Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1483
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: 60337
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:4124 original size:27 final size:27
Alignment explanation
Indices: 4094--4271 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
4084 ATATTGAGCC
* * *
4094 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
4121 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
4148 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
4176 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
4203 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
4230 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
4257 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4272 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:4187 original size:55 final size:55
Alignment explanation
Indices: 4094--4271 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
4084 ATATTGAGCC
* * *
4094 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
4148 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
4203 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
4257 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4272 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:4233 original size:82 final size:81
Alignment explanation
Indices: 4115--4270 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
4105 TGCTATACAA
* * *
4115 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
4180 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
4197 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
4261 CACTTAGTGC
65 CACTTAGTGC
4271 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:7365 original size:29 final size:29
Alignment explanation
Indices: 7330--7403 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
7320 GTTGTGAGAT
* *
7330 TGGCACTAAGTGTGCGCGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
7359 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
7388 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
7404 TTGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:7773 original size:40 final size:40
Alignment explanation
Indices: 7718--7955 Score: 214
Period size: 40 Copynumber: 6.0 Consensus size: 40
7708 TTGAATGATG
**
7718 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCGCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-CGCA
* *
7758 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACGCA
* * *
7798 TCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACGCA
** * ***
7838 TCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACGCA
* ** * * *
7878 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATG--
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTG--ACGCA
* * *
7918 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGACG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACG
7956 TGTATTCGGG
Statistics
Matches: 170, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.01
40 153 0.90
41 7 0.04
42 8 0.05
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACGCA
Found at i:7856 original size:80 final size:80
Alignment explanation
Indices: 7718--7953 Score: 269
Period size: 80 Copynumber: 3.0 Consensus size: 80
7708 TTGAATGATG
* * *
7718 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCGCATCCGGGCTAAGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TGTATCCGGGCTAAGTCCCGAAGAGCA
*
7781 TTCATGCTAGTGATGTA
64 TTCATGCTAGTGATATA
* * **
7798 TCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTTCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
7863 CGTGCTAGTGATATA
66 CATGCTAGTGATATA
* ** * * * * * *
7878 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATGTCCGGGCTAGGTCCCGAAGAGCAAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
7943 CATGCTGGTGA
66 CATGCTAGTGA
7954 CGTGTATTCG
Statistics
Matches: 130, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
80 117 0.90
81 7 0.05
82 6 0.05
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
CATGCTAGTGATATA
Found at i:11208 original size:47 final size:47
Alignment explanation
Indices: 11143--11829 Score: 950
Period size: 47 Copynumber: 14.4 Consensus size: 47
11133 CAGCCAAGAG
*
11143 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11190 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11237 AGTGTATGTATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11286 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11337 AGTATATGTATATATGT-ATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AG----TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11387 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11434 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11481 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11532 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11579 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11626 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATG-ATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11672 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
11719 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * * *
11766 A--GTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
11811 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
11830 TCCCGAAAGG
Statistics
Matches: 590, Mismatches: 34, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
45 37 0.06
46 54 0.09
47 320 0.54
49 43 0.07
50 33 0.06
51 99 0.17
53 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:11559 original size:145 final size:143
Alignment explanation
Indices: 11143--11768 Score: 976
Period size: 145 Copynumber: 4.3 Consensus size: 143
11133 CAGCCAAGAG
11143 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA--GTGTATATATGTAAT
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTATATATGTAAT
* * *
11206 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCTGA
66 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA--TATATGTGATAAGGCCTAATAGCCGA
*
11271 TGTGATGAATGTGAA
129 CGTGATGAATGTGAA
* * *
11286 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGTATATA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG--TGTGTATATA
* *
11351 TGT-ATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAG
60 TGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAG
11415 CCGACGTGATGAATGTGAA
125 CCGACGTGATGAATGTGAA
11434 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TGTATATATGTA
*
11499 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
64 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGA
11564 CGTGATGAATGTGAA
129 CGTGATGAATGTGAA
11579 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA--GTGTATATATGTAAT
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTATATATGTAAT
* * *
11642 AAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
66 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACG
*
11706 CGATGAATGTGAA
131 TGATGAATGTGAA
* *
11719 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
11769 ATATATGTGA
Statistics
Matches: 450, Mismatches: 20, Indels: 27
0.91 0.04 0.05
Matches are distributed among these distances:
140 96 0.21
141 36 0.08
142 1 0.00
143 2 0.00
144 56 0.12
145 128 0.28
146 1 0.00
147 44 0.10
148 38 0.08
150 37 0.08
151 11 0.02
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (143 bp):
AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTATATATGTAAT
AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACG
TGATGAATGTGAA
Found at i:12003 original size:37 final size:37
Alignment explanation
Indices: 11947--12025 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
11937 CCGAGCTCTA
* * *
11947 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
11984 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
12021 AAGAC
1 AAGAC
12026 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20968 original size:30 final size:30
Alignment explanation
Indices: 20927--20987 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
20917 TCTACCATAG
*
20927 TGTTGGTACTCAGGCTTATTAGACCTAGCA
1 TGTTGGCACTCAGGCTTATTAGACCTAGCA
20957 TGTTGGCACTCAGGCTTATTAGACCTAGCA
1 TGTTGGCACTCAGGCTTATTAGACCTAGCA
20987 T
1 T
20988 TACCAACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TGTTGGCACTCAGGCTTATTAGACCTAGCA
Found at i:22532 original size:42 final size:42
Alignment explanation
Indices: 22473--22597 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
22463 ATCAAGACTA
22473 TGTGTAAAACCATATTTGGGATATTGCATC-ATTATGAGATTT
1 TGTGTAAAACCATATTTGGGATATTGCATCGA-TATGAGATTT
* *
22515 TGTGTAAGACCATATTTGGGATATGGCATCGATATGAGATTT
1 TGTGTAAAACCATATTTGGGATATTGCATCGATATGAGATTT
* * *
22557 TGTGTAAAACCATAGTTGGGCTATTGGCATCGAAATGAGAT
1 TGTGTAAAACCATATTTGGGATATT-GCATCGATATGAGAT
22598 CTCATATAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 59 0.80
43 15 0.20
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (42 bp):
TGTGTAAAACCATATTTGGGATATTGCATCGATATGAGATTT
Found at i:22612 original size:43 final size:42
Alignment explanation
Indices: 22519--22628 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 42
22509 AGATTTTGTG
* * * ** *
22519 TAAGACCATATTTGGGATATGGCATCGATATGAGATTTTGTG
1 TAAGACCATAGTTGGGATATGGCATCGAAATGAGATCTCATA
* *
22561 TAAAACCATAGTTGGGCTATTGGCATCGAAATGAGATCTCATA
1 TAAGACCATAGTTGGGATA-TGGCATCGAAATGAGATCTCATA
*
22604 TAAGACCATA-TCTGGGATGTGGCAT
1 TAAGACCATAGT-TGGGATATGGCAT
22629 TGGTGTGGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
42 23 0.42
43 32 0.58
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
TAAGACCATAGTTGGGATATGGCATCGAAATGAGATCTCATA
Found at i:22620 original size:85 final size:84
Alignment explanation
Indices: 22473--22628 Score: 206
Period size: 85 Copynumber: 1.8 Consensus size: 84
22463 ATCAAGACTA
* * * ** * *
22473 TGTGTAAAACCATATTTGGGATATTGCATCATTATGAGATTTTGTGTAAGACCATATTTGGGATA
1 TGTGTAAAACCATAGTTGGGATATTGCATCATAATGAGATCTCATATAAGACCATATCTGGGATA
22538 TGGCATCGATATGAGATTT
66 TGGCATCGATATGAGATTT
*
22557 TGTGTAAAACCATAGTTGGGCTATTGGCATCGA-AATGAGATCTCATATAAGACCATATCTGGGA
1 TGTGTAAAACCATAGTTGGGATATT-GCATC-ATAATGAGATCTCATATAAGACCATATCTGGGA
*
22621 TGTGGCAT
64 TATGGCAT
22629 TGGTGTGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 23 0.38
85 37 0.61
86 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (84 bp):
TGTGTAAAACCATAGTTGGGATATTGCATCATAATGAGATCTCATATAAGACCATATCTGGGATA
TGGCATCGATATGAGATTT
Found at i:24964 original size:19 final size:19
Alignment explanation
Indices: 24940--24985 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
24930 GCAGTGTGAG
24940 CCACACGGATATATGGGCC
1 CCACACGGATATATGGGCC
*
24959 CCACACGGATATGTGGGCC
1 CCACACGGATATATGGGCC
24978 CCACACGG
1 CCACACGG
24986 GTTAACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.13
Consensus pattern (19 bp):
CCACACGGATATATGGGCC
Found at i:25346 original size:81 final size:81
Alignment explanation
Indices: 25209--25415 Score: 326
Period size: 81 Copynumber: 2.6 Consensus size: 81
25199 CACTAATAGA
* * * *
25209 TAAAATGATTCTTTTGCCCTTATGAGGTAAAATGACTGTTTTTCCCTTATGAGGTAAAATGACTG
1 TAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGAGGTAAAATGACTA
25274 TTTTGCCCTTATATGG
66 TTTTGCCCTTATATGG
*
25290 TAAAATGATTGTTTTGCCCTTATGTGGTAAAATGCCTGTTTTGCCCTTAT-ATGGTAAAATGACT
1 TAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGA-GGTAAAATGACT
*
25354 ATTTTTCCCTTATATGG
65 ATTTTGCCCTTATATGG
* *
25371 TAAAATGATTGTTTTGCCCTTATGTGGTAAGATGATTGTTTTGCC
1 TAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTGCC
25416 TCTATGTGCA
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 1 0.01
81 115 0.99
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (81 bp):
TAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGAGGTAAAATGACTA
TTTTGCCCTTATATGG
Found at i:25421 original size:27 final size:27
Alignment explanation
Indices: 25209--25423 Score: 279
Period size: 27 Copynumber: 8.0 Consensus size: 27
25199 CACTAATAGA
* *
25209 TAAAATGATTCTTTTGCCCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
* * *
25236 TAAAATGACTGTTTTTCCCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
* *
25263 TAAAATGACTGTTTTGCCCTTATATGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
25290 TAAAATGATTGTTTTGCCCTTATGTGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
** *
25317 TAAAATGCCTGTTTTGCCCTTATATGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
* * * *
25344 TAAAATGACTATTTTTCCCTTATATGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
25371 TAAAATGATTGTTTTGCCCTTATGTGG
1 TAAAATGATTGTTTTGCCCTTATGTGG
*
25398 TAAGATGATTGTTTTG-CCTCTATGTG
1 TAAAATGATTGTTTTGCCCT-TATGTG
25424 CAGTATATAT
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 3 0.02
27 165 0.98
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (27 bp):
TAAAATGATTGTTTTGCCCTTATGTGG
Found at i:31432 original size:33 final size:32
Alignment explanation
Indices: 31383--31446 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
31373 CTCGCTGCAA
* *
31383 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
31416 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
31447 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:31460 original size:27 final size:26
Alignment explanation
Indices: 31408--31467 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
31398 ACATATATAT
*
31408 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
31434 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
31461 ATATCTG
1 ATATCTG
31468 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:35536 original size:42 final size:42
Alignment explanation
Indices: 35473--35568 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
35463 CGAGACTATA
* *
35473 TGTAAGACCATATCTGAGATATGGCATCATTATGAGATTTCG
1 TGTAAGACCATATATGAGATATGGCATCAATATGAGATTTCG
* *
35515 TGTAAAACCATATAT-AGGATATGGCATCAATATGAGATTTTG
1 TGTAAGACCATATATGA-GATATGGCATCAATATGAGATTTCG
35557 TGTAAGACCATA
1 TGTAAGACCATA
35569 GCTAGGCTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATATATGAGATATGGCATCAATATGAGATTTCG
Found at i:54239 original size:37 final size:37
Alignment explanation
Indices: 54189--54267 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54179 TTATTATGAA
* * *
54189 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54226 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54263 GTCTT
1 GTCTT
54268 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54464 original size:47 final size:47
Alignment explanation
Indices: 54386--54722 Score: 521
Period size: 47 Copynumber: 7.1 Consensus size: 47
54376 CCCTTCGGGA
* * * * * *
54386 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54433 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54480 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54527 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54576 CTTATCTCATATATACGCTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54623 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54670 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54719 CTTA
1 CTTA
54723 CTATCATTTC
Statistics
Matches: 266, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 179 0.67
49 87 0.33
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54655 original size:143 final size:143
Alignment explanation
Indices: 54388--54722 Score: 548
Period size: 143 Copynumber: 2.4 Consensus size: 143
54378 CTTCGGGACT
* * * * * * *
54388 TATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
54451 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
54516 GGCCATTAGGCCC
131 GGCCATTAGGCCC
* *
54529 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACGC
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
54594 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
54659 GGCCATTAGGCCT
131 GGCCATTAGGCCC
54672 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
54723 CTATCATTTC
Statistics
Matches: 180, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
141 8 0.04
142 1 0.01
143 171 0.95
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (143 bp):
TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCC
Found at i:54722 original size:96 final size:94
Alignment explanation
Indices: 54386--54719 Score: 524
Period size: 96 Copynumber: 3.5 Consensus size: 94
54376 CCCTTCGGGA
* * * * * * *
54386 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
54451 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
54480 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATAC
54545 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
54576 CTTATCTCATATATACGCTTTCACATTCATCACATTGGCCATTAGGCCTTATCACGTATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
54641 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
54670 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
54720 TTACTATCAT
Statistics
Matches: 221, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
94 93 0.42
96 128 0.58
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Done.