Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3250
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: 59314
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1001 original size:70 final size:73
Alignment explanation
Indices: 766--1188 Score: 342
Period size: 78 Copynumber: 5.5 Consensus size: 73
756 CAGACTCACT
*
766 ACTCA-CTCTCGCAATATGAGTTGATTCTTTTAAAAAGCAAAAAATTGAAAATACCTCAGCGTGT
1 ACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAAA--AAAAAATTGAAAATACCTCAGCGTGT
*
830 CCCGAGGCTCA
63 CCTGAGGCTCA
** *
841 ACTCACCTCTCGCAATATGAGTTGATTTTTTTTGATAAAAATAGAATTTTGAAAATATCTCAGCG
1 ACTCACCTCTCGCAATATGAGTTGA---TTTTTGA-AAAAA-A-AAAATTGAAAATACCTCAGCG
*
906 TGTCCTGAGTC-CA
60 TGTCCTGAGGCTCA
* *
919 ACTCACCTCTCGCAATATGAGTTGA-TTTTGACAAAAAAAAATTGAAATTACCTCAGCGT-T-CT
1 ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAAATTGAAAATACCTCAGCGTGTCCT
981 GAGGCTCA
66 GAGGCTCA
* * **
989 ACTCACTTCTCGCAATATGAGTTTATTTTTTTTTGAAACATAAATTAAAAAACGAAAATTGAAAA
1 ACTCACCTCTCGCAATATGAGTTGA----TTTTTG-AA-A-AAA--AAAAATTGAAAA-T-----
1054 ACCTCAGC-TGTCCTGAGGCTCA
51 ACCTCAGCGTGTCCTGAGGCTCA
**
1076 ACTCACCTC-CGCAATATGATGTTGA-AATT-AAAAAACACAAATATTGAAAATACCGTCAGCGT
1 ACTCACCTCTCGCAATATGA-GTTGATTTTTGAAAAAA-A-AAA-ATTGAAAATACC-TCAGCGT
* *
1138 GCCCCGAGGCTCA
61 GTCCTGAGGCTCA
*
1151 ACTCACCTCTTGCAATATGAGCTGCTGATTTTTGAAAA
1 ACTCACCTCTCGCAATATGAG-T--TGATTTTTGAAAA
1189 GTAGAAATTA
Statistics
Matches: 281, Mismatches: 30, Indels: 69
0.74 0.08 0.18
Matches are distributed among these distances:
69 6 0.02
70 26 0.09
71 18 0.06
72 1 0.00
73 7 0.02
74 11 0.04
75 32 0.11
76 30 0.11
77 3 0.01
78 45 0.16
79 42 0.15
80 15 0.05
81 1 0.00
82 2 0.01
85 1 0.00
86 19 0.07
87 22 0.08
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (73 bp):
ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAAATTGAAAATACCTCAGCGTGTCCT
GAGGCTCA
Found at i:1150 original size:75 final size:71
Alignment explanation
Indices: 1030--1170 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 71
1020 TTTGAAACAT
* * *
1030 AAATTAAAAAACGAAAATTGAAAAACCTCAGCTGTCCTGAGGCTCAACTCACCTC-CGCAATATG
1 AAATTAAAAAACCAAAATTGAAAAACCTCAGCTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
1094 ATGTTG
66 ATGTTG
*
1100 AAATTAAAAAACACAAATATTGAAAATACCGTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCA
1 AAATTAAAAAAC-CAAA-ATTGAAAA-ACC-TCAGC-TGCCCCGAGGCTCAACTCACCTCTCGCA
1165 ATATGA
61 ATATGA
1171 GCTGCTGATT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
70 12 0.20
71 3 0.05
72 8 0.13
73 3 0.05
74 5 0.08
75 21 0.34
76 9 0.15
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAAACCAAAATTGAAAAACCTCAGCTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
ATGTTG
Found at i:1423 original size:75 final size:73
Alignment explanation
Indices: 1325--1656 Score: 458
Period size: 75 Copynumber: 4.5 Consensus size: 73
1315 AGTGTGTAAT
*
1325 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAGAAATTGAAAATACCTC
*
1390 AGCATGTGAAC
66 AGC--GTG-TC
*
1401 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTG-AAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-AAAACAGAAATTGAAAATACCT
*
1464 CAACGTGT-
65 CAGCGTGTC
* * * * *
1472 CTGAGGCTCAACTCA-TTCTCGCAATATAAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAGAAATTGAAAATACCTC
1535 AGCGTGTC
66 AGCGTGTC
** *
1543 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTAA-AACAGAAATTGAAAATACC
1608 TCAGCGTGTC
64 TCAGCGTGTC
*
1618 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1657 GAAAACAAAA
Statistics
Matches: 233, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
69 13 0.06
70 18 0.08
71 34 0.15
72 31 0.13
73 3 0.01
74 10 0.04
75 110 0.47
76 14 0.06
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (73 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAGAAATTGAAAATACCTC
AGCGTGTC
Found at i:1609 original size:145 final size:145
Alignment explanation
Indices: 1324--1672 Score: 485
Period size: 145 Copynumber: 2.4 Consensus size: 145
1314 CAGTGTGTAA
* * *
1324 TCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAGAAATTGAAAATACCT
1 TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAAATACCT
1389 CAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
65 CAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
1454 TGAAATACCTCAACGTG
129 TGAAATACCTCAACGTG
* * *
1471 TCTGAGGCTCAACTCA-TTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC
1 TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTC
* ** * *
1535 AGC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAAT
66 AGCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAA-AACAGAAAT
*
1598 TGAAATTACCTCAGCGTG
129 TGAAA-TACCTCAACGTG
*
1616 TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAACA-AAATT-AAAA
1 T-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAA
1673 GGCTTAACTC
Statistics
Matches: 181, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
142 2 0.01
143 42 0.23
144 17 0.09
145 46 0.25
146 44 0.24
147 30 0.17
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (145 bp):
TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTC
AGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTG
AAATACCTCAACGTG
Found at i:1811 original size:70 final size:68
Alignment explanation
Indices: 1672--1843 Score: 204
Period size: 70 Copynumber: 2.5 Consensus size: 68
1662 CAAAATTAAA
* * * * * **
1672 AGGCTTAACTCA-TCTCGCAATATGAG-TCAATTTAAACATAAACTAAAAATACCTCGGCGTGCC
1 AGGCTCAACTCATTCTCGCAATATGAGTTGATTTTAAAAAAAAACTAAAAATACCTCAACGTGCC
1735 CCG
66 CCG
*
1738 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCA-TTCTCGCAATATGAGTTGATTTT-AAAAAAAAACTAAAAATACCTCAACGTG
* **
1803 TCTTG
64 CCCCG
1808 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCAT-TCTCGCAATATGAGTTGATTTT
1844 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
66 11 0.12
68 14 0.16
69 6 0.07
70 59 0.66
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (68 bp):
AGGCTCAACTCATTCTCGCAATATGAGTTGATTTTAAAAAAAAACTAAAAATACCTCAACGTGCC
CCG
Found at i:10166 original size:24 final size:24
Alignment explanation
Indices: 10134--10228 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
10124 CAATGATGTG
*
10134 AATAATAAAATATATAAAATATAA
1 AATATTAAAATATATAAAATATAA
*
10158 AATATTAAAATAT-CAAAATATCAA
1 AATATTAAAATATATAAAATAT-AA
*
10182 AATATTAGAATA-ATAATAAT-T--
1 AATATTAAAATATATAA-AATATAA
10203 AATATTGAAAA-ATA-AAAA-ATAA
1 AATATT-AAAATATATAAAATATAA
10225 AATA
1 AATA
10229 GAAATAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.05
21 9 0.16
22 8 0.14
23 7 0.12
24 28 0.48
25 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AATATTAAAATATATAAAATATAA
Found at i:10168 original size:8 final size:8
Alignment explanation
Indices: 10134--10193 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
10124 CAATGATGTG
*
10134 AATAATAA
1 AATATTAA
10142 AATATATAA
1 AATAT-TAA
10151 AATA-TAA
1 AATATTAA
10158 AATATTAA
1 AATATTAA
*
10166 AATATCAA
1 AATATTAA
*
10174 AATATCAA
1 AATATTAA
*
10182 AATATTAG
1 AATATTAA
10190 AATA
1 AATA
10194 ATAATAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.15
8 32 0.70
9 7 0.15
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (8 bp):
AATATTAA
Found at i:10372 original size:25 final size:23
Alignment explanation
Indices: 10344--10406 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
10334 CGTGATAATA
10344 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATA--TACATAATATAGTG
10369 TTAAAAATATACATAATATA--G
1 TTAAAAATATACATAATATAGTG
*
10390 TTAAGATATATACATAA
1 TTAA-AAATATACATAA
10407 GATAACATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 11 0.31
25 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (23 bp):
TTAAAAATATACATAATATAGTG
Found at i:10461 original size:25 final size:25
Alignment explanation
Indices: 10427--10560 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 25
10417 AGAAAAATAT
10427 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
10452 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
10477 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
10503 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
10525 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
10548 AAATAT-AATAATA
1 ATATATAAATAATA
10561 ACAAAAAAGG
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 18 0.21
24 5 0.06
25 33 0.39
26 2 0.02
27 10 0.12
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:10495 original size:27 final size:27
Alignment explanation
Indices: 10375--10495 Score: 97
Period size: 27 Copynumber: 4.6 Consensus size: 27
10365 AGTGTTAAAA
* *
10375 ATATACATAATATAGT-TAAGATATAT
1 ATATAAATAATATAGTATAAAATATAT
* * *
10401 ACATAAGATAACAT-GTAGAAAAATATAT
1 ATATAA-ATAATATAGTA-TAAAATATAT
* * *
10429 ATATAAATAATATAATAT-TAA-AGAT
1 ATATAAATAATATAGTATAAAATATAT
*
10454 ATATAAATAAAATAGTATAAAATATAT
1 ATATAAATAATATAGTATAAAATATAT
**
10481 ATATACGTAATATAG
1 ATATAAATAATATAG
10496 AATTTAAAAT
Statistics
Matches: 71, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
25 19 0.27
26 10 0.14
27 27 0.38
28 15 0.21
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.33
Consensus pattern (27 bp):
ATATAAATAATATAGTATAAAATATAT
Found at i:11080 original size:30 final size:30
Alignment explanation
Indices: 11044--11158 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
11034 TAGGTACAAG
* *
11044 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
11074 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
11104 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
11134 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
11159 TGAGAAAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:12570 original size:26 final size:26
Alignment explanation
Indices: 12528--12581 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12518 AGATATTTTT
*
12528 AAAAATTAAAATCATTAACATTATTA
1 AAAAATTAAAATAATTAACATTATTA
* *
12554 AAAAATATAAAA-AATTAATATTTTTA
1 AAAAAT-TAAAATAATTAACATTATTA
12580 AA
1 AA
12582 TTTTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATTAAAATAATTAACATTATTA
Found at i:18515 original size:34 final size:31
Alignment explanation
Indices: 18468--18534 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
18458 TAAACACTTA
*
18468 TAAAATTTTAAAGTATATTTATATTAATTTTAATT
1 TAAAATTTTAAAGT-T-TATATATT--TTTTAATT
18503 TAAAA-TTTAAAGTTTATATATTTTTTAATT
1 TAAAATTTTAAAGTTTATATATTTTTTAATT
18533 TA
1 TA
18535 TTCAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 10 0.32
32 7 0.23
33 1 0.03
34 8 0.26
35 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TAAAATTTTAAAGTTTATATATTTTTTAATT
Found at i:23806 original size:5 final size:5
Alignment explanation
Indices: 23771--23804 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
23761 ATATAATCTC
* *
23771 AAATG AAATG AAATG AAATG AAATA AAATA AAAT
1 AAATG AAATG AAATG AAATG AAATG AAATG AAAT
23805 AATTATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:36773 original size:42 final size:42
Alignment explanation
Indices: 36722--36868 Score: 179
Period size: 42 Copynumber: 3.3 Consensus size: 42
36712 CACAGTTCAA
36722 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACAT-ATCGATGCCATAGCCCAG
* * * *
36764 CTATAGTCTTACACCTATTCATATATCGATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
36806 CTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---AT--C-T-TCACATATCGATGCCATAGCCCAG
36855 CTATGGTCTTACAC
1 CTATGGTCTTACAC
36869 GAATCACATA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.02
42 48 0.54
45 1 0.01
48 1 0.01
49 37 0.42
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
Found at i:36850 original size:49 final size:48
Alignment explanation
Indices: 36740--36911 Score: 200
Period size: 49 Copynumber: 3.7 Consensus size: 48
36730 TTACACATCT
* *
36740 TCACATAAT-GATGCCATAGCCCAGCTATAGTCTTACAC----C-TAT-
1 TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
*
36782 TCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATA
36831 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
* * * *
36879 TCTCA-CT-GATGCCATATCCCAGATATGGTCTTA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
36912 TACAGTAGCA
Statistics
Matches: 114, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
41 2 0.02
42 33 0.29
46 24 0.21
47 2 0.02
48 15 0.13
49 38 0.33
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (48 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
Found at i:36942 original size:47 final size:46
Alignment explanation
Indices: 36749--36954 Score: 195
Period size: 47 Copynumber: 4.5 Consensus size: 46
36739 TTCACATAAT
* * * * *
36749 GATGCCATAGCCCAGCTATAGTCTTACACCTAT-TCATAT---ATC
1 GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
* *
36791 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCAC--ACC
* * * *
36840 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACT
1 GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
* * * *
36886 GATGCCATATCCCAGATATGGTCTTATACAGTAGCAAATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACACC
* *
36933 GATGCCATATCCCAAATATGGT
1 GATGCCATAGCCCAGATATGGT
36955 TTTATGCGAA
Statistics
Matches: 140, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
42 29 0.21
43 2 0.01
44 5 0.04
46 27 0.19
47 33 0.24
48 11 0.08
49 33 0.24
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (46 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
Found at i:36969 original size:95 final size:92
Alignment explanation
Indices: 36791--36978 Score: 200
Period size: 95 Copynumber: 2.0 Consensus size: 92
36781 TTCATATATC
* * * * **
36791 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAGC
1 GATGCCATAGCCCAGATATGGTCTTACACGTAAGCAAATATCACA-ACCGATGCCATAGCCCAAA
36856 TATGGTCTTACACGAATCACATATCTCACT
65 TATGGTCTTACACGAATCAC-T-TCTCACT
* * *
36886 GATGCCATATCCCAGATATGGTCTTATACAGT-AGCAAATATCAC-ACCGATGCCATATCCCAAA
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTAAGCAAATATCACAACCGATGCCATAGCCCAAA
* **
36949 TATGGTTTTATGCGAAAATCACTTCTCACT
65 TATGGTCTTACACG--AATCACTTCTCACT
36979 TGTCACTTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
93 33 0.42
94 1 0.01
95 42 0.54
96 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (92 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTAAGCAAATATCACAACCGATGCCATAGCCCAAAT
ATGGTCTTACACGAATCACTTCTCACT
Found at i:37030 original size:31 final size:31
Alignment explanation
Indices: 36987--37135 Score: 226
Period size: 31 Copynumber: 4.8 Consensus size: 31
36977 CTTGTCACTT
* * *
36987 GTAGTCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
37018 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
37049 GTAGCTGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
37080 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
37111 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
37136 TGTCATTGAT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:39617 original size:26 final size:26
Alignment explanation
Indices: 39588--39695 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
39578 TGGTACAAAT
*
39588 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATGGA-TTAGGTAAATATTCCA
39614 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
*
39640 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
* *
39666 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATATTCCA
39692 TGAT
1 TGAT
39696 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 75 0.97
27 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATATTCCA
Found at i:45946 original size:26 final size:26
Alignment explanation
Indices: 45907--46014 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
45897 TGATACAAAT
45907 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
45933 TGATAATGGATTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
45959 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
45985 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
46011 TGAT
1 TGAT
46015 GGGAATTTCG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:47666 original size:54 final size:54
Alignment explanation
Indices: 47602--47717 Score: 232
Period size: 54 Copynumber: 2.1 Consensus size: 54
47592 AAACCAACCC
47602 ACCTAAACACTAACCCACAACCAGCAGAGCCCAAATTACAACCAAACCTAATTA
1 ACCTAAACACTAACCCACAACCAGCAGAGCCCAAATTACAACCAAACCTAATTA
47656 ACCTAAACACTAACCCACAACCAGCAGAGCCCAAATTACAACCAAACCTAATTA
1 ACCTAAACACTAACCCACAACCAGCAGAGCCCAAATTACAACCAAACCTAATTA
47710 ACCTAAAC
1 ACCTAAAC
47718 CCAAAATCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.47, C:0.35, G:0.05, T:0.13
Consensus pattern (54 bp):
ACCTAAACACTAACCCACAACCAGCAGAGCCCAAATTACAACCAAACCTAATTA
Found at i:48175 original size:8 final size:8
Alignment explanation
Indices: 48162--48193 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
48152 TTATTTGCAA
48162 AAAAAAAT
1 AAAAAAAT
48170 -AAAAAAT
1 AAAAAAAT
48177 AAAAAAAT
1 AAAAAAAT
48185 AAAAAAAT
1 AAAAAAAT
48193 A
1 A
48194 CCTTTCGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:48193 original size:16 final size:15
Alignment explanation
Indices: 48162--48190 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48152 TTATTTGCAA
48162 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
48177 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
48191 ATACCTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:48961 original size:18 final size:18
Alignment explanation
Indices: 48940--48988 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
48930 TTATTATAAC
48940 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
48958 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
48976 TA-TTATATATATC
1 TATTTATATATATC
48989 TATATATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:48961 original size:33 final size:35
Alignment explanation
Indices: 48924--48988 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
48914 CCTATTATTA
48924 TTATTAT-TA-TTATAAC-TATTTATATATATCATC
1 TTATTATATATTTATAACTTA-TTATATATATCATC
*
48957 TTATTATATATTTATATCTTATTATATATATC
1 TTATTATATATTTATAACTTATTATATATATC
48989 TATATATCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 2 0.07
35 17 0.61
36 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATTATATATTTATAACTTATTATATATATCATC
Done.