Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:141090 original size:13 final size:12
Alignment explanation
Indices: 141069--141103 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
141059 AAATAATCTC
*
141069 ATTATTTATTTA
1 ATTATTTATATA
141081 ATTAATTTATATA
1 ATT-ATTTATATA
141094 ATTATTTATA
1 ATTATTTATA
141104 AAAATATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATTTATATA
Found at i:141329 original size:20 final size:20
Alignment explanation
Indices: 141304--141341 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
141294 TAGTATTTAT
* *
141304 AAATTAAATTTTTTTTAAAA
1 AAATTAAAATTTATTTAAAA
141324 AAATTAAAATTTATTTAA
1 AAATTAAAATTTATTTAA
141342 TTAATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTAAAATTTATTTAAAA
Found at i:142866 original size:16 final size:16
Alignment explanation
Indices: 142847--142904 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
142837 ATGTATAAAT
142847 ATATTAATTTTATATA
1 ATATTAATTTTATATA
*
142863 ATATAAATTATTA-AT-
1 ATATTAATT-TTATATA
*
142878 ATATTAAATTTATATA
1 ATATTAATTTTATATA
*
142894 TATAATAATTT
1 -ATATTAATTT
142905 AAAATAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 10 0.30
17 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTAATTTTATATA
Found at i:142882 original size:31 final size:31
Alignment explanation
Indices: 142835--142898 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
142825 CCCAATATGG
*
142835 AAATGTATAAATATATTAATTTTATATAATAT
1 AAATGTATAAATATATTAAATTTATAT-ATAT
*
142867 AAAT-TATTAATATATTAAATTTATATATAT
1 AAATGTATAAATATATTAAATTTATATATAT
142897 AA
1 AA
142899 TAATTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.20
31 20 0.67
32 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
AAATGTATAAATATATTAAATTTATATATAT
Found at i:142894 original size:15 final size:15
Alignment explanation
Indices: 142845--142896 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
142835 AAATGTATAA
*
142845 ATATATTAATTTTAT
1 ATATATTAAATTTAT
142860 ATA-ATATAAA-TTATT
1 ATATAT-TAAATTTA-T
142875 AATATATTAAATTTAT
1 -ATATATTAAATTTAT
142891 ATATAT
1 ATATAT
142897 AATAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 5 0.16
15 13 0.42
16 8 0.26
17 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATTAAATTTAT
Found at i:143081 original size:21 final size:21
Alignment explanation
Indices: 143040--143079 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
143030 GCGGCATGGA
143040 ATTTAATATTTGAAGACTTTC
1 ATTTAATATTTGAAGACTTTC
143061 ATTT-ATATTTGTAAG-CTTT
1 ATTTAATATTTG-AAGACTTT
143080 TCTATCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTAATATTTGAAGACTTTC
Found at i:143356 original size:25 final size:23
Alignment explanation
Indices: 143301--143357 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
143291 AAAATTAAAC
*
143301 TATTA-AATTAAATATATATTTT
1 TATTATAATTAAATATATATTTA
*
143323 TATTAATAATTATAATATTTAATTTA
1 TATT-ATAATTA-AATATAT-ATTTA
143349 TATTATAAT
1 TATTATAAT
143358 ACTTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 1 0.03
24 5 0.17
25 11 0.38
26 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTATAATTAAATATATATTTA
Found at i:143366 original size:24 final size:21
Alignment explanation
Indices: 143331--143389 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
143321 TTTATTAATA
*
143331 ATTATAATATTTAA-TTTA-T
1 ATTATAATAATTAATTTTATT
*
143350 ATTATAATACTTAATTTTATT
1 ATTATAATAATTAATTTTATT
143371 ATTATAATAATTAATTTTA
1 ATTATAATAATTAATTTTA
143390 CCGTCACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.36
20 4 0.11
21 19 0.53
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATAATTAATTTTATT
Found at i:144464 original size:11 final size:11
Alignment explanation
Indices: 144431--144473 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
144421 ATAAAGCATG
*
144431 AAATAAAATAA
1 AAATAATATAA
*
144442 AATATTATATAA
1 AA-ATAATATAA
144454 AAATAATATAA
1 AAATAATATAA
*
144465 AATTAATAT
1 AAATAATAT
144474 TAATATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATAA
Found at i:144501 original size:28 final size:27
Alignment explanation
Indices: 144433--144495 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
144423 AAAGCATGAA
*
144433 ATAAAATAAAATATTATATAAAAATAAT
1 ATAAAAT-TAATATTATATAAAAATAAT
*
144461 ATAAAATTAATATTAATATATAAAT-AT
1 ATAAAATTAATATT-ATATAAAAATAAT
*
144488 ATTAAATT
1 ATAAAATT
144496 TTATATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAAAATTAATATTATATAAAAATAAT
Found at i:144594 original size:14 final size:14
Alignment explanation
Indices: 144563--144595 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
144553 TATAATTTTA
*
144563 AAATAAAAAAATAT
1 AAATTAAAAAATAT
144577 -AATTAAAAAATAT
1 AAATTAAAAAATAT
144590 AAATTA
1 AAATTA
144596 TCTGATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATTAAAAAATAT
Found at i:154616 original size:18 final size:17
Alignment explanation
Indices: 154589--154625 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
154579 AAATGTGAAA
*
154589 TAATTTTTTAAATATTT
1 TAATTTTTTAAATAATT
154606 TAATATTTTTAAATAATT
1 TAAT-TTTTTAAATAATT
154624 TA
1 TA
154626 TAGATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTTTAAATAATT
Found at i:154935 original size:18 final size:17
Alignment explanation
Indices: 154907--154952 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
154897 TAATTTTAAA
*
154907 TATAAATATATTATATT
1 TATAAACATATTATATT
154924 TATTAAACATATTATATT
1 TA-TAAACATATTATATT
154942 TAT-AACATATT
1 TATAAACATATT
154953 TTTATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.30
17 3 0.11
18 16 0.59
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAAACATATTATATT
Found at i:157130 original size:47 final size:47
Alignment explanation
Indices: 157061--157151 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
157051 TAGAGTTTTG
* *
157061 TTCATCTGCTCTGTCACTCCATTTTGTTGAGGTGTGTAAGCCGCACT
1 TTCATCCGCTCTGCCACTCCATTTTGTTGAGGTGTGTAAGCCGCACT
157108 TTCATCCGCTCTGCCACTCCATTTTGTTGAGGTGTGTAAGCCGC
1 TTCATCCGCTCTGCCACTCCATTTTGTTGAGGTGTGTAAGCCGC
157152 GCTAAATTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.36
Consensus pattern (47 bp):
TTCATCCGCTCTGCCACTCCATTTTGTTGAGGTGTGTAAGCCGCACT
Found at i:158769 original size:22 final size:22
Alignment explanation
Indices: 158742--158788 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
158732 CGTTTCATTT
158742 GGCATCGTCCGTTATCTCACTC
1 GGCATCGTCCGTTATCTCACTC
158764 GGCATCGTCCGTTATCTCACTC
1 GGCATCGTCCGTTATCTCACTC
158786 GGC
1 GGC
158789 CTCTCTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.13, C:0.36, G:0.21, T:0.30
Consensus pattern (22 bp):
GGCATCGTCCGTTATCTCACTC
Found at i:159318 original size:50 final size:49
Alignment explanation
Indices: 159244--159443 Score: 238
Period size: 50 Copynumber: 4.0 Consensus size: 49
159234 AGTTGCTTCG
* * * * *
159244 AGTCAATAATTATTGTCACATCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTA-AGTCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* * * * * *
159294 AATCAACGATTATAGCCACCTCTCTCGATTGTCAAACGTTGGTAAAGAAT
1 AGTCAACAATTA-AGTCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* *
159344 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAATGTTAGTGAAGAAT
1 AGTCAACAATTAAG-TCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
*
159394 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTA-AGTCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
159444 TATTAATAAT
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 128 0.98
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (49 bp):
AGTCAACAATTAAGTCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
Found at i:159369 original size:100 final size:100
Alignment explanation
Indices: 159259--159443 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 100
159249 ATAATTATTG
* * * *
159259 TCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATAATCAACGATTATAGCCACCTCTCTCGATT
1 TCACATCTCTCGATTGTCAAAGGTTAGTGAAGAATAATCAACAATTACAGCCACCTCTCTCGATT
*
159324 GTCAAACGTTGGTAAAGAATAGTCAACAATTACGA
66 GTCAAACGTTAGTAAAGAATAGTCAACAATTACGA
* * * * *
159359 TCACCTCTCTCGATTGTCAAATGTTAGTGAAGAATAGTCAACAATTACGGTCACCTCTCTCGATT
1 TCACATCTCTCGATTGTCAAAGGTTAGTGAAGAATAATCAACAATTACAGCCACCTCTCTCGATT
* *
159424 GTCAAAGGTTAGTGAAGAAT
66 GTCAAACGTTAGTAAAGAAT
159444 TATTAATAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (100 bp):
TCACATCTCTCGATTGTCAAAGGTTAGTGAAGAATAATCAACAATTACAGCCACCTCTCTCGATT
GTCAAACGTTAGTAAAGAATAGTCAACAATTACGA
Found at i:159552 original size:8 final size:10
Alignment explanation
Indices: 159525--159574 Score: 84
Period size: 10 Copynumber: 5.0 Consensus size: 10
159515 TTAACTGTTA
159525 AAAAATATAT
1 AAAAATATAT
159535 AAAAATATAT
1 AAAAATATAT
159545 AAAAATATAT
1 AAAAATATAT
159555 AAAAATATA-
1 AAAAATATAT
159564 AAATAATATAT
1 AAA-AATATAT
159575 TTTATATTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 3 0.08
10 35 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:159774 original size:13 final size:13
Alignment explanation
Indices: 159733--159778 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 13
159723 TTGATTTTTG
159733 AATAAATTATTAA
1 AATAAATTATTAA
159746 AATAATATTAATTTAA
1 AATAA-ATT-A-TTAA
159762 AATAAATTATTAA
1 AATAAATTATTAA
159775 AATA
1 AATA
159779 TTATTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 4 0.13
16 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAAATTATTAA
Found at i:159886 original size:31 final size:32
Alignment explanation
Indices: 159828--159943 Score: 94
Period size: 38 Copynumber: 3.5 Consensus size: 32
159818 TATGTAAATT
*
159828 TTATAATTATTATAATTTT-TAATAATTAAATGA
1 TTATAATT-TTA-AATTTTAAAATAATTAAATGA
* *
159861 TTGT-ATTTTAAATTTTAAAATAATTAAATTA
1 TTATAATTTTAAATTTTAAAATAATTAAATGA
*
159892 TTATAATTTTTAATTTAAATTTAAAAATAATTAAATGA
1 TTATAA----T--TTTAAATTTTAAAATAATTAAATGA
*
159930 TAATAA-TTTAAATT
1 TTATAATTTTAAATT
159944 AAATATTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
30 6 0.09
31 26 0.38
32 4 0.06
33 3 0.04
36 1 0.01
38 28 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATAATTTTAAATTTTAAAATAATTAAATGA
Found at i:159910 original size:38 final size:37
Alignment explanation
Indices: 159867--159958 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
159857 ATGATTGTAT
* * *
159867 TTTAAATTTTAAAATAATTAAATTATTATAATTTTTAA
1 TTTAAATTTTAAAATAATTAAATGATAATAA-TTTAAA
*
159905 TTTAAATTTAAAAATAATTAAATGATAATAATTTAAA
1 TTTAAATTTTAAAATAATTAAATGATAATAATTTAAA
*
159942 TTAAATATTTTAAAATA
1 TTTAA-ATTTTAAAATA
159959 TTATATAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 9 0.19
38 38 0.81
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTAAATTTTAAAATAATTAAATGATAATAATTTAAA
Found at i:160086 original size:19 final size:19
Alignment explanation
Indices: 160039--160089 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
160029 AAAAAGTATT
*
160039 ATTTATTTA-TAATAATATT
1 ATTT-TTTATTAATAATATA
*
160058 ATCTTTTATTAATAATATA
1 ATTTTTTATTAATAATATA
160077 ATTTTTTATTAAT
1 ATTTTTTATTAAT
160090 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTTATTAATAATATA
Found at i:160211 original size:23 final size:22
Alignment explanation
Indices: 160171--160213 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
160161 TAATAATTAC
160171 TAAAATATTTAATAATTTTATG
1 TAAAATATTTAATAATTTTATG
* *
160193 TAAAATTTATTAATTATTTTA
1 TAAAATAT-TTAATAATTTTA
160214 AAAATTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAAATATTTAATAATTTTATG
Found at i:160246 original size:32 final size:32
Alignment explanation
Indices: 160177--160246 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
160167 TTACTAAAAT
* * *
160177 ATTTAATAATTTTATGTAAAATTTATTAATTA
1 ATTTAAAAATTTTATGAAAAATTTATCAATTA
* *
160209 TTTTAAAAATTGTTAT-AAAAATTTATCAGTTA
1 ATTTAAAAATT-TTATGAAAAATTTATCAATTA
160241 ATTTAA
1 ATTTAA
160247 TATTTTTGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
32 27 0.87
33 4 0.13
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (32 bp):
ATTTAAAAATTTTATGAAAAATTTATCAATTA
Found at i:161645 original size:17 final size:18
Alignment explanation
Indices: 161611--161653 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
161601 AAGAAAGAAA
*
161611 AAAAAAAAAGCCAAAGAC
1 AAAACAAAAGCCAAAGAC
*
161629 AAAACAAAAG-CATAGAC
1 AAAACAAAAGCCAAAGAC
*
161646 AAGACAAA
1 AAAACAAA
161654 TCTTTAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.70, C:0.16, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAACAAAAGCCAAAGAC
Found at i:161930 original size:14 final size:14
Alignment explanation
Indices: 161911--161937 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
161901 AATATTAAAA
161911 AATATTTTTATATT
1 AATATTTTTATATT
161925 AATATTTTTATAT
1 AATATTTTTATAT
161938 ATTTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:162074 original size:17 final size:18
Alignment explanation
Indices: 162024--162076 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
162014 CAATTCAAAC
* *
162024 AAATTAAATCAAATAAAT
1 AAATTTAATCATATAAAT
*
162042 -AATTT-ATCTTATAAAT
1 AAATTTAATCATATAAAT
162058 AAATTTAATCATA-AAAT
1 AAATTTAATCATATAAAT
162075 AA
1 AA
162077 CCACTAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 9 0.31
17 15 0.52
18 5 0.17
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTAATCATATAAAT
Found at i:162233 original size:17 final size:18
Alignment explanation
Indices: 162203--162244 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
162193 ATATATTAAA
162203 ATATTTATTAAAAAATATT
1 ATATTTATTAAAAAAT-TT
162222 AT-TTTATT-AAAAATTT
1 ATATTTATTAAAAAATTT
162238 ATATTTA
1 ATATTTA
162245 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 6 0.27
19 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTATTAAAAAATTT
Found at i:162242 original size:18 final size:19
Alignment explanation
Indices: 162206--162257 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
162196 TATTAAAATA
*
162206 TTTATTAAAAA-ATATTAT
1 TTTATTAAAAATTTATTAT
162224 TTTATTAAAAATTTA-TAT
1 TTTATTAAAAATTTATTAT
*
162242 TTAATTTTAAAAATTT
1 TT--TATTAAAAATTT
162258 TAATAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 16 0.55
19 2 0.07
20 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTAAAAATTTATTAT
Found at i:164662 original size:2 final size:2
Alignment explanation
Indices: 164657--164690 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
164647 GAGGAATTAA
164657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
164691 GCAGCTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168180 original size:12 final size:13
Alignment explanation
Indices: 168141--168189 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 13
168131 TAAACAACAA
168141 AAATAATAATAATAT
1 AAAT-ATAATAA-AT
168156 AATATATAATAAAT
1 AA-ATATAATAAAT
168170 AAATA-AATAAAT
1 AAATATAATAAAT
*
168182 AAAAATAA
1 AAATATAA
168190 GCTTAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 11 0.35
13 5 0.16
14 4 0.13
15 9 0.29
16 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAATAAAT
Found at i:172714 original size:4 final size:4
Alignment explanation
Indices: 172705--172774 Score: 72
Period size: 4 Copynumber: 17.8 Consensus size: 4
172695 TTCAGCCAAA
* * * *
172705 AAAG AAAG AAAG AAAG AAA- AAAA AAAG AAAAA AAAG AAAG AAAA AAAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
*
172753 AAAG AAA- AATG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAA
172775 AAAATATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
3 5 0.09
4 48 0.86
5 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:172730 original size:23 final size:22
Alignment explanation
Indices: 172703--172770 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
172693 TGTTCAGCCA
172703 AAAAAGAAAGAAAGAAAGAAAA-A
1 AAAAAGAAAGAAA-AAA-AAAAGA
172726 AAAAAGAAA-AAAAAGAAAGAA-A
1 AAAAAGAAAGAAAAA-AAA-AAGA
**
172748 AAAAA-AAAGAAAAATGAAAGA
1 AAAAAGAAAGAAAAAAAAAAGA
172769 AA
1 AA
172771 GAAAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.05
21 11 0.28
22 17 0.44
23 9 0.23
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (22 bp):
AAAAAGAAAGAAAAAAAAAAGA
Found at i:172740 original size:24 final size:24
Alignment explanation
Indices: 172702--172778 Score: 111
Period size: 25 Copynumber: 3.1 Consensus size: 24
172692 GTGTTCAGCC
*
172702 AAAAAAG-AAAGAAAGAAAGAAAA
1 AAAAAAGAAAAAAAAGAAAGAAAA
172725 AAAAAAGAAAAAAAAGAAAGAAAAA
1 AAAAAAGAAAAAAAAGAAAG-AAAA
172750 AAAAAAGAAAAATGAAAGAAAGAAAA
1 AAAAAAGAAAAA--AAAGAAAGAAAA
172776 AAA
1 AAA
172779 TATTTATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
23 7 0.14
24 11 0.22
25 16 0.33
26 7 0.14
27 8 0.16
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAGAAAGAAAA
Found at i:172757 original size:36 final size:37
Alignment explanation
Indices: 172705--172776 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
172695 TTCAGCCAAA
* * *
172705 AAAGAAAGAAAGAAAGAAAAAAAAAAGAAAA-AAAAG
1 AAAGAAAAAAAAAAAGAAAAAAAAAAGAAAGAAAAAG
**
172741 AAAGAAAAAAAAAAAGAAAAATGAAAGAAAGAAAAA
1 AAAGAAAAAAAAAAAGAAAAAAAAAAGAAAGAAAAA
172777 AATATTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (37 bp):
AAAGAAAAAAAAAAAGAAAAAAAAAAGAAAGAAAAAG
Found at i:172841 original size:32 final size:30
Alignment explanation
Indices: 172813--172872 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
172803 ATTTTTTACT
*
172813 TAAAATATTATATTTTTATATAAATTTTTAA
1 TAAAATAATA-ATTTTTATATAAATTTTTAA
* * *
172844 TATAATAATAATTTTTATGTATATTTTTA
1 TAAAATAATAATTTTTATATAAATTTTTA
172873 TACGTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TAAAATAATAATTTTTATATAAATTTTTAA
Found at i:173094 original size:16 final size:14
Alignment explanation
Indices: 173067--173105 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
173057 TTTAAAGTAT
*
173067 TATAAATTTATATA
1 TATATATTTATATA
173081 -ATAT-TTTATATA
1 TATATATTTATATA
173093 TATATATTTATAT
1 TATATATTTATAT
173106 TGTCATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 8 0.36
13 7 0.32
14 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:173142 original size:22 final size:22
Alignment explanation
Indices: 173114--173155 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
173104 ATTGTCATAT
*
173114 TTATTTTTATATTATATTTTAA
1 TTATTTTCATATTATATTTTAA
*
173136 TTATTTTCATGTTATATTTT
1 TTATTTTCATATTATATTTT
173156 TATTTTCCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTCATATTATATTTTAA
Found at i:173560 original size:15 final size:16
Alignment explanation
Indices: 173542--173571 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
173532 TTTTATAAAA
173542 AAAGAAAAAG-GAAAG
1 AAAGAAAAAGAGAAAG
173557 AAAGAAAAAGAGAAA
1 AAAGAAAAAGAGAAA
173572 AAATTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAG
Found at i:174109 original size:15 final size:16
Alignment explanation
Indices: 174089--174118 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
174079 TTTTTAAATA
174089 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
174104 AATTTTATTTAATTA
1 AATTTTATTTAATTA
174119 AAAATCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:174467 original size:19 final size:18
Alignment explanation
Indices: 174443--174487 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
174433 CATGTAATTA
174443 TAAATATAATAAAAAATAT
1 TAAATATAAT-AAAAATAT
* *
174462 TAAATAT-ATTAAAATTT
1 TAAATATAATAAAAATAT
174479 TAAATATAA
1 TAAATATAA
174488 ATATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 3 0.13
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATAATAAAAATAT
Found at i:174502 original size:17 final size:17
Alignment explanation
Indices: 174456--174508 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
174446 ATATAATAAA
*
174456 AAATATTAAATATAT-T
1 AAATATTATATATATAT
*
174472 AAA-ATT-T-TAAATAT
1 AAATATTATATATATAT
174486 AAATATTATATATATAT
1 AAATATTATATATATAT
*
174503 ATATAT
1 AAATAT
174509 ATTGCATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 6 0.21
16 4 0.14
17 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTATATATATAT
Found at i:176509 original size:14 final size:15
Alignment explanation
Indices: 176492--176524 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
176482 AAAATTTAAA
*
176492 TAAAAAAA-TAATAT
1 TAAAAAAAGTAAAAT
176506 TAAAAAAAGTAAAAT
1 TAAAAAAAGTAAAAT
176521 TAAA
1 TAAA
176525 TTCTTATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAAAAGTAAAAT
Found at i:177260 original size:28 final size:28
Alignment explanation
Indices: 177183--177265 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 28
177173 TGAAATTTGT
* * *
177183 AAATACTATAATATTAAATATAATATGAA
1 AAATAATATAA-ATTTAGTATAATATGAA
** *
177212 AAATTTTAATAAATATATAGTATAATATTAA
1 AAATAAT-ATAAAT-T-TAGTATAATATGAA
177243 AAATAATATAAATTTAGTATAAT
1 AAATAATATAAATTTAGTATAAT
177266 TATATAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.20
29 8 0.18
30 11 0.25
31 16 0.36
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATAATATAAATTTAGTATAATATGAA
Found at i:177277 original size:37 final size:35
Alignment explanation
Indices: 177182--177307 Score: 83
Period size: 37 Copynumber: 3.3 Consensus size: 35
177172 CTGAAATTTG
* *
177182 TAAATACTAT-AATATTAAATATAATATGAAAAATTTTAA
1 TAAATA-TATAAATATTAAAAAT-A-AT-AAAAATTAT-A
*
177221 TAAATATATAGTATAATATTAAAAATAATATAAATTTAGTA
1 T-AA-ATATA-TA-AATATTAAAAATAATA-AAAATTA-TA
* * * *
177262 TAATTATATAAATATTTAATATATTAAAAATTATA
1 TAAATATATAAATATTAAAAATAATAAAAATTATA
177297 TAAATATATAA
1 TAAATATATAA
177308 TTTTTAAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
35 12 0.17
36 6 0.08
37 13 0.18
38 2 0.03
39 5 0.07
40 7 0.10
41 13 0.18
42 2 0.03
43 11 0.15
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (35 bp):
TAAATATATAAATATTAAAAATAATAAAAATTATA
Found at i:177294 original size:27 final size:27
Alignment explanation
Indices: 177261--177331 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
177251 TAAATTTAGT
*
177261 ATAATTATATAAATATTTAATATATTAA
1 ATAATTATATAAATATATAAT-TATTAA
*
177289 A-AATTATATAAATATATAATTTTTAA
1 ATAATTATATAAATATATAATTATTAA
* *
177315 ATATTTTTATAAATATA
1 ATAATTATATAAATATA
177332 AAAAAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 6 0.16
27 31 0.82
28 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAATTATATAAATATATAATTATTAA
Found at i:177298 original size:46 final size:42
Alignment explanation
Indices: 177236--177346 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 42
177226 ATATAGTATA
177236 ATATTAAAAATAATATAAATTTAGTATAATTATATAAATATTTAAT
1 ATATTAAAAATAATATAAA--TA-TATAATT-TATAAATATTTAAT
* * *
177282 ATATTAAAAATTATATAAATATATAATTTTTAAATATTTTTAT
1 ATATTAAAAATAATATAAATATATAATTTATAAATA-TTTAAT
*
177325 AAATATAAAAA-AATATAAATAT
1 ATAT-TAAAAATAATATAAATAT
177347 GAAATAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 7 0.12
43 25 0.43
44 8 0.14
46 18 0.31
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (42 bp):
ATATTAAAAATAATATAAATATATAATTTATAAATATTTAAT
Found at i:177306 original size:35 final size:36
Alignment explanation
Indices: 177260--177346 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 36
177250 ATAAATTTAG
*
177260 TATAATTATATAAATATTT-AATA-TATTAAAAATTA
1 TATAAATATATAAATATTTAAATATTATTAAAAA-TA
* * *
177295 TATAAATATAT-AATTTTTAAATATTTTTATAAATA
1 TATAAATATATAAATATTTAAATATTATTAAAAATA
* *
177330 TAAAAAAATATAAATAT
1 TATAAATATATAAATAT
177347 GAAATAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
34 6 0.14
35 25 0.60
36 11 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TATAAATATATAAATATTTAAATATTATTAAAAATA
Found at i:177343 original size:16 final size:17
Alignment explanation
Indices: 177322--177358 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
177312 TAAATATTTT
177322 TATAAATAT-AAAAAAA
1 TATAAATATGAAAAAAA
*
177338 TATAAATATGAAATAAA
1 TATAAATATGAAAAAAA
177355 TATA
1 TATA
177359 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TATAAATATGAAAAAAA
Found at i:177750 original size:32 final size:30
Alignment explanation
Indices: 177697--177792 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 30
177687 TGCTAATCTA
*
177697 AAAATATTAAAATTTAAATTTAAGATTAAATTT
1 AAAATATTAAAAATT--ATTTAA-ATTAAATTT
* *
177730 AATAAT-TTAAATAATTATTTAAAATATA-TT
1 AA-AATATTAAA-AATTATTTAAATTAAATTT
*
177760 AAAATATTAAAAATTATTTTATATTAATATTT
1 AAAATATTAAAAATTA-TTTAAATTAA-ATTT
177792 A
1 A
177793 TACATATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
29 8 0.16
30 16 0.31
31 5 0.10
32 9 0.18
33 7 0.14
34 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
AAAATATTAAAAATTATTTAAATTAAATTT
Found at i:178469 original size:16 final size:15
Alignment explanation
Indices: 178448--178538 Score: 50
Period size: 14 Copynumber: 6.1 Consensus size: 15
178438 TATATTAAAA
*
178448 TAATATCATGTTATTT
1 TAATAT-ATATTATTT
178464 TAATATATATTATTT
1 TAATATATATTATTT
*
178479 T-TTATAT-TATATTT
1 TAATATATAT-TATTT
*
178493 TAAT-TAT-TTTTTAT
1 TAATATATATTATT-T
*
178507 TATTCATAT-TTATTT
1 TAAT-ATATATTATTT
*
178522 T-ATATAATAATATTT
1 TAATAT-ATATTATTT
178537 TA
1 TA
178539 TTTAATATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
13 6 0.10
14 22 0.37
15 18 0.31
16 13 0.22
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (15 bp):
TAATATATATTATTT
Found at i:178484 original size:12 final size:12
Alignment explanation
Indices: 178469--178506 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
178459 TATTTTAATA
178469 TATATTATTTTT
1 TATATTATTTTT
*
178481 TATATTATATTT
1 TATATTATTTTT
178493 TA-ATTATTTTT
1 TATATTATTTTT
178504 TAT
1 TAT
178507 TATTCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATATTATTTTT
Found at i:178498 original size:23 final size:25
Alignment explanation
Indices: 178472--178517 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
178462 TTTAATATAT
178472 ATTATTTTTTA-TATT-ATATTTTA
1 ATTATTTTTTATTATTCATATTTTA
178495 ATTATTTTTTATTATTCATATTT
1 ATTATTTTTTATTATTCATATTT
178518 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.52
24 4 0.19
25 6 0.29
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTATTTTTTATTATTCATATTTTA
Found at i:178516 original size:30 final size:28
Alignment explanation
Indices: 178458--178527 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 28
178448 TAATATCATG
* *
178458 TTATTTTAATATATATTATTTTTTATAT
1 TTATTTTAATATATATTATTATTCATAT
* *
178486 TATATTTTAATTATTTTTTATTATTCATAT
1 T-TATTTTAA-TATATATTATTATTCATAT
178516 TTATTTT-ATATA
1 TTATTTTAATATA
178528 ATAATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.09
28 2 0.06
29 14 0.40
30 16 0.46
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTTTAATATATATTATTATTCATAT
Found at i:179101 original size:18 final size:16
Alignment explanation
Indices: 179078--179117 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
179068 AACTGTTTGA
*
179078 ATTAATCGATATATTTCG
1 ATTAATCGAT-TAATT-G
179096 ATTAATCGATTAATTG
1 ATTAATCGATTAATTG
179112 ATTAAT
1 ATTAAT
179118 AATTCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (16 bp):
ATTAATCGATTAATTG
Found at i:181663 original size:17 final size:17
Alignment explanation
Indices: 181633--181666 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
181623 AATTAAAATA
*
181633 TTTTATTAAAAATAATT
1 TTTTAATAAAAATAATT
*
181650 TTTTAATAATAATAATT
1 TTTTAATAAAAATAATT
181667 CAAATTATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAATAAAAATAATT
Found at i:181707 original size:28 final size:29
Alignment explanation
Indices: 181676--181730 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
181666 TCAAATTATC
* * *
181676 ATATTTATATTATTTTAATA-TTATAATT
1 ATATTTAAAATATCTTAATATTTATAATT
181704 ATATTTAAAATATCTTAATATTTATAA
1 ATATTTAAAATATCTTAATATTTATAA
181731 AATTTTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTAAAATATCTTAATATTTATAATT
Found at i:181762 original size:18 final size:18
Alignment explanation
Indices: 181731--181797 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
181721 ATATTTATAA
181731 AATTT-TAATCATATTAAT
1 AATTTATAAT-ATATTAAT
181749 AATTTATAATATA-T-A-
1 AATTTATAATATATTAAT
*
181764 AATTTA-AATATATTTAT
1 AATTTATAATATATTAAT
*
181781 ACATTAATAATATATTA
1 A-ATTTATAATATATTA
181798 TATTTTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
15 7 0.17
16 2 0.05
17 2 0.05
18 12 0.29
19 12 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTATAATATATTAAT
Found at i:181805 original size:18 final size:16
Alignment explanation
Indices: 181732--181818 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 16
181722 TATTTATAAA
*
181732 ATTTTAATCATATTAAT
1 ATTTTAAT-ATATTTAT
*
181749 AATTTATAATATA--TAA
1 -ATTT-TAATATATTTAT
*
181765 ATTTAAATATATTTAT
1 ATTTTAATATATTTAT
**
181781 ACATTAATAATATATTAT
1 ATTTTAAT-ATAT-TTAT
181799 ATTTTAAT-TATTTTAT
1 ATTTTAATATA-TTTAT
181815 ATTT
1 ATTT
181819 ATATACTATA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
14 6 0.11
15 4 0.07
16 18 0.33
17 5 0.09
18 17 0.31
19 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTAATATATTTAT
Found at i:181811 original size:33 final size:32
Alignment explanation
Indices: 181726--181811 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
181716 TCTTAATATT
* *
181726 TATA-AAATTTTAATCATATTAATAATTTATAA
1 TATATAAATTTTAAT-ATATTTATAATTAATAA
*
181758 TATATAAATTTAAATATATTTATACATTAATAA
1 TATATAAATTTTAATATATTTATA-ATTAATAA
*
181791 TATATTATATTTTAAT-TATTT
1 TATA-TAAATTTTAATATATTT
181812 TATATTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.26
33 25 0.54
34 9 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATAAATTTTAATATATTTATAATTAATAA
Found at i:184385 original size:31 final size:31
Alignment explanation
Indices: 184327--184396 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
184317 TAAAATGATC
* *
184327 ATAAA-TTGATAAATATTAAAGATAATTATTC
1 ATAAATTTAATAAATATT-AAGATAATTATTA
*
184358 GTAAATTTAATAAATATT-AGATAAATTATTA
1 ATAAATTTAATAAATATTAAGAT-AATTATTA
184389 ATAAATTT
1 ATAAATTT
184397 GAGAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.12
31 18 0.55
32 11 0.33
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (31 bp):
ATAAATTTAATAAATATTAAGATAATTATTA
Found at i:184463 original size:29 final size:31
Alignment explanation
Indices: 184429--184491 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
184419 TTTTATTATT
* *
184429 TAAATTTATATTG-ATTTTCT-TATAATTGA
1 TAAATTTATATTGAATATTATATATAATTGA
* *
184458 TAAATTTTTTTTGAATATTATATATAATTGA
1 TAAATTTATATTGAATATTATATATAATTGA
184489 TAA
1 TAA
184492 GTATTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.39
30 5 0.18
31 12 0.43
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (31 bp):
TAAATTTATATTGAATATTATATATAATTGA
Found at i:184525 original size:14 final size:15
Alignment explanation
Indices: 184508--184537 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
184498 AATATATAAA
184508 ATTTATTTTAT-TTT
1 ATTTATTTTATATTT
184522 ATTTATTTTATATTT
1 ATTTATTTTATATTT
184537 A
1 A
184538 AAAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTTTATATTT
Found at i:186142 original size:20 final size:19
Alignment explanation
Indices: 186117--186164 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
186107 AAGATATAAA
*
186117 TATATATATGTGTTAAAATT
1 TATATATATATG-TAAAATT
* *
186137 TATATAAATATGTAATATT
1 TATATATATATGTAAAATT
186156 T-TATATATA
1 TATATATATA
186165 ATTATGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 7 0.29
19 7 0.29
20 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TATATATATATGTAAAATT
Found at i:186396 original size:17 final size:17
Alignment explanation
Indices: 186376--186408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
186366 ATATGATTAT
186376 AATATAAAAATAATACA
1 AATATAAAAATAATACA
*
186393 AATATAAAATTAATAC
1 AATATAAAAATAATAC
186409 GGAGCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AATATAAAAATAATACA
Found at i:186813 original size:17 final size:19
Alignment explanation
Indices: 186783--186817 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
186773 ATTTTAATTT
186783 ATTTTATATGTATTTTTAA
1 ATTTTATATGTATTTTTAA
186802 ATTTTA-AT-TATTTTTA
1 ATTTTATATGTATTTTTA
186818 TTTAACTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTATATGTATTTTTAA
Found at i:187008 original size:20 final size:20
Alignment explanation
Indices: 186979--187020 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
186969 GAAAGGATGT
* *
186979 ATTTTTATTTTATATTTATA
1 ATTTTAATTTTAAATTTATA
*
186999 ATTTTAATTTTAAATTTTTA
1 ATTTTAATTTTAAATTTATA
187019 AT
1 AT
187021 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTAATTTTAAATTTATA
Found at i:187545 original size:22 final size:24
Alignment explanation
Indices: 187520--187568 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
187510 TTTTTTTATA
187520 TTATAATTATATT-TA-AAATATT
1 TTATAATTATATTATATAAATATT
** *
187542 TTATTTTTATATTATATAAATTTT
1 TTATAATTATATTATATAAATATT
187566 TTA
1 TTA
187569 AAAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATAATTATATTATATAAATATT
Found at i:188197 original size:23 final size:21
Alignment explanation
Indices: 188144--188198 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
188134 TCTATATTCT
*
188144 TATT-TTAATAAAAATAATTA
1 TATTATTAATAAAAAAAATTA
*
188164 TATTTTATAATAATAAAAAATTA
1 TATTAT-TAATAA-AAAAAATTA
188187 TATATATTAATA
1 TAT-TATTAATA
188199 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 1 0.03
22 6 0.21
23 16 0.55
24 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTATTAATAAAAAAAATTA
Found at i:190537 original size:15 final size:14
Alignment explanation
Indices: 190497--190537 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
190487 CAATTTATTT
190497 AATTTAATAAATTA
1 AATTTAATAAATTA
*
190511 AATTTATTTAAATTA
1 AATTTA-ATAAATTA
190526 AATTTACATAAA
1 AATTTA-ATAAA
190538 AATTTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTAATAAATTA
Found at i:190620 original size:25 final size:25
Alignment explanation
Indices: 190562--190636 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
190552 AATTGACTTG
* * *
190562 ATAAAAATTATTATTTAA-ATAATA
1 ATAAATATTATTATTTAATTTAATT
*
190586 ATAAATTATTTTTATTTAATTTAATT
1 ATAAA-TATTATTATTTAATTTAATT
* *
190612 ATAAATATTAATATATAATTTAATT
1 ATAAATATTATTATTTAATTTAATT
190637 TTTTTAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 5 0.12
25 28 0.67
26 9 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAAATATTATTATTTAATTTAATT
Found at i:190624 original size:39 final size:38
Alignment explanation
Indices: 190581--190667 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 38
190571 ATTATTTAAA
* *
190581 TAATAATAAATTATTTTTATTTAAT-TTAATTATAAATAT
1 TAATAATAAATTAATTTT-TTTAATATT-ATTATAAATAG
* *
190620 TAATATATAATTTAATTTTTTTAATATTATTTTAAATAG
1 TAATA-ATAAATTAATTTTTTTAATATTATTATAAATAG
190659 TAAT-ATAAA
1 TAATAATAAA
190668 CGTTTACACT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
37 4 0.10
39 24 0.59
40 13 0.32
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
TAATAATAAATTAATTTTTTTAATATTATTATAAATAG
Found at i:191156 original size:23 final size:23
Alignment explanation
Indices: 191124--191176 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
191114 AATATAAAAA
*
191124 TAAT-TTTATATATTATTT-TTAT
1 TAATATTTATATATT-TTTATAAT
191146 TAATATTTATATATTTTTATAAT
1 TAATATTTATATATTTTTATAAT
191169 TAA-ATTTA
1 TAATATTTA
191177 AATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATATTTATATATTTTTATAAT
Found at i:191226 original size:26 final size:25
Alignment explanation
Indices: 191166--191228 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
191156 ATATTTTTAT
* *
191166 AATTAAATTTAAATAAATATTATTA
1 AATTAAATTTAAATAAATATAATCA
*
191191 AATAACAATTTAAATCAAA-ATAAATCA
1 AATTA-AATTTAAAT-AAATAT-AATCA
191218 AATTAAATTTA
1 AATTAAATTTA
191229 TAAAACTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 17 0.55
27 10 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
AATTAAATTTAAATAAATATAATCA
Found at i:194648 original size:2 final size:2
Alignment explanation
Indices: 194641--194679 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
194631 TTATTCACAA
194641 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
194680 CTTACTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:195656 original size:15 final size:15
Alignment explanation
Indices: 195626--195686 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
195616 CGTTAAATAC
*
195626 ATATTACATGTATTTA
1 ATATTA-ATATATTTA
195642 ATATTAATATATTTA
1 ATATTAATATATTTA
195657 AT-TT--T-TATTTA
1 ATATTAATATATTTA
**
195668 ATATTTTTATATTT-
1 ATATTAATATATTTA
195682 ATATT
1 ATATT
195687 TAAAGAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 8 0.20
12 3 0.08
14 8 0.20
15 15 0.38
16 6 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (15 bp):
ATATTAATATATTTA
Found at i:195660 original size:20 final size:20
Alignment explanation
Indices: 195636--195686 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
195626 ATATTACATG
195636 TATTTAATATTAATATATTTA
1 TATTT-ATATTAATATATTTA
* *
195657 -ATTTTTATTTAATATTTTTA
1 TATTTATA-TTAATATATTTA
195677 TATTTATATT
1 TATTTATATT
195687 TAAAGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTATATTAATATATTTA
Found at i:195665 original size:26 final size:27
Alignment explanation
Indices: 195636--195687 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
195626 ATATTACATG
195636 TATTTAATATTAATATATTTA-ATTTT
1 TATTTAATATTAATATATTTATATTTT
**
195662 TATTTAATATTTTTATATTTATATTT
1 TATTTAATATTAATATATTTATATTT
195688 AAAGAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TATTTAATATTAATATATTTATATTTT
Found at i:195766 original size:3 final size:3
Alignment explanation
Indices: 195758--195789 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
195748 AAATAAGTAC
*
195758 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
195790 GATGAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:196216 original size:15 final size:16
Alignment explanation
Indices: 196189--196219 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
196179 TTTTTTAAAG
196189 TTTAAATTTAATTTAA
1 TTTAAATTTAATTTAA
196205 TTTAAA-TTAATTTAA
1 TTTAAATTTAATTTAA
196220 AAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAATTTAA
Found at i:196226 original size:18 final size:19
Alignment explanation
Indices: 196203--196241 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
196193 AATTTAATTT
196203 AATTTAAATTA-ATTTAAA
1 AATTTAAATTATATTTAAA
*
196221 AATTTATATTATTATTTAAA
1 AATTTAAATTA-TATTTAAA
196241 A
1 A
196242 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTAAATTATATTTAAA
Found at i:196309 original size:28 final size:30
Alignment explanation
Indices: 196229--196331 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 30
196219 AAAATTTATA
196229 TTATTATTTAAAATAATATTTAAAATATAAATT
1 TTATTATTT-AAATAA-A-TTAAAATATAAATT
* * * *
196262 TTA-TAATTAATTAAAATAAAATA-AAGTT
1 TTATTATTTAAATAAATTAAAATATAAATT
*
196290 TTATTATTTAAAT-AATTAAAATTATAAATA
1 TTATTATTTAAATAAATTAAAA-TATAAATT
196320 TTATTAATTTAA
1 TTATT-ATTTAA
196332 TTTAATTTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 14 0.25
29 16 0.28
30 9 0.16
31 11 0.19
32 4 0.07
33 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TTATTATTTAAATAAATTAAAATATAAATT
Found at i:196500 original size:66 final size:68
Alignment explanation
Indices: 196425--196558 Score: 227
Period size: 66 Copynumber: 2.0 Consensus size: 68
196415 ATAAATTTGG
* *
196425 TGGATATATTAAAAGTTTTTATTTTTAATATTGCGTCACT-A-CGTGTCGGAATTGAACTCAGGA
1 TGGATATATTAAAAGCTTTTATTTTCAATATTGCGTCACTAACCGTGTCGGAATTGAACTCAGGA
196488 TTC
66 TTC
*
196491 TGGATATATTAAAAGCTTTTATTTTCAATATTGCGTCACTAACCGTGTCGGAATTGAACTCCGGA
1 TGGATATATTAAAAGCTTTTATTTTCAATATTGCGTCACTAACCGTGTCGGAATTGAACTCAGGA
196556 TTC
66 TTC
196559 ACCGAATCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 38 0.60
67 1 0.02
68 24 0.38
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (68 bp):
TGGATATATTAAAAGCTTTTATTTTCAATATTGCGTCACTAACCGTGTCGGAATTGAACTCAGGA
TTC
Found at i:199614 original size:14 final size:14
Alignment explanation
Indices: 199567--199623 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
199557 TTAAACTTAT
199567 TTTAAA-ATT-AAA
1 TTTAAATATTAAAA
*
199579 TTTATAATAATAATAA
1 TTTA-AATATTAA-AA
*
199595 -TAAAATATTAAAA
1 TTTAAATATTAAAA
199608 TTTAAATA-TAAAA
1 TTTAAATATTAAAA
199621 TTT
1 TTT
199624 CTTAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.11
13 12 0.33
14 15 0.42
15 3 0.08
16 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAATATTAAAA
Found at i:200262 original size:21 final size:21
Alignment explanation
Indices: 200236--200300 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
200226 AATGATGATA
*
200236 AAAATTAATTA-TATTAATAAT
1 AAAATTAAATATTA-TAATAAT
200257 AAAATTAAATATTATAATAAT
1 AAAATTAAATATTATAATAAT
* * *
200278 AATA-TATATATTAAAAT-AT
1 AAAATTAAATATTATAATAAT
200297 AAAA
1 AAAA
200301 ATAATGATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 5 0.13
20 11 0.29
21 20 0.53
22 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTAAATATTATAATAAT
Found at i:201025 original size:21 final size:21
Alignment explanation
Indices: 200986--201040 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
200976 AAAGATATAT
** *
200986 TTGGATGAAATGATGCATTGA
1 TTGGATGAAAAAATACATTGA
**
201007 TTGGATGAAAAAATACATTTT
1 TTGGATGAAAAAATACATTGA
*
201028 TTGAATGAAAAAA
1 TTGGATGAAAAAA
201041 ATGTAACTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.33
Consensus pattern (21 bp):
TTGGATGAAAAAATACATTGA
Found at i:209747 original size:15 final size:16
Alignment explanation
Indices: 209705--209754 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
209695 ATATTTTATT
*
209705 ATTAAAAATTAATATA
1 ATTAATAATTAATATA
*
209721 ACTT-ATATTTAA-ATA
1 A-TTAATAATTAATATA
*
209736 ATTAATAATTAATTTA
1 ATTAATAATTAATATA
209752 ATT
1 ATT
209755 TATGAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 12 0.44
17 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAATAATTAATATA
Found at i:210207 original size:14 final size:13
Alignment explanation
Indices: 210171--210204 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
210161 ATCATTTAAA
*
210171 AATTTTTTATTTT
1 AATTTTTTAATTT
*
210184 TATTTTTTAATTT
1 AATTTTTTAATTT
210197 AATTTTTT
1 AATTTTTT
210205 TAAATATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTTTTAATTT
Found at i:210605 original size:6 final size:6
Alignment explanation
Indices: 210588--210657 Score: 61
Period size: 6 Copynumber: 10.8 Consensus size: 6
210578 TTAATATTAA
* *
210588 TATATT TA-ATT TATATT TAATTTTT TATATT TAAAAATTT ATATATT
1 TATATT TATATT TATATT T-A-TATT TATATT T--ATA-TT -TATATT
210635 TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATAT
210658 AAAATATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 5 0.09
6 33 0.62
7 4 0.08
8 8 0.15
9 2 0.04
10 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:210607 original size:26 final size:24
Alignment explanation
Indices: 210575--210657 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 24
210565 AATAAAAACG
210575 TATTTAATATTAATATATTTAATTTA
1 TATTTAATATT--TATATTTAATTTA
*
210601 TATTTAATTTTTTATATTTAAAAATTTA
1 TATTTAA-TATTTATATTT---AATTTA
*
210629 TATATTTATATTTATATTTATATTTA
1 TAT-TTAATATTTATATTTA-ATTTA
210655 TAT
1 TAT
210658 AAAATATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
25 8 0.17
26 15 0.31
27 3 0.06
28 19 0.40
29 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTAATATTTATATTTAATTTA
Found at i:210641 original size:14 final size:14
Alignment explanation
Indices: 210575--210658 Score: 70
Period size: 12 Copynumber: 6.1 Consensus size: 14
210565 AATAAAAACG
*
210575 TATTTAATATTAATA
1 TATTT-ATATTTATA
210590 TATTTA-ATTTATA
1 TATTTATATTTATA
* *
210603 T-TTAAT-TTTTTA
1 TATTTATATTTATA
*
210615 TATTTAAAAATTTATA
1 TATTT--ATATTTATA
210631 TATTTATA-TT-TA
1 TATTTATATTTATA
210643 TATTTATATTTATA
1 TATTTATATTTATA
210657 TA
1 TA
210659 AAATATAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
12 19 0.35
13 13 0.24
14 7 0.13
15 6 0.11
16 10 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTATATTTATA
Found at i:210658 original size:20 final size:21
Alignment explanation
Indices: 210575--210651 Score: 81
Period size: 20 Copynumber: 3.8 Consensus size: 21
210565 AATAAAAACG
*
210575 TATTTAATATTAATATATTTA
1 TATTTAATATTTATATATTTA
*
210596 -ATTT-ATATTTA-ATTTTTTA
1 TATTTAATATTTATA-TATTTA
*
210615 TATTTAAAAATTTATATATTTA
1 TATTT-AATATTTATATATTTA
210637 TATTT-ATATTTATAT
1 TATTTAATATTTATAT
210652 TTATATAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 11 0.24
20 17 0.37
22 16 0.35
23 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTAATATTTATATATTTA
Found at i:212300 original size:33 final size:30
Alignment explanation
Indices: 212276--212365 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 30
212266 TTAAATTTTT
212276 TTAAAAATATTA-ATTTGATATAATTAATGTA
1 TTAAAAATATTATATTT--TATAATTAATGTA
*
212307 TTAAAAATATTATATTTTATAATTTTATCG-A
1 TTAAAAATATTATATTTTATAA-TTAAT-GTA
* *
212338 TTAAAAAATAATATATCATTATAATTAA
1 TT-AAAAATATTATAT-TTTATAATTAA
212366 ATTTTAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
30 5 0.10
31 19 0.38
32 20 0.40
33 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (30 bp):
TTAAAAATATTATATTTTATAATTAATGTA
Found at i:212341 original size:31 final size:31
Alignment explanation
Indices: 212276--212363 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
212266 TTAAATTTTT
212276 TTAAAAATATTA-ATTTGATATAA-TTAATGTA
1 TTAAAAATATTATATTT--TATAATTTAATGTA
*
212307 TTAAAAATATTATATTTTATAATTTTATCG-A
1 TTAAAAATATTATATTTTATAATTTAAT-GTA
* *
212338 TTAAAAAATAATATATCATTATAATT
1 TT-AAAAATATTATAT-TTTATAATT
212364 AAATTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
30 5 0.10
31 19 0.39
32 17 0.35
33 8 0.16
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
TTAAAAATATTATATTTTATAATTTAATGTA
Found at i:212695 original size:20 final size:21
Alignment explanation
Indices: 212676--212747 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 21
212666 ACCTGTATTT
*
212676 AATATTAATATATTTAATTTA
1 AATATTAATATATTTAATATA
*
212697 TAT-TTAAATAAATATTTAATATA
1 AATATT-AAT--ATATTTAATATA
*
212720 AATATTAA-ATATTAAATATA
1 AATATTAATATATTTAATATA
212740 AATATTAA
1 AATATTAA
212748 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 21 0.49
21 5 0.12
23 15 0.35
24 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTAATATATTTAATATA
Found at i:212713 original size:12 final size:12
Alignment explanation
Indices: 212696--212730 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
212686 TATTTAATTT
212696 ATATTTAAATAA
1 ATATTTAAATAA
212708 ATATTTAATATAA
1 ATATTTAA-ATAA
212721 ATA-TTAAATA
1 ATATTTAAATA
212731 TTAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 12 0.55
13 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTTAAATAA
Found at i:212722 original size:13 final size:13
Alignment explanation
Indices: 212671--212738 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
212661 ATATTACCTG
212671 TATTTAATATTAATA
1 TATTTAATA-TAA-A
*
212686 TATTTAAT-T-TA
1 TATTTAATATAAA
212697 TATTTAA-ATAAA
1 TATTTAATATAAA
212709 TATTTAATATAAA
1 TATTTAATATAAA
*
212722 TATTAAATATTAAA
1 TATTTAATA-TAAA
212736 TAT
1 TAT
212739 AAATATTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
11 9 0.20
12 8 0.17
13 14 0.30
14 7 0.15
15 8 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTTAATATAAA
Found at i:212728 original size:7 final size:7
Alignment explanation
Indices: 212705--212748 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
212695 TATATTTAAA
212705 TAAATAT
1 TAAATAT
*
212712 TTAATA-
1 TAAATAT
212718 TAAATAT
1 TAAATAT
212725 TAAATAT
1 TAAATAT
212732 TAAATA-
1 TAAATAT
212738 TAAATAT
1 TAAATAT
212745 TAAA
1 TAAA
212749 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAATAT
Found at i:212748 original size:13 final size:13
Alignment explanation
Indices: 212704--212744 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
212694 TTATATTTAA
*
212704 ATAAATATTTAAT
1 ATAAATATTAAAT
212717 ATAAATATTAAAT
1 ATAAATATTAAAT
212730 ATTAAATA-TAAAT
1 A-TAAATATTAAAT
212743 AT
1 AT
212745 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 1 0.04
13 19 0.73
14 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAAATATTAAAT
Found at i:212748 original size:20 final size:20
Alignment explanation
Indices: 212705--212748 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
212695 TATATTTAAA
*
212705 TAAATATTTAATATAAATAT
1 TAAATATTAAATATAAATAT
212725 TAAATATTAAATATAAATAT
1 TAAATATTAAATATAAATAT
212745 TAAA
1 TAAA
212749 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTAAATATAAATAT
Found at i:212807 original size:3 final size:3
Alignment explanation
Indices: 212799--212825 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
212789 AATGAAGTAC
212799 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
212826 ATGAAGGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:213239 original size:16 final size:18
Alignment explanation
Indices: 213202--213260 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 18
213192 TTTTTTATTT
213202 TTTAAAGTTTAAATTTAA
1 TTTAAAGTTTAAATTTAA
213220 -TTAAA-TTTAAA-TTAA
1 TTTAAAGTTTAAATTTAA
* *
213235 TTTAAAAGTTTATATTATTA
1 TTT-AAAGTTTAAATT-TAA
213255 TTTAAA
1 TTTAAA
213261 ATAATATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 8 0.24
18 5 0.15
19 4 0.12
20 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAAGTTTAAATTTAA
Found at i:213284 original size:27 final size:23
Alignment explanation
Indices: 213254--213305 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
213244 TTATATTATT
213254 ATTTAAAATAATATTTAAAATATATAA
1 ATTTAAAAT--TATTTAAAA-ATA-AA
*
213281 ATTTATAATTATTTAAAAATAAA
1 ATTTAAAATTATTTAAAAATAAA
213304 AT
1 AT
213306 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 3 0.12
25 9 0.38
27 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAAAATTATTTAAAAATAAA
Found at i:213316 original size:23 final size:25
Alignment explanation
Indices: 213261--213309 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
213251 ATTATTTAAA
*
213261 ATAA-TATTTAAAATATATAAATTT
1 ATAATTATTTAAAATATATAAATAT
213285 ATAATTATTTAAAA-ATA-AAATAT
1 ATAATTATTTAAAATATATAAATAT
213308 AT
1 AT
213310 TTTTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAATTATTTAAAATATATAAATAT
Found at i:213332 original size:29 final size:29
Alignment explanation
Indices: 213224--213337 Score: 83
Period size: 31 Copynumber: 3.7 Consensus size: 29
213214 ATTTAATTAA
* *
213224 ATTTAAATTAATTTAAAAGTTTA-TATTATT
1 ATTTAAA-TAATTTAAAA-TATATTTTTATT
213254 ATTTAAAATAATATTTAAAATATATAAATTTATAATT
1 ATTT-AAAT-A-ATTTAAAATATAT---TTT-T-ATT
213291 ATTTAAA-AA--TAAAATATATTTTTATT
1 ATTTAAATAATTTAAAATATATTTTTATT
*
213317 ATTTAAATAATTTAAATTATA
1 ATTTAAATAATTTAAAATATA
213338 AATATTATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
26 10 0.14
27 3 0.04
28 3 0.04
29 8 0.12
30 5 0.07
31 17 0.25
32 8 0.12
33 1 0.01
34 1 0.01
35 2 0.03
36 4 0.06
37 7 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTTAAATAATTTAAAATATATTTTTATT
Found at i:213350 original size:23 final size:24
Alignment explanation
Indices: 213324--213368 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
213314 ATTATTTAAA
*
213324 TAATTTAAATT-ATAAATATTATT
1 TAATTTAAATTAATAAAAATTATT
*
213347 TAATTTAATTTAATAAAAATTA
1 TAATTTAAATTAATAAAAATTA
213369 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTTAAATTAATAAAAATTATT
Found at i:213372 original size:16 final size:17
Alignment explanation
Indices: 213348--213380 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
213338 AATATTATTT
*
213348 AATTTAATTT-AATAAA
1 AATTAAATTTAAATAAA
213364 AATTAAATTTAAATAAA
1 AATTAAATTTAAATAAA
213381 TTTTTATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAAATTTAAATAAA
Found at i:215662 original size:18 final size:18
Alignment explanation
Indices: 215640--215705 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 18
215630 TATATATTTT
215640 TAAAAATTATTATAAATA
1 TAAAAATTATTATAAATA
*
215658 -AAAAATAATTA-ATAATA
1 TAAAAATTATTATA-AATA
215675 TAAAAATTATT-TAAATA
1 TAAAAATTATTATAAATA
215692 TTAAAAATATATTA
1 -TAAAAAT-TATTA
215706 ATATTATGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 1 0.03
17 18 0.45
18 17 0.43
19 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATTATTATAAATA
Found at i:215861 original size:17 final size:17
Alignment explanation
Indices: 215828--215875 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
215818 TTAATATTTA
215828 AATTATT-TTTTCAATATT
1 AATTATTATTTT--ATATT
215846 -ATTAATTATTTTATATT
1 AATT-ATTATTTTATATT
215863 AATTATTATTTTA
1 AATTATTATTTTA
215876 AAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 17 0.63
18 6 0.22
19 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATTATTTTATATT
Found at i:215899 original size:15 final size:16
Alignment explanation
Indices: 215870--215904 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
215860 ATTAATTATT
215870 ATTTTAAAAATATTAA
1 ATTTTAAAAATATTAA
215886 ATTTTAAAAA-ATTAA
1 ATTTTAAAAATATTAA
215901 ATTT
1 ATTT
215905 AATAATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTAAAAATATTAA
Found at i:216062 original size:3 final size:3
Alignment explanation
Indices: 216054--216090 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
216044 TAATCAAAAT
216054 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
216091 TTCGTCTTTC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:216319 original size:16 final size:18
Alignment explanation
Indices: 216300--216333 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
216290 TTAAATTAAA
216300 TTTAAAT-A-TTTAATTT
1 TTTAAATAAGTTTAATTT
216316 TTTAAATAAGTTTAATTT
1 TTTAAATAAGTTTAATTT
216334 GAATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAAATAAGTTTAATTT
Found at i:217135 original size:12 final size:12
Alignment explanation
Indices: 217120--217154 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
217110 TTTAATAAAT
217120 AATTTAATTTAA
1 AATTTAATTTAA
*
217132 AATTTATTTTAA
1 AATTTAATTTAA
*
217144 AATTAAATTTA
1 AATTTAATTTA
217155 TAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTAATTTAA
Found at i:217142 original size:17 final size:17
Alignment explanation
Indices: 217097--217143 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
217087 AAAATATTAT
217097 ATTTAAAATTTATTTTA
1 ATTTAAAATTTATTTTA
*
217114 A--T-AAA--TAATTTA
1 ATTTAAAATTTATTTTA
217126 ATTTAAAATTTATTTTA
1 ATTTAAAATTTATTTTA
217143 A
1 A
217144 AATTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
12 7 0.30
14 4 0.17
15 4 0.17
17 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAAAATTTATTTTA
Found at i:217152 original size:29 final size:31
Alignment explanation
Indices: 217088--217156 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
217078 TCTAAATTAA
217088 AAATATTATATTTAAAATTTATTTTAATAAAT
1 AAAT-TTATATTTAAAATTTATTTTAATAAAT
*
217120 -AATTTA-ATTTAAAATTTATTTTAA-AATT
1 AAATTTATATTTAAAATTTATTTTAATAAAT
217148 AAATTTATA
1 AAATTTATA
217157 ATAATAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 3 0.09
29 24 0.71
30 4 0.12
31 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
AAATTTATATTTAAAATTTATTTTAATAAAT
Found at i:217943 original size:2 final size:2
Alignment explanation
Indices: 217936--217962 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
217926 CTAACAAATA
217936 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
217963 GAATATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218066 original size:21 final size:18
Alignment explanation
Indices: 218030--218088 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
218020 AATAAATATT
* *
218030 ATTAATATTAAAAATAAA
1 ATTAAAATTAATAATAAA
218048 ATTAAATATTATAATAATAAA
1 ATTAAA-A-T-TAATAATAAA
218069 ATTAAAATTAATAATAAA
1 ATTAAAATTAATAATAAA
218087 AT
1 AT
218089 ATATGTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 17 0.47
19 2 0.06
20 2 0.06
21 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAATTAATAATAAA
Found at i:218069 original size:27 final size:28
Alignment explanation
Indices: 218022--218079 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
218012 ATAATGATAA
*
218022 TAAATATTATTAATATTAAAAATAAAAT
1 TAAATATTATTAATAATAAAAATAAAAT
*
218050 TAAATATTA-TAATAATAAAATTAAAAT
1 TAAATATTATTAATAATAAAAATAAAAT
218077 TAA
1 TAA
218080 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATATTATTAATAATAAAAATAAAAT
Found at i:219237 original size:13 final size:13
Alignment explanation
Indices: 219221--219246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
219211 AATATTAATA
219221 TAAAATAATTTTT
1 TAAAATAATTTTT
219234 TAAAATAATTTTT
1 TAAAATAATTTTT
219247 GAAGTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAAATAATTTTT
Found at i:222582 original size:15 final size:16
Alignment explanation
Indices: 222551--222581 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
222541 ATGCGAGCAA
222551 AATTGTTTTTCTTTTT
1 AATTGTTTTTCTTTTT
*
222567 AATTTTTTTTCTTTT
1 AATTGTTTTTCTTTT
222582 AGAAAAAGGC
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:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
AATTGTTTTTCTTTTT
Done.