Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2280
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: 24279
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:5790 original size:71 final size:70
Alignment explanation
Indices: 5695--5940 Score: 349
Period size: 71 Copynumber: 3.5 Consensus size: 70
5685 TGATGTTTTT
* *
5695 ATTTCTGTTTCAAAAAATTCAACTCATACTG-GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 ATTTCTGTTTC-AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAAACGCTGAGG
5759 TAATTTCA
63 TAATTTCA
* *
5767 ATTTTTGTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GACGCTGAGTGT
1 ATTTCTGTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAAACGCTGAG-GT
5831 AATTTCA
64 AATTTCA
*
5838 A-TTCTGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT-AACCTCGGGAGAACGCTGAGGT
1 ATTTCTGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGA-AACGCTGAGGT
5901 AATTTCA
64 AATTTCA
5908 ATTTCTGTTTCAAAAATCAACTCATATT-CGAGA
1 ATTTCTGTTTCAAAAATCAACTCATATTGCGAGA
5941 CACTGCTGAG
Statistics
Matches: 161, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
68 5 0.03
69 35 0.22
70 29 0.18
71 58 0.36
72 32 0.20
73 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (70 bp):
ATTTCTGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAAACGCTGAGGTAA
TTTCA
Found at i:5985 original size:51 final size:53
Alignment explanation
Indices: 5893--5992 Score: 145
Period size: 51 Copynumber: 1.9 Consensus size: 53
5883 TCGGGAGAAC
5893 GCTGAGGTAATTTCAATTTCTGTTTCAAAAATCAACTCATATT-CGAGACACT
1 GCTGAGGTAATTTCAATTTCTGTTTCAAAAATCAACTCATATTGCGAGACACT
*
5945 GCTGAGGT-ATTT-AATTTCTGTTTTTAAAAATTCAA-TCATATTGCGAGA
1 GCTGAGGTAATTTCAATTTCTG-TTTCAAAAA-TCAACTCATATTGCGAGA
5993 AATGAGTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
50 8 0.18
51 19 0.43
52 17 0.39
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (53 bp):
GCTGAGGTAATTTCAATTTCTGTTTCAAAAATCAACTCATATTGCGAGACACT
Found at i:6064 original size:74 final size:72
Alignment explanation
Indices: 5938--6321 Score: 379
Period size: 74 Copynumber: 5.5 Consensus size: 72
5928 CTCATATTCG
* *
5938 AGACACTGCTGAGGTA-TTTAATTTCTGTTTTTAAAAATTCAA-TCATATTGCGAGAAATGAGTT
1 AGACAC-GCTGAGGTATTTTAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTT
6001 GAGCCTCA
65 GAGCCTCA
* * **
6009 AGACACG-TGAGGTATTTTTAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAG
1 AGACACGCTGAGGTA-TTTTAATTTCTGT-TTTC-AAAAAATCAACTCATATTGCGAGAAATGAG
6073 TTGAGCCTCA
63 TTGAGCCTCA
* * * *
6083 GGACACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCAAGAAATGAGT
1 AGACACGCTGAGGT-ATTTTAATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAAATGAGT
6148 TGAGCCTCA
64 TGAGCCTCA
* * * *
6157 GGACACGCTGAGGTAATTCAA-TTCTGTTTTC-AAAATTCAACTCATATTGCGAG--ATGAGTTG
1 AGACACGCTGAGGTATTTTAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTG
6218 AG-CTCA
66 AGCCTCA
* * * * **
6224 A-ACATGCTGAGGT-TTTTCATTTTTTTTTTTC-AAAAATCAACT-ATATTGCGAG-GGTGAGTT
1 AGACACGCTGAGGTATTTT-AATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTT
6284 --GCCTC-
65 GAGCCTCA
* * *
6289 GGACACGCTGAGGTAATTCAATTT-TGTTTTCAA
1 AGACACGCTGAGGTATTTTAATTTCTGTTTTCAA
6322 TCAATCATAT
Statistics
Matches: 265, Mismatches: 33, Indels: 35
0.80 0.10 0.11
Matches are distributed among these distances:
65 9 0.03
66 41 0.15
67 30 0.11
68 10 0.04
69 7 0.03
70 21 0.08
71 19 0.07
72 10 0.04
73 15 0.06
74 83 0.31
75 19 0.07
76 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (72 bp):
AGACACGCTGAGGTATTTTAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTG
AGCCTCA
Found at i:6135 original size:148 final size:138
Alignment explanation
Indices: 5938--6349 Score: 436
Period size: 148 Copynumber: 3.0 Consensus size: 138
5928 CTCATATTCG
*
5938 AGACACTGCTGAGGTATTT-AATTTCTGTTTTTAAAAATTCAA-TCATATTGCGAGAAATGAGTT
1 AGACAC-GCTGAGGTATTTCAATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAAATGAGTT
* * *
6001 GAGCCTCAAGACACG-TGAGGTATTTTTAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGA
65 GAGCCTCAAGACACGCTGAGGTA-ATTCAA-TTCTGT-TTTC--AAAAATCAACTCATACTGCGA
6065 GAGGTGAGTTGAGCCTC
125 GA--TGAGTTGAG-CTC
* *
6082 AGGACACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCAAGAAATGAG
1 A-GACACGCTGAGGT-ATTTCAATTTCTGTT-TTTAAAAAATCAACTCATATTGCGAGAAATGAG
* * *
6147 TTGAGCCTCAGGACACGCTGAGGTAATTCAATTCTGTTTTCAAAATTCAACTCATATTGCGAGAT
63 TTGAGCCTCAAGACACGCTGAGGTAATTCAATTCTGTTTTCAAAAATCAACTCATACTGCGAGAT
6212 GAGTTGAGCTC
128 GAGTTGAGCTC
* * * * * * **
6223 AAACATGCTGAGGTTTTTC-ATTTTTTTTTTTCAAAAATCAACT-ATATTGCGAG-GGTGAGTT-
1 AGACACGCTGAGGTATTTCAATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAAATGAGTTG
* * * *
6284 -GCCTC-GGACACGCTGAGGTAATTCAATTTTGTTTTC---AATCAA-TCATATTGCGAGGTGAG
66 AGCCTCAAGACACGCTGAGGTAATTCAATTCTGTTTTCAAAAATCAACTCATACTGCGAGATGAG
6343 TTGAGCT
131 TTGAGCT
6350 TAAATCAACA
Statistics
Matches: 240, Mismatches: 22, Indels: 28
0.83 0.08 0.10
Matches are distributed among these distances:
128 23 0.10
129 5 0.02
132 30 0.12
133 5 0.02
135 6 0.03
136 9 0.04
137 13 0.05
138 7 0.03
139 4 0.02
140 11 0.05
141 4 0.02
142 9 0.04
144 30 0.12
145 9 0.04
146 14 0.06
147 16 0.07
148 38 0.16
149 7 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (138 bp):
AGACACGCTGAGGTATTTCAATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAAATGAGTTG
AGCCTCAAGACACGCTGAGGTAATTCAATTCTGTTTTCAAAAATCAACTCATACTGCGAGATGAG
TTGAGCTC
Found at i:7170 original size:22 final size:21
Alignment explanation
Indices: 7145--7207 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 21
7135 AAAAGCCCAT
*
7145 TAACCCTCCCAAAAAAAAAATC
1 TAACCC-CCCAAAAAAAAAACC
7167 TAACCCCCCAAAAAAAAAAAAACC
1 TAACCCCCC---AAAAAAAAAACC
7191 TAACCCCCCAAAAAAAA
1 TAACCCCCCAAAAAAAA
7208 GAAAAACTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 11 0.30
22 6 0.16
24 20 0.54
ACGTcount: A:0.59, C:0.33, G:0.00, T:0.08
Consensus pattern (21 bp):
TAACCCCCCAAAAAAAAAACC
Found at i:7183 original size:25 final size:23
Alignment explanation
Indices: 7155--7233 Score: 113
Period size: 25 Copynumber: 3.3 Consensus size: 23
7145 TAACCCTCCC
*
7155 AAAAAAAAAATCTAACCCCCCAA
1 AAAAAAAAAAACTAACCCCCCAA
7178 AAAAAAAAAAACCTAACCCCCCAA
1 AAAAAAAAAAA-CTAACCCCCCAA
*
7202 AAAAAAGAAAAACTTAACCCCCCCA
1 AAAAAA-AAAAAC-TAACCCCCCAA
7227 AAAAAAA
1 AAAAAAA
7234 CCAAGAAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.20
24 20 0.39
25 21 0.41
ACGTcount: A:0.63, C:0.29, G:0.01, T:0.06
Consensus pattern (23 bp):
AAAAAAAAAAACTAACCCCCCAA
Found at i:7489 original size:13 final size:13
Alignment explanation
Indices: 7473--7497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7463 TTTTACTCTT
7473 TTTTTTATTTTTA
1 TTTTTTATTTTTA
7486 TTTTTTATTTTT
1 TTTTTTATTTTT
7498 TCCTTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:7561 original size:13 final size:13
Alignment explanation
Indices: 7535--7584 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
7525 TATATACATC
7535 ATAATAAAAA-AT
1 ATAATAAAAATAT
7547 ATAATAAAAATAT
1 ATAATAAAAATAT
* *
7560 ATATACAAAACAAAT
1 ATA-ATAAAA-ATAT
7575 ATAA-AAAAAT
1 ATAATAAAAAT
7585 TACCTTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 11 0.34
13 9 0.28
14 6 0.19
15 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:7997 original size:11 final size:11
Alignment explanation
Indices: 7981--8010 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7971 GTATATATTG
7981 TATATATTATA
1 TATATATTATA
*
7992 TTTATATTATA
1 TATATATTATA
8003 TATATATT
1 TATATATT
8011 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:8065 original size:21 final size:23
Alignment explanation
Indices: 8039--8081 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
8029 ATACTTCTTG
*
8039 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
8060 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
8082 CGAAATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:8418 original size:16 final size:15
Alignment explanation
Indices: 8394--8428 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
8384 TAATTATTAT
8394 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
8410 TATTTTAATATTTTA
1 TATTCTAATATTTTA
8425 TATT
1 TATT
8429 ATTCACATCA
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:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:16761 original size:16 final size:17
Alignment explanation
Indices: 16729--16762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16719 CAAACATTAT
*
16729 AAAGGAAGAAGGAAAAA
1 AAAGGAAGAAAGAAAAA
16746 AAAGGAA-AAAGAAAAA
1 AAAGGAAGAAAGAAAAA
16762 A
1 A
16763 GAGAGAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGGAAGAAAGAAAAA
Found at i:17098 original size:28 final size:27
Alignment explanation
Indices: 17037--17126 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 27
17027 ATCAACTTGG
* *
17037 GAAAAAAGTAGTTTAGGTACAAATTGT
1 GAAAAAAGAAGTTTAGGTACAAATGGT
*
17064 GATAAAAAAAAGTTTAGGTACCAAGATGGT
1 GA-AAAAAGAAGTTTAGGTA-CAA-ATGGT
** *
17094 GAAAAGGGTATAGTTTAGGTACCAATGTGT
1 GAAAAAAG-A-AGTTTAGGTACAAATG-GT
17124 GAA
1 GAA
17127 TTATAAGCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
27 2 0.04
28 15 0.30
29 9 0.18
30 14 0.28
31 10 0.20
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.27
Consensus pattern (27 bp):
GAAAAAAGAAGTTTAGGTACAAATGGT
Found at i:17155 original size:2 final size:2
Alignment explanation
Indices: 17145--17220 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
17135 CTTTTTTTAA
17145 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17186 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17221 TTGGATAAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:18434 original size:24 final size:23
Alignment explanation
Indices: 18404--18515 Score: 84
Period size: 24 Copynumber: 4.8 Consensus size: 23
18394 TAAAAAAATG
**
18404 ATAGTAAAATAATAATAGGAAAA
1 ATAGTAAAATAATAATAACAAAA
* *
18427 ATTAGTAAAAGTGATAATAACAGAA
1 A-TAGTAAAA-TAATAATAACAAAA
***
18452 ATAGT--AATAATAATAATGTAA
1 ATAGTAAAATAATAATAACAAAA
* *
18473 ATAGTAATAAGAATAATAACGAAA
1 ATAGTAA-AATAATAATAACAAAA
*
18497 ATAGTAATGATAATAATAA
1 ATAGTAA-AATAATAATAA
18516 TATCTGATAG
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.21
22 2 0.03
23 1 0.01
24 42 0.59
25 11 0.15
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (23 bp):
ATAGTAAAATAATAATAACAAAA
Found at i:18466 original size:21 final size:21
Alignment explanation
Indices: 18440--18512 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
18430 AGTAAAAGTG
18440 ATAATAAC-AGAAATAGTAATA
1 ATAATAACGA-AAATAGTAATA
* *
18461 ATAATAATGTAAATAGTAATAAGA
1 ATAATAACGAAAATAGTAAT---A
*
18485 ATAATAACGAAAATAGTAATG
1 ATAATAACGAAAATAGTAATA
18506 ATAATAA
1 ATAATAA
18513 TAATATCTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 24 0.56
24 19 0.44
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (21 bp):
ATAATAACGAAAATAGTAATA
Found at i:20935 original size:9 final size:10
Alignment explanation
Indices: 20891--20935 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
20881 AACCAAAATT
20891 AATTAATAAAA
1 AATT-ATAAAA
20902 TAATTATAATAA
1 -AATTATAA-AA
20914 AATTATAAAA
1 AATTATAAAA
*
20924 AAATATAAAA
1 AATTATAAAA
20934 AA
1 AA
20936 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 13 0.42
11 12 0.39
12 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATTATAAAA
Found at i:21214 original size:21 final size:22
Alignment explanation
Indices: 21171--21212 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21161 ATTTTGAAGT
* * *
21171 AAAAAAAGTTGTGCTCACTTTA
1 AAAAAAAATTATGCTAACTTTA
21193 AAAAAAAATTATGCTAACTT
1 AAAAAAAATTATGCTAACTT
21213 AATTGATGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAAAAAATTATGCTAACTTTA
Done.