Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold240
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: 37325
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Found at i:4063 original size:27 final size:27
Alignment explanation
Indices: 4027--4170 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 27
4017 CGCAACTCCA
4027 AGTGCT-CATAATCAACTCGCACACTT
1 AGTGCTACATAATCAACTCGCACACTT
* *
4053 AGT-CTGACATAATCAACAC-CTGAAACTT
1 AGTGCT-ACATAATCAACTCGC--ACACTT
* *
4081 ATTGCTACAATAGTCAAC-CGCACACTT
1 AGTGCTAC-ATAATCAACTCGCACACTT
*
4108 AGTGCCTACATAGTCCAAACTCGCACACTT
1 AGTG-CTACATAAT-C-AACTCGCACACTT
* *
4138 AG-GCTACATAGCTCAATTCGCACACTT
1 AGTGCTACATA-ATCAACTCGCACACTT
4165 AGTGCT
1 AGTGCT
4171 GCACAATTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
25 2 0.02
26 4 0.04
27 38 0.39
28 26 0.27
29 16 0.16
30 11 0.11
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (27 bp):
AGTGCTACATAATCAACTCGCACACTT
Found at i:13227 original size:27 final size:27
Alignment explanation
Indices: 13171--13298 Score: 151
Period size: 27 Copynumber: 4.8 Consensus size: 27
13161 CGATATAAAT
*
13171 TCAACTCG-ACACTTA--GCTAACATTAA
1 TCAACTCGCACACTTAGTGCT-ACA-TAG
13197 TCAAACTCGCACACTTAGTGCTACA-AG
1 TC-AACTCGCACACTTAGTGCTACATAG
13224 TCAACTTCGCACACTTAGTGCTACATAG
1 TCAAC-TCGCACACTTAGTGCTACATAG
13252 TCAAACTCG--CACTTAGTGCTACATAG
1 TC-AACTCGCACACTTAGTGCTACATAG
*
13278 TCAATTCGCACACTTAGTGCT
1 TCAACTCGCACACTTAGTGCT
13299 GCACATTTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 17
0.83 0.02 0.15
Matches are distributed among these distances:
25 5 0.05
26 24 0.26
27 39 0.43
28 14 0.15
29 6 0.07
30 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (27 bp):
TCAACTCGCACACTTAGTGCTACATAG
Found at i:13316 original size:53 final size:53
Alignment explanation
Indices: 13208--13316 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 53
13198 CAAACTCGCA
* *
13208 CACTTAGTGCTACAAGTCAACTTCGCACACTTAGTGCTACATAGTCAAACTCG
1 CACTTAGTGCTACAAGTCAACTTCGCACACTTAGTGCTACACAGTCAAACCCG
* * *
13261 CACTTAGTGCTACATAGTCAA-TTCGCACACTTAGTGCTGCACATTTAAACCCG
1 CACTTAGTGCTACA-AGTCAACTTCGCACACTTAGTGCTACACAGTCAAACCCG
13314 CAC
1 CAC
13317 ACTAGCGCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 44 0.88
54 6 0.12
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (53 bp):
CACTTAGTGCTACAAGTCAACTTCGCACACTTAGTGCTACACAGTCAAACCCG
Found at i:21272 original size:28 final size:27
Alignment explanation
Indices: 21209--21360 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
21199 ATATTAAGTC
* * *
21209 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
21236 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
21264 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
21291 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
21319 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
21346 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21361 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:21293 original size:55 final size:55
Alignment explanation
Indices: 21209--21360 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
21199 ATATTAAGTC
* * *
21209 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
21264 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
21319 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
21361 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:30031 original size:39 final size:39
Alignment explanation
Indices: 29817--30036 Score: 293
Period size: 40 Copynumber: 5.6 Consensus size: 39
29807 AAACCAAGTA
** * *
29817 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCAC-AATG
**
29856 CCTTCGAAACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAA-TG
*
29896 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGTACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAA-TG
*
29936 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATG
*
29975 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AATG
30015 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
30037 CAATCCGAAT
Statistics
Matches: 165, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
39 63 0.38
40 102 0.62
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATG
Done.