Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_pilon, 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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 21
Found at i:11947 original size:18 final size:18
Alignment explanation
Indices: 11921--11993 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
11911 AAATTATATA
11921 ATATATAGTTTTGAAAAC
1 ATATATAGTTTTGAAAAC
* *
11939 ATGTATAGTTTTTAAAAC
1 ATATATAGTTTTGAAAAC
* *
11957 ATATATA-TAATTTTAAAAT
1 ATATATAGT--TTTGAAAAC
*
11976 ATATATTGTTTTGAAAAC
1 ATATATAGTTTTGAAAAC
11994 CTAGATGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 1 0.02
18 29 0.64
19 14 0.31
20 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATATAGTTTTGAAAAC
Found at i:11970 original size:19 final size:18
Alignment explanation
Indices: 11921--11981 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
11911 AAATTATATA
11921 ATATATAGTTTTGAAAACAT
1 ATATATA-TTTT-AAAACAT
*
11941 GTATAGT-TTTTAAAACAT
1 ATATA-TATTTTAAAACAT
*
11959 ATATATAATTTTAAAATAT
1 ATATAT-ATTTTAAAACAT
11978 ATAT
1 ATAT
11982 TGTTTTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 18 0.51
20 4 0.11
21 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (18 bp):
ATATATATTTTAAAACAT
Found at i:13323 original size:11 final size:11
Alignment explanation
Indices: 13307--13333 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13297 ATATGACTAA
13307 AATAAAATAAT
1 AATAAAATAAT
13318 AATAAAATAAT
1 AATAAAATAAT
13329 AATAA
1 AATAA
13334 TTAAAGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:19856 original size:42 final size:41
Alignment explanation
Indices: 19793--19879 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 41
19783 AAAATAACTC
* *
19793 TAAACTTTTATTTATTATTTTTATAGGTTTTTTTCGTAGATT
1 TAAACTTTTATTTATTATTTTTA-AGGGTTTATTCGTAGATT
*
19835 TAAACTTTTATTTATTGTTTTTAAGGGTTTATTCGTAGATT
1 TAAACTTTTATTTATTATTTTTAAGGGTTTATTCGTAGATT
19876 TAAA
1 TAAA
19880 AATTACGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 20 0.48
42 22 0.52
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.57
Consensus pattern (41 bp):
TAAACTTTTATTTATTATTTTTAAGGGTTTATTCGTAGATT
Found at i:25119 original size:122 final size:124
Alignment explanation
Indices: 24908--25137 Score: 313
Period size: 122 Copynumber: 1.9 Consensus size: 124
24898 AAATCTAAAA
* * *
24908 GTCTAAACTCTAAATGGGAGAAACAATGGGGGTTTTCATTAAATTTGACCATTTAAATTATAACA
1 GTCTAAAATCTAAATAGGAGAAACAATGGGGGTTTTCATTAAATTTGACCATTTAAATTAAAACA
* * * *
24973 CAAGTATGGGAGTGAGTAGTGTAATTTAGCCATGTCTATTAAAACATAAACATGCATTC
66 CAAATATGGGAGTGAGTAGCGTAATTTACCCATGTATATTAAAACATAAACATGCATTC
* * * *
25032 GTCTAAAATCTAAATAGGAGAAACTATGAGGGG-TTT-ATT-GATTTGGCCATTTAAATTAAAAT
1 GTCTAAAATCTAAATAGGAGAAACAATG-GGGGTTTTCATTAAATTTGACCATTTAAATTAAAAC
* *
25094 ACAAATATGGGTGTGGGTAGCGTAATTTACCCATGTATATTAAA
65 ACAAATATGGGAGTGAGTAGCGTAATTTACCCATGTATATTAAA
25138 GCACAGGCGC
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
122 57 0.62
123 3 0.03
124 28 0.30
125 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (124 bp):
GTCTAAAATCTAAATAGGAGAAACAATGGGGGTTTTCATTAAATTTGACCATTTAAATTAAAACA
CAAATATGGGAGTGAGTAGCGTAATTTACCCATGTATATTAAAACATAAACATGCATTC
Found at i:26665 original size:15 final size:15
Alignment explanation
Indices: 26645--26761 Score: 125
Period size: 15 Copynumber: 8.1 Consensus size: 15
26635 ATTTAGTTTT
26645 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
26660 CTGGAATTTGAATTA
1 CTGGAAAATGAATTA
**
26675 CTGGAATTTGAATTA
1 CTGGAAAATGAATTA
26690 CTGG--AATGAATTA
1 CTGGAAAATGAATTA
**
26703 CTGGAATTTGAATTA
1 CTGGAAAATGAATTA
26718 CTGG-AAATGAATTA
1 CTGGAAAATGAATTA
**
26732 CTGGAATTTGAATT-
1 CTGGAAAATGAATTA
*
26746 CTAGAAAATGAATTA
1 CTGGAAAATGAATTA
26761 C
1 C
26762 ATTTCTAGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.13
14 23 0.27
15 51 0.60
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (15 bp):
CTGGAAAATGAATTA
Found at i:26699 original size:43 final size:42
Alignment explanation
Indices: 26651--26738 Score: 158
Period size: 43 Copynumber: 2.1 Consensus size: 42
26641 TTTTCTGGAA
*
26651 AATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTGG
1 AATGAATTACTGGAATTTGAATTACTGGAA-ATGAATTACTGG
26694 AATGAATTACTGGAATTTGAATTACTGGAAATGAATTACTGG
1 AATGAATTACTGGAATTTGAATTACTGGAAATGAATTACTGG
26736 AAT
1 AAT
26739 TTGAATTCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (42 bp):
AATGAATTACTGGAATTTGAATTACTGGAAATGAATTACTGG
Found at i:26708 original size:28 final size:28
Alignment explanation
Indices: 26653--26745 Score: 159
Period size: 28 Copynumber: 3.2 Consensus size: 28
26643 TTCTGGAAAA
26653 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAA--TGAATTACTGGAATT
26683 TGAATTACTGGAATGAATTACTGGAATT
1 TGAATTACTGGAATGAATTACTGGAATT
26711 TGAATTACTGGAAATGAATTACTGGAATT
1 TGAATTACTGG-AATGAATTACTGGAATT
26740 TGAATT
1 TGAATT
26746 CTAGAAAATG
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
28 26 0.42
29 23 0.37
30 13 0.21
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (28 bp):
TGAATTACTGGAATGAATTACTGGAATT
Found at i:26736 original size:29 final size:29
Alignment explanation
Indices: 26653--26761 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
26643 TTCTGGAAAA
*
26653 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAA-ATGAATTACTGGAATT
26683 TGAATTACTGG-AATGAATTACTGGAATT
1 TGAATTACTGGAAATGAATTACTGGAATT
26711 TGAATTACTGGAAATGAATTACTGGAATT
1 TGAATTACTGGAAATGAATTACTGGAATT
*
26740 TGAATT-CTAGAAAATGAATTAC
1 TGAATTACT-GGAAATGAATTAC
26762 ATTTCTAGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
28 28 0.37
29 36 0.48
30 11 0.15
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (29 bp):
TGAATTACTGGAAATGAATTACTGGAATT
Found at i:27281 original size:23 final size:24
Alignment explanation
Indices: 27254--27314 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 24
27244 AAATAATATT
27254 AAATATTAAATAAATCAA-AGAAA
1 AAATATTAAATAAATCAAGAGAAA
*
27277 AAATAATAAAATAATAAATCAAGAGAAA
1 AAAT-AT--TA-AATAAATCAAGAGAAA
*
27305 AAAAATTAAA
1 AAATATTAAA
27315 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 1 0.03
26 1 0.03
27 12 0.40
28 8 0.27
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (24 bp):
AAATATTAAATAAATCAAGAGAAA
Found at i:27294 original size:27 final size:28
Alignment explanation
Indices: 27262--27315 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
27252 TTAAATATTA
27262 AATAAATCAA-AGAAAAAATAA-TAAAAT
1 AATAAATCAAGAGAAAAAA-AATTAAAAT
27289 AATAAATCAAGAGAAAAAAAATTAAAA
1 AATAAATCAAGAGAAAAAAAATTAAAA
27316 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (28 bp):
AATAAATCAAGAGAAAAAAAATTAAAAT
Found at i:27319 original size:12 final size:12
Alignment explanation
Indices: 27302--27326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27292 AAATCAAGAG
27302 AAAAAAAATTAA
1 AAAAAAAATTAA
27314 AAAAAAAATTAA
1 AAAAAAAATTAA
27326 A
1 A
27327 TAAGTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:27322 original size:27 final size:27
Alignment explanation
Indices: 27260--27322 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
27250 TATTAAATAT
27260 TAAATAAATCAAAGAAAAAATAATAAAA
1 TAAA-AAATCAAAGAAAAAATAATAAAA
*
27288 TAATAAATCAAGAGAAAAAA-AATTAAAA
1 TAAAAAATCAA-AGAAAAAATAA-TAAAA
27316 -AAAAAAT
1 TAAAAAAT
27323 TAAATAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (27 bp):
TAAAAAATCAAAGAAAAAATAATAAAA
Found at i:27388 original size:11 final size:11
Alignment explanation
Indices: 27372--27410 Score: 50
Period size: 9 Copynumber: 3.9 Consensus size: 11
27362 AAGTCAAAGA
27372 AAATAAATAAT
1 AAATAAATAAT
27383 AAATAAATAAT
1 AAATAAATAAT
27394 -AAT-AATAA-
1 AAATAAATAAT
27402 AAA-AAATAA
1 AAATAAATAA
27411 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 12 0.46
10 3 0.12
11 11 0.42
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:27399 original size:17 final size:15
Alignment explanation
Indices: 27371--27417 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 15
27361 CAAGTCAAAG
27371 AAAATAAATAATAAATA
1 AAAAT-AATAATAAA-A
27388 AATAATAATAATAAAA
1 AA-AATAATAATAAAA
27404 AAAATAA-AATAAAA
1 AAAATAATAATAAAA
27418 CTTAGACGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.24
15 5 0.17
16 3 0.10
17 11 0.38
18 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAATAATAAAA
Found at i:28945 original size:84 final size:85
Alignment explanation
Indices: 28838--28995 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
28828 AAAATTTTAT
* * * * *
28838 TGACAAATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTAG-AGCTGAGCATAGT
1 TGACAAATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCCTAGAAGCTGAGCATAAT
28902 CAAACTCGAAGGTCTTTTGG
66 CAAACTCGAAGGTCTTTTGG
* * * **
28922 TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAAATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCCTAGAAGCTGAGCATAAT
28987 CAAACTCGA
66 CAAACTCGA
28996 GGGTTTGGTG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 44 0.70
85 19 0.30
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (85 bp):
TGACAAATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCCTAGAAGCTGAGCATAAT
CAAACTCGAAGGTCTTTTGG
Found at i:29046 original size:39 final size:36
Alignment explanation
Indices: 28999--29093 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
28989 AACTCGAGGG
*
28999 TTTG-GTGTTTTAAGAGAAA-AATTTTCAAAGGTTTTT
1 TTTGTGTGTTTCAAGAGAAACAA-TTTC-AAGGTTTTT
*
29035 TGTGTGTGTGTTTCAAGAGAAACAATTTCGAGGTTTTT
1 T-T-TGTGTGTTTCAAGAGAAACAATTTCAAGGTTTTT
*
29073 TTTTTGTGTTTCAAGAGAAAC
1 TTTGTGTGTTTCAAGAGAAAC
29094 TGTCTCAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
36 19 0.37
37 2 0.04
38 11 0.21
39 18 0.35
40 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.44
Consensus pattern (36 bp):
TTTGTGTGTTTCAAGAGAAACAATTTCAAGGTTTTT
Found at i:29166 original size:22 final size:21
Alignment explanation
Indices: 29131--29184 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
29121 AAAAGAAACT
29131 GTCTCAA-GAGAGACAAAACTTA
1 GTCTCAAGGA-AGACAAAA-TTA
* *
29153 GTCTCAAGGAAGACGAAATTT
1 GTCTCAAGGAAGACAAAATTA
*
29174 GTTTCAAGGAA
1 GTCTCAAGGAA
29185 AAGATATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.43
22 14 0.50
23 2 0.07
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (21 bp):
GTCTCAAGGAAGACAAAATTA
Found at i:29224 original size:29 final size:29
Alignment explanation
Indices: 29192--29349 Score: 74
Period size: 37 Copynumber: 5.2 Consensus size: 29
29182 GAAAAGATAT
29192 TCAAAGATTTTGTTTCAAGGGAAACTGTC
1 TCAAAGATTTTGTTTCAAGGGAAACTGTC
29221 TCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTC
1 TC-------A-AAGATTTTGTTTCAAGGGAAACTGTC
* * * *
29258 TCAAA-A-CTCGTTTTAAGGGGAACTGAT-
1 TCAAAGATTTTGTTTCAAGGGAAACTG-TC
* * *
29285 TTAAATATTTTTGTTTCAAGGGAAA-TGTTT
1 TCAAAGA-TTTTGTTTCAAGGGAAACTG-TC
* * * *
29315 TC-AAGGTTTATGTTTCAAGAGAAAATATC
1 TCAAAGATTT-TGTTTCAAGGGAAACTGTC
29344 TCAAAG
1 TCAAAG
29350 GAGACAAAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
27 19 0.20
28 6 0.06
29 25 0.26
30 18 0.19
36 1 0.01
37 28 0.29
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (29 bp):
TCAAAGATTTTGTTTCAAGGGAAACTGTC
Found at i:29381 original size:37 final size:36
Alignment explanation
Indices: 29326--29411 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
29316 CAAGGTTTAT
*
29326 GTTTCAAGAGAAAATATCTCAA-AGGAGACAAAATTTC
1 GTTTCAAGGGAAAATATCTCAAGA-GAGACAAAA-TTC
*
29363 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAAATATCTCAAGAGAGACAAAATTC
* *
29399 ATTTCAAAGGAAA
1 GTTTCAAGGGAAA
29412 TGTTTTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 14 0.32
37 29 0.66
38 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (36 bp):
GTTTCAAGGGAAAATATCTCAAGAGAGACAAAATTC
Found at i:29414 original size:102 final size:102
Alignment explanation
Indices: 29298--29710 Score: 578
Period size: 102 Copynumber: 4.1 Consensus size: 102
29288 AATATTTTTG
* * * *
29298 TTTCAAGGGAAATGTTTTCAAGGTTTATGTTTCAAGAGAAAATATCTCAAAGGAGACAAAATTTC
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
*
29363 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
* * *
29400 TTTCAAAGGAAATGTTTTCAATGTTGATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* * * *
29464 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
29501 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* ** * *
29566 GTTTCAAGGGAAACTATCTCGATTGAGATAGAATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
*
29603 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* ** * * * *
29668 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAA-TTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
29704 GTTTCAA
1 -TTTCAA
29711 TGAAAACATA
Statistics
Matches: 276, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
101 96 0.35
102 180 0.65
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
Found at i:29477 original size:36 final size:36
Alignment explanation
Indices: 29427--29710 Score: 113
Period size: 36 Copynumber: 8.2 Consensus size: 36
29417 TCAATGTTGA
29427 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
* ** * * * *
29463 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
* * * *
29499 TATTTCAAGGGAAA-TGTTTTCAA---TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAATTT
29527 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTT
* * * * ** *
29565 CGTTTCAAGGGAAACTATCTCGATTGAGATAGAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACA-AATTT
* * * *
29601 TATTTCAAGGGAAA-TGTTTTCAA---TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAATTT
29629 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTT
* * * *
29667 AGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTT
*
29703 AGTTTCAA
1 TGTTTCAA
29711 TGAAAACATA
Statistics
Matches: 181, Mismatches: 41, Indels: 52
0.66 0.15 0.19
Matches are distributed among these distances:
28 4 0.02
29 34 0.19
30 4 0.02
32 2 0.01
33 2 0.01
35 2 0.01
36 73 0.40
37 54 0.30
38 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
Found at i:29516 original size:101 final size:102
Alignment explanation
Indices: 29298--29666 Score: 587
Period size: 102 Copynumber: 3.6 Consensus size: 102
29288 AATATTTTTG
* * * *
29298 TTTCAAGGGAAATGTTTTCAAGGTTTATGTTTCAAGAGAAAATATCTCAAAGGAGACAAAATTTC
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* *
29363 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTA
* * *
29400 TTTCAAAGGAAATGTTTTCAATGTTGATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* * *
29464 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTA
29501 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
* ** *
29566 GTTTCAAGGGAAACTATCTCGATTGAGATAGAATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTA
29603 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
29667 AGTTCCAAAA
Statistics
Matches: 245, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
101 93 0.38
102 152 0.62
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTA
Found at i:30063 original size:82 final size:84
Alignment explanation
Indices: 29919--30087 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 84
29909 TCCGCCGTGA
* * *
29919 AGTTAAAATTGGCTCTGGAACTAGGAAATTGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAG
1 AGTTAAAATTGGCTCTCGAAATAGGAAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAG
* *
29984 TTGAGCTTGTGCTGTCTCG
66 TTGAACTTGTGCTCTCTCG
* * * * *
30003 AGTTGAAATTGGCTC-CGAAATTGGAAATTGTTT-TTGACAACCAGTCGTCCCTTCGTTGTGAAG
1 AGTTAAAATTGGCTCTCGAAATAGGAAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAG
*
30066 TTGAACTTGTGTTCTCTCG
66 TTGAACTTGTGCTCTCTCG
30085 AGT
1 AGT
30088 CCAATATCCT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 45 0.61
83 15 0.20
84 14 0.19
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (84 bp):
AGTTAAAATTGGCTCTCGAAATAGGAAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAG
TTGAACTTGTGCTCTCTCG
Found at i:30834 original size:32 final size:32
Alignment explanation
Indices: 30798--30860 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
30788 CCCAAAGATG
* * *
30798 CCCCAATATTCGATGTTGAATCTCAAAAAATT
1 CCCCAACATTCGATGTTAAATCTAAAAAAATT
*
30830 CCCCAACATTTGATGTTAAATCTAAAAAAAT
1 CCCCAACATTCGATGTTAAATCTAAAAAAAT
30861 GGCCAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (32 bp):
CCCCAACATTCGATGTTAAATCTAAAAAAATT
Found at i:30867 original size:31 final size:32
Alignment explanation
Indices: 30798--30888 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
30788 CCCAAAGATG
* * *
30798 CCCCAATATTCGATGTTGAATCTCAAAAAATT
1 CCCCAACATTTGATGTTGAATCTCAAAAAAAT
*
30830 CCCCAACATTTGATGTTAAATCT-AAAAAAAT
1 CCCCAACATTTGATGTTGAATCTCAAAAAAAT
** *
30861 GGCCAACATTTGATATTGAATCTTCAAA
1 CCCCAACATTTGATGTTGAATC-TCAAA
30889 GATGCCCTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 25 0.51
32 21 0.43
33 3 0.06
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (32 bp):
CCCCAACATTTGATGTTGAATCTCAAAAAAAT
Found at i:31923 original size:69 final size:69
Alignment explanation
Indices: 31812--31949 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
31802 TGTCTCTCTC
* *
31812 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATAGTGCTTGATCAATC
31877 TCAT
66 TCAT
* * *
31881 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATGATAGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATAGTGCTTGATCAATC
31946 TCAT
66 TCAT
31950 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATAGTGCTTGATCAATC
TCAT
Found at i:32049 original size:13 final size:13
Alignment explanation
Indices: 32021--32072 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
32011 TTTTCTTCAA
32021 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
32033 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
32045 ATTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
32059 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
32071 TT
1 TT
32073 CTTTTTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.30
13 24 0.65
14 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:32059 original size:26 final size:25
Alignment explanation
Indices: 32020--32070 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
32010 TTTTTCTTCA
32020 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
32045 ATTTTCTCTTTGTTTTTTCTCTTTTT
1 ATTTTC-CTTTGTTTTTTCTCTTTTT
32071 TTCTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:38168 original size:23 final size:24
Alignment explanation
Indices: 38130--38182 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
38120 CTTTTTTTCT
*
38130 TTTCCTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
38154 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
38177 TTTCTT
1 TTTCTT
38183 TTCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.09, C:0.19, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:41062 original size:9 final size:9
Alignment explanation
Indices: 41048--41077 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
41038 AAATCAAGAG
41048 AAAAAAATT
1 AAAAAAATT
41057 AAAAAAATT
1 AAAAAAATT
41066 AAAAAAATT
1 AAAAAAATT
41075 AAA
1 AAA
41078 TAAGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAAATT
Found at i:41157 original size:20 final size:17
Alignment explanation
Indices: 41126--41173 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 17
41116 CAAGTCAAAG
41126 AAAAT-AAATAATAAATT
1 AAAATAAAATAATAAA-T
41143 AATAATAATAATAATAAAT
1 AA-AATAA-AATAATAAAT
41162 AAAATAAAATAA
1 AAAATAAAATAA
41174 AACTTAGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 4 0.14
20 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAAATAATAAAT
Found at i:42328 original size:22 final size:22
Alignment explanation
Indices: 42309--42352 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42299 ATTAATTAGT
42309 ATATTTTAAATTATTTATTAAA
1 ATATTTTAAATTATTTATTAAA
* *
42331 ATATATTAGATTATTATATTAA
1 ATATTTTAAATTATT-TATTAA
42353 TATTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTAAATTATTTATTAAA
Found at i:42373 original size:27 final size:26
Alignment explanation
Indices: 42353--42431 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
42343 ATTATATTAA
42353 TATTAAATATATAAATAATTAT-TCT
1 TATTAAATATATAAATAATTATATCT
* *
42378 TATTAAATATATAAAAAATTATATATT
1 TATTAAATATATAAATAATTATAT-CT
*
42405 TATTGAAATA-A-AAAT-ATAATATCT
1 TATT-AAATATATAAATAATTATATCT
42429 TAT
1 TAT
42432 ATTATAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.09
25 27 0.59
26 4 0.09
27 6 0.13
28 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
TATTAAATATATAAATAATTATATCT
Found at i:42454 original size:20 final size:21
Alignment explanation
Indices: 42431--42506 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 21
42421 TAATATCTTA
* *
42431 TATTATAATATTGAT-TATTT
1 TATTATAATATTAATATATAT
42451 TATTATAATATTAATAATATAT
1 TATTATAATATTAAT-ATATAT
42473 TATTATAAATATTAATAAATATAT
1 TATTAT-AATATTAAT--ATATAT
42497 T-TTA-AATATT
1 TATTATAATATT
42507 TTAATAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.28
21 6 0.12
22 10 0.20
23 12 0.24
24 8 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
TATTATAATATTAATATATAT
Found at i:42476 original size:14 final size:13
Alignment explanation
Indices: 42431--42505 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 13
42421 TAATATCTTA
42431 TATTATAATATTGAT
1 TATTATAATA-T-AT
* * *
42446 TATTTTATTATAA
1 TATTATAATATAT
42459 TATTAATAATATAT
1 TATT-ATAATATAT
42473 TATTATAA-ATAT
1 TATTATAATATAT
*
42485 TAATA-AATATAT
1 TATTATAATATAT
42497 T-TTA-AATAT
1 TATTATAATAT
42506 TTTAATAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.18
12 13 0.26
13 9 0.18
14 11 0.22
15 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (13 bp):
TATTATAATATAT
Found at i:42510 original size:23 final size:23
Alignment explanation
Indices: 42446--42559 Score: 83
Period size: 24 Copynumber: 4.7 Consensus size: 23
42436 TAATATTGAT
42446 TATTTTATTATAATATTAAT-AATA
1 TATTTTA-TA-AATATTAATAAATA
42470 TATTATTATAAATATTAATAAATA
1 TATT-TTATAAATATTAATAAATA
* *
42494 TATTTTA-AATATTTTAATAATTAA
1 TATTTTATAA-ATATTAATAAAT-A
*
42518 TATTTTGATGAAA-ATGATATTAAA-A
1 TATTTT-AT-AAATAT--TAATAAATA
*
42543 TATTTTATTAATATTAA
1 TATTTTATAAATATTAA
42560 ATTCATAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
22 4 0.05
23 24 0.33
24 25 0.34
25 12 0.16
26 1 0.01
27 7 0.10
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
TATTTTATAAATATTAATAAATA
Found at i:43481 original size:3 final size:3
Alignment explanation
Indices: 43473--43636 Score: 248
Period size: 3 Copynumber: 54.7 Consensus size: 3
43463 TGTCCACCAG
43473 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
43520 CTT CTTT CTT CTCT CTTT CTT CTCT CTT CTT CTTT CTT CTT CTT CTT
1 CTT C-TT CTT CT-T C-TT CTT CT-T CTT CTT C-TT CTT CTT CTT CTT
43567 C-T CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
43612 CTT CTT CTT CTT C-T CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
43637 CTTTTACTTT
Statistics
Matches: 151, Mismatches: 0, Indels: 20
0.88 0.00 0.12
Matches are distributed among these distances:
2 10 0.07
3 127 0.84
4 13 0.09
5 1 0.01
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:45533 original size:27 final size:28
Alignment explanation
Indices: 45487--45547 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
45477 AGACTAATAA
45487 AATAATAAGTCAAAATAAATAAATAAAAGT
1 AATAATAAGTCAAAATAAATAAA-AAAA-T
45517 AATAATAA-T-AAAA-AAATAAAAAAAT
1 AATAATAAGTCAAAATAAATAAAAAAAT
45542 AA-AATA
1 AATAATA
45548 GAATATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 4 0.13
27 7 0.23
28 4 0.13
29 1 0.03
30 8 0.26
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (28 bp):
AATAATAAGTCAAAATAAATAAAAAAAT
Found at i:45565 original size:30 final size:31
Alignment explanation
Indices: 45498--45569 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
45488 ATAATAAGTC
* *
45498 AAAATAAATAAATAAAAGTAATAATAATAAA
1 AAAATAAAAAAATAAAAGTAAGAATAATAAA
**
45529 AAAATAAAAAAATAAAA-T-AGAATATATACG
1 AAAATAAAAAAATAAAAGTAAGAATA-ATAAA
45559 AAAATAAAAAA
1 AAAATAAAAAA
45570 GGGTTAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 5 0.14
30 15 0.42
31 16 0.44
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (31 bp):
AAAATAAAAAAATAAAAGTAAGAATAATAAA
Found at i:45594 original size:8 final size:8
Alignment explanation
Indices: 45583--45616 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
45573 TTAAATTTTG
45583 AAATAAAA
1 AAATAAAA
45591 AAATAAAA
1 AAATAAAA
*
45599 AAA-ATAA
1 AAATAAAA
45606 AAATAAAA
1 AAATAAAA
45614 AAA
1 AAA
45617 GAAGTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:45668 original size:5 final size:5
Alignment explanation
Indices: 45658--45691 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
45648 AACATGCTCG
*
45658 AAATA AAATA AAATA AAATA AAATA AAATG AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
45692 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:46979 original size:31 final size:32
Alignment explanation
Indices: 46930--47006 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 32
46920 AAAATTATAA
**
46930 TATATATATATATATTAAAAATA-TTTTTTAAAC
1 TATATAT-TATATATTAAAAA-AGTTTTCAAAAC
46963 TATATATTATAT-TTAAAAAAGTTTTCAAAAC
1 TATATATTATATATTAAAAAAGTTTTCAAAAC
46994 TATATATTATATA
1 TATATATTATATA
47007 GTTTTCAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 1 0.03
31 27 0.68
32 5 0.12
33 7 0.17
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (32 bp):
TATATATTATATATTAAAAAAGTTTTCAAAAC
Found at i:47100 original size:37 final size:37
Alignment explanation
Indices: 46884--47369 Score: 361
Period size: 37 Copynumber: 13.3 Consensus size: 37
46874 ATTTTTAAAA
* * *** *
46884 AAAACTATATATTATA-AGTATTTCAAAAACGGTTTA
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
* *
46920 AAAATTATA-ATATATATATATATATT-AAAAATATTTTT
1 AAAACTATATAT-TATATA-AT-TTTTCAAAAATATTTTT
* *
46958 TAAACTATATA-T-TAT-A--TTT-AAAAA-AGTTTTC
1 AAAACTATATATTATATAATTTTTCAAAAATA-TTTTT
*
46989 AAAACTATATATTATAT-AGTTTTC---AATATGTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATAT-TTTT
* * *
47023 -AAA--A-ATATTACATAAGTTTTCAAAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTC--AAAAATATTTTT
*
47058 GAAACTATATATTATATAATTTTTCAAAAATATTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
*
47095 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
*
47132 AAAACTATATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAAC--TATATATTATATAATTTTTCAAAAATATTTTT
*
47171 AAAACTATATATTATATAATTTTTCAAAAA-AGTTTTA
1 AAAACTATATATTATATAATTTTTCAAAAATA-TTTTT
* * * *
47208 AAAATTATATATTATATAAGTTTTC-AAAATGTTTTA
1 AAAACTATATATTATATAATTTTTCAAAAATATTTTT
* *
47244 AAAACTATATAATATATATATATATTT-AAAAATATTTTCA
1 AAAACTATAT-AT-TATATA-ATTTTTCAAAAATATTTT-T
* * * *
47284 AAAACTATATAATATATAAATTTTCGAAAATCGTTTTCT
1 AAAACTATATATTATATAATTTTTCAAAAAT-ATTTT-T
* * * *
47323 AAAAATTATATATTATAT--TTTGTCAAAAACATTTTC
1 -AAAACTATATATTATATAATTTTTCAAAAATATTTTT
47359 ACAAACTATAT
1 A-AAACTATAT
47370 TACCATATAC
Statistics
Matches: 369, Mismatches: 45, Indels: 72
0.76 0.09 0.15
Matches are distributed among these distances:
30 9 0.02
31 29 0.08
32 1 0.00
33 10 0.03
34 5 0.01
35 10 0.03
36 48 0.13
37 115 0.31
38 42 0.11
39 74 0.20
40 26 0.07
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATAATTTTTCAAAAATATTTTT
Found at i:47107 original size:76 final size:73
Alignment explanation
Indices: 46884--47369 Score: 382
Period size: 76 Copynumber: 6.6 Consensus size: 73
46874 ATTTTTAAAA
* * * * * * * *
46884 AAAACTATATATTATA-AGTATTTCAAAAACGGTTTAAAAATTATAATATATATATATA-TATTA
1 AAAACTATATATTATATAATTTTTCAAAAAAGTTTTTAAAACTAT-ATAT-TATATA-AGTTTTC
46947 AAAATATTTTT
63 AAAATATTTTT
* *
46958 TAAACTATATA-T-TAT-A--TTT-AAAAAAGTTTTCAAAACTATATATTATAT-AGTTTTC--A
1 AAAACTATATATTATATAATTTTTCAAAAAAGTTTTTAAAACTATATATTATATAAGTTTTCAAA
47014 ATATGTTTT
66 ATAT-TTTT
* * * *
47023 -AAA--A-ATATTACATAAGTTTTCAAAAAAATGTTTTTGAAACTATATATTATATAATTTTTCA
1 AAAACTATATATTATATAATTTTTC-AAAAAA-GTTTTTAAAACTATATATTATATAAGTTTTC-
47084 AAAATATTTTT
63 AAAATATTTTT
* *
47095 AAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATATTATATAATTTTTCA
1 AAAACTATATATTATATAATTTTTCAAAAAAGTTTTTAAAAC--TATATATTATATAAGTTTTC-
*
47160 AAAATGTTTTT
63 AAAATATTTTT
* *
47171 AAAACTATATATTATATAATTTTTCAAAAAAGTTTTAAAAATTATATATTATATAAGTTTTCAAA
1 AAAACTATATATTATATAATTTTTCAAAAAAGTTTTTAAAACTATATATTATATAAGTTTTCAAA
* *
47236 ATGTTTTA
66 ATATTTTT
* * * *
47244 AAAACTATATAATATATATATATATTT-AAAAATA-TTTTCAAAAACTATATAATATATAAATTT
1 AAAACTATAT-AT-TATATA-ATTTTTCAAAAA-AGTTTT-TAAAACTATATATTATATAAGTTT
*
47307 TCGAAAATCGTTTTCT
61 TC-AAAAT-ATTTT-T
* * *
47323 AAAAATTATATATTATAT--TTTGTCAAAAACA-TTTTCACAAACTATAT
1 -AAAACTATATATTATATAATTTTTCAAAAA-AGTTTTTA-AAACTATAT
47370 TACCATATAC
Statistics
Matches: 348, Mismatches: 32, Indels: 62
0.79 0.07 0.14
Matches are distributed among these distances:
61 3 0.01
62 2 0.01
63 2 0.01
64 9 0.03
65 5 0.01
66 6 0.02
67 5 0.01
68 10 0.03
69 37 0.11
70 9 0.03
72 6 0.02
73 29 0.08
74 41 0.12
75 25 0.07
76 133 0.38
77 5 0.01
78 10 0.03
79 2 0.01
80 9 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (73 bp):
AAAACTATATATTATATAATTTTTCAAAAAAGTTTTTAAAACTATATATTATATAAGTTTTCAAA
ATATTTTT
Found at i:47176 original size:113 final size:112
Alignment explanation
Indices: 46868--47340 Score: 405
Period size: 113 Copynumber: 4.3 Consensus size: 112
46858 ATAGTTTCAA
* * * * *
46868 AAAAATATTTTTAAAA-AAAACTATATATTATAAGTATTTCAAAAACGGTTTAAAAATTATA-AT
1 AAAAATATTTTTAAAATTATA-TAT-TA-TATAAGT-TTTC-AAAATGTTTTAAAAACTATATAT
* * *
46931 A-TATATATATATATT-AAAAATATTTTTTAAACTATATA-T-TAT-A--TTT-
61 ATTATATA-AT-TTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTC
* * *
46977 AAAAA-AGTTTTCAAAACTATATATTATAT-AGTTTTCAATATGTTTT---AA--A-A-ATATTA
1 AAAAATA-TTTTTAAAATTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATATTA
* * *
47033 CATAAGTTTTCAAAAAAATGTTTTTGAAACTATATATTATATAATTTTTC
65 TATAATTTTTC--AAAAATGTTTTTAAAACTATATATTATATAATTTTTC
* * *
47083 AAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATATTA
1 AAAAATATTTTTAAAATTATATATTATATAAGTTTTC-AAAATGTTTTAAAAACTATATATATTA
47148 TATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTC
65 TATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTC
*
47196 AAAAA-AGTTTTAAAAATTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATA-ATAT
1 AAAAATA-TTTTTAAAATTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATAT-T
* * * * *
47259 ATATATATATTT-AAAAATATTTTCAAAAACTATATAATATATAAATTTTC
64 ATATA-ATTTTTCAAAAATGTTTT-TAAAACTATATATTATATAATTTTTC
* *
47309 GAAAATCGTTTTCTAAAAATTATATATTATAT
1 AAAAAT-ATTTT-T-AAAATTATATATTATAT
47341 TTTGTCAAAA
Statistics
Matches: 305, Mismatches: 29, Indels: 53
0.79 0.07 0.14
Matches are distributed among these distances:
97 3 0.01
98 5 0.02
99 6 0.02
100 21 0.07
101 3 0.01
102 3 0.01
103 1 0.00
104 7 0.02
105 7 0.02
106 29 0.10
107 10 0.03
108 12 0.04
109 16 0.05
110 2 0.01
111 4 0.01
112 38 0.12
113 101 0.33
114 5 0.02
115 15 0.05
116 17 0.06
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (112 bp):
AAAAATATTTTTAAAATTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATATTAT
ATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTC
Found at i:47973 original size:33 final size:33
Alignment explanation
Indices: 47931--48091 Score: 182
Period size: 33 Copynumber: 4.8 Consensus size: 33
47921 TTTTTTTGTG
* * *
47931 TGTGTTTCAAGAGAAACAATTTCATATGTTTTT
1 TGTGTTTCAAGATAAACAATTTCAAAGGTTTTT
47964 TGTGTTTCAAGATAAACAATTTCAAAGGTTTTT
1 TGTGTTTCAAGATAAACAATTTCAAAGGTTTTT
** *
47997 TGTGTTTCAAGATAAACTTTTTTTTC-AA-TTTTTT
1 TGTGTTTCAAGATAAAC---AATTTCAAAGGTTTTT
* * *
48031 TTTATTTCAAGATAAGCAATTTCAAAGGTTTTTT
1 TGTGTTTCAAGATAAACAATTTCAAAGG-TTTTT
*
48065 TGTGTTTCAAGAGAAACAATTTCAAAG
1 TGTGTTTCAAGATAAACAATTTCAAAG
48092 ATTGGTGTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
31 4 0.04
32 2 0.02
33 47 0.44
34 47 0.44
35 2 0.02
36 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTGTTTCAAGATAAACAATTTCAAAGGTTTTT
Found at i:48051 original size:67 final size:70
Alignment explanation
Indices: 47950--48081 Score: 207
Period size: 67 Copynumber: 1.9 Consensus size: 70
47940 AGAGAAACAA
* *
47950 TTTCATATGTTTTTTGTGTTTCAAGATAAACAATTTCAAAGG-TTTTTTGTGTTTCAAGATAAAC
1 TTTCATATGTTTTTTGTATTTCAAGATAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAAC
48014 TTTTT
66 TTTTT
* *
48019 TTTCA-AT-TTTTTTTTATTTCAAGATAAGCAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAAC
1 TTTCATATGTTTTTTGTATTTCAAGATAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAAC
48082 AATTTCAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 30 0.52
68 23 0.40
69 5 0.09
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (70 bp):
TTTCATATGTTTTTTGTATTTCAAGATAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAAC
TTTTT
Found at i:48090 original size:34 final size:34
Alignment explanation
Indices: 47886--48091 Score: 172
Period size: 34 Copynumber: 5.9 Consensus size: 34
47876 AACTCAAAGG
47886 TTTTGTGTTTCAAGAGAAAC-ATTCTCAAAGGGTTTTTTTT
1 TTTTGTGTTTCAAGAGAAACAATT-TCAAA-GG-----TTT
* *
47926 TTGTGTGTGTTTCAAGAGAAACAATTTCATATG-TT
1 TT-T-TGTGTTTCAAGAGAAACAATTTCAAAGGTTT
*
47961 TTTTGTGTTTCAAGATAAACAATTTCAAAGG-TT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
* **
47994 TTTTGTGTTTCAAGATAAACTTTTTTTTC-AA--TTT
1 TTTTGTGTTTCAAGAGAAAC---AATTTCAAAGGTTT
* * * *
48028 TTTTTTATTTCAAGATAAGCAATTTCAAAGGTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
48062 TTTTGTGTTTCAAGAGAAACAATTTCAAAG
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAG
48092 ATTGGTGTTT
Statistics
Matches: 140, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
31 4 0.03
32 2 0.01
33 47 0.34
34 49 0.35
35 6 0.04
36 4 0.03
40 2 0.01
41 2 0.01
42 21 0.15
43 3 0.02
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (34 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
Found at i:48175 original size:39 final size:37
Alignment explanation
Indices: 48097--48184 Score: 124
Period size: 37 Copynumber: 2.3 Consensus size: 37
48087 CAAAGATTGG
*
48097 TGTTTCAAGAGAAACTGTTTCAAGAGAGACATAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACATAACTT
*
48134 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAACATAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG---ACATAACTT
48173 TGTTTCAAGAGA
1 TGTTTCAAGAGA
48185 GACCAAACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
37 26 0.58
39 13 0.29
40 6 0.13
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACATAACTT
Found at i:48213 original size:61 final size:59
Alignment explanation
Indices: 48112--48224 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 59
48102 CAAGAGAAAC
* * **
48112 TGTTTCAAGAGAGACATAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAACATAATT
1 TGTTTCAAGAGAGACATAACTTAGTTCCAAAAGAAACTGTCTC--GAGAGACAACATAATT
*
48173 TGTTTCAAGAGAGACCA-AACTTAGTTCCAAAAGAAGCTGTCTCGAGAGACAA
1 TGTTTCAAGAGAGA-CATAACTTAGTTCCAAAAGAAACTGTCTCGAGAGACAA
48225 AATTTGTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 9 0.20
61 35 0.76
62 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (59 bp):
TGTTTCAAGAGAGACATAACTTAGTTCCAAAAGAAACTGTCTCGAGAGACAACATAATT
Found at i:48359 original size:36 final size:36
Alignment explanation
Indices: 48260--48512 Score: 302
Period size: 36 Copynumber: 7.1 Consensus size: 36
48250 AAAGCTTTCA
*
48260 TTTCAAG-GAAACTCTCTCAAGAGAGACAAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTG
48296 TTTCAATG-GAAACTG--T--AGAGAGACAAAATTTG
1 TTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
48328 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
48364 TTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTT-CAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
48401 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * * * *
48437 TTTTAAGAGAAAATGTCTCAAGAAATACAAAACTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
48473 TTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
48510 TTT
1 TTT
48513 TGAGTAAATT
Statistics
Matches: 186, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.01
32 21 0.11
33 8 0.04
34 1 0.01
35 1 0.01
36 110 0.59
37 44 0.24
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:48455 original size:109 final size:104
Alignment explanation
Indices: 48259--48512 Score: 321
Period size: 109 Copynumber: 2.4 Consensus size: 104
48249 CAAAGCTTTC
* * *
48259 ATTTC-AAGGAAACTCTCTCAAGAGAGACAAAAATTTGTTTCAATGGAAACTGTAGAGAGACAAA
1 ATTTCAAAAGAAACTATCTCAAGAGAGAC-AAAATTTGTTTCAAGGGAAACTGTAGAGAGACAAA
* *
48323 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
65 ATTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTT
* * *
48363 ATTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 ATTT-CAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTG--T--AGAGAGA
* *
48428 CAAAATTTGTTTTAAGAGAAAATGTCTCAAGAAATACAAAACTT
61 CAAAATTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTT
* * *
48472 GTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTT
1 ATTTCAAAAGAAACTATCTCAAGAGAGACAAAA-TTTGTTT
48513 TGAGTAAATT
Statistics
Matches: 128, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
104 4 0.03
105 22 0.17
106 20 0.16
107 1 0.01
108 24 0.19
109 57 0.45
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (104 bp):
ATTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTAGAGAGACAAAA
TTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTT
Found at i:50033 original size:95 final size:95
Alignment explanation
Indices: 49837--50075 Score: 284
Period size: 95 Copynumber: 2.5 Consensus size: 95
49827 CATAAAGCCA
* * * * **
49837 GGGCATTTAACCAATTACTCTAGAGGGACAACTTAGTATCATTGTATAG-ATATTATAATTGCAT
1 GGGCGTTTAACCAATTACTCTAGAGGGACAACTCA--AGC-TT-TATTGTATATTATAATCACAT
* *
49901 TTATCATGCTAGCTAAATATTATCCATAAAGTTG
62 TTAGCAGGCTAGCTAAATATTATCCATAAAGTTG
* *
49935 GGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTAG
1 GGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACATTTAG
* *
50000 CAGGCTAGCTGAATCTTATCCATAAA-TTCG
66 CAGGCTAGCTAAATATTATCCATAAAGTT-G
* * *
50030 GGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGTTTTATTGT
1 GGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGT
50076 GTGTATATAT
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
94 6 0.05
95 84 0.68
96 2 0.02
98 32 0.26
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
GGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACATTTAG
CAGGCTAGCTAAATATTATCCATAAAGTTG
Found at i:53985 original size:43 final size:43
Alignment explanation
Indices: 53937--54018 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
53927 GAAAAACAAC
*
53937 AAAGTAATAGACTAATAA-AAT-AATAAGTCAAAATA-AATAAATA
1 AAAGTAATA-A-TAATAATAATAAATAA-ACAAAATAGAATAAATA
53980 AAAGTAATAATAATAATAATAAATAAACAAAATAGAATA
1 AAAGTAATAATAATAATAATAAATAAACAAAATAGAATA
54019 TATACGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
41 6 0.17
42 11 0.31
43 18 0.51
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (43 bp):
AAAGTAATAATAATAATAATAAATAAACAAAATAGAATAAATA
Found at i:53997 original size:18 final size:20
Alignment explanation
Indices: 53949--54001 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
53939 AGTAATAGAC
53949 TAATAA-AATAATAAGTCAA
1 TAATAATAATAATAAGTCAA
53968 -AATAAATAAATAA-AAGT-AA
1 TAAT-AAT-AATAATAAGTCAA
53987 TAATAATAATAATAA
1 TAATAATAATAATAA
54002 ATAAACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 7 0.24
21 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
TAATAATAATAATAAGTCAA
Found at i:54004 original size:13 final size:12
Alignment explanation
Indices: 53950--54006 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 12
53940 GTAATAGACT
53950 AATAAAATAATA
1 AATAAAATAATA
*
53962 AGTCAAAATAAATA
1 AAT-AAAAT-AATA
53976 AATAAAAGTAAT-
1 AATAAAA-TAATA
53988 AATAATAATAATA
1 AATAA-AATAATA
54001 AATAAA
1 AATAAA
54007 CAAAATAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 12 0.32
13 19 0.50
14 7 0.18
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:54079 original size:8 final size:8
Alignment explanation
Indices: 54048--54072 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54038 TTAAATTTTG
54048 AAATAAAA
1 AAATAAAA
54056 AAATAAAA
1 AAATAAAA
54064 AAATAAAA
1 AAATAAAA
54072 A
1 A
54073 TAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:55241 original size:3 final size:3
Alignment explanation
Indices: 55207--55271 Score: 60
Period size: 3 Copynumber: 20.7 Consensus size: 3
55197 TGACCCTGAA
* *
55207 AAT AAA AAT AA- AAT AAAT AAT AAAT AAA AAT AAT AAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT -AAT -AAT AAT
*
55255 ACT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
55272 ATAAATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 37 0.71
4 13 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:55271 original size:26 final size:27
Alignment explanation
Indices: 55205--55280 Score: 109
Period size: 26 Copynumber: 2.8 Consensus size: 27
55195 TTTGACCCTG
*
55205 AAAATAAAAATAAAATAAATAATAAATA
1 AAAATAATAAT-AAATAAATAATAAATA
*
55233 AAAATAATAATAAATAAATAAT-ACTA
1 AAAATAATAATAAATAAATAATAAATA
*
55259 ATAATAATAATAAATAAATAAT
1 AAAATAATAATAAATAAATAAT
55281 TGTTAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 24 0.53
27 11 0.24
28 10 0.22
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAATAATAATAAATAAATAATAAATA
Found at i:55278 original size:23 final size:23
Alignment explanation
Indices: 55208--55280 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
55198 GACCCTGAAA
55208 ATAAA-AATAA-AATAAATAATAA
1 ATAAATAATAATAAT-AATAATAA
55230 ATAAA-AATAATAAT-A-AATAA
1 ATAAATAATAATAATAATAATAA
*
55250 AT-AATACTAATAATAATAATAA
1 ATAAATAATAATAATAATAATAA
55272 ATAAATAAT
1 ATAAATAAT
55281 TGTTAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.05
20 15 0.34
21 2 0.05
22 17 0.39
23 8 0.18
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAATAATAATAATAATAATAA
Found at i:55317 original size:39 final size:38
Alignment explanation
Indices: 55274--55353 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
55264 AATAATAAAT
55274 AAATAATTGTTAAAAAACCATATAATATA-TAGTTTCAAA
1 AAAT-ATTGTTAAAAAACCATATAATATACTA-TTTCAAA
* * * *
55313 AAATATTTTTTAAAAACTATATATTATACGTATTTCAAA
1 AAATATTGTTAAAAAACCATATAATATAC-TATTTCAAA
55352 AA
1 AA
55354 CATCTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 20 0.57
39 13 0.37
40 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (38 bp):
AAATATTGTTAAAAAACCATATAATATACTATTTCAAA
Found at i:55370 original size:36 final size:34
Alignment explanation
Indices: 55321--55771 Score: 223
Period size: 37 Copynumber: 12.6 Consensus size: 34
55311 AAAAATATTT
55321 TTTAAAAACTATATATTATACGTA-TTTCAAAAACA
1 TTTAAAAACTATATATTATA--TATTTTCAAAAACA
* *
55356 TCTTAAAAATTATATATTATATATTTTCAAAAATA
1 T-TTAAAAACTATATATTATATATTTTCAAAAACA
** * **
55391 TTTTTAAACTATATATTATA-A--TTAAAAAAGT
1 TTTAAAAACTATATATTATATATTTTCAAAAACA
* * **
55422 TTTCAAAACTATATATTATATAGTTTTTAAAAAGTGT
1 TTTAAAAACTATATATTATATA-TTTTCAAAAA--CA
* * **
55459 TTTTAAAATTATATATTATATAATTTTTCAAAAATGT
1 TTTAAAAACTATATATTATAT-A-TTTTCAAAAA-CA
* **
55496 TTTTAAAACTATATATTATATAATTTTCAAAAATGT
1 TTTAAAAACTATATATTATAT-ATTTTCAAAAA-CA
* **
55532 TTTTAAAACTATATATTATATAATTTTTCAAAAATGT
1 TTTAAAAACTATATATTATAT-A-TTTTCAAAAA-CA
* **
55569 TTTTAAAACTATATATATTATATAATTTTTCAAAAATGT
1 TTTAAAAAC--TATATATTATAT-A-TTTTCAAAAA-CA
* * * * **
55608 TTTTAAAACTATATATTTTTTAATTTTTTAAAAATGT
1 TTTAAAAACTATATATTATAT-A-TTTTCAAAAA-CA
* * ***
55645 TTTAAAAATTATATACTATATAAGTTTTCAAAATGT
1 TTTAAAAACTATATATTATAT-A-TTTTCAAAAACA
* * *
55681 TTTAAAAACTATATAATATATAAATGTTTTAAAAATA
1 TTTAAAAACTATAT-AT-TATATAT-TTTCAAAAACA
**
55718 TTTTCGAAACTATATATTATATA-TTT-AAAAA-A
1 -TTTAAAAACTATATATTATATATTTTCAAAAACA
* *
55750 TTCAAAAACTATATAATATATA
1 TTTAAAAACTATATATTATATA
55772 AATTTTCGAA
Statistics
Matches: 359, Mismatches: 41, Indels: 36
0.82 0.09 0.08
Matches are distributed among these distances:
31 43 0.12
32 2 0.01
33 6 0.02
34 21 0.06
35 19 0.05
36 75 0.21
37 130 0.36
38 26 0.07
39 37 0.10
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (34 bp):
TTTAAAAACTATATATTATATATTTTCAAAAACA
Found at i:55472 original size:37 final size:36
Alignment explanation
Indices: 55361--55740 Score: 450
Period size: 37 Copynumber: 10.5 Consensus size: 36
55351 AAACATCTTA
* * *
55361 AAAATTATATATTATAT-ATTTTCAAAAATATTTTT
1 AAAACTATATATTATATAATTTTTAAAAATGTTTTT
* *
55396 -AAACTATATA-T-TATAA---TTAAAAAAGTTTTC
1 AAAACTATATATTATATAATTTTTAAAAATGTTTTT
*
55426 AAAACTATATATTATATAGTTTTTAAAAAGTGTTTTT
1 AAAACTATATATTATATAATTTTTAAAAA-TGTTTTT
*
55463 AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTT-AAAAATGTTTTT
*
55500 AAAACTATATATTATATAATTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTAAAAATGTTTTT
55536 AAAACTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTT-AAAAATGTTTTT
55573 AAAACTATATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAAC--TATATATTATATAATTTTT-AAAAATGTTTTT
* * *
55612 AAAACTATATATTTTTTAATTTTTTAAAAATGTTTTA
1 AAAACTATATATTATATAA-TTTTTAAAAATGTTTTT
* * * * *
55649 AAAATTATATACTATATAAGTTTTCAAAATGTTTTA
1 AAAACTATATATTATATAATTTTTAAAAATGTTTTT
* * *
55685 AAAACTATATAATATATAAATGTTTTAAAAATATTTTC
1 AAAACTATATATTATAT-AAT-TTTTAAAAATGTTTTT
*
55723 GAAACTATATATTATATA
1 AAAACTATATATTATATA
55741 TTTAAAAAAT
Statistics
Matches: 300, Mismatches: 30, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.03
31 10 0.03
32 4 0.01
33 6 0.02
34 9 0.03
36 72 0.24
37 114 0.38
38 38 0.13
39 37 0.12
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
AAAACTATATATTATATAATTTTTAAAAATGTTTTT
Found at i:55609 original size:149 final size:147
Alignment explanation
Indices: 55319--55734 Score: 503
Period size: 149 Copynumber: 2.9 Consensus size: 147
55309 CAAAAAATAT
** * ** *
55319 TTTTTAAAAACTATATATTATA-CGTATTTCAAAAACATCTTAAAAATTATATATTATAT-ATTT
1 TTTTT-AAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAATTATATATTATATAATTT
* *
55382 TCAAAAATATTTTT-AAACTATATAT-TATAA---TTAAAAAAGTTTTCAAAAC--TATATATTA
65 TCAAAAATGTTTTTAAAACTATATATATATAATTTTTAAAAATGTTTTCAAAACTATATATATTA
*
55440 TATAGTTTTTAAAAAGTG
130 TATAATTTTTAAAAAGTG
* * *
55458 TTTTTAAAATTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTT
1 TTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAATTATATATTATATAATTTT
*
55523 CAAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATATT
66 CAAAAATGTTTTTAAAACTATATA-TATATAATTTTT-AAAAATGTTTTCAAAACTATATATATT
55588 ATATAATTTTTCAAAAA-TG
129 ATATAATTTTT-AAAAAGTG
* * * *
55607 TTTTTAAAACTATATATTTTTTAATTTTTTAAAAATGTTTTAAAAATTATATACTATATAAGTTT
1 TTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAATTATATATTATATAA-TTT
* * *
55672 TC-AAAATGTTTTAAAAACTATATAATATATAAATGTTTTAAAAATATTTTCGAAACTATATAT
65 TCAAAAATGTTTTTAAAACTATAT-ATATAT-AAT-TTTTAAAAATGTTTTCAAAACTATATAT
55735 TATATATTTA
Statistics
Matches: 237, Mismatches: 24, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
138 15 0.06
139 34 0.14
140 17 0.07
141 10 0.04
142 1 0.00
143 5 0.02
146 2 0.01
147 15 0.06
149 99 0.42
150 35 0.15
151 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (147 bp):
TTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAATTATATATTATATAATTTT
CAAAAATGTTTTTAAAACTATATATATATAATTTTTAAAAATGTTTTCAAAACTATATATATTAT
ATAATTTTTAAAAAGTG
Found at i:55842 original size:2 final size:2
Alignment explanation
Indices: 55835--55908 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
55825 TTATTATTAT
*
55835 TA TA TA TA TA TA TA TA -A TA AA TA -A TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55874 TA TA TA TA -A 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
55909 AACAAAATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56191 original size:27 final size:27
Alignment explanation
Indices: 56139--56191 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56129 AACCCACAGC
* *
56139 CCAAAGTATTTATAATTTTTTATATAG
1 CCAAACTATTTATAATTTTCTATATAG
56166 CCAAACTATTTATAATTTGTCT-TATA
1 CCAAACTATTTATAATTT-TCTATATA
56192 ATTTATGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (27 bp):
CCAAACTATTTATAATTTTCTATATAG
Found at i:56912 original size:11 final size:11
Alignment explanation
Indices: 56896--56921 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56886 ATTAGATAAC
56896 AAATATTAAAT
1 AAATATTAAAT
56907 AAATATTAAAT
1 AAATATTAAAT
56918 AAAT
1 AAAT
56922 CAAAGGGCAA
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):
AAATATTAAAT
Found at i:56959 original size:17 final size:17
Alignment explanation
Indices: 56937--56973 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
56927 GGCAAAAGAG
* *
56937 AAAAAATAATATATAAT
1 AAAAAATAAAATAAAAT
56954 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
56971 AAA
1 AAA
56974 TCAAAAGGAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:56999 original size:29 final size:29
Alignment explanation
Indices: 56937--57056 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 29
56927 GGCAAAAGAG
* *
56937 AAAAAATAATAT-ATAATAAAAAATA-A-A
1 AAAAAATAA-ATCAAAAGAAAAAATATATA
* *
56964 ATAAAATAAATCAAAAGGAAAAATATATA
1 AAAAAATAAATCAAAAGAAAAAATATATA
**
56993 AAAAAATATGTCAAAAGAAAAAATATATTA
1 AAAAAATAAATCAAAAGAAAAAATATA-TA
* * *
57023 AATAAATAAA--AAAA-CAAAAATAAATA
1 AAAAAATAAATCAAAAGAAAAAATATATA
*
57049 AAAGAATA
1 AAAAAATA
57057 TTAATGTAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
26 10 0.14
27 26 0.35
28 5 0.07
29 24 0.32
30 9 0.12
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (29 bp):
AAAAAATAAATCAAAAGAAAAAATATATA
Found at i:57117 original size:15 final size:15
Alignment explanation
Indices: 57064--57123 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
57054 ATATTAATGT
*
57064 AAAAATAAATGAATA
1 AAAAATAAAAGAATA
*
57079 AAGATAAGTAAAATTGAGTA
1 AA-A-AA-TAAAA--GAATA
57099 AAAAATAAAAGAATA
1 AAAAATAAAAGAATA
57114 AAAAATAAAA
1 AAAAATAAAA
57124 AAATGAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
15 16 0.43
16 1 0.03
17 7 0.19
18 6 0.16
19 1 0.03
20 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (15 bp):
AAAAATAAAAGAATA
Found at i:58681 original size:84 final size:84
Alignment explanation
Indices: 58554--59624 Score: 1252
Period size: 84 Copynumber: 12.8 Consensus size: 84
58544 CTGAATGGAA
* * * * * * * *
58554 TCGAACTCGAAGGT-TTTTGTTGGCAGATAGCCTTTTTTGCCTTGAGCTGTGCTGCAAATAATGC
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
58618 GCCTTGGAGCTGAGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* *
58637 TCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
58702 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
58721 TCGAACTCGAAGGTCTTTTGTTGACAAAATAACCCTTCGT-GCCTTGAGCTATGTTGTAAATGAT
1 TCGAACTCGAAGGTCTTTTGTTGGC-AGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAATGAT
58785 GTGCCTTGGAGCTGAGCGTAG
64 GTGCCTTGGAGCTGAGCGTAG
* * * * * *
58806 TCGAACTCAAAGGTATTTTGTTGACAGATAACCCTTCTAGCCTTGATTTATGCTGGAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
58871 GCCTTTGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
58890 TCGAACTTGAAAGTCTTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATACTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
**
58955 GCCTTTAAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
58974 TCGAACTTGAAGGTCTTTGGTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
59039 GCCTTTGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
59058 TCGAACTCGAAGGTCTTTTGTTGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
59123 GTCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * ** *
59142 TCGAACTCGAAGGTCTTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATATTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
59207 GTCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
59226 TCAAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTAACCTTGAGTTATACTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
59291 GCCTTTGAGCTGAGCGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
59310 TCAAACTCGAAGGAT-TTTTGTTGGTAAATAGA-CCTTCTTGCCTTCAGCTATGTTGCAAATGAT
1 TCGAACTCGAAGG-TCTTTTGTTGGCAGATA-ACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* *
59373 GTCCCTTGGAGCTGAACGTAG
64 GTGCCTTGGAGCTGAGCGTAG
* * * * * * * *
59394 TCGAACTCGAAGGCCTTTGGTTGGCAGATATCCCTTCTGGACTTAAGCTATGCTGCAAATGATGA
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * ** *
59459 GTCTTTGAGTTGAGTATAA
66 GCCTTGGAGCTGAGCGTAG
* * *
59478 TCAAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
59542 GCCTTGGAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* *
59561 TCGAACTCGAAGGTTTTTTGTTGGCAGATAAACCTTCTAGCCTTGAGTTATGCTGCAAATGATG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
59625 GTTTCTTAAA
Statistics
Matches: 851, Mismatches: 128, Indels: 17
0.85 0.13 0.02
Matches are distributed among these distances:
83 82 0.10
84 690 0.81
85 78 0.09
86 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:60917 original size:94 final size:92
Alignment explanation
Indices: 60721--60978 Score: 268
Period size: 93 Copynumber: 2.7 Consensus size: 92
60711 GGCTAGCTGA
* * * * * *
60721 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTTAA--TATCATTGTATAGA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAAGGACAACTCAAGCT-TTATTGTATAG-
* * * *
60784 TATTATAATTACTTTATCAGGGTAGTTGGATTTT
64 ----AT-ATTACTTTATCAGGCTAGCTGAATCTT
* * * *
60818 ATCCATAAAGTCGGGGCGTTTTCACCAATTACTCTAGAGGGATAACTCACGCTTTATTGTATAGA
1 ATCCATAAAGTCGGGGCG-TTTAACCAATTACTCTAGAAGGACAACTCAAGCTTTATTGTATAGA
60883 TATTACCTTTATCAGGCTAGCTGAATCTT
65 TATTA-CTTTATCAGGCTAGCTGAATCTT
* * *
60912 ATCCATAAAGTCGGGGCGTTTAACCAATTTCTTTAGAAGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAAGGACAACTCAAGCTTTATTGTATAGAT
60977 AT
66 AT
60979 AATATTATAA
Statistics
Matches: 138, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
93 46 0.33
94 39 0.28
97 16 0.12
98 26 0.19
99 10 0.07
100 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (92 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAAGGACAACTCAAGCTTTATTGTATAGAT
ATTACTTTATCAGGCTAGCTGAATCTT
Found at i:63693 original size:28 final size:30
Alignment explanation
Indices: 63631--63688 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
63621 TAAAATAAAT
*
63631 CAAAAGGAAAAATATATTAAAAAAATATTG
1 CAAAAGAAAAAATATATTAAAAAAATATTG
*
63661 CAAAAGAAAAAATATATTAAATAAATAT
1 CAAAAGAAAAAATATATTAAAAAAATAT
63689 GAAAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (30 bp):
CAAAAGAAAAAATATATTAAAAAAATATTG
Found at i:63698 original size:28 final size:30
Alignment explanation
Indices: 63638--63715 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
63628 AATCAAAAGG
*
63638 AAAAATATATTAAAAAAATATTGCAAAAGA
1 AAAAATATATTAAAAAAATATTGCAAAACA
*
63668 AAAAATATATTAAATAAATA-TG-AAAAC-
1 AAAAATATATTAAAAAAATATTGCAAAACA
* *
63695 AAAAATA-AATAAAAGAATATT
1 AAAAATATATTAAAAAAATATT
63716 AATATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 9 0.21
27 8 0.19
28 4 0.10
29 2 0.05
30 19 0.45
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (30 bp):
AAAAATATATTAAAAAAATATTGCAAAACA
Found at i:63779 original size:7 final size:7
Alignment explanation
Indices: 63756--63797 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
63746 TAAAATTGAG
63756 TAAAAAA
1 TAAAAAA
63763 TAAAAGAA
1 TAAAA-AA
63771 TAAAAAA
1 TAAAAAA
*
63778 T-ATAAA
1 TAAAAAA
63784 TAAAAAA
1 TAAAAAA
63791 TAAAAAA
1 TAAAAAA
63798 ATGAAGTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 19 0.61
8 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:67831 original size:29 final size:30
Alignment explanation
Indices: 67770--67838 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
67760 TGATTTTTTT
* *
67770 AAAAT-AATTATTATAATTTGAATTATTGA
1 AAAATGAATTATTAGAATTTGAATTACTGA
* *
67799 AAAATGAATTATTGGAATTTGAATT-CTGG
1 AAAATGAATTATTAGAATTTGAATTACTGA
67828 AAAATGAATTA
1 AAAATGAATTA
67839 CATTTCTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.46, C:0.01, G:0.13, T:0.39
Consensus pattern (30 bp):
AAAATGAATTATTAGAATTTGAATTACTGA
Found at i:67835 original size:14 final size:15
Alignment explanation
Indices: 67788--67839 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
67778 TATTATAATT
* *
67788 TGAATTATTGAAAAA
1 TGAATTACTGGAAAA
* **
67803 TGAATTATTGGAATT
1 TGAATTACTGGAAAA
67818 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
67832 TGAATTAC
1 TGAATTAC
67840 ATTTCTGGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:68029 original size:22 final size:21
Alignment explanation
Indices: 68004--68079 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
67994 AAATAATAAA
68004 TAATATTATTTATTATAAAACT
1 TAATATTATTTATTATAAAA-T
* *
68026 TAATATTATTATTTTATAATAT
1 TAATATTATT-TATTATAAAAT
* * **
68048 TAAAATAATTTATT-TATTAT
1 TAATATTATTTATTATAAAAT
68068 TAAATATTATTT
1 T-AATATTATTT
68080 TATAATTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.14
21 11 0.25
22 19 0.43
23 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTATTTATTATAAAAT
Found at i:68087 original size:18 final size:18
Alignment explanation
Indices: 68032--68087 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
68022 AACTTAATAT
68032 TATTATTTTATAATATTAAAA
1 TATTATTTTAT-A-ATT-AAA
*
68053 TAATT-TATTTATTATTAAA
1 T-ATTAT-TTTATAATTAAA
68072 TATTATTTTATAATTA
1 TATTATTTTATAATTA
68088 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 12 0.40
19 5 0.17
20 3 0.10
21 2 0.07
22 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTTTATAATTAAA
Found at i:68102 original size:34 final size:34
Alignment explanation
Indices: 68063--68148 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 34
68053 TAATTTATTT
68063 ATTATTAAATATTATTTTATAATTAT-ATT-TTAAA
1 ATTATTAAATATTATTTTA-AA-TATCATTATTAAA
* *
68097 ATTATTAATTAGTATATTTTAAATATCTTTATTAAA
1 ATTATTAAATA-T-TATTTTAAATATCATTATTAAA
68133 A-TATTAAAATATTATT
1 ATTATT-AAATATTATT
68149 ATATTAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
34 17 0.39
35 10 0.23
36 17 0.39
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (34 bp):
ATTATTAAATATTATTTTAAATATCATTATTAAA
Found at i:68214 original size:27 final size:28
Alignment explanation
Indices: 68150--68214 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
68140 AATATTATTA
*
68150 TATTA-ATATTAAATACATAAATAATAT
1 TATTATATATTAAATACATAAAAAATAT
*
68177 TATTCAT-TATTAAATATATAAAAAAT-T
1 TATT-ATATATTAAATACATAAAAAATAT
68204 TATTATATATT
1 TATTATATATT
68215 TATTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 13 0.39
28 18 0.55
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTATATATTAAATACATAAAAAATAT
Found at i:68289 original size:14 final size:15
Alignment explanation
Indices: 68270--68325 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
68260 ATTATTTTAT
68270 TATAATATTAA-AAA
1 TATAATATTAATAAA
* *
68284 TATAATATTATATTAT
1 TATAATATTA-ATAAA
68300 TATAAATATTAATAAA
1 TAT-AATATTAATAAA
68316 TAT-ATATTAA
1 TATAATATTAA
68326 ATATTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 17 0.49
15 1 0.03
16 10 0.29
17 7 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATATTAATAAA
Found at i:68295 original size:22 final size:23
Alignment explanation
Indices: 68267--68345 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 23
68257 TTGATTATTT
68267 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
68289 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
* * *
68312 TA-AATATATATTAAATATTTTAA
1 TATTATA-ATATTAAAAATATTAA
*
68335 TAAT-TAATATT
1 TATTATAATATT
68346 TTGATGAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 25 0.54
23 21 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:68300 original size:30 final size:31
Alignment explanation
Indices: 68240--68343 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 31
68230 ATAATATCTT
* *
68240 ATATTATTATAATATAATTGATTATTTTATTATA
1 ATATTAATA-AATATAA-T-ATTATATTATTATA
68274 ATATTAA-AAATATAATATTATATTATTATAA
1 ATATTAATAAATATAATATTATATTATTAT-A
* *
68305 ATATTAATAAATAT-ATATTA-AATATTTTA
1 ATATTAATAAATATAATATTATATTATTATA
68334 ATAATTAATA
1 AT-ATTAATA
68344 TTTTGATGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.05
30 25 0.40
31 15 0.24
32 13 0.21
33 1 0.02
34 6 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATATTAATAAATATAATATTATATTATTATA
Found at i:68323 original size:23 final size:22
Alignment explanation
Indices: 68268--68345 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
68258 TGATTATTTT
68268 ATTATAATATTAAAA-ATATAAT-
1 ATTAT-ATATTAAAATAT-TAATA
68290 ATTATATTATTATAAATATTAATA
1 ATTATA-TATTA-AAATATTAATA
* *
68314 AATATATATTAAATATTTTAATA
1 ATTATATATTAAA-ATATTAATA
68337 ATTA-ATATT
1 ATTATATATT
68346 TTGATGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 1 0.02
22 17 0.35
23 23 0.48
24 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATATATTAAAATATTAATA
Found at i:68600 original size:41 final size:41
Alignment explanation
Indices: 68553--68633 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
68543 CAAACACCGG
*
68553 AAAATATTTTCCGGAAAACGAATTACGTGAAACAAACACAA
1 AAAATATTTTCCGGAAAACGAATTACATGAAACAAACACAA
*
68594 AAAATATTTTTCGGAAAACGAATTACATGAAACAAACACA
1 AAAATATTTTCCGGAAAACGAATTACATGAAACAAACACA
68634 GGATTTCGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (41 bp):
AAAATATTTTCCGGAAAACGAATTACATGAAACAAACACAA
Found at i:69505 original size:32 final size:26
Alignment explanation
Indices: 69442--69508 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
69432 AGTTTAAGCT
*
69442 TTTCGAGTTTAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
69468 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
69494 TTTCGAGTTCGAGTT
1 TTTCGAGTTCAAGTT
69509 GAACTTGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:72722 original size:2 final size:2
Alignment explanation
Indices: 72717--72746 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
72707 ACACACATTC
72717 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
72747 ACTACTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75140 original size:3 final size:3
Alignment explanation
Indices: 75132--75181 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
75122 TATCCCGGTT
* *
75132 TTA TTA TTA TTA TAA TTA TT- TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
75179 TTA
1 TTA
75182 CTAAATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:80912 original size:20 final size:16
Alignment explanation
Indices: 80869--80901 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
80859 GATCAATACC
80869 TTTTGCATACATTCAT
1 TTTTGCATACATTCAT
80885 TTTTGCATACATTCAT
1 TTTTGCATACATTCAT
80901 T
1 T
80902 ATCCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTTGCATACATTCAT
Found at i:88263 original size:8 final size:8
Alignment explanation
Indices: 88252--88289 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
88242 AAGAAAAATG
88252 AAAAAGAA
1 AAAAAGAA
88260 AAAAAGAA
1 AAAAAGAA
88268 AAAAAGGAA
1 AAAAA-GAA
*
88277 AAAAGGAA
1 AAAAAGAA
88285 AAAAA
1 AAAAA
88290 TGATGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:88269 original size:13 final size:16
Alignment explanation
Indices: 88234--88279 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
88224 ATATTATGCT
*
88234 TGAAGAAGAAGAAAAA
1 TGAAAAAGAAGAAAAA
88250 TGAAAAAGAA-AAAAA
1 TGAAAAAGAAGAAAAA
88265 -GAAAAA-AAGGAAAAA
1 TGAAAAAGAA-GAAAAA
88280 AGGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 6 0.22
15 10 0.37
16 9 0.33
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
TGAAAAAGAAGAAAAA
Found at i:88272 original size:24 final size:25
Alignment explanation
Indices: 88239--88289 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
88229 ATGCTTGAAG
*
88239 AAGAAGAAAAATG-AAAAA-GAAAAA
1 AAGAA-AAAAAGGAAAAAAGGAAAAA
88263 AAGAAAAAAAGGAAAAAAGGAAAAA
1 AAGAAAAAAAGGAAAAAAGGAAAAA
88288 AA
1 AA
88290 TGATGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 10 0.42
25 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (25 bp):
AAGAAAAAAAGGAAAAAAGGAAAAA
Found at i:88277 original size:17 final size:16
Alignment explanation
Indices: 88252--88289 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
88242 AAGAAAAATG
88252 AAAAAGAAAAAAAGAA
1 AAAAAGAAAAAAAGAA
*
88268 AAAAAGGAAAAAAGGAA
1 AAAAA-GAAAAAAAGAA
88285 AAAAA
1 AAAAA
88290 TGATGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAGAA
Found at i:90285 original size:122 final size:118
Alignment explanation
Indices: 89870--90302 Score: 444
Period size: 110 Copynumber: 3.7 Consensus size: 118
89860 TGGATCAATA
* * *
89870 TTTCCAGAGTAAGTTCATAATGAGAAAAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GGAGAAGAAGTTCATAATGAGA
* ** *
89935 AGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGAT---CATC-A--
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACGAGATAGATCAACATCAACT
* * *
89983 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTAAAGAA-G-GAAGAAGTTCATAATGAGA
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGA
* ** * *
90045 AGAACTTGGTCAACCTTTTGCTCGAATTCATCACTTGATAGATCAGCATTAACT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACGAGATAGATCAACATCAACT
* * *
90099 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGAAAGAGGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAGAAGAAGTTCATAATGAGA
*
90163 AGAACTTGTTCAACCTTTTGCAT-G-ACTCTATCACAGAAGGAGATAGATCAACATCAA-T
65 AGAACTTGTTCAACCTTTTGC-TCGAATTC-ATCAC-----GAGATAGATCAACATCAACT
** * *
90221 ATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATATGAAGAAGGAGAAGAAGTTTATAATGAGA
1 -TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGA
*
90285 AGAATTTGTTCAAACCTT
65 AGAACTTGTTC-AACCTT
90303 GCCTTAATTC
Statistics
Matches: 269, Mismatches: 30, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
110 59 0.22
112 1 0.00
113 38 0.14
114 1 0.00
115 1 0.00
116 34 0.13
117 4 0.01
118 44 0.16
119 1 0.00
122 56 0.21
123 30 0.11
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (118 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCTCGAATTCATCACGAGATAGATCAACATCAACT
Found at i:90659 original size:3 final size:3
Alignment explanation
Indices: 90645--90696 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
90635 TATCCCGGTT
* * *
90645 TTA TTA TCA TTA TTA ATA TTA TTA TAA TTA TT- TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90691 TTA TTA
1 TTA TTA
90697 CTAAATAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:92109 original size:31 final size:29
Alignment explanation
Indices: 92040--92112 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
92030 TTTTAAATAT
* *
92040 TTTTATTTATTTTTAATTACAAGTTTTAC
1 TTTTATTTATTTTTAAATACAAGTTTTAA
* *
92069 TGCTT-TTTATATTTTAAATATATAGTTTTAA
1 T-TTTATTTAT-TTTTAAATACA-AGTTTTAA
92100 TTTTATTTATTTT
1 TTTTATTTATTTT
92113 AGTCACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
29 6 0.17
30 16 0.46
31 13 0.37
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTTATTTATTTTTAAATACAAGTTTTAA
Found at i:92192 original size:2 final size:2
Alignment explanation
Indices: 92185--92217 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
92175 TTATTATTAT
*
92185 TA TA TA TA TA TA TA TA TA TA TA TA -A TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92218 AATTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:97835 original size:60 final size:60
Alignment explanation
Indices: 97768--97881 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
97758 AAATGATTCC
* * *
97768 TAATTATATGACATTGTTTT-TTAAAAT-TTTCTTACTATTAAAAGTTATAAAATAATCCCT
1 TAATTATAGGACATTATTTTGTT-AAATCTTT-TGACTATTAAAAGTTATAAAATAATCCCT
* * *
97828 TAATTATAGGACATTATTTTGTTGAGTCTTTTGACTATTAAAAGTTGTAAAATA
1 TAATTATAGGACATTATTTTGTTAAATCTTTTGACTATTAAAAGTTATAAAATA
97882 GTCACTCAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (60 bp):
TAATTATAGGACATTATTTTGTTAAATCTTTTGACTATTAAAAGTTATAAAATAATCCCT
Found at i:104628 original size:31 final size:32
Alignment explanation
Indices: 104592--104652 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
104582 TTTTACTTAT
*
104592 ACTAACTAATTTT-TTT-TATTTGTTTGTGTAC
1 ACTAACTAATTTTATTTCT-TTTGATTGTGTAC
*
104623 ACTAACTTATTTTATTTCTTTTGATTGTGT
1 ACTAACTAATTTTATTTCTTTTGATTGTGT
104653 CATTTTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 12 0.46
32 13 0.50
33 1 0.04
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (32 bp):
ACTAACTAATTTTATTTCTTTTGATTGTGTAC
Found at i:109134 original size:15 final size:15
Alignment explanation
Indices: 109111--109140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109101 CTCATGAAAC
109111 AATAACCATCTTTGA
1 AATAACCATCTTTGA
*
109126 AATACCCATCTTTGA
1 AATAACCATCTTTGA
109141 GTTTGTTTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (15 bp):
AATAACCATCTTTGA
Found at i:109216 original size:68 final size:63
Alignment explanation
Indices: 109133--109261 Score: 161
Period size: 68 Copynumber: 2.0 Consensus size: 63
109123 TGAAATACCC
*
109133 ATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAACATCTTTGAGAT-AGTTTCCCTTGAAACGAA
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAAC---CATCTTTGAG-TCA-TTT-CCTTGAAACGAA
109197 TTAA
60 TTAA
** *
109201 ATCTTTGAGTCTGTTTCTTTTGAAACAAAACCATCTTTGAGTCATTTCCTTGAAATGAATT
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAACCATCTTTGAGTCATTTCCTTGAAACGAATT
109262 TTGTCTCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
63 13 0.23
64 4 0.07
65 11 0.20
68 28 0.50
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACCATCTTTGAGTCATTTCCTTGAAACGAATTAA
Found at i:109217 original size:33 final size:34
Alignment explanation
Indices: 109132--109255 Score: 107
Period size: 35 Copynumber: 3.7 Consensus size: 34
109122 TTGAAATACC
109132 CATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAG-TTGTTTCCCTTGAAACAAAACAAA
* * **
109167 CATCTTTGAGATAGTTTCCCTTGAAAC-GAATTAA
1 CATCTTTGAG-TTGTTTCCCTTGAAACAAAACAAA
**
109201 -ATCTTTGAGTCTGTTTCTTTTGAAACAAAAC---
1 CATCTTTGAGT-TGTTTCCCTTGAAACAAAACAAA
**
109232 CATCTTTGAGTCATTT-CCTTGAAA
1 CATCTTTGAGTTGTTTCCCTTGAAA
109256 TGAATTTTGT
Statistics
Matches: 72, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
30 6 0.08
31 3 0.04
32 11 0.15
33 21 0.29
34 6 0.08
35 25 0.35
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (34 bp):
CATCTTTGAGTTGTTTCCCTTGAAACAAAACAAA
Found at i:109805 original size:132 final size:127
Alignment explanation
Indices: 109395--109794 Score: 407
Period size: 126 Copynumber: 3.1 Consensus size: 127
109385 CATCGCATAT
* ** * * * * ** *
109395 GAGCAGTGTCAACCCCAGATAACCAGCCGTCCCCAACAGAGT-GGAACAATGTTATCACCCCTAG
1 GAGCTGTGTCAACCTAAGATAACCAGCCGTCCTCATCA-CGTAGAAACCGTGTTATCACCCTTAG
* * * * * *
109459 ATGGACAAGACTCATGAACAGATGAGCAGTGTCGTCACATGA-TCAGATCTCCTCATTATGTAG
65 ATGGCCAAGACTCATCAACAGATGAGCAGTGTCATCCCCTGACT-AGATCTCCTCATCATGTAG
*
109522 GAGCTGTGTCAA-CTAAGATAACCAACCGTCCTCATCACGTAGAAACCGTGTTATCACCCTTAGA
1 GAGCTGTGTCAACCTAAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCACCCTTAGA
* *
109586 TGGCTAAGACTCATGAACAGATGAGCAGTGTCATCACCC-GACCT-GATCTCCTCATCATGTAG
66 TGGCCAAGACTCATCAACAGATGAGCAGTGTCATC-CCCTGA-CTAGATCTCCTCATCATGTAG
* ** * *
109648 GAGCAGTGTCAACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCT
1 GAGCTGTGTCAACCTAAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCACCC-T--T
* *
109713 AAAGATGGCCAAGATTCATCATA-ATATGAGCAGTGTCATCCCCTGACTAGATCTCCTCATCATG
63 --AGATGGCCAAGACTCATCA-ACAGATGAGCAGTGTCATCCCCTGACTAGATCTCCTCATCATG
*
109777 TAT
125 TAG
* *
109780 GAGTTGTTTCAACCT
1 GAGCTGTGTCAACCT
109795 TAGACGACCA
Statistics
Matches: 228, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
125 2 0.01
126 101 0.44
127 54 0.24
128 2 0.01
130 1 0.00
131 5 0.02
132 62 0.27
133 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (127 bp):
GAGCTGTGTCAACCTAAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCACCCTTAGA
TGGCCAAGACTCATCAACAGATGAGCAGTGTCATCCCCTGACTAGATCTCCTCATCATGTAG
Found at i:109885 original size:3 final size:3
Alignment explanation
Indices: 109879--109915 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
109869 CTAAAAAAAC
109879 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
109916 AACATTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:113187 original size:12 final size:13
Alignment explanation
Indices: 113161--113193 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
113151 AAGAAAAGAC
113161 AATACAAATTAAA
1 AATACAAATTAAA
*
113174 AATA-AAATTTAA
1 AATACAAATTAAA
113186 AATACAAA
1 AATACAAA
113194 AAAGATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AATACAAATTAAA
Found at i:118463 original size:16 final size:15
Alignment explanation
Indices: 118428--118465 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
118418 GGATAGGAAG
*
118428 AGTACTCTGCCATTA
1 AGTACTTTGCCATTA
118443 AGTACTTTGCCATTAA
1 AGTACTTTGCCATT-A
118459 AGTACTT
1 AGTACTT
118466 AGTTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (15 bp):
AGTACTTTGCCATTA
Found at i:125150 original size:26 final size:26
Alignment explanation
Indices: 125108--125158 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
125098 CCAGAAGGCG
125108 CGCTGACTAGATCTTCTAGAAACTGT
1 CGCTGACTAGATCTTCTAGAAACTGT
*
125134 CGCTGACTGGA-CATTCTAGAAACTG
1 CGCTGACTAGATC-TTCTAGAAACTG
125159 GCACGCCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGT
Found at i:129137 original size:16 final size:16
Alignment explanation
Indices: 129112--129146 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
129102 TGCTCAATCG
129112 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
* *
129128 AAATATAATAAAATTA
1 AAATAAAATAAAAATA
129144 AAA
1 AAA
129147 ACAATGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:140795 original size:15 final size:15
Alignment explanation
Indices: 140775--140808 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
140765 TCAGTTCTGA
*
140775 TCGGGTTGGATCAGG
1 TCGGGTCGGATCAGG
*
140790 TCGGGTCGGATCGGG
1 TCGGGTCGGATCAGG
140805 TCGG
1 TCGG
140809 ACATGCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.50, T:0.24
Consensus pattern (15 bp):
TCGGGTCGGATCAGG
Found at i:141385 original size:30 final size:30
Alignment explanation
Indices: 141320--141385 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
141310 GTTTGAGAAT
* * *
141320 AAATTTAACTAAAATTTTATTTTGGTATTC
1 AAATTTAACTAAAATTTCAGTTTAGTATTC
* *
141350 GAATTTAATTAAAATTTCAGTTTAGT-TCTC
1 AAATTTAACTAAAATTTCAGTTTAGTAT-TC
141380 AAATTT
1 AAATTT
141386 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (30 bp):
AAATTTAACTAAAATTTCAGTTTAGTATTC
Found at i:143285 original size:4 final size:4
Alignment explanation
Indices: 143254--143342 Score: 65
Period size: 4 Copynumber: 22.8 Consensus size: 4
143244 ATAAACATAC
* * * *
143254 ACAT ACAC ACAT ACAC ACAT ATAT ACAT ACAT ACAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * *
143302 --AT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
143343 AATATCAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
4 72 0.97
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (4 bp):
ACAT
Found at i:143285 original size:20 final size:20
Alignment explanation
Indices: 143254--143302 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
143244 ATAAACATAC
*
143254 ACATACACACATACACACAT
1 ACATACATACATACACACAT
*
143274 ATATACATACATACACACAT
1 ACATACATACATACACACAT
143294 ACATACATA
1 ACATACATA
143303 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
ACATACATACATACACACAT
Found at i:143305 original size:2 final size:2
Alignment explanation
Indices: 143300--143332 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
143290 ACATACATAC
143300 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
143333 CATACATACA
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:155071 original size:16 final size:16
Alignment explanation
Indices: 155046--155081 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
155036 CTCTCGGCTT
155046 AAAA-GAAAATAAAAG
1 AAAAGGAAAATAAAAG
155061 AAAAGGAAAATAAAAG
1 AAAAGGAAAATAAAAG
155077 AAAAG
1 AAAAG
155082 AATTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAAGGAAAATAAAAG
Found at i:157563 original size:19 final size:20
Alignment explanation
Indices: 157528--157569 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
157518 ATGGGTACCT
157528 AAACAAATCAAAGAAAAACAA
1 AAACAAATC-AAGAAAAACAA
*
157549 AAACAAATC-AGAAAAATAA
1 AAACAAATCAAGAAAAACAA
157568 AA
1 AA
157570 TTGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.76, C:0.12, G:0.05, T:0.07
Consensus pattern (20 bp):
AAACAAATCAAGAAAAACAA
Found at i:158031 original size:12 final size:12
Alignment explanation
Indices: 158016--158045 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
158006 AAAAGATTCC
158016 AAAGAAGATTAA
1 AAAGAAGATTAA
*
158028 AAAGAATATTAA
1 AAAGAAGATTAA
158040 AAAGAA
1 AAAGAA
158046 AATTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (12 bp):
AAAGAAGATTAA
Found at i:158586 original size:16 final size:16
Alignment explanation
Indices: 158565--158596 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
158555 CGACTTTAAA
*
158565 GAAAATTAAAGAAAAT
1 GAAAATAAAAGAAAAT
158581 GAAAATAAAAGAAAAT
1 GAAAATAAAAGAAAAT
158597 AATTTTTGTT
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:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (16 bp):
GAAAATAAAAGAAAAT
Found at i:161772 original size:21 final size:21
Alignment explanation
Indices: 161748--161791 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
161738 ATCGGATTCA
161748 GATCTG-AATATTTGGATATCC
1 GATCTGAAAT-TTTGGATATCC
161769 GATCTGAAATTTTGGATATCC
1 GATCTGAAATTTTGGATATCC
161790 GA
1 GA
161792 ATTTTTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (21 bp):
GATCTGAAATTTTGGATATCC
Done.