Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold935
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: 38964
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:4500 original size:27 final size:27
Alignment explanation
Indices: 4470--4625 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
4460 TGCTATTCAC
* *
4470 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
4497 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
4524 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
4552 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
4579 TCTTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
4606 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
4626 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:4541 original size:55 final size:55
Alignment explanation
Indices: 4475--4626 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
4465 TTCACTCAAC
* *
4475 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTAGAT
* ** * ***
4530 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
* *
4584 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
4627 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
Found at i:6999 original size:48 final size:44
Alignment explanation
Indices: 6931--7110 Score: 177
Period size: 48 Copynumber: 4.0 Consensus size: 44
6921 TCACATAGTA
*
6931 ATATGCCAACGCCATATCCCAGATATGGTCTTACATGGGATCACAACT
1 ATATGCCAATGCCATATCCCAGATATGGTCTTACATGGGAT--C-A-T
* *
6979 CTATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCAT
1 ATATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCAT
**
7023 ATAT--CAATGCCATATCCCAGATATGGTCTTACATGATAAAAT-AT
1 ATATGCCAATGCCATATCCCAGATATGGTCTTACATG---GGATCAT
* * * *
7067 ATGGATGCCGATGCCATATCCTAGATATGGTCTTATACGGGATC
1 AT--ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATC
7111 TCATCACCCC
Statistics
Matches: 111, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 30 0.27
44 8 0.07
45 5 0.05
46 3 0.03
48 65 0.59
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
ATATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCAT
Found at i:7093 original size:90 final size:89
Alignment explanation
Indices: 6941--7110 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 89
6931 ATATGCCAAC
* * * *
6941 GCCATATCCCAGATATGGTCTTACATGGGATCACAACTCTATGCCAATGCCATGTCCCAGATATG
1 GCCATATCCCAGATATGGTCTTACAT-GGATCAAAAATATATGCCAATGCCATATCCCAGATATG
*
7006 GTCTTACATGGGATCATATATCAAT
65 GTCTTACACGGGATCATATATCAAT
* *
7031 GCCATATCCCAGATATGGTCTTACAT-GAT-AAAATATATGGATGCCGATGCCATATCCTAGATA
1 GCCATATCCCAGATATGGTCTTACATGGATCAAAA-ATAT--ATGCCAATGCCATATCCCAGATA
*
7094 TGGTCTTATACGGGATC
63 TGGTCTTACACGGGATC
7111 TCATCACCCC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
87 3 0.04
88 5 0.07
90 61 0.88
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (89 bp):
GCCATATCCCAGATATGGTCTTACATGGATCAAAAATATATGCCAATGCCATATCCCAGATATGG
TCTTACACGGGATCATATATCAAT
Found at i:14878 original size:27 final size:27
Alignment explanation
Indices: 14841--14925 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
14831 TATTTCTCTC
*
14841 AGAGTTCACCAGACATACTATTCCTTT
1 AGAGTTCACCATACATACTATTCCTTT
* * *
14868 CGAGTTTACCATACGTACTATTCCTTT
1 AGAGTTCACCATACATACTATTCCTTT
* *
14895 AGAGTTCACCATACATACTAGTCCTTC
1 AGAGTTCACCATACATACTATTCCTTT
14922 AGAG
1 AGAG
14926 CTAGCTACAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (27 bp):
AGAGTTCACCATACATACTATTCCTTT
Found at i:15108 original size:27 final size:27
Alignment explanation
Indices: 15075--15144 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
15065 AGATCACCAT
*
15075 AAAGGCTTCCATTTCATAGATTGCCAC
1 AAAGGCTTCCATTTCATAGACTGCCAC
* *
15102 AATGGCTTTCATTTCATAGACTGCCAC
1 AAAGGCTTCCATTTCATAGACTGCCAC
15129 AAAGGCTTCCATTTCA
1 AAAGGCTTCCATTTCA
15145 CATCTACCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (27 bp):
AAAGGCTTCCATTTCATAGACTGCCAC
Found at i:22878 original size:68 final size:64
Alignment explanation
Indices: 22664--22916 Score: 203
Period size: 68 Copynumber: 3.8 Consensus size: 64
22654 CATAATTTTG
* * *
22664 GCTCTCTTGTAC-ACACGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTA-TCTCG
1 GCTCTCTTGT-CTACATGGTGTACAC-TAGTACCACCCATGTGACCTAGCTACA-TATATTCTCG
22725 TA
63 TA
* * * ** * *
22727 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCATGCATGCGACCTAGCTACATATA-TCCC
1 GCTCTCTTGTCTACATGGTG---TACA-CTAGTACCACCCATGTGACCTAGCTACATATATTCTC
22791 GTA
62 GTA
*
22794 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGTGACCTAGCTACATCATAATGTCTC
1 GCTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGTGACCTAGCTACAT-AT-AT-TCTC
22859 GTA
62 GTA
* * * **
22862 GCTCTCTTGTAC-ACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGTGACCTAGCTACATA
22917 CCATCTGTAT
Statistics
Matches: 152, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 25 0.16
65 2 0.01
66 21 0.14
67 32 0.21
68 52 0.34
69 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGTGACCTAGCTACATATATTCTCGTA
Found at i:23417 original size:29 final size:29
Alignment explanation
Indices: 23385--23440 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
23375 TAACTCAAAC
23385 TTTTGAAAAATTACAATTTTGCCCCTAAA
1 TTTTGAAAAATTACAATTTTGCCCCTAAA
* * * *
23414 TTTTGCATATTTACACTTTTGCCCCTA
1 TTTTGAAAAATTACAATTTTGCCCCTA
23441 GGCTCGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTGAAAAATTACAATTTTGCCCCTAAA
Found at i:30171 original size:26 final size:26
Alignment explanation
Indices: 30141--30191 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
30131 ACCAATGAAC
*
30141 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
30167 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
30192 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:30231 original size:103 final size:103
Alignment explanation
Indices: 30047--30268 Score: 367
Period size: 103 Copynumber: 2.2 Consensus size: 103
30037 AATGGATATC
30047 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
30112 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACATAGCACCACC-ATAAACCGGGGAATCA
30151 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
*
30215 GGATCA-CGCACATAGCACCACCATAAATCGGGGAATCA
66 GGAT-ATCGCACATAGCACCACCATAAACCGGGGAATCA
**
30253 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
30269 TTTATATACA
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 28 0.25
103 66 0.59
104 18 0.16
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCATAAACCGGGGAATCA
Found at i:30630 original size:29 final size:29
Alignment explanation
Indices: 30597--30660 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
30587 TAATCCACCA
30597 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
30626 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
30656 CCCAA
1 CCCAA
30661 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:30634 original size:30 final size:30
Alignment explanation
Indices: 30604--30660 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30594 CCACCCAACT
30604 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
30633 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
30661 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:37540 original size:26 final size:26
Alignment explanation
Indices: 37504--37556 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
37494 CACCACTGAA
* *
37504 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
37530 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
37556 T
1 T
37557 TTTCATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:37697 original size:23 final size:24
Alignment explanation
Indices: 37671--37718 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
37661 CACCAATGAA
*
37671 CGGGGAATCAGCA-TTAGCAACCC
1 CGGGGAATCAGCACATAGCAACCC
37694 CGGGGAATCAGCACATAGCAACCC
1 CGGGGAATCAGCACATAGCAACCC
37718 C
1 C
37719 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.10
Consensus pattern (24 bp):
CGGGGAATCAGCACATAGCAACCC
Found at i:37705 original size:95 final size:97
Alignment explanation
Indices: 37588--37779 Score: 311
Period size: 95 Copynumber: 2.0 Consensus size: 97
37578 GATATCGCAC
*
37588 TTAGCAACCCTCGGGGAATCAGCACATAGCAA-CCCTTTCAATTTCAAAGATATGGTGGAT-ATG
1 TTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCTTTC-ATTTCAAAGATATGGTGGATCACG
* *
37651 CACTTAGCACCACCAATGAA-CGGGGAATCAGCA
65 CACATAGCACCACC-ATAAATCGGGGAATCAGCA
37684 TTAGCAACCC-CGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAAGATATGGTGGATCACGC
1 TTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAAGATATGGTGGATCACGC
37748 ACATAGCACCACCATAAATCGGGGAATCAGCA
66 ACATAGCACCACCATAAATCGGGGAATCAGCA
37780 CACAGCAACC
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
95 45 0.50
96 45 0.50
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (97 bp):
TTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAAGATATGGTGGATCACGC
ACATAGCACCACCATAAATCGGGGAATCAGCA
Found at i:38148 original size:28 final size:29
Alignment explanation
Indices: 38116--38178 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
38106 TAATCCACCA
38116 CCCAACTTTTTG-AAAATTACAATTTTG-C
1 CCCAAC-TTTTGCAAAATTACAATTTTGTC
* *
38144 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGTC
38174 CCCAA
1 CCCAA
38179 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
29 18 0.60
30 4 0.13
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGTC
Found at i:38152 original size:29 final size:30
Alignment explanation
Indices: 38123--38178 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
38113 CCACCCAACT
38123 TTTTG-AAAATTACAATTTTG-CCCCAAAC
1 TTTTGCAAAATTACAATTTTGTCCCCAAAC
* *
38151 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGTCCCCAA
38179 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGTCCCCAAAC
Done.