Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold472
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: 529027
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:504525 original size:90 final size:87
Alignment explanation
Indices: 504352--504609 Score: 270
Period size: 90 Copynumber: 2.9 Consensus size: 87
504342 ATGGTACTTT
* * * * *
504352 TTTTTTTAAGTTTACAACTTCATGGTACCTTCTTTTTTAAGTCAACAACTCCATGGCACCTTTTT
1 TTTTTTTAAGTTCACAACTTCGTGGTACC-TC-TTTTTAAATCCACAACTCCATAGCACCTTTTT
504417 AAAAAATCCACAACTCCGTGCCACCC
64 --AAAATCCACAACTCCGTGCCACCC
* *
504443 TCTTTTTTAAGTTCACAACTTCGTGGCACCTCTTTTTAAATCCACAACTCTATAGCACTATCTTT
1 T-TTTTTTAAGTTCACAACTTCGTGGTACCTCTTTTTAAATCCACAACTCCATAGCAC---CTTT
* * *
504508 TT-AAGTCCACAATTCCGTGGCACCC
62 TTAAAATCCACAACTCCGTGCCACCC
* * *
504533 TTTTTTAAAAGTTCACAACTTTGTGGTACCT-TTTTTAAAGTCCACAACTCCA-AGGCACCCTTT
1 TTTTTT-TAAGTTCACAACTTCGTGGTACCTCTTTTTAAA-TCCACAACTCCATA-GCACCTTTT
*
504596 TAAAATCAACAACT
63 TAAAATCCACAACT
504610 TTATAGCACC
Statistics
Matches: 141, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
87 5 0.04
88 9 0.06
89 14 0.10
90 79 0.56
91 3 0.02
92 25 0.18
93 6 0.04
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (87 bp):
TTTTTTTAAGTTCACAACTTCGTGGTACCTCTTTTTAAATCCACAACTCCATAGCACCTTTTTAA
AATCCACAACTCCGTGCCACCC
Found at i:504538 original size:59 final size:59
Alignment explanation
Indices: 504382--504541 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 59
504372 CATGGTACCT
* * * * * *
504382 TCTTTTTTAAGTCAACAACTCCATGGCACCTTTTTAAAAAATCCACAACTCCGTGCCACCC
1 TCTTTTTTAAGTCCACAATTCCGTGGCACCTTTTT--TAAATCCACAACTCCATGCCACCA
* * *
504443 TCTTTTTTAAGTTCACAACTT-CGTGGCACCTCTTTTTAAATCCACAACTCTATAG-CACTA
1 TCTTTTTTAAGTCCACAA-TTCCGTGGCACCT-TTTTTAAATCCACAACTCCAT-GCCACCA
504503 TC-TTTTTAAGTCCACAATTCCGTGGCACCCTTTTTTAAA
1 TCTTTTTTAAGTCCACAATTCCGTGGCA-CCTTTTTTAAA
504542 AGTTCACAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 29 0.35
60 22 0.26
61 26 0.31
62 5 0.06
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.36
Consensus pattern (59 bp):
TCTTTTTTAAGTCCACAATTCCGTGGCACCTTTTTTAAATCCACAACTCCATGCCACCA
Found at i:504607 original size:28 final size:28
Alignment explanation
Indices: 504565--504641 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
504555 GTGGTACCTT
*
504565 TTTTAAAGTCCACAACTCCA-AGGCACCC
1 TTTTAAAATCCACAACTCCATA-GCACCC
* **
504593 TTTTAAAATCAACAACTTTATAGCACCC
1 TTTTAAAATCCACAACTCCATAGCACCC
*
504621 TTTTACAATCCACAACTCCAT
1 TTTTAAAATCCACAACTCCAT
504642 GGAATCCCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (28 bp):
TTTTAAAATCCACAACTCCATAGCACCC
Found at i:504775 original size:30 final size:30
Alignment explanation
Indices: 504645--505017 Score: 368
Period size: 30 Copynumber: 12.5 Consensus size: 30
504635 ACTCCATGGA
* *
504645 ATCCCTTTTCAAAGCCCACAAGTTAGTGGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* *
504675 ATCCTTTTTTTTAAAGCCCACAAGTTAGTGGC
1 ATCC--CTTTTTAAAGCCCACAAGTCAGTGGC
* *
504707 ATCCTTTTTCTAAAGCCCACAAGTCAATGGC
1 ATCCCTTTT-TAAAGCCCACAAGTCAGTGGC
* * *
504738 A-CCCTTTTTAAATCCTACAAGTTAGTGGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* *
504767 ATCCCTTTTCAAAGCCCACAAGCCAGTGG-
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* * *
504796 AACCC-TTTTAAAACTCACAAGTCAGTGGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* *
504825 A-CCC-TTTTAAAGCCCACAAGTGAGTAGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
*
504853 ATCCC-TTTTAAAGCCCACAAGTCAATGGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* **
504882 ATCCCTTTTTAAAGCCCATAAGTCAGTAAC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
** *
504912 ATCTTTTTTTTAAAAGCCCACAAATCAGT-G-
1 ATC-CCTTTTT-AAAGCCCACAAGTCAGTGGC
* * *
504942 A-CACTATTTAAAGCCCACAAGTTAGTGGC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
* *
504971 ATCCCTTTTTAAAGCCCACAAGTTAGTGAC
1 ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
*
505001 ATCCTTTTTTTAAAGCC
1 ATCC-CTTTTTAAAGCC
505018 AACAGGTAAG
Statistics
Matches: 286, Mismatches: 44, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
27 15 0.05
28 48 0.17
29 54 0.19
30 90 0.31
31 36 0.13
32 43 0.15
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
ATCCCTTTTTAAAGCCCACAAGTCAGTGGC
Found at i:504980 original size:59 final size:58
Alignment explanation
Indices: 504649--504998 Score: 300
Period size: 59 Copynumber: 5.9 Consensus size: 58
504639 CATGGAATCC
* * *
504649 CTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTTTTTAAAGCCCACAAGTTAGTGGCATC-
1 CTTTT-AAAGCCCACAAGTCAGTGGCATCC--CTTTTTAAAGCCCACAAGTCAGTGGCA-CA
* * * * *
504710 CTTTTTCTAAAGCCCACAAGTCAATGGCA-CCCTTTTTAAATCCTACAAGTTAGTGGCATCC
1 C--TTT-TAAAGCCCACAAGTCAGTGGCATCCCTTTTTAAAGCCCACAAGTCAGTGGCA-CA
* * * * *
504771 CTTTTCAAAGCCCACAAGCCAGTGG-AACCC-TTTTAAAACTCACAAGTCAGTGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCATCCCTTTTTAAAGCCCACAAGTCAGTGGCACA
* * * *
504828 CTTTTAAAGCCCACAAGTGAGTAGCATCCC-TTTTAAAGCCCACAAGTCAATGGCATCC
1 CTTTTAAAGCCCACAAGTCAGTGGCATCCCTTTTTAAAGCCCACAAGTCAGTGGCA-CA
* ** ** *
504886 CTTTTTAAAGCCCATAAGTCAGTAACATCTTTTTTTTAAAAGCCCACAAATCAGT-G-ACA
1 C-TTTTAAAGCCCACAAGTCAGTGGCATC-CCTTTTT-AAAGCCCACAAGTCAGTGGCACA
* *
504945 CTATTTAAAGCCCACAAGTTAGTGGCATCCCTTTTTAAAGCCCACAAGTTAGTG
1 CT-TTTAAAGCCCACAAGTCAGTGGCATCCCTTTTTAAAGCCCACAAGTCAGTG
504999 ACATCCTTTT
Statistics
Matches: 241, Mismatches: 34, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
56 16 0.07
57 48 0.20
58 32 0.13
59 71 0.29
60 27 0.11
61 7 0.03
62 17 0.07
63 22 0.09
64 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (58 bp):
CTTTTAAAGCCCACAAGTCAGTGGCATCCCTTTTTAAAGCCCACAAGTCAGTGGCACA
Found at i:505157 original size:33 final size:33
Alignment explanation
Indices: 505047--505149 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 33
505037 TCACAAGTTG
*
505047 GTGGCAACTC-TTTC-AAAGCCCATACAAGTC-
1 GTGGCAACCCTTTTCAAAAGCCCATACAAGTCA
* *
505077 GATGGTAACCCTTTTCAAAAGCCCACACAAGTCA
1 G-TGGCAACCCTTTTCAAAAGCCCATACAAGTCA
505111 GTGGCAACCCTTTTCAAAAGCCCATACAAGTCA
1 GTGGCAACCCTTTTCAAAAGCCCATACAAGTCA
505144 GTGGCA
1 GTGGCA
505150 TCTCTTTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 7 0.11
32 4 0.06
33 51 0.80
34 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (33 bp):
GTGGCAACCCTTTTCAAAAGCCCATACAAGTCA
Found at i:509732 original size:33 final size:33
Alignment explanation
Indices: 509695--509761 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
509685 TTCAACGATT
509695 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
509728 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
509761 T
1 T
509762 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:509733 original size:13 final size:13
Alignment explanation
Indices: 509715--509739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509705 CATAAAATGT
509715 TGTATCGATACAA
1 TGTATCGATACAA
509728 TGTATCGATACA
1 TGTATCGATACA
509740 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:509820 original size:13 final size:13
Alignment explanation
Indices: 509802--509826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509792 ATTACTCACA
509802 TGTATCGATACAT
1 TGTATCGATACAT
509815 TGTATCGATACA
1 TGTATCGATACA
509827 CTGATCTTTG
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:509891 original size:52 final size:52
Alignment explanation
Indices: 509835--509955 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
509825 CACTGATCTT
*
509835 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
509887 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
509939 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
509956 TAACCCTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:513058 original size:32 final size:32
Alignment explanation
Indices: 512995--513058 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
512985 CCTCATTTGC
* *
512995 CCTATCGCCGGGGTCGAGCGCACGTTACGACA
1 CCTATCGCCGGAGTCGAGCGCACGTCACGACA
* *
513027 CCTATCGCTGGAGTCGAGCGCACGTCGCGACA
1 CCTATCGCCGGAGTCGAGCGCACGTCACGACA
513059 AAGATACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (32 bp):
CCTATCGCCGGAGTCGAGCGCACGTCACGACA
Found at i:515228 original size:13 final size:13
Alignment explanation
Indices: 515210--515234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515200 TTCAACGATT
515210 TGTATCGATACAG
1 TGTATCGATACAG
515223 TGTATCGATACA
1 TGTATCGATACA
515235 TTACTCAAAT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:521141 original size:52 final size:52
Alignment explanation
Indices: 521060--521180 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
521050 TGAAAAGTTA
*
521060 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
521112 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
521164 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
521181 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:521193 original size:52 final size:51
Alignment explanation
Indices: 521060--521200 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
521050 TGAAAAGTTA
521060 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
521112 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
521164 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
521201 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:521207 original size:13 final size:13
Alignment explanation
Indices: 521189--521213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
521179 CAAAGATCAG
521189 TGTATCGATACAA
1 TGTATCGATACAA
521202 TGTATCGATACA
1 TGTATCGATACA
521214 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:521318 original size:33 final size:33
Alignment explanation
Indices: 521254--521323 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
521244 GGCAGTAGCT
*
521254 TACATTGTATCGATACAAAAAAATATTTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
521287 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
521320 TACA
1 TACA
521324 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:522410 original size:19 final size:20
Alignment explanation
Indices: 522386--522441 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
522376 ACATTATGCT
* **
522386 TTGTATTGATACATGTTC-A
1 TTGTATCGATACATGGACAA
522405 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
522425 TTGTATCGATACATGGA
1 TTGTATCGATACATGGA
522442 ACTGGCAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Done.