Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold655
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: 13196
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2465 original size:21 final size:21
Alignment explanation
Indices: 2398--2466 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
2388 CAAAACAAGG
2398 AAAAAGTATCGATACCAA-AAC
1 AAAAA-TATCGATACCAATAAC
* **
2419 AAAAGGTATCGATACCTTTTAA-
1 AAAA-ATATCGATACC-AATAAC
*
2441 AAAAATATCGATACCAATGAC
1 AAAAATATCGATACCAATAAC
2462 AAAAA
1 AAAAA
2467 CAATACCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 2 0.05
21 29 0.78
22 4 0.11
23 2 0.05
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (21 bp):
AAAAATATCGATACCAATAAC
Found at i:3210 original size:41 final size:40
Alignment explanation
Indices: 3119--3217 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
3109 AAAAACACTG
** * **
3119 CTATTACTTTACCTTTAACGGCGTTTATGAAAAAATGCGG
1 CTATTACTTTACCTTTTGCGACGTTTATGAAAAAATGCCA
* * *
3159 TTGTTGCTTTACCTTTTGCGACGTTTATGAGAAAAATGCCA
1 CTATTACTTTACCTTTTGCGACGTTTATGA-AAAAATGCCA
3200 CTATTACTTTACCTTTTG
1 CTATTACTTTACCTTTTG
3218 TGGCTTTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
40 24 0.51
41 23 0.49
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (40 bp):
CTATTACTTTACCTTTTGCGACGTTTATGAAAAAATGCCA
Found at i:3227 original size:41 final size:40
Alignment explanation
Indices: 3092--3234 Score: 124
Period size: 41 Copynumber: 3.5 Consensus size: 40
3082 TAAAAAAATA
* ** **
3092 TTTGCGGCATTTATGGAAAAAACACTGCTATTACTTTACCT
1 TTTGCGGCGTTTAT-GAAAAAATGCCACTATTACTTTACCT
** *** * *
3133 TTAACGGCGTTTATGAAAAAATGCGGTTGTTGCTTTACCT
1 TTTGCGGCGTTTATGAAAAAATGCCACTATTACTTTACCT
*
3173 TTTGCGACGTTTATGAGAAAAATGCCACTATTACTTTACCT
1 TTTGCGGCGTTTATGA-AAAAATGCCACTATTACTTTACCT
* * *
3214 TTTGTGGCTTTTATGCAAAAA
1 TTTGCGGCGTTTATGAAAAAA
3235 CGTTACTAAT
Statistics
Matches: 80, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
40 38 0.47
41 42 0.52
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (40 bp):
TTTGCGGCGTTTATGAAAAAATGCCACTATTACTTTACCT
Found at i:4784 original size:16 final size:16
Alignment explanation
Indices: 4765--4796 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4755 ATTTAATCCC
*
4765 CATTTGTTATTATTAT
1 CATTTATTATTATTAT
4781 CATTTATTATTATTAT
1 CATTTATTATTATTAT
4797 ATATATATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (16 bp):
CATTTATTATTATTAT
Found at i:4833 original size:28 final size:30
Alignment explanation
Indices: 4784--4839 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
4774 TTATTATCAT
4784 TTATTATTATTATATATATATACATACACA
1 TTATTATTATTATATATATATACATACACA
4814 TTATT-TT-TTATA-ATAGTATACATACA
1 TTATTATTATTATATATA-TATACATACA
4840 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 15 0.60
29 2 0.08
30 5 0.20
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (30 bp):
TTATTATTATTATATATATATACATACACA
Found at i:5051 original size:2 final size:2
Alignment explanation
Indices: 5044--5076 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5034 TTTCATAATT
*
5044 TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5077 GTTTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5058 original size:14 final size:14
Alignment explanation
Indices: 5041--5086 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
5031 ATATTTCATA
5041 ATTTATATATATAT
1 ATTTATATATATAT
5055 ATTTATATATATAT
1 ATTTATATATATAT
* * *
5069 ATATATATGTTTAT
1 ATTTATATATATAT
5083 ATTT
1 ATTT
5087 TTCTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
ATTTATATATATAT
Found at i:5063 original size:12 final size:12
Alignment explanation
Indices: 5046--5084 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5036 TCATAATTTA
5046 TATATATATATT
1 TATATATATATT
5058 TATATATATA--
1 TATATATATATT
*
5068 TATATATATGTT
1 TATATATATATT
5080 TATAT
1 TATAT
5085 TTTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATATATATT
Found at i:5367 original size:27 final size:27
Alignment explanation
Indices: 5332--5385 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5322 CATGTATATA
* *
5332 TTTTGTATTTTTTTTC-TCTTTATGTTT
1 TTTTGTATTTATTTCCTTCTTT-TGTTT
*
5359 TTTTTTATTTATTTCCTTCTTTTGTTT
1 TTTTGTATTTATTTCCTTCTTTTGTTT
5386 ATCGATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.07, C:0.09, G:0.06, T:0.78
Consensus pattern (27 bp):
TTTTGTATTTATTTCCTTCTTTTGTTT
Found at i:6469 original size:27 final size:27
Alignment explanation
Indices: 6434--6486 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6424 ATACTTTCTA
*
6434 AATAATTTTAATAATTTTTATTTTTAC
1 AATAATTTTAATAATTTTAATTTTTAC
* * *
6461 AATATTTTTTATCATTTTAATTTTTA
1 AATAATTTTAATAATTTTAATTTTTA
6487 AAAATTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
AATAATTTTAATAATTTTAATTTTTAC
Found at i:12057 original size:164 final size:161
Alignment explanation
Indices: 11668--12968 Score: 953
Period size: 164 Copynumber: 8.0 Consensus size: 161
11658 ACAAGTATTC
* * * * * * * *
11668 TAAAAGATACATAATTTGAAAACCAATTTGCATATTAAAATAATATACAAAATAAGTATTTATAA
1 TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAA-AAACAAAATAAGCATTTATAA
* * * *
11733 TAAAAT-ACGGGTTTAGGTATAGTAAAAGGTGTATGTTTTCAATAACCAAAG-AAAATAAGCATT
65 TAAAATGA--GGTTTAGGTATAGT-AAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATT
* * * * *
11796 TATAAGACACGATGGAGTATAGA-TTT-AGTCGTCGT
127 TATAA-ACACAATGAAATATAAACTTTAAGT-ATCGT
* * * *
11831 TAAAAGATATCTAATTCGAAAACCATCTTACTTA--ATAATAAAAACAAAATAAGCATTTATAAT
1 TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAAT
* * * * * *
11894 AAAATGCAAGTTTAAGTATAATACAAGATGTATGATTCCGATAACAAAAGCGAAATAAGTATTTA
66 AAAATG-AGGTTTAGGTATAGTA-AAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATTTA
* *
11959 TGAAACACGATGGAATATAAACTTTAAGTATCGT
129 T-AAACACAATGAAATATAAACTTTAAGTATCGT
* *
11993 TAAAAGATATATAAATT-GAAAACCATTTTATTTATTAAAACAAAAACAAAATAATCATTTATAA
1 TAAAAGATATAT-AATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAA
* * * * * *
12057 TAAAATACAAGTTTAGGTATTGTAAA-----A-GA---AG-TAA-AATAAGC---AT---T-TAT
65 TAAAAT-GAGGTTTAGGTATAGTAAAGGTGTATGATTCCGATAACCA-AAGCAAAATAAGTATTT
** *
12104 A-AAGTACGATGAAATATAAACTTTAAGTATCGT
128 ATAAACACAATGAAATATAAACTTTAAGTATCGT
* *
12137 TAAAAGATATATAATTC-ATTATAATTCAAAAATCATTATACTTATTAAAATAAAAACAAAAGTA
1 TAAAAGATATATAATTCGA--A-AA--C------CATTTTACTTATTAAAACAAAAACAAAA-TA
* * * *
12201 AGCATCTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGGATGATTCCGATAACGAAAGAAA
54 AGCATTTATAATAAAAT-GAGGTTTAGGTATAGT-AAAGGTGTATGATTCCGATAACCAAAGCAA
* *
12266 AATTAA-CATTTATAGTACACAATGAAATATAAACTTTAAGTATCGT
117 AA-TAAGTATTTATA-AACACAATGAAATATAAACTTTAAGTATCGT
* * * * * *
12312 TGAAAGATATATAATTTGAAAACCGTCTTACTTATTAAAAGAGAAACAAAATAAGCATTTATAAT
1 TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAAT
* ** *
12377 AAAATAGAGGTTTACGTATAGCGGAAGGTGTATGATTCCTATAACCAAAGCAAAATAAGTATTTA
66 AAAAT-GAGGTTTAGGTATAG-TAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATTTA
** *
12442 TATAACACTCGTAAAATATAAACTTTAAGTATCGT
129 TA-AACAC-AATGAAATATAAACTTTAAGTATCGT
* * *
12477 TAAAAGATATCTAATTTGAAAACC-TATTTACTTATTGAAACAAAAACAAAATAAGC----ATAA
1 TAAAAGATATATAATTCGAAAACCAT-TTTACTTATTAAAACAAAAACAAAATAAGCATTTATAA
*
12537 TAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGAAAAATAAGTATTT
65 TAAAAT-GAGGTTTAGGTATAGT-AAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATTT
* ** *
12602 ATATA-AC-AT-CCAT-GAAA---T-A-TATCGT
128 ATAAACACAATGAAATATAAACTTTAAGTATCGT
* * * * *
12627 TAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACGCATTTATAAC
1 TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAAT
* * * * * * *
12692 AGAATAGAGATATAGATATGGTGAAAGGTGTATGATTCCGAAAACCAAAGCAAAATAAGCATTTA
66 AAAAT-GAGGTTTAGGTATAGT-AAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATTTA
* * *
12757 TAATATATAATGAAATATAAATTTTAAGTATCGT
129 TAA-ACACAATGAAATATAAACTTTAAGTATCGT
* * * * * * *
12791 TAAAGGATATATAATTCGAAAATCGTTCTACTTATT-AAA-AAAAATAAAGTACGCATTTATAAT
1 TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAAT
* * *
12854 AAAATAGAGGTATAGGTATGGTGAAAGGTGAAAGGTGTATGATTTCGATAACCAAAGCAAAACAA
66 AAAAT-GAGGT-T---TA-GGT-ATA-GT-AAAGGTGTATGATTCCGATAACCAAAGCAAAATAA
* * * * *
12919 GCATTTATATAACACTCATAAAATATAAACTTTAAGCATAGT
122 GTATTTATA-AACAC-AATGAAATATAAACTTTAAGTATCGT
*
12961 TGAAAGAT
1 TAAAAGAT
12969 GTAGTTTAGG
Statistics
Matches: 927, Mismatches: 135, Indels: 145
0.77 0.11 0.12
Matches are distributed among these distances:
143 5 0.01
144 41 0.04
145 1 0.00
146 5 0.01
147 1 0.00
148 1 0.00
150 56 0.06
151 2 0.00
152 3 0.00
153 7 0.01
154 89 0.10
155 35 0.04
156 6 0.01
157 5 0.01
158 3 0.00
159 6 0.01
160 58 0.06
161 101 0.11
162 69 0.07
163 43 0.05
164 156 0.17
165 95 0.10
166 8 0.01
167 3 0.00
168 1 0.00
169 47 0.05
170 29 0.03
171 1 0.00
173 5 0.01
174 2 0.00
175 42 0.05
176 1 0.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.30
Consensus pattern (161 bp):
TAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAAT
AAAATGAGGTTTAGGTATAGTAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGTATTTATA
AACACAATGAAATATAAACTTTAAGTATCGT
Found at i:12756 original size:154 final size:151
Alignment explanation
Indices: 12471--12945 Score: 474
Period size: 154 Copynumber: 3.0 Consensus size: 151
12461 AAACTTTAAG
* * * *
12471 TATCGTTAAAAGATATCTAATTTGAAAA-CCTATTTACTTATTGAAACAAAAACAAAATAAGCA-
1 TATCGTTAAAAGATATATAATTCGAAAATCGT-TTTACTTATT-AAACAAAAACAAAATACGCAT
* * * * * *
12534 TAAT-AAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGAAAAATAAGT
64 TTATAAAAATAGAGATATAGGTATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGC
*
12598 ATTTATATAACATCCATGAAATA
129 ATTTATATAACATCCATAAAATA
*
12621 TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACGCATT
1 TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATT-AAACAAAAACAAAATACGCATT
* *
12686 TATAACAGAATAGAGATATAGATATGGTGAAAGGTGTATGATTCCGAAAACCAAAGCAAAATAAG
65 TATAA-A-AATAGAGATATAGGTATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
* **
12751 CATTTATAATATATAATGAAATATAAATTTTAA
128 CATTTAT-ATA-A-CAT-CCATA-AAA---T-A
* * * *
12784 GTATCGTTAAAGGATATATAATTCGAAAATCGTTCTACTTATTAAA-AAAAATAAAGTACGCATT
1 -TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAACAAAAACAAAATACGCATT
* *
12848 TATAATAAAATAGAGGTATAGGTATGGTGAAAGGTGAAAGGTGTATGATTTCGATAACCAAAGCA
65 TAT-A-AAAATAGA-G-ATA--TA-GGT--ATGGTGAAAGGTGTATGATTCCGATAACCAAAGCA
*
12913 AAACAAGCATTTATATAACA-CTCATAAAATA
121 AAATAAGCATTTATATAACATC-CATAAAATA
12944 TA
1 TA
12946 AACTTTAAGC
Statistics
Matches: 270, Mismatches: 30, Indels: 41
0.79 0.09 0.12
Matches are distributed among these distances:
150 54 0.20
151 5 0.02
152 1 0.00
153 1 0.00
154 57 0.21
155 3 0.01
156 1 0.00
157 2 0.01
158 2 0.01
159 5 0.02
160 1 0.00
161 1 0.00
162 26 0.10
163 7 0.03
164 47 0.17
165 3 0.01
166 3 0.01
167 3 0.01
168 3 0.01
169 45 0.17
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.30
Consensus pattern (151 bp):
TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAACAAAAACAAAATACGCATTT
ATAAAAATAGAGATATAGGTATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAGCAT
TTATATAACATCCATAAAATA
Found at i:13085 original size:65 final size:66
Alignment explanation
Indices: 13011--13146 Score: 247
Period size: 66 Copynumber: 2.1 Consensus size: 66
13001 GCAGATTTAA
13011 GTATAGTGAAAGGTGTATAATT-CCGATAATCAAAGTAAAAAAAGTATTTATATAACACCCACAA
1 GTATAGTGAAAGGTGTATAATTCCCGATAATCAAAGTAAAAAAAGTATTTATATAACACCCACAA
13075 C
66 C
* *
13076 GTATAGTGAAAGGTGTATAATTCCCGATAATCAAAGTAAAATAAGTATTTATGTAACACCCACAA
1 GTATAGTGAAAGGTGTATAATTCCCGATAATCAAAGTAAAAAAAGTATTTATATAACACCCACAA
13141 C
66 C
13142 GTATA
1 GTATA
13147 AACTAATTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 22 0.32
66 46 0.68
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (66 bp):
GTATAGTGAAAGGTGTATAATTCCCGATAATCAAAGTAAAAAAAGTATTTATATAACACCCACAA
C
Done.