Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1398
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: 18000
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Found at i:1184 original size:20 final size:20
Alignment explanation
Indices: 1159--1197 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1149 TTACTTCTTC
1159 TTTACTTA-TTGTCTTACTTG
1 TTTACTTACTTG-CTTACTTG
1179 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
1198 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.15, C:0.18, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:1524 original size:50 final size:50
Alignment explanation
Indices: 1446--1593 Score: 161
Period size: 50 Copynumber: 3.0 Consensus size: 50
1436 TGTTTCGTGT
* * * * * **
1446 AGTGCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATC
1 AGTGCCAACGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATATC
* * * * * *
1496 AGTGCCCATGCCATGTTCTAGACATAGTCTTACGGGGGACCTCTCATCTC
1 AGTGCCAACGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATATC
* *
1546 GGTGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 AGTGCCAACGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATA
1594 ACCTCAATAA
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
AGTGCCAACGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATATC
Found at i:5087 original size:11 final size:11
Alignment explanation
Indices: 5071--5109 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
5061 CAATTTAATA
5071 CAATTCATATT
1 CAATTCATATT
5082 CAATTCATATT
1 CAATTCATATT
5093 CAATTCA-ATT
1 CAATTCATATT
5103 CAATTCA
1 CAATTCA
5110 CATCCTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (11 bp):
CAATTCATATT
Found at i:5098 original size:5 final size:5
Alignment explanation
Indices: 5060--5109 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
5050 TAAATTTAGA
* *
5060 TCAAT TTAAT ACAAT TCATAT TCAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
5110 CATCCTAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (5 bp):
TCAAT
Found at i:5100 original size:16 final size:15
Alignment explanation
Indices: 5060--5109 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
5050 TAAATTTAGA
* *
5060 TCAATTTAATACAAT
1 TCAATTCAATTCAAT
5075 TCATATTCAATTCATAT
1 TCA-ATTCAATTCA-AT
5092 TCAATTCAATTCAAT
1 TCAATTCAATTCAAT
5107 TCA
1 TCA
5110 CATCCTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.26
16 18 0.58
17 5 0.16
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (15 bp):
TCAATTCAATTCAAT
Found at i:5279 original size:20 final size:20
Alignment explanation
Indices: 5256--5306 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
5246 CCAATTAATT
5256 CATAAATTTTATAATTTTTC
1 CATAAATTTTATAATTTTTC
5276 CATAAATTTTATAATTTTTC
1 CATAAATTTTATAATTTTTC
5296 CATAAATTTTA
1 CATAAATTTTA
5307 CATCTTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
CATAAATTTTATAATTTTTC
Found at i:5285 original size:11 final size:10
Alignment explanation
Indices: 5254--5305 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
5244 GCCCAATTAA
5254 TTCATAAATT
1 TTCATAAATT
*
5264 TT-ATAATTT
1 TTCATAAATT
5273 TTCCATAAATT
1 TT-CATAAATT
*
5284 TT-ATAATTT
1 TTCATAAATT
5293 TTCCATAAATT
1 TT-CATAAATT
5304 TT
1 TT
5306 ACATCTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
9 16 0.47
10 2 0.06
11 16 0.47
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.56
Consensus pattern (10 bp):
TTCATAAATT
Found at i:5681 original size:22 final size:22
Alignment explanation
Indices: 5656--5704 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5646 TATTTATCAT
*
5656 ATTTTATTATTTCCACTTTCCA
1 ATTTTATCATTTCCACTTTCCA
* * **
5678 ATTTAATCATTTTCTTTTTCCA
1 ATTTTATCATTTCCACTTTCCA
5700 ATTTT
1 ATTTT
5705 CCATTGATGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTATCATTTCCACTTTCCA
Found at i:8567 original size:27 final size:27
Alignment explanation
Indices: 8550--8727 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
8540 ATATTAAGTC
8550 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
8577 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
8604 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
8632 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
8659 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
8686 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
8713 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
8728 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:8689 original size:82 final size:81
Alignment explanation
Indices: 8571--8726 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
8561 TGCTATATAA
* *
8571 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
8636 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
8653 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
8717 CACTTAGTGC
65 CACTTAGTGC
8727 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:8710 original size:54 final size:54
Alignment explanation
Indices: 8550--8726 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
8540 ATATTAAGTC
* * * *
8550 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
8604 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
8659 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
8713 CGCACACTTAGTGC
1 CGCACACTTAGTGC
8727 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:16369 original size:27 final size:27
Alignment explanation
Indices: 16339--16516 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16329 ATATTGAGTC
* * * *
16339 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16366 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16393 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16421 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16448 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16475 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16502 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16517 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16478 original size:82 final size:81
Alignment explanation
Indices: 16360--16515 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16350 TGCTATATAA
* *
16360 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16425 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16442 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16506 CACTTAGTGC
65 CACTTAGTGC
16516 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.