Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 123 of 279
Found at i:38902073 original size:72 final size:72
Alignment explanation
Indices: 38901946--38902084 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 72
38901936 AAAAACCATA
* *
38901946 AAATTGATAAATAAAATGGCAAAAAAGTCATTACATAAATACAAAGTTAACTATTTAAATTGCAA
1 AAATTGATAAATAAAATGGCAAAAAAGTCATTACATAAATACAAAGTGAACTATTTAAATTACAA
38902011 AAAAATT
66 AAAAATT
* * * * *
38902018 AAATTGTTAATTAAAAT-GCTAAAAAATTCATTACATAAATA-AATA-TGAAGTTATTTATATTA
1 AAATTGATAAATAAAATGGC-AAAAAAGTCATTACATAAATACAA-AGTGAA-CTATTTAAATTA
38902080 CAAAA
63 CAAAA
38902085 CCCCCTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
71 7 0.12
72 50 0.88
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (72 bp):
AAATTGATAAATAAAATGGCAAAAAAGTCATTACATAAATACAAAGTGAACTATTTAAATTACAA
AAAAATT
Found at i:38902249 original size:72 final size:72
Alignment explanation
Indices: 38902132--38902274 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
38902122 GGTATATTTT
* ** * *
38902132 TGTGGAGCTCGACGTTCACGTTGCGGGCGATTACGGTGATCAACATTCTCTTCATCCGTATGTGG
1 TGTGGAGCTCGACGTTCACGTTGCGGGCGACTACGACGATCAACATTCTCTTCATCCATATGTAG
38902197 GGGTGTG
66 GGGTGTG
* *
38902204 TGTGGAGCTCGACGTTCACGTTGTGGGCGACTACGACGATCAACATTCTCTTCGTCCATATGTAG
1 TGTGGAGCTCGACGTTCACGTTGCGGGCGACTACGACGATCAACATTCTCTTCATCCATATGTAG
38902269 GGGTGT
66 GGGTGT
38902275 AGAGAATGTC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.30
Consensus pattern (72 bp):
TGTGGAGCTCGACGTTCACGTTGCGGGCGACTACGACGATCAACATTCTCTTCATCCATATGTAG
GGGTGTG
Found at i:38902516 original size:12 final size:12
Alignment explanation
Indices: 38902493--38902541 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
38902483 TCTGGCCGCC
*
38902493 GCTCTGGGTCCG
1 GCTCTGGCTCCG
* *
38902505 GCACTGCCTCCG
1 GCTCTGGCTCCG
*
38902517 GCTCTGGCTCTG
1 GCTCTGGCTCCG
38902529 GCTCTGGCTCCG
1 GCTCTGGCTCCG
38902541 G
1 G
38902542 AGTTGGTGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.39, G:0.35, T:0.24
Consensus pattern (12 bp):
GCTCTGGCTCCG
Found at i:38905074 original size:19 final size:18
Alignment explanation
Indices: 38905052--38905091 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
38905042 AAAATATAAT
38905052 AAAATAATAATATTTAAAA
1 AAAATAATAATA-TTAAAA
* *
38905071 AAAATTATATTATTAAAA
1 AAAATAATAATATTAAAA
38905089 AAA
1 AAA
38905092 TGGGTCGCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAATAATATTAAAA
Found at i:38910032 original size:271 final size:273
Alignment explanation
Indices: 38909525--38910074 Score: 739
Period size: 271 Copynumber: 2.0 Consensus size: 273
38909515 TACATATAAG
* * ** *
38909525 AGCTTATACAATTTTAGGAGTTAAATAACTCCTAAATTGATCAAGCACATGCCTCCCGGTGCTAA
1 AGCTTGTACAATTTAAGGAGTTAAATAACTCCTAAATTGATCAAGCACACACCTCCCGATGCTAA
* * * * * * **
38909590 ATGTAGACTCTAAAGCAACCGTAGAAATCGATATAACTAACATATCTTTGGCCACATTAGAAAGA
66 ATGCAGACTCTAAACCAACCGTAGAAACCGATACAACTAACACATCTCTAACCACATTAGAAAGA
*
38909655 GTGGGAAATCTAAGGCTATTCAATTTCCACCACAATAAAATATCAAAAACTTCAATAAAATTCTC
131 GTGGGAAATCTAAGGCTATTCAATTTCCACCACAATAAAATATCAAAAACTTCAACAAAATTCTC
* * * ** * *
38909720 ATTAGCCTCAGCTGGATATTTCTCCAATTCAGATGTTTTATCCTCAACTCTATTTTCTAACTCAT
196 ATTAGCCTCAGCTAGATACTTATCCAATTCAGACATTTTATCCTCAACACCATTTTCTAACTCAT
*
38909785 GCTTTTTATACAA
261 GCATTTTATACAA
* *
38909798 AGCTTGTACAAATTTAAGG-GTTAAATGACTCCTAAATTGATCAAGCACACACC-CTCGATGCTA
1 AGCTTGTAC-AATTTAAGGAGTTAAATAACTCCTAAATTGATCAAGCACACACCTCCCGATGCTA
* * * * *
38909861 AATGCAGACTTTGAACCAACTGTAGAAACCGGTACAACTAACACATCTCTAACCATC-TTTGAAA
65 AATGCAGACTCTAAACCAACCGTAGAAACCGATACAACTAACACATCTCTAACCA-CATTAGAAA
* * *
38909925 GAGT-GGAAATCTAGGGCTATTCACTTTCCACCACAATAAAATATCAAAATCTTCAACAAAATTC
129 GAGTGGGAAATCTAAGGCTATTCAATTTCCACCACAATAAAATATCAAAAACTTCAACAAAATTC
* * *
38909989 TCATTAGCTTCTGCTAGATACTTATCCAATTCAGACATTTTATCCTCACCACCATTTTCTAACTC
194 TCATTAGCCTCAGCTAGATACTTATCCAATTCAGACATTTTATCCTCAACACCATTTTCTAACTC
38910054 ATGCATTTTATACAA
259 ATGCATTTTATACAA
38910069 AGCTTG
1 AGCTTG
38910075 CATATGCCTT
Statistics
Matches: 240, Mismatches: 35, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
271 131 0.55
272 61 0.25
273 40 0.17
274 8 0.03
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (273 bp):
AGCTTGTACAATTTAAGGAGTTAAATAACTCCTAAATTGATCAAGCACACACCTCCCGATGCTAA
ATGCAGACTCTAAACCAACCGTAGAAACCGATACAACTAACACATCTCTAACCACATTAGAAAGA
GTGGGAAATCTAAGGCTATTCAATTTCCACCACAATAAAATATCAAAAACTTCAACAAAATTCTC
ATTAGCCTCAGCTAGATACTTATCCAATTCAGACATTTTATCCTCAACACCATTTTCTAACTCAT
GCATTTTATACAA
Found at i:38910298 original size:13 final size:13
Alignment explanation
Indices: 38910280--38910304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38910270 CTAGGGTCTA
38910280 AAACACAAGCAAC
1 AAACACAAGCAAC
38910293 AAACACAAGCAA
1 AAACACAAGCAA
38910305 ATTTATCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.28, G:0.08, T:0.00
Consensus pattern (13 bp):
AAACACAAGCAAC
Found at i:38911629 original size:28 final size:27
Alignment explanation
Indices: 38911574--38911631 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
38911564 ATTGTATTTC
*
38911574 AAATATTATATATTTATATACATTTTA
1 AAATATTATATATTTATATACATCTTA
38911601 AAAT-TTAT-TATTTGATATATCGATCTTA
1 AAATATTATATATTT-ATATA-C-ATCTTA
38911629 AAA
1 AAA
38911632 CCTTTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.19
26 9 0.33
27 5 0.19
28 8 0.30
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (27 bp):
AAATATTATATATTTATATACATCTTA
Found at i:38922963 original size:19 final size:19
Alignment explanation
Indices: 38922939--38922975 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
38922929 ACATCATAAG
38922939 TTCAATTCGTGTAAACAAT
1 TTCAATTCGTGTAAACAAT
38922958 TTCAATTCGTGTAAACAA
1 TTCAATTCGTGTAAACAA
38922976 GAACAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (19 bp):
TTCAATTCGTGTAAACAAT
Found at i:38924538 original size:16 final size:16
Alignment explanation
Indices: 38924517--38924550 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38924507 TATTTCCTTT
38924517 TTTTCCGTCACTCATC
1 TTTTCCGTCACTCATC
38924533 TTTTCCGTCACTCATC
1 TTTTCCGTCACTCATC
38924549 TT
1 TT
38924551 CAAAATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTTCCGTCACTCATC
Found at i:38928459 original size:6 final size:6
Alignment explanation
Indices: 38928448--38928472 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38928438 TTCCTACTTA
38928448 CCAAGC CCAAGC CCAAGC CCAAGC C
1 CCAAGC CCAAGC CCAAGC CCAAGC C
38928473 TTAACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CCAAGC
Found at i:38931414 original size:10 final size:10
Alignment explanation
Indices: 38931399--38931437 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
38931389 TTTTTGCTTT
38931399 AATTATAAAA
1 AATTATAAAA
38931409 AATTATAGAAA
1 AATTATA-AAA
*
38931420 AA-TAAAAAA
1 AATTATAAAA
38931429 AATTATAAA
1 AATTATAAA
38931438 TTTTCCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.20
10 15 0.60
11 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
AATTATAAAA
Found at i:38953927 original size:10 final size:10
Alignment explanation
Indices: 38953912--38953939 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
38953902 TTCATGGAGT
38953912 GAGAGGTCTC
1 GAGAGGTCTC
38953922 GAGAGGTCTC
1 GAGAGGTCTC
38953932 GAGAGGTC
1 GAGAGGTC
38953940 CTGGAACCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.43, T:0.18
Consensus pattern (10 bp):
GAGAGGTCTC
Found at i:38959027 original size:46 final size:45
Alignment explanation
Indices: 38958952--38959081 Score: 181
Period size: 46 Copynumber: 2.9 Consensus size: 45
38958942 ATAACCAAAT
*
38958952 ACTTTAATACAAAAAAAAATCAATTTCTATCATGCACATGCCATAC
1 ACTTTAATAC-AAAAAAAATCCATTTCTATCATGCACATGCCATAC
* * *
38958998 ATTTTAATACAATAAAAAATCCATGTCTATCATGCACATGTCATAC
1 ACTTTAATACAA-AAAAAATCCATTTCTATCATGCACATGCCATAC
* *
38959044 ACTTTAACAC-AAACAAATCCATTTCTATCATGCACATG
1 ACTTTAATACAAAAAAAATCCATTTCTATCATGCACATG
38959082 ACAGACAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 25 0.33
45 3 0.04
46 47 0.63
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.30
Consensus pattern (45 bp):
ACTTTAATACAAAAAAAATCCATTTCTATCATGCACATGCCATAC
Found at i:38961315 original size:35 final size:35
Alignment explanation
Indices: 38961276--38961575 Score: 325
Period size: 35 Copynumber: 8.6 Consensus size: 35
38961266 TATGGCAAAG
*
38961276 TGTGAAACGTAGGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
38961311 TGTGAAACGTAGGTATGGTATCATCTATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
*
38961346 TGTGAAACGTAGGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
*
38961381 TGTGAAACGTAGGTATGGTATT-TCCATACCGAGC
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * ** ** *
38961415 TATGAAACGTAGGTATGGCATCGTCCATATTGAGC
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * ** *
38961450 TATGATACGTAGGTATGGTATCGTCCATACCAAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* ** * *
38961485 TATGAAATATAGGTATGATATTTTCCATACCGAG-
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
** * * * **
38961519 CATGAAAAGTAGGTATGGTGTTTTCCATAAAGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
38961554 TGTGAAACGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
38961576 TCAATGAGGA
Statistics
Matches: 226, Mismatches: 37, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
34 56 0.25
35 170 0.75
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
Found at i:38961460 original size:69 final size:70
Alignment explanation
Indices: 38961278--38961575 Score: 330
Period size: 69 Copynumber: 4.3 Consensus size: 70
38961268 TGGCAAAGTG
* * * * *
38961278 TGAAACGTAGGTATGGTATTAACCATACCGAGTTGTGAAACGTAGGTATGGTATCATCTATACCG
1 TGAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAACGTAGGTATGGTATCTTCCATACCG
*
38961343 AGTTG
66 AGTTA
* * *
38961348 TGAAACGTAGGTATGGTATTAACCATACCGAGTTGTGAAACGTAGGTATGGTAT-TTCCATACCG
1 TGAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAACGTAGGTATGGTATCTTCCATACCG
*
38961412 AGCTA
66 AGTTA
* ** ** * * *
38961417 TGAAACGTAGGTATGGCATCGTCCATATTGAGCTATGATACGTAGGTATGGTATCGTCCATACCA
1 TGAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAACGTAGGTATGGTATCTTCCATACCG
38961482 AGTTA
66 AGTTA
** * * * * * **
38961487 TGAAATATAGGTATGATATTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATAAAG
1 TGAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAACGTAGGTATGGTATCTTCCATACCG
*
38961551 AGTTG
66 AGTTA
38961556 TGAAACGTAGGTATGGTATT
1 TGAAACGTAGGTATGGTATT
38961576 TCAATGAGGA
Statistics
Matches: 191, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
69 100 0.52
70 91 0.48
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (70 bp):
TGAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAACGTAGGTATGGTATCTTCCATACCG
AGTTA
Found at i:38961460 original size:104 final size:104
Alignment explanation
Indices: 38961276--38961574 Score: 321
Period size: 104 Copynumber: 2.9 Consensus size: 104
38961266 TATGGCAAAG
* * * * *
38961276 TGTGAAACGTAGGTATGGTATTAACCATACCGAGTTGTGAAACGTAGGTATGGTATCATCTATAC
1 TGTGAAACGTAGGTATGGTATT-TCCATACCGAGCTATGAAACGTAGGTATGGCATCATCCATAC
* * * *
38961341 CGAGTTGTGAAACGTAGGTATGGTATTAACCATACCGAGT
65 CGAGCTATGAAACGTAGGTATGGTATCAACCATACCAAGT
* **
38961381 TGTGAAACGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGCATCGTCCATATT
1 TGTGAAACGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGCATCATCCATACC
* **
38961446 GAGCTATGATACGTAGGTATGGTATCGTCCATACCAAGT
66 GAGCTATGAAACGTAGGTATGGTATCAACCATACCAAGT
* ** * * ** ** *
38961485 TATGAAATATAGGTATGATATTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATAA
1 TGTGAAACGTAGGTATGGTA-TTTCCATACCGAGCTATGAAACGTAGGTATGGCATCATCCATAC
* * *
38961549 AGAGTTGTGAAACGTAGGTATGGTAT
65 CGAGCTATGAAACGTAGGTATGGTAT
38961575 TTCAATGAGG
Statistics
Matches: 164, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
104 128 0.78
105 36 0.22
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (104 bp):
TGTGAAACGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGCATCATCCATACC
GAGCTATGAAACGTAGGTATGGTATCAACCATACCAAGT
Found at i:38964512 original size:43 final size:43
Alignment explanation
Indices: 38964464--38964642 Score: 211
Period size: 43 Copynumber: 4.4 Consensus size: 43
38964454 AATTATCATT
* *
38964464 TCACCGGCATTACGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
38964507 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
38964550 TCACCGGCACTATG-C--CTA-G--C----GCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
38964583 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
38964625 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
38964643 GGGATTTATC
Statistics
Matches: 117, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
33 26 0.22
34 1 0.01
36 3 0.03
37 2 0.02
39 2 0.02
40 3 0.03
41 15 0.13
42 3 0.03
43 62 0.53
ACGTcount: A:0.28, C:0.35, G:0.23, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:38964579 original size:33 final size:33
Alignment explanation
Indices: 38964537--38964599 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
38964527 AGGCACGAAG
*
38964537 GCCCGAATACACATCACCGGCACTATGCCTAGC
1 GCCCGAATACACATCACCGGCACTAAGCCTAGC
38964570 GCCCGAATACACATCACCGGCACTAAGCCT
1 GCCCGAATACACATCACCGGCACTAAGCCT
38964600 GCTAGGCACG
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:0.29, C:0.40, G:0.17, T:0.14
Consensus pattern (33 bp):
GCCCGAATACACATCACCGGCACTAAGCCTAGC
Found at i:38967925 original size:24 final size:24
Alignment explanation
Indices: 38967909--38967992 Score: 118
Period size: 24 Copynumber: 3.5 Consensus size: 24
38967899 TTTGAGTGGA
38967909 ACTATGTGTGCGTATTTGTATGGC
1 ACTATGTGTGCGTATTTGTATGGC
*
38967933 ACTATGTGTGCGTATATGTATGGC
1 ACTATGTGTGCGTATTTGTATGGC
*
38967957 ACTATGTGTGCAGAATTAT-T-TGGC
1 ACTATGTGTGC-GTATT-TGTATGGC
38967981 ACTATGTGTGCG
1 ACTATGTGTGCG
38967993 GAGTTGAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
23 1 0.02
24 49 0.89
25 4 0.07
26 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (24 bp):
ACTATGTGTGCGTATTTGTATGGC
Found at i:38976862 original size:30 final size:30
Alignment explanation
Indices: 38976828--38976884 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
38976818 AAATATTCAC
38976828 TTAA-TAATCATGTAATT-AAAAAATAATTTT
1 TTAATTAA-CATG-AATTAAAAAAATAATTTT
*
38976858 TTAATTAACTTGAATTAAAAAAATAAT
1 TTAATTAACATGAATTAAAAAAATAAT
38976885 AGTATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.17
30 17 0.71
31 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAATTAACATGAATTAAAAAAATAATTTT
Found at i:38981678 original size:23 final size:21
Alignment explanation
Indices: 38981652--38981699 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
38981642 AGGCACTTTA
38981652 TGTGAAGTATTTCAAGCACCTCG
1 TGTGAAGTA--TCAAGCACCTCG
** *
38981675 TGTGTCGTATCAGGCACCTCG
1 TGTGAAGTATCAAGCACCTCG
38981696 TGTG
1 TGTG
38981700 TCGTTTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (21 bp):
TGTGAAGTATCAAGCACCTCG
Found at i:38981693 original size:21 final size:21
Alignment explanation
Indices: 38981667--38981726 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
38981657 AGTATTTCAA
38981667 GCACCTCGTGTGTCGTATCAG
1 GCACCTCGTGTGTCGTATCAG
* *
38981688 GCACCTCGTGTGTCGTTTTAG
1 GCACCTCGTGTGTCGTATCAG
* **
38981709 GCACTTTATGTGTCGTAT
1 GCACCTCGTGTGTCGTAT
38981727 ACTGATCAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (21 bp):
GCACCTCGTGTGTCGTATCAG
Found at i:38989096 original size:25 final size:25
Alignment explanation
Indices: 38989013--38989104 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 25
38989003 CAAATGTAAT
* *
38989013 TTTATTATTTT-AATA-ATTTATATC
1 TTTATTATTTTAAATATATATATA-A
*
38989037 TTTATAAATTTTAAATGATATATATAA
1 TTTAT-TATTTTAAAT-ATATATATAA
38989064 TTTCTATTATTTTAAATATATATATAA
1 -TT-TATTATTTTAAATATATATATAA
*
38989091 TTTATTAATTTAAA
1 TTTATTATTTTAAA
38989105 ATTTTAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.09
25 16 0.28
26 5 0.09
27 11 0.19
28 17 0.30
29 3 0.05
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTATTATTTTAAATATATATATAA
Found at i:39000445 original size:21 final size:20
Alignment explanation
Indices: 39000392--39000447 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
39000382 CATAATATCA
39000392 AAATACAA-AC-AATGTCTC
1 AAATACAACACAAATGTCTC
* *
39000410 AAATACATCATAAATGTCTTC
1 AAATACAACACAAATGTC-TC
*
39000431 AAATGCAACACAAATGT
1 AAATACAACACAAATGT
39000448 AAAACTTCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 7 0.23
19 1 0.03
20 6 0.20
21 16 0.53
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (20 bp):
AAATACAACACAAATGTCTC
Found at i:39003746 original size:26 final size:25
Alignment explanation
Indices: 39003700--39003759 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
39003690 TATATTTATA
*
39003700 TTATATCATTTTAATATTTAATATTT
1 TTATAT-ATTTTAATATTTAAAATTT
* *
39003726 TTATATATTTTTATTTATTAAAATTT
1 TTATATATTTTAATAT-TTAAAATTT
*
39003752 TTTTATAT
1 TTATATAT
39003760 AGTGATCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATATTTTAATATTTAAAATTT
Found at i:39003815 original size:14 final size:15
Alignment explanation
Indices: 39003796--39003829 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
39003786 TACATTAGAG
39003796 TAATATTATATA-TT
1 TAATATTATATATTT
39003810 TAATA-TATATATTT
1 TAATATTATATATTT
39003824 TAATAT
1 TAATAT
39003830 GTTCTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATATTATATATTT
Found at i:39005276 original size:44 final size:43
Alignment explanation
Indices: 39005213--39005301 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 43
39005203 TAAATTAGAT
39005213 AAACCAAAAGTTGATAAGTTAACATATTTAAATGTATTTTTTAA
1 AAACCAAAAGTTGATAAGTTAACATATTTAAATGTA-TTTTTAA
39005257 AAACCAAAAGTTGATAAGTTAACATATTTAAATGTATTTTTAA
1 AAACCAAAAGTTGATAAGTTAACATATTTAAATGTATTTTTAA
39005300 AA
1 AA
39005302 CCAGATAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 9 0.20
44 36 0.80
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (43 bp):
AAACCAAAAGTTGATAAGTTAACATATTTAAATGTATTTTTAA
Found at i:39021497 original size:16 final size:16
Alignment explanation
Indices: 39021448--39021491 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
39021438 GTAGTCAATT
*
39021448 AATTAAAAAAGGACTA
1 AATTGAAAAAGGACTA
39021464 AATTGAAAAAGGACTA
1 AATTGAAAAAGGACTA
39021480 AATTGAAAAAGG
1 AATTGAAAAAGG
39021492 TGTAAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (16 bp):
AATTGAAAAAGGACTA
Found at i:39022768 original size:57 final size:57
Alignment explanation
Indices: 39022691--39022824 Score: 232
Period size: 57 Copynumber: 2.4 Consensus size: 57
39022681 CATATAAAGG
*
39022691 ATTTAGCCTGGACTGGTAATCCGACAAAGCCCTTAGAGTATATGCGATACAAGCAAA
1 ATTTAGCCTGGACTGGTAATCCGACAAAGCCCTTAGAGTATATGCGATACAAACAAA
* * *
39022748 ATTTGGCCCGGACTGGTAATCCGACAAAGCCCTTAGAGTATATGCTATACAAACAAA
1 ATTTAGCCTGGACTGGTAATCCGACAAAGCCCTTAGAGTATATGCGATACAAACAAA
39022805 ATTTAGCCTGGACTGGTAAT
1 ATTTAGCCTGGACTGGTAAT
39022825 TCTGCTGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (57 bp):
ATTTAGCCTGGACTGGTAATCCGACAAAGCCCTTAGAGTATATGCGATACAAACAAA
Found at i:39029641 original size:159 final size:156
Alignment explanation
Indices: 39029355--39029669 Score: 488
Period size: 159 Copynumber: 2.0 Consensus size: 156
39029345 AGCAACATAG
*
39029355 CACCAATTAACTTTTTCCTTTTTTTTATGAATTAAAATAAGGCACACGTGATGTTGACGAAATGA
1 CACCAATTAACTTTTTCCTTTTTTCTATGAATTAAAATAAGGCACACGTGATGTTGACGAAATGA
* * * * * *
39029420 TGAACACGGTGACTAGAACGATATCATATTGAAAGGCGGAGGCGATCCAAGCTGGATTTTCCACT
66 TGAACACAGTGACTAGAACGAGATCACATCGAAAAGCGGAGGCGATCCAAGCAGGATTTTCCACT
39029485 GAGACTTTTACTCGGTTGTAGCTCCA
131 GAGACTTTTACTCGGTTGTAGCTCCA
* * *
39029511 CACCAATTAACTTTTTCC-TTTTTCTATGATTTAAAATAAGGCACACGTTATATTAAGTGACGAA
1 CACCAATTAACTTTTTCCTTTTTTCTATGAATTAAAATAAGGCACACGTGAT-GT---TGACGAA
39029575 ATGATGAACACAGTGACTAGAACGAGATCACATCGAAAAGCGGAGGCGATCCAAGCAGGATTTTC
62 ATGATGAACACAGTGACTAGAACGAGATCACATCGAAAAGCGGAGGCGATCCAAGCAGGATTTTC
*
39029640 CACTGAGACTTTTACTCTGTTGTAGCTCCA
127 CACTGAGACTTTTACTCGGTTGTAGCTCCA
39029670 AGTAGTTCCT
Statistics
Matches: 144, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
155 30 0.21
156 19 0.13
159 95 0.66
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (156 bp):
CACCAATTAACTTTTTCCTTTTTTCTATGAATTAAAATAAGGCACACGTGATGTTGACGAAATGA
TGAACACAGTGACTAGAACGAGATCACATCGAAAAGCGGAGGCGATCCAAGCAGGATTTTCCACT
GAGACTTTTACTCGGTTGTAGCTCCA
Found at i:39031198 original size:13 final size:13
Alignment explanation
Indices: 39031177--39031215 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
39031167 AAACATAATT
39031177 AAATATTAATAAC
1 AAATATTAATAAC
* * *
39031190 AACTATTAAAAAT
1 AAATATTAATAAC
39031203 AAATATTAATAAC
1 AAATATTAATAAC
39031216 TCTCAAATTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATTAATAAC
Found at i:39031199 original size:30 final size:27
Alignment explanation
Indices: 39031143--39031215 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 27
39031133 TATAATAATT
**
39031143 AAATAAATATTAATAA-ATTTATTTAAA
1 AAATAAATATTAATAACAACTATTT-AA
39031170 CATAATTAAATATTAATAACAACTA-TTAA
1 -A-AA-TAAATATTAATAACAACTATTTAA
39031199 AAATAAATATTAATAAC
1 AAATAAATATTAATAAC
39031216 TCTCAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 14 0.35
27 2 0.05
28 2 0.05
29 4 0.10
30 15 0.38
31 3 0.08
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATAAATATTAATAACAACTATTTAA
Found at i:39033319 original size:20 final size:24
Alignment explanation
Indices: 39033294--39033339 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 24
39033284 CAAAAAATGG
39033294 TTTCTCA-A-TTTC-TCAT-TTCT
1 TTTCTCACATTTTCTTCATCTTCT
39033314 TTTCTCACATTTTCTTCATCTTCT
1 TTTCTCACATTTTCTTCATCTTCT
39033338 TT
1 TT
39033340 AAAGTTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 1 0.05
22 4 0.18
23 4 0.18
24 6 0.27
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCTCACATTTTCTTCATCTTCT
Found at i:39037764 original size:15 final size:16
Alignment explanation
Indices: 39037744--39037786 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39037734 TTTAATCTTT
39037744 TAAAAATTATAAAA-A
1 TAAAAATTATAAAATA
*
39037759 TAAAAACTATTAAAATA
1 TAAAAATTA-TAAAATA
*
39037776 TTAAAATTATA
1 TAAAAATTATA
39037787 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATTATAAAATA
Found at i:39045208 original size:58 final size:57
Alignment explanation
Indices: 39045085--39045253 Score: 268
Period size: 58 Copynumber: 2.9 Consensus size: 57
39045075 GTGCCCACTG
*
39045085 ACCGATCTCGCACACATAGTGCTCGGTTGAA-GAACTTGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAA-TTGCACACACAGTGCCTCAATT
*
39045142 ACCAATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATT-GCACACACAGTGCCTCAATT
* *
39045200 ACTGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACATAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAA-TTGCACACACAGTGCCTC
39045254 TAATCATTCG
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
57 31 0.30
58 71 0.68
59 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (57 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTGCACACACAGTGCCTCAATT
Found at i:39045241 original size:29 final size:28
Alignment explanation
Indices: 39045092--39045250 Score: 119
Period size: 29 Copynumber: 5.5 Consensus size: 28
39045082 CTGACCGATC
39045092 TCGCACACATAGTGCTCGGTTGAA-GAACT
1 TCGCACACATAGTGCTCGGTT-AAGGAA-T
* ** **
39045121 T-GCACACACAGTGCCTCAATT-ACCAAT
1 TCGCACACATAGTG-CTCGGTTAAGGAAT
39045148 CTCGCACACATAGTGCTCGGTTAAAGGAAT
1 -TCGCACACATAGTGCTCGGTT-AAGGAAT
* ** **
39045178 TCGCACACACAGTGCCTCAATTACTG-AT
1 TCGCACACATAGTG-CTCGGTTAAGGAAT
39045206 CTCGCACACATAGTGCTCGGTTAAAGGAAT
1 -TCGCACACATAGTGCTCGGTT-AAGGAAT
*
39045236 TTGCACACATAGTGC
1 TCGCACACATAGTGC
39045251 CTCTAATCAT
Statistics
Matches: 100, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
27 2 0.02
28 26 0.26
29 61 0.61
30 11 0.11
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGGTTAAGGAAT
Found at i:39045468 original size:43 final size:43
Alignment explanation
Indices: 39045419--39045689 Score: 325
Period size: 43 Copynumber: 6.3 Consensus size: 43
39045409 CACCAGTATT
*
39045419 AAGCCTGCTAAGCACGAAGACCCGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
* * *
39045462 AAGCCTGCTAGGCACGAA-AGCCTGAATACACATCACCGACATG
1 AAGCCTGCTAGGCACGAAGA-CCCGAATACACATCACCGGCACG
* * * *
39045505 AAGCAT-CTAGGCACGAAG-GCCGAATACATATCACTGGCACG
1 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
* * * * **
39045546 AAGCCTGTTAGGCACGAAGGCCCAAATACACATCATCGATACG
1 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
* *
39045589 AAGCCTGCTAGGCACGAA-AGCCCTAATACACATCATCGGCACG
1 AAGCCTGCTAGGCACGAAGA-CCCGAATACACATCACCGGCACG
* * *
39045632 AAGCCTGTTAGGCACGAAGGCACGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
39045675 AAGCCTGCTAGGCAC
1 AAGCCTGCTAGGCAC
39045690 AAAGCCTGCT
Statistics
Matches: 191, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
41 22 0.12
42 23 0.12
43 146 0.76
ACGTcount: A:0.34, C:0.31, G:0.23, T:0.13
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
Found at i:39045645 original size:86 final size:84
Alignment explanation
Indices: 39045419--39045695 Score: 367
Period size: 86 Copynumber: 3.2 Consensus size: 84
39045409 CACCAGTATT
* * *
39045419 AAGCCTGCTAAGCACGAAGACCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAAGCC
1 AAGCCTGCTAGGCACGAAG-CCCGAATACACATCA-CGGCACGAAGCCTGTTAGGCACGAAGGCC
* *
39045484 TGAATACACATCACCGACATG
64 CGAATACACATCACCGACACG
* * *
39045505 AAGCAT-CTAGGCACGAAGGCCGAATACATATCACTGGCACGAAGCCTGTTAGGCACGAAGGCCC
1 AAGCCTGCTAGGCACGAAGCCCGAATACACATCAC-GGCACGAAGCCTGTTAGGCACGAAGGCCC
* * *
39045569 AAATACACATCATCGATACG
65 GAATACACATCACCGACACG
* *
39045589 AAGCCTGCTAGGCACGAAAGCCCTAATACACATCATCGGCACGAAGCCTGTTAGGCACGAAGGCA
1 AAGCCTGCTAGGCACG-AAGCCCGAATACACATCA-CGGCACGAAGCCTGTTAGGCACGAAGGCC
*
39045654 CGAATACACATCACCGGCACG
64 CGAATACACATCACCGACACG
*
39045675 AAGCCTGCTAGGCACAAAGCC
1 AAGCCTGCTAGGCACGAAGCC
39045696 TGCTAGGCAC
Statistics
Matches: 166, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
83 1 0.01
84 60 0.36
85 25 0.15
86 79 0.48
87 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (84 bp):
AAGCCTGCTAGGCACGAAGCCCGAATACACATCACGGCACGAAGCCTGTTAGGCACGAAGGCCCG
AATACACATCACCGACACG
Found at i:39045694 original size:16 final size:16
Alignment explanation
Indices: 39045669--39045705 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39045659 ACACATCACC
*
39045669 GGCACGAAGCCTGCTA
1 GGCACAAAGCCTGCTA
39045685 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
39045701 GGCAC
1 GGCAC
39045706 GAAGGCCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.11
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:39063881 original size:21 final size:21
Alignment explanation
Indices: 39063857--39063936 Score: 151
Period size: 21 Copynumber: 3.8 Consensus size: 21
39063847 TTTCAAGCAT
39063857 CTCGTGTGTCGTATCAGGCAC
1 CTCGTGTGTCGTATCAGGCAC
39063878 CTCGTGTGTCGTATCAGGCAC
1 CTCGTGTGTCGTATCAGGCAC
39063899 CTCGTGTGTCGTATCAGGCAC
1 CTCGTGTGTCGTATCAGGCAC
*
39063920 CTCGTGTGTCGTCTCAG
1 CTCGTGTGTCGTATCAG
39063937 TAACTTATGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.30
Consensus pattern (21 bp):
CTCGTGTGTCGTATCAGGCAC
Found at i:39065779 original size:19 final size:20
Alignment explanation
Indices: 39065755--39065793 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
39065745 TCTTATTTTT
39065755 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
39065774 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
39065794 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:39065811 original size:25 final size:23
Alignment explanation
Indices: 39065755--39065819 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
39065745 TCTTATTTTT
*
39065755 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
39065774 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
39065797 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
39065820 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 6 0.15
24 3 0.08
25 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:39073285 original size:75 final size:72
Alignment explanation
Indices: 39073163--39073333 Score: 215
Period size: 75 Copynumber: 2.4 Consensus size: 72
39073153 GTTTTCCTCA
* * * * **
39073163 TTGA-AATACCATACCTACATTTTACAACTCGGTATGGGAAATGCCATACCTACATTTCTTAACT
1 TTGATAATACCATACCTACATTTCACAACTCAGTATGAGAAATACCATACCTACATTTCACAACT
39073227 CAGTATGG
66 CAGTAT-G
39073235 ATTTGATAATACCATACCTACATTTCACAACTCAGTAT-AGATAATACCATACCTACATTTCACA
1 --TTGATAATACCATACCTACATTTCACAACTCAGTATGAGA-AATACCATACCTACATTTCACA
*
39073299 ACTCGGTATG
63 ACTCAGTATG
39073309 --GATAATACCATACCTACATTTCACA
1 TTGATAATACCATACCTACATTTCACA
39073334 CTTTTCCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 25 0.28
74 7 0.08
75 56 0.64
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (72 bp):
TTGATAATACCATACCTACATTTCACAACTCAGTATGAGAAATACCATACCTACATTTCACAACT
CAGTATG
Found at i:39073345 original size:35 final size:35
Alignment explanation
Indices: 39073167--39073333 Score: 210
Period size: 35 Copynumber: 4.6 Consensus size: 35
39073157 TCCTCATTGA
* *
39073167 AATACCATACCTACATTTTACAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
39073202 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
39073242 AATACCATACCTACATTTCACAACTCAGTATAGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
39073277 AATACCATACCTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
39073312 AATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
39073334 CTTTTCCATG
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
35 86 0.74
39 2 0.02
40 28 0.24
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:39080729 original size:13 final size:13
Alignment explanation
Indices: 39080707--39080739 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39080697 AAGGATTTGT
39080707 TTAT-TAAACTAA
1 TTATCTAAACTAA
39080719 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39080732 TTAACTAA
1 TTATCTAA
39080740 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39083589 original size:222 final size:222
Alignment explanation
Indices: 39083201--39083644 Score: 834
Period size: 222 Copynumber: 2.0 Consensus size: 222
39083191 AATAATGCAA
39083201 AAAATTAGGTTTCATGTTCACCCCCTCACACTTAAGATGTACATTGCCCTCAATGTACAGAGATA
1 AAAATTAGGTTTCATGTTCACCCCCTCACACTTAAGATGTACATTGCCCTCAATGTACAGAGATA
39083266 GATTATTCAAAATAAAGAAAATCATAAGAGGAAAGGAGGTGAAATTCCCTGTTATATGGATGTGG
66 GATTATTCAAAATAAAGAAAATCATAAGAGGAAAGGAGGTGAAATTCCCTGTTATATGGATGTGG
* **
39083331 AGCTTGATTTTGAGGATGGAGTGTTCGGGCAAAGTGGTAGCTGCCATTGTTCTTGGCTAGATGAA
131 AGCTTGATTTTGAGGATAGAGTGTTCGGAAAAAGTGGTAGCTGCCATTGTTCTTGGCTAGATGAA
*
39083396 GAAATTGGGTCGTTGAACATGGAACTC
196 GAAATTGGGTCATTGAACATGGAACTC
39083423 AAAATTAGGTTTCATGTTCACCCCCTCACACTTAAGATGTACATTGCCCTCAATGTACAGAGATA
1 AAAATTAGGTTTCATGTTCACCCCCTCACACTTAAGATGTACATTGCCCTCAATGTACAGAGATA
39083488 GATTATTCAAAATAAAGAAAATCATAAGAGGAAAGGAGGTGAAATTCCCTGTTATATGGATGTGG
66 GATTATTCAAAATAAAGAAAATCATAAGAGGAAAGGAGGTGAAATTCCCTGTTATATGGATGTGG
*
39083553 AGCTTGATTTTGAGGATAGAGTGTTTGGAAAAAGTGGTAGCTGCCATTGTTCTTGGCTAGATGAA
131 AGCTTGATTTTGAGGATAGAGTGTTCGGAAAAAGTGGTAGCTGCCATTGTTCTTGGCTAGATGAA
*
39083618 GAAATTGGGTCATTGAACATGGTACTC
196 GAAATTGGGTCATTGAACATGGAACTC
39083645 GTGAGGTATT
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
222 216 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (222 bp):
AAAATTAGGTTTCATGTTCACCCCCTCACACTTAAGATGTACATTGCCCTCAATGTACAGAGATA
GATTATTCAAAATAAAGAAAATCATAAGAGGAAAGGAGGTGAAATTCCCTGTTATATGGATGTGG
AGCTTGATTTTGAGGATAGAGTGTTCGGAAAAAGTGGTAGCTGCCATTGTTCTTGGCTAGATGAA
GAAATTGGGTCATTGAACATGGAACTC
Found at i:39083858 original size:6 final size:5
Alignment explanation
Indices: 39083829--39083926 Score: 69
Period size: 5 Copynumber: 18.8 Consensus size: 5
39083819 TATGTCTTTC
* *
39083829 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAG AAAA-
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT AAAAT
*
39083875 AGAAAA ATAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT AAGAAT -AAAT
1 A-AAAT A-AAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT
39083923 AAAA
1 AAAA
39083927 AATAGGAGGA
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 40 0.52
6 30 0.39
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39083930 original size:17 final size:16
Alignment explanation
Indices: 39083829--39083927 Score: 91
Period size: 16 Copynumber: 6.2 Consensus size: 16
39083819 TATGTCTTTC
39083829 AAAATAAAAT--AATA
1 AAAATAAAATAAAATA
* *
39083843 AAATTGAAATGAAAATA
1 AAAATAAAAT-AAAATA
* *
39083860 AAAATCAAAAGAAAAAGA
1 AAAAT-AAAA-TAAAATA
39083878 AAAAT-AAATAAAAT-
1 AAAATAAAATAAAATA
39083892 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
39083908 AAAATAAGAAT-AAATA
1 AAAATAA-AATAAAATA
39083924 AAAA
1 AAAA
39083928 ATAGGAGGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
14 13 0.19
15 13 0.19
16 19 0.28
17 11 0.16
18 13 0.19
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:39089072 original size:24 final size:25
Alignment explanation
Indices: 39089025--39089072 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
39089015 TAATATAGAG
*
39089025 TTAAAAATACATACATAATGTAATTA
1 TTAAAAATA-ATACATAATATAATTA
*
39089051 TTAAAAAT-ATATATAATATAAT
1 TTAAAAATAATACATAATATAAT
39089073 AAAATATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
26 8 0.40
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TTAAAAATAATACATAATATAATTA
Found at i:39089087 original size:21 final size:20
Alignment explanation
Indices: 39089054--39089156 Score: 68
Period size: 19 Copynumber: 5.0 Consensus size: 20
39089044 GTAATTATTA
39089054 AAAATATAT-ATAATATAAT
1 AAAATATATAATAATATAAT
*
39089073 AAAATATATGAATAATAGGATAT
1 AAAATATAT-AATAATA-TA-AT
39089096 AAAAATATATACATAATAT-AT
1 -AAAATATATA-ATAATATAAT
* * * * *
39089117 AAAAAATTTACTATTTTAA-
1 AAAATATATAATAATATAAT
39089136 AAAATAATATAGATAATATAA
1 AAAAT-ATATA-ATAATATAA
39089157 GAGTATTTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
19 17 0.27
20 13 0.21
21 14 0.22
22 1 0.02
23 3 0.05
24 15 0.24
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATATATAATAATATAAT
Found at i:39089302 original size:21 final size:21
Alignment explanation
Indices: 39089278--39089343 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
39089268 GTATATACGT
* *
39089278 ATAACAATGATAAAAATAATA
1 ATAATAATAATAAAAATAATA
* *
39089299 ATAATAATTATGAAAATAATA
1 ATAATAATAATAAAAATAATA
*
39089320 A-ATATAATAATAAATATAATA
1 ATA-ATAATAATAAAAATAATA
39089341 ATA
1 ATA
39089344 GAAACGATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (21 bp):
ATAATAATAATAAAAATAATA
Found at i:39089328 original size:12 final size:12
Alignment explanation
Indices: 39089313--39089421 Score: 65
Period size: 12 Copynumber: 9.3 Consensus size: 12
39089303 TAATTATGAA
39089313 AATAATAAATAT
1 AATAATAAATAT
39089325 AATAATAAATAT
1 AATAATAAATAT
*
39089337 AATAATAGAA-AC
1 AATAATA-AATAT
* *
39089349 GATAAT-ACTAT
1 AATAATAAATAT
39089360 -ATAA-AAAGTAT
1 AATAATAAA-TAT
*
39089371 -ATATATACATAT
1 AATA-ATAAATAT
39089383 -ATAATAAA-AT
1 AATAATAAATAT
39089393 -AT-ATACCAATATT
1 AATAATA--AATA-T
39089406 AATAATAAATAT
1 AATAATAAATAT
39089418 AATA
1 AATA
39089422 TTATAATACT
Statistics
Matches: 78, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
9 3 0.04
10 10 0.13
11 13 0.17
12 38 0.49
13 9 0.12
14 2 0.03
15 3 0.04
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:39089404 original size:20 final size:21
Alignment explanation
Indices: 39089371--39089422 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
39089361 TAAAAAGTAT
39089371 ATATATACATATA-TAATAAA
1 ATATATACATATATTAATAAA
39089391 ATATATACCA-ATATTAATAATA
1 ATATATA-CATATATTAATAA-A
39089413 A-ATATA-ATAT
1 ATATATACATAT
39089423 TATAATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.04
20 12 0.43
21 13 0.46
22 2 0.07
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATATACATATATTAATAAA
Found at i:39089538 original size:3 final size:3
Alignment explanation
Indices: 39089525--39089581 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
39089515 ACTAATATAT
* * * * *
39089525 ATA AAA ATA ATA ATA ATA ATA TTG ATA ATA TTA ATA ATA TTA GA-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
39089570 ATA ATA ATA ATA
1 ATA ATA ATA ATA
39089582 TTTAATAAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39089552 original size:18 final size:19
Alignment explanation
Indices: 39089531--39089583 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 19
39089521 ATATATAAAA
39089531 ATAATAATAATAATATT-G
1 ATAATAATAATAATATTAG
*
39089549 ATAATATTAATAATATTAG
1 ATAATAATAATAATATTAG
39089568 A-AATAATAATAATATT
1 ATAATAATAATAATATT
39089584 TAATAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 30 0.94
19 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAATAATAATAATATTAG
Found at i:39090729 original size:27 final size:28
Alignment explanation
Indices: 39090659--39090740 Score: 114
Period size: 27 Copynumber: 2.9 Consensus size: 28
39090649 TGATATAATT
39090659 GGGTTTTGGGTTTAATT-TTGAGTGGGCTAA
1 GGGTTTTGGG--T-ATTGTTGAGTGGGCTAA
*
39090689 GGGTTTTGGATATTGTTGAGTGGGCT-A
1 GGGTTTTGGGTATTGTTGAGTGGGCTAA
39090716 GGGTTTTGGGTATTGTTGAGTGGGC
1 GGGTTTTGGGTATTGTTGAGTGGGC
39090741 CAAAATTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
27 28 0.57
28 12 0.24
30 9 0.18
ACGTcount: A:0.13, C:0.04, G:0.41, T:0.41
Consensus pattern (28 bp):
GGGTTTTGGGTATTGTTGAGTGGGCTAA
Found at i:39091832 original size:22 final size:22
Alignment explanation
Indices: 39091807--39091852 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39091797 ACTGTGCGAT
39091807 TGATTTCTTCGTCAAAAAGTAA
1 TGATTTCTTCGTCAAAAAGTAA
39091829 TGATTTCTTCGTCAAAAAGTAA
1 TGATTTCTTCGTCAAAAAGTAA
39091851 TG
1 TG
39091853 GTCCTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (22 bp):
TGATTTCTTCGTCAAAAAGTAA
Found at i:39092246 original size:13 final size:13
Alignment explanation
Indices: 39092223--39092256 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39092213 AGGGTTTGTT
*
39092223 TTAATTAAACTAA
1 TTAACTAAACTAA
*
39092236 TTATCTAAACTAA
1 TTAACTAAACTAA
39092249 TTAACTAA
1 TTAACTAA
39092257 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:39093689 original size:35 final size:36
Alignment explanation
Indices: 39093578--39093698 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 36
39093568 TCCTCATTGA
* * *
39093578 AATACCATACCTACATTTTACAACTCGGTTTGGGA-
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
** **
39093613 AATGTCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGG----GAT
39093653 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
39093688 AATACCATACC
1 AATACCATACC
39093699 AAAATTTCGC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
35 40 0.57
39 3 0.04
40 27 0.39
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (36 bp):
AATACCATACCTACATTTCACAACTCAGTATGGGAT
Found at i:39093699 original size:40 final size:39
Alignment explanation
Indices: 39093578--39093691 Score: 105
Period size: 40 Copynumber: 3.0 Consensus size: 39
39093568 TCCTCATTGA
* * *
39093578 AATACCATACCTACATTTTACAACTCGGTTTGGGA--AAT
1 AATACCATACCTACATTTCACAACTCAGTAT-GGATTAAT
* ** *
39093616 -GT--CATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGA-TTAAT
39093653 AATACCATACCTACATTTCACAACTCAGTATGGA-TAAT
1 AATACCATACCTACATTTCACAACTCAGTATGGATTAAT
39093691 A
1 A
39093692 CCATACCAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
34 3 0.05
35 21 0.36
37 3 0.05
38 5 0.08
40 27 0.46
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (39 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATTAAT
Found at i:39096959 original size:29 final size:29
Alignment explanation
Indices: 39096904--39096959 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
39096894 TTAATAAAAA
* *
39096904 ATAAAATTGTATTTTAATCCTTCAAAATG
1 ATAAAATTGTAATTTAATCATTCAAAATG
* * *
39096933 ATAAAATTTTAATTTAATTATTTAAAA
1 ATAAAATTGTAATTTAATCATTCAAAA
39096960 ATTATAAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (29 bp):
ATAAAATTGTAATTTAATCATTCAAAATG
Found at i:39097667 original size:28 final size:28
Alignment explanation
Indices: 39097635--39097691 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
39097625 AAAATTCTAC
*
39097635 TTTGACTTT-TTTTTTTAAATTATAAAAA
1 TTTGA-TTTATTTTTTAAAATTATAAAAA
39097663 TTTGATTTAAATTTTTTAAAATTATAAAA
1 TTTGATTT--ATTTTTTAAAATTATAAAA
39097692 TATAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 5 0.20
30 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTGATTTATTTTTTAAAATTATAAAAA
Found at i:39097699 original size:15 final size:16
Alignment explanation
Indices: 39097679--39097718 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
39097669 TTAAATTTTT
39097679 TAAAATTATAAAAT-A
1 TAAAATTATAAAATAA
*
39097694 TAAAATT-TTAAATAA
1 TAAAATTATAAAATAA
39097709 TAAAATTATA
1 TAAAATTATA
39097719 TTTCAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 5 0.24
15 15 0.71
16 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTATAAAATAA
Found at i:39098004 original size:39 final size:39
Alignment explanation
Indices: 39097961--39098038 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39097951 AATAAAAAAG
39097961 AATAAACTAACCTTAATGATAATGACAGTAGTGATTGAA
1 AATAAACTAACCTTAATGATAATGACAGTAGTGATTGAA
39098000 AATAAACTAACCTTAATGATAATGACAGTAGTGATTGAA
1 AATAAACTAACCTTAATGATAATGACAGTAGTGATTGAA
39098039 TCTAACTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (39 bp):
AATAAACTAACCTTAATGATAATGACAGTAGTGATTGAA
Found at i:39101819 original size:20 final size:19
Alignment explanation
Indices: 39101794--39101836 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
39101784 TTTTGGACTA
*
39101794 ATTAATAGTTATATACATAT
1 ATTAATAGTTATA-AAATAT
*
39101814 ATTAATAGTTTTAAAATAT
1 ATTAATAGTTATAAAATAT
39101833 ATTA
1 ATTA
39101837 TTACATTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTAATAGTTATAAAATAT
Found at i:39102377 original size:26 final size:25
Alignment explanation
Indices: 39102342--39102390 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
39102332 AACTAAAAGT
*
39102342 AAAAACCTAAATTCTAAAATCATAA
1 AAAAACCTAAATTCCAAAATCATAA
39102367 AAAAACCCTAAATTCCAAAATCAT
1 AAAAA-CCTAAATTCCAAAATCAT
39102391 TGAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAACCTAAATTCCAAAATCATAA
Found at i:39102570 original size:26 final size:26
Alignment explanation
Indices: 39102541--39102592 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39102531 ATTTTATAGG
*
39102541 TTGTAATAATTAT-TAATTATATATAT
1 TTGTAATAAATATATAATTATA-ATAT
*
39102567 TTGTTATAAATATATAATTATAATAT
1 TTGTAATAAATATATAATTATAATAT
39102593 GAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TTGTAATAAATATATAATTATAATAT
Found at i:39105988 original size:3 final size:3
Alignment explanation
Indices: 39105980--39106007 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39105970 AAGATGCTAC
39105980 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39106008 ATTTTATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39106211 original size:26 final size:25
Alignment explanation
Indices: 39106177--39106252 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
39106167 GAATAAATAA
39106177 AAAGAAAGAAAAACAAGAAAAAGAAAC
1 AAAG-AAGAAAAA-AAGAAAAAGAAAC
* * * *
39106204 AAAGAAGAAACGAAATAGAAAGAAAG
1 AAAGAAGAAA-AAAAGAAAAAGAAAC
39106230 AAAGAAGAAAAGAAAAGAAAAAG
1 AAAGAAG-AAA-AAAAGAAAAAG
39106253 GAGAAATTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 23 0.59
27 16 0.41
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.01
Consensus pattern (25 bp):
AAAGAAGAAAAAAAGAAAAAGAAAC
Found at i:39109493 original size:39 final size:39
Alignment explanation
Indices: 39109439--39109551 Score: 163
Period size: 39 Copynumber: 2.8 Consensus size: 39
39109429 GTGCTGATTG
39109439 TTATCGTATATTGATTGCATGTAAGCATGCCAATAAATA
1 TTATCGTATATTGATTGCATGTAAGCATGCCAATAAATA
* *
39109478 TTATCGTATATTGATTGCATGTAAGCATGCCATTGAATA
1 TTATCGTATATTGATTGCATGTAAGCATGCCAATAAATA
* *
39109517 TTACCGTACATGTTGATTGCATGTAAAGCATGCCA
1 TTATCGT--ATATTGATTGCATGT-AAGCATGCCA
39109552 CCGATATTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 43 0.64
41 14 0.21
42 10 0.15
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (39 bp):
TTATCGTATATTGATTGCATGTAAGCATGCCAATAAATA
Found at i:39110662 original size:15 final size:15
Alignment explanation
Indices: 39110639--39110669 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39110629 ATAATTTTTT
39110639 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
*
39110654 TATATAATTCTAAAA
1 TATAAAATTCTAAAA
39110669 T
1 T
39110670 TCTAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:39110784 original size:31 final size:32
Alignment explanation
Indices: 39110718--39110786 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
39110708 ACTTGAAATT
* * *
39110718 TATATACTTTTTTTAATTTTTTATATATATTA
1 TATATACTTTTTTTAATTTTTAATACATATAA
*
39110750 TATATA-TTTTTTTACA-TTTTAATCCATATAA
1 TATATACTTTTTTTA-ATTTTTAATACATATAA
39110781 TATATA
1 TATATA
39110787 ATATTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATACTTTTTTTAATTTTTAATACATATAA
Found at i:39111083 original size:8 final size:8
Alignment explanation
Indices: 39111070--39111110 Score: 59
Period size: 7 Copynumber: 5.2 Consensus size: 8
39111060 AATAAATTTT
39111070 TTATAAAA
1 TTATAAAA
39111078 TTATAAAA
1 TTATAAAA
39111086 TT-TAAAA
1 TTATAAAA
39111093 TTATAAAAA
1 TTAT-AAAA
39111102 TT-TAAAA
1 TTATAAAA
39111109 TT
1 TT
39111111 CAAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 13 0.42
8 12 0.39
9 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:39111093 original size:7 final size:7
Alignment explanation
Indices: 39111073--39111116 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
39111063 AAATTTTTTA
39111073 TAAAATT
1 TAAAATT
39111080 ATAAAATT
1 -TAAAATT
39111088 TAAAATT
1 TAAAATT
39111095 ATAAAAATT
1 -T-AAAATT
39111104 TAAAATT
1 TAAAATT
*
39111111 CAAAAT
1 TAAAAT
39111117 AATATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 18 0.55
8 9 0.27
9 6 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (7 bp):
TAAAATT
Found at i:39111093 original size:15 final size:16
Alignment explanation
Indices: 39111073--39111110 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
39111063 AAATTTTTTA
39111073 TAAAATTAT-AAAATT
1 TAAAATTATAAAAATT
39111088 TAAAATTATAAAAATT
1 TAAAATTATAAAAATT
39111104 TAAAATT
1 TAAAATT
39111111 CAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTATAAAAATT
Found at i:39111100 original size:23 final size:23
Alignment explanation
Indices: 39111070--39111116 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39111060 AATAAATTTT
*
39111070 TTAT-AAAATTATAAAATTTAAAA
1 TTATAAAAATT-TAAAATTCAAAA
39111093 TTATAAAAATTTAAAATTCAAAA
1 TTATAAAAATTTAAAATTCAAAA
39111116 T
1 T
39111117 AATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATAAAAATTTAAAATTCAAAA
Found at i:39111115 original size:15 final size:14
Alignment explanation
Indices: 39111073--39111116 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
39111063 AAATTTTTTA
39111073 TAAAATTATAAAATT
1 TAAAATTA-AAAATT
39111088 TAAAATTATAAAAATT
1 TAAAA-T-TAAAAATT
*
39111104 TAAAATTCAAAAT
1 TAAAATTAAAAAT
39111117 AATATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 12 0.46
17 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAATTAAAAATT
Found at i:39111162 original size:17 final size:19
Alignment explanation
Indices: 39111121--39111164 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
39111111 CAAAATAATA
* *
39111121 TATAAAAATTGATAAATGT
1 TATAAAAATTGATAAAAGG
39111140 TATAAAAA-TGA-AAAAGG
1 TATAAAAATTGATAAAAGG
39111157 TATAAAAA
1 TATAAAAA
39111165 AAACTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (19 bp):
TATAAAAATTGATAAAAGG
Found at i:39111365 original size:20 final size:19
Alignment explanation
Indices: 39111342--39111387 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
39111332 GTTTTTTAGA
39111342 TTATATA-TATTTCTGATTTT
1 TTATATATTATTTCT-A-TTT
39111362 TTATATATTTATTTCTATTT
1 TTATATA-TTATTTCTATTT
39111382 TTATAT
1 TTATAT
39111388 TTTCTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTATTTCTATTT
Found at i:39111374 original size:22 final size:20
Alignment explanation
Indices: 39111343--39111387 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
39111333 TTTTTTAGAT
39111343 TATATATATTTCTGATTTTTTA
1 TATATATATTTCT-A-TTTTTA
*
39111365 TATATTTATTTCTATTTTTA
1 TATATATATTTCTATTTTTA
39111385 TAT
1 TAT
39111388 TTTCTAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
TATATATATTTCTATTTTTA
Found at i:39114430 original size:30 final size:27
Alignment explanation
Indices: 39114396--39114461 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
39114386 TTCAACTAAT
*
39114396 TTATTTTTAATTATCAAATTTTTTAATAAA
1 TTATTTTT-ATTAT-AAATTATTT-ATAAA
*
39114426 TTATTTTTTTTATAAATTATTTATAAA
1 TTATTTTTATTATAAATTATTTATAAA
39114453 TTATATTTT
1 TTAT-TTTT
39114462 TTTCATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 9 0.27
28 12 0.36
29 4 0.12
30 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATTTTTATTATAAATTATTTATAAA
Found at i:39114433 original size:16 final size:16
Alignment explanation
Indices: 39114414--39114447 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39114404 AATTATCAAA
39114414 TTTTTTAATAAATTAT
1 TTTTTTAATAAATTAT
*
39114430 TTTTTTTATAAATTAT
1 TTTTTTAATAAATTAT
39114446 TT
1 TT
39114448 ATAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTAATAAATTAT
Found at i:39114456 original size:27 final size:29
Alignment explanation
Indices: 39114396--39114472 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 29
39114386 TTCAACTAAT
* *
39114396 TTATTTTTAATTATCAAATTTTTTAATAAA
1 TTATTTTT-TTTATCAAATTATTTAATAAA
39114426 TTATTTTTTTTAT-AAATTATTT-ATAAA
1 TTATTTTTTTTATCAAATTATTTAATAAA
* *
39114453 TTATATTTTTT-TCATATTAT
1 TTATTTTTTTTATCAAATTAT
39114473 ATATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 21 0.50
28 8 0.19
29 4 0.10
30 8 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATTTTTTTTATCAAATTATTTAATAAA
Found at i:39114494 original size:19 final size:20
Alignment explanation
Indices: 39114472--39114519 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
39114462 TTTCATATTA
*
39114472 TATATATTT-TTTAGTTTTT
1 TATATATTTATTTACTTTTT
39114491 TATATATTTATTTACTTTTT
1 TATATATTTATTTACTTTTT
39114511 TATAT-TTTA
1 TATATATTTA
39114520 ATGTTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TATATATTTATTTACTTTTT
Found at i:39114518 original size:28 final size:29
Alignment explanation
Indices: 39114453--39114518 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
39114443 TATTTATAAA
*
39114453 TTATATTTTTTTCATATTATATATATTTT
1 TTATATTTTTATCATATTATATATATTTT
*
39114482 TTAGT-TTTTTAT-ATATT-TATTTACTTTT
1 TTA-TATTTTTATCATATTATATATA-TTTT
39114510 TTATATTTT
1 TTATATTTT
39114519 AATGTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 6 0.19
28 16 0.50
29 9 0.28
30 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (29 bp):
TTATATTTTTATCATATTATATATATTTT
Found at i:39116834 original size:13 final size:13
Alignment explanation
Indices: 39116772--39116833 Score: 79
Period size: 13 Copynumber: 4.7 Consensus size: 13
39116762 TTAAACCAAA
39116772 TTTTTCAAAAGCAC
1 TTTTT-AAAAGCAC
*
39116786 TTTTCAAAAGCAC
1 TTTTTAAAAGCAC
* *
39116799 TTTTTCACAGCAC
1 TTTTTAAAAGCAC
*
39116812 TTTTTAAAAACAC
1 TTTTTAAAAGCAC
39116825 TTTTTAAAA
1 TTTTTAAAA
39116834 ATATTGCCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
13 37 0.90
14 4 0.10
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (13 bp):
TTTTTAAAAGCAC
Found at i:39135968 original size:3 final size:3
Alignment explanation
Indices: 39135962--39135991 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39135952 CTTTTTTTTT
39135962 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
39135992 ATTTTCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:39136919 original size:7 final size:7
Alignment explanation
Indices: 39136907--39136953 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
39136897 AACTATAATG
39136907 ACCATCC
1 ACCATCC
39136914 ACCATCC
1 ACCATCC
39136921 ACCATCC
1 ACCATCC
39136928 ACCATCC
1 ACCATCC
39136935 ACCATCC
1 ACCATCC
39136942 ACCATCC
1 ACCATCC
39136949 ACCAT
1 ACCAT
39136954 TACATCCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCATCC
Found at i:39146776 original size:23 final size:22
Alignment explanation
Indices: 39146739--39146781 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
39146729 ATTTTTTTTA
39146739 TTTTATATATATATGTATATGT
1 TTTTATATATATATGTATATGT
*
39146761 TTTTAATATATTTATGTATAT
1 TTTT-ATATATATATGTATAT
39146782 ACTTATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTATATATATATGTATATGT
Found at i:39146874 original size:30 final size:30
Alignment explanation
Indices: 39146819--39146893 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
39146809 TTTATCCCTA
*
39146819 ATAT-TTATGTATTATGTAAATATTTTA-AT
1 ATATATTATGTA-TATCTAAATATTTTATAT
* * *
39146848 ATTATATTATGTATATCTATATATTTTTTGT
1 A-TATATTATGTATATCTAAATATTTTATAT
39146879 ATATATTATGTATAT
1 ATATATTATGTATAT
39146894 ATGTTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 29 0.74
31 9 0.23
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (30 bp):
ATATATTATGTATATCTAAATATTTTATAT
Found at i:39146894 original size:24 final size:25
Alignment explanation
Indices: 39146865--39146937 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 25
39146855 TATGTATATC
39146865 TATATATTTTTTGTATATATTATG-
1 TATATATTTTTTGTATATATTATGT
* **
39146889 TATATATGTTTTCAATAT-TGTATGT
1 TATATATTTTTTGTATATAT-TATGT
39146914 TATATATATTATTGTGTATATATT
1 TATATAT-TT-TT-TGTATATATT
39146938 TTAACATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
23 1 0.03
24 19 0.51
25 7 0.19
26 1 0.03
27 2 0.05
28 6 0.16
29 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.59
Consensus pattern (25 bp):
TATATATTTTTTGTATATATTATGT
Found at i:39147001 original size:19 final size:19
Alignment explanation
Indices: 39146977--39147013 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39146967 CTATTTTATA
*
39146977 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
39146996 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
39147014 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:39147098 original size:9 final size:9
Alignment explanation
Indices: 39147080--39147115 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
39147070 TCATTTCTAA
39147080 TATATATAT
1 TATATATAT
*
39147089 TATATGTAT
1 TATATATAT
*
39147098 TTTATATAT
1 TATATATAT
39147107 TATATATAT
1 TATATATAT
39147116 ATTTTAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
TATATATAT
Found at i:39147103 original size:20 final size:20
Alignment explanation
Indices: 39147079--39147121 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
39147069 ATCATTTCTA
*
39147079 ATATATATATTATATGTATTTT
1 ATATAT-TA-TATATATATTTT
39147101 ATATATTATATATATATTTT
1 ATATATTATATATATATTTT
39147121 A
1 A
39147122 ATGTTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATATTATATATATATTTT
Found at i:39163758 original size:15 final size:16
Alignment explanation
Indices: 39163726--39163760 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39163716 ATGGAAGCTG
*
39163726 TATTTTTATAATTCAA
1 TATTTTTATAAATCAA
39163742 TATTTTTATAAAT-AA
1 TATTTTTATAAATCAA
39163757 TATT
1 TATT
39163761 ATTGGAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTTATAAATCAA
Found at i:39165074 original size:18 final size:18
Alignment explanation
Indices: 39165051--39165085 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39165041 AAAACTTTGG
39165051 TTTTTATACTTTTATTAT
1 TTTTTATACTTTTATTAT
39165069 TTTTTATACTTTTATTA
1 TTTTTATACTTTTATTA
39165086 AAATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATACTTTTATTAT
Found at i:39165082 original size:26 final size:25
Alignment explanation
Indices: 39165063--39165136 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 25
39165053 TTTATACTTT
*
39165063 TATTATTTTTTATACTTTTATTAAAA
1 TATTATTTTTTATACTTTTA-TATAA
39165089 TATTATTTTTTATACTTTTATAAATAA
1 TATTATTTTTTATACTTTTAT--ATAA
39165116 TATTATTTTTTATACTTTTAT
1 TATTATTTTTTATACTTTTAT
39165137 TAAAATATCA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 1 0.02
26 20 0.44
27 24 0.53
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATTTTTTATACTTTTATATAA
Found at i:39165143 original size:26 final size:26
Alignment explanation
Indices: 39165063--39165144 Score: 146
Period size: 26 Copynumber: 3.1 Consensus size: 26
39165053 TTTATACTTT
39165063 TATTATTTTTTATACTTTTATTAAAA
1 TATTATTTTTTATACTTTTATTAAAA
*
39165089 TATTATTTTTTATACTTTTATAAATAA
1 TATTATTTTTTATACTTTTATTAA-AA
39165116 TATTATTTTTTATACTTTTATTAAAA
1 TATTATTTTTTATACTTTTATTAAAA
39165142 TAT
1 TAT
39165145 CATAATATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
26 28 0.53
27 25 0.47
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATTTTTTATACTTTTATTAAAA
Found at i:39167291 original size:34 final size:34
Alignment explanation
Indices: 39167247--39167377 Score: 97
Period size: 34 Copynumber: 3.9 Consensus size: 34
39167237 GTAATATAGA
39167247 ATGCTTATAACAAATCAATACAGTAGCAATTTAT
1 ATGCTTATAACAAATCAATACAGTAGCAATTTAT
* * * * *
39167281 ATGCTCATAACAATTCGATAC-GATAGCAAATAAT
1 ATGCTTATAACAAATCAATACAG-TAGCAATTTAT
*** * *
39167315 ATGCTTATAATGGATCAATACAAT-G-ACATTTAAC
1 ATGCTTATAACAAATCAATACAGTAGCA-ATTT-AT
* * *
39167349 ATGCTGATAAGAAATCAATACACTAGCAA
1 ATGCTTATAACAAATCAATACAGTAGCAA
39167378 AAGACATGCT
Statistics
Matches: 71, Mismatches: 20, Indels: 11
0.70 0.20 0.11
Matches are distributed among these distances:
32 1 0.01
33 4 0.06
34 63 0.89
35 2 0.03
36 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (34 bp):
ATGCTTATAACAAATCAATACAGTAGCAATTTAT
Found at i:39169983 original size:28 final size:28
Alignment explanation
Indices: 39169951--39170006 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
39169941 AGTGCACTAA
39169951 CTACTTAACCATTAAGCCTAGGTGATTT
1 CTACTTAACCATTAAGCCTAGGTGATTT
*
39169979 CTACTTAACCGTTAAGCCTAGGTGATTT
1 CTACTTAACCATTAAGCCTAGGTGATTT
39170007 TCTTGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (28 bp):
CTACTTAACCATTAAGCCTAGGTGATTT
Found at i:39173282 original size:32 final size:30
Alignment explanation
Indices: 39173244--39173308 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
39173234 ACTTAACAAG
39173244 CAAATGCCTCTAAAATAATAATAATAAATTAA
1 CAAATGCCTCTAAAATAATAA-AA-AAATTAA
* *
39173276 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
39173306 CAA
1 CAA
39173309 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 10 0.32
31 1 0.03
32 20 0.65
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:39173364 original size:22 final size:22
Alignment explanation
Indices: 39173339--39173381 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39173329 TATTCAAACA
39173339 ATAACAATAAAAT-AGTAGCAAC
1 ATAACAATAAAATGA-TAGCAAC
* *
39173361 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATGATAGCAA
39173382 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATGATAGCAAC
Found at i:39196379 original size:6 final size:6
Alignment explanation
Indices: 39196340--39196487 Score: 73
Period size: 6 Copynumber: 23.7 Consensus size: 6
39196330 ATTTAAGGTT
* * * * * *
39196340 ATTTCG ATTCTG ATTCTG ATTCTG ATTCTG ATTTTG ATTTCG ATTTCT-
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT-TG
**
39196388 ATTTTG ATTTTG ATTTCA ATTTTG AAATACTCATTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG --AT--T--TTG ATTTTG ATTTTG
* ** * ** * * *
39196436 ATTTTG GTTTCA ATTTTG ATCTCA ATTTAG CTTTAG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
39196484 ATTT
1 ATTT
39196488 CAATTTGGAT
Statistics
Matches: 110, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
5 1 0.01
6 100 0.91
8 3 0.03
10 3 0.03
12 3 0.03
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (6 bp):
ATTTTG
Found at i:39196427 original size:42 final size:41
Alignment explanation
Indices: 39196376--39196493 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 41
39196366 TCTGATTTTG
*
39196376 ATTTCGATTTCTATTTTGATTTTGATTTCAATTTTGAAATACTC-
1 ATTTAGATTT-TATTTTGATTTTGATTTCAATTTTG--AT-CTCA
*
39196420 A-TT-GATTTTGATTTTGATTTTGGTTTCAATTTTGATCTCA
1 ATTTAGATTTT-ATTTTGATTTTGATTTCAATTTTGATCTCA
* *
39196460 ATTTAGCTTTAGATTTTGATTTTGATTTCAATTT
1 ATTTAGATTT-TATTTTGATTTTGATTTCAATTT
39196494 GGATTTCGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
39 3 0.05
40 3 0.05
41 3 0.05
42 53 0.82
43 2 0.03
44 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.57
Consensus pattern (41 bp):
ATTTAGATTTTATTTTGATTTTGATTTCAATTTTGATCTCA
Found at i:39196453 original size:18 final size:18
Alignment explanation
Indices: 39196370--39196505 Score: 76
Period size: 18 Copynumber: 6.9 Consensus size: 18
39196360 TCTGATTCTG
* *
39196370 ATTTTGATTTCGATTTCT
1 ATTTTGATTTTGATTTCA
39196388 ATTTTGATTTTGATTTCA
1 ATTTTGATTTTGATTTCA
**
39196406 ATTTTGAAATACTCATTGATTTTG
1 ATTTTG--AT--T--TTGATTTCA
*
39196430 ATTTTGATTTTGGTTTCA
1 ATTTTGATTTTGATTTCA
*
39196448 ATTTTGATCTCAATTTAGCTTT-A
1 ATTTTGA--T---TTT-GATTTCA
39196471 GATTTTGATTTTGATTTCA
1 -ATTTTGATTTTGATTTCA
* *
39196490 ATTTGGATTTCGATTT
1 ATTTTGATTTTGATTT
39196506 GTATGACACA
Statistics
Matches: 93, Mismatches: 11, Indels: 28
0.70 0.08 0.21
Matches are distributed among these distances:
18 53 0.57
19 4 0.04
20 4 0.04
22 4 0.04
23 4 0.04
24 24 0.26
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (18 bp):
ATTTTGATTTTGATTTCA
Found at i:39196598 original size:48 final size:48
Alignment explanation
Indices: 39196543--39196663 Score: 179
Period size: 48 Copynumber: 2.5 Consensus size: 48
39196533 CATATGCATG
*
39196543 ATGTTTATTATTTGTATCTGCCATTGTATGGATGCCATTATCAAACTA
1 ATGTTTATTATTTGTATCTGCAATTGTATGGATGCCATTATCAAACTA
* * *
39196591 ATGTTTATTTTTTGTATCTGCAATTGTATGGATGTCATTATCAAACTG
1 ATGTTTATTATTTGTATCTGCAATTGTATGGATGCCATTATCAAACTA
* * *
39196639 ATGTTTATTGTGTATATCTGCAATT
1 ATGTTTATTATTTGTATCTGCAATT
39196664 TTTTGTATCC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (48 bp):
ATGTTTATTATTTGTATCTGCAATTGTATGGATGCCATTATCAAACTA
Found at i:39196789 original size:89 final size:89
Alignment explanation
Indices: 39196622--39196787 Score: 246
Period size: 89 Copynumber: 1.9 Consensus size: 89
39196612 AATTGTATGG
* * *
39196622 ATGTCATTATCAAACTGATGTTTATTGTGTATATCTGCAATTTTTTGTATCCAAGCTGCTATATT
1 ATGTCATTATCAAACTGATGTTTATTGTATATATCTGCAATTGTTTGTATCCAAACTGCTATATT
39196687 GTATATGGCAAAATCAAAATTTGA
66 GTATATGGCAAAATCAAAATTTGA
* *
39196711 ATGTCATTATCAAACTGATGTTTGTTGTATATATTTGTC-ATTGTTT-TATCCAAACTGCTATAT
1 ATGTCATTATCAAACTGATGTTTATTGTATATATCTG-CAATTGTTTGTATCCAAACTGCTATAT
* *
39196774 TGTATGTTGCAAAA
65 TGTATATGGCAAAA
39196788 ATGGTTGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
88 28 0.41
89 40 0.58
90 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (89 bp):
ATGTCATTATCAAACTGATGTTTATTGTATATATCTGCAATTGTTTGTATCCAAACTGCTATATT
GTATATGGCAAAATCAAAATTTGA
Found at i:39197022 original size:15 final size:15
Alignment explanation
Indices: 39197002--39197051 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
39196992 GAATAAGACA
39197002 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
39197017 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
** **
39197032 CATCTGAAAGTGATG
1 TGTCTGGTAGTGATG
39197047 TGTCT
1 TGTCT
39197052 AATAGGATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.18, C:0.10, G:0.34, T:0.38
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:39198836 original size:26 final size:26
Alignment explanation
Indices: 39198776--39198839 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
39198766 TGGTGTGTTG
* *
39198776 ACTATTTTTTAATATGCATTTAGTGA
1 ACTATTTTTTAATATGCATATAATGA
* *
39198802 GCTTTTTTTTATAATATGCATATAAT-A
1 AC-TATTTTT-TAATATGCATATAATGA
39198829 ACTATTTTTTA
1 ACTATTTTTTA
39198840 GGGGATGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.07
26 7 0.23
27 8 0.27
28 13 0.43
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (26 bp):
ACTATTTTTTAATATGCATATAATGA
Found at i:39198836 original size:28 final size:27
Alignment explanation
Indices: 39198780--39198838 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
39198770 GTGTTGACTA
* * *
39198780 TTTTTTAATATGCATTTAGTGAGCTTT
1 TTTTTTAATATGCATATAATGAACTTT
*
39198807 TTTTTATAATATGCATATAAT-AACTAT
1 TTTTT-TAATATGCATATAATGAACTTT
39198834 TTTTT
1 TTTTT
39198839 AGGGGATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (27 bp):
TTTTTTAATATGCATATAATGAACTTT
Found at i:39201839 original size:21 final size:21
Alignment explanation
Indices: 39201775--39201843 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
39201765 AATGCTAATA
* *
39201775 ATAACAATCTAATATAAAACC
1 ATAATAATTTAATATAAAACC
* **
39201796 ATAAT--GTTAAT-TAATAATT
1 ATAATAATTTAATATAA-AACC
39201815 ATAATAATTTAATATAAAACC
1 ATAATAATTTAATATAAAACC
39201836 ATAATAAT
1 ATAATAAT
39201844 AATCATAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.31
21 19 0.53
22 3 0.08
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (21 bp):
ATAATAATTTAATATAAAACC
Found at i:39201843 original size:30 final size:30
Alignment explanation
Indices: 39201807--39201865 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39201797 TAATGTTAAT
* *
39201807 TAATAATTATAATAAT-TTAATATAAAACCA
1 TAATAATAATAATAATAAT-ATATAAAACCA
*
39201837 TAATAATAATCATAATAATATATAAAACC
1 TAATAATAATAATAATAATATATAAAACC
39201866 TAAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (30 bp):
TAATAATAATAATAATAATATATAAAACCA
Found at i:39202325 original size:21 final size:21
Alignment explanation
Indices: 39202270--39202325 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
39202260 AAGTTGGTGT
*
39202270 CCCAACTCAGCAACAAGCTAC
1 CCCAACTCAGCAAGAAGCTAC
*
39202291 CCCAAATCAGCAAGAGAG-TAC
1 CCCAACTCAGCAAGA-AGCTAC
*
39202312 CCCAACTCAACAAG
1 CCCAACTCAGCAAG
39202326 CTGCCCCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.41, C:0.38, G:0.12, T:0.09
Consensus pattern (21 bp):
CCCAACTCAGCAAGAAGCTAC
Found at i:39202353 original size:21 final size:21
Alignment explanation
Indices: 39202327--39202399 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
39202317 CTCAACAAGC
39202327 TGCCCCAACTCAGTTACCTAG
1 TGCCCCAACTCAGTTACCTAG
* * *
39202348 TGCCCCAACTCA-TCAACAAG
1 TGCCCCAACTCAGTTACCTAG
*
39202368 CTGCCCCAACTCAGTTACCTAA
1 -TGCCCCAACTCAGTTACCTAG
39202390 TGCCCCAACT
1 TGCCCCAACT
39202400 TATCAATAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.12
21 34 0.79
22 4 0.09
ACGTcount: A:0.27, C:0.41, G:0.11, T:0.21
Consensus pattern (21 bp):
TGCCCCAACTCAGTTACCTAG
Found at i:39202373 original size:42 final size:42
Alignment explanation
Indices: 39202318--39202415 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
39202308 GTACCCCAAC
*
39202318 TCAACAAGCTGCCCCAACTCAGTTACCTAGTGCCCCAACTCA
1 TCAACAAGCTGCCCCAACTCAGTTACCTAATGCCCCAACTCA
*
39202360 TCAACAAGCTGCCCCAACTCAGTTACCTAATGCCCCAACTTA
1 TCAACAAGCTGCCCCAACTCAGTTACCTAATGCCCCAACTCA
*
39202402 TCAATAAGCTGCCC
1 TCAACAAGCTGCCC
39202416 TAAGAGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (42 bp):
TCAACAAGCTGCCCCAACTCAGTTACCTAATGCCCCAACTCA
Found at i:39202414 original size:21 final size:21
Alignment explanation
Indices: 39202318--39202415 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
39202308 GTACCCCAAC
*
39202318 TCAACAAGCTGCCCCAACTCA
1 TCAATAAGCTGCCCCAACTCA
* *
39202339 GTTACCT-AG-TGCCCCAACTCA
1 -TCA-ATAAGCTGCCCCAACTCA
*
39202360 TCAACAAGCTGCCCCAACTCA
1 TCAATAAGCTGCCCCAACTCA
* * *
39202381 GTTACCTAA--TGCCCCAACTTA
1 -TCA-ATAAGCTGCCCCAACTCA
39202402 TCAATAAGCTGCCC
1 TCAATAAGCTGCCC
39202416 TAAGAGAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 40 0.70
22 6 0.11
23 2 0.04
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (21 bp):
TCAATAAGCTGCCCCAACTCA
Found at i:39203451 original size:3 final size:3
Alignment explanation
Indices: 39203443--39203514 Score: 92
Period size: 3 Copynumber: 24.3 Consensus size: 3
39203433 TCCATTTTTC
*
39203443 TCT TCT TCT TCT TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
39203490 TCC TCC TCT TAT TAT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
39203515 TTCCTTTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:39210710 original size:99 final size:99
Alignment explanation
Indices: 39210536--39210718 Score: 269
Period size: 99 Copynumber: 1.8 Consensus size: 99
39210526 ATAAAAACGT
* * *
39210536 TTGTTCAATTATGCATTTTCTAAAATGTTAATTTAGTTCTATTTATTGAGTTTTGATATTAAGTG
1 TTGTTCAATTATGCATTTTCTAAAACGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAGTG
*
39210601 AAACCATTTATTCTATTATACAAAGTAAAACCAC
66 AAACCATTTATTCAATTATACAAAGTAAAACCAC
** *
39210635 TTGTTCAATTATGTGTTTTTTAAAACGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAGT-
1 TTGTTCAATTATGCATTTTCTAAAACGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAGTG
**
39210699 AGAACTGTTTATTCAATTAT
66 A-AACCATTTATTCAATTAT
39210719 GTGTTTTTGA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
98 1 0.01
99 73 0.99
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (99 bp):
TTGTTCAATTATGCATTTTCTAAAACGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAGTG
AAACCATTTATTCAATTATACAAAGTAAAACCAC
Found at i:39210722 original size:72 final size:72
Alignment explanation
Indices: 39210623--39210791 Score: 221
Period size: 72 Copynumber: 2.3 Consensus size: 72
39210613 CTATTATACA
* * * * *
39210623 AAGTAAAACCACTTGTTCAATTATGTGTTTTTTAAAACGTTAATTTAGTTCAATTTATTGAATTT
1 AAGTAAAACCATTTATTCAATTATGTGTTTTTGAAAACGCTAATTTAGTTCAATTCATTGAATTT
*
39210688 TGATATT
66 CGATATT
* ** * * *
39210695 AAGTAGAACTGTTTATTCAATTATGTGTTTTTGAAAAGGCTATTTTAGTTCAATTCATTGAGTTT
1 AAGTAAAACCATTTATTCAATTATGTGTTTTTGAAAACGCTAATTTAGTTCAATTCATTGAATTT
39210760 CGATATT
66 CGATATT
39210767 AAGTAAAACCATTTATTCAAGTTAT
1 AAGTAAAACCATTTATTCAA-TTAT
39210792 ACGTTTTGAG
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 77 0.95
73 4 0.05
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (72 bp):
AAGTAAAACCATTTATTCAATTATGTGTTTTTGAAAACGCTAATTTAGTTCAATTCATTGAATTT
CGATATT
Found at i:39215731 original size:29 final size:26
Alignment explanation
Indices: 39215670--39215731 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
39215660 TTCAATATAC
*
39215670 TAAAATTTATTATTTTATGTTTTTAT
1 TAAAATTTATTATTTTATGCTTTTAT
*
39215696 TATAATTTATTCATTTTATATGACTTTT-T
1 TAAAATTTATT-A-TTT-TATG-CTTTTAT
39215725 TAAAATT
1 TAAAATT
39215732 ATTTTCATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 10 0.34
27 1 0.03
28 3 0.10
29 11 0.38
30 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (26 bp):
TAAAATTTATTATTTTATGCTTTTAT
Done.