Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3897
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: 16743
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:105 original size:11 final size:13
Alignment explanation
Indices: 89--159 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 13
79 TTGGAGTAAC
89 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
100 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
114 AAAAAAAATTGATTGA
1 AAAAAAAA-T--TCGA
130 AAAAAAAATTC-A
1 AAAAAAAATTCGA
*
142 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
154 AAAAAA
1 AAAAAA
160 TCGAGCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
11 8 0.16
12 19 0.38
13 1 0.02
14 9 0.18
15 2 0.04
16 9 0.18
17 2 0.04
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:106 original size:12 final size:12
Alignment explanation
Indices: 89--159 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 12
79 TTGGAGTAAC
89 AAAAAAAATCAA
1 AAAAAAAATCAA
*
101 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
114 AAAAAAAATTGATTGA
1 AAAAAAAA-TCA---A
130 AAAAAAAATTCAA
1 AAAAAAAA-TCAA
* *
143 AAAAAAAGTGAA
1 AAAAAAAATCAA
155 AAAAA
1 AAAAA
160 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 17 0.35
13 18 0.38
14 1 0.02
16 12 0.25
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:116 original size:14 final size:14
Alignment explanation
Indices: 99--149 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 14
89 AAAAAAAATC
99 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
113 AAAAAAAAATT-GA
1 AAAAAAAAATTCGA
126 TTGAAAAAAAAATTC-A
1 ---AAAAAAAAATTCGA
142 AAAAAAAA
1 AAAAAAAA
150 GTGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.30
14 11 0.33
16 12 0.36
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:199 original size:29 final size:26
Alignment explanation
Indices: 141--210 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 26
131 AAAAAAATTC
*
141 AAAAAAAAAGTGAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAATCAAGCA
*
167 AAAAAAAAAGGTGACAAAAAAATCAAG-T
1 AAAAAAAAA-GTG--AAAAAAATCAAGCA
*
195 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
211 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.11
26 9 0.24
27 6 0.16
28 8 0.21
29 11 0.29
ACGTcount: A:0.70, C:0.06, G:0.14, T:0.10
Consensus pattern (26 bp):
AAAAAAAAAGTGAAAAAAATCAAGCA
Found at i:1117 original size:17 final size:16
Alignment explanation
Indices: 1097--1134 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1087 GTGAGCGAGA
1097 AAATGAAAAAGAAAAAG
1 AAATG-AAAAGAAAAAG
1114 AAATG-AAAGAAAAAG
1 AAATGAAAAGAAAAAG
*
1129 AGATGA
1 AAATGA
1135 GTGTGAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 14 0.74
17 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
AAATGAAAAGAAAAAG
Found at i:1124 original size:15 final size:15
Alignment explanation
Indices: 1104--1134 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1094 AGAAAATGAA
1104 AAAGAAAAAGAAATG
1 AAAGAAAAAGAAATG
*
1119 AAAGAAAAAGAGATG
1 AAAGAAAAAGAAATG
1134 A
1 A
1135 GTGTGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (15 bp):
AAAGAAAAAGAAATG
Found at i:1249 original size:17 final size:18
Alignment explanation
Indices: 1217--1250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1207 AAAAGAGAGT
*
1217 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
1235 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
1251 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:2500 original size:20 final size:20
Alignment explanation
Indices: 2471--2524 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2461 TTAGTTTTCC
*
2471 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
2491 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
2511 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
2525 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:2505 original size:30 final size:30
Alignment explanation
Indices: 2471--2544 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
2461 TTAGTTTTCC
2471 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
2501 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
2531 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
2545 TGGCTAAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:2534 original size:20 final size:20
Alignment explanation
Indices: 2471--2535 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2461 TTAGTTTTCC
* * * *
2471 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
2491 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
2510 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
2531 AGCTC
1 AGCTC
2536 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:5946 original size:20 final size:19
Alignment explanation
Indices: 5923--5987 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
5913 AAGCTCAAAC
5923 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
5943 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
5963 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
5983 GAGCT
1 GAGCT
5988 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:7271 original size:17 final size:18
Alignment explanation
Indices: 7249--7282 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7239 ACAACACTCC
*
7249 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
7266 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
7283 ACTCTCTTTT
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:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:7390 original size:15 final size:16
Alignment explanation
Indices: 7365--7396 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
7355 TATCTCACAC
7365 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
7381 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
7396 T
1 T
7397 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:8368 original size:12 final size:12
Alignment explanation
Indices: 8353--8424 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 12
8343 TTTTGCTCGA
*
8353 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
8365 TTTTTTTTGAATT
1 TTTTTTTTCAA-T
8378 TTTTTTTCAATCAATT
1 TTTTTTT---TCAA-T
8394 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
*
8407 TTTTTTTT-GAT
1 TTTTTTTTCAAT
8418 TTTTTTT
1 TTTTTTT
8425 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.18
12 9 0.18
13 19 0.37
14 2 0.04
16 12 0.24
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:8381 original size:14 final size:14
Alignment explanation
Indices: 8364--8414 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
8354 TTTTTTTCAC
8364 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
* *
8378 TTTTTTTCAATCAATT
1 TTTTTTT--TTGAATT
*
8394 TTTTTTTTCGAATT
1 TTTTTTTTTGAATT
8408 TTTTTTT
1 TTTTTTT
8415 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:8419 original size:11 final size:13
Alignment explanation
Indices: 8353--8424 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 13
8343 TTTTGCTCGA
*
8353 TTTTTTTTC-ACT
1 TTTTTTTTCGAAT
8365 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
8377 TTTTTTTTCAATCAATT
1 TTTTTTTTC---GAA-T
8394 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
8407 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
8418 TTTTTTT
1 TTTTTTT
8425 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 9 0.18
12 19 0.37
13 9 0.18
14 2 0.04
16 2 0.04
17 10 0.20
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:10031 original size:20 final size:19
Alignment explanation
Indices: 10008--10072 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
9998 AAGCTCAAAC
10008 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
10028 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
10048 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
10068 GAGCT
1 GAGCT
10073 GGGAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:14010 original size:11 final size:11
Alignment explanation
Indices: 13989--14019 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
13979 TGCAATTTTT
13989 TTTTCTTTTCAA
1 TTTT-TTTTCAA
14001 TTTTTTTTCAA
1 TTTTTTTTCAA
14012 TTTTTTTT
1 TTTTTTTT
14020 TCGAACTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAA
Done.