Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1276
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: 176520
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:152516 original size:83 final size:83
Alignment explanation
Indices: 152418--152762 Score: 305
Period size: 83 Copynumber: 4.2 Consensus size: 83
152408 CGTGGACTAG
* *
152418 AAGCTGCTGCTGGTGTTGGTTTTAGATGCTTC-TGCTG-CTGGAAGCTGCTGTCGATGTTAGTTT
1 AAGCTGCTGCTGGTGTTGGTTTCAGATGC-TCGTG--GACTGGAAACTGCTGTCGATGTTAGTTT
* *
152481 TTT-TATGCTCCTACTGTTGA
63 TTTCGATGCTCCTACTGCTGA
* * *
152501 AAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGATTGGAAACTGCTGTCGGTGTTAGTTTTTT
1 AAGCTGCTGCTGGTGTTGGTTTCAGATGCTCGTGGACTGGAAACTGCTGTCGATGTTAGTTTTTT
*
152566 CGATGCTCCTACTGCTGG
66 CGATGCTCCTACTGCTGA
** * * * * * *
152584 AAGCTGCTGCTGGCATTGG-TTCTGGGTGCTCGTGGACTGG-AA--GCTGTTGCTGGTA-TTGGT
1 AAGCTGCTGCTGGTGTTGGTTTC-AGATGCTCGTGGACTGGAAACTGCTGTCGATGTTAGTT-TT
* *
152644 TTCGGATGCTCTTGCTGCTGA
64 TTC-GATGCTCCTACTGCTGA
* * * * * * * *
152665 AAGCTGCTGTTGGTGTTGGTTTCGGGTGCTCGTGGACTGGAAGCTGTTGTTGGTGTT-GGTTTTT
1 AAGCTGCTGCTGGTGTTGGTTTCAGATGCTCGTGGACTGGAAACTGCTGTCGATGTTAGTTTTTT
* *
152729 -GATGCTCCTACTACTGG
66 CGATGCTCCTACTGCTGA
*
152746 AAGCTGCTGCTGATGTT
1 AAGCTGCTGCTGGTGTT
152763 TTTTTCTTTG
Statistics
Matches: 217, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
79 2 0.01
80 14 0.06
81 76 0.35
82 37 0.17
83 78 0.36
84 10 0.05
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (83 bp):
AAGCTGCTGCTGGTGTTGGTTTCAGATGCTCGTGGACTGGAAACTGCTGTCGATGTTAGTTTTTT
CGATGCTCCTACTGCTGA
Found at i:152531 original size:123 final size:123
Alignment explanation
Indices: 152298--152592 Score: 403
Period size: 123 Copynumber: 2.4 Consensus size: 123
152288 TATTGGACAT
* * * *
152298 TGCTGATGGTGTTGGTTTCAGATGCTCCTACTGCTGGAAGCTACTGTCGGTGTTGGTTTTTTTTA
1 TGCTG-TGGTGTTGGTTTTAGATGCTCCTACTGCTGGAAGCTGCTGTCGATGTTAGTTTTTTTTA
* * ** *
152363 TGCTCCTGCTGTTGGAAGCTGCTGCTGGTGTTGGTTTTGGGTGCTCGTGGACTAGAAGC
65 TGCTCCTACTGTTGAAAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGACTAGAAAC
* *
152422 TGCTGCTGGTGTTGGTTTTAGATGCTTCTGCTGCTGGAAGCTGCTGTCGATGTTAG-TTTTTTTA
1 TGCTG-TGGTGTTGGTTTTAGATGCTCCTACTGCTGGAAGCTGCTGTCGATGTTAGTTTTTTTTA
* *
152486 TGCTCCTACTGTTGAAAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGATTGGAAAC
65 TGCTCCTACTGTTGAAAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGACTAGAAAC
* *
152545 TGCTGTCGGTGTTAGTTTTTTCGATGCTCCTACTGCTGGAAGCTGCTG
1 TGCTGT-GGTGTT-G-GTTTTAGATGCTCCTACTGCTGGAAGCTGCTG
152593 CTGGCATTGG
Statistics
Matches: 150, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
122 1 0.01
123 71 0.47
124 50 0.33
125 28 0.19
ACGTcount: A:0.12, C:0.17, G:0.32, T:0.39
Consensus pattern (123 bp):
TGCTGTGGTGTTGGTTTTAGATGCTCCTACTGCTGGAAGCTGCTGTCGATGTTAGTTTTTTTTAT
GCTCCTACTGTTGAAAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGACTAGAAAC
Found at i:152556 original size:206 final size:206
Alignment explanation
Indices: 152298--152674 Score: 526
Period size: 206 Copynumber: 1.8 Consensus size: 206
152288 TATTGGACAT
* * **
152298 TGCTGATGGTGTTGGTTTCAGATGCTCCTACTGCTGGAAGCTACTGTCGGTGTTGGTTTTTTTTA
1 TGCTGATGGTGTTGGTTTCAGATGCTCCTACT-CTGGAAACTACTGTCGGTGTTAGTTTTTTCGA
* * ** *
152363 TGCTCCTGCTGTTGGAAGCTGCTGCTGGTGTTGGTTTTGGGTGCTCGTGGACTAGAAGCTGCTGC
65 TGCTCCTACTGCTGGAAGCTGCTGCTGGCATTGGTTCTGGGTGCTCGTGGACTAGAAGCTGCTGC
* * *
152428 TGGTGTTGGTTTTAGATGCT-TCTGCTGCTGGAAGCTGCTGTCGATGTTAGTTTTTTTATGCTCC
130 TGGTATTGGTTTCAGATGCTCT-TGCTGCTGAAAGCTGCTGTCGATGTTAGTTTTTTTATGCTCC
152492 TACTGTTGAAAGC
194 TACTGTTGAAAGC
* * * *
152505 TGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGA-T-TGGAAACTGCTGTCGGTGTTAGTTTTTTCG
1 TGCTGATGGTGTTGGTTTCAGATGCTCCT--ACTCTGGAAACTACTGTCGGTGTTAGTTTTTTCG
* *
152568 ATGCTCCTACTGCTGGAAGCTGCTGCTGGCATTGGTTCTGGGTGCTCGTGGACTGGAAGCTGTTG
64 ATGCTCCTACTGCTGGAAGCTGCTGCTGGCATTGGTTCTGGGTGCTCGTGGACTAGAAGCTGCTG
*
152633 CTGGTATTGGTTTCGGATGCTCTTGCTGCTGAAAGCTGCTGT
129 CTGGTATTGGTTTCAGATGCTCTTGCTGCTGAAAGCTGCTGT
152675 TGGTGTTGGT
Statistics
Matches: 148, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
206 119 0.80
207 27 0.18
208 1 0.01
209 1 0.01
ACGTcount: A:0.12, C:0.18, G:0.32, T:0.38
Consensus pattern (206 bp):
TGCTGATGGTGTTGGTTTCAGATGCTCCTACTCTGGAAACTACTGTCGGTGTTAGTTTTTTCGAT
GCTCCTACTGCTGGAAGCTGCTGCTGGCATTGGTTCTGGGTGCTCGTGGACTAGAAGCTGCTGCT
GGTATTGGTTTCAGATGCTCTTGCTGCTGAAAGCTGCTGTCGATGTTAGTTTTTTTATGCTCCTA
CTGTTGAAAGC
Found at i:152684 original size:81 final size:79
Alignment explanation
Indices: 152485--152762 Score: 315
Period size: 81 Copynumber: 3.4 Consensus size: 79
152475 TAGTTTTTTT
* * * * *
152485 ATGCTCCTACTGTTGAAAGCTGCTGCTGGTGTTGGTTTCAGGTGCTCGTGGATTGGAAACTGCTG
1 ATGCTCCTACTGCTGAAAGCTGCTGCTGGTGTTGGTTTCGGGTGCTCGTGGACTGGAAGCTGTTG
*
152550 TCGGTGTTAGTTTTTTCG
66 T-GGTGTT-G--GTTTCG
* **
152568 ATGCTCCTACTGCTGGAAGCTGCTGCTGGCATTGG-TTCTGGGTGCTCGTGGACTGGAAGCTGTT
1 ATGCTCCTACTGCTGAAAGCTGCTGCTGGTGTTGGTTTC-GGGTGCTCGTGGACTGGAAGCTGTT
*
152632 GCTGGTATTGGTTTCGG
65 G-TGGTGTTGGTTTC-G
* * *
152649 ATGCTCTTGCTGCTGAAAGCTGCTGTTGGTGTTGGTTTCGGGTGCTCGTGGACTGGAAGCTGTTG
1 ATGCTCCTACTGCTGAAAGCTGCTGCTGGTGTTGGTTTCGGGTGCTCGTGGACTGGAAGCTGTTG
*
152714 TTGGTGTTGGTTTTTG
66 -TGGTGTTGG-TTTCG
* * *
152730 ATGCTCCTACTACTGGAAGCTGCTGCTGATGTT
1 ATGCTCCTACTGCTGAAAGCTGCTGCTGGTGTT
152763 TTTTTCTTTG
Statistics
Matches: 165, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
80 4 0.02
81 92 0.56
82 10 0.06
83 58 0.35
84 1 0.01
ACGTcount: A:0.12, C:0.18, G:0.33, T:0.37
Consensus pattern (79 bp):
ATGCTCCTACTGCTGAAAGCTGCTGCTGGTGTTGGTTTCGGGTGCTCGTGGACTGGAAGCTGTTG
TGGTGTTGGTTTCG
Found at i:153237 original size:22 final size:22
Alignment explanation
Indices: 153212--153256 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
153202 TTTTTTTTGG
*
153212 ATTTTGATTTTTC-ATTGTTATT
1 ATTTT-ATTATTCGATTGTTATT
*
153234 ATTTTATTATTCGATTTTTATT
1 ATTTTATTATTCGATTGTTATT
153256 A
1 A
153257 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (22 bp):
ATTTTATTATTCGATTGTTATT
Found at i:154496 original size:54 final size:54
Alignment explanation
Indices: 154407--154520 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 54
154397 TAAATAGGAA
* *
154407 AAGAAACGGCATTTCATGCATGTTTTCACACATGAACATGGAGGCTGAAGAAAC
1 AAGAAACGGCATTTCACGCATGCTTTCACACATGAACATGGAGGCTGAAGAAAC
***
154461 AAGAAACGGCATTTCACGCATGCTTTCATGTATGAACATGGAGGCTGAAGAAAC
1 AAGAAACGGCATTTCACGCATGCTTTCACACATGAACATGGAGGCTGAAGAAAC
154515 AAGAAA
1 AAGAAA
154521 TGGTAGCATG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (54 bp):
AAGAAACGGCATTTCACGCATGCTTTCACACATGAACATGGAGGCTGAAGAAAC
Found at i:154702 original size:23 final size:23
Alignment explanation
Indices: 154676--154723 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
154666 AATAAGAAGT
*
154676 AATAGCTACAATTAAGCTGCTGA
1 AATAGATACAATTAAGCTGCTGA
*
154699 AATAGATGCAATTAAGCTGCTGA
1 AATAGATACAATTAAGCTGCTGA
154722 AA
1 AA
154724 CAACTGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (23 bp):
AATAGATACAATTAAGCTGCTGA
Found at i:154731 original size:23 final size:23
Alignment explanation
Indices: 154684--154733 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
154674 GTAATAGCTA
*
154684 CAATTAAGCTGCTGAAATAGATG
1 CAATTAAGCTGCTGAAACAGATG
154707 CAATTAAGCTGCTGAAACA-ACTG
1 CAATTAAGCTGCTGAAACAGA-TG
154730 CAAT
1 CAAT
154734 GCAACAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
CAATTAAGCTGCTGAAACAGATG
Found at i:154777 original size:26 final size:26
Alignment explanation
Indices: 154748--154807 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
154738 CAAGAACGAA
*
154748 ACAGCTGCAATGAAGAGAAGAAATCG
1 ACAGCTGCAACGAAGAGAAGAAATCG
*
154774 ACAGCTACAACGAAGAGAAGAAATCG
1 ACAGCTGCAACGAAGAGAAGAAATCG
154800 ACAGCTGC
1 ACAGCTGC
154808 TGAAATGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (26 bp):
ACAGCTGCAACGAAGAGAAGAAATCG
Found at i:155396 original size:24 final size:25
Alignment explanation
Indices: 155353--155399 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
155343 AACAAAGAGG
155353 GCAAGCAAAAAAAGAAAAAAAAACA
1 GCAAGCAAAAAAAGAAAAAAAAACA
*
155378 GCAAGC-AAATAAGAAAAAAAAA
1 GCAAGCAAAAAAAGAAAAAAAAA
155400 GTTCACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.74, C:0.11, G:0.13, T:0.02
Consensus pattern (25 bp):
GCAAGCAAAAAAAGAAAAAAAAACA
Found at i:161112 original size:15 final size:15
Alignment explanation
Indices: 161092--161121 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
161082 GATACATTAG
161092 TATTGTATCGATACA
1 TATTGTATCGATACA
161107 TATTGTATCGATACA
1 TATTGTATCGATACA
161122 AATTACATTG
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:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TATTGTATCGATACA
Found at i:161181 original size:48 final size:49
Alignment explanation
Indices: 161110--161217 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 49
161100 CGATACATAT
* *
161110 TGTATCGATACAAATTACATTGTATTGATACGA-TCT-GGAAAACCCAAA
1 TGTATCGATACAAATTACATTGTATCGATAC-ATTCTAGAAAAACCCAAA
* * *
161158 TGTATCGATACAAGTTACATTGTATCGATACATTCTAGAAAAATCCAGA
1 TGTATCGATACAAATTACATTGTATCGATACATTCTAGAAAAACCCAAA
161207 TGTATCGATAC
1 TGTATCGATAC
161218 TTTGAACAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 1 0.02
48 32 0.60
49 20 0.38
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (49 bp):
TGTATCGATACAAATTACATTGTATCGATACATTCTAGAAAAACCCAAA
Found at i:165920 original size:38 final size:38
Alignment explanation
Indices: 165869--165946 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
165859 TCATAGTCAA
*
165869 GTGTAAGCATACTTATCTTTGATTCCTCGACTTGATTT
1 GTGTAACCATACTTATCTTTGATTCCTCGACTTGATTT
*
165907 GTGTAACCATACTTATCTTTGATTCCTTGACTTGATTT
1 GTGTAACCATACTTATCTTTGATTCCTCGACTTGATTT
165945 GT
1 GT
165947 TCCTTCATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (38 bp):
GTGTAACCATACTTATCTTTGATTCCTCGACTTGATTT
Found at i:167076 original size:13 final size:13
Alignment explanation
Indices: 167058--167083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
167048 CAATTTTTTG
167058 TGTATCGATACAT
1 TGTATCGATACAT
167071 TGTATCGATACAT
1 TGTATCGATACAT
167084 ACTTTGTGTA
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:167095 original size:32 final size:33
Alignment explanation
Indices: 167038--167101 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
167028 TACAAGCCAA
**
167038 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
167071 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
167102 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:169621 original size:13 final size:13
Alignment explanation
Indices: 169603--169627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169593 ATAATCCCTC
169603 TGTATCGATACAG
1 TGTATCGATACAG
169616 TGTATCGATACA
1 TGTATCGATACA
169628 AAGAAAAATG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:175829 original size:13 final size:13
Alignment explanation
Indices: 175811--175836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175801 CAATTTTTTG
175811 TGTATCGATACAT
1 TGTATCGATACAT
175824 TGTATCGATACAT
1 TGTATCGATACAT
175837 ACTTTGTGTA
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:175848 original size:32 final size:33
Alignment explanation
Indices: 175791--175854 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
175781 TACAAGCCAA
**
175791 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
175824 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
175855 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:175952 original size:20 final size:19
Alignment explanation
Indices: 175906--175958 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
175896 ACAATCTTTT
* *
175906 CATGTATCGATACATTGCA
1 CATGTATCGATACTTTGAA
175925 CATGTATCGATACTTTGAA
1 CATGTATCGATACTTTGAA
*
175944 CTGTGTATCGATACT
1 C-ATGTATCGATACT
175959 GTTAAGGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (19 bp):
CATGTATCGATACTTTGAA
Done.