Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2430
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: 16395
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:1302 original size:33 final size:32
Alignment explanation
Indices: 1257--1806 Score: 345
Period size: 33 Copynumber: 17.6 Consensus size: 32
1247 GCTCTTCTCA
*
1257 AAGT-CACAACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1289 AAGTCCACGACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
** *
1322 AAGTCCATGACTCCATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCCTTTT
* *
1356 AAGTCCATAA-TTCGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
*
1382 ATGTCCACAACT-CGTGGCACAC----CCTTTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTCCTTTT
* * *
1410 ATGTCCACAA-TCTGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTCCTTTT
*
1442 AAGCCCACAACT-CGTGGCAACCTTGTTTCCTTTT
1 AAGTCCACAACTCCGTGGC-ACC-T-TTTCCTTTT
* ** *
1476 AAGTCTACAACTTTGTGGTACTCTTTTTCC-TTT
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCCTTTT
** *
1509 AAGTCCACAACTCTATGGTA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1536 AAGTCCACAATTCC-TGGCATCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
*
1567 AAGTCCACAACTTCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * *
1600 GAGTCCACAACTTCATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCCTTTT
*
1634 AAGTGCACAACTCCGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1661 AAGTCCACAACT--TTAGGCATCTTTTCC-TTT
1 AAGTCCACAACTCCGT-GGCACCTTTTCCTTTT
* * * * *
1691 ACGTCCACAACTCTGCGACACC-GTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
1722 AAATCCACAACTCC-AGGCACTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1753 AAGTCCACGACTCCGGGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT-CCTTTT
*
1787 AAG-CCTACACCTCCGTGGCA
1 AAGTCC-ACAACTCCGTGGCA
1807 TCCATTTATC
Statistics
Matches: 420, Mismatches: 56, Indels: 82
0.75 0.10 0.15
Matches are distributed among these distances:
25 1 0.00
26 31 0.07
27 36 0.09
28 23 0.05
29 1 0.00
30 22 0.05
31 59 0.14
32 37 0.09
33 111 0.26
34 88 0.21
35 11 0.03
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:1379 original size:26 final size:27
Alignment explanation
Indices: 1350--1419 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
1340 CACTCTTTTT
* * *
1350 CCTTTTAAGTCCATAATTCGTGG-CAC
1 CCTTTTATGTCCACAACTCGTGGACAC
1376 CCTTTTATGTCCACAACTCGTGGCACAC
1 CCTTTTATGTCCACAACTCGTGG-ACAC
1404 CCTTTTATGTCCACAA
1 CCTTTTATGTCCACAA
1420 TCTGTGGCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 20 0.51
28 19 0.49
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (27 bp):
CCTTTTATGTCCACAACTCGTGGACAC
Found at i:1413 original size:28 final size:27
Alignment explanation
Indices: 1350--1428 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 27
1340 CACTCTTTTT
* *
1350 CCTTTTAAGTCCATAATTCGTGG--CAC
1 CCTTTTATGTCCACAA-TCGTGGCACAC
1376 CCTTTTATGTCCACAACTCGTGGCACAC
1 CCTTTTATGTCCACAA-TCGTGGCACAC
1404 CCTTTTATGTCCACAATCTGTGGCA
1 CCTTTTATGTCCACAATC-GTGGCA
1429 TCTTTTTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
26 20 0.43
27 2 0.04
28 25 0.53
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (27 bp):
CCTTTTATGTCCACAATCGTGGCACAC
Found at i:1517 original size:67 final size:65
Alignment explanation
Indices: 1257--1789 Score: 313
Period size: 67 Copynumber: 8.6 Consensus size: 65
1247 GCTCTTCTCA
* * * * * *
1257 AAGT-CACAACTCCATGGCACCTTG-TTCCTTTTAAGTCCACGACTCCATGGCACCTTGTTCCTT
1 AAGTCCACAACT-CGTGGCACCTTGTTTCCTTTTAAGTCCAC-AATTCGTGGCATCTTTTTCCTT
1320 TT
64 TT
** * *
1322 AAGTCCATGACTCCATGGCACTCTT-TTTCCTTTTAAGTCCATAATTCGTGGCA-C-----CCTT
1 AAGTCCACAACT-CGTGGCAC-CTTGTTTCCTTTTAAGTCCACAATTCGTGGCATCTTTTTCCTT
1380 TT
64 TT
* *
1382 ATGTCCACAACTCGTGGCACAC------CCTTTTATGTCCACAA-TCTGTGGCATCTTTTTCCTT
1 AAGTCCACAACTCGTGGCAC-CTTGTTTCCTTTTAAGTCCACAATTC-GTGGCATCTTTTTCCTT
1440 TT
64 TT
* * * *
1442 AAGCCCACAACTCGTGGCAACCTTGTTTCCTTTTAAGTCTACAACTTTGTGGTACTCTTTTTCC-
1 AAGTCCACAACTCGTGGC-ACCTTGTTTCCTTTTAAGTCCACAA-TTCGTGGCA-TCTTTTTCCT
1506 TTT
63 TTT
* ** *
1509 AAGTCCACAACTC-T---A--TGGTACCCTTTTAAGTCCACAATTCCTGGCATC-TTTTCCTTTT
1 AAGTCCACAACTCGTGGCACCTTGTTTCCTTTTAAGTCCACAATTCGTGGCATCTTTTTCCTTTT
* *
1567 AAGTCCACAACTTCGTGGCACCTTG-TTCCTTTTGAGTCCACAACTTCATGGCACTCTTTTTCCT
1 AAGTCCACAAC-TCGTGGCACCTTGTTTCCTTTTAAGTCCACAA-TTCGTGGCA-TCTTTTTCCT
1631 TTT
63 TTT
*
1634 AAGTGCACAACTCCGTGGCA-C------CCTTTTAAGTCCACAACTT--TAGGCATC-TTTTCC-
1 AAGTCCACAACT-CGTGGCACCTTGTTTCCTTTTAAGTCCACAA-TTCGT-GGCATCTTTTTCCT
1688 TTT
63 TTT
* * * ** *
1691 ACGTCCACAACTC-TGCGACACC--G-TTCCTTTTAAATCCACAACTCCAGGCA-CTTTTTCTTT
1 AAGTCCACAACTCGTG-G-CACCTTGTTTCCTTTTAAGTCCACAATTCGTGGCATCTTTTTCCTT
1751 TT
64 TT
* * *
1753 AAGTCCACGACTCCGGGGCACCCTT-TTCCCTTTTAAG
1 AAGTCCACAACT-CGTGGCA-CCTTGTTTCCTTTTAAG
1790 CCTACACCTC
Statistics
Matches: 374, Mismatches: 45, Indels: 98
0.72 0.09 0.19
Matches are distributed among these distances:
53 2 0.01
54 20 0.05
55 3 0.01
56 2 0.01
57 21 0.06
58 23 0.06
59 19 0.05
60 63 0.17
61 44 0.12
62 16 0.04
63 5 0.01
64 16 0.04
65 24 0.06
66 41 0.11
67 65 0.17
68 10 0.03
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.36
Consensus pattern (65 bp):
AAGTCCACAACTCGTGGCACCTTGTTTCCTTTTAAGTCCACAATTCGTGGCATCTTTTTCCTTTT
Found at i:1643 original size:125 final size:123
Alignment explanation
Indices: 1283--1779 Score: 445
Period size: 125 Copynumber: 4.0 Consensus size: 123
1273 GCACCTTGTT
* * * ** * *
1283 CCTTTTAAGTCCACGACTCCATGGCACCTTGTTCCTTTTAAGTCCATGACTCCATGGCACTCTTT
1 CCTTTTAAGTCCAC-AATTC-TGGCATCTT-TTCCTTTTAAGTCCACAACT-CGTGGCAC-CTTG
* * * *
1348 TTCCTTTTAAGTCCATAA-TTCGTGGCA--C-----CCTTTTATGTCCACAACT-CGTGGCACAC
61 TTCCTTTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGG--CAC
* * *
1404 CCTTTTATGTCCACAATCTGTGGCATCTTTTTCCTTTTAAGCCCACAACTCGTGGCAACCTTGTT
1 CCTTTTAAGTCCACAAT-TCTGGCATC-TTTTCCTTTTAAGTCCACAACTCGTGGC-ACCTTG-T
* ** * * *
1469 TCCTTTTAAGTCTACAACTTTGTGGTACTCTTTTTCC-TTTAAGTCCACAACTCTATGGTAC
62 TCCTTTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1530 CCTTTTAAGTCCACAATTCCTGGCATCTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTTGTTC
1 CCTTTTAAGTCCACAATT-CTGGCATCTTTTCCTTTTAAGTCCACAAC-TCGTGGCACCTTGTTC
* * *
1595 CTTTTGAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTGCACAACTCCGTGGCAC
64 CTTTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
*
1655 CCTTTTAAGTCCACAACTT-TAGGCATCTTTTCC-TTTACGTCCACAACTC-TGCGACACC--GT
1 CCTTTTAAGTCCACAA-TTCT-GGCATCTTTTCCTTTTAAGTCCACAACTCGTG-G-CACCTTGT
* * * * **
1715 TCCTTTTAAATCCACAACTCCA-GGCA--CTTTTTCTTTTTAAGTCCACGACTCCGGGGCAC
62 TCCTTTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1774 CCTTTT
1 CCTTTT
1780 CCCTTTTAAG
Statistics
Matches: 318, Mismatches: 38, Indels: 42
0.80 0.10 0.11
Matches are distributed among these distances:
119 43 0.14
120 43 0.14
121 26 0.08
122 23 0.07
123 4 0.01
124 51 0.16
125 75 0.24
126 34 0.11
127 14 0.04
128 5 0.02
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (123 bp):
CCTTTTAAGTCCACAATTCTGGCATCTTTTCCTTTTAAGTCCACAACTCGTGGCACCTTGTTCCT
TTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
Found at i:1913 original size:44 final size:42
Alignment explanation
Indices: 1825--1918 Score: 125
Period size: 44 Copynumber: 2.2 Consensus size: 42
1815 TCTTTTTTCT
* **
1825 CACCTTTAAGTCCAATATCGCTGGCCTGAATCAGCACATTGA
1 CACCTTTAAATCCAATATCAATGGCCTGAATCAGCACATTGA
* *
1867 CACCTTTAAATCCAATATCAATGGGCATTGAATCAGCAGATTGA
1 CACCTTTAAATCCAATATCAAT-GGC-CTGAATCAGCACATTGA
1911 CACCTTTA
1 CACCTTTA
1919 CCATCTTGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
42 19 0.42
43 3 0.07
44 23 0.51
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
CACCTTTAAATCCAATATCAATGGCCTGAATCAGCACATTGA
Found at i:1999 original size:49 final size:47
Alignment explanation
Indices: 1828--2944 Score: 779
Period size: 49 Copynumber: 23.7 Consensus size: 47
1818 TTTTTCTCAC
* *
1828 CTTTAAGTCCAATATCGCTGGCC-TGAATCAGCACATTGACA-C---
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* ** * * *
1870 CTTTAAATCCAATATCAATGGGCATTGAATCAGCAGATTGACACCTTT
1 CTTTAAGTCCAATATCGCT-GGCCTTGAATCAGCATATTGGCACCTTT
* * * *
1918 ACCATCTTGACTCCAATATCGTTGGCCTTGAATCAGCATAGTTGGCATCTTGT
1 --C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TTGGCACCTT-T
* * * * *
1971 CTTTAAGACCAATGTCGCTGGCTTTGAATCAGCACATTAGCA-C--T
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* * * *
2015 -ATTAAGTCC-ATATCTCTAGCCTTGAATCAACATATTGGCACCTTGT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
* * * * *
2061 CTTTAAGTCCAATGTCGTTAGCCTTGAATAAGCA-CTTGGCA-C---
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* *
2103 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGACACCTTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* * **
2150 ACCATCTTGAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTGT
1 --C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
* * *
2202 CTTTAAGACCAATGTGCGGCTGGCCTTGAATCAGCACATTGGCA-C---
1 CTTTAAGTCCAATAT-C-GCTGGCCTTGAATCAGCATATTGGCACCTTT
2247 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
* * *
2295 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACC-TT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
** *
2341 -TAGAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* *
2387 ACCATCATGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
1 --C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
* * * *
2439 CTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-----
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* *
2481 ---TAAG-CCAATATCGCTGGCC-TGAATCAACATATTGGCACTTTAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
* *
2524 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-----
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* *
2566 ---GAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T
* ** * * * *
2612 CTTTAAGACTGATGTCGTTGGCCTTGAATCAGCACATTGACACCTTAACCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-----T
* * * * * * *
2664 TTTTAAGTCCAATGTCGCTGGGCTTGAATAAGGACATTGGCATC-TT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
*
2710 CATCTTAAGGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 C-T-TTAA-GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T
** * *
2762 CTTTAAAACCATTATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T
* * * * *
2811 CTTTAAGTCCGACATCGTTGGCCTTGAATTAGCATATTGGCATCTTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
* ** * *
2858 AACATTCCTAAG-CCTAATGTCGCTGGCCTTGTCTCAGCACATTGGCA-TTCTT
1 --C-TT--TAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TT
* * * *
2910 CTTCAAGTCTAATGTCGCTGGCCATGAATCAGCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
2945 GTTGTCATTC
Statistics
Matches: 855, Mismatches: 139, Indels: 157
0.74 0.12 0.14
Matches are distributed among these distances:
37 16 0.02
38 14 0.02
39 40 0.05
42 70 0.08
43 41 0.05
44 21 0.02
45 51 0.06
46 10 0.01
47 55 0.06
48 133 0.16
49 174 0.20
50 35 0.04
51 102 0.12
52 92 0.11
53 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (47 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
Found at i:2256 original size:93 final size:92
Alignment explanation
Indices: 2159--2944 Score: 425
Period size: 101 Copynumber: 8.3 Consensus size: 92
2149 TACCATCTTG
* ** *
2159 AGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTGTCTTTAAGACCAATGTGCGGCTG
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGT-C-GCTA
2224 GCCTTGAATCAGCACATTGGCACCTTT-A
64 GCCTTGAATCAGCACATTGGCACCTTTAA
*
2252 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTAGC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGC
2317 CTTGAATCAGCACATTGGCACCTTTAGA
66 CTTGAATCAGCACATTGGCACCTTTA-A
* * * * *
2345 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTT-TACCATCATGAGTCCAATATCGC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--C-T-TTAAGACCAATGTCGC
* * *
2409 TGGCCTTGAATCAGCATATTGGCACCTTGTCTCTA
62 TAGCCTTGAATCAGCACATTGGCACC-T-T-T-AA
* * * * *
2444 AGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---------TAAG-CCAATATCGCTGGC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGC
* *
2499 C-TGAATCAACATATTGGCA-CTTTATCTTTA
66 CTTGAATCAGCACATTGGCACCTTTA-----A
* * * * *
2529 AGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA----G-----AAGCCCAATATCGCTGGC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGC
* *
2585 CTTGAATCAGCATATTGGCACCTTCATCTTTA
66 CTTGAATCAGCACATTGGCA-C--C-T-TTAA
* ** * * * * * * *
2617 AGACTGATGTCGTTGGCCTTGAATCAGCACATTGACACCTTAACCATTTTTAAGTCCAATGTCGC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT----GTCTTTAAGACCAATGTCGC
* * * *
2682 TGGGCTTGAATAAGGACATTGGCATCTTCATCTTAA
62 TAGCCTTGAATCAGCACATTGGCA-C--C-T-TTAA
* * * * * * *
2718 GGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAAACCATTATCGCTGG
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTCGCTAG
* *
2783 CCTTGAATCAGCATATTGGCACCTTCACCTTTA
65 CCTTGAATCAGCACATTGGCACC-T----TTAA
* * * * *
2816 AGTCCGACATCGTTGGCCTTGAATTAGCATATTGGCATCTT-TAACATTCCTAAG-CCTAATGTC
1 AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--C-TT--TAAGACC-AATGTC
* ** * *
2879 GCTGGCCTTGTCTCAGCACATTGGCATTCTTCTTCA
60 GCTAGCCTTGAATCAGCACATTGGCA--CCT-TTAA
* * *
2915 AGTCTAATGTCGCTGGCCATGAATCAGCAT
1 AGTCCAATATCGCTGGCCTTGAATCAGCAT
2945 GTTGTCATTC
Statistics
Matches: 570, Mismatches: 74, Indels: 92
0.77 0.10 0.12
Matches are distributed among these distances:
81 1 0.00
82 1 0.00
83 1 0.00
84 1 0.00
85 57 0.10
86 30 0.05
87 20 0.04
88 33 0.06
91 31 0.05
92 3 0.01
93 97 0.17
94 1 0.00
95 3 0.01
96 38 0.07
97 4 0.01
98 75 0.13
99 64 0.11
100 2 0.00
101 104 0.18
102 3 0.01
103 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (92 bp):
AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGC
CTTGAATCAGCACATTGGCACCTTTAA
Found at i:2291 original size:144 final size:140
Alignment explanation
Indices: 1825--2943 Score: 644
Period size: 144 Copynumber: 8.0 Consensus size: 140
1815 TCTTTTTTCT
* * *
1825 CACCTTTAAGTCCAATATCGCTGGCC-TGAATCAGCACATTGACA-C----CT-TTAAATCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTAAGTCCAAT
** * * * * * * * *
1883 ATCAATGGGCATTGAATCAGCAGATTGACACCTT-TACCATCTTGACTCCAATATCGTTGGCCTT
66 ATCGCT-AGCCTTGAATCAGCACATTGGCACCTTGT--C-T-TTAAGTCCAATGTCGCTGGCCTT
*
1947 GAATCAGCATAGTTGG
126 GAATCAGCACA-TTGG
* * * * * *
1963 CATCTTGTCTTTAAGACCAATGTCGCTGGCTTTGAATCAGCACATTAGCA------CTATTAAGT
1 CA-C----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTAAGT
* * * * *
2022 CC-ATATCTCTAGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGTCCAATGTCGTTAGCCTT
61 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTGTCTTTAAGTCCAATGTCGCTGGCCTT
*
2086 GAATAAGCAC-TTGG
126 GAATCAGCACATTGG
* * *
2100 CACCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGACACCTT-TACCATCTTGAGTCC
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--C-TCTTAAGTCC
* ** *
2164 AATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTGTCTTTAAGACCAATGTGCGGCTGGCCTT
63 AATATCGCTAGCCTTGAATCAGCACATTGGCACCTTGTCTTTAAGTCCAATGT-C-GCTGGCCTT
2229 GAATCAGCACATTGG
126 GAATCAGCACATTGG
2244 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCT-TTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTAAGTCCAAT
* ** *
2308 GTCGCTAGCCTTGAATCAGCACATTGGCACC-T-T-TAGAAGTCCAATATCGCTGGCCTTGAATC
66 ATCGCTAGCCTTGAATCAGCACATTGGCACCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATC
* *
2370 AGCATATTGA
131 AGCACATTGG
2380 CACCTTTACCATCATGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTC-TA
1 CACC-TT----T-A--AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTA
* * * *
2444 AGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---------TAAG-CCAATATCGCTGGC
58 AGTCCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTGTCTTTAAGTCCAATGTCGCTGGC
* *
2499 C-TGAATCAACATATTGG
123 CTTGAATCAGCACATTGG
* * *
2516 CACTTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA----G------AAGC
1 CAC-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTAAGT
* * * * ** *
2571 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACTGATGTCGTTGGCCT
61 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTT-GTCTTTAAGTCCAATGTCGCTGGCCT
*
2636 TGAATCAGCACATTGACAC
125 TGAATCAGCACATTG---G
* * * * * *
2655 CTTAACCATTTTTAAGTCCAATGTCGCTGGGCTTGAATAAGGACATTGGCATC-T-TCATCTTAA
1 C---ACC---TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTC-TCTTAA
* * * * ** * *
2718 GGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAAACCATTATCGCTGG
59 -GTCCAATATCGCTAGCCTTGAATCAGCACATTGGCACC-TTGTCTTTAAGTCCAATGTCGCTGG
*
2783 CCTTGAATCAGCATATTGG
122 CCTTGAATCAGCACATTGG
* * * * * *
2802 CACCTTCACCTTTAAGTCCGACATCGTTGGCCTTGAATTAGCATATTGGCATCTT-TAACATTCC
1 ------CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--C--TCT
* * ** * * *
2866 TAAG-CCTAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCGC
56 TAAGTCC-AATATCGCTAGCCTTGAATCAGCACATTGGCACCTT-GTCTTTAAGTCCAATGTCGC
*
2928 TGGCCATGAATCAGCA
119 TGGCCTTGAATCAGCA
2944 TGTTGTCATT
Statistics
Matches: 797, Mismatches: 104, Indels: 150
0.76 0.10 0.14
Matches are distributed among these distances:
124 35 0.04
129 1 0.00
132 35 0.04
133 35 0.04
134 4 0.01
135 12 0.02
136 58 0.07
137 25 0.03
138 15 0.02
139 31 0.04
140 48 0.06
141 87 0.11
142 27 0.03
143 46 0.06
144 156 0.20
145 1 0.00
147 37 0.05
148 30 0.04
149 4 0.01
150 102 0.13
151 7 0.01
153 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (140 bp):
CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTTAAGTCCAAT
ATCGCTAGCCTTGAATCAGCACATTGGCACCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATC
AGCACATTGG
Found at i:2400 original size:237 final size:234
Alignment explanation
Indices: 1828--2943 Score: 1189
Period size: 237 Copynumber: 4.8 Consensus size: 234
1818 TTTTTCTCAC
* * **
1828 CTTTAAGTCCAATATCGCTGGCC-TGAATCAGCACATTGACACCTTTAAA-TCCAATATCAATGG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAAGTCCAATATCGCT-G
* * * *
1891 GCATTGAATCAGCAGATTGACACCTTTACCATCTTGACTCCAATATCGTTGGCCTTGAATCAGCA
65 GCCTTGAATCAGCATATTGACACCTTTACCATCTTGAGTCCAATATCGCTGGCCTTGAATCAGCA
* * *
1956 TAGTTGGCATCTTGTCTTTAAGACCAATGTCGCTGGCTTTGAATCAGCACATTAGCACTATTAAG
130 TA-TTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTATTAAG
* * *
2021 TCC-ATATCTCTAGCCTTGAATCAACATATTGGCACCTTGT
194 TCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTAT
* * *
2061 CTTTAAGTCCAATGTCGTTAGCCTTGAATAAGCAC-TTGGCACCTTT-AAGTCCAATATCGCTGG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAAGTCCAATATCGCTGG
* *
2124 CCTTGAATTAGCATATTGACACCTTTACCATCTTGAGTCCAATATCGCTAGCCTTGAATCAGCAT
66 CCTTGAATCAGCATATTGACACCTTTACCATCTTGAGTCCAATATCGCTGGCCTTGAATCAGCAT
**
2189 ATTGGTGCCTTGTCTTTAAGACCAATGTGCGGCTGGCCTTGAATCAGCACATTGGCACCT-TTAA
131 ATTGGCACCTTGTCTTTAAGACCAATGT-C-GCTGGCCTTGAATCAGCACATTGGCA-CTATTAA
* *
2253 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
193 GTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTAT
*
2295 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAGAAGTCCAATATCGCTG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA-AAGTCCAATATCGCTG
*
2360 GCCTTGAATCAGCATATTGACACCTTTACCATCATGAGTCCAATATCGCTGGCCTTGAATCAGCA
65 GCCTTGAATCAGCATATTGACACCTTTACCATCTTGAGTCCAATATCGCTGGCCTTGAATCAGCA
*
2425 TATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG--C-A-TAAG-
130 TATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTATTAAGT
*
2485 CCAATATCGCTGGCC-TGAATCAACATATTGGCACTTTAT
195 CCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTAT
* * * *
2524 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-----GAAGCCCAATATCGCTGG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAAGTCCAATATCGCTGG
* * * ** * *
2584 CCTTGAATCAGCATATTGGCACC-TT--CATCTTTAAGACTGATGTCGTTGGCCTTGAATCAGCA
66 CCTTGAATCAGCATATTGACACCTTTACCATC-TTGAGTCCAATATCGCTGGCCTTGAATCAGCA
* * * * * * * *
2646 CATTGACACCTTAACCATTTTTAAGTCCAATGTCGCTGGGCTTGAATAAGGACATTGGCATCTTC
130 TATTGGCACCTT----GTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-T-
* *
2711 ATCTTAAGGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
188 A--TTAA-GTCCAATATCGCTGGCCTTGAATCAACATATTGGCACC-TTAT
** * * * * * *
2762 CTTTAAAACCATTATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCGACATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T----TTAAAGTCCAATATC
* * * * * * * * **
2827 GTTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAG-CCTAATGTCGCTGGCCTTGTC
61 GCTGGCCTTGAATCAGCATATTGACACCTTTACCA-TCTTGAGTCC-AATATCGCTGGCCTTGAA
* * * * * *
2891 TCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCA
124 TCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCA
2944 TGTTGTCATT
Statistics
Matches: 758, Mismatches: 82, Indels: 73
0.83 0.09 0.08
Matches are distributed among these distances:
220 4 0.01
221 35 0.05
222 2 0.00
223 38 0.05
225 35 0.05
228 1 0.00
229 60 0.08
230 15 0.02
231 29 0.04
232 66 0.09
233 72 0.09
234 82 0.11
235 36 0.05
236 15 0.02
237 122 0.16
238 43 0.06
246 29 0.04
248 34 0.04
249 4 0.01
250 1 0.00
251 33 0.04
252 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (234 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAAGTCCAATATCGCTGG
CCTTGAATCAGCATATTGACACCTTTACCATCTTGAGTCCAATATCGCTGGCCTTGAATCAGCAT
ATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTATTAAGTC
CAATATCGCTGGCCTTGAATCAACATATTGGCACCTTAT
Found at i:2543 original size:85 final size:87
Alignment explanation
Indices: 2399--2650 Score: 391
Period size: 85 Copynumber: 2.9 Consensus size: 87
2389 CATCATGAGT
* * *
2399 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTATCTTTAAGACCAATGTCGCTGGCCTT
*
2464 GAATCAGCACATTGGCATAAG-
66 GAATCAGCACATTGGCAGAAGC
*
2485 CCAATATCGCTGGCC-TGAATCAACATATTGGCACTTTATCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTATCTTTAAGACCAATGTCGCTGGCCTT
*
2549 GAATCAGCATATTGGCAGAAGC
66 GAATCAGCACATTGGCAGAAGC
* ** *
2571 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACTGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTATCTTTAAGACCAATGTCGCTGGCCT
2636 TGAATCAGCACATTG
65 TGAATCAGCACATTG
2651 ACACCTTAAC
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
85 64 0.42
86 30 0.20
87 17 0.11
88 40 0.26
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTATCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCAGAAGC
Found at i:2879 original size:199 final size:197
Alignment explanation
Indices: 2575--2944 Score: 485
Period size: 199 Copynumber: 1.9 Consensus size: 197
2565 AGAAGCCCAA
* * **
2575 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACTGATGTCGTTGGCCTTGAA
1 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCGACATCGTTGGCCTTGAA
** * *
2640 TCAGCACATTGACACCTTAACCATTTTTAAGTCCAATGTCGCTGGGCTTGAATAAGGACATTGGC
66 TCAGCACATTGACACCTTAACCATTCCTAAGTCCAATGTCGCTGGCCTTGAATAAGCACATTGGC
* * *
2705 A-TCTTCATCTTAAGGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAA
131 ATTCTTC-T-TCAA-GTCCAATATCGCTGGCCATGAATCAGCATATTGGCACCTTTATCTTTAAA
2769 ACCAT
193 ACCAT
*
2774 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCGACATCGTTGGCCTTGAA
1 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCGACATCGTTGGCCTTGAA
* * * * ** *
2839 TTAGCATATTGGCATCTTTAA-CATTCCTAAG-CCTAATGTCGCTGGCCTTGTCTCAGCACATTG
66 TCAGCACATTGACA-CCTTAACCATTCCTAAGTCC-AATGTCGCTGGCCTTGAATAAGCACATTG
* *
2902 GCATTCTTCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCAT
129 GCATTCTTCTTCAAGTCCAATATCGCTGGCCATGAATCAGCAT
2945 GTTGTCATTC
Statistics
Matches: 147, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
197 25 0.17
198 5 0.03
199 107 0.73
200 10 0.07
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (197 bp):
TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCGACATCGTTGGCCTTGAA
TCAGCACATTGACACCTTAACCATTCCTAAGTCCAATGTCGCTGGCCTTGAATAAGCACATTGGC
ATTCTTCTTCAAGTCCAATATCGCTGGCCATGAATCAGCATATTGGCACCTTTATCTTTAAAACC
AT
Found at i:2881 original size:150 final size:146
Alignment explanation
Indices: 2571--2943 Score: 367
Period size: 150 Copynumber: 2.5 Consensus size: 146
2561 TGGCAGAAGC
* * * *
2571 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACTGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACTCATATCGCTGGCCT
** * *
2636 TGAATCAGCACATTGACACCTTAACCATTTTTAAGTCCAATGTCGCTGGGCTTGAATAAGGACAT
66 TGAATCAGCACATTGACACCTTAACC--TTTTAAGTCCAACATCGCTGGCCTTGAATAAGCACAT
*
2701 TGGCATCTTCATCTTAAGG
129 TGGCATCTTCATCCTAA-G
* *
2720 TCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAAAC-CATTATCGCTGGC
1 -CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACTCA-TATCGCTGGC
* * * * * * *
2784 CTTGAATCAGCATATTGGCACCTTCACC-TTTAAGTCCGACATCGTTGGCCTTGAATTAGCATAT
64 CTTGAATCAGCACATTGACACCTTAACCTTTTAAGTCCAACATCGCTGGCCTTGAATAAGCACAT
2848 TGGCATCTTTAACATTCCTAAG
129 TGGCATC-TT--CA-TCCTAAG
* ** * * * ** * *
2870 CCTAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCGCTGGCC
1 CC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACTCATATCGCTGGCC
*
2933 ATGAATCAGCA
65 TTGAATCAGCA
2944 TGTTGTCATT
Statistics
Matches: 185, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
147 35 0.19
148 31 0.17
149 4 0.02
150 110 0.59
151 5 0.03
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (146 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACTCATATCGCTGGCCT
TGAATCAGCACATTGACACCTTAACCTTTTAAGTCCAACATCGCTGGCCTTGAATAAGCACATTG
GCATCTTCATCCTAAG
Found at i:4718 original size:28 final size:28
Alignment explanation
Indices: 4673--5768 Score: 1194
Period size: 28 Copynumber: 38.6 Consensus size: 28
4663 TTGAAAGGGT
* *
4673 ATGCCATTGACTTGTGGGTTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
4701 ATACCACTGACTTATGGGCTTTG-AAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
4728 ATGCCACTGACTTGTAGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
4756 ATGCCACTAACTTAT-GGCTTTGAAAT-
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
4782 AGTGCTACTGACTTGTGGGCTTTTAAATG
1 A-TGCCACTGACTTGTGGGCTTTGAAATG
* *
4811 TTGCCACTGACTTGTGGACTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
4839 ATGCCACTGACTTGTGGGCATTAAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * * * * *
4867 ATACTACTAACCTGTAGGCTTTGAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
4895 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
4923 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* **
4951 ATGCCACTAACTCATGGGCTTTGAAATGG
1 ATGCCACTGACTTGTGGGCTTTGAAAT-G
*
4980 TTGCCACTGACTTGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
5008 CTGCCACTGACTTGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
5036 ATGCCACTGA-TTCGTGGGCTTTGAAATG
1 ATGCCACTGACTT-GTGGGCTTTGAAATG
*
5064 ATGCCACTGACTCGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* ** *
5092 ATGCCACTAACTCATGGGCTTTGAAAAG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
5120 ACGCCACTGACTTATGGGTTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5148 GTGCCACTGACTTGTGAGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
5176 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5204 ATGCCGCTGACTTGTGGGCTTTGTAAT-
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5231 AGTGCCACTAACTTGTGGGGTTTGAAATG
1 A-TGCCACTGACTTGTGGGCTTTGAAATG
* *
5260 ATGCCACTGACTTGTGGGCTTTAAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
** * * *
5288 ATGCTTCTAACTTGTTGGCTTTGAAAGG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
5316 ATGACACTGACTTGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5344 GTGCCACTGACTTATGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
5372 GTGCCACTGAGTTGTGGGCTTTGAAAAG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
*
5400 ATGCCATTGACTTGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
5428 ATGCCACTGACTTGTGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
5456 ATGCCCCTGACTTTTAGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* * *
5484 ATGTCACTGATTTATGGGCTTTGAAATG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5512 ATGCCATTGACTTGTGGGCTTTGAAAAG
1 ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5540 AGTTGCCACCGACTTGTGTGGACTTTGAAAAG
1 A--TGCCACTGACTTGTG-GG-CTTTGAAATG
* ** *
5572 AGTGCCACTAACTTGTAAGCTTTGAAAAGG
1 A-TGCCACTGACTTGTGGGCTTTG-AAATG
* * * **
5602 GTGCCACTAACTTGTAGGCTTTAGAAGGG
1 ATGCCACTGACTTGTGGGCTTT-GAAATG
* *
5631 AATGCCATTGACTTGTGGGCTTTGAAAAG
1 -ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5660 AGTTGCCACCGACTTGTGTGGACTTTGAAAAG
1 A--TGCCACTGACTTGTG-GG-CTTTGAAATG
* *
5692 AGTGCCACTGACTTGTGAGCTTTGAAAAGG
1 A-TGCCACTGACTTGTGGGCTTTG-AAATG
* * **
5722 GTGCCACTAACTTGTGGGCTTTAGAAGGG
1 ATGCCACTGACTTGTGGGCTTT-GAAATG
*
5751 AATGCCATTGACTTGTGG
1 -ATGCCACTGACTTGTGG
5769 ACTTAAAAAG
Statistics
Matches: 906, Mismatches: 139, Indels: 44
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.00
27 48 0.05
28 648 0.72
29 87 0.10
30 70 0.08
31 30 0.03
32 22 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (28 bp):
ATGCCACTGACTTGTGGGCTTTGAAATG
Found at i:4908 original size:84 final size:84
Alignment explanation
Indices: 4607--6225 Score: 1168
Period size: 84 Copynumber: 19.1 Consensus size: 84
4597 GCTTTTAAAA
* * * * * *
4607 AAAAGG-TGCCACTAACTTGTGTGATTTGAAAAGAGTTGCTACCGACTTGTATGGGC-TTGAAAG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTG--TGGGCTTTGAAA-
* * *
4670 GGTATGCCATTGACTTGTGGGTTTT
61 TG-ATGCCACTGACTTGTGGGCTTT
* * * * *
4695 GAAATGATACCACTGACTTATGGGCTTTG-AAGGATGCCACTGACTTGTAGGCTTTGAAATGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
* *
4759 CCACTAACTTAT-GGCTTT
66 CCACTGACTTGTGGGCTTT
* * * * *
4777 GAAATA-G-TGCTACTGACTTGTGGGCTTTTAAATGTTGCCACTGACTTGTGGACTTTGAAATGA
1 -AAA-AGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGA
*
4840 TGCCACTGACTTGTGGGCATT
64 TGCCACTGACTTGTGGGCTTT
* * * * * *
4861 AAAAGGATACTACTAACCTGTAGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
4926 CCACTGACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * ** * *
4945 GAAAGGATGCCACTAACTCATGGGCTTTGAAATGGTTGCCACTGACTTGTGGGCTTTGAAATGCT
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAATGAT
5010 GCCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * *
5030 GAAATGATGCCACTGA-TTCGTGGGCTTTGAAATGATGCCACTGACTCGTGGGCTTTGAAATGAT
1 AAAAGGATGCCACTGACTT-GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGAT
* **
5094 GCCACTAACTCATGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * *
5114 GAAAA-GACGCCACTGACTTATGGGTTTTGAAATGG-TGCCACTGACTTGTGAGCTTTGAAATGA
1 -AAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAATGA
5177 TGCCACTGACTTGTGGGCTTT
64 TGCCACTGACTTGTGGGCTTT
* * * *
5198 GAAAGGATGCCGCTGACTTGTGGGCTTTGTAATA-G-TGCCACTAACTTGTGGGGTTTGAAATGA
1 AAAAGGATGCCACTGACTTGTGGGCTTTG-AA-AGGATGCCACTGACTTGTGGGCTTTGAAATGA
5261 TGCCACTGACTTGTGGGCTTT
64 TGCCACTGACTTGTGGGCTTT
** * * * *
5282 AAAAGGATGCTTCTAACTTGTTGGCTTTGAAAGGATGACACTGACTTGTGGGCTTTGAAATGGTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
*
5347 CCACTGACTTATGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * *
5366 GAAATGG-TGCCACTGAGTTGTGGGCTTTGAAAAGATGCCATTGACTTGTGGGCTTTGAAATGAT
1 -AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGAT
5430 GCCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * * * * * *
5450 GAAATGATGCCCCTGACTTTTAGGCTTTGAAATGATGTCACTGATTTATGGGCTTTGAAATGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
*
5515 CCATTGACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * * **
5534 GAAAAGAGTTGCCACCGACTTGTGTGGACTTTGAAAAGAGTGCCACTAACTTGTAAGCTTTGAAA
1 -AAAAG-GATGCCACTGACTTGTG-GG-CTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AA
* * * *
5599 AGGGTGCCACTAACTTGTAGGCTTT
60 ATGATGCCACTGACTTGTGGGCTTT
* * * *
5624 AGAAGGGAATGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGACTTTGAA
1 A-AAAGG-ATGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTG-GG-CTTTGAA
* *
5689 AAGAGTGCCACTGACTTGTGAGCTTT
60 ATGA-TGCCACTGACTTGTGGGCTTT
* * * * * * *
5715 GAAAAGGGTGCCACTAACTTGTGGGCTTTAGAAGGGAATGCCATTGACTTGTGGAC-TTAAAAAG
1 -AAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGG-ATGCCACTGACTTGTGGGCTTTGAAATG
* *
5779 AGTGCCAC-GAAGTTGTGGAC-TT
63 A-TGCCACTG-ACTTGTGGGCTTT
* * * * * * * * * * * *
5801 AAAAGGGTGTCA-TAGAGTTGTAGACTTTAAAAAGG-TGCCACGGACTTATGGACTTTAAAAGGG
1 AAAAGGATGCCACT-GACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTGAAATGA
* *
5864 TGCCACAGACTTGTGGACTTT
64 TGCCACTGACTTGTGGGCTTT
* * *** * * * * * ** * * *
5885 AAAAGGGTGCCA-TGGAGC-TCTAAACTTTAAAAGGGTACCACGGAGTTGTGGAATTTAAAAGGG
1 AAAAGGATGCCACT-GA-CTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGA
* * *
5948 TGCCACAGAGTTGTGGACTTT
64 TGCCACTGACTTGTGGGCTTT
* * * * * * * * * * *
5969 AAAAAGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCA-TAAAGTTGTGGACTTAG-AAGGAT
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAATGAT
* * *
6032 GCCACGGAGTTGTGGACTTT
65 GCCACTGACTTGTGGGCTTT
** * * * * * * * *
6052 AACAAGG-TGCCACAAAGTTGTGGAC-TTAAAAGGATGCCACTAAGTTGTGGAC-TTAAAAGGAT
1 AA-AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGAT
* * * * *
6114 GTCACGGAGTTATGGACTTT
65 GCCACTGACTTGTGGGCTTT
* * * * ** * * * *
6134 AAAAGGATGCCACAGAATTATGGACTTAAAAAGGATGCCAC-GATGTTGTGGAC-TTAAAAGGAT
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGA-CTTGTGGGCTTTGAAATGAT
* * *
6197 GCCACAGAGTTGTGGAC-TT
65 GCCACTGACTTGTGGGCTTT
6216 AAAAGGATGC
1 AAAAGGATGC
6226 AATGGAGTCG
Statistics
Matches: 1267, Mismatches: 212, Indels: 110
0.80 0.13 0.07
Matches are distributed among these distances:
81 5 0.00
82 103 0.08
83 195 0.15
84 604 0.48
85 123 0.10
86 28 0.02
87 27 0.02
88 20 0.02
89 54 0.04
90 79 0.06
91 28 0.02
92 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (84 bp):
AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
CCACTGACTTGTGGGCTTT
Found at i:5794 original size:28 final size:28
Alignment explanation
Indices: 5763--6219 Score: 314
Period size: 28 Copynumber: 16.5 Consensus size: 28
5753 TGCCATTGAC
5763 TTGTGGACTTAAAAAGAGTGCCACGAAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* * *
5791 TTGTGGACTT-AAAAGGGTGTCA-TAGAG
1 TTGTGGACTTAAAAAGAGTGCCACGA-AG
* * *
5818 TTGTAGACTTTAAAAAG-GTGCCACGGAC
1 TTGTGGAC-TTAAAAAGAGTGCCACGAAG
* * * *
5846 TTATGGACTTTAAAAGGGTGCCAC-AGAC
1 TTGTGGACTTAAAAAGAGTGCCACGA-AG
* * * *
5874 TTGTGGACTTTAAAAGGGTGCCATGGAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* * ** * * * *
5902 CTCTAAACTTTAAAAGGGTACCACGGAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* * *
5930 TTGTGGAATTTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTTAAAAAGAGTGCCACGA-AG
*
5958 TTGTGGACTTTAAAAAGA-TGCCACGGAG
1 TTGTGGAC-TTAAAAAGAGTGCCACGAAG
* * **
5986 TTGTGGACTTTAAAAGGGTGCCATAAAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* * *
6014 TTGTGGACTTAGAAGGA-TGCCACGGAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* *
6041 TTGTGGACTTTAACAAG-GTGCCACAAAG
1 TTGTGGAC-TTAAAAAGAGTGCCACGAAG
* *
6069 TTGTGGACTTAAAAGGA-TGCCACTAAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* * *
6096 TTGTGGACTTAAAAGGA-TGTCACGGAG
1 TTGTGGACTTAAAAAGAGTGCCACGAAG
* *
6123 TTATGGACTTTAAAAG-GATGCCACAGAA-
1 TTGTGGACTTAAAAAGAG-TGCCAC-GAAG
* *
6151 TTATGGACTTAAAAAG-GATGCCACGATG
1 TTGTGGACTTAAAAAGAG-TGCCACGAAG
*
6179 TTGTGGACTTAAAAGGA-TGCCAC-AGAG
1 TTGTGGACTTAAAAAGAGTGCCACGA-AG
6206 TTGTGGACTTAAAA
1 TTGTGGACTTAAAA
6220 GGATGCAATG
Statistics
Matches: 343, Mismatches: 66, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.01
27 123 0.36
28 204 0.59
29 14 0.04
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.25
Consensus pattern (28 bp):
TTGTGGACTTAAAAAGAGTGCCACGAAG
Found at i:5842 original size:55 final size:56
Alignment explanation
Indices: 5676--6219 Score: 484
Period size: 56 Copynumber: 9.8 Consensus size: 56
5666 CACCGACTTG
* * * * *
5676 TGTGGACTTTGAAAA-GAGTGCCACTGACTTGT-GAGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGACTTT-AAAAGGA-TGCCACAGAGTTGTGGA-CTTT-AAAAAGGTGCCACGAAGT
* * ** *
5734 TGTGGGCTTTAGAAGGGAATGCCATTGACTTGTGGAC-TTAAAAAGAGTGCCACGAAGT
1 TGTGGACTTTA-AAAGG-ATGCCACAGAGTTGTGGACTTTAAAAAG-GTGCCACGAAGT
* * * * * *
5792 TGTGGAC-TTAAAAGGGTGTCATAGAGTTGTAGACTTTAAAAAGGTGCCACGGACT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* * * * * * *
5847 TATGGACTTTAAAAGGGTGCCACAGACTTGTGGACTTTAAAAGGGTGCCATGGAGC
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* ** * * * * *
5903 TCTAAACTTTAAAAGGGTACCACGGAGTTGTGGAATTTAAAAGGGTGCCAC-AGAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGA-AGT
* * * **
5959 TGTGGACTTTAAAAAGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATAAAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* * * *
6015 TGTGGAC-TTAGAAGGATGCCACGGAGTTGTGGACTTTAACAAGGTGCCACAAAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* *
6070 TGTGGAC-TTAAAAGGATGCCACTA-AGTTGTGGAC-TT-AAAAGGATGTCACGGAGT
1 TGTGGACTTTAAAAGGATGCCAC-AGAGTTGTGGACTTTAAAAAGG-TGCCACGAAGT
* * * *
6124 TATGGACTTTAAAAGGATGCCACAGAATTATGGAC-TTAAAAAGGATGCCACGATGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGG-TGCCACGAAGT
6180 TGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAA
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAA
6220 GGATGCAATG
Statistics
Matches: 410, Mismatches: 62, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.01
54 17 0.04
55 160 0.39
56 171 0.42
57 10 0.02
58 29 0.07
59 15 0.04
60 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.26
Consensus pattern (56 bp):
TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
Found at i:6254 original size:55 final size:55
Alignment explanation
Indices: 5676--6256 Score: 441
Period size: 55 Copynumber: 10.4 Consensus size: 55
5666 CACCGACTTG
* * * *
5676 TGTGGACTTTGAAAA-GAGTGCCACTGACTTGT-GAGCTTTGAAAAGGGTGCCACTA-ACT
1 TGTGGACTTT-AAAAGGA-TGCCACAGAGTTGTGGA-C-TT-AAAAGGATGCCAC-AGAGT
* * ** * *
5734 TGTGGGCTTTAGAAGGGAATGCCATTGACTTGTGGACTTAAAAAGAGTGCCAC-GAAGT
1 TGTGGACTTTA-AAAGG-ATGCCACAGAGTTGTGGACTTAAAAGGA-TGCCACAG-AGT
* * * * * *
5792 TGTGGAC-TTAAAAGGGTGTCATAGAGTTGTAGACTTTAAAAAGG-TGCCACGGACT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TT-AAAAGGATGCCACAGAGT
* * * * ** *
5847 TATGGACTTTAAAAGGGTGCCACAGACTTGTGGACTTTAAAAGGGTGCCATGGAGC
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACAGAGT
* ** * * * * *
5903 TCTAAACTTTAAAAGGGTACCACGGAGTTGTGGAATTTAAAAGGGTGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGG-ACTTAAAAGGATGCCACAGAGT
* * * * *
5959 TGTGGACTTTAAAAAGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATAAAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACAGAGT
* * *
6015 TGTGGAC-TTAGAAGGATGCCACGGAGTTGTGGACTTTAACAAGG-TGCCACAAAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAA-AAGGATGCCACAGAGT
* *
6070 TGTGGAC-TTAAAAGGATGCCACTA-AGTTGTGGACTTAAAAGGATGTCACGGAGT
1 TGTGGACTTTAAAAGGATGCCAC-AGAGTTGTGGACTTAAAAGGATGCCACAGAGT
* * *
6124 TATGGACTTTAAAAGGATGCCACAGAATTATGGACTTAAAAAGGATGCCAC-GATGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTT-AAAAGGATGCCACAGA-GT
* **
6180 TGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCAATGGAGT
1 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGT
* *
6234 CGT-GACTTTAAAAGAAATGCCAC
1 TGTGGACTTTAAAAG-GATGCCAC
6257 TGAATCATGG
Statistics
Matches: 438, Mismatches: 61, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
53 7 0.02
54 41 0.09
55 169 0.39
56 161 0.37
57 15 0.03
58 27 0.06
59 15 0.03
60 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.25
Consensus pattern (55 bp):
TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGT
Found at i:9975 original size:22 final size:23
Alignment explanation
Indices: 9931--9979 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
9921 TTCAATATAT
9931 ATATATAATAAATAAAACAGCAA
1 ATATATAATAAATAAAACAGCAA
*
9954 ATATGATAATAAA-AAAA-TGCAA
1 ATAT-ATAATAAATAAAACAGCAA
9976 ATAT
1 ATAT
9980 CACCAAGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 8 0.33
24 8 0.33
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (23 bp):
ATATATAATAAATAAAACAGCAA
Found at i:15776 original size:21 final size:21
Alignment explanation
Indices: 15751--15791 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
15741 AAAAATAACA
15751 AAAATGACAATATTAGAGACC
1 AAAATGACAATATTAGAGACC
15772 AAAATGACAATATTAGAGAC
1 AAAATGACAATATTAGAGAC
15792 ATATATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAATGACAATATTAGAGACC
Done.