Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3277
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: 6061
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:747 original size:16 final size:15
Alignment explanation
Indices: 721--755 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
711 AATAAAATAT
721 AATATAAAATATTAA
1 AATATAAAATATTAA
*
736 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
752 AATA
1 AATA
756 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:924 original size:19 final size:19
Alignment explanation
Indices: 869--925 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 19
859 ATACTACATC
869 AATATGTACATATATAAAA
1 AATATGTACATATATAAAA
* *
888 AATAATACGT-GATAATATTAAA
1 AAT-AT--GTACAT-ATATAAAA
910 AATATGTACATATATA
1 AATATGTACATATATA
926 GTGTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
21 4 0.14
22 12 0.41
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (19 bp):
AATATGTACATATATAAAA
Found at i:932 original size:24 final size:25
Alignment explanation
Indices: 905--952 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
895 CGTGATAATA
**
905 TTAAAAATATGTACAT-ATATAGTG
1 TTAAAAATACATACATAATATAGTG
929 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
953 TAAGATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:997 original size:29 final size:29
Alignment explanation
Indices: 957--1023 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
947 TATAGTTAAG
*
957 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* *
986 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
*
1015 ATACATAAA
1 ATATATAAA
1024 ATAGTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:1014 original size:25 final size:25
Alignment explanation
Indices: 899--1117 Score: 113
Period size: 25 Copynumber: 9.0 Consensus size: 25
889 ATAATACGTG
* *
899 ATAATATTAAAAATATGTACAT-AT
1 ATAATATTAAAGATATATACATAAT
* * * *
923 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
948 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
970 ATAACATGTAAAATATATATATAAATAAT
1 ATAATAT-T--AA-AGATATATACATAAT
*
999 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
1024 ATAGTA-TAATATATATATACGTAAT
1 ATAATATTAA-AGATATATACATAAT
* *
1049 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
1072 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
1094 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
1117 A
1 A
1118 ACAAAAAAGG
Statistics
Matches: 151, Mismatches: 28, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.19
24 29 0.19
25 39 0.26
26 4 0.03
28 2 0.01
29 18 0.12
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:1648 original size:29 final size:30
Alignment explanation
Indices: 1594--1763 Score: 235
Period size: 29 Copynumber: 5.8 Consensus size: 30
1584 TAGGTACAAG
* * *
1594 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1624 TGGTGGTGGAAAAAG-GTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1653 TGGTGGTGG-AAAAG-GTGTGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTG-GCTAGTGGAGT
1682 TGGTGGTGG-AAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
* *
1711 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
1741 T-GTGGT-GAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGT
1764 TGAGAAAAGT
Statistics
Matches: 132, Mismatches: 5, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
28 24 0.18
29 73 0.55
30 35 0.27
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:1688 original size:58 final size:60
Alignment explanation
Indices: 1594--1763 Score: 287
Period size: 58 Copynumber: 2.9 Consensus size: 60
1584 TAGGTACAAG
*
1594 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAG-GTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1653 TGGTGGTGGAAAAGGTGT-GCTAGTGGAGTTGGTGGTGG-AAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
1711 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTT-GTGGT-GAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
1764 TGAGAAAAGT
Statistics
Matches: 106, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
57 6 0.06
58 71 0.67
59 29 0.27
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.26
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:1746 original size:87 final size:88
Alignment explanation
Indices: 1594--1763 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 88
1584 TAGGTACAAG
* *
1594 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGGTGGCTAGTGGAGTTGGTGG
1 TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGGTGGCTAGTGGAGTTGGTGG
*
1659 TGGAAAAGGTGT-GCTAGTGGAGT
66 T-GAAAAGGAGTGGCTAGTGGAGT
*
1682 TGGTGGTGGA-AAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTT-GTG
1 TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAG-GTGGCTAGTGGAGTTGGTG
1745 GTGAAAAGGAGTGGCTAGT
65 GTGAAAAGGAGTGGCTAGT
1764 TGAGAAAAGT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
86 9 0.12
87 42 0.55
88 25 0.33
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.26
Consensus pattern (88 bp):
TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGGTGGCTAGTGGAGTTGGTGG
TGAAAAGGAGTGGCTAGTGGAGT
Found at i:2527 original size:14 final size:14
Alignment explanation
Indices: 2508--2556 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2498 GAGTTGATTT
* *
2508 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
2522 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
2536 TTGAAAAAGCA-AAA
1 TTGAAAAA-CAGAAA
2550 TT-AAAAA
1 TTGAAAAA
2557 GACCTCAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 5 0.16
14 25 0.78
15 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2784 original size:74 final size:74
Alignment explanation
Indices: 2547--2819 Score: 315
Period size: 74 Copynumber: 3.7 Consensus size: 74
2537 TGAAAAAGCA
*
2547 AAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCGCAATATGAGTT-ATTTT
1 AAATTAAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
2611 TGACAAACAG
65 TGACAAACAG
* ** * *
2621 AAATTGAAATTACCTCAGC-GTG-TCCGGAGGCTCAACTCACCTTTCG-AATATGAGTTGATTTT
1 AAATTAAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
2683 TGAAAAACAG
65 TGACAAACAG
* * *
2693 AAATTTAAAAAATACCTCAGC-GTG-TCCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
1 AAA-TT-AAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
* *
2756 TTTTTACGAACAG
62 TTTTGACAAACAG
* *
2769 AAATTGAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAA
1 AAATTAAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTCGCAA
2820 AAGTAGATTT
Statistics
Matches: 170, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
71 12 0.07
72 38 0.22
73 2 0.01
74 64 0.38
75 14 0.08
76 38 0.22
77 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (74 bp):
AAATTAAAAAGACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GACAAACAG
Found at i:2938 original size:14 final size:14
Alignment explanation
Indices: 2900--2938 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2890 TGAAAAATAT
*
2900 AAATTAAAAAACAG
1 AAATTAAAAAGCAG
*
2914 AAATTGAAAAGCAG
1 AAATTAAAAAGCAG
2928 AAATTAAAAAG
1 AAATTAAAAAG
2939 ACCTCAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (14 bp):
AAATTAAAAAGCAG
Found at i:3085 original size:14 final size:14
Alignment explanation
Indices: 3063--3094 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3053 AGTTGATTTT
3063 AAAAACAGAAATTG
1 AAAAACAGAAATTG
*
3077 AAAACCAGAAATTG
1 AAAAACAGAAATTG
3091 AAAA
1 AAAA
3095 TACCTCAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.09, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAACAGAAATTG
Found at i:3100 original size:157 final size:160
Alignment explanation
Indices: 2906--3222 Score: 437
Period size: 157 Copynumber: 2.0 Consensus size: 160
2896 ATATAAATTA
* *
2906 AAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGA-GCTCAACT-CAC
1 AAAAACAGAAATTGAAAACCAGAAATTAAAAAGACCTCAGCAT-TGAGCCAAGGCTCAACTCCAC
* * ** *
2969 CTCTCGCAATATGAG-TGA-TTTTGACAAACAGAAATTTGAAATTACCTCAGTGTGTCCCGAGGC
65 CTCTCGCAATATGAGCTAATTTTTGACAAACAGAAA-TTAAAACCACCTCAGCGTGTCCCGAGGC
*
3032 TCAACTCA-CTCTCGCAATATGAGTTGATTTT
129 TCAACTCACCTCTCGCAATATAAGTTGATTTT
* * *
3063 AAAAACAGAAATTGAAAACCAGAAATTGAAAATACCTCAGCGTTGAGCCAAGGCTCAACTCCACC
1 AAAAACAGAAATTGAAAACCAGAAATTAAAAAGACCTCAGCATTGAGCCAAGGCTCAACTCCACC
* ** * *
3128 TCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTC
66 TCTCGCAATATGAGCTAATTTTTGACAAACAGAAATTAAAACCACCTCAGCGTGTCCCGAGGCTC
3193 AACTCACCTCTCGCAATATAAGTTGATTTT
131 AACTCACCTCTCGCAATATAAGTTGATTTT
3223 TTTGAAAATC
Statistics
Matches: 139, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
156 7 0.05
157 47 0.34
158 17 0.12
159 33 0.24
160 35 0.25
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (160 bp):
AAAAACAGAAATTGAAAACCAGAAATTAAAAAGACCTCAGCATTGAGCCAAGGCTCAACTCCACC
TCTCGCAATATGAGCTAATTTTTGACAAACAGAAATTAAAACCACCTCAGCGTGTCCCGAGGCTC
AACTCACCTCTCGCAATATAAGTTGATTTT
Done.