Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1242
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: 41322
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:2783 original size:26 final size:26
Alignment explanation
Indices: 2740--2808 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
2730 GTAACTATGA
2740 AAATATCAAATTTT-ATTATTTAATAT
1 AAATAT-AAATTTTAATTATTTAATAT
* *
2766 AAATATAATTTTTAATTATTTATTAT
1 AAATATAAATTTTAATTATTTAATAT
*
2792 ATATATAAATTTTAATT
1 AAATATAAATTTTAATT
2809 TAATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 6 0.16
26 32 0.84
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATATAAATTTTAATTATTTAATAT
Found at i:2823 original size:30 final size:29
Alignment explanation
Indices: 2759--2824 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 29
2749 ATTTTATTAT
* *
2759 TTAATATAAATATAATTTTTAA-TT-AT-
1 TTAATATATATATAAATTTTAATTTAATA
*
2785 TTATTATATATATAAATTTTAATTTAATA
1 TTAATATATATATAAATTTTAATTTAATA
2814 TATAATATATA
1 T-TAATATATA
2825 AACTTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.59
27 2 0.06
28 2 0.06
29 1 0.03
30 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTAATATATATATAAATTTTAATTTAATA
Found at i:4275 original size:167 final size:167
Alignment explanation
Indices: 3928--4284 Score: 380
Period size: 167 Copynumber: 2.1 Consensus size: 167
3918 AATTTTCATG
* ** ** *
3928 GGTTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATACATGTTAAATCATTTTTCAAGAA
1 GGTTTAAAATTTTTAAAATTCATAAAATATTATCATTTAATACAAATTAAATCAGCTTTCAAAAA
** * * ** *
3993 TTTACTCATCTTCATGAGTTTTTGATTTTTTTCCTTGAAATTTTTCTATTTTTGAAATACGGAAT
66 TGAAATCATCTTCATGAGTTTTTGATTTTTTTCCTTGAAATTCTTCTATTTTCAAAAAACGGAAT
** * *
4058 TTTTTACTCTGTAAATGTGTTCGGGGTGATATTTCTT
131 TTTTTACTCCATAAATGTGTTCGGAGTGATATTTCTC
** ** * * *
4095 GGTTTTTAATTTTTAAAATTTGTAAAATATTATCATTTAATTCAAATTAAATTAGCTTTGAAAAA
1 GGTTTAAAATTTTTAAAATTCATAAAATATTATCATTTAATACAAATTAAATCAGCTTTCAAAAA
* *
4160 TGAAATTATTTTCATGAG-TTTTGAATTTTTTT-CTTCGAAATTCTTCTATTTTCAAAAAACGG-
66 TGAAATCATCTTCATGAGTTTTTG-ATTTTTTTCCTT-GAAATTCTTCTATTTTCAAAAAACGGA
* * * *
4222 ATTTTTCTACTCCATAAATATTTTTTGGAG-GATTTTTCTC
129 ATTTTT-TACTCCATAAAT-GTGTTCGGAGTGATATTTCTC
4262 GGTTTAAAATTTTTAAAATTCAT
1 GGTTTAAAATTTTTAAAATTCAT
4285 CTAATATTGT
Statistics
Matches: 152, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
166 14 0.09
167 132 0.87
168 6 0.04
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (167 bp):
GGTTTAAAATTTTTAAAATTCATAAAATATTATCATTTAATACAAATTAAATCAGCTTTCAAAAA
TGAAATCATCTTCATGAGTTTTTGATTTTTTTCCTTGAAATTCTTCTATTTTCAAAAAACGGAAT
TTTTTACTCCATAAATGTGTTCGGAGTGATATTTCTC
Found at i:6109 original size:152 final size:157
Alignment explanation
Indices: 5822--6260 Score: 485
Period size: 152 Copynumber: 2.8 Consensus size: 157
5812 TTTAATCAAT
* * * * *
5822 TTTTCTAATCTTTTATATTCCTATGGGTATCTGTAGGGATATAAAAGATTTCAAAAACTTTTTAT
1 TTTT-TAATCTTTTATATTCTTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCAT
* * * * * * ** * *
5887 AACTTTTTGAACTTCCGTTAAGGTACGAAATAGTTTTTTTGAAAATAAATAAAATAAAATTACAT
65 ATCTTTTCGGACTTCCATTAAGGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTAAAT
* *
5952 TAACACTTTCATAATC-G-AGA-TAA-A
130 AAACACTTTCATAATCAGAAAATTAATA
* ** *
5976 -TTTTAATCTTTTATATTCTTATAGGCATCCACAGGGGTATAAAAGATTTCAAAAACTTTTCGTA
1 TTTTTAATCTTTTATATTCTTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCATA
* * * *
6040 TCTTGTCGGGCTTCCACTAAGGTACAAAATGGTATTTTCAAAAATAAATAAAATTAAATTAAATA
66 TCTTTTCGGACTTCCATTAAGGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTAAATA
*
6105 AACACTTTCGTAATCAAGATAAATTTTAATTA
131 AACACTTTCATAATC-AGA-AAA--TTAA-TA
* *
6137 TTTTTAATCTTTTATATTCTTATGGGCATTCGTA-AGGTATAAAAGATTTCAAAAACTTTTCATA
1 TTTTTAATCTTTTATATTCTTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCATA
* * * *
6201 TCTTTTCGGATTTTCATTAAGGTACGAAATGATATTTTCAAGAAAGAAATAAAATTAAAT
66 TCTTTTCGGACTTCCATTAAGGTACGAAATGGTATTTTCAA-AAATAAATAAAATTAAAT
6261 ATAATAATAA
Statistics
Matches: 234, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
152 116 0.50
153 3 0.01
154 1 0.00
156 2 0.01
159 3 0.01
161 63 0.27
162 46 0.20
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (157 bp):
TTTTTAATCTTTTATATTCTTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCATA
TCTTTTCGGACTTCCATTAAGGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTAAATA
AACACTTTCATAATCAGAAAATTAATA
Found at i:7541 original size:13 final size:13
Alignment explanation
Indices: 7523--7548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7513 CAATTTTTTG
7523 TGTATCGATACAT
1 TGTATCGATACAT
7536 TGTATCGATACAT
1 TGTATCGATACAT
7549 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7613 original size:21 final size:21
Alignment explanation
Indices: 7587--7662 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
7577 CTGCCAAGAA
*
7587 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
7608 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
7628 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
7649 ATGTATCGATACAT
1 ATGTATCGATACAT
7663 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:7633 original size:20 final size:20
Alignment explanation
Indices: 7608--7680 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
7598 CATCTTTTTT
7608 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
7628 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
7649 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
7669 ATGTATCGATAC
1 ATGTATCGATAC
7681 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:7644 original size:41 final size:41
Alignment explanation
Indices: 7587--7680 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
7577 CTGCCAAGAA
*
7587 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
7628 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
7669 ATGTATCGATAC
1 ATGTATCGATAC
7681 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:8335 original size:30 final size:30
Alignment explanation
Indices: 8301--8360 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
8291 CCCGTTTATT
8301 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
8331 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
8361 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.27
Consensus pattern (30 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCA
Found at i:9152 original size:47 final size:47
Alignment explanation
Indices: 9080--9173 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
9070 ATTGAATTTT
*
9080 GAAATAATAAACCAAAAAGGTGCCCATCTCACTTAGGGGTGTAATCA
1 GAAATAATAAACCAAAAAGGAGCCCATCTCACTTAGGGGTGTAATCA
*
9127 GAAATAATAGACCAAAAAGGAGCCCATCTCACTTAGGGGTGTAATCA
1 GAAATAATAAACCAAAAAGGAGCCCATCTCACTTAGGGGTGTAATCA
9174 AGCTGTAAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (47 bp):
GAAATAATAAACCAAAAAGGAGCCCATCTCACTTAGGGGTGTAATCA
Found at i:12157 original size:2 final size:2
Alignment explanation
Indices: 12134--12271 Score: 132
Period size: 2 Copynumber: 69.0 Consensus size: 2
12124 GATCAAAATC
* * * * * * *
12134 AT AT CT AT AT CT AT AT AA AT AT AT AT AG AT AT AA AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
12176 AT AT AT CT CT AC AA AT AT AT AT AT AT AA AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
12218 AT AT AT AT AT CT AT AT TT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12260 AT AT AT AT AT AT
1 AT AT AT AT AT AT
12272 CGTATGTTAA
Statistics
Matches: 107, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13447 original size:19 final size:19
Alignment explanation
Indices: 13423--13463 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
13413 ATCCAATAAA
13423 AAAAATGATTGTACGAAAC
1 AAAAATGATTGTACGAAAC
13442 AAAAATGATTGTACGAAAC
1 AAAAATGATTGTACGAAAC
13461 AAA
1 AAA
13464 CTCTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (19 bp):
AAAAATGATTGTACGAAAC
Found at i:14728 original size:17 final size:19
Alignment explanation
Indices: 14706--14743 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
14696 TCTAAAATTT
14706 TAAAAT-ATAAGTTAG-TA
1 TAAAATAATAAGTTAGATA
*
14723 TAAAATAATAATTTAGATA
1 TAAAATAATAAGTTAGATA
14742 TA
1 TA
14744 TTTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TAAAATAATAAGTTAGATA
Found at i:14973 original size:16 final size:17
Alignment explanation
Indices: 14934--14974 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
14924 TATTATTATT
*
14934 ATTATTTAAAATAAAAA
1 ATTATTCAAAATAAAAA
14951 ATT-TTCAAAA-AAAAA
1 ATTATTCAAAATAAAAA
*
14966 TTTATTCAA
1 ATTATTCAA
14975 GTTTTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 11 0.52
17 3 0.14
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATTCAAAATAAAAA
Found at i:16711 original size:3 final size:3
Alignment explanation
Indices: 16703--16737 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16693 AAGGTATGGT
16703 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16738 TCAATCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17209 original size:18 final size:18
Alignment explanation
Indices: 17155--17202 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
17145 AAACCAAAGG
*
17155 ATAAACATAAAAAAAATACAC
1 ATAAACA-AAAGAAAA-A-AC
17176 ATAAACAAAAGAAAAAAC
1 ATAAACAAAAGAAAAAAC
*
17194 ATTAACAAA
1 ATAAACAAA
17203 GGTAAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 7 0.28
21 7 0.28
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.12
Consensus pattern (18 bp):
ATAAACAAAAGAAAAAAC
Found at i:17328 original size:15 final size:15
Alignment explanation
Indices: 17308--17337 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17298 CTAGGAAAAG
17308 GTACAAAGGAACCAA
1 GTACAAAGGAACCAA
17323 GTACAAAGGAACCAA
1 GTACAAAGGAACCAA
17338 TATGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (15 bp):
GTACAAAGGAACCAA
Found at i:25084 original size:34 final size:34
Alignment explanation
Indices: 25038--25222 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
25028 GTAAAAACCA
*
25038 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
25072 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
25106 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
25140 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
25174 CCATTTAGTCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
25207 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
25223 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:29315 original size:19 final size:19
Alignment explanation
Indices: 29288--29350 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
29278 TCACGTGTAC
* *
29288 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
29307 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
29326 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
29345 AGTACC
1 AGTACC
29351 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:29698 original size:34 final size:34
Alignment explanation
Indices: 29652--29835 Score: 255
Period size: 34 Copynumber: 5.4 Consensus size: 34
29642 GTAAAAACCA
*
29652 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
29686 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
29720 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
29754 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
29788 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
29821 CCATTTAATCAACAA
1 CCATTTAATCAACAA
29836 AAATAGCCAC
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:32583 original size:22 final size:19
Alignment explanation
Indices: 32558--32609 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 19
32548 TAGAGATGCA
32558 ATTATATTTTTACTTTAATTAT
1 ATTATATTTTTA-TTT-ATT-T
32580 ATTATATTATTTATTTATTT
1 ATTATATT-TTTATTTATTT
32600 ATTAATATTT
1 ATT-ATATTT
32610 AATTTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
22 11 0.39
23 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATATTTTTATTTATTT
Found at i:41182 original size:29 final size:30
Alignment explanation
Indices: 41124--41192 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
41114 GTTTTTGTAC
41124 CAAAATACTATTAAATTTAAAACAAATTAT
1 CAAAATACTATTAAATTTAAAACAAATTAT
* * * *
41154 CAAAATAGTA-TAATTTTGAAACAATTTAT
1 CAAAATACTATTAAATTTAAAACAAATTAT
41183 CAAAATACTA
1 CAAAATACTA
41193 CCATTTTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (30 bp):
CAAAATACTATTAAATTTAAAACAAATTAT
Done.