Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1365
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: 36839
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:51 original size:17 final size:18
Alignment explanation
Indices: 25--58 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15 ACTTGTTTAT
*
25 ATAATTAGAGA-AAAAAA
1 ATAATAAGAGAGAAAAAA
42 ATAATAAGAGAGAAAAA
1 ATAATAAGAGAGAAAAA
59 CTCATTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (18 bp):
ATAATAAGAGAGAAAAAA
Found at i:4821 original size:29 final size:29
Alignment explanation
Indices: 4788--4845 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4778 AAAACCATTA
4788 ACCTTTTGATTAAAGATCACCTCTTGATC
1 ACCTTTTGATTAAAGATCACCTCTTGATC
4817 ACCTTTTGATTAAAGATCACCTCTTGATC
1 ACCTTTTGATTAAAGATCACCTCTTGATC
4846 TACCAACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (29 bp):
ACCTTTTGATTAAAGATCACCTCTTGATC
Found at i:6703 original size:5 final size:5
Alignment explanation
Indices: 6693--6723 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
6683 TTTGATTGGG
6693 GCCTT GCCTT GCCTT GCCTT GCCTT GCCTT G
1 GCCTT GCCTT GCCTT GCCTT GCCTT GCCTT G
6724 GCGGGACTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.23, T:0.39
Consensus pattern (5 bp):
GCCTT
Found at i:7782 original size:43 final size:40
Alignment explanation
Indices: 7695--7782 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
7685 AATCACTATT
* *
7695 TATTAATAAAAAATATATTTTTATTTAAATTTAATTATATAA
1 TATTAATAAAAAATATATTTTTATTT--ATTTAATAATAAAA
7737 TATTAATATAAAAATAATATTTTTAGTTT-TTTAAATAATAAAA
1 TATTAATA-AAAAAT-ATATTTTTA-TTTATTT-AATAATAAAA
7780 TAT
1 TAT
7783 GTCGTTGAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
42 11 0.28
43 17 0.43
44 9 0.22
45 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
TATTAATAAAAAATATATTTTTATTTATTTAATAATAAAA
Found at i:8970 original size:13 final size:13
Alignment explanation
Indices: 8952--9010 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
8942 ACATTATGCT
8952 TTGTATCGATACA
1 TTGTATCGATACA
8965 TTGTATCGATACACA
1 TTGTATCGAT--ACA
8980 CCTAGATGTATCGATACA
1 --T---TGTATCGATACA
8998 TTGTATCGATACA
1 TTGTATCGATACA
9011 CACCTAGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.56
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
20 9 0.23
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8975 original size:33 final size:32
Alignment explanation
Indices: 8953--9031 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 32
8943 CATTATGCTT
8953 TGTATCGATACATTGTATCGATACACACCTAGA
1 TGTATCGATACATTGTATCGATACACACCTA-A
8986 TGTATCGATACATTGTATCGATACACACCTAGA
1 TGTATCGATACATTGTATCGATACACACCTA-A
9019 TGTATCGATACAT
1 TGTATCGATACAT
9032 ATTCATTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACACACCTAA
Found at i:8991 original size:20 final size:20
Alignment explanation
Indices: 8966--9030 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
8956 ATCGATACAT
8966 TGTATCGATACACACCTAGA
1 TGTATCGATACACACCTAGA
8986 TGTATCGAT--ACA--T---
1 TGTATCGATACACACCTAGA
8999 TGTATCGATACACACCTAGA
1 TGTATCGATACACACCTAGA
9019 TGTATCGATACA
1 TGTATCGATACA
9031 TATTCATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
20 21 0.55
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACACCTAGA
Found at i:9043 original size:19 final size:20
Alignment explanation
Indices: 9019--9070 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9009 CACACCTAGA
**
9019 TGTATCGATACATATTC-AT
1 TGTATCGATACATAGACAAT
* *
9038 TGTATCGATATATGGACAAT
1 TGTATCGATACATAGACAAT
9058 TGTATCGATACAT
1 TGTATCGATACAT
9071 GAAATTGGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATAGACAAT
Found at i:9125 original size:20 final size:19
Alignment explanation
Indices: 9100--9166 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
9090 CTACCACTGT
9100 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTA-A
9120 TTGTATCGATAC-----AA
1 TTGTATCGATACATGGTAA
9134 -TGTATCGATACATGGTGAA
1 TTGTATCGATACATGGT-AA
9153 TTGTATCGATACAT
1 TTGTATCGATACAT
9167 TACTTCTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
15 1 0.03
19 2 0.05
20 25 0.62
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGGTAA
Found at i:9137 original size:13 final size:13
Alignment explanation
Indices: 9116--9145 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9106 CGATACATGG
*
9116 TACATTGTATCGA
1 TACAATGTATCGA
9129 TACAATGTATCGA
1 TACAATGTATCGA
9142 TACA
1 TACA
9146 TGGTGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:9143 original size:33 final size:33
Alignment explanation
Indices: 9101--9165 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
9091 TACCACTGTT
9101 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGGTGA-ATTGTATCGATACAA
9134 TGTATCGATACATGGTGAATTGTATCGATACA
1 TGTATCGATACATGGTGAATTGTATCGATACA
9166 TTACTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGTGAATTGTATCGATACAA
Found at i:17843 original size:13 final size:13
Alignment explanation
Indices: 17825--17851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17815 ACATTATGCT
17825 TTGTATCGATACA
1 TTGTATCGATACA
17838 TTGTATCGATACA
1 TTGTATCGATACA
17851 T
1 T
17852 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:20921 original size:18 final size:17
Alignment explanation
Indices: 20879--20933 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
20869 TATCTAATTT
* *
20879 TATAATTATTAGATAAT
1 TATATTTATTAGATAAA
*
20896 TATATTTATTAGGTAAA
1 TATATTTATTAGATAAA
20913 TATTATTTATTAAGATAAA
1 TA-TATTTATT-AGATAAA
20932 TA
1 TA
20934 AGGAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 16 0.50
18 8 0.25
19 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATTTATTAGATAAA
Found at i:23713 original size:51 final size:51
Alignment explanation
Indices: 23553--23723 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
23543 GAAATAACGA
* * * *
23553 GGTTGGAGTATCCTCGGTTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
23605 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
23658 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
23709 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
23724 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 39 0.41
52 15 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:23769 original size:27 final size:28
Alignment explanation
Indices: 23706--23781 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
23696 AAAATAAAGT
*
23706 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
23734 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
23761 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
23782 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:26034 original size:55 final size:55
Alignment explanation
Indices: 25939--26616 Score: 1034
Period size: 55 Copynumber: 12.3 Consensus size: 55
25929 ATAAATTGTA
* * * * * *
25939 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
25994 TGCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
26049 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
26104 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
26159 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
26214 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
26269 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
26324 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
26379 TCCTGCTCCTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
26434 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
26489 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
26544 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
26599 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
26617 AAAAAGCGGA
Statistics
Matches: 585, Mismatches: 27, Indels: 22
0.92 0.04 0.03
Matches are distributed among these distances:
53 2 0.00
54 12 0.02
55 559 0.96
56 10 0.02
57 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:27602 original size:1 final size:1
Alignment explanation
Indices: 27598--27654 Score: 69
Period size: 1 Copynumber: 57.0 Consensus size: 1
27588 CTTTTCTCTC
* * * * *
27598 TTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27655 GAAGAGAAGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.04, G:0.05, T:0.91
Consensus pattern (1 bp):
T
Found at i:27611 original size:9 final size:9
Alignment explanation
Indices: 27584--27654 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
27574 TAAGTAGGTT
27584 TTTTCTTTTC
1 TTTT-TTTTC
*
27594 TCTCTTTTTC
1 T-TTTTTTTC
* *
27604 TTTGTTTTG
1 TTTTTTTTC
*
27613 TTTTTTTTGT
1 TTTTTTTT-C
27623 TTTTTTTTC
1 TTTTTTTTC
27632 TTTTTTTT-
1 TTTTTTTTC
27640 TTTTTTTT-
1 TTTTTTTTC
27648 TTTTTTT
1 TTTTTTT
27655 GAAGAGAAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
8 15 0.29
9 20 0.38
10 15 0.29
11 2 0.04
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.87
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:27616 original size:14 final size:12
Alignment explanation
Indices: 27582--27653 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 12
27572 CTTAAGTAGG
27582 TTTTTTCTTTTCTC
1 TTTTTT-TTTT-TC
* * *
27596 TCTTTTTCTTTG
1 TTTTTTTTTTTC
27608 TTTTGTTTTTTT-
1 TTTT-TTTTTTTC
*
27620 TGTTTTTTTTTC
1 TTTTTTTTTTTC
27632 TTTTTTTTTTT-
1 TTTTTTTTTTTC
27643 TTTTTTTTTTT
1 TTTTTTTTTTT
27654 TGAAGAGAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 18 0.37
12 17 0.35
13 9 0.18
14 5 0.10
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:27630 original size:28 final size:25
Alignment explanation
Indices: 27598--27654 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 25
27588 CTTTTCTCTC
27598 TTTTTCTTTGTTTTGTTTTTTTTGTTTT
1 TTTTTCTTT-TTTT-TTTTTTTT-TTTT
27626 TTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTTTTT
27651 TTTT
1 TTTT
27655 GAAGAGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 8 0.28
26 8 0.28
27 4 0.14
28 9 0.31
ACGTcount: A:0.00, C:0.04, G:0.05, T:0.91
Consensus pattern (25 bp):
TTTTTCTTTTTTTTTTTTTTTTTTT
Done.