Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 20 of 21
Found at i:2359360 original size:2 final size:2
Alignment explanation
Indices: 2359355--2359389 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2359345 AAATAGGAAT
2359355 TA TA TA 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 TA TA TA T
2359390 GTATTCAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2361848 original size:32 final size:32
Alignment explanation
Indices: 2361807--2361870 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2361797 ATCATACAAA
2361807 CCCTGACGATCTTCTTGTTCTGGAGATTGCTC
1 CCCTGACGATCTTCTTGTTCTGGAGATTGCTC
2361839 CCCTGACGATCTTCTTGTTCTGGAGATTGCTC
1 CCCTGACGATCTTCTTGTTCTGGAGATTGCTC
2361871 ATATCATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (32 bp):
CCCTGACGATCTTCTTGTTCTGGAGATTGCTC
Found at i:2364180 original size:11 final size:10
Alignment explanation
Indices: 2364129--2364217 Score: 53
Period size: 9 Copynumber: 8.9 Consensus size: 10
2364119 ATAATTTTAA
2364129 ATATTAATAT
1 ATATTAATAT
*
2364139 AT-TTAATAA
1 ATATTAATAT
* *
2364148 ATATAAAAAT
1 ATATTAATAT
*
2364158 ATCTCATAATAT
1 ATAT--TAATAT
2364170 ATTATTAATAT
1 A-TATTAATAT
*
2364181 ATATTATATTT
1 ATATTA-ATAT
2364192 ATATTTAA-A-
1 ATA-TTAATAT
2364201 AT-TTAATAT
1 ATATTAATAT
2364210 AT-TTAATA
1 ATATTAATA
2364218 ATTTATATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 18 0.30
10 14 0.23
11 14 0.23
12 8 0.13
13 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATTAATAT
Found at i:2364195 original size:6 final size:6
Alignment explanation
Indices: 2364178--2364242 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
2364168 ATATTATTAA
*
2364178 TATATAT TATATT TATATT TAAAATT TA-A-- TATATT TAATAATT TATATT
1 TATAT-T TATATT TATATT T-ATATT TATATT TATATT T-AT-ATT TATATT
2364227 T-TATT TATATT TATAT
1 TATATT TATATT TATAT
2364243 AATTATTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 6 0.12
6 23 0.46
7 14 0.28
8 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:2364212 original size:16 final size:17
Alignment explanation
Indices: 2364191--2364222 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2364181 ATATTATATT
2364191 TATATTTAA-AATTTAA
1 TATATTTAATAATTTAA
2364207 TATATTTAATAATTTA
1 TATATTTAATAATTTA
2364223 TATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTAATAATTTAA
Found at i:2364225 original size:16 final size:16
Alignment explanation
Indices: 2364191--2364243 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2364181 ATATTATATT
2364191 TATATTTAA-AATTTAA
1 TATATTTAATAATTT-A
2364207 TATATTTAATAATTTA
1 TATATTTAATAATTTA
*
2364223 TAT-TTTATTTATATTTA
1 TATATTTA-ATA-ATTTA
2364240 TATA
1 TATA
2364244 ATTATTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.12
16 15 0.47
17 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTAATAATTTA
Found at i:2364925 original size:19 final size:21
Alignment explanation
Indices: 2364898--2364951 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
2364888 TTGATTTAAA
*
2364898 TTTAAATTTAAATTT-ATT-T
1 TTTATATTTAAATTTAATTAT
*
2364917 TTTATATTTTAATTTAATTAT
1 TTTATATTTAAATTTAATTAT
2364938 TATTATAATTTAAA
1 T-TTAT-ATTTAAA
2364952 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 13 0.46
20 3 0.11
21 2 0.07
22 4 0.14
23 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATATTTAAATTTAATTAT
Found at i:2369798 original size:3 final size:3
Alignment explanation
Indices: 2369790--2369822 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2369780 AACTATCCTT
2369790 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2369823 CTACTTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2377209 original size:52 final size:54
Alignment explanation
Indices: 2377147--2377249 Score: 140
Period size: 52 Copynumber: 1.9 Consensus size: 54
2377137 AAAATGGTTG
2377147 ATTTTATATTTATCTTAATCATTAACCT-AATCAAATTT-AAA-AAATATAATCA
1 ATTTTATATTTATCTTAATCATTAA-CTAAATCAAATTTGAAATAAATATAATCA
* * * *
2377199 ATTTTGTATTTATTTTAATCATTAATTAAATTAAATTTGAAATAAATATAA
1 ATTTTATATTTATCTTAATCATTAACTAAATCAAATTTGAAATAAATATAA
2377250 AATAACTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 1 0.02
52 32 0.73
53 3 0.07
54 8 0.18
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (54 bp):
ATTTTATATTTATCTTAATCATTAACTAAATCAAATTTGAAATAAATATAATCA
Found at i:2377383 original size:2 final size:2
Alignment explanation
Indices: 2377378--2377407 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2377368 ACATGTGTGT
2377378 TA TA 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 TA TA
2377408 ATACATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2377814 original size:2 final size:2
Alignment explanation
Indices: 2377807--2377832 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2377797 AAAATGTTAT
2377807 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
2377833 AGCAGTAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2381864 original size:23 final size:23
Alignment explanation
Indices: 2381838--2381902 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
2381828 AATAATATTA
2381838 AATTTTATTTTATATAAATATAT
1 AATTTTATTTTATATAAATATAT
* * *
2381861 AA-TTAAATTTAAATAAA-ATAT
1 AATTTTATTTTATATAAATATAT
2381882 AATTTT-TTAATTATATAAATA
1 AATTTTATT--TTATATAAATA
2381903 GAGTTGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
21 7 0.22
22 14 0.44
23 10 0.31
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTTTATTTTATATAAATATAT
Found at i:2382089 original size:27 final size:27
Alignment explanation
Indices: 2382059--2382110 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2382049 TGTCATAATT
2382059 TAAAAA-ATTTTAAATTTTATATATTAA
1 TAAAAATATTTTAAATTTTA-ATATTAA
**
2382086 TAAAAATATTTTTTATTTTAATATT
1 TAAAAATATTTTAAATTTTAATATT
2382111 TATATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAAAAATATTTTAAATTTTAATATTAA
Found at i:2382115 original size:21 final size:21
Alignment explanation
Indices: 2382091--2382133 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2382081 ATTAATAAAA
*
2382091 ATATT-TTTTATTTTAATATTT
1 ATATTATTTTATATTAA-ATTT
2382112 ATATTATTTTATATTAAATTT
1 ATATTATTTTATATTAAATTT
2382133 A
1 A
2382134 AATAAAAAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATATTATTTTATATTAAATTT
Found at i:2386848 original size:3 final size:3
Alignment explanation
Indices: 2386806--2386836 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2386796 ATCATGAATG
2386806 ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
2386837 GTCTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2388035 original size:23 final size:24
Alignment explanation
Indices: 2388000--2388046 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2387990 TACCAATTTT
*
2388000 AATATTTAATTTTTAAATTTATTA
1 AATATTTAATTTTTAAAATTATTA
*
2388024 AATA-TTATTTTTTAAAATTATTA
1 AATATTTAATTTTTAAAATTATTA
2388047 TATAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATATTTAATTTTTAAAATTATTA
Found at i:2388673 original size:27 final size:29
Alignment explanation
Indices: 2388620--2388672 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
2388610 TCTCTTTTGA
2388620 TTTTATGTTAATATTTAATTAATAAAATT
1 TTTTATGTTAATATTTAATTAATAAAATT
2388649 TTTTAT-TTAA-ATTTAATT-ATAAAA
1 TTTTATGTTAATATTTAATTAATAAAA
2388673 AATATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.25
27 8 0.33
28 4 0.17
29 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTTATGTTAATATTTAATTAATAAAATT
Found at i:2390520 original size:19 final size:20
Alignment explanation
Indices: 2390469--2390517 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2390459 ACTGACCAAA
*
2390469 TAATTGAATTAATTTTATTTT
1 TAATTGAATTAA-TTTAGTTT
2390490 TAATT-AATTAATTTAGTTT
1 TAATTGAATTAATTTAGTTT
2390509 TAATTGAAT
1 TAATTGAAT
2390518 AATAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 9 0.35
21 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TAATTGAATTAATTTAGTTT
Found at i:2391237 original size:17 final size:17
Alignment explanation
Indices: 2391215--2391248 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2391205 TCATTATCCG
2391215 ATTTTAAATAAATATTA
1 ATTTTAAATAAATATTA
*
2391232 ATTTTAATTAAATATTA
1 ATTTTAAATAAATATTA
2391249 TAATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAATAAATATTA
Found at i:2391281 original size:22 final size:22
Alignment explanation
Indices: 2391215--2391282 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
2391205 TCATTATCCG
*
2391215 ATTTTAAATAAATATTAA-TTTT
1 ATTTTAAAT-AATAATAATTTTT
*
2391237 A-ATTAAATATTATAAT-ATATTTT
1 ATTTTAAATA--ATAATAAT-TTTT
2391260 ATTTTAAATAATAATAATTTTT
1 ATTTTAAATAATAATAATTTTT
2391282 A
1 A
2391283 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 15 0.41
23 7 0.19
24 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTAAATAATAATAATTTTT
Found at i:2391282 original size:45 final size:41
Alignment explanation
Indices: 2391215--2391312 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
2391205 TCATTATCCG
* * **
2391215 ATTTTAAATAAATATTAATTTTAATTAAATATTATAATATATTTT
1 ATTTTAAAT-AATAATAATTTTAA-TAAA-A-TAAAATATATTAA
2391260 ATTTTAAATAATAATAATTTTTAATAAAATAAAATATATTAA
1 ATTTTAAATAATAATAA-TTTTAATAAAATAAAATATATTAA
2391302 ATTTTAAATAA
1 ATTTTAAATAA
2391313 ACAATTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 21 0.44
43 1 0.02
44 11 0.23
45 15 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (41 bp):
ATTTTAAATAATAATAATTTTAATAAAATAAAATATATTAA
Found at i:2391323 original size:42 final size:44
Alignment explanation
Indices: 2391215--2391324 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 44
2391205 TCATTATCCG
* * * **
2391215 ATTTTAAATAAATATTAATTTTAATTAAATATTATAATATATTTT
1 ATTTTAAATAAAAATT-TTTTTAATTAAATATTAAAATATATTAA
* *
2391260 ATTTTAAATAATAATAATTTTTAA-TAAA-A-TAAAATATATTAA
1 ATTTTAAATAAAAAT-TTTTTTAATTAAATATTAAAATATATTAA
2391302 ATTTTAAATAAACAATTTTTTTA
1 ATTTTAAATAAA-AATTTTTTTA
2391325 CAGTTCAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
42 27 0.50
43 4 0.07
44 4 0.07
45 19 0.35
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (44 bp):
ATTTTAAATAAAAATTTTTTTAATTAAATATTAAAATATATTAA
Found at i:2391907 original size:17 final size:17
Alignment explanation
Indices: 2391877--2391917 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
2391867 ATATAAAAAC
2391877 TAATTTTCATTTATCTTT
1 TAATTTTCATTTAT-TTT
*
2391895 TGATTTT-ATTTATTTT
1 TAATTTTCATTTATTTT
2391911 TAATTTT
1 TAATTTT
2391918 TGATTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (17 bp):
TAATTTTCATTTATTTT
Found at i:2391918 original size:17 final size:18
Alignment explanation
Indices: 2391877--2391918 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2391867 ATATAAAAAC
*
2391877 TAATTTTCATTTATCTTT
1 TAATTTTTATTTATCTTT
*
2391895 TGA-TTTTATTTAT-TTT
1 TAATTTTTATTTATCTTT
2391911 TAATTTTT
1 TAATTTTT
2391919 GATTCCAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 5 0.25
17 13 0.65
18 2 0.10
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (18 bp):
TAATTTTTATTTATCTTT
Found at i:2392910 original size:14 final size:14
Alignment explanation
Indices: 2392893--2392942 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
2392883 TTTTAAGTTT
2392893 TTAATTTTTTATTA
1 TTAATTTTTTATTA
**
2392907 TTAATAATTTATTA
1 TTAATTTTTTATTA
*
2392921 -TAATTTATTA-TA
1 TTAATTTTTTATTA
*
2392933 ATAATTTTTT
1 TTAATTTTTT
2392943 TATATTTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 2 0.07
13 15 0.52
14 12 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATTTTTTATTA
Found at i:2392925 original size:10 final size:10
Alignment explanation
Indices: 2392904--2392934 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
2392894 TAATTTTTTA
2392904 TTATTAATAAT
1 TTATT-ATAAT
2392915 TTATTATAAT
1 TTATTATAAT
2392925 TTATTATAAT
1 TTATTATAAT
2392935 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATTATAAT
Found at i:2392949 original size:23 final size:24
Alignment explanation
Indices: 2392900--2392960 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
2392890 TTTTTAATTT
2392900 TTTATTATTAATAA-TTTATTATAA
1 TTTATTA-TAATAATTTTATTATAA
*
2392924 TTTATTATAATAATTTTTTTAT-A
1 TTTATTATAATAATTTTATTATAA
* *
2392947 TTTATAATGATAAT
1 TTTATTATAATAAT
2392961 AAATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTATTATAATAATTTTATTATAA
Found at i:2392978 original size:14 final size:15
Alignment explanation
Indices: 2392949--2392981 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2392939 TTTTTATATT
*
2392949 TATAATGATAATAAA
1 TATAATGATAAAAAA
2392964 TATAAT-ATAAAAAA
1 TATAATGATAAAAAA
2392978 TATA
1 TATA
2392982 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAATGATAAAAAA
Found at i:2393109 original size:19 final size:20
Alignment explanation
Indices: 2393085--2393126 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
2393075 TTAAATTAAT
2393085 TTAAAA-TTTTATATTTATA
1 TTAAAATTTTTATATTTATA
2393104 TTAAAATTTTTTATATTTATA
1 TTAAAA-TTTTTATATTTATA
2393125 TT
1 TT
2393127 TATAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTTATATTTATA
Found at i:2393153 original size:27 final size:27
Alignment explanation
Indices: 2393076--2393163 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
2393066 AAATTAAGAT
* *
2393076 TAAATTAATTTAA-AATTTTATATTTA
1 TAAATAAATTTAATTATTTTATATTTA
* *
2393102 T-ATTAAAATTT-TTTATATTTATATTTA
1 TAAAT-AAATTTAATTAT-TTTATATTTA
* *
2393129 TAAATAAATTTAATTATTTTTTATTATT
1 TAAATAAATTTAATTATTTTATATT-TA
2393157 TAAATAA
1 TAAATAA
2393164 TAATTTAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 24 0.50
28 14 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TAAATAAATTTAATTATTTTATATTTA
Found at i:2395882 original size:27 final size:24
Alignment explanation
Indices: 2395834--2395883 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
2395824 ACTTTATAAT
2395834 TATTTATATTTTTTTATCAAATTA
1 TATTTATATTTTTTTATCAAATTA
*
2395858 TATTTAATATTATATTTTATTAAATT
1 TATTT-ATATT-T-TTTTATCAAATT
2395884 TGATACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 5 0.23
26 1 0.05
27 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTATATTTTTTTATCAAATTA
Found at i:2395967 original size:21 final size:22
Alignment explanation
Indices: 2395934--2395976 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2395924 TATTTATATA
*
2395934 TTTAACTATATTTATATCTTAT
1 TTTAACTATATTTATATATTAT
* *
2395956 TTTAATTA-ATTTTTATATTAT
1 TTTAACTATATTTATATATTAT
2395977 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAACTATATTTATATATTAT
Found at i:2395979 original size:23 final size:22
Alignment explanation
Indices: 2395927--2395982 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2395917 ATTAAAATAT
2395927 TTATATATTTAACTATATTTATA
1 TTATAT-TTTAACTATATTTATA
* *
2395950 TCT-TATTTTAATTAATTTTTATA
1 T-TATATTTTAACT-ATATTTATA
2395973 TTATATTTTA
1 TTATATTTTA
2395983 TTTTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTTTAACTATATTTATA
Found at i:2395982 original size:12 final size:12
Alignment explanation
Indices: 2395927--2396020 Score: 55
Period size: 12 Copynumber: 8.4 Consensus size: 12
2395917 ATTAAAATAT
2395927 TTATATATTTA-A
1 TTATAT-TTTATA
*
2395939 CTATA-TTTATA
1 TTATATTTTATA
2395950 TCT-TATTTTA-A
1 T-TATATTTTATA
2395961 TTA-ATTTTTATA
1 TTATA-TTTTATA
2395973 TTATATTTTAT-
1 TTATATTTTATA
*
2395984 TT-TA-TATA-A
1 TTATATTTTATA
*
2395993 TTATA-ATTATA
1 TTATATTTTATA
*
2396004 TTATATTTAATA
1 TTATATTTTATA
2396016 TTATA
1 TTATA
2396021 GTAAACCCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
9 5 0.08
10 12 0.19
11 18 0.28
12 28 0.44
13 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:2396002 original size:19 final size:18
Alignment explanation
Indices: 2395926--2396009 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 18
2395916 TATTAAAATA
2395926 TTTATATATT-TAACTATAT
1 TTTATATATTATAA-T-TAT
* *
2395945 TTATATCTTATTTTAATTAAT
1 TT-TAT-ATATTATAATT-AT
*
2395966 TTT-TATATTATATTTTAT
1 TTTATATATTATA-ATTAT
2395984 TTTATATAATTATAATTAT
1 TTTATAT-ATTATAATTAT
*
2396003 ATTATAT
1 TTTATAT
2396010 TTAATATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
18 11 0.21
19 18 0.35
20 11 0.21
21 9 0.17
22 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATATTATAATTAT
Found at i:2396006 original size:31 final size:30
Alignment explanation
Indices: 2395926--2396020 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
2395916 TATTAAAATA
* *
2395926 TTTATAT-ATTTAACTATATTTATATCTTAT
1 TTTATATAATTTAATTATA-TTATATTTTAT
2395956 TTTA-ATTAATTT--TTATATTATATTTTAT
1 TTTATA-TAATTTAATTATATTATATTTTAT
*
2395984 TTTATATAATTATAATTATATTATATTTAAT
1 TTTATATAATT-TAATTATATTATATTTTAT
*
2396015 ATTATA
1 TTTATA
2396021 GTAAACCCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
28 19 0.35
29 7 0.13
30 5 0.09
31 24 0.44
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTATATAATTTAATTATATTATATTTTAT
Found at i:2396010 original size:26 final size:25
Alignment explanation
Indices: 2395923--2396016 Score: 72
Period size: 26 Copynumber: 3.8 Consensus size: 25
2395913 AAATATTAAA
*
2395923 ATATT-TA-TATATTTAACTATATTT
1 ATATTATATTATATTTAA-TATAATT
* * *
2395947 ATATCT-TATTTTAATTAAT-T-TTT
1 ATAT-TATATTATATTTAATATAATT
* *
2395970 ATATTATATTTTATTTTATATAATT
1 ATATTATATTATATTTAATATAATT
2395995 ATAATTATATTATATTTAATAT
1 AT-ATTATATTATATTTAATAT
2396017 TATAGTAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.02
23 18 0.32
24 6 0.11
25 8 0.14
26 24 0.42
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATTATATTATATTTAATATAATT
Found at i:2396400 original size:26 final size:24
Alignment explanation
Indices: 2396356--2396416 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
2396346 AATGCACACA
*
2396356 TTAAAAAATATTTTGTATTTTTTT
1 TTAAAAAATATTTTGTATTTTATT
2396380 TTAAAAAATATACTTAT-TATTTTA-T
1 TTAAAAAATAT--TT-TGTATTTTATT
*
2396405 TTGAAAAATATT
1 TTAAAAAATATT
2396417 ATTTTATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 11 0.34
25 11 0.34
26 8 0.25
27 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
TTAAAAAATATTTTGTATTTTATT
Found at i:2399710 original size:9 final size:11
Alignment explanation
Indices: 2399685--2399714 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
2399675 AGAAATTTTT
2399685 TAAAAATATAA
1 TAAAAATATAA
2399696 TAAAAATA-AA
1 TAAAAATATAA
2399706 TAAAAATAT
1 TAAAAATAT
2399715 GTGATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:2407030 original size:124 final size:126
Alignment explanation
Indices: 2406805--2407030 Score: 275
Period size: 126 Copynumber: 1.8 Consensus size: 126
2406795 ATAACGAATT
* * *
2406805 CACCTACAATCATCATTCAATAACCTTAACAATGTACAATATTACCTATATATATAGTTTCAGTC
1 CACCTACAATCATCATTCAATAACCTTAACAATGCACAACATTACCTATATATATAGTTTCAGCC
*
2406870 AATCAGATTCGACACTACATCTTCCAAATATGAAAAAAAAAAAATTAATATAAAGACAATG
66 AATCAGATTCAACACTACATCTTCCAAATATGAAAAAAAAAAAATTAATATAAAGACAATG
* * *
2406931 CACCTACAATCATCATT-ACATATTCC-TAATAATGCACTACATTACCTAT-T-TATAGTTTCAG
1 CACCTACAATCATCATTCA-ATA-ACCTTAACAATGCACAACATTACCTATATATATAGTTTCAG
* * * * *
2406992 CCACCTC-TATTCAATACTATATCTTTCAAATA-GAAAAAA
64 CCA-ATCAGATTCAACACTACATCTTCCAAATATGAAAAAA
2407031 GAATTAGTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
123 7 0.08
124 33 0.39
125 4 0.05
126 39 0.46
127 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.31
Consensus pattern (126 bp):
CACCTACAATCATCATTCAATAACCTTAACAATGCACAACATTACCTATATATATAGTTTCAGCC
AATCAGATTCAACACTACATCTTCCAAATATGAAAAAAAAAAAATTAATATAAAGACAATG
Found at i:2409017 original size:13 final size:13
Alignment explanation
Indices: 2408999--2409024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2408989 TTATAATTTT
2408999 AAATATAATATAA
1 AAATATAATATAA
2409012 AAATATAATATAA
1 AAATATAATATAA
2409025 GTGTGACATG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:2409116 original size:18 final size:17
Alignment explanation
Indices: 2409076--2409122 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2409066 TATGATTAAA
*
2409076 AAATAAATTTAATTTAT
1 AAATTAATTTAATTTAT
*
2409093 ATATTACATTTATATTTA-
1 AAATTA-ATTTA-ATTTAT
2409111 AAATTAATTTAA
1 AAATTAATTTAA
2409123 ATTCATAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.04
17 9 0.36
18 10 0.40
19 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTAATTTAATTTAT
Found at i:2409444 original size:3 final size:3
Alignment explanation
Indices: 2409436--2409462 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2409426 TTAAATCGTA
2409436 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2409463 TATTGCTTTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2410129 original size:2 final size:2
Alignment explanation
Indices: 2410122--2410171 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2410112 AGACAAGAAC
2410122 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2410164 GA GA GA GA
1 GA GA GA GA
2410172 TAATCACTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2410702 original size:20 final size:20
Alignment explanation
Indices: 2410679--2410752 Score: 52
Period size: 21 Copynumber: 3.9 Consensus size: 20
2410669 AAATTTATAT
2410679 AATATAAATTATTATATTAA
1 AATATAAATTATTATATTAA
*
2410699 AATA-AAA--A-TAT-TTTA
1 AATATAAATTATTATATTAA
*
2410714 AATAT-AATTATAATATAATAA
1 AATATAAATTAT--TATATTAA
*
2410735 AATATATAAATATTATAT
1 AATATA-AATTATTATAT
2410753 GAATATACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 17
0.65 0.08 0.27
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 2 0.05
19 3 0.08
20 7 0.17
21 11 0.28
23 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAAATTATTATATTAA
Found at i:2410757 original size:29 final size:27
Alignment explanation
Indices: 2410680--2410759 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 27
2410670 AATTTATATA
*
2410680 ATATAAATTATTATATTAAAAT-AAAAAT
1 ATATAAA-TATTATA-TAATATAAAAAAT
* *
2410708 ATTTTAAATATAATTATAATATAATAAAAT
1 A-TATAAATATTA-TATAATATAA-AAAAT
2410738 ATATAAATATTATATGAATATA
1 ATATAAATATTATAT-AATATA
2410760 CTTATAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
28 13 0.31
29 23 0.55
30 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATATAAATATTATATAATATAAAAAAT
Found at i:2410758 original size:40 final size:37
Alignment explanation
Indices: 2410668--2410766 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 37
2410658 ATATATTTTT
*
2410668 AAAAT-TTATATAATATAAATTAT--TATATTAAAATA
1 AAAATATTATATAATAT-AATTATAATATAATAAAATA
*
2410703 AAAATATTTTA-AATATAATTATAATATAATAAAATA
1 AAAATATTATATAATATAATTATAATATAATAAAATA
*
2410739 TATAAATATTATATGAATATACTTATAA
1 -A-AAATATTATAT-AATATAATTATAA
2410767 GCATATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
34 6 0.11
35 10 0.19
36 15 0.28
37 1 0.02
38 9 0.17
40 12 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (37 bp):
AAAATATTATATAATATAATTATAATATAATAAAATA
Found at i:2415187 original size:16 final size:16
Alignment explanation
Indices: 2415166--2415200 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2415156 GTCCTAGAAA
2415166 AGGGAGGGGGACAGGG
1 AGGGAGGGGGACAGGG
2415182 AGGGAGGGGGACAGGG
1 AGGGAGGGGGACAGGG
2415198 AGG
1 AGG
2415201 ACTTAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.69, T:0.00
Consensus pattern (16 bp):
AGGGAGGGGGACAGGG
Found at i:2425021 original size:16 final size:18
Alignment explanation
Indices: 2424985--2425026 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2424975 TTAATTTAAA
2424985 AAATATAAAAAATTATAT
1 AAATATAAAAAATTATAT
*
2425003 AAATATAAAATATT-T-T
1 AAATATAAAAAATTATAT
2425019 AAATATAA
1 AAATATAA
2425027 TTATAACGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATAAAAAATTATAT
Found at i:2425058 original size:56 final size:57
Alignment explanation
Indices: 2424946--2425062 Score: 143
Period size: 56 Copynumber: 2.1 Consensus size: 57
2424936 AATAAAAGAG
* **
2424946 AAATATATGAATATTTTAAATATATAATATTAATTTAAAAAATATAAAAAATTATAT
1 AAATATATAAATATTTTAAATATATAATATTAACGTAAAAAATATAAAAAATTATAT
*
2425003 AAATATA-AAATATTTTAAATATA-ATTA-TAACGTAATAAAATA-AAAAATATATATAT
1 AAATATATAAATATTTTAAATATATAATATTAACGTAA-AAAATATAAAAA-AT-TATAT
2425059 AAAT
1 AAAT
2425063 TTTCATGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 11 0.21
55 11 0.21
56 24 0.45
57 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (57 bp):
AAATATATAAATATTTTAAATATATAATATTAACGTAAAAAATATAAAAAATTATAT
Found at i:2425570 original size:33 final size:32
Alignment explanation
Indices: 2425515--2425608 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 32
2425505 AATAGTTAAA
*
2425515 ATAAA-ATA-TAAAATATGATATAATATAAATAT
1 ATAAATATATTAAAAT-TTATATAATATAAAT-T
*
2425547 ATAAATATTTTAAAATTTATATAATA-AAATT
1 ATAAATATATTAAAATTTATATAATATAAATT
* *
2425578 ATTAATATATTAAAATTTAAATAAATATAAA
1 ATAAATATATTAAAATTTATAT-AATATAAA
2425609 ATTTTTTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
31 20 0.38
32 13 0.25
33 14 0.26
34 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAAATATATTAAAATTTATATAATATAAATT
Found at i:2425608 original size:17 final size:17
Alignment explanation
Indices: 2425570--2425612 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2425560 AATTTATATA
* *
2425570 ATAAAATTATTAATATAT
1 ATAAAATT-TAAATAAAT
2425588 -TAAAATTTAAATAAAT
1 ATAAAATTTAAATAAAT
2425604 ATAAAATTT
1 ATAAAATTT
2425613 TTTTGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTAAATAAAT
Found at i:2426624 original size:19 final size:19
Alignment explanation
Indices: 2426586--2426624 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2426576 TAATAAATCA
**
2426586 ATTTAAATGTAAAATTTTT
1 ATTTAAATGTAAAAAATTT
*
2426605 ATTTAAATTTAAAAAATTT
1 ATTTAAATGTAAAAAATTT
2426624 A
1 A
2426625 AATTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTAAATGTAAAAAATTT
Found at i:2426656 original size:17 final size:17
Alignment explanation
Indices: 2426636--2426671 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2426626 ATTATTATTT
* *
2426636 AATTTGATTTATAAATA
1 AATTTAATTTAAAAATA
2426653 AATTTAATTTAAAAATA
1 AATTTAATTTAAAAATA
2426670 AA
1 AA
2426672 AAATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTTAATTTAAAAATA
Found at i:2426814 original size:22 final size:22
Alignment explanation
Indices: 2426789--2426833 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2426779 AGATTTTAAA
2426789 TTTTAATAATTATAATTT-ATTG
1 TTTTAA-AATTATAATTTCATTG
* *
2426811 TTTTTAAATTATGATTTCATTG
1 TTTTAAAATTATAATTTCATTG
2426833 T
1 T
2426834 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTAAAATTATAATTTCATTG
Found at i:2429449 original size:20 final size:18
Alignment explanation
Indices: 2429421--2429462 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2429411 AAAGCTTAGC
*
2429421 TTTTTTTTTTTAAATTTG
1 TTTTTTTTTTTTAATTTG
*
2429439 TTTTTTGTTTTTTACTTTG
1 TTTTTT-TTTTTTAATTTG
2429458 TTTTT
1 TTTTT
2429463 AATGTTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTTTAATTTG
Found at i:2431077 original size:2 final size:2
Alignment explanation
Indices: 2431070--2431100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2431060 AAGCATGAAC
2431070 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
2431101 GAGAGAGAGA
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:2431105 original size:2 final size:2
Alignment explanation
Indices: 2431100--2431126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2431090 ATATATATAT
2431100 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 A
2431127 AGAATCCAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2431494 original size:2 final size:2
Alignment explanation
Indices: 2431489--2431521 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2431479 ATATATATAT
2431489 AG AG AG AG AG -G 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 AG
2431522 TATAGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2433131 original size:12 final size:12
Alignment explanation
Indices: 2433114--2433186 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 12
2433104 AATTAAAATA
2433114 ATTAAATTTAAT
1 ATTAAATTTAAT
*
2433126 ATTAAAATT-AT
1 ATTAAATTTAAT
* **
2433137 ATTTAATAAAAT
1 ATTAAATTTAAT
2433149 A-TAAATTTAA-
1 ATTAAATTTAAT
2433159 ACTTAAATTT-AT
1 A-TTAAATTTAAT
*
2433171 -TTAAATCTAA-
1 ATTAAATTTAAT
2433181 ATTAAA
1 ATTAAA
2433187 AGTTCAGTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
10 8 0.17
11 20 0.43
12 18 0.39
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:2433158 original size:28 final size:27
Alignment explanation
Indices: 2433126--2433187 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
2433116 TAAATTTAAT
*
2433126 ATTAAAATTATATTTAATAAAATATAA
1 ATTAAAATTAAATTTAATAAAATATAA
* * * *
2433153 ATTTAAACTTAAATTTATTTAAATCTAA
1 A-TTAAAATTAAATTTAATAAAATATAA
2433181 ATTAAAA
1 ATTAAAA
2433188 GTTCAGTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTAAAATTAAATTTAATAAAATATAA
Found at i:2433220 original size:23 final size:23
Alignment explanation
Indices: 2433163--2433221 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
2433153 ATTTAAACTT
*
2433163 AAATTTATTTAAATCTAAATTAA
1 AAATTTAATTAAATCTAAATTAA
* * *
2433186 AAGTTCAGTTAAA-CTTAAATTAA
1 AAATTTAATTAAATC-TAAATTAA
2433209 AAATTTAATTAAA
1 AAATTTAATTAAA
2433222 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (23 bp):
AAATTTAATTAAATCTAAATTAA
Found at i:2433250 original size:16 final size:16
Alignment explanation
Indices: 2433208--2433253 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2433198 ACTTAAATTA
2433208 AAAATTTAATTAAAAT
1 AAAATTTAATTAAAAT
2433224 AAAA---AA-T--AAT
1 AAAATTTAATTAAAAT
2433234 AAAATTTAATTAAAAT
1 AAAATTTAATTAAAAT
2433250 AAAA
1 AAAA
2433254 AAATGCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 7 0.29
12 1 0.04
13 4 0.17
14 1 0.04
16 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTTAATTAAAAT
Found at i:2435434 original size:18 final size:18
Alignment explanation
Indices: 2435411--2435447 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2435401 TGATTTAAAG
2435411 TATTATTATTGTTTTAAT
1 TATTATTATTGTTTTAAT
* *
2435429 TATTATTTTTTTTTTAAT
1 TATTATTATTGTTTTAAT
2435447 T
1 T
2435448 TTTGAACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TATTATTATTGTTTTAAT
Found at i:2436933 original size:17 final size:17
Alignment explanation
Indices: 2436900--2436938 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2436890 ATAAAAAATT
2436900 TTAAA-AATATTTAAAA
1 TTAAATAATATTTAAAA
2436916 TTAAATAATAATTT-AAA
1 TTAAATAAT-ATTTAAAA
2436933 TTAAAT
1 TTAAAT
2436939 TTTATCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAATATTTAAAA
Found at i:2438899 original size:32 final size:32
Alignment explanation
Indices: 2438863--2438926 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2438853 CTTATGATGA
2438863 TATGGCATAGAATTGGAACTTACTGCAGAAGT
1 TATGGCATAGAATTGGAACTTACTGCAGAAGT
2438895 TATGGCATAGAATTGGAACTTACTGCAGAAGT
1 TATGGCATAGAATTGGAACTTACTGCAGAAGT
2438927 ATCTAGCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (32 bp):
TATGGCATAGAATTGGAACTTACTGCAGAAGT
Found at i:2440272 original size:20 final size:20
Alignment explanation
Indices: 2440247--2440285 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2440237 CCCAATACGA
*
2440247 TTTGTTTCAAGCAATGTCTG
1 TTTGTTTCAAACAATGTCTG
2440267 TTTGTTTCAAACAATGTCT
1 TTTGTTTCAAACAATGTCT
2440286 CCTCCTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTGTTTCAAACAATGTCTG
Found at i:2440566 original size:24 final size:24
Alignment explanation
Indices: 2440534--2440582 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2440524 GGCCTTGCAG
2440534 ATTGCCTTTTTTCGCGGCTTTCCT
1 ATTGCCTTTTTTCGCGGCTTTCCT
2440558 ATTGCCTTTTTTCGCGGCTTTCCT
1 ATTGCCTTTTTTCGCGGCTTTCCT
2440582 A
1 A
2440583 AAGGTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.29, G:0.16, T:0.49
Consensus pattern (24 bp):
ATTGCCTTTTTTCGCGGCTTTCCT
Found at i:2444146 original size:2 final size:2
Alignment explanation
Indices: 2444139--2444171 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2444129 TAATGTAAGC
2444139 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
2444172 AAAGAGTGAC
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:2446438 original size:2 final size:2
Alignment explanation
Indices: 2446431--2446463 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2446421 TGCATAGTGC
2446431 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
2446464 CCAGCTATTA
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:2447371 original size:2 final size:2
Alignment explanation
Indices: 2447364--2447406 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2447354 TGATCTAAGT
2447364 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2447406 T
1 T
2447407 TAATTTGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2453080 original size:3 final size:3
Alignment explanation
Indices: 2453072--2453108 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2453062 GTAACTTCTC
2453072 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2453109 ACATTAGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2454059 original size:4 final size:4
Alignment explanation
Indices: 2454050--2454081 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
2454040 CACTTTGCGA
2454050 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2454082 CATTTTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:2454739 original size:2 final size:2
Alignment explanation
Indices: 2454734--2454763 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2454724 ATAAAAAACT
2454734 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2454764 AACAAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2455314 original size:11 final size:10
Alignment explanation
Indices: 2455293--2455318 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2455283 CAGATATTTG
2455293 CCCCCCTCCC
1 CCCCCCTCCC
2455303 CCCCCCTCCC
1 CCCCCCTCCC
2455313 CCCCCC
1 CCCCCC
2455319 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.92, G:0.00, T:0.08
Consensus pattern (10 bp):
CCCCCCTCCC
Found at i:2456329 original size:23 final size:22
Alignment explanation
Indices: 2456292--2456348 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
2456282 TTTGTTTTTA
2456292 AATTAATTTTTATTT-TCAAAATAT
1 AATTAA-TTTTATTTAT-AAAAT-T
*
2456316 ATTTAATTTTATTTATAAAATT
1 AATTAATTTTATTTATAAAATT
2456338 AATTAATTTTA
1 AATTAATTTTA
2456349 AATAATCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.37
23 13 0.43
24 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTAATTTTATTTATAAAATT
Found at i:2456825 original size:2 final size:2
Alignment explanation
Indices: 2456818--2456851 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2456808 TCCACTTGCA
* *
2456818 TC TC TC TC TC CC TC TC TC TC TC TC TG TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2456852 ATTTCTGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:2464817 original size:3 final size:3
Alignment explanation
Indices: 2464809--2464840 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2464799 GCATCATGGC
2464809 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2464841 AAAGCTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2470319 original size:13 final size:13
Alignment explanation
Indices: 2470301--2470327 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2470291 AGAAACTTTG
2470301 CTGTAAAAGCCAT
1 CTGTAAAAGCCAT
2470314 CTGTAAAAGCCAT
1 CTGTAAAAGCCAT
2470327 C
1 C
2470328 ACTCCAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (13 bp):
CTGTAAAAGCCAT
Found at i:2471645 original size:17 final size:17
Alignment explanation
Indices: 2471604--2471647 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2471594 TCTGTCAGAA
*
2471604 AAAGCCCATTGAAATCC
1 AAAGCCCATTCAAATCC
*
2471621 AAACCCCATTCAAAT-C
1 AAAGCCCATTCAAATCC
2471637 ACAAGCCCATT
1 A-AAGCCCATT
2471648 TATAAACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.41, C:0.34, G:0.07, T:0.18
Consensus pattern (17 bp):
AAAGCCCATTCAAATCC
Found at i:2474197 original size:87 final size:87
Alignment explanation
Indices: 2474051--2474226 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
2474041 ATCAGCATTT
2474051 ACATAGTTTCTAAAAAATGCACTTAAGAACAGAAGAATTATTTAAGTTACCAAGGGAGGTATATG
1 ACATAGTTTCTAAAAAATGCACTTAAGAACAGAAGAATTATTTAAGTTACCAAGGGAGGTATATG
2474116 AGCACGAGAAGCCCCCTGAGCA
66 AGCACGAGAAGCCCCCTGAGCA
2474138 ACATAGTTTCTAAAAAATGCACTTAAGAACAGAAGAATTATTTAAGTTACCAAGGGAGGTATATG
1 ACATAGTTTCTAAAAAATGCACTTAAGAACAGAAGAATTATTTAAGTTACCAAGGGAGGTATATG
2474203 AGCACGAGAAGCCCCCTGAGCA
66 AGCACGAGAAGCCCCCTGAGCA
2474225 AC
1 AC
2474227 TGTTTCAGCC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (87 bp):
ACATAGTTTCTAAAAAATGCACTTAAGAACAGAAGAATTATTTAAGTTACCAAGGGAGGTATATG
AGCACGAGAAGCCCCCTGAGCA
Found at i:2480831 original size:2 final size:2
Alignment explanation
Indices: 2480826--2480863 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2480816 ATATATATAT
2480826 AG AG AG 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 AG AG AG
2480864 TGAGTGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2481022 original size:14 final size:14
Alignment explanation
Indices: 2480999--2481029 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2480989 ATAATAATAA
*
2480999 TTAATTAAATATTT
1 TTAATGAAATATTT
2481013 TTAATGAAATATTT
1 TTAATGAAATATTT
2481027 TTA
1 TTA
2481030 TTTGTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTAATGAAATATTT
Found at i:2481369 original size:22 final size:22
Alignment explanation
Indices: 2481341--2481426 Score: 78
Period size: 21 Copynumber: 4.1 Consensus size: 22
2481331 TAATTATATG
2481341 ATTTAAATATAATATAAAAAAT
1 ATTTAAATATAATATAAAAAAT
*
2481363 ATTTAAA-ATAAAATAAAAAAT
1 ATTTAAATATAATATAAAAAAT
*
2481384 A--T-GATATAATAT-AAAAAT
1 ATTTAAATATAATATAAAAAAT
*
2481402 AATATAAATAT-ATA-AAAAACAT
1 -ATTTAAATATAATATAAAAA-AT
2481424 ATT
1 ATT
2481427 ACAAAGTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
18 7 0.13
19 8 0.15
21 24 0.46
22 13 0.25
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (22 bp):
ATTTAAATATAATATAAAAAAT
Found at i:2481399 original size:17 final size:17
Alignment explanation
Indices: 2481369--2481418 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
2481359 AAATATTTAA
2481369 AATA-AAATA-AAAAAT
1 AATATAAATATAAAAAT
2481384 -ATGATATAATATAAAAAT
1 AAT-ATA-AATATAAAAAT
2481402 AATATAAATATATAAAA
1 AATATAAATATA-AAAA
2481419 AACATATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.07
15 1 0.03
16 1 0.03
17 10 0.34
18 13 0.45
19 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
AATATAAATATAAAAAT
Found at i:2482658 original size:3 final size:3
Alignment explanation
Indices: 2482650--2482674 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2482640 AACATATTCG
2482650 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
2482675 AGTTAAAAGG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2483517 original size:5 final size:5
Alignment explanation
Indices: 2483507--2483534 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2483497 GAATAATGCC
2483507 CTTGG CTTGG CTTGG CTTGG CTTGG CTT
1 CTTGG CTTGG CTTGG CTTGG CTTGG CTT
2483535 TGACAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.36, T:0.43
Consensus pattern (5 bp):
CTTGG
Found at i:2484158 original size:2 final size:2
Alignment explanation
Indices: 2484151--2484176 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2484141 AACTGACAAC
2484151 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2484177 CCAGATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2487915 original size:3 final size:3
Alignment explanation
Indices: 2487907--2487945 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2487897 CTTCTTTTCT
2487907 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2487946 TATTTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2488215 original size:2 final size:2
Alignment explanation
Indices: 2488208--2488241 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2488198 TTTTAAAGGT
2488208 TA TA TA TA 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 TA TA TA TA
2488242 AAGTTTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2488602 original size:3 final size:3
Alignment explanation
Indices: 2488596--2488641 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
2488586 AGAATAATAA
* *
2488596 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAG TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
2488642 ATACAATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2493767 original size:2 final size:2
Alignment explanation
Indices: 2493760--2493789 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2493750 AATAGTGTGA
2493760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2493790 CCAAGCTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2500284 original size:13 final size:13
Alignment explanation
Indices: 2500268--2500293 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2500258 ACCGATTTTT
2500268 TAAAAAAGAAAAA
1 TAAAAAAGAAAAA
2500281 TAAAAAAGAAAAA
1 TAAAAAAGAAAAA
2500294 CTTACCACCG
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
TAAAAAAGAAAAA
Found at i:2501321 original size:19 final size:19
Alignment explanation
Indices: 2501276--2501321 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2501266 TCATCACTAG
*
2501276 ATATTAATTAATATTTTTT
1 ATATTAATTAATAATTTTT
*
2501295 ATAGTAATTAAATAATTTTT
1 ATATTAATT-AATAATTTTT
2501315 A-ATTAAT
1 ATATTAAT
2501322 ATTTATATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTAATTAATAATTTTT
Found at i:2501783 original size:234 final size:235
Alignment explanation
Indices: 2501336--2501787 Score: 766
Period size: 234 Copynumber: 1.9 Consensus size: 235
2501326 ATATACATAA
*
2501336 ATTAATTTGATTTTTTTTATAAAATATTTGAAATTTTGATATGAACTTTTGTCAAATTATTATTT
1 ATTAATTTGATTTTTCTTATAAAATATTTGAAATTTTGATATGAACTTTTGTCAAATTATTATTT
*
2501401 AAATTTGTTTTCAACCGTTAACAATTATTAAAGAGTTTATTCTTACTAATTTTTTAAAAATAACC
66 AAATTTGTTTTCAACCGTTAACAATTATTAAAGAGTTTATTCTTACAAATTTTTTAAAAATAACC
* * *
2501466 TTTTATTATGCTAATGATACTTGTTTAGATGTTAATATTAAAGTAGTAAAAAAATAAAATATATT
131 TTTTATTATGCTAATGATACTTGTTTAAATGTTAATATTAAAATAATAAAAAAATAAAATATATT
*
2501531 ATTAATGCAAGAATTATGATCTGCACATATCATATCTATT
196 ACTAATGCAAGAATTATGATCTGCACATATCATATCTATT
2501571 ATTAATTTGATTCTTTCTTATAAAATATTTGAAATTTTGATATGAACTTTTGTCAAATTATTATT
1 ATTAATTTGATT-TTTCTTATAAAATATTTGAAATTTTGATATGAACTTTTGTCAAATTATTATT
* *
2501636 TAAATTTTTTTTCAACC-TTAACAATTATTAAAGAGTTTATTCTTACCAAATTTTTTTAAAA-AA
65 TAAATTTGTTTTCAACCGTTAACAATTATTAAAGAGTTTATTCTTA-CAAATTTTTTAAAAATAA
* * *
2501699 -TTTTTTTTATGCTAATGATATTTGTTTAAATGTTAATATTAAAATAATAAAAAAATAAAATATA
129 CCTTTTATTATGCTAATGATACTTGTTTAAATGTTAATATTAAAATAATAAAAAAATAAAATATA
2501763 TTACTAATGCAAGAATTATGATCTG
194 TTACTAATGCAAGAATTATGATCTG
2501788 TATATATTAT
Statistics
Matches: 204, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
234 82 0.40
235 42 0.21
236 80 0.39
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (235 bp):
ATTAATTTGATTTTTCTTATAAAATATTTGAAATTTTGATATGAACTTTTGTCAAATTATTATTT
AAATTTGTTTTCAACCGTTAACAATTATTAAAGAGTTTATTCTTACAAATTTTTTAAAAATAACC
TTTTATTATGCTAATGATACTTGTTTAAATGTTAATATTAAAATAATAAAAAAATAAAATATATT
ACTAATGCAAGAATTATGATCTGCACATATCATATCTATT
Found at i:2506039 original size:14 final size:14
Alignment explanation
Indices: 2506020--2506053 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2506010 TTTTTTATGT
2506020 AATTTGTATAATTG
1 AATTTGTATAATTG
* *
2506034 AATTTGTATCATTT
1 AATTTGTATAATTG
2506048 AATTTG
1 AATTTG
2506054 ATTTGTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (14 bp):
AATTTGTATAATTG
Found at i:2506550 original size:2 final size:2
Alignment explanation
Indices: 2506543--2506575 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2506533 TTCCATTTCA
2506543 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
2506576 AAAGAAAAGG
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:2509160 original size:12 final size:12
Alignment explanation
Indices: 2509139--2509172 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2509129 AAAATTAAAG
*
2509139 TTTTGATTTTAT
1 TTTTAATTTTAT
*
2509151 TTTTAGTTTTAT
1 TTTTAATTTTAT
2509163 TTTTAATTTT
1 TTTTAATTTT
2509173 CAACTGTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
TTTTAATTTTAT
Found at i:2511833 original size:5 final size:5
Alignment explanation
Indices: 2511806--2511856 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
2511796 TTAATATAAA
* *
2511806 TATAT TTTAA TATAT T-T-T TATAT TATAT TATATTT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA--T TATAT TATAT TATAT
2511856 T
1 T
2511857 TTTTTATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 29 0.76
7 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:2511843 original size:17 final size:17
Alignment explanation
Indices: 2511806--2511858 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
2511796 TTAATATAAA
* *
2511806 TATATTTTAATATATTTT
1 TATATTATATTATA-TTT
2511824 TATATTATATTATATTT
1 TATATTATATTATATTT
2511841 TATATTATATTATATTT
1 TATATTATATTATATTT
2511858 T
1 T
2511859 TTTATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATTATATTATATTT
Found at i:2513354 original size:49 final size:52
Alignment explanation
Indices: 2513251--2513355 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 52
2513241 TCAACTTCTT
2513251 TTACACCGAGCTCGATTATCATAAACTAAGGTTAGTCTAAATGCCCGACCTCTAA
1 TTACACCGAGCTCGATTATCAT-AAC-AA-GTTAGTCTAAATGCCCGACCTCTAA
2513306 TTACACCGAGCTCGATTATCAT-A-AA-TTAGTCTAAATGCCCGACCTCTAA
1 TTACACCGAGCTCGATTATCATAACAAGTTAGTCTAAATGCCCGACCTCTAA
2513355 T
1 T
2513356 GGTGATCTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
49 25 0.50
51 2 0.04
53 1 0.02
55 22 0.44
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (52 bp):
TTACACCGAGCTCGATTATCATAACAAGTTAGTCTAAATGCCCGACCTCTAA
Found at i:2515667 original size:15 final size:16
Alignment explanation
Indices: 2515636--2515669 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2515626 GTGAGTTTGG
2515636 ATATAAATATTTATTTA
1 ATATAAATA-TTATTTA
2515653 ATATAAATA-TATTTA
1 ATATAAATATTATTTA
2515668 AT
1 AT
2515670 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAAATATTATTTA
Found at i:2516394 original size:4 final size:4
Alignment explanation
Indices: 2516385--2516415 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2516375 AATAAACTTC
2516385 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2516416 AACAAGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2518673 original size:3 final size:3
Alignment explanation
Indices: 2518665--2518721 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
2518655 CTCAACCTTG
* * * *
2518665 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATTC TTA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
2518711 ATA ATA ATA AT
1 ATA ATA ATA AT
2518722 TCTATCTGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 44 0.98
4 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2518707 original size:25 final size:25
Alignment explanation
Indices: 2518675--2518724 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2518665 ATAATAATAA
2518675 TAATAATAACAATAATAATAATTCT
1 TAATAATAACAATAATAATAATTCT
2518700 TAATAATAACAATAATAATAATTCT
1 TAATAATAACAATAATAATAATTCT
2518725 ATCTGGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (25 bp):
TAATAATAACAATAATAATAATTCT
Found at i:2528366 original size:33 final size:33
Alignment explanation
Indices: 2528322--2528396 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
2528312 CTAAGAGGCT
* *
2528322 TGAAGAAGAGGAGCAAGACGGAGCAAGCAAACA
1 TGAAGAAGAGGAGCAAGAAGAAGCAAGCAAACA
* * **
2528355 TGAAGATGAGGAGCAGGAAGAAGCAAGTTAACA
1 TGAAGAAGAGGAGCAAGAAGAAGCAAGCAAACA
2528388 TGAAGAAGA
1 TGAAGAAGA
2528397 TGAAGGCAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.11, G:0.33, T:0.08
Consensus pattern (33 bp):
TGAAGAAGAGGAGCAAGAAGAAGCAAGCAAACA
Found at i:2532624 original size:50 final size:50
Alignment explanation
Indices: 2532569--2532752 Score: 264
Period size: 50 Copynumber: 3.7 Consensus size: 50
2532559 TTTTCTATTA
*
2532569 TCAAAGGTTGATGAAGAATAGTCAACAATTACGATCAACTCTCTCGATTG
1 TCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAACTCTCTCGATTG
* * *
2532619 TCAAAGGTTGGTGAGGAATAGTTAACAATTAC-AGTCACCTCTCTCGATTG
1 TCAAAGGTTGGTGAAGAATAGTCAACAATTACGA-TCAACTCTCTCGATTG
* * *
2532669 TTAAAGGTTGGTGAAGAATAGTCAATAATTACGGT-AACTTCTCTCGATTG
1 TCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAAC-TCTCTCGATTG
*
2532719 TCAAAGGTTGGTGAAGAATAATCAACAATTACGA
1 TCAAAGGTTGGTGAAGAATAGTCAACAATTACGA
2532753 CCACTTCTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
49 3 0.03
50 114 0.97
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (50 bp):
TCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAACTCTCTCGATTG
Found at i:2532712 original size:100 final size:100
Alignment explanation
Indices: 2532538--2532750 Score: 311
Period size: 100 Copynumber: 2.1 Consensus size: 100
2532528 AGATGCTTAG
* * *
2532538 AGTTAACAATTACAGTCACCTTTTTCTATTATCAAAGGTTGATGAAGAATAGTCAACAATTACGA
1 AGTTAACAATTACAGTCACCTCTCTCGATTATCAAAGGTTGATGAAGAATAGTCAACAATTACGA
*
2532603 TCAACTCTCTCGATTGTCAAAGGTTGGTGAGGAAT
66 TCAACTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * * *
2532638 AGTTAACAATTACAGTCACCTCTCTCGATTGTTAAAGGTTGGTGAAGAATAGTCAATAATTACGG
1 AGTTAACAATTACAGTCACCTCTCTCGATTATCAAAGGTTGATGAAGAATAGTCAACAATTACGA
2532703 T-AACTTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
66 TCAAC-TCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
2532738 AATCAACAATTAC
1 AGTTAACAATTAC
2532751 GACCACTTCT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
99 3 0.03
100 98 0.97
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (100 bp):
AGTTAACAATTACAGTCACCTCTCTCGATTATCAAAGGTTGATGAAGAATAGTCAACAATTACGA
TCAACTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:2533562 original size:22 final size:22
Alignment explanation
Indices: 2533534--2533576 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2533524 AGACATTTCC
2533534 TTCCTCTCATTTTCATCGCTAT
1 TTCCTCTCATTTTCATCGCTAT
2533556 TTCCTCTCATTTTCATCGCTA
1 TTCCTCTCATTTTCATCGCTA
2533577 GGACACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.33, G:0.05, T:0.49
Consensus pattern (22 bp):
TTCCTCTCATTTTCATCGCTAT
Found at i:2538671 original size:13 final size:13
Alignment explanation
Indices: 2538653--2538680 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2538643 GAAGCTAGAA
2538653 AATATGGTTGAAG
1 AATATGGTTGAAG
2538666 AATATGGTTGAAG
1 AATATGGTTGAAG
2538679 AA
1 AA
2538681 AGGATCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (13 bp):
AATATGGTTGAAG
Found at i:2539164 original size:40 final size:39
Alignment explanation
Indices: 2539105--2539182 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
2539095 GGTAAAAAGA
* *
2539105 CATAATGTATCGATATATTGAAGAATATATTGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
2539144 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
2539183 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:2539172 original size:20 final size:20
Alignment explanation
Indices: 2539108--2539179 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2539098 AAAAAGACAT
*
2539108 AATGTATCGATATATTGAAG
1 AATGTATCGATATATTGAAA
* * * * *
2539128 AATATATTGATACATTCATA
1 AATGTATCGATATATTGAAA
*
2539148 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTGAAA
2539168 AATGTATCGATA
1 AATGTATCGATA
2539180 CATCTGGGTA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATATATTGAAA
Found at i:2540756 original size:50 final size:50
Alignment explanation
Indices: 2540662--2540829 Score: 176
Period size: 50 Copynumber: 3.3 Consensus size: 50
2540652 ATGTTTAGAG
* ** * *
2540662 TCAACAATTACGATCACCTTTTTTTTATTATCAAAAGTTGATAAAAAATAA
1 TCAACAATTACAATCACC-TTTTTCAATTATCAAAAATTAATAAAAAATAA
* *
2540713 TCAACAATTACAATCACCTTTTTCGATTATCAAAATTTAATAAAAAATAA
1 TCAACAATTACAATCACCTTTTTCAATTATCAAAAATTAATAAAAAATAA
* * * * * * *
2540763 TTAATAATTACGATTACCTCTCTCAATTATCAAAAAATAATAAAAAATAGA
1 TCAACAATTACAATCACCTTTTTCAATTATCAAAAATTAATAAAAAATA-A
*
2540814 T-AATAATTACAATCAC
1 TCAACAATTACAATCAC
2540830 TTCTCTGTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
50 81 0.81
51 19 0.19
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.34
Consensus pattern (50 bp):
TCAACAATTACAATCACCTTTTTCAATTATCAAAAATTAATAAAAAATAA
Found at i:2543082 original size:5 final size:5
Alignment explanation
Indices: 2543072--2543100 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2543062 TCATGGATCT
2543072 AACCC AACCC AACCC AACCC AACCC AACC
1 AACCC AACCC AACCC AACCC AACCC AACC
2543101 ATAGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:2544335 original size:37 final size:35
Alignment explanation
Indices: 2544244--2544338 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 35
2544234 GAAAAAATCA
* *
2544244 TATATTTGTAT-T-TATATTTTTTATTTAAAATAT
1 TATATTTTTATATATATATTTTTTATATAAAATAT
*
2544277 TATATTTTTATATA-AT-TTTTTTATATATTAATAAT
1 TATATTTTTATATATATATTTTTTATATA-AAAT-AT
2544312 TAT-TTTATTATATATATATTTTTTATA
1 TATATTT-TTATATATATATTTTTTATA
2544339 CATGTATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
33 20 0.38
34 9 0.17
35 12 0.23
36 2 0.04
37 9 0.17
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (35 bp):
TATATTTTTATATATATATTTTTTATATAAAATAT
Found at i:2544490 original size:24 final size:24
Alignment explanation
Indices: 2544463--2544509 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2544453 TTTTTAAATA
*
2544463 TTAAT-TATTAATTTAATTTATATT
1 TTAATATATTAATGT-ATTTATATT
*
2544487 TTAATATATTTATGTATTTATAT
1 TTAATATATTAATGTATTTATAT
2544510 CATAATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTAATATATTAATGTATTTATATT
Found at i:2544775 original size:21 final size:20
Alignment explanation
Indices: 2544749--2544798 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
2544739 AGTTTCTTTT
2544749 AAGAAAAAAAGGAAAAAAAAA
1 AAGAAAAAAA-GAAAAAAAAA
* *
2544770 AAGAAAAGAAAGAAAAAGACA
1 AAGAAAA-AAAGAAAAAAAAA
2544791 AAGAAAAA
1 AAGAAAAA
2544799 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAGAAAAAAAAA
Found at i:2544785 original size:16 final size:16
Alignment explanation
Indices: 2544767--2544796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2544757 AAGGAAAAAA
2544767 AAAAAGA-AAAGAAAG
1 AAAAAGACAAAGAAAG
2544782 AAAAAGACAAAGAAA
1 AAAAAGACAAAGAAA
2544797 AATTAAAAAA
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:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGACAAAGAAAG
Found at i:2544886 original size:16 final size:14
Alignment explanation
Indices: 2544853--2544895 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
2544843 ATGACTTAAA
*
2544853 ATAT-TATAAATTT
1 ATATATATATATTT
2544866 ATATA-ATAT-TTT
1 ATATATATATATTT
2544878 ATATATATATATTT
1 ATATATATATATTT
2544892 ATAT
1 ATAT
2544896 GTTATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.31
13 11 0.42
14 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATATATATTT
Found at i:2544943 original size:22 final size:20
Alignment explanation
Indices: 2544917--2544967 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2544907 TGTGTCATTT
2544917 ATTTTTTATATTATATTTTA
1 ATTTTTTATATTATATTTTA
* *
2544937 ATTTTTTATATCATATTTTT
1 ATTTTTTATATTATATTTTA
*
2544957 ATATTTTATAT
1 ATTTTTTATAT
2544968 ATTTAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTATATTATATTTTA
Done.