Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1398
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: 90993
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:2136 original size:20 final size:20
Alignment explanation
Indices: 2103--2142 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2093 ATTGTTTAAA
2103 ATATGAAAAATATAT-TTTT
1 ATATGAAAAATATATATTTT
*
2122 ATATTAAAAATTATATATTTT
1 ATATGAAAAA-TATATATTTT
2143 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATGAAAAATATATATTTT
Found at i:10258 original size:17 final size:19
Alignment explanation
Indices: 10230--10264 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10220 ATTAAAAATA
10230 TTAAATTAAAAAT-TAATT
1 TTAAATTAAAAATGTAATT
10248 TTAAA-TAAAAATGTAAT
1 TTAAATTAAAAATGTAAT
10265 CTCATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TTAAATTAAAAATGTAATT
Found at i:10358 original size:16 final size:16
Alignment explanation
Indices: 10333--10376 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
10323 ACTCAATTTA
10333 TAATTATATAATATAT
1 TAATTATATAATATAT
* * *
10349 TAATTTTATATTTTAT
1 TAATTATATAATATAT
*
10365 TAATTAGATAAT
1 TAATTATATAAT
10377 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TAATTATATAATATAT
Found at i:10465 original size:16 final size:17
Alignment explanation
Indices: 10417--10476 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
10407 TATTATAATG
* *
10417 TAAATATTAAAAATATAT
1 TAAAAATTATAAAT-TAT
*
10435 TAAATTATT-TAAATT-T
1 TAAA-AATTATAAATTAT
*
10451 TGAAAATTATAAATTAT
1 TAAAAATTATAAATTAT
10468 TAAAAATTA
1 TAAAAATTA
10477 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 10 0.29
18 8 0.23
19 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAAATTATAAATTAT
Found at i:11015 original size:30 final size:31
Alignment explanation
Indices: 10952--11019 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
10942 TAATAATTAC
* ** *
10952 ACTTTTAATGTTAAATGTTTGTGTATGTTTA
1 ACTTTTAATCTTAAACATCTGTGTATGTTTA
10983 ACTTTTAATCTTAAACATCTGTGTAT-TTTA
1 ACTTTTAATCTTAAACATCTGTGTATGTTTA
11013 ACTTTTA
1 ACTTTTA
11020 GTTTAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (31 bp):
ACTTTTAATCTTAAACATCTGTGTATGTTTA
Found at i:11559 original size:20 final size:20
Alignment explanation
Indices: 11531--11568 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11521 TCACATTGAG
* *
11531 TTTTTTTTTTTTTTTAGTAA
1 TTTTGTTTTTCTTTTAGTAA
11551 TTTTGTTTTTCTTTTAGT
1 TTTTGTTTTTCTTTTAGT
11569 TTTTGACTCT
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:0.11, C:0.03, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTAGTAA
Found at i:12265 original size:39 final size:39
Alignment explanation
Indices: 12222--12297 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
12212 GAAAAATACT
* *
12222 CAAAATATTCTCCTATTTAATTAATGTTTTGTTTTTTTC
1 CAAAATATTCTCCTAGTTAATTAATGTTGTGTTTTTTTC
12261 CAAAATATTCTCCTAGTTAATTAATGTTGTGTTTTTT
1 CAAAATATTCTCCTAGTTAATTAATGTTGTGTTTTTT
12298 CTTTTGTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (39 bp):
CAAAATATTCTCCTAGTTAATTAATGTTGTGTTTTTTTC
Found at i:12329 original size:2 final size:2
Alignment explanation
Indices: 12322--12347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12312 GTAATCAACC
12322 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
12348 GGGTGAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13480 original size:23 final size:25
Alignment explanation
Indices: 13440--13499 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 25
13430 AAACTTCAAC
13440 ATAATTGATATTTATATAAATTTTA
1 ATAATTGATATTTATATAAATTTTA
13465 ATAATT-AT-TTTATATAAATTTTA
1 ATAATTGATATTTATATAAATTTTA
*
13488 ATATATTTATAT
1 ATA-ATTGATAT
13500 GTTTATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 18 0.56
24 5 0.16
25 8 0.25
26 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATAATTGATATTTATATAAATTTTA
Found at i:13487 original size:11 final size:11
Alignment explanation
Indices: 13450--13492 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
13440 ATAATTGATA
13450 TTTATATAAAT
1 TTTATATAAAT
13461 TTTA-ATAATTAT
1 TTTATATAA--AT
13473 TTTATATAAAT
1 TTTATATAAAT
13484 TTTAATATA
1 TTT-ATATA
13493 TTTATATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 9 0.32
12 11 0.39
13 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTATATAAAT
Found at i:13523 original size:12 final size:13
Alignment explanation
Indices: 13501--13538 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
13491 TATTTATATG
13501 TTTATATTATTAT
1 TTTATATTATTAT
13514 TTTA-ATTATT-T
1 TTTATATTATTAT
13525 TTTATATTA-TAT
1 TTTATATTATTAT
13537 TT
1 TT
13539 GTATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 13 0.57
13 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATTATTAT
Found at i:15052 original size:2 final size:2
Alignment explanation
Indices: 15045--15077 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15035 GAGAAGTTAA
15045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15078 CATCCTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17789 original size:32 final size:32
Alignment explanation
Indices: 17732--17812 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
17722 TTTAATACAA
* * * *
17732 ATATA-ATATATATATAAATATATTAAATTTT
1 ATATATATAAATATATAAAAAAATTAAAATTT
17763 ATATGATATAAAT-TATAAAAAAATTAAAATTT
1 ATAT-ATATAAATATATAAAAAAATTAAAATTT
*
17795 ATATATATATATATATAA
1 ATATATATAAATATATAA
17813 TAATTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 11 0.26
32 26 0.62
33 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
ATATATATAAATATATAAAAAAATTAAAATTT
Found at i:17817 original size:24 final size:22
Alignment explanation
Indices: 17790--17837 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 22
17780 AAAAAATTAA
17790 AATTTATATATATATATATATAA-T
1 AATTTATA-ATATA-AT-TATAACT
17814 AA-TTATAATATAATTATAACT
1 AATTTATAATATAATTATAACT
17835 AAT
1 AAT
17838 AAAAATACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 5 0.23
23 5 0.23
24 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTATAATATAATTATAACT
Found at i:18227 original size:20 final size:21
Alignment explanation
Indices: 18204--18305 Score: 61
Period size: 21 Copynumber: 4.8 Consensus size: 21
18194 TAATTTAAAT
18204 AAATAATATTTT-AT-TTAGTA
1 AAATAATATTTTAATATTA-TA
*
18224 AAATTAT-TTTTAATAATTATA
1 AAATAATATTTTAAT-ATTATA
**
18245 AAATAATATTAAATATATTATTA
1 AAATAATATTTTA-ATATTA-TA
* *
18268 GTAA-AATAATTTAATA-TATA
1 -AAATAATATTTTAATATTATA
*
18288 TTAATAATATTTTAATAT
1 -AAATAATATTTTAATAT
18306 ATTCTGTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.06
20 13 0.21
21 21 0.33
22 13 0.21
23 10 0.16
24 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATAATATTTTAATATTATA
Found at i:18272 original size:26 final size:25
Alignment explanation
Indices: 18239--18290 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
18229 ATTTTTAATA
18239 ATTATAAAATAATATTAA-ATATATT
1 ATTATAAAATAAT-TTAATATATATT
18264 ATTAGTAAAATAATTTAATATATATT
1 ATTA-TAAAATAATTTAATATATATT
18290 A
1 A
18291 ATAATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTATAAAATAATTTAATATATATT
Found at i:18275 original size:23 final size:23
Alignment explanation
Indices: 18232--18308 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 23
18222 TAAAATTATT
18232 TTTAATA-ATTA-TAA-AATAATA
1 TTTAATATATTATTAATAA-AATA
* *
18253 TTAAATATATTATTAGTAAAATAA
1 TTTAATATATTATTAATAAAAT-A
*
18277 TTTAATATA-TATTAATAATAT-
1 TTTAATATATTATTAATAAAATA
18298 TTTAATATATT
1 TTTAATATATT
18309 CTGTTTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 15 0.33
22 5 0.11
23 15 0.33
24 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
TTTAATATATTATTAATAAAATA
Found at i:18416 original size:21 final size:18
Alignment explanation
Indices: 18385--18432 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
18375 AAATTTTAAA
*
18385 TTATAATTAAAATAATATT
1 TTATTATTAAAA-AATATT
*
18404 TTCATTTATTAAAAATTATT
1 TT-A-TTATTAAAAAATATT
18424 TTATTATTA
1 TTATTATTA
18433 TTTTGTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 8 0.32
21 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTATTAAAAAATATT
Found at i:18433 original size:21 final size:23
Alignment explanation
Indices: 18384--18434 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
18374 TAAATTTTAA
*
18384 ATTATAATTAAAATAATATTTTC
1 ATTATTATTAAAATAATATTTTC
*
18407 A-T-TTATTAAAA-ATTATTTT-
1 ATTATTATTAAAATAATATTTTC
18426 ATTATTATT
1 ATTATTATT
18435 TTGTAACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 13 0.54
22 1 0.04
23 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATTATTAAAATAATATTTTC
Found at i:21242 original size:16 final size:18
Alignment explanation
Indices: 21215--21252 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
21205 TAAATCATCC
*
21215 AAATGATATTTT-AAATA
1 AAATGATATTTTGAAAGA
21232 AAATG-TATTTTGAAAGA
1 AAATGATATTTTGAAAGA
21249 AAAT
1 AAAT
21253 TAATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
AAATGATATTTTGAAAGA
Found at i:22390 original size:3 final size:3
Alignment explanation
Indices: 22384--22432 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
22374 TTGGTTTAGA
22384 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22432 A
1 A
22433 ATAAAACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:22725 original size:2 final size:2
Alignment explanation
Indices: 22716--22748 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
22706 AAAAAATGAG
*
22716 AT AT -T AT AT AT AT GT 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
22749 GATCAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:24033 original size:17 final size:17
Alignment explanation
Indices: 24011--24045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24001 AATTAACTAA
*
24011 TAAAAAAACATTAAAAT
1 TAAAAAAACAATAAAAT
*
24028 TAAAAAATCAATAAAAT
1 TAAAAAAACAATAAAAT
24045 T
1 T
24046 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAACAATAAAAT
Found at i:24319 original size:18 final size:18
Alignment explanation
Indices: 24298--24333 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24288 AATTGAGCGA
24298 AAAAAATAATTAAAAATT
1 AAAAAATAATTAAAAATT
* *
24316 AAAAATTAATTATAAATT
1 AAAAAATAATTAAAAATT
24334 TTAATCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATAATTAAAAATT
Found at i:24816 original size:34 final size:34
Alignment explanation
Indices: 24747--24928 Score: 161
Period size: 34 Copynumber: 5.4 Consensus size: 34
24737 CTCATCCATC
* * *
24747 TTGTTGATTAAAT-GGTGATTTAGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
* **
24780 TTGTTGATTAAATGGGTGATTTGGTGGTTTGTCA
1 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
* * ** *
24814 TTGTTGACTAAATAGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
* * * *
24848 TTATTGATTAAATGGATAATTTGGTGGCTTACTA
1 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
* * * **
24882 TTATTGACTAAATGGGAGATTTGGTAGG-TTGTCA
1 TTGTTGATTAAATGGGTGATTTGGT-GGCTTACCA
24916 TTGTTGATTAAAT
1 TTGTTGATTAAAT
24929 AGTGGTTTTT
Statistics
Matches: 119, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
33 13 0.11
34 104 0.87
35 2 0.02
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
Found at i:24855 original size:68 final size:67
Alignment explanation
Indices: 24747--24928 Score: 204
Period size: 68 Copynumber: 2.7 Consensus size: 67
24737 CTCATCCATC
* * * * * * **
24747 TTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGG-TTTG
1 TTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGATAATTTGGTGGCTTAC
24811 TCA
66 T-A
* *
24814 TTGTTGACTAAATAGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATAATTTGGTGGCTTA
1 TTGTTGACTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGGATAATTTGGTGGCTTA
24879 CTA
65 CTA
* * **
24882 TTATTGACTAAATGGGAGATTTGGTAGGTTGTCATTGTTGATTAAAT
1 TTGTTGACTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAAT
24929 AGTGGTTTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
67 12 0.12
68 81 0.84
69 3 0.03
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (67 bp):
TTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGATAATTTGGTGGCTTAC
TA
Found at i:25285 original size:19 final size:19
Alignment explanation
Indices: 25222--25285 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
25212 TTGGTTGTCG
25222 AGTTACTATTTACGTATAC
1 AGTTACTATTTACGTATAC
*
25241 AGGTACTATTTACGTATAC
1 AGTTACTATTTACGTATAC
* *
25260 GAG-TACTATTTAAGTATAT
1 -AGTTACTATTTACGTATAC
25279 AGTTACT
1 AGTTACT
25286 GTACACGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.05
19 36 0.90
20 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (19 bp):
AGTTACTATTTACGTATAC
Found at i:29339 original size:1 final size:1
Alignment explanation
Indices: 29333--29490 Score: 118
Period size: 1 Copynumber: 158.0 Consensus size: 1
29323 AAATCTTCAC
* * ** * * * **
29333 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** * * * **
29398 TTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
29463 TTTTTGTTTTGTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
29491 CCTTTTGCCA
Statistics
Matches: 121, Mismatches: 36, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 121 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:29375 original size:32 final size:32
Alignment explanation
Indices: 29333--29496 Score: 294
Period size: 32 Copynumber: 5.1 Consensus size: 32
29323 AAATCTTCAC
29333 TTTTTT-TTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
29364 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
29396 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
29428 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTG--TTTTTTTTTTCTTTTTCCTT
29462 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTG-TTTTTTTTTTCTTTTTCCTT
29495 TT
1 TT
29497 GCCATGCATC
Statistics
Matches: 130, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.05
32 69 0.53
33 23 0.18
34 32 0.25
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.85
Consensus pattern (32 bp):
TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
Found at i:29512 original size:98 final size:95
Alignment explanation
Indices: 29333--29512 Score: 238
Period size: 98 Copynumber: 1.9 Consensus size: 95
29323 AAATCTTCAC
29333 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTT
1 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTT
*** ** **
29398 TTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
66 CCATGTCATGCATTTTTTTTCTTTTTCCTT
29428 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCC
1 TTTTTT-TTTTG--TTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG-TTTTTTTTTTCTTTTTCC
29493 TTTTGCCATG-CAT-CATTTTT
62 TTTT-CCATGTCATGCATTTTT
29513 CCTCTTGTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
95 6 0.08
96 5 0.07
98 37 0.51
99 23 0.32
100 2 0.03
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (95 bp):
TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTT
CCATGTCATGCATTTTTTTTCTTTTTCCTT
Found at i:39845 original size:34 final size:34
Alignment explanation
Indices: 39776--39994 Score: 269
Period size: 34 Copynumber: 6.5 Consensus size: 34
39766 AAGTGCGAGA
* *
39776 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
* * * * *
39809 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
*
39843 ATTGTTGACTAAATGGGAGATTTAGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
* * * *
39877 ATTATTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
* *
39911 ATTGTTGATTAAATGGGTGATTTAGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
* * * *
39945 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
39979 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
39995 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 27, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
33 14 0.09
34 144 0.91
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTAGTAGCTTACC
Found at i:39869 original size:68 final size:67
Alignment explanation
Indices: 39776--39994 Score: 305
Period size: 68 Copynumber: 3.2 Consensus size: 67
39766 AAGTGCGAGA
* *
39776 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TT
39840 GCC
65 GCC
* * * * * *
39843 ATTGTTGACTAAATGGGAGATTTAGTAGCTTACCATTATTGATTAAATGAGAAATTTGGTAGCTT
1 ATTGTTGATTAAATGGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
*
39908 ACC
65 GCC
* *
39911 ATTGTTGATTAAATGGGTGATTTAGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAATGGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
39976 GCC
65 GCC
39979 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
39995 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
67 13 0.10
68 118 0.89
69 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTG
CC
Found at i:39929 original size:102 final size:101
Alignment explanation
Indices: 39780--39994 Score: 322
Period size: 102 Copynumber: 2.1 Consensus size: 101
39770 GCGAGAATTG
** * * * *
39780 TTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCAT
39845 TGTTGACTAAATGGGAGATTTAGTAGCTTACCATTA
66 TGTTGACTAAATGGGAGATTTAGTAGCTTACCATTA
*
39881 TTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCA
1 TTGATTAAATG-GAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCA
* * * *
39946 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTG
65 TTGTTGACTAAATGGGAGATTTAGTAGCTTACCATTA
39983 TTGATTAAATGG
1 TTGATTAAATGG
39995 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
101 12 0.12
102 90 0.88
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
TTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCAT
TGTTGACTAAATGGGAGATTTAGTAGCTTACCATTA
Found at i:40795 original size:20 final size:22
Alignment explanation
Indices: 40758--40803 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
40748 TTATTTTAAG
40758 TATTTTAATTAGATAAATTT-A
1 TATTTTAATTAGATAAATTTGA
*
40779 TATTTTTATTA-ATAAATTTGA
1 TATTTTAATTAGATAAATTTGA
40800 TATT
1 TATT
40804 AATTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTAATTAGATAAATTTGA
Found at i:43158 original size:33 final size:33
Alignment explanation
Indices: 43121--43189 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
43111 CACCTGCAGA
43121 TATAAACAAATTGAATATCTAATCATATTAAAT
1 TATAAACAAATTGAATATCTAATCATATTAAAT
43154 TATAAACAAATTGAATATCTAATCATATTAAAT
1 TATAAACAAATTGAATATCTAATCATATTAAAT
43187 TAT
1 TAT
43190 TATTTACCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (33 bp):
TATAAACAAATTGAATATCTAATCATATTAAAT
Found at i:43615 original size:2 final size:2
Alignment explanation
Indices: 43608--43636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43598 AAGTGAATTT
43608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43637 GTTATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43862 original size:18 final size:19
Alignment explanation
Indices: 43829--43868 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
43819 AAATATAATT
*
43829 ATAATACATGAAATATGTAA
1 ATAATACA-GAAATATATAA
43849 ATAATACA-AAATATATAA
1 ATAATACAGAAATATATAA
43867 AT
1 AT
43869 TATCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAATACAGAAATATATAA
Found at i:44585 original size:60 final size:59
Alignment explanation
Indices: 44454--44590 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 59
44444 TATAATTATA
44454 TAAATATAA-TAT-ATATAAATTAATTAAAATATAAAATAATATAATAAAAATATATTT
1 TAAATATAATTATAATATAAATTAATTAAAATATAAAATAATATAATAAAAATATATTT
* * *
44511 TAAAAAT-ATATATAATATAAATT-ATTAATATATCAAAATTTATATAAATAAAAA-ATATTT
1 TAAATATAAT-TATAATATAAATTAATTAAAATAT-AAAA-TAATAT-AATAAAAATATATTT
44571 TAAATATAATTATAATATAA
1 TAAATATAATTATAATATAA
44591 TAATATATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
56 1 0.01
57 6 0.09
58 12 0.17
59 13 0.19
60 27 0.39
61 10 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (59 bp):
TAAATATAATTATAATATAAATTAATTAAAATATAAAATAATATAATAAAAATATATTT
Found at i:44626 original size:17 final size:17
Alignment explanation
Indices: 44443--44632 Score: 82
Period size: 17 Copynumber: 11.1 Consensus size: 17
44433 ATGATTTTAG
*
44443 ATATAATTATATAAAT-
1 ATATAAATATATAAATA
*
44459 ATA-ATATATATAAATTA
1 ATATAAATATATAAA-TA
44476 AT-TAAA-ATATAAAATA
1 ATATAAATATAT-AAATA
44492 ATAT-AATA-A-AAATA
1 ATATAAATATATAAATA
* * *
44506 TATTTTAAAAATATATATA
1 -A-TATAAATATATAAATA
*
44525 ATATAAAT-TATTAAT-
1 ATATAAATATATAAATA
44540 ATATCAAAATTTATATAAATA
1 ATAT--AAA--TATATAAATA
*
44561 A-A-AAATATTTTAAAT-
1 ATATAAATA-TATAAATA
44576 ATAATTATAATATA-ATAATA
1 AT-A-TA-AATATATA-AATA
*
44596 TATATATATATATAAATA
1 -ATATAAATATATAAATA
*
44614 ATATAAATTTATAAATA
1 ATATAAATATATAAATA
44631 AT
1 AT
44633 TATGTTACGT
Statistics
Matches: 131, Mismatches: 16, Indels: 53
0.65 0.08 0.26
Matches are distributed among these distances:
14 5 0.04
15 17 0.13
16 28 0.21
17 41 0.31
18 12 0.09
19 13 0.10
20 12 0.09
21 3 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAATATATAAATA
Found at i:44631 original size:21 final size:21
Alignment explanation
Indices: 44573--44631 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
44563 AAATATTTTA
44573 AATAT-AA-TTAT-AATATAAT
1 AATATAAATTTATAAATA-AAT
* * *
44592 AATATATATATATATATAAAT
1 AATATAAATTTATAAATAAAT
44613 AATATAAATTTATAAATAA
1 AATATAAATTTATAAATAA
44632 TTATGTTACG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 5 0.16
20 1 0.03
21 22 0.71
22 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATAAATTTATAAATAAAT
Found at i:47726 original size:11 final size:11
Alignment explanation
Indices: 47710--47753 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
47700 TTTTAATTAA
47710 AATATAAATAT
1 AATATAAATAT
47721 AATATAAAT-T
1 AATATAAATAT
47731 -AT-TAAATAT
1 AATATAAATAT
*
47740 AATTTAAATA-
1 AATATAAATAT
47750 AATA
1 AATA
47754 ATGACTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
8 5 0.17
9 3 0.10
10 6 0.21
11 15 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAAATAT
Found at i:48212 original size:10 final size:10
Alignment explanation
Indices: 48197--48243 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
48187 TAATTAAAAA
48197 TTTTAATTAT
1 TTTTAATTAT
48207 TTTTAATTA-
1 TTTTAATTAT
*
48216 --TTAA-AAT
1 TTTTAATTAT
48223 TTTTAATTAT
1 TTTTAATTAT
48233 TTTTAATTAT
1 TTTTAATTAT
48243 T
1 T
48244 AAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
6 1 0.03
7 4 0.13
9 4 0.13
10 22 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:48218 original size:26 final size:26
Alignment explanation
Indices: 48189--48254 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
48179 TAAAAATATA
48189 ATTAAAAATTTTAATTATTTTTAATT
1 ATTAAAAATTTTAATTATTTTTAATT
*
48215 ATTAAAATTTTTAATTATTTTTAATT
1 ATTAAAAATTTTAATTATTTTTAATT
48241 ATTAAAAATTTTAA
1 ATTAAAAATTTTAA
48255 AATAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTAAAAATTTTAATTATTTTTAATT
Found at i:48361 original size:22 final size:22
Alignment explanation
Indices: 48331--48372 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
48321 TTAAATTTTT
48331 AATATTAAAAATTTAAATTAATA
1 AATATT-AAAATTTAAATTAATA
*
48354 AATA-TAAAATTTTAATTAA
1 AATATTAAAATTTAAATTAA
48373 ATTATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 1 0.06
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATTAAAATTTAAATTAATA
Found at i:48547 original size:17 final size:18
Alignment explanation
Indices: 48525--48582 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
48515 TAATTTAAAT
*
48525 AATAATTTTA-GATATAA
1 AATAATTATATGATATAA
48542 AATAATTATATGATATAA
1 AATAATTATATGATATAA
48560 ATATAA-TATA--A-ATAA
1 A-ATAATTATATGATATAA
48575 AATAATTA
1 AATAATTA
48583 AAATATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 4 0.11
15 7 0.19
16 1 0.03
17 9 0.24
18 12 0.32
19 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATAATTATATGATATAA
Found at i:48563 original size:11 final size:11
Alignment explanation
Indices: 48549--48710 Score: 89
Period size: 11 Copynumber: 15.5 Consensus size: 11
48539 TAAAATAATT
*
48549 ATATGATATAA
1 ATATAATATAA
48560 ATATAATATAA
1 ATATAATATAA
48571 ATA-AA-ATAA
1 ATATAATATAA
* *
48580 TTAAAATAT-A
1 ATATAATATAA
*
48590 ATATGATAT-A
1 ATATAATATAA
48600 A-AT-ATATAA
1 ATATAATATAA
48609 ATAT-AT-TAA
1 ATATAATATAA
* *
48618 ATTTAAAATAA
1 ATATAATATAA
* *
48629 AAATAAATTATTA
1 ATAT-AA-TATAA
*
48642 ATATATTA-AA
1 ATATAATATAA
48652 ATAT-ATA-AA
1 ATATAATATAA
*
48661 TATATAATAT-T
1 -ATATAATATAA
*
48672 TTA-AATATAA
1 ATATAATATAA
*
48682 TTATAATATTAA
1 ATATAATA-TAA
48694 ATATAATATAA
1 ATATAATATAA
48705 ATATAA
1 ATATAA
48711 AATATATTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 28
0.72 0.12 0.17
Matches are distributed among these distances:
8 4 0.03
9 25 0.21
10 32 0.27
11 38 0.32
12 13 0.11
13 6 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:48609 original size:25 final size:23
Alignment explanation
Indices: 48554--48716 Score: 84
Period size: 25 Copynumber: 6.7 Consensus size: 23
48544 TAATTATATG
48554 ATAT-AAATATAATATAAATAAA
1 ATATAAAATATAATATAAATAAA
*
48576 ATAATTAAAATATAATATGATATAAA
1 AT-A-TAAAATATAATAT-AAATAAA
*
48602 TATATAAATATATTAAATTTAAAATAAA
1 -ATATAAA-ATA-T-AATAT-AAATAAA
* *
48630 A-ATAAATTATTAATAT-ATTAAA
1 ATATAAAATA-TAATATAAATAAA
** *
48652 ATATATAAATAT-ATAATATTTTAA
1 ATATA-AAATATAAT-ATAAATAAA
* *
48676 ATAT-AATTATAATATTAAATATA
1 ATATAAAATATAATA-TAAATAAA
*
48699 ATATAAATATAAAATATA
1 ATATAAA-ATATAATATA
48717 TTTTTTTTTC
Statistics
Matches: 108, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
22 16 0.15
23 17 0.16
24 21 0.19
25 25 0.23
26 15 0.14
27 4 0.04
28 10 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
ATATAAAATATAATATAAATAAA
Found at i:48658 original size:59 final size:59
Alignment explanation
Indices: 48564--48717 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 59
48554 ATATAAATAT
* *
48564 AATATAAATAAAATAATTAAAATATAATATGATATAAATATATAAATATATTAAATTTAA
1 AATAAAAATAAAATAATTAAAATATAAAATGATATAAATATAT-AATATATTAAATTTAA
* * * *
48624 AATAAAAAT-AAATTATTAATATATTAAAAT-ATATAAATATATAATATTTTAAATATAA
1 AATAAAAATAAAATAATTAAAATA-TAAAATGATATAAATATATAATATATTAAATTTAA
* * *
48682 TTATAATATTAAATATAA-TATAAATATAAAAT-ATAT
1 -AATAAAAATAAA-ATAATTA-AAATATAAAATGATAT
48718 TTTTTTTTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
58 14 0.18
59 30 0.38
60 27 0.35
61 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (59 bp):
AATAAAAATAAAATAATTAAAATATAAAATGATATAAATATATAATATATTAAATTTAA
Found at i:48662 original size:51 final size:54
Alignment explanation
Indices: 48589--48718 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 54
48579 ATTAAAATAT
*
48589 AATATGATATAAATATATAAATATATTAA-ATTTAAAATAAAAATA-AATTATT-
1 AATATAATATAAATATATAAATATATTAATATTTAAAATAAAAATATAA-TATTA
* * * *
48641 AATATATTA-AAATATATAAATATA-TAATATTTTAAATATAATTATAATATTA
1 AATATAATATAAATATATAAATATATTAATATTTAAAATAAAAATATAATATTA
48693 AATATAATATAAATATA-AAATATATT
1 AATATAATATAAATATATAAATATATT
48719 TTTTTTTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
50 3 0.04
51 32 0.48
52 24 0.36
53 8 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (54 bp):
AATATAATATAAATATATAAATATATTAATATTTAAAATAAAAATATAATATTA
Found at i:48689 original size:45 final size:45
Alignment explanation
Indices: 48541--48715 Score: 122
Period size: 45 Copynumber: 3.9 Consensus size: 45
48531 TTTAGATATA
* * *
48541 AAAT-AATTATATGATA-TAAATATAATAT-AA-ATAAAATAATTA
1 AAATAAATTAT-TAATATTAAATATAATATAAATATAAAATATTTT
* *
48583 AAATATAATATGATATAAATATATAAATAT-AT-TAAATTTAAAATA---A
1 AAATA-AAT-T-AT-T-AATAT-TAAATATAATATAAATATAAAATATTTT
*
48629 AAATAAATTATTAATATATTAAA-AT-ATATAAATATATAATATTTT
1 AAATAAATTATT-A-ATATTAAATATAATATAAATATAAAATATTTT
48674 AAATATAATTA-TAATATTAAATATAATATAAATATAAAATAT
1 AAATA-AATTATTAATATTAAATATAATATAAATATAAAATAT
48716 ATTTTTTTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 31
0.75 0.04 0.21
Matches are distributed among these distances:
41 4 0.04
42 22 0.20
43 14 0.13
44 7 0.06
45 26 0.24
46 15 0.14
47 4 0.04
48 4 0.04
49 14 0.13
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (45 bp):
AAATAAATTATTAATATTAAATATAATATAAATATAAAATATTTT
Found at i:48716 original size:18 final size:18
Alignment explanation
Indices: 48536--48716 Score: 97
Period size: 18 Copynumber: 10.7 Consensus size: 18
48526 ATAATTTTAG
* *
48536 ATATAAAATA-ATTATATG
1 ATATAAAATATAATATA-A
48554 ATAT-AAATATAATAT-A
1 ATATAAAATATAATATAA
48570 A-AT-AAA-ATAAT-TAA
1 ATATAAAATATAATATAA
* *
48584 A-ATATAATATGATATAA
1 ATATAAAATATAATATAA
48601 ATATATAAATAT-AT-TAA
1 ATATA-AAATATAATATAA
* *
48618 ATTTAAAATA-AAAATAA
1 ATATAAAATATAATATAA
* *
48635 AT-TATTAATATATTA-AA
1 ATATA-AAATATAATATAA
*
48652 ATATATAAATAT-ATA-AT
1 ATATA-AAATATAATATAA
* *
48669 ATTTTAAATATAAT-TATA
1 ATATAAAATATAATATA-A
*
48687 ATATTAAATATAATATAA
1 ATATAAAATATAATATAA
48705 ATATAAAATATA
1 ATATAAAATATA
48717 TTTTTTTTTC
Statistics
Matches: 129, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.01
14 9 0.07
15 7 0.05
16 19 0.15
17 38 0.29
18 48 0.37
19 7 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
ATATAAAATATAATATAA
Found at i:50557 original size:16 final size:16
Alignment explanation
Indices: 50536--50566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50526 AAGTATAATA
*
50536 TAATTATAAATGTAAG
1 TAATTATAAAAGTAAG
50552 TAATTATAAAAGTAA
1 TAATTATAAAAGTAA
50567 ATATTTTCAA
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:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
TAATTATAAAAGTAAG
Found at i:51750 original size:27 final size:27
Alignment explanation
Indices: 51702--51767 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
51692 AGTTGTCTCT
51702 TCTCCACCACCATCATCACCACCCCCA
1 TCTCCACCACCATCATCACCACCCCCA
* * * * *
51729 TCTCCTCCACCTTCCTCTCCACCTCCA
1 TCTCCACCACCATCATCACCACCCCCA
*
51756 TCGCCACCACCA
1 TCTCCACCACCA
51768 CCTCCGCCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.59, G:0.02, T:0.20
Consensus pattern (27 bp):
TCTCCACCACCATCATCACCACCCCCA
Found at i:51765 original size:15 final size:15
Alignment explanation
Indices: 51747--51813 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
51737 ACCTTCCTCT
*
51747 CCACCTCCATCGCCA
1 CCACCACCATCGCCA
51762 CCACCACC-TCCGCCA
1 CCACCACCAT-CGCCA
* *
51777 CC-GCA--ATCCCCA
1 CCACCACCATCGCCA
* *
51789 CCTCCTCCATCGCCA
1 CCACCACCATCGCCA
51804 CCACCACCAT
1 CCACCACCAT
51814 TTCCTTCACC
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
12 6 0.15
13 2 0.05
14 3 0.08
15 28 0.72
ACGTcount: A:0.21, C:0.61, G:0.06, T:0.12
Consensus pattern (15 bp):
CCACCACCATCGCCA
Found at i:51810 original size:21 final size:21
Alignment explanation
Indices: 51750--51811 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
51740 TTCCTCTCCA
51750 CCTCCATCGCCACCACCACCT
1 CCTCCATCGCCACCACCACCT
* * *
51771 CCGCCACCGCAATCC-CCACCT
1 CCTCCATCGCCA-CCACCACCT
51792 CCTCCATCGCCACCACCACC
1 CCTCCATCGCCACCACCACC
51812 ATTTCCTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.63, G:0.06, T:0.11
Consensus pattern (21 bp):
CCTCCATCGCCACCACCACCT
Found at i:53234 original size:2 final size:2
Alignment explanation
Indices: 53227--53256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53217 TTTAAAAACT
53227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53257 AATAGTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53435 original size:17 final size:17
Alignment explanation
Indices: 53412--53453 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
53402 TATTTATATT
53412 TTTTATATCATAA-TTATA
1 TTTTATAT-A-AATTTATA
53430 -TTTATATAAATTTATA
1 TTTTATATAAATTTATA
53446 TTTTATAT
1 TTTTATAT
53454 TTATATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 6 0.27
17 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTATATAAATTTATA
Found at i:53479 original size:18 final size:17
Alignment explanation
Indices: 53445--53499 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
53435 ATAAATTTAT
53445 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
53462 ATTTTAATATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
53479 A-TTTATA-TTATATAT
1 ATTTTATATTTATATAA
53494 ATTTTA
1 ATTTTA
53500 AGATATTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 4 0.12
16 7 0.22
17 7 0.22
18 6 0.19
19 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:54865 original size:10 final size:11
Alignment explanation
Indices: 54836--54898 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 11
54826 AAAATTTTAA
54836 ATTTAAATTTGT
1 ATTT-AATTTGT
*
54848 AGTTAATTTG-
1 ATTTAATTTGT
54858 ATTTAATTTGT
1 ATTTAATTTGT
54869 AAATTTAAATTAT-T
1 --ATTT-AATT-TGT
54883 ATTTAATTT-T
1 ATTTAATTTGT
54893 ATTTAA
1 ATTTAA
54899 AAATATTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 17 0.39
11 10 0.23
12 7 0.16
13 4 0.09
14 5 0.11
15 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (11 bp):
ATTTAATTTGT
Found at i:54878 original size:35 final size:34
Alignment explanation
Indices: 54828--54898 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
54818 GCCATTTAAA
54828 AATTTTAAATTTAAATT-TGTAGTTAATTTGATTT
1 AATTTTAAATTTAAATTAT-TAGTTAATTTGATTT
* *
54862 AATTTGTAAATTTAAATTATTATTTAATTTTATTT
1 AATTT-TAAATTTAAATTATTAGTTAATTTGATTT
54897 AA
1 AA
54899 AAATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 5 0.15
35 27 0.82
36 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (34 bp):
AATTTTAAATTTAAATTATTAGTTAATTTGATTT
Found at i:54977 original size:19 final size:19
Alignment explanation
Indices: 54949--54995 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
54939 TTTAATTAAA
*
54949 TTTAAATAAAATATATTAT
1 TTTAATTAAAATATATTAT
*
54968 TTTAATTAAAATTTATTAT
1 TTTAATTAAAATATATTAT
54987 TTTAGATTA
1 TTTA-ATTA
54996 GGCCAGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTAATTAAAATATATTAT
Found at i:55354 original size:21 final size:23
Alignment explanation
Indices: 55329--55390 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
55319 TATCAAAATT
* **
55329 TATATAAATATAA-ATATTTTAA
1 TATATAAATATAATATAATAAAA
*
55351 -ATATAATTATAATATAATAAAA
1 TATATAAATATAATATAATAAAA
55373 TATATAAATATAATATAA
1 TATATAAATATAATATAA
55391 ATTTATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 11 0.33
22 6 0.18
23 16 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATAAATATAATATAATAAAA
Found at i:55368 original size:5 final size:5
Alignment explanation
Indices: 55350--55390 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
55340 AAATATTTTA
*
55350 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
55391 ATTTATGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 20 0.65
6 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:55734 original size:13 final size:13
Alignment explanation
Indices: 55718--55772 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
55708 TTATTTTGAA
55718 ATATTATATTTTT
1 ATATTATATTTTT
55731 ATA-TATTATTTTT
1 ATATTA-TATTTTT
*
55744 AAAATTA-ATTTTT
1 -ATATTATATTTTT
*
55757 ATATATATATATTT
1 ATAT-TATATTTTT
55771 AT
1 AT
55773 TTCATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
12 5 0.15
13 18 0.53
14 9 0.26
15 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTATATTTTT
Found at i:55764 original size:28 final size:28
Alignment explanation
Indices: 55707--55762 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 28
55697 ATCTTGTAAA
55707 ATTATTTTGAAATATTATATTTTTATAT
1 ATTATTTTGAAATATTATATTTTTATAT
*
55735 ATTATTTTTAAA-ATTA-ATTTTTATAT
1 ATTATTTTGAAATATTATATTTTTATAT
55761 AT
1 AT
55763 ATATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.44
27 4 0.15
28 11 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTATTTTGAAATATTATATTTTTATAT
Found at i:59394 original size:174 final size:174
Alignment explanation
Indices: 59104--59452 Score: 653
Period size: 174 Copynumber: 2.0 Consensus size: 174
59094 ACATGCTAGA
*
59104 AACATAAATGGCATTATTTGATAAAGACGGATTAAGATACAATGCCTTTGAGAAAGAAATAAAAT
1 AACATAAATGGCATTATTTGATAAAGACGGATTAAGATACAATACCTTTGAGAAAGAAATAAAAT
*
59169 TCAAAAATTTCTTTGTGAAGCATAATTCTCAATATGATGCCTCATGCATGTGTTCATTATGCCAT
66 TCAAAAATTTCTTTGTGAAACATAATTCTCAATATGATGCCTCATGCATGTGTTCATTATGCCAT
59234 AAAAGTGGACATACCTTTTACACATGCAATTATAAAATAAATAC
131 AAAAGTGGACATACCTTTTACACATGCAATTATAAAATAAATAC
*
59278 AACATAAATGGCATTCTTTGATAAAGACGGATTAAGATACAATACCTTTGAGAAAGAAATAAAAT
1 AACATAAATGGCATTATTTGATAAAGACGGATTAAGATACAATACCTTTGAGAAAGAAATAAAAT
* *
59343 TCAAGAATTTCTTTGTTAAACATAATTCTCAATATGATGCCTCATGCATGTGTTCATTATGCCAT
66 TCAAAAATTTCTTTGTGAAACATAATTCTCAATATGATGCCTCATGCATGTGTTCATTATGCCAT
59408 AAAAGTGGACATACCTTTTACACATGCAATTATAAAATAAATAC
131 AAAAGTGGACATACCTTTTACACATGCAATTATAAAATAAATAC
59452 A
1 A
59453 TTTAGAGGTA
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 170 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (174 bp):
AACATAAATGGCATTATTTGATAAAGACGGATTAAGATACAATACCTTTGAGAAAGAAATAAAAT
TCAAAAATTTCTTTGTGAAACATAATTCTCAATATGATGCCTCATGCATGTGTTCATTATGCCAT
AAAAGTGGACATACCTTTTACACATGCAATTATAAAATAAATAC
Found at i:65753 original size:13 final size:13
Alignment explanation
Indices: 65735--65759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65725 ATGTTGCTTA
65735 GTATCGATACATT
1 GTATCGATACATT
65748 GTATCGATACAT
1 GTATCGATACAT
65760 GTTCTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:65756 original size:33 final size:32
Alignment explanation
Indices: 65714--65775 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
65704 CATGTCTAAA
65714 TGTATCGATACATGTTGCTTAGTATCGATACAT
1 TGTATCGATACATGTT-CTTAGTATCGATACAT
*
65747 TGTATCGATACATGTTCTTTGTATCGATA
1 TGTATCGATACATGTTCTTAGTATCGATA
65776 TACCATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTTCTTAGTATCGATACAT
Found at i:67736 original size:20 final size:21
Alignment explanation
Indices: 67697--67736 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
67687 ATTAAAAAGA
*
67697 TTATATTTTTAAAATATTATT
1 TTATATTTTCAAAATATTATT
*
67718 TTATATTTTCCAAAT-TTAT
1 TTATATTTTCAAAATATTAT
67737 AATTTTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTTTCAAAATATTATT
Found at i:67874 original size:21 final size:20
Alignment explanation
Indices: 67830--67874 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
67820 TAGATTTAAT
* * *
67830 TTTTATTTTTTAAATTGTTG
1 TTTTAATTTTTAAATTATTA
67850 TTTTAATTTTTAAATTTATTA
1 TTTTAATTTTTAAA-TTATTA
67871 TTTT
1 TTTT
67875 TATAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTAATTTTTAAATTATTA
Found at i:71265 original size:47 final size:44
Alignment explanation
Indices: 71180--71268 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 44
71170 TAGTTCAGGA
* *
71180 ATTTTTTAGTTTTTTAATATTTTATTTTTCCTTTTTATGGTACC
1 ATTTTTTAGTATTTTAATATTTTATTTTTCCTTCTTATGGTACC
* *
71224 ATTTATTTAGTATTTTAATATATTATTTTTTTTCTTCTTATGGTA
1 ATTT-TTTAGTATTTTAATAT-TT-TATTTTTCCTTCTTATGGTA
71269 TCACTTCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 4 0.11
45 15 0.39
46 2 0.05
47 17 0.45
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (44 bp):
ATTTTTTAGTATTTTAATATTTTATTTTTCCTTCTTATGGTACC
Found at i:73168 original size:2 final size:2
Alignment explanation
Indices: 73161--73197 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
73151 TATATCTTCC
73161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73198 CTTCCTAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74544 original size:14 final size:15
Alignment explanation
Indices: 74527--74561 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
74517 ATATTATTAT
74527 TTATATATGT-AAAA
1 TTATATATGTAAAAA
*
74541 TTATTTATGTAAAAA
1 TTATATATGTAAAAA
74556 TTATAT
1 TTATAT
74562 TTATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
TTATATATGTAAAAA
Found at i:74809 original size:16 final size:17
Alignment explanation
Indices: 74790--74823 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
74780 ATTTAATTTT
*
74790 AAAT-TAATTTTTTTAA
1 AAATATAATTTATTTAA
74806 AAATATAATTTATTTAA
1 AAATATAATTTATTTAA
74823 A
1 A
74824 TAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATAATTTATTTAA
Found at i:75668 original size:12 final size:12
Alignment explanation
Indices: 75653--75677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75643 ATATATATTT
75653 AATAATTAAATA
1 AATAATTAAATA
75665 AATAATTAAATA
1 AATAATTAAATA
75677 A
1 A
75678 TTTATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATTAAATA
Found at i:75780 original size:22 final size:22
Alignment explanation
Indices: 75755--75810 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
75745 AAAATTTTGA
75755 ATTTATAAATATAAT-AATTATT
1 ATTTATAAAT-TAATAAATTATT
* *
75777 ATTTATTAAATTTATAAATTTTT
1 ATTTA-TAAATTAATAAATTATT
75800 ATTT-TAAATTA
1 ATTTATAAATTA
75811 TTTTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTATAAATTAATAAATTATT
Found at i:75828 original size:20 final size:19
Alignment explanation
Indices: 75805--75875 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
75795 TTTTTATTTT
75805 AAATTATTTTAATATTAATA
1 AAATTATTTTAAT-TTAATA
75825 AAATGTA-TTTAATTT-ATAA
1 AAAT-TATTTTAATTTAAT-A
*
75844 ATAAATATTTTAATTTAATTA
1 A-AATTATTTTAATTTAA-TA
75865 AAATT-TTTTAA
1 AAATTATTTTAA
75876 AAATAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
18 2 0.05
19 12 0.28
20 23 0.53
21 5 0.12
22 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
AAATTATTTTAATTTAATA
Found at i:75872 original size:18 final size:19
Alignment explanation
Indices: 75803--75875 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
75793 AATTTTTATT
*
75803 TTAAATTATTTTAATATTAA
1 TTAAAATATTTTAAT-TTAA
*
75823 -TAAAATGTATTTAATTT-A
1 TTAAAATAT-TTTAATTTAA
*
75841 TAAATAAATATTTTAATTTAA
1 T-TA-AAATATTTTAATTTAA
*
75862 TTAAAATTTTTTAA
1 TTAAAATATTTTAA
75876 AAATAAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.02
19 18 0.43
20 16 0.38
21 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
TTAAAATATTTTAATTTAA
Found at i:76390 original size:23 final size:21
Alignment explanation
Indices: 76357--76399 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
76347 AAATTTGAAA
76357 AATAAAAAATAAAAAATTAAT
1 AATAAAAAATAAAAAATTAAT
*
76378 AATAATAATAATAAAATATTAA
1 AATAA-AA-AATAAAAAATTAA
76400 ATAAGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAAAAATAAAAAATTAAT
Found at i:77983 original size:2 final size:2
Alignment explanation
Indices: 77978--78021 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
77968 ACTCCCTGCA
* *
77978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78020 AT
1 AT
78022 GTTGAAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80245 original size:5 final size:5
Alignment explanation
Indices: 80221--80259 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
80211 AATTAAATTC
*
80221 ATTTAA ATTTAA ATTCA ATTTA ATTTA ATTTA ATTTA AT
1 ATTT-A ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA AT
80260 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 22 0.71
6 9 0.29
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (5 bp):
ATTTA
Found at i:80245 original size:16 final size:16
Alignment explanation
Indices: 80213--80259 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
80203 TCAATCCAAA
80213 TTAAATTC-ATTTAAAT
1 TTAAATTCAATTT-AAT
80229 TTAAATTCAATTTAAT
1 TTAAATTCAATTTAAT
*
80245 TT-AATTTAATTTAAT
1 TTAAATTCAATTTAAT
80260 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 12 0.41
16 13 0.45
17 4 0.14
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTCAATTTAAT
Found at i:80313 original size:17 final size:16
Alignment explanation
Indices: 80289--80323 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
80279 AATCAATTCA
*
80289 AATTTAAAATAATTTG
1 AATTTTAAATAATTTG
*
80305 AATTTTAAATGATTTG
1 AATTTTAAATAATTTG
80321 AAT
1 AAT
80324 AATTAACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
AATTTTAAATAATTTG
Found at i:80737 original size:13 final size:13
Alignment explanation
Indices: 80719--80745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
80709 TGTCACATTT
80719 TTATTTTTTAATG
1 TTATTTTTTAATG
80732 TTATTTTTTAATG
1 TTATTTTTTAATG
80745 T
1 T
80746 CTTTGGTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TTATTTTTTAATG
Found at i:81624 original size:9 final size:10
Alignment explanation
Indices: 81583--81616 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
81573 TTACAAATTC
81583 AAATATAATTAA
1 AAATATAA--AA
81595 AAATATAAAA
1 AAATATAAAA
81605 AAATATAAAA
1 AAATATAAAA
81615 AA
1 AA
81617 CTTAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
12 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATATAAAA
Found at i:81735 original size:31 final size:30
Alignment explanation
Indices: 81650--81735 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
81640 TTTAAAAAGC
*
81650 TTAAAATTTTAAAAAATATA-TAAATAAATA
1 TTAAAA-TTTAAAAAATAAATTAAATAAATA
* * * * * *
81680 TCAAAAATTAAAATTATTATTTAAATATATAA
1 TTAAAATTTAAAA-AATAAATTAAATAAAT-A
81712 TTAAAATTTAAAAAATAAATTAAA
1 TTAAAATTTAAAAAATAAATTAAA
81736 AAAAAAGAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
29 6 0.15
30 7 0.17
31 16 0.39
32 12 0.29
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
TTAAAATTTAAAAAATAAATTAAATAAATA
Found at i:82085 original size:13 final size:13
Alignment explanation
Indices: 82067--82101 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
82057 CCCTTTTCCT
*
82067 TTTTTTTTCTCTC
1 TTTTTTTTCTCCC
82080 TTTTTTTTCTCCC
1 TTTTTTTTCTCCC
82093 TTTTCTTTT
1 TTTT-TTTT
82102 TTGATTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCTCCC
Found at i:82458 original size:18 final size:17
Alignment explanation
Indices: 82428--82509 Score: 82
Period size: 18 Copynumber: 4.9 Consensus size: 17
82418 GTTCTTTTTT
82428 ATTTTATAGATTTTTTACA
1 ATTTTATA-ATTTTTTA-A
82447 ATTTTATAATTTTTT--
1 ATTTTATAATTTTTTAA
*
82462 ATTTT-TAAATTTTTAA
1 ATTTTATAATTTTTTAA
* *
82478 ATTTTATTAATTTTTGAT
1 ATTTTA-TAATTTTTTAA
82496 ATTTTAT-ATTTTTT
1 ATTTTATAATTTTTT
82510 TCTAAATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.15
15 5 0.09
16 11 0.20
17 1 0.02
18 21 0.39
19 8 0.15
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTATAATTTTTTAA
Found at i:82460 original size:34 final size:33
Alignment explanation
Indices: 82422--82549 Score: 108
Period size: 34 Copynumber: 3.8 Consensus size: 33
82412 TTCGATGTTC
*
82422 TTTTTTATTTTATAGATTTTTTACAATTTTA-TAA
1 TTTTTTATTTTATA-AATTTTTA-AATTTTATTAA
82456 TTTTTTATTTT-TAAATTTTTAAATTTTATTAA
1 TTTTTTATTTTATAAATTTTTAAATTTTATTAA
**
82488 TTTTTGATATTTTATATTTTTTTCTAAA-TTT-TT-A
1 TTTTT--TATTTTATA-AATTTT-TAAATTTTATTAA
82522 TTTTATT-TTTTA-AAATTTTTAAAATTTT
1 TTTT-TTATTTTATAAATTTTT-AAATTTT
82550 TCTTTTTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
29 1 0.01
30 7 0.09
31 11 0.14
32 20 0.25
33 3 0.04
34 22 0.28
35 5 0.06
36 7 0.09
37 4 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (33 bp):
TTTTTTATTTTATAAATTTTTAAATTTTATTAA
Found at i:82506 original size:16 final size:16
Alignment explanation
Indices: 82422--82508 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 16
82412 TTCGATGTTC
82422 TTTTT-TATTTTATAGA
1 TTTTTATATTTTATA-A
*
82438 TTTTTTACAATTTTATAA
1 -TTTTTA-TATTTTATAA
82456 TTTTT-TATTTT-TAAA
1 TTTTTATATTTTAT-AA
*
82471 TTTTTAAATTTTATTAA
1 TTTTTATATTTTA-TAA
82488 TTTTTGATATTTTAT-A
1 TTTTT-ATATTTTATAA
82504 TTTTT
1 TTTTT
82509 TTCTAAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.02
15 12 0.20
16 11 0.19
17 18 0.31
18 9 0.15
19 8 0.14
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTATATTTTATAA
Found at i:82520 original size:20 final size:21
Alignment explanation
Indices: 82497--82542 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
82487 ATTTTTGATA
82497 TTTTATATTT-TTTTCT-AAAT
1 TTTTAT-TTTATTTTCTAAAAT
*
82517 TTTTATTTTATTTTTTAAAAT
1 TTTTATTTTATTTTCTAAAAT
82538 TTTTA
1 TTTTA
82543 AAATTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 11 0.48
21 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATTTTATTTTCTAAAAT
Found at i:82567 original size:28 final size:28
Alignment explanation
Indices: 82513--82590 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
82503 ATTTTTTTCT
* * **
82513 AAATTTTTATTTTATTTTTTAAAATTTTTA
1 AAATTTTTCTTTT-TTTTTT-GAATTTAAA
82543 AAATTTTTCTTTTTTTTTTGAATTTAAA
1 AAATTTTTCTTTTTTTTTTGAATTTAAA
* * *
82571 AAATTATTCTTATATTTTTG
1 AAATTTTTCTTTTTTTTTTG
82591 TTGACTTGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 23 0.56
29 6 0.15
30 12 0.29
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (28 bp):
AAATTTTTCTTTTTTTTTTGAATTTAAA
Found at i:83623 original size:3 final size:3
Alignment explanation
Indices: 83615--83639 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
83605 GATTTGTTAC
83615 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
83640 TATGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:86725 original size:13 final size:13
Alignment explanation
Indices: 86707--86732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86697 AACGGAAGGC
86707 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
86720 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
86733 GAAAGAGGAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:89110 original size:21 final size:21
Alignment explanation
Indices: 89080--89119 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
89070 AACCCTTAAA
89080 AATTAATAAATTTA-AATTTT
1 AATTAATAAATTTATAATTTT
89100 AATTAGATAAATTTATAATT
1 AATTA-ATAAATTTATAATT
89120 ATATGATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AATTAATAAATTTATAATTTT
Found at i:89813 original size:1 final size:1
Alignment explanation
Indices: 89807--89917 Score: 159
Period size: 1 Copynumber: 111.0 Consensus size: 1
89797 AAGATAATAT
* *
89807 AAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *** *
89872 AAAAAAAAAAAAGAAAAAAAGCTAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
89918 GCCACCAATA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 98 1.00
ACGTcount: A:0.94, C:0.01, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Done.