Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014680.1 Kokia drynarioides strain JFW-HI SEQ_129719, whole genome shotgun sequence
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: 28823
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1355 original size:28 final size:29
Alignment explanation
Indices: 1315--1370 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1305 AGATGTCGAA
*
1315 ATTTTTTTGAAAAATTATCGAGTTAAATT
1 ATTTTTTTGAAAAATTATCGAATTAAATT
* *
1344 ATTTTTTT-AAAATTTATCTAATTAAAT
1 ATTTTTTTGAAAAATTATCGAATTAAAT
1371 AAAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTTTTTGAAAAATTATCGAATTAAATT
Found at i:5879 original size:30 final size:29
Alignment explanation
Indices: 5847--6117 Score: 186
Period size: 30 Copynumber: 9.3 Consensus size: 29
5837 AAAGTGTGAT
*
5847 TTTTTGGAAATTCGAGGGT-AAAATGATAA
1 TTTTTGGAAATTTGAGGGTAAAAATG-TAA
* * *
5876 TTTTTGG-AAGTCGAGGGGTAAAAATGTGA
1 TTTTTGGAAATTTGA-GGGTAAAAATGTAA
* *
5905 -TTTTGAGAAGTTTG-GGGT-AAAATGTGA
1 TTTTTG-GAAATTTGAGGGTAAAAATGTAA
*
5932 -TTTT-GAAAGTTTG-GGGTAAAAATATAA
1 TTTTTGGAAA-TTTGAGGGTAAAAATGTAA
*
5959 TTTTT-GAAAGTTTG-GTTGTAAAAATGTAA
1 TTTTTGGAAA-TTTGAG-GGTAAAAATGTAA
** *
5988 TTTTTGGAAAGTTCAAGGGTTAAAATGTAA
1 TTTTTGGAAA-TTTGAGGGTAAAAATGTAA
*
6018 TTTTTGGAAAATTT-AGGGTTAAAATGTAA
1 TTTTTGG-AAATTTGAGGGTAAAAATGTAA
* * * *
6047 TTTTTAGAAAATTTGAGAGTCAAAATATAA
1 TTTTT-GGAAATTTGAGGGTAAAAATGTAA
* * * *
6077 TTTTTGAGAAAGTTTGAGAGTCAACATGTAG
1 TTTTTG-GAAA-TTTGAGGGTAAAAATGTAA
6108 TTTTTGGAAA
1 TTTTTGGAAA
6118 GTTCAGGACC
Statistics
Matches: 204, Mismatches: 23, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
25 3 0.01
26 8 0.04
27 20 0.10
28 29 0.14
29 57 0.28
30 61 0.30
31 26 0.13
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTTGGAAATTTGAGGGTAAAAATGTAA
Found at i:6021 original size:59 final size:57
Alignment explanation
Indices: 5862--6122 Score: 196
Period size: 59 Copynumber: 4.5 Consensus size: 57
5852 GGAAATTCGA
* * *
5862 GGGTAAAATGATAATTTTTGG-AAG-TCGAGGGGTAAAAATGTGA-TTTT-GAGAAGTTT
1 GGGTAAAATG-TAATTTTTGGAAAGTTC-AAGGGTAAAAATATAATTTTTGGA-AAGTTT
* **
5918 GGGGTAAAATGTGA-TTTT-GAAAGTT-TGGGGTAAAAATATAATTTTT-GAAAGTTT
1 -GGGTAAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTGGAAAGTTT
* * *
5972 GGTTGTAAAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAATGTAATTTTTGGAAAATTT
1 GG--GT-AAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTGGAAAGTTT
* * ** * *
6032 AGGGTTAAAATGTAATTTTTAGAAAATTTGAGAGTCAAAATATAATTTTTGAGAAAGTTT
1 -GGG-TAAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTG-GAAAGTTT
* *
6092 GAGAGTCAACATGTAGTTTTTGGAAAGTTCA
1 G-G-GT-AAAATGTAATTTTTGGAAAGTTCA
6123 GGACCTTCTG
Statistics
Matches: 164, Mismatches: 24, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
53 2 0.01
54 20 0.12
55 15 0.09
56 11 0.07
57 14 0.09
58 7 0.04
59 57 0.35
60 17 0.10
61 21 0.13
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTGGAAAGTTT
Found at i:6036 original size:29 final size:29
Alignment explanation
Indices: 5847--6120 Score: 190
Period size: 29 Copynumber: 9.4 Consensus size: 29
5837 AAAGTGTGAT
*
5847 TTTTTGGAAA-TTCGAGGG-TAAAATGATAA
1 TTTTTGGAAAGTT-TAGGGTTAAAATG-TAA
** * *
5876 TTTTTGG-AAGTCGAGGGGTAAAAATGTGA
1 TTTTTGGAAAGTTTA-GGGTTAAAATGTAA
* *
5905 -TTTT-GAGAAGTTT-GGGGTAAAATGTGA
1 TTTTTGGA-AAGTTTAGGGTTAAAATGTAA
* * *
5932 -TTTT-GAAAGTTTGGGGTAAAAATATAA
1 TTTTTGGAAAGTTTAGGGTTAAAATGTAA
*
5959 TTTTT-GAAAGTTT-GGTTGTAAAAATGTAA
1 TTTTTGGAAAGTTTAGG--GTTAAAATGTAA
*
5988 TTTTTGGAAAGTTCAAGGGTTAAAATGTAA
1 TTTTTGGAAAGTT-TAGGGTTAAAATGTAA
*
6018 TTTTTGGAAAATTTAGGGTTAAAATGTAA
1 TTTTTGGAAAGTTTAGGGTTAAAATGTAA
* * * * *
6047 TTTTTAGAAAATTTGAGAGTCAAAATATAA
1 TTTTTGGAAAGTTT-AGGGTTAAAATGTAA
* * * *
6077 TTTTTGAGAAAGTTTGAGAGTCAACATGTAG
1 TTTTTG-GAAAGTTT-AGGGTTAAAATGTAA
6108 TTTTTGGAAAGTT
1 TTTTTGGAAAGTT
6121 CAGGACCTTC
Statistics
Matches: 206, Mismatches: 25, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.03
27 31 0.15
28 20 0.10
29 61 0.30
30 60 0.29
31 26 0.13
32 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTTGGAAAGTTTAGGGTTAAAATGTAA
Found at i:7946 original size:11 final size:12
Alignment explanation
Indices: 7922--7998 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 12
7912 TTTTAAACTC
7922 AATTTAAAATTA
1 AATTTAAAATTA
7934 AATTTAGAATAAATTTA
1 AATTT---A-AAA-TTA
7951 AATTTAAAA-TA
1 AATTTAAAATTA
7962 AATTTAAAATTA
1 AATTTAAAATTA
*
7974 AACTTAAAA-TA
1 AATTTAAAATTA
7985 AATTTAAAATTA
1 AATTTAAAATTA
7997 AA
1 AA
7999 GATTGGGCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
11 21 0.38
12 19 0.34
13 3 0.05
14 1 0.02
15 1 0.02
16 3 0.05
17 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (12 bp):
AATTTAAAATTA
Found at i:7948 original size:23 final size:23
Alignment explanation
Indices: 7943--7998 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
7933 AAATTTAGAA
*
7943 TAAATTTAAATTTAAAATAAATT
1 TAAAATTAAATTTAAAATAAATT
*
7966 TAAAATTAAACTTAAAATAAATT
1 TAAAATTAAATTTAAAATAAATT
7989 TAAAATTAAA
1 TAAAATTAAA
7999 GATTGGGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATTAAATTTAAAATAAATT
Found at i:7958 original size:40 final size:40
Alignment explanation
Indices: 7913--7998 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
7903 TATTTGGACT
* * * *
7913 TTTAAACTCAATTTAAAATTAAATTTAGAATAAATTTAAA
1 TTTAAAATAAATTTAAAATTAAACTTAAAATAAATTTAAA
7953 TTTAAAATAAATTTAAAATTAAACTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAAATTAAACTTAAAATAAATTTAAA
*
7993 ATTAAA
1 TTTAAA
7999 GATTGGGCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (40 bp):
TTTAAAATAAATTTAAAATTAAACTTAAAATAAATTTAAA
Found at i:7998 original size:17 final size:17
Alignment explanation
Indices: 7926--7994 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
7916 AAACTCAATT
* *
7926 TAAAATTAAATTTAGAA
1 TAAATTTAAATTTAAAA
7943 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
7960 TAAATTTAAAATTAAACT
1 TAAATTTAAATTTAAA-A
*
7978 TAAA-ATAAATTTAAAA
1 TAAATTTAAATTTAAAA
7994 T
1 T
7995 TAAAGATTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.02
17 39 0.89
18 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:8735 original size:208 final size:208
Alignment explanation
Indices: 8372--9319 Score: 991
Period size: 208 Copynumber: 4.6 Consensus size: 208
8362 TTCATCTCTC
* * * * * *
8372 GGTCTACTTCTCTGTATCTCATCAGGAATATTATCGCATCACTTGTTTTAATCCGCTTCTTTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
* * * * ** *
8437 TCTCATTAGGAAGATGGATTTGGTTCACTTCTTTGTATCTCATTAGGAAAACT-ACCGCTATATT
66 TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGG-AAGGTAACCGCTTTATT
* * * * **
8501 GCTTCAACCCGCTTCTTAGAATCTCATCAGGAAGCTGGGGTTCGAATTTTTGCTCA-TATCT-AG
130 GCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT-T-TGAG
* *
8564 CTTTGTTTCCTTGATTT
193 C-CTGTTTCATTGATTT
*
8581 GGTCTACTTCTCAGTATCTCAT-AGGAAGATGACCGCATCACTTGTTTTAATCCCCTTCTCTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
* *
8645 TCTCATCAGAAAGACGGATTTGGTTCACTTCTCTATATCTCATCAGGAAGGTAACCGCTTTATTG
66 TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTG
* *
8710 CTTTGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT
131 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT
8775 GATTTCATTGATTT
196 G-TTTCATTGATTT
* ** * ** * *
8789 GGTCTACTTCTCAGTATCTCATCAAGAAGATGACTACCT-TGTTGTTTTGATCCACTTTTCTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
* * * *
8853 TCTTATCAGGAAGACGGATCTGGTACACTTCTCTGTATCTCATCAGGAAGGTAACTGCTTTATTG
66 TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTG
* ** *
8918 CTTCGACCTGCTTCTCAATATCTCATCAGGAAGCCAGGGTTCGAAGATTTGCTCACTTTGAACCT
131 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT
*
8983 GGTTCAATAT-ATTT
196 GTTTC-AT-TGATTT
* * * * * *
8997 GGTCTACTTCTCAGTATCTCATCAGGAATATGACCGCCTC-GTTATTTTGATCCACTTCTCTGCA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
* * * * * * * *
9061 TCGCATCAGGAAGATGGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGATCACTTTATTG
66 TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTG
* * * * * * *
9126 CTTTGA-CTCACTTCTCAGTATCTTATCAGGAAGAT-AGGTTCGAAG-TTTCACTCACATTGAGC
131 CTTCGACCT-GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCACTTTGAGC
* * * *
9188 TTTGCTTCAATGATAT
194 -CTGTTTCATTGATTT
* ** * * *
9204 GGTCTTCTTCTTTGTATCTCATCAGAAAGATGACCGCATCAC-TGTTTCAATCCGCTTCTCTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
* * * *** * *
9268 TCTAATCAGAAAGACGAATTTGACCCATTTCTCTGTATCTTATCAGGAAGGT
66 TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGT
9320 GACCATTTTA
Statistics
Matches: 621, Mismatches: 105, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
206 4 0.01
207 124 0.20
208 458 0.74
209 35 0.06
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (208 bp):
GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
TCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTG
CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT
GTTTCATTGATTT
Found at i:9822 original size:50 final size:50
Alignment explanation
Indices: 9750--10263 Score: 413
Period size: 50 Copynumber: 10.3 Consensus size: 50
9740 GCAGTAACGA
* * * * * * *
9750 CCTCAATCTTTTCCATCGCATCTTTTTAGATACCGAGTTCGCCGTGGCGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
* *
9800 CCGCAACCTTTCCCTTCACATCTTCTTAGGTACC-AGGTTCGCTGTTGCGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGA-GTTCGCCGTTGCGG
* ** * * *
9850 CCTCAACCTTTCCTTTTGCATCTTTTTAAGGTATC-AGATTCGCCGTTGTGG
1 CCTCAACCTTTCCCTTCACATCTTCTT-AGGTACCGAG-TTCGCCGTTGCGG
* * * * * *
9901 CCTCAA--TTCTCCCCTGTCATC-TCTTCAT-GGTACTGGGTTCACTGTTGCGA
1 CCTCAACCTT-T-CCCT-TCA-CATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
* *
9951 CCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
* * **
10001 CGTCAACCTTTCCCTTCACATCTTCTTAGGTACC-AGGTTCGTCGTTAAGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGA-GTTCGCCGTTGCGG
* * * * * * *
10051 TCTCAACCTTTCCCTTTACATCTTCAT-GGTACCGGGTTCACCGTTACGA
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
*
10100 CCTCAACCTTTCCCATCACATCTTCTTAGGTACC-AGGTTCGCCGTTGCGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGA-GTTCGCCGTTGCGG
* * * * * * * *
10150 CCTCAACTTTTCCCATCATATCTTTTTAGGTACTGGGTTCGGCGTTGTGG
1 CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
* * * *
10200 CCTCAACCTTTCCTTTCA-ATCTT-TTATGGTACCG-GATTTGCCGTCGGGG
1 CCTCAACCTTTCCCTTCACATCTTCTTA-GGTACCGAG-TTCGCCGTTGCGG
*
10249 CCTCAATCTTTCCCT
1 CCTCAACCTTTCCCT
10264 ATCAAACCTG
Statistics
Matches: 370, Mismatches: 75, Indels: 39
0.76 0.15 0.08
Matches are distributed among these distances:
48 5 0.01
49 84 0.23
50 243 0.66
51 29 0.08
52 8 0.02
53 1 0.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.35
Consensus pattern (50 bp):
CCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGAGTTCGCCGTTGCGG
Found at i:10132 original size:149 final size:148
Alignment explanation
Indices: 9803--10234 Score: 546
Period size: 149 Copynumber: 2.9 Consensus size: 148
9793 GTGGCGGCCG
* * * **
9803 CAACCTTTCCCTTCACATCTTCTTAGGTACCAGGTTCGCTGTTGCGGCCTCAACCTTTCCTTTTG
1 CAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA
* * *
9868 CATCTTTTTAAGGTATCAGATTCGCCGTTGTGGCCTCAA--TTCTCCCCTGTCATCTCTTCATGG
66 CATCTTTTT-AGGTACCAGGTTCGCCGTTGTGGCCTCAACCTT-T-CCCTTTCA--TCTTCATGG
* * *
9931 TACTGGGTTCACTGTTGCGACCT
126 TACCGGGTTCACCGTTACGACCT
* *
9954 CAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCGTCAACCTTTCCCTTCA
1 CAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA
* * ** *
10019 CATCTTCTTAGGTACCAGGTTCGTCGTTAAGGTCTCAACCTTTCCCTTTACATCTTCATGGTACC
66 CATCTTTTTAGGTACCAGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTT-CATCTTCATGGTACC
10084 GGGTTCACCGTTACGACCT
130 GGGTTCACCGTTACGACCT
* *
10103 CAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACTTTTCCCATCA
1 CAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA
* ** * *
10168 TATCTTTTTAGGTACTGGGTTCGGCGTTGTGGCCTCAACCTTT-CCTTTCAATCTTTTATGGTAC
66 CATCTTTTTAGGTACCAGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTC-ATC-TTCATGGTAC
10232 CGG
129 CGG
10235 ATTTGCCGTC
Statistics
Matches: 245, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
147 1 0.00
148 8 0.03
149 137 0.56
150 28 0.11
151 69 0.28
152 2 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (148 bp):
CAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA
CATCTTTTTAGGTACCAGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTCATCTTCATGGTACCG
GGTTCACCGTTACGACCT
Found at i:10222 original size:99 final size:100
Alignment explanation
Indices: 9750--10267 Score: 494
Period size: 99 Copynumber: 5.2 Consensus size: 100
9740 GCAGTAACGA
* * * * * * *
9750 CCTCAATCTTTTCCATCGCATCTTTTTAGATACCGAGTTCGCCGTGGCGGCCGCAACCTTTCCCT
1 CCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
*
9815 TCACATCTTCTTAGGTACCAGGTTCGCTGTTGCGG
66 TCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
** ** * * * *
9850 CCTCAACCTTTCCTTTTGCATCTTTTTAAGGTATCAGATTCGCCGTTGTGGCCTCAA--TTCTCC
1 CCTCAACCTTTCCCATCACATCTTTTT-AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTT-T-C
* ** * * *
9913 CCTGTCATC-TCTTCAT-GGTACTGGGTTCACTGTTGCGA
63 CCT-TCA-CATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
* *
9951 CCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCGTCAACCTTTCCCT
1 CCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
* **
10016 TCACATCTTCTTAGGTACCAGGTTCGTCGTTAAGG
66 TCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
* * * ** * * * *
10051 TCTCAACCTTTCCCTTTACATCTTCAT-GGTACCGGGTTCACCGTTACGACCTCAACCTTTCCCA
1 CCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
10115 TCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
66 TCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
* * * * * *
10150 CCTCAACTTTTCCCATCATATCTTTTTAGGTACTGGGTTCGGCGTTGTGGCCTCAACCTTTCCTT
1 CCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
* * *
10215 TCA-ATCTT-TTATGGTACC-GGATTTGCCGTCGGGG
66 TCACATCTTCTTA-GGTACCAGG-TTCGCCGTTGCGG
*
10249 CCTCAATCTTTCCCTATCA
1 CCTCAACCTTTCCC-ATCA
10268 AACCTGTATA
Statistics
Matches: 336, Mismatches: 69, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
98 6 0.02
99 128 0.38
100 124 0.37
101 66 0.20
102 11 0.03
103 1 0.00
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (100 bp):
CCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
TCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGG
Found at i:15029 original size:96 final size:96
Alignment explanation
Indices: 14856--15133 Score: 459
Period size: 96 Copynumber: 2.9 Consensus size: 96
14846 AGGGTATTCT
* *** ***
14856 ATTATCCCGATTTTAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAACAAAAGAT
1 ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
*
14921 -AAAGAAACATTGTCTCGATTTAAGGGAATCG
66 AAAAG-AATATTGTCTCGATTTAAGGGAATCG
14952 ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
1 ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
15017 AAAAGAATATTGTCTCGATTTAAGGGAATCG
66 AAAAGAATATTGTCTCGATTTAAGGGAATCG
15048 ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
1 ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
*
15113 AAAAGAATATTGCCTCGATTT
66 AAAAGAATATTGTCTCGATTT
15134 TTAAATATTT
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
96 168 0.98
97 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (96 bp):
ATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAGAT
AAAAGAATATTGTCTCGATTTAAGGGAATCG
Found at i:15451 original size:30 final size:28
Alignment explanation
Indices: 15385--15451 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
15375 TTTCAGAGAG
* *
15385 TTTGGGATGAAAACATAATTTTAGAAAG
1 TTTGGGATCAAAACATAATTTTAGAAAA
* *
15413 TTTAGGGATCAAAATCATAGTTATTGGAAAA
1 TTT-GGGATCAAAA-CATAATT-TTAGAAAA
15444 TTTGGGAT
1 TTTGGGAT
15452 TAAAGCCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 9 0.28
30 11 0.34
31 9 0.28
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (28 bp):
TTTGGGATCAAAACATAATTTTAGAAAA
Found at i:15569 original size:58 final size:58
Alignment explanation
Indices: 15507--15711 Score: 195
Period size: 58 Copynumber: 3.5 Consensus size: 58
15497 AAAAATTCGA
* *
15507 GGGTAAAATGGTAATTTTTGG-AAGTTCGGGAGCAAAAATGTGATTTTTGAGAAGTTTG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTTG
** * * * *
15565 GGGTAAAAACATGATTTTT-GAAAGTT-TAGAGGTAAAAATATAATTTTTGA-AAGTTTG
1 GGGT-AAAATGTAATTTTTGGAAAGTTCGAGA-GCAAAAATGTAATTTTTGAGAAGTTTG
* *
15622 GTGGTCAAAATGTAATTTTTGGAAAGTTTGAGAGTC-AAAATGTAATTTTTGAGAAAGTTCAG
1 G-GGT-AAAATGTAATTTTTGGAAAGTTCGAGAG-CAAAAATGTAATTTTTGAG-AAGTT-TG
*
15684 GGGTTAACATGTAATTTTTGGAAAGTTC
1 GGG-TAAAATGTAATTTTTGGAAAGTTC
15712 AAGGACCTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
57 11 0.09
58 46 0.39
59 27 0.23
60 3 0.03
61 28 0.24
62 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGAAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTTG
Found at i:15696 original size:31 final size:31
Alignment explanation
Indices: 15578--15712 Score: 129
Period size: 30 Copynumber: 4.5 Consensus size: 31
15568 TAAAAACATG
* * *
15578 ATTTTT-GAAAGTTTAGAG-GTAAAAATATA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
** *
15607 ATTTTT-GAAAGTTTGGTG-GTCAAAATGTA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
*
15636 ATTTTTGGAAAGTT-TGAGAGTCAAAATGTA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
* * *
15666 ATTTTTGAGAAAGTTCAG-GGGTTAACATGTA
1 ATTTTTG-GAAAGTTCAGAGAGTCAAAATGTA
15697 ATTTTTGGAAAGTTCA
1 ATTTTTGGAAAGTTCA
15713 AGGACCTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
29 33 0.36
30 34 0.37
31 24 0.26
32 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.39
Consensus pattern (31 bp):
ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
Found at i:15712 original size:30 final size:29
Alignment explanation
Indices: 15507--15710 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 29
15497 AAAAATTCGA
*
15507 GGGT-AAAATGGTAATTTTTGG-AAGTTCG
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTAG
* *
15535 GGAG-CAAAAATGTGATTTTT-GAGAAGTTTG
1 GG-GTC-AAAATGTAATTTTTGGA-AAGTTAG
* ** *
15565 GGGTAAAAACATGATTTTT-GAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGGAAAG-TTAG
* * * *
15594 AGGTAAAAATATAATTTTT-GAAAGTTTG
1 GGGTCAAAATGTAATTTTTGGAAAGTTAG
*
15622 GTGGTCAAAATGTAATTTTTGGAAAGTTTG
1 G-GGTCAAAATGTAATTTTTGGAAAGTTAG
*
15652 AGAGTCAAAATGTAATTTTTGAGAAAGTTCAG
1 -GGGTCAAAATGTAATTTTTG-GAAAGTT-AG
* *
15684 GGGTTAACATGTAATTTTTGGAAAGTT
1 GGGTCAAAATGTAATTTTTGGAAAGTT
15711 CAAGGACCTT
Statistics
Matches: 146, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
28 9 0.06
29 64 0.44
30 47 0.32
31 25 0.17
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTAG
Found at i:18760 original size:18 final size:18
Alignment explanation
Indices: 18737--18773 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18727 TTTGTGATCA
18737 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
18755 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
18773 A
1 A
18774 TATGAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:19575 original size:93 final size:93
Alignment explanation
Indices: 19416--19602 Score: 338
Period size: 93 Copynumber: 2.0 Consensus size: 93
19406 CGTAGGTATA
* *
19416 AGACCTCCGAGAAGTTAAGGTTGGTCTAGGTGCTTCTCATCAAATTACATCAACATCGAAAGATT
1 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
19481 GCAAAATAAGGTATATTTATTTTGTGTG
66 GCAAAATAAGGTATATTTATTTTGTGTG
*
19509 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGGAAGATT
1 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
*
19574 GCAAAATAATGTATATTTATTTTGTGTG
66 GCAAAATAAGGTATATTTATTTTGTGTG
19602 A
1 A
19603 AATGACATGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (93 bp):
AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
GCAAAATAAGGTATATTTATTTTGTGTG
Found at i:20571 original size:11 final size:12
Alignment explanation
Indices: 20555--20616 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 12
20545 TATTTGGATT
*
20555 TTTAAACTT-AA
1 TTTAAAATTAAA
20566 TTTAAAATTAAA
1 TTTAAAATTAAA
*
20578 TTTAGGATAAATTTAA
1 TTT---A-AAATTAAA
20594 TTTAAAA-TAAA
1 TTTAAAATTAAA
20605 TTTAAAATTAAA
1 TTTAAAATTAAA
20617 GATTGAGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 18 0.43
12 12 0.29
13 1 0.02
15 1 0.02
16 10 0.24
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:20595 original size:16 final size:16
Alignment explanation
Indices: 20570--20609 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20560 ACTTAATTTA
* **
20570 AAATTAAATTTAGGAT
1 AAATTTAATTTAAAAT
20586 AAATTTAATTTAAAAT
1 AAATTTAATTTAAAAT
20602 AAATTTAA
1 AAATTTAA
20610 AATTAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Found at i:22279 original size:30 final size:28
Alignment explanation
Indices: 22213--22279 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
22203 TTTCAGAGAG
* *
22213 TTTGGGATGAAAACATAATTTTAGAAAG
1 TTTGGGATCAAAACATAATTTTAGAAAA
* *
22241 TTTAGGGATCAAAATCATAGTTATTGGAAAA
1 TTT-GGGATCAAAA-CATAATT-TTAGAAAA
22272 TTTGGGAT
1 TTTGGGAT
22280 TAAAGCCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 9 0.28
30 11 0.34
31 9 0.28
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (28 bp):
TTTGGGATCAAAACATAATTTTAGAAAA
Found at i:22397 original size:58 final size:58
Alignment explanation
Indices: 22335--22539 Score: 195
Period size: 58 Copynumber: 3.5 Consensus size: 58
22325 AAAAATTCGA
* *
22335 GGGTAAAATGGTAATTTTTGG-AAGTTCGGGAGCAAAAATGTGATTTTTGAGAAGTTTG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTTG
** * * * *
22393 GGGTAAAAACATGATTTTT-GAAAGTT-TAGAGGTAAAAATATAATTTTTGA-AAGTTTG
1 GGGT-AAAATGTAATTTTTGGAAAGTTCGAGA-GCAAAAATGTAATTTTTGAGAAGTTTG
* *
22450 GTGGTCAAAATGTAATTTTTGGAAAGTTTGAGAGTC-AAAATGTAATTTTTGAGAAAGTTCAG
1 G-GGT-AAAATGTAATTTTTGGAAAGTTCGAGAG-CAAAAATGTAATTTTTGAG-AAGTT-TG
*
22512 GGGTTAACATGTAATTTTTGGAAAGTTC
1 GGG-TAAAATGTAATTTTTGGAAAGTTC
22540 AAGGACCTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
57 11 0.09
58 46 0.39
59 27 0.23
60 3 0.03
61 28 0.24
62 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGAAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTTG
Found at i:22524 original size:31 final size:31
Alignment explanation
Indices: 22406--22540 Score: 129
Period size: 30 Copynumber: 4.5 Consensus size: 31
22396 TAAAAACATG
* * *
22406 ATTTTT-GAAAGTTTAGAG-GTAAAAATATA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
** *
22435 ATTTTT-GAAAGTTTGGTG-GTCAAAATGTA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
*
22464 ATTTTTGGAAAGTT-TGAGAGTCAAAATGTA
1 ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
* * *
22494 ATTTTTGAGAAAGTTCAG-GGGTTAACATGTA
1 ATTTTTG-GAAAGTTCAGAGAGTCAAAATGTA
22525 ATTTTTGGAAAGTTCA
1 ATTTTTGGAAAGTTCA
22541 AGGACCTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
29 33 0.36
30 34 0.37
31 24 0.26
32 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.39
Consensus pattern (31 bp):
ATTTTTGGAAAGTTCAGAGAGTCAAAATGTA
Found at i:22540 original size:30 final size:29
Alignment explanation
Indices: 22335--22538 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 29
22325 AAAAATTCGA
*
22335 GGGT-AAAATGGTAATTTTTGG-AAGTTCG
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTAG
* *
22363 GGAG-CAAAAATGTGATTTTT-GAGAAGTTTG
1 GG-GTC-AAAATGTAATTTTTGGA-AAGTTAG
* ** *
22393 GGGTAAAAACATGATTTTT-GAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGGAAAG-TTAG
* * * *
22422 AGGTAAAAATATAATTTTT-GAAAGTTTG
1 GGGTCAAAATGTAATTTTTGGAAAGTTAG
*
22450 GTGGTCAAAATGTAATTTTTGGAAAGTTTG
1 G-GGTCAAAATGTAATTTTTGGAAAGTTAG
*
22480 AGAGTCAAAATGTAATTTTTGAGAAAGTTCAG
1 -GGGTCAAAATGTAATTTTTG-GAAAGTT-AG
* *
22512 GGGTTAACATGTAATTTTTGGAAAGTT
1 GGGTCAAAATGTAATTTTTGGAAAGTT
22539 CAAGGACCTT
Statistics
Matches: 146, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
28 9 0.06
29 64 0.44
30 47 0.32
31 25 0.17
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTAG
Found at i:25588 original size:18 final size:18
Alignment explanation
Indices: 25565--25601 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25555 TTTGTGATCA
25565 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
25583 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
25601 A
1 A
25602 TATGAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:26403 original size:93 final size:93
Alignment explanation
Indices: 26244--26430 Score: 338
Period size: 93 Copynumber: 2.0 Consensus size: 93
26234 CGTAGGTATA
* *
26244 AGACCTCCGAGAAGTTAAGGTTGGTCTAGGTGCTTCTCATCAAATTACATCAACATCGAAAGATT
1 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
26309 GCAAAATAAGGTATATTTATTTTGTGTG
66 GCAAAATAAGGTATATTTATTTTGTGTG
*
26337 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGGAAGATT
1 AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
*
26402 GCAAAATAATGTATATTTATTTTGTGTG
66 GCAAAATAAGGTATATTTATTTTGTGTG
26430 A
1 A
26431 AATGACATGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (93 bp):
AGACCTCCGAGAAGTTAAGGTTGGACTAGGTGCTTCGCATCAAATTACATCAACATCGAAAGATT
GCAAAATAAGGTATATTTATTTTGTGTG
Found at i:27399 original size:11 final size:12
Alignment explanation
Indices: 27383--27444 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 12
27373 TATTTGGATT
*
27383 TTTAAACTT-AA
1 TTTAAAATTAAA
27394 TTTAAAATTAAA
1 TTTAAAATTAAA
*
27406 TTTAGGATAAATTTAA
1 TTT---A-AAATTAAA
27422 TTTAAAA-TAAA
1 TTTAAAATTAAA
27433 TTTAAAATTAAA
1 TTTAAAATTAAA
27445 GATTGAGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 18 0.43
12 12 0.29
13 1 0.02
15 1 0.02
16 10 0.24
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:27423 original size:16 final size:16
Alignment explanation
Indices: 27398--27437 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
27388 ACTTAATTTA
* **
27398 AAATTAAATTTAGGAT
1 AAATTTAATTTAAAAT
27414 AAATTTAATTTAAAAT
1 AAATTTAATTTAAAAT
27430 AAATTTAA
1 AAATTTAA
27438 AATTAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Done.