Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold598
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: 66628
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:3894 original size:6 final size:7
Alignment explanation
Indices: 3861--3917 Score: 50
Period size: 6 Copynumber: 8.4 Consensus size: 7
3851 ATAATCTATT
3861 TATTATTA
1 TATTA-TA
3869 TATTAT-
1 TATTATA
*
3875 TTTTATA
1 TATTATA
3882 TATTATA
1 TATTATA
3889 -ATTATA
1 TATTATA
*
3895 T-TTAAAA
1 TATT-ATA
3902 TATTATA
1 TATTATA
3909 TATT-TA
1 TATTATA
3915 TAT
1 TAT
3918 AAAATTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 18 0.44
7 16 0.39
8 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTATA
Found at i:3906 original size:20 final size:20
Alignment explanation
Indices: 3864--3922 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3854 ATCTATTTAT
* *
3864 TATTAT-ATTAT-TTTTATA
1 TATTATAATTATATTTAAAA
3882 TATTATAATTATATTTAAAA
1 TATTATAATTATATTTAAAA
*
3902 TATTATATATT-TATATAAAA
1 TATTATA-ATTATATTTAAAA
3922 T
1 T
3923 TTAATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.17
19 5 0.14
20 21 0.60
21 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATAATTATATTTAAAA
Found at i:3924 original size:27 final size:26
Alignment explanation
Indices: 3876--3942 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
3866 TTATATTATT
* *
3876 TTTATATA-TTATAATTATATTTAAAA
1 TTTATATATTTAT-ATAAAATTTAAAA
*
3902 TATTATATATTTATATAAAATTTAATA
1 T-TTATATATTTATATAAAATTTAAAA
*
3929 TTTA-AAATTTATAT
1 TTTATATATTTATAT
3943 TATATAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 9 0.26
26 4 0.11
27 18 0.51
28 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTATATATTTATATAAAATTTAAAA
Found at i:6502 original size:11 final size:11
Alignment explanation
Indices: 6486--6534 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
6476 TCGATAATTT
6486 TAAATATAATA
1 TAAATATAATA
6497 TAAATATAAT-
1 TAAATATAATA
6507 TAAATTATAATA
1 TAAA-TATAATA
*
6519 TTTAAATGTAATA
1 --TAAATATAATA
6532 TAA
1 TAA
6535 TTTAAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 4 0.12
11 19 0.58
13 6 0.18
14 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATATAATA
Found at i:6646 original size:20 final size:22
Alignment explanation
Indices: 6608--6652 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
6598 TAAAATTTAT
*
6608 ATATAAAAAATATTTTAAATAC
1 ATATAAAAAATATTATAAATAC
6630 ATAT-AAAAATA-TATAAATAC
1 ATATAAAAAATATTATAAATAC
6650 ATA
1 ATA
6653 GATTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAAAAATATTATAAATAC
Found at i:7002 original size:160 final size:161
Alignment explanation
Indices: 6738--7055 Score: 512
Period size: 160 Copynumber: 2.0 Consensus size: 161
6728 TCTTTCATGG
*
6738 CCCTACTCAAAGAAACTTCCTATTAACTCTGTTAACCAACCCCTTGGTCCTCTCCAATCCAATTC
1 CCCTACTCAAAGAAACTTCCTATTAACTCTGTTAACCAACCCCTTGGTCCTCTCCAATCCAACTC
* * * *
6803 CACGAGTGGAAATGGTTAGCTGGCTGTATGAGCACTAGCCTAGA-AGCTGATCTAGTTTTTCAGA
66 CACGAGTGGAAATGATTAGCTGGCCGTAGGAGCACTAGCCTAGATAGCCGATCTAGTTTTTCAGA
* *
6867 GTTAATTTTATTTTAGGGAAGATTTATTATC
131 GTTAATTTTATTGTAGGGAAGACTTATTATC
* * * ** *
6898 CCCTACTCAAGGAAACTTCCTATTAACTCTGTTAACCAAGCCCTTGGTCCTCTTCTTTTCAACTC
1 CCCTACTCAAAGAAACTTCCTATTAACTCTGTTAACCAACCCCTTGGTCCTCTCCAATCCAACTC
6963 CACGAGTGGAAATGATTAGCTGGCCGTAGGAGCACTAGCCTAGATAGCCGATCTAGTTTTTCAGA
66 CACGAGTGGAAATGATTAGCTGGCCGTAGGAGCACTAGCCTAGATAGCCGATCTAGTTTTTCAGA
7028 GTTAATTTTATTGTAGGGAAGACTTATT
131 GTTAATTTTATTGTAGGGAAGACTTATT
7056 TCTCCGAAAG
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
160 99 0.69
161 45 0.31
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (161 bp):
CCCTACTCAAAGAAACTTCCTATTAACTCTGTTAACCAACCCCTTGGTCCTCTCCAATCCAACTC
CACGAGTGGAAATGATTAGCTGGCCGTAGGAGCACTAGCCTAGATAGCCGATCTAGTTTTTCAGA
GTTAATTTTATTGTAGGGAAGACTTATTATC
Found at i:12099 original size:13 final size:13
Alignment explanation
Indices: 12068--12117 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
12058 TATATTACAG
12068 ATTTAT-TTTAATTT
1 ATTTATATTTAA--T
12082 ATTTATATTTAAT
1 ATTTATATTTAAT
12095 ATTTATA-TTAA-
1 ATTTATATTTAAT
*
12106 ATATATATTTAA
1 ATTTATATTTAA
12118 ATGTAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.18
12 8 0.24
13 8 0.24
14 6 0.18
15 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTATATTTAAT
Found at i:12113 original size:17 final size:18
Alignment explanation
Indices: 12093--12128 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12083 TTTATATTTA
*
12093 ATATTTATAT-TAAATAT
1 ATATTTAAATGTAAATAT
12110 ATATTTAAATGTAAATAT
1 ATATTTAAATGTAAATAT
12128 A
1 A
12129 AAAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTTAAATGTAAATAT
Found at i:12130 original size:24 final size:24
Alignment explanation
Indices: 12085--12136 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
12075 TTAATTTATT
* * *
12085 TATATTTAATATTTATATTAAATA
1 TATATTTAATATGTAAATTAAAAA
12109 TATATTTAA-ATGTAAATATAAAAA
1 TATATTTAATATGTAAAT-TAAAAA
12133 TATA
1 TATA
12137 ATTATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATTTAATATGTAAATTAAAAA
Found at i:12756 original size:3 final size:3
Alignment explanation
Indices: 12750--12774 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12740 CTGCATCATC
12750 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
12775 AAGAAAAAGT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12968 original size:22 final size:22
Alignment explanation
Indices: 12916--12957 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12906 TATATTTTAT
*
12916 ATATTAT-T-TTTTTATTTAAA
1 ATATTATATATTTTTATATAAA
12936 ATATTATATATTTTTATATAAA
1 ATATTATATATTTTTATATAAA
12958 TTTTGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATATATTTTTATATAAA
Found at i:16767 original size:34 final size:34
Alignment explanation
Indices: 16721--16938 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
16711 GTAAAAACCA
*
16721 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
16755 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
16789 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
16823 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
16856 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
16890 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
16923 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
16939 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:16835 original size:68 final size:67
Alignment explanation
Indices: 16719--16938 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
16709 TGGTAAAAAC
* * *
16719 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
16784 AT
66 AT
* * *
16786 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
16851 AAT
65 AAT
* * * * * *
16854 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
16919 AT
66 AT
16921 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
16939 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:21400 original size:34 final size:34
Alignment explanation
Indices: 21354--21571 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
21344 GTAAAAACCA
*
21354 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
21388 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
21422 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
21456 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
21489 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
21523 CCATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
21556 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
21572 TTGGTTATAG
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 114 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:21468 original size:68 final size:67
Alignment explanation
Indices: 21352--21571 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
21342 TGGTAAAAAC
* * *
21352 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
21417 AT
66 AT
* * *
21419 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
21484 AAT
65 AAT
* * * * * * *
21487 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGATAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
21552 AT
66 AT
21554 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
21572 TTGGTTATAG
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:22113 original size:26 final size:27
Alignment explanation
Indices: 22084--22172 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
22074 ACGTAAACTT
22084 CATA-TTTAAAAATTATATAAATATAA
1 CATACTTTAAAAATTATATAAATATAA
**
22110 CATACAATAAAAA-TA-ATAAA-AT-A
1 CATACTTTAAAAATTATATAAATATAA
* * *
22133 TATAATTTAAAATTTATATAAATATAA
1 CATACTTTAAAAATTATATAAATATAA
* *
22160 AATATTTTAAAAA
1 CATACTTTAAAAA
22173 ATAATTATTA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 9 0.19
24 4 0.08
25 10 0.21
26 8 0.17
27 17 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
CATACTTTAAAAATTATATAAATATAA
Found at i:22163 original size:31 final size:33
Alignment explanation
Indices: 22120--22202 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 33
22110 CATACAATAA
*
22120 AAATAATAAAATATATAATT-TAAAAT-TTATAT
1 AAATAATAAAATATATAATTAAAAAATATTAT-T
22152 AAAT-ATAAAATAT-T--TTAAAAAATAATTATT
1 AAATAATAAAATATATAATTAAAAAAT-ATTATT
22182 AAATAATAAAATATATAATTA
1 AAATAATAAAATATATAATTA
22203 TAATATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
30 6 0.14
31 22 0.51
32 5 0.12
34 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAATAATAAAATATATAATTAAAAAATATTATT
Found at i:22212 original size:19 final size:18
Alignment explanation
Indices: 22184--22223 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
22174 TAATTATTAA
* *
22184 ATAATAAAATATATAATT
1 ATAATAAAATAAACAATT
22202 ATAATATAAATAAACAATT
1 ATAATA-AAATAAACAATT
22221 ATA
1 ATA
22224 TTTCATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATAAAATAAACAATT
Found at i:25150 original size:21 final size:22
Alignment explanation
Indices: 25126--25169 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
25116 CATCTAACTT
25126 AAATTAT-AAT-TTAATAATAAA
1 AAATTATAAATATTAAT-ATAAA
25147 AAATTATAAATATTAATATAAA
1 AAATTATAAATATTAATATAAA
25169 A
1 A
25170 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTATAAATATTAATATAAA
Found at i:25169 original size:20 final size:21
Alignment explanation
Indices: 25126--25172 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
25116 CATCTAACTT
*
25126 AAATTATAATTTAATAATAAA
1 AAATTATAATATAATAATAAA
* *
25147 AAATTATAA-ATATTAATATA
1 AAATTATAATATAATAATAAA
25167 AAATTA
1 AAATTA
25173 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTATAATATAATAATAAA
Found at i:26427 original size:2 final size:2
Alignment explanation
Indices: 26420--26448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26410 GCAGGCTTTC
26420 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
26449 GCACACTAAA
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:26515 original size:16 final size:16
Alignment explanation
Indices: 26484--26531 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
26474 TGTTTCATTA
*
26484 TAAAAAAAT-ATGAAT
1 TAAAAAAATAATAAAT
**
26499 TTTAAAAATAATAAAT
1 TAAAAAAATAATAAAT
26515 TAAAAAAATAAGTAAAT
1 TAAAAAAATAA-TAAAT
26532 ACTTTTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 7 0.27
16 14 0.54
17 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (16 bp):
TAAAAAAATAATAAAT
Found at i:27074 original size:18 final size:18
Alignment explanation
Indices: 27053--27104 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 18
27043 AAAGAAATTT
27053 ATTTAATTTATAAAATAA
1 ATTTAATTTATAAAATAA
*
27071 ATTT-A---ATAAGATAA
1 ATTTAATTTATAAAATAA
*
27085 A-TAAATTTATAAAATAA
1 ATTTAATTTATAAAATAA
27102 ATT
1 ATT
27105 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 10
0.67 0.08 0.26
Matches are distributed among these distances:
13 1 0.04
14 10 0.38
17 10 0.38
18 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTTAATTTATAAAATAA
Found at i:27084 original size:14 final size:13
Alignment explanation
Indices: 27057--27104 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
27047 AAATTTATTT
27057 AATTTATAAAATA
1 AATTTATAAAATA
27070 AATTTAATAAGATAAATA
1 AATTT-AT---A-AAATA
27088 AATTTATAAAATA
1 AATTTATAAAATA
27101 AATT
1 AATT
27105 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 14 0.47
14 3 0.10
17 3 0.10
18 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTTATAAAATA
Found at i:27107 original size:18 final size:17
Alignment explanation
Indices: 27065--27126 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 17
27055 TTAATTTATA
*
27065 AAATAAATTTAATAAGAT
1 AAATAAATTT-ATAAAAT
27083 AAATAAATTTATAAAAT
1 AAATAAATTTATAAAAT
27100 AAATTAAAATTTAATTAAAAAT
1 AAA-T-AAATTT-A-T-AAAAT
27122 AAATA
1 AAATA
27127 TATTCTATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 9 0.24
18 11 0.29
19 6 0.16
20 2 0.05
21 2 0.05
22 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATAAATTTATAAAAT
Found at i:27420 original size:20 final size:20
Alignment explanation
Indices: 27386--27423 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27376 AAAAAATATT
27386 TTAATTTTTATATTATTAAA
1 TTAATTTTTATATTATTAAA
27406 TTAATATTTTA-ATTATTA
1 TTAAT-TTTTATATTATTA
27424 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTTTTATATTATTAAA
Found at i:27458 original size:16 final size:18
Alignment explanation
Indices: 27432--27472 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
27422 TATATTTTTT
*
27432 AAAATT-ATAATAAATAAA
1 AAAATTAATAAT-ATTAAA
27450 AAAATTAATAATATTAAA
1 AAAATTAATAATATTAAA
27468 AAAAT
1 AAAAT
27473 ATTTTACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTAATAATATTAAA
Found at i:27499 original size:25 final size:24
Alignment explanation
Indices: 27470--27535 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
27460 ATATTAAAAA
*
27470 AATATTTTACTATCGAT-AAAATTTT
1 AATATTTTA-TAT-AATAAAAATTTT
*
27495 AATATATTATATAATAAAAATTTT
1 AATATTTTATATAATAAAAATTTT
27519 AA-ATTTTATATAA-AAAA
1 AATATTTTATATAATAAAA
27536 TTTAAACCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 13 0.35
25 8 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATTTTATATAATAAAAATTTT
Found at i:27538 original size:21 final size:24
Alignment explanation
Indices: 27487--27535 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
27477 TACTATCGAT
27487 AAAATTTTAATATATTATATAATA
1 AAAATTTTAATATATTATATAATA
*
27511 AAAATTTTAA-ATTTTATATAA-A
1 AAAATTTTAATATATTATATAATA
27533 AAA
1 AAA
27536 TTTAAACCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 10 0.42
24 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTTTAATATATTATATAATA
Found at i:31109 original size:12 final size:12
Alignment explanation
Indices: 31092--31116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31082 TATTTGAAAG
31092 ATCATAACTTAT
1 ATCATAACTTAT
31104 ATCATAACTTAT
1 ATCATAACTTAT
31116 A
1 A
31117 CCTATATTCG
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCATAACTTAT
Found at i:32738 original size:17 final size:17
Alignment explanation
Indices: 32712--32750 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
32702 TTCATGTGTC
*
32712 ATTT-TAAATTAAATTT
1 ATTTATAAATTAAATTA
*
32728 ATTTATAAATTAAGTTA
1 ATTTATAAATTAAATTA
32745 ATTTAT
1 ATTTAT
32751 TTTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTATAAATTAAATTA
Found at i:34732 original size:21 final size:23
Alignment explanation
Indices: 34688--34732 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
34678 CGATCATAAC
* *
34688 ATAAAATTTTTAATTTTATTTAT
1 ATAAAATTTTAAATTTTATATAT
34711 ATAAAA-TTTAAATTTTA-ATAT
1 ATAAAATTTTAAATTTTATATAT
34732 A
1 A
34733 GGCTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAAAATTTTAAATTTTATATAT
Found at i:35072 original size:2 final size:2
Alignment explanation
Indices: 35065--35096 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35055 GTAACGTGGG
35065 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
35097 GGATTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35459 original size:6 final size:7
Alignment explanation
Indices: 35450--35515 Score: 50
Period size: 6 Copynumber: 9.4 Consensus size: 7
35440 TCAAATGCCC
35450 TTATAT-
1 TTATATA
35456 TTATATA
1 TTATATA
35463 TTAT-TA
1 TTATATA
35469 TTATATCCA
1 TTATAT--A
**
35478 ACATATA
1 TTATATA
35485 -TATATA
1 TTATATA
35491 -TATATA
1 TTATATA
35497 TATATATA
1 T-TATATA
35505 TATATATA
1 T-TATATA
35513 TTA
1 TTA
35516 AGATTTGAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
6 23 0.45
7 8 0.16
8 15 0.29
9 5 0.10
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (7 bp):
TTATATA
Found at i:35487 original size:2 final size:2
Alignment explanation
Indices: 35480--35513 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35470 TATATCCAAC
35480 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
35514 TAAGATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36767 original size:35 final size:35
Alignment explanation
Indices: 36727--36845 Score: 98
Period size: 35 Copynumber: 3.2 Consensus size: 35
36717 AATATTATAT
36727 TTATATAAATTTTTGTTATAATTATATTAAAAATATTA
1 TTATATAAATTTTTGTTATAATTATATT-AAAA-A-TA
* * ** *
36765 TATATTTTATAAATTTTAGTATGTTAAAAATATT--ATATA
1 T-TA---TATAAATTTTTGT-T-ATAATTATATTAAAAATA
36804 TTATATAAATTTTTGTTATAATTATATTAAAAATA
1 TTATATAAATTTTTGTTATAATTATATTAAAAATA
36839 TTATATA
1 TTATATA
36846 TTATATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
33 8 0.13
34 1 0.02
35 23 0.37
38 3 0.05
39 5 0.08
40 1 0.02
41 1 0.02
42 12 0.19
43 1 0.02
44 8 0.13
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TTATATAAATTTTTGTTATAATTATATTAAAAATA
Found at i:36781 original size:42 final size:42
Alignment explanation
Indices: 36717--36858 Score: 201
Period size: 42 Copynumber: 3.6 Consensus size: 42
36707 AACGTGTATT
36717 AATATTATAT-TTATATAAATTTTTGTTATAATTATATTAAA
1 AATATTATATATTATATAAATTTTTGTTATAATTATATTAAA
* * *
36758 AATATTATATATTTTATAAA----T-TT-T-AGTATGTTAAA
1 AATATTATATATTATATAAATTTTTGTTATAATTATATTAAA
36793 AATATTATATATTATATAAATTTTTGTTATAATTATATTAAA
1 AATATTATATATTATATAAATTTTTGTTATAATTATATTAAA
36835 AATATTATATATTATATAAATTTT
1 AATATTATATATTATATAAATTTT
36859 AGTATGTTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
35 28 0.32
36 1 0.01
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 11 0.13
42 41 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (42 bp):
AATATTATATATTATATAAATTTTTGTTATAATTATATTAAA
Found at i:36837 original size:77 final size:76
Alignment explanation
Indices: 36717--36875 Score: 300
Period size: 77 Copynumber: 2.1 Consensus size: 76
36707 AACGTGTATT
*
36717 AATATTATATTTATATAAATTTTTGTTATAATTATATTAAAAATATTATATATTTTATAAATTTT
1 AATATTATATTTATATAAATTTTTGTTATAATTATATTAAAAATATTATATATTATATAAATTTT
36782 AGTATGTTAAA
66 AGTATGTTAAA
36793 AATATTATATATTATATAAATTTTTGTTATAATTATATTAAAAATATTATATATTATATAAATTT
1 AATATTATAT-TTATATAAATTTTTGTTATAATTATATTAAAAATATTATATATTATATAAATTT
36858 TAGTATGTTAAA
65 TAGTATGTTAAA
36870 AATATT
1 AATATT
36876 TTAATAAATT
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
76 10 0.12
77 71 0.88
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (76 bp):
AATATTATATTTATATAAATTTTTGTTATAATTATATTAAAAATATTATATATTATATAAATTTT
AGTATGTTAAA
Found at i:38617 original size:21 final size:20
Alignment explanation
Indices: 38592--38633 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
38582 AATATTTTTT
38592 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAA-ATA
*
38613 TAAATATTTATATAAAAATA
1 TAAATATTAATATAAAAATA
38633 T
1 T
38634 TTTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:40117 original size:2 final size:2
Alignment explanation
Indices: 40110--40143 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
40100 GAAAGTTGAA
*
40110 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
40144 GAAAAGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40587 original size:14 final size:14
Alignment explanation
Indices: 40558--40596 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
40548 CGGGTTTTCA
*
40558 TAAAAATATGTATAT
1 TAAATATAT-TATAT
40573 TAAATATATTATAT
1 TAAATATATTATAT
*
40587 TAATTATATT
1 TAAATATATT
40597 TAAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TAAATATATTATAT
Found at i:40745 original size:28 final size:29
Alignment explanation
Indices: 40689--40760 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
40679 ATCACATGAG
*
40689 ATAAAATAT-AAATA-TTTTAAAATTTTT
1 ATAAAATATAAAATATTTTTAAAATTATT
40716 AT-AAATATAAAATATTTTTAAAATTATT
1 ATAAAATATAAAATATTTTTAAAATTATT
40744 ATAAAATAATAAAATAT
1 ATAAAAT-ATAAAATAT
40761 ATAATATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 6 0.15
27 7 0.17
28 14 0.35
29 4 0.10
30 9 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATAAAATATAAAATATTTTTAAAATTATT
Found at i:41420 original size:16 final size:16
Alignment explanation
Indices: 41399--41429 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41389 TGGTACGATA
*
41399 AAAAAATTTAAAAAAT
1 AAAAAATTGAAAAAAT
41415 AAAAAATTGAAAAAA
1 AAAAAATTGAAAAAA
41430 AGTGAGAAAG
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:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAATTGAAAAAAT
Found at i:41514 original size:48 final size:47
Alignment explanation
Indices: 41436--41541 Score: 110
Period size: 48 Copynumber: 2.2 Consensus size: 47
41426 AAAAAGTGAG
* ** *
41436 AAAGATAAAAGAAATATTTTTTATTTTTATTAGTTTATT-TGGTTTAAAA
1 AAAG-TAAAAAAAATATTTTTTATACTTATTA-TTTATTAT-GATTAAAA
*
41485 AAAGTAAAAAAAATATTTTTT-TCACTTATTATTTGTTATGATTAAAA
1 AAAGTAAAAAAAATATTTTTTAT-ACTTATTATTTATTATGATTAAAA
41532 AAA-TAAAAAA
1 AAAGTAAAAAA
41542 TTATTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 7 0.14
47 16 0.32
48 23 0.46
49 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (47 bp):
AAAGTAAAAAAAATATTTTTTATACTTATTATTTATTATGATTAAAA
Found at i:41739 original size:31 final size:29
Alignment explanation
Indices: 41703--41775 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 29
41693 TATATATATA
41703 TTTTTTACTTTTTCATCCTCTCTTTTTTTTT
1 TTTTTTACTTTTTCATCCTCTC--TTTTTTT
41734 TTTTTTACTTTTTCATCCTCTCTTTTTTT
1 TTTTTTACTTTTTCATCCTCTCTTTTTTT
41763 TTTTTTACTTTTT
1 TTTTTTACTTTTT
41776 TTATCTTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 20 0.48
31 22 0.52
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTTTACTTTTTCATCCTCTCTTTTTTT
Found at i:41754 original size:29 final size:31
Alignment explanation
Indices: 41703--41775 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
41693 TATATATATA
*
41703 TTTTTTACTTTTTCATCCTCTCTTTTTTTTT
1 TTTTTTACTTTTTCATCCTCTCTCTTTTTTT
41734 TTTTTTACTTTTTCAT-C-CTCTCTTTTTTT
1 TTTTTTACTTTTTCATCCTCTCTCTTTTTTT
41763 TTTTTTACTTTTT
1 TTTTTTACTTTTT
41776 TTATCTTACC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 24 0.59
30 1 0.02
31 16 0.39
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTTTACTTTTTCATCCTCTCTCTTTTTTT
Found at i:42186 original size:13 final size:12
Alignment explanation
Indices: 42168--42203 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
42158 TAATATGTTA
42168 ATATATTTATATT
1 ATATATTTAT-TT
42181 ATATATTTATTT
1 ATATATTTATTT
42193 -TATATTTATTT
1 ATATATTTATTT
42204 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 2 0.09
13 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATATTTATTT
Found at i:43388 original size:217 final size:214
Alignment explanation
Indices: 43000--43432 Score: 516
Period size: 217 Copynumber: 2.0 Consensus size: 214
42990 AAAGTGCCTG
* * * * * *
43000 GCCAATTACCGTGGGCTTTTGTGTATGGTGTTGTGAAGAAATATGAATGACAAACCTTACCATCT
1 GCCAATTACCATGGGCTTTTGTCTATGATGTTATGAAGAAAAATGAACGACAAACCTTACCATCT
* *
43065 ACTTTAAAAGAAGATAGGCAACAGTCTCACTGACCAAGATCAATTTCTGAGCTACAAGAATTCAC
66 ACTTTAAAAGAAGATAGGCAACAGTCTCACTAACCAAGATCAATTTCTGAGCTACAAGAATGCAC
* * * ** * **
43130 CATGTATGTTAAGCTGGGTAGTAAGCACTCTAAGGGCAGCTCATGTCGATGAAAGTACTTTCAGG
131 CA-GCATGTTAAGCTAGGTAGTAAGCACTCCAACAGCAGCTCATATCGATGAAAGTACTTTCAAA
43195 TG-TCAGAAAAGGCTCACATA
195 TGCT-AGAAAAGGCTCACATA
* * *
43215 GCCAATTACCATGGGC-TTTGTCTATGATTTTATGAAGAAAAATGAACGAGAAGCCTTACCATCT
1 GCCAATTACCATGGGCTTTTGTCTATGATGTTATGAAGAAAAATGAACGACAAACCTTACCATCT
* * **
43279 ACTTTAAAAGAATATAGTCAGCAACA-TCTTCACTAACCAAGATCAATTTCTGAGCTGCCTGAAT
66 ACTTTAAAAGAAGATAG---GCAACAGTC-TCACTAACCAAGATCAATTTCTGAGCTACAAGAAT
* * *
43343 GCACTGCA-CATTTTAAGCTAGGTAGTAAGC-CATCCAACAGCAGCTCATATTGATGAAAGTATT
127 GCAC--CAGCATGTTAAGCTAGGTAGTAAGCAC-TCCAACAGCAGCTCATATCGATGAAAGTACT
43406 TTCAAATGCTAGAAAAGGCTCACATA
189 TTCAAATGCTAGAAAAGGCTCACATA
43432 G
1 G
43433 ACAAAGGTAA
Statistics
Matches: 184, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
214 56 0.30
215 15 0.08
216 3 0.02
217 107 0.58
218 1 0.01
219 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (214 bp):
GCCAATTACCATGGGCTTTTGTCTATGATGTTATGAAGAAAAATGAACGACAAACCTTACCATCT
ACTTTAAAAGAAGATAGGCAACAGTCTCACTAACCAAGATCAATTTCTGAGCTACAAGAATGCAC
CAGCATGTTAAGCTAGGTAGTAAGCACTCCAACAGCAGCTCATATCGATGAAAGTACTTTCAAAT
GCTAGAAAAGGCTCACATA
Found at i:45491 original size:16 final size:16
Alignment explanation
Indices: 45470--45664 Score: 74
Period size: 16 Copynumber: 12.0 Consensus size: 16
45460 CTCGTATCAA
45470 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
45486 TTTAAATTT-AATTGAGT
1 TTTAAATTTAAATT-A-T
*
45503 CGAATTGAATATTTAAATTA-
1 ----TTTAA-ATTTAAATTAT
*
45523 ATTAAATTTAAAATTA-
1 TTTAAATTT-AAATTAT
* *
45539 ATTAATTTTAATAATTAAT
1 TTTAAATTT-A-AATT-AT
*
45558 TTTATCGAGTTT-AATTAT
1 TTTA---AATTTAAATTAT
* *
45576 TTTAAA-TTGAATCAT
1 TTTAAATTTAAATTAT
45591 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
*
45607 TTTAAGTTTAAGA-TA-
1 TTTAAATTTAA-ATTAT
*
45622 --T---TTT-GATTAT
1 TTTAAATTTAAATTAT
45632 TTTAAATTTAAATTATT
1 TTTAAATTTAAATTA-T
45649 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
45665 AAATTTTTTA
Statistics
Matches: 139, Mismatches: 13, Indels: 54
0.67 0.06 0.26
Matches are distributed among these distances:
8 1 0.01
9 2 0.01
10 3 0.02
12 1 0.01
13 1 0.01
14 2 0.01
15 23 0.17
16 53 0.38
17 22 0.16
18 7 0.05
19 7 0.05
21 4 0.03
22 9 0.06
23 4 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:45498 original size:15 final size:15
Alignment explanation
Indices: 45470--45664 Score: 86
Period size: 15 Copynumber: 13.0 Consensus size: 15
45460 CTCGTATCAA
45470 TTTAAATTTAAATTAT
1 TTTAAATTT-AATTAT
45486 TTTAAATTTAATTGA-
1 TTTAAATTTAATT-AT
* ** *
45501 GTCGAATTGAA-TA-
1 TTTAAATTTAATTAT
*
45514 TTTAAA-TTAATTAAA
1 TTTAAATTTAATT-AT
*
45529 TTTAAAATTAATTAAT
1 TTTAAATTTAATT-AT
*
45545 TTTAATAATTAATT-T
1 TTTAA-ATTTAATTAT
** *
45560 TATCGAGTTTAATTAT
1 T-TTAAATTTAATTAT
* *
45576 TTTAAATTGAATCAT
1 TTTAAATTTAATTAT
45591 TTTAAATTTAAATTAT
1 TTTAAATTT-AATTAT
* *
45607 TTTAAGTTTAA-GA-
1 TTTAAATTTAATTAT
* *
45620 --T-ATTTTGATTAT
1 TTTAAATTTAATTAT
45632 TTTAAATTTAAATTATT
1 TTTAAATTT-AATTA-T
45649 TTTAAATTTAAATTAT
1 TTTAAATTT-AATTAT
45665 AAATTTTTTA
Statistics
Matches: 136, Mismatches: 27, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
10 5 0.04
11 2 0.01
12 3 0.02
13 5 0.04
14 4 0.03
15 48 0.35
16 45 0.33
17 24 0.18
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (15 bp):
TTTAAATTTAATTAT
Found at i:45555 original size:13 final size:13
Alignment explanation
Indices: 45537--45561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45527 AATTTAAAAT
45537 TAATTAATTTTAA
1 TAATTAATTTTAA
45550 TAATTAATTTTA
1 TAATTAATTTTA
45562 TCGAGTTTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTAATTTTAA
Found at i:45630 original size:25 final size:25
Alignment explanation
Indices: 45602--45693 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
45592 TTAAATTTAA
*
45602 ATTATTTTAAGTTTAAGA-TATTTTG
1 ATTATTTTAAATTTAA-ATTATTTTG
45627 ATTATTTTAAATTTAAATTATTTT-
1 ATTATTTTAAATTTAAATTATTTTG
* * *
45651 -TAAATTTAAATTATAAATT-TTTTA
1 ATTATTTTAAATT-TAAATTATTTTG
**
45675 ATTAAATTAAATTTAAATT
1 ATTATTTTAAATTTAAATT
45694 TAATTGAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
23 14 0.24
24 13 0.22
25 31 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
ATTATTTTAAATTTAAATTATTTTG
Found at i:45653 original size:17 final size:17
Alignment explanation
Indices: 45627--45664 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
45617 AGATATTTTG
45627 ATTA-TTTTAAATTTAA
1 ATTATTTTTAAATTTAA
45643 ATTATTTTTAAATTTAA
1 ATTATTTTTAAATTTAA
45660 ATTAT
1 ATTAT
45665 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTTTAAATTTAA
Found at i:45669 original size:7 final size:6
Alignment explanation
Indices: 45632--45696 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
45622 TTTTGATTAT
** *
45632 TTTAAA TTTAAA -TTATT TTTAAA TTTAAA TTATAAA TTTTTTAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA --TTTAAA TTTAAA
45681 -TTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
45697 TTGAATTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 12 0.25
6 27 0.56
7 4 0.08
8 3 0.06
9 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:47633 original size:23 final size:21
Alignment explanation
Indices: 47603--47646 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
47593 TTAAAATTTA
*
47603 TTTTTAATTAATATTTATATAT
1 TTTTTAATTAA-ATTTAAATAT
47625 TTTTATAATTAAATTTAAATAT
1 TTTT-TAATTAAATTTAAATAT
47647 AAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTAATTAAATTTAAATAT
Found at i:47640 original size:22 final size:22
Alignment explanation
Indices: 47589--47646 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
47579 TTATTTAAAA
* *
47589 AATATTAAAATTTATTTTTAATT
1 AATATTTAAATAT-TTTTTAATT
*
47612 AATATTTATATATTTTTATAATT
1 AATATTTAAATATTTTT-TAATT
47635 AA-ATTTAAATAT
1 AATATTTAAATAT
47647 AAAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTTAAATATTTTTTAATT
Found at i:48783 original size:3 final size:3
Alignment explanation
Indices: 48775--48799 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48765 CTCATTAGGG
48775 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
48800 AACTTTAGAG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:49110 original size:25 final size:25
Alignment explanation
Indices: 49048--49115 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 25
49038 TGAACTCTTT
*
49048 TTTA-ATTATATATTGTA-TATTATT
1 TTTATATTATATA-TGTATTATTATA
49072 TTTATATT-TAATATGTATTATGTA-A
1 TTTATATTAT-ATATGTATTAT-TATA
49097 TTTATATTATATATAGTAT
1 TTTATATTATATAT-GTAT
49116 AATATTACGT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 9 0.24
25 21 0.57
26 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (25 bp):
TTTATATTATATATGTATTATTATA
Found at i:49540 original size:22 final size:21
Alignment explanation
Indices: 49512--49574 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
49502 ATAACTTTTC
49512 AAAAACTCTTTAAATATATTAA
1 AAAAAC-CTTTAAATATATTAA
* *
49534 AAAAA-CTTAAAAAATATTAA
1 AAAAACCTTTAAATATATTAA
49554 AAATAACCGTGTTAAATATAT
1 AAA-AACC-T-TTAAATATAT
49575 ATATCTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 6 0.18
23 1 0.03
24 8 0.24
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAAACCTTTAAATATATTAA
Found at i:52220 original size:2 final size:2
Alignment explanation
Indices: 52213--52242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52203 TGATAATTGG
52213 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
52243 CACACACATC
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:58925 original size:28 final size:26
Alignment explanation
Indices: 58865--58917 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
58855 AATGAATCTT
* *
58865 ATTATAATTTATTATAATAAATATTA
1 ATTATAATTTAATATAATAAAAATTA
58891 ATTATAATATTAATATAA-AAAAATTA
1 ATTATAAT-TTAATATAATAAAAATTA
58917 A
1 A
58918 AATTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTATAATTTAATATAATAAAAATTA
Found at i:59206 original size:20 final size:19
Alignment explanation
Indices: 59178--59223 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
59168 GTTTAGTTAA
59178 AAAAATTTTAATA-CAAAAT
1 AAAAATTTTAATATC-AAAT
59197 AAATAATTTTAATATCAAAT
1 AAA-AATTTTAATATCAAAT
59217 AAAAATT
1 AAAAATT
59224 AAATATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTTTAATATCAAAT
Found at i:59256 original size:17 final size:17
Alignment explanation
Indices: 59236--59274 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
59226 ATATAGTTAG
59236 TATTTAATAGAAAT-ATA
1 TATTTAAT-GAAATGATA
*
59253 TATTTAATTAAATGATA
1 TATTTAATGAAATGATA
59270 TATTT
1 TATTT
59275 TTTAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TATTTAATGAAATGATA
Found at i:61854 original size:2 final size:2
Alignment explanation
Indices: 61847--61884 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
61837 AAACTGAATA
*
61847 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61885 GCATATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64008 original size:20 final size:21
Alignment explanation
Indices: 63967--64019 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
63957 GAAATTTGAT
*
63967 ATAA-AAATATAAATTAATAA
1 ATAATAAATATAAATTAAAAA
63987 AT-ATAAATATAAGA-TAAAAA
1 ATAATAAATATAA-ATTAAAAA
*
64007 ATAATTAATATAA
1 ATAATAAATATAA
64020 TATGTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 17 0.61
21 10 0.36
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAATAAATATAAATTAAAAA
Found at i:64909 original size:29 final size:28
Alignment explanation
Indices: 64891--64962 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
64881 AAAATATGTA
64891 TATAT-TTATATTAATTTTTTAAATTATAT
1 TATATATTA-ATTAATTTTTTAAA-TATAT
*
64920 TATATATTAATT-ATTTTTTATATTATAT
1 TATATATTAATTAATTTTTTA-AATATAT
*
64948 TTTATTATATAATTA
1 TATA-TAT-TAATTA
64963 TTTCGTAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
28 16 0.44
29 12 0.33
30 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TATATATTAATTAATTTTTTAAATATAT
Found at i:64924 original size:23 final size:22
Alignment explanation
Indices: 64891--64948 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
64881 AAAATATGTA
64891 TATATTTATATTAATT-TTTTAAAT
1 TATATTTATATTAATTATTTT---T
64915 TATATTATATATTAATTATTTTT
1 TATATT-TATATTAATTATTTTT
64938 TATA-TTATATT
1 TATATTTATATT
64949 TTATTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 5 0.16
24 6 0.19
25 10 0.31
26 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTTATATTAATTATTTTT
Found at i:64927 original size:25 final size:23
Alignment explanation
Indices: 64891--64955 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
64881 AAAATATGTA
64891 TATATT-TATATTAATT-TTTTAAAT
1 TATATTATATATTAATTATTTT---T
64915 TATATTATATATTAATTATTTTT
1 TATATTATATATTAATTATTTTT
*
64938 TATATTATAT-TTTATTAT
1 TATATTATATATTAATTAT
64956 ATAATTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 7 0.18
23 11 0.29
24 6 0.16
25 10 0.26
26 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTATATATTAATTATTTTT
Found at i:64963 original size:23 final size:23
Alignment explanation
Indices: 64889--64963 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 23
64879 TTAAAATATG
*
64889 TATATATTTATATTA-A-TTT-T
1 TATATAATTATATTATATTTTAT
*
64909 T-TA-AATTATATTATATATTAAT
1 TATATAATTATATTATAT-TTTAT
**
64931 TAT-TTTTTATATTATATTTTAT
1 TATATAATTATATTATATTTTAT
64953 TATATAATTAT
1 TATATAATTAT
64964 TTCGTAAGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
18 9 0.22
19 3 0.07
20 1 0.02
21 2 0.05
22 9 0.22
23 17 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATAATTATATTATATTTTAT
Found at i:64963 original size:30 final size:28
Alignment explanation
Indices: 64877--64965 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 28
64867 TGTGTCAAAA
64877 TTTTAAA--ATATGTATATATTTATATTAATT
1 TTTTAAATTATAT-TATATA-TTA-ATT-ATT
64907 TTTTAAATTATATTATATATTAATTATT
1 TTTTAAATTATATTATATATTAATTATT
* *
64935 TTTTATATTATATTTTATTATATAATTATT
1 TTTTAAATTATATTATA-TAT-TAATTATT
64965 T
1 T
64966 CGTAAGGTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
28 18 0.34
29 6 0.11
30 19 0.36
31 6 0.11
32 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTAAATTATATTATATATTAATTATT
Found at i:65481 original size:130 final size:131
Alignment explanation
Indices: 65329--65563 Score: 302
Period size: 132 Copynumber: 1.8 Consensus size: 131
65319 TTTTTTTAAC
** * *
65329 CCAATAATGTATATTTTTTAATAGAA-AA-A-ATGGGTATTTGAGAT-TGAAGTAATGAATTTCA
1 CCAATAATGTATATTTTTTAATA-AACAATAGAAAGGTATTTGAAATAAG-AGTAATGAATTTCA
*
65390 AT-TAGTCATCAATTTCGTCCCATTTTCATTTAAATGTGCCAATTATATGTCAAGTAATTCTTTT
64 ATAT-GTCATCAATTT-GTCCCATTTTCACTTAAATGTGCCAATTATATGTCAAGTAATTCTTTT
65454 AGGAT
127 AGGAT
*
65459 CCAATAATGTA-ATTTTTTTAATAAACAATAGAAAGTTATTTGAAATAAGAGTAATGAATTTCAA
1 CCAATAATGTATA-TTTTTTAATAAACAATAGAAAGGTATTTGAAATAAGAGTAATGAATTTCAA
* * *
65523 TATGTGATCAATTTGTCCTATTTTCACTTATATGTGCCAAT
65 TATGTCATCAATTTGTCCCATTTTCACTTAAATGTGCCAAT
65564 GATAGGAGAC
Statistics
Matches: 90, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
129 3 0.03
130 23 0.26
131 25 0.28
132 37 0.41
133 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (131 bp):
CCAATAATGTATATTTTTTAATAAACAATAGAAAGGTATTTGAAATAAGAGTAATGAATTTCAAT
ATGTCATCAATTTGTCCCATTTTCACTTAAATGTGCCAATTATATGTCAAGTAATTCTTTTAGGA
T
Found at i:66497 original size:34 final size:33
Alignment explanation
Indices: 66459--66530 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
66449 TTTTATTTTT
*
66459 AAATTAAAGATTTT-TAAAAAATAAAATAATAAAA
1 AAATT-AAGATTTTAAAAAAAATAAAA-AATAAAA
**
66493 AAATTATTATTTTAAAAAAAATAAAAAATAAAA
1 AAATTAAGATTTTAAAAAAAATAAAAAATAAAA
66526 AAATT
1 AAATT
66531 GATAATGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
AAATTAAGATTTTAAAAAAAATAAAAAATAAAA
Done.