Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00981.F3
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: 4027
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Found at i:1698 original size:21 final size:21
Alignment explanation
Indices: 1645--1714 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
1635 CAGGACCTTC
*
1645 TAGTCCACCTTCAAGAGGAGT
1 TAGTCCACCTCCAAGAGGAGT
*
1666 TAG-CCCCACTCCAAGAGGAGT
1 TAGTCCAC-CTCCAAGAGGAGT
*
1687 TAGTCTACCTCCAAG-GGAAGT
1 TAGTCCACCTCCAAGAGG-AGT
*
1708 CAGTCCA
1 TAGTCCA
1715 ACTCAGATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 5 0.12
21 33 0.82
22 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (21 bp):
TAGTCCACCTCCAAGAGGAGT
Found at i:1800 original size:21 final size:21
Alignment explanation
Indices: 1770--1823 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1760 ACTTCAGTTC
*
1770 TCAGTTCAACTTCAAGAGG-AG
1 TCAGTCCAACTTCAAG-GGTAG
*
1791 TCAGTCCAACTCCAAGGGTAG
1 TCAGTCCAACTTCAAGGGTAG
*
1812 TGAGTCCAACTT
1 TCAGTCCAACTT
1824 GGATGAGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTTCAAGGGTAG
Found at i:1865 original size:105 final size:105
Alignment explanation
Indices: 1677--1907 Score: 309
Period size: 105 Copynumber: 2.2 Consensus size: 105
1667 AGCCCCACTC
* * * * * *
1677 CAAGAGGAGTTAGTCTACCTCCAAGGGAAGTCAGTCCAACTCAGATTAGGACATCCATCCCATCA
1 CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
* *
1742 AGTCAATCCCAAAACTCAACTTCAGTTCTCAGTTCAACTT
66 AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
* * ** * **
1782 CAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTTGGATGAGAACATCGAGCTTATCA
1 CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
* *
1847 AGTCAATCCCATAGCTCAACTTCAGTTATAAGTTCAACTT
66 AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
1887 CAAGAGGAGTCAGTCCAACTC
1 CAAGAGGAGTCAGTCCAACTC
1908 GGATGAGGGC
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
Found at i:1965 original size:84 final size:84
Alignment explanation
Indices: 1797--1985 Score: 231
Period size: 84 Copynumber: 2.2 Consensus size: 84
1787 GGAGTCAGTC
* * * * *
1797 CAACTCCAAG-GGTAGTGAGTCCAACTTGGATGAGAACATCGAGCTTATCAAGTCAATCCCATAG
1 CAACTTCAAGAGG-AGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAG
*
1861 CTCAACTTCAGTTATAAGTT
65 CTCAACTCCAGTTATAAGTT
**
1881 CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGC
1 CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGC
* *
1946 TCAGCTCCAG-TAGTTAGTT
66 TCAACTCCAGTTA-TAAGTT
*
1965 CAACTTTAAGA-GAGGTCAGTC
1 CAACTTCAAGAGGA-GTCAGTC
1986 TTACTCCAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
83 4 0.04
84 85 0.93
85 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGC
TCAACTCCAGTTATAAGTT
Found at i:2047 original size:189 final size:186
Alignment explanation
Indices: 1695--2093 Score: 455
Period size: 189 Copynumber: 2.1 Consensus size: 186
1685 GTTAGTCTAC
* *
1695 CTCCAAG-GGAAGTCAGTCCAACTCAGATTAGGACATCCATCCCATCAAGTCAATCCCAAAACTC
1 CTCCAAGAGG-AGTCAGTCCAACTCAGATGAGGACATCCAACCCATCAAGTCAATCCCAAAACTC
* * * * *
1759 AACTTCAGTTCTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTT
65 AACTCCAGTACTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTC
* * * *
1824 GGATGAGAACATCGAGCTTATCAAGTCAATCCCATAGCTCAACTTCAGTTATAAGTTCAA
130 GAATGAGAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCA---ATAAGTTCAA
* * * * * *
1884 CTTCAAGAGGAGTCAGTCCAACTCGGATGAGGGCAT-CAACCTTATCAAGTCAATCCCATAGCTC
1 CTCCAAGAGGAGTCAGTCCAACTCAGATGAGGACATCCAACC-CATCAAGTCAATCCCAAAACTC
* * * * **
1948 AGCTCCAGTAGTTAGTTCAACTTTAAGA-GAGGTCAGTCTTACTCCAAGGGTAATCAGTCCAACT
65 AACTCCAGTACTCAGTTCAACTTCAAGAGGA-GTCAGTCCAACTCCAAGGGTAATCAGTCCAACT
** * *
2012 CGAATGAGGAA-ATCAACCTCATTGAGTCTATCCCATAGCTCAACTTCAATTAGTTCAA
129 CGAATGA-GAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATAAGTTCAA
*
2070 CTCCAAGAGGAGTCAATCCAACTC
1 CTCCAAGAGGAGTCAGTCCAACTC
2094 CAAGCGTAGT
Statistics
Matches: 177, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
186 31 0.18
188 6 0.03
189 135 0.76
190 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (186 bp):
CTCCAAGAGGAGTCAGTCCAACTCAGATGAGGACATCCAACCCATCAAGTCAATCCCAAAACTCA
ACTCCAGTACTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCG
AATGAGAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATAAGTTCAA
Found at i:2215 original size:21 final size:21
Alignment explanation
Indices: 2166--2218 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2156 ACTTCAGTTA
*
2166 TCAGTTCAACTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
*
2187 TCATTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
2208 TGAGTCCAACT
1 TCAGTCCAACT
2219 GGGATGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:2254 original size:207 final size:205
Alignment explanation
Indices: 1894--2408 Score: 538
Period size: 207 Copynumber: 2.5 Consensus size: 205
1884 CTTCAAGAGG
* * * * *
1894 AGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCAG-TA
1 AGTCAGTCCAACTC-GATAAGGACATC-ACC-TATCAAGTCAATCCCATAGTTCAACTTCAGTTA
** **
1958 GTTAGTTCAACTTTAAGA-GAGGTCAGTCTTACTCCAAGGGTAATCAGTCCAACTCGAATGAGGA
63 -TTAGTTCAACTCCAAGAGGA-GTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGA
** *
2022 AATCAACCTCATTGAGTCTATCCCATAGCTCAACTTCAATT-AGTTCAACTCC-AAGAGGAGTCA
126 AATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATTCAGTTCAAC-CCTAAGAGGAGTCA
2085 ATCCAACTCCAAGCGT
190 ATCCAACTCCAAGCGT
*
2101 AGTGAGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGTTCAACTTCAGTTA
1 AGTCAGTCCAACTC-GATAAGGACAT-CACCT-ATCAAGTCAATCCCATAGTTCAACTTCAGTTA
* * * * * * *
2166 TCAGTTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACA
63 TTAGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAA
* * * *
2231 TCCACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACATTTCAACCCTAAGAGGAGTCAG
128 TCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATT--CAGTTCAACCCTAAGAGGAGTCAA
* * *
2296 TCCAATTTCAAGGGT
191 TCCAACTCCAAGCGT
* * * * * *
2311 AGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTT-GACTTCAGTT
1 AGTCAGTCCAACTCG-ATAAGGACAT-CA-CCTATCAAGTCAATCCCATAG-TTCAACTTCAGTT
*
2375 ATTGGTTCAACTCCAA-AGGTAGTCAGTCCAACTC
62 ATTAGTTCAACTCCAAGAGG-AGTCAGTCCAACTC
2409 GGATGGGAAC
Statistics
Matches: 257, Mismatches: 39, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
206 1 0.00
207 136 0.53
208 5 0.02
209 6 0.02
210 105 0.41
211 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (205 bp):
AGTCAGTCCAACTCGATAAGGACATCACCTATCAAGTCAATCCCATAGTTCAACTTCAGTTATTA
GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAATCA
ACCTCATCAAGTCAATCCCATAGCTCAACTTCAATTCAGTTCAACCCTAAGAGGAGTCAATCCAA
CTCCAAGCGT
Found at i:2454 original size:84 final size:85
Alignment explanation
Indices: 2304--2492 Score: 242
Period size: 84 Copynumber: 2.3 Consensus size: 85
2294 AGTCCAATTT
* **
2304 CAAG-GGTAGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTTGAC
1 CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTCAAC
**
2368 TTCAGTTATTGGTTCAACTC
66 TTCAGTTATCAGTTCAACTC
* ** * *
2388 CAA-AGGTAGTCAGTCCAACTCGGATGGGAACATCCA-CCTCATCGAGTCAATCCCATAGCTCAA
1 CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCAT-ATCGAGCCAATCCCATAGCTCAA
2451 CTTCAGTTATCAGTTCAACTC
65 CTTCAGTTATCAGTTCAACTC
*
2472 CAAGAGG-AGTAAGTCCAACTC
1 CAAGAGGTAGTCAGTCCAACTC
2493 CAAATGTTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
83 2 0.02
84 86 0.95
85 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (85 bp):
CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTCAAC
TTCAGTTATCAGTTCAACTC
Found at i:2504 original size:42 final size:42
Alignment explanation
Indices: 2456--2537 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2446 CTCAACTTCA
2456 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
* * *
2498 GTTATCATTTCAATTCCAAGAGGAGTCAGTCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
2538 TCAGGACATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
Found at i:2536 original size:21 final size:21
Alignment explanation
Indices: 2460--2537 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
2450 ACTTCAGTTA
*
2460 TCAGTTCAACTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
* *
2481 TAAGTCCAACTCCAA-ATGTTA-
1 TCAGTCCAACTCCAAGA-G-GAG
* * *
2502 TCATTTCAATTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
2523 TCAGTCCAACTCCAA
1 TCAGTCCAACTCCAA
2538 TCAGGACATC
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:2597 original size:126 final size:126
Alignment explanation
Indices: 2380--2621 Score: 391
Period size: 126 Copynumber: 1.9 Consensus size: 126
2370 CAGTTATTGG
** *
2380 TTCAACTCCAAAGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATA
1 TTCAACTCCAAAGGTAGTCAGTCCAACTCCAATAGGAACATCCACCTCATCGAGTCAATCCCATA
2445 GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TAAGTCCAACTCCAAATGTTATCAT
66 GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTAAGTCCAACTCCAAATGTTATCAT
*
2506 TTCAATTCCAAGAGG-AGTCAGTCCAACTCCAATCAGG-ACATCCACCTCATCGAGTCAATCCCA
1 TTCAACTCCAA-AGGTAGTCAGTCCAACTCCAAT-AGGAACATCCACCTCATCGAGTCAATCCCA
*
2569 TAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTCAGTCCAACTCCAA
64 TAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTAAGTCCAACTCCAA
2622 GGGTAGTTAG
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
125 1 0.01
126 102 0.94
127 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.24
Consensus pattern (126 bp):
TTCAACTCCAAAGGTAGTCAGTCCAACTCCAATAGGAACATCCACCTCATCGAGTCAATCCCATA
GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTAAGTCCAACTCCAAATGTTATCAT
Found at i:2616 original size:21 final size:21
Alignment explanation
Indices: 2586--2639 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2576 ACTTCAGTTA
*
2586 TCAGTTCAACTCCAAGAGG-GT
1 TCAGTCCAACTCCAAG-GGAGT
2607 TCAGTCCAACTCCAAGGGTAGT
1 TCAGTCCAACTCCAAGGG-AGT
2629 T-AGTCCAACTC
1 TCAGTCCAACTC
2640 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGGGAGT
Found at i:2721 original size:21 final size:21
Alignment explanation
Indices: 2692--2744 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2682 CTTCAGTTAT
*
2692 CAGTTCAACTCCAAGAGG-AGC
1 CAGTCCAACTCCAAG-GGTAGC
*
2713 CAGTCCAACTCCAAGGGTAGT
1 CAGTCCAACTCCAAGGGTAGC
*
2734 TAGTCCAACTC
1 CAGTCCAACTC
2745 AGATGAGGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
CAGTCCAACTCCAAGGGTAGC
Found at i:2828 original size:105 final size:104
Alignment explanation
Indices: 1881--2810 Score: 801
Period size: 105 Copynumber: 8.9 Consensus size: 104
1871 GTTATAAGTT
* * * * *
1881 CAACTTCAAGAGG-AGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAG
1 CAACTCCAAG-GGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAG
* * * **
1945 CTCAGCTCCAG-TAGTTAGTTCAACTTTAAGA-GAGGTCAGTC
64 CTCAACTTCAGTTA-TCAGTTCAACTCCAAGAGGA-GTCAGTC
** * * * * *
1986 TTACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAATCAACCTCATTGAGTCTATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTCG-ATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
* *
2051 TCAACTTCA---ATTAGTTCAACTCCAAGAGGAGTCAATC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* * * * * *
2088 CAACTCCAAGCGTAGTGAGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGT
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
2153 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCATTC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* * *
2193 CAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACATCCACCTCATCAAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACT-CGATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
2258 TCAACTTCAGTTCA-CATTTCAAC-CCTAAGAGGAGTCAGTC
65 TCAACTTCAGTT-ATCAGTTCAACTCC-AAGAGGAGTCAGTC
* * * * * * *
2298 CAATTTCAAGGGTAGTCAGTCCAATTCGAATAAGAACATCCAGCAT-ATCGAGCCAATCCCATAG
1 CAACTCCAAGGGTAGTCAGTCCAACTCG-ATGAGGACATCCA-CCTCATCGAGTCAATCCCATAG
** **
2362 CTTGACTTCAGTTATTGGTTCAACTCCAA-AGGTAGTCAGTC
64 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-AGTCAGTC
* * * * * * * * * *
2403 CAACTCGGATGGG-A-ACA-TCCACCTC-ATCGA-GTCAATCC-CAT-AGCTCAACTTCAGT--T
1 CAACTC-CAAGGGTAGTCAGTCCAACTCGAT-GAGGAC-ATCCACCTCA--TCGA-GTCAATCCC
* * ** * * * * *
2459 ATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA-ATGTTA-TCATTT
60 AT-AGCTCAACTTC-AG-TTA-TCAGTTCAACTCCAAGA-G-GAGTCAGTC
* * *
2508 CAATTCCAAGAGG-AGTCAGTCCAACTCCAATCAGGACATCCACCTCATCGAGTCAATCCCATAG
1 CAACTCCAAG-GGTAGTCAGTCCAACT-CGATGAGGACATCCACCTCATCGAGTCAATCCCATAG
2572 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTCAGTC
64 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TCAGTC
*
2613 CAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
* *
2678 TCCACTTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* *
2718 CAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCATCTCATCGAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
2783 TCAACTTCAGTTA-CAAGTCCAACTCCAA
65 TCAACTTCAGTTATC-AGTTCAACTCCAA
2811 TGGTAGCTAG
Statistics
Matches: 671, Mismatches: 110, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 95 0.14
103 15 0.02
104 19 0.03
105 478 0.71
106 16 0.02
107 12 0.02
108 18 0.03
109 8 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (104 bp):
CAACTCCAAGGGTAGTCAGTCCAACTCGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCT
CAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
Found at i:2855 original size:84 final size:83
Alignment explanation
Indices: 2713--2978 Score: 406
Period size: 84 Copynumber: 3.2 Consensus size: 83
2703 CAAGAGGAGC
* * * *
2713 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCATCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCCC
2778 ATAGCTCAACTTCAGTTA
66 ATAGCTCAACTTCAGTTA
*
2796 CAAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCT
1 C-AGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCC
*
2861 CATAGCTCAACTTCTGTTA
65 CATAGCTCAACTTCAGTTA
* *
2880 CCAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATAAGGACGTCCACCTCATCGAATCAATCC
1 -CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCC
* *
2945 CATAGCTCGACCTCAGTTA
65 CATAGCTCAACTTCAGTTA
*
2964 TCAGTTCAACTCCAA
1 -CAGTCCAACTCCAA
2979 GAGGAGTCAG
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 165 0.99
85 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (83 bp):
CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCCC
ATAGCTCAACTTCAGTTA
Found at i:2912 original size:420 final size:420
Alignment explanation
Indices: 2105--2894 Score: 1164
Period size: 420 Copynumber: 1.9 Consensus size: 420
2095 AAGCGTAGTG
*
2105 AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGTTCAACTTCAGTTATCAG
1 AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCAG
* *
2170 TTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACATCCA
66 TTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATCCA
* *
2235 CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACATTTCAACCCTAAGAGGAGTCAGTCCA
131 CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACAGTTCAACCCTAAGAGGAGCCAGTCCA
* * * *
2300 ATTTCAAGGGTAGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTT
196 ACTCCAAGGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTC
* *** * *
2365 GACTTCAGTTATTGGTTCAACTCCAAAGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCAT
261 AACTTCAGTTACAAGTCCAACTCCAAAGGTAGTCAGTCCAACTCAGATGGGAACATCCACCTCAT
* *
2430 CGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCA
326 CGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAAGAGGAGTAAGTCCAACTCCA
2495 AATGTTATCATTTCAATTCCAAGAGGAGTC
391 AATGTTATCATTTCAATTCCAAGAGGAGTC
* * *
2525 AGTCCAACTCCA-ATCAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
1 AGTCCAACT-CAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCA
*
2589 GTTCAACTCCAAGAGG-GTTCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATC
65 GTTCAACTCCAAGAGGAG-TCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATC
* *
2653 CACCTCATCGAGTCAATCCCATAGCTCCACTTCAGTT-ATCAGTTCAACTCC-AAGAGGAGCCAG
129 CACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCA-CAGTTCAAC-CCTAAGAGGAGCCAG
* * * * *
2716 TCCAACTCCAAGGGTAGTTAGTCCAACTC-AGATGAGGACATCCATC-TCATCGAGTCAATCCCA
192 TCCAACTCCAAGGGTAGTCAGTCCAACTCGA-ATAAGAACATCCAGCAT-ATCGAGCCAATCCCA
* *
2779 TAGCTCAACTTCAGTTACAAGTCCAACTCCAATGGTAG-CTAGTCCAACTCAGATGAGG-ACGTC
255 TAGCTCAACTTCAGTTACAAGTCCAACTCCAAAGGTAGTC-AGTCCAACTCAGATG-GGAACATC
* *
2842 CACCTCATCGAGTCAATCTCATAGCTCAACTTCTGTTACCAGTCCAACTCCAA
318 CACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAA
2895 TGGTAGCTAG
Statistics
Matches: 330, Mismatches: 32, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
419 5 0.02
420 319 0.97
421 6 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (420 bp):
AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCAG
TTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATCCA
CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACAGTTCAACCCTAAGAGGAGCCAGTCCA
ACTCCAAGGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTC
AACTTCAGTTACAAGTCCAACTCCAAAGGTAGTCAGTCCAACTCAGATGGGAACATCCACCTCAT
CGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAAGAGGAGTAAGTCCAACTCCA
AATGTTATCATTTCAATTCCAAGAGGAGTC
Found at i:2994 original size:21 final size:21
Alignment explanation
Indices: 2964--3017 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2954 ACCTCAGTTA
*
2964 TCAGTTCAACTCCAAGAGG-AG
1 TCAGTCCAACTCCAAG-GGTAG
2985 TCAGTCCAACTCCAAGGGTAG
1 TCAGTCCAACTCCAAGGGTAG
*
3006 TTAGTCCAACTC
1 TCAGTCCAACTC
3018 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGGGTAG
Found at i:2995 original size:105 final size:105
Alignment explanation
Indices: 2881--3074 Score: 300
Period size: 105 Copynumber: 1.8 Consensus size: 105
2871 CTTCTGTTAC
* *
2881 CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATAAGGACGTCCACCTCATCGAATCAATCCC
1 CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
* *
2946 ATAGCTCGAC-CTCAGTTATCAGTTCAACTCCAAGAGGAGT
66 ATAGCTCAACTC-CAGATATCAGTTCAACTCCAAGAGGAGT
* * * *
2986 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
3051 ATAGCTCAACTCCAGATATCAGTT
66 ATAGCTCAACTCCAGATATCAGTT
3075 TTATCACTGA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 79 0.99
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
ATAGCTCAACTCCAGATATCAGTTCAACTCCAAGAGGAGT
Done.