Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 35 of 106
Found at i:6537066 original size:26 final size:26
Alignment explanation
Indices: 6537036--6537091 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
6537026 AGGAAAGAAG
6537036 AATAAAAACAAAATAATAATAATAAT
1 AATAAAAACAAAATAATAATAATAAT
* ** * *
6537062 AATAATAGTAATATAATAATAATGAT
1 AATAAAAACAAAATAATAATAATAAT
6537088 AATA
1 AATA
6537092 GTAATATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
AATAAAAACAAAATAATAATAATAAT
Found at i:6537077 original size:23 final size:20
Alignment explanation
Indices: 6537051--6537204 Score: 123
Period size: 21 Copynumber: 7.3 Consensus size: 20
6537041 AAACAAAATA
6537051 ATAATAATAATAATAATAGTAAT
1 ATAAT-ATAAT-ATAATA-TAAT
6537074 ATAATAATAATGATAATAGTAAT
1 ATAAT-ATAAT-ATAATA-TAAT
*
6537097 ATAATATACTAT-A-ATAAT
1 ATAATATAATATAATATAAT
* * *
6537115 ATAACATCATATACTATAAT
1 ATAATATAATATAATATAAT
*
6537135 ATAATAATAATATAGTATAAT
1 ATAAT-ATAATATAATATAAT
* *
6537156 GGTAATATAGTAATAATATAAT
1 -ATAATATAAT-ATAATATAAT
**
6537178 ATAATATGCTATAATAATAAT
1 ATAATATAATATAAT-ATAAT
6537199 ATAATA
1 ATAATA
6537205 ATAGTATAGT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
18 13 0.12
19 1 0.01
20 15 0.14
21 37 0.34
22 17 0.15
23 27 0.25
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
ATAATATAATATAATATAAT
Found at i:6537143 original size:8 final size:8
Alignment explanation
Indices: 6537048--6537207 Score: 73
Period size: 8 Copynumber: 19.1 Consensus size: 8
6537038 TAAAAACAAA
6537048 ATAATAAT
1 ATAATAAT
6537056 AATAATAAT
1 -ATAATAAT
*
6537065 AATAGTAAT
1 -ATAATAAT
6537074 ATAATAAT
1 ATAATAAT
*
6537082 AATGATAAT
1 -ATAATAAT
6537091 AGTAAT-AT
1 A-TAATAAT
*
6537099 A-ATATACT
1 ATA-ATAAT
6537107 ATAATAAT
1 ATAATAAT
*
6537115 ATAA-CAT
1 ATAATAAT
*
6537122 CAT-ATACT
1 -ATAATAAT
6537130 ATAAT-AT
1 ATAATAAT
6537137 AATAATAAT
1 -ATAATAAT
6537146 ATAGTATAAT
1 ATA--ATAAT
*
6537156 GGTAAT-AT
1 -ATAATAAT
6537164 AGTAATAAT
1 A-TAATAAT
6537173 ATAATATAAT
1 AT-A-ATAAT
**
6537183 ATGCT-AT
1 ATAATAAT
6537190 AATAATAAT
1 -ATAATAAT
6537199 ATAATAAT
1 ATAATAAT
6537207 A
1 A
6537208 GTATAGTAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 39
0.68 0.09 0.23
Matches are distributed among these distances:
6 1 0.01
7 10 0.09
8 54 0.47
9 37 0.32
10 12 0.10
11 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:6537169 original size:27 final size:27
Alignment explanation
Indices: 6537052--6537204 Score: 79
Period size: 26 Copynumber: 5.8 Consensus size: 27
6537042 AACAAAATAA
**
6537052 TAATAATAATAATAATAGTAATATAATAA
1 TAAT-ATAATAATAATA-TAATATAATGG
* **
6537081 TAATGATAATAGTAATATAATATACTATAA
1 TAAT-ATAATAATAATATAATATA--ATGG
* * * *
6537111 TAATATAA-CATCATATACTATAAT-A
1 TAATATAATAATAATATAATATAATGG
*
6537136 T-A-ATAATAAT-A--TAGTATAATGG
1 TAATATAATAATAATATAATATAATGG
* *
6537158 TAATATAGTAATAATATAATATAAT-A
1 TAATATAATAATAATATAATATAATGG
**
6537184 TGCTATAATAATAATATAATA
1 TAATATAATAATAATATAATA
6537205 ATAGTATAGT
Statistics
Matches: 100, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
21 8 0.08
22 1 0.01
23 6 0.06
24 10 0.10
25 3 0.03
26 20 0.20
27 8 0.08
28 17 0.17
29 19 0.19
30 8 0.08
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
TAATATAATAATAATATAATATAATGG
Found at i:6537824 original size:28 final size:29
Alignment explanation
Indices: 6537782--6537839 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
6537772 GCTTGACTTG
6537782 ATCGATCTCCTAATGTACTAAATCGATCC
1 ATCGATCTCCTAATGTACTAAATCGATCC
6537811 ATCGATC-CCTAATGTACTAAATCGATCC
1 ATCGATCTCCTAATGTACTAAATCGATCC
6537839 A
1 A
6537840 ATCTATTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (29 bp):
ATCGATCTCCTAATGTACTAAATCGATCC
Found at i:6544169 original size:23 final size:23
Alignment explanation
Indices: 6544120--6544167 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6544110 AGGGAGAGAA
*
6544120 TTTGTGAATATTTGCTAATGGCT
1 TTTGTGAATATTTGCTAATGCCT
*
6544143 TTTGTGAATATTTG-TTATGCCT
1 TTTGTGAATATTTGCTAATGCCT
6544165 TTT
1 TTT
6544168 TGCTATGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (23 bp):
TTTGTGAATATTTGCTAATGCCT
Found at i:6546643 original size:38 final size:37
Alignment explanation
Indices: 6546568--6546643 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
6546558 ATTTTAAATT
* ** *
6546568 TTAATTTTTTAAAATATTCAAAATTTATTCATTTTAA
1 TTAAATTTTTAAAATATTCAAAAAATATTCATGTTAA
6546605 TTAAATTTTT-AAATATTCAATAAAATATGTCATGTTAA
1 TTAAATTTTTAAAATATTCAA-AAAATAT-TCATGTTAA
6546643 T
1 T
6546644 GTCATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 10 0.30
37 14 0.42
38 9 0.27
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (37 bp):
TTAAATTTTTAAAATATTCAAAAAATATTCATGTTAA
Found at i:6549538 original size:101 final size:101
Alignment explanation
Indices: 6549322--6549744 Score: 353
Period size: 103 Copynumber: 4.1 Consensus size: 101
6549312 TAAGGTCATA
* * * * * * *
6549322 AAAATAATATTATTACAAAAAAGGTTTTTGTAACCAAATTTT-TGGTTGTTAAAATGCAATTAAA
1 AAAATAATATTGTTACATAAGA-GTTTTTATAACCAAATTTTATAGTTGCTAAAATGAAATTAAA
* *
6549386 ATGATGACATTTAAT-TGTTACAAAATATTTTATGTAA-T
65 A--ATGACATTTAATCT-TTACAAAATATGTTATATAACT
6549424 CAAAATAATATTGTTACAAATAA-AGTTTTTATAACCAAATTTTATAGTTGCTAAAATGAAATT-
1 -AAAATAATATTGTTAC--ATAAGAGTTTTTATAACCAAATTTTATAGTTGCTAAAATGAAATTA
*
6549487 AAAATGACATTTAATCTTTTCAAAATATGTTATATAACT
63 AAAATGACATTTAATCTTTACAAAATATGTTATATAACT
* * * * *
6549526 AAAATAATATTGTTACTTAAGAGTTTTTATAA-TAAACTTTTATGGTTGCTAAAAAGCAATTTAA
1 AAAATAATATTGTTACATAAGAGTTTTTATAACCAAA-TTTTATAGTTGCTAAAATG-AAATTAA
** * *
6549590 CAAACAATATTTAATCATTACAAAATATGTTATATAAC-
64 -AAATGACATTTAATCTTTACAAAATATGTTATATAACT
* * * * * * * *
6549628 AACAATCATATGGTTACGTAAGAGTATTTGTAACCAAATTCTATAGTTGCTGAAA--AAGTTAAA
1 AA-AATAATATTGTTACATAAGAGTTTTTATAACCAAATTTTATAGTTGCTAAAATGAAATT-AA
* * * * * *
6549691 ACAATGTCGTGTT-ATCATTACAAAATATTTTATGTAACA
64 A-AATGACAT-TTAATCTTTACAAAATATGTTATATAACT
6549730 AAAATAATATTGTTA
1 AAAATAATATTGTTA
6549745 TGTCATAGTT
Statistics
Matches: 266, Mismatches: 38, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
99 6 0.02
100 33 0.12
101 88 0.33
102 9 0.03
103 107 0.40
104 20 0.08
105 3 0.01
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (101 bp):
AAAATAATATTGTTACATAAGAGTTTTTATAACCAAATTTTATAGTTGCTAAAATGAAATTAAAA
ATGACATTTAATCTTTACAAAATATGTTATATAACT
Found at i:6551703 original size:24 final size:24
Alignment explanation
Indices: 6551673--6551721 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6551663 ATGGCTCTAG
* *
6551673 TATATTATATTATTAAATTTATTA
1 TATATTATATTAATAAAATTATTA
*
6551697 TATATTATTTTAATAAAATTATTA
1 TATATTATATTAATAAAATTATTA
6551721 T
1 T
6551722 TTGATATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTATATTAATAAAATTATTA
Found at i:6553760 original size:22 final size:23
Alignment explanation
Indices: 6553704--6553762 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
6553694 TTTATGAGCA
**
6553704 AATAAGTTTAGTGTTGTAATTTT
1 AATAAGTTTAGTGTTGTAATGCT
*
6553727 AGTATAATTTTAGTGTTGTAA-GCT
1 A--ATAAGTTTAGTGTTGTAATGCT
6553751 AATAAGTTTAGT
1 AATAAGTTTAGT
6553763 ACAACTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.33
23 1 0.03
24 2 0.07
25 17 0.57
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (23 bp):
AATAAGTTTAGTGTTGTAATGCT
Found at i:6558430 original size:2 final size:2
Alignment explanation
Indices: 6558423--6558455 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6558413 CTTTCATTAA
6558423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6558456 AGAAGTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6565090 original size:23 final size:25
Alignment explanation
Indices: 6565045--6565093 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
6565035 TAAAATAAAA
**
6565045 TTTTTTCTTTTTTTTTTTCTTGTTC
1 TTTTTTCTTTTTTAATTTCTTGTTC
6565070 TTTTTT-TTTTTTAATTT-TTGTTC
1 TTTTTTCTTTTTTAATTTCTTGTTC
6565093 T
1 T
6565094 CACTTTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 9 0.41
25 6 0.27
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.84
Consensus pattern (25 bp):
TTTTTTCTTTTTTAATTTCTTGTTC
Found at i:6565875 original size:22 final size:22
Alignment explanation
Indices: 6565811--6565875 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 22
6565801 AAGGATGATG
*
6565811 TTTCTAAGATAAAAATGCAGT-
1 TTTCTAAGATAAAAATGCAATA
* *
6565832 CTTCGTTA-A-AAAAATG-AA-A
1 TTTC-TAAGATAAAAATGCAATA
6565851 TTTCTAAGATAAAAATGCAATA
1 TTTCTAAGATAAAAATGCAATA
6565873 TTT
1 TTT
6565876 ATTGGAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 11
0.67 0.10 0.22
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 14 0.42
21 6 0.18
22 6 0.18
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (22 bp):
TTTCTAAGATAAAAATGCAATA
Found at i:6565982 original size:40 final size:40
Alignment explanation
Indices: 6565929--6566022 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
6565919 GAAAACATAG
*
6565929 TCTTTGTTGAAAAGAGAATGTTTTTACA-AAAAAAATACAA
1 TCTTTGTTGAAAAGAGAATGTTTCTA-AGAAAAAAATACAA
* * * *
6565969 TCTTTGTTGAAAAGATAGTGTTTCTAAGATAAAAATACAG
1 TCTTTGTTGAAAAGAGAATGTTTCTAAGAAAAAAATACAA
*
6566009 TCTTTATTGAAAAG
1 TCTTTGTTGAAAAG
6566023 CCAACATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (40 bp):
TCTTTGTTGAAAAGAGAATGTTTCTAAGAAAAAAATACAA
Found at i:6566402 original size:26 final size:26
Alignment explanation
Indices: 6566364--6566416 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6566354 AGATTAAGCC
*
6566364 TTAAATTTTATTTGTAT-TTTAATTTT
1 TTAAATTTAATTT-TATGTTTAATTTT
* *
6566390 TTAAGTTTAATTTTCTGTTTAATTTT
1 TTAAATTTAATTTTATGTTTAATTTT
6566416 T
1 T
6566417 GCTTTTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (26 bp):
TTAAATTTAATTTTATGTTTAATTTT
Found at i:6567097 original size:21 final size:21
Alignment explanation
Indices: 6567071--6567166 Score: 70
Period size: 20 Copynumber: 4.5 Consensus size: 21
6567061 TTTATTTGCC
6567071 TAATATATTTGTTTGCATGAT
1 TAATATATTTGTTTGCATGAT
* * *
6567092 TAATATATTTATTTGTGTTATTTAT
1 TAATATATTT-GTT-TG-CA-TGAT
* ** *
6567117 TAATACATTTGCATG-ATTAT
1 TAATATATTTGTTTGCATGAT
*
6567137 TAATATATTTATTTGCATGAT
1 TAATATATTTGTTTGCATGAT
6567158 T-ATATATTT
1 TAATATATTT
6567167 AATTGCATAT
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
20 23 0.40
21 16 0.28
22 2 0.03
23 4 0.07
24 1 0.02
25 12 0.21
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.55
Consensus pattern (21 bp):
TAATATATTTGTTTGCATGAT
Found at i:6567162 original size:20 final size:21
Alignment explanation
Indices: 6567071--6567174 Score: 86
Period size: 21 Copynumber: 4.9 Consensus size: 21
6567061 TTTATTTGCC
*
6567071 TAATATATTTGTTTGCATGAT
1 TAATATATTTATTTGCATGAT
** *
6567092 TAATATATTTATTTGTGTTAT
1 TAATATATTTATTTGCATGAT
* **
6567113 TTAT-TAATACATTTGCATGATTAT
1 TAATAT-ATTTATTTGCATG---AT
6567137 TAATATATTTATTTGCATGAT
1 TAATATATTTATTTGCATGAT
*
6567158 T-ATATATTTAATTGCAT
1 TAATATATTTATTTGCAT
6567175 ATTTATTTGC
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
20 16 0.25
21 31 0.48
24 16 0.25
25 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (21 bp):
TAATATATTTATTTGCATGAT
Found at i:6567180 original size:20 final size:20
Alignment explanation
Indices: 6567134--6567180 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6567124 TTTGCATGAT
* *
6567134 TATTAATATATTTATTTGCA
1 TATTTATATATTTAATTGCA
6567154 TGA-TTATATATTTAATTGCA
1 T-ATTTATATATTTAATTGCA
6567174 TATTTAT
1 TATTTAT
6567181 TTGCATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (20 bp):
TATTTATATATTTAATTGCA
Found at i:6567217 original size:55 final size:55
Alignment explanation
Indices: 6567123--6567380 Score: 304
Period size: 55 Copynumber: 4.6 Consensus size: 55
6567113 TTATTAATAC
*
6567123 ATTTGCATGATTATTA-ATATATTTATTTGCATGATTATATATTTAATTGCATATTT
1 ATTTGCATGATTAATATAT-TA-TTATTTGCATGATTATATATTTAATTGCATATTT
* * *
6567179 ATTTGCATGATTAATACATTACTATCTGCATGATTATATATTTAATTGCATATTT
1 ATTTGCATGATTAATATATTATTATTTGCATGATTATATATTTAATTGCATATTT
* * * * * *
6567234 ATTTGCATGGTTTATATATTTTTATTTGTATGACTATATATTTAATTGCATGTTT
1 ATTTGCATGATTAATATATTATTATTTGCATGATTATATATTTAATTGCATATTT
* * * *
6567289 ATTTGCATGATTATTAATATTATTATTAGCATGATTATATATTTGATTGCATGTTT
1 ATTTGCATGATTAAT-ATATTATTATTTGCATGATTATATATTTAATTGCATATTT
* * *
6567345 AATTGCATGATTATTA-ATTTATTTATTTGTATGATT
1 ATTTGCATGATTAATATA-TTA-TTATTTGCATGATT
6567381 GCTTGATTAT
Statistics
Matches: 175, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
54 1 0.01
55 94 0.54
56 78 0.45
57 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (55 bp):
ATTTGCATGATTAATATATTATTATTTGCATGATTATATATTTAATTGCATATTT
Found at i:6567382 original size:32 final size:32
Alignment explanation
Indices: 6567346--6567412 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
6567336 TGCATGTTTA
*
6567346 ATTGCATGATTATTAAT-TTATTTATTTGTATG
1 ATTGCATGATTATTAATATTATTTA-TTGCATG
* *
6567378 ATTGCTTGATTATTAATATTTTTTATTGCATG
1 ATTGCATGATTATTAATATTATTTATTGCATG
6567410 ATT
1 ATT
6567413 ATATATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (32 bp):
ATTGCATGATTATTAATATTATTTATTGCATG
Found at i:6567425 original size:20 final size:20
Alignment explanation
Indices: 6567402--6567465 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
6567392 AATATTTTTT
6567402 ATTGCATGATTATATATTTA
1 ATTGCATGATTATATATTTA
6567422 ATTGCATG------T--TTA
1 ATTGCATGATTATATATTTA
6567434 ATT-CATGATTATATATTTA
1 ATTGCATGATTATATATTTA
6567453 ATTGCATGATTAT
1 ATTGCATGATTAT
6567466 TAATTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 18
0.66 0.00 0.34
Matches are distributed among these distances:
11 4 0.11
12 6 0.17
14 1 0.03
17 1 0.03
19 6 0.17
20 17 0.49
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTGCATGATTATATATTTA
Found at i:6567550 original size:24 final size:25
Alignment explanation
Indices: 6567510--6567556 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
6567500 ATATATTTAT
*
6567510 TTGCATAGTTATTTA-TTATTATTA
1 TTGCATAATTATTTATTTATTATTA
6567534 TTGCATAATT-TTATATTTATTAT
1 TTGCATAATTATT-TATTTATTAT
6567557 ATAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 11 0.55
25 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (25 bp):
TTGCATAATTATTTATTTATTATTA
Found at i:6567699 original size:18 final size:19
Alignment explanation
Indices: 6567671--6567744 Score: 75
Period size: 18 Copynumber: 4.0 Consensus size: 19
6567661 ATTACATAAT
6567671 TATTAATATATTTGCATGA
1 TATTAATATATTTGCATGA
*
6567690 TATT-ATATATTTACATGA
1 TATTAATATATTTGCATGA
*
6567708 T-TGTTAT-TA-TTGCATGA
1 TAT-TAATATATTTGCATGA
*
6567725 TAATTAATATATTTGTATGA
1 T-ATTAATATATTTGCATGA
6567745 CATTCTTGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
17 9 0.20
18 20 0.44
19 9 0.20
20 7 0.16
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (19 bp):
TATTAATATATTTGCATGA
Found at i:6567704 original size:38 final size:36
Alignment explanation
Indices: 6567639--6567738 Score: 98
Period size: 38 Copynumber: 2.7 Consensus size: 36
6567629 TTATTGTGTG
* *
6567639 TATA-ATTGCATGAT-TATATTTAATTACATAATTAT
1 TATATATTGCATGATAT-TATATATTTACATAATTAT
* *
6567674 TAATATATTTGCATGATATTATATATTTACATGATTGT
1 T-ATATA-TTGCATGATATTATATATTTACATAATTAT
6567712 TAT-TATTGCATGATAATTAATATATTT
1 TATATATTGCATGAT-ATT-ATATATTT
6567739 GTATGACATT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
35 10 0.18
36 8 0.15
37 11 0.20
38 25 0.45
39 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (36 bp):
TATATATTGCATGATATTATATATTTACATAATTAT
Found at i:6578880 original size:12 final size:12
Alignment explanation
Indices: 6578855--6578886 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6578845 ATAGATCTTT
6578855 TTACTGGT--GA
1 TTACTGGTGAGA
6578865 TTACTGGTGAGA
1 TTACTGGTGAGA
6578877 TTACTGGTGA
1 TTACTGGTGA
6578887 TCAACTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (12 bp):
TTACTGGTGAGA
Found at i:6580596 original size:22 final size:21
Alignment explanation
Indices: 6580551--6580603 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
6580541 GTGTATGATT
* *
6580551 ATATTTGAAATGTTATAATGC
1 ATATTTAAAATGTTATAATAC
*
6580572 ATATTTAAAATAGTTATATTAC
1 ATATTTAAAAT-GTTATAATAC
*
6580594 ATACTTAAAA
1 ATATTTAAAA
6580604 AAAAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (21 bp):
ATATTTAAAATGTTATAATAC
Found at i:6584091 original size:22 final size:22
Alignment explanation
Indices: 6584032--6584102 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
6584022 GTTATCAGTA
*
6584032 ATTTACTA-TGAATTTATAAATA
1 ATTTACTATTGAA-TTATAAATG
* *
6584054 ATTTACCATTGAATTATGAATG
1 ATTTACTATTGAATTATAAATG
* *
6584076 GTTTACTATTGAATTATTAATG
1 ATTTACTATTGAATTATAAATG
6584098 ATTTA
1 ATTTA
6584103 TTACTAAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 37 0.90
23 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (22 bp):
ATTTACTATTGAATTATAAATG
Found at i:6584904 original size:22 final size:22
Alignment explanation
Indices: 6584683--6585016 Score: 108
Period size: 22 Copynumber: 15.3 Consensus size: 22
6584673 AGATTAACTA
* *
6584683 ATTTATTACTAAATTATCACTA
1 ATTTACTACTAAATTATCACTG
* * *
6584705 ATCTA-TAACTAAATTATCAATT
1 ATTTACT-ACTAAATTATCACTG
** * * *
6584727 ATTTAAAACTAAGTTATTAATG
1 ATTTACTACTAAATTATCACTG
* * ** * *
6584749 ATATACTATTATGTTATTAGTG
1 ATTTACTACTAAATTATCACTG
* * *
6584771 ATTTATTACTAAATTACCAATG
1 ATTTACTACTAAATTATCACTG
* * * * *
6584793 ATTTATTATTATACTATTA-TG
1 ATTTACTACTAAATTATCACTG
* ** *
6584814 CA-TTACTATTATGTTATCATTG
1 -ATTTACTACTAAATTATCACTG
* * * * *
6584836 ATTTACTACTTAGTCATCAATT
1 ATTTACTACTAAATTATCACTG
* * **
6584858 ATTTACTACAAAATTATTAAAG
1 ATTTACTACTAAATTATCACTG
*
6584880 ATTTATTACTAAATTATC-CATG
1 ATTTACTACTAAATTATCAC-TG
* * *
6584902 ATTCACTACCAAATTATCACTC
1 ATTTACTACTAAATTATCACTG
* *
6584924 ATTTA-TATTAAATTATCTA-TA
1 ATTTACTACTAAATTATC-ACTG
* *
6584945 ATTTACTATTAAATTATCATTG
1 ATTTACTACTAAATTATCACTG
* * * *
6584967 ATTTACTATTAAGTTATTAATG
1 ATTTACTACTAAATTATCACTG
* *
6584989 GTTTACTAC-AAAGTTAT-ATTG
1 ATTTACTACTAAA-TTATCACTG
6585010 ATTTACT
1 ATTTACT
6585017 TTCAAGTTTC
Statistics
Matches: 235, Mismatches: 66, Indels: 23
0.73 0.20 0.07
Matches are distributed among these distances:
21 45 0.19
22 189 0.80
23 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTACTACTAAATTATCACTG
Found at i:6584959 original size:43 final size:44
Alignment explanation
Indices: 6584880--6584983 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 44
6584870 ATTATTAAAG
* * *
6584880 ATTTATTACTAAATTATCCATGATTCACTACCAAATTATCACTC
1 ATTTACTATTAAATTATCCATAATTCACTACCAAATTATCACTC
* * ** * *
6584924 ATTTA-TATTAAATTATCTATAATTTACTATTAAATTATCATTG
1 ATTTACTATTAAATTATCCATAATTCACTACCAAATTATCACTC
*
6584967 ATTTACTATTAAGTTAT
1 ATTTACTATTAAATTAT
6584984 TAATGGTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 35 0.70
44 15 0.30
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (44 bp):
ATTTACTATTAAATTATCCATAATTCACTACCAAATTATCACTC
Found at i:6585011 original size:43 final size:44
Alignment explanation
Indices: 6584906--6585109 Score: 163
Period size: 44 Copynumber: 4.7 Consensus size: 44
6584896 TCCATGATTC
* * * * * *
6584906 ACTACCAAATTATCACTCATTTA-TATTAAATTATCT-ATAATTT
1 ACTACTAAATTATCATTGATTTACTATTAAGTTAT-TAATAGTTA
* * *
6584949 ACTATTAAATTATCATTGATTTACTATTAAGTTATTAATGGTTT
1 ACTACTAAATTATCATTGATTTACTATTAAGTTATTAATAGTTA
*
6584993 ACTAC-AAAGTTAT-ATTGATTTACT-TTCAAGTT-TCCAATAGTTA
1 ACTACTAAA-TTATCATTGATTTACTATT-AAGTTAT-TAATAGTTA
* * *
6585036 ACTACTAAATTTTCATTGATTTACTATTAAGTTATTTATAATT-
1 ACTACTAAATTATCATTGATTTACTATTAAGTTATTAATAGTTA
* *
6585079 TCTACTAAATTTATCAATT-AATTACTATTAA
1 ACTACTAAA-TTATC-ATTGATTTACTATTAA
6585110 ACTAAAACTA
Statistics
Matches: 132, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
42 3 0.02
43 61 0.46
44 62 0.47
45 6 0.05
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (44 bp):
ACTACTAAATTATCATTGATTTACTATTAAGTTATTAATAGTTA
Found at i:6585456 original size:22 final size:22
Alignment explanation
Indices: 6585428--6586104 Score: 287
Period size: 22 Copynumber: 31.3 Consensus size: 22
6585418 GAATAAAAGC
* *
6585428 ATTATCAATGATTAACAATTAA
1 ATTATCAATGATTTACTATTAA
*
6585450 ATTATCAATGATTTACTATTAT
1 ATTATCAATGATTTACTATTAA
* * *
6585472 TTTATCAATAATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
* * *
6585494 ACTACCAATGATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
*
6585516 ATTATCATTGATTTACTATTAA
1 ATTATCAATGATTTACTATTAA
* * *
6585538 ATTATGAGTGATTTACCA-T--
1 ATTATCAATGATTTACTATTAA
* * *
6585557 -TTATAAATAATTTACCATTAA
1 ATTATCAATGATTTACTATTAA
*** *
6585578 ATTATTGGTGATTTACAATTAA
1 ATTATCAATGATTTACTATTAA
* ** * *
6585600 GTTATTGATAATTTATTA-TAA
1 ATTATCAATGATTTACTATTAA
* *
6585621 AGTTAT-AATTGATGTACTACTAA
1 A-TTATCAA-TGATTTACTATTAA
* * *
6585644 ATTATCACTAATTTACAACTT-A
1 ATTATCAATGATTTACTA-TTAA
* * * * *
6585666 GTTATTAGTAATTTACTATTAT
1 ATTATCAATGATTTACTATTAA
* * * *
6585688 ATTATTAGTGATTTATTACTAA
1 ATTATCAATGATTTACTATTAA
* * *
6585710 GTTATCAATAATTTATTATTAA
1 ATTATCAATGATTTACTATTAA
* *
6585732 ATTATTAATGATTTACTATTAT
1 ATTATCAATGATTTACTATTAA
* * * *
6585754 AGTAT-TATGTATTTACTACTAT
1 ATTATCAATG-ATTTACTATTAA
* *
6585776 TTTATCATTGATTTACTACTT-A
1 ATTATCAATGATTTACTA-TTAA
* * * *
6585798 ATTTTCAATTATTTAGTA-CAA
1 ATTATCAATGATTTACTATTAA
*** *
6585819 ATTATCACCAATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
* * **
6585841 ATTTTTC-ATAATTTACTACCAA
1 A-TTATCAATGATTTACTATTAA
*
6585863 ATTATCACTGATTTA-TATTAA
1 ATTATCAATGATTTACTATTAA
*
6585884 ATTAT-ATATTATTTACTATTAA
1 ATTATCA-ATGATTTACTATTAA
* * *
6585906 GTTATTAATGAATTACTATTAA
1 ATTATCAATGATTTACTATTAA
* * * * *
6585928 GTTAT-ACTAATTTGCTTTTAA
1 ATTATCAATGATTTACTATTAA
* * * * *
6585949 GTTTTTAATGATTAACTACTAA
1 ATTATCAATGATTTACTATTAA
* * *
6585971 ATTATCAGTTATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
* *
6585993 GTTAT-AATTGATTTACTACTAA
1 ATTATCAA-TGATTTACTATTAA
* **
6586015 GTTATTTATGATTTAC---T--
1 ATTATCAATGATTTACTATTAA
* *
6586032 ATTATCAATTAATTACTATTAA
1 ATTATCAATGATTTACTATTAA
* ** * *
6586054 ACTAAAAGTGATTTATTATTAA
1 ATTATCAATGATTTACTATTAA
* *
6586076 ATTATCACTAATTTACTATTAA
1 ATTATCAATGATTTACTATTAA
*
6586098 GTTATCA
1 ATTATCA
6586105 TTAGTTTATT
Statistics
Matches: 490, Mismatches: 137, Indels: 56
0.72 0.20 0.08
Matches are distributed among these distances:
17 11 0.02
18 14 0.03
19 2 0.00
20 2 0.00
21 59 0.12
22 387 0.79
23 15 0.03
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.47
Consensus pattern (22 bp):
ATTATCAATGATTTACTATTAA
Found at i:6585899 original size:43 final size:44
Alignment explanation
Indices: 6585730--6585933 Score: 132
Period size: 43 Copynumber: 4.7 Consensus size: 44
6585720 ATTTATTATT
* * * * *
6585730 AAATTATTAATGATTTACTATTATAGTAT-TATGTATTTACTACT
1 AAATTATCACTGATTTACTATTAAATTATATAT-TATTTACTACC
** * * *
6585774 ATTTTATCATTGATTTACTACTT-AATTTTCA-ATTATTTAGTA-C
1 AAATTATCACTGATTTACTA-TTAAATTAT-ATATTATTTACTACC
** * * *
6585817 AAATTATCACCAATTTACTACTAAATT-TTTCATAATTTACTACC
1 AAATTATCACTGATTTACTATTAAATTATAT-ATTATTTACTACC
**
6585861 AAATTATCACTGATTTA-TATTAAATTATATATTATTTACTATT
1 AAATTATCACTGATTTACTATTAAATTATATATTATTTACTACC
* * * * *
6585904 AAGTTATTAATGAATTACTATTAAGTTATA
1 AAATTATCACTGATTTACTATTAAATTATA
6585934 CTAATTTGCT
Statistics
Matches: 121, Mismatches: 30, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
42 2 0.02
43 59 0.49
44 56 0.46
45 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.48
Consensus pattern (44 bp):
AAATTATCACTGATTTACTATTAAATTATATATTATTTACTACC
Found at i:6586112 original size:22 final size:22
Alignment explanation
Indices: 6586064--6586124 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
6586054 ACTAAAAGTG
*
6586064 ATTTATTATTAAATTATCACTA
1 ATTTATTATTAAGTTATCACTA
* *
6586086 ATTTACTATTAAGTTATCATTA
1 ATTTATTATTAAGTTATCACTA
*
6586108 GTTTATTATTAAGTTAT
1 ATTTATTATTAAGTTAT
6586125 TAATAACTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTTATTATTAAGTTATCACTA
Found at i:6586113 original size:44 final size:43
Alignment explanation
Indices: 6586064--6586180 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 43
6586054 ACTAAAAGTG
* *
6586064 ATTTATTATTAAATTATCACTAATTTACTATTAAGTTATCATT
1 ATTTATTATTAAGTTATCACTAATTTACTATTAAGTAATCATT
* * * * *
6586107 AGTTTATTATTAAGTTATTAATAACTAACTACTAAGTAATCATT
1 A-TTTATTATTAAGTTATCACTAATTTACTATTAAGTAATCATT
6586151 ATTT-TTA-TAACGTTATC-CATAATTTACTAT
1 ATTTATTATTAA-GTTATCAC-TAATTTACTAT
6586181 GCATTTACAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.05
42 16 0.27
43 4 0.07
44 36 0.61
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (43 bp):
ATTTATTATTAAGTTATCACTAATTTACTATTAAGTAATCATT
Found at i:6586124 original size:11 final size:11
Alignment explanation
Indices: 6586066--6586126 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
6586056 TAAAAGTGAT
*
6586066 TTATTATTAAA
1 TTATTATTAAG
* * *
6586077 TTATCACTAAT
1 TTATTATTAAG
*
6586088 TTACTATTAAG
1 TTATTATTAAG
*
6586099 TTATCATT-AG
1 TTATTATTAAG
6586109 TTTATTATTAAG
1 -TTATTATTAAG
6586121 TTATTA
1 TTATTA
6586127 ATAACTAACT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
10 2 0.05
11 34 0.89
12 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (11 bp):
TTATTATTAAG
Found at i:6586221 original size:22 final size:22
Alignment explanation
Indices: 6586196--6586271 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
6586186 TACAACTACA
*
6586196 TTATAATTAATTTATTACTAAG
1 TTATAATTAATTTATTATTAAG
* ** * *
6586218 TTATTATGCATTTACTATTATG
1 TTATAATTAATTTATTATTAAG
* *
6586240 TTATTATTGATTTATTATTAAG
1 TTATAATTAATTTATTATTAAG
6586262 TTATCAATTA
1 TTAT-AATTA
6586272 TTGACTATTA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 38 0.93
23 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (22 bp):
TTATAATTAATTTATTATTAAG
Found at i:6586227 original size:44 final size:44
Alignment explanation
Indices: 6586178--6586265 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
6586168 CATAATTTAC
6586178 TATGCATTTACAACTACATTATAATTAATTTATTACTAAGTTAT
1 TATGCATTTACAACTACATTATAATTAATTTATTACTAAGTTAT
* * ** * * *
6586222 TATGCATTTACTATTATGTTATTATTGATTTATTATTAAGTTAT
1 TATGCATTTACAACTACATTATAATTAATTTATTACTAAGTTAT
6586266 CAATTATTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (44 bp):
TATGCATTTACAACTACATTATAATTAATTTATTACTAAGTTAT
Found at i:6586265 original size:11 final size:11
Alignment explanation
Indices: 6586196--6586265 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
6586186 TACAACTACA
* *
6586196 TTATAATTAAT
1 TTATTATTAAG
*
6586207 TTATTACTAAG
1 TTATTATTAAG
** *
6586218 TTATTATGCAT
1 TTATTATTAAG
* *
6586229 TTACTATTATG
1 TTATTATTAAG
* *
6586240 TTATTATTGAT
1 TTATTATTAAG
6586251 TTATTATTAAG
1 TTATTATTAAG
6586262 TTAT
1 TTAT
6586266 CAATTATTGA
Statistics
Matches: 41, Mismatches: 18, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (11 bp):
TTATTATTAAG
Found at i:6586279 original size:44 final size:44
Alignment explanation
Indices: 6586196--6586281 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
6586186 TACAACTACA
* *
6586196 TTATAATTAATTTATTACTAAGTTATTATGCATTTACTATTATG
1 TTATAATTAATTTATTACTAAGTTATAATGCATTGACTATTATG
* * * *
6586240 TTATTATTGATTTATTATTAAGTTATCAAT-TATTGACTATTA
1 TTATAATTAATTTATTACTAAGTTAT-AATGCATTGACTATTA
6586282 AATTATCAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 33 0.94
45 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (44 bp):
TTATAATTAATTTATTACTAAGTTATAATGCATTGACTATTATG
Found at i:6586280 original size:22 final size:22
Alignment explanation
Indices: 6586255--6586311 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
6586245 ATTGATTTAT
* *
6586255 TATTAAGTTATCAATTATTGAC
1 TATTAAATTATCAATCATTGAC
* *
6586277 TATTAAATTATCAGTCATTTAC
1 TATTAAATTATCAATCATTGAC
6586299 TATTAAATTATCA
1 TATTAAATTATCA
6586312 CTAAATTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (22 bp):
TATTAAATTATCAATCATTGAC
Found at i:6586439 original size:25 final size:26
Alignment explanation
Indices: 6586380--6586439 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
6586370 TACTACTAAG
* * *
6586380 TTATACTAATTACTTTTAAGTTTTTAA
1 TTAT-CTAATTACTTATAAGTTATCAA
*
6586407 TGAT-TAATTAC-TATAAGTTATCAA
1 TTATCTAATTACTTATAAGTTATCAA
6586431 TTATCTAAT
1 TTATCTAAT
6586440 CTTACATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
27 3 0.11
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (26 bp):
TTATCTAATTACTTATAAGTTATCAA
Found at i:6589887 original size:14 final size:14
Alignment explanation
Indices: 6589843--6589891 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
6589833 AATAAACAAA
6589843 CTTCATATAATTGT
1 CTTCATATAATTGT
**
6589857 CTT--T-TAATACT
1 CTTCATATAATTGT
6589868 -TTCATATAATTGT
1 CTTCATATAATTGT
6589881 CTTCATATAAT
1 CTTCATATAAT
6589892 GCTTCGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 5 0.19
12 2 0.07
13 5 0.19
14 13 0.48
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (14 bp):
CTTCATATAATTGT
Found at i:6591340 original size:23 final size:23
Alignment explanation
Indices: 6591314--6591358 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
6591304 TAATTAAATA
6591314 TTTT-AAAATTGAAAAATATTTAT
1 TTTTAAAAATTGAAAAAT-TTTAT
*
6591337 TTTTAAAAATTTAAAAATTTTA
1 TTTTAAAAATTGAAAAATTTTA
6591359 AATTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTAAAAATTGAAAAATTTTAT
Found at i:6591364 original size:23 final size:24
Alignment explanation
Indices: 6591313--6591364 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6591303 ATAATTAAAT
* *
6591313 ATTTTAAAATTGAAAAATATTTAT
1 ATTTAAAAATTGAAAAATATTTAA
* *
6591337 TTTTAAAAATTTAAAAAT-TTTAA
1 ATTTAAAAATTGAAAAATATTTAA
6591360 ATTTA
1 ATTTA
6591365 TTAATAATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTAAAAATTGAAAAATATTTAA
Found at i:6593042 original size:30 final size:30
Alignment explanation
Indices: 6593007--6593067 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
6592997 AAAAAATTTA
6593007 AATTCGATTCAATTATTATAAATTCGATTC
1 AATTCGATTCAATTATTATAAATTCGATTC
*
6593037 AATTCGATTCGATTATTATAAATTCGATTC
1 AATTCGATTCAATTATTATAAATTCGATTC
6593067 A
1 A
6593068 TCGATCGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (30 bp):
AATTCGATTCAATTATTATAAATTCGATTC
Found at i:6593061 original size:15 final size:15
Alignment explanation
Indices: 6593013--6593065 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
6593003 TTTAAATTCG
*
6593013 ATTCAATTATTATAA
1 ATTCGATTATTATAA
* **
6593028 ATTCGATTCAAT-TCG
1 ATTCGATT-ATTATAA
6593043 ATTCGATTATTATAA
1 ATTCGATTATTATAA
6593058 ATTCGATT
1 ATTCGATT
6593066 CATCGATCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.07
15 25 0.86
16 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (15 bp):
ATTCGATTATTATAA
Found at i:6594834 original size:14 final size:14
Alignment explanation
Indices: 6594815--6594850 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
6594805 CTGATTTCTC
6594815 ATGTGAACAAGAGA
1 ATGTGAACAAGAGA
6594829 ATGTG-A-AAGAGA
1 ATGTGAACAAGAGA
6594841 ATGTGAACAA
1 ATGTGAACAA
6594851 TGGCAACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.55
13 2 0.10
14 7 0.35
ACGTcount: A:0.50, C:0.06, G:0.28, T:0.17
Consensus pattern (14 bp):
ATGTGAACAAGAGA
Found at i:6595637 original size:10 final size:10
Alignment explanation
Indices: 6595622--6595657 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6595612 TCAATTCTAA
6595622 AATATTTTAG
1 AATATTTTAG
* *
6595632 AATATTCTAA
1 AATATTTTAG
6595642 AATATTTTAG
1 AATATTTTAG
6595652 AATATT
1 AATATT
6595658 CTAAAAGCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (10 bp):
AATATTTTAG
Found at i:6595640 original size:20 final size:20
Alignment explanation
Indices: 6595615--6595663 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
6595605 ATAAAAGTCA
6595615 ATTCTAAAATATTTTAGAAT
1 ATTCTAAAATATTTTAGAAT
6595635 ATTCTAAAATATTTTAGAAT
1 ATTCTAAAATATTTTAGAAT
6595655 ATTCTAAAA
1 ATTCTAAAA
6595664 GCTCACACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTCTAAAATATTTTAGAAT
Found at i:6600049 original size:2 final size:2
Alignment explanation
Indices: 6600044--6600070 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6600034 TGCAGAAAAA
6600044 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6600071 GTTAGATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6602043 original size:24 final size:24
Alignment explanation
Indices: 6602016--6602072 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
6602006 AAAGTTTTTC
6602016 AAATAATTTATTATAA-TATTTAAT
1 AAATAATTTA-TATAATTATTTAAT
*
6602040 AAATCATTTATATAATTATTTAAT
1 AAATAATTTATATAATTATTTAAT
6602064 AAACTAATT
1 AAA-TAATT
6602073 AATAGATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 20 0.69
25 4 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATAATTTATATAATTATTTAAT
Found at i:6602812 original size:145 final size:144
Alignment explanation
Indices: 6602651--6602961 Score: 412
Period size: 145 Copynumber: 2.1 Consensus size: 144
6602641 TTAATTTCAA
* *
6602651 AATATTTTATGATTTTTGATGCATTTGAAATCACAGCAGTATCC-TGAAAAGTTTAAAATTACCA
1 AATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTA-CCTTGAAAAGTATAAAATTACCA
* *
6602715 AAATACCCCTATAAGGGTATTTTTGTAATTT-ATCCTTCTTGAGCTC-AGATTTTCATGAAACTT
65 AAATACCCCTATAAGGGTAATTTTGTAATTTAAT--TTCTCGAGCTCGA-ATTTTCATGAAACTT
* *
6602778 TTCAGATCTTAATTTTTT
127 TTCAGATCTCAATTTTAT
** * ** * *
6602796 AATATTTCATGATTTTTGATTTATTTGAAATCATAGCAGTACCTTGTGAAGTATGAAATTACTAA
1 AATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTACCTTGAAAAGTATAAAATTACCAA
* *
6602861 TATACCCTTATAAGGGTAATTTTGTAATTTGAATTTCTCGAGCTCGAATTTTCATGAAACTTTTC
66 AATACCCCTATAAGGGTAATTTTGTAATTT-AATTTCTCGAGCTCGAATTTTCATGAAACTTTTC
6602926 AGATCTCAATTTTAT
130 AGATCTCAATTTTAT
*
6602941 AATAGTTCATGATTTTTGATG
1 AATATTTCATGATTTTTGATG
6602962 TTTTAAAATC
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
144 2 0.01
145 140 0.97
146 1 0.01
147 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (144 bp):
AATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTACCTTGAAAAGTATAAAATTACCAA
AATACCCCTATAAGGGTAATTTTGTAATTTAATTTCTCGAGCTCGAATTTTCATGAAACTTTTCA
GATCTCAATTTTAT
Found at i:6612029 original size:25 final size:26
Alignment explanation
Indices: 6611992--6612079 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 26
6611982 GATGATTATA
6611992 AAAAAAGAAAAAAAATCAAAATCAAT
1 AAAAAAGAAAAAAAATCAAAATCAAT
*
6612018 AAAAAAG-TAAAAAATCAAAATCAAAAT
1 AAAAAAGAAAAAAAATCAAAATC--AAT
* * *
6612045 AAAAATGAAAATAAAAACAAAAACAA-
1 AAAAAAGAAAA-AAAATCAAAATCAAT
6612071 AAACAAAGA
1 AAA-AAAGA
6612080 GAAGCTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
25 14 0.27
26 10 0.20
27 15 0.29
28 2 0.04
29 10 0.20
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (26 bp):
AAAAAAGAAAAAAAATCAAAATCAAT
Found at i:6612048 original size:18 final size:18
Alignment explanation
Indices: 6612027--6612077 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
6612017 TAAAAAAGTA
*
6612027 AAAAATCAAAATCAAAAT
1 AAAAATCAAAATCAAAAC
* *
6612045 AAAAATGAAAATAAAAAC
1 AAAAATCAAAATCAAAAC
*
6612063 AAAAA-CAAAAACAAA
1 AAAAATCAAAATCAAA
6612078 GAGAAGCTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (18 bp):
AAAAATCAAAATCAAAAC
Found at i:6612049 original size:12 final size:12
Alignment explanation
Indices: 6612028--6612066 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6612018 AAAAAAGTAA
*
6612028 AAAATCAAAATC
1 AAAATAAAAATC
*
6612040 AAAATAAAAATG
1 AAAATAAAAATC
6612052 AAAATAAAAA-C
1 AAAATAAAAATC
6612063 AAAA
1 AAAA
6612067 ACAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:6612060 original size:31 final size:31
Alignment explanation
Indices: 6612003--6612061 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
6611993 AAAAAGAAAA
*
6612003 AAAATCAAAATCAATAAAAAAGTAAAAAATC
1 AAAATCAAAATCAATAAAAAAATAAAAAATC
6612034 AAAATCAAAAT-AA-AAATGAAAATAAAAA
1 AAAATCAAAATCAATAAA--AAAATAAAAA
6612062 CAAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 2 0.08
31 20 0.80
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (31 bp):
AAAATCAAAATCAATAAAAAAATAAAAAATC
Found at i:6612067 original size:12 final size:12
Alignment explanation
Indices: 6612027--6612077 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
6612017 TAAAAAAGTA
*
6612027 AAAAATCAAAATC
1 AAAAAT-AAAAAC
*
6612040 -AAAATAAAAAT
1 AAAAATAAAAAC
*
6612051 GAAAATAAAAAC
1 AAAAATAAAAAC
*
6612063 AAAAACAAAAAC
1 AAAAATAAAAAC
6612075 AAA
1 AAA
6612078 GAGAAGCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (12 bp):
AAAAATAAAAAC
Found at i:6612448 original size:9 final size:9
Alignment explanation
Indices: 6612434--6612463 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6612424 TCAAATGTTC
6612434 AAAAAAAAG
1 AAAAAAAAG
6612443 AAAAAAAAG
1 AAAAAAAAG
*
6612452 CAAAAAAAG
1 AAAAAAAAG
6612461 AAA
1 AAA
6612464 GACATGCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:6612657 original size:136 final size:131
Alignment explanation
Indices: 6612392--6612866 Score: 491
Period size: 130 Copynumber: 3.6 Consensus size: 131
6612382 TGGAATCCAA
*
6612392 AGAATTCAAGAAATTGATTGCTAAAGATGAAGTCAAATGTT-CAAAAAAAAGAAAA-AAAAGCAA
1 AGAATTCAAGAAATTGATTGCTAAAGATGAAGTCAAATATTCCAAAAAAAA-AAAAGAAAAG-AA
* * * * * * * *
6612455 AA-AAAGAAAGACATGCACCTCAAAAATGAAAGTTTATGGCAAAAAGTGAATGATGCCT-CAAGA
64 AAGAAAGAAAGAAATGCACTTAAAAAATGAAAGTCTAAGGTAAAAAGTGAATGAAGCTTCCAA-A
6612518 AAAT
128 AAAT
*
6612522 AGAATTCAAGAAATTGATTGTTAAAGATGAAGTCAAATATTCCTAAAAAAAAAAGAAGGGGAAAA
1 AGAATTCAAGAAATTGATTGCTAAAGATGAAGTCAAATATTCC-AAAAAAAAAA-AA---GAAAA
* * *
6612587 GAAAAGAAAGAAAGAAATACACTTAAAAAATGAGAGTCCAAGGTAAAAAGTGAATGAAGCTTCCA
61 GAAAAGAAAGAAAGAAATGCACTTAAAAAATGAAAGTCTAAGGTAAAAAGTGAATGAAGCTTCCA
6612652 AAAAAT
126 AAAAAT
* * * *
6612658 AGAATT-AAAAGAATTGATTGCTAAAGATGAAGTCAAATGTCCCAAAAAAAAAAAAG-AAAGCAA
1 AGAATTCAAGA-AATTGATTGCTAAAGATGAAGTCAAATATTCCAAAAAAAAAAAAGAAAAGAAA
* * ** * * *
6612721 AGAAATAAAGAAATGCATTTTGAAAATGAAAGTCTAGGGTAATAAGTGAATGAAGCTTCAAAAAA
65 AGAAAGAAAGAAATGCACTTAAAAAATGAAAGTCTAAGGTAAAAAGTGAATGAAGCTTCCAAAAA
6612786 AT
130 AT
* * * * *
6612788 AAAATTAAAGAAAGTTAAATGCTAAA-ATTGAAGTCTAATATTTCCAAAAAAGAAAAAA-AAAA-
1 AGAATTCAAGAAA-TTGATTGCTAAAGA-TGAAGTCAAATA-TTCCAAAAAA-AAAAAAGAAAAG
*
6612850 AAAAAAAAGCAAAGAAA
62 AAAAGAAAG-AAAGAAA
6612867 AAAAGGTATG
Statistics
Matches: 290, Mismatches: 38, Indels: 31
0.81 0.11 0.09
Matches are distributed among these distances:
130 110 0.38
131 27 0.09
132 25 0.09
133 16 0.06
134 2 0.01
135 17 0.06
136 90 0.31
137 3 0.01
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.19
Consensus pattern (131 bp):
AGAATTCAAGAAATTGATTGCTAAAGATGAAGTCAAATATTCCAAAAAAAAAAAAGAAAAGAAAA
GAAAGAAAGAAATGCACTTAAAAAATGAAAGTCTAAGGTAAAAAGTGAATGAAGCTTCCAAAAAA
T
Found at i:6614319 original size:42 final size:41
Alignment explanation
Indices: 6614253--6614333 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
6614243 TTTACATTCA
*
6614253 CATCTACATCACAAAAAAGACATTCCTATTTGCATCACTTG
1 CATCTACATCACAAAAAAGACATTCCTATTTACATCACTTG
* *
6614294 CATCTGCATCACACAAAAAGACATTCGTATTTACATCACT
1 CATCTACATCACA-AAAAAGACATTCCTATTTACATCACT
6614334 CGTATTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 12 0.33
42 24 0.67
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.28
Consensus pattern (41 bp):
CATCTACATCACAAAAAAGACATTCCTATTTACATCACTTG
Found at i:6614821 original size:2 final size:2
Alignment explanation
Indices: 6614816--6614848 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6614806 AAATAAAAAA
6614816 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6614849 ATGAATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6615167 original size:106 final size:105
Alignment explanation
Indices: 6615046--6615324 Score: 375
Period size: 105 Copynumber: 2.6 Consensus size: 105
6615036 CAAGACTTTC
* **
6615046 AGGCAAAACATTTTAAATTTTTAAAATTTCT-ATGCCTCTATTATGAGAAGCATTCAAAGATTTT
1 AGGCAAAACATTTTAAATTTTTAAAGTTT-TAACACCTCTATTATGAGAAGCATTCAAAGATTTT
**
6615110 TAAGATTTGTAAGACCT-TAGGGCATATATTTCCAAGACATCT
65 TAAGATTTGTAAGACCTCT-GGAAATA-ATTTCCAAGACATCT
* * * *
6615152 GGGCAAAACCTTTTAAATTTTTAAAGTTTTAACACCTTTAATATGAGGAA-CATTCAAAGATTTT
1 AGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCTCTATTATGA-GAAGCATTCAAAGATTTT
* *
6615216 TTAGATTTGTAAGACCTCTGGAAATAATTTCCAAGACCTCT
65 TAAGATTTGTAAGACCTCTGGAAATAATTTCCAAGACATCT
* * *
6615257 AGGCAAAATATTTTAAATTTTTAAAGTTTTAACACCTCTTTTATGAGGAGCATTCAAAGATTTTT
1 AGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCTCTATTATGAGAAGCATTCAAAGATTTTT
6615322 AAG
66 AAG
6615325 TTCTTTGGGC
Statistics
Matches: 150, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
104 2 0.01
105 72 0.48
106 72 0.48
107 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (105 bp):
AGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCTCTATTATGAGAAGCATTCAAAGATTTTT
AAGATTTGTAAGACCTCTGGAAATAATTTCCAAGACATCT
Found at i:6615284 original size:105 final size:106
Alignment explanation
Indices: 6615027--6615324 Score: 374
Period size: 106 Copynumber: 2.8 Consensus size: 106
6615017 TGGCACCCAG
* * * ** *
6615027 ATATATTTTCAAGAC-TTTCAGGCAAAACATTTTAAATTTTTAAAATTTCT-ATGCCTCTATTAT
1 ATATATTTCCAAGACATCT-AGGCAAAACATTTTAAATTTTTAAAGTTT-TAACACCTTTATTAT
**
6615090 GA-GAAGCATTCAAAGATTTTTAAGATTTGTAAGACCTTAGGGC
64 GAGGAA-CATTCAAAGATTTTTAAGATTTGTAAGACCTTAGGAA
* * *
6615133 ATATATTTCCAAGACATCTGGGCAAAACCTTTTAAATTTTTAAAGTTTTAACACCTTTAATATGA
1 ATATATTTCCAAGACATCTAGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCTTTATTATGA
*
6615198 GGAACATTCAAAGATTTTTTAGATTTGTAAGACCTCT-GGAA
66 GGAACATTCAAAGATTTTTAAGATTTGTAAGACCT-TAGGAA
* *
6615239 ATA-ATTTCCAAGACCTCTAGGCAAAATATTTTAAATTTTTAAAGTTTTAACACCTCTT-TTATG
1 ATATATTTCCAAGACATCTAGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCT-TTATTATG
*
6615302 AGGAGCATTCAAAGATTTTTAAG
65 AGGAACATTCAAAGATTTTTAAG
6615325 TTCTTTGGGC
Statistics
Matches: 168, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
105 74 0.44
106 88 0.52
107 6 0.04
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (106 bp):
ATATATTTCCAAGACATCTAGGCAAAACATTTTAAATTTTTAAAGTTTTAACACCTTTATTATGA
GGAACATTCAAAGATTTTTAAGATTTGTAAGACCTTAGGAA
Found at i:6615447 original size:62 final size:62
Alignment explanation
Indices: 6615355--6615481 Score: 184
Period size: 62 Copynumber: 2.0 Consensus size: 62
6615345 AGTCCTTTAA
* * * * *
6615355 GCAAGATTTGTAAGTCTTTTGAGCTGAATCTATTTTAATTTTGAGATTTATAAGTCTTTTGG
1 GCAAGATTCGTAAGTCTTTTAAGCTAAATCTATTTTAATTTTGAGATTTATAAGACCTTTGG
*
6615417 GCAAGATTCGTAAG-CTTTTCAAGCTAAATCTATTTTAATTTTGAGATTTGTAAGACCTTTGG
1 GCAAGATTCGTAAGTCTTTT-AAGCTAAATCTATTTTAATTTTGAGATTTATAAGACCTTTGG
6615479 GCA
1 GCA
6615482 TGATCTCTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 5 0.09
62 53 0.91
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (62 bp):
GCAAGATTCGTAAGTCTTTTAAGCTAAATCTATTTTAATTTTGAGATTTATAAGACCTTTGG
Found at i:6615579 original size:7 final size:7
Alignment explanation
Indices: 6615569--6615642 Score: 55
Period size: 7 Copynumber: 10.4 Consensus size: 7
6615559 TAAAAAAAAT
*
6615569 AAAAATA
1 AAAAACA
6615576 AAAAACA
1 AAAAACA
*
6615583 AACAACA
1 AAAAACA
*
6615590 AAAAAAA
1 AAAAACA
6615597 AGCAAAACA
1 A--AAAACA
*
6615606 AAAAAAA
1 AAAAACA
6615613 ATGAAAAC-
1 A--AAAACA
6615621 AAAAAC-
1 AAAAACA
6615627 AAAAAC-
1 AAAAACA
6615633 AAAAACA
1 AAAAACA
6615640 AAA
1 AAA
6615643 GCAAAACAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
6 17 0.31
7 27 0.49
8 1 0.02
9 10 0.18
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (7 bp):
AAAAACA
Found at i:6615609 original size:6 final size:6
Alignment explanation
Indices: 6615576--6615667 Score: 81
Period size: 6 Copynumber: 16.3 Consensus size: 6
6615566 AATAAAAATA
* * *
6615576 AAAAAC AAACAAC AAAAA- AAAAGC -AAAAC -AAAA- AAAAAT GAAAAC
1 AAAAAC AAA-AAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
* *
6615621 AAAAAC AAAAAC AAAAAC AAAAGC -AAAAC -AAAAC -ATAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
6615666 AA
1 AA
6615668 GTTCAAAGCC
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
5 29 0.40
6 37 0.51
7 6 0.08
ACGTcount: A:0.79, C:0.15, G:0.03, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:6615609 original size:45 final size:45
Alignment explanation
Indices: 6615560--6615653 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
6615550 ATTAATTTAT
6615560 AAAAAAAATAAAAATAAAAAACAAACAACAAAAA-AAAAGCAAAACA
1 AAAAAAAATAAAAA-AAAAAACAAA-AACAAAAACAAAAGCAAAACA
* *
6615606 AAAAAAAATGAAAACAAAAACAAAAACAAAAACAAAAGCAAAACA
1 AAAAAAAATAAAAAAAAAAACAAAAACAAAAACAAAAGCAAAACA
6615651 AAA
1 AAA
6615654 CATAACAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 8 0.18
45 24 0.53
46 13 0.29
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (45 bp):
AAAAAAAATAAAAAAAAAAACAAAAACAAAAACAAAAGCAAAACA
Found at i:6615652 original size:5 final size:5
Alignment explanation
Indices: 6615586--6615663 Score: 66
Period size: 5 Copynumber: 14.4 Consensus size: 5
6615576 AAAAACAAAC
* * *
6615586 AACAA AAAAA AAGCAA AACAA AAAAA AATGAA AACAAA AACAAA AACAAA
1 AACAA AACAA AA-CAA AACAA AACAA AA-CAA AAC-AA AAC-AA AAC-AA
*
6615636 AACAA AAGCAA AACAA AACAT AACAA AA
1 AACAA AA-CAA AACAA AACAA AACAA AA
6615664 ACAAGTTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
5 32 0.52
6 30 0.48
ACGTcount: A:0.79, C:0.14, G:0.04, T:0.03
Consensus pattern (5 bp):
AACAA
Found at i:6615664 original size:16 final size:16
Alignment explanation
Indices: 6615576--6615667 Score: 82
Period size: 16 Copynumber: 5.5 Consensus size: 16
6615566 AATAAAAATA
6615576 AAAAACAAACAACAAAA-
1 AAAAAC-AA-AACAAAAC
6615593 AAAAAGCAAAACAAAA-
1 AAAAA-CAAAACAAAAC
*
6615609 AAAAATGAAAACAAAAAC
1 AAAAA-CAAAAC-AAAAC
6615627 AAAAACAAAAACAAAAGC
1 AAAAAC-AAAACAAAA-C
*
6615645 -AAAACAAAACATAAC
1 AAAAACAAAACAAAAC
6615660 AAAAACAA
1 AAAAACAA
6615668 GTTCAAAGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.02
16 32 0.49
17 20 0.31
18 12 0.18
ACGTcount: A:0.79, C:0.15, G:0.03, T:0.02
Consensus pattern (16 bp):
AAAAACAAAACAAAAC
Found at i:6615665 original size:45 final size:45
Alignment explanation
Indices: 6615560--6615667 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
6615550 ATTAATTTAT
* *
6615560 AAAAAAAATAAAAATAAAAAACAAACAACAAAAAAAAAGCAAAACA
1 AAAAAAAACAAAAA-CAAAAACAAACAACAAAAAAAAAGCAAAACA
**
6615606 AAAAAAAATGAAAACAAAAACAAA-AACAAAAACAAAAGCAAAACA
1 AAAAAAAACAAAAACAAAAACAAACAACAAAAA-AAAAGCAAAACA
* *
6615651 AAACATAACAAAAACAA
1 AAAAAAAACAAAAACAA
6615668 GTTCAAAGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 8 0.15
45 34 0.62
46 13 0.24
ACGTcount: A:0.81, C:0.13, G:0.03, T:0.04
Consensus pattern (45 bp):
AAAAAAAACAAAAACAAAAACAAACAACAAAAAAAAAGCAAAACA
Found at i:6615715 original size:37 final size:37
Alignment explanation
Indices: 6615669--6615754 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
6615659 CAAAAACAAG
6615669 TTCAAAGCCTCTATTCAGAAGAAGCCATTTTCAAAGT
1 TTCAAAGCCTCTATTCAGAAGAAGCCATTTTCAAAGT
* * ** * * *
6615706 TTCAAAGCCTTTGTTCAGGGGGATCTATTTTCAAAGT
1 TTCAAAGCCTCTATTCAGAAGAAGCCATTTTCAAAGT
6615743 TTCAAAGCCTCT
1 TTCAAAGCCTCT
6615755 TTTTAAGGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (37 bp):
TTCAAAGCCTCTATTCAGAAGAAGCCATTTTCAAAGT
Found at i:6615765 original size:37 final size:38
Alignment explanation
Indices: 6615694--6615791 Score: 121
Period size: 37 Copynumber: 2.6 Consensus size: 38
6615684 CAGAAGAAGC
*
6615694 CATTTTCAAAGTTTCAAAGCCT-TTGTTCAGGGGGA-T
1 CATTTTCAAAGTTTCAAAGCCTCTTGTTCAAGGGGATT
*
6615730 CTATTTTCAAAGTTTCAAAGCCTCTT-TTTAAGGGGATT
1 C-ATTTTCAAAGTTTCAAAGCCTCTTGTTCAAGGGGATT
* * *
6615768 CATTTTCAAAATTTTAAAACCTCT
1 CATTTTCAAAGTTTCAAAGCCTCT
6615792 ATTTGAGAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 49 0.91
38 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (38 bp):
CATTTTCAAAGTTTCAAAGCCTCTTGTTCAAGGGGATT
Found at i:6615921 original size:58 final size:58
Alignment explanation
Indices: 6615831--6615941 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
6615821 TTTTAAAGTT
* *
6615831 TCAAAGTCTCTGTTTAGAGAGAGTCATTTTCAAACAAGATTTATAAAAAAAAATAGTG
1 TCAAAGCCTCTGTTTAGAGAGAGTCATTTTCAAACAAGATTTAAAAAAAAAAATAGTG
* *
6615889 TCAAAGCCTCTGTTTAGGGGGAG-CAATTTTCAAACAAGATTTAAAAAAAAAAA
1 TCAAAGCCTCTGTTTAGAGAGAGTC-ATTTTCAAACAAGATTTAAAAAAAAAAA
6615942 AAATTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (58 bp):
TCAAAGCCTCTGTTTAGAGAGAGTCATTTTCAAACAAGATTTAAAAAAAAAAATAGTG
Found at i:6616359 original size:22 final size:22
Alignment explanation
Indices: 6616318--6616361 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6616308 ACCCAAAGTC
*
6616318 AACTCTAGTCAAAATTATACAA
1 AACTCTAGTCAAAATAATACAA
6616340 AACT-TAGTCAAAATGAATACAA
1 AACTCTAGTCAAAAT-AATACAA
6616362 TCGAGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (22 bp):
AACTCTAGTCAAAATAATACAA
Found at i:6618568 original size:15 final size:16
Alignment explanation
Indices: 6618540--6618569 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6618530 TAATGATGAT
6618540 GATGATGAAAATTTTC
1 GATGATGAAAATTTTC
6618556 GATGATG-AAATTTT
1 GATGATGAAAATTTT
6618570 AAAGAAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (16 bp):
GATGATGAAAATTTTC
Found at i:6620374 original size:18 final size:19
Alignment explanation
Indices: 6620351--6620390 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6620341 ATTAATGTCT
6620351 TTAATTGTAAATAAA-TTA
1 TTAATTGTAAATAAATTTA
* *
6620369 TTAATTTTTAATAAATTTA
1 TTAATTGTAAATAAATTTA
6620388 TTA
1 TTA
6620391 TTTGATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAATTGTAAATAAATTTA
Found at i:6626679 original size:30 final size:30
Alignment explanation
Indices: 6626638--6626695 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6626628 TGAAGATGGA
*
6626638 AGGGGAAAGTAGACATATAAAGTTTATTAT
1 AGGGAAAAGTAGACATATAAAGTTTATTAT
*
6626668 AGGGAAAAGTAGACATATGAAGTTTATT
1 AGGGAAAAGTAGACATATAAAGTTTATT
6626696 CTATCTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.29
Consensus pattern (30 bp):
AGGGAAAAGTAGACATATAAAGTTTATTAT
Found at i:6629298 original size:2 final size:2
Alignment explanation
Indices: 6629291--6629317 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6629281 TAAACCAGTT
6629291 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6629318 TTCATTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6629615 original size:23 final size:25
Alignment explanation
Indices: 6629589--6629634 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6629579 AGATTTATGC
*
6629589 AAAAAT-TA-ATAACAACAATTTTT
1 AAAAATATATATAACAAAAATTTTT
6629612 AAAAATATATATAACAAAAATTT
1 AAAAATATATATAACAAAAATTT
6629635 GAAATCCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATATATATAACAAAAATTTTT
Found at i:6629947 original size:25 final size:26
Alignment explanation
Indices: 6629913--6629979 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
6629903 TTGAAAGCCA
* *
6629913 TAAACTGAAATGCC-AAA-TAAAACCT
1 TAAAATGAAAT-CCTAAACTAAAACCC
6629938 TAAAATGAAATCCTAAACTAAAACCC
1 TAAAATGAAATCCTAAACTAAAACCC
*
6629964 TAGAATGAAA-CCTAAA
1 TAAAATGAAATCCTAAA
6629980 ATGAAATCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 2 0.05
25 19 0.51
26 16 0.43
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (26 bp):
TAAAATGAAATCCTAAACTAAAACCC
Found at i:6629954 original size:13 final size:13
Alignment explanation
Indices: 6629938--6629990 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
6629928 AATAAAACCT
6629938 TAAAATGAAATCC
1 TAAAATGAAATCC
* * *
6629951 TAAACTAAAACCC
1 TAAAATGAAATCC
*
6629964 TAGAATGAAA-CC
1 TAAAATGAAATCC
6629976 TAAAATGAAATCC
1 TAAAATGAAATCC
6629989 TA
1 TA
6629991 GGTGAAATCC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
12 11 0.34
13 21 0.66
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.21
Consensus pattern (13 bp):
TAAAATGAAATCC
Found at i:6629990 original size:25 final size:26
Alignment explanation
Indices: 6629927--6630000 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
6629917 CTGAAATGCC
* *
6629927 AAATAAAACCTTAAAATGAAATCCTA
1 AAATAAAACCCTAGAATGAAATCCTA
*
6629953 AACTAAAACCCTAGAATGAAA-CCTA
1 AAATAAAACCCTAGAATGAAATCCTA
* * *
6629978 AAATGAAATCCTAG-GTGAAATCC
1 AAATAAAACCCTAGAATGAAATCC
6630001 GAAACCTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 5 0.12
25 17 0.43
26 18 0.45
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.20
Consensus pattern (26 bp):
AAATAAAACCCTAGAATGAAATCCTA
Found at i:6630011 original size:19 final size:18
Alignment explanation
Indices: 6629989--6630069 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
6629979 AATGAAATCC
6629989 TAGGTGAAATCCGAAACCT
1 TAGGTGAAA-CCGAAACCT
* *
6630008 TAGGTCAAACAGTAAACCT
1 TAGGTGAAACCG-AAACCT
* ** *
6630027 TAGGTAAAATCTTAAATCT
1 TAGGTGAAA-CCGAAACCT
* *
6630046 TAGTTGAAACTCTAAACCT
1 TAGGTGAAAC-CGAAACCT
6630065 TAGGT
1 TAGGT
6630070 AAAGTCCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.06
19 44 0.92
20 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (18 bp):
TAGGTGAAACCGAAACCT
Found at i:6630280 original size:19 final size:20
Alignment explanation
Indices: 6630235--6630273 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
6630225 CATATTTTAA
6630235 AATAATAATAAAATTAAATC
1 AATAATAATAAAATTAAATC
6630255 AATAATAA-AAAATTAAATC
1 AATAATAATAAAATTAAATC
6630274 TTAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAATAATAAAATTAAATC
Found at i:6642893 original size:59 final size:58
Alignment explanation
Indices: 6642739--6642893 Score: 168
Period size: 59 Copynumber: 2.6 Consensus size: 58
6642729 ATAGAAATAT
* * *
6642739 ATAACCAAAACCACAATAATTTTAACAAATATAAAACCAACAAAAACTCAACAAATTG
1 ATAACCAAAACCAAAAAAATTTTAACAAATATATAACCAACAAAAACTCAACAAATTG
* * * * * * *
6642797 ATAACCAAAACCCAAATAAATTTCAACAAATAAATAACTAACAAAAACTCCATACATT-
1 ATAACCAAAA-CCAAAAAAATTTTAACAAATATATAACCAACAAAAACTCAACAAATTG
* *
6642855 AGTAACCAAAACCAAAACAAATTTTACCAAATTTATAAC
1 A-TAACCAAAACCAAAA-AAATTTTAACAAATATATAAC
6642894 AAAAAAGTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
58 16 0.20
59 63 0.80
ACGTcount: A:0.57, C:0.21, G:0.01, T:0.21
Consensus pattern (58 bp):
ATAACCAAAACCAAAAAAATTTTAACAAATATATAACCAACAAAAACTCAACAAATTG
Found at i:6642936 original size:12 final size:11
Alignment explanation
Indices: 6642915--6642947 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
6642905 CCCTAAACTT
6642915 AATAAACATAA
1 AATAAACATAA
6642926 AATACAACATAA
1 AATA-AACATAA
6642938 AATAAA-ATAA
1 AATAAACATAA
6642948 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
AATAAACATAA
Found at i:6647390 original size:17 final size:16
Alignment explanation
Indices: 6647367--6647407 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
6647357 TATCATGTTG
*
6647367 ATTTATCTTTTTAATT
1 ATTTATCTGTTTAATT
*
6647383 ATTTTATCTGTTTAGTT
1 A-TTTATCTGTTTAATT
6647400 ATTTATCT
1 ATTTATCT
6647408 AGGTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (16 bp):
ATTTATCTGTTTAATT
Found at i:6648119 original size:13 final size:12
Alignment explanation
Indices: 6648091--6648126 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
6648081 TAGACTTTGG
*
6648091 TATTTATTTTAC
1 TATTTATTTTTC
6648103 TATTTATTTTTC
1 TATTTATTTTTC
6648115 TTATTTATTTTT
1 -TATTTATTTTT
6648127 AATTGTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (12 bp):
TATTTATTTTTC
Found at i:6648450 original size:3 final size:3
Alignment explanation
Indices: 6648438--6648468 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6648428 GAAAATTTAG
6648438 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6648469 TAGTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6653803 original size:15 final size:15
Alignment explanation
Indices: 6653783--6653816 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6653773 AACTCATGCA
6653783 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
*
6653798 AAAAAAAAGAAAAGG
1 AAAAAAAAAAAAAGG
6653813 AAAA
1 AAAA
6653817 GGAAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:6655897 original size:84 final size:84
Alignment explanation
Indices: 6655743--6655898 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 84
6655733 AGTCCTCCAG
* * * * *
6655743 GCATGATTCATATGTCTTCCAAGCTGAATCTATTTTAAAGTTAGGATTTGTAAGACCTCTTGACA
1 GCATGATTCATAAGTCTTCCAAGCTGAATCTATTTTAAAATTAAGATTCGTAAGACCTCTGGACA
*
6655808 TAATCTCTAAGTCTTTATA
66 AAATCTCTAAGTCTTTATA
* * * *
6655827 GCATGATTCATAAGTCTTCTAAGCTTAATTTGTTTTAAAATTAAGATTCGTAAGACCTCTAGGA-
1 GCATGATTCATAAGTCTTCCAAGCTGAATCTATTTTAAAATTAAGATTCGTAAGACCTCT-GGAC
6655891 AAAATCTC
65 AAAATCTC
6655899 CTAGTTCTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 59 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (84 bp):
GCATGATTCATAAGTCTTCCAAGCTGAATCTATTTTAAAATTAAGATTCGTAAGACCTCTGGACA
AAATCTCTAAGTCTTTATA
Found at i:6656270 original size:16 final size:16
Alignment explanation
Indices: 6656249--6656281 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6656239 CCAATTGTGG
6656249 AATTTT-GTTTTATTTT
1 AATTTTAGTTTT-TTTT
6656265 AATTTTAGTTTTTTTT
1 AATTTTAGTTTTTTTT
6656281 A
1 A
6656282 TTATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (16 bp):
AATTTTAGTTTTTTTT
Found at i:6658412 original size:12 final size:12
Alignment explanation
Indices: 6658395--6658423 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
6658385 TTAAGTCTAT
6658395 GTCTAGCAATAG
1 GTCTAGCAATAG
6658407 GTCTAGCAATAG
1 GTCTAGCAATAG
6658419 GTCTA
1 GTCTA
6658424 CAAATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (12 bp):
GTCTAGCAATAG
Found at i:6667782 original size:7 final size:6
Alignment explanation
Indices: 6667770--6668076 Score: 90
Period size: 7 Copynumber: 47.3 Consensus size: 6
6667760 CTCATGAAAC
** *
6667770 CCTAAA CCATAAA CCTAAA CCTAAA CCTTAAA CCCT-AA TTTTAA CCTTAAAA
1 CCTAAA CC-TAAA CCTAAA CCTAAA CC-TAAA -CCTAAA CCTAAA CC-T-AAA
* * **
6667822 CCTAAAA CC-AAA CTTTAAA CCCTAAA TCC-CAA CACTAAA CAAAAA CCCTAAA
1 CCT-AAA CCTAAA C-CTAAA -CCTAAA -CCTAAA C-CTAAA CCTAAA -CCTAAA
* * *
6667874 CCCTTAA -CTAAA CCATAAA -CTAACC CCAAAA CCTAAA CAC-AAA CCCTAAA
1 -CCTAAA CCTAAA CC-TAAA CCTAA-A CCTAAA CCTAAA C-CTAAA -CCTAAA
*
6667924 CCTAAA CCTCAAA CCCTAAA CCCTAAA CCCTAAA CCTTAAA CCCAAA CTCTAAA
1 CCTAAA CCT-AAA -CCTAAA -CCTAAA -CCTAAA CC-TAAA CCTAAA C-CTAAA
* * * * *
6667978 CCTTAG TCTAAA CCCTAAA CCAAAAA CCCCAAA TCCTAAA -CTAAAA CCCTAAA
1 CCTAAA CCTAAA -CCTAAA CC-TAAA -CCTAAA -CCTAAA CCT-AAA -CCTAAA
* * * * *
6668031 CCCTAAA CCCAAA CGTAGA CTTTAAA CC-AAC CCTAAA CCCTAAA CC
1 -CCTAAA CCTAAA CCTAAA C-CTAAA CCTAAA CCTAAA -CCTAAA CC
6668077 AACTTCCAAT
Statistics
Matches: 228, Mismatches: 41, Indels: 64
0.68 0.12 0.19
Matches are distributed among these distances:
5 19 0.08
6 75 0.33
7 120 0.53
8 14 0.06
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (6 bp):
CCTAAA
Found at i:6667788 original size:13 final size:12
Alignment explanation
Indices: 6667770--6668076 Score: 90
Period size: 13 Copynumber: 23.7 Consensus size: 12
6667760 CTCATGAAAC
6667770 CCTAAACCATAAA
1 CCTAAACC-TAAA
6667783 CCTAAACCTAAA
1 CCTAAACCTAAA
6667795 CCTTAAACCCT-AA
1 CC-TAAA-CCTAAA
** *
6667808 TTTTAACCTTAAAA
1 CCTAAACC-T-AAA
6667822 CCTAAAACC-AAA
1 CCT-AAACCTAAA
*
6667834 CTTTAAACCCTAAA
1 C-CTAAA-CCTAAA
*
6667848 TCC-CAACACTAAA
1 -CCTAAAC-CTAAA
**
6667861 CAAAAACCCTAAA
1 CCTAAA-CCTAAA
*
6667874 CCCTTAA-CTAAA
1 -CCTAAACCTAAA
*
6667886 CCATAAA-CTAACC
1 CC-TAAACCTAA-A
*
6667899 CCAAAACCTAAA
1 CCTAAACCTAAA
6667911 CAC-AAACCCTAAA
1 C-CTAAA-CCTAAA
6667924 CCTAAACCTCAAA
1 CCTAAACCT-AAA
6667937 CCCTAAACCCTAAA
1 -CCTAAA-CCTAAA
6667951 CCCTAAACCTTAAA
1 -CCTAAACC-TAAA
*
6667965 CCCAAACTCTAAA
1 CCTAAAC-CTAAA
* **
6667978 CCTTAGTCTAAA
1 CCTAAACCTAAA
*
6667990 CCCTAAACCAAAAA
1 -CCTAAACC-TAAA
*
6668004 CCCCAAATCCTAAA
1 -CCTAAA-CCTAAA
6668018 -CTAAAACCCTAAA
1 CCT-AAA-CCTAAA
*
6668031 CCCTAAACCCAAA
1 -CCTAAACCTAAA
* * *
6668044 CGTAGACTTTAAA
1 CCTAAAC-CTAAA
*
6668057 CC-AACCCTAAA
1 CCTAAACCTAAA
6668068 CCCTAAACC
1 -CCTAAACC
6668077 AACTTCCAAT
Statistics
Matches: 219, Mismatches: 41, Indels: 68
0.67 0.12 0.21
Matches are distributed among these distances:
11 8 0.04
12 57 0.26
13 93 0.42
14 49 0.22
15 12 0.05
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (12 bp):
CCTAAACCTAAA
Found at i:6667806 original size:20 final size:20
Alignment explanation
Indices: 6667770--6668039 Score: 116
Period size: 20 Copynumber: 13.4 Consensus size: 20
6667760 CTCATGAAAC
*
6667770 CCTAAACCATAAA-CCTAAA
1 CCTAAACCTTAAACCCTAAA
6667789 CCTAAACCTTAAACCCT-AA
1 CCTAAACCTTAAACCCTAAA
** * *
6667808 TTTTAACCTTAAAACCTAAAA
1 CCTAAACCTTAAACCCT-AAA
*
6667829 CC-AAACTTTAAACCCTAAA
1 CCTAAACCTTAAACCCTAAA
* **
6667848 TCCCAACACTAAACAAAAACCCTAAA
1 -CCTAA-AC----CTTAAACCCTAAA
* *
6667874 CCCTTAA-C-TAAACCATAAA
1 -CCTAAACCTTAAACCCTAAA
** *
6667893 -CT-AACCCCAAAACCTAAA
1 CCTAAACCTTAAACCCTAAA
*
6667911 CAC-AAACCCTAAA-CCTAAA
1 C-CTAAACCTTAAACCCTAAA
*
6667930 CCTCAAACCCTAAACCCTAAA
1 CCT-AAACCTTAAACCCTAAA
6667951 CCCTAAACCTTAAACCC-AAA
1 -CCTAAACCTTAAACCCTAAA
**
6667971 CTCTAAACCTT--AGTCTAAA
1 C-CTAAACCTTAAACCCTAAA
** *
6667990 CCCTAAACCAAAAACCCCAAA
1 -CCTAAACCTTAAACCCTAAA
*
6668011 TCCTAAA-CTAAAACCCTAAA
1 -CCTAAACCTTAAACCCTAAA
6668031 CCCTAAACC
1 -CCTAAACC
6668040 CAAACGTAGA
Statistics
Matches: 192, Mismatches: 34, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.01
17 3 0.02
18 11 0.06
19 57 0.30
20 66 0.34
21 34 0.18
22 5 0.03
25 1 0.01
26 13 0.07
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (20 bp):
CCTAAACCTTAAACCCTAAA
Found at i:6668018 original size:14 final size:13
Alignment explanation
Indices: 6667766--6668044 Score: 120
Period size: 13 Copynumber: 21.3 Consensus size: 13
6667756 ATTTCTCATG
6667766 AAACCCTAAACCAT
1 AAACCCTAAACC-T
6667780 AAA-CCTAAACCT
1 AAACCCTAAACCT
*
6667792 AAACCTTAAACCCT
1 AAACCCTAAA-CCT
** *
6667806 -AA-TTTTAACCTT
1 AAACCCTAAACC-T
*
6667818 AAAACCTAAAACC-
1 AAACCCT-AAACCT
**
6667831 AAACTTTAAACCCT
1 AAACCCTAAA-CCT
6667845 AAATCCC--AACACT
1 AAA-CCCTAAAC-CT
**
6667858 AAA-CAAAAACCCT
1 AAACCCTAAA-CCT
*
6667871 AAACCCTTAA-CT
1 AAACCCTAAACCT
*
6667883 AAACCATAAA-CT
1 AAACCCTAAACCT
* *
6667895 AACCCCAAAACCT
1 AAACCCTAAACCT
*
6667908 AAACAC-AAACCCT
1 AAACCCTAAA-CCT
6667921 AAA-CCTAAACCT
1 AAACCCTAAACCT
6667933 CAAACCCTAAACCCT
1 -AAACCCTAAA-CCT
6667948 AAACCCTAAACCTT
1 AAACCCTAAACC-T
6667962 AAACCC-AAACTCT
1 AAACCCTAAAC-CT
* **
6667975 AAA-CCTTAGTCT
1 AAACCCTAAACCT
*
6667987 AAACCCTAAACCAA
1 AAACCCTAAACC-T
*
6668001 AAACCCCAAATCCT
1 AAACCCTAAA-CCT
6668015 AAA--CTAAAACCCT
1 AAACCCT-AAA-CCT
*
6668028 AAACCCTAAACCC
1 AAACCCTAAACCT
6668041 AAAC
1 AAAC
6668045 GTAGACTTTA
Statistics
Matches: 201, Mismatches: 35, Indels: 59
0.68 0.12 0.20
Matches are distributed among these distances:
11 3 0.01
12 47 0.23
13 86 0.43
14 53 0.26
15 12 0.06
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:6668044 original size:20 final size:20
Alignment explanation
Indices: 6667895--6668076 Score: 122
Period size: 20 Copynumber: 8.9 Consensus size: 20
6667885 ACCATAAACT
* * *
6667895 AACCCCAAAACCTAAACACA
1 AACCCTAAACCCTAAACCCA
6667915 AACCCTAAA-CCTAAACCTCA
1 AACCCTAAACCCTAAACC-CA
6667935 AACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCC-A
* *
6667956 AACCTTAAACCC-AAACTCTA
1 AACCCTAAACCCTAAAC-CCA
*
6667976 AACCTTAGTCTAAACCCTAAACCAAA
1 AACC-----CTAAACCCTAAACC-CA
* * **
6668002 AACCCCAAATCCTAAACTAA
1 AACCCTAAACCCTAAACCCA
6668022 AACCCTAAACCCTAAACCCA
1 AACCCTAAACCCTAAACCCA
* * **
6668042 AA-CGTAGACTTTAAA-CC-
1 AACCCTAAACCCTAAACCCA
6668059 AACCCTAAACCCTAAACC
1 AACCCTAAACCCTAAACC
6668077 AACTTCCAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.02
18 11 0.09
19 17 0.13
20 49 0.38
21 32 0.25
25 8 0.06
26 9 0.07
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.15
Consensus pattern (20 bp):
AACCCTAAACCCTAAACCCA
Found at i:6669311 original size:49 final size:48
Alignment explanation
Indices: 6669190--6669332 Score: 155
Period size: 49 Copynumber: 2.9 Consensus size: 48
6669180 CAATATATTA
* *
6669190 AAAAATTAAGGAAAAAGTTGAAATATTAATTTTTTTTCTTAAATTGCTTTTG
1 AAAAATTAAGGAAAATGTTGAAATA-TAA---TTTTTCTTAAATAGCTTTTG
* * *
6669242 AAATACTAA-GAAAAGTGTTGAAATATCAATCTTTTCTTAAA-AGTTTTTG
1 AAAAATTAAGGAAAA-TGTTGAAATAT-AAT-TTTTCTTAAATAGCTTTTG
6669291 AAAAATTAAGGAAAATGTTGAAATATAGATTTTTCTTAAATA
1 AAAAATTAAGGAAAATGTTGAAATATA-ATTTTTCTTAAATA
6669333 AAATTTTTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
48 11 0.14
49 28 0.36
50 15 0.19
51 6 0.08
52 18 0.23
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (48 bp):
AAAAATTAAGGAAAATGTTGAAATATAATTTTTCTTAAATAGCTTTTG
Found at i:6688115 original size:53 final size:53
Alignment explanation
Indices: 6688026--6688127 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
6688016 TTAACAAATC
* * *
6688026 ATCAATAATCTGTCGATAATTGTTTGATAATGCATCAATAAAAGCTGATTTCT
1 ATCAATAATCTATCGATAATTGGTTGATAATCCATCAATAAAAGCTGATTTCT
* * *
6688079 ATCAATAATCTATTGATAATTGGTTGGTAATCCATCAATAAAGGCTGAT
1 ATCAATAATCTATCGATAATTGGTTGATAATCCATCAATAAAAGCTGAT
6688128 CTTCATTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (53 bp):
ATCAATAATCTATCGATAATTGGTTGATAATCCATCAATAAAAGCTGATTTCT
Found at i:6688156 original size:23 final size:22
Alignment explanation
Indices: 6688129--6688175 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
6688119 AAGGCTGATC
*
6688129 TTCATTGATAAATTCATTGGTAA
1 TTCATCGATAAATT-ATTGGTAA
* *
6688152 TTCATCGATAAGTTGTTGGTAA
1 TTCATCGATAAATTATTGGTAA
6688174 TT
1 TT
6688176 GCTAATTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.45
Consensus pattern (22 bp):
TTCATCGATAAATTATTGGTAA
Found at i:6691722 original size:17 final size:16
Alignment explanation
Indices: 6691669--6691733 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 16
6691659 TTCTCAAAAG
6691669 TTTTTTTTCTT--TTT
1 TTTTTTTTCTTGATTT
**
6691683 TAGTTTTTCTTGATTT
1 TTTTTTTTCTTGATTT
*
6691699 GATTTTTTTCTTGATTT
1 -TTTTTTTTCTTGATTT
6691716 TTGTTTTTT-TT-ATTT
1 TT-TTTTTTCTTGATTT
6691731 TTT
1 TTT
6691734 GATTTGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
14 10 0.24
15 6 0.15
16 6 0.15
17 19 0.46
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTGATTT
Found at i:6691731 original size:25 final size:23
Alignment explanation
Indices: 6691719--6691767 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
6691709 TTGATTTTTG
6691719 TTTTTT-TTATTTTTTGATTTGATT
1 TTTTTTGTTATTTTTTGATTT--TT
6691743 TTTTTTGTTATTTTTTGATTTTT
1 TTTTTTGTTATTTTTTGATTTTT
6691766 TT
1 TT
6691768 AATTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.17
24 6 0.25
25 14 0.58
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (23 bp):
TTTTTTGTTATTTTTTGATTTTT
Found at i:6691748 original size:41 final size:42
Alignment explanation
Indices: 6691669--6691768 Score: 118
Period size: 41 Copynumber: 2.4 Consensus size: 42
6691659 TTCTCAAAAG
6691669 TTTTTT-TTCTTTTTTAGTTTTTCTTGATTTGATTTTTTTCTTGA
1 TTTTTTGTT-TTTTTTAG-TTTTCTTGATTTGATTTTTTTCTT-A
*
6691713 -TTTTTGTTTTTTTTA-TTTT-TTGATTTGATTTTTTTTGTTA
1 TTTTTTGTTTTTTTTAGTTTTCTTGATTTGA-TTTTTTTCTTA
*
6691753 TTTTTTGATTTTTTTA
1 TTTTTTGTTTTTTTTA
6691769 ATTAATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
40 10 0.20
41 27 0.53
43 12 0.24
44 2 0.04
ACGTcount: A:0.10, C:0.03, G:0.09, T:0.78
Consensus pattern (42 bp):
TTTTTTGTTTTTTTTAGTTTTCTTGATTTGATTTTTTTCTTA
Found at i:6691756 original size:40 final size:43
Alignment explanation
Indices: 6691669--6691768 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 43
6691659 TTCTCAAAAG
6691669 TTTTTT-TTCTTTTTTAGTTTTTCTTGATTTGATTTTTTTCTTGA
1 TTTTTTGTT-TTTTTTAG-TTTTCTTGATTTGATTTTTTTCTTGA
*
6691713 -TTTTTGTTTTTTTTA-TTTT-TTGATTTGATTTTTTT-TGTTA
1 TTTTTTGTTTTTTTTAGTTTTCTTGATTTGATTTTTTTCT-TGA
*
6691753 TTTTTTGATTTTTTTA
1 TTTTTTGTTTTTTTTA
6691769 ATTAATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
39 1 0.02
40 18 0.35
41 18 0.35
43 12 0.24
44 2 0.04
ACGTcount: A:0.10, C:0.03, G:0.09, T:0.78
Consensus pattern (43 bp):
TTTTTTGTTTTTTTTAGTTTTCTTGATTTGATTTTTTTCTTGA
Found at i:6691777 original size:20 final size:20
Alignment explanation
Indices: 6691696--6691794 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
6691686 TTTTTCTTGA
* *
6691696 TTTGATTTTTTT-CTTGATT
1 TTTGATTTTTTTAATTAATT
* **
6691715 TTTG-TTTTTTTTATTTTTT
1 TTTGATTTTTTTAATTAATT
** *
6691734 GATTTGATTTTTTTTGTTATTT
1 --TTTGATTTTTTTAATTAATT
6691756 TTTGATTTTTTTAATTAATT
1 TTTGATTTTTTTAATTAATT
* *
6691776 TTTAAATTTTTTAATTAAT
1 TTTGATTTTTTTAATTAAT
6691795 AAATTTAACC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.11
19 8 0.12
20 34 0.52
21 4 0.06
22 13 0.20
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTGATTTTTTTAATTAATT
Found at i:6691777 original size:33 final size:31
Alignment explanation
Indices: 6691713--6691778 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 31
6691703 TTTTTCTTGA
* *
6691713 TTTTTGTTTTTTTTATTTTTTGATTTGATTT
1 TTTTTGTTTTTTTTATTTTTTGAATTAATTT
*
6691744 TTTTTGTTATTTTTTGATTTTTTTAATTAATTT
1 TTTTTGTT-TTTTTT-ATTTTTTGAATTAATTT
6691777 TT
1 TT
6691779 AAATTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 8 0.27
32 6 0.20
33 16 0.53
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.79
Consensus pattern (31 bp):
TTTTTGTTTTTTTTATTTTTTGAATTAATTT
Found at i:6691955 original size:22 final size:22
Alignment explanation
Indices: 6691925--6691972 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6691915 ACTCGAAAGA
*
6691925 CTTAGAGATTATACCCAGAGGT
1 CTTAAAGATTATACCCAGAGGT
* *
6691947 CTTAAAGATTATGCCTAGAGGT
1 CTTAAAGATTATACCCAGAGGT
6691969 CTTA
1 CTTA
6691973 CAAATCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTAAAGATTATACCCAGAGGT
Found at i:6692198 original size:53 final size:53
Alignment explanation
Indices: 6692112--6692222 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
6692102 TTAAAAAAGA
* **
6692112 AAAAAAAAACTTGTCTAAAAATTGCTCTTCATAAACAAAGGCTTTGGAACTTT
1 AAAAAAAAACTTATCTAAAAATTGCTCCCCATAAACAAAGGCTTTGGAACTTT
* * **
6692165 AAAAAAAATCTTATCTAAAAATTGCTCCCCATAAATAGGGGCTTTGGAACTTT
1 AAAAAAAAACTTATCTAAAAATTGCTCCCCATAAACAAAGGCTTTGGAACTTT
6692218 AAAAA
1 AAAAA
6692223 TTTAAAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (53 bp):
AAAAAAAAACTTATCTAAAAATTGCTCCCCATAAACAAAGGCTTTGGAACTTT
Found at i:6692604 original size:22 final size:22
Alignment explanation
Indices: 6692549--6692626 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
6692539 ATCTTAGTGA
6692549 TGCCAACTAATCTAGGCTTAAGG
1 TGCCAACTAATCTAGGCTT-AGG
* **
6692572 TGCTAGTTAATCTAGGCTTAGG
1 TGCCAACTAATCTAGGCTTAGG
* *
6692594 TGCCGACTAATCTAGGCTTGGG
1 TGCCAACTAATCTAGGCTTAGG
*
6692616 TGCCAGCTAAT
1 TGCCAACTAAT
6692627 TTGGGTTTAG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 29 0.64
23 16 0.36
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (22 bp):
TGCCAACTAATCTAGGCTTAGG
Found at i:6692717 original size:23 final size:23
Alignment explanation
Indices: 6692686--6692746 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
6692676 TGGGTGCAAC
* *
6692686 TAAACTGGGCTTAAAGTGCCAAA
1 TAAATTGGGTTTAAAGTGCCAAA
**
6692709 TAAATTGGGTTTAAAGTGCCAGT
1 TAAATTGGGTTTAAAGTGCCAAA
6692732 TAAATTGGGTTTAAA
1 TAAATTGGGTTTAAA
6692747 ATCTTAACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (23 bp):
TAAATTGGGTTTAAAGTGCCAAA
Found at i:6692857 original size:21 final size:22
Alignment explanation
Indices: 6692801--6692863 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
6692791 GCCACCTAAA
6692801 CTGAACTTAGGTGCCAA-CTAGT
1 CTGAACTTAGGTG-CAAGCTAGT
* * *
6692823 CTCAGCTAAGGTGCAAGCTA-T
1 CTGAACTTAGGTGCAAGCTAGT
*
6692844 CTGAACTTAGGTGCCAGCTA
1 CTGAACTTAGGTGCAAGCTA
6692864 ATCTAGGCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (22 bp):
CTGAACTTAGGTGCAAGCTAGT
Found at i:6693172 original size:23 final size:23
Alignment explanation
Indices: 6693116--6693195 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
6693106 TAGACTTACT
* *
6693116 TTTCTCTTTTTGCCCTTTTTT-TT
1 TTTCT-TTTTTTCCCTTTTTTCTC
*
6693139 TTTGCTATTTTTCCCTTTTTTCTC
1 TTT-CTTTTTTTCCCTTTTTTCTC
*
6693163 TTTCTTTTTTT--TTGTTTTTCTC
1 TTTCTTTTTTTCCCT-TTTTTCTC
6693185 TTT-TTTTTTTC
1 TTTCTTTTTTTC
6693196 AAACTCTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 8 0.17
22 11 0.23
23 23 0.48
24 6 0.12
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTCTTTTTTTCCCTTTTTTCTC
Found at i:6693173 original size:16 final size:17
Alignment explanation
Indices: 6693154--6693192 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
6693144 TATTTTTCCC
6693154 TTTTTTCTCTTTCT-TT
1 TTTTTTCTCTTTCTCTT
* *
6693170 TTTTTTGTTTTTCTCTT
1 TTTTTTCTCTTTCTCTT
6693187 TTTTTT
1 TTTTTT
6693193 TTCAAACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTCTCTTTCTCTT
Found at i:6693191 original size:32 final size:32
Alignment explanation
Indices: 6693115--6693190 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
6693105 ATAGACTTAC
* *
6693115 TTTTCTCTTTTTGCCCTTTTTTTTTTTGCTAT
1 TTTTCTCTTTTTTCCCTTTCTTTTTTTGCTAT
* * * *
6693147 TTTTCCCTTTTTTCTCTTTCTTTTTTT-TTGT
1 TTTTCTCTTTTTTCCCTTTCTTTTTTTGCTAT
6693178 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
6693191 TTTTCAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (32 bp):
TTTTCTCTTTTTTCCCTTTCTTTTTTTGCTAT
Found at i:6694983 original size:146 final size:141
Alignment explanation
Indices: 6694716--6694992 Score: 353
Period size: 146 Copynumber: 1.9 Consensus size: 141
6694706 TCTTTCTTTC
*
6694716 TTTGCTCTTTTTTTTTAGAAATATTTGACTTCAATTTTTTACTTTCTTAAATTCTATCTTTTTTT
1 TTTGCTCTTTTTTTTTAGAAATATTTGACTTCAATTTTTTACTTTCTTAAATTCTA-CTTTTCTT
* *
6694781 TTTTACTTGAGATTCTAATTGAAACTTATTCATTTTTTACCTCGGGCTCTCATCTCTAAGGTGCA
65 TTTTACTTGAGATTATAATTGAAACTTATTCATTTTTTACCTCGGACTCTCATCTCTAAGGTGCA
6694846 TACCTTCATATA
130 TACCTTCATATA
* *
6694858 TTTGCT-TTTTTTTTTTGAAATATTTGATTTCAACTTTAACGTTGTACTTTCTTAAATTCTA-TT
1 TTTGCTCTTTTTTTTTAGAAATATTTGACTTCAA-TTT----TT-TACTTTCTTAAATTCTACTT
* * * * * *
6694921 TTCTTTTTTACTTG-GAATTATAATTGAAGCTTTATTCATTTTTTGCCTTGGACTTTTATCTCTG
60 TTCTTTTTTACTTGAG-ATTATAATTGAAAC-TTATTCATTTTTTACCTCGGACTCTCATCTCTA
6694985 AGGTGCAT
123 AGGTGCAT
6694993 GTCTTTCTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
141 25 0.22
142 9 0.08
144 1 0.01
145 27 0.23
146 37 0.32
147 17 0.15
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (141 bp):
TTTGCTCTTTTTTTTTAGAAATATTTGACTTCAATTTTTTACTTTCTTAAATTCTACTTTTCTTT
TTTACTTGAGATTATAATTGAAACTTATTCATTTTTTACCTCGGACTCTCATCTCTAAGGTGCAT
ACCTTCATATA
Found at i:6695127 original size:123 final size:120
Alignment explanation
Indices: 6694886--6695333 Score: 486
Period size: 123 Copynumber: 3.6 Consensus size: 120
6694876 AATATTTGAT
* * * * * * * *
6694886 TTCAACTTTAACGTTGTACTTTCTTAAATTCTATTTTCTTTTTTACTTGGAATTATAATTGAAGC
1 TTCAACTTTAGCATTCTACTTTCTTAAATTCTA-TTT-TTTTTTACTTGAAATTCTAACTAAAAC
* * * * *
6694951 TTTATTCATTTTTTGCCTTGGACTTTTATCTCTGAGGTGCATGTCTTTCTTTTTTTGAC
64 TTTATTCACTTTTTGCC-TAGACTCTTATCTCTGAGGTGCATGTC-TTATTTTTTTAAC
* * * *
6695010 TTCAACTTTAGCATTTTACTTTTTTGAATTCTATTTTCTTTTTACTTGAAATTCTAACTAAAATT
1 TTCAACTTTAGCATTCTACTTTCTTAAATTCTATTTT-TTTTTACTTGAAATTCTAACTAAAACT
* * *
6695075 TTATTTACTTTTTGCCTCGAACTCTCAAT-TCTGAGGTGCATGTCTCTATTTTTTTAAC
65 TTATTCACTTTTTGCCTAG-ACTCT-TATCTCTGAGGTGCATGTCT-TATTTTTTTAAC
* *
6695133 TTCAACTTTAGCATTCTACTTTCTTAAATTGTATTCTTTTTTACTT-AGAATTCTAACTAAAACT
1 TTCAACTTTAGCATTCTACTTTCTTAAATTCTATTTTTTTTTACTTGA-AATTCTAACTAAAACT
* * * *
6695197 TTATTCACTTTTTATCCTAGACTCTTATCTCTAAAGTGCATGTCTTTTTTTCTTTAAC
65 TTATTCACTTTTT-GCCTAGACTCTTATCTCTGAGGTGCATGTCTTATTTT-TTTAAC
* * * *
6695255 TTTAACTTTAGCATTCTACTTTCTTGAATTCTATCTTATTTTTTACTTGAAATTCTAGCTGAAAC
1 TTCAACTTTAGCATTCTACTTTCTTAAATTCTAT-TT-TTTTTTACTTGAAATTCTAACTAAAAC
*
6695320 TTTATTCATTTTTT
64 TTTATTCACTTTTT
6695334 ACCCTTGATT
Statistics
Matches: 275, Mismatches: 38, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
121 8 0.03
122 96 0.35
123 104 0.38
124 66 0.24
125 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (120 bp):
TTCAACTTTAGCATTCTACTTTCTTAAATTCTATTTTTTTTTACTTGAAATTCTAACTAAAACTT
TATTCACTTTTTGCCTAGACTCTTATCTCTGAGGTGCATGTCTTATTTTTTTAAC
Found at i:6696149 original size:20 final size:20
Alignment explanation
Indices: 6696124--6696164 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6696114 TTATCAAATT
6696124 ATAACAAGGTTCACAAGTTG
1 ATAACAAGGTTCACAAGTTG
6696144 ATAACAAGGTTCACAAGTTG
1 ATAACAAGGTTCACAAGTTG
6696164 A
1 A
6696165 AATTCATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (20 bp):
ATAACAAGGTTCACAAGTTG
Found at i:6700674 original size:25 final size:24
Alignment explanation
Indices: 6700646--6700710 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
6700636 TAAACATTTC
6700646 TATTTTGTATATTATTAACAATAAA
1 TATTTT-TATATTATTAACAATAAA
* *
6700671 TATTTTTAATATT-TCAATAATAAA
1 TATTTTT-ATATTATTAACAATAAA
*
6700695 TAGTTTTATATTATTA
1 TATTTTTATATTATTA
6700711 TAATAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.15
24 18 0.53
25 11 0.32
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (24 bp):
TATTTTTATATTATTAACAATAAA
Found at i:6700716 original size:26 final size:24
Alignment explanation
Indices: 6700646--6700722 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 24
6700636 TAAACATTTC
*
6700646 TATTTTGT-ATATTATTAACAATAAA
1 TATTTT-TAATATTA-TAATAATAAA
6700671 TATTTTTAATATT-TCAATAATAAA
1 TATTTTTAATATTAT-AATAATAAA
*
6700695 TAGTTTTATATTATTATAATAATAAA
1 TA-TTTT-TAATATTATAATAATAAA
6700721 TA
1 TA
6700723 ACAAATGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
23 1 0.02
24 11 0.24
25 15 0.33
26 17 0.38
27 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (24 bp):
TATTTTTAATATTATAATAATAAA
Done.