Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1123
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: 15062
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:8638 original size:49 final size:49
Alignment explanation
Indices: 8566--8902 Score: 490
Period size: 49 Copynumber: 6.9 Consensus size: 49
8556 CTGACACAAT
8566 TTGGCC-TTCAGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 TTGGCCATTC-GGCCTTATCACATATATATACACTTTCACATTCATCACA
8615 TTGGCCATTCGGCCTTATCAC--ATATATACACTTTCAACATTCAATCACA
1 TTGGCCATTCGGCCTTATCACATATATATACACTTTC-ACATTC-ATCACA
* * *
8664 CTCGGCCATTAGGCCTTATCACATATATATGCACTTTCACATTCATCACA
1 -TTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
8714 TCGGCCATTAGGCCTTATCACATATATATACAACTTTCACATTCATATCACA
1 TTGGCCATTCGGCCTTATCACATATATATAC-ACTTTCACATTC--ATCACA
8766 TTCGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
1 TT-GGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
8814 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 TTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
8863 TTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATT
1 TTGGCCATTCGGCCTTATCACATATATATACACTTTCACATT
8903 TATTCAAATA
Statistics
Matches: 266, Mismatches: 10, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
47 51 0.19
48 13 0.05
49 98 0.37
50 52 0.20
51 14 0.05
52 20 0.08
53 18 0.07
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (49 bp):
TTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
Found at i:8848 original size:149 final size:148
Alignment explanation
Indices: 8575--8902 Score: 558
Period size: 149 Copynumber: 2.2 Consensus size: 148
8565 TTTGGCCTTC
8575 AGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAT
1 AGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAT
*
8640 ATACACTTTCAACATTCAATCACACTCGGCCATTAGGCCTTATCACATATATATGCACTTTCACA
66 ATACACTTTCAACATTCAATCACACTCGGCCATTAGGCCTTATCACATATATATACACTTTCACA
8705 TTCATCACATCGGCCATT
131 TTCATCACATCGGCCATT
8723 AGGCCTTATCACATATATATACAACTTTCACATTCATATCACATTCGGCCATTCGGCCTTATCAC
1 AGGCCTTATCACATATATATAC-ACTTTCACATTC--ATCACATT-GGCCATTCGGCCTTATCAC
8788 ATATATACACTTTC-ACATTC-ATCACA-TCGGCCATTAGGCCTTATCACATATATATACACTTT
62 ATATATACACTTTCAACATTCAATCACACTCGGCCATTAGGCCTTATCACATATATATACACTTT
*
8850 CACATTCATCACATTGGCCATT
127 CACATTCATCACATCGGCCATT
*
8872 CGGCCTTATCAC--ATATATACACTTTCACATT
1 AGGCCTTATCACATATATATACACTTTCACATT
8903 TATTCAAATA
Statistics
Matches: 173, Mismatches: 3, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
146 11 0.06
147 8 0.05
148 22 0.13
149 79 0.46
150 6 0.03
151 14 0.08
152 33 0.19
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (148 bp):
AGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAT
ATACACTTTCAACATTCAATCACACTCGGCCATTAGGCCTTATCACATATATATACACTTTCACA
TTCATCACATCGGCCATT
Found at i:13725 original size:46 final size:45
Alignment explanation
Indices: 13675--13847 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
13665 TGGTTGAGCA
*
13675 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAACG
* * *
13721 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AA--A--CG
* *
13768 TCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATGAGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGA-AACG
* *
13814 -CCGGAGCTCGTTGAGTTGATTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
13848 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 57 0.54
47 28 0.27
48 3 0.03
49 1 0.01
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAACG
Found at i:13831 original size:93 final size:93
Alignment explanation
Indices: 13672--13842 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 93
13662 GGATGGTTGA
* *
13672 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
13737 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
13765 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATG-AGAACG-CCGGAGCTCGTTGA
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCA-AACGTCC-GAACTCGTTGA
*
13828 GTTGATTCCGAGTTC
64 GTTGAGTCCGAGTTC
13843 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.