Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1082
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: 45433
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1661 original size:13 final size:13
Alignment explanation
Indices: 1643--1667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1633 AATGTTTTTG
1643 TGTATCGATACAT
1 TGTATCGATACAT
1656 TGTATCGATACA
1 TGTATCGATACA
1668 AGTTTGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2077 original size:18 final size:18
Alignment explanation
Indices: 2045--2115 Score: 99
Period size: 18 Copynumber: 3.9 Consensus size: 18
2035 TCCTAACAAT
2045 TATTATATT-ATATATTC
1 TATTATATTAATATATTC
2062 TATTATATTAATATATTC
1 TATTATATTAATATATTC
* *
2080 TATTATATTAATTCTATTT
1 TATTATATTAA-TATATTC
2099 TATATATATTAATATAT
1 TAT-TATATTAATATAT
2116 ATTCTAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
17 9 0.19
18 19 0.40
19 12 0.25
20 8 0.17
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATATTAATATATTC
Found at i:2086 original size:30 final size:27
Alignment explanation
Indices: 2045--2121 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 27
2035 TCCTAACAAT
2045 TATTATATTATATATTCTATTATATTAATA
1 TATT-TATTATATATTCTATTATA-T-ATA
*
2075 TATTCTATTATATTAATTCTATTTTATATA
1 TATT-TATTATA-T-ATTCTATTATATATA
*
2105 TA-TTAATATATATTCTA
1 TATTTATTATATATTCTA
2122 ATTTAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.14
27 1 0.02
28 6 0.14
29 1 0.02
30 16 0.38
31 2 0.05
32 10 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTATTATATATTCTATTATATATA
Found at i:6108 original size:8 final size:8
Alignment explanation
Indices: 6095--6126 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
6085 TCACTTTGAA
6095 TTCGAATG
1 TTCGAATG
6103 TTCGAATG
1 TTCGAATG
6111 TTCGAATG
1 TTCGAATG
6119 TTCGAATG
1 TTCGAATG
6127 AAATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (8 bp):
TTCGAATG
Found at i:6407 original size:11 final size:12
Alignment explanation
Indices: 6380--6409 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6370 ATAATTGAAA
6380 AAAAAAATTATG
1 AAAAAAATTATG
*
6392 AAAAATATTATG
1 AAAAAAATTATG
6404 AAAAAA
1 AAAAAA
6410 GATAGAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (12 bp):
AAAAAAATTATG
Found at i:8053 original size:14 final size:14
Alignment explanation
Indices: 8034--8080 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
8024 GAAATATATC
*
8034 TTATAATAATTATA
1 TTATAATAAGTATA
*
8048 TTATAATTAGTATA
1 TTATAATAAGTATA
*
8062 TTATACTAAGTATA
1 TTATAATAAGTATA
8076 -TATAA
1 TTATAA
8081 ATACTAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (14 bp):
TTATAATAAGTATA
Found at i:9133 original size:21 final size:20
Alignment explanation
Indices: 9109--9155 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
9099 TGAATTGATG
9109 CCATGAATAAAGAGATTATGT
1 CCATGAA-AAAGAGATTATGT
*
9130 CCATG--AAATAGATTATGT
1 CCATGAAAAAGAGATTATGT
9148 CCATGAAA
1 CCATGAAA
9156 GATAATGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 17 0.74
20 1 0.04
21 5 0.22
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (20 bp):
CCATGAAAAAGAGATTATGT
Found at i:9144 original size:18 final size:18
Alignment explanation
Indices: 9121--9155 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9111 ATGAATAAAG
9121 AGATTATGTCCATGAAAT
1 AGATTATGTCCATGAAAT
9139 AGATTATGTCCATGAAA
1 AGATTATGTCCATGAAA
9156 GATAATGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
AGATTATGTCCATGAAAT
Found at i:10165 original size:19 final size:20
Alignment explanation
Indices: 10132--10180 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
10122 GATACATTGG
* *
10132 ATCGATAAATGCTC-ATTAT
1 ATCGATACATACTCAATTAT
*
10151 ATCGATACATACTCAATTGT
1 ATCGATACATACTCAATTAT
*
10171 ATTGATACAT
1 ATCGATACAT
10181 GAAATTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCGATACATACTCAATTAT
Found at i:18615 original size:19 final size:19
Alignment explanation
Indices: 18588--18643 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
18578 TGTATCGATA
*
18588 CATTATATCGATACATGCT
1 CATTGTATCGATACATGCT
*
18607 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
18626 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
18644 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:32858 original size:18 final size:18
Alignment explanation
Indices: 32837--32882 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
32827 ATTGATTTTT
32837 ATGAAAAAGTGTA-TTTAG
1 ATGAAAAA-TGTATTTTAG
32855 ATGAAAGAATGTATTTTTAG
1 ATGAAA-AATGTA-TTTTAG
32875 ATGAAAAA
1 ATGAAAAA
32883 AATGTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
20 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33
Consensus pattern (18 bp):
ATGAAAAATGTATTTTAG
Found at i:32888 original size:21 final size:20
Alignment explanation
Indices: 32837--32888 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
32827 ATTGATTTTT
*
32837 ATGAAAAAGTGTA--TTTAG
1 ATGAAAAAATGTATTTTTAG
*
32855 ATGAAAGAATGTATTTTTAG
1 ATGAAAAAATGTATTTTTAG
32875 ATGAAAAAAATGTA
1 ATG-AAAAAATGTA
32889 ACTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
20 8 0.29
21 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGAAAAAATGTATTTTTAG
Found at i:37368 original size:20 final size:20
Alignment explanation
Indices: 37343--37398 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
37333 TTTTCACAAT
37343 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
37363 TTGTATCGATACATT-ATCA
1 TTGTATCGATACATTGTTCA
*
37382 TTGTATCGATGCATTGT
1 TTGTATCGATACATTGT
37399 ATCGATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:37396 original size:13 final size:13
Alignment explanation
Indices: 37380--37409 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37370 GATACATTAT
*
37380 CATTGTATCGATG
1 CATTGTATCGATA
37393 CATTGTATCGATA
1 CATTGTATCGATA
37406 CATT
1 CATT
37410 CTGGGTTTAC
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:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:39906 original size:79 final size:79
Alignment explanation
Indices: 39788--40037 Score: 265
Period size: 79 Copynumber: 3.2 Consensus size: 79
39778 TTTTCATAAT
* * * *
39788 CGGGAATACTCTAACCCCGACATTATTTCTAAAATATTGATTTCTCACAGTCGGAGATACTCCAA
1 CGGGGATACTCCAACCCCGACATTATTTCTAAAACATTGATTTCTCACAATCGGAGATACTCCAA
*
39853 CCCCGTTATTTTCG
66 CCCCGTTATTTTCA
* * * * *
39867 CGGGGATACTCCAACCCCGACCTTATTTCTAAAGCATTGATTTTTCACAATCGGGGATATTCCAA
1 CGGGGATACTCCAACCCCGACATTATTTCTAAAACATTGATTTCTCACAATCGGAGATACTCCAA
39932 CCCCGTTATTTTCA
66 CCCCGTTATTTTCA
* * ** ** *
39946 AGGGGATACTCCAACCCTGATTTTATTT-TCAAAACACCGATTT-TCTATAATCAGG-GATACTC
1 CGGGGATACTCCAACCCCGACATTATTTCT-AAAACATTGATTTCTC-ACAATC-GGAGATACTC
*
40008 CAACCCTGTTA-TTTCTA
63 CAACCCCGTTATTTTC-A
*
40025 AGGGGATACTCCA
1 CGGGGATACTCCA
40038 TCCCTGATTT
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
78 7 0.05
79 138 0.94
80 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGACATTATTTCTAAAACATTGATTTCTCACAATCGGAGATACTCCAA
CCCCGTTATTTTCA
Found at i:40043 original size:79 final size:79
Alignment explanation
Indices: 39843--40088 Score: 291
Period size: 79 Copynumber: 3.1 Consensus size: 79
39833 CACAGTCGGA
** * ** * **
39843 GATACTCCAACCCCGTTATTTTCGCGGGGATACTCCAACCCCGACCTTA-TTTCTAAAGCATTGA
1 GATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTC-AAAACACCGA
* * *
39907 TTTTTCACAATCGGG
65 TTTTTAATAATCAGG
*
39922 GATATTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGAT
1 GATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGAT
39987 TTTCT-ATAATCAGG
66 TTT-TAATAATCAGG
* * * *
40001 GATACTCCAACCCTGTTA-TTTCTAAGGGGATACTCCATCCCTGATTTTATTTTCAGAACACTGA
1 GATACTCCAACCCCGTTATTTTC-AAGGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGA
*
40065 TTTTTAATAATCAGA
65 TTTTTAATAATCAGG
40080 GATACTCCA
1 GATACTCCA
40089 GTCCCGTCGT
Statistics
Matches: 146, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.03
79 136 0.93
80 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGAT
TTTTAATAATCAGG
Found at i:41835 original size:320 final size:320
Alignment explanation
Indices: 41253--41873 Score: 1188
Period size: 320 Copynumber: 1.9 Consensus size: 320
41243 ATTCAAAGTC
41253 TTATCATTTTTTCTATTTCAAAGAGCTTTTATATTCATTGTTGTTATTCTTTGAAAGCTCATTTG
1 TTATCATTTTTTCTATTTCAAAGAGCTTTTATATTCATTGTTGTTATTCTTTGAAAGCTCATTTG
41318 TATTCCTTTGTGCTTATACTTTCACAAACACTAGCCTACTTAGAGGCAATTCTCGTTTGTAAAAT
66 TATTCCTTTGTGCTTATACTTTCACAAACACTAGCCTACTTAGAGGCAATTCTCGTTTGTAAAAT
41383 TTCTTTGTGTTGTATAAGGTTTTATTCAACATTGGGTTACAATCTCTTAAGAATTTTAGGTATAA
131 TTCTTTGTGTTGTATAAGGTTTTATTCAACATTGGGTTACAATCTCTTAAGAATTTTAGGTATAA
41448 TTCTTGAAGAGAATAAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTGTTGTAAGGTTATACCT
196 TTCTTGAAGAGAATAAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTGTTGTAAGGTTATACCT
41513 TTTCCTGAAAGGTAAATGATTCGAGTAGTGAATTGTGGTATTCTTTTATATTCATTGTTG
261 TTTCCTGAAAGGTAAATGATTCGAGTAGTGAATTGTGGTATTCTTTTATATTCATTGTTG
* *
41573 TTATCATTTTTTCTATTTCAAAGAGCTTTTATATTCATTGTTGTTATTCTTTGAAAGGTTATTTG
1 TTATCATTTTTTCTATTTCAAAGAGCTTTTATATTCATTGTTGTTATTCTTTGAAAGCTCATTTG
*
41638 TATTCCTTTGTGCTTATACTTTCACAAACACTAGCCTACTTAGAGGTAATTCTCGTTTGTAAAAT
66 TATTCCTTTGTGCTTATACTTTCACAAACACTAGCCTACTTAGAGGCAATTCTCGTTTGTAAAAT
* *
41703 TTCTTTGTGTTGTATAAGGTTTTATTCAACCTTGGGTTACAATCTCTTAAGAATTTTGGGTATAA
131 TTCTTTGTGTTGTATAAGGTTTTATTCAACATTGGGTTACAATCTCTTAAGAATTTTAGGTATAA
*
41768 TTCTTGAAGAGAATGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTGTTGTAAGGTTATACCT
196 TTCTTGAAGAGAATAAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTGTTGTAAGGTTATACCT
41833 TTTCCTGAAAGGTAAATGATTCGAGTAGTGAATTGTGGTAT
261 TTTCCTGAAAGGTAAATGATTCGAGTAGTGAATTGTGGTAT
41874 ACATTCGAAA
Statistics
Matches: 295, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
320 295 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.43
Consensus pattern (320 bp):
TTATCATTTTTTCTATTTCAAAGAGCTTTTATATTCATTGTTGTTATTCTTTGAAAGCTCATTTG
TATTCCTTTGTGCTTATACTTTCACAAACACTAGCCTACTTAGAGGCAATTCTCGTTTGTAAAAT
TTCTTTGTGTTGTATAAGGTTTTATTCAACATTGGGTTACAATCTCTTAAGAATTTTAGGTATAA
TTCTTGAAGAGAATAAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTGTTGTAAGGTTATACCT
TTTCCTGAAAGGTAAATGATTCGAGTAGTGAATTGTGGTATTCTTTTATATTCATTGTTG
Done.