATCAACTAATAGTTAGTGAGTCAATGCTCCA
3565356 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
1 AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
* *
3565421 CATCGAGTCAATACTGCAAGTCATTGCTAACATTAACTAATAGTTTGTGAGTCAATGCTCCAAGT
66 CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTGAGTCAATGCT-CAAG-
3565486 CATTGCTAACATT
129 CATTGCTAACATT
3565499 GCTAACATTT
Statistics
Matches: 369, Mismatches: 10, Indels: 11
0.95 0.03 0.03
Matches are distributed among these distances:
241 33 0.09
242 198 0.54
243 2 0.01
244 2 0.01
245 115 0.31
246 19 0.05
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (243 bp):
AGTCATTGCTAACATTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGT
CATCGAGTCAATGCTGCAAGTCATTGCTAACATTAACTAATAGTTAGTGAGTCAATGCTCAAGCA
TTGCTAACATTTGTACAAAACATTAAATTATGGAAAAAAATAATTAATAGGCATCGAGTCAATAC
TGCAAGTCATTGCTAACATCAACTAATAGTTAGTGAGTCAATGCTCCA
Found at i:3572478 original size:17 final size:18
Alignment explanation
Indices: 3572407--3572482 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
3572397 CTGTCATTTC
* *
3572407 TTTTCTTTTTTTTTTCTT
1 TTTTCCTTTTTCTTTCTT
*
3572425 TCTTCCTTTTTCTTT-TT
1 TTTTCCTTTTTCTTTCTT
**
3572442 CTTTT-CTATTTTCCACTCTT
1 -TTTTCCT-TTTT-CTTTCTT
3572462 TTTTCCTTTTT-TTTCTT
1 TTTTCCTTTTTCTTTCTT
3572479 TTTT
1 TTTT
3572483 TTAAATATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
17 12 0.27
18 19 0.42
19 10 0.22
20 4 0.09
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCCTTTTTCTTTCTT
Found at i:3573073 original size:9 final size:9
Alignment explanation
Indices: 3573061--3573146 Score: 72
Period size: 10 Copynumber: 9.4 Consensus size: 9
3573051 CAATTTTTAC
3573061 CTTTTTTTT
1 CTTTTTTTT
3573070 CTTTTTTTTT
1 C-TTTTTTTT
3573080 CTCTTTTTTT
1 CT-TTTTTTT
3573090 C---TTTTT
1 CTTTTTTTT
*
3573096 C-TCTTTTT
1 CTTTTTTTT
*
3573104 CTTTTCTTT
1 CTTTTTTTT
3573113 CTTTGTTTTTT
1 C-TT-TTTTTT
3573124 CCTTTTTTTT
1 -CTTTTTTTT
*
3573134 CTCTTTTTT
1 CTTTTTTTT
3573143 CTTT
1 CTTT
3573147 CATTTTTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
6 6 0.09
8 6 0.09
9 19 0.30
10 25 0.39
11 7 0.11
12 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:3573074 original size:8 final size:8
Alignment explanation
Indices: 3573062--3573146 Score: 57
Period size: 8 Copynumber: 10.2 Consensus size: 8
3573052 AATTTTTACC
3573062 TTTTTT-T
1 TTTTTTCT
*
3573069 TCTTTT-T
1 TTTTTTCT
*
3573076 TTTTCTCT
1 TTTTTTCT
3573084 TTTTTTCT
1 TTTTTTCT
*
3573092 TTTTCTCTTT
1 TTTT-T-TCT
3573102 TTCTTTTCT
1 TT-TTTTCT
* *
3573111 TTCTTTGT
1 TTTTTTCT
*
3573119 TTTTTCCTT
1 TTTTTTC-T
3573128 TTTTTTCT
1 TTTTTTCT
3573136 CTTTTTTCT
1 -TTTTTTCT
3573145 TT
1 TT
3573147 CATTTTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
7 10 0.17
8 23 0.38
9 20 0.33
10 5 0.08
11 2 0.03
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3573108 original size:34 final size:31
Alignment explanation
Indices: 3573062--3573156 Score: 93
Period size: 34 Copynumber: 2.9 Consensus size: 31
3573052 AATTTTTACC
*
3573062 TTTTTTTTCTTTTTTTTTCTCTTTTTTTCTTT
1 TTTTTTTTCTTTTTTTTTCT-TTTTTTTCCTT
*
3573094 TTCTCTTTTTCTTTTCTTTCTT-TGTTTTTTCCTT
1 TT-T-TTTTTCTTTT-TTT-TTCTTTTTTTTCCTT
*
3573128 TTTTTTCTCTTTTTTCTTTCATTTTTTTT
1 TTTTTTTTCTTTTTT-TTTC-TTTTTTTT
3573157 AACTTAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
31 4 0.08
32 12 0.23
33 9 0.17
34 21 0.40
35 4 0.08
36 2 0.04
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.82
Consensus pattern (31 bp):
TTTTTTTTCTTTTTTTTTCTTTTTTTTCCTT
Found at i:3573156 original size:27 final size:26
Alignment explanation
Indices: 3573064--3573146 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 26
3573054 TTTTTACCTT
3573064 TTTTTTCTTTTTTTTTCTCTTTTTTTC
1 TTTTTTCTTTTTTTTTCTC-TTTTTTC
* *
3573091 TTTTTCTCTTTTTCTTTTCT-TTCTTTG
1 TTTTT-TCTTTTT-TTTTCTCTTTTTTC
*
3573118 TTTTTTCCTTTTTTTTCTCTTTTTTC
1 TTTTTTCTTTTTTTTTCTCTTTTTTC
3573144 TTT
1 TTT
3573147 CATTTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
25 6 0.12
26 14 0.29
27 15 0.31
28 7 0.15
29 6 0.12
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (26 bp):
TTTTTTCTTTTTTTTTCTCTTTTTTC
Found at i:3585963 original size:18 final size:20
Alignment explanation
Indices: 3585940--3585981 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
3585930 AAAAAAAACT
3585940 AAAAAGAAAT-GAGAAAA-A
1 AAAAAGAAATAGAGAAAAGA
3585958 AAAAAGAAATAGGAGAAAAGA
1 AAAAAGAAATA-GAGAAAAGA
3585979 AAA
1 AAA
3585982 TGCACCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (20 bp):
AAAAAGAAATAGAGAAAAGA
Found at i:3592093 original size:21 final size:21
Alignment explanation
Indices: 3592069--3592219 Score: 50
Period size: 21 Copynumber: 7.2 Consensus size: 21
3592059 GGGCCACTTA
3592069 TCCTACTCTCCTTCATTATTG
1 TCCTACTCTCCTTCATTATTG
** **
3592090 TCCTCACAAGTCACAACATTA-T-
1 TCCT-AC-TCTC-CTTCATTATTG
3592112 -CCTACTCTCCTTCATTATTG
1 TCCTACTCTCCTTCATTATTG
** **
3592132 TCCTCACAAGTCACAACATTA-T-
1 TCCT-AC-TCTC-CTTCATTATTG
3592154 -CCTACTCTCCTTCATTATTG
1 TCCTACTCTCCTTCATTATTG
** **
3592174 TCCTCACAAGTCACAACATTA-T-
1 TCCT-AC-TCTC-CTTCATTATTG
3592196 -CCTACTCTCCTTCATTATTG
1 TCCTACTCTCCTTCATTATTG
3592216 TCCT
1 TCCT
3592220 CACAAGTCAC
Statistics
Matches: 88, Mismatches: 24, Indels: 36
0.59 0.16 0.24
Matches are distributed among these distances:
18 18 0.20
19 9 0.10
20 6 0.07
21 22 0.25
22 6 0.07
23 9 0.10
24 18 0.20
ACGTcount: A:0.24, C:0.34, G:0.05, T:0.38
Consensus pattern (21 bp):
TCCTACTCTCCTTCATTATTG
Found at i:3592125 original size:42 final size:42
Alignment explanation
Indices: 3592066--3592236 Score: 333
Period size: 42 Copynumber: 4.0 Consensus size: 42
3592056 ATGGGGCCAC
3592066 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
1 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
3592108 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
1 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
3592150 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
1 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
3592192 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAAACA
1 TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCAC-AACA
3592235 TT
1 TT
3592237 CTTTCGCAAG
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
42 122 0.95
43 6 0.05
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (42 bp):
TTATCCTACTCTCCTTCATTATTGTCCTCACAAGTCACAACA
Found at i:3601366 original size:23 final size:23
Alignment explanation
Indices: 3601332--3601379 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3601322 TTCACGCCTC
*
3601332 TTTCTCCTTCTCCTTCTTTTTCTT
1 TTTCTCCTTCTCCTT-TTGTTCTT
3601356 TTTCT-CTTCTCCTTTTGTTCTT
1 TTTCTCCTTCTCCTTTTGTTCTT
3601378 TT
1 TT
3601380 AATTTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
23 9 0.39
24 5 0.22
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTCTCCTTCTCCTTTTGTTCTT
Found at i:3602302 original size:15 final size:15
Alignment explanation
Indices: 3602282--3602312 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3602272 AACAAAAAGC
3602282 AAACTTTATTATATT
1 AAACTTTATTATATT
3602297 AAACTTTATTATATT
1 AAACTTTATTATATT
3602312 A
1 A
3602313 GCATTACATC
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:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
AAACTTTATTATATT
Found at i:3608977 original size:64 final size:64
Alignment explanation
Indices: 3608888--3609016 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 64
3608878 TCATTTGTCC
* *
3608888 TACCTACTTCACCGTGGACCTCATTTTATAATCTTTCAAACGAACCAGGCCAGAAATTATGTAA
1 TACCTACTCCACCATGGACCTCATTTTATAATCTTTCAAACGAACCAGGCCAGAAATTATGTAA
* * * * * *
3608952 TACCTACTCCACCATGGGCCTCATTTTCTAATCTTTCACATGAACCGGGCGAGAAATTATGTAA
1 TACCTACTCCACCATGGACCTCATTTTATAATCTTTCAAACGAACCAGGCCAGAAATTATGTAA
3609016 T
1 T
3609017 TATGTAAGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (64 bp):
TACCTACTCCACCATGGACCTCATTTTATAATCTTTCAAACGAACCAGGCCAGAAATTATGTAA
Found at i:3609471 original size:26 final size:26
Alignment explanation
Indices: 3609442--3609494 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
3609432 ATATATATAG
3609442 AAAT-ATAAGGTACAAGATGA-TGATGA
1 AAATCATAAGGTA-AAGAT-ATTGATGA
*
3609468 AAATCATTAGGTAAAGATATTGATGA
1 AAATCATAAGGTAAAGATATTGATGA
3609494 A
1 A
3609495 GATGACATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (26 bp):
AAATCATAAGGTAAAGATATTGATGA
Found at i:3610201 original size:73 final size:73
Alignment explanation
Indices: 3610110--3610256 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
3610100 CACACTTTAC
3610110 ATTGAGCACTAATGGGCATTTCGTTTTCTGTATTTTGGTTTATTTTCTTATCTGGGGTGTAGTTA
1 ATTGAGCACTAATGGGCATTTCGTTTTCTGTATTTTGGTTTATTTTCTTATCTGGGGTGTAGTTA
3610175 CATATAAA
66 CATATAAA
3610183 ATTGAGCACTAATGGGCATTTCGTTTTCTGTATTTTGGTTTATTTTCTTATCTGGGGTGTAGTTA
1 ATTGAGCACTAATGGGCATTTCGTTTTCTGTATTTTGGTTTATTTTCTTATCTGGGGTGTAGTTA
3610248 CATATAAA
66 CATATAAA
3610256 A
1 A
3610257 AAAAATTAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.46
Consensus pattern (73 bp):
ATTGAGCACTAATGGGCATTTCGTTTTCTGTATTTTGGTTTATTTTCTTATCTGGGGTGTAGTTA
CATATAAA
Found at i:3613418 original size:8 final size:8
Alignment explanation
Indices: 3613405--3613439 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
3613395 TAAATTATTT
3613405 TTTTAATA
1 TTTTAATA
3613413 TTTTAATA
1 TTTTAATA
3613421 TTTTAATCA
1 TTTTAAT-A
*
3613430 TATTAATA
1 TTTTAATA
3613438 TT
1 TT
3613440 AATAATGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTAATA
Found at i:3613435 original size:17 final size:16
Alignment explanation
Indices: 3613405--3613439 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3613395 TAAATTATTT
*
3613405 TTTTAATATTTTAATA
1 TTTTAATATATTAATA
3613421 TTTTAATCATATTAATA
1 TTTTAAT-ATATTAATA
3613438 TT
1 TT
3613440 AATAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAATATATTAATA
Found at i:3613485 original size:25 final size:27
Alignment explanation
Indices: 3613434--3613487 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3613424 TAATCATATT
3613434 AATATTAATAATGTTAAATTATATATAA
1 AATATTAATAATGTTAAA-TATATATAA
* *
3613462 AATATTAAT-ATTTTAAA-ATTTATAA
1 AATATTAATAATGTTAAATATATATAA
3613487 A
1 A
3613488 TAATTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
27 7 0.29
28 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AATATTAATAATGTTAAATATATATAA
Found at i:3616161 original size:21 final size:22
Alignment explanation
Indices: 3616135--3616175 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3616125 ATGTTAATGC
3616135 AATTATCTTTTTT-TTTTATTT
1 AATTATCTTTTTTATTTTATTT
*
3616156 AATTATTTTTTTTATTTTAT
1 AATTATCTTTTTTATTTTAT
3616176 GATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
AATTATCTTTTTTATTTTATTT
Found at i:3616208 original size:17 final size:17
Alignment explanation
Indices: 3616146--3616209 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
3616136 ATTATCTTTT
* *
3616146 TTTTTTATTTAATTATT
1 TTTTTTATTTTATTATA
*
3616163 TTTTTTATTTTATGATA
1 TTTTTTATTTTATTATA
3616180 TTTTTTCA--TTATTATA
1 TTTTTT-ATTTTATTATA
3616196 TTTTTTATTTTATT
1 TTTTTTATTTTATT
3616210 CCTTATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.03
16 13 0.32
17 25 0.62
18 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTATTATA
Found at i:3616221 original size:23 final size:23
Alignment explanation
Indices: 3616178--3616224 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3616168 TATTTTATGA
3616178 TATTTTTTCATTATTATATTTTT
1 TATTTTTTCATTATTATATTTTT
*
3616201 TATTTTATTCCTTATTA-ATTTTT
1 TATTTT-TTCATTATTATATTTTT
3616224 T
1 T
3616225 GTATACCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTTTTCATTATTATATTTTT
Found at i:3616347 original size:3 final size:3
Alignment explanation
Indices: 3616328--3616409 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
3616318 AGAAACTTAT
* * * *
3616328 TTA TTA TCA TT- TT- TTA TTA TTA TTA TTT TTA TATA TTT TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
3616372 TT- TTT TTA TTA TTA TT- TT- TTA TTA TTG TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3616410 GATTTTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
2 12 0.19
3 48 0.76
4 3 0.05
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3616352 original size:19 final size:19
Alignment explanation
Indices: 3616328--3616387 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
3616318 AGAAACTTAT
3616328 TTATTATCATTTTTTATTA
1 TTATTATCATTTTTTATTA
*
3616347 TTATTAT--TTTTATA-TA
1 TTATTATCATTTTTTATTA
*
3616363 TTTTTATCATTTTTTTATTA
1 TTATTATCA-TTTTTTATTA
3616383 TTATT
1 TTATT
3616388 TTTTATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
19 13 0.39
20 6 0.18
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTATCATTTTTTATTA
Found at i:3616405 original size:11 final size:11
Alignment explanation
Indices: 3616324--3616408 Score: 77
Period size: 11 Copynumber: 7.5 Consensus size: 11
3616314 ACTGAGAAAC
3616324 TTATTTATTATCA
1 TTATTT-TTAT-A
*
3616337 TTTTTTATTATTA
1 TTATTT-TTA-TA
3616350 TTATTTTTATA
1 TTATTTTTATA
3616361 -TATTTTTATCA
1 TTATTTTTAT-A
3616372 TT-TTTTTATTA
1 TTATTTTTA-TA
3616383 TTATTTTT-TA
1 TTATTTTTATA
*
3616393 TTATTGTTATA
1 TTATTTTTATA
3616404 TTATT
1 TTATT
3616409 AGATTTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
10 18 0.29
11 19 0.30
12 10 0.16
13 15 0.24
14 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:3616415 original size:24 final size:24
Alignment explanation
Indices: 3616364--3616415 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3616354 TTTTATATAT
* * **
3616364 TTTTATCATTTTTTTATTATTATT
1 TTTTATCATTGTTATATTATTAGA
*
3616388 TTTTATTATTGTTATATTATTAGA
1 TTTTATCATTGTTATATTATTAGA
3616412 TTTT
1 TTTT
3616416 TTTTTTTAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTTATCATTGTTATATTATTAGA
Found at i:3616718 original size:22 final size:20
Alignment explanation
Indices: 3616675--3616718 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3616665 ATTTGAATCA
* *
3616675 TTATTATTTTTTTATTTTAT
1 TTATTATTTTTTTATATGAT
3616695 TTATTATATTTTTTAATATGAT
1 TTATTAT-TTTTTT-ATATGAT
3616717 TT
1 TT
3616719 TCGTATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTATTTTTTTATATGAT
Found at i:3616968 original size:28 final size:30
Alignment explanation
Indices: 3616903--3616973 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 30
3616893 TCATGATATT
* *
3616903 TTATTATTATTT-TTCCTTTTTTATTATCA
1 TTATTATTATTTATTCATTTTTTATTATAA
*
3616932 TTATT-TTATTTATT-ATTTTTTTTTATAA
1 TTATTATTATTTATTCATTTTTTATTATAA
*
3616960 TT-TTATTATATATT
1 TTATTATTATTTATT
3616974 TGTAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.06
28 27 0.75
29 7 0.19
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (30 bp):
TTATTATTATTTATTCATTTTTTATTATAA
Found at i:3616971 original size:13 final size:13
Alignment explanation
Indices: 3616921--3616971 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
3616911 ATTTTTCCTT
*
3616921 TTTTATTATCATTA
1 TTTTATTAT-ATAA
*
3616935 TTTTATT-TATTA
1 TTTTATTATATAA
* *
3616947 TTTTTTTTTATAA
1 TTTTATTATATAA
3616960 TTTTATTATATA
1 TTTTATTATATA
3616972 TTTGTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 10 0.31
13 15 0.47
14 7 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTATATAA
Found at i:3617119 original size:21 final size:22
Alignment explanation
Indices: 3617094--3617144 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
3617084 TCAATTTCCT
*
3617094 AAATTTAAATTGTCAT-CTAAA
1 AAATTTAAAATGTCATACTAAA
*
3617115 AAATTTAAAATGTTATACTAAA
1 AAATTTAAAATGTCATACTAAA
3617137 ATAATTTA
1 A-AATTTA
3617145 GAACAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATTTAAAATGTCATACTAAA
Found at i:3619443 original size:2 final size:2
Alignment explanation
Indices: 3619436--3619480 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3619426 ANNNNNNNNN
3619436 AT AT AT AT 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 AT AT AT AT
3619478 AT A
1 AT A
3619481 AGTAACCCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3620123 original size:131 final size:138
Alignment explanation
Indices: 3619866--3620137 Score: 337
Period size: 131 Copynumber: 2.0 Consensus size: 138
3619856 TGTCAATCAT
* *
3619866 TCTTTTTATTTTATTTTATTTACTCGTCTTTACTGTATTTTATTATTATTTTTTTAATTATTTTA
1 TCTTTCTATTTTATTTTATTTACTCGTCTTTACTG-ATGTTATTATTATTTTTTTAATTATTTTA
* * * *
3619931 GGTTGATATTGAGTCAAATTAATTAAGTTTAAGTAACTTGAGCCCATTAAAGTTGTAAGTGCAAA
65 GGTTGATATTGACTCAAATTAATTAAG--T-AG-AACTTGAACCCATTAAAATTGGAAGTGCAAA
*
3619996 GCTCTATCAATGG
126 GCTCGATCAATGG
3620009 TCTTTCTATTTTATTTTATTTACT-GATCTTTACTG-TGTT-TTATT-TTTTTTTAATTATTTTA
1 TCTTTCTATTTTATTTTATTTACTCG-TCTTTACTGATGTTATTATTATTTTTTTAATTATTTTA
* *
3620070 GGTTGA-A-TGACTCAAAGTT-ATTAAG-A-ACCTTGAACCCATTAAAATTGGCAGTGCAAAGCT
65 GGTTGATATTGACTCAAA-TTAATTAAGTAGAACTTGAACCCATTAAAATTGGAAGTGCAAAGCT
3620130 CGATCAAT
129 CGATCAAT
3620138 ATAAATTCGA
Statistics
Matches: 118, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
131 36 0.31
133 1 0.01
137 14 0.12
138 3 0.03
139 23 0.19
140 5 0.04
141 3 0.03
142 1 0.01
143 32 0.27
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (138 bp):
TCTTTCTATTTTATTTTATTTACTCGTCTTTACTGATGTTATTATTATTTTTTTAATTATTTTAG
GTTGATATTGACTCAAATTAATTAAGTAGAACTTGAACCCATTAAAATTGGAAGTGCAAAGCTCG
ATCAATGG
Found at i:3626515 original size:15 final size:15
Alignment explanation
Indices: 3626495--3626529 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3626485 TACCTTTTAA
3626495 TAAATTT-AAAACTTT
1 TAAATTTAAAAAC-TT
3626510 TAAATTTAAAAACTT
1 TAAATTTAAAAACTT
3626525 TAAAT
1 TAAAT
3626530 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTTAAAAACTT
Found at i:3648296 original size:52 final size:52
Alignment explanation
Indices: 3648220--3648324 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
3648210 TGCATTAGCA
*
3648220 ATATTTTCTGAATTATTATTTTAATCCCAGCTAATTAAATTATAACCATATT
1 ATATTTTCTGAATTATTATATTAATCCCAGCTAATTAAATTATAACCATATT
3648272 ATATTTTCTGAATTATTATATTAATCCCAGCTAATTAAATTATAACCATATT
1 ATATTTTCTGAATTATTATATTAATCCCAGCTAATTAAATTATAACCATATT
3648324 A
1 A
3648325 GTAGAAATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (52 bp):
ATATTTTCTGAATTATTATATTAATCCCAGCTAATTAAATTATAACCATATT
Found at i:3694386 original size:2 final size:2
Alignment explanation
Indices: 3694379--3694409 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3694369 AGGTGTAACT
3694379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3694410 GCATGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3715758 original size:32 final size:32
Alignment explanation
Indices: 3715717--3715779 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3715707 ACAGAATTCA
*
3715717 CCTGCGTTACTCAAGGGGAATTTTCCAAGTCC
1 CCTGCGTTACTCAAAGGGAATTTTCCAAGTCC
*
3715749 CCTGCGTTACTCAAAGGGAATTTTCTAAGTC
1 CCTGCGTTACTCAAAGGGAATTTTCCAAGTC
3715780 TACAGTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (32 bp):
CCTGCGTTACTCAAAGGGAATTTTCCAAGTCC
Found at i:3717518 original size:19 final size:18
Alignment explanation
Indices: 3717479--3717524 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
3717469 CGATTACGGG
*
3717479 TAAAAGAATATTTTAGAA
1 TAAAATAATATTTTAGAA
3717497 TAAAATAATATTTTATGAA
1 TAAAATAATATTTTA-GAA
3717516 TAAAATAAT
1 TAAAATAAT
3717525 GTTAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAAATAATATTTTAGAA
Found at i:3718476 original size:20 final size:18
Alignment explanation
Indices: 3718451--3718541 Score: 80
Period size: 20 Copynumber: 4.9 Consensus size: 18
3718441 ACCCATATCC
3718451 AAGAAGAAAAGAGAAAGGA
1 AAGAAG-AAAGAGAAAGGA
* *
3718470 GAAGAAGGAA-AGAAAGAA
1 -AAGAAGAAAGAGAAAGGA
3718488 AAG-AGAAAG-GAAAGGA
1 AAGAAGAAAGAGAAAGGA
3718504 AAGAAAGAAAAGAGAAAGGA
1 AAG-AAG-AAAGAGAAAGGA
*
3718524 AAGGAAAGAAAGAAAAAG
1 AA-G-AAGAAAGAGAAAG
3718542 AAGGAAAGGA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.22
17 3 0.05
18 9 0.15
19 6 0.10
20 24 0.40
21 5 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAGAGAAAGGA
Found at i:3718500 original size:5 final size:5
Alignment explanation
Indices: 3718474--3718556 Score: 77
Period size: 5 Copynumber: 17.2 Consensus size: 5
3718464 AAAGGAGAAG
* *
3718474 AAGGA AA-GA AAGAA AAGAGA AAGGA AAGGA AA-GA AAGAA AAGAGA AAGGA
1 AAGGA AAGGA AAGGA AAG-GA AAGGA AAGGA AAGGA AAGGA AAG-GA AAGGA
* *
3718524 AAGGA AA-GA AAGAA AAAG- AAGGA AAGG- AAGGA A
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA A
3718557 GGCTCGGTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
4 19 0.30
5 36 0.57
6 8 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:3718502 original size:25 final size:25
Alignment explanation
Indices: 3718454--3718552 Score: 148
Period size: 25 Copynumber: 3.9 Consensus size: 25
3718444 CATATCCAAG
3718454 AAGAAAAGAGAAAGGAGAAGAAGGAAAGA
1 AAGAAAAGAGAAA-G-G-A-AAGGAAAGA
3718483 AAGAAAAGAGAAAGGAAAGGAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGA
3718508 AAGAAAAGAGAAAGGAAAGGAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGA
3718533 AAGAAAA-AG-AAGGAAAGGAA
1 AAGAAAAGAGAAAGGAAAGGAA
3718553 GGAAGGCTCG
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.16
24 2 0.03
25 41 0.59
26 1 0.01
27 1 0.01
28 1 0.01
29 13 0.19
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
AAGAAAAGAGAAAGGAAAGGAAAGA
Found at i:3725590 original size:11 final size:12
Alignment explanation
Indices: 3725574--3725602 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3725564 AGAGTGTGAA
3725574 TGAGAGAAAA-T
1 TGAGAGAAAATT
3725585 TGAGAGAAAATT
1 TGAGAGAAAATT
3725597 TGAGAG
1 TGAGAG
3725603 TTTGAGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (12 bp):
TGAGAGAAAATT
Found at i:3730953 original size:35 final size:35
Alignment explanation
Indices: 3730907--3730976 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3730897 AGAGATTCAC
*
3730907 GTAACTAACCACCTTCTTCTATACTTCAAGGTTTT
1 GTAACTAACCACCTTCTTCTATACGTCAAGGTTTT
*
3730942 GTAACTAACCACCTTTTTCTATACGTCAAGGTTTT
1 GTAACTAACCACCTTCTTCTATACGTCAAGGTTTT
3730977 CACAATGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (35 bp):
GTAACTAACCACCTTCTTCTATACGTCAAGGTTTT
Found at i:3738794 original size:157 final size:157
Alignment explanation
Indices: 3738508--3738794 Score: 502
Period size: 157 Copynumber: 1.8 Consensus size: 157
3738498 ATTGACATTA
*
3738508 GTAAGGCTATCTGTCATGCCACATCACATACGAGCCAAACCAAATGAGATGGTATAGGATTTCCT
1 GTAAGGCTATCTCTCATGCCACATCACATACGAGCCAAACCAAATGAGATGGTATAGGATTTCCT
* *
3738573 TCTTTGATAACTGCATTGTGTGCGAAAGCTGATGTGTGATGGAGTAATAAAGAGGAGCTGCAACA
66 TCTTTGATAACTACATTGTGTGCGAAAGCTAATGTGTGATGGAGTAATAAAGAGGAGCTGCAACA
3738638 TGACATACAAGCCAAACCAAATGAGTG
131 TGACATACAAGCCAAACCAAATGAGTG
* *
3738665 GTAAGGCTATCTCTCATGCCACATTACATACGGGCCAAACCAAATGAGATGGTATAGGATTTCCT
1 GTAAGGCTATCTCTCATGCCACATCACATACGAGCCAAACCAAATGAGATGGTATAGGATTTCCT
* * *
3738730 TCTTTGATAACTACATTGTGTGTGAAAGCTAATGTGTGATGGAGTGATAAAGAGGAGTTGCAACA
66 TCTTTGATAACTACATTGTGTGCGAAAGCTAATGTGTGATGGAGTAATAAAGAGGAGCTGCAACA
3738795 ACCAAAAATC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 122 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (157 bp):
GTAAGGCTATCTCTCATGCCACATCACATACGAGCCAAACCAAATGAGATGGTATAGGATTTCCT
TCTTTGATAACTACATTGTGTGCGAAAGCTAATGTGTGATGGAGTAATAAAGAGGAGCTGCAACA
TGACATACAAGCCAAACCAAATGAGTG
Found at i:3741649 original size:28 final size:28
Alignment explanation
Indices: 3741615--3741681 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
3741605 TTTAGTTCTA
3741615 TTGATTTTTATCGAATTTTAGTTT-TGCT
1 TTGATTTTTATCGAATTTTA-TTTCTGCT
3741643 TTGATTTTTATCGAATTTTATTTCTGCT
1 TTGATTTTTATCGAATTTTATTTCTGCT
3741671 TTGATTTTTAT
1 TTGATTTTTAT
3741682 TTTTGTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 3 0.08
28 35 0.92
ACGTcount: A:0.18, C:0.07, G:0.12, T:0.63
Consensus pattern (28 bp):
TTGATTTTTATCGAATTTTATTTCTGCT
Found at i:3747018 original size:14 final size:14
Alignment explanation
Indices: 3746999--3747026 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3746989 AGTAAGATTC
3746999 TTTTGTTATCAGAA
1 TTTTGTTATCAGAA
3747013 TTTTGTTATCAGAA
1 TTTTGTTATCAGAA
3747027 ATAAGAGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTTGTTATCAGAA
Found at i:3748598 original size:38 final size:39
Alignment explanation
Indices: 3748491--3748685 Score: 203
Period size: 39 Copynumber: 5.0 Consensus size: 39
3748481 TATTATCTTT
* **
3748491 TTTTGGTGTGTATTCATATGATGAAGAGTGATTTACAAATG
1 TTTTGGT-T-TATTCATATGATGAAGATTGATTTATGAATG
* *
3748532 TTTTAGTTCATTCATATGATGAAGATTGA-TTATGAATG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* * * *
3748570 CTTTGGTTTATTCATATGATAAAAATTGATTTATGAAAG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* * **
3748609 TTTTGGTTTATTAATATGACGAAGATTGATTTACAAATG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* * * * *
3748648 TTTTGGTCTATTCATACGATGAATACTGATTGATGAAT
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAAT
3748686 TTGATGAAAT
Statistics
Matches: 125, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
38 31 0.25
39 87 0.70
40 1 0.01
41 6 0.05
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (39 bp):
TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
Found at i:3748633 original size:77 final size:78
Alignment explanation
Indices: 3748492--3748663 Score: 195
Period size: 77 Copynumber: 2.2 Consensus size: 78
3748482 ATTATCTTTT
* * * *
3748492 TTTGGTGTGTATTCATATGATGAAGAGTGATTTACAAATGTTTTAGTTCATTCATATGATGAAGA
1 TTTGGT-T-TATTCATATGATAAAAAGTGATTTACAAATGTTTTAGTTCATTAATATGACGAAGA
**
3748557 TTGA-TTATGAATGC
64 TTGATTTACAAATGC
* * * *
3748571 TTTGGTTTATTCATATGATAAAAATTGATTTATGAAA-GTTTTGGTTTATTAATATGACGAAGAT
1 TTTGGTTTATTCATATGATAAAAAGTGATTTA-CAAATGTTTTAGTTCATTAATATGACGAAGAT
*
3748635 TGATTTACAAATGT
65 TGATTTACAAATGC
*
3748649 TTTGGTCTATTCATA
1 TTTGGTTTATTCATA
3748664 CGATGAATAC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
77 48 0.61
78 25 0.32
79 6 0.08
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (78 bp):
TTTGGTTTATTCATATGATAAAAAGTGATTTACAAATGTTTTAGTTCATTAATATGACGAAGATT
GATTTACAAATGC
Found at i:3749434 original size:26 final size:26
Alignment explanation
Indices: 3749398--3749451 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3749388 ATAACATGTA
3749398 CTTGTAATCACATGTCATTCATAAAT
1 CTTGTAATCACATGTCATTCATAAAT
*
3749424 CTTGTAATCACATTTCATTCATAAAT
1 CTTGTAATCACATGTCATTCATAAAT
3749450 CT
1 CT
3749452 GTGAGTGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (26 bp):
CTTGTAATCACATGTCATTCATAAAT
Done.