Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1098
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: 45673
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Found at i:945 original size:27 final size:27
Alignment explanation
Indices: 914--1091 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
904 TAAATTGTAC
914 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
941 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
967 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
995 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1023 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1050 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1077 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1092 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:1028 original size:82 final size:81
Alignment explanation
Indices: 915--1070 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
905 AAATTGTACA
* *
915 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
979 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
996 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1061 TGCGAGTTGA
65 TGCGAATTGA
1071 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1082 original size:82 final size:81
Alignment explanation
Indices: 911--1091 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
901 GATTAAATTG
* *
911 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
976 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
992 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1056 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
1074 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1092 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:8139 original size:27 final size:27
Alignment explanation
Indices: 8108--8284 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
8098 TAAATTGTAC
*
8108 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
8135 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
8161 ATGCACTAAATGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
8189 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
8217 AGCACTAAGTGTGC-AATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
8243 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
8270 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8285 GACTCAATAT
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 22 0.18
27 81 0.65
28 21 0.17
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:8256 original size:81 final size:81
Alignment explanation
Indices: 8109--8263 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
8099 AAATTGTACA
* *
8109 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAATGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
8174 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* * *
8190 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGC-AATTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
8253 GTGCGAGTTGA
64 GTGCGAATTGA
8264 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 1 0.02
81 41 0.62
82 24 0.36
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:8275 original size:81 final size:81
Alignment explanation
Indices: 8105--8284 Score: 220
Period size: 81 Copynumber: 2.2 Consensus size: 81
8095 GATTAAATTG
* *
8105 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
8170 ATGTGCGAATTGACCA
66 ATGTGCGAATTGACCA
* * * *
8186 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGC-AATTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * **
8249 AAGTGTGCGAGTTGATTA
64 AAATGTGCGAATTGACCA
* *
8267 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
8285 GACTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 1 0.01
81 58 0.70
82 24 0.29
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
ATGTGCGAATTGACCA
Found at i:16094 original size:27 final size:27
Alignment explanation
Indices: 16041--16094 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
16031 ATATATAAAT
* *
16041 ATTATAAAATAATTATTTTGTACTTAA
1 ATTATAAAATAATTAATTTGTAATTAA
*
16068 ATTATTAACATAATTAATTT-TAATTAA
1 ATTA-TAAAATAATTAATTTGTAATTAA
16095 TTTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATAAAATAATTAATTTGTAATTAA
Found at i:17820 original size:26 final size:26
Alignment explanation
Indices: 17781--17850 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
17771 GCCAACACAC
**
17781 CAATATCGTGGCAAAGCTACAAGTAAT
1 CAATATCGCAGCAAAGCTACAAGT-AT
* *
17808 -AATATCGCAGCAAAGCTGCCAGTAT
1 CAATATCGCAGCAAAGCTACAAGTAT
* *
17833 CAGTAACGCAGCAAAGCT
1 CAATATCGCAGCAAAGCT
17851 GCCAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 2 0.06
26 34 0.94
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTACAAGTAT
Found at i:17851 original size:26 final size:26
Alignment explanation
Indices: 17813--17863 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17803 GTAATAATAT
*
17813 CGCAGCAAAGCTGCCAGTATCAGTAA
1 CGCAGCAAAGCTGCCAATATCAGTAA
17839 CGCAGCAAAGCTGCCAATATCAGTA
1 CGCAGCAAAGCTGCCAATATCAGTA
17864 TATGTGGCCA
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:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAATATCAGTAA
Found at i:22525 original size:31 final size:31
Alignment explanation
Indices: 22466--22530 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
22456 TTTGAGCCTT
* * *
22466 TAACTCCACAAGTTCTTTCGATGTCATTCCA
1 TAACTCCACAAGCTATTTCGATGCCATTCCA
* * *
22497 TAACTCCACAAGCTATTTTGGTGCCATTCTA
1 TAACTCCACAAGCTATTTCGATGCCATTCCA
22528 TAA
1 TAA
22531 GGGGCAATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (31 bp):
TAACTCCACAAGCTATTTCGATGCCATTCCA
Found at i:25605 original size:28 final size:28
Alignment explanation
Indices: 25542--25723 Score: 276
Period size: 28 Copynumber: 6.5 Consensus size: 28
25532 ATATTAAGTC
*
25542 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
25569 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
25597 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
25625 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
25653 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
25681 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
25710 CGTACACTTAGTGC
1 CGCACACTTAGTGC
25724 CAATCTCATG
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
27 21 0.15
28 104 0.73
29 18 0.13
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33746 original size:28 final size:28
Alignment explanation
Indices: 33651--33800 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
33641 ATATTAAGTC
*
33651 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
33678 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
33706 -GCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
33733 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
33761 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
33790 CGCACACTTAG
1 CGCACACTTAG
33801 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 47 0.42
28 50 0.44
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33754 original size:55 final size:56
Alignment explanation
Indices: 33651--33800 Score: 223
Period size: 55 Copynumber: 2.7 Consensus size: 56
33641 ATATTAAGTC
*
33651 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
*
33706 -GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
* * * *
33761 CGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAG
1 CGCACACTTAGTGCTATATAA-TCAAACTCGCACACTTAG
33801 CGCCAATCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
54 21 0.24
55 31 0.36
56 18 0.21
57 16 0.19
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (56 bp):
CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:41801 original size:29 final size:28
Alignment explanation
Indices: 41713--41867 Score: 204
Period size: 28 Copynumber: 5.5 Consensus size: 28
41703 ATATTAAGTC
* *
41713 CGCACACTCAGTGCTATATAAAC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41740 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41768 TGCACACTTAGTGCTCATATAATCAAACT
1 CGCACACTTAGTGCT-ATATAATCAAACT
41797 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41825 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
41854 CGTACACTTAGTGC
1 CGCACACTTAGTGC
41868 CAAATTCATG
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
27 20 0.18
28 50 0.44
29 44 0.39
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41805 original size:57 final size:55
Alignment explanation
Indices: 41713--41839 Score: 200
Period size: 57 Copynumber: 2.3 Consensus size: 55
41703 ATATTAAGTC
*
41713 CGCACACTCAGTGCTATATAAACAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAAACAACTCGCACACTTAGTGCTACATAATCAAACT
* * *
41768 TGCACACTTAGTGCTCATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCT-ATATAAAC-AACTCGCACACTTAGTGCTACATAATCAAACT
41825 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41840 GTACAATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 13 0.20
56 7 0.11
57 45 0.69
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTATATAAACAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:41861 original size:57 final size:57
Alignment explanation
Indices: 41713--41867 Score: 181
Period size: 57 Copynumber: 2.8 Consensus size: 57
41703 ATATTAAGTC
* * * *
41713 CGCACACTCAGTGCT-ATATAAAC-AACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTCATACAATCAAACCCGCACACTTAGTGCTACATAATCAAACT
* * * *
41768 TGCACACTTAGTGCTCATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTCATACAATCAAACCCGCACACTTAGTGCTACATAATCAAACT
* * *
41825 CGCACACTTAGTGCT-GTACAATTTAAACCCGTACACTTAGTGC
1 CGCACACTTAGTGCTCATACAA-TCAAACCCGCACACTTAGTGC
41868 CAAATTCATG
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
55 13 0.15
56 11 0.13
57 63 0.72
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (57 bp):
CGCACACTTAGTGCTCATACAATCAAACCCGCACACTTAGTGCTACATAATCAAACT
Done.