Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397276.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_106.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2845708
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.30
Warning! 346660 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:1124725 original size:10 final size:10
Alignment explanation
Indices: 1124710--1124753 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
1124700 TCTCTTTTTA
1124710 TTTTTTCCTT
1 TTTTTTCCTT
1124720 TTTTTTCTCTT
1 TTTTTTC-CTT
*
1124731 TTTTTCCCTT
1 TTTTTTCCTT
*
1124741 CTTTTTCCTT
1 TTTTTTCCTT
1124751 TTT
1 TTT
1124754 ATTTATTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:1124735 original size:20 final size:20
Alignment explanation
Indices: 1124675--1124753 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
1124665 TCCTTTTATA
*
1124675 TTTTTT-CCTTCATTTTCCT
1 TTTTTTCCCTTCTTTTTCCT
*
1124694 TTATTTT--C-TCTTTTT--A
1 TT-TTTTCCCTTCTTTTTCCT
*
1124710 TTTTTT-CCTTTTTTTTCTCT
1 TTTTTTCCCTTCTTTTTC-CT
1124730 TTTTTTCCCTTCTTTTTCCT
1 TTTTTTCCCTTCTTTTTCCT
1124750 TTTT
1 TTTT
1124754 ATTTATTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
15 4 0.08
16 3 0.06
17 6 0.12
18 6 0.12
19 3 0.06
20 16 0.33
21 10 0.21
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTCCCTTCTTTTTCCT
Found at i:1124911 original size:22 final size:24
Alignment explanation
Indices: 1124885--1124936 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1124875 TATACTAAAC
1124885 CCTTTTA-TTTTCTT-TTTTTTCT
1 CCTTTTATTTTTCTTATTTTTTCT
* *
1124907 CCTTTTATTTTTTTTATTTTTTTT
1 CCTTTTATTTTTCTTATTTTTTCT
1124931 CCTTTT
1 CCTTTT
1124937 CCTTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 7 0.27
23 6 0.23
24 13 0.50
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (24 bp):
CCTTTTATTTTTCTTATTTTTTCT
Found at i:1124945 original size:24 final size:25
Alignment explanation
Indices: 1124898--1124945 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1124888 TTTATTTTCT
* *
1124898 TTTTTTTCTCCTTTTATTTTTTTTA
1 TTTTTTTCTCCTTTTACTTCTTTTA
*
1124923 TTTTTTT-TCCTTTTCCTTCTTTT
1 TTTTTTTCTCCTTTTACTTCTTTT
1124946 TTCTTTCTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTTCTCCTTTTACTTCTTTTA
Found at i:1125001 original size:10 final size:10
Alignment explanation
Indices: 1124987--1125023 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1124977 TTTTTTTATT
1124987 TTTTCCTTTA
1 TTTTCCTTTA
1124997 TTTTCCTTTA
1 TTTTCCTTTA
1125007 -TTT-CTCTTA
1 TTTTCCT-TTA
1125016 TTTTCCTT
1 TTTTCCTT
1125024 CTTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.08
9 6 0.25
10 14 0.58
11 2 0.08
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTCCTTTA
Found at i:1125029 original size:10 final size:9
Alignment explanation
Indices: 1124985--1125036 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
1124975 TTTTTTTTTA
1124985 TTTTTTCCT
1 TTTTTTCCT
1124994 TTATTTTCCT
1 TT-TTTTCCT
*
1125004 TTATTTCTCT
1 TTTTTTC-CT
*
1125014 TATTTTCCT
1 TTTTTTCCT
*
1125023 TCTTTTTTCT
1 T-TTTTTCCT
1125033 TTTT
1 TTTT
1125037 CTTTTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 12 0.34
10 23 0.66
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:1125123 original size:28 final size:28
Alignment explanation
Indices: 1125071--1125125 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1125061 CCTTCATAAG
**
1125071 TATACTAAACCCATTTATTTTTTTATTT
1 TATACTAAACCCATTTATTCATTTATTT
*
1125099 TATACTAAACCCTTTTATTCATTTATT
1 TATACTAAACCCATTTATTCATTTATT
1125126 CTTTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (28 bp):
TATACTAAACCCATTTATTCATTTATTT
Found at i:1125299 original size:17 final size:17
Alignment explanation
Indices: 1125251--1125316 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
1125241 CTCCTTTTAT
*
1125251 TTTTTTATTTTTTCCTTG
1 TTTTTTA-TTTTTCCTTC
* *
1125269 TTTCCTTCTTTTTTTCTTTC
1 TTT--TT-TATTTTTCCTTC
1125289 TTTTTTATTTTTCCTTC
1 TTTTTTATTTTTCCTTC
*
1125306 TTTTTTCTTTT
1 TTTTTTATTTT
1125317 CCCTCCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 20 0.51
18 5 0.13
20 13 0.33
21 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTTCCTTC
Found at i:1125369 original size:83 final size:85
Alignment explanation
Indices: 1125269--1125435 Score: 205
Period size: 86 Copynumber: 2.0 Consensus size: 85
1125259 TTTTTCCTTG
* ** *
1125269 TTTCCTTCTTTTTTTCTTTCTTTTTTATTT-TTCCTTCTTTTT-TCTT-TTCCCTCCATTATAAG
1 TTTCCTTCTATTTTTCTTT-TTTCCTATTTCTTCCTTCTTTTTCTATTGTTCCCTCCATTATAAG
1125331 TATACTAAACCCTTTTATTTT
65 TATACTAAACCCTTTTATTTT
* * ** *
1125352 TTTCCTTCTATTTTTCTTTTTTCCTCTTTCTTTCTTCTTTTTCCTATTGTTTTCTCCTTTATAAG
1 TTTCCTTCTATTTTTCTTTTTTCCTATTTCTTCCTTCTTTTT-CTATTGTTCCCTCCATTATAAG
*
1125417 TATATTAAACCCTTTTATT
65 TATACTAAACCCTTTTATT
1125436 CTTATTCCCC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
82 7 0.10
83 29 0.41
85 3 0.04
86 31 0.44
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.63
Consensus pattern (85 bp):
TTTCCTTCTATTTTTCTTTTTTCCTATTTCTTCCTTCTTTTTCTATTGTTCCCTCCATTATAAGT
ATACTAAACCCTTTTATTTT
Found at i:1125371 original size:20 final size:19
Alignment explanation
Indices: 1125343--1125396 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1125333 TACTAAACCC
*
1125343 TTTTATTTTTTTCCTTCTAT
1 TTTTCTTTTTTTCCTTCT-T
1125363 TTTTC-TTTTTTCC-TCTT
1 TTTTCTTTTTTTCCTTCTT
1125380 TCTTTCTTCTTTTTCCT
1 T-TTTCTT-TTTTTCCT
1125397 ATTGTTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 7 0.24
19 9 0.31
20 11 0.38
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTTTTCCTTCTT
Found at i:1125405 original size:20 final size:20
Alignment explanation
Indices: 1125369--1125411 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1125359 CTATTTTTCT
* *
1125369 TTTTTCCTCTTTCTTTCTTC
1 TTTTTCCTATTTCTTTCTCC
1125389 TTTTTCCTATTGT-TTTCTCC
1 TTTTTCCTATT-TCTTTCTCC
1125409 TTT
1 TTT
1125412 ATAAGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTCCTATTTCTTTCTCC
Found at i:1125487 original size:9 final size:9
Alignment explanation
Indices: 1125475--1125528 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
1125465 TTTTTTATTA
1125475 TTTTCTTTT
1 TTTTCTTTT
1125484 TTTTCTTCATT
1 TTTTCTT--TT
*
1125495 TTTTCCTTT
1 TTTTCTTTT
1125504 TTTTCTTCATT
1 TTTTCTT--TT
*
1125515 TTTTCCTTT
1 TTTTCTTTT
1125524 TTTTC
1 TTTTC
1125529 CATGCTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 22 0.58
11 16 0.42
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:1125498 original size:11 final size:11
Alignment explanation
Indices: 1125482--1125519 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1125472 TTATTTTCTT
1125482 TTTTTTCTTCA
1 TTTTTTCTTCA
*
1125493 TTTTTTC--CT
1 TTTTTTCTTCA
1125502 TTTTTTCTTCA
1 TTTTTTCTTCA
1125513 TTTTTTC
1 TTTTTTC
1125520 CTTTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTCTTCA
Found at i:1125504 original size:20 final size:20
Alignment explanation
Indices: 1125475--1125528 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125465 TTTTTTATTA
*
1125475 TTTTCTTTTTTTTCTTCATT
1 TTTTCCTTTTTTTCTTCATT
1125495 TTTTCCTTTTTTTCTTCATT
1 TTTTCCTTTTTTTCTTCATT
1125515 TTTTCCTTTTTTTC
1 TTTTCCTTTTTTTC
1125529 CATGCTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCCTTTTTTTCTTCATT
Found at i:1125633 original size:22 final size:22
Alignment explanation
Indices: 1125608--1125714 Score: 92
Period size: 22 Copynumber: 4.6 Consensus size: 22
1125598 GTCATTTTTA
*
1125608 TTTTTTCCTTTTTTTTTCCTTT
1 TTTTTTCCTTCTTTTTTCCTTT
*
1125630 TTTTTT-CTTCCTTTTCTCCTTTT
1 TTTTTTCCTT-CTTTTTTCC-TTT
*
1125653 ATTTTTTCCCTTCTTTTTT-CTCTA
1 -TTTTTT-CCTTCTTTTTTCCT-TT
*
1125677 TTTTTTCCTTCTTTTTTCTTTT
1 TTTTTTCCTTCTTTTTTCCTTT
*
1125699 TCATTTTTCCTCCTTT
1 T--TTTTTCCTTCTTT
1125715 ATAAGTATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.04
22 26 0.38
23 11 0.16
24 20 0.29
25 6 0.09
26 3 0.04
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTCCTTCTTTTTTCCTTT
Found at i:1125658 original size:14 final size:12
Alignment explanation
Indices: 1125603--1125693 Score: 64
Period size: 11 Copynumber: 7.7 Consensus size: 12
1125593 ATTTAGTCAT
1125603 TTTTATTTTTTCC
1 TTTT-TTTTTTCC
1125616 -TTTTTTTTTCC
1 TTTTTTTTTTCC
1125627 -TTTTTTTTT-C
1 TTTTTTTTTTCC
** *
1125637 TTCCTTTTCTCC
1 TTTTTTTTTTCC
1125649 TTTTATTTTTTCC
1 TTTT-TTTTTTCC
* *
1125662 CTTCTTTTTT-C
1 TTTTTTTTTTCC
* *
1125673 TCTATTTTTTCC
1 TTTTTTTTTTCC
1125685 TTCTTTTTT
1 TT-TTTTTT
1125694 CTTTTTCATT
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
10 1 0.02
11 31 0.52
12 14 0.23
13 14 0.23
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTTCC
Found at i:1125681 original size:47 final size:46
Alignment explanation
Indices: 1125603--1125714 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 46
1125593 ATTTAGTCAT
* *
1125603 TTTTATTTTTTCCTTTTTTTTTCCTT-TTTTTTTCTTCCTTTTCTCC
1 TTTTATTTTTTCCTTCTTTTTTCCTTATTTTTTCCTT-CTTTTCTCC
* *
1125649 TTTTATTTTTTCCCTTCTTTTTT-CTCTATTTTTTCCTTCTTTTTTCT
1 TTTTATTTTTT-CCTTCTTTTTTCCT-TATTTTTTCCTTCTTTTCTCC
*
1125696 TTTTCA-TTTTTCCTCCTTT
1 TTTT-ATTTTTTCCTTCTTT
1125715 ATAAGTATAC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
46 20 0.35
47 27 0.47
48 10 0.18
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (46 bp):
TTTTATTTTTTCCTTCTTTTTTCCTTATTTTTTCCTTCTTTTCTCC
Found at i:1125770 original size:10 final size:9
Alignment explanation
Indices: 1125732--1125810 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
1125722 TACTATACCC
*
1125732 TTTTATTTT
1 TTTTCTTTT
1125741 TTTTCTTTT
1 TTTTCTTTT
1125750 ATTTTCCTTTT
1 -TTTT-CTTTT
*
1125761 TTCTCTTTT
1 TTTTCTTTT
*
1125770 TCCTTCTTTT
1 T-TTTCTTTT
**
1125780 TTAAC--TT
1 TTTTCTTTT
1125787 TTTTCTTTT
1 TTTTCTTTT
*
1125796 TTCTCTTTGT
1 TTTTCTTT-T
1125806 TTTTC
1 TTTTC
1125811 CTTTATAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
7 5 0.09
9 24 0.45
10 19 0.36
11 5 0.09
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:1125770 original size:16 final size:16
Alignment explanation
Indices: 1125751--1125803 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
1125741 TTTTCTTTTA
1125751 TTTTCCTTTTTTCTCT
1 TTTTCCTTTTTTCTCT
*
1125767 TTTTCCTTCTTTTTTAACT
1 TTTTCCTT-TTTTCT--CT
*
1125786 TTTTTCTTTTTTCTCT
1 TTTTCCTTTTTTCTCT
1125802 TT
1 TT
1125804 GTTTTTCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.39
17 5 0.16
18 5 0.16
19 9 0.29
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCCTTTTTTCTCT
Found at i:1125808 original size:19 final size:18
Alignment explanation
Indices: 1125732--1125810 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
1125722 TACTATACCC
* *
1125732 TTTTATTTTTTTTCTTTT
1 TTTTCTTTTTTCTCTTTT
1125750 ATTTTCCTTTTTTCTCTTTT
1 -TTTT-CTTTTTTCTCTTTT
* **
1125770 TCCTTCTTTTTTAAC--TT
1 T-TTTCTTTTTTCTCTTTT
1125787 TTTTCTTTTTTCTCTTTGT
1 TTTTCTTTTTTCTCTTT-T
1125806 TTTTC
1 TTTTC
1125811 CTTTATAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
16 10 0.21
17 3 0.06
18 1 0.02
19 19 0.40
20 14 0.30
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTTCTCTTTT
Found at i:1125983 original size:51 final size:51
Alignment explanation
Indices: 1125863--1125985 Score: 128
Period size: 51 Copynumber: 2.4 Consensus size: 51
1125853 GGTCATGTTT
* * * *
1125863 ATTT-TTTTA-CTTTTTCTTTCTCCTTGATAAGTATACTAAACCTTTTTATTT
1 ATTTCTTTTATCTTTTT-TTT-TCCCTCATAAGTATACTAAACCCTTTTATTC
* *
1125914 TTTTCATTTT-T-TTCTTTTTTTCCCTCATATGTATACTAAACCCTTTTATTC
1 ATTTC-TTTTATCTT-TTTTTTTCCCTCATAAGTATACTAAACCCTTTTATTC
1125965 ATTTCTTTTATCTTTTTTTTT
1 ATTTCTTTTATCTTTTTTTTT
1125986 TCAAAGTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
50 4 0.07
51 41 0.69
52 7 0.12
53 7 0.12
ACGTcount: A:0.18, C:0.17, G:0.02, T:0.63
Consensus pattern (51 bp):
ATTTCTTTTATCTTTTTTTTTCCCTCATAAGTATACTAAACCCTTTTATTC
Found at i:1127359 original size:3 final size:3
Alignment explanation
Indices: 1127351--1127382 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1127341 TCATGCAAAT
*
1127351 TTC TTC TTC TTC TTC TTC GTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1127383 TTTTTTGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:1128433 original size:2 final size:2
Alignment explanation
Indices: 1128428--1128471 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1128418 AAAGAAGGAA
1128428 AT AT AT 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
1128470 AT
1 AT
1128472 TGAAATGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1132513 original size:119 final size:119
Alignment explanation
Indices: 1132302--1132520 Score: 350
Period size: 119 Copynumber: 1.8 Consensus size: 119
1132292 TGATGATGAC
* *
1132302 CAAATAGCAATAAAATAACTGTAATGGAAAGGAAATTTTTAACAAGTTCTAGAACATCATATATC
1 CAAATAGCAATAAAACAACTGTAATGGAAAGGAAATTTTTAACAAGTTCTAGAACAACATATATC
1132367 AACCAATGCTAAGACATAATAGCCATATGATTTTCACTATAAAGTGTTCATTAG
66 AACCAATGCTAAGACATAATAGCCATATGATTTTCACTATAAAGTGTTCATTAG
** *
1132421 CAAATAGCAATAAAACAACTGTAATGGAAAGGAAATTTTTAGGAAGTTCTAGATA-AACATGTAT
1 CAAATAGCAATAAAACAACTGTAATGGAAAGGAAATTTTTAACAAGTTCTAGA-ACAACATATAT
** *
1132485 CAAGTAATGGTAAGACATAATAGCCATATGATTTTC
65 CAACCAATGCTAAGACATAATAGCCATATGATTTTC
1132521 GTCATAGAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 90 0.99
120 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (119 bp):
CAAATAGCAATAAAACAACTGTAATGGAAAGGAAATTTTTAACAAGTTCTAGAACAACATATATC
AACCAATGCTAAGACATAATAGCCATATGATTTTCACTATAAAGTGTTCATTAG
Found at i:1136997 original size:18 final size:18
Alignment explanation
Indices: 1136976--1137015 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1136966 TTAATTAATT
1136976 GTGTTAATCAT-TTTAAAC
1 GTGTT-ATCATGTTTAAAC
1136994 GTGTTATCATGTTTAAAC
1 GTGTTATCATGTTTAAAC
1137012 GTGT
1 GTGT
1137016 ATACGTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (18 bp):
GTGTTATCATGTTTAAAC
Found at i:1138494 original size:29 final size:29
Alignment explanation
Indices: 1138454--1138524 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1138444 ATTTCTGAAG
* * * *
1138454 TCAAGATTAAGCGCCAGCGAAGTTCGTGA
1 TCAAGATCAAGCGCCAACAAAGTTCATGA
1138483 TCAAGATCAAGCGCCAACAAAGTTCATGA
1 TCAAGATCAAGCGCCAACAAAGTTCATGA
1138512 TCAAG-TGCAAGCG
1 TCAAGAT-CAAGCG
1138525 AAGTTCGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (29 bp):
TCAAGATCAAGCGCCAACAAAGTTCATGA
Found at i:1138528 original size:23 final size:25
Alignment explanation
Indices: 1138502--1138560 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1138492 AGCGCCAACA
1138502 AAGTTCATGATCAA-GT-GCAAGCG
1 AAGTTCATGATCAAGGTAGCAAGCG
* * *
1138525 AAGTTCGTGATTAAGGTATCAAGCG
1 AAGTTCATGATCAAGGTAGCAAGCG
1138550 AAGTTCATGAT
1 AAGTTCATGAT
1138561 TAAGATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 12 0.40
24 2 0.07
25 16 0.53
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (25 bp):
AAGTTCATGATCAAGGTAGCAAGCG
Found at i:1138685 original size:24 final size:23
Alignment explanation
Indices: 1138641--1138685 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1138631 TCTTGAAGTG
*
1138641 AAGATTAAGCGAAGTTTGTGATC
1 AAGATTAAGCGAAGTTCGTGATC
1138664 AAGATTAAGTCCG-AGTTCGTGA
1 AAGATTAAG--CGAAGTTCGTGA
1138686 CTCTTGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 8 0.42
25 2 0.11
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (23 bp):
AAGATTAAGCGAAGTTCGTGATC
Found at i:1141024 original size:20 final size:20
Alignment explanation
Indices: 1140999--1141042 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1140989 AGTTTTCTTT
* *
1140999 TCATTCCTCTGCTGGTTTTA
1 TCATTCCTCTACTAGTTTTA
*
1141019 TCATTCCTTTACTAGTTTTA
1 TCATTCCTCTACTAGTTTTA
1141039 TCAT
1 TCAT
1141043 GGTATCAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.09, T:0.52
Consensus pattern (20 bp):
TCATTCCTCTACTAGTTTTA
Found at i:1143144 original size:2 final size:2
Alignment explanation
Indices: 1143131--1143165 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1143121 TCACTTTTAC
*
1143131 AT AT AC 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 AT A
1143166 ATAGAGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1159019 original size:2 final size:2
Alignment explanation
Indices: 1159012--1159036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1159002 ATTGATAAAT
1159012 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1159037 GGATTTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1161495 original size:33 final size:33
Alignment explanation
Indices: 1161453--1161518 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1161443 ATATTAGAGT
1161453 ACAAATCTCATTCATCATAACTTGAATGTGAAG
1 ACAAATCTCATTCATCATAACTTGAATGTGAAG
1161486 ACAAATCTCATTCATCATAACTTGAATGTGAAG
1 ACAAATCTCATTCATCATAACTTGAATGTGAAG
1161519 CATATTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (33 bp):
ACAAATCTCATTCATCATAACTTGAATGTGAAG
Found at i:1170550 original size:15 final size:15
Alignment explanation
Indices: 1170530--1170568 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1170520 ATTACGTATG
*
1170530 AAATATTCTATTCCT
1 AAATATTCTATTCCA
1170545 AAATATTCTATTCCA
1 AAATATTCTATTCCA
1170560 AAATATTCT
1 AAATATTCT
1170569 TTTCGTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTCTATTCCA
Found at i:1180860 original size:80 final size:80
Alignment explanation
Indices: 1180717--1180867 Score: 241
Period size: 80 Copynumber: 1.9 Consensus size: 80
1180707 CATGAGTTCC
* * * *
1180717 ATTTATGAGATTATGATATGTATGCCATGAGATGTATGTGTTGAAAATGTCATGTACATTATGGG
1 ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTTGAAAATGTCATATACACTATGGG
1180782 CTAAGTGTGCAAATG
66 CTAAGTGTGCAAATG
1180797 ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTTG-AAATAGTCATATACACTATGG
1 ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTTGAAAAT-GTCATATACACTATGG
*
1180861 GGTAAGT
65 GCTAAGT
1180868 ATATAATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 4 0.06
80 61 0.94
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (80 bp):
ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTTGAAAATGTCATATACACTATGGG
CTAAGTGTGCAAATG
Found at i:1183303 original size:31 final size:31
Alignment explanation
Indices: 1183254--1183328 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
1183244 AAAAATAGAG
* *
1183254 GGACTAAAGTGGAGAAAAATTTACA-GTATAA
1 GGACTAAAGTGAAGAAAAATTCA-ATGTATAA
* *
1183285 GGACTAATGTGAATAAAAATTCAATGTATAA
1 GGACTAAAGTGAAGAAAAATTCAATGTATAA
* *
1183316 GGACAAAATTGAA
1 GGACTAAAGTGAA
1183329 CTAAAATTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (31 bp):
GGACTAAAGTGAAGAAAAATTCAATGTATAA
Found at i:1184059 original size:2 final size:2
Alignment explanation
Indices: 1184052--1184078 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1184042 GAAAGGTAGC
1184052 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1184079 GCAAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1184936 original size:21 final size:21
Alignment explanation
Indices: 1184912--1184964 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
1184902 TAATAGGAAG
1184912 TTCACTTGCACAAGCAGTAGC
1 TTCACTTGCACAAGCAGTAGC
* *
1184933 TTCACTTGGTGCACTAGTAGTAGC
1 TTCAC-T--TGCACAAGCAGTAGC
1184957 TTCACTTG
1 TTCACTTG
1184965 GTGCATCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 1 0.04
24 18 0.67
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (21 bp):
TTCACTTGCACAAGCAGTAGC
Found at i:1184954 original size:24 final size:24
Alignment explanation
Indices: 1184918--1184985 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
1184908 GAAGTTCACT
* *
1184918 TGCACAAGCAGTAGCTTCACTTGG
1 TGCACTAGTAGTAGCTTCACTTGG
1184942 TGCACTAGTAGTAGCTTCACTTGG
1 TGCACTAGTAGTAGCTTCACTTGG
*
1184966 TGCA-TCAGTAGCAGCTTCAC
1 TGCACT-AGTAGTAGCTTCAC
1184986 CCACTCTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (24 bp):
TGCACTAGTAGTAGCTTCACTTGG
Found at i:1195535 original size:30 final size:28
Alignment explanation
Indices: 1195499--1195574 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
1195489 AACCATTAAT
* *
1195499 TATAAGGGCTTATTTGATTCAAAATAAATG
1 TATAAGGGCTTATTTGATGC--AATAAAAG
*
1195529 TATAAGGGCTTGTTTGAATGCAATAAAAG
1 TATAAGGGCTTATTTG-ATGCAATAAAAG
*
1195558 TATAAAGGCTTATTTGA
1 TATAAGGGCTTATTTGA
1195575 ATTTTCATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 21 0.52
30 15 0.38
31 3 0.08
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (28 bp):
TATAAGGGCTTATTTGATGCAATAAAAG
Found at i:1198412 original size:23 final size:25
Alignment explanation
Indices: 1198363--1198413 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
1198353 TGAAAAATGC
*
1198363 AATATGACCATATCATCATGTCCCATT
1 AATATGACCAAATCATCATG--CCATT
1198390 AATAT-ACCAAATCATCATG-CATT
1 AATATGACCAAATCATCATGCCATT
1198413 A
1 A
1198414 TGACATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
26 13 0.57
27 5 0.22
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (25 bp):
AATATGACCAAATCATCATGCCATT
Found at i:1198540 original size:30 final size:28
Alignment explanation
Indices: 1198502--1198569 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
1198492 GTTATAAAAA
* *
1198502 CTTATTTGACTCAAAATAAAAGTATAAGGG
1 CTTATTTGACGC--AATAAAAGTATAAAGG
*
1198532 CTTGTTTGAACGCAATAAAAGTATAAAGG
1 CTTATTTG-ACGCAATAAAAGTATAAAGG
1198561 CTTATTTGA
1 CTTATTTGA
1198570 ATTTTTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 22 0.67
30 7 0.21
31 3 0.09
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (28 bp):
CTTATTTGACGCAATAAAAGTATAAAGG
Found at i:1208499 original size:20 final size:20
Alignment explanation
Indices: 1208454--1208492 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1208444 ATTTAGATAG
1208454 GGAAAAATAAAGCTAGTGAA
1 GGAAAAATAAAGCTAGTGAA
1208474 GGAAAAATAAAGCTAGTGA
1 GGAAAAATAAAGCTAGTGA
1208493 GAGAAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (20 bp):
GGAAAAATAAAGCTAGTGAA
Found at i:1211890 original size:20 final size:20
Alignment explanation
Indices: 1211867--1211905 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1211857 GAGTTTTCTC
1211867 TCACTAACTTTATTTTTCCT
1 TCACTAACTTTATTTTTCCT
**
1211887 TCACTAGTTTTATTTTTCC
1 TCACTAACTTTATTTTTCC
1211906 CTATCTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (20 bp):
TCACTAACTTTATTTTTCCT
Found at i:1212767 original size:29 final size:28
Alignment explanation
Indices: 1212694--1212781 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
1212684 ATGAGTTTAC
**
1212694 GCCTAATCCTTGAAAAGGCAATAGGTTCC
1 GCCTAATCCTTGAAAAGGCAA-AGGTTAT
* *
1212723 ACCTGATCCTTGAAAAGGCAAGAGGTTAT
1 GCCTAATCCTTGAAAAGGCAA-AGGTTAT
* *
1212752 GCCTAATCGTTCAAAAGGCAAAGGGTTAT
1 GCCTAATCCTTGAAAAGGCAAA-GGTTAT
1212781 G
1 G
1212782 TTTGCTCTCG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 1 0.02
29 48 0.98
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (28 bp):
GCCTAATCCTTGAAAAGGCAAAGGTTAT
Found at i:1212814 original size:34 final size:33
Alignment explanation
Indices: 1212774--1212839 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
1212764 AAAAGGCAAA
** *
1212774 GGGTTATGTTTGCTCTCGTGGAAAGGCATTGTGT
1 GGGTTATACTTGCTCACGT-GAAAGGCATTGTGT
*
1212808 GGGTTATACTTGCTCACGTGAAATGCATTGTG
1 GGGTTATACTTGCTCACGTGAAAGGCATTGTG
1212840 AGGTTTGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (33 bp):
GGGTTATACTTGCTCACGTGAAAGGCATTGTGT
Found at i:1221347 original size:30 final size:29
Alignment explanation
Indices: 1221248--1221350 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 29
1221238 AACAAGTCAT
*
1221248 TACCTTTTCAAGGTTAAA-TCACAACTTATC
1 TACCTTTTCAAGG-TAAAGT-ACAACCTATC
* * * *
1221278 TACCTTTTGCAA--TAGAGGTATAACCAAGC
1 TACCTTTT-CAAGGTA-AAGTACAACCTATC
*
1221307 TTACTTTTTCAAGGCTAAAGTACAACCTATC
1 -TACCTTTTCAAGG-TAAAGTACAACCTATC
1221338 TACCTTTTCAAGG
1 TACCTTTTCAAGG
1221351 ACATAAAACC
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
28 2 0.04
29 10 0.18
30 28 0.51
31 13 0.24
32 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (29 bp):
TACCTTTTCAAGGTAAAGTACAACCTATC
Found at i:1242968 original size:73 final size:68
Alignment explanation
Indices: 1242836--1242971 Score: 191
Period size: 73 Copynumber: 1.9 Consensus size: 68
1242826 ACTTTCTTCG
* * *
1242836 CATAAACACTAAACTTGTTGTTGGTACTATAAAAGCAATTAGGGACATTCTTGGAAACATCATCT
1 CATAAACACTAAACTTGTTGGTGGTACTATAAAAGCAATTACGAACATTCTTGGAAACATCATCT
1242901 CGA
66 CGA
*
1242904 CATAAACACTAAACTTCTTGTTGGTGGTACTATAAAAAAGCAATTACGAACTTTCTTGGAAACAT
1 CATAAACACTAAA---CTTGTTGGTGGTACTAT--AAAAGCAATTACGAACATTCTTGGAAACAT
1242969 CAT
61 CAT
1242972 TTTCTCTCTC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
68 13 0.22
71 16 0.27
73 30 0.51
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (68 bp):
CATAAACACTAAACTTGTTGGTGGTACTATAAAAGCAATTACGAACATTCTTGGAAACATCATCT
CGA
Found at i:1244098 original size:26 final size:27
Alignment explanation
Indices: 1244069--1244121 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1244059 ATTCAAAAAA
**
1244069 ATTTAAAT-AAATTTTTATTTTTTATT
1 ATTTAAATCAAATTTTTAGATTTTATT
* *
1244095 ATTTTAATCAAGTTTTTAGATTTTATT
1 ATTTAAATCAAATTTTTAGATTTTATT
1244122 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTAAATCAAATTTTTAGATTTTATT
Found at i:1245518 original size:26 final size:25
Alignment explanation
Indices: 1245476--1245584 Score: 78
Period size: 26 Copynumber: 4.1 Consensus size: 25
1245466 TAACAAAATA
* * *
1245476 TTTTTGAATATGGCGTGTAATA-ACT
1 TTTTTTAATATGACGTGTAACATA-T
1245501 TTTTTTAATCATGACGTGTAACATAT
1 TTTTTTAAT-ATGACGTGTAACATAT
*
1245527 TTTTGT-ATATGACGTGTAAAAACAGTATT
1 TTTTTTAATATGACGTGT---AACA-TA-T
* *
1245556 TTTTTTAACCATGGCGTGTAACATAT
1 TTTTTTAA-TATGACGTGTAACATAT
1245582 TTT
1 TTT
1245585 GGTACATGAC
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
24 9 0.13
25 10 0.15
26 21 0.31
27 7 0.10
28 6 0.09
29 6 0.09
30 1 0.01
31 8 0.12
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (25 bp):
TTTTTTAATATGACGTGTAACATAT
Found at i:1245537 original size:50 final size:51
Alignment explanation
Indices: 1245473--1245584 Score: 136
Period size: 55 Copynumber: 2.1 Consensus size: 51
1245463 GTGTAACAAA
* * *
1245473 ATATTTTTGAATATGGCGTGTAATAAC-TTTTTTTAATCATGACGTGTAAC
1 ATATTTTTGAATATGACGTGTAAAAACATTTTTTTAACCATGACGTGTAAC
* *
1245523 ATATTTTTGTATATGACGTGTAAAAACAGTATTTTTTTTAACCATGGCGTGTAAC
1 ATATTTTTGAATATGACGTGTAAAAAC---A-TTTTTTTAACCATGACGTGTAAC
1245578 ATATTTT
1 ATATTTT
1245585 GGTACATGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 24 0.46
55 28 0.54
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (51 bp):
ATATTTTTGAATATGACGTGTAAAAACATTTTTTTAACCATGACGTGTAAC
Found at i:1245538 original size:24 final size:24
Alignment explanation
Indices: 1245473--1245545 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1245463 GTGTAACAAA
* * *
1245473 ATATTTTTGAATATGGCGTGTAAT
1 ATATTTTTGTATATGACGTGTAAC
*
1245497 A-ACTTTTTTTAATCATGACGTGTAAC
1 ATA-TTTTTGT-AT-ATGACGTGTAAC
1245523 ATATTTTTGTATATGACGTGTAA
1 ATATTTTTGTATATGACGTGTAA
1245546 AAACAGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
23 1 0.03
24 17 0.43
25 4 0.10
26 17 0.43
27 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.45
Consensus pattern (24 bp):
ATATTTTTGTATATGACGTGTAAC
Found at i:1245758 original size:48 final size:48
Alignment explanation
Indices: 1245700--1245796 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
1245690 ACAACTTAAC
*
1245700 CATAACGTGTCACATATTTTTGTATCTGACATATAACATGTTTCTATA
1 CATAACGTGTCACATATTTTTGTATCTAACATATAACATGTTTCTATA
1245748 CATAACGTGTCACATATTTTTGTATCTAACATATAACATGTTTCTATA
1 CATAACGTGTCACATATTTTTGTATCTAACATATAACATGTTTCTATA
1245796 C
1 C
1245797 TCAACTCACC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (48 bp):
CATAACGTGTCACATATTTTTGTATCTAACATATAACATGTTTCTATA
Found at i:1245777 original size:24 final size:24
Alignment explanation
Indices: 1245702--1245777 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1245692 AACTTAACCA
1245702 TAACGTGTCACATATTTTTGTATC
1 TAACGTGTCACATATTTTTGTATC
* * * * * * *
1245726 TGACATATAACATGTTTCTATA-C
1 TAACGTGTCACATATTTTTGTATC
1245749 ATAACGTGTCACATATTTTTGTATC
1 -TAACGTGTCACATATTTTTGTATC
1245774 TAAC
1 TAAC
1245778 ATATAACATG
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (24 bp):
TAACGTGTCACATATTTTTGTATC
Found at i:1245786 original size:24 final size:24
Alignment explanation
Indices: 1245711--1245786 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1245701 ATAACGTGTC
*
1245711 ACATATTTTTGTATCTGACATATA
1 ACATATTTTTGTATCTAACATATA
* * * * * *
1245735 ACATGTTTCTATA-CATAACGTGTC
1 ACATATTTTTGTATC-TAACATATA
1245759 ACATATTTTTGTATCTAACATATA
1 ACATATTTTTGTATCTAACATATA
1245783 ACAT
1 ACAT
1245787 GTTTCTATAC
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (24 bp):
ACATATTTTTGTATCTAACATATA
Found at i:1247235 original size:15 final size:15
Alignment explanation
Indices: 1247215--1247274 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
1247205 TAATTTTATA
1247215 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
1247230 ATTAAAATAAAATATAT
1 ATTAAAATAAAA-A-AT
* * *
1247247 AATAAAAGAATAAAAA
1 ATTAAAATAA-AAAAT
1247263 ATTAAAATAAAA
1 ATTAAAATAAAA
1247275 TAAAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 14 0.38
16 10 0.27
17 11 0.30
18 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:1247267 original size:33 final size:33
Alignment explanation
Indices: 1247211--1247276 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1247201 TTTATAATTT
* *
1247211 TATAATTAAAATAAAAAATATTAAAATAAAATA
1 TATAATTAAAAGAAAAAAAATTAAAATAAAATA
1247244 TATAA-TAAAAGAATAAAAAATTAAAATAAAATA
1 TATAATTAAAAGAA-AAAAAATTAAAATAAAATA
1247277 AAATATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (33 bp):
TATAATTAAAAGAAAAAAAATTAAAATAAAATA
Found at i:1247294 original size:33 final size:36
Alignment explanation
Indices: 1247219--1247294 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 36
1247209 TTTATAATTA
*
1247219 AAATAAAAAATATTAAAATAAAATATATAATAAAAG
1 AAATTAAAAATATTAAAATAAAATATATAATAAAAG
*
1247255 -AA-TAAAAA-ATTAAAATAAAATA-A-AATATAAG
1 AAATTAAAAATATTAAAATAAAATATATAATAAAAG
1247286 AAATTAAAA
1 AAATTAAAA
1247295 TTTGTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
31 7 0.19
32 3 0.08
33 19 0.53
34 5 0.14
35 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (36 bp):
AAATTAAAAATATTAAAATAAAATATATAATAAAAG
Found at i:1248637 original size:73 final size:66
Alignment explanation
Indices: 1248486--1248646 Score: 198
Period size: 73 Copynumber: 2.3 Consensus size: 66
1248476 CCCTTCGCAT
* *
1248486 GAACTTTCTTCGAAACATCATTGACGTAAACACTAAACTTGTTGTCGGTACTATAAAAGCAATTA
1 GAACTTTCTTGGAAACATCATTGACATAAACACTAAACTTGTTGTCGGTACTATAAAAGCAATTA
*
1248551 G
66 C
* *
1248552 GGACATTCTTGGAAACATCATCTCGACATAAACACTAAACTTCTTGTTGGT-GGTACTATAAAAA
1 GAACTTTCTTGGAAACATCAT-T-GACATAAACACTAAA---CTTGTT-GTCGGTACTAT--AAA
1248616 AGCAATTAC
58 AGCAATTAC
1248625 GAACTTTCTTGGAAACATCATT
1 GAACTTTCTTGGAAACATCATT
1248647 TTCTCTCTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
66 18 0.22
67 1 0.01
68 14 0.17
71 14 0.17
72 3 0.04
73 30 0.38
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (66 bp):
GAACTTTCTTGGAAACATCATTGACATAAACACTAAACTTGTTGTCGGTACTATAAAAGCAATTA
C
Found at i:1249811 original size:17 final size:17
Alignment explanation
Indices: 1249752--1249802 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1249742 TTATATTTTA
1249752 TTTTAAATTAAATATAT
1 TTTTAAATTAAATATAT
*
1249769 TTTTATATT---T-TA-
1 TTTTAAATTAAATATAT
1249781 TTTTAAATTAAATATAT
1 TTTTAAATTAAATATAT
1249798 TTTTA
1 TTTTA
1249803 TATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 1 0.04
15 1 0.04
16 2 0.07
17 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAATTAAATATAT
Found at i:1249820 original size:29 final size:29
Alignment explanation
Indices: 1249738--1249807 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
1249728 TTTCTATCAA
1249738 ATTTTTATATTTTATTTTAAATTAAATAT
1 ATTTTTATATTTTATTTTAAATTAAATAT
1249767 ATTTTTATATTTTATTTTAAATTAAATAT
1 ATTTTTATATTTTATTTTAAATTAAATAT
1249796 ATTTTTATATTT
1 ATTTTTATATTT
1249808 AATAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
ATTTTTATATTTTATTTTAAATTAAATAT
Found at i:1251392 original size:14 final size:14
Alignment explanation
Indices: 1251373--1251399 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1251363 CTGGATATTC
1251373 AGTTTAATTAATGA
1 AGTTTAATTAATGA
1251387 AGTTTAATTAATG
1 AGTTTAATTAATG
1251400 TGAGATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
AGTTTAATTAATGA
Found at i:1251968 original size:30 final size:30
Alignment explanation
Indices: 1251912--1251970 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1251902 AACTATTAGT
* *
1251912 TGTAAAGGCTTATTTAAGTCGAAATAAAAG
1 TGTAAAGGCCTATTTAACTCGAAATAAAAG
*
1251942 TGTAAAGGCCTATTTGACTC-AGAATAAAA
1 TGTAAAGGCCTATTTAACTCGA-AATAAAA
1251971 ATATGAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (30 bp):
TGTAAAGGCCTATTTAACTCGAAATAAAAG
Found at i:1252110 original size:27 final size:26
Alignment explanation
Indices: 1252059--1252129 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 26
1252049 GATATTATGC
*
1252059 CTTTTATTTTTTATTTCTTTCATTTT
1 CTTTTATTTTTTATTTCTTTCATTTG
*
1252085 TTTTTATTTTTCCTAATTT-TTT-ATTTG
1 CTTTTATTTTT--T-ATTTCTTTCATTTG
1252112 CTTTTATTATCTTTATTT
1 CTTTTATT-T-TTTATTT
1252130 TGTGGAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
26 14 0.38
27 12 0.32
28 5 0.14
29 6 0.16
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.75
Consensus pattern (26 bp):
CTTTTATTTTTTATTTCTTTCATTTG
Found at i:1252724 original size:20 final size:20
Alignment explanation
Indices: 1252699--1252736 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1252689 TTGACCAAGT
1252699 TGACATGGTACTAATAAAAA
1 TGACATGGTACTAATAAAAA
1252719 TGACATGGTACTAATAAA
1 TGACATGGTACTAATAAA
1252737 TATGTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (20 bp):
TGACATGGTACTAATAAAAA
Found at i:1253840 original size:18 final size:18
Alignment explanation
Indices: 1253814--1253867 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
1253804 TGATTCATTC
1253814 GGAAACATTCGAAGATTG
1 GGAAACATTCGAAGATTG
* *
1253832 GGAAGCATTCGAAGATTC
1 GGAAACATTCGAAGATTG
*
1253850 GAAAACATTCGAAGATTG
1 GGAAACATTCGAAGATTG
1253868 AGAGCATTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (18 bp):
GGAAACATTCGAAGATTG
Found at i:1253883 original size:36 final size:36
Alignment explanation
Indices: 1253810--1253883 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1253800 ATTTTGATTC
* * *
1253810 ATTCGGAAACATTCGAAGATTGGGAAGCATTCGAAG
1 ATTCGAAAACATTCGAAGATTGAGAAGCATTCAAAG
1253846 ATTCGAAAACATTCGAAGATTGAG-AGCATTTCAAAG
1 ATTCGAAAACATTCGAAGATTGAGAAGCA-TTCAAAG
1253882 AT
1 AT
1253884 CAAGAAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (36 bp):
ATTCGAAAACATTCGAAGATTGAGAAGCATTCAAAG
Found at i:1254092 original size:99 final size:97
Alignment explanation
Indices: 1253931--1254211 Score: 400
Period size: 99 Copynumber: 2.9 Consensus size: 97
1253921 GGCAACAAAA
* * * *
1253931 TTCGTGATCAAGATCGAGTCGTGAAGACCCTTGAAGCAAAAATAAAGTGTTCGTGATCAAGATCA
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATCA
* *
1253996 AGTTGTAACGACCCTTGAAGTGAAAATCAAGTG
66 AGTTGTAA-GACCCTTGAAGCGAAAATCAAGAG
1254029 TTCGTGATCAAGATCAAGTCGTGAAGACCCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATC
1 TTCGTGATCAAGATCAAGTCGTGAAGA-CCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATC
* *
1254094 AAGTCGTGAAGACCCTTGAAGCGAAGATCAAGAG
65 AAGTTGT-AAGACCCTTGAAGCGAAAATCAAGAG
* ** * * *
1254128 TTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAATGAAGGTCAAGTATTCGTGATCAAGATTA
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATCA
1254193 AGTTGTAATGACCCTTGAA
66 AGTTGTAA-GACCCTTGAA
1254212 AACGAAAGAT
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
97 2 0.01
98 74 0.45
99 87 0.53
100 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (97 bp):
TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATCA
AGTTGTAAGACCCTTGAAGCGAAAATCAAGAG
Found at i:1254206 original size:148 final size:147
Alignment explanation
Indices: 1253931--1254211 Score: 404
Period size: 148 Copynumber: 1.9 Consensus size: 147
1253921 GGCAACAAAA
* *
1253931 TTCGTGATCAAGATCGAGTCGTGAAGACCCTTGAAGCAAAAATAAAGTGTTCGTGATCAAGATCA
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCAAAAATAAAGAGTTCGTGATCAAGATCA
* * *
1253996 AGTTGTAACGACCCTTGAAGTGAAAATCAAGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCCT
66 AGTCGTAACGACCCTTGAAATGAAAATCAAGTATTCGTGATCAAGATCAAGTCGTGAAGA-CCCT
1254061 TGAAGCGAAGATCAAGTG
130 TGAAGCGAAGATCAAGTG
* * * *
1254079 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGAGTTCGTGATCAAGATTA
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCAAAAATAAAGAGTTCGTGATCAAGATCA
** * *
1254144 AGTCGTGAA-GACCCTTGAAATGAAGGTCAAGTATTCGTGATCAAGATTAAGTTGT-AATGACCC
66 AGTCGT-AACGACCCTTGAAATGAAAATCAAGTATTCGTGATCAAGATCAAGTCGTGAA-GACCC
1254207 TTGAA
129 TTGAA
1254212 AACGAAAGAT
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
147 10 0.08
148 106 0.90
149 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (147 bp):
TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCAAAAATAAAGAGTTCGTGATCAAGATCA
AGTCGTAACGACCCTTGAAATGAAAATCAAGTATTCGTGATCAAGATCAAGTCGTGAAGACCCTT
GAAGCGAAGATCAAGTG
Found at i:1254212 original size:49 final size:49
Alignment explanation
Indices: 1253931--1254211 Score: 386
Period size: 49 Copynumber: 5.7 Consensus size: 49
1253921 GGCAACAAAA
* * * *
1253931 TTCGTGATCAAGATCGAGTCGTGAAGACCCTTGAAGCAAAAATAAAGTG
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTG
* * *
1253980 TTCGTGATCAAGATCAAGTTGT-AACGACCCTTGAAGTGAAAATCAAGTG
1 TTCGTGATCAAGATCAAGTCGTGAA-GACCCTTGAAGCGAAGATCAAGTG
1254029 TTCGTGATCAAGATCAAGTCGTGAAGACCCCTTGAAGCGAAGATCAAGTG
1 TTCGTGATCAAGATCAAGTCGTGAAGA-CCCTTGAAGCGAAGATCAAGTG
*
1254079 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGAG
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTG
* ** * *
1254128 TTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAATGAAGGTCAAGTA
1 TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTG
* *
1254177 TTCGTGATCAAGATTAAGTTGT-AATGACCCTTGAA
1 TTCGTGATCAAGATCAAGTCGTGAA-GACCCTTGAA
1254212 AACGAAAGAT
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
48 4 0.02
49 159 0.75
50 49 0.23
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (49 bp):
TTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTG
Found at i:1256099 original size:63 final size:62
Alignment explanation
Indices: 1256019--1256215 Score: 274
Period size: 62 Copynumber: 3.2 Consensus size: 62
1256009 GCTACACCCA
*
1256019 AAAAAAAAAAAGCCTACTAAGTTGAAAATCCTT-ACTAGGACGACTTAGGCAAAACTTAAGGC
1 AAAAAAAAAAAGCCTACTAAGTTGAAAATCCTTAAC-AGGACGACTTAGGCAAAAGTTAAGGC
* *
1256081 ACAAAAAAAAAAGCCTACTAAGTTG-AAATCCTTAACAGGATGACTTAGGAAAAAGTTAAGGC
1 A-AAAAAAAAAAGCCTACTAAGTTGAAAATCCTTAACAGGACGACTTAGGCAAAAGTTAAGGC
** * * *
1256143 AAATTAAAAAATCCTATTAAGTTGAAAATCCTTAACAGGAAC-ACTTAGGCAAAAGTTAAGGG
1 AAAAAAAAAAAGCCTACTAAGTTGAAAATCCTTAACAGG-ACGACTTAGGCAAAAGTTAAGGC
1256205 AAAAAAAAAAA
1 AAAAAAAAAAA
1256216 AAGATATGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
61 19 0.16
62 74 0.62
63 26 0.22
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (62 bp):
AAAAAAAAAAAGCCTACTAAGTTGAAAATCCTTAACAGGACGACTTAGGCAAAAGTTAAGGC
Found at i:1258994 original size:18 final size:18
Alignment explanation
Indices: 1258968--1259037 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
1258958 CGATTCATTC
* *
1258968 GGAAACATTCGAAGATTG
1 GGAAGCATTCAAAGATTG
*
1258986 GGAAGCATTCAAAGATTC
1 GGAAGCATTCAAAGATTG
*
1259004 GAAAGCATTCAAAGATTG
1 GGAAGCATTCAAAGATTG
*
1259022 AG-AGCATTTCAAAGAT
1 GGAAGCA-TTCAAAGAT
1259038 CAAGAAGAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 4 0.09
18 40 0.91
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (18 bp):
GGAAGCATTCAAAGATTG
Found at i:1259004 original size:36 final size:36
Alignment explanation
Indices: 1258964--1259037 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
1258954 ATTTCGATTC
* *
1258964 ATTCGGAAA-CATTCGAAGATTGGGAAGCA-TTCAAAG
1 ATTC-GAAAGCATTCAAAGATTGAG-AGCATTTCAAAG
1259000 ATTCGAAAGCATTCAAAGATTGAGAGCATTTCAAAG
1 ATTCGAAAGCATTCAAAGATTGAGAGCATTTCAAAG
1259036 AT
1 AT
1259038 CAAGAAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 8 0.24
36 26 0.76
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (36 bp):
ATTCGAAAGCATTCAAAGATTGAGAGCATTTCAAAG
Found at i:1259222 original size:15 final size:15
Alignment explanation
Indices: 1259202--1259231 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1259192 AAGATCAAGT
1259202 CGTGAAGACCCTTGA
1 CGTGAAGACCCTTGA
*
1259217 CGTGAAGACCTTTGA
1 CGTGAAGACCCTTGA
1259232 AGCGAAGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (15 bp):
CGTGAAGACCCTTGA
Found at i:1259254 original size:64 final size:64
Alignment explanation
Indices: 1259153--1259285 Score: 203
Period size: 64 Copynumber: 2.1 Consensus size: 64
1259143 AAGATCAAGT
* * *
1259153 CGTGAAGACCCTTGAAACAAAGATCAAGTGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGA
1 CGTGAAGACCCTTGAAACAAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGA
* * *
1259217 CGTGAAGACCTTTGAAGCGAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGA
1 CGTGAAGACCCTTGAAACAAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGA
*
1259281 AGTGA
1 CGTGA
1259286 TGATCAAGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (64 bp):
CGTGAAGACCCTTGAAACAAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGA
Found at i:1259260 original size:113 final size:112
Alignment explanation
Indices: 1259115--1259336 Score: 318
Period size: 113 Copynumber: 2.0 Consensus size: 112
1259105 GTTAAGACTC
* * * *
1259115 TTGAAGTGAAAATCAGGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAACAAAGATCAA
1 TTGAAGCGAAAATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGAAACAAAGATCAA
* *
1259180 GTGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGACGTGAAGACCT
66 GTG-TTGTGAACAAGATCAAGTCGTGAAGACCCTTGAAGTGAAGACCT
* *** *
1259228 TTGAAGCGAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGAAGTGATGATCAA
1 TTGAAGCGAAAATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGAAACAAAGATCAA
* *
1259293 GTGTTGTTAACAAGATCATGTCGTGAAGACCCTTGAAGTGAAGA
66 GTGTTGTGAACAAGATCAAGTCGTGAAGACCCTTGAAGTGAAGA
1259337 TCAAGAGTTC
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
112 37 0.39
113 59 0.61
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (112 bp):
TTGAAGCGAAAATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGAAACAAAGATCAA
GTGTTGTGAACAAGATCAAGTCGTGAAGACCCTTGAAGTGAAGACCT
Found at i:1259281 original size:49 final size:49
Alignment explanation
Indices: 1259217--1259476 Score: 308
Period size: 49 Copynumber: 5.3 Consensus size: 49
1259207 AGACCCTTGA
* * *
1259217 CGTGAAGACCTTTGAAGCGAAGATCAAGTGTTCGTGATAAAGATCAAGT
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGT
* * * * * * *
1259266 CCTGAAGACCCTTGAAGTGATGATCAAGTGTT-GTTAACAAGATCATGT
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGT
* * *
1259314 CGTGAAGACCCTTGAAGTGAAGATCAAGAGTTCATGATCAAGATTAAGT
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGT
* * *
1259363 CGTGAAGACCCTTGAAGCGAAAATCAAGTGTTCATTATCAAGATTAAGT
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGT
* * *
1259412 CGTAAAGACCCTTG-AGACGAAGGTTAAGTGTTCGTGATCAAGATTAAGT
1 CGTGAAGACCCTTGAAG-CGAAGATCAAGTGTTCGTGATCAAGATTAAGT
* *
1259461 CGTAAAGATCCTTGAA
1 CGTGAAGACCCTTGAA
1259477 AATGAAGATC
Statistics
Matches: 181, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
48 43 0.24
49 137 0.76
50 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (49 bp):
CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGT
Found at i:1259336 original size:97 final size:98
Alignment explanation
Indices: 1259217--1259476 Score: 326
Period size: 97 Copynumber: 2.7 Consensus size: 98
1259207 AGACCCTTGA
* * * *
1259217 CGTGAAGACCTTTGAAGCGAAGATCAAGTGTTCGTGATAAAGATCAAGTCCTGAAGACCCTTGAA
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAA
* ** * *
1259282 GTGATGATCAAGTGTT-GTTAACAAGATCATGT
66 GCGAAAATCAAGTGTTCATTAACAAGATCAAGT
* * *
1259314 CGTGAAGACCCTTGAAGTGAAGATCAAGAGTTCATGATCAAGATTAAGTCGTGAAGACCCTTGAA
1 CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAA
* *
1259379 GCGAAAATCAAGTGTTCATTATCAAGATTAAGT
66 GCGAAAATCAAGTGTTCATTAACAAGATCAAGT
* * * * *
1259412 CGTAAAGACCCTTG-AGACGAAGGTTAAGTGTTCGTGATCAAGATTAAGTCGTAAAGATCCTTGA
1 CGTGAAGACCCTTGAAG-CGAAGATCAAGTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGA
1259476 A
65 A
1259477 AATGAAGATC
Statistics
Matches: 139, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
97 73 0.53
98 66 0.47
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (98 bp):
CGTGAAGACCCTTGAAGCGAAGATCAAGTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAA
GCGAAAATCAAGTGTTCATTAACAAGATCAAGT
Found at i:1266673 original size:18 final size:18
Alignment explanation
Indices: 1266631--1266666 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1266621 CAAGGCACAA
1266631 ACATTTTACCAGTGATAT
1 ACATTTTACCAGTGATAT
1266649 ACATTTTACCAGTGATAT
1 ACATTTTACCAGTGATAT
1266667 GATTTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
ACATTTTACCAGTGATAT
Found at i:1275697 original size:26 final size:26
Alignment explanation
Indices: 1275668--1275719 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1275658 GAGTAGGCCG
1275668 AATGTCACATCGAGATAGTGTGACCC
1 AATGTCACATCGAGATAGTGTGACCC
*
1275694 AATGTCGCATCGAGATAGTGTGACCC
1 AATGTCACATCGAGATAGTGTGACCC
1275720 TTGTATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (26 bp):
AATGTCACATCGAGATAGTGTGACCC
Found at i:1286882 original size:2 final size:2
Alignment explanation
Indices: 1286847--1286871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1286837 TTGACTATGC
1286847 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1286872 CGATTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1297107 original size:64 final size:63
Alignment explanation
Indices: 1297034--1297190 Score: 215
Period size: 64 Copynumber: 2.4 Consensus size: 63
1297024 AATTTTACTC
* *
1297034 ACTACCTTTTGAAGGCTACAGTATAACCTCTATGCCTTTCAAGGATCAAGCACAACCTTTATAT
1 ACTACCTTTTGAAGGCTA-AGTATAACCTCTATCCCTTTCAAGGATCAAGCACAACCTTTAAAT
**
1297098 ACTACCTTTTGAATTCTAAGGTATAACCTCTATCCCTTTCAAGGATCAAGCACAACCTTTAAAT
1 ACTACCTTTTGAAGGCTAA-GTATAACCTCTATCCCTTTCAAGGATCAAGCACAACCTTTAAAT
* * * *
1297162 ACTAGCTTATGGAGGCTAAATTATAACCT
1 ACTACCTTTTGAAGGCT-AAGTATAACCT
1297191 TTTTCTCTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.96
65 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (63 bp):
ACTACCTTTTGAAGGCTAAGTATAACCTCTATCCCTTTCAAGGATCAAGCACAACCTTTAAAT
Found at i:1303113 original size:19 final size:19
Alignment explanation
Indices: 1303064--1303111 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1303054 TTAATATTTT
1303064 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
1303083 AATATTATTTTATTCA-AA
1 AATATTATTTTATTCATAA
*
1303101 AATATTCTTTT
1 AATATTATTTT
1303112 TACTTGTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:1303568 original size:2 final size:2
Alignment explanation
Indices: 1303561--1303590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1303551 AACATTAACC
1303561 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
1303591 GGCAACAACA
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:1307062 original size:21 final size:21
Alignment explanation
Indices: 1306973--1307055 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
1306963 AAGGAGGTTT
* *
1306973 AAAACTAATTTAAGCAAGTTT-
1 AAAACTCATTCAAGCAA-TTTC
1306994 AAAAGCT-ATTCAAGCAATTTC
1 AAAA-CTCATTCAAGCAATTTC
*
1307015 AAAAATCATTCAAGCAATTTC
1 AAAACTCATTCAAGCAATTTC
*
1307036 AAAACTCATTCAAGTAATTT
1 AAAACTCATTCAAGCAATTT
1307056 TGAAACTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.07
21 49 0.89
22 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (21 bp):
AAAACTCATTCAAGCAATTTC
Found at i:1307265 original size:20 final size:21
Alignment explanation
Indices: 1307240--1307305 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
1307230 TTTAAAAACA
1307240 CATTCAAACAACTTCAAA-AT
1 CATTCAAACAACTTCAAAGAT
*
1307260 CATTCAAACAAGTTCAAAGAT
1 CATTCAAACAACTTCAAAGAT
** *
1307281 CCCTCAAACAACTTTAAAGAT
1 CATTCAAACAACTTCAAAGAT
1307302 CATT
1 CATT
1307306 GAAGCAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (21 bp):
CATTCAAACAACTTCAAAGAT
Found at i:1310950 original size:39 final size:39
Alignment explanation
Indices: 1310896--1310989 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
1310886 GTGGACATAG
*
1310896 AAAGGTAATCTAATAAAAAAGAGAATAAAATTTCACACA
1 AAAGGTAATCTAATAAAAAAAAGAATAAAATTTCACACA
1310935 AAAGGTAATCTAATAAAAAAAAGAATAAAATTTCACACA
1 AAAGGTAATCTAATAAAAAAAAGAATAAAATTTCACACA
1310974 AAAGGTAATCTAATAA
1 AAAGGTAATCTAATAA
1310990 TCTTAAGTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (39 bp):
AAAGGTAATCTAATAAAAAAAAGAATAAAATTTCACACA
Found at i:1312378 original size:19 final size:19
Alignment explanation
Indices: 1312354--1312394 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1312344 TATATTTTTC
*
1312354 AAAATATATTGATAAAATT
1 AAAATATATTGATAAAAGT
1312373 AAAATATATTGATAAAAGT
1 AAAATATATTGATAAAAGT
1312392 AAA
1 AAA
1312395 GGACACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
AAAATATATTGATAAAAGT
Found at i:1320620 original size:21 final size:22
Alignment explanation
Indices: 1320585--1320628 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1320575 CTTTTAAAGT
1320585 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1320607 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1320628 A
1 A
1320629 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1320843 original size:9 final size:9
Alignment explanation
Indices: 1320829--1320868 Score: 80
Period size: 9 Copynumber: 4.4 Consensus size: 9
1320819 TTATAGATAC
1320829 ATGTTCATA
1 ATGTTCATA
1320838 ATGTTCATA
1 ATGTTCATA
1320847 ATGTTCATA
1 ATGTTCATA
1320856 ATGTTCATA
1 ATGTTCATA
1320865 ATGT
1 ATGT
1320869 ATTGATACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (9 bp):
ATGTTCATA
Found at i:1321905 original size:68 final size:68
Alignment explanation
Indices: 1321792--1322005 Score: 216
Period size: 68 Copynumber: 3.1 Consensus size: 68
1321782 ATGCCATAAA
** *
1321792 ATTATGTATATGATGTAAATTCCATACACCATATGGGATAATTAAGTATACATGATGTATACTAC
1 ATTATGTATATGATGTAAATTCCATACACCATATGGGATAATTAAGTATACATGATAAATACCAC
1321857 AAG
66 AAG
* * * *
1321860 ATTGTGTATATGATGTAAATTCCATATACCATATGAGG-TGATTAAGTATGCATGATAAATACCA
1 ATTATGTATATGATGTAAATTCCATACACCATATG-GGATAATTAAGTATACATGATAAATACCA
**
1321924 TGAG
65 CAAG
* * * * * * * * *
1321928 ATTATTTATATGATGTATATTCCATACACTACATGAGATGATTGAG-AAAGCATGATAAATGCCA
1 ATTATGTATATGATGTAAATTCCATACACCATATGGGATAATTAAGTATA-CATGATAAATACCA
**
1321992 TGAG
65 CAAG
1321996 ATTATGTATA
1 ATTATGTATA
1322006 CGACGTATTG
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
67 2 0.02
68 118 0.97
69 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (68 bp):
ATTATGTATATGATGTAAATTCCATACACCATATGGGATAATTAAGTATACATGATAAATACCAC
AAG
Found at i:1322020 original size:68 final size:67
Alignment explanation
Indices: 1321909--1322036 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 67
1321899 GATTAAGTAT
* * *
1321909 GCATGATAAATACCATGAGATTATTTATATGATGTATATTCCA-TACACTACATGAGATGATTGA
1 GCATGATAAATACCATGAGATTATGTATACGACGTATATTCCAGTAC-CT-CATGAGATGATTGA
1321973 GAAA
64 GAAA
*
1321977 GCATGATAAATGCCATGAGATTATGTATACGACGTAT-TGTCCATGTACCTCATGAGATGA
1 GCATGATAAATACCATGAGATTATGTATACGACGTATAT-TCCA-GTACCTCATGAGATGA
1322037 GTAAGCTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
67 1 0.02
68 47 0.89
69 2 0.04
70 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (67 bp):
GCATGATAAATACCATGAGATTATGTATACGACGTATATTCCAGTACCTCATGAGATGATTGAGA
AA
Found at i:1324041 original size:29 final size:28
Alignment explanation
Indices: 1323963--1324099 Score: 125
Period size: 29 Copynumber: 4.7 Consensus size: 28
1323953 TAAGACAACA
*
1323963 CTTGTCTTTAATTAAGACAAAAATAT-TTTAT
1 CTTGTC-TAAATTAAGAC--AAATATGTTT-T
* * *
1323994 CTTATCTGAATTGAGACAAATATGTTTT
1 CTTGTCTAAATTAAGACAAATATGTTTT
* *
1324022 CTTGTCTTAAATTAAGACAAATATATTTG
1 CTTGTC-TAAATTAAGACAAATATGTTTT
*
1324051 CTTGTCTAAATTAAGACCAAACATGTCTTT
1 CTTGTCTAAATTAAGA-CAAATATGT-TTT
*
1324081 -TCGTCTAAATTAAGACAAA
1 CTTGTCTAAATTAAGACAAA
1324100 CATATTGAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
28 26 0.29
29 48 0.53
30 11 0.12
31 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
CTTGTCTAAATTAAGACAAATATGTTTT
Found at i:1324097 original size:57 final size:58
Alignment explanation
Indices: 1323966--1324105 Score: 151
Period size: 57 Copynumber: 2.4 Consensus size: 58
1323956 GACAACACTT
* * * * * *
1323966 GTCTTTAATTAAGACAAAAATATTTTATCTTATCTGAATTGAGACAAATATGTTTTCTT
1 GTCTTAAATTAAGACAAAAATA-TTTAGCTTATCTAAATTAAGACAAACATGTTTTCTC
* *
1324025 GTCTTAAATTAAGACAAATATATTT-GCTTGTCTAAATTAAGACCAAACATGTCTTT-TC
1 GTCTTAAATTAAGACAAAAATATTTAGCTTATCTAAATTAAGA-CAAACATGT-TTTCTC
*
1324083 GTC-TAAATTAAGACAAACATATT
1 GTCTTAAATTAAGACAAAAATATT
1324106 GAAGCTGCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 32 0.46
58 15 0.21
59 23 0.33
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (58 bp):
GTCTTAAATTAAGACAAAAATATTTAGCTTATCTAAATTAAGACAAACATGTTTTCTC
Found at i:1327230 original size:2 final size:2
Alignment explanation
Indices: 1327223--1327262 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1327213 TGCACTAAGC
1327223 CA CA CA CA CA 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 CA CA CA CA CA
1327263 TATAGTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1329868 original size:17 final size:17
Alignment explanation
Indices: 1329830--1329870 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1329820 TGCATTCAAG
1329830 TATTTT-TTTTTCTTTC
1 TATTTTCTTTTTCTTTC
*
1329846 TGTTTTCTTTTTCATTT-
1 TATTTTCTTTTTC-TTTC
1329863 TATTTTCT
1 TATTTTCT
1329871 ATCGTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (17 bp):
TATTTTCTTTTTCTTTC
Found at i:1330364 original size:37 final size:36
Alignment explanation
Indices: 1330283--1330364 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 36
1330273 TTCTCATGAT
*
1330283 TTTA-TTTATTTATTATTTTTAATTAATAAATTTTAT
1 TTTATTTTATTTATTATTTTTAATT-ATAAATTTTAA
1330319 TTTATTTTATTTATT-TATTTTAATT-TGAAATTTATAA
1 TTTATTTTATTTATTAT-TTTTAATTAT-AAATTT-TAA
*
1330356 TTTGTTTTA
1 TTTATTTTA
1330365 ATAGAGTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 1 0.03
36 11 0.28
37 28 0.70
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (36 bp):
TTTATTTTATTTATTATTTTTAATTATAAATTTTAA
Found at i:1345620 original size:127 final size:127
Alignment explanation
Indices: 1345394--1345648 Score: 456
Period size: 127 Copynumber: 2.0 Consensus size: 127
1345384 AAGAGATGCC
* *
1345394 ACCTAAAGAGGGTTTATAGTAAATGAGAAATCCTTACTGGGTTTACGGTAGATGTGAGATTTCTA
1 ACCTAAAGAGGGTTTATAGTAAATGAGAAATCCCTACTAGGTTTACGGTAGATGTGAGATTTCTA
* * *
1345459 TTGGTTTGTTTTTGAATTACTATGGTAAGTTAGTGGATTCCTTATCAAAGGCCTATAAATAT
66 TTGGTTTGTTTCTGAATTACTATGGTAAATTAGTGGATTCCTTATCAAAGGCCTACAAATAT
1345521 ACCTAAAGAGGGTTTATAGTAAATGAGAAATCCCTACTAGGTTTACGGTAGATGTGAGATTTCTA
1 ACCTAAAGAGGGTTTATAGTAAATGAGAAATCCCTACTAGGTTTACGGTAGATGTGAGATTTCTA
*
1345586 TTGGTTTGTTTCTGAATTACTGTGGTAAATTAGTGGATTCCTTATCAAAGGCCTACAAATAT
66 TTGGTTTGTTTCTGAATTACTATGGTAAATTAGTGGATTCCTTATCAAAGGCCTACAAATAT
1345648 A
1 A
1345649 ATTGTGACTA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (127 bp):
ACCTAAAGAGGGTTTATAGTAAATGAGAAATCCCTACTAGGTTTACGGTAGATGTGAGATTTCTA
TTGGTTTGTTTCTGAATTACTATGGTAAATTAGTGGATTCCTTATCAAAGGCCTACAAATAT
Found at i:1364211 original size:27 final size:27
Alignment explanation
Indices: 1364173--1364253 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
1364163 GAATAGTTAG
1364173 ATTGACTTCATTGTTGACCTTAGATAA
1 ATTGACTTCATTGTTGACCTTAGATAA
*
1364200 ATTGGCTTCATTGTTGACCTTAGATAA
1 ATTGACTTCATTGTTGACCTTAGATAA
1364227 ATTGACTTCATTGTTGACCTTAGATAA
1 ATTGACTTCATTGTTGACCTTAGATAA
1364254 TATCCTATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (27 bp):
ATTGACTTCATTGTTGACCTTAGATAA
Found at i:1368150 original size:209 final size:208
Alignment explanation
Indices: 1367790--1368196 Score: 654
Period size: 209 Copynumber: 2.0 Consensus size: 208
1367780 CATTTTTATT
* *
1367790 TCTTTCTTCTTCTTTTCTTTCCTTTGTTTATTGCATGTGTCTCTTTAAATTTTCTCTCCATTATA
1 TCTTTCTTCTTCTCTTCTTTCCTTTGTTTACTGCATGTGTCTCTTTAAATTTTCTCTCCATTATA
** *
1367855 GCAGCAACTATGCCATGTCTTTCTCTCTTTTGGCCTCCACACAAACACCATAACACCTCTATCAT
66 GCAGCAACTATGCCACATCCTTCTCTCTTTTGGCCTCCACACAAACACCATAACACCTCTATCAT
* * * *
1367920 TCCTTCACCTCACGACTAGCACCCAAGCTTCCGTTTCCTCATTCTTTTACTTCTCTTCATGGAAT
131 TCCTTCACCTCACAACTAGCACCCAAGCTTCCATCTCCT-ATTCTCTTACTTCTCTTCATGGAAT
1367985 TTAAGCTAATAGTA
195 TTAAGCTAATAGTA
* *
1367999 TCTTTCTTCTTCTCTTCTTTCCTTTGTTTGCTGCATGTGTCTCTTTAAATTTTCTCTCCATTGTA
1 TCTTTCTTCTTCTCTTCTTTCCTTTGTTTACTGCATGTGTCTCTTTAAATTTTCTCTCCATTATA
* **
1368064 GCAGCAACTATGCCACATCCTTCTCTCTTTTGGCCTCCACACAAACATCATAATGCCT-TCATCA
66 GCAGCAACTATGCCACATCCTTCTCTCTTTTGGCCTCCACACAAACACCATAACACCTCT-ATCA
*
1368128 TTCCTTCACCTCACAACTAGCACCCAAGCTTCCATCTCCTGTTCTCTTACTTCTCTTCATGGAAT
130 TTCCTTCACCTCACAACTAGCACCCAAGCTTCCATCTCCTATTCTCTTACTTCTCTTCATGGAAT
1368193 TTAA
195 TTAA
1368197 TCCAATAATA
Statistics
Matches: 182, Mismatches: 15, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
208 28 0.15
209 154 0.85
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (208 bp):
TCTTTCTTCTTCTCTTCTTTCCTTTGTTTACTGCATGTGTCTCTTTAAATTTTCTCTCCATTATA
GCAGCAACTATGCCACATCCTTCTCTCTTTTGGCCTCCACACAAACACCATAACACCTCTATCAT
TCCTTCACCTCACAACTAGCACCCAAGCTTCCATCTCCTATTCTCTTACTTCTCTTCATGGAATT
TAAGCTAATAGTA
Found at i:1369631 original size:59 final size:61
Alignment explanation
Indices: 1369556--1369710 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 61
1369546 CCTCGACTTC
* *
1369556 TATTTGGTGGCGTAGGGAGTTCCTACAAGTAGGT-AAAGGGAACCTAAAGCCTC-AATTTA
1 TATTTGGTGGCGTAGGGAGTTCCCACAAGTAGGTGAAAGGGAACCTAAAGCCCCGAATTTA
* * * * * *
1369615 TATTTGATGGCATAGGGAGTTCCCACAATTAGGTGAAGGGGGACCTAAAGCCCCGATTTTA
1 TATTTGGTGGCGTAGGGAGTTCCCACAAGTAGGTGAAAGGGAACCTAAAGCCCCGAATTTA
* *
1369676 TATTTGGTGGGGT-GGGAGTTCCCACGAGTAGGTGA
1 TATTTGGTGGCGTAGGGAGTTCCCACAAGTAGGTGA
1369711 TGATGTTATT
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 30 0.37
60 36 0.44
61 15 0.19
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.27
Consensus pattern (61 bp):
TATTTGGTGGCGTAGGGAGTTCCCACAAGTAGGTGAAAGGGAACCTAAAGCCCCGAATTTA
Found at i:1376628 original size:2 final size:2
Alignment explanation
Indices: 1376621--1376653 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1376611 AAGTATTAAC
1376621 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
1376654 AAAGACCCAA
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:1384271 original size:30 final size:32
Alignment explanation
Indices: 1384212--1384272 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1384202 TACTTGCTTA
1384212 AGTGGTTATACTTTAAGCAATAGAAAAGGTAG
1 AGTGGTTATACTTTAAGCAATAGAAAAGGTAG
* *
1384244 AGTGGTTATGCTTTAA-CCATA-AAAAGGTA
1 AGTGGTTATACTTTAAGCAATAGAAAAGGTA
1384273 TTGTATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 15 0.56
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (32 bp):
AGTGGTTATACTTTAAGCAATAGAAAAGGTAG
Found at i:1386837 original size:25 final size:25
Alignment explanation
Indices: 1386778--1386837 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1386768 GTGGTTGCAA
*
1386778 CCACGTATATCAACTTGTGGCCTAG
1 CCACGTATATCAACCTGTGGCCTAG
** * *
1386803 CCACAAATATCATCCTGTGGCCTTG
1 CCACGTATATCAACCTGTGGCCTAG
1386828 CCACGTATAT
1 CCACGTATAT
1386838 AAATCACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (25 bp):
CCACGTATATCAACCTGTGGCCTAG
Found at i:1388996 original size:16 final size:16
Alignment explanation
Indices: 1388975--1389006 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1388965 TTTTTGGTTT
*
1388975 ATTTCATTTGCATTTC
1 ATTTCATATGCATTTC
1388991 ATTTCATATGCATTTC
1 ATTTCATATGCATTTC
1389007 CTTTTAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTCATATGCATTTC
Found at i:1391872 original size:22 final size:22
Alignment explanation
Indices: 1391842--1391887 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1391832 TTAGCTTGAG
1391842 TTCCACACAT-ATAGTTCACCAT
1 TTCCACACATCATAG-TCACCAT
*
1391864 TTCCTCACATCCATAGTCACCAT
1 TTCCACACAT-CATAGTCACCAT
1391887 T
1 T
1391888 GCTGCCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (22 bp):
TTCCACACATCATAGTCACCAT
Found at i:1393671 original size:11 final size:11
Alignment explanation
Indices: 1393655--1393679 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1393645 CTCAATAAGA
1393655 TATTATTATTT
1 TATTATTATTT
1393666 TATTATTATTT
1 TATTATTATTT
1393677 TAT
1 TAT
1393680 CGCACATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:1419814 original size:60 final size:60
Alignment explanation
Indices: 1419674--1419960 Score: 183
Period size: 60 Copynumber: 4.8 Consensus size: 60
1419664 TACTTATGGG
* * * ** * * *
1419674 AACTCCTTATGCCACCAAATATAAATTGAAGCTTCAGGTGTCTCTATACATACTCTTGGGA
1 AACTCCCTATGCCACCAAATATAAATTGAGGCTTCAAGTCCCTCTTTACCTACTCGT-GGA
* * * **
1419735 AA-TCCCCATACCACGAAATATAAATTGAGGCTTC-AGATCCCTCTTTACCTACTCGTACA
1 AACTCCCTATGCCACCAAATATAAATTGAGGCTTCAAG-TCCCTCTTTACCTACTCGTGGA
* * * * * * *
1419794 AACTTCTTATGCCACCAAATAAAAATT-AGGGCTTTAAGTCCC-CTTTTAGCTACTCATGGG
1 AACTCCCTATGCCACCAAATATAAATTGA-GGCTTCAAGTCCCTC-TTTACCTACTCGTGGA
* * * * *
1419854 AACTTCCTATGCCACTAAATATAAA-TCAGAGCTTTAAGTCCCCCTTTACCTACTCGTGG-
1 AACTCCCTATGCCACCAAATATAAATTGAG-GCTTCAAGTCCCTCTTTACCTACTCGTGGA
* * * * * *
1419913 GACTACCC-ATGCCACCAAATTTCAAGTCGAGGCTTCAACTCCTTCTTT
1 AACT-CCCTATGCCACCAAATAT-AAATTGAGGCTTCAAGTCCCTCTTT
1419961 TGCTTACTTG
Statistics
Matches: 174, Mismatches: 41, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
59 23 0.13
60 144 0.83
61 7 0.04
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (60 bp):
AACTCCCTATGCCACCAAATATAAATTGAGGCTTCAAGTCCCTCTTTACCTACTCGTGGA
Found at i:1420557 original size:21 final size:21
Alignment explanation
Indices: 1420512--1420557 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1420502 TAGATTCAAG
**
1420512 TATTCAAAAGAGATATGCATG
1 TATTCAAAAGAGATATGCACA
* *
1420533 TATTCAAACGAGATATGTACA
1 TATTCAAAAGAGATATGCACA
1420554 TATT
1 TATT
1420558 ATAATTCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (21 bp):
TATTCAAAAGAGATATGCACA
Found at i:1422763 original size:4 final size:4
Alignment explanation
Indices: 1422748--1422809 Score: 92
Period size: 4 Copynumber: 15.8 Consensus size: 4
1422738 GCTTAGAAGC
1422748 AAAG AGAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
1422797 GAA- AAAG -AAG AAA
1 AAAG AAAG AAAG AAA
1422810 AAACAATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 5 0.09
4 44 0.83
5 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1424088 original size:25 final size:25
Alignment explanation
Indices: 1424060--1424116 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
1424050 ACATGGCTGG
*
1424060 GGCCATAGTTTGTGATACGTGGCAA
1 GGCCATAGGTTGTGATACGTGGCAA
** * * *
1424085 GGCCACGGGTTGTTATATGTGGCTA
1 GGCCATAGGTTGTGATACGTGGCAA
1424110 GGCCATA
1 GGCCATA
1424117 AGTGATATTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (25 bp):
GGCCATAGGTTGTGATACGTGGCAA
Found at i:1426544 original size:28 final size:28
Alignment explanation
Indices: 1426512--1426595 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
1426502 GAAGTAGGAA
1426512 AACATTACGATGGACTTTATGATGGGGT
1 AACATTACGATGGACTTTATGATGGGGT
*
1426540 AACATTACGATGGACTTTATGATGAGGT
1 AACATTACGATGGACTTTATGATGGGGT
*
1426568 AACATTATGATGGACTTTATGATGGGGT
1 AACATTACGATGGACTTTATGATGGGGT
1426596 TATGTCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (28 bp):
AACATTACGATGGACTTTATGATGGGGT
Found at i:1427945 original size:73 final size:72
Alignment explanation
Indices: 1427778--1427951 Score: 172
Period size: 73 Copynumber: 2.4 Consensus size: 72
1427768 GTTTTGACAA
* * * *
1427778 GAAAAATGTATTCTATTGCAAAAGTTTTGATACCTAAGAGAAAGTTATCGATACTTAGTGGGCAA
1 GAAAAAAGTATTCTATTG-AAAAGTATCGATACCTAAAAGAAAGTTATCGATACTTAGTGGGCAA
1427843 AATGCCTT
65 AATGCCTT
* ** * * *
1427851 TAAAAAAAAATTCTACATGAAAGGTATCGATACCTTAAAAGAAAG-TATCGATACTTAGT-GTCT
1 GAAAAAAGTATTCTA-TTGAAAAGTATCGATACC-TAAAAGAAAGTTATCGATACTTAGTGGGC-
*
1427914 TAAATGCCTT
63 AAAATGCCTT
**
1427924 GGGAAAAGTATTCTATGTGAAAAGTATC
1 GAAAAAAGTATTCTAT-TGAAAAGTATC
1427952 AATATTTGTC
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
72 2 0.03
73 66 0.84
74 11 0.14
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (72 bp):
GAAAAAAGTATTCTATTGAAAAGTATCGATACCTAAAAGAAAGTTATCGATACTTAGTGGGCAAA
ATGCCTT
Found at i:1436867 original size:12 final size:12
Alignment explanation
Indices: 1436850--1436875 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1436840 TATGCATATG
1436850 TTGAGAGGGAGA
1 TTGAGAGGGAGA
1436862 TTGAGAGGGAGA
1 TTGAGAGGGAGA
1436874 TT
1 TT
1436876 TTAAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (12 bp):
TTGAGAGGGAGA
Found at i:1446366 original size:17 final size:17
Alignment explanation
Indices: 1446337--1446369 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1446327 TTCTTGATGA
1446337 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
1446354 AATAATAAC-TCTTATT
1 AATAA-AACTTCTTATT
1446370 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:1446573 original size:28 final size:28
Alignment explanation
Indices: 1446532--1446590 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1446522 ATTAAGATAA
*
1446532 AAATATTTTATCTTGTCTAAATTGAGAC
1 AAATATTTTATCTTGTCTAAATTAAGAC
*
1446560 AAATATGTTT-TCTTGTCTCAATTAAGAC
1 AAATAT-TTTATCTTGTCTAAATTAAGAC
1446588 AAA
1 AAA
1446591 CAATATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (28 bp):
AAATATTTTATCTTGTCTAAATTAAGAC
Found at i:1446635 original size:29 final size:28
Alignment explanation
Indices: 1446598--1446667 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 28
1446588 AAACAATATT
**
1446598 AGACAAACATATTTTCTTATCAAAATTA
1 AGACAAACATATTTGATTATCAAAATTA
* * *
1446626 AGACCAAACATGTTTGATTGTCTAAATTA
1 AGA-CAAACATATTTGATTATCAAAATTA
1446655 AGACAAACATATT
1 AGACAAACATATT
1446668 AAAGTTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (28 bp):
AGACAAACATATTTGATTATCAAAATTA
Found at i:1446675 original size:29 final size:29
Alignment explanation
Indices: 1446620--1446675 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1446610 TTTCTTATCA
* **
1446620 AAATTAAGACCAAACATGTTTGATTGTCT
1 AAATTAAGACCAAACATATTAAATTGTCT
1446649 AAATTAAGA-CAAACATATTAAAGTTGT
1 AAATTAAGACCAAACATATTAAA-TTGT
1446676 TATTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATTAAGACCAAACATATTAAATTGTCT
Found at i:1449459 original size:21 final size:19
Alignment explanation
Indices: 1449423--1449463 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1449413 ACATGTTGAG
1449423 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
1449442 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
1449463 T
1 T
1449464 GTTTTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:1455468 original size:21 final size:21
Alignment explanation
Indices: 1455435--1455484 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1455425 ACATGTTGAG
1455435 TAGTT-AA-TTTAAGTTATTT
1 TAGTTAAATTTTAAGTTATTT
1455454 TAGTTAAATTTTAAGTTATTT
1 TAGTTAAATTTTAAGTTATTT
1455475 T-GTTTAAATT
1 TAG-TTAAATT
1455485 ACTTTAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.18
20 3 0.11
21 20 0.71
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (21 bp):
TAGTTAAATTTTAAGTTATTT
Found at i:1459868 original size:3 final size:3
Alignment explanation
Indices: 1459860--1459899 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1459850 GCACTGTCTC
*
1459860 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAA TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1459900 GGTAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (3 bp):
TAG
Done.