Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold712
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: 9023
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:1051 original size:4 final size:4
Alignment explanation
Indices: 1042--1068 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1032 ATATGAGAGA
1042 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1069 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1741 original size:44 final size:44
Alignment explanation
Indices: 1693--1918 Score: 180
Period size: 44 Copynumber: 5.2 Consensus size: 44
1683 AAAATTTAGC
* *
1693 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGACAGAATCTGCA
* * * *
1737 ATCTTCAACCTACTCCCCTACTGCTTAGGGAGATAGGAT-T--A
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGACAGAATCTGCA
* * * * * *
1778 A-CGGCTCAATGTACTCCACTA-T-CTT-GGGAAGATAAGATTC-ACC
1 ATC--TTCAATCTACTCCACTACTGCTTAGGG-AGA-CAGAATCTGCA
* *
1821 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTTGCA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGACAGAATC-TGCA
* * * * *
1866 ATCTTCAACCTACTCCACTACTGCTTAGGGAAATAGGATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGACAGAATCTGCA
1910 ATCTTCAAT
1 ATCTTCAAT
1919 TCATTCCACT
Statistics
Matches: 139, Mismatches: 30, Indels: 26
0.71 0.15 0.13
Matches are distributed among these distances:
39 3 0.02
40 7 0.05
41 6 0.04
42 26 0.19
43 8 0.06
44 51 0.37
45 38 0.27
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTTAGGGAGACAGAATCTGCA
Found at i:2071 original size:95 final size:95
Alignment explanation
Indices: 1921--2103 Score: 307
Period size: 95 Copynumber: 1.9 Consensus size: 95
1911 TCTTCAATTC
* *
1921 ATTCCACTGCTACCTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAG
1 ATTCCACTGCAACCTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAAGGAG
1986 GTAAAATCTATC-ATATTTAATCTTTAGTCT
66 GTAAAATCT-TCTATATTTAATCTTTAGTCT
2016 ATTCCACTGCCAACC-AGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAAGGA
1 ATTCCACTG-CAACCTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAAGGA
*
2080 GGTAAAATCTTCTATATTTGATCT
65 GGTAAAATCTTCTATATTTAATCT
2104 GCCCCGCTGT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
94 2 0.02
95 77 0.93
96 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (95 bp):
ATTCCACTGCAACCTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAAGGAG
GTAAAATCTTCTATATTTAATCTTTAGTCT
Found at i:2350 original size:44 final size:44
Alignment explanation
Indices: 2212--2439 Score: 171
Period size: 44 Copynumber: 5.2 Consensus size: 44
2202 TAATGCAGGA
* *
2212 AGGCCAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAATCGAGAG
* * * * * * *
2256 AGGTAATG-TTTG-TGTCTTCGATCTGCTTCGCTGTCAAT-GCAG-G
1 AGGCAA-GATCTGTTGTCTTCAACCAGCTCCGCT-ACAATCG-AGAG
*
2299 AAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAATCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAATCGAGAG
* * * * * * * *
2344 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCAAT-GCAGAA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-ACAATCG-AGAG
* * *
2388 AGGCAAGATCGGTTGTCTTCAACCAGCTCCACCACAATCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAATCGAGAG
2432 AGGCAAGA
1 AGGCAAGA
2440 CTTTATTTTC
Statistics
Matches: 135, Mismatches: 37, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
43 35 0.26
44 67 0.50
45 33 0.24
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAATCGAGAG
Found at i:2407 original size:45 final size:45
Alignment explanation
Indices: 2180--2407 Score: 155
Period size: 44 Copynumber: 5.2 Consensus size: 45
2170 GCAAGGTTTG
* * * * *
2180 TGTCTTCGACCTGCTTCGATGTTAATGCAGGAAGGCCAGATCTGT
1 TGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGT
* * * * * * * * *
2225 TGTCTTCAACCAGCTCCGCT-ACAA-CCGAGAGAGGTAATG-TTTG-
1 TGTCTTCGATCTGCTTCGCTGTCAATGC-AGAAAGGCAA-GATCTGT
*
2268 TGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGT
1 TGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGT
* * * * * * * * *
2313 TGTCTTCAACCAGCTCCACT-ACAAT-CGAGAGAGGCAAGGTTTG-
1 TGTCTTCGATCTGCTTCGCTGTCAATGC-AGAAAGGCAAGATCTGT
*
2356 TGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCGGT
1 TGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGT
2401 TGTCTTC
1 TGTCTTC
2408 AACCAGCTCC
Statistics
Matches: 131, Mismatches: 42, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
43 34 0.26
44 56 0.43
45 41 0.31
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (45 bp):
TGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGT
Found at i:2506 original size:87 final size:87
Alignment explanation
Indices: 2118--3082 Score: 1359
Period size: 87 Copynumber: 11.1 Consensus size: 87
2108 CGCTGTCGAT
* * * * * * **
2118 GCAGGAGGGCAATATCTGCTGTCCTCATCCAGCTCCACCACAACCGA-GAGAGGCAAGG-TTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT
* * *
2181 GTCTTCGACCTGCTTCGATGTTAAT
65 -T-TTCGATCTGCTTCGCTGTTAAC
* * * * * * * *
2206 GCAGGAAGGCCAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGA-GAGAGGTAATG-TTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT
* *
2269 GTCTTCGATCTGCTTCGCTGTCAAT
65 -T-TTCGATCTGCTTCGCTGTTAAC
* * * * *
2294 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAATCGA-GAGAGGCAAGG-TTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT
* *
2357 GTCTTCGATCTGCTTCGCTGTCAAT
65 -T-TTCGATCTGCTTCGCTGTTAAC
* * * * * ** * * *
2382 GCAGAAAGGCAAGATCGGTTGTCTTCAACCAGCTCCACCACAATCGA-GAGAGGCAAGACTTTAT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT
*
2446 TTTCGATCTGCTTCGTTGTTAAC
65 TTTCGATCTGCTTCGCTGTTAAC
* *
2469 GCCGGAAGGCAAGATCTGCTATCTCTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
2534 TTCGATCTGCTTCGCTGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2556 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
* *
2621 TTCGATCTGCTTTGCTGGTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2643 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
*
2708 TTCGATCTGCTTCGCCGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2730 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
*
2795 TTCGATCTGCTTCGCCGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2817 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
*
2882 TTCGATCTGCTTCGCCGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2904 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
*
2969 TTCGATCTGCTTCGCCGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
2991 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
*
3056 TTCGATCTGCTTCGCCGTTAAC
66 TTCGATCTGCTTCGCTGTTAAC
3078 GCAGG
1 GCAGG
3083 CCTTCTTGCC
Statistics
Matches: 829, Mismatches: 46, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
87 611 0.74
88 214 0.26
89 4 0.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (87 bp):
GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
TTCGATCTGCTTCGCTGTTAAC
Found at i:4087 original size:16 final size:15
Alignment explanation
Indices: 4059--4103 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
4049 TTAGCCTCTC
*
4059 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
4073 CATTTTTTTCATTTTT
1 CA-TTTTTTCATTTTT
4089 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
4104 TTCATCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:4116 original size:11 final size:9
Alignment explanation
Indices: 4068--4115 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
4058 CCATTTTTAC
4068 TTTTTCATT
1 TTTTTCATT
4077 TTTTTCA--
1 TTTTTCATT
4084 TTTTTCA-T
1 TTTTTCATT
4092 TTTTTCATT
1 TTTTTCATT
4101 TTTTTCATCT
1 TTTTTCAT-T
4111 TTTTT
1 TTTTT
4116 TTTACTCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 16 0.44
10 6 0.17
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCATT
Found at i:4118 original size:24 final size:24
Alignment explanation
Indices: 4059--4113 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
4049 TTAGCCTCTC
*
4059 CATTTTT-ACTTTTTCATTTTTTT
1 CATTTTTCATTTTTTCATTTTTTT
4082 CATTTTTCATTTTTTCATTTTTTT
1 CATTTTTCATTTTTTCATTTTTTT
4106 CATCTTTT
1 CAT-TTTT
4114 TTTTTACTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 18 0.62
25 4 0.14
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.73
Consensus pattern (24 bp):
CATTTTTCATTTTTTCATTTTTTT
Found at i:4979 original size:9 final size:9
Alignment explanation
Indices: 4961--5039 Score: 90
Period size: 9 Copynumber: 8.6 Consensus size: 9
4951 TATTTTTGAC
4961 TTTGATTTT
1 TTTGATTTT
*
4970 TTTTATTTT
1 TTTGATTTT
4979 TTTGATTTT
1 TTTGATTTT
4988 TTTGA-TTT
1 TTTGATTTT
4996 TTTGA-TTT
1 TTTGATTTT
5004 TTTGATTTTT
1 TTTGA-TTTT
5014 TGATTGATTTTT
1 T--TTGA-TTTT
*
5026 TTTTATTTT
1 TTTGATTTT
5035 TTTGA
1 TTTGA
5040 GTCTGAACTC
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
8 16 0.26
9 29 0.47
10 7 0.11
12 10 0.16
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (9 bp):
TTTGATTTT
Found at i:4980 original size:8 final size:8
Alignment explanation
Indices: 4967--5037 Score: 65
Period size: 8 Copynumber: 8.9 Consensus size: 8
4957 TGACTTTGAT
4967 TTTTTTTA
1 TTTTTTTA
4975 TTTTTTTGA
1 TTTTTTT-A
4984 TTTTTTTGA
1 TTTTTTT-A
*
4993 TTTTTTGA
1 TTTTTTTA
*
5001 TTTTTTGA
1 TTTTTTTA
*
5009 TTTTTTGA
1 TTTTTTTA
**
5017 -TTGATT-
1 TTTTTTTA
5023 TTTTTTTA
1 TTTTTTTA
5031 TTTTTTT
1 TTTTTTT
5038 GAGTCTGAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 7 0.13
8 31 0.57
9 16 0.30
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:6453 original size:352 final size:353
Alignment explanation
Indices: 5798--6506 Score: 1402
Period size: 352 Copynumber: 2.0 Consensus size: 353
5788 TAAAAGAATA
5798 ATCATTCAAGAAATGAAAGAATATTGGTTCAAAAGATCGCAAAGATGCATTCCATTAAAATAATG
1 ATCATTCAAGAAATGAAAGAATATTGGTTCAAAAGATCGCAAAGATGCATTCCATTAAAATAATG
*
5863 ACGTTCAGACATAAGCCTATTTCACAAAGGAATTTCTATCATTTCTAGGCTAAAAACAACAAAAT
66 ACGTTCAGACATAAGCCTATTTCACAAAAGAATTTCTATCATTTCTAGGCTAAAAACAACAAAAT
5928 GTTCTGAACATTACTCTAGATAAGCCCTAAAAACTATAGGGATTTCTTCTGCAGTCTAATTGCTT
131 GTTCTGAACATTACTCTAGATAAGCCCTAAAAACTATAGGGATTTCTTCTGCAGTCTAATTGCTT
5993 AGAACACTCCAGATTTATAAGGGCAGATATCTAACAAGGTTCCTTTTCATTCGTTTGTGCATTTC
196 AGAACACTCCAGATTTATAAGGGCAGATATCTAACAAGGTTCCTTTTCATTCGTTTGTGCATTTC
6058 ACTCACTCCACTCGTCAATTATGGTTGGGTAATGGATTTTCCTCAGTGGAGGAATCATCAAATTT
261 ACTCACTCCACTCGTCAATTATGGTTGGGTAATGGATTTTCCTCAGTGGAGGAATCATCAAATTT
6123 AACGACGCCCATACTGATAAGCCTTTCG
326 AACGACGCCCATACTGATAAGCCTTTCG
6151 ATCATTCAAG-AATGAAAGAATATTGGTTCAAAAGATCGCAAAGATGCATTCCATTAAAATAATG
1 ATCATTCAAGAAATGAAAGAATATTGGTTCAAAAGATCGCAAAGATGCATTCCATTAAAATAATG
6215 ACGTTCAGACATAAGCCTATTTCACAAAAGAATTTCTATCATTTCTAGGCTAAAAACAACAAAAT
66 ACGTTCAGACATAAGCCTATTTCACAAAAGAATTTCTATCATTTCTAGGCTAAAAACAACAAAAT
6280 GTTCTGAACATTACTCTAGATAAGCCCTAAAAACTATAGGGATTTCTTCTGCAGTCTAATTGCTT
131 GTTCTGAACATTACTCTAGATAAGCCCTAAAAACTATAGGGATTTCTTCTGCAGTCTAATTGCTT
6345 AGAACACTCCAGATTTATAAGGGCAGATATCTAACAAGGTTCCTTTTCATTCGTTTGTGCATTTC
196 AGAACACTCCAGATTTATAAGGGCAGATATCTAACAAGGTTCCTTTTCATTCGTTTGTGCATTTC
6410 ACTCACTCCACTCGTCAATTATGGTTGGGTAATGGATTTTCCTCAGTGGAGGAATCATCAAATTT
261 ACTCACTCCACTCGTCAATTATGGTTGGGTAATGGATTTTCCTCAGTGGAGGAATCATCAAATTT
6475 AACGACGCCCATACTGATAAGCCTTTCG
326 AACGACGCCCATACTGATAAGCCTTTCG
6503 ATCA
1 ATCA
6507 GTTTCTTAAA
Statistics
Matches: 355, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
352 345 0.97
353 10 0.03
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (353 bp):
ATCATTCAAGAAATGAAAGAATATTGGTTCAAAAGATCGCAAAGATGCATTCCATTAAAATAATG
ACGTTCAGACATAAGCCTATTTCACAAAAGAATTTCTATCATTTCTAGGCTAAAAACAACAAAAT
GTTCTGAACATTACTCTAGATAAGCCCTAAAAACTATAGGGATTTCTTCTGCAGTCTAATTGCTT
AGAACACTCCAGATTTATAAGGGCAGATATCTAACAAGGTTCCTTTTCATTCGTTTGTGCATTTC
ACTCACTCCACTCGTCAATTATGGTTGGGTAATGGATTTTCCTCAGTGGAGGAATCATCAAATTT
AACGACGCCCATACTGATAAGCCTTTCG
Done.