Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2358
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: 5035
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Found at i:2527 original size:51 final size:48
Alignment explanation
Indices: 2431--2547 Score: 123
Period size: 51 Copynumber: 2.4 Consensus size: 48
2421 AATTCTCCGC
*
2431 AATCGGGGATA-TCCCAACTCTGATTTCATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTTCAAAACACTAA-TTT-T-T
* *
2482 AATCGGGGATACTCCAACTCCGATTTTA-TTTCTAGAACA-TCAATTTTT
1 AATCGGGGATACTCCAACTCCGATTTCATTTTC-AAAACACT-AATTTTT
*
2530 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
2548 CCCGTTAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
48 18 0.31
49 1 0.02
50 8 0.14
51 31 0.53
52 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (48 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTTCAAAACACTAATTTTT
Found at i:2602 original size:28 final size:28
Alignment explanation
Indices: 2529--2603 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2519 CATCAATTTT
2529 TCATC-GGGGATACTCCAACCCCGTTAA
1 TCATCAGGGGATACTCCAACCCCGTTAA
2556 TCATCA-GGGATACTCCAACCCCGTT-A
1 TCATCAGGGGATACTCCAACCCCGTTAA
**
2582 TTTTCGAGGGGATACTCCAACC
1 TCATC-AGGGGATACTCCAACC
2604 TCCGGCTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 4 0.09
27 25 0.58
28 14 0.33
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (28 bp):
TCATCAGGGGATACTCCAACCCCGTTAA
Found at i:2711 original size:80 final size:78
Alignment explanation
Indices: 2562--2736 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 78
2552 TTAATCATCA
* * * *
2562 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCCGGCTTTATTTCTAAAATATT
1 GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCTCAGGCTTTATTTCTAAAATATG
*
2627 ATTTTCTCATAATCG
66 ATTTT-TC-GAATCG
* *
2642 GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACC-CAGGTTTTATTTC-CAAATCAT
1 GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCTCAGGCTTTATTTCTAAAAT-AT
2705 CGATTTTTCGAATCG
65 -GATTTTTCGAATCG
2720 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
2737 ACTTTATTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 26 0.30
79 15 0.17
80 45 0.52
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCTCAGGCTTTATTTCTAAAATATG
ATTTTTCGAATCG
Found at i:2829 original size:52 final size:49
Alignment explanation
Indices: 2669--2837 Score: 178
Period size: 52 Copynumber: 3.3 Consensus size: 49
2659 TTATCTCCGA
* * * * *
2669 GGGGATACTCCAACCCAGGTTTTATTTCCAAATCATCGATTTTTCGAATC
1 GGGGATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTTCCAATC
* *
2719 GGGGATACTCCAACCCCGACTTTATTTTCAAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACACCAATTTTTCC---AATC
*
2771 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAACACCAATTTTTC-CAATC
*
2823 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2838 TCGTTATTTC
Statistics
Matches: 100, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
49 5 0.05
50 29 0.29
51 5 0.05
52 45 0.45
53 10 0.10
54 5 0.05
55 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (49 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTTCCAATC
Found at i:2848 original size:31 final size:28
Alignment explanation
Indices: 2823--2896 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
2813 TTTCACAATT
*
2823 GAGGATACTCCAACCTCGTTATTTCATC
1 GAGGATACTCCAACCCCGTTATTTCATC
**
2851 GAGGATACTCCAACCCCGTTACCTC--C
1 GAGGATACTCCAACCCCGTTATTTCATC
2877 GAGGGGATACTCCAACCCCG
1 GA--GGATACTCCAACCCCG
2897 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
28 38 0.93
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
GAGGATACTCCAACCCCGTTATTTCATC
Found at i:2945 original size:289 final size:285
Alignment explanation
Indices: 2430--3026 Score: 776
Period size: 289 Copynumber: 2.1 Consensus size: 285
2420 CAATTCTCCG
* * *
2430 CAATCGGGGATA-TCCCAACTCTGATTTCATTTTCAAAACACTAATTTTCTATAATCGGGGATAC
1 CAATCGGGGATACT-CCAACCCCGATTTCATTTTCAAAACACCAATTTTCTATAATCGGGGATAC
* * * *
2494 TCCAACTCCGATTTTATTTCTAGAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTAATCA
65 TCCAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCA
** * * *
2559 TCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCCGGCTTTATTTCTAAAAT
130 TCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCTCCGGCTTTATTCCCAAAAT
* * * * *
2624 ATTATTTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCC-AG
195 ATCAATTTCTCATAATCAGGGATACTCCAACCCCGTTATCTCCGAGAGGATACTCCAATCCCGAT
* *
2687 GTTTTATTTCCAAATCATCGATTTTTC-
260 GTTTT-TCT-CAAATCATCGATTTCTCA
* *
2714 GAATCGGGGATACTCCAACCCCGACTTT-ATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
1 CAATCGGGGATACTCCAACCCCGA-TTTCATTTTCAAAACACCAATTTT-CTATAATCGGGGATA
* *
2778 CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAACCTCGTT
64 CTCCAACTCCGATTTTATTT-CAAAAACACCAATTTTT--C-ATCGAGGATACTCCAACCCCGTT
*
2843 ATTTCATC-GAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACC-CCGGCTTTATTC
125 A-ATCATCAG-GGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCTCCGGCTTTATTC
* * *
2906 CCAAAATATCAATTTCTCATAATTAGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAA
188 CCAAAATATCAATTTCTCATAATCAGGGATACTCCAACCCCGTTATCTCCGAGAGGATACTCCAA
*
2971 TCCCGATGTTTTTCTCTAATCATCGATTTCTCA
253 TCCCGATGTTTTTCTCAAATCATCGATTTCTCA
* *
3004 CAACCGGGGATACTCCAGCCCCG
1 CAATCGGGGATACTCCAACCCCG
3027 TCATTTTCAA
Statistics
Matches: 270, Mismatches: 31, Indels: 18
0.85 0.10 0.06
Matches are distributed among these distances:
284 38 0.14
285 38 0.14
286 14 0.05
288 1 0.00
289 105 0.39
290 68 0.25
291 6 0.02
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (285 bp):
CAATCGGGGATACTCCAACCCCGATTTCATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCAT
CAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCTCCGGCTTTATTCCCAAAATA
TCAATTTCTCATAATCAGGGATACTCCAACCCCGTTATCTCCGAGAGGATACTCCAATCCCGATG
TTTTTCTCAAATCATCGATTTCTCA
Found at i:2962 original size:107 final size:107
Alignment explanation
Indices: 2771--2975 Score: 263
Period size: 107 Copynumber: 1.9 Consensus size: 107
2761 TCCTTTAATC
* * *
2771 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGAGGATACTCCAA
*
2836 CCTCGTTATTTCATCGAGGATACTCCAACCCCGTTACCTCCGA
66 CCCCGTTATTTCA-CGAGGATACTCCAACCCCGTTACCTCCGA
* * * * *
2879 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATCAATTTCTCATAATT-AGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGA-GGATACTCCA
*
2942 ACCCCGTTATTTTCGA-GAGGATACTCCAATCCCG
65 ACCCCGTTA-TTTC-ACGAGGATACTCCAACCCCG
2976 ATGTTTTTCT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
106 1 0.01
107 57 0.68
108 25 0.30
109 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGAGGATACTCCAA
CCCCGTTATTTCACGAGGATACTCCAACCCCGTTACCTCCGA
Found at i:3000 original size:79 final size:79
Alignment explanation
Indices: 2853--3054 Score: 212
Period size: 79 Copynumber: 2.6 Consensus size: 79
2843 ATTTCATCGA
** *
2853 GGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCAA
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCAA
* **
2918 TTTCTCATAATTAG
66 TTTCTCACAACCAG
* * * *
2932 GGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAATCCCGATG-TTT-TTCTC-TAATCAT
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT-AT
* *
2994 CGATTTCTCACAACCGG
63 CAATTTCTCACAACCAG
* * * *
3011 GGATACTCCAGCCCCGTCATTTTCAAGGGGACACTCCAACCCCG
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
3055 TTATTATCTC
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 3 0.03
79 95 0.93
80 3 0.03
81 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCAA
TTTCTCACAACCAG
Found at i:4051 original size:19 final size:20
Alignment explanation
Indices: 4027--4068 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4017 GCACGTTGCG
4027 ACACCTT-AAATGTATCGAT
1 ACACCTTCAAATGTATCGAT
*
4046 ACACCTTCAGATGTATCGAT
1 ACACCTTCAAATGTATCGAT
4066 ACA
1 ACA
4069 TAATGCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (20 bp):
ACACCTTCAAATGTATCGAT
Found at i:4096 original size:13 final size:13
Alignment explanation
Indices: 4078--4102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4068 ATAATGCACA
4078 GTATCGATACATT
1 GTATCGATACATT
4091 GTATCGATACAT
1 GTATCGATACAT
4103 GACCATTGTA
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:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:4209 original size:13 final size:13
Alignment explanation
Indices: 4191--4216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4181 ACATACAAGA
4191 TGTATCGATACAT
1 TGTATCGATACAT
4204 TGTATCGATACAT
1 TGTATCGATACAT
4217 GACTAAATGT
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:4232 original size:33 final size:32
Alignment explanation
Indices: 4171--4238 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
4161 CCTTAACTGT
4171 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
4203 TTGTATCGATACATGACTAA-ATGTATCGATACA
1 TTGTATCGATACAT-AC-AAGATGTATCGATACA
4236 TTG
1 TTG
4239 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Done.