Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2149
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: 45417
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:5074 original size:40 final size:40
Alignment explanation
Indices: 4990--5213 Score: 242
Period size: 40 Copynumber: 5.6 Consensus size: 40
4980 TTGAATGCTG
* *
4990 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
** * * *
5029 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
5070 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5110 TCCGGGTTAAGTCCTGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* ** *
5150 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
5190 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5214 GAATGAGTTA
Statistics
Matches: 160, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
39 3 0.02
40 145 0.91
41 12 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:5234 original size:39 final size:39
Alignment explanation
Indices: 5070--5260 Score: 136
Period size: 40 Copynumber: 4.8 Consensus size: 39
5060 AGTTATTAAT
* ** * *
5070 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
* * ** * *
5110 TCCGGGTTAAGTCCTGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
5150 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* *
5190 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
5230 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
5261 GAGCTAAATC
Statistics
Matches: 133, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 30 0.23
40 103 0.77
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:8031 original size:27 final size:27
Alignment explanation
Indices: 8001--8056 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
7991 GTACCTAGAC
8001 CCCCTA-ATTGGAAAAATAACTGAAATG
1 CCCCTACA-TGGAAAAATAACTGAAATG
* * *
8028 CCCCTACATGGTAAAATGACTGATATG
1 CCCCTACATGGAAAAATAACTGAAATG
8055 CC
1 CC
8057 TTATGAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (27 bp):
CCCCTACATGGAAAAATAACTGAAATG
Found at i:10273 original size:56 final size:56
Alignment explanation
Indices: 10213--10339 Score: 209
Period size: 56 Copynumber: 2.3 Consensus size: 56
10203 TCCTAGACAG
* *
10213 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACAT
1 GGTCTTACTCGCACACATATATCAGAGTCACATATCGATACCAACGTATTAAACAT
* * *
10269 GGTCTTACTCGTACACATATATCAGAGTCACATATCGATACCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAGTCACATATCGATACCAACGTATTAAACAT
10325 GGTCTTACTCGCACA
1 GGTCTTACTCGCACA
10340 TCAAAGATCG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAGTCACATATCGATACCAACGTATTAAACAT
Found at i:13905 original size:29 final size:29
Alignment explanation
Indices: 13873--13949 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
13863 AATCATATTC
* *
13873 ATATGACCTATTAGGCCCAAATCACCTGT
1 ATATGACCCATTAGGCCCAAATCACATGT
* * *
13902 ATATGGCCCATTAGGCCTAAATCACATTT
1 ATATGACCCATTAGGCCCAAATCACATGT
* * *
13931 ATATGGCCCGTTAAGCCCA
1 ATATGACCCATTAGGCCCA
13950 GTCACATTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (29 bp):
ATATGACCCATTAGGCCCAAATCACATGT
Found at i:16583 original size:29 final size:29
Alignment explanation
Indices: 16517--16644 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
16507 AATTTCACAT
* * *
16517 ACCTGTATCTGGCGCATTAAGCCC-AATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
**
16545 ATAT-TCATATGGCCCATTAGGCCCAAATC
1 ACCTGT-ATATGGCCCATTAGGCCCAAATC
* *
16574 ACCTGTATATGGCCTATTAGGCCTAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
*
16603 ACCTGTATATTGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
* *
16632 ACATTTATATGGC
1 ACCTGTATATGGC
16645 TTGTTAGGCC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.01
28 17 0.21
29 63 0.77
30 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (29 bp):
ACCTGTATATGGCCCATTAGGCCCAAATC
Found at i:16651 original size:29 final size:29
Alignment explanation
Indices: 16551--16656 Score: 131
Period size: 29 Copynumber: 3.7 Consensus size: 29
16541 AATCATATTC
* *
16551 ATATGGCCCATTAGGCCCAAATCACCTGT
1 ATATGGCCTATTAGGCCCAAATCACATGT
* *
16580 ATATGGCCTATTAGGCCTAAATCACCTGT
1 ATATGGCCTATTAGGCCCAAATCACATGT
* * *
16609 ATATTGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCTATTAGGCCCAAATCACATGT
* *
16638 ATATGGCTTGTTAGGCCCA
1 ATATGGCCTATTAGGCCCA
16657 GTCACATTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (29 bp):
ATATGGCCTATTAGGCCCAAATCACATGT
Found at i:25709 original size:28 final size:27
Alignment explanation
Indices: 25678--25740 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
25668 AATTACTAGA
* *
25678 ATACCCCTAAGTATGGAAAATTACCATT
1 ATACCCCTAAG-ATGCAAAATGACCATT
*
25706 ATACCCCT-AGGTGCAAAATGACCATT
1 ATACCCCTAAGATGCAAAATGACCATT
*
25732 TTACCCCTA
1 ATACCCCTA
25741 GGGTTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 20 0.67
27 2 0.07
28 8 0.27
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATGACCATT
Found at i:27607 original size:37 final size:36
Alignment explanation
Indices: 27538--27614 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 36
27528 TACGTGCATT
*
27538 ATGTGCAATTCAGGGGTACTAAATACAAGCAGGGGC
1 ATGTGCAATGCAGGGGTACTAAATACAAGCAGGGGC
* *
27574 ATGTTCAATGCAGGGGTACTGAAGTACAAGCAGGGGC
1 ATGTGCAATGCAGGGGTACT-AAATACAAGCAGGGGC
27611 ATGT
1 ATGT
27615 ATATGCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 18 0.49
37 19 0.51
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.21
Consensus pattern (36 bp):
ATGTGCAATGCAGGGGTACTAAATACAAGCAGGGGC
Found at i:33889 original size:40 final size:40
Alignment explanation
Indices: 33839--34028 Score: 267
Period size: 40 Copynumber: 4.8 Consensus size: 40
33829 AATATAGCTT
* *
33839 CTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAG
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAA
* *
33879 TTCGCACAAATGCCTTCGAGACTTAGCCCGG-ATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAA
* *
33919 CTCGCACAAATGCCTTCGGGACTTATCCCAGAATTAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA
* *
33959 CTCGTACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA
*
33999 CTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CTCGCACAAATGCCTTCGGGACTTAGCCCG
34029 TTATCATCCG
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA
Found at i:41899 original size:40 final size:40
Alignment explanation
Indices: 41863--42012 Score: 232
Period size: 40 Copynumber: 3.8 Consensus size: 40
41853 GGATATAGCT
*
41863 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
**
41903 GTTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
41943 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
41983 ACTAGCACAAATGCCTTCGGGACTTA-CCCG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCG
42013 TTATCATCCG
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 4 0.04
40 96 0.94
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:41991 original size:80 final size:79
Alignment explanation
Indices: 41837--42012 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 79
41827 AAACCAAGTA
* * *
41837 CCTTCGGGATTTAACCGG-ATATAGCT-ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTACCCGGAAT-TAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
41900 GTAGTTCGCACAAATG
64 GTAGCTAGCACAAATG
41916 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTA
1 CCTTCGGGACTTA-CCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TA
41980 GTCA-CTAGCACAAATG
64 GT-AGCTAGCACAAATG
41996 CCTTCGGGACTTACCCG
1 CCTTCGGGACTTACCCG
42013 TTATCATCCG
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
79 18 0.21
80 66 0.76
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTACCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AGCTAGCACAAATG
Done.