Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2126
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: 37583
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4887 original size:26 final size:27
Alignment explanation
Indices: 4848--5025 Score: 155
Period size: 27 Copynumber: 6.6 Consensus size: 27
4838 ATATTGAGTC
* *
4848 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
4875 CGCAC-CTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
4901 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
4929 CGCACACTTAGTGCCGCAATGGTCAATT
1 CGCACACTTAGTGCTAC-ATAATCAACT
**
4957 CGCACACTTAGTGCATCACAT--TCATTT
1 CGCACACTTAGTGC-T-ACATAATCAACT
* * *
4984 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
5011 CGCATACTTAGTGCT
1 CGCACACTTAGTGCT
5026 GTACAATTTA
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.03
26 22 0.18
27 56 0.45
28 35 0.28
29 7 0.06
30 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:6909 original size:38 final size:38
Alignment explanation
Indices: 6858--6934 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
6848 GTGCTGGTAG
6858 AGATATCACGATTTGTGATGATTAAATATCTAAAGGAA
1 AGATATCACGATTTGTGATGATTAAATATCTAAAGGAA
6896 AGATATCACGATTTGTGATGATTAAATATCTAAAGGAA
1 AGATATCACGATTTGTGATGATTAAATATCTAAAGGAA
6934 A
1 A
6935 CCATGATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (38 bp):
AGATATCACGATTTGTGATGATTAAATATCTAAAGGAA
Found at i:7203 original size:45 final size:45
Alignment explanation
Indices: 7132--7365 Score: 284
Period size: 45 Copynumber: 5.2 Consensus size: 45
7122 CAGGCTTCGG
7132 GCCT-GCAGGC-ATTGATGCCGGTGAAATACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTA-TGATGCCGGTGAAATACTATTCGGGCCTTTGA
7176 GCCTAGCAGGCTATTGATGCCGG-GAAATGACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTA-TGATGCCGGTGAAAT-ACTATTCGGGCCTTTGA
* * * *
7222 GCCTAGCAAGCTATGATGCTGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
* * *
7267 GCCTAGCAGGCTATAATGCCGGTGAGATACTATTCTGG-CTTTCGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTT-GA
* * *
7312 GCCTAGTAGGCTATAATGCCGGTGAAATGA-TA-TCGGGCC-TCGA
1 GCCTAGCAGGCTATGATGCCGGTGAAAT-ACTATTCGGGCCTTTGA
7355 GCCTAGCAGGC
1 GCCTAGCAGGC
7366 GAATGCTGGT
Statistics
Matches: 169, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
43 12 0.07
44 13 0.08
45 99 0.59
46 45 0.27
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (45 bp):
GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
Found at i:13491 original size:33 final size:33
Alignment explanation
Indices: 13452--13517 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
13442 TTAATAATAA
13452 AATTTAATGTAACTAACGAAATAACTAGACAAT
1 AATTTAATGTAACTAACGAAATAACTAGACAAT
*
13485 AATTTAATGTAATTAACGAAATAACTAGACAAT
1 AATTTAATGTAACTAACGAAATAACTAGACAAT
13518 CACACTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (33 bp):
AATTTAATGTAACTAACGAAATAACTAGACAAT
Found at i:14023 original size:13 final size:13
Alignment explanation
Indices: 13995--14042 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
13985 CATCATGTGC
*
13995 TTTTACCATATTAA
1 TTTTATCAT-TTAA
14009 TTTTATCATTTAA
1 TTTTATCATTTAA
*
14022 TTTTAT-AATTAA
1 TTTTATCATTTAA
14034 TTTTTATCA
1 -TTTTATCA
14043 CTTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 5 0.17
13 16 0.53
14 9 0.30
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTATCATTTAA
Found at i:15007 original size:32 final size:32
Alignment explanation
Indices: 14948--15012 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
14938 TTAGATTGAA
*
14948 TTTTAAAAAGTTGAGAATTTATAGATAAAATT
1 TTTTAAAAAGTTGAGAATTCATAGATAAAATT
* *
14980 TTTTAAAAATTTGAGAATCTCA-GGATAAAATT
1 TTTTAAAAAGTTGAGAAT-TCATAGATAAAATT
15012 T
1 T
15013 ACATTCCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (32 bp):
TTTTAAAAAGTTGAGAATTCATAGATAAAATT
Found at i:19218 original size:30 final size:30
Alignment explanation
Indices: 19184--19241 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
19174 TAGGCACTTC
19184 CACACAGGT-GATCCACACGCCCGTGTGTGA
1 CACACAGGTAGA-CCACACGCCCGTGTGTGA
* *
19214 CACACGGGTAGACCACATGCCCGTGTGT
1 CACACAGGTAGACCACACGCCCGTGTGT
19242 CATGGCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (30 bp):
CACACAGGTAGACCACACGCCCGTGTGTGA
Found at i:23277 original size:47 final size:47
Alignment explanation
Indices: 23226--23464 Score: 374
Period size: 47 Copynumber: 5.1 Consensus size: 47
23216 TTAGGATTTT
* *
23226 ATGTGATGAATGTAAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
*
23273 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
23320 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
*
23367 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
23414 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
23459 ATGTGA
1 ATGTGA
23465 AATATATATA
Statistics
Matches: 179, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 25 0.14
47 154 0.86
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:23279 original size:22 final size:22
Alignment explanation
Indices: 23251--23373 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 22
23241 ACATGCATAT
23251 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
23273 ATGTGATAAATGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
23297 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * *
23320 ATGTGATGAATGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
23344 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
23367 ATGTGAT
1 ATGTGAT
23374 GAATGTGAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
22 23 0.31
23 18 0.24
24 18 0.24
25 16 0.21
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:23422 original size:25 final size:25
Alignment explanation
Indices: 23347--23422 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
23337 ATGCATATAT
23347 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
23372 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
23394 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
23419 GTGA
1 GTGA
23423 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:23496 original size:50 final size:49
Alignment explanation
Indices: 23423--23519 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
23413 AATGTGGTGA
23423 ATATGAACATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATAT
1 ATATGAACATGCATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATAT
* * *
23472 ATATGAGATATGCATATGTGGTAAAGTCGAATGGCTAGTGTGAAATAT
1 ATATGA-ACATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
23520 GTAGGCGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 6 0.14
50 36 0.84
51 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (49 bp):
ATATGAACATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATATAT
Found at i:23814 original size:37 final size:37
Alignment explanation
Indices: 23674--23813 Score: 228
Period size: 37 Copynumber: 3.8 Consensus size: 37
23664 TATATTCTGG
23674 GTAAGACCCGATGACTACGTGTGGAGATTATGTCC-A
1 GTAAGACCCGATGACTACGTGTGGAGATTATGTCCGA
*
23710 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGG
1 -GTAAGACCCGATGACTACGTGTGGAGATTATGTCCGA
*
23748 GTAAGACCCGATGACTACGTGTGGAGATTTTGTCCGA
1 GTAAGACCCGATGACTACGTGTGGAGATTATGTCCGA
* *
23785 GTAAGACCCGATAACTTCGTGTGGAGATT
1 GTAAGACCCGATGACTACGTGTGGAGATT
23814 TCGTCTGAGC
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
GTAAGACCCGATGACTACGTGTGGAGATTATGTCCGA
Found at i:27517 original size:92 final size:93
Alignment explanation
Indices: 27405--27575 Score: 301
Period size: 92 Copynumber: 1.8 Consensus size: 93
27395 CGCCCATAAG
*
27405 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
27469 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
27498 CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
27562 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
27576 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
91 2 0.03
92 66 0.88
93 7 0.09
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:27570 original size:46 final size:46
Alignment explanation
Indices: 27398--27572 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
27388 TGTAACCCGC
* *
27398 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
27444 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
27494 -C-TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
27536 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
27573 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 2 0.02
45 8 0.07
46 76 0.70
47 6 0.06
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:35042 original size:92 final size:92
Alignment explanation
Indices: 34912--35081 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 92
34902 CGCCCATAAG
*
34912 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34977 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
35004 CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
35068 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
35082 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 20 0.27
92 55 0.73
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:35061 original size:46 final size:46
Alignment explanation
Indices: 34905--35078 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
34895 TGTAACCCGC
* *
34905 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
34950 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
35000 -C-TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
35042 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
35079 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 21
0.78 0.06 0.15
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 2 0.02
45 40 0.37
46 44 0.40
47 6 0.06
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.