Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold942
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: 113128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1003 original size:47 final size:47
Alignment explanation
Indices: 952--1204 Score: 162
Period size: 46 Copynumber: 5.4 Consensus size: 47
942 GATGTCATAT
* * *
952 CCCAGATATGGTCTTACACTGGCTCA-CATCTC-AAGTCGATGCCATGG
1 CCCAGACATGGTCTTACACTGGCT-ATCATATCGAAGCCGATG-CATGG
* * *
999 CCCAGACATGGTCTTACACTGACTATCATATCGTAGCCGATGCATGT
1 CCCAGACATGGTCTTACACTGGCTATCATATCGAAGCCGATGCATGG
* * * * * *
1046 CCCAGACAT-GTCTTACACTGGCT-TACGTCTTGAGGCCAATGCATGT
1 CCCAGACATGGTCTTACACTGGCTAT-CATATCGAAGCCGATGCATGG
* * * * * * * * *
1092 CCCATACAT-GTTTTACACTAGTTCTCGTCTC-AATGCCAATGCCATGT
1 CCCAGACATGGTCTTACACTGGCTATCATATCGAA-GCCGATG-CATGG
* ** * *
1139 CCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCATGT
1 CCCAGACATGGTCTTACACTGGCTATCAT-ATCGAAGCCGATGCATGG
1186 CCCAGACAT-GTCTTACACT
1 CCCAGACATGGTCTTACACT
1205 AGTCAACAGT
Statistics
Matches: 168, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.01
46 70 0.42
47 68 0.40
48 27 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
CCCAGACATGGTCTTACACTGGCTATCATATCGAAGCCGATGCATGG
Found at i:1088 original size:46 final size:45
Alignment explanation
Indices: 994--1204 Score: 172
Period size: 46 Copynumber: 4.5 Consensus size: 45
984 AAGTCGATGC
* * * * * *
994 CATGGCCCAGACATGGTCTTACACTGACTATCATATCGTA-GCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCT-TCGTCTTG-AGGCCAATG
1041 CATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGCTT-CGTCTTGAGGCCAATG
* * * * ** *
1087 CATGTCCCATACATGTTTTACACTAGTTCTCGTCTCAATGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGCT-TCGTCTTGAGGCCAATG
* ** * **
1133 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCT-TCGTCTTGAGGCCAATG
1181 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
1205 AGTCAACAGT
Statistics
Matches: 133, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
45 2 0.02
46 70 0.53
47 41 0.31
48 20 0.15
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTTCGTCTTGAGGCCAATG
Found at i:1101 original size:93 final size:94
Alignment explanation
Indices: 938--1163 Score: 219
Period size: 93 Copynumber: 2.4 Consensus size: 94
928 GTGGGTAAAG
* * * * *
938 TGCCGATGTCATATCCCAGATATGGTCTTACACTGGCTCACATCTCAAGTCGATGCCATGGCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGCCAATGCCATGGCCCA
*
1003 GACATGGTCTTACACT-GACTATCATATC-G
66 GACAT-GTCTTACACTAG-CTATCATATCAA
* * * * *
1032 TAGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTTGAGGCCAATG-CATGTCC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATC-TCAAGCCAATGCCATGGCC
* * * * * *
1094 CATACATGTTTTACACTAGTTCTCGTCTCAA
64 CAGACATGTCTTACACTAGCTATCATATCAA
*
1125 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1164 TCATAATGTG
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
92 21 0.19
93 46 0.43
94 34 0.31
95 7 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGCCAATGCCATGGCCCA
GACATGTCTTACACTAGCTATCATATCAA
Found at i:3266 original size:95 final size:94
Alignment explanation
Indices: 3143--3317 Score: 255
Period size: 95 Copynumber: 1.9 Consensus size: 94
3133 CATATCTGTG
* * *
3143 CCGATGCCATGTCCCAGACATGTCTTACACTGGCT-TACGT-CTCGAGGCCGATGCATGTCCCAT
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCT-CATAAT-GAGGCCGATGCATGTCCCAA
3206 ACATGTCTTACACTAGCACTTGTCTTAAATA
64 ACATGTCTTACACTAGCACTTGTCTTAAATA
* * *
3237 CCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAAA
1 CCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAAA
3302 CATGTCTTACACTAGC
65 CATGTCTTACACTAGC
3318 TCACAATAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
94 20 0.28
95 50 0.69
96 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAAAC
ATGTCTTACACTAGCACTTGTCTTAAATA
Found at i:5209 original size:27 final size:28
Alignment explanation
Indices: 5171--5225 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
5161 TCCTTTTGTA
5171 AATTATGGATGTTAATT-TTAGTACTTT
1 AATTATGGATGTTAATTCTTAGTACTTT
5198 AATTATGGATGTTAATTCTTAGTACTTT
1 AATTATGGATGTTAATTCTTAGTACTTT
5226 TGATCTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (28 bp):
AATTATGGATGTTAATTCTTAGTACTTT
Found at i:5803 original size:40 final size:40
Alignment explanation
Indices: 5758--5858 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
5748 TTAACAATTG
*
5758 CCAAAATTTCTATGACTTTACCAA-ATAATCCAATGATTTA
1 CCAAAATTTCTATGACTTTACCAAGAT-ATCCAACGATTTA
* ** *
5798 CCAAAATATCTAAAACTTTACCAAGATATCTAACGATTTA
1 CCAAAATTTCTATGACTTTACCAAGATATCCAACGATTTA
* *
5838 CCAGAATTTCTAATGAATTTA
1 CCAAAATTTCT-ATGACTTTA
5859 TCAATATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 41 0.84
41 8 0.16
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (40 bp):
CCAAAATTTCTATGACTTTACCAAGATATCCAACGATTTA
Found at i:5837 original size:20 final size:18
Alignment explanation
Indices: 5774--6019 Score: 93
Period size: 20 Copynumber: 12.4 Consensus size: 18
5764 TTTCTATGAC
*
5774 TTTACCAAATAATCCAATGA
1 TTTACCAAAT-ATCTAA-GA
*
5794 TTTACCAAAATATCTAAAA
1 TTTACC-AAATATCTAAGA
5813 CTTTACCAAGATATCTAACGA
1 -TTTACCAA-ATATCTAA-GA
*
5834 TTTACCAGAATTTCTAATGAA
1 TTTACCA-AATATCTAA-G-A
* * * *
5855 TTTATCAATATTTATAAGC
1 TTTACCAA-ATATCTAAGA
5874 TTATACCAAA-AGTCTTATAGA
1 TT-TACCAAATA-TC-TA-AGA
* **
5895 -TTACCACAATTTCTATTA
1 TTTACCA-AATATCTAAGA
*
5913 CTTTACCAAAAATCTAAAGGA
1 -TTTACCAAATATCT-AA-GA
5934 -TTACCAAATTATCTAAGA
1 TTTACCAAA-TATCTAAGA
*
5952 TTTTACCAATATTTCTAAGGA
1 -TTTACCAA-ATATCTAA-GA
* *
5973 TTTACCAAATTATATAAAA
1 TTTACCAAA-TATCTAAGA
* *
5992 CTTTACCTGAATTTCTAACGA
1 -TTTACC-AAATATCTAA-GA
6013 TTTACCA
1 TTTACCA
6020 TTACTTTTAA
Statistics
Matches: 171, Mismatches: 29, Indels: 53
0.68 0.11 0.21
Matches are distributed among these distances:
18 3 0.02
19 31 0.18
20 108 0.63
21 29 0.17
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTACCAAATATCTAAGA
Found at i:5980 original size:40 final size:40
Alignment explanation
Indices: 5912--6019 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
5902 AATTTCTATT
** * *
5912 ACTTTACC-AAAAATCTAAAGGA-TTACCAAATTATCTAAG
1 ACTTTACCTAAATTTCT-AAGGATTTACCAAATTATATAAA
*
5951 ATTTTACC-AATATTTCTAAGGATTTACCAAATTATATAAA
1 ACTTTACCTAA-ATTTCTAAGGATTTACCAAATTATATAAA
* *
5991 ACTTTACCTGAATTTCTAACGATTTACCA
1 ACTTTACCTAAATTTCTAAGGATTTACCA
6020 TTACTTTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.24
40 43 0.74
41 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (40 bp):
ACTTTACCTAAATTTCTAAGGATTTACCAAATTATATAAA
Found at i:6231 original size:20 final size:20
Alignment explanation
Indices: 6169--6321 Score: 79
Period size: 20 Copynumber: 7.7 Consensus size: 20
6159 GTCTTACCAA
*
6169 TTACCAAAATTT-TTATAACT
1 TTACCAAAATTTCTTA-GACT
* *
6189 TTATCAAAATAT-TTA-ACGAT
1 TTACCAAAATTTCTTAGAC--T
6209 TTACCAAAATTTCTTAGACT
1 TTACCAAAATTTCTTAGACT
* *
6229 TTACTC-AAATATCTAAG-CT
1 TTAC-CAAAATTTCTTAGACT
*
6248 TTACCAAATTTTCTTAGGA-T
1 TTACCAAAATTTCTTA-GACT
* *
6268 TTACCAAAATATCTAATGA-T
1 TTACCAAAATTTCTTA-GACT
* * *
6288 TTA-CAAGAATTTCTAACAAT
1 TTACCAA-AATTTCTTAGACT
*
6308 TTACCAATATTTCT
1 TTACCAAAATTTCT
6322 AGGCATATAT
Statistics
Matches: 106, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.03
19 17 0.16
20 77 0.73
21 7 0.07
22 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (20 bp):
TTACCAAAATTTCTTAGACT
Found at i:6261 original size:39 final size:41
Alignment explanation
Indices: 6169--6291 Score: 134
Period size: 39 Copynumber: 3.1 Consensus size: 41
6159 GTCTTACCAA
*
6169 TTACCAAAATTTT-TATA-ACTTTA-TCAAAATATTTAACGAT
1 TTACC-AAATTTTCT-TAGACTTTACTCAAAATATCTAACGAT
* *
6209 TTACCAAAATTTCTTAGACTTTACTC-AAATATCTAA-GCT
1 TTACCAAATTTTCTTAGACTTTACTCAAAATATCTAACGAT
*
6248 TTACCAAATTTTCTTAGGA-TTTAC-CAAAATATCTAATGAT
1 TTACCAAATTTTCTTA-GACTTTACTCAAAATATCTAACGAT
6288 TTAC
1 TTAC
6292 AAGAATTTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
38 1 0.01
39 40 0.56
40 29 0.40
41 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (41 bp):
TTACCAAATTTTCTTAGACTTTACTCAAAATATCTAACGAT
Found at i:6339 original size:20 final size:20
Alignment explanation
Indices: 6295--6363 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
6285 GATTTACAAG
*
6295 AATTTCTAA-CAATTTACC-A
1 AATTTCTAAGC-ATATACCGA
* *
6314 ATATTTCTAGGCATATATCGA
1 A-ATTTCTAAGCATATACCGA
*
6335 AATTTCTAAGCCTATACCGA
1 AATTTCTAAGCATATACCGA
6355 AATTTCTAA
1 AATTTCTAA
6364 AATTTCTCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 37 0.90
21 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (20 bp):
AATTTCTAAGCATATACCGA
Found at i:6493 original size:29 final size:29
Alignment explanation
Indices: 6449--6519 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
6439 AACACTTTAC
*
6449 CAAAATATCTAGGAGTTTACAAATATTTT
1 CAAAATATCTAAGAGTTTACAAATATTTT
*
6478 CAAAATATCTAAGAGTTTACTAATATTTT
1 CAAAATATCTAAGAGTTTACAAATATTTT
*
6507 CAAAATTTCTAAG
1 CAAAATATCTAAG
6520 CACATACCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (29 bp):
CAAAATATCTAAGAGTTTACAAATATTTT
Found at i:7006 original size:20 final size:20
Alignment explanation
Indices: 6966--7054 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
6956 TACCATGTCT
* *
6966 TAACAA-TTATCAAAATATC
1 TAACAATTTATCAATATTTC
* *
6985 TAACAATTTATTACTATTTC
1 TAACAATTTATCAATATTTC
** * *
7005 TAGTACTTTATCAATATTTT
1 TAACAATTTATCAATATTTC
* *
7025 TAACAATTTATCAAAATTTG
1 TAACAATTTATCAATATTTC
*
7045 TAATAATTTA
1 TAACAATTTA
7055 CTGTTATTTA
Statistics
Matches: 53, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
19 6 0.11
20 47 0.89
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (20 bp):
TAACAATTTATCAATATTTC
Found at i:19190 original size:23 final size:21
Alignment explanation
Indices: 19151--19193 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
19141 TTTAAATCTA
19151 TCAAATTTAAAAAATTTATCC
1 TCAAATTTAAAAAATTTATCC
19172 TCAATATTTATAAAAATTTATC
1 TCAA-ATTTA-AAAAATTTATC
19194 AATTAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
TCAAATTTAAAAAATTTATCC
Found at i:21423 original size:41 final size:39
Alignment explanation
Indices: 21349--21463 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 39
21339 ATAAATAACA
*
21349 AAAAACTATTTTAAAAATAAAAAAATAAAAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAAT-AAAAAA-AATAAAAAAAGTATTTT
21392 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAA-TAAAAAAAA-TAAAAAAAGTATTTT
*
21433 AAAAGTATTTTAAAATAAAAAAAATAAAAAA
1 AAAAATATTTTAAAATAAAAAAAATAAAAAA
21464 TATATATTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
39 7 0.10
40 11 0.16
41 38 0.56
42 7 0.10
43 5 0.07
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (39 bp):
AAAAATATTTTAAAATAAAAAAAATAAAAAAAGTATTTT
Found at i:21436 original size:11 final size:11
Alignment explanation
Indices: 21422--21447 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21412 AAAAATTAAA
21422 AAAAGTATTTT
1 AAAAGTATTTT
21433 AAAAGTATTTT
1 AAAAGTATTTT
21444 AAAA
1 AAAA
21448 TAAAAAAAAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:24459 original size:18 final size:17
Alignment explanation
Indices: 24337--24470 Score: 75
Period size: 18 Copynumber: 7.9 Consensus size: 17
24327 AATACTAAGA
24337 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
24354 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
24370 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
24384 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* * *
24403 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
**
24419 ATTTTAAAAAATTCATAT
1 ATTTTATTAAATT-ATAT
24437 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
24454 ATTTTTATTAAATTATA
1 A-TTTTATTAAATTATA
24471 GTTAATAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 8 0.09
16 9 0.10
17 18 0.21
18 39 0.45
19 2 0.02
20 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:24722 original size:46 final size:44
Alignment explanation
Indices: 24630--24723 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
24620 ATTACAACAT
* * **
24630 CATTCCATTTAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACAAAAGAATACTATTACACCTCTATTC
*
24674 CATTCCATTCAACCAAACAAAAGGATTAGCTATTACACCTCTATTC
1 CATTCCATTCAACCAAACAAAA-GAATA-CTATTACACCTCTATTC
24720 CATT
1 CATT
24724 ACGCCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 20 0.47
45 4 0.09
46 19 0.44
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCATTCAACCAAACAAAAGAATACTATTACACCTCTATTC
Found at i:24730 original size:16 final size:16
Alignment explanation
Indices: 24705--24742 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
24695 AGGATTAGCT
24705 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
24721 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
24737 ATTACA
1 ATTACA
24743 GCGAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:34476 original size:20 final size:20
Alignment explanation
Indices: 34447--34489 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34437 AAAATAAACA
* **
34447 TATAATTATTCATTTAATAT
1 TATAACTATTCAAATAATAT
34467 TATAACTATTCAAATAATAT
1 TATAACTATTCAAATAATAT
34487 TAT
1 TAT
34490 TTAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAACTATTCAAATAATAT
Found at i:39627 original size:26 final size:26
Alignment explanation
Indices: 39596--39649 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
39586 GAATTTACAA
39596 AAGTAAATCTATATAATATATAAAAC
1 AAGTAAATCTATATAATATATAAAAC
39622 AAGTAAATCTATATAATATATAAAAC
1 AAGTAAATCTATATAATATATAAAAC
39648 AA
1 AA
39650 ACTCCCCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (26 bp):
AAGTAAATCTATATAATATATAAAAC
Found at i:45836 original size:33 final size:33
Alignment explanation
Indices: 45799--45863 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
45789 TTTAGGCTAC
* *
45799 TTTGATAAAGACTATTATTGTAATTGATGTGTA
1 TTTGATAAAGACTATAATCGTAATTGATGTGTA
* *
45832 TTTGATGAGGACTATAATCGTAATTGATGTGT
1 TTTGATAAAGACTATAATCGTAATTGATGTGT
45864 CTCCAGCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTGATAAAGACTATAATCGTAATTGATGTGTA
Found at i:46017 original size:16 final size:16
Alignment explanation
Indices: 45996--46031 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
45986 TGTGGACAAT
45996 TTTTTTTAATTTTT-AA
1 TTTTTTT-ATTTTTCAA
46012 TTTTTTTATTTTTCAA
1 TTTTTTTATTTTTCAA
46028 TTTT
1 TTTT
46032 CTTTTCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTCAA
Found at i:50328 original size:16 final size:16
Alignment explanation
Indices: 50309--50344 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
50299 GATTGAAAAG
50309 AAAATTGAAAAA-TAAA
1 AAAATT-AAAAATTAAA
50325 AAAATTAAAAATTAAA
1 AAAATTAAAAATTAAA
50341 AAAA
1 AAAA
50345 ATTGTCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATTAAAAATTAAA
Found at i:50514 original size:33 final size:33
Alignment explanation
Indices: 50477--50541 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
50467 TGGGCTGGAG
* *
50477 ACACATCAATTACGATTATAGTCCTCATCAAAT
1 ACACATCAATTACAATAATAGTCCTCATCAAAT
* *
50510 ACACATCAATTACAATAATAGTCTTTATCAAA
1 ACACATCAATTACAATAATAGTCCTCATCAAA
50542 GTAGCCTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.31
Consensus pattern (33 bp):
ACACATCAATTACAATAATAGTCCTCATCAAAT
Found at i:54215 original size:27 final size:27
Alignment explanation
Indices: 54177--54230 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
54167 TTTCTAGGTT
* *
54177 TGAGATATAAAGAGAGAAGCTTAAGGC
1 TGAGATATAAAGAGAAAAGCATAAGGC
54204 TGAGATATAAAGAGAAAAGCATAAGGC
1 TGAGATATAAAGAGAAAAGCATAAGGC
54231 CCCTATCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.28, T:0.17
Consensus pattern (27 bp):
TGAGATATAAAGAGAAAAGCATAAGGC
Found at i:66702 original size:26 final size:26
Alignment explanation
Indices: 66666--66717 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
66656 CAATCTTTTT
66666 AACTTGAATGAATTAAAATAATAAAA
1 AACTTGAATGAATTAAAATAATAAAA
66692 AACTTGAATGAATTAAAATAATAAAA
1 AACTTGAATGAATTAAAATAATAAAA
66718 CATTCTTATT
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:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (26 bp):
AACTTGAATGAATTAAAATAATAAAA
Found at i:70109 original size:5 final size:5
Alignment explanation
Indices: 70071--70124 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
70061 TGTTTTATAA
* *
70071 ATATT AT-TT -TATT ATATAAT ATAAT ATATT ATATT ATATT GTATT ATATT
1 ATATT ATATT ATATT ATAT--T ATATT ATATT ATATT ATATT ATATT ATATT
70121 ATAT
1 ATAT
70125 AAGTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 32 0.78
7 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:70143 original size:6 final size:6
Alignment explanation
Indices: 70132--70160 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
70122 TATAAGTAAA
70132 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
70161 AGATGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:70961 original size:3 final size:3
Alignment explanation
Indices: 70947--70993 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
70937 GATAAAAATT
* * * *
70947 TTA TTT TTA TTA TTA TTG TTA ATA TAA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
70994 TTTAATGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:72405 original size:16 final size:16
Alignment explanation
Indices: 72384--72414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
72374 AAGAAACGAT
*
72384 AAATATGTATATATAA
1 AAATATGTACATATAA
72400 AAATATGTACATATA
1 AAATATGTACATATA
72415 TATGGGTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATATGTACATATAA
Found at i:72968 original size:3 final size:3
Alignment explanation
Indices: 72954--73000 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
72944 AACATAAACA
* *
72954 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAA AAA AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72999 AA
1 AA
73001 AGTGGCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:74786 original size:46 final size:45
Alignment explanation
Indices: 74667--74964 Score: 221
Period size: 46 Copynumber: 6.8 Consensus size: 45
74657 TAGGATAGTG
* * * *
74667 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATGAGATCT--CT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** *
74710 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* * *
74757 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * * *
74800 --TGTGATCTTCTCTACTGTAA-CTTCAGAGAGAT---A-C-G-AT
1 TCTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * * * *
74837 CCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
*
74880 ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
74927 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
74965 CCTGTATTAT
Statistics
Matches: 197, Mismatches: 39, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
36 2 0.01
37 1 0.01
38 1 0.01
39 22 0.11
40 2 0.01
41 24 0.12
42 1 0.01
43 1 0.01
44 69 0.35
45 1 0.01
46 70 0.36
47 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:74913 original size:44 final size:44
Alignment explanation
Indices: 74636--74964 Score: 202
Period size: 44 Copynumber: 7.6 Consensus size: 44
74626 TTTAATCCAT
* * * *
74636 TCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGC
1 TCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGATCTGC
* * ** **
74679 TCCGCTGTAATCTCAGGGAGATGAGATCT-CTGGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGATCTGC
* * * *
74723 TCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCTGT
1 TCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGATCTGC
* * *
74769 TCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TGTGATCTTC
1 TCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGATCTGC
* * * * *
74810 TCTACTGTAA-CTTCAGAGAGATACGA-T-C---CTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGATCTGC
* * *
74849 TCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGC
* * * *
74893 TCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCTGT
1 TCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGATCTGC
74939 TCCACTGTAATCTCAGGGAGATAAGA
1 TCCACTGTAATCTCAGGGAGATAAGA
74965 CCTGTATTAT
Statistics
Matches: 221, Mismatches: 45, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
39 25 0.11
40 3 0.01
41 29 0.13
43 21 0.10
44 72 0.33
45 3 0.01
46 68 0.31
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGC
Found at i:83310 original size:13 final size:14
Alignment explanation
Indices: 83292--83320 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
83282 CACAAAATAT
83292 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
83305 TTATAATTGTTTAA
1 TTATAATTGTTTAA
83319 TT
1 TT
83321 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:83787 original size:21 final size:21
Alignment explanation
Indices: 83734--83788 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
83724 ACTTAGAGCG
*
83734 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
*
83755 GCGGCA-CGAGCGAGGGAGGCA
1 GAGGCAGC-AGCGAGGGAGGCA
83776 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
83789 TGGCAGCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.51, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:84082 original size:31 final size:31
Alignment explanation
Indices: 84036--84102 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
84026 TTGTTGTATT
* *
84036 TTTTATGCTAAATTTGATGTTTTTGGCTGCA
1 TTTTATACTAAATTTGATGTATTTGGCTGCA
* * * *
84067 TTTTATACTATATTTGTTGTATTTGGTTGGA
1 TTTTATACTAAATTTGATGTATTTGGCTGCA
84098 TTTTA
1 TTTTA
84103 ATGCAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.06, G:0.18, T:0.57
Consensus pattern (31 bp):
TTTTATACTAAATTTGATGTATTTGGCTGCA
Found at i:89006 original size:13 final size:13
Alignment explanation
Indices: 88973--89026 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
88963 ATTTGTTTCA
88973 AAATAAAATATTT
1 AAATAAAATATTT
* *
88986 -TATTAAATATTT
1 AAATAAAATATTT
88998 AAATAAAATATCTT
1 AAATAAAATAT-TT
*
89012 TAAT-AAATA-TT
1 AAATAAAATATTT
89023 AAAT
1 AAAT
89027 TTATAATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
11 5 0.15
12 10 0.30
13 13 0.39
14 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAAAATATTT
Found at i:89007 original size:25 final size:25
Alignment explanation
Indices: 88973--89026 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
88963 ATTTGTTTCA
*
88973 AAATAAAATAT-TTTATTAAATATTT
1 AAATAAAATATCTTTAATAAATA-TT
88998 AAATAAAATATCTTTAATAAATATT
1 AAATAAAATATCTTTAATAAATATT
89023 AAAT
1 AAAT
89027 TTATAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATAAAATATCTTTAATAAATATT
Found at i:89305 original size:9 final size:9
Alignment explanation
Indices: 89271--89304 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
89261 TATTTTTAAA
89271 ATTAAAAAT
1 ATTAAAAAT
89280 ATTAAAAAT
1 ATTAAAAAT
89289 ATTAAAAAT
1 ATTAAAAAT
89298 A-TAAAAA
1 ATTAAAAA
89305 AAACCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:91377 original size:20 final size:19
Alignment explanation
Indices: 91354--91396 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
91344 TAAATAACAG
*
91354 TAAATTATTACAAATTTTGA
1 TAAATTATTA-AAATATTGA
*
91374 TAAATTGTTAAAATATTGA
1 TAAATTATTAAAATATTGA
91393 TAAA
1 TAAA
91397 GTACTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (19 bp):
TAAATTATTAAAATATTGA
Found at i:91435 original size:20 final size:20
Alignment explanation
Indices: 91354--91441 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
91344 TAAATAACAG
* * *
91354 TAAATTATTACAAATTTTGA
1 TAAATTGTTAGAAATATTGA
91374 TAAATTGTTA-AAATATTGA
1 TAAATTGTTAGAAATATTGA
* ** * *
91393 TAAAGTACTAGAAATAGTAA
1 TAAATTGTTAGAAATATTGA
* *
91413 TAAATTGTTAGATATTTTGA
1 TAAATTGTTAGAAATATTGA
91433 T-AATTGTTA
1 TAAATTGTTA
91442 AGACATGGTA
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
19 23 0.43
20 30 0.57
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAATTGTTAGAAATATTGA
Found at i:91942 original size:30 final size:28
Alignment explanation
Indices: 91894--91955 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
91884 GCTTAAGAAA
*
91894 TTTGAAATATTAGTAAACTCTTAGATAT
1 TTTGAAATATTAGTAAACTCCTAGATAT
*
91922 TTTGAAAATATTTTGTAAACTCCTAGATAT
1 TTTG-AAATA-TTAGTAAACTCCTAGATAT
91952 TTTG
1 TTTG
91956 GTAAAGTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.13
29 5 0.17
30 21 0.70
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTGAAATATTAGTAAACTCCTAGATAT
Found at i:92065 original size:20 final size:20
Alignment explanation
Indices: 92040--92087 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
92030 CAGAGAAATT
*
92040 TTAGAAATTTCGGTATAGGC
1 TTAGAAATTTCGATATAGGC
*
92060 TTAGAAATTTCGATATATGC
1 TTAGAAATTTCGATATAGGC
*
92080 CTAGAAAT
1 TTAGAAAT
92088 ATTGGTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
TTAGAAATTTCGATATAGGC
Found at i:92145 original size:39 final size:38
Alignment explanation
Indices: 92118--92194 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
92108 TCTTGTAATA
92118 ATTAGATATTTTG-GTAAA-TCCTAAGAAAATTTGGTAAAG
1 ATTAGATA-TTTGAGTAAAGT-CTAAG-AAATTTGGTAAAG
*
92157 CTTAGATATTTGAGTAAAGTCTAAGAAATTTTGGTAAA
1 ATTAGATATTTGAGTAAAGTCTAAGAAA-TTTGGTAAA
92195 TCGTTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
38 7 0.21
39 26 0.76
40 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.36
Consensus pattern (38 bp):
ATTAGATATTTGAGTAAAGTCTAAGAAATTTGGTAAAG
Found at i:92152 original size:20 final size:20
Alignment explanation
Indices: 92127--92196 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
92117 AATTAGATAT
92127 TTTGGTAAATCCTAAGAAAA
1 TTTGGTAAATCCTAAGAAAA
* * *
92147 TTTGGTAAA-GCTTAG-ATA
1 TTTGGTAAATCCTAAGAAAA
*
92165 TTTGAGTAAAGT-CTAAGAAAT
1 TTTG-GTAAA-TCCTAAGAAAA
92186 TTTGGTAAATC
1 TTTGGTAAATC
92197 GTTAAATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 6 0.15
19 10 0.26
20 18 0.46
21 5 0.13
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (20 bp):
TTTGGTAAATCCTAAGAAAA
Found at i:92207 original size:21 final size:20
Alignment explanation
Indices: 92182--92234 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
92172 AAAGTCTAAG
92182 AAATTTTGGTAAATCGTTA-AA
1 AAATTTTGGTAAA--GTTATAA
* *
92203 TAATTTTGATAAAGTTATAA
1 AAATTTTGGTAAAGTTATAA
92223 AAATTTTGGTAA
1 AAATTTTGGTAA
92235 TTGGTAAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 12 0.44
21 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (20 bp):
AAATTTTGGTAAAGTTATAA
Found at i:92229 original size:20 final size:20
Alignment explanation
Indices: 92182--92230 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
92172 AAAGTCTAAG
*
92182 AAATTTTGGTAAATCGTTAAA
1 AAATTTTGATAAA-CGTTAAA
*
92203 TAATTTTGATAAA-GTTATAA
1 AAATTTTGATAAACGTTA-AA
92223 AAATTTTG
1 AAATTTTG
92231 GTAATTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (20 bp):
AAATTTTGATAAACGTTAAA
Found at i:92449 original size:40 final size:41
Alignment explanation
Indices: 92342--92491 Score: 109
Period size: 40 Copynumber: 3.7 Consensus size: 41
92332 TGTCAGAATT
*
92342 TTTGGTAAATAATTA-AATATTTTGGTAAAGTCTTAAAAGTAA
1 TTTGGTAAATCATTAGAATA--TTGGTAAAGTCTTAAAAGTAA
* * **
92384 --TGGTAAATCGTTAGAA-ATTCAGGTAAAGTTTTTTAA-TAA
1 TTTGGTAAATCATTAGAATATT--GGTAAAGTCTTAAAAGTAA
* *
92423 TTTGGTAAATCATTAGAATATTGGTAAAATCTT-AGA-TAA
1 TTTGGTAAATCATTAGAATATTGGTAAAGTCTTAAAAGTAA
* * *
92462 TTTGGT-AATCCTTTAGATTTTTGGTAAAGT
1 TTTGGTAAAT-CATTAGAATATTGGTAAAGT
92492 AATAGAAATT
Statistics
Matches: 87, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
38 5 0.06
39 29 0.33
40 33 0.38
41 17 0.20
42 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (41 bp):
TTTGGTAAATCATTAGAATATTGGTAAAGTCTTAAAAGTAA
Found at i:92466 original size:20 final size:21
Alignment explanation
Indices: 92419--92469 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
92409 AAGTTTTTTA
92419 ATAATTTGGT-AAATCATTAG
1 ATAATTTGGTAAAATCATTAG
92439 --AATATTGGTAAAATC-TTAG
1 ATAAT-TTGGTAAAATCATTAG
92458 ATAATTTGGTAA
1 ATAATTTGGTAA
92470 TCCTTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 3 0.11
19 9 0.33
20 12 0.44
21 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (21 bp):
ATAATTTGGTAAAATCATTAG
Found at i:92588 original size:20 final size:19
Alignment explanation
Indices: 92547--92630 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 19
92537 TAAATATTGA
*
92547 TAAATTCATTAGAAATTCTGG
1 TAAA-TCATTAGATATT-TGG
*
92568 TAAATCGTTAGATATCTTGG
1 TAAATCATTAGATAT-TTGG
*
92588 TAAAGT-TTTAGATATTTTGG
1 TAAA-TCATTAGATA-TTTGG
92608 TAAATCATT-GATTATTTGG
1 TAAATCATTAGA-TATTTGG
92627 TAAA
1 TAAA
92631 AGTCATAGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
19 12 0.22
20 35 0.65
21 7 0.13
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.43
Consensus pattern (19 bp):
TAAATCATTAGATATTTGG
Found at i:92633 original size:40 final size:40
Alignment explanation
Indices: 92555--92647 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
92545 GATAAATTCA
* * *
92555 TTAGAAATTCTGGTAAATCGTTAGATATCTTGGTAAAGTT
1 TTAGAAATTTTGGTAAATCATTAGATATCTTGGTAAAGTC
*
92595 TTAGATATTTTGGTAAATCATT-GATTAT-TTGGTAAAAGTC
1 TTAGAAATTTTGGTAAATCATTAGA-TATCTTGGT-AAAGTC
*
92635 ATAGAAATTTTGG
1 TTAGAAATTTTGG
92648 CAATTGTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 7 0.16
40 38 0.84
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (40 bp):
TTAGAAATTTTGGTAAATCATTAGATATCTTGGTAAAGTC
Found at i:93226 original size:27 final size:28
Alignment explanation
Indices: 93179--93233 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
93169 CTAAGATCAA
93179 AAAGTACTAAGAATTAACATCCATAATT
1 AAAGTACTAAGAATTAACATCCATAATT
93207 AAAGTACTAA-AATTAACATCCATAATT
1 AAAGTACTAAGAATTAACATCCATAATT
93234 TACAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAGTACTAAGAATTAACATCCATAATT
Done.