Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2261
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: 63841
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:62 original size:22 final size:22
Alignment explanation
Indices: 35--84 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
25 CAAACATATA
35 TAAAAATAAAATAAATTTAAAAT
1 TAAAAATAAAA-AAATTTAAAAT
* * *
58 TAAAAATCAAACAATTTTAAAT
1 TAAAAATAAAAAAATTTAAAAT
80 TAAAA
1 TAAAA
85 TATTTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATAAAAAAATTTAAAAT
Found at i:76 original size:23 final size:22
Alignment explanation
Indices: 35--84 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
25 CAAACATATA
*
35 TAAAAATAAAATAAATTTAAAAT
1 TAAAAATAAAACAAATTT-AAAT
* *
58 TAAAAATCAAACAATTTTAAAT
1 TAAAAATAAAACAAATTTAAAT
80 TAAAA
1 TAAAA
85 TATTTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATAAAACAAATTTAAAT
Found at i:4207 original size:2 final size:2
Alignment explanation
Indices: 4200--4262 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
4190 ATAACATTAA
4200 AT AT AT AT 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 AT AT AT AT
4242 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
4263 AAAAGGGCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6767 original size:164 final size:164
Alignment explanation
Indices: 6496--6825 Score: 633
Period size: 164 Copynumber: 2.0 Consensus size: 164
6486 TTAAAAGATT
6496 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
1 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
*
6561 CACCTTTATGAGGCTACATACAGACTGAAAAATGTTGAAAAAGTGGATGTTTAAGTTATAGTACG
66 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
6626 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
131 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
*
6660 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTGGTCTGAACAAGTAATGCAGCTTATTTAA
1 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
*
6725 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAGGTTATAGTACG
66 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
6790 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
131 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
6824 AG
1 AG
6826 GAAGTGTTTG
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 163 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (164 bp):
AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
Found at i:7752 original size:20 final size:21
Alignment explanation
Indices: 7723--7780 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 21
7713 GTAAAAAGAC
7723 AGAATGTATCGATACATT-AA
1 AGAATGTATCGATACATTGAA
*
7743 AGAATATATCGATACATTGAA
1 AGAATGTATCGATACATTGAA
7764 A-AATGTATCGATACATT
1 AGAATGTATCGATACATT
7781 TGGGTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 32 0.91
21 3 0.09
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
AGAATGTATCGATACATTGAA
Found at i:7791 original size:71 final size:71
Alignment explanation
Indices: 7675--7830 Score: 224
Period size: 71 Copynumber: 2.2 Consensus size: 71
7665 TTTTAACTAG
* * * * *
7675 ATATATTGATATATTGCAAAATGTATCGATATATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
7740 T-AAAGA
66 TGAAA-A
*
7746 ATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAGACAGAATATATCGATACAT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
7811 TGAAAA
66 TGAAAA
* *
7817 ATATACCAATACAT
1 ATATATCGATACAT
7831 CTGGATAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
71 73 0.96
72 3 0.04
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (71 bp):
ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
TGAAAA
Found at i:7798 original size:51 final size:51
Alignment explanation
Indices: 7743--7841 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
7733 GATACATTAA
* * * * *
7743 AGAATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAGAC
1 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAAGAC
7794 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAA
1 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAA
7842 TGTGACTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (51 bp):
AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAAGAC
Found at i:10438 original size:11 final size:11
Alignment explanation
Indices: 10416--10461 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
10406 ATAGTAATTT
*
10416 TTATATTAATA
1 TTATATTTATA
*
10427 TTGTATTTATA
1 TTATATTTATA
*
10438 TTATTTTTATA
1 TTATATTTATA
*
10449 TTATAATTATA
1 TTATATTTATA
10460 TT
1 TT
10462 TAAATATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATATTTATA
Found at i:10441 original size:22 final size:22
Alignment explanation
Indices: 10416--10524 Score: 62
Period size: 22 Copynumber: 4.9 Consensus size: 22
10406 ATAGTAATTT
* *
10416 TTATATTAATATTGTATTTATA
1 TTATATTAATATTATAATTATA
* *
10438 TTATTTTTATATTATAATTATA
1 TTATATTAATATTATAATTATA
10460 TT-TA--AATATTATGAATTTATA
1 TTATATTAATATTAT-AA-TTATA
* * * *
10481 TATATTTTGACATTAATAACTCATA
1 T-TATATTAATATT-ATAA-TTATA
* *
10506 TTATAATAATTTTATAATT
1 TTATATTAATATTATAATT
10525 TTTAGTTGTA
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
19 7 0.11
20 2 0.03
21 7 0.11
22 22 0.35
23 5 0.08
24 7 0.11
25 11 0.17
26 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATATTAATATTATAATTATA
Found at i:17084 original size:2 final size:2
Alignment explanation
Indices: 17077--17110 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17067 TAGCTTTTGC
17077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17111 TTTATCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19534 original size:3 final size:3
Alignment explanation
Indices: 19526--19565 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
19516 TTACGGAAAT
*
19526 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
19566 GATATTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20904 original size:2 final size:2
Alignment explanation
Indices: 20897--20927 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20887 AAATCACATG
20897 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20928 CGCAGGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21714 original size:3 final size:3
Alignment explanation
Indices: 21706--21735 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21696 AAGCTGAATG
21706 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21736 TAGGCTTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23425 original size:21 final size:20
Alignment explanation
Indices: 23399--23442 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
23389 ATTAAAATTT
23399 ATATAATTAT-ATAATATTTTA
1 ATATAATTATAAT-AT-TTTTA
23420 ATATAATTATAATATTTTTA
1 ATATAATTATAATATTTTTA
23440 ATA
1 ATA
23443 ATATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 12 0.55
22 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATAATTATAATATTTTTA
Found at i:25016 original size:25 final size:25
Alignment explanation
Indices: 24982--25034 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
24972 GTCATGATGT
24982 CAATTGAGAAATAATTATGTTACAA
1 CAATTGAGAAATAATTATGTTACAA
25007 CAATTGAGAAATAATTATGTTACAA
1 CAATTGAGAAATAATTATGTTACAA
25032 CAA
1 CAA
25035 CACCCACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (25 bp):
CAATTGAGAAATAATTATGTTACAA
Found at i:25213 original size:2 final size:2
Alignment explanation
Indices: 25206--25242 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25196 TTAAATTTAC
25206 AT AT 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 AT AT A
25243 AAAGGAGCTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25857 original size:2 final size:2
Alignment explanation
Indices: 25850--25889 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25840 ACATGCATGC
25850 AT AT AT 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 AT AT AT
25890 TCAAACATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26075 original size:15 final size:16
Alignment explanation
Indices: 26043--26076 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
26033 TTATTTCATA
*
26043 TGTTATTAAAAAGGAG
1 TGTTATTAAAAAGAAG
26059 TGTTATT-AAAAGAAG
1 TGTTATTAAAAAGAAG
26074 TGT
1 TGT
26077 AAAAATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (16 bp):
TGTTATTAAAAAGAAG
Found at i:26119 original size:3 final size:3
Alignment explanation
Indices: 26111--26151 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
26101 TGTCAAGCAT
26111 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
26152 CAAAAATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29202 original size:16 final size:18
Alignment explanation
Indices: 29162--29204 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
29152 AAAAATAACA
29162 TTTATAATAACAAAATAT
1 TTTATAATAACAAAATAT
**
29180 TACATAATAA-AAAAT-T
1 TTTATAATAACAAAATAT
29196 TTTATAATA
1 TTTATAATA
29205 TCGCGTACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
18 8 0.38
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTATAATAACAAAATAT
Found at i:30221 original size:3 final size:3
Alignment explanation
Indices: 30213--30253 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
30203 CTGACTCAAC
30213 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30254 GATTTTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31994 original size:8 final size:8
Alignment explanation
Indices: 31981--32012 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
31971 GTCTTTGGAG
31981 AAAAAAAT
1 AAAAAAAT
31989 AAAAAAAT
1 AAAAAAAT
31997 AAAATAAAT
1 AAAA-AAAT
32006 AAAAAAA
1 AAAAAAA
32013 GTTAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:32007 original size:17 final size:16
Alignment explanation
Indices: 31981--32012 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
31971 GTCTTTGGAG
31981 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
31997 AAAATAAATAAAAAAA
1 AAAA-AAATAAAAAAA
32013 GTTAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:33185 original size:8 final size:8
Alignment explanation
Indices: 33172--33202 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
33162 GTCAAAGTAT
33172 AATATATA
1 AATATATA
33180 AATATATA
1 AATATATA
33188 AATATATA
1 AATATATA
*
33196 TATATAT
1 AATATAT
33203 CATTAACTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATATA
Found at i:33810 original size:1 final size:1
Alignment explanation
Indices: 33806--33840 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
33796 CCCAAAAATG
33806 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33841 CGAAGCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35461 original size:3 final size:3
Alignment explanation
Indices: 35448--35503 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
35438 CTGGAAAATG
35448 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35495 AAT AAT AAT
1 AAT AAT AAT
35504 TTGAGCTGGC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36082 original size:2 final size:2
Alignment explanation
Indices: 36075--36113 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
36065 AAGTTTGGAG
*
36075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36114 AATCTACCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36371 original size:2 final size:2
Alignment explanation
Indices: 36366--36403 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
36356 CATTCAATAC
* *
36366 AT AT AT AT AT AT AG AT AT AG AT A- 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 AT AT AT A
36404 AGAAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:44014 original size:2 final size:2
Alignment explanation
Indices: 44007--44036 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43997 AATTCTGCAA
*
44007 AT AT AT AT AT AC 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
44037 TGAAATTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44272 original size:3 final size:3
Alignment explanation
Indices: 44259--44308 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
44249 GATTCTCTTC
*
44259 ATT ACT 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
44307 AT
1 AT
44309 ATCATCACTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:46657 original size:2 final size:2
Alignment explanation
Indices: 46650--46676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46640 TACGTGTATG
46650 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 T
46677 CAAAGGCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47228 original size:18 final size:18
Alignment explanation
Indices: 47193--47246 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
47183 TTTAAAAAAT
*
47193 TATATTTAATAATTTAATA
1 TATATTTAA-ATTTTAATA
47212 TATATTTAAATTTTAATA
1 TATATTTAAATTTTAATA
*
47230 T-TATTTTAAATTATAAT
1 TATA-TTTAAATTTTAAT
47247 TTTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 2 0.06
18 21 0.66
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTTAAATTTTAATA
Found at i:47398 original size:2 final size:2
Alignment explanation
Indices: 47391--47417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47381 TGAATTTGAA
47391 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
47418 AAACTTGAAA
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:48035 original size:24 final size:24
Alignment explanation
Indices: 47986--48043 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
47976 TATATTTAAT
* *
47986 ATATAATTATATAATTAAATATAA
1 ATATAAATATATAATTAAATAAAA
48010 ATATAAATATATAATTTAAA-AAAA
1 ATATAAATATATAA-TTAAATAAAA
*
48034 ATAAAAATAT
1 ATATAAATAT
48044 TTATATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAAATATATAATTAAATAAAA
Found at i:48095 original size:63 final size:63
Alignment explanation
Indices: 47977--48094 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
47967 TAAATTATTT
*
47977 ATATTTAATATATAATTATATAATTAAATATAAATATAAATATATAATTTAAAAAAAATAAAA
1 ATATTTAATATATAAATATATAATTAAATATAAATATAAATATATAATTTAAAAAAAATAAAA
* * *
48040 ATATTT-ATATAGTAAATATTTATTTAAATAT-AA-AT-AATATATATTTTAAAAAAAA
1 ATATTTAATATA-TAAATATATAATTAAATATAAATATAAATATATAATTTAAAAAAAA
48095 ATTCTATCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 19 0.38
61 2 0.04
62 7 0.14
63 22 0.44
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (63 bp):
ATATTTAATATATAAATATATAATTAAATATAAATATAAATATATAATTTAAAAAAAATAAAA
Found at i:49332 original size:34 final size:34
Alignment explanation
Indices: 49286--49470 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
49276 GTAAAAACCA
*
49286 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
49320 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
49354 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
49388 CTATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
49422 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
49455 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
49471 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 18 0.14
34 111 0.83
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:53930 original size:34 final size:34
Alignment explanation
Indices: 53884--54066 Score: 242
Period size: 34 Copynumber: 5.4 Consensus size: 34
53874 GTAAAAACCA
* *
53884 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
53918 CCATTTAGTCAACAATGGTAAACTATCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
53952 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
53986 CTATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
54020 CCATTTAGTCAACAATGATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
54053 CCATTTAATCAACA
1 CCATTTAATCAACA
54067 TTTTTTACGG
Statistics
Matches: 129, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 13 0.10
34 116 0.90
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:54822 original size:13 final size:13
Alignment explanation
Indices: 54804--54829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54794 GATGGATTTA
54804 AAATTAATTAATT
1 AAATTAATTAATT
54817 AAATTAATTAATT
1 AAATTAATTAATT
54830 TTTTTATTTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:55087 original size:21 final size:22
Alignment explanation
Indices: 55038--55088 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
55028 TTTAAAAGAG
* * *
55038 TTAAAAATGATCAATAATTATT
1 TTAAAAATGATAAAAAATTATC
*
55060 TTCAAAA-GATAAAAAATTATC
1 TTAAAAATGATAAAAAATTATC
55081 TTAAAAAT
1 TTAAAAAT
55089 TTTAAAAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
TTAAAAATGATAAAAAATTATC
Found at i:56289 original size:22 final size:22
Alignment explanation
Indices: 56248--56327 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
56238 AAAATATATT
*
56248 TATTTAAAT-TTAATTTTAAAAA
1 TATTTAAATATTAA-TATAAAAA
*
56270 TATTTAAATATTAATATAAATA
1 TATTTAAATATTAATATAAAAA
*
56292 T-TTTTAATAATTAAATATTAAAATA
1 TATTTAAAT-ATT-AATA-TAAAA-A
56317 TATTTTAAATA
1 TA-TTTAAATA
56328 ATAAAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 6 0.13
22 19 0.41
23 8 0.17
24 4 0.09
25 2 0.04
26 1 0.02
27 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAAATATTAATATAAAAA
Found at i:56325 original size:48 final size:46
Alignment explanation
Indices: 56237--56344 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 46
56227 TATTTAAAAT
* * * *
56237 AAAAATATATTTATTTA-AATTTAATTTTAAAAATATTTAAATATTAA
1 AAAAATA-ATTT-TTAATAATTAAATATTAAAAATATTTAAATAATAA
*
56284 TATAAAT-ATTTTTAATAATTAAATATTAAAATATATTTTAAATAATAA
1 -AAAAATAATTTTTAATAATTAAATATTAAAA-ATA-TTTAAATAATAA
56332 AAAAATAATTTTT
1 AAAAATAATTTTT
56345 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
45 3 0.06
46 17 0.34
47 8 0.16
48 22 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (46 bp):
AAAAATAATTTTTAATAATTAAATATTAAAAATATTTAAATAATAA
Found at i:57037 original size:146 final size:147
Alignment explanation
Indices: 56748--57038 Score: 487
Period size: 147 Copynumber: 2.0 Consensus size: 147
56738 TTGACAAATG
**
56748 AAAAATTAAACAAATTAAATTTTTTCCATCAAAATTTTTTATTGGATTACTTAAAATTAAATGAT
1 AAAAATTAAACAAATTAAATTTTTTCCATCAAAATTTTTTATTAAATTACTTAAAATTAAATGAT
* *
56813 TTTTTCTATACATATAAATGAAGTGTTAGATTTTCTTTCATTATTTTTTTATTTATTACTTTTAA
66 TTTTTCTATACATATAAATGAAGTATTAGATTTTCTTTCATTATTTTTATATTTATTACTTTTAA
56878 TATATATTTATGAACCA
131 TATATATTTATGAACCA
* *
56895 AAAAATTAAATAAATTAAATTTTTTCCATCAAAATTTTTTATTAAATTATTTAAAAGTTAAATGA
1 AAAAATTAAACAAATTAAATTTTTTCCATCAAAATTTTTTATTAAATTACTTAAAA-TTAAATGA
* *
56960 -TTTTTCTATACATATAAATGAAGTATTA-ATTTTCTTTCATTCTTTTTATATTTATTATTTTTA
65 TTTTTTCTATACATATAAATGAAGTATTAGATTTTCTTTCATTATTTTTATATTTATTACTTTTA
57023 ATATATATTTATGAAC
130 ATATATATTTATGAAC
57039 ACCGTTTAAA
Statistics
Matches: 135, Mismatches: 8, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
146 48 0.36
147 79 0.59
148 8 0.06
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.50
Consensus pattern (147 bp):
AAAAATTAAACAAATTAAATTTTTTCCATCAAAATTTTTTATTAAATTACTTAAAATTAAATGAT
TTTTTCTATACATATAAATGAAGTATTAGATTTTCTTTCATTATTTTTATATTTATTACTTTTAA
TATATATTTATGAACCA
Found at i:57086 original size:3 final size:3
Alignment explanation
Indices: 57078--57103 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57068 AATTATGAAA
57078 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
57104 GAATATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58318 original size:2 final size:2
Alignment explanation
Indices: 58305--58339 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
58295 TTCAAATTAA
*
58305 AT AT AA 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 AT A
58340 CTTGTAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:58560 original size:3 final size:3
Alignment explanation
Indices: 58552--58595 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58542 CACTTTCAAA
58552 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58596 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58600 original size:4 final size:4
Alignment explanation
Indices: 58591--58616 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
58581 TAATAATAAT
58591 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
58617 AGCTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:59235 original size:34 final size:34
Alignment explanation
Indices: 59162--59344 Score: 187
Period size: 34 Copynumber: 5.4 Consensus size: 34
59152 ACAACCTTAT
* * * * *
59162 TTGTTGATTAAA-AGGTGATTTAGTAGTTTACCA
1 TTGTTGATTAAATGGGTAATTTGGTGGCTTACCA
* *
59195 TTGTTGATTAAATGGGTAATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTAATTTGGTGGCTTACCA
* * *
59229 TTGTTGACTAAAT--GAAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTA-ATTTGGTGGCTTACCA
*
59262 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTAATTTGGTGGCTTACCA
* *
59296 TTGTTGACTAAATGGG-AGATTTGGTAGG-TTGCCA
1 TTGTTGATTAAATGGGTA-ATTTGGT-GGCTTACCA
59330 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
59345 TGGTTTTTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
32 2 0.02
33 37 0.29
34 84 0.67
35 3 0.02
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTAATTTGGTGGCTTACCA
Found at i:59260 original size:67 final size:68
Alignment explanation
Indices: 59178--59344 Score: 255
Period size: 67 Copynumber: 2.5 Consensus size: 68
59168 ATTAAAAGGT
* * * *
59178 GATTTAGTAGTTTACCATTGTTGATTAAATGGGTAATTTGGTGGTTTGCCATTGTTGACTAAAT-
1 GATTTGGTAGCTTACCATTGTTGATTAAATGGGTAATTTGGTGGCTTACCATTGTTGACTAAATG
59242 GAA
66 GAA
*
59245 GATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATG
1 GATTTGGTAGCTTACCATTGTTGATTAAATGGGTAATTTGGTGGCTTACCATTGTTGACTAAATG
*
59310 GGA
66 GAA
* *
59313 GATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 GATTTGGTAGCTTACCATTGTTGATTAAATGG
59345 TGGTTTTTTA
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 59 0.65
68 32 0.35
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (68 bp):
GATTTGGTAGCTTACCATTGTTGATTAAATGGGTAATTTGGTGGCTTACCATTGTTGACTAAATG
GAA
Found at i:59297 original size:101 final size:100
Alignment explanation
Indices: 59162--59343 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 100
59152 ACAACCTTAT
* *
59162 TTGTTGATTAAAAGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTA-ATTTGGT-GGTTT
1 TTGTTGATTAAAAGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGG-AGATTTGGTAGG-TT
59225 GCCATTGTTGACTAAATGAAGATTTGGTAGCTTACCA
64 GCCATTGTTGACTAAATGAAGATTTGGTAGCTTACCA
* * *
59262 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTG
1 TTGTTGATTAAA-AGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTG
*
59327 CCATTGTTGATTAAATG
65 CCATTGTTGACTAAATG
59344 GTGGTTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 13 0.18
101 58 0.79
102 2 0.03
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (100 bp):
TTGTTGATTAAAAGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
CATTGTTGACTAAATGAAGATTTGGTAGCTTACCA
Done.