Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2464
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: 10206
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Found at i:1072 original size:20 final size:22
Alignment explanation
Indices: 1034--1128 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
1024 TTTGACAAAA
* * *
1034 GGGGAGAAATGCGTTGATTAAG
1 GGGGAGAAATTCTTTAATTAAG
* * *
1056 GAGGAGAAA-T-TTTGATTAAA
1 GGGGAGAAATTCTTTAATTAAG
*
1076 GGGGATAAATTCTTTAATTAAG
1 GGGGAGAAATTCTTTAATTAAG
1098 GGGGAGAAATTCTTTAATTAAG
1 GGGGAGAAATTCTTTAATTAAG
1120 GGGGAGAAA
1 GGGGAGAAA
1129 AACGAAAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
20 15 0.24
21 1 0.02
22 46 0.74
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (22 bp):
GGGGAGAAATTCTTTAATTAAG
Found at i:1077 original size:42 final size:44
Alignment explanation
Indices: 1031--1128 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 44
1021 AGATTTGACA
* *
1031 AAAGGGGAGAAATGCGTTGATTAAGGAGGAGAAA-T-TTTGATT
1 AAAGGGGAGAAATGCGTTAATTAAGGAGGAGAAATTCTTTAATT
* * * *
1073 AAAGGGGATAAATTCTTTAATTAAGGGGGAGAAATTCTTTAATT
1 AAAGGGGAGAAATGCGTTAATTAAGGAGGAGAAATTCTTTAATT
*
1117 AAGGGGGAGAAA
1 AAAGGGGAGAAA
1129 AACGAAAACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 29 0.63
43 1 0.02
44 16 0.35
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.27
Consensus pattern (44 bp):
AAAGGGGAGAAATGCGTTAATTAAGGAGGAGAAATTCTTTAATT
Found at i:1677 original size:71 final size:71
Alignment explanation
Indices: 1561--1714 Score: 274
Period size: 71 Copynumber: 2.2 Consensus size: 71
1551 ATACTTCAAA
1561 GTATCGATACATTGGTATTTGTATCGATACATTATGGTTGACTTAGGGTACAAAGGTCAAAACCC
1 GTATCGATACATTGGTATTTGTATCGATACATTATGGTTGACTTAGGGTACAAAGGTCAAAACCC
1626 TTGAAT
66 TTGAAT
* *
1632 GTATCGATACATT-ATGCTTTGTATCGATACATTATGGTTGACTTAGGGTACAAAGGTCAAAACC
1 GTATCGATACATTGGT-ATTTGTATCGATACATTATGGTTGACTTAGGGTACAAAGGTCAAAACC
1696 CTTGAAT
65 CTTGAAT
1703 GTATCGATACAT
1 GTATCGATACAT
1715 GTTCATTGTA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
70 1 0.01
71 79 0.99
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (71 bp):
GTATCGATACATTGGTATTTGTATCGATACATTATGGTTGACTTAGGGTACAAAGGTCAAAACCC
TTGAAT
Found at i:1730 original size:19 final size:20
Alignment explanation
Indices: 1702--1754 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1692 AACCCTTGAA
**
1702 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGGCAAT
*
1721 TGTATTGATACATGGGCAAT
1 TGTATCGATACATGGGCAAT
1741 TGTATCGATACATG
1 TGTATCGATACATG
1755 AGATTGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGGCAAT
Found at i:1809 original size:20 final size:20
Alignment explanation
Indices: 1784--1849 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1774 TGCCACTGTT
1784 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
1804 TGTATCGATACA---T----
1 TGTATCGATACATGGTACAA
1817 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
1837 TGTATCGATACAT
1 TGTATCGATACAT
1850 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
16 1 0.03
17 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:1820 original size:13 final size:13
Alignment explanation
Indices: 1799--1884 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
1789 CGATACATGG
*
1799 TACAATGTATCGA
1 TACATTGTATCGA
1812 TACATTGTATCGA
1 TACATTGTATCGA
1825 TACA-TG----G-
1 TACATTGTATCGA
*
1832 TACAATGTATCGA
1 TACATTGTATCGA
1845 TACATTGTATCGA
1 TACATTGTATCGA
1858 TACA-TG-AT-G-
1 TACATTGTATCGA
1867 -A-ATTGTATCGA
1 TACATTGTATCGA
1878 TACATTG
1 TACATTG
1885 CTTGTAACGG
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
7 5 0.08
8 6 0.10
9 2 0.03
10 2 0.03
11 2 0.03
12 6 0.10
13 36 0.61
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1825 original size:33 final size:33
Alignment explanation
Indices: 1783--1884 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
1773 CTGCCACTGT
1783 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
1816 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
* *
1849 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGGT-ACAATGTATCGATACA
1882 TTG
1 TTG
1885 CTTGTAACGG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 65 0.98
34 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGGTACAATGTATCGATACA
Found at i:6373 original size:79 final size:80
Alignment explanation
Indices: 6290--6517 Score: 238
Period size: 77 Copynumber: 2.9 Consensus size: 80
6280 ATCCCCTTGA
* * *
6290 AAATAACGGGGTTGGAGTATCCCCGGTTGAGAAAAATCGATGATTAGGAAATAAAATCGGGATTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGAGAAAAATCTATGTTTAGGAAATAAAATCGGGATTG
6355 GAGTATTCCCTC-A-G
66 GAGTATT-CCTCGATG
* * * * **
6369 AAATAACGGGGTTGGAGTATCCCCAATT-ATGAGAAATCTAT-TTTA-AAAAT-AAAGCCAGAGT
1 AAATAACGGGGTTGGAGTATCCCCGATTGA-GAAAAATCTATGTTTAGGAAATAAAATCGGGA-T
6430 TGGAGTA-TCCTCGATG
64 TGGAGTATTCCTCGATG
* * * *
6446 AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAAT-TAGTGTTTTTGGAAATAAAATCGGGGT
1 AAATAACGGGGTTGGAGTATCCCCGATTGAGAAAAATCTA-TG-TTTAGGAAATAAAATCGGGAT
6510 TGGAGTAT
64 TGGAGTAT
6518 CCCCGATTGT
Statistics
Matches: 119, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
75 4 0.03
76 10 0.08
77 46 0.39
78 4 0.03
79 38 0.32
80 12 0.10
81 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (80 bp):
AAATAACGGGGTTGGAGTATCCCCGATTGAGAAAAATCTATGTTTAGGAAATAAAATCGGGATTG
GAGTATTCCTCGATG
Found at i:6570 original size:51 final size:51
Alignment explanation
Indices: 6455--6685 Score: 351
Period size: 51 Copynumber: 4.6 Consensus size: 51
6445 GAAATAACGA
* *
6455 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTG-TTTTAGAAATAAAACCGG
*
6507 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
* *
6558 GGTTGGAGTATCCCCAATTGTGGAAAA-T--TGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * *
6606 GGTTGAAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
*
6657 GGTTGGAGTATCCCCGATTATGAAAAATT
1 GGTTGGAGTATCCCCGATTGTGAAAAATT
6686 GAGAAACTTA
Statistics
Matches: 164, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
48 44 0.27
49 1 0.01
50 1 0.01
51 85 0.52
52 33 0.20
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:6621 original size:99 final size:100
Alignment explanation
Indices: 6455--6686 Score: 349
Period size: 99 Copynumber: 2.3 Consensus size: 100
6445 GAAATAACGA
* * *
6455 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAA-T--TGTTTTTAGAAATAAAACCGGGGTTGAAGTATCC
**
6520 CCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
63 CCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAG
* *
6558 GGTTGGAGTATCCCCAATTGTGGAAAATTG-TTTTAGAAATAAAACCGGGGTTGAAGTATCCCCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGTTTTTAGAAATAAAACCGGGGTTGAAGTATCCCCG
*
6622 ATTGTGGAAAATTAGTGTTTTAGAAATAAAACCAG
66 ATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAG
*
6657 GGTTGGAGTATCCCCGATTATGAAAAATTG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTG
6687 AGAAACTTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
99 90 0.76
100 2 0.02
102 1 0.01
103 25 0.21
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (100 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGTTTTTAGAAATAAAACCGGGGTTGAAGTATCCCCG
ATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAG
Found at i:7156 original size:79 final size:77
Alignment explanation
Indices: 7050--7319 Score: 280
Period size: 79 Copynumber: 3.4 Consensus size: 77
7040 AATTTAATAT
*
7050 TTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAGTT
1 TTTGGAAATAA-AATCGGGGTTGGAGTATCCCCTTG-AAATAACGGGGTTGGAGTATCCCCAGTT
7114 GA-GAAAAATCGATGA
64 -ATGAAAAATCGAT-A
* * * *
7129 TTAGGAAATAAAATCGGGATTGGAGTAT-CCCTTCGGAAATAGCGGGGTTGGAGTATCCCCAATT
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTT--GAAATAACGGGGTTGGAGTATCCCCAGTT
* *
7193 ATGAGAAATCAATA
64 ATGAAAAATCGATA
* * * *
7207 TTTTGAAA-ATAAAGCTGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCC-GA
1 TTTGGAAATA-AAATC-GGGGTTGGAGTATCCCC-TTGAAATAACGGGGTTGGAGTATCCCCAG-
* *
7270 TTATGAAAAATTGGTATT
62 TTATGAAAAA-TCG-ATA
7288 TTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCC
7320 GATTGTGAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 23
0.78 0.10 0.11
Matches are distributed among these distances:
77 1 0.01
78 19 0.12
79 101 0.64
80 22 0.14
81 14 0.09
82 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (77 bp):
TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTGAAATAACGGGGTTGGAGTATCCCCAGTTAT
GAAAAATCGATA
Found at i:7368 original size:51 final size:51
Alignment explanation
Indices: 7253--7435 Score: 285
Period size: 51 Copynumber: 3.6 Consensus size: 51
7243 GAAATAACGA
* * * *
7253 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTAGAAATAAAACCGG
* *
7305 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* *
7356 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
7407 GGTTGGAGTATCCCCGATTATGAAAAATT
1 GGTTGGAGTATCCCCGATTATGAAAAATT
7436 GAGAAACTTA
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
51 91 0.75
52 30 0.25
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:7907 original size:79 final size:78
Alignment explanation
Indices: 7800--8068 Score: 296
Period size: 78 Copynumber: 3.4 Consensus size: 78
7790 AATTTAATAT
* * *
7800 TTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTT
1 TTTGGAAATAA-AATCGGGGTTGGAGTATCCCCTTG-AAATAACGAGGTTGGAGTATCCCCGATT
7864 GA-GAAAAATCGATGA
64 -ATGAAAAATCGATGA
* * *
7879 TTAGGAAATAAAATCGGGATTGGAGTAT-CCCTTCGGAAATAACGAGGTTGGAGTATCCCCAATT
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTT--GAAATAACGAGGTTGGAGTATCCCCGATT
* *
7943 ATGAGAAATCAAT-A
64 ATGAAAAATCGATGA
* * **
7957 TTTGAAAAT-AAAGCTGGGGTTGGAGTATTCCCGATGAAATAACGAGGTTGGAGTATCCCCGATT
1 TTTGGAAATAAAATC-GGGGTTGGAGTA-TCCCCTTGAAATAACGAGGTTGGAGTATCCCCGATT
* * *
8021 ATGAAAAATTGGTGTT
64 ATGAAAAATCGATG-A
8037 TTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCC
8069 GATTGTGAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
77 4 0.03
78 64 0.41
79 61 0.39
80 24 0.15
81 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (78 bp):
TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTGAAATAACGAGGTTGGAGTATCCCCGATTAT
GAAAAATCGATGA
Found at i:8117 original size:51 final size:51
Alignment explanation
Indices: 8002--8184 Score: 294
Period size: 51 Copynumber: 3.6 Consensus size: 51
7992 GAAATAACGA
* * *
8002 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTAGAAATAAAACCGG
* *
8054 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* *
8105 GGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
8156 GGTTGGAGTATCCCCGATTATGAAAAATT
1 GGTTGGAGTATCCCCGATTATGAAAAATT
8185 GAGAAACTTA
Statistics
Matches: 122, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 91 0.75
52 31 0.25
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
Done.