Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3202
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: 29006
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1428 original size:36 final size:36
Alignment explanation
Indices: 1356--1432 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
1346 TTATTACGAA
* *
1356 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATC-G
*
1393 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
1428 GTCTT
1 GTCTT
1433 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 6 0.16
36 13 0.35
37 18 0.49
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (36 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
Found at i:1674 original size:47 final size:47
Alignment explanation
Indices: 1546--2397 Score: 1423
Period size: 47 Copynumber: 18.1 Consensus size: 47
1536 TGCCCTTCGG
* * * * * * *
1546 CTTATCAAATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
1593 CCTGTCACATATATTACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
1641 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1688 CCTATCAATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1736 C-TATCACATATATACACTTTCACATTCATCACATCGTCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1782 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1829 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1875 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1922 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1971 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2018 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2065 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2112 CTTAACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2159 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2206 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2255 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2302 CTTAT--C--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2345 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2394 CTTA
1 CTTA
2398 CTATCATTTA
Statistics
Matches: 767, Mismatches: 22, Indels: 30
0.94 0.03 0.04
Matches are distributed among these distances:
43 42 0.05
45 40 0.05
46 47 0.06
47 386 0.50
48 117 0.15
49 135 0.18
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2126 original size:237 final size:237
Alignment explanation
Indices: 1546--2397 Score: 1420
Period size: 237 Copynumber: 3.6 Consensus size: 237
1536 TGCCCTTCGG
* * * * * * * * *
1546 CTTATCAAATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATTACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA-TACA
* *
1611 CTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTAACACATATATACACTTTCACATTCATCACAT
*
1676 CGGCCATTAGGCCCTATCA-ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCC-TA
130 CGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
1739 TCACATATATACACTTTCACATTCATCACATCGTCCATTAGGC
195 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1782 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-C-TATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
1844 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTAACACATATATACACTTTCACATTCATCACA
1909 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
129 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1974 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
194 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2018 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
2083 TTTCACATTCATCACATCGGCCATTAGGCCTTAACATATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTAACACATATATACACTTTCACATTCATCACATC
2148 GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
2211 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
196 CAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2255 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--C--ATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
2316 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTA--ACACATATATACACTTTCACATTCATCACA
2381 TCGGCCATTAGGCCTTA
129 TCGGCCATTAGGCCTTA
2398 CTATCATTTA
Statistics
Matches: 592, Mismatches: 13, Indels: 23
0.94 0.02 0.04
Matches are distributed among these distances:
233 41 0.07
234 86 0.15
235 190 0.32
236 48 0.08
237 227 0.38
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (237 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTAACACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:15054 original size:24 final size:22
Alignment explanation
Indices: 15001--15090 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 22
14991 AGCTCATATG
*
15001 AGCTTACTGATATATCAACTCGTAA
1 AGCTTACTG-T-T-TCAGCTCGTAA
15026 GAGCTTACTGTTCTCAGCTCGTATA
1 -AGCTTACTGTT-TCAGCTCGTA-A
*
15051 AGCTTACTGTTT-AGCTCTTCAA
1 AGCTTACTGTTTCAGCTCGT-AA
*
15073 AGCTTACTGTTTTAGCTC
1 AGCTTACTGTTTCAGCTC
15091 AATAGAGCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
22 19 0.33
23 7 0.12
24 21 0.36
25 2 0.03
26 9 0.16
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (22 bp):
AGCTTACTGTTTCAGCTCGTAA
Found at i:20264 original size:46 final size:46
Alignment explanation
Indices: 20214--20389 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
20204 TGGTTGAGCA
20214 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20260 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
20305 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20353 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20390 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20348 original size:93 final size:93
Alignment explanation
Indices: 20211--20382 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
20201 GGATGGTTGA
* * *
20211 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20276 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
20304 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20369 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20383 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27828 original size:46 final size:46
Alignment explanation
Indices: 27778--27953 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
27768 TGGTTGAGCA
27778 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27824 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
27869 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27917 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27954 CGGGTTACAT
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27934 original size:93 final size:93
Alignment explanation
Indices: 27775--27946 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
27765 GGATGGTTGA
* *
27775 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27840 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27868 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27933 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
27947 CTTATGGCGG
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:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.