Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 92 of 173
Found at i:28849001 original size:18 final size:17
Alignment explanation
Indices: 28848967--28849003 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
28848957 ATTATTAAGA
28848967 ATTTTATTAAATCATAT
1 ATTTTATTAAATCATAT
28848984 ATTTTATTTAAA--ATAT
1 ATTTTA-TTAAATCATAT
28849000 ATTT
1 ATTT
28849004 AATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATCATAT
Found at i:28849115 original size:18 final size:17
Alignment explanation
Indices: 28849087--28849121 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28849077 ATTATTAAGA
*
28849087 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28849104 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28849122 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28849341 original size:44 final size:45
Alignment explanation
Indices: 28849278--28849374 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
28849268 CTATTACACC
*
28849278 TCCATTCCATTCAACCAAAC-ATAAGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAAT-AGATATACTATTACGCCTCTAT
* * *
28849322 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
*
28849367 TCTATTAC
1 TCCATTAC
28849375 GCCTCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 21 0.46
45 25 0.54
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:28849373 original size:16 final size:16
Alignment explanation
Indices: 28849352--28849390 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
28849342 AATTGATTTG
28849352 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
28849368 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
28849384 CTATTAC
1 CTATTAC
28849391 TGCGAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:28849548 original size:32 final size:32
Alignment explanation
Indices: 28849512--28849573 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
28849502 GTGACAGTTA
28849512 AAAAAATTATTATAATAATAAATTTAACCCAC
1 AAAAAATTATTATAATAATAAATTTAACCCAC
28849544 AAAAAATTATTATAATAATAAATTTAACCC
1 AAAAAATTATTATAATAATAAATTTAACCC
28849574 TCAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAAAATTATTATAATAATAAATTTAACCCAC
Found at i:28852438 original size:20 final size:20
Alignment explanation
Indices: 28852371--28852440 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
28852361 ATTAAGTTAT
* *
28852371 TAAAATATTGAAAAATTAAAAA
1 TAAAATATT-AAAAAGT-AATA
* * *
28852393 TAAATTATAAAAAAGGAAT-
1 TAAAATATTAAAAAGTAATA
*
28852412 TATAATATTAAAAAGTAATA
1 TAAAATATTAAAAAGTAATA
28852432 TAAAATATT
1 TAAAATATT
28852441 TAATATGGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
19 15 0.41
20 10 0.27
21 5 0.14
22 7 0.19
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (20 bp):
TAAAATATTAAAAAGTAATA
Found at i:28855476 original size:45 final size:45
Alignment explanation
Indices: 28855373--28855488 Score: 169
Period size: 45 Copynumber: 2.6 Consensus size: 45
28855363 TTTGGATTGA
* **
28855373 GAAATAAGAAAGAAGATGGTTGAAAGATGCCATGACATTATACCC
1 GAAATGAGAAAGACCATGGTTGAAAGATGCCATGACATTATACCC
* * *
28855418 GAAACGAGAAAGACTATGGTTGAAAGATGCCATGGCATTATACCC
1 GAAATGAGAAAGACCATGGTTGAAAGATGCCATGACATTATACCC
*
28855463 GAAATGAGAAAGACCATAGTTGAAAG
1 GAAATGAGAAAGACCATGGTTGAAAG
28855489 CAACTATGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (45 bp):
GAAATGAGAAAGACCATGGTTGAAAGATGCCATGACATTATACCC
Found at i:28855498 original size:45 final size:45
Alignment explanation
Indices: 28855373--28855544 Score: 159
Period size: 45 Copynumber: 3.8 Consensus size: 45
28855363 TTTGGATTGA
* ** * * *
28855373 GAAATAAGAAAGAAGATGGTTGAAAGATGCCATGACATTATACCC
1 GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
* * * *
28855418 GAAACGAGAAAGACTATGGTTGAAAGATGCCATGGCATTATACCC
1 GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
* * * *
28855463 GAAATGAGAAAGACCATAGTTGAAAGCA-ACTATGGCACTATATCA
1 GAAATGAGAAAGACCATAGTTGAAAG-ATACCATGGCATTATACCC
* * *
28855508 GAAATGTA-TAAGACCATAGTTGAAATATACTATGGCA
1 GAAATG-AGAAAGACCATAGTTGAAAGATACCATGGCA
28855545 ATACATCGAC
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.01
45 106 0.97
46 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.22
Consensus pattern (45 bp):
GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
Found at i:28855564 original size:45 final size:44
Alignment explanation
Indices: 28855463--28855589 Score: 123
Period size: 45 Copynumber: 2.8 Consensus size: 44
28855453 CATTATACCC
* *
28855463 GAAATGAGA-AAGACCATAGTTGAAAGCAACTATGGCACTATATCA
1 GAAATGA-ATAAGACCATAGTTGAAA-CAACTATGGCAATACATCA
* *
28855508 GAAATGTATAAGACCATAGTTGAAATATACTATGGCAATACATC-
1 GAAATGAATAAGACCATAGTTGAAACA-ACTATGGCAATACATCA
* * * *
28855552 GACAATGAATAAGACTACAGTTTAAAGAGACTATGGCA
1 GA-AATGAATAAGACCATAGTTGAAACA-ACTATGGCA
28855590 TCACTTTGGA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 4 0.06
45 65 0.94
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (44 bp):
GAAATGAATAAGACCATAGTTGAAACAACTATGGCAATACATCA
Found at i:28863765 original size:21 final size:22
Alignment explanation
Indices: 28863725--28863771 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
28863715 ATAAATATGA
*
28863725 CAATTCAAAATACATGTATAATT
1 CAATTCAAAATACATATAT-ATT
28863748 CAATT-AAAA-ACATATATATT
1 CAATTCAAAATACATATATATT
28863768 CAAT
1 CAAT
28863772 ATAATTACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 4 0.17
23 5 0.22
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (22 bp):
CAATTCAAAATACATATATATT
Found at i:28881058 original size:45 final size:45
Alignment explanation
Indices: 28880991--28881199 Score: 265
Period size: 45 Copynumber: 4.6 Consensus size: 45
28880981 TTGATTTGAG
* ** * * *
28880991 GAAAAGGAAAAAATGATTATTGAAATATATCATTGCATTATAATC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* *
28881036 AAAAAGGAAAATACCATGATTGAAAGATATCATGGCATTATAATC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* ** ** *
28881081 TAAAAGGAAAAGACTGTGATTGAAAGATATCAAAGCATTATAATT
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
*
28881126 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATACTC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* *
28881171 GAAAAGAAAAAGACCATGGTTGAAAGATA
1 GAAAAGGAAAAGACCATGATTGAAAGATA
28881200 CTATGACATC
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 141 1.00
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (45 bp):
GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
Found at i:28883408 original size:22 final size:23
Alignment explanation
Indices: 28883379--28883421 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28883369 TTAGGGGTGT
28883379 TACATTTAG-TGG-TATCAAAGC
1 TACATTTAGTTGGTTATCAAAGC
28883400 TACAGTTTAGTTGGTTATCAAA
1 TACA-TTTAGTTGGTTATCAAA
28883422 CTGAATGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 3 0.16
24 7 0.37
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (23 bp):
TACATTTAGTTGGTTATCAAAGC
Found at i:28903449 original size:9 final size:9
Alignment explanation
Indices: 28903435--28903465 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28903425 GTTAAACGAA
28903435 TCGAGTTAT
1 TCGAGTTAT
*
28903444 TCGAGTTAA
1 TCGAGTTAT
28903453 TCGAGTTAT
1 TCGAGTTAT
28903462 TCGA
1 TCGA
28903466 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28903545 original size:9 final size:9
Alignment explanation
Indices: 28903518--28903554 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28903508 TGAGTTTTCG
28903518 AATTCGAAT
1 AATTCGAAT
* *
28903527 AACTCAAAT
1 AATTCGAAT
28903536 AATTCGAAT
1 AATTCGAAT
28903545 AATTCGAAT
1 AATTCGAAT
28903554 A
1 A
28903555 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28903802 original size:30 final size:31
Alignment explanation
Indices: 28903768--28903827 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
28903758 AAACCTTTTA
28903768 TTTTCCCCCCAAAA-TTTTACTCCC-TCCCAC
1 TTTT-CCCCCAAAACTTTTACTCCCTTCCCAC
* *
28903798 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28903828 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:28904761 original size:29 final size:29
Alignment explanation
Indices: 28904716--28904772 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
28904706 CATCAATAAA
*
28904716 GATAACCACAAAAAACATATGTAAATTAG
1 GATAACCACAAAAAACATAAGTAAATTAG
* *
28904745 GATAACTACAAAGAACATAAGTAAATTA
1 GATAACCACAAAAAACATAAGTAAATTA
28904773 CAGAAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.11, T:0.21
Consensus pattern (29 bp):
GATAACCACAAAAAACATAAGTAAATTAG
Found at i:28907765 original size:9 final size:9
Alignment explanation
Indices: 28907751--28907805 Score: 76
Period size: 9 Copynumber: 6.2 Consensus size: 9
28907741 TTTGGTTAAA
*
28907751 AATTACCCG
1 AATTAACCG
*
28907760 AATTACCCG
1 AATTAACCG
28907769 -ATTAACCG
1 AATTAACCG
28907777 AATTAACCG
1 AATTAACCG
28907786 AATTAACCG
1 AATTAACCG
*
28907795 AATTACCCG
1 AATTAACCG
28907804 AA
1 AA
28907806 AATTACCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
8 7 0.16
9 36 0.84
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:28907792 original size:18 final size:18
Alignment explanation
Indices: 28907751--28907805 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
28907741 TTTGGTTAAA
*
28907751 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
*
28907769 -ATTAACCGAATTAACCG
1 AATTAACCGAATTACCCG
28907786 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
28907804 AA
1 AA
28907806 AATTACCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:28908236 original size:14 final size:16
Alignment explanation
Indices: 28908217--28908248 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28908207 TAAGTCATAA
28908217 ATAATATA-AA-ATTT
1 ATAATATATAACATTT
28908231 ATAATATATAACATTT
1 ATAATATATAACATTT
28908247 AT
1 AT
28908249 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATAACATTT
Found at i:28908537 original size:13 final size:15
Alignment explanation
Indices: 28908503--28908536 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28908493 ATGTAAATTA
28908503 TTTTTTATAATGAAC
1 TTTTTTATAATGAAC
*
28908518 TTTTTTATTAT-AAC
1 TTTTTTATAATGAAC
28908532 TTTTT
1 TTTTT
28908537 ACAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTTATAATGAAC
Found at i:28913890 original size:26 final size:28
Alignment explanation
Indices: 28913838--28913890 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
28913828 TTAAGAAATC
*
28913838 TATTATTATTTTTTTATTATACTTATTCA
1 TATTATTATATTTTTATTATAC-TATTCA
*
28913867 TATTATTGTATTTTT-TTATA-TATT
1 TATTATTATATTTTTATTATACTATT
28913891 TGTTCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
28 5 0.23
29 13 0.59
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTATTATATTTTTATTATACTATTCA
Found at i:28918745 original size:23 final size:24
Alignment explanation
Indices: 28918717--28918762 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28918707 TATACGCTAT
*
28918717 ATTTTTGT-TGAATAAAATCAACA
1 ATTTTTATGTGAATAAAATCAACA
*
28918740 ATTTTTATGTGAATAATATCAAC
1 ATTTTTATGTGAATAAAATCAAC
28918763 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (24 bp):
ATTTTTATGTGAATAAAATCAACA
Found at i:28919597 original size:30 final size:31
Alignment explanation
Indices: 28919534--28919597 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
28919524 TAGTAAAGAT
*
28919534 AAAATTATATTTTAATCCTTTTTAAAATTATA
1 AAAATTATAATTTAATCC-TTTTAAAATTATA
28919566 AAAATT-TAATTTAATCC-TTTAAAATTTATA
1 AAAATTATAATTTAATCCTTTTAAAA-TTATA
28919596 AA
1 AA
28919598 GATAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 7 0.23
30 7 0.23
31 10 0.33
32 6 0.20
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
AAAATTATAATTTAATCCTTTTAAAATTATA
Found at i:28922182 original size:30 final size:30
Alignment explanation
Indices: 28922146--28922203 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28922136 CGGGTAACCT
*
28922146 TGATATAATGTCAGCTTGTGTGAGCAATCC
1 TGATATAATATCAGCTTGTGTGAGCAATCC
* *
28922176 TGATATACTATTAGCTTGTGTGAGCAAT
1 TGATATAATATCAGCTTGTGTGAGCAAT
28922204 TTATTCACAT
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:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (30 bp):
TGATATAATATCAGCTTGTGTGAGCAATCC
Found at i:28927119 original size:15 final size:15
Alignment explanation
Indices: 28927091--28927131 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
28927081 TTATCCAATC
28927091 AAATAAAG-AAAAAT
1 AAATAAAGCAAAAAT
28927105 AAATAAAGCAAAAAT
1 AAATAAAGCAAAAAT
* *
28927120 GAATAAAACAAA
1 AAATAAAGCAAA
28927132 GAAGCTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (15 bp):
AAATAAAGCAAAAAT
Found at i:28927905 original size:26 final size:26
Alignment explanation
Indices: 28927861--28927935 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
28927851 AAATTAAACC
28927861 TAAACCCAAGTT-ACC-AGCCCAAAAT
1 TAAACCCAA-TTAACCTAGCCCAAAAT
*
28927886 CT-AACCCAATTAACCTAGCCCAAACT
1 -TAAACCCAATTAACCTAGCCCAAAAT
* *
28927912 TAAACCCAACTACATCTAGCCCAA
1 TAAACCCAATTA-ACCTAGCCCAA
28927936 CTATCATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 19 0.45
27 10 0.24
ACGTcount: A:0.41, C:0.36, G:0.05, T:0.17
Consensus pattern (26 bp):
TAAACCCAATTAACCTAGCCCAAAAT
Found at i:28929495 original size:22 final size:21
Alignment explanation
Indices: 28929465--28929507 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28929455 AATTCATTTT
28929465 TTTTTAAAAAGCTTACTTATG
1 TTTTTAAAAAGCTTACTTATG
28929486 TTTTTAAAAAGCTTACTTATG
1 TTTTTAAAAAGCTTACTTATG
28929507 T
1 T
28929508 ATGAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTTTAAAAAGCTTACTTATG
Found at i:28931756 original size:16 final size:16
Alignment explanation
Indices: 28931737--28931767 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28931727 TTATTTTTAA
28931737 ATAAATCTAATTAAAT
1 ATAAATCTAATTAAAT
28931753 ATAAATCTAATTAAA
1 ATAAATCTAATTAAA
28931768 AGATTTATTT
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:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATCTAATTAAAT
Found at i:28934454 original size:126 final size:126
Alignment explanation
Indices: 28934247--28934541 Score: 432
Period size: 126 Copynumber: 2.4 Consensus size: 126
28934237 AGTGTTAATT
* * * *
28934247 TAAAA-AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCT-CTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
* * * * *
28934310 ACGTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGCAGGATGCTTTGTTAGGAAAAATAC
66 ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
* * *
28934371 TGAAAGAAGCTCTCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
* *
28934436 ACGGTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAGGACGCTTTGTCAGCAAAAGTAC
66 ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
* *
28934497 TAAAAGAAGCTCCCACATGGATGCGCTTTTGCTACAGTAGTTCCT
1 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCT
28934542 GTTTGGCCTG
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 4 0.03
125 33 0.22
126 114 0.75
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGAAG
ACGGTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTCAGCAAAAATAC
Found at i:28937795 original size:34 final size:36
Alignment explanation
Indices: 28937717--28937813 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 36
28937707 ATTTAAAAGA
* *
28937717 ATTTCTATTATATTAAA-AATGTAAAAGTAAATTTCT
1 ATTT-TATTACATTAAATAATATAAAAGTAAATTTCT
28937753 ATTTTATTACATTAAATAATATAAAAG-AAATTT-T
1 ATTTTATTACATTAAATAATATAAAAGTAAATTTCT
*
28937787 ATTTTATTACATCAAATAATATCAAAA
1 ATTTTATTACATTAAATAATAT-AAAA
28937814 TATTCAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
34 22 0.39
35 21 0.38
36 13 0.23
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (36 bp):
ATTTTATTACATTAAATAATATAAAAGTAAATTTCT
Found at i:28938258 original size:18 final size:18
Alignment explanation
Indices: 28938232--28938274 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28938222 GACTAGAAAA
* * *
28938232 AGGAAACATAGAAGGGTT
1 AGGATACATAAAAGGGCT
28938250 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
28938268 AGGATAC
1 AGGATAC
28938275 GCACCTGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:28938909 original size:7 final size:7
Alignment explanation
Indices: 28938899--28938923 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28938889 CATAATACAT
28938899 AATACTA
1 AATACTA
28938906 AATACTA
1 AATACTA
28938913 AATACTA
1 AATACTA
28938920 AATA
1 AATA
28938924 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28940180 original size:10 final size:10
Alignment explanation
Indices: 28940138--28940184 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 10
28940128 TTTTTAAGAG
*
28940138 GAAATTGAAA
1 GAAATTGAGA
28940148 GGAAATTGAGA
1 -GAAATTGAGA
28940159 GAATATTGGAGA
1 GAA-ATT-GAGA
28940171 GAAATTGAGA
1 GAAATTGAGA
28940181 GAAA
1 GAAA
28940185 GGATTTAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 11 0.33
11 15 0.45
12 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:28940869 original size:54 final size:52
Alignment explanation
Indices: 28940781--28940891 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 52
28940771 CCTTTGGTTT
28940781 TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATT-TATAA
1 TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATTCT-TAA
* * * *
28940833 TTTTGTTTCAAAATTTTGAA-TTTGATTGATGCATCTTAAAATTCGAATTCTTAA
1 TTTTG-TTCAAAA-TTTAAATTTTG-TTGAGGAATCTTAAAATTCAAATTCTTAA
28940887 TTTTG
1 TTTTG
28940892 ATTTTATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
52 5 0.10
53 11 0.22
54 34 0.67
55 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (52 bp):
TTTTGTTCAAAATTTAAATTTTGTTGAGGAATCTTAAAATTCAAATTCTTAA
Found at i:28943643 original size:14 final size:14
Alignment explanation
Indices: 28943624--28943651 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28943614 TCGCGAAATT
28943624 GTTGTGTGTCCATG
1 GTTGTGTGTCCATG
28943638 GTTGTGTGTCCATG
1 GTTGTGTGTCCATG
28943652 CGAGTCTCTT
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:0.07, C:0.14, G:0.36, T:0.43
Consensus pattern (14 bp):
GTTGTGTGTCCATG
Found at i:28944255 original size:7 final size:7
Alignment explanation
Indices: 28944243--28944267 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28944233 GAACATGTGT
28944243 GTTATGG
1 GTTATGG
28944250 GTTATGG
1 GTTATGG
28944257 GTTATGG
1 GTTATGG
28944264 GTTA
1 GTTA
28944268 ACATTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (7 bp):
GTTATGG
Found at i:28945142 original size:15 final size:15
Alignment explanation
Indices: 28945104--28945169 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
28945094 GAAGTCTAAG
* *
28945104 AAATAAAAATAACAC
1 AAATAAAAATAAAAA
*
28945119 AACTAAAAA-AAAGTAA
1 AAATAAAAATAAA--AA
* *
28945135 AAGTAAAAGTAAAAA
1 AAATAAAAATAAAAA
28945150 AAATAAAAATAAAAA
1 AAATAAAAATAAAAA
*
28945165 TAATA
1 AAATA
28945170 TTGAAAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 2 0.05
15 27 0.68
16 8 0.20
17 3 0.08
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (15 bp):
AAATAAAAATAAAAA
Found at i:28945150 original size:22 final size:21
Alignment explanation
Indices: 28945104--28945163 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
28945094 GAAGTCTAAG
*
28945104 AAATAAAAATAACACAACTAAAAA
1 AAATAAAAAT-A-A-AAGTAAAAA
*
28945128 AAAGTAAAAGTAAAAGTAAAAA
1 AAA-TAAAAATAAAAGTAAAAA
28945150 AAATAAAAATAAAA
1 AAATAAAAATAAAA
28945164 ATAATATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 10 0.31
22 11 0.34
23 1 0.03
24 4 0.12
25 6 0.19
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (21 bp):
AAATAAAAATAAAAGTAAAAA
Found at i:28946820 original size:16 final size:16
Alignment explanation
Indices: 28946755--28946818 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
28946745 GAATAACAAT
*
28946755 AATAAGAATAAGAATAA
1 AATAAAAATAA-AATAA
28946772 ATACTAAAAATAAAATAA
1 A-A-TAAAAATAAAATAA
* *
28946790 AAGAAAGATAAAATAA
1 AATAAAAATAAAATAA
28946806 AATAAGAAATAAA
1 AATAA-AAATAAA
28946819 TAGATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 16 0.41
17 8 0.21
18 7 0.18
19 8 0.21
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:28946826 original size:25 final size:25
Alignment explanation
Indices: 28946755--28946827 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
28946745 GAATAACAAT
*
28946755 AATAAGAATAAG-AATAAATA-CTAAA
1 AATAA-AATAAGAAATAAATAGAT-AA
*
28946780 AATAAAAT-A-AAA-GAA-AGATAA
1 AATAAAATAAGAAATAAATAGATAA
28946801 AATAAAATAAGAAATAAATAGATAA
1 AATAAAATAAGAAATAAATAGATAA
28946826 AA
1 AA
28946828 AGGGTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
21 11 0.28
22 4 0.10
23 6 0.15
24 5 0.13
25 13 0.33
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (25 bp):
AATAAAATAAGAAATAAATAGATAA
Found at i:28948840 original size:50 final size:50
Alignment explanation
Indices: 28948765--28948962 Score: 225
Period size: 50 Copynumber: 3.8 Consensus size: 50
28948755 CTTTCTTTAC
* * **
28948765 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *** *
28948815 TGCCCATGCCATGTCCTAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
28948865 TGCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
28948921 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28948963 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 79 0.65
53 2 0.02
56 41 0.34
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28951630 original size:20 final size:20
Alignment explanation
Indices: 28951567--28951632 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
28951557 TACTTCGGTA
* *
28951567 CCTTCGATTACACATACGTGC
1 CCTT-GATTGCACTTACGTGC
* * * *
28951588 CCCTGTTTGTACTT-CGATAC
1 CCTTGATTGCACTTACG-TGC
28951608 CCTTGATTGCACTTACGTGC
1 CCTTGATTGCACTTACGTGC
28951628 CCTTG
1 CCTTG
28951633 TTTACATTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.06
20 26 0.79
21 5 0.15
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.35
Consensus pattern (20 bp):
CCTTGATTGCACTTACGTGC
Found at i:28951635 original size:40 final size:39
Alignment explanation
Indices: 28951525--28951635 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
28951515 TATGTAAATT
*
28951525 ATACCC-TGATTGCACATACGTGACCCTATTTGTACTTCG
1 ATACCCTTGATTGCACATACGTG-CCCTGTTTGTACTTCG
* *
28951564 GTA-CCTTCGATTACACATACGTGCCCCTGTTTGTACTTCG
1 ATACCCTT-GATTGCACATACGTG-CCCTGTTTGTACTTCG
*
28951604 ATACCCTTGATTGCACTTACGTGCCCTTGTTT
1 ATACCCTTGATTGCACATACGTGCCC-TGTTT
28951636 ACATTTTGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.03
39 6 0.10
40 49 0.80
41 4 0.07
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (39 bp):
ATACCCTTGATTGCACATACGTGCCCTGTTTGTACTTCG
Found at i:28952965 original size:17 final size:17
Alignment explanation
Indices: 28952940--28952972 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28952930 GTTCAAAAAT
*
28952940 ATTTTTTTAATTTAATA
1 ATTTATTTAATTTAATA
28952957 ATTTATTTAATTTAAT
1 ATTTATTTAATTTAAT
28952973 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTTAATTTAATA
Found at i:28956404 original size:7 final size:7
Alignment explanation
Indices: 28956366--28956414 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
28956356 AAATAAGAAA
28956366 TAGGGTT
1 TAGGGTT
*
28956373 TAGTGTT
1 TAGGGTT
*
28956380 TAAGGTT
1 TAGGGTT
*
28956387 T-GGATT
1 TAGGGTT
28956393 T-GGGTT
1 TAGGGTT
28956399 TAGGGTT
1 TAGGGTT
28956406 TAGGGTT
1 TAGGGTT
28956413 TA
1 TA
28956415 TAGTTTGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 9 0.26
7 26 0.74
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:28957949 original size:25 final size:24
Alignment explanation
Indices: 28957921--28957968 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
28957911 TAGATTTAGT
28957921 TTTGATTTGGGGATTCAATTTCAAG
1 TTTGATTTGGGGATTC-ATTTCAAG
* * *
28957946 TTTGGTTTGTGGTTTCATTTCAA
1 TTTGATTTGGGGATTCATTTCAA
28957969 AGACCTTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (24 bp):
TTTGATTTGGGGATTCATTTCAAG
Found at i:28958741 original size:143 final size:143
Alignment explanation
Indices: 28958483--28958767 Score: 462
Period size: 143 Copynumber: 2.0 Consensus size: 143
28958473 CATCTTACGC
*
28958483 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTG
1 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
*
28958548 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTGGGGTCTGGTTTGGGGTTTTAGATTCG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
*
28958613 TCTACGATTTGGG
131 TCCACGATTTGGG
* * *
28958626 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATTTGTTC
1 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
* * * * *
28958691 ACAGCTTTAATTTGGGATTTTGAGTTATGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
*
28958756 TCCATGATTTGG
131 TCCACGATTTGG
28958768 TGATTTGATT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 130 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (143 bp):
TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
TCCACGATTTGGG
Found at i:28962047 original size:671 final size:679
Alignment explanation
Indices: 28959638--28963063 Score: 2668
Period size: 705 Copynumber: 4.9 Consensus size: 679
28959628 ATCTATAATT
* *
28959638 TTTATATTCTATA-TTTCAAAACCTCAATT-ACTTTTTGCTCATTTTAAGTTATCAAAACTCTAT
1 TTTATATTCTATATTTTCAGAATCTC-ATTGACTTTTTGCTCATTTTAAGTTATCAAAA--CTAT
** * * * * *
28959701 GGTCTTTCAAAAATTTGGTGGTTTTAATAATATTAATTTAGAGCTGAAATTTAATTCTAAAATAA
63 ACTCTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTTTAAAAAAA
* * * * * *
28959766 -GAAATTTTGTTTGATCAAAAAGAGTAACCAAAAGCCTAAGATTCGAGGCTTAAAACATTCAAAA
128 TAAAATTTT-TTTTATCAAAAAGAGTAACCAAAAGCCTAAAATTCGGGGCTTAAAACTTTAAAAA
* * * * * *
28959830 TCGTCACAATTTG-CTCAAAATTTCAAAGTTTTCTATTTCAAGTAGGCTACTTTGGGAGCTTGGT
192 TCGTCACAACTTGCCT-AGAATTTCAAAGTTTTCTGTTTCAAGTAGACTACTTTCGGAGCTAGGT
* * * * * * * **
28959894 TCTTTTAAGACACAACATAATTTGGCTTGGAAAACATACTAATGGAAAGATCACAGTTAATACAA
256 TCTTTTAACACAGAACTTATTTTGGCTTGGAAAACATACCAATGAAAAGAT-GCA-TTTCTACAA
* * * * ** * ** * *
28959959 TATAAATCATCTCACGTTCGACTAAAATGAAAAATAATAAAAGGTTTTTTAAAGCCTTATATTTA
319 TAGAAATAATCTCATGTTCGACTAGAATGAGCAACAATAAAAGGTTTTAGAAAGCTTTAAATTTA
* * ** *
28960024 GTTACCCAAATCTATTGAAAGCCTTAAATTAGGA--ATT-T-TGATATA-GGTTTCACTTTAGGG
384 G-----CAAA-CTGTTG-AA-CCTT-AA-TA-GATTATTATATTAT-TAGGGTTT-GGTTTGGGG
*** * * * * * *
28960084 TTTTAGATTTGGTTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATCCAAAG-C
436 TTTTAGATTCAATTTCAATATGGGGAGTCAATTTCAAGTTTGGTATGTGCTTTCGATTCAAAGTC
* *
28960148 TCTTTTGGTTGTTCGATAACCTCCAGAGGAACTAAACAAGTG-TGACAATTCTATAAGTTTGTAA
501 T-TTTTAGTTGTTCGATAACCTCC-GAGCAACTAAACAAGTGTTGA-AATTCTATAAGTTTGTAA
* * * *
28960212 TATATACAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATAATGTTTACCTTAA
563 TATATATAAATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATGATGTTTACATTAA
* ** * * * * * * **
28960277 TAAAAAATTGTTTGACCAACAACAATAATAATATGGAATAAAATCTAAAG-TT
628 TAAAACATAATTTGGCCAACAATAATATTAAAATGAAATAAAAT-AAAAGAAA
* * * *
28960329 TTTATA-AC-ATATATTTCAGAACCTCAATGACTTTTTCACTCATTTTAAGTTATCAAAACTCTA
1 TTTATATTCTATAT-TTTCAGAATCTCATTGACTTTTT-GCTCATTTTAAGTTATCAAAA--CTA
* * * * *
28960392 TGA-TCTTTCAAAATTTTGGTGGTTTTAATAATATTAATTTAGAGTTGGAATGTAATTCTAAAAC
62 T-ACTCTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTTTAAAAA
* * * * * * * * *
28960456 AA-AAAATTTTGCTTGATAAAAAAGAGTAACCGAAAGCCTAACACTCAGGGCTTAAAACATTCAA
126 AATAAAATTTT-TTTTATCAAAAAGAGTAACCAAAAGCCTAAAATTCGGGGCTTAAAACTTTAAA
* * * * *
28960520 AATCGTCACAA-TTGGCTCAAAATGTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GAGAGCTT
190 AATCGTCACAACTTGCCT-AGAATTTCAAAGTTTTCTGTTTCAAGTAGACTACTTTCG-GAGCTA
* * * ** * * *
28960583 GGTTCTTTTAAGAAACAACACAATTTGGCTTGGAAAAACATACTAATGGAAAGATCGCATTTCAT
253 GGTTCTTTTAACACAGAACTTATTTTGGCTTGG-AAAACATACCAATGAAAAGAT-GCATTTC-T
* ** * * * *
28960648 ACAATACAAATCCTCTCACT-TTCAATTAGAATGAGAAAAAATAAAAGGTTTCT-GAAAGCCTTT
315 ACAATAGAAATAATCTCA-TGTTCGACTAGAATGAGCAACAATAAAAGGTTT-TAGAAAG-CTTT
** * * *
28960711 -AATTTAGTTACCCAAATCTAATGAAAGCCTTAAATTTGGGATTTCGACATAGGTTTTGAATTTA
377 AAATTTAG-----CAAA-CTGTTG-AA-CCTT-AA--T-AGA-TT--A-TTA--TATT--A-TTA
* **** * * * * *
28960775 GGTTTTTGGTTT-GGGTTTTAGATTTGGCTTCAATTTGGGGATTCAAGTTCAATTTTGGTTTGTG
421 GG-GTTTGGTTTGGGGTTTTAGATTCAATTTCAATATGGGGAGTCAATTTCAAGTTTGGTATGTG
* * * * * * * * * * * * *
28960839 GTTGCAATTCGAAGCCCTTTTGGTTATTCGGTAACCTCCGGAGTAGCTAAACAAGTGTGGCAATT
485 CTTTCGATTCAAAGTCTTTTTAGTTGTTCGATAACCTCC-GAGCAACTAAACAAGTGTTGAAATT
*
28960904 CTATAAGTTTGTAATATATATAAATATATATATATTCAACAAAAAAATTTTAAAAATTAGTTTAA
549 CTATAAGTTTGTAATATATATAAATATATA-A-ATTCAAC-AAAAAATTTTAAAAATTAATTTAA
* *
28960969 TATGATGTTTATC-TTAATAAAACATAATTTGACCAACAATAATATTAAAATAAAATAAAAT---
611 TATGATGTTTA-CATTAATAAAACATAATTTGGCCAACAATAATATTAAAATGAAATAAAATAAA
*
28961030 CG-AA
675 AGAAA
* * * *
28961034 TTTTTATTATTATATATTTCAGAATCTCCA-TAACTTTTTGACTCATTTTAAGCTATCAAAATTC
1 TTTATATT-CTATAT-TTTCAGAATCT-CATTGACTTTTTG-CTCATTTTAAGTTATCAAAA--C
* *
28961098 TATACTCTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTCAAATGTAATTCTAAAA
60 TATACTCTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTTTAAAA
* ** ** *
28961163 CAAT---A-TTTTTTTATCAAACAA-AGTAACCAAAAGCCTAAGGTTCAAGGCTTAAAACTTTGA
125 AAATAAAATTTTTTTTATCAAA-AAGAGTAACCAAAAGCCTAAAATTCGGGGCTTAAAACTTTAA
* * * *
28961223 AAATCGTCACAACTTGCCCAGAATTTTAAAG-TTTCTTGTTTCAAGTAGACTACTTTGGGAGCTT
189 AAATCGTCACAACTTGCCTAGAATTTCAAAGTTTTC-TGTTTCAAGTAGACTACTTTCGGAGCTA
* * ** * * * *
28961287 GGTTATTTTAACATAGAACACATTTTGGCATGGAAAATAGACAAATGAAAAGATGACATTTTCTA
253 GGTTCTTTTAACACAGAACTTATTTTGGCTTGGAAAACATACCAATGAAAAGATG-CA-TTTCTA
* * * *
28961352 CAATAGAAATAACCTCACGTTCGACTAGAATGAGCAACAATAGAAGGATTTAGAAAGCTTTAAAT
316 CAATAGAAATAATCTCATGTTCGACTAGAATGAGCAACAATAAAAGGTTTTAGAAAGCTTTAAAT
* *
28961417 TT-G-AGA-TTTTG-A-CTT-A-AG-TT-TTA-A-T-TTAGGGTTTTGGTTT-GGGTTTTAGATT
381 TTAGCAAACTGTTGAACCTTAATAGATTATTATATTATTAGGG-TTTGGTTTGGGGTTTTAGATT
* * * * *
28961469 CAATTTCGATATGGGGAGT-AGATTT-ATGTTTTGGTCT-TGCCTTTTGATTCGAAGGTC-TTTT
445 CAATTTCAATATGGGGAGTCA-ATTTCAAG-TTTGGTATGTG-CTTTCGATTC-AAAGTCTTTTT
* * * *
28961530 AGTTGTTCGATAACCT-C-A-CAACTAAACAATTGTTGTAATTCTATAAGTTTGTAATATATTTT
506 AGTTGTTCGATAACCTCCGAGCAACTAAACAAGTGTTGAAATTCTATAAGTTTGTAATATATATA
* * *
28961592 AATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATTATATTTACATGAATAAAACAT
571 AATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATGATGTTTACATTAATAAAACAT
28961657 AATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAA
636 AATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAA
* *
28961701 TTTATATTCTATATTTTC-GAATCTCATTGACTTTTTAGCTCATTTTAAGTTACCAAAACTCTAC
1 TTTATATTCTATATTTTCAGAATCTCATTGACTTTTT-GCTCATTTTAAGTTATCAAAACTATAC
* * *
28961765 TCTTTCAAAAATTTGGTGGTTTTAATAATAATAATAATTTATAGTTGAAATGTAATTTTAAAATA
65 TCTTTCAAAAATTTGGTTGTTTTAATAAT-AT--TAATTTAGAGTTGAAATGTAATTTTAAAAAA
* * * * * * *
28961830 ATAAAATTTTTGTTTAATCAAAAAGAGTAATCAAATGCCAAAAATTTGGGGGTAAAAAAATTT-A
127 ATAAAATTTTT-TTT-ATCAAAAAGAGTAACCAAAAGCCTAAAATTCGGGGCT-TAAAACTTTAA
* *
28961894 AAATCGTCACAACTTGCCTAGAATTTCAAAGTTTTCTGTTTCAAGTACG-CTAATTTCGGTGCTA
189 AAATCGTCACAACTTGCCTAGAATTTCAAAGTTTTCTGTTTCAAGTA-GACTACTTTCGGAGCTA
* *
28961958 GGTTCTTTTAACACAGAACTTATTTTGGCTTGCAAAACATACCAATGGAAAGATCGCATTTCATA
253 GGTTCTTTTAACACAGAACTTATTTTGGCTTGGAAAACATACCAATGAAAAGAT-GCATTTC-TA
* * * * *
28962023 CAACAGATATCATCTCATGTTCGACTAGAATGA-CAAACAATAAAAGGTTTTAAAAAGCCTTAAA
316 CAATAGAAATAATCTCATGTTCGACTAGAATGAGC-AACAATAAAAGGTTTTAGAAAGCTTTAAA
28962087 TTTAGTTACCCAAACCTGTTGAAAGCCTTCAATTTGAGATTTCAACTTATATTTCAAATTAGGGT
380 TTTAG-----CAAA-CTGTTG-AA-CCTT-AA--T-AGA-TT--A-TTATA-TT---ATTAGGGT
* * * * *
28962152 TTGGTTTGGGGTTTTATATTCGATTTCAATTTGGGGATTCAATTTCAAGTTTGGTATGTGGTTTC
425 TTGGTTTGGGGTTTTAGATTCAATTTCAATATGGGGAGTCAATTTCAAGTTTGGTATGTGCTTTC
* * *
28962217 GATTCAAAGTCTTTTTGGTTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGAAATTCTATA
490 GATTCAAAGTCTTTTTAGTTGTTCGATAACCTCC-GAGCAACTAAACAAGTGTTGAAATTCTATA
* * *
28962282 AGTTTGTAACATATATATAAATATATAAATTTAACAAAAAAATTTAAAAATTAATTTAGTATGAT
554 AGTTTGT-A-ATATATATAAATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATGAT
* ** *
28962347 GTTTATATTAATAAAACATAATTTGGAAAACAATAATATTAAAATGAAATAATATAAAA-AAA
617 GTTTACATTAATAAAACATAATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAA
* * *
28962409 -TTGTATTCTATA-TTTCAGAATCTCATAGACTTTTTGGTTCATTTTAAGTTATCAAAACTTTAT
1 TTTATATTCTATATTTTCAGAATCTCATTGACTTTTT-GCTCATTTTAAGTTATCAAAAC--TAT
* * * *
28962472 GCTCTTTCAAAAATTTGATTGTTTTAATAGTATTAATTTAGAGTTGAAATGTAATTCTAAAAAAA
63 ACTCTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTGAAATGTAATT-TTAAAAAA
* * *
28962537 ATAAAATTTTTTTTATCAAATAGAGTAACCAAAAGCCTAATATTCGGTGCTTAAAACTTTAAAAA
127 ATAAAATTTTTTTTATCAAAAAGAGTAACCAAAAGCCTAAAATTCGGGGCTTAAAACTTTAAAAA
** * *
28962602 TTATCACAACTTGCCTAGAATTTGAAAGTTTTCTATTTCAAGTAGACTACTTTCGGAGC-ATGGT
192 TCGTCACAACTTGCCTAGAATTTCAAAGTTTTCTGTTTCAAGTAGACTACTTTCGGAGCTA-GGT
* * * *
28962666 TCTTTTAACACAG-AGTTCATTTTGACTTGGAAAACATGCCAATGAAAAGATTGCATTTTGTACA
256 TCTTTTAACACAGAACTT-ATTTTGGCTTGGAAAACATACCAATGAAAAGA-TGCA-TTTCTACA
* *
28962730 ATAGAAATAATCTCATGTTCGACTAGAATGAGCAACAATATAAGGTTTTAGAAAGTTTTAAATTT
318 ATAGAAATAATCTCATGTTCGACTAGAATGAGCAACAATAAAAGGTTTTAGAAAGCTTT-AA---
* * * *
28962795 ATTTACCCAAATCTATTGAAAGCCTTAAATTTGATATTTTGACTTAGGTTTCAATTTAGGGTTTT
379 ATTTA-GCAAA-CTGTTG-AA-CCTT-AA-TAGAT-TATT-A--TA---TT--A-TTAGGG-TTT
* ** * * * * * * *
28962860 TGTTTGGGGTTTTAGATTCAATTTTTATCA-GGTGATTCAATTT-TAGTTTTGATTTATGGTTTC
427 GGTTTGGGGTTTTAGATTCAATTTCAAT-ATGGGGAGTCAATTTCAAG-TTTGGTATGTGCTTTC
** * * * * * * * *
28962923 GATTTGAAGGC-ATTTGGTTTTTCGATAACCTCTTGAGTAACTAAACAAGGGTTGTAATTCTATA
490 GATTCAAAGTCTTTTTAGTTGTTCGATAACCTC-CGAGCAACTAAACAAGTGTTGAAATTCTATA
* *
28962987 AGTTTGTAATATATATAAATATATAAATTCAACAAAATA-TTT-AAAATTTATTTAATATGATGT
554 AGTTTGTAATATATATAAATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATGATGT
28963050 TTACATTAATAAAA
619 TTACATTAATAAAA
28963064 TTGTTGGTTT
Statistics
Matches: 2273, Mismatches: 313, Indels: 288
0.79 0.11 0.10
Matches are distributed among these distances:
662 34 0.01
663 81 0.04
664 39 0.02
665 35 0.02
666 51 0.02
667 10 0.00
668 1 0.00
669 9 0.00
670 80 0.04
671 184 0.08
672 14 0.01
674 1 0.00
678 4 0.00
680 4 0.00
682 3 0.00
684 4 0.00
686 1 0.00
688 1 0.00
689 3 0.00
690 8 0.00
691 28 0.01
692 229 0.10
693 103 0.05
694 11 0.00
696 5 0.00
697 1 0.00
699 2 0.00
700 3 0.00
701 33 0.01
702 24 0.01
703 177 0.08
704 140 0.06
705 284 0.12
706 228 0.10
707 105 0.05
708 122 0.05
709 210 0.09
710 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (679 bp):
TTTATATTCTATATTTTCAGAATCTCATTGACTTTTTGCTCATTTTAAGTTATCAAAACTATACT
CTTTCAAAAATTTGGTTGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTTTAAAAAAATAA
AATTTTTTTTATCAAAAAGAGTAACCAAAAGCCTAAAATTCGGGGCTTAAAACTTTAAAAATCGT
CACAACTTGCCTAGAATTTCAAAGTTTTCTGTTTCAAGTAGACTACTTTCGGAGCTAGGTTCTTT
TAACACAGAACTTATTTTGGCTTGGAAAACATACCAATGAAAAGATGCATTTCTACAATAGAAAT
AATCTCATGTTCGACTAGAATGAGCAACAATAAAAGGTTTTAGAAAGCTTTAAATTTAGCAAACT
GTTGAACCTTAATAGATTATTATATTATTAGGGTTTGGTTTGGGGTTTTAGATTCAATTTCAATA
TGGGGAGTCAATTTCAAGTTTGGTATGTGCTTTCGATTCAAAGTCTTTTTAGTTGTTCGATAACC
TCCGAGCAACTAAACAAGTGTTGAAATTCTATAAGTTTGTAATATATATAAATATATAAATTCAA
CAAAAAATTTTAAAAATTAATTTAATATGATGTTTACATTAATAAAACATAATTTGGCCAACAAT
AATATTAAAATGAAATAAAATAAAAGAAA
Found at i:28966905 original size:16 final size:18
Alignment explanation
Indices: 28966873--28966905 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
28966863 ATATATTATA
28966873 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
28966891 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
28966906 AAAAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:28968046 original size:25 final size:25
Alignment explanation
Indices: 28968018--28968065 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28968008 TGTCATTGAC
*
28968018 ATTGAAATGGCAAAGATGAGAAAAT
1 ATTGAAATGACAAAGATGAGAAAAT
*
28968043 ATTGAAATGACAAATATGAGAAA
1 ATTGAAATGACAAAGATGAGAAA
28968066 TGATTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (25 bp):
ATTGAAATGACAAAGATGAGAAAAT
Found at i:28969373 original size:49 final size:49
Alignment explanation
Indices: 28969301--28969394 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
28969291 TCAAGAAGGG
* *
28969301 ATAAATAGTGATAAGAGTGTAGATAATGGAAGACTAAATTTAGCAATGT
1 ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCAATGT
* *
28969350 ATAAATAGTGATAAAAGTGTAGATAGTGGAAGACCAATTTTAGCA
1 ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCA
28969395 TTGCATAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (49 bp):
ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCAATGT
Found at i:28972151 original size:119 final size:120
Alignment explanation
Indices: 28971969--28972191 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
28971959 TCCTCGTTCA
*
28971969 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
28972034 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
28972089 AATGCCTTC-GGACTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
28972151 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
28972192 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 69 0.77
120 17 0.19
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:28972191 original size:40 final size:40
Alignment explanation
Indices: 28971967--28972191 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
28971957 ACTCCTCGTT
* *
28971967 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28972007 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28972047 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28972087 CCAATGCCTTC-GGACTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
28972126 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28972167 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28972192 CATCATTCAA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 37 0.22
40 116 0.70
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28977643 original size:16 final size:18
Alignment explanation
Indices: 28977622--28977655 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
28977612 TGTAGCTAAT
28977622 TAAATTTT-TG-AATTAG
1 TAAATTTTGTGAAATTAG
28977638 TAAATTTTGTGAAATTAG
1 TAAATTTTGTGAAATTAG
28977656 GAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TAAATTTTGTGAAATTAG
Found at i:28977881 original size:16 final size:18
Alignment explanation
Indices: 28977849--28977881 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
28977839 ATATATTATA
28977849 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
28977867 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
28977882 AAAAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:28977930 original size:13 final size:13
Alignment explanation
Indices: 28977912--28977942 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28977902 CATGCAAATT
28977912 AGAAAAGAAAAAA
1 AGAAAAGAAAAAA
*
28977925 AGAAAAGAAAGAA
1 AGAAAAGAAAAAA
28977938 AGAAA
1 AGAAA
28977943 TGGAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAAAA
Found at i:28978680 original size:25 final size:25
Alignment explanation
Indices: 28978632--28978680 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
28978622 CATAATTGAA
* * *
28978632 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
28978657 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
28978681 ATGTGTGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:28981422 original size:100 final size:99
Alignment explanation
Indices: 28981248--28981436 Score: 272
Period size: 100 Copynumber: 1.9 Consensus size: 99
28981238 TAAAATATTG
* * *
28981248 AATGTTTAAATGTTTAAATGTTTCCGATTGTATGGTAATGCTCCATAACCCTAATCTAGCGACGG
1 AATGTTTAAATGTTTAAATGTTTCCGATTGTACGGTAATGCTCCATAACCCTAATCCAGCGACGA
* *
28981313 AGACGGGTTAGGGGTGTTACATTTAGAAATTTTTC
66 AGACAGGTTAGGGATGTTAC-TTTAGAAATTTTTC
* * * *
28981348 AATGTTTAAATGTTTAAATGTTTTCGATTGTACGGTAATGCAT-CGTAACCCTAATCCAGTGATG
1 AATGTTTAAATGTTTAAATGTTTCCGATTGTACGGTAATGC-TCCATAACCCTAATCCAGCGACG
28981412 AAGACAGGTTAGGGATGTTACTTTA
65 AAGACAGGTTAGGGATGTTACTTTA
28981437 TATGTAGGTA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
99 4 0.05
100 74 0.94
101 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (99 bp):
AATGTTTAAATGTTTAAATGTTTCCGATTGTACGGTAATGCTCCATAACCCTAATCCAGCGACGA
AGACAGGTTAGGGATGTTACTTTAGAAATTTTTC
Found at i:28998424 original size:15 final size:14
Alignment explanation
Indices: 28998405--28998449 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
28998395 TTTGAAGGAC
28998405 TAAAAAGAAGAAAA
1 TAAAAAGAAGAAAA
* *
28998419 GAAAAAGAACAAAAA
1 TAAAAAGAA-GAAAA
28998434 TAAAAAGAAAGAAAA
1 TAAAAAG-AAGAAAA
28998449 T
1 T
28998450 GGAAGAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 8 0.32
15 15 0.60
16 2 0.08
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (14 bp):
TAAAAAGAAGAAAA
Found at i:29001320 original size:11 final size:11
Alignment explanation
Indices: 29001304--29001329 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29001294 AGGTCCAAGG
29001304 TAAGTTGATTT
1 TAAGTTGATTT
29001315 TAAGTTGATTT
1 TAAGTTGATTT
29001326 TAAG
1 TAAG
29001330 GTTGTTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (11 bp):
TAAGTTGATTT
Found at i:29005195 original size:32 final size:32
Alignment explanation
Indices: 29005159--29005241 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
29005149 ACAATTATGG
* * *
29005159 AACCTAGTTTTGAGGTTTACTTATGATTTAA-A
1 AACCTAGTTGTGAGGCTTACTGATGA-TTAATA
*
29005191 AACCTAGTTGTAAGGCTTACTGATGATTAATA
1 AACCTAGTTGTGAGGCTTACTGATGATTAATA
29005223 AACCTAGTTGTGAGGCTTA
1 AACCTAGTTGTGAGGCTTA
29005242 TTGAGGTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (32 bp):
AACCTAGTTGTGAGGCTTACTGATGATTAATA
Found at i:29005598 original size:31 final size:32
Alignment explanation
Indices: 29005563--29005627 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
29005553 AAGCCGAGCA
*
29005563 TTAAGGTCCATATTAA-TTTATAA-ACCTAGTT
1 TTAAGGCCCATATTAATTTTA-AAGACCTAGTT
* *
29005594 TTAAGGCCCATTTTTATTTTAAAGACCTAGTT
1 TTAAGGCCCATATTAATTTTAAAGACCTAGTT
29005626 TT
1 TT
29005628 GACATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (32 bp):
TTAAGGCCCATATTAATTTTAAAGACCTAGTT
Found at i:29011471 original size:29 final size:30
Alignment explanation
Indices: 29011432--29011492 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
29011422 CAAATTTTTT
29011432 TATATAAAATT-ACATAAAACCAAAATTTA
1 TATATAAAATTAACATAAAACCAAAATTTA
* * *
29011461 TATATACAATTACACATTAAACCATAATTTA
1 TATATAAAATTA-ACATAAAACCAAAATTTA
29011492 T
1 T
29011493 TTTGCCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
31 17 0.63
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
TATATAAAATTAACATAAAACCAAAATTTA
Found at i:29014664 original size:11 final size:11
Alignment explanation
Indices: 29014648--29014673 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29014638 GTAGGAAGGG
29014648 GAAAGAAAAAA
1 GAAAGAAAAAA
29014659 GAAAGAAAAAA
1 GAAAGAAAAAA
29014670 GAAA
1 GAAA
29014674 TTATTAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:29014799 original size:23 final size:23
Alignment explanation
Indices: 29014767--29014831 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
29014757 TAGATTTTTC
*
29014767 CTAAACATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
29014790 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
29014813 CTAAATATTATCACTAAAT
1 CTAAATATTATCACTAAAT
29014832 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:29014808 original size:13 final size:13
Alignment explanation
Indices: 29014767--29014831 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
29014757 TAGATTTTTC
*
29014767 CTAAACATTATCA
1 CTAAATATTATCA
*
29014780 CTAAATA--AT-T
1 CTAAATATTATCA
29014790 CTAAATATTATCA
1 CTAAATATTATCA
*
29014803 CTAAATA--AT-T
1 CTAAATATTATCA
29014813 CTAAATATTATCA
1 CTAAATATTATCA
29014826 CTAAAT
1 CTAAAT
29014832 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
10 14 0.34
11 4 0.10
12 4 0.10
13 19 0.46
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:29020121 original size:23 final size:23
Alignment explanation
Indices: 29020070--29020115 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29020060 TAGATTTTTC
*
29020070 CTAAACATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
29020093 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
29020116 TGAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:29020148 original size:12 final size:12
Alignment explanation
Indices: 29020131--29020155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29020121 TTTAAAAATT
29020131 GAATTTAAACTA
1 GAATTTAAACTA
29020143 GAATTTAAACTA
1 GAATTTAAACTA
29020155 G
1 G
29020156 TTACAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (12 bp):
GAATTTAAACTA
Found at i:29022690 original size:20 final size:20
Alignment explanation
Indices: 29022665--29022711 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
29022655 ATATCTCGTT
29022665 TTGATTTGATTTTAATCAAA
1 TTGATTTGATTTTAATCAAA
*
29022685 TTGATTTGATTTTATTCAAA
1 TTGATTTGATTTTAATCAAA
29022705 TTGATTT
1 TTGATTT
29022712 AAAGGCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (20 bp):
TTGATTTGATTTTAATCAAA
Found at i:29023120 original size:6 final size:6
Alignment explanation
Indices: 29023093--29023158 Score: 98
Period size: 6 Copynumber: 11.0 Consensus size: 6
29023083 ATTTGTTCAA
**
29023093 ATATTT -TATTT AATATAA ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT -ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
29023141 ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT
29023159 GTTTGCTAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.09
6 46 0.85
7 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:29025070 original size:76 final size:77
Alignment explanation
Indices: 29024944--29025097 Score: 247
Period size: 76 Copynumber: 2.0 Consensus size: 77
29024934 GTTTGGGTAA
* *
29024944 TCCACGGGCAATTAGAAGACTCCGGCATGTGTTGAAGATGTATAATCCCCAAGTAG-TCTTTTTT
1 TCCACGGGCAATTAGAAAACTCCGGCATGTGCTGAAGATGTATAATCCCCAAGTAGTTCTTTTTT
29025008 GTGGAGACTAAG
66 GTGGAGACTAAG
* * * *
29025020 TCCACGGGCAGTTAGAAAACTTCGGCATGTGCTGAAGATGTATAATCCCCAGGTAGTTTTTTTTT
1 TCCACGGGCAATTAGAAAACTCCGGCATGTGCTGAAGATGTATAATCCCCAAGTAGTTCTTTTTT
29025085 GTGGAGACTAAG
66 GTGGAGACTAAG
29025097 T
1 T
29025098 TATGCAAGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 51 0.72
77 20 0.28
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (77 bp):
TCCACGGGCAATTAGAAAACTCCGGCATGTGCTGAAGATGTATAATCCCCAAGTAGTTCTTTTTT
GTGGAGACTAAG
Found at i:29036912 original size:31 final size:31
Alignment explanation
Indices: 29036868--29036944 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
29036858 ATCACACTAG
* *
29036868 TAGTC-TCCTAACTATTAGTCAATTTCTTTTT
1 TAGTCATCC-AACTATTAGTAAATTTATTTTT
29036899 TAGTCATCCAACTATTAGTAAATTTATTTTT
1 TAGTCATCCAACTATTAGTAAATTTATTTTT
* *
29036930 TGGTCATCTAACTAT
1 TAGTCATCCAACTAT
29036945 GAAAAGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (31 bp):
TAGTCATCCAACTATTAGTAAATTTATTTTT
Found at i:29037522 original size:18 final size:17
Alignment explanation
Indices: 29037494--29037527 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
29037484 TTAATCACTT
29037494 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
29037511 TAATATTTAAATTTAAT
1 TAATA-TTAAATTTAAT
29037528 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:29039587 original size:29 final size:29
Alignment explanation
Indices: 29039554--29039614 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
29039544 ACAAAATTGA
*
29039554 ATAATTAGGTGATCATTCTGTAACTTTTC
1 ATAATTAGGTGACCATTCTGTAACTTTTC
* *
29039583 ATAATTGGGTGACCATTTTGTAACTTTTC
1 ATAATTAGGTGACCATTCTGTAACTTTTC
29039612 ATA
1 ATA
29039615 TTTGAGTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (29 bp):
ATAATTAGGTGACCATTCTGTAACTTTTC
Found at i:29041118 original size:47 final size:47
Alignment explanation
Indices: 29041047--29041136 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
29041037 ACCTGCAAAC
* *
29041047 CCCTATCACCAAATACCTACGAACACCTATTACTAGACACATGTGAA
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGTGAA
* **
29041094 CCCTATCACCAGATACCTGTGAACACCTATCACCAGACACATG
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATG
29041137 CAAAACACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.36, C:0.34, G:0.10, T:0.20
Consensus pattern (47 bp):
CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGTGAA
Found at i:29041179 original size:24 final size:23
Alignment explanation
Indices: 29041047--29041181 Score: 108
Period size: 24 Copynumber: 5.7 Consensus size: 23
29041037 ACCTGCAAAC
* * * *
29041047 CCCTATCACCAAATACCTACGAA
1 CCCTATCACCAGACACATGCGAA
* * *
29041070 CACCTATTACTAGACACATGTGAA
1 C-CCTATCACCAGACACATGCGAA
* * *
29041094 CCCTATCACCAGATACCTGTGAA
1 CCCTATCACCAGACACATGCGAA
*
29041117 CACCTATCACCAGACACATGCAAAA
1 C-CCTATCACCAGACACATGC-GAA
* * *
29041142 CACTACCACTAGACACATGCGAA
1 CCCTATCACCAGACACATGCGAA
29041165 CCCATATCACCAGACAC
1 CCC-TATCACCAGACAC
29041182 CTGTAAATCC
Statistics
Matches: 86, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
23 24 0.28
24 59 0.69
25 3 0.03
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.17
Consensus pattern (23 bp):
CCCTATCACCAGACACATGCGAA
Found at i:29043229 original size:46 final size:46
Alignment explanation
Indices: 29043175--29043288 Score: 169
Period size: 46 Copynumber: 2.5 Consensus size: 46
29043165 AGTGTATTGA
* *
29043175 ATCGGGCCTTGAGCCTAGCAGGTTTTATGCCGGTGTATTTTAATGT
1 ATCGGGCCTTGAGCCTAGCAGGTTTTATGCCGGTGTACTGTAATGT
29043221 ATCGGGCCTT-ATGCCTAGCAGGTTTTATGCCGGTGTACTGTAATGT
1 ATCGGGCCTTGA-GCCTAGCAGGTTTTATGCCGGTGTACTGTAATGT
*
29043267 ATCAGGCCTTGTA-CCTAGCAGG
1 ATCGGGCCTTG-AGCCTAGCAGG
29043289 CTTCATATCG
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
45 1 0.02
46 60 0.97
48 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.33
Consensus pattern (46 bp):
ATCGGGCCTTGAGCCTAGCAGGTTTTATGCCGGTGTACTGTAATGT
Found at i:29044731 original size:23 final size:24
Alignment explanation
Indices: 29044683--29044782 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
29044673 GTGTTACAAT
* ***
29044683 CCCTATCACCAGACACCTGCAAAC
1 CCCTATCACCAGACACATATGAAC
* *
29044707 CCCTAT-ACCAGACACCTATGGAC
1 CCCTATCACCAGACACATATGAAC
*
29044730 CCCTATCACTAGACACATATGAAC
1 CCCTATCACCAGACACATATGAAC
** * **
29044754 CCCTATTTCCAGATACATGCGAAC
1 CCCTATCACCAGACACATATGAAC
29044778 CCCTA
1 CCCTA
29044783 CAGTGAACCC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
23 19 0.31
24 43 0.69
ACGTcount: A:0.32, C:0.39, G:0.10, T:0.19
Consensus pattern (24 bp):
CCCTATCACCAGACACATATGAAC
Found at i:29046927 original size:17 final size:16
Alignment explanation
Indices: 29046907--29046946 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
29046897 ATGGAATTAG
29046907 AATTTACTTGAAAAAAT
1 AATTTAC-TGAAAAAAT
29046924 AATTTAACTGAAAAAAT
1 AATTT-ACTGAAAAAAT
*
29046941 TATTTA
1 AATTTA
29046947 AATTCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.86
18 2 0.10
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (16 bp):
AATTTACTGAAAAAAT
Found at i:29046947 original size:17 final size:17
Alignment explanation
Indices: 29046915--29046947 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29046905 AGAATTTACT
29046915 TGAAAAAATAATTTAAC
1 TGAAAAAATAATTTAAC
*
29046932 TGAAAAAATTATTTAA
1 TGAAAAAATAATTTAA
29046948 ATTCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
TGAAAAAATAATTTAAC
Found at i:29050353 original size:24 final size:24
Alignment explanation
Indices: 29050297--29050372 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
29050287 CCGGATAATA
* *
29050297 TAACGGGAAGCTCACAAAGAGC-CT
1 TAACGGGTAGCTC-CAAAGAGCAAT
29050321 ATAAC-GGTAGCTCCAAAGAGCAAT
1 -TAACGGGTAGCTCCAAAGAGCAAT
29050345 TAACGGGTAGCTCCAAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGCAAT
29050369 TAAC
1 TAAC
29050373 AGGAAGCACC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.26
24 31 0.66
25 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGCAAT
Found at i:29050465 original size:26 final size:26
Alignment explanation
Indices: 29050422--29050482 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
29050412 ATCACTAATA
*
29050422 GGAAGCTCACAAAGAGCC-TTTAATCG
1 GGAAGCTCACAAAGAGCCATATAA-CG
*
29050448 GGAAGCTCACGATA-AGCCATATAACG
1 GGAAGCTCAC-AAAGAGCCATATAACG
*
29050474 GGACGCTCA
1 GGAAGCTCA
29050483 TAAGAGCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATATAACG
Found at i:29052690 original size:25 final size:24
Alignment explanation
Indices: 29052662--29052709 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
29052652 AGATACTTTT
*
29052662 TTTATTATAAAATATCACATTTTAG
1 TTTATTATAAAATAT-AAATTTTAG
29052687 TTTATTATAAAATATAAATTTTA
1 TTTATTATAAAATATAAATTTTA
29052710 AAAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATTATAAAATATAAATTTTAG
Found at i:29052742 original size:22 final size:20
Alignment explanation
Indices: 29052709--29052748 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
29052699 TATAAATTTT
*
29052709 AAAAATGTAAAATTTTATTA
1 AAAAATGTAAAAGTTTATTA
29052729 AAAATATGTAAAAAGTTTAT
1 AAAA-ATGT-AAAAGTTTAT
29052749 AATGTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAAATGTAAAAGTTTATTA
Found at i:29053624 original size:23 final size:23
Alignment explanation
Indices: 29053596--29053639 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29053586 TAATACTATT
29053596 TAATAA-TGGTAACAATAGTAAAA
1 TAATAAGTGG-AACAATAGTAAAA
*
29053619 TAATAAGTGGAACATTAGTAA
1 TAATAAGTGGAACAATAGTAA
29053640 TAACCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (23 bp):
TAATAAGTGGAACAATAGTAAAA
Found at i:29055406 original size:28 final size:27
Alignment explanation
Indices: 29055359--29055411 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
29055349 TTTTTATTAA
29055359 TTTTTATATTTAAAATTTTTAAAATGT
1 TTTTTATATTTAAAATTTTTAAAATGT
*
29055386 TTTTATATATTTTTAAA-TTTTAAAAT
1 TTTT-TATA-TTTAAAATTTTTAAAAT
29055412 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 13 0.57
29 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTATATTTAAAATTTTTAAAATGT
Found at i:29067827 original size:30 final size:30
Alignment explanation
Indices: 29067773--29067830 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29067763 GCGTTTTAGT
*
29067773 AAAACCGGACCATTCCCATTATTTTTTTAA
1 AAAACCGGACCATTCCCATAATTTTTTTAA
* * *
29067803 AAAAGCGGCCCATTTCCATAATTTTTTT
1 AAAACCGGACCATTCCCATAATTTTTTT
29067831 TAGAAATGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (30 bp):
AAAACCGGACCATTCCCATAATTTTTTTAA
Found at i:29070096 original size:24 final size:24
Alignment explanation
Indices: 29070055--29070139 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
29070045 GAAGATGGAA
* * *
29070055 ATGAAGACGAAAATGAGGGTAGAG
1 ATGAAGATGAAGACGAGGGTAGAG
*
29070079 ATGAAGATGAAGACGAGGG-ACTAG
1 ATGAAGATGAAGACGAGGGTA-GAG
* * *
29070103 ATGAAGATGAATAC-AGGGATCGGG
1 ATGAAGATGAAGACGAGGG-TAGAG
*
29070127 GTGAAGATGAAGA
1 ATGAAGATGAAGA
29070140 AGATGAAGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.10
24 43 0.90
ACGTcount: A:0.42, C:0.06, G:0.38, T:0.14
Consensus pattern (24 bp):
ATGAAGATGAAGACGAGGGTAGAG
Found at i:29079561 original size:23 final size:24
Alignment explanation
Indices: 29079522--29079569 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
29079512 TTTATTTGAT
29079522 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
29079547 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
29079569 A
1 A
29079570 GTTGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:29080685 original size:23 final size:24
Alignment explanation
Indices: 29080646--29080693 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
29080636 TTTATTTGAT
29080646 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
29080671 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
29080693 A
1 A
29080694 GTTGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:29084245 original size:138 final size:138
Alignment explanation
Indices: 29083997--29084555 Score: 793
Period size: 138 Copynumber: 4.1 Consensus size: 138
29083987 TAGAAAAAAG
* *
29083997 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
29084062 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
66 TATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
29084126 CTATATATT
131 C-ATATATT
* * * * *
29084135 AATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTGACTGAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* ** *
29084200 TATAACTGATTATATTAATAAATTCGGTAATATATATGTAATTAATATTTTTTATGAATCAAATT
66 TATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
29084265 CATATATT
131 CATATATT
* * *
29084273 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTATTTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
** * * * *
29084338 TATGTCT-ATTTATATTATTAAATTAGGTAAAATATATATAATTAATATTTT-TATGAATCACAT
66 TATAACTGA-TTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
*
29084401 TCAGATATT
130 TCATATATT
* * *
29084410 AATTATATTCTTTCCAAAAGAATATTAATTGCTATATCTTTTATATTTTGA-TCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACT-GAAATTAATTA
* * * *
29084474 ATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTATTATTTTGTATGAATCAAAT
65 ATATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
29084539 TCATATATT
130 TCATATATT
29084548 AATTATAT
1 AATTATAT
29084556 CTATGTTCTC
Statistics
Matches: 371, Mismatches: 45, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.00
137 119 0.32
138 249 0.67
139 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
TATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:29084536 original size:275 final size:276
Alignment explanation
Indices: 29083997--29084555 Score: 820
Period size: 275 Copynumber: 2.0 Consensus size: 276
29083987 TAGAAAAAAG
*
29083997 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
29084062 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
66 TATAATTACTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
* * *
29084127 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTGACTGAAA
131 TAGATATTAATTATATTCTTCCCAAAAGAAAATTAATTGCTATATCTTTAATATTTTGACTGAAA
* ** *
29084192 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATGTAATTAATATTTTTTATGA
196 TTAATCAATATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGA
29084257 ATCAAATTCATATATT
261 ATCAAATTCATATATT
* * * *
29084273 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTATTTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
29084338 TAT-GTCTATTTATATTATTAAATTAGGTAAAATATATATAATTAATATTTT-TATGAATCACAT
66 TATAAT-TACTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
* * *
29084401 -TCAGATATTAATTATATTCTTTCCAAAAGAATATTAATTGCTATATCTTTTATATTTTGA-TCG
130 CT-AGATATTAATTATATTCTTCCCAAAAGAAAATTAATTGCTATATCTTTAATATTTTGACT-G
* * * * *
29084464 AAATTAATTAATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTATTATTTTGTA
193 AAATTAATCAATATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTA
29084529 TGAATCAAATTCATATATT
258 TGAATCAAATTCATATATT
29084548 AATTATAT
1 AATTATAT
29084556 CTATGTTCTC
Statistics
Matches: 253, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
274 2 0.01
275 148 0.58
276 103 0.41
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (276 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTACTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
TAGATATTAATTATATTCTTCCCAAAAGAAAATTAATTGCTATATCTTTAATATTTTGACTGAAA
TTAATCAATATAACTGATTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGA
ATCAAATTCATATATT
Found at i:29085912 original size:14 final size:15
Alignment explanation
Indices: 29085883--29085914 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29085873 AGGTTTGGGT
29085883 AGAAATATTGAAGGG
1 AGAAATATTGAAGGG
29085898 AGAAATATT-AAGGG
1 AGAAATATTGAAGGG
29085912 AGA
1 AGA
29085915 TTGTAAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (15 bp):
AGAAATATTGAAGGG
Found at i:29087758 original size:12 final size:12
Alignment explanation
Indices: 29087741--29087768 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29087731 TTAACATGTT
29087741 ACCTCATTAAAA
1 ACCTCATTAAAA
29087753 ACCTCATTAAAA
1 ACCTCATTAAAA
29087765 ACCT
1 ACCT
29087769 TACTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (12 bp):
ACCTCATTAAAA
Found at i:29093007 original size:64 final size:64
Alignment explanation
Indices: 29092890--29093061 Score: 215
Period size: 64 Copynumber: 2.7 Consensus size: 64
29092880 GAATGGCTAC
* * * *
29092890 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAGTAGTGATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAATAGTAATATGATCGACACA
* * *
29092953 CAA-CCATCAGTAATGGTAATATGATTGACACAAAGCCATCAGTAAT-GATAATATGATCGGCAC
1 -AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAATAG-TAATATGATCGACAC
29093016 A
64 A
* * *
29093017 AAGCCATCAGTAACGGTAATATTATCGGCACAAAGCCATTAGTAA
1 AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAA
29093062 CATCCCAGTA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 10 0.11
64 83 0.89
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (64 bp):
AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAATAGTAATATGATCGACACA
Found at i:29093062 original size:32 final size:32
Alignment explanation
Indices: 29092890--29093062 Score: 188
Period size: 32 Copynumber: 5.4 Consensus size: 32
29092880 GAATGGCTAC
* * *
29092890 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*** * *
29092921 AAGCCATCAGTAGTAGTGATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
29092953 CAA-CCATCAGTAATGGTAATATGATTGACACA
1 -AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
29092985 AAGCCATCAGTAATGATAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
29093017 AAGCCATCAGTAACGGTAATATTATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
29093049 AAGCCATTAGTAAC
1 AAGCCATCAGTAAC
29093063 ATCCCAGTAA
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.10
32 108 0.89
33 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:29093101 original size:26 final size:26
Alignment explanation
Indices: 29093071--29093142 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
29093061 ACATCCCAGT
*
29093071 AAAGCTACCAGCAATAGTATCACAGC
1 AAAGCTGCCAGCAATAGTATCACAGC
* *
29093097 AAAGCTGCCAGCAACAGTATCGCAGC
1 AAAGCTGCCAGCAATAGTATCACAGC
*
29093123 AAAGCTGCCAGTAATAGTAT
1 AAAGCTGCCAGCAATAGTAT
29093143 ATGTGGCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAGCTGCCAGCAATAGTATCACAGC
Found at i:29093181 original size:26 final size:27
Alignment explanation
Indices: 29093130--29093188 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
29093120 AGCAAAGCTG
*
29093130 CCAGTAATAGTATATGTGGCCAAGCCA
1 CCAGTAATAGTAGATGTGGCCAAGCCA
29093157 CCAGTAATAGT-GATGTGG-CAGAGCCA
1 CCAGTAATAGTAGATGTGGCCA-AGCCA
29093183 CCAGTA
1 CCAGTA
29093189 CAAAACTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.57
27 11 0.37
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAATAGTAGATGTGGCCAAGCCA
Found at i:29093418 original size:27 final size:27
Alignment explanation
Indices: 29093335--29093479 Score: 161
Period size: 27 Copynumber: 5.4 Consensus size: 27
29093325 GGGGAAAAAT
*
29093335 AGTCA-TTTACCCTCCAGGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
*
29093361 -GATCATTTTACCCTACA-AGGCATTAC
1 AG-TCATTTTACCCTACAGGGGCATTAC
*
29093387 GGTCATTTTACCCTACAGGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
* *
29093414 AGTCATTTTACCCTATAGGGGCATTAT
1 AGTCATTTTACCCTACAGGGGCATTAC
* * * *
29093441 GGTCATTTTGCCTTACAAGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
* *
29093468 AGTTATTATACC
1 AGTCATTTTACC
29093480 TATTTTAGGG
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 26 0.26
27 72 0.73
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (27 bp):
AGTCATTTTACCCTACAGGGGCATTAC
Found at i:29098767 original size:3 final size:3
Alignment explanation
Indices: 29098759--29098827 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
29098749 TATTTTTTAG
* * * *
29098759 ATT ATT ATT ATT ATC ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
29098807 ATT ATT ATC ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
29098828 TTGTTTTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:29100048 original size:23 final size:23
Alignment explanation
Indices: 29100022--29100070 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29100012 TCTTCTGCCT
*
29100022 TTTCTATCTTTCTTTTT-CTTTCA
1 TTTCTATC-TTCTTTTTACTTTAA
*
29100045 TTTCTTTCTTCTTTTTACTTTAA
1 TTTCTATCTTCTTTTTACTTTAA
29100068 TTT
1 TTT
29100071 GCATGCCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTCTATCTTCTTTTTACTTTAA
Found at i:29118718 original size:21 final size:18
Alignment explanation
Indices: 29118680--29118725 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
29118670 TTTATGCAGT
29118680 AATAGTATTTTAATTTTATA
1 AATA-TATTTTAATTTTA-A
29118700 ACATATATTTTATATTTTAA
1 A-ATATATTTTA-ATTTTAA
29118720 AATATA
1 AATATA
29118726 ATTATCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATATATTTTAATTTTAA
Found at i:29122919 original size:15 final size:15
Alignment explanation
Indices: 29122899--29122929 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29122889 TTAGCTTCTA
29122899 TTCACAAATTGTTGG
1 TTCACAAATTGTTGG
29122914 TTCACAAATTGTTGG
1 TTCACAAATTGTTGG
29122929 T
1 T
29122930 ACATCAGAAG
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:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TTCACAAATTGTTGG
Found at i:29122974 original size:24 final size:24
Alignment explanation
Indices: 29122941--29122994 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
29122931 CATCAGAAGA
29122941 GGCACACAAAATGAGAGATATCGTG
1 GGCA-ACAAAATGAGAGATATCGTG
* *
29122966 GGCAACAAAATGTGAGATATTGTG
1 GGCAACAAAATGAGAGATATCGTG
*
29122990 AGCAA
1 GGCAA
29122995 TAAATAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.19
Consensus pattern (24 bp):
GGCAACAAAATGAGAGATATCGTG
Found at i:29125717 original size:31 final size:29
Alignment explanation
Indices: 29125679--29125755 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
29125669 TTAATGGCTC
* * *
29125679 AGTGACTAAAATGTTACAATATGATAACGTA
1 AGTGACTAAAATGTAAC-ATATCA-AACATA
* *
29125710 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATCAAACATA
*
29125739 AGTGACTAAAATATAAC
1 AGTGACTAAAATGTAAC
29125756 TTAAGATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.51
30 4 0.10
31 15 0.38
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATCAAACATA
Found at i:29133028 original size:24 final size:25
Alignment explanation
Indices: 29132975--29133042 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
29132965 TAACACATTA
29132975 AATAAATA-AAAA-ATATAAAATTTC
1 AATAAATATAAAATATATAAAA-TTC
29132999 AATAAATATAAAATATATAAAA-T-
1 AATAAATATAAAATATATAAAATTC
*
29133022 AATTAAATATTAAATAT-TAAA
1 AA-TAAATATAAAATATATAAA
29133043 TTAAAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 6 0.15
24 22 0.55
25 4 0.10
26 8 0.20
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAATATAAAATATATAAAATTC
Found at i:29134590 original size:6 final size:6
Alignment explanation
Indices: 29134579--29134604 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29134569 ATTTTTTAAT
29134579 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
29134605 TTATTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:29138214 original size:27 final size:27
Alignment explanation
Indices: 29138174--29138352 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
29138164 TAAATTGTAC
29138174 AGCACTAAAGTGTGCGATTTGACTATGT
1 AGCACT-AAGTGTGCGATTTGACTATGT
* ** *
29138202 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29138228 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29138256 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29138284 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29138311 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29138338 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29138353 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
27 101 0.78
28 28 0.22
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29138316 original size:82 final size:82
Alignment explanation
Indices: 29138175--29138331 Score: 228
Period size: 82 Copynumber: 1.9 Consensus size: 82
29138165 AAATTGTACA
* *
29138175 GCACTAAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 GCACTAAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
29138240 TGCGAATTGACCATGCG
66 TGCGAATTGACCATGCG
** *
29138257 GCACT-AAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAG
1 GCACTAAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAG
*
29138320 TGTGCGAGTTGA
64 TGTGCGAATTGA
29138332 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 11 0.16
82 56 0.84
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (82 bp):
GCACTAAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
TGCGAATTGACCATGCG
Found at i:29138343 original size:82 final size:81
Alignment explanation
Indices: 29138171--29138352 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
29138161 GAGTAAATTG
* *
29138171 TACAGCACTAAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTA
1 TACAGCACT-AAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
29138236 AGTGTGCGAATTGACCA
65 AGTGTGCGAATTGACCA
* * ** *
29138253 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29138317 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29138335 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29138353 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 11 0.13
82 73 0.87
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29145564 original size:2 final size:2
Alignment explanation
Indices: 29145557--29145591 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
29145547 CATATTCGGC
* *
29145557 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29145592 GTAAGCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:29146385 original size:27 final size:27
Alignment explanation
Indices: 29146351--29146528 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29146341 TAAATTGTAC
29146351 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29146378 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29146404 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29146432 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29146460 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29146487 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29146514 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29146529 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29146465 original size:82 final size:81
Alignment explanation
Indices: 29146352--29146507 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29146342 AAATTGTACA
* *
29146352 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29146416 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29146433 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29146498 TGCGAGTTGA
65 TGCGAATTGA
29146508 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29146519 original size:82 final size:81
Alignment explanation
Indices: 29146348--29146528 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29146338 GAGTAAATTG
* *
29146348 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29146413 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29146429 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29146493 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29146511 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29146529 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29158841 original size:31 final size:33
Alignment explanation
Indices: 29158764--29158844 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 33
29158754 TTATTATTTT
* * *
29158764 TTACCTTGTTGATTATTTTTTTATTCTTTTTAG
1 TTACCTTGTTAATTATTATTTTATTCTTTTTAC
* *
29158797 TTA-ATTAGATAATT-TTATTTTATT-TTTTTAC
1 TTACCTT-GTTAATTATTATTTTATTCTTTTTAC
29158828 TTACCTTGTTAATTATT
1 TTACCTTGTTAATTATT
29158845 GGATTTAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
31 15 0.39
32 15 0.39
33 8 0.21
ACGTcount: A:0.22, C:0.07, G:0.06, T:0.64
Consensus pattern (33 bp):
TTACCTTGTTAATTATTATTTTATTCTTTTTAC
Found at i:29169721 original size:41 final size:41
Alignment explanation
Indices: 29169660--29169827 Score: 169
Period size: 41 Copynumber: 4.1 Consensus size: 41
29169650 GTACAATTTG
* * **
29169660 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
1 CCTGATACAATACACTGGCACGAAGCCTGCTAGGCACAAAA
* *
29169701 CTTGATACAATACACTGGCACGAAGCCTTCTAGGCACAAAA
1 CCTGATACAATACACTGGCACGAAGCCTGCTAGGCACAAAA
* * *
29169742 CCTGATACAATACACTAGCATGAAGCCGGCTAGGCA-AAAA
1 CCTGATACAATACACTGGCACGAAGCCTGCTAGGCACAAAA
* * * * * *
29169782 CCCTGATCCAAGACACCGGTACGAAGCC-GACTGGGCTCAAAA
1 -CCTGATACAATACACTGGCACGAAGCCTG-CTAGGCACAAAA
29169824 CCTG
1 CCTG
29169828 CTAGGCTCAA
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
40 5 0.05
41 96 0.91
42 4 0.04
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.15
Consensus pattern (41 bp):
CCTGATACAATACACTGGCACGAAGCCTGCTAGGCACAAAA
Found at i:29179165 original size:27 final size:27
Alignment explanation
Indices: 29179127--29179179 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
29179117 CTGATGTCGA
29179127 TTGCCATAGAAAAGATACTATTAAGTG
1 TTGCCATAGAAAAGATACTATTAAGTG
* *
29179154 TTGCCATAGAAAATATACTGTTAAGT
1 TTGCCATAGAAAAGATACTATTAAGT
29179180 TATAGGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (27 bp):
TTGCCATAGAAAAGATACTATTAAGTG
Found at i:29187419 original size:17 final size:17
Alignment explanation
Indices: 29187388--29187420 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29187378 GTACTGATTT
29187388 TGACATTCTTATGTCAA
1 TGACATTCTTATGTCAA
29187405 TGACAATTCTT-TGTCA
1 TGAC-ATTCTTATGTCA
29187421 TCAATCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACATTCTTATGTCAA
Found at i:29190491 original size:27 final size:25
Alignment explanation
Indices: 29190461--29190512 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
29190451 TTCATTTTTC
*
29190461 ATTTCCCATCTCATATTCATTTCTCAT
1 ATTTCCCATCTCA-ATAC-TTTCTCAT
* *
29190488 ATTTTCCATTTCAATACTTTCTCAT
1 ATTTCCCATCTCAATACTTTCTCAT
29190513 CTCATATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
27 11 0.50
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTCCCATCTCAATACTTTCTCAT
Found at i:29190516 original size:43 final size:43
Alignment explanation
Indices: 29190462--29190546 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
29190452 TCATTTTTCA
29190462 TTTCCCATCTCATATTCATTTCTCATATTT-TCCATTTCAATAC
1 TTTCCCATCTCATATTCATTTCTCATATTTGT-CATTTCAATAC
* *
29190505 TTTCTCATCTCATATTCATTTCTCATCTTTGTCATTTCAATA
1 TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATA
29190547 TCAATAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.01, T:0.51
Consensus pattern (43 bp):
TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATAC
Done.