Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1381
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: 48264
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:1510 original size:40 final size:40
Alignment explanation
Indices: 1368--1549 Score: 210
Period size: 39 Copynumber: 4.6 Consensus size: 40
1358 TCCTCGTTCA
* * * * *
1368 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
1407 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
1447 -CTGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
1485 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
1525 AAGGCCTTC-GGATCTTAATCCGGAT
1 AATGCCTTCGGGA-CTTAACCCGGAT
1550 ATATTCACTT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
38 28 0.22
39 51 0.41
40 46 0.37
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:1596 original size:40 final size:41
Alignment explanation
Indices: 1520--1596 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
1510 TTAGTATCTC
* * *
1520 GCACAAAGGCCTTCGGATCTTAATCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAACCCGGACACATTCACTTA
*
1561 GCACAAA-GCCTTCGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGATCTTAACCCGGACA-CATTCA
1597 ATTAATCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 10 0.32
40 14 0.45
41 7 0.23
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAACCCGGACACATTCACTTA
Found at i:9368 original size:40 final size:40
Alignment explanation
Indices: 9192--9414 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
9182 TCCTCGTTCA
* * * * *
9192 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
9231 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
9271 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
9311 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
9351 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
9391 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9415 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11312 original size:17 final size:17
Alignment explanation
Indices: 11290--11322 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11280 TAGTTGTCAC
11290 ATGAATTAAATTAATTG
1 ATGAATTAAATTAATTG
*
11307 ATGAATTAATTTAATT
1 ATGAATTAAATTAATT
11323 TGATAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
ATGAATTAAATTAATTG
Found at i:11705 original size:136 final size:135
Alignment explanation
Indices: 11384--11801 Score: 651
Period size: 138 Copynumber: 3.1 Consensus size: 135
11374 AGAGAACATA
* *
11384 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGTATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA-TTTACCGAATTTAT
* * *** *
11449 TAATATAAACAATTATATTAATTAATTTCTAACAAAATATAAAAGACATGATAATTAATATTCTT
65 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACA-GAAAATTAATATTCTT
11514 TTGGAAAG
129 TT-GAAAG
*
11522 AATATAATTAATATATGAATTTGATTCGTACAAAATATTAATTGTATATAGTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA-TTTACCGAATTTAT
* *
11587 TAATATAAATAGTTATATTAAATAATTTCGGTCAAAATATAAAAAACACGAAAATTAATATT-TT
65 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACA-GAAAATTAATATTCTT
11651 TTGAAAG
129 TTGAAAG
11658 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTGTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATT-TACCGAATTTAT
11723 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACAG-AAATTAATATTCTTT
65 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACAGAAAATTAATATTCTTT
*
11787 TGCAAG
130 TGAAAG
*
11793 AACATAATT
1 AATATAATT
11802 CATTTTTCTA
Statistics
Matches: 260, Mismatches: 18, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
134 11 0.04
135 19 0.07
136 112 0.43
137 4 0.02
138 114 0.44
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (135 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTACCGAATTTATT
AATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACAGAAAATTAATATTCTTTT
GAAAG
Found at i:29985 original size:25 final size:25
Alignment explanation
Indices: 29956--30042 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 25
29946 ACGAGCTATA
29956 AATGATAAGCTCCTCTGAGCTGAAT
1 AATGATAAGCTCCTCTGAGCTGAAT
* * *
29981 AATGATAAGCTCTTCCGAGTTGAAT
1 AATGATAAGCTCCTCTGAGCTGAAT
* * * *
30006 AACGGTAAGCTCCT-TCAAACTGAAT
1 AATGATAAGCTCCTCT-GAGCTGAAT
*
30031 AATGGTAAGCTC
1 AATGATAAGCTC
30043 ATACGAATGA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (25 bp):
AATGATAAGCTCCTCTGAGCTGAAT
Found at i:35927 original size:42 final size:42
Alignment explanation
Indices: 35868--36094 Score: 187
Period size: 43 Copynumber: 5.4 Consensus size: 42
35858 TTTCCCGAGG
* ** *
35868 GGTTGCTAAGTGTTGATTCCCCAAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATTATTGATTGTAAAGGT
35910 GGTTGCTAAGTGCTGATTCCACCGTA-TATTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATTA-TTGATTGT-AAAGGT
* * * * * * **
35953 GATTGCTATGTGCTGATTCCCCGTATCACTGAATATAAATAT
1 GGTTGCTAAGTGCTGATTCCCCGTATTATTGATTGTAAAGGT
*
35995 GGTTGCTAAGTGCTGATTCCACCATATCT-TTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTAT-TATTGATTGT-AAAGGT
* * * * *
36038 AGTTGATATGTGCTGATTCCCCGTATCACTGAATT-T-AAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATTATTG-ATTGTAAAGGT
36079 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
36095 ATCCACCGAG
Statistics
Matches: 144, Mismatches: 30, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
40 4 0.03
41 16 0.11
42 57 0.40
43 59 0.41
44 8 0.06
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATTATTGATTGTAAAGGT
Found at i:36013 original size:85 final size:84
Alignment explanation
Indices: 35903--36102 Score: 303
Period size: 85 Copynumber: 2.4 Consensus size: 84
35893 TTATTGATTC
* *
35903 TAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGG-GATTGCTATGTGCT
1 TAAAGATGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGAG-TTGATATGTGCT
35967 GATTCCCCGTATCACTGAAT
65 GATTCCCCGTATCACTGAAT
* * *
35987 ATAAATATGGTTGCTAAGTGCTGATTCCACCATATCTTTGATTGTGAAAGGAGTTGATATGTGCT
1 -TAAAGATGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGAGTTGATATGTGCT
36052 GATTCCCCGTATCACTGAAT
65 GATTCCCCGTATCACTGAAT
* * *
36072 TTAAGGTGGTTGCTAAGTGCTGAATCCACCG
1 TAAAGATGGTTGCTAAGTGCTGATTCCACCG
36103 AGTAACGGAT
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
84 26 0.25
85 77 0.74
86 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (84 bp):
TAAAGATGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGAGTTGATATGTGCTG
ATTCCCCGTATCACTGAAT
Found at i:39450 original size:25 final size:25
Alignment explanation
Indices: 39338--39457 Score: 127
Period size: 25 Copynumber: 4.8 Consensus size: 25
39328 TAGGGACACT
*
39338 GTAAGCTACTT-CGAGCTGAGTAACG
1 GTAAGCT-CTTACGAGCTGAATAACG
* * *
39363 GTAAGCTCTTCCGAGCTAAATAATG
1 GTAAGCTCTTACGAGCTGAATAACG
* * * *
39388 GTAAGCTCCTCCAAGCTAAATAACG
1 GTAAGCTCTTACGAGCTGAATAACG
*
39413 GTAAGCTCATACGAGCTGAATAACG
1 GTAAGCTCTTACGAGCTGAATAACG
39438 GTAAG-TCTTTACGAGCTGAA
1 GTAAGCTC-TTACGAGCTGAA
39458 ATTGGTAACC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.06
25 77 0.94
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
GTAAGCTCTTACGAGCTGAATAACG
Found at i:43575 original size:78 final size:78
Alignment explanation
Indices: 43452--43672 Score: 258
Period size: 78 Copynumber: 2.8 Consensus size: 78
43442 GCTCCTCGTT
* * *
43452 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATCTCGCACAATGCCTTCGGGACTTAGCCCG
43515 GATTAGTAACTCGCA
64 GATTAGTAACTCGCA
43530 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCAC-AATGCCTTCGGGACTTAGCCCGG
*
43593 AATTAGTATCTCGCA
65 -ATTAGTAACTCGCA
* * * *
43608 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCACAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTAATC-TCGCACAATGCCTTCGGGACTTAGCCC
43670 GGA
63 GGA
43673 CATCATTCAA
Statistics
Matches: 127, Mismatches: 7, Indels: 18
0.84 0.05 0.12
Matches are distributed among these distances:
76 2 0.02
77 28 0.22
78 63 0.50
79 25 0.20
80 9 0.07
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAATGCCTTCGGGACTTAGCCCGGA
TTAGTAACTCGCA
Found at i:43633 original size:117 final size:118
Alignment explanation
Indices: 43452--43672 Score: 276
Period size: 117 Copynumber: 1.9 Consensus size: 118
43442 GCTCCTCGTT
*
43452 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAATGCCTTCGGGACTTAACCCGGA
*
43517 T-TAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 TATAGTAACTTAGCAC-AA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* **
43569 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAAT-TCGCAC-AATGCCTTCGGGA-CTTAACC
* *
43630 CGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAGCCCGGA
62 CGGATATAGTAACTTAGCACAAGCCTTCGGGACTTAGCCCGGA
43673 CATCATTCAA
Statistics
Matches: 90, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
115 3 0.03
116 22 0.24
117 42 0.47
118 18 0.20
119 5 0.06
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (118 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCACAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:43672 original size:39 final size:39
Alignment explanation
Indices: 43452--43672 Score: 226
Period size: 39 Copynumber: 5.7 Consensus size: 39
43442 GCTCCTCGTT
* * *
43452 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTGT-ATTCGCA
* * *
43492 C-AATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTGT-ATTCGCA
43530 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATT-GTAT-TCGCA
43569 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATT-GTAT-TCGCA
* *
43608 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTGT-A-TTCGCA
43649 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43673 CATCATTCAA
Statistics
Matches: 161, Mismatches: 10, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
38 26 0.16
39 107 0.66
40 18 0.11
41 9 0.06
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTGTATTCGCA
Done.