Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold870
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: 46754
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3475 original size:40 final size:39
Alignment explanation
Indices: 3352--3572 Score: 259
Period size: 39 Copynumber: 5.6 Consensus size: 39
3342 TCCTCGTTCA
* * * * *
3352 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
3391 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
3429 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
3469 GAATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
3508 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
3549 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3573 CAGCATTCAA
Statistics
Matches: 161, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 11 0.07
39 85 0.53
40 57 0.35
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:3488 original size:79 final size:78
Alignment explanation
Indices: 3350--3572 Score: 277
Period size: 79 Copynumber: 2.8 Consensus size: 78
3340 GCTCCTCGTT
* * * * *
3350 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
3415 TTTAAAACTCGCA
66 TTTAAAACTCGCA
*
3428 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
*
3493 ATTTATAACTCGCA
65 ATTTAAAACTCGCA
* * * * * * * *
3507 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
3571 GA
64 GA
3573 CAGCATTCAA
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
78 38 0.30
79 83 0.66
80 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAAAACTCGCA
Found at i:11262 original size:39 final size:40
Alignment explanation
Indices: 11219--11440 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
11209 TCCTCGTTCA
* * * * *
11219 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11258 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11298 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
11338 AATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
11377 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
11417 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11441 CAGCATTCAA
Statistics
Matches: 163, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.02
39 64 0.39
40 88 0.54
41 8 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11320 original size:79 final size:78
Alignment explanation
Indices: 11217--11440 Score: 270
Period size: 79 Copynumber: 2.8 Consensus size: 78
11207 GCTCCTCGTT
* * * *
11217 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
11282 TTTAATAACTCGCA
66 TTTAAT-ACTCGCA
* *
11296 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCGG
*
11361 ATTTAGTACTCGCA
65 ATTTAATACTCGCA
* * * * * * * *
11375 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCA-CACAATGCCTTCGGGACTTAACCCG
11439 GA
64 GA
11441 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
78 3 0.02
79 90 0.72
80 32 0.26
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTAATACTCGCA
Found at i:11394 original size:119 final size:119
Alignment explanation
Indices: 11219--11440 Score: 288
Period size: 119 Copynumber: 1.9 Consensus size: 119
11209 TCCTCGTTCA
* * * *
11219 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
* *
11284 TAATAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAATAACTTAGCAC-AAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
11338 AATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CTTAACCCGGA
* * *
11401 TATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATAATAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
11441 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
118 10 0.11
119 73 0.83
120 5 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
TAATAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:13714 original size:17 final size:18
Alignment explanation
Indices: 13681--13714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13671 TTCAAAGAAG
13681 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
13699 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
13715 CTCCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:15983 original size:35 final size:35
Alignment explanation
Indices: 15937--16006 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
15927 TCGATAGGTA
15937 CACTTGCCTTCATCGTGATAATAGTTAGTTTCAAG
1 CACTTGCCTTCATCGTGATAATAGTTAGTTTCAAG
15972 CACTTGCCTTCATCGTGATAATAGTTAGTTTCAAG
1 CACTTGCCTTCATCGTGATAATAGTTAGTTTCAAG
16007 AACGATTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (35 bp):
CACTTGCCTTCATCGTGATAATAGTTAGTTTCAAG
Found at i:19692 original size:54 final size:54
Alignment explanation
Indices: 19644--19783 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
19634 GGTATCTCGG
19644 TAATTCTA-CCTTACAGGGGTATTTCGGTAATTCTACCCTAC-AGTGGTATTTTAA
1 TAATTCTATCC-TACAGGGGTATTTCGGTAATTCTACCCTACAAG-GGTATTTTAA
* *
19698 TAATTCTATCCCACAGGGGTATTTCGGTAATCCTACCCTACAAGGGTATTTTAA
1 TAATTCTATCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAA
*
19752 TAATTCTATCCTACAGGGGTATTTCGATAATT
1 TAATTCTATCCTACAGGGGTATTTCGGTAATT
19784 TTGTAAATCG
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
54 75 0.95
55 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (54 bp):
TAATTCTATCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAA
Found at i:19747 original size:27 final size:27
Alignment explanation
Indices: 19623--19783 Score: 155
Period size: 27 Copynumber: 6.0 Consensus size: 27
19613 ATGGTAATAT
* * *
19623 TACCCCACAAGGGTATCTCGGTAATTC
1 TACCCTACAAGGGTATTTCGATAATTC
* * *
19650 TACCTTACAGGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGATAATTC
**
19677 TACCCTAC-AGTGGTATTTTAATAATTC
1 TACCCTACAAG-GGTATTTCGATAATTC
* * *
19704 TATCCC-ACAGGGGTATTTCGGTAATCC
1 TA-CCCTACAAGGGTATTTCGATAATTC
**
19731 TACCCTACAAGGGTATTTTAATAATTC
1 TACCCTACAAGGGTATTTCGATAATTC
* *
19758 TATCCTACAGGGGTATTTCGATAATT
1 TACCCTACAAGGGTATTTCGATAATT
19784 TTGTAAATCG
Statistics
Matches: 107, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
26 4 0.04
27 99 0.93
28 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
TACCCTACAAGGGTATTTCGATAATTC
Found at i:19765 original size:81 final size:81
Alignment explanation
Indices: 19626--19775 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
19616 GTAATATTAC
* * * ** *
19626 CCCACAAGGGTATCTCGGTAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCCTACAGTGGT
1 CCCACAAGGGTATCTCGGTAATCCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGT
19691 ATTTTAATAATTCTAT
66 ATTTTAATAATTCTAT
* * * *
19707 CCCACAGGGGTATTTCGGTAATCCTACCCTACAAGGGTATTTTAATAATTCTATCCTACAGGGGT
1 CCCACAAGGGTATCTCGGTAATCCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGT
19772 ATTT
66 ATTT
19776 CGATAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (81 bp):
CCCACAAGGGTATCTCGGTAATCCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGT
ATTTTAATAATTCTAT
Found at i:19925 original size:27 final size:27
Alignment explanation
Indices: 19822--19971 Score: 108
Period size: 27 Copynumber: 5.6 Consensus size: 27
19812 TATAAATTGA
* * * *
19822 GGGTACTTTGGTAATTTTACAAGT-TG
1 GGGTATTTTAGTAATTTTACAAATCAG
* **
19848 AGGGTATTTCAGTAATTTTACAGGTC-G
1 -GGGTATTTTAGTAATTTTACAAATCAG
* **
19875 AAGGTATTTTAACAATTTTACAAATCAG
1 -GGGTATTTTAGTAATTTTACAAATCAG
* * *
19903 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTAGTAATTTTACAAATCAG
* * *
19930 GGGTATTTTCA-TAATTTTATAAACCAA
1 GGGTATTTT-AGTAATTTTACAAATCAG
19957 GGGTATTTTAGTAAT
1 GGGTATTTTAGTAAT
19972 CTACAGGGGC
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 99 0.98
28 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAATCAG
Found at i:22485 original size:19 final size:20
Alignment explanation
Indices: 22453--22490 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22443 TGTTTAAAAA
*
22453 TTTTTATTTATTATTTTATG
1 TTTTTACTTATTATTTTATG
22473 TTTTTACTT-TTATTTTAT
1 TTTTTACTTATTATTTTAT
22491 TTTAAGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTACTTATTATTTTATG
Found at i:26589 original size:48 final size:48
Alignment explanation
Indices: 26534--27155 Score: 962
Period size: 48 Copynumber: 12.9 Consensus size: 48
26524 TATATAGGTG
26534 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
*
26582 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
* *
26630 TGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
*
26678 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTGTA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
*
26726 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGA-ATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATAT-ATATGAGATATGTATA
* *
26774 TGTGGTAAAGCCGAATGGTTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
* *
26822 TGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
* *
26870 TGTGGTAAAGTCGAATGGCTAATGTGATATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
*
26918 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGA-ATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATAT-ATATGAGATATGTATA
* *
26966 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGA-ATGAGATATGTATT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATAT-ATATGAGATATGTATA
* *
27014 TGTGGTAAAGCCGAATGGCTAGTGTGAAGTGAAATATGAATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAA---ATATAT--ATGAGATATGTATA
* *
27067 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
* * *
27115 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGAT
27156 GTGTGTATAT
Statistics
Matches: 540, Mismatches: 25, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
48 489 0.91
49 2 0.00
50 5 0.01
51 3 0.01
53 41 0.08
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
Found at i:31908 original size:16 final size:16
Alignment explanation
Indices: 31887--31918 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31877 GGCAAATCCC
*
31887 GAAATGTCGAAAAGCT
1 GAAATGCCGAAAAGCT
31903 GAAATGCCGAAAAGCT
1 GAAATGCCGAAAAGCT
31919 AAAAGTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.16
Consensus pattern (16 bp):
GAAATGCCGAAAAGCT
Found at i:32143 original size:29 final size:28
Alignment explanation
Indices: 32090--32178 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
32080 ATTGCATGAC
* *
32090 TATGAATGTGATTGGGTCC-GATGGGCCA
1 TATGAATGAGATTGGG-CCTAATGGGCCA
**
32118 TATGAATTTGATTTGGGCCTAATGGGCCA
1 TATGAATGAGA-TTGGGCCTAATGGGCCA
*
32147 TATGAATGAGATTGGGCCTAGTGGGCCA
1 TATGAATGAGATTGGGCCTAATGGGCCA
32175 TATG
1 TATG
32179 CATGTATGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 32 0.59
29 22 0.41
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (28 bp):
TATGAATGAGATTGGGCCTAATGGGCCA
Found at i:36109 original size:28 final size:28
Alignment explanation
Indices: 36077--36146 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
36067 AATGAGATTG
*
36077 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
36105 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
36133 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
36147 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:46152 original size:28 final size:28
Alignment explanation
Indices: 46120--46189 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
46110 AATGAGATTG
*
46120 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
46148 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
46176 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
46190 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Done.