Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 25
Found at i:2911903 original size:25 final size:26
Alignment explanation
Indices: 2911835--2911903 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
2911825 AATCATTAAA
2911835 AATTAAAATTT-TTATTTTAAGAAGT
1 AATTAAAATTTATTATTTTAAGAAGT
**
2911860 AATTTTAATTTATTAATTTTAA-AA-T
1 AATTAAAATTTATT-ATTTTAAGAAGT
2911885 AATTAAAATTTTATTATTT
1 AATTAAAA-TTTATTATTT
2911904 CAATTATTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 20 0.54
26 10 0.27
27 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
AATTAAAATTTATTATTTTAAGAAGT
Found at i:2912647 original size:23 final size:23
Alignment explanation
Indices: 2912595--2912649 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2912585 CCTTTCTATT
** *
2912595 TTCTCTTTTGTTTTGCTCTTTCG
1 TTCTCTTTTACTTTCCTCTTTCG
*
2912618 TTGTCTTTTACTTTCCTCGTTTC-
1 TTCTCTTTTACTTTCCTC-TTTCG
2912641 TTCTCTTTT
1 TTCTCTTTT
2912650 GGGGGTGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.02, C:0.24, G:0.09, T:0.65
Consensus pattern (23 bp):
TTCTCTTTTACTTTCCTCTTTCG
Found at i:2916850 original size:23 final size:23
Alignment explanation
Indices: 2916824--2916867 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2916814 AATATTTATT
2916824 TTTTATAA-AATTATAAAAAATTG
1 TTTTATAAGAATT-TAAAAAATTG
*
2916847 TTTTTTAAGAATTTAAAAAAT
1 TTTTATAAGAATTTAAAAAAT
2916868 ATAAACTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTTATAAGAATTTAAAAAATTG
Found at i:2926396 original size:3 final size:3
Alignment explanation
Indices: 2926368--2926415 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
2926358 CCATCGCTAC
* *
2926368 CTT CTT -TT CTT -AT CTT CTTT CCT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
2926412 CTT C
1 CTT C
2926416 CATTTTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 32 0.84
4 3 0.08
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2930119 original size:27 final size:28
Alignment explanation
Indices: 2930067--2930119 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
2930057 GATAAAAATT
* *
2930067 AAATTATTTAAATTTGTTTTATTAATAA
1 AAATAATTTAAATTTGTTATATTAATAA
2930095 AAATAATTT-AATTT-TTATATATAAT
1 AAATAATTTAAATTTGTTATAT-TAAT
2930120 TTTTAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 5 0.23
27 9 0.41
28 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AAATAATTTAAATTTGTTATATTAATAA
Found at i:2930174 original size:20 final size:20
Alignment explanation
Indices: 2930145--2930184 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2930135 TATGTTCAAA
*
2930145 TTTAAAATTAAATTAAAATT
1 TTTAAAATTAAATAAAAATT
*
2930165 TTTAATATTAAATAAAAATT
1 TTTAAAATTAAATAAAAATT
2930185 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAATTAAATAAAAATT
Found at i:2944142 original size:2 final size:2
Alignment explanation
Indices: 2944135--2944160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2944125 AGCTGTTGCC
2944135 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
2944161 TAATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2953706 original size:21 final size:21
Alignment explanation
Indices: 2953649--2953706 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
2953639 TTATAAGTAA
2953649 ATAAGTTATTTTTATTAAAAAT
1 ATAA-TTATTTTTATTAAAAAT
* ***
2953671 ATTA-TATAAAATATTAAAAAT
1 ATAATTAT-TTTTATTAAAAAT
2953692 ATAATTATTTTTATT
1 ATAATTATTTTTATT
2953707 TTATAGTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 5
0.67 0.21 0.13
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATAATTATTTTTATTAAAAAT
Found at i:2966214 original size:36 final size:35
Alignment explanation
Indices: 2966159--2966241 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 35
2966149 GCATTTATAT
*
2966159 CTAATCTCAAATATGATCCCTTTCATCTAATTATTA
1 CTAATCTCAAATATAATCCCTTTCATCTAA-TATTA
* * *
2966195 CTAATCTCAGATATAATCCCTTTCATTTAATATTG
1 CTAATCTCAAATATAATCCCTTTCATCTAATATTA
2966230 CTAATCTCAAAT
1 CTAATCTCAAAT
2966242 CTCCTGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 15 0.36
36 27 0.64
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.41
Consensus pattern (35 bp):
CTAATCTCAAATATAATCCCTTTCATCTAATATTA
Found at i:2971453 original size:36 final size:36
Alignment explanation
Indices: 2971406--2971474 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
2971396 CAATTTCCTT
2971406 GCTCTTAGATTGGCTACATAATGAATAGTCAAAGTC
1 GCTCTTAGATTGGCTACATAATGAATAGTCAAAGTC
*
2971442 GCTCTTAGATTGGCTACGTAATGAATAGTCAAA
1 GCTCTTAGATTGGCTACATAATGAATAGTCAAA
2971475 TTTAACTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTCTTAGATTGGCTACATAATGAATAGTCAAAGTC
Found at i:2982251 original size:2 final size:2
Alignment explanation
Indices: 2982244--2982269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2982234 GCCTAAAGGG
2982244 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
2982270 CCTAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2989584 original size:2 final size:2
Alignment explanation
Indices: 2989577--2989603 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2989567 GCTTTTCAGA
2989577 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 A
2989604 AACATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2989815 original size:13 final size:13
Alignment explanation
Indices: 2989799--2989823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2989789 AACAAGGGAT
2989799 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
2989812 TTTTCTTTTCTT
1 TTTTCTTTTCTT
2989824 TTCATACAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:2997689 original size:10 final size:10
Alignment explanation
Indices: 2997671--2997716 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
2997661 ATTATTTAAG
*
2997671 TAATAATTTT
1 TAATTATTTT
2997681 TAATTATTTTT
1 TAATTA-TTTT
2997692 TAATATATATTT
1 TAAT-TAT-TTT
2997704 TAATTATTTT
1 TAATTATTTT
2997714 TAA
1 TAA
2997717 AAATAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 11 0.34
11 12 0.38
12 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TAATTATTTT
Found at i:2997693 original size:11 final size:11
Alignment explanation
Indices: 2997677--2997714 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
2997667 TAAGTAATAA
2997677 TTTTTAATTAT
1 TTTTTAATTAT
2997688 TTTTTAATATAT
1 TTTTTAAT-TAT
*
2997700 ATTTTAATTAT
1 TTTTTAATTAT
2997711 TTTT
1 TTTT
2997715 AAAAATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTAATTAT
Found at i:2997693 original size:25 final size:23
Alignment explanation
Indices: 2997671--2997714 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2997661 ATTATTTAAG
2997671 TAATA-AT-TTTTAATTATTTTT
1 TAATATATATTTTAATTATTTTT
2997692 TAATATATATTTTAATTATTTTT
1 TAATATATATTTTAATTATTTTT
2997715 AAAAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TAATATATATTTTAATTATTTTT
Found at i:2997728 original size:25 final size:23
Alignment explanation
Indices: 2997678--2997721 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2997668 AAGTAATAAT
* *
2997678 TTTTAATTATTTTTTAATATATA
1 TTTTAATTATTTTTAAAAATATA
2997701 TTTTAATTATTTTTAAAAATA
1 TTTTAATTATTTTTAAAAATA
2997722 ACTATTTATG
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAATTATTTTTAAAAATATA
Found at i:2999929 original size:2 final size:2
Alignment explanation
Indices: 2999922--2999947 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2999912 CAAACTTCAA
2999922 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
2999948 TTACTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3002169 original size:2 final size:2
Alignment explanation
Indices: 3002162--3002193 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3002152 TATCAAATAC
3002162 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
3002194 TTTGCTTTTA
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:3008818 original size:2 final size:2
Alignment explanation
Indices: 3008811--3008846 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3008801 AAAATTGAGA
*
3008811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3008847 TTTGTCGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3010186 original size:20 final size:20
Alignment explanation
Indices: 3010163--3010225 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
3010153 ATATATATTT
3010163 TTATATATTAATAAATTATA
1 TTATATATTAATAAATTATA
** *
3010183 TTATATAAGAATTAAAATAT-
1 TTATATATTAA-TAAATTATA
**
3010203 TTATATTATTTTTAAATTATA
1 TTATA-TATTAATAAATTATA
3010224 TT
1 TT
3010226 TTAATTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATATATTAATAAATTATA
Found at i:3013337 original size:2 final size:2
Alignment explanation
Indices: 3013330--3013372 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
3013320 ATAAGAACAA
* * *
3013330 AT AT AT AT AT AT AT GT AT AT GT AT AT GT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3013371 AT
1 AT
3013373 GCAGTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3013354 original size:12 final size:12
Alignment explanation
Indices: 3013333--3013367 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3013323 AGAACAAATA
3013333 TATATATATATG
1 TATATATATATG
*
3013345 TATATGTATATG
1 TATATATATATG
3013357 TATATATATAT
1 TATATATATAT
3013368 AATATGCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:3021521 original size:34 final size:34
Alignment explanation
Indices: 3021464--3021528 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
3021454 TATTAAATTT
*
3021464 TTTTATATTTTTATAATTAAATTTAAATAAAAAA
1 TTTTATATTATTATAATTAAATTTAAATAAAAAA
* *
3021498 TTTTGTATTATTAT-ATTATAATTTAATTAAA
1 TTTTATATTATTATAATTA-AATTTAAATAAA
3021529 TTGAATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTTATATTATTATAATTAAATTTAAATAAAAAA
Found at i:3022090 original size:17 final size:18
Alignment explanation
Indices: 3022056--3022092 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3022046 TAAATTTTTA
3022056 AATTTTAAATCATGATTT
1 AATTTTAAATCATGATTT
3022074 AATTTATAAA-CAT-ATTT
1 AATTT-TAAATCATGATTT
3022091 AA
1 AA
3022093 ATGTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTTTAAATCATGATTT
Found at i:3022517 original size:22 final size:25
Alignment explanation
Indices: 3022481--3022528 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
3022471 ATATTTATAA
3022481 TTTAATTATTATATGTAATA-AATT
1 TTTAATTATTATATGTAATATAATT
3022505 TTTAATT-TT-TATGTAATATAATT
1 TTTAATTATTATATGTAATATAATT
3022528 T
1 T
3022529 GAATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 7 0.30
24 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTAATTATTATATGTAATATAATT
Found at i:3028936 original size:24 final size:23
Alignment explanation
Indices: 3028909--3028962 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3028899 AATACAAATT
*
3028909 TTTTTAATGTTAATAATT-TATATA
1 TTTTTAATATT-ATAATTATA-ATA
*
3028933 TTTTATTATATTATAATTATAATA
1 TTTT-TAATATTATAATTATAATA
3028957 TTTTTA
1 TTTTTA
3028963 TTTATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTAATATTATAATTATAATA
Found at i:3028967 original size:26 final size:24
Alignment explanation
Indices: 3028921--3028969 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3028911 TTTAATGTTA
3028921 ATAATTTATATATTTTATTATATT
1 ATAATTTATATATTTTATTATATT
3028945 ATAA-TTATAATATTTTTATTTATAT
1 ATAATTTAT-ATA-TTTTA-TTATAT
3028970 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 7 0.32
25 5 0.23
26 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATAATTTATATATTTTATTATATT
Found at i:3030850 original size:3 final size:3
Alignment explanation
Indices: 3030837--3030866 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3030827 GAAATTTTAA
*
3030837 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3030867 GTTTTGGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3033227 original size:73 final size:73
Alignment explanation
Indices: 3033108--3033254 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
3033098 CCAATTAGAA
3033108 AACAATTTTACAAATAAAATTCCTCTATCAATCCGACTGGAAGAACAGTAATTATTTTTTACAAT
1 AACAATTTTACAAATAAAATTCCTCTATCAATCCGACTGGAAGAACAGTAATTATTTTTTACAAT
3033173 ATATATAT
66 ATATATAT
3033181 AACAATTTTACAAATAAAATTCCTCTATCAATCCGACTGGAAGAACAGTAATTATTTTTTACAAT
1 AACAATTTTACAAATAAAATTCCTCTATCAATCCGACTGGAAGAACAGTAATTATTTTTTACAAT
3033246 ATATATAT
66 ATATATAT
3033254 A
1 A
3033255 TATATATCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (73 bp):
AACAATTTTACAAATAAAATTCCTCTATCAATCCGACTGGAAGAACAGTAATTATTTTTTACAAT
ATATATAT
Found at i:3038220 original size:26 final size:26
Alignment explanation
Indices: 3038184--3038235 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3038174 CTAGTCATAG
3038184 AAATTGTATAAGTTTGCATGAGAAAT
1 AAATTGTATAAGTTTGCATGAGAAAT
3038210 AAATTGTATAAGTTTGCATGAGAAAT
1 AAATTGTATAAGTTTGCATGAGAAAT
3038236 TATCTATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (26 bp):
AAATTGTATAAGTTTGCATGAGAAAT
Found at i:3042553 original size:2 final size:2
Alignment explanation
Indices: 3042546--3042578 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3042536 AGTCAAAGTA
3042546 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
3042579 GAAAGGTTTG
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:3048903 original size:21 final size:21
Alignment explanation
Indices: 3048864--3048903 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3048854 ATATATTTTT
*
3048864 AATTTTTATTTAATTTAATTA
1 AATTTTTATTTAATATAATTA
3048885 AATTTTTATTTTAA-ATAAT
1 AATTTTTA-TTTAATATAAT
3048904 AAAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTATTTAATATAATTA
Found at i:3048984 original size:29 final size:30
Alignment explanation
Indices: 3048936--3049008 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
3048926 TTTATGAATT
*
3048936 AATTAAAAATTAAATATTTATTTAAATATA
1 AATTAAAAATTAAATATTTATGTAAATATA
*
3048966 AATTAAAAA-TAAA-AGTTTATGTAAATGTA
1 AATTAAAAATTAAATA-TTTATGTAAATATA
* *
3048995 AATTATAGATTAAA
1 AATTAAAAATTAAA
3049009 AATTGAGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 23 0.62
30 13 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (30 bp):
AATTAAAAATTAAATATTTATGTAAATATA
Found at i:3054896 original size:14 final size:14
Alignment explanation
Indices: 3054877--3054924 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3054867 ATTTTAAAAA
3054877 ATAATATAAATTAT
1 ATAATATAAATTAT
* *
3054891 ATAATAAAAAATAT
1 ATAATATAAATTAT
3054905 ATAAATATAATATT-T
1 AT-AATATAA-ATTAT
3054920 ATAAT
1 ATAAT
3054925 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 17 0.61
15 9 0.32
16 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATAAATTAT
Found at i:3055530 original size:12 final size:12
Alignment explanation
Indices: 3055505--3055538 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
3055495 AAATTTTATT
3055505 ATAATTAA-AAA
1 ATAATTAATAAA
3055516 ATAATTAATAAA
1 ATAATTAATAAA
3055528 ATAATT-ATAAA
1 ATAATTAATAAA
3055539 TTTCTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATTAATAAA
Found at i:3055744 original size:20 final size:19
Alignment explanation
Indices: 3055686--3055752 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 19
3055676 TAAAAATAAA
3055686 TTTTTATATTATATTATGTAT
1 TTTTTATATT-TATTAT-TAT
*
3055707 TATTATTAAATATTATTATTAT
1 T-TT-TTATAT-TTATTATTAT
*
3055729 TTTTTATATGTTATTAATAT
1 TTTTTATAT-TTATTATTAT
3055749 TTTT
1 TTTT
3055753 AATTTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 18 0.46
21 3 0.08
22 6 0.15
23 11 0.28
24 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTATATTTATTATTAT
Found at i:3056357 original size:15 final size:15
Alignment explanation
Indices: 3056334--3056365 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3056324 AAAATTTTAT
3056334 ATTAATCATATTAAA
1 ATTAATCATATTAAA
*
3056349 ATTATTCATATTAAA
1 ATTAATCATATTAAA
3056364 AT
1 AT
3056366 AAATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATCATATTAAA
Found at i:3057863 original size:45 final size:39
Alignment explanation
Indices: 3057793--3057892 Score: 96
Period size: 45 Copynumber: 2.4 Consensus size: 39
3057783 GAATTTTTAT
3057793 TTAA-AATATTATTATTAAAAAAAATTTATATATTATTAATAAA
1 TTAATAATATTATT-TTAAAAAAAATTT-TA-A-TATTAA-AAA
* *
3057836 TTATATAATATTATTTTAATGATAAATTTTAATATTAAAAA
1 TTA-ATAATATTATTTTAA-AAAAAATTTTAATATTAAAAA
3057877 TTAATAAT-TATATTTT
1 TTAATAATAT-TATTTT
3057893 TCATGCACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
39 1 0.02
40 11 0.22
41 6 0.12
42 6 0.12
43 4 0.08
44 7 0.14
45 16 0.31
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
TTAATAATATTATTTTAAAAAAAATTTTAATATTAAAAA
Found at i:3058544 original size:2 final size:2
Alignment explanation
Indices: 3058537--3058570 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3058527 TATGTCTGTG
*
3058537 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
3058571 TTTTACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3059630 original size:2 final size:2
Alignment explanation
Indices: 3059623--3059662 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3059613 TTAATGCTTC
3059623 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
3059663 TGCTCCGGCT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3061664 original size:27 final size:27
Alignment explanation
Indices: 3061592--3061667 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
3061582 AACAACAAGT
* * *
3061592 CACCATTTTTTACAAATAAAAAGGAAC
1 CACCATTTTTTACAAACACAAAGAAAC
* * *
3061619 TATCATTTTTGACAAACACAAAGAAAC
1 CACCATTTTTTACAAACACAAAGAAAC
*
3061646 CACCATTTTTTATAAACACAAA
1 CACCATTTTTTACAAACACAAA
3061668 CGGTGGCTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (27 bp):
CACCATTTTTTACAAACACAAAGAAAC
Found at i:3063576 original size:21 final size:21
Alignment explanation
Indices: 3063538--3063579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3063528 ATCTGTTGAA
* **
3063538 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
3063559 ACTCCACCTGCTGCGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
3063580 TACTTGTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTCCACCTGCTGCGGAGTAT
Found at i:3066144 original size:27 final size:27
Alignment explanation
Indices: 3066114--3066177 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3066104 ATTTTAACAA
* * *
3066114 AAAAATATTATTATTTTTGATAAGTAT
1 AAAAATATTACTATTTTTGACAAATAT
* *
3066141 AAAAAAATCACTATTTTTGACAAATAT
1 AAAAATATTACTATTTTTGACAAATAT
3066168 AAAAAGTATT
1 AAAAA-TATT
3066178 TTTTATTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (27 bp):
AAAAATATTACTATTTTTGACAAATAT
Found at i:3067480 original size:62 final size:64
Alignment explanation
Indices: 3067377--3067506 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 64
3067367 TTCAGCTGTT
* *
3067377 CTCCATCCAACAGGGTTTTACTGTTTAAAACCTCGTGGCATTGAC-A-TATGTAGCAAGTTTTG
1 CTCCATCCAACAGGGTTTTACCGTTTAAAACCTCATGGCATTGACTACTATGTAGCAAGTTTTG
* * *
3067439 CTCCATCCCACATGGTTTTACCGTTTAAAACCTCATTGCATTGACTTACGTATGTAGCAAGTTTT
1 CTCCATCCAACAGGGTTTTACCGTTTAAAACCTCATGGCATTGAC-TAC-TATGTAGCAAGTTTT
3067504 G
64 G
3067505 CT
1 CT
3067507 GTTGATAGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
62 40 0.68
64 1 0.02
66 18 0.31
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (64 bp):
CTCCATCCAACAGGGTTTTACCGTTTAAAACCTCATGGCATTGACTACTATGTAGCAAGTTTTG
Found at i:3068942 original size:20 final size:20
Alignment explanation
Indices: 3068914--3068971 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3068904 AATAAAAATT
*
3068914 ATTACAAAATTTAAATATAA
1 ATTATAAAATTTAAATATAA
*
3068934 ATTATAAAATAATAAA-ATAA
1 ATTATAAAAT-TTAAATATAA
3068954 ATATATAATAA-TTAAATA
1 AT-TATAA-AATTTAAATA
3068972 CACCTTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 19 0.61
21 10 0.32
22 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTATAAAATTTAAATATAA
Found at i:3068963 original size:19 final size:20
Alignment explanation
Indices: 3068872--3068971 Score: 61
Period size: 19 Copynumber: 5.1 Consensus size: 20
3068862 TTTAATTATT
3068872 TAAATTA-AAAATAATAAAAACA
1 TAAATTATAAAATAAT--AAA-A
3068894 TAAA-TATTAAAAT-A-AAAA
1 TAAATTA-TAAAATAATAAAA
* * *
3068912 T-TATTACAAAAT-TTAAATA
1 TAAATTATAAAATAATAAA-A
3068931 TAAATTATAAAATAATAAAA
1 TAAATTATAAAATAATAAAA
* *
3068951 TAAA-TATATAATAATTAAA
1 TAAATTATAAAATAATAAAA
3068970 TA
1 TA
3068972 CACCTTAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
17 6 0.10
18 7 0.11
19 20 0.32
20 14 0.22
21 6 0.10
22 5 0.08
23 5 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATTATAAAATAATAAAA
Found at i:3080735 original size:15 final size:16
Alignment explanation
Indices: 3080704--3080738 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3080694 CAAGGAGGAA
3080704 AAATTGACTAAACTAC
1 AAATTGACTAAACTAC
*
3080720 AAATTGACT-CACTAC
1 AAATTGACTAAACTAC
3080735 AAAT
1 AAAT
3080739 ATGGCCAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATTGACTAAACTAC
Found at i:3081987 original size:18 final size:17
Alignment explanation
Indices: 3081964--3081999 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
3081954 TTGTAAAAAT
3081964 AAATATTTATTTATTTAA
1 AAATATTTATTT-TTTAA
3081982 AAATATTTATTTTTTAA
1 AAATATTTATTTTTTAA
3081999 A
1 A
3082000 TATCAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTTATTTTTTAA
Found at i:3081992 original size:22 final size:22
Alignment explanation
Indices: 3081951--3081997 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3081941 AAAAATAAAA
3081951 TTATTGTAAAAATAAATATTTAT
1 TTATTGTAAAAATAAATATTT-T
**
3081974 TTATT-TAAAAATATTTATTTT
1 TTATTGTAAAAATAAATATTTT
3081995 TTA
1 TTA
3081998 AATATCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTGTAAAAATAAATATTTT
Found at i:3082262 original size:23 final size:23
Alignment explanation
Indices: 3082226--3082304 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
3082216 AGGTTCAATT
* *
3082226 AATTTGATTAATTAATTATATAA
1 AATTTAATTTATTAATTATATAA
* **
3082249 AATTTTATTTATTAATT-TAATTT
1 AATTTAATTTATTAATTAT-ATAA
3082272 AATTTAATTT-TTAATTATTATATA
1 AATTTAATTTATTAATTA-TATA-A
*
3082296 AATTAAATT
1 AATTTAATT
3082305 ATAAATTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
22 7 0.16
23 28 0.64
24 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
AATTTAATTTATTAATTATATAA
Found at i:3082315 original size:23 final size:23
Alignment explanation
Indices: 3082284--3082332 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
3082274 TTTAATTTTT
3082284 AATTATTATATAAATTAAATTATA
1 AATTATTATATAAATTAAATTA-A
*
3082308 AATT-TTATATTAATTAAATTAA
1 AATTATTATATAAATTAAATTAA
3082330 AAT
1 AAT
3082333 GATTCATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 16 0.67
24 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATTATATAAATTAAATTAA
Found at i:3082325 original size:28 final size:28
Alignment explanation
Indices: 3082232--3082330 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
3082222 AATTAATTTG
*
3082232 ATTAATT-AATTATA-TA-AAATTTTATTT
1 ATTAATTAAATTAAATTATAAATTTTA--T
* * *
3082259 ATTAATTTAATTTAATT-TAATTTTTA-
1 ATTAATTAAATTAAATTATAAATTTTAT
3082285 ATTATTATATAAATTAAATTATAAATTTTAT
1 ATTA--AT-TAAATTAAATTATAAATTTTAT
3082316 ATTAATTAAATTAAA
1 ATTAATTAAATTAAA
3082331 ATGATTCATG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.07
27 7 0.12
28 16 0.28
29 19 0.33
30 8 0.14
31 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTAATTAAATTAAATTATAAATTTTAT
Found at i:3082873 original size:15 final size:17
Alignment explanation
Indices: 3082830--3082881 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 17
3082820 AGTTTGATTT
*
3082830 AATTTAAAATTT--TAA
1 AATTTAAAATTTAATTA
*
3082845 AATTTAAAATTTAATTT
1 AATTTAAAATTTAATTA
3082862 AATTT-AAA-TTAATTA
1 AATTTAAAATTTAATTA
3082877 AATTT
1 AATTT
3082882 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 23 0.72
16 3 0.09
17 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAAATTTAATTA
Found at i:3083827 original size:13 final size:13
Alignment explanation
Indices: 3083775--3083828 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3083765 TTATATAATA
3083775 ATTTATAATAAAT
1 ATTTATAATAAAT
3083788 -TTTAATAATAAAT
1 ATTT-ATAATAAAT
* *
3083801 ATTAATAAT-TAT
1 ATTTATAATAAAT
*
3083813 ATTTTTAATAAAT
1 ATTTATAATAAAT
3083826 ATT
1 ATT
3083829 CTCTTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 12 0.36
13 19 0.58
14 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTATAATAAAT
Found at i:3084344 original size:2 final size:2
Alignment explanation
Indices: 3084339--3084368 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3084329 CGTGTGTGTG
3084339 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
3084369 TTTATTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3086832 original size:53 final size:54
Alignment explanation
Indices: 3086769--3086879 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
3086759 TAATAAGTTC
3086769 ATATATTGTGTTCTTTCAATA-A-ATTTTTCTGATGCAATAAAATATATATAAAA
1 ATATATTGTGTTCTTTCAATATAGATTTTT-TGATGCAATAAAATATATATAAAA
* *
3086822 ATATGTTGTGTTCTTTCAATATAGCTTTTTTGATGCAATAAAATATATATAAAA
1 ATATATTGTGTTCTTTCAATATAGATTTTTTGATGCAATAAAATATATATAAAA
3086876 ATAT
1 ATAT
3086880 TAAACAACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
53 20 0.37
54 29 0.54
55 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (54 bp):
ATATATTGTGTTCTTTCAATATAGATTTTTTGATGCAATAAAATATATATAAAA
Found at i:3087134 original size:118 final size:120
Alignment explanation
Indices: 3086924--3087153 Score: 385
Period size: 118 Copynumber: 1.9 Consensus size: 120
3086914 AAAATATTAT
3086924 ATATTATTTAATTTATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTT
1 ATATTATTTAATTTATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTT
* * *
3086989 AAACTTAAGTGCTCTAATAGTCATCTTTAACATTTAAATAATTACTAATCCATAA
66 AAACTTAAGTACTCCAATAGCCATCTTTAACATTTAAATAATTACTAATCCATAA
3087044 ATATTATTTAATTTATTTTGAAAATAAAAAT-AA-AAATAAATAAATAAATGCATTTTCAAATTT
1 ATATTATTTAATTTATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTT
* *
3087107 AAGCTTAAGTACTCCAAT-GCCCATCTTTAATATTTAAATAATTACTA
66 AAACTTAAGTACTCCAATAG-CCATCTTTAACATTTAAATAATTACTA
3087154 GCCCACAAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
117 1 0.01
118 70 0.67
119 2 0.02
120 31 0.30
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (120 bp):
ATATTATTTAATTTATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTT
AAACTTAAGTACTCCAATAGCCATCTTTAACATTTAAATAATTACTAATCCATAA
Found at i:3087191 original size:118 final size:120
Alignment explanation
Indices: 3086932--3087181 Score: 335
Period size: 118 Copynumber: 2.1 Consensus size: 120
3086922 ATATATTATT
*
3086932 TAATTTATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTTAAACTTAA
1 TAATTAATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTTAAACTTAA
* * * * * * ** *
3086997 GTGCTCTAATAGTCATCTTTAACATTTAAATAATTACTAATCCATAAATATTATT
66 GTACTCCAATAGCCATCTTTAACATTTAAATAATTACTAACCCACAAAAAAAATC
* *
3087052 TAATTTATTTTGAAAATAAAAAT-AA-AAATAAATAAATAAATGCATTTTCAAATTTAAGCTTAA
1 TAATTAATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTTAAACTTAA
* *
3087115 GTACTCCAAT-GCCCATCTTTAATATTTAAATAATTACTAGCCCACAAAAAAAATC
66 GTACTCCAATAG-CCATCTTTAACATTTAAATAATTACTAACCCACAAAAAAAATC
3087170 TAATATAATTTT
1 TAAT-TAATTTT
3087182 AAGTTAAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
117 1 0.01
118 83 0.72
119 8 0.07
120 23 0.20
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (120 bp):
TAATTAATTTTGAAAATAAAAATAAATAAATAAATAAATAAATGCATTTTCAAATTTAAACTTAA
GTACTCCAATAGCCATCTTTAACATTTAAATAATTACTAACCCACAAAAAAAATC
Found at i:3089278 original size:62 final size:60
Alignment explanation
Indices: 3089197--3089320 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 60
3089187 TTCAGCAGTT
3089197 CTCCATCCCACGGGATTTTACTGTTTAAAACC-TCGTGGCATTGACATATGTAGCAAGTTTTG
1 CTCCATCCCACGGGATTTTACTGTTTAAAACCATC---GCATTGACATATGTAGCAAGTTTTG
*
3089259 CTCCATCCCACATGG-TTTTACTGTTTAAAACCATCGCATTGACATATGTAGCAAGTTTTG
1 CTCCATCCCAC-GGGATTTTACTGTTTAAAACCATCGCATTGACATATGTAGCAAGTTTTG
3089319 CT
1 CT
3089321 GTTGATAGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
60 27 0.46
62 28 0.47
63 4 0.07
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (60 bp):
CTCCATCCCACGGGATTTTACTGTTTAAAACCATCGCATTGACATATGTAGCAAGTTTTG
Found at i:3091670 original size:2 final size:2
Alignment explanation
Indices: 3091663--3091700 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3091653 CAAATACCTA
3091663 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
3091701 GTAAAGAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3097698 original size:1 final size:1
Alignment explanation
Indices: 3097692--3097716 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3097682 ATATCTCATT
3097692 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
3097717 TAAAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3097979 original size:3 final size:3
Alignment explanation
Indices: 3097971--3098002 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3097961 ACTTTATTAA
3097971 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3098003 AGATATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3103580 original size:16 final size:16
Alignment explanation
Indices: 3103547--3103623 Score: 77
Period size: 16 Copynumber: 4.7 Consensus size: 16
3103537 TCACATTATT
3103547 ATAAAAATATTATAAAAA
1 ATAAAAATA-T-TAAAAA
*
3103565 ATTAAAATATTAAAAA
1 ATAAAAATATTAAAAA
* *
3103581 ATATATAT-TTAAAATA
1 ATAAAAATATTAAAA-A
3103597 ATAAAAAT-TTAAAAA
1 ATAAAAATATTAAAAA
3103612 TATAAAAATATT
1 -ATAAAAATATT
3103624 TTATTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
15 7 0.14
16 32 0.64
17 3 0.06
18 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAAATATTAAAAA
Found at i:3103601 original size:39 final size:39
Alignment explanation
Indices: 3103558--3103633 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
3103548 TAAAAATATT
3103558 ATAAAAAATT-AAAATATTAAAAA-ATATATATTTAAAATA
1 ATAAAAAATTAAAAATA-TAAAAATAT-TATATTTAAAATA
* *
3103597 ATAAAAATTTAAAAATATAAAAATATTTTATTTAAAA
1 ATAAAAAATTAAAAATATAAAAATATTATATTTAAAA
3103634 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 25 0.76
40 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (39 bp):
ATAAAAAATTAAAAATATAAAAATATTATATTTAAAATA
Found at i:3103613 original size:30 final size:32
Alignment explanation
Indices: 3103553--3103615 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 32
3103543 TATTATAAAA
3103553 ATATTATAAAAAATTAAAATATTAAAAAATAT
1 ATATTATAAAAAATTAAAATATTAAAAAATAT
*
3103585 ATATT-TAAAATAA-TAAAA-ATTTAAAAATAT
1 ATATTATAAAA-AATTAAAATATTAAAAAATAT
3103615 A
1 A
3103616 AAAATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 12 0.41
31 10 0.34
32 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
ATATTATAAAAAATTAAAATATTAAAAAATAT
Found at i:3113184 original size:20 final size:20
Alignment explanation
Indices: 3113159--3113202 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3113149 TGTCACTATC
3113159 ATCAAGAAAAAAATAAATCT
1 ATCAAGAAAAAAATAAATCT
*
3113179 ATCAAGAAAAAATTAAATCT
1 ATCAAGAAAAAAATAAATCT
3113199 ATCA
1 ATCA
3113203 TTGTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (20 bp):
ATCAAGAAAAAAATAAATCT
Found at i:3116566 original size:2 final size:2
Alignment explanation
Indices: 3116559--3116584 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3116549 CGATGAACGT
3116559 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3116585 AGCCGATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3117094 original size:20 final size:20
Alignment explanation
Indices: 3117069--3117106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3117059 AATAAATCTC
3117069 AATTTAAAATAAAATATAAA
1 AATTTAAAATAAAATATAAA
**
3117089 AATTTAATTTAAAATATA
1 AATTTAAAATAAAATATA
3117107 TTAAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTAAAATAAAATATAAA
Found at i:3117628 original size:42 final size:43
Alignment explanation
Indices: 3117550--3117630 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
3117540 GATTTAATTA
*
3117550 ACTAAAATGTGAAATCATGGAAAAAAAAAATTATGACCCATTG
1 ACTAAAACGTGAAATCATGGAAAAAAAAAATTATGACCCATTG
3117593 ACTAAAACGTGAAATCAT-GAAAAAAAAAATTATGACCC
1 ACTAAAACGTGAAATCATGGAAAAAAAAAATTATGACCC
3117631 CCCACCCCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 20 0.54
43 17 0.46
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (43 bp):
ACTAAAACGTGAAATCATGGAAAAAAAAAATTATGACCCATTG
Found at i:3119061 original size:34 final size:34
Alignment explanation
Indices: 3118994--3119209 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
3118984 TGGTACCTAC
* * *
3118994 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
3119027 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3119061 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3119094 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
3119128 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
3119162 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
3119196 TGTTGATTAAATGG
1 TGTTGATTAAATGG
3119210 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:3119175 original size:68 final size:67
Alignment explanation
Indices: 3118994--3119211 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
3118984 TGGTACCTAC
* * * * *
3118994 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
3119059 AT
66 AT
* * * *
3119061 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
3119126 AT
66 AT
* * *
3119128 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
3119193 CAT
65 CAT
3119196 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
3119212 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:3123682 original size:34 final size:34
Alignment explanation
Indices: 3123613--3123830 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
3123603 AAGTGGGAGA
* * *
3123613 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3123646 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3123680 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3123713 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3123747 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3123781 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3123815 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3123831 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3123796 original size:68 final size:67
Alignment explanation
Indices: 3123613--3123832 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
3123603 AAGTGGGAGA
* * * * *
3123613 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
3123678 CC
66 CC
* * * *
3123680 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
3123745 CC
66 CC
* * *
3123747 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
3123812 GCC
65 GCC
3123815 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
3123833 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:3124365 original size:20 final size:20
Alignment explanation
Indices: 3124342--3124381 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3124332 CTTGAAGAAT
3124342 GGATAATTGCCTGGAAGACC
1 GGATAATTGCCTGGAAGACC
3124362 GGATAATTGCCTGGAAGACC
1 GGATAATTGCCTGGAAGACC
3124382 AAACTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
GGATAATTGCCTGGAAGACC
Found at i:3128561 original size:15 final size:14
Alignment explanation
Indices: 3128527--3128568 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3128517 ATTTTTTCTT
*
3128527 TAAATTCTAATAAA
1 TAAATTTTAATAAA
3128541 -AAATTTTAATTAAA
1 TAAATTTTAA-TAAA
3128555 TAAATTTTAGATAA
1 TAAATTTTA-ATAA
3128569 TTTATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 8 0.33
14 4 0.17
15 11 0.46
16 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
TAAATTTTAATAAA
Found at i:3128645 original size:13 final size:13
Alignment explanation
Indices: 3128627--3128663 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3128617 AAATTTTTTA
3128627 ATTTTATTAAATT
1 ATTTTATTAAATT
3128640 ATTTTATTAAATT
1 ATTTTATTAAATT
*
3128653 TTTATTATTAA
1 ATT-TTATTAA
3128664 TAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTATTAAATT
Found at i:3128694 original size:14 final size:14
Alignment explanation
Indices: 3128624--3128700 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 14
3128614 CCTAAATTTT
*
3128624 TTAATTTTATTAAA
1 TTAATTATATTAAA
*
3128638 TT-ATTTTATTAAA
1 TTAATTATATTAAA
* *
3128651 TTTTTATTATTAATAAA
1 --TTAATTA-TATTAAA
*
3128668 TTAAATCAT-TTAAA
1 TT-AATTATATTAAA
3128682 TTAATTATATTAAA
1 TTAATTATATTAAA
3128696 -TAATT
1 TTAATT
3128701 TTAATAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
13 21 0.41
14 13 0.25
15 5 0.10
16 6 0.12
17 6 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTATATTAAA
Found at i:3128720 original size:17 final size:17
Alignment explanation
Indices: 3128700--3128762 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
3128690 ATTAAATAAT
3128700 TTTAATAAAAAAATTAA
1 TTTAATAAAAAAATTAA
3128717 TTTAAAATATAAATAAATTAA
1 TTT--AATA-AAA-AAATTAA
* *
3128738 TTTATTAAAAATAA-AAA
1 TTTAATAAAAA-AATTAA
3128755 TTTAATAA
1 TTTAATAA
3128763 TATAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 13 0.34
18 5 0.13
19 7 0.18
20 3 0.08
21 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAATAAAAAAATTAA
Found at i:3128739 original size:25 final size:25
Alignment explanation
Indices: 3128678--3128755 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
3128668 TTAAATCATT
* *
3128678 TAAATTAATTATATTAAATAATTTTAA
1 TAAATTAATTA-ATTAAA-AATATAAA
** *
3128705 TAAAAAAATTAATTTAAAATATAAA
1 TAAATTAATTAATTAAAAATATAAA
* *
3128730 TAAATTAATTTATTAAAAATAAAAA
1 TAAATTAATTAATTAAAAATATAAA
3128755 T
1 T
3128756 TTAATAATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 27 0.66
26 5 0.12
27 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAATTAATTAATTAAAAATATAAA
Found at i:3128747 original size:38 final size:39
Alignment explanation
Indices: 3128692--3128767 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
3128682 TTAATTATAT
*
3128692 TAAATAATTTTAATAAAAA-AATTAATTTAA-AATATAAA
1 TAAATAATTTTAATAAAAATAA-AAATTTAATAATATAAA
*
3128730 TAAATTAA-TTTATTAAAAATAAAAATTTAATAATATAA
1 TAAA-TAATTTTAATAAAAATAAAAATTTAATAATATAA
3128768 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
38 21 0.64
39 12 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (39 bp):
TAAATAATTTTAATAAAAATAAAAATTTAATAATATAAA
Found at i:3128755 original size:21 final size:20
Alignment explanation
Indices: 3128707--3128760 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
3128697 AATTTTAATA
*
3128707 AAAAAATTAATTTAAAATAT
1 AAAAAATTAATTTAAAAAAT
3128727 AAATAAATTAATTTATTAAAAAT
1 AAA-AAATTAATTTA--AAAAAT
*
3128750 AAAAATTTAAT
1 AAAAAATTAAT
3128761 AATATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 11 0.38
22 7 0.24
23 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTAATTTAAAAAAT
Found at i:3128762 original size:30 final size:31
Alignment explanation
Indices: 3128728--3128792 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
3128718 TTAAAATATA
*
3128728 AATAAAT-TAATTTATTAAAAA-TAAAAATTT
1 AATAAATATAATTTA-AAAAAATTAAAAATTT
3128758 AAT-AATATAATTTAAAAAAATTAAAAATTT
1 AATAAATATAATTTAAAAAAATTAAAAATTT
*
3128788 TATAA
1 AATAA
3128793 TTTTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 8 0.27
30 21 0.70
31 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AATAAATATAATTTAAAAAAATTAAAAATTT
Found at i:3128793 original size:30 final size:30
Alignment explanation
Indices: 3128735--3128804 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
3128725 ATAAATAAAT
*
3128735 TAATTTATTAAAAATAAAAATTTAATAATA
1 TAATTTATAAAAAATAAAAATTTAATAATA
*
3128765 TAATTTA-AAAAAATTAAAAATTTTATAAT-
1 TAATTTATAAAAAA-TAAAAATTTAATAATA
3128794 T--TTTATAAAAA
1 TAATTTATAAAAA
3128805 TTCATACGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 4 0.11
28 5 0.14
29 6 0.17
30 21 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATTTATAAAAAATAAAAATTTAATAATA
Found at i:3131285 original size:2 final size:2
Alignment explanation
Indices: 3131278--3131324 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3131268 ATGAATCTGA
3131278 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
3131320 AT AT A
1 AT AT A
3131325 AAATAAGATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3133556 original size:12 final size:12
Alignment explanation
Indices: 3133539--3133569 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3133529 ATAATTTTAG
3133539 TAATTTTTAATA
1 TAATTTTTAATA
*
3133551 TAATTTTTAATG
1 TAATTTTTAATA
3133563 TAATTTT
1 TAATTTT
3133570 GATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:3133723 original size:21 final size:21
Alignment explanation
Indices: 3133698--3133807 Score: 106
Period size: 21 Copynumber: 5.2 Consensus size: 21
3133688 ATTTTTATAT
3133698 ATTTTAATAATATTTGTAATA
1 ATTTTAATAATATTTGTAATA
*
3133719 CTTTTAATAACT-TTTCGT-ATA
1 ATTTTAATAA-TATTT-GTAATA
3133740 ATTTTAATAATATTTGTAATA
1 ATTTTAATAATATTTGTAATA
*
3133761 ATTTT--TAATATTTTTAAATATA
1 ATTTTAATAATATTTGT--A-ATA
3133783 ATTTTAATAA-ATTT-TATATA
1 ATTTTAATAATATTTGTA-ATA
3133803 ATTTT
1 ATTTT
3133808 TGATAACTCT
Statistics
Matches: 77, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
19 9 0.12
20 13 0.17
21 36 0.47
22 12 0.16
23 4 0.05
24 3 0.04
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTTAATAATATTTGTAATA
Found at i:3133759 original size:12 final size:11
Alignment explanation
Indices: 3133696--3133813 Score: 67
Period size: 11 Copynumber: 11.1 Consensus size: 11
3133686 TCATTTTTAT
3133696 ATATTTTAATA
1 ATATTTTAATA
3133707 ATATTTGTAAT-
1 ATATTT-TAATA
*
3133718 A-CTTTTAATA
1 ATATTTTAATA
* **
3133728 A-CTTTTCGT-
1 ATATTTTAATA
3133737 ATAATTTTAATA
1 AT-ATTTTAATA
3133749 ATATTTGTAATA
1 ATATTT-TAATA
3133761 AT-TTTTAAT-
1 ATATTTTAATA
3133770 AT-TTTTAA-A
1 ATATTTTAATA
3133779 TATAATTTTAATA
1 -AT-ATTTTAATA
3133792 A-ATTTTATATA
1 ATATTTTA-ATA
*
3133803 AT-TTTTGATA
1 ATATTTTAATA
3133813 A
1 A
3133814 CTCTTATTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
9 13 0.15
10 26 0.30
11 27 0.31
12 20 0.23
13 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:3133855 original size:21 final size:21
Alignment explanation
Indices: 3133693--3133855 Score: 90
Period size: 21 Copynumber: 7.7 Consensus size: 21
3133683 TTATCATTTT
3133693 TATATATTTTAATAATATTTG-
1 TATA-ATTTTAATAATATTTGA
*
3133714 TAATACTTTTAATAACT-TTTCG-
1 T-ATAATTTTAATAA-TATTT-GA
3133736 TATAATTTTAATAATATTTG-
1 TATAATTTTAATAATATTTGA
* *
3133756 TAATAATTTTTAAT-ATTTTTAAA
1 T-ATAA-TTTTAATAATATTT-GA
*
3133779 TATAATTTTAATAA-ATTTTA
1 TATAATTTTAATAATATTTGA
* *
3133799 TATAATTTTTGATAACT-CTT-A
1 TATAA-TTTTAATAA-TATTTGA
* ** *
3133820 TTTTAATGATGATAATATTTGA
1 -TATAATTTTAATAATATTTGA
3133842 TATAATTTTAATAA
1 TATAATTTTAATAA
3133856 CTTTCATCAT
Statistics
Matches: 111, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
20 10 0.09
21 75 0.68
22 25 0.23
23 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (21 bp):
TATAATTTTAATAATATTTGA
Found at i:3133875 original size:42 final size:42
Alignment explanation
Indices: 3133693--3133877 Score: 148
Period size: 42 Copynumber: 4.4 Consensus size: 42
3133683 TTATCATTTT
* *
3133693 TATATATTTTAATAATATTTGTAAT-ACTTTTAATAACTTTTCG
1 TATA-ATTTTAATAATATTTGTAATAATTTTTAATAAC-TTTCA
** *
3133736 TATAATTTTAATAATATTTGTAATAATTTTTAATATTTTTAAA
1 TATAATTTTAATAATATTTGTAATAATTTTTAATAACTTT-CA
*
3133779 TATAATTTTAATAA-ATTT-TATATAATTTTTGATAACTCTT-A
1 TATAATTTTAATAATATTTGTA-ATAATTTTTAATAACT-TTCA
* ** *
3133820 TTTTAATGATGATAATATTTG-ATATAA-TTTTAATAACTTTCA
1 -TATAATTTTAATAATATTTGTA-ATAATTTTTAATAACTTTCA
* *
3133862 TCATCATTTTGATAAT
1 T-ATAATTTTAATAAT
3133878 CGTGAAAAGA
Statistics
Matches: 116, Mismatches: 17, Indels: 19
0.76 0.11 0.12
Matches are distributed among these distances:
41 6 0.05
42 71 0.61
43 39 0.34
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (42 bp):
TATAATTTTAATAATATTTGTAATAATTTTTAATAACTTTCA
Found at i:3134489 original size:32 final size:31
Alignment explanation
Indices: 3134431--3134522 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 31
3134421 AAATTAATTG
3134431 TTTAAGTCATTTTAAGTTT-GAGTTATTTCAAGT
1 TTTAA-TCATTTTAA-TTTAGA-TTATTTCAAGT
*
3134464 TTTAATCATTTTACATTTAGATTATTTTAAGT
1 TTTAATCATTTTA-ATTTAGATTATTTCAAGT
** *
3134496 TCGAATCATTCTAAATTTAGATTATTT
1 TTTAATCATT-TTAATTTAGATTATTT
3134523 TAAACTCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
32 42 0.81
33 10 0.19
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTAATCATTTTAATTTAGATTATTTCAAGT
Found at i:3134523 original size:32 final size:32
Alignment explanation
Indices: 3134453--3134525 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
3134443 TAAGTTTGAG
* ** * *
3134453 TTATTTCAAGTTTTAATCATTTTACATTTAGA
1 TTATTTTAAGTTCGAATCATTCTAAATTTAGA
3134485 TTATTTTAAGTTCGAATCATTCTAAATTTAGA
1 TTATTTTAAGTTCGAATCATTCTAAATTTAGA
3134517 TTATTTTAA
1 TTATTTTAA
3134526 ACTCGAATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (32 bp):
TTATTTTAAGTTCGAATCATTCTAAATTTAGA
Found at i:3134532 original size:32 final size:32
Alignment explanation
Indices: 3134467--3134533 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
3134457 TTCAAGTTTT
* * **
3134467 AATCATTTTACATTTAGATTATTTTAAGTTCG
1 AATCATTCTAAATTTAGATTATTTTAAACTCG
3134499 AATCATTCTAAATTTAGATTATTTTAAACTCG
1 AATCATTCTAAATTTAGATTATTTTAAACTCG
3134531 AAT
1 AAT
3134534 TGATTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (32 bp):
AATCATTCTAAATTTAGATTATTTTAAACTCG
Found at i:3134939 original size:22 final size:21
Alignment explanation
Indices: 3134914--3134958 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3134904 AAAAAAATTT
*
3134914 TAAAATTAAAATAATTAAAAAA
1 TAAAA-TAAAATAAATAAAAAA
* *
3134936 TAAAATGATATAAATAAAAAA
1 TAAAATAAAATAAATAAAAAA
3134957 TA
1 TA
3134959 CCTAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAATAAAATAAATAAAAAA
Found at i:3136964 original size:16 final size:15
Alignment explanation
Indices: 3136943--3137057 Score: 74
Period size: 16 Copynumber: 7.0 Consensus size: 15
3136933 CATATAATAA
3136943 TTATATTTAATATATT
1 TTATATTT-ATATATT
3136959 TTATATTTATATTAATT
1 TTATATTTATA-T-ATT
3136976 TTAATATATTA-ATATT
1 TT-ATAT-TTATATATT
*
3136992 TTATATTATATAAATT
1 TTATATT-TATATATT
3137008 TTAAAATATTTATATA-T
1 TT---ATATTTATATATT
*
3137025 TTATATCGTATCATATT
1 TTATAT-TTAT-ATATT
3137042 TTAATTATTT-TATATT
1 TT-A-TATTTATATATT
3137058 ATATTAATAT
Statistics
Matches: 81, Mismatches: 4, Indels: 28
0.72 0.04 0.25
Matches are distributed among these distances:
14 5 0.06
15 12 0.15
16 28 0.35
17 13 0.16
18 12 0.15
19 11 0.14
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:3136972 original size:27 final size:27
Alignment explanation
Indices: 3136924--3137002 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 27
3136914 TTTTTTATAC
*
3136924 ATATTTTATCATATAATAATTATATTTAAT
1 ATATTTTAT-AT-TTAT-ATTATATTTAAT
3136954 ATATTTTATATTTATATTA-ATTTTAAT
1 ATATTTTATATTTATATTATA-TTTAAT
*
3136981 ATA-TTAATATTTTATATTATAT
1 ATATTTTATA-TTTATATTATAT
3137003 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.14
27 23 0.52
28 4 0.09
29 2 0.05
30 9 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATATTTTATATTTATATTATATTTAAT
Found at i:3136996 original size:33 final size:33
Alignment explanation
Indices: 3136954--3137030 Score: 111
Period size: 32 Copynumber: 2.3 Consensus size: 33
3136944 TATATTTAAT
* *
3136954 ATATTTTATATTTATATTAATTTTAATATATTA
1 ATATTTTATATTTATATAAATTTTAAAATATTA
*
3136987 ATATTTTATA-TTATATAAATTTTAAAATATTT
1 ATATTTTATATTTATATAAATTTTAAAATATTA
3137019 ATATATTTATAT
1 ATAT-TTTATAT
3137031 CGTATCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
ATATTTTATATTTATATAAATTTTAAAATATTA
Found at i:3137008 original size:32 final size:31
Alignment explanation
Indices: 3136954--3137086 Score: 108
Period size: 33 Copynumber: 4.1 Consensus size: 31
3136944 TATATTTAAT
*
3136954 ATATTTTATATTTATATTAATTTTAATATATTA
1 ATATTTTATA-TTATATAAATTTTAAT-TATTA
* *
3136987 ATATTTTATATTATATAAATTTTAAAATATTT
1 ATATTTTATATTATATAAATTTT-AATTATTA
** *
3137019 ATATATTTATATCGTATCATATTTTAATTATT-
1 ATAT-TTTATATTATAT-AAATTTTAATTATTA
* * *
3137051 TTATATTATATTA-ATATAATTATTAATTAATA
1 ATATTTTATATTATATA-AATT-TTAATTATTA
3137083 ATAT
1 ATAT
3137087 GAGAAATGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
29 1 0.01
30 5 0.06
31 14 0.17
32 26 0.32
33 28 0.35
34 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
ATATTTTATATTATATAAATTTTAATTATTA
Found at i:3142285 original size:88 final size:90
Alignment explanation
Indices: 3142146--3142326 Score: 285
Period size: 89 Copynumber: 2.0 Consensus size: 90
3142136 TCCTGCAGTG
* *
3142146 TATCATTGTCAAAAACCCGAAAGGATGTATTTGGAGTTAAATGTTATAATGTTTG-TCAAACTTT
1 TATCATTGTCAAAAACCCGAAAGGATGTATTTGGAGTTAAATGTTACAATGTTTGTTAAAACTTT
*
3142210 TCTGGTCTTTCTAGATAGAAATTGA
66 TCTGGTCTTTCTAAATAGAAATTGA
* * *
3142235 TATCATTGTCAAGAGCCCGAGAGGATGTA-TTGGAGTTAAATGTTACAATGTTTGTTAAAACTTT
1 TATCATTGTCAAAAACCCGAAAGGATGTATTTGGAGTTAAATGTTACAATGTTTGTTAAAACTTT
*
3142299 TCTGGTCTTTCTAAATCGAAATTGA
66 TCTGGTCTTTCTAAATAGAAATTGA
3142324 TAT
1 TAT
3142327 GTTCAAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 24 0.29
89 60 0.71
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (90 bp):
TATCATTGTCAAAAACCCGAAAGGATGTATTTGGAGTTAAATGTTACAATGTTTGTTAAAACTTT
TCTGGTCTTTCTAAATAGAAATTGA
Found at i:3148894 original size:21 final size:21
Alignment explanation
Indices: 3148869--3148915 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3148859 CCACCACCAG
3148869 CTTGCCCCGCATGTCC-TCCAC
1 CTTGCCCCGCATG-CCATCCAC
*
3148890 CTTGCCCTGCATGCCATCCAC
1 CTTGCCCCGCATGCCATCCAC
3148911 CTTGC
1 CTTGC
3148916 TCTGGCTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.11, C:0.49, G:0.15, T:0.26
Consensus pattern (21 bp):
CTTGCCCCGCATGCCATCCAC
Found at i:3148925 original size:21 final size:20
Alignment explanation
Indices: 3148883--3148947 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
3148873 CCCCGCATGT
*
3148883 CCTCCACCTTGCCCT-GCATG
1 CCTCCACCTTGCTCTGGC-TG
3148903 CCATCCACCTTGCTCTGGCTG
1 CC-TCCACCTTGCTCTGGCTG
*
3148924 CCTACCTCCTTGCTCTGGCTG
1 CCT-CCACCTTGCTCTGGCTG
3148945 CCT
1 CCT
3148948 TCCTCCGTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.08
21 35 0.88
22 2 0.05
ACGTcount: A:0.08, C:0.46, G:0.17, T:0.29
Consensus pattern (20 bp):
CCTCCACCTTGCTCTGGCTG
Found at i:3148952 original size:21 final size:21
Alignment explanation
Indices: 3148901--3148953 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3148891 TTGCCCTGCA
* *
3148901 TGCCATCCACCTTGCTCTGGC
1 TGCCTTCCTCCTTGCTCTGGC
*
3148922 TGCCTACCTCCTTGCTCTGGC
1 TGCCTTCCTCCTTGCTCTGGC
3148943 TGCCTTCCTCC
1 TGCCTTCCTCC
3148954 GTGCAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.45, G:0.17, T:0.32
Consensus pattern (21 bp):
TGCCTTCCTCCTTGCTCTGGC
Found at i:3149968 original size:2 final size:2
Alignment explanation
Indices: 3149961--3149992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3149951 TTTTAAAATG
3149961 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
3149993 TAGATTATGA
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:3150615 original size:11 final size:11
Alignment explanation
Indices: 3150601--3150626 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3150591 AAATATAGGT
3150601 TAAAATATTAA
1 TAAAATATTAA
3150612 TAAAATATTAA
1 TAAAATATTAA
3150623 TAAA
1 TAAA
3150627 GTCAGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:3154715 original size:16 final size:16
Alignment explanation
Indices: 3154694--3154733 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3154684 TCGTTTTGGC
3154694 TTTGATATTGATAAAT
1 TTTGATATTGATAAAT
* *
3154710 TTTGATATTGTTATAT
1 TTTGATATTGATAAAT
*
3154726 TTTAATAT
1 TTTGATAT
3154734 AGTTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
TTTGATATTGATAAAT
Found at i:3155024 original size:9 final size:9
Alignment explanation
Indices: 3155012--3155036 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3155002 TAAAAATTAA
3155012 TAAAATAAG
1 TAAAATAAG
3155021 TAAAATAAG
1 TAAAATAAG
3155030 TAAAATA
1 TAAAATA
3155037 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (9 bp):
TAAAATAAG
Found at i:3155447 original size:16 final size:17
Alignment explanation
Indices: 3155402--3155447 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3155392 TATTAATAAT
*
3155402 TATATTATTAAATTAAA
1 TATATTATTATATTAAA
3155419 TATAATT-TT-TATTAAA
1 TAT-ATTATTATATTAAA
3155435 TAT-TTATTATATT
1 TATATTATTATATT
3155448 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 2 0.08
15 2 0.08
16 13 0.52
17 5 0.20
18 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATTATATTAAA
Found at i:3155580 original size:2 final size:2
Alignment explanation
Indices: 3155575--3155599 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3155565 ATATATATAT
3155575 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3155600 TAGCAGGCGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3157779 original size:2 final size:2
Alignment explanation
Indices: 3157766--3157816 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
3157756 ATGTAAACAA
* *
3157766 AT AT AC AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3157807 AT AT AT AT AT
1 AT AT AT AT AT
3157817 CTTTTATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3162622 original size:20 final size:20
Alignment explanation
Indices: 3162585--3162622 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3162575 CGAGTTTTAT
*
3162585 TAGCAAATATAATCTTCTTA
1 TAGCAAATATAATATTCTTA
3162605 TAGCAAATA-ATATATTCT
1 TAGCAAATATA-ATATTCT
3162623 GAGAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
TAGCAAATATAATATTCTTA
Found at i:3163099 original size:233 final size:232
Alignment explanation
Indices: 3162662--3163357 Score: 1180
Period size: 233 Copynumber: 3.0 Consensus size: 232
3162652 AGAAAAGGTA
*
3162662 TTTTTTATTAAATAATATCACCTTATTAATTCATTGTTTTAATAT-TGCATTACTTAGAATTAAG
1 TTTTTTATTAAATAATATCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
* * * *
3162726 AAATAATAATTTCTATTATATATTATATCTTTGTGTATAAGAATAAGAATATGAT-AAATGATTC
66 AAATAATAATTTTTATTATATATTATATCTTTGTATATAAGAATAAGAATACGATAAAATAATT-
*
3162790 TTTTATATATAATTGGTCAAAATTTATCTTTTCTTTCATTGTTACTGTAAATATATGAAAGTTAT
130 TTTTATATATAATTGGTCAAAATTTATCTTTTCTTTCATTGTTACTTTAAATATATGAAAGTTAT
*
3162855 TTTGCAGGATAAAATAAGTAACATGTTAATAAGGGTCT
195 TTTGAAGGATAAAATAAGTAACATGTTAATAAGGGTCT
*
3162893 TTTTTTACTAAATAATATCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
1 TTTTTTATTAAATAATATCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
3162958 AAATAATAATTTTTATTATATATTATATCTTTGTATATAAGAATAAGAATACGATAAAATTAATT
66 AAATAATAATTTTTATTATATATTATATCTTTGTATATAAGAATAAGAATACGATAAAA-TAATT
* * *
3163023 TTTTATATATATTTTGTCAAAATTTATCTTTTCTTTCATTGTTACTTTAAATATATGAAAATTAT
130 TTTTATATATAATTGGTCAAAATTTATCTTTTCTTTCATTGTTACTTTAAATATATGAAAGTTAT
*
3163088 TTTGAAGGATAAAATAAGTAATATGTTAATAAGGGTCT
195 TTTGAAGGATAAAATAAGTAACATGTTAATAAGGGTCT
*
3163126 TTTTTTATTAAATAATACCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
1 TTTTTTATTAAATAATATCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
* *
3163191 AAATAATAATTTTTATTATATATTATATCTTTGTATATAAAAATAAAAATACGATAAAATAATTT
66 AAATAATAATTTTTATTATATATTATATCTTTGTATATAAGAATAAGAATACGATAAAATAA-TT
* *
3163256 TTTTATATATAATTGGTCAAAATTTATCTTTTTTTTTCATTATTACTTTAAATATATGAAAGTTA
130 TTTTATATATAATTGGTCAAAATTTATC-TTTTCTTTCATTGTTACTTTAAATATATGAAAGTTA
*
3163321 TTTTGAAAGATAAAATAAGTAACATGTTAATAAGGGT
194 TTTTGAAGGATAAAATAAGTAACATGTTAATAAGGGT
3163358 ATTTAACATA
Statistics
Matches: 437, Mismatches: 23, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
231 43 0.10
232 74 0.17
233 248 0.57
234 72 0.16
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (232 bp):
TTTTTTATTAAATAATATCATCTTATTAATTCATTGTTTTAATATGTGCATTACTTAGAATTAAG
AAATAATAATTTTTATTATATATTATATCTTTGTATATAAGAATAAGAATACGATAAAATAATTT
TTTATATATAATTGGTCAAAATTTATCTTTTCTTTCATTGTTACTTTAAATATATGAAAGTTATT
TTGAAGGATAAAATAAGTAACATGTTAATAAGGGTCT
Found at i:3166799 original size:2 final size:2
Alignment explanation
Indices: 3166758--3166782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3166748 ATTACTCTGG
3166758 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
3166783 CTGATTATTG
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:3175678 original size:15 final size:16
Alignment explanation
Indices: 3175658--3175688 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3175648 TTCAAATATT
3175658 AACTAATTT-GATTTA
1 AACTAATTTAGATTTA
3175673 AACTAATTTAGATTTA
1 AACTAATTTAGATTTA
3175689 GATTTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
AACTAATTTAGATTTA
Found at i:3175774 original size:3 final size:3
Alignment explanation
Indices: 3175766--3175798 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3175756 CACTAATCGC
3175766 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3175799 GCACTTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3179494 original size:2 final size:2
Alignment explanation
Indices: 3179487--3179522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3179477 TTTCAAAGTG
3179487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3179523 CACACGCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3182521 original size:29 final size:28
Alignment explanation
Indices: 3182476--3182559 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
3182466 AAAAAAAGCC
**
3182476 TATTAATTAATAATAATATATTCATTAA
1 TATTAATTAATGCTAATATATTCATTAA
* *
3182504 TATTTAATTAATGCTAATATATTCGTCAA
1 TA-TTAATTAATGCTAATATATTCATTAA
3182533 TATTAATTAATGCTAATATATTCATTA
1 TATTAATTAATGCTAATATATTCATTA
3182560 TTACCGGAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 25 0.51
29 24 0.49
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
TATTAATTAATGCTAATATATTCATTAA
Found at i:3186609 original size:14 final size:13
Alignment explanation
Indices: 3186585--3186617 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3186575 TAAAATAAAA
3186585 ATTTTTTAAATAT
1 ATTTTTTAAATAT
3186598 ATTTTTTAAA-AT
1 ATTTTTTAAATAT
*
3186610 ATCTTTTA
1 ATTTTTTA
3186618 TTTCTATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTTTTAAATAT
Found at i:3186611 original size:12 final size:12
Alignment explanation
Indices: 3186580--3186617 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3186570 CTGTTTAAAA
3186580 TAAAA-ATTTTT
1 TAAAATATTTTT
3186591 TAAATATATTTTT
1 TAAA-ATATTTTT
*
3186604 TAAAATATCTTT
1 TAAAATATTTTT
3186616 TA
1 TA
3186618 TTTCTATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 10 0.42
13 10 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:3186975 original size:11 final size:11
Alignment explanation
Indices: 3186959--3187020 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
3186949 GATGTAAATA
3186959 TATATTTATAT
1 TATATTTATAT
3186970 TATA-TTATTAT
1 TATATTTA-TAT
* *
3186981 TATTTTTTTTAT
1 TA-TATTTATAT
3186993 TATATTT-TAAT
1 TATATTTAT-AT
3187004 TAT-TTTATAT
1 TATATTTATAT
3187014 TATATTT
1 TATATTT
3187021 TTTTCATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 12 0.29
11 22 0.52
12 6 0.14
13 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3187006 original size:34 final size:36
Alignment explanation
Indices: 3186957--3187024 Score: 97
Period size: 34 Copynumber: 1.9 Consensus size: 36
3186947 ATGATGTAAA
3186957 TATATATTTATATTATATTATTATTAT-TTTTTTTAT
1 TATATATTTATATTATATTA-TATTATATTTTTTTAT
*
3186993 TATAT-TTTA-ATTATTTTATATTATATTTTTTT
1 TATATATTTATATTATATTATATTATATTTTTTT
3187025 CATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 6 0.20
34 15 0.50
35 4 0.13
36 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (36 bp):
TATATATTTATATTATATTATATTATATTTTTTTAT
Done.