Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold184
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: 2218657
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.30
Warning! 156408 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:2195919 original size:128 final size:126
Alignment explanation
Indices: 2195740--2195985 Score: 325
Period size: 128 Copynumber: 1.9 Consensus size: 126
2195730 AAATAACGGG
**
2195740 GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAGGCCGGGGTTGAAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGAT-ATTTAGAAATAAAACCGGGGTTGAAGTATCCCC
* * * *
2195805 TTGGAAATAACGGGGTTGGAGTATCCCCTATTGTGAAAAATTGGTGTTTTAGAAATAAAATCAAA
65 TTGAAAATAACGGGGTTAGAGTATCCCCGA---TGAAAAATTGATGTTTTAGAAATAAAATCAAA
* * * * *
2195870 GTTGGAGTATCCCCGATTG-G-AAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATTCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATA-TTTAGAAATAAAACCGGGGTTGAAGTATCCCC
*
2195933 TTGAAAATAACGGGGTTAGAGTATCCCCGATGAAAAATTGATGTTTTGGAAAT
65 TTGAAAATAACGGGGTTAGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAT
2195986 CAAACCGGGA
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
125 21 0.20
127 1 0.01
128 61 0.59
129 1 0.01
130 19 0.18
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (126 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGATATTTAGAAATAAAACCGGGGTTGAAGTATCCCCT
TGAAAATAACGGGGTTAGAGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAATCAAA
Found at i:2195923 original size:49 final size:51
Alignment explanation
Indices: 2195815--2195928 Score: 169
Period size: 49 Copynumber: 2.3 Consensus size: 51
2195805 TTGGAAATAA
* *
2195815 CGGGGTTGGAGTATCCCCTATTGTGAAAAATTGGTGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAAT
***
2195866 CAAAGTTGGAGTATCCCCGATTG-G-AAAATTGGTATTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAAT
2195915 CGGGGTTGGAGTAT
1 CGGGGTTGGAGTAT
2195929 TCCCTTGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 35 0.64
50 1 0.02
51 19 0.35
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAAT
Found at i:2198336 original size:20 final size:20
Alignment explanation
Indices: 2198311--2198364 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2198301 AAAATGCCTG
*
2198311 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGCA-A
2198331 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
2198351 AATGTATCGATACA
1 AATGTATCGATACA
2198365 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:2198457 original size:20 final size:20
Alignment explanation
Indices: 2198383--2198455 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2198373 AACTTCCTAG
2198383 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
*
2198403 ATGTATCGATACAAAGATCG
1 ATGTATCGATACAAAGATCA
**
2198423 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACAAAG-ATCA
2198443 ATGTATCGATACA
1 ATGTATCGATACA
2198456 TTTCCTTAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 46 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGATCA
Found at i:2198910 original size:79 final size:79
Alignment explanation
Indices: 2198801--2198969 Score: 182
Period size: 79 Copynumber: 2.1 Consensus size: 79
2198791 TGTCTACAGG
* * * * *
2198801 GGATACTCAAACTCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTTTCAAAATA-CTG
1 GGATACTCCAACCCCATTATTTCTCAGGGGATACTCCAACCCCGACTTTATTTTCAAAATATC-G
*
2198865 A-TTTCTCATAATCGA
65 ATTTTCT-ATAATAGA
* * * * *
2198880 GGATACTCCAACCCCATTATTT-TCATGGGGATATTCCAATCCCGATTTTATTTTTAAAGTATCG
1 GGATACTCCAACCCCATTATTTCTCA-GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCG
*
2198944 ATTTTCTATAATAGG
65 ATTTTCTATAATAGA
2198959 GGATACTCCAA
1 GGATACTCCAA
2198970 TCTCGATTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.03
79 67 0.89
80 6 0.08
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (79 bp):
GGATACTCCAACCCCATTATTTCTCAGGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGA
TTTTCTATAATAGA
Found at i:2198969 original size:51 final size:51
Alignment explanation
Indices: 2198906--2199020 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
2198896 TTATTTTCAT
* * * *
2198906 GGGGATATTCCAATCCCGATTTTATTTTTAAAGT-ATCGA-TTTTCTATAATA
1 GGGGATACTCCAATCCCGATTTTATTTCTAAA-TCATCAATTTTTC-ACAATA
* *
2198957 GGGGATACTCCAATCTCGATTTTATTTCTAAATCATCAATTTTTCACAATC
1 GGGGATACTCCAATCCCGATTTTATTTCTAAATCATCAATTTTTCACAATA
2199008 GGGGATACTCCAA
1 GGGGATACTCCAA
2199021 CCCCATTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 50 0.89
52 5 0.09
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (51 bp):
GGGGATACTCCAATCCCGATTTTATTTCTAAATCATCAATTTTTCACAATA
Found at i:2203605 original size:14 final size:15
Alignment explanation
Indices: 2203586--2203614 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2203576 TTTGTTTTAG
2203586 AAAAATAGT-AATTT
1 AAAAATAGTGAATTT
2203600 AAAAATAGTGAATTT
1 AAAAATAGTGAATTT
2203615 GAAACTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
AAAAATAGTGAATTT
Found at i:2206255 original size:23 final size:22
Alignment explanation
Indices: 2206229--2206287 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
2206219 TATACTTATT
*
2206229 TATTTAATATTTAAAATTATTTA
1 TATTTAATATTTAAAATT-TTAA
* *
2206252 TATTAAATATTTATAATTTTAA
1 TATTTAATATTTAAAATTTTAA
*
2206274 GATTT-ATATTTAAA
1 TATTTAATATTTAAA
2206288 TACAAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 8 0.27
22 6 0.20
23 16 0.53
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTTAATATTTAAAATTTTAA
Found at i:2206264 original size:13 final size:14
Alignment explanation
Indices: 2206229--2206289 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
2206219 TATACTTATT
2206229 TATTTAATATTTAAAA
1 TATTT-ATATTT-AAA
2206245 TTATTTATA-TTAAA
1 -TATTTATATTTAAA
*
2206259 TATTTATAATTTTAA
1 TATTTAT-ATTTAAA
*
2206274 GATTTATATTTAAA
1 TATTTATATTTAAA
2206288 TA
1 TA
2206290 CAAACATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 7 0.18
14 11 0.29
15 12 0.32
16 3 0.08
17 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TATTTATATTTAAA
Found at i:2207435 original size:7 final size:7
Alignment explanation
Indices: 2207423--2207467 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
2207413 GGATAAAATC
*
2207423 ATAGATA
1 ATAGATT
2207430 ATAGATT
1 ATAGATT
*
2207437 ATAAATT
1 ATAGATT
*
2207444 ATAAATT
1 ATAGATT
2207451 ATAGATT
1 ATAGATT
2207458 ATAGATT
1 ATAGATT
2207465 ATA
1 ATA
2207468 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (7 bp):
ATAGATT
Found at i:2207453 original size:14 final size:14
Alignment explanation
Indices: 2207434--2207484 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
2207424 TAGATAATAG
2207434 ATTATAAATTATAA
1 ATTATAAATTATAA
* *
2207448 ATTATAGATTATAG
1 ATTATAAATTATAA
2207462 ATTAT-AA-TA-AA
1 ATTATAAATTATAA
*
2207473 AATATAAATTAT
1 ATTATAAATTAT
2207485 TTACTTTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.17
12 4 0.14
13 3 0.10
14 17 0.59
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
ATTATAAATTATAA
Found at i:2207837 original size:20 final size:19
Alignment explanation
Indices: 2207802--2207841 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2207792 TTATATCACA
2207802 TATTTAATTTTAAAATTATT
1 TATTTAATTTTAAAA-TATT
2207822 TATTTAATATTT-AAATATT
1 TATTTAAT-TTTAAAATATT
2207841 T
1 T
2207842 TCCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 11 0.58
21 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTAATTTTAAAATATT
Found at i:2208231 original size:16 final size:15
Alignment explanation
Indices: 2208213--2208253 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
2208203 GTTCAAATTT
*
2208213 TTTTTAATTTGAGTC
1 TTTTTAATTTGAATC
2208228 TTTTTAGATTTGAATC
1 TTTTTA-ATTTGAATC
2208244 TTTTTAATTT
1 TTTTTAATTT
2208254 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTTTAATTTGAATC
Found at i:2210045 original size:20 final size:21
Alignment explanation
Indices: 2210020--2210058 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2210010 ATTGTTTCTA
*
2210020 TATTTATGT-TTTTTAATGCT
1 TATTTATGTAGTTTTAATGCT
2210040 TATTTATGTAGTTTTAATG
1 TATTTATGTAGTTTTAATG
2210059 ATTTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.62
Consensus pattern (21 bp):
TATTTATGTAGTTTTAATGCT
Found at i:2210297 original size:23 final size:23
Alignment explanation
Indices: 2210271--2210315 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2210261 TTTCTTTAAA
* *
2210271 AAATTATTTATTTTTTAAAATTT
1 AAATCATTTATTTTTAAAAATTT
2210294 AAATCATTTATTTTTAAAAATT
1 AAATCATTTATTTTTAAAAATT
2210316 ATTGTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATCATTTATTTTTAAAAATTT
Done.