Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 20 of 20
Found at i:2637979 original size:7 final size:7
Alignment explanation
Indices: 2637964--2638015 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
2637954 AAGTGTCATC
*
2637964 TAAAATT
1 TAAATTT
2637971 TAAATTT
1 TAAATTT
2637978 TAAA-TT
1 TAAATTT
2637984 TAAATTT
1 TAAATTT
2637991 TAAATTT
1 TAAATTT
2637998 TAAATTT
1 TAAATTT
*
2638005 TAAAATT
1 TAAATTT
2638012 TAAA
1 TAAA
2638016 ATTTGAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TAAATTT
Found at i:2637981 original size:14 final size:14
Alignment explanation
Indices: 2637964--2638015 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
2637954 AAGTGTCATC
2637964 TAAAATTTAAATTT
1 TAAAATTTAAATTT
2637978 T-AAATTTAAATTT
1 TAAAATTTAAATTT
*
2637991 TAAATTTTAAATTT
1 TAAAATTTAAATTT
2638005 TAAAATTTAAA
1 TAAAATTTAAA
2638016 ATTTGAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.37
14 22 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAATTTAAATTT
Found at i:2637982 original size:13 final size:13
Alignment explanation
Indices: 2637966--2638015 Score: 82
Period size: 13 Copynumber: 3.7 Consensus size: 13
2637956 GTGTCATCTA
2637966 AAATTTAAATTTT
1 AAATTTAAATTTT
2637979 AAATTTAAATTTT
1 AAATTTAAATTTT
2637992 AAATTTTAAATTTT
1 AAA-TTTAAATTTT
2638006 AAAATTTAAA
1 -AAATTTAAA
2638016 ATTTGAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 16 0.46
14 16 0.46
15 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:2639163 original size:26 final size:25
Alignment explanation
Indices: 2639134--2639217 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
2639124 AAAAATTTTA
2639134 AAATAATTTTATTAATTTAATATAAT
1 AAATAATTTTATTAATTT-ATATAAT
* **
2639160 AAATAA-ATTATATAATTT-TACGAT
1 AAATAATTTTAT-TAATTTATATAAT
*
2639184 AAATAAATTTTATTATTTTATATAAT
1 AAAT-AATTTTATTAATTTATATAAT
2639210 AAAGTAAT
1 AAA-TAAT
2639218 ATCTTAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
24 8 0.17
25 11 0.24
26 26 0.57
27 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATAATTTTATTAATTTATATAAT
Found at i:2639190 original size:24 final size:24
Alignment explanation
Indices: 2639158--2639203 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2639148 ATTTAATATA
2639158 ATAAATAAATTATATAATTTTACG
1 ATAAATAAATTATATAATTTTACG
* *
2639182 ATAAATAAATTTTATTATTTTA
1 ATAAATAAATTATATAATTTTA
2639204 TATAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
ATAAATAAATTATATAATTTTACG
Found at i:2639703 original size:27 final size:31
Alignment explanation
Indices: 2639673--2639737 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
2639663 CTCATTTCAC
2639673 TTTTTAA-TTT-TATTTA-TTT-TTAAATTA
1 TTTTTAATTTTATATTTATTTTATTAAATTA
*
2639700 TTTTTAATTTTTATATTTATTTTATTAATTTA
1 TTTTTAA-TTTTATATTTATTTTATTAAATTA
2639732 TTTTTA
1 TTTTTA
2639738 GATAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.22
29 3 0.09
30 6 0.19
31 3 0.09
32 13 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTTAATTTTATATTTATTTTATTAAATTA
Found at i:2639803 original size:26 final size:27
Alignment explanation
Indices: 2639748--2639808 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
2639738 GATAAAAATA
*
2639748 TAATTTTAGTAAATTTTAATTATTATT
1 TAATATTAGTAAATTTTAATTATTATT
* *
2639775 TAATATTAGTATATTTT-TTTATTATT
1 TAATATTAGTAAATTTTAATTATTATT
2639801 TAATATTA
1 TAATATTA
2639809 AAATTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (27 bp):
TAATATTAGTAAATTTTAATTATTATT
Found at i:2643207 original size:94 final size:94
Alignment explanation
Indices: 2643046--2643269 Score: 322
Period size: 94 Copynumber: 2.4 Consensus size: 94
2643036 TCCTTCATTA
* * * * * *
2643046 GGGATGCTCCAACCCCATTATTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGTCAAGATAA
1 GGGATACTCCAACCCCATTCTTTCGAGAGGATACTCCAACCCCGTTTTCAAACTTATCAAGATAA
**
2643111 TTCTTATTTTTGCTTAAATTGTCATTGTC
66 TTCTTATTTTTGCTTAAATTGTCATCATC
* * *
2643140 GGGATACTCCAATCCCATTCTTTCGAGAGGATACTCCAATCCCGTTTTCAAACTTATTAAGATAA
1 GGGATACTCCAACCCCATTCTTTCGAGAGGATACTCCAACCCCGTTTTCAAACTTATCAAGATAA
2643205 TTCTTATTTTTGCTTAAATTGTCATCATC
66 TTCTTATTTTTGCTTAAATTGTCATCATC
* * *
2643234 GGGATACTCTAACCCCATTCATTCGAGAAGATACTC
1 GGGATACTCCAACCCCATTCTTTCGAGAGGATACTC
2643270 TAGCCCCATT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 115 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (94 bp):
GGGATACTCCAACCCCATTCTTTCGAGAGGATACTCCAACCCCGTTTTCAAACTTATCAAGATAA
TTCTTATTTTTGCTTAAATTGTCATCATC
Found at i:2644283 original size:30 final size:32
Alignment explanation
Indices: 2644228--2644356 Score: 82
Period size: 33 Copynumber: 3.8 Consensus size: 32
2644218 TTTATTTTAA
* *
2644228 TTATTATTTAATATTAATGCAATATT-ATTATTT
1 TTATTATTTAATATAAAT--AATATTAATAATTT
2644261 TTATTATTTAATATAAAT-ATATTGAATAATTTTT
1 TTATTATTTAATATAAATAATATT-AATAA--TTT
* * *
2644295 AATTATTATTTAACATAAATATAATTTTTATAATTT
1 --TTATTATTTAATAT-AA-ATAATATTAATAATTT
* *
2644331 TTATTTATTTATTATATATAAATATT
1 TTA-TTATTTAATATAAAT-AATATT
2644357 TTAATTTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
30 5 0.07
32 3 0.04
33 19 0.25
34 12 0.16
35 9 0.12
36 16 0.21
37 2 0.03
38 6 0.08
39 4 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (32 bp):
TTATTATTTAATATAAATAATATTAATAATTT
Found at i:2644301 original size:36 final size:38
Alignment explanation
Indices: 2644261--2644355 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 38
2644251 ATTATTATTT
2644261 TTATTATTTAATATAAATAT-A-TTGAATAATTTTTAA
1 TTATTATTTAATATAAATATAATTTGAATAATTTTTAA
* ** *
2644297 TTATTATTTAACATAAATATAATTTTTATAATTTTTAT
1 TTATTATTTAATATAAATATAATTTGAATAATTTTTAA
2644335 TTATT-TATTATATATAAATAT
1 TTATTAT-TTA-ATATAAATAT
2644356 TTTAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
36 19 0.38
37 2 0.04
38 20 0.40
39 9 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (38 bp):
TTATTATTTAATATAAATATAATTTGAATAATTTTTAA
Found at i:2644339 original size:38 final size:36
Alignment explanation
Indices: 2644260--2644339 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
2644250 TATTATTATT
*
2644260 TTTATTATTTAATATAAATATATTGAATAATTTTTA
1 TTTATTATTTAACATAAATATATTGAATAATTTTTA
* **
2644296 ATTATTATTTAACATAAATATAATTTTTATAATTTTTA
1 TTTATTATTTAACATAAATAT-A-TTGAATAATTTTTA
2644334 TTTATT
1 TTTATT
2644340 TATTATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 19 0.51
37 1 0.03
38 17 0.46
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTATTATTTAACATAAATATATTGAATAATTTTTA
Found at i:2645498 original size:14 final size:14
Alignment explanation
Indices: 2645451--2645498 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2645441 TTTATATTTA
2645451 TTTTAAATAT--AT
1 TTTTAAATATAAAT
2645463 TTTTAAATATAAAT
1 TTTTAAATATAAAT
* **
2645477 ATAAAAATATAAAT
1 TTTTAAATATAAAT
2645491 TTTTAAAT
1 TTTTAAAT
2645499 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 10 0.36
14 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTAAATATAAAT
Found at i:2646184 original size:21 final size:22
Alignment explanation
Indices: 2646160--2646203 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2646150 TTGATAAACT
2646160 TTTCTCAAAATA-TTTTATTTA
1 TTTCTCAAAATAGTTTTATTTA
* *
2646181 TTTCTCAATATAGTTTTTTTTA
1 TTTCTCAAAATAGTTTTATTTA
2646203 T
1 T
2646204 AAGATTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTCTCAAAATAGTTTTATTTA
Found at i:2648780 original size:24 final size:26
Alignment explanation
Indices: 2648753--2648809 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
2648743 TTATTTTAAA
* *
2648753 ATTTTTAATT-ATTTAA-AAATATAT
1 ATTTATAATTAATATAATAAATATAT
*
2648777 ATTTATATTTAATATAATAAATATAT
1 ATTTATAATTAATATAATAAATATAT
*
2648803 AATTATA
1 ATTTATA
2648810 TAATGATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 8 0.30
25 5 0.19
26 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTATAATTAATATAATAAATATAT
Found at i:2659506 original size:16 final size:17
Alignment explanation
Indices: 2659485--2659516 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2659475 TAATAATTTT
2659485 TAAAA-TATTTTTATTA
1 TAAAATTATTTTTATTA
2659501 TAAAATTATTTTTATT
1 TAAAATTATTTTTATT
2659517 TCTTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAAATTATTTTTATTA
Found at i:2661706 original size:23 final size:23
Alignment explanation
Indices: 2661678--2661749 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
2661668 TTTGAATTAT
2661678 TAAATTTATCATTATTATTTTTA
1 TAAATTTATCATTATTATTTTTA
** *
2661701 TAAATTATAAAATT-TTAATTTTA
1 TAAATT-TATCATTATTATTTTTA
* * *
2661724 TTAAATTAATCATCA-AATTTTTA
1 -TAAATTTATCATTATTATTTTTA
2661747 TAA
1 TAA
2661750 TTAATAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
22 3 0.08
23 23 0.62
24 11 0.30
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTATCATTATTATTTTTA
Found at i:2661934 original size:13 final size:14
Alignment explanation
Indices: 2661905--2661938 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2661895 AAAATTAGTA
2661905 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
2661919 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
2661932 TTAATAA
1 TTAATAA
2661939 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:2661966 original size:28 final size:29
Alignment explanation
Indices: 2661905--2661973 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 29
2661895 AAAATTAGTA
2661905 TTAAT-AA-TAAAAATTTAATAATATAAT
1 TTAATAAATTAAAAATTTAATAATATAAT
*
2661932 TTAATAAAATTAAAAATTT-ATATTA-AAT
1 TTAAT-AAATTAAAAATTTAATAATATAAT
2661960 TTAATAAATTAAAA
1 TTAATAAATTAAAA
2661974 TATTATCGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
27 14 0.37
28 8 0.21
29 7 0.18
30 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TTAATAAATTAAAAATTTAATAATATAAT
Found at i:2662187 original size:13 final size:14
Alignment explanation
Indices: 2662163--2662197 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2662153 AAATTTAATT
2662163 TATTTAATTATTTA
1 TATTTAATTATTTA
2662177 TATTT-ATTATTTA
1 TATTTAATTATTTA
*
2662190 TAATTAAT
1 TATTTAAT
2662198 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTAATTATTTA
Found at i:2662276 original size:51 final size:51
Alignment explanation
Indices: 2662160--2662282 Score: 123
Period size: 51 Copynumber: 2.4 Consensus size: 51
2662150 ATTAAATTTA
*
2662160 ATTTATTTAATTATTTATATTTATTATTTATAATTAATAAAAAATTTAAAAAT
1 ATTT-TTTAATTATTAATATTTATTATTTATAATTAATAAAAAA-TTAAAAAT
*
2662213 -TATTTTT-A-TATTAAT-TTTATTTATTTTATAATTAA-ATTAAAA-TAAAAAT
1 AT-TTTTTAATTATTAATATTTA-TTA-TTTATAATTAATA-AAAAATTAAAAAT
2662262 ATTTTTTAATTATTAAATATT
1 ATTTTTTAATTATT-AATATT
2662283 AATTTATATC
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
49 16 0.27
50 12 0.20
51 20 0.34
52 7 0.12
53 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (51 bp):
ATTTTTTAATTATTAATATTTATTATTTATAATTAATAAAAAATTAAAAAT
Found at i:2662459 original size:45 final size:42
Alignment explanation
Indices: 2662409--2662519 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 42
2662399 TTTTAAAATT
*
2662409 TATATAATATAAATTATTAATATATTAAAAAATTTTTAAATATAAA
1 TATATAATATAAATTATTAAT-TATTAAAAAA---TAAAATATAAA
* *
2662455 -ATAT-ATA-AAA-TATT-ATTTTTATAAAATAAAATATAAA
1 TATATAATATAAATTATTAATTATTAAAAAATAAAATATAAA
*
2662492 TATATAATATAAATATATAAATTATTAA
1 TATATAATATAAAT-TATTAATTATTAA
2662520 GTTTAATTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
37 10 0.19
38 4 0.08
39 3 0.06
40 11 0.21
41 2 0.04
42 7 0.13
43 9 0.17
44 3 0.06
45 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (42 bp):
TATATAATATAAATTATTAATTATTAAAAAATAAAATATAAA
Found at i:2662468 original size:34 final size:34
Alignment explanation
Indices: 2662403--2662469 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2662393 AAATATTTTT
* *
2662403 AAAATTTATATAATATAAATTATTAATATATTAA
1 AAAATTTATATAATATAAAATATTAAAATATTAA
*
2662437 AAAATTTTTA-AATATAAAATATATAAAATATTA
1 AAAATTTATATAATATAAAATAT-TAAAATATTA
2662470 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAATTTATATAATATAAAATATTAAAATATTAA
Found at i:2662502 original size:13 final size:13
Alignment explanation
Indices: 2662474--2662511 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2662464 ATATTATTTT
*
2662474 TATAAA-ATAAAA
1 TATAAATATATAA
2662486 TATAAATATATAA
1 TATAAATATATAA
2662499 TATAAATATATAA
1 TATAAATATATAA
2662512 ATTATTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TATAAATATATAA
Found at i:2663930 original size:2 final size:2
Alignment explanation
Indices: 2663923--2663956 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2663913 CATTGATTTA
*
2663923 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2663957 GAGGTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2664844 original size:2 final size:2
Alignment explanation
Indices: 2664837--2664867 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2664827 CTTAAACCCT
2664837 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 T
2664868 TAATCCAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2666194 original size:2 final size:2
Alignment explanation
Indices: 2666183--2666227 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2666173 ATTCCCCATC
2666183 AT AT -T AT AT AT 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 AT AT AT AT AT AT
2666224 AT AT
1 AT AT
2666228 CAGTGGAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2668531 original size:21 final size:21
Alignment explanation
Indices: 2668497--2668552 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2668487 ACAATCAATC
* * *
2668497 AATAAA-CCAACATATAATTG
1 AATAAATCAAACATAAAATTA
2668517 AATAAATCAAACATAAAATTA
1 AATAAATCAAACATAAAATTA
2668538 AATCAAATTCAAACA
1 AAT-AAA-TCAAACA
2668553 GAATAAGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 3 0.10
23 7 0.23
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAAATCAAACATAAAATTA
Found at i:2669311 original size:29 final size:30
Alignment explanation
Indices: 2669269--2669333 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
2669259 CGATGAGATG
* *
2669269 AAAA-ACATATATGATAAGATTGTAATCAT
1 AAAATACATATATGATAAAATCGTAATCAT
*
2669298 AAAATACA-ATATGATAAAATCGTATTCAT
1 AAAATACATATATGATAAAATCGTAATCAT
2669327 AAAATAC
1 AAAATAC
2669334 GACCCTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (30 bp):
AAAATACATATATGATAAAATCGTAATCAT
Found at i:2673065 original size:219 final size:219
Alignment explanation
Indices: 2672686--2673124 Score: 833
Period size: 219 Copynumber: 2.0 Consensus size: 219
2672676 TAAAGATCGA
* *
2672686 GAAGTCGTCGAAAACAGCCCTTAACTATTCCAAATAAATCTACATATAGTTAAGAGAGCATGATG
1 GAAGTCGTCGAAAACAGCCCTCAACTATTCCAAATAAATCTACAAATAGTTAAGAGAGCATGATG
* *
2672751 TTCGAAACCTTTTATTATAGGAATAAGAAGAAGGGTCAACGCTTGAACTTGCAGGGAAAATTTAT
66 TTCAAAACCTTTTATTATAGGAATAAGAAGAAGGATCAACGCTTGAACTTGCAGGGAAAATTTAT
2672816 CTGTCATGCTTATACTTCCCTTTTCTCTCAATGGCTTTAGAAAGAAATCCAATTAAGGTTCAGTG
131 CTGTCATGCTTATACTTCCCTTTTCTCTCAATGGCTTTAGAAAGAAATCCAATTAAGGTTCAGTG
2672881 CTTGGAACTCAGAGAATCATGGTT
196 CTTGGAACTCAGAGAATCATGGTT
*
2672905 GAAGTCGTCGAAAACAGCCCTCAACTATTCCAAATAAATCTACAAATAGTTAGGAGAGCATGATG
1 GAAGTCGTCGAAAACAGCCCTCAACTATTCCAAATAAATCTACAAATAGTTAAGAGAGCATGATG
2672970 TTCAAAACCTTTTATTATAGGAATAAGAAGAAGGATCAACGCTTGAACTTGCAGGGAAAATTTAT
66 TTCAAAACCTTTTATTATAGGAATAAGAAGAAGGATCAACGCTTGAACTTGCAGGGAAAATTTAT
2673035 CTGTCATGCTTATACTTCCCTTTTCTCTCAATGGCTTTAGAAAGAAATCCAATTAAGGTTCAGTG
131 CTGTCATGCTTATACTTCCCTTTTCTCTCAATGGCTTTAGAAAGAAATCCAATTAAGGTTCAGTG
2673100 CTTGGAACTCAGAGAATCATGGTT
196 CTTGGAACTCAGAGAATCATGGTT
2673124 G
1 G
2673125 CACTTTTCTC
Statistics
Matches: 215, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 215 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (219 bp):
GAAGTCGTCGAAAACAGCCCTCAACTATTCCAAATAAATCTACAAATAGTTAAGAGAGCATGATG
TTCAAAACCTTTTATTATAGGAATAAGAAGAAGGATCAACGCTTGAACTTGCAGGGAAAATTTAT
CTGTCATGCTTATACTTCCCTTTTCTCTCAATGGCTTTAGAAAGAAATCCAATTAAGGTTCAGTG
CTTGGAACTCAGAGAATCATGGTT
Found at i:2676769 original size:21 final size:22
Alignment explanation
Indices: 2676734--2676774 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2676724 TATCAATATA
2676734 ATTTTATAGATTTATATTTTTC
1 ATTTTATAGATTTATATTTTTC
*
2676756 ATTTTAT-TATTTATATTTT
1 ATTTTATAGATTTATATTTT
2676775 ATGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTTTATAGATTTATATTTTTC
Found at i:2677076 original size:10 final size:10
Alignment explanation
Indices: 2677058--2677108 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
2677048 AATTATTTTA
2677058 AAATA-ACAT
1 AAATATACAT
2677067 AAATATACAT
1 AAATATACAT
2677077 --ATATACAT
1 AAATATACAT
*
2677085 AAATATATAT
1 AAATATACAT
*
2677095 AAATA-ACTT
1 AAATATACAT
2677104 AAATA
1 AAATA
2677109 CCCCTTACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
9 12 0.33
10 16 0.44
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATACAT
Found at i:2677218 original size:3 final size:3
Alignment explanation
Indices: 2677210--2677246 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2677200 TAATCACAAA
*
2677210 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2677247 CTTTAATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2677645 original size:2 final size:2
Alignment explanation
Indices: 2677638--2677679 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2677628 TATGTTTGTT
2677638 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
2677680 AGGTTTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2678436 original size:18 final size:18
Alignment explanation
Indices: 2678413--2678449 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2678403 TACATATCGA
2678413 TTTTAAAATAAAATAAAT
1 TTTTAAAATAAAATAAAT
2678431 TTTTAAAATAAAATAAAT
1 TTTTAAAATAAAATAAAT
2678449 T
1 T
2678450 ATTATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTAAAATAAAATAAAT
Found at i:2678675 original size:21 final size:21
Alignment explanation
Indices: 2678650--2678700 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2678640 TTGATCTTAA
2678650 TTAATAATAATTTATTATATT
1 TTAATAATAATTTATTATATT
2678671 TTAATAATAATTTATTATATT
1 TTAATAATAATTTATTATATT
2678692 TTAATAATA
1 TTAATAATA
2678701 TTTGTATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATAATAATTTATTATATT
Found at i:2678701 original size:11 final size:11
Alignment explanation
Indices: 2678650--2678703 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
2678640 TTGATCTTAA
*
2678650 TTAATAATAAT
1 TTAATAATATT
*
2678661 TT-ATTATATT
1 TTAATAATATT
*
2678671 TTAATAATAAT
1 TTAATAATATT
*
2678682 TT-ATTATATT
1 TTAATAATATT
2678692 TTAATAATATT
1 TTAATAATATT
2678703 T
1 T
2678704 GTATACTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
10 16 0.47
11 18 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAATAATATT
Found at i:2682389 original size:5 final size:5
Alignment explanation
Indices: 2682379--2682405 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2682369 TTTTGATTTT
2682379 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
2682406 CTAAGACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:2683155 original size:154 final size:153
Alignment explanation
Indices: 2682686--2683155 Score: 433
Period size: 154 Copynumber: 3.0 Consensus size: 153
2682676 TTCGACTTAT
* * * * * * *
2682686 AAGTATCTCGGTAACCTTAAAGGACAAAAAAAGATCATTAATAGGACGAACCTATCCCAAATGCA
1 AAGTATCTCGGTAACCCTAAAGGACAAGAAAAGATTAGTAAAAGGATGAACCTATCCTAAATGCA
* * * * *
2682751 CA-TCTTAGGCATAAAAGCAA-CCGCGTGATGACCTAAAACTCGATTTTAGGGAAATTACAAAAT
66 CACTTTTA-GCATAAAAGCAACCCG-GTGATGACCTAAGACTTGATTTTA-AGAAATTA-AAAAA
* * *
2682814 TACTTTTAAGGTATACCTTCAACGTGA
127 TGCCTTTAGGGTATACCTTCAACGTGA
* ** ** * * * *
2682841 AAGTACCTCAATAACCCTAAAACACGAGCAAAGATTAGTAAAAGAATAAACCTATCCTAAATGCA
1 AAGTATCTCGGTAACCCTAAAGGACAAGAAAAGATTAGTAAAAGGATGAACCTATCCTAAATGCA
* * * * * * * *
2682906 CACATTTGGCATAAAAGCGACCCAGTGAT-AACTTAGAATTCGATTCTAAGAAATTAATAAAATG
66 CACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTT-GATTTTAAGAAATTAA-AAAATG
* ** ** *
2682970 CCTTTCGGGTATATTTTTGATGTGA
129 CCTTTAGGGTATACCTTCAACGTGA
* * * *
2682995 ACGTATCTTGGTAACCCTAAAGGACATGAAAAGATTAGTAAAAGGATGAACATATCCTAAATGCA
1 AAGTATCTCGGTAACCCTAAAGGACAAGAAAAGATTAGTAAAAGGATGAACCTATCCTAAATGCA
* *
2683060 CACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGGTTTTAAAAAATTATAAAAATGC
66 CACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGATTTTAAGAAATTA-AAAAATGC
* * *
2683125 CCTTGGGGTATACCTTCAACATGA
130 CTTTAGGGTATACCTTCAACGTGA
2683149 AAGTATC
1 AAGTATC
2683156 CTAGTATTCC
Statistics
Matches: 239, Mismatches: 70, Indels: 13
0.74 0.22 0.04
Matches are distributed among these distances:
153 1 0.00
154 152 0.64
155 82 0.34
156 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (153 bp):
AAGTATCTCGGTAACCCTAAAGGACAAGAAAAGATTAGTAAAAGGATGAACCTATCCTAAATGCA
CACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGATTTTAAGAAATTAAAAAATGCC
TTTAGGGTATACCTTCAACGTGA
Found at i:2684635 original size:25 final size:24
Alignment explanation
Indices: 2684583--2684637 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
2684573 TTTAGGCTTT
* * * *
2684583 TTTCCTTTATTTTTCTTTTTTTTT
1 TTTCATTTATTTTTCTTATTGTTA
2684607 TTTCATTTATATTTTCTTATTGTTA
1 TTTCATTTAT-TTTTCTTATTGTTA
2684632 TTTCAT
1 TTTCAT
2684638 AAAAAGATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTCATTTATTTTTCTTATTGTTA
Found at i:2684808 original size:30 final size:30
Alignment explanation
Indices: 2684777--2684855 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 30
2684767 TAACTAGTTA
2684777 AAAATAAAAATTAAAAAT-TAAAAAAATTT
1 AAAATAAAAATTAAAAATATAAAAAAATTT
* *
2684806 -AAATTAGAATTAAAAATCATAAAAAAATTT
1 AAAATAAAAATTAAAAAT-ATAAAAAAATTT
*
2684836 AGAAATGAAATAATAAAAAA
1 A-AAAT-AAA-AATTAAAAA
2684856 AATCTTGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 15 0.38
30 11 0.28
32 4 0.10
33 1 0.03
34 8 0.21
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (30 bp):
AAAATAAAAATTAAAAATATAAAAAAATTT
Found at i:2688907 original size:21 final size:21
Alignment explanation
Indices: 2688881--2688925 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2688871 CTATGAATAT
2688881 TTATGCACTAAAATTAGACAC
1 TTATGCACTAAAATTAGACAC
* *
2688902 TTATGCACTAACATTGGACAC
1 TTATGCACTAAAATTAGACAC
2688923 TTA
1 TTA
2688926 ATGTCCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (21 bp):
TTATGCACTAAAATTAGACAC
Found at i:2690855 original size:24 final size:24
Alignment explanation
Indices: 2690828--2690883 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
2690818 TCTTAGTGTG
2690828 AAACCATTTTCATTATTAATG-TTA
1 AAACCATTTTCATT-TTAATGATTA
*
2690852 AAA-CATTTTTTATTTTAATGTATTA
1 AAACCA-TTTTCATTTTAATG-ATTA
2690877 AAACCAT
1 AAACCAT
2690884 GGACTGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
23 8 0.30
24 10 0.37
25 7 0.26
26 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (24 bp):
AAACCATTTTCATTTTAATGATTA
Found at i:2696989 original size:16 final size:16
Alignment explanation
Indices: 2696947--2696989 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2696937 CTCAAATCCG
2696947 AAAGAATCC-AAACCTA
1 AAAGAA-CCTAAACCTA
*
2696963 AAAGAAGCTAAACCTA
1 AAAGAACCTAAACCTA
*
2696979 ATAGAACCTAA
1 AAAGAACCTAA
2696990 GATTGACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAGAACCTAAACCTA
Found at i:2698309 original size:13 final size:13
Alignment explanation
Indices: 2698291--2698316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2698281 CAATTTTTTG
2698291 TGTATCGATACAT
1 TGTATCGATACAT
2698304 TGTATCGATACAT
1 TGTATCGATACAT
2698317 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2700698 original size:21 final size:21
Alignment explanation
Indices: 2700674--2700720 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2700664 TTTAATGCTG
2700674 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
2700694 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
2700715 ATTTTG
1 ATTTTG
2700721 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:2700866 original size:20 final size:20
Alignment explanation
Indices: 2700841--2700917 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
2700831 ATAATCACCC
2700841 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
2700861 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
2700886 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
2700906 TGTATCGATACA
1 TGTATCGATACA
2700918 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:2702945 original size:15 final size:15
Alignment explanation
Indices: 2702925--2702955 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2702915 ATTTCGTTTG
*
2702925 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2702940 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2702955 G
1 G
2702956 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2704788 original size:21 final size:21
Alignment explanation
Indices: 2704759--2704803 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2704749 AAGTTTTCAT
*
2704759 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2704779 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2704801 TTT
1 TTT
2704804 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2707039 original size:13 final size:13
Alignment explanation
Indices: 2707021--2707078 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
2707011 CAATTTTTTG
2707021 TGTATCGATACAT
1 TGTATCGATACAT
2707034 TGTATCGATACATACTT
1 TGTATCGATAC--A--T
2707051 GCTGTATCGATACAT
1 --TGTATCGATACAT
2707066 TGTATCGATACAT
1 TGTATCGATACAT
2707079 ATTTGGCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
15 2 0.05
17 2 0.05
19 11 0.28
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2708288 original size:16 final size:17
Alignment explanation
Indices: 2708264--2708300 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2708254 TTTAATTTGT
2708264 ATTTAAATTAAA-ATATA
1 ATTTAAATTAAATAT-TA
2708281 ATTT-AATTAAATATTA
1 ATTTAAATTAAATATTA
2708297 ATTT
1 ATTT
2708301 GATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATTAAATATTA
Found at i:2709012 original size:18 final size:18
Alignment explanation
Indices: 2708989--2709024 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2708979 TAAATTATTT
*
2708989 AAAAATTAATTTTATATA
1 AAAAATTAATTATATATA
2709007 AAAAATTAATTATATATA
1 AAAAATTAATTATATATA
2709025 TAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATTAATTATATATA
Found at i:2709110 original size:31 final size:30
Alignment explanation
Indices: 2709042--2709110 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
2709032 AAATATAAAT
* *
2709042 TTTAATAA-ATAAATATATTAAAAATATCA
1 TTTAATAATAAAAATATATTAAAAATAACA
* *
2709071 TGTT-ATAATAAAAATTTACTTAAAAGTAACA
1 T-TTAATAATAAAAATATA-TTAAAAATAACA
2709102 TTTAATAAT
1 TTTAATAAT
2709111 TTACTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
29 5 0.16
30 11 0.34
31 16 0.50
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (30 bp):
TTTAATAATAAAAATATATTAAAAATAACA
Found at i:2710655 original size:21 final size:21
Alignment explanation
Indices: 2710629--2710670 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2710619 AGCTACTGCC
*
2710629 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCCATACATT
*
2710650 AAGGAAGTGTATCCATACATT
1 AAGGAAATGTATCCATACATT
2710671 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCCATACATT
Found at i:2723502 original size:28 final size:28
Alignment explanation
Indices: 2723469--2723570 Score: 152
Period size: 28 Copynumber: 3.6 Consensus size: 28
2723459 TTTCACAATT
2723469 GGGGATACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCATC
**
2723497 GGGGATACTCCAACCCTATTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCATC
* *
2723525 GGGGATACTCCAACCCAGTTATTTCCA-A
1 GGGGATACTCCAACCCCGTTATTT-CATC
2723553 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2723571 GCTTTATTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 65 0.97
29 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCATC
Found at i:2723629 original size:51 final size:51
Alignment explanation
Indices: 2723554--2723671 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
2723544 TATTTCCAAG
* *
2723554 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
* * **
2723605 GGGATAC-CTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTG
1 GGGATACTC-CAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
2723656 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
2723672 ATTATTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:2723857 original size:130 final size:128
Alignment explanation
Indices: 2723522--2723858 Score: 329
Period size: 130 Copynumber: 2.6 Consensus size: 128
2723512 CTATTATTTC
* * *
2723522 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTC-AGGGGATACTCCAACCCC-GTTTTATTTCCAAAAT
* * *
2723587 ATTGATTTCTCACAATCAGGGATACCTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATA
64 ATTAATTTCTCACAATCAGGGACACCTCAACCCCGACCTTATTTCTAAAATATCGATTTCTCATA
* * *** * *** *
2723652 ATTGGGGATACTCCAACCCCATTATTTTCACAATGATACTCCAACCCCGATTCTATTTTTGAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTCA-GGGGATACTCCAACCCCG-TTTTATTTCCAAAAT
* * * * * * *
2723717 ATCTATTTTCT-ATAATCGGGGACACTTCAACCCTTG-CCTTCTTTCT-AAATCATCGATTTTTC
64 AT-TAATTTCTCACAATCAGGGACACCTCAACCC-CGACCTTATTTCTAAAAT-ATCGATTTCTC
2723779 ATA
126 ATA
** *
2723782 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTTCGTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTC-AGGGGATACTCCAACCCCGTT-TTATTTCCAAAAT
2723847 ATTAAATTTCTC
64 ATT-AATTTCTC
2723859 GTCGGGAGAT
Statistics
Matches: 161, Mismatches: 37, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
129 9 0.06
130 144 0.89
131 8 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (128 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCAGGGGATACTCCAACCCCGTTTTATTTCCAAAATAT
TAATTTCTCACAATCAGGGACACCTCAACCCCGACCTTATTTCTAAAATATCGATTTCTCATA
Found at i:2725906 original size:4 final size:4
Alignment explanation
Indices: 2725897--2725927 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2725887 TTTTGAGGTG
2725897 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2725928 GTTTTGTTTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.