Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2693
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: 45721
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2905 original size:16 final size:17
Alignment explanation
Indices: 2881--2918 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2871 AAAATGCTTC
2881 ATTTTCA-T-TAAAATT
1 ATTTTCATTATAAAATT
2896 ATTTTGCATTATAAAATT
1 ATTTT-CATTATAAAATT
2914 ATTTT
1 ATTTT
2919 TATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 2 0.10
17 1 0.05
18 12 0.60
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTCATTATAAAATT
Found at i:4262 original size:11 final size:11
Alignment explanation
Indices: 4246--4312 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
4236 ATAAAATAAA
4246 ATATATTTTAT
1 ATATATTTTAT
4257 ATATATTTT-T
1 ATATATTTTAT
*
4267 A-AAATTTTA-
1 ATATATTTTAT
4276 ATATATTTAATAAT
1 ATATATTT--T-AT
* *
4290 TTATATTATAT
1 ATATATTTTAT
*
4301 TTATATTTTAT
1 ATATATTTTAT
4312 A
1 A
4313 ATTAATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
9 7 0.16
10 7 0.16
11 21 0.48
12 2 0.05
13 1 0.02
14 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATATTTTAT
Found at i:4284 original size:17 final size:19
Alignment explanation
Indices: 4252--4314 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
4242 TAAAATATAT
*
4252 TTTATATATATTTTTAA-AA
1 TTTATA-ATATATTTAATAA
4271 TTT-TAATATATTTAATAA
1 TTTATAATATATTTAATAA
* *
4289 TTTATATTATATTT-ATAT
1 TTTATAATATATTTAATAA
4307 TTTATAAT
1 TTTATAAT
4315 TAATAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 9 0.24
18 17 0.45
19 12 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATAATATATTTAATAA
Found at i:4417 original size:2 final size:2
Alignment explanation
Indices: 4410--4445 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4400 TTCTGATCTT
4410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4446 AAACTTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5737 original size:6 final size:6
Alignment explanation
Indices: 5728--5770 Score: 56
Period size: 5 Copynumber: 7.5 Consensus size: 6
5718 AAAAATTTTT
5728 ATTTAA ATTT-A ATTT-A ATTTAA A-TTAA ATTATAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATT
5771 ATTAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.44
6 13 0.38
7 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:7313 original size:25 final size:25
Alignment explanation
Indices: 7261--7323 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
7251 TTTTAAAAAA
* * *
7261 AATAAATATTAAAAAATTTATTTTT
1 AATAAATATAAAAAAATTAATTTCT
7286 AATAAA-ATAAAAAAATTAATTTACT
1 AATAAATATAAAAAAATTAATTT-CT
7311 AATAATATATAAA
1 AATAA-ATATAAA
7324 TTTATATACC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 14 0.44
25 12 0.38
26 1 0.03
27 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAAATATAAAAAAATTAATTTCT
Found at i:7317 original size:23 final size:24
Alignment explanation
Indices: 7265--7317 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
7255 AAAAAAAATA
* * *
7265 AATATTAAAAAATTTATTTTTAAT
1 AATAATAAAAAAATTATATTTAAT
*
7289 AA-AATAAAAAAATTA-ATTTACT
1 AATAATAAAAAAATTATATTTAAT
7311 AATAATA
1 AATAATA
7318 TATAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAATAAAAAAATTATATTTAAT
Found at i:7566 original size:19 final size:19
Alignment explanation
Indices: 7544--7596 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
7534 TAAAATTTTC
7544 AAATTTTAATAAAATTAAA
1 AAATTTTAATAAAATTAAA
** * *
7563 AAATTACAAATATAA-TAAT
1 AAATT-TTAATAAAATTAAA
7582 AAATTTTAATAAAAT
1 AAATTTTAATAAAAT
7597 AAATGATCGA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
18 6 0.24
19 13 0.52
20 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTTTAATAAAATTAAA
Found at i:8085 original size:23 final size:24
Alignment explanation
Indices: 8052--8101 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
8042 AAATATAAAA
* * *
8052 ATAATATAATATAATATTTTTAGT
1 ATAATATAATAAAATATGTTTAAT
8076 ATAAT-TAATAAAATATGTTTAAT
1 ATAATATAATAAAATATGTTTAAT
8099 ATA
1 ATA
8102 TGTTTTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAATATAATAAAATATGTTTAAT
Found at i:9060 original size:7 final size:7
Alignment explanation
Indices: 9044--9101 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
9034 AAATATCTTA
9044 TAAA-TT
1 TAAATTT
9050 TAAATTT
1 TAAATTT
9057 TAAATTT
1 TAAATTT
9064 TAAATTT
1 TAAATTT
9071 TAATAATTT
1 T-A-AATTT
*
9080 ATAATTTTT
1 -TAA-ATTT
*
9089 TTAATTT
1 TAAATTT
9096 TAAATT
1 TAAATT
9102 CTGATCTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
6 4 0.09
7 25 0.58
8 4 0.09
9 9 0.21
10 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:9101 original size:16 final size:16
Alignment explanation
Indices: 9054--9101 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
9044 TAAATTTAAA
*
9054 TTTTAAATTTTAAATT
1 TTTTTAATTTTAAATT
**
9070 TTAATAA-TTTATAATT
1 TTTTTAATTTTA-AATT
9086 TTTTTAATTTTAAATT
1 TTTTTAATTTTAAATT
9102 CTGATCTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAATTTTAAATT
Found at i:10196 original size:12 final size:12
Alignment explanation
Indices: 10149--10203 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
10139 AAATTTTTTA
10149 TTTAAAT-TTAT
1 TTTAAATATTAT
10160 TTATAAATATTA-
1 TT-TAAATATTAT
* * *
10172 ATAAAAAATTAT
1 TTTAAATATTAT
*
10184 TTTTAATATTAT
1 TTTAAATATTAT
10196 TTTAAATA
1 TTTAAATA
10204 ATAAAATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 9 0.27
12 21 0.64
13 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAAATATTAT
Found at i:10231 original size:11 final size:11
Alignment explanation
Indices: 10215--10247 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10205 TAAAATAAAT
10215 ATTTAAATTAA
1 ATTTAAATTAA
10226 ATTTAAATT-A
1 ATTTAAATTAA
*
10236 ACTTAAATTAA
1 ATTTAAATTAA
10247 A
1 A
10248 GTAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:10493 original size:15 final size:15
Alignment explanation
Indices: 10473--10510 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
10463 ATATTATATA
10473 TTTATAATTTA-AATT
1 TTTAT-ATTTATAATT
10488 TTTATATTTATAATT
1 TTTATATTTATAATT
10503 TTT-TATTT
1 TTTATATTT
10511 TCAAACTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATATTTATAATT
Found at i:10511 original size:21 final size:20
Alignment explanation
Indices: 10463--10503 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
10453 TTTTTAAAAA
*
10463 ATATTATATATTTATAATTT
1 ATATTTTATATTTATAATTT
*
10483 AAATTTTTATATTTATAATTT
1 ATA-TTTTATATTTATAATTT
10504 TTTATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTTATATTTATAATTT
Found at i:10569 original size:42 final size:42
Alignment explanation
Indices: 10481--10574 Score: 95
Period size: 42 Copynumber: 2.2 Consensus size: 42
10471 TATTTATAAT
* * *
10481 TTAAATTTTTATATTTATAATTTTTTATTTTCAAACTGTAAT
1 TTAAAATTTTATATTTATAATTTTTTATTATCAAACTGTAAA
*
10523 TTAAAATTTTATA-TTATTATTATTATTATTAT-AAAGCTG-AAA
1 TTAAAATTTTATATTTATAATT-TT-TTATTATCAAA-CTGTAAA
*
10565 TTAAAGTTTT
1 TTAAAATTTT
10575 TTTTTGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 7 0.16
42 28 0.64
43 9 0.20
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.55
Consensus pattern (42 bp):
TTAAAATTTTATATTTATAATTTTTTATTATCAAACTGTAAA
Found at i:11777 original size:22 final size:21
Alignment explanation
Indices: 11749--11790 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
11739 TATTAAAAAA
11749 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
11769 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
11790 A
1 A
11791 AATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:11833 original size:10 final size:10
Alignment explanation
Indices: 11818--11843 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11808 GAAAAATTCA
11818 AATTAATCTG
1 AATTAATCTG
11828 AATTAATCTG
1 AATTAATCTG
11838 AATTAA
1 AATTAA
11844 AAAAATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (10 bp):
AATTAATCTG
Found at i:12640 original size:19 final size:20
Alignment explanation
Indices: 12604--12641 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12594 ATCTGTTTTA
* *
12604 TTTATTTAATATATTTTAAT
1 TTTATTTAATAAAATTTAAT
12624 TTTATTT-ATAAAATTTAA
1 TTTATTTAATAAAATTTAA
12642 AAAATTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATTTAATAAAATTTAAT
Found at i:14149 original size:34 final size:34
Alignment explanation
Indices: 14094--14310 Score: 233
Period size: 34 Copynumber: 6.4 Consensus size: 34
14084 AAGGGGTCCG
**
14094 TGTTGATTAAAT-GGTGATTTGGTAG-TATATTAT
1 TGTTGATTAAATGGGTGATTTGGTAGCT-TACCAT
* * **
14127 TGTTGATTAAATGGGTGATTTGGTGGTTTGTCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
14161 TGTAGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * ** *
14195 TGTTAATTAAATGAGAAATTTGATAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
*
14229 TATTGATTAAATGGGTGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
14263 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
14297 TGTTGATTAAATGG
1 TGTTGATTAAATGG
14311 TGGTTTTTAC
Statistics
Matches: 153, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
33 15 0.10
34 136 0.89
35 2 0.01
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:18775 original size:34 final size:34
Alignment explanation
Indices: 18718--18936 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
18708 AAGTGGGAGA
*
18718 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
18751 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
18785 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
18819 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
18853 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
18887 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
18921 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
18937 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 143 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:18861 original size:102 final size:101
Alignment explanation
Indices: 18718--18936 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
18708 AAGTGGGAGA
** * * * *
18718 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
18783 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
18819 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * **
18884 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
18921 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
18937 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:21938 original size:16 final size:17
Alignment explanation
Indices: 21912--21945 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21902 CAAACTCAGT
*
21912 TAAAAATTTTATAATAA
1 TAAAAATTTTAAAATAA
21929 TAAAAA-TTTAAAATAA
1 TAAAAATTTTAAAATAA
21945 T
1 T
21946 GAAATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTTTAAAATAA
Found at i:22995 original size:29 final size:29
Alignment explanation
Indices: 22962--23053 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
22952 AATTATTATT
22962 TAAATAATAATTTTAAAAAATTTTAATTA
1 TAAATAATAATTTTAAAAAATTTTAATTA
* * * *
22991 TAAATATTAA-TATAATAATATTTTTAATAA
1 TAAATAATAATTTTAA-AA-AATTTTAATTA
*
23021 TAATATAA-AATTTTAAATTAA-TTTAATTA
1 TAA-ATAATAATTTTAAA-AAATTTTAATTA
23050 -AAAT
1 TAAAT
23054 TAAATTTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 18 0.37
30 16 0.33
31 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAATAATAATTTTAAAAAATTTTAATTA
Found at i:23059 original size:16 final size:15
Alignment explanation
Indices: 23035--23068 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
23025 ATAAAATTTT
*
23035 AAATTAATTTAATTA
1 AAATTAATTTAAATA
23050 AAATTAAATTTAAATA
1 AAATT-AATTTAAATA
23066 AAA
1 AAA
23069 AAATTTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTAATTTAAATA
Found at i:23758 original size:17 final size:18
Alignment explanation
Indices: 23733--23766 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23723 TTTTATTTTT
23733 TAAATTATATCTTTTATC
1 TAAATTATATCTTTTATC
*
23751 TAAA-TATATTTTTTAT
1 TAAATTATATCTTTTAT
23767 TAATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAATTATATCTTTTATC
Found at i:28396 original size:18 final size:18
Alignment explanation
Indices: 28373--28410 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28363 AATCAAGTTC
*
28373 ATATTAAATTTAAATATA
1 ATATTAAAATTAAATATA
28391 ATATTAAAATTAAATATA
1 ATATTAAAATTAAATATA
28409 AT
1 AT
28411 TATTTGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAAAATTAAATATA
Found at i:28541 original size:19 final size:20
Alignment explanation
Indices: 28517--28554 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
28507 TATATTAATT
28517 TTTTATAATTT-ATTTTTAC
1 TTTTATAATTTAATTTTTAC
28536 TTTTATAATTTAATTTTTA
1 TTTTATAATTTAATTTTTA
28555 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTAATTTTTAC
Found at i:28559 original size:15 final size:15
Alignment explanation
Indices: 28536--28569 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28526 TTATTTTTAC
28536 TTTTATAATTTAAT-
1 TTTTATAATTTAATA
28550 TTTTATTAATTTAATA
1 TTTTA-TAATTTAATA
28566 TTTT
1 TTTT
28570 TTTATTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 9 0.50
16 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATAATTTAATA
Found at i:28677 original size:25 final size:26
Alignment explanation
Indices: 28649--28697 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
28639 TATGATAAAA
28649 AATACATTATATATAATA-TAAAATT
1 AATACATTATATATAATAGTAAAATT
* *
28674 AATATATTTTATATAATAGTAAAA
1 AATACATTATATATAATAGTAAAA
28698 AATAAGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
AATACATTATATATAATAGTAAAATT
Found at i:28849 original size:18 final size:19
Alignment explanation
Indices: 28814--28851 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28804 TATTCAAATT
28814 TTTTTAAATATAAGATAAA
1 TTTTTAAATATAAGATAAA
*
28833 TTTTTAAATTTAA-ATAAA
1 TTTTTAAATATAAGATAAA
28851 T
1 T
28852 AATTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TTTTTAAATATAAGATAAA
Found at i:28857 original size:19 final size:19
Alignment explanation
Indices: 28816--28858 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28806 TTCAAATTTT
*
28816 TTTAAATATAAGATAAATT
1 TTTAAATATAAGATAAATA
*
28835 TTTAAATTTAA-ATAAATAA
1 TTTAAATATAAGATAAAT-A
28854 TTTAA
1 TTTAA
28859 TTTTTGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTAAATATAAGATAAATA
Found at i:33357 original size:21 final size:21
Alignment explanation
Indices: 33333--33378 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33323 GATGAAATGC
*
33333 TGCATTAGTTGGATGAAAGAA
1 TGCATTAGTTGGATGAAAAAA
**
33354 TGCATTTTTTGGATGAAAAAA
1 TGCATTAGTTGGATGAAAAAA
33375 TGCA
1 TGCA
33379 ACTTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (21 bp):
TGCATTAGTTGGATGAAAAAA
Found at i:33384 original size:21 final size:21
Alignment explanation
Indices: 33341--33384 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33331 GCTGCATTAG
* **
33341 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
33362 TTGGATGAAAAAATGCAACTT
1 TTGGATGAAAAAATGCAACTT
33383 TT
1 TT
33385 AATAACCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:38408 original size:21 final size:21
Alignment explanation
Indices: 38382--38433 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
38372 AAAGATTTAT
38382 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
38403 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
38424 TTGGATGAAA
1 TTGGATGAAA
38434 AAAGCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:38445 original size:21 final size:21
Alignment explanation
Indices: 38403--38445 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38393 GATGCATTGG
* *
38403 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAAAGCACTTT
38424 TTGGATGAAA-AAAGCAACTTT
1 TTGGATGAAAGAAAGC-ACTTT
38445 T
1 T
38446 AATAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (21 bp):
TTGGATGAAAGAAAGCACTTT
Found at i:41238 original size:14 final size:14
Alignment explanation
Indices: 41219--41245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41209 TTTATCCAAA
41219 TGTATCGATACATT
1 TGTATCGATACATT
41233 TGTATCGATACAT
1 TGTATCGATACAT
41246 CCTACAAATG
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
TGTATCGATACATT
Found at i:41325 original size:19 final size:19
Alignment explanation
Indices: 41301--41368 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
41291 AATTCAACAA
41301 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
41320 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
41335 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
41352 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
41369 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:41340 original size:13 final size:13
Alignment explanation
Indices: 41322--41346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41312 ACATAAGTTT
41322 TGTATCGATACAA
1 TGTATCGATACAA
41335 TGTATCGATACA
1 TGTATCGATACA
41347 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:41344 original size:32 final size:32
Alignment explanation
Indices: 41303--41365 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
41293 TTCAACAATT
*
41303 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
41335 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
41366 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:41426 original size:13 final size:13
Alignment explanation
Indices: 41408--41433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41398 CATTTTTCTG
41408 TGTATCGATACAT
1 TGTATCGATACAT
41421 TGTATCGATACAT
1 TGTATCGATACAT
41434 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:41430 original size:33 final size:33
Alignment explanation
Indices: 41388--41454 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
41378 GCCAAGGAAA
***
41388 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
41421 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
41454 T
1 T
41455 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:45206 original size:12 final size:13
Alignment explanation
Indices: 45177--45215 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
45167 AAAAATAATG
*
45177 AATATATATCAAAT
1 AATATATAT-ATAT
45191 AATATATATATA-
1 AATATATATATAT
45203 AATATATATATAT
1 AATATATATATAT
45216 TAGAACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 12 0.52
13 2 0.09
14 9 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATATATATAT
Found at i:45215 original size:14 final size:16
Alignment explanation
Indices: 45178--45215 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
45168 AAAATAATGA
45178 ATATATATCAAATAAT
1 ATATATATCAAATAAT
45194 ATATATAT-AAAT-AT
1 ATATATATCAAATAAT
45208 ATATATAT
1 ATATATAT
45216 TAGAACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATCAAATAAT
Done.