Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1550
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: 32978
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Found at i:6619 original size:40 final size:40
Alignment explanation
Indices: 6582--6765 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
6572 GCTACTCGTT
*
6582 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
6622 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * **
6662 CCAATGCCTTCTGG-CTTAGCCC-GAAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * * *
6701 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
*
6742 CAAA-GCCTTCGGGACTTAGGCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
6766 ACATCATTCG
Statistics
Matches: 120, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
38 3 0.03
39 29 0.24
40 72 0.60
41 16 0.13
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:6750 original size:79 final size:80
Alignment explanation
Indices: 6582--6760 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 80
6572 GCTACTCGTT
* **
6582 CAAATGCCTTCGGGACATAGCCCG-GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGAAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
6646 GATTTAGTAACTCGCAC
64 GATATAGTAACTAGCAC
* * ** *
6663 CAATGCCTTCTGG-CTTAGCCCGAAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCTGG
1 CAAAGCCTTCGGGACTTAGCCCGAAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
6726 ATATGGTCACTTAGCA-
65 ATATAGTAAC-TAGCAC
6742 CAAAGCCTTCGGGACTTAG
1 CAAAGCCTTCGGGACTTAG
6761 GCCGGACATC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
78 3 0.04
79 56 0.70
80 18 0.22
81 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTAGCAC
Found at i:15069 original size:11 final size:10
Alignment explanation
Indices: 15043--15076 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
15033 GGAGAGCACC
*
15043 AAGAGTCAAA
1 AAGAGCCAAA
15053 AAGAGCCAAA
1 AAGAGCCAAA
15063 AATGAGCCAAA
1 AA-GAGCCAAA
15074 AAG
1 AAG
15077 GGACAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.06
Consensus pattern (10 bp):
AAGAGCCAAA
Found at i:15268 original size:13 final size:13
Alignment explanation
Indices: 15250--15279 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15240 CTGGCAATCA
15250 TGTCACACGGCCG
1 TGTCACACGGCCG
*
15263 TGTCACACGGGCG
1 TGTCACACGGCCG
15276 TGTC
1 TGTC
15280 CCTGCTGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.33, G:0.33, T:0.20
Consensus pattern (13 bp):
TGTCACACGGCCG
Found at i:25506 original size:29 final size:28
Alignment explanation
Indices: 25451--25539 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
25441 GTGAGCATGA
*
25451 ATATGAATGTGA-TTGGGCCTAACGGGCC
1 ATAT-AATGTGATTTGGGCCTAATGGGCC
25479 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATAT-AATGTGATTTGGGCCTAATGGGCC
* * * *
25508 ACATAAGGTGATTCGTGCCTAATGGGCC
1 ATATAATGTGATTTGGGCCTAATGGGCC
25536 ATAT
1 ATAT
25540 GAAAATGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
28 35 0.66
29 18 0.34
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (28 bp):
ATATAATGTGATTTGGGCCTAATGGGCC
Found at i:26999 original size:40 final size:40
Alignment explanation
Indices: 26928--27151 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
26918 GCTACTCGTT
*
26928 CAAATGCCTT-GGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
26967 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
27007 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27047 CAAATG-CTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
27086 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
27127 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27152 CATCATTCAA
Statistics
Matches: 168, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
38 3 0.02
39 42 0.25
40 109 0.65
41 14 0.08
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27071 original size:79 final size:80
Alignment explanation
Indices: 26928--27151 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 80
26918 GCTACTCGTT
*
26928 CAAATGCCTT-GGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
26992 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* **
27007 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATG-CTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
*
27069 GGATTTAGTAACTCGTA
64 GGATTTAGTAACTCGCA
* ** * * * * *
27086 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CATAACCCGGTTATAGT-AACTCGCACAAATGCCTTCGGGACTTAACCC
27149 GGA
64 GGA
27152 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 7 0.06
79 59 0.47
80 54 0.43
81 5 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Done.