Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1674
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: 17109
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:928 original size:5 final size:5
Alignment explanation
Indices: 902--1087 Score: 73
Period size: 4 Copynumber: 41.2 Consensus size: 5
892 CCCCAGAAAA
* *
902 ACCCC A-CCA ACCCC ACCCC ACCGCAC CCCCC ACCCC -CTCCC -CCCC
1 ACCCC ACCCC ACCCC ACCCC ACC-C-C ACCCC ACCCC AC-CCC ACCCC
* * *
947 ACCCCC CCCCC ACACCC ACTCC ACCCCC CCCCC ACCCC -CCCC -CCCC
1 A-CCCC ACCCC AC-CCC ACCCC A-CCCC ACCCC ACCCC ACCCC ACCCC
993 -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC
1 ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC
1033 -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC -CCCC
1 ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC
* *
1073 -CCCC CCCCC CCCCC A
1 ACCCC ACCCC ACCCC A
1088 AAAAAAAAAA
Statistics
Matches: 161, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
4 99 0.61
5 45 0.28
6 14 0.09
7 3 0.02
ACGTcount: A:0.08, C:0.90, G:0.01, T:0.01
Consensus pattern (5 bp):
ACCCC
Found at i:938 original size:1 final size:1
Alignment explanation
Indices: 927--1086 Score: 239
Period size: 1 Copynumber: 160.0 Consensus size: 1
917 CCCCACCGCA
* * * * * * * * *
927 CCCCCCACCCCCTCCCCCCCACCCCCCCCCCACACCCACTCCACCCCCCCCCCACCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
992 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1057 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1087 AAAAAAAAAA
Statistics
Matches: 141, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 141 1.00
ACGTcount: A:0.04, C:0.94, G:0.00, T:0.01
Consensus pattern (1 bp):
C
Found at i:4031 original size:26 final size:26
Alignment explanation
Indices: 3979--4030 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3969 AAATATGATA
* *
3979 TAATAAAAATTATTTTCTTTTATTTT
1 TAATAAAAAATATTATCTTTTATTTT
4005 TAATAAAAAATATTAT-TTTTATTTT
1 TAATAAAAAATATTATCTTTTATTTT
4030 T
1 T
4031 TTACTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TAATAAAAAATATTATCTTTTATTTT
Found at i:9876 original size:3 final size:3
Alignment explanation
Indices: 9868--9892 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9858 ATCTTACTCC
9868 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
9893 GATTAACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10203 original size:12 final size:14
Alignment explanation
Indices: 10181--10238 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 14
10171 TTAAAATATA
*
10181 AATTTTATTTTT-T
1 AATTATATTTTTAT
10194 -ATTATATTTTTAT
1 AATTATATTTTTAT
*
10207 AATTAAATTTTTA-
1 AATTATATTTTTAT
*
10220 AA-AATATTTTTATT
1 AATTATATTTTTA-T
10234 AATTA
1 AATTA
10239 AATATTGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 18 0.51
13 3 0.09
14 13 0.37
15 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTATATTTTTAT
Found at i:10553 original size:21 final size:21
Alignment explanation
Indices: 10501--10555 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
10491 ATAATAGTAA
* *
10501 TAATGAAATTAATTATTATAT
1 TAATGAAATTAAATGTTATAT
*
10522 TGATGAAATTAAATGTTATAT
1 TAATGAAATTAAATGTTATAT
10543 TAAT-AATATTAAA
1 TAATGAA-ATTAAA
10556 AATTTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TAATGAAATTAAATGTTATAT
Found at i:11036 original size:53 final size:53
Alignment explanation
Indices: 10979--11081 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
10969 TTATTTTAAG
* * *
10979 TTCAAATTATT-TTAATTTCGGATCAACCAAGTTTAAAATTAAAATTAATCGTA
1 TTCAAATTATTCTAAATTT-AGATCAACCAAATTTAAAATTAAAATTAATCGTA
* * *
11032 TTCAAATTATTCTAAATTTAGATCAATCAAATTTAACATTAAGATTAATC
1 TTCAAATTATTCTAAATTTAGATCAACCAAATTTAAAATTAAAATTAATC
11082 AAATTTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 37 0.86
54 6 0.14
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.40
Consensus pattern (53 bp):
TTCAAATTATTCTAAATTTAGATCAACCAAATTTAAAATTAAAATTAATCGTA
Found at i:13052 original size:3 final size:3
Alignment explanation
Indices: 13044--13074 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13034 TTAGAGGAGT
13044 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13075 GAAAATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.