Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1558
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: 24737
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:1571 original size:13 final size:13
Alignment explanation
Indices: 1553--1577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1543 CATATGCTTG
1553 TGTATCGATACAA
1 TGTATCGATACAA
1566 TGTATCGATACA
1 TGTATCGATACA
1578 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1597 original size:33 final size:33
Alignment explanation
Indices: 1531--1597 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1521 TACACACCCA
* *
1531 AATGTATCGATACATATGCTTGTGTATCGATAC
1 AATGTATCGATACATATGCATGTGTATCAATAC
* *
1564 AATGTATCGATACATGTTCAT-TGTATCCAATAC
1 AATGTATCGATACATATGCATGTGTAT-CAATAC
1597 A
1 A
1598 TGGACAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATATGCATGTGTATCAATAC
Found at i:1616 original size:20 final size:20
Alignment explanation
Indices: 1562--1619 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1552 GTGTATCGAT
*
1562 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
1581 TC-ATTGTATCCAATACATGG
1 ACAATTGTAT-CGATACATGG
1601 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
1620 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 6 0.19
20 17 0.55
21 7 0.23
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:5842 original size:20 final size:20
Alignment explanation
Indices: 5814--5864 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5804 CAGAAGAATT
* *
5814 TATCGATACATTCACACATG
1 TATCGATACATTCAAAAATG
* *
5834 TATCAATACATTGAAAAATG
1 TATCGATACATTCAAAAATG
5854 TATCGATACAT
1 TATCGATACAT
5865 CTGGGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:7632 original size:13 final size:13
Alignment explanation
Indices: 7614--7638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7604 ATTACTCAAA
7614 TGTATCGATACAT
1 TGTATCGATACAT
7627 TGTATCGATACA
1 TGTATCGATACA
7639 CTCATCTTTG
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):
TGTATCGATACAT
Found at i:13815 original size:23 final size:25
Alignment explanation
Indices: 13785--13831 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
13775 TTCTTTTCCA
13785 AAAAAAGAA-ACAA-AAAAAAAAAG
1 AAAAAAGAAGACAAGAAAAAAAAAG
*
13808 AAAAAAGAAGAGAAGAAAAAAAAA
1 AAAAAAGAAGACAAGAAAAAAAAA
13832 AGAAGGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAGACAAGAAAAAAAAAG
Found at i:14856 original size:34 final size:34
Alignment explanation
Indices: 14816--15301 Score: 475
Period size: 34 Copynumber: 14.9 Consensus size: 34
14806 ATCTCTTCTC
14816 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
14850 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
14884 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
14918 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * * * * *
14954 AAAGTCCACGACCCCGTGGAACCTTGTTCCTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
14988 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
*
15023 -AAGTCCACAACTCCGTAGCACC-----C-TTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
15050 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
*
15084 -AAGTCCACAACTCTGTGGCACC-----C-TTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
15111 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
* * *
15145 -AAGTCCACAACTCTGTGGCACCTTGTTCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
** *
15178 -AAGTCCATGACTCCGTGGCACC---TTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
15208 AAAGTCCACAACTCCGTGGCACC---TTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
15239 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
15273 AAAG-CCACAACTCTGTGGCA-CTTTTTCTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTT
15302 CTCAAAGCTC
Statistics
Matches: 392, Mismatches: 39, Indels: 44
0.83 0.08 0.09
Matches are distributed among these distances:
27 46 0.12
28 4 0.01
30 6 0.02
31 50 0.13
32 9 0.02
33 48 0.12
34 187 0.48
35 20 0.05
36 22 0.06
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:15047 original size:27 final size:27
Alignment explanation
Indices: 15017--15070 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
15007 CACTCTTTTT
*
15017 CCTTCTAAGTCCACAACTCCGTAGCAC
1 CCTTCTAAGCCCACAACTCCGTAGCAC
* *
15044 CCTTTTAAGCCCACAACTCCGTGGCAC
1 CCTTCTAAGCCCACAACTCCGTAGCAC
15071 TCTTTTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.41, G:0.13, T:0.22
Consensus pattern (27 bp):
CCTTCTAAGCCCACAACTCCGTAGCAC
Found at i:15063 original size:61 final size:61
Alignment explanation
Indices: 14993--15293 Score: 351
Period size: 61 Copynumber: 4.8 Consensus size: 61
14983 CTTTCAAAGT
*
14993 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTAGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* *
15054 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* *
15115 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCTTGTTCCTTTTAA
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAA
*
15180 GT
60 GC
** * *
15182 CCATGACTCCGTGGCAC-CTTCTT--TTCAAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC--CTTTT--AAGC
* * *
15244 CCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAG-CCACAACTCTGTGGCAC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCGTGGCAC
15294 TTTTTCTTCT
Statistics
Matches: 208, Mismatches: 19, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
58 1 0.00
60 5 0.02
61 106 0.51
62 24 0.12
63 1 0.00
64 40 0.19
65 3 0.01
66 5 0.02
67 23 0.11
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (61 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
Found at i:15083 original size:138 final size:133
Alignment explanation
Indices: 14816--15285 Score: 394
Period size: 138 Copynumber: 3.6 Consensus size: 133
14806 ATCTCTTCTC
* * * * ** *
14816 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGTCCACAACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCCT
* *
14881 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTT
66 TCTAAAGCCCACAACTCCGTAGCACC----TCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTT
14946 TCCCTTTT
126 TCCCTTTT
*
14954 AAAGTCCACGACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGTCCACAACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCAC-CTTTTTCC
*
15019 TTCT-AAGTCCACAACTCCGTAGCACC-CTTTT-AAGCCCACAACTCCGTGGCACTCTTTTT-CC
65 TTCTAAAGCCCACAACTCCGTAGCACCTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
15080 TTTT
130 TTTT
* * * * * *
15084 -AAGTCCACAACTCTGTGGCA-C-----CCTTT-TAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGTCCACAACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCAC-CTTTTTCC
* * * * **
15141 TTCT-AAGTCCACAACTCTGTGGCACCTTGTTCCTTTT-AAGTCCATGACTCCGTGGCAC-C---
65 TTCTAAAGCCCACAACTCCGTAGCACC----T-CTTTTAAAGCCCACAACTCCGTGGCACTCTTT
15200 TT--CTTTT
125 TTCCCTTTT
* * * * *
15207 CAAAGTCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT
1 -AAAGTCCACAACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCC
*
15269 TTTTAAAG-CCACAACTC
65 TTCTAAAGCCCACAACTC
15286 TGTGGCACTT
Statistics
Matches: 289, Mismatches: 29, Indels: 38
0.81 0.08 0.11
Matches are distributed among these distances:
122 52 0.18
123 10 0.03
124 2 0.01
125 19 0.07
126 1 0.00
127 1 0.00
128 47 0.16
129 39 0.13
130 6 0.02
131 28 0.10
133 5 0.02
138 69 0.24
139 10 0.03
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (133 bp):
AAAGTCCACAACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCCT
TCTAAAGCCCACAACTCCGTAGCACCTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
TTT
Found at i:15093 original size:95 final size:94
Alignment explanation
Indices: 14947--15303 Score: 315
Period size: 95 Copynumber: 3.8 Consensus size: 94
14937 CACTCTTTTT
* * * * *
14947 CCCTTTTAAAGTCCACGACCCCGTGGAACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACTC
1 CCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTT-TAAGTCCACAACTCCGTGGCAC-C
*
15012 TTTTTCCTTCTAAGTCCACAACTCCGTAGCA
64 TTTTTCCTTCTAAGTCCACAACTCCGTGGCA
* *
15043 CCCTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA-C-
1 CCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCT
* * *
15105 ----CCTTTTAAGCCCACAACTCTGTGGCA
65 TTTTCCTTCTAAGTCCACAACTCCGTGGCA
* * * * **
15131 CTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCTTGTTCCTTTTAAGTCCATGACTCCGTGG
1 C-C--CTT--TT-AAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGG
* *
15196 CACCTTCTT--TTCAAAGTCCACAACTCCGTGGCA
60 CACCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA
* * *
15229 CCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAG-CCACAACTCTGTGGCA
1 CC--CTTTT-AAAGCCCACAACTCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCA
15293 -CTTTTT-CTTCT
62 CCTTTTTCCTTCT
15304 CAAAGCTCAC
Statistics
Matches: 212, Mismatches: 33, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
88 23 0.11
89 1 0.00
91 2 0.01
93 3 0.01
94 33 0.16
95 104 0.49
96 20 0.09
97 5 0.02
98 21 0.10
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (94 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTT
TTTCCTTCTAAGTCCACAACTCCGTGGCA
Found at i:15348 original size:33 final size:33
Alignment explanation
Indices: 15299--15499 Score: 311
Period size: 33 Copynumber: 6.2 Consensus size: 33
15289 GGCACTTTTT
* *
15299 CTTCTC-AAAGCTCACACAAGTTGGTGGCAACC
1 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
*
15331 CTTTTCTAAAGCCCACACAAGTCGGTGGCAA-C
1 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
15363 CTTCTTCTAAAGCCCACACAAGTCGGTGGCAA-C
1 CTTC-TCTAAAGCCCACACAAGTCGGTGGCAACC
* *
15396 CTTCCTCTAAAACCCACACAAGTTGGTGGCAACC
1 CTT-CTCTAAAGCCCACACAAGTCGGTGGCAACC
15430 CTTCTC-AAAGCCCACACAAGTCGGTGGCAACC
1 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
15462 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
15495 CTTCT
1 CTTCT
15500 AAGCCCAATA
Statistics
Matches: 156, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
32 39 0.25
33 112 0.72
34 5 0.03
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.21
Consensus pattern (33 bp):
CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:15461 original size:98 final size:99
Alignment explanation
Indices: 15311--15494 Score: 336
Period size: 98 Copynumber: 1.9 Consensus size: 99
15301 TCTCAAAGCT
*
15311 CACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCTAAAG
1 CACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC-TCTAAAG
15375 CCCACACAAGTCGGTGGCAACCTTCCTCTAAAACC
65 CCCACACAAGTCGGTGGCAACCTTCCTCTAAAACC
15410 CACACAAGTTGGTGGCAACCCTTCTC-AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
1 CACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
15474 CCACACAAGTCGGTGGCAACC
66 CCACACAAGTCGGTGGCAACC
15495 CTTCTAAGCC
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
98 53 0.64
99 30 0.36
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.19
Consensus pattern (99 bp):
CACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
CCACACAAGTCGGTGGCAACCTTCCTCTAAAACC
Found at i:15470 original size:65 final size:65
Alignment explanation
Indices: 15299--15506 Score: 316
Period size: 65 Copynumber: 3.2 Consensus size: 65
15289 GGCACTTTTT
* * *
15299 CTTCTCAAAGCTCACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAA-C
1 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
* *
15363 CTTCTTCTAAAGCCCACACAAGTCGGTGGCAA-CCTTCCTCTAAAACCCACACAAGTTGGTGGCA
1 CTTC-TC-AAAGCCCACACAAGTCGGTGGCAACCCTT-CTCTAAAGCCCACACAAGTCGGTGGCA
15427 ACC
63 ACC
15430 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
15495 CTTCT--AAGCCCA
1 CTTCTCAAAGCCCA
15507 ATATAGCTGG
Statistics
Matches: 132, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
63 7 0.05
64 4 0.03
65 63 0.48
66 53 0.40
67 5 0.04
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (65 bp):
CTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:15590 original size:21 final size:20
Alignment explanation
Indices: 15566--15633 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
15556 ATGTAGCTGG
15566 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
15587 CCTTTAAGTC--CAATATAGCTA
1 CCTTGAA-TCAGCAAT-TGGC-A
15608 GCCTTGAATCAGCATATTGGCA
1 -CCTTGAATCAGCA-ATTGGCA
15630 CCTT
1 CCTT
15634 CATCTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:15606 original size:43 final size:43
Alignment explanation
Indices: 15545--16002 Score: 504
Period size: 43 Copynumber: 10.1 Consensus size: 43
15535 GCACCTTCAT
*
15545 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
15588 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
15635 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATGAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
15680 CTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCA----C
* *
15727 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATGAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
15772 TTTTATGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
15819 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
15864 CTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
15911 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
15956 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
15999 CTTT
1 CTTT
16003 TCCATCTTTA
Statistics
Matches: 352, Mismatches: 37, Indels: 52
0.80 0.08 0.12
Matches are distributed among these distances:
43 193 0.55
44 1 0.00
45 4 0.01
47 4 0.01
48 1 0.00
49 149 0.42
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:15661 original size:92 final size:92
Alignment explanation
Indices: 15494--16055 Score: 937
Period size: 92 Copynumber: 6.1 Consensus size: 92
15484 CGGTGGCAAC
*
15494 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
15559 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
15587 CCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
15652 AGCTGGCCTTGAATGAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
15679 CCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
15743 TAGCTGGCCTTGAATGAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
15771 CTTTTATGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
15836 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
15863 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
15928 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
15955 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
16020 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
16050 TCCTTT
1 -CCTTT
16056 TTCTCATCTT
Statistics
Matches: 443, Mismatches: 20, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
92 388 0.88
93 5 0.01
94 2 0.00
95 43 0.10
96 5 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:16026 original size:52 final size:55
Alignment explanation
Indices: 15956--16093 Score: 176
Period size: 52 Copynumber: 2.6 Consensus size: 55
15946 ACATTGGCAC
*
15956 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-AGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA-CATCCTTTTTCTCAT
* *
16008 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * *
16063 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
16094 ACATATTGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 37 0.51
53 3 0.04
54 5 0.07
55 28 0.38
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:16965 original size:33 final size:33
Alignment explanation
Indices: 16923--16987 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
16913 TCAACGATTT
16923 GTATCGATACATAAAGTGTTGTATCGATACAAC
1 GTATCGATACATAAAGTGTTGTATCGATACAAC
*** *
16956 GTATCGATACATATTTTTTTGTATCGATACAA
1 GTATCGATACATAAAGTGTTGTATCGATACAA
16988 TTTAAGCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (33 bp):
GTATCGATACATAAAGTGTTGTATCGATACAAC
Found at i:20311 original size:13 final size:13
Alignment explanation
Indices: 20293--20317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20283 ATTCATCATG
20293 TATCGATACAATT
1 TATCGATACAATT
20306 TATCGATACAAT
1 TATCGATACAAT
20318 GTGCCATGTA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATCGATACAATT
Found at i:20315 original size:33 final size:33
Alignment explanation
Indices: 20268--20333 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
20258 CCGTTTAAAG
20268 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
*
20301 CAATTTATCGATACAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
20334 TAAACAGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:20390 original size:20 final size:20
Alignment explanation
Indices: 20365--20422 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
20355 CTGCCAGTTT
*
20365 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
* *
20385 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGTA
20404 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
20423 TCGATACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 14 0.44
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:20424 original size:13 final size:13
Alignment explanation
Indices: 20406--20430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20396 ACAATGAACA
20406 TGTATCGATACAT
1 TGTATCGATACAT
20419 TGTATCGATACA
1 TGTATCGATACA
20431 AAGCATAATG
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):
TGTATCGATACAT
Done.