Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold392_ERROPOS132712
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: 132712
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:6834 original size:40 final size:40
Alignment explanation
Indices: 6790--7012 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
6780 GCTCCTCGTT
* * *
6790 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
*
6830 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
*
6870 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
*
6909 CAAATGCCTTCGGG-CTTAACCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
** * * *
6948 CAAA-GCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TCGCA
*
6988 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7013 CATCATTCAA
Statistics
Matches: 164, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
37 2 0.01
38 17 0.10
39 54 0.33
40 88 0.54
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
Found at i:6918 original size:79 final size:79
Alignment explanation
Indices: 6790--7012 Score: 285
Period size: 79 Copynumber: 2.8 Consensus size: 79
6780 GCTCCTCGTT
* *
6790 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
6855 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
6870 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTATCTCGCACAAATGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAACCCGG
*
6933 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * *
6948 CAAA-GCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAACCC
7010 GGA
63 GGA
7013 CATCATTCAA
Statistics
Matches: 127, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
76 3 0.02
77 16 0.13
78 41 0.32
79 43 0.34
80 24 0.19
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:9635 original size:27 final size:27
Alignment explanation
Indices: 9618--9824 Score: 216
Period size: 27 Copynumber: 7.6 Consensus size: 27
9608 ATATTAAGTC
9618 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
9645 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
9673 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
9700 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
9728 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
9755 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * * *
9783 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
*
9810 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
9825 GCACAATTTA
Statistics
Matches: 173, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
27 93 0.54
28 80 0.46
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:9702 original size:55 final size:55
Alignment explanation
Indices: 9618--9824 Score: 369
Period size: 55 Copynumber: 3.8 Consensus size: 55
9608 ATATTAAGTC
* * * *
9618 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
9673 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
9728 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
9783 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
9825 GCACAATTTA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:14221 original size:59 final size:60
Alignment explanation
Indices: 14138--14339 Score: 162
Period size: 62 Copynumber: 3.2 Consensus size: 60
14128 AATCACTTTA
* * * *
14138 TTATTAAATTGATATAATACTTATC-AAGAAAAATATTATATTAAATTTAATATTAAATC
1 TTATTAAATTAATAGAATACTTATCTAAGAAAAAGATTAAATTAAATTTAATATTAAATC
* *
14197 TTATTAAATTAATAGAATATTTATCTATAAGATAAAGATTAAATTAAATTTAATATTAAGATAAT
1 TTATTAAATTAATAGAATACTTATC--TAAGAAAAAGATTAAATTAAATTTAATATT---A-AAT
14262 CAC
60 --C
* * *
14265 TTTAATATTAAATTAATAAAATAC-TAT-TAAG-ATAAGTATTAAATTAAATTAAATATTAAATC
1 --T--TATTAAATTAATAGAATACTTATCTAAGAAAAAG-ATTAAATTAAATTTAATATTAAATC
*
14327 -TATTAAAATAATA
1 TTATTAAATTAATA
14340 TTATTTTTGG
Statistics
Matches: 117, Mismatches: 12, Indels: 30
0.74 0.08 0.19
Matches are distributed among these distances:
57 12 0.10
59 22 0.19
62 27 0.23
64 3 0.03
65 2 0.02
66 3 0.03
67 3 0.03
68 24 0.21
70 1 0.01
71 3 0.03
72 17 0.15
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (60 bp):
TTATTAAATTAATAGAATACTTATCTAAGAAAAAGATTAAATTAAATTTAATATTAAATC
Found at i:14281 original size:20 final size:18
Alignment explanation
Indices: 14234--14282 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
14224 TAAGATAAAG
14234 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
14251 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
14271 ATTAAATTAATA
1 ATTAAATTAATA
14283 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:14339 original size:68 final size:71
Alignment explanation
Indices: 14198--14342 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 71
14188 TATTAAATCT
*
14198 TATTAAATTAATAGAATATTTATCTATAAGATAAAGATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAGAATA-TTATCTATAAGATAAAGATTAAATTAAATTAAATATTAAGATAATC
***
14263 ACTTTAA
65 AAAATAA
*
14270 TATTAAATTAATA-AA-A-TA-CTATTAAGAT-AAGTATTAAATTAAATTAAATATTAA-ATCTA
1 TATTAAATTAATAGAATATTATCTA-TAAGATAAAG-ATTAAATTAAATTAAATATTAAGAT-AA
*
14329 TTAAAATAA
63 TCAAAATAA
14338 TATTA
1 TATTA
14343 TTTTTGGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
67 8 0.12
68 40 0.62
70 1 0.02
71 2 0.03
72 13 0.20
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (71 bp):
TATTAAATTAATAGAATATTATCTATAAGATAAAGATTAAATTAAATTAAATATTAAGATAATCA
AAATAA
Found at i:26733 original size:93 final size:93
Alignment explanation
Indices: 26621--26792 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
26611 CGCCCATAAG
* *
26621 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
26686 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
26714 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
26779 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
26793 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:26789 original size:46 final size:46
Alignment explanation
Indices: 26614--26789 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
26604 TGTAACCCGC
* * *
26614 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
26660 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
26710 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
26753 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
26790 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:34284 original size:93 final size:93
Alignment explanation
Indices: 34172--34343 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
34162 CGCCCATAAG
* *
34172 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
34237 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
34265 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
34330 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
34344 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:34340 original size:46 final size:46
Alignment explanation
Indices: 34165--34340 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
34155 TGTAACCCGC
* * *
34165 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
34211 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
34261 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
34304 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
34341 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:37693 original size:37 final size:38
Alignment explanation
Indices: 37570--37693 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 38
37560 GTTGAGCATC
37570 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAATG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTT--ATG-G-ATG
* * * *
37612 TCCGAACTCGTTGAGTTGAGTCCG-GTTCAATAGATGCATC
1 --CGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATG
37652 CGAAC-CGTTGAGTTGAGTCCGAGTTCACTTATGGATG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
37689 CGAAC
1 CGAAC
37694 GCCCGAGCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 26 0.37
38 11 0.16
40 2 0.03
42 3 0.04
43 6 0.09
44 22 0.31
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (38 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
Found at i:37715 original size:83 final size:83
Alignment explanation
Indices: 37565--37723 Score: 259
Period size: 83 Copynumber: 1.9 Consensus size: 83
37555 GGATGGTTGA
* *
37565 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAATGTCCGAACTCGTTGAGTTG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAACGCCCGAACTCGTTGAGTTG
37630 AGTCCG-GTTCAATAGAT
66 AGTCCGAGTTCAATAGAT
*
37647 GCATCCGAAC-CGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-T-TGGATGCGAACGCCCGAACTCGTTGAGT
37711 TGAGTCCGAGTTC
64 TGAGTCCGAGTTC
37724 GCTTATGGGC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
81 23 0.32
82 11 0.15
83 33 0.46
84 4 0.06
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.28
Consensus pattern (83 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCAATAGAT
Found at i:45061 original size:46 final size:46
Alignment explanation
Indices: 45009--45136 Score: 211
Period size: 46 Copynumber: 2.8 Consensus size: 46
44999 GGTTGAGCAT
* *
45009 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
45055 CTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
45101 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45137 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:49730 original size:42 final size:43
Alignment explanation
Indices: 49653--49783 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 43
49643 TCTTACTTGT
*
49653 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATATCGATGCCACTGTCCCAAACAGGGTCTTACACGA
* * *
49696 AATCAAATA-CGATGCCGA-TGTTCCAAACATGGTCTTACACATA
1 AATCAAATATCGATGCC-ACTGTCCCAAACAGGGTCTTACAC-GA
* * *
49739 AATCTCAA-ATCGATGCCAAC-GTCCCAGA-TGTGGTCTTACACGA
1 AATC-AAATATCGATGCC-ACTGTCCCAAACAG-GGTCTTACACGA
49782 AA
1 AA
49784 ACACATATTG
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
42 26 0.37
43 19 0.27
44 26 0.37
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
AATCAAATATCGATGCCACTGTCCCAAACAGGGTCTTACACGA
Found at i:52559 original size:18 final size:18
Alignment explanation
Indices: 52536--52571 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52526 AAAAGATTGA
52536 AACAAAATTGAGAGTAAT
1 AACAAAATTGAGAGTAAT
52554 AACAAAATTGAGAGTAAT
1 AACAAAATTGAGAGTAAT
52572 CCACCTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (18 bp):
AACAAAATTGAGAGTAAT
Found at i:54523 original size:52 final size:52
Alignment explanation
Indices: 54444--54550 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
54434 AAGTTCTTGT
* *
54444 ATGGATTAAAAGTATTTTTATATGTTAAATGTGTGCCTATTGGTTTGTTACC
1 ATGGATTAAAAGTATTTTTATACGTTAAATGTGTGCCTATTGGTTTGCTACC
*
54496 ATGGATTAAAAGTATTTTTATACGTTAAATGTGTGCCTATTTGTTTGCTACC
1 ATGGATTAAAAGTATTTTTATACGTTAAATGTGTGCCTATTGGTTTGCTACC
54548 ATG
1 ATG
54551 TTGGCATTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (52 bp):
ATGGATTAAAAGTATTTTTATACGTTAAATGTGTGCCTATTGGTTTGCTACC
Found at i:59002 original size:62 final size:62
Alignment explanation
Indices: 58836--59015 Score: 179
Period size: 62 Copynumber: 2.9 Consensus size: 62
58826 TTGGTCTAAT
** * * * * *
58836 AACAAATTTAGCTATCTAATATTTAC-ACATTCTATCAA-TTTGATTCTAAATCT-AAAAAATTT
1 AACAAATTTAGCCCTC-AATATTTACAAAATT-TATCAACTTAG-TTATAATTCTAAAAAAATTC
* * ** *
58898 AACAAATTTAGCCCTCAATGTTTACAAAATTTTTCATTTTAGTCTA-AGTTCTAAAAAAATTC
1 AACAAATTTAGCCCTCAATATTTACAAAATTTATCAACTTAGT-TATAATTCTAAAAAAATTC
*
58960 AATAAATTTAGCCCTCAATATTTACAAAATTTATCAACTTAGTTATAATTCTAAAA
1 AACAAATTTAGCCCTCAATATTTACAAAATTTATCAACTTAGTTATAATTCTAAAA
59016 TTTTCAAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
61 19 0.20
62 77 0.80
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAATATTTACAAAATTTATCAACTTAGTTATAATTCTAAAAAAATTC
Found at i:59287 original size:24 final size:25
Alignment explanation
Indices: 59246--59292 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
59236 ATTAAATTCC
*
59246 TATAAAAAATATTTTTTTAAAGTAT
1 TATAAAAAATATTATTTTAAAGTAT
* *
59271 TATAAAACA-ATTATTTTGAAGT
1 TATAAAAAATATTATTTTAAAGT
59293 TTTTTTCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
TATAAAAAATATTATTTTAAAGTAT
Found at i:62242 original size:18 final size:19
Alignment explanation
Indices: 62205--62243 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
62195 CAAAAAAGTA
* *
62205 CAAACTCTCAATTGAAAAC
1 CAAAATCTCAAATGAAAAC
62224 CAAAATCTCAAAT-AAAAC
1 CAAAATCTCAAATGAAAAC
62242 CA
1 CA
62244 TAATTAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.18
Consensus pattern (19 bp):
CAAAATCTCAAATGAAAAC
Found at i:64911 original size:20 final size:20
Alignment explanation
Indices: 64886--64923 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
64876 CAACACTCTT
64886 CCCCCAGGATCCATTTCAAG
1 CCCCCAGGATCCATTTCAAG
64906 CCCCCAGGATCCATTTCA
1 CCCCCAGGATCCATTTCA
64924 GGAAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (20 bp):
CCCCCAGGATCCATTTCAAG
Found at i:66503 original size:26 final size:27
Alignment explanation
Indices: 66466--66520 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
66456 CCGCAGCCAA
66466 TTCAAGATCATGCATTGGATAATTCCC
1 TTCAAGATCATGCATTGGATAATTCCC
*
66493 TTCAA-ATCATGCGTTGGATAATTCCC
1 TTCAAGATCATGCATTGGATAATTCCC
66519 TT
1 TT
66521 TATGTGTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (27 bp):
TTCAAGATCATGCATTGGATAATTCCC
Found at i:73017 original size:42 final size:42
Alignment explanation
Indices: 72969--73059 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
72959 AGATAACGCT
*
72969 CAACTCCCCACTAATAACTCAATCTCAATCACCTCAGAATTC
1 CAACTCCCCACTAATAACTCAATCTCAATCACCTCAAAATTC
* * *
73011 TAACTCCCCACTAATAACTCAATCTTAGTCACCTCAAAATTC
1 CAACTCCCCACTAATAACTCAATCTCAATCACCTCAAAATTC
73053 CAACTCC
1 CAACTCC
73060 ACTGAAACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.25
Consensus pattern (42 bp):
CAACTCCCCACTAATAACTCAATCTCAATCACCTCAAAATTC
Found at i:87943 original size:190 final size:190
Alignment explanation
Indices: 87620--87997 Score: 711
Period size: 190 Copynumber: 2.0 Consensus size: 190
87610 GTAACTTAGG
* *
87620 TAAGTTAAATTAATGACTTGTTGATGTTGAATACTAGGGAACAATCAAAGAATGGGTAAGATGTA
1 TAAGTTAAATTAATGAATTGTTGATGTTGAATACCAGGGAACAATCAAAGAATGGGTAAGATGTA
87685 ACAAAAGCATGGATTATGACTATGATGTTGCTAGTGTTGTAAGCTATCATCTATGTCTCAATACA
66 ACAAAAGCATGGATTATGACTATGATGTTGCTAGTGTTGTAAGCTATCATCTATGTCTCAATACA
87750 AGAGGTTACCGAGCTCTAATATACAGGTTACACTTTTGCTTGCTTACAGCACTCGCCAGC
131 AGAGGTTACCGAGCTCTAATATACAGGTTACACTTTTGCTTGCTTACAGCACTCGCCAGC
87810 TAAGTTAAATTAATGAATTGTTGATGTTGAATACCAGGGAACAATCAAAGAATGGGTAAGATGTA
1 TAAGTTAAATTAATGAATTGTTGATGTTGAATACCAGGGAACAATCAAAGAATGGGTAAGATGTA
87875 ACAAAAGCATGGATTATGACTATGATGTTGCTAGTGTTGTAAGCTATCATCTATGTCTCAATACA
66 ACAAAAGCATGGATTATGACTATGATGTTGCTAGTGTTGTAAGCTATCATCTATGTCTCAATACA
* * *
87940 AGAGGTTACCGAGCTCTAATATACGGGTTACACTTTTTCTTGCTTACAGCTCTCGCCA
131 AGAGGTTACCGAGCTCTAATATACAGGTTACACTTTTGCTTGCTTACAGCACTCGCCA
87998 TCTCAATTAT
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
190 183 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (190 bp):
TAAGTTAAATTAATGAATTGTTGATGTTGAATACCAGGGAACAATCAAAGAATGGGTAAGATGTA
ACAAAAGCATGGATTATGACTATGATGTTGCTAGTGTTGTAAGCTATCATCTATGTCTCAATACA
AGAGGTTACCGAGCTCTAATATACAGGTTACACTTTTGCTTGCTTACAGCACTCGCCAGC
Found at i:90906 original size:24 final size:24
Alignment explanation
Indices: 90879--90954 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
90869 ATGGTAAGAA
90879 TGCTTTAATCCGCTTTAAACTTGG
1 TGCTTTAATCCGCTTTAAACTTGG
* * * *
90903 TGCTTT-ATCAGATGGT-AA---GAA
1 TGCTTTAATCCGCT-TTAAACTTG-G
90924 TGCTTTAATCCGCTTTAAACTTGG
1 TGCTTTAATCCGCTTTAAACTTGG
90948 TGCTTTA
1 TGCTTTA
90955 TCTGTTGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 7 0.19
23 7 0.19
24 14 0.38
25 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TGCTTTAATCCGCTTTAAACTTGG
Found at i:90927 original size:45 final size:45
Alignment explanation
Indices: 90863--90956 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
90853 GCTCAAGCAA
90863 TATCAGATGGTAAGAATGCTTTAATCCGCTTTAAACTTGGTGCTT
1 TATCAGATGGTAAGAATGCTTTAATCCGCTTTAAACTTGGTGCTT
90908 TATCAGATGGTAAGAATGCTTTAATCCGCTTTAAACTTGGTGCTT
1 TATCAGATGGTAAGAATGCTTTAATCCGCTTTAAACTTGGTGCTT
90953 TATC
1 TATC
90957 TGTTGTTTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (45 bp):
TATCAGATGGTAAGAATGCTTTAATCCGCTTTAAACTTGGTGCTT
Found at i:101605 original size:14 final size:14
Alignment explanation
Indices: 101586--101613 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
101576 CAACTTATAC
101586 ATCAAGCACTCATG
1 ATCAAGCACTCATG
101600 ATCAAGCACTCATG
1 ATCAAGCACTCATG
101614 TTTAACCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
ATCAAGCACTCATG
Found at i:103049 original size:25 final size:25
Alignment explanation
Indices: 103021--103073 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
103011 TTATGTAAAA
103021 TACATGGATGGTCATAAGCATAACT
1 TACATGGATGGTCATAAGCATAACT
103046 TACATGGATGGTCATAAGCATAACT
1 TACATGGATGGTCATAAGCATAACT
103071 TAC
1 TAC
103074 TCACTTTCCT
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:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (25 bp):
TACATGGATGGTCATAAGCATAACT
Found at i:105300 original size:65 final size:65
Alignment explanation
Indices: 105196--105326 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
105186 CCCCTAAGGT
105196 TAAGGTTGACCTGAATGCATGTTTGACTATTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTATTACTATTTACTGCATGCCATGTTATTATTATCTGA
* * *
105261 TAAGGTTGACCTGAATGCGTGTTTGACTGTTACTATTTACTTCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTATTACTATTTACTGCATGCCATGTTATTATTATCTGA
105326 T
1 T
105327 GCATGGGACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATGTTTGACTATTACTATTTACTGCATGCCATGTTATTATTATCTGA
Found at i:106515 original size:49 final size:49
Alignment explanation
Indices: 106422--106552 Score: 149
Period size: 49 Copynumber: 2.7 Consensus size: 49
106412 ACATCAAAGT
* * *
106422 CGATGCCATGTCCCAGACAGGTTTTACACTGATTTTCATATATCGAG-GC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GTGC
* * * * *
106471 CGATGTCGTGTCCCAGGCAGGTCTTACACT-AGCTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTCTCATATATCGGTGC
*
106520 CGATGCCATGTCCTAGACAGGTCTTACACTGAC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAC
106553 ACACAACAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 64 0.96
50 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.29
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGC
Found at i:107414 original size:20 final size:18
Alignment explanation
Indices: 107377--107427 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
107367 CTATAGCAAC
107377 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
107394 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
107414 TTACAACTTTACAA
1 TCACAA-TTTACAA
107428 AATAGCCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:110800 original size:21 final size:21
Alignment explanation
Indices: 110776--110824 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
110766 CACGCTGTAC
* * *
110776 GAAGTAGGGATACGGCCGTGT
1 GAAGCAGGGACACGACCGTGT
110797 GAAGCAGGGACACGACCGTGT
1 GAAGCAGGGACACGACCGTGT
110818 GAA-CAGG
1 GAAGCAGG
110825 CCATGTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (21 bp):
GAAGCAGGGACACGACCGTGT
Found at i:112565 original size:40 final size:39
Alignment explanation
Indices: 112521--112742 Score: 275
Period size: 40 Copynumber: 5.6 Consensus size: 39
112511 GCCACTAGCT
*
112521 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
112561 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
112600 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
** *
112640 CAAACACCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
112680 CGAATGCCTTCGGGACTTAGCCCGGAATCAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTAT-AGTAACTCGCA
112720 CAAATG-CTCTCGGGACTTAGCCC
1 CAAATGCCT-TCGGGACTTAGCCC
112743 AGTTATCATC
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 41 0.25
40 122 0.75
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:112619 original size:79 final size:80
Alignment explanation
Indices: 112521--112705 Score: 282
Period size: 79 Copynumber: 2.3 Consensus size: 80
112511 GCCACTAGCT
* * * **
112521 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACACCTTCGGGACTTAGCCCGG
112586 -TATAATAACTCGCA
66 ATATAATAACTCGCA
*
112600 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACACCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACACCTTCGGGACTTAGCCCGG
* *
112665 ATATAGTAGCTCGCA
66 ATATAATAACTCGCA
*
112680 CGAATGCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
112706 ATCAGCCACT
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 59 0.61
80 37 0.39
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACACCTTCGGGACTTAGCCCGG
ATATAATAACTCGCA
Found at i:114859 original size:15 final size:15
Alignment explanation
Indices: 114841--114887 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
114831 AAAGAAAGTA
114841 AAAAATAATAGA-AAT
1 AAAAATAATA-ATAAT
*
114856 AAAAGTAATAATAAT
1 AAAAATAATAATAAT
* *
114871 AAAATTAATAACAAT
1 AAAAATAATAATAAT
114886 AA
1 AA
114888 CCAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:119038 original size:40 final size:39
Alignment explanation
Indices: 118838--119058 Score: 265
Period size: 40 Copynumber: 5.7 Consensus size: 39
118828 TTGAATGATG
* * *
118838 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* *
118878 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
118917 TTCCGGG-TAAG-CCCGAAGGCATTTGTGCGAG-TACTAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
118954 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
*
118993 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* *
119033 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
119059 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
36 6 0.04
37 29 0.18
38 23 0.14
39 20 0.12
40 76 0.47
41 8 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:126888 original size:40 final size:40
Alignment explanation
Indices: 126844--127056 Score: 338
Period size: 40 Copynumber: 5.3 Consensus size: 40
126834 AGACTAAGAT
* *
126844 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTA
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
126884 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
126924 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
* *
126964 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
* * * *
127004 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGTTAAGTC
127044 CCGAAGGCATTTG
1 CCGAAGGCATTTG
127057 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.01
40 163 0.99
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
Done.