Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 10 of 77
Found at i:1470952 original size:19 final size:20
Alignment explanation
Indices: 1470907--1470958 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1470897 TATTTATAAA
*
1470907 TAAAAT-AATAATAATTTAT
1 TAAAATAAATATTAATTTAT
1470926 TAATAAATAAATATTAATTT-T
1 T-A-AAATAAATATTAATTTAT
1470947 TAAAATAAATAT
1 TAAAATAAATAT
1470959 ATATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 6 0.21
22 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATAAATATTAATTTAT
Found at i:1471092 original size:31 final size:29
Alignment explanation
Indices: 1471052--1471158 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 29
1471042 TGATTCAATG
1471052 ATAATATATAAAATTTATATATTAATAATAT
1 ATAA-ATATAAAATTTATATATT-ATAATAT
* *
1471083 ATCAAATATAAATTTTTTTATATTATAATAT
1 AT-AAATATAAA-ATTTATATATTATAATAT
*
1471114 ATAAATTATTAATAATTTATATATTTATATTAT
1 ATAAA-TA-TAA-AATTTATATA-TTATAATAT
*
1471147 ATTAATATAAAA
1 ATAAATATAAAA
1471159 ATATAATATA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
30 5 0.08
31 23 0.36
32 23 0.36
33 13 0.20
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATATAAAATTTATATATTATAATAT
Found at i:1471137 original size:24 final size:25
Alignment explanation
Indices: 1471071--1471134 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
1471061 AAAATTTATA
*
1471071 TATTAATAATATATCAA-ATATAAAT
1 TATTAATAATTTAT-AATATATAAAT
* *
1471096 T-TT-TTTATATTATAATATATAAAT
1 TATTAATAAT-TTATAATATATAAAT
1471120 TATTAATAATTTATA
1 TATTAATAATTTATA
1471135 TATTTATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
23 5 0.17
24 14 0.47
25 8 0.27
26 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTAATAATTTATAATATATAAAT
Found at i:1471224 original size:21 final size:21
Alignment explanation
Indices: 1471167--1471212 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1471157 AAATATAATA
* *
1471167 TATATTTAATTTTATTAAATT
1 TATATATAATTTTATTAAAAT
1471188 TATATATAATTTTATTAAAAT
1 TATATATAATTTTATTAAAAT
1471209 TATA
1 TATA
1471213 AAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATAATTTTATTAAAAT
Found at i:1473828 original size:15 final size:14
Alignment explanation
Indices: 1473797--1473835 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1473787 TTATTATATC
*
1473797 ATTATTAAATTGTA
1 ATTATTAAATAGTA
1473811 ATTATTAAATAAGTA
1 ATTATTAAAT-AGTA
*
1473826 ATTAATAAAT
1 ATTATTAAAT
1473836 TATAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATTATTAAATAGTA
Found at i:1474469 original size:18 final size:19
Alignment explanation
Indices: 1474446--1474489 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1474436 ATAAATACAT
*
1474446 AAAAATTTAATTTT-TTAA
1 AAAAATATAATTTTATTAA
*
1474464 AAAAATATATTTTTATTAA
1 AAAAATATAATTTTATTAA
*
1474483 TAAAATA
1 AAAAATA
1474490 ATATCGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATATAATTTTATTAA
Found at i:1474777 original size:7 final size:7
Alignment explanation
Indices: 1474746--1474788 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
1474736 TATTAAGATA
1474746 TTTATTT
1 TTTATTT
1474753 TGTTGATGTT
1 T-TT-AT-TT
*
1474763 TTTGTTT
1 TTTATTT
1474770 TTTATTT
1 TTTATTT
1474777 TTTATTT
1 TTTATTT
1474784 TTTAT
1 TTTAT
1474789 CTTCTCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 21 0.68
8 3 0.10
9 4 0.13
10 3 0.10
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:1475718 original size:22 final size:21
Alignment explanation
Indices: 1475676--1475728 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1475666 TAACTATTTG
*
1475676 ATTATTATAAAATAATAAATAT
1 ATTATTA-AAAATAATAAATAA
1475698 ATTATTAAAATATTAAT-AATAA
1 ATTATTAAAA-A-TAATAAATAA
*
1475720 AATATTAAA
1 ATTATTAAA
1475729 GAACTAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 20 0.74
23 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTAAAAATAATAAATAA
Found at i:1475722 original size:14 final size:14
Alignment explanation
Indices: 1475686--1475727 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1475676 ATTATTATAA
1475686 AATAATAAATATATT
1 AATAATAAA-ATATT
1475701 -AT--TAAAATATT
1 AATAATAAAATATT
1475712 AATAATAAAATATT
1 AATAATAAAATATT
1475726 AA
1 AA
1475728 AGAACTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
14 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATAAAATATT
Found at i:1480210 original size:38 final size:39
Alignment explanation
Indices: 1480115--1480217 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 39
1480105 CTAAAATTCT
* * *
1480115 TAAATTTTGGGATTAAATTCAAAGAATTCCAAAAATCTC
1 TAAATTTTGGGATTAAATTCCAAGAAGTCCAAAAATCCC
* * * * **
1480154 TTAATTCTGGCATCAAATTCCAAGGCGTCC-AAAATCCC
1 TAAATTTTGGGATTAAATTCCAAGAAGTCCAAAAATCCC
*
1480192 TAAATTTTGGGATTAAATTTCAAGAA
1 TAAATTTTGGGATTAAATTCCAAGAA
1480218 ACCCAATAAC
Statistics
Matches: 48, Mismatches: 16, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
38 26 0.54
39 22 0.46
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (39 bp):
TAAATTTTGGGATTAAATTCCAAGAAGTCCAAAAATCCC
Found at i:1482490 original size:11 final size:11
Alignment explanation
Indices: 1482439--1482504 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 11
1482429 CGATTTTTTT
*
1482439 ATTAGATTTAA
1 ATTAAATTTAA
*
1482450 ATTAAATTCAGA
1 ATTAAATTTA-A
*
1482462 TATTAAATATATAT
1 -ATTAAAT-T-TAA
1482476 ATTAAATTTAA
1 ATTAAATTTAA
1482487 ATTAAATTTTAA
1 ATTAAA-TTTAA
1482499 ATTAAA
1 ATTAAA
1482505 AAGTGAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
11 16 0.36
12 13 0.29
13 14 0.31
14 1 0.02
15 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:1482500 original size:18 final size:18
Alignment explanation
Indices: 1482444--1482501 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1482434 TTTTTATTAG
* *
1482444 ATTTAAATTAAA-TTCAG
1 ATTTAAATTAAATTTTAA
* *
1482461 ATATTAAATATATATATTAA
1 AT-TTAAAT-TAAATTTTAA
1482481 ATTTAAATTAAATTTTAA
1 ATTTAAATTAAATTTTAA
1482499 ATT
1 ATT
1482502 AAAAAGTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.06
18 17 0.53
19 9 0.28
20 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTAAATTAAATTTTAA
Found at i:1483421 original size:3 final size:3
Alignment explanation
Indices: 1483413--1483498 Score: 102
Period size: 3 Copynumber: 27.7 Consensus size: 3
1483403 ATAGACTCAT
1483413 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA
* * *
1483460 TTTA TTT TTA TTA TTTA CTG TTA -TA TTA TTA TTA TTA TT
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
1483499 TTTTGATTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.03
3 58 0.81
4 12 0.17
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1483925 original size:20 final size:20
Alignment explanation
Indices: 1483902--1483948 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1483892 AAAATTGAAT
1483902 TTTTCGACCAAATTTTTCAA
1 TTTTCGACCAAATTTTTCAA
***
1483922 TTTTCGATGTAATTTTTCAA
1 TTTTCGACCAAATTTTTCAA
1483942 TTTTCGA
1 TTTTCGA
1483949 TTAAACATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTTCGACCAAATTTTTCAA
Found at i:1483949 original size:20 final size:20
Alignment explanation
Indices: 1483912--1483949 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1483902 TTTTCGACCA
1483912 AATTTTTCAATTTTCGATGT
1 AATTTTTCAATTTTCGATGT
1483932 AATTTTTCAATTTTCGAT
1 AATTTTTCAATTTTCGAT
1483950 TAAACATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (20 bp):
AATTTTTCAATTTTCGATGT
Found at i:1484298 original size:3 final size:3
Alignment explanation
Indices: 1484292--1484323 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1484282 TTTTTTTCAT
1484292 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1484324 GCTTATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1484380 original size:15 final size:15
Alignment explanation
Indices: 1484362--1484391 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1484352 TATTCCTTAA
1484362 TTTATTATTTTTGTT
1 TTTATTATTTTTGTT
*
1484377 TTTATTTTTTTTGTT
1 TTTATTATTTTTGTT
1484392 AATGATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTATTATTTTTGTT
Found at i:1484504 original size:60 final size:60
Alignment explanation
Indices: 1484434--1484780 Score: 368
Period size: 60 Copynumber: 5.8 Consensus size: 60
1484424 ATTATTTTTG
* *
1484434 AAATATTTTTGA-AGAAAAGTTGGAAGTACCAA-TTTTCTTTAAAAATAAAAATTATCAAGAA
1 AAATA-TTTTGAGA-AAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAAATTATCAAGAA
* * * * *
1484495 AAGTATTTTGAG-GAAAGTTGAAAGTATAAATTTTTCTT-GAAATTAAAATTA--AA-AA
1 AAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAA
*
1484550 AATATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
1 AA-ATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAA
* * * * * * * ** *
1484611 AAGTATTTTGAGGAAAAGCTAAAAGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAA
1 AAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATT-ATCAAGAA
* * * *
1484672 AAACATTTTGAGAAAAAGTTGGAAGTATCAATTTTCCTTAAAAATAAAGATTATCAAGAA
1 AAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAA
* * *
1484732 AAACATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTT-AAAATAAAAA
1 AAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAA
1484781 CCTCCAAAAT
Statistics
Matches: 234, Mismatches: 43, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
55 4 0.02
56 11 0.05
57 23 0.10
58 22 0.09
59 25 0.11
60 95 0.41
61 54 0.23
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (60 bp):
AAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAA
Found at i:1484712 original size:121 final size:117
Alignment explanation
Indices: 1484440--1484780 Score: 479
Period size: 121 Copynumber: 2.9 Consensus size: 117
1484430 TTTGAAATAT
*
1484440 TTTTGA-AGAAAAGTTGGAAGTACCAATTTTCTTTAAAAATAAAAATTATCAAGAAAAGTATTTT
1 TTTTGAGA-AAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTATCAAGAAAAGTATTTT
* * * *
1484504 GAGG-AAAGTTGAAAGTATAAATTTTTCTTGAAATTAAAATTAAAAAAATATA
65 GAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAATTAAAAAAAAACA
* *
1484556 TTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTG
1 TTTTGAGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTATCAAGAAAAGTATTTTG
*
1484621 AGGAAAAGCTAAAAGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAAACA
66 AGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAA-TT---AAAAAAAAACA
* * ** *
1484677 TTTTGAGAAAAAGTTGGAAGTATCAATTTTCCTTAAAAATAAAGATTATCAAGAAAAACATTTTA
1 TTTTGAGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTATCAAGAAAAGTATTTTG
* * *
1484742 AGAAAAAGTTAAAAGTATCAATTTTTCTTAAAATAAAAA
66 AGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAA
1484781 CCTCCAAAAT
Statistics
Matches: 200, Mismatches: 19, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
116 63 0.31
117 33 0.17
118 2 0.01
121 102 0.51
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (117 bp):
TTTTGAGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTATCAAGAAAAGTATTTTG
AGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAATTAAAAAAAAACA
Found at i:1490715 original size:11 final size:11
Alignment explanation
Indices: 1490699--1490723 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1490689 ATCAAGTTAG
1490699 ATGTCAAATAT
1 ATGTCAAATAT
1490710 ATGTCAAATAT
1 ATGTCAAATAT
1490721 ATG
1 ATG
1490724 CCAGCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (11 bp):
ATGTCAAATAT
Found at i:1492785 original size:21 final size:21
Alignment explanation
Indices: 1492747--1492790 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1492737 TTAGCCAACA
*
1492747 TTTGAATAGCATGCATTGAAT
1 TTTGAATAGCATACATTGAAT
* * *
1492768 TTTGCATAGCATATATTGCAT
1 TTTGAATAGCATACATTGAAT
1492789 TT
1 TT
1492791 AGGAAAGCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (21 bp):
TTTGAATAGCATACATTGAAT
Found at i:1493101 original size:41 final size:40
Alignment explanation
Indices: 1493039--1493204 Score: 172
Period size: 42 Copynumber: 4.0 Consensus size: 40
1493029 AAGGGGCATT
* *
1493039 CATTTA-TTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
1 CATTTATTTTTCAAAGTCGTGGAGCCTCTGTTTAGAGGAG
* *
1493078 CAATTTATTTTTCAAAGTCGTGGTTGCCTCTGTTTAGATGAG
1 C-ATTTATTTTTCAAAGTCGTGG-AGCCTCTGTTTAGAGGAG
* * *
1493120 CATTTATTTCTTTAAAAGTTGTGGAGCTTCTGTTTAGAGGAG
1 CATTTA-TT-TTTCAAAGTCGTGGAGCCTCTGTTTAGAGGAG
* * * *
1493162 CATTTATTTCTTCAAAAGTCATTGAGCCTTTGCTTAGAGGAG
1 CATTTATTT-TTC-AAAGTCGTGGAGCCTCTGTTTAGAGGAG
1493204 C
1 C
1493205 TTTGTTTATT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 6 0.06
41 23 0.22
42 64 0.60
43 12 0.11
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (40 bp):
CATTTATTTTTCAAAGTCGTGGAGCCTCTGTTTAGAGGAG
Found at i:1493180 original size:42 final size:40
Alignment explanation
Indices: 1493039--1493177 Score: 181
Period size: 42 Copynumber: 3.4 Consensus size: 40
1493029 AAGGGGCATT
1493039 CATTTA-TTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
1 CATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
* *
1493078 CAATTTATTTTTCAAAGTCGTGGTTGCCTCTGTTTAGATGAG
1 C-ATTTATTTTTCAAAGTTGTGG-TGCCTCTGTTTAGAGGAG
* * *
1493120 CATTTATTTCTTTAAAAGTTGTGGAGCTTCTGTTTAGAGGAG
1 CATTTA-TT-TTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
1493162 CATTTATTTCTTCAAA
1 CATTTATTT-TTCAAA
1493178 AGTCATTGAG
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 6 0.07
41 26 0.30
42 41 0.48
43 12 0.14
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (40 bp):
CATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
Found at i:1493199 original size:42 final size:43
Alignment explanation
Indices: 1493061--1493333 Score: 214
Period size: 42 Copynumber: 6.3 Consensus size: 43
1493051 AAGTTGTGGT
* * * *
1493061 GCCTCTGTTTAGAGGAGCAATTTATTT-TTC-AAAGTCGTGGTT
1 GCCTCTGTTTAGAGGAGCTATTTATTTCTTCAAAAGTCATTG-A
* * ** *
1493103 GCCTCTGTTTAGATGAGC-ATTTATTTCTTTAAAAGTTGTGGA
1 GCCTCTGTTTAGAGGAGCTATTTATTTCTTCAAAAGTCATTGA
*
1493145 GCTTCTGTTTAGAGGAGC-ATTTATTTCTTCAAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGCTATTTATTTCTTCAAAAGTCATTGA
* * * * * * **
1493187 GCCTTTGCTTAGAGGAGCTTTGTTTATTTCTTTAAAAATTATAAA
1 GCCTCTGTTTAGAGGAGC--TATTTATTTCTTCAAAAGTCATTGA
* *
1493232 GCCTCTGTTTAGAAGAGCTTTATTTATTTTTCTCAAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGC--TATTTATTTCT-TCAAAAGTCATTGA
* * *
1493278 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTC-AAAGTCATTGA
1 GCCTCTGTTTAGAGGAGC--TATTTATTTCTTCAAAAGTCATTGA
* *
1493322 ACCTCTGCTTAG
1 GCCTCTGTTTAG
1493334 GAGAGCTTTG
Statistics
Matches: 191, Mismatches: 34, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
41 8 0.04
42 70 0.37
43 9 0.05
44 21 0.11
45 46 0.24
46 37 0.19
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (43 bp):
GCCTCTGTTTAGAGGAGCTATTTATTTCTTCAAAAGTCATTGA
Found at i:1493199 original size:84 final size:85
Alignment explanation
Indices: 1493050--1493296 Score: 257
Period size: 84 Copynumber: 2.8 Consensus size: 85
1493040 ATTTATTTTC
* * * * * *
1493050 AAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAGTCGTGGTTGCCTCTGTTTA
1 AAAGTTGTGGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAAGTCATTG-AGCCTCTGATTA
*
1493114 GATGAGC-ATTTATTTCTTTA
65 GAGGAGCTATTTATTTCTTTA
* * *
1493134 AAAGTTGTGGAGCTTCTGTTTAGAGGAGC-ATTTATTTCTTCAAAAGTCATTGAGCCTTTGCTTA
1 AAAGTTGTGGAGCCTCTGTTTAGAGGAGCTATTTATTT-TTCAAAAGTCATTGAGCCTCTGATTA
*
1493198 GAGGAGCTTTGTTTATTTCTTTA
65 GAGGAGC--TATTTATTTCTTTA
* * ** *
1493221 AAAATTATAAAGCCTCTGTTTAGAAGAGCTTTATTTATTTTTCTCAAAAGTCATTGAGCCTCTGA
1 AAAGTTGTGGAGCCTCTGTTTAGAGGAGC--TATTTA-TTTT-TCAAAAGTCATTGAGCCTCTGA
1493286 TTAGAGGAGCT
62 TTAGAGGAGCT
1493297 TTGTTTATTT
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
83 8 0.06
84 45 0.33
85 8 0.06
87 35 0.26
89 1 0.01
90 6 0.04
91 33 0.24
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (85 bp):
AAAGTTGTGGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAAGTCATTGAGCCTCTGATTAG
AGGAGCTATTTATTTCTTTA
Found at i:1493292 original size:91 final size:87
Alignment explanation
Indices: 1493061--1493306 Score: 259
Period size: 91 Copynumber: 2.8 Consensus size: 87
1493051 AAGTTGTGGT
* * * * * *
1493061 GCCTCTGTTTAGAGGAGCAATTTATTT-TTC-AAAGTCGTGGTTGCCTCTGTTTAGATGAGC---
1 GCCTCTGTTTAGAAGAGC-ATTTATTTCTTCAAAAGTCATTG-AGCCTCTGATTAGAGGAGCTTT
* * * **
1493121 ATTTATTTCTTTAAAAGTTGTGGA
64 GTTTATTTCTTTAAAAATTATAAA
* * * *
1493145 GCTTCTGTTTAGAGGAGCATTTATTTCTTCAAAAGTCATTGAGCCTTTGCTTAGAGGAGCTTTGT
1 GCCTCTGTTTAGAAGAGCATTTATTTCTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTGT
1493210 TTATTTCTTTAAAAATTATAAA
66 TTATTTCTTTAAAAATTATAAA
*
1493232 GCCTCTGTTTAGAAGAGCTTTATTTATTTTTCTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCT
1 GCCTCTGTTTAGAAGAGC---ATTTATTTCT-TCAAAAGTCATTGAGCCTCTGATTAGAGGAGCT
1493297 TTGTTTATTT
62 TTGTTTATTT
1493307 TTTCAAAGTC
Statistics
Matches: 136, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
83 8 0.06
84 35 0.26
85 8 0.06
87 35 0.26
90 9 0.07
91 41 0.30
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (87 bp):
GCCTCTGTTTAGAAGAGCATTTATTTCTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTGT
TTATTTCTTTAAAAATTATAAA
Found at i:1493296 original size:46 final size:45
Alignment explanation
Indices: 1493121--1493342 Score: 206
Period size: 45 Copynumber: 5.0 Consensus size: 45
1493111 TTAGATGAGC
** * * *
1493121 ATTTATTTCTTT-AAAAGTTGTGGAGCTTCTGTTTAGAGGAGC---
1 ATTTATTT-TTTCAAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTT
* *
1493163 ATTTATTTCTTCAAAAGTCATTGAGCCTTTGCTTAGAGGAGCTTT
1 ATTTATTTTTTCAAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTT
* * * ** * *
1493208 GTTTATTTCTTT-AAAAATTATAAAGCCTCTGTTTAGAAGAGCTTT
1 ATTTATTT-TTTCAAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTT
*
1493253 ATTTATTTTTCTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
1 ATTTATTTTT-TCAAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTT
* *
1493299 GTTTATTTTTTC-AAAGTCATTGAACCTCTGCTTAG-GAGAGCTTT
1 ATTTATTTTTTCAAAAGTCATTGAGCCTCTGCTTAGAG-GAGCTTT
1493343 GATCAAAATC
Statistics
Matches: 146, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.01
42 32 0.22
43 1 0.01
44 30 0.21
45 43 0.29
46 38 0.26
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.43
Consensus pattern (45 bp):
ATTTATTTTTTCAAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTT
Found at i:1493377 original size:16 final size:15
Alignment explanation
Indices: 1493358--1493408 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1493348 AAATCTTAAC
*
1493358 AAAAAAAAACCAAAA
1 AAAAAAAAAACAAAA
1493373 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
**
1493388 CAAAAAAAAGGCAAAA
1 -AAAAAAAAAACAAAA
1493404 AAAAA
1 AAAAA
1493409 GTGTCAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:1493561 original size:3 final size:3
Alignment explanation
Indices: 1493553--1493675 Score: 94
Period size: 3 Copynumber: 41.3 Consensus size: 3
1493543 AAGATGGGCC
* * *
1493553 TAT TAT TAT TAT TAT TAT T-T TAT TTT TAT TAT CAT TAT T-T TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
1493599 TAT TGT TTT TCT GT-T TAT TATT TAT TTT TAT TATT TAC TAT TA- TAT
1 TAT TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
*
1493645 TAT TACT TA- TGT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
1493676 TTGATTGATT
Statistics
Matches: 97, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
2 8 0.08
3 79 0.81
4 10 0.10
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1493581 original size:20 final size:20
Alignment explanation
Indices: 1493553--1493677 Score: 101
Period size: 20 Copynumber: 6.0 Consensus size: 20
1493543 AAGATGGGCC
*
1493553 TATTATTATTATTATTATTT
1 TATTTTTATTATTATTATTT
*
1493573 TATTTTTATTATCATTATTT
1 TATTTTTATTATTATTATTT
* * *
1493593 T-TTTATTATTGTTTTTCTGTT
1 TATTT-TTATTATTATTAT-TT
*
1493614 TATTATTTATTTTTATTA-TT
1 TATT-TTTATTATTATTATTT
* *
1493634 TACTATTATATTATTACTTATGT
1 TA-T-TTTTATTATTA-TTATTT
*
1493657 TATTATTATTATTATTATTT
1 TATTTTTATTATTATTATTT
1493677 T
1 T
1493678 GATTGATTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
19 3 0.04
20 38 0.46
21 21 0.26
22 16 0.20
23 4 0.05
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTTTTATTATTATTATTT
Found at i:1493669 original size:52 final size:50
Alignment explanation
Indices: 1493555--1493686 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 50
1493545 GATGGGCCTA
* *
1493555 TTATTATTATTATTATTTTATTTTTATTA--TCATTATTTTTTTATTATTG
1 TTATTATTATTATTA-TTTATTTTTATTATTTCATTATATTATTATTATTG
* *
1493604 TTTTTCTGT-TTATTATTTATTTTTATTATTTACTATTATATTATTACTTA-TG
1 TTATTAT-TATTATTATTTATTTTTATTATTT-C-ATTATATTATTA-TTATTG
*
1493656 TTATTATTATTATTA-TTATTTTGATTGATTT
1 TTATTATTATTATTATTTATTTTTATT-ATTT
1493687 TATCTTTCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
48 13 0.19
49 11 0.16
50 2 0.03
51 12 0.18
52 27 0.40
53 3 0.04
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (50 bp):
TTATTATTATTATTATTTATTTTTATTATTTCATTATATTATTATTATTG
Found at i:1494494 original size:3 final size:3
Alignment explanation
Indices: 1494486--1494511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1494476 ATTTATTTAT
1494486 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1494512 TCTACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1494759 original size:60 final size:57
Alignment explanation
Indices: 1494620--1494950 Score: 355
Period size: 56 Copynumber: 5.7 Consensus size: 57
1494610 TTTTTTTTTA
* *
1494620 AAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTT-AAA-AAAAATTTC
1 AAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTC
* * *
1494676 TAAAAAATATTTTTGAGGAAAAGTTGGAAGTATTAATTTTTCTTAAAAATAAAAATTATC
1 AAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAAATT-TC
* * * * * *
1494736 AAGACAAGTATTTTGAGGAAAAGTAGAACGTATCAATTTTTCTTGAAATTAAAATTTC
1 AA-AAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTC
* * * *
1494794 AAAAAAAAAATTTGA-GAAAAATTGAAAGTATCAATTTTTCTTAAAATTAAAATTTC
1 AAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTC
* * *
1494850 AGAAAAAAATATTTTGAGGAGAAGTTGGAAGT-TCCAATTTTTCTTAAAAATAAAGATTATC
1 --AAAAAAATATTTTGAGGAAAAGTTGAAAGTAT-CAATTTTTCTT-AAAATAAAAATT-TC
* *
1494911 AAGAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTT
1 AA-AAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTT
1494951 CTCTGTACAA
Statistics
Matches: 229, Mismatches: 33, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
56 76 0.33
57 9 0.04
58 21 0.09
59 41 0.18
60 74 0.32
61 8 0.03
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (57 bp):
AAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTC
Found at i:1494769 original size:116 final size:114
Alignment explanation
Indices: 1494620--1494950 Score: 348
Period size: 116 Copynumber: 2.8 Consensus size: 114
1494610 TTTTTTTTTA
* *
1494620 AAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTT-AAAAAAAATTTCTAAAAAAT
1 AAAAAAATA-TTTTGAGGAAAAGTTAGAAGTATCAATTTTTCTTAAAAAAAAATTTC-AAAAAAT
* *
1494684 ATTTTTGAGGAAAAGTTGGAAGTATTAATTTTTCTTAAAAATAAAAATTATCA-
64 A-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAAATT-TCAG
* * * **
1494737 AGACAAGTATTTTGAGGAAAAG-TAGAACGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAA
1 AAAAAAATATTTTGAGGAAAAGTTAGAA-GTATCAATTTTTCTT-AAAAAAAAATTTC-AAAAAA
* * * *
1494801 AAATTTGA-GAAAAATTGAAAGTATCAATTTTTCTTAAAATTAAAATTTCAG
63 TATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTCAG
* *
1494852 AAAAAAATATTTTGAGGAGAAGTTGGAAGT-TCCAATTTTTCTTAAAAATAAAGATTATCAAGAA
1 AAAAAAATATTTTGAGGAAAAGTTAGAAGTAT-CAATTTTTCTTAAAAA-AAA-ATT-TC-A-AA
* *
1494916 AAATATTTTAAGAAAAAGTTGAAAGTATCAATTTT
60 AAATATTTTGAGGAAAAGTTGAAAGTATCAATTTT
1494951 CTCTGTACAA
Statistics
Matches: 177, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
114 7 0.04
115 49 0.28
116 58 0.33
117 15 0.08
118 27 0.15
119 21 0.12
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (114 bp):
AAAAAAATATTTTGAGGAAAAGTTAGAAGTATCAATTTTTCTTAAAAAAAAATTTCAAAAAATAT
TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAAATTTCAG
Found at i:1494891 original size:175 final size:173
Alignment explanation
Indices: 1494631--1494950 Score: 475
Period size: 175 Copynumber: 1.8 Consensus size: 173
1494621 AAAAAATATT
*
1494631 TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAAAATTTCTAAAAAATATTTTTGAGGAA
1 TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAAAATTTCAAAAAAATATTTTTGAGGAA
* * * * *
1494696 AAGTTGGAAGTATTAATTTTTCTTAAAAATAAAAATTATCAAGACAAGTATTTTGAGGAAAAGTA
66 AAGTTGGAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAAAAATATTTTAAGAAAAAGTA
*
1494761 GAACGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAA
131 GAAAGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAA
*
1494804 TTTGAGAAAAA-TTGAAAGTATCAATTTTTCTTAAAATTAAAATTTCAGAAAAAA-ATATTTTGA
1 TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAA--AAAATTTCA-AAAAAATAT-TTTTGA
* *
1494867 GGAGAAGTTGGAAGT-TCCAATTTTTCTTAAAAATAAAGATTATCAAGAAAAATATTTTAAGAAA
62 GGAAAAGTTGGAAGTAT-CAATTTTTCTTAAAAATAAAAATTATCAAGAAAAATATTTTAAGAAA
*
1494931 AAGTTGAAAGTATCAATTTT
126 AAGTAGAAAGTATCAATTTT
1494951 CTCTGTACAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
172 24 0.18
173 11 0.08
174 11 0.08
175 85 0.65
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (173 bp):
TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAAAATTTCAAAAAAATATTTTTGAGGAA
AAGTTGGAAGTATCAATTTTTCTTAAAAATAAAAATTATCAAGAAAAATATTTTAAGAAAAAGTA
GAAAGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAA
Found at i:1495994 original size:2 final size:2
Alignment explanation
Indices: 1495987--1496012 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1495977 GCTCTATGCA
1495987 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1496013 TGTATCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1498509 original size:2 final size:2
Alignment explanation
Indices: 1498504--1498533 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1498494 TGATCTCTCC
1498504 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1498534 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1499915 original size:4 final size:4
Alignment explanation
Indices: 1499908--1499932 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1499898 TTATATATAT
1499908 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1499933 GCACATCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1500380 original size:17 final size:18
Alignment explanation
Indices: 1500346--1500381 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1500336 AATTGCATTA
1500346 TATATTTTTATTAATTTTT
1 TATATTTTTA-TAATTTTT
1500365 TATATTTTTA-AATTTTT
1 TATATTTTTATAATTTTT
1500382 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATATTTTTATAATTTTT
Found at i:1501648 original size:2 final size:2
Alignment explanation
Indices: 1501641--1501666 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1501631 GCTCTATGCA
1501641 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1501667 CCAATGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1502561 original size:21 final size:21
Alignment explanation
Indices: 1502517--1502563 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1502507 TAATTTAAAT
**
1502517 TTTAATAAAAATTATATATAA
1 TTTAATAAAAAAAATATATAA
*
1502538 TTTAATAAAATAAAATATATAT
1 TTTAATAAAA-AAAATATATAA
1502560 TTTA
1 TTTA
1502564 TATTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATAAAAAAAATATATAA
Found at i:1503898 original size:9 final size:9
Alignment explanation
Indices: 1503886--1503915 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1503876 AGATATTTAT
1503886 TAATTAAAA
1 TAATTAAAA
1503895 TAATTAAAA
1 TAATTAAAA
1503904 TATATTAAAA
1 TA-ATTAAAA
1503914 TA
1 TA
1503916 TAAAAGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:1503912 original size:10 final size:10
Alignment explanation
Indices: 1503888--1503917 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1503878 ATATTTATTA
1503888 ATTAAAATA-
1 ATTAAAATAT
1503897 ATTAAAATAT
1 ATTAAAATAT
1503907 ATTAAAATAT
1 ATTAAAATAT
1503917 A
1 A
1503918 AAAGTTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1506865 original size:23 final size:24
Alignment explanation
Indices: 1506839--1506888 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1506829 TTATATTTTA
1506839 ATTTATTAATTAATTATTCAA-TG
1 ATTTATTAATTAATTATTCAATTG
* *
1506862 ATTTATTAGTTAATTATTTAATTG
1 ATTTATTAATTAATTATTCAATTG
1506886 ATT
1 ATT
1506889 ATATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTTATTAATTAATTATTCAATTG
Found at i:1513199 original size:25 final size:25
Alignment explanation
Indices: 1513169--1513217 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1513159 TGTATAATTA
*
1513169 TATTATATTTTATATAAAAATTAAG
1 TATTATAATTTATATAAAAATTAAG
* *
1513194 TATTATAATTTATATTAATATTAA
1 TATTATAATTTATATAAAAATTAA
1513218 AATATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTATAATTTATATAAAAATTAAG
Found at i:1515017 original size:64 final size:64
Alignment explanation
Indices: 1514943--1515152 Score: 235
Period size: 64 Copynumber: 3.3 Consensus size: 64
1514933 TAATTTATAA
* *
1514943 TATAATTTATAAAACATCATCAATTAAGGTGTTTCTTAATATGAACACCTTAATTGACACATTT
1 TATAATTTATAAAACATCATCAATTAAGGCGTTTGTTAATATGAACACCTTAATTGACACATTT
* ** * * ** *
1515007 TATAATTTATAAAATATCATCAAACAAGGCGTTTGTTAACAGGAATGCCTTAATTGACA-GTTT
1 TATAATTTATAAAACATCATCAATTAAGGCGTTTGTTAATATGAACACCTTAATTGACACATTT
* * ** *
1515070 TAT-ATTCTTTAAAACATCATCAATTAAGACACTTGTTAATATGAACACCTTAATTGATACATTT
1 TATAATT-TATAAAACATCATCAATTAAGGCGTTTGTTAATATGAACACCTTAATTGACACA-TT
1515134 CT
64 -T
*
1515136 TATCATTTATAAAACAT
1 TATAATTTATAAAACAT
1515153 GAGAAGACAT
Statistics
Matches: 117, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
62 3 0.03
63 46 0.39
64 50 0.43
65 2 0.02
66 13 0.11
67 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (64 bp):
TATAATTTATAAAACATCATCAATTAAGGCGTTTGTTAATATGAACACCTTAATTGACACATTT
Found at i:1515281 original size:64 final size:65
Alignment explanation
Indices: 1515180--1515310 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 65
1515170 CATGAATATC
*
1515180 ATCAATTAAGGCCTTTGTTAATATGAACGCCCTAATTGATCT-TTTTTTTAATTTATAAAACATG
1 ATCAATTAAGGCCTTTGTTAATATGAACGCCCTAATTGATCTATTTTTATAATTTATAAAACATG
* * **
1515244 ATCAATTAAGGCGTTTGTTATTATGAACGCTTTAATTGATCTATTTTTATAATTTATAAAACATG
1 ATCAATTAAGGCCTTTGTTAATATGAACGCCCTAATTGATCTATTTTTATAATTTATAAAACATG
1515309 AT
1 AT
1515311 GTGTTTGTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 38 0.62
65 23 0.38
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (65 bp):
ATCAATTAAGGCCTTTGTTAATATGAACGCCCTAATTGATCTATTTTTATAATTTATAAAACATG
Found at i:1515384 original size:57 final size:58
Alignment explanation
Indices: 1515323--1515433 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 58
1515313 GTTTGTTAAT
* * *
1515323 ATGAATGCCTTAATTGATGTATATATAT-TTTTTAAAACAAGATCAATAAAGGCTTTC
1 ATGAATGCCTTAATTGATATATATATATATATTTAAAACAACATCAATAAAGGCTTTC
* *
1515380 ATGAATGCCTTAATTGATATATATATATATATTTAAAACATCATCAATTAAGGC
1 ATGAATGCCTTAATTGATATATATATATATATTTAAAACAACATCAATAAAGGC
1515434 ATTTGTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 27 0.56
58 21 0.44
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (58 bp):
ATGAATGCCTTAATTGATATATATATATATATTTAAAACAACATCAATAAAGGCTTTC
Found at i:1517898 original size:21 final size:21
Alignment explanation
Indices: 1517869--1517909 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1517859 TAATATATTA
1517869 TTTCA-TTTTAACTATTTATCT
1 TTTCATTTTTAACT-TTTATCT
*
1517890 TTTCCTTTTTAACTTTTATC
1 TTTCATTTTTAACTTTTATC
1517910 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCATTTTTAACTTTTATCT
Found at i:1518742 original size:13 final size:13
Alignment explanation
Indices: 1518699--1518761 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
1518689 AATAAAAATT
1518699 AATTTTATATTAA
1 AATTTTATATTAA
1518712 AA-TTTAT-TT-A
1 AATTTTATATTAA
1518722 AA---TATATTAA
1 AATTTTATATTAA
1518732 AATTTTATATTAA
1 AATTTTATATTAA
**
1518745 AATAATATA-TAA
1 AATTTTATATTAA
1518757 AATTT
1 AATTT
1518762 AAAAAATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 6 0.15
11 2 0.05
12 11 0.27
13 17 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTTTATATTAA
Found at i:1521989 original size:45 final size:45
Alignment explanation
Indices: 1521919--1522053 Score: 216
Period size: 45 Copynumber: 3.0 Consensus size: 45
1521909 TGCTAAAGCC
*
1521919 AAAGACAAGGTTTCAGAGACTGCACATGAAGCTAAAGAGAAGGTT
1 AAAGACAAGGTTTCAGAGACCGCACATGAAGCTAAAGAGAAGGTT
* * *
1521964 AAAGACAAGGTTTGAGAAACCGCACATGAAGCTAAAGAGAAGGTC
1 AAAGACAAGGTTTCAGAGACCGCACATGAAGCTAAAGAGAAGGTT
* *
1522009 AAAGACAAGTTTTCAGAGACCGCACATGAAGCTAAATAGAAGGTT
1 AAAGACAAGGTTTCAGAGACCGCACATGAAGCTAAAGAGAAGGTT
1522054 TCAGAAACCG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (45 bp):
AAAGACAAGGTTTCAGAGACCGCACATGAAGCTAAAGAGAAGGTT
Found at i:1522064 original size:33 final size:33
Alignment explanation
Indices: 1522009--1522086 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
1521999 AGAGAAGGTC
* * * *
1522009 AAAGACAAGTTTTCAGAGACCGCACATGAAGCT
1 AAAGAGAAGGTTTCAGAAACCGCACAAGAAGCT
* *
1522042 AAATAGAAGGTTTCAGAAACCGCACAAGAAGTT
1 AAAGAGAAGGTTTCAGAAACCGCACAAGAAGCT
1522075 AAAGAGAAGGTT
1 AAAGAGAAGGTT
1522087 AAGGGTACTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (33 bp):
AAAGAGAAGGTTTCAGAAACCGCACAAGAAGCT
Found at i:1530761 original size:49 final size:49
Alignment explanation
Indices: 1530689--1530788 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 49
1530679 TTACATGTTT
* ** * * * *
1530689 TAATTTTTTTTATTTATAATGACGGTTAACGTCTTTCAGTATAGACTTG
1 TAATTTTTCTTACCTATAATGACGCTTAACATCTGTCAGTATAGAATTG
* *
1530738 TAATTTTTCTTACCTATATTGACGCTTAGCATCTGTCAGTATAGAATTG
1 TAATTTTTCTTACCTATAATGACGCTTAACATCTGTCAGTATAGAATTG
1530787 TA
1 TA
1530789 TGCTTTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (49 bp):
TAATTTTTCTTACCTATAATGACGCTTAACATCTGTCAGTATAGAATTG
Found at i:1532741 original size:63 final size:63
Alignment explanation
Indices: 1532560--1532740 Score: 181
Period size: 63 Copynumber: 2.9 Consensus size: 63
1532550 TTTATCAACT
** * * *
1532560 AAAATGCCTTGAATAATCCTGTC-TAAAAAAT-TAGAATGATGATTAAAGGTATTTTTGGTAA
1 AAAATGCCTTGAATAATCCCCTCATAAAAAATATAGGATGATTATTGAAGGTATTTTTGGTAA
* * * * * * * *
1532621 AAAATACCTTAAATAATCCCTTCATAAAAATAGATAGG-GGATTGTTGAAGGCATTTTTGGTAG
1 AAAATGCCTTGAATAATCCCCTCATAAAAA-ATATAGGATGATTATTGAAGGTATTTTTGGTAA
* * *
1532684 ACAATGCCTTGAGTAATCCCCTCATAAAAAATAT-GGATGATTATTGAAGGTGTTTTT
1 AAAATGCCTTGAATAATCCCCTCATAAAAAATATAGGATGATTATTGAAGGTATTTTT
1532741 TTGCCAAAAA
Statistics
Matches: 94, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
61 21 0.22
62 25 0.27
63 45 0.48
64 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (63 bp):
AAAATGCCTTGAATAATCCCCTCATAAAAAATATAGGATGATTATTGAAGGTATTTTTGGTAA
Found at i:1533143 original size:63 final size:64
Alignment explanation
Indices: 1532996--1533149 Score: 177
Period size: 63 Copynumber: 2.4 Consensus size: 64
1532986 ATTCAATGCT
* * * *
1532996 TTTTCTAGCAAAAAACGTCTTCAATAATCCATTCAAAAAATTTTGAAAAGAGATTATTGAAGATA
1 TTTT-TAGCTAAAAACGCCTTCAATAATCAATTCAAAAAATTTTGAAAAGAGATTATTGAAGACA
* * * * *
1533061 TTTTTGGTTAAAAACGCCTTCAATAATCAATAT-AAAAAATTTT-AGAAGAGATTGTTGAAGGCA
1 TTTTTAGCTAAAAACGCCTTCAATAATCAAT-TCAAAAAATTTTGAAAAGAGATTATTGAAGACA
* *
1533124 TTTTTAGCTAGAAATGCCTTCAATAA
1 TTTTTAGCTAAAAACGCCTTCAATAA
1533150 CCCCATTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 38 0.51
64 32 0.43
65 5 0.07
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (64 bp):
TTTTTAGCTAAAAACGCCTTCAATAATCAATTCAAAAAATTTTGAAAAGAGATTATTGAAGACA
Found at i:1537288 original size:127 final size:126
Alignment explanation
Indices: 1537154--1537468 Score: 350
Period size: 126 Copynumber: 2.5 Consensus size: 126
1537144 AGACGAGACT
* * * * *
1537154 ATTGAAGGCGTTTGTGACTAAAAATACCTTCAATAATCACCGGATAAAATATTGGAGGGGATTAT
1 ATTGAAGGTGTTTTTGACTAAAAACACCTTCAATAATC-CCTGATAAAAAATTGGAGGGGATTAT
** *
1537219 TAAAGGTATTTTCTACAAAAAAA-AGGCCTTCAATAA-TTTCTTTTAAAATTTTATAATGGATA
65 TAAAGACATTTTCTACAAAAAAATA--ACTTCAATAAGTTTCTTTTAAAATTTTATAATGGATA
* * *
1537281 ATTGAAGGTGTTTTTGACTAAAAACGCCTTCAATAATCCCATGATAAAAAATT-AAAGGGATTAT
1 ATTGAAGGTGTTTTTGACTAAAAACACCTTCAATAATCCC-TGATAAAAAATTGGAGGGGATTAT
* * *** * * *
1537345 TAAAGACATTTTCTATAAAAAAATAACTTCAATAAGTTTTTTTTTTGATTTTTTAGTGGATT
65 TAAAGACATTTTCTACAAAAAAATAACTTCAATAAGTTTCTTTTAAAATTTTATAATGGATA
* * * *
1537407 ATTGAAGGTATTTTTCACTAAAAACA-CTTCAACAACCCCCTGATAAAAAATTGGAGGGGATT
1 ATTGAAGGTGTTTTTGACTAAAAACACCTTCAATAA-TCCCTGATAAAAAATTGGAGGGGATT
1537469 GTTGAAGGCG
Statistics
Matches: 157, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
125 29 0.18
126 83 0.53
127 45 0.29
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (126 bp):
ATTGAAGGTGTTTTTGACTAAAAACACCTTCAATAATCCCTGATAAAAAATTGGAGGGGATTATT
AAAGACATTTTCTACAAAAAAATAACTTCAATAAGTTTCTTTTAAAATTTTATAATGGATA
Found at i:1537609 original size:63 final size:64
Alignment explanation
Indices: 1537492--1537611 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
1537482 TTTGCAAAAA
* *
1537492 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTTTCAATGGATTATTGAAGGTATGTTCTGC
1 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTATGTTCTGC
* * ** *
1537556 AAAAAAAATACCTTTAATAAGTTTTTTTAAAATTTGT-AGTAGATTATTGAAGGTAT
1 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTAT
1537612 TTTTTATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 17 0.35
64 32 0.65
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (64 bp):
AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTATGTTCTGC
Found at i:1537623 original size:63 final size:64
Alignment explanation
Indices: 1537492--1537625 Score: 162
Period size: 64 Copynumber: 2.1 Consensus size: 64
1537482 TTTGCAAAAA
* * *
1537492 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTTTCAATGGATTATTGAAGGTATGTTCTGC
1 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTATGTTCTAC
* * ** * * * *
1537556 AAAAAAAATACCTTTAATAAGTTTTTTTAAAATTTGT-AGTAGATTATTGAAGGTATTTTTTAT
1 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTATGTTCTAC
1537619 AAAAAAA
1 AAAAAAA
1537626 TGCCTTCAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
63 27 0.46
64 32 0.54
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (64 bp):
AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTGTCAATAGATTATTGAAGGTATGTTCTAC
Found at i:1537664 original size:63 final size:60
Alignment explanation
Indices: 1537492--1537679 Score: 144
Period size: 63 Copynumber: 3.0 Consensus size: 60
1537482 TTTGCAAAAA
* * * ** * **
1537492 AAAAAAAAAACCTTTAATAAATTCCTTTAAAATTTTTCAATGGATTATTGAAGGTATGTTCTGC
1 AAAAAAAATACCTTCAATAAGTTTGTCTAAAA-TTTT-AATGGATTATTGAAGGTAT-TT-TTT
* * * * *
1537556 AAAAAAAATACCTTTAATAAGTTTTTTTAAAATTTGTAGTAGATTATTGAAGGTATTTTTT
1 AAAAAAAATACCTTCAATAAGTTTGTCTAAAATTT-TAATGGATTATTGAAGGTATTTTTT
* * *
1537617 ATAAAAAAATGCCTTCAATAA-TTTCGTCTAAAAGTTTTAAATGGATTATTAAAGGTGTTTTTT
1 A-AAAAAAATACCTTCAATAAGTTT-GTCTAAAA-TTTT-AATGGATTATTGAAGGTATTTTTT
1537680 CAATAATTTC
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
61 5 0.05
62 26 0.25
63 43 0.42
64 29 0.28
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (60 bp):
AAAAAAAATACCTTCAATAAGTTTGTCTAAAATTTTAATGGATTATTGAAGGTATTTTTT
Found at i:1544385 original size:162 final size:159
Alignment explanation
Indices: 1544036--1544625 Score: 655
Period size: 162 Copynumber: 3.7 Consensus size: 159
1544026 GGTACTAATG
* * * * * * * *
1544036 CAAATTTATAGTTATAGTTCTATTTTAATAGTTTTGATAGTTTTAATACATGATATTAATCTT-A
1 CAAATTTGTAGTTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGT
* * * * * *
1544100 TCTAAATTATTAACCTTAGTTTCCACAGTTGATATGTATGAAAAAGTTATTGTTTACATCTATTT
66 TC-GAATGATTAAACTTGGTTTCCACAGTTGATATGTGTGAAAAAGTTATTGTTTACGTCTATTT
* * *
1544165 AGGACATTTTGTGCCGTTAATAGGTAAAAATA
130 AGGACATTTTATG-CTTTAAAAGGT-AAAATA
*** * * * *
1544197 CAAATTTAG-ACAAATTATTTTATTTTAAAAGTTTGGATAGCTCCAATACATGATATTAAACTTG
1 CAAATTT-GTAGTTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTG
* * *
1544261 TTCGAATGATTGAACTTGGTTTCCACAATTGATATGTGTGAAAAAAATTATTGTTTACGTCTATT
65 TTCGAATGATTAAACTTGGTTTCCACAGTTGATATGTGTG-AAAAAGTTATTGTTTACGTCTATT
* * * *
1544326 TAAGACTTTTTATGCTATTAAGAGGTAAACATG
129 TAGGACATTTTATGCT-TTAAAAGGTAAA-ATA
* **
1544359 CAAATTTGTTGTTATTGTTCTATTTTAACAGTTTACATAGCTTCAATACATGATATTAAACTTGT
1 CAAATTTGTAGTTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGT
* * * * * *** *
1544424 TGGAATAATTAAAATTGGTTTCCACAGTTGATATATGTGAAAAAGCTAACATTTACGTCTGTTTA
66 TCGAATGATTAAACTTGGTTTCCACAGTTGATATGTGTGAAAAAGTTATTGTTTACGTCTATTTA
**
1544489 GGACATTTTATGCCTTTAAAAGACAAAATA
131 GGACATTTTATG-CTTTAAAAGGTAAAATA
1544519 CAAATTTGATA-TTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTG
1 CAAATTTG-TAGTTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTG
* *
1544583 TCCGAATGATTAAACTTGGTTTCTACAGTTGATATGTGTGAAA
65 TTCGAATGATTAAACTTGGTTTCCACAGTTGATATGTGTGAAA
1544626 GGCCCAAATG
Statistics
Matches: 355, Mismatches: 66, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
160 98 0.28
161 124 0.35
162 133 0.37
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (159 bp):
CAAATTTGTAGTTATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGT
TCGAATGATTAAACTTGGTTTCCACAGTTGATATGTGTGAAAAAGTTATTGTTTACGTCTATTTA
GGACATTTTATGCTTTAAAAGGTAAAATA
Found at i:1549435 original size:12 final size:12
Alignment explanation
Indices: 1549415--1549456 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1549405 TTTTTTTGAA
1549415 TTATTTATTTG-
1 TTATTTATTTGT
*
1549426 TTATTTTATTTAT
1 TTA-TTTATTTGT
1549439 TTATTTATTTGGT
1 TTATTTATTT-GT
1549452 TTATT
1 TTATT
1549457 ATTAGATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 3 0.12
12 14 0.54
13 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:1549494 original size:23 final size:23
Alignment explanation
Indices: 1549468--1549512 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1549458 TTAGATATCG
1549468 TTTTTAATATTCTTTTTA-TATTA
1 TTTTTAATATT-TTTTTACTATTA
**
1549491 TTTTTTTTATTTTTTTACTATT
1 TTTTTAATATTTTTTTACTATT
1549513 CCTAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTAATATTTTTTTACTATTA
Found at i:1549513 original size:34 final size:35
Alignment explanation
Indices: 1549468--1549541 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
1549458 TTAGATATCG
* **
1549468 TTTTTAATATTCTTTTTATATTATTTT-TTTTATT
1 TTTTTAATATTCCTAATATATTATTTTATTTTATT
* *
1549502 TTTTTACTATTCCTAATATATTTTTTTATTTTATT
1 TTTTTAATATTCCTAATATATTATTTTATTTTATT
1549537 TTTTT
1 TTTTT
1549542 TCCTTTTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.74
Consensus pattern (35 bp):
TTTTTAATATTCCTAATATATTATTTTATTTTATT
Found at i:1549570 original size:22 final size:20
Alignment explanation
Indices: 1549520--1549571 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
1549510 ATTCCTAATA
*
1549520 TATTTTTTTATTTTATTTTT
1 TATTTTTTCATTTTATTTTT
1549540 T-TTCCTTTTCACTTTTATTGTTT
1 TATT--TTTTCA-TTTTATT-TTT
1549563 TATTTTTTC
1 TATTTTTTC
1549572 CATCTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 5 0.19
22 12 0.46
23 4 0.15
24 2 0.08
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.77
Consensus pattern (20 bp):
TATTTTTTCATTTTATTTTT
Found at i:1549662 original size:58 final size:56
Alignment explanation
Indices: 1549567--1549803 Score: 302
Period size: 58 Copynumber: 4.1 Consensus size: 56
1549557 TTGTTTTATT
* *
1549567 TTTTCCATCTAAAAATAAATTTTCAAAAAAGGA-TTTTGAGGAAAAGTTGAAAGTATC-A
1 TTTTCC-T-TAAAAATAAATTTCCAAAAAA-TATTTTTG-GGAAAAGTTGAAAGTATCAA
*
1549625 TTTTCCTTGAAAATCAAAGTTTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA
1 TTTTCCTTAAAAAT-AAA-TTTCCAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAA
*
1549684 TTTTCCTTAAAAATAAAATTTTCAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAA
1 TTTTCCTTAAAAAT-AAA-TTTCCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAA
*
1549742 TTTTTCTTAAAAATAAA-TT-CAAAAAATCATTTTTGGGAAAAAGTTGAAAGTATCAA
1 TTTTCCTTAAAAATAAATTTCCAAAAAAT-ATTTTTGGG-AAAAGTTGAAAGTATCAA
1549798 TTTTCC
1 TTTTCC
1549804 CTACATAAGA
Statistics
Matches: 163, Mismatches: 10, Indels: 14
0.87 0.05 0.07
Matches are distributed among these distances:
54 7 0.04
55 11 0.07
56 29 0.18
57 8 0.05
58 73 0.45
59 35 0.21
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (56 bp):
TTTTCCTTAAAAATAAATTTCCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAA
Found at i:1549719 original size:116 final size:115
Alignment explanation
Indices: 1549567--1549803 Score: 333
Period size: 116 Copynumber: 2.1 Consensus size: 115
1549557 TTGTTTTATT
*
1549567 TTTTCCATCTAAAAATAAATTTTCAAAAAAGGA-TTTTGAGGAAAAGTTGAAAGTATC-ATTTTC
1 TTTTCCATCTAAAAATAAATTTTCAAAAAAAGATTTTTG-GGAAAAGTTGAAAGTATCAATTTTC
*
1549630 CTTGAAAATCAAAGTTTCCAAAAAAT-ATTTTTGAGG-AAAAGTTGAAAGTATCAA
65 CTTAAAAAT-AAA--TT-CAAAAAATCATTTTTG-GGAAAAAGTTGAAAGTATCAA
* *
1549684 TTTTCC-T-TAAAAATAAAATTTTCAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTT
1 TTTTCCATCTAAAAAT-AAATTTTCAAAAAAAGATTTTTGGGAAAAGTTGAAAGTATCAATTTTC
1549747 CTTAAAAATAAATTCAAAAAATCATTTTTGGGAAAAAGTTGAAAGTATCAA
65 CTTAAAAATAAATTCAAAAAATCATTTTTGGGAAAAAGTTGAAAGTATCAA
1549798 TTTTCC
1 TTTTCC
1549804 CTACATAAGA
Statistics
Matches: 111, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
113 10 0.09
114 33 0.30
115 7 0.06
116 37 0.33
117 24 0.22
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (115 bp):
TTTTCCATCTAAAAATAAATTTTCAAAAAAAGATTTTTGGGAAAAGTTGAAAGTATCAATTTTCC
TTAAAAATAAATTCAAAAAATCATTTTTGGGAAAAAGTTGAAAGTATCAA
Found at i:1560227 original size:19 final size:19
Alignment explanation
Indices: 1560215--1560312 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
1560205 GAAAAAAATG
* *
1560215 AAAAAATGAGAAAATGAAA
1 AAAAAATGAAAAAATGAGA
*
1560234 AAAAATGATGAAAAAATAAGA
1 AAAAA--ATGAAAAAATGAGA
**
1560255 AAACGA-GAAAAAAATGATG-
1 AAAAAATG-AAAAAATGA-GA
1560274 AAAAAATGAAAAAAT--GA
1 AAAAAATGAAAAAATGAGA
1560291 AAAAAATGAAAAAATGA-A
1 AAAAAATGAAAAAATGAGA
1560309 AAAA
1 AAAA
1560313 GAAAAAGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.02
17 15 0.24
18 6 0.10
19 25 0.40
20 2 0.03
21 14 0.22
ACGTcount: A:0.73, C:0.01, G:0.14, T:0.11
Consensus pattern (19 bp):
AAAAAATGAAAAAATGAGA
Found at i:1560266 original size:30 final size:29
Alignment explanation
Indices: 1560212--1560296 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 29
1560202 CTTGAAAAAA
*
1560212 ATGAAAAAATGAGAAAATGAAAAAAAATG
1 ATGAAAAAATAAGAAAATGAAAAAAAATG
*
1560241 ATGAAAAAATAAGAAAACGAGAAAAAAATG
1 ATGAAAAAATAAGAAAATGA-AAAAAAATG
1560271 ATGAAAAAATGAA-AAAATGAAAAAAA
1 ATGAAAAAAT-AAGAAAATGAAAAAAA
1560297 TGAAAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 24 0.47
30 25 0.49
31 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.15, T:0.12
Consensus pattern (29 bp):
ATGAAAAAATAAGAAAATGAAAAAAAATG
Found at i:1560326 original size:59 final size:56
Alignment explanation
Indices: 1560204--1560327 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 56
1560194 ATACTATGCT
* ** * *
1560204 TGAAAAAAATGAAAAAATGAGAAAATGAAAAAAAATGATGAAAAAATAAGAAAACG
1 TGAAAAAAATGAAAAAATGAAAAAATGAAAAAAAATGAAAAAAAAAAAAGAAAAAG
*
1560260 AGAAAAAAATGATGAAAAAATGAAAAAATG-AAAAAAATGAAAAAATGAAAAAAGAAAAAG
1 TG-AAAAAA--ATGAAAAAATGAAAAAATGAAAAAAAATGAAAAAA--AAAAAAGAAAAAG
1560320 TGAAAAAA
1 TGAAAAAA
1560328 GAGGACTCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
56 1 0.02
57 6 0.11
58 13 0.23
59 24 0.43
60 12 0.21
ACGTcount: A:0.73, C:0.01, G:0.15, T:0.11
Consensus pattern (56 bp):
TGAAAAAAATGAAAAAATGAAAAAATGAAAAAAAATGAAAAAAAAAAAAGAAAAAG
Found at i:1560328 original size:9 final size:8
Alignment explanation
Indices: 1560207--1560327 Score: 103
Period size: 8 Copynumber: 15.8 Consensus size: 8
1560197 CTATGCTTGA
1560207 AAAAAATG
1 AAAAAATG
1560215 AAAAAATG
1 AAAAAATG
*
1560223 AGAAAATG
1 AAAAAATG
1560231 -AAAAA--
1 AAAAAATG
**
1560236 AAATGATG
1 AAAAAATG
1560244 AAAAAAT-
1 AAAAAATG
*
1560251 AAGAAAACG
1 AA-AAAATG
*
1560260 AGAAAA--
1 AAAAAATG
**
1560266 AAATGATG
1 AAAAAATG
1560274 AAAAAATG
1 AAAAAATG
1560282 AAAAAATG
1 AAAAAATG
1560290 AAAAAAATG
1 -AAAAAATG
1560299 AAAAAATG
1 AAAAAATG
1560307 AAAAAA-G
1 AAAAAATG
*
1560314 AAAAAGTG
1 AAAAAATG
1560322 AAAAAA
1 AAAAAA
1560328 GAGGACTCAA
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
6 6 0.07
7 12 0.13
8 62 0.70
9 9 0.10
ACGTcount: A:0.74, C:0.01, G:0.15, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:1561371 original size:41 final size:41
Alignment explanation
Indices: 1561326--1561657 Score: 360
Period size: 41 Copynumber: 8.0 Consensus size: 41
1561316 GTCAATGAGT
*
1561326 AATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGC
1 AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* *
1561367 AATTTACTTTTCAAAGCCGTGGTGCCTTTGTTTAGAGGAGC
1 AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
** *
1561408 AATTTGTTTTTCAAAGTCGTGGTGCATCTGTTTAGAGGAGC
1 AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* *
1561449 -ATTTACTTTTCAAAGTCGTGATGCCTCTATTTAGAGGAGC
1 AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* *
1561489 AATTTACTTTCCAAAGTCGTGGTGCCTTTGTTTAGAGGAGC
1 AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* * * * * **
1561530 AGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAAAAGC
1 AATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* * * * * *
1561572 CATTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAGATGAGC
1 AATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* * * * *
1561615 CATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTCAGAGGAGC
1 AATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1561658 TTTGATCAAA
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
40 35 0.14
41 115 0.45
42 35 0.14
43 69 0.27
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
AATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
Found at i:1561593 original size:43 final size:43
Alignment explanation
Indices: 1561532--1561646 Score: 196
Period size: 43 Copynumber: 2.7 Consensus size: 43
1561522 AGAGGAGCAG
*
1561532 TTTAT-TTTTTCAAAGTCGTTGAGCCTCTGATTAGAAAAGCCA
1 TTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAGAAAAGCCA
**
1561574 TTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAGATGAGCCA
1 TTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAGAAAAGCCA
1561617 TTTATGTTTCTCAAAGTCGTTGAGCCTCTG
1 TTTATGTTTCTCAAAGTCGTTGAGCCTCTG
1561647 TTCAGAGGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 5 0.07
43 64 0.93
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (43 bp):
TTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAGAAAAGCCA
Found at i:1561868 original size:19 final size:19
Alignment explanation
Indices: 1561844--1561893 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1561834 GGTAAGTCTG
*
1561844 TATTTTT-TTTTCTTCATTT
1 TATTTTTATTTT-TTCAATT
*
1561863 TATTTTTATTTTTTTAATT
1 TATTTTTATTTTTTCAATT
1561882 TATTTTTATTTT
1 TATTTTTATTTT
1561894 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (19 bp):
TATTTTTATTTTTTCAATT
Found at i:1561871 original size:6 final size:6
Alignment explanation
Indices: 1561860--1561931 Score: 83
Period size: 6 Copynumber: 11.5 Consensus size: 6
1561850 TTTTTCTTCA
1561860 TTTTAT TTTTAT TTTT-T TAATTTAT TTTTAT TTTATAT TTTTAT ATTTTAT
1 TTTTAT TTTTAT TTTTAT T--TTTAT TTTTAT TTT-TAT TTTTAT -TTTTAT
* *
1561911 TTTTAT TATTAT TATTAT TTT
1 TTTTAT TTTTAT TTTTAT TTT
1561932 ATATATGTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
5 2 0.03
6 40 0.68
7 15 0.25
8 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:1561876 original size:13 final size:13
Alignment explanation
Indices: 1561860--1561931 Score: 69
Period size: 13 Copynumber: 5.7 Consensus size: 13
1561850 TTTTTCTTCA
1561860 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
*
1561872 TTTT-TTAATTTAT
1 TTTTATT-TTTTAT
*
1561885 TTTTATTTTATAT
1 TTTTATTTTTTAT
*
1561898 TTTTATATTTTAT
1 TTTTATTTTTTAT
*
1561911 TTTTA-TTATTAT
1 TTTTATTTTTTAT
*
1561923 TATTATTTT
1 TTTTATTTT
1561932 ATATATGTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
12 14 0.30
13 31 0.66
14 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:1561902 original size:19 final size:18
Alignment explanation
Indices: 1561860--1561931 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 18
1561850 TTTTTCTTCA
1561860 TTTTATTTTTATTTTT-T
1 TTTTATTTTTATTTTTAT
1561877 TAATTTATTTTTATTTTATAT
1 T--TTTATTTTTATTTT-TAT
1561898 TTTTATATTTTATTTTTAT
1 TTTTAT-TTTTATTTTTAT
* *
1561917 TATTATTATTATTTT
1 TTTTATTTTTATTTT
1561932 ATATATGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
17 1 0.02
18 8 0.17
19 27 0.56
20 10 0.21
21 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTATTTTTAT
Found at i:1561902 original size:38 final size:38
Alignment explanation
Indices: 1561860--1561972 Score: 117
Period size: 38 Copynumber: 2.9 Consensus size: 38
1561850 TTTTTCTTCA
*
1561860 TTTTAT-TTTTATTTTT-TTAATTTATTTTTATTTTATAT
1 TTTTATATTTTATTTTTATT-A-TTATTATTATTTTATAT
1561898 TTTTATATTTTATTTTTATTATTATTATTATTTTATAT
1 TTTTATATTTTATTTTTATTATTATTATTATTTTATAT
*
1561936 ATGTATATATATTTT-TCTTTTCTT-TTATTATTATTTT
1 -T-T-T-TATATTTTAT-TTTTATTATTATTATTATTTT
1561973 TTAGGATTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
38 22 0.33
39 12 0.18
40 3 0.05
41 15 0.23
42 14 0.21
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (38 bp):
TTTTATATTTTATTTTTATTATTATTATTATTTTATAT
Found at i:1561916 original size:32 final size:33
Alignment explanation
Indices: 1561863--1561937 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
1561853 TTCTTCATTT
*
1561863 TATTTTTAT-TTTTTTAATTTATTTTTATT-TTA
1 TATTTTTATATTTTTT-ATTTATTATTATTATTA
1561895 TATTTTTATATTTTATT-TTTATTATTATTATTA
1 TATTTTTATATTTT-TTATTTATTATTATTATTA
*
1561928 T-TTTATATAT
1 TATTTTTATAT
1561938 GTATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 28 0.74
33 8 0.21
34 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (33 bp):
TATTTTTATATTTTTTATTTATTATTATTATTA
Found at i:1561947 original size:50 final size:50
Alignment explanation
Indices: 1561893--1562031 Score: 126
Period size: 50 Copynumber: 2.8 Consensus size: 50
1561883 ATTTTTATTT
1561893 TATATTTTTATATTTTATTTTTATTATTATTATTATTTTATATATGTA-TA
1 TATATTTTTATATTTTATTTTTATTATT-TTATTATTTTATATATGTAGTA
* * * *
1561943 TATATTTTTCT-TTTCT-TTTATTATTATTTT-TTAGGATTTATGTATTTAGTA
1 TATATTTTTATATTT-TATTT-TTATTATTTTATTA--TTTTATATATGTAGTA
* * *
1561994 -ATATGTATATATCTTTATTATTATTATTTTATTATTTT
1 TATATTTTTATAT-TTTATTTTTATTATTTTATTATTTT
1562032 TTTCTTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
48 3 0.04
49 8 0.11
50 39 0.55
51 14 0.20
52 7 0.10
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (50 bp):
TATATTTTTATATTTTATTTTTATTATTTTATTATTTTATATATGTAGTA
Found at i:1561950 original size:19 final size:18
Alignment explanation
Indices: 1561893--1561950 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
1561883 ATTTTTATTT
1561893 TATATTTT-TATATT-T-
1 TATATTTTATATATTATA
1561908 TAT-TTTTAT-TATTAT-
1 TATATTTTATATATTATA
1561923 TATTATTTTATATATGTATA
1 TA-TATTTTATATAT-TATA
1561943 TATATTTT
1 TATATTTT
1561951 TCTTTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.22
15 7 0.19
16 1 0.03
17 6 0.17
18 3 0.08
19 9 0.25
20 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TATATTTTATATATTATA
Found at i:1562960 original size:4 final size:4
Alignment explanation
Indices: 1562953--1563084 Score: 81
Period size: 4 Copynumber: 31.0 Consensus size: 4
1562943 TTTTTTTTGA
* * * *
1562953 ATTT ATTT ATTT GTTT ATTT ATTT ATTT TTTT ATTT ATTA AATT AGGTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A--TTT
* *
1563003 ATTT AATATT CTTT -TTAT ATTT ATTTT ATTT -TTAT ATTT ATTT TTTT
1 ATTT -AT-TT ATTT ATT-T ATTT A-TTT ATTT ATT-T ATTT ATTT ATTT
*
1563050 ACTTT CCTTT ATTT -TTT ATTT ATTTT ATTTT ATTT
1 A-TTT -ATTT ATTT ATTT ATTT A-TTT A-TTT ATTT
1563085 TTTCTTTTCA
Statistics
Matches: 102, Mismatches: 13, Indels: 26
0.72 0.09 0.18
Matches are distributed among these distances:
3 7 0.07
4 64 0.63
5 26 0.25
6 5 0.05
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1563029 original size:11 final size:11
Alignment explanation
Indices: 1563000--1563085 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
1562990 TTAAATTAGG
*
1563000 TTTATTTAATA
1 TTTATTTTATA
1563011 TTCT-TTTTATA
1 TT-TATTTTATA
*
1563022 TTTATTTTATT
1 TTTATTTTATA
1563033 TTTATATTTAT-
1 TTTAT-TTTATA
* *
1563044 TTT-TTTACTTTCC
1 TTTATTT--TAT-A
*
1563057 TTTATTTTTTA
1 TTTATTTTATA
1563068 TTTATTTTAT-
1 TTTATTTTATA
1563078 TTTATTTT
1 TTTATTTT
1563086 TTCTTTTCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.03
10 10 0.16
11 35 0.56
12 9 0.15
13 3 0.05
14 3 0.05
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTTATA
Found at i:1563032 original size:5 final size:5
Alignment explanation
Indices: 1563015--1563118 Score: 65
Period size: 5 Copynumber: 20.8 Consensus size: 5
1563005 TTAATATTCT
* * *
1563015 TTTTA TATTTA TTTTA TTTTTA TATTTA -TTT- TTTTA CTTTC CTTTA
1 TTTTA T-TTTA TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA
* * * *
1563061 TTTTT TATTTA TTTTA TTTTA TTTT- TTCT- TTTCA CTTTTA TTTTG TTTTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
1563111 TTTT- TTTT
1 TTTTA TTTT
1563119 CCTCTAAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
4 15 0.19
5 42 0.53
6 22 0.28
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1563104 original size:24 final size:21
Alignment explanation
Indices: 1562954--1563118 Score: 53
Period size: 20 Copynumber: 7.8 Consensus size: 21
1562944 TTTTTTTGAA
*
1562954 TTTATTTA-TTT-GTTTATTT
1 TTTATTTATTTTATTTTATTT
*
1562973 ATTTATTT-TTTTA-TTTATTAA
1 -TTTATTTATTTTATTTTATT-T
* * * *
1562994 ATTAGGTTTATTTAATATTCTTT
1 TTTA--TTTATTTTATTTTATTT
*
1563017 TTATATTTATTTTATTTT-TATA
1 TT-TATTTATTTTATTTTAT-TT
**
1563039 TTTATTT-TTTTACTTTCCTTT
1 TTTATTTATTTTA-TTTTATTT
1563060 ATTT-TTTA-TTTATTTTATTT
1 -TTTATTTATTTTATTTTATTT
* *
1563080 TATTTTTTCTTTTCACTTTTATTT
1 T-TTATTTATTTT-A-TTTTATTT
*
1563104 TGT-TTTATTTT-TTTT
1 TTTATTTATTTTATTTT
1563119 CCTCTAAAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 37
0.67 0.10 0.23
Matches are distributed among these distances:
19 5 0.05
20 32 0.29
21 20 0.18
22 31 0.28
23 7 0.06
24 15 0.14
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTATTTATTTTATTTTATTT
Found at i:1563229 original size:61 final size:59
Alignment explanation
Indices: 1563114--1563290 Score: 216
Period size: 61 Copynumber: 2.9 Consensus size: 59
1563104 TGTTTTATTT
1563114 TTTTTCCTCTAAAAATAAAATTTCAAAAAAAAAG-ATTTTTGAGGAAAAGTTGAAAGTATCAA
1 TTTTT-CT-TAAAAATAAAATTT--AAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAA
*
1563176 TTTTTCTTAAAAATAAAATTTAAAAAAAAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAA
1 TTTTTCTTAAAAATAAAATTTAAAAAAAA-G-TATTTTTGAGGAAAAGTTGAAAGTATCAA
* * * **
1563237 TTTTCCTTGAAAATCAAAGTTT-TCAAAAA-TATTTTTGAGGAAAAGTTGAAAGTA
1 TTTTTCTTAAAAAT-AAAATTTAAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTA
1563291 AGGTTTTTTT
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
58 32 0.31
59 1 0.01
60 14 0.13
61 46 0.44
62 11 0.11
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (59 bp):
TTTTTCTTAAAAATAAAATTTAAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAA
Found at i:1563298 original size:86 final size:87
Alignment explanation
Indices: 1563203--1563376 Score: 323
Period size: 86 Copynumber: 2.0 Consensus size: 87
1563193 ATTTAAAAAA
* *
1563203 AAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCAAAAATA
1 AAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAAATA
1563268 TTTTTGAGGAAAAGTTGAAAGT
66 TTTTTGAGGAAAAGTTGAAAGT
1563290 AAGG-TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAAATA
1 AAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAAATA
1563354 TTTTTGAGGAAAAGTTGAAAGT
66 TTTTTGAGGAAAAGTTGAAAGT
1563376 A
1 A
1563377 TCAATTTTCC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 81 0.95
87 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (87 bp):
AAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAAATA
TTTTTGAGGAAAAGTTGAAAGT
Found at i:1563364 original size:58 final size:58
Alignment explanation
Indices: 1563296--1563566 Score: 334
Period size: 58 Copynumber: 4.5 Consensus size: 58
1563286 AAGTAAGGTT
*
1563296 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAAATA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAAAAATA
* *
1563354 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCAAAAAAAGTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTC-CAAAAA-TA
*
1563413 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAATA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCC--AAAAATA
* **
1563473 TTTCTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAA-AAACAATTTAAAAAAAATTCAA
1 TTT-TTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAA-AATTT-CCAAAAA-T--A
*
1563536 TTTTCG-GAGAAAAGTTGAAAGTATCAATTTT
1 TTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
1563567 TTCTGCACAA
Statistics
Matches: 189, Mismatches: 11, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
57 7 0.04
58 46 0.24
59 41 0.22
60 21 0.11
61 44 0.23
62 25 0.13
63 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (58 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAAAAATA
Found at i:1563414 original size:117 final size:119
Alignment explanation
Indices: 1563293--1563566 Score: 405
Period size: 117 Copynumber: 2.3 Consensus size: 119
1563283 TGAAAGTAAG
*
1563293 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCC-AAAAATATTT
1 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAAAAAATATTT
*
1563357 -TTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA-AATTTCAAAAAAA
66 CTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAACAATTT-AAAAAAA
*
1563410 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAATATT
1 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCC-AAAAAATATT
1563475 TCTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAACAATTTAAAAAAA
65 TCTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAACAATTTAAAAAAA
* *
1563530 ATTCAATTTTCG-GAGAAAAGTTGAAAGTATCAATTTT
1 GTT---TTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
1563567 TTCTGCACAA
Statistics
Matches: 143, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
117 52 0.36
119 12 0.08
120 45 0.31
121 5 0.03
122 1 0.01
123 28 0.20
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (119 bp):
GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAAAAAATATTT
CTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAACAATTTAAAAAAA
Found at i:1565537 original size:31 final size:30
Alignment explanation
Indices: 1565465--1565541 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
1565455 ATTGAAACCA
1565465 AATTAATATAATATTGTAATTAAAAAATTTT
1 AATTAATATAATATT-TAATTAAAAAATTTT
* * *
1565496 --TTAGTATAATATTTAATTATAAATTTATT
1 AATTAATATAATATTTAATTAAAAAATT-TT
1565525 AATTAATATAATATTTA
1 AATTAATATAATATTTA
1565542 CAAATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 11 0.28
29 14 0.36
31 14 0.36
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
AATTAATATAATATTTAATTAAAAAATTTT
Found at i:1567490 original size:12 final size:13
Alignment explanation
Indices: 1567467--1567499 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1567457 TATTAATAAT
1567467 TTATATATTTATA
1 TTATATATTTATA
1567480 TTATA-ATTTATA
1 TTATATATTTATA
1567492 TTGATATA
1 TT-ATATA
1567500 AAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 8 0.44
14 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:1569782 original size:80 final size:79
Alignment explanation
Indices: 1569624--1569783 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 79
1569614 AATATAATTT
* * *
1569624 TAATATTTTTTAATAAATATTACGTTTTTTATCTAAAAAATAACATTTTTGTTCAATTCTAAAAA
1 TAATATTTTTTAATAAAAATTACGTTTTTAATCTAAAAAATAACATTTTTGTTCAATTATAAAAA
* *
1569689 ATAAAATTTTAAAA
66 ACAAAATTATAAAA
* **
1569703 TAATATATTTTTAATAAAAATTACGTTTTTAATCTTAAAAAT-ATTTTTATTG-TCGAAATTATA
1 TAATAT-TTTTTAATAAAAATTACGTTTTTAATCTAAAAAATAACATTT-TTGTTC--AATTATA
1569766 AAAAACAAAA-TATAAAA
62 AAAAACAAAATTATAAAA
1569783 T
1 T
1569784 TATTTCATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 12 0.17
80 42 0.61
81 15 0.22
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (79 bp):
TAATATTTTTTAATAAAAATTACGTTTTTAATCTAAAAAATAACATTTTTGTTCAATTATAAAAA
ACAAAATTATAAAA
Found at i:1572242 original size:2 final size:2
Alignment explanation
Indices: 1572237--1572275 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1572227 TCTCTATAAA
* *
1572237 AT AT AT AT AT AA AT AT AA AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1572276 GGCATCAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1572726 original size:20 final size:19
Alignment explanation
Indices: 1572703--1572814 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 19
1572693 TTAGGTACAA
1572703 GTAAATATATTAATAATCAT
1 GTAAATATATTAATAAT-AT
1572723 GTAAATATTACTTATATAAT-T
1 GTAAATA-TA-TTA-ATAATAT
** *
1572744 AAAAATATAATAATGTAAATAT
1 GTAAATATATTAA--T-AATAT
* * *
1572766 -TCAATATATTGATAATCAC
1 GTAAATATATTAATAAT-AT
*
1572785 GTAAATATATTATTAATTAT
1 GTAAATATATTAATAA-TAT
1572805 GTAAATATAT
1 GTAAATATAT
1572815 GCAATAAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
18 4 0.06
19 4 0.06
20 33 0.47
21 20 0.29
22 4 0.06
23 5 0.07
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (19 bp):
GTAAATATATTAATAATAT
Found at i:1574710 original size:22 final size:22
Alignment explanation
Indices: 1574682--1574726 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1574672 TAAACATTAG
1574682 TGTCTAGTTCAGAGATATCTTA
1 TGTCTAGTTCAGAGATATCTTA
1574704 TGTCTAGTTCAGAGATATCTTA
1 TGTCTAGTTCAGAGATATCTTA
1574726 T
1 T
1574727 AGGGTAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (22 bp):
TGTCTAGTTCAGAGATATCTTA
Found at i:1578311 original size:3 final size:3
Alignment explanation
Indices: 1578305--1578334 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1578295 ATTATTATTA
1578305 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1578335 CTATTATTAT
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:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1579347 original size:25 final size:24
Alignment explanation
Indices: 1579316--1579407 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 24
1579306 TTATTTTTTT
1579316 AATCAAAATAAATCACAAAATTAA
1 AATCAAAATAAATCACAAAATTAA
* *
1579340 AATCCAAACTAAATCTA-AAACTTAA
1 AAT-CAAAATAAATC-ACAAAATTAA
*
1579365 AATTAAAATTAAA--ATCAAAATTAA
1 AATCAAAA-TAAATCA-CAAAATTAA
* *
1579389 AATTAAAATCAAATTACAA
1 AATCAAAAT-AAATCACAA
1579408 CTAAAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 24 0.44
25 27 0.49
26 2 0.04
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (24 bp):
AATCAAAATAAATCACAAAATTAA
Found at i:1579370 original size:6 final size:6
Alignment explanation
Indices: 1579332--1579397 Score: 71
Period size: 6 Copynumber: 10.8 Consensus size: 6
1579322 AATAAATCAC
* * * *
1579332 AAAATT AAAATC CAAACT -AAATCT AAAACTT AAAATT AAAATT AAAATC
1 AAAATT AAAATT AAAATT AAAAT-T AAAA-TT AAAATT AAAATT AAAATT
1579381 AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAAT
1579398 CAAATTACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 3 0.06
6 38 0.76
7 8 0.16
8 1 0.02
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:1579386 original size:18 final size:18
Alignment explanation
Indices: 1579332--1579401 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
1579322 AATAAATCAC
* *
1579332 AAAATTAAAATCCAAACT
1 AAAATTAAAATCAAAATT
*
1579350 -AAATCTAAAACTTAAAATT
1 AAAAT-TAAAA-TCAAAATT
1579369 AAAATTAAAATCAAAATT
1 AAAATTAAAATCAAAATT
1579387 AAAATTAAAATCAAA
1 AAAATTAAAATCAAA
1579402 TTACAACTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.09
18 27 0.60
19 10 0.22
20 4 0.09
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAAAATCAAAATT
Found at i:1579414 original size:18 final size:18
Alignment explanation
Indices: 1579363--1579415 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1579353 TCTAAAACTT
*
1579363 AAAATTAAAATTAAAATC
1 AAAATTAAAATAAAAATC
*
1579381 AAAATTAAAATTAAAATC
1 AAAATTAAAATAAAAATC
*
1579399 -AAATTACAACTAAAAAT
1 AAAATTA-AAATAAAAAT
1579416 TTTAACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAAAATAAAAATC
Found at i:1581852 original size:13 final size:14
Alignment explanation
Indices: 1581834--1581862 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1581824 ACTAATAATA
1581834 ATAATG-ATTTATG
1 ATAATGAATTTATG
1581847 ATAATGAATTTATG
1 ATAATGAATTTATG
1581861 AT
1 AT
1581863 TTTAAAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
ATAATGAATTTATG
Found at i:1583836 original size:14 final size:14
Alignment explanation
Indices: 1583817--1583845 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1583807 CCTATTCATA
1583817 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
1583831 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
1583845 T
1 T
1583846 TTCCTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTCTCTCTCTCTT
Found at i:1597910 original size:19 final size:19
Alignment explanation
Indices: 1597888--1597930 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1597878 TTTTTTTATT
* * *
1597888 TATAAAAATTTAAAATATA
1 TATAAAAAATAAAAAAATA
1597907 TATAAAAAATAAAAAAATA
1 TATAAAAAATAAAAAAATA
1597926 TATAA
1 TATAA
1597931 TTTGGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TATAAAAAATAAAAAAATA
Found at i:1604665 original size:4 final size:4
Alignment explanation
Indices: 1604656--1604685 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1604646 TAGATAATCA
1604656 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
1604686 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:1610273 original size:25 final size:25
Alignment explanation
Indices: 1610238--1610307 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
1610228 CAGTAATGTG
* *
1610238 CTTAGACACACCCTTTAGCAAACCA
1 CTTAGAAACACCATTTAGCAAACCA
*
1610263 CTTAGAAACACCATTTAGTAAACCA
1 CTTAGAAACACCATTTAGCAAACCA
* * *
1610288 ATCAGAAACACCATTCAGCA
1 CTTAGAAACACCATTTAGCA
1610308 TATGATTCAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (25 bp):
CTTAGAAACACCATTTAGCAAACCA
Found at i:1610280 original size:13 final size:13
Alignment explanation
Indices: 1610239--1610302 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
1610229 AGTAATGTGC
* *
1610239 TTAGACACACCCT
1 TTAGAAACACCAT
* *
1610252 TTAGCAA-ACCAC
1 TTAGAAACACCAT
1610264 TTAGAAACACCAT
1 TTAGAAACACCAT
* *
1610277 TTAGTAA-ACCAA
1 TTAGAAACACCAT
*
1610289 TCAGAAACACCAT
1 TTAGAAACACCAT
1610302 T
1 T
1610303 CAGCATATGA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
12 18 0.47
13 20 0.53
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (13 bp):
TTAGAAACACCAT
Found at i:1611291 original size:125 final size:126
Alignment explanation
Indices: 1611082--1611339 Score: 317
Period size: 125 Copynumber: 2.1 Consensus size: 126
1611072 AATAATCTCA
* * *
1611082 AAAATTTTAAGAGAAAATTATTGAATGCATTTGTTCTAAAAAAAACACTTTCAATAATTATGTAC
1 AAAATTTTAAAAGAAAATTATTGAAGGCATTTGTTCTAAAAAAAACACTTTCAATAATTATCTAC
* * * * *
1611147 GTAAATTAGAAGGAATTAGTGAAGATGTTTTTCTAGAATAAATGCCTTCACT-AATCGTCTT
66 ATAAATTAGAAGAAATTAGTAAAGATATTTTTCTAGAATAAATGCATTCACTAAAT-GTCTT
* * * ** *
1611208 AAAATTTTAAAA-AGAAATTATTTAAGGCGTTTGTTCT-CAAAAAATGCTTTTAATAATTATACT
1 AAAATTTTAAAAGA-AAATTATTGAAGGCATTTGTTCTAAAAAAAACACTTTCAATAATTAT-CT
* *
1611271 -CATAAATTAGAATAAATTAGTAAAGGTATTTTTCTAGAATAAATGCATTCACTAAATGTCTT
64 ACATAAATTAGAAGAAATTAGTAAAGATATTTTTCTAGAATAAATGCATTCACTAAATGTCTT
1611333 AAAATTT
1 AAAATTT
1611340 GAGTTGTGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
125 78 0.69
126 35 0.31
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (126 bp):
AAAATTTTAAAAGAAAATTATTGAAGGCATTTGTTCTAAAAAAAACACTTTCAATAATTATCTAC
ATAAATTAGAAGAAATTAGTAAAGATATTTTTCTAGAATAAATGCATTCACTAAATGTCTT
Found at i:1611859 original size:185 final size:183
Alignment explanation
Indices: 1611208--1612004 Score: 1001
Period size: 184 Copynumber: 4.3 Consensus size: 183
1611198 TAATCGTCTT
* * * * * *
1611208 AAAATTTTAAAAAGAAATTATTTAAGGCGTTTGTTCTCAAAAAATGCTTTTAATAATTATACTCA
1 AAAATTTTAAAAA-AAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTAT-GTCG
* * **
1611273 TAAATTAGAATAAATTAGTAAAGGTATTTTTCTAGAATAAATGCATTCACTAAATGTCTTAAAAT
64 TAAATTAAAAGAAATTAGTAAAGGTATTTTTCTAGAATAAACACATTCACTAAATGTCTTAAAAT
* * *
1611338 TTGAGTTGTGAAAAATTGAAAACATTTTTCACTCGAA-ACCCTTTAATAATCCCA
129 TTGAGTTGTGAAAAATTGAAAGCGTTTTTCACTGGAAGACCCTTTAATAATCCCA
* *
1611392 AAAATTTTAAAAAAAAATTATTGAAGGCGTTTGTTCTCAAAAAATGCCTTTAATAATTATGCTCG
1 AAAATTTT-AAAAAAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTATG-TCG
* **
1611457 TAAATTAGAAGAAATTAGTAAAGGTATTTTTCTAGAATAAATGCATTCACTAAATGTCTTAAAAT
64 TAAATTAAAAGAAATTAGTAAAGGTATTTTTCTAGAATAAACACATTCACTAAATGTCTTAAAAT
* *
1611522 TTGAGTTGTAAAAAATTGAAGGCGTTTTTCACTGGAAGACCCTTTTAATAATCCCAAA
129 TTGAGTTGTGAAAAATTGAAAGCGTTTTTCACTGGAAGACCC-TTTAATAATCCC--A
* * **
1611580 AAAATTTTAAAAAAAATTACTGAAGACATTTGTTCT-AAAAAACACCTTCAATAATTATGTACGT
1 AAAATTTTAAAAAAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTATGT-CGT
* * * *
1611644 AAATTAAAAGAAATTAGTGAAGGTATTTTTCTAGAATAAACACCTTCACTAACTATCTTAAAATT
65 AAATTAAAAGAAATTAGTAAAGGTATTTTTCTAGAATAAACACATTCACTAAATGTCTTAAAATT
* * * * **
1611709 TGAGTTGTGAAAAAGTGAATGTGTTTTTTACTGGAA-ACGCCTTTAATAATCTTA
130 TGAGTTGTGAAAAATTGAAAGCGTTTTTCACTGGAAGAC-CCTTTAATAATCCCA
* *
1611763 AAAATTTTAAGAAGAAATTATTGAAGGCATTTATTCTCAAAAAATGCCTTCAATAATTATGTACG
1 AAAATTTTAA-AAAAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTATGT-CG
* * * *
1611828 TAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACACATTCACTAACTGTCTTAAAAT
64 TAAATTAAAAGAAATTAGTAAAGGTATTTTTCTAGAATAAACACATTCACTAAATGTCTTAAAAT
* * * *
1611893 TTGAGTTGTGGAATATT-AAAG-GCATTTTCACTGGAAGATGCCTTTAATAATCCCA
129 TTGAGTTGTGAAAAATTGAAAGCG-TTTTTCACTGGAAGA-CCCTTTAATAATCCCA
* ** * *
1611948 AAAATTTTAAAAAAAATTATTAAACCCATTTGTTCTCAAAAAACGCCTTCACTAATT
1 AAAATTTTAAAAAAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATT
1612005 GTCTTAAAGT
Statistics
Matches: 544, Mismatches: 56, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
183 12 0.02
184 226 0.42
185 146 0.27
186 126 0.23
187 25 0.05
188 9 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (183 bp):
AAAATTTTAAAAAAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTATGTCGTA
AATTAAAAGAAATTAGTAAAGGTATTTTTCTAGAATAAACACATTCACTAAATGTCTTAAAATTT
GAGTTGTGAAAAATTGAAAGCGTTTTTCACTGGAAGACCCTTTAATAATCCCA
Found at i:1620091 original size:34 final size:34
Alignment explanation
Indices: 1619946--1620113 Score: 140
Period size: 34 Copynumber: 4.9 Consensus size: 34
1619936 AGTTTATCAA
** *
1619946 AAATACAAACATCGCTAATATAGTGACATTTTTC
1 AAATACAAACGCCGCTAATATAGCGACATTTTTC
* * **
1619980 AGATACAAACACCATTAATATAGCGACATTTTTC
1 AAATACAAACGCCGCTAATATAGCGACATTTTTC
** ** ***
1620014 TCATACAAACGCCATTAATATAGCGGTGTTTTTC
1 AAATACAAACGCCGCTAATATAGCGACATTTTTC
* ** *
1620048 ATATACAAATTCTGCTAATATAGCGACATTTTTC
1 AAATACAAACGCCGCTAATATAGCGACATTTTTC
* *
1620082 AAATACAAATGCCGCTAATGTAGC-AGCATTTT
1 AAATACAAACGCCGCTAATATAGCGA-CATTTT
1620114 ATAGAAAATG
Statistics
Matches: 108, Mismatches: 25, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
33 1 0.01
34 107 0.99
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (34 bp):
AAATACAAACGCCGCTAATATAGCGACATTTTTC
Found at i:1626755 original size:4 final size:4
Alignment explanation
Indices: 1626740--1626781 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
1626730 CAAAATTTTG
*
1626740 ATTT AATT ATTT ATTT ATTT ATTT ATTT AGTTT ATTAT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATT-T ATTT
1626782 TTTTTTCTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:1627941 original size:20 final size:21
Alignment explanation
Indices: 1627918--1627964 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1627908 TTTGCATGAT
1627918 TAAATTTAGGA-AAAATAAAA
1 TAAATTTAGGATAAAATAAAA
**
1627938 TAAA-AAAGGATAAAATAAAA
1 TAAATTTAGGATAAAATAAAA
1627958 TAAATTT
1 TAAATTT
1627965 TGAAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
TAAATTTAGGATAAAATAAAA
Found at i:1628050 original size:25 final size:24
Alignment explanation
Indices: 1627993--1628050 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
1627983 ATTCAATGAT
1627993 GAAATTT-ATAAAAATTTTAAATG
1 GAAATTTCATAAAAATTTTAAATG
* *
1628016 GTAAATTTTCATAAAATTTTTAATTG
1 G-AAA-TTTCATAAAAATTTTAAATG
1628042 AGAAATTTC
1 -GAAATTTC
1628051 TCTAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 7 0.24
26 17 0.59
27 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (24 bp):
GAAATTTCATAAAAATTTTAAATG
Found at i:1640046 original size:62 final size:62
Alignment explanation
Indices: 1639967--1640087 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
1639957 TTAGAGGAGC
* * *
1639967 TTTGTTTATTTTTTTCAAAGTCGCTGAACCTCTTATTATAAGAGCTTTGTTTATTTTTTCCT
1 TTTGTTTATTTTTTTCAAAGTCGCTGAACCTCTGATTAAAAAAGCTTTGTTTATTTTTTCCT
*
1640029 TTTGTTTATTTTTTTCAAAGTCGTTGAACCTCTGATTAAAAAAGCTTTGTTTATTTTTT
1 TTTGTTTATTTTTTTCAAAGTCGCTGAACCTCTGATTAAAAAAGCTTTGTTTATTTTTT
1640088 TCAAAGTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (62 bp):
TTTGTTTATTTTTTTCAAAGTCGCTGAACCTCTGATTAAAAAAGCTTTGTTTATTTTTTCCT
Found at i:1640300 original size:45 final size:44
Alignment explanation
Indices: 1640029--1640315 Score: 226
Period size: 45 Copynumber: 6.5 Consensus size: 44
1640019 ATTTTTTCCT
* * * * **
1640029 TTTGTTTATTTTTTTC-AAAGTCGTTGAACCTCTGATTAAAAAAGC
1 TTTGTTTA--TTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
** * * * *
1640074 TTTGTTTATTTTTTTC-AAAGTTGTTGAACCTCTGCTTAAAGAAGC
1 TTTGTTTA--TTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
* ** * * *
1640119 TTTGTTTTTTTTTTTC-AAAGTTGTTAAGCCTCTGATTAGAAGAGC
1 TTTG--TTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
*
1640164 TTTTGTTTATTTTTTC-AAAG-CATTTAGCCTCTGTTTAGAGGAGC
1 -TTTGTTTA-TTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
* * *
1640208 TTTGTTTACTTTTCAAAA-TCATGGAGCCTCTGCTTAGAGGAGC
1 TTTGTTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
*
1640251 TTTGTTTATTTTTCAAAAAGTCATTGAGCCTCTGTTTAGAGGAGT
1 TTTGTTTATTTTTC-AAAAGTCATTGAGCCTCTGTTTAGAGGAGC
* *
1640296 TTTGTTCATTCTTCAAAAGT
1 TTTGTTTATTTTTCAAAAGT
1640316 TATGAACATC
Statistics
Matches: 208, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
42 5 0.02
43 45 0.22
44 32 0.15
45 119 0.57
46 4 0.02
47 3 0.01
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (44 bp):
TTTGTTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGC
Found at i:1640311 original size:88 final size:87
Alignment explanation
Indices: 1640145--1640313 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 87
1640135 AAAGTTGTTA
*
1640145 AGCCTCTGATTAGAAGAGCTTTTGTTTATTTTTTCAAAGCATTTAGCCTCTGTTTAGAGGAGCTT
1 AGCCTCTGATTAGAAGAGCTTTTGTTTATTTTTTCAAAGCATTGAGCCTCTGTTTAGAGGAGCTT
*
1640210 TGTTTACTTTTCAAAATCATGG
66 TGTTCACTTTTCAAAATCATGG
* *
1640232 AGCCTCTGCTTAGAGGAGC-TTTGTTTA-TTTTTCAAAAAGTCATTGAGCCTCTGTTTAGAGGAG
1 AGCCTCTGATTAGAAGAGCTTTTGTTTATTTTTTC--AAAG-CATTGAGCCTCTGTTTAGAGGAG
*
1640295 TTTTGTTCA-TTCTTCAAAA
63 CTTTGTTCACTT-TTCAAAA
1640314 GTTATGAACA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
85 6 0.08
86 8 0.11
87 23 0.32
88 36 0.49
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (87 bp):
AGCCTCTGATTAGAAGAGCTTTTGTTTATTTTTTCAAAGCATTGAGCCTCTGTTTAGAGGAGCTT
TGTTCACTTTTCAAAATCATGG
Found at i:1640552 original size:15 final size:14
Alignment explanation
Indices: 1640529--1640572 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1640519 AAAATTTTGG
*
1640529 TTTAATTATTTCTTT
1 TTTATTTATTT-TTT
1640544 TTTATTTA-TTTTT
1 TTTATTTATTTTTT
1640557 TTT-TTTATTTTTT
1 TTTATTTATTTTTT
1640570 TTT
1 TTT
1640573 CTTCTAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 4 0.15
13 14 0.52
14 2 0.07
15 7 0.26
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTATTTATTTTTT
Found at i:1640562 original size:16 final size:15
Alignment explanation
Indices: 1640541--1640572 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1640531 TAATTATTTC
1640541 TTTTTTATTTATTTTT
1 TTTTTTATTT-TTTTT
1640557 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
1640572 T
1 T
1640573 CTTCTAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTTATTTTTTTT
Found at i:1640571 original size:12 final size:12
Alignment explanation
Indices: 1640541--1640572 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1640531 TAATTATTTC
*
1640541 TTTTTTATTTAT
1 TTTTTTTTTTAT
1640553 TTTTTTTTTTAT
1 TTTTTTTTTTAT
1640565 TTTTTTTT
1 TTTTTTTT
1640573 CTTCTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:1641549 original size:5 final size:5
Alignment explanation
Indices: 1641539--1641572 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1641529 AATTTTAGGA
*
1641539 AAAAT AAAAT AAAAT AAGGAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAA
1641573 TTTTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1652916 original size:4 final size:4
Alignment explanation
Indices: 1652907--1652949 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1652897 TCTTCTTTAC
* * * *
1652907 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATTT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1652950 GATAGATAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (4 bp):
ATAT
Found at i:1652918 original size:6 final size:6
Alignment explanation
Indices: 1652907--1652949 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1652897 TCTTCTTTAC
* * * *
1652907 ATATAT ATATAT ATATAT ATATAT GTATGT ATGTAT ATTTAT A
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
1652950 GATAGATAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (6 bp):
ATATAT
Done.