Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1806
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: 15320
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Found at i:52 original size:15 final size:15
Alignment explanation
Indices: 32--67 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
22 TTTAATTTTC
32 AAAATTTCAAAAAA-A
1 AAAATTT-AAAAAATA
47 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
62 AAAATT
1 AAAATT
68 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:126 original size:30 final size:29
Alignment explanation
Indices: 63--161 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 29
53 TAAAAAATAA
* *
63 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGA-CCCTAAACTTTCT-TT
93 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCTTT
* * *
123 AAATTTCACTTAGACCCTAAA-TTTCATT
1 AAATTTCATTTTGACCCTAAACTTTCTTT
151 AAATTTCATTT
1 AAATTTCATTT
162 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.26
29 7 0.11
30 37 0.61
31 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCTTT
Found at i:156 original size:28 final size:28
Alignment explanation
Indices: 92--173 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
82 AAACTTTTCC
* *
92 TAAATTTCATTTTGACCCTTAAACTTTCTT
1 TAAATTTCATTTAGACCC-TAAA-TTTCAT
*
122 TAAATTTCACTTAGACCCTAAATTTCAT
1 TAAATTTCATTTAGACCCTAAATTTCAT
*
150 TAAATTTCATTTA-ATCCTAAATTT
1 TAAATTTCATTTAGACCCTAAATTT
174 TCTAAAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
27 10 0.21
28 17 0.36
29 4 0.09
30 16 0.34
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.46
Consensus pattern (28 bp):
TAAATTTCATTTAGACCCTAAATTTCAT
Found at i:175 original size:28 final size:27
Alignment explanation
Indices: 78--176 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 27
68 GCATTTTGAC
* *
78 CCCTAAACTTTTCCTAAATTTCATTTTGA
1 CCCTAAA-TTTTCTTAAATTTCA-TTTAA
* *
107 CCCTTAAACTTTCTTTAAATTTCACTTAGA
1 CCC-TAAATTTTC-TTAAATTTCATTTA-A
137 CCCTAAA-TTTCATTAAATTTCATTTAA
1 CCCTAAATTTTC-TTAAATTTCATTTAA
*
164 TCCTAAATTTTCT
1 CCCTAAATTTTCT
177 AAAAATGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 8 0.14
28 21 0.36
29 13 0.22
30 17 0.29
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.45
Consensus pattern (27 bp):
CCCTAAATTTTCTTAAATTTCATTTAA
Found at i:1514 original size:16 final size:16
Alignment explanation
Indices: 1466--1514 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
1456 TTTCTTTCTA
*
1466 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
1482 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
1499 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
1515 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:1514 original size:24 final size:26
Alignment explanation
Indices: 1491--1538 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1481 CAAAAATTTC
1491 CGTG-TTTC-AAAAAT-TCGTGTTTT
1 CGTGTTTTCAAAAAATCTCGTGTTTT
1514 CGTGTTTTCAAAAAATCTCGTGTTT
1 CGTGTTTTCAAAAAATCTCGTGTTT
1539 CAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 6 0.27
26 8 0.36
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.46
Consensus pattern (26 bp):
CGTGTTTTCAAAAAATCTCGTGTTTT
Found at i:1554 original size:8 final size:8
Alignment explanation
Indices: 1541--1588 Score: 64
Period size: 8 Copynumber: 6.0 Consensus size: 8
1531 TCGTGTTTCA
1541 AAAAAAAT
1 AAAAAAAT
1549 AAAAAAAT
1 AAAAAAAT
1557 --AAAAAT
1 AAAAAAAT
1563 AAAAAAAT
1 AAAAAAAT
1571 AATAAAAAAT
1 -A-AAAAAAT
1581 AAAAAAAT
1 AAAAAAAT
1589 TTCGTGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.17
8 21 0.58
9 2 0.06
10 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1561 original size:18 final size:16
Alignment explanation
Indices: 1541--1588 Score: 64
Period size: 14 Copynumber: 3.0 Consensus size: 16
1531 TCGTGTTTCA
1541 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
1557 --AAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
1571 AATAAAAAATAAAAAAAT
1 -A-AAAAAATAAAAAAAT
1589 TTCGTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.50
18 14 0.50
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:1566 original size:11 final size:11
Alignment explanation
Indices: 1541--1587 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
1531 TCGTGTTTCA
1541 AAAAAAATAA-
1 AAAAAAATAAT
*
1551 AAAAATAAAAAT
1 AAAAA-AATAAT
1563 AAAAAAATAAT
1 AAAAAAATAAT
1574 -AAAAAATAA-
1 AAAAAAATAAT
1583 AAAAA
1 AAAAA
1588 TTTCGTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 18 0.56
11 9 0.28
12 5 0.16
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:1586 original size:25 final size:24
Alignment explanation
Indices: 1540--1585 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1530 CTCGTGTTTC
1540 AAAAAAAATAAAAAAATAAAAATA
1 AAAAAAAATAAAAAAATAAAAATA
1564 AAAAAATAAT-AAAAAATAAAAA
1 AAAAAA-AATAAAAAAATAAAAA
1586 AATTTCGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAAAATAAAAAAATAAAAATA
Found at i:1671 original size:18 final size:18
Alignment explanation
Indices: 1650--2081 Score: 218
Period size: 18 Copynumber: 25.0 Consensus size: 18
1640 AAATTTTGTG
1650 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1668 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
1686 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
1704 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
1721 TTTTCGTGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
* *
1740 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
1758 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
1775 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
1793 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
1809 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
1827 TTCTCGCGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
**
1847 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
1865 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
*
1879 TTTT-GT-TTTT--TAAA
1 TTTTCGTGTTTTCAAAAA
1893 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
1907 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
1924 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
1941 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
1958 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
1977 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
1995 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
2014 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
2031 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
2047 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
2065 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
2082 AAAACTTTCG
Statistics
Matches: 317, Mismatches: 62, Indels: 71
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.00
12 5 0.02
13 4 0.01
14 9 0.03
15 1 0.00
16 21 0.07
17 108 0.34
18 115 0.36
19 39 0.12
20 14 0.04
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:1731 original size:17 final size:17
Alignment explanation
Indices: 1650--2081 Score: 206
Period size: 17 Copynumber: 25.0 Consensus size: 17
1640 AAATTTTGTG
1650 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
1668 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
1686 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
1704 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
1721 TTTTCGTGTTTAAAAAAAA
1 TTTTCGTGTTT--CAAAAA
* *
1740 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
1758 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
1775 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
1793 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
1809 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
1827 TTCTCGCGTTTAAAAAAAAA
1 TTTTCGTGTTT---CAAAAA
**
1847 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
1865 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
**
1879 TTTT-GT-TTT-TTAAA
1 TTTTCGTGTTTCAAAAA
1893 ---TCGTGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
* * *
1907 ATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
1924 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
* * *
1941 TTTCCCTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
**
1958 TTCCCGTGTTTCAAAAAAA
1 TTTTCGTGTTTC--AAAAA
* * *
1977 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* *
1995 ATTTCGTTTTTTCTAAAAA
1 TTTTCG-TGTTTC-AAAAA
*
2014 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
2031 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
*
2047 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* *
2065 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
2082 AAAACTTTCG
Statistics
Matches: 317, Mismatches: 67, Indels: 61
0.71 0.15 0.14
Matches are distributed among these distances:
11 1 0.00
12 5 0.02
13 4 0.01
14 9 0.03
15 1 0.00
16 15 0.05
17 129 0.41
18 96 0.30
19 40 0.13
20 17 0.05
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:14122 original size:52 final size:53
Alignment explanation
Indices: 14040--14141 Score: 188
Period size: 52 Copynumber: 1.9 Consensus size: 53
14030 AGGTAATTTC
*
14040 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTT
14093 AATTTCTGTTTTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
14142 CAGGCACGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 35 0.73
53 13 0.27
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (53 bp):
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTT
Found at i:14237 original size:51 final size:50
Alignment explanation
Indices: 14156--14257 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 50
14146 CACGCAGGTA
**
14156 TTTTAATTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
1 TTTTAATTTATGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTAAGCC
*
14206 TTTTAATTT-TGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTATGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTAAGCC
14257 T
1 T
14258 CAGACACGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
49 6 0.13
50 9 0.19
51 32 0.68
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (50 bp):
TTTTAATTTATGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:14493 original size:71 final size:70
Alignment explanation
Indices: 14206--14817 Score: 942
Period size: 71 Copynumber: 8.8 Consensus size: 70
14196 GAGTTAAGCC
**
14206 TTTT-AATTT-TGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTG
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTG
14269 AGGTA
66 AGGTA
*
14274 TTTTCAATTTCTGTTTTAAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTCAGACACGCTG
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTG
14337 AGGTA
66 AGGTA
*
14342 ATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTCAGGACACGCT
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GACACGCT
14405 GAGGTA
65 GAGGTA
*
14411 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCT
14476 GAGGTA
65 GAGGTA
* *
14482 ATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTG
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTG
14547 AGGTA
66 AGGTA
*
14552 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCT
14617 GAGGTA
65 GAGGTA
*
14623 -TTTCAATTT-TGTTTTCAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAGACACG-TG
1 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTG
14684 AGGTA
66 AGGTA
14689 TTTTCAATTTCTGTTTTCAATTCAAAATCAA-TCATATTGCGAGAAATGAGTTGAGCCTCAG-CA
1 TTTTCAATTTCTG--TT---TTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACA
14752 CGCTGAGGTA
61 CGCTGAGGTA
* **
14762 TTTTCAATTTTTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTCAA--TTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
14818 TTTAATTTTT
Statistics
Matches: 512, Mismatches: 13, Indels: 35
0.91 0.02 0.06
Matches are distributed among these distances:
66 7 0.01
67 16 0.03
68 100 0.20
69 85 0.17
70 118 0.23
71 121 0.24
72 17 0.03
73 43 0.08
75 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (70 bp):
TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTG
AGGTA
Found at i:14592 original size:141 final size:139
Alignment explanation
Indices: 14210--14817 Score: 964
Period size: 141 Copynumber: 4.3 Consensus size: 139
14200 TAAGCCTTTT
*
14210 AATTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTAT
1 AATTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTAT
*
14275 TTTCAATTTCTGTTTTAAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTCAGACACGCTGA
66 TTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTGA
14338 GGTAATTTC
131 GGTAATTTC
14347 AATTTCTGTTTTCAAAATCAACTCATATTGCGAG-A-TGAGTTGAGCCTCAGGACACGCTGAGGT
1 AATTT-TGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-GACACGCTGAGGT
*
14410 ATTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
64 ATTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGC
14475 TGAGGTAATTTC
128 TGAGGTAATTTC
* *
14487 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTA
1 AATTT-TGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTA
*
14552 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
65 TTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCT
14617 GAGGT-ATTTC
129 GAGGTAATTTC
14627 AATTTTGTTTTCAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAGACACG-TGAGGTAT
1 AATTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTAT
14690 TTTCAATTTCTGTTTTCAATTCAAAATCAA-TCATATTGCGAGAAATGAGTTGAGCCTCAG-CAC
66 TTTCAATTTCTG--TT---TTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACAC
*
14753 GCTGAGGTATTTTC
126 GCTGAGGTAATTTC
*
14767 AATTTTTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AA---TTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
14818 TTTAATTTTT
Statistics
Matches: 446, Mismatches: 8, Indels: 27
0.93 0.02 0.06
Matches are distributed among these distances:
136 14 0.03
137 77 0.17
138 49 0.11
139 54 0.12
140 71 0.16
141 112 0.25
142 25 0.06
143 31 0.07
144 13 0.03
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (139 bp):
AATTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTAT
TTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTGA
GGTAATTTC
Found at i:14836 original size:278 final size:277
Alignment explanation
Indices: 14212--14817 Score: 974
Period size: 278 Copynumber: 2.2 Consensus size: 277
14202 AGCCTTTTAA
*
14212 TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTT
1 TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAC-TTGAGGTATTT
14277 TCAATTTCTGTTTTAAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAGGTA
65 TCAATTTCTGTTTTAAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAGGTA
14342 ATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGGACACGCTGA
130 ATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGGACACGCTGA
14407 GGTATTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
195 GGTATTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
*
14472 CGTTGAGGTAATTTCAAT
260 CGCTGAGGTAATTTCAAT
* **
14490 TTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTATTT
1 TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAC-TTGAGGTATTT
* *
14555 TCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
65 TCAATTTCTGTTTTAAAAATCAACTCATATTGCGAG--ATGAGTTGAGCCTC-AGACACGCTGAG
14620 GT-ATTTCAATTT-TGTTTTCAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCA-GACACG
127 GTAATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGA-TGAGTTGAGCCTCAGGACACG
14682 -TGAGGTATTTTCAATTTCTGTTTTCAATTCAAAATCAA-TCATATTGCGAGAAATGAGTTGAGC
191 CTGAGGTATTTTCAATTTCTG--TT---TTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
*
14745 CTC-AG-CACGCTGAGGTATTTTCAATTT
251 CTCAAGACACGCTGAGGTAATTTCAA--T
14772 TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
14818 TTTAATTTTT
Statistics
Matches: 306, Mismatches: 11, Indels: 18
0.91 0.03 0.05
Matches are distributed among these distances:
278 116 0.38
279 35 0.11
280 57 0.19
281 15 0.05
282 72 0.24
283 11 0.04
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (277 bp):
TTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACTTGAGGTATTTT
CAATTTCTGTTTTAAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAGGTAA
TTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGGACACGCTGAG
GTATTTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
GCTGAGGTAATTTCAAT
Found at i:14932 original size:49 final size:50
Alignment explanation
Indices: 14773--15064 Score: 342
Period size: 49 Copynumber: 5.9 Consensus size: 50
14763 TTTCAATTTT
14773 TTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
1 TTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
14823 TTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--
1 --TTTG-TTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
*
14875 TCAT-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTTTAA
1 T-TTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
*
14924 TTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTT--
1 TTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
* * *
14972 TCTATTTTC--AAT----T--TTTTGCGAGAGGTGAGTTGAGCCTTTTGCAA
1 TTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AA
*
15016 TTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 TT-TGTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
15065 GGCTCACTGC
Statistics
Matches: 207, Mismatches: 11, Indels: 41
0.80 0.04 0.16
Matches are distributed among these distances:
40 25 0.12
42 1 0.00
44 1 0.00
45 6 0.03
46 3 0.01
47 5 0.02
48 41 0.20
49 46 0.22
50 6 0.03
51 1 0.00
52 4 0.02
53 6 0.03
54 39 0.19
55 23 0.11
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (50 bp):
TTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA
Found at i:14980 original size:97 final size:99
Alignment explanation
Indices: 14777--15064 Score: 409
Period size: 97 Copynumber: 2.9 Consensus size: 99
14767 AATTTTTTTG
14777 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTCAAAAATC
1 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAA--TTTG-TTTTCAAAAATC
*
14842 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCAT
63 AACTCATATTGCGAGAAGTGAGTTGAGCCTTTTTCAT
14879 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTTTAATTTGTTTTC-AAAATCAAC
1 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTGTTTTCAAAAATCAAC
14942 TCATATTGCGAGAAGTGAGTTGAGCCTTTTTC-T
66 TCATATTGCGAGAAGTGAGTTGAGCCTTTTTCAT
*
14975 ATTTTC--AAT----T--TTTTGCGAGAGGTGAGTTGAGCCTTTTGCAATTCTGTTTTCAAAAAA
1 -TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AATT-TGTTTTC-AAAAA
15032 TCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
61 TCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
15065 GGCTCACTGC
Statistics
Matches: 177, Mismatches: 2, Indels: 21
0.88 0.01 0.10
Matches are distributed among these distances:
89 20 0.11
90 5 0.03
91 1 0.01
92 4 0.02
93 7 0.04
95 40 0.23
96 1 0.01
97 45 0.25
98 5 0.03
99 4 0.02
101 7 0.04
102 38 0.21
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (99 bp):
TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTGTTTTCAAAAATCAAC
TCATATTGCGAGAAGTGAGTTGAGCCTTTTTCAT
Done.