Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold988
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: 62075
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Found at i:7325 original size:54 final size:54
Alignment explanation
Indices: 7267--7413 Score: 156
Period size: 54 Copynumber: 2.7 Consensus size: 54
7257 ACTCAACTCA
* *
7267 CACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGATTC-
1 CACACTTAGTGCCACAT-ATCAAATCGCACACTTAGTGCTATCATA-TTAGATTCG
* * * ***
7321 CACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTTTTCG
1 CACACTTAGTGCCACAT-ATCAAATCGCACACTTAGTGCTATCATATTAGATTCG
* *
7375 CACACTTAGTGCAACATATCGAATCGCACACTTAGTGCT
1 CACACTTAGTGCCACATATCAAATCGCACACTTAGTGCT
7414 GTACAATTTA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 24 0.32
54 52 0.68
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (54 bp):
CACACTTAGTGCCACATATCAAATCGCACACTTAGTGCTATCATATTAGATTCG
Found at i:7328 original size:27 final size:27
Alignment explanation
Indices: 7267--7412 Score: 129
Period size: 27 Copynumber: 5.4 Consensus size: 27
7257 ACTCAACTCA
* * *
7267 CACACTTAGTGCCACGTAATCAAATCG
1 CACACTTAGTGCCACATAGTCAATTCG
* * *
7294 CACCCTTAGTGCTACATAGTTAGATTC-
1 CACACTTAGTGCCACATAGTCA-ATTCG
* *
7321 CACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCCACATAGTCAATTCG
* **
7348 CACACTTAGTG-CATCATATTCTTTTCG
1 CACACTTAGTGCCA-CATAGTCAATTCG
*
7375 CACACTTAGTGCAACATA-TCGAA-TCG
1 CACACTTAGTGCCACATAGTC-AATTCG
7401 CACACTTAGTGC
1 CACACTTAGTGC
7413 TGTACAATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
26 22 0.23
27 69 0.73
28 4 0.04
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (27 bp):
CACACTTAGTGCCACATAGTCAATTCG
Found at i:10150 original size:68 final size:66
Alignment explanation
Indices: 10078--10254 Score: 189
Period size: 67 Copynumber: 2.7 Consensus size: 66
10068 CATCATGTGT
* * * * *
10078 ACAAGAGAGCTACGAGATACTATGTGGCAGCTAGGTCACATGTGT-GAT-ACGGGATGTATACCA
1 ACAAGAGAGCTACGAGATA-AATGT---AGCTAGGTCACATGTGTGGATCAAGGGAAGGACACCA
10141 TGTAG
62 TGTAG
* * * *
10146 ACAAGAGAGCTACGGGATAAATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGAT-CAAGGGAAGGACACCATGT
10211 AG
65 AG
* *
10213 ACAAGAGAGCTACGAGATAAA-GTGGCTAGGTCACATGGGTGG
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGG
10255 TACTAAGTGT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 16 0.17
65 2 0.02
66 18 0.19
67 39 0.42
68 18 0.19
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATCAAGGGAAGGACACCATGTA
G
Found at i:20789 original size:25 final size:25
Alignment explanation
Indices: 20760--20809 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20750 GAAGTAAATG
20760 ATTTAAATAAAACAAAAGAGTTCTA
1 ATTTAAATAAAACAAAAGAGTTCTA
20785 ATTTAAATAAAACAAAAGAGTTCTA
1 ATTTAAATAAAACAAAAGAGTTCTA
20810 GTGCATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (25 bp):
ATTTAAATAAAACAAAAGAGTTCTA
Found at i:24162 original size:49 final size:49
Alignment explanation
Indices: 24051--24230 Score: 166
Period size: 49 Copynumber: 3.7 Consensus size: 49
24041 GGGATAAGAT
* * * ** * *
24051 GCCGACGCCATGTCCCAGACATGGTCTTACACAGGCTAGC--ACATCAAA
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGACTCTCATATATCAAG
* * * * **
24099 GTCGATGCCATGTCCTAGACAAGTCTTACACTGACTTTCATATATTGAG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAAG
* * * * *
24148 GCCGATGCCGTGTCCCAAACAGGTCTTACACTGGCTCTCATCTATCAAT
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAAG
*
24197 GTCGATGCCATGTCCCAGACAGGTCTTACACTGA
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGA
24231 AACACAACAA
Statistics
Matches: 103, Mismatches: 27, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
47 13 0.13
48 18 0.17
49 72 0.70
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAAG
Found at i:24223 original size:98 final size:97
Alignment explanation
Indices: 24051--24230 Score: 254
Period size: 98 Copynumber: 1.8 Consensus size: 97
24041 GGGATAAGAT
* *
24051 GCCGACGCCATGTCCCAGACATGGTCTTACACAGGCTAGCACATCAAAGTCGATGCCATGTCCTA
1 GCCGACGCCATGTCCCAAACATGGTCTTACACAGGCTAGCACATCAAAGTCGATGCCATGTCCCA
24116 GACAAGTCTTACACTGACTTTCATATATTGAG
66 GACAAGTCTTACACTGACTTTCATATATTGAG
* * * ** *
24148 GCCGATGCCGTGTCCCAAACA-GGTCTTACACTGGCTCTCATCTATCAATGTCGATGCCATGTCC
1 GCCGACGCCATGTCCCAAACATGGTCTTACACAGGCTAGCA-C-ATCAAAGTCGATGCCATGTCC
*
24212 CAGACAGGTCTTACACTGA
64 CAGACAAGTCTTACACTGA
24231 AACACAACAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
96 16 0.22
97 19 0.26
98 37 0.51
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (97 bp):
GCCGACGCCATGTCCCAAACATGGTCTTACACAGGCTAGCACATCAAAGTCGATGCCATGTCCCA
GACAAGTCTTACACTGACTTTCATATATTGAG
Found at i:24818 original size:20 final size:18
Alignment explanation
Indices: 24781--24831 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
24771 CTATAGCAAC
24781 TCACAATTTA-AATTATT
1 TCACAATTTACAATTATT
24798 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
24818 TTACAACTTTACAA
1 TCACAA-TTTACAA
24832 AATAGCCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 3 0.10
20 16 0.55
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:27129 original size:147 final size:147
Alignment explanation
Indices: 26889--27198 Score: 557
Period size: 147 Copynumber: 2.1 Consensus size: 147
26879 TCACAGGCTA
* * *
26889 GCCACACGGTCGTGTGACCCCTATAGGGAAATATTTTTCGATCACGCACGAGGTTGTAATTAAGT
1 GCCACATGGTCGTGTGACCCCTATAGGGAAATATTTTTCAATCACGCACAAGGTTGTAATTAAGT
*
26954 CACATGGTCCTGTTATCTAGCCATAGGACTGTGTCCCTTAGTCATACACTGTCACACAGTCTGGA
66 CACATGGTCCTGTTATCTAGCCACAGGACTGTGTCCCTTAGTCATACACTGTCACACAGTCTGGA
*
27019 CCCTCCCACACGGCCCG
131 CCCTCCCACACAGCCCG
27036 GCCACATGGTCGTGTGACCCCTATAGGGAAATATTTTTCAATCACGCACAAGGTTGTAATTAAGT
1 GCCACATGGTCGTGTGACCCCTATAGGGAAATATTTTTCAATCACGCACAAGGTTGTAATTAAGT
*
27101 CACATGGTCGTGTTATCTAGCCACAGGACTGTGTCCCTTAGTCATACACTGTCACACAGTCTGGA
66 CACATGGTCCTGTTATCTAGCCACAGGACTGTGTCCCTTAGTCATACACTGTCACACAGTCTGGA
27166 CCCTCCCACACAGCCCG
131 CCCTCCCACACAGCCCG
*
27183 ACCACATGGTCGTGTG
1 GCCACATGGTCGTGTG
27199 GCTTTGTTTT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 156 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (147 bp):
GCCACATGGTCGTGTGACCCCTATAGGGAAATATTTTTCAATCACGCACAAGGTTGTAATTAAGT
CACATGGTCCTGTTATCTAGCCACAGGACTGTGTCCCTTAGTCATACACTGTCACACAGTCTGGA
CCCTCCCACACAGCCCG
Found at i:33778 original size:43 final size:43
Alignment explanation
Indices: 33730--33896 Score: 266
Period size: 43 Copynumber: 3.9 Consensus size: 43
33720 CCGGCATTAC
33730 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
**
33773 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
* *
33816 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
* *
33859 GCCTGCTAGGCACGAAGGCCTGAATATA-AT-ACCAGCAC
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCAC
33897 TAGGTGTAAC
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
41 7 0.06
42 2 0.02
43 108 0.92
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
Found at i:35266 original size:27 final size:27
Alignment explanation
Indices: 35235--35457 Score: 203
Period size: 27 Copynumber: 8.5 Consensus size: 27
35225 ATTGAGTCCG
* *
35235 GCACACTCAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTACATAATCAACTC
* *
35262 GCACACTTAGTGCTACGTAATCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
*
35289 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAATC-AACTC
** ** *
35317 GCACACTTAGTGCCGCATGGTCAATTC
1 GCACACTTAGTGCTACATAATCAACTC
* **
35344 GCACACTTAGTGC-ATCATATTCATTTC
1 GCACACTTAGTGCTA-CATAATCAACTC
*
35371 G--CACTTAGTGCAACAT--T----TC
1 GCACACTTAGTGCTACATAATCAACTC
* *
35390 GCACACTTAGTGCTACATAGTCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
* *
35417 GCACACTTAGTGCTACATAGTCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
35444 GCACACTTAGTGCT
1 GCACACTTAGTGCT
35458 GTACAATTTA
Statistics
Matches: 169, Mismatches: 16, Indels: 22
0.82 0.08 0.11
Matches are distributed among these distances:
19 3 0.02
21 14 0.08
23 2 0.01
25 13 0.08
26 1 0.01
27 113 0.67
28 23 0.14
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAATCAACTC
Found at i:35389 original size:19 final size:20
Alignment explanation
Indices: 35365--35407 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
35355 GCATCATATT
35365 CATTTCG-CACTTAGTGCAA
1 CATTTCGACACTTAGTGCAA
*
35384 CATTTCGCACACTTAGTGCTA
1 CATTTCG-ACACTTAGTGCAA
35405 CAT
1 CAT
35408 AGTCAAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (20 bp):
CATTTCGACACTTAGTGCAA
Found at i:35446 original size:73 final size:74
Alignment explanation
Indices: 35315--35456 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 74
35305 ATAGTCAAAC
* * * * **
35315 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATATTCATTTCG-CACTTAG
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCATCATAGTCAAATCGACACTTAG
35379 TGCAACATT
66 TGCAACATT
*
35388 TCGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC-TACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCAT-CATAGTCAAATCG-ACACTT
35452 AGTGC
64 AGTGC
35457 TGTACAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.02
73 48 0.81
75 10 0.17
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (74 bp):
TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCATCATAGTCAAATCGACACTTAG
TGCAACATT
Found at i:43255 original size:27 final size:27
Alignment explanation
Indices: 43225--43428 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
43215 ATATTGAGTC
* * * *
43225 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43252 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43279 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43307 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43334 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43361 CGCACACTTAGTGCAACATAGTC-AAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43387 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43414 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43429 GTACAATTTA
Statistics
Matches: 155, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.15
27 108 0.70
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43317 original size:55 final size:54
Alignment explanation
Indices: 43225--43428 Score: 250
Period size: 55 Copynumber: 3.8 Consensus size: 54
43215 ATATTGAGTC
* * * * *
43225 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
** * *
43279 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAAT
* ** *
43334 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTC-AAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
*
43387 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
43429 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
53 38 0.30
54 44 0.35
55 45 0.35
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
Found at i:43364 original size:82 final size:80
Alignment explanation
Indices: 43225--43428 Score: 248
Period size: 82 Copynumber: 2.5 Consensus size: 80
43215 ATATTGAGTC
* * * * * *
43225 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAG
1 CGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAG
*
43290 TGCTACATAGTCAAACT
66 TGCAACATAGTC-AA-T
* * * * **
43307 CGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTA
1 CGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTA
43371 GTGCAACATAGTCAAT
65 GTGCAACATAGTCAAT
*
43387 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCT
43429 GTACAATTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
80 38 0.37
81 3 0.03
82 63 0.61
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (80 bp):
CGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAG
TGCAACATAGTCAAT
Found at i:51198 original size:27 final size:27
Alignment explanation
Indices: 51168--51371 Score: 248
Period size: 27 Copynumber: 7.6 Consensus size: 27
51158 ATATTGAGTC
* * * *
51168 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
51195 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
51222 CGCACACTTAGTGCTTCATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
51249 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
51276 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
51303 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
51330 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
51357 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
51372 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
27 154 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:56118 original size:40 final size:40
Alignment explanation
Indices: 56070--56235 Score: 264
Period size: 40 Copynumber: 4.2 Consensus size: 40
56060 GGACTAAGAT
*
56070 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
56110 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
*
56150 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * *
56190 CCGAAGGCATTTGTGTGAGTTG-TTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTC
56229 CCGAAGG
1 CCGAAGG
56236 TACTTGGGTT
Statistics
Matches: 119, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.13
40 103 0.87
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
Done.