Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1154
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: 38101
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:13697 original size:53 final size:54
Alignment explanation
Indices: 13615--13731 Score: 175
Period size: 53 Copynumber: 2.2 Consensus size: 54
13605 TGAAACGAAA
*
13615 TCGCACACACATGCCCACTGACCGATCTCGCACACATATTGCTCGATTAAAGAAT
1 TCGCACACACATG-CCACTGACCGATCTCGCACACATAGTGCTCGATTAAAGAAT
* *
13670 TCGCACACACAGTG-C-CTGACCTATCTCGCACACATAGTGCTCGGTTAAAGAAT
1 TCGCACACACA-TGCCACTGACCGATCTCGCACACATAGTGCTCGATTAAAGAAT
13723 TCGCACACA
1 TCGCACACA
13732 GTGCCTCAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 44 0.76
54 1 0.02
55 11 0.19
56 2 0.03
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.21
Consensus pattern (54 bp):
TCGCACACACATGCCACTGACCGATCTCGCACACATAGTGCTCGATTAAAGAAT
Found at i:13728 original size:28 final size:27
Alignment explanation
Indices: 13642--13731 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
13632 CTGACCGATC
*
13642 TCGCACACATATTGCTCGATTAAAGAAT
1 TCGCACACATAGTGCTCG-TTAAAGAAT
* * ***
13670 TCGCACACACAGTGC-C--TGACCTAT
1 TCGCACACATAGTGCTCGTTAAAGAAT
13694 CTCGCACACATAGTGCTCGGTTAAAGAAT
1 -TCGCACACATAGTGCTC-GTTAAAGAAT
13723 TCGCACACA
1 TCGCACACA
13732 GTGCCTCAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
24 4 0.09
25 14 0.30
26 1 0.02
27 1 0.02
28 22 0.48
29 4 0.09
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (27 bp):
TCGCACACATAGTGCTCGTTAAAGAAT
Found at i:13751 original size:23 final size:24
Alignment explanation
Indices: 13721--13773 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
13711 CGGTTAAAGA
13721 ATTCGCA-CACAGTGCCTCA-ATTC
1 ATTCGCACCACAGTGCCT-ATATTC
*
13744 ATTCGCACCCATAGTGCCTATATTC
1 ATTCGCA-CCACAGTGCCTATATTC
13769 ATTCG
1 ATTCG
13774 TTATTACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 1 0.04
25 18 0.69
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (24 bp):
ATTCGCACCACAGTGCCTATATTC
Found at i:13751 original size:51 final size:52
Alignment explanation
Indices: 13639--13760 Score: 158
Period size: 53 Copynumber: 2.3 Consensus size: 52
13629 CCACTGACCG
* * *
13639 ATCTCGCACACATATTGCTCGATTAAAGAATTCGCACACACAGTGCCTGACCT
1 ATCTCGCACACATAGTGCTCGATTAAAGAATTCG-ACACACAGTGCCTCAACT
* *
13692 ATCTCGCACACATAGTGCTCGGTTAAAGAATTCG-CACACAGTGCCTCAATT
1 ATCTCGCACACATAGTGCTCGATTAAAGAATTCGACACACAGTGCCTCAACT
*
13743 CAT-TCGCACCCATAGTGC
1 -ATCTCGCACACATAGTGC
13761 CTATATTCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 28 0.45
52 2 0.03
53 32 0.52
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (52 bp):
ATCTCGCACACATAGTGCTCGATTAAAGAATTCGACACACAGTGCCTCAACT
Found at i:13953 original size:43 final size:43
Alignment explanation
Indices: 13892--14034 Score: 187
Period size: 43 Copynumber: 3.3 Consensus size: 43
13882 CTTTGCTCGA
** * *
13892 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCAAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
13935 ATCACCGGCACGAAGCCTGCTAGGAACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* * * ** *
13978 ATCACCAGCACAAAGCCTGCTAGGCATGAAGGCATGATTACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
14021 ATCACCGGCACGAA
1 ATCACCGGCACGAA
14035 TGCCCTTCAG
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:14088 original size:40 final size:40
Alignment explanation
Indices: 14023--14143 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
14013 GATTACACAT
* * * * *
14023 CACCGGCACGAATGCCCTTCAGGACTTAGCCCATATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCAGATATAA
*
14063 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCAGATATAA
*
14103 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCAGATATAA
14143 C
1 C
14144 TCTCAATTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCAGATATAA
Found at i:20546 original size:10 final size:10
Alignment explanation
Indices: 20531--20589 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
20521 TATAATGAGT
20531 ATATCATAGC
1 ATATCATAGC
*
20541 ATATCATGTGC
1 ATATCAT-AGC
* *
20552 ATATCGTAAC
1 ATATCATAGC
*
20562 ATATCATAAC
1 ATATCATAGC
*
20572 ATATCATGTGC
1 ATATCAT-AGC
20583 ATATCAT
1 ATATCAT
20590 GTCCTATCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
10 24 0.60
11 16 0.40
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (10 bp):
ATATCATAGC
Found at i:20597 original size:10 final size:11
Alignment explanation
Indices: 20539--20601 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 11
20529 GTATATCATA
20539 GCATATCATGT
1 GCATATCATGT
20550 GCATATC--GT
1 GCATATCATGT
* *
20559 AACATATCAT-A
1 -GCATATCATGT
*
20570 ACATATCATGT
1 GCATATCATGT
20581 GCATATCATGT
1 GCATATCATGT
*
20592 -CCTATCATGT
1 GCATATCATGT
20602 ATATCAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 2 0.05
10 24 0.56
11 17 0.40
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (11 bp):
GCATATCATGT
Found at i:20599 original size:31 final size:31
Alignment explanation
Indices: 20531--20589 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
20521 TATAATGAGT
* *
20531 ATATCATAGCATATCATGTGCATATCGTAAC
1 ATATCATAACATATCATGTGCATATCATAAC
20562 ATATCATAACATATCATGTGCATATCAT
1 ATATCATAACATATCATGTGCATATCAT
20590 GTCCTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (31 bp):
ATATCATAACATATCATGTGCATATCATAAC
Found at i:24844 original size:47 final size:47
Alignment explanation
Indices: 24781--25216 Score: 719
Period size: 47 Copynumber: 9.3 Consensus size: 47
24771 CCCTTCGGGA
* *
24781 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
24828 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
24875 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
24922 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
24969 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
25016 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
25063 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
25110 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
25157 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
25204 CTTATCACATATA
1 CTTATCACATATA
25217 CATATCTTGT
Statistics
Matches: 359, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 359 1.00
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:27548 original size:46 final size:46
Alignment explanation
Indices: 27426--27555 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 46
27416 TGTAACCCGC
27426 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG-ATTCCTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAATTCCTAG-T
* *
27472 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A-T
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGA-ATTC-CTAGT
*
27519 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
27556 TGCTCAACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
45 2 0.03
46 31 0.42
47 32 0.44
48 2 0.03
49 5 0.07
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAATTCCTAGT
Found at i:27574 original size:46 final size:44
Alignment explanation
Indices: 27434--27574 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 44
27424 GCCCATAAGC
*
27434 GAACTCGGACTCAACTCAACGAGTTCGGATTCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATTCC-A---ACCATCT-AGT
* *
27481 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATTC-CAACCATCTAGT
*
27527 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATTC-CAACCAT-CTAGT
27573 GA
1 GA
27575 CATGTCACTT
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
49 5 0.06
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATTCCAACCATCTAGT
Found at i:33496 original size:85 final size:84
Alignment explanation
Indices: 33353--33522 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 84
33343 GGCCGGCCAT
33353 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
33418 GTAAGGATTAATAAAATAAA
66 -TAAGGATTAATAAAATAAA
33438 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
33503 TAAGGATTAATAAAATAAA
66 TAAGGATTAATAAAATAAA
33522 G
1 G
33523 GTATGGGCAA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 20 0.24
85 65 0.76
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (84 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
TAAGGATTAATAAAATAAA
Found at i:35843 original size:49 final size:47
Alignment explanation
Indices: 35788--35989 Score: 320
Period size: 49 Copynumber: 4.3 Consensus size: 47
35778 TATATTGATG
*
35788 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TA
*
35837 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
35884 TATA-GTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG--TA
*
35932 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG--AGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
35977 TATATGTGATAAG
1 TATATGTGATAAG
35990 TGATGAATGT
Statistics
Matches: 146, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
45 15 0.10
46 39 0.27
47 10 0.07
48 6 0.04
49 76 0.52
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:35898 original size:95 final size:93
Alignment explanation
Indices: 35786--35989 Score: 365
Period size: 95 Copynumber: 2.2 Consensus size: 93
35776 AATATATTGA
35786 TGTATAT-GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
1 TGTATATAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
35850 GCCTAATGGCCGATGTGATGAATGTGAAAG
66 GCCTAATGGCCGATGTGATGAATGTG--AG
*
35880 TGTATATAGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
1 TGTATATAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
35945 GCCTAATGGCCGATGTGATGAATGTGAG
66 GCCTAATGGCCGATGTGATGAATGTGAG
35973 TGTATATATGTGATAAG
1 TGTATATA-GTGATAAG
35990 TGATGAATGT
Statistics
Matches: 107, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
93 10 0.09
94 15 0.14
95 82 0.77
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (93 bp):
TGTATATAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
GCCTAATGGCCGATGTGATGAATGTGAG
Found at i:35994 original size:30 final size:31
Alignment explanation
Indices: 35959--36021 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 31
35949 AATGGCCGAT
35959 GTGATGAATGTG-AGTGTATATATGTGATAA
1 GTGATGAATGTGAAGTGTATATATGTGATAA
35989 GTGATGAATGTGAAAGTGTATATATGTGATAA
1 GTGATGAATGTG-AAGTGTATATATGTGATAA
36021 G
1 G
36022 GCCTAATGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 12 0.39
32 19 0.61
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (31 bp):
GTGATGAATGTGAAGTGTATATATGTGATAA
Found at i:36001 original size:16 final size:17
Alignment explanation
Indices: 35971--36021 Score: 72
Period size: 16 Copynumber: 3.1 Consensus size: 17
35961 GATGAATGTG
35971 AGTGTATATATGTGATA
1 AGTGTATATATGTGATA
35988 AGTG-ATGA-ATGTGA-A
1 AGTGTAT-ATATGTGATA
36003 AGTGTATATATGTGATA
1 AGTGTATATATGTGATA
36020 AG
1 AG
36022 GCCTAATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.20
16 16 0.53
17 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.35
Consensus pattern (17 bp):
AGTGTATATATGTGATA
Found at i:36031 original size:172 final size:172
Alignment explanation
Indices: 35815--36161 Score: 610
Period size: 172 Copynumber: 2.0 Consensus size: 172
35805 AATGGCCAAT
35815 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 GTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
35880 TGTATATA-GTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAA
65 TGTATATATGTGATAAGGCC-AATGGCCAATGTGATGAATGTG-AAG-GTATATATATGTGATAA
35944 GGCCTAATGGCCGATGTGATGAATGTG-AGTGTATATATGTGATAA
127 GGCCTAATGGCCGATGTGATGAATGTGAAGTGTATATATGTGATAA
35989 GTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
* *
36053 GTATATATGTGATAAGGCCGATGGCCAATGTGATGAATGTGAAGGTATATATATGTGGTAAGGCC
66 GTATATATGTGATAAGGCCAATGGCCAATGTGATGAATGTGAAGGTATATATATGTGATAAGGCC
36118 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
131 TAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGATAA
36161 G
1 G
36162 GCCTAATGGC
Statistics
Matches: 168, Mismatches: 2, Indels: 8
0.94 0.01 0.04
Matches are distributed among these distances:
170 43 0.26
171 3 0.02
172 93 0.55
173 11 0.07
174 18 0.11
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (172 bp):
GTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
GTATATATGTGATAAGGCCAATGGCCAATGTGATGAATGTGAAGGTATATATATGTGATAAGGCC
TAATGGCCGATGTGATGAATGTGAAGTGTATATATGTGATAA
Found at i:36039 original size:77 final size:79
Alignment explanation
Indices: 35910--36161 Score: 328
Period size: 93 Copynumber: 3.0 Consensus size: 79
35900 AATGGCCAAT
35910 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AGT
1 GTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGT
35974 GTATATATGTGATAA
65 GTATATATGTGATAA
35989 GTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAGT
36053 GTATATATGTGATAA
65 GTATATATGTGATAA
* *
36068 GGCCGATGGCCAATGTGATGAATGTGAAGGTATATATATGTGGTAAGGCCTAATGGCCGATGTGA
1 -G-TGAT-G--AATGTGA--AA-GT----G-ATATATATGTGATAAGGCCTAATGGCCGATGTGA
36133 TGAATGTGAAAGTGTATATATGTGATAA
53 TGAATGTG-AAGTGTATATATGTGATAA
36161 G
1 G
36162 GCCTAATGGC
Statistics
Matches: 155, Mismatches: 2, Indels: 19
0.88 0.01 0.11
Matches are distributed among these distances:
77 41 0.26
79 36 0.23
80 1 0.01
81 3 0.02
82 1 0.01
84 7 0.05
86 2 0.01
87 2 0.01
91 1 0.01
92 1 0.01
93 60 0.39
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (79 bp):
GTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGTG
TATATATGTGATAA
Found at i:36042 original size:47 final size:47
Alignment explanation
Indices: 35989--36254 Score: 401
Period size: 47 Copynumber: 5.7 Consensus size: 47
35979 TATGTGATAA
35989 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
36036 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCC-GATGGCCAAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * *
36082 GTGATGAATGTGAAGGTATATATATGTGGTAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
36129 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * *
36176 GTGATG-ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
36222 GTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAG
36255 TCCCGAAGGG
Statistics
Matches: 198, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
46 81 0.41
47 117 0.59
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.29
Consensus pattern (47 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
Found at i:36090 original size:93 final size:94
Alignment explanation
Indices: 35989--36254 Score: 401
Period size: 93 Copynumber: 2.9 Consensus size: 94
35979 TATGTGATAA
35989 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
36054 TATATATGTGATAAGGCC-GATGGCCAAT
66 TATATATGTGATAAGGCCTAATGGCCAAT
* * *
36082 GTGATGAATGTGAAGGTATATATATGTGGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
36147 TATATATGTGATAAGGCCTAATGGCCGAT
66 TATATATGTGATAAGGCCTAATGGCCAAT
* * * * * * *
36176 GTGATG-ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
36240 TATAAATGTGATAAG
66 TATATATGTGATAAG
36255 TCCCGAAGGG
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
93 142 0.91
94 14 0.09
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.29
Consensus pattern (94 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
TATATATGTGATAAGGCCTAATGGCCAAT
Found at i:36151 original size:140 final size:140
Alignment explanation
Indices: 35989--36254 Score: 444
Period size: 140 Copynumber: 1.9 Consensus size: 140
35979 TATGTGATAA
35989 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTG
* * * * *
36054 TATATATGTGATAAGGCCGA-TGGCCAATGTGATGAATGTGAAGGTATATATATGTGGTAAGGCC
65 TATATATGTGACAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTATATAAATGTGATAAGGCC
36118 TAATGGCCGAT
130 TAATGGCCGAT
36129 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGT
* * *
36194 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 ATATATGTGACAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTATATAAATGTGATAAG
36255 TCCCGAAGGG
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
139 29 0.25
140 88 0.75
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.29
Consensus pattern (140 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGT
ATATATGTGACAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTATATAAATGTGATAAGGCCT
AATGGCCGAT
Found at i:36452 original size:37 final size:37
Alignment explanation
Indices: 36369--36510 Score: 200
Period size: 36 Copynumber: 3.9 Consensus size: 37
36359 CCGAGCTCTA
* *
36369 AAGACCCGATGACTACGTGTGGAGAGTATGTCC-GGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
36405 AAGACCCGATGACTACGTGTGGAGATTTTGCCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
36442 AAGACCCGATGACTACGTGTGGAG-TTTTGTTCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* * *
36478 AAGA-CCGATAACTTCGTGTAGAGATTTTGTCCG
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCG
36511 AGCTAAAGGT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 16 0.17
36 52 0.55
37 27 0.28
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:36454 original size:73 final size:72
Alignment explanation
Indices: 36369--36506 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
36359 CCGAGCTCTA
* *
36369 AAGACCCGATGACTACGTGTGGAGAGTATG-TCCGGTAAGACCCGATGACTACGTGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAG-GTATGTTCCGGTAAGA-CCGATAACTACGTGTAGAGATTT
36433 TGCCCGGGT
64 TGCCCGGGT
* * * *
36442 AAGACCCGATGACTACGTGTGGAGTTTTGTTCGGGTAAGACCGATAACTTCGTGTAGAGATTTTG
1 AAGACCCGATGACTACGTGTGGAGGTATGTTCCGGTAAGACCGATAACTACGTGTAGAGATTTTG
36507 TCCGAGCTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 25 0.43
73 33 0.57
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (72 bp):
AAGACCCGATGACTACGTGTGGAGGTATGTTCCGGTAAGACCGATAACTACGTGTAGAGATTTTG
CCCGGGT
Done.