Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2278
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: 34604
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:5516 original size:29 final size:29
Alignment explanation
Indices: 5482--5553 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
5472 ATCAACCGCG
* * *
5482 CACACTTAGTGCCATGCACTTTAAACTCA
1 CACACTTAGTGCCATACAATTTAAACCCA
** *
5511 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCCATACAATTTAAACCCA
5540 CACACTTAGTGCCA
1 CACACTTAGTGCCA
5554 ATCTCATGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CACACTTAGTGCCATACAATTTAAACCCA
Found at i:24268 original size:16 final size:15
Alignment explanation
Indices: 24242--24276 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
24232 TGATGTGAAT
24242 AATATAAAATATTAA
1 AATATAAAATATTAA
*
24257 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
24273 AATA
1 AATA
24277 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:24448 original size:20 final size:20
Alignment explanation
Indices: 24391--24450 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
24381 AATACTACAT
24391 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
24410 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
24433 AAATATGTACATAATATA
1 AAATATGTACATAATATA
24451 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:24489 original size:22 final size:23
Alignment explanation
Indices: 24428--24498 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
24418 ACGTGATAAT
*
24428 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
24451 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
24476 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
24498 A
1 A
24499 CATGTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:24570 original size:25 final size:26
Alignment explanation
Indices: 24513--24571 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
24503 TAAAAAAAAT
* *
24513 ATATATATATAAATAATATAGTATTA
1 ATATATATATAAATAAAATAATATTA
* *
24539 A-AGATATATACATAAAATAATA-TA
1 ATATATATATAAATAAAATAATATTA
24563 ATATATATA
1 ATATATATA
24572 CGTAATATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.11
25 23 0.85
26 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (26 bp):
ATATATATATAAATAAAATAATATTA
Found at i:26048 original size:30 final size:30
Alignment explanation
Indices: 26012--26070 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
26002 TGCAAAGCAT
26012 AAATT-AAAAGACTCAACTCAACTCTCGCAG
1 AAATTAAAAAG-CTCAACTCAACTCTCGCAG
* *
26042 AAATTAAAAAGCTCAACTCACCTTTCGCA
1 AAATTAAAAAGCTCAACTCAACTCTCGCA
26071 ATATGAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.22
Consensus pattern (30 bp):
AAATTAAAAAGCTCAACTCAACTCTCGCAG
Found at i:26474 original size:170 final size:167
Alignment explanation
Indices: 26273--27022 Score: 466
Period size: 150 Copynumber: 4.8 Consensus size: 167
26263 ATAAATTGAA
* * *
26273 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
*
26338 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
26402 TGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
127 TGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
* * * * *
26443 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGTAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
* * * *
26508 AACAGAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
26572 -TTTTTTT-------A-AAA---AAACA-G-AAATTG
131 TTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
* * * * ** * **
26595 AAAATACTTCAGCATGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTTTTTTTTTTTGA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAG-TTGATTTTTTTG-
* * * * * * * **
26658 AAAATAGAAATTGAAAATACCTTAGCATGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTG
64 AAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
26723 A----ATTTTGAAA-ACAGAAATT-------G-AAA-T-
129 ATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
* * * ** * *
26747 ----TACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
* * * * * **
26804 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
26868 ATTTTTTT--------GAAA--G--ACA-G-AAATTG
131 TTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
* * ** *
26891 AAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCATAATATGAGTTGA--TTTTTGA
1 AAAATACCTCAGCGTGTG-ACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGA
* * * * **
26953 AAACAGAAATTGGAAATACCTCAACGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA
65 AAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
27018 ATTTT
130 TTTTT
27023 GAAAACAGAA
Statistics
Matches: 492, Mismatches: 59, Indels: 77
0.78 0.09 0.12
Matches are distributed among these distances:
140 4 0.01
142 4 0.01
143 1 0.00
144 60 0.12
145 5 0.01
147 6 0.01
148 53 0.11
150 127 0.26
151 14 0.03
152 78 0.16
153 2 0.00
154 8 0.02
156 1 0.00
157 6 0.01
158 1 0.00
165 7 0.01
166 2 0.00
167 37 0.08
169 18 0.04
170 58 0.12
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (167 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
Found at i:26779 original size:72 final size:72
Alignment explanation
Indices: 26437--27106 Score: 766
Period size: 72 Copynumber: 9.0 Consensus size: 72
26427 TGAAAAACGA
* * *** * *
26437 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGTAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TT
*
26502 TTTGACAACAG
62 TTTGAAAACAG
* * * **
26513 AAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTTT
*
26578 TAAAAAAACAG
64 T--GAAAACAG
* * **
26589 AAATTGAAAATACTTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTTTTTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG---TTGATTT
*
26654 TTGAAAAATAG
63 TTG-AAAACAG
* * * *
26665 AAATTGAAAATACCTTAGCATGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
26730 AAAACAG
66 AAAACAG
* * *
26737 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
26802 AAAACAG
66 AAAACAG
* *
26809 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-A--TTT
26874 TTGAAAGACAG
63 TTGAAA-ACAG
* * ** **
26885 AAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCATAATATGAGTTGATTT
1 AAATTGAAAATACCTCAGC--GTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
26949 TTGAAAACAG
63 TTGAAAACAG
* * * *
26959 AAATTGGAAATACCTCAACGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
27024 AAAACAG
66 AAAACAG
* ** *
27031 AAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATTTCTTGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTTT
27096 TGAAAACAG
64 TGAAAACAG
27105 AA
1 AA
27107 GTAACAACAT
Statistics
Matches: 520, Mismatches: 58, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
71 1 0.00
72 226 0.43
73 8 0.02
74 75 0.14
75 17 0.03
76 153 0.29
77 6 0.01
78 31 0.06
79 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (72 bp):
AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
AAAACAG
Found at i:27009 original size:222 final size:219
Alignment explanation
Indices: 26437--27106 Score: 914
Period size: 222 Copynumber: 3.0 Consensus size: 219
26427 TGAAAAACGA
* * * *
26437 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGTAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAGCATGTGACC-GAGGCTCAACTCACCTCTCGTAATATGAGTTGA--TT
* * * * **
26502 TTTGACAACAGAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
63 TTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
* * * * *
26567 GTTGATTTTTTTAAAAAAACAGAAATTGAAAATACTTCAGCATGTCTTGAGGCTCAACTCATTTC
128 GTTGA--ATTTT--GAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTC
** *
26632 TCGCAATATGAGTTTTTTTTTTTTGAAAAATAG
189 TCGCAATATGAG-TTGATTTTTTTG-AAAACAG
* * * ** * *
26665 AAATTGAAAATACCTTAGCATGT--CTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTT
1 AAATTGAAAATACCTCAGCATGTGAC-CGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
26728 TGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
65 TGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
*
26793 TGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
130 TGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAA
26858 TATGAGTTGAATTTTTTTGAAAGACAG
195 TATGAGTTG-ATTTTTTTGAAA-ACAG
*
26885 AAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCATAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAGCATGTG-ACCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
*
26950 TGAAAACAGAAATTGGAAA-TACCTCAACGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAG
65 TGAAAACAGAAATT-GAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
** *
27014 TTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATTTCTTGCA
129 TTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCA
27079 ATATGAGTTGATTTTTTTGAAAACAG
194 ATATGAGTTGATTTTTTTGAAAACAG
27105 AA
1 AA
27107 GTAACAACAT
Statistics
Matches: 396, Mismatches: 39, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
219 5 0.01
220 97 0.24
221 12 0.03
222 164 0.41
223 5 0.01
224 65 0.16
226 28 0.07
228 20 0.05
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (219 bp):
AAATTGAAAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
GAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
GAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
ATGAGTTGATTTTTTTGAAAACAG
Done.