Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012400.1 Kokia drynarioides strain JFW-HI SEQ_127404, 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: 195259
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 201 characters in sequence are not A, C, G, or T
Found at i:2348 original size:29 final size:29
Alignment explanation
Indices: 2305--2382 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2295 AAAATATACA
*
2305 CTTTAATTCTA-TTTTTTTAAAATTAAGTC
1 CTTTTATTCTATTTTTTTTAAAATTAA-TC
* **
2334 C-TTTATTTTATTTTTTTTAATTTTAATC
1 CTTTTATTCTATTTTTTTTAAAATTAATC
2362 CTTTTATTCTATTTTTATTTA
1 CTTTTATTCTATTTTT-TTTA
2383 TTTATTGACC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 10 0.24
29 27 0.66
30 4 0.10
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.65
Consensus pattern (29 bp):
CTTTTATTCTATTTTTTTTAAAATTAATC
Found at i:2386 original size:28 final size:28
Alignment explanation
Indices: 2305--2386 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
2295 AAAATATACA
* * *
2305 CTTTAATTCTATTTTTTTAAAATTAAGTC
1 CTTTTATTCTATTTTTTT-TATTTAAGTC
*
2334 C-TTTATTTTATTTTTTTTAATTTTAA-TC
1 CTTTTATTCTATTTTTTTT-A-TTTAAGTC
2362 CTTTTATTCTATTTTTATTTATTTA
1 CTTTTATTCTATTTTT-TTTATTTA
2387 TTGACCCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
28 22 0.50
29 19 0.43
30 3 0.07
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (28 bp):
CTTTTATTCTATTTTTTTTATTTAAGTC
Found at i:3337 original size:29 final size:29
Alignment explanation
Indices: 3277--3337 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3267 TTTACATTAG
* *
3277 GTTACATTTTAGTCACTTATGTTTGACAT
1 GTTACATTTTAGTCACTTACGTTTAACAT
*
3306 GTTACATTTTAGTCACTTTACG-TTAACGT
1 GTTACATTTTAGTCAC-TTACGTTTAACAT
3335 GTT
1 GTT
3338 GTAACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTACGTTTAACAT
Found at i:8605 original size:21 final size:20
Alignment explanation
Indices: 8575--8622 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
8565 GTTTTTCAGT
8575 TTCAAATTTTAAATTAAATG
1 TTCAAATTTTAAATTAAATG
**
8595 TTCAACATTTTCTATTAAAT-
1 TTCAA-ATTTTAAATTAAATG
8615 TT-AAATTT
1 TTCAAATTT
8623 ATTATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 2 0.08
20 7 0.28
21 12 0.48
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (20 bp):
TTCAAATTTTAAATTAAATG
Found at i:14300 original size:25 final size:25
Alignment explanation
Indices: 14272--14322 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
14262 TGATTTAGGT
* *
14272 AATTTAAAGAAA-ATAAATTATTAAA
1 AATTTAAA-AAATAAAAAATATTAAA
14297 AATTTAAAAAATAAAAAATATTAAA
1 AATTTAAAAAATAAAAAATATTAAA
14322 A
1 A
14323 GCTGATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
AATTTAAAAAATAAAAAATATTAAA
Found at i:31574 original size:38 final size:36
Alignment explanation
Indices: 31530--31654 Score: 115
Period size: 38 Copynumber: 3.3 Consensus size: 36
31520 AAAGTGGAAT
* *
31530 ACTGATTACACTGAATATTGGCTCAAATGAGTGAATTC
1 ACTGATTATACTGAAT-TT-GCTCAAATGAGTGAATCC
* * * *
31568 ATTGATTATATTGAATTCTTGCTCAAGTGAGCGAATCC
1 ACTGATTATACTGAA-T-TTGCTCAAATGAGTGAATCC
* *
31606 ACTAATTATACTGAATGCTTGCTCAACTGAGTGAATCC
1 ACTGATTATACTGAAT--TTGCTCAAATGAGTGAATCC
*
31644 ACTAATTATAC
1 ACTGATTATAC
31655 CAAATGCTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 69 0.95
39 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (36 bp):
ACTGATTATACTGAATTTGCTCAAATGAGTGAATCC
Found at i:31637 original size:76 final size:76
Alignment explanation
Indices: 31550--31768 Score: 228
Period size: 76 Copynumber: 2.9 Consensus size: 76
31540 CTGAATATTG
* * * **
31550 GCTCAAATGAGTGAATTCATTGATTATATTGAATTCTTGCTCAAGTGAGCGAATCCACTAATTAT
1 GCTCAAATGAGTGAATACACTGATTATATTGAATGCTTGCTCAAACGAGCGAATCCACTAATTAT
*
31615 ACTGAATGCTT-
66 ACGGAATG-TTC
* * * *** * * *
31626 GCTCAACTGAGTGAATCCACTAATTATACCAAATGCTTGTTAAAACGAGCGAATCCACTAATTTT
1 GCTCAAATGAGTGAATACACTGATTATATTGAATGCTTGCTCAAACGAGCGAATCCACTAATTAT
*
31691 TCGGAATGTTC
66 ACGGAATGTTC
31702 GCTCAAATGAGT-AATAACTACTGATTATATTGAATGCTTGCTCAAACGAGC-ATTATCCACTAA
1 GCTCAAATGAGTGAAT-AC-ACTGATTATATTGAATGCTTGCTCAAACGAGCGA--ATCCACTAA
31765 TTAT
62 TTAT
31769 TCTAAATAAG
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
75 5 0.04
76 71 0.62
77 26 0.23
78 12 0.11
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
GCTCAAATGAGTGAATACACTGATTATATTGAATGCTTGCTCAAACGAGCGAATCCACTAATTAT
ACGGAATGTTC
Found at i:31661 original size:38 final size:38
Alignment explanation
Indices: 31585--31688 Score: 138
Period size: 38 Copynumber: 2.7 Consensus size: 38
31575 ATATTGAATT
* **
31585 CTTGCTCAAGTGAGCGAATCCACTAATTATACTGAATG
1 CTTGCTCAACTGAGCGAATCCACTAATTATACCAAATG
*
31623 CTTGCTCAACTGAGTGAATCCACTAATTATACCAAATG
1 CTTGCTCAACTGAGCGAATCCACTAATTATACCAAATG
* *
31661 CTTGTTAAAAC-GAGCGAATCCACTAATT
1 CTTGCT-CAACTGAGCGAATCCACTAATT
31689 TTTCGGAATG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 55 0.95
39 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (38 bp):
CTTGCTCAACTGAGCGAATCCACTAATTATACCAAATG
Found at i:38689 original size:17 final size:18
Alignment explanation
Indices: 38658--38691 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38648 ACTGATTTTT
*
38658 TAATTTTTTTGAAAATAA
1 TAATTTTATTGAAAATAA
38676 TAATTTTATT-AAAATA
1 TAATTTTATTGAAAATA
38692 TTTTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTTTATTGAAAATAA
Found at i:39787 original size:26 final size:26
Alignment explanation
Indices: 39753--39806 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
39743 ATTGTTGTTG
* *
39753 TTGTATTTAATTAATTATATTTATGT
1 TTGTATTTAACTAATTATACTTATGT
*
39779 TTGTATTTAACTAATTATGCTTATGT
1 TTGTATTTAACTAATTATACTTATGT
39805 TT
1 TT
39807 AGAGTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (26 bp):
TTGTATTTAACTAATTATACTTATGT
Found at i:39820 original size:7 final size:7
Alignment explanation
Indices: 39810--39857 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
39800 TATGTTTAGA
39810 GTTTAAG
1 GTTTAAG
*
39817 GTTTATG
1 GTTTAAG
* *
39824 ATTTAGG
1 GTTTAAG
39831 GTTTAAG
1 GTTTAAG
*
39838 GTTTTAGG
1 G-TTTAAG
39846 GTTTAAG
1 GTTTAAG
39853 GTTTA
1 GTTTA
39858 GAACTTGGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (7 bp):
GTTTAAG
Found at i:39829 original size:21 final size:20
Alignment explanation
Indices: 39799--39841 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
39789 CTAATTATGC
39799 TTATGTTTAGAGTTTAAGGT
1 TTATGTTTAGAGTTTAAGGT
*
39819 TTATGATTTAGGGTTTAAGGT
1 TTATG-TTTAGAGTTTAAGGT
39840 TT
1 TT
39842 TAGGGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (20 bp):
TTATGTTTAGAGTTTAAGGT
Found at i:39845 original size:15 final size:15
Alignment explanation
Indices: 39825--39856 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39815 AGGTTTATGA
39825 TTTAGGGTTTAAGGT
1 TTTAGGGTTTAAGGT
39840 TTTAGGGTTTAAGGT
1 TTTAGGGTTTAAGGT
39855 TT
1 TT
39857 AGAACTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTAAGGT
Found at i:44829 original size:23 final size:22
Alignment explanation
Indices: 44801--44869 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
44791 AATTAATCTT
44801 TATTTAATCAATAAAAATATATA
1 TATTTAAT-AATAAAAATATATA
* * *
44824 TTTTTAAGTTATAAAAATACAT-
1 TATTTAA-TAATAAAAATATATA
*
44846 TATTTAAAGAATAAAAA-ATATA
1 TATTT-AATAATAAAAATATATA
44868 TA
1 TA
44870 AAAACCATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
21 3 0.08
22 13 0.36
23 19 0.53
24 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (22 bp):
TATTTAATAATAAAAATATATA
Found at i:52291 original size:9 final size:9
Alignment explanation
Indices: 52277--52303 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
52267 TAAATTTTAA
52277 AAAAATTAT
1 AAAAATTAT
52286 AAAAATTAT
1 AAAAATTAT
52295 AAAAATTAT
1 AAAAATTAT
52304 TTTAACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54318 original size:3 final size:3
Alignment explanation
Indices: 54310--54336 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54300 GGAGTGTTAA
54310 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
54337 TAAGAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54735 original size:13 final size:11
Alignment explanation
Indices: 54707--54749 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
54697 AGTTAAATAT
54707 TATTTTATTAA
1 TATTTTATTAA
54718 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
54731 TA-TTTATTAT
1 TATTTTATTAA
54741 TATTTTATT
1 TATTTTATT
54750 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:54736 original size:23 final size:23
Alignment explanation
Indices: 54710--54753 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54700 TAAATATTAT
54710 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
54733 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
54754 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:56278 original size:16 final size:16
Alignment explanation
Indices: 56257--56288 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56247 TGACTTTTTT
*
56257 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
56273 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
56289 TTTGTAAGGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:56868 original size:52 final size:52
Alignment explanation
Indices: 56752--56989 Score: 261
Period size: 52 Copynumber: 4.6 Consensus size: 52
56742 TAAATTCAAA
* * * * *
56752 AGGTTCGATGACTTTGTGTTATCGTGAGTATATGAA-CCTTTA-CAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGA-ATTACG
* *
56803 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACT-AATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTA-TGAATTACG
* * *
56855 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCTTTTATGAAGTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTACG
* * * *
56907 AGG-CCTGATGACTATGTGTTATCGTGAATATATGAATCCTTTATGGATTATG
1 AGGTCC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTACG
* *
56959 AGGAT-CGATGACTATGTATCTTCGTGAGTAT
1 AGG-TCCGATGACTATGTGTCATCGTGAGTAT
56990 TAAATGAGAA
Statistics
Matches: 162, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
51 37 0.23
52 123 0.76
53 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTACG
Found at i:61469 original size:16 final size:16
Alignment explanation
Indices: 61448--61479 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61438 TGAAAATTTT
*
61448 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
61464 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
61480 CTTGTACGGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:62222 original size:52 final size:52
Alignment explanation
Indices: 61940--62219 Score: 411
Period size: 52 Copynumber: 5.4 Consensus size: 52
61930 TAAATGTAAA
* *
61940 AGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGGATGATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
61992 AGGTCCGATGAC--TGTGTCATCGTGAGTATATGAATCTTTTATGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
62042 AGGTCCAATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
62094 AGGTCCGATGACTATGTGTTATCGTGAGTATATGAATCCATTACGAATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
62146 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTTTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
62198 AGGTTCGATGACTATGTGTCAT
1 AGGTCCGATGACTATGTGTCAT
62220 TGTATCACCC
Statistics
Matches: 207, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 45 0.22
52 162 0.78
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:68040 original size:21 final size:20
Alignment explanation
Indices: 68016--68055 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
68006 GAAGAAAAAG
68016 AAAGAAAAAGAAAGATAGAAT
1 AAAGAAAAAGAAAGA-AGAAT
* *
68037 AAAGAAGATGAAAGAAGAA
1 AAAGAAAAAGAAAGAAGAA
68056 ATGGGGGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAAT
Found at i:69253 original size:21 final size:21
Alignment explanation
Indices: 69214--69263 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
69204 TTTTTAGTAC
* * *
69214 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATCACTTGTAT
*
69235 CGGTAGAAGCTTCACTTGTAT
1 CGGTAGAAGCATCACTTGTAT
*
69256 CGATAGAA
1 CGGTAGAA
69264 CTGTCATAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
CGGTAGAAGCATCACTTGTAT
Found at i:71971 original size:18 final size:19
Alignment explanation
Indices: 71914--71972 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
71904 CCTGTTGATC
*
71914 GACCCAACTCAAAGCTGTT
1 GACCCAACTCAAACCTGTT
*
71933 GACCCAACTCAAACCTATT
1 GACCCAACTCAAACCTGTT
* *
71952 GACCGAACTC-GACCTGTT
1 GACCCAACTCAAACCTGTT
71970 GAC
1 GAC
71973 TGTTGACTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
18 9 0.26
19 26 0.74
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (19 bp):
GACCCAACTCAAACCTGTT
Found at i:73066 original size:3 final size:3
Alignment explanation
Indices: 73058--73089 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
73048 TATACTTTGG
73058 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
73090 GGGTTGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:79237 original size:17 final size:17
Alignment explanation
Indices: 79215--79253 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
79205 CTATAGTATA
*
79215 ATTGTCCCTGCATTATT
1 ATTGTCACTGCATTATT
* *
79232 ATTGTCATTGCATTTTT
1 ATTGTCACTGCATTATT
79249 ATTGT
1 ATTGT
79254 TGCTGCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (17 bp):
ATTGTCACTGCATTATT
Found at i:79253 original size:34 final size:34
Alignment explanation
Indices: 79215--79280 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
79205 CTATAGTATA
*
79215 ATTGTCCCTGCAT-TATTATTGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CATTGTCATTGCATTTTT
**
79249 ATTGTTGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACATTGTCATTGCATTT
79281 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACATTGTCATTGCATTTTT
Found at i:85390 original size:13 final size:14
Alignment explanation
Indices: 85358--85397 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
85348 ACTCGACCTA
*
85358 TTGACTGTTGACAG
1 TTGACCGTTGACAG
*
85372 TTGACCGTTGAC-T
1 TTGACCGTTGACAG
85385 TTGACCGTTGACA
1 TTGACCGTTGACA
85398 TTTTCCAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (14 bp):
TTGACCGTTGACAG
Found at i:89417 original size:10 final size:10
Alignment explanation
Indices: 89399--89427 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
89389 AGAGCATTTG
89399 AGAGC-AAAA
1 AGAGCAAAAA
89408 AGAGCAAAAA
1 AGAGCAAAAA
89418 AGAGCAAAAA
1 AGAGCAAAAA
89428 TCAAAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAGCAAAAA
Found at i:90595 original size:20 final size:21
Alignment explanation
Indices: 90560--90598 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
90550 CTTCTATTAC
*
90560 TTTAATCATTTTTATTTTTGT
1 TTTAATCATTTGTATTTTTGT
90581 TTTAAT-ATTTGTATTTTT
1 TTTAATCATTTGTATTTTT
90599 CTAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTAATCATTTGTATTTTTGT
Found at i:94041 original size:18 final size:16
Alignment explanation
Indices: 94010--94043 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
94000 TGTTTATAAT
94010 TTTAAAAATTAATTAA
1 TTTAAAAATTAATTAA
94026 TTTAAATAATTTAATTAA
1 TTTAAA-AA-TTAATTAA
94044 AGTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAAATTAATTAA
Found at i:98325 original size:23 final size:23
Alignment explanation
Indices: 98299--98465 Score: 181
Period size: 23 Copynumber: 7.0 Consensus size: 23
98289 ATCACATATT
* *
98299 AATCACATGAATATTTCAGCATA
1 AATCACATTAATATTTAAGCATA
* * *
98322 AATCATATTAACATTTAAGTATAAATATA
1 AATCACATTAATATTTAAG----CA--TA
*
98351 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
98374 AATCACATTAACATTTAAGTATA
1 AATCACATTAATATTTAAGCATA
*
98397 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
98420 AATCACATTAATATTTAAGGACA
1 AATCACATTAATATTTAAGCATA
98443 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
98466 TAACGCATGA
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
23 98 0.82
25 1 0.01
27 1 0.01
29 20 0.17
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.35
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:98351 original size:29 final size:29
Alignment explanation
Indices: 98319--98376 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
98309 ATATTTCAGC
*
98319 ATAAATCATATTAACATTTAAGTATAAAT
1 ATAAATCATATTAACATTTAAGCATAAAT
*
98348 ATAAATCATATTAATATTTAAGCATAAAT
1 ATAAATCATATTAACATTTAAGCATAAAT
98377 CACATTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAAATCATATTAACATTTAAGCATAAAT
Found at i:98397 original size:46 final size:46
Alignment explanation
Indices: 98299--98465 Score: 208
Period size: 46 Copynumber: 3.5 Consensus size: 46
98289 ATCACATATT
* * *
98299 AATCACATGAATATTTCAGCATAAATCATATTAACATTTAAGTATAAATATA
1 AATCACATTAATATTTAAGCATAAATCACATTAACATTTAAG------TATA
*
98351 AATCATATTAATATTTAAGCATAAATCACATTAACATTTAAGTATA
1 AATCACATTAATATTTAAGCATAAATCACATTAACATTTAAGTATA
* * * *
98397 AATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGGACA
1 AATCACATTAATATTTAAGCATAAATCACATTAACATTTAAGTATA
98443 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
98466 TAACGCATGA
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
46 69 0.64
52 38 0.36
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.35
Consensus pattern (46 bp):
AATCACATTAATATTTAAGCATAAATCACATTAACATTTAAGTATA
Found at i:99257 original size:10 final size:10
Alignment explanation
Indices: 99229--99363 Score: 110
Period size: 10 Copynumber: 12.6 Consensus size: 10
99219 TTTAACACAA
99229 CACATATTAAT
1 CACAT-TTAAT
*
99240 TACATTTAAT
1 CACATTTAAT
*
99250 CACCTTTAAT
1 CACATTTAAT
*
99260 CACATATAAT
1 CACATTTAAT
*
99270 CACA-TTAGT
1 CACATTTAAT
*
99279 CACATGATTATTT
1 CACAT--TTA-AT
99292 CAGCATTTATCACAT
1 CA-CA-TT-T-A-AT
99307 CACATATTAAT
1 CACAT-TTAAT
*
99318 CACATTTAGT
1 CACATTTAAT
99328 CACATTTAAT
1 CACATTTAAT
*
99338 CACATTTAGT
1 CACATTTAAT
99348 CACATTTAAT
1 CACATTTAAT
99358 CACATT
1 CACATT
99364 GGTCACATGA
Statistics
Matches: 101, Mismatches: 14, Indels: 19
0.75 0.10 0.14
Matches are distributed among these distances:
9 7 0.07
10 62 0.61
11 11 0.11
12 4 0.04
13 6 0.06
14 6 0.06
15 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.39
Consensus pattern (10 bp):
CACATTTAAT
Found at i:99299 original size:78 final size:79
Alignment explanation
Indices: 99196--99362 Score: 219
Period size: 78 Copynumber: 2.1 Consensus size: 79
99186 ATTAATTGCA
* * * * * *
99196 TTAATCACATAAGTACTTAAGCATTTAACACAACACATATTAATTACATTTAATCACCTTTAATC
1 TTAATCACATGATTATTTCAGCATTTAACACAACACATATTAATCACATTTAATCACATTTAATC
99261 ACATATAATCACA-
66 ACATATAATCACAT
* * * *
99274 TTAGTCACATGATTATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACATTTAATC
1 TTAATCACATGATTATTTCAGCATTTAACACAACACATATTAATCACATTTAATCACATTTAATC
* *
99339 ACATTTAGTCACAT
66 ACATATAATCACAT
99353 TTAATCACAT
1 TTAATCACAT
99363 TGGTCACATG
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 66 0.88
79 9 0.12
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (79 bp):
TTAATCACATGATTATTTCAGCATTTAACACAACACATATTAATCACATTTAATCACATTTAATC
ACATATAATCACAT
Found at i:99317 original size:68 final size:70
Alignment explanation
Indices: 99241--99547 Score: 233
Period size: 68 Copynumber: 4.4 Consensus size: 70
99231 CATATTAATT
* *
99241 ACAT-TTAATCACCTTTAATCACATA-TAATCACA-TTAGTCACATGATTATTTCAGCATTTATC
1 ACATATTAATCACATTTAATCACATATTAATCACATTTAGTCACATGAATATTTCAGCATTTATC
99303 ACATC
66 ACATC
* * * **
99308 ACATATTAATCACATTTAGTCACAT-TTAATCACATTTAGTCACAT--TTA-ATCA-CATTGGTC
1 ACATATTAATCACATTTAATCACATATTAATCACATTTAGTCACATGAATATTTCAGCATTTATC
*
99368 ACATG
66 ACATC
* *
99373 A-ATATT-TTAACATTTATCACGTCACATATTAATCACATTTAGTCACATTTAACCACATGAATA
1 ACATATTAATCACATTTA--A--TCACATATTAATCACATTTAG-------T---CACATGAATA
* *
99436 TTTCAGTATTTATCGCATC
52 TTTCAGCATTTATCACATC
* * * * *
99455 ACATATTAATCACATTTAGTCACA-ATTAATCACA-CTGGTCACATGAATATTCCAACATTTATC
1 ACATATTAATCACATTTAATCACATATTAATCACATTTAGTCACATGAATATTTCAGCATTTATC
*
99518 ACATT
66 ACATC
*
99523 AGATATTAATCACATTTAATCACAT
1 ACATATTAATCACATTTAATCACAT
99548 GAATATTTTA
Statistics
Matches: 187, Mismatches: 28, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
63 8 0.04
64 5 0.03
65 11 0.06
66 3 0.02
67 13 0.07
68 86 0.46
69 10 0.05
71 1 0.01
75 1 0.01
78 7 0.04
79 10 0.05
80 7 0.04
81 3 0.02
82 9 0.05
83 5 0.03
84 8 0.04
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (70 bp):
ACATATTAATCACATTTAATCACATATTAATCACATTTAGTCACATGAATATTTCAGCATTTATC
ACATC
Found at i:99333 original size:88 final size:88
Alignment explanation
Indices: 99241--99430 Score: 299
Period size: 88 Copynumber: 2.2 Consensus size: 88
99231 CATATTAATT
* * *
99241 ACATTTAATCACCTTTAATCACATATAATCACATTAGTCACATGATTATTTCAGCATTTATCACA
1 ACATTTAATCACATTTAATCACATATAATCACATTAGTCACATGAATATTTCAACATTTATCACA
99306 TCACATATTAATCACATTTAGTC
66 TCACATATTAATCACATTTAGTC
* * * * *
99329 ACATTTAATCACATTTAGTCACATTTAATCACATTGGTCACATGAATATTTTAACATTTATCACG
1 ACATTTAATCACATTTAATCACATATAATCACATTAGTCACATGAATATTTCAACATTTATCACA
99394 TCACATATTAATCACATTTAGTC
66 TCACATATTAATCACATTTAGTC
*
99417 ACATTTAACCACAT
1 ACATTTAATCACAT
99431 GAATATTTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 93 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (88 bp):
ACATTTAATCACATTTAATCACATATAATCACATTAGTCACATGAATATTTCAACATTTATCACA
TCACATATTAATCACATTTAGTC
Found at i:99447 original size:59 final size:58
Alignment explanation
Indices: 99336--99547 Score: 201
Period size: 59 Copynumber: 3.5 Consensus size: 58
99326 GTCACATTTA
* * ** *
99336 ATCACAT-TTAGTCACATTTAATCACATTGGTCACATGAATATTTTAACATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATTAATCACATGAATATTTCAACATTTATCAC
* * ** *
99393 GTCACATATTAATCACATTTAGTCACATTTAACCACATGAATATTTCAGTATTTATCGC
1 ATCACATATTAATCACATTTAGTCACA-TTAATCACATGAATATTTCAACATTTATCAC
99452 ATCACATATTAATCACATTTAGTCACAATTAATCACACTGGTCACATGAATATTCCAACATTTAT
1 ATCACATATTAATCACATTTAGTCAC-ATTAATCACA-T-G--A-AT--AT-TT-CAACATTTAT
99517 CAC
56 CAC
* * *
99520 ATTAGATATTAATCACATTTAATCACAT
1 ATCACATATTAATCACATTTAGTCACAT
99548 GAATATTTTA
Statistics
Matches: 125, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
57 6 0.05
58 17 0.14
59 57 0.46
60 2 0.02
61 1 0.01
63 1 0.01
64 2 0.02
66 2 0.02
67 4 0.03
68 33 0.26
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (58 bp):
ATCACATATTAATCACATTTAGTCACATTAATCACATGAATATTTCAACATTTATCAC
Found at i:99468 original size:11 final size:11
Alignment explanation
Indices: 99452--99488 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
99442 TATTTATCGC
99452 ATCACATATTA
1 ATCACATATTA
99463 ATCACAT-TTA
1 ATCACATATTA
*
99473 GTCACA-ATTA
1 ATCACATATTA
99483 ATCACA
1 ATCACA
99489 CTGGTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.32
Consensus pattern (11 bp):
ATCACATATTA
Found at i:99606 original size:23 final size:23
Alignment explanation
Indices: 99580--99645 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
99570 TCATATTAAC
*
99580 ATTTAAGCATAAATCACAATAAT
1 ATTTAAACATAAATCACAATAAT
* * *
99603 ATTTAAATATAAATTACATTAAT
1 ATTTAAACATAAATCACAATAAT
99626 ATTTAACACATATAATCACA
1 ATTTAA-ACATA-AATCACA
99646 GTCAAACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 25 0.71
24 4 0.11
25 6 0.17
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTTAAACATAAATCACAATAAT
Found at i:102624 original size:10 final size:10
Alignment explanation
Indices: 102597--102644 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
102587 CATTTATCAC
*
102597 ATCACATATGA
1 ATCACAT-TTA
102608 ATCACATTTA
1 ATCACATTTA
*
102618 GTCACATTTA
1 ATCACATTTA
102628 ATCACATTTA
1 ATCACATTTA
102638 ATCACAT
1 ATCACAT
102645 GAATATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 27 0.79
11 7 0.21
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (10 bp):
ATCACATTTA
Found at i:102664 original size:23 final size:23
Alignment explanation
Indices: 102637--102774 Score: 188
Period size: 23 Copynumber: 6.0 Consensus size: 23
102627 AATCACATTT
*
102637 AATCACATGAATATTTCAA-CATA
1 AATCACATTAATATTT-AAGCATA
*
102660 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* * *
102683 AATCATATTAACATTTAAGTATA
1 AATCACATTAATATTTAAGCATA
*
102706 AATCACATTAATATTTAAGCACA
1 AATCACATTAATATTTAAGCATA
*
102729 AATCACATTAATATTTAAACATA
1 AATCACATTAATATTTAAGCATA
*
102752 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
102775 TAATGCATGA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
22 2 0.02
23 100 0.98
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:102739 original size:69 final size:69
Alignment explanation
Indices: 102637--102770 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 69
102627 AATCACATTT
* * *
102637 AATCACATGAATATTTCAACATAAATCATATTAATATTTAAGCATAAATCATATTAACATTTAAG
1 AATCACATGAATATTTCAACACAAATCACATTAATATTTAAACATAAATCATATTAACATTTAAG
102702 TATA
66 TATA
* *
102706 AATCACATTAATATTT-AAGCACAAATCACATTAATATTTAAACATAAATCATATTAATATTTAA
1 AATCACATGAATATTTCAA-CACAAATCACATTAATATTTAAACATAAATCATATTAACATTTAA
102770 G
65 G
102771 CATATAATGC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 2 0.03
69 57 0.97
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (69 bp):
AATCACATGAATATTTCAACACAAATCACATTAATATTTAAACATAAATCATATTAACATTTAAG
TATA
Found at i:103720 original size:19 final size:19
Alignment explanation
Indices: 103696--103792 Score: 140
Period size: 19 Copynumber: 5.1 Consensus size: 19
103686 AAGACTCTGA
* *
103696 AGCGATACTGGCTTGTAAG
1 AGCGATACTAGCTCGTAAG
*
103715 AGCGATACTAGCTTGTAAG
1 AGCGATACTAGCTCGTAAG
103734 AGCGATACTAGCTCGTAAG
1 AGCGATACTAGCTCGTAAG
103753 AGCGATACTAGCTCGTAAG
1 AGCGATACTAGCTCGTAAG
* * *
103772 AGCGATAGTGGCTCATAAG
1 AGCGATACTAGCTCGTAAG
103791 AG
1 AG
103793 TTAAAAATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.23
Consensus pattern (19 bp):
AGCGATACTAGCTCGTAAG
Found at i:103847 original size:35 final size:35
Alignment explanation
Indices: 103797--103876 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
103787 TAAGAGTTAA
* * *
103797 AAATTACTGGGAATCTTGAAGAGCTCGTATGAGTT
1 AAATTATTGGAAATCTTGAAGAACTCGTATGAGTT
103832 AAATTATTGGAAATCTTGAAGAACTCGTATGAGTT
1 AAATTATTGGAAATCTTGAAGAACTCGTATGAGTT
*
103867 AAATCATTGG
1 AAATTATTGG
103877 GAGACTAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (35 bp):
AAATTATTGGAAATCTTGAAGAACTCGTATGAGTT
Found at i:103888 original size:35 final size:35
Alignment explanation
Indices: 103808--103889 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
103798 AATTACTGGG
* * *
103808 AATCTTGAAGAGCTCGTATGAGTTAAATTATTGGA
1 AATCTAGAAGAACTCGTATGAGTTAAATCATTGGA
*
103843 AATCTTGAAGAACTCGTATGAGTTAAATCATTGGGA
1 AATCTAGAAGAACTCGTATGAGTTAAATCATT-GGA
*
103879 GA-CTAGAAGAA
1 AATCTAGAAGAA
103890 ATCTACTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 38 0.90
36 4 0.10
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (35 bp):
AATCTAGAAGAACTCGTATGAGTTAAATCATTGGA
Found at i:106088 original size:22 final size:23
Alignment explanation
Indices: 106046--106089 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
106036 AATTTGATTT
*
106046 ACTTTTAGTTGCACTGACAATTA
1 ACTTTTAGTTACACTGACAATTA
*
106069 ACTTTTA-TTACATTGACAATT
1 ACTTTTAGTTACACTGACAATT
106090 TTAACAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (23 bp):
ACTTTTAGTTACACTGACAATTA
Found at i:115080 original size:13 final size:13
Alignment explanation
Indices: 115064--115113 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
115054 CTTGAAAAAG
115064 AGAAAAAAAAATA
1 AGAAAAAAAAATA
* *
115077 AGAAAAATAAA-G
1 AGAAAAAAAAATA
* *
115089 AGAAAAGAAAAGA
1 AGAAAAAAAAATA
115102 AGAAAAAAAAAT
1 AGAAAAAAAAAT
115114 TATTGCTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AGAAAAAAAAATA
Found at i:115089 original size:25 final size:25
Alignment explanation
Indices: 115060--115108 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
115050 GTCACTTGAA
*
115060 AAAGAGAAAAAAAAATAAGAAAAAT
1 AAAGAGAAAAAAAAAGAAGAAAAAT
*
115085 AAAGAGAAAAGAAAAGAAGAAAAA
1 AAAGAGAAAAAAAAAGAAGAAAAA
115109 AAAATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (25 bp):
AAAGAGAAAAAAAAAGAAGAAAAAT
Found at i:118201 original size:24 final size:23
Alignment explanation
Indices: 118174--118218 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
118164 GAACTCTGAC
118174 AAATT-CAAATAATTTTGAATTTTT
1 AAATTACAAAT-ATTTT-AATTTTT
*
118198 AAATTATAAATATTTTAATTT
1 AAATTACAAATATTTTAATTT
118219 CAAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTACAAATATTTTAATTTTT
Found at i:118844 original size:32 final size:32
Alignment explanation
Indices: 118753--118888 Score: 133
Period size: 32 Copynumber: 4.5 Consensus size: 32
118743 AAGATAACAG
* * *
118753 TTGGTACCTAAACTTGATA-CTTTTTACTAAT
1 TTGGTACCTAAACTTGACATTTTTTTTCTAAT
* *
118784 TTGGTACCTAAAC-T----TTTTTTGTCCAAT
1 TTGGTACCTAAACTTGACATTTTTTTTCTAAT
*
118811 TTGGTACCCAAACTTGACATTTTTTTTCTAAT
1 TTGGTACCTAAACTTGACATTTTTTTTCTAAT
* * *
118843 TTGGTACCTAAACTTGGCAATTTTTTT-TAAG
1 TTGGTACCTAAACTTGACATTTTTTTTCTAAT
*
118874 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
118889 TTTGAGGTCT
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
27 20 0.23
28 1 0.01
30 1 0.01
31 30 0.34
32 35 0.40
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (32 bp):
TTGGTACCTAAACTTGACATTTTTTTTCTAAT
Found at i:119155 original size:31 final size:31
Alignment explanation
Indices: 119118--119285 Score: 104
Period size: 31 Copynumber: 5.5 Consensus size: 31
119108 AAAAAAGCTT
*
119118 AGGTACCAAACTAAGAAAAAATGTCAAGTTC
1 AGGTACCAAATTAAGAAAAAATGTCAAGTTC
* *
119149 AGGTACCAAATT-GGATCCAAAAA----AAGTTT
1 AGGTACCAAATTAAGA---AAAAATGTCAAGTTC
* *
119178 AGGTACTAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAAGAAAAAATGTCAAGTTC
* *
119209 AAGTACCAAATTAAGTAAAAAA----AA-TTT
1 AGGTACCAAATTAAG-AAAAAATGTCAAGTTC
* *
119236 AGGTACCAAATTAAAAAAAAAAGTATCAAGTTC
1 AGGTACCAAATT-AAGAAAAAA-TGTCAAGTTC
* *
119269 AAGTATCAATATTAAGA
1 AGGTACCAA-ATTAAGA
119286 CTTTATTATA
Statistics
Matches: 103, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
27 23 0.22
28 4 0.04
29 16 0.16
30 4 0.04
31 29 0.28
32 7 0.07
33 17 0.17
34 3 0.03
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (31 bp):
AGGTACCAAATTAAGAAAAAATGTCAAGTTC
Found at i:119182 original size:60 final size:58
Alignment explanation
Indices: 119107--119284 Score: 205
Period size: 60 Copynumber: 3.0 Consensus size: 58
119097 GAATCTTGAG
* * * *
119107 AAAAAAAGCTTAGGTACCAAACTAAGAAAAAATGTCAAGTTCAGGTACCAAATT-GGAT
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTAAG-T
* *
119165 CCAAAAAAAGTTTAGGTACTAAATTAAGAAAAAGTGTCAAGTTCAAGTACCAAATTAAGT
1 --AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTAAGT
* * * *
119225 AAAAAAAATTTAGGTACCAAATTAAAAAAAAAAGTATCAAGTTCAAGTATCAATATTAAG
1 AAAAAAAGTTTAGGTACCAAATT-AAGAAAAAA-TGTCAAGTTCAAGTACCAA-ATTAAG
119285 ACTTTATTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 21 0.21
59 7 0.07
60 67 0.66
61 7 0.07
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTAAGT
Found at i:119335 original size:21 final size:21
Alignment explanation
Indices: 119287--119342 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
119277 ATATTAAGAC
*
119287 TTTATTATAATATATAATATA
1 TTTATAATAATATATAATATA
* * * *
119308 ATAATAATTATATATATTATA
1 TTTATAATAATATATAATATA
119329 TTTATAA-AATATAT
1 TTTATAATAATATAT
119343 TATTTCATCA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTATAATAATATATAATATA
Found at i:119762 original size:12 final size:11
Alignment explanation
Indices: 119737--119773 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
119727 CATTTGAAAG
119737 TAATATATATA
1 TAATATATATA
119748 T-ATATAT-TA
1 TAATATATATA
119757 TAATATATAATA
1 TAATATAT-ATA
119769 TAATA
1 TAATA
119774 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 12 0.52
11 1 0.04
12 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATATATATA
Found at i:119777 original size:18 final size:20
Alignment explanation
Indices: 119737--119778 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
119727 CATTTGAAAG
*
119737 TAATATATATATATATATTA
1 TAATATATATATATATATAA
119757 TAATATATA-ATATA-ATAA
1 TAATATATATATATATATAA
119775 TAAT
1 TAAT
119779 TAAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATATATATATATATAA
Found at i:119876 original size:148 final size:149
Alignment explanation
Indices: 119602--120048 Score: 371
Period size: 166 Copynumber: 2.9 Consensus size: 149
119592 ATATTTTTTA
* * * *
119602 ATTATAATCTATAATATAATAATAGTTATATACAATAGCAATACATTATATATTACTTAATATTA
1 ATTATAATATATAATATAATAATAATTAAATACAAAAGCAATACATTATATATTA--TAATATTA
* * * * *
119667 TATATTATTGTTTGTTATTATACTATTTGAAATGTGCTCGAAGTTTCTTTGCTTTTCGTACATTT
64 TATATTATTGTTTATTATTATACTAGTTGAAATATGCTCGAAGTTTCTATACTTTTCGTACATTT
119732 GAAAGTAATATATATATATAT
129 GAAAGTAATATATATATATAT
* ** ** * *
119753 ATTATAATATATAATATAATAATAATTAAATAGAAAAGTTATATGTTATATATTA-ATTATTATG
1 ATTATAATATATAATATAATAATAATTAAATACAAAAGCAATACATTATATATTATAATATTATA
* * * *
119817 TATTATTGTTTATTATTATATTAGTTGAAATATGCTCTAA-TTTCCTATATTTTTTGTACATTTG
66 TATTATTGTTTATTATTATACTAGTTGAAATATGCTCGAAGTTT-CTATACTTTTCGTACATTTG
* * *
119881 AAAGTTAATTTTTCTACTATAT
130 AAAG-TAATATATATA-TATAT
* *
119903 -TATATAATGTTATATCATATCATATAATAAATTAATAGTTATATATAA-CAGAAGTACATTATA
1 AT-TATAA---TATATAATAT-A-ATAAT-AATTAA-A--TACA-A-AAGC--AA-TACATTATA
* * * * * *
119966 TATTACATATTATTATATATCATTGTTTATTATTATACTAGTTGAAATATGTTCTAAATCTCTAT
51 TATT--ATAATATTATATATTATTGTTTATTATTATACTAGTTGAAATATGCTCGAAGTTTCTAT
* *
120031 ACTTTTCATACATCTGAA
114 ACTTTTCGTACATTTGAA
120049 CGTTAATCCT
Statistics
Matches: 236, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
147 3 0.01
148 62 0.26
149 9 0.04
150 10 0.04
151 46 0.19
153 9 0.04
154 1 0.00
155 5 0.02
156 6 0.03
157 1 0.00
159 3 0.01
160 1 0.00
161 2 0.01
162 1 0.00
163 11 0.05
165 1 0.00
166 63 0.27
167 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (149 bp):
ATTATAATATATAATATAATAATAATTAAATACAAAAGCAATACATTATATATTATAATATTATA
TATTATTGTTTATTATTATACTAGTTGAAATATGCTCGAAGTTTCTATACTTTTCGTACATTTGA
AAGTAATATATATATATAT
Found at i:120218 original size:25 final size:25
Alignment explanation
Indices: 120181--120228 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
120171 ATCTATATTA
*
120181 TAATAATAGTTATATATAATATTTT
1 TAATAATAATTATATATAATATTTT
*
120206 TAATAATAATTATATATTATATT
1 TAATAATAATTATATATAATATT
120229 ATTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATAATAATTATATATAATATTTT
Found at i:120229 original size:12 final size:12
Alignment explanation
Indices: 120175--120230 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
120165 ATTATAATCT
120175 ATATTATA-ATA
1 ATATTATATATA
120186 ATAGTTATATATA
1 ATA-TTATATATA
*
120199 ATATT-TTTAATA
1 ATATTATAT-ATA
*
120211 ATAATTATATATT
1 AT-ATTATATATA
120224 ATATTAT
1 ATATTAT
120231 TATTTTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.14
12 17 0.46
13 13 0.35
14 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATATTATATATA
Found at i:120487 original size:16 final size:16
Alignment explanation
Indices: 120466--120504 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
120456 AAAAAATATC
120466 ATTAATAATTTTTCCT
1 ATTAATAATTTTTCCT
120482 ATTAATAATTTTTCCT
1 ATTAATAATTTTTCCT
*
120498 ATAAATA
1 ATTAATA
120505 TGAAATGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATAATTTTTCCT
Found at i:138083 original size:21 final size:21
Alignment explanation
Indices: 138045--138084 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
138035 TCTTTATTTT
*
138045 TACGTATTTCGACTTGTCCTG
1 TACGTATTTCGACGTGTCCTG
* *
138066 TACGTATTTGGCCGTGTCC
1 TACGTATTTCGACGTGTCC
138085 GACGAGTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (21 bp):
TACGTATTTCGACGTGTCCTG
Found at i:139293 original size:17 final size:17
Alignment explanation
Indices: 139271--139307 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
139261 ATTTTTTTAT
*
139271 TAAAAAAATAAAAATAC
1 TAAAAAAAAAAAAATAC
*
139288 TAAAAAAAAAAAAATGC
1 TAAAAAAAAAAAAATAC
139305 TAA
1 TAA
139308 TAACATGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
TAAAAAAAAAAAAATAC
Found at i:153395 original size:26 final size:26
Alignment explanation
Indices: 153366--153447 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
153356 ATCATCGAAC
153366 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* * * * **
153392 CTCACAATGACATATA-G-TT-ATCGGA
1 CTCATAAT-CCGTAAAGGATTCAT-ATA
153417 CCTCATAATCCGTAAAGGATTCATATA
1 -CTCATAATCCGTAAAGGATTCATATA
153444 CTCA
1 CTCA
153448 CGATGACACA
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
24 2 0.05
25 7 0.18
26 20 0.53
27 7 0.18
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:153471 original size:52 final size:52
Alignment explanation
Indices: 153136--153471 Score: 437
Period size: 52 Copynumber: 6.5 Consensus size: 52
153126 CATTTAATAT
* * * * * * *
153136 TCACGATAACACAAAATCATCGAACCTTA-AATCCGAAAAAGGATTCATATGC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCG-TAAAGGATTCATATAC
* * *
153188 TCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGAGTCAAATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* * * *
153240 TCACGATGACACATAATCATCGAACCTCATAATCTGTAAAGAATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* *
153292 TCACGATGAC-CATAGTCATCGGATCTCATAATCCGTAAAAGATT--TATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* *
153341 TCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* * *
153393 TCACAATGACATATAGTTATCGGACCTCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
*
153445 TCACGATGACACATAGTCATCAGACCT
1 TCACGATGACACATAGTCATCGGACCT
153472 TTTCCGTTTA
Statistics
Matches: 246, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
49 15 0.06
50 30 0.12
51 28 0.11
52 168 0.68
53 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
Found at i:154582 original size:23 final size:23
Alignment explanation
Indices: 154556--154627 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
154546 ATAGAAATTA
154556 ATCACAAAATTAAATAATTCCAC
1 ATCACAAAATTAAATAATTCCAC
** *
154579 ATCA-ATTATATAATAGAAATT--A-
1 ATCACAAAAT-TAA-A-TAATTCCAC
154601 ATCACAAAATTAAATAATTCCAC
1 ATCACAAAATTAAATAATTCCAC
154624 ATCA
1 ATCA
154628 TTTCTATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 11 0.31
23 15 0.42
24 1 0.03
25 4 0.11
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (23 bp):
ATCACAAAATTAAATAATTCCAC
Found at i:154592 original size:45 final size:45
Alignment explanation
Indices: 154541--154627 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
154531 ATTAATAAGA
154541 ATATAATAGAAATTAATCACAAAATTAAATAATTCCACATCAATT
1 ATATAATAGAAATTAATCACAAAATTAAATAATTCCACATCAATT
154586 ATATAATAGAAATTAATCACAAAATTAAATAATTCCACATCA
1 ATATAATAGAAATTAATCACAAAATTAAATAATTCCACATCA
154628 TTTCTATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (45 bp):
ATATAATAGAAATTAATCACAAAATTAAATAATTCCACATCAATT
Found at i:158711 original size:14 final size:14
Alignment explanation
Indices: 158682--158726 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
158672 CACAAACAAT
158682 TATACGAATGAATAAA
1 TATACGAA--AATAAA
158698 TATACGAAAATAAA
1 TATACGAAAATAAA
*
158712 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
158727 ATATGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:158810 original size:21 final size:19
Alignment explanation
Indices: 158773--158811 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
158763 AGATCAATTC
158773 AAAATAATAATAAAAAGTT
1 AAAATAATAATAAAAAGTT
*
158792 AAAATTATATATACAAAAGT
1 AAAATAATA-ATA-AAAAGT
158812 CGAAGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATAATAATAAAAAGTT
Found at i:158960 original size:56 final size:54
Alignment explanation
Indices: 158835--159189 Score: 248
Period size: 56 Copynumber: 6.2 Consensus size: 54
158825 AATGGGGTCG
* * * * * * *
158835 AAAAT-TAAGTTTCGGAGAGTTCAGGGCTAAAACGTAATTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTAGGA-AGTTCAAGG-TAAAATGTGATTTTTGAAAGTTTGA-GG-A
158892 AAAATGTAATTTTAGGAAGTTCAAGGTAAATATGTGATTTTTGAGAAGTTTGAGGA
1 AAAATGTAATTTTAGGAAGTTCAAGGTAAA-ATGTGATTTTTGA-AAGTTTGAGGA
* * * * *
158948 AAAATGTCATTTTTGGAAGTTCAGGGGTAAAAATGTGATTTTTGAAAGTTTGGGGG
1 AAAATGTAATTTTAGGAAGTTCA-AGGT-AAAATGTGATTTTTGAAAGTTTGAGGA
* * *
159004 AAAATGTAAATTTTAAGAAGTTTAAGGGTAAAATTGTGATTTTT-AAAGTTCGAGGGA
1 AAAATGT-AATTTTAGGAAGTTCAA-GGTAAAA-TGTGATTTTTGAAAGTTTGA-GGA
* * * * * *
159061 AAAATGTAATTTTTGGAAGTTTAGGGTTAAAATGTAATTTTTGGAAGTTTAAGGGTTA
1 AAAATGTAATTTTAGGAAGTTCAAGG-TAAAATGTGATTTTTGAAAGTTTGA-GG--A
* ** * * * *
159119 AAAA-ATAATTTTTAAAAAGTTTAATGGTTAAAATGTAATTTTTAGAGAGTTTGAGGTC
1 AAAATGTAA-TTTTAGGAAGTTCAA-GG-TAAAATGTGATTTTT-GAAAGTTTGAGG-A
159177 AAAATGTAATTTT
1 AAAATGTAATTTT
159190 TTGAAAGTTT
Statistics
Matches: 244, Mismatches: 37, Indels: 33
0.78 0.12 0.11
Matches are distributed among these distances:
55 11 0.05
56 81 0.33
57 78 0.32
58 44 0.18
59 23 0.09
60 7 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (54 bp):
AAAATGTAATTTTAGGAAGTTCAAGGTAAAATGTGATTTTTGAAAGTTTGAGGA
Found at i:159200 original size:29 final size:28
Alignment explanation
Indices: 158863--159203 Score: 242
Period size: 29 Copynumber: 11.9 Consensus size: 28
158853 GTTCAGGGCT
* * *
158863 AAAACGTAATTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTGAAAGTTTGA-GGTA
* * **
158892 AAAATGTAATTTTAGGAAGTTCAAGGTA
1 AAAATGTAATTTTTGAAAGTTTGAGGTA
* *
158920 AATATGTGATTTTTGAGAAGTTTGAGG-A
1 AAAATGTAATTTTTGA-AAGTTTGAGGTA
* * * *
158948 AAAATGTCATTTTTGGAAGTTCAGGGGTA
1 AAAATGTAATTTTTGAAAGTT-TGAGGTA
* **
158977 AAAATGTGATTTTTGAAAGTTTG-GGGG
1 AAAATGTAATTTTTGAAAGTTTGAGGTA
* * *
159004 AAAATGTAAATTTTAAGAAGTTTAAGGGTA
1 AAAATGTAATTTTTGA-AAGTTTGA-GGTA
* * * *
159034 AAATTGTGATTTTT-AAAGTTCGAGGGA
1 AAAATGTAATTTTTGAAAGTTTGAGGTA
* *
159061 AAAATGTAATTTTTGGAAGTTT-AGGGTT
1 AAAATGTAATTTTTGAAAGTTTGA-GGTA
* *
159089 AAAATGTAATTTTTGGAAGTTTAAGGGTTA
1 AAAATGTAATTTTTGAAAGTTTGA-GG-TA
* * * *
159119 AAAA-ATAATTTTTAAAAAGTTTAATGGTT
1 AAAATGTAATTTTT-GAAAGTTTGA-GGTA
* *
159148 AAAATGTAATTTTTAGAGAGTTTGAGGTC
1 AAAATGTAATTTTT-GAAAGTTTGAGGTA
159177 AAAATGTAATTTTTTGAAAGTTTGAGG
1 AAAATGTAA-TTTTTGAAAGTTTGAGG
159204 ACTACATAGA
Statistics
Matches: 249, Mismatches: 50, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
27 36 0.14
28 75 0.30
29 89 0.36
30 49 0.20
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAGTTTGAGGTA
Found at i:159732 original size:10 final size:9
Alignment explanation
Indices: 159712--159745 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
159702 TCAAAAAATC
159712 CTCTCTTTT
1 CTCTCTTTT
159721 CTCTCTTTT
1 CTCTCTTTT
159730 -TCTCTTTT
1 CTCTCTTTT
159738 CTCT-TTTT
1 CTCTCTTTT
159746 TGAGTGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
CTCTCTTTT
Found at i:159735 original size:17 final size:16
Alignment explanation
Indices: 159713--159746 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
159703 CAAAAAATCC
159713 TCTCTTTTCTCTCTTTT
1 TCTCTTTTCTCT-TTTT
159730 TCTCTTTTCTCTTTTT
1 TCTCTTTTCTCTTTTT
159746 T
1 T
159747 GAGTGAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTCTTTTCTCTTTTT
Found at i:160654 original size:52 final size:52
Alignment explanation
Indices: 160598--161051 Score: 685
Period size: 52 Copynumber: 8.7 Consensus size: 52
160588 TCCAAAAAAA
** * *
160598 GATTCATATGTTCACTATGACACATAGTCATCGGACC-CAATAATCCATAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTC-ATAATCCGTAAAG
*
160650 GATTCATATACTCACGATGACACATAATCATCGGACCTCATAATCCGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
*
160702 GATTCATATACTCACGATGACACATAATCATCGGACCTCATAATCCGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
* **
160754 GATTCACATACTCACGATGACACATAGTCATCAAACCTCATAATCCGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
*
160806 GATTCATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
* ** * *
160858 GATTCATATACTCACGATGACATATAGTCATCAAATCTCATAATCCGTAAAT
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
* * * **
160910 GTTTCATATACTCATGATGACACATAGTCACCGGACCTCATAATTTGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
* *
160962 GATTCATATACTCATGATGACACATAGTCATCGGAACTCATAATCCGTAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
*
161014 GATTCATATACTCACGATGACACATAGTCATCGAACCT
1 GATTCATATACTCACGATGACACATAGTCATCGGACCT
161052 TTTCCATTCA
Statistics
Matches: 368, Mismatches: 33, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
52 367 1.00
53 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (52 bp):
GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG
Found at i:164797 original size:24 final size:23
Alignment explanation
Indices: 164750--164798 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
164740 ATCGTTGGAT
* * *
164750 AAAAAAAGTGACCGTTGGATTCA
1 AAAAAAAATGACCATTGGAATCA
164773 AAAAAAAATGACCATTGGACATCA
1 AAAAAAAATGACCATTGGA-ATCA
164797 AA
1 AA
164799 TTTTGGGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAAAAAATGACCATTGGAATCA
Found at i:165197 original size:109 final size:108
Alignment explanation
Indices: 165073--165322 Score: 330
Period size: 109 Copynumber: 2.3 Consensus size: 108
165063 AACGTTGCCT
* * *
165073 TTTTCCTTTTTATCTCTGTTTTTAGTTTTAGATATATGCTTCTTTTTACTT-TAATTTTCAATGG
1 TTTTCCTTTTCATCTCTGTTTTTAGTTTCAGATATATGCTTCTTTTTAATTCT-ATTTTCAATGG
* * * *
165137 GTTTTTGTCAGGGTTTTTGGTTTCCAGATTTAGATATCCTTTATC
65 G-TTTTGTCAAGGTTTTTGGTTTCCAAACTTAGAGATCCTTTATC
*
165182 TTTTCATTTTCATCTCTGTTTTTAGTTTCAGATATATGCTTCTTTTTAATTCTATTTTCAATGGG
1 TTTTCCTTTTCATCTCTGTTTTTAGTTTCAGATATATGCTTCTTTTTAATTCTATTTTCAATGGG
* ** *
165247 TTTTGTCAAGTTTTTTGGTTTTTAAACTTAGAGATCCTTTGTC
66 TTTTGTCAAGGTTTTTGGTTTCCAAACTTAGAGATCCTTTATC
*
165290 ----CCTCTTCATCTCTGTTTTTAGTTTCAGATATAT
1 TTTTCCTTTTCATCTCTGTTTTTAGTTTCAGATATAT
165323 CCTCATTTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
104 31 0.25
108 35 0.28
109 59 0.47
110 1 0.01
ACGTcount: A:0.18, C:0.14, G:0.13, T:0.56
Consensus pattern (108 bp):
TTTTCCTTTTCATCTCTGTTTTTAGTTTCAGATATATGCTTCTTTTTAATTCTATTTTCAATGGG
TTTTGTCAAGGTTTTTGGTTTCCAAACTTAGAGATCCTTTATC
Found at i:167029 original size:21 final size:21
Alignment explanation
Indices: 166978--167031 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
166968 GGTTGGAGTT
* *
166978 TAGGGTTCGGGTTTAGGGCTT
1 TAGGGTTCGGGTCTAGGGCTG
*
166999 TGGGGTTCGGGTCTAGGG-TG
1 TAGGGTTCGGGTCTAGGGCTG
167019 TAGGGTGTCGGGT
1 TAGGGT-TCGGGT
167032 GTGGAACCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.07, C:0.09, G:0.50, T:0.33
Consensus pattern (21 bp):
TAGGGTTCGGGTCTAGGGCTG
Found at i:168097 original size:21 final size:21
Alignment explanation
Indices: 168063--168107 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
168053 AGGTAGCCTT
**
168063 AAAGTGACTGTTGGATAAAAA
1 AAAGTGACAATTGGATAAAAA
* *
168084 AAAGTGACAATTGGTTTAAAA
1 AAAGTGACAATTGGATAAAAA
168105 AAA
1 AAA
168108 TAAAAAGTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.24
Consensus pattern (21 bp):
AAAGTGACAATTGGATAAAAA
Found at i:168487 original size:109 final size:108
Alignment explanation
Indices: 168355--168633 Score: 274
Period size: 109 Copynumber: 2.6 Consensus size: 108
168345 AATGTTGCCT
* * *
168355 TTTTCCTTTCCATCTATGTTTTTAGTTTTAGATATATGCTTCTTTTTACTTTAATTTTCAATGGG
1 TTTTCCTTTTCATCTATGATTTTAGTTTCAGATATATGCTTCTTTTTA-TTTAATTTTCAATGGG
*
168420 TTTTTGT-AATGGTTTTTAGTTTTCAGATTTAAAGATCCTTTGTC
65 TTTTTGTCAA-GGTTTTTAGTTTTCAAATTTAAAGATCCTTTGTC
* * * * * *
168464 TTTTCATTTTCATCTCTGATTTTAGTTTCAGATATATGTTTCGTTTTAATTCT-ATTTTCAGTGA
1 TTTTCCTTTTCATCTATGATTTTAGTTTCAGATATATGCTTC-TTTTTATT-TAATTTTCAATGG
* * * *
168528 G--CTTGTCAAGGTTTTTGGTTTTTAAATTTAGAGATCCTTTGTC
64 GTTTTTGTCAAGGTTTTTAGTTTTCAAATTTAAAGATCCTTTGTC
* * *
168571 ----CCTCTTCATCTTTGATTTTAGTTTCATATATAT-C--CTTTTTATTTGAATTTTTCAATGG
1 TTTTCCTTTTCATCTATGATTTTAGTTTCAGATATATGCTTCTTTTTATTT-AA-TTTTCAATGG
168629 GTTTT
64 GTTTT
168634 CGTTCGCATT
Statistics
Matches: 139, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
98 1 0.01
99 7 0.05
100 2 0.01
101 9 0.06
103 30 0.22
107 34 0.24
108 2 0.01
109 48 0.35
110 6 0.04
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (108 bp):
TTTTCCTTTTCATCTATGATTTTAGTTTCAGATATATGCTTCTTTTTATTTAATTTTCAATGGGT
TTTTGTCAAGGTTTTTAGTTTTCAAATTTAAAGATCCTTTGTC
Found at i:168922 original size:21 final size:22
Alignment explanation
Indices: 168885--168926 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
168875 TCGTTTCCGC
168885 TATTTTTGGTTTGGTTGGGTTT
1 TATTTTTGGTTTGGTTGGGTTT
168907 TATTTTTGGTTT-GTTGGGTT
1 TATTTTTGGTTTGGTTGGGTT
168927 CGATTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.05, C:0.00, G:0.31, T:0.64
Consensus pattern (22 bp):
TATTTTTGGTTTGGTTGGGTTT
Found at i:171578 original size:2 final size:2
Alignment explanation
Indices: 171571--171612 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
171561 TATCACTATG
171571 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
171613 TAGATTTTAC
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):
AT
Found at i:173538 original size:60 final size:59
Alignment explanation
Indices: 173472--173590 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
173462 AAAATTAGAA
*
173472 ATTTTGTATTAATAGGATTTTAGATTGAATTATTAACTTTAAGGAGGGCGTATGAATTAG
1 ATTTTGTATTAATAGGATTTTAGATTGAA-TAATAACTTTAAGGAGGGCGTATGAATTAG
173532 ATTTTGTATTAATAGGATTTTAGATTGAATAATAACTTTAAGGAGGGCGTATGAATTAG
1 ATTTTGTATTAATAGGATTTTAGATTGAATAATAACTTTAAGGAGGGCGTATGAATTAG
173591 GGTCAATTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 29 0.50
60 29 0.50
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.40
Consensus pattern (59 bp):
ATTTTGTATTAATAGGATTTTAGATTGAATAATAACTTTAAGGAGGGCGTATGAATTAG
Found at i:179582 original size:2 final size:2
Alignment explanation
Indices: 179575--179606 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
179565 CTGTTTACAA
179575 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
179607 TAAAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183628 original size:24 final size:23
Alignment explanation
Indices: 183591--183644 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
183581 CAGTCACAGT
*
183591 ATTGCACGAAGTGTTA-TATTTCA
1 ATTGCACGAAGTGTCATTA-TTCA
183614 ATTGCACTGAAGTGTCATTATTCA
1 ATTGCAC-GAAGTGTCATTATTCA
183638 ATTGCAC
1 ATTGCAC
183645 CAAAATGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.25
24 19 0.68
25 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (23 bp):
ATTGCACGAAGTGTCATTATTCA
Found at i:184214 original size:30 final size:30
Alignment explanation
Indices: 184180--184238 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
184170 ATGCTTGGAG
*
184180 AAAACCTTTTCTTCTTTTTTCACTCCTTGA
1 AAAACCTTTTCTTCTGTTTTCACTCCTTGA
*
184210 AAAACTTTTTCTTCTGTTTTCACTCCTTG
1 AAAACCTTTTCTTCTGTTTTCACTCCTTG
184239 GCTACTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.05, T:0.51
Consensus pattern (30 bp):
AAAACCTTTTCTTCTGTTTTCACTCCTTGA
Found at i:188184 original size:87 final size:87
Alignment explanation
Indices: 188068--188228 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
188058 AGCCATTTGA
* * * * *
188068 GAGTCCCTTCTAGACTTTATTGAGCTTTTCCTTGATGTCCCTCATAGACTCTTCAAGAGTGACCA
1 GAGTCCCTCCTAGACTTCATCGAGCTTTTCCTTAATGTCCCACATAGACTCTTCAAGAGTGACCA
188133 CTCCATTTTTCGACCCACTTGG
66 CTCCATTTTTCGACCCACTTGG
* * *
188155 GAGTCCCTCCTCGACTTCATCGAGCTTTTCCTTAATGTCCCACATGGACTCTTTAAGAGTGACCA
1 GAGTCCCTCCTAGACTTCATCGAGCTTTTCCTTAATGTCCCACATAGACTCTTCAAGAGTGACCA
*
188220 CTCGATTTT
66 CTCCATTTT
188229 CCAAAGTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (87 bp):
GAGTCCCTCCTAGACTTCATCGAGCTTTTCCTTAATGTCCCACATAGACTCTTCAAGAGTGACCA
CTCCATTTTTCGACCCACTTGG
Found at i:190355 original size:23 final size:22
Alignment explanation
Indices: 190283--190429 Score: 97
Period size: 23 Copynumber: 6.4 Consensus size: 22
190273 CATTAGCGCG
*
190283 CTCTCTGTTTAGCACGTTT-TGTG
1 CTCTCTG-TTAGCAC-TTTGTGTA
*
190306 CCCTCTGATTAGCACTTTGTG-A
1 CTCTCTG-TTAGCACTTTGTGTA
*
190328 GCTCTCTGATTAGTACTTTGTGTA
1 -CTCTCTG-TTAGCACTTTGTGTA
* * *
190352 CTCTTTGTTTAGCACTGTGTGTG
1 CTCTCTG-TTAGCACTTTGTGTA
190375 CTCTCTGTTGCCCAGCACTTATGTG--
1 CTCTCTGTT----AGCACTT-TGTGTA
*
190400 CTCTCTGTTAGTACTTTG-GTA
1 CTCTCTGTTAGCACTTTGTGTA
190421 CTCTCTGTT
1 CTCTCTGTT
190430 TGTTCCGTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 15 0.15
22 5 0.05
23 58 0.57
24 1 0.01
25 9 0.09
26 6 0.06
27 4 0.04
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (22 bp):
CTCTCTGTTAGCACTTTGTGTA
Found at i:195236 original size:2 final size:2
Alignment explanation
Indices: 195229--195259 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
195219 CATGAGATTC
195229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.