Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1125
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: 19299
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:6406 original size:20 final size:20
Alignment explanation
Indices: 6366--6419 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
6356 CATTTCAAGC
*
6366 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTT
6386 ATGTATCGATACATTGC-CTT
1 ATGTATCGATACATT-CACTT
*
6406 ATTGTACCGATACA
1 A-TGTATCGATACA
6420 AAATATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:9546 original size:19 final size:19
Alignment explanation
Indices: 9522--9559 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9512 ATAAACATAA
9522 GCCAAAAACACTTTTTTTT
1 GCCAAAAACACTTTTTTTT
9541 GCCAAAAACACTTTTTTTT
1 GCCAAAAACACTTTTTTTT
9560 CTCTTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (19 bp):
GCCAAAAACACTTTTTTTT
Found at i:12019 original size:48 final size:48
Alignment explanation
Indices: 11905--12246 Score: 362
Period size: 48 Copynumber: 7.1 Consensus size: 48
11895 CGTTTAACCA
* *
11905 TATTGGCGTTAGGACCTGGTCAAACTCTTCATTAATCCCTCATTTGACTG
1 TATTGGCGTTAGGGCCTGGTCAAACTCTT--TTCATCCCTCATTTGACTG
*
11955 TATTGGCATTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
* * * ** *
12003 TATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTTGTTTGACTA
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
* * *
12051 TATTGGTGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGATTG
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
* * ** * ** *
12099 CATTGGAGTTAGGGCCTAATCAAACTCTTTTCATGCCTTGTTTGACTA
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
* * * * *
12147 TATTAGCATTAGGGCCTAGTTAAACTCTTTTTATCCCTCATTTGACTG
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
* * * * * * * *
12195 CATTGGTGTTAGGGCTTGGTTAAACTCTTTGCA-CCTTCGTTTGACTA
1 TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
12242 TATTG
1 TATTG
12247 ATGATAGAAC
Statistics
Matches: 244, Mismatches: 48, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
47 15 0.06
48 202 0.83
50 27 0.11
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (48 bp):
TATTGGCGTTAGGGCCTGGTCAAACTCTTTTCATCCCTCATTTGACTG
Found at i:12073 original size:96 final size:96
Alignment explanation
Indices: 11906--12246 Score: 427
Period size: 96 Copynumber: 3.5 Consensus size: 96
11896 GTTTAACCAT
* * * * *
11906 ATTGGCGTT-AGGACCTGGTCAAACTCTTCATTAATCCCTCATTTGACTGTATTGGCATTAGGGC
1 ATTGGTGTTAAGG-CCTGGTCAAACTCTT--TTCATCCTTCGTTTGACTATATTGGCATTAGGGC
* *
11970 CTGGTCAAACTCTTTTCATCCCTCATTTGACTGT
63 CTAGTCAAACTCTTTTCATCCCTCATTTGACTGC
* **
12004 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTTGTTTGACTATATTGGTGTTAGGGCCTA
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTCGTTTGACTATATTGGCATTAGGGCCTA
*
12069 GTCAAACTCTTTTCATCCCTCATTTGATTGC
66 GTCAAACTCTTTTCATCCCTCATTTGACTGC
* * ** *
12100 ATTGGAGTTAGGGCCTAATCAAACTCTTTTCATGCCTT-GTTTGACTATATTAGCATTAGGGCCT
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCAT-CCTTCGTTTGACTATATTGGCATTAGGGCCT
* *
12164 AGTTAAACTCTTTTTATCCCTCATTTGACTGC
65 AGTCAAACTCTTTTCATCCCTCATTTGACTGC
* * * *
12196 ATTGGTGTTAGGGCTTGGTTAAACTCTTTGCA-CCTTCGTTTGACTATATTG
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTCGTTTGACTATATTG
12247 ATGATAGAAC
Statistics
Matches: 212, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
94 4 0.02
95 13 0.06
96 165 0.78
97 4 0.02
98 23 0.11
99 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (96 bp):
ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTCGTTTGACTATATTGGCATTAGGGCCTA
GTCAAACTCTTTTCATCCCTCATTTGACTGC
Found at i:12621 original size:83 final size:84
Alignment explanation
Indices: 12505--12693 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 84
12495 TTAGTCTCGG
* ** * * *
12505 GTAAA-TCCTTTACCCTTTATTGACTTATTGGTTCA-CCTTGGTCAACCATT-TATCACTTGTTT
1 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACC-TTCCATCACTTGTTT
* *
12567 ACTTGGCAGTTTAGTGCCCA
65 ACCTAGCAGTTTAGTGCCCA
*
12587 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCCCTTGTTTA
1 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCACTTGTTTA
* * **
12652 CCTATCATTTTAGTGCCTG
66 CCTAGCAGTTTAGTGCCCA
* * *
12671 GTAAACTCGTTTATCCTGTGTTG
1 GTAAACTCCTTTACCCTTTGTTG
12694 GTTTGTTGGT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
82 5 0.06
83 29 0.33
84 54 0.61
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (84 bp):
GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCACTTGTTTA
CCTAGCAGTTTAGTGCCCA
Found at i:13993 original size:163 final size:162
Alignment explanation
Indices: 13779--14900 Score: 738
Period size: 163 Copynumber: 7.1 Consensus size: 162
13769 TTAAAGATTT
* * * * * * * *
13779 TCAAATATTATCATTAATT-TTCATTAAATAAAATTTTAAAACTTTATTCATTTTTATTCATTTT
1 TCAAATATTATTATTTATTCAT-ATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCATTTT
** *
13843 TAATTTTTCCTAAAAATTTTCCTATTTTCGAAATACAGAGTTTTCTACTCTGTAATTTTTTTCGA
65 TAATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAGAGTTTTCTACTCTGTAATTTTTTTCGA
13908 GAGATTTTTCTTGGCTTTTAA-TTTTAAAATTCA
130 GAGATTTTTCTTGG-TTTTAATTTTTAAAATTCA
13941 TCAAATATTATTATTTATGTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCAAGAGTT--
1 TCAAATATTATTATTTAT-TCATATTAAATCAATTTTTAAAAATTCATTCATTTTC---A-TTCA
* * * * *
14004 TTTTTATTTTTTCCTTAAAATTTTCCTA-TTTCTAAAATACGGAGTTTTCTATTTCAT-AAATTT
61 TTTTTAATTTTTCCTTGAAATTTTCCTATTTTC-AAAATACAGAGTTTTCTA-CTC-TGTAATTT
* *
14067 TTTTGGATAGATTTTTCTTGGTTTTCAATTTTTAAAATTCA
123 TTTTCGAGAGATTTTTCTTGGTTTT-AATTTTTAAAATTCA
* * * *
14108 TTAAATATTATTATTTACTTCATATTAAATC-ACTTTT-AAAATTCATTCATTTTCA-TAAGTTT
1 TCAAATATTATTATTTA-TTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCATTTT
* * * * * * *
14170 TCATTTTTCCTCGAAA-TTTCTCTATTTCCAAAATA-TGAAGTTTTTTACTCTGTAATTTCTTTA
65 TAATTTTTCCTTGAAATTTTC-CTATTTTCAAAATACAG-AGTTTTCTACTCTGTAATTTTTTTC
* *
14233 G-GGGA----TCTTGGTTTTTAATTTTTAAAATTTA
128 GAGAGATTTTTCTTGG-TTTTAATTTTTAAAATTCA
* **
14264 TCAAATATTATTATTTATT--TTTTAAA--AA--TTT----ATTCATTTCA---GGAGTT--TTT
1 TCAAATATTATTATTTATTCATATTAAATCAATTTTTAAAAATTCA-TTCATTTTCA-TTCATTT
* * * * * * * * *
14314 TT-GTTTTTCTTTCAAATTCTCATATTTTCGAAATACAGAGTTTTCTGCTTTGTTGA-TTTTTTC
64 TTAATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAGAGTTTTCTACTCTG-TAATTTTTTTC
* *
14377 AGAGGGATTTTTCTTGGTTTTGAATTTTTAAAATCCA
128 -GAGAGATTTTTCTTGGTTTT-AATTTTTAAAATTCA
* * * *
14414 T-AAA-A-TATTA--T-TT-ATATTAACTTATTTTTTAAAACTTCATTCA-TTT--TTCA---TT
1 TCAAATATTATTATTTATTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCATTTTT
* ** * * ** ** *
14466 --TTTTT-CTCGAAA-TTTCCTATTTT-TTAATACAAAGCTTTCTACTCCATAATTTTTTGGGGG
66 AATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAGAGTTTTCTACTCTGTAATTTTTTTCGAG
*
14526 AGATTTTTCTTAGTTTTTAATTTTTAAAATTCA
131 AGATTTTTCTT-GGTTTTAATTTTTAAAATTCA
* ** * *
14559 TCAAATATTATTATTTATTTCATAGTAAATCTTTTTTTAAAAATTCATTTATTTTCA-TGAGTTT
1 TCAAATATTATTATTTA-TTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCA-TTT
* * * * * **
14623 TTTATTTTTTCTTGAAATTTCCCTATTTTCAAAATAC-GAAATTTTCGACTGCAATAAATTTTTT
64 TTAATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAG-AGTTTTCTACT-CTGT-AATTTTTT
* * *
14687 TCGAGGGATTTTTATTGGTTTT--TTTTTAAAAATCA
126 TCGAGAGATTTTTCTTGGTTTTAATTTTTAAAATTCA
* * *
14722 TCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATTCATTTT
1 TCAAATATTATTATTTA-TTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCATTTT
* * * * * ** * *
14787 TCATTTTTTACTTGAAATTTTCTTATTTTGAAAA-ACTGAGTTTTCTACTCCATAAATGTTTTCG
65 T-AATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAGAGTTTTCTACTCTGTAATTTTTTTC-
* * * *
14851 GAGGGA-TTTTCTTGATTTAAAATTTTTAAAATTTA
128 GAGAGATTTTTCTTGGTTT-TAATTTTTAAAATTCA
* *
14886 TCTAATATTGTTATT
1 TCAAATATTATTATT
14901 AACCTTTCAT
Statistics
Matches: 754, Mismatches: 128, Indels: 154
0.73 0.12 0.15
Matches are distributed among these distances:
144 39 0.05
145 47 0.06
146 32 0.04
147 22 0.03
148 14 0.02
149 15 0.02
150 26 0.03
151 2 0.00
152 7 0.01
153 34 0.05
154 3 0.00
155 4 0.01
156 36 0.05
157 4 0.01
159 2 0.00
160 4 0.01
161 39 0.05
162 64 0.08
163 121 0.16
164 71 0.09
165 71 0.09
166 53 0.07
167 43 0.06
168 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (162 bp):
TCAAATATTATTATTTATTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCATTCATTTTT
AATTTTTCCTTGAAATTTTCCTATTTTCAAAATACAGAGTTTTCTACTCTGTAATTTTTTTCGAG
AGATTTTTCTTGGTTTTAATTTTTAAAATTCA
Found at i:14879 original size:164 final size:160
Alignment explanation
Indices: 14449--14959 Score: 459
Period size: 163 Copynumber: 3.1 Consensus size: 160
14439 TTTTTAAAAC
* ** * * *
14449 TTCATTCATTTTTCATTTTTTTCTCGAAA-TTTCCTATTTTTTAATACAAAGCTTTCTACTCCAT
1 TTCATTCATTTTTCA-TTTTTTCTTGAAATTTTCCTATTTTCAAAAAC-GAGTTTTCTACTCCAT
* * *
14513 -AATTTTTTGGGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAT
64 AAATTTTTCGGAGG-GATTTTTCTT-G-ATTTAATTTTTAAAATTCATCAAATATTATTATTTAT
* * *
14577 TTCATAGTAAATCT-TTTTTTAAAAATTCATTTATT
126 TTCATATTAAAT-TAATTTTCAAAAATTCATTTATT
* * * * * *
14612 TTCA-TGAGTTTTTTATTTTTTCTTGAAATTTCCCTATTTTCAAAATACGAAATTTTCGACTGCA
1 TTCATTCA-TTTTTCATTTTTTCTTGAAATTTTCCTATTTTCAAAA-ACG-AGTTTTCTACT-CC
* * * *
14676 ATAAATTTTTTTC-GAGGGATTTTTATTGGTTT-TTTTTTAAAAATCATCAAATATTATTATTTA
62 ATAAA--TTTTTCGGAGGGATTTTTCTTGATTTAATTTTTAAAATTCATCAAATATTATTATTTA
* *
14739 TTTCATATTAAATTAGTTTTCAAAAATTCATTCATT
125 TTTCATATTAAATTAATTTTCAAAAATTCATTTATT
* *
14775 TTCATTCATTTTTCATTTTTTACTTGAAATTTTCTTATTTTGAAAAACTGAGTTTTCTACTCCAT
1 TTCATTCATTTTTCATTTTTT-CTTGAAATTTTCCTATTTTCAAAAAC-GAGTTTTCTACTCCAT
* * * *
14840 AAATGTTTTCGGAGGGA-TTTTCTTGATTTAAAATTTTTAAAATTTATCTAATATTGTTATTAAC
64 AAAT-TTTTCGGAGGGATTTTTCTTGATTT--AATTTTTAAAATTCATCAAATATTATTATTTA-
14904 CTTTC--ATTAAA-TAATTTTCAAAAAATTCAATTTA-T
125 -TTTCATATTAAATTAATTTTC-AAAAATTC-ATTTATT
** *
14939 TTCATGAATTTTTAATTTTTT
1 TTCATTCATTTTTCATTTTTT
14960 TGTATACATT
Statistics
Matches: 284, Mismatches: 43, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
160 1 0.00
161 15 0.05
162 27 0.10
163 115 0.40
164 95 0.33
165 8 0.03
166 15 0.05
167 3 0.01
168 5 0.02
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (160 bp):
TTCATTCATTTTTCATTTTTTCTTGAAATTTTCCTATTTTCAAAAACGAGTTTTCTACTCCATAA
ATTTTTCGGAGGGATTTTTCTTGATTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCAT
ATTAAATTAATTTTCAAAAATTCATTTATT
Found at i:15293 original size:9 final size:9
Alignment explanation
Indices: 15281--15325 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
15271 AAAAAAAAAA
*
15281 AAAAGAGAG
1 AAAAGAAAG
15290 AAAAGAAAG
1 AAAAGAAAG
15299 AAAAGAAAG
1 AAAAGAAAG
15308 --AAGAAA-
1 AAAAGAAAG
15314 AAAAGAAA-
1 AAAAGAAAG
15322 AAAA
1 AAAA
15326 TAGTGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 6 0.18
8 10 0.30
9 17 0.52
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:15318 original size:20 final size:20
Alignment explanation
Indices: 15271--15325 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
15261 GCAACTCAGC
15271 AAAAAAA-AAAAAAAGAGAG
1 AAAAAAAGAAAAAAAGAGAG
15290 AAAAGAAAGAAAAGAAAGA-AG
1 AAAA-AAAGAAAA-AAAGAGAG
15311 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
15326 TAGTGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.21
20 11 0.33
21 10 0.30
22 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAGAGAG
Done.