Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 6 of 290
Found at i:1989152 original size:29 final size:29
Alignment explanation
Indices: 1989107--1989171 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
1989097 TTCGGTCACT
*
1989107 CAACTATGAAAAATTATAAAATGATCATC
1 CAACTATGAAAAATTATAAAACGATCATC
* *
1989136 CAACTAT-AAAAAGTTATAAAACGGTCATT
1 CAACTATGAAAAA-TTATAAAACGATCATC
1989165 CAACTAT
1 CAACTAT
1989172 TCAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (29 bp):
CAACTATGAAAAATTATAAAACGATCATC
Found at i:1993103 original size:3 final size:3
Alignment explanation
Indices: 1993095--1993130 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1993085 GAATTTGACC
1993095 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1993131 CCTGAATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1995794 original size:46 final size:46
Alignment explanation
Indices: 1995738--1995837 Score: 191
Period size: 46 Copynumber: 2.2 Consensus size: 46
1995728 AATGACCCAA
1995738 ATTGAGTCTCTAAAACTTTGACTGAAGCCTAAAGGCAAAATGCAAAT
1 ATTG-GTCTCTAAAACTTTGACTGAAGCCTAAAGGCAAAATGCAAAT
1995785 ATTGGTCTCTAAAACTTTGACTGAAGCCTAAAGGCAAAATGCAAAT
1 ATTGGTCTCTAAAACTTTGACTGAAGCCTAAAGGCAAAATGCAAAT
1995831 ATTGGTC
1 ATTGGTC
1995838 CTATAAATGA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 49 0.92
47 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (46 bp):
ATTGGTCTCTAAAACTTTGACTGAAGCCTAAAGGCAAAATGCAAAT
Found at i:2006596 original size:23 final size:23
Alignment explanation
Indices: 2006566--2006611 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2006556 ATTAAATTAT
2006566 TAAATATTAAATTAAAAATAATA
1 TAAATATTAAATTAAAAATAATA
***
2006589 TAAATATTTTTTTAAAAATAATA
1 TAAATATTAAATTAAAAATAATA
2006612 CAAGTGAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATATTAAATTAAAAATAATA
Found at i:2023662 original size:7 final size:7
Alignment explanation
Indices: 2023650--2023674 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2023640 ATTTAAACAT
2023650 AAAATAA
1 AAAATAA
2023657 AAAATAA
1 AAAATAA
2023664 AAAATAA
1 AAAATAA
2023671 AAAA
1 AAAA
2023675 AGAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:2026293 original size:11 final size:11
Alignment explanation
Indices: 2026277--2026304 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2026267 ACTATTTTTG
2026277 ATTTTTTAATA
1 ATTTTTTAATA
2026288 ATTTTTTAATA
1 ATTTTTTAATA
2026299 ATTTTT
1 ATTTTT
2026305 CTATATCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:2026404 original size:21 final size:21
Alignment explanation
Indices: 2026378--2026420 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2026368 CTTCAACTAC
*
2026378 ACTTACTGTTCCTATTATCTA
1 ACTTACTGTTCCTATTAGCTA
2026399 ACTTACTGTTCCTATTAGCTA
1 ACTTACTGTTCCTATTAGCTA
2026420 A
1 A
2026421 TCAATGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (21 bp):
ACTTACTGTTCCTATTAGCTA
Found at i:2030721 original size:47 final size:47
Alignment explanation
Indices: 2030612--2030722 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
2030602 CCGGGATAAG
* * *
2030612 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
2030659 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
2030706 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
2030723 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:2037940 original size:47 final size:47
Alignment explanation
Indices: 2037831--2037941 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
2037821 CCGGGATAAG
* *
2037831 CACATAGTGCTTCATCGGAATAAATCCGAAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
2037878 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
2037925 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
2037942 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:2040514 original size:25 final size:26
Alignment explanation
Indices: 2040477--2040528 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
2040467 ATAAATAATT
*
2040477 TAAAAATATAAAAATATTCA-AAAAAA
1 TAAAAATATAAAAAAATT-ATAAAAAA
*
2040503 TAAAAGTA-AAAAAAATTATAAAAAA
1 TAAAAATATAAAAAAATTATAAAAAA
2040528 T
1 T
2040529 TATAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.04
25 15 0.65
26 7 0.30
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (26 bp):
TAAAAATATAAAAAAATTATAAAAAA
Found at i:2040528 original size:10 final size:10
Alignment explanation
Indices: 2040512--2040536 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2040502 ATAAAAGTAA
2040512 AAAAAATTAT
1 AAAAAATTAT
2040522 AAAAAATTAT
1 AAAAAATTAT
2040532 AAAAA
1 AAAAA
2040537 TTCAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:2040643 original size:28 final size:27
Alignment explanation
Indices: 2040596--2040667 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
2040586 AAATATCTCA
* ** *
2040596 AAAAAAGAAAAATTCGATTTTTGTTTT
1 AAAAAATAAAAATTAAATTTTTATTTT
*
2040623 AAAAAGTCAAAAATTAAA--TTTATTTT
1 AAAAAAT-AAAAATTAAATTTTTATTTT
*
2040649 AAAAAATAATAATTAAATT
1 AAAAAATAAAAATTAAATT
2040668 GATAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
25 9 0.26
26 13 0.37
27 5 0.14
28 8 0.23
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (27 bp):
AAAAAATAAAAATTAAATTTTTATTTT
Found at i:2040648 original size:26 final size:25
Alignment explanation
Indices: 2040619--2040667 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2040609 TCGATTTTTG
*
2040619 TTTTAAAAAGTCAAAAATTAAATTTA
1 TTTTAAAAAAT-AAAAATTAAATTTA
*
2040645 TTTTAAAAAATAATAATTAAATT
1 TTTTAAAAAATAAAAATTAAATT
2040668 GATAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTTAAAAAATAAAAATTAAATTTA
Found at i:2041335 original size:23 final size:22
Alignment explanation
Indices: 2041309--2041365 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2041299 TAAAAGTTAC
2041309 AAAAATTATTAAAATTTAATAA
1 AAAAATTATTAAAATTTAATAA
* *
2041331 AAAAACTACTTAAAATTTATTAA
1 AAAAATTA-TTAAAATTTAATAA
2041354 AAACTAATTATT
1 AAA--AATTATT
2041366 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 16 0.55
24 2 0.07
25 4 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATTATTAAAATTTAATAA
Found at i:2041726 original size:9 final size:9
Alignment explanation
Indices: 2041712--2041749 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2041702 CCATTTTATA
2041712 TTTTATAAT
1 TTTTATAAT
2041721 TTTTATAAT
1 TTTTATAAT
2041730 TTTTA-AA-
1 TTTTATAAT
*
2041737 TATTATAAT
1 TTTTATAAT
2041746 TTTT
1 TTTT
2041750 TGTCACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 4 0.16
8 4 0.16
9 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2054862 original size:28 final size:28
Alignment explanation
Indices: 2054831--2054886 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2054821 AAAAAGGAAG
2054831 TTGATTTCCAACCACAAAAACAACCAAA
1 TTGATTTCCAACCACAAAAACAACCAAA
2054859 TTGATTTCCAACCACAAAAACAACCAAA
1 TTGATTTCCAACCACAAAAACAACCAAA
2054887 CATTTATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.29, G:0.04, T:0.18
Consensus pattern (28 bp):
TTGATTTCCAACCACAAAAACAACCAAA
Found at i:2054946 original size:33 final size:33
Alignment explanation
Indices: 2054890--2054962 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
2054880 AACCAAACAT
* * *
2054890 TTATAGAGTGACAGTACCTATGAGATCCCTGTA
1 TTATAGGGTGACACTACCCATGAGATCCCTGTA
* *
2054923 TTATAGGGTGAGACTACCCATGAGATCCTTGTA
1 TTATAGGGTGACACTACCCATGAGATCCCTGTA
2054956 TTATAGG
1 TTATAGG
2054963 AGTTGTATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (33 bp):
TTATAGGGTGACACTACCCATGAGATCCCTGTA
Found at i:2058386 original size:17 final size:18
Alignment explanation
Indices: 2058353--2058386 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2058343 ATAACATTTA
2058353 AATAAATAATTAAAAATC
1 AATAAATAATTAAAAATC
*
2058371 AATAAA-AATTATAAAT
1 AATAAATAATTAAAAAT
2058387 AAATTTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAATAATTAAAAATC
Found at i:2063773 original size:16 final size:16
Alignment explanation
Indices: 2063752--2063801 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
2063742 TTTTATGTTT
2063752 TATAAATTATAATATA
1 TATAAATTATAATATA
*
2063768 TATAAATAGCATAATATA
1 TATAAAT--TATAATATA
*
2063786 -ATATATTATAA-ATA
1 TATAAATTATAATATA
2063800 TA
1 TA
2063802 GAAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TATAAATTATAATATA
Found at i:2063809 original size:23 final size:23
Alignment explanation
Indices: 2063760--2063810 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2063750 TTTATAAATT
* *
2063760 ATAATATATATAAATAGCATAAT
1 ATAATATATATAAATAGCAGAAA
*
2063783 ATAATATATTATAAATA-TAGAAA
1 ATAATATA-TATAAATAGCAGAAA
2063806 ATAAT
1 ATAAT
2063811 TTAGGCTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAATATATATAAATAGCAGAAA
Found at i:2064335 original size:30 final size:29
Alignment explanation
Indices: 2064262--2064340 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
2064252 AAATGTGCTC
* *
2064262 AAATAAAGGTCAAA-TTTTTCAAAATAGTC
1 AAATAAAGGT-AAACTTTTTCAAAATACTA
* *
2064291 AAATAAGGGCTAAACCTTTTCAAAAATACTA
1 AAATAAAGG-TAAACTTTTTC-AAAATACTA
2064322 AAATAAAGGTAAACTTTTT
1 AAATAAAGGTAAACTTTTT
2064341 TAAATGTGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 11 0.27
30 15 0.37
31 15 0.37
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.30
Consensus pattern (29 bp):
AAATAAAGGTAAACTTTTTCAAAATACTA
Found at i:2064359 original size:29 final size:30
Alignment explanation
Indices: 2064247--2064357 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 30
2064237 GGGTTTAATC
2064247 TTTACAAATGTGCTCAAATAAAGGTCAAA-TT
1 TTTA-AAATGTGCTCAAATAAAGGT-AAACTT
* *
2064278 TTTCAAAAT-AG-TCAAATAAGGGCTAAACCTT
1 TTT-AAAATGTGCTCAAATAAAGG-TAAA-CTT
* * * *
2064309 TTCAAAA-ATACTAAAATAAAGGTAAACTT
1 TTTAAAATGTGCTCAAATAAAGGTAAACTT
*
2064338 TTTTAAATGTGCTCAAATAA
1 TTTAAAATGTGCTCAAATAA
2064358 GGGCTTCTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
29 21 0.34
30 19 0.31
31 20 0.33
32 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (30 bp):
TTTAAAATGTGCTCAAATAAAGGTAAACTT
Found at i:2079711 original size:31 final size:31
Alignment explanation
Indices: 2079639--2079713 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
2079629 TAATTTTATA
*
2079639 CAATTATACACATGAAACTTTGATCGTGGAT
1 CAATTATACACATGAAACTTTGATCATGGAT
* * * * *
2079670 CAAGTGTACACATGTAATTTTGATTAT-GATT
1 CAATTATACACATGAAACTTTGATCATGGA-T
2079701 CAATTATACACAT
1 CAATTATACACAT
2079714 TTAAATAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
CAATTATACACATGAAACTTTGATCATGGAT
Found at i:2083069 original size:18 final size:19
Alignment explanation
Indices: 2083035--2083071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2083025 TTTCCATCTT
2083035 TTTAATTGTGCAAAAAAAAA
1 TTTAATTGT-CAAAAAAAAA
2083055 TTTAATTGT-AAAAAAAA
1 TTTAATTGTCAAAAAAAA
2083072 TAAATCACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTAATTGTCAAAAAAAAA
Found at i:2084524 original size:86 final size:87
Alignment explanation
Indices: 2084415--2084579 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 87
2084405 AAAAAATACA
* * *
2084415 TATAAAGATTCGAAAATT-AAAAAAACTATATATTATTTATTCCTTAAATGATAATAAGGTCAAT
1 TATAAAGAATCAAAAATTAAAAAAAACTATATATTATTTACTCCTTAAATGATAATAAGGTCAAT
2084479 CTAAAGTTTGAAGTATCCATTT
66 CTAAAGTTTGAAGTATCCATTT
*
2084501 TATAAAGAATCAAAAATTTAAAAAAAAAACTATATATTATTTACTCCTTAAATGGTAATAAGGTC
1 TATAAAGAATCAAAAA-TT--AAAAAAAACTATATATTATTTACTCCTTAAATGATAATAAGGTC
2084566 AATCTAAAGTTTGA
63 AATCTAAAGTTTGA
2084580 CGCGTCTAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
86 14 0.20
87 2 0.03
90 55 0.77
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (87 bp):
TATAAAGAATCAAAAATTAAAAAAAACTATATATTATTTACTCCTTAAATGATAATAAGGTCAAT
CTAAAGTTTGAAGTATCCATTT
Found at i:2084961 original size:10 final size:10
Alignment explanation
Indices: 2084946--2084972 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2084936 ACGACAATTA
2084946 AAATTTTAAG
1 AAATTTTAAG
2084956 AAATTTTAAG
1 AAATTTTAAG
2084966 AAATTTT
1 AAATTTT
2084973 TTGTACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (10 bp):
AAATTTTAAG
Found at i:2089111 original size:39 final size:41
Alignment explanation
Indices: 2089068--2089151 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
2089058 CCAACACATA
* *
2089068 TTTTAG-TTTCG-TATCATATCTAAAATGGATATTTAGCCC
1 TTTTAGTTTTCGATATCATATCTAAAATGAATATTTAGCAC
2089107 TTTTAGTTTTCGATATCATATCTAAAATGAATATTTAGCAC
1 TTTTAGTTTTCGATATCATATCTAAAATGAATATTTAGCAC
2089148 TTTT
1 TTTT
2089152 TAACCTCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 6 0.15
40 5 0.12
41 30 0.73
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (41 bp):
TTTTAGTTTTCGATATCATATCTAAAATGAATATTTAGCAC
Found at i:2090608 original size:15 final size:16
Alignment explanation
Indices: 2090590--2090621 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2090580 TTAATAAATC
2090590 ATATGTTAA-ATATTA
1 ATATGTTAATATATTA
2090605 ATATGTTAATATATTA
1 ATATGTTAATATATTA
2090621 A
1 A
2090622 CAATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATGTTAATATATTA
Found at i:2096958 original size:11 final size:11
Alignment explanation
Indices: 2096938--2096967 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2096928 TCAAAGTCAT
2096938 AAAA-ATATAA
1 AAAATATATAA
2096948 AAAATATATAA
1 AAAATATATAA
2096959 AAAATATAT
1 AAAATATAT
2096968 TTAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATATATAA
Found at i:2103140 original size:23 final size:23
Alignment explanation
Indices: 2103113--2103157 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2103103 GCCCAAACCA
*
2103113 TAATTATCCAAAGTGACCAAAAT
1 TAATTATCCAAACTGACCAAAAT
2103136 TAATTATCCAAACTGACCAAAA
1 TAATTATCCAAACTGACCAAAA
2103158 ATTGAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (23 bp):
TAATTATCCAAACTGACCAAAAT
Found at i:2114844 original size:348 final size:352
Alignment explanation
Indices: 2114184--2114894 Score: 1205
Period size: 348 Copynumber: 2.0 Consensus size: 352
2114174 TTCCAGTTTT
* *
2114184 TCCGGCTACAGTTTCAGTTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
1 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
2114249 TTGTTATAAATTCAGCCATGATCACATTACTGCAAGTAATATCATTTTCATATCATTTTTTACAA
66 TTGTTATAAATTCAGCCATGATCACATTACTGCAAG----ATCA---T-ATATCATTTTTTACAA
* * * *
2114314 CGCCACCTAGGCTGAATCTGAAAAAAGTTATAGTGGTGGGCGAAAACTTCAGTTGTTAAGTCTAT
123 CGCCACCTAGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTAC
*
2114379 GGAGAGCAAACAGCAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGG
188 GGAGAGCAAACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGG
2114444 GTTTATATCTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACC-TTTTTTTTTTTTAAATCAG
253 GTTTATATCTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTTAAATCAG
2114508 ATTATAAGATTGTAAACAGATATAAACCTTCCATC
318 ATTATAAGATTGTAAACAGATATAAACCTTCCATC
2114543 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
1 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
*
2114608 TTGTTATAACTTCAGCCATGATCACATTACTGCAAG-T-A-ATATCATTTTTTACAACGCCACCT
66 TTGTTATAAATTCAGCCATGATCACATTACTGCAAGATCATATATCATTTTTTACAACGCCACCT
* * *
2114670 AGGCTGAATCTGAAAAAGGTTACAGTGGTGGGTGAAAACTTTAATTGTTAACTCTACGGAGAGCA
131 AGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTACGGAGAGCA
2114735 AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
196 AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
*
2114800 CTTGGGTAAGAAACTAGAAATGAATCAAGTTGGAACCATTTTTTTTTTTTAAATCAGATTATAAG
261 CTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTTAAATCAGATTATAAG
*
2114865 ATTGTAAACAGGTATAAACCTTCCATC
326 ATTGTAAACAGATATAAACCTTCCATC
2114892 TCC
1 TCC
2114895 AGCAGAAGCC
Statistics
Matches: 338, Mismatches: 13, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
348 182 0.54
349 56 0.17
353 1 0.00
354 1 0.00
359 98 0.29
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (352 bp):
TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
TTGTTATAAATTCAGCCATGATCACATTACTGCAAGATCATATATCATTTTTTACAACGCCACCT
AGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTACGGAGAGCA
AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
CTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTTAAATCAGATTATAAG
ATTGTAAACAGATATAAACCTTCCATC
Found at i:2115664 original size:3 final size:3
Alignment explanation
Indices: 2115656--2115683 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2115646 AACGTTAAAT
2115656 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2115684 AAAATACTAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2117032 original size:30 final size:30
Alignment explanation
Indices: 2116996--2117052 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2116986 GCTCCCCTAA
2116996 ATTCGCCCCTGAA-TAGGATCTAGTTAATAG
1 ATTCGCCCCT-AACTAGGATCTAGTTAATAG
2117026 ATTCGCCCCTAACTAGGATCTAGTTAA
1 ATTCGCCCCTAACTAGGATCTAGTTAA
2117053 GCCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (30 bp):
ATTCGCCCCTAACTAGGATCTAGTTAATAG
Found at i:2122463 original size:9 final size:9
Alignment explanation
Indices: 2122449--2122476 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2122439 TCACTTAGGC
2122449 TAGCACATT
1 TAGCACATT
2122458 TAGCACATT
1 TAGCACATT
2122467 TAGCACATT
1 TAGCACATT
2122476 T
1 T
2122477 TTGTGCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (9 bp):
TAGCACATT
Found at i:2127073 original size:22 final size:23
Alignment explanation
Indices: 2127026--2127084 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2127016 AAGGCCAAGC
*
2127026 TATATACGAATAATTTTAAAGAAAA
1 TATATAC-AATAAATTT-AAGAAAA
2127051 TATATACAATAAATTT-AGAAAA
1 TATATACAATAAATTTAAGAAAA
*
2127073 TATTTAC-ATAAA
1 TATATACAATAAA
2127085 ATAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 12 0.38
24 8 0.25
25 7 0.22
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (23 bp):
TATATACAATAAATTTAAGAAAA
Found at i:2127927 original size:27 final size:25
Alignment explanation
Indices: 2127896--2127948 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2127886 TCACGCAAAA
*
2127896 AGAAAATGAAAGAATAATAACAAAATC
1 AGAAAAGGAAAGAA-AATAA-AAAATC
* *
2127923 AGAAAGGGAAAGAAACTAAAAAATC
1 AGAAAAGGAAAGAAAATAAAAAATC
2127948 A
1 A
2127949 CCTTTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.11
Consensus pattern (25 bp):
AGAAAAGGAAAGAAAATAAAAAATC
Found at i:2129308 original size:53 final size:53
Alignment explanation
Indices: 2129228--2129333 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
2129218 CATTTCCATA
* *
2129228 TAATATGACATTTGATCATAGGTAAGCAATCAATTTACTCAATTGGTTTTTTC
1 TAATATGACATTAGATCATAGATAAGCAATCAATTTACTCAATTGGTTTTTTC
** ***
2129281 TAATATGACATTAGATTGTAGATAAGCAATTGCTTTACTCAATTGGTTTTTTC
1 TAATATGACATTAGATCATAGATAAGCAATCAATTTACTCAATTGGTTTTTTC
2129334 AAAATCGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (53 bp):
TAATATGACATTAGATCATAGATAAGCAATCAATTTACTCAATTGGTTTTTTC
Found at i:2142115 original size:23 final size:22
Alignment explanation
Indices: 2142083--2142148 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
2142073 AAAGTTTTAG
2142083 AATTAAAATTAAGATTTTATAT
1 AATTAAAATTAAGATTTTATAT
* ** *
2142105 AACTTTAAATTGATATTTTTTATTT
1 AA-TTAAAATT-A-AGATTTTATAT
2142130 AATTAAAATTAAGATTTTA
1 AATTAAAATTAAGATTTTA
2142149 GAATTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
22 8 0.24
23 8 0.24
24 8 0.24
25 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTAAAATTAAGATTTTATAT
Found at i:2142155 original size:24 final size:23
Alignment explanation
Indices: 2142083--2142155 Score: 58
Period size: 24 Copynumber: 3.1 Consensus size: 23
2142073 AAAGTTTTAG
*
2142083 AATTAAAATTAAGATTTTATA-T
1 AATTAAAATTAAGATTTTAAATT
* * * * *
2142105 AACTTTAAATTGATATTTTTTATTT
1 AA-TTAAAATTAAGA-TTTTAAATT
2142130 AATTAAAATTAAGATTTTAGAATT
1 AATTAAAATTAAGATTTTA-AATT
2142154 AA
1 AA
2142156 AATTTTGGAT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
22 2 0.06
23 13 0.36
24 18 0.50
25 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTAAAATTAAGATTTTAAATT
Found at i:2144854 original size:28 final size:29
Alignment explanation
Indices: 2144803--2144858 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
2144793 TGTGATTGAG
2144803 TTTTGGAGTACTTAATAAAATTTTTAAACT
1 TTTTGGAGTA-TTAATAAAATTTTTAAACT
* *
2144833 TTTTGGAGT-TTAATGAATTTTTTAAA
1 TTTTGGAGTATTAATAAAATTTTTAAA
2144859 AAAATAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
30 9 0.38
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTTGGAGTATTAATAAAATTTTTAAACT
Found at i:2162928 original size:29 final size:29
Alignment explanation
Indices: 2162895--2162951 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2162885 TATGCATAAG
2162895 TAAGACTAAAAAAGTGCTACAATAATAGT
1 TAAGACTAAAAAAGTGCTACAATAATAGT
2162924 TAAGACTAAAAAAGTGCTACAATAATAG
1 TAAGACTAAAAAAGTGCTACAATAATAG
2162952 ACAAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (29 bp):
TAAGACTAAAAAAGTGCTACAATAATAGT
Found at i:2165950 original size:17 final size:18
Alignment explanation
Indices: 2165928--2165962 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2165918 GCGGATTTAA
*
2165928 TTAAAA-TAATTTGAAAT
1 TTAAAATTAATTTAAAAT
2165945 TTAAAATTAATTTAAAAT
1 TTAAAATTAATTTAAAAT
2165963 CTCTAAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TTAAAATTAATTTAAAAT
Found at i:2177440 original size:5 final size:5
Alignment explanation
Indices: 2177425--2177483 Score: 109
Period size: 5 Copynumber: 11.6 Consensus size: 5
2177415 TTTATTATAA
2177425 AATTGT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATT-T AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
2177476 AATTT AAT
1 AATTT AAT
2177484 AAAATCATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 49 0.92
6 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:2180333 original size:27 final size:28
Alignment explanation
Indices: 2180302--2180437 Score: 93
Period size: 27 Copynumber: 4.8 Consensus size: 28
2180292 ACATTTTTTT
2180302 TCTAATTTGGTACCTAAACTTTTTTGGC
1 TCTAATTTGGTACCTAAACTTTTTTGGC
*
2180330 -CTAATTTGGTA-CTGAAA-TGTTTTTTGC
1 TCTAATTTGGTACCT-AAACT-TTTTTGGC
* * **
2180357 TCCAAGTTGGTACCTAAACTTAACATTTTTTTC
1 TCTAATTTGGTACCTAAAC-T----TTTTTGGC
* * *
2180390 CCTAATTTGGTACCTATA-TTTTTTAGGT
1 TCTAATTTGGTACCTAAACTTTTTT-GGC
2180418 TC-AATTTGGTACCTAAACTT
1 TCTAATTTGGTACCTAAACTT
2180438 GTTAATACAA
Statistics
Matches: 83, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
26 3 0.04
27 40 0.48
28 15 0.18
29 2 0.02
30 1 0.01
31 1 0.01
33 21 0.25
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (28 bp):
TCTAATTTGGTACCTAAACTTTTTTGGC
Found at i:2188174 original size:27 final size:27
Alignment explanation
Indices: 2188142--2188196 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2188132 GTGAAAAAAA
2188142 AAACATTTATACGTGTTTATTAAAAGT
1 AAACATTTATACGTGTTTATTAAAAGT
2188169 AAACATTTATACGTGTTTATTAAAAGT
1 AAACATTTATACGTGTTTATTAAAAGT
2188196 A
1 A
2188197 TCTCACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (27 bp):
AAACATTTATACGTGTTTATTAAAAGT
Found at i:2188504 original size:2 final size:2
Alignment explanation
Indices: 2188497--2188521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2188487 TTTATACATT
2188497 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2188522 TCTCTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2190023 original size:19 final size:18
Alignment explanation
Indices: 2189979--2190025 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2189969 TTTTGGAATT
2189979 TAAATTTTAAATTTTATA
1 TAAATTTTAAATTTTATA
* *
2189997 TGATTTTTAGAATTTTAT-
1 TAAATTTTA-AATTTTATA
2190015 TAAAATTTTAA
1 T-AAATTTTAA
2190026 TATATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TAAATTTTAAATTTTATA
Found at i:2198459 original size:21 final size:21
Alignment explanation
Indices: 2198433--2198477 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2198423 CCCATAGGCC
2198433 AATATTCATAATTAT-TACATT
1 AATATT-ATAATTATATACATT
* *
2198454 AATATTATATTTATATATATT
1 AATATTATAATTATATACATT
2198475 AAT
1 AAT
2198478 GTTTATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATAATTATATACATT
Found at i:2213974 original size:20 final size:23
Alignment explanation
Indices: 2213918--2213982 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 23
2213908 GTAAGATTTT
*
2213918 TGAATTATTAATAAAAAATAATAA
1 TGAATTATTAAT-AAAAACAATAA
2213942 TGAATTATTAATAAAAACAATAA
1 TGAATTATTAATAAAAACAATAA
2213965 T-AA-T-TTAATAAAAACAAT
1 TGAATTATTAATAAAAACAAT
2213983 TTATACAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 14 0.35
21 1 0.03
22 2 0.05
23 11 0.28
24 12 0.30
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (23 bp):
TGAATTATTAATAAAAACAATAA
Found at i:2219545 original size:45 final size:45
Alignment explanation
Indices: 2219496--2219590 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
2219486 TTTTACATTA
*
2219496 TATTATCAAATCAAATTCACAGTATTTTAAATTAATTATTTTTAT
1 TATTATCAAATCAAATTCACAATATTTTAAATTAATTATTTTTAT
*
2219541 TATTATCAAATCAAATTCACAATTTTTTAAATTAATTATTTTTAT
1 TATTATCAAATCAAATTCACAATATTTTAAATTAATTATTTTTAT
2219586 TATTA
1 TATTA
2219591 GTTTCGATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (45 bp):
TATTATCAAATCAAATTCACAATATTTTAAATTAATTATTTTTAT
Found at i:2219656 original size:23 final size:23
Alignment explanation
Indices: 2219612--2219657 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2219602 GTTAAAAATA
* *
2219612 TTTATTTTTAATTTTATGATTTT
1 TTTATATTTAATTTTATAATTTT
2219635 TTTATATTTAATATTT-TAATTTT
1 TTTATATTTAAT-TTTATAATTTT
2219658 ATCCTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTATATTTAATTTTATAATTTT
Found at i:2220563 original size:30 final size:30
Alignment explanation
Indices: 2220501--2220573 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 30
2220491 ATATACAGTA
*
2220501 AAATT-ATCTTTT-AAAATAAAAAAATTAT
1 AAATTAATTTTTTAAAAATAAAAAAATTAT
*
2220529 ---TTAATTTTTTAAAAATAATAAAATTAT
1 AAATTAATTTTTTAAAAATAAAAAAATTAT
*
2220556 AAATTAATATGTTTAAAA
1 AAATTAAT-TTTTTAAAA
2220574 TTTATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 2 0.06
26 6 0.17
27 15 0.42
30 5 0.14
31 8 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
AAATTAATTTTTTAAAAATAAAAAAATTAT
Found at i:2224335 original size:22 final size:22
Alignment explanation
Indices: 2224310--2224353 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2224300 TATTCATGAC
*
2224310 CAAATATATATGATACAA-ATAT
1 CAAATATA-ATAATACAATATAT
2224332 CAAATATAATAATACAATATAT
1 CAAATATAATAATACAATATAT
2224354 TTTTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (22 bp):
CAAATATAATAATACAATATAT
Found at i:2227525 original size:28 final size:28
Alignment explanation
Indices: 2227472--2227526 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2227462 TGAAAGGAAT
* *
2227472 TAAATCTCAAATTTTAAAGTACTATAAC
1 TAAATCTCAAATTCTAAAGAACTATAAC
*
2227500 TAAATCTCAAATTCTAAAGAAGTATAA
1 TAAATCTCAAATTCTAAAGAACTATAA
2227527 GGACTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (28 bp):
TAAATCTCAAATTCTAAAGAACTATAAC
Found at i:2232826 original size:153 final size:153
Alignment explanation
Indices: 2232540--2232827 Score: 407
Period size: 153 Copynumber: 1.9 Consensus size: 153
2232530 GAACGGAAAA
* *
2232540 TTTCCTCTTTTTACTTGAACAACTAACGATTTCAACATCTGGGCATCTTTCCTTTCCCTTCAAAT
1 TTTCCTCTTTATACTTGAACAACTAACGATTTCAACATCTGGGCATCTTTCCTTTCCCTCCAAAT
* ** * * *
2232605 CGACACCAAAAACAACACTTCCTGAGTTTGTGAAGTTTTCTGTTTCTTTCTCGGGAAACCCAATA
66 CGACACCAAAAACAACACTTCCTGACTCGGTGAAATTTTCCGTTTCTTTCTCGGGAAACCCAAAA
2232670 TCAAAAACGACATTGGGGCTTCT
131 TCAAAAACGACATTGGGGCTTCT
* ** * *
2232693 TTTCGTCTTTATACTTGAAGGACTAACGATTTCAACA-CTTGGGCTTCTTTCCTTTCTCTCCAAA
1 TTTCCTCTTTATACTTGAACAACTAACGATTTCAACATC-TGGGCATCTTTCCTTTCCCTCCAAA
* ** *
2232757 TCGACACCAAGAACAACACTTTGTGACTCGGTGAAATTTTCCGTTTGTTTCTCGGGAAACCCAAA
65 TCGACACCAAAAACAACACTTCCTGACTCGGTGAAATTTTCCGTTTCTTTCTCGGGAAACCCAAA
2232822 ATCAAA
130 ATCAAA
2232828 CCCCCAAAAC
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
152 1 0.01
153 116 0.99
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (153 bp):
TTTCCTCTTTATACTTGAACAACTAACGATTTCAACATCTGGGCATCTTTCCTTTCCCTCCAAAT
CGACACCAAAAACAACACTTCCTGACTCGGTGAAATTTTCCGTTTCTTTCTCGGGAAACCCAAAA
TCAAAAACGACATTGGGGCTTCT
Found at i:2236153 original size:18 final size:18
Alignment explanation
Indices: 2236111--2236154 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2236101 TTAAATTTAA
*
2236111 ATTAATTATAAAAATATT
1 ATTAAATATAAAAATATT
*
2236129 AAT-AATATAAAAATATT
1 ATTAAATATAAAAATATT
*
2236146 TTTAAATAT
1 ATTAAATAT
2236155 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAATATAAAAATATT
Found at i:2244286 original size:11 final size:11
Alignment explanation
Indices: 2244267--2244323 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
2244257 ATATTATACA
2244267 AAAACTATAAAT
1 AAAA-TATAAAT
2244279 AAAATATAAAT
1 AAAATATAAAT
*
2244290 ATAA-AT-AA-
1 AAAATATAAAT
2244298 AAAATATAAAT
1 AAAATATAAAT
2244309 AAAATA-AAAT
1 AAAATATAAAT
2244319 AAAAT
1 AAAAT
2244324 TTATTTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 3 0.08
9 4 0.10
10 13 0.32
11 16 0.40
12 4 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:2244291 original size:6 final size:5
Alignment explanation
Indices: 2244275--2244323 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
2244265 CAAAAACTAT
*
2244275 AAATA AAATA TAAATA TAAATA AAA-A ATAT- AAATA AAATA AAATA AAAT
1 AAATA AAATA -AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAAT
2244324 TTATTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 6 0.15
5 22 0.56
6 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:2244294 original size:17 final size:17
Alignment explanation
Indices: 2244272--2244323 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 17
2244262 ATACAAAAAC
2244272 TATAAATAAAATATAAA
1 TATAAATAAAATATAAA
2244289 TATAAATAAAAAATATAAA
1 TATAAAT--AAAATATAAA
2244308 TA-AAATAAAATA-AAA
1 TATAAATAAAATATAAA
2244323 T
1 T
2244324 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 7 0.21
18 4 0.12
19 12 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAATAAAATATAAA
Found at i:2244306 original size:30 final size:28
Alignment explanation
Indices: 2244266--2244323 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 28
2244256 TATATTATAC
*
2244266 AAAAACTATAAATAAAATATAAATATAAAT
1 AAAAAATATAAATAAAATA-AAATA-AAAT
2244296 AAAAAATATAAATAAAATAAAATAAAAT
1 AAAAAATATAAATAAAATAAAATAAAAT
2244324 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 18 0.67
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (28 bp):
AAAAAATATAAATAAAATAAAATAAAAT
Found at i:2248878 original size:5 final size:6
Alignment explanation
Indices: 2248863--2248887 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2248853 CAAAGCTTGA
2248863 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
2248888 GACCGGCGCT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2250114 original size:11 final size:11
Alignment explanation
Indices: 2250098--2250129 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2250088 TAAGACGAGG
2250098 AAGGAAAAGAA
1 AAGGAAAAGAA
2250109 AAGGAAAAGAA
1 AAGGAAAAGAA
*
2250120 AAAGAAAAGA
1 AAGGAAAAGA
2250130 TTGTTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAGGAAAAGAA
Found at i:2250838 original size:26 final size:27
Alignment explanation
Indices: 2250808--2250862 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
2250798 TTTTTTAGTC
*
2250808 AAAT-AAACTTTTAATTTGTATTAATT
1 AAATAAAACTTATAATTTGTATTAATT
2250834 AAATAACCAAACTTATAATTTGTATTAAT
1 AAAT-A--AAACTTATAATTTGTATTAAT
2250863 CCCAACATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
30 20 0.83
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (27 bp):
AAATAAAACTTATAATTTGTATTAATT
Found at i:2257869 original size:22 final size:22
Alignment explanation
Indices: 2257844--2257913 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
2257834 AATTATGTAT
2257844 TTAAATTTAAAAATAATATATA
1 TTAAATTTAAAAATAATATATA
*
2257866 TTAAATATAAAAAT-ATATATGA
1 TTAAATTTAAAAATAATATAT-A
*
2257888 TTTGAAA-TTAATAATAATATTATA
1 -TT-AAATTTAAAAATAATA-TATA
2257912 TT
1 TT
2257914 TATAATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.15
22 14 0.35
23 10 0.25
24 7 0.17
25 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (22 bp):
TTAAATTTAAAAATAATATATA
Found at i:2265337 original size:11 final size:12
Alignment explanation
Indices: 2265307--2265340 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2265297 AGCGTTGAAT
2265307 TTTAAAAATACA
1 TTTAAAAATACA
*
2265319 TTTAAAAATATA
1 TTTAAAAATACA
2265331 TTTAAAAATA
1 TTTAAAAATA
2265341 AGGTTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTAAAAATACA
Found at i:2273460 original size:19 final size:20
Alignment explanation
Indices: 2273436--2273479 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2273426 ATTTTTAAAA
*
2273436 AAAAATTGTTAAAAA-TAAT
1 AAAAATTGTAAAAAAGTAAT
*
2273455 AAAAA-TGTAAAAAAGTATT
1 AAAAATTGTAAAAAAGTAAT
2273474 AAAAAT
1 AAAAAT
2273480 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAATTGTAAAAAAGTAAT
Found at i:2273498 original size:40 final size:40
Alignment explanation
Indices: 2273444--2273523 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
2273434 AAAAAAATTG
*
2273444 TTAAAAATAATAAAAATGTA-AAAAAG-TATTAAAAATATAT
1 TTAAAAATAAT-AAAAT-TATAAAAAGTTATAAAAAATATAT
** *
2273484 TTAAAAATTGTAAAATTATTAAAAGTTATAAAAAATATAT
1 TTAAAAATAATAAAATTATAAAAAGTTATAAAAAATATAT
2273524 AATTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
38 2 0.06
39 10 0.29
40 22 0.65
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (40 bp):
TTAAAAATAATAAAATTATAAAAAGTTATAAAAAATATAT
Found at i:2273517 original size:19 final size:20
Alignment explanation
Indices: 2273444--2273523 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 20
2273434 AAAAAAATTG
* *
2273444 TTAAAAATAATAAAAATGTA
1 TTAAAAATTATAAAAATATA
*
2273464 --AAAAAGTATTAAAAATATA
1 TTAAAAATTA-TAAAAATATA
*
2273483 TTTAAAAATTGT-AAAAT-TA
1 -TTAAAAATTATAAAAATATA
*
2273502 TTAAAAGTTATAAAAAATATA
1 TTAAAAATTAT-AAAAATATA
2273523 T
1 T
2273524 AATTTTTTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
18 15 0.33
19 11 0.24
20 10 0.22
21 4 0.09
22 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAAAATTATAAAAATATA
Found at i:2273641 original size:30 final size:29
Alignment explanation
Indices: 2273607--2273663 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2273597 TTGAAAATAC
* * *
2273607 TTTTTAATCATTTTTACAATTTTTAAAATT
1 TTTTTAATAACTTTTAC-ATTTTAAAAATT
2273637 TTTTTAATAACTTTTACATTTTAAAAA
1 TTTTTAATAACTTTTACATTTTAAAAA
2273664 AAAATTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTTAATAACTTTTACATTTTAAAAATT
Found at i:2273717 original size:19 final size:20
Alignment explanation
Indices: 2273686--2273741 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
2273676 TAGTAATTTT
2273686 TTTTACAAATTTT-TAATAAA
1 TTTTACAAATTTTCT-ATAAA
2273706 TTTTAC-AATTTTCTATAAA
1 TTTTACAAATTTTCTATAAA
*
2273725 TTTTAATAAATTTTCTA
1 TTTT-ACAAATTTTCTA
2273742 ACTTTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 15 0.47
20 8 0.25
21 9 0.28
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTACAAATTTTCTATAAA
Found at i:2273814 original size:19 final size:20
Alignment explanation
Indices: 2273784--2273834 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2273774 ATGACATTAG
*
2273784 AAATTCTAGTATC-ACTTAA
1 AAATTTTAGTATCGACTTAA
* **
2273803 AAATTTTGGTATCGTGTTAA
1 AAATTTTAGTATCGACTTAA
2273823 AAATTTTAGTAT
1 AAATTTTAGTAT
2273835 TGGTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (20 bp):
AAATTTTAGTATCGACTTAA
Found at i:2273904 original size:20 final size:20
Alignment explanation
Indices: 2273879--2274025 Score: 95
Period size: 20 Copynumber: 7.4 Consensus size: 20
2273869 TTGGTATTAC
* *
2273879 TTAGAAATCTGGATATCATG
1 TTAGAAATATTGATATCATG
2273899 TTAGAAATATTGATATCCAT-
1 TTAGAAATATTGATAT-CATG
* *
2273919 TATA-AAATTTTGATATCATA
1 T-TAGAAATATTGATATCATG
* *
2273939 TTAGAAGTATTGATATCACG
1 TTAGAAATATTGATATCATG
* *
2273959 TTAGAAACT-TTGGTATTA-G
1 TTAGAAA-TATTGATATCATG
* * ***
2273978 TTAAAAATTTTGATATCGCC
1 TTAGAAATATTGATATCATG
* *
2273998 TTAGAAGTATTGATATCACG
1 TTAGAAATATTGATATCATG
*
2274018 TTAAAAAT
1 TTAGAAAT
2274026 TTTAGTATTA
Statistics
Matches: 98, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
19 18 0.18
20 73 0.74
21 6 0.06
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (20 bp):
TTAGAAATATTGATATCATG
Found at i:2274004 original size:59 final size:60
Alignment explanation
Indices: 2273922--2274059 Score: 190
Period size: 59 Copynumber: 2.3 Consensus size: 60
2273912 TATCCATTAT
* * *
2273922 AAAATTTTGATATCATATTAGAAGTATTGATATCACGTTAGAAACTTTGGTATTA-GTTA
1 AAAATTTTGATATCACATTAGAAGTATTGATATCACGTTAAAAACTTTAGTATTACGTTA
* * *
2273981 AAAATTTTGATATCGCCTTAGAAGTATTGATATCACGTTAAAAATTTTAGTATTACGTTA
1 AAAATTTTGATATCACATTAGAAGTATTGATATCACGTTAAAAACTTTAGTATTACGTTA
* *
2274041 GAAATTTTAATATC-CATTA
1 AAAATTTTGATATCACATTA
2274060 AAAATTTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 53 0.77
60 16 0.23
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (60 bp):
AAAATTTTGATATCACATTAGAAGTATTGATATCACGTTAAAAACTTTAGTATTACGTTA
Found at i:2274066 original size:19 final size:20
Alignment explanation
Indices: 2274018--2274066 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2274008 TGATATCACG
* *
2274018 TTAAAAATTTTAGTATTACG
1 TTAAAAATTTTAATATTACA
* *
2274038 TTAGAAATTTTAATA-TCCA
1 TTAAAAATTTTAATATTACA
2274057 TTAAAAATTT
1 TTAAAAATTT
2274067 AAAAACACTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (20 bp):
TTAAAAATTTTAATATTACA
Found at i:2275399 original size:6 final size:6
Alignment explanation
Indices: 2275388--2275414 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2275378 TTTAGTAAAT
2275388 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
2275415 AAAGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:2276592 original size:44 final size:44
Alignment explanation
Indices: 2276520--2276611 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
2276510 CTGAAGTAAC
*
2276520 AGTAACAGTACGACACACAATGTGCCTCATCGACTCGAA-GTCGA
1 AGTAACAGTACGACACACAATGTGCCTCATCGACT-GAAGGCCGA
** *
2276564 AGTAACAGTACGACAC-TTATAGTTCCTCATCGACTGAAGGCCGA
1 AGTAACAGTACGACACACAAT-GTGCCTCATCGACTGAAGGCCGA
2276608 AGTA
1 AGTA
2276612 TTCCTGAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 5 0.12
44 37 0.88
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (44 bp):
AGTAACAGTACGACACACAATGTGCCTCATCGACTGAAGGCCGA
Found at i:2277177 original size:44 final size:44
Alignment explanation
Indices: 2277105--2277196 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
2277095 CTGAAGTAAC
*
2277105 AGTAACAGTACGACACACAATATGCCTCATCGACTCGAA-GTCGA
1 AGTAACAGTACGACACACAATATGCCTCATCGACT-GAAGGCCGA
** *
2277149 AGTAACAGTACGACAC-TTATAGTTCCTCATCGACTGAAGGCCGA
1 AGTAACAGTACGACACACAATA-TGCCTCATCGACTGAAGGCCGA
2277193 AGTA
1 AGTA
2277197 TTACTGAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 6 0.14
44 36 0.86
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (44 bp):
AGTAACAGTACGACACACAATATGCCTCATCGACTGAAGGCCGA
Found at i:2277395 original size:585 final size:585
Alignment explanation
Indices: 2276285--2277454 Score: 2223
Period size: 585 Copynumber: 2.0 Consensus size: 585
2276275 ATTGTTATTT
2276285 AATAACAATCAGTTATTCAGTATCAAACTATCAATACCAATCAGTTATTCAGTCCAGTAATAAAG
1 AATAACAATCAGTTATTCAGTATCAAACTATCAATACCAATCAGTTATTCAGTCCAGTAATAAAG
*
2276350 TCATTCAATTATTCAGTGCAATTGTTTACCCCTATTAACATAACTCGGACTTAGACAGATATATG
66 CCATTCAATTATTCAGTGCAATTGTTTACCCCTATTAACATAACTCGGACTTAGACAGATATATG
* *
2276415 GATCCAACCAACAAACCAGTATGGCACTCAGTGCCTCATCGGCTTTGCCGAAGTAAACAGTAGTA
131 GATCCAACCAACAAACCAGTACGGCACTCAGTGCCTCATCGGCTTTGCCGAAGTAAAAAGTAGTA
*
2276480 GTACAGTACTTAGTACCTCATTGGATTAAACTGAAGTAACAGTAACAGTACGACACACAATGTGC
196 GTACAGTACTTAGTACCTCATTGGATTAAACTGAAGTAACAGTAACAGTACGACACACAATATGC
2276545 CTCATCGACTCGAAGTCGAAGTAACAGTACGACACTTATAGTTCCTCATCGACTGAAGGCCGAAG
261 CTCATCGACTCGAAGTCGAAGTAACAGTACGACACTTATAGTTCCTCATCGACTGAAGGCCGAAG
* *
2276610 TATTCCTGAACACTTCCAATCCTATGGCATGCCAACTATATCTGACTCAACCCAATACAGTTAAT
326 TATTACTGAACACTTCCAATCCTATGGCATGCCAACTATATCCGACTCAACCCAATACAGTTAAT
*
2276675 AGGGTATTCAATTCATTTCTCAATTCATAGTAATTAATTATTTCAATACCTATTTCACAATAATC
391 AGGGTATTCAATTCATTTCTCAATTCACAGTAATTAATTATTTCAATACCTATTTCACAATAATC
*
2276740 ACAAATTCACATACATTCAATTCAATATCAAAACACTAATACTTACCTTAATATCTTTCCATATA
456 ACAAATTCACATACATTCAATTCAATATCAAAACACTAATACTGACCTTAATATCTTTCCATATA
* *
2276805 CATCAAATAATAACATCAAAAATTTAAATGTTAAGTTCGGTTTATAGAAATACAAACCGTAATTC
521 CATCAAATAATAAAATAAAAAATTTAAATGTTAAGTTCGGTTTATAGAAATACAAACCGTAATTC
*
2276870 AATAACAATCAGTTATTCAGTATCAAACTATCAATATCAATCAGTTATTCAGTCCAGTAATAAAG
1 AATAACAATCAGTTATTCAGTATCAAACTATCAATACCAATCAGTTATTCAGTCCAGTAATAAAG
2276935 CCATTCAATTATTCAGTGCAATTGTTTACCCCTATTAACATAACTCGGACTTAGACAGATATATG
66 CCATTCAATTATTCAGTGCAATTGTTTACCCCTATTAACATAACTCGGACTTAGACAGATATATG
2277000 GATCCAACCAACAAACCAGTACGGCACTCAGTGCCTCATCGGCTTTGCCGAAGTAAAAAGTAGTA
131 GATCCAACCAACAAACCAGTACGGCACTCAGTGCCTCATCGGCTTTGCCGAAGTAAAAAGTAGTA
*
2277065 GTACGGTACTTAGTACCTCATTGGATTAAACTGAAGTAACAGTAACAGTACGACACACAATATGC
196 GTACAGTACTTAGTACCTCATTGGATTAAACTGAAGTAACAGTAACAGTACGACACACAATATGC
2277130 CTCATCGACTCGAAGTCGAAGTAACAGTACGACACTTATAGTTCCTCATCGACTGAAGGCCGAAG
261 CTCATCGACTCGAAGTCGAAGTAACAGTACGACACTTATAGTTCCTCATCGACTGAAGGCCGAAG
2277195 TATTACTGAACACTTCCAATCCTATGGCATGCCAACTATATCCGACTCAACCCAATACAGTTAAT
326 TATTACTGAACACTTCCAATCCTATGGCATGCCAACTATATCCGACTCAACCCAATACAGTTAAT
*
2277260 AGGGTATTCAATTCATTTCTCAATTCACAGTAATTAATTATTTCAATATCTATTTCACAATAATC
391 AGGGTATTCAATTCATTTCTCAATTCACAGTAATTAATTATTTCAATACCTATTTCACAATAATC
2277325 ACAAATTCACATACATTCAATTCAATATCAAAACACTAATACTGACCTTAATATCTTTCCATATA
456 ACAAATTCACATACATTCAATTCAATATCAAAACACTAATACTGACCTTAATATCTTTCCATATA
2277390 CATCAAATAATAAAATAAAAAATTTAAATGTTAAGTTCGGTTTATAGAAATACAAACCGTAATTC
521 CATCAAATAATAAAATAAAAAATTTAAATGTTAAGTTCGGTTTATAGAAATACAAACCGTAATTC
2277455 TCGGATTACT
Statistics
Matches: 572, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
585 572 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (585 bp):
AATAACAATCAGTTATTCAGTATCAAACTATCAATACCAATCAGTTATTCAGTCCAGTAATAAAG
CCATTCAATTATTCAGTGCAATTGTTTACCCCTATTAACATAACTCGGACTTAGACAGATATATG
GATCCAACCAACAAACCAGTACGGCACTCAGTGCCTCATCGGCTTTGCCGAAGTAAAAAGTAGTA
GTACAGTACTTAGTACCTCATTGGATTAAACTGAAGTAACAGTAACAGTACGACACACAATATGC
CTCATCGACTCGAAGTCGAAGTAACAGTACGACACTTATAGTTCCTCATCGACTGAAGGCCGAAG
TATTACTGAACACTTCCAATCCTATGGCATGCCAACTATATCCGACTCAACCCAATACAGTTAAT
AGGGTATTCAATTCATTTCTCAATTCACAGTAATTAATTATTTCAATACCTATTTCACAATAATC
ACAAATTCACATACATTCAATTCAATATCAAAACACTAATACTGACCTTAATATCTTTCCATATA
CATCAAATAATAAAATAAAAAATTTAAATGTTAAGTTCGGTTTATAGAAATACAAACCGTAATTC
Found at i:2277535 original size:6 final size:6
Alignment explanation
Indices: 2277524--2277554 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2277514 GTTAACTACG
2277524 AAAATA AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA A
2277555 TTTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:2279189 original size:46 final size:46
Alignment explanation
Indices: 2279139--2279265 Score: 209
Period size: 46 Copynumber: 2.8 Consensus size: 46
2279129 TGTTTGGGCA
*
2279139 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
2279185 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
2279231 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTAT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
2279266 AGGCGGGTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:2283528 original size:13 final size:13
Alignment explanation
Indices: 2283512--2283564 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2283502 TTTAAATTAA
*
2283512 ACTTTTCAAAAAT
1 ACTTTTCAAAAAC
*
2283525 ACTTCTT-AAAAGC
1 ACTT-TTCAAAAAC
* *
2283538 ACTTTTCTATAAC
1 ACTTTTCAAAAAC
2283551 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
2283564 A
1 A
2283565 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:2287075 original size:38 final size:39
Alignment explanation
Indices: 2287029--2287105 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
2287019 GGTGATTAAG
* *
2287029 ATGAATGTATTTAG-GAAGTAGTCAT-TTAATTAAGATGT
1 ATGAATGTA-TTAGACAAATAGTCATGTTAATTAAGATGT
2287067 ATGAATGTATTAGACCAAATAGTCATGTTAATTAAGATG
1 ATGAATGTATTAGA-CAAATAGTCATGTTAATTAAGATG
2287106 CATGTTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 4 0.12
38 9 0.26
39 9 0.26
40 12 0.35
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (39 bp):
ATGAATGTATTAGACAAATAGTCATGTTAATTAAGATGT
Found at i:2289640 original size:24 final size:24
Alignment explanation
Indices: 2289613--2289675 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 24
2289603 CAACTCAAAA
* *
2289613 GAGCGTCCTATTATTAGCTCTCAG
1 GAGCATCCTATTATTAGCTCTCAC
*
2289637 GAGCATCC-ATTTATTTGGCTCTCAC
1 GAGCATCCTA-TTA-TTAGCTCTCAC
* *
2289662 GAGCTTCCTGTTAT
1 GAGCATCCTATTAT
2289676 ATGGTTCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.03
24 11 0.35
25 19 0.61
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
GAGCATCCTATTATTAGCTCTCAC
Found at i:2289675 original size:25 final size:25
Alignment explanation
Indices: 2289629--2289699 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
2289619 CCTATTATTA
* * *
2289629 GCTCTCAGGAGCATCCAT-TTATTTG
1 GCTCTCACGAGCTTCC-TGTTATATG
2289654 GCTCTCACGAGCTTCCTGTTATATG
1 GCTCTCACGAGCTTCCTGTTATATG
* ** *
2289679 GTTCTTGCGAGCTTCCCGTTA
1 GCTCTCACGAGCTTCCTGTTA
2289700 ATAACTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (25 bp):
GCTCTCACGAGCTTCCTGTTATATG
Found at i:2289939 original size:25 final size:24
Alignment explanation
Indices: 2289910--2289983 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
2289900 CTCGCTTGAA
2289910 CTTCCCGATTACAGCTCTTATGAG
1 CTTCCCGATTACAGCTCTTATGAG
* * *
2289934 CTTTCCAATATACAGCTC-AATTGAG
1 CTTCCCGAT-TACAGCTCTTA-TGAG
*
2289959 CTTCCCG-TTATATGCTCTTATGAG
1 CTTCCCGATTACA-GCTCTTATGAG
2289983 C
1 C
2289984 ATTCTTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.08
24 18 0.46
25 18 0.46
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (24 bp):
CTTCCCGATTACAGCTCTTATGAG
Found at i:2290788 original size:21 final size:22
Alignment explanation
Indices: 2290748--2290790 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2290738 TTAAGGCTTG
2290748 ATATTGGTTTGAATTGAATGTGAT
1 ATATTGGTTTG-A-TGAATGTGAT
2290772 ATATTGGTTTG-TGAATGTG
1 ATATTGGTTTGATGAATGTG
2290791 TTAAAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (22 bp):
ATATTGGTTTGATGAATGTGAT
Found at i:2292974 original size:24 final size:23
Alignment explanation
Indices: 2292941--2292998 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2292931 AGTTGAAAAG
2292941 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
2292965 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
2292987 TATATATAATAA
1 TATA-ATAATAA
2292999 TGCTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:2293351 original size:49 final size:48
Alignment explanation
Indices: 2293269--2293426 Score: 264
Period size: 49 Copynumber: 3.2 Consensus size: 48
2293259 CTTACTTTGA
*
2293269 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
2293316 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
*
2293365 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCAGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
2293414 GAATGTGATAAGT
1 GAATGTGA-AAGT
2293427 CCCGAAGGGC
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
47 13 0.12
49 88 0.84
50 4 0.04
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:2293599 original size:37 final size:37
Alignment explanation
Indices: 2293543--2293621 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2293533 CCGAGCTCTA
* * *
2293543 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
2293580 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
2293617 AAGAC
1 AAGAC
2293622 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:2299782 original size:18 final size:18
Alignment explanation
Indices: 2299761--2299822 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2299751 ATATATAGAT
2299761 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
2299779 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
2299798 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
2299813 ATA-ATAATAA
1 ATATATAATAA
2299823 TAATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:2299813 original size:35 final size:33
Alignment explanation
Indices: 2299758--2299822 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
2299748 GAGATATATA
2299758 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
2299793 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
2299823 TAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:2301674 original size:43 final size:43
Alignment explanation
Indices: 2301618--2301728 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 43
2301608 AATCCGCTCT
* * * *
2301618 ACTGTAACTTCAGGGAGATAGGATA-GTGTCTTCGATCTGATCC
1 ACTGTAAC-TCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
* *
2301661 GCTGTAATCTCAGGGAGATAAGATATCTGGCTTCAATCTGCTCC
1 ACTGTAA-CTCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
2301705 ACTGTAACCTCAGGGAGATAAGAT
1 ACTGTAA-CTCAGGGAGATAAGAT
2301729 CTGAAATTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 21 0.36
44 37 0.64
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
ACTGTAACTCAGGGAGATAAGATATCTGGCTTCAATCTGATCC
Found at i:2301764 original size:46 final size:45
Alignment explanation
Indices: 2301697--2301943 Score: 187
Period size: 46 Copynumber: 5.7 Consensus size: 45
2301687 CTGGCTTCAA
* *
2301697 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGG
* * * *
2301743 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGTGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGG
* * * **
2301784 TCTTTTCTACTGTAA-CTTCAGAGAGATAAGATC------CTTTAA
1 TCTGTTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTTGG
* * * * * * *
2301823 TCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGG
* *
2301867 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGG
2301913 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
2301944 CCTGTATAAT
Statistics
Matches: 159, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
39 25 0.16
40 2 0.01
41 30 0.19
44 33 0.21
45 1 0.01
46 66 0.42
47 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
TCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGG
Found at i:2312435 original size:21 final size:21
Alignment explanation
Indices: 2312393--2312435 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2312383 TTCACTATAC
*
2312393 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
2312414 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
2312435 A
1 A
2312436 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:2341974 original size:24 final size:24
Alignment explanation
Indices: 2341950--2342030 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
2341940 TTTTTATATT
*
2341950 ATTATTTATATAAATATATAAATTA
1 ATTATATATATAAATAT-TAAATTA
* *
2341975 ATTATAAAGTAT-ATTATTAAATTA
1 ATTATATA-TATAAATATTAAATTA
*
2341999 ATTATAT-TATAAATATTATATT-
1 ATTATATATATAAATATTAAATTA
2342021 ATTATATATA
1 ATTATATATA
2342031 AAAGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 10 0.21
26 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATATATATAAATATTAAATTA
Found at i:2341982 original size:11 final size:11
Alignment explanation
Indices: 2341966--2342004 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2341956 TATATAAATA
2341966 TATAAATTAAT
1 TATAAATTAAT
*
2341977 TATAAAGTATAT
1 TATAAATTA-AT
2341989 TATTAAATTAAT
1 TA-TAAATTAAT
2342001 TATA
1 TATA
2342005 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:2342006 original size:17 final size:15
Alignment explanation
Indices: 2341949--2342029 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 15
2341939 ATTTTTATAT
2341949 TATTAT-TTATATAAA
1 TATTATATTAT-TAAA
*
2341964 TATATAAATTAATTATAA
1 TAT-TATATT-ATTA-AA
*
2341982 -AGTATATTATTAAA
1 TATTATATTATTAAA
2341996 TTAATTATATTA-TAAA
1 -T-ATTATATTATTAAA
*
2342012 TATTATATTATTATA
1 TATTATATTATTAAA
2342027 TAT
1 TAT
2342030 AAAAGAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 11 0.21
17 13 0.25
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATTATTAAA
Found at i:2342016 original size:14 final size:16
Alignment explanation
Indices: 2341984--2342022 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
2341974 AATTATAAAG
2341984 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
2342001 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
2342015 TATATTAT
1 TATATTAT
2342023 TATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 4 0.18
17 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:2343353 original size:3 final size:3
Alignment explanation
Indices: 2343345--2343380 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2343335 GTGAGGTAAG
2343345 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2343381 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2343563 original size:24 final size:27
Alignment explanation
Indices: 2343531--2343589 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2343521 CGGATTAATT
2343531 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
2343554 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
2343581 ATTGAATTG
1 ATTGAATTG
2343590 GGATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:2343793 original size:37 final size:39
Alignment explanation
Indices: 2343734--2343829 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
2343724 CGGATAGATT
* * * *
2343734 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
2343771 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
2343810 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
2343830 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:2348755 original size:29 final size:32
Alignment explanation
Indices: 2348714--2348786 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
2348704 TAAAAAAAAC
*
2348714 TAAAAATATTAAAATT-TATAATT-T-ATTTTA
1 TAAAAATATT-AAATTATATAATTATAATTATA
*
2348744 TAAAATTA-TAAATTATATAATTATAATTATA
1 TAAAAATATTAAATTATATAATTATAATTATA
2348775 TAAAAA-ATTAAA
1 TAAAAATATTAAA
2348787 AACCATGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.14
29 8 0.22
30 9 0.25
31 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAAAAATATTAAATTATATAATTATAATTATA
Found at i:2351519 original size:16 final size:17
Alignment explanation
Indices: 2351500--2351539 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
2351490 CCTTTTTCTT
2351500 TTCCTT-AATGGGAAAA
1 TTCCTTGAATGGGAAAA
2351516 TTCCTTTGAATGGGAAAA
1 TTCC-TTGAATGGGAAAA
2351534 TTCCTT
1 TTCCTT
2351540 TCACTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (17 bp):
TTCCTTGAATGGGAAAA
Found at i:2351529 original size:18 final size:18
Alignment explanation
Indices: 2351506--2351540 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2351496 TCTTTTCCTT
2351506 AATGGGAAAATTCCTTTG
1 AATGGGAAAATTCCTTTG
2351524 AATGGGAAAATTCCTTT
1 AATGGGAAAATTCCTTT
2351541 CACTTTCTCG
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:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (18 bp):
AATGGGAAAATTCCTTTG
Found at i:2356177 original size:39 final size:39
Alignment explanation
Indices: 2356131--2356209 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2356121 AAATTTTTAC
2356131 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
1 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
2356170 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
1 TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
2356209 T
1 T
2356210 GTTGAGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (39 bp):
TTACAATATACTTAATAATACTTTATGAAAATTCATGTT
Found at i:2357420 original size:21 final size:21
Alignment explanation
Indices: 2357394--2357433 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2357384 CTAGGTTTTG
2357394 GGTTTTTACAAGAAAAAACCT
1 GGTTTTTACAAGAAAAAACCT
**
2357415 GGTTTTTACATTAAAAAAC
1 GGTTTTTACAAGAAAAAAC
2357434 TATTTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
GGTTTTTACAAGAAAAAACCT
Found at i:2364425 original size:44 final size:44
Alignment explanation
Indices: 2364337--2364422 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
2364327 ATAATTTTAA
** *
2364337 ATTAAATTATAATTATTTTTAAATGTGTAATTATCATAATTTCT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCAGAATTTCT
*
2364381 ATTAAATTATAATTATTTTTAAATGTACAATTTTCACGAATT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCA-GAATT
2364423 CTACTTTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (44 bp):
ATTAAATTATAATTATTTTTAAATGTACAATTATCAGAATTTCT
Found at i:2370123 original size:26 final size:24
Alignment explanation
Indices: 2370082--2370149 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 24
2370072 TGTATAAGAG
* *
2370082 TTTTAAAATGTTTAAAAATATTTATT
1 TTTTAAAAT-TTTAAAAATATGTA-A
2370108 TTTATAAAATTTTAAAAATATGTAA
1 TTT-TAAAATTTTAAAAATATGTAA
2370133 TTTT-AAATTTTAAAAAT
1 TTTTAAAATTTTAAAAAT
2370150 TCAAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.33
24 1 0.03
25 3 0.08
26 16 0.41
27 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
TTTTAAAATTTTAAAAATATGTAA
Found at i:2370385 original size:14 final size:14
Alignment explanation
Indices: 2370360--2370402 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
2370350 ACTTAATTCT
2370360 TTTGTA-AATTTTA
1 TTTGTATAATTTTA
2370373 TTTGTATAATTTTA
1 TTTGTATAATTTTA
2370387 -TT-TATAATTTATA
1 TTTGTATAATTT-TA
2370400 TTT
1 TTT
2370403 TTTTCTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.30
13 10 0.37
14 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTGTATAATTTTA
Found at i:2370420 original size:21 final size:22
Alignment explanation
Indices: 2370396--2370449 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
2370386 ATTTATAATT
2370396 TATATTTTTTTCT-AGA-TTTTA
1 TATATTTTTTTCTGA-ATTTTTA
2370417 TATA-TTTTTTCTGAATTTTTA
1 TATATTTTTTTCTGAATTTTTA
2370438 TATATTTATTTT
1 TATATTT-TTTT
2370450 TTTACATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.31
21 14 0.48
22 2 0.07
23 4 0.14
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TATATTTTTTTCTGAATTTTTA
Found at i:2370439 original size:19 final size:19
Alignment explanation
Indices: 2370394--2370440 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2370384 TTATTTATAA
2370394 TTTATATTTTTTTCTAGATT
1 TTTATA-TTTTTTCTAGATT
2370414 TTATATATTTTTTCT-GAATT
1 TT-TATATTTTTTCTAG-ATT
2370434 TTTATAT
1 TTTATAT
2370441 ATTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTATATTTTTTCTAGATT
Found at i:2378398 original size:21 final size:22
Alignment explanation
Indices: 2378372--2378418 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2378362 CTCTGCTCAA
*
2378372 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
2378393 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
2378415 ACTC
1 ACTC
2378419 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:2390556 original size:3 final size:3
Alignment explanation
Indices: 2390548--2390577 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2390538 TCACTACCTG
2390548 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2390578 AATGACTGTT
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2395302 original size:21 final size:22
Alignment explanation
Indices: 2395273--2395319 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2395263 CAGAAGGAGT
*
2395273 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2395295 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2395316 GAGT
1 GAGT
2395320 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:2400032 original size:40 final size:40
Alignment explanation
Indices: 2399960--2400108 Score: 221
Period size: 40 Copynumber: 3.7 Consensus size: 40
2399950 TATTTGGATG
* * *
2399960 ATAACCGGGCTAAAGTCCCGAAGGCATGTGTGCTAGTGACT
1 ATAACCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACT
*
2400001 ATATA-CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
2400041 ATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
2400081 ATAACCGGGCT-AGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
2400109 AGCAAGTAGA
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
39 18 0.18
40 73 0.73
41 8 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:2409857 original size:13 final size:13
Alignment explanation
Indices: 2409839--2409868 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2409829 ATATTATATT
2409839 TATACACTGATAA
1 TATACACTGATAA
2409852 TATACACTGATAA
1 TATACACTGATAA
2409865 TATA
1 TATA
2409869 TAATTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (13 bp):
TATACACTGATAA
Found at i:2417752 original size:5 final size:5
Alignment explanation
Indices: 2417720--2417749 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2417710 AGAGAATTAC
*
2417720 GCTTG GCTTG GCTTG GCTTG GCTTG CCTTG
1 GCTTG GCTTG GCTTG GCTTG GCTTG GCTTG
2417750 CCTAGTGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.37, T:0.40
Consensus pattern (5 bp):
GCTTG
Found at i:2419225 original size:22 final size:22
Alignment explanation
Indices: 2419173--2419226 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2419163 TGAAATTATT
*
2419173 AATTAAAATATAATAACTATTA
1 AATTAAAATATAATAACTATAA
* * *
2419195 ATTTTAAATATAATTA-TATAAA
1 AATTAAAATATAATAACTAT-AA
2419217 AATTAAAATA
1 AATTAAAATA
2419227 GTTAACCACA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAAAATATAATAACTATAA
Found at i:2419487 original size:25 final size:26
Alignment explanation
Indices: 2419459--2419512 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
2419449 GGCAAACAAT
*
2419459 TTTTTATATTTAATATCTTTAAA-TA
1 TTTTTAAATTTAATATCTTTAAACTA
*
2419484 TTTTTAAATTTAATTTCTTTAAACTA
1 TTTTTAAATTTAATATCTTTAAACTA
2419510 TTT
1 TTT
2419513 AAATCAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTAAATTTAATATCTTTAAACTA
Found at i:2432437 original size:15 final size:15
Alignment explanation
Indices: 2432399--2432441 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2432389 TTAAGGTAAG
*
2432399 TAATTAAAATAT-TA
1 TAATTAAAATATAAA
* *
2432413 TATTTTAAATATAAA
1 TAATTAAAATATAAA
2432428 TAATTAAAATATAA
1 TAATTAAAATATAA
2432442 TATGAGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTAAAATATAAA
Done.