Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1822
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: 39855
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:8684 original size:47 final size:47
Alignment explanation
Indices: 8630--8955 Score: 476
Period size: 47 Copynumber: 7.0 Consensus size: 47
8620 TTAGGATTTT
** * * **
8630 ATGTGATGAATGTGAATGTGGATATATGAGATAAGGCCGAATGGAAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
8677 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
8724 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
8771 ATGTGATGAATGTGAACATGCGTA-GTGTGGTAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
8817 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
8864 ATGTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
8911 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGC
8956 TAATACGAAA
Statistics
Matches: 256, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
46 44 0.17
47 209 0.82
48 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.25
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:8705 original size:25 final size:25
Alignment explanation
Indices: 8677--8755 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
8667 CGAATGGAAA
8677 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * *
8702 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
8724 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
*
8749 GTGTGAT
1 ATGTGAT
8756 AAGGCCGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 14 0.35
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:8823 original size:140 final size:140
Alignment explanation
Indices: 8661--8920 Score: 475
Period size: 140 Copynumber: 1.9 Consensus size: 140
8651 ATATATGAGA
8661 TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
1 TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
* * *
8726 GTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
66 GTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAATGTGAACATG
8791 CGTAGTGTGG
131 CGTAGTGTGG
**
8801 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
1 TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
8866 GTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAA
66 GTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAA
8921 CGTGGAAGTG
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 115 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (140 bp):
TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
GTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAATGTGAACATG
CGTAGTGTGG
Found at i:8990 original size:46 final size:46
Alignment explanation
Indices: 8934--9070 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
8924 GGAAGTGTAT
* *
8934 ATATGTGGTAAAGCCGAATGGCTAATACGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
8980 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATAAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * * *
9026 ACATGCGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
9071 TGTATATATA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.36, C:0.10, G:0.30, T:0.24
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:8998 original size:187 final size:186
Alignment explanation
Indices: 8630--9006 Score: 483
Period size: 187 Copynumber: 2.0 Consensus size: 186
8620 TTAGGATTTT
** *
8630 ATGTGATGAATGTGAATGTGGATATATGAGATAAGGCCGAATGGAAAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGAAAATGTGATGAATGTGAACA
* * * * *
8695 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
66 TGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCATATATGTGATAAAG
** * *
8760 CCGAATGGCCAATGTGATGAATGTGAACATGCGTAGTGTGGTAAGGCCGAATGGCCA
131 CCGAATGGCCAATACGA-GAATGTGAACATGCGTAGTGAGGTAAAGCCGAATGGCCA
* **
8817 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGAAAATGTGATGAATGTGAACA
* * *
8882 TGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGGAA-GTGTATATATGTGGTAAA
66 TGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAACGT-GAACATGCATATATGTGATAAA
* * *
8946 GCCGAATGGCTAATACGA-AATGTGTATGAGATG-GATA-TGAGGTAAAGCCGAATGGCTA
130 GCCGAATGGCCAATACGAGAATGTG-A--ACATGCG-TAGTGAGGTAAAGCCGAATGGCCA
9004 ATG
1 ATG
9007 CGAAACGTGT
Statistics
Matches: 164, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
185 6 0.04
186 1 0.01
187 148 0.90
188 9 0.05
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (186 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGAAAATGTGATGAATGTGAACA
TGCATATATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCATATATGTGATAAAG
CCGAATGGCCAATACGAGAATGTGAACATGCGTAGTGAGGTAAAGCCGAATGGCCA
Found at i:9001 original size:140 final size:139
Alignment explanation
Indices: 8684--8969 Score: 405
Period size: 140 Copynumber: 2.1 Consensus size: 139
8674 AAAATGTGAT
*
8684 GAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT
1 GAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT
* * * * * * *
8749 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTAGTGTGGTAAGGCCGAATGG
66 ATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCATAATGTGGTAAAGCCGAATGG
**
8814 CCAATGTGA
131 CCAATACGA
*
8823 TGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATA
1 -GAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATA
* *
8888 TATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAA
65 TATGTGACAAGGCAGAATGGCCAATGTGATGAACGT-GAACATGCATA-ATGTGGTAAAGCCGAA
*
8952 TGGCTAATACGA
128 TGGCCAATACGA
8964 -AATGTG
1 GAATGTG
8970 TATGAGATGG
Statistics
Matches: 132, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
139 6 0.05
140 100 0.76
141 26 0.20
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (139 bp):
GAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT
ATGTGACAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCATAATGTGGTAAAGCCGAATGG
CCAATACGA
Found at i:12145 original size:17 final size:17
Alignment explanation
Indices: 12123--12160 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
12113 TCCACCCTAA
12123 TTCCAACGGAGGATCTT
1 TTCCAACGGAGGATCTT
12140 TTCCAACGGAGGATCTT
1 TTCCAACGGAGGATCTT
12157 TTCC
1 TTCC
12161 CTCTCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (17 bp):
TTCCAACGGAGGATCTT
Found at i:14817 original size:42 final size:43
Alignment explanation
Indices: 14760--14861 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
14750 TGAGATTTAC
*
14760 GTGTAAGATCATGTCTGAGACA-TCGGCATC-ATATTTGATTTT
1 GTGTAAGACCATGTCTGAGACAGT-GGCATCGATATTTGATTTT
* * **
14802 GTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCATGTCTGAGACAGTGGCATCGATATTTGATTTT
* *
14845 ATGTAAGACCACGTCTG
1 GTGTAAGACCATGTCTG
14862 GGACGTTGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGAGACAGTGGCATCGATATTTGATTTT
Found at i:14838 original size:43 final size:42
Alignment explanation
Indices: 14739--14873 Score: 125
Period size: 43 Copynumber: 3.1 Consensus size: 42
14729 TCTGGGTCGT
* * *
14739 TGGCATCA-ATTTGAGATTTACGTGTAAGATCATGTCTGAGACA-
1 TGGCATCATATTT--GA-TTACGTGTAAGACCCTGTCTGGGACAG
**
14782 TCGGCATCATATTTGATTTTGTGTAAGACCCTGTCTGGGACAG
1 T-GGCATCATATTTGATTACGTGTAAGACCCTGTCTGGGACAG
*
14825 TGGCATCGATATTTGATTACATGTAAGACCAC-GTCTGGGAC-G
1 TGGCATC-ATATTTGATTACGTGTAAGACC-CTGTCTGGGACAG
14867 TTGGCAT
1 -TGGCAT
14874 TGTGTGACCT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
42 28 0.36
43 38 0.49
44 8 0.10
45 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGGCATCATATTTGATTACGTGTAAGACCCTGTCTGGGACAG
Found at i:17551 original size:13 final size:13
Alignment explanation
Indices: 17533--17561 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17523 AACTAACGTT
17533 AAAATAGTAAATG
1 AAAATAGTAAATG
17546 AAAATAGTAAATG
1 AAAATAGTAAATG
17559 AAA
1 AAA
17562 TAATATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAATAGTAAATG
Found at i:20844 original size:23 final size:23
Alignment explanation
Indices: 20817--20870 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
20807 GTAAATGGAT
20817 CCCGCAAGTGTAGCGCCTGCTCC
1 CCCGCAAGTGTAGCGCCTGCTCC
20840 CCCGCAAGTGTAGCGCCTGCTCC
1 CCCGCAAGTGTAGCGCCTGCTCC
20863 CCCGCAAG
1 CCCGCAAG
20871 GGACAGCGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.44, G:0.26, T:0.15
Consensus pattern (23 bp):
CCCGCAAGTGTAGCGCCTGCTCC
Found at i:20878 original size:24 final size:23
Alignment explanation
Indices: 20817--20879 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
20807 GTAAATGGAT
* *
20817 CCCGCAAGTGTAGCGCCTGCTCC
1 CCCGCAAGGGCAGCGCCTGCTCC
* *
20840 CCCGCAAGTGTAGCGCCTGCTCC
1 CCCGCAAGGGCAGCGCCTGCTCC
20863 CCCGCAAGGGACAGCGC
1 CCCGCAAGGG-CAGCGC
20880 AGGCTAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
23 32 0.86
24 5 0.14
ACGTcount: A:0.16, C:0.43, G:0.29, T:0.13
Consensus pattern (23 bp):
CCCGCAAGGGCAGCGCCTGCTCC
Found at i:26999 original size:28 final size:28
Alignment explanation
Indices: 26967--27094 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
26957 ATAGTAAGTC
*
26967 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
26995 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
27024 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
27052 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
27081 CGCACACTTAGTGC
1 CGCACACTTAGTGC
27095 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:27057 original size:57 final size:57
Alignment explanation
Indices: 26966--27094 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
26956 TATAGTAAGT
*
26966 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
27023 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
27080 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
27095 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:30081 original size:39 final size:40
Alignment explanation
Indices: 30036--30203 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
30026 CGGGGTTTAG
* * *
30036 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
30075 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
30115 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
30155 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
30196 CCGGATAT
1 CCGGATAT
30204 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:30186 original size:41 final size:40
Alignment explanation
Indices: 30059--30203 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
30049 CTCGCACAAG
* * * * *
30059 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
30099 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
30139 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
30180 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
30204 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:38263 original size:28 final size:28
Alignment explanation
Indices: 38231--38358 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
38221 ATAGTAAGTC
*
38231 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38259 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
38288 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
38316 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
38345 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38359 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38321 original size:57 final size:57
Alignment explanation
Indices: 38230--38358 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
38220 TATAGTAAGT
*
38230 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
38287 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
38344 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
38359 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Done.