Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 5 of 32
Found at i:2129067 original size:23 final size:22
Alignment explanation
Indices: 2129021--2129073 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2129011 TTTTTTAATT
* *
2129021 AAAAAATATATTTTCAATGGAA
1 AAAAAATAAATTTTCAATGCAA
*
2129043 AAAAAATAAATATTTCAATTCAA
1 AAAAAATAAAT-TTTCAATGCAA
*
2129066 AATAAATA
1 AAAAAATA
2129074 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAAATAAATTTTCAATGCAA
Found at i:2129083 original size:15 final size:17
Alignment explanation
Indices: 2129045--2129086 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
2129035 CAATGGAAAA
2129045 AAAATAAATATTTCAATT
1 AAAATAAATATTT-AATT
2129063 CAAAATAAATATTT-ATT
1 -AAAATAAATATTTAATT
2129080 -AAATAAA
1 AAAATAAA
2129087 AAACCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
17 3 0.13
19 13 0.57
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATAAATATTTAATT
Found at i:2134930 original size:14 final size:15
Alignment explanation
Indices: 2134911--2134943 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2134901 AAAAGAAGAG
2134911 CTCTTTCTCTTTC-T
1 CTCTTTCTCTTTCGT
2134925 CTCTTTCTCTTTCGT
1 CTCTTTCTCTTTCGT
2134940 CTCT
1 CTCT
2134944 GTGCTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (15 bp):
CTCTTTCTCTTTCGT
Found at i:2136505 original size:18 final size:18
Alignment explanation
Indices: 2136477--2136514 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2136467 AAGGATGTGC
2136477 AAATACAAACCAAATCGAA
1 AAATACAAACCAAATC-AA
2136496 AAAT-CAAACCAAATCAA
1 AAATACAAACCAAATCAA
2136513 AA
1 AA
2136515 TGGGGTCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.66, C:0.21, G:0.03, T:0.11
Consensus pattern (18 bp):
AAATACAAACCAAATCAA
Found at i:2136787 original size:13 final size:12
Alignment explanation
Indices: 2136756--2136788 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2136746 TATTTATCAA
2136756 TATTTTTAATAT
1 TATTTTTAATAT
2136768 T-TTTTTAATAT
1 TATTTTTAATAT
2136779 TAATTTTTAA
1 T-ATTTTTAA
2136789 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 1 0.05
13 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTTAATAT
Found at i:2145111 original size:22 final size:22
Alignment explanation
Indices: 2145086--2145145 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2145076 ACGAGTCTCG
2145086 TAATATCTAAAAACTAGTAACA
1 TAATATCTAAAAACTAGTAACA
* * *
2145108 TAATGTCTAAAGACTAGTAATA
1 TAATATCTAAAAACTAGTAACA
* * *
2145130 CAATACCTAATAACTA
1 TAATATCTAAAAACTA
2145146 ATTGATTCGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (22 bp):
TAATATCTAAAAACTAGTAACA
Found at i:2145806 original size:28 final size:29
Alignment explanation
Indices: 2145761--2145819 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
2145751 GTTAAATATG
* *
2145761 AAAATAAAATAATCAAATAATATATTTAT
1 AAAATAAAATAATAAAATAAAATATTTAT
*
2145790 AAAATAAATTAA-AAAATAAAATATTTAT
1 AAAATAAAATAATAAAATAAAATATTTAT
2145818 AA
1 AA
2145820 TTTCAAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAATAAAATAATAAAATAAAATATTTAT
Found at i:2149329 original size:6 final size:6
Alignment explanation
Indices: 2149318--2149343 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2149308 AACATAATCG
2149318 CATTTC CATTTC CATTTC CATTTC CA
1 CATTTC CATTTC CATTTC CATTTC CA
2149344 ATCAAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
CATTTC
Found at i:2173475 original size:16 final size:16
Alignment explanation
Indices: 2173454--2173492 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2173444 TGCATTATCA
* *
2173454 TTTTTACTTGCTTTAT
1 TTTTTACCTGCTTGAT
2173470 TTTTTACCTGCTTGAT
1 TTTTTACCTGCTTGAT
*
2173486 TTATTAC
1 TTTTTAC
2173493 GTAATTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (16 bp):
TTTTTACCTGCTTGAT
Found at i:2181925 original size:60 final size:57
Alignment explanation
Indices: 2181851--2181961 Score: 159
Period size: 60 Copynumber: 1.9 Consensus size: 57
2181841 TATTTTTAAT
* *
2181851 TTGTATTAATAATTTAATAAAAAAATATTTTAAGACTTCATTAAAAATATATATAACATA
1 TTGTATTAAAAATTTAATAAAAAAAT-TTTT-AGACTTCACTAAAAA-ATATATAACATA
* *
2181911 TTGTATTAAAAATTTAATAAAAAAATTTTTTGAGTTCACTAAAAAATATAT
1 TTGTATTAAAAATTTAATAAAAAAATTTTTAGACTTCACTAAAAAATATAT
2181962 GTAATATGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
57 6 0.13
58 12 0.26
59 4 0.09
60 25 0.53
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (57 bp):
TTGTATTAAAAATTTAATAAAAAAATTTTTAGACTTCACTAAAAAATATATAACATA
Found at i:2210284 original size:19 final size:20
Alignment explanation
Indices: 2210260--2210301 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2210250 AACTTTACTT
*
2210260 AAACAAAAACTAAAG-GAGA
1 AAACAAAAACGAAAGAGAGA
*
2210279 AAACAAAAAGGAAAGAGAGA
1 AAACAAAAACGAAAGAGAGA
2210299 AAA
1 AAA
2210302 GGGTTGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.71, C:0.07, G:0.19, T:0.02
Consensus pattern (20 bp):
AAACAAAAACGAAAGAGAGA
Found at i:2211205 original size:2 final size:2
Alignment explanation
Indices: 2211198--2211222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2211188 TTTTTACCGC
2211198 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 A
2211223 ATTATAATTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2215816 original size:74 final size:74
Alignment explanation
Indices: 2215695--2215841 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
2215685 AATAATTGTG
2215695 ACGGTTTAACAATTAATAATATTTAATTTTACGGCTTAATTTTCCCTTCAATCATGTGTATGAAA
1 ACGGTTTAACAATTAATAATATTTAATTTTACGGCTTAATTTTCCCTTCAATCATGTGTATGAAA
2215760 CTATCTATC
66 CTATCTATC
2215769 ACGGTTTAACAATTAATAATATTTAATTTTACGGCTTAATTTTCCCTTCAATCATGTGTATGAAA
1 ACGGTTTAACAATTAATAATATTTAATTTTACGGCTTAATTTTCCCTTCAATCATGTGTATGAAA
2215834 CTATCTAT
66 CTATCTAT
2215842 TTTTAGAGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (74 bp):
ACGGTTTAACAATTAATAATATTTAATTTTACGGCTTAATTTTCCCTTCAATCATGTGTATGAAA
CTATCTATC
Found at i:2239871 original size:3 final size:3
Alignment explanation
Indices: 2239863--2239887 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2239853 TTATTTTTTC
2239863 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2239888 CTTTTTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2242193 original size:3 final size:3
Alignment explanation
Indices: 2242185--2242215 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2242175 CATACCAAGT
2242185 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2242216 ATGAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2243013 original size:15 final size:15
Alignment explanation
Indices: 2242993--2243039 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
2242983 GAAAACTTTC
2242993 GGTAATGTGATTGCA
1 GGTAATGTGATTGCA
2243008 GGTAATGTGATTGCA
1 GGTAATGTGATTGCA
* *
2243023 AGTAATGTGATTACA
1 GGTAATGTGATTGCA
2243038 GG
1 GG
2243040 GAAAATAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (15 bp):
GGTAATGTGATTGCA
Found at i:2243267 original size:29 final size:27
Alignment explanation
Indices: 2243235--2243315 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 27
2243225 TAAATATATT
2243235 TTTAATATCATATATTTTATTTTTAATTA
1 TTTAATAT-AT-TATTTTATTTTTAATTA
*
2243264 TTTAA-ATATTTATATTTATTTTTAAATA
1 TTTAATATA-TTAT-TTTATTTTTAATTA
2243292 TTT-ATAT-TTATTATTATTTTTAAT
1 TTTAATATATTATT-TTATTTTTAAT
2243316 AATATCATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
25 1 0.02
26 14 0.30
27 5 0.11
28 21 0.46
29 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTAATATATTATTTTATTTTTAATTA
Found at i:2243289 original size:20 final size:21
Alignment explanation
Indices: 2243250--2243306 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
2243240 TATCATATAT
*
2243250 TTTATTTTTAATTATTTAAATA
1 TTTATATTT-ATTATTTAAATA
2243272 TTTATATTTATT-TTTAAATA
1 TTTATATTTATTATTTAAATA
2243292 TTTATATTTATTATT
1 TTTATATTTATTATT
2243307 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 20 0.61
21 5 0.15
22 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATTTATTATTTAAATA
Found at i:2243308 original size:26 final size:27
Alignment explanation
Indices: 2243247--2243314 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
2243237 TAATATCATA
*
2243247 TATT-TTATTTTTAATTATTTAAATATT
1 TATTATTATTTTTAAATATTT-AATATT
2243274 TA-TATTTATTTTTAAATATTT-ATATT
1 TATTA-TTATTTTTAAATATTTAATATT
2243300 TATTATTATTTTTAA
1 TATTATTATTTTTAA
2243315 TAATATCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 18 0.49
27 4 0.11
28 15 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTATTATTTTTAAATATTTAATATT
Found at i:2243319 original size:28 final size:28
Alignment explanation
Indices: 2243247--2243520 Score: 79
Period size: 26 Copynumber: 10.4 Consensus size: 28
2243237 TAATATCATA
2243247 TATT-TTATTTTTAAT--TATTTAAATATT
1 TATTATTATTTTTAATAATATTT--ATATT
2243274 TA-TATTTATTTTT-A-AATATTTATATT
1 TATTA-TTATTTTTAATAATATTTATATT
*
2243300 TATTATTATTTTTAATAATA-TCAT-TCT
1 TATTATTATTTTTAATAATATTTATAT-T
* *
2243327 TA-AATATATTTTTAAT-GTCATATT-T-TT
1 TATTAT-TATTTTTAATAAT-AT-TTATATT
* * *
2243354 TATTTTTAATTATTATATAATTTTTATATT
1 TATTATT-ATTTTTA-ATAATATTTATATT
* * * *
2243384 TATT-TTA-ATATATTTATATTTATA-T
1 TATTATTATTTTTAATAATATTTATATT
*
2243409 TATTA--ATTTTTATATAATA-TCATATT
1 TATTATTATTTTTA-ATAATATTTATATT
* *
2243435 T-TAATATATTTTTAAT-GTA--TATATT
1 TATTAT-TATTTTTAATAATATTTATATT
*
2243460 TATT-TTATTTATTATTAA-ATTT-TA--
1 TATTATTATTT-TTAATAATATTTATATT
2243484 TATTATTA--TTTAAT-A-ATTTATATTT
1 TATTATTATTTTTAATAATATTTATA-TT
*
2243509 TATTATAATTTT
1 TATTATTATTTT
2243521 ATATAATCAT
Statistics
Matches: 182, Mismatches: 28, Indels: 74
0.64 0.10 0.26
Matches are distributed among these distances:
21 5 0.03
22 6 0.03
23 1 0.01
24 10 0.05
25 36 0.20
26 40 0.22
27 34 0.19
28 36 0.20
29 7 0.04
30 7 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TATTATTATTTTTAATAATATTTATATT
Found at i:2243387 original size:30 final size:30
Alignment explanation
Indices: 2243352--2243527 Score: 89
Period size: 30 Copynumber: 5.8 Consensus size: 30
2243342 TGTCATATTT
2243352 TTTATTTTTAATTATTATATAATTTTTATA
1 TTTATTTTTAATTATTATATAATTTTTATA
*
2243382 TTTA-TTTTAATATATT-TAT-ATTTATATTA
1 TTTATTTTTAAT-TATTATATAATTTTTA-TA
* * *
2243411 TTAATTTTT-A-TATAATATCATATTTTA-A
1 TTTATTTTTAATTATTATATAAT-TTTTATA
* * *
2243439 TATATTTTTAATGTATATATTTATTTTATTTATTA
1 TTTATTTTTAAT-TAT-TATATA-ATT-TTTA-TA
* * * *
2243474 TTAAATTTTATATTATTATTTAATAATTTATA
1 TTTATTTTTA-ATTATTATATAAT-TTTTATA
*
2243506 TTT-TATTATAATT-TTATATAAT
1 TTTAT-TTTTAATTATTATATAAT
2243528 CATTTCTTAA
Statistics
Matches: 110, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
27 3 0.03
28 17 0.15
29 19 0.17
30 24 0.22
31 6 0.05
32 12 0.11
33 10 0.09
34 6 0.05
35 11 0.10
36 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTATTTTTAATTATTATATAATTTTTATA
Found at i:2243401 original size:29 final size:30
Alignment explanation
Indices: 2243346--2243938 Score: 134
Period size: 28 Copynumber: 20.7 Consensus size: 30
2243336 TTTTAATGTC
*
2243346 ATATTTTTTATTTTTAAT-TATTATATAATTT
1 ATATTATTTA-TTTTAATATATTATAT-ATTT
*
2243377 TTA-TATTTATTTTAATATATT-TATATTT
1 ATATTATTTATTTTAATATATTATATATTT
* * *
2243405 ATATTATTAATTTTTATATAATATCATATTT
1 ATATTATTTATTTTAATATATTAT-ATATTT
*
2243436 -TA--ATATATTTT--TA-ATGTATATATTT
1 ATATTATTTATTTTAATATAT-TATATATTT
* *
2243461 ATTTTATTTATTATTAA-ATTTTATAT-TATT
1 ATATTATTTATT-TTAATATATTATATAT-TT
* * * *
2243491 AT-TTAATAATTTATATTTTATTATA-ATTTT
1 ATATTATTTATTT-TAATATATTATATA-TTT
* * * *
2243521 ATATAATCATT-TCTTAA-ATATT-TTTAATGTC
1 ATATTAT--TTATTTTAATATATTATAT-AT-TT
*
2243552 ATA-T-TTTATTATT-AT-TATTATTAAATTT
1 ATATTATTTATT-TTAATATATTA-TATATTT
*
2243580 TTA-T-TTTATTTTAATATA-T-TATATTT
1 ATATTATTTATTTTAATATATTATATATTT
* *
2243606 ATATTA-TTAATTT-ATATAATATCATATTT
1 ATATTATTTATTTTAATATATTAT-ATATTT
* *
2243635 A-A--ATATATTTTAATGTCA-TAT-TA-TT
1 ATATTATTTATTTTAATAT-ATTATATATTT
2243660 -TA-T-TTTA-TTT-AT-TATTATA-ATTT
1 ATATTATTTATTTTAATATATTATATATTT
2243683 ATA-TATTTATTTTAATAT-TAT-TATATTT
1 ATATTATTTATTTTAATATAT-TATATATTT
* * *
2243711 -TATTATTAATTTTTATATA-TATCATTTCTT
1 ATATTATTTATTTTAATATATTAT-ATAT-TT
* * * * *
2243741 AAATATATTTTAATGTCATATATTTTATTATTT
1 ATAT-TA-TTTATTTTAATATATTATA-TATTT
*
2243774 AT-TTATTATATTTT-ATAT-TT-TATTTTT
1 ATATTATT-TATTTTAATATATTATATATTT
2243801 A-ATATATTTATATTTAAT-TATTA-AT-TTT
1 ATAT-TATTTAT-TTTAATATATTATATATTT
* * * *
2243829 ATATAATATCATTTCCTAAATATATTTTA-ATATC
1 ATATTAT-TTATTT--T-AATATATTATATAT-TT
* * *
2243863 ATA-TATTT-TATTATTATTTTATATATTT
1 ATATTATTTATTTTAATATATTATATATTT
2243891 -TA-TATTTTATTTTTAATATATT-TATATTT
1 ATATTA-TTTA-TTTTAATATATTATATATTT
*
2243920 ATATTATTAATTTT-ATATA
1 ATATTATTTATTTTAATATA
2243939 ATATCATTTT
Statistics
Matches: 413, Mismatches: 67, Indels: 167
0.64 0.10 0.26
Matches are distributed among these distances:
21 1 0.00
22 5 0.01
23 4 0.01
24 6 0.01
25 17 0.04
26 25 0.06
27 38 0.09
28 102 0.25
29 83 0.20
30 61 0.15
31 34 0.08
32 10 0.02
33 19 0.05
34 8 0.02
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (30 bp):
ATATTATTTATTTTAATATATTATATATTT
Found at i:2243506 original size:63 final size:60
Alignment explanation
Indices: 2243391--2243809 Score: 159
Period size: 61 Copynumber: 6.9 Consensus size: 60
2243381 ATTTATTTTA
*
2243391 ATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAATATATTTTTAATGT
1 ATATATTTATATTTATATTATTAAATTTTATAT-ATAT-ATATTTTAATATATTTTTAATGT
*
2243453 ATATATTTAT-TTTATTTATTATTAAATTTTATAT-TAT-TATTTAATAATTTATATTTT-AT-T
1 ATATATTTATATTTA--TATTATTAAATTTTATATATATATATTT--TAATATAT-TTTTAATGT
* * * * * *
2243513 ATA-ATTT-TATATAATCATTTCTTAAATATTTTTA-ATGTCATATTTTATTATTATTATT-AT-
1 ATATATTTATAT-TTAT-A-TTATTAAAT-TTTATATATAT-ATATTTTAATA-TATTTTTAATG
2243573 T
60 T
* * * * * * * *
2243574 AAATTTTTAT-TTTATTTTAATATATTATATTTATATTATTAATTTATATAATATCATATTTAA-
1 ATATATTTATATTTATATTATTAAATTTTATATATA-TA-T-A-TT-T-TAATAT-ATTTTTAAT
*
2243637 AT
59 GT
* * * * *
2243639 ATAT-TTTA-ATGTCATATTATT-TATTTTATTTATTATTATAATTTATATATTTATTTTAA--T
1 ATATATTTATAT-TTATATTATTAAATTTTATATA-TA-TATATTTTA-ATATAT-TTTTAATGT
*
2243699 AT-TA-TTATATTT-TATTATTAATTTTTATATATATCAT-TTCTTAA-ATATATTTTAATGT
1 ATATATTTATATTTATATTATTAAATTTTATATATAT-ATATT-TTAATATAT-TTTTAATGT
* *
2243757 CATATATTTTATTATTTAT-TTATTATATTTTATAT-TTTAT-TTTTAATATATTT
1 -ATATA-TTTA-TATTTATATTATTAAATTTTATATATATATATTTTAATATATTT
2243810 ATATTTAATT
Statistics
Matches: 272, Mismatches: 40, Indels: 92
0.67 0.10 0.23
Matches are distributed among these distances:
56 10 0.04
57 3 0.01
58 20 0.07
59 35 0.13
60 32 0.12
61 56 0.21
62 29 0.11
63 45 0.17
64 25 0.09
65 17 0.06
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (60 bp):
ATATATTTATATTTATATTATTAAATTTTATATATATATATTTTAATATATTTTTAATGT
Found at i:2243508 original size:104 final size:103
Alignment explanation
Indices: 2243192--2244301 Score: 1180
Period size: 105 Copynumber: 10.9 Consensus size: 103
2243182 AGTTAATAAT
** * * *
2243192 TTTATTATTATTTTTTTTATATAATATCATTCCTAAATATATTTTTAATATCATATATTT-TATT
1 TTTA-TATTATTAATTTTATATAATATCATT-TTTAA-ATATTTTTAATGTCATATATTTAT-TT
*
2243256 T-TTAATTATTTAAATATTTATA-TTTATTTTTAA-ATATTTATA
62 TATTTATTA-TTAAAT-TTTATATTTTA-TTTTAATATATTTATA
* * *
2243298 -TT-TATTATTATTTTTA-ATAATATCATTCTTAAATATATTTTTAATGTCATATTTTTTATTTT
1 TTTATATTATTAATTTTATATAATATCATT-TTTAA-ATATTTTTAATGTCATA-TATTTA-TTT
* *
2243360 TAATTATTATATAATTTTTATA-TTTATTTTAATATATTTATA
62 TATTTATTAT-TAAATTTTATATTTTATTTTAATATATTTATA
2243402 TTTATATTATTAATTTTTATATAATATCATATTTTAATATATTTTTAATGT-ATATATTTATTTT
1 TTTATATTATTAA-TTTTATATAATATCAT-TTTTAA-ATATTTTTAATGTCATATATTTATTTT
2243466 ATTTATTATTAAATTTTATATTATTA-TTTAATA-ATTTATA
63 ATTTATTATTAAATTTTATATT-TTATTTTAATATATTTATA
2243506 TTT-TATTA-TAATTTTATAT-A-ATCATTTCTTAAATATTTTTAATGTCATAT-TTTATTATTA
1 TTTATATTATTAATTTTATATAATATCATTT-TTAAATATTTTTAATGTCATATATTTATT-TTA
2243566 -TTATTATTAAATTTT-TATTTTATTTTAATATA-TTATA
64 TTTATTATTAAATTTTATATTTTATTTTAATATATTTATA
*
2243603 TTTATATTATTAA-TTTATATAATATCATATTTAAATATATTTTAATGTCATATTATTTATTTTA
1 TTTATATTATTAATTTTATATAATATCATTTTTAAATAT-TTTTAATGTCATA-TATTTATTTTA
2243667 TTTATTATTATAA-TTTATATATTTATTTTAATAT-TATTATA
64 TTTATTATTA-AATTTTATAT-TTTATTTTAATATAT-TTATA
*
2243708 TTT-TATTATTAATTTT-TATATATATCATTTCTTAAATATATTTTAATGTCATATATTT-TATT
1 TTTATATTATTAATTTTATATA-ATATCATTT-TTAAATAT-TTTTAATGTCATATATTTATTTT
*
2243770 ATTTATTTATTATATTTTATATTTTATTTTTAATATATTTATA
63 ATTTA-TTATTAAATTTTATATTTTA-TTTTAATATATTTATA
* *
2243813 TTTA-ATTATTAATTTTATATAATATCATTTCCTAAATATATTTTAATATCATATATTTTATTAT
1 TTTATATTATTAATTTTATATAATATCATTT-TTAAATAT-TTTTAATGTCATATA-TTTATT-T
*
2243877 TA-TT-TTA-TATATTTTATATTTTATTTTTAATATATTTATA
62 TATTTATTATTAAATTTTATATTTTA-TTTTAATATATTTATA
*
2243917 TTTATATTATTAATTTTATATAATATCATTTTTAAATATATTTAATGTCATATTATTTA-TTTAT
1 TTTATATTATTAATTTTATATAATATCATTTTTAAATATTTTTAATGTCATA-TATTTATTTTA-
* *
2243981 TTTATTA-TATATTTAAT-TTTTA-TTTAATATA-TTATA
64 TTTATTATTAAATTTTATATTTTATTTTAATATATTTATA
* *
2244017 --TATA-TATTAA-TTTATATAATATCATTTTAAAATATATTTAAT-TC--ATA--TATTTTATT
1 TTTATATTATTAATTTTATATAATATCATTTTTAAATATTTTTAATGTCATATATTTATTTTATT
*
2244073 T-TTATT--A-TATA-ATTTTATTTTAAT-TATTTTATA
66 TATTATTAAATTTTATATTTTATTTTAATATA-TTTATA
* *
2244106 TTT-TTTTA-TAATTTTATATAATATCATTTCTAAATATATTTTTAATGTCATATATTTTATTTT
1 TTTATATTATTAATTTTATATAATATCATTT-TTAA-ATATTTTTAATGTCATATA-TTTATTTT
2244169 ATTTATTATTAATATTTTATATTTTATTTTTAATATATTTATA
63 ATTTATTATTAA-ATTTTATATTTTA-TTTTAATATATTTATA
*
2244212 --TATATTATTAATTTTATATAATATCATTTCTAAATATATTTTAATGTCA-ATATTT-TATTTA
1 TTTATATTATTAATTTTATATAATATCATTTTTAAATAT-TTTTAATGTCATATATTTAT-TTTA
*
2244273 TTT-TATATTAATTTTATATATTTTATTTT
64 TTTAT-TATTAAATTT-TATATTTTATTTT
2244302 TATTTCTTAA
Statistics
Matches: 891, Mismatches: 33, Indels: 164
0.82 0.03 0.15
Matches are distributed among these distances:
87 9 0.01
88 7 0.01
89 8 0.01
90 10 0.01
91 24 0.03
92 6 0.01
93 11 0.01
94 2 0.00
95 2 0.00
96 37 0.04
97 25 0.03
98 53 0.06
99 38 0.04
100 30 0.03
101 24 0.03
102 64 0.07
103 81 0.09
104 151 0.17
105 184 0.21
106 80 0.09
107 13 0.01
108 31 0.03
109 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (103 bp):
TTTATATTATTAATTTTATATAATATCATTTTTAAATATTTTTAATGTCATATATTTATTTTATT
TATTATTAAATTTTATATTTTATTTTAATATATTTATA
Found at i:2243514 original size:22 final size:23
Alignment explanation
Indices: 2243458--2243515 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2243448 AATGTATATA
*
2243458 TTTATTTTATT-TATTATTAAAT
1 TTTATTTTATTATATTAATAAAT
*
2243480 TTTATATTATTAT-TTAAT-AAT
1 TTTATTTTATTATATTAATAAAT
2243501 TTATATTTTATTATA
1 TT-TATTTTATTATA
2243516 ATTTTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.17
22 24 0.80
23 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTTATTATATTAATAAAT
Found at i:2243631 original size:77 final size:76
Alignment explanation
Indices: 2243545--2244238 Score: 276
Period size: 77 Copynumber: 9.1 Consensus size: 76
2243535 TAAATATTTT
* *
2243545 TAATGTCATATTTTATTATTATTATTATTAAATTTTTATTTTATTTTAATATATTATATTTATAT
1 TAATATCATATTTTATTATTATT-TTATTATATTTTTATTTTATTTTAATATATTATATTTATAT
2243610 TATTAATTTATA
65 TATTAATTTATA
* *
2243622 TAATATCATATTTAAATA-TATTTTAATGTCATATTATTTATTTTA-TTT-AT-TATTATAATTT
1 TAATATCATATTTTATTATTATTTT-AT-T-ATATT-TTTATTTTATTTTAATATATTAT-ATTT
*
2243683 ATA-TATTTATTT-TAA
61 ATATTATTAATTTAT-A
* * * * *
2243698 TATTATTATATTTTATTATTAATTTTTATATATATCATTTCTTAAATATATTTTAATGTCA-TAT
1 TAATATCATATTTTATTATT-A--TTT-TAT-TAT-ATTT-TT-ATTTTATTTTAATAT-ATTAT
*
2243762 ATTT-TATTATTTATTTAT-
57 ATTTATATTATTAATTTATA
* * * * * * *
2243780 TATATTTTATATTTTATTTTTAATATATTTATATTTAATTA-TTAATTTT-ATATAATATCATTT
1 TA-ATATCATATTTTATTATTATTTTA-TTATATTT--TTATTTTATTTTAATATATTAT-ATTT
* * *
2243843 CCTA-AATATATTTTA-A
61 -ATATTAT-TAATTTATA
2243859 T-ATCAT-ATATTTTATTATTATTTTA-TATATTTTATATTTTATTTTTAATATATTTATATTTA
1 TAAT-ATCATATTTTATTATTATTTTATTATATTTT-TATTTTA-TTTTAATATA-TTATATTTA
2243921 TATTATTAATTTTATA
62 TATTATTAA-TTTATA
* *
2243937 TAATATCAT-TTTTA-AATATATTTAATGTCATATTATTTA-TTTATTTT-AT-TA-TATATTTA
1 TAATATCATATTTTATTAT-TATTTTAT-T-ATATT-TTTATTTTATTTTAATATATTATATTTA
*
2243996 -ATT-TTTATTTA-A
62 TATTATTAATTTATA
* * * ***
2244008 T-ATATTATA-TATA-TATTAATTTATATAATATCATTTTAAAATATATTTAAT-TCA-TATATT
1 TAATATCATATTTTATTATT-ATTT-TATTATAT--TTTTATTTTAT-TTTAATAT-ATTATATT
*
2244068 T-TATT-TTTA-TTATA
60 TATATTATTAATTTATA
* * * * *
2244082 TAAT-T-TTATTTTA--ATTATTTTA-TAT-TTTTT-TATAATTTT-ATATAATATCATTTCTA-
1 TAATATCATATTTTATTATTATTTTATTATATTTTTATTTTATTTTAATATATTAT-ATTTATAT
*
2244138 -AATATATTT-T-
65 TATTA-ATTTATA
*
2244148 TAATGTCATATATTTTATT-TTATTTATTATTAATATTTTATATTTTATTTTTAATATATT-TAT
1 TAATATC--ATATTTTATTATTA-TT-TTATT-ATATTTT-TATTTTA-TTTTAATATATTATAT
*
2244211 ATATATTATTAATTTTATA
59 TTATATTATTAA-TTTATA
2244230 TAATATCAT
1 TAATATCAT
2244239 TTCTAAATAT
Statistics
Matches: 473, Mismatches: 59, Indels: 167
0.68 0.08 0.24
Matches are distributed among these distances:
64 3 0.01
65 7 0.01
66 12 0.03
67 9 0.02
68 2 0.00
69 6 0.01
70 28 0.06
71 13 0.03
72 13 0.03
73 18 0.04
74 27 0.06
75 26 0.05
76 53 0.11
77 74 0.16
78 44 0.09
79 41 0.09
80 32 0.07
81 13 0.03
82 16 0.03
83 30 0.06
84 5 0.01
85 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (76 bp):
TAATATCATATTTTATTATTATTTTATTATATTTTTATTTTATTTTAATATATTATATTTATATT
ATTAATTTATA
Found at i:2243669 original size:9 final size:10
Alignment explanation
Indices: 2243653--2243717 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 10
2243643 TTTAATGTCA
2243653 TATTATTTAT
1 TATTATTTAT
2243663 T-TTATTTAT
1 TATTATTTAT
*
2243672 TATTA-TAATT
1 TATTATTTA-T
2243682 TATATATTTAT
1 TAT-TATTTAT
*
2243693 T-TTA-ATAT
1 TATTATTTAT
2243701 TATTATATT-T
1 TATTAT-TTAT
2243711 TATTATT
1 TATTATT
2243718 AATTTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
8 4 0.09
9 17 0.39
10 16 0.36
11 5 0.11
12 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATTTAT
Found at i:2243901 original size:187 final size:186
Alignment explanation
Indices: 2243675--2244316 Score: 632
Period size: 198 Copynumber: 3.3 Consensus size: 186
2243665 TATTTATTAT
* *
2243675 TATAATTTATATATTTATTTTA-ATATTATTATATTTTATTATTAATTTTTATATATATCATTTC
1 TATATTTTAT-TA-TTATTTTATATATT-TTATATTTTATTTTTAATTTTTATATATATCATTTC
2243739 TTAAATATA-TTTTAATGTCATATATTTTATTATTTATTTATTATATTTTATATTTTATTTTTAA
63 TTAAATATATTTTTAATGTCATATATTTTATTATTTATTTATTATATTTTATATTTTATTTTTAA
2243803 TATATTTATATTTAATTATTAATTTTATATAATATCATTTCCTAAATATATTTTAATATCA
128 TATATTTATATTTAATTATTAATTTTATATAATATCATTT-CTAAATATATTTTAAT-TCA
*
2243864 TATATTTTATTATTATTTTATATATTTTATATTTTATTTTTAATATATTTATATTTATATTATTA
1 TATATTTTATTATTATTTTATATATTTTATATTTTATTTTTAAT-T-TTTATA--TATATCA-T-
* * * * * *
2243929 ATTTTATATAATATCATTTTTAAATAT-ATTTAATGTCATATTATTTATTTATTTTATTATATAT
60 -TTCT-TA-AATAT-ATTTTT-AATGTCATAT-AT-T-TTATTATTTATTTATTATATTTTATAT
* * *
2243993 TTAATTTTT-ATTTA-ATATATTATATATATATTAA-TTTATATAATATCATTT-TAAA-ATATA
117 TTTATTTTTAATATATTTATATT-TA-AT-TATTAATTTTATATAATATCATTTCTAAATATAT-
2244053 TTTAATTCA
178 TTTAATTCA
* * *
2244062 TATATTTTATTTTTATTATATAATTTTATTTTAATTATTTTATATTTTTTTATAATTTTATATAA
1 TATATTTTATTATTATT-T-T-A-TATATTTT-A-TA-TTT-TA--TTTTTA-ATTTTTATAT-A
2244127 TATCATTTC-TAAATATATTTTTAATGTCATATATTTTATTTTATTTA-TTATTAATATTTTATA
54 TATCATTTCTTAAATATATTTTTAATGTCATATATTTTA--TTATTTATTTATT-ATATTTTATA
*
2244190 TTTTATTTTTAATATATTTATATAT-ATTATTAATTTTATATAATATCATTTCTAAATATATTTT
116 TTTTATTTTTAATATATTTATATTTAATTATTAATTTTATATAATATCATTTCTAAATATATTTT
2244254 AATGTCA
181 AAT-TCA
2244261 -ATATTTTA-T-TTATTTTATATTAATTTTATATATTTTATTTTT-ATTTCTTA-ATATAT
1 TATATTTTATTATTATTTTATA-T-A-TTT-TATATTTTATTTTTAATTT-TTATATATAT
2244317 TTTTATATTA
Statistics
Matches: 378, Mismatches: 28, Indels: 96
0.75 0.06 0.19
Matches are distributed among these distances:
187 29 0.08
188 13 0.03
189 18 0.05
190 5 0.01
191 6 0.02
192 4 0.01
193 5 0.01
194 7 0.02
195 7 0.02
196 19 0.05
197 27 0.07
198 78 0.21
199 44 0.12
200 18 0.05
201 54 0.14
202 13 0.03
203 3 0.01
204 2 0.01
205 5 0.01
206 7 0.02
207 6 0.02
208 7 0.02
209 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (186 bp):
TATATTTTATTATTATTTTATATATTTTATATTTTATTTTTAATTTTTATATATATCATTTCTTA
AATATATTTTTAATGTCATATATTTTATTATTTATTTATTATATTTTATATTTTATTTTTAATAT
ATTTATATTTAATTATTAATTTTATATAATATCATTTCTAAATATATTTTAATTCA
Found at i:2243970 original size:46 final size:45
Alignment explanation
Indices: 2243899--2244280 Score: 167
Period size: 46 Copynumber: 7.9 Consensus size: 45
2243889 TTTATATTTT
*
2243899 ATTTTT-AATATATTTATATTTATATTATTAATTTTATATAATATC
1 ATTTTTAAATATATTTA-ATTCATATTATTAATTTTATATAATATC
* *
2243944 ATTTTTAAATATATTTAATGTCATATTATTTATTTATTTTATTATATATTTA
1 ATTTTTAAATATATTTAAT-TCATATTA-TTA---ATTTTA-TATA-ATATC
2243996 ATTTTTATTTAATATA-TT-A-T-ATATATATTAA-TTTATATAATATC
1 ATTTTTA---AATATATTTAATTCATAT-TATTAATTTTATATAATATC
* * * *
2244040 ATTTTAAAATATATTTAATTCATATATTTTATTTTTAT-TATATAATT
1 ATTTTTAAATATATTTAATTCATAT-TATTAATTTTATATA-AT-ATC
* * * *
2244087 TTATTTTAATTAT-TTTATATT-TTTTTA-TAATTTTATATAATATC
1 AT-TTTTAAATATATTTA-ATTCATATTATTAATTTTATATAATATC
* * * *
2244131 ATTTCTAAATATATTTTTAATGTCATATATTTTATTTTATTTATTATTAATATTTT
1 ATTTTTAAATATA--TTTAAT-TCATAT-TATTA--AT-TTTA-TA-TAATA--TC
2244187 ATATTTTATTTTTAATATATTT-ATAT-ATATTATTAATTTTATATAATATC
1 AT-TTTTA-----AATATATTTAAT-TCATATTATTAATTTTATATAATATC
* *
2244237 ATTTCTAAATATATTTTAATGTCAATATTTTATTTATTTTATAT
1 ATTTTTAAATATA-TTTAAT-TC-ATA--TTATTAATTTTATAT
2244281 TAATTTTATA
Statistics
Matches: 256, Mismatches: 33, Indels: 91
0.67 0.09 0.24
Matches are distributed among these distances:
41 6 0.02
42 2 0.01
43 9 0.04
44 19 0.07
45 38 0.15
46 39 0.15
47 15 0.06
48 15 0.06
49 6 0.02
50 30 0.12
51 8 0.03
52 19 0.07
53 5 0.02
54 11 0.04
55 7 0.03
56 3 0.01
57 8 0.03
58 4 0.02
59 3 0.01
60 3 0.01
62 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (45 bp):
ATTTTTAAATATATTTAATTCATATTATTAATTTTATATAATATC
Found at i:2244076 original size:31 final size:31
Alignment explanation
Indices: 2243944--2244076 Score: 78
Period size: 31 Copynumber: 4.2 Consensus size: 31
2243934 ATATAATATC
2243944 ATTTTT-AAATATATTTAATGTCATATTATTTAT
1 ATTTTTAAAATATATTTAAT-TCATA-TATTT-T
* ** * *
2243977 TTATTTTATTATATATTTAATT--TTTATTTA
1 AT-TTTTAAAATATATTTAATTCATATATTTT
* * * * *
2244007 ATATATT-ATATATATATTAATTTATATAATATC
1 AT-TTTTAAAATATAT-TTAATTCATAT-ATTTT
2244040 A-TTTTAAAATATATTTAATTCATATATTTT
1 ATTTTTAAAATATATTTAATTCATATATTTT
2244070 ATTTTTA
1 ATTTTTA
2244077 TTATATAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
29 7 0.09
30 15 0.20
31 23 0.30
32 10 0.13
33 5 0.07
34 5 0.07
35 11 0.14
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTTAAAATATATTTAATTCATATATTTT
Found at i:2244099 original size:9 final size:10
Alignment explanation
Indices: 2244068--2244124 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 10
2244058 TTCATATATT
2244068 TTATTTT-TA
1 TTATTTTATA
* * *
2244077 TTATATAATT
1 TTATTTTATA
2244087 TTATTTTA-A
1 TTATTTTATA
2244096 TTATTTTATA
1 TTATTTTATA
2244106 TT-TTTT-TA
1 TTATTTTATA
*
2244114 TAATTTTATA
1 TTATTTTATA
2244124 T
1 T
2244125 AATATCATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
8 3 0.08
9 21 0.57
10 13 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTTATA
Found at i:2244141 original size:91 final size:89
Alignment explanation
Indices: 2243907--2244199 Score: 278
Period size: 91 Copynumber: 3.2 Consensus size: 89
2243897 TTATTTTTAA
* * *
2243907 TATATTTATATTTATATTATTAATTTTATATAATATCATTTTTAAATATA-TTTAATGTCATATT
1 TATATTT-TATTTTTTTTA-TAATTTTATATAATATCATTTTAAAATATATTTTAATGTCATA-T
*
2243971 ATTTATTTATTTTATTATATATTTAAT-TTT
63 A--T-TTTATTTTATT-TATAATTAATATTT
* *
2244001 TAT-TTAATATATTATATATATATTAA-TTTATATAATATCATTTTAAAATATA-TTTAAT-TCA
1 TATATT--T-TATT-T-TTTTTA-TAATTTTATATAATATCATTTTAAAATATATTTTAATGTCA
*
2244062 TATATTTTATTTTTATTATATAATT-TTATTT
60 TATATTTTA-TTTTATT-TATAATTAATATTT
2244093 TAATTATTTTATATTTTTTTATAATTTTATATAATATCATTTCT-AAATATATTTTTAATGTCAT
1 T-A-TATTTTAT-TTTTTTTATAATTTTATATAATATCATTT-TAAAATATA-TTTTAATGTCAT
*
2244157 ATATTTTATTTTATTTATTATTAATATTT
61 ATATTTTATTTTATTTATAATTAATATTT
2244186 TATATTTTATTTTT
1 TATATTTTATTTTT
2244200 AATATATTTA
Statistics
Matches: 172, Mismatches: 11, Indels: 36
0.79 0.05 0.16
Matches are distributed among these distances:
90 7 0.04
91 41 0.24
92 31 0.18
93 24 0.14
94 18 0.10
95 13 0.08
96 32 0.19
97 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (89 bp):
TATATTTTATTTTTTTTATAATTTTATATAATATCATTTTAAAATATATTTTAATGTCATATATT
TTATTTTATTTATAATTAATATTT
Found at i:2244160 original size:54 final size:53
Alignment explanation
Indices: 2244102--2244280 Score: 178
Period size: 54 Copynumber: 3.4 Consensus size: 53
2244092 TTAATTATTT
*
2244102 TATATTTTTTTATAATTTTATATAATATCATTTCTAAATATATTTTTAATGTCA
1 TATATTTTATT-TAATTTTATATAATATCATTTCTAAATATATTTTTAATGTCA
* * * * *
2244156 TATATTTTATTTTA-TTTAT-TATTAAT-ATTT-TATATTTTATTTTTAATAT-A
1 TATATTTTATTTAATTTTATATAAT-ATCATTTCTA-AATATATTTTTAATGTCA
2244206 TTTATATATATTA-TTAATTTTATATAATATCATTTCTAAATATA-TTTTAATGTCA
1 --TATAT-T-TTATTTAATTTTATATAATATCATTTCTAAATATATTTTTAATGTCA
2244261 -ATATTTTATTT-ATTTTATAT
1 TATATTTTATTTAATTTTATAT
2244281 TAATTTTATA
Statistics
Matches: 102, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
50 15 0.15
51 23 0.23
52 16 0.16
53 6 0.06
54 28 0.27
55 12 0.12
56 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (53 bp):
TATATTTTATTTAATTTTATATAATATCATTTCTAAATATATTTTTAATGTCA
Found at i:2244181 original size:30 final size:30
Alignment explanation
Indices: 2244142--2244198 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2244132 TTTCTAAATA
* *
2244142 TATTTTTAATGTCATATATTTTATTTTATT
1 TATTATTAATATCATATATTTTATTTTATT
**
2244172 TATTATTAATATTTTATATTTTATTTT
1 TATTATTAATATCATATATTTTATTTT
2244199 TAATATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
TATTATTAATATCATATATTTTATTTTATT
Found at i:2244186 original size:18 final size:18
Alignment explanation
Indices: 2244163--2244223 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 18
2244153 TCATATATTT
2244163 TATTTTATTTATTATTAA
1 TATTTTATTTATTATTAA
*
2244181 TATTTTATATTTTATTTTTAA
1 TA-TTT-TA-TTTATTATTAA
2244202 TATATTTATATATATTATTAA
1 TAT-TTTAT-T-TATTATTAA
2244223 T
1 T
2244224 TTTATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 6 0.17
21 23 0.66
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTATTTATTATTAA
Found at i:2244282 original size:106 final size:108
Alignment explanation
Indices: 2244075--2244336 Score: 337
Period size: 106 Copynumber: 2.4 Consensus size: 108
2244065 ATTTTATTTT
* * *
2244075 TATTATATAATTTTA-TTTTAAT-TATTTTATATTTTTTTATAATTTTATATAATATCATTTCTA
1 TATTTTAT-ATTTTATTTTTAATATATTTTATA-TATTAT-TAATTTTATATAATATCATTTCTA
2244138 AATATATTTTTAATGTCATATATTTTATTTTATTTATT-A-TTA-A
63 AATATATTTTTAATGTCATATATTTTATTTTATTTATTAATTTATA
2244181 TATTTTATATTTTATTTTTAATATATTTATATATATTATTAATTTTATATAATATCATTTCTAAA
1 TATTTTATATTTTATTTTTAATATATTT-TATATATTATTAATTTTATATAATATCATTTCTAAA
*
2244246 TATA-TTTTAATGTCA-ATATTTTATTTATTTTATATTAATTTTATA
65 TATATTTTTAATGTCATATATTTTATTT-TATT-TATTAA-TTTATA
2244291 TATTTTAT-TTTTATTTCTTAATATATTTT-TATATTA-TATATTTTAT
1 TATTTTATATTTTATTT-TTAATATATTTTATATATTATTA-ATTTTAT
2244337 TTTAATTGTT
Statistics
Matches: 141, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
104 11 0.08
105 20 0.14
106 48 0.34
107 12 0.09
108 18 0.13
109 12 0.09
110 20 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (108 bp):
TATTTTATATTTTATTTTTAATATATTTTATATATTATTAATTTTATATAATATCATTTCTAAAT
ATATTTTTAATGTCATATATTTTATTTTATTTATTAATTTATA
Found at i:2244286 original size:11 final size:10
Alignment explanation
Indices: 2244262--2244298 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
2244252 TTAATGTCAA
2244262 TATTTTAT-T
1 TATTTTATAT
2244271 TATTTTATAT
1 TATTTTATAT
2244281 TAATTTTATA-
1 T-ATTTTATAT
2244291 TATTTTAT
1 TATTTTAT
2244299 TTTTATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 15 0.58
10 3 0.12
11 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTATAT
Found at i:2244306 original size:20 final size:20
Alignment explanation
Indices: 2244262--2244339 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
2244252 TTAATGTCAA
* *
2244262 TATTTTATTTATTTTATATT
1 TATTTTATATATTTTATTTT
*
2244282 AATTTTATATATTTTATTTT
1 TATTTTATATATTTTATTTT
*
2244302 TATTTCT-TA-A-TATATTTT
1 TATTT-TATATATTTTATTTT
*
2244320 TATATTATATATTTTATTTT
1 TATTTTATATATTTTATTTT
2244340 AATTGTTTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.28
19 2 0.04
20 30 0.64
21 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTATATATTTTATTTT
Found at i:2244317 original size:293 final size:286
Alignment explanation
Indices: 2243681--2244335 Score: 788
Period size: 293 Copynumber: 2.3 Consensus size: 286
2243671 TTATTATAAT
* * * * *
2243681 TTATATATTTATTTTAATAT-TATTATATTTTATTA-TTAAT-TTTTATATATATCATTTCT-TA
1 TTATTTATTTATTTTATTATATATT-TAATTT-TTATTTAATATATTATATATAT-ATTTTTATA
* * * *
2243742 -AATATATTTTAATGTCATATATTTTATTATTTATTTATTATATTTTATATTTTATTTTTAATAT
63 TAATATATTTTAA---AATATATTTAATTATATATTTATTATATTATATATTTTATTTTTAATAT
2243806 ATTTATATTTAATTATTAATTTTATATAATATCATTTCCTAAATATATTTTAATATCATATATTT
125 ATTTATATTTAATTATTAATTTTATATAATATCATTTCCTAAATATATTTTAATATCATATATTT
2243871 TATTATTATTTTATATATTTTATATTTTATTTTTAATATATTTATATTTATATTATTAATTTTAT
190 TATTATTATTTTATATATTTTATATTTTATTTTTAATATATTTATA-TTATATTATTAATTTTAT
*
2243936 ATAATATCATTTTTAAATATATTTAATGTCATA
254 ATAATATCATTTCTAAATATATTTAATGTCATA
2243969 TTATTTATTTATTTTATTATATATTTAATTTTTATTTAATATATTATATATATATTAATTTATAT
1 TTATTTATTTATTTTATTATATATTTAATTTTTATTTAATATATTATATATATATT--TTTATAT
*
2244034 AATATCATTTTAAAATATATTTAATTCATATATTTTATTTTTATTATATAATTTTA-TTTTAAT-
64 AATAT-ATTTTAAAATATATTTAATT-ATATA-TTTA-TTATATTATAT-ATTTTATTTTTAATA
** *
2244097 TATTTTATATTTTTTTA-TAATTTTATATAATATCATTT-CTAAATATATTTTTAATGTCATATA
124 TA-TTTATATTTAATTATTAATTTTATATAATATCATTTCCTAAATATA-TTTTAATATCATATA
2244160 TTTTATT-TTATTTATTATTAATATTTTATATTTTATTTTTAATATATTTATA-TATATTATTAA
187 TTTTATTATTA-TT-TTA-T-ATATTTTATATTTTATTTTTAATATATTTATATTATATTATTAA
2244223 TTTTATATAATATCATTTCTAAATATATTTTAATGTCA-A
248 TTTTATATAATATCATTTCTAAATATA-TTTAATGTCATA
* *
2244262 -TATTTTATTTATTTTA-TAT-TAATTTTATATATTTTATTT-TTAT-TTCT-TAATATATTTTT
1 TTA-TTTATTTATTTTATTATAT-A-TTTA-AT-TTTTATTTAATATATTATAT-ATATATTTTT
*
2244321 ATATTATATATTTTA
60 ATATAATATATTTTA
2244336 TTTTAATTGT
Statistics
Matches: 325, Mismatches: 17, Indels: 48
0.83 0.04 0.12
Matches are distributed among these distances:
287 3 0.01
288 31 0.10
289 15 0.05
290 19 0.06
291 30 0.09
292 62 0.19
293 103 0.32
294 22 0.07
295 40 0.12
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (286 bp):
TTATTTATTTATTTTATTATATATTTAATTTTTATTTAATATATTATATATATATTTTTATATAA
TATATTTTAAAATATATTTAATTATATATTTATTATATTATATATTTTATTTTTAATATATTTAT
ATTTAATTATTAATTTTATATAATATCATTTCCTAAATATATTTTAATATCATATATTTTATTAT
TATTTTATATATTTTATATTTTATTTTTAATATATTTATATTATATTATTAATTTTATATAATAT
CATTTCTAAATATATTTAATGTCATA
Found at i:2244366 original size:49 final size:48
Alignment explanation
Indices: 2244317--2244420 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 48
2244307 CTTAATATAT
2244317 TTTTATATTATATATTTTATTTTAA-TTGTTTACCTATATTAATAAATATTAA
1 TTTTATATT-T-TATTTTA-TTTAATTTGTTT-CCTATATTAATAAATATT-A
* * *
2244369 TTTTATATTTTATTTTATTTAATTTGTTTCTTATATT-ATATATTTTA
1 TTTTATATTTTATTTTATTTAATTTGTTTCCTATATTAATAAATATTA
2244416 TTTTA
1 TTTTA
2244421 ATTATAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
47 6 0.12
48 7 0.15
49 12 0.25
50 13 0.27
51 1 0.02
52 9 0.19
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (48 bp):
TTTTATATTTTATTTTATTTAATTTGTTTCCTATATTAATAAATATTA
Found at i:2244381 original size:108 final size:110
Alignment explanation
Indices: 2244075--2244393 Score: 273
Period size: 106 Copynumber: 3.0 Consensus size: 110
2244065 ATTTTATTTT
* * *
2244075 TATTATATAATTTTA-TTTTAAT-TATTT-TATATTTTTTTATAATTTTATATAATATCATTTCT
1 TATTTTAT-ATTTTATTTTTAATATATTTATATA-TATTAT-TAATTTTATATAATATCATTTCT
* * *
2244137 AAATATAT-T---T-TTAATGTCATATATTTTATTTTATTT-ATTATTAA
63 AAATATATATAAATATCAATAT-TTATATTTTATTTTATTTAATT-TTAA
2244181 TATTTTATATTTTATTTTTAATATATTTATATATATTATTAATTTTATATAATATCATTTCTAAA
1 TATTTTATATTTTATTTTTAATATATTTATATATATTATTAATTTTATATAATATCATTTCTAAA
* * *
2244246 TATATTTTAATGTCAATATTT-TA-TTTATTTTATATTAATTTTATA
66 TATATATAAATATCAATATTTATATTTTATTTTAT-TTAATTTTA-A
* *
2244291 TATTTTAT-TTTTATTTCTTAATATATTT-T-TATATTA-TATATTTTATTTTAAT-T-GTTTAC
1 TATTTTATATTTTATTT-TTAATATATTTATATATATTATTA-ATTTTA-TATAATATCATTT--
* *
2244350 CTATAT-TA-ATAAATATTAAT-TTTATATTTTATTTTATTTAATTT
61 CTAAATATATATAAATATCAATATTTATATTTTATTTTATTTAATTT
2244394 GTTTCTTATA
Statistics
Matches: 182, Mismatches: 13, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
105 6 0.03
106 48 0.26
107 32 0.18
108 40 0.22
109 26 0.14
110 25 0.14
111 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (110 bp):
TATTTTATATTTTATTTTTAATATATTTATATATATTATTAATTTTATATAATATCATTTCTAAA
TATATATAAATATCAATATTTATATTTTATTTTATTTAATTTTAA
Found at i:2261204 original size:24 final size:25
Alignment explanation
Indices: 2261165--2261217 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
2261155 AAAATGAAAA
2261165 AAATTATTTATATTTTATTT-AATT
1 AAATTATTTATATTTTATTTAAATT
2261189 AAATT-TTTATATTTTTATTTAAATT
1 AAATTATTTATA-TTTTATTTAAATT
2261214 AAAT
1 AAAT
2261218 AAAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.22
24 13 0.48
25 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
AAATTATTTATATTTTATTTAAATT
Found at i:2261207 original size:29 final size:29
Alignment explanation
Indices: 2261169--2261227 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2261159 TGAAAAAAAT
* * * *
2261169 TATTTATATTTTATTTAATTAAATTTTTA
1 TATTTATATTTAAATTAAATAAAATTTTA
*
2261198 TATTTTTATTTAAATTAAATAAAATTTTA
1 TATTTATATTTAAATTAAATAAAATTTTA
2261227 T
1 T
2261228 GAATAATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTATATTTAAATTAAATAAAATTTTA
Found at i:2286782 original size:62 final size:63
Alignment explanation
Indices: 2286691--2286818 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 63
2286681 CCAATAGTGT
2286691 TACTTATTATTAGG-ATATATATATATATATATATTGGGTTATTGTGAATGCAAGTTCCAATA
1 TACTTATTATTAGGAATATATATATATATATATATTGGGTTATTGTGAATGCAAGTTCCAATA
2286753 TACTTATTATTAGGATATATATATATATATATATATTGGGTTATTGTGAATGCAAGTTCCAATA
1 TACTTATTATTAGGA-ATATATATATATATATATATTGGGTTATTGTGAATGCAAGTTCCAATA
2286817 TA
1 TA
2286819 GAATTGTTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 14 0.22
64 50 0.78
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (63 bp):
TACTTATTATTAGGAATATATATATATATATATATTGGGTTATTGTGAATGCAAGTTCCAATA
Found at i:2287306 original size:32 final size:33
Alignment explanation
Indices: 2287250--2287313 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2287240 TTTTAAATGT
* *
2287250 ATTAAATATGATTATATACGAAAT-ATATTAAA
1 ATTAAATATGAATATACACGAAATAATATTAAA
2287282 ATTAAATATGAATATGACAC-AAATAATATTAA
1 ATTAAATATGAATAT-ACACGAAATAATATTAA
2287314 TATCTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (33 bp):
ATTAAATATGAATATACACGAAATAATATTAAA
Found at i:2294819 original size:13 final size:14
Alignment explanation
Indices: 2294795--2294824 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2294785 CCAGGAACCA
2294795 AAAAAAGAAAAAGG
1 AAAAAAGAAAAAGG
2294809 AAAAAAG-AAAAGG
1 AAAAAAGAAAAAGG
2294822 AAA
1 AAA
2294825 GCAATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:2316587 original size:3 final size:3
Alignment explanation
Indices: 2316579--2316605 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2316569 AGATTGAATC
2316579 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
2316606 CCGCGTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2324388 original size:18 final size:17
Alignment explanation
Indices: 2324343--2324379 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2324333 GTTAAAATTA
*
2324343 TAAAAA-ATATTATTTT
1 TAAAAATATTTTATTTT
2324359 TAAAAATATTTTATTTT
1 TAAAAATATTTTATTTT
2324376 TAAA
1 TAAA
2324380 GATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAAATATTTTATTTT
Found at i:2348708 original size:31 final size:31
Alignment explanation
Indices: 2348667--2348725 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2348657 TATGTTAGTC
*
2348667 TTTTCTCTTTATATAAAGAAATCCCTCTTTA
1 TTTTCTCTTTATATAAAGAAATACCTCTTTA
* *
2348698 TTTTTTCTTTATGTAAAGAAATACCTCT
1 TTTTCTCTTTATATAAAGAAATACCTCT
2348726 CTCTCGCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTCTCTTTATATAAAGAAATACCTCTTTA
Found at i:2348895 original size:2 final size:2
Alignment explanation
Indices: 2348890--2348914 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2348880 TGTGTGTATG
2348890 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
2348915 GTCTTGGCAT
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:2351671 original size:2 final size:2
Alignment explanation
Indices: 2351664--2351689 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2351654 GACTAATTTT
2351664 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2351690 GTGTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2355007 original size:74 final size:74
Alignment explanation
Indices: 2354870--2355010 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
2354860 CATTAAGTGG
* *
2354870 CTCTAGAACTGATTTTAATATTCAATAAACACCACCCTTAATTTGAGACTCAACAGTTCTCTATG
1 CTCTAGAACTGATTTTAATATTCAATAAACAACACCCTTAATTCGAGACTCAACAGTTCTCTATG
2354935 CAATACAGA
66 CAATACAGA
* * * * *
2354944 CTCTGGAAGTGATTTTAATATTCAATAAATAACACCCTTGATTCGTGACTCAACAGCTT-TCTAT
1 CTCTAGAACTGATTTTAATATTCAATAAACAACACCCTTAATTCGAGACTCAACAG-TTCTCTAT
2355008 GCA
65 GCA
2355011 GTGCTAGTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 57 0.97
75 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (74 bp):
CTCTAGAACTGATTTTAATATTCAATAAACAACACCCTTAATTCGAGACTCAACAGTTCTCTATG
CAATACAGA
Found at i:2355717 original size:12 final size:12
Alignment explanation
Indices: 2355678--2355720 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2355668 GCCCTTTTAA
2355678 AATTTTTAAAAT
1 AATTTTTAAAAT
* * *
2355690 TATATATAAAAT
1 AATTTTTAAAAT
2355702 -ATTTTTAAAAT
1 AATTTTTAAAAT
2355713 AATTTTTA
1 AATTTTTA
2355721 TTTAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTTTAAAAT
Found at i:2355741 original size:24 final size:26
Alignment explanation
Indices: 2355714--2355767 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
2355704 TTTTAAAATA
2355714 ATTTTTATTTAGTA-ATTAATA-TTT
1 ATTTTTATTTAGTATATTAATATTTT
* *
2355738 ATTTTTATTTATTATATTTATATTTT
1 ATTTTTATTTAGTATATTAATATTTT
2355764 ATTT
1 ATTT
2355768 ATTCGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 13 0.50
25 6 0.23
26 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
ATTTTTATTTAGTATATTAATATTTT
Found at i:2355744 original size:20 final size:20
Alignment explanation
Indices: 2355721--2355764 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2355711 ATAATTTTTA
2355721 TTTAGTAATTAATATTTAT-T
1 TTTAGTAATT-ATATTTATAT
* *
2355741 TTTATTTATTATATTTATAT
1 TTTAGTAATTATATTTATAT
2355761 TTTA
1 TTTA
2355765 TTTATTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTAGTAATTATATTTATAT
Found at i:2355782 original size:23 final size:20
Alignment explanation
Indices: 2355732--2355770 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2355722 TTAGTAATTA
2355732 ATATTTAT-TTTTATTTATT
1 ATATTTATATTTTATTTATT
2355751 ATATTTATATTTTATTTATT
1 ATATTTATATTTTATTTATT
2355771 CGTATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATATTTATATTTTATTTATT
Found at i:2357900 original size:45 final size:45
Alignment explanation
Indices: 2357752--2357907 Score: 116
Period size: 45 Copynumber: 3.4 Consensus size: 45
2357742 TAGCATGTAA
* * *
2357752 TAATAATATTTTTTTAACAT-GACGTGTGACAACCTAACCATGACGTG
1 TAAT-ATATTTTTGT-ACATAG-CGTGTAACAACCTAACCATAACGTG
* * * *** * * * * * *
2357799 TAACATGTGTTTGTACATAATATATAATAACTTAATCATACCATG
1 TAATATATTTTTGTACATAGCGTGTAACAACCTAACCATAACGTG
* *
2357844 TCATATGTTTTTGTACATAGCGTGTAACAACCTAACCATAACGTG
1 TAATATATTTTTGTACATAGCGTGTAACAACCTAACCATAACGTG
*
2357889 TAATATATTTTTATACATA
1 TAATATATTTTTGTACATA
2357908 ATGTACATTT
Statistics
Matches: 78, Mismatches: 30, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
45 68 0.87
46 7 0.09
47 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (45 bp):
TAATATATTTTTGTACATAGCGTGTAACAACCTAACCATAACGTG
Found at i:2362192 original size:24 final size:25
Alignment explanation
Indices: 2362137--2362204 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
2362127 AATTATTTAA
*
2362137 TTAAAGTTATAATATAATATCAATAG
1 TTAAAATTATAATATAATATC-ATAG
*
2362163 TT--AATTATATTATAATATC-TAG
1 TTAAAATTATAATATAATATCATAG
**
2362185 TTAAAATTATACGATAATAT
1 TTAAAATTATAATATAATAT
2362205 TACTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.14
24 29 0.81
26 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
TTAAAATTATAATATAATATCATAG
Found at i:2372232 original size:27 final size:27
Alignment explanation
Indices: 2372202--2372260 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
2372192 ACAACTACAG
* *
2372202 GCTTTAGTCTAGGCACTACAACCCCGA
1 GCTTTACTCTAGGCACTACAACCACGA
* *
2372229 GCTTTTCTCTAGGCACTACAACCATGA
1 GCTTTACTCTAGGCACTACAACCACGA
2372256 GCTTT
1 GCTTT
2372261 TCTCCCGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (27 bp):
GCTTTACTCTAGGCACTACAACCACGA
Found at i:2372261 original size:27 final size:27
Alignment explanation
Indices: 2372209--2372290 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
2372199 CAGGCTTTAG
**
2372209 TCTAGGCACTACAACCCCGAGCTTTTC
1 TCTAGGCACTACAACCATGAGCTTTTC
2372236 TCTAGGCACTACAACCATGAGCTTTTC
1 TCTAGGCACTACAACCATGAGCTTTTC
** * * *
2372263 TCCCGGCACCACGACCGTGAGCTTTTC
1 TCTAGGCACTACAACCATGAGCTTTTC
2372290 T
1 T
2372291 TCAGGTACTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (27 bp):
TCTAGGCACTACAACCATGAGCTTTTC
Found at i:2385372 original size:74 final size:74
Alignment explanation
Indices: 2385251--2385400 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
2385241 TTGAAATTTG
2385251 ATCGATAATTAAGTGGACTTATTTAAATGTTGGCGGGTTATAACGGCTATAATGGCAGTTTGTAA
1 ATCGATAATTAAGTGGACTTATTTAAATGTTGGCGGGTTATAACGGCTATAATGGCAGTTTGTAA
2385316 CTTGGTTCT
66 CTTGGTTCT
*
2385325 ATCGATAATTAAGTGGACTTATTTAAATGTTGGCGGGTTTTAACGGCTATAATGGCAGTTTGTAA
1 ATCGATAATTAAGTGGACTTATTTAAATGTTGGCGGGTTATAACGGCTATAATGGCAGTTTGTAA
2385390 CTTGGTTCT
66 CTTGGTTCT
2385399 AT
1 AT
2385401 GTTTAATACA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (74 bp):
ATCGATAATTAAGTGGACTTATTTAAATGTTGGCGGGTTATAACGGCTATAATGGCAGTTTGTAA
CTTGGTTCT
Found at i:2395187 original size:13 final size:13
Alignment explanation
Indices: 2395169--2395194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2395159 TTTTCTACTT
2395169 ACAGATATTTATA
1 ACAGATATTTATA
2395182 ACAGATATTTATA
1 ACAGATATTTATA
2395195 GAGGTAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGATATTTATA
Found at i:2398350 original size:2 final size:2
Alignment explanation
Indices: 2398343--2398390 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2398333 TTAACATTTA
2398343 AT AT AT AT AT -T AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2398382 AT AT AT AT A
1 AT AT AT AT A
2398391 CTTGCTTAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2404127 original size:13 final size:14
Alignment explanation
Indices: 2404108--2404141 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2404098 GCATTTAAAG
2404108 GAAAAAGAAAAGAA
1 GAAAAAGAAAAGAA
*
2404122 -AAAAAGAAGAGAA
1 GAAAAAGAAAAGAA
2404135 GAAAAAG
1 GAAAAAG
2404142 TGGTAATCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAGAA
Found at i:2407368 original size:20 final size:20
Alignment explanation
Indices: 2407316--2407369 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2407306 ATTTTAAATT
2407316 AAATA-TATTTATATAATTAA
1 AAATATTATTTAT-TAATTAA
*
2407336 AATTAATTA-TTATTAATTAA
1 AAAT-ATTATTTATTAATTAA
2407356 AAATATTATTTATT
1 AAATATTATTTATT
2407370 TTTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 5 0.17
22 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTATTTATTAATTAA
Found at i:2413206 original size:21 final size:21
Alignment explanation
Indices: 2413180--2413219 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2413170 CATTACTTCT
2413180 GAAGA-CAAGCAAGGTGATGAC
1 GAAGACCAAG-AAGGTGATGAC
2413201 GAAGACCAAGAAGGTGATG
1 GAAGACCAAGAAGGTGATG
2413220 GAAGTGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.10
Consensus pattern (21 bp):
GAAGACCAAGAAGGTGATGAC
Found at i:2416385 original size:2 final size:2
Alignment explanation
Indices: 2416380--2416411 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2416370 ATATATATAT
2416380 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2416412 GTACTTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2421115 original size:2 final size:2
Alignment explanation
Indices: 2421105--2421137 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2421095 TGAAATATAT
*
2421105 AG AG GG 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
2421138 TGAAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2429015 original size:15 final size:15
Alignment explanation
Indices: 2428990--2429044 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
2428980 GATTGAATTA
* *
2428990 CATTAAAAGACTAAT
1 CATTGAAAGACTGAT
*
2429005 CACTGAAAGACTGAT
1 CATTGAAAGACTGAT
*
2429020 CATTGAAAGATTGAT
1 CATTGAAAGACTGAT
2429035 CATTGAAAGA
1 CATTGAAAGA
2429045 TTGAATCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (15 bp):
CATTGAAAGACTGAT
Found at i:2435729 original size:46 final size:47
Alignment explanation
Indices: 2435662--2435751 Score: 132
Period size: 46 Copynumber: 1.9 Consensus size: 47
2435652 TATGATCATA
2435662 ATCTAAGATATAACCAAAGATCGTTAATATCTTA-ATT-ATAATTATG
1 ATCTAAGATATAACCAAAGATCGTTAATAT-TTATATTAATAATTATG
*
2435708 ATCTAAGATATAACTC-AAGATCGTTACTATTTATATTAATAATT
1 ATCTAAGATATAAC-CAAAGATCGTTAATATTTATATTAATAATT
2435752 TATTTATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 3 0.08
46 30 0.75
47 7 0.17
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (47 bp):
ATCTAAGATATAACCAAAGATCGTTAATATTTATATTAATAATTATG
Found at i:2442240 original size:22 final size:22
Alignment explanation
Indices: 2442205--2442267 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
2442195 TTATTTTTTA
2442205 TTTATAAATAATTAACTTTATAT
1 TTTATAAAT-ATTAACTTTATAT
* *
2442228 TTTAAAAATATTAAAATTT-TAT
1 TTTATAAATATT-AACTTTATAT
*
2442250 TATATAAATATT-ACTTTA
1 TTTATAAATATTAACTTTA
2442268 AAAAATAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.12
22 16 0.48
23 13 0.39
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATAAATATTAACTTTATAT
Found at i:2443104 original size:18 final size:19
Alignment explanation
Indices: 2443070--2443105 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2443060 TTTATTAATA
2443070 TTCAAAATAAATAATTTGT
1 TTCAAAATAAATAATTTGT
*
2443089 TTCAAAA-AAATTATTTG
1 TTCAAAATAAATAATTTG
2443106 CTAGTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (19 bp):
TTCAAAATAAATAATTTGT
Found at i:2457715 original size:11 final size:11
Alignment explanation
Indices: 2457701--2457731 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
2457691 TTATTTTTAC
2457701 AAAAATTAAAA
1 AAAAATTAAAA
2457712 AAAAA-TAAAA
1 AAAAATTAAAA
2457722 AAAAATTAAA
1 AAAAATTAAA
2457732 TCTGTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATTAAAA
Found at i:2460448 original size:2 final size:2
Alignment explanation
Indices: 2460441--2460473 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2460431 TTGCACAAAT
2460441 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2460474 GGTTTGATTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2462251 original size:3 final size:3
Alignment explanation
Indices: 2462245--2462288 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2462235 GAGTTTTTTT
* * *
2462245 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TGA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2462289 TTTATTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2465173 original size:20 final size:20
Alignment explanation
Indices: 2465148--2465185 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2465138 GCATCGCAAT
* *
2465148 TAAATTGTAATTTATTTTCA
1 TAAATTATAATATATTTTCA
2465168 TAAATTATAATATATTTT
1 TAAATTATAATATATTTT
2465186 TAAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAATTATAATATATTTTCA
Found at i:2465192 original size:20 final size:20
Alignment explanation
Indices: 2465149--2465192 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2465139 CATCGCAATT
* * *
2465149 AAATTGTAATTTATTTTCAT
1 AAATTATAATATATTTTCAA
*
2465169 AAATTATAATATATTTTTAA
1 AAATTATAATATATTTTCAA
2465189 AAAT
1 AAAT
2465193 ATTGATAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATTATAATATATTTTCAA
Found at i:2499269 original size:2 final size:2
Alignment explanation
Indices: 2499262--2499287 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2499252 AATTAATAGC
2499262 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2499288 ACGGCAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2509672 original size:2 final size:2
Alignment explanation
Indices: 2509665--2509693 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2509655 GTTAGAGTAT
2509665 TA 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 TA T
2509694 GTGACTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2515060 original size:26 final size:26
Alignment explanation
Indices: 2515024--2515095 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
2515014 AGGAGGGAGA
*
2515024 TCCAGTCAGAGCAGGATCTGGCACTC
1 TCCAGTCAGAGCCGGATCTGGCACTC
2515050 TCCAGTCAGAGCCGGATCTGGCACTC
1 TCCAGTCAGAGCCGGATCTGGCACTC
*
2515076 TCCAATCAGAGCCGGATCTG
1 TCCAGTCAGAGCCGGATCTG
2515096 AGGGTACAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.19
Consensus pattern (26 bp):
TCCAGTCAGAGCCGGATCTGGCACTC
Found at i:2530463 original size:2 final size:2
Alignment explanation
Indices: 2530456--2530486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2530446 TTGCCTTCTC
2530456 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 A
2530487 GTTGGCAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2545553 original size:30 final size:29
Alignment explanation
Indices: 2545519--2545591 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
2545509 GACTAATAGT
*
2545519 TATAAAATTTTATTTGATTCAAAATAAAAA
1 TATAAAATTTTATTTGAAT-AAAATAAAAA
* * *
2545549 TATAAAACTTGA-TTGAATATAATAAAAA
1 TATAAAATTTTATTTGAATAAAATAAAAA
2545577 TAT-AAATATTTATTT
1 TATAAAAT-TTTATTT
2545592 AAAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.09
28 15 0.43
29 7 0.20
30 10 0.29
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (29 bp):
TATAAAATTTTATTTGAATAAAATAAAAA
Found at i:2545598 original size:11 final size:12
Alignment explanation
Indices: 2545579--2545634 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 12
2545569 AATAAAAATA
2545579 TAAATATTTATT
1 TAAATATTTATT
2545591 TAAA-ATTT-TT
1 TAAATATTTATT
2545601 TAAATA---ATT
1 TAAATATTTATT
2545610 TAAATATTT-TT
1 TAAATATTTATT
2545621 TAAATATTATATT
1 TAAATATT-TATT
2545634 T
1 T
2545635 TTATTTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
9 8 0.22
10 6 0.16
11 15 0.41
12 5 0.14
13 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAATATTTATT
Found at i:2545610 original size:19 final size:20
Alignment explanation
Indices: 2545588--2545626 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2545578 ATAAATATTT
2545588 ATTTAAA-ATTTTTTAAATA
1 ATTTAAATATTTTTTAAATA
2545607 ATTTAAATATTTTTTAAATA
1 ATTTAAATATTTTTTAAATA
2545627 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAATATTTTTTAAATA
Found at i:2550155 original size:25 final size:25
Alignment explanation
Indices: 2550127--2550187 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
2550117 TGGATGGAAG
2550127 GTTGAATATTT-AAGATAAAAAAAAT
1 GTTGAATATTTAAAG-TAAAAAAAAT
* * *
2550152 GTTGTATATTGAAAGTAAAAAAATT
1 GTTGAATATTTAAAGTAAAAAAAAT
*
2550177 ATT-AATATTTA
1 GTTGAATATTTA
2550188 TGAATTTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 6 0.21
25 20 0.69
26 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (25 bp):
GTTGAATATTTAAAGTAAAAAAAAT
Found at i:2550778 original size:15 final size:16
Alignment explanation
Indices: 2550758--2550791 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2550748 TATATATATA
2550758 ATTAATAAT-TTTGTT
1 ATTAATAATATTTGTT
*
2550773 ATTAATAATATTTTTT
1 ATTAATAATATTTGTT
2550789 ATT
1 ATT
2550792 TTATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTAATAATATTTGTT
Found at i:2550780 original size:22 final size:22
Alignment explanation
Indices: 2550710--2550781 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 22
2550700 AAAAAAATTA
2550710 AATTAATAATTTTAGTTATTTTAAT
1 AATTAATAATTTT-GTTA--TTAAT
*
2550735 AATT-AT-ATATAT-TTATATATAT
1 AATTAATAAT-TTTGTTAT-TA-AT
2550757 AATTAATAATTTTGTTATTAAT
1 AATTAATAATTTTGTTATTAAT
2550779 AAT
1 AAT
2550782 ATTTTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
20 1 0.03
21 2 0.05
22 14 0.36
23 8 0.21
24 10 0.26
25 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
AATTAATAATTTTGTTATTAAT
Found at i:2550782 original size:47 final size:45
Alignment explanation
Indices: 2550710--2550799 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 45
2550700 AAAAAAATTA
*
2550710 AATTAATAATTTTAGTTATTTTAATAATTATATATATTTATATATAT
1 AATTAATAATTTTAGTTATTATAAT-ATTATATAT-TTTATATATAT
* *
2550757 AATTAATAATTTT-GTTATTAATAATATTTTTTATTTTATATAT
1 AATTAATAATTTTAGTTATT-ATAATATTATATATTTTATATAT
2550800 TTTAATACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 9 0.23
46 13 0.33
47 17 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (45 bp):
AATTAATAATTTTAGTTATTATAATATTATATATTTTATATATAT
Found at i:2551056 original size:19 final size:19
Alignment explanation
Indices: 2551011--2551057 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
2551001 TATATACTTA
*
2551011 TATTTATAGGATTGTAATT
1 TATTTATAGGATTGAAATT
2551030 TATGTTATA-GATTGAAATTT
1 TAT-TTATAGGATTGAAA-TT
2551050 TATTTATA
1 TATTTATA
2551058 TTTGATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TATTTATAGGATTGAAATT
Found at i:2551075 original size:24 final size:24
Alignment explanation
Indices: 2551048--2551105 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
2551038 AGATTGAAAT
2551048 TTTATTTATATTT-GATATAATTTA
1 TTTATTTATATTTAG-TATAATTTA
*
2551072 TTTATTTATGTTTAGTATAATTTA
1 TTTATTTATATTTAGTATAATTTA
2551096 TTTATTTATA
1 TTTATTTATA
2551106 ATATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (24 bp):
TTTATTTATATTTAGTATAATTTA
Found at i:2551110 original size:20 final size:20
Alignment explanation
Indices: 2551048--2551123 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
2551038 AGATTGAAAT
*
2551048 TTTATTTATATT-TGATATAA
1 TTTATTTAT-TTATAATATAA
*
2551068 TTTATTTATTTATGTTTAGTATAA
1 TTTATTTATTTA----TAATATAA
2551092 TTTATTTATTTATAATAT-A
1 TTTATTTATTTATAATATAA
*
2551111 TTTTTATTATTTA
1 TTTAT-TTATTTA
2551124 ATTTATGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
19 7 0.15
20 21 0.46
24 18 0.39
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTATTTATTTATAATATAA
Found at i:2553904 original size:32 final size:32
Alignment explanation
Indices: 2553862--2553936 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
2553852 GAATTCCATC
*
2553862 ATAATGAAAAATATTTCTT-ATAAAAAAATCTAA
1 ATAATAAAAAATATTT-TTGATAAAAAAAT-TAA
***
2553895 ATAATAAAAAATATTTTTGATAATTTAATTAA
1 ATAATAAAAAATATTTTTGATAAAAAAATTAA
2553927 ATAATAAAAA
1 ATAATAAAAA
2553937 TGTTAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 15 0.41
33 22 0.59
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (32 bp):
ATAATAAAAAATATTTTTGATAAAAAAATTAA
Found at i:2560732 original size:39 final size:39
Alignment explanation
Indices: 2560678--2560755 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2560668 AATAGAAAAA
2560678 GTCTGCCAAATTGGATATATGGATACTTGAAATTTTAAT
1 GTCTGCCAAATTGGATATATGGATACTTGAAATTTTAAT
2560717 GTCTGCCAAATTGGATATATGGATACTTGAAATTTTAAT
1 GTCTGCCAAATTGGATATATGGATACTTGAAATTTTAAT
2560756 ATGTAAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (39 bp):
GTCTGCCAAATTGGATATATGGATACTTGAAATTTTAAT
Found at i:2564031 original size:14 final size:14
Alignment explanation
Indices: 2564012--2564039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2564002 GCAGTATCGT
2564012 ACTTTTGTTACTGC
1 ACTTTTGTTACTGC
2564026 ACTTTTGTTACTGC
1 ACTTTTGTTACTGC
2564040 TTTGTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
ACTTTTGTTACTGC
Found at i:2564402 original size:30 final size:29
Alignment explanation
Indices: 2564361--2564421 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
2564351 TTGCATTGTC
* *
2564361 CTGCAGGAGAGTCTGGCTTGGATCTTTATA
1 CTGCAGCAGAGTCTGGCTTGAATCTTT-TA
2564391 CTGCAGCAGAGTCTGGCTTGAATCTTTTA
1 CTGCAGCAGAGTCTGGCTTGAATCTTTTA
2564420 CT
1 CT
2564422 ATATCTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (29 bp):
CTGCAGCAGAGTCTGGCTTGAATCTTTTA
Found at i:2582914 original size:12 final size:13
Alignment explanation
Indices: 2582899--2582931 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
2582889 TATATTTTGT
2582899 AATAATTTTTA-A
1 AATAATTTTTATA
2582911 AATAATTTTTATTA
1 AATAATTTTTA-TA
2582925 AATAATT
1 AATAATT
2582932 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTTTTATA
Found at i:2583266 original size:15 final size:16
Alignment explanation
Indices: 2583248--2583282 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2583238 TTATTATGTG
*
2583248 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
2583263 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
2583279 AATT
1 AATT
2583283 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:2583272 original size:21 final size:21
Alignment explanation
Indices: 2583229--2583274 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2583219 TATCATGATT
* *
2583229 TTTTATTTTTTATTATGTGAA
1 TTTTATTTTTAATAATGTGAA
* *
2583250 TTTTATTTTTAATAATTTTAA
1 TTTTATTTTTAATAATGTGAA
2583271 TTTT
1 TTTT
2583275 TAAAAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTATTTTTAATAATGTGAA
Found at i:2583513 original size:14 final size:13
Alignment explanation
Indices: 2583494--2583550 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 13
2583484 TATATATATC
2583494 ATATTTAATTATTT
1 ATATTTAA-TATTT
*
2583508 ATATTTTATATATT
1 ATATTTAATAT-TT
2583522 ATAATTTAATATTT
1 AT-ATTTAATATTT
2583536 AATATTATAA-ATTT
1 -ATATT-TAATATTT
2583550 A
1 A
2583551 AATATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 4 0.11
14 20 0.54
15 13 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:2583534 original size:28 final size:29
Alignment explanation
Indices: 2583486--2583541 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2583476 TTATTAATTA
2583486 TATATATCATATTTAATTATTT-ATATTT
1 TATATATCATATTTAATTATTTAATATTT
*
2583514 TATATATTATAATTTAA-TATTTAATATT
1 TATATATCAT-ATTTAATTATTTAATATT
2583542 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TATATATCATATTTAATTATTTAATATTT
Found at i:2583542 original size:20 final size:22
Alignment explanation
Indices: 2583504--2583551 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2583494 ATATTTAATT
2583504 ATTT-ATATTTTATATATTAT-A
1 ATTTAATA-TTTATATATTATAA
2583525 ATTTAATATTTA-ATATTATAA
1 ATTTAATATTTATATATTATAA
2583546 ATTTAA
1 ATTTAA
2583552 ATATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAATATTTATATATTATAA
Found at i:2583558 original size:20 final size:20
Alignment explanation
Indices: 2583517--2583576 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2583507 TATATTTTAT
*
2583517 ATATTAT-AATTTAATATTTA
1 ATATTATAAATTTAA-ATATA
2583537 ATATTATAAATTTAAATATA
1 ATATTATAAATTTAAATATA
**
2583557 ATAAAATAAATATTAAATAT
1 ATATTATAAAT-TTAAATAT
2583577 TAATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATAAATTTAAATATA
Found at i:2595002 original size:29 final size:29
Alignment explanation
Indices: 2594970--2595055 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 29
2594960 AACCAAAATG
* * *
2594970 TTTTTGAATATGGCATGTAATAACAATAT
1 TTTTTGAACATGACATGTAACAACAATAT
* * *
2594999 TTTTTTAACATGACGTGTAACAACAGTATTTT
1 TTTTTGAACATGACATGTAACAACA--A-TAT
*
2595031 TTTTTGCAACATGACGTGTAACAAC
1 TTTTTG-AACATGACATGTAACAAC
2595056 CTTTTTTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 20 0.43
31 1 0.02
32 7 0.15
33 18 0.39
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (29 bp):
TTTTTGAACATGACATGTAACAACAATAT
Found at i:2595062 original size:30 final size:29
Alignment explanation
Indices: 2594985--2595055 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 29
2594975 GAATATGGCA
* *
2594985 TGTAATAACAATATTTTTTTAACATGACG
1 TGTAACAACAATTTTTTTTTAACATGACG
2595014 TGTAACAACAGTATTTTTTTTTGCAACATGACG
1 TGTAACAACA--ATTTTTTTTT--AACATGACG
2595047 TGTAACAAC
1 TGTAACAAC
2595056 CTTTTTTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 9 0.25
31 9 0.25
33 18 0.50
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (29 bp):
TGTAACAACAATTTTTTTTTAACATGACG
Found at i:2595097 original size:24 final size:24
Alignment explanation
Indices: 2595070--2595146 Score: 57
Period size: 25 Copynumber: 3.0 Consensus size: 24
2595060 TTTAACCATG
2595070 ATGTATAACATATTTTTGTACATA
1 ATGTATAACATATTTTTGTACATA
* *
2595094 ATGTGTAATAGTA-ATATTTTTTTTAACATG
1 A--TGT-ATA--ACATA-TTTTTGT-ACATA
*
2595124 ATGTGTAACATATTTTTGTACAT
1 ATGTATAACATATTTTTGTACAT
2595147 GACGTGTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
24 5 0.12
25 7 0.17
26 6 0.15
27 5 0.12
28 6 0.15
29 7 0.17
30 5 0.12
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (24 bp):
ATGTATAACATATTTTTGTACATA
Found at i:2595147 original size:24 final size:24
Alignment explanation
Indices: 2595066--2595157 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 24
2595056 CTTTTTTAAC
*
2595066 CATGATGTATAACATATTTTTGTA
1 CATGATGTGTAACATATTTTTGTA
* * *
2595090 CATAATGTGTAATAGTAATATTTTTTTTAA
1 CATGATGTGT-A-A--CATA-TTTTTGT-A
2595120 CATGATGTGTAACATATTTTTGTA
1 CATGATGTGTAACATATTTTTGTA
*
2595144 CATGACGTGTAACA
1 CATGATGTGTAACA
2595158 ATCTAACCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
24 22 0.41
25 7 0.13
26 4 0.07
28 4 0.07
29 7 0.13
30 10 0.19
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (24 bp):
CATGATGTGTAACATATTTTTGTA
Found at i:2595267 original size:38 final size:38
Alignment explanation
Indices: 2595213--2595312 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 38
2595203 ACCTAATCAT
*
2595213 GTGTCACATGTTTTTGTACATGACATGTTAGGCTAGAC
1 GTGTAACATGTTTTTGTACATGACATGTTAGGCTAGAC
* *
2595251 GTGTAACATGTTTTTGTACAT-AGCATGTTAGGTTAGGC
1 GTGTAACATGTTTTTGTACATGA-CATGTTAGGCTAGAC
* *
2595289 ATGTAACATGTATTTGTACATGAC
1 GTGTAACATGTTTTTGTACATGAC
2595313 GTGTCACATG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.02
38 53 0.96
39 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (38 bp):
GTGTAACATGTTTTTGTACATGACATGTTAGGCTAGAC
Found at i:2595429 original size:45 final size:42
Alignment explanation
Indices: 2595318--2595438 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
2595308 ATGACGTGTC
* * * **
2595318 ACATGTTTTTATACATGACGTATAACAACTTAATCATGTGTC
1 ACATGTTTTTGTACATGACGTGTAACAACCTAATCATGTGGA
* *
2595360 ACATGTTTTTGTATATGACATGTAACAACCTAATCATGGCGTGGA
1 ACATGTTTTTGTACATGACGTGTAACAACCTAATCAT---GTGGA
* * *
2595405 ATATGTTTCTGTACATGACGTGTAATAACCTAAT
1 ACATGTTTTTGTACATGACGTGTAACAACCTAAT
2595439 TATAACGTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 32 0.50
45 32 0.50
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (42 bp):
ACATGTTTTTGTACATGACGTGTAACAACCTAATCATGTGGA
Found at i:2595509 original size:24 final size:24
Alignment explanation
Indices: 2595450--2595517 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
2595440 ATAACGTCAT
*
2595450 ATATTTTTATACAT-AGCGTATAAC
1 ATATTTTTATACATGA-CGTGTAAC
*
2595474 A-A-TTTAAT-CATGACGTGTAAC
1 ATATTTTTATACATGACGTGTAAC
*
2595495 ATATTTTTATACATGACATGTAA
1 ATATTTTTATACATGACGTGTAA
2595518 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 11 0.31
22 7 0.19
23 6 0.17
24 12 0.33
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (24 bp):
ATATTTTTATACATGACGTGTAAC
Found at i:2596558 original size:27 final size:27
Alignment explanation
Indices: 2596491--2596559 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
2596481 TTATTAATGA
*
2596491 TAATATCT-TTATATATTCATAATATAT
1 TAATAT-TATTATATAATCATAATATAT
* *
2596518 TAGACATTAATATATAAT-ATAATATATT
1 TA-ATATTATTATATAATCATAATATA-T
2596546 TAATATTATTATAT
1 TAATATTATTATAT
2596560 TGTAAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (27 bp):
TAATATTATTATATAATCATAATATAT
Found at i:2596691 original size:15 final size:15
Alignment explanation
Indices: 2596671--2596715 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2596661 ATATGTTAAT
2596671 TTTATATAGTATATA
1 TTTATATAGTATATA
2596686 TTTATAT-GTAT-TA
1 TTTATATAGTATATA
2596699 TTTTATTATA-TATATA
1 -TTTA-TATAGTATATA
2596715 T
1 T
2596716 GAAATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 14 0.54
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
TTTATATAGTATATA
Found at i:2596701 original size:29 final size:28
Alignment explanation
Indices: 2596661--2596715 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
2596651 AGTATAAGTA
2596661 ATATGTTAATTTTA-TATAGTATATATTT
1 ATATGTTAATTTTATTATA-TATATATTT
*
2596689 ATATGTATTATTTTATTATATATATAT
1 ATATGT-TAATTTTATTATATATATAT
2596716 GAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 14 0.58
30 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
ATATGTTAATTTTATTATATATATATTT
Found at i:2600726 original size:28 final size:28
Alignment explanation
Indices: 2600688--2600816 Score: 122
Period size: 27 Copynumber: 4.7 Consensus size: 28
2600678 TCATAACAAG
*
2600688 TAATAATTAAATTTTTCAACATGACGTA
1 TAATAACTAAATTTTTCAACATGACGTA
* *
2600716 TAACAACTAAATGTTT-AACATGACGTA
1 TAATAACTAAATTTTTCAACATGACGTA
* *
2600743 TAATAATTATATTTTTCAACATG--GTA
1 TAATAACTAAATTTTTCAACATGACGTA
* * *
2600769 TGTAATAACTAAA-TTTTCAACATAATGTG
1 --TAATAACTAAATTTTTCAACATGACGTA
* *
2600798 TAATAATTATATTTTTCAA
1 TAATAACTAAATTTTTCAA
2600817 TATAGTATGT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
26 3 0.04
27 42 0.51
28 35 0.43
29 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (28 bp):
TAATAACTAAATTTTTCAACATGACGTA
Found at i:2600757 original size:55 final size:52
Alignment explanation
Indices: 2600688--2600900 Score: 175
Period size: 55 Copynumber: 3.9 Consensus size: 52
2600678 TCATAACAAG
*
2600688 TAATAATTAAATTTTTCAACATGACGTA-TAACAACTAAATGTTTAACATGACGTA
1 TAATAATTATATTTTTCAACATGA-GTAGTAACAACTAAAT-TTTAACAT-A-GTA
* *
2600743 TAATAATTATATTTTTCAACATG-GTATGTAATAACTAAATTTTCAACATAATGTG
1 TAATAATTATATTTTTCAACATGAGTA-GTAACAACTAAATTTT-AACAT-A-GTA
* * * *
2600798 TAATAATTATATTTTTCAATAT-AGTATGTAACAATTAAAATTTCAACATAATAA
1 TAATAATTATATTTTTCAACATGAGTA-GTAACAACT-AAATTTTAACATAGT-A
* *
2600852 GTGATAATTACATTTTT-AACCATGACGTA-TAACAACTAAATTTTTAACA
1 -TAATAATTATATTTTTCAA-CATGA-GTAGTAACAACTAAA-TTTTAACA
2600901 CAGCGTGTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
53 4 0.03
54 9 0.07
55 108 0.82
56 7 0.05
57 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (52 bp):
TAATAATTATATTTTTCAACATGAGTAGTAACAACTAAATTTTAACATAGTA
Found at i:2600799 original size:27 final size:27
Alignment explanation
Indices: 2600687--2600867 Score: 112
Period size: 27 Copynumber: 6.6 Consensus size: 27
2600677 ATCATAACAA
* *
2600687 GTAATAATTAAATTTTTCAACATGACGT
1 GTAATAATTAAA-TTTTCAACATAATGT
* * * * *
2600715 ATAACAACTAAATGTTT-AACATGACGT
1 GTAATAATTAAAT-TTTCAACATAATGT
* * ** *
2600742 ATAATAATTATATTTTTCAACATGGTAT
1 GTAATAATTA-AATTTTCAACATAATGT
*
2600770 GTAATAACTAAATTTTCAACATAATGT
1 GTAATAATTAAATTTTCAACATAATGT
* * * *
2600797 GTAATAATTATATTTTTCAATATAGTAT
1 GTAATAATTA-AATTTTCAACATAATGT
* * **
2600825 GTAACAATTAAAATTTCAACATAATAA
1 GTAATAATTAAATTTTCAACATAATGT
* *
2600852 GTGATAATTACATTTT
1 GTAATAATTAAATTTT
2600868 TAACCATGAC
Statistics
Matches: 119, Mismatches: 30, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
27 68 0.57
28 51 0.43
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (27 bp):
GTAATAATTAAATTTTCAACATAATGT
Found at i:2600827 original size:28 final size:28
Alignment explanation
Indices: 2600743--2600868 Score: 121
Period size: 27 Copynumber: 4.6 Consensus size: 28
2600733 ACATGACGTA
*
2600743 TAATAATTATATTTTTCAACATGGTATG
1 TAATAATTATATTTTTCAACATAGTATG
* * * *
2600771 TAATAACTA-AATTTTCAACATAATGTG
1 TAATAATTATATTTTTCAACATAGTATG
*
2600798 TAATAATTATATTTTTCAATATAGTATG
1 TAATAATTATATTTTTCAACATAGTATG
* ** * *
2600826 TAACAATTA-AAATTTCAACATAATAAG
1 TAATAATTATATTTTTCAACATAGTATG
* *
2600853 TGATAATTACATTTTT
1 TAATAATTATATTTTT
2600869 AACCATGACG
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
27 42 0.55
28 34 0.45
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (28 bp):
TAATAATTATATTTTTCAACATAGTATG
Found at i:2603224 original size:14 final size:14
Alignment explanation
Indices: 2603170--2603217 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2603160 AAAAAATTAT
**
2603170 AAATAATAAATTAA
1 AAATAATATTTTAA
*
2603184 AGATAATTATTTTAA
1 AAATAA-TATTTTAA
*
2603199 AAATAATATTTTTA
1 AAATAATATTTTAA
2603213 AAATA
1 AAATA
2603218 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATAATATTTTAA
Found at i:2603391 original size:6 final size:6
Alignment explanation
Indices: 2603382--2603430 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
2603372 TTCTTATCCC
* * * *
2603382 GTCTCT GTCTCT GTGTCC GTCTCT GTCTCT GTCTGT CTCTCT AGTCTCT
1 GTCTCT GTCTCT GTCTCT GTCTCT GTCTCT GTCTCT GTCTCT -GTCTCT
2603431 CCCTCGCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.02, C:0.33, G:0.18, T:0.47
Consensus pattern (6 bp):
GTCTCT
Found at i:2603618 original size:539 final size:538
Alignment explanation
Indices: 2602882--2603894 Score: 1556
Period size: 539 Copynumber: 1.9 Consensus size: 538
2602872 AGTCCATCTC
* * * *
2602882 TCTCTCTGTCTCTCCCTCGCTCAAACACAGTAAACGTCAGCTCTGCGCTCGGCCTGGTTTCTAGA
1 TCTCTCTGTCTCTCCCTCGCTCAAACAAAGTAAACGTCAGATCCGCGCTCGGCCTGGTTTCTAAA
* * *
2602947 AATTTATTGTAAACAAATTCGCACCATGTGAATAAAACATGATGCACACCAAGGTGGATAGCTGC
66 AATTTAGTGTAAACAAATTAGAACCATGTGAATAAAACATGATGCACACCAAGGTGGATAGCTGC
* * * * * *
2603012 GACTTGGTTGGTGATGATCAAGGATATATATATCAGGTTACTTGAGCGGTGCCCCGCTTCGACGG
131 GACTCGATTGGTGAAGATCAAGGATACATATATCAAGTTACTTGAGCGGTGCCCCGCTTCCACGG
* * *
2603077 GTGTTGACTTTTTTATTAAAAATATTTTTAAATTACATAATATTATAAATAATTATAATAAAAGA
196 GTGTTGACTTTTTTATTAAAAATAATTTTAAATTACATAATATTATAAATAATAATAACAAAAGA
*
2603142 AAAATAATTTTAAATTT-AA-A-A-AAATTATAA-A-TAATAAATTAAAGATAATTATTTTAAAA
261 AAAATAATTTTAAATTTAAAGAGATAAATAATAATAGTAATAAATTAAAGATAATTATTTTAAAA
** *
2603201 ATAATATTTTTAAAATATTTTTTTATATAAGCTAAATTTTTTATTTCAAT-ATTTTTTAAAAAAA
326 ATAATATTTTTAAAATATTTTTAAATATAAGCTAAATTTTTTATTTAAATAATTTTTT--AAAAA
*
2603265 TATTTGATTTTTTATATCTTAATGTATGCTAATATTGATATAATCATATTTTGTTAATTACATTA
389 TATTTGATTTTTTATAT-TTAATATATGCTAAT-TTGATATAATCATATTTTGTTAATTACATTA
2603330 TTCTAATAACGAAATAAAATTTACATTATTCTAATTACATTATTCTTATCCCGTCTCTGTCTCTG
452 TTCTAATAACGAAATAAAATTTACATTATTCTAATTACATTATTCTTATCCCGTCTCTGTCTCTG
2603395 TGTCCGTCTCTGTCTCTGTCTG
517 TGTCCGTCTCTGTCTCTGTCTG
* *
2603417 TCTCTCTAGTCTCTCCCTCGCTCAAACAAAGTAAACGTCAGATCCGTGCTGGGCCTGGTTTCTAA
1 TCTCTCT-GTCTCTCCCTCGCTCAAACAAAGTAAACGTCAGATCCGCGCTCGGCCTGGTTTCTAA
*
2603482 AAATTTTAGTGTAAACAAATTAGAACCATGTGAATAAAACGTGATGCACACCAAGG-GGATGATT
65 AAA-TTTAGTGTAAACAAATTAGAACCATGTGAATAAAACATGATGCACACCAAGGTGGAT-A--
* * * *
2603546 GCTGCGACTCGATTGGTGAAGGTTAAGGATACATATATTAAGTTACTTGAGTGGTGCCCCGCTTC
126 GCTGCGACTCGATTGGTGAAGATCAAGGATACATATATCAAGTTACTTGAGCGGTGCCCCGCTTC
* *
2603611 CACGGGTGTTGATTTTTTTATTAAAAATAATTTTAAATTACATTATATTATAAATAATAATAACA
191 CACGGGTGTTGACTTTTTTATTAAAAATAATTTTAAATTACATAATATTATAAATAATAATAACA
2603676 AAAGAAAAATAATTTTAAATTTAAAAGTATGATAAATAATAATAGTAATAAATTAAAGATAATTA
256 AAAGAAAAATAATTTTAAATTT-AAAG-A-GATAAATAATAATAGTAATAAATTAAAGATAATTA
* *
2603741 TTTTAAAAATAATATTTTTTAAATATTTTTAAATGTAAGCTAAATTTTTTATTTAAATAATTTTT
318 TTTTAAAAATAATATTTTTAAAATATTTTTAAATATAAGCTAAATTTTTTATTTAAATAATTTTT
* *
2603806 TTAAAATATTTGATTTTTTATATTTAATATATGCTAATTTGATATAATCATATTTTGTTAATTAT
383 TAAAAATATTTGATTTTTTATATTTAATATATGCTAATTTGATATAATCATATTTTGTTAATTAC
2603871 ATTATTCTAATAACGAAATAAAAT
448 ATTATTCTAATAACGAAATAAAAT
2603895 ATATATTGAG
Statistics
Matches: 429, Mismatches: 34, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
535 7 0.02
536 58 0.14
537 49 0.11
539 137 0.32
541 2 0.00
543 1 0.00
545 51 0.12
546 22 0.05
547 22 0.05
548 73 0.17
549 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (538 bp):
TCTCTCTGTCTCTCCCTCGCTCAAACAAAGTAAACGTCAGATCCGCGCTCGGCCTGGTTTCTAAA
AATTTAGTGTAAACAAATTAGAACCATGTGAATAAAACATGATGCACACCAAGGTGGATAGCTGC
GACTCGATTGGTGAAGATCAAGGATACATATATCAAGTTACTTGAGCGGTGCCCCGCTTCCACGG
GTGTTGACTTTTTTATTAAAAATAATTTTAAATTACATAATATTATAAATAATAATAACAAAAGA
AAAATAATTTTAAATTTAAAGAGATAAATAATAATAGTAATAAATTAAAGATAATTATTTTAAAA
ATAATATTTTTAAAATATTTTTAAATATAAGCTAAATTTTTTATTTAAATAATTTTTTAAAAATA
TTTGATTTTTTATATTTAATATATGCTAATTTGATATAATCATATTTTGTTAATTACATTATTCT
AATAACGAAATAAAATTTACATTATTCTAATTACATTATTCTTATCCCGTCTCTGTCTCTGTGTC
CGTCTCTGTCTCTGTCTG
Found at i:2604281 original size:14 final size:15
Alignment explanation
Indices: 2604251--2604283 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2604241 TAATTCATAC
*
2604251 ATAAAAAAATTACAA
1 ATAAAAAAAATACAA
2604266 ATAAAAAAAATA-AA
1 ATAAAAAAAATACAA
2604280 ATAA
1 ATAA
2604284 CTAAACCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAAAAATACAA
Done.